VMD-L Mailing List

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About this archive

Starting: Thu Dec 19 1996 - 11:40:41 CST
Ending: Mon Oct 21 2024 - 06:24:29 CDT

ffTK Water Int tab generated .inp Charge 0 Mult 1 INQUIRY? Joel Subach (Mon Oct 21 2024 - 06:24:11 CDT)
Automatic PSF Builder on Windows Mustafa Tekpinar (Sun Oct 13 2024 - 11:38:23 CDT)
- Re: Automatic PSF Builder on Windows Ivan Gregoretti (Sun Oct 13 2024 - 14:29:22 CDT)
- Re: Automatic PSF Builder on Windows PaweÅ‚ KÄ™dzierski (Mon Oct 14 2024 - 05:15:32 CDT)
PBC wrap (close to the boundaries) Manuel Perez Escribano (Mon Oct 07 2024 - 12:55:43 CDT)
Two different type of color set for potential map of overlapped molecules Nakshatra Upadhyay (Wed Oct 02 2024 - 04:13:38 CDT)
- Re: Two different type of color set for potential map of overlapped molecules Diego Gomes (Wed Oct 02 2024 - 14:04:50 CDT)
  - Re: Two different type of color set for potential map of overlapped molecules Nakshatra Upadhyay (Fri Oct 04 2024 - 02:16:54 CDT)
FFTK partial charge assignment weak acid ONOH (HNO2) - Water Shift settings Marinus Veldhuizen (Wed Oct 02 2024 - 03:15:05 CDT)
- Re: FFTK partial charge assignment weak acid ONOH (HNO2) - Water Shift settings Marinus Veldhuizen (Thu Oct 03 2024 - 07:44:33 CDT)
  - Re: Re: FFTK partial charge assignment weak acid ONOH (HNO2) - Water Shift settings Gumbart, JC (Sun Oct 06 2024 - 07:26:26 CDT)
    - Re: Re: FFTK partial charge assignment weak acid ONOH (HNO2) - Water Shift settings Marinus Veldhuizen (Mon Oct 07 2024 - 09:30:35 CDT)
VMD 1.9.4 NAMDEnergy plugin query Roni Saiba (Thu Sep 26 2024 - 22:56:50 CDT)
- Re: VMD 1.9.4 NAMDEnergy plugin query Diego Gomes (Mon Sep 30 2024 - 10:15:56 CDT)
  - Re: VMD 1.9.4 NAMDEnergy plugin query Roni Saiba (Mon Sep 30 2024 - 23:39:10 CDT)
FFTK error - empty string not an operand of * Harini S H (Wed Sep 25 2024 - 13:46:40 CDT)
- Re: FFTK error - empty string not an operand of * Gumbart, JC (Thu Sep 26 2024 - 14:21:24 CDT)
  - Re: FFTK error - empty string not an operand of * Harini S H (Fri Sep 27 2024 - 04:27:42 CDT)
.str file generation of nitrile group containing ligands Hideyuki Miyatake (Tue Sep 24 2024 - 20:55:26 CDT)
- Re: .str file generation of nitrile group containing ligands Josh Vermaas (Wed Sep 25 2024 - 09:09:41 CDT)
  - Re: .str file generation of nitrile group containing ligands Hideyuki Miyatake (Wed Sep 25 2024 - 21:14:12 CDT)
    - Re: .str file generation of nitrile group containing ligands Klimkowski, V (Thu Sep 26 2024 - 21:04:11 CDT)
  - Re: .str file generation of nitrile group containing ligands Hideyuki Miyatake (Fri Sep 27 2024 - 06:59:30 CDT)
Artifacts in GLSL rendering mode: deformation and noisy shading of atom spheres Zilong HE (Tue Sep 24 2024 - 02:00:00 CDT)
- Re: Artifacts in GLSL rendering mode: deformation and noisy shading of atom spheres Zilong HE (Wed Sep 25 2024 - 04:21:31 CDT)
Visualizing elastic network proteins Samapika Sahu (P20CY011) (Mon Sep 16 2024 - 13:49:31 CDT)
- Re: Visualizing elastic network proteins Raman Preet Singh (Tue Sep 17 2024 - 01:49:40 CDT)
FFTK charge optimisation: ORCA issue - cant use empty string as an operand of '*' Harini S H (Mon Sep 16 2024 - 08:36:56 CDT)
retaining HETAM and conect records in pdb files Bennion, Brian (Fri Sep 13 2024 - 17:14:37 CDT)
VMD ORCA 6 Update Mcguire, Kelly (Fri Sep 06 2024 - 17:09:29 CDT)
- Re: VMD ORCA 6 Update Diego Gomes (Fri Sep 13 2024 - 10:13:59 CDT)
FFTK Opt. Torsions End of File Issue Mcguire, Kelly (Wed Sep 04 2024 - 00:54:05 CDT)
FFTK Opt. Torsions End of File Issue Mcguire, Kelly (Wed Sep 04 2024 - 00:29:13 CDT)
- Re: FFTK Opt. Torsions End of File Issue McGuire, Kelly (Wed Sep 04 2024 - 10:13:53 CDT)
- Re: FFTK Opt. Torsions End of File Issue McGuire, Kelly (Thu Sep 05 2024 - 11:13:34 CDT)
FFTK Calc. Bonded ORCA Issue Mcguire, Kelly (Sat Aug 31 2024 - 17:54:33 CDT)
Re: ffTK Opt Charge APPLICATION HALTING ON ERROR Inquiry Joel Subach (Sat Aug 24 2024 - 10:53:04 CDT)
- Re: Re: ffTK Opt Charge APPLICATION HALTING ON ERROR Inquiry Joel Subach (Mon Aug 26 2024 - 10:03:14 CDT)
  - Re: Re: ffTK Opt Charge APPLICATION HALTING ON ERROR Inquiry Joel Subach (Thu Aug 29 2024 - 03:14:59 CDT)
    - Re: Re: ffTK Opt Charge APPLICATION HALTING ON ERROR Inquiry Joel Subach (Thu Aug 29 2024 - 09:55:15 CDT)
    - Re: Re: ffTK Opt Charge APPLICATION HALTING ON ERROR Inquiry Joel Subach (Fri Aug 30 2024 - 03:35:02 CDT)
Problem with pbctools join Laura Ernstsen (Wed Aug 21 2024 - 03:41:33 CDT)
Problem with pbctools join Laura Ernstsen (Wed Aug 21 2024 - 01:54:04 CDT)
Re: Select atoms on surface of sphere Vermaas, Josh (Fri Aug 16 2024 - 11:11:34 CDT)
- Re: Select atoms on surface of sphere Raman Preet Singh (Mon Aug 19 2024 - 03:38:33 CDT)
Select atoms on surface of sphere Raman Preet Singh (Fri Aug 16 2024 - 09:05:20 CDT)
residue torsion angles Alexei Rossokhin (Wed Aug 14 2024 - 05:55:57 CDT)
altloc pdb entries Bennion, Brian (Tue Aug 13 2024 - 19:47:41 CDT)
- Re: altloc pdb entries Josh Vermaas (Wed Aug 14 2024 - 09:44:24 CDT)
  - Re: altloc pdb entries Bennion, Brian (Thu Aug 15 2024 - 00:33:18 CDT)
Reminder: Hands-On Workshop on Computational Biophysics in Auburn, AL Sinclair, Matt (Mon Aug 12 2024 - 13:10:07 CDT)
pbc box unwrapping/wrapping error infinite bond angles/box sides Ryan Woltz (Fri Aug 09 2024 - 17:58:42 CDT)
- Re: pbc box unwrapping/wrapping error infinite bond angles/box sides Vermaas, Josh (Mon Aug 12 2024 - 09:42:09 CDT)
  - Re: pbc box unwrapping/wrapping error infinite bond angles/box sides Ryan Woltz (Mon Aug 12 2024 - 14:42:56 CDT)
Re: Re: flipping a .inp file for a water interaction INQUIRY Joel Subach (Sun Aug 04 2024 - 05:04:33 CDT)
- Re: Re: flipping a .inp file for a water interaction INQUIRY Joel Subach (Sun Aug 04 2024 - 06:10:59 CDT)
  - Re: Re: flipping a .inp file for a water interaction INQUIRY Daniel Fellner (Fri Aug 16 2024 - 21:45:53 CDT)
    - Re: Re: flipping a .inp file for a water interaction INQUIRY Joel Subach (Sat Aug 17 2024 - 05:03:19 CDT)
    - Re: Re: flipping a .inp file for a water interaction INQUIRY Joel Subach (Sun Aug 18 2024 - 04:47:22 CDT)
Re: flipping a .inp file for a water interaction INQUIRY Daniel Fellner (Thu Aug 01 2024 - 20:48:58 CDT)
CHGCAR file read in VMD SKM (Wed Jul 31 2024 - 22:06:25 CDT)
- Re: CHGCAR file read in VMD Diego Gomes (Fri Aug 02 2024 - 12:08:46 CDT)
- Re: CHGCAR file read in VMD Diego Gomes (Wed Aug 07 2024 - 10:16:25 CDT)
selecting first instance of a ligand from several in pdb file Bennion, Brian (Sat Jul 27 2024 - 18:10:43 CDT)
- Re: selecting first instance of a ligand from several in pdb file Josh Vermaas (Mon Jul 29 2024 - 09:42:33 CDT)
  - Re: selecting first instance of a ligand from several in pdb file Bennion, Brian (Mon Jul 29 2024 - 13:49:39 CDT)
  - VMD reads vasp files with variable cells incorrectly Ronald Cohen (Mon Jul 29 2024 - 14:06:41 CDT)
Query on networkview plugin Sruthi Sudhakar (Fri Jul 26 2024 - 07:13:21 CDT)
fftk, ORCA, Bond and Angle Optimization, error As a subsequent Frequencies calculation has been requested Vardan Vardanyan (Tue Jul 23 2024 - 15:29:09 CDT)
- Re: fftk, ORCA, Bond and Angle Optimization, error As a subsequent Frequencies calculation has been requested Gumbart, JC (Thu Jul 25 2024 - 12:46:36 CDT)
  - Re: fftk, ORCA, Bond and Angle Optimization, error As a subsequent Frequencies calculation has been requested Joel Subach (Thu Jul 25 2024 - 13:05:15 CDT)
    - Re: fftk, ORCA, Bond and Angle Optimization, error As a subsequent Frequencies calculation has been requested Vardan Vardanyan (Thu Aug 15 2024 - 11:11:19 CDT)
How can a known point be moved to the origin of the screen? Pacci Evaristo, Felipe Fabricio (Sun Jul 21 2024 - 23:19:36 CDT)
Compiling CUDAMarchingCubes.cu build error Chris Taylor (Sun Jul 21 2024 - 20:53:43 CDT)
- Re: Compiling CUDAMarchingCubes.cu build error Vermaas, Josh (Mon Jul 22 2024 - 20:16:50 CDT)
  - Re: Compiling CUDAMarchingCubes.cu build error Chris Taylor (Tue Jul 23 2024 - 20:02:18 CDT)
Working with trajectory and updating frames dependents on current frame Laura X Sepulveda (Thu Jul 18 2024 - 12:52:06 CDT)
- Re: Working with trajectory and updating frames dependents on current frame Roni Saiba (Thu Jul 18 2024 - 14:26:32 CDT)
  - Re: Working with trajectory and updating frames dependents on current frame Vermaas, Josh (Thu Jul 18 2024 - 15:56:01 CDT)
TkConsol mohamed marzouk (Wed Jul 17 2024 - 15:02:37 CDT)
- Re: TkConsol Isralewitz, Barry (Wed Jul 17 2024 - 18:46:04 CDT)
  - Re: TkConsol mohamed marzouk (Wed Jul 17 2024 - 21:12:51 CDT)
Opening file after i downloaded vmd Micah Watson (Tue Jul 16 2024 - 20:33:06 CDT)
- Re: Opening file after i downloaded vmd Giacomo Fiorin (Wed Jul 17 2024 - 09:54:02 CDT)
  - Re: Opening file after i downloaded vmd Micah Watson (Wed Jul 17 2024 - 12:14:41 CDT)
- Re: Opening file after i downloaded vmd Diego Gomes (Wed Jul 17 2024 - 13:27:31 CDT)
pbc get -all fails Ronald Cohen (Tue Jul 16 2024 - 08:47:25 CDT)
- Re: pbc get -all fails Ronald Cohen (Tue Jul 16 2024 - 09:04:29 CDT)
PBC issue Aditi Gotkhindikar (Tue Jul 16 2024 - 03:22:20 CDT)
- Re: PBC issue Vermaas, Josh (Tue Jul 16 2024 - 06:18:47 CDT)
FFTK water molecules overlapped and charge optimisation error MARIA MILANESI (Mon Jul 15 2024 - 04:06:27 CDT)
- Re: FFTK water molecules overlapped and charge optimisation error Gumbart, JC (Sun Jul 21 2024 - 22:13:21 CDT)
  - Re: FFTK water molecules overlapped and charge optimisation error Joel Subach (Tue Jul 23 2024 - 02:18:55 CDT)
Re: ffTK Water Int Tab .inp File Flipping a Waters Coordinates Inquiry Joel Subach (Sun Jul 14 2024 - 12:19:46 CDT)
- Re: ffTK Water Int Tab .inp File Flipping a Waters Coordinates Inquiry Joel Subach (Mon Jul 15 2024 - 09:09:18 CDT)
ffTK Water Int Tab Optimization INTERACTION DISTANCE INQUIRY Joel Subach (Sun Jul 07 2024 - 05:35:12 CDT)
- Re: ffTK Water Int Tab Optimization INTERACTION DISTANCE INQUIRY PaweÅ‚ KÄ™dzierski (Mon Jul 08 2024 - 01:38:32 CDT)
  - Re: ffTK Water Int Tab Optimization INTERACTION DISTANCE INQUIRY Joel Subach (Mon Jul 08 2024 - 03:47:52 CDT)
    - Re: ffTK Water Int Tab Optimization INTERACTION DISTANCE INQUIRY PaweÅ‚ KÄ™dzierski (Mon Jul 08 2024 - 04:51:34 CDT)
    - Re: ffTK Water Int Tab Optimization INTERACTION DISTANCE INQUIRY Joel Subach (Mon Jul 08 2024 - 12:04:35 CDT)
loading multiple pdbs as frames and the filenames Ryan Woltz (Wed Jun 26 2024 - 13:03:11 CDT)
- Re: loading multiple pdbs as frames and the filenames Gianluca Interlandi (Wed Jun 26 2024 - 16:10:05 CDT)
  - Re: loading multiple pdbs as frames and the filenames Ryan Woltz (Wed Jun 26 2024 - 18:29:44 CDT)
    - Re: loading multiple pdbs as frames and the filenames Ryan Woltz (Wed Jun 26 2024 - 18:41:17 CDT)
- Re: loading multiple pdbs as frames and the filenames Diego Gomes (Wed Jun 26 2024 - 16:57:58 CDT)
wrapping atoms along a specific axis with pbctools SHIVAM TIWARI (Wed Jun 26 2024 - 03:30:19 CDT)
Potential Bug Using NAMD Energy Plugin from the Command Line Jacob Graham (Tue Jun 18 2024 - 14:59:45 CDT)
- Re: Potential Bug Using NAMD Energy Plugin from the Command Line Diego Gomes (Sat Jun 22 2024 - 09:57:34 CDT)
bonding across periodic walls Kevin Wittkowski (Thu Jun 13 2024 - 14:34:08 CDT)
- Re: bonding across periodic walls Giacomo Fiorin (Thu Jun 13 2024 - 16:37:32 CDT)
  - Re: bonding across periodic walls Kevin Wittkowski (Fri Jun 14 2024 - 02:43:55 CDT)
VMD receives Segmentation Fault After NVIDIA Driver Update GIANG NGUYEN (Fri Jun 07 2024 - 04:15:10 CDT)
- Re: VMD receives Segmentation Fault After NVIDIA Driver Update Diego Gomes (Fri Jun 07 2024 - 11:15:23 CDT)
Display both-signed portions of isosurface jimkress_58_at_kressworks.org (Sun Jun 02 2024 - 01:02:52 CDT)
- Re: Display both-signed portions of isosurface Vermaas, Josh (Sun Jun 02 2024 - 15:24:39 CDT)
  - RE: Display both-signed portions of isosurface jimkress_58_at_kressworks.org (Sun Jun 02 2024 - 23:19:29 CDT)
Issue sending forces to atoms with IMD and LAMMPS Tom (Fri May 31 2024 - 12:55:12 CDT)
- Re: Issue sending forces to atoms with IMD and LAMMPS Josh Vermaas (Fri May 31 2024 - 14:51:44 CDT)
  - Re: Issue sending forces to atoms with IMD and LAMMPS Tom (Fri May 31 2024 - 15:29:37 CDT)
Deleting portions of isosurfaces jimkress_58_at_kressworks.org (Thu May 23 2024 - 18:30:11 CDT)
pbc wrap for nonbonded group of atoms SHRAVANI NETHI . (Mon May 20 2024 - 06:40:34 CDT)
Deleting portions of isosurfaces jimkress_58_at_kressworks.org (Sat May 18 2024 - 00:12:45 CDT)
namdenergy plugin energy values Ravithree Senanayake (Tue May 14 2024 - 12:48:23 CDT)
NUMLP NUMLPH section eliminated by VMD 1.9.4a57 DENILSON FERREIRA DE OLIVEIRA (Tue May 14 2024 - 08:06:59 CDT)
- Re: NUMLP NUMLPH section eliminated by VMD 1.9.4a57 Diego Gomes (Tue May 14 2024 - 10:18:44 CDT)
  - Re: NUMLP NUMLPH section eliminated by VMD 1.9.4a57 DENILSON FERREIRA DE OLIVEIRA (Wed May 15 2024 - 07:07:12 CDT)
Adding an Implicit Solvation Compatible with below ffTK suggested Methods INQUIRY Joel Subach (Tue May 07 2024 - 13:26:58 CDT)
- Re: Adding an Implicit Solvation Compatible with below ffTK suggested Methods INQUIRY Joel Subach (Wed May 08 2024 - 14:06:02 CDT)
  - Re: Adding an Implicit Solvation Compatible with below ffTK suggested Methods INQUIRY Joel Subach (Sat May 11 2024 - 10:49:03 CDT)
saving a PDB in a different order than it was loaded Ryan Woltz (Thu May 02 2024 - 21:30:39 CDT)
- Re: saving a PDB in a different order than it was loaded Axel Kohlmeyer (Thu May 02 2024 - 22:30:44 CDT)
  - Re: saving a PDB in a different order than it was loaded Diego Gomes (Fri May 03 2024 - 10:38:56 CDT)
  - Re: saving a PDB in a different order than it was loaded Josh Vermaas (Fri May 03 2024 - 11:12:21 CDT)
    - Re: saving a PDB in a different order than it was loaded Ryan Woltz (Fri May 03 2024 - 11:21:01 CDT)
restarting calculations anytime within Equilibration and MD simulations steps in QwikMD Sefcikova, Jana (Tue Apr 30 2024 - 12:58:34 CDT)
- Re: restarting calculations anytime within Equilibration and MD simulations steps in QwikMD Giacomo Fiorin (Tue Apr 30 2024 - 14:42:21 CDT)
  - RE: restarting calculations anytime within Equilibration and MD simulations steps in QwikMD Sefcikova, Jana (Tue Apr 30 2024 - 16:05:52 CDT)
    - Re: restarting calculations anytime within Equilibration and MD simulations steps in QwikMD Giacomo Fiorin (Tue Apr 30 2024 - 16:09:48 CDT)
    - RE: restarting calculations anytime within Equilibration and MD simulations steps in QwikMD Sefcikova, Jana (Tue Apr 30 2024 - 17:41:39 CDT)
Reminder: Hands-On Workshop on Computational Biophysics in Auburn, AL Sinclair, Matt (Mon Apr 29 2024 - 12:39:54 CDT)
is ! RI-MP2 6-31G* TightSCF opt autoaux rijcosx compatibile with ffTK CHARMM INQUIRY Joel Subach (Sat Apr 27 2024 - 02:03:24 CDT)
- Re: is ! RI-MP2 6-31G* TightSCF opt autoaux rijcosx compatibile with ffTK CHARMM INQUIRY Joel Subach (Sat May 11 2024 - 10:55:20 CDT)
ffTK HF/6-31G Base Set QM or a Different QM Base Set? Joel Subach (Wed Apr 24 2024 - 05:07:16 CDT)
- Re: ffTK HF/6-31G Base Set QM or a Different QM Base Set? Joel Subach (Wed Apr 24 2024 - 06:37:51 CDT)
  - Re: Re: ffTK HF/6-31G Base Set QM or a Different QM Base Set? Vermaas, Josh (Wed Apr 24 2024 - 08:35:29 CDT)
mol addfile CHARLES MCCALLUM (Thu Apr 18 2024 - 13:18:51 CDT)
- Re: mol addfile Roni Saiba (Fri Apr 19 2024 - 22:05:43 CDT)
  - Re: mol addfile Diego Gomes (Mon Apr 22 2024 - 13:33:07 CDT)
    - Re: mol addfile CHARLES MCCALLUM (Tue Apr 23 2024 - 14:04:23 CDT)
MD Videos and fixing the view into a certain perspective Lohry, David Patrick (Thu Apr 18 2024 - 10:53:24 CDT)
- Re: MD Videos and fixing the view into a certain perspective Josh Vermaas (Thu Apr 18 2024 - 12:05:24 CDT)
  - Re: MD Videos and fixing the view into a certain perspective Lohry, David Patrick (Thu Apr 18 2024 - 12:14:52 CDT)
VMD 1.9.4a53 on Windows 11 crashing frequently Lohry, David Patrick (Tue Apr 16 2024 - 17:45:45 CDT)
- Re: VMD 1.9.4a53 on Windows 11 crashing frequently Jason Smith (Tue Apr 16 2024 - 21:21:57 CDT)
  - Re: VMD 1.9.4a53 on Windows 11 crashing frequently Lohry, David Patrick (Wed Apr 17 2024 - 07:48:45 CDT)
    - Re: VMD 1.9.4a53 on Windows 11 crashing frequently Diego Gomes (Thu May 02 2024 - 10:01:42 CDT)
Problems with â€˜Surfâ€™ as a â€œDrawing methodâ€ for protein in VMD installed to a local folder Dmitry Suplatov (Thu Apr 11 2024 - 08:04:45 CDT)
- Re: Problems with â€˜Surfâ€™ as a â€œDrawing methodâ€ for protein in VMD installed to a local folder Diego Gomes (Thu Apr 11 2024 - 10:14:05 CDT)
  - Re: Problems with â€˜Surfâ€™ as a â€œDrawing methodâ€ for protein in VMD installed to a local folder Diego Gomes (Thu Apr 11 2024 - 11:38:36 CDT)
    - Re: Problems with â€˜Surfâ€™ as a â€œDrawing methodâ€ for protein in VMD installed to a local folder Dmitry Suplatov (Thu Apr 11 2024 - 12:02:22 CDT)
    - Re: Problems with â€˜Surfâ€™ as a â€œDrawing methodâ€ for protein in VMD installed to a local folder Diego Gomes (Thu Apr 11 2024 - 12:56:15 CDT)
Can not run VMD in interactive mode on the supercomputer from Mac mohamed marzouk (Thu Apr 11 2024 - 01:16:59 CDT)
- Re: Can not run VMD in interactive mode on the supercomputer from Mac Diego Gomes (Thu Apr 11 2024 - 09:48:49 CDT)
VR Movies Collette Riviere (Wed Apr 03 2024 - 23:04:15 CDT)
- Re: VR Movies Diego Gomes (Fri Apr 05 2024 - 05:20:50 CDT)
Index extractor Python Code Sam Fredrick (Wed Apr 03 2024 - 19:47:55 CDT)
- Re: Index extractor Python Code Smith, Harper (Wed Apr 03 2024 - 20:34:25 CDT)
error during membrane mixing: can't read "toplist": no such variable Tvedt, Nathan (Fri Mar 29 2024 - 14:03:14 CDT)
Atom selection based on center of sphere Peter (Tue Mar 26 2024 - 17:04:45 CDT)
- Re: Atom selection based on center of sphere Peter (Wed Mar 27 2024 - 01:29:46 CDT)
  - RE: Atom selection based on center of sphere Joaquim Rui de Castro Rodrigues (Wed Mar 27 2024 - 06:23:54 CDT)
    - Re: Atom selection based on center of sphere Peter (Wed Mar 27 2024 - 16:14:08 CDT)
Can't connect to BioCORE M Suma (Tue Mar 26 2024 - 02:03:14 CDT)
Atoms poorly guessed after applying a patch in Psfgen Kyle Billings (Mon Mar 25 2024 - 12:28:59 CDT)
- Re: Atoms poorly guessed after applying a patch in Psfgen Josh Vermaas (Mon Mar 25 2024 - 15:01:52 CDT)
  - Re: Atoms poorly guessed after applying a patch in Psfgen Vermaas, Josh (Wed Mar 27 2024 - 09:51:49 CDT)
    - Re: Atoms poorly guessed after applying a patch in Psfgen Kyle Billings (Thu Mar 28 2024 - 15:15:23 CDT)
    - Re: Atoms poorly guessed after applying a patch in Psfgen Josh Vermaas (Fri Mar 29 2024 - 09:47:58 CDT)
  - Re: Atoms poorly guessed after applying a patch in Psfgen Josh Vermaas (Fri Mar 29 2024 - 11:58:43 CDT)
Problem to launch vmd1.9.4 (v2022-04-27) in wsl linux Roozbeh (Fri Mar 22 2024 - 20:17:28 CDT)
- Re: Problem to launch vmd1.9.4 (v2022-04-27) in wsl linux Roozbeh (Tue Mar 26 2024 - 05:09:21 CDT)
NMWiz Arrow Colors Mcguire, Kelly (Thu Mar 21 2024 - 17:50:01 CDT)
save/load visualization for data file é³å¿ƒç‘¶ (Sun Mar 17 2024 - 07:40:35 CDT)
- Re: save/load visualization for data file Vermaas, Josh (Mon Mar 18 2024 - 08:32:26 CDT)
FFTK - Dihedral doesn't fit the QM target data francesco quilli (Mon Mar 11 2024 - 10:12:52 CDT)
- Re: FFTK - Dihedral doesn't fit the QM target data Ernesto Aleksei Delgado Hurtado (Mon Mar 11 2024 - 17:21:46 CDT)
  - Re: FFTK - Dihedral doesn't fit the QM target data Gumbart, JC (Mon Mar 11 2024 - 21:43:51 CDT)
Re: looking for help to solve FATAL ERRORQ=BC=9A_Didn=27t_find_vdw_parameter_for_atom_type_C11?= Josh Vermaas (Thu Mar 07 2024 - 13:18:13 CST)
- Re: Re: looking for help to solve FATAL ERRORï¼š Didn't find vdw parameter for atom type C11 Cindy Cregier (Mon Mar 11 2024 - 20:03:24 CDT)
  - Re: Re: looking for help to solve FATAL ERRORï¼š Didn't find vdw parameter for atom type C11 Yixin Chen (Tue Mar 12 2024 - 10:30:55 CDT)
issue with wrapping water molecules Yuan Xue (Wed Mar 06 2024 - 20:47:01 CST)
How to define an atom selection for a dynamic space Jacob Layton (Wed Mar 06 2024 - 13:43:16 CST)
- Re: How to define an atom selection for a dynamic space Josh Vermaas (Wed Mar 06 2024 - 15:15:26 CST)
looking for help to solve FATAL ERRORï¼š Didn't find vdw parameter for atom type C11 Yixin Chen (Wed Mar 06 2024 - 08:12:31 CST)
- Re: looking for help to solve FATAL ERRORï¼š Didn't find vdw parameter for atom type C11 Vermaas, Josh (Wed Mar 06 2024 - 09:36:55 CST)
VR Movie Rendering Collette Riviere (Tue Mar 05 2024 - 22:05:16 CST)
Water molecules cling to protein in last frame Yuan Xue (Sat Mar 02 2024 - 10:42:54 CST)
Problems generating movies for vmd 1.9.4a53 Kung, Ryan (Thu Feb 29 2024 - 09:54:53 CST)
- Re: Problems generating movies for vmd 1.9.4a53 Diego Gomes (Thu Feb 29 2024 - 17:09:42 CST)
  - Re: Problems generating movies for vmd 1.9.4a53 Kung, Ryan (Sat Mar 02 2024 - 11:35:49 CST)
    - Re: Problems generating movies for vmd 1.9.4a53 Diego Gomes (Mon Mar 04 2024 - 13:23:46 CST)
Fwd: bond lengths and angle display SKM (Wed Feb 28 2024 - 21:43:52 CST)
- Re: Fwd: bond lengths and angle display Diego Gomes (Thu Feb 29 2024 - 22:10:19 CST)
  - Re: Fwd: bond lengths and angle display Diego Gomes (Fri Mar 01 2024 - 10:08:19 CST)
How to access the Lable tab's info of atoms? Big Chungus (Wed Feb 28 2024 - 20:57:11 CST)
- Re: How to access the Lable tab's info of atoms? Vermaas, Josh (Thu Feb 29 2024 - 07:51:51 CST)
Error in Molefacture 2.0: Unable to write PSF and PDB files Sarthak Mohanty (Mon Feb 26 2024 - 02:19:07 CST)
bug when starting VMD on MACOS ARM Maud Jusot (Wed Feb 21 2024 - 08:24:02 CST)
- Re: bug when starting VMD on MACOS ARM Isralewitz, Barry (Wed Feb 21 2024 - 12:06:57 CST)
  - Re: bug when starting VMD on MACOS ARM Maud Jusot (Thu Feb 22 2024 - 04:32:55 CST)
Anyone Completed ffTK Calc Bonded Tab using ORCA gbw instead of Gaussian chk? Joel Subach (Mon Feb 19 2024 - 14:08:30 CST)
- Re: Anyone Completed ffTK Calc Bonded Tab using ORCA gbw instead of Gaussian chk? PaweÅ‚ KÄ™dzierski (Tue Feb 20 2024 - 01:32:05 CST)
  - Re: Anyone Completed ffTK Calc Bonded Tab using ORCA gbw instead of Gaussian chk? Joel Subach (Tue Feb 20 2024 - 02:01:03 CST)
  - Re: Anyone Completed ffTK Calc Bonded Tab using ORCA gbw instead of Gaussian chk? Joel Subach (Tue Feb 20 2024 - 05:43:11 CST)
- Re: Anyone Completed ffTK Calc Bonded Tab using ORCA gbw instead of Gaussian chk? Joel Subach (Thu Feb 22 2024 - 03:08:29 CST)
atomselection near periodic boundaries Amir (Sun Feb 18 2024 - 14:54:49 CST)
- Re: atomselection near periodic boundaries SHIVAM TIWARI (Mon Feb 19 2024 - 00:41:43 CST)
  - Re: atomselection near periodic boundaries Axel Kohlmeyer (Mon Feb 19 2024 - 06:55:01 CST)
    - Re: atomselection near periodic boundaries Amir (Mon Feb 19 2024 - 12:49:35 CST)
VMD Programmer position available at TCBG / University of Illinois Isralewitz, Barry (Thu Feb 15 2024 - 08:54:20 CST)
Re: ffTK Calc Bonded Tab gbw file not recognized INQUIRY Joel Subach (Wed Feb 14 2024 - 05:40:24 CST)
- Re: ffTK Calc Bonded Tab gbw file not recognized INQUIRY Joel Subach (Fri Feb 16 2024 - 07:50:37 CST)
  - Re: ffTK Calc Bonded Tab gbw file not recognized INQUIRY Joel Subach (Tue Feb 20 2024 - 05:55:28 CST)
ffTK Opt. Charge Run QM Target Data WATER INTERACTION ENERGY DATA INQUIRY Joel Subach (Tue Feb 06 2024 - 09:43:16 CST)
- Re: ffTK Opt. Charge Run QM Target Data WATER INTERACTION ENERGY DATA INQUIRY Joel Subach (Fri Feb 09 2024 - 11:47:09 CST)
parseFEP and solvate pulgins in VMD 1.9.3 Gianluca Interlandi (Mon Feb 05 2024 - 12:58:01 CST)
- Re: parseFEP and solvate pulgins in VMD 1.9.3 Josh (Mon Feb 05 2024 - 14:54:25 CST)
  - Re: parseFEP and solvate pulgins in VMD 1.9.3 Gianluca Interlandi (Mon Feb 05 2024 - 15:30:55 CST)
    - Re: parseFEP and solvate pulgins in VMD 1.9.3 Vermaas, Josh (Mon Feb 05 2024 - 19:27:14 CST)
    - Re: parseFEP and solvate pulgins in VMD 1.9.3 Gianluca Interlandi (Mon Feb 05 2024 - 19:33:47 CST)
unable to open VMD as normal He, Xibing (Mon Feb 05 2024 - 11:41:38 CST)
- Re: unable to open VMD as normal Axel Kohlmeyer (Mon Feb 05 2024 - 16:58:07 CST)
  - Re: unable to open VMD as normal He, Xibing (Mon Feb 05 2024 - 17:35:11 CST)
  - Re: unable to open VMD as normal Diego Gomes (Wed Feb 07 2024 - 02:13:14 CST)
Coarse Grain Setup Mcguire, Kelly (Mon Feb 05 2024 - 00:01:55 CST)
ffTK Opt. Charge Run Optimization Error PSF File Problem INQUIRY Joel Subach (Sat Feb 03 2024 - 08:36:02 CST)
- Re: ffTK Opt. Charge Run Optimization Error PSF File Problem INQUIRY Vermaas, Josh (Mon Feb 05 2024 - 09:25:25 CST)
  - Re: ffTK Opt. Charge Run Optimization Error PSF File Problem INQUIRY Joel Subach (Mon Feb 05 2024 - 11:32:15 CST)
- Re: ffTK Opt. Charge Run Optimization Error PSF File Problem INQUIRY Joel Subach (Mon Feb 05 2024 - 11:39:02 CST)
NAMDenergy plugin Alexei Rossokhin (Fri Jan 26 2024 - 07:38:58 CST)
- Re: NAMDenergy plugin Diego Gomes (Mon Jan 29 2024 - 10:17:37 CST)
  - Re: NAMDenergy plugin Diego Gomes (Tue Jan 30 2024 - 10:12:10 CST)
Re: working out the output files from Timeline jing liang (Wed Jan 24 2024 - 23:58:11 CST)
working out the output files from Timeline jing liang (Mon Jan 22 2024 - 11:44:48 CST)
ffTK charge optimization error francesco quilli (Mon Jan 08 2024 - 08:38:31 CST)
- Re: ffTK charge optimization error Gumbart, JC (Tue Jan 09 2024 - 21:54:57 CST)
  - Re: ffTK charge optimization error Gumbart, JC (Fri Jan 12 2024 - 18:13:38 CST)
<< Hbonds distances >> I. Camps (Fri Jan 05 2024 - 14:06:06 CST)
- Re: << Hbonds distances >> Diego Gomes (Mon Jan 08 2024 - 11:00:08 CST)
assigning segment id or a unique identity in lammps data file SHIVAM TIWARI (Wed Jan 03 2024 - 11:27:38 CST)
- Re: assigning segment id or a unique identity in lammps data file Axel Kohlmeyer (Wed Jan 03 2024 - 12:58:48 CST)
  - Re: assigning segment id or a unique identity in lammps data file SHIVAM TIWARI (Thu Jan 04 2024 - 02:26:56 CST)
M1 Mac menu issues Corey Taylor (Wed Dec 27 2023 - 05:22:48 CST)
- Re: M1 Mac menu issues Vermaas, Josh (Wed Dec 27 2023 - 12:48:58 CST)
  - Re: M1 Mac menu issues Corey Taylor (Thu Dec 28 2023 - 01:51:07 CST)
    - Re: M1 Mac menu issues Diego Gomes (Fri Jan 05 2024 - 15:04:59 CST)
    - Re: M1 Mac menu issues Barry Isralewitz (Fri Jan 05 2024 - 16:29:08 CST)
Total charge from *.psf alone Francesco Pietra (Thu Dec 21 2023 - 15:07:35 CST)
Visualization of new bonds created in LAMMPS simulation Roni Saiba (Thu Dec 21 2023 - 01:05:23 CST)
- Re: Visualization of new bonds created in LAMMPS simulation Axel Kohlmeyer (Wed Jan 03 2024 - 13:04:34 CST)
Re: ffTK Water Interactions Ligand Atom Hydrogen Bond Acceptors Acting as Donors Inquiry Joel Subach (Thu Dec 14 2023 - 06:19:45 CST)
Missing operand error in vmd pathways plugin Ananya Nayak (Thu Dec 14 2023 - 01:29:56 CST)
- Re: Missing operand error in vmd pathways plugin Diego Gomes (Wed Dec 20 2023 - 09:31:18 CST)
Re: ffTK vmd Index Atom Numbering via ORCA .inp and .out Files Inquiry Joel Subach (Wed Dec 13 2023 - 03:46:25 CST)
- Re: ffTK vmd Index Atom Numbering via ORCA .inp and .out Files Inquiry Joel Subach (Wed Dec 13 2023 - 04:30:37 CST)
(no subject) Ananya Nayak (Tue Dec 12 2023 - 23:06:48 CST)
Please help me understand the .dx file generated when using PME Electrostatics Analysis Jester Itliong (Sat Dec 09 2023 - 11:46:29 CST)
- Re: Please help me understand the .dx file generated when using PME Electrostatics Analysis Axel Kohlmeyer (Sat Dec 09 2023 - 14:48:21 CST)
  - Re: Please help me understand the .dx file generated when using PME Electrostatics Analysis Jester Itliong (Sat Dec 09 2023 - 20:02:02 CST)
VMD for macOS -- easy install with new code-signed versions Isralewitz, Barry (Fri Dec 01 2023 - 19:29:06 CST)
- Re: VMD for macOS -- easy install with new code-signed versions Isralewitz, Barry (Fri Dec 01 2023 - 20:54:59 CST)
- Re: VMD for macOS -- easy install with new code-signed versions Tru Huynh (Sat Dec 02 2023 - 11:38:23 CST)
VMD for macOS - easy install with new code-signed versions Barry Isralewitz (Fri Dec 01 2023 - 17:29:19 CST)
how to control "offset" and "midpoint" of color scale simultaneously using tk-console Suleman Ansari (P19PH004) (Fri Dec 01 2023 - 00:54:05 CST)
- Re: how to control "offset" and "midpoint" of color scale simultaneously using tk-console Diego Gomes (Thu Dec 07 2023 - 09:22:00 CST)
  - Re: how to control "offset" and "midpoint" of color scale simultaneously using tk-console Suleman Ansari (P19PH004) (Thu Dec 07 2023 - 10:53:27 CST)
Startup position of OpenGL Display window and VMD console window æŽå®‰é‚¦ (Wed Nov 29 2023 - 20:44:29 CST)
- Re: Startup position of OpenGL Display window and VMD console window Hasdemir, Hale Siir (Thu Nov 30 2023 - 10:15:14 CST)
  - Re: Startup position of OpenGL Display window and VMD console window æŽå®‰é‚¦ (Fri Dec 01 2023 - 00:41:40 CST)
Re: Interactive MD - 3DSystems Touch Trollmann, Marius (Tue Nov 28 2023 - 01:44:48 CST)
- Re: Interactive MD - 3DSystems Touch Trollmann, Marius (Wed Nov 29 2023 - 03:23:23 CST)
  - Re: Interactive MD - 3DSystems Touch John Stone (Fri Dec 01 2023 - 13:33:52 CST)
    - Re: Interactive MD - 3DSystems Touch Trollmann, Marius (Mon Dec 04 2023 - 12:34:51 CST)
Interactive MD - 3DSystems Touch Trollmann, Marius (Sun Nov 26 2023 - 07:19:56 CST)
- Re: Interactive MD - 3DSystems Touch Trollmann, Marius (Mon Nov 27 2023 - 10:24:50 CST)
SASA Cutoff Value for Residues on Protein Surface Kevin Lin (Tue Nov 21 2023 - 18:08:58 CST)
- Re: SASA Cutoff Value for Residues on Protein Surface Roni Saiba (Tue Nov 21 2023 - 22:02:41 CST)
- Re: SASA Cutoff Value for Residues on Protein Surface Josh (Wed Nov 22 2023 - 11:20:46 CST)
Issue assigning impropers with topotools SHIVAM TIWARI (Tue Nov 21 2023 - 00:21:27 CST)
- Re: Issue assigning impropers with topotools Diego Gomes (Thu Dec 07 2023 - 09:31:44 CST)
  - Re: Issue assigning impropers with topotools SHIVAM TIWARI (Thu Dec 07 2023 - 09:37:08 CST)
Re: How to evaluate VMD performance properly? Vermaas, Josh (Mon Nov 20 2023 - 08:57:13 CST)
- Re: How to evaluate VMD performance properly? Diego Gomes (Mon Nov 20 2023 - 22:30:15 CST)
  - Re: How to evaluate VMD performance properly? Frederico De Santana Pontes (Tue Nov 21 2023 - 03:39:12 CST)
- Re: How to evaluate VMD performance properly? Frederico De Santana Pontes (Tue Nov 21 2023 - 07:39:39 CST)
  - Re: How to evaluate VMD performance properly? Vermaas, Josh (Tue Nov 21 2023 - 09:01:11 CST)
  - Re: How to evaluate VMD performance properly? Frederico De Santana Pontes (Thu Nov 23 2023 - 05:23:51 CST)
How to evaluate VMD performance properly? Frederico De Santana Pontes (Mon Nov 20 2023 - 06:03:40 CST)
Smoothing PBC jumps across PBC Patrick Charchar (Wed Nov 15 2023 - 23:27:39 CST)
- Re: Smoothing PBC jumps across PBC Jason Smith (Thu Nov 16 2023 - 15:28:49 CST)
  - Re: Re: Smoothing PBC jumps across PBC Diego Gomes (Mon Nov 20 2023 - 22:34:43 CST)
Commands runs manually but not as a script Bill McIntyre (Fri Nov 03 2023 - 10:58:11 CDT)
- Re: Commands runs manually but not as a script Diego Gomes (Tue Nov 07 2023 - 09:19:01 CST)
- Re: Commands runs manually but not as a script CHARLES MCCALLUM (Fri Nov 24 2023 - 19:23:05 CST)
STRIDE breaks after 100,000 protein atoms Vasista (Wed Nov 01 2023 - 06:36:38 CDT)
- Re: STRIDE breaks after 100,000 protein atoms Diego Gomes (Thu Nov 02 2023 - 12:58:25 CDT)
  - Re: STRIDE breaks after 100,000 protein atoms Diego Gomes (Thu Nov 02 2023 - 13:57:33 CDT)
Error on VMD Tkconsole : syntax error near unexpected token Yixin Chen (Tue Oct 31 2023 - 10:55:22 CDT)
- Re: Error on VMD Tkconsole : syntax error near unexpected token Josh (Thu Nov 02 2023 - 15:36:48 CDT)
  - Re: Error on VMD Tkconsole : syntax error near unexpected token Yixin Chen (Fri Nov 03 2023 - 05:11:19 CDT)
VMD openGL over ssh from a server with NVIDIA Gianluca Interlandi (Mon Oct 30 2023 - 19:13:02 CDT)
- Re: VMD openGL over ssh from a server with NVIDIA Victor Kwan (Tue Oct 31 2023 - 16:44:58 CDT)
  - Re: VMD openGL over ssh from a server with NVIDIA Gianluca Interlandi (Tue Oct 31 2023 - 17:05:44 CDT)
MacOS VMD1.9.4.a55 crashes- malloc: can't allocate region Subha Kalyaanamoorthy (Mon Oct 30 2023 - 11:01:09 CDT)
Molefacture 2 does not generate angles & dihedrals PaweÅ‚ KÄ™dzierski (Mon Oct 30 2023 - 02:54:26 CDT)
- Re: Molefacture 2 does not generate angles & dihedrals Pawel Kedzierski (Mon Oct 30 2023 - 07:22:18 CDT)
  - Re: Molefacture 2 does not generate angles & dihedrals Jirui Yang (Mon Oct 30 2023 - 12:20:33 CDT)
Creating Dummy Atoms in VMD Using TCL Script Kevin Lin (Fri Oct 27 2023 - 15:16:45 CDT)
- Re: Creating Dummy Atoms in VMD Using TCL Script Smith, Harper E. (Fri Oct 27 2023 - 15:40:40 CDT)
ffTK Tabs for Just Dihedral Optimization Can I Just Use Scan and Opt Tabs Inquiry? Joel Subach (Fri Oct 27 2023 - 11:18:02 CDT)
- Re: ffTK Tabs for Just Dihedral Optimization Can I Just Use Scan and Opt Tabs Inquiry? Joel Subach (Tue Feb 20 2024 - 06:04:23 CST)
ffTK Scan Torsions Scan +/-and Step Size Inquiry which are Best Values? Joel Subach (Fri Oct 27 2023 - 11:12:38 CDT)
Re: ffTK Opt Torsions Tab Hysteresis Problem in the QM Calculation Inquiry or Phase Periodicity error? Joel Subach (Thu Oct 26 2023 - 11:09:03 CDT)
- Re: ffTK Opt Torsions Tab Hysteresis Problem in the QM Calculation Inquiry or Phase Periodicity error? Joel Subach (Tue Feb 20 2024 - 06:06:29 CST)
Tcl/Tk misbehave after upgrading MacOS to Sonoma (14.0) Cassiano Langini (Mon Oct 23 2023 - 05:17:56 CDT)
Script to Build Cyclic Peptides Bill McIntyre (Sun Oct 22 2023 - 17:38:30 CDT)
- Re: Script to Build Cyclic Peptides Josh (Mon Oct 23 2023 - 07:57:20 CDT)
  - Re: Script to Build Cyclic Peptides Bill McIntyre (Tue Oct 24 2023 - 00:52:02 CDT)
ffTK Opt Torsions Refine Section i.e. PERIODICITY, PHASE SHIFT Values? Joel Subach (Sun Oct 22 2023 - 07:21:10 CDT)
- Re: ffTK Opt Torsions Refine Section i.e. PERIODICITY, PHASE SHIFT Values? Josh (Mon Oct 23 2023 - 07:51:12 CDT)
  - Re: ffTK Opt Torsions Refine Section i.e. PERIODICITY, PHASE SHIFT Values? Joel Subach (Tue Oct 24 2023 - 10:40:24 CDT)
ffTK Parameter Selection i.e. just Scan and Opt Torsion Selection Viable? Joel Subach (Wed Oct 18 2023 - 06:13:50 CDT)
- Re: ffTK Parameter Selection i.e. just Scan and Opt Torsion Selection Viable? Joel Subach (Tue Feb 20 2024 - 06:09:32 CST)
  - Re: Re: ffTK Parameter Selection i.e. just Scan and Opt Torsion Selection Viable? Ebru Ã‡etin (Tue Feb 20 2024 - 07:03:03 CST)
  - Re: Re: ffTK Parameter Selection i.e. just Scan and Opt Torsion Selection Viable? PaweÅ‚ KÄ™dzierski (Tue Feb 20 2024 - 07:29:39 CST)
    - Re: Re: ffTK Parameter Selection i.e. just Scan and Opt Torsion Selection Viable? Joel Subach (Tue Feb 20 2024 - 07:33:37 CST)
Update structure on-the-fly Raman Preet Singh (Mon Oct 16 2023 - 02:18:14 CDT)
- Re: Update structure on-the-fly Josh (Mon Oct 16 2023 - 08:54:23 CDT)
VMD APBS Plugin Issues Kevin Lin (Sun Oct 15 2023 - 19:15:01 CDT)
ffTK FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS Inquiry Joel Subach (Fri Oct 13 2023 - 06:52:49 CDT)
- Re: ffTK FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS Inquiry Gumbart, JC (Fri Oct 13 2023 - 21:49:24 CDT)
ERROR: UNABLE TO FIND IMPROPER PARAMETERS Inquiry Joel Subach (Wed Oct 11 2023 - 09:05:22 CDT)
- Re: ERROR: UNABLE TO FIND IMPROPER PARAMETERS Inquiry Joel Subach (Fri Oct 13 2023 - 06:46:37 CDT)
Total H-bond occupancy analysis Neena Susan Eappen (Mon Sep 25 2023 - 14:14:33 CDT)
- Re: Total H-bond occupancy analysis PaweÅ‚ KÄ™dzierski (Tue Sep 26 2023 - 05:32:52 CDT)
  - Re: Total H-bond occupancy analysis Vermaas, Josh (Tue Sep 26 2023 - 08:06:02 CDT)
    - Re: Total H-bond occupancy analysis Neena Susan Eappen (Thu Sep 28 2023 - 14:34:14 CDT)
<<cionize on macOS error>> ROPÓN-PALACIOS G. G. (Sun Sep 24 2023 - 06:57:26 CDT)
- Re: <<cionize on macOS error>> Castro Martinez, Camila (Mon Sep 25 2023 - 01:49:52 CDT)
  - Re: <<cionize on macOS error>> RopÃ³n-Palacios G. (Mon Sep 25 2023 - 14:52:05 CDT)
<<measure command>> RopÃ³n-Palacios G. (Thu Sep 21 2023 - 16:21:11 CDT)
- Re: <<measure command>> Diego Gomes (Fri Sep 22 2023 - 11:07:32 CDT)
  - Re: <<measure command>> ROPÃ“N-PALACIOS G. G. (Sat Sep 23 2023 - 09:16:15 CDT)
Angle between a vector and a plane Castro Martinez, Camila (Wed Sep 20 2023 - 02:53:52 CDT)
- Re: Angle between a vector and a plane Ashar Malik (Wed Sep 20 2023 - 04:13:25 CDT)
  - Re: Angle between a vector and a plane Vermaas, Josh (Wed Sep 20 2023 - 06:54:23 CDT)
  - Re: Angle between a vector and a plane Vermaas, Josh (Wed Sep 20 2023 - 08:06:25 CDT)
    - Re: Angle between a vector and a plane Castro Martinez, Camila (Wed Sep 20 2023 - 08:42:24 CDT)
    - Re: Angle between a vector and a plane Diego Gomes (Thu Sep 21 2023 - 12:50:19 CDT)
Generate Trajectory using Gaussian Cube Files Jia-Yang Lim (Tue Sep 19 2023 - 23:51:39 CDT)
Viewing Van der Waals bonds of a protein ligand in complex inquiry Joel Subach (Sun Sep 10 2023 - 07:38:30 CDT)
- Re: Viewing Van der Waals bonds of a protein ligand in complex inquiry Vermaas, Josh (Mon Sep 11 2023 - 09:00:34 CDT)
  - Re: Viewing Van der Waals bonds of a protein ligand in complex inquiry Joel Subach (Mon Sep 11 2023 - 10:06:31 CDT)
reading chain labels from amber prmtop Baker, Joseph (Fri Sep 08 2023 - 07:15:42 CDT)
Error in porcupine plot Sanjay Kumar Paul (Thu Aug 31 2023 - 04:06:46 CDT)
- Re: Error in porcupine plot Diego Gomes (Tue Sep 05 2023 - 13:55:55 CDT)
How to shortening bonds length in a molecule ? maxim todoru (Thu Aug 31 2023 - 01:28:26 CDT)
- Re: How to shortening bonds length in a molecule ? Daipayan Sarkar (Thu Aug 31 2023 - 03:00:20 CDT)
  - Re: How to shortening bonds length in a molecule ? maxim todoru (Thu Aug 31 2023 - 04:16:04 CDT)
    - Re: How to shortening bonds length in a molecule ? PaweÅ‚ KÄ™dzierski (Thu Aug 31 2023 - 08:34:35 CDT)
    - Re: How to shortening bonds length in a molecule ? Josh (Thu Aug 31 2023 - 09:15:35 CDT)
Issues with urea and autopsf Simone Gargano (Tue Aug 29 2023 - 07:17:49 CDT)
- Re: Issues with urea and autopsf Josh (Tue Aug 29 2023 - 09:15:58 CDT)
Pulling and Anchoring residues Jeevan Patra (Wed Aug 16 2023 - 06:33:45 CDT)
define custom colours for posX gradient Yogesh Sharma (Wed Aug 16 2023 - 06:30:49 CDT)
Unable to use plots with QwikMD Javier Badilla (Fri Aug 11 2023 - 08:09:42 CDT)
- Re: Unable to use plots with QwikMD Diego Gomes (Sun Aug 13 2023 - 15:18:25 CDT)
FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HB2 CT1 NH3 (ATOMS 1 5 8) SONAL GAHLAWAT (Thu Aug 10 2023 - 13:32:17 CDT)
Diffusion Coefficient calculation Nakshatra Upadhyay (Wed Aug 09 2023 - 11:25:19 CDT)
- Re: Diffusion Coefficient calculation Josh (Wed Aug 09 2023 - 13:49:47 CDT)
  - Re: Diffusion Coefficient calculation Nakshatra Upadhyay (Wed Aug 09 2023 - 15:04:29 CDT)
Custom selection variable Bart Bruininks (Tue Aug 08 2023 - 09:12:23 CDT)
- Re: Custom selection variable Josh (Fri Aug 11 2023 - 08:32:12 CDT)
QwikMD - Steered Molecular Dynamics Query Jeevan Patra (Sun Jul 30 2023 - 09:18:11 CDT)
- Re: QwikMD - Steered Molecular Dynamics Query Sinclair, Matt (Sun Jul 30 2023 - 13:03:28 CDT)
  - Re: QwikMD - Steered Molecular Dynamics Query Jeevan Patra (Mon Jul 31 2023 - 12:49:20 CDT)
ffTK Load Dihedral Scan Output for Visualization Inquiry Joel Subach (Sun Jul 30 2023 - 07:05:50 CDT)
Drawing ellipsoids Johannes Haataja (Tue Jul 25 2023 - 14:10:29 CDT)
converting NAMD trajectories GAGANJYOT KAUR BAKSHI (Tue Jul 25 2023 - 01:46:59 CDT)
Re: keeping two ligands in a box Vermaas, Josh (Sun Jul 23 2023 - 03:45:49 CDT)
- Re: keeping two ligands in a box Ackad, Edward (Sun Jul 23 2023 - 07:55:48 CDT)
  - Re: keeping two ligands in a box Vermaas, Josh (Sun Jul 23 2023 - 16:28:50 CDT)
    - Re: keeping two ligands in a box Ackad, Edward (Mon Jul 24 2023 - 08:06:19 CDT)
    - Re: keeping two ligands in a box Vermaas, Josh (Tue Jul 25 2023 - 06:08:36 CDT)
keeping two ligands in a box Ackad, Edward (Sat Jul 22 2023 - 09:00:19 CDT)
Constant pH MD with NAMD Hoang, Oanh Tu (Wed Jul 19 2023 - 08:15:22 CDT)
FW: VMD Programmer Position available at TCBG/UIUC Tajkhorshid, Emad (Thu Jul 13 2023 - 09:20:35 CDT)
(no subject) Alexei Rossokhin (Mon Jul 10 2023 - 07:26:50 CDT)
VMD error - molefacture Hasdemir, Hale Siir (Fri Jul 07 2023 - 10:00:29 CDT)
Problem with converting from lammpstrj to dcd using CatDCD Zuzanna Jedlinska (Fri Jul 07 2023 - 08:54:50 CDT)
covalent bond Alexei Rossokhin (Wed Jul 05 2023 - 09:18:37 CDT)
CHARMM36 and water: can the H-H "bond" be added to the wat.top file used by solvate.tcl? Cindy Cregier (Wed Jul 05 2023 - 01:14:37 CDT)
- Re: CHARMM36 and water: can the H-H "bond" be added to the wat.top file used by solvate.tcl? Gumbart, JC (Wed Jul 05 2023 - 12:32:43 CDT)
OH- Drude parameters Shah, Tanooj (Mon Jul 03 2023 - 17:09:42 CDT)
Fix the Header of DCD File After Merging Multiple Trajectories Efthymiou, Christos (Mon Jul 03 2023 - 04:19:11 CDT)
Re: Concatenate DCD Files with Different Numbers of Atoms Nick Bayhi (Sat Jul 01 2023 - 17:32:29 CDT)
- Re: Concatenate DCD Files with Different Numbers of Atoms Efthymiou, Christos (Wed Jul 05 2023 - 02:53:00 CDT)
Concatenate DCD Files with Different Numbers of Atoms Efthymiou, Christos (Sat Jul 01 2023 - 16:04:35 CDT)
- Re: Concatenate DCD Files with Different Numbers of Atoms Strahs, Dr. Daniel Bernard (Sat Jul 01 2023 - 21:40:55 CDT)
location of light sources in vmd Yogesh Sharma (Mon Jun 26 2023 - 01:58:45 CDT)
Has anyone successfully executed ORCA instead of Gaussian for ffTK? Joel Subach (Sun Jun 25 2023 - 06:28:49 CDT)
network analysis for gromacs jing liang (Sat Jun 24 2023 - 02:44:51 CDT)
Re: ffTK Opt Torsions .log file input Inquiry Joel Subach (Thu Jun 22 2023 - 07:43:40 CDT)
- Re: Re: ffTK Opt Torsions .log file input Inquiry Joel Subach (Sun Jun 25 2023 - 06:20:01 CDT)
  - Re: Re: ffTK Opt Torsions .log file input Inquiry Joel Subach (Tue Feb 20 2024 - 06:15:00 CST)
network analysis on Windows 11 jing liang (Thu Jun 22 2023 - 04:51:45 CDT)
ffTK Scan Torsions Generate Dihedral Scan Input OUTPUT Inquiry Joel Subach (Mon Jun 19 2023 - 09:50:49 CDT)
Converting namd trajectory to desmond trajectory GAGANJYOT KAUR BAKSHI (Tue Jun 13 2023 - 14:56:58 CDT)
- Re: Converting namd trajectory to desmond trajectory Hasdemir, Hale Siir (Tue Jun 13 2023 - 17:00:25 CDT)
- Re: Converting namd trajectory to desmond trajectory Diego Gomes (Wed Jun 14 2023 - 14:33:50 CDT)
  - Re: Converting namd trajectory to desmond trajectory GAGANJYOT KAUR BAKSHI (Wed Jun 14 2023 - 14:40:04 CDT)
    - Re: Converting namd trajectory to desmond trajectory Hasdemir, Hale Siir (Wed Jun 14 2023 - 17:05:39 CDT)
ORCA within ffTK Dihedral Angle Optimization Inquiry Joel Subach (Sat Jun 10 2023 - 05:11:26 CDT)
- Re: ORCA within ffTK Dihedral Angle Optimization Inquiry Gumbart, JC (Sun Jun 11 2023 - 15:16:02 CDT)
- Re: ORCA within ffTK Dihedral Angle Optimization Inquiry Joel Subach (Mon Jun 19 2023 - 08:42:54 CDT)
Two postdoctoral positions available at the computational core of the Pittsburgh Center for HIV Protein Interactions External Juan R. Perilla (Thu Jun 08 2023 - 08:37:45 CDT)
Tachyon dat file as input? Shayna Hilburg (Thu Jun 01 2023 - 01:09:47 CDT)
Convert trajectory GAGANJYOT KAUR BAKSHI (Wed May 24 2023 - 21:08:06 CDT)
- Re: Convert trajectory Joel Subach (Thu May 25 2023 - 01:38:07 CDT)
  - Re: Convert trajectory GAGANJYOT KAUR BAKSHI (Thu May 25 2023 - 01:40:01 CDT)
    - Re: Convert trajectory Joel Subach (Thu May 25 2023 - 02:26:17 CDT)
- Re: Convert trajectory Diego Gomes (Wed May 31 2023 - 09:49:07 CDT)
Reminder: Hands-On Workshop On Computational Biophysics in Auburn, AL Mariano Spivak (Fri May 19 2023 - 12:31:05 CDT)
VMD DMS plugin Siyoung Kim (Mon May 15 2023 - 09:08:38 CDT)
VMD DMS plugin Siyoung Kim (Mon May 15 2023 - 09:03:32 CDT)
version 1.9.3 elham sattarinezhad (Fri May 12 2023 - 09:31:35 CDT)
Trajectory Smoothing and length of hydrogen bonds Gabby Leonard (Thu May 11 2023 - 14:54:23 CDT)
- Re: Trajectory Smoothing and length of hydrogen bonds Vermaas, Josh (Thu May 11 2023 - 16:13:12 CDT)
  - Re: Trajectory Smoothing and length of hydrogen bonds Gabby Leonard (Thu May 11 2023 - 16:27:33 CDT)
- Re: Trajectory Smoothing and length of hydrogen bonds Bennion, Brian (Thu May 11 2023 - 16:52:32 CDT)
Question about using fftk with files from QM calculations from Gaussian 16 Matteo Lambrughi (Thu May 11 2023 - 02:52:31 CDT)
- Re: Question about using fftk with files from QM calculations from Gaussian 16 Mariano Spivak (Mon May 15 2023 - 13:22:50 CDT)
VMD BFEE namdbin error Janni Christensen (Tue May 09 2023 - 02:03:44 CDT)
- Re: VMD BFEE namdbin error Gumbart, JC (Wed May 24 2023 - 11:09:20 CDT)
Cartoon representation in VMD with amber netcd file Hoang, Oanh Tu (Fri May 05 2023 - 05:41:15 CDT)
- Re: Cartoon representation in VMD with amber netcd file John Stone (Mon May 08 2023 - 00:12:26 CDT)
Restarting a simulation GAGANJYOT KAUR BAKSHI (Wed May 03 2023 - 06:29:22 CDT)
Missing Bond at Periodic Boundary Reza Namakian (Mon May 01 2023 - 09:04:06 CDT)
Random Sudden Increase in RMSD Near End of Simulation Efthymiou, Christos (Fri Apr 28 2023 - 01:58:28 CDT)
- Re: Random Sudden Increase in RMSD Near End of Simulation Vermaas, Josh (Fri Apr 28 2023 - 04:20:23 CDT)
  - Re: Random Sudden Increase in RMSD Near End of Simulation Efthymiou, Christos (Mon May 01 2023 - 11:43:33 CDT)
    - Re: Random Sudden Increase in RMSD Near End of Simulation Josh Vermaas (Mon May 01 2023 - 12:02:21 CDT)
    - Re: Random Sudden Increase in RMSD Near End of Simulation Efthymiou, Christos (Mon May 01 2023 - 13:39:12 CDT)
Formatting of text in label Roshan Shrestha (Fri Apr 21 2023 - 09:14:41 CDT)
Selecting atom of given residue in namdenergy plugin Francesco Pietra (Wed Apr 19 2023 - 05:39:58 CDT)
- Re: namd-l: Selecting atom of given residue in namdenergy plugin Peter Freddolino (Wed Apr 19 2023 - 09:50:00 CDT)
  - Re: Re: namd-l: Selecting atom of given residue in namdenergy plugin Francesco Pietra (Wed Apr 19 2023 - 12:17:37 CDT)
    - Fwd: Re: namd-l: Selecting atom of given residue in namdenergy plugin Francesco Pietra (Wed Apr 19 2023 - 12:41:18 CDT)
Re: Re: Executing ORCA within ffTK Opt Geometry Tab Inquiry Joel Subach (Tue Apr 18 2023 - 11:41:35 CDT)
Re: Executing ORCA within ffTK Opt Geometry Tab Inquiry Joel Subach (Tue Apr 18 2023 - 07:53:13 CDT)
Combining multiple psf into one for collagen protein SONAL GAHLAWAT (Mon Apr 17 2023 - 11:42:20 CDT)
Re: Python crash VMD1.9.4 Vermaas, Josh (Wed Apr 12 2023 - 09:30:56 CDT)
- Re: Python crash VMD1.9.4 Dominique Mias-Lucquin (Thu Apr 13 2023 - 05:05:45 CDT)
  - Re: Python crash VMD1.9.4 Vermaas, Josh (Thu Apr 13 2023 - 08:11:14 CDT)
Python crash VMD1.9.4 Dominique Mias-Lucquin (Wed Apr 12 2023 - 08:02:19 CDT)
- Re: Python crash VMD1.9.4 Axel Kohlmeyer (Wed Apr 12 2023 - 09:57:28 CDT)
Create bonds in VMD Rajorshi Chattopadhyay (Tue Apr 11 2023 - 15:21:54 CDT)
- Re: Create bonds in VMD Giacomo Fiorin (Tue Apr 11 2023 - 16:16:29 CDT)
Gaussian09 install on macOS Inquiry Joel Subach (Tue Apr 11 2023 - 07:47:02 CDT)
- Re: Gaussian09 install on macOS Inquiry Axel Kohlmeyer (Tue Apr 11 2023 - 08:31:28 CDT)
  - Re: Gaussian09 install on macOS Inquiry Joel Subach (Tue Apr 11 2023 - 08:35:27 CDT)
    - Re: Gaussian09 install on macOS Inquiry Axel Kohlmeyer (Tue Apr 11 2023 - 08:43:23 CDT)
  - Re: Gaussian09 install on macOS Inquiry Giacomo Fiorin (Tue Apr 11 2023 - 10:03:39 CDT)
Re: fftk-Tutorial Writing psf and pdb files from a CGenFF .str File Inquiry Joel Subach (Fri Apr 07 2023 - 07:24:56 CDT)
- Re: fftk-Tutorial Writing psf and pdb files from a CGenFF .str File Inquiry Joel Subach (Fri Apr 07 2023 - 11:35:41 CDT)
Render straight to ffmpeg/NVENC ? Diego Gomes (Wed Apr 05 2023 - 15:08:10 CDT)
- Re: Render straight to ffmpeg/NVENC ? John Stone (Wed Apr 05 2023 - 23:05:51 CDT)
Node selection in network view GAGANJYOT KAUR BAKSHI (Tue Apr 04 2023 - 00:29:10 CDT)
vmd mpi parallel rendering with SLURM RenÃ© Hafner TUK (Thu Mar 30 2023 - 02:28:18 CDT)
- Re: vmd mpi parallel rendering with SLURM John Stone (Wed Apr 05 2023 - 23:38:27 CDT)
  - Re: vmd mpi parallel rendering with SLURM Chris Taylor (Thu Apr 06 2023 - 21:14:08 CDT)
Cannot open parm7 file through tcl script, but can open via graphic interface Fernando Amrein (Mon Mar 27 2023 - 19:15:54 CDT)
Re: ffTK Opt Torsions Refine Section EDIT ENTRY SECTION PROBLEM Joel Subach (Mon Mar 27 2023 - 07:25:41 CDT)
- Re: Re: ffTK Opt Torsions Refine Section EDIT ENTRY SECTION PROBLEM Gumbart, JC (Tue Mar 28 2023 - 18:04:16 CDT)
  - Re: Re: ffTK Opt Torsions Refine Section EDIT ENTRY SECTION PROBLEM Gumbart, JC (Tue Mar 28 2023 - 18:06:57 CDT)
Atoms dropped on running AutoPSF Priyanshu Gupta (Fri Mar 24 2023 - 12:52:46 CDT)
- Re: Atoms dropped on running AutoPSF Ashar Malik (Fri Mar 24 2023 - 19:38:09 CDT)
Show tcl console selections in VMD graphical display Alexandre Suman de AraÃºjo (Thu Mar 23 2023 - 04:06:05 CDT)
- Re: Show tcl console selections in VMD graphical display Diego Gomes (Thu Mar 23 2023 - 09:11:43 CDT)
  - Re: Show tcl console selections in VMD graphical display Alexandre Suman de AraÃºjo (Thu Mar 23 2023 - 09:53:42 CDT)
Select waters inside cylinder ROPÃ“N-PALACIOS G. (Tue Mar 21 2023 - 16:25:47 CDT)
calculation of rotation angle Sangita Kachhap (Tue Mar 21 2023 - 13:05:05 CDT)
- Re: calculation of rotation angle Ashar Malik (Tue Mar 21 2023 - 15:50:07 CDT)
- Re: calculation of rotation angle Norbert Straeter (Wed Mar 22 2023 - 03:35:17 CDT)
  - Re: calculation of rotation angle Giacomo Fiorin (Wed Mar 22 2023 - 05:27:42 CDT)
Re: No ffTK .gau Extension in Determine File Type in VMD for Visualization Problem? Joel Subach (Fri Mar 17 2023 - 16:04:23 CDT)
- Re: Re: No ffTK .gau Extension in Determine File Type in VMD for Visualization Problem? Gumbart, JC (Wed Mar 22 2023 - 16:40:10 CDT)
  - Re: Re: No ffTK .gau Extension in Determine File Type in VMD for Visualization Problem? Gumbart, JC (Thu Mar 23 2023 - 10:50:53 CDT)
  - Re: Re: No ffTK .gau Extension in Determine File Type in VMD for Visualization Problem? Gumbart, JC (Thu Mar 23 2023 - 13:29:13 CDT)
    - Re: Re: No ffTK .gau Extension in Determine File Type in VMD for Visualization Problem? Joel Subach (Thu Mar 23 2023 - 13:45:28 CDT)
PDB with CONECT records Raman Preet Singh (Tue Mar 14 2023 - 08:18:34 CDT)
ffTK Inquiry Joel Subach (Mon Mar 13 2023 - 20:28:51 CDT)
- Re: ffTK Inquiry Vardan Vardanyan (Mon Mar 13 2023 - 21:36:38 CDT)
  - Re: ffTK Inquiry Joel Subach (Tue Mar 14 2023 - 06:32:30 CDT)
Two questions: reordering molecule IDs and deleting frames with TCL commands Strahs, Dr. Daniel Bernard (Sat Mar 11 2023 - 17:03:09 CST)
- Re: Two questions: reordering molecule IDs and deleting frames with TCL commands Axel Kohlmeyer (Sat Mar 11 2023 - 23:23:27 CST)
  - Re: Two questions: reordering molecule IDs and deleting frames with TCL commands Axel Kohlmeyer (Sat Mar 11 2023 - 23:49:00 CST)
Error with Catdcd Efthymiou, Christos (Tue Mar 07 2023 - 16:47:47 CST)
- Re: Error with Catdcd Victor Kwan (Wed Mar 08 2023 - 02:18:40 CST)
can't build VMD on MacOs Ventura: use of undeclared identifier 'msms' Alexander Beerhoff (Tue Mar 07 2023 - 08:56:42 CST)
- Re: can't build VMD on MacOs Ventura: use of undeclared identifier 'msms' John Stone (Tue Mar 07 2023 - 12:55:57 CST)
  - Re: can't build VMD on MacOs Ventura: use of undeclared identifier 'msms' Alexander Beerhoff (Tue Mar 07 2023 - 19:55:15 CST)
helix content colvar for a 3-10 helix Diship Srivastava (Tue Mar 07 2023 - 00:46:08 CST)
Autopsf Not Generating Atom Numbers Beyond 99999 Stefan Lyne Oliver (Wed Mar 01 2023 - 13:41:26 CST)
New Cartoon representation - Ubuntu 16.zdsmith_at_gmail.com (Wed Mar 01 2023 - 12:09:48 CST)
Font size of the colorbar legends and rotation of the colorscale bar bibhab majumdar (Sun Feb 26 2023 - 22:44:56 CST)
Rotation of the color scale bar in VMD bibhab majumdar (Sun Feb 26 2023 - 22:21:11 CST)
Set constant length scale to molecules in boxes of different sizes Pacci Evaristo, Felipe Fabricio (Sun Feb 26 2023 - 14:39:37 CST)
Question about NMD file visualization Sruthi Sudhakar (Sun Feb 26 2023 - 04:18:50 CST)
Fwd: Problem building vmd with ospray - OSPRayRenderer.h error: â€˜OSPModelâ€™ does not name a typ Alexander Beerhoff (Thu Feb 23 2023 - 22:47:16 CST)
- Re: Fwd: Problem building vmd with ospray - OSPRayRenderer.h error: â€˜OSPModelâ€™ does not name a typ Axel Kohlmeyer (Thu Feb 23 2023 - 23:55:57 CST)
  - Re: Re: Fwd: Problem building vmd with ospray - OSPRayRenderer.h error: â€˜OSPModelâ€™ does not name a typ Alexander Beerhoff (Fri Feb 24 2023 - 16:09:58 CST)
    - Re: Re: Re: Fwd: Problem building vmd with ospray - OSPRayRenderer.h error: ???OSPModel??? does not name a typ John Stone (Fri Feb 24 2023 - 20:03:54 CST)
- Re: Fwd: Problem building vmd with ospray - OSPRayRenderer.h error: â€˜OSPModelâ€™ does not name a typ Vermaas, Josh (Fri Feb 24 2023 - 00:19:28 CST)
Problem with make_trajectory_movie_files script for lammps trajectory with -dispdev text Marin Paolo Virgile Vatin (Fri Feb 17 2023 - 04:46:15 CST)
- Re: Problem with make_trajectory_movie_files script for lammps trajectory with -dispdev text Axel Kohlmeyer (Fri Feb 17 2023 - 06:45:21 CST)
VMD 64-bit Windows OSPRay Initialization Error Possible Fix Mortimer Hemmit (Tue Feb 14 2023 - 16:12:48 CST)
- Re: VMD 64-bit Windows OSPRay Initialization Error Possible Fix Chris Taylor (Tue Feb 14 2023 - 22:41:23 CST)
  - Re: VMD 64-bit Windows OSPRay Initialization Error Possible Fix Mortimer Hemmit (Thu May 04 2023 - 16:05:59 CDT)
Viewing post script images GAGANJYOT KAUR BAKSHI (Mon Feb 13 2023 - 05:43:29 CST)
- Re: Viewing post script images John Stone (Mon Feb 13 2023 - 09:15:20 CST)
ChatGPT knows basic VMD scripting... John Stone (Sun Feb 12 2023 - 22:45:01 CST)
- Re: ChatGPT knows basic VMD scripting... Dusan Racko (Mon Feb 13 2023 - 07:27:29 CST)
- Re: ChatGPT knows basic VMD scripting... EDUARDO JOSÃ‰ AZEVEDO CORREA (Mon Feb 13 2023 - 09:37:06 CST)
- Re: ChatGPT knows basic VMD scripting... Bennion, Brian (Mon Feb 13 2023 - 11:28:20 CST)
VMD on Windows 11 Pol Garcia-Segura (Wed Feb 08 2023 - 11:58:56 CST)
- Re: VMD on Windows 11 Axel Kohlmeyer (Wed Feb 08 2023 - 12:57:05 CST)
  - Re: VMD on Windows 11 Pol Garcia-Segura (Wed Feb 08 2023 - 13:18:56 CST)
    - Re: VMD on Windows 11 Atanu Acharya (Wed Feb 08 2023 - 15:39:47 CST)
BFEE Francesco Coppola (Wed Feb 08 2023 - 11:33:42 CST)
1-Nanotube Zigzag and 2-saving coordinates problem srikasi.qut_at_gmail.com (Tue Feb 07 2023 - 00:00:41 CST)
Uninstalling VMD Sarthak Mohanty (Mon Feb 06 2023 - 01:40:43 CST)
- Re: Uninstalling VMD Giacomo Fiorin (Mon Feb 06 2023 - 07:46:44 CST)
fftk Improper fitting Rizal Sinaga (Thu Feb 02 2023 - 18:12:52 CST)
How to change stride of trajectory initially loaded in CaFE Plugin Efthymiou, Christos (Thu Feb 02 2023 - 17:45:36 CST)
Nanopore Sequencing Tutorial Problem Andrew Doig (Thu Feb 02 2023 - 19:07:57 CST)
Image render in VMD GAGANJYOT KAUR BAKSHI (Tue Jan 31 2023 - 05:31:53 CST)
- Re: Image render in VMD amin sagar (Tue Jan 31 2023 - 07:58:50 CST)
- Re: Image render in VMD Geist, Norman (Tue Jan 31 2023 - 08:22:44 CST)
- Re: Image render in VMD Josh Vermaas (Tue Jan 31 2023 - 09:02:35 CST)
  - Re: Image render in VMD GAGANJYOT KAUR BAKSHI (Tue Jan 31 2023 - 09:04:48 CST)
Running VMD 1.9.4alpha on newer GPUs that require CUDA 11+ and OptiX 7+ Brendan Dennis (Mon Jan 30 2023 - 20:16:39 CST)
- Re: Running VMD 1.9.4alpha on newer GPUs that require CUDA 11+ and OptiX 7+ Josh Vermaas (Tue Jan 31 2023 - 08:58:37 CST)
  - Re: Running VMD 1.9.4alpha on newer GPUs that require CUDA 11+ and OptiX 7+ Brendan Dennis (Tue Jan 31 2023 - 13:16:41 CST)
  - Re: Running VMD 1.9.4alpha on newer GPUs that require CUDA 11+ and OptiX 7+ Brendan Dennis (Wed Feb 01 2023 - 13:51:43 CST)
    - Re: Running VMD 1.9.4alpha on newer GPUs that require CUDA 11+ and OptiX 7+ Rudy Richardson (Wed Feb 01 2023 - 15:59:36 CST)
- Re: Running VMD 1.9.4alpha on newer GPUs that require CUDA 11+ and OptiX 7+ Rudy Richardson (Tue Jan 31 2023 - 10:22:04 CST)
bash calling multiple python scripts that open vmd pauses Ryan Woltz (Sat Jan 21 2023 - 04:30:13 CST)
- Re: bash calling multiple python scripts that open vmd pauses Ashar Malik (Sat Jan 21 2023 - 05:36:52 CST)
  - Re: bash calling multiple python scripts that open vmd pauses Ryan Woltz (Sat Jan 21 2023 - 17:26:02 CST)
    - Re: bash calling multiple python scripts that open vmd pauses Ryan Woltz (Sat Jan 21 2023 - 21:47:48 CST)
fftk, charge optimization, fragmentation Vardan Vardanyan (Thu Jan 19 2023 - 13:39:33 CST)
- Re: fftk, charge optimization, fragmentation Ernesto Aleksei Delgado Hurtado (Thu Jan 19 2023 - 18:09:44 CST)
get "x y z" from smoothed coordinates Diego Gomes (Wed Jan 18 2023 - 15:20:37 CST)
- Re: get "x y z" from smoothed coordinates Geist, Norman (Thu Jan 19 2023 - 04:05:29 CST)
Regarding Network Analysis GAGANJYOT KAUR BAKSHI (Wed Jan 18 2023 - 02:01:29 CST)
PCA/NMA/Secondary structure analysis with bigdcd Hocine el khaoudi enyoury (Tue Jan 17 2023 - 03:53:21 CST)
Vmd Hardware Requirements long MD visual/analysis Hocine el khaoudi enyoury (Mon Jan 16 2023 - 07:27:18 CST)
- Re: Vmd Hardware Requirements long MD visual/analysis Vermaas, Josh (Mon Jan 16 2023 - 09:22:38 CST)
TCL Script for PCA? Efthymiou, Christos (Mon Jan 09 2023 - 15:24:06 CST)
Aligning of ions and DNA angad sharma (Sun Jan 08 2023 - 03:00:11 CST)
measure sasa algorithm? Alvea Tasneem (Fri Jan 06 2023 - 11:25:23 CST)
Labels on top of atoms Pierpaolo Pravatto (Mon Jan 02 2023 - 02:27:13 CST)
coloring Fateme Aghaei (Fri Dec 30 2022 - 15:45:45 CST)
- Re: coloring Axel Kohlmeyer (Fri Dec 30 2022 - 19:16:49 CST)
<< Centering/aligning several molecules >> I. Camps (Thu Dec 29 2022 - 13:26:04 CST)
- Re: << Centering/aligning several molecules >> John Stone (Thu Dec 29 2022 - 13:54:56 CST)
- Re: << Centering/aligning several molecules >> Giacomo Fiorin (Thu Dec 29 2022 - 14:24:54 CST)
  - Re: << Centering/aligning several molecules >> I. Camps (Fri Dec 30 2022 - 14:43:28 CST)
- Re: << Centering/aligning several molecules >> Vermaas, Josh (Fri Dec 30 2022 - 11:00:34 CST)
<< thresholds for drawing bonds >> I. Camps (Wed Dec 21 2022 - 13:49:48 CST)
- Re: << thresholds for drawing bonds >> John Stone (Tue Dec 27 2022 - 10:10:24 CST)
  - Re: << thresholds for drawing bonds >> I. Camps (Tue Dec 27 2022 - 14:54:19 CST)
    - Re: << thresholds for drawing bonds >> Axel Kohlmeyer (Tue Dec 27 2022 - 16:12:10 CST)
(no subject) Ivan Franzoni (Tue Dec 20 2022 - 12:01:20 CST)
Error in merging two PSFs and PDBs using a TCL script Sarthak Mohanty (Fri Dec 16 2022 - 11:59:06 CST)
BFEE calculations for protein-protein complexes Deepshikha Ghosh 19310001 (Mon Dec 12 2022 - 04:23:41 CST)
Issue install VMD 1.9.3 Spack Arsene Marian Alain (Mon Dec 05 2022 - 01:34:27 CST)
- Re: Issue install VMD 1.9.3 Spack Axel Kohlmeyer (Mon Dec 05 2022 - 05:45:24 CST)
  - Re: Issue install VMD 1.9.3 Spack Vermaas, Josh (Mon Dec 05 2022 - 10:13:17 CST)
Question about code Raag Saluja (Sun Dec 04 2022 - 13:43:40 CST)
- Re: Question about code Jason Smith (Sun Dec 04 2022 - 15:25:23 CST)
Generating single amino acid using PSFGEN Huang, Caleb (Fri Dec 02 2022 - 16:23:54 CST)
- Re: Generating single amino acid using PSFGEN PaweÅ‚ KÄ™dzierski (Sat Dec 03 2022 - 05:19:10 CST)
Unknown variable modifier. while running vmd Diship Srivastava (Tue Nov 29 2022 - 23:33:40 CST)
- Re: Unknown variable modifier. while running vmd John Stone (Thu Dec 29 2022 - 11:20:31 CST)
vmd-l@ks.uiuc.edu angad sharma (Tue Nov 22 2022 - 05:06:23 CST)
- Re: vmd-l@ks.uiuc.edu angad sharma (Fri Nov 25 2022 - 00:33:20 CST)
  - Re: Re: vmd-l@ks.uiuc.edu Raman Preet Singh (Sun Nov 27 2022 - 08:01:01 CST)
Listing solvent accessible surface area per residue Bill McIntyre (Sat Nov 19 2022 - 13:55:14 CST)
- Re: Listing solvent accessible surface area per residue Diego Gomes (Fri Dec 09 2022 - 14:14:44 CST)
NewCartoon or NewRibbons Secondary Structure methods don't work with latest updated Mesa 22.2.3 David Carrasco de Busturia (Sat Nov 19 2022 - 05:48:51 CST)
- Re: NewCartoon or NewRibbons Secondary Structure methods don't work with latest updated Mesa 22.2.3 John Stone (Thu Dec 29 2022 - 11:17:52 CST)
  - Re: NewCartoon or NewRibbons Secondary Structure methods don't work with latest updated Mesa 22.2.3 David Carrasco de Busturia (Wed Jan 25 2023 - 02:10:51 CST)
Residence time calculation angad sharma (Thu Nov 17 2022 - 23:21:43 CST)
C atom projection calculation Kodituwakku,Dimuthu Nirmani (Wed Nov 16 2022 - 22:23:23 CST)
- Re: C atom projection calculation Giacomo Fiorin (Thu Nov 17 2022 - 08:03:42 CST)
Coloring/material of ply files Bart Bruininks (Tue Nov 15 2022 - 09:29:59 CST)
Atomselect entire water molecule using pbwithin Huang, Caleb (Fri Nov 11 2022 - 14:51:53 CST)
- Re: Atomselect entire water molecule using pbwithin Josh Vermaas (Fri Nov 11 2022 - 16:46:51 CST)
Hbonds details every frame Nick Bayhi (Thu Nov 10 2022 - 16:57:02 CST)
- Re: Hbonds details every frame Gumbart, JC (Fri Nov 11 2022 - 14:24:10 CST)
Parametrization of sulfur-containing compound with ffTK Trollmann, Marius (Thu Nov 10 2022 - 10:36:32 CST)
Residence time of ions angad sharma (Thu Nov 10 2022 - 00:32:40 CST)
- Re: Residence time of ions Daipayan Sarkar (Thu Nov 10 2022 - 08:02:17 CST)
MacOS VMD1.9.4.a55 crashes- malloc: can't allocate region Subha Kalyaanamoorthy (Wed Nov 09 2022 - 11:36:29 CST)
- Re: MacOS VMD1.9.4.a55 crashes- malloc: can't allocate region John Stone (Wed Nov 09 2022 - 19:36:57 CST)
Topotools "guessangles" not assigning angles utku.ozkan_at_bilkent.edu.tr (Wed Nov 09 2022 - 00:05:50 CST)
- Re: Topotools "guessangles" not assigning angles Axel Kohlmeyer (Wed Nov 09 2022 - 03:07:42 CST)
  - Re: Topotools "guessangles" not assigning angles utku.ozkan_at_bilkent.edu.tr (Wed Nov 09 2022 - 04:29:16 CST)
Error with PCA Calculation using Normal Mode Wizard Efthymiou, Christos (Tue Nov 08 2022 - 12:06:45 CST)
Linux HiDPI screens FX (Mon Nov 07 2022 - 08:33:18 CST)
can not visualize bond in vmd Chunli Yan (Fri Nov 04 2022 - 12:49:26 CDT)
visualisation of molecular orbitals in VMD jing liang (Fri Nov 04 2022 - 06:37:41 CDT)
- Re: visualisation of molecular orbitals in VMD Marcelo C. R. Melo (Fri Nov 04 2022 - 10:28:52 CDT)
Extracting hydrogen bond information of water Ata Madanchi (Thu Nov 03 2022 - 14:28:43 CDT)
- Re: Extracting hydrogen bond information of water Josh Vermaas (Thu Nov 03 2022 - 15:29:05 CDT)
VMD 1.9.4.a53 crashes on windows 11 Atanu Acharya (Thu Nov 03 2022 - 11:01:49 CDT)
- Re: VMD 1.9.4.a53 crashes on windows 11 John Stone (Thu Nov 03 2022 - 13:44:56 CDT)
3d visualization VMD / NVIDIA / Linux Vlad Cojocaru (Wed Nov 02 2022 - 05:26:47 CDT)
- Re: 3d visualization VMD / NVIDIA / Linux John Stone (Thu Dec 29 2022 - 11:51:40 CST)
Simple MDFF Tutorial - 1ake does not fit into map Stefan Lyne Oliver (Tue Nov 01 2022 - 22:09:45 CDT)
- RE: Simple MDFF Tutorial - 1ake does not fit into map Stefan Lyne Oliver (Fri Nov 04 2022 - 18:52:47 CDT)
  - Re: RE: Simple MDFF Tutorial - 1ake does not fit into map Gumbart, JC (Sun Nov 06 2022 - 15:28:50 CST)
Question about running script for hydrogen bonding analysis Daniel Adrion (Sat Oct 29 2022 - 09:04:33 CDT)
Re: Obtaining a list of surface exposed residues Bill McIntyre (Fri Oct 28 2022 - 02:36:24 CDT)
helix orientation angle CPMAS Chen (Thu Oct 27 2022 - 20:55:45 CDT)
- Re: helix orientation angle JÃ©rÃ´me HÃ©nin (Mon Oct 31 2022 - 07:24:55 CDT)
  - Re: helix orientation angle CPMAS Chen (Wed Nov 02 2022 - 14:42:48 CDT)
QMMM Update Mcguire, Kelly (Fri Oct 21 2022 - 11:41:42 CDT)
QMMM Update Mcguire, Kelly (Fri Oct 21 2022 - 11:36:06 CDT)
- Re: QMMM Update Mcguire, Kelly (Sun Oct 23 2022 - 11:53:16 CDT)
QMMM Update Mcguire, Kelly (Thu Oct 20 2022 - 20:29:15 CDT)
- Re: QMMM Update Mcguire, Kelly (Fri Oct 21 2022 - 14:42:37 CDT)
  - Re: QMMM Update Mcguire, Kelly (Fri Oct 21 2022 - 14:42:53 CDT)
    - Re: QMMM Update Bennion, Brian (Fri Oct 21 2022 - 14:44:12 CDT)
    - Re: QMMM Update Mcguire, Kelly (Fri Oct 21 2022 - 14:45:18 CDT)
Two Proteins Question Mcguire, Kelly (Wed Oct 19 2022 - 16:23:37 CDT)
- Re: Two Proteins Question JÃ©rÃ´me HÃ©nin (Thu Oct 20 2022 - 04:12:11 CDT)
Use VMD to produce images and videos to sell Henrique Fernandes (Sun Oct 16 2022 - 10:02:52 CDT)
- Re: Use VMD to produce images and videos to sell Diego Gomes (Tue Oct 18 2022 - 08:29:18 CDT)
  - Re: Use VMD to produce images and videos to sell John Stone (Tue Oct 18 2022 - 15:12:00 CDT)
    - Re: Use VMD to produce images and videos to sell Henrique Fernandes (Wed Oct 19 2022 - 12:22:19 CDT)
Protein breaks after automatic psf builder Neeraj Dhandia (Fri Oct 14 2022 - 06:45:08 CDT)
- Re: Protein breaks after automatic psf builder PaweÅ‚ KÄ™dzierski (Mon Oct 17 2022 - 07:11:35 CDT)
When should I use NTER and NNEU as a patch? Derman BaÅŸtÃ¼rk (Tue Oct 11 2022 - 23:38:26 CDT)
- Re: When should I use NTER and NNEU as a patch? Daniel Fellner (Wed Oct 12 2022 - 01:38:40 CDT)
Using BigDCD on Simulation Files Located on Mapped Network Drive Efthymiou, Christos (Tue Oct 11 2022 - 13:33:08 CDT)
- Re: Using BigDCD on Simulation Files Located on Mapped Network Drive Norbert Straeter (Tue Oct 11 2022 - 14:05:57 CDT)
  - Re: Using BigDCD on Simulation Files Located on Mapped Network Drive Efthymiou, Christos (Tue Oct 11 2022 - 14:15:52 CDT)
- Re: Using BigDCD on Simulation Files Located on Mapped Network Drive Georcki Ropon (Thu Oct 13 2022 - 14:31:37 CDT)
How to get a file of trajectories and velocities in VMD? Eduardo Estevez (Mon Oct 10 2022 - 16:53:39 CDT)
Losing atoms while solvating Rajat Chakraborty (Mon Oct 10 2022 - 13:06:00 CDT)
QwikMD Error in VMD 1.9.4a53 on Windows 10 Computer Efthymiou, Christos (Mon Oct 10 2022 - 12:04:46 CDT)
Mopac VMD McGuire, Kelly (Sun Oct 09 2022 - 15:13:35 CDT)
Installing VMD store using tkconsole in VMD in Windows 10 Madhavan Narayanan (Sat Oct 08 2022 - 11:31:32 CDT)
Query regarding WISP extension in VMD Sruthi Sudhakar (Thu Oct 06 2022 - 01:31:58 CDT)
- Re: Query regarding WISP extension in VMD Giacomo Fiorin (Thu Oct 06 2022 - 08:52:32 CDT)
Extracting Voxel-based or STL from QuickSurf Representation Max Win (Wed Oct 05 2022 - 15:13:51 CDT)
- Re: Extracting Voxel-based or STL from QuickSurf Representation Josh Vermaas (Wed Oct 05 2022 - 16:51:57 CDT)
VMD disables audio? Strahs, Dr. Daniel Bernard (Wed Oct 05 2022 - 11:50:17 CDT)
- Re: VMD disables audio? John Stone (Wed Oct 05 2022 - 12:58:43 CDT)
  - Re: VMD disables audio? Jason Smith (Wed Oct 05 2022 - 15:20:09 CDT)
Maximum Stride Possible for Publishable Results Efthymiou, Christos (Mon Oct 03 2022 - 13:50:17 CDT)
- Re: Maximum Stride Possible for Publishable Results Ashar Malik (Mon Oct 03 2022 - 23:47:24 CDT)
  - Re: Maximum Stride Possible for Publishable Results Efthymiou, Christos (Tue Oct 04 2022 - 12:43:17 CDT)
Overriding default bond heuristics Raman Preet Singh (Mon Oct 03 2022 - 12:50:36 CDT)
- Re: Overriding default bond heuristics Axel Kohlmeyer (Mon Oct 03 2022 - 13:39:22 CDT)
- Re: Overriding default bond heuristics Josh Vermaas (Mon Oct 03 2022 - 14:36:53 CDT)
  - Re: Overriding default bond heuristics Raman Preet Singh (Tue Oct 04 2022 - 01:48:28 CDT)
Re: Label all atoms using script Raman Preet Singh (Sat Oct 01 2022 - 11:40:20 CDT)
Label all atoms using script Raman Preet Singh (Sat Oct 01 2022 - 08:55:36 CDT)
How to calculate number of water molecules close to a nanostructure Eduardo Estevez (Sat Oct 01 2022 - 06:52:56 CDT)
- Re: How to calculate number of water molecules close to a nanostructure Josh Vermaas (Mon Oct 03 2022 - 09:03:37 CDT)
VMD1.9.4a57 crashes when main console moved to second display Chan, Matthew (Thu Sep 29 2022 - 16:37:35 CDT)
dealing with large pdb files Morteza Chehel Amirani (Tue Sep 27 2022 - 15:50:47 CDT)
INITIALIZATION ERROR --> OSPRay not yet initialized - WIN64, version 1.9.4a53 Chris Taylor (Mon Sep 26 2022 - 18:31:01 CDT)
Part of my molecule isn't rendering in New Cartoon Nick Bayhi (Fri Sep 23 2022 - 16:22:49 CDT)
- Re: Part of my molecule isn't rendering in New Cartoon Vermaas, Josh (Sat Sep 24 2022 - 12:25:01 CDT)
  - Re: Part of my molecule isn't rendering in New Cartoon Trifan, Anda (Sun Sep 25 2022 - 09:03:02 CDT)
Period images not appearing Ackad, Edward (Fri Sep 23 2022 - 13:29:45 CDT)
- Re: Period images not appearing Nathan Kern (Fri Sep 23 2022 - 15:13:43 CDT)
  - Re: Period images not appearing Ackad, Edward (Mon Sep 26 2022 - 14:38:12 CDT)
Ramachandran Dihedral Angles Suspiciously Constant Amanda Jenkins (Fri Sep 23 2022 - 05:14:30 CDT)
- Re: Ramachandran Dihedral Angles Suspiciously Constant Josh Vermaas (Fri Sep 23 2022 - 07:54:53 CDT)
  - Re: Ramachandran Dihedral Angles Suspiciously Constant Josh Vermaas (Fri Sep 23 2022 - 15:36:58 CDT)
  - Re: Ramachandran Dihedral Angles Suspiciously Constant Michael Robinson (Mon Sep 26 2022 - 08:53:11 CDT)
Calculating time variation of potential. Pranjal Sur (Fri Sep 23 2022 - 04:47:39 CDT)
tcl measure bond length script Ryan Woltz (Tue Sep 13 2022 - 17:25:08 CDT)
- Re: tcl measure bond length script Josh Vermaas (Wed Sep 14 2022 - 08:05:29 CDT)
Installation problem on MacOS Monterey Suman Chakrabarty (Sun Sep 11 2022 - 12:16:22 CDT)
- Re: Installation problem on MacOS Monterey FX (Sun Sep 11 2022 - 14:35:32 CDT)
  - Re: Installation problem on MacOS Monterey Suman Chakrabarty (Sun Sep 11 2022 - 22:19:30 CDT)
Multiple Programmer Positions to develop VMD and NAMD Tajkhorshid, Emad (Sun Sep 11 2022 - 10:15:14 CDT)
Rendering structures with Hydrogen Bonds using Tachyon Saumyak Mukherjee (Fri Sep 09 2022 - 08:18:21 CDT)
- Re: Rendering structures with Hydrogen Bonds using Tachyon Diego Gomes (Fri Sep 09 2022 - 13:44:38 CDT)
  - Re: Rendering structures with Hydrogen Bonds using Tachyon Saumyak Mukherjee (Mon Sep 12 2022 - 02:25:16 CDT)
Most relevant VMD install Klimkowski, V (Tue Sep 06 2022 - 20:52:51 CDT)
- Re: Most relevant VMD install Giacomo Fiorin (Wed Sep 07 2022 - 07:55:56 CDT)
- Re: Most relevant VMD install Josh Vermaas (Wed Sep 07 2022 - 07:56:34 CDT)
- Re: Most relevant VMD install Gumbart, JC (Wed Sep 07 2022 - 10:13:18 CDT)
  - Re: Most relevant VMD install Klimkowski, V (Thu Sep 08 2022 - 10:29:47 CDT)
QwikMD QM Tut - FATAL ERROR: Error running command for QM forces calculation hgkrug1_at_gmail.com (Tue Sep 06 2022 - 10:30:58 CDT)
- QwikMD QM Tut - FATAL ERROR: Error running command for QM forces calculation hgkrug1_at_gmail.com (Fri Sep 09 2022 - 02:31:37 CDT)
  - QwikMD QM Tut - FATAL ERROR: Error running command for QM forces calculation hgkrug1_at_gmail.com (Fri Sep 09 2022 - 03:46:55 CDT)
    - QwikMD QM Tut - FATAL ERROR: Error running command for QM forces calculation hgkrug1_at_gmail.com (Mon Sep 12 2022 - 08:38:15 CDT)
Using Molefacture plugin in batch mode Enrico Martinez (Tue Sep 06 2022 - 03:22:44 CDT)
- Re: Using Molefacture plugin in batch mode Peter Freddolino (Tue Sep 06 2022 - 16:42:35 CDT)
  - Re: Using Molefacture plugin in batch mode Enrico Martinez (Wed Sep 07 2022 - 02:44:47 CDT)
    - Re: Using Molefacture plugin in batch mode Peter Freddolino (Wed Sep 07 2022 - 07:52:54 CDT)
    - Re: Using Molefacture plugin in batch mode Enrico Martinez (Wed Sep 07 2022 - 08:53:25 CDT)
patching of sucrose Akash Mondal (Sat Sep 03 2022 - 01:14:51 CDT)
- Re: patching of sucrose Akash Mondal (Sat Sep 03 2022 - 01:37:41 CDT)
Automation of Analysis from QwikMD and Loading Trajectory Without Water in QwikMD Efthymiou, Christos (Thu Sep 01 2022 - 08:48:31 CDT)
- Re: Automation of Analysis from QwikMD and Loading Trajectory Without Water in QwikMD Diego Gomes (Wed Sep 07 2022 - 16:43:28 CDT)
Chains x, y, and z cannot be selected Charles McAnany (Wed Aug 31 2022 - 14:27:29 CDT)
How to choose solid color in clipping plane render with POV-Ray Prateek Bansal (Tue Aug 30 2022 - 11:10:42 CDT)
- Re: How to choose solid color in clipping plane render with POV-Ray John Stone (Tue Aug 30 2022 - 11:42:31 CDT)
  - Re: How to choose solid color in clipping plane render with POV-Ray Carlos Simmerling (Tue Aug 30 2022 - 12:42:58 CDT)
    - Re: How to choose solid color in clipping plane render with POV-Ray John Stone (Tue Aug 30 2022 - 14:45:43 CDT)
Add Topology and Parameters in QwikMD Efthymiou, Christos (Tue Aug 30 2022 - 10:09:37 CDT)
Problem with measure bond command returning -NaN for some frames Norbert Straeter (Mon Aug 29 2022 - 07:32:17 CDT)
- Re: Problem with measure bond command returning -NaN for some frames Vermaas, Josh (Mon Aug 29 2022 - 08:49:37 CDT)
  - Re: Re: Problem with measure bond command returning -NaN for some frames Norbert Straeter (Mon Aug 29 2022 - 11:00:01 CDT)
Correlation matrix illustration via heating map Maghsoud, Yazdan (Sun Aug 28 2022 - 11:08:11 CDT)
DisRG Plugin Availability Efthymiou, Christos (Thu Aug 25 2022 - 10:43:10 CDT)
- Re: DisRG Plugin Availability Trifan, Anda (Thu Aug 25 2022 - 11:56:11 CDT)
- Re: DisRG Plugin Availability Axel Kohlmeyer (Thu Aug 25 2022 - 17:45:01 CDT)
rdf with respect to a specific point michaelmorgan937_at_gmail.com (Wed Aug 24 2022 - 13:17:33 CDT)
- Re: rdf with respect to a specific point Axel Kohlmeyer (Wed Aug 24 2022 - 17:16:42 CDT)
  - RE: rdf with respect to a specific point michaelmorgan937_at_gmail.com (Thu Aug 25 2022 - 17:15:07 CDT)
    - Re: rdf with respect to a specific point Axel Kohlmeyer (Thu Aug 25 2022 - 17:37:03 CDT)
Mutation of Amino Acid Akash Mondal (Sat Aug 20 2022 - 01:11:34 CDT)
CaFE VMD Plugin Errors at PB Calculation Step Efthymiou, Christos (Fri Aug 19 2022 - 04:03:25 CDT)
Error in FFTK charges optimization (Run Optimization) Chenbo Yan (Thu Aug 18 2022 - 21:31:59 CDT)
- Re: Error in FFTK charges optimization (Run Optimization) Pang, Yui Tik (Fri Aug 19 2022 - 08:40:30 CDT)
  - Re: Error in FFTK charges optimization (Run Optimization) Chenbo Yan (Sat Aug 20 2022 - 07:43:52 CDT)
    - RE: Error in FFTK charges optimization (Run Optimization) Pang, Yui Tik (Sun Aug 28 2022 - 20:03:48 CDT)
CaFE Plugin - Didn't Find vDW Parameter for Atom Type HT1 Error Efthymiou, Christos (Thu Aug 18 2022 - 11:11:35 CDT)
- Re: CaFE Plugin - Didn't Find vDW Parameter for Atom Type HT1 Error Geist, Norman (Thu Aug 18 2022 - 12:50:18 CDT)
  - Re: CaFE Plugin - Didn't Find vDW Parameter for Atom Type HT1 Error Efthymiou, Christos (Thu Aug 18 2022 - 15:16:34 CDT)
Angle Cutoff variable for Hydrogen Bonds David Carrasco de Busturia (Thu Aug 18 2022 - 05:41:30 CDT)
- Re: Angle Cutoff variable for Hydrogen Bonds Josh Vermaas (Thu Aug 18 2022 - 08:29:35 CDT)
Protein residue read as solvent Arthur Pereira da Fonseca (Tue Aug 16 2022 - 18:49:52 CDT)
- Re: Protein residue read as solvent Axel Kohlmeyer (Wed Aug 17 2022 - 07:48:42 CDT)
- Re: Protein residue read as solvent Josh Vermaas (Wed Aug 17 2022 - 08:23:19 CDT)
  - RES: Protein residue read as solvent Arthur Pereira da Fonseca (Wed Aug 17 2022 - 10:21:48 CDT)
Re: atomselect for interacting hydroxyl groups Vermaas, Josh (Tue Aug 16 2022 - 12:53:40 CDT)
atomselect for interacting hydroxyl groups Huang, Caleb (Tue Aug 16 2022 - 11:36:40 CDT)
- Re: atomselect for interacting hydroxyl groups Ashar Malik (Tue Aug 16 2022 - 12:53:49 CDT)
problems with OSX 64-bit installation Charlie Mcdowell (Mon Aug 15 2022 - 23:05:09 CDT)
OSPRay error on startup Windows11 Chris Taylor (Thu Aug 11 2022 - 17:26:42 CDT)
Adding Topology+Parameter For Small Molecule in QwikMD Efthymiou, Christos (Tue Aug 09 2022 - 08:09:41 CDT)
Hetero Chain not Recognized by Structure Manipulation Window Efthymiou, Christos (Mon Aug 08 2022 - 11:10:16 CDT)
- Re: Hetero Chain not Recognized by Structure Manipulation Window Efthymiou, Christos (Tue Aug 09 2022 - 05:01:28 CDT)
Preparing Simulation Files Quickly Using QwikMD Efthymiou, Christos (Fri Aug 05 2022 - 03:46:56 CDT)
Multi-core CPU does not work with VMD. toshiaki.tomimori_at_uniadex.co.jp (Wed Aug 03 2022 - 06:10:01 CDT)
- Re: Multi-core CPU does not work with VMD. John Stone (Sat Aug 06 2022 - 01:34:08 CDT)
  - RE: Multi-core CPU does not work with VMD. toshiaki.tomimori_at_uniadex.co.jp (Mon Aug 08 2022 - 02:59:23 CDT)
    - Re: Multi-core CPU does not work with VMD. John Stone (Mon Aug 08 2022 - 22:14:56 CDT)
Unable to Delete Macro QwikMD Error Efthymiou, Christos (Mon Aug 01 2022 - 03:55:53 CDT)
compiling VMD 1.9.3 under Ubuntu 22.04LTS: modern C library issues Strahs, Dr. Daniel Bernard (Sat Jul 30 2022 - 14:04:38 CDT)
- Re: compiling VMD 1.9.3 under Ubuntu 22.04LTS: modern C library issues Axel Kohlmeyer (Sat Jul 30 2022 - 16:04:14 CDT)
Question about Network Analysis tutorial chanyann06_at_stu.scu.edu.cn (Fri Jul 29 2022 - 07:12:07 CDT)
Color change in VMD Saikat Pal (Wed Jul 27 2022 - 10:33:12 CDT)
- Re: Color change in VMD Smith, Harper E. (Wed Jul 27 2022 - 10:48:58 CDT)
  - Display point charges jimkress_58_at_kressworks.org (Wed Aug 24 2022 - 13:55:01 CDT)
Create CHARMM COR files with VMD Prathit Chatterjee (Tue Jul 26 2022 - 08:50:27 CDT)
- Re: Create CHARMM COR files with VMD Axel Kohlmeyer (Tue Jul 26 2022 - 12:09:13 CDT)
Color Coding by Residue Type Peter (Mon Jul 25 2022 - 15:28:58 CDT)
- Re: Color Coding by Residue Type Satyan Sharma (Tue Jul 26 2022 - 04:46:49 CDT)
  - Re: Color Coding by Residue Type Peter (Thu Jul 28 2022 - 09:06:13 CDT)
<< multiple atom selection >> I. Camps (Sat Jul 23 2022 - 11:13:55 CDT)
- Re: << multiple atom selection >> Ashar Malik (Sat Jul 23 2022 - 12:14:54 CDT)
- Re: << multiple atom selection >> Zachary SMITH (Sat Jul 23 2022 - 12:20:13 CDT)
- Re: << multiple atom selection >> Axel Kohlmeyer (Sat Jul 23 2022 - 13:02:47 CDT)
  - Re: << multiple atom selection >> Axel Kohlmeyer (Sat Jul 23 2022 - 13:03:27 CDT)
- Re: << multiple atom selection >> I. Camps (Sat Jul 23 2022 - 16:48:32 CDT)
VMD 1.9.4a57 on Linux ? Thibault TUBIANA (Fri Jul 22 2022 - 09:08:56 CDT)
NAMDEnergy Plugin in VMD Kartik Tulsian (Sat Jul 16 2022 - 05:11:00 CDT)
- Re: NAMDEnergy Plugin in VMD Ashar Malik (Sat Jul 16 2022 - 08:22:11 CDT)
Permanent position Research Software HPC Engineer at the University of Delaware Juan R. Perilla (Thu Jul 14 2022 - 09:19:01 CDT)
Cannot write parm7 file with type parm7 Prathit Chatterjee (Thu Jul 14 2022 - 08:54:37 CDT)
Cafe 1.0 plugin does not recognize commands DENILSON FERREIRA DE OLIVEIRA (Mon Jul 11 2022 - 09:07:19 CDT)
- Re: Cafe 1.0 plugin does not recognize commands John Stone (Tue Jul 12 2022 - 17:19:33 CDT)
  - Re: Cafe 1.0 plugin does not recognize commands DENILSON FERREIRA DE OLIVEIRA (Wed Jul 13 2022 - 02:40:55 CDT)
    - Re: Cafe 1.0 plugin does not recognize commands PaweÅ‚ KÄ™dzierski (Wed Jul 13 2022 - 04:09:11 CDT)
    - Re: Cafe 1.0 plugin does not recognize commands DENILSON FERREIRA DE OLIVEIRA (Wed Jul 13 2022 - 12:43:56 CDT)
PROBLEM INSTALLING VMD Edivaldo Rodrigues (Mon Jul 11 2022 - 06:53:09 CDT)
- Re: PROBLEM INSTALLING VMD John Stone (Tue Jul 12 2022 - 17:16:21 CDT)
  - Re: PROBLEM INSTALLING VMD Edivaldo Rodrigues (Fri Jul 15 2022 - 13:23:10 CDT)
(no subject) Edivaldo Rodrigues (Thu Jul 07 2022 - 16:12:53 CDT)
(no subject) Huertas, Jan (Wed Jul 06 2022 - 12:04:35 CDT)
- Re: Chris Neale (Thu Jul 07 2022 - 21:25:56 CDT)
Multiseq doesn't work on mac Carlos Guardia (Fri Jul 01 2022 - 17:38:05 CDT)
- Re: Multiseq doesn't work on mac Scazzocchio, Claudio (Sat Jul 02 2022 - 01:04:02 CDT)
  - Re: Multiseq doesn't work on mac Carlos Guardia (Wed Jul 06 2022 - 11:45:26 CDT)
Calculate Free Binding Energy of Protein-Protein Complex: CaFE Extension Efthymiou, Christos (Tue Jun 28 2022 - 14:26:49 CDT)
MultiSeq QR structure factorization on the command line Christian Seitz (Tue Jun 28 2022 - 14:07:41 CDT)
- Re: MultiSeq QR structure factorization on the command line Vermaas, Josh (Tue Jun 28 2022 - 16:03:06 CDT)
  - Re: MultiSeq QR structure factorization on the command line Christian Seitz (Wed Jun 29 2022 - 18:23:55 CDT)
    - Re: MultiSeq QR structure factorization on the command line Josh Vermaas (Wed Jun 29 2022 - 20:47:32 CDT)
Re: Re: Visualisation of CG bonds Vermaas, Josh (Mon Jun 27 2022 - 07:52:11 CDT)
- Re: Re: Visualisation of CG bonds Roshan Shrestha (Mon Jun 27 2022 - 08:47:31 CDT)
- Re: Re: Visualisation of CG bonds Diego Gomes (Mon Jun 27 2022 - 11:21:34 CDT)
Visualisation of CG bonds Raman Preet Singh (Sun Jun 26 2022 - 13:07:45 CDT)
- Re: Visualisation of CG bonds Smith, Harper E. (Sun Jun 26 2022 - 17:49:38 CDT)
  - Re: Re: Visualisation of CG bonds Peter Freddolino (Mon Jun 27 2022 - 09:41:15 CDT)
protein residue not being recognized as protein Ryan Woltz (Fri Jun 17 2022 - 17:12:28 CDT)
Error with CaFE VMD Plugin Efthymiou, Christos (Thu Jun 16 2022 - 05:30:17 CDT)
- Re: Error with CaFE VMD Plugin Ashar Malik (Thu Jun 16 2022 - 06:32:12 CDT)
  - Re: Error with CaFE VMD Plugin John Stone (Thu Jun 16 2022 - 09:39:35 CDT)
  - Re: Error with CaFE VMD Plugin Jason Smith (Thu Jun 16 2022 - 10:50:03 CDT)
How to reduce the size of a .dcd file? Efthymiou, Christos (Thu Jun 16 2022 - 05:14:03 CDT)
- Re: How to reduce the size of a .dcd file? Geist, Norman (Thu Jun 16 2022 - 07:01:13 CDT)
- Re: How to reduce the size of a .dcd file? Raman Preet Singh (Thu Jun 16 2022 - 08:23:34 CDT)
water bridges Alexei Rossokhin (Wed Jun 15 2022 - 09:14:46 CDT)
Different results in using GUI or script Timelime Leonardo Palmieri (Fri Jun 10 2022 - 11:15:34 CDT)
- Re: Different results in using GUI or script Timelime Roni Saiba (Mon Jun 13 2022 - 02:06:32 CDT)
simple script question michaelmorgan937_at_gmail.com (Fri Jun 10 2022 - 00:02:39 CDT)
- Re: simple script question Ashar Malik (Fri Jun 10 2022 - 02:08:03 CDT)
- Re: simple script question Geist, Norman (Fri Jun 10 2022 - 02:05:21 CDT)
  - Re: simple script question Geist, Norman (Sun Jun 12 2022 - 14:11:15 CDT)
- RES: simple script question Arthur Pereira da Fonseca (Sun Jun 12 2022 - 11:54:27 CDT)
GPU-accelerated MSD calculation Max Win (Thu Jun 09 2022 - 12:20:20 CDT)
- Re: GPU-accelerated MSD calculation RenÃ© Hafner TUK (Fri Jun 10 2022 - 01:47:58 CDT)
Unable to useTachyon-Optix renderer when VMD is installed in Windows Subsystem for Linux (WSL) Vaidehi Doke (Wed Jun 08 2022 - 06:56:04 CDT)
- Re: Unable to useTachyon-Optix renderer when VMD is installed in Windows Subsystem for Linux (WSL) Vermaas, Josh (Wed Jun 08 2022 - 08:23:15 CDT)
  - Re: Unable to useTachyon-Optix renderer when VMD is installed in Windows Subsystem for Linux (WSL) John Stone (Wed Jun 15 2022 - 00:01:03 CDT)
    - Re: Unable to useTachyon-Optix renderer when VMD is installed in Windows Subsystem for Linux (WSL) Vaidehi Doke (Wed Jun 15 2022 - 01:47:03 CDT)
Script Modification to Print Phi and Psi Angles Oscar Bastidas (Mon Jun 06 2022 - 23:12:08 CDT)
- Re: Script Modification to Print Phi and Psi Angles Geist, Norman (Tue Jun 07 2022 - 00:59:28 CDT)
  - Re: Script Modification to Print Phi and Psi Angles Geist, Norman (Tue Jun 07 2022 - 01:01:55 CDT)
  - Re: Script Modification to Print Phi and Psi Angles Geist, Norman (Wed Jun 08 2022 - 00:19:52 CDT)
- Re: Script Modification to Print Phi and Psi Angles Roni Saiba (Tue Jun 07 2022 - 02:08:34 CDT)
Clarification on RMSF Calculation Efthymiou, Christos (Mon May 30 2022 - 14:08:16 CDT)
- Re: Clarification on RMSF Calculation Vermaas, Josh (Mon May 30 2022 - 15:52:12 CDT)
  - Re: Clarification on RMSF Calculation Efthymiou, Christos (Mon May 30 2022 - 16:01:41 CDT)
Movie Maker plugin parallel MPI rendering Chris Taylor (Sun May 29 2022 - 17:33:46 CDT)
- Re: Movie Maker plugin parallel MPI rendering Axel Kohlmeyer (Sun May 29 2022 - 18:49:42 CDT)
  - Re: Movie Maker plugin parallel MPI rendering Chris Taylor (Mon May 30 2022 - 13:12:09 CDT)
- Re: Movie Maker plugin parallel MPI rendering John Stone (Wed Jun 15 2022 - 00:19:43 CDT)
Re: Tcl Scripts Fails Unless Run in Tkconsole Alexander Adams (Thu May 26 2022 - 19:35:44 CDT)
Tcl Scripts Fails Unless Run in Tkconsole Alexander Adams (Thu May 26 2022 - 17:50:41 CDT)
- Re: Tcl Scripts Fails Unless Run in Tkconsole John Stone (Thu May 26 2022 - 19:46:00 CDT)
  - Re: Tcl Scripts Fails Unless Run in Tkconsole Alexander Adams (Thu May 26 2022 - 19:53:58 CDT)
QFilesize_limit_exceeded_(core_dumped)=94_with_VMD_on_?= Linux Dourna Jamshideasli (Thu May 26 2022 - 11:21:50 CDT)
- Re: ?Filesize limit exceeded (core dumped)? with VMD on Linux John Stone (Thu May 26 2022 - 11:47:37 CDT)
- Re: â€œFilesize limit exceeded (core dumped)Q=80=9D_with_VMD_on_Linux?= Axel Kohlmeyer (Thu May 26 2022 - 12:09:10 CDT)
Why the restype color of Gly residue in protein is green (polar)? Daniel Marin (Tue May 24 2022 - 04:28:35 CDT)
- Re: Why the restype color of Gly residue in protein is green (polar)? John Stone (Tue May 24 2022 - 08:40:01 CDT)
  - Re: Why the restype color of Gly residue in protein is green (polar)? Daniel Marin (Tue May 24 2022 - 13:48:54 CDT)
measure sasa and memory issue Ackad, Edward (Sun May 22 2022 - 10:54:55 CDT)
- Re: measure sasa and memory issue Axel Kohlmeyer (Sun May 22 2022 - 12:24:04 CDT)
  - Re: measure sasa and memory issue Ackad, Edward (Mon May 23 2022 - 08:47:00 CDT)
Launching VMD Gui from WSL Centos compiled from source manuel mourato (Sat May 21 2022 - 07:58:43 CDT)
- Re: Launching VMD Gui from WSL Centos compiled from source Axel Kohlmeyer (Sat May 21 2022 - 11:07:29 CDT)
  - Re: Launching VMD Gui from WSL Centos compiled from source manuel mourato (Sat May 21 2022 - 13:26:21 CDT)
    - Re: Launching VMD Gui from WSL Centos compiled from source John Stone (Mon May 23 2022 - 09:51:05 CDT)
Plot RMSD/RMSF/SASA Results from Multiple Trajectories on Same Plot Efthymiou, Christos (Thu May 19 2022 - 14:53:57 CDT)
Calculate Free Energy of Protein-Protein Binding Efthymiou, Christos (Thu May 12 2022 - 13:55:43 CDT)
- Re: Calculate Free Energy of Protein-Protein Binding Giacomo Fiorin (Thu May 12 2022 - 15:23:05 CDT)
FFTK Opt.Bonded error: unmatched open quote in list Zakaria Bouchouireb (Tue May 10 2022 - 03:14:24 CDT)
- Re: FFTK Opt.Bonded error: unmatched open quote in list Gumbart, JC (Mon May 23 2022 - 17:33:14 CDT)
Parsing exit code from TCL script to bash bypassing VMD GIUSEPPE LEONARDO LICARI (Mon May 09 2022 - 08:20:59 CDT)
- Re: Parsing exit code from TCL script to bash bypassing VMD Axel Kohlmeyer (Mon May 09 2022 - 09:17:29 CDT)
  - Re: Parsing exit code from TCL script to bash bypassing VMD GIUSEPPE LEONARDO LICARI (Tue May 10 2022 - 03:59:03 CDT)
Non-functional RMSD Visualizer in 1.9.4a53, windows Jason Smith (Fri May 06 2022 - 14:37:56 CDT)
- Re: Non-functional RMSD Visualizer in 1.9.4a53, windows John Stone (Tue Jul 05 2022 - 23:02:21 CDT)
remove atoms in a geometric shape using VMD Mohammed GOUNZARI (Fri May 06 2022 - 14:26:06 CDT)
- Re: remove atoms in a geometric shape using VMD Vermaas, Josh (Fri May 06 2022 - 15:44:01 CDT)
Using VMD from a Chrome Web Browser manuel mourato (Fri May 06 2022 - 06:23:59 CDT)
- Re: Using VMD from a Chrome Web Browser John Stone (Fri May 06 2022 - 09:06:39 CDT)
  - Re: Using VMD from a Chrome Web Browser manuel mourato (Fri May 06 2022 - 11:49:41 CDT)
FFTK Parameterization of Halogenated Molecule Bassam Haddad (Thu May 05 2022 - 11:24:24 CDT)
- RE: FFTK Parameterization of Halogenated Molecule Pang, Yui Tik (Fri May 06 2022 - 10:00:10 CDT)
  - Re: FFTK Parameterization of Halogenated Molecule Pang, Yui Tik (Fri May 06 2022 - 12:08:43 CDT)
Parallel rendering example from tutorial, "VMD parallel commands" Chris Taylor (Mon May 02 2022 - 21:49:45 CDT)
- Re: Parallel rendering example from tutorial, "VMD parallel commands" John Stone (Wed May 04 2022 - 15:11:39 CDT)
  - Re: Parallel rendering example from tutorial, "VMD parallel commands" Chris Taylor (Wed May 04 2022 - 22:46:28 CDT)
    - Re: Parallel rendering example from tutorial, "VMD parallel commands" John Stone (Wed May 04 2022 - 23:16:21 CDT)
  - Re: Parallel rendering example from tutorial, "VMD parallel commands" John Stone (Fri May 06 2022 - 00:36:13 CDT)
    - Re: Parallel rendering example from tutorial, "VMD parallel commands" Chris Taylor (Fri May 06 2022 - 20:07:16 CDT)
- Movie Maker plugin parallel MPI rendering Chris Taylor (Thu May 26 2022 - 21:23:39 CDT)
Unable to reload a saved state in VMD 1.9.3 Debostuti Ghoshdastidar (Mon May 02 2022 - 07:17:12 CDT)
- Re: Unable to reload a saved state in VMD 1.9.3 John Stone (Mon May 02 2022 - 12:51:30 CDT)
  - Re: Unable to reload a saved state in VMD 1.9.3 Debostuti Ghoshdastidar (Mon May 02 2022 - 13:26:46 CDT)
    - Re: Unable to reload a saved state in VMD 1.9.3 John Stone (Thu May 05 2022 - 23:21:28 CDT)
    - Re: Unable to reload a saved state in VMD 1.9.3 Debostuti Ghoshdastidar (Fri May 06 2022 - 01:18:10 CDT)
question on increasing font size on VMD main menu Lei Qian (Sat Apr 30 2022 - 12:21:13 CDT)
- Re: question on increasing font size on VMD main menu Axel Kohlmeyer (Sat Apr 30 2022 - 15:18:13 CDT)
how to analyse a trajectory without loading it Leonardo Palmieri (Tue Apr 26 2022 - 14:12:18 CDT)
- Re: how to analyse a trajectory without loading it John Stone (Tue Apr 26 2022 - 14:17:02 CDT)
  - Re: how to analyse a trajectory without loading it Leonardo Palmieri (Tue Apr 26 2022 - 14:35:41 CDT)
Errors using 'replicateCrystal.tcl' tutorial script Linda Ravazzano (Tue Apr 26 2022 - 09:10:39 CDT)
- Re: Errors using 'replicateCrystal.tcl' tutorial script John Stone (Fri May 06 2022 - 00:11:44 CDT)
FFTK baOpt electronic effects Aleksei (Wed Apr 13 2022 - 22:28:14 CDT)
FFTK baOpt electronic effects Daniel Fellner (Wed Apr 13 2022 - 12:33:04 CDT)
- Re: FFTK baOpt electronic effects Aleksei (Wed Apr 13 2022 - 20:53:46 CDT)
  - Re: FFTK baOpt electronic effects Daniel Fellner (Wed Apr 13 2022 - 21:39:00 CDT)
sched_setaffinity error message when using srun to give VMD only a portion of the cores on a node [SOLVED] Neale, Christopher Andrew (Tue Apr 12 2022 - 10:52:15 CDT)
VMD dumps core after OSPRay render completes Chris Taylor (Sun Apr 10 2022 - 15:46:02 CDT)
- Re: VMD dumps core after OSPRay render completes John Stone (Sun Apr 10 2022 - 20:04:38 CDT)
  - Re: VMD dumps core after OSPRay render completes Chris Taylor (Tue Apr 12 2022 - 01:14:35 CDT)
- Use VMDOSPRAYMPI env variable and OSPray render method Chris Taylor (Sun Apr 17 2022 - 02:09:04 CDT)
  - Use VMDOSPRAYMPI env variable and OSPray render method Chris Taylor (Mon Apr 18 2022 - 21:17:08 CDT)
ffTK can't use empty string as operand of "*" vmd194a53win64-SetupV7.exe Rahul Nikhar (Tue Apr 05 2022 - 18:46:47 CDT)
- Re: ffTK can't use empty string as operand of "*" vmd194a53win64-SetupV7.exe Gumbart, JC (Thu Apr 07 2022 - 08:34:27 CDT)
  - Re: ffTK can't use empty string as operand of "*" vmd194a53win64-SetupV7.exe Gumbart, JC (Sat Apr 09 2022 - 20:40:03 CDT)
error 1114 when loading plugins Eric Ledieu (Tue Apr 05 2022 - 12:07:49 CDT)
- Re: error 1114 when loading plugins John Stone (Tue Apr 05 2022 - 12:16:34 CDT)
  - Re: error 1114 when loading plugins Giacomo Fiorin (Tue Apr 05 2022 - 13:52:31 CDT)
- Re: error 1114 when loading plugins Giacomo Fiorin (Tue Apr 05 2022 - 13:21:56 CDT)
- Re: error 1114 when loading plugins Axel Kohlmeyer (Tue Apr 05 2022 - 13:36:18 CDT)
VMD 1.9.4 crashes after running the "Merge Structures" plugin (with psfgen 2.0) yjcoshc (Mon Apr 04 2022 - 10:06:35 CDT)
- Re: VMD 1.9.4 crashes after running the "Merge Structures" plugin (with psfgen 2.0) John Stone (Mon Apr 04 2022 - 10:11:51 CDT)
  - Re: VMD 1.9.4 crashes after running the "Merge Structures" plugin (with psfgen 2.0) yjcoshc (Mon Apr 04 2022 - 10:14:48 CDT)
    - Re: VMD 1.9.4 crashes after running the "Merge Structures" plugin (with psfgen 2.0) John Stone (Mon Apr 04 2022 - 10:20:26 CDT)
- Re: VMD 1.9.4 crashes after running the "Merge Structures" plugin (with psfgen 2.0) Josh Vermaas (Mon Apr 04 2022 - 11:15:30 CDT)
  - Re: VMD 1.9.4 crashes after running the "Merge Structures" plugin (with psfgen 2.0) yjcoshc (Mon Apr 04 2022 - 11:18:41 CDT)
VMD MPI error Lenz Fiedler (Mon Apr 04 2022 - 09:39:17 CDT)
- Re: VMD MPI error John Stone (Mon Apr 04 2022 - 10:04:05 CDT)
  - Re: VMD MPI error Lenz Fiedler (Mon Apr 04 2022 - 10:45:52 CDT)
Unable to rename material Vasista (Mon Apr 04 2022 - 05:40:43 CDT)
GPU-accelerated RDF Calculation Max Win (Thu Mar 31 2022 - 16:52:56 CDT)
- Re: GPU-accelerated RDF Calculation Axel Kohlmeyer (Thu Mar 31 2022 - 18:10:50 CDT)
- Re: GPU-accelerated RDF Calculation Josh Vermaas (Thu Mar 31 2022 - 19:12:38 CDT)
<< memory issue? >> I. Camps (Wed Mar 30 2022 - 20:04:47 CDT)
- Re: << memory issue? >> Axel Kohlmeyer (Wed Mar 30 2022 - 21:05:09 CDT)
How to increase bond length maximum ? maxim todoru (Tue Mar 29 2022 - 06:00:37 CDT)
- Re: How to increase bond length maximum ? Axel Kohlmeyer (Wed Mar 30 2022 - 08:15:31 CDT)
  - Re: How to increase bond length maximum ? maxim todoru (Tue Mar 29 2022 - 20:04:45 CDT)
    - Re: How to increase bond length maximum ? Axel Kohlmeyer (Thu Mar 31 2022 - 09:05:33 CDT)
FFTK Charge Optimization Target Data Daniel Fellner (Wed Mar 30 2022 - 02:13:08 CDT)
- Re: FFTK Charge Optimization Target Data Gumbart, JC (Thu Mar 31 2022 - 10:51:07 CDT)
  - Re: FFTK Charge Optimization Target Data Daniel Fellner (Fri Apr 01 2022 - 02:52:01 CDT)
Timeline/H-Bond broken OS X CHARLES MCCALLUM (Tue Mar 29 2022 - 19:03:08 CDT)
- Re: Timeline/H-Bond broken OS X John Stone (Fri May 06 2022 - 00:41:10 CDT)
  - Re: Timeline/H-Bond broken OS X CHARLES MCCALLUM (Fri May 06 2022 - 11:25:52 CDT)
    - Re: Timeline/H-Bond broken OS X John Stone (Fri May 06 2022 - 11:28:08 CDT)
    - Re: Timeline/H-Bond broken OS X CHARLES MCCALLUM (Fri May 06 2022 - 12:16:06 CDT)
Changing color scale bar location in VMD Ahmad Alqaisi (Fri Mar 25 2022 - 20:30:06 CDT)
- Re: Changing color scale bar location in VMD John Stone (Fri May 06 2022 - 01:06:40 CDT)
Issue in wat_hbond.tcl script Alvea Tasneem (Thu Mar 24 2022 - 12:47:24 CDT)
Distances with respect to principal axis Peter Mawanga (Mon Mar 21 2022 - 09:30:57 CDT)
How to read netcdf files on Windows version of VMD? Suchetana Gupta (Mon Mar 14 2022 - 00:08:49 CDT)
- Re: How to read netcdf files on Windows version of VMD? Axel Kohlmeyer (Mon Mar 14 2022 - 02:45:43 CDT)
- Re: How to read netcdf files on Windows version of VMD? Axel Kohlmeyer (Mon Mar 14 2022 - 03:02:28 CDT)
Re: VMD 1.9.4 as a Python Module Vermaas, Josh (Thu Mar 10 2022 - 08:50:16 CST)
VMD 1.9.4 as a Python Module Dominique Mias-Lucquin (Wed Mar 09 2022 - 05:15:39 CST)
Problem w/ DCD Title Block When Saving - Using 'Animate Write' vs Saving Via GUI Adam Gross (Tue Mar 08 2022 - 11:39:05 CST)
- Re: Problem w/ DCD Title Block When Saving - Using 'Animate Write' vs Saving Via GUI John Stone (Tue Mar 08 2022 - 12:16:36 CST)
  - Re: Problem w/ DCD Title Block When Saving - Using 'Animate Write' vs Saving Via GUI Adam Gross (Tue Mar 08 2022 - 13:13:32 CST)
    - Re: Problem w/ DCD Title Block When Saving - Using 'Animate Write' vs Saving Via GUI Vermaas, Josh (Tue Mar 08 2022 - 14:58:18 CST)
PSF Script Mcguire, Kelly (Sat Mar 05 2022 - 11:50:08 CST)
- Re: PSF Script Peter Freddolino (Sat Mar 05 2022 - 18:33:13 CST)
- Re: PSF Script Mcguire, Kelly (Mon Mar 07 2022 - 12:23:46 CST)
  - Re: PSF Script Mcguire, Kelly (Mon Mar 07 2022 - 13:15:35 CST)
Check DCD finish Georcki Ropon (Tue Mar 01 2022 - 11:06:02 CST)
read setting from text file Marco Di Gennaro (TME) (Tue Mar 01 2022 - 07:59:38 CST)
- Re: read setting from text file Axel Kohlmeyer (Tue Mar 01 2022 - 09:00:17 CST)
  - Re: read setting from text file Vermaas, Josh (Tue Mar 01 2022 - 09:08:04 CST)
    - RE: read setting from text file Marco Di Gennaro (TME) (Wed Mar 02 2022 - 03:48:17 CST)
Water molecule ID in Hydrogen bond plugin SYEDA SABIHA SULTANA LUBNA . (Mon Feb 28 2022 - 03:38:01 CST)
- Re: Water molecule ID in Hydrogen bond plugin Gumbart, JC (Tue Mar 01 2022 - 13:30:26 CST)
- Re: Water molecule ID in Hydrogen bond plugin CHARLES MCCALLUM (Tue Mar 01 2022 - 15:01:32 CST)
- Re: Water molecule ID in Hydrogen bond plugin CHARLES MCCALLUM (Tue Mar 01 2022 - 14:58:06 CST)
get coordinates for each frame in a trjectory Alessandro Ruda (Sun Feb 27 2022 - 08:03:44 CST)
- Re: get coordinates for each frame in a trjectory Giacomo Fiorin (Sun Feb 27 2022 - 09:11:40 CST)
Re: command measure inertia Vermaas, Josh (Sat Feb 26 2022 - 11:57:31 CST)
command measure inertia Alessandro Ruda (Sat Feb 26 2022 - 09:59:14 CST)
MMPBSA Question Mcguire, Kelly (Mon Feb 21 2022 - 15:44:57 CST)
RSCB assembly formatting change - chain names with hyphens and numbers not recognized in VMD Evelyn Maizels (Thu Feb 17 2022 - 19:17:06 CST)
- Re: RSCB assembly formatting change - chain names with hyphens and numbers not recognized in VMD Evelyn Maizels (Fri Feb 18 2022 - 10:14:25 CST)
VMD Visualizers and AutoPSF unusable on Mac BigSur and VMD1.9.4a55 Paula Schneider (Thu Feb 17 2022 - 14:27:31 CST)
- Re: VMD Visualizers and AutoPSF unusable on Mac BigSur and VMD1.9.4a55 John Stone (Fri May 06 2022 - 01:23:03 CDT)
Molecular orbitals from molden files florian.naegele_at_uni-ulm.de (Thu Feb 17 2022 - 03:39:37 CST)
VMD Install Samuel Canner (Mon Feb 14 2022 - 16:44:00 CST)
Questions - Running vmd on a supercomputer emerson p l (Mon Feb 14 2022 - 08:01:02 CST)
- Re: Questions - Running vmd on a supercomputer Giacomo Fiorin (Mon Feb 14 2022 - 08:52:14 CST)
  - Re: Questions - Running vmd on a supercomputer emerson p l (Mon Feb 14 2022 - 12:50:13 CST)
hmassrepart Artur Hermano (Thu Feb 10 2022 - 16:05:12 CST)
- Re: hmassrepart CHARLES MCCALLUM (Thu Feb 10 2022 - 17:03:56 CST)
  - Re: hmassrepart Artur Hermano (Thu Feb 10 2022 - 17:32:28 CST)
tkcon behavior in OS X / selection Q Mike McCallum (Tue Feb 08 2022 - 11:57:59 CST)
- Re: tkcon behavior in OS X / selection Q Giacomo Fiorin (Tue Feb 08 2022 - 13:11:58 CST)
  - Re: tkcon behavior in OS X / selection Q Mike McCallum (Tue Feb 08 2022 - 13:18:54 CST)
Puzzle with "small molecule" ligand structure in nucleotide environments Francesco Pietra (Sun Feb 06 2022 - 01:59:52 CST)
autopsf question McGuire, Kelly (Sat Feb 05 2022 - 16:33:09 CST)
- Re: autopsf question Peter Freddolino (Sat Feb 05 2022 - 18:27:49 CST)
  - Re: autopsf question McGuire, Kelly (Sat Feb 05 2022 - 19:22:13 CST)
PDBx and chain IDs in VMD 1.9.4a55 Whitford, Paul (Fri Feb 04 2022 - 10:28:32 CST)
- Re: PDBx and chain IDs in VMD 1.9.4a55 Whitford, Paul (Thu Jun 23 2022 - 22:29:17 CDT)
Any TCL script to identify specific MD water molecules with their respective IDs, forming hbond with certain residues in every frame Alvea Tasneem (Wed Feb 02 2022 - 11:48:23 CST)
Regarding Periodic MSM calculation Subhasish Mallick (Wed Feb 02 2022 - 02:08:16 CST)
- Re: Regarding Periodic MSM calculation John Stone (Thu Feb 03 2022 - 23:14:43 CST)
Issue running vmd and tk commands on my computer through script Huebert, David Nicolas (Wed Feb 02 2022 - 00:19:31 CST)
- Re: Issue running vmd and tk commands on my computer through script Smith, Harper E. (Wed Feb 02 2022 - 09:55:43 CST)
  - Re: Issue running vmd and tk commands on my computer through script John Stone (Thu Feb 03 2022 - 23:17:21 CST)
Protein-ligand interactions Maryam (Mon Jan 31 2022 - 10:39:44 CST)
- Re: Protein-ligand interactions Josh Vermaas (Mon Jan 31 2022 - 11:43:36 CST)
  - Re: Protein-ligand interactions Maryam (Mon Jan 31 2022 - 13:17:01 CST)
    - Re: Protein-ligand interactions Vermaas, Josh (Mon Jan 31 2022 - 14:52:57 CST)
Needing to visualize lots of spheres during solution steps Ali Sheikholeslam (Tue Jan 25 2022 - 13:34:14 CST)
- Re: Needing to visualize lots of spheres during solution steps John Stone (Thu Feb 03 2022 - 23:32:45 CST)
pbc wrap issue Aditi Gotkhindikar (Sun Jan 23 2022 - 23:55:55 CST)
- Fwd: pbc wrap issue Aditi Gotkhindikar (Tue Jan 25 2022 - 00:11:51 CST)
  - Re: Fwd: pbc wrap issue RenÃ© Hafner TUK (Tue Jan 25 2022 - 01:25:13 CST)
Error in tcl script Kiana Jahani (Sun Jan 23 2022 - 05:13:46 CST)
- Re: Error in tcl script Peter Freddolino (Sun Jan 23 2022 - 09:41:25 CST)
  - Re: Error in tcl script Kiana Jahani (Mon Jan 24 2022 - 00:35:23 CST)
PDBx/CIF Problem on New PDBs Andrew White (Thu Jan 20 2022 - 10:38:44 CST)
- Re: PDBx/CIF Problem on New PDBs Jason Smith (Sat Jan 22 2022 - 14:55:29 CST)
Problems with charmm36 modified nucleotides for psfgen and namd Francesco Pietra (Thu Jan 20 2022 - 08:26:48 CST)
- Fwd: Problems with charmm36 modified nucleotides for psfgen and namd Francesco Pietra (Thu Jan 20 2022 - 08:31:36 CST)
  - Fwd: Problems with charmm36 modified nucleotides for psfgen and namd Francesco Pietra (Thu Jan 20 2022 - 08:43:12 CST)
Visualize a lammpstrij file Otakandza Glenn (Thu Jan 20 2022 - 05:52:50 CST)
- Re: Visualize a lammpstrij file Axel Kohlmeyer (Thu Jan 20 2022 - 06:45:18 CST)
Where to find top_all36_cgenff.rtf/prm version 4.5? Francesco Pietra (Wed Jan 19 2022 - 08:39:20 CST)
Issue with Timeline Plugin related to "geometry manager pack" Aaron Blanchard, Ph.D. (Mon Jan 17 2022 - 23:23:51 CST)
- Re: Issue with Timeline Plugin related to "geometry manager pack" Mariano Spivak (Tue Jan 18 2022 - 10:07:09 CST)
MOLECULE DESTROYED BY FATAL ERROR Eduardo Estevez (Sun Jan 16 2022 - 14:54:00 CST)
- Re: MOLECULE DESTROYED BY FATAL ERROR Axel Kohlmeyer (Sun Jan 16 2022 - 15:40:25 CST)
Place multiple proteins into membrane Georcki Ropon (Tue Jan 11 2022 - 14:31:08 CST)
Problem selecting atoms MacOS VMD 1.9.4a55 for MacOS X, 64-bit Intel x86 (x86_64) Sergio Perez (Tue Jan 11 2022 - 10:21:12 CST)
QMMM simulation orbitals visualization step by step francisca andrea salas sepulveda (Tue Jan 11 2022 - 08:17:20 CST)
"Error: no indices found in file." in carma.indices using NetworkView Nick Bayhi (Fri Jan 07 2022 - 14:19:55 CST)
Failure of autopsf with modified nucleotides Francesco Pietra (Thu Jan 06 2022 - 03:12:44 CST)
- Re: Failure of autopsf with modified nucleotides Peter Freddolino (Thu Jan 06 2022 - 07:55:42 CST)
  - Re: Failure of autopsf with modified nucleotides Francesco Pietra (Thu Jan 06 2022 - 08:45:26 CST)
  - Re: Failure of autopsf with modified nucleotides Francesco Pietra (Thu Jan 06 2022 - 09:44:32 CST)
mail about VMD installation vidhya sankar (Fri Dec 31 2021 - 08:29:44 CST)
- Re: mail about VMD installation Pacci Evaristo, Felipe Fabricio (Fri Dec 31 2021 - 14:00:29 CST)
  - Re: mail about VMD installation Giacomo Fiorin (Fri Dec 31 2021 - 14:55:05 CST)
issue with protein- ligand psfgen Aditi Gotkhindikar (Mon Dec 27 2021 - 05:39:04 CST)
- Fwd: issue with protein- ligand psfgen Aditi Gotkhindikar (Mon Dec 27 2021 - 22:33:03 CST)
Question about error while using QwikMD files Ahmad Alqaisi (Fri Dec 24 2021 - 15:25:30 CST)
- Re: Question about error while using QwikMD files Mariano Spivak (Fri Dec 24 2021 - 17:11:54 CST)
Vmd on Monterey Osman, Roman (Thu Dec 23 2021 - 22:31:03 CST)
- Re: Vmd on Monterey Nathan Kern (Fri Dec 24 2021 - 10:02:34 CST)
  - Re: Vmd on Monterey John Stone (Sat Dec 25 2021 - 00:18:50 CST)
    - Re: Vmd on Monterey Osman, Roman (Sat Dec 25 2021 - 07:57:55 CST)
    - Re: Vmd on Monterey John Stone (Sun Dec 26 2021 - 23:36:21 CST)
How to write a netcdf file in vmd from already loaded netcdf/dcd trajectory Prathit Chatterjee (Thu Dec 23 2021 - 05:00:44 CST)
- Re: How to write a netcdf file in vmd from already loaded netcdf/dcd trajectory Axel Kohlmeyer (Thu Dec 23 2021 - 06:16:31 CST)
  - Re: How to write a netcdf file in vmd from already loaded netcdf/dcd trajectory Prathit Chatterjee (Thu Dec 23 2021 - 09:08:51 CST)
  - Re: How to write a netcdf file in vmd from already loaded netcdf/dcd trajectory John Stone (Sat Dec 25 2021 - 00:27:21 CST)
Too many nested evaluations Hamish Swanson (Mon Dec 20 2021 - 03:58:35 CST)
- Re: Too many nested evaluations John Stone (Mon Dec 20 2021 - 17:07:26 CST)
Problem with rendering proper colors in linux Soumik Ghosh (Fri Dec 17 2021 - 08:21:25 CST)
VMD license Arthur Pereira da Fonseca (Thu Dec 16 2021 - 08:37:57 CST)
- Re: VMD license Nuno Cerqueira (Thu Dec 16 2021 - 11:55:55 CST)
  - Re: VMD license John Stone (Thu Dec 16 2021 - 12:34:12 CST)
- Re: VMD license John Stone (Thu Dec 16 2021 - 12:15:08 CST)
  - Re: VMD license Giacomo Fiorin (Thu Dec 16 2021 - 13:18:41 CST)
    - RES: VMD license Arthur Pereira da Fonseca (Fri Dec 17 2021 - 17:32:10 CST)
VMD warning: ignoring out of range atom #*** with id *** Jiabin You (Wed Dec 15 2021 - 08:37:17 CST)
- Re: VMD warning: ignoring out of range atom #*** with id *** Axel Kohlmeyer (Wed Dec 15 2021 - 09:28:58 CST)
Open VMD in current terminal directory Pacci Evaristo, Felipe Fabricio (Tue Dec 14 2021 - 16:57:13 CST)
- Re: Open VMD in current terminal directory John Stone (Thu Dec 16 2021 - 22:52:35 CST)
  - Re: Open VMD in current terminal directory FX (Fri Dec 17 2021 - 00:42:05 CST)
    - Re: Open VMD in current terminal directory Pacci Evaristo, Felipe Fabricio (Tue Dec 21 2021 - 13:10:55 CST)
Avoid atom indices reassignment Liel Sapir (Mon Dec 13 2021 - 08:46:42 CST)
- Re: Avoid atom indices reassignment JÃ©rÃ´me HÃ©nin (Mon Dec 13 2021 - 09:42:33 CST)
  - Re: Avoid atom indices reassignment Liel Sapir (Wed Dec 15 2021 - 03:04:01 CST)
Paper request : Assembly and Analysis of Cell-Scale Membrane Envelopes Georcki Ropon (Mon Dec 06 2021 - 15:40:55 CST)
Distance from surface Raman Preet Singh (Mon Dec 06 2021 - 12:07:40 CST)
- Re: Distance from surface Giacomo Fiorin (Mon Dec 06 2021 - 12:57:32 CST)
color by molecule number Marco Di Gennaro (TME) (Mon Dec 06 2021 - 04:50:41 CST)
Re: L-DOPA and non-natural amino acids incorporation Hideyuki Miyatake (Mon Dec 06 2021 - 04:30:50 CST)
- Re: L-DOPA and non-natural amino acids incorporation Michael Robinson (Mon Dec 06 2021 - 05:41:07 CST)
Fatal error: Unable to find dihedral parameters Kiana Jahani (Sun Dec 05 2021 - 06:26:46 CST)
- Re: Fatal error: Unable to find dihedral parameters Peter Freddolino (Sun Dec 05 2021 - 10:14:11 CST)
  - Re: Fatal error: Unable to find dihedral parameters Kiana Jahani (Mon Dec 06 2021 - 02:19:29 CST)
L-DOPA and non-natural amino acids incorporation Hideyuki Miyatake (Sat Dec 04 2021 - 06:00:11 CST)
FFTK segmentation fault when guessing charge groups Bassam Haddad (Fri Dec 03 2021 - 02:35:30 CST)
- Re: FFTK segmentation fault when guessing charge groups Gumbart, JC (Fri Dec 03 2021 - 07:07:48 CST)
  - Re: FFTK segmentation fault when guessing charge groups Bassam Haddad (Fri Dec 03 2021 - 07:09:39 CST)
    - Re: FFTK segmentation fault when guessing charge groups Pang, Yui Tik (Tue Dec 07 2021 - 15:12:20 CST)
- Re: FFTK segmentation fault when guessing charge groups Pang, Yui Tik (Fri Dec 03 2021 - 09:05:49 CST)
  - L-DOPA incorporation Hideyuki Miyatake (Sat Dec 04 2021 - 04:25:59 CST)
NYT article on SARS-CoV-2 aerosol+virion simulations w/ NAMD+VMD John Stone (Wed Dec 01 2021 - 13:11:51 CST)
- Re: NYT article on SARS-CoV-2 aerosol+virion simulations w/ NAMD+VMD Strahs, Dr. Daniel Bernard (Thu Dec 02 2021 - 09:49:34 CST)
molfile plugin compilation for webassembly Kochnev, Iurii K (Wed Dec 01 2021 - 12:49:27 CST)
- Re: molfile plugin compilation for webassembly Axel Kohlmeyer (Wed Dec 01 2021 - 22:22:57 CST)
  - Re: molfile plugin compilation for webassembly John Stone (Wed Dec 01 2021 - 23:16:17 CST)
    - Re: molfile plugin compilation for webassembly Peter Schmidtke (Thu Dec 02 2021 - 07:58:11 CST)
Error 1327.Invalid Drive: F youtux (Tue Nov 30 2021 - 08:54:36 CST)
- Re: Error 1327.Invalid Drive: F John Stone (Tue Nov 30 2021 - 11:31:47 CST)
Multiseq / stamp alignment on Windows 1.9.4alpha Stefan Boresch (Tue Nov 30 2021 - 07:45:40 CST)
- Re: Multiseq / stamp alignment on Windows 1.9.4alpha Phillip Compeau (Tue Nov 30 2021 - 10:27:03 CST)
- How can I incorporate non-natural amino acids into proteins? Hideyuki Miyatake (Tue Nov 30 2021 - 20:15:05 CST)
  - Re: How can I incorporate non-natural amino acids into proteins? Georcki Ropon (Tue Nov 30 2021 - 21:22:00 CST)
  - Re: How can I incorporate non-natural amino acids into proteins? Michael Robinson (Tue Nov 30 2021 - 21:45:06 CST)
    - Re: How can I incorporate non-natural amino acids into proteins? Michael Robinson (Tue Nov 30 2021 - 21:52:27 CST)
    - Re: How can I incorporate non-natural amino acids into proteins? Hideyuki Miyatake (Tue Nov 30 2021 - 21:59:13 CST)
- Re: Multiseq / stamp alignment on Windows 1.9.4alpha John Stone (Wed Dec 01 2021 - 00:49:28 CST)
  - Re: Multiseq / stamp alignment on Windows 1.9.4alpha Stefan Boresch (Wed Dec 01 2021 - 03:23:47 CST)
Dynamic bonds across PBC MD Simulation (Sat Nov 27 2021 - 07:01:37 CST)
- Re: Dynamic bonds across PBC Axel Kohlmeyer (Sat Nov 27 2021 - 07:45:18 CST)
  - Re: Dynamic bonds across PBC MD Simulation (Sat Nov 27 2021 - 07:46:25 CST)
Issue with STAMP Alignment Phillip Compeau (Fri Nov 26 2021 - 22:05:02 CST)
- Re: Issue with STAMP Alignment John Stone (Wed Dec 01 2021 - 00:42:12 CST)
  - Re: Issue with STAMP Alignment John Stone (Thu Dec 02 2021 - 14:32:51 CST)
  - Re: Issue with STAMP Alignment John Stone (Mon Dec 20 2021 - 00:51:18 CST)
    - Re: Issue with STAMP Alignment Phillip Compeau (Mon Dec 20 2021 - 17:22:00 CST)
basic procedure for ABF-PMF calculation Yogesh Sharma (Fri Nov 26 2021 - 11:53:01 CST)
- Re: basic procedure for ABF-PMF calculation JÃ©rÃ´me HÃ©nin (Mon Nov 29 2021 - 06:30:58 CST)
Absolute ruler or position limits of the current view Philip Loche (Thu Nov 25 2021 - 07:50:20 CST)
- Re: Absolute ruler or position limits of the current view John Stone (Wed Dec 01 2021 - 00:55:03 CST)
CNT structure formation Kibria Imtiaz Shabbir (Thu Nov 25 2021 - 03:52:13 CST)
- Re: CNT structure formation Kibria Imtiaz Shabbir (Fri Nov 26 2021 - 21:48:21 CST)
  - Re: Re: CNT structure formation Axel Kohlmeyer (Sat Nov 27 2021 - 14:03:46 CST)
    - Re: Re: CNT structure formation Philippe Bopp (Sat Nov 27 2021 - 17:32:46 CST)
    - Re: Re: CNT structure formation Raman Preet Singh (Mon Nov 29 2021 - 03:11:57 CST)
VMD 1.9.4 (RTRT) with python3 and numpy on Ubuntu Bruininks, B.M.H. (Thu Nov 25 2021 - 03:25:12 CST)
VMD GUI Francesco Pietra (Thu Nov 25 2021 - 02:15:38 CST)
- Re: VMD GUI John Stone (Wed Dec 01 2021 - 00:38:32 CST)
support for gromacs topology files Bennion, Brian (Wed Nov 24 2021 - 14:20:11 CST)
- Re: support for gromacs topology files Giacomo Fiorin (Wed Nov 24 2021 - 16:47:45 CST)
  - Re: support for gromacs topology files Raman Preet Singh (Thu Nov 25 2021 - 06:23:34 CST)
  - Re: support for gromacs topology files Vermaas, Josh (Fri Nov 26 2021 - 18:38:58 CST)
    - Re: support for gromacs topology files Axel Kohlmeyer (Fri Nov 26 2021 - 19:25:44 CST)
Select a molecule with multiple indexes Otakandza Glenn (Mon Nov 22 2021 - 09:17:27 CST)
- Re: Select a molecule with multiple indexes Vermaas, Josh (Mon Nov 22 2021 - 10:42:48 CST)
Autoionize with non water solvent Francesco Pietra (Sat Nov 20 2021 - 09:11:49 CST)
- Re: Autoionize with non water solvent Nathan Kern (Sat Nov 20 2021 - 13:16:21 CST)
- Re: Autoionize with non water solvent Georcki Ropon (Sat Nov 20 2021 - 13:35:42 CST)
namd minimization looking for wrong angle Francesco Pietra (Thu Nov 18 2021 - 02:27:31 CST)
- Re: namd-l: namd minimization looking for wrong angle Francesco Pietra (Thu Nov 18 2021 - 04:02:10 CST)
  - Re: namd-l: namd minimization looking for wrong angle Peter Freddolino (Thu Nov 18 2021 - 08:03:40 CST)
autopsfgen looking for wrong angle Francesco Pietra (Thu Nov 18 2021 - 02:21:33 CST)
- Fwd: autopsfgen looking for wrong angle Francesco Pietra (Thu Nov 18 2021 - 02:28:25 CST)
Change Atom serial Atom Georcki Ropon (Wed Nov 17 2021 - 19:04:32 CST)
- Re: Change Atom serial Atom Axel Kohlmeyer (Wed Nov 17 2021 - 20:14:48 CST)
  - Re: Change Atom serial Atom Georcki Ropon (Wed Nov 17 2021 - 20:18:09 CST)
- Re: Change Atom serial Atom Vermaas, Josh (Wed Nov 17 2021 - 20:34:02 CST)
  - Re: Change Atom serial Atom Georcki Ropon (Wed Nov 17 2021 - 20:42:25 CST)
    - Re: Change Atom serial Atom Vermaas, Josh (Wed Nov 17 2021 - 20:50:42 CST)
    - Re: Change Atom serial Atom Georcki Ropon (Thu Nov 18 2021 - 11:07:13 CST)
chloroform box ChARMM Francesco Pietra (Wed Nov 17 2021 - 04:41:24 CST)
AWS for VMD and NAMD no longer working? Chapman, John O. (Wed Nov 10 2021 - 16:25:23 CST)
- Re: AWS for VMD and NAMD no longer working? John Stone (Thu Dec 09 2021 - 23:40:31 CST)
(Semi-)transparent windows on installation on a virtual server Per Larsson (Tue Nov 09 2021 - 14:33:47 CST)
- Re: (Semi-)transparent windows on installation on a virtual server John Stone (Tue Nov 09 2021 - 15:36:18 CST)
  - Re: (Semi-)transparent windows on installation on a virtual server Per Larsson (Wed Nov 10 2021 - 02:07:52 CST)
    - Re: (Semi-)transparent windows on installation on a virtual server Per Larsson (Thu Nov 18 2021 - 14:21:04 CST)
    - Re: (Semi-)transparent windows on installation on a virtual server John Stone (Thu Nov 18 2021 - 14:30:25 CST)
Cluster analysis SYEDA SABIHA SULTANA LUBNA . (Mon Nov 08 2021 - 04:49:50 CST)
- Re: Cluster analysis John Stone (Tue Nov 09 2021 - 16:11:52 CST)
  - Re: Re: Cluster analysis OZGE ENGIN (Tue Feb 05 2008 - 06:29:17 CST)
Angle between molecular dipole and nanotube axis. Yogesh Sharma (Mon Nov 08 2021 - 03:19:45 CST)
- Re: Angle between molecular dipole and nanotube axis. John Stone (Tue Nov 09 2021 - 16:14:49 CST)
  - Re: Angle between molecular dipole and nanotube axis. Yogesh Sharma (Mon Nov 29 2021 - 12:51:18 CST)
Where found QwikMD 2.0? Georcki Ropon (Sat Nov 06 2021 - 23:28:08 CDT)
- Re: Where found QwikMD 2.0? John Stone (Tue Nov 09 2021 - 16:17:55 CST)
Remote IMD simulation Georcki Ropon (Sat Nov 06 2021 - 12:03:57 CDT)
- Re: Remote IMD simulation Axel Kohlmeyer (Sat Nov 06 2021 - 13:38:23 CDT)
Install of VMD on amazon linux2 NICE DCV server Ben Cossins (Sat Nov 06 2021 - 10:56:34 CDT)
- Re: Install of VMD on amazon linux2 NICE DCV server Axel Kohlmeyer (Sat Nov 06 2021 - 11:41:25 CDT)
- Re: Install of VMD on amazon linux2 NICE DCV server Tru Huynh (Sun Nov 07 2021 - 09:13:46 CST)
  - Re: Install of VMD on amazon linux2 NICE DCV server John Stone (Tue Nov 09 2021 - 16:05:16 CST)
    - Re: Install of VMD on amazon linux2 NICE DCV server Ben Cossins (Sun Nov 14 2021 - 13:29:37 CST)
Color Transition in VMD maxim todoru (Sat Nov 06 2021 - 09:46:26 CDT)
- Re: Color Transition in VMD Giacomo Fiorin (Sat Nov 06 2021 - 10:30:33 CDT)
Error reading fep.tcl file in namd SYEDA SABIHA SULTANA LUBNA . (Fri Oct 29 2021 - 06:52:39 CDT)
- Re: Error reading fep.tcl file in namd John Stone (Fri Oct 29 2021 - 10:25:00 CDT)
  - Re: Error reading fep.tcl file in namd SYEDA SABIHA SULTANA LUBNA . (Sat Oct 30 2021 - 01:58:38 CDT)
Re: namd-l: RMSD and RMSF of ligand Only Mi Yang (Thu Oct 28 2021 - 08:35:40 CDT)
- Re: Re: namd-l: RMSD and RMSF of ligand Only Ashar Malik (Thu Oct 28 2021 - 09:26:11 CDT)
How to create a color ramp in VMD? anas forum (Wed Oct 27 2021 - 06:55:37 CDT)
- Re: How to create a color ramp in VMD? Josh Vermaas (Thu Oct 28 2021 - 09:12:57 CDT)
  - Re: How to create a color ramp in VMD? John Stone (Thu Oct 28 2021 - 09:22:04 CDT)
  - Re: How to create a color ramp in VMD? John Stone (Tue Nov 09 2021 - 15:57:32 CST)
RMSD and RMSF of ligand Only Mi Yang (Thu Oct 28 2021 - 04:48:37 CDT)
- Re: RMSD and RMSF of ligand Only Ashar Malik (Thu Oct 28 2021 - 06:28:27 CDT)
energy partitioning Alexei Rossokhin (Tue Oct 26 2021 - 06:19:49 CDT)
- Re: energy partitioning John Stone (Wed Oct 27 2021 - 21:32:37 CDT)
  - Re: energy partitioning Peter Freddolino (Wed Oct 27 2021 - 23:55:46 CDT)
    - Re: energy partitioning Peter Freddolino (Wed Oct 27 2021 - 23:57:32 CDT)
  - Re: energy partitioning Peter Freddolino (Thu Oct 28 2021 - 07:56:37 CDT)
    - Re: energy partitioning Alexei Rossokhin (Thu Oct 28 2021 - 09:14:27 CDT)
protein and lipid jumping Ryan Woltz (Fri Oct 22 2021 - 15:05:58 CDT)
- Re: protein and lipid jumping Ashar Malik (Fri Oct 22 2021 - 21:34:47 CDT)
  - Re: protein and lipid jumping Ryan Woltz (Fri Oct 22 2021 - 21:57:27 CDT)
Script for contact Vs Freq Mi Yang (Thu Oct 21 2021 - 12:41:06 CDT)
Fwd: Fwd: namd-l: impropers for protonated 1-methyladenosine Francesco Pietra (Wed Oct 20 2021 - 08:40:14 CDT)
- Re: Fwd: Fwd: namd-l: impropers for protonated 1-methyladenosine Francesco Pietra (Thu Oct 21 2021 - 04:15:56 CDT)
  - Re: Fwd: Fwd: namd-l: impropers for protonated 1-methyladenosine Ashar Malik (Thu Oct 21 2021 - 05:04:03 CDT)
    - Re: Fwd: Fwd: namd-l: impropers for protonated 1-methyladenosine Francesco Pietra (Thu Oct 21 2021 - 07:56:06 CDT)
    - Re: Fwd: Fwd: namd-l: impropers for protonated 1-methyladenosine Ashar Malik (Thu Oct 21 2021 - 08:51:20 CDT)
calculate radius of empty space between selected residue Yogesh Sharma (Wed Oct 20 2021 - 04:31:59 CDT)
contactvFreq TCL script not running Mi Yang (Wed Oct 20 2021 - 00:57:01 CDT)
Early access to VMD builds with full-time interactive ray tracing display mode (Tachyon RTX RTRT) John Stone (Tue Oct 19 2021 - 13:27:56 CDT)
- Re: Early access to VMD builds with full-time interactive ray tracing display mode (Tachyon RTX RTRT) Gumbart, JC (Tue Oct 19 2021 - 19:58:12 CDT)
  - Re: Early access to VMD builds with full-time interactive ray tracing display mode (Tachyon RTX RTRT) John Stone (Tue Oct 19 2021 - 20:51:07 CDT)
Coloring rings with paperchain Xiang Gao (Mon Oct 18 2021 - 16:47:56 CDT)
- Re: Coloring rings with paperchain John Stone (Mon Oct 18 2021 - 17:05:36 CDT)
  - Re: Coloring rings with paperchain Xiang Gao (Mon Oct 18 2021 - 17:24:08 CDT)
    - Re: Coloring rings with paperchain Vermaas, Josh (Mon Oct 18 2021 - 19:23:39 CDT)
    - Re: Coloring rings with paperchain Xiang Gao (Tue Oct 19 2021 - 02:33:01 CDT)
VMD Movie Plugin for MacOS Mahsa (Sat Oct 16 2021 - 13:27:50 CDT)
- Re: VMD Movie Plugin for MacOS John Stone (Mon Oct 18 2021 - 11:41:56 CDT)
mac OS Bigsur version 11.6 intel netcdf extension Sunidhi Lenka (Fri Oct 15 2021 - 13:47:32 CDT)
How can I make VMD use the correct graphics card in a Remote Desktop session? Alexander Balaeff (Thu Oct 14 2021 - 15:17:59 CDT)
- Re: How can I make VMD use the correct graphics card in a Remote Desktop session? John Stone (Mon Oct 18 2021 - 11:46:18 CDT)
CAFE plugin JosÃ© VillalaÃn (Wed Oct 13 2021 - 06:27:18 CDT)
- Re: CAFE plugin Giacomo Fiorin (Wed Oct 13 2021 - 08:31:26 CDT)
Re: vmd-l digest V1 #4449 tatyanasysoeva_at_gmail.com (Tue Oct 12 2021 - 19:48:30 CDT)
Generating silanol group on silica Javier Ivan Wong Romero (Tue Oct 12 2021 - 18:40:44 CDT)
Change Tkconsole brackground Georcki Ropon (Sun Oct 10 2021 - 14:19:12 CDT)
- Re: Change Tkconsole brackground John Stone (Mon Oct 18 2021 - 12:02:21 CDT)
partially loading all dcd files using animatedcds X_ChangeProperty: BadValue Ryan Woltz (Sun Oct 10 2021 - 10:27:00 CDT)
- Re: partially loading all dcd files using animatedcds X_ChangeProperty: BadValue John Stone (Mon Oct 18 2021 - 12:13:47 CDT)
  - Re: partially loading all dcd files using animatedcds X_ChangeProperty: BadValue Ryan Woltz (Fri Oct 22 2021 - 14:41:40 CDT)
Creation of SiC NP Francesco Coppola (Fri Oct 08 2021 - 11:37:59 CDT)
save the secondary structure and rmsd Runak R (Fri Oct 08 2021 - 10:18:17 CDT)
- Re: save the secondary structure and rmsd John Stone (Mon Oct 18 2021 - 12:17:09 CDT)
Density profile of MICELLE . sheikh sameer (Fri Oct 08 2021 - 09:55:58 CDT)
- Re: Density profile of MICELLE . Giacomo Fiorin (Fri Oct 08 2021 - 11:05:29 CDT)
Problem running CAFE for MMPBSA using CHARMM PB Radius Javier Ivan Wong Romero (Thu Oct 07 2021 - 20:38:11 CDT)
Merge frames of PDB asymmetric unit to biological assembly Chris Taylor (Tue Oct 05 2021 - 22:10:14 CDT)
- Re: Merge frames of PDB asymmetric unit to biological assembly Axel Kohlmeyer (Tue Oct 05 2021 - 23:42:45 CDT)
  - RE: Merge frames of PDB asymmetric unit to biological assembly Chris Taylor (Wed Oct 06 2021 - 21:02:58 CDT)
- Angle parameters Hideyuki Miyatake (Sat Dec 11 2021 - 22:59:50 CST)
Quikmd hangs on new install of vmd 1.9.4 on BigSur Carolyn Fitch (Sat Oct 02 2021 - 07:57:21 CDT)
- Re: Quikmd hangs on new install of vmd 1.9.4 on BigSur Carolyn Fitch (Sun Oct 03 2021 - 08:02:20 CDT)
- Re: Quikmd hangs on new install of vmd 1.9.4 on BigSur John Stone (Mon Oct 18 2021 - 12:20:17 CDT)
  - Re: Quikmd hangs on new install of vmd 1.9.4 on BigSur John Stone (Tue Oct 19 2021 - 15:08:54 CDT)
    - Re: Quikmd hangs on new install of vmd 1.9.4 on BigSur Mike McCallum (Tue Oct 19 2021 - 16:33:31 CDT)
  - Re: Quikmd hangs on new install of vmd 1.9.4 on BigSur John Stone (Tue Oct 19 2021 - 16:55:04 CDT)
Postdoctoral fellowship Computational Drug Discovery Marawan Hussien (Fri Oct 01 2021 - 12:50:10 CDT)
Multiseq unusable on M1 Mac Raul Araya (Fri Oct 01 2021 - 07:55:09 CDT)
- Re: Multiseq unusable on M1 Mac John Stone (Fri Oct 01 2021 - 13:04:50 CDT)
Re: time dependent plot for stride output file Santanu Santra (Tue Sep 28 2021 - 00:37:42 CDT)
time dependent plot for stride output file Santanu Santra (Sat Sep 25 2021 - 09:22:02 CDT)
Structure factor and Steinhardt order parameter Arpita Srivastava (Wed Sep 22 2021 - 11:54:54 CDT)
VMD/QMTool generating multiple outputs Daniel Fellner (Wed Sep 22 2021 - 03:02:06 CDT)
- Re: VMD/QMTool generating multiple outputs PaweÅ‚ KÄ™dzierski (Wed Sep 22 2021 - 04:56:10 CDT)
Changing residue name for a resid Kiana Jahani (Sat Sep 18 2021 - 06:08:41 CDT)
- Re: Changing residue name for a resid Vermaas, Josh (Sun Sep 19 2021 - 15:10:03 CDT)
Umbrella sampling windows run Ropon-Palacios G. (Wed Sep 15 2021 - 17:39:31 CDT)
How to get tensionless LIPID BILAYER automatically ? sheikh sameer (Tue Sep 14 2021 - 10:25:37 CDT)
running TCL script Bakary N'tji Diallo (Tue Sep 14 2021 - 04:19:12 CDT)
- Re: running TCL script Ashar Malik (Tue Sep 14 2021 - 05:30:01 CDT)
- Re: running TCL script Roshan Shrestha (Tue Sep 14 2021 - 05:35:25 CDT)
Re: Regarding atom index in VMD Vermaas, Josh (Mon Sep 13 2021 - 15:19:31 CDT)
Regarding atom index in VMD Arpita Srivastava (Mon Sep 13 2021 - 14:20:59 CDT)
- Re: Regarding atom index in VMD Smith, Harper E. (Tue Sep 14 2021 - 09:30:53 CDT)
Question about secondary structure analysis Runak R (Mon Sep 13 2021 - 11:36:43 CDT)
- Re: Question about secondary structure analysis John Stone (Fri Sep 17 2021 - 22:43:04 CDT)
FFTK - ORCA Bassam Haddad (Mon Sep 13 2021 - 04:41:40 CDT)
- Re: FFTK - ORCA Bassam Haddad (Sat Sep 18 2021 - 11:02:25 CDT)
  - Re: FFTK - ORCA Mariano Spivak (Sun Sep 19 2021 - 13:20:05 CDT)
    - Re: FFTK - ORCA Bassam Haddad (Tue Sep 21 2021 - 10:34:26 CDT)
  - Re: FFTK - ORCA Mariano Spivak (Tue Sep 28 2021 - 14:43:29 CDT)
autopsf with many modifiers Francesco Pietra (Sat Sep 11 2021 - 09:21:24 CDT)
- Fwd: autopsf with many modifiers Francesco Pietra (Mon Sep 13 2021 - 04:58:30 CDT)
  - Fwd: autopsf with many modifiers Francesco Pietra (Mon Sep 13 2021 - 09:25:31 CDT)
Issues with multiseq Raul Araya (Fri Sep 10 2021 - 14:16:46 CDT)
- Re: Issues with multiseq Lindsey Prignano (Fri Sep 10 2021 - 16:34:30 CDT)
Re: VMD installation on Mac OSx 11 Bug Sur Mauro Boero (Wed Sep 08 2021 - 06:44:35 CDT)
- Re: VMD installation on Mac OSx 11 Bug Sur John Stone (Sat Sep 18 2021 - 10:29:30 CDT)
VMD installation on Mac OSx 11 Bug Sur Mauro Boero (Mon Sep 06 2021 - 02:08:46 CDT)
Re: Umbrella sampling windows Vermaas, Josh (Sat Sep 04 2021 - 16:10:37 CDT)
- Re: Umbrella sampling windows Ropon-Palacios G. (Sat Sep 04 2021 - 16:24:03 CDT)
  - Re: Umbrella sampling windows Giacomo Fiorin (Sat Sep 04 2021 - 19:50:44 CDT)
    - Re: Umbrella sampling windows Ropon-Palacios G. (Sat Sep 04 2021 - 22:05:10 CDT)
    - Re: Umbrella sampling windows Giacomo Fiorin (Sun Sep 05 2021 - 00:32:12 CDT)
Umbrella sampling windows Ropon-Palacios G. (Sat Sep 04 2021 - 13:19:49 CDT)
loading movies of ply files Prof. Eddie (Thu Sep 02 2021 - 10:35:03 CDT)
- Re: loading movies of ply files Axel Kohlmeyer (Thu Sep 02 2021 - 11:14:40 CDT)
Tachyon not rendering large scenes Jason Hlozek (Thu Sep 02 2021 - 07:29:11 CDT)
- Re: Tachyon not rendering large scenes John Stone (Thu Sep 02 2021 - 08:43:49 CDT)
  - Re: Tachyon not rendering large scenes Jason Hlozek (Thu Sep 02 2021 - 10:33:43 CDT)
Visualizing segmentation/labeling without python dependency Bruininks, B.M.H. (Wed Sep 01 2021 - 08:35:14 CDT)
- Re: Visualizing segmentation/labeling without python dependency Vermaas, Josh (Wed Sep 01 2021 - 10:51:53 CDT)
  - Re: Visualizing segmentation/labeling without python dependency Bruininks, B.M.H. (Thu Sep 02 2021 - 04:15:40 CDT)
Phosphate ions Raman Preet Singh (Sat Aug 28 2021 - 08:43:43 CDT)
VMD not displaying Gromacs TRR format traj Prithwish Nandi (Thu Aug 26 2021 - 11:36:12 CDT)
- Re: VMD not displaying Gromacs TRR format traj Giacomo Fiorin (Thu Aug 26 2021 - 12:44:50 CDT)
FFTK dihedral scan discontinuities Daniel Fellner (Thu Aug 26 2021 - 10:18:17 CDT)
- Re: FFTK dihedral scan discontinuities JÃ©rÃ´me HÃ©nin (Fri Aug 27 2021 - 07:35:26 CDT)
  - Re: FFTK dihedral scan discontinuities Daniel Fellner (Fri Apr 08 2022 - 01:29:41 CDT)
VMD Error: vecsub: two vectors don't have the same size Amir Zeb (Thu Aug 26 2021 - 02:03:51 CDT)
- Re: VMD Error: vecsub: two vectors don't have the same size Ropon-Palacios G. (Thu Aug 26 2021 - 19:45:47 CDT)
VR movie Amnah Alalmaie (Wed Aug 25 2021 - 21:18:01 CDT)
- Re: VR movie John Stone (Wed Aug 25 2021 - 21:45:51 CDT)
Changing Tk console background Manasa Yadavalli (Wed Aug 25 2021 - 15:46:57 CDT)
- Re: Changing Tk console background Victor Kwan (Wed Aug 25 2021 - 18:05:26 CDT)
- Re: Changing Tk console background Lindsey Prignano (Wed Aug 25 2021 - 18:38:01 CDT)
Tk console not responding to keystrokes Manasa Yadavalli (Wed Aug 25 2021 - 15:46:18 CDT)
Asymmetric concentration gradient Ropon-Palacios G. (Mon Aug 23 2021 - 21:08:19 CDT)
- Re: Asymmetric concentration gradient Jason Smith (Tue Aug 24 2021 - 12:11:09 CDT)
- Re: Asymmetric concentration gradient Alec Zander (Tue Aug 24 2021 - 13:01:21 CDT)
  - Re: Asymmetric concentration gradient Georcki Ropon (Tue Aug 24 2021 - 13:05:05 CDT)
VMD Tachyon Render fails with new material Prateek Bansal (Mon Aug 23 2021 - 10:21:48 CDT)
- Re: VMD Tachyon Render fails with new material Vermaas, Josh (Mon Aug 23 2021 - 11:47:22 CDT)
  - Re: VMD Tachyon Render fails with new material Jason Smith (Mon Aug 23 2021 - 12:44:15 CDT)
    - Re: VMD Tachyon Render fails with new material John Stone (Mon Aug 23 2021 - 13:52:41 CDT)
Hexameric periodic box Georcki Ropon (Fri Aug 20 2021 - 17:36:43 CDT)
high-dpi monitor issue Raul Araya (Fri Aug 20 2021 - 15:19:42 CDT)
Mutated model development in VMD SYEDA SABIHA SULTANA LUBNA . (Thu Aug 19 2021 - 06:34:02 CDT)
Glycosphingolipids structure Ropon-Palacios G. (Tue Aug 17 2021 - 15:42:38 CDT)
- Re: Glycosphingolipids structure Nathan Kern (Wed Aug 18 2021 - 09:39:58 CDT)
Understanding the positional difference of all atoms between two frames SYEDA SABIHA SULTANA LUBNA . (Tue Aug 17 2021 - 03:02:23 CDT)
Alascan plugin error Brandon Havranek (Fri Aug 13 2021 - 23:23:25 CDT)
Voltool Averaging Maps Mcguire, Kelly (Fri Aug 13 2021 - 19:23:36 CDT)
- Re: Voltool Averaging Maps Josh Vermaas (Mon Aug 16 2021 - 10:00:14 CDT)
Funnel metadynamics Prithwish Nandi (Fri Aug 13 2021 - 06:14:45 CDT)
- Re: Funnel metadynamics Ashar Malik (Fri Aug 13 2021 - 07:20:50 CDT)
  - Re: Funnel metadynamics Prithwish Nandi (Fri Aug 13 2021 - 07:59:36 CDT)
FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CD2R6A LPA1 zeynab hosseini (Fri Aug 13 2021 - 03:28:24 CDT)
- Re: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CD2R6A LPA1 Michael Robinson (Sun Aug 15 2021 - 22:55:51 CDT)
  - Re: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CD2R6A LPA1 zeynab hosseini (Mon Aug 16 2021 - 01:19:35 CDT)
Re: Stripping water from psf Vermaas, Josh (Thu Aug 12 2021 - 14:55:03 CDT)
- Re: Stripping water from psf Raman Preet Singh (Fri Aug 13 2021 - 08:41:18 CDT)
Stripping water from psf Raman Preet Singh (Thu Aug 12 2021 - 12:44:46 CDT)
Add specific h-bonds Dawid das (Thu Aug 12 2021 - 08:59:35 CDT)
- Re: Add specific h-bonds Jason Smith (Thu Aug 12 2021 - 10:47:28 CDT)
Joining nonlinear chain fragments from LAMMPS data file Clement Fang Jin Koh (Wed Aug 11 2021 - 12:32:56 CDT)
Re: Protein Alignment Question Vermaas, Josh (Wed Aug 11 2021 - 09:10:49 CDT)
How to generate random velocities? Seera Suryanarayana (Wed Aug 11 2021 - 04:57:19 CDT)
- Re: How to generate random velocities? Georcki Ropon (Wed Aug 11 2021 - 11:41:51 CDT)
Protein Alignment Question Mcguire, Kelly (Wed Aug 11 2021 - 01:09:13 CDT)
Problem loading file in VMD Caitlin Hetherington (Tue Aug 10 2021 - 09:18:17 CDT)
Print array Ropon-Palacios G. (Mon Aug 09 2021 - 17:54:01 CDT)
Write umbrella windows Ropon-Palacios G. (Sun Aug 08 2021 - 23:31:54 CDT)
- Re: Write umbrella windows Vermaas, Josh (Mon Aug 09 2021 - 08:00:36 CDT)
  - Re: Write umbrella windows Ropon-Palacios G. (Mon Aug 09 2021 - 10:58:46 CDT)
Flying metal ion in QWIKMD ( NAMD/ORCA) QM/MM Herald Delis (Sat Aug 07 2021 - 14:01:27 CDT)
Hydrogen mass repartition PSFGen2.0 Ropon-Palacios G. (Fri Aug 06 2021 - 13:52:10 CDT)
- Re: Hydrogen mass repartition PSFGen2.0 RenÃ© Hafner TUK (Sat Aug 07 2021 - 04:20:23 CDT)
  - Re: Hydrogen mass repartition PSFGen2.0 Georcki Ropon (Sat Aug 07 2021 - 11:55:41 CDT)
  - Re: Hydrogen mass repartition PSFGen2.0 Geist, Norman (Sat Aug 07 2021 - 13:43:23 CDT)
how to solvate the membrane in vmd?? Amir Zeb (Thu Aug 05 2021 - 07:55:38 CDT)
- Re: how to solvate the membrane in vmd?? Ashar Malik (Thu Aug 05 2021 - 08:54:20 CDT)
dipole watcher plugin kazimieras tamoliunas (Thu Aug 05 2021 - 04:51:56 CDT)
psfgen 2.0 zeynab hosseini (Wed Aug 04 2021 - 12:06:36 CDT)
- Re: psfgen 2.0 zeynab hosseini (Wed Aug 04 2021 - 14:17:11 CDT)
- Re: psfgen 2.0 Victor Kwan (Wed Aug 04 2021 - 16:16:26 CDT)
  - Re: psfgen 2.0 zeynab hosseini (Thu Aug 05 2021 - 04:25:41 CDT)
Re: psfgen 2.0 and Drude Gumbart, JC (Tue Aug 03 2021 - 14:44:09 CDT)
psfgen 2.0 and Drude Gumbart, JC (Tue Aug 03 2021 - 14:22:37 CDT)
Shannon entropy in MultiSeq? Aaron Oakley (Tue Aug 03 2021 - 00:11:26 CDT)
MultiSeq Database Downloading Error Alexander Howard (Fri Jul 30 2021 - 19:03:22 CDT)
VMD high DPI Yujie Wu (Thu Jul 29 2021 - 23:54:33 CDT)
- Re: VMD high DPI Miro Astore (Fri Jul 30 2021 - 00:28:03 CDT)
  - Re: VMD high DPI Michael Von Domaros (Fri Jul 30 2021 - 02:03:22 CDT)
    - Re: VMD high DPI Alin-Marin Elena - STFC UKRI (Fri Jul 30 2021 - 03:06:33 CDT)
- Re: VMD high DPI Dow Hurst (Fri Sep 03 2021 - 12:45:22 CDT)
  - Re: VMD high DPI John Stone (Fri Sep 17 2021 - 23:58:30 CDT)
    - Re: VMD high DPI yjcoshc (Sat Sep 18 2021 - 07:21:13 CDT)
    - Re: VMD high DPI John Stone (Sat Sep 18 2021 - 10:10:19 CDT)
Problem with Psfgen 2.0 to create Drude FF .psf file for amino acid zeynab hosseini (Thu Jul 29 2021 - 11:57:11 CDT)
- Re: Problem with Psfgen 2.0 to create Drude FF .psf file for amino acid zeynab hosseini (Fri Jul 30 2021 - 04:47:35 CDT)
Does CHARMM-GUI Drude-Prepper input generator work for MD simulation of carbon nanotubes? zeynab hosseini (Mon Jul 26 2021 - 14:08:52 CDT)
- Re: Does CHARMM-GUI Drude-Prepper input generator work for MD simulation of carbon nanotubes? Raman Preet Singh (Tue Jul 27 2021 - 02:03:23 CDT)
- Re: Does CHARMM-GUI Drude-Prepper input generator work for MD simulation of carbon nanotubes? Stefan Boresch (Tue Jul 27 2021 - 02:38:19 CDT)
Could not read file problem Igor Gordiy (Fri Jul 23 2021 - 04:33:46 CDT)
- Re: Could not read file problem Vermaas, Josh (Fri Jul 23 2021 - 08:39:58 CDT)
  - Re: Could not read file problem Chris Neale (Fri Jul 23 2021 - 09:42:54 CDT)
- Re: Could not read file problem PaweÅ‚ KÄ™dzierski (Fri Jul 23 2021 - 10:55:22 CDT)
FFTk GUI unresponsive Hamish Swanson (Thu Jul 22 2021 - 09:30:58 CDT)
- Re: FFTk GUI unresponsive Gumbart, JC (Tue Jul 27 2021 - 10:42:19 CDT)
  - Re: Re: FFTk GUI unresponsive PaweÅ‚ KÄ™dzierski (Wed Jul 28 2021 - 06:05:27 CDT)
Discrepancy in value of dihedral angles of a sugar molecule by VMD tools chiessi_at_uniroma2.it (Thu Jul 22 2021 - 05:55:17 CDT)
- Re: Discrepancy in value of dihedral angles of a sugar molecule by VMD tools Axel Kohlmeyer (Thu Jul 22 2021 - 07:41:39 CDT)
  - Re: Discrepancy in value of dihedral angles of a sugar molecule by VMD tools chiessi_at_uniroma2.it (Thu Jul 22 2021 - 08:38:25 CDT)
- Re: Discrepancy in value of dihedral angles of a sugar molecule by VMD tools Josh Vermaas (Thu Jul 22 2021 - 08:44:49 CDT)
- RE: Discrepancy in value of dihedral angles of a sugar molecule by VMD tools Joaquim Rui de Castro Rodrigues (Thu Jul 22 2021 - 09:56:53 CDT)
  - Re: Discrepancy in value of dihedral angles of a sugar molecule by VMD tools chiessi_at_uniroma2.it (Fri Jul 23 2021 - 04:42:54 CDT)
Errors in exporting average structure to a .pdb file Francesco Pietra (Tue Jul 20 2021 - 11:28:24 CDT)
Error while making th trajectory movie Nancy Singh (Tue Jul 20 2021 - 10:26:47 CDT)
RE:MolID error using fftk with VMD 1.94a49 on windows 10 - [Solved] ABEL Stephane (Sun Jul 18 2021 - 09:25:50 CDT)
Re: [External] Re: troubles in setting pbc on m1 mac version Fujie Tang (Thu Jul 15 2021 - 08:53:54 CDT)
- Re: [External] Re: troubles in setting pbc on m1 mac version Axel Kohlmeyer (Thu Jul 15 2021 - 09:50:28 CDT)
  - Re: [External] Re: troubles in setting pbc on m1 mac version Fujie Tang (Thu Jul 15 2021 - 16:27:57 CDT)
Adding oxygen molecules Kiana Jahani (Thu Jul 15 2021 - 04:12:50 CDT)
troubles in setting pbc on m1 mac version Fujie Tang (Wed Jul 14 2021 - 12:01:27 CDT)
loading PDBs with multiple states having different numbers of atoms in VMD Stefan Ivanov (Wed Jul 14 2021 - 02:00:24 CDT)
- Re: loading PDBs with multiple states having different numbers of atoms in VMD PaweÅ‚ KÄ™dzierski (Wed Jul 14 2021 - 04:30:29 CDT)
Re: Unwrap for diffusion phenomena? Vermaas, Josh (Tue Jul 13 2021 - 15:49:35 CDT)
- Re: Unwrap for diffusion phenomena? Ropon-Palacios G. (Tue Jul 13 2021 - 15:53:39 CDT)
- Re: Unwrap for diffusion phenomena? Georcki Ropon (Fri Jul 16 2021 - 00:51:47 CDT)
Unwrap for diffusion phenomena? Ropon-Palacios G. (Tue Jul 13 2021 - 14:01:04 CDT)
- Re: Unwrap for diffusion phenomena? Ropon-Palacios G. (Tue Jul 13 2021 - 15:36:43 CDT)
Extracellular Salt Bridges Manas Kohli (Tue Jul 13 2021 - 12:02:52 CDT)
- Re: Extracellular Salt Bridges Carlos Simmerling (Tue Jul 13 2021 - 16:21:28 CDT)
TR : MolID error using fftk with VMD 1.94a49 on windows 10 ABEL Stephane (Tue Jul 13 2021 - 08:51:45 CDT)
- Re: MolID error using fftk with VMD 1.94a49 on windows 10 Jason Smith (Tue Jul 13 2021 - 10:56:36 CDT)
  - RE:MolID error using fftk with VMD 1.94a49 on windows 10 ABEL Stephane (Tue Jul 13 2021 - 12:35:20 CDT)
showing bonds in .xyz files Yiyan Kuang (Tue Jul 06 2021 - 22:13:38 CDT)
- Re: showing bonds in .xyz files Jason Smith (Wed Jul 07 2021 - 11:29:00 CDT)
- Re: showing bonds in .xyz files Axel Kohlmeyer (Wed Jul 07 2021 - 12:32:32 CDT)
Molecular Design Interface Software Development Position Joao Vieira-Ribeiro (Tue Jul 06 2021 - 15:00:34 CDT)
Randomly select molecules and delete them fan li (Tue Jul 06 2021 - 05:23:48 CDT)
- Re: Randomly select molecules and delete them Jason Smith (Tue Jul 06 2021 - 10:28:03 CDT)
  - Re: Randomly select molecules and delete them fan li (Tue Jul 06 2021 - 15:06:26 CDT)
Autopsf error Amir Zeb (Mon Jul 05 2021 - 21:48:42 CDT)
FFTK kList no such variable Hamish Swanson (Mon Jul 05 2021 - 05:49:38 CDT)
- Re: FFTK kList no such variable Gumbart, JC (Mon Jul 05 2021 - 10:25:16 CDT)
  - Re: FFTK kList no such variable Smith, Harper E. (Mon Jul 05 2021 - 11:01:21 CDT)
    - Re: FFTK kList no such variable Hamish Swanson (Mon Jul 05 2021 - 12:03:23 CDT)
Problem in Installing the linus version of VMD Nancy Singh (Thu Jul 01 2021 - 08:21:06 CDT)
VMD H-bond Plugin error Nancy Singh (Tue Jun 29 2021 - 09:22:39 CDT)
- Re: VMD H-bond Plugin error Mariano Spivak (Tue Jun 29 2021 - 11:00:12 CDT)
  - Re: VMD H-bond Plugin error John Stone (Fri Jul 02 2021 - 11:31:29 CDT)
    - Re: VMD H-bond Plugin error Nancy Singh (Mon Jul 05 2021 - 05:55:37 CDT)
Residue numbers changing after addition of simulation boxes below and above membrane cell Nagendra Prasad (Sun Jun 20 2021 - 05:10:31 CDT)
- Re: Residue numbers changing after addition of simulation boxes below and above membrane cell Josh Vermaas (Mon Jun 21 2021 - 07:54:41 CDT)
Measure helicity at each frame Roni Saiba (Fri Jun 18 2021 - 21:09:24 CDT)
- RE: Measure helicity at each frame Joaquim Rui de Castro Rodrigues (Sat Jun 19 2021 - 07:24:19 CDT)
  - Re: Measure helicity at each frame Roni Saiba (Sat Jun 19 2021 - 11:21:25 CDT)
[topotools]writelammpsdata å†¯è‰ºæ¼© (Fri Jun 18 2021 - 07:04:46 CDT)
- Re: [topotools]writelammpsdata Axel Kohlmeyer (Fri Jun 18 2021 - 07:58:55 CDT)
  - Re: Re: [topotools]writelammpsdata Axel Kohlmeyer (Fri Jun 18 2021 - 08:52:30 CDT)
    - Re: Re: [topotools]writelammpsdata John Stone (Fri Jul 02 2021 - 11:33:19 CDT)
Unable to open VMD on Mac Anirudh Nandakumar (Wed Jun 16 2021 - 08:34:31 CDT)
topotools lammps style sphere - write molecules MD Simulation (Mon Jun 14 2021 - 10:05:35 CDT)
- Re: topotools lammps style sphere - write molecules Axel Kohlmeyer (Mon Jun 14 2021 - 10:52:29 CDT)
  - Re: topotools lammps style sphere - write molecules MD Simulation (Mon Jun 14 2021 - 10:54:16 CDT)
Jarzynski analysis Ropon-Palacios G. (Sun Jun 13 2021 - 22:26:03 CDT)
- Re: Jarzynski analysis JÃ©rÃ´me HÃ©nin (Tue Jul 27 2021 - 07:25:25 CDT)
  - Re: Jarzynski analysis Georcki Ropon (Tue Jul 27 2021 - 11:23:34 CDT)
Wrapping creates extra bonds..! zeynab hosseini (Sun Jun 13 2021 - 15:06:41 CDT)
wraping creates extra bonds! zeynab hoseyni (Sun Jun 13 2021 - 14:49:48 CDT)
- Re: wraping creates extra bonds! Peter Freddolino (Sun Jun 13 2021 - 19:22:32 CDT)
  - Re: wraping creates extra bonds! zeynab hoseyni (Mon Jun 14 2021 - 00:38:35 CDT)
Building micelles Raman Preet Singh (Sun Jun 13 2021 - 13:29:34 CDT)
- RE:Building micelles ABEL Stephane (Mon Jun 14 2021 - 04:42:05 CDT)
Found bad contact Ropon-Palacios G. (Thu Jun 10 2021 - 10:19:13 CDT)
- Re: Found bad contact Vermaas, Josh (Thu Jun 10 2021 - 10:20:24 CDT)
  - Re: Found bad contact Ropon-Palacios G. (Thu Jun 10 2021 - 10:23:46 CDT)
    - Re: Found bad contact Josh Vermaas (Thu Jun 10 2021 - 10:35:11 CDT)
  - Re: Re: Found bad contact Diship Srivastava (Thu Jun 10 2021 - 11:11:59 CDT)
loading multiple different topologies into the same "molecule" Chris Neale (Wed Jun 09 2021 - 18:34:22 CDT)
- Re: loading multiple different topologies into the same "molecule" Pawel Kedzierski (Thu Jun 10 2021 - 02:00:01 CDT)
  - Re: loading multiple different topologies into the same "molecule" Raman Preet Singh (Thu Jun 10 2021 - 05:02:58 CDT)
- Re: loading multiple different topologies into the same "molecule" Vermaas, Josh (Thu Jun 10 2021 - 09:19:11 CDT)
  - Re: loading multiple different topologies into the same "molecule" Chris Neale (Thu Jun 10 2021 - 12:26:39 CDT)
Lipid Packing Defect in vmd Diship Srivastava (Sun Jun 06 2021 - 04:57:06 CDT)
Status of VR in VMD Paulo E. Abreu (Tue Jun 01 2021 - 13:46:01 CDT)
- Re: Status of VR in VMD John Stone (Thu Jun 10 2021 - 16:10:23 CDT)
  - Re: Status of VR in VMD Paulo E. Abreu (Tue Sep 07 2021 - 04:04:30 CDT)
VMD Timeline Plug-in Selection in Hydrogen Bonds Calculations Ebru Cetin (Fri May 28 2021 - 11:55:09 CDT)
Fwd: VMD Timeline Plug-in Selection in Hydrogen Bonds Calculations Ebru Cetin (Wed May 26 2021 - 04:33:46 CDT)
Atom selection with asterisk atom name Saikat Pal (Wed May 26 2021 - 02:00:59 CDT)
- Re: Atom selection with asterisk atom name Vermaas, Josh (Wed May 26 2021 - 10:57:06 CDT)
  - Re: Atom selection with asterisk atom name Vermaas, Josh (Fri May 28 2021 - 10:49:25 CDT)
VMD in "Big DCD mode" Leonardo Palmieri (Fri May 21 2021 - 12:55:57 CDT)
QwikMD error Giuseppe Ermondi (Fri May 21 2021 - 07:47:45 CDT)
- Re: QwikMD error John Stone (Fri Jul 02 2021 - 11:34:11 CDT)
Generating parameter files Arthur Pereira da Fonseca (Wed May 19 2021 - 12:04:33 CDT)
- Re: Generating parameter files Smith, Harper E. (Wed May 19 2021 - 13:01:13 CDT)
- Re: Generating parameter files Pawel Kedzierski (Wed May 19 2021 - 15:00:34 CDT)
FFTK: dihedral containing hydrogen? Smith, Harper E. (Tue May 18 2021 - 15:42:21 CDT)
- Re: FFTK: dihedral containing hydrogen? Gumbart, JC (Tue May 18 2021 - 19:03:04 CDT)
VMD and NAMD survey invitations coming to your inbox... John Stone (Tue May 18 2021 - 14:21:55 CDT)
Re: Angles generated by AutoPSF? Vermaas, Josh (Mon May 17 2021 - 14:23:20 CDT)
Angles generated by AutoPSF? Smith, Harper E. (Mon May 17 2021 - 12:15:15 CDT)
- Re: Angles generated by AutoPSF? Pawel Kedzierski (Mon May 17 2021 - 14:50:37 CDT)
  - Re: Angles generated by AutoPSF? Smith, Harper E. (Mon May 17 2021 - 14:57:28 CDT)
REMOVE WATER MOLECULES WITH A SPECIFIC DISTANCE Eduardo Estevez (Sun May 16 2021 - 13:13:06 CDT)
- Re: REMOVE WATER MOLECULES WITH A SPECIFIC DISTANCE Karteek K. Bejagam (Sun May 16 2021 - 14:15:17 CDT)
Nanotube builder bug Pawel Kedzierski (Thu May 13 2021 - 08:06:06 CDT)
Place complex in the center Amnah Alalmaie (Wed May 12 2021 - 14:13:11 CDT)
Clustering by RMSD Lilian Esmeralda Araujo Arcos (Wed May 12 2021 - 12:16:56 CDT)
- Re: Clustering by RMSD Smith, Harper E. (Wed May 12 2021 - 13:27:57 CDT)
[topotool] writelammpsdata : custom order for atom types Yann Claveau (Wed May 12 2021 - 03:37:29 CDT)
- Re: [topotool] writelammpsdata : custom order for atom types Axel Kohlmeyer (Wed May 12 2021 - 04:30:22 CDT)
  - Re: [topotool] writelammpsdata : custom order for atom types Yann Claveau (Wed May 12 2021 - 04:37:01 CDT)
  - Re: [topotool] writelammpsdata : custom order for atom types Yann Claveau (Wed May 12 2021 - 08:12:59 CDT)
Question about error while using QwikMD files Ahmad Alqaisi (Mon May 10 2021 - 03:12:25 CDT)
- Re: Question about error while using QwikMD files Mariano Spivak (Mon May 10 2021 - 10:48:21 CDT)
  - Re: Question about error while using QwikMD files John Stone (Mon May 10 2021 - 11:25:30 CDT)
Auto PSF problem with VMD 1.9.4a48-Catalina-Rev7 Patrick Osmer (Sun May 09 2021 - 14:29:00 CDT)
- Re: Auto PSF problem with VMD 1.9.4a48-Catalina-Rev7 Peter Freddolino (Sun May 09 2021 - 19:17:26 CDT)
  - Re: Auto PSF problem with VMD 1.9.4a48-Catalina-Rev7 John Stone (Mon May 10 2021 - 01:01:05 CDT)
Quicksurf crashes VMD on newest Mac version David Kastner (Thu May 06 2021 - 23:29:03 CDT)
- Re: Quicksurf crashes VMD on newest Mac version John Stone (Mon May 10 2021 - 11:27:26 CDT)
  - Re: Quicksurf crashes VMD on newest Mac version FX (Mon May 10 2021 - 14:50:46 CDT)
    - Re: Quicksurf crashes VMD on newest Mac version John Stone (Mon May 10 2021 - 15:39:22 CDT)
    - Re: Quicksurf crashes VMD on newest Mac version FX (Mon May 10 2021 - 16:05:59 CDT)
  - Re: Quicksurf crashes VMD on newest Mac version David Kastner (Mon May 10 2021 - 14:58:23 CDT)
Tcl Scripting Question Mcguire, Kelly (Tue May 04 2021 - 12:45:55 CDT)
- Re: Tcl Scripting Question RenÃ© Hafner TUK (Tue May 04 2021 - 13:57:07 CDT)
- Re: Tcl Scripting Question Ashar Malik (Tue May 04 2021 - 14:11:45 CDT)
- Re: Tcl Scripting Question Vermaas, Josh (Tue May 04 2021 - 14:48:00 CDT)
  - Re: Tcl Scripting Question John Stone (Tue May 04 2021 - 15:44:24 CDT)
rendering with a very large scene description file Vlad Cojocaru (Sun May 02 2021 - 13:10:50 CDT)
- Re: rendering with a very large scene description file Vlad Cojocaru (Sun May 02 2021 - 16:55:07 CDT)
  - Re: Re: rendering with a very large scene description file John Stone (Mon May 03 2021 - 16:10:00 CDT)
    - Re: Re: rendering with a very large scene description file Vlad Cojocaru (Tue May 04 2021 - 18:09:52 CDT)
Printing simulation box vectors to the display window Andrew DeYoung (Wed Apr 28 2021 - 15:46:29 CDT)
Problem with Calc. inter-sel. contacts NICOLÃS DÃAZ ROUSSEL (Fri Apr 23 2021 - 07:12:40 CDT)
Compilation error: stride_LINUXAMD64', surf_LINUXAMD64, tachyon_LINUXAMD64 : No such file or directory Chintapalli, Sree vamsee (Thu Apr 22 2021 - 14:45:29 CDT)
- Re: Compilation error: stride_LINUXAMD64', surf_LINUXAMD64, tachyon_LINUXAMD64 : No such file or directory Axel Kohlmeyer (Thu Apr 22 2021 - 15:34:04 CDT)
BFEE plugin error: 'measure center: bad weight sum would cause divide by zero' Jovana Stelkic (Thu Apr 22 2021 - 01:25:22 CDT)
- Re: BFEE plugin error: 'measure center: bad weight sum would cause divide by zero' Pawel Kedzierski (Thu Apr 22 2021 - 08:42:25 CDT)
  - Re: BFEE plugin error: 'measure center: bad weight sum would cause divide by zero' Pawel Kedzierski (Thu Apr 22 2021 - 10:43:27 CDT)
- Re: BFEE plugin error: 'measure center: bad weight sum would cause divide by zero' Axel Kohlmeyer (Thu Apr 22 2021 - 12:59:51 CDT)
  - Re: BFEE plugin error: 'measure center: bad weight sum would cause divide by zero' Jovana Stelkic (Thu Apr 22 2021 - 13:34:48 CDT)
Tachyon Render not working juan.velasquez (Mon Apr 19 2021 - 04:58:18 CDT)
Using QwikMD with latest CHARMM36 force fields Andreas Kukol (Sat Apr 17 2021 - 03:58:22 CDT)
vecsub: two vectors don't have the same size Francesco Pietra (Fri Apr 16 2021 - 04:36:38 CDT)
- Re: vecsub: two vectors don't have the same size Ashar Malik (Fri Apr 16 2021 - 05:31:31 CDT)
  - Re: vecsub: two vectors don't have the same size Francesco Pietra (Fri Apr 16 2021 - 10:30:35 CDT)
Re: Error while compiling vmd: "libmolfile_plugin.h" Vermaas, Josh (Thu Apr 15 2021 - 13:47:19 CDT)
Error while compiling vmd: "libmolfile_plugin.h" Chintapalli, Sree vamsee (Thu Apr 15 2021 - 12:08:04 CDT)
Rendering using GPU Nikhil Maroli (Thu Apr 15 2021 - 02:31:50 CDT)
- Re: Rendering using GPU Paul O'Leary (Thu Apr 15 2021 - 03:45:02 CDT)
- Re: Rendering using GPU Geist, Norman (Thu Apr 15 2021 - 03:45:48 CDT)
  - Re: Rendering using GPU John Stone (Thu Apr 15 2021 - 10:20:42 CDT)
Re: ethanol solvation box Vermaas, Josh (Wed Apr 14 2021 - 18:35:05 CDT)
- Re: Re: ethanol solvation box Raisa Carmen Andeme Ela (Wed Apr 14 2021 - 19:31:56 CDT)
  - Re: Re: ethanol solvation box Vermaas, Josh (Wed Apr 14 2021 - 19:38:18 CDT)
    - Re: Re: ethanol solvation box Raisa Carmen Andeme Ela (Thu Apr 15 2021 - 13:37:45 CDT)
A question about atomic symbol and cell-border width using VMD Hamza Bouafia (Tue Apr 13 2021 - 18:29:03 CDT)
stride not showing all helix section after VMD crash Carlos Simmerling (Tue Apr 13 2021 - 16:28:22 CDT)
- Re: stride not showing all helix section after VMD crash John Stone (Thu Apr 15 2021 - 11:51:36 CDT)
CIonize Not Installed on Windows VMD Arash Firouzbakht (Tue Apr 13 2021 - 14:33:15 CDT)
Visual Help Mcguire, Kelly (Sun Apr 11 2021 - 20:38:48 CDT)
- Re: Visual Help Robin Betz (Sun Apr 11 2021 - 23:18:38 CDT)
  - Re: Visual Help Jason Smith (Mon Apr 12 2021 - 00:47:52 CDT)
Loading files Karteek K. Bejagam (Wed Apr 07 2021 - 12:55:49 CDT)
- Re: Loading files Ali Osman Acar (Wed Apr 07 2021 - 14:07:11 CDT)
  - Re: Loading files Axel Kohlmeyer (Wed Apr 07 2021 - 14:59:25 CDT)
  - Re: Loading files Vermaas, Josh (Wed Apr 07 2021 - 15:23:52 CDT)
- Re: Loading files Axel Kohlmeyer (Wed Apr 07 2021 - 15:02:28 CDT)
VMD web/email outage today Tuesday 4/6 John Stone (Tue Apr 06 2021 - 12:57:55 CDT)
secondary structure of a protein containing non-canonical residues Arash Firouzbakht (Tue Apr 06 2021 - 09:59:48 CDT)
(no subject) Kabir Biswas (Mon Apr 05 2021 - 17:45:40 CDT)
VMD 1.9.4 won't open .crd files Alex Nazlidis (Mon Apr 05 2021 - 15:31:11 CDT)
- Re: VMD 1.9.4 won't open .crd files John Stone (Mon Apr 05 2021 - 15:33:19 CDT)
  - Re: VMD 1.9.4 won't open .crd files Alex Nazlidis (Mon Apr 05 2021 - 15:41:45 CDT)
Ultra-violet environment simulation in NAMD Faisal, H M Nasrullah (Mon Apr 05 2021 - 10:55:08 CDT)
- Re: Ultra-violet environment simulation in NAMD Jason Smith (Mon Apr 05 2021 - 13:31:05 CDT)
histidine protonation Francesco Pietra (Fri Apr 02 2021 - 11:52:43 CDT)
- Re: histidine protonation Vermaas, Josh (Fri Apr 02 2021 - 13:26:13 CDT)
  - Re: histidine protonation Gumbart, JC (Fri Apr 02 2021 - 15:43:20 CDT)
pbwithin a defined coordinate MD Simulation (Tue Mar 30 2021 - 08:48:51 CDT)
Electrostatic Potential membrane pores Satyan Sharma (Tue Mar 30 2021 - 03:52:44 CDT)
change color sequence used in label graphs? Carlos Simmerling (Mon Mar 29 2021 - 14:00:55 CDT)
- Re: change color sequence used in label graphs? Mariano Spivak (Mon Mar 29 2021 - 16:52:11 CDT)
Moment of inertia script David Gae (Fri Mar 26 2021 - 15:11:54 CDT)
Switching from MP2 in FFTK? Smith, Harper E. (Fri Mar 26 2021 - 11:15:10 CDT)
- Re: Switching from MP2 in FFTK? Bennion, Brian (Fri Mar 26 2021 - 13:19:52 CDT)
- Re: Switching from MP2 in FFTK? Jason Smith (Fri Mar 26 2021 - 13:25:14 CDT)
  - Re: Switching from MP2 in FFTK? Smith, Harper E. (Fri Mar 26 2021 - 13:55:44 CDT)
- Re: Switching from MP2 in FFTK? Aleksei (Fri Mar 26 2021 - 14:19:52 CDT)
parameterizing a peptide with a methylated backbone nitrogen SHIVAM TIWARI (Thu Mar 25 2021 - 04:28:36 CDT)
(no subject) soumadwip ghosh (Thu Mar 25 2021 - 02:57:21 CDT)
- Re: Axel Kohlmeyer (Fri Mar 26 2021 - 14:01:39 CDT)
attachment file size limit for the mailing list SHIVAM TIWARI (Thu Mar 25 2021 - 00:19:00 CDT)
- Re: attachment file size limit for the mailing list John Stone (Fri Mar 26 2021 - 00:12:37 CDT)
Problem in opening VMD on macOS Catalina Mahsa (Wed Mar 24 2021 - 07:02:09 CDT)
- Re: Problem in opening VMD on macOS Catalina Mortimer Hemmit (Fri Mar 26 2021 - 13:50:17 CDT)
modify and save updated PSF and CRD files soumadwip ghosh (Wed Mar 24 2021 - 04:02:20 CDT)
VMD web/email outage most of Tuesday March 23rd John Stone (Mon Mar 22 2021 - 22:45:54 CDT)
how to generate different starting points to do the md simulations Seera Suryanarayana (Mon Mar 22 2021 - 02:02:18 CDT)
FFTK: Dihedral scan trans/cis Daniel Fellner (Sun Mar 21 2021 - 06:28:55 CDT)
- Re: FFTK: Dihedral scan trans/cis Gumbart, JC (Mon Mar 22 2021 - 22:48:09 CDT)
Why do the coordinates of my atoms change when writing to a pdb file? Ramon Mendoza Uriarte (Sat Mar 20 2021 - 23:15:56 CDT)
- Re: Why do the coordinates of my atoms change when writing to a pdb file? Axel Kohlmeyer (Sun Mar 21 2021 - 00:18:28 CDT)
  - Re: Why do the coordinates of my atoms change when writing to a pdb file? Ramon Mendoza Uriarte (Sun Mar 21 2021 - 00:57:03 CDT)
Problem with the Box Amnah Alalmaie (Thu Mar 18 2021 - 15:43:30 CDT)
- Re: Problem with the Box Ashar Malik (Thu Mar 18 2021 - 18:02:35 CDT)
Could not load .nc file in MAC installed VMD Prathit Chatterjee (Wed Mar 17 2021 - 03:03:39 CDT)
- Re: Could not load .nc file in MAC installed VMD Mortimer Hemmit (Wed Mar 17 2021 - 12:45:15 CDT)
  - Re: Could not load .nc file in MAC installed VMD Prathit Chatterjee (Thu Mar 18 2021 - 01:46:47 CDT)
cannot visualize GROMACS trajectories in VMD 1.9.4 on MacOS Big Sur Davide Marchi (Tue Mar 16 2021 - 05:48:35 CDT)
- Re: cannot visualize GROMACS trajectories in VMD 1.9.4 on MacOS Big Sur alberto (Tue Mar 16 2021 - 06:37:37 CDT)
  - Re: cannot visualize GROMACS trajectories in VMD 1.9.4 on MacOS Big Sur Chang, Christopher (Tue Mar 16 2021 - 10:54:00 CDT)
    - Re: cannot visualize GROMACS trajectories in VMD 1.9.4 on MacOS Big Sur John Stone (Tue Mar 16 2021 - 11:48:14 CDT)
    - Re: cannot visualize GROMACS trajectories in VMD 1.9.4 on MacOS Big Sur Davide Marchi (Tue Mar 16 2021 - 13:33:02 CDT)
set non-zero box sizes for GAMESS output marco di gennaro (Tue Mar 16 2021 - 03:06:35 CDT)
- set non-zero box sizes for GAMESS output marco di gennaro (Tue Mar 16 2021 - 04:42:35 CDT)
- Re: set non-zero box sizes for GAMESS output John Stone (Tue Mar 16 2021 - 11:55:50 CDT)
  - Re: set non-zero box sizes for GAMESS output Axel Kohlmeyer (Tue Mar 16 2021 - 13:30:53 CDT)
Problems MacOS Big Sur Sergio Perez (Mon Mar 15 2021 - 02:06:51 CDT)
- Re: Problems MacOS Big Sur John Stone (Wed Mar 17 2021 - 00:30:40 CDT)
  - Re: Problems MacOS Big Sur Sergio Perez (Wed Mar 17 2021 - 02:31:34 CDT)
    - Re: Problems MacOS Big Sur Sergio Perez (Tue Apr 20 2021 - 02:01:26 CDT)
Re: Molefacture and writegmxtop stops with no error fan li (Sun Mar 14 2021 - 13:12:00 CDT)
Trouble launching VMD in Apple M1 Neelanjana Sengupta (Fri Mar 12 2021 - 21:54:49 CST)
- Re: Trouble launching VMD in Apple M1 John Stone (Wed Mar 17 2021 - 00:35:42 CDT)
  - Re: Trouble launching VMD in Apple M1 Neelanjana Sengupta (Fri Mar 19 2021 - 21:51:52 CDT)
TCL script to measure distance between two points in space William Howe (Wed Mar 10 2021 - 17:19:18 CST)
- Re: TCL script to measure distance between two points in space Ashar Malik (Wed Mar 10 2021 - 18:01:10 CST)
Re: Solvating with Pre-equilibration ethanol box Raisa Carmen Andeme Ela (Tue Mar 09 2021 - 15:43:10 CST)
psfgen on console missing dihedral parameters for standard residues Prof. Eddie (Tue Mar 09 2021 - 13:00:06 CST)
fftk wat. opt. when charges overlap Prof. Eddie (Mon Mar 08 2021 - 08:46:07 CST)
- Re: fftk wat. opt. when charges overlap Jason Smith (Mon Mar 08 2021 - 11:04:23 CST)
- Re: fftk wat. opt. when charges overlap Pawel Kedzierski (Tue Mar 09 2021 - 05:51:15 CST)
  - Re: fftk wat. opt. when charges overlap Prof. Eddie (Tue Mar 09 2021 - 08:28:34 CST)
    - Re: fftk wat. opt. when charges overlap Pawel Kedzierski (Tue Mar 09 2021 - 11:19:20 CST)
Surf drawing representation fails after negative circle radius Christian Seitz (Mon Mar 08 2021 - 01:50:03 CST)
- Re: Surf drawing representation fails after negative circle radius John Stone (Mon Mar 08 2021 - 01:58:43 CST)
PBC Shift Center Mcguire, Kelly (Sun Mar 07 2021 - 14:31:30 CST)
Custom particle shapes Johannes Haataja (Sat Mar 06 2021 - 06:27:04 CST)
- Re: Custom particle shapes John Stone (Sat Mar 06 2021 - 12:46:29 CST)
  - Re: Custom particle shapes Johannes Haataja (Sat Mar 06 2021 - 13:58:14 CST)
how to change working directory for viewmaster? Carlos Simmerling (Fri Mar 05 2021 - 09:56:07 CST)
- Re: how to change working directory for viewmaster? John Stone (Fri Mar 05 2021 - 10:12:50 CST)
  - Re: how to change working directory for viewmaster? John Stone (Sat Mar 06 2021 - 12:41:54 CST)
    - Re: how to change working directory for viewmaster? Carlos Simmerling (Sat Mar 06 2021 - 16:35:29 CST)
Problems MacOS Big Sur Sergio Perez (Fri Mar 05 2021 - 02:13:18 CST)
Error defining "clusters" in NetworkView? Smith, Harper E. (Thu Mar 04 2021 - 18:18:26 CST)
VMD Compilation with LEPTON & C++11 to support COLVARS "customFunction" RenÃ© Hafner TUK (Thu Mar 04 2021 - 14:21:27 CST)
- Re: VMD Compilation with LEPTON & C++11 to support COLVARS "customFunction" Giacomo Fiorin (Fri Mar 05 2021 - 11:46:59 CST)
  - Re: VMD Compilation with LEPTON & C++11 to support COLVARS "customFunction" WORKS now --- FLTK issue now RenÃ© Hafner TUK (Sat Mar 06 2021 - 10:14:12 CST)
Redundant entries in force field parameters generated by paratool plugin in VMD Mandayam Bharathi, Harsha (Wed Mar 03 2021 - 12:03:25 CST)
- Re: Redundant entries in force field parameters generated by paratool plugin in VMD John Stone (Wed Mar 03 2021 - 21:30:41 CST)
  - Re: Redundant entries in force field parameters generated by paratool plugin in VMD John Stone (Thu Mar 04 2021 - 09:39:23 CST)
Using writelammpsdata in 1.9.4 Robert Chan-Jobe (Tue Mar 02 2021 - 19:11:58 CST)
- Re: Using writelammpsdata in 1.9.4 Axel Kohlmeyer (Tue Mar 02 2021 - 20:05:55 CST)
  - Re: Using writelammpsdata in 1.9.4 Axel Kohlmeyer (Tue Mar 02 2021 - 20:49:54 CST)
    - Re: Using writelammpsdata in 1.9.4 John Stone (Tue Mar 02 2021 - 20:52:20 CST)
Render image background-free Pacci Evaristo, Felipe Fabricio (Tue Mar 02 2021 - 13:43:02 CST)
- Re: Render image background-free Pawel Kedzierski (Tue Mar 02 2021 - 14:58:22 CST)
- Re: Render image background-free Vermaas, Josh (Tue Mar 02 2021 - 15:17:59 CST)
  - Re: Render image background-free John Stone (Tue Mar 02 2021 - 15:40:11 CST)
    - Re: Render image background-free Pacci Evaristo, Felipe Fabricio (Tue Mar 02 2021 - 15:52:59 CST)
trouble with multiseq Hedlund, Erik (Tue Mar 02 2021 - 10:34:01 CST)
- Re: trouble with multiseq John Stone (Wed Mar 17 2021 - 00:54:12 CDT)
Reduce Waterbox Dimensions Post Simulation Mcguire, Kelly (Mon Mar 01 2021 - 18:13:04 CST)
- Re: Reduce Waterbox Dimensions Post Simulation Aaron Oakley (Mon Mar 01 2021 - 20:07:39 CST)
Custom residue in mutate psfgen Prof. Eddie (Mon Mar 01 2021 - 14:10:15 CST)
- Re: Custom residue in mutate psfgen Michael Robinson (Tue Mar 02 2021 - 05:53:35 CST)
  - Re: Custom residue in mutate psfgen Prof. Eddie (Tue Mar 02 2021 - 07:56:53 CST)
Fwd: Problem with QwikMD analysis Ranabir Majumder (Mon Mar 01 2021 - 13:29:03 CST)
- Re: Fwd: Problem with QwikMD analysis Mariano Spivak (Mon Mar 01 2021 - 15:25:19 CST)
  - Re: Fwd: Problem with QwikMD analysis Ranabir Majumder (Wed Mar 03 2021 - 07:14:13 CST)
(no subject) soumadwip ghosh (Mon Mar 01 2021 - 03:13:50 CST)
New User Cannot Access VMD on Windows Phelan Jr., Frederick R. Dr. (Fed) (Fri Feb 26 2021 - 18:20:29 CST)
- Re: New User Cannot Access VMD on Windows Axel Kohlmeyer (Fri Feb 26 2021 - 18:59:05 CST)
  - RE: New User Cannot Access VMD on Windows Phelan Jr., Frederick R. Dr. (Fed) (Fri Feb 26 2021 - 19:09:01 CST)
Couldn't read internal coordinate table and list index out of range Ruijie Darius Teo (Tue Feb 23 2021 - 13:58:49 CST)
- Re: Couldn't read internal coordinate table and list index out of range Gumbart, JC (Tue Feb 23 2021 - 19:00:32 CST)
  - Re: Couldn't read internal coordinate table and list index out of range Ruijie Darius Teo (Tue Feb 23 2021 - 19:24:42 CST)
    - Re: Couldn't read internal coordinate table and list index out of range Gumbart, JC (Tue Feb 23 2021 - 19:28:33 CST)
    - Re: Couldn't read internal coordinate table and list index out of range Ruijie Darius Teo (Tue Feb 23 2021 - 20:23:57 CST)
Problem in DISPLAY of VMD from remote server in local Mac Machine Prathit Chatterjee (Tue Feb 23 2021 - 07:20:39 CST)
- Re: Problem in DISPLAY of VMD from remote server in local Mac Machine John Stone (Tue Feb 23 2021 - 13:42:35 CST)
question about RDF parinaz bashirbanaem (Fri Feb 19 2021 - 11:19:36 CST)
question about RDF parinaz bashirbanaem (Fri Feb 19 2021 - 10:46:32 CST)
Plotting orbitals from Molden file Chang, Christopher (Tue Feb 16 2021 - 16:53:56 CST)
- Re: Plotting orbitals from Molden file John Stone (Fri Feb 19 2021 - 02:23:43 CST)
  - Re: Plotting orbitals from Molden file Chang, Christopher (Fri Feb 19 2021 - 13:35:02 CST)
Native contacts tcl script crashed Sunita Patel (Tue Feb 16 2021 - 05:01:30 CST)
- Re: Native contacts tcl script crashed Axel Kohlmeyer (Tue Feb 16 2021 - 05:12:14 CST)
  - Re: Native contacts tcl script crashed Sunita Patel (Thu Feb 18 2021 - 00:36:29 CST)
Calculation of residue pair energy values Daniel STERBULEAC (Sun Feb 14 2021 - 16:46:12 CST)
Calculation of residue pair energy values Manas Kohli (Sun Feb 14 2021 - 07:54:51 CST)
- Re: Calculation of residue pair energy values Daniel Fellner (Sun Feb 14 2021 - 19:23:10 CST)
  - Re: Calculation of residue pair energy values Manas Kohli (Mon Feb 15 2021 - 08:51:54 CST)
ffTK torsion scan? Smith, Harper E. (Thu Feb 11 2021 - 18:30:51 CST)
- Re: ffTK torsion scan? Gumbart, JC (Mon Feb 15 2021 - 09:55:07 CST)
  - Re: ffTK torsion scan? Smith, Harper E. (Mon Feb 15 2021 - 15:50:41 CST)
    - Re: ffTK torsion scan? Gumbart, JC (Thu Feb 18 2021 - 18:12:36 CST)
Problem in VMD Big Sur Sherif Arafa (Thu Feb 11 2021 - 14:41:37 CST)
VMD. PSF and lone pairs JosÃ© VillalaÃn (Thu Feb 11 2021 - 08:23:50 CST)
- Re: VMD. PSF and lone pairs David Hardy (Thu Feb 11 2021 - 08:49:53 CST)
Topology for carbon nanotube compatible to Amber Shilpa Gupta (Wed Feb 10 2021 - 02:56:34 CST)
- Re: Topology for carbon nanotube compatible to Amber Raman Preet Singh (Wed Feb 10 2021 - 06:34:27 CST)
- Re: Topology for carbon nanotube compatible to Amber Nathan Kern (Wed Feb 10 2021 - 09:11:50 CST)
No residue of segment error Isuru Herath (Sun Feb 07 2021 - 14:16:26 CST)
Test email Giuseppe Licari (Fri Feb 05 2021 - 12:24:38 CST)
- Re: Test email John Stone (Fri Feb 05 2021 - 12:30:37 CST)
  - Re: Test email Giuseppe Licari (Fri Feb 05 2021 - 12:44:46 CST)
    - Re: Test email John Stone (Fri Feb 05 2021 - 13:37:11 CST)
Test email GIUSEPPE LEONARDO LICARI (Fri Feb 05 2021 - 12:04:17 CST)
Pbc box on, default Henrik Hariman (Wed Feb 03 2021 - 12:42:28 CST)
- Re: Pbc box on, default Axel Kohlmeyer (Wed Feb 03 2021 - 13:07:03 CST)
- Re: Pbc box on, default Dallas Warren (Wed Feb 03 2021 - 16:51:51 CST)
Angles between two groups of atoms Enzo Claudino (Wed Feb 03 2021 - 12:19:00 CST)
fftk and charmmgui vdW parameters Prof. Eddie (Wed Feb 03 2021 - 10:29:56 CST)
- Re: fftk and charmmgui vdW parameters Daniel Fellner (Wed Feb 03 2021 - 17:02:50 CST)
  - Re: fftk and charmmgui vdW parameters Prof. Eddie (Sat Feb 06 2021 - 08:11:04 CST)
Creating PDB files of binding pockets that lists ligands first within the file William Howe (Tue Feb 02 2021 - 18:14:55 CST)
- Re: Creating PDB files of binding pockets that lists ligands first within the file Ashar Malik (Tue Feb 02 2021 - 19:22:51 CST)
how to search for existing topology SHIVAM TIWARI (Sun Jan 31 2021 - 06:22:14 CST)
- Re: how to search for existing topology Gumbart, JC (Mon Feb 01 2021 - 09:57:27 CST)
  - Re: how to search for existing topology Vermaas, Josh (Mon Feb 01 2021 - 10:40:27 CST)
  - Re: how to search for existing topology Nathan Kern (Mon Feb 01 2021 - 11:06:18 CST)
Dealing with lone pairs in fftk Emma Wu (Sat Jan 30 2021 - 20:31:30 CST)
Deselecting the atoms Yuvam Bhateja (Fri Jan 29 2021 - 10:11:33 CST)
- Re: Deselecting the atoms Smith, Harper E. (Fri Jan 29 2021 - 10:18:48 CST)
- Re: Deselecting the atoms Rafael Bernardi (Fri Jan 29 2021 - 11:21:07 CST)
Electrostatic potential values Araz Jakalian (Fri Jan 29 2021 - 08:29:12 CST)
- Re: Electrostatic potential values John Stone (Fri Jan 29 2021 - 14:37:42 CST)
setting coloring and drawing methods Magnus Andersson (Fri Jan 29 2021 - 08:05:24 CST)
- Re: setting coloring and drawing methods Vermaas, Josh (Fri Jan 29 2021 - 09:37:38 CST)
  - Re: setting coloring and drawing methods Peter Freddolino (Fri Jan 29 2021 - 10:29:40 CST)
- Re: setting coloring and drawing methods Magnus Andersson (Fri Jan 29 2021 - 09:20:48 CST)
launching fftk Prof. Eddie (Wed Jan 27 2021 - 16:36:47 CST)
- Re: launching fftk John Stone (Thu Jan 28 2021 - 15:28:35 CST)
PBC wrap with an octahedral water box Benedetta Sampoli Benitez (Wed Jan 27 2021 - 11:44:46 CST)
novel residue creation and parameterization Prof. Eddie (Wed Jan 27 2021 - 08:33:12 CST)
- Re: novel residue creation and parameterization Raman Preet Singh (Wed Jan 27 2021 - 11:28:56 CST)
- Re: novel residue creation and parameterization Smith, Harper E. (Wed Jan 27 2021 - 11:42:22 CST)
- Re: novel residue creation and parameterization Vermaas, Josh (Wed Jan 27 2021 - 12:01:29 CST)
  - Re: novel residue creation and parameterization Prof. Eddie (Wed Jan 27 2021 - 17:46:11 CST)
Compiling VMD with the TNG plugin Dominic Hayward (Mon Jan 25 2021 - 11:46:41 CST)
- Re: Compiling VMD with the TNG plugin Vermaas, Josh (Mon Jan 25 2021 - 13:02:19 CST)
  - Re: Compiling VMD with the TNG plugin Dominic Hayward (Tue Jan 26 2021 - 04:08:29 CST)
    - Re: Compiling VMD with the TNG plugin John Stone (Tue Jan 26 2021 - 08:51:45 CST)
    - Re: Compiling VMD with the TNG plugin Dominic Hayward (Tue Jan 26 2021 - 12:11:11 CST)
Netcdf files mohamed marzouk (Mon Jan 25 2021 - 04:57:34 CST)
- Re: Netcdf files John Stone (Tue Jan 26 2021 - 00:26:00 CST)
Problem with visualizing trajectory produced in Amber Christopher Gaughan (Mon Jan 25 2021 - 02:05:51 CST)
- Re: Problem with visualizing trajectory produced in Amber John Stone (Tue Jan 26 2021 - 00:24:25 CST)
Re: OpenGL window not rendering over ssh but works when connecting from other computers and works fine locally Maria Dimitrova (Thu Jan 21 2021 - 06:32:59 CST)
- Re: OpenGL window not rendering over ssh but works when connecting from other computers and works fine locally Axel Kohlmeyer (Thu Jan 21 2021 - 07:15:46 CST)
- Re: OpenGL window not rendering over ssh but works when connecting from other computers and works fine locally Maria Dimitrova (Fri Jan 22 2021 - 02:21:56 CST)
  - Re: OpenGL window not rendering over ssh but works when connecting from other computers and works fine locally John Stone (Sat Jan 23 2021 - 14:07:28 CST)
    - Re: OpenGL window not rendering over ssh but works when connecting from other computers and works fine locally Maria Dimitrova (Sun Jan 24 2021 - 03:20:17 CST)
OpenGL window not rendering over ssh but works when connecting from other computers and works fine locally Maria Dimitrova (Thu Jan 21 2021 - 05:22:57 CST)
How to keep particular water molecules within the cut off during the simulations Seera Suryanarayana (Wed Jan 20 2021 - 23:15:37 CST)
- Re: How to keep particular water molecules within the cut off during the simulations Jason Smith (Thu Jan 21 2021 - 10:54:12 CST)
Coarse-Graining Protein with Ion Ligands Isuru Herath (Wed Jan 20 2021 - 21:12:31 CST)
- Re: Coarse-Graining Protein with Ion Ligands Raman Preet Singh (Thu Jan 21 2021 - 00:48:57 CST)
Fixing Memory Overflow Issue with LJ Parameter Assignment Timothy Leong (Wed Jan 20 2021 - 12:23:53 CST)
- Re: Fixing Memory Overflow Issue with LJ Parameter Assignment Peter Freddolino (Thu Jan 21 2021 - 00:33:44 CST)
  - Re: Fixing Memory Overflow Issue with LJ Parameter Assignment John Stone (Tue Jan 26 2021 - 01:30:38 CST)
Fwd: Naming Atoms in VMD David Alejandro RincÃ³n Daza (Tue Jan 19 2021 - 16:27:44 CST)
- Re: Fwd: Naming Atoms in VMD Daniel Fellner (Tue Jan 19 2021 - 19:47:08 CST)
- Re: Fwd: Naming Atoms in VMD Pawel Kedzierski (Wed Jan 20 2021 - 08:19:46 CST)
  - Re: Fwd: Naming Atoms in VMD David Alejandro RincÃ³n Daza (Thu Jan 21 2021 - 15:57:41 CST)
    - Re: Fwd: Naming Atoms in VMD Axel Kohlmeyer (Thu Jan 21 2021 - 16:36:16 CST)
    - Re: Fwd: Naming Atoms in VMD David Alejandro RincÃ³n Daza (Thu Jan 21 2021 - 20:22:56 CST)
Flipping vector in orient Raul Araya (Tue Jan 19 2021 - 09:21:39 CST)
Unable to fit dihedral to QM target data in FFTK Akash Banerjee (Mon Jan 18 2021 - 16:31:20 CST)
- Re: Unable to fit dihedral to QM target data in FFTK Akash Banerjee (Thu Jan 28 2021 - 16:28:57 CST)
  - Re: Re: Unable to fit dihedral to QM target data in FFTK Gumbart, JC (Mon Feb 01 2021 - 09:49:35 CST)
Clipping plane Edgar Galicia (Mon Jan 18 2021 - 11:58:43 CST)
- Re: Clipping plane John Stone (Mon Jan 25 2021 - 23:55:19 CST)
Tachyon sometimes suddenly freezes up when rendering epotential images Soumik Ghosh (Sun Jan 17 2021 - 11:00:56 CST)
- Re: Tachyon sometimes suddenly freezes up when rendering epotential images Vermaas, Josh (Mon Jan 18 2021 - 08:41:44 CST)
  - Re: Tachyon sometimes suddenly freezes up when rendering epotential images John Stone (Mon Jan 25 2021 - 23:59:30 CST)
Question about NAMD configuration files Tiglath Moradkhan (Fri Jan 15 2021 - 18:37:04 CST)
- Re: Question about NAMD configuration files Jason Smith (Fri Jan 15 2021 - 22:17:41 CST)
- Re: Question about NAMD configuration files Rafael Bernardi (Sat Jan 16 2021 - 14:29:33 CST)
Packing periodic simulation using Pbc wrap error Rakesh K (Thu Jan 14 2021 - 06:41:38 CST)
- Re: Packing periodic simulation using Pbc wrap error John Stone (Tue Jan 26 2021 - 00:37:41 CST)
  - Re: Packing periodic simulation using Pbc wrap error Anthony Cruz-Balberdy (Tue Jan 26 2021 - 11:25:45 CST)
Moving Graphics Primitives to Front/Back Timothy Leong (Tue Jan 12 2021 - 09:18:16 CST)
- Re: Moving Graphics Primitives to Front/Back John Stone (Tue Jan 26 2021 - 00:14:25 CST)
vector flips Raul Araya (Mon Jan 11 2021 - 15:56:27 CST)
- Re: vector flips John Stone (Tue Jan 26 2021 - 00:18:09 CST)
Update on email sent last week Tiglath Moradkhan (Mon Jan 11 2021 - 12:00:46 CST)
- Re: Update on email sent last week John Stone (Mon Jan 11 2021 - 12:11:34 CST)
- Re: Update on email sent last week SHIVAM TIWARI (Mon Jan 11 2021 - 12:48:22 CST)
NAMD RBCG Tutorial dssp Isuru Herath (Sun Jan 10 2021 - 12:58:16 CST)
Problem when rendering within a tcl loop Arham Amouie (Sun Jan 10 2021 - 04:17:35 CST)
- Re: Problem when rendering within a tcl loop John Stone (Mon Jan 11 2021 - 16:29:09 CST)
  - Re: Problem when rendering within a tcl loop John Stone (Mon Jan 25 2021 - 23:47:58 CST)
Problem with running NAMD configuration file Tiglath Moradkhan (Fri Jan 08 2021 - 18:07:43 CST)
- Re: Problem with running NAMD configuration file Jason Smith (Mon Jan 11 2021 - 12:50:38 CST)
  - Re: Problem with running NAMD configuration file Tiglath Moradkhan (Mon Jan 11 2021 - 13:43:00 CST)
- Re: Problem with running NAMD configuration file John Stone (Mon Jan 11 2021 - 16:22:09 CST)
FFTK Issue: Not able to visualize dihedral scan Akash Banerjee (Fri Jan 08 2021 - 17:41:07 CST)
- Re: FFTK Issue: Not able to visualize dihedral scan Gumbart, JC (Sun Jan 10 2021 - 06:52:25 CST)
  - Re: FFTK Issue: Not able to visualize dihedral scan Akash Banerjee (Sun Jan 10 2021 - 08:43:12 CST)
model with TIP4 water minimization getting crashed every time Faisal, H M Nasrullah (Thu Jan 07 2021 - 21:56:25 CST)
Problem with following NAMD tutorial Tiglath Moradkhan (Thu Jan 07 2021 - 19:17:22 CST)
- Re: Problem with following NAMD tutorial Jason Smith (Thu Jan 07 2021 - 20:19:01 CST)
  - Re: Problem with following NAMD tutorial Tiglath Moradkhan (Thu Jan 07 2021 - 20:50:52 CST)
  - Re: Problem with following NAMD tutorial Peter Freddolino (Thu Jan 07 2021 - 21:09:52 CST)
(no subject) K Jan (Thu Jan 07 2021 - 18:18:59 CST)
FFTK dihedral paramterization Akash Banerjee (Thu Jan 07 2021 - 16:06:23 CST)
- Re: FFTK dihedral paramterization Gumbart, JC (Thu Jan 07 2021 - 17:49:26 CST)
  - Re: FFTK dihedral paramterization Akash Banerjee (Fri Jan 08 2021 - 07:30:11 CST)
Change Font on VMD Main Window -- Linux Rudy Richardson (Thu Jan 07 2021 - 14:42:13 CST)
- Re: Change Font on VMD Main Window -- Linux John Stone (Mon Jan 11 2021 - 16:36:35 CST)
Running equilibration MD simulation Tiglath Moradkhan (Tue Jan 05 2021 - 15:06:41 CST)
- Re: Running equilibration MD simulation Rafael Bernardi (Tue Jan 05 2021 - 22:23:27 CST)
RE: Install VMD from source on Amazon EC2 instance Chris Taylor (Mon Jan 04 2021 - 18:54:26 CST)
- RE: Install VMD from source on Amazon EC2 instance Chris Taylor (Thu Jan 07 2021 - 16:20:21 CST)
  - Re: RE: Install VMD from source on Amazon EC2 instance Axel Kohlmeyer (Thu Jan 07 2021 - 16:48:47 CST)
/usr/local/lib/vmd/vmd_LINUXAMD64: error while loading shared libraries: libOpenGL.so.0: Mi Yang (Mon Jan 04 2021 - 08:40:42 CST)
- Re: /usr/local/lib/vmd/vmd_LINUXAMD64: error while loading shared libraries: libOpenGL.so.0: John Stone (Mon Jan 11 2021 - 16:42:59 CST)
Tk Console dsspcmbi file Isuru Herath (Sat Jan 02 2021 - 15:38:04 CST)
Install VMD with goal of enabling Intel OSPray renderer Chris Taylor (Fri Jan 01 2021 - 03:59:34 CST)
- Re: Install VMD with goal of enabling Intel OSPray renderer Josh Vermaas (Fri Jan 01 2021 - 13:13:55 CST)
Random deletions of molecules Tiglath Moradkhan (Wed Dec 30 2020 - 16:22:15 CST)
- Re: Random deletions of molecules Daniel Fellner (Wed Dec 30 2020 - 19:20:08 CST)
  - Re: Random deletions of molecules John Stone (Thu Dec 31 2020 - 10:49:49 CST)
CHARMM parameters for ADP-ribosylated arginine? Smith, Harper E. (Tue Dec 29 2020 - 16:03:51 CST)
- Re: CHARMM parameters for ADP-ribosylated arginine? Aaron Oakley (Tue Dec 29 2020 - 18:03:21 CST)
  - Re: CHARMM parameters for ADP-ribosylated arginine? Josh Vermaas (Tue Dec 29 2020 - 18:28:59 CST)
- Re: CHARMM parameters for ADP-ribosylated arginine? SHIVAM TIWARI (Wed Dec 30 2020 - 01:15:40 CST)
Error with RESP in ffTK Emma Wu (Sun Dec 27 2020 - 22:00:35 CST)
- Re: Error with RESP in ffTK Gumbart, JC (Mon Dec 28 2020 - 00:20:51 CST)
  - Re: Error with RESP in ffTK Gumbart, JC (Mon Dec 28 2020 - 20:39:05 CST)
    - Re: Error with RESP in ffTK Emma Wu (Wed Dec 30 2020 - 17:52:56 CST)
    - Re: Error with RESP in ffTK Gumbart, JC (Wed Dec 30 2020 - 18:25:03 CST)
Windows VMD 1.9.4a Version Failing Emma Wu (Sun Dec 27 2020 - 19:16:24 CST)
- Re: Windows VMD 1.9.4a Version Failing Daniel Fellner (Mon Dec 28 2020 - 20:05:45 CST)
- Re: Windows VMD 1.9.4a Version Failing John Stone (Thu Dec 31 2020 - 11:08:43 CST)
  - Re: Windows VMD 1.9.4a Version Failing Emma Wu (Thu Jan 07 2021 - 19:43:27 CST)
    - Re: Windows VMD 1.9.4a Version Failing Minh Ho (Fri Jan 15 2021 - 15:21:52 CST)
    - Re: Windows VMD 1.9.4a Version Failing John Stone (Fri Jan 15 2021 - 15:25:35 CST)
VMD NetCDF plugin on POWER9 CPUs (like ORNL Summit) Chris Neale (Sat Dec 26 2020 - 11:49:32 CST)
- Re: VMD NetCDF plugin on POWER9 CPUs (like ORNL Summit) John Stone (Thu Dec 31 2020 - 11:12:14 CST)
  - Re: VMD NetCDF plugin on POWER9 CPUs (like ORNL Summit) Chris Neale (Mon Jan 04 2021 - 19:47:17 CST)
PSF Files Giving Long Bonds Isuru Herath (Fri Dec 25 2020 - 08:23:49 CST)
- Re: PSF Files Giving Long Bonds Peter Freddolino (Fri Dec 25 2020 - 12:05:00 CST)
  - Re: PSF Files Giving Long Bonds Isuru Herath (Fri Dec 25 2020 - 21:21:28 CST)
Fake angles created by AutoPSF Francesco Pietra (Wed Dec 23 2020 - 08:52:35 CST)
- Fwd: Fake angles created by AutoPSF Francesco Pietra (Wed Dec 23 2020 - 08:55:08 CST)
  - Re: Fwd: Fake angles created by AutoPSF Peter Freddolino (Wed Dec 23 2020 - 20:35:40 CST)
Query regarding 'Protein:ligand Standard Binding Free Energies' tutorial Faisal, H M Nasrullah (Tue Dec 22 2020 - 14:39:15 CST)
- Re: namd-l: Query regarding 'Protein:ligand Standard Binding Free Energies' tutorial Gumbart, JC (Tue Dec 22 2020 - 20:43:36 CST)
  - Re: namd-l: Query regarding 'Protein:ligand Standard Binding Free Energies' tutorial Faisal, H M Nasrullah (Tue Dec 22 2020 - 20:52:34 CST)
Molecule is shown with too many bonds Domenico Riolfi Barzotto (Fri Dec 18 2020 - 08:32:48 CST)
- Re: Molecule is shown with too many bonds John Stone (Fri Dec 18 2020 - 10:15:13 CST)
  - Re: Molecule is shown with too many bonds Domenico Riolfi Barzotto (Fri Dec 18 2020 - 11:22:56 CST)
    - Re: Molecule is shown with too many bonds Jason Smith (Fri Dec 18 2020 - 12:37:51 CST)
- Re: Molecule is shown with too many bonds vermaasj (Fri Dec 18 2020 - 10:32:43 CST)
PDB Format McGuire, Kelly (Thu Dec 17 2020 - 18:52:37 CST)
- Re: PDB Format Bennion, Brian (Thu Dec 17 2020 - 22:44:26 CST)
  - Re: Re: PDB Format John Stone (Thu Dec 17 2020 - 22:54:15 CST)
    - Re: Re: PDB Format Raman Preet Singh (Fri Dec 18 2020 - 00:45:47 CST)
- Re: PDB Format Peter Freddolino (Thu Dec 17 2020 - 22:50:15 CST)
Qurry Regarding Vizualization of two data sets Shubham Agarwal (Thu Dec 17 2020 - 04:38:15 CST)
- Re: Qurry Regarding Vizualization of two data sets John Stone (Thu Dec 17 2020 - 09:51:04 CST)
  - Re: Qurry Regarding Vizualization of two data sets Shubham Agarwal (Mon Dec 21 2020 - 09:58:35 CST)
    - Re: Qurry Regarding Vizualization of two data sets Rafael Bernardi (Mon Dec 21 2020 - 12:16:45 CST)
    - Re: Qurry Regarding Vizualization of two data sets John Stone (Thu Dec 31 2020 - 11:53:09 CST)
Dipole Moment Measurement Hamish Swanson (Wed Dec 16 2020 - 08:04:59 CST)
- Re: Dipole Moment Measurement John Stone (Thu Dec 17 2020 - 00:44:32 CST)
  - Re: Dipole Moment Measurement John Stone (Thu Dec 17 2020 - 09:37:00 CST)
VMD and BigSur Alex Peralvarez Marin (Wed Dec 16 2020 - 08:32:01 CST)
- Re: VMD and BigSur John Stone (Thu Dec 17 2020 - 00:38:53 CST)
  - Re: VMD and BigSur Alex Peralvarez Marin (Thu Dec 17 2020 - 00:46:10 CST)
1.9.4a50 - unable to open DCDs win64 Jason Smith (Wed Dec 16 2020 - 19:35:18 CST)
- Re: 1.9.4a50 - unable to open DCDs win64 John Stone (Wed Dec 16 2020 - 20:32:27 CST)
- Re: 1.9.4a50 - unable to open DCDs win64 John Stone (Thu Dec 17 2020 - 09:43:05 CST)
  - Re: 1.9.4a50 - unable to open DCDs win64 Jason Smith (Thu Dec 17 2020 - 21:11:57 CST)
- Re: 1.9.4a50 - unable to open DCDs win64 John Stone (Thu Dec 17 2020 - 22:49:39 CST)
Identifying salt bridges between chains Tiglath Moradkhan (Wed Dec 16 2020 - 14:32:10 CST)
- Re: Identifying salt bridges between chains John Stone (Fri Dec 18 2020 - 11:12:19 CST)
Qurry Regarding Vizualization og two data sets Shubham Agarwal (Tue Dec 15 2020 - 09:05:05 CST)
VMD 1.9.4a50 64-bit Windows test build posted John Stone (Mon Dec 14 2020 - 23:46:50 CST)
- Re: VMD 1.9.4a50 64-bit Windows test build posted Stefan Boresch (Tue Dec 15 2020 - 04:11:28 CST)
  - Re: VMD 1.9.4a50 64-bit Windows test build posted John Stone (Tue Dec 15 2020 - 09:17:09 CST)
VMD aborts when setting up MD simulation Tiglath Moradkhan (Mon Dec 14 2020 - 12:36:01 CST)
- Re: VMD aborts when setting up MD simulation John Stone (Fri Dec 18 2020 - 10:40:07 CST)
VMD 1.9.4a50 test versions for MacOS Big Sur -- both x86 and ARM64 (M1) John Stone (Mon Dec 14 2020 - 01:55:40 CST)
- Re: VMD 1.9.4a50 test versions for MacOS Big Sur -- both x86 and ARM64 (M1) Pacci Evaristo, Felipe Fabricio (Mon Dec 14 2020 - 09:37:03 CST)
  - Re: VMD 1.9.4a50 test versions for MacOS Big Sur -- both x86 and ARM64 (M1) John Stone (Mon Dec 14 2020 - 09:56:07 CST)
    - Re: VMD 1.9.4a50 test versions for MacOS Big Sur -- both x86 and ARM64 (M1) Pacci Evaristo, Felipe Fabricio (Mon Dec 14 2020 - 11:27:17 CST)
  - Re: VMD 1.9.4a50 test versions for MacOS Big Sur -- both x86 and ARM64 (M1) John Stone (Thu Dec 31 2020 - 12:00:07 CST)
SBCG of molecules Raman Preet Singh (Sat Dec 12 2020 - 12:29:43 CST)
- Re: SBCG of molecules John Stone (Fri Dec 18 2020 - 10:43:13 CST)
  - Re: SBCG of molecules Peter Freddolino (Fri Dec 18 2020 - 11:36:08 CST)
    - Re: SBCG of molecules Raman Preet Singh (Fri Dec 18 2020 - 11:50:00 CST)
ProDy issue with QMonly.psf/dcd from QMMM NAMD-ORCA simulations Francesco Pietra (Sat Dec 12 2020 - 10:39:41 CST)
- Re: ProDy issue with QMonly.psf/dcd from QMMM NAMD-ORCA simulations John Stone (Sat Dec 12 2020 - 11:52:57 CST)
FW: Seeking assistance Onur Alptürk (Sat Dec 12 2020 - 08:01:31 CST)
- Re: FW: Seeking assistance Pawel Kedzierski (Sat Dec 12 2020 - 11:27:04 CST)
  - Re: FW: Seeking assistance Pawel Kedzierski (Sat Dec 12 2020 - 12:34:37 CST)
- Re: FW: Seeking assistance John Stone (Sat Dec 12 2020 - 11:44:47 CST)
Incorrect visualization of system after catdcd Kandarp Sojitra (Sat Dec 12 2020 - 06:36:45 CST)
- Re: Incorrect visualization of system after catdcd Peter Freddolino (Sat Dec 12 2020 - 20:03:27 CST)
VMD junt won't work on Windows Gustavo Scheiffer (Sat Dec 12 2020 - 01:01:30 CST)
- Re: VMD junt won't work on Windows John Stone (Tue Dec 15 2020 - 00:46:32 CST)
  - Re: VMD junt won't work on Windows Gustavo Scheiffer (Tue Dec 15 2020 - 13:03:45 CST)
Manipulating volumes in VMD Bassam Haddad (Thu Dec 10 2020 - 16:18:23 CST)
- Re: Manipulating volumes in VMD John Stone (Fri Dec 18 2020 - 10:50:56 CST)
  - Re: Manipulating volumes in VMD Bassam Haddad (Fri Dec 18 2020 - 13:21:00 CST)
Problem with rendering modified bond label position with Tachyon Antonija TomiÄ‡ (Thu Dec 10 2020 - 12:38:20 CST)
- Re: Problem with rendering modified bond label position with Tachyon John Stone (Thu Dec 31 2020 - 13:01:59 CST)
(no subject) Ashma Khan (Thu Dec 10 2020 - 10:16:13 CST)
- Re: John Stone (Thu Dec 31 2020 - 12:58:56 CST)
confusing about the residue number Ashma Khan (Wed Dec 09 2020 - 22:43:18 CST)
- Re: confusing about the residue number Roshan Shrestha (Wed Dec 09 2020 - 23:18:50 CST)
  - Re: confusing about the residue number Ashma Khan (Wed Dec 09 2020 - 23:24:36 CST)
    - Re: confusing about the residue number vermaasj (Thu Dec 10 2020 - 09:47:00 CST)
    - Re: confusing about the residue number Ashma Khan (Thu Dec 10 2020 - 10:07:56 CST)
Problem resolved Tiglath Moradkhan (Wed Dec 09 2020 - 15:33:42 CST)
- Re: Problem resolved John Stone (Wed Dec 09 2020 - 16:37:25 CST)
My Protein is a homology model Tiglath Moradkhan (Wed Dec 09 2020 - 13:32:18 CST)
- Re: My Protein is a homology model John Stone (Wed Dec 09 2020 - 13:55:59 CST)
VMD version Tiglath Moradkhan (Wed Dec 09 2020 - 12:25:44 CST)
- Re: VMD version John Stone (Wed Dec 09 2020 - 13:13:58 CST)
Ongoing problem with QwickMD plugin Tiglath Moradkhan (Wed Dec 09 2020 - 12:09:04 CST)
- Re: Ongoing problem with QwickMD plugin John Stone (Wed Dec 09 2020 - 12:14:54 CST)
Movie Making Troubles Demy Hernandez (Tue Dec 08 2020 - 18:48:07 CST)
- Re: Movie Making Troubles Josh Vermaas (Tue Dec 08 2020 - 20:00:30 CST)
  - Re: Movie Making Troubles Josh Vermaas (Wed Dec 09 2020 - 10:54:39 CST)
  - Re: Movie Making Troubles Geist, Norman (Wed Dec 09 2020 - 02:45:35 CST)
    - Re: Movie Making Troubles John Stone (Thu Dec 10 2020 - 11:47:29 CST)
Problems with QwickMD plugin Tiglath Moradkhan (Tue Dec 08 2020 - 16:23:48 CST)
- Re: Problems with QwickMD plugin Rafael Bernardi (Tue Dec 08 2020 - 23:05:56 CST)
RMSF Trajectory extraction script Mi Yang (Tue Dec 08 2020 - 05:39:33 CST)
- Re: RMSF Trajectory extraction script John Stone (Thu Dec 31 2020 - 12:59:52 CST)
  - Re: RMSF Trajectory extraction script Mustafa Tekpinar (Thu Dec 31 2020 - 15:43:35 CST)
How to measure several angles? David Alejandro RincÃ³n Daza (Mon Dec 07 2020 - 15:55:19 CST)
- Re: How to measure several angles? Patrick Charchar (Mon Dec 07 2020 - 19:48:48 CST)
  - Re: How to measure several angles? David Alejandro RincÃ³n Daza (Tue Dec 22 2020 - 11:00:39 CST)
VMD for macOS Big Sur Pacci Evaristo, Felipe Fabricio (Sun Dec 06 2020 - 16:35:36 CST)
- Re: VMD for macOS Big Sur John Stone (Mon Dec 07 2020 - 12:01:06 CST)
  - Re: VMD for macOS Big Sur Pacci Evaristo, Felipe Fabricio (Mon Dec 07 2020 - 12:10:17 CST)
  - Re: VMD for macOS Big Sur John Stone (Thu Dec 10 2020 - 14:40:29 CST)
(no subject) Arthur Pereira da Fonseca (Sat Dec 05 2020 - 15:31:30 CST)
- Re: Axel Kohlmeyer (Sat Dec 05 2020 - 17:08:10 CST)
Re: [EXTERNAL]Re: h-bond plugin with QMMM Rafael Bernardi (Thu Dec 03 2020 - 10:44:37 CST)
- Re: [EXTERNAL]Re: h-bond plugin with QMMM Francesco Pietra (Thu Dec 03 2020 - 13:44:20 CST)
  - Re: [EXTERNAL]Re: h-bond plugin with QMMM Marcelo C. R. Melo (Thu Dec 03 2020 - 15:52:18 CST)
Dipole Moment calculation Shounak Mukherjee (Wed Dec 02 2020 - 04:16:34 CST)
- Re: Dipole Moment calculation John Stone (Thu Dec 03 2020 - 01:25:14 CST)
  - Re: Dipole Moment calculation Shounak Mukherjee (Tue Dec 08 2020 - 13:13:29 CST)
h-bond plugin with QMMM Francesco Pietra (Wed Dec 02 2020 - 03:56:05 CST)
- Re: h-bond plugin with QMMM Rafael Bernardi (Wed Dec 02 2020 - 12:48:28 CST)
Error tachyon rendering Mac Catalina fabio trovato (Sat Nov 28 2020 - 19:22:27 CST)
- Re: Error tachyon rendering Mac Catalina John Stone (Wed Dec 02 2020 - 01:03:32 CST)
VMD crash due to large volume of .dcd file Mi Yang (Sat Nov 28 2020 - 13:49:16 CST)
- Re: VMD crash due to large volume of .dcd file Emma Wu (Sat Nov 28 2020 - 16:53:30 CST)
  - Re: VMD crash due to large volume of .dcd file Aravinda Munasinghe (Sun Nov 29 2020 - 08:56:43 CST)
Readpsf Error Isuru Herath (Sat Nov 28 2020 - 13:01:55 CST)
- Re: Readpsf Error Peter Freddolino (Sat Nov 28 2020 - 18:03:01 CST)
  - Re: Readpsf Error Isuru Herath (Sun Nov 29 2020 - 08:56:47 CST)
- Re: Readpsf Error Aravinda Munasinghe (Sun Nov 29 2020 - 08:48:32 CST)
  - Re: Readpsf Error Isuru Herath (Sun Nov 29 2020 - 09:03:17 CST)
    - Re: Readpsf Error Aravinda Munasinghe (Sun Nov 29 2020 - 09:11:45 CST)
    - Re: Readpsf Error Aravinda Munasinghe (Sun Nov 29 2020 - 09:20:28 CST)
Gaussian aborting during ffTK - Calc.Bonded Jason Smith (Wed Nov 25 2020 - 23:18:10 CST)
Packing periodic simulation using Pbc wrap error Rakesh K (Tue Nov 24 2020 - 12:22:26 CST)
Possible memory leak in vmd 1.9.4a38 or FFTK on Linux Pawel Kedzierski (Tue Nov 24 2020 - 07:35:35 CST)
- Re: Possible memory leak in vmd 1.9.4a38 or FFTK on Linux John Stone (Tue Nov 24 2020 - 08:40:22 CST)
Number of water molecules as a function of residue Akash Pandya (Tue Nov 24 2020 - 04:07:02 CST)
Glycoprotein simulation answer Daniel STERBULEAC (Fri Nov 20 2020 - 23:51:08 CST)
- Re: Glycoprotein simulation answer Raman Preet Singh (Sat Nov 21 2020 - 01:09:10 CST)
Outdated Tutorial Files? Eashan C (Fri Nov 20 2020 - 23:17:00 CST)
- Re: Outdated Tutorial Files? Peter Freddolino (Mon Nov 23 2020 - 08:50:56 CST)
Glycoprotein simulation Manas Kohli (Fri Nov 20 2020 - 14:25:18 CST)
- Re: Glycoprotein simulation Pratik Narain Srivastava (Sun Nov 22 2020 - 02:04:59 CST)
- Re: Glycoprotein simulation Krishna Vkm (Sun Nov 22 2020 - 05:55:05 CST)
  - Re: Glycoprotein simulation Manas Kohli (Sun Nov 22 2020 - 09:12:01 CST)
Ambient occlusion / Electrostatic surfaces Lothar Esser (Fri Nov 20 2020 - 12:30:57 CST)
- Re: Ambient occlusion / Electrostatic surfaces John Stone (Fri Nov 20 2020 - 12:58:14 CST)
  - Re: Ambient occlusion / Electrostatic surfaces John Stone (Fri Nov 20 2020 - 14:19:24 CST)
  - Re: Ambient occlusion / Electrostatic surfaces John Stone (Thu Dec 31 2020 - 13:44:41 CST)
AVX512 support on Linux. Zhu Liang (Thu Nov 19 2020 - 10:33:42 CST)
- Re: AVX512 support on Linux. John Stone (Thu Nov 19 2020 - 11:04:31 CST)
- Re: AVX512 support on Linux. Josh Vermaas (Thu Nov 19 2020 - 11:15:29 CST)
Trajectory analysis without loading all frames Raman Preet Singh (Thu Nov 19 2020 - 08:35:23 CST)
- Re: Trajectory analysis without loading all frames Smith, Harper E. (Thu Nov 19 2020 - 09:02:54 CST)
  - Re: Re: Trajectory analysis without loading all frames Peter Freddolino (Thu Nov 19 2020 - 15:14:08 CST)
- Re: Trajectory analysis without loading all frames Ashar Malik (Thu Nov 19 2020 - 09:29:43 CST)
  - Re: Trajectory analysis without loading all frames Pratik Narain Srivastava (Sun Nov 22 2020 - 02:07:30 CST)
charge opt not converged Lokendra Poudel (Wed Nov 18 2020 - 10:12:40 CST)
- Re: charge opt not converged Gumbart, JC (Wed Nov 18 2020 - 14:35:01 CST)
VMD running on Mac OS Big Sur Atreyo Pal (Tue Nov 17 2020 - 20:28:30 CST)
- Re: VMD running on Mac OS Big Sur John Stone (Wed Nov 18 2020 - 00:27:17 CST)
  - Re: VMD running on Mac OS Big Sur Mortimer Hemmit (Wed Nov 18 2020 - 08:10:13 CST)
extended system file not found Eashan C (Tue Nov 17 2020 - 18:36:59 CST)
- RE: extended system file not found Pang, Yui Tik (Tue Nov 17 2020 - 20:36:02 CST)
  - Re: extended system file not found Eashan C (Tue Nov 17 2020 - 20:41:14 CST)
Startup problem on Windows Stefan Boresch (Tue Nov 17 2020 - 03:39:20 CST)
- Re: Startup problem on Windows Chang, Christopher (Tue Nov 17 2020 - 10:18:07 CST)
- Re: Startup problem on Windows John Stone (Tue Nov 17 2020 - 11:00:06 CST)
  - Re: Startup problem on Windows Stefan Boresch (Tue Nov 17 2020 - 14:57:25 CST)
- Re: Startup problem on Windows John Stone (Wed Nov 18 2020 - 00:35:12 CST)
  - Re: Startup problem on Windows Stefan Boresch (Fri Nov 20 2020 - 02:17:52 CST)
Error "vecscale: parameters must have data" in water interaction step of FFTK Alexandre Suman de AraÃºjo (Mon Nov 16 2020 - 08:49:36 CST)
- Re: Error "vecscale: parameters must have data" in water interaction step of FFTK Pang, Yui Tik (Wed Nov 18 2020 - 15:15:10 CST)
  - Re: Error "vecscale: parameters must have data" in water interaction step of FFTK Alexandre Suman de AraÃºjo (Wed Nov 18 2020 - 15:44:56 CST)
    - Re: Error "vecscale: parameters must have data" in water interaction step of FFTK Mariano Spivak (Mon Nov 23 2020 - 17:24:53 CST)
Saving updated trajectory coordinates of selected atoms SHRAVANI NETHI . (Mon Nov 16 2020 - 07:07:46 CST)
- Re: Saving updated trajectory coordinates of selected atoms Axel Kohlmeyer (Mon Nov 16 2020 - 07:42:46 CST)
  - Re: Saving updated trajectory coordinates of selected atoms SHRAVANI NETHI . (Mon Nov 16 2020 - 08:04:04 CST)
    - Re: Saving updated trajectory coordinates of selected atoms Axel Kohlmeyer (Mon Nov 16 2020 - 09:02:07 CST)
Sorting as an increasing function of the integers in suffices Prathit Chatterjee (Mon Nov 16 2020 - 05:31:29 CST)
- Re: Sorting as an increasing function of the integers in suffices Axel Kohlmeyer (Mon Nov 16 2020 - 07:47:14 CST)
  - Re: Sorting as an increasing function of the integers in suffices John Stone (Mon Nov 16 2020 - 13:18:19 CST)
    - Re: Sorting as an increasing function of the integers in suffices Prathit Chatterjee (Mon Nov 16 2020 - 14:23:42 CST)
(no subject) Eashan C (Mon Nov 16 2020 - 00:32:30 CST)
- Re: Abhishek TYAGI (Mon Nov 16 2020 - 01:05:52 CST)
Translation Script Demy Hernandez (Tue Nov 10 2020 - 10:55:28 CST)
- Re: Translation Script Peter Freddolino (Wed Nov 11 2020 - 11:17:19 CST)
  - Re: Translation Script Peter Freddolino (Wed Nov 11 2020 - 19:09:58 CST)
cionize plugin VMD Atreyo Pal (Mon Nov 09 2020 - 11:33:51 CST)
- Re: cionize plugin VMD Peter Freddolino (Mon Nov 09 2020 - 14:34:37 CST)
Windows Server 2019 support issue of VMD and NAMD Gawtak Kim (Sun Nov 08 2020 - 20:44:53 CST)
- Re: Windows Server 2019 support issue of VMD and NAMD John Stone (Sun Nov 08 2020 - 21:24:44 CST)
  - Re: Windows Server 2019 support issue of VMD and NAMD Gawtak Kim (Mon Nov 09 2020 - 17:27:41 CST)
Discrepancy in interaction energy of amber coordinate trajectories of a system Prathit Chatterjee (Sat Nov 07 2020 - 07:22:40 CST)
- Re: Discrepancy in interaction energy of amber coordinate trajectories of a system Peter Freddolino (Sat Nov 07 2020 - 19:35:23 CST)
  - Re: Discrepancy in interaction energy of amber coordinate trajectories of a system Prathit Chatterjee (Sun Nov 08 2020 - 21:50:23 CST)
VMD clustering of conformations Jeff Saxon (Sat Nov 07 2020 - 04:57:59 CST)
- Re: VMD clustering of conformations Roshan Shrestha (Sat Nov 07 2020 - 05:37:31 CST)
  - Re: VMD clustering of conformations Jeff Saxon (Sat Nov 07 2020 - 07:18:23 CST)
Error in charge optimization Nibedita Ray Chaudhuri (Fri Nov 06 2020 - 05:22:09 CST)
- Re: Error in charge optimization Gumbart, JC (Wed Nov 11 2020 - 23:48:15 CST)
  - Re: Error in charge optimization Gumbart, JC (Thu Nov 12 2020 - 15:46:45 CST)
Re: Potential bugs in ffTK dihedral optimization Mariano Spivak (Thu Nov 05 2020 - 14:53:51 CST)
- Re: Potential bugs in ffTK dihedral optimization Hao Wu (Thu Nov 05 2020 - 14:56:21 CST)
  - Re: Potential bugs in ffTK dihedral optimization John Stone (Thu Nov 05 2020 - 15:02:19 CST)
    - Re: Potential bugs in ffTK dihedral optimization Hao Wu (Tue Nov 24 2020 - 11:17:18 CST)
Analysis of DLG filles Jeff Saxon (Thu Nov 05 2020 - 10:45:19 CST)
- Re: Analysis of DLG filles John Stone (Thu Nov 05 2020 - 10:49:39 CST)
- Re: Analysis of DLG filles Paolo Conflitti (Fri Nov 06 2020 - 03:00:43 CST)
  - Re: Analysis of DLG filles Jeff Saxon (Fri Nov 06 2020 - 06:27:51 CST)
    - Re: Analysis of DLG filles Paolo Conflitti (Fri Nov 06 2020 - 07:26:01 CST)
    - Re: Analysis of DLG filles Jeff Saxon (Fri Nov 06 2020 - 07:40:58 CST)
Visualizing forces from .forcedcd files? Smith, Harper E. (Wed Nov 04 2020 - 12:52:17 CST)
Restraining selected atoms with multimer Francesco Pietra (Wed Nov 04 2020 - 04:36:11 CST)
- Fwd: Restraining selected atoms with multimer Francesco Pietra (Wed Nov 04 2020 - 04:46:42 CST)
- Re: Restraining selected atoms with multimer Michael Robinson (Mon Nov 16 2020 - 21:29:22 CST)
Re: VMD 1.9.4 a48 fails to build from source yjcoshc (Wed Nov 04 2020 - 03:22:28 CST)
Pulling vector direction in SMD miyatake_at_riken.jp (Wed Nov 04 2020 - 02:57:00 CST)
Pulling vector direction in SMD miyatake_at_riken.jp (Wed Nov 04 2020 - 02:51:09 CST)
VMD 1.9.4 a48 fails to build from source yjcoshc (Tue Nov 03 2020 - 19:22:56 CST)
Autopsf Failed on end of segment Francesco Pietra (Tue Nov 03 2020 - 06:55:01 CST)
- Re: Autopsf Failed on end of segment Peter Freddolino (Tue Nov 03 2020 - 11:07:14 CST)
  - Re: Autopsf Failed on end of segment Francesco Pietra (Tue Nov 03 2020 - 12:52:28 CST)
  - Pulling vector direction in SMD miyatake_at_riken.jp (Tue Nov 03 2020 - 19:17:30 CST)
    - Re: Pulling vector direction in SMD Peter Freddolino (Wed Nov 04 2020 - 08:05:49 CST)
Re: Molefacture 2.0 - missing functionality? Pawel Kedzierski (Fri Oct 30 2020 - 14:54:21 CDT)
- Re: Molefacture 2.0 - missing functionality? John Stone (Sun Nov 01 2020 - 01:43:46 CST)
- Re: Molefacture 2.0 - missing functionality? John Stone (Tue Jan 12 2021 - 00:46:06 CST)
Molefacture 2.0 - missing functionality? Pawel Kedzierski (Fri Oct 30 2020 - 07:17:00 CDT)
PSFGEN vs AUTOPSF White, Mark (Thu Oct 29 2020 - 18:10:37 CDT)
- Re: PSFGEN vs AUTOPSF Peter Freddolino (Fri Oct 30 2020 - 08:00:10 CDT)
Unknown atom type while running psfgen Arusha Acharyya (Mon Oct 26 2020 - 20:37:20 CDT)
Ospray vs Optix McGuire, Kelly (Fri Oct 23 2020 - 03:27:11 CDT)
- Re: Ospray vs Optix John Stone (Fri Oct 30 2020 - 18:49:32 CDT)
PBC Wrapping McGuire, Kelly (Thu Oct 22 2020 - 16:06:22 CDT)
- Re: PBC Wrapping RenÃ© Hafner TUK (Fri Oct 23 2020 - 03:25:46 CDT)
  - Re: PBC Wrapping McGuire, Kelly (Fri Oct 23 2020 - 03:33:17 CDT)
Calculating mean square displacement and removing PBC RonitS Chem (Thu Oct 22 2020 - 13:09:34 CDT)
- Re: Calculating mean square displacement and removing PBC Axel Kohlmeyer (Thu Oct 22 2020 - 13:47:24 CDT)
  - Re: Calculating mean square displacement and removing PBC RonitS Chem (Thu Oct 22 2020 - 14:16:06 CDT)
Failing to load AMBER parameter files in VMD Prathit Chatterjee (Thu Oct 22 2020 - 06:11:34 CDT)
"atomsel: set: bad data in 0th element" ffTK Emma Wu (Thu Oct 22 2020 - 00:25:01 CDT)
- Re: "atomsel: set: bad data in 0th element" ffTK Pang, Yui Tik (Thu Nov 12 2020 - 00:07:15 CST)
  - Re: Re: "atomsel: set: bad data in 0th element" ffTK Emma Wu (Thu Nov 12 2020 - 18:42:29 CST)
VMD Align command Daniel STERBULEAC (Mon Oct 19 2020 - 15:33:46 CDT)
- Re: VMD Align command Bassam Haddad (Mon Oct 19 2020 - 17:07:54 CDT)
  - Re: VMD Align command Daniel STERBULEAC (Mon Oct 19 2020 - 17:42:41 CDT)
Colors in VMd graphics Remya Ann (Sat Oct 17 2020 - 13:46:52 CDT)
- Re: Colors in VMd graphics Ashar Malik (Sat Oct 17 2020 - 22:22:49 CDT)
  - Re: Colors in VMd graphics Remya Ann (Sun Oct 18 2020 - 02:36:33 CDT)
  - Re: Colors in VMd graphics Remya Ann (Sun Oct 18 2020 - 05:37:25 CDT)
    - Re: Colors in VMd graphics John Stone (Mon Oct 19 2020 - 14:38:45 CDT)
Combining fragments for parameterization Emma Wu (Thu Oct 15 2020 - 00:50:30 CDT)
- Re: Combining fragments for parameterization Daniel Fellner (Thu Oct 15 2020 - 01:05:34 CDT)
  - Re: Combining fragments for parameterization Emma Wu (Fri Oct 30 2020 - 23:47:35 CDT)
    - Re: Combining fragments for parameterization Daniel Fellner (Sat Oct 31 2020 - 03:15:46 CDT)
Error in PSFGEN Bassam Haddad (Wed Oct 14 2020 - 18:15:45 CDT)
- Re: Error in PSFGEN Josh Vermaas (Wed Oct 14 2020 - 19:58:08 CDT)
  - Re: Error in PSFGEN Bassam Haddad (Wed Oct 14 2020 - 20:22:12 CDT)
    - Re: Error in PSFGEN Bassam Haddad (Mon Oct 19 2020 - 12:38:16 CDT)
    - Re: Error in PSFGEN Gianfranco Abrusci (Mon Oct 19 2020 - 15:36:50 CDT)
  - Re: Error in PSFGEN Gianfranco Abrusci (Mon Oct 19 2020 - 15:43:46 CDT)
    - Re: Error in PSFGEN Bassam Haddad (Mon Oct 19 2020 - 15:45:28 CDT)
Unable to open TkConsole, Possible bug! Adupa Vasista (Wed Oct 14 2020 - 01:51:21 CDT)
- Re: Unable to open TkConsole, Possible bug! John Stone (Wed Oct 14 2020 - 08:56:53 CDT)
  - Re: Unable to open TkConsole, Possible bug! Adupa Vasista (Wed Oct 14 2020 - 09:27:24 CDT)
charge optimization Lokendra Poudel (Tue Oct 13 2020 - 17:55:20 CDT)
- Re: charge optimization JC Gumbart (Sun Oct 18 2020 - 18:37:03 CDT)
error in reading Gaussian log file Lokendra Poudel (Tue Oct 13 2020 - 14:15:39 CDT)
- Re: error in reading Gaussian log file John Stone (Tue Oct 13 2020 - 14:25:04 CDT)
  - Re: error in reading Gaussian log file Lokendra Poudel (Tue Oct 13 2020 - 15:04:44 CDT)
videostream command? Josh Vermaas (Sat Oct 10 2020 - 17:58:41 CDT)
- Re: videostream command? John Stone (Sat Oct 10 2020 - 18:19:23 CDT)
Error in building a psf file for nanoparticle Yuvam Bhateja (Sat Oct 10 2020 - 03:04:41 CDT)
- Re: Error in building a psf file for nanoparticle Peter Freddolino (Tue Oct 13 2020 - 18:40:42 CDT)
Formation of a nanoparticle-ligand complex Yuvam Bhateja (Fri Oct 09 2020 - 14:10:08 CDT)
Set molecule ID by topo tools fan li (Fri Oct 09 2020 - 11:26:04 CDT)
- Re: Set molecule ID by topo tools John Stone (Wed Oct 21 2020 - 13:44:04 CDT)
VMD images/movies of SARS-CoV-2 work in NYT... John Stone (Fri Oct 09 2020 - 11:07:32 CDT)
Bond/angle optimization using FFTK Minh Ho (Thu Oct 08 2020 - 16:39:46 CDT)
covalent atomic radii customization fulvio ciriaco (Thu Oct 08 2020 - 14:18:30 CDT)
- Re: covalent atomic radii customization John Stone (Wed Oct 21 2020 - 13:42:10 CDT)
QwikMD premature exit John Keller (Wed Oct 07 2020 - 16:30:11 CDT)
- Re: QwikMD premature exit John Keller (Wed Oct 07 2020 - 18:49:51 CDT)
  - Re: QwikMD premature exit John Stone (Thu Dec 31 2020 - 14:25:47 CST)
Glu-Lys Isopeptide Bond Parameters? Smith, Harper E. (Wed Oct 07 2020 - 13:44:43 CDT)
- Re: Glu-Lys Isopeptide Bond Parameters? Josh Vermaas (Wed Oct 07 2020 - 14:48:53 CDT)
  - Re: Glu-Lys Isopeptide Bond Parameters? Smith, Harper E. (Wed Oct 07 2020 - 15:28:52 CDT)
FFTK: Water Interactions, Steric Clashes Emma Wu (Tue Oct 06 2020 - 22:13:31 CDT)
- Re: FFTK: Water Interactions, Steric Clashes Daniel Fellner (Tue Oct 06 2020 - 22:51:15 CDT)
  - Re: FFTK: Water Interactions, Steric Clashes Emma Wu (Wed Oct 07 2020 - 23:20:54 CDT)
shifting of ions from +z to -z in a single frame(1ps) Basanta Acharya (Tue Oct 06 2020 - 21:39:01 CDT)
- Re: shifting of ions from +z to -z in a single frame(1ps) Axel Kohlmeyer (Tue Oct 06 2020 - 22:13:37 CDT)
Silver nanoparticle with coating of protein. Yuvam Bhateja (Tue Oct 06 2020 - 11:17:26 CDT)
- Re: Silver nanoparticle with coating of protein. Raman Preet Singh (Tue Oct 06 2020 - 12:57:28 CDT)
placing graphics objects at fixed locations on the display Goedde, Chris (Mon Oct 05 2020 - 14:39:02 CDT)
- Re: placing graphics objects at fixed locations on the display John Stone (Tue Oct 06 2020 - 10:46:04 CDT)
  - Re: [EXT] placing graphics objects at fixed locations on the display Goedde, Chris (Tue Oct 06 2020 - 15:32:23 CDT)
Vmd uninstallation and reinstallation achchirangeebi (Sat Oct 03 2020 - 05:23:49 CDT)
- Re: Vmd uninstallation and reinstallation John Stone (Tue Oct 06 2020 - 10:39:57 CDT)
  - Re: Vmd uninstallation and reinstallation Basanta Acharya (Tue Oct 06 2020 - 21:43:56 CDT)
Errors at Charge Opt. (Charge-2 step from FFTK Screencast) Minh Ho (Fri Oct 02 2020 - 18:29:40 CDT)
- Re: Errors at Charge Opt. (Charge-2 step from FFTK Screencast) Daniel Fellner (Fri Oct 02 2020 - 18:39:32 CDT)
  - Re: Errors at Charge Opt. (Charge-2 step from FFTK Screencast) Minh Ho (Fri Oct 02 2020 - 18:44:37 CDT)
How select atoms from mol 0 within "x" of mol 1? Asghar Razavi (Thu Oct 01 2020 - 12:20:19 CDT)
- Re: How select atoms from mol 0 within "x" of mol 1? Josh Vermaas (Thu Oct 01 2020 - 19:01:07 CDT)
  - Re: How select atoms from mol 0 within "x" of mol 1? John Stone (Tue Oct 06 2020 - 10:55:54 CDT)
TCL force script Basanta Acharya (Thu Oct 01 2020 - 02:29:01 CDT)
- Re: TCL force script Adupa Vasista (Thu Oct 01 2020 - 02:57:45 CDT)
- Re: TCL force script Karteek K. Bejagam (Thu Oct 01 2020 - 03:02:18 CDT)
TCL script for creating multiple representations on the same molecule William Howe (Wed Sep 30 2020 - 19:17:54 CDT)
- Re: TCL script for creating multiple representations on the same molecule Peter Freddolino (Wed Sep 30 2020 - 21:22:36 CDT)
  - Re: TCL script for creating multiple representations on the same molecule John Stone (Tue Oct 06 2020 - 11:12:27 CDT)
Converting electron density data from .map to .dx in vmd Faisal, H M Nasrullah (Wed Sep 30 2020 - 11:16:29 CDT)
- Re: Converting electron density data from .map to .dx in vmd JC Gumbart (Wed Sep 30 2020 - 13:35:30 CDT)
- Re: Converting electron density data from .map to .dx in vmd John Stone (Tue Oct 06 2020 - 20:57:44 CDT)
  - Re: Converting electron density data from .map to .dx in vmd Faisal, H M Nasrullah (Tue Oct 06 2020 - 22:07:28 CDT)
    - Re: Converting electron density data from .map to .dx in vmd John Stone (Tue Oct 06 2020 - 23:52:59 CDT)
    - Re: Converting electron density data from .map to .dx in vmd Faisal, H M Nasrullah (Wed Oct 07 2020 - 09:48:20 CDT)
high quality videos omid gh (Wed Sep 30 2020 - 11:03:01 CDT)
- Re: high quality videos Adupa Vasista (Wed Sep 30 2020 - 11:45:08 CDT)
increase the resolution of images omid gh (Tue Sep 29 2020 - 13:34:31 CDT)
- Re: increase the resolution of images Fernando Vallejos-Burgos (Tue Sep 29 2020 - 18:06:33 CDT)
  - Re: increase the resolution of images omid gh (Wed Sep 30 2020 - 04:46:21 CDT)
    - Re: increase the resolution of images Pawel Kedzierski (Wed Sep 30 2020 - 06:27:03 CDT)
Converting electron density data from .map to .dx in vmd Faisal, H M Nasrullah (Tue Sep 29 2020 - 08:54:29 CDT)
Converting electron density data from .map to .dx in vmd Faisal, H M Nasrullah (Mon Sep 28 2020 - 16:33:26 CDT)
- Fw: Converting electron density data from .map to .dx in vmd Faisal, H M Nasrullah (Mon Sep 28 2020 - 16:36:57 CDT)
Converting electron density data from .map to .dx in vmd Faisal, H M Nasrullah Faisal, H M Nasrullah (Mon Sep 28 2020 - 13:58:18 CDT)
- Re: Converting electron density data from .map to .dx in vmd Faisal, H M Nasrullah Faisal, H M Nasrullah (Mon Sep 28 2020 - 16:31:59 CDT)
Converting electron density data from .map to .dx in vmd Faisal, H M Nasrullah (Mon Sep 28 2020 - 13:56:46 CDT)
FFTK Opt Torsions: can not find channel named "" Almeida-Hernández, Yasser, Dr. (Mon Sep 28 2020 - 05:45:50 CDT)
- Re: FFTK Opt Torsions: can not find channel named "" Almeida-Hernández, Yasser, Dr. (Tue Sep 29 2020 - 04:25:09 CDT)
  - Re: Re: FFTK Opt Torsions: can not find channel named "" JC Gumbart (Tue Sep 29 2020 - 11:41:11 CDT)
    - Re: Re: FFTK Opt Torsions: can not find channel named "" Almeida-Hernández, Yasser, Dr. (Tue Sep 29 2020 - 11:49:53 CDT)
FFTK Charge Opt Indoles Daniel Fellner (Sun Sep 27 2020 - 20:15:46 CDT)
Script for Finding Point Group Symmetry of Molecule and Saving the Ideal coordinate Shivang Agarwal (Sat Sep 26 2020 - 00:31:16 CDT)
FFTK Gaussian Input Generator - Bug? Daniel Fellner (Thu Sep 24 2020 - 20:20:36 CDT)
- Re: FFTK Gaussian Input Generator - Bug? Daniel Fellner (Thu Sep 24 2020 - 21:22:39 CDT)
  - Re: FFTK Gaussian Input Generator - Bug? JC Gumbart (Thu Sep 24 2020 - 23:08:50 CDT)
How to make the trajectory file show the right bonds information in VMD åˆ˜å¿—ä¼Ÿ (Thu Sep 24 2020 - 06:00:44 CDT)
- Re: How to make the trajectory file show the right bonds information in VMD Josh Vermaas (Thu Sep 24 2020 - 09:57:06 CDT)
compile vmd for windows 10 omid gh (Tue Sep 22 2020 - 06:43:36 CDT)
- Re: compile vmd for windows 10 Raman Preet Singh (Tue Sep 22 2020 - 07:33:20 CDT)
  - Re: compile vmd for windows 10 Axel Kohlmeyer (Tue Sep 22 2020 - 09:07:27 CDT)
Unusual coordinates in PDB files exracted from dcd file Mark Zottola (Sun Sep 20 2020 - 02:01:08 CDT)
- Re: Unusual coordinates in PDB files exracted from dcd file Bassam Haddad (Sun Sep 20 2020 - 17:21:56 CDT)
  - Re: Unusual coordinates in PDB files exracted from dcd file Mark Zottola (Sun Sep 20 2020 - 20:17:39 CDT)
lammpstrj move out zoom alberto (Fri Sep 18 2020 - 08:53:22 CDT)
- Re: lammpstrj move out zoom John Stone (Thu Dec 31 2020 - 15:04:46 CST)
  - Re: lammpstrj move out zoom Axel Kohlmeyer (Fri Jan 01 2021 - 11:03:26 CST)
1.9.4_a43: chemical2vmd should use /tmp instead of /usr/tmp Francisco Ramos (Thu Sep 17 2020 - 06:33:30 CDT)
1.9.4_a43 mixes g++ and gcc during building and ignores LDFLAGS Francisco Ramos (Thu Sep 17 2020 - 06:26:43 CDT)
Conformation assignment Navid Shervani-Tabar (Wed Sep 16 2020 - 14:01:30 CDT)
1.9.4_a43 parallel build issues with high -j Francisco Ramos (Wed Sep 16 2020 - 06:32:59 CDT)
- Re: 1.9.4_a43 parallel build issues with high -j John Stone (Wed Sep 16 2020 - 11:44:29 CDT)
  - Re: 1.9.4_a43 parallel build issues with high -j Giacomo Fiorin (Wed Sep 16 2020 - 12:55:38 CDT)
    - Re: 1.9.4_a43 parallel build issues with high -j John Stone (Wed Sep 16 2020 - 13:38:35 CDT)
The Fe2+ parameter for NAMD simulation sunyeping (Tue Sep 15 2020 - 23:08:25 CDT)
topo tool guess bond algorithm omid gh (Tue Sep 15 2020 - 13:39:34 CDT)
- Re: topo tool guess bond algorithm Josh Vermaas (Tue Sep 15 2020 - 15:12:00 CDT)
  - Re: topo tool guess bond algorithm omid gh (Tue Sep 15 2020 - 15:22:15 CDT)
    - Re: topo tool guess bond algorithm Axel Kohlmeyer (Tue Sep 15 2020 - 19:07:28 CDT)
    - Re: topo tool guess bond algorithm omid gh (Wed Sep 16 2020 - 04:34:47 CDT)
Regarding arsorite files Basanta Acharya (Tue Sep 15 2020 - 06:59:12 CDT)
- Re: Regarding arsorite files Axel Kohlmeyer (Tue Sep 15 2020 - 08:10:10 CDT)
- Re: Regarding arsorite files Raman Preet Singh (Tue Sep 15 2020 - 08:15:13 CDT)
  - Re: Regarding arsorite files Yogesh Sharma (Tue Sep 15 2020 - 10:02:19 CDT)
Questions about using VMD to modify/alter nucleic acid structures CHIRANJEEV BURMA (Sun Sep 13 2020 - 12:01:20 CDT)
- Re: Questions about using VMD to modify/alter nucleic acid structures Ashar Malik (Mon Sep 14 2020 - 03:48:25 CDT)
Distance between multiple residues as heat plot Raman Preet Singh (Fri Sep 11 2020 - 06:21:21 CDT)
hide bonds omid gh (Thu Sep 10 2020 - 02:45:18 CDT)
- RE: hide bonds Raman Preet Singh (Thu Sep 10 2020 - 05:02:28 CDT)
  - Re: hide bonds omid gh (Thu Sep 10 2020 - 06:12:51 CDT)
VMD write pdb error Arthur Pereira da Fonseca (Wed Sep 09 2020 - 12:16:46 CDT)
- Re: VMD write pdb error Josh Vermaas (Wed Sep 09 2020 - 13:40:17 CDT)
Tachyon freezing up Soumik Ghosh (Tue Sep 08 2020 - 16:02:18 CDT)
Re: finding number of atoms within a radius Rogers Swai (Mon Sep 07 2020 - 04:56:37 CDT)
finding number of atoms within a radius Saikat Pal (Mon Sep 07 2020 - 00:54:08 CDT)
Do different version of NAMD would give different results? Krishna Vkm (Sun Sep 06 2020 - 14:38:26 CDT)
- Re: Do different version of NAMD would give different results? Josh Vermaas (Sun Sep 06 2020 - 17:00:53 CDT)
  - Re: Do different version of NAMD would give different results? Peter Freddolino (Sun Sep 06 2020 - 19:00:34 CDT)
  - Re: Do different version of NAMD would give different results? Krishna Vkm (Mon Sep 07 2020 - 04:56:11 CDT)
topotool lammps data_file viewing omid gh (Sun Sep 06 2020 - 06:20:02 CDT)
- Re: topotool lammps data_file viewing Amir Suhail (Sun Sep 06 2020 - 06:50:38 CDT)
VMD python3 version Pacho Ramos (Sat Sep 05 2020 - 07:16:15 CDT)
- Re: VMD python3 version John Stone (Sat Sep 05 2020 - 08:26:20 CDT)
  - Re: VMD python3 version Francisco Ramos (Sat Sep 05 2020 - 12:04:17 CDT)
- Re: VMD python3 version Josh Vermaas (Sat Sep 05 2020 - 14:29:29 CDT)
Re: Error in NAMD plot John Stone (Mon Aug 31 2020 - 11:45:27 CDT)
Fwd: N-glycosylation in AutoPSF Adupa Vasista (Sat Aug 29 2020 - 03:21:23 CDT)
- Re: Fwd: N-glycosylation in AutoPSF Peter Freddolino (Sat Aug 29 2020 - 23:21:49 CDT)
  - Re: Fwd: N-glycosylation in AutoPSF Adupa Vasista (Sun Aug 30 2020 - 02:20:32 CDT)
    - Re: Fwd: N-glycosylation in AutoPSF JC Gumbart (Sun Aug 30 2020 - 06:39:36 CDT)
Loading AMBER coordinates in VMD text mode Prathit Chatterjee (Fri Aug 28 2020 - 00:39:33 CDT)
Copying the new alpha sources of VMD into the installation directory Faisal, H M Nasrullah (Tue Aug 25 2020 - 19:09:19 CDT)
Shadows in TachyonLOptiXInternal vs TachyonLOptiXInteractive Soeren von Buelow (Tue Aug 25 2020 - 09:06:03 CDT)
command line options for video in vmd Remya Ann (Mon Aug 24 2020 - 02:05:49 CDT)
NT in bilayer RAHUL SURESH (Sun Aug 23 2020 - 15:19:33 CDT)
Using MDFF 0.6 in VMD 1.9.4a Conrad F Li (Fri Aug 21 2020 - 11:19:41 CDT)
FEP simulation analysis error Mckellan S Gonzales (Thu Aug 20 2020 - 11:49:03 CDT)
VMD display freezing Yogesh Sharma (Thu Aug 20 2020 - 09:32:46 CDT)
MDFF tutorial is not working Faisal, H M Nasrullah (Thu Aug 20 2020 - 09:09:24 CDT)
- Re: MDFF tutorial is not working JC Gumbart (Mon Aug 24 2020 - 17:51:31 CDT)
Non-natural amino acid issues with autopsf Paul O'Leary (Thu Aug 20 2020 - 04:19:38 CDT)
How do I define "collision only" atoms using MSMS? Shang,Emily (Wed Aug 19 2020 - 10:24:08 CDT)
- AW: How do I define "collision only" atoms using MSMS? Norman Geist (Thu Aug 20 2020 - 02:24:05 CDT)
  - Re: How do I define "collision only" atoms using MSMS? Shang,Emily (Thu Aug 20 2020 - 10:12:18 CDT)
    - Re: How do I define "collision only" atoms using MSMS? Giacomo Fiorin (Thu Aug 20 2020 - 10:58:44 CDT)
    - Re: How do I define "collision only" atoms using MSMS? Shang,Emily (Thu Aug 20 2020 - 11:03:37 CDT)
New LAMMPS atom style for TopoTools Yasser Almeida-Hernandez (Wed Aug 19 2020 - 09:19:59 CDT)
- Re: New LAMMPS atom style for TopoTools Axel Kohlmeyer (Wed Aug 19 2020 - 10:10:46 CDT)
  - Re: New LAMMPS atom style for TopoTools Almeida-Hernández, Yasser, Dr. (Thu Aug 20 2020 - 03:16:52 CDT)
No NetCDF file type for Mac Catalina Luis Claudio Pessoa Dias (Wed Aug 19 2020 - 09:10:39 CDT)
- Re: No NetCDF file type for Mac Catalina John Stone (Sat Aug 22 2020 - 00:28:02 CDT)
  - Re: No NetCDF file type for Mac Catalina Luis Claudio Pessoa Dias (Sun Aug 23 2020 - 10:29:04 CDT)
Any tutorial/manual for Dowser for membrane protein modeling Faisal, H M Nasrullah (Tue Aug 18 2020 - 12:14:05 CDT)
- Re: Any tutorial/manual for Dowser for membrane protein modeling JC Gumbart (Wed Aug 19 2020 - 06:37:40 CDT)
  - Re: Any tutorial/manual for Dowser for membrane protein modeling Giacomo Fiorin (Wed Aug 19 2020 - 07:32:14 CDT)
    - Re: Any tutorial/manual for Dowser for membrane protein modeling JC Gumbart (Wed Aug 19 2020 - 10:04:21 CDT)
Error in fftk during bond opt using VMD 1.9.3 Faisal, H M Nasrullah (Mon Aug 17 2020 - 10:08:37 CDT)
- Re: Error in fftk during bond opt using VMD 1.9.3 JC Gumbart (Mon Aug 17 2020 - 12:17:12 CDT)
Molecular Surface Restricted Shang,Emily (Fri Aug 14 2020 - 19:14:59 CDT)
different RMSD number in VMD and charmm Michael Morgan (Fri Aug 14 2020 - 17:31:09 CDT)
- Re: different RMSD number in VMD and charmm Peter Freddolino (Sat Aug 15 2020 - 20:30:19 CDT)
PME boolean Debajeet Ghosh (Fri Aug 14 2020 - 02:14:30 CDT)
- Re: PME boolean Ashar Malik (Fri Aug 14 2020 - 03:03:02 CDT)
  - Re: PME boolean Peter Freddolino (Fri Aug 14 2020 - 07:27:01 CDT)
Nanotube in lipid bilayer RAHUL SURESH (Thu Aug 13 2020 - 06:08:42 CDT)
- Re: Nanotube in lipid bilayer Mortimer Hemmit (Thu Aug 13 2020 - 20:21:55 CDT)
  - Re: Nanotube in lipid bilayer Mortimer Hemmit (Sat Aug 15 2020 - 17:17:49 CDT)
    - Re: Nanotube in lipid bilayer RAHUL SURESH (Tue Aug 18 2020 - 06:05:04 CDT)
    - Re: Nanotube in lipid bilayer Mortimer Hemmit (Fri Aug 21 2020 - 09:03:30 CDT)
Coarse graining disordered protein Ritu Arora (Wed Aug 12 2020 - 12:34:41 CDT)
- Re: Coarse graining disordered protein Peter Freddolino (Tue Aug 18 2020 - 00:32:47 CDT)
FFTK Dihedrals Opt - Multiplicity modification Yasser Almeida-Hernandez (Wed Aug 12 2020 - 09:34:59 CDT)
- Re: FFTK Dihedrals Opt - Multiplicity modification JC Gumbart (Wed Aug 12 2020 - 14:25:50 CDT)
Using VolMap for center of mass amin sagar (Mon Aug 10 2020 - 11:16:29 CDT)
No file upon rendering Holland J.O. (Mon Aug 10 2020 - 06:22:06 CDT)
- Re: No file upon rendering Axel Kohlmeyer (Mon Aug 10 2020 - 10:26:23 CDT)
FFTK - issue after hessian loading during bonds/angles optimization Yasser Almeida-Hernandez (Mon Aug 10 2020 - 04:41:58 CDT)
- Re: FFTK - issue after hessian loading during bonds/angles optimization JC Gumbart (Mon Aug 10 2020 - 16:19:18 CDT)
  - Re: FFTK - issue after hessian loading during bonds/angles optimization Yasser Almeida-Hernandez (Tue Aug 11 2020 - 05:32:05 CDT)
TR: DUCHER Roland (Thu Aug 06 2020 - 03:03:12 CDT)
Creating a .tpr file from NAMD files Error Ethan Croitoru (Wed Aug 05 2020 - 10:23:49 CDT)
- Re: Creating a .tpr file from NAMD files Error Josh Vermaas (Wed Aug 05 2020 - 11:54:56 CDT)
  - Re: Creating a .tpr file from NAMD files Error Ethan Croitoru (Wed Aug 05 2020 - 13:30:05 CDT)
    - Re: Creating a .tpr file from NAMD files Error Josh Vermaas (Wed Aug 05 2020 - 13:45:27 CDT)
Error Qbug=3F=29=20with=20Simulated=20annealing=20in?= QFFTK-Bond/Angle=20opt?= Yasser Almeida-Hernandez (Tue Aug 04 2020 - 05:17:06 CDT)
- Re: Error (bug?) with Simulated annealing in FFTK-Bond/Angle opt Peter Freddolino (Wed Aug 05 2020 - 21:46:46 CDT)
  - Re: Error Qbug=3F=29=20with=20Simulated=20anne?= aling in FFTK-Bond/Angle opt Yasser Almeida-Hernandez (Thu Aug 06 2020 - 01:36:32 CDT)
FFTK bonded parameter optimization with ORCA Marcelo C. R. Melo (Mon Aug 03 2020 - 17:26:11 CDT)
LAMMPS output with VMD Keister, Bradley (Mon Aug 03 2020 - 09:12:26 CDT)
- Re: LAMMPS output with VMD Axel Kohlmeyer (Mon Aug 03 2020 - 09:57:20 CDT)
- Re: LAMMPS output with VMD Nathan Kern (Mon Aug 03 2020 - 10:28:15 CDT)
building VMD with Ubuntu 18.04 Keister, Bradley (Mon Aug 03 2020 - 09:12:25 CDT)
- Re: building VMD with Ubuntu 18.04 Axel Kohlmeyer (Mon Aug 03 2020 - 09:52:16 CDT)
- Re: building VMD with Ubuntu 18.04 Josh Vermaas (Mon Aug 03 2020 - 10:18:55 CDT)
  - Re: building VMD with Ubuntu 18.04 Keister, Bradley (Mon Aug 03 2020 - 10:26:34 CDT)
    - Re: building VMD with Ubuntu 18.04 Michael Bielecki (Mon Aug 03 2020 - 12:33:46 CDT)
    - Re: building VMD with Ubuntu 18.04 Keister, Bradley (Mon Aug 03 2020 - 12:46:15 CDT)
FFTK Angle optimization error Yasser Almeida-Hernandez (Mon Aug 03 2020 - 06:46:49 CDT)
- Re: FFTK Angle optimization error JC Gumbart (Mon Aug 03 2020 - 09:28:00 CDT)
  - Re: FFTK Angle optimization error Yasser Almeida-Hernandez (Mon Aug 03 2020 - 09:46:12 CDT)
  - Re: FFTK Angle optimization error Yasser Almeida-Hernandez (Mon Aug 03 2020 - 11:27:40 CDT)
Merge Structure changes coordinates to 0 Raman Preet Singh (Mon Aug 03 2020 - 01:58:25 CDT)
- RE: Merge Structure changes coordinates to 0 Raman Preet Singh (Wed Aug 12 2020 - 12:47:51 CDT)
  - Re: Merge Structure changes coordinates to 0 B (Wed Nov 11 2020 - 19:40:09 CST)
Color specific frames with specific colors in a trajectory Ameya Harmalkar (Sat Aug 01 2020 - 17:58:24 CDT)
- Re: Color specific frames with specific colors in a trajectory Josh Vermaas (Sun Aug 02 2020 - 16:44:16 CDT)
Displaying disulfide bonds with updated VMD Francesco Pietra (Sat Aug 01 2020 - 12:04:20 CDT)
- Re: Displaying disulfide bonds with updated VMD Josh Vermaas (Sat Aug 01 2020 - 16:48:19 CDT)
  - Re: Displaying disulfide bonds with updated VMD Francesco Pietra (Sun Aug 02 2020 - 01:16:00 CDT)
Non-standard solvents in Solvate Raman Preet Singh (Thu Jul 30 2020 - 13:29:52 CDT)
- Re: Non-standard solvents in Solvate Peter Freddolino (Thu Jul 30 2020 - 15:44:22 CDT)
  - Re: Non-standard solvents in Solvate Josh Vermaas (Thu Jul 30 2020 - 16:26:05 CDT)
    - RE: Non-standard solvents in Solvate Raman Preet Singh (Wed Aug 12 2020 - 12:44:32 CDT)
Problem with Residue Based Coarse Grain tutorial Manas Kohli (Mon Jul 27 2020 - 04:57:59 CDT)
- Re: Problem with Residue Based Coarse Grain tutorial Peter Freddolino (Mon Jul 27 2020 - 22:25:08 CDT)
  - Re: Problem with Residue Based Coarse Grain tutorial Manas Kohli (Tue Jul 28 2020 - 09:11:29 CDT)
  - Re: Problem with Residue Based Coarse Grain tutorial Peter Freddolino (Wed Jul 29 2020 - 14:15:24 CDT)
Error with initiation of additional production simulation using Qwikmd jrhau lung (Mon Jul 27 2020 - 04:19:54 CDT)
- Re: Error with initiation of additional production simulation using Qwikmd jrhau lung (Thu Jul 30 2020 - 06:48:11 CDT)
  - Re: Re: Error with initiation of additional production simulation using Qwikmd Peter Freddolino (Thu Jul 30 2020 - 10:02:09 CDT)
  - Re: Re: Error with initiation of additional production simulation using Qwikmd Josh Vermaas (Thu Jul 30 2020 - 16:33:10 CDT)
    - Re: Re: Error with initiation of additional production simulation using Qwikmd jrhau lung (Thu Jul 30 2020 - 18:44:45 CDT)
writing a new trajectory with selected atoms Yogesh Sharma (Fri Jul 24 2020 - 01:05:46 CDT)
- Re: writing a new trajectory with selected atoms Smith, Harper E. (Fri Jul 24 2020 - 01:34:26 CDT)
resizing display exits vmd Miro Astore (Thu Jul 23 2020 - 19:11:24 CDT)
- Re: resizing display exits vmd Michael Robinson (Thu Jul 23 2020 - 21:56:31 CDT)
  - Re: resizing display exits vmd John Stone (Fri Jul 24 2020 - 13:33:20 CDT)
    - Re: resizing display exits vmd Michael Robinson (Sat Jul 25 2020 - 00:00:54 CDT)
Configuring Tkcon in VMD for Catalina to access history with up arrow Chang, Christopher (Thu Jul 23 2020 - 17:16:32 CDT)
- Re: Configuring Tkcon in VMD for Catalina to access history with up arrow John Stone (Fri Jul 24 2020 - 13:36:24 CDT)
  - Re: Configuring Tkcon in VMD for Catalina to access history with up arrow Chang, Christopher (Fri Jul 24 2020 - 14:31:02 CDT)
    - Re: Configuring Tkcon in VMD for Catalina to access history with up arrow John Stone (Fri Jul 24 2020 - 14:40:45 CDT)
Molefacture does not write bond angles and dihedral angles info in the psf file Valentin Gogonea (Thu Jul 23 2020 - 16:10:38 CDT)
- Re: Molefacture does not write bond angles and dihedral angles info in the psf file John Stone (Thu Jul 23 2020 - 16:47:56 CDT)
  - Re: Molefacture does not write bond angles and dihedral angles info in the psf file Valentin Gogonea (Thu Jul 23 2020 - 17:13:01 CDT)
FFTK Fragment Charge Opt. Daniel Fellner (Wed Jul 22 2020 - 03:46:59 CDT)
Create Binding Pocket of Every PDB File In A Directory Using TCL Scripts and Atomselect Command protein and within 4 of resname LIG William Howe (Mon Jul 20 2020 - 11:12:54 CDT)
- Re: Create Binding Pocket of Every PDB File In A Directory Using TCL Scripts and Atomselect Command protein and within 4 of resname LIG Bassam Haddad (Mon Jul 20 2020 - 12:58:36 CDT)
  - Re: Create Binding Pocket of Every PDB File In A Directory Using TCL Scripts and Atomselect Command protein and within 4 of resname LIG Bassam Haddad (Mon Jul 20 2020 - 13:31:24 CDT)
- Re: Create Binding Pocket of Every PDB File In A Directory Using TCL Scripts and Atomselect Command protein and within 4 of resname LIG Ashar Malik (Mon Jul 20 2020 - 16:06:03 CDT)
FFTK Opt Torsions MM Trajectory Daniel Fellner (Wed Jul 15 2020 - 07:11:20 CDT)
- VMD on Catalina miyatake (Fri Jul 17 2020 - 02:20:18 CDT)
Phi and Psi angles for particular residues as a function of time Akash Pandya (Tue Jul 14 2020 - 10:38:28 CDT)
- Re: Phi and Psi angles for particular residues as a function of time Ashar Malik (Tue Jul 14 2020 - 11:27:50 CDT)
Trajectory smoothing Maximilian Ebert (Mon Jul 13 2020 - 20:53:09 CDT)
- Re: Trajectory smoothing Axel Kohlmeyer (Mon Jul 13 2020 - 22:06:24 CDT)
  - Re: Trajectory smoothing Maximilian Ebert (Mon Jul 13 2020 - 22:08:50 CDT)
    - Re: Trajectory smoothing Axel Kohlmeyer (Mon Jul 13 2020 - 22:41:55 CDT)
Difficulty downloading databases for MultiSeq Julia Steckner (Mon Jul 13 2020 - 11:34:50 CDT)
- Re: Difficulty downloading databases for MultiSeq John Stone (Mon Nov 02 2020 - 14:30:33 CST)
RBCG models using Martini forces - psf file Alilovic,Kata (Mon Jul 13 2020 - 09:13:19 CDT)
- Re: RBCG models using Martini forces - psf file Peter Freddolino (Mon Jul 13 2020 - 11:35:03 CDT)
Pore lining residues over a trajactory. Yogesh Sharma (Mon Jul 13 2020 - 06:34:58 CDT)
How to get a transparent background with Tachyon Soumik Ghosh (Mon Jul 13 2020 - 02:26:34 CDT)
- Re: How to get a transparent background with Tachyon Nathan Kern (Mon Jul 13 2020 - 11:29:51 CDT)
- Re: How to get a transparent background with Tachyon John Stone (Thu Jul 30 2020 - 00:19:15 CDT)
seeking suggestion in simulation analysis for pore lining residues in channel protein Yogesh Sharma (Sat Jul 11 2020 - 08:49:42 CDT)
unable to access vmd through ssh x11 forward using mobaxterm SHRAVANI NETHI . (Sat Jul 11 2020 - 02:25:29 CDT)
- Re: unable to access vmd through ssh x11 forward using mobaxterm John Stone (Thu Jul 30 2020 - 00:18:24 CDT)
Best way to extend molfile plugin Peter Schmidtke (Tue Jul 07 2020 - 07:28:19 CDT)
- Re: Best way to extend molfile plugin Axel Kohlmeyer (Tue Jul 07 2020 - 08:15:37 CDT)
PhD Position In Computational Structural Biology Of Membrane Proteins Marawan Hussien (Mon Jul 06 2020 - 22:07:44 CDT)
QwikMD problem to continue new production simulation session jrhau lung (Mon Jul 06 2020 - 18:33:57 CDT)
FF parameters for EtSNO Ritu Arora (Mon Jul 06 2020 - 11:34:50 CDT)
- Re: FF parameters for EtSNO JC Gumbart (Mon Jul 06 2020 - 18:57:17 CDT)
  - Re: FF parameters for EtSNO JC Gumbart (Mon Jul 06 2020 - 19:21:36 CDT)
Fwd: namd-l: Re: scripts to generate initial boxes of solvents Francesco Pietra (Mon Jul 06 2020 - 11:09:14 CDT)
- Fwd: Fwd: namd-l: Re: scripts to generate initial boxes of solvents Francesco Pietra (Mon Jul 06 2020 - 11:57:16 CDT)
  - Re: Fwd: namd-l: Re: scripts to generate initial boxes of solvents Peter Freddolino (Tue Jul 07 2020 - 00:00:06 CDT)
    - Re: Fwd: namd-l: Re: scripts to generate initial boxes of solvents Francesco Pietra (Tue Jul 07 2020 - 01:01:15 CDT)
    - Fwd: Fwd: namd-l: Re: scripts to generate initial boxes of solvents Francesco Pietra (Tue Jul 07 2020 - 01:58:10 CDT)
getting VMD to obey me Francesco Pietra (Sun Jul 05 2020 - 10:38:46 CDT)
- Re: getting VMD to obey me Josh Vermaas (Sun Jul 05 2020 - 15:33:12 CDT)
  - Re: getting VMD to obey me Francesco Pietra (Mon Jul 06 2020 - 04:39:22 CDT)
VMD: error in ffTK torsion angle optimization Valentin Gogonea (Sun Jul 05 2020 - 10:23:42 CDT)
- Re: VMD: error in ffTK torsion angle optimization JC Gumbart (Mon Jul 06 2020 - 18:51:42 CDT)
  - Re: VMD: error in ffTK torsion angle optimization JC Gumbart (Sat Jul 11 2020 - 18:18:47 CDT)
  - Re: VMD: error in ffTK torsion angle optimization JC Gumbart (Tue Aug 04 2020 - 20:26:58 CDT)
    - Re: VMD: error in ffTK torsion angle optimization Valentin Gogonea (Tue Aug 04 2020 - 21:17:02 CDT)
1.9.4a43-Catalina-Rev6 TkConsole Up Arrow History Mortimer Hemmit (Fri Jul 03 2020 - 20:11:22 CDT)
- Re: 1.9.4a43-Catalina-Rev6 TkConsole Up Arrow History Mortimer Hemmit (Mon Jul 13 2020 - 10:04:19 CDT)
  - Re: 1.9.4a43-Catalina-Rev6 TkConsole Up Arrow History FX (Mon Jul 13 2020 - 11:03:01 CDT)
  - Re: 1.9.4a43-Catalina-Rev6 TkConsole Up Arrow History Karl Lundquist (Mon Jul 13 2020 - 11:32:18 CDT)
    - Re: 1.9.4a43-Catalina-Rev6 TkConsole Up Arrow History John Stone (Mon Jul 13 2020 - 13:36:59 CDT)
EPYC and GTX selection for VMD and NAMD jrhau lung (Fri Jul 03 2020 - 06:33:35 CDT)
Unable to create PSF file Alilovic,Kata (Thu Jul 02 2020 - 16:04:29 CDT)
- Re: Unable to create PSF file Peter Freddolino (Thu Jul 02 2020 - 19:05:20 CDT)
  - VMD 1.9.4a43 Rev 6 for MacOS X Catalina miyatake (Thu Jul 02 2020 - 22:09:01 CDT)
  - Re: Unable to create PSF file Alilovic,Kata (Fri Jul 03 2020 - 12:55:10 CDT)
    - Re: Unable to create PSF file Peter Freddolino (Fri Jul 03 2020 - 13:01:33 CDT)
hydrogen bonding calculation Snehasis Chatterjee (Thu Jul 02 2020 - 15:54:47 CDT)
How to visualize unusual amino acid in VMD with Cartoon or ribbon representation Chetna Tyagi (Wed Jul 01 2020 - 09:29:46 CDT)
- Re: How to visualize unusual amino acid in VMD with Cartoon or ribbon representation Dallas Warren (Wed Jul 01 2020 - 17:55:56 CDT)
VMD on HPC Adupa Vasista (Wed Jul 01 2020 - 00:00:28 CDT)
- Re: VMD on HPC Ashar Malik (Wed Jul 01 2020 - 03:19:24 CDT)
  - Re: VMD on HPC Adupa Vasista (Wed Jul 01 2020 - 04:06:33 CDT)
selection of molecules in dynamic region SHRAVANI NETHI . (Mon Jun 29 2020 - 03:05:10 CDT)
- Re: selection of molecules in dynamic region Axel Kohlmeyer (Mon Jun 29 2020 - 06:13:44 CDT)
  - Fw: selection of molecules in dynamic region SHRAVANI NETHI (Wed Jul 01 2020 - 10:16:11 CDT)
Dangerous bug with pbwithin selection? Norman Geist (Fri Jun 26 2020 - 06:24:02 CDT)
Potential map of Electric field of charged gas mohammad rezaei (Wed Jun 24 2020 - 03:31:16 CDT)
- Re: Potential map of Electric field of charged gas Giacomo Fiorin (Wed Jun 24 2020 - 08:52:23 CDT)
  - Re: Potential map of Electric field of charged gas mohammad rezaei (Wed Jun 24 2020 - 11:35:56 CDT)
How to change the center of Radial coloring method fan li (Tue Jun 23 2020 - 14:50:09 CDT)
Orientational correlation function SHIVAM TIWARI (Mon Jun 22 2020 - 05:50:10 CDT)
VMD Failing to Recognize Path Nisler, Collin R. (Sat Jun 20 2020 - 16:21:28 CDT)
Atomic bond counting wuth VMD Otakandza Glenn (Fri Jun 19 2020 - 06:11:03 CDT)
- Re: Atomic bond counting wuth VMD Josh Vermaas (Fri Jun 19 2020 - 08:55:59 CDT)
  - Re: Atomic bond counting wuth VMD Josh Vermaas (Fri Jun 19 2020 - 15:47:22 CDT)
FFTK sulfur ChargeOpt Daniel Fellner (Thu Jun 18 2020 - 23:17:42 CDT)
- Re: FFTK sulfur ChargeOpt JC Gumbart (Fri Jun 19 2020 - 15:08:14 CDT)
  - Re: FFTK sulfur ChargeOpt Daniel Fellner (Fri Jun 19 2020 - 17:52:54 CDT)
Movie Maker in VMD Seibold, Steve Allan (Thu Jun 18 2020 - 10:38:50 CDT)
- Re: Movie Maker in VMD Josh Vermaas (Thu Jun 18 2020 - 12:16:55 CDT)
orientational correlation function for protein SHIVAM TIWARI (Thu Jun 18 2020 - 06:20:10 CDT)
Child killed error: unknown signal Mintare Cesiunaite (Tue Jun 16 2020 - 23:15:36 CDT)
- Re: Child killed error: unknown signal John Stone (Tue Jun 16 2020 - 23:31:47 CDT)
Visualizing Molecule-Molecule RDFs instead of atom-atom Rameswar Bhattacharjee (Tue Jun 16 2020 - 15:31:58 CDT)
- Re: Visualizing Molecule-Molecule RDFs instead of atom-atom Axel Kohlmeyer (Tue Jun 16 2020 - 16:01:39 CDT)
  - Re: Visualizing Molecule-Molecule RDFs instead of atom-atom Rameswar Bhattacharjee (Tue Jun 16 2020 - 16:15:39 CDT)
    - Re: Visualizing Molecule-Molecule RDFs instead of atom-atom Axel Kohlmeyer (Tue Jun 16 2020 - 16:58:45 CDT)
how to keep the bond , angle , dihedral and improper type after solvating the lammps data fan li (Fri Jun 12 2020 - 14:19:23 CDT)
- Re: how to keep the bond , angle , dihedral and improper type after solvating the lammps data Axel Kohlmeyer (Fri Jun 12 2020 - 15:04:44 CDT)
VMD 1.9.4 alpha 43 test builds posted... John Stone (Thu Jun 11 2020 - 15:24:45 CDT)
Regarding Distance measurements DHEERAJ CHITARA (Thu Jun 11 2020 - 05:57:49 CDT)
Radial distribution function calculation Rameswar Bhattacharjee (Wed Jun 10 2020 - 23:01:30 CDT)
- Re: Radial distribution function calculation Axel Kohlmeyer (Wed Jun 10 2020 - 23:59:10 CDT)
  - Re: Radial distribution function calculation Rameswar Bhattacharjee (Thu Jun 11 2020 - 00:35:06 CDT)
error: can't read "w" no such variable. æŽå‰å¼˜ (Wed Jun 10 2020 - 08:16:23 CDT)
- Re: error: can't read "w" no such variable. yjcoshc (Wed Jun 10 2020 - 17:08:56 CDT)
VRAM memory piling up OPTIX 1.9.4a42 rendering consecutive frames Bart Bruininks (Wed Jun 10 2020 - 08:05:10 CDT)
- Re: VRAM memory piling up OPTIX 1.9.4a42 rendering consecutive frames Bart Bruininks (Wed Jun 10 2020 - 08:37:09 CDT)
- Re: VRAM memory piling up OPTIX 1.9.4a42 rendering consecutive frames John Stone (Wed Jun 10 2020 - 10:05:54 CDT)
  - Re: VRAM memory piling up OPTIX 1.9.4a42 rendering consecutive frames John Stone (Wed Jun 10 2020 - 11:11:36 CDT)
    - Re: VRAM memory piling up OPTIX 1.9.4a42 rendering consecutive frames John Stone (Thu Jun 11 2020 - 15:59:34 CDT)
  - Re: VRAM memory piling up OPTIX 1.9.4a42 rendering consecutive frames Bart Bruininks (Wed Jun 10 2020 - 11:07:58 CDT)
Black screen OPTIX interactive rendering Bart Bruininks (Wed Jun 10 2020 - 05:22:39 CDT)
- Re: Black screen OPTIX interactive rendering Bart Bruininks (Wed Jun 10 2020 - 08:20:49 CDT)
- Re: Black screen OPTIX interactive rendering John Stone (Wed Jun 10 2020 - 09:57:06 CDT)
Visualizing Vibrational Modes MD Simulation (Tue Jun 09 2020 - 16:43:38 CDT)
- Re: Visualizing Vibrational Modes Axel Kohlmeyer (Tue Jun 09 2020 - 17:23:13 CDT)
  - Re: Visualizing Vibrational Modes MD Simulation (Tue Jun 09 2020 - 17:47:15 CDT)
    - Re: Visualizing Vibrational Modes Axel Kohlmeyer (Tue Jun 09 2020 - 18:08:29 CDT)
Fixed atoms Hélder Bandarra Tavares (Tue Jun 09 2020 - 09:35:48 CDT)
- Re: Fixed atoms Michael Robinson (Tue Jun 09 2020 - 22:14:48 CDT)
  - Re: Fixed atoms Hélder Bandarra Tavares (Wed Jun 10 2020 - 05:55:09 CDT)
Finding gas migration pathways in protein using ILS method. Muhammad tariq (Tue Jun 09 2020 - 04:51:21 CDT)
FFTK: Charge Optimisation partial charges Daniel Fellner (Mon Jun 08 2020 - 23:15:15 CDT)
- Re: FFTK: Charge Optimisation partial charges JC Gumbart (Tue Jun 09 2020 - 12:33:39 CDT)
  - Re: FFTK: Charge Optimisation partial charges JC Gumbart (Wed Jun 10 2020 - 06:19:28 CDT)
  - Re: FFTK: Charge Optimisation partial charges JC Gumbart (Wed Jun 10 2020 - 06:44:05 CDT)
    - Re: FFTK: Charge Optimisation partial charges Daniel Fellner (Wed Jun 10 2020 - 07:01:37 CDT)
Action halted on error in ffTK: The following output QM was not recognized Valentin Gogonea (Mon Jun 08 2020 - 18:16:55 CDT)
- Re: Action halted on error in ffTK: The following output QM was not recognized JC Gumbart (Tue Jun 09 2020 - 12:27:22 CDT)
  - Re: Action halted on error in ffTK: The following output QM was not recognized JC Gumbart (Tue Jun 09 2020 - 18:03:55 CDT)
    - Re: Action halted on error in ffTK: The following output QM was not recognized Valentin Gogonea (Tue Jun 09 2020 - 20:05:05 CDT)
    - Re: Action halted on error in ffTK: The following output QM was not recognized JC Gumbart (Tue Jun 09 2020 - 20:12:50 CDT)
Fixed atoms question Hélder Bandarra Tavares (Mon Jun 08 2020 - 12:51:07 CDT)
atoms inside a Nanotube, Deleting Nima Soltani (Sun Jun 07 2020 - 22:49:58 CDT)
volmap computation_ILS method Muhammad tariq (Sat Jun 06 2020 - 12:08:27 CDT)
- Re: volmap computation_ILS method Ashar Malik (Sat Jun 06 2020 - 17:42:31 CDT)
implicit ligand sampling method Muhammad tariq (Sat Jun 06 2020 - 09:58:00 CDT)
resname X and pbwithin resname X excluding intramolecular Bart Bruininks (Fri Jun 05 2020 - 08:14:43 CDT)
- Re: resname X and pbwithin resname X excluding intramolecular Josh Vermaas (Fri Jun 05 2020 - 10:34:36 CDT)
  - Re: resname X and pbwithin resname X excluding intramolecular Bart Bruininks (Sat Jun 06 2020 - 14:47:30 CDT)
monomer to tatramer conversion Yogesh Sharma (Thu Jun 04 2020 - 09:55:23 CDT)
- Re: monomer to tatramer conversion Josh Vermaas (Thu Jun 04 2020 - 13:06:02 CDT)
Selecting first three characters of a variable with tcl in VMD Prathit Chatterjee (Thu Jun 04 2020 - 01:37:54 CDT)
- RE: Selecting first three characters of a variable with tcl in VMD Joaquim Rui de Castro Rodrigues (Thu Jun 04 2020 - 03:24:22 CDT)
  - Re: Selecting first three characters of a variable with tcl in VMD Prathit Chatterjee (Thu Jun 04 2020 - 21:20:56 CDT)
Selecting first three characters of a variable with tcl in VMD Prathit Chatterjee (Wed Jun 03 2020 - 22:56:41 CDT)
- Re: Selecting first three characters of a variable with tcl in VMD Ashar Malik (Wed Jun 03 2020 - 23:53:46 CDT)
  - Re: Selecting first three characters of a variable with tcl in VMD Prathit Chatterjee (Thu Jun 04 2020 - 02:59:49 CDT)
VMD crashes when files are drag-and-dropped - any resolution? Oleg Stroganov (Wed Jun 03 2020 - 22:14:54 CDT)
PSFGEN David Alejandro RincÃ³n Daza (Tue Jun 02 2020 - 16:51:19 CDT)
- Re: PSFGEN Josh Vermaas (Wed Jun 03 2020 - 11:32:06 CDT)
  - Re: PSFGEN David Alejandro RincÃ³n Daza (Wed Jun 03 2020 - 15:10:47 CDT)
    - Re: PSFGEN Josh Vermaas (Wed Jun 03 2020 - 16:12:53 CDT)
    - Re: PSFGEN David Alejandro RincÃ³n Daza (Wed Jun 03 2020 - 16:43:26 CDT)
Re: Fw: Hbond extension Axel Kohlmeyer (Tue Jun 02 2020 - 12:43:54 CDT)
analyzing amino acids forming pore constrictions in a channel protein Yogesh Sharma (Tue Jun 02 2020 - 04:46:41 CDT)
- Re: analyzing amino acids forming pore constrictions in a channel protein Bassam Haddad (Tue Jun 02 2020 - 11:44:55 CDT)
  - Re: analyzing amino acids forming pore constrictions in a channel protein Bassam Haddad (Tue Jun 02 2020 - 12:33:03 CDT)
How to determine a molecule's conformation in solution Hélder Bandarra Tavares (Mon Jun 01 2020 - 11:00:09 CDT)
- Re: How to determine a molecule's conformation in solution Daniel Fellner (Mon Jun 01 2020 - 11:14:29 CDT)
  - Re: How to determine a molecule's conformation in solution Hélder Bandarra Tavares (Mon Jun 01 2020 - 11:24:27 CDT)
    - Re: How to determine a molecule's conformation in solution Daniel Fellner (Mon Jun 01 2020 - 21:04:57 CDT)
    - Re: How to determine a molecule's conformation in solution Hélder Bandarra Tavares (Tue Jun 02 2020 - 04:39:16 CDT)
NAMD energy plugin reference Aashish Bhatt (Mon Jun 01 2020 - 06:30:56 CDT)
- Re: NAMD energy plugin reference John Stone (Sat Jun 06 2020 - 00:23:53 CDT)
  - Re: NAMD energy plugin reference Peter Freddolino (Sat Jun 06 2020 - 22:21:32 CDT)
FFTK: Opt. Charges Error Daniel Fellner (Sat May 30 2020 - 02:58:43 CDT)
- Re: FFTK: Opt. Charges Error Gumbart, JC (Sat May 30 2020 - 11:48:23 CDT)
  - Re: FFTK: Opt. Charges Error Gumbart, JC (Sat May 30 2020 - 11:49:45 CDT)
    - Re: FFTK: Opt. Charges Error Daniel Fellner (Sat May 30 2020 - 20:33:32 CDT)
    - Re: FFTK: Opt. Charges Error Gumbart, JC (Sun May 31 2020 - 15:20:52 CDT)
VMD 1.9.4a42 test builds posted... John Stone (Fri May 29 2020 - 16:51:53 CDT)
- Re: VMD 1.9.4a42 test builds posted... FX (Sat May 30 2020 - 04:04:48 CDT)
  - Re: VMD 1.9.4a42 test builds posted... John Stone (Sat May 30 2020 - 16:31:14 CDT)
  - Re: VMD 1.9.4a42 test builds posted... John Stone (Sat May 30 2020 - 16:28:54 CDT)
measure gofr non-orthogonal MD Simulation (Wed May 27 2020 - 19:40:26 CDT)
Re: Fwd: Fwd: Fwd: Electrostatic potential maps Sebastian Reiter (Wed May 27 2020 - 09:36:37 CDT)
- Re: Fwd: Fwd: Fwd: Electrostatic potential maps Francesco Pietra (Fri May 29 2020 - 05:07:20 CDT)
  - Re: Fwd: Fwd: Fwd: Electrostatic potential maps John Stone (Fri May 29 2020 - 21:50:01 CDT)
Unable to install vmdICE plugin in VMD gagandeep singh (Wed May 27 2020 - 15:37:11 CDT)
- Re: Unable to install vmdICE plugin in VMD Giacomo Fiorin (Wed May 27 2020 - 09:28:30 CDT)
Extrabonds issue Hélder Bandarra Tavares (Wed May 27 2020 - 05:19:12 CDT)
- Re: Extrabonds issue Josh Vermaas (Wed May 27 2020 - 10:49:31 CDT)
  - Re: Extrabonds issue Hélder Bandarra Tavares (Mon Jun 01 2020 - 08:31:51 CDT)
Transparent QuickSurf ali.kamrani91_at_REMOVE_yahoo.com (Tue May 26 2020 - 12:29:29 CDT)
Issues using AutoPSF Hélder Bandarra Tavares (Tue May 26 2020 - 08:59:08 CDT)
Issues generating a .psf file Hélder Bandarra Tavares (Tue May 26 2020 - 08:47:56 CDT)
- Re: Issues generating a .psf file Josh Vermaas (Tue May 26 2020 - 09:50:12 CDT)
  - Re: Issues generating a .psf file Hélder Bandarra Tavares (Tue May 26 2020 - 10:14:44 CDT)
  - Re: Issues generating a .psf file Peter Freddolino (Tue May 26 2020 - 11:52:02 CDT)
VMD charmm paramters files: par_all36m_prot.prm RenÃ© Hafner TUK (Tue May 26 2020 - 06:48:44 CDT)
- Re: VMD charmm paramters files: par_all36m_prot.prm Gumbart, JC (Tue May 26 2020 - 13:29:05 CDT)
  - Re: VMD charmm paramters files: par_all36m_prot.prm RenÃ© Hafner TUK (Wed May 27 2020 - 01:34:51 CDT)
Failed to create Optix rendering context ERROR: Invalid value (OptiXRenderer.C:1214 Lorenzo Casalino (Mon May 25 2020 - 15:28:53 CDT)
- Re: Failed to create Optix rendering context ERROR: Invalid value (OptiXRenderer.C:1214 John Stone (Mon May 25 2020 - 23:16:04 CDT)
  - Re: Failed to create Optix rendering context ERROR: Invalid value (OptiXRenderer.C:1214 John Stone (Wed May 27 2020 - 16:26:16 CDT)
    - Re: Failed to create Optix rendering context ERROR: Invalid value (OptiXRenderer.C:1214 John Stone (Fri May 29 2020 - 16:46:33 CDT)
  - Re: Failed to create Optix rendering context ERROR: Invalid value (OptiXRenderer.C:1214 John Stone (Thu Jun 11 2020 - 21:56:17 CDT)
Get atoms in each ring MD Simulation (Mon May 25 2020 - 11:31:12 CDT)
- Re: Get atoms in each ring Giacomo Fiorin (Mon May 25 2020 - 12:32:27 CDT)
Create covalent bonds between 2 atoms via Tk console Hélder Bandarra Tavares (Mon May 25 2020 - 09:29:15 CDT)
- Re: Create covalent bonds between 2 atoms via Tk console Josh Vermaas (Mon May 25 2020 - 11:19:29 CDT)
Electrostatic potential maps Francesco Pietra (Sat May 23 2020 - 03:20:02 CDT)
- Fwd: Electrostatic potential maps Francesco Pietra (Sun May 24 2020 - 08:58:49 CDT)
  - Re: Fwd: Electrostatic potential maps Mortimer Hemmit (Sun May 24 2020 - 16:31:50 CDT)
cgenff atom type issue Stefano Guglielmo (Fri May 22 2020 - 11:50:36 CDT)
- Re: cgenff atom type issue Krishna Vkm (Fri May 22 2020 - 12:40:29 CDT)
- Re: cgenff atom type issue Josh Vermaas (Fri May 22 2020 - 13:16:15 CDT)
  - Re: cgenff atom type issue Stefano Guglielmo (Sun May 24 2020 - 05:51:55 CDT)
FFTK: Charge Optimization (Water Int.) Daniel Fellner (Fri May 22 2020 - 01:24:18 CDT)
- Re: FFTK: Charge Optimization (Water Int.) Aleksei (Fri May 22 2020 - 11:50:36 CDT)
  - Re: FFTK: Charge Optimization (Water Int.) Daniel Fellner (Sun May 24 2020 - 21:24:40 CDT)
    - Re: FFTK: Charge Optimization (Water Int.) Aleksei (Thu May 28 2020 - 01:39:15 CDT)
Writing DCD files using animate HEMANTH H (Thu May 21 2020 - 00:18:46 CDT)
- Re: Writing DCD files using animate John Stone (Sat May 23 2020 - 02:17:05 CDT)
  - Re: Writing DCD files using animate HEMANTH H (Sat May 23 2020 - 07:27:08 CDT)
Re: VMD patch, console w/ built-in command editing Giacomo Fiorin (Wed May 20 2020 - 10:06:50 CDT)
- Re: Re: VMD patch, console w/ built-in command editing John Stone (Wed May 20 2020 - 10:26:21 CDT)
  - Re: Re: VMD patch, console w/ built-in command editing John Stone (Wed May 20 2020 - 10:33:45 CDT)
    - Re: Re: VMD patch, console w/ built-in command editing Giacomo Fiorin (Wed May 20 2020 - 11:09:16 CDT)
    - Re: Re: VMD patch, console w/ built-in command editing John Stone (Wed May 20 2020 - 11:45:03 CDT)
- Re: VMD patch, console w/ built-in command editing John Stone (Fri May 22 2020 - 10:56:18 CDT)
RDF from a trajectory generated by SIESTA Linda Sheila Medondjio (Tue May 19 2020 - 14:10:32 CDT)
- Re: RDF from a trajectory generated by SIESTA Giacomo Fiorin (Tue May 19 2020 - 15:12:53 CDT)
Windows version, system out of memory Dallas Warren (Mon May 18 2020 - 02:39:32 CDT)
- Re: Windows version, system out of memory John Stone (Tue May 19 2020 - 15:18:13 CDT)
  - Re: Windows version, system out of memory Chris Broomell (Tue May 19 2020 - 16:39:41 CDT)
    - Re: Windows version, system out of memory John Stone (Tue May 19 2020 - 21:53:15 CDT)
  - Re: Windows version, system out of memory Dallas Warren (Tue May 19 2020 - 18:30:17 CDT)
vmd console linux shell mode Michael Morgan (Wed May 13 2020 - 20:52:04 CDT)
- Re: vmd console linux shell mode John Stone (Wed May 13 2020 - 21:46:33 CDT)
new type cross terms in topo tool omid gh (Sat May 09 2020 - 13:46:15 CDT)
- Re: new type cross terms in topo tool Axel Kohlmeyer (Sat May 09 2020 - 16:14:11 CDT)
Regarding zinc parameters in CHARMM force field varun dewaker (Sat May 09 2020 - 12:40:52 CDT)
- Re: Regarding zinc parameters in CHARMM force field Gumbart, JC (Mon May 11 2020 - 14:12:25 CDT)
VMD-L Regarding Zinc parameters varun dewaker (Sat May 09 2020 - 12:38:00 CDT)
VMD-L Entropy calculation in VMD varun dewaker (Sat May 09 2020 - 12:31:03 CDT)
- Re: VMD-L Entropy calculation in VMD Giacomo Fiorin (Sat May 09 2020 - 18:12:29 CDT)
delete angle type with topo tool omid gh (Sat May 09 2020 - 11:46:22 CDT)
- Re: delete angle type with topo tool Axel Kohlmeyer (Sat May 09 2020 - 16:12:13 CDT)
How to download high-quality images from MEMBPLUGIN -> "Membrane thickness map" Sunidhi IIITD (Sat May 09 2020 - 06:58:21 CDT)
- Re: How to download high-quality images from MEMBPLUGIN -> "Membrane thickness map" John Stone (Sat May 23 2020 - 02:23:03 CDT)
MDAnalysis/VMD discrepancy Alexandra Ringsby (Fri May 08 2020 - 15:22:28 CDT)
- Re: MDAnalysis/VMD discrepancy Josh Vermaas (Fri May 08 2020 - 16:02:50 CDT)
  - Re: MDAnalysis/VMD discrepancy Alexandra Ringsby (Fri May 08 2020 - 16:44:31 CDT)
    - Re: MDAnalysis/VMD discrepancy Giacomo Fiorin (Fri May 08 2020 - 17:56:57 CDT)
visualizing bonds in lammps output reaxff Udeshini Manatunga (Fri May 08 2020 - 03:46:25 CDT)
- Re: visualizing bonds in lammps output reaxff Giacomo Fiorin (Fri May 08 2020 - 09:42:56 CDT)
  - Re: visualizing bonds in lammps output reaxff Udeshini Manatunga (Fri May 08 2020 - 21:09:01 CDT)
Drawing multiple frames Neena Susan Eappen (Thu May 07 2020 - 17:58:22 CDT)
- Re: Drawing multiple frames John Stone (Sat May 23 2020 - 02:24:52 CDT)
VMD Slices Amali Guruge (Wed May 06 2020 - 19:38:02 CDT)
- Re: VMD Slices John Stone (Sat May 23 2020 - 02:21:15 CDT)
Explain Script Neena Susan Eappen (Wed May 06 2020 - 16:54:37 CDT)
- Re: Explain Script Nathan Kern (Wed May 06 2020 - 18:43:22 CDT)
Bypassing MM parameterization of ligand in QMMM Francesco Pietra (Wed May 06 2020 - 02:49:55 CDT)
- Fwd: Bypassing MM parameterization of ligand in QMMM Francesco Pietra (Wed May 06 2020 - 03:10:29 CDT)
entropy calculation varun dewaker (Tue May 05 2020 - 00:33:14 CDT)
error with make movie mohammad rezaei (Mon May 04 2020 - 05:54:47 CDT)
- Re: error with make movie Dallas Warren (Mon May 04 2020 - 17:55:59 CDT)
  - Re: error with make movie mohammad rezaei (Tue May 05 2020 - 04:14:29 CDT)
coloured surface Ivana (Sun May 03 2020 - 11:49:03 CDT)
- Re: coloured surface John Stone (Sat May 23 2020 - 02:09:17 CDT)
  - Re: coloured surface Ivana (Sat May 23 2020 - 12:51:01 CDT)
Solvation in mixed solvent HOUSTON Douglas (Thu Apr 30 2020 - 06:17:23 CDT)
- Re: Solvation in mixed solvent Josh Vermaas (Thu Apr 30 2020 - 07:45:14 CDT)
qwrap installation Alexander Adams (Tue Apr 28 2020 - 12:36:40 CDT)
- Re: qwrap installation Ivan Gregoretti (Tue Apr 28 2020 - 14:09:42 CDT)
  - Re: qwrap installation Ashar Malik (Tue Apr 28 2020 - 15:03:51 CDT)
  - Re: qwrap installation Giacomo Fiorin (Tue Apr 28 2020 - 15:20:04 CDT)
    - Re: qwrap installation Alexander Adams (Wed Apr 29 2020 - 14:30:31 CDT)
DNA on RMSD Trajectory Tool Seojin You (Tue Apr 28 2020 - 03:11:26 CDT)
- Re: DNA on RMSD Trajectory Tool Ashar Malik (Tue Apr 28 2020 - 04:57:54 CDT)
Problem with Surf representation in the latest version macOS Catalina Neda Rafieiolhosseini (Mon Apr 27 2020 - 12:56:54 CDT)
- Re: Problem with Surf representation in the latest version macOS Catalina Josh Vermaas (Mon Apr 27 2020 - 15:25:36 CDT)
  - Re: Problem with Surf representation in the latest version macOS Catalina John Stone (Mon Apr 27 2020 - 16:04:29 CDT)
STRIDE issues on Windows mfeiglab_at_gmail.com (Mon Apr 27 2020 - 12:51:01 CDT)
- Re: STRIDE issues on Windows John Stone (Wed Apr 29 2020 - 01:16:19 CDT)
  - Re: STRIDE issues on Windows John Stone (Wed Apr 29 2020 - 01:20:47 CDT)
  - RE: STRIDE issues on Windows mfeiglab_at_gmail.com (Wed Apr 29 2020 - 08:58:38 CDT)
Convert problem mohamed marzouk (Sat Apr 25 2020 - 03:31:23 CDT)
- Re: Convert problem Giacomo Fiorin (Sat Apr 25 2020 - 09:45:29 CDT)
  - Re: Convert problem mohamed marzouk (Sat Apr 25 2020 - 11:38:23 CDT)
- Re: Convert problem Pawel Kedzierski (Sat Apr 25 2020 - 10:45:18 CDT)
  - Re: Convert problem mohamed marzouk (Sat Apr 25 2020 - 11:44:09 CDT)
    - Re: Convert problem Mike McCallum (Wed Apr 29 2020 - 22:47:43 CDT)
mapping values on protein structure Aiswarya Pawar (Fri Apr 24 2020 - 00:44:24 CDT)
- Re: mapping values on protein structure Ashar Malik (Fri Apr 24 2020 - 01:51:44 CDT)
  - Re: mapping values on protein structure Aiswarya Pawar (Fri Apr 24 2020 - 02:47:37 CDT)
    - Re: mapping values on protein structure Josh Vermaas (Fri Apr 24 2020 - 08:37:53 CDT)
  - Re: mapping values on protein structure Aiswarya Pawar (Fri Apr 24 2020 - 11:23:53 CDT)
    - Re: mapping values on protein structure Ashar Malik (Fri Apr 24 2020 - 11:49:33 CDT)
Re: Calculating Bias for Well-tempered metadynamics Giacomo Fiorin (Thu Apr 23 2020 - 19:00:11 CDT)
- Re: Calculating Bias for Well-tempered metadynamics Giacomo Fiorin (Fri Apr 24 2020 - 13:37:28 CDT)
- Re: Calculating Bias for Well-tempered metadynamics Giacomo Fiorin (Sat Apr 25 2020 - 19:51:01 CDT)
vmd 1.9.4 omid gh (Thu Apr 23 2020 - 12:10:59 CDT)
FFTK Characterising Distortions Daniel Fellner (Thu Apr 23 2020 - 02:32:58 CDT)
- Re: FFTK Characterising Distortions JC Gumbart (Thu Apr 23 2020 - 19:48:37 CDT)
Re: new cartoon representation resid selection Owen Vickery (Mon Apr 20 2020 - 05:08:47 CDT)
Assign active site Nada Afiva (Sun Apr 19 2020 - 16:50:17 CDT)
- Re: Assign active site Ashar Malik (Sun Apr 19 2020 - 17:20:40 CDT)
  - Re: Assign active site Nada Afiva (Sun Apr 19 2020 - 17:50:51 CDT)
label placement with smoothed trajectory Miro Astore (Sat Apr 18 2020 - 20:29:41 CDT)
Trouble in installing VMD Gardezi,Shahbaz (Fri Apr 17 2020 - 22:11:55 CDT)
- Re: Trouble in installing VMD John Stone (Fri Apr 17 2020 - 23:06:51 CDT)
Re: Early VMD 1.9.4 alpha builds for MacOS X Catalina (e.g., 10.15.4) John Stone (Fri Apr 17 2020 - 16:04:27 CDT)
- Re: Early VMD 1.9.4 alpha builds for MacOS X Catalina (e.g., 10.15.4) FX (Fri Apr 17 2020 - 17:42:29 CDT)
  - Re: Early VMD 1.9.4 alpha builds for MacOS X Catalina (e.g., 10.15.4) John Stone (Fri Apr 17 2020 - 22:23:30 CDT)
- Re: Early VMD 1.9.4 alpha builds for MacOS X Catalina (e.g., 10.15.4) John Stone (Sat Apr 25 2020 - 22:07:53 CDT)
  - Re: Early VMD 1.9.4 alpha builds for MacOS X Catalina (e.g., 10.15.4) FX (Sun Apr 26 2020 - 04:27:14 CDT)
- Re: Early VMD 1.9.4 alpha builds for MacOS X Catalina (e.g., 10.15.4) John Stone (Tue Apr 28 2020 - 11:29:38 CDT)
  - Re: Early VMD 1.9.4 alpha builds for MacOS X Catalina (e.g., 10.15.4) FX (Tue Apr 28 2020 - 13:18:37 CDT)
    - Re: Early VMD 1.9.4 alpha builds for MacOS X Catalina (e.g., 10.15.4) John Stone (Tue Apr 28 2020 - 13:25:08 CDT)
    - Re: Early VMD 1.9.4 alpha builds for MacOS X Catalina (e.g., 10.15.4) FX (Sun May 03 2020 - 07:16:23 CDT)
Early VMD 1.9.4 alpha builds for MacOS X Catalina (e.g., 10.15.4) John Stone (Fri Apr 17 2020 - 14:30:59 CDT)
- Re: Early VMD 1.9.4 alpha builds for MacOS X Catalina (e.g., 10.15.4) Mustafa Tekpinar (Sat Apr 25 2020 - 19:37:45 CDT)
  - Re: Early VMD 1.9.4 alpha builds for MacOS X Catalina (e.g., 10.15.4) John Stone (Sat Apr 25 2020 - 21:55:20 CDT)
Counting the number of ligand molecules around my protein Akash Pandya (Thu Apr 16 2020 - 07:17:02 CDT)
- Re: Counting the number of ligand molecules around my protein Adupa Vasista (Thu Apr 16 2020 - 08:24:27 CDT)
  - Re: Counting the number of ligand molecules around my protein Akash Pandya (Thu Apr 16 2020 - 09:22:00 CDT)
new cartoon representation resid selection Owen Vickery (Thu Apr 16 2020 - 05:04:27 CDT)
ATOM LPH Francesco Pietra (Tue Apr 14 2020 - 12:57:04 CDT)
- Fwd: ATOM LPH Francesco Pietra (Tue Apr 14 2020 - 14:48:26 CDT)
  - Fwd: ATOM LPH Francesco Pietra (Tue Apr 14 2020 - 14:52:10 CDT)
    - Fwd: ATOM LPH Francesco Pietra (Wed Apr 15 2020 - 05:10:09 CDT)
- Re: ATOM LPH Aleksei (Tue Apr 14 2020 - 15:19:45 CDT)
fftk dihedrals error Andrej Tekel (Sun Apr 12 2020 - 03:32:05 CDT)
- Re: fftk dihedrals error JC Gumbart (Sun Apr 12 2020 - 16:03:29 CDT)
  - Re: fftk dihedrals error JC Gumbart (Fri Apr 17 2020 - 18:03:45 CDT)
Setting graphical representations from the command line Ross Williams (Fri Apr 10 2020 - 14:36:07 CDT)
- Re: Setting graphical representations from the command line Josh Vermaas (Fri Apr 10 2020 - 15:19:21 CDT)
  - Re: Setting graphical representations from the command line Peter Freddolino (Fri Apr 10 2020 - 18:24:05 CDT)
compiling VMD with cuda from source Oleksii Zdorevskyi (Fri Apr 10 2020 - 10:28:57 CDT)
- Re: compiling VMD with cuda from source Josh Vermaas (Fri Apr 10 2020 - 11:21:31 CDT)
  - Re: compiling VMD with cuda from source Oleksii Zdorevskyi (Mon Apr 13 2020 - 04:28:00 CDT)
Re: namd-l: .coor and .vel output files not generated Josh Vermaas (Thu Apr 09 2020 - 22:04:49 CDT)
VMD Compatible with Windows with 64-bit OS? Alex Hummels (Thu Apr 09 2020 - 15:44:24 CDT)
- Re: VMD Compatible with Windows with 64-bit OS? John Stone (Thu Apr 09 2020 - 16:21:37 CDT)
- Re: VMD Compatible with Windows with 64-bit OS? Josh Vermaas (Thu Apr 09 2020 - 16:23:38 CDT)
- Re: VMD Compatible with Windows with 64-bit OS? ccbroomell_at_gmail.com (Thu Apr 09 2020 - 16:43:29 CDT)
Peptides with Linkage between N-Terminus and Side Chain Hendrik SchrÃ¶der (Tue Apr 07 2020 - 13:17:07 CDT)
- Re: Peptides with Linkage between N-Terminus and Side Chain Josh Vermaas (Tue Apr 07 2020 - 15:29:25 CDT)
  - Re: Peptides with Linkage between N-Terminus and Side Chain Josh Vermaas (Thu Apr 09 2020 - 17:04:14 CDT)
(no subject) Marcos Verissimo Alves (Mon Apr 06 2020 - 12:04:07 CDT)
Register some cell information in XYZ files FX (Mon Apr 06 2020 - 05:01:55 CDT)
- Re: Register some cell information in XYZ files Luthaf (Mon Apr 06 2020 - 09:37:45 CDT)
VMD Crash Czarny,Ryan (Fri Apr 03 2020 - 12:42:08 CDT)
Segfault in VMD 1.9.4a38 in DrawMolItem::draw_volume_isosurface_points FX (Fri Apr 03 2020 - 06:18:01 CDT)
- Re: Segfault in VMD 1.9.4a38 in DrawMolItem::draw_volume_isosurface_points John Stone (Fri Apr 03 2020 - 09:24:28 CDT)
  - Re: Segfault in VMD 1.9.4a38 in DrawMolItem::draw_volume_isosurface_points FX (Fri Apr 03 2020 - 10:26:17 CDT)
    - Re: Segfault in VMD 1.9.4a38 in DrawMolItem::draw_volume_isosurface_points John Stone (Fri Apr 03 2020 - 11:11:56 CDT)
Dangling Bonds Anthony Ruth (Thu Apr 02 2020 - 14:46:33 CDT)
- Re: Dangling Bonds Josh Vermaas (Thu Apr 02 2020 - 15:55:08 CDT)
  - Re: Dangling Bonds Anthony Ruth (Fri Apr 03 2020 - 10:29:06 CDT)
    - Re: Dangling Bonds John Stone (Fri Apr 03 2020 - 10:58:36 CDT)
MDFF chirality restrain error - measure imprp: empty atom index Indrajit Deb (Wed Apr 01 2020 - 15:41:49 CDT)
- Re: MDFF chirality restrain error - measure imprp: empty atom index Josh Vermaas (Wed Apr 01 2020 - 18:26:44 CDT)
  - Re: MDFF chirality restrain error - measure imprp: empty atom index Indrajit Deb (Wed Apr 01 2020 - 21:24:17 CDT)
    - Re: MDFF chirality restrain error - measure imprp: empty atom index Josh Vermaas (Mon Apr 06 2020 - 12:04:07 CDT)
Problem compiling VMD 1.9.3 on macOS Catalina 10.15.3 Neda Rafieiolhosseini (Wed Apr 01 2020 - 03:23:13 CDT)
- Re: Problem compiling VMD 1.9.3 on macOS Catalina 10.15.3 JC Gumbart (Wed Apr 01 2020 - 19:23:31 CDT)
  - Re: Problem compiling VMD 1.9.3 on macOS Catalina 10.15.3 Neda Rafieiolhosseini (Thu Apr 02 2020 - 03:35:16 CDT)
VMD Energy analysis surya narayanan (Tue Mar 31 2020 - 16:45:40 CDT)
Loading Chemical Component Dictionary File Crashes VMD Mortimer Hemmit (Mon Mar 30 2020 - 14:42:05 CDT)
- Re: Loading Chemical Component Dictionary File Crashes VMD John Stone (Wed Apr 01 2020 - 00:42:28 CDT)
Memory Pool Size - can I optimize this? Chris Broomell (Mon Mar 30 2020 - 10:55:08 CDT)
- Re: Memory Pool Size - can I optimize this? Axel Kohlmeyer (Mon Mar 30 2020 - 12:12:32 CDT)
  - Re: Memory Pool Size - can I optimize this? ccbroomell_at_gmail.com (Mon Mar 30 2020 - 12:31:27 CDT)
faced error in operating vmd Ram Krishna Adhikari (Fri Mar 27 2020 - 11:45:42 CDT)
- Re: faced error in operating vmd John Stone (Fri Mar 27 2020 - 11:56:58 CDT)
  - Re: faced error in operating vmd Ram Krishna Adhikari (Mon Apr 06 2020 - 10:36:17 CDT)
    - Re: faced error in operating vmd Josh Vermaas (Mon Apr 06 2020 - 12:00:22 CDT)
Lipids generated by VMD could not use "coordpdb" to read jiali wang (Thu Mar 26 2020 - 23:42:27 CDT)
- Re: Lipids generated by VMD could not use "coordpdb" to read JC Gumbart (Fri Mar 27 2020 - 17:17:58 CDT)
  - Re: Lipids generated by VMD could not use "coordpdb" to read JC Gumbart (Mon Mar 30 2020 - 12:48:52 CDT)
    - Re: Lipids generated by VMD could not use "coordpdb" to read jiali wang (Mon Mar 30 2020 - 14:40:04 CDT)
Visualizing coarse grained particles in VMD Borne, Vincent (Thu Mar 26 2020 - 12:07:21 CDT)
- Re: Visualizing coarse grained particles in VMD Josh Vermaas (Thu Mar 26 2020 - 19:00:48 CDT)
  - Re: Visualizing coarse grained particles in VMD John Stone (Fri Mar 27 2020 - 00:16:37 CDT)
rmsdtt 'batch mode' Philippe Bopp (Tue Mar 24 2020 - 08:14:22 CDT)
- Re: rmsdtt 'batch mode' Giacomo Fiorin (Tue Mar 24 2020 - 09:04:25 CDT)
  - Re: rmsdtt 'batch mode' Giacomo Fiorin (Tue Mar 24 2020 - 13:19:16 CDT)
CIF file reader FX (Sun Mar 22 2020 - 17:00:35 CDT)
- Re: CIF file reader Mortimer Hemmit (Mon Mar 23 2020 - 15:57:20 CDT)
  - FW: RE: Re: CIF file reader John Keller (Sun Mar 29 2020 - 02:55:42 CDT)
- Re: CIF file reader John Stone (Tue Mar 24 2020 - 11:06:27 CDT)
  - Re: CIF file reader FX (Sat Mar 28 2020 - 13:29:56 CDT)
Running Hydrogen Bonding Analysis with Script åˆ˜å®¸å®‡ (Sun Mar 22 2020 - 02:04:34 CDT)
- Re: Running Hydrogen Bonding Analysis with Script JÃ©rÃ´me HÃ©nin (Sun Mar 22 2020 - 08:06:47 CDT)
- Re: Running Hydrogen Bonding Analysis with Script åˆ˜å®¸å®‡ (Sun Mar 22 2020 - 16:53:21 CDT)
Pair interaction calculation is not supported in CUDA version Adupa Vasista (Sun Mar 15 2020 - 12:10:53 CDT)
- Re: namd-l: Pair interaction calculation is not supported in CUDA version Josh Vermaas (Sun Mar 15 2020 - 14:58:45 CDT)
  - Re: namd-l: Pair interaction calculation is not supported in CUDA version Adupa Vasista (Sun Mar 15 2020 - 23:48:52 CDT)
Recommended Hardware Morgan Hoffman (Sat Mar 14 2020 - 19:56:09 CDT)
- Re: Recommended Hardware Josh Vermaas (Sat Mar 14 2020 - 23:14:06 CDT)
- RE: Recommended Hardware Jason Hogrefe (Mon Mar 16 2020 - 11:52:08 CDT)
Saving visualization state coordinates Peter Mawanga (Fri Mar 13 2020 - 11:00:16 CDT)
- Re: Saving visualization state coordinates Josh Vermaas (Fri Mar 13 2020 - 15:06:39 CDT)
  - Re: Saving visualization state coordinates Peter Mawanga (Fri Mar 13 2020 - 16:43:38 CDT)
Re: Qwikmd for QMMM simulations Joao Ribeiro (Thu Mar 12 2020 - 15:33:17 CDT)
Re: Increasing cores in QwiKMD Joao Ribeiro (Thu Mar 12 2020 - 15:28:23 CDT)
KS UIUC isn't accessible in new Firefox viktor drobot (Thu Mar 12 2020 - 09:47:11 CDT)
- Re: KS UIUC isn't accessible in new Firefox John Stone (Thu Mar 12 2020 - 13:22:27 CDT)
Steered Molecular Dynamics for Metal-organic frameworks Achar, Sid (Mon Mar 09 2020 - 11:15:14 CDT)
Qwikmd for QMMM simulations jing liang (Mon Mar 09 2020 - 10:37:34 CDT)
Increasing cores in QwiKMD Naeem Mahmood Ashraf (Sun Mar 08 2020 - 06:22:04 CDT)
Re: reseting namd library and uploading new topology file Joao Ribeiro (Fri Mar 06 2020 - 11:00:48 CST)
reseting namd library and uploading new topology file soodabeh ghaffari (Thu Mar 05 2020 - 09:33:28 CST)
Angular energy term Paula Mihaljevic-Juric (Thu Mar 05 2020 - 08:06:15 CST)
- Re: Angular energy term Giacomo Fiorin (Thu Mar 05 2020 - 12:23:00 CST)
Cionize Plugin - Output Options? Michael Robinson (Tue Mar 03 2020 - 23:57:34 CST)
Rendering resolution Norouzi, Seyed (Mon Mar 02 2020 - 10:02:46 CST)
- Re: Rendering resolution Josh Vermaas (Mon Mar 02 2020 - 12:50:48 CST)
  - Re: Rendering resolution Giacomo Fiorin (Mon Mar 02 2020 - 13:34:42 CST)
Regarding adding extra strand in a beta barrel Shashank Ranjan Srivastava (Mon Mar 02 2020 - 03:59:13 CST)
Minmax command Yogesh Sharma (Sun Mar 01 2020 - 08:38:20 CST)
- Re: Minmax command Giacomo Fiorin (Sun Mar 01 2020 - 10:19:15 CST)
  - Re: Minmax command Bassam Haddad (Sun Mar 01 2020 - 12:09:38 CST)
MSMS in VMD Mandar Kulkarni (Fri Feb 28 2020 - 07:59:54 CST)
- Re: MSMS in VMD John Stone (Fri Feb 28 2020 - 09:58:08 CST)
  - Re: MSMS in VMD Mandar Kulkarni (Fri Feb 28 2020 - 10:02:45 CST)
How to increase the number of core Naeem Mahmood Ashraf (Tue Feb 25 2020 - 05:47:53 CST)
- Re: How to increase the number of core Adupa Vasista (Tue Feb 25 2020 - 23:28:13 CST)
- AW: How to increase the number of core Norman Geist (Wed Feb 26 2020 - 01:59:33 CST)
VMD doesn't handle AMBER Restart files correct viktor drobot (Sun Feb 23 2020 - 14:09:09 CST)
- Re: VMD doesn't handle AMBER Restart files correct Josh Vermaas (Sun Feb 23 2020 - 16:36:58 CST)
  - Re: VMD doesn't handle AMBER Restart files correct viktor drobot (Tue Mar 03 2020 - 02:28:39 CST)
  - Re: VMD doesn't handle AMBER Restart files correct viktor (Mon Oct 19 2020 - 16:02:03 CDT)
Build graphene sheets using VMD Amir Afshar (Thu Feb 20 2020 - 15:47:46 CST)
- Re: Build graphene sheets using VMD Axel Kohlmeyer (Thu Feb 20 2020 - 15:54:39 CST)
  - Re: Build graphene sheets using VMD Amir Afshar (Thu Feb 20 2020 - 16:12:17 CST)
    - Re: Build graphene sheets using VMD Axel Kohlmeyer (Thu Feb 20 2020 - 16:22:12 CST)
FFTK: What is the correct charge calculation setup for carbonyl compounds David SÃ¡ez (Wed Feb 19 2020 - 10:06:54 CST)
- Re: FFTK: What is the correct charge calculation setup for carbonyl compounds Giacomo Fiorin (Wed Feb 19 2020 - 10:47:26 CST)
  - Re: FFTK: What is the correct charge calculation setup for carbonyl compounds JC Gumbart (Thu Feb 20 2020 - 08:10:32 CST)
vmd on raspberry pi Joe Konecny (Wed Feb 19 2020 - 09:39:31 CST)
- Re: vmd on raspberry pi John Stone (Wed Feb 19 2020 - 13:00:49 CST)
  - Re: vmd on raspberry pi Joe Konecny (Wed Feb 19 2020 - 14:06:27 CST)
  - Re: vmd on raspberry pi Joe Konecny (Thu Feb 20 2020 - 13:13:47 CST)
atomselect moveby: non-numeric in vector Adupa Vasista (Tue Feb 18 2020 - 09:32:22 CST)
- RE: atomselect moveby: non-numeric in vector Joaquim Rui de Castro Rodrigues (Tue Feb 18 2020 - 10:46:13 CST)
  - Re: atomselect moveby: non-numeric in vector Adupa Vasista (Tue Feb 18 2020 - 10:59:21 CST)
    - Re: [EXT] Re: atomselect moveby: non-numeric in vector Goedde, Chris (Tue Feb 18 2020 - 11:28:35 CST)
    - Re: [EXT] Re: atomselect moveby: non-numeric in vector Adupa Vasista (Tue Feb 18 2020 - 11:29:49 CST)
- Re: atomselect moveby: non-numeric in vector JÃ©rÃ´me HÃ©nin (Tue Feb 18 2020 - 11:34:37 CST)
  - Re: atomselect moveby: non-numeric in vector Adupa Vasista (Tue Feb 18 2020 - 11:43:16 CST)
SDS molecules agglomeration. Mikhail Suyetin (Tue Feb 18 2020 - 03:02:38 CST)
- Re: SDS molecules agglomeration. Josh Vermaas (Tue Feb 18 2020 - 08:59:16 CST)
  - Re: SDS molecules agglomeration. Ashar Malik (Tue Feb 18 2020 - 11:21:52 CST)
Keeping molecules intact when unwrapping Minjung Godfrey (Sat Feb 15 2020 - 17:39:49 CST)
- Re: Keeping molecules intact when unwrapping Giacomo Fiorin (Sun Feb 16 2020 - 12:30:19 CST)
  - Re: Keeping molecules intact when unwrapping Axel Kohlmeyer (Sun Feb 16 2020 - 17:37:22 CST)
    - Re: Keeping molecules intact when unwrapping JÃ©rÃ´me HÃ©nin (Tue Feb 18 2020 - 11:23:08 CST)
Check and remove the overlapping between atoms Amir Afshar (Sat Feb 15 2020 - 10:26:43 CST)
- Re: Check and remove the overlapping between atoms Giacomo Fiorin (Sat Feb 15 2020 - 11:14:47 CST)
  - Re: Check and remove the overlapping between atoms Amir Afshar (Sat Feb 15 2020 - 13:31:55 CST)
    - Re: Check and remove the overlapping between atoms Giacomo Fiorin (Sat Feb 15 2020 - 14:57:49 CST)
- Re: Check and remove the overlapping between atoms Axel Kohlmeyer (Sat Feb 15 2020 - 11:09:48 CST)
  - Re: Check and remove the overlapping between atoms Amir Afshar (Sat Feb 15 2020 - 15:18:32 CST)
  - Re: Check and remove the overlapping between atoms Amir Afshar (Sat Feb 15 2020 - 17:14:23 CST)
    - Re: Check and remove the overlapping between atoms Axel Kohlmeyer (Sun Feb 16 2020 - 17:47:25 CST)
VMD rendering colors Francesco Pietra (Thu Feb 13 2020 - 11:28:10 CST)
- Re: VMD rendering colors John Stone (Thu Feb 13 2020 - 12:13:49 CST)
  - Re: VMD rendering colors Francesco Pietra (Fri Feb 14 2020 - 11:30:02 CST)
    - Re: VMD rendering colors Robin Betz (Fri Feb 14 2020 - 13:36:23 CST)
    - Re: VMD rendering colors Francesco Pietra (Sat Feb 15 2020 - 01:46:54 CST)
Visulizing subunits Francesco Pietra (Tue Feb 11 2020 - 09:11:47 CST)
- Fwd: Visulizing subunits Francesco Pietra (Tue Feb 11 2020 - 10:10:07 CST)
  - Re: Fwd: Visulizing subunits John Stone (Tue Feb 11 2020 - 10:41:58 CST)
voltool mask usage Matthieu (Fri Feb 07 2020 - 19:11:03 CST)
- Re: voltool mask usage Bassam Haddad (Sat Feb 08 2020 - 03:10:55 CST)
  - Re: voltool mask usage Matthieu (Sun Feb 09 2020 - 18:43:15 CST)
Showing TkConsole on VMD Startup David Nicholson (Fri Feb 07 2020 - 12:44:08 CST)
- Re: Showing TkConsole on VMD Startup John Stone (Fri Feb 07 2020 - 12:55:12 CST)
Generating Images for Several Structures Thyagarajan, Raghuram (Thu Feb 06 2020 - 14:08:34 CST)
- Re: Generating Images for Several Structures John Stone (Thu Feb 06 2020 - 20:20:54 CST)
atomselect: cannot parse selection text: Viviane CorrÃªa (Thu Feb 06 2020 - 11:13:25 CST)
- Re: atomselect: cannot parse selection text: John Stone (Thu Feb 06 2020 - 11:21:21 CST)
  - Re: atomselect: cannot parse selection text: Viviane CorrÃªa (Thu Feb 06 2020 - 11:31:06 CST)
Gaussian16 support issue of ffTK Gawtak Kim (Wed Feb 05 2020 - 01:31:49 CST)
- Re: Gaussian16 support issue of ffTK David SÃ¡ez (Wed Feb 05 2020 - 04:07:17 CST)
  - Re: Gaussian16 support issue of ffTK giuseppe_at_ks.uiuc.edu (Wed Feb 05 2020 - 10:09:08 CST)
Tk startup error in X forwarding George Mogami (Tue Feb 04 2020 - 19:44:13 CST)
- Re: Tk startup error in X forwarding John Stone (Wed Feb 05 2020 - 15:04:07 CST)
  - Re: Tk startup error in X forwarding George Mogami (Wed Feb 05 2020 - 23:00:10 CST)
    - Re: Tk startup error in X forwarding John Stone (Thu Feb 06 2020 - 10:28:29 CST)
Removing water molecules from nanotubes RAHUL SURESH (Mon Feb 03 2020 - 04:56:45 CST)
AutoPSF error vecsub Francesco Pietra (Sat Feb 01 2020 - 14:59:02 CST)
- Re: AutoPSF error vecsub Peter Freddolino (Sun Feb 02 2020 - 08:04:37 CST)
Moving a molecule, regarding RAHUL SURESH (Sat Feb 01 2020 - 09:28:53 CST)
compilation of vmd from source on armv8 RK3399 processor Joey Gehring (Fri Jan 31 2020 - 22:54:40 CST)
- Re: compilation of vmd from source on armv8 RK3399 processor Pawel Kedzierski (Sat Feb 01 2020 - 05:06:47 CST)
Re: question about an error in QuickMD Joao Ribeiro (Wed Jan 29 2020 - 15:38:58 CST)
- Re: question about an error in QuickMD Joao Ribeiro (Wed Jan 29 2020 - 15:54:30 CST)
  - Re: question about an error in QuickMD soodabeh ghaffari (Wed Jan 29 2020 - 16:05:13 CST)
    - Re: question about an error in QuickMD Joao Ribeiro (Wed Jan 29 2020 - 16:11:01 CST)
    - Re: question about an error in QuickMD soodabeh ghaffari (Wed Jan 29 2020 - 16:13:01 CST)
question about an error in QuickMD soodabeh ghaffari (Wed Jan 29 2020 - 15:23:20 CST)
radial atom distribution faride badalkhani (Mon Jan 27 2020 - 06:12:50 CST)
- RE: radial atom distribution James Kress (Mon Jan 27 2020 - 10:36:52 CST)
  - Re: radial atom distribution faride badalkhani (Mon Jan 27 2020 - 14:20:37 CST)
FFTK dihedral parametrization David SÃ¡ez (Fri Jan 24 2020 - 23:07:00 CST)
- Re: FFTK dihedral parametrization Gumbart, JC (Mon Jan 27 2020 - 19:52:53 CST)
  - Re: FFTK dihedral parametrization David SÃ¡ez (Wed Jan 29 2020 - 07:57:40 CST)
    - Re: FFTK dihedral parametrization Gumbart, JC (Wed Jan 29 2020 - 11:54:19 CST)
  - Re: FFTK dihedral parametrization Adupa Vasista (Wed Jan 29 2020 - 08:24:27 CST)
    - Re: FFTK dihedral parametrization David SÃ¡ez (Wed Jan 29 2020 - 08:58:11 CST)
    - Re: FFTK dihedral parametrization Adupa Vasista (Wed Jan 29 2020 - 09:34:57 CST)
Re: VMD 1.9.3 compiled from source does not work Oleksii Zdorevskyi (Fri Jan 24 2020 - 11:06:12 CST)
- Re: VMD 1.9.3 compiled from source does not work John Stone (Fri Jan 24 2020 - 22:56:16 CST)
replacing an existig residue with a novel residue LOKI LOKI (Fri Jan 24 2020 - 00:24:36 CST)
- Re: replacing an existig residue with a novel residue Peter Freddolino (Fri Jan 24 2020 - 07:28:40 CST)
could not read file no atoms found error Yogesh Sharma (Thu Jan 23 2020 - 02:56:10 CST)
- Re: could not read file no atoms found error Adupa Vasista (Thu Jan 23 2020 - 04:51:21 CST)
  - Re: could not read file no atoms found error RAHUL SURESH (Thu Jan 23 2020 - 05:17:37 CST)
- Re: could not read file no atoms found error Ashar Malik (Thu Jan 23 2020 - 05:13:57 CST)
writing psf file without any coordinates Miro Astore (Wed Jan 22 2020 - 19:19:44 CST)
- Re: writing psf file without any coordinates Axel Kohlmeyer (Wed Jan 22 2020 - 20:23:25 CST)
  - Re: writing psf file without any coordinates Miro Astore (Wed Jan 22 2020 - 21:14:10 CST)
VMD 1.9.3 compiled from source does not work Oleksii Zdorevskyi (Wed Jan 22 2020 - 15:24:58 CST)
stuttering movies with snapshot Sebastian Reiter (Wed Jan 22 2020 - 12:03:31 CST)
- Re: stuttering movies with snapshot John Stone (Wed Jan 22 2020 - 12:35:50 CST)
- Re: stuttering movies with snapshot Robin Betz (Wed Jan 22 2020 - 13:51:57 CST)
  - Re: stuttering movies with snapshot Sebastian Reiter (Thu Jan 23 2020 - 10:03:06 CST)
  - Re: stuttering movies with snapshot John Stone (Thu Jan 23 2020 - 10:50:08 CST)
NAMD and VMD Armv8-A Joey Gehring (Tue Jan 21 2020 - 20:24:12 CST)
- Re: NAMD and VMD Armv8-A John Stone (Wed Jan 22 2020 - 12:38:31 CST)
  - Re: NAMD and VMD Armv8-A Joey Gehring (Wed Jan 22 2020 - 13:45:43 CST)
Restrain a molecule in movie Saikat Pal (Mon Jan 20 2020 - 08:56:30 CST)
- Re: Restrain a molecule in movie Ashar Malik (Mon Jan 20 2020 - 09:42:10 CST)
save contact map residue-residue distance plot SHAHEE ISLAM (Mon Jan 20 2020 - 03:36:22 CST)
- Re: save contact map residue-residue distance plot Axel Kohlmeyer (Mon Jan 20 2020 - 08:28:11 CST)
  - Re: save contact map residue-residue distance plot SHAHEE ISLAM (Mon Jan 20 2020 - 23:38:19 CST)
    - Re: save contact map residue-residue distance plot Souvik Sinha (Tue Jan 21 2020 - 00:37:34 CST)
conversion of vmd generated (C36) bilayer to gromac format Yogesh Sharma (Sun Jan 19 2020 - 01:04:27 CST)
- Re: conversion of vmd generated (C36) bilayer to gromac format Miro Astore (Sun Jan 19 2020 - 16:35:54 CST)
orienting aquaporin in bilayer Yogesh Sharma (Sat Jan 18 2020 - 05:53:55 CST)
- Re: orienting aquaporin in bilayer Ashar Malik (Sat Jan 18 2020 - 08:37:54 CST)
Selection by Atom Number or Fragments Roshan Shrestha (Sat Jan 18 2020 - 02:55:47 CST)
- Re: Selection by Atom Number or Fragments John Stone (Wed Jan 22 2020 - 12:43:25 CST)
Workshop on Free Energy calculations in Muenster March 11-13 2020 Vlad Cojocaru (Fri Jan 17 2020 - 03:32:53 CST)
pore visualization in throughout trajectory Yogesh Sharma (Thu Jan 16 2020 - 12:43:46 CST)
settings for labels Francesco Pietra (Thu Jan 16 2020 - 09:41:16 CST)
Using namdEnergy from an external python script Ackad, Edward (Wed Jan 15 2020 - 13:23:09 CST)
- Re: Using namdEnergy from an external python script Adupa Vasista (Wed Jan 15 2020 - 23:08:49 CST)
- Re: Using namdEnergy from an external python script PaweÅ‚ KÄ™dzierski (Thu Jan 16 2020 - 03:36:20 CST)
  - Re: Using namdEnergy from an external python script Ackad, Edward (Thu Jan 16 2020 - 10:05:10 CST)
    - Re: Using namdEnergy from an external python script Brian Radak (Thu Jan 16 2020 - 12:25:37 CST)
adding modified residue into psf file from pdb Bennion, Brian (Mon Jan 13 2020 - 17:20:32 CST)
Unable to view protein as cartoon or trace or tube Igor Leontyev (Mon Jan 13 2020 - 03:18:45 CST)
- Re: Unable to view protein as cartoon or trace or tube jiali wang (Mon Jan 13 2020 - 17:31:33 CST)
How to take care of charges while attaching two monomers to form a polymer chain MUNUBARTHI KRANTHI KUMAR (Thu Jan 09 2020 - 05:10:08 CST)
- How to take care of charges while attaching two monomers to form a polymer chain MUNUBARTHI KRANTHI KUMAR (Sun Jan 12 2020 - 23:11:30 CST)
ignore gpu on startup Miro Astore (Thu Jan 09 2020 - 03:07:13 CST)
- Re: ignore gpu on startup John Stone (Thu Jan 09 2020 - 08:43:29 CST)
PBC wrap deleting PBC boundaries during wrapping Christian Seitz (Mon Jan 06 2020 - 18:37:42 CST)
- Re: PBC wrap deleting PBC boundaries during wrapping John Stone (Tue Jan 07 2020 - 14:27:38 CST)
  - Re: PBC wrap deleting PBC boundaries during wrapping Christian Seitz (Tue Jan 07 2020 - 17:37:24 CST)
    - Re: PBC wrap deleting PBC boundaries during wrapping Adupa Vasista (Wed Jan 08 2020 - 04:41:12 CST)
Re: Fwd: RMSD pluging error Joao Ribeiro (Mon Jan 06 2020 - 09:20:56 CST)
New OSX Requires 64-bit DMG Alex Saad-Falcon (Fri Jan 03 2020 - 11:42:11 CST)
- Re: New OSX Requires 64-bit DMG Gumbart, JC (Fri Jan 03 2020 - 16:02:44 CST)
SMD specifying atom selection surya narayanan chandrasekaran (Wed Jan 01 2020 - 22:57:48 CST)
- Re: SMD specifying atom selection John Stone (Tue Jan 07 2020 - 14:20:02 CST)
RMSD pluging error Francesco Pietra (Mon Dec 30 2019 - 10:16:46 CST)
- Fwd: RMSD pluging error Francesco Pietra (Mon Dec 30 2019 - 10:21:28 CST)
Wrong net charge after patch Reinke.Patrick_at_mh-hannover.de (Sat Dec 21 2019 - 12:26:37 CST)
Select Nucleic Acid sequence Dominique Mias-Lucquin (Fri Dec 20 2019 - 07:37:15 CST)
- Re: Select Nucleic Acid sequence John Stone (Tue Jan 07 2020 - 14:15:51 CST)
  - Re: Select Nucleic Acid sequence Dominique Mias-Lucquin (Thu Jan 09 2020 - 02:28:07 CST)
    - Re: Select Nucleic Acid sequence Ashar Malik (Thu Jan 09 2020 - 04:43:56 CST)
RMSD per residue vs RMSF Ashraya Ravikumar (Wed Dec 18 2019 - 12:34:19 CST)
- Re: RMSD per residue vs RMSF John Stone (Tue Jan 07 2020 - 14:34:51 CST)
amber generated netcdf trajectories Vlad Cojocaru (Wed Dec 18 2019 - 07:25:11 CST)
- Re: amber generated netcdf trajectories John Stone (Wed Dec 18 2019 - 10:19:26 CST)
  - Re: amber generated netcdf trajectories Vlad Cojocaru (Thu Dec 19 2019 - 03:46:08 CST)
Installing VMD 1.9.3 on Linux - Missing Console Travis Meyer (Tue Dec 17 2019 - 15:25:27 CST)
- Re: Installing VMD 1.9.3 on Linux - Missing Console Dallas Warren (Tue Dec 17 2019 - 16:50:34 CST)
vmd draw material affects previous drawings Norouzi, Seyed (Mon Dec 16 2019 - 12:59:28 CST)
- Re: vmd draw material affects previous drawings Axel Kohlmeyer (Mon Dec 16 2019 - 13:50:25 CST)
  - Re: vmd draw material affects previous drawings Norouzi, Seyed (Mon Dec 16 2019 - 14:25:58 CST)
Re: Charm++ fatal error: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CG321 NG301 (ATOMS 6407 6408) .. ERROR) Error connecting to localhost on port 3000 Joao Ribeiro (Mon Dec 16 2019 - 09:26:08 CST)
Charm++ fatal error: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CG321 NG301 (ATOMS 6407 6408) .. ERROR) Error connecting to localhost on port 3000 Mubarak Alamri (Sat Dec 14 2019 - 18:30:51 CST)
VMD 1.9.3 Linux installation Chang, Christopher (Fri Dec 13 2019 - 18:27:05 CST)
- Re: VMD 1.9.3 Linux installation John Stone (Tue Jan 07 2020 - 14:50:52 CST)
  - Re: VMD 1.9.3 Linux installation John Stone (Tue Jan 07 2020 - 15:21:49 CST)
Two questions regarding VMD 1.9.3 Windows NetCDF plugin Li, Zhen (Fri Dec 13 2019 - 16:17:30 CST)
- Re: Two questions regarding VMD 1.9.3 Windows NetCDF plugin John Stone (Tue Jan 07 2020 - 14:53:13 CST)
Re: Running RMSF script on compute canada Joao Ribeiro (Thu Dec 12 2019 - 16:18:58 CST)
- RE: Running RMSF script on compute canada crockett c.h. (chc2g16) (Thu Dec 12 2019 - 20:09:49 CST)
  - RE: Running RMSF script on compute canada Vermaas, Joshua (Fri Dec 13 2019 - 11:00:44 CST)
- Re: Running RMSF script on compute canada Vermaas, Joshua (Fri Dec 13 2019 - 12:34:23 CST)
Running RMSF script on compute canada crockett c.h. (chc2g16) (Thu Dec 12 2019 - 12:43:26 CST)
Name / permissions of Optix Diskcache Stefan Boresch (Wed Dec 11 2019 - 01:59:17 CST)
- Re: Name / permissions of Optix Diskcache John Stone (Wed Dec 11 2019 - 08:22:01 CST)
  - Re: Name / permissions of Optix Diskcache Stefan Boresch (Thu Dec 12 2019 - 06:37:29 CST)
    - Re: Name / permissions of Optix Diskcache John Stone (Thu Dec 12 2019 - 09:04:06 CST)
Using RMSD for individual residues script (as seen in the NAMD tutorial) and bigdcd crockett c.h. (chc2g16) (Mon Dec 09 2019 - 17:28:46 CST)
- Re: Using RMSD for individual residues script (as seen in the NAMD tutorial) and bigdcd Ashar Malik (Mon Dec 09 2019 - 21:43:23 CST)
problem with installing OPTIX ray tracing giulia palermo (Mon Dec 09 2019 - 16:33:18 CST)
- Re: problem with installing OPTIX ray tracing Giacomo Fiorin (Tue Dec 10 2019 - 08:35:12 CST)
  - Re: problem with installing OPTIX ray tracing John Stone (Wed Dec 11 2019 - 08:28:34 CST)
OPTIX ray tracing option not showing up YOGESH NARKHEDE (Fri Dec 06 2019 - 13:55:37 CST)
- RE: OPTIX ray tracing option not showing up Vermaas, Joshua (Fri Dec 06 2019 - 17:57:25 CST)
  - Re: OPTIX ray tracing option not showing up YOGESH NARKHEDE (Fri Dec 06 2019 - 20:26:01 CST)
    - Re: OPTIX ray tracing option not showing up John Stone (Sat Dec 07 2019 - 10:53:26 CST)
Files not written during OptiX ray tracing Bart Bruininks (Thu Dec 05 2019 - 10:56:54 CST)
- Re: Files not written during OptiX ray tracing Dallas Warren (Thu Dec 05 2019 - 19:02:31 CST)
- Re: Files not written during OptiX ray tracing John Stone (Fri Dec 13 2019 - 00:53:31 CST)
  - Re: Files not written during OptiX ray tracing Bart Bruininks (Fri Dec 13 2019 - 05:01:18 CST)
    - Re: Files not written during OptiX ray tracing John Stone (Tue Jan 07 2020 - 14:54:46 CST)
Loading large trajectories using multiple threads/direct calls? Bart Bruininks (Thu Dec 05 2019 - 05:54:10 CST)
- Re: Loading large trajectories using multiple threads/direct calls? John Stone (Thu Dec 05 2019 - 10:07:50 CST)
  - Re: Loading large trajectories using multiple threads/direct calls? Bart Bruininks (Thu Dec 05 2019 - 11:00:50 CST)
    - Re: Loading large trajectories using multiple threads/direct calls? John Stone (Thu Dec 05 2019 - 12:41:06 CST)
    - Re: Loading large trajectories using multiple threads/direct calls? Bart Bruininks (Thu Dec 05 2019 - 17:06:26 CST)
  - RE: Loading large trajectories using multiple threads/direct calls? Vermaas, Joshua (Thu Dec 05 2019 - 12:12:45 CST)
VMD 1.9.4a38 build for macOS Catalina FX (Thu Dec 05 2019 - 04:46:46 CST)
- Re: VMD 1.9.4a38 build for macOS Catalina FX (Thu Dec 05 2019 - 07:58:46 CST)
- Re: VMD 1.9.4a38 build for macOS Catalina FX (Sat Dec 07 2019 - 07:32:21 CST)
Cross correlation Paula Mihaljevic-Juric (Tue Dec 03 2019 - 08:17:02 CST)
- RE: Cross correlation Vermaas, Joshua (Tue Dec 03 2019 - 11:12:45 CST)
  - Re: Cross correlation John Stone (Thu Dec 05 2019 - 16:44:33 CST)
Using bigdcd and .tcl scripts crockett c.h. (chc2g16) (Wed Nov 27 2019 - 09:23:39 CST)
- RE: Using bigdcd and .tcl scripts Vermaas, Joshua (Wed Nov 27 2019 - 17:19:17 CST)
Getting list of arguments for TCL console Edward Ditler (Tue Nov 26 2019 - 02:23:58 CST)
- Re: Getting list of arguments for TCL console Gianfranco Abrusci (Tue Nov 26 2019 - 04:20:29 CST)
- Re: Getting list of arguments for TCL console John Stone (Tue Nov 26 2019 - 10:33:10 CST)
  - Re: Getting list of arguments for TCL console Edward Ditler (Wed Nov 27 2019 - 05:22:16 CST)
    - Re: Getting list of arguments for TCL console John Stone (Wed Nov 27 2019 - 09:03:46 CST)
Dynamical network analysis-NetworkView-error Aliakbartehrani Zahra (Mon Nov 25 2019 - 04:56:22 CST)
how to get VMD plugins for 1.9.3 Brian Guthrie (Sun Nov 24 2019 - 22:06:40 CST)
- Re: how to get VMD plugins for 1.9.3 John Stone (Sun Nov 24 2019 - 22:43:51 CST)
Filetype for Kinetic Monte Carlo Anthony Ruth (Fri Nov 22 2019 - 09:07:31 CST)
- Re: Filetype for Kinetic Monte Carlo Axel Kohlmeyer (Fri Nov 22 2019 - 10:29:22 CST)
  - Re: Filetype for Kinetic Monte Carlo Giacomo Fiorin (Fri Nov 22 2019 - 11:05:51 CST)
    - Re: Filetype for Kinetic Monte Carlo Anthony Ruth (Mon Nov 25 2019 - 08:19:44 CST)
Overlap of volume maps in VMD Saumik Sen (Thu Nov 21 2019 - 05:39:16 CST)
- Re: Overlap of volume maps in VMD John Stone (Thu Nov 21 2019 - 09:27:22 CST)
  - Re: Overlap of volume maps in VMD Saumik Sen (Wed Nov 27 2019 - 14:45:34 CST)
Coarse grain modelling problem Hasan Mahmud (Tue Nov 19 2019 - 14:26:30 CST)
add new color index do VMD Nuno Cerqueira (Tue Nov 19 2019 - 10:54:52 CST)
- RE: add new color index do VMD Vermaas, Joshua (Wed Nov 20 2019 - 09:47:04 CST)
Protein is not read in VMD Normal Mode Wizard plugin Chetna Tyagi (Mon Nov 18 2019 - 07:53:02 CST)
Problem in rendering CG bonds with VMD leila karami (Tue Nov 12 2019 - 15:18:08 CST)
- RE: Problem in rendering CG bonds with VMD Vermaas, Joshua (Tue Nov 12 2019 - 18:01:55 CST)
VMD download page down davidiniming . (Mon Nov 11 2019 - 00:24:16 CST)
- Re: VMD download page down John Stone (Mon Nov 11 2019 - 09:27:19 CST)
volmap to find free volume MD Simulation (Fri Nov 08 2019 - 14:57:35 CST)
- Re: volmap to find free volume John Stone (Wed Nov 13 2019 - 00:22:54 CST)
specifying path of add on program Dhiraj Srivastava (Fri Nov 08 2019 - 14:57:07 CST)
Change color scale data range William Glass (Fri Nov 08 2019 - 04:32:03 CST)
- RE: Change color scale data range Vermaas, Joshua (Fri Nov 08 2019 - 10:51:39 CST)
Re: namd-l: flexible fitting for helical structure Giacomo Fiorin (Tue Nov 05 2019 - 20:09:25 CST)
Reg: RMSF Adupa Vasista (Tue Nov 05 2019 - 10:25:13 CST)
- Re: Reg: RMSF John Stone (Wed Nov 13 2019 - 00:33:24 CST)
  - Re: Reg: RMSF Adupa Vasista (Wed Nov 13 2019 - 02:40:29 CST)
Compilation and installation of VMD on Mac OS Catalina fabio trovato (Sun Nov 03 2019 - 05:36:37 CST)
Molecule occupies the lower-bottom corner of the main window fabio trovato (Sat Nov 02 2019 - 11:03:40 CDT)
- Re: Molecule occupies the lower-bottom corner of the main window John Stone (Wed Nov 13 2019 - 00:37:10 CST)
visualising the bonds which indicated by "connect" order in pdb files Hoda Shirzad (Sat Nov 02 2019 - 00:43:18 CDT)
- Re: visualising the bonds which indicated by "connect" order in pdb files John Stone (Wed Nov 13 2019 - 00:38:47 CST)
VMD for Mac stopped working after updating to Catalina fabio trovato (Fri Nov 01 2019 - 20:43:09 CDT)
- Re: [EXT] VMD for Mac stopped working after updating to Catalina Goedde, Chris (Mon Nov 04 2019 - 09:50:29 CST)
  - Re: [EXT] VMD for Mac stopped working after updating to Catalina John Stone (Wed Nov 06 2019 - 23:42:17 CST)
    - Re: [EXT] VMD for Mac stopped working after updating to Catalina fabio trovato (Thu Nov 07 2019 - 03:07:59 CST)
VMD 1.9.3 Only Loads 2 Plugins Mortimer Hemmit (Thu Oct 31 2019 - 19:23:04 CDT)
- Re: VMD 1.9.3 Only Loads 2 Plugins John Stone (Thu Oct 31 2019 - 20:48:13 CDT)
VMD for Catalina Krishna Suresh (Wed Oct 30 2019 - 17:35:22 CDT)
Query on preferred encoder/settings for producing MPEG files GRANT KENNY (Sun Oct 27 2019 - 10:00:27 CDT)
- Re: Query on preferred encoder/settings for producing MPEG files Nathan Kern (Sun Oct 27 2019 - 11:22:36 CDT)
  - RE: Query on preferred encoder/settings for producing MPEG files Vermaas, Joshua (Sun Oct 27 2019 - 13:35:12 CDT)
- Re: Query on preferred encoder/settings for producing MPEG files Dallas Warren (Mon Oct 28 2019 - 19:08:59 CDT)
catdcd Henrik Hariman (Thu Oct 24 2019 - 22:34:12 CDT)
Is it possible to use VMD to plot RDFs where the cell volume/parameter changes at each time step? Sarah Fowler (Wed Oct 23 2019 - 11:25:03 CDT)
- RE: Is it possible to use VMD to plot RDFs where the cell volume/parameter changes at each time step? Vermaas, Joshua (Wed Oct 23 2019 - 13:07:18 CDT)
  - RE: Is it possible to use VMD to plot RDFs where the cell volume/parameter changes at each time step? Vermaas, Joshua (Wed Oct 23 2019 - 14:35:24 CDT)
  - RE: Is it possible to use VMD to plot RDFs where the cell volume/parameter changes at each time step? Vermaas, Joshua (Wed Oct 23 2019 - 15:19:38 CDT)
- Re: Is it possible to use VMD to plot RDFs where the cell volume/parameter changes at each time step? Axel Kohlmeyer (Wed Oct 23 2019 - 15:49:48 CDT)
VMD RMSD Plot Selection ê¹€ë¯¼ìž¬ (Mon Oct 21 2019 - 10:53:46 CDT)
Unit for RMSD cut-off in clustering tool Neena Susan Eappen (Fri Oct 18 2019 - 10:53:58 CDT)
- RE: Unit for RMSD cut-off in clustering tool Vermaas, Joshua (Fri Oct 18 2019 - 14:05:12 CDT)
query on centering the pbc and cut the shell Santhosh Ranga (Thu Oct 17 2019 - 08:28:53 CDT)
Periodic image Samuel Canner (Wed Oct 16 2019 - 23:17:13 CDT)
- Re: Periodic image Axel Kohlmeyer (Thu Oct 17 2019 - 04:40:39 CDT)
SSrestraints Paula Mihaljevic-Juric (Wed Oct 16 2019 - 12:19:19 CDT)
- RE: SSrestraints Vermaas, Joshua (Wed Oct 16 2019 - 14:10:10 CDT)
regarding inner volume of a micelle Snehasis Chatterjee (Tue Oct 15 2019 - 15:38:28 CDT)
Joining fragments Raul Araya (Mon Oct 14 2019 - 07:51:30 CDT)
- RE: Joining fragments Vermaas, Joshua (Mon Oct 14 2019 - 09:26:56 CDT)
Create Straight Peptide Molefacture Protein Builder Mortimer Hemmit (Sat Oct 12 2019 - 16:31:04 CDT)
- Re: Create Straight Peptide Molefacture Protein Builder Miro Astore (Sat Oct 12 2019 - 17:14:12 CDT)
vmd 1.9.3 won't open in mac after catalina update this morning Evelyn Maizels (Tue Oct 08 2019 - 11:15:22 CDT)
- Re: vmd 1.9.3 won't open in mac after catalina update this morning Tru Huynh (Tue Oct 08 2019 - 13:28:58 CDT)
  - Re: vmd 1.9.3 won't open in mac after catalina update this morning John Stone (Mon Oct 14 2019 - 22:11:49 CDT)
splitting pdb Stefano Guglielmo (Tue Oct 08 2019 - 10:30:02 CDT)
- Re: splitting pdb Ashar Malik (Tue Oct 08 2019 - 23:20:52 CDT)
Transform structure to Bakary N'tji Diallo (Tue Oct 08 2019 - 01:20:35 CDT)
- RE: Transform structure to Vermaas, Joshua (Tue Oct 08 2019 - 11:29:15 CDT)
query on how to allow the protein to interact with the water molecules Santhosh Ranga (Sun Oct 06 2019 - 23:45:36 CDT)
- Re: query on how to allow the protein to interact with the water molecules Adupa Vasista (Mon Oct 07 2019 - 02:26:32 CDT)
  - RE: query on how to allow the protein to interact with the water molecules James Kress (Mon Oct 07 2019 - 10:06:23 CDT)
  - Re: query on how to allow the protein to interact with the water molecules Joao Ribeiro (Tue Oct 08 2019 - 09:01:51 CDT)
- Absolute scaling? "Scale to #" does this? Dallas Warren (Mon Oct 07 2019 - 15:28:34 CDT)
  - Re: Absolute scaling? "Scale to #" does this? Dallas Warren (Thu Oct 17 2019 - 04:12:08 CDT)
Question for Installing Plugin for VMD on Mac Oscar Bastidas (Sun Oct 06 2019 - 12:41:08 CDT)
- Re: [EXT] Question for Installing Plugin for VMD on Mac Goedde, Chris (Mon Oct 07 2019 - 10:07:46 CDT)
macOS Catalina Reza Esmaeeli (Sun Oct 06 2019 - 11:09:24 CDT)
- Re: macOS Catalina John Stone (Mon Oct 14 2019 - 22:16:56 CDT)
NAMD .coor file to pdb, WRITE PDB ERROR. Amir Suhail (Thu Oct 03 2019 - 05:27:35 CDT)
- RE: NAMD .coor file to pdb, WRITE PDB ERROR. Vermaas, Joshua (Thu Oct 03 2019 - 11:44:50 CDT)
  - RE: NAMD .coor file to pdb, WRITE PDB ERROR. Vermaas, Joshua (Wed Oct 09 2019 - 08:51:59 CDT)
solvate protein in triclinic box Amir Suhail (Wed Oct 02 2019 - 10:37:26 CDT)
lammps data file simulation box center and VMD origin Madhur Aggarwal (Wed Oct 02 2019 - 09:53:05 CDT)
- Re: lammps data file simulation box center and VMD origin Giacomo Fiorin (Wed Oct 02 2019 - 10:28:54 CDT)
- Re: lammps data file simulation box center and VMD origin Bassam Haddad (Wed Oct 02 2019 - 11:18:32 CDT)
  - Re: lammps data file simulation box center and VMD origin Madhur Aggarwal (Wed Oct 02 2019 - 12:51:54 CDT)
(no subject) anupama sharma (Wed Oct 02 2019 - 07:53:27 CDT)
- Re: Chitrak Gupta (Wed Oct 02 2019 - 09:24:07 CDT)
- Re: Giacomo Fiorin (Wed Oct 02 2019 - 09:26:45 CDT)
- RE: Vermaas, Joshua (Wed Oct 02 2019 - 09:43:30 CDT)
  - Re: John Stone (Wed Oct 02 2019 - 10:08:43 CDT)
GBIS parameters Paula Mihaljevic-Juric (Wed Oct 02 2019 - 07:24:17 CDT)
- Re: GBIS parameters John Stone (Wed Oct 02 2019 - 09:30:35 CDT)
network path analysis Naveen BK (Tue Oct 01 2019 - 04:52:52 CDT)
- Re: network path analysis Tamas Hegedus (Tue Oct 01 2019 - 12:10:48 CDT)
  - Re: network path analysis Naveen BK (Tue Oct 15 2019 - 00:17:56 CDT)
VMD on multi-projector digital planetarium dome Peter van Heusden (Mon Sep 30 2019 - 07:53:15 CDT)
MultiSeq: STAMP fails Aaron Oakley (Thu Sep 26 2019 - 20:40:31 CDT)
- RE: MultiSeq: STAMP fails Vermaas, Joshua (Fri Sep 27 2019 - 13:23:03 CDT)
Calculate CC in MDFF Mihaljevic-Juric Paula (Mme) (Wed Sep 25 2019 - 10:26:41 CDT)
- Re: Calculate CC in MDFF John Stone (Wed Sep 25 2019 - 10:34:27 CDT)
XenoView saved file (.car/.mdf file) Patrik MolnÃ¡r (Tue Sep 24 2019 - 10:49:39 CDT)
- Re: XenoView saved file (.car/.mdf file) Axel Kohlmeyer (Tue Sep 24 2019 - 11:20:18 CDT)
  - Re: XenoView saved file (.car/.mdf file) John Stone (Thu Sep 26 2019 - 13:48:38 CDT)
XenoView saved file (.car/.mdf file) Patrik MolnÃ¡r (Tue Sep 24 2019 - 01:11:46 CDT)
Decrease in CC during MDFF Paula Mihaljevic-Juric (Fri Sep 20 2019 - 04:45:38 CDT)
- Re: Decrease in CC during MDFF Ryan McGreevy (Fri Sep 20 2019 - 07:34:34 CDT)
AW: Re: namd-l: Is there someway to render protein picture without background color? Norman Geist (Thu Sep 19 2019 - 04:13:05 CDT)
- Re: Re: namd-l: Is there someway to render protein picture without background color? John Stone (Thu Sep 19 2019 - 10:13:52 CDT)
  - Re: Re: namd-l: Is there someway to render protein picture without background color? Geist, Norman (Thu Sep 26 2019 - 03:14:48 CDT)
    - Re: Re: namd-l: Is there someway to render protein picture without background color? John Stone (Thu Sep 26 2019 - 13:33:30 CDT)
colormaps available for color by volume Thomas Sommerfeld (Thu Sep 19 2019 - 09:26:14 CDT)
- Re: colormaps available for color by volume John Stone (Thu Sep 19 2019 - 09:37:44 CDT)
  - Re: colormaps available for color by volume John Stone (Fri Sep 20 2019 - 08:57:18 CDT)
    - Re: colormaps available for color by volume Thomas Sommerfeld (Fri Sep 20 2019 - 15:01:11 CDT)
Parameterization strategy with fragmentation in fftk Per Larsson (Thu Sep 19 2019 - 06:14:37 CDT)
- RE: Parameterization strategy with fragmentation in fftk Vermaas, Joshua (Thu Sep 19 2019 - 11:50:39 CDT)
  - Re: Parameterization strategy with fragmentation in fftk Per Larsson (Fri Sep 20 2019 - 04:31:50 CDT)
exporting 3D model of a volume-based colored mesh Walter Rocchia (Wed Sep 18 2019 - 16:10:18 CDT)
- RE: exporting 3D model of a volume-based colored mesh Luc Boisvert (Wed Sep 18 2019 - 17:36:22 CDT)
- RE: exporting 3D model of a volume-based colored mesh Luciano Abriata (Thu Sep 19 2019 - 02:37:07 CDT)
  - Re: exporting 3D model of a volume-based colored mesh Walter Rocchia (Thu Sep 19 2019 - 08:39:00 CDT)
  - Re: exporting 3D model of a volume-based colored mesh John Stone (Thu Sep 19 2019 - 10:43:17 CDT)
    - Re: exporting 3D model of a volume-based colored mesh John Stone (Thu Sep 19 2019 - 10:53:26 CDT)
- Re: exporting 3D model of a volume-based colored mesh John Stone (Thu Sep 19 2019 - 10:35:35 CDT)
  - Re: exporting 3D model of a volume-based colored mesh Walter Rocchia (Thu Sep 19 2019 - 10:42:44 CDT)
subopt/network analysis Tamas Hegedus (Tue Sep 17 2019 - 04:31:40 CDT)
correct "origin" in VMD Michael Morgan (Mon Sep 16 2019 - 16:44:47 CDT)
- RE: correct "origin" in VMD Vermaas, Joshua (Mon Sep 16 2019 - 18:17:44 CDT)
  - Re: correct "origin" in VMD John Stone (Mon Sep 16 2019 - 20:11:43 CDT)
VMD segmentation fault (core dumped) Kliuchnikov, Evgenii (Mon Sep 16 2019 - 12:53:42 CDT)
- Re: VMD segmentation fault (core dumped) Miro Astore (Mon Sep 16 2019 - 17:44:53 CDT)
  - RE: VMD segmentation fault (core dumped) Kliuchnikov, Evgenii (Mon Sep 16 2019 - 17:51:16 CDT)
For calculating the number of osmolytes molecules Ashma Khan (Mon Sep 16 2019 - 04:51:51 CDT)
- Re: For calculating the number of osmolytes molecules Ashma Khan (Mon Sep 16 2019 - 09:47:08 CDT)
  - Re: For calculating the number of osmolytes molecules Joao Ribeiro (Mon Sep 16 2019 - 09:35:59 CDT)
  - Re: For calculating the number of osmolytes molecules Gianfranco Abrusci (Mon Sep 16 2019 - 12:37:00 CDT)
VMD not reading plain mdcrd trajectories viktor drobot (Sun Sep 15 2019 - 08:43:38 CDT)
- VMD not reading plain mdcrd trajectories viktor drobot (Fri Sep 20 2019 - 09:41:40 CDT)
  - Re: VMD not reading plain mdcrd trajectories John Stone (Fri Sep 20 2019 - 09:50:02 CDT)
  - Re: VMD not reading plain mdcrd trajectories Axel Kohlmeyer (Fri Sep 20 2019 - 10:26:47 CDT)
    - Re: VMD not reading plain mdcrd trajectories viktor drobot (Fri Sep 20 2019 - 10:53:18 CDT)
Is there someway to render protein picture without background color? jiali wang (Sat Sep 14 2019 - 20:25:54 CDT)
- Re: namd-l: Is there someway to render protein picture without background color? Chitrak Gupta (Sat Sep 14 2019 - 20:52:08 CDT)
  - Re: Re: namd-l: Is there someway to render protein picture without background color? John Stone (Tue Sep 17 2019 - 16:11:48 CDT)
Change of colour for bond distance Suchetana Gupta (Fri Sep 13 2019 - 00:26:30 CDT)
- RE: Change of colour for bond distance Vermaas, Joshua (Fri Sep 13 2019 - 08:34:51 CDT)
  - Re: Change of colour for bond distance Suchetana Gupta (Fri Sep 13 2019 - 09:07:05 CDT)
Normal mode analysis Kliuchnikov, Evgenii (Thu Sep 12 2019 - 18:11:16 CDT)
generation of amber topology of Carbon nanotube Shilpa Gupta (Mon Sep 09 2019 - 07:08:58 CDT)
Errors in FFTK during bond opt using VMD 1.9.4a37 #YEO JINGJIE# (Mon Sep 09 2019 - 02:17:54 CDT)
- Re: Errors in FFTK during bond opt using VMD 1.9.4a37 mariano spivak (Mon Sep 09 2019 - 13:34:33 CDT)
  - Re: Errors in FFTK during bond opt using VMD 1.9.4a37 #YEO JINGJIE# (Mon Sep 09 2019 - 20:08:27 CDT)
perform hbond analysis in the terminal Saikat Pal (Sat Sep 07 2019 - 02:30:43 CDT)
Querying Residue Numbers that are Alphanumeric Wallace Chan (Fri Sep 06 2019 - 12:56:35 CDT)
Tcl foreach/for loop error Alex Hummels (Thu Sep 05 2019 - 16:28:51 CDT)
- Re: Tcl foreach/for loop error JÃ©rÃ´me HÃ©nin (Fri Sep 06 2019 - 04:34:26 CDT)
  - Re: Tcl foreach/for loop error Alex Hummels (Fri Sep 06 2019 - 07:23:54 CDT)
VMD 1.9.4 crash on MacOS Adam MatÄ›j (Thu Sep 05 2019 - 02:55:20 CDT)
planned support for Catalina? Gumbart, JC (Thu Aug 29 2019 - 14:53:05 CDT)
- Re: planned support for Catalina? John Stone (Thu Aug 29 2019 - 15:24:40 CDT)
  - Re: planned support for Catalina? Gumbart, JC (Thu Aug 29 2019 - 17:03:28 CDT)
    - Re: planned support for Catalina? John Stone (Thu Aug 29 2019 - 22:10:32 CDT)
<< Different values of RMSD >> I. Camps (Thu Aug 29 2019 - 12:39:09 CDT)
- RE: << Different values of RMSD >> Vermaas, Joshua (Thu Aug 29 2019 - 17:39:58 CDT)
  - RE: << Different values of RMSD >> Vermaas, Joshua (Thu Aug 29 2019 - 20:25:40 CDT)
    - Re: << Different values of RMSD >> I. Camps (Sat Aug 31 2019 - 21:32:53 CDT)
ssrestraints errors ridaka jannat (Wed Aug 28 2019 - 12:01:28 CDT)
- Re: ssrestraints errors Ryan McGreevy (Wed Aug 28 2019 - 12:50:35 CDT)
  - Re: ssrestraints errors ridaka jannat (Wed Aug 28 2019 - 12:56:51 CDT)
    - Re: ssrestraints errors Ryan McGreevy (Wed Aug 28 2019 - 13:18:08 CDT)
<< Loading trajectory file in Windows fails >> I. Camps (Wed Aug 28 2019 - 07:39:34 CDT)
- Re: << Loading trajectory file in Windows fails >> Axel Kohlmeyer (Wed Aug 28 2019 - 09:08:53 CDT)
- RE: << Loading trajectory file in Windows fails >> Vermaas, Joshua (Wed Aug 28 2019 - 10:09:27 CDT)
- Re: << Loading trajectory file in Windows fails >> I. Camps (Thu Aug 29 2019 - 12:40:22 CDT)
clustering tool is not working Saikat Pal (Tue Aug 27 2019 - 00:38:21 CDT)
Postdoctoral researcher position in computational virology. Juan R. Perilla (Mon Aug 26 2019 - 10:32:44 CDT)
Acetylation AutoPSF Reinke.Patrick_at_mh-hannover.de (Mon Aug 26 2019 - 10:13:01 CDT)
- Re: Acetylation AutoPSF Ernesto Aleksei Delgado Hurtado (Mon Aug 26 2019 - 17:54:26 CDT)
- Re: Acetylation AutoPSF Peter Freddolino (Mon Aug 26 2019 - 19:26:17 CDT)
Keeping Dotted Structure when Rendering using PovRay Nick Palmer (Fri Aug 23 2019 - 10:25:31 CDT)
How the suboptimal path length is computed in NetworkView plugin Yuchen Yuan (Tue Aug 20 2019 - 20:35:51 CDT)
Reduce size/number of nodes/image quality while rendering VRML 2.0 file Wei-Lan Lin (Tue Aug 20 2019 - 17:10:13 CDT)
NetCDF (Amber MMTK) plugin Weatherby,Gerard (Tue Aug 20 2019 - 12:41:34 CDT)
Mailing list for Postdoctoral opportunities in Simulations Peter Mawanga (Tue Aug 20 2019 - 01:24:38 CDT)
Re: Extract Most Frequently found structure Joao Ribeiro (Fri Aug 16 2019 - 08:11:56 CDT)
- Re: Extract Most Frequently found structure Neena Susan Eappen (Fri Aug 16 2019 - 11:42:32 CDT)
  - Re: Extract Most Frequently found structure Neena Susan Eappen (Fri Aug 23 2019 - 09:27:18 CDT)
    - RE: Extract Most Frequently found structure Vermaas, Joshua (Fri Aug 23 2019 - 10:39:59 CDT)
    - Re: Extract Most Frequently found structure Neena Susan Eappen (Fri Aug 23 2019 - 19:13:22 CDT)
Extract Most Frequently found structure Neena Susan Eappen (Thu Aug 15 2019 - 22:31:08 CDT)
Atoms on top of each in wrapped trajectory Alex Hummels (Thu Aug 15 2019 - 14:42:02 CDT)
- RE: Atoms on top of each in wrapped trajectory Vermaas, Joshua (Thu Aug 15 2019 - 15:56:09 CDT)
  - Re: Atoms on top of each in wrapped trajectory Alex Hummels (Thu Aug 15 2019 - 16:18:57 CDT)
- Re: Atoms on top of each in wrapped trajectory JÃ©rÃ´me HÃ©nin (Thu Aug 15 2019 - 16:06:53 CDT)
How the Within Command Works Alex Hummels (Thu Aug 08 2019 - 09:28:30 CDT)
- RE: How the Within Command Works Vermaas, Joshua (Thu Aug 08 2019 - 12:18:32 CDT)
- Re: How the Within Command Works Robin Betz (Thu Aug 08 2019 - 12:41:10 CDT)
Problem in Network analysis PRITI ROY (Sun Aug 04 2019 - 01:51:30 CDT)
wrapping with bigdcd Monika Kumari (Wed Jul 31 2019 - 00:22:34 CDT)
Bond Length and Bond Angle as a Function of Steps ehsan shahini (Tue Jul 30 2019 - 02:29:41 CDT)
Local isosurface JÃ©rÃ´me Claverie (Sat Jul 27 2019 - 13:02:14 CDT)
- Re: Local isosurface John Stone (Mon Jul 29 2019 - 13:38:13 CDT)
  - Re: Local isosurface Ryan McGreevy (Mon Jul 29 2019 - 14:34:30 CDT)
Scripting with volumes Bassam Haddad (Thu Jul 25 2019 - 16:45:32 CDT)
- Re: Scripting with volumes Giacomo Fiorin (Fri Jul 26 2019 - 07:08:42 CDT)
  - Re: Scripting with volumes Bassam Haddad (Fri Jul 26 2019 - 15:19:02 CDT)
Fwd: Charu Sharma (JRF) (Wed Jul 24 2019 - 03:03:06 CDT)
- Re: Fwd: Charu Sharma (JRF) (Wed Jul 24 2019 - 03:57:31 CDT)
  - Re: Fwd: John Stone (Wed Jul 24 2019 - 08:42:45 CDT)
    - Re: Fwd: Charu Sharma (JRF) (Wed Jul 24 2019 - 08:59:05 CDT)
    - Re: Fwd: John Stone (Mon Jul 29 2019 - 12:55:54 CDT)
sub : considering waters with in 5A of solute Lara rajam (Tue Jul 23 2019 - 10:10:42 CDT)
- Re: sub : considering waters with in 5A of solute Ashar Malik (Tue Jul 23 2019 - 15:30:18 CDT)
  - Re: sub : considering waters with in 5A of solute Lara rajam (Wed Jul 24 2019 - 11:16:03 CDT)
    - Re: sub : considering waters with in 5A of solute Axel Kohlmeyer (Wed Jul 24 2019 - 12:24:05 CDT)
Periodic boundary conditions for multimeric systems Maryam X (Mon Jul 22 2019 - 07:38:47 CDT)
- Re: Periodic boundary conditions for multimeric systems Philippe Bopp (Mon Jul 22 2019 - 10:47:24 CDT)
  - Re: Periodic boundary conditions for multimeric systems Maryam X (Tue Jul 23 2019 - 10:34:18 CDT)
- Re: Periodic boundary conditions for multimeric systems Axel Kohlmeyer (Mon Jul 22 2019 - 11:58:08 CDT)
followup: atomselect one liner Philippe Bopp (Sat Jul 20 2019 - 04:09:27 CDT)
- Re: followup: atomselect one liner Ashar Malik (Sat Jul 20 2019 - 05:15:51 CDT)
atomselect one liner Philippe Bopp (Sat Jul 20 2019 - 02:22:12 CDT)
- Re: atomselect one liner Axel Kohlmeyer (Sat Jul 20 2019 - 03:22:13 CDT)
Creation of Thin Amorphous SiO2 using Inorganic Builder-VMD Sina Zarepakzad (Fri Jul 19 2019 - 07:32:39 CDT)
Tcl Almira Ovagimyan (Thu Jul 18 2019 - 07:36:15 CDT)
- Re: Tcl Almira Ovagimyan (Fri Jul 19 2019 - 02:14:51 CDT)
  - Re: Re: Tcl John Stone (Tue Jul 23 2019 - 23:31:12 CDT)
VMD 1.9.4a31 segmentation fault on OpenSUSE 15.1 Steven Wang (Tue Jul 16 2019 - 14:43:55 CDT)
- Re: VMD 1.9.4a31 segmentation fault on OpenSUSE 15.1 John Stone (Tue Jul 16 2019 - 15:37:23 CDT)
Re: Generate QM Region Topology in QwikMD for metal ions to perform QM/MM Joao Ribeiro (Tue Jul 16 2019 - 09:29:31 CDT)
Generate QM Region Topology in QwikMD for metal ions to perform QM/MM Umut Gerlevik (Tue Jul 16 2019 - 05:56:15 CDT)
(no subject) Nirmitee Mulgaonkar (Sat Jul 13 2019 - 21:45:50 CDT)
- Re: Adupa Vasista (Sun Jul 14 2019 - 04:31:25 CDT)
Re: vmd moveby command inside loop Joao Ribeiro (Thu Jul 11 2019 - 09:23:32 CDT)
vmd moveby command inside loop surya narayanan chandrasekaran (Thu Jul 11 2019 - 05:36:07 CDT)
- Re: vmd moveby command inside loop Giacomo Fiorin (Thu Jul 11 2019 - 09:43:59 CDT)
  - Re: vmd moveby command inside loop surya narayanan chandrasekaran (Fri Jul 12 2019 - 01:35:08 CDT)
New version of Molefacture -small molecule modeling tool- posted Joao Ribeiro (Wed Jul 10 2019 - 16:59:50 CDT)
New VMD 1.9.4 test versions posted with many new updates/features... John Stone (Wed Jul 10 2019 - 15:29:12 CDT)
- Re: New VMD 1.9.4 test versions posted with many new updates/features... Dallas Warren (Sun Jul 14 2019 - 20:10:43 CDT)
Fwd: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT Adupa Vasista (Wed Jul 10 2019 - 10:32:16 CDT)
Re: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT Joao Ribeiro (Wed Jul 10 2019 - 09:49:09 CDT)
FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT é»„æ´‹ (Wed Jul 10 2019 - 09:03:44 CDT)
- Re: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT Aravinda Munasinghe (Wed Jul 10 2019 - 11:18:51 CDT)
Re: How to incorporate new probe molecules in DruGui? Joao Ribeiro (Tue Jul 09 2019 - 09:07:48 CDT)
How to incorporate new probe molecules in DruGui? Nirmitee Mulgaonkar (Sat Jul 06 2019 - 17:17:45 CDT)
AutoPSF charge generation Adupa Vasista (Sat Jul 06 2019 - 04:28:55 CDT)
- Re: AutoPSF charge generation Peter Freddolino (Sat Jul 06 2019 - 21:00:48 CDT)
Getting the topology,PSF files Adupa Vasista (Thu Jul 04 2019 - 14:54:25 CDT)
- Re: Getting the topology,PSF files Peter Freddolino (Thu Jul 04 2019 - 17:09:41 CDT)
  - Re: Getting the topology,PSF files Peter Freddolino (Fri Jul 05 2019 - 08:02:29 CDT)
    - Re: Getting the topology,PSF files Adupa Vasista (Fri Jul 05 2019 - 08:23:33 CDT)
    - Re: Getting the topology,PSF files Adupa Vasista (Sun Jul 07 2019 - 08:38:25 CDT)
Rotating a molecule to make it parallel to another bond Monika Madhavi (Wed Jul 03 2019 - 12:10:22 CDT)
- Re: Rotating a molecule to make it parallel to another bond Giacomo Fiorin (Wed Jul 03 2019 - 13:32:12 CDT)
Sub: making a trajectory with frames having different number of water molecules. Lara rajam (Mon Jul 01 2019 - 19:44:18 CDT)
- Re: Sub: making a trajectory with frames having different number of water molecules. John Stone (Mon Jul 08 2019 - 00:33:04 CDT)
using martini forcefields for DNA in NAMD Parth Chaturvedi (Mon Jul 01 2019 - 18:34:51 CDT)
failure of charge optimization by fftk WT Ren (Sun Jun 30 2019 - 09:42:13 CDT)
- Re: failure of charge optimization by fftk mariano spivak (Sun Jun 30 2019 - 11:01:20 CDT)
  - Re: failure of charge optimization by fftk WT Ren (Sun Jun 30 2019 - 20:58:24 CDT)
  - Re: failure of charge optimization by fftk mariano spivak (Tue Jul 09 2019 - 17:56:47 CDT)
    - Re: failure of charge optimization by fftk WT Ren (Thu Jul 11 2019 - 11:00:57 CDT)
Change Label Font Gajanan Kanagalingam (Sun Jun 30 2019 - 04:14:13 CDT)
- Re: Change Label Font John Stone (Mon Jul 08 2019 - 00:54:13 CDT)
Adaptive real time selection and coloring in default display Bart Bruininks (Thu Jun 27 2019 - 10:05:11 CDT)
- Re: Adaptive real time selection and coloring in default display Giacomo Fiorin (Thu Jun 27 2019 - 11:03:11 CDT)
- RE: Adaptive real time selection and coloring in default display Vermaas, Joshua (Thu Jun 27 2019 - 12:04:01 CDT)
  - RE: Adaptive real time selection and coloring in default display Vermaas, Joshua (Thu Jun 27 2019 - 17:54:01 CDT)
    - Re: Adaptive real time selection and coloring in default display John Stone (Fri Jun 28 2019 - 11:12:44 CDT)
Increasing the number of bonds per atom Wasim Abdul (Thu Jun 27 2019 - 06:54:17 CDT)
- Re: Increasing the number of bonds per atom Axel Kohlmeyer (Thu Jun 27 2019 - 07:31:22 CDT)
  - Re: Increasing the number of bonds per atom John Stone (Thu Jun 27 2019 - 09:09:23 CDT)
atoms within a radius cutoff and a percentage cutoff of a trajectory Amendra Fernando Hewa Dewage (Fri Jun 21 2019 - 15:27:01 CDT)
- Re: atoms within a radius cutoff and a percentage cutoff of a trajectory Aravinda Munasinghe (Sun Jun 23 2019 - 11:48:15 CDT)
Error compiling 1.9.3 with CUDA Weatherby,Gerard (Thu Jun 20 2019 - 12:54:53 CDT)
- RE: Error compiling 1.9.3 with CUDA Vermaas, Joshua (Thu Jun 20 2019 - 14:40:07 CDT)
  - Re: Error compiling 1.9.3 with CUDA Weatherby,Gerard (Thu Jun 20 2019 - 15:18:43 CDT)
    - RE: Error compiling 1.9.3 with CUDA Vermaas, Joshua (Thu Jun 20 2019 - 17:21:51 CDT)
Immediate postdoc opening in Bio-molecular simulation, University of Alberta, Canada Marawan Hussien (Wed Jun 19 2019 - 19:16:26 CDT)
NAMD Developer Meeting 2019 giuseppe_at_ks.uiuc.edu (Wed Jun 19 2019 - 16:59:58 CDT)
- Reminder NAMD Developer Meeting 2019 giuseppe_at_ks.uiuc.edu (Tue Jul 09 2019 - 10:55:30 CDT)
basal spacing Hasnain Shabbir (Wed Jun 19 2019 - 13:25:20 CDT)
Re: Error during minimizazion - Number of atoms in fixed atoms PDB... Joao Ribeiro (Tue Jun 18 2019 - 09:38:50 CDT)
Error during minimizazion - Number of atoms in fixed atoms PDB... Alessandro Ruda (Mon Jun 17 2019 - 17:12:26 CDT)
How to get box information from file.dcd. Parviz Seifpanahi Shabane (Mon Jun 17 2019 - 14:16:45 CDT)
- Re: How to get box information from file.dcd. John Stone (Mon Jun 17 2019 - 16:36:15 CDT)
Merging two proteins John H (Mon Jun 17 2019 - 10:56:24 CDT)
- Re: Merging two proteins Bassam Haddad (Mon Jun 17 2019 - 15:50:19 CDT)
  - Re: Merging two proteins John Stone (Mon Jun 17 2019 - 15:57:21 CDT)
    - Re: Merging two proteins John H (Mon Jun 17 2019 - 16:38:06 CDT)
How to calculate water density. Parviz Seifpanahi Shabane (Mon Jun 17 2019 - 09:34:57 CDT)
- Re: How to calculate water density. Bennion, Brian (Mon Jun 17 2019 - 10:44:55 CDT)
  - Re: How to calculate water density. Bennion, Brian (Mon Jun 17 2019 - 14:38:04 CDT)
catdcd error Roshan Shrestha (Sat Jun 15 2019 - 04:02:46 CDT)
- Re: catdcd error Ashar Malik (Sat Jun 15 2019 - 17:05:15 CDT)
reg: PHI HEOM tool surya narayanan chandrasekaran (Tue Jun 11 2019 - 05:12:30 CDT)
Visualization State Issue With Secondary Structure Elizabeth Wait (Thu Jun 06 2019 - 15:46:40 CDT)
- RE: Visualization State Issue With Secondary Structure Vermaas, Joshua (Thu Jun 06 2019 - 17:33:14 CDT)
  - Re: Visualization State Issue With Secondary Structure John Stone (Thu Jun 06 2019 - 22:45:26 CDT)
    - Re: Visualization State Issue With Secondary Structure Elizabeth Wait (Tue Jun 11 2019 - 11:16:04 CDT)
Re: namd-l: vecsub:two vectors don't have the same size Joao Ribeiro (Thu Jun 06 2019 - 09:21:58 CDT)
VMD on Mac OS Catalina (10.15 beta): Bad CPU type in executable Tai Bui (Thu Jun 06 2019 - 08:17:58 CDT)
Request for help in command line in VMD priyaranjini ranju (Thu Jun 06 2019 - 04:30:37 CDT)
SASA calculation for sidechains of my peptide residues Daeun Noh (Wed Jun 05 2019 - 17:44:20 CDT)
- RE: SASA calculation for sidechains of my peptide residues Vermaas, Joshua (Thu Jun 06 2019 - 11:05:15 CDT)
  - Re: SASA calculation for sidechains of my peptide residues Daeun Noh (Thu Jun 06 2019 - 15:42:13 CDT)
User-defined coloring Mustafa Tekpinar (Wed Jun 05 2019 - 10:55:24 CDT)
- Re: User-defined coloring Bassam Haddad (Thu Jun 06 2019 - 15:41:21 CDT)
Problem with visualization of structure in amber coordinate format sunyeping (Mon Jun 03 2019 - 23:32:30 CDT)
VMD alpha builds JÃ©rÃ´me HÃ©nin (Mon Jun 03 2019 - 09:01:03 CDT)
- Re: VMD alpha builds John Stone (Mon Jun 03 2019 - 23:12:21 CDT)
how to draw boxes with semi-transparent sides Abolfazl Musavi (Sat Jun 01 2019 - 21:58:10 CDT)
- Re: how to draw boxes with semi-transparent sides Dallas Warren (Sun Jun 02 2019 - 17:57:21 CDT)
  - Re: how to draw boxes with semi-transparent sides Abolfazl Musavi (Sun Jun 02 2019 - 18:47:26 CDT)
- Re: how to draw boxes with semi-transparent sides Strahs, Dr. Daniel Bernard (Sun Jun 02 2019 - 19:13:53 CDT)
- Re: how to draw boxes with semi-transparent sides Axel Kohlmeyer (Sun Jun 02 2019 - 20:21:05 CDT)
  - Re: how to draw boxes with semi-transparent sides Abolfazl Musavi (Wed Jun 05 2019 - 11:46:01 CDT)
Problem While Visualising the Trajectory File from LAMMPS Simulation LIGESH B (Sat Jun 01 2019 - 06:38:18 CDT)
- Re: Problem While Visualising the Trajectory File from LAMMPS Simulation Giacomo Fiorin (Sat Jun 01 2019 - 18:28:42 CDT)
  - Re: Problem While Visualising the Trajectory File from LAMMPS Simulation LIGESH B (Sun Jun 02 2019 - 23:36:37 CDT)
parameter file for dUTP sunyeping (Thu May 30 2019 - 08:03:03 CDT)
PDB manipulation options Roshan Shrestha (Wed May 29 2019 - 12:41:37 CDT)
- Re: PDB manipulation options Peter Freddolino (Wed May 29 2019 - 14:12:16 CDT)
Re: Re: psfgen problems of many segment complex Joao Ribeiro (Tue May 28 2019 - 08:45:26 CDT)
- Re: Re: psfgen problems of many segment complex Takeru KAMEDA (Tue May 28 2019 - 09:16:46 CDT)
- Re: Re: psfgen problems of many segment complex Takeru KAMEDA (Tue May 28 2019 - 09:51:24 CDT)
Get number of fragments MD Simulation (Mon May 27 2019 - 05:57:25 CDT)
- Re: Get number of fragments Ashar Malik (Mon May 27 2019 - 09:48:23 CDT)
- Re: Get number of fragments Giacomo Fiorin (Mon May 27 2019 - 10:05:02 CDT)
Check if the lysine residues are deprotonated or not inside the membrane ? Roshan Shrestha (Fri May 24 2019 - 08:55:40 CDT)
VMD installation Saikat Pal (Fri May 24 2019 - 06:55:34 CDT)
psfgen problems of many segment complex Takeru KAMEDA (Fri May 24 2019 - 00:57:38 CDT)
- Re: psfgen problems of many segment complex Peter Freddolino (Fri May 24 2019 - 07:22:38 CDT)
- RE: psfgen problems of many segment complex Vermaas, Joshua (Fri May 24 2019 - 07:52:55 CDT)
  - Re: psfgen problems of many segment complex Takeru KAMEDA (Fri May 24 2019 - 10:14:43 CDT)
Cionize plugin Paula Mihaljevic-Juric (Tue May 21 2019 - 09:46:53 CDT)
CG Martini File for Cholesterol Alexander Adams (Mon May 20 2019 - 10:45:50 CDT)
- Re: CG Martini File for Cholesterol Fotis Baltoumas (Mon May 20 2019 - 11:07:44 CDT)
volutil option xiaoyu qing (Sun May 19 2019 - 03:46:15 CDT)
- Re: volutil option Ryan McGreevy (Mon May 20 2019 - 08:36:26 CDT)
regarding cionize san kumar (Fri May 17 2019 - 09:56:50 CDT)
- Re: regarding cionize Peter Freddolino (Fri May 17 2019 - 12:01:23 CDT)
  - Re: regarding cionize xiaoyu qing (Sun May 19 2019 - 03:30:07 CDT)
Tachyon-OptiX Rendering User Defined Clipping Planes? Dallas Warren (Wed May 15 2019 - 18:22:26 CDT)
Partial rendering of periodic cells` Nick Palmer (Wed May 15 2019 - 16:14:07 CDT)
- RE: Partial rendering of periodic cells` Vermaas, Joshua (Wed May 15 2019 - 17:17:20 CDT)
- Re: Partial rendering of periodic cells` Dallas Warren (Wed May 15 2019 - 18:23:57 CDT)
Alpha to beta conversion Kalyanashis Jana (Wed May 15 2019 - 04:17:08 CDT)
- Re: Alpha to beta conversion Giacomo Fiorin (Wed May 15 2019 - 08:45:46 CDT)
Defining a layer for a micelle Nick Palmer (Mon May 13 2019 - 11:26:22 CDT)
- Re: Defining a layer for a micelle Alec Zander (Mon May 13 2019 - 12:12:42 CDT)
  - RE: Defining a layer for a micelle Vermaas, Joshua (Mon May 13 2019 - 13:35:32 CDT)
- AW: Defining a layer for a micelle Norman Geist (Tue May 14 2019 - 01:17:08 CDT)
- Re: Defining a layer for a micelle Nick Palmer (Wed May 15 2019 - 11:08:33 CDT)
  - RE: Re: Defining a layer for a micelle Vermaas, Joshua (Wed May 15 2019 - 12:12:22 CDT)
VMD process Windows Endri Kastrati (Fri May 10 2019 - 00:01:22 CDT)
How to add ions to a system with non-water solvents sting (Thu May 09 2019 - 21:22:55 CDT)
- Re: How to add ions to a system with non-water solvents McGuire, Kelly (Thu May 09 2019 - 23:44:19 CDT)
  - Re:Re: How to add ions to a system with non-water solvents sting (Mon May 13 2019 - 07:37:46 CDT)
measure rmsd with non-serial atom ordering between two selections Patrick Charchar (Tue May 07 2019 - 17:54:41 CDT)
- RE: measure rmsd with non-serial atom ordering between two selections Vermaas, Joshua (Tue May 07 2019 - 19:11:08 CDT)
  - RE: measure rmsd with non-serial atom ordering between two selections Vermaas, Joshua (Tue May 07 2019 - 19:17:57 CDT)
    - RE: measure rmsd with non-serial atom ordering between two selections Patrick Charchar (Tue May 07 2019 - 20:16:32 CDT)
Issues with Tcl script for MD Prep Matt Veter (Tue May 07 2019 - 13:28:49 CDT)
- Re: Issues with Tcl script for MD Prep Bassam Haddad (Tue May 28 2019 - 14:29:05 CDT)
  - Re: Issues with Tcl script for MD Prep Roessler, Bryan C (Wed Jun 19 2019 - 14:19:03 CDT)
    - Re: Issues with Tcl script for MD Prep John Stone (Wed Jun 19 2019 - 16:42:06 CDT)
Find Hydrogens not participating in H-bond Neena Susan Eappen (Wed May 01 2019 - 17:11:11 CDT)
Amide peptide capping group lost in VMD Neena Susan Eappen (Wed May 01 2019 - 16:54:29 CDT)
- Re: Amide peptide capping group lost in VMD Neena Susan Eappen (Sat May 11 2019 - 09:05:49 CDT)
Autopsfgen verbose error output? Francesco Pietra (Wed May 01 2019 - 13:24:31 CDT)
- Re: Autopsfgen verbose error output? Peter Freddolino (Wed May 01 2019 - 14:54:52 CDT)
  - Re: Autopsfgen verbose error output? Francesco Pietra (Wed May 01 2019 - 16:56:22 CDT)
    - Re: Autopsfgen verbose error output? Peter Freddolino (Wed May 01 2019 - 21:26:03 CDT)
regarding capsid inner volume san kumar (Tue Apr 30 2019 - 16:24:23 CDT)
MD Simulations with GROMACS/NAMD/AMBER/VMD: Seasonal School in Stockholm 10-13 June Joao Ribeiro (Tue Apr 30 2019 - 09:43:46 CDT)
(no subject) Steven De Volder (Mon Apr 29 2019 - 08:57:40 CDT)
- RE: Vermaas, Joshua (Mon Apr 29 2019 - 11:15:05 CDT)
- Re: JÃ©rÃ´me HÃ©nin (Mon Apr 29 2019 - 11:15:44 CDT)
Some bugs and questions about the 1.9.4a29 version Bart Bruininks (Mon Apr 29 2019 - 03:57:59 CDT)
Query regarding H-bond Saikat Pal (Sat Apr 27 2019 - 08:06:19 CDT)
- Re: Query regarding H-bond Roshan Shrestha (Sat Apr 27 2019 - 08:45:33 CDT)
  - RE: Query regarding H-bond Vermaas, Joshua (Mon Apr 29 2019 - 11:17:35 CDT)
Postdoc Position at Penn in Chromosome Modeling Hemant Kumar (Fri Apr 26 2019 - 13:41:25 CDT)
obj/mtl and isosurface as wireframe, possibly a small bug Luciano Abriata (Fri Apr 26 2019 - 02:54:40 CDT)
- RE: obj/mtl and isosurface as wireframe, possibly a small bug Luciano Abriata (Mon May 13 2019 - 12:13:27 CDT)
Re: Bugs and Questions Joao Ribeiro (Thu Apr 25 2019 - 13:39:32 CDT)
- Re: Bugs and Questions Joao Ribeiro (Thu Apr 25 2019 - 14:22:44 CDT)
  - Re: Bugs and Questions McGuire, Kelly (Thu Apr 25 2019 - 14:25:02 CDT)
- Re: Bugs and Questions McGuire, Kelly (Thu Apr 25 2019 - 14:10:36 CDT)
- Re: Bugs and Questions Joao Ribeiro (Thu Apr 25 2019 - 14:14:17 CDT)
  - Re: Bugs and Questions McGuire, Kelly (Thu Apr 25 2019 - 14:15:36 CDT)
Re: QwikMD Glycoside Hydrolase Tutorial step 2 Joao Ribeiro (Thu Apr 25 2019 - 13:31:40 CDT)
- RE: QwikMD Glycoside Hydrolase Tutorial step 2 Andreas Kukol (Fri Apr 26 2019 - 04:30:30 CDT)
- Re: QwikMD Glycoside Hydrolase Tutorial step 2 Joao Ribeiro (Fri Apr 26 2019 - 08:57:56 CDT)
QwikMD Glycoside Hydrolase Tutorial step 2 Andreas Kukol (Thu Apr 25 2019 - 10:35:16 CDT)
Questions and Bugs McGuire, Kelly (Thu Apr 25 2019 - 10:22:33 CDT)
Bugs and Questions McGuire, Kelly (Thu Apr 25 2019 - 10:14:02 CDT)
VMD window doesn't show up ëŒ€í•™ì› í™”í•™ê³µí•™ê³¼ (Thu Apr 25 2019 - 06:44:52 CDT)
- Re: VMD window doesn't show up John Stone (Thu Apr 25 2019 - 07:46:04 CDT)
  - Re: VMD window doesn't show up ëŒ€í•™ì› í™”í•™ê³µí•™ê³¼ (Thu Apr 25 2019 - 19:08:55 CDT)
  - Re: VMD window doesn't show up ëŒ€í•™ì› í™”í•™ê³µí•™ê³¼ (Thu Apr 25 2019 - 20:00:39 CDT)
Track H-bonds at a site in a trajectory Neena Susan Eappen (Wed Apr 24 2019 - 12:44:39 CDT)
- RE: Track H-bonds at a site in a trajectory Vermaas, Joshua (Wed Apr 24 2019 - 15:39:47 CDT)
How to transfer Anton trajectory to AMBER trajectory. Parviz Seifpanahi Shabane (Mon Apr 22 2019 - 09:29:14 CDT)
- Re: How to transfer Anton trajectory to AMBER trajectory. Giacomo Fiorin (Mon Apr 22 2019 - 12:47:02 CDT)
Umbrella Sampling in PLUMED + NAMD Mikhail Suyetin (Mon Apr 22 2019 - 01:33:04 CDT)
- RE: namd-l: Umbrella Sampling in PLUMED + NAMD Vermaas, Joshua (Mon Apr 22 2019 - 11:50:56 CDT)
OpenGL acceleration from eGPU? Ross Gunderson (Thu Apr 18 2019 - 10:08:22 CDT)
- Re: OpenGL acceleration from eGPU? John Stone (Thu Apr 18 2019 - 22:11:31 CDT)
OBJ rendering with multiple colors and transparency Luc Boisvert (Wed Apr 17 2019 - 17:41:52 CDT)
- Re: OBJ rendering with multiple colors and transparency John Stone (Fri Apr 19 2019 - 11:52:54 CDT)
Re: Problem with QwikMD automatic NTER patch Joao Ribeiro (Wed Apr 17 2019 - 16:59:41 CDT)
Problem with QwikMD automatic NTER patch Pablo Alfonso Madero Ayala (Wed Apr 17 2019 - 16:45:37 CDT)
Rasterized default display rendering vs ray-tracing (interactive) Bart Bruininks (Wed Apr 17 2019 - 06:02:46 CDT)
- Re: Rasterized default display rendering vs ray-tracing (interactive) John Stone (Wed Apr 17 2019 - 08:41:53 CDT)
SASA calculation with periodic images Projesh Roy (Tue Apr 16 2019 - 05:04:49 CDT)
- RE: SASA calculation with periodic images Vermaas, Joshua (Tue Apr 16 2019 - 12:17:26 CDT)
Re: Query regarding qwrap JÃ©rÃ´me HÃ©nin (Tue Apr 16 2019 - 02:57:13 CDT)
- Re: Query regarding qwrap Angana Ray (Tue Apr 16 2019 - 14:20:04 CDT)
  - Re: Query regarding qwrap JÃ©rÃ´me HÃ©nin (Wed Apr 17 2019 - 01:59:02 CDT)
Question Cristian Bogaciu (Fri Apr 12 2019 - 20:44:32 CDT)
- RE: Question Vermaas, Joshua (Sat Apr 13 2019 - 13:36:35 CDT)
  - Re: Question Ajasja LjubetiÄ (Tue Apr 16 2019 - 00:00:41 CDT)
    - Re: Question John Stone (Tue Apr 16 2019 - 09:09:27 CDT)
Regarding PBC unwrap Angana Ray (Fri Apr 12 2019 - 17:44:45 CDT)
- Re: Regarding PBC unwrap Gumbart, JC (Sat Apr 13 2019 - 07:34:59 CDT)
Tcl Almira Ovagimyan (Thu Apr 11 2019 - 15:20:42 CDT)
- RE: Tcl Vermaas, Joshua (Thu Apr 11 2019 - 19:16:36 CDT)
File Format McGuire, Kelly (Wed Apr 10 2019 - 15:15:17 CDT)
- Re: File Format John Stone (Wed Apr 10 2019 - 15:54:50 CDT)
Re: Creating and using a tk button Joao Ribeiro (Mon Apr 08 2019 - 07:25:50 CDT)
- Re: Creating and using a tk button Ali Morshedi (Tue Apr 09 2019 - 01:22:22 CDT)
Creating and using a tk button Ali Morshedi (Sun Apr 07 2019 - 03:34:39 CDT)
Tk-console Anjali Patel (Sat Apr 06 2019 - 03:45:37 CDT)
- Re: Tk-console John Stone (Sat Apr 06 2019 - 23:01:51 CDT)
Tk-Console Anjali Patel (Sat Apr 06 2019 - 02:54:34 CDT)
- haptic/force feedback devices and 3D viz Thomas C Bishop (Wed Apr 10 2019 - 14:52:26 CDT)
is VMD portable? Michael Morgan (Wed Apr 03 2019 - 21:04:17 CDT)
- Re: is VMD portable? John Stone (Thu Apr 04 2019 - 23:51:48 CDT)
calculate the percentage of beta-sheet and alpha helix with time evolution Saikat Pal (Wed Apr 03 2019 - 00:24:11 CDT)
- Re: calculate the percentage of beta-sheet and alpha helix with time evolution John Stone (Thu Apr 04 2019 - 23:55:04 CDT)
BOND distance Aashish Bhatt (Sat Mar 30 2019 - 06:23:35 CDT)
- Re: BOND distance Giacomo Fiorin (Sat Mar 30 2019 - 18:13:26 CDT)
  - Re: BOND distance Karteek Kumar (Sat Mar 30 2019 - 22:14:27 CDT)
- Re: BOND distance Ernesto Aleksei Delgado Hurtado (Sat Mar 30 2019 - 21:46:36 CDT)
  - Re: BOND distance Aashish Bhatt (Sun Mar 31 2019 - 04:55:13 CDT)
Topotools - silicon (110) creation Sina Zarepakzad (Thu Mar 28 2019 - 11:18:43 CDT)
- Re: Topotools - silicon (110) creation Axel Kohlmeyer (Thu Mar 28 2019 - 11:56:12 CDT)
  - Re: Topotools - silicon (110) creation Sina Zarepakzad (Sat Mar 30 2019 - 05:10:34 CDT)
    - Re: Topotools - silicon (110) creation Axel Kohlmeyer (Sat Mar 30 2019 - 06:05:07 CDT)
Re: FFTK Water Interaction mariano spivak (Thu Mar 28 2019 - 09:25:13 CDT)
- Re: FFTK Water Interaction McGuire, Kelly (Thu Mar 28 2019 - 15:30:56 CDT)
  - Re: FFTK Water Interaction McGuire, Kelly (Fri Mar 29 2019 - 00:48:51 CDT)
    - Re: FFTK Water Interaction mariano spivak (Fri Mar 29 2019 - 09:17:25 CDT)
    - Re: FFTK Water Interaction Mayne, Christopher G (Fri Apr 05 2019 - 17:32:33 CDT)
FFTK Water Interaction McGuire, Kelly (Wed Mar 27 2019 - 23:57:34 CDT)
Re: VMD on a WINDOWS 7 64-bit computer Stefan Boresch (Wed Mar 27 2019 - 03:01:06 CDT)
- Re: Re: VMD on a WINDOWS 7 64-bit computer Peter Freddolino (Wed Mar 27 2019 - 20:42:37 CDT)
Re: Visualization Question Joao Ribeiro (Tue Mar 26 2019 - 08:16:02 CDT)
- Re: Visualization Question McGuire, Kelly (Tue Mar 26 2019 - 10:15:25 CDT)
  - Re: Visualization Question John Stone (Thu Mar 28 2019 - 22:44:13 CDT)
VMD psfgen lonepair handling Aravinda Munasinghe (Mon Mar 25 2019 - 21:37:32 CDT)
- Re: VMD psfgen lonepair handling Brian Radak (Tue Mar 26 2019 - 08:28:21 CDT)
  - Re: VMD psfgen lonepair handling Joao Ribeiro (Tue Mar 26 2019 - 08:33:21 CDT)
    - Re: VMD psfgen lonepair handling Brian Radak (Tue Mar 26 2019 - 10:32:10 CDT)
Visualization Question McGuire, Kelly (Mon Mar 25 2019 - 19:05:45 CDT)
Re: Idle script error Joao Ribeiro (Mon Mar 25 2019 - 09:11:52 CDT)
- RE: Idle script error Simon Wheeler (Thu Mar 28 2019 - 05:39:37 CDT)
Idle script error Simon Wheeler (Mon Mar 25 2019 - 06:07:58 CDT)
Measre dihedral angle of a certain type M K (Mon Mar 25 2019 - 00:42:37 CDT)
- Re: Measre dihedral angle of a certain type M K (Tue Apr 09 2019 - 19:19:18 CDT)
  - Re: Measre dihedral angle of a certain type M K (Tue Apr 09 2019 - 19:46:23 CDT)
    - Re: Measre dihedral angle of a certain type Ashar Malik (Tue Apr 09 2019 - 20:52:47 CDT)
    - Re: Measre dihedral angle of a certain type Brian Radak (Wed Apr 10 2019 - 05:48:10 CDT)
Re: ORCA Plugin Ernesto Aleksei Delgado Hurtado (Sun Mar 24 2019 - 11:54:16 CDT)
ORCA Plugin McGuire, Kelly (Sat Mar 23 2019 - 23:03:50 CDT)
VMD OrcaPlugin Bug McGuire, Kelly (Thu Mar 21 2019 - 13:49:29 CDT)
- Re: VMD OrcaPlugin Bug McGuire, Kelly (Thu Mar 21 2019 - 14:09:08 CDT)
  - RE: VMD OrcaPlugin Bug Vermaas, Joshua (Thu Mar 21 2019 - 16:41:52 CDT)
Fwd: hydrogen bond calculations Sasthi Charan Mandal (Sun Mar 17 2019 - 03:58:09 CDT)
hydrogen bond calculations Sasthi Charan Mandal (Sun Mar 17 2019 - 02:07:16 CDT)
32bit memory problems on Mac OS Tom Bartl (Sat Mar 16 2019 - 14:10:48 CDT)
- Re: 32bit memory problems on Mac OS John Stone (Sun Mar 17 2019 - 19:14:31 CDT)
  - Re: 32bit memory problems on Mac OS Tom Bartl (Mon Mar 18 2019 - 09:50:54 CDT)
    - Re: 32bit memory problems on Mac OS Tom Bartl (Thu Mar 28 2019 - 12:11:05 CDT)
    - Re: 32bit memory problems on Mac OS John Stone (Thu Mar 28 2019 - 21:39:03 CDT)
Source code for ringsize? MD Simulation (Fri Mar 15 2019 - 14:30:07 CDT)
- Re: Source code for ringsize? Robin Betz (Fri Mar 15 2019 - 16:04:23 CDT)
- RE: Source code for ringsize? Vermaas, Joshua (Fri Mar 15 2019 - 16:25:45 CDT)
ORCA Orbital Bug McGuire, Kelly (Fri Mar 15 2019 - 11:02:30 CDT)
- Re: ORCA Orbital Bug John Stone (Sat Mar 16 2019 - 01:13:06 CDT)
  - Re: ORCA Orbital Bug McGuire, Kelly (Sat Mar 16 2019 - 18:34:51 CDT)
Fixing coordinates for visualization Eugenio Gil (Thu Mar 14 2019 - 08:22:14 CDT)
- RE: Fixing coordinates for visualization Vermaas, Joshua (Thu Mar 14 2019 - 12:43:48 CDT)
How to fix the position of the lipid bilayer in the trajectories Rabeta Yeasmin (Wed Mar 13 2019 - 14:38:00 CDT)
- Re: How to fix the position of the lipid bilayer in the trajectories Giacomo Fiorin (Wed Mar 13 2019 - 15:34:12 CDT)
  - Re: How to fix the position of the lipid bilayer in the trajectories Axel Kohlmeyer (Wed Mar 13 2019 - 16:18:12 CDT)
PSF File Hasnain Shabbir (Wed Mar 13 2019 - 02:12:13 CDT)
- Re: PSF File Ashar Malik (Wed Mar 13 2019 - 03:25:10 CDT)
  - Setting up remote GPU jhamre (Wed Mar 13 2019 - 06:23:53 CDT)
- RE: PSF File soroush ziaei (Wed Mar 13 2019 - 12:31:21 CDT)
- Re: PSF File Axel Kohlmeyer (Wed Mar 13 2019 - 19:54:21 CDT)
Research Programmer for VMD/NAMD at UIUC JoÃ£o Ribeiro (Tue Mar 12 2019 - 13:20:10 CDT)
VMD Multiprocessing McGuire, Kelly (Sun Mar 10 2019 - 17:55:43 CDT)
- RE: VMD Multiprocessing Vermaas, Joshua (Mon Mar 11 2019 - 12:49:28 CDT)
- Re: VMD Multiprocessing John Stone (Mon Mar 11 2019 - 15:39:34 CDT)
read vector lammps with VMD alberto (Fri Mar 08 2019 - 04:14:34 CST)
VMD Text Mode McGuire, Kelly (Thu Mar 07 2019 - 18:02:28 CST)
- RE: VMD Text Mode Bennion, Brian (Thu Mar 07 2019 - 19:07:49 CST)
  - Re: VMD Text Mode McGuire, Kelly (Thu Mar 07 2019 - 19:12:34 CST)
  - Re: RE: VMD Text Mode Joshua Moore (Thu Mar 07 2019 - 23:33:35 CST)
    - Re: RE: VMD Text Mode McGuire, Kelly (Thu Mar 07 2019 - 23:38:20 CST)
- Re: VMD Text Mode Mike McCallum (Thu Mar 07 2019 - 19:19:59 CST)
center of mass 4 rdf VMD alberto (Thu Mar 07 2019 - 09:42:48 CST)
qwikmd can't load pdb file, locate "P:/" drive Brittany Lott (Mon Mar 04 2019 - 20:24:54 CST)
- Re: qwikmd can't load pdb file, locate "P:/" drive JoÃ£o Ribeiro (Tue Mar 05 2019 - 09:21:08 CST)
Clipping plane redering issues Korey R (Mon Mar 04 2019 - 10:46:00 CST)
- Re: Clipping plane redering issues Korey R (Thu Mar 07 2019 - 18:53:54 CST)
Windows build newer than 1.9.3 Stefan Boresch (Mon Mar 04 2019 - 01:54:58 CST)
- Re: Windows build newer than 1.9.3 Ashar Malik (Mon Mar 04 2019 - 03:03:59 CST)
  - Re: Windows build newer than 1.9.3 Stefan Boresch (Tue Mar 05 2019 - 02:39:54 CST)
FFTK Possible Bug McGuire, Kelly (Sat Mar 02 2019 - 20:28:38 CST)
- Re: FFTK Possible Bug McGuire, Kelly (Sat Mar 02 2019 - 20:55:31 CST)
  - Re: FFTK Possible Bug McGuire, Kelly (Sat Mar 02 2019 - 22:00:33 CST)
BIMac2019 Dusan Racko (Thu Feb 28 2019 - 08:39:19 CST)
Changing isosurface wireframe thickness when rendering with Tachyon Matthieu Benoit (Wed Feb 27 2019 - 23:44:27 CST)
GolP-CHARMM Mikhail Suyetin (Wed Feb 27 2019 - 10:24:21 CST)
Centering an atom over the length of a trajectory Nick Palmer (Tue Feb 26 2019 - 15:11:55 CST)
- Re: Centering an atom over the length of a trajectory Bassam Haddad (Tue Feb 26 2019 - 16:25:15 CST)
  - Re: Centering an atom over the length of a trajectory Bassam Haddad (Tue Feb 26 2019 - 16:30:29 CST)
- RE: Centering an atom over the length of a trajectory Vermaas, Joshua (Tue Feb 26 2019 - 16:33:31 CST)
RDF witth center of mass as selection alberto (Tue Feb 26 2019 - 10:08:03 CST)
- Re: RDF witth center of mass as selection JÃ©rÃ´me HÃ©nin (Tue Feb 26 2019 - 11:10:38 CST)
  - Re: RDF witth center of mass as selection alberto (Tue Feb 26 2019 - 12:04:15 CST)
RTX-accelerated VMD 1.9.4 test build for 64-bit Linux posted... John Stone (Mon Feb 25 2019 - 20:40:16 CST)
- Re: RTX-accelerated VMD 1.9.4 test build for 64-bit Linux posted... Casalino, Lorenzo (Tue Feb 26 2019 - 13:02:03 CST)
- Updated RTX-accelerated VMD 1.9.4 test build for 64-bit Linux posted... John Stone (Fri Mar 15 2019 - 16:31:14 CDT)
- Re: RTX-accelerated VMD 1.9.4 test build for 64-bit Linux posted... Dallas Warren (Mon Apr 29 2019 - 18:52:15 CDT)
  - Re: RTX-accelerated VMD 1.9.4 test build for 64-bit Linux posted... Dallas Warren (Mon Apr 29 2019 - 18:59:40 CDT)
    - Re: RTX-accelerated VMD 1.9.4 test build for 64-bit Linux posted... Dallas Warren (Mon Apr 29 2019 - 19:00:35 CDT)
    - Re: RTX-accelerated VMD 1.9.4 test build for 64-bit Linux posted... John Stone (Mon Apr 29 2019 - 20:50:31 CDT)
  - QuickSurf error Re: RTX-accelerated VMD 1.9.4 test build for 64-bit Linux posted... John Stone (Mon Apr 29 2019 - 21:09:42 CDT)
Incorrect charge in VMD from PSF? Udaya Dahal (Mon Feb 25 2019 - 11:57:47 CST)
- RE: Incorrect charge in VMD from PSF? Vermaas, Joshua (Mon Feb 25 2019 - 15:44:31 CST)
  - Re: Incorrect charge in VMD from PSF? Udaya Dahal (Mon Feb 25 2019 - 16:28:18 CST)
Calculate the bond and angle energy of a glucosidic linkage using NAMD Energy plugin Ern Ong (Mon Feb 25 2019 - 04:39:21 CST)
- Re: Calculate the bond and angle energy of a glucosidic linkage using NAMD Energy plugin Peter Freddolino (Mon Feb 25 2019 - 07:47:05 CST)
TCL For Loop Problem McGuire, Kelly (Sun Feb 24 2019 - 21:47:16 CST)
- Re: TCL For Loop Problem Axel Kohlmeyer (Sun Feb 24 2019 - 22:18:12 CST)
  - Re: TCL For Loop Problem McGuire, Kelly (Sun Feb 24 2019 - 22:25:03 CST)
- Re: TCL For Loop Problem Ashar Malik (Sun Feb 24 2019 - 22:24:08 CST)
Possible Bug McGuire, Kelly (Sat Feb 23 2019 - 00:32:30 CST)
- Re: Possible Bug John Stone (Sat Feb 23 2019 - 20:54:38 CST)
  - Re: Possible Bug McGuire, Kelly (Sat Feb 23 2019 - 23:19:28 CST)
    - Re: Possible Bug John Stone (Sun Feb 24 2019 - 19:22:55 CST)
Query regarding contact map Saikat Pal (Sat Feb 23 2019 - 00:18:40 CST)
Re: [EXTERNAL] RE: pbctools installation error Tripathi, Ashutosh (Fri Feb 22 2019 - 16:10:30 CST)
- RE: [EXTERNAL] RE: pbctools installation error Vermaas, Joshua (Fri Feb 22 2019 - 16:15:14 CST)
  - Re: [EXTERNAL] RE: pbctools installation error Tripathi, Ashutosh (Fri Feb 22 2019 - 16:28:37 CST)
    - Re: Re: [EXTERNAL] RE: pbctools installation error John Stone (Fri Feb 22 2019 - 17:30:33 CST)
pbctools installation error Tripathi, Ashutosh (Fri Feb 22 2019 - 14:27:40 CST)
- RE: pbctools installation error Vermaas, Joshua (Fri Feb 22 2019 - 16:05:03 CST)
VMD RTX hardware accelerated ray tracing update! John Stone (Thu Feb 21 2019 - 23:24:40 CST)
extracting 1-D data from a volumetric file Bassam Haddad (Thu Feb 21 2019 - 12:47:04 CST)
- Re: extracting 1-D data from a volumetric file Giacomo Fiorin (Thu Feb 21 2019 - 13:31:40 CST)
- RE: extracting 1-D data from a volumetric file Vermaas, Joshua (Thu Feb 21 2019 - 14:22:21 CST)
  - Re: extracting 1-D data from a volumetric file Bassam Haddad (Thu Feb 21 2019 - 16:02:08 CST)
Query regarding contact map Saikat Pal (Wed Feb 20 2019 - 22:56:10 CST)
TIP4P Water box ê¹€ë¯¼ìž¬ (Tue Feb 19 2019 - 19:51:03 CST)
Move volumetric data with their associated PDB Matthieu Benoit (Tue Feb 19 2019 - 12:21:37 CST)
- Re: Move volumetric data with their associated PDB Ryan McGreevy (Tue Feb 19 2019 - 12:33:06 CST)
  - Re: Move volumetric data with their associated PDB Matthieu Benoit (Tue Feb 19 2019 - 13:04:38 CST)
    - Re: Move volumetric data with their associated PDB Ryan McGreevy (Tue Feb 19 2019 - 13:17:05 CST)
- RE: Move volumetric data with their associated PDB Vermaas, Joshua (Tue Feb 19 2019 - 13:37:20 CST)
  - RE: Move volumetric data with their associated PDB Matthieu Benoit (Tue Feb 19 2019 - 19:23:39 CST)
Error: invalid command name "voltool" Montserrat Fabrega Ferrer (Tue Feb 19 2019 - 10:40:59 CST)
- Re: Error: invalid command name "voltool" Ashar Malik (Tue Feb 19 2019 - 11:14:49 CST)
  - RE: Error: invalid command name "voltool" Vermaas, Joshua (Tue Feb 19 2019 - 12:35:31 CST)
    - Re: Error: invalid command name "voltool" John Stone (Tue Feb 19 2019 - 13:33:12 CST)
- Re: Error: invalid command name "voltool" Ryan McGreevy (Tue Feb 19 2019 - 10:57:35 CST)
1CA2 autoionization ê¹€ë¯¼ìž¬ (Tue Feb 19 2019 - 08:44:29 CST)
- Re: 1CA2 autoionization Ernesto Aleksei Delgado Hurtado (Tue Feb 19 2019 - 12:17:23 CST)
Difference in ParseFEP result with versions 1.9.2 and 2.1 Amy Rice (Mon Feb 18 2019 - 15:16:00 CST)
- Re: Difference in ParseFEP result with versions 1.9.2 and 2.1 Brian Radak (Mon Feb 18 2019 - 16:31:07 CST)
  - Re: Difference in ParseFEP result with versions 1.9.2 and 2.1 Amy Rice (Tue Feb 19 2019 - 10:34:03 CST)
    - Re: Difference in ParseFEP result with versions 1.9.2 and 2.1 JÃ©rÃ´me HÃ©nin (Tue Feb 19 2019 - 11:48:04 CST)
    - Re: Difference in ParseFEP result with versions 1.9.2 and 2.1 Brian Radak (Tue Feb 19 2019 - 11:44:01 CST)
- Re: Difference in ParseFEP result with versions 1.9.2 and 2.1 JÃ©rÃ´me HÃ©nin (Mon Feb 18 2019 - 16:44:16 CST)
Namdinator - a web service for automatic MDFF simulations Rune Thomas Kidmose (Mon Feb 18 2019 - 13:22:17 CST)
Topo tools error in dihedral guess Ø§Ø³ØØ§Ù‚ Ø®Ø¯Ø§Ù¾Ø±Ø³Øª Ø³ÛŒØ§Ù‡Ù…Ø²Ú¯ÛŒ (Mon Feb 18 2019 - 07:06:42 CST)
- Re: Topo tools error in dihedral guess Axel Kohlmeyer (Mon Feb 18 2019 - 08:46:13 CST)
  - Re: Topo tools error in dihedral guess Axel Kohlmeyer (Mon Feb 18 2019 - 13:14:00 CST)
  - Re: Topo tools error in dihedral guess Axel Kohlmeyer (Tue Feb 19 2019 - 01:59:57 CST)
Regarding image quality in vmd Saikat Pal (Mon Feb 18 2019 - 04:35:08 CST)
- Re: Regarding image quality in vmd Dallas Warren (Mon Feb 18 2019 - 14:51:11 CST)
3d visualization setup Anthony Cruz-Balberdy (Sat Feb 16 2019 - 13:47:29 CST)
- Re: 3d visualization setup Anthony Cruz-Balberdy (Thu Feb 21 2019 - 08:00:02 CST)
  - RE: Re: 3d visualization setup Jordi Bujons (Thu Feb 21 2019 - 10:02:31 CST)
    - Re: Re: 3d visualization setup Anthony Cruz-Balberdy (Sat Feb 23 2019 - 08:35:24 CST)
PDB structures of peptides Mikhail Suyetin (Thu Feb 14 2019 - 03:05:15 CST)
- Re: PDB structures of peptides Aravinda Munasinghe (Thu Feb 14 2019 - 18:26:40 CST)
Cannot merge psf and pdb files using psfgen Ern Ong (Wed Feb 13 2019 - 05:12:41 CST)
- RE: Cannot merge psf and pdb files using psfgen Vermaas, Joshua (Wed Feb 13 2019 - 09:55:21 CST)
  - RE: Cannot merge psf and pdb files using psfgen Ern Ong (Wed Feb 13 2019 - 22:20:53 CST)
Cannot merge psf and pdb files using psfgen Ern Ong (Wed Feb 13 2019 - 03:52:42 CST)
MSD of membrane lipids Villalain Boullon, Jose (Mon Feb 11 2019 - 10:35:46 CST)
minimal distance between atoms in all frame alberto (Tue Feb 05 2019 - 12:04:43 CST)
measure distance atom from plane alberto (Tue Feb 05 2019 - 04:54:20 CST)
- Re: measure distance atom from plane Ashar Malik (Tue Feb 05 2019 - 05:50:15 CST)
Coloring different isosurfaces with user-defined colors Ellis, Matthew (Sat Feb 02 2019 - 04:38:32 CST)
QwikMD and CUDA10 jrhau lung (Thu Jan 31 2019 - 05:43:53 CST)
- Re: QwikMD and CUDA10 JoÃ£o Ribeiro (Thu Jan 31 2019 - 09:04:40 CST)
  - Re: QwikMD and CUDA10 John Stone (Thu Jan 31 2019 - 09:21:04 CST)
  - Re: QwikMD and CUDA10 jrhau lung (Thu Jan 31 2019 - 17:58:24 CST)
    - Re: QwikMD and CUDA10 JoÃ£o Ribeiro (Fri Feb 01 2019 - 08:59:31 CST)
    - Re: QwikMD and CUDA10 jrhau lung (Fri Feb 01 2019 - 17:33:45 CST)
calculating number of water and osmolytes molecules at particular distance from protein surface. ISHRAT JAHAN (Wed Jan 30 2019 - 23:09:41 CST)
- Re: calculating number of water and osmolytes molecules at particular distance from protein surface. Ashar Malik (Thu Jan 31 2019 - 00:00:10 CST)
regarding radius of a 3D sphere san kumar (Tue Jan 29 2019 - 11:55:01 CST)
Conversion from gromacs trr trajectory into charmm trajectory Roshan Shrestha (Mon Jan 28 2019 - 23:14:21 CST)
- RE: Conversion from gromacs trr trajectory into charmm trajectory Vermaas, Joshua (Tue Jan 29 2019 - 11:25:50 CST)
Bug fixed in volmap Giacomo Fiorin (Thu Jan 24 2019 - 21:30:23 CST)
Uncertainty estimate of g(r) using measure gofr function Jim Parker (Mon Jan 21 2019 - 21:48:42 CST)
Pause script, make display interactive, then resume script after user input Patrick Charchar (Wed Jan 16 2019 - 19:59:54 CST)
- Re: Pause script, make display interactive, then resume script after user input John Stone (Fri Jan 18 2019 - 16:44:29 CST)
  - Re: Pause script, make display interactive, then resume script after user input John Stone (Wed Jan 23 2019 - 23:45:27 CST)
FEP tutorial plot error surya narayanan chandrasekaran (Wed Jan 16 2019 - 07:00:25 CST)
- RE: FEP tutorial plot error soroush ziaei (Thu Jan 17 2019 - 06:57:21 CST)
  - Re: FEP tutorial plot error surya narayanan chandrasekaran (Thu Jan 17 2019 - 23:07:35 CST)
    - Re: FEP tutorial plot error Brian Radak (Thu Jan 24 2019 - 13:37:07 CST)
regarding the coordinate transformation on a curved surface to plane surface Subbarao Kanchi (Tue Jan 08 2019 - 18:01:28 CST)
- AW: regarding the coordinate transformation on a curved surface to plane surface Norman Geist (Wed Jan 09 2019 - 02:13:09 CST)
  - Re: regarding the coordinate transformation on a curved surface to plane surface Subbarao Kanchi (Wed Jan 09 2019 - 02:30:46 CST)
orient package problem Prabir Khatua (Wed Jan 02 2019 - 17:15:56 CST)
- RE: orient package problem Vermaas, Joshua (Wed Jan 02 2019 - 18:33:14 CST)
  - RE: orient package problem Vermaas, Joshua (Thu Jan 03 2019 - 12:32:02 CST)
Parsing error in TkConsole Seibold, Steve Allan (Wed Jan 02 2019 - 13:44:08 CST)
- Re: Parsing error in TkConsole JoÃ£o Ribeiro (Wed Jan 02 2019 - 14:46:56 CST)
  - RE: Parsing error in TkConsole Seibold, Steve Allan (Wed Jan 02 2019 - 15:03:47 CST)
- Re: Parsing error in TkConsole Ashar Malik (Wed Jan 02 2019 - 15:14:44 CST)
- RE: Parsing error in TkConsole Vermaas, Joshua (Wed Jan 02 2019 - 15:17:33 CST)
Calculation of gofr for non-orthorhombic boxes HEMANTH H 18310019 (Tue Jan 01 2019 - 02:55:14 CST)
- Re: Calculation of gofr for non-orthorhombic boxes Axel Kohlmeyer (Tue Jan 01 2019 - 22:55:07 CST)
Problem in loading netcdf file from LAMMPS output in VMD LIGESH B (Tue Jan 01 2019 - 00:05:34 CST)
- Re: Problem in loading netcdf file from LAMMPS output in VMD Axel Kohlmeyer (Tue Jan 01 2019 - 23:52:35 CST)
  - Re: Problem in loading netcdf file from LAMMPS output in VMD John Stone (Fri Jan 04 2019 - 11:34:55 CST)
h-bond soroush ziaei (Sat Dec 22 2018 - 17:04:03 CST)
- RE: h-bond Vermaas, Joshua (Sun Dec 23 2018 - 07:40:26 CST)
  - RE: h-bond soroush ziaei (Sun Dec 23 2018 - 09:51:17 CST)
Problems with rendering with POV-Ray Oliver Sørensen Siig (Sat Dec 22 2018 - 07:12:41 CST)
- Re: Problems with rendering with POV-Ray John Stone (Fri Jan 04 2019 - 13:10:53 CST)
beta barrel structure generation Prabir Khatua (Fri Dec 21 2018 - 16:41:42 CST)
- Re: beta barrel structure generation Ashar Malik (Fri Dec 21 2018 - 21:45:16 CST)
- Re: beta barrel structure generation Geist, Norman (Sat Dec 22 2018 - 02:06:44 CST)
MDFF through VMD Error FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT Somnath Dutta (Fri Dec 21 2018 - 09:39:40 CST)
- Re: MDFF through VMD Error FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT Ryan McGreevy (Fri Dec 21 2018 - 10:44:42 CST)
- RE: MDFF through VMD Error FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT Vermaas, Joshua (Fri Dec 21 2018 - 11:08:31 CST)
Dynamical Network Analysis ÐÐ»ÐµÐºÑÐ°Ð½Ð´Ñ€ ÐšÐ¾ÑˆÐºÐ°Ñ€Ð¾Ð² (Thu Dec 20 2018 - 02:53:47 CST)
- Re: Dynamical Network Analysis liushiyong (Thu Dec 20 2018 - 04:36:04 CST)
atom types depend on PSF/PDB reading order Gumbart, JC (Wed Dec 19 2018 - 18:46:23 CST)
- RE: atom types depend on PSF/PDB reading order Vermaas, Joshua (Thu Dec 20 2018 - 08:42:52 CST)
vrpn and vmd 1.9.3 - which version to use ? Paulo E. Abreu (Wed Dec 19 2018 - 03:41:42 CST)
ring-like structure formation with distance restraints Prabir Khatua (Tue Dec 18 2018 - 21:32:48 CST)
- RE: ring-like structure formation with distance restraints Vermaas, Joshua (Wed Dec 19 2018 - 12:53:31 CST)
  - RE: ring-like structure formation with distance restraints Vermaas, Joshua (Wed Dec 19 2018 - 17:27:58 CST)
Error in Loading atom_style hybrid LAMMPS data file in VMD LIGESH B (Mon Dec 17 2018 - 08:27:34 CST)
- Re: Error in Loading atom_style hybrid LAMMPS data file in VMD Axel Kohlmeyer (Mon Dec 17 2018 - 09:13:01 CST)
fftk problem in opt. bonded step NicolÃ¡s Veiga (Fri Dec 14 2018 - 14:57:59 CST)
- Re: fftk problem in opt. bonded step Gumbart, JC (Fri Dec 14 2018 - 16:51:59 CST)
  - Re: fftk problem in opt. bonded step Gumbart, JC (Fri Dec 14 2018 - 18:04:17 CST)
ARM Joey Gehring (Thu Dec 13 2018 - 10:29:58 CST)
- Re: ARM John Stone (Sat Dec 15 2018 - 14:46:08 CST)
Assertion failure OS X 10.14 Per Larsson (Thu Dec 13 2018 - 03:11:53 CST)
Free Energy Perturbation Analysis using VMD HOCHEOL LIM (Thu Dec 13 2018 - 01:24:02 CST)
- Re: Free Energy Perturbation Analysis using VMD Brian Radak (Fri Dec 14 2018 - 10:24:22 CST)
Heme PSF file generation and hydrogen peroxide parameter files HOCHEOL LIM (Thu Dec 13 2018 - 01:13:53 CST)
Fwd: Extensions not working Francesco Pietra (Sun Dec 09 2018 - 01:29:24 CST)
Patch DISU fails for MARTINIZED protein segments Manish Agarwal (Tue Dec 04 2018 - 01:45:08 CST)
- Re: Patch DISU fails for MARTINIZED protein segments Peter Freddolino (Tue Dec 04 2018 - 07:22:26 CST)
  - Re: Patch DISU fails for MARTINIZED protein segments Manish Agarwal (Tue Dec 04 2018 - 10:54:14 CST)
vmd error time too large/small to represent Stephani Macalino (Mon Dec 03 2018 - 20:49:06 CST)
- RE: vmd error time too large/small to represent Vermaas, Joshua (Tue Dec 04 2018 - 11:42:01 CST)
  - Re: vmd error time too large/small to represent Stephani Macalino (Tue Dec 04 2018 - 19:22:44 CST)
regarding h-bod calculation in tk console Jai Kumar (Sun Dec 02 2018 - 00:17:49 CST)
Extensions not working Francesco Pietra (Sat Dec 01 2018 - 09:17:03 CST)
- Re: Extensions not working John Stone (Mon Dec 03 2018 - 15:21:05 CST)
mol representation Isosurface - Parameters? MD Simulation (Fri Nov 30 2018 - 06:36:17 CST)
- RE: mol representation Isosurface - Parameters? Vermaas, Joshua (Fri Nov 30 2018 - 13:31:19 CST)
selection of water molecules around particular number of atoms Ashma Khan (Wed Nov 28 2018 - 23:54:42 CST)
VMD - Measure water flow The Cromicus Productions (Wed Nov 28 2018 - 11:41:40 CST)
REG building non standard solvent simulation box. surya narayanan chandrasekaran (Wed Nov 28 2018 - 03:27:16 CST)
- Re: REG building non standard solvent simulation box. Peter Freddolino (Wed Nov 28 2018 - 07:51:17 CST)
  - Re: REG building non standard solvent simulation box. surya narayanan chandrasekaran (Thu Nov 29 2018 - 06:08:46 CST)
implicit membrane in QwikMD? Armando Jerome de Jesus (Tue Nov 27 2018 - 09:37:15 CST)
- Re: implicit membrane in QwikMD? JoÃ£o Ribeiro (Tue Nov 27 2018 - 11:27:28 CST)
  - Re: implicit membrane in QwikMD? Armando Jerome de Jesus (Tue Nov 27 2018 - 14:52:08 CST)
Inverted measure fit of ring atoms mish (Tue Nov 27 2018 - 08:58:09 CST)
- Re: Inverted measure fit of ring atoms mish (Tue Nov 27 2018 - 09:25:29 CST)
  - Re: Re: Inverted measure fit of ring atoms John Stone (Tue Nov 27 2018 - 10:12:23 CST)
How to add bond between atoms of same same or type in every molecule Remya Ann (Tue Nov 27 2018 - 07:14:59 CST)
Cant use NAMDplot to plot Artur Duque Rossi (Sat Nov 24 2018 - 16:34:18 CST)
Compiling VMD 1.9.3 64-bit on MacOS 10.13.6 Alex Sha (Fri Nov 23 2018 - 00:48:06 CST)
- Re: Compiling VMD 1.9.3 64-bit on MacOS 10.13.6 Alex Sha (Mon Nov 26 2018 - 00:28:12 CST)
gopython with python3 Guilherme da Silva (Thu Nov 22 2018 - 11:53:11 CST)
- Re: gopython with python3 Giacomo Fiorin (Thu Nov 22 2018 - 19:25:45 CST)
  - Re: gopython with python3 Giacomo Fiorin (Thu Nov 22 2018 - 19:45:55 CST)
  - Re: gopython with python3 Robin Betz (Thu Nov 22 2018 - 20:33:50 CST)
CUDA 10 JÃ©rÃ´me HÃ©nin (Thu Nov 22 2018 - 06:47:27 CST)
- Re: CUDA 10 John Stone (Thu Nov 22 2018 - 09:12:31 CST)
  - Re: CUDA 10 JÃ©rÃ´me HÃ©nin (Thu Nov 22 2018 - 11:30:53 CST)
Creating a pdb of periodic images of a unit cell Monika Madhavi (Tue Nov 20 2018 - 23:19:09 CST)
- Re: Creating a pdb of periodic images of a unit cell Devanand T (Wed Nov 21 2018 - 00:19:11 CST)
  - RE: Creating a pdb of periodic images of a unit cell Vermaas, Joshua (Wed Nov 21 2018 - 11:43:43 CST)
VMD crashes when drag-and-dropping files in Windows Oleg Stroganov (Tue Nov 13 2018 - 04:16:09 CST)
Patching for bond between protein and organic ligand Francesco Pietra (Mon Nov 12 2018 - 01:50:29 CST)
- RE: Patching for bond between protein and organic ligand Vermaas, Joshua (Mon Nov 12 2018 - 11:28:21 CST)
  - Re: Patching for bond between protein and organic ligand Brian Radak (Mon Nov 12 2018 - 12:19:08 CST)
Concatenate Outputs McGuire, Kelly (Fri Nov 09 2018 - 14:12:21 CST)
- Re: Concatenate Outputs McGuire, Kelly (Sat Nov 10 2018 - 14:52:45 CST)
how to change material and color of an atom selection in TkConsole Abolfazl Musavi (Thu Nov 08 2018 - 16:11:17 CST)
- RE: how to change material and color of an atom selection in TkConsole Vermaas, Joshua (Thu Nov 08 2018 - 18:55:32 CST)
  - Re: how to change material and color of an atom selection in TkConsole Abolfazl Musavi (Thu Nov 08 2018 - 19:16:41 CST)
autopsf ERROR FRANCESCO TORRICELLA (Thu Nov 08 2018 - 08:58:57 CST)
- Re: autopsf ERROR Peter Freddolino (Thu Nov 08 2018 - 11:29:36 CST)
Create new atoms Michail Lazaratos (Wed Nov 07 2018 - 13:45:21 CST)
- Re: Create new atoms Axel Kohlmeyer (Wed Nov 07 2018 - 14:32:13 CST)
- Re: Create new atoms John Stone (Wed Nov 07 2018 - 14:30:01 CST)
VMD hangs on startup (MacOSX 10.14) Nathan M. Lim (UCI) (Wed Nov 07 2018 - 12:42:01 CST)
- Re: VMD hangs on startup (MacOSX 10.14) Nathan M. Lim (UCI) (Sun Nov 11 2018 - 00:00:45 CST)
VMD does not display bonds Behnam Ghalami (Wed Nov 07 2018 - 02:26:03 CST)
- RE: VMD does not display bonds Vermaas, Joshua (Wed Nov 07 2018 - 12:09:47 CST)
  - RE: VMD does not display bonds Vermaas, Joshua (Thu Nov 08 2018 - 11:45:59 CST)
    - Re: VMD does not display bonds Peter Kroon (Fri Nov 09 2018 - 06:15:55 CST)
    - Re: VMD does not display bonds Behnam Ghalami (Fri Nov 09 2018 - 13:27:27 CST)
Save specific atoms from multiple frame pdb Abhik Ghosh Moulick (Wed Nov 07 2018 - 01:33:10 CST)
- Re: Save specific atoms from multiple frame pdb John Stone (Wed Nov 07 2018 - 14:34:53 CST)
  - Re: Save specific atoms from multiple frame pdb John Stone (Thu Nov 08 2018 - 21:47:29 CST)
PSFgen failure Anatoly Chernyshev (Mon Nov 05 2018 - 07:13:11 CST)
- Re: PSFgen failure JoÃ£o Ribeiro (Mon Nov 12 2018 - 10:27:28 CST)
Question McGuire, Kelly (Sun Nov 04 2018 - 17:16:27 CST)
- Re: Question Axel Kohlmeyer (Sun Nov 04 2018 - 18:56:26 CST)
creating topology for a unique structure soroush ziaei (Sun Nov 04 2018 - 05:49:31 CST)
unknown residue type Francesco Pietra (Sun Nov 04 2018 - 03:08:49 CST)
- Re: unknown residue type Peter Freddolino (Sun Nov 04 2018 - 07:48:48 CST)
  - Re: unknown residue type Francesco Pietra (Mon Nov 05 2018 - 00:36:38 CST)
Newby unable to see secondary structure in New Cartoon Gary Turner (Sat Nov 03 2018 - 12:40:19 CDT)
- Re: Newby unable to see secondary structure in New Cartoon John Stone (Sun Nov 04 2018 - 20:59:58 CST)
  - Re: Newby unable to see secondary structure in New Cartoon Gary Turner (Tue Nov 06 2018 - 14:44:59 CST)
Building amino acid simulation box. surya narayanan chandrasekaran (Thu Nov 01 2018 - 23:45:39 CDT)
Dynamic Bonds Question McGuire, Kelly (Wed Oct 31 2018 - 12:58:01 CDT)
- Re: Dynamic Bonds Question McGuire, Kelly (Wed Oct 31 2018 - 13:46:04 CDT)
- RE: Dynamic Bonds Question Vermaas, Joshua (Wed Oct 31 2018 - 14:20:13 CDT)
  - Re: Dynamic Bonds Question McGuire, Kelly (Wed Oct 31 2018 - 14:52:09 CDT)
    - RE: Dynamic Bonds Question Vermaas, Joshua (Wed Oct 31 2018 - 15:46:23 CDT)
    - Re: Re: Dynamic Bonds Question Brian Radak (Wed Oct 31 2018 - 17:42:53 CDT)
selecting residues in a heterodimer Raag Saluja (Mon Oct 29 2018 - 01:42:50 CDT)
- Re: selecting residues in a heterodimer amin sagar (Mon Oct 29 2018 - 02:47:31 CDT)
  - Re: selecting residues in a heterodimer Raag Saluja (Mon Oct 29 2018 - 02:51:27 CDT)
Problem of saving .trj file in vmd Sasthi Charan Mandal (Sat Oct 27 2018 - 08:00:43 CDT)
- RE: Problem of saving .trj file in vmd Vermaas, Joshua (Sun Oct 28 2018 - 18:01:29 CDT)
  - RE: Problem of saving .trj file in vmd Vermaas, Joshua (Mon Oct 29 2018 - 09:35:18 CDT)
    - Re: Problem of saving .trj file in vmd John Stone (Tue Oct 30 2018 - 09:16:43 CDT)
    - Re: Problem of saving .trj file in vmd Sasthi Charan Mandal (Tue Oct 30 2018 - 10:01:08 CDT)
Unknown atom type CG205 with CGenFF by psfgen Francesco Pietra (Fri Oct 26 2018 - 10:09:08 CDT)
- Fwd: Unknown atom type CG205 with CGenFF by psfgen Francesco Pietra (Fri Oct 26 2018 - 10:11:20 CDT)
  - Re: Fwd: Unknown atom type CG205 with CGenFF by psfgen Gumbart, James C (Fri Oct 26 2018 - 12:06:15 CDT)
    - Re: Fwd: Unknown atom type CG205 with CGenFF by psfgen Francesco Pietra (Fri Oct 26 2018 - 14:30:59 CDT)
- RE: Unknown atom type CG205 with CGenFF by psfgen Vermaas, Joshua (Fri Oct 26 2018 - 12:21:06 CDT)
Domain error in parseFEP Kevin Song (Tue Oct 23 2018 - 11:58:47 CDT)
Problems with CGenFF and oxetane ring Francesco Pietra (Tue Oct 23 2018 - 11:04:27 CDT)
Pressure Control Norge Cruz HernÃ¡ndez (Tue Oct 23 2018 - 09:26:09 CDT)
- Re: Pressure Control Gumbart, James C (Thu Oct 25 2018 - 12:53:03 CDT)
  - RE: Pressure Control Vermaas, Joshua (Thu Oct 25 2018 - 18:35:17 CDT)
AutoPSF error with glycana (end of segment error) Steinar Halldorsson (Mon Oct 22 2018 - 08:58:12 CDT)
- Re: AutoPSF error with glycana (end of segment error) JoÃ£o Ribeiro (Mon Oct 22 2018 - 10:05:01 CDT)
  - Re: AutoPSF error with glycana (end of segment error) Steinar Halldorsson (Mon Oct 22 2018 - 10:16:32 CDT)
Measure Center Question McGuire, Kelly (Sat Oct 20 2018 - 18:20:57 CDT)
- AW: Measure Center Question Norman Geist (Sun Oct 21 2018 - 04:02:15 CDT)
error in analyse fep simulation (parse fep) soroush ziaei (Fri Oct 19 2018 - 08:54:44 CDT)
Ambient/direct light missing after adding Glow lights to a tachyon scene with glow_lights.tcl Oliver Grant (Fri Oct 19 2018 - 06:04:37 CDT)
- Re: Ambient/direct light missing after adding Glow lights to a tachyon scene with glow_lights.tcl John Stone (Fri Oct 19 2018 - 08:37:46 CDT)
  - Re: Ambient/direct light missing after adding Glow lights to a tachyon scene with glow_lights.tcl Oliver Grant (Fri Oct 19 2018 - 10:07:41 CDT)
Dipole Watcher Plugin - atom selection not updated at every frame when drawing dipoles Eric Lang (Thu Oct 18 2018 - 06:31:41 CDT)
- Re: Dipole Watcher Plugin - atom selection not updated at every frame when drawing dipoles Axel Kohlmeyer (Thu Oct 18 2018 - 08:05:04 CDT)
  - Re: Dipole Watcher Plugin - atom selection not updated at every frame when drawing dipoles Eric Lang (Thu Oct 18 2018 - 08:39:14 CDT)
    - Re: Dipole Watcher Plugin - atom selection not updated at every frame when drawing dipoles Axel Kohlmeyer (Mon Oct 22 2018 - 10:15:14 CDT)
3D hardware Rubner, Oliver (Wed Oct 17 2018 - 03:52:54 CDT)
psfgen patching protein-ligand Francesco Pietra (Tue Oct 16 2018 - 10:13:08 CDT)
- Re: psfgen patching protein-ligand JoÃ£o Ribeiro (Tue Oct 16 2018 - 10:21:24 CDT)
  - Re: psfgen patching protein-ligand Francesco Pietra (Tue Oct 16 2018 - 10:47:35 CDT)
Library to display molecule into Qt widget Endri Kastrati (Thu Oct 11 2018 - 20:00:27 CDT)
- Re: Library to display molecule into Qt widget John Stone (Thu Oct 11 2018 - 21:08:19 CDT)
Display representations with Tk Console Michail Lazaratos (Thu Oct 11 2018 - 12:19:13 CDT)
- Re: Display representations with Tk Console Giacomo Fiorin (Thu Oct 11 2018 - 13:11:43 CDT)
- RE: Display representations with Tk Console Vermaas, Joshua (Thu Oct 11 2018 - 13:53:23 CDT)
  - Re: Display representations with Tk Console Giacomo Fiorin (Thu Oct 11 2018 - 14:35:26 CDT)
- AW: Display representations with Tk Console Daniel MÃ¶ller (Thu Oct 11 2018 - 14:54:29 CDT)
VMD Tk Console Columns McGuire, Kelly (Wed Oct 10 2018 - 14:26:18 CDT)
- Re: VMD Tk Console Columns Giacomo Fiorin (Wed Oct 10 2018 - 15:19:05 CDT)
  - Re: VMD Tk Console Columns McGuire, Kelly (Wed Oct 10 2018 - 19:14:04 CDT)
    - Re: VMD Tk Console Columns Souvik Sinha (Thu Oct 11 2018 - 02:54:11 CDT)
    - Re: VMD Tk Console Columns McGuire, Kelly (Thu Oct 11 2018 - 14:05:56 CDT)
Advantages of new RTX/Turing NVidia cards? Pawel Kedzierski (Wed Oct 10 2018 - 03:55:13 CDT)
- Re: Advantages of new RTX/Turing NVidia cards? John Stone (Wed Oct 10 2018 - 10:21:13 CDT)
  - Re: Advantages of new RTX/Turing NVidia cards? Pawel Kedzierski (Thu Oct 11 2018 - 06:13:47 CDT)
IFD complex for solvation Stephani Macalino (Tue Oct 09 2018 - 02:08:30 CDT)
- Re: IFD complex for solvation Fotis Baltoumas (Tue Oct 09 2018 - 05:18:14 CDT)
What does pbc get -now do Mayank (Sun Oct 07 2018 - 09:36:41 CDT)
- Re: What does pbc get -now do Stefan Doerr (Sun Oct 07 2018 - 12:06:37 CDT)
- Re: What does pbc get -now do Chitrak Gupta (Sun Oct 07 2018 - 12:40:21 CDT)
topotools in place of patching Francesco Pietra (Thu Oct 04 2018 - 09:07:48 CDT)
- RE: topotools in place of patching Vermaas, Joshua (Thu Oct 04 2018 - 14:21:40 CDT)
  - Re: topotools in place of patching Brian Radak (Thu Oct 04 2018 - 15:32:20 CDT)
    - Re: topotools in place of patching Francesco Pietra (Fri Oct 05 2018 - 12:00:09 CDT)
Fwd: Diffusion coefficient calculation Kinkini Jayasundara (Sat Sep 29 2018 - 11:30:47 CDT)
- RE: Fwd: Diffusion coefficient calculation Vermaas, Joshua (Sun Sep 30 2018 - 18:06:15 CDT)
RTX for raytracing Stefan Doerr (Thu Sep 27 2018 - 05:20:51 CDT)
- Re: RTX for raytracing Giacomo Fiorin (Thu Sep 27 2018 - 09:12:41 CDT)
  - Re: RTX for raytracing John Stone (Thu Sep 27 2018 - 10:02:42 CDT)
    - Re: RTX for raytracing Stefan Doerr (Thu Sep 27 2018 - 10:24:35 CDT)
    - Re: RTX for raytracing John Stone (Wed Oct 10 2018 - 10:29:37 CDT)
measuring all the bonds and angles in /Tcl hosein geraili (Tue Sep 25 2018 - 14:48:52 CDT)
RBCG Builder Lewis, Kimberly A (Mon Sep 24 2018 - 13:27:06 CDT)
- Re: RBCG Builder Fotis Baltoumas (Mon Sep 24 2018 - 14:37:34 CDT)
- Re: RBCG Builder Peter Freddolino (Mon Sep 24 2018 - 21:59:09 CDT)
  - Re: RBCG Builder Fotis Baltoumas (Tue Sep 25 2018 - 02:01:04 CDT)
First "Hands-On" Workshop on Structural DNA Nanotechnology JoÃ£o Ribeiro (Mon Sep 24 2018 - 09:13:30 CDT)
- Re: First "Hands-On" Workshop on Structural DNA Nanotechnology Dudo (Mon Sep 24 2018 - 09:49:19 CDT)
Mail about TCL script subramanian vidhyasankar (Sun Sep 23 2018 - 06:36:17 CDT)
reg membrane hydration using tcl script of vmd subramanian vidhyasankar (Sat Sep 22 2018 - 08:14:09 CDT)
mail about renumbering of residues subramanian vidhyasankar (Sat Sep 22 2018 - 08:08:18 CDT)
- Re: mail about renumbering of residues Giacomo Fiorin (Mon Sep 24 2018 - 06:47:57 CDT)
  - Re: mail about renumbering of residues John Stone (Mon Sep 24 2018 - 10:02:58 CDT)
Query about PME data in .dx format Peter Mawanga (Fri Sep 14 2018 - 04:32:10 CDT)
- Re: Query about PME data in .dx format Giacomo Fiorin (Fri Sep 14 2018 - 08:44:08 CDT)
  - Re: Query about PME data in .dx format Peter Mawanga (Fri Sep 14 2018 - 10:55:42 CDT)
problem with Catdcd Sonibare, Kolawole (Mon Sep 10 2018 - 14:13:34 CDT)
- Re: problem with Catdcd Axel Kohlmeyer (Wed Sep 12 2018 - 23:50:14 CDT)
Enhanced Sampling and Free-Energy Calculations Lectures JoÃ£o Ribeiro (Mon Sep 10 2018 - 12:02:42 CDT)
- Re: Enhanced Sampling and Free-Energy Calculations Lectures JoÃ£o Ribeiro (Wed Sep 12 2018 - 08:56:28 CDT)
problem of calculating hydrogen bonds Sasthi Charan Mandal (Sat Sep 08 2018 - 02:19:13 CDT)
- RE: problem of calculating hydrogen bonds Vermaas, Joshua (Sat Sep 08 2018 - 21:45:52 CDT)
  - Re: problem of calculating hydrogen bonds Sasthi Charan Mandal (Sun Sep 09 2018 - 02:33:25 CDT)
    - Re: problem of calculating hydrogen bonds Ashar Malik (Sun Sep 09 2018 - 03:16:05 CDT)
    - Re: problem of calculating hydrogen bonds Sasthi Charan Mandal (Sun Sep 09 2018 - 08:44:18 CDT)
Error at Dihedral Optimization using fftk RABIUL ISLAM (Fri Sep 07 2018 - 04:30:51 CDT)
- Re: Error at Dihedral Optimization using fftk RABIUL ISLAM (Fri Sep 07 2018 - 12:42:29 CDT)
  - RE: Re: Error at Dihedral Optimization using fftk Vermaas, Joshua (Fri Sep 07 2018 - 13:32:40 CDT)
- Re: Error at Dihedral Optimization using fftk Pawel Kedzierski (Wed Dec 12 2018 - 10:09:45 CST)
  - Re: Error at Dihedral Optimization using fftk Gumbart, JC (Wed Dec 12 2018 - 19:15:54 CST)
    - Re: Error at Dihedral Optimization using fftk Pawel Kedzierski (Thu Dec 13 2018 - 09:01:46 CST)
RMSD for specific residue abhik.ghosh_at_bose.res.in (Wed Sep 05 2018 - 09:42:29 CDT)
- Re: RMSD for specific residue John Stone (Fri Sep 07 2018 - 14:28:17 CDT)
Connect particular residues with a line Raag Saluja (Sat Sep 01 2018 - 12:39:02 CDT)
- Re: Connect particular residues with a line Ashar Malik (Sat Sep 01 2018 - 22:39:17 CDT)
Different bond styles in VMD Patzschke, Dr. Michael (Fri Aug 31 2018 - 09:01:28 CDT)
- Re: Different bond styles in VMD Patzschke, Dr. Michael (Mon Sep 03 2018 - 03:37:35 CDT)
MDFF Check CCC problem Rune Thomas Kidmose (Thu Aug 30 2018 - 03:13:28 CDT)
- Re: MDFF Check CCC problem Ryan McGreevy (Thu Aug 30 2018 - 10:20:49 CDT)
  - Re: MDFF Check CCC problem Ryan McGreevy (Fri Aug 31 2018 - 15:57:15 CDT)
Plugins show no text Peter Kroon (Tue Aug 28 2018 - 05:04:06 CDT)
- RE: Plugins show no text Vermaas, Joshua (Tue Aug 28 2018 - 07:21:00 CDT)
  - Re: Plugins show no text Peter Kroon (Wed Aug 29 2018 - 10:04:02 CDT)
  - RE: Plugins show no text P C Kroon (Thu Aug 30 2018 - 04:25:46 CDT)
RE: truncated atom types with fftk v.1.93 - Resolved ABEL Stephane (Mon Aug 27 2018 - 10:45:37 CDT)
- Re: RE: truncated atom types with fftk v.1.93 - Resolved JC Gumbart (Mon Aug 27 2018 - 15:59:23 CDT)
truncated atom types with fftk v.1.93 ABEL Stephane (Mon Aug 27 2018 - 08:48:47 CDT)
- Re: truncated atom types with fftk v.1.93 JC Gumbart (Mon Aug 27 2018 - 15:55:20 CDT)
Nvidia 3D vision not working in Windows 10 Carlos Simmerling (Mon Aug 27 2018 - 08:26:35 CDT)
- Re: Nvidia 3D vision not working in Windows 10 John Stone (Mon Aug 27 2018 - 10:10:00 CDT)
  - Re: Nvidia 3D vision not working in Windows 10 Carlos Simmerling (Mon Aug 27 2018 - 10:20:02 CDT)
(no subject) CMP (Mon Aug 27 2018 - 05:45:29 CDT)
- QwikMD and GROMOS Re: John Stone (Mon Aug 27 2018 - 10:12:44 CDT)
  - Re: QwikMD and GROMOS Re: Brian Radak (Mon Aug 27 2018 - 11:04:26 CDT)
Solvate Plugin Error - Reg Mani Kandan (Mon Aug 27 2018 - 04:31:18 CDT)
- RE: Solvate Plugin Error - Reg Vermaas, Joshua (Mon Aug 27 2018 - 07:56:56 CDT)
  - Re: Solvate Plugin Error - Reg Mani Kandan (Mon Aug 27 2018 - 10:56:31 CDT)
    - Re: Solvate Plugin Error - Reg John Stone (Mon Aug 27 2018 - 11:04:24 CDT)
Secondary structure representation stays static Peter Mawanga (Mon Aug 27 2018 - 02:41:22 CDT)
- Re: Secondary structure representation stays static JÃ©rÃ´me HÃ©nin (Mon Aug 27 2018 - 04:05:58 CDT)
- AW: Secondary structure representation stays static Daniel MÃ¶ller (Mon Aug 27 2018 - 04:31:42 CDT)
  - Re: Secondary structure representation stays static Peter Mawanga (Mon Aug 27 2018 - 04:41:46 CDT)
1.9.4 beta version of VMD ABEL Stephane (Sun Aug 26 2018 - 07:43:43 CDT)
- Re: 1.9.4 beta version of VMD Giacomo Fiorin (Sun Aug 26 2018 - 09:32:31 CDT)
  - RE: 1.9.4 beta version of VMD ABEL Stephane (Sun Aug 26 2018 - 10:12:23 CDT)
    - Re: 1.9.4 beta version of VMD John Stone (Mon Aug 27 2018 - 09:55:17 CDT)
  - Re: 1.9.4 beta version of VMD John Stone (Mon Aug 27 2018 - 11:35:47 CDT)
Running Cionize1.0 Archana Sonawani-Jagtap (Sat Aug 25 2018 - 15:27:45 CDT)
- Re: Running Cionize1.0 Peter Freddolino (Sat Aug 25 2018 - 20:44:35 CDT)
Network Path Backtraces amin sagar (Sat Aug 18 2018 - 13:13:41 CDT)
h-bond water molecules Adriano Santana Sanchez (Sat Aug 18 2018 - 08:54:38 CDT)
Determining energies between two different molecules Nick Palmer (Thu Aug 16 2018 - 10:58:05 CDT)
Atomselection with the position selected conditions inside the loop is not working properly fan li (Thu Aug 16 2018 - 05:47:22 CDT)
- Re: Atomselection with the position selected conditions inside the loop is not working properly Ashar Malik (Thu Aug 16 2018 - 06:50:38 CDT)
  - Re: Atomselection with the position selected conditions inside the loop is not working properly fan li (Thu Aug 16 2018 - 08:05:38 CDT)
    - Re: Atomselection with the position selected conditions inside the loop is not working properly Ashar Malik (Thu Aug 16 2018 - 08:43:50 CDT)
- Re: Atomselection with the position selected conditions inside the loop is not working properly Axel Kohlmeyer (Thu Aug 16 2018 - 08:14:03 CDT)
  - Re: Atomselection with the position selected conditions inside the loop is not working properly JoÃ£o Ribeiro (Thu Aug 16 2018 - 08:23:51 CDT)
Userani.tcl script jumps frame after no play sperez14_at_us.es (Wed Aug 15 2018 - 09:26:52 CDT)
- AW: Userani.tcl script jumps frame after no play Norman Geist (Thu Aug 16 2018 - 01:41:22 CDT)
Unexpected results after loop added to the script fan li (Tue Aug 14 2018 - 11:32:26 CDT)
display residues near ligand Graham Jackson (Sat Aug 11 2018 - 02:38:55 CDT)
- Re: display residues near ligand amin sagar (Sat Aug 11 2018 - 03:14:12 CDT)
Research Programmers Positions Available JoÃ£o Ribeiro (Fri Aug 10 2018 - 13:30:28 CDT)
[VMD] Cannot find "cionize" plugin The Cromicus Productions (Fri Aug 10 2018 - 02:07:11 CDT)
- Re: [VMD] Cannot find "cionize" plugin The Cromicus Productions (Fri Aug 10 2018 - 02:35:45 CDT)
  - Re: [VMD] Cannot find "cionize" plugin JC Gumbart (Sun Aug 12 2018 - 10:44:49 CDT)
    - Re: [VMD] Cannot find "cionize" plugin The Cromicus Productions (Mon Aug 13 2018 - 00:03:23 CDT)
Rendering Images from VMD Phuong Chau (Tue Aug 07 2018 - 12:20:48 CDT)
Derivation of parameters for a ligand with a Cl atom with fftk ABEL Stephane (Mon Aug 06 2018 - 08:21:57 CDT)
- Re: Derivation of parameters for a ligand with a Cl atom with fftk JC Gumbart (Mon Aug 06 2018 - 11:34:48 CDT)
  - RE: Derivation of parameters for a ligand with a Cl atom with fftk ABEL Stephane (Tue Aug 07 2018 - 05:17:10 CDT)
VMD help - select model shyama Prasad rao (Mon Aug 06 2018 - 01:03:18 CDT)
Updates McGuire, Kelly (Sun Aug 05 2018 - 14:06:26 CDT)
Where to save the script Funzo_at_seznam.cz (Sun Aug 05 2018 - 10:38:14 CDT)
- Re: Where to save the script Ashar Malik (Sun Aug 05 2018 - 20:38:47 CDT)
  - Re: Where to save the script Funzo_at_seznam.cz (Mon Aug 06 2018 - 04:02:58 CDT)
Molden orbitals: how to increase the bounding box size? Vladimir Stegailov (Sat Aug 04 2018 - 07:10:18 CDT)
- Re: Molden orbitals: how to increase the bounding box size? John Stone (Sat Aug 04 2018 - 09:59:04 CDT)
Vibrational spectra script Aashish Bhatt (Sat Aug 04 2018 - 03:59:48 CDT)
Charge opt in FFTK Ushasi Pramanik 1710228 (Fri Aug 03 2018 - 05:25:34 CDT)
Alascan, psfgen errors Matthew Kenney (Thu Aug 02 2018 - 17:19:16 CDT)
Please remove me from mailing list Christine Horejs (Wed Aug 01 2018 - 04:59:12 CDT)
- Re: Please remove me from mailing list John Stone (Thu Aug 02 2018 - 12:00:45 CDT)
Rendering incompletion during Tachyon rendering Tony Myung Keun Cho (Tue Jul 31 2018 - 19:22:46 CDT)
- Re: Rendering incompletion during Tachyon rendering John Stone (Tue Jul 31 2018 - 21:41:59 CDT)
request for provide a script of rmsf Sasthi Charan Mandal (Tue Jul 31 2018 - 10:21:20 CDT)
- Re: request for provide a script of rmsf Ashar Malik (Tue Jul 31 2018 - 19:40:09 CDT)
  - Re: request for provide a script of rmsf Sasthi Charan Mandal (Wed Aug 01 2018 - 03:17:04 CDT)
Solvate plugin Error - reg Mani Kandan (Tue Jul 31 2018 - 06:24:53 CDT)
- Re: Solvate plugin Error - reg John Stone (Tue Jul 31 2018 - 11:53:39 CDT)
  - Re: Solvate plugin Error - reg John Stone (Tue Jul 31 2018 - 11:57:52 CDT)
VR McGuire, Kelly (Mon Jul 30 2018 - 19:38:07 CDT)
- Re: VR John Stone (Tue Jul 31 2018 - 14:03:29 CDT)
  - Re: VR McGuire, Kelly (Tue Jul 31 2018 - 14:06:36 CDT)
- Re: VR Alin Marin Elena - UKRI STFC (Wed Aug 22 2018 - 15:49:22 CDT)
"Hands-on" Workshop on Enhanced Sampling and Free-Energy Calculation at Urbana, IL, September 10-14, 2018 JoÃ£o Ribeiro (Mon Jul 30 2018 - 16:15:45 CDT)
Force Field Toolkit (ffTK) Norge Cruz HernÃ¡ndez (Mon Jul 30 2018 - 05:32:39 CDT)
- Re: Force Field Toolkit (ffTK) JC Gumbart (Mon Jul 30 2018 - 06:57:51 CDT)
  - Re: Force Field Toolkit (ffTK) Norge Cruz HernÃ¡ndez (Wed Aug 08 2018 - 11:43:40 CDT)
request for provide a script of rmsf Sasthi Charan Mandal (Mon Jul 30 2018 - 04:24:22 CDT)
split multi frame pdb abhik.ghosh_at_bose.res.in (Mon Jul 30 2018 - 00:18:10 CDT)
- Re: split multi frame pdb amin sagar (Mon Jul 30 2018 - 00:57:09 CDT)
  - Re: split multi frame pdb abhik.ghosh_at_bose.res.in (Mon Jul 30 2018 - 01:01:47 CDT)
Farewell VMD Vlastimil ZÃma (Sun Jul 29 2018 - 14:02:54 CDT)
- Re: Farewell VMD Giacomo Fiorin (Mon Jul 30 2018 - 08:40:36 CDT)
  - Re: Farewell VMD Ivan Gregoretti (Mon Jul 30 2018 - 11:33:01 CDT)
    - Re: Farewell VMD John Stone (Mon Jul 30 2018 - 11:56:46 CDT)
    - Re: Farewell VMD Giacomo Fiorin (Mon Jul 30 2018 - 13:03:55 CDT)
  - RE: Farewell VMD Vermaas, Joshua (Mon Jul 30 2018 - 12:38:26 CDT)
reg compilation of vmd 1.9.3 subramanian vidhyasankar (Sun Jul 29 2018 - 08:38:56 CDT)
- Re: reg compilation of vmd 1.9.3 John Stone (Mon Jul 30 2018 - 14:37:17 CDT)
Mail reg compilation of vmd 1.9.3 plugin subramanian vidhyasankar (Sat Jul 28 2018 - 03:10:19 CDT)
- Re: Mail reg compilation of vmd 1.9.3 plugin Giacomo Fiorin (Sat Jul 28 2018 - 08:30:00 CDT)
Fusing proteins together Nick Palmer (Thu Jul 26 2018 - 13:53:48 CDT)
- Re: Fusing proteins together Ashar Malik (Thu Jul 26 2018 - 16:01:55 CDT)
  - Re: Fusing proteins together Dhiraj Srivastava (Thu Jul 26 2018 - 16:50:55 CDT)
    - Re: Fusing proteins together Ashar Malik (Thu Jul 26 2018 - 19:33:48 CDT)
    - Re: Fusing proteins together Nick Palmer (Fri Jul 27 2018 - 10:05:31 CDT)
Porcupine plot with nmwiz Funzo_at_seznam.cz (Thu Jul 26 2018 - 09:34:19 CDT)
- Re: Porcupine plot with nmwiz John Stone (Tue Jul 31 2018 - 10:03:14 CDT)
  - Re: Porcupine plot with nmwiz Funzo_at_seznam.cz (Tue Jul 31 2018 - 11:06:17 CDT)
    - Re: Porcupine plot with nmwiz John Stone (Tue Jul 31 2018 - 11:38:16 CDT)
Timeline error Jordi Bujons (Tue Jul 24 2018 - 12:13:01 CDT)
- Re: Timeline error SebastiÃ¡n GutiÃ©rrez (Tue Aug 07 2018 - 15:01:11 CDT)
psfgen building fails due to locale Stefan Doerr (Mon Jul 23 2018 - 07:28:16 CDT)
- Re: psfgen building fails due to locale Axel Kohlmeyer (Mon Jul 23 2018 - 08:12:37 CDT)
  - Re: psfgen building fails due to locale Stefan Doerr (Mon Jul 23 2018 - 08:15:25 CDT)
IR spectral density calculation Aashish Bhatt (Sun Jul 22 2018 - 12:53:34 CDT)
- Re: IR spectral density calculation Axel Kohlmeyer (Sun Jul 22 2018 - 14:26:45 CDT)
(no subject) abhik.ghosh_at_bose.res.in (Sun Jul 22 2018 - 05:16:07 CDT)
- Re: Ashar Malik (Sun Jul 22 2018 - 05:48:29 CDT)
(no subject) abhik.ghosh_at_bose.res.in (Sun Jul 22 2018 - 05:00:41 CDT)
Building Al2O3 or Fe2O3 Morrissey, Liam S. (Sat Jul 21 2018 - 15:59:29 CDT)
New Cartoon and Simulation Question McGuire, Kelly (Wed Jul 18 2018 - 19:18:34 CDT)
- Re: New Cartoon and Simulation Question Robin Betz (Wed Jul 18 2018 - 20:14:47 CDT)
  - Re: New Cartoon and Simulation Question McGuire, Kelly (Wed Jul 18 2018 - 20:23:03 CDT)
  - Re: New Cartoon and Simulation Question McGuire, Kelly (Wed Jul 18 2018 - 20:22:06 CDT)
Deleting a given bond type by topo tool Amir Hossein Saeedi Dehaghani (Wed Jul 18 2018 - 07:15:40 CDT)
- Re: Deleting a given bond type by topo tool Axel Kohlmeyer (Wed Jul 18 2018 - 08:27:37 CDT)
Fwd: problemas con la opt de los enlaces dalpizar_at_fbio.uh.cu (Tue Jul 17 2018 - 15:05:07 CDT)
- Re: Fwd: problemas con la opt de los enlaces Fotis Baltoumas (Tue Jul 17 2018 - 16:30:45 CDT)
  - Re: Fwd: problemas con la opt de los enlaces JC Gumbart (Wed Jul 18 2018 - 09:02:33 CDT)
    - Re: Fwd: problemas con la opt de los enlaces dalpizar_at_fbio.uh.cu (Wed Jul 18 2018 - 10:38:52 CDT)
- Re: Fwd: problemas con la opt de los enlaces JC Gumbart (Tue Jul 17 2018 - 16:46:10 CDT)
Autopsf CGenFF input Stamatia Zavitsanou (Tue Jul 17 2018 - 03:59:29 CDT)
- Re: Autopsf CGenFF input Peter Freddolino (Tue Jul 17 2018 - 08:00:32 CDT)
  - Re: Autopsf CGenFF input Stamatia Zavitsanou (Tue Jul 17 2018 - 08:56:10 CDT)
Deleting a given bond type by topo tool Amir Hossein Saeedi Dehaghani (Tue Jul 17 2018 - 02:58:20 CDT)
Dowser Availability McGuire, Kelly (Mon Jul 16 2018 - 14:54:05 CDT)
- Re: Dowser Availability Giacomo Fiorin (Mon Jul 16 2018 - 15:53:03 CDT)
  - Re: Dowser Availability Giacomo Fiorin (Mon Jul 16 2018 - 16:14:13 CDT)
    - Re: Dowser Availability John Stone (Mon Jul 16 2018 - 17:50:50 CDT)
Fully Visual Docker Container for VMD Matthew Kenney (Mon Jul 16 2018 - 10:00:16 CDT)
- Re: Fully Visual Docker Container for VMD John Stone (Mon Jul 16 2018 - 15:06:35 CDT)
  - Re: Fully Visual Docker Container for VMD Matthew Kenney (Mon Jul 16 2018 - 15:37:32 CDT)
    - Re: Fully Visual Docker Container for VMD Matthew Kenney (Mon Jul 16 2018 - 15:49:49 CDT)
maiil about installation of vmd1.9.3 from source code subramanian vidhyasankar (Fri Jul 13 2018 - 09:47:28 CDT)
- Re: maiil about installation of vmd1.9.3 from source code Joaquim Rui de Castro Rodrigues (Fri Jul 13 2018 - 10:39:54 CDT)
Issue with visualizing model Yu,Wenjin (Thu Jul 12 2018 - 10:35:57 CDT)
- Re: Issue with visualizing model Axel Kohlmeyer (Sat Jul 14 2018 - 01:16:28 CDT)
Problem with parametrization using ffTK Ushasi Pramanik 1710228 (Thu Jul 12 2018 - 04:58:55 CDT)
- RE: Problem with parametrization using ffTK Vermaas, Joshua (Fri Jul 13 2018 - 20:43:10 CDT)
Reopening the Discussion on visual VMD container: GLX now enabled Matthew Kenney (Tue Jul 10 2018 - 16:47:00 CDT)
Fixing Martini PSF Ganne, Akshatha (Mon Jul 09 2018 - 18:00:38 CDT)
Gamma Silicon Nitrite Crystal - Reg Mani Kandan (Mon Jul 09 2018 - 12:48:32 CDT)
Tachyon with DoF ignores FocalLength Peter Kroon (Mon Jul 09 2018 - 09:36:14 CDT)
- Re: Tachyon with DoF ignores FocalLength Peter Kroon (Wed Aug 01 2018 - 03:48:45 CDT)
  - RE: Re: Tachyon with DoF ignores FocalLength Vermaas, Joshua (Wed Aug 01 2018 - 06:02:13 CDT)
    - Re: Re: Tachyon with DoF ignores FocalLength Peter Kroon (Thu Aug 02 2018 - 05:03:21 CDT)
    - RE: Re: Tachyon with DoF ignores FocalLength Vermaas, Joshua (Thu Aug 02 2018 - 09:12:47 CDT)
  - Re: Re: Tachyon with DoF ignores FocalLength John Stone (Thu Aug 02 2018 - 11:58:08 CDT)
"Prepare Parameterization from CGenFF Program Output" in ffTK Ushasi Pramanik 1710228 (Sun Jul 08 2018 - 23:04:00 CDT)
- Re: "Prepare Parameterization from CGenFF Program Output" in ffTK Hazel, Justin (Mon Jul 09 2018 - 08:09:02 CDT)
  - Re: "Prepare Parameterization from CGenFF Program Output" in ffTK Hazel, Justin (Mon Jul 09 2018 - 12:59:00 CDT)
Merge Structures Bug McGuire, Kelly (Fri Jul 06 2018 - 16:34:43 CDT)
- RE: Merge Structures Bug Vermaas, Joshua (Mon Jul 09 2018 - 09:35:32 CDT)
Issue with NVIDIA GPU Cloud VMD Container Matthew Kenney (Fri Jul 06 2018 - 15:50:59 CDT)
- Re: Issue with NVIDIA GPU Cloud VMD Container John Stone (Fri Jul 06 2018 - 16:04:51 CDT)
  - Re: Issue with NVIDIA GPU Cloud VMD Container John Stone (Fri Jul 06 2018 - 16:07:05 CDT)
  - Re: Issue with NVIDIA GPU Cloud VMD Container Matthew Kenney (Fri Jul 06 2018 - 16:20:05 CDT)
    - Re: Issue with NVIDIA GPU Cloud VMD Container Matthew Kenney (Fri Jul 06 2018 - 17:13:59 CDT)
Importing .str file generated by ParamChem to molefacture in VMD Ushasi Pramanik 1710228 (Fri Jul 06 2018 - 05:43:07 CDT)
- Re: Importing .str file generated by ParamChem to molefacture in VMD Hazel, Justin (Fri Jul 06 2018 - 09:55:10 CDT)
Re: Problem with QwikMD and glycans JoÃ£o Ribeiro (Thu Jul 05 2018 - 13:28:00 CDT)
Membrane Protein Tutorial Bug McGuire, Kelly (Thu Jul 05 2018 - 10:24:41 CDT)
- Re: Membrane Protein Tutorial Bug JoÃ£o Ribeiro (Thu Jul 05 2018 - 13:01:24 CDT)
- Re: Membrane Protein Tutorial Bug John Stone (Thu Jul 05 2018 - 15:12:20 CDT)
Ph.D. candidate position in biomolecular modeling or bioinformatics Jan Brezovsky (Wed Jul 04 2018 - 05:33:36 CDT)
grid mode in vmd? Murpholino Peligro (Tue Jul 03 2018 - 18:26:11 CDT)
- Re: grid mode in vmd? John Stone (Thu Jul 05 2018 - 09:07:37 CDT)
Possible to run VMD in parallel - Reg Mani Kandan (Tue Jul 03 2018 - 13:42:21 CDT)
- Re: Possible to run VMD in parallel - Reg John Stone (Thu Jul 05 2018 - 09:09:51 CDT)
  - Re: Possible to run VMD in parallel - Reg Mani Kandan (Thu Jul 05 2018 - 09:50:31 CDT)
    - Re: Possible to run VMD in parallel - Reg John Stone (Thu Jul 05 2018 - 15:09:01 CDT)
    - Re: Possible to run VMD in parallel - Reg Mani Kandan (Thu Jul 05 2018 - 21:03:55 CDT)
How to define charge group and pass it to topo writegmxtop fan li (Mon Jul 02 2018 - 05:17:56 CDT)
- Re: How to define charge group and pass it to topo writegmxtop Axel Kohlmeyer (Mon Jul 02 2018 - 06:07:08 CDT)
distance-based selections applied to velDCD Mike McCallum (Fri Jun 29 2018 - 16:01:56 CDT)
- RE: distance-based selections applied to velDCD Vermaas, Joshua (Fri Jun 29 2018 - 18:28:58 CDT)
- Re: distance-based selections applied to velDCD Mike McCallum (Sat Jun 30 2018 - 12:00:27 CDT)
  - Re: distance-based selections applied to velDCD Mike McCallum (Tue Jul 03 2018 - 15:25:42 CDT)
Different colors of a residue at different frames Cruzeiro,Vinicius Wilian D (Thu Jun 28 2018 - 16:13:29 CDT)
- RE: Different colors of a residue at different frames Vermaas, Joshua (Thu Jun 28 2018 - 17:53:00 CDT)
- RE: Different colors of a residue at different frames Vermaas, Joshua (Fri Jun 29 2018 - 12:27:47 CDT)
  - Re: Different colors of a residue at different frames Cruzeiro,Vinicius Wilian D (Sun Jul 01 2018 - 11:00:50 CDT)
Inorganic builder in no display mode - Reg Mani Kandan (Wed Jun 27 2018 - 10:32:00 CDT)
- Re: Inorganic builder in no display mode - Reg John Stone (Tue Jul 03 2018 - 11:41:10 CDT)
  - Re: Inorganic builder in no display mode - Reg Mani Kandan (Tue Jul 03 2018 - 13:17:22 CDT)
Error in PCA analysis Aravind Ravichandran (Wed Jun 27 2018 - 05:26:18 CDT)
- Re: Error in PCA analysis John Stone (Tue Jul 03 2018 - 11:46:14 CDT)
Error: not possible to build nodeSelString: () and () Sophie Mader (Tue Jun 26 2018 - 04:27:04 CDT)
- AW: Error: not possible to build nodeSelString: () and () Sophie Mader (Thu Jun 28 2018 - 07:37:02 CDT)
  - Re: AW: Error: not possible to build nodeSelString: () and () John Stone (Tue Jul 03 2018 - 11:14:40 CDT)
Frame out of range when trying to edit .psf Francesco Pietra (Sat Jun 23 2018 - 11:46:37 CDT)
- Re: Frame out of range when trying to edit .psf Francesco Pietra (Sun Jun 24 2018 - 03:29:24 CDT)
catdcd error opening reading index file Francesco Pietra (Sat Jun 23 2018 - 04:11:57 CDT)
- Fwd: catdcd error opening reading index file Francesco Pietra (Sat Jun 23 2018 - 09:01:53 CDT)
  - Fwd: catdcd error opening reading index file Francesco Pietra (Sat Jun 23 2018 - 09:45:23 CDT)
Strange Bond Behavior Question McGuire, Kelly (Fri Jun 22 2018 - 15:42:20 CDT)
- Re: namd-l: Strange Bond Behavior Question JoÃ£o Ribeiro (Fri Jun 22 2018 - 16:08:07 CDT)
Opt. Bonded: Angle in multiple rings dalpizar_at_fbio.uh.cu (Fri Jun 22 2018 - 11:15:59 CDT)
- Re: Opt. Bonded: Angle in multiple rings John Stone (Fri Jun 22 2018 - 11:21:01 CDT)
vmd keeps crashing Graham Jackson (Fri Jun 22 2018 - 04:31:28 CDT)
- Re: vmd keeps crashing John Stone (Fri Jun 22 2018 - 04:45:37 CDT)
Solvation using Charmm36 TIP3P Muthukumaran Rajagopalan (Fri Jun 22 2018 - 02:31:54 CDT)
- Re: Solvation using Charmm36 TIP3P JoÃ£o Ribeiro (Fri Jun 22 2018 - 09:07:03 CDT)
Z-axis data extraction Aashish Bhatt (Thu Jun 21 2018 - 23:13:00 CDT)
Amber rst7 not loading Sophia Hirakis (Wed Jun 20 2018 - 20:25:28 CDT)
(no subject) Mohammadi, Mohammadjavad (Wed Jun 20 2018 - 20:12:40 CDT)
- Re: John Stone (Thu Jun 21 2018 - 13:19:56 CDT)
  - RE: Mohammadjavad Mohammadi (Fri Jun 22 2018 - 10:26:18 CDT)
    - Re: John Stone (Fri Jun 22 2018 - 11:09:56 CDT)
QwikMD Restraints Question McGuire, Kelly (Wed Jun 20 2018 - 17:37:28 CDT)
- Re: QwikMD Restraints Question JoÃ£o Ribeiro (Wed Jun 20 2018 - 17:56:49 CDT)
  - Re: QwikMD Restraints Question McGuire, Kelly (Wed Jun 20 2018 - 18:07:50 CDT)
Atom Selections in QwikMD SM Bargeen A Turzo (Wed Jun 20 2018 - 14:28:03 CDT)
- Re: Atom Selections in QwikMD JoÃ£o Ribeiro (Wed Jun 20 2018 - 17:06:36 CDT)
  - Re: Atom Selections in QwikMD JoÃ£o Ribeiro (Thu Jun 21 2018 - 10:03:44 CDT)
Connecting new residues to old residues in topology file Nick Palmer (Wed Jun 20 2018 - 13:28:08 CDT)
- Re: Connecting new residues to old residues in topology file Peter Freddolino (Wed Jun 20 2018 - 21:10:23 CDT)
Vmd tcl versions Bennion, Brian (Mon Jun 18 2018 - 11:04:01 CDT)
- Re: Vmd tcl versions John Stone (Mon Jun 18 2018 - 14:57:10 CDT)
mail about installation of vmd 1.9 in cluster subramanian vidhyasankar (Mon Jun 18 2018 - 02:20:09 CDT)
- Re: mail about installation of vmd 1.9 in cluster John Stone (Wed Jun 20 2018 - 14:51:37 CDT)
z-direction selection Aashish Bhatt (Mon Jun 18 2018 - 00:33:50 CDT)
- AW: z-direction selection Norman Geist (Mon Jun 18 2018 - 02:38:44 CDT)
(no subject) shyam sharma (Sun Jun 17 2018 - 03:24:35 CDT)
tcl script to pull pdb file from tgz Bennion, Brian (Fri Jun 15 2018 - 10:08:50 CDT)
- Re: tcl script to pull pdb file from tgz John Stone (Thu Jun 21 2018 - 21:40:58 CDT)
  - Re: tcl script to pull pdb file from tgz Axel Kohlmeyer (Thu Jun 21 2018 - 22:18:58 CDT)
    - Re: tcl script to pull pdb file from tgz Bennion, Brian (Fri Jun 22 2018 - 11:19:24 CDT)
Easy way to add hydrogens and get their internal coordinates? Nick Palmer (Thu Jun 14 2018 - 13:27:56 CDT)
- RE: Easy way to add hydrogens and get their internal coordinates? Vermaas, Joshua (Fri Jun 15 2018 - 04:51:49 CDT)
  - Re: Easy way to add hydrogens and get their internal coordinates? Nick Palmer (Wed Jun 20 2018 - 12:42:00 CDT)
- Re: Easy way to add hydrogens and get their internal coordinates? Peter Freddolino (Fri Jun 15 2018 - 12:27:16 CDT)
  - Re: Easy way to add hydrogens and get their internal coordinates? Nick Palmer (Wed Jun 20 2018 - 12:38:12 CDT)
ribbon on different thickness Graham Jackson (Wed Jun 13 2018 - 10:29:45 CDT)
- Re: ribbon on different thickness John Stone (Fri Jun 22 2018 - 03:25:25 CDT)
Chiral indices in VMD Nanotube Builder Akif Ramzan (Wed Jun 13 2018 - 08:10:11 CDT)
How to apply uniform surface charge ? Mani Kandan (Mon Jun 11 2018 - 22:37:08 CDT)
topotools/topogromacs Francesco Pietra (Mon Jun 11 2018 - 15:30:51 CDT)
- Re: topotools/topogromacs John Stone (Mon Jun 11 2018 - 15:53:42 CDT)
  - RE: topotools/topogromacs Vermaas, Joshua (Wed Jun 13 2018 - 04:53:57 CDT)
Protein mutation issues Bose, Ritwika (Sun Jun 10 2018 - 23:27:29 CDT)
- Re: Protein mutation issues Ashar Malik (Mon Jun 11 2018 - 00:22:13 CDT)
  - Re: Protein mutation issues JoÃ£o Ribeiro (Wed Jun 13 2018 - 09:24:26 CDT)
(no subject) shyam sharma (Sat Jun 09 2018 - 12:14:07 CDT)
Calculation of pair distribution function shyam sharma (Sat Jun 09 2018 - 00:19:21 CDT)
vmd startup sequence Goedde, Chris (Thu Jun 07 2018 - 17:03:51 CDT)
- RE: vmd startup sequence Vermaas, Joshua (Fri Jun 08 2018 - 00:06:54 CDT)
  - Re: vmd startup sequence Goedde, Chris (Fri Jun 08 2018 - 10:53:45 CDT)
Custom VMD script development service for fee Neeraj (Thu Jun 07 2018 - 15:08:32 CDT)
- Re: Custom VMD script development service for fee Andrew Dalke (Fri Jun 08 2018 - 06:57:14 CDT)
VMD Update Questions McGuire, Kelly (Tue Jun 05 2018 - 12:11:42 CDT)
- Re: VMD Update Questions John Stone (Mon Jun 11 2018 - 10:32:19 CDT)
  - Re: VMD Update Questions McGuire, Kelly (Mon Jun 11 2018 - 12:05:08 CDT)
Flipping a molecule around its geometrical center Lorenzo Casalino (Mon Jun 04 2018 - 21:38:37 CDT)
- Re: Flipping a molecule around its geometrical center Ashar Malik (Mon Jun 04 2018 - 23:29:51 CDT)
  - Re: Flipping a molecule around its geometrical center Casalino, Lorenzo (Mon Jun 04 2018 - 23:37:12 CDT)
- Re: Flipping a molecule around its geometrical center JC Gumbart (Mon Jun 04 2018 - 23:39:24 CDT)
- RE: Flipping a molecule around its geometrical center Vermaas, Joshua (Tue Jun 05 2018 - 07:55:00 CDT)
Issue with "measure rmsf" command Peter Mawanga (Mon Jun 04 2018 - 10:49:11 CDT)
- RE: Issue with "measure rmsf" command Vermaas, Joshua (Mon Jun 04 2018 - 11:46:56 CDT)
  - Re: Issue with "measure rmsf" command Peter Mawanga (Mon Jun 04 2018 - 11:58:32 CDT)
    - RE: Issue with "measure rmsf" command Vermaas, Joshua (Mon Jun 04 2018 - 12:03:22 CDT)
- Re: Issue with "measure rmsf" command Peter Mawanga (Mon Jun 04 2018 - 11:39:37 CDT)
problem with mol IDs when running script from same VMD session. Rune Thomas Kidmose (Sun Jun 03 2018 - 14:02:31 CDT)
- Re: problem with mol IDs when running script from same VMD session. Ashar Malik (Sun Jun 03 2018 - 14:29:11 CDT)
  - Sv: problem with mol IDs when running script from same VMD session. Rune Thomas Kidmose (Sun Jun 03 2018 - 14:33:45 CDT)
    - Re: problem with mol IDs when running script from same VMD session. Ryan McGreevy (Sun Jun 03 2018 - 14:40:31 CDT)
NAMD and FFTK on a Mac tclick_at_nctu.edu.tw (Fri Jun 01 2018 - 07:24:41 CDT)
- Re: NAMD and FFTK on a Mac JC Gumbart (Sat Jun 02 2018 - 20:07:26 CDT)
  - Re: NAMD and FFTK on a Mac JC Gumbart (Sun Jun 03 2018 - 22:26:04 CDT)
VMD 1.9.4 for Windows? Pawel Kedzierski (Fri Jun 01 2018 - 02:54:26 CDT)
PMF Question McGuire, Kelly (Thu May 31 2018 - 13:39:07 CDT)
- Re: PMF Question JÃ©rÃ´me HÃ©nin (Mon Jun 04 2018 - 07:26:33 CDT)
  - Re: PMF Question McGuire, Kelly (Mon Jun 04 2018 - 09:35:28 CDT)
Re: Alignment with RMSD trajectory tool Ashar Malik (Tue May 29 2018 - 21:00:08 CDT)
Alignment with RMSD trajectory tool Gulce Kalyoncu (Tue May 29 2018 - 20:42:15 CDT)
ABF lowerboundary upperboundary McGuire, Kelly (Tue May 29 2018 - 13:54:39 CDT)
Large number of harmonic distance restraints Nick Palmer (Tue May 29 2018 - 11:04:27 CDT)
- Re: Large number of harmonic distance restraints Giacomo Fiorin (Tue May 29 2018 - 11:30:34 CDT)
alpha-quartz with hydrogen bond Suu Kyi, Myat Noe (Tue May 29 2018 - 10:46:49 CDT)
Reading DL_POLY trajectory Ali Ahmed (Sat May 26 2018 - 20:02:17 CDT)
- Re: Reading DL_POLY trajectory Ashar Malik (Sat May 26 2018 - 20:28:34 CDT)
ABF Question McGuire, Kelly (Sat May 26 2018 - 13:44:20 CDT)
Creating a constraints file(.pdb) from NMR constraints file(.mr) Nick Palmer (Thu May 24 2018 - 15:40:08 CDT)
alter crosshair appearance Daniel Strahs (Thu May 24 2018 - 12:48:30 CDT)
- Re: alter crosshair appearance John Stone (Fri Jun 22 2018 - 03:15:09 CDT)
  - Re: alter crosshair appearance Barry Isralewitz (Fri Jun 22 2018 - 13:18:31 CDT)
ABF Calculations Question 1 McGuire, Kelly (Thu May 24 2018 - 12:10:34 CDT)
- Re: ABF Calculations Question 1 JÃ©rÃ´me HÃ©nin (Fri May 25 2018 - 07:43:40 CDT)
- Re: ABF Calculations Question 1 Giacomo Fiorin (Fri May 25 2018 - 08:09:32 CDT)
  - Re: ABF Calculations Question 1 McGuire, Kelly (Fri May 25 2018 - 10:30:48 CDT)
    - Re: ABF Calculations Question 1 Brian Radak (Fri May 25 2018 - 12:40:32 CDT)
    - Re: ABF Calculations Question 1 McGuire, Kelly (Fri May 25 2018 - 19:22:03 CDT)
Adding a hydrogen through the command line and Molefacture David Stevens (Thu May 24 2018 - 11:58:39 CDT)
- Re: Adding a hydrogen through the command line and Molefacture Peter Freddolino (Thu May 24 2018 - 21:57:32 CDT)
Scan Torsions McGuire, Kelly (Wed May 23 2018 - 13:28:01 CDT)
- RE: Scan Torsions Vermaas, Joshua (Wed May 23 2018 - 16:39:44 CDT)
  - Re: Scan Torsions McGuire, Kelly (Wed May 23 2018 - 21:19:54 CDT)
- Re: Scan Torsions Peter Freddolino (Wed May 23 2018 - 22:07:13 CDT)
  - Re: Scan Torsions Giacomo Fiorin (Thu May 24 2018 - 08:33:37 CDT)
Finding Local Kinetic Energy or Velocities Nick Palmer (Wed May 23 2018 - 10:28:53 CDT)
- Re: Finding Local Kinetic Energy or Velocities Axel Kohlmeyer (Wed May 23 2018 - 10:55:36 CDT)
NAMD Energy Plugin: Cutoff error Peter Mawanga (Wed May 23 2018 - 08:42:05 CDT)
- Re: NAMD Energy Plugin: Cutoff error Fotis Baltoumas (Wed May 23 2018 - 09:37:49 CDT)
  - Re: NAMD Energy Plugin: Cutoff error Peter Mawanga (Mon Jun 04 2018 - 10:24:09 CDT)
SPC/E Water models Mani Kandan (Wed May 23 2018 - 04:36:36 CDT)
- Re: SPC/E Water models Peter Freddolino (Wed May 23 2018 - 11:19:35 CDT)
  - Re: SPC/E Water models Mani Kandan (Wed May 23 2018 - 11:36:20 CDT)
    - Re: SPC/E Water models Manoj Dhiman (Wed May 23 2018 - 11:49:44 CDT)
How autoionzie plugin works? Mani Kandan (Tue May 22 2018 - 12:44:47 CDT)
- Re: How autoionzie plugin works? JoÃ£o Ribeiro (Tue May 22 2018 - 13:25:25 CDT)
  - Re: How autoionzie plugin works? JoÃ£o Ribeiro (Tue May 22 2018 - 13:43:05 CDT)
How can I redefine fragments in VMD fan li (Tue May 22 2018 - 11:43:38 CDT)
- RE: How can I redefine fragments in VMD Vermaas, Joshua (Tue May 22 2018 - 13:40:54 CDT)
RMSF_Calculation_Error_Using script Rinky Parakra (Mon May 21 2018 - 19:32:48 CDT)
Need FFTK Help from Someone w/ Gaussian Alex Saad-Falcon (Mon May 21 2018 - 13:05:32 CDT)
- Re: Need FFTK Help from Someone w/ Gaussian jrhau lung (Mon May 21 2018 - 19:22:37 CDT)
FFTK Tutorial Charge Opt Question McGuire, Kelly (Fri May 18 2018 - 23:59:48 CDT)
- RE: FFTK Tutorial Charge Opt Question Vermaas, Joshua (Sat May 19 2018 - 13:43:41 CDT)
  - Re: FFTK Tutorial Charge Opt Question McGuire, Kelly (Sat May 19 2018 - 14:21:07 CDT)
FFTK Charge Optimization McGuire, Kelly (Fri May 18 2018 - 11:58:14 CDT)
- RE: FFTK Charge Optimization Vermaas, Joshua (Fri May 18 2018 - 13:25:05 CDT)
  - Re: FFTK Charge Optimization McGuire, Kelly (Fri May 18 2018 - 13:36:22 CDT)
invalid command name "La::mevsvd_br" SHAHEE ISLAM (Fri May 18 2018 - 00:43:54 CDT)
- Re: invalid command name "La::mevsvd_br" SHAHEE ISLAM (Fri May 18 2018 - 01:03:50 CDT)
  - RE: Re: invalid command name "La::mevsvd_br" Vermaas, Joshua (Fri May 18 2018 - 07:19:11 CDT)
- Re: invalid command name "La::mevsvd_br" Jim Parker (Fri May 18 2018 - 16:34:59 CDT)
rst7 as input file bug James Kress (Thu May 17 2018 - 18:36:27 CDT)
- Re: rst7 as input file bug Robin Betz (Thu May 17 2018 - 19:45:20 CDT)
  - RE: rst7 as input file bug James Kress (Thu May 17 2018 - 21:24:15 CDT)
QwikMD Add Topo+Param Question McGuire, Kelly (Thu May 17 2018 - 12:40:08 CDT)
- Re: QwikMD Add Topo+Param Question JoÃ£o Ribeiro (Mon May 21 2018 - 09:57:49 CDT)
.js file format for point cloud data TRINH Minh Hieu (Wed May 16 2018 - 20:35:56 CDT)
- RE: .js file format for point cloud data Vermaas, Joshua (Thu May 17 2018 - 12:14:24 CDT)
diffusion coefficient tool Suresh Ghimire (Wed May 16 2018 - 02:32:55 CDT)
- Re: diffusion coefficient tool Roshan Shrestha (Wed May 16 2018 - 06:21:40 CDT)
How can I create the water Solvate in vmd fan li (Tue May 15 2018 - 16:59:11 CDT)
- RE: How can I create the water Solvate in vmd Vermaas, Joshua (Tue May 15 2018 - 18:07:47 CDT)
- Re: How can I create the water Solvate in vmd Dallas Warren (Tue May 15 2018 - 20:23:27 CDT)
  - Re: How can I create the water Solvate in vmd fan li (Wed May 16 2018 - 16:56:21 CDT)
    - RE: How can I create the water Solvate in vmd Vermaas, Joshua (Wed May 16 2018 - 17:45:13 CDT)
Error: vecscale: parameters must have data dalpizar_at_fbio.uh.cu (Fri May 11 2018 - 15:17:11 CDT)
- Re: Error: vecscale: parameters must have data JC Gumbart (Fri May 11 2018 - 17:56:00 CDT)
  - Re: Error: vecscale: parameters must have data JC Gumbart (Fri May 18 2018 - 09:51:53 CDT)
Error loading .phi file Andy Liu (Thu May 10 2018 - 19:03:43 CDT)
- Re: Error loading .phi file John Stone (Tue May 15 2018 - 14:53:22 CDT)
Diagnosing vmd startup problems Goedde, Chris (Mon May 07 2018 - 11:29:36 CDT)
- Re: Diagnosing vmd startup problems John Stone (Mon May 07 2018 - 14:47:22 CDT)
  - Re: Diagnosing vmd startup problems Goedde, Chris (Mon May 07 2018 - 15:44:18 CDT)
    - Re: Diagnosing vmd startup problems John Stone (Mon May 07 2018 - 15:46:32 CDT)
    - Re: Diagnosing vmd startup problems Goedde, Chris (Mon May 07 2018 - 16:03:45 CDT)
A fill for "bodies" build out of surfacs Daniel Möller (Mon May 07 2018 - 05:12:40 CDT)
- Re: A fill for "bodies" build out of surfacs John Stone (Mon May 07 2018 - 14:40:52 CDT)
  - AW: A fill for "bodies" build out of surfacs Daniel Möller (Mon May 07 2018 - 16:31:37 CDT)
    - Re: A fill for "bodies" build out of surfacs John Stone (Mon May 07 2018 - 16:49:44 CDT)
VMD in OS X Yosemite version 10.1.1.5 locuswendy (Sat May 05 2018 - 23:04:19 CDT)
- Re: VMD in OS X Yosemite version 10.1.1.5 Ashar Malik (Sat May 05 2018 - 23:45:48 CDT)
  - Re: VMD in OS X Yosemite version 10.1.1.5 locuswendy (Sun May 06 2018 - 07:26:51 CDT)
    - Re: VMD in OS X Yosemite version 10.1.1.5 Jacob F. Tande (Sun May 06 2018 - 10:58:19 CDT)
    - Re: VMD in OS X Yosemite version 10.1.1.5 Ashar Malik (Sun May 06 2018 - 15:40:51 CDT)
Coloring Scheme Spectrum McGuire, Kelly (Sat May 05 2018 - 09:49:09 CDT)
- Re: Coloring Scheme Spectrum John Stone (Sun May 06 2018 - 21:13:55 CDT)
  - Re: Coloring Scheme Spectrum John Stone (Sun May 06 2018 - 21:20:13 CDT)
  - Re: Coloring Scheme Spectrum McGuire, Kelly (Sun May 06 2018 - 23:34:32 CDT)
RMSD Question McGuire, Kelly (Fri May 04 2018 - 17:47:31 CDT)
- RE: RMSD Question Vermaas, Joshua (Fri May 04 2018 - 18:46:41 CDT)
- Re: RMSD Question Ashar Malik (Fri May 04 2018 - 19:07:17 CDT)
How to change the coordinates of the dummy atoms in readvarxyz Remya Ann (Fri May 04 2018 - 10:55:35 CDT)
- Re: How to change the coordinates of the dummy atoms in readvarxyz John Stone (Fri May 04 2018 - 11:07:04 CDT)
  - Re: How to change the coordinates of the dummy atoms in readvarxyz Axel Kohlmeyer (Fri May 04 2018 - 11:17:19 CDT)
  - Re: How to change the coordinates of the dummy atoms in readvarxyz Remya Ann (Fri May 04 2018 - 11:15:01 CDT)
Automating VMD Oscar Bastidas (Thu May 03 2018 - 16:51:01 CDT)
- Re: Automating VMD Ashar Malik (Thu May 03 2018 - 17:40:36 CDT)
QwikMD - psfgen: patch and autogenerate Rose, Stuart Wallace (Thu May 03 2018 - 11:50:07 CDT)
- Re: QwikMD - psfgen: patch and autogenerate JoÃ£o Ribeiro (Fri May 04 2018 - 17:09:55 CDT)
Unable to load molecule ê¹€ë¯¼ìž¬ (Thu May 03 2018 - 05:16:28 CDT)
- Re: Unable to load molecule Ajasja LjubetiÄ (Thu May 03 2018 - 06:31:23 CDT)
CellPack McGuire, Kelly (Wed May 02 2018 - 23:03:31 CDT)
- Re: CellPack John Stone (Thu May 03 2018 - 10:22:22 CDT)
  - Re: CellPack McGuire, Kelly (Thu May 03 2018 - 11:20:26 CDT)
  - Re: CellPack McGuire, Kelly (Thu May 03 2018 - 18:53:18 CDT)
Displaying gaussian cube file produced by Delphi Andy Liu (Mon Apr 30 2018 - 17:04:24 CDT)
- Re: Displaying gaussian cube file produced by Delphi John Stone (Mon Apr 30 2018 - 22:06:29 CDT)
coloring method User for graphics like tubes? Daniel Möller (Mon Apr 30 2018 - 04:39:25 CDT)
- RE: coloring method User for graphics like tubes? Vermaas, Joshua (Mon Apr 30 2018 - 08:06:49 CDT)
  - Re: coloring method User for graphics like tubes? John Stone (Mon Apr 30 2018 - 22:07:41 CDT)
DCD Question McGuire, Kelly (Sun Apr 29 2018 - 16:45:35 CDT)
- Re: DCD Question Fernando Vallejos-Burgos (Sun Apr 29 2018 - 18:37:16 CDT)
  - Re: DCD Question McGuire, Kelly (Sun Apr 29 2018 - 20:31:18 CDT)
Waters per residue in ion channel McGuire, Kelly (Sat Apr 28 2018 - 18:26:48 CDT)
excluding atoms Doaa Saayed (Sat Apr 28 2018 - 05:29:58 CDT)
- Re: excluding atoms Ashar Malik (Sat Apr 28 2018 - 08:12:45 CDT)
RMSD of lipid molecules Sadegh Faramarzi Ganjabad (Thu Apr 26 2018 - 23:30:21 CDT)
- Re: RMSD of lipid molecules Giacomo Fiorin (Fri Apr 27 2018 - 07:01:36 CDT)
  - Re: RMSD of lipid molecules Brian Radak (Fri Apr 27 2018 - 08:59:34 CDT)
Measure Distance Script Question McGuire, Kelly (Thu Apr 26 2018 - 23:27:47 CDT)
- AW: Measure Distance Script Question Norman Geist (Fri Apr 27 2018 - 02:07:09 CDT)
  - Re: Measure Distance Script Question McGuire, Kelly (Fri Apr 27 2018 - 09:08:41 CDT)
Re: Fixing VMD build with recent FLTK on macOS John Stone (Thu Apr 26 2018 - 17:30:17 CDT)
FEP with intermediary segments Francesco Pietra (Thu Apr 26 2018 - 10:20:21 CDT)
- Fwd: FEP with intermediary segments Francesco Pietra (Fri May 04 2018 - 00:37:18 CDT)
  - Re: Fwd: FEP with intermediary segments Brian Radak (Fri May 04 2018 - 08:01:28 CDT)
MOPAC Orbitals McGuire, Kelly (Tue Apr 24 2018 - 12:13:29 CDT)
NAMD Developer Workshop at Urbana IL, June 11-12, 2018 JoÃ£o Ribeiro (Tue Apr 24 2018 - 08:57:57 CDT)
- Re: NAMD Developer Workshop at Urbana IL, June 11-12, 2018 JoÃ£o Ribeiro (Wed May 02 2018 - 09:17:31 CDT)
PSFGEN 1.6.4 autogenerate PATCH keyword not available Thomas C. Bishop (Mon Apr 23 2018 - 19:57:47 CDT)
- Re: PSFGEN 1.6.4 autogenerate PATCH keyword not available Brian Radak (Tue Apr 24 2018 - 07:34:01 CDT)
  - RE: namd-l: Re: PSFGEN 1.6.4 autogenerate PATCH keyword not available Vermaas, Joshua (Tue Apr 24 2018 - 10:59:35 CDT)
    - Re: namd-l: Re: PSFGEN 1.6.4 autogenerate PATCH keyword not available Brian Radak (Tue Apr 24 2018 - 11:23:47 CDT)
    - RE: namd-l: Re: PSFGEN 1.6.4 autogenerate PATCH keyword not available Vermaas, Joshua (Tue Apr 24 2018 - 12:08:20 CDT)
Resp on VMD SM Bargeen A Turzo (Mon Apr 23 2018 - 15:46:20 CDT)
- Re: Resp on VMD Axel Kohlmeyer (Mon Apr 23 2018 - 16:27:52 CDT)
- Re: Resp on VMD JC Gumbart (Mon Apr 23 2018 - 17:36:36 CDT)
  - Re: Resp on VMD JC Gumbart (Fri Apr 27 2018 - 11:30:06 CDT)
    - Re: Resp on VMD SM Bargeen A Turzo (Fri Apr 27 2018 - 11:41:53 CDT)
RESP2.4 and FFTK SM Bargeen A Turzo (Mon Apr 23 2018 - 14:22:38 CDT)
RESP PATH SM Bargeen A Turzo (Mon Apr 23 2018 - 12:49:56 CDT)
Calculating Diffusion Coefficient Using VMD Sonibare, Kolawole (Mon Apr 23 2018 - 10:58:56 CDT)
- Re: Calculating Diffusion Coefficient Using VMD Giacomo Fiorin (Mon Apr 23 2018 - 11:12:49 CDT)
Calculating Diffusion Coefficient using VMD Sonibare, Kolawole (Mon Apr 23 2018 - 08:56:34 CDT)
PDB Question McGuire, Kelly (Sun Apr 22 2018 - 18:40:00 CDT)
- Re: PDB Question jrhau lung (Mon Apr 23 2018 - 06:56:53 CDT)
  - Re: PDB Question McGuire, Kelly (Mon Apr 23 2018 - 12:05:44 CDT)
    - Re: PDB Question Bennion, Brian (Mon Apr 23 2018 - 12:34:18 CDT)
- Re: PDB Question Giacomo Fiorin (Mon Apr 23 2018 - 06:40:11 CDT)
dynamic cross-correlation Map(DCCM)? Gu, Wenze (Sat Apr 21 2018 - 21:48:02 CDT)
- Re: dynamic cross-correlation Map(DCCM)? John Stone (Tue Apr 24 2018 - 16:56:19 CDT)
Problem using topo writegmxtop fan li (Sat Apr 21 2018 - 08:57:35 CDT)
- RE: Problem using topo writegmxtop Vermaas, Joshua (Sat Apr 21 2018 - 13:52:20 CDT)
  - RE: Problem using topo writegmxtop Vermaas, Joshua (Mon Apr 23 2018 - 10:51:27 CDT)
  - RE: Problem using topo writegmxtop Vermaas, Joshua (Wed Apr 25 2018 - 17:11:42 CDT)
VMD Install Question McGuire, Kelly (Fri Apr 20 2018 - 13:24:08 CDT)
- RE: VMD Install Question Vermaas, Joshua (Fri Apr 20 2018 - 14:00:30 CDT)
  - Re: VMD Install Question McGuire, Kelly (Fri Apr 20 2018 - 14:06:13 CDT)
problem with adding ions Olya Kravchenko (Fri Apr 20 2018 - 12:33:14 CDT)
- Re: problem with adding ions JoÃ£o Ribeiro (Fri Apr 20 2018 - 12:57:04 CDT)
VMD 1.9.4 Linux McGuire, Kelly (Fri Apr 20 2018 - 10:57:29 CDT)
the number of hydrogen bonds per residue Qasim Pars (Fri Apr 20 2018 - 08:27:07 CDT)
- Re: the number of hydrogen bonds per residue Qasim Pars (Fri May 04 2018 - 11:09:48 CDT)
  - Re: the number of hydrogen bonds per residue Fotis Baltoumas (Fri May 04 2018 - 11:16:45 CDT)
Smoothing McGuire, Kelly (Thu Apr 19 2018 - 16:12:01 CDT)
- RE: Smoothing Vermaas, Joshua (Thu Apr 19 2018 - 17:39:37 CDT)
  - Re: Smoothing McGuire, Kelly (Thu Apr 19 2018 - 17:48:05 CDT)
    - RE: Smoothing Vermaas, Joshua (Thu Apr 19 2018 - 18:58:57 CDT)
macosx 10.6 compilation issue andre padilla (Thu Apr 19 2018 - 07:23:47 CDT)
- Re: macosx 10.6 compilation issue John Stone (Tue May 08 2018 - 14:32:40 CDT)
About loading multiple XYZ trajectories Gulce Kalyoncu (Wed Apr 18 2018 - 10:51:04 CDT)
- Re: About loading multiple XYZ trajectories Giacomo Fiorin (Wed Apr 18 2018 - 12:18:02 CDT)
vmd tcl script writing issue Sandip Mondal (Wed Apr 18 2018 - 09:29:43 CDT)
- Re: vmd tcl script writing issue Ashar Malik (Wed Apr 18 2018 - 09:53:53 CDT)
- Re: vmd tcl script writing issue Giacomo Fiorin (Wed Apr 18 2018 - 09:57:57 CDT)
- Re: vmd tcl script writing issue Chitrak Gupta (Wed Apr 18 2018 - 10:14:18 CDT)
  - Re: vmd tcl script writing issue Sandip Mondal (Wed Apr 18 2018 - 13:18:42 CDT)
making a movie of multiple molecules Sahithya Iyer (Wed Apr 18 2018 - 08:50:54 CDT)
- RE: making a movie of multiple molecules Vermaas, Joshua (Wed Apr 18 2018 - 11:33:52 CDT)
NAMD Color By Velocity McGuire, Kelly (Tue Apr 17 2018 - 13:28:19 CDT)
- Re: NAMD Color By Velocity Axel Kohlmeyer (Tue Apr 17 2018 - 14:03:22 CDT)
source download andre padilla (Mon Apr 16 2018 - 08:17:40 CDT)
- Re: source download Axel Kohlmeyer (Mon Apr 16 2018 - 08:43:31 CDT)
reverting coarse-grained system to all-atom system Rabeta Yeasmin (Sun Apr 15 2018 - 18:57:10 CDT)
- Re: reverting coarse-grained system to all-atom system Peter Freddolino (Sun Apr 15 2018 - 20:14:26 CDT)
  - Re: reverting coarse-grained system to all-atom system Rabeta Yeasmin (Mon Apr 16 2018 - 10:43:25 CDT)
Re: namd-l: Re: Bug with FEP? Francesco Pietra (Sun Apr 15 2018 - 02:48:10 CDT)
- Re: Re: namd-l: Re: Bug with FEP? Brian Radak (Mon Apr 16 2018 - 11:31:45 CDT)
  - Re: Re: namd-l: Re: Bug with FEP? Francesco Pietra (Tue Apr 17 2018 - 00:05:38 CDT)
    - Re: Re: namd-l: Re: Bug with FEP? Brian Radak (Tue Apr 17 2018 - 09:42:46 CDT)
build virus envelope sunyeping (Thu Apr 12 2018 - 23:34:06 CDT)
hollow sphere Doaa Saayed (Thu Apr 12 2018 - 12:14:56 CDT)
- Re: hollow sphere Mike McCallum (Thu Apr 12 2018 - 13:20:30 CDT)
Change in reaction coordinate value after doing solvation from that of the crystal structure Sheena Singh (Thu Apr 12 2018 - 10:07:09 CDT)
- RE: Change in reaction coordinate value after doing solvation from that of the crystal structure Vermaas, Joshua (Thu Apr 12 2018 - 14:55:26 CDT)
water molecules amber force field Stefano Guglielmo (Thu Apr 12 2018 - 09:03:51 CDT)
- Re: water molecules amber force field Brian Radak (Thu Apr 12 2018 - 12:23:35 CDT)
  - RE: water molecules amber force field Vermaas, Joshua (Thu Apr 12 2018 - 14:57:32 CDT)
Diffusion Coefficient calculation Jeams Anderson (Wed Apr 11 2018 - 08:14:59 CDT)
- Re: Diffusion Coefficient calculation Rabeta Yeasmin (Wed Apr 11 2018 - 10:52:54 CDT)
  - Re: Diffusion Coefficient calculation A. M.M (Wed Apr 11 2018 - 11:27:31 CDT)
    - Re: Diffusion Coefficient calculation A. M.M (Wed Apr 11 2018 - 11:37:01 CDT)
    - Re: Diffusion Coefficient calculation A. M.M (Wed Apr 11 2018 - 11:37:52 CDT)
- RE: Diffusion Coefficient calculation Vermaas, Joshua (Wed Apr 11 2018 - 11:07:32 CDT)
(no subject) JOHN FLANAGAN (Tue Apr 10 2018 - 16:36:48 CDT)
- (no subject) Ashar Malik (Tue Apr 10 2018 - 18:51:32 CDT)
- Re: t.shivam_at_iitg.ernet.in (Wed Apr 11 2018 - 04:01:52 CDT)
Drastically different number of suboptimal paths in similar simulations amin sagar (Tue Apr 10 2018 - 10:17:54 CDT)
Proper use of psfgen "mutate"? Brian Radak (Tue Apr 10 2018 - 08:58:47 CDT)
- Re: Proper use of psfgen "mutate"? Francesco Pietra (Tue Apr 10 2018 - 09:20:20 CDT)
- Re: namd-l: Proper use of psfgen "mutate"? JÃ©rÃ´me HÃ©nin (Tue Apr 10 2018 - 09:23:20 CDT)
  - Re: namd-l: Proper use of psfgen "mutate"? Brian Radak (Tue Apr 10 2018 - 09:41:54 CDT)
Re: namd-l: ParseFEP error with FEP in segments at different lambda schedule Brian Radak (Tue Apr 10 2018 - 07:56:40 CDT)
ParseFEP error with FEP in segments at different lambda schedule Francesco Pietra (Sun Apr 08 2018 - 08:46:35 CDT)
TCBG Workshop lecture videos JoÃ£o Ribeiro (Sat Apr 07 2018 - 10:45:12 CDT)
Query for coarse grain system Abhishek TYAGI (Thu Apr 05 2018 - 09:53:36 CDT)
unable to install VMD on OSX Raag Saluja (Wed Apr 04 2018 - 12:40:18 CDT)
- RE: unable to install VMD on OSX Ray, William (Wed Apr 04 2018 - 14:19:30 CDT)
Regarding RDF and Cordination number calculatin Jeams Anderson (Wed Apr 04 2018 - 02:40:42 CDT)
- Re: Regarding RDF and Cordination number calculatin Axel Kohlmeyer (Wed Apr 04 2018 - 05:04:34 CDT)
ATOM VELOCITY HIGH ERROR in Coarse grained Simulation RAKESH (Fri Mar 30 2018 - 08:39:40 CDT)
- Re: ATOM VELOCITY HIGH ERROR in Coarse grained Simulation Axel Kohlmeyer (Fri Mar 30 2018 - 09:41:50 CDT)
  - Re: ATOM VELOCITY HIGH ERROR in Coarse grained Simulation Rabeta Yeasmin (Fri Mar 30 2018 - 10:19:32 CDT)
Secondary structure not being rendered for 1O82 Simon DÃ¼rr (Fri Mar 30 2018 - 04:56:50 CDT)
Connecting VMD to a supercomputer center SM Bargeen A Turzo (Thu Mar 29 2018 - 14:04:59 CDT)
Solvent PDB and PSF Files Alex Saad-Falcon (Thu Mar 29 2018 - 10:50:45 CDT)
- Re: Solvent PDB and PSF Files Brian Radak (Thu Mar 29 2018 - 11:40:26 CDT)
  - Re: Solvent PDB and PSF Files Axel Kohlmeyer (Thu Mar 29 2018 - 12:58:02 CDT)
- Re: Solvent PDB and PSF Files Vermaas, Joshua (Thu Mar 29 2018 - 12:28:40 CDT)
Coloring of a trajectory with atom types more than 9 Amin Koochaki (Thu Mar 29 2018 - 05:12:36 CDT)
- Re: Coloring of a trajectory with atom types more than 9 Vermaas, Joshua (Thu Mar 29 2018 - 12:19:41 CDT)
  - Re: Coloring of a trajectory with atom types more than 9 Amin Koochaki (Thu Mar 29 2018 - 14:58:09 CDT)
Is there a way to create atom selection for a list of atom indices? Jeffrey A Tibbitt (Thu Mar 29 2018 - 01:43:43 CDT)
- Re: Is there a way to create atom selection for a list of atom indices? Monika Madhavi (Thu Mar 29 2018 - 02:23:53 CDT)
  - Re: Is there a way to create atom selection for a list of atom indices? Jeffrey A Tibbitt (Thu Mar 29 2018 - 03:29:19 CDT)
Fwd: Protein backbone representation for non standard residues / molecules Dallas Warren (Wed Mar 28 2018 - 22:21:46 CDT)
labels with sub/superscripts or even symbols sperez14_at_us.es (Tue Mar 27 2018 - 01:50:05 CDT)
- Re: labels with sub/superscripts or even symbols John Stone (Mon May 07 2018 - 16:24:28 CDT)
Using radial coloring method from user-defined center Miguel Caro (Mon Mar 26 2018 - 10:09:27 CDT)
- Re: Using radial coloring method from user-defined center Vermaas, Joshua (Mon Mar 26 2018 - 13:59:16 CDT)
  - Re: Using radial coloring method from user-defined center Miguel Caro (Tue Mar 27 2018 - 02:32:59 CDT)
NAMD simulation Denish Poudyal (Sun Mar 25 2018 - 20:25:03 CDT)
i thought I could run a 100 ns NAMD simulation in my laptop for a protein-hormone system containing around 2000 atoms in its pdb file(4lnx.pdb). But even to run a simulation for four hundred fifty thousand steps, it has taken almost 4700 minutes. is this normal or its low? the device has 4 cores with 16 gigs of ram and 4 gigs of gpu(amd). Or any suggestions to run it faster??? Denish Poudyal (Sun Mar 25 2018 - 20:22:34 CDT)
- Re: i thought I could run a 100 ns NAMD simulation in my laptop for a protein-hormone system containing around 2000 atoms in its pdb file(4lnx.pdb). But even to run a simulation for four hundred fifty thousand steps, it has taken almost 4700 minutes. is this normal or its low? the device has 4 cores with 16 gigs of ram and 4 gigs of gpu(amd). Or any suggestions to run it faster??? Ashar Malik (Sun Mar 25 2018 - 20:44:48 CDT)
Binding free energy calculations varun dewaker (Sat Mar 24 2018 - 08:12:17 CDT)
Regarding installation of DruGui SM Bargeen A Turzo (Sat Mar 24 2018 - 06:30:29 CDT)
- Re: Regarding installation of DruGui Brian Radak (Mon Mar 26 2018 - 11:12:57 CDT)
  - Re: Regarding installation of DruGui Pratik Narain Srivastava (Tue Mar 27 2018 - 02:03:09 CDT)
    - Re: Regarding installation of DruGui Fotis Baltoumas (Tue Mar 27 2018 - 04:11:36 CDT)
Regarding Installation of DruGui SM Bargeen A Turzo (Fri Mar 23 2018 - 23:23:04 CDT)
- Re: Regarding Installation of DruGui John Stone (Sun Mar 25 2018 - 11:52:48 CDT)
FFTK, recognize wildcard atom types in forcefields Bryan Roessler (Fri Mar 23 2018 - 19:38:06 CDT)
- Re: FFTK, recognize wildcard atom types in forcefields JC Gumbart (Sat Mar 24 2018 - 08:56:35 CDT)
Parallelization to an axis Sandip Mondal (Fri Mar 23 2018 - 09:31:48 CDT)
- Re: Parallelization to an axis Axel Kohlmeyer (Fri Mar 23 2018 - 09:57:52 CDT)
  - Re: Parallelization to an axis Sandip Mondal (Fri Mar 23 2018 - 12:42:45 CDT)
- Re: Parallelization to an axis Vermaas, Joshua (Fri Mar 23 2018 - 12:26:59 CDT)
  - Re: Parallelization to an axis Sandip Mondal (Fri Mar 23 2018 - 12:44:13 CDT)
ParseFEP for restating FEP Francesco Pietra (Fri Mar 23 2018 - 02:05:41 CDT)
- Fwd: ParseFEP for restating FEP Francesco Pietra (Fri Mar 23 2018 - 09:00:15 CDT)
  - Re: Fwd: ParseFEP for restating FEP Brian Radak (Fri Mar 23 2018 - 10:48:17 CDT)
[VMD-NAMD] Question about Dipole of DNA / Dipole Moment Watcher Plugin The Cromicus Productions (Thu Mar 22 2018 - 18:17:30 CDT)
- Re: [VMD-NAMD] Question about Dipole of DNA / Dipole Moment Watcher Plugin Brian Radak (Fri Mar 23 2018 - 10:59:05 CDT)
  - Re: [VMD-NAMD] Question about Dipole of DNA / Dipole Moment Watcher Plugin The Cromicus Productions (Sun Mar 25 2018 - 20:31:45 CDT)
Decompose Transformation Matrix to Rotations and Translations along XYZ axes Peter Mawanga (Wed Mar 21 2018 - 11:12:20 CDT)
- Re: Decompose Transformation Matrix to Rotations and Translations along XYZ axes Ashar Malik (Wed Mar 21 2018 - 13:29:17 CDT)
- Re: Decompose Transformation Matrix to Rotations and Translations along XYZ axes Vermaas, Joshua (Fri Mar 23 2018 - 12:24:42 CDT)
  - Re: Decompose Transformation Matrix to Rotations and Translations along XYZ axes Peter Mawanga (Fri Mar 30 2018 - 12:51:59 CDT)
Changing isosurface wireframe thickness when rendering with TachyonL Rune Thomas Kidmose (Wed Mar 21 2018 - 07:39:19 CDT)
- Re: Changing isosurface wireframe thickness when rendering with TachyonL John Stone (Wed Mar 21 2018 - 10:36:54 CDT)
Command to save visualization state. sperez14_at_us.es (Wed Mar 21 2018 - 05:47:38 CDT)
- Re: Command to save visualization state. John Stone (Wed Mar 21 2018 - 10:27:25 CDT)
polyhedra representation + periodic images sperez14_at_us.es (Wed Mar 21 2018 - 05:44:55 CDT)
- Re: polyhedra representation + periodic images John Stone (Wed Mar 21 2018 - 10:32:18 CDT)
Average structure Williams Miranda (Wed Mar 21 2018 - 01:37:13 CDT)
- Re: Average structure Ashar Malik (Wed Mar 21 2018 - 02:55:20 CDT)
- AW: Average structure Norman Geist (Wed Mar 21 2018 - 04:02:14 CDT)
2-Dimensional map of a lipid molecule around the protein Shashank Ranjan Srivastava (Wed Mar 21 2018 - 01:16:55 CDT)
- Re: 2-Dimensional map of a lipid molecule around the protein Giacomo Fiorin (Wed Mar 21 2018 - 09:06:36 CDT)
  - Re: 2-Dimensional map of a lipid molecule around the protein Giacomo Fiorin (Thu Mar 22 2018 - 10:04:10 CDT)
    - Re: 2-Dimensional map of a lipid molecule around the protein Chris Neale (Thu Mar 22 2018 - 10:31:06 CDT)
  - Re: 2-Dimensional map of a lipid molecule around the protein Giacomo Fiorin (Mon Mar 26 2018 - 09:01:18 CDT)
Propagating PDB coordinates using Quaternion matrix Peter Mawanga (Tue Mar 20 2018 - 09:29:06 CDT)
- Re: Propagating PDB coordinates using Quaternion matrix Ashar Malik (Tue Mar 20 2018 - 10:00:57 CDT)
  - Re: Propagating PDB coordinates using Quaternion matrix Ashar Malik (Tue Mar 20 2018 - 12:15:10 CDT)
    - Re: Propagating PDB coordinates using Quaternion matrix Peter Mawanga (Tue Mar 20 2018 - 13:22:18 CDT)
    - Re: Propagating PDB coordinates using Quaternion matrix Ashar Malik (Wed Mar 21 2018 - 01:16:18 CDT)
  - Re: Propagating PDB coordinates using Quaternion matrix Peter Mawanga (Wed Mar 21 2018 - 12:27:40 CDT)
    - Re: Propagating PDB coordinates using Quaternion matrix Ashar Malik (Wed Mar 21 2018 - 13:34:12 CDT)
Adding Hydroxide Ions to the simulation box Aman Jindal (Tue Mar 20 2018 - 01:56:10 CDT)
- Re: Adding Hydroxide Ions to the simulation box Brian Radak (Tue Mar 20 2018 - 09:42:54 CDT)
  - Re: Adding Hydroxide Ions to the simulation box Francesco Pietra (Tue Mar 20 2018 - 10:55:21 CDT)
    - Re: Adding Hydroxide Ions to the simulation box Aman Jindal (Wed Mar 21 2018 - 00:56:31 CDT)
    - Re: Adding Hydroxide Ions to the simulation box Brian Radak (Wed Mar 21 2018 - 09:15:30 CDT)
Text mode data extraction without trajectory update Udaya Dahal (Sun Mar 18 2018 - 01:31:36 CDT)
- Re: Text mode data extraction without trajectory update Ashar Malik (Sun Mar 18 2018 - 07:50:26 CDT)
  - Re: Text mode data extraction without trajectory update Udaya Dahal (Sun Mar 18 2018 - 09:44:33 CDT)
    - Re: Text mode data extraction without trajectory update Vermaas, Joshua (Fri Mar 23 2018 - 12:01:22 CDT)
"'Hands-on" Workshop on Computational Biophysics at Pittsburgh, PA, May 21-25, 2018 JoÃ£o Ribeiro (Fri Mar 16 2018 - 15:47:15 CDT)
Occupancy volume quantitation Lizelle Lubbe (Fri Mar 16 2018 - 09:31:37 CDT)
- Re: Occupancy volume quantitation Giacomo Fiorin (Fri Mar 16 2018 - 10:10:31 CDT)
  - Re: Occupancy volume quantitation Lizelle Lubbe (Mon Mar 19 2018 - 02:47:27 CDT)
how to merge two pdb in a single file SHAHEE ISLAM (Fri Mar 16 2018 - 09:20:03 CDT)
- Re: how to merge two pdb in a single file SHAHEE ISLAM (Fri Mar 16 2018 - 09:26:27 CDT)
- Re: how to merge two pdb in a single file Giacomo Fiorin (Fri Mar 16 2018 - 09:58:51 CDT)
non-heme iron coordination with His in NAMD2 Anna Petroff (Thu Mar 15 2018 - 10:33:15 CDT)
- Re: non-heme iron coordination with His in NAMD2 Vermaas, Joshua (Thu Mar 15 2018 - 12:21:21 CDT)
  - Re: non-heme iron coordination with His in NAMD2 Anna Petroff (Thu Mar 15 2018 - 13:45:40 CDT)
  - Re: non-heme iron coordination with His in NAMD2 JC Gumbart (Thu Mar 15 2018 - 13:48:51 CDT)
    - Re: non-heme iron coordination with His in NAMD2 Anna Petroff (Thu Mar 15 2018 - 14:31:27 CDT)
Query for the VolMap plugin Saikat Pal (Thu Mar 15 2018 - 07:16:49 CDT)
- Re: Query for the VolMap plugin Giacomo Fiorin (Thu Mar 15 2018 - 08:39:14 CDT)
  - Re: Query for the VolMap plugin Giacomo Fiorin (Thu Mar 15 2018 - 09:09:18 CDT)
Writing all transformed coordinates into single file Peter Mawanga (Wed Mar 14 2018 - 14:23:05 CDT)
- Re: Writing all transformed coordinates into single file Vermaas, Joshua (Wed Mar 14 2018 - 15:51:06 CDT)
  - Re: Writing all transformed coordinates into single file Peter Mawanga (Thu Mar 15 2018 - 07:35:36 CDT)
Membrane tutorial regarding RAHUL SURESH (Wed Mar 14 2018 - 10:54:23 CDT)
- Re: Membrane tutorial regarding Vermaas, Joshua (Wed Mar 14 2018 - 12:00:01 CDT)
Building plugins with _USE_ZLIB (how to activate preprocessor macro) Christian Leitold (Tue Mar 13 2018 - 14:19:48 CDT)
- Re: Building plugins with _USE_ZLIB (how to activate preprocessor macro) John Stone (Tue Mar 13 2018 - 14:29:20 CDT)
  - Re: Building plugins with _USE_ZLIB (how to activate preprocessor macro) Christian Leitold (Tue Mar 13 2018 - 15:25:36 CDT)
  - Re: Building plugins with _USE_ZLIB (how to activate preprocessor macro) Axel Kohlmeyer (Tue Mar 13 2018 - 16:32:37 CDT)
- Re: Building plugins with _USE_ZLIB (how to activate preprocessor macro) Axel Kohlmeyer (Tue Mar 13 2018 - 16:30:12 CDT)
  - Re: Building plugins with _USE_ZLIB (how to activate preprocessor macro) Christian Leitold (Tue Mar 13 2018 - 17:33:24 CDT)
Graphics card requirement for VMD Debostuti Ghoshdastidar (Tue Mar 13 2018 - 07:05:32 CDT)
- Re: Graphics card requirement for VMD Abhishek TYAGI (Tue Mar 13 2018 - 07:13:06 CDT)
- Re: Graphics card requirement for VMD John Stone (Tue Mar 13 2018 - 09:36:16 CDT)
  - Re: Graphics card requirement for VMD Debostuti Ghoshdastidar (Tue Mar 13 2018 - 09:55:26 CDT)
Graphics Requirement for VMD Debostuti Ghoshdastidar (Tue Mar 13 2018 - 06:29:47 CDT)
MDFF multiple PDB and PSF Rune Thomas Kidmose (Mon Mar 12 2018 - 09:14:32 CDT)
- Re: MDFF multiple PDB and PSF Ryan McGreevy (Mon Mar 12 2018 - 11:35:40 CDT)
  - Re: MDFF multiple PDB and PSF Rune Thomas Kidmose (Mon Mar 12 2018 - 11:49:41 CDT)
    - Re: MDFF multiple PDB and PSF JC Gumbart (Tue Mar 13 2018 - 17:04:54 CDT)
(no subject) shyam sharma (Fri Mar 09 2018 - 01:15:48 CST)
- Re: t.shivam_at_iitg.ernet.in (Fri Mar 09 2018 - 02:04:47 CST)
How to hide water in mdcrd file? Gu, Wenze (Thu Mar 08 2018 - 12:48:00 CST)
- Re: How to hide water in mdcrd file? Ashar Malik (Thu Mar 08 2018 - 13:21:20 CST)
- Re: How to hide water in mdcrd file? Robin Betz (Thu Mar 08 2018 - 14:21:11 CST)
  - Re: How to hide water in mdcrd file? Gu, Wenze (Thu Mar 08 2018 - 15:31:44 CST)
VMD quit unexpectedly on Mac Gu, Wenze (Thu Mar 08 2018 - 12:42:19 CST)
- Re: VMD quit unexpectedly on Mac John Stone (Thu Mar 08 2018 - 13:15:44 CST)
  - Re: VMD quit unexpectedly on Mac Gu, Wenze (Thu Mar 08 2018 - 15:33:45 CST)
(no subject) shyam sharma (Thu Mar 08 2018 - 06:29:59 CST)
Creating VR-movies with tachyon renderer Per Larsson (Thu Mar 08 2018 - 03:49:38 CST)
Multiseq: Perform peptide trajectory clustering Peter Mawanga (Wed Mar 07 2018 - 11:09:19 CST)
TachyonL-optix rendering question Rune Thomas Kidmose (Wed Mar 07 2018 - 09:49:40 CST)
- Re: TachyonL-optix rendering question John Stone (Wed Mar 07 2018 - 10:19:21 CST)
  - Sv: TachyonL-optix rendering question Rune Thomas Kidmose (Wed Mar 07 2018 - 12:59:54 CST)
    - Re: Sv: TachyonL-optix rendering question John Stone (Wed Mar 14 2018 - 23:59:31 CDT)
Re: namd-l: Fwd: parseFEP domain error Francesco Pietra (Wed Mar 07 2018 - 08:39:49 CST)
VMD Segfault Fedora 27 iamcool777able . (Tue Mar 06 2018 - 13:12:01 CST)
- Re: VMD Segfault Fedora 27 Ivan Gregoretti (Tue Mar 06 2018 - 14:11:41 CST)
  - Re: VMD Segfault Fedora 27 John Stone (Tue Mar 06 2018 - 14:28:46 CST)
  - RE: VMD Segfault Fedora 27 Bennion, Brian (Tue Mar 06 2018 - 15:01:16 CST)
- Re: VMD Segfault Fedora 27 John Stone (Tue Mar 06 2018 - 13:49:16 CST)
Creating VR-movies with tachyon renderer Per Larsson (Tue Mar 06 2018 - 06:52:54 CST)
- Re: Creating VR-movies with tachyon renderer Vermaas, Joshua (Tue Mar 06 2018 - 11:53:35 CST)
- Re: Creating VR-movies with tachyon renderer Dallas Warren (Tue Mar 06 2018 - 14:23:07 CST)
  - Re: Creating VR-movies with tachyon renderer Per Larsson (Wed Mar 07 2018 - 02:09:16 CST)
    - Re: Creating VR-movies with tachyon renderer Dallas Warren (Wed Mar 07 2018 - 16:04:53 CST)
  - Re: Creating VR-movies with tachyon renderer Per Larsson (Wed Mar 07 2018 - 08:09:49 CST)
Ph.D. and Post-doc positions in molecular simulations and structural bioinformatics Jan Brezovsky (Mon Mar 05 2018 - 11:10:28 CST)
Running vmd Mahmood Naderan (Sun Mar 04 2018 - 09:20:14 CST)
- Re: Running vmd Giacomo Fiorin (Sun Mar 04 2018 - 13:58:37 CST)
  - Re: Running vmd Mahmood Naderan (Mon Mar 05 2018 - 04:26:16 CST)
netcdf for plugins Mahmood Naderan (Sun Mar 04 2018 - 07:11:08 CST)
- Re: netcdf for plugins Axel Kohlmeyer (Sun Mar 04 2018 - 07:34:44 CST)
  - Re: netcdf for plugins Mahmood Naderan (Sun Mar 04 2018 - 07:45:51 CST)
    - Re: netcdf for plugins Axel Kohlmeyer (Sun Mar 04 2018 - 07:49:42 CST)
- Re: netcdf for plugins John Stone (Mon Mar 05 2018 - 09:50:33 CST)
vmd error related to tcl.h Mahmood Naderan (Sat Mar 03 2018 - 13:47:07 CST)
- Re: vmd error related to tcl.h Axel Kohlmeyer (Sun Mar 04 2018 - 07:42:32 CST)
  - Re: vmd error related to tcl.h John Stone (Mon Mar 05 2018 - 00:28:08 CST)
Problem reading mdcrd file Gu, Wenze (Sat Mar 03 2018 - 10:52:29 CST)
- Re: Problem reading mdcrd file David Gae (Sat Mar 03 2018 - 14:03:09 CST)
VMD stops furing loading of DCD trajectory Rose, Stuart Wallace (Fri Mar 02 2018 - 16:07:07 CST)
- Re: VMD stops furing loading of DCD trajectory Ashar Malik (Fri Mar 02 2018 - 17:25:43 CST)
  - RE: VMD stops furing loading of DCD trajectory Rose, Stuart Wallace (Fri Mar 02 2018 - 17:26:51 CST)
    - RE: VMD stops furing loading of DCD trajectory Ashar Malik (Fri Mar 02 2018 - 17:53:43 CST)
- Re: VMD stops furing loading of DCD trajectory Vermaas, Joshua (Fri Mar 02 2018 - 18:15:11 CST)
parseFEP domain error Francesco Pietra (Fri Mar 02 2018 - 09:47:42 CST)
- Fwd: parseFEP domain error Francesco Pietra (Sat Mar 03 2018 - 11:44:06 CST)
  - Fwd: parseFEP domain error Francesco Pietra (Mon Mar 05 2018 - 14:17:56 CST)
    - Re: Fwd: parseFEP domain error Brian Radak (Mon Mar 05 2018 - 15:43:15 CST)
PSFGEN: Residue addition not working Peter Mawanga (Fri Mar 02 2018 - 04:05:45 CST)
- Re: PSFGEN: Residue addition not working Vermaas, Joshua (Fri Mar 02 2018 - 13:55:19 CST)
visualization of a normal mode analysis Albert (Wed Feb 28 2018 - 14:44:25 CST)
Unable to build a symmetric (m=0) zigzag BN nanotube in VMD Aman Jindal (Wed Feb 28 2018 - 01:29:20 CST)
- Re: Unable to build a symmetric (m=0) zigzag BN nanotube in VMD Axel Kohlmeyer (Wed Feb 28 2018 - 02:15:29 CST)
Error merging the pdbs and psfs Denish Poudyal (Mon Feb 26 2018 - 20:26:08 CST)
- Re: Error merging the pdbs and psfs John Stone (Mon Mar 05 2018 - 14:51:53 CST)
MDFF rotation Rune Thomas Kidmose (Mon Feb 26 2018 - 03:48:08 CST)
- Re: MDFF rotation Ryan McGreevy (Mon Feb 26 2018 - 07:47:24 CST)
  - Sv: MDFF rotation Rune Thomas Kidmose (Mon Feb 26 2018 - 08:12:57 CST)
video 360 vmd Laine Tereza (Fri Feb 23 2018 - 14:37:09 CST)
- Re: video 360 vmd John Stone (Fri Feb 23 2018 - 14:50:35 CST)
Atom type information is not incremented after merging two molecules. Manoj Dhiman (Fri Feb 23 2018 - 03:34:16 CST)
- Re: Atom type information is not incremented after merging two molecules. Axel Kohlmeyer (Fri Feb 23 2018 - 04:02:27 CST)
  - Re: Atom type information is not incremented after merging two molecules. Manoj Dhiman (Fri Feb 23 2018 - 09:22:18 CST)
VISUALIZE HYDROGEN BOND BETWEEN PROTEIN AND LIGAND Neha Gupta (Wed Feb 21 2018 - 05:08:07 CST)
VMD crashes on Macbook with Intel Graphics theblueone_at_web.de (Wed Feb 21 2018 - 02:27:47 CST)
- Re: VMD crashes on Macbook with Intel Graphics John Stone (Thu Feb 22 2018 - 17:16:23 CST)
  - Aw: Re: VMD crashes on Macbook with Intel Graphics theblueone_at_web.de (Fri Feb 23 2018 - 07:23:58 CST)
    - Re: Re: VMD crashes on Macbook with Intel Graphics John Stone (Fri Feb 23 2018 - 10:07:37 CST)
How to identify the index number of some particular atoms Jeams Anderson (Tue Feb 20 2018 - 01:31:18 CST)
- Re: How to identify the index number of some particular atoms Ashar Malik (Tue Feb 20 2018 - 03:35:19 CST)
VMD TCL Script to save last frame of a trajectory using bash+tcl scripts Dive, Aniruddha Mukund (Mon Feb 19 2018 - 16:37:33 CST)
- Re: VMD TCL Script to save last frame of a trajectory using bash+tcl scripts John Stone (Tue Feb 20 2018 - 10:49:00 CST)
  - Re: VMD TCL Script to save last frame of a trajectory using bash+tcl scripts Dive, Aniruddha Mukund (Wed Feb 21 2018 - 12:18:02 CST)
    - Re: VMD TCL Script to save last frame of a trajectory using bash+tcl scripts Goedde, Chris (Wed Feb 21 2018 - 12:46:31 CST)
    - Re: VMD TCL Script to save last frame of a trajectory using bash+tcl scripts Giacomo Fiorin (Wed Feb 21 2018 - 13:07:40 CST)
salvation of heavy water Suresh Ghimire (Mon Feb 19 2018 - 09:12:33 CST)
- Re: salvation of heavy water Axel Kohlmeyer (Mon Feb 19 2018 - 09:45:18 CST)
Obtaining VMD view matrices for tcl script Rune Thomas Kidmose (Mon Feb 19 2018 - 01:18:59 CST)
- AW: Obtaining VMD view matrices for tcl script Norman Geist (Mon Feb 19 2018 - 02:39:47 CST)
  - Re: AW: Obtaining VMD view matrices for tcl script Rune Thomas Kidmose (Mon Feb 19 2018 - 04:15:43 CST)
    - Re: Obtaining VMD view matrices for tcl script Barry Isralewitz (Wed Feb 21 2018 - 13:55:31 CST)
Re: problem compiling vmd from source. sperez14_at_us.es (Sun Feb 18 2018 - 14:10:24 CST)
- Re: Re: problem compiling vmd from source. Vermaas, Joshua (Sun Feb 18 2018 - 23:41:17 CST)
  - Re: Re: problem compiling vmd from source. sperez14_at_us.es (Mon Feb 19 2018 - 13:17:11 CST)
    - Re: Re: problem compiling vmd from source. Vermaas, Joshua (Mon Feb 19 2018 - 14:34:35 CST)
FFTK Bond/Angle Optimization issue with namd2 Gabi Heller (Fri Feb 16 2018 - 06:05:00 CST)
- Re: FFTK Bond/Angle Optimization issue with namd2 JC Gumbart (Tue Feb 20 2018 - 01:20:50 CST)
  - Re: FFTK Bond/Angle Optimization issue with namd2 JC Gumbart (Tue Feb 20 2018 - 09:43:21 CST)
  - Re: FFTK Bond/Angle Optimization issue with namd2 JC Gumbart (Tue Feb 20 2018 - 10:27:53 CST)
setting up POPS or POPG in VMD Rabeta Yeasmin (Mon Feb 12 2018 - 16:32:33 CST)
- Re: setting up POPS or POPG in VMD Brian Radak (Tue Feb 13 2018 - 10:31:47 CST)
  - Re: setting up POPS or POPG in VMD Rabeta Yeasmin (Tue Feb 13 2018 - 13:05:15 CST)
Ph.D. and Post-doc positions in molecular simulations and structural bioinformatics Jan Brezovsky (Sun Feb 11 2018 - 15:58:39 CST)
Color scale bar Malvika K (Thu Feb 08 2018 - 11:15:46 CST)
- Re: Color scale bar John Stone (Thu Feb 08 2018 - 14:08:04 CST)
how to align simulated peptide in complex structure. Seera Suryanarayana (Thu Feb 08 2018 - 01:13:20 CST)
"Hands-on" Workshop on Enhanced Sampling and Free-Energy Calculation at Urbana, IL, September 10-14, 2018 JoÃ£o Ribeiro (Wed Feb 07 2018 - 10:46:51 CST)
NAMD Developer Workshop at Urbana IL, June 11-12, 2018 JoÃ£o Ribeiro (Wed Feb 07 2018 - 10:46:41 CST)
"Hands-On" Workshop on QM/MM Simulations at Urbana, IL, April 5-7, 2018 JoÃ£o Ribeiro (Wed Feb 07 2018 - 10:44:57 CST)
- Re: "Hands-On" Workshop on QM/MM Simulations at Urbana, IL, April 5-7, 2018 JoÃ£o Ribeiro (Tue Feb 27 2018 - 08:08:16 CST)
metalloprotein simulation t.shivam_at_iitg.ernet.in (Wed Feb 07 2018 - 10:11:39 CST)
Can specden produce the autocorrelation and not only the powerspectrum? sperez14_at_us.es (Tue Feb 06 2018 - 12:13:34 CST)
- Re: Can specden produce the autocorrelation and not only the powerspectrum? Axel Kohlmeyer (Tue Feb 06 2018 - 12:46:27 CST)
  - Re: Can specden produce the autocorrelation and not only the powerspectrum? Giacomo Fiorin (Wed Feb 07 2018 - 08:51:27 CST)
- Re: Can specden produce the autocorrelation and not only the powerspectrum? Giacomo Fiorin (Tue Feb 06 2018 - 13:10:44 CST)
Question regarding VMD In-situ Remote Visualization on clusters Feng Chen (Mon Feb 05 2018 - 11:28:41 CST)
How to copy/paste a membrane patch to create a larger membrane? thiagorrg UFC (Mon Feb 05 2018 - 08:34:15 CST)
- Re: How to copy/paste a membrane patch to create a larger membrane? Giacomo Fiorin (Mon Feb 05 2018 - 08:55:50 CST)
  - Re: How to copy/paste a membrane patch to create a larger membrane? Devanand T (Mon Feb 05 2018 - 09:26:40 CST)
  - Re: How to copy/paste a membrane patch to create a larger membrane? Ashar Malik (Mon Feb 05 2018 - 10:14:19 CST)
- Re: How to copy/paste a membrane patch to create a larger membrane? Stefan Doerr (Mon Feb 05 2018 - 09:10:55 CST)
- Re: How to copy/paste a membrane patch to create a larger membrane? thiagorrg UFC (Mon Feb 05 2018 - 12:34:43 CST)
"adding polymer to CNT" soroush ziaei (Fri Feb 02 2018 - 07:21:00 CST)
- Re: "adding polymer to CNT" Giacomo Fiorin (Fri Feb 02 2018 - 09:21:52 CST)
  - Re: "adding polymer to CNT" Giacomo Fiorin (Tue Feb 13 2018 - 09:38:45 CST)
AutoPSF formatted PDB: wrong residue order Bryan Roessler (Fri Feb 02 2018 - 04:09:33 CST)
- Re: AutoPSF formatted PDB: wrong residue order Pawel Kedzierski (Fri Feb 02 2018 - 05:45:47 CST)
  - Re: AutoPSF formatted PDB: wrong residue order Bryan Roessler (Fri Feb 02 2018 - 14:04:43 CST)
OS X Connection between VMD and AutoIMD De Winter Hans (Thu Feb 01 2018 - 03:17:27 CST)
- Re: OS X Connection between VMD and AutoIMD John Stone (Thu Feb 08 2018 - 16:24:26 CST)
- Re: OS X Connection between VMD and AutoIMD Ryan McGreevy (Fri Feb 09 2018 - 09:27:03 CST)
Affordable 3D stereo. sperez14_at_us.es (Tue Jan 30 2018 - 06:12:02 CST)
- AW: Affordable 3D stereo. Norman Geist (Wed Jan 31 2018 - 01:08:09 CST)
  - Re: Affordable 3D stereo. John Stone (Wed Jan 31 2018 - 11:17:54 CST)
Superimpose Protein Structure Wong Li Zhe (Tue Jan 30 2018 - 03:20:14 CST)
Molecule limit Windle,Stephen (Mon Jan 29 2018 - 18:20:31 CST)
- Re: Molecule limit Ashar Malik (Mon Jan 29 2018 - 19:06:53 CST)
- Re: Molecule limit Vermaas, Joshua (Mon Jan 29 2018 - 19:44:42 CST)
  - Re: Molecule limit John Stone (Mon Jan 29 2018 - 23:23:33 CST)
disulfide bonds are not showimg in vmd Shahee Islam (Mon Jan 29 2018 - 00:01:25 CST)
- Re: disulfide bonds are not showimg in vmd Shahee Islam (Mon Jan 29 2018 - 01:41:15 CST)
  - Re: disulfide bonds are not showimg in vmd Souvik Sinha (Mon Jan 29 2018 - 02:27:09 CST)
  - Re: disulfide bonds are not showimg in vmd Shahee Islam (Mon Jan 29 2018 - 02:34:29 CST)
    - Re: disulfide bonds are not showimg in vmd Vermaas, Joshua (Mon Jan 29 2018 - 13:06:34 CST)
Having problem with geometrical structure parinaz bashirbanaem (Sun Jan 28 2018 - 04:16:44 CST)
Colvars module doesn't work Michael Morin (Fri Jan 26 2018 - 14:11:29 CST)
- Re: Colvars module doesn't work Giacomo Fiorin (Fri Jan 26 2018 - 14:58:35 CST)
  - Re: Colvars module doesn't work Vermaas, Joshua (Fri Jan 26 2018 - 17:39:32 CST)
- Re: Colvars module doesn't work Vermaas, Joshua (Fri Jan 26 2018 - 15:14:46 CST)
Vmd coefficient tool Suresh Ghimire (Thu Jan 25 2018 - 03:39:56 CST)
Alignment issues Heather Carson (Wed Jan 24 2018 - 07:18:44 CST)
- Re: Alignment issues Ashar Malik (Wed Jan 24 2018 - 08:02:02 CST)
Superimpose Structures Wong Li Zhe (Tue Jan 23 2018 - 20:49:59 CST)
- Re: Superimpose Structures Ashar Malik (Wed Jan 24 2018 - 01:42:55 CST)
MSD for water inside CNT Suresh Ghimire (Tue Jan 23 2018 - 02:28:15 CST)
- Re: MSD for water inside CNT Vermaas, Joshua (Tue Jan 23 2018 - 11:30:12 CST)
Re: [phenixbb] secondary structure presentation in VMD CPMAS Chen (Mon Jan 22 2018 - 15:58:44 CST)
- Re: Re: [phenixbb] secondary structure presentation in VMD John Stone (Mon Jan 22 2018 - 16:03:48 CST)
  - Re: Re: [phenixbb] secondary structure presentation in VMD CPMAS Chen (Tue Jan 23 2018 - 11:01:48 CST)
    - Re: Re: [phenixbb] secondary structure presentation in VMD John Stone (Tue Jan 23 2018 - 11:12:12 CST)
    - Re: Re: [phenixbb] secondary structure presentation in VMD CPMAS Chen (Tue Jan 23 2018 - 11:38:16 CST)
VMD ffTK: The determination of a correct spin multiplicity value Ern Ong (Mon Jan 22 2018 - 02:14:54 CST)
- Re: VMD ffTK: The determination of a correct spin multiplicity value Giacomo Fiorin (Mon Jan 22 2018 - 08:31:45 CST)
saving velocities with VMD Marcela Madrid (Sun Jan 21 2018 - 14:55:30 CST)
secondary structure new cartoon presentation CPMAS Chen (Sun Jan 21 2018 - 08:55:56 CST)
VMD ffTK plugin: Error termination occurred at Gaussian input files generated for water interaction Ern Ong (Sat Jan 20 2018 - 07:09:26 CST)
- Re: VMD ffTK plugin: Error termination occurred at Gaussian input files generated for water interaction Mayne, Christopher G (Sat Jan 20 2018 - 20:05:43 CST)
MultiSeq conflicting with DYLD_LYBRARY_PATH fabio trovato (Thu Jan 18 2018 - 04:05:02 CST)
- Re: MultiSeq conflicting with DYLD_LYBRARY_PATH Ajasja LjubetiÄ (Thu Jan 18 2018 - 06:12:12 CST)
  - Re: MultiSeq conflicting with DYLD_LYBRARY_PATH fabio trovato (Thu Jan 18 2018 - 06:40:54 CST)
Parameter and topology Suresh Ghimire (Wed Jan 17 2018 - 23:59:37 CST)
Isosurface wireframe & solid surface representation Vincent Ustach (Wed Jan 17 2018 - 10:02:22 CST)
- Re: Isosurface wireframe & solid surface representation John Stone (Wed Jan 17 2018 - 12:07:23 CST)
  - Re: Isosurface wireframe & solid surface representation Vincent Ustach (Wed Jan 17 2018 - 15:40:12 CST)
Rotate a specific residue and save the coordinates in VMD Roshan Shrestha (Tue Jan 16 2018 - 22:25:01 CST)
- Re: Rotate a specific residue and save the coordinates in VMD Giacomo Fiorin (Wed Jan 17 2018 - 10:22:37 CST)
  - Re: Rotate a specific residue and save the coordinates in VMD Ashar Malik (Wed Jan 17 2018 - 17:44:21 CST)
catdcd plugin for Windows users Ern Ong (Tue Jan 16 2018 - 00:51:57 CST)
- Re: catdcd plugin for Windows users Ashar Malik (Tue Jan 16 2018 - 01:58:45 CST)
View sidechains in VMD Roshan Shrestha (Mon Jan 15 2018 - 22:51:22 CST)
- Re: View sidechains in VMD Ashar Malik (Tue Jan 16 2018 - 01:52:23 CST)
- Re: View sidechains in VMD Pawel Kedzierski (Tue Jan 16 2018 - 02:49:38 CST)
contact map in Rainbow scale Roshan Shrestha (Fri Jan 12 2018 - 11:55:56 CST)
- Re: contact map in Rainbow scale Vermaas, Joshua (Fri Jan 12 2018 - 13:10:25 CST)
Loading multiple dcd files crashes VMD Peter Mawanga (Thu Jan 11 2018 - 07:46:33 CST)
- Re: Loading multiple dcd files crashes VMD Ajasja LjubetiÄ (Thu Jan 11 2018 - 08:17:22 CST)
selecting residues within 5-10A of another molecule Rabeta Yeasmin (Wed Jan 10 2018 - 15:22:26 CST)
- Re: selecting residues within 5-10A of another molecule Vermaas, Joshua (Wed Jan 10 2018 - 17:02:01 CST)
- Re: selecting residues within 5-10A of another molecule amin sagar (Wed Jan 10 2018 - 23:57:28 CST)
- Re: selecting residues within 5-10A of another molecule Ashar Malik (Wed Jan 10 2018 - 23:05:01 CST)
How to calculate head group and acyl chain contact (separately) within 5 Anstrom of a particular protein residue? Robert Nairn (Wed Jan 10 2018 - 08:20:14 CST)
- Re: How to calculate head group and acyl chain contact (separately) within 5 Anstrom of a particular protein residue? Chitrak Gupta (Wed Jan 10 2018 - 10:15:00 CST)
  - Re: How to calculate head group and acyl chain contact (separately) within 5 Anstrom of a particular protein residue? Vermaas, Joshua (Wed Jan 10 2018 - 12:31:02 CST)
having problem with disulfide bond Shahee Islam (Tue Jan 09 2018 - 00:04:01 CST)
- Re: having problem with disulfide bond Ashar Malik (Tue Jan 09 2018 - 00:48:54 CST)
  - Re: having problem with disulfide bond Shahee Islam (Tue Jan 09 2018 - 01:21:24 CST)
    - Re: having problem with disulfide bond Souvik Sinha (Tue Jan 09 2018 - 02:05:47 CST)
    - Re: having problem with disulfide bond John Stone (Tue Jan 09 2018 - 11:25:28 CST)
ppm image conversion gpu dependent? Dow Hurst (Mon Jan 08 2018 - 17:22:03 CST)
(no subject) Suresh Ghimire (Sat Jan 06 2018 - 06:06:46 CST)
- Re: Jadzia Dax (Sat Jan 06 2018 - 06:52:54 CST)
- Re: Ashar Malik (Sat Jan 06 2018 - 07:04:01 CST)
  - Re: Vermaas, Joshua (Mon Jan 08 2018 - 11:58:15 CST)
(no subject) Suresh Ghimire (Sat Jan 06 2018 - 05:49:07 CST)
vector passing through a point and parallel to z axis, TCL code Rabeta Yeasmin (Thu Jan 04 2018 - 18:57:39 CST)
- Re: vector passing through a point and parallel to z axis, TCL code t.shivam_at_iitg.ernet.in (Thu Jan 04 2018 - 23:28:16 CST)
Improper terms in topology files processed by psfgen Jadzia Dax (Tue Jan 02 2018 - 01:29:30 CST)
- Re: Improper terms in topology files processed by psfgen Peter Freddolino (Tue Jan 02 2018 - 09:31:43 CST)
  - Re: Improper terms in topology files processed by psfgen Jadzia Dax (Wed Jan 03 2018 - 03:15:39 CST)
Problem drawing cylinders with a foreach loop - TCL syntax issue. Jeffrey A Tibbitt (Mon Jan 01 2018 - 20:16:26 CST)
- Re: Problem drawing cylinders with a foreach loop - TCL syntax issue. Jeffrey A Tibbitt (Wed Jan 03 2018 - 03:40:39 CST)
TCL equivalent for ---> Mouse Pick Mode Center Jeffrey A Tibbitt (Mon Jan 01 2018 - 18:55:49 CST)
(no subject) Suresh Ghimire (Sun Dec 31 2017 - 21:52:35 CST)
question about point substitution Aâ†’U parinaz bashirbanaem (Sat Dec 30 2017 - 12:32:03 CST)
- Re: question about point substitution A$B"*(BU Vermaas, Joshua (Tue Jan 02 2018 - 10:48:52 CST)
Save contact map data in other formats besides postscript Roshan Shrestha (Wed Dec 20 2017 - 17:20:23 CST)
vector passing through a point and parallel to z axis, TCL code Rabeta Yeasmin (Wed Dec 20 2017 - 17:12:38 CST)
removing rotation in trajectories Seibold, Steve Allan (Wed Dec 20 2017 - 10:11:12 CST)
- Re: removing rotation in trajectories Ajasja LjubetiÄ (Wed Dec 20 2017 - 10:29:56 CST)
- Re: removing rotation in trajectories Axel Kohlmeyer (Wed Dec 20 2017 - 10:38:40 CST)
Location of measure command script divyabharathi korlepara (Wed Dec 20 2017 - 03:43:12 CST)
- Re: Location of measure command script Vermaas, Joshua (Wed Dec 20 2017 - 12:23:07 CST)
tcl script not executed when submitted using a slurm script Stephen Thomas (Tue Dec 19 2017 - 23:55:17 CST)
- Re: tcl script not executed when submitted using a slurm script Ashar Malik (Wed Dec 20 2017 - 01:38:26 CST)
  - Re: tcl script not executed when submitted using a slurm script Stephen Thomas (Wed Dec 20 2017 - 08:40:05 CST)
    - Re: tcl script not executed when submitted using a slurm script John Stone (Wed Dec 20 2017 - 08:58:09 CST)
    - Re: tcl script not executed when submitted using a slurm script Stephen Thomas (Wed Dec 20 2017 - 08:59:11 CST)
- Re: tcl script not executed when submitted using a slurm script John Stone (Wed Dec 20 2017 - 09:08:23 CST)
  - Re: tcl script not executed when submitted using a slurm script Ashar Malik (Wed Dec 20 2017 - 09:50:11 CST)
    - Re: tcl script not executed when submitted using a slurm script Stephen Thomas (Wed Dec 20 2017 - 10:14:35 CST)
    - Re: tcl script not executed when submitted using a slurm script Bennion, Brian (Wed Dec 20 2017 - 10:45:35 CST)
  - Re: tcl script not executed when submitted using a slurm script Stephen Thomas (Wed Dec 20 2017 - 09:26:52 CST)
Contact map using VMD Contact Map Plugin Roshan Shrestha (Tue Dec 19 2017 - 20:49:22 CST)
Crack generation in Grapehene sheet sumit nagar (Tue Dec 19 2017 - 03:56:32 CST)
- Re: Crack generation in Grapehene sheet Giacomo Fiorin (Tue Dec 19 2017 - 07:49:40 CST)
How can I measure bond length with â€œname ** and resid **" in scripts? æœ¬æ‘è‚‡ (Tue Dec 19 2017 - 01:56:45 CST)
- Re: How can I measure bond length with â€œname ** and resid **" in scripts? Ashar Malik (Tue Dec 19 2017 - 02:42:41 CST)
  - Re: How can I measure bond length with Q=80=9Cname_**_and_resid_**=22_in_scripts=3F?= æœ¬æ‘è‚‡ (Tue Dec 19 2017 - 03:03:19 CST)
Using python interpreter with VMD sumit nagar (Mon Dec 18 2017 - 23:46:43 CST)
- Re: Using python interpreter with VMD sumit nagar (Mon Dec 18 2017 - 23:58:00 CST)
  - Re: Re: Using python interpreter with VMD John Stone (Tue Dec 19 2017 - 00:02:04 CST)
- Re: Using python interpreter with VMD Giacomo Fiorin (Tue Dec 19 2017 - 07:33:26 CST)
Suspected bug in BaseMolecule::default_mass Peter Jensen Husen (Mon Dec 18 2017 - 03:35:44 CST)
- Re: Suspected bug in BaseMolecule::default_mass John Stone (Mon Dec 18 2017 - 09:49:23 CST)
(no subject) Suresh Ghimire (Sun Dec 17 2017 - 06:57:45 CST)
- Re: John Stone (Mon Dec 18 2017 - 10:02:05 CST)
  - Re: Suresh Ghimire (Mon Dec 25 2017 - 22:29:46 CST)
    - Re: Tim Lo (Fri Dec 29 2017 - 20:38:47 CST)
Cycling between files using the same output file Windle,Stephen (Fri Dec 15 2017 - 16:39:25 CST)
- Re: Cycling between files using the same output file Ashar Malik (Fri Dec 15 2017 - 17:34:44 CST)
  - Re: Cycling between files using the same output file Vermaas, Joshua (Fri Dec 15 2017 - 20:03:57 CST)
    - Re: Cycling between files using the same output file Windle,Stephen (Sun Dec 17 2017 - 13:21:09 CST)
distance between two groups of atoms Rabeta Yeasmin (Fri Dec 15 2017 - 14:39:06 CST)
- Re: distance between two groups of atoms Vermaas, Joshua (Fri Dec 15 2017 - 15:37:27 CST)
- Re: distance between two groups of atoms Karteek Kumar (Fri Dec 15 2017 - 15:23:39 CST)
  - Re: distance between two groups of atoms Souvik Sinha (Sat Dec 16 2017 - 04:33:25 CST)
    - Re: distance between two groups of atoms Rabeta Yeasmin (Mon Dec 18 2017 - 10:02:23 CST)
Same starting configuration gives two starting values of backbone RMSD Monika Madhavi (Fri Dec 15 2017 - 05:52:39 CST)
FFTK, regarding RAHUL SURESH (Fri Dec 15 2017 - 05:45:54 CST)
- Re: FFTK, regarding Giacomo Fiorin (Fri Dec 15 2017 - 09:07:26 CST)
  - Re: FFTK, regarding Vermaas, Joshua (Fri Dec 15 2017 - 12:25:57 CST)
Same starting configuration gives two values of backbone RMSD Monika Madhavi (Fri Dec 15 2017 - 04:55:54 CST)
- Re: Same starting configuration gives two values of backbone RMSD Ashar Malik (Fri Dec 15 2017 - 06:10:00 CST)
  - Re: Same starting configuration gives two values of backbone RMSD Monika Madhavi (Fri Dec 15 2017 - 06:30:24 CST)
I would like to get a trajectory file in PDB. Can I use like data frame in VMD? æœ¬æ‘è‚‡ (Wed Dec 13 2017 - 00:41:56 CST)
- Re: I would like to get a trajectory file in PDB. Can I use like data frame in VMD? Ashar Malik (Wed Dec 13 2017 - 02:37:16 CST)
  - Re: I would like to get a trajectory file in PDB. Can I use like data frame in VMD? Ashar Malik (Wed Dec 13 2017 - 02:40:25 CST)
- Re: I would like to get a trajectory file in PDB. Can I use like data frame in VMD? Vermaas, Joshua (Wed Dec 13 2017 - 12:24:47 CST)
Nonbond energy between 3 part jrhau lung (Mon Dec 11 2017 - 20:52:21 CST)
- Re: Nonbond energy between 3 part Giacomo Fiorin (Mon Dec 11 2017 - 21:51:19 CST)
  - Re: Nonbond energy between 3 part jrhau lung (Tue Dec 12 2017 - 01:13:10 CST)
Missing substituents in the converted pdb format Lalehan Ozalp (Mon Dec 11 2017 - 03:01:46 CST)
How to calculate density profile M K (Sun Dec 10 2017 - 23:21:39 CST)
GUI mod request Dow Hurst (Sat Dec 09 2017 - 10:06:37 CST)
- Re: GUI mod request JÃ©rÃ´me HÃ©nin (Sat Dec 09 2017 - 10:57:55 CST)
  - Re: GUI mod request Dow Hurst (Sat Dec 09 2017 - 11:10:58 CST)
    - Re: GUI mod request JÃ©rÃ´me HÃ©nin (Sun Dec 10 2017 - 05:31:52 CST)
Water molar mass in autoionize.tcl Peter Jensen Husen (Fri Dec 08 2017 - 07:16:07 CST)
- Re: Water molar mass in autoionize.tcl JC Gumbart (Sat Dec 09 2017 - 07:52:15 CST)
  - Re: Water molar mass in autoionize.tcl Peter Jensen Husen (Mon Dec 18 2017 - 03:26:09 CST)
measure rmsf - relative to what? Gudrun Gygli (Fri Dec 08 2017 - 06:54:33 CST)
- Re: measure rmsf - relative to what? Giacomo Fiorin (Fri Dec 08 2017 - 07:16:59 CST)
FFTK plugin: domain error: argument not in valid range David Fischermeier (Fri Dec 08 2017 - 06:14:49 CST)
- Re: FFTK plugin: domain error: argument not in valid range David Fischermeier (Sat Dec 09 2017 - 05:32:50 CST)
  - Re: FFTK plugin: domain error: argument not in valid range JC Gumbart (Sat Dec 09 2017 - 07:33:39 CST)
    - Re: FFTK plugin: domain error: argument not in valid range Mayne, Christopher G (Sat Dec 09 2017 - 12:56:18 CST)
VMD interface and TkConsole font Yanxiao Han (Thu Dec 07 2017 - 16:58:01 CST)
- Re: VMD interface and TkConsole font Giacomo Fiorin (Fri Dec 08 2017 - 07:15:24 CST)
  - Re: VMD interface and TkConsole font JoÃ£o Ribeiro (Fri Dec 08 2017 - 08:47:09 CST)
    - Re: VMD interface and TkConsole font Giacomo Fiorin (Fri Dec 08 2017 - 09:28:50 CST)
    - Re: VMD interface and TkConsole font Barry Isralewitz (Fri Dec 08 2017 - 15:36:09 CST)
Regarding RDF calculation Aashish Bhatt (Fri Dec 01 2017 - 09:32:36 CST)
- Re: Regarding RDF calculation Philippe Bopp (Fri Dec 01 2017 - 11:27:33 CST)
Changing the format of atom labels from %f.3 to something else sperez14_at_us.es (Thu Nov 30 2017 - 04:40:09 CST)
- Re: Changing the format of atom labels from %f.3 to something else Giacomo Fiorin (Thu Nov 30 2017 - 09:13:09 CST)
Changing the format of atom labels from %f.3 to something else sperez14_at_us.es (Thu Nov 30 2017 - 02:43:50 CST)
Remote indirect GLX, Xquartz and nvidia drivers Osman BarÄ±ÅŸ MalcÄ±oÄŸlu (Wed Nov 29 2017 - 03:42:49 CST)
creation of psf t.shivam_at_iitg.ernet.in (Mon Nov 27 2017 - 02:40:53 CST)
- Re: creation of psf Vermaas, Joshua (Thu Nov 30 2017 - 13:15:38 CST)
  - Re: creation of psf t.shivam_at_iitg.ernet.in (Thu Nov 30 2017 - 22:10:49 CST)
Re: Timeline SASA Lizelle Lubbe (Thu Nov 23 2017 - 06:21:07 CST)
Timeline SASA Lizelle Lubbe (Thu Nov 23 2017 - 04:48:39 CST)
Topotools guessing angle and bond topology from CONNECT info in PDB files Vaidyanathan Sethuraman (Tue Nov 21 2017 - 23:40:33 CST)
- Re: Topotools guessing angle and bond topology from CONNECT info in PDB files Axel Kohlmeyer (Wed Nov 22 2017 - 00:41:16 CST)
  - Re: Topotools guessing angle and bond topology from CONNECT info in PDB files Yesica Pena (Wed Nov 22 2017 - 11:50:03 CST)
    - Re: Topotools guessing angle and bond topology from CONNECT info in PDB files Axel Kohlmeyer (Wed Nov 22 2017 - 13:25:20 CST)
  - Re: Topotools guessing angle and bond topology from CONNECT info in PDB files Vaidyanathan Sethuraman (Thu Nov 23 2017 - 02:15:32 CST)
error : invalid command name "psfgen" in 6pti tutorial æœ¬æ‘è‚‡ (Mon Nov 20 2017 - 21:47:25 CST)
- Re: error : invalid command name "psfgen" in 6pti tutorial Ashar Malik (Mon Nov 20 2017 - 23:22:31 CST)
  - Re: error : invalid command name "psfgen" in 6pti tutorial æœ¬æ‘è‚‡ (Mon Nov 20 2017 - 23:34:40 CST)
- Re: error : invalid command name "psfgen" in 6pti tutorial Axel Kohlmeyer (Mon Nov 20 2017 - 23:47:19 CST)
Exocyclic dihedral MD Simulation (Mon Nov 20 2017 - 12:13:22 CST)
graphics in VMD and overlay Nuno Sousa Cerqueira (Tue Nov 14 2017 - 12:21:21 CST)
- AW: graphics in VMD and overlay Norman Geist (Wed Nov 15 2017 - 01:24:53 CST)
SMD: constant velocity output analysis (Force and displacement plot from output file) Keshab Thapa (Sun Nov 12 2017 - 23:44:48 CST)
How to plot LOAD vs DISPLACEMENT from SMD output result using VMD Keshab Thapa (Thu Nov 09 2017 - 00:38:24 CST)
Gas migration pathway Lizelle Lubbe (Wed Nov 08 2017 - 12:43:15 CST)
- Re: Gas migration pathway Vermaas, Joshua (Wed Nov 08 2017 - 14:19:21 CST)
Order of atom indexes for a Fragment Clement Fang Jin Koh (Sun Nov 05 2017 - 22:18:22 CST)
- Re: Order of atom indexes for a Fragment Vermaas, Joshua (Mon Nov 06 2017 - 11:39:57 CST)
  - Re: Order of atom indexes for a Fragment Vermaas, Joshua (Mon Nov 06 2017 - 14:42:45 CST)
  - Re: Order of atom indexes for a Fragment Vermaas, Joshua (Mon Nov 06 2017 - 15:12:53 CST)
    - Re: Order of atom indexes for a Fragment Clement Fang Jin Koh (Mon Nov 06 2017 - 15:46:07 CST)
    - Re: Order of atom indexes for a Fragment Vermaas, Joshua (Mon Nov 06 2017 - 15:49:48 CST)
sqm not active in molefacture t.shivam_at_iitg.ernet.in (Thu Nov 02 2017 - 05:26:30 CDT)
- Re: sqm not active in molefacture Peter Freddolino (Thu Nov 02 2017 - 09:08:09 CDT)
  - Re: sqm not active in molefacture t.shivam_at_iitg.ernet.in (Thu Nov 02 2017 - 10:19:17 CDT)
Fwd: Topotools to keep atomtypes same Vaidyanathan Sethuraman (Wed Nov 01 2017 - 16:34:33 CDT)
- Re: Fwd: Topotools to keep atomtypes same Axel Kohlmeyer (Wed Nov 01 2017 - 17:38:50 CDT)
  - Re: Fwd: Topotools to keep atomtypes same Axel Kohlmeyer (Wed Nov 01 2017 - 21:03:27 CDT)
    - Re: Fwd: Topotools to keep atomtypes same Vaidyanathan Sethuraman (Wed Nov 01 2017 - 22:40:07 CDT)
Error using psfgen "unknown residue type SOD" Charles Hoying (Wed Nov 01 2017 - 04:59:23 CDT)
- Re: Error using psfgen "unknown residue type SOD" Vermaas, Joshua (Wed Nov 01 2017 - 11:45:04 CDT)
Re: Computing atom distances Ashar Malik (Tue Oct 31 2017 - 17:00:25 CDT)
Computing atom distances Windle,Stephen (Tue Oct 31 2017 - 15:52:54 CDT)
- Re: Computing atom distances Chitrak Gupta (Tue Oct 31 2017 - 17:27:38 CDT)
- Re: Computing atom distances Vermaas, Joshua (Tue Oct 31 2017 - 18:03:12 CDT)
  - Re: Computing atom distances Windle,Stephen (Fri Nov 03 2017 - 16:29:48 CDT)
Trajectory Smoothing Window Zize with implicit solvent Fabian Gonzalez (Tue Oct 31 2017 - 09:50:54 CDT)
Render in spherical equirectangular projection Dallas Warren (Mon Oct 30 2017 - 20:08:00 CDT)
- Re: Render in spherical equirectangular projection Dallas Warren (Tue Nov 07 2017 - 17:16:12 CST)
  - Re: Render in spherical equirectangular projection John Stone (Fri Nov 10 2017 - 22:16:35 CST)
Atoms in rings MD Simulation (Fri Oct 27 2017 - 09:31:41 CDT)
- Re: Atoms in rings Vermaas, Joshua (Fri Oct 27 2017 - 11:44:43 CDT)
  - Re: Atoms in rings John Stone (Fri Oct 27 2017 - 14:30:14 CDT)
- Re: Atoms in rings John Stone (Fri Oct 27 2017 - 12:54:31 CDT)
how to turn on antialiasing yx38 (Thu Oct 26 2017 - 23:31:06 CDT)
pbc wrapping problem Seibold, Steve Allan (Thu Oct 26 2017 - 10:37:56 CDT)
Moving atoms so that origin is at fixed position with respect to the display Miguel Caro (Thu Oct 26 2017 - 08:39:07 CDT)
- Re: Moving atoms so that origin is at fixed position with respect to the display Vermaas, Joshua (Thu Oct 26 2017 - 12:49:41 CDT)
  - Re: Moving atoms so that origin is at fixed position with respect to the display Ashar Malik (Thu Oct 26 2017 - 14:41:59 CDT)
    - Re: Moving atoms so that origin is at fixed position with respect to the display Miguel Caro (Fri Oct 27 2017 - 08:43:14 CDT)
Wrapping molecules in unit box Seibold, Steve Allan (Wed Oct 25 2017 - 11:43:23 CDT)
- Re: Wrapping molecules in unit box Dallas Warren (Sun Oct 29 2017 - 15:26:54 CDT)
  - Re: Wrapping molecules in unit box Ashar Malik (Sun Oct 29 2017 - 18:27:54 CDT)
Water atoms' explosion out of solvate box in my RBCG simulation on NAMD ThatMind TV (Mon Oct 23 2017 - 05:53:23 CDT)
write a new dcd file for a sub selection of atoms Monika Madhavi (Mon Oct 23 2017 - 01:24:03 CDT)
- Re: write a new dcd file for a sub selection of atoms Ashar Malik (Mon Oct 23 2017 - 02:05:30 CDT)
  - Re: write a new dcd file for a sub selection of atoms Monika Madhavi (Mon Oct 23 2017 - 17:55:21 CDT)
    - Re: write a new dcd file for a sub selection of atoms Ashar Malik (Mon Oct 23 2017 - 18:10:26 CDT)
    - Re: write a new dcd file for a sub selection of atoms Chitrak Gupta (Tue Oct 24 2017 - 07:25:33 CDT)
vmd-I: Creating PSF from PDB files Shehan Parmar (Sun Oct 22 2017 - 17:57:00 CDT)
problems reading rst file as amber7 restart with VMD 1.9.3 Capponi, Sara (Fri Oct 20 2017 - 12:27:48 CDT)
- Re: problems reading rst file as amber7 restart with VMD 1.9.3 Vermaas, Joshua (Fri Oct 20 2017 - 14:43:09 CDT)
  - Re: problems reading rst file as amber7 restart with VMD 1.9.3 Vermaas, Joshua (Fri Oct 20 2017 - 15:14:39 CDT)
FFTK Dihedral Optimization Error Nikolaos Galanakis (Fri Oct 20 2017 - 11:50:39 CDT)
- Re: FFTK Dihedral Optimization Error JC Gumbart (Fri Oct 20 2017 - 16:54:15 CDT)
  - Re: FFTK Dihedral Optimization Error JC Gumbart (Tue Oct 24 2017 - 17:21:14 CDT)
VMD error loading dcd files Daipayan Sarkar (Wed Oct 18 2017 - 21:01:39 CDT)
vmd not working on remote server POTTER T.D. (Tue Oct 17 2017 - 08:20:07 CDT)
- Re: vmd not working on remote server John Stone (Tue Oct 17 2017 - 14:10:00 CDT)
  - Re: vmd not working on remote server POTTER T.D. (Wed Oct 18 2017 - 05:31:53 CDT)
VMD contact map - long helical structure Zyla Dawid (Mon Oct 16 2017 - 03:41:44 CDT)
calculate g(r) melika_ bm85 (Sun Oct 15 2017 - 05:49:12 CDT)
- Re: calculate g(r) Monika Madhavi (Sun Oct 15 2017 - 07:14:20 CDT)
  - Re: calculate g(r) melika_ bm85 (Sun Oct 15 2017 - 07:36:10 CDT)
    - Re: calculate g(r) Monika Madhavi (Sun Oct 15 2017 - 07:44:44 CDT)
    - Re: calculate g(r) Axel Kohlmeyer (Sun Oct 15 2017 - 08:42:56 CDT)
  - Re: calculate g(r) melika_ bm85 (Sun Oct 15 2017 - 09:29:56 CDT)
    - Re: calculate g(r) Axel Kohlmeyer (Sun Oct 15 2017 - 14:09:46 CDT)
- Re: calculate g(r) Axel Kohlmeyer (Sun Oct 15 2017 - 07:00:57 CDT)
Fwd: Problem with Loading Bond Angle Optimization Gaussian .log file into the fftk Matt Albertolle (Thu Oct 12 2017 - 11:30:04 CDT)
- Re: Fwd: Problem with Loading Bond Angle Optimization Gaussian .log file into the fftk JC Gumbart (Fri Oct 20 2017 - 17:15:01 CDT)
  - Re: Fwd: Problem with Loading Bond Angle Optimization Gaussian .log file into the fftk Matt Albertolle (Mon Oct 23 2017 - 18:40:54 CDT)
  - Re: Fwd: Problem with Loading Bond Angle Optimization Gaussian .log file into the fftk Matt Albertolle (Thu Nov 02 2017 - 09:27:35 CDT)
    - Re: Fwd: Problem with Loading Bond Angle Optimization Gaussian .log file into the fftk JC Gumbart (Fri Nov 03 2017 - 10:39:20 CDT)
Bug report for NAMDgui plugin in VMD (1.9.4 alpha 8) Pawel Kedzierski (Wed Oct 11 2017 - 04:10:20 CDT)
- Re: Bug report for NAMDgui plugin in VMD (1.9.4 alpha 8) Pawel Kedzierski (Wed Oct 11 2017 - 08:07:35 CDT)
  - Re: Bug report for NAMDgui plugin in VMD (1.9.4 alpha 8) John Stone (Wed Oct 11 2017 - 09:57:26 CDT)
PDB loading in old vmd versions Stefan Boresch (Wed Oct 11 2017 - 01:40:25 CDT)
- Re: PDB loading in old vmd versions Ashar Malik (Wed Oct 11 2017 - 03:18:41 CDT)
  - Re: PDB loading in old vmd versions Stefan Boresch (Wed Oct 11 2017 - 03:52:04 CDT)
  - Re: PDB loading in old vmd versions John Stone (Wed Oct 11 2017 - 09:46:50 CDT)
HOW TO VISUALIZE HBOND AFTER SIMULATIONS THROUGH VMD Neha Gupta (Wed Oct 11 2017 - 00:04:10 CDT)
- Re: HOW TO VISUALIZE HBOND AFTER SIMULATIONS THROUGH VMD Ashar Malik (Wed Oct 11 2017 - 03:24:28 CDT)
  - Re: HOW TO VISUALIZE HBOND AFTER SIMULATIONS THROUGH VMD Neha Gupta (Thu Oct 26 2017 - 09:43:29 CDT)
Question about fftk Luba Simhaev (Tue Oct 10 2017 - 15:52:41 CDT)
- Re: Question about fftk JC Gumbart (Tue Oct 10 2017 - 18:12:32 CDT)
  - Re: Question about fftk JC Gumbart (Sun Oct 15 2017 - 07:24:45 CDT)
Smoothening labels in vmd Vikas Dubey (Tue Oct 10 2017 - 07:09:01 CDT)
- Re: Smoothening labels in vmd John Stone (Tue Oct 10 2017 - 10:15:31 CDT)
  - Re: Smoothening labels in vmd amin sagar (Tue Oct 10 2017 - 10:57:57 CDT)
VMD from remote workstation Pawel Kedzierski (Tue Oct 10 2017 - 03:45:58 CDT)
- Re: VMD from remote workstation (followup: crash with Intel drivers) Pawel Kedzierski (Tue Oct 10 2017 - 06:21:30 CDT)
  - Re: VMD from remote workstation (followup: crash with Intel drivers) John Stone (Tue Oct 10 2017 - 10:10:58 CDT)
    - Re: VMD from remote workstation (followup: crash with Intel drivers) Pawel Kedzierski (Wed Oct 11 2017 - 03:39:23 CDT)
Stuttering in video with TachyonL-Optix Dallas Warren (Mon Oct 09 2017 - 20:43:57 CDT)
- Re: Stuttering in video with TachyonL-Optix Dallas Warren (Mon Oct 09 2017 - 20:53:18 CDT)
- Re: Stuttering in video with TachyonL-Optix John Stone (Mon Oct 09 2017 - 22:17:24 CDT)
  - Re: Stuttering in video with TachyonL-Optix Dallas Warren (Tue Oct 10 2017 - 15:54:40 CDT)
how to calculate rmsd? Seera Suryanarayana (Mon Oct 09 2017 - 00:18:06 CDT)
- Re: how to calculate rmsd? Vermaas, Joshua (Mon Oct 09 2017 - 10:09:04 CDT)
Fwd: Klaus Schulten Memorial Symposium, registration and accommodation David Hardy (Thu Oct 05 2017 - 15:29:08 CDT)
Re: Unable to load O'Reilly Science Art (Thu Oct 05 2017 - 13:43:16 CDT)
- Re: Unable to load O'Reilly Science Art (Thu Oct 05 2017 - 13:25:01 CDT)
- Re: Unable to load John Stone (Thu Oct 05 2017 - 13:49:28 CDT)
  - Re: Unable to load O'Reilly Science Art (Thu Oct 05 2017 - 17:20:24 CDT)
Unable to load O'Reilly Science Art (Thu Oct 05 2017 - 13:07:21 CDT)
Start in VMD luiz beline (Wed Oct 04 2017 - 13:31:43 CDT)
- Re: Start in VMD Dallas Warren (Wed Oct 04 2017 - 16:40:29 CDT)
an continuous increased pattern for RMSD curve after long run fatehi_at_eng.uk.ac.ir (Tue Oct 03 2017 - 13:08:44 CDT)
- Re: an continuous increased pattern for RMSD curve after long run John Stone (Tue Oct 03 2017 - 13:20:57 CDT)
  - Re: an continuous increased pattern for RMSD curve after long run Vermaas, Joshua (Thu Oct 05 2017 - 11:47:11 CDT)
  - Re: an continuous increased pattern for RMSD curve after long run Vermaas, Joshua (Fri Oct 06 2017 - 10:58:48 CDT)
- Re: an continuous increased pattern for RMSD curve after long run Vermaas, Joshua (Tue Oct 03 2017 - 14:49:16 CDT)
a question about force field toolkit Albert (Tue Oct 03 2017 - 12:47:03 CDT)
- Re: a question about force field toolkit John Stone (Tue Oct 03 2017 - 13:20:16 CDT)
  - RE: a question about force field toolkit James Kress (Tue Oct 03 2017 - 16:48:11 CDT)
    - Re: a question about force field toolkit Mayne, Christopher G (Wed Oct 04 2017 - 01:33:51 CDT)
  - Re: a question about force field toolkit JC Gumbart (Tue Oct 03 2017 - 17:25:20 CDT)
Visualising Molecular Vibrations Mo Rahman (Tue Oct 03 2017 - 08:29:13 CDT)
- Re: Visualising Molecular Vibrations Giacomo Fiorin (Tue Oct 03 2017 - 15:18:34 CDT)
Improper angle-ffTK, regarding RAHUL SURESH (Tue Oct 03 2017 - 05:44:49 CDT)
- Re: Improper angle-ffTK, regarding JC Gumbart (Tue Oct 03 2017 - 17:21:52 CDT)
  - Re: Improper angle-ffTK, regarding JC Gumbart (Wed Oct 04 2017 - 15:01:47 CDT)
    - Re: Improper angle-ffTK, regarding Mayne, Christopher G (Thu Oct 05 2017 - 01:21:10 CDT)
    - Re: Improper angle-ffTK, regarding RAHUL SURESH (Thu Oct 05 2017 - 01:23:19 CDT)
VMD with sensible phantom haptic device using VRPN Xiaohu Hu (Mon Oct 02 2017 - 13:30:36 CDT)
- Re: VMD with sensible phantom haptic device using VRPN Xiaohu Hu (Mon Oct 02 2017 - 14:58:03 CDT)
  - Re: VMD with sensible phantom haptic device using VRPN John Stone (Tue Oct 03 2017 - 13:41:52 CDT)
    - Re: VMD with sensible phantom haptic device using VRPN Xiaohu Hu (Tue Oct 03 2017 - 13:44:51 CDT)
    - Re: VMD with sensible phantom haptic device using VRPN Xiaohu Hu (Wed Oct 04 2017 - 16:09:27 CDT)
Tachyon OptiX vs OSPRay for isosurface and clipping control Rune Thomas Kidmose (Sun Oct 01 2017 - 14:20:13 CDT)
- Re: Tachyon OptiX vs OSPRay for isosurface and clipping control Rune Thomas Kidmose (Mon Oct 02 2017 - 06:14:05 CDT)
ffTK, regarding RAHUL SURESH (Sun Oct 01 2017 - 02:22:19 CDT)
- Re: ffTK, regarding JC Gumbart (Sun Oct 01 2017 - 07:15:49 CDT)
Rendering 3D 360 Movies at higher resolution Dallas Warren (Wed Sep 27 2017 - 23:01:17 CDT)
- Re: Rendering 3D 360 Movies at higher resolution Dallas Warren (Sun Oct 01 2017 - 06:46:06 CDT)
  - Re: Rendering 3D 360 Movies at higher resolution Vermaas, Joshua (Mon Oct 02 2017 - 12:22:25 CDT)
Rgarding the output for dx file of occupancy(VolMap) Sheena Singh (Mon Sep 18 2017 - 10:38:19 CDT)
- Re: Rgarding the output for dx file of occupancy(VolMap) Giacomo Fiorin (Mon Sep 18 2017 - 11:20:04 CDT)
  - Re: Rgarding the output for dx file of occupancy(VolMap) Brian Radak (Mon Sep 18 2017 - 12:35:38 CDT)
    - Re: Rgarding the output for dx file of occupancy(VolMap) Axel Kohlmeyer (Mon Sep 18 2017 - 14:17:22 CDT)
  - Re: Rgarding the output for dx file of occupancy(VolMap) Giacomo Fiorin (Tue Sep 19 2017 - 09:47:35 CDT)
    - Re: Rgarding the output for dx file of occupancy(VolMap) Sheena Singh (Tue Sep 19 2017 - 10:27:37 CDT)
VMD installation RAHUL SURESH (Mon Sep 18 2017 - 05:07:39 CDT)
- Re: VMD installation JoÃ£o Ribeiro (Mon Sep 18 2017 - 07:39:09 CDT)
  - Re: VMD installation John Stone (Mon Sep 18 2017 - 10:14:00 CDT)
Error in merging two PDB files Aishwarya Smriti (Sun Sep 17 2017 - 04:05:44 CDT)
- Re: Error in merging two PDB files John Stone (Mon Sep 18 2017 - 10:18:06 CDT)
  - Re: Error in merging two PDB files Aishwarya Smriti (Mon Sep 18 2017 - 10:23:36 CDT)
Error in merging two PDB files Aishwarya Smriti (Sat Sep 16 2017 - 05:19:34 CDT)
MDFF Check -ccc in different VMD versions Rune Thomas Kidmose (Fri Sep 15 2017 - 05:36:46 CDT)
- Re: MDFF Check -ccc in different VMD versions Ryan McGreevy (Fri Sep 15 2017 - 08:56:03 CDT)
  - Sv: MDFF Check -ccc in different VMD versions Rune Thomas Kidmose (Wed Jan 17 2018 - 14:36:12 CST)
    - Re: MDFF Check -ccc in different VMD versions Ryan McGreevy (Wed Jan 17 2018 - 14:49:09 CST)
vmd not able to generate new cartoon representation t.shivam_at_iitg.ernet.in (Fri Sep 15 2017 - 00:46:10 CDT)
- Re: vmd not able to generate new cartoon representation John Stone (Tue Sep 19 2017 - 14:55:58 CDT)
  - Re: vmd not able to generate new cartoon representation t.shivam_at_iitg.ernet.in (Wed Sep 20 2017 - 02:37:31 CDT)
parallel processing in vmd Monika Madhavi (Thu Sep 14 2017 - 20:20:43 CDT)
- Re: parallel processing in vmd John Stone (Thu Sep 14 2017 - 21:35:59 CDT)
- Re: parallel processing in vmd Christopher Neale (Thu Sep 14 2017 - 22:34:52 CDT)
Change atom types in topotools Rajesh (Thu Sep 14 2017 - 08:07:12 CDT)
- Re: Change atom types in topotools Giacomo Fiorin (Thu Sep 14 2017 - 09:05:38 CDT)
polar hydrogens Albers, Thomas (Wed Sep 13 2017 - 12:07:46 CDT)
- Re: polar hydrogens Karteek Kumar (Wed Sep 13 2017 - 12:39:35 CDT)
  - Re: polar hydrogens Giacomo Fiorin (Wed Sep 13 2017 - 14:04:46 CDT)
    - Re: [EXTERNAL] Re: polar hydrogens Albers, Thomas (Thu Sep 14 2017 - 10:20:12 CDT)
- Re: polar hydrogens Vermaas, Joshua (Wed Sep 13 2017 - 13:41:30 CDT)
libX11.so.6 error Francesco Pietra (Wed Sep 13 2017 - 10:04:00 CDT)
- Re: libX11.so.6 error John Stone (Wed Sep 13 2017 - 11:02:27 CDT)
  - Re: libX11.so.6 error Francesco Pietra (Wed Sep 13 2017 - 11:31:25 CDT)
    - Re: libX11.so.6 error John Stone (Wed Sep 13 2017 - 15:51:42 CDT)
segname field in pdb files Goedde, Chris (Tue Sep 12 2017 - 15:46:09 CDT)
- Re: segname field in pdb files Vermaas, Joshua (Tue Sep 12 2017 - 17:00:33 CDT)
  - Re: segname field in pdb files Albers, Thomas (Wed Sep 13 2017 - 11:22:25 CDT)
Unable to visualize the solid isosurfaces Shivanand Malaganvi (Tue Sep 12 2017 - 10:46:00 CDT)
Electrostatic interaction calculations using the NAMD Energy Plugin and PME Michael LeVine (Tue Sep 12 2017 - 09:37:30 CDT)
- Re: Electrostatic interaction calculations using the NAMD Energy Plugin and PME John Stone (Wed Sep 13 2017 - 11:51:55 CDT)
intel_do_flush_locked failed: Cannot allocate memory Saikat Pal (Sat Sep 09 2017 - 00:07:35 CDT)
- Re: intel_do_flush_locked failed: Cannot allocate memory John Stone (Sat Sep 09 2017 - 15:15:38 CDT)
Creating PSF from PDB files Shehan Parmar (Thu Sep 07 2017 - 22:15:34 CDT)
Select Atoms that are bonded to specific atom type Arthur Vale (Thu Sep 07 2017 - 15:09:20 CDT)
- Re: Select Atoms that are bonded to specific atom type Vermaas, Joshua (Thu Sep 07 2017 - 16:38:29 CDT)
Re: VRML files from VMD are malformed John Stone (Wed Sep 06 2017 - 21:48:06 CDT)
tcl command "lremove" not working in VMD text mode Devanand T (Wed Sep 06 2017 - 16:08:44 CDT)
- Re: tcl command "lremove" not working in VMD text mode John Stone (Wed Sep 06 2017 - 16:33:52 CDT)
  - Re: tcl command "lremove" not working in VMD text mode Devanand T (Wed Sep 06 2017 - 16:38:31 CDT)
ACS COMP awards announcement John Stone (Wed Sep 06 2017 - 14:27:41 CDT)
VMD Seg fault on startup in Fedora 26 sooraj achar (Sun Sep 03 2017 - 17:19:26 CDT)
- Re: VMD Seg fault on startup in Fedora 26 John Stone (Sun Sep 03 2017 - 20:52:44 CDT)
  - Re: VMD Seg fault on startup in Fedora 26 sooraj achar (Sun Sep 03 2017 - 21:39:39 CDT)
    - Re: VMD Seg fault on startup in Fedora 26 John Stone (Tue Sep 05 2017 - 09:54:32 CDT)
Study the hydrogen bond in VMD Roshan Shrestha (Sat Sep 02 2017 - 06:19:11 CDT)
- RE: Study the hydrogen bond in VMD Bennion, Brian (Tue Sep 05 2017 - 10:31:57 CDT)
rlwrap: Command not found. Saikat Pal (Sat Sep 02 2017 - 01:07:17 CDT)
- RE: rlwrap: Command not found. Bennion, Brian (Tue Sep 05 2017 - 10:31:58 CDT)
- Re: rlwrap: Command not found. John Stone (Tue Sep 05 2017 - 13:27:31 CDT)
  - Bad reply-to email field Re: rlwrap: Command not found. John Stone (Tue Sep 05 2017 - 13:30:52 CDT)
    - Re: Bad reply-to email field Re: rlwrap: Command not found. John Stone (Wed Sep 06 2017 - 14:37:21 CDT)
install VMD IN parallel Saikat Pal (Fri Sep 01 2017 - 05:59:37 CDT)
- Re: install VMD IN parallel Ajasja LjubetiÄ (Fri Sep 01 2017 - 06:34:59 CDT)
  - Re: install VMD IN parallel John Stone (Fri Sep 01 2017 - 13:12:19 CDT)
    - Re: install VMD IN parallel Axel Kohlmeyer (Fri Sep 01 2017 - 14:10:44 CDT)
    - Re: install VMD IN parallel John Stone (Fri Sep 01 2017 - 14:34:31 CDT)
Cannot show the simulation box lan hoa Trinh (Thu Aug 31 2017 - 17:21:01 CDT)
- Re: Cannot show the simulation box John Stone (Thu Aug 31 2017 - 17:34:57 CDT)
  - Re: Cannot show the simulation box lan hoa Trinh (Thu Aug 31 2017 - 17:51:12 CDT)
FfTK RAHUL SURESH (Thu Aug 31 2017 - 10:35:21 CDT)
electrostatic potential along channel axis Williams Miranda (Wed Aug 30 2017 - 16:25:28 CDT)
- electrostatic potential along channel axis Williams Miranda (Thu Aug 31 2017 - 09:55:39 CDT)
- Re: electrostatic potential along channel axis Vermaas, Joshua (Thu Aug 31 2017 - 11:59:40 CDT)
VMD 1.9.4 alpha 8 posted for download... John Stone (Wed Aug 30 2017 - 12:14:19 CDT)
Unable to visualize the solid isosurfaces Shivanand Malaganvi (Wed Aug 30 2017 - 07:12:33 CDT)
780Ti and NAMD2 jrhau lung (Wed Aug 30 2017 - 06:14:54 CDT)
- Re: 780Ti and NAMD2 David Hardy (Wed Aug 30 2017 - 10:21:40 CDT)
Error while using Alanine Scanning Plugin amin sagar (Tue Aug 29 2017 - 08:37:47 CDT)
- Re: Error while using Alanine Scanning Plugin JC Gumbart (Tue Aug 29 2017 - 19:40:47 CDT)
  - Re: Error while using Alanine Scanning Plugin amin sagar (Thu Aug 31 2017 - 01:28:35 CDT)
    - Re: Error while using Alanine Scanning Plugin JoÃ£o Ribeiro (Thu Aug 31 2017 - 09:57:41 CDT)
  - Re: Error while using Alanine Scanning Plugin JoÃ£o Ribeiro (Fri Sep 01 2017 - 08:19:06 CDT)
    - Re: Error while using Alanine Scanning Plugin amin sagar (Fri Sep 01 2017 - 08:33:17 CDT)
Is it possible to use colvars module in VMD python mode? yjcoshc_at_gmail.com (Fri Aug 25 2017 - 20:30:33 CDT)
- Re: Is it possible to use colvars module in VMD python mode? Vermaas, Joshua (Sun Aug 27 2017 - 13:39:21 CDT)
  - Re: Is it possible to use colvars module in VMD python mode? yjcoshc (Mon Aug 28 2017 - 03:03:42 CDT)
    - Re: Is it possible to use colvars module in VMD python mode? Giacomo Fiorin (Thu Aug 31 2017 - 09:50:57 CDT)
Selection Text for two C atoms with a double bond Arthur Vale (Thu Aug 24 2017 - 16:55:20 CDT)
- Selection Text for two C atoms with a double bond Arthur Vale (Thu Aug 24 2017 - 17:09:22 CDT)
  - Re: Selection Text for two C atoms with a double bond Vermaas, Joshua (Thu Aug 24 2017 - 18:11:13 CDT)
    - RE: Selection Text for two C atoms with a double bond Arthur Vale (Thu Aug 24 2017 - 18:17:29 CDT)
    - Re: Selection Text for two C atoms with a double bond Vermaas, Joshua (Thu Aug 24 2017 - 18:30:23 CDT)
VMD not starting after nvidia update Remya Ann (Wed Aug 23 2017 - 05:52:36 CDT)
- Re: VMD not starting after nvidia update John Stone (Wed Aug 23 2017 - 10:37:03 CDT)
  - Re: VMD not starting after nvidia update Remya Ann (Thu Aug 24 2017 - 03:29:44 CDT)
TachyonL-OptiX Dallas Warren (Mon Aug 21 2017 - 19:20:00 CDT)
- Re: TachyonL-OptiX Vermaas, Joshua (Mon Aug 21 2017 - 20:18:40 CDT)
  - Re: TachyonL-OptiX Dallas Warren (Mon Aug 21 2017 - 20:59:58 CDT)
Functionalizing Mohsen Farshad (Mon Aug 21 2017 - 09:30:19 CDT)
bond updating in VMD Albert (Sat Aug 19 2017 - 00:20:27 CDT)
- Re: bond updating in VMD Ashar Malik (Sat Aug 19 2017 - 01:27:26 CDT)
  - Re: bond updating in VMD Jana, Suvamay (Sat Aug 19 2017 - 04:00:40 CDT)
    - Re: bond updating in VMD Albert (Sat Aug 19 2017 - 04:11:22 CDT)
    - Re: bond updating in VMD stefdoerr_at_gmail.com (Sat Aug 19 2017 - 04:41:54 CDT)
Visualize temperature Manish Gupta (Fri Aug 18 2017 - 12:04:54 CDT)
- Re: Visualize temperature Chris Neale (Fri Aug 18 2017 - 14:53:11 CDT)
  - Re: Visualize temperature Manish Gupta (Fri Aug 18 2017 - 15:02:36 CDT)
  - AW: Visualize temperature Norman Geist (Mon Aug 21 2017 - 00:08:08 CDT)
- Re: Visualize temperature Vermaas, Joshua (Fri Aug 18 2017 - 14:35:14 CDT)
  - Re: Visualize temperature Manish Gupta (Fri Aug 18 2017 - 14:57:29 CDT)
convert frames to nano seconds Saikat Pal (Wed Aug 16 2017 - 08:31:58 CDT)
- Re: convert frames to nano seconds Ashar Malik (Wed Aug 16 2017 - 09:53:19 CDT)
  - Re: convert frames to nano seconds Ashar Malik (Thu Aug 17 2017 - 07:58:49 CDT)
  - Re: convert frames to nano seconds Chitrak Gupta (Thu Aug 17 2017 - 17:13:45 CDT)
Optimal path calculation using NetworkView Souvik Sinha (Mon Aug 14 2017 - 03:59:07 CDT)
ffTK RAHUL SURESH (Mon Aug 14 2017 - 03:14:35 CDT)
- Re: ffTK Abhishek TYAGI (Mon Aug 14 2017 - 06:41:21 CDT)
Problem loading Amber trajectory George Tzotzos (Sun Aug 13 2017 - 08:40:50 CDT)
- Re: Problem loading Amber trajectory Axel Kohlmeyer (Sun Aug 13 2017 - 09:22:54 CDT)
Is occulus rift plug-and-play with VMD yet? If so, what are the capabilities? Christopher Neale (Sat Aug 12 2017 - 11:29:49 CDT)
- Re: Is occulus rift plug-and-play with VMD yet? If so, what are the capabilities? John Stone (Thu Aug 24 2017 - 15:37:18 CDT)
How to get 3D figure of solvent accessible surface area from APBS output Rabeta Yeasmin (Fri Aug 11 2017 - 17:19:24 CDT)
- Re: How to get 3D figure of solvent accessible surface area from APBS output John Stone (Thu Aug 31 2017 - 17:18:19 CDT)
ffTK RAHUL SURESH (Fri Aug 11 2017 - 02:04:38 CDT)
- Re: ffTK JC Gumbart (Sat Aug 12 2017 - 08:37:56 CDT)
  - Re: ffTK RAHUL SURESH (Sat Aug 12 2017 - 10:57:02 CDT)
Finding atoms in protein-lipid system having electrostatic interaction Rabeta Yeasmin (Wed Aug 09 2017 - 13:33:44 CDT)
- Re: Finding atoms in protein-lipid system having electrostatic interaction Ashar Malik (Wed Aug 09 2017 - 14:27:48 CDT)
  - Re: Finding atoms in protein-lipid system having electrostatic interaction Rabeta Yeasmin (Wed Aug 09 2017 - 15:22:53 CDT)
- Re: Finding atoms in protein-lipid system having electrostatic interaction Philippe Bopp (Wed Aug 09 2017 - 15:14:56 CDT)
  - Re: Finding atoms in protein-lipid system having electrostatic interaction Rabeta Yeasmin (Wed Aug 09 2017 - 15:29:27 CDT)
Software for molecular electrostatic calculations Rabeta Yeasmin (Wed Aug 09 2017 - 13:07:34 CDT)
vmd smooth trajectory distorted molecule Albert (Wed Aug 09 2017 - 03:59:33 CDT)
- Re: vmd smooth trajectory distorted molecule Axel Kohlmeyer (Wed Aug 09 2017 - 05:40:02 CDT)
  - Re: vmd smooth trajectory distorted molecule Albert (Wed Aug 09 2017 - 09:00:59 CDT)
RDF analysis using GROMACS trajectory faride badalkhani (Mon Aug 07 2017 - 08:02:05 CDT)
- Re: RDF analysis using GROMACS trajectory John Stone (Tue Aug 15 2017 - 12:18:20 CDT)
RE: autoionize not neutralizing the system Albers, Thomas (Sun Aug 06 2017 - 12:26:58 CDT)
autoionize not neutralizing the system t.shivam_at_iitg.ernet.in (Sun Aug 06 2017 - 09:51:29 CDT)
- Re: autoionize not neutralizing the system Giacomo Fiorin (Sun Aug 06 2017 - 10:46:37 CDT)
  - Re: autoionize not neutralizing the system t.shivam_at_iitg.ernet.in (Sun Aug 06 2017 - 21:30:32 CDT)
- Re: autoionize not neutralizing the system Chitrak Gupta (Sun Aug 06 2017 - 11:50:54 CDT)
- Re: autoionize not neutralizing the system Ashar Malik (Sun Aug 06 2017 - 11:11:45 CDT)
  - Re: autoionize not neutralizing the system Roshan Shrestha (Sun Aug 06 2017 - 11:50:49 CDT)
FFTK gaussian log Laura Joana (Thu Aug 03 2017 - 17:40:27 CDT)
- Re: FFTK gaussian log JC Gumbart (Mon Aug 07 2017 - 12:23:17 CDT)
identifying the specific coordinates of a voxel Daniel Strahs (Thu Aug 03 2017 - 12:30:30 CDT)
- Re: identifying the specific coordinates of a voxel John Stone (Wed Aug 30 2017 - 14:50:24 CDT)
Problem with cionize Sebastian Reiter (Tue Aug 01 2017 - 14:57:23 CDT)
- Re: Problem with cionize Peter Freddolino (Tue Aug 01 2017 - 22:01:30 CDT)
  - Re: Problem with cionize Sebastian Reiter (Wed Aug 02 2017 - 06:00:46 CDT)
Molecule builder for large number of molecules t.shivam_at_iitg.ernet.in (Mon Jul 31 2017 - 07:32:56 CDT)
- Re: Molecule builder for large number of molecules Fernando Vallejos-Burgos (Mon Jul 31 2017 - 09:17:47 CDT)
- Re: Molecule builder for large number of molecules Vermaas, Joshua (Mon Jul 31 2017 - 12:42:10 CDT)
  - Re: Molecule builder for large number of molecules t.shivam_at_iitg.ernet.in (Fri Aug 04 2017 - 01:29:09 CDT)
    - Re: Molecule builder for large number of molecules Vermaas, Joshua (Fri Aug 04 2017 - 12:05:29 CDT)
ffTk, regarding RAHUL SURESH (Mon Jul 31 2017 - 05:13:44 CDT)
- Fwd: ffTk, regarding RAHUL SURESH (Mon Jul 31 2017 - 05:38:55 CDT)
Viewing single lipid layer in vmd Roshan Shrestha (Mon Jul 31 2017 - 03:42:05 CDT)
ffTK, regarding RAHUL SURESH (Sat Jul 29 2017 - 03:15:46 CDT)
FFTk, dihedral optimization RAHUL SURESH (Sat Jul 29 2017 - 02:45:46 CDT)
- Re: FFTk, dihedral optimization Mayne, Christopher G (Sat Jul 29 2017 - 09:43:05 CDT)
  - Re: FFTk, dihedral optimization RAHUL SURESH (Sat Jul 29 2017 - 10:04:57 CDT)
    - Re: FFTk, dihedral optimization Mayne, Christopher G (Sat Jul 29 2017 - 10:10:51 CDT)
VMD text Nuno Sousa Cerqueira (Fri Jul 28 2017 - 05:33:44 CDT)
- Re: VMD text John Stone (Fri Jul 28 2017 - 11:38:57 CDT)
Protein move out of the water box in a QwikMD setup MD simulation using explicit solvent condition jrhau lung (Wed Jul 26 2017 - 20:37:32 CDT)
- Re: Protein move out of the water box in a QwikMD setup MD simulation using explicit solvent condition JoÃ£o Ribeiro (Thu Jul 27 2017 - 12:42:39 CDT)
sparse volumetric file format r xu (Wed Jul 26 2017 - 15:53:07 CDT)
Re: Unequal atoms size Afnan Sultan (Wed Jul 26 2017 - 03:08:01 CDT)
- Re: Re: Unequal atoms size Ashar Malik (Wed Jul 26 2017 - 03:37:36 CDT)
  - Re: Re: Unequal atoms size John Stone (Wed Jul 26 2017 - 09:49:44 CDT)
ffTK: neutral pyruvate group and charged pyruvate group at beta-D-mannose Ern Ong (Wed Jul 26 2017 - 01:40:49 CDT)
- Re: ffTK: neutral pyruvate group and charged pyruvate group at beta-D-mannose Mayne, Christopher G (Thu Jul 27 2017 - 22:52:49 CDT)
ffTK: neutral pyruvate group and charged pyruvate group at beta-D-mannose Ern Ong (Wed Jul 26 2017 - 01:37:37 CDT)
mol pdbload failing Mike McCallum (Tue Jul 25 2017 - 23:40:14 CDT)
- Re: mol pdbload failing Ashar Malik (Wed Jul 26 2017 - 00:35:27 CDT)
  - Re: mol pdbload failing Ashar Malik (Wed Jul 26 2017 - 00:39:09 CDT)
  - Re: mol pdbload failing Mike McCallum (Wed Jul 26 2017 - 01:51:58 CDT)
    - Re: mol pdbload failing JoÃ£o Ribeiro (Wed Jul 26 2017 - 08:29:15 CDT)
- Re: mol pdbload failing John Stone (Wed Jul 26 2017 - 09:53:12 CDT)
  - Re: mol pdbload failing Steven(Yuhang) Wang (Wed Jul 26 2017 - 20:50:37 CDT)
    - Re: mol pdbload failing John Stone (Tue Aug 15 2017 - 11:51:53 CDT)
    - RE: mol pdbload failing Wang, Steven (Tue Aug 15 2017 - 11:55:54 CDT)
- Re: mol pdbload failing Mike McCallum (Wed Jul 26 2017 - 09:50:28 CDT)
how draw color bar? Arham Amouie (Mon Jul 24 2017 - 09:35:18 CDT)
- Re: how draw color bar? Arham Amouie (Mon Jul 24 2017 - 15:10:44 CDT)
fftk - MM/QM distances not converging Kitzmiller, Nate (Sat Jul 22 2017 - 23:44:30 CDT)
fftk - MM/QM distances not converging McCullough, Scott (Sat Jul 22 2017 - 15:36:35 CDT)
- Re: fftk - MM/QM distances not converging Mayne, Christopher G (Mon Jul 24 2017 - 22:28:54 CDT)
VMD Error in Mac OSX Janakiraman Balachandran (Fri Jul 21 2017 - 13:14:22 CDT)
- Re: VMD Error in Mac OSX John Stone (Fri Jul 21 2017 - 13:58:50 CDT)
  - Re: VMD Error in Mac OSX Janakiraman Balachandran (Fri Jul 21 2017 - 14:06:02 CDT)
Building HMMM using patch files Arthur Vale (Thu Jul 20 2017 - 15:19:54 CDT)
- Re: Building HMMM using patch files Vermaas, Joshua (Thu Jul 20 2017 - 16:35:15 CDT)
(no subject) Siddharth Girdhar (Thu Jul 20 2017 - 01:42:01 CDT)
- Re: Ashar Malik (Thu Jul 20 2017 - 03:23:39 CDT)
  - Re: Giacomo Fiorin (Thu Jul 20 2017 - 09:40:20 CDT)
"Hands-on" Workshop on Enhanced Sampling and Free-Energy Calculation at Urbana, IL JoÃ£o Ribeiro (Mon Jul 17 2017 - 14:45:43 CDT)
(no subject) sesha surya vara prasad reddy karri (Mon Jul 17 2017 - 01:16:48 CDT)
- Re: Tim Lo (Fri Jul 21 2017 - 20:29:08 CDT)
Addforces Sourav Pal (Mon Jul 17 2017 - 01:11:55 CDT)
(no subject) sesha surya vara prasad reddy karri (Mon Jul 17 2017 - 01:10:17 CDT)
- Re: Tim Lo (Fri Jul 21 2017 - 20:19:32 CDT)
  - RE: McCullough, Scott (Sat Jul 22 2017 - 12:14:26 CDT)
file.dat and file.out from AMBER Martina Devi (Sat Jul 15 2017 - 01:13:10 CDT)
overriding predifined types for coloring sperez14_at_us.es (Wed Jul 12 2017 - 04:10:12 CDT)
regarding the python interface of vmd Pallab Dutta (Tue Jul 11 2017 - 00:45:48 CDT)
- Re: regarding the python interface of vmd Giacomo Fiorin (Tue Jul 11 2017 - 07:39:33 CDT)
  - Re: regarding the python interface of vmd Vermaas, Joshua (Tue Jul 11 2017 - 12:50:35 CDT)
    - Re: regarding the python interface of vmd Giacomo Fiorin (Tue Jul 11 2017 - 18:46:00 CDT)
simulation box moves in VMD when read lammps trajectory ruiyan (Mon Jul 10 2017 - 17:34:40 CDT)
coloring different polymers with different (random) colors Valerio Sorichetti (Mon Jul 10 2017 - 04:13:03 CDT)
- Re: coloring different polymers with different (random) colors Tim Moore (Mon Jul 10 2017 - 08:44:41 CDT)
  - Re: coloring different polymers with different (random) colors Valerio Sorichetti (Mon Jul 10 2017 - 09:05:57 CDT)
    - Re: coloring different polymers with different (random) colors Axel Kohlmeyer (Mon Jul 10 2017 - 09:46:33 CDT)
    - Re: coloring different polymers with different (random) colors Valerio Sorichetti (Mon Jul 10 2017 - 10:32:44 CDT)
Attaching NBD label to residues mutated to cysteine in VMD Satyaki Chatterjee (Sat Jul 08 2017 - 11:41:45 CDT)
HOLE-VMD installation Sourav Pal (Tue Jul 04 2017 - 05:31:17 CDT)
- Re: HOLE-VMD installation Dallas Warren (Thu Jul 13 2017 - 20:07:58 CDT)
Get empirical formula of fragment MD Simulation (Sat Jul 01 2017 - 20:12:31 CDT)
- Re: Get empirical formula of fragment Vermaas, Joshua (Mon Jul 03 2017 - 13:28:39 CDT)
- Re: Get empirical formula of fragment Axel Kohlmeyer (Mon Jul 03 2017 - 14:19:13 CDT)
  - Re: Get empirical formula of fragment MD Simulation (Mon Jul 03 2017 - 14:27:23 CDT)
Fragment determination MD Simulation (Sat Jul 01 2017 - 11:19:01 CDT)
dynamic bond making/breaking formats MD Simulation (Fri Jun 30 2017 - 17:11:24 CDT)
- Re: dynamic bond making/breaking formats Axel Kohlmeyer (Fri Jun 30 2017 - 17:49:12 CDT)
- Re: dynamic bond making/breaking formats Vermaas, Joshua (Fri Jun 30 2017 - 18:04:29 CDT)
namd plot not showing full range of data? Olya Kravchenko (Fri Jun 30 2017 - 15:38:45 CDT)
Re: psfgen error with "auto angles dihe patch" Ashar Malik (Thu Jun 29 2017 - 14:30:57 CDT)
- Re: psfgen error with "auto angles dihe patch" Vermaas, Joshua (Thu Jun 29 2017 - 16:02:22 CDT)
psfgen error with "auto angles dihe patch" Mary Lowe (Thu Jun 29 2017 - 13:41:08 CDT)
color bar problem in VMD Geng (Thu Jun 29 2017 - 12:44:11 CDT)
- Re: color bar problem in VMD Vermaas, Joshua (Thu Jun 29 2017 - 14:10:24 CDT)
  - RE: color bar problem in VMD Geng (Thu Jun 29 2017 - 17:19:24 CDT)
- Re: color bar problem in VMD Robin Betz (Thu Jun 29 2017 - 16:16:04 CDT)
  - RE: color bar problem in VMD Geng (Thu Jun 29 2017 - 16:34:57 CDT)
Running VMD on Blue Waters Jaime Guevara (Thu Jun 29 2017 - 11:09:46 CDT)
- Re: Running VMD on Blue Waters John Stone (Thu Jun 29 2017 - 13:08:52 CDT)
  - Re: Running VMD on Blue Waters Jaime Guevara (Thu Jul 06 2017 - 11:52:21 CDT)
PSF and PDB files do not show up Ghosh, Shreya (Wed Jun 28 2017 - 12:45:25 CDT)
- Re: PSF and PDB files do not show up Ashar Malik (Wed Jun 28 2017 - 13:37:28 CDT)
"Hands-on" Workshop on Enhanced Sampling and Free-Energy Calculation at Urbana, IL JoÃ£o Ribeiro (Tue Jun 27 2017 - 13:46:57 CDT)
Micelle formation visualisation Prapti Lohi (Tue Jun 27 2017 - 13:29:49 CDT)
- Re: Micelle formation visualisation Ashar Malik (Tue Jun 27 2017 - 14:28:30 CDT)
pdb download bug Albers, Thomas (Mon Jun 26 2017 - 13:44:07 CDT)
- Re: pdb download bug John Stone (Tue Jun 27 2017 - 20:32:36 CDT)
Re: Salt-Bridge Calculation PRITI ROY (Fri Jun 23 2017 - 02:10:40 CDT)
pbc wrap + within VS pbwithin Hemanth Vemuri (Wed Jun 21 2017 - 14:08:08 CDT)
convert psf to top with topotools Qinghua Liao (Wed Jun 21 2017 - 12:20:43 CDT)
- Re: convert psf to top with topotools Axel Kohlmeyer (Wed Jun 21 2017 - 13:04:40 CDT)
  - Re: convert psf to top with topotools Qinghua Liao (Wed Jun 21 2017 - 16:58:52 CDT)
- Re: convert psf to top with topotools Vermaas, Joshua (Wed Jun 21 2017 - 13:30:42 CDT)
  - Re: convert psf to top with topotools Qinghua Liao (Wed Jun 21 2017 - 13:35:12 CDT)
dihedral angles of nonpolar hydrogen in FFTK saeed amini (Sun Jun 18 2017 - 07:37:51 CDT)
- Re: dihedral angles of nonpolar hydrogen in FFTK Mayne, Christopher G (Mon Jun 19 2017 - 10:19:54 CDT)
  - Re: dihedral angles of nonpolar hydrogen in FFTK Mayne, Christopher G (Tue Jun 20 2017 - 09:12:15 CDT)
VMD display problems Seibold, Steve Allan (Fri Jun 16 2017 - 12:26:48 CDT)
VMD display problems. Seibold, Steve Allan (Fri Jun 16 2017 - 10:33:20 CDT)
- Re: VMD display problems. Vermaas, Joshua (Fri Jun 16 2017 - 13:11:38 CDT)
  - Re: VMD display problems. John Stone (Fri Jun 16 2017 - 14:46:55 CDT)
problem of displaying simulation box ruiyan (Fri Jun 16 2017 - 10:04:30 CDT)
- Re: problem of displaying simulation box Axel Kohlmeyer (Fri Jun 16 2017 - 11:20:00 CDT)
  - Re: Re: problem of displaying simulation box ruiyan (Fri Jun 16 2017 - 12:21:42 CDT)
NeutronRefTools ? Claire Loison (Fri Jun 16 2017 - 05:45:51 CDT)
- Re: NeutronRefTools ? Fotis Baltoumas (Fri Jun 16 2017 - 06:40:41 CDT)
Tachyon Craig Amundsen (Wed Jun 14 2017 - 11:18:12 CDT)
- Re: Tachyon John Stone (Wed Jun 14 2017 - 11:22:06 CDT)
  - Re: Tachyon Craig Amundsen (Wed Jun 14 2017 - 11:53:41 CDT)
    - Re: Tachyon John Stone (Mon Jun 19 2017 - 13:24:57 CDT)
    - Re: Tachyon Craig Amundsen (Mon Jun 19 2017 - 14:27:37 CDT)
CG builder in script JÃ¡nos SzÃ¶vÃ©rfi (Wed Jun 14 2017 - 03:26:06 CDT)
- Re: CG builder in script Ajasja LjubetiÄ (Wed Jun 14 2017 - 04:42:40 CDT)
- Re: CG builder in script Fotis Baltoumas (Wed Jun 14 2017 - 04:50:49 CDT)
  - Re: CG builder in script JÃ¡nos SzÃ¶vÃ©rfi (Wed Jun 14 2017 - 04:58:06 CDT)
Extract coordinates from a pdb file Roshan Shrestha (Mon Jun 12 2017 - 04:19:00 CDT)
- Re: Extract coordinates from a pdb file jrhau lung (Mon Jun 12 2017 - 05:07:14 CDT)
  - Re: Extract coordinates from a pdb file Ashar Malik (Mon Jun 12 2017 - 06:04:53 CDT)
    - Re: Extract coordinates from a pdb file Ashar Malik (Tue Jun 13 2017 - 08:27:08 CDT)
vmd-1.9.3 problem with nvidia driver 375 Robert Wohlhueter (Sat Jun 10 2017 - 21:06:04 CDT)
- Re: vmd-1.9.3 problem with nvidia driver 375 Vermaas, Joshua (Mon Jun 12 2017 - 10:36:14 CDT)
Ignore all the errors and load severely wrong structure in XYZ format Bharat Sharma (Sat Jun 10 2017 - 09:48:06 CDT)
- Re: Ignore all the errors and load severely wrong structure in XYZ format Bharat Sharma (Sat Jun 10 2017 - 16:07:40 CDT)
VMD crashed during reading the trajectory file Sidra Rafi (Sat Jun 10 2017 - 00:34:34 CDT)
- Re: VMD crashed during reading the trajectory file Ashar Malik (Sat Jun 10 2017 - 02:15:30 CDT)
- Re: VMD crashed during reading the trajectory file Pawel Kedzierski (Sat Jun 10 2017 - 05:33:58 CDT)
H-bond angle Shashank Ranjan Srivastava (Thu Jun 08 2017 - 09:52:38 CDT)
- Re: H-bond angle Ashar Malik (Thu Jun 08 2017 - 10:58:40 CDT)
Opening GROMACS Simulation File Norfarisha Mohd Fadil (Wed Jun 07 2017 - 20:04:51 CDT)
inorganic builder Barbault Florent (Wed Jun 07 2017 - 03:31:16 CDT)
different hydrogen bond results for the same system Sadegh Faramarzi Ganjabad (Tue Jun 06 2017 - 14:42:33 CDT)
different hydrogen bond results for the same system Sadegh Faramarzi Ganjabad (Mon Jun 05 2017 - 15:27:57 CDT)
errors starting vmd 1.9.3 Robert Wohlhueter (Sun Jun 04 2017 - 12:44:43 CDT)
Cutting and replacing in VMD Kalyan Madanapalli (Sat Jun 03 2017 - 16:26:45 CDT)
Re: winvmd stopped working Ashar Malik (Fri Jun 02 2017 - 18:59:03 CDT)
winvmd stopped working Fernando Bonilla Millan (Fri Jun 02 2017 - 16:40:26 CDT)
Suggested fix for 'restore_reps' command Robert Elder (Fri Jun 02 2017 - 14:12:43 CDT)
Three dcdplugin.c questions, and the DCD binary format. Charles McAnany (Thu Jun 01 2017 - 12:39:48 CDT)
Average structure using multiple frame trajectory Shashank Ranjan Srivastava (Thu May 25 2017 - 05:24:07 CDT)
- Re: Average structure using multiple frame trajectory Ashar Malik (Thu May 25 2017 - 06:07:34 CDT)
vmd script running from command line JÃ¡nos SzÃ¶vÃ©rfi (Thu May 25 2017 - 02:38:44 CDT)
- Re: vmd script running from command line Giacomo Fiorin (Thu May 25 2017 - 09:16:25 CDT)
Unable to remove sudden RMSD jumps between two segments Peter Mawanga (Thu May 25 2017 - 02:13:12 CDT)
- Re: Unable to remove sudden RMSD jumps between two segments Giacomo Fiorin (Thu May 25 2017 - 09:19:09 CDT)
  - Re: Unable to remove sudden RMSD jumps between two segments Peter Mawanga (Thu May 25 2017 - 21:02:18 CDT)
    - Re: Unable to remove sudden RMSD jumps between two segments Giacomo Fiorin (Thu May 25 2017 - 22:27:42 CDT)
    - Re: Unable to remove sudden RMSD jumps between two segments JÃ©rÃ´me HÃ©nin (Fri May 26 2017 - 10:55:22 CDT)
Re: Atoms moving too fast Ashar Malik (Wed May 24 2017 - 20:49:05 CDT)
- Re: Atoms moving too fast JoÃ£o Ribeiro (Thu May 25 2017 - 08:37:59 CDT)
Atoms moving too fast Pratik Narain Srivastava (Wed May 24 2017 - 14:36:45 CDT)
MDFF time line ccc score Karol KASZUBA (Wed May 24 2017 - 02:49:25 CDT)
- Re: MDFF time line ccc score Ryan McGreevy (Wed May 24 2017 - 09:16:19 CDT)
  - RE: MDFF time line ccc score Karol KASZUBA (Wed May 24 2017 - 09:42:34 CDT)
Drawing hollow circles Peter Mawanga (Tue May 23 2017 - 19:02:28 CDT)
- Re: Drawing hollow circles Karteek Kumar (Tue May 23 2017 - 19:37:56 CDT)
  - Re: Drawing hollow circles Peter Mawanga (Tue May 23 2017 - 20:58:32 CDT)
Selection of lipids not in contact with polymer Mihaela Drenscko (Sat May 20 2017 - 18:39:32 CDT)
- Re: Selection of lipids not in contact with polymer Ashar Malik (Sun May 21 2017 - 18:00:34 CDT)
Periodic Conditions for Hexagonal Membrane System Arthur Oliveira Vale (Fri May 19 2017 - 18:52:11 CDT)
- Re: Periodic Conditions for Hexagonal Membrane System Axel Kohlmeyer (Fri May 19 2017 - 19:40:24 CDT)
Selecting all residues based on z-axis coordinate in a protein Marko Sever (Fri May 19 2017 - 03:12:23 CDT)
- Re: Selecting all residues based on z-axis coordinate in a protein JÃ©rÃ´me HÃ©nin (Fri May 19 2017 - 05:08:15 CDT)
FFTK charge optimisation does not converge Siladitya Padhi (Sun May 14 2017 - 15:55:41 CDT)
- Re: FFTK charge optimisation does not converge Mayne, Christopher G (Tue May 16 2017 - 13:59:52 CDT)
  - Re: FFTK charge optimisation does not converge Siladitya Padhi (Thu May 18 2017 - 21:30:55 CDT)
    - Re: FFTK charge optimisation does not converge Mayne, Christopher G (Thu May 18 2017 - 21:46:03 CDT)
Reordering atomselection before saving trajectory Jacob D Durrant (Sat May 13 2017 - 19:28:32 CDT)
- Re: Reordering atomselection before saving trajectory John Stone (Wed May 31 2017 - 16:37:47 CDT)
  - Re: Reordering atomselection before saving trajectory JÃ©rÃ´me HÃ©nin (Thu Jun 01 2017 - 14:45:52 CDT)
    - Re: Reordering atomselection before saving trajectory Jacob D Durrant (Wed Jun 21 2017 - 18:49:34 CDT)
[VMD] Measure distance between two selections The Cromicus Productions (Sat May 13 2017 - 17:33:14 CDT)
- Re: [VMD] Measure distance between two selections John Stone (Wed May 31 2017 - 16:34:50 CDT)
Re: Accessing Mapped Drive Files on iMac Barry Isralewitz (Fri May 12 2017 - 12:01:17 CDT)
- Re: Accessing Mapped Drive Files on iMac Barry Isralewitz (Fri May 12 2017 - 14:11:13 CDT)
CG builder for martini force field Karteek Kumar (Fri May 12 2017 - 10:37:45 CDT)
- Re: CG builder for martini force field Peter Freddolino (Fri May 12 2017 - 15:33:54 CDT)
  - Re: CG builder for martini force field Peter Freddolino (Sat May 13 2017 - 21:36:21 CDT)
  - Re: CG builder for martini force field Peter Freddolino (Thu May 25 2017 - 22:10:03 CDT)
using inorganic builder for amorphous silica Diez Fernandez, Amanda (Thu May 11 2017 - 07:35:11 CDT)
Minimum distance between atoms within representation Dawid das (Fri May 05 2017 - 12:22:07 CDT)
- RE: Minimum distance between atoms within representation Radak, Brian K (Fri May 05 2017 - 15:15:55 CDT)
substitute one residue without rebuilding the structure? Olya Kravchenko (Thu May 04 2017 - 16:58:38 CDT)
- Re: substitute one residue without rebuilding the structure? Vermaas, Joshua (Thu May 04 2017 - 18:26:11 CDT)
  - Re: substitute one residue without rebuilding the structure? Olya Kravchenko (Thu May 04 2017 - 22:00:20 CDT)
Finding .vmdrc in LINUX(UBUNTU) Roshan Shrestha (Sat Apr 29 2017 - 01:31:54 CDT)
- Re: Finding .vmdrc in LINUX(UBUNTU) Dallas Warren (Sun Apr 30 2017 - 16:16:30 CDT)
  - Re: Finding .vmdrc in LINUX(UBUNTU) Vermaas, Joshua (Mon May 01 2017 - 11:32:53 CDT)
Writing velocities in lammps dump file Karteek Kumar (Thu Apr 27 2017 - 00:40:02 CDT)
- Re: Writing velocities in lammps dump file Axel Kohlmeyer (Thu Apr 27 2017 - 06:28:09 CDT)
Bug in VMD 1.9.3? Arham Amouie (Wed Apr 26 2017 - 07:07:20 CDT)
- Re: Bug in VMD 1.9.3? John Stone (Wed Apr 26 2017 - 10:03:28 CDT)
  - Re: Bug in VMD 1.9.3? Arham Amouie (Wed Apr 26 2017 - 10:37:58 CDT)
    - Re: Bug in VMD 1.9.3? John Stone (Wed Apr 26 2017 - 10:52:03 CDT)
    - Re: Bug in VMD 1.9.3? Arham Amouie (Wed Apr 26 2017 - 11:17:55 CDT)
Error when find salt bridges EGIDEA PUTI DEVINA (Tue Apr 25 2017 - 22:02:16 CDT)
NAMD developer workshop - Chicago, May 22-23, 2017 JoÃ£o Ribeiro (Tue Apr 25 2017 - 07:45:59 CDT)
Within X1 of Y but not within X2 of Y Kamps, M. (Mon Apr 24 2017 - 06:28:46 CDT)
- Re: Within X1 of Y but not within X2 of Y JÃ©rÃ´me HÃ©nin (Mon Apr 24 2017 - 09:12:33 CDT)
Visualizing volumetric data only for the small portion of a system reza vatan (Sat Apr 22 2017 - 18:03:21 CDT)
access to molfile plugin source code Peter Schmidtke (Sat Apr 22 2017 - 16:20:52 CDT)
- Re: access to molfile plugin source code Peter Schmidtke (Sat Apr 22 2017 - 17:44:42 CDT)
Meaning of computer graphic terms Arham Amouie (Wed Apr 19 2017 - 12:33:18 CDT)
- Re: Meaning of computer graphic terms Arham Amouie (Wed Apr 19 2017 - 12:42:41 CDT)
RE: Creating 3D PDF files James Kress (Wed Apr 19 2017 - 09:06:56 CDT)
NAMD developer workshop - Chicago, May 22-23, 2017 JoÃ£o Ribeiro (Tue Apr 18 2017 - 07:45:04 CDT)
TCBG Live Computational Biophysics Workshop Lectures JoÃ£o Ribeiro (Mon Apr 17 2017 - 09:13:24 CDT)
Re: Disable OSPRay for VMD on AMD CPU John Stone (Mon Apr 17 2017 - 07:59:29 CDT)
Re: Behavior of TachyonLOptiXInternal Renderer Vermaas, Joshua (Thu Apr 13 2017 - 20:53:52 CDT)
- Re: Re: Behavior of TachyonLOptiXInternal Renderer John Stone (Fri Apr 14 2017 - 02:29:36 CDT)
  - Re: Re: Behavior of TachyonLOptiXInternal Renderer John Stone (Fri Apr 14 2017 - 05:03:15 CDT)
Playing trajectories using HMDs Philip Loche (Wed Apr 12 2017 - 04:48:49 CDT)
- Re: Playing trajectories using HMDs John Stone (Wed May 31 2017 - 16:48:16 CDT)
Need help in NAMD Energy plugin jrhau lung (Tue Apr 11 2017 - 20:03:14 CDT)
- Re: Need help in NAMD Energy plugin Peter Freddolino (Tue Apr 11 2017 - 22:16:52 CDT)
Crating 3D PDF files James Kress (Tue Apr 11 2017 - 13:36:56 CDT)
- Re: Crating 3D PDF files John Stone (Mon Apr 17 2017 - 08:46:11 CDT)
RDF and RMSD calculation Jeams Anderson (Tue Apr 11 2017 - 04:06:48 CDT)
- Re: RDF and RMSD calculation Axel Kohlmeyer (Tue Apr 11 2017 - 09:54:28 CDT)
~1,5 million system Steven Neumann (Tue Apr 11 2017 - 03:51:17 CDT)
Fwd: vmd-1 Sharav Desai (Tue Apr 11 2017 - 03:32:09 CDT)
- Re: Fwd: vmd-1 JoÃ£o Ribeiro (Tue Apr 11 2017 - 07:50:39 CDT)
How to change the font size in VMD? ì •ìˆ™ì˜ (Tue Apr 11 2017 - 02:55:52 CDT)
- Re: How to change the font size in VMD? John Stone (Tue Apr 11 2017 - 02:58:37 CDT)
  - Re: How to change the font size in VMD? ì •ìˆ™ì˜ (Tue Apr 11 2017 - 03:18:08 CDT)
Unable to Render modified positions of labels with Tachyon Peter Mawanga (Mon Apr 10 2017 - 20:33:11 CDT)
- Re: Unable to Render modified positions of labels with Tachyon John Stone (Tue Apr 11 2017 - 02:57:14 CDT)
Unable to Render modified positions of labels with Tachyon Peter Mawanga (Mon Apr 10 2017 - 20:22:17 CDT)
Re: how to have an array of snapshots in an image file? Arham Amouie (Mon Apr 10 2017 - 15:24:09 CDT)
how to have an array of snapshots in an image file? Arham Amouie (Mon Apr 10 2017 - 14:55:21 CDT)
- Re: how to have an array of snapshots in an image file? Vermaas, Joshua (Mon Apr 10 2017 - 16:22:12 CDT)
function returned by atomselect; use global atomselect function from proc scope Eric Smoll (Mon Apr 10 2017 - 10:30:03 CDT)
function returned by atomselect; use global atomselect function from proc scope Eric Smoll (Mon Apr 10 2017 - 10:27:23 CDT)
TCBG Live Computational Biophysics Workshop Lectures JoÃ£o Ribeiro (Mon Apr 10 2017 - 08:24:13 CDT)
Problems of generating the psf file with a protein that has a structural calcium Guanyu Wang (Thu Apr 06 2017 - 17:46:24 CDT)
- Re: Problems of generating the psf file with a protein that has a structural calcium JoÃ£o Ribeiro (Thu Apr 06 2017 - 18:44:37 CDT)
  - Re: Problems of generating the psf file with a protein that has a structural calcium JoÃ£o Ribeiro (Thu Apr 06 2017 - 19:13:34 CDT)
NAMD Developer Workshop at Chicago IL, May 22-23, 2017 JoÃ£o Ribeiro (Thu Apr 06 2017 - 08:18:23 CDT)
psfgen giving wrong structure in the autopdb file Harish Srinivasan (Thu Apr 06 2017 - 01:37:29 CDT)
- Re: namd-l: psfgen giving wrong structure in the autopdb file JoÃ£o Ribeiro (Thu Apr 06 2017 - 19:06:36 CDT)
  - Re: namd-l: psfgen giving wrong structure in the autopdb file Peter Freddolino (Fri Apr 07 2017 - 07:58:04 CDT)
- Re: namd-l: psfgen giving wrong structure in the autopdb file Peter Freddolino (Thu Apr 06 2017 - 19:50:01 CDT)
(no subject) udit0000_at_gmail.com (Wed Apr 05 2017 - 09:36:00 CDT)
- Re: Ajasja LjubetiÄ (Wed Apr 05 2017 - 10:06:54 CDT)
- Re: Chitrak Gupta (Wed Apr 05 2017 - 10:43:55 CDT)
  - Re: Udit Aswal (Thu Apr 06 2017 - 00:54:35 CDT)
Regarding membrane thickness Shashank Ranjan Srivastava (Wed Apr 05 2017 - 06:46:29 CDT)
- Re: Regarding membrane thickness John Stone (Wed Apr 05 2017 - 14:27:11 CDT)
  - Re: Regarding membrane thickness John Stone (Tue Apr 11 2017 - 03:13:10 CDT)
    - Re: Regarding membrane thickness Ramon GuixÃ (Tue Apr 11 2017 - 03:59:52 CDT)
psfgen error with charmm36 parameters? Magnus Andersson (Wed Apr 05 2017 - 04:48:25 CDT)
- Re: psfgen error with charmm36 parameters? Ashar Malik (Wed Apr 05 2017 - 05:15:38 CDT)
- Re: psfgen error with charmm36 parameters? Pawel Kedzierski (Wed Apr 05 2017 - 06:23:50 CDT)
(no subject) udit0000_at_gmail.com (Tue Apr 04 2017 - 23:33:52 CDT)
Center of Mass RMSD in a trajectory Daniela Rivas (Mon Apr 03 2017 - 02:58:54 CDT)
- Re: Center of Mass RMSD in a trajectory Felipe Merino (Mon Apr 03 2017 - 03:51:46 CDT)
  - Re: Center of Mass RMSD in a trajectory Daniela Rivas (Mon Apr 03 2017 - 03:59:30 CDT)
Accessing tachyon optix from commandline and dat file generation Amit Gupta (Mon Apr 03 2017 - 01:41:09 CDT)
- Re: Accessing tachyon optix from commandline and dat file generation Andrea Spitaleri (Mon Apr 03 2017 - 02:36:37 CDT)
  - Re: Accessing tachyon optix from commandline and dat file generation Amit Gupta (Mon Apr 03 2017 - 04:16:44 CDT)
vmdrc file not loaded when the filename is a command line argument Dimitrova, Maria (Sat Apr 01 2017 - 10:49:55 CDT)
- Re: vmdrc file not loaded when the filename is a command line argument Vermaas, Joshua (Sat Apr 01 2017 - 21:30:33 CDT)
  - Re: vmdrc file not loaded when the filename is a command line argument Dimitrova, Maria (Sun Apr 02 2017 - 07:12:30 CDT)
  - Re: vmdrc file not loaded when the filename is a command line argument Stefan Kuczera (Mon Apr 03 2017 - 09:15:22 CDT)
modify the plugin in MACOS X H. Lee (Sat Apr 01 2017 - 08:28:11 CDT)
- Re: modify the plugin in MACOS X John Stone (Mon Apr 03 2017 - 09:47:12 CDT)
  - Re: modify the plugin in MACOS X H. Lee (Mon Apr 03 2017 - 10:11:43 CDT)
    - Re: modify the plugin in MACOS X John Stone (Mon Apr 03 2017 - 10:16:14 CDT)
    - Re: modify the plugin in MACOS X H. Lee (Mon Apr 03 2017 - 12:20:57 CDT)
vicinity analysis Udit Aswal (Fri Mar 31 2017 - 02:03:59 CDT)
- Re: vicinity analysis Ramon GuixÃ (Fri Mar 31 2017 - 03:14:11 CDT)
  - Re: vicinity analysis Udit Aswal (Fri Mar 31 2017 - 04:32:20 CDT)
(no subject) Udit Aswal (Fri Mar 31 2017 - 01:37:54 CDT)
How to extract data from log file Monika Madhavi (Thu Mar 30 2017 - 01:21:22 CDT)
- Re: How to extract data from log file Ashar Malik (Thu Mar 30 2017 - 02:18:27 CDT)
  - Re: How to extract data from log file Ajasja LjubetiÄ (Thu Mar 30 2017 - 02:54:05 CDT)
- Re: How to extract data from log file Daniela Rivas (Mon Apr 03 2017 - 08:30:17 CDT)
  - Re: How to extract data from log file Monika Madhavi (Mon Apr 03 2017 - 23:02:14 CDT)
VMD 1.9.2 crashing at startup in Mac OS X El Capitan Janakiraman Balachandran (Wed Mar 29 2017 - 08:57:41 CDT)
- Re: VMD 1.9.2 crashing at startup in Mac OS X El Capitan John Stone (Fri Mar 31 2017 - 13:29:29 CDT)
video streaming Ramon GuixÃ (Wed Mar 29 2017 - 05:02:37 CDT)
- Re: video streaming Vermaas, Joshua (Wed Mar 29 2017 - 11:47:52 CDT)
  - Re: video streaming Ramon GuixÃ (Thu Mar 30 2017 - 05:23:31 CDT)
    - Re: video streaming Axel Kohlmeyer (Thu Mar 30 2017 - 06:01:19 CDT)
    - Re: video streaming Ramon GuixÃ (Thu Mar 30 2017 - 06:25:44 CDT)
  - Re: video streaming Ramon GuixÃ (Thu Mar 30 2017 - 17:36:14 CDT)
    - Re: video streaming Ramon GuixÃ (Thu Mar 30 2017 - 17:41:52 CDT)
- Re: video streaming John Stone (Thu Mar 30 2017 - 15:11:41 CDT)
"spiral cylinders" instead of bonds when rendering with Tachyon? Brian Radak (Thu Mar 23 2017 - 14:34:16 CDT)
- Re: "spiral cylinders" instead of bonds when rendering with Tachyon? Vermaas, Joshua (Thu Mar 23 2017 - 17:32:41 CDT)
Volarea command line options Ban Arn (Wed Mar 22 2017 - 14:33:37 CDT)
- Re: Volarea command line options JoÃ£o Ribeiro KS (Wed Mar 22 2017 - 14:46:08 CDT)
Hands-On Workshop on Computational Biophysics: May 30 - June 2 in Pittsburgh, PA JoÃ£o Ribeiro KS (Wed Mar 22 2017 - 10:15:41 CDT)
Workshop on MD simulation software design Giacomo Fiorin (Tue Mar 21 2017 - 13:44:34 CDT)
VMD 1.9.3 GLSL rendering not available on Linux cluster Install Muralikrishna Raju (Mon Mar 20 2017 - 22:25:08 CDT)
- Re: VMD 1.9.3 GLSL rendering not available on Linux cluster Install Vermaas, Joshua (Tue Mar 21 2017 - 09:55:47 CDT)
replicating a trajectory in VMD Aman Jindal (Sun Mar 19 2017 - 06:01:28 CDT)
- Re: replicating a trajectory in VMD Philippe Bopp (Sun Mar 19 2017 - 09:10:12 CDT)
- Re: replicating a trajectory in VMD Axel Kohlmeyer (Sun Mar 19 2017 - 10:55:51 CDT)
measure inertia (Eigenvalues and Eigenvectors) Cardenas Lizana, Paul Antonio (Sat Mar 18 2017 - 13:30:07 CDT)
Numerical data from electrostatic calculations horst_at_lillig.de (Fri Mar 17 2017 - 02:53:37 CDT)
- Re: Numerical data from electrostatic calculations John Stone (Fri Mar 17 2017 - 11:10:03 CDT)
- Re: Numerical data from electrostatic calculations Brian Radak (Fri Mar 17 2017 - 11:09:18 CDT)
VMD and latest XQuartz update Ryan P. Steele (Thu Mar 16 2017 - 14:50:53 CDT)
- Re: VMD and latest XQuartz update John Stone (Thu Mar 16 2017 - 14:56:10 CDT)
  - Re: VMD and latest XQuartz update Ryan P. Steele (Thu Mar 16 2017 - 15:28:19 CDT)
WG: zoom and focus on on a selection Daniel MÃ¶ller (Tue Mar 14 2017 - 15:14:50 CDT)
zoom and focus on on a selection Thomas Evangelidis (Tue Mar 14 2017 - 07:35:00 CDT)
- RE: zoom and focus on on a selection Bennion, Brian (Tue Mar 14 2017 - 10:31:59 CDT)
Restart after press Finish in QwikMD simulation jrhau lung (Tue Mar 14 2017 - 04:08:04 CDT)
- Re: Restart after press Finish in QwikMD simulation JoÃ£o Ribeiro KS (Tue Mar 14 2017 - 07:18:16 CDT)
  - Re: Restart after press Finish in QwikMD simulation JoÃ£o Ribeiro KS (Tue Mar 14 2017 - 07:35:06 CDT)
Timeline / Sequence View not functional Vlad Cojocaru (Mon Mar 13 2017 - 08:11:17 CDT)
- Re: Timeline / Sequence View not functional Caio S. Souza (Mon Mar 13 2017 - 09:16:40 CDT)
  - Re: Timeline / Sequence View not functional Vlad Cojocaru (Mon Mar 13 2017 - 09:17:52 CDT)
- Re: Timeline / Sequence View not functional Vlad Cojocaru (Mon Mar 13 2017 - 09:16:25 CDT)
Importing Surface Mesh into VMD? Daniel Brooks (Mon Mar 13 2017 - 02:22:18 CDT)
- Re: Importing Surface Mesh into VMD? Vermaas, Joshua (Mon Mar 13 2017 - 11:25:21 CDT)
  - Re: Importing Surface Mesh into VMD? Daniel Brooks (Mon Mar 13 2017 - 16:05:15 CDT)
VMD and cuda 7.5 Hamid (Sat Mar 11 2017 - 04:33:51 CST)
- Re: VMD and cuda 7.5 John Stone (Fri Mar 17 2017 - 15:38:08 CDT)
Problem with CG Builder/AutoPSF extension in VMD Emiliano Fratini (Thu Mar 09 2017 - 05:34:41 CST)
- Re: Problem with CG Builder/AutoPSF extension in VMD Peter Freddolino (Thu Mar 09 2017 - 07:06:56 CST)
PSFGEN error "failed to parse autogenerate statement" Chitrak Gupta (Wed Mar 08 2017 - 13:45:28 CST)
Problem with N-glycosylation Daniela Rivas (Tue Mar 07 2017 - 20:40:19 CST)
- Re: Problem with N-glycosylation Vermaas, Joshua (Wed Mar 08 2017 - 09:54:21 CST)
  - Re: Problem with N-glycosylation Daniela Rivas (Wed Mar 08 2017 - 18:14:18 CST)
Re: Usage of the Orient package sunyeping (Tue Mar 07 2017 - 19:49:31 CST)
Localhost port 3000 error Kanishk Jain (Tue Mar 07 2017 - 17:08:09 CST)
- Re: Localhost port 3000 error JoÃ£o Ribeiro KS (Tue Mar 07 2017 - 17:25:26 CST)
- Re: Localhost port 3000 error Kanishk Jain (Wed Mar 08 2017 - 14:48:18 CST)
  - Re: Localhost port 3000 error Axel Kohlmeyer (Wed Mar 08 2017 - 15:26:21 CST)
Usage of the Orient package sunyeping (Mon Mar 06 2017 - 21:32:25 CST)
- RE: Usage of the Orient package Bennion, Brian (Tue Mar 07 2017 - 12:07:27 CST)
- RE: Usage of the Orient package Yogesh Sharma (Mon Dec 06 2021 - 14:08:28 CST)
Body elene shopova (Mon Mar 06 2017 - 11:18:40 CST)
- Re: Body Axel Kohlmeyer (Mon Mar 06 2017 - 12:10:52 CST)
scale angstroms to pixels (or mm, inches, etc.) Lachele Foley (Mon Mar 06 2017 - 07:55:01 CST)
Workshop on Computational Biophysics, Urbana, IL: Application Deadline March 10th JoÃ£o Ribeiro KS (Sat Mar 04 2017 - 15:55:57 CST)
convert .mrc map to .dx format Karol KASZUBA (Fri Mar 03 2017 - 09:51:29 CST)
- Re: convert .mrc map to .dx format Ryan McGreevy (Fri Mar 03 2017 - 10:08:58 CST)
- Re: convert .mrc map to .dx format Steven Cohen (Fri Mar 03 2017 - 10:49:47 CST)
  - RE: convert .mrc map to .dx format Karol KASZUBA (Sat Mar 04 2017 - 05:49:53 CST)
Zoom-to-fit before rendering Stefan Doerr (Thu Mar 02 2017 - 04:30:10 CST)
- AW: Zoom-to-fit before rendering Norman Geist (Thu Mar 02 2017 - 07:19:40 CST)
  - Re: Zoom-to-fit before rendering Stefan Doerr (Thu Mar 02 2017 - 08:04:36 CST)
    - Re: Zoom-to-fit before rendering Stefan Doerr (Thu Mar 02 2017 - 08:13:37 CST)
    - AW: Zoom-to-fit before rendering Norman Geist (Fri Mar 03 2017 - 02:24:46 CST)
Center camera rotation on a molid TUBIANA Thibault CNRS (Thu Mar 02 2017 - 04:00:03 CST)
- AW: Center camera rotation on a molid Norman Geist (Thu Mar 02 2017 - 07:30:55 CST)
Building NAMD 2.12 from Source with IB and CUDA Greipel.Joachim_at_mh-hannover.de (Thu Mar 02 2017 - 02:57:01 CST)
- AW: Building NAMD 2.12 from Source with IB and CUDA Norman Geist (Thu Mar 02 2017 - 04:37:40 CST)
  - AW: Building NAMD 2.12 from Source with IB and CUDA Greipel.Joachim_at_mh-hannover.de (Thu Mar 02 2017 - 05:53:58 CST)
creating the center of mass pdb file Mehdi Bagherpour (Tue Feb 28 2017 - 13:22:23 CST)
- Re: creating the center of mass pdb file Ashar Malik (Tue Feb 28 2017 - 15:27:07 CST)
Fwd: Termination when using QuickSurf, libGL no version info, and CUDA Error in start up Dallas Warren (Mon Feb 27 2017 - 18:32:54 CST)
- Re: Fwd: Termination when using QuickSurf, libGL no version info, and CUDA Error in start up John Stone (Tue Feb 28 2017 - 12:53:46 CST)
  - Re: Fwd: Termination when using QuickSurf, libGL no version info, and CUDA Error in start up Dallas Warren (Mon Mar 06 2017 - 22:08:56 CST)
  - Re: Fwd: Termination when using QuickSurf, libGL no version info, and CUDA Error in start up Dallas Warren (Tue Mar 07 2017 - 19:21:08 CST)
    - Re: Fwd: Termination when using QuickSurf, libGL no version info, and CUDA Error in start up Dallas Warren (Tue Mar 07 2017 - 19:31:27 CST)
    - Re: Fwd: Termination when using QuickSurf, libGL no version info, and CUDA Error in start up Dallas Warren (Tue Mar 07 2017 - 19:36:13 CST)
- Re: Fwd: Termination when using QuickSurf, libGL no version info, and CUDA Error in start up Dallas Warren (Tue Feb 28 2017 - 19:08:46 CST)
  - Re: Fwd: Termination when using QuickSurf, libGL no version info, and CUDA Error in start up Vermaas, Joshua (Wed Mar 01 2017 - 10:35:37 CST)
    - Re: Fwd: Termination when using QuickSurf, libGL no version info, and CUDA Error in start up Dallas Warren (Mon Mar 06 2017 - 20:12:11 CST)
- Re: Fwd: Termination when using QuickSurf, libGL no version info, and CUDA Error in start up Dallas Warren (Mon Mar 06 2017 - 21:09:54 CST)
placing text labels near atoms using draw text Garold Murdachaew (Mon Feb 27 2017 - 10:35:04 CST)
- Re: placing text labels near atoms using draw text John Stone (Tue Feb 28 2017 - 16:55:41 CST)
Re: How to remove rmsd spikes due to PB Ashar Malik (Sat Feb 25 2017 - 14:43:39 CST)
How to remove rmsd spikes due to PB zoran matovic (Sat Feb 25 2017 - 13:40:12 CST)
VMD 1.9.3 crashes during loading GROMACS trr trajectory in linux. yjcoshc_at_gmail.com (Fri Feb 24 2017 - 20:54:27 CST)
- Re: VMD 1.9.3 crashes during loading GROMACS trr trajectory in linux. John Stone (Tue Feb 28 2017 - 12:57:57 CST)
  - Re: VMD 1.9.3 crashes during loading GROMACS trr trajectory in linux. yjcoshc_at_gmail.com (Tue Feb 28 2017 - 22:11:21 CST)
NAMD developer workshop at Chicago IL, May 22-23, 2017 JoÃ£o Ribeiro KS (Fri Feb 24 2017 - 19:23:08 CST)
Issue viewing GRO file in VMD Sanim Rahman (Fri Feb 24 2017 - 17:44:31 CST)
- Re: Issue viewing GRO file in VMD Ashar Malik (Fri Feb 24 2017 - 19:10:53 CST)
  - Re: Issue viewing GRO file in VMD John Stone (Tue Feb 28 2017 - 16:28:07 CST)
ReadVarXYZ and measure gofr Tyler Westland (Fri Feb 24 2017 - 14:47:15 CST)
- Re: ReadVarXYZ and measure gofr Axel Kohlmeyer (Fri Feb 24 2017 - 15:12:28 CST)
hbonds with noncommon atom names Sadegh Faramarzi Ganjabad (Thu Feb 23 2017 - 23:52:24 CST)
- Re: hbonds with noncommon atom names John Stone (Tue Feb 28 2017 - 17:02:52 CST)
  - Re: hbonds with noncommon atom names Sadegh Faramarzi Ganjabad (Tue Feb 28 2017 - 18:34:33 CST)
remote visualization Thomas C. Bishop (Wed Feb 22 2017 - 17:38:45 CST)
trr generated by catdcd Stefano Guglielmo (Mon Feb 20 2017 - 19:25:11 CST)
- Re: trr generated by catdcd Vermaas, Joshua (Tue Feb 21 2017 - 11:23:33 CST)
  - Re: trr generated by catdcd Stefano Guglielmo (Tue Feb 21 2017 - 15:36:03 CST)
MSD calculation Nikhil Maroli (Mon Feb 20 2017 - 06:39:44 CST)
Charge Optimization error Lakshmikanth Srinivasamurthy (Sun Feb 19 2017 - 03:13:35 CST)
- Re: Charge Optimization error Mayne, Christopher G (Mon Feb 20 2017 - 14:23:09 CST)
QMtool gaussian 09 MARIA JOSE ALIAGA GOSALVEZ (Sat Feb 18 2017 - 14:34:23 CST)
- Re: QMtool gaussian 09 John Stone (Tue Feb 28 2017 - 17:05:43 CST)
Hands-On Workshop on Computational Biophysics: April 17-21 in Urbana, IL JoÃ£o Ribeiro KS (Fri Feb 17 2017 - 16:57:08 CST)
- Re: Hands-On Workshop on Computational Biophysics: April 17-21 in Urbana, IL JoÃ£o Ribeiro KS (Fri Feb 24 2017 - 09:12:05 CST)
measure surface usage Albers, Thomas (Fri Feb 17 2017 - 14:47:07 CST)
- Re: measure surface usage Vermaas, Joshua (Fri Feb 17 2017 - 18:38:01 CST)
Delete water 5 Angstrom away of ligand konda003 . (Fri Feb 17 2017 - 08:34:24 CST)
Simulation the binding affinity between DNA or RNA with non-natural nucleic acid acid jrhau lung (Thu Feb 16 2017 - 02:59:41 CST)
- Re: Simulation the binding affinity between DNA or RNA with non-natural nucleic acid acid Giacomo Fiorin (Thu Feb 16 2017 - 07:44:40 CST)
(no subject) MARIA JOSE ALIAGA GOSALVEZ (Tue Feb 14 2017 - 14:02:28 CST)
incorrect bonds Statics Eng (Tue Feb 14 2017 - 06:01:12 CST)
How to choose CVs along DNA axis? Mehdi Bagherpour (Mon Feb 13 2017 - 11:32:53 CST)
- Re: How to choose CVs along DNA axis? JÃ©rÃ´me HÃ©nin (Tue Feb 14 2017 - 08:36:11 CST)
Binding affinity simulation of a mutation structure. jrhau lung (Sun Feb 12 2017 - 19:14:28 CST)
- Re: Binding affinity simulation of a mutation structure. JoÃ£o Ribeiro KS (Sun Feb 12 2017 - 23:32:52 CST)
chain seprating and jumping because of periodic bound sunyeping (Sat Feb 11 2017 - 13:45:42 CST)
How to set the representations in batch in VMD? sunyeping (Sat Feb 11 2017 - 13:06:18 CST)
- Re: How to set the representations in batch in VMD? Axel Kohlmeyer (Sat Feb 11 2017 - 13:42:12 CST)
VolMap data format Karl Decker (Fri Feb 10 2017 - 14:32:22 CST)
- Re: VolMap data format John Stone (Fri Feb 10 2017 - 14:34:31 CST)
- Re: VolMap data format Vermaas, Joshua (Fri Feb 10 2017 - 15:52:31 CST)
  - Re: VolMap data format John Stone (Fri Feb 10 2017 - 16:06:32 CST)
    - Re: VolMap data format Vermaas, Joshua (Fri Feb 10 2017 - 16:36:10 CST)
Error Running NAMD Danu Fajar (Thu Feb 09 2017 - 22:53:46 CST)
- Re: Error Running NAMD JoÃ£o Ribeiro KS (Fri Feb 10 2017 - 07:23:23 CST)
  - Re: Error Running NAMD JoÃ£o Ribeiro KS (Fri Feb 10 2017 - 09:52:29 CST)
patching residues Lara rajam (Thu Feb 09 2017 - 15:07:11 CST)
- Re: patching residues Giacomo Fiorin (Thu Feb 09 2017 - 16:13:02 CST)
  - Re: patching residues Lara rajam (Thu Feb 09 2017 - 16:42:11 CST)
is there any plugin or software to combine PMF trajectory with VMD image? Olya Kravchenko (Wed Feb 08 2017 - 11:11:16 CST)
- Re: is there any plugin or software to combine PMF trajectory with VMD image? Vermaas, Joshua (Wed Feb 08 2017 - 14:28:31 CST)
  - Re: is there any plugin or software to combine PMF trajectory with VMD image? Olya Kravchenko (Wed Feb 08 2017 - 14:45:52 CST)
memory sharing in VMD Karl Decker (Tue Feb 07 2017 - 14:13:06 CST)
- Re: memory sharing in VMD John Stone (Tue Feb 07 2017 - 14:22:59 CST)
- Re: memory sharing in VMD Vermaas, Joshua (Tue Feb 07 2017 - 15:51:32 CST)
  - Re: memory sharing in VMD John Stone (Tue Feb 07 2017 - 16:02:12 CST)
  - Re: memory sharing in VMD Karl Decker (Fri Feb 10 2017 - 15:51:02 CST)
    - Re: memory sharing in VMD Vermaas, Joshua (Fri Feb 10 2017 - 16:17:49 CST)
    - Re: memory sharing in VMD Robin Betz (Fri Feb 10 2017 - 17:25:01 CST)
Using variables inside Atomselect Udaya Dahal (Tue Feb 07 2017 - 07:20:08 CST)
- Re: Using variables inside Atomselect JÃ©rÃ´me HÃ©nin (Tue Feb 07 2017 - 08:03:21 CST)
  - Re: Using variables inside Atomselect Ajasja LjubetiÄ (Tue Feb 07 2017 - 08:35:38 CST)
    - Re: Using variables inside Atomselect Udaya Dahal (Tue Feb 07 2017 - 08:41:46 CST)
- Re: Using variables inside Atomselect Ashar Malik (Tue Feb 07 2017 - 08:15:44 CST)
Topo file Statics Eng (Tue Feb 07 2017 - 06:39:33 CST)
- Re: Topo file John Stone (Tue Feb 07 2017 - 10:13:35 CST)
  - Re: Topo file Axel Kohlmeyer (Tue Feb 07 2017 - 10:45:30 CST)
    - Re: Topo file John Stone (Tue Feb 07 2017 - 10:57:52 CST)
    - Re: Topo file Axel Kohlmeyer (Tue Feb 07 2017 - 11:14:14 CST)
VMD animating spindensity Negar Ashari Astani (Tue Feb 07 2017 - 04:28:31 CST)
vmd cannot display cartoon/ribbon representations of part of a protein in gro/trr format å™ä¸šå¹³ (Sun Feb 05 2017 - 08:11:19 CST)
vmd cannot display part of the protein in gromacs gro/trr file format sunyeping (Fri Feb 03 2017 - 02:44:20 CST)
- Re: vmd cannot display part of the protein in gromacs gro/trr file format John Stone (Fri Feb 03 2017 - 10:31:45 CST)
  - Re: vmd cannot display part of the protein in gromacs gro/trr file format sunyeping (Sun Feb 05 2017 - 08:16:49 CST)
Interacting H-bond between two dimer PRITI ROY (Thu Feb 02 2017 - 23:58:56 CST)
- Re: Interacting H-bond between two dimer Chitrak Gupta (Fri Feb 03 2017 - 10:45:02 CST)
  - Re: Interacting H-bond between two dimer Chitrak Gupta (Sat Feb 04 2017 - 19:30:12 CST)
    - Re: Interacting H-bond between two dimer PRITI ROY (Sun Feb 12 2017 - 13:10:36 CST)
    - Re: Interacting H-bond between two dimer Vermaas, Joshua (Sun Feb 12 2017 - 22:13:45 CST)
.gro files written with python script not displayed until strange modification Benjamin Joseph Coscia (Thu Feb 02 2017 - 14:51:44 CST)
- Re: .gro files written with python script not displayed until strange modification Vermaas, Joshua (Thu Feb 02 2017 - 16:40:25 CST)
atomsel : setbonds: Need one bondlist for each selected atom leila karami (Wed Feb 01 2017 - 01:44:26 CST)
AW: SASA area Norman Geist (Wed Feb 01 2017 - 01:44:51 CST)
metadynamics potential vs pmf Stefano Guglielmo (Tue Jan 31 2017 - 20:02:51 CST)
- Re: metadynamics potential vs pmf Giacomo Fiorin (Wed Feb 01 2017 - 08:43:26 CST)
  - Re: metadynamics potential vs pmf Giacomo Fiorin (Thu Feb 02 2017 - 21:21:19 CST)
    - Re: metadynamics potential vs pmf Stefano Guglielmo (Fri Feb 03 2017 - 02:01:33 CST)
RMSF calculation with reference structure update Dmitry Suplatov (Tue Jan 31 2017 - 11:32:04 CST)
- Re: RMSF calculation with reference structure update Dmitry Suplatov (Thu Feb 02 2017 - 05:59:35 CST)
  - Re: RMSF calculation with reference structure update Vermaas, Joshua (Thu Feb 02 2017 - 11:03:32 CST)
Amber visualization problem Albert (Tue Jan 31 2017 - 10:09:50 CST)
- RE: Amber visualization problem Radak, Brian K (Tue Jan 31 2017 - 14:05:37 CST)
  - Re: Amber visualization problem Hannes Loeffler (Wed Feb 01 2017 - 03:09:52 CST)
    - Re: Amber visualization problem John Stone (Thu Feb 02 2017 - 23:53:12 CST)
AW: SASA area Norman Geist (Tue Jan 31 2017 - 09:35:48 CST)
SASA area Anna Battisti (Tue Jan 31 2017 - 01:28:16 CST)
- AW: SASA area Norman Geist (Tue Jan 31 2017 - 05:05:52 CST)
charmm36 vs charmm27/22 topology Neeraj Agrawal (Mon Jan 30 2017 - 11:29:19 CST)
- Re: charmm36 vs charmm27/22 topology Vermaas, Joshua (Mon Jan 30 2017 - 13:49:16 CST)
  - Re: charmm36 vs charmm27/22 topology Neeraj Agrawal (Mon Jan 30 2017 - 14:14:28 CST)
    - Re: charmm36 vs charmm27/22 topology Vermaas, Joshua (Mon Jan 30 2017 - 15:13:17 CST)
colvars module Stefano Guglielmo (Sun Jan 29 2017 - 17:40:53 CST)
- Re: colvars module JÃ©rÃ´me HÃ©nin (Mon Jan 30 2017 - 07:13:49 CST)
  - Re: colvars module Stefano Guglielmo (Mon Jan 30 2017 - 09:06:14 CST)
  - Re: colvars module Stefano Guglielmo (Mon Jan 30 2017 - 17:26:38 CST)
- Re: colvars module Stefano Guglielmo (Mon Jan 30 2017 - 16:05:23 CST)
reading rst7 files generated by cpptraj Vlad Cojocaru (Fri Jan 27 2017 - 04:28:30 CST)
- Re: reading rst7 files generated by cpptraj John Stone (Fri Feb 03 2017 - 00:18:05 CST)
Running out of memory due to multiple mol addfile's (?) Alexander Balaeff (Fri Jan 27 2017 - 00:03:15 CST)
- Re: Running out of memory due to multiple mol addfile's (?) Ashar Malik (Fri Jan 27 2017 - 02:01:13 CST)
  - Re: Running out of memory due to multiple mol addfile's (?) Alexander Balaeff (Fri Jan 27 2017 - 12:59:17 CST)
Optimization of torsion angles with fftk, large force constant ABEL Stephane (Thu Jan 26 2017 - 03:37:43 CST)
- Re: Optimization of torsion angles with fftk, large force constant Mayne, Christopher G (Wed Feb 01 2017 - 14:29:33 CST)
  - Re: Optimization of torsion angles with fftk, large force constant Mayne, Christopher G (Tue May 16 2017 - 14:07:20 CDT)
HBonds Plugin - Hbonds criteria #ANG YUN MEI ELISA# (Tue Jan 24 2017 - 18:24:49 CST)
- AW: HBonds Plugin - Hbonds criteria Norman Geist (Wed Jan 25 2017 - 02:19:24 CST)
Commandline file processed before vmdrc read in Stefan Kuczera (Tue Jan 24 2017 - 09:47:49 CST)
- Re: Commandline file processed before vmdrc read in Stefan Kuczera (Wed Jan 25 2017 - 07:35:34 CST)
Viewing Isosurface from g_spatial on VMD Badmos, Sakiru (Mon Jan 23 2017 - 13:04:44 CST)
RDFs Calculation incorporating PBC Mehta, Rushita (Mon Jan 23 2017 - 05:58:53 CST)
- Re: RDFs Calculation incorporating PBC Axel Kohlmeyer (Mon Jan 23 2017 - 06:43:25 CST)
minimizing each structure of a DCD file saeed amini (Sun Jan 22 2017 - 06:43:24 CST)
- Re: minimizing each structure of a DCD file Ashar Malik (Sun Jan 22 2017 - 07:48:30 CST)
ffTK Hessian calculation error outputting to Gaussian input Sze May Yee (Fri Jan 20 2017 - 05:02:22 CST)
- Re: ffTK Hessian calculation error outputting to Gaussian input JC Gumbart (Fri Jan 20 2017 - 10:48:13 CST)
  - Re: ffTK Hessian calculation error outputting to Gaussian input John Stone (Fri Jan 20 2017 - 10:55:24 CST)
Feature request: "Apply to all molecules" option in graphical representation window Bryan Roessler (Wed Jan 18 2017 - 17:06:48 CST)
- Re: Feature request: "Apply to all molecules" option in graphical representation window John Stone (Wed Jan 18 2017 - 17:17:50 CST)
  - Re: Feature request: "Apply to all molecules" option in graphical representation window Bryan Roessler (Wed Jan 18 2017 - 17:44:29 CST)
psf for a DNA chain saeed amini (Wed Jan 18 2017 - 06:44:21 CST)
- Re: psf for a DNA chain Ashar Malik (Wed Jan 18 2017 - 07:12:54 CST)
writegmxtop error invalid command name "..." Igor Ariz (Tue Jan 17 2017 - 03:30:36 CST)
- Re: writegmxtop error invalid command name "..." Axel Kohlmeyer (Tue Jan 17 2017 - 07:14:29 CST)
  - Re: writegmxtop error invalid command name "..." Vermaas, Joshua (Tue Jan 17 2017 - 14:07:19 CST)
atom selection in cv module of VMD Bin Sun (Sun Jan 15 2017 - 18:36:22 CST)
- Re: atom selection in cv module of VMD JÃ©rÃ´me HÃ©nin (Tue Jan 17 2017 - 07:17:02 CST)
working on VMD for Analysis.. maria khan (Sat Jan 14 2017 - 13:55:01 CST)
working with VMD maria khan (Sat Jan 14 2017 - 07:50:04 CST)
- Re: working with VMD Ashar Malik (Sat Jan 14 2017 - 11:59:46 CST)
working with VMD maria khan (Sat Jan 14 2017 - 07:43:43 CST)
results analysis by VMD. maria khan (Sat Jan 14 2017 - 05:11:04 CST)
How to read Scattered Volume Data hirak chatterjee (Fri Jan 13 2017 - 23:52:28 CST)
- Re: How to read Scattered Volume Data John Stone (Fri Jan 13 2017 - 23:58:12 CST)
  - Re: How to read Scattered Volume Data hirak chatterjee (Sat Jan 14 2017 - 00:05:10 CST)
    - Re: How to read Scattered Volume Data John Stone (Sat Jan 14 2017 - 00:20:59 CST)
Rendering images like those shown on VMD home page Amit Gupta (Fri Jan 13 2017 - 22:57:34 CST)
- Re: Rendering images like those shown on VMD home page John Stone (Fri Jan 13 2017 - 23:18:08 CST)
  - Re: Rendering images like those shown on VMD home page Amit Gupta (Sat Jan 14 2017 - 00:32:03 CST)
Analyzing results of simulation done by gromacs maria khan (Fri Jan 13 2017 - 15:44:31 CST)
- Re: Analyzing results of simulation done by gromacs Ashar Malik (Fri Jan 13 2017 - 16:41:27 CST)
  - Re: Analyzing results of simulation done by gromacs John Stone (Fri Jan 13 2017 - 23:28:26 CST)
    - Re: Analyzing results of simulation done by gromacs maria khan (Sat Jan 14 2017 - 04:32:11 CST)
    - Re: Analyzing results of simulation done by gromacs Ashar Malik (Sat Jan 14 2017 - 06:15:12 CST)
Polymer helix wrapping on the outer surface of carbon nanotube konda003 . (Fri Jan 13 2017 - 14:32:43 CST)
- Re: Polymer helix wrapping on the outer surface of carbon nanotube Tim Lo (Fri Jan 13 2017 - 20:38:12 CST)
Re: VMD very slow on DELL workstation with Quadro M4000 Vlad Cojocaru (Thu Jan 12 2017 - 09:02:31 CST)
- Re: VMD very slow on DELL workstation with Quadro M4000 John Stone (Thu Jan 12 2017 - 12:32:42 CST)
  - Re: VMD very slow on DELL workstation with Quadro M4000 Vlad Cojocaru (Fri Jan 13 2017 - 03:50:09 CST)
VMD very slow on DELL workstation with Quadro M4000 Vlad Cojocaru (Thu Jan 12 2017 - 07:40:45 CST)
isosurface stays gray after using "surface_color" command and "rebuild" Fux Samuel (ID SIS) (Wed Jan 11 2017 - 07:18:39 CST)
- Re: isosurface stays gray after using "surface_color" command and "rebuild" John Stone (Wed Jan 11 2017 - 08:07:56 CST)
Quad buffered stereo from Quadro M4000 to HDMI monitor Vlad Cojocaru (Wed Jan 11 2017 - 04:15:32 CST)
- Re: Quad buffered stereo from Quadro M4000 to HDMI monitor John Stone (Thu Jan 12 2017 - 12:20:50 CST)
  - AW: Quad buffered stereo from Quadro M4000 to HDMI monitor Greipel.Joachim_at_mh-hannover.de (Tue Jan 17 2017 - 07:12:12 CST)
    - Re: AW: Quad buffered stereo from Quadro M4000 to HDMI monitor Vlad Cojocaru (Tue Jan 17 2017 - 07:55:03 CST)
compiling VMD 1.9.3 with OSPRay support Vlad Cojocaru (Tue Jan 10 2017 - 07:25:10 CST)
- Re: compiling VMD 1.9.3 with OSPRay support John Stone (Tue Jan 10 2017 - 07:59:38 CST)
  - Re: compiling VMD 1.9.3 with OSPRay support Vlad Cojocaru (Tue Jan 10 2017 - 08:32:55 CST)
why vmd cannot load the dcd trajectory? sunyeping (Tue Jan 10 2017 - 01:06:08 CST)
- AW: why vmd cannot load the dcd trajectory? Norman Geist (Tue Jan 10 2017 - 02:43:17 CST)
pbc unwrap doesn't work sunyeping (Sun Jan 08 2017 - 07:44:14 CST)
water permeation across the channel Nikhil Maroli (Sun Jan 08 2017 - 06:56:48 CST)
orient - winVMD Stefano Guglielmo (Sat Jan 07 2017 - 05:33:49 CST)
- Re: orient - winVMD John Stone (Sun Jan 15 2017 - 02:44:45 CST)
FFTK for diazonium-modified tyrosine #YEO JINGJIE# (Fri Jan 06 2017 - 12:52:40 CST)
- Re: FFTK for diazonium-modified tyrosine JC Gumbart (Fri Jan 06 2017 - 14:52:50 CST)
  - Re: FFTK for diazonium-modified tyrosine #YEO JINGJIE# (Fri Jan 06 2017 - 15:47:00 CST)
reading big xtc file Smolin, Nikolai (Thu Jan 05 2017 - 15:58:26 CST)
- Re: reading big xtc file Axel Kohlmeyer (Thu Jan 05 2017 - 16:25:48 CST)
- Re: reading big xtc file Vermaas, Joshua (Thu Jan 05 2017 - 17:14:17 CST)
  - Re: reading big xtc file Ajasja LjubetiÄ (Fri Jan 06 2017 - 02:14:07 CST)
    - Re: reading big xtc file Smolin, Nikolai (Fri Jan 06 2017 - 09:15:49 CST)
DNA .dcd file analysis brataraj ghosh (Thu Jan 05 2017 - 07:33:07 CST)
- Re: DNA .dcd file analysis Karl Decker (Thu Jan 05 2017 - 14:46:29 CST)
veldcd file fatehi_at_eng.uk.ac.ir (Thu Jan 05 2017 - 02:52:29 CST)
- AW: veldcd file Norman Geist (Thu Jan 05 2017 - 04:49:12 CST)
- Re: veldcd file fatehi_at_eng.uk.ac.ir (Sat Jan 07 2017 - 06:30:21 CST)
  - Re: veldcd file John Stone (Sun Jan 15 2017 - 02:47:25 CST)
autoionize plugin parsing error (vmd 1.9.3 ) Wang, Steven (Wed Jan 04 2017 - 16:57:19 CST)
- Re: autoionize plugin parsing error (vmd 1.9.3 ) Peter Freddolino (Wed Jan 04 2017 - 20:01:57 CST)
topotools readlammpsdata redefining xyz coordinates? matt wessel (Wed Jan 04 2017 - 16:32:11 CST)
- Re: topotools readlammpsdata redefining xyz coordinates? Axel Kohlmeyer (Wed Jan 04 2017 - 17:49:44 CST)
  - Re: topotools readlammpsdata redefining xyz coordinates? matt wessel (Wed Jan 04 2017 - 18:05:20 CST)
plug-in for DNA .dcd brataraj ghosh (Tue Jan 03 2017 - 02:05:25 CST)
Contacts among two sets of atoms saeed amini (Mon Jan 02 2017 - 10:19:08 CST)
- Re: Contacts among two sets of atoms Vermaas, Joshua (Tue Jan 03 2017 - 10:54:03 CST)
Acetone as solvent Jonasz Sowada (Sat Dec 31 2016 - 17:34:33 CST)
[VMD] Power-spectrum calculation The Cromicus Productions (Tue Dec 27 2016 - 03:12:38 CST)
ffTK has halted on error. The optimizer has returned an empty result, indicating an abnormal termination. Ern Ong (Mon Dec 26 2016 - 22:31:47 CST)
- Re: ffTK has halted on error. The optimizer has returned an empty result, indicating an abnormal termination. JC Gumbart (Wed Dec 28 2016 - 16:52:28 CST)
  - Re: ffTK has halted on error. The optimizer has returned an empty result, indicating an abnormal termination. JC Gumbart (Sat Dec 31 2016 - 22:12:49 CST)
Fwd: namd-l: Modifying the equilibrium distance for a specific region of carbon nanotube in the parameter file zeynab hoseyni (Mon Dec 26 2016 - 06:45:28 CST)
- Re: namd-l: Modifying the equilibrium distance for a specific region of carbon nanotube in the parameter file Abhishek TYAGI (Mon Dec 26 2016 - 08:59:58 CST)
Problem while using multiseq amin_at_imtech.res.in (Thu Dec 22 2016 - 08:01:57 CST)
- RE: Problem while using multiseq Lai, Jonathan (Thu Dec 22 2016 - 09:46:16 CST)
  - RE: Problem while using multiseq amin_at_imtech.res.in (Sun Dec 25 2016 - 07:57:03 CST)
psf file of graphene Mohsen Farshad (Wed Dec 21 2016 - 15:16:44 CST)
- Re: psf file of graphene nabaneeta mukhopadhyay (Wed Dec 21 2016 - 16:20:25 CST)
trajectory smoothing with periodic images in VMD Chris Neale (Wed Dec 21 2016 - 12:52:39 CST)
How to determine periodicity and phase shift for ffTK dihedral parameter optimization? Ern Ong (Wed Dec 21 2016 - 03:02:05 CST)
- Re: How to determine periodicity and phase shift for ffTK dihedral parameter optimization? Vermaas, Joshua (Thu Dec 22 2016 - 08:49:59 CST)
  - RE: How to determine periodicity and phase shift for ffTK dihedral parameter optimization? Ern Ong (Thu Dec 22 2016 - 18:19:58 CST)
    - Re: How to determine periodicity and phase shift for ffTK dihedral parameter optimization? Vermaas, Joshua (Sat Dec 24 2016 - 08:40:07 CST)
Automate QwikMD? Danny Xu (Tue Dec 20 2016 - 15:23:28 CST)
- Re: Automate QwikMD? Vermaas, Joshua (Tue Dec 20 2016 - 16:43:39 CST)
  - Re: Automate QwikMD? JoÃ£o Ribeiro KS (Tue Dec 20 2016 - 17:19:22 CST)
AW: Draw arrows in trajectory file Norman Geist (Tue Dec 20 2016 - 07:55:37 CST)
Fw: Draw arrows in trajectory file Amit Gupta (Tue Dec 20 2016 - 03:45:40 CST)
- Re: Fw: Draw arrows in trajectory file Ashar Malik (Tue Dec 20 2016 - 06:19:33 CST)
  - Re: Fw: Draw arrows in trajectory file Amit Gupta (Tue Dec 20 2016 - 06:28:54 CST)
Draw arrows in trajectory file Amit Gupta (Tue Dec 20 2016 - 00:31:18 CST)
- AW: Draw arrows in trajectory file Norman Geist (Tue Dec 20 2016 - 02:37:41 CST)
Atom label offset Dimitrova, Maria (Mon Dec 19 2016 - 03:12:14 CST)
[VMD] Obtaining phonon spectrum of DNA The Cromicus Productions (Sat Dec 17 2016 - 00:00:44 CST)
vmd1.9.23 rlwrap: No match Francesco Pietra (Fri Dec 16 2016 - 01:43:12 CST)
- Fwd: vmd1.9.23 rlwrap: No match Francesco Pietra (Fri Dec 16 2016 - 03:49:21 CST)
  - Re: Fwd: vmd1.9.23 rlwrap: No match John Stone (Fri Dec 16 2016 - 14:14:50 CST)
psfgen - pdbalias when using readpsf Brian Radak (Thu Dec 15 2016 - 14:28:56 CST)
- Re: namd-l: psfgen - pdbalias when using readpsf Peter Freddolino (Thu Dec 15 2016 - 14:40:40 CST)
  - Re: namd-l: psfgen - pdbalias when using readpsf Brian Radak (Thu Dec 15 2016 - 14:48:01 CST)
(no subject) Karl Decker (Thu Dec 15 2016 - 11:13:26 CST)
- Re: John Stone (Thu Dec 15 2016 - 11:27:01 CST)
  - Re: Karl Decker (Fri Dec 16 2016 - 10:36:42 CST)
Atom selections for measure - index sorting Brian Radak (Wed Dec 14 2016 - 15:49:03 CST)
- Re: Atom selections for measure - index sorting Ajasja LjubetiÄ (Thu Dec 15 2016 - 02:31:16 CST)
  - Re: Atom selections for measure - index sorting Brian Radak (Thu Dec 15 2016 - 09:33:06 CST)
    - Re: Atom selections for measure - index sorting Axel Kohlmeyer (Thu Dec 15 2016 - 10:24:15 CST)
VMD crashing on OS X El Capitan 64 bit K. Aurelia Ball (Wed Dec 14 2016 - 15:27:35 CST)
- Re: VMD crashing on OS X El Capitan 64 bit John Stone (Wed Dec 14 2016 - 16:44:00 CST)
rlwrap: Command not found. /usr/local/lib/vmd/vmd_LINUX: Command not found. Atila Petrosian (Fri Dec 09 2016 - 13:29:11 CST)
- Re: rlwrap: Command not found. /usr/local/lib/vmd/vmd_LINUX: Command not found. Axel Kohlmeyer (Fri Dec 09 2016 - 13:50:14 CST)
  - Re: rlwrap: Command not found. /usr/local/lib/vmd/vmd_LINUX: Command not found. Axel Kohlmeyer (Fri Dec 09 2016 - 13:51:56 CST)
- Re: rlwrap: Command not found. /usr/local/lib/vmd/vmd_LINUX: Command not found. John Stone (Fri Dec 09 2016 - 13:46:00 CST)
NAMD Check points Naeem Mahmood Ashraf (Fri Dec 09 2016 - 08:25:29 CST)
- Re: NAMD Check points Peter Freddolino (Fri Dec 09 2016 - 10:12:25 CST)
- Re: NAMD Check points Brian Radak (Fri Dec 09 2016 - 10:17:47 CST)
rlwrap: Command not found. /usr/local/lib/vmd/vmd_LINUX: Command not found. Atila Petrosian (Fri Dec 09 2016 - 01:49:42 CST)
- Re: rlwrap: Command not found. /usr/local/lib/vmd/vmd_LINUX: Command not found. Atila Petrosian (Fri Dec 09 2016 - 01:55:18 CST)
  - Re: Re: rlwrap: Command not found. /usr/local/lib/vmd/vmd_LINUX: Command not found. John Stone (Fri Dec 09 2016 - 10:10:53 CST)
Unable to set coordinates in pdb - AutoPSF Harish Srinivasan (Thu Dec 08 2016 - 21:10:50 CST)
- Re: Unable to set coordinates in pdb - AutoPSF Peter Freddolino (Sun Dec 11 2016 - 14:46:51 CST)
Points of interaction in DNA linked proteins Roshan Shrestha (Thu Dec 08 2016 - 20:46:04 CST)
Trying to Use AutoPSF on Hundreds of pdb Files Eric A Brenner (Thu Dec 08 2016 - 17:27:58 CST)
- Re: Trying to Use AutoPSF on Hundreds of pdb Files Peter Freddolino (Thu Dec 08 2016 - 19:58:04 CST)
  - Re: Trying to Use AutoPSF on Hundreds of pdb Files Eric A Brenner (Thu Dec 08 2016 - 20:14:13 CST)
    - Re: Trying to Use AutoPSF on Hundreds of pdb Files Peter Freddolino (Thu Dec 08 2016 - 21:00:34 CST)
    - Re: Trying to Use AutoPSF on Hundreds of pdb Files Vermaas, Joshua (Fri Dec 09 2016 - 13:30:38 CST)
  - Re: Trying to Use AutoPSF on Hundreds of pdb Files Eric A Brenner (Fri Dec 09 2016 - 18:40:15 CST)
    - Re: Trying to Use AutoPSF on Hundreds of pdb Files Peter Freddolino (Sun Dec 11 2016 - 14:32:00 CST)
    - Re: Trying to Use AutoPSF on Hundreds of pdb Files Eric A Brenner (Mon Dec 12 2016 - 11:01:25 CST)
geometry optimization with SQM M.H. Taheri (Thu Dec 08 2016 - 10:43:29 CST)
- Re: geometry optimization with SQM Fotis Baltoumas (Thu Dec 08 2016 - 13:26:21 CST)
  - Re: geometry optimization with SQM Peter Freddolino (Thu Dec 08 2016 - 16:31:52 CST)
Delete the residue and reassign the residue numbers Karteek Kumar (Wed Dec 07 2016 - 01:23:53 CST)
Use of CUDA with AMD GPU Harish Srinivasan (Tue Dec 06 2016 - 22:59:44 CST)
- Re: Use of CUDA with AMD GPU John Stone (Tue Dec 06 2016 - 23:24:23 CST)
  - Re: Use of CUDA with AMD GPU Harish Srinivasan (Tue Dec 06 2016 - 23:52:56 CST)
OpenGL Display not working spandu K (Tue Dec 06 2016 - 22:02:16 CST)
- Re: OpenGL Display not working John Stone (Tue Dec 06 2016 - 22:11:30 CST)
  - Re: OpenGL Display not working spandu K (Tue Dec 06 2016 - 22:39:31 CST)
    - Re: OpenGL Display not working John Stone (Tue Dec 06 2016 - 22:49:00 CST)
    - Re: OpenGL Display not working spandu K (Tue Dec 06 2016 - 22:53:46 CST)
VMD HBonds plugin Ern Ong (Tue Dec 06 2016 - 21:38:26 CST)
- Re: VMD HBonds plugin Karteek Kumar (Tue Dec 06 2016 - 22:07:46 CST)
  - RE: VMD HBonds plugin Ern Ong (Tue Dec 06 2016 - 22:17:45 CST)
Invalid repid? Ignacio FernÃ¡ndez GalvÃ¡n (Tue Dec 06 2016 - 11:49:47 CST)
- Re: Invalid repid? John Stone (Fri Dec 09 2016 - 14:32:31 CST)
  - Re: Invalid repid? Ignacio FernÃ¡ndez GalvÃ¡n (Fri Dec 16 2016 - 08:53:42 CST)
Reordering atom numbers on a XYZ file Alexandre Barrozo (Mon Dec 05 2016 - 18:39:01 CST)
change_tkconsole_color_of_background_and_foreground Panagiotis Lagarias (Sun Dec 04 2016 - 04:48:07 CST)
- Re: change_tkconsole_color_of_background_and_foreground Aman Jindal (Sun Dec 04 2016 - 07:15:31 CST)
  - Re: change_tkconsole_color_of_background_and_foreground Ashar Malik (Sun Dec 04 2016 - 10:53:47 CST)
- Re: change_tkconsole_color_of_background_and_foreground Aman Jindal (Sun Dec 04 2016 - 06:26:33 CST)
AMBER trajectory visualization James Kress (Sat Dec 03 2016 - 20:33:16 CST)
- Re: AMBER trajectory visualization John Stone (Sat Dec 03 2016 - 22:48:02 CST)
  - RE: AMBER trajectory visualization James Kress (Sun Dec 04 2016 - 20:40:39 CST)
    - Re: AMBER trajectory visualization John Stone (Sun Dec 04 2016 - 21:25:34 CST)
Distribute evenly n-molecules at m-angstroem from protein surface Ebert Maximilian (Fri Dec 02 2016 - 21:55:50 CST)
- Re: Distribute evenly n-molecules at m-angstroem from protein surface John Stone (Sat Dec 03 2016 - 23:38:11 CST)
  - Re: Distribute evenly n-molecules at m-angstroem from protein surface Axel Kohlmeyer (Sun Dec 04 2016 - 00:29:54 CST)
    - Re: Distribute evenly n-molecules at m-angstroem from protein surface Vermaas, Joshua (Sun Dec 04 2016 - 11:17:09 CST)
Re: chlorine atom: Cl or CL ? Denilson F. Oliveira (Fri Dec 02 2016 - 12:03:00 CST)
Capture query data Eric Smoll (Fri Dec 02 2016 - 06:20:52 CST)
- Re: Capture query data JÃ©rÃ´me HÃ©nin (Fri Dec 02 2016 - 06:52:20 CST)
(no subject) Denilson F. Oliveira (Fri Dec 02 2016 - 05:51:38 CST)
VMD 1.9.3 on 64-bit macOS FX (Fri Dec 02 2016 - 05:25:07 CST)
- Some macOS code simplification FX (Fri Dec 02 2016 - 07:42:09 CST)
  - Re: Some macOS code simplification John Stone (Tue Dec 06 2016 - 17:55:01 CST)
- Re: VMD 1.9.3 on 64-bit macOS John Stone (Tue Dec 06 2016 - 17:49:43 CST)
  - Re: VMD 1.9.3 on 64-bit macOS FX (Thu Dec 15 2016 - 05:05:59 CST)
XYZ Bashir (Thu Dec 01 2016 - 10:52:03 CST)
- Re: XYZ M K (Thu Dec 01 2016 - 17:33:23 CST)
Setting user field for time varying parameters? Brian Radak (Thu Dec 01 2016 - 14:05:28 CST)
- Re: Setting user field for time varying parameters? John Stone (Thu Dec 01 2016 - 15:09:27 CST)
- Re: Setting user field for time varying parameters? Vermaas, Joshua (Thu Dec 01 2016 - 15:11:56 CST)
  - Re: Setting user field for time varying parameters? Brian Radak (Thu Dec 01 2016 - 15:24:45 CST)
    - Re: Setting user field for time varying parameters? John Stone (Thu Dec 01 2016 - 15:40:57 CST)
CUDA acceleration for Tachyon rendering? Eiros Zamora, Juan (Thu Dec 01 2016 - 13:41:59 CST)
- Re: CUDA acceleration for Tachyon rendering? John Stone (Thu Dec 01 2016 - 15:06:03 CST)
  - AW: CUDA acceleration for Tachyon rendering? Norman Geist (Fri Dec 02 2016 - 01:51:05 CST)
    - Re: CUDA acceleration for Tachyon rendering? Eiros Zamora, Juan (Fri Dec 02 2016 - 04:48:37 CST)
- Re: CUDA acceleration for Tachyon rendering? Vermaas, Joshua (Thu Dec 01 2016 - 15:20:44 CST)
VMD 1.9.3 released! John Stone (Thu Dec 01 2016 - 01:30:55 CST)
- Re: VMD 1.9.3 released! jrhau lung (Thu Dec 01 2016 - 02:04:04 CST)
Superimpose Wong Li Zhe (Wed Nov 30 2016 - 23:53:25 CST)
- Re: Superimpose Ashar Malik (Thu Dec 01 2016 - 02:42:56 CST)
  - Re: Superimpose Wong Li Zhe (Tue Dec 06 2016 - 18:03:04 CST)
    - Re: Superimpose John Stone (Tue Dec 06 2016 - 22:37:04 CST)
  - Re: Superimpose Ashar Malik (Tue Dec 06 2016 - 22:56:55 CST)
    - Re: Superimpose Wong Li Zhe (Thu Dec 08 2016 - 18:37:12 CST)
    - Re: Superimpose John Stone (Thu Dec 08 2016 - 21:24:45 CST)
OpenGL spandu K (Tue Nov 29 2016 - 16:59:42 CST)
- Re: OpenGL John Stone (Tue Nov 29 2016 - 17:07:16 CST)
qwikmd, some dropdown menus missing Stefan Boresch (Mon Nov 28 2016 - 04:35:31 CST)
- Re: qwikmd, some dropdown menus missing Stefan Boresch (Mon Nov 28 2016 - 06:31:30 CST)
  - Re: qwikmd, some dropdown menus missing JoÃ£o Ribeiro KS (Mon Nov 28 2016 - 07:40:33 CST)
error during the Gaussian optimization of the Water interaction in fftk Ghazaleh Zamani Maimian (Fri Nov 25 2016 - 03:25:42 CST)
Close contacts upon solvation of XYZ file. Dawid das (Thu Nov 24 2016 - 10:30:50 CST)
- Re: Close contacts upon solvation of XYZ file. John Stone (Thu Nov 24 2016 - 12:18:43 CST)
  - Re: Close contacts upon solvation of XYZ file. Dawid das (Fri Nov 25 2016 - 01:52:10 CST)
  - Re: Close contacts upon solvation of XYZ file. Pawel Kedzierski (Fri Nov 25 2016 - 03:20:37 CST)
- Re: Close contacts upon solvation of XYZ file. Pawel Kedzierski (Fri Nov 25 2016 - 01:27:57 CST)
Superimpose Models Wong Li Zhe (Wed Nov 23 2016 - 23:37:45 CST)
- Superimpose Models Wong Li Zhe (Thu Nov 24 2016 - 00:40:01 CST)
  - Re: Superimpose Models Vermaas, Joshua (Thu Nov 24 2016 - 11:27:49 CST)
- AW: Superimpose Models Norman Geist (Thu Nov 24 2016 - 01:39:44 CST)
VMD problems on Linux Cinnamon Mint (Sarah) Madaras ErzsÃ©bet (Wed Nov 23 2016 - 16:00:00 CST)
- Re: VMD problems on Linux Cinnamon Mint (Sarah) John Stone (Wed Nov 23 2016 - 16:16:32 CST)
  - Re: VMD problems on Linux Cinnamon Mint (Sarah) Madaras ErzsÃ©bet (Thu Nov 24 2016 - 06:42:09 CST)
vmd installation Archana Sonawani-Jagtap (Wed Nov 23 2016 - 01:34:45 CST)
- Re: vmd installation John Stone (Wed Nov 23 2016 - 01:44:00 CST)
  - Re: vmd installation Archana Sonawani-Jagtap (Thu Nov 24 2016 - 01:12:42 CST)
X3D render NewRibbons only in blue Jean Richelle (Wed Nov 23 2016 - 00:19:29 CST)
- Re: X3D render NewRibbons only in blue John Stone (Wed Nov 23 2016 - 01:08:01 CST)
  - Re: X3D render NewRibbons only in blue Jean Richelle (Thu Nov 24 2016 - 10:04:44 CST)
    - Re: X3D render NewRibbons only in blue John Stone (Fri Nov 25 2016 - 01:02:21 CST)
    - Re: X3D render NewRibbons only in blue Jean Richelle (Fri Nov 25 2016 - 08:59:19 CST)
GPU rendering of molecular orbitals Matt Watkins (Tue Nov 22 2016 - 15:03:38 CST)
- Re: GPU rendering of molecular orbitals John Stone (Tue Nov 22 2016 - 16:01:27 CST)
  - Re: GPU rendering of molecular orbitals Matt Watkins (Tue Nov 22 2016 - 16:31:28 CST)
    - Re: GPU rendering of molecular orbitals John Stone (Tue Nov 22 2016 - 17:27:12 CST)
how to find vander waal interactions in vmd? Seera Suryanarayana (Tue Nov 22 2016 - 05:52:49 CST)
- Re: how to find vander waal interactions in vmd? John Stone (Mon Nov 28 2016 - 00:15:51 CST)
error loading PDB Anna Lohning (Tue Nov 22 2016 - 00:56:00 CST)
- Re: error loading PDB John Stone (Tue Nov 22 2016 - 17:33:14 CST)
  - Re: error loading PDB John Stone (Tue Nov 22 2016 - 17:36:08 CST)
  - Re: error loading PDB Anna Lohning (Tue Nov 22 2016 - 17:44:03 CST)
    - Re: error loading PDB Ashar Malik (Tue Nov 22 2016 - 18:13:11 CST)
    - RE: error loading PDB Anna Lohning (Tue Nov 22 2016 - 18:33:21 CST)
GPU conf file Naeem Mahmood Ashraf (Sun Nov 20 2016 - 02:18:43 CST)
- Re: GPU conf file John Stone (Mon Nov 28 2016 - 00:21:34 CST)
Change browsing directory in mac Estefania Gonzalez Solveyra (Fri Nov 18 2016 - 11:31:28 CST)
- Re: Change browsing directory in mac John Stone (Mon Nov 28 2016 - 00:24:53 CST)
What is the reasonable GPU usage when running simulation in VMD? jrhau lung (Wed Nov 16 2016 - 23:58:37 CST)
- Re: What is the reasonable GPU usage when running simulation in VMD? jrhau lung (Thu Nov 17 2016 - 06:47:43 CST)
  - Re: What is the reasonable GPU usage when running simulation in VMD? JoÃ£o Ribeiro KS (Thu Nov 17 2016 - 08:41:03 CST)
Hands-On Workshop on Integrative Modeling and Simulations Jodi Ann Hadden (Wed Nov 16 2016 - 11:28:03 CST)
Fast PBC wrapping in VMD JÃ©rÃ´me HÃ©nin (Wed Nov 16 2016 - 07:54:39 CST)
- Re: Fast PBC wrapping in VMD Grace Brannigan (Wed Nov 16 2016 - 09:11:51 CST)
- AW: Fast PBC wrapping in VMD Norman Geist (Thu Nov 17 2016 - 02:05:46 CST)
  - Re: Fast PBC wrapping in VMD JÃ©rÃ´me HÃ©nin (Thu Nov 17 2016 - 03:09:14 CST)
which water models are inbult in namd? can I use SPCE if yes how? Raviteja Kurapati (Wed Nov 16 2016 - 06:18:33 CST)
- Re: which water models are inbult in namd? can I use SPCE if yes how? Peter Freddolino (Wed Nov 16 2016 - 08:57:32 CST)
exact number of solvent molecule in simulation box Raviteja Kurapati (Tue Nov 15 2016 - 08:20:00 CST)
- Re: exact number of solvent molecule in simulation box Ashar Malik (Tue Nov 15 2016 - 09:07:20 CST)
  - Re: exact number of solvent molecule in simulation box Ashar Malik (Tue Nov 15 2016 - 09:10:39 CST)
VMD and Spacenavigator in OSX Fernando Vallejos-Burgos (Sun Nov 13 2016 - 18:45:27 CST)
- Re: VMD and Spacenavigator in OSX John Stone (Mon Nov 28 2016 - 01:42:14 CST)
  - Re: VMD and Spacenavigator in OSX Madaras ErzsÃ©bet (Tue Dec 06 2016 - 04:12:40 CST)
ffTK: How to determine the optimized bond and angle parameters Ern Ong (Sun Nov 13 2016 - 02:43:12 CST)
- Re: ffTK: How to determine the optimized bond and angle parameters JC Gumbart (Mon Nov 14 2016 - 23:20:09 CST)
  - RE: ffTK: How to determine the optimized bond and angle parameters Ern Ong (Mon Nov 14 2016 - 23:32:47 CST)
  - RE: ffTK: How to determine the optimized bond and angle parameters Ern.Ong_at_student.adfa.edu.au (Thu Nov 17 2016 - 03:38:59 CST)
    - Re: ffTK: How to determine the optimized bond and angle parameters JC Gumbart (Thu Nov 17 2016 - 11:56:18 CST)
PhD position available Ashar Malik (Sat Nov 12 2016 - 19:17:08 CST)
Location of 'mol bondsrecalc' in source code Dhritiman Talukdar (Sat Nov 12 2016 - 00:05:08 CST)
- Re: Location of 'mol bondsrecalc' in source code Vermaas, Joshua (Sat Nov 12 2016 - 17:07:03 CST)
Rendering with Tachyon GPU enabled (TachyonLOptiXInternal) with options Ben Lowe (Fri Nov 11 2016 - 11:32:47 CST)
- Re: Rendering with Tachyon GPU enabled (TachyonLOptiXInternal) with options Vermaas, Joshua (Sat Nov 12 2016 - 16:46:14 CST)
  - Re: Rendering with Tachyon GPU enabled (TachyonLOptiXInternal) with options Ben Lowe (Tue Nov 15 2016 - 12:44:53 CST)
    - Re: Rendering with Tachyon GPU enabled (TachyonLOptiXInternal) with options Vermaas, Joshua (Tue Nov 15 2016 - 13:12:23 CST)
    - Re: Rendering with Tachyon GPU enabled (TachyonLOptiXInternal) with options John Stone (Sun Nov 27 2016 - 23:58:33 CST)
Re: Fwd: Compile / Configure VMD with the Oculus Rift DK2 John Stone (Fri Nov 11 2016 - 10:03:12 CST)
Problem of compiling VMD with options Le Liu (Wed Nov 09 2016 - 13:41:00 CST)
- Re: Problem of compiling VMD with options John Stone (Wed Nov 09 2016 - 14:10:23 CST)
  - Re: Problem of compiling VMD with options Le Liu (Wed Nov 09 2016 - 14:27:59 CST)
Limits of the VMD Visualisation Jan Janssen (Wed Nov 09 2016 - 10:59:56 CST)
- Re: Limits of the VMD Visualisation Axel Kohlmeyer (Wed Nov 09 2016 - 12:21:13 CST)
  - Re: Limits of the VMD Visualisation Jan Janssen (Thu Nov 10 2016 - 01:29:50 CST)
MD movie making of fluent movements Kevin C Chan (Fri Nov 04 2016 - 05:26:21 CDT)
- Re: MD movie making of fluent movements Ajasja LjubetiÄ (Fri Nov 04 2016 - 05:54:32 CDT)
  - Re: MD movie making of fluent movements Vermaas, Joshua (Fri Nov 04 2016 - 09:43:31 CDT)
    - Re: MD movie making of fluent movements Axel Kohlmeyer (Fri Nov 04 2016 - 10:35:30 CDT)
    - Re: MD movie making of fluent movements Tabris Chun Chan (Fri Nov 04 2016 - 10:55:48 CDT)
3D projection of vmd window Cyril Bauvais (Thu Nov 03 2016 - 18:18:50 CDT)
- Re: 3D projection of vmd window Cyril Bauvais (Thu Nov 24 2016 - 04:08:16 CST)
  - Re: 3D projection of vmd window John Stone (Mon Nov 28 2016 - 00:07:15 CST)
Rotate molecular system without rotating objects added with the graphics command Eric Smoll (Thu Nov 03 2016 - 17:07:14 CDT)
- Re: Rotate molecular system without rotating objects added with the graphics command John Stone (Fri Nov 04 2016 - 09:53:00 CDT)
Fwd: Research Position at Acellera, Barcelona JoÃ£o M. Damas (Thu Nov 03 2016 - 08:26:49 CDT)
Compile / Configure VMD with the Oculus Rift DK2 Jan Janssen (Thu Nov 03 2016 - 02:42:43 CDT)
Tachyon Render and MacOS segfault Issue Ashley Bennett (Wed Nov 02 2016 - 16:39:20 CDT)
Remembering Klaus Schulten Thomas C. Bishop (Tue Nov 01 2016 - 09:33:31 CDT)
FFTK measure bond error Eisenhart, Andrew (eisenhaw) (Mon Oct 31 2016 - 13:15:24 CDT)
- Re: FFTK measure bond error JC Gumbart (Mon Oct 31 2016 - 21:38:12 CDT)
  - Re: FFTK measure bond error Mayne, Christopher G (Tue Nov 01 2016 - 10:45:28 CDT)
VMD 1.9.3 beta 4 posted for download... John Stone (Sat Oct 29 2016 - 00:31:18 CDT)
The new molecule file browser M K (Fri Oct 28 2016 - 20:51:59 CDT)
- Re: The new molecule file browser John Stone (Fri Oct 28 2016 - 21:35:00 CDT)
Error connecting to localhost on port 3000 and IMD connection ended unexpectedly; connection terminated. jrhau lung (Thu Oct 27 2016 - 05:05:38 CDT)
- Re: Error connecting to localhost on port 3000 and IMD connection ended unexpectedly; connection terminated. jrhau lung (Thu Oct 27 2016 - 06:19:56 CDT)
- AW: Error connecting to localhost on port 3000 and IMD connection ended unexpectedly; connection terminated. Norman Geist (Thu Oct 27 2016 - 07:50:51 CDT)
VMDFORCECPUCOUNT csu1505110121_at_163.com (Wed Oct 26 2016 - 22:47:42 CDT)
Zinc ion visualization from Amber trajectory Aditya Padhi (Tue Oct 25 2016 - 19:44:12 CDT)
- Re: Zinc ion visualization from Amber trajectory JC Gumbart (Tue Nov 01 2016 - 14:42:04 CDT)
Two open positions related to molecular visualization developments Marc Baaden (Tue Oct 25 2016 - 11:19:23 CDT)
MDFF using Martini Steven Neumann (Thu Oct 20 2016 - 21:07:37 CDT)
- Re: MDFF using Martini Ryan McGreevy (Mon Oct 24 2016 - 16:58:47 CDT)
problem with molfacture plugin 1.3 Raviteja Kurapati (Thu Oct 20 2016 - 07:27:34 CDT)
- Re: problem with molfacture plugin 1.3 Peter Freddolino (Thu Oct 20 2016 - 08:43:21 CDT)
  - Re: problem with molfacture plugin 1.3 Peter Freddolino (Fri Oct 21 2016 - 00:24:33 CDT)
- Re: problem with molfacture plugin 1.3 John Stone (Thu Oct 20 2016 - 12:42:15 CDT)
  - Re: problem with molfacture plugin 1.3 Raviteja Kurapati (Thu Oct 20 2016 - 13:29:37 CDT)
OptiX AO rendering Parker de Waal (Wed Oct 19 2016 - 11:50:39 CDT)
- Re: OptiX AO rendering Mayne, Christopher G (Wed Oct 19 2016 - 14:39:51 CDT)
  - Re: OptiX AO rendering Mayne, Christopher G (Thu Oct 20 2016 - 10:51:00 CDT)
Problem with Autopsf tool of vmd Life Sciences Inc (Wed Oct 19 2016 - 11:13:07 CDT)
- Re: Problem with Autopsf tool of vmd Life Sciences Inc (Wed Oct 19 2016 - 11:33:32 CDT)
  - Re: Re: Problem with Autopsf tool of vmd Ashar Malik (Wed Oct 19 2016 - 17:12:33 CDT)
    - Re: Re: Problem with Autopsf tool of vmd Life Sciences Inc (Wed Oct 19 2016 - 17:48:27 CDT)
    - Re: Re: Problem with Autopsf tool of vmd Peter Freddolino (Wed Oct 19 2016 - 20:14:58 CDT)
- Re: Problem with Autopsf tool of vmd Peter Freddolino (Wed Oct 19 2016 - 14:25:49 CDT)
  - Re: Problem with Autopsf tool of vmd Life Sciences Inc (Wed Oct 19 2016 - 17:47:53 CDT)
Calculate angles using fit_angle.tcl amin_at_imtech.res.in (Sat Oct 15 2016 - 03:25:48 CDT)
for surface area calculation Abhishek TYAGI (Fri Oct 14 2016 - 08:36:56 CDT)
selection atoms depending on bonding, selection of 'new' molecules Francesca Lønstad Bleken (Fri Oct 14 2016 - 05:39:58 CDT)
- Re: selection atoms depending on bonding, selection of 'new' molecules Axel Kohlmeyer (Fri Oct 14 2016 - 09:52:54 CDT)
  - Re: selection atoms depending on bonding, selection of 'new' molecules John Stone (Fri Oct 14 2016 - 10:05:05 CDT)
    - Re: selection atoms depending on bonding, selection of 'new' molecules Francesca Lønstad Bleken (Fri Oct 14 2016 - 10:58:01 CDT)
selection atoms depending on bonding, selection of 'new' molecules Francesca Lønstad Bleken (Fri Oct 14 2016 - 04:30:56 CDT)
- Re: selection atoms depending on bonding, selection of 'new' molecules John Stone (Fri Oct 14 2016 - 09:41:12 CDT)
aligning molecules with modes from ProDy L. Signorile (Thu Oct 13 2016 - 06:32:24 CDT)
helix orientation Qasim Pars (Wed Oct 12 2016 - 07:42:28 CDT)
- Re: helix orientation Vermaas, Joshua (Wed Oct 12 2016 - 10:36:21 CDT)
  - Re: helix orientation Qasim Pars (Wed Oct 12 2016 - 11:19:09 CDT)
Error when loading log files into ffTK Torsion Explorer david kastner (Mon Oct 10 2016 - 22:52:59 CDT)
- Re: Error when loading log files into ffTK Torsion Explorer Mayne, Christopher G (Tue Oct 11 2016 - 08:51:45 CDT)
  - Re: Error when loading log files into ffTK Torsion Explorer david kastner (Tue Oct 11 2016 - 22:42:49 CDT)
    - Re: Error when loading log files into ffTK Torsion Explorer Mayne, Christopher G (Thu Oct 20 2016 - 11:54:10 CDT)
Size of POPC membrane Roshan Shrestha (Fri Oct 07 2016 - 04:27:11 CDT)
- Re: Size of POPC membrane Ajasja LjubetiÄ (Fri Oct 07 2016 - 04:49:36 CDT)
  - Re: Size of POPC membrane Chitrak Gupta (Fri Oct 07 2016 - 05:52:26 CDT)
Visual of a box and/or scale of distance in VMD graphics Harish Srinivasan (Fri Oct 07 2016 - 01:03:17 CDT)
- Re: Visual of a box and/or scale of distance in VMD graphics Fernando Vallejos-Burgos (Fri Oct 07 2016 - 06:03:34 CDT)
Simulations cutting out due to per-atom velocity Steven Cohen (Thu Oct 06 2016 - 14:52:05 CDT)
- Re: Simulations cutting out due to per-atom velocity Ryan McGreevy (Thu Oct 06 2016 - 15:08:44 CDT)
POPC membrane equilibration Roshan Shrestha (Mon Oct 03 2016 - 08:11:23 CDT)
- Re: POPC membrane equilibration Vermaas, Joshua (Mon Oct 03 2016 - 15:00:55 CDT)
Save work in the middle of chirality correction jrhau lung (Fri Sep 30 2016 - 02:35:43 CDT)
- Re: Save work in the middle of chirality correction Ryan McGreevy (Fri Sep 30 2016 - 11:39:04 CDT)
QUESTION about NMWizad Guo, Jiasen (MU-Student) (Thu Sep 29 2016 - 18:33:41 CDT)
- Re: QUESTION about NMWizad John Stone (Mon Oct 03 2016 - 15:39:24 CDT)
Adding residues to dowser nikolaev_at_spbau.ru (Thu Sep 29 2016 - 16:32:10 CDT)
- Re: Adding residues to dowser John Stone (Mon Oct 03 2016 - 15:42:23 CDT)
Colouring atoms individually Albers, Thomas (Thu Sep 29 2016 - 16:31:24 CDT)
- Re: Colouring atoms individually Vermaas, Joshua (Fri Sep 30 2016 - 09:53:41 CDT)
  - Re: Colouring atoms individually John Stone (Mon Oct 03 2016 - 15:32:26 CDT)
QwikMD and platform choice James Kress (Thu Sep 29 2016 - 10:30:53 CDT)
- Re: QwikMD and platform choice JoÃ£o Ribeiro KS (Thu Sep 29 2016 - 10:44:23 CDT)
calculate the angle between two principal axes from two selecton sunyeping (Thu Sep 29 2016 - 04:49:57 CDT)
TNG Plugin Niels Müller (Thu Sep 29 2016 - 03:49:51 CDT)
- Re: TNG Plugin John Stone (Mon Oct 03 2016 - 15:52:01 CDT)
Hands-On Workshop on Computational Biophysics: November 14-18 in Atlanta, GA Jodi Ann Hadden (Thu Sep 29 2016 - 00:27:46 CDT)
Apply for ACS Comp travel awards for Spring 2017 meeting in San Francisco John Stone (Wed Sep 28 2016 - 11:16:51 CDT)
Fwd: Dihedral fitting -FFTK-shift in minima Mohan maruthi sena (Wed Sep 28 2016 - 05:19:09 CDT)
- Re: Dihedral fitting -FFTK-shift in minima Mayne, Christopher G (Wed Sep 28 2016 - 09:35:46 CDT)
Alignment and RMSD calculation Tran, Tran (Tue Sep 27 2016 - 20:18:31 CDT)
- Re: Alignment and RMSD calculation Ashar Malik (Tue Sep 27 2016 - 21:46:17 CDT)
  - Re: Alignment and RMSD calculation John Stone (Mon Oct 03 2016 - 16:02:47 CDT)
    - Re: Alignment and RMSD calculation Tran, Tran (Tue Oct 04 2016 - 11:12:15 CDT)
chain identifier change in the pdb files generated by the "solvate" and "Add Ions" plugin sunyeping (Mon Sep 26 2016 - 21:46:54 CDT)
- Re: chain identifier change in the pdb files generated by the "solvate" and "Add Ions" plugin John Stone (Mon Oct 03 2016 - 16:10:19 CDT)
  - Re: chain identifier change in the pdb files generated by the "solvate" and "Add Ions" plugin sunyeping (Mon Oct 10 2016 - 21:04:45 CDT)
- Re: chain identifier change in the pdb files generated by the "solvate" and "Add Ions" plugin Stefan Doerr (Tue Oct 04 2016 - 09:25:39 CDT)
Q=BD=AC=E5=8F=91=EF=BC=9A__by_using_Ax?= el's HOOMD plugin, convert pdb to xml and missing bond information Darren Li (Mon Sep 26 2016 - 01:45:01 CDT)
- Re: by using Axel's HOOMD plugin, convert pdb to xml and missing bond information Axel Kohlmeyer (Mon Sep 26 2016 - 06:11:58 CDT)
  - Q=9B=9E=E5=A4=8D=EF=BC=9A__by_using_Ax?= el's HOOMD plugin, convert pdb to xml and missing bond information Darren Li (Mon Sep 26 2016 - 09:08:56 CDT)
by using Axel's HOOMD plugin, convert pdb to xml and missing bond information Darren Li (Sun Sep 25 2016 - 22:40:02 CDT)
- Re: by using Axel's HOOMD plugin, convert pdb to xml and missing bond information Axel Kohlmeyer (Sun Sep 25 2016 - 23:20:00 CDT)
mkdir command in vmd sunyeping (Sun Sep 25 2016 - 21:02:17 CDT)
- Re: mkdir command in vmd Axel Kohlmeyer (Sun Sep 25 2016 - 22:05:45 CDT)
  - Re: mkdir command in vmd Vermaas, Joshua (Mon Sep 26 2016 - 10:51:00 CDT)
  - Re: mkdir command in vmd sunyeping (Tue Sep 27 2016 - 22:05:23 CDT)
measuring angle between two domains of protein Felicia Jiang (Thu Sep 22 2016 - 17:18:19 CDT)
- Re: measuring angle between two domains of protein Ashar Malik (Fri Sep 23 2016 - 06:40:58 CDT)
compiling VMD from CVS 2016 09 21 Vlad Cojocaru (Wed Sep 21 2016 - 07:42:06 CDT)
- Re: compiling VMD from CVS 2016 09 21 Axel Kohlmeyer (Wed Sep 21 2016 - 08:10:58 CDT)
  - Re: compiling VMD from CVS 2016 09 21 Vlad Cojocaru (Wed Sep 21 2016 - 08:26:17 CDT)
pdb reader plugin error checking Bennion, Brian (Tue Sep 20 2016 - 13:47:26 CDT)
- Re: pdb reader plugin error checking John Stone (Tue Sep 20 2016 - 16:17:47 CDT)
  - Re: pdb reader plugin error checking John Stone (Thu Sep 22 2016 - 12:05:16 CDT)
    - RE: pdb reader plugin error checking Bennion, Brian (Thu Sep 22 2016 - 13:28:07 CDT)
    - Re: pdb reader plugin error checking John Stone (Thu Sep 22 2016 - 15:14:12 CDT)
dcd File and bounds Christian Wohlschlager (Mon Sep 19 2016 - 08:00:53 CDT)
- Re: dcd File and bounds Axel Kohlmeyer (Mon Sep 19 2016 - 09:47:15 CDT)
Hands-On Workshop on Computational Biophysics: October 17-21 in Urbana, IL Jodi Ann Hadden (Fri Sep 16 2016 - 15:35:45 CDT)
Using pbc wrap with bigdcd Thomas Griffiths (Thu Sep 15 2016 - 20:56:49 CDT)
- Re: Using pbc wrap with bigdcd Thomas Griffiths (Fri Sep 16 2016 - 23:28:34 CDT)
Error of NAMD simulation when the structure including azide Chia-Ju Hsieh (Thu Sep 15 2016 - 10:15:34 CDT)
- Re: Error of NAMD simulation when the structure including azide Vermaas, Joshua (Thu Sep 15 2016 - 11:23:17 CDT)
  - Re: Error of NAMD simulation when the structure including azide Chia-Ju Hsieh (Fri Sep 16 2016 - 15:03:43 CDT)
setting secondary structure Chitrak Gupta (Fri Sep 09 2016 - 17:31:27 CDT)
Setting Default Colors in vmdrc Tyler Westland (Thu Sep 08 2016 - 10:17:53 CDT)
- Re: Setting Default Colors in vmdrc John Stone (Thu Sep 08 2016 - 11:57:19 CDT)
- Re: Setting Default Colors in vmdrc Tyler Westland (Tue Sep 20 2016 - 15:45:15 CDT)
IR Spectrum Units marvin.hoffmann_at_stud.uni-heidelberg.de (Wed Sep 07 2016 - 08:46:59 CDT)
- Re: IR Spectrum Units Axel Kohlmeyer (Wed Sep 07 2016 - 09:16:06 CDT)
Re: Lammps data visualization with VMD Axel Kohlmeyer (Mon Sep 05 2016 - 22:01:25 CDT)
Clustering algorithm Abramyan, Tigran (Fri Sep 02 2016 - 12:27:59 CDT)
Re: How to choose a ligand conformation to generate a CgenFF parameter jrhau lung (Fri Sep 02 2016 - 09:17:59 CDT)
- Re: How to choose a ligand conformation to generate a CgenFF parameter JoÃ£o Ribeiro KS (Fri Sep 02 2016 - 09:31:02 CDT)
How to choose a ligand conformation to generate a CgenFF parameter jrhau lung (Fri Sep 02 2016 - 00:12:03 CDT)
- Re: How to choose a ligand conformation to generate a CgenFF parameter Vermaas, Joshua (Fri Sep 02 2016 - 10:54:00 CDT)
Atom Selection based on angular criterion Sangkha Borah (Thu Sep 01 2016 - 03:10:37 CDT)
- Re: Atom Selection based on angular criterion Ashar Malik (Thu Sep 01 2016 - 07:02:34 CDT)
Error when using orient command #YEO JINGJIE# (Wed Aug 31 2016 - 16:46:17 CDT)
- Re: Error when using orient command John Stone (Wed Sep 07 2016 - 11:32:32 CDT)
generating images without shading Eric Smoll (Wed Aug 31 2016 - 13:52:43 CDT)
- Re: generating images without shading Ky Wildermuth (Wed Aug 31 2016 - 15:37:42 CDT)
  - Re: generating images without shading John Stone (Wed Sep 07 2016 - 11:35:47 CDT)
Problem when loading 1QRA in QwiKMD jrhau lung (Mon Aug 29 2016 - 19:18:27 CDT)
- Re: Problem when loading 1QRA in QwiKMD jrhau lung (Thu Sep 01 2016 - 21:48:37 CDT)
AW: AW: AW: How to smooth atom labels in a MD trajectory? Norman Geist (Mon Aug 22 2016 - 08:42:30 CDT)
- Re: AW: AW: AW: How to smooth atom labels in a MD trajectory? sunyeping (Mon Aug 22 2016 - 09:12:01 CDT)
AW: AW: AW: How to smooth atom labels in a MD trajectory? Norman Geist (Mon Aug 22 2016 - 08:32:34 CDT)
representation for multiple molecules Akshay Bhatnagar (Sun Aug 21 2016 - 21:23:15 CDT)
- Re: representation for multiple molecules Vermaas, Joshua (Mon Aug 22 2016 - 11:28:50 CDT)
How to smooth atom labels in a MD trajectory? å™ä¸šå¹³ (Sat Aug 20 2016 - 13:06:37 CDT)
- AW: How to smooth atom labels in a MD trajectory? Norman Geist (Mon Aug 22 2016 - 01:04:04 CDT)
  - Re: AW: How to smooth atom labels in a MD trajectory? sunyeping (Mon Aug 22 2016 - 07:17:19 CDT)
how to change the color of all the C atoms in the newly created copy of representation sunyeping (Fri Aug 19 2016 - 07:54:55 CDT)
getting list of correct indices? Olya Kravchenko (Thu Aug 18 2016 - 14:54:16 CDT)
- Re: getting list of correct indices? Olya Kravchenko (Thu Aug 18 2016 - 15:37:55 CDT)
- Re: getting list of correct indices? Chitrak Gupta (Thu Aug 18 2016 - 16:07:18 CDT)
- Re: getting list of correct indices? Crystal Liu (Thu Aug 18 2016 - 17:00:29 CDT)
  - Re: getting list of correct indices? Olya Kravchenko (Thu Aug 18 2016 - 17:01:15 CDT)
Lipid Bilayer Shearing Sachin Natesh (Tue Aug 16 2016 - 12:01:15 CDT)
Minimization--Number of Timesteps Jackson Cavett (Fri Aug 12 2016 - 13:27:27 CDT)
- Re: Minimization--Number of Timesteps Vermaas, Joshua (Fri Aug 12 2016 - 14:45:00 CDT)
VMD 1.9.3 omnidirectional rendering Sebastian Schneider (Fri Aug 12 2016 - 10:18:04 CDT)
- Re: VMD 1.9.3 omnidirectional rendering John Stone (Fri Aug 12 2016 - 14:23:17 CDT)
  - Re: VMD 1.9.3 omnidirectional rendering Sebastian Schneider (Mon Aug 15 2016 - 14:59:40 CDT)
OptiXRenderer) ERROR: Launch failed Levi Pierce (Thu Aug 11 2016 - 14:08:23 CDT)
- Re: OptiXRenderer) ERROR: Launch failed John Stone (Thu Aug 11 2016 - 14:57:07 CDT)
using vslab in vmd Anjela Manandhar (Thu Aug 11 2016 - 10:56:54 CDT)
- Re: using vslab in vmd John Stone (Thu Aug 11 2016 - 15:45:31 CDT)
  - Re: using vslab in vmd Nuno Sousa Cerqueira (Fri Aug 12 2016 - 15:25:30 CDT)
    - Re: using vslab in vmd Anjela Manandhar (Mon Aug 15 2016 - 09:45:56 CDT)
processing a large "molecule" Arham Amouie (Sat Aug 06 2016 - 13:12:18 CDT)
- Re: processing a large "molecule" Axel Kohlmeyer (Sat Aug 06 2016 - 13:49:48 CDT)
  - Re: processing a large "molecule" Arham Amouie (Sun Aug 07 2016 - 03:13:52 CDT)
Water segid split JosÃ© GÃ³mez (Thu Aug 04 2016 - 16:50:03 CDT)
- Re: Water segid split Chitrak Gupta (Thu Aug 04 2016 - 18:15:02 CDT)
  - Re: Water segid split Chitrak Gupta (Thu Aug 04 2016 - 18:20:19 CDT)
- Re: Water segid split Vermaas, Joshua (Thu Aug 04 2016 - 18:11:15 CDT)
Script runs slow afterwards Sangkha Borah (Thu Aug 04 2016 - 00:56:43 CDT)
- Re: Script runs slow afterwards Ajasja LjubetiÄ (Thu Aug 04 2016 - 03:31:05 CDT)
Aligning a dcd file of a protein consisting two chains kim, stephanie S. (Wed Aug 03 2016 - 11:31:37 CDT)
- Re: Aligning a dcd file of a protein consisting two chains Vermaas, Joshua (Wed Aug 03 2016 - 13:24:32 CDT)
  - Re: Aligning a dcd file of a protein consisting two chains kim, stephanie S. (Thu Aug 04 2016 - 09:02:38 CDT)
    - Re: Aligning a dcd file of a protein consisting two chains Vermaas, Joshua (Thu Aug 04 2016 - 11:06:56 CDT)
  - Re: Aligning a dcd file of a protein consisting two chains Vermaas, Joshua (Tue Aug 09 2016 - 11:42:07 CDT)
Cartoon represenation for non-standard residue Simon DÃ¼rr (Tue Aug 02 2016 - 07:01:01 CDT)
- Re: Cartoon represenation for non-standard residue Simon DÃ¼rr (Tue Aug 02 2016 - 09:53:50 CDT)
over-long bonds only in multi-frame trajectory Ming-Tsung Lee (Mon Aug 01 2016 - 17:55:37 CDT)
Fwd: namd-l: water permeation through nanotube in lipid bilayer Nikhil Maroli (Fri Jul 29 2016 - 10:59:23 CDT)
vmd linking error Richard Overstreet (Fri Jul 29 2016 - 11:53:57 CDT)
AW: merging independent dcd files, Norman Geist (Thu Jul 28 2016 - 02:42:45 CDT)
- Re: merging independent dcd files, Aliasghar Alizadeh-Mojarad (Thu Jul 28 2016 - 14:35:26 CDT)
Which phosphoserine patch to use: SP1 or SP2? Devanand T (Wed Jul 27 2016 - 02:33:10 CDT)
- Re: Which phosphoserine patch to use: SP1 or SP2? Devanand T (Wed Jul 27 2016 - 05:26:07 CDT)
Parallel analysis using dynamic atom selections Patrick Charchar (Tue Jul 26 2016 - 23:01:01 CDT)
merging independent dcd files, Aliasghar Alizadeh-Mojarad (Tue Jul 26 2016 - 22:05:10 CDT)
- AW: merging independent dcd files, Norman Geist (Wed Jul 27 2016 - 02:04:09 CDT)
calculation of geometric centers of the rings Vikas Varshney (Tue Jul 26 2016 - 08:15:13 CDT)
Custom Water Box Jackson Cavett (Mon Jul 25 2016 - 20:34:31 CDT)
- RE: Custom Water Box James Kress (Mon Jul 25 2016 - 22:00:08 CDT)
  - Re: Custom Water Box Jackson Cavett (Tue Jul 26 2016 - 19:13:32 CDT)
topotools: write a particular selection into a lammps data file M K (Sun Jul 24 2016 - 23:08:25 CDT)
list structure in measure cluster output Bennion, Brian (Fri Jul 22 2016 - 11:25:50 CDT)
PorcupinePlot: invalid command name error Shubhangi Gupta (Fri Jul 22 2016 - 05:42:57 CDT)
Linking 4 proteins Aditya Padhi (Thu Jul 21 2016 - 22:49:35 CDT)
strange output from measure cluster Bennion, Brian (Thu Jul 21 2016 - 17:31:46 CDT)
- Re: strange output from measure cluster Axel Kohlmeyer (Thu Jul 21 2016 - 18:11:24 CDT)
rendering with povray in mac Irem Altan (Thu Jul 21 2016 - 15:04:24 CDT)
- rendering with povray in mac Irem Altan (Thu Jul 21 2016 - 15:25:33 CDT)
- Re: rendering with povray in mac John Stone (Thu Jul 21 2016 - 15:31:05 CDT)
VMD 1.9.3 beta 1 posted for download... John Stone (Wed Jul 20 2016 - 23:33:49 CDT)
- RE: VMD 1.9.3 beta 1 posted for download... James Kress (Thu Jul 21 2016 - 08:21:13 CDT)
  - Re: VMD 1.9.3 beta 1 posted for download... John Stone (Thu Jul 21 2016 - 14:11:16 CDT)
- Re: VMD 1.9.3 beta 1 posted for download... Bruce D'Amora (Thu Jul 21 2016 - 11:04:32 CDT)
- Re: VMD 1.9.3 beta 1 posted for download... John Stone (Thu Jul 21 2016 - 16:35:01 CDT)
Changing atom colouring by a non-standard property Thomas Aldershof (Wed Jul 20 2016 - 01:36:21 CDT)
- Re: Changing atom colouring by a non-standard property John Stone (Thu Jul 21 2016 - 16:54:54 CDT)
  - Re: Changing atom colouring by a non-standard property Thomas Aldershof (Tue Jul 26 2016 - 23:10:44 CDT)
Periodic cell has become too small for original patch grid Tahmina Akter (Tue Jul 19 2016 - 11:38:23 CDT)
Problerm with STAMP Scazzocchio, Claudio (Sun Jul 17 2016 - 11:46:54 CDT)
- Re: Problerm with STAMP John Stone (Thu Jul 21 2016 - 17:02:26 CDT)
  - Re: Problerm with STAMP Scazzocchio, Claudio (Fri Jul 22 2016 - 02:22:27 CDT)
Inconsistent frame output with TMD simulations Steven Cohen (Thu Jul 14 2016 - 15:38:55 CDT)
- Re: Inconsistent frame output with TMD simulations John Stone (Thu Jul 21 2016 - 17:05:49 CDT)
  - Re: Inconsistent frame output with TMD simulations Steven Cohen (Wed Jul 27 2016 - 07:46:38 CDT)
VMD window turning black with Nvidia 3d vision on ASUS monitor Vlad Cojocaru (Wed Jul 13 2016 - 05:06:23 CDT)
- Re: VMD window turning black with Nvidia 3d vision on ASUS monitor Matic Kisovec (Thu Jul 14 2016 - 01:53:27 CDT)
  - Re: VMD window turning black with Nvidia 3d vision on ASUS monitor Vlad Cojocaru (Thu Jul 14 2016 - 03:04:49 CDT)
    - Re: VMD window turning black with Nvidia 3d vision on ASUS monitor John Stone (Thu Jul 14 2016 - 09:43:52 CDT)
How to compile for Python 3 Caio S. Souza (Tue Jul 12 2016 - 17:03:21 CDT)
- Re: How to compile for Python 3 John Stone (Thu Jul 14 2016 - 11:00:47 CDT)
  - Re: How to compile for Python 3 Caio S. Souza (Sat Oct 29 2016 - 10:09:58 CDT)
Re: About snapshot rendering in VMD-1.9.2 Remya Ann (Tue Jul 12 2016 - 12:22:08 CDT)
- Re: Re: About snapshot rendering in VMD-1.9.2 John Stone (Wed Jul 13 2016 - 01:19:05 CDT)
  - Re: Re: About snapshot rendering in VMD-1.9.2 Remya Ann (Wed Jul 13 2016 - 02:09:17 CDT)
Q=80=9CGraphical_Representation=E2=80=9D_question_?= Nuno Sousa Cerqueira (Tue Jul 12 2016 - 07:13:35 CDT)
VMD called from python hangs on Windows Pawel Kedzierski (Mon Jul 11 2016 - 15:35:40 CDT)
- Re: VMD called from python hangs on Windows John Stone (Wed Jul 13 2016 - 01:35:55 CDT)
  - Re: VMD called from python hangs on Windows Pawel Kedzierski (Wed Jul 13 2016 - 03:46:22 CDT)
VMD failed after FFTW installation anu chandra (Mon Jul 11 2016 - 11:37:34 CDT)
- Re: VMD failed after FFTW installation John Stone (Mon Jul 11 2016 - 12:00:33 CDT)
psf file is changed Tahmina Akter (Sat Jul 09 2016 - 11:15:52 CDT)
- Re: psf file is changed Ashar Malik (Sat Jul 09 2016 - 12:01:42 CDT)
Question: VMD sasa calculation of the hydrophobic surface area on segname P2 Tran, Tran (Thu Jul 07 2016 - 23:46:37 CDT)
Atom names aliased after psfgen Kevin C Chan (Thu Jul 07 2016 - 04:51:42 CDT)
- Re: Atom names aliased after psfgen Stefan Doerr (Thu Jul 07 2016 - 05:19:47 CDT)
  - Re: Atom names aliased after psfgen Stefan Doerr (Thu Jul 07 2016 - 05:22:17 CDT)
how to explore the frame number in clustering analysis by the clustering plugin sunyeping (Thu Jul 07 2016 - 03:54:16 CDT)
- RE: how to explore the frame number in clustering analysis by the clustering plugin Bennion, Brian (Thu Jul 07 2016 - 16:05:37 CDT)
Inconsistent atom count Laura Joana (Tue Jul 05 2016 - 12:04:44 CDT)
- Re: Inconsistent atom count John Stone (Tue Jul 05 2016 - 12:54:26 CDT)
I want to change back ground color Seera Suryanarayana (Tue Jul 05 2016 - 01:16:24 CDT)
- Re: I want to change back ground color Fernando Vallejos-Burgos (Tue Jul 05 2016 - 02:22:17 CDT)
changing molid number Benjamin Hill (Mon Jul 04 2016 - 16:02:27 CDT)
- Re: changing molid number Axel Kohlmeyer (Mon Jul 04 2016 - 16:27:37 CDT)
Installing VMD-1.9.2 in Ubuntu 16.04-32bit Remya Ann (Mon Jul 04 2016 - 01:39:17 CDT)
- Re: Installing VMD-1.9.2 in Ubuntu 16.04-32bit Matic Kisovec (Mon Jul 04 2016 - 06:09:12 CDT)
On CHARMM angle bending potential Mr Bernard Ramos (Sun Jul 03 2016 - 22:56:38 CDT)
- Re: On CHARMM angle bending potential Peter Freddolino (Mon Jul 04 2016 - 16:09:39 CDT)
  - Re: On CHARMM angle bending potential Axel Kohlmeyer (Tue Jul 05 2016 - 08:37:15 CDT)
    - Re: On CHARMM angle bending potential Peter Freddolino (Tue Jul 05 2016 - 08:45:15 CDT)
  - Re: On CHARMM angle bending potential Mr Bernard Ramos (Fri Jul 15 2016 - 19:39:14 CDT)
PSA & Rg values Naeem Mahmood Ashraf (Sun Jul 03 2016 - 02:42:57 CDT)
Energy between desired selected molecules Faezeh Pousaneh (Fri Jul 01 2016 - 02:41:40 CDT)
- Re: Energy between desired selected molecules John Stone (Tue Jul 05 2016 - 12:46:48 CDT)
  - Re: Energy between desired selected molecules Faezeh Pousaneh (Tue Jul 05 2016 - 13:40:07 CDT)
Image Flags Sachin Natesh (Thu Jun 30 2016 - 20:36:07 CDT)
K-means clustering algorithm for multiple frames in C Sourav Ray (Thu Jun 30 2016 - 07:54:04 CDT)
- Re: K-means clustering algorithm for multiple frames in C Chitrak Gupta (Fri Jul 01 2016 - 13:40:54 CDT)
  - Re: K-means clustering algorithm for multiple frames in C Sourav Ray (Sat Jul 02 2016 - 09:45:25 CDT)
making cluster for simulations Naeem Mahmood Ashraf (Wed Jun 29 2016 - 11:56:33 CDT)
- Re: making cluster for simulations Ashar Malik (Wed Jun 29 2016 - 13:15:26 CDT)
- Re: making cluster for simulations Gianluca Interlandi (Wed Jun 29 2016 - 13:41:11 CDT)
Exactly align view direction to coordinate axes Zhang, Dansong (Wed Jun 29 2016 - 10:45:15 CDT)
- AW: Exactly align view direction to coordinate axes Norman Geist (Thu Jun 30 2016 - 01:30:04 CDT)
MultiSeq error Andreas Tosstorff (Wed Jun 29 2016 - 03:26:50 CDT)
secondary structure script Qasim Pars (Tue Jun 28 2016 - 19:31:58 CDT)
- Re: secondary structure script Chitrak Gupta (Tue Jun 28 2016 - 20:38:47 CDT)
generating autopsf Tahmina Akter (Tue Jun 28 2016 - 13:07:20 CDT)
- Re: generating autopsf Ashar Malik (Tue Jun 28 2016 - 13:50:48 CDT)
  - Re: generating autopsf Pawel Kedzierski (Tue Jun 28 2016 - 15:10:23 CDT)
VMD 1.9.3 Sebastian Schneider (Tue Jun 28 2016 - 12:07:28 CDT)
- Re: VMD 1.9.3 Bruce D'Amora (Tue Jun 28 2016 - 14:48:43 CDT)
  - Re: VMD 1.9.3 Sebastian Schneider (Tue Jun 28 2016 - 15:33:26 CDT)
    - Re: VMD 1.9.3 John Stone (Wed Jun 29 2016 - 09:45:22 CDT)
QwikMD/IMD Error connecting to localhost on port 3000 Kevin C Chan (Tue Jun 28 2016 - 08:24:19 CDT)
- Re: QwikMD/IMD Error connecting to localhost on port 3000 JoÃ£o Ribeiro KS (Tue Jun 28 2016 - 08:51:15 CDT)
  - Re: QwikMD/IMD Error connecting to localhost on port 3000 John Stone (Tue Jun 28 2016 - 09:55:55 CDT)
System requirement for MD 10ns Naeem Mahmood Ashraf (Tue Jun 28 2016 - 07:24:04 CDT)
- Re: System requirement for MD 10ns Ajasja LjubetiÄ (Tue Jun 28 2016 - 07:57:07 CDT)
  - Re: System requirement for MD 10ns Fernando Vallejos-Burgos (Tue Jun 28 2016 - 08:27:42 CDT)
- Re: System requirement for MD 10ns JÃ©rÃ´me HÃ©nin (Tue Jun 28 2016 - 08:15:34 CDT)
- RE: System requirement for MD 10ns Richard Wood (Tue Jun 28 2016 - 08:19:59 CDT)
- Re: System requirement for MD 10ns Ashar Malik (Tue Jun 28 2016 - 11:03:49 CDT)
VMD TkConsole font size Kotaro Tanaka (Tue Jun 28 2016 - 02:24:58 CDT)
- Re: VMD TkConsole font size faride badalkhani (Tue Jun 28 2016 - 08:38:51 CDT)
  - Re: VMD TkConsole font size Kotaro Tanaka (Tue Jun 28 2016 - 08:45:28 CDT)
TLS handshake failed Gianluca Interlandi (Mon Jun 27 2016 - 20:45:45 CDT)
- Re: TLS handshake failed John Stone (Tue Jun 28 2016 - 10:04:27 CDT)
Shortening a Simulation Jackson Cavett (Mon Jun 27 2016 - 19:11:05 CDT)
- Re: Shortening a Simulation John Stone (Tue Jun 28 2016 - 10:15:00 CDT)
Move center of volmap.dx Jean-Patrick Francoia (Sun Jun 26 2016 - 15:00:34 CDT)
GPU acceleration on tachyon rendering Kevin C Chan (Fri Jun 24 2016 - 05:05:16 CDT)
- Re: GPU acceleration on tachyon rendering Ajasja LjubetiÄ (Fri Jun 24 2016 - 06:52:47 CDT)
  - Re: GPU acceleration on tachyon rendering John Stone (Tue Jun 28 2016 - 11:34:40 CDT)
  - Re: GPU acceleration on tachyon rendering Kevin C Chan (Thu Jun 30 2016 - 09:16:51 CDT)
troubles with openGL Stefano Guglielmo (Thu Jun 23 2016 - 07:08:09 CDT)
- Fwd: troubles with openGL Stefano Guglielmo (Fri Jun 24 2016 - 03:16:22 CDT)
  - Re: Fwd: troubles with openGL John Stone (Tue Jun 28 2016 - 11:43:21 CDT)
    - Re: Fwd: troubles with openGL Stefano Guglielmo (Tue Jul 05 2016 - 13:19:24 CDT)
AW: Selecting atoms of same type in a certain distance (between X and Y angstroms away) Norman Geist (Thu Jun 23 2016 - 01:22:06 CDT)
Render VR scenes in VMD 1.9.2 (possible?) Fernando Vallejos-Burgos (Wed Jun 22 2016 - 22:07:49 CDT)
- Re: Render VR scenes in VMD 1.9.2 (possible?) John Stone (Wed Jun 22 2016 - 22:38:36 CDT)
Selecting atoms of same type in a certain distance (between X and Y angstroms away) Simon DÃ¼rr (Wed Jun 22 2016 - 08:42:50 CDT)
- Re: Selecting atoms of same type in a certain distance (between X and Y angstroms away) Simon DÃ¼rr (Wed Jun 22 2016 - 08:58:28 CDT)
- AW: Selecting atoms of same type in a certain distance (between X and Y angstroms away) Norman Geist (Wed Jun 22 2016 - 10:58:55 CDT)
catdcd Paul Schlesinger (Wed Jun 22 2016 - 06:11:00 CDT)
- Re: catdcd Axel Kohlmeyer (Wed Jun 22 2016 - 07:21:37 CDT)
Isosurface Render - No Color? Foster, Clay A. (Mon Jun 20 2016 - 18:06:37 CDT)
- AW: Isosurface Render - No Color? Daniel Möller (Tue Jun 21 2016 - 07:45:00 CDT)
- Re: Isosurface Render - No Color? Axel Kohlmeyer (Tue Jun 21 2016 - 08:19:27 CDT)
Positioning protein on membrane-water interface Allen, Caley R (Fri Jun 17 2016 - 14:27:23 CDT)
Setting atom coordinates in VMD Vishnu K (Fri Jun 17 2016 - 02:37:11 CDT)
Can't read DCD files generated using NAMD. Richard Wood (Thu Jun 16 2016 - 11:12:53 CDT)
- Re: Can't read DCD files generated using NAMD. John Stone (Thu Jun 16 2016 - 15:02:42 CDT)
  - RE: Can't read DCD files generated using NAMD. Richard Wood (Thu Jun 16 2016 - 16:53:11 CDT)
Density profile tool plugin Faezeh Pousaneh (Thu Jun 16 2016 - 02:12:50 CDT)
SURF Stefano Guglielmo (Wed Jun 15 2016 - 19:42:01 CDT)
zooming into a chosen atom Irem Altan (Wed Jun 15 2016 - 15:56:29 CDT)
- AW: zooming into a chosen atom Norman Geist (Thu Jun 16 2016 - 02:53:57 CDT)
  - AW: zooming into a chosen atom Norman Geist (Thu Jun 16 2016 - 04:39:19 CDT)
(no subject) Eric Smoll (Wed Jun 15 2016 - 15:41:27 CDT)
- RE: Bennion, Brian (Wed Jun 15 2016 - 16:40:08 CDT)
segmentation fault on OSX El capitan Peter Schmidtke (Tue Jun 14 2016 - 03:00:50 CDT)
- RE: segmentation fault on OSX El capitan Vermaas, Joshua V (Tue Jun 14 2016 - 18:35:32 CDT)
frequecy of inter-residue contact Anjela Manandhar (Mon Jun 13 2016 - 16:12:15 CDT)
CatDCD refuses to work (mac) Heather Boltz (Fri Jun 10 2016 - 22:05:39 CDT)
- Re: CatDCD refuses to work (mac) Strahs, Dr. Daniel Bernard (Fri Jun 10 2016 - 23:20:51 CDT)
  - Re: CatDCD refuses to work (mac) Heather Boltz (Sun Jun 12 2016 - 07:42:29 CDT)
  - Re: CatDCD refuses to work (mac) Heather Boltz (Mon Jun 13 2016 - 20:13:32 CDT)
hiding atoms outside the unit cell Irem Altan (Thu Jun 09 2016 - 10:16:29 CDT)
- AW: hiding atoms outside the unit cell Norman Geist (Fri Jun 10 2016 - 01:55:01 CDT)
VMD XYZ plugin: add support for reading velocities Christian Leitold (Thu Jun 09 2016 - 10:06:55 CDT)
- Re: VMD XYZ plugin: add support for reading velocities Axel Kohlmeyer (Thu Jun 09 2016 - 10:45:58 CDT)
  - Re: VMD XYZ plugin: add support for reading velocities Christian Leitold (Thu Jun 09 2016 - 11:12:10 CDT)
Saving variable information Murilo Kramar (Wed Jun 08 2016 - 15:49:45 CDT)
Script to generate PSF: ERROR, additional atoms Francesco Greco (Wed Jun 08 2016 - 07:52:42 CDT)
- Re: Script to generate PSF: ERROR, additional atoms Ashar Malik (Wed Jun 08 2016 - 15:31:40 CDT)
pyvmd: Highlevel python library for VMD Vlastimil ZÃma (Wed Jun 08 2016 - 06:33:59 CDT)
radius of gyration autocorrelation function faride badalkhani (Tue Jun 07 2016 - 15:40:10 CDT)
- Re: radius of gyration autocorrelation function Ajasja LjubetiÄ (Tue Jun 07 2016 - 17:08:46 CDT)
How to extract residue names and resid from serial numbers in vmd using tcl? Devanand T (Tue Jun 07 2016 - 13:07:39 CDT)
Using VMD in Java application Luis Omar Alvarez Mures (Tue Jun 07 2016 - 07:40:30 CDT)
bond Label position Parvez Mh (Mon Jun 06 2016 - 12:21:00 CDT)
psfgen error with "auto angles dihe patch" Chitrak Gupta (Mon Jun 06 2016 - 10:47:01 CDT)
trr generated by catdcd Stefano Guglielmo (Sun Jun 05 2016 - 04:17:51 CDT)
- Re: trr generated by catdcd Axel Kohlmeyer (Sun Jun 05 2016 - 07:06:53 CDT)
much larger diameter of ssDNA, Aliasghar Alizadeh-Mojarad (Sat Jun 04 2016 - 04:22:41 CDT)
namdenergy and bigdcd Grant Schauer (Fri Jun 03 2016 - 15:55:26 CDT)
- Re: namdenergy and bigdcd Peter Freddolino (Sat Jun 04 2016 - 20:58:06 CDT)
rmsf calculation Stefano Guglielmo (Fri Jun 03 2016 - 03:01:50 CDT)
radius of gyration autocorrelation function faride badalkhani (Thu Jun 02 2016 - 14:23:28 CDT)
non-standard solvents faride badalkhani (Thu Jun 02 2016 - 12:54:20 CDT)
how to plot multiple namd log files using NAMD plot sunyeping (Wed Jun 01 2016 - 22:07:54 CDT)
Running a source script from a C shell Ky Wildermuth (Wed Jun 01 2016 - 21:52:38 CDT)
- RE: Running a source script from a C shell Bennion, Brian (Thu Jun 02 2016 - 12:53:41 CDT)
  - Re: Running a source script from a C shell Kyle Wildermuth (Thu Jun 02 2016 - 13:38:04 CDT)
Disabling VMD logo Bryan Roessler (Tue May 31 2016 - 20:40:27 CDT)
- Re: Disabling VMD logo Bryan Roessler (Tue May 31 2016 - 20:47:21 CDT)
vmd 1.9.3 beta release-regd Mohan maruthi sena (Tue May 31 2016 - 01:06:00 CDT)
VMD with EGL Bruce D'Amora (Sun May 29 2016 - 07:34:56 CDT)
Wrapping problem Ajasja LjubetiÄ (Fri May 27 2016 - 11:10:05 CDT)
- Re: Wrapping problem Chitrak Gupta (Fri May 27 2016 - 12:47:36 CDT)
  - AW: Wrapping problem Norman Geist (Mon May 30 2016 - 00:51:46 CDT)
non-water solvent prepared by VMD Deng, Jinxia (Nancy) (Thu May 26 2016 - 12:22:45 CDT)
- Re: non-water solvent prepared by VMD John Stone (Thu May 26 2016 - 12:32:21 CDT)
How to make the script that shows simulation time on a movie work sunyeping (Thu May 26 2016 - 11:08:23 CDT)
- Re: How to make the script that shows simulation time on a movie work John Stone (Thu May 26 2016 - 11:19:50 CDT)
  - Re: How to make the script that shows simulation time on a movie work SebastiÃ¡n GutiÃ©rrez (Thu May 26 2016 - 13:36:40 CDT)
cpptraj-nastruct + VMD Thomas C. Bishop (Wed May 25 2016 - 18:30:18 CDT)
defining/updating atom selection within loop Chitrak Gupta (Wed May 25 2016 - 13:07:49 CDT)
- Re: defining/updating atom selection within loop John Stone (Wed May 25 2016 - 21:52:21 CDT)
  - Re: defining/updating atom selection within loop Chitrak Gupta (Wed May 25 2016 - 22:05:21 CDT)
tkcon cursors not working Ruggero Cortini (Wed May 25 2016 - 03:36:47 CDT)
- Re: tkcon cursors not working Ruggero Cortini (Tue Jan 31 2017 - 09:41:50 CST)
some vmd mail list webpage cannot be accessed sunyeping (Wed May 25 2016 - 02:19:57 CDT)
- Re: some vmd mail list webpage cannot be accessed John Stone (Thu May 26 2016 - 11:31:29 CDT)
write vel binary file from dcd (command line) Laura Joana (Tue May 24 2016 - 10:41:05 CDT)
- Re: write vel binary file from dcd (command line) Maxim Belkin (Tue May 24 2016 - 10:55:28 CDT)
  - Re: write vel binary file from dcd (command line) Laura Joana (Tue May 24 2016 - 10:57:58 CDT)
Namdenergy BUG: Namd started without initial box info, pairlist invalid Norman Geist (Tue May 24 2016 - 03:02:26 CDT)
- Re: Namdenergy BUG: Namd started without initial box info, pairlist invalid Peter Freddolino (Tue May 24 2016 - 07:40:30 CDT)
vmd install on ubuntu 15.04 -- no display Liviu Zarbo (Mon May 23 2016 - 03:03:52 CDT)
- Re: vmd install on ubuntu 15.04 -- no display Josh Vermaas (Mon May 23 2016 - 16:37:38 CDT)
- Re: vmd install on ubuntu 15.04 -- no display John Stone (Wed May 25 2016 - 00:57:24 CDT)
  - Re: vmd install on ubuntu 15.04 -- no display Liviu Zarbo (Thu May 26 2016 - 07:15:52 CDT)
how to find dihedral parameter yanxiao han (Sat May 21 2016 - 12:51:19 CDT)
CPU comparison Gianluca Interlandi (Fri May 20 2016 - 22:09:16 CDT)
Parameters for HS(CH2)11NH2 Natnael Doilicho (Fri May 20 2016 - 19:07:28 CDT)
- Re: Parameters for HS(CH2)11NH2 Seth Axen (Sat May 21 2016 - 00:02:24 CDT)
FFTK dihedrals and problematic intermolecular H-bonds LOISON CLAIRE (Fri May 20 2016 - 04:29:14 CDT)
- Re: FFTK dihedrals and problematic intermolecular H-bonds Mayne, Christopher G (Fri May 20 2016 - 10:11:46 CDT)
  - Re: FFTK dihedrals and problematic intermolecular H-bonds Seth Axen (Sat May 21 2016 - 13:45:08 CDT)
  - Re: FFTK dihedrals and problematic intermolecular H-bonds JC Gumbart (Sat May 21 2016 - 18:57:07 CDT)
    - RE: FFTK dihedrals and problematic intermolecular H-bonds LOISON CLAIRE (Tue May 24 2016 - 06:24:43 CDT)
Bondlist limit Ivan Moncayo (Thu May 19 2016 - 11:44:24 CDT)
- Re: Bondlist limit Axel Kohlmeyer (Thu May 19 2016 - 12:35:29 CDT)
  - Re: Bondlist limit Ivan Moncayo (Wed Jun 15 2016 - 12:05:16 CDT)
    - Re: Bondlist limit Axel Kohlmeyer (Wed Jun 15 2016 - 14:39:52 CDT)
MDFF with two symmetry groups Benjamin.Haberl_at_physik.uni-muenchen.de (Tue May 17 2016 - 14:48:19 CDT)
ffTK fitting dihedrals Seth Axen (Tue May 17 2016 - 13:23:41 CDT)
- Re: ffTK fitting dihedrals Mayne, Christopher G (Tue May 17 2016 - 15:45:02 CDT)
  - Re: ffTK fitting dihedrals Seth Axen (Wed May 18 2016 - 14:04:29 CDT)
TCL script to track molecules moving within a specified region each time frame Dive, Aniruddha Mukund (Mon May 16 2016 - 02:52:14 CDT)
- Re: TCL script to track molecules moving within a specified region each time frame Chitrak Gupta (Mon May 16 2016 - 11:30:33 CDT)
  - Re: TCL script to track molecules moving within a specified region each time frame Dive, Aniruddha Mukund (Mon May 16 2016 - 12:57:18 CDT)
CHARMM36 alleged missing CC CT1 NH2 angle params Francesco Pietra (Mon May 16 2016 - 02:45:55 CDT)
- Re: CHARMM36 alleged missing CC CT1 NH2 angle params Francesco Pietra (Mon May 16 2016 - 04:30:29 CDT)
  - Re: CHARMM36 alleged missing CC CT1 NH2 angle params Peter Freddolino (Mon May 16 2016 - 07:46:47 CDT)
labeling index of atoms of a particular type Aman Jindal (Sat May 14 2016 - 05:19:40 CDT)
Force field tool kit - calculation of enthalpy of vaporization Mohan maruthi sena (Thu May 12 2016 - 12:42:51 CDT)
- Re: Force field tool kit - calculation of enthalpy of vaporization Mayne, Christopher G (Mon May 16 2016 - 10:26:03 CDT)
periodical boundary condition associated chain seperating? sunyeping (Thu May 12 2016 - 04:02:24 CDT)
Rendering usong Tachyon with Tcl scripting Remya Ann (Tue May 10 2016 - 07:29:02 CDT)
- Re: Rendering usong Tachyon with Tcl scripting Felipe Merino (Tue May 10 2016 - 08:37:18 CDT)
  - Re: Rendering usong Tachyon with Tcl scripting John Stone (Tue May 10 2016 - 10:11:05 CDT)
Random placement of molecules within a defined region Sourav Ray (Sat May 07 2016 - 11:11:17 CDT)
- Re: Random placement of molecules within a defined region John Stone (Wed May 11 2016 - 23:24:05 CDT)
Unable to create psf Roshan Shrestha (Sat May 07 2016 - 09:43:03 CDT)
- Re: Unable to create psf Sourav Ray (Sat May 07 2016 - 10:40:24 CDT)
intermolecular salt bridge Chitrak Gupta (Thu May 05 2016 - 16:25:20 CDT)
- Re: intermolecular salt bridge John Stone (Wed May 11 2016 - 23:26:40 CDT)
  - Re: intermolecular salt bridge Chitrak Gupta (Fri May 13 2016 - 09:53:36 CDT)
Coarse Grain model for graphene Abhishek TYAGI (Wed May 04 2016 - 22:20:34 CDT)
TP2 Phosphotyrosine Patch Issue David E. Heppner (Tue May 03 2016 - 15:29:22 CDT)
- Re: TP2 Phosphotyrosine Patch Issue Josh Vermaas (Tue May 03 2016 - 16:29:00 CDT)
  - Re: TP2 Phosphotyrosine Patch Issue David E. Heppner (Wed May 04 2016 - 05:02:00 CDT)
SMD Force TCL Script in NAMD Allen, Caley R (Sun May 01 2016 - 19:54:09 CDT)
Superimposing 2 dcd files Devanand T (Sat Apr 30 2016 - 16:29:01 CDT)
- Re: Superimposing 2 dcd files Josh Vermaas (Mon May 02 2016 - 09:23:10 CDT)
  - Re: Superimposing 2 dcd files Axel Kohlmeyer (Mon May 02 2016 - 09:46:11 CDT)
Unable to view protein as cartoon or trace or tube surendra jain (Fri Apr 29 2016 - 21:34:47 CDT)
- Re: Unable to view protein as cartoon or trace or tube John Stone (Fri Apr 29 2016 - 21:53:46 CDT)
  - Re: Unable to view protein as cartoon or trace or tube John Stone (Mon May 02 2016 - 10:57:03 CDT)
    - Re: Unable to view protein as cartoon or trace or tube Maxim Belkin (Mon May 02 2016 - 12:25:44 CDT)
LAMMPS tutorial and Materials Simulation Symposium @ Temple, August 15-19, 2016 Axel Kohlmeyer (Fri Apr 29 2016 - 21:11:16 CDT)
VMD Molden plugin crashes Dimitrova, Maria (Fri Apr 29 2016 - 06:27:58 CDT)
- Re: VMD Molden plugin crashes John Stone (Fri Apr 29 2016 - 09:43:29 CDT)
mail about visualization state subramanian vidhyasankar (Fri Apr 29 2016 - 03:20:03 CDT)
- Re: mail about visualization state Axel Kohlmeyer (Fri Apr 29 2016 - 03:43:45 CDT)
- Re: mail about visualization state Karteek Kumar (Fri Apr 29 2016 - 03:43:00 CDT)
hbonds vs measure hbonds Sahu, Subin (Wed Apr 27 2016 - 11:05:04 CDT)
- Re: hbonds vs measure hbonds Sahu, Subin (Thu Apr 28 2016 - 07:15:32 CDT)
Re: VMD HBonds Plugin Produce Duplicate Results Anthony Ma (Tue Apr 26 2016 - 17:57:06 CDT)
- Re: Re: VMD HBonds Plugin Produce Duplicate Results Josh Vermaas (Tue Apr 26 2016 - 20:45:09 CDT)
Finding waters near a protein Mihaela Drenscko (Tue Apr 26 2016 - 16:46:02 CDT)
- Re: Finding waters near a protein Axel Kohlmeyer (Tue Apr 26 2016 - 17:14:43 CDT)
- RE: Finding waters near a protein Bennion, Brian (Tue Apr 26 2016 - 17:26:05 CDT)
  - Re: Finding waters near a protein Mihaela Drenscko (Tue Apr 26 2016 - 18:06:24 CDT)
Set minimum distance cutoff for dynamic bonds Shangmin Xiong (Sun Apr 24 2016 - 22:46:44 CDT)
pbc wrap command for two chain protein structure Z. Erge Akbas (Sun Apr 24 2016 - 14:30:29 CDT)
how do I keep graphics/representations in their designated frames? (they all show up in all frames) Lena Simine (Sun Apr 24 2016 - 00:46:23 CDT)
- Re: how do I keep graphics/representations in their designated frames? (they all show up in all frames) JÃ©rÃ´me HÃ©nin (Sun Apr 24 2016 - 04:34:57 CDT)
Why wrapped and unwrapped trajectories show different energies over the time? zeynab hoseyni (Sat Apr 23 2016 - 09:32:06 CDT)
Changing atoms diameter ehsan shahini (Fri Apr 22 2016 - 04:26:46 CDT)
- Re: Changing atoms diameter Axel Kohlmeyer (Fri Apr 22 2016 - 05:18:28 CDT)
backbone selection failing Stefan Doerr (Thu Apr 21 2016 - 11:27:19 CDT)
- Re: backbone selection failing Ashar Malik (Thu Apr 21 2016 - 13:28:42 CDT)
- Re: backbone selection failing Samuel Bowerman (Thu Apr 21 2016 - 13:45:53 CDT)
  - Re: backbone selection failing Stefan Doerr (Fri Apr 22 2016 - 04:05:10 CDT)
    - Re: backbone selection failing Ashar Malik (Fri Apr 22 2016 - 04:32:13 CDT)
    - Re: backbone selection failing Stefan Doerr (Fri Apr 22 2016 - 04:34:16 CDT)
adding a representation for a selection which is varying from frame to frame in a trajectory Lena Simine (Thu Apr 21 2016 - 02:19:24 CDT)
adding free Fe(II) ions? Olya Kravchenko (Wed Apr 20 2016 - 15:01:39 CDT)
- Re: adding free Fe(II) ions? Ashar Malik (Thu Apr 21 2016 - 05:07:04 CDT)
  - Re: adding free Fe(II) ions? Olya Kravchenko (Mon Apr 25 2016 - 14:25:32 CDT)
output data file problem çŽ‹å¦™éƒ¡ (Tue Apr 19 2016 - 15:05:35 CDT)
- Re: output data file problem Axel Kohlmeyer (Tue Apr 19 2016 - 15:38:21 CDT)
  - Re: output data file problem çŽ‹å¦™éƒ¡ (Fri Apr 22 2016 - 09:34:46 CDT)
solvate fails to set coordinates for the first few residues of the first chain? Olya Kravchenko (Tue Apr 19 2016 - 14:59:01 CDT)
- Re: solvate fails to set coordinates for the first few residues of the first chain? Josh Vermaas (Tue Apr 19 2016 - 16:27:38 CDT)
  - Re: solvate fails to set coordinates for the first few residues of the first chain? Josh Vermaas (Tue Apr 19 2016 - 17:09:00 CDT)
- Re: solvate fails to set coordinates for the first few residues of the first chain? Ashar Malik (Tue Apr 19 2016 - 16:17:17 CDT)
multiseq doesn't work sunyeping (Mon Apr 18 2016 - 21:21:55 CDT)
- Re: multiseq doesn't work Scazzocchio, Claudio (Tue Apr 19 2016 - 03:06:21 CDT)
HOMO and LUMO visualization DR. WOON KAI LIN (Mon Apr 18 2016 - 20:56:51 CDT)
Early bird extended! ISQBP2016 meeting - Bergen Norway Vlad Cojocaru (Mon Apr 18 2016 - 14:34:56 CDT)
Need help in atoms selection Khuong Truong Gia (Sun Apr 17 2016 - 04:32:53 CDT)
- Re: Need help in atoms selection JÃ©rÃ´me HÃ©nin (Mon Apr 18 2016 - 04:17:27 CDT)
  - Re: Need help in atoms selection Khuong Truong Gia (Mon Apr 18 2016 - 06:34:57 CDT)
colvars problem - different values in VMD and NAMD Laura Joana (Fri Apr 15 2016 - 09:19:09 CDT)
- Re: colvars problem - different values in VMD and NAMD Karteek Kumar (Fri Apr 15 2016 - 09:50:19 CDT)
  - Re: colvars problem - different values in VMD and NAMD JÃ©rÃ´me HÃ©nin (Fri Apr 15 2016 - 11:50:32 CDT)
  - Re: colvars problem - different values in VMD and NAMD Laura Joana (Tue Apr 19 2016 - 04:17:09 CDT)
    - Re: colvars problem - different values in VMD and NAMD Laura Joana (Wed Apr 20 2016 - 09:53:13 CDT)
- Re: colvars problem - different values in VMD and NAMD JÃ©rÃ´me HÃ©nin (Fri Apr 15 2016 - 09:50:05 CDT)
  - Re: colvars problem - different values in VMD and NAMD Philippe Bopp (Fri Apr 15 2016 - 11:29:02 CDT)
problems with ligands Scazzocchio, Claudio (Thu Apr 14 2016 - 05:29:16 CDT)
- Re: problems with ligands Cesar Millan (Thu Apr 14 2016 - 06:02:29 CDT)
  - Re: problems with ligands Scazzocchio, Claudio (Thu Apr 14 2016 - 06:12:42 CDT)
Qres portion of MultiSeq for vmd 1.9.2 Shyno Mathew (Wed Apr 13 2016 - 20:26:51 CDT)
- Re: Qres portion of MultiSeq for vmd 1.9.2 Shyno Mathew (Fri Apr 15 2016 - 14:49:45 CDT)
  - RE: Re: Qres portion of MultiSeq for vmd 1.9.2 Lai, Jonathan (Fri Apr 15 2016 - 15:47:58 CDT)
    - Re: Re: Qres portion of MultiSeq for vmd 1.9.2 Shyno Mathew (Fri Apr 15 2016 - 16:07:24 CDT)
Modifying vmd permeation.tcl script Sadegh Faramarzi Ganjabad (Wed Apr 13 2016 - 01:21:48 CDT)
Atom ID Change ahmed sengab (Mon Apr 11 2016 - 12:45:41 CDT)
- Re: Atom ID Change Axel Kohlmeyer (Mon Apr 11 2016 - 13:12:20 CDT)
how to tackle atoms in a PDB with multiple occupancies Akshay Bhatnagar (Sat Apr 09 2016 - 04:22:08 CDT)
Installation Issue Nate Abraham (Fri Apr 08 2016 - 17:01:39 CDT)
- Re: Installation Issue Peter Freddolino (Sat Apr 09 2016 - 20:30:43 CDT)
VMD with VRPN 7.33 and Phantom Omni on Windows 7 Sebastian Schneider (Fri Apr 08 2016 - 10:47:22 CDT)
Clonerep GUI issue with VMD CVS JÃ©rÃ´me HÃ©nin (Fri Apr 08 2016 - 04:28:03 CDT)
- Re: Clonerep GUI issue with VMD CVS Josh Vermaas (Fri Apr 08 2016 - 09:22:36 CDT)
- Re: Clonerep GUI issue with VMD CVS John Stone (Fri Apr 08 2016 - 09:14:42 CDT)
  - Re: Clonerep GUI issue with VMD CVS Nuno Sousa Cerqueira (Fri Apr 08 2016 - 09:56:57 CDT)
How to determine angle between two helices? Anjela Manandhar (Wed Apr 06 2016 - 15:09:46 CDT)
- Re: How to determine angle between two helices? Ashar Malik (Wed Apr 06 2016 - 20:54:17 CDT)
setting up a 4k HD TV for passive stereoscopic 3d Yoav Atsmon-Raz (Wed Apr 06 2016 - 13:45:49 CDT)
- Re: setting up a 4k HD TV for passive stereoscopic 3d John Stone (Wed Apr 06 2016 - 14:31:51 CDT)
  - RE: setting up a 4k HD TV for passive stereoscopic 3d Yoav Atsmon-Raz (Wed Apr 06 2016 - 14:49:10 CDT)
Volume slice rendering TachyonOptiX Kyle Mills (Wed Apr 06 2016 - 06:36:21 CDT)
- Re: Volume slice rendering TachyonOptiX John Stone (Wed Apr 06 2016 - 19:14:37 CDT)
Animate Molekul Christian Wohlschlager (Tue Apr 05 2016 - 08:12:17 CDT)
- AW: Animate Molekul Norman Geist (Tue Apr 05 2016 - 09:53:28 CDT)
- Re: Animate Molekul Maxim Belkin (Tue Apr 05 2016 - 10:24:47 CDT)
constructing spherical molecule? Olya Kravchenko (Mon Apr 04 2016 - 15:16:12 CDT)
- Re: constructing spherical molecule? Josh Vermaas (Mon Apr 04 2016 - 17:06:46 CDT)
  - Re: constructing spherical molecule? Olya Kravchenko (Tue Apr 05 2016 - 10:23:46 CDT)
    - Re: constructing spherical molecule? Josh Vermaas (Tue Apr 05 2016 - 11:05:11 CDT)
Making a Skewed graphene sheet via VMD Majid Shahbabaei (Mon Apr 04 2016 - 05:10:25 CDT)
Reading from file divyabharathi korlepara (Mon Apr 04 2016 - 00:51:49 CDT)
- Re: Reading from file Ashar Malik (Mon Apr 04 2016 - 01:36:25 CDT)
psfgen on proteins with multiple chains Akshay Bhatnagar (Sun Apr 03 2016 - 11:17:30 CDT)
- Re: psfgen on proteins with multiple chains Akshay Bhatnagar (Sun Apr 03 2016 - 11:19:07 CDT)
  - Re: Re: psfgen on proteins with multiple chains Stefan Doerr (Sun Apr 03 2016 - 12:04:32 CDT)
  - Re: Re: psfgen on proteins with multiple chains Peter Freddolino (Mon Apr 04 2016 - 13:19:38 CDT)
Rendering high quality obj, x3d and other files for use in other 3D representation systems James Kress (Sat Apr 02 2016 - 16:09:00 CDT)
- Re: Rendering high quality obj, x3d and other files for use in other 3D representation systems John Stone (Sat Apr 02 2016 - 21:20:57 CDT)
  - RE: Rendering high quality obj, x3d and other files for use in other 3D representation systems James Kress (Sat Apr 02 2016 - 22:14:08 CDT)
Wrapping molecules in simulation of an aggregation phenomenon Sourav Ray (Fri Apr 01 2016 - 16:28:45 CDT)
issue drawing a PBC box centered on a selection Ky Wildermuth (Thu Mar 31 2016 - 19:14:48 CDT)
- AW: issue drawing a PBC box centered on a selection Daniel MÃ¶ller (Fri Apr 01 2016 - 03:10:31 CDT)
protein from protein sequence in VMD chin chun (Thu Mar 31 2016 - 08:40:44 CDT)
- Re: protein from protein sequence in VMD Ashar Malik (Thu Mar 31 2016 - 09:47:27 CDT)
  - Re: protein from protein sequence in VMD Stefan Doerr (Thu Mar 31 2016 - 10:10:54 CDT)
    - Re: protein from protein sequence in VMD Stefan Doerr (Thu Mar 31 2016 - 10:16:11 CDT)
    - Re: protein from protein sequence in VMD Peter Freddolino (Thu Mar 31 2016 - 14:06:46 CDT)
Depth of field with movie maker Kyle Mills (Thu Mar 31 2016 - 07:27:50 CDT)
- Re: Depth of field with movie maker John Stone (Thu Mar 31 2016 - 10:19:22 CDT)
  - Re: Depth of field with movie maker Kyle Mills (Mon Apr 04 2016 - 16:37:55 CDT)
VDM and two SpaceNavigators Jesper Lykkegaard Karlsen (Thu Mar 31 2016 - 04:33:46 CDT)
- Re: VDM and two SpaceNavigators John Stone (Thu Mar 31 2016 - 10:27:56 CDT)
concatenate two pdb files? Akshay Bhatnagar (Wed Mar 30 2016 - 23:08:34 CDT)
- Re: concatenate two pdb files? Subbarao Kanchi (Wed Mar 30 2016 - 23:51:00 CDT)
Residence Time Script (v2.) MannyEful E (Wed Mar 30 2016 - 19:51:48 CDT)
- Re: Residence Time Script (v2.) John Stone (Thu Mar 31 2016 - 10:38:07 CDT)
  - Re: Residence Time Script (v2.) MannyEful E (Sat Apr 02 2016 - 12:28:06 CDT)
"Jump" in Energy and Volume graphs of my MD Daniela Rivas (Wed Mar 30 2016 - 15:01:39 CDT)
- Re: "Jump" in Energy and Volume graphs of my MD John Stone (Thu Mar 31 2016 - 10:32:34 CDT)
FFTK dihedral fitting Mohan maruthi sena (Wed Mar 30 2016 - 09:37:49 CDT)
- Re: FFTK dihedral fitting Mayne, Christopher G (Thu Mar 31 2016 - 10:05:02 CDT)
  - Re: Re: FFTK dihedral fitting Mohan maruthi sena (Thu Mar 31 2016 - 22:55:00 CDT)
    - Re: Re: FFTK dihedral fitting Mayne, Christopher G (Mon Apr 04 2016 - 10:09:06 CDT)
how to find phi-psi angles of residue of our interest in NMR structure? Seera Suryanarayana (Wed Mar 30 2016 - 04:23:17 CDT)
making a movie of a atomselection of a very large trajectory Monika Madhavi (Tue Mar 29 2016 - 21:42:41 CDT)
- AW: making a movie of a atomselection of a very large trajectory Norman Geist (Wed Mar 30 2016 - 03:57:05 CDT)
error loading dcd Stefano Guglielmo (Tue Mar 29 2016 - 17:48:41 CDT)
- Re: error loading dcd Ajasja LjubetiÄ (Wed Mar 30 2016 - 02:45:46 CDT)
- Re: error loading dcd Abhishek TYAGI (Wed Mar 30 2016 - 04:14:05 CDT)
RE: How to draw a box in VMD and plot the coordinates of the system ABHISHEK GUPTA (Mon Mar 28 2016 - 00:50:24 CDT)
- Re: RE: How to draw a box in VMD and plot the coordinates of the system Karteek Kumar (Mon Mar 28 2016 - 01:15:55 CDT)
Unable to patch RNA to obtain DNA #YEO JINGJIE# (Wed Mar 23 2016 - 14:48:35 CDT)
Residue numbers in outfiles PDB/GRO Norman Geist (Wed Mar 23 2016 - 06:19:22 CDT)
- Re: Residue numbers in outfiles PDB/GRO John Stone (Thu Mar 31 2016 - 11:03:04 CDT)
  - AW: Residue numbers in outfiles PDB/GRO Daniel Möller (Thu Mar 31 2016 - 13:31:36 CDT)
    - Re: Residue numbers in outfiles PDB/GRO John Stone (Thu Mar 31 2016 - 14:49:49 CDT)
  - AW: Residue numbers in outfiles PDB/GRO Norman Geist (Fri Apr 01 2016 - 01:54:51 CDT)
    - Re: Residue numbers in outfiles PDB/GRO John Stone (Fri Apr 01 2016 - 13:42:27 CDT)
Radial distribution function from center of mass Sadegh Faramarzi Ganjabad (Tue Mar 22 2016 - 11:35:24 CDT)
How to work on multiple pdbs by tcl script? Seera Suryanarayana (Tue Mar 22 2016 - 03:53:41 CDT)
- Re: How to work on multiple pdbs by tcl script? Ajasja LjubetiÄ (Tue Mar 22 2016 - 05:26:44 CDT)
  - Re: How to work on multiple pdbs by tcl script? Axel Kohlmeyer (Tue Mar 22 2016 - 05:47:43 CDT)
    - Re: How to work on multiple pdbs by tcl script? Ajasja LjubetiÄ (Tue Mar 22 2016 - 06:04:25 CDT)
- AW: How to work on multiple pdbs by tcl script? Norman Geist (Tue Mar 22 2016 - 07:04:36 CDT)
DNA mutation Kalyanashis Jana (Sat Mar 19 2016 - 02:32:08 CDT)
- Re: DNA mutation Vlad Cojocaru (Sat Mar 19 2016 - 03:34:16 CDT)
  - Re: DNA mutation JoÃ£o Ribeiro KS (Mon Mar 21 2016 - 11:33:43 CDT)
rlwrap problem Laura Joana (Fri Mar 18 2016 - 10:37:10 CDT)
- Re: rlwrap problem Josh Vermaas (Fri Mar 18 2016 - 13:42:51 CDT)
  - Re: rlwrap problem Laura Joana (Mon Mar 21 2016 - 08:44:43 CDT)
    - Re: rlwrap problem Josh Vermaas (Mon Mar 21 2016 - 09:08:04 CDT)
    - Re: rlwrap problem Laura Joana (Wed Mar 23 2016 - 12:16:57 CDT)
Gaussian *.log/out visualize Parvez Mh (Thu Mar 17 2016 - 17:57:44 CDT)
- Re: Gaussian *.log/out visualize Mayne, Christopher G (Fri Mar 18 2016 - 09:35:59 CDT)
  - AW: Gaussian *.log/out visualize Norman Geist (Mon Mar 21 2016 - 02:41:13 CDT)
    - Re: Gaussian *.log/out visualize Parvez Mh (Mon Mar 21 2016 - 18:26:47 CDT)
  - Re: Gaussian *.log/out visualize Parvez Mh (Sun Mar 27 2016 - 20:04:01 CDT)
2016 ISQBP Meeting: early registration / abstract submission deadline approaching Vlad Cojocaru (Thu Mar 17 2016 - 03:48:59 CDT)
Adding hydrogens breaks "protein" atomselection and bonds Stefan Doerr (Wed Mar 16 2016 - 06:25:01 CDT)
- Re: Adding hydrogens breaks "protein" atomselection and bonds Peter Freddolino (Wed Mar 16 2016 - 08:55:12 CDT)
  - Re: Adding hydrogens breaks "protein" atomselection and bonds Stefan Doerr (Wed Mar 16 2016 - 09:01:22 CDT)
- Re: Adding hydrogens breaks "protein" atomselection and bonds Josh Vermaas (Wed Mar 16 2016 - 09:29:31 CDT)
AW: Unable to visualize my polymer chains generated using RIS theory using VMD properly Norman Geist (Wed Mar 16 2016 - 04:56:34 CDT)
- Re: Unable to visualize my polymer chains generated using RIS theory using VMD properly John Stone (Wed Mar 16 2016 - 11:25:51 CDT)
  - Re: Unable to visualize my polymer chains generated using RIS theory using VMD properly ABHISHEK GUPTA (Sat Mar 19 2016 - 00:06:59 CDT)
    - Re: Unable to visualize my polymer chains generated using RIS theory using VMD properly Chitrak Gupta (Sun Mar 20 2016 - 17:27:42 CDT)
  - Re: Unable to visualize my polymer chains generated using RIS theory using VMD properly Chitrak Gupta (Tue Mar 29 2016 - 08:11:27 CDT)
speed of pbc join is slow Deng, Jinxia (Nancy) (Tue Mar 15 2016 - 15:48:41 CDT)
- AW: speed of pbc join is slow Norman Geist (Wed Mar 16 2016 - 04:52:28 CDT)
Visualization problem of random Polyethylene chains in VMD. ABHISHEK GUPTA (Tue Mar 15 2016 - 01:17:07 CDT)
default drawing style Parvez Mh (Mon Mar 14 2016 - 21:15:10 CDT)
- Re: default drawing style Axel Kohlmeyer (Mon Mar 14 2016 - 22:04:59 CDT)
Units of moments of inertia Sadegh Faramarzi Ganjabad (Mon Mar 14 2016 - 17:43:06 CDT)
- Re: Units of moments of inertia Josh Vermaas (Tue Mar 15 2016 - 10:00:00 CDT)
  - Re: Units of moments of inertia Sadegh Faramarzi Ganjabad (Fri Mar 18 2016 - 14:00:43 CDT)
Fwd: ISQBP 2016 meeting - registration opened! Vlad Cojocaru (Mon Mar 14 2016 - 03:13:37 CDT)
AW: NAMD 2.11 Cuda does not work with Quadro FX 3800 Norman Geist (Sun Mar 13 2016 - 12:37:40 CDT)
Unable to visualize my polymer chains generated using RIS theory using VMD properly ABHISHEK GUPTA (Fri Mar 11 2016 - 21:09:52 CST)
- AW: Unable to visualize my polymer chains generated using RIS theory using VMD properly Norman Geist (Tue Mar 15 2016 - 02:53:21 CDT)
default drawing style Parvez Mh (Fri Mar 11 2016 - 01:02:06 CST)
- Re: default drawing style Pawel Kedzierski (Fri Mar 11 2016 - 02:43:29 CST)
  - Re: default drawing style Parvez Mh (Tue Mar 15 2016 - 08:28:27 CDT)
NAMD 2.11 Cuda does not work with Quadro FX 3800 Greipel.Joachim_at_mh-hannover.de (Thu Mar 10 2016 - 01:57:06 CST)
error while trying to run the first tutorial for NAMD using VMD Mochena, Mogus D. (Wed Mar 09 2016 - 11:59:13 CST)
Fast PBC wrapping JÃ©rÃ´me HÃ©nin (Tue Mar 08 2016 - 11:13:38 CST)
- Re: Fast PBC wrapping JÃ©rÃ´me HÃ©nin (Wed Mar 09 2016 - 13:05:56 CST)
open position in Computational Physics Andrea Spitaleri (Tue Mar 08 2016 - 06:00:24 CST)
Wrap with PBCTools Kevin C Chan (Tue Mar 08 2016 - 03:20:46 CST)
- Re: Wrap with PBCTools Josh Vermaas (Tue Mar 08 2016 - 09:59:30 CST)
  - Re: Wrap with PBCTools Kevin C Chan (Tue Mar 08 2016 - 21:49:34 CST)
printing out trajectories with some random indices of atoms renamed frame by frame Sangkha Borah (Fri Mar 04 2016 - 13:55:43 CST)
- AW: printing out trajectories with some random indices of atoms renamed frame by frame Norman Geist (Mon Mar 07 2016 - 01:07:22 CST)
Trouble launching VMD 1.9.2 from the dock in Mac OS X el capitan Peter Monson (Thu Mar 03 2016 - 15:10:33 CST)
- Re: Trouble launching VMD 1.9.2 from the dock in Mac OS X el capitan John Stone (Fri Apr 01 2016 - 00:46:01 CDT)
FFTK - bond parameters Mohan maruthi sena (Thu Mar 03 2016 - 11:32:24 CST)
- Re: FFTK - bond parameters Mayne, Christopher G (Mon Mar 07 2016 - 12:30:26 CST)
  - Re: FFTK - bond parameters Mohan maruthi sena (Tue Mar 08 2016 - 05:11:53 CST)
tcl8.6 Nuno Sousa Cerqueira (Thu Mar 03 2016 - 10:28:43 CST)
- Re: tcl8.6 Nuno Sousa Cerqueira (Thu Mar 03 2016 - 11:19:13 CST)
  - Re: tcl8.6 Axel Kohlmeyer (Thu Mar 03 2016 - 12:52:12 CST)
a question about g(r) Richard Wood (Thu Mar 03 2016 - 09:04:07 CST)
- Re: a question about g(r) Ana Celia Vila Verde (Thu Mar 03 2016 - 09:30:18 CST)
  - RE: a question about g(r) Richard Wood (Thu Mar 03 2016 - 09:35:00 CST)
Asking VMD to show bonds between periodic images reza vatan (Thu Mar 03 2016 - 00:40:07 CST)
FFTK: Obj value in bond optimization Soumya Lipsa Rath (Wed Mar 02 2016 - 20:36:04 CST)
- Re: FFTK: Obj value in bond optimization Mayne, Christopher G (Mon Mar 07 2016 - 12:24:58 CST)
catdcd error Daniela Rivas (Wed Mar 02 2016 - 12:11:07 CST)
- Re: catdcd error Chitrak Gupta (Fri Mar 04 2016 - 17:21:47 CST)
  - Re: catdcd error Josh Vermaas (Fri Mar 04 2016 - 18:49:23 CST)
    - Re: catdcd error Dani (Wed Mar 16 2016 - 16:50:47 CDT)
Fwd: distance using pbc Sangkha Borah (Tue Mar 01 2016 - 10:18:58 CST)
- AW: Fwd: distance using pbc Norman Geist (Wed Mar 02 2016 - 01:53:56 CST)
visualizing MDFF results with explicit solvent Bylund, Tatsiana (NIH/NIAID) [F] (Tue Mar 01 2016 - 09:34:34 CST)
- Re: visualizing MDFF results with explicit solvent John Stone (Tue Mar 01 2016 - 09:50:56 CST)
  - Re: visualizing MDFF results with explicit solvent Bylund, Tatsiana (NIH/NIAID) [F] (Tue Mar 01 2016 - 10:03:44 CST)
  - Re: visualizing MDFF results with explicit solvent Josh Vermaas (Tue Mar 01 2016 - 10:14:21 CST)
    - Re: visualizing MDFF results with explicit solvent Bylund, Tatsiana (NIH/NIAID) [F] (Tue Mar 01 2016 - 10:32:54 CST)
- how to analyze fitting structure into density map Bylund, Tatsiana (NIH/NIAID) [F] (Tue Mar 01 2016 - 10:35:36 CST)
  - Re: how to analyze fitting structure into density map Ryan McGreevy (Tue Mar 01 2016 - 11:09:45 CST)
pbc to keep membrane in center Deng, Jinxia (Nancy) (Tue Mar 01 2016 - 09:03:27 CST)
- AW: pbc to keep membrane in center Norman Geist (Wed Mar 02 2016 - 01:41:01 CST)
vmd and proxy settings Greipel.Joachim_at_mh-hannover.de (Tue Mar 01 2016 - 05:59:03 CST)
- Re: vmd and proxy settings John Stone (Tue Mar 01 2016 - 10:22:15 CST)
Re: Not all frames loaded Josh Vermaas (Mon Feb 29 2016 - 15:35:40 CST)
- Re: Not all frames loaded Davit Hakobyan (Tue Mar 01 2016 - 04:37:49 CST)
  - Re: Not all frames loaded Ajasja LjubetiÄ (Tue Mar 01 2016 - 05:02:32 CST)
    - Re: Not all frames loaded Davit Hakobyan (Tue Mar 01 2016 - 14:11:45 CST)
    - Re: Not all frames loaded Davit Hakobyan (Tue Mar 01 2016 - 23:39:41 CST)
Not all frames loaded Davit Hakobyan (Mon Feb 29 2016 - 13:28:03 CST)
- Re: Not all frames loaded Ashar Malik (Mon Feb 29 2016 - 15:24:14 CST)
Re: New atom types in VMD Josh Vermaas (Mon Feb 29 2016 - 08:43:14 CST)
- Re: New atom types in VMD Josh Vermaas (Mon Feb 29 2016 - 09:50:45 CST)
New atom types in VMD Nash, Anthony (Mon Feb 29 2016 - 00:56:29 CST)
Problem wit solvating carbon nano-tube, psfgen) error reading atoms from psf file zeynab hoseyni (Sun Feb 28 2016 - 11:16:58 CST)
- Re: Problem wit solvating carbon nano-tube, psfgen) error reading atoms from psf file Axel Kohlmeyer (Sun Feb 28 2016 - 11:48:58 CST)
  - Re: Problem wit solvating carbon nano-tube, psfgen) error reading atoms from psf file zeynab hoseyni (Sun Feb 28 2016 - 13:22:47 CST)
Creating Carbon Nano-tube psf file.. zeynab hoseyni (Sun Feb 28 2016 - 06:32:00 CST)
Showing wall potential Mahdi Moosaei (Thu Feb 25 2016 - 09:43:27 CST)
Suitable VMD version for OS X EI Capitan, Version 10.11.3 Mahdieh Hadi (Mon Feb 22 2016 - 17:04:44 CST)
- RE: Suitable VMD version for OS X EI Capitan, Version 10.11.3 Mahdieh Hadi (Tue Feb 23 2016 - 03:35:01 CST)
  - Re: RE: Suitable VMD version for OS X EI Capitan, Version 10.11.3 John Stone (Tue Feb 23 2016 - 10:11:08 CST)
    - RE: RE: Suitable VMD version for OS X EI Capitan, Version 10.11.3 Mahdieh Hadi (Wed Feb 24 2016 - 02:33:17 CST)
Define the percentage of zoom M K (Mon Feb 22 2016 - 05:21:36 CST)
- Re: Define the percentage of zoom John Stone (Mon Feb 22 2016 - 09:51:52 CST)
  - Re: Define the percentage of zoom M K (Mon Feb 22 2016 - 17:54:14 CST)
    - AW: Define the percentage of zoom Norman Geist (Tue Feb 23 2016 - 01:35:16 CST)
CD spectra Prof. Eddie (Fri Feb 19 2016 - 10:34:02 CST)
wrapping multi chain proteins Nicolas Martin (Fri Feb 19 2016 - 08:30:12 CST)
- Re: wrapping multi chain proteins Josh Vermaas (Fri Feb 19 2016 - 09:50:34 CST)
  - Re: wrapping multi chain proteins Nicolas Martin (Fri Feb 19 2016 - 11:48:59 CST)
Bond Optimization FFTK error Soumya Lipsa Rath (Thu Feb 18 2016 - 18:18:04 CST)
- Re: Bond Optimization FFTK error Mayne, Christopher G (Fri Feb 26 2016 - 11:58:10 CST)
Re: Re: Molecule not visible in VMD 1.9.2 MAC OS X El Capitan Nixon Raj (Wed Feb 17 2016 - 04:21:33 CST)
Molecule not visible in VMD 1.9.2 MAC OS X El Capitan Nixon Raj (Mon Feb 15 2016 - 20:56:53 CST)
- Re: Molecule not visible in VMD 1.9.2 MAC OS X El Capitan Nixon Raj (Mon Feb 15 2016 - 20:58:13 CST)
hydrophobic interaction between peptide vs membrane Deng, Jinxia (Nancy) (Mon Feb 15 2016 - 10:51:28 CST)
editing distance.tcl debra ragland (Mon Feb 15 2016 - 08:23:38 CST)
moving atoms and updating distances jing liang (Sat Feb 13 2016 - 11:15:34 CST)
- AW: moving atoms and updating distances Norman Geist (Mon Feb 15 2016 - 00:14:22 CST)
Tachyon renderer memory error Eiros Zamora, Juan (Tue Feb 09 2016 - 04:44:38 CST)
- Re: Tachyon renderer memory error Axel Kohlmeyer (Tue Feb 09 2016 - 05:09:50 CST)
  - Re: Tachyon renderer memory error Eiros Zamora, Juan (Tue Feb 09 2016 - 10:15:34 CST)
Changing molecule number Irem Altan (Mon Feb 08 2016 - 09:02:03 CST)
- Re: Changing molecule number Maxim Belkin (Mon Feb 08 2016 - 09:34:27 CST)
Regarding pbc tool: pbc join fragment -bondlist + topo tool M K (Sat Feb 06 2016 - 07:23:08 CST)
- Re: Regarding pbc tool: pbc join fragment -bondlist + topo tool Axel Kohlmeyer (Sat Feb 06 2016 - 07:41:31 CST)
vmd console problem Reza Shakouri (Fri Feb 05 2016 - 14:31:04 CST)
- Re: vmd console problem Josh Vermaas (Fri Feb 05 2016 - 15:08:26 CST)
  - Re: vmd console problem Reza Shakouri (Sat Feb 06 2016 - 05:29:06 CST)
    - Re: vmd console problem Peter Freddolino (Sat Feb 06 2016 - 19:38:22 CST)
    - Re: vmd console problem Peter Freddolino (Sat Feb 06 2016 - 19:40:22 CST)
AW: loading electron density maps with a script Norman Geist (Fri Feb 05 2016 - 02:30:05 CST)
FFTK and the divide and conquer strategy fvlieffe (Thu Feb 04 2016 - 03:37:02 CST)
- Re: FFTK and the divide and conquer strategy Mayne, Christopher G (Thu Feb 04 2016 - 10:10:25 CST)
loading electron density maps with a script Irem Altan (Wed Feb 03 2016 - 16:02:48 CST)
- AW: loading electron density maps with a script Norman Geist (Thu Feb 04 2016 - 01:33:21 CST)
What is the correct way of using "pbcwrap" with "atomselect [within]"? Monika Madhavi (Tue Feb 02 2016 - 01:34:46 CST)
- Re: What is the correct way of using "pbcwrap" with "atomselect [within]"? Axel Kohlmeyer (Tue Feb 02 2016 - 02:07:21 CST)
Updating atomselections in every frame and write to a pdb Monika Madhavi (Mon Feb 01 2016 - 18:01:41 CST)
- Re: Updating atomselections in every frame and write to a pdb Peter Freddolino (Mon Feb 01 2016 - 20:51:30 CST)
  - Re: Updating atomselections in every frame and write to a pdb Monika Madhavi (Mon Feb 01 2016 - 21:12:45 CST)
can't read "viewplist": no such variable Dimitrova, Maria (Mon Feb 01 2016 - 09:05:41 CST)
- Re: can't read "viewplist": no such variable John Stone (Mon Feb 01 2016 - 10:31:41 CST)
VMD Hbond criterion vs. other software debra ragland (Mon Feb 01 2016 - 07:24:40 CST)
- Re: VMD Hbond criterion vs. other software Josh Vermaas (Mon Feb 01 2016 - 08:56:09 CST)
  - Re: VMD Hbond criterion vs. other software debra ragland (Mon Feb 01 2016 - 09:32:05 CST)
A nanosphere with mass Shubham Mishra (Mon Feb 01 2016 - 02:25:09 CST)
A nanosphere with mass Shubham Mishra (Mon Feb 01 2016 - 02:24:21 CST)
A nanosphere with mass Shubham Mishra (Mon Feb 01 2016 - 01:29:43 CST)
- Re: A nanosphere with mass Axel Kohlmeyer (Mon Feb 01 2016 - 01:47:00 CST)
  - Re: A nanosphere with mass Shubham Mishra (Mon Feb 01 2016 - 12:19:37 CST)
- Re: A nanosphere with mass Ana Celia Vila Verde (Mon Feb 01 2016 - 01:55:14 CST)
  - Re: A nanosphere with mass Ashar Malik (Mon Feb 01 2016 - 03:51:35 CST)
    - Re: A nanosphere with mass Shubham Mishra (Mon Feb 01 2016 - 04:32:50 CST)
    - Re: A nanosphere with mass Ashar Malik (Mon Feb 01 2016 - 05:30:30 CST)
FFTK Diherdal Scan error Soumya Lipsa Rath (Mon Feb 01 2016 - 00:27:26 CST)
- Re: FFTK Diherdal Scan error Mayne, Christopher G (Mon Feb 01 2016 - 12:34:42 CST)
  - Re: FFTK Diherdal Scan error Soumya Lipsa Rath (Mon Feb 01 2016 - 18:19:22 CST)
building a solvent/gas filled simulation box, no protein inside Olya Kravchenko (Fri Jan 29 2016 - 13:17:28 CST)
- Re: building a solvent/gas filled simulation box, no protein inside Maxim Belkin (Fri Jan 29 2016 - 13:26:21 CST)
  - Re: building a solvent/gas filled simulation box, no protein inside Olya Kravchenko (Fri Jan 29 2016 - 13:36:24 CST)
selection of atoms/residues across multiple molecules... Shashidhar Rao (Fri Jan 29 2016 - 10:45:07 CST)
- Re: selection of atoms/residues across multiple molecules... Ashar Malik (Sat Jan 30 2016 - 23:26:21 CST)
  - Re: selection of atoms/residues across multiple molecules... Shashidhar Rao (Mon Feb 01 2016 - 10:57:37 CST)
atomselect: cannot parse selection text: index Monika Madhavi (Thu Jan 28 2016 - 23:11:57 CST)
making a movie in a tcl script using graphics commands Nima Emadi (Thu Jan 28 2016 - 14:10:33 CST)
- Re: making a movie in a tcl script using graphics commands Josh Vermaas (Thu Jan 28 2016 - 14:52:33 CST)
  - Re: making a movie in a tcl script using graphics commands Nima Emadi (Thu Jan 28 2016 - 15:37:23 CST)
    - Re: making a movie in a tcl script using graphics commands Axel Kohlmeyer (Thu Jan 28 2016 - 17:16:48 CST)
    - AW: making a movie in a tcl script using graphics commands Norman Geist (Fri Jan 29 2016 - 05:02:16 CST)
- Re: making a movie in a tcl script using graphics commands Nima Emadi (Thu Jan 28 2016 - 14:50:50 CST)
Feature request: Change printf( to fprintf(stderr, in molfile plugins Charles McAnany (Thu Jan 28 2016 - 12:23:46 CST)
- Re: Feature request: Change printf( to fprintf(stderr, in molfile plugins John Stone (Thu Jan 28 2016 - 16:11:55 CST)
  - Re: Feature request: Change printf( to fprintf(stderr, in molfile plugins Charles McAnany (Fri Jan 29 2016 - 11:13:40 CST)
how to save coordinates from others molecule files Marta Wisniewska (Thu Jan 28 2016 - 11:08:19 CST)
Extracting velocity information from .gro or .trr files Davide Mercadante (Thu Jan 28 2016 - 10:30:47 CST)
- Re: Extracting velocity information from .gro or .trr files John Stone (Thu Jan 28 2016 - 21:57:04 CST)
  - Re: Extracting velocity information from .gro or .trr files Davide Mercadante (Fri Jan 29 2016 - 03:48:55 CST)
Specify stride from command line Eiros Zamora, Juan (Thu Jan 28 2016 - 10:07:43 CST)
- Re: Specify stride from command line Ashar Malik (Thu Jan 28 2016 - 14:19:13 CST)
  - Re: Specify stride from command line Eiros Zamora, Juan (Tue Feb 02 2016 - 04:15:57 CST)
    - Re: Specify stride from command line Josh Vermaas (Tue Feb 02 2016 - 09:40:56 CST)
tcl scripting for adding hydrogens to particular atoms in multiple pdb files Shoresh Shafei (Wed Jan 27 2016 - 10:15:58 CST)
- Re: tcl scripting for adding hydrogens to particular atoms in multiple pdb files Peter Freddolino (Thu Jan 28 2016 - 00:00:28 CST)
  - Re: tcl scripting for adding hydrogens to particular atoms in multiple pdb files Shoresh Shafei (Thu Jan 28 2016 - 06:52:10 CST)
    - Re: tcl scripting for adding hydrogens to particular atoms in multiple pdb files Peter Freddolino (Thu Jan 28 2016 - 14:21:18 CST)
VMD 1.9.2 Crashes (CUDA,VRPN) Munir Ahmad (Wed Jan 27 2016 - 07:35:50 CST)
- Re: VMD 1.9.2 Crashes (CUDA,VRPN) John Stone (Thu Jan 28 2016 - 10:28:17 CST)
  - Re: VMD 1.9.2 Crashes (CUDA,VRPN) Munir Ahmad (Tue Feb 02 2016 - 04:49:27 CST)
tcl command to write amber format files Akshay Bhatnagar (Tue Jan 26 2016 - 22:40:18 CST)
- AW: tcl command to write amber format files Norman Geist (Wed Jan 27 2016 - 03:10:18 CST)
- AW: tcl command to write amber format files Norman Geist (Wed Jan 27 2016 - 03:12:33 CST)
- Re: tcl command to write amber format files Ajasja LjubetiÄ (Wed Jan 27 2016 - 03:28:24 CST)
vmd does not start Kris Feher (Mon Jan 25 2016 - 11:41:09 CST)
- Re: vmd does not start Josh Vermaas (Mon Jan 25 2016 - 12:57:00 CST)
select atoms within a sphere - atomselect Monika Madhavi (Sun Jan 24 2016 - 23:31:07 CST)
- Re: select atoms within a sphere - atomselect Ashar Malik (Mon Jan 25 2016 - 00:51:22 CST)
  - Re: select atoms within a sphere - atomselect Monika Madhavi (Mon Feb 01 2016 - 06:02:36 CST)
- AW: select atoms within a sphere - atomselect Norman Geist (Mon Jan 25 2016 - 01:09:42 CST)
  - Re: select atoms within a sphere - atomselect M K (Mon Jan 25 2016 - 03:35:42 CST)
Running atomselect made a seg fault yong zhou (Thu Jan 21 2016 - 09:11:24 CST)
- Re: Running atomselect made a seg fault John Stone (Thu Jan 21 2016 - 09:34:15 CST)
  - Re: Running atomselect made a seg fault yong zhou (Thu Jan 21 2016 - 21:15:49 CST)
    - Re: Running atomselect made a seg fault John Stone (Thu Jan 28 2016 - 22:11:31 CST)
Obscure bug in RMSD tool (the original) Tristan Croll (Thu Jan 21 2016 - 02:41:42 CST)
Manipulating the pdb file Mohsen Farshad (Wed Jan 20 2016 - 18:34:01 CST)
- Re: Manipulating the pdb file Ashar Malik (Wed Jan 20 2016 - 19:03:05 CST)
  - Re: Manipulating the pdb file M K (Wed Jan 20 2016 - 20:13:02 CST)
"user add key" feature Eric Smoll (Wed Jan 20 2016 - 18:02:41 CST)
Showing atom index in vmd reza vatan (Wed Jan 20 2016 - 16:28:36 CST)
- Re: Showing atom index in vmd Samuel Bowerman (Wed Jan 20 2016 - 16:54:23 CST)
  - Re: Showing atom index in vmd reza vatan (Wed Jan 20 2016 - 20:18:42 CST)
VMD stereo NVIDIA 3D vision with Composite Vlad Cojocaru (Wed Jan 20 2016 - 11:45:30 CST)
- Re: VMD stereo NVIDIA 3D vision with Composite John Stone (Wed Jan 20 2016 - 16:00:59 CST)
  - Re: VMD stereo NVIDIA 3D vision with Composite Vlad Cojocaru (Thu Jan 21 2016 - 03:02:49 CST)
    - Re: VMD stereo NVIDIA 3D vision with Composite John Stone (Thu Jan 21 2016 - 09:56:36 CST)
    - Re: VMD stereo NVIDIA 3D vision with Composite Vlad Cojocaru (Thu Jan 21 2016 - 17:20:22 CST)
which version!? Reza Shakouri (Tue Jan 19 2016 - 09:29:36 CST)
- Re: which version!? John Stone (Tue Jan 19 2016 - 10:16:49 CST)
No error details for VMD compilation from Source. Munir Ahmad (Thu Jan 14 2016 - 15:40:53 CST)
- Re: No error details for VMD compilation from Source. John Stone (Thu Jan 14 2016 - 15:50:29 CST)
  - Re: No error details for VMD compilation from Source. Munir Ahmad (Fri Jan 15 2016 - 12:04:48 CST)
    - Re: No error details for VMD compilation from Source. Munir Ahmad (Thu Jan 21 2016 - 09:45:35 CST)
    - Re: No error details for VMD compilation from Source. John Stone (Thu Jan 21 2016 - 10:12:42 CST)
pdb was not generated Albert (Thu Jan 14 2016 - 11:53:36 CST)
- Re: pdb was not generated Josh Vermaas (Thu Jan 14 2016 - 13:41:00 CST)
Recommended method to attach labels to atoms in VMD Eric Smoll (Wed Jan 13 2016 - 15:33:47 CST)
- Re: Recommended method to attach labels to atoms in VMD Josh Vermaas (Wed Jan 13 2016 - 16:39:19 CST)
question about reading more volumes via atomselect or removing of them Daniel Möller (Wed Jan 13 2016 - 08:33:13 CST)
- Re: question about reading more volumes via atomselect or removing of them John Stone (Wed Jan 13 2016 - 13:38:27 CST)
  - AW: question about reading more volumes via atomselect or removing of them Daniel Möller (Thu Jan 14 2016 - 05:37:52 CST)
Show additional data Matthias Ernst (Fri Jan 08 2016 - 12:55:49 CST)
- Re: Show additional data John Stone (Wed Jan 13 2016 - 12:05:37 CST)
  - Re: Show additional data Matthias Ernst (Thu Jan 14 2016 - 10:38:28 CST)
    - Re: Show additional data John Stone (Thu Jan 14 2016 - 15:36:04 CST)
PhD and postdoctoral positions in biomolecular simulation Allison, Jane (Thu Jan 07 2016 - 15:50:48 CST)
removing water from inside the membranes in a duplicate membrane system Olya Kravchenko (Wed Jan 06 2016 - 15:51:47 CST)
Bugs in solvate plugin Vlastimil ZÃma (Wed Jan 06 2016 - 03:27:41 CST)
- Re: Bugs in solvate plugin Peter Freddolino (Fri Jan 08 2016 - 13:57:47 CST)
-fpascal-strings flag when compiling with TDCONNEXION option Tristan Croll (Wed Jan 06 2016 - 01:50:30 CST)
- Re: -fpascal-strings flag when compiling with TDCONNEXION option Tristan Croll (Wed Jan 06 2016 - 01:58:40 CST)
  - Re: Re: -fpascal-strings flag when compiling with TDCONNEXION option John Stone (Wed Jan 13 2016 - 13:29:06 CST)
    - Re: Re: -fpascal-strings flag when compiling with TDCONNEXION option Tristan Croll (Wed Jan 13 2016 - 13:31:47 CST)
error message MultiSeq - sequence alignement Marie Erard (Tue Jan 05 2016 - 15:52:06 CST)
- Re: error message MultiSeq - sequence alignement John Stone (Wed Jan 13 2016 - 13:31:48 CST)
Possible bug in topotools plugin Morteza Jalalvand (Sun Jan 03 2016 - 10:53:44 CST)
- Re: Possible bug in topotools plugin Axel Kohlmeyer (Sun Jan 03 2016 - 11:17:49 CST)
  - Re: Possible bug in topotools plugin Morteza Jalalvand (Sun Jan 03 2016 - 11:24:45 CST)
mdff: tutorial Rose, Stuart Wallace (Wed Dec 30 2015 - 09:55:01 CST)
- Re: mdff: tutorial Ryan McGreevy (Wed Dec 30 2015 - 10:51:33 CST)
  - RE: mdff: tutorial Rose, Stuart Wallace (Wed Dec 30 2015 - 12:11:49 CST)
  - Re: mdff: tutorial Ryan McGreevy (Tue Jan 05 2016 - 00:47:27 CST)
Improving movie clarity anu chandra (Tue Dec 29 2015 - 18:05:58 CST)
- Re: Improving movie clarity Josh Vermaas (Tue Dec 29 2015 - 19:17:08 CST)
  - Re: Improving movie clarity anu chandra (Thu Dec 31 2015 - 06:34:57 CST)
    - Re: Improving movie clarity Josh Vermaas (Thu Dec 31 2015 - 08:28:32 CST)
    - Re: Improving movie clarity anu chandra (Thu Dec 31 2015 - 15:32:22 CST)
TCL code for psf file Mohsen Farshad (Sun Dec 27 2015 - 12:01:38 CST)
- Re: TCL code for psf file Ashar Malik (Sun Dec 27 2015 - 12:57:33 CST)
calculating RMSD for a trajectory file Mai Aamer (Mon Dec 21 2015 - 04:44:53 CST)
- Re: calculating RMSD for a trajectory file Ashar Malik (Mon Dec 21 2015 - 05:20:43 CST)
importing deMon2k "molden" files into VMD Urquhart, Stephen (Sat Dec 19 2015 - 17:22:27 CST)
- Re: importing deMon2k "molden" files into VMD Axel Kohlmeyer (Sat Dec 19 2015 - 17:48:31 CST)
mol add url Thomas C Bishop (Fri Dec 18 2015 - 16:41:24 CST)
- Re: mol add url Josh Vermaas (Fri Dec 18 2015 - 18:00:02 CST)
  - Re: mol add url John Stone (Tue Dec 22 2015 - 09:52:51 CST)
    - Re: mol add url Thomas C Bishop (Tue Dec 22 2015 - 23:58:30 CST)
Number of pdb and psf atoms are not the same! Francesco Pietra (Wed Dec 16 2015 - 09:23:41 CST)
- Re: Number of pdb and psf atoms are not the same! Ashar Malik (Wed Dec 16 2015 - 09:57:47 CST)
  - Re: Number of pdb and psf atoms are not the same! Francesco Pietra (Wed Dec 16 2015 - 10:14:12 CST)
Request for atom sequence followed by topo tools Swamy Sumanth (Mon Dec 14 2015 - 23:59:25 CST)
Coarse-graining: Inability to assign charge to C-terminus using fix_martini_psf.tcl Sourav Ray (Mon Dec 14 2015 - 17:51:46 CST)
- Re: Coarse-graining: Inability to assign charge to C-terminus using fix_martini_psf.tcl Sourav Ray (Mon Dec 14 2015 - 18:22:50 CST)
Steinhardt order parameter and clustering algorithms MannyEful E (Sat Dec 12 2015 - 13:04:18 CST)
- Re: Steinhardt order parameter and clustering algorithms conor parks (Sat Dec 12 2015 - 17:01:42 CST)
  - Re: Steinhardt order parameter and clustering algorithms conor parks (Sun Dec 13 2015 - 15:11:11 CST)
VMD-NAMD and PDB element column Francesco Pietra (Sat Dec 12 2015 - 09:09:55 CST)
- Re: namd-l: VMD-NAMD and PDB element column Jim Phillips (Sun Dec 13 2015 - 12:17:57 CST)
  - Re: Re: namd-l: VMD-NAMD and PDB element column Francesco Pietra (Sun Dec 13 2015 - 13:39:11 CST)
NetCDF plug-in for VMD Wanlei Wei (Fri Dec 11 2015 - 07:49:43 CST)
- Re: NetCDF plug-in for VMD John Stone (Fri Dec 11 2015 - 09:07:15 CST)
  - Re: NetCDF plug-in for VMD Wanlei Wei (Fri Dec 11 2015 - 20:20:15 CST)
Problems with GLUP and ASPP with CHARMM36 Francesco Pietra (Fri Dec 11 2015 - 05:07:03 CST)
- Re: namd-l: Problems with GLUP and ASPP with CHARMM36 Josh Vermaas (Fri Dec 11 2015 - 08:45:00 CST)
  - Re: namd-l: Problems with GLUP and ASPP with CHARMM36 Francesco Pietra (Fri Dec 11 2015 - 09:35:48 CST)
  - Re: namd-l: Problems with GLUP and ASPP with CHARMM36 Francesco Pietra (Fri Dec 11 2015 - 09:21:34 CST)
    - Re: namd-l: Problems with GLUP and ASPP with CHARMM36 Josh Vermaas (Fri Dec 11 2015 - 09:25:11 CST)
Unable to access config file Julio Cantu (Thu Dec 10 2015 - 17:36:05 CST)
- Re: Unable to access config file Ashar Malik (Thu Dec 10 2015 - 22:57:56 CST)
  - Re: Unable to access config file Ajasja LjubetiÄ (Fri Dec 11 2015 - 02:31:41 CST)
  - Re: Unable to access config file Pawel Kedzierski (Fri Dec 11 2015 - 03:52:26 CST)
PRES and water-ions issues with charmm36 Francesco Pietra (Thu Dec 10 2015 - 15:30:14 CST)
- Re: PRES and water-ions issues with charmm36 Brian Radak (Thu Dec 10 2015 - 15:58:49 CST)
Ubuntu launcher and WM_CLASS Peter Husen (Thu Dec 10 2015 - 06:07:44 CST)
- Re: Ubuntu launcher and WM_CLASS John Stone (Thu Dec 10 2015 - 08:54:22 CST)
[lammps-users] NPT/ Missing bonds / atoms & atom overlap Georgia Tsagkaropoulou (Wed Dec 09 2015 - 11:19:25 CST)
Defining space coordinates for multiple structures Mariano Smoler (Tue Dec 08 2015 - 13:08:15 CST)
- Re: Defining space coordinates for multiple structures Axel Kohlmeyer (Tue Dec 08 2015 - 13:45:12 CST)
- RE: Defining space coordinates for multiple structures Joaquim Rui de Castro Rodrigues (Tue Dec 08 2015 - 14:17:13 CST)
residue-residue interaction energy elena ermakova (Tue Dec 08 2015 - 02:48:04 CST)
- Re: residue-residue interaction energy John Stone (Tue Dec 08 2015 - 14:06:14 CST)
Fwd: couldn't execute "psfgen": no such file or directory zeynab hoseyni (Sun Dec 06 2015 - 07:39:17 CST)
- Re: couldn't execute "psfgen": no such file or directory Axel Kohlmeyer (Mon Dec 07 2015 - 07:03:19 CST)
  - Re: couldn't execute "psfgen": no such file or directory zeynab hoseyni (Wed Dec 09 2015 - 12:50:37 CST)
    - Re: couldn't execute "psfgen": no such file or directory John Stone (Thu Dec 10 2015 - 11:34:05 CST)
couldn't execute "psfgen": no such file or directory zeynab hoseyni (Sun Dec 06 2015 - 07:02:21 CST)
- Re: couldn't execute "psfgen": no such file or directory Axel Kohlmeyer (Sun Dec 06 2015 - 07:26:56 CST)
  - Re: couldn't execute "psfgen": no such file or directory zeynab hoseyni (Sun Dec 06 2015 - 07:46:33 CST)
alignment of two the same structures Marta Wisniewska (Fri Dec 04 2015 - 11:45:39 CST)
- Re: alignment of two the same structures Tristan Croll (Tue Dec 08 2015 - 00:59:06 CST)
IR Spectral Density Tool Dive, Aniruddha Mukund (Thu Dec 03 2015 - 20:39:11 CST)
(no subject) Abhijit Ghosh (Thu Dec 03 2015 - 12:35:43 CST)
- Re: John Stone (Thu Dec 03 2015 - 12:43:51 CST)
minimizing text console on startup (Windows) Jason Quenneville (Thu Dec 03 2015 - 10:02:30 CST)
Measure atom position directly from index Tristan Croll (Wed Dec 02 2015 - 19:20:53 CST)
- Re: Measure atom position directly from index Axel Kohlmeyer (Wed Dec 02 2015 - 19:56:14 CST)
  - Re: Measure atom position directly from index Tristan Croll (Wed Dec 02 2015 - 20:05:31 CST)
Amber calculated structure(PDB) visualization in pymol vs chimera vs vmd V. Kumar (Wed Dec 02 2015 - 17:16:46 CST)
measure contacts not working as expected Bryan Roessler (Wed Dec 02 2015 - 16:51:04 CST)
- Re: measure contacts not working as expected Bryan Roessler (Thu Dec 03 2015 - 19:34:39 CST)
  - Re: measure contacts not working as expected Peter Freddolino (Thu Dec 03 2015 - 21:14:13 CST)
Loading .vel files into vmd Ben Rousseau (Wed Dec 02 2015 - 11:42:00 CST)
- Re: Loading .vel files into vmd Josh Vermaas (Wed Dec 02 2015 - 13:14:37 CST)
  - Re: Loading .vel files into vmd John Stone (Wed Dec 02 2015 - 15:22:07 CST)
- Re: Loading .vel files into vmd Maxim Belkin (Wed Dec 02 2015 - 12:24:05 CST)
Guessbonds and retype bonds Karteek Kumar (Tue Dec 01 2015 - 23:12:30 CST)
- Re: Guessbonds and retype bonds John Stone (Wed Dec 02 2015 - 15:19:11 CST)
- Re: Guessbonds and retype bonds Axel Kohlmeyer (Wed Dec 02 2015 - 15:46:43 CST)
new structure file James Lord (Mon Nov 30 2015 - 05:27:35 CST)
- AW: new structure file Norman Geist (Mon Nov 30 2015 - 23:51:22 CST)
  - AW: new structure file Norman Geist (Tue Dec 01 2015 - 01:26:52 CST)
Re: namd-l: Fwd: TIP4P and CHARMM27 Francesco Pietra (Fri Nov 27 2015 - 10:18:28 CST)
- Re: namd-l: Fwd: TIP4P and CHARMM27 Francesco Pietra (Fri Nov 27 2015 - 11:35:25 CST)
- Re: namd-l: Fwd: TIP4P and CHARMM27 Francesco Pietra (Fri Nov 27 2015 - 15:54:56 CST)
Possible memory leak with adding and deleting molecules frequently Daniel Möller (Fri Nov 27 2015 - 04:33:06 CST)
- Re: Possible memory leak with adding and deleting molecules frequently John Stone (Wed Dec 02 2015 - 15:52:53 CST)
  - Re: Possible memory leak with adding and deleting molecules frequently John Stone (Tue Feb 23 2016 - 14:45:50 CST)
TIP4P and CHARMM27 Francesco Pietra (Thu Nov 26 2015 - 15:50:52 CST)
- Fwd: TIP4P and CHARMM27 Francesco Pietra (Fri Nov 27 2015 - 09:17:35 CST)
  - Re: namd-l: Fwd: TIP4P and CHARMM27 Jim Phillips (Mon Nov 30 2015 - 16:21:44 CST)
vmd killed - memory problems? Frank Zack (Thu Nov 26 2015 - 06:30:57 CST)
- Re: vmd killed - memory problems? Axel Kohlmeyer (Thu Nov 26 2015 - 07:27:01 CST)
  - Re: vmd killed - memory problems? Frank Zack (Fri Nov 27 2015 - 10:35:04 CST)
    - Re: vmd killed - memory problems? Frank Zack (Fri Nov 27 2015 - 11:12:59 CST)
    - Re: vmd killed - memory problems? Axel Kohlmeyer (Fri Nov 27 2015 - 12:01:38 CST)
Re: fitting a line to 3D data points Vlad Cojocaru (Thu Nov 26 2015 - 02:18:55 CST)
- Re: fitting a line to 3D data points Ajasja LjubetiÄ (Thu Nov 26 2015 - 02:41:44 CST)
fitting a line to 3D data points Vlad Cojocaru (Wed Nov 25 2015 - 10:10:30 CST)
- Re: fitting a line to 3D data points Simon DÃ¼rr (Thu Nov 26 2015 - 08:37:45 CST)
Problem visualizing a pdbqt file generated by AutoDockTools Gustavo Seabra (Wed Nov 25 2015 - 06:59:53 CST)
- RE: Problem visualizing a pdbqt file generated by AutoDockTools Bennion, Brian (Wed Nov 25 2015 - 08:54:10 CST)
  - Re: Problem visualizing a pdbqt file generated by AutoDockTools Gustavo Seabra (Wed Nov 25 2015 - 10:41:57 CST)
Stride for large structures Tristan Croll (Wed Nov 25 2015 - 02:04:50 CST)
- Re: Stride for large structures John Stone (Wed Nov 25 2015 - 09:25:11 CST)
  - RE: Stride for large structures Tristan Croll (Wed Nov 25 2015 - 16:49:34 CST)
Minimum content/format of PSF file to specify bonds? Bret Hess (Mon Nov 23 2015 - 10:55:22 CST)
- Re: Minimum content/format of PSF file to specify bonds? Axel Kohlmeyer (Mon Nov 23 2015 - 11:29:58 CST)
  - Re: Minimum content/format of PSF file to specify bonds? Bret Hess (Mon Nov 23 2015 - 11:46:31 CST)
    - Re: Minimum content/format of PSF file to specify bonds? JÃ©rÃ´me HÃ©nin (Mon Nov 23 2015 - 12:31:57 CST)
- Re: Minimum content/format of PSF file to specify bonds? JÃ©rÃ´me HÃ©nin (Mon Nov 23 2015 - 11:52:04 CST)
  - Re: Minimum content/format of PSF file to specify bonds? Bret Hess (Mon Nov 23 2015 - 11:59:22 CST)
- Re: Minimum content/format of PSF file to specify bonds? Josh Vermaas (Mon Nov 23 2015 - 13:43:08 CST)
possible issue with specden package Ana Celia Vila Verde (Mon Nov 23 2015 - 09:19:35 CST)
output of salt bridge plugin Shyno Mathew (Sun Nov 22 2015 - 22:40:44 CST)
- Re: output of salt bridge plugin Shyno Mathew (Mon Nov 23 2015 - 11:10:26 CST)
Attractive or repulsive with Namd Energy? sunyeping (Sun Nov 22 2015 - 20:15:06 CST)
- Re: Attractive or repulsive with Namd Energy? JÃ©rÃ´me HÃ©nin (Mon Nov 23 2015 - 03:33:30 CST)
volmap parameters JhonY. I. (Sat Nov 21 2015 - 20:52:10 CST)
periodic boundry in movie James Lord (Fri Nov 20 2015 - 02:45:52 CST)
- Re: periodic boundry in movie Josh Vermaas (Fri Nov 20 2015 - 07:54:16 CST)
Using the -updatesel parameter in namdenergy Atreya Dey (Fri Nov 20 2015 - 01:49:58 CST)
Changing the color of some atoms Majid Shahbabaei (Thu Nov 19 2015 - 22:54:49 CST)
loading a several structures in the same time Marta Wisniewska (Wed Nov 18 2015 - 16:46:01 CST)
- Re: loading a several structures in the same time Josh Vermaas (Wed Nov 18 2015 - 18:09:19 CST)
  - Re: loading a several structures in the same time Lela Vukovic (Wed Nov 18 2015 - 19:08:35 CST)
extract certain part of atoms into separate file Albert (Wed Nov 18 2015 - 09:49:53 CST)
- Re: extract certain part of atoms into separate file Ryan McGreevy (Wed Nov 18 2015 - 10:26:45 CST)
  - Re: extract certain part of atoms into separate file Albert (Thu Nov 19 2015 - 01:46:40 CST)
    - RE: extract certain part of atoms into separate file Morgan, Brittany (Thu Nov 19 2015 - 08:41:14 CST)
    - Re: extract certain part of atoms into separate file Ryan McGreevy (Thu Nov 19 2015 - 08:41:56 CST)
Fwd: Compiling VMD with python interpreter on MacOSX kskeby (Wed Nov 18 2015 - 08:29:45 CST)
- Re: Fwd: Compiling VMD with python interpreter on MacOSX Josh Vermaas (Wed Nov 18 2015 - 09:45:12 CST)
  - Re: Fwd: Compiling VMD with python interpreter on MacOSX kskeby (Wed Nov 18 2015 - 10:43:22 CST)
    - Re: Fwd: Compiling VMD with python interpreter on MacOSX Maxim Belkin (Wed Nov 18 2015 - 10:52:52 CST)
FFTK dihedral scan Chitrak Gupta (Wed Nov 18 2015 - 08:07:57 CST)
- Re: FFTK dihedral scan Mayne, Christopher G (Wed Nov 18 2015 - 14:08:51 CST)
  - Re: FFTK dihedral scan Chitrak Gupta (Wed Nov 18 2015 - 14:31:22 CST)
Error while opening dump file Dive, Aniruddha Mukund (Tue Nov 17 2015 - 19:05:10 CST)
- Re: Error while opening dump file M K (Tue Nov 17 2015 - 20:18:05 CST)
vmd 1.9.3 A Christian Wohlschlager (Tue Nov 17 2015 - 01:31:46 CST)
- Re: vmd 1.9.3 A John Stone (Tue Nov 24 2015 - 12:54:08 CST)
Error (incompatible tcl8.5.so) when installing VMD plugins Xinqiang Ding (Sat Nov 14 2015 - 07:09:59 CST)
- Re: Error (incompatible tcl8.5.so) when installing VMD plugins Axel Kohlmeyer (Sat Nov 14 2015 - 09:31:15 CST)
- Re: Error (incompatible tcl8.5.so) when installing VMD plugins Arash Azari (Sat Nov 14 2015 - 10:34:34 CST)
Re: namd-l: On-the-fly modification of tclforces script? Tristan Croll (Fri Nov 13 2015 - 16:48:21 CST)
- Re: namd-l: On-the-fly modification of tclforces script? Tristan Croll (Fri Nov 13 2015 - 18:14:28 CST)
  - Re: Re: namd-l: On-the-fly modification of tclforces script? John Stone (Fri Nov 13 2015 - 19:05:34 CST)
VDW-radius-and-Interstitial-Space Chowdhury, Sanjib Chandra (Tue Nov 10 2015 - 19:10:18 CST)
- Re: VDW-radius-and-Interstitial-Space Josh Vermaas (Tue Nov 10 2015 - 20:21:34 CST)
what is difference between "TOTAL", â€œTOTAL2" and "POTENTIAL" in the VMD plugin NAMD Plot? sunyeping (Mon Nov 09 2015 - 02:22:23 CST)
- Re: what is difference between "TOTAL", Q=80=9cTOTAL2=22_and_=22POTENTIAL=22_in_the_VMD_plugin_NAMD_Plo?= t? Pawel Kedzierski (Mon Nov 09 2015 - 04:09:48 CST)
can I change the axes type to look like something like a graduated coordinate? Nima Soltani (Sun Nov 08 2015 - 15:23:51 CST)
- Re: can I change the axes type to look like something like a graduated coordinate? Tristan Croll (Sun Nov 08 2015 - 19:33:17 CST)
VMD script variable is dipak sanap (Fri Nov 06 2015 - 03:56:41 CST)
- Re: VMD script variable is Josh Vermaas (Fri Nov 06 2015 - 10:07:48 CST)
velocity array accessible for any loaded molecule? JC Gumbart (Thu Nov 05 2015 - 19:56:46 CST)
- Re: velocity array accessible for any loaded molecule? John Stone (Thu Nov 05 2015 - 20:13:06 CST)
- Re: velocity array accessible for any loaded molecule? JC Gumbart (Thu Nov 05 2015 - 23:43:12 CST)
  - Re: velocity array accessible for any loaded molecule? John Stone (Fri Nov 06 2015 - 00:09:36 CST)
    - Re: velocity array accessible for any loaded molecule? JC Gumbart (Fri Nov 06 2015 - 08:13:56 CST)
Re: Query for eliminating proteins with unusual amino acids Akshay Bhatnagar (Thu Nov 05 2015 - 18:25:59 CST)
- Re: Query for eliminating proteins with unusual amino acids Akshay Bhatnagar (Thu Nov 05 2015 - 22:24:24 CST)
  - RE: Query for eliminating proteins with unusual amino acids Tristan Croll (Thu Nov 05 2015 - 22:37:24 CST)
Fwd: Query for eliminating proteins with unusual amino acids Akshay Bhatnagar (Thu Nov 05 2015 - 18:19:18 CST)
Query for eliminating proteins with unusual amino acids Akshay Bhatnagar (Wed Nov 04 2015 - 23:46:02 CST)
- RE: Query for eliminating proteins with unusual amino acids Tristan Croll (Thu Nov 05 2015 - 16:28:31 CST)
Charge optimization in ffTK Amira Yu (Wed Nov 04 2015 - 09:09:39 CST)
- Re: Charge optimization in ffTK Mayne, Christopher G (Wed Nov 04 2015 - 13:51:00 CST)
  - Re: Charge optimization in ffTK Amira Yu (Wed Nov 04 2015 - 14:05:26 CST)
    - Re: Charge optimization in ffTK Pawel Kedzierski (Thu Nov 05 2015 - 02:04:17 CST)
    - Re: Charge optimization in ffTK Amira Yu (Thu Nov 05 2015 - 07:20:32 CST)
RMSD per residue of docked molecule Evandro Semighini (Wed Nov 04 2015 - 07:08:34 CST)
Shifting the Geometric Center of entire set of molecules to origin Sourav Ray (Wed Nov 04 2015 - 04:33:58 CST)
- Re: Shifting the Geometric Center of entire set of molecules to origin Tristan Croll (Wed Nov 04 2015 - 05:38:44 CST)
- RE: Shifting the Geometric Center of entire set of molecules to origin Joaquim Rui de Castro Rodrigues (Wed Nov 04 2015 - 06:14:13 CST)
- Re: Shifting the Geometric Center of entire set of molecules to origin Tim Lo (Fri Nov 06 2015 - 22:38:19 CST)
Tracing on color by properties Tristan Croll (Wed Nov 04 2015 - 02:54:49 CST)
- Re: Tracing on color by properties Tristan Croll (Wed Nov 04 2015 - 03:51:42 CST)
Best VMD install for El Capitan OS X? Eiros Zamora, Juan (Mon Nov 02 2015 - 03:35:36 CST)
- Re: Best VMD install for El Capitan OS X? John Stone (Mon Nov 02 2015 - 10:35:29 CST)
  - Re: Best VMD install for El Capitan OS X? Eiros Zamora, Juan (Fri Nov 06 2015 - 09:32:57 CST)
    - Re: Best VMD install for El Capitan OS X? John Stone (Fri Nov 06 2015 - 09:53:56 CST)
Need help in selection Kshatresh Dutta Dubey (Mon Nov 02 2015 - 03:12:13 CST)
- Re: Need help in selection Karteek Kumar (Mon Nov 02 2015 - 03:22:00 CST)
  - Re: Need help in selection Kshatresh Dutta Dubey (Mon Nov 02 2015 - 03:37:42 CST)
    - Re: Need help in selection M K (Mon Nov 02 2015 - 04:11:35 CST)
Problems with vmd plugin namdenergy output sunyeping (Mon Nov 02 2015 - 03:06:32 CST)
- Re: Problems with vmd plugin namdenergy output Fotis Baltoumas (Mon Nov 02 2015 - 04:48:11 CST)
  - Re: Problems with vmd plugin namdenergy output sunyeping (Mon Nov 02 2015 - 05:54:58 CST)
    - Re: Re: Problems with vmd plugin namdenergy output John Stone (Mon Nov 02 2015 - 10:32:27 CST)
  - Re: Problems with vmd plugin namdenergy output sunyeping (Wed Nov 04 2015 - 05:11:10 CST)
- Re: Problems with vmd plugin namdenergy output Axel Kohlmeyer (Mon Nov 02 2015 - 10:51:24 CST)
Making high quality pictures: How to increase the number of samples? Lai, Jonathan (Sun Nov 01 2015 - 16:34:45 CST)
- Re: Making high quality pictures: How to increase the number of samples? John Stone (Sun Nov 01 2015 - 22:22:16 CST)
www.tcl.tk DNS taken by cybersquatter... John Stone (Fri Oct 30 2015 - 16:47:17 CDT)
ffTK charge optimizations Amira Yu (Fri Oct 30 2015 - 09:22:24 CDT)
netcdf trajectory file Atila Petrosian (Fri Oct 30 2015 - 02:22:12 CDT)
- Re: netcdf trajectory file Diego Vazquez (Fri Oct 30 2015 - 04:02:57 CDT)
  - Re: netcdf trajectory file Atila Petrosian (Fri Oct 30 2015 - 06:17:27 CDT)
Molefacture & Six-Character Atom Types Eric Schibli (Wed Oct 28 2015 - 21:52:09 CDT)
fftk using Terachem? Tristan Croll (Wed Oct 28 2015 - 20:25:55 CDT)
- Re: fftk using Terachem? Mayne, Christopher G (Thu Oct 29 2015 - 07:59:31 CDT)
  - Re: fftk using Terachem? Tristan Croll (Thu Oct 29 2015 - 18:42:53 CDT)
Including two parameters for protein-ligand simulation Nikhil Maroli (Wed Oct 28 2015 - 01:52:30 CDT)
- Re: namd-l: Including two parameters for protein-ligand simulation Abhishek TYAGI (Wed Oct 28 2015 - 01:59:21 CDT)
  - Re: Re: namd-l: Including two parameters for protein-ligand simulation Payal Chatterjee (Wed Oct 28 2015 - 03:08:16 CDT)
FFTK abort charge calculation. Eric Schibli (Tue Oct 27 2015 - 16:38:56 CDT)
- Re: FFTK abort charge calculation. Mayne, Christopher G (Tue Oct 27 2015 - 17:10:11 CDT)
how to measure the thickness of the water shell sunyeping (Tue Oct 27 2015 - 00:50:48 CDT)
- AW: how to measure the thickness of the water shell Norman Geist (Tue Oct 27 2015 - 06:28:09 CDT)
  - Re: AW: how to measure the thickness of the water shell sunyeping (Tue Oct 27 2015 - 09:11:59 CDT)
script for plotting trajectories Aris Marcolongo (Mon Oct 26 2015 - 06:02:27 CDT)
- Re: script for plotting trajectories Aris Marcolongo (Mon Oct 26 2015 - 15:06:07 CDT)
  - Re: script for plotting trajectories Axel Kohlmeyer (Mon Oct 26 2015 - 15:39:37 CDT)
Errors in display yunshi11 . (Mon Oct 26 2015 - 00:19:59 CDT)
Writing Wrapped coordinates to a xyz file using TCL script Abhishek Bagusetty (Sat Oct 24 2015 - 14:19:36 CDT)
catdcd in VMD JhonY. I. (Sat Oct 24 2015 - 10:26:53 CDT)
- Re: catdcd in VMD Axel Kohlmeyer (Sat Oct 24 2015 - 10:57:48 CDT)
PLO2 Patch Francesco Greco (Sat Oct 24 2015 - 09:44:14 CDT)
CHARMM parameters for iodide and bromide Stojanoski, Vlatko (Fri Oct 23 2015 - 12:10:58 CDT)
- Re: CHARMM parameters for iodide and bromide Stojanoski, Vlatko (Sat Oct 24 2015 - 09:37:45 CDT)
- Re: CHARMM parameters for iodide and bromide Mayne, Christopher G (Mon Oct 26 2015 - 19:29:41 CDT)
GPU accelerated MD Nikhil Maroli (Fri Oct 23 2015 - 04:12:24 CDT)
- AW: GPU accelerated MD Norman Geist (Fri Oct 23 2015 - 07:18:01 CDT)
gromacs to charmm conversion Francesco Pietra (Fri Oct 23 2015 - 02:34:15 CDT)
- Re: gromacs to charmm conversion Ajasja LjubetiÄ (Fri Oct 23 2015 - 03:28:28 CDT)
Problem of VMD in ubuntu 14.04 Bonakala Satyanarayana (Fri Oct 23 2015 - 01:46:40 CDT)
- Re: Problem of VMD in ubuntu 14.04 Pawel Kedzierski (Fri Oct 23 2015 - 03:17:14 CDT)
VMD: Problems loading PDB Files from behind a proxy server Greipel.Joachim_at_mh-hannover.de (Fri Oct 23 2015 - 01:15:53 CDT)
Tcl script for hydration shell of backbone carbonyl oxygen for whole trajectory. dipak sanap (Thu Oct 22 2015 - 01:06:39 CDT)
- Re: Tcl script for hydration shell of backbone carbonyl oxygen for whole trajectory. M K (Thu Oct 22 2015 - 04:10:36 CDT)
Double bond in VMD Parvez Mh (Wed Oct 21 2015 - 17:45:25 CDT)
Topology for drugs to do MD after docking Nikhil Maroli (Wed Oct 21 2015 - 11:40:04 CDT)
- Re: Topology for drugs to do MD after docking Mayne, Christopher G (Wed Oct 21 2015 - 14:44:18 CDT)
  - Re: Topology for drugs to do MD after docking Mayne, Christopher G (Thu Oct 22 2015 - 09:39:02 CDT)
assign bond color based on bond type Zhang, Tao (Wed Oct 21 2015 - 10:53:26 CDT)
- Re: assign bond color based on bond type John Stone (Wed Oct 21 2015 - 14:49:36 CDT)
  - RE: assign bond color based on bond type Zhang, Tao (Wed Oct 21 2015 - 14:54:11 CDT)
    - Re: assign bond color based on bond type John Stone (Wed Oct 21 2015 - 14:58:10 CDT)
Regarding generating force field Saumik Sen (Wed Oct 21 2015 - 01:50:33 CDT)
TachyonL-Optix render command Edoardo Baldi (Tue Oct 20 2015 - 12:45:31 CDT)
- Re: TachyonL-Optix render command Josh Vermaas (Tue Oct 20 2015 - 13:24:13 CDT)
  - Re: TachyonL-Optix render command John Stone (Wed Oct 21 2015 - 15:04:47 CDT)
Problem on merging multi-psf files into one wliu (Tue Oct 20 2015 - 00:47:12 CDT)
- Re: Problem on merging multi-psf files into one Axel Kohlmeyer (Tue Oct 20 2015 - 05:58:07 CDT)
  - RE: Problem on merging multi-psf files into one Joaquim Rui de Castro Rodrigues (Tue Oct 20 2015 - 07:24:14 CDT)
Plot waters vs time in a trajectory Daniela Rivas (Mon Oct 19 2015 - 15:05:24 CDT)
- Re: Plot waters vs time in a trajectory Axel Kohlmeyer (Mon Oct 19 2015 - 15:51:23 CDT)
- Re: Plot waters vs time in a trajectory Chitrak Gupta (Mon Oct 19 2015 - 16:36:15 CDT)
  - Re: Plot waters vs time in a trajectory M K (Tue Oct 20 2015 - 20:04:27 CDT)
    - Re: Plot waters vs time in a trajectory M K (Tue Oct 20 2015 - 20:08:49 CDT)
- Re: Plot waters vs time in a trajectory Diego Vazquez (Tue Oct 20 2015 - 21:44:05 CDT)
How can I trace an oxygen atom in VMD? Majid Shahbabaei (Mon Oct 19 2015 - 00:52:11 CDT)
- Re: How can I trace an oxygen atom in VMD? Ashar Malik (Mon Oct 19 2015 - 01:42:45 CDT)
  - Re: How can I trace an oxygen atom in VMD? Majid Shahbabaei (Mon Oct 19 2015 - 02:08:37 CDT)
  - Re: How can I trace an oxygen atom in VMD? Majid Shahbabaei (Wed Oct 28 2015 - 22:03:38 CDT)
problem of x3d in chrome and IE Albert (Sun Oct 18 2015 - 13:11:26 CDT)
- Re: problem of x3d in chrome and IE John Stone (Sun Oct 18 2015 - 16:40:36 CDT)
  - Re: problem of x3d in chrome and IE John Stone (Sun Oct 18 2015 - 16:43:36 CDT)
viewMaster plugin Nuno Sousa Cerqueira (Sun Oct 18 2015 - 12:11:41 CDT)
Re: namd-l: Problem on merging multi-psf files into one Axel Kohlmeyer (Sun Oct 18 2015 - 09:39:43 CDT)
can we export VMD scene as webGL file? Albert (Fri Oct 16 2015 - 16:22:59 CDT)
- Re: can we export VMD scene as webGL file? John Stone (Fri Oct 16 2015 - 16:34:10 CDT)
  - Re: can we export VMD scene as webGL file? Albert (Fri Oct 16 2015 - 16:52:19 CDT)
Regarding generating psf file Saumik Sen (Thu Oct 15 2015 - 03:49:50 CDT)
- Re: Regarding generating psf file Chitrak Gupta (Thu Oct 15 2015 - 08:14:38 CDT)
  - Re: Regarding generating psf file Saumik Sen (Thu Oct 15 2015 - 08:41:39 CDT)
    - Re: Regarding generating psf file Chitrak Gupta (Thu Oct 15 2015 - 09:32:29 CDT)
Consistent size Eric Smoll (Wed Oct 14 2015 - 21:33:58 CDT)
- Re: Consistent size Maxim Belkin (Thu Oct 15 2015 - 09:44:09 CDT)
- Re: Consistent size Josh Vermaas (Thu Oct 15 2015 - 11:33:43 CDT)
Ideal charge optimization strategy for atoms with existing ff parameters Bryan Roessler (Tue Oct 13 2015 - 14:08:02 CDT)
- Re: Ideal charge optimization strategy for atoms with existing ff parameters Mayne, Christopher G (Fri Oct 16 2015 - 02:50:39 CDT)
  - Re: Ideal charge optimization strategy for atoms with existing ff parameters Bryan Roessler (Fri Oct 16 2015 - 10:01:53 CDT)
Cyclic peptide nanotube psf second mail Nikhil Maroli (Tue Oct 13 2015 - 00:42:55 CDT)
- RE: Cyclic peptide nanotube psf second mail Tristan Croll (Tue Oct 13 2015 - 02:00:43 CDT)
AW: query regarding phi-psi range for asigning secondary structure Norman Geist (Mon Oct 12 2015 - 01:44:23 CDT)
Problems with S-Adenosyl-L-Methionine / SAM Topology & Parameter for MD simulations Daan Mevius (Sun Oct 11 2015 - 06:20:19 CDT)
- Re: Problems with S-Adenosyl-L-Methionine / SAM Topology & Parameter for MD simulations Pawel Kedzierski (Sun Oct 11 2015 - 08:33:33 CDT)
  - Re: Problems with S-Adenosyl-L-Methionine / SAM Topology & Parameter for MD simulations Daan Mevius (Tue Oct 13 2015 - 09:23:50 CDT)
query regarding phi-psi range for asigning secondary structure Atanu Maity (Fri Oct 09 2015 - 01:43:43 CDT)
- AW: query regarding phi-psi range for asigning secondary structure Norman Geist (Fri Oct 09 2015 - 02:56:42 CDT)
  - Re: query regarding phi-psi range for asigning secondary structure Atanu Maity (Fri Oct 09 2015 - 04:44:24 CDT)
    - AW: query regarding phi-psi range for asigning secondary structure Norman Geist (Fri Oct 09 2015 - 05:29:00 CDT)
Change color of drawn object Ebert Maximilian (Thu Oct 08 2015 - 13:48:07 CDT)
- Re: Change color of drawn object John Stone (Thu Oct 08 2015 - 14:11:16 CDT)
  - Re: Change color of drawn object Ebert Maximilian (Sat Oct 10 2015 - 20:34:33 CDT)
    - Re: Change color of drawn object Axel Kohlmeyer (Sun Oct 11 2015 - 09:53:37 CDT)
catdcd - writing DCD with box info from namdbin and xsc files? Brian Radak (Thu Oct 08 2015 - 10:03:58 CDT)
about opls-aam ff for small molecules Francesco Pietra (Wed Oct 07 2015 - 16:16:15 CDT)
Draw cylinder with two different diameters for the endpoints (cone) Ebert Maximilian (Wed Oct 07 2015 - 11:21:08 CDT)
- RE: Draw cylinder with two different diameters for the endpoints (cone) Ebert Maximilian (Wed Oct 07 2015 - 11:35:27 CDT)
  - Re: RE: Draw cylinder with two different diameters for the endpoints (cone) John Stone (Wed Oct 07 2015 - 16:38:27 CDT)
Re: namd-l: Regarding problem in psfgen of heparin Tristan Croll (Tue Oct 06 2015 - 18:44:21 CDT)
Announcement: call for abstracts (**extended deadline**): SC15 workshop "Producing High-Performance and Sustainable Software for Molecular Simulation" Arno Proeme (Mon Oct 05 2015 - 19:33:18 CDT)
VMD 1.9.2 32 bit Linux Gianluca Interlandi (Fri Oct 02 2015 - 18:00:35 CDT)
- Re: VMD 1.9.2 32 bit Linux John Stone (Fri Oct 02 2015 - 22:03:22 CDT)
Re: VMD Tricky selection of protein water bridge (2 bridge waters) Yarrow Madrona (Fri Oct 02 2015 - 17:21:23 CDT)
- Re: Re: VMD Tricky selection of protein water bridge (2 bridge waters) Ashar Malik (Fri Oct 02 2015 - 18:17:31 CDT)
- Re: Re: VMD Tricky selection of protein water bridge (2 bridge waters) Josh Vermaas (Mon Oct 05 2015 - 11:06:14 CDT)
OpenDX file format website down: What do the three values at each grid point represent Ebert Maximilian (Fri Oct 02 2015 - 12:36:27 CDT)
- Re: OpenDX file format website down: What do the three values at each grid point represent Axel Kohlmeyer (Fri Oct 02 2015 - 13:09:36 CDT)
  - Re: OpenDX file format website down: What do the three values at each grid point represent Ebert Maximilian (Mon Oct 05 2015 - 10:05:29 CDT)
    - Re: OpenDX file format website down: What do the three values at each grid point represent Axel Kohlmeyer (Mon Oct 05 2015 - 10:57:17 CDT)
    - Re: OpenDX file format website down: What do the three values at each grid point represent Arash Azari (Tue Oct 06 2015 - 00:47:38 CDT)
  - Re: OpenDX file format website down: What do the three values at each grid point represent Ebert Maximilian (Tue Oct 06 2015 - 14:38:43 CDT)
Cyclic peptide Nanotube Nikhil Maroli (Fri Oct 02 2015 - 08:52:59 CDT)
script error Nikhil Maroli (Fri Oct 02 2015 - 08:44:13 CDT)
- Re: script error John Stone (Fri Oct 02 2015 - 10:10:56 CDT)
sqlite and vmd Nuno Sousa Cerqueira (Fri Oct 02 2015 - 08:39:08 CDT)
- Re: sqlite and vmd John Stone (Fri Oct 02 2015 - 10:01:04 CDT)
PSF for cyclic peptide nanotube Nikhil Maroli (Fri Oct 02 2015 - 08:36:47 CDT)
VMD with XTC trajectory and stride Ebert Maximilian (Thu Oct 01 2015 - 11:56:13 CDT)
- Re: VMD with XTC trajectory and stride John Stone (Tue Oct 13 2015 - 14:52:23 CDT)
Re: namd-l: Atomselect within radial pair distribution function g(r) Chitrak Gupta (Wed Sep 30 2015 - 08:09:16 CDT)
scipt for loading multiple copies in psfgen Prof. Eddie (Tue Sep 29 2015 - 12:59:40 CDT)
Re: VMD crash when opening sunyeping (Tue Sep 29 2015 - 11:39:27 CDT)
VMD crash when opening sunyeping (Tue Sep 29 2015 - 11:22:46 CDT)
multiple parameterized ligands Prof. Eddie (Mon Sep 28 2015 - 18:57:37 CDT)
- Re: multiple parameterized ligands Chitrak Gupta (Mon Sep 28 2015 - 20:56:21 CDT)
  - Re: multiple parameterized ligands Prof. Eddie (Tue Sep 29 2015 - 10:39:22 CDT)
- Re: multiple parameterized ligands Mayne, Christopher G (Mon Sep 28 2015 - 21:26:00 CDT)
  - Re: multiple parameterized ligands Prof. Eddie (Tue Sep 29 2015 - 10:42:58 CDT)
    - Re: multiple parameterized ligands Tim Lo (Fri Oct 02 2015 - 21:35:39 CDT)
ffTK & transition metals Francesco Pietra (Sun Sep 27 2015 - 13:20:28 CDT)
- Re: ffTK & transition metals JC Gumbart (Thu Oct 01 2015 - 16:38:01 CDT)
  - Re: ffTK & transition metals Francesco Pietra (Fri Oct 02 2015 - 01:03:27 CDT)
Re: Why can VMD not be opened? sunyeping (Sun Sep 27 2015 - 13:03:32 CDT)
- Re: Re: Why can VMD not be opened? John Stone (Mon Sep 28 2015 - 09:14:28 CDT)
  - Re: Re: Why can VMD not be opened? sunyeping (Tue Sep 29 2015 - 09:40:21 CDT)
Why can VMD not be opened? sunyeping (Sun Sep 27 2015 - 12:07:50 CDT)
psf for cyclic peptide nanotube:psf ready for one ring but required for 8 ring Nikhil Maroli (Sat Sep 26 2015 - 06:50:31 CDT)
PSF for CYCLIC PEPTIDE : Nikhil Maroli (Sat Sep 26 2015 - 05:45:17 CDT)
Problems_calling_VMD_remotely_from_cluster Payal Chatterjee (Fri Sep 25 2015 - 17:32:25 CDT)
- Re: Problems_calling_VMD_remotely_from_cluster John Stone (Tue Sep 29 2015 - 10:23:30 CDT)
  - Re: Problems_calling_VMD_remotely_from_cluster Andrea Spitaleri (Tue Sep 29 2015 - 10:58:41 CDT)
  - Re: Problems_calling_VMD_remotely_from_cluster Payal Chatterjee (Tue Sep 29 2015 - 11:15:12 CDT)
REG: adding hydrogens using TCL surya narayanan chandrasekaran (Fri Sep 25 2015 - 11:11:41 CDT)
- Re: REG: adding hydrogens using TCL John Stone (Fri Sep 25 2015 - 15:02:07 CDT)
  - Re: REG: adding hydrogens using TCL surya narayanan chandrasekaran (Fri Sep 25 2015 - 15:34:23 CDT)
Segmentation fault error only when executing command within script Eric Smoll (Thu Sep 24 2015 - 21:15:28 CDT)
- Re: Segmentation fault error only when executing command within script John Stone (Fri Sep 25 2015 - 15:04:34 CDT)
fftk and impropers Prof. Eddie (Thu Sep 24 2015 - 08:04:42 CDT)
- Re: fftk and impropers Mayne, Christopher G (Thu Sep 24 2015 - 08:53:36 CDT)
Implicit Ligand Sampling: How to get energy along a reaction coordinate? Ebert Maximilian (Wed Sep 23 2015 - 14:11:06 CDT)
- Re: Implicit Ligand Sampling: How to get energy along a reaction coordinate? John Stone (Wed Sep 23 2015 - 14:33:09 CDT)
  - Re: Implicit Ligand Sampling: How to get energy along a reaction coordinate? Ebert Maximilian (Wed Sep 23 2015 - 15:09:55 CDT)
SSD vs SSHD vs mechanical Gianluca Interlandi (Wed Sep 23 2015 - 13:22:06 CDT)
- Re: SSD vs SSHD vs mechanical John Stone (Wed Sep 23 2015 - 13:37:27 CDT)
  - Re: SSD vs SSHD vs mechanical Gianluca Interlandi (Wed Sep 23 2015 - 13:57:22 CDT)
- RE: SSD vs SSHD vs mechanical James Kress (Thu Sep 24 2015 - 10:09:31 CDT)
visualising unit cell "plus a little more" Francesca Lønstad Bleken (Wed Sep 23 2015 - 04:34:52 CDT)
- RE: visualising unit cell "plus a little more" Morgan, Brittany (Wed Sep 23 2015 - 08:36:21 CDT)
  - RE: visualising unit cell "plus a little more" Francesca Lønstad Bleken (Thu Sep 24 2015 - 01:37:00 CDT)
  - AW: RE: visualising unit cell "plus a little more" Norman Geist (Thu Sep 24 2015 - 02:31:36 CDT)
Cannot Remote Display on Ubuntu Christian Wohlschlager (Tue Sep 22 2015 - 02:30:12 CDT)
Cannot Remote Display on Ububtu Christian Wohlschlager (Tue Sep 22 2015 - 00:54:34 CDT)
volutil: -combinepmf - Bug? Simon DÃ¼rr (Mon Sep 21 2015 - 13:39:30 CDT)
mergemols not combining topology information Frank Zack (Mon Sep 21 2015 - 07:06:02 CDT)
- Re: mergemols not combining topology information Axel Kohlmeyer (Mon Sep 21 2015 - 08:20:25 CDT)
Which VMD AND NAMD should install Nikhil Maroli (Sat Sep 19 2015 - 01:57:30 CDT)
- Re: Which VMD AND NAMD should install John Stone (Tue Sep 22 2015 - 14:07:17 CDT)
error with tutorial beginer required help Nikhil Maroli (Fri Sep 18 2015 - 02:42:58 CDT)
How to remove the simulation box M K (Thu Sep 17 2015 - 22:22:52 CDT)
- Re: How to remove the simulation box Axel Kohlmeyer (Thu Sep 17 2015 - 22:46:33 CDT)
  - Re: How to remove the simulation box M K (Wed Oct 14 2015 - 20:44:14 CDT)
Plugin to read DCD files Gianluca Interlandi (Thu Sep 17 2015 - 17:35:29 CDT)
- Re: Plugin to read DCD files Josh Vermaas (Thu Sep 17 2015 - 18:26:37 CDT)
- RE: Plugin to read DCD files Bennion, Brian (Fri Sep 18 2015 - 10:05:38 CDT)
ffTK: Charge optimization Amy Rice (Thu Sep 17 2015 - 14:39:05 CDT)
- Re: ffTK: Charge optimization Mayne, Christopher G (Thu Sep 17 2015 - 16:21:12 CDT)
  - Re: ffTK: Charge optimization Amy Rice (Tue Sep 22 2015 - 11:26:48 CDT)
    - Re: ffTK: Charge optimization Mayne, Christopher G (Wed Sep 23 2015 - 09:36:08 CDT)
-restrict option in measure sasa Chitrak Gupta (Wed Sep 16 2015 - 12:42:26 CDT)
- Re: -restrict option in measure sasa Josh Vermaas (Thu Sep 17 2015 - 09:27:36 CDT)
  - Re: -restrict option in measure sasa Chitrak Gupta (Fri Sep 18 2015 - 11:51:03 CDT)
Bonds appearing as elongated lines Sourav Ray (Wed Sep 16 2015 - 04:34:43 CDT)
- Re: Bonds appearing as elongated lines conor parks (Wed Sep 16 2015 - 11:59:14 CDT)
- Re: Bonds appearing as elongated lines Josh Vermaas (Thu Sep 17 2015 - 09:32:23 CDT)
PMEPot plugin: epilon-surface Anders Gabrielsson (Wed Sep 16 2015 - 04:29:29 CDT)
psfgen error: FAILED TO RECOGNIZE LONEPAIR Monika Madhavi (Wed Sep 16 2015 - 04:10:11 CDT)
align molecules using "anchor" atoms Xing (Tue Sep 15 2015 - 10:34:25 CDT)
- Re: align molecules using "anchor" atoms John Stone (Tue Sep 15 2015 - 10:58:02 CDT)
  - Re: align molecules using "anchor" atoms Xing (Tue Sep 15 2015 - 12:08:03 CDT)
    - Re: align molecules using "anchor" atoms Axel Kohlmeyer (Tue Sep 15 2015 - 15:41:30 CDT)
    - Re: align molecules using "anchor" atoms Xing (Tue Sep 15 2015 - 22:10:11 CDT)
Autopsf problem Kevin C Chan (Tue Sep 15 2015 - 08:53:57 CDT)
- Re: Autopsf problem Josh Vermaas (Tue Sep 15 2015 - 09:48:02 CDT)
  - Re: Autopsf problem Kevin Chan (Tue Sep 15 2015 - 21:24:16 CDT)
  - Re: Autopsf problem Kevin Chan (Tue Sep 15 2015 - 21:30:24 CDT)
fftk Bond guassian input for hessian calculation fvlieffe (Tue Sep 15 2015 - 06:07:14 CDT)
- Re: fftk Bond guassian input for hessian calculation Mayne, Christopher G (Tue Sep 15 2015 - 08:07:10 CDT)
  - Re: fftk Bond guassian input for hessian calculation Chitrak Gupta (Tue Sep 15 2015 - 10:47:52 CDT)
- fftk: prepare from CGENFF and improper fvlieffe (Fri Oct 16 2015 - 08:01:49 CDT)
  - Re: fftk: prepare from CGENFF and improper Mayne, Christopher G (Fri Oct 16 2015 - 09:58:51 CDT)
conversion of topology entries from charmm str format to vmd psfgen format Monika Madhavi (Tue Sep 15 2015 - 05:40:06 CDT)
New user encounter an error as follows ;please guide me :: Tutorial Nikhil Maroli (Tue Sep 15 2015 - 02:56:47 CDT)
New user encounter an error as follows ;please guide me :: Tutorial Nikhil Maroli (Tue Sep 15 2015 - 00:37:12 CDT)
Align only translation not rotation Simon DÃ¼rr (Mon Sep 14 2015 - 10:16:08 CDT)
- AW: Align only translation not rotation Norman Geist (Tue Sep 15 2015 - 01:40:02 CDT)
  - Re: Align only translation not rotation Ajasja LjubetiÄ (Tue Sep 15 2015 - 03:20:41 CDT)
Merge PDB files to create a single PDB and PSF file Ern Seang Ong (Mon Sep 14 2015 - 02:10:22 CDT)
ILS: Problems with the alignment Simon DÃ¼rr (Fri Sep 11 2015 - 15:42:26 CDT)
- Re: ILS: Problems with the alignment Simon DÃ¼rr (Mon Sep 21 2015 - 13:19:10 CDT)
ILS: clash exclusion distance Simon DÃ¼rr (Fri Sep 11 2015 - 12:25:46 CDT)
FFTK Bond optimization Chitrak Gupta (Fri Sep 11 2015 - 08:26:42 CDT)
- Re: FFTK Bond optimization Mayne, Christopher G (Mon Sep 14 2015 - 08:34:39 CDT)
  - Re: FFTK Bond optimization Chitrak Gupta (Tue Sep 22 2015 - 18:06:30 CDT)
Out of memory when loading 700 MB trajectory file Lee-Ping Wang (Fri Sep 11 2015 - 04:35:12 CDT)
- Re: Out of memory when loading 700 MB trajectory file Benjamin Kaduk (Fri Sep 11 2015 - 11:59:13 CDT)
- Re: Out of memory when loading 700 MB trajectory file John Stone (Fri Sep 11 2015 - 11:35:35 CDT)
psfgen error: FAILED TO RECOGNIZE LONEPAIR Monika Madhavi (Fri Sep 11 2015 - 00:48:51 CDT)
Fwd: Inviting applications for a new PhD program in Quantitative Biosciences at Georgia Tech JC Gumbart (Wed Sep 09 2015 - 18:15:34 CDT)
- Re: Fwd: Inviting applications for a new PhD program in Quantitative Biosciences at Georgia Tech Sourav Ray (Wed Sep 09 2015 - 22:51:54 CDT)
How to display frames title ? Ã‰ric Germaneau (Wed Sep 09 2015 - 16:43:44 CDT)
- Re: How to display frames title ? John Stone (Thu Sep 10 2015 - 15:26:33 CDT)
  - Re: How to display frames title ? Ã‰ric Germaneau (Fri Sep 11 2015 - 01:09:13 CDT)
    - Re: How to display frames title ? John Stone (Fri Sep 11 2015 - 01:17:55 CDT)
    - VMD in hubzero Thomas C Bishop (Mon Sep 14 2015 - 15:40:26 CDT)
Please vote for VMD in HPCWire Reader's Choice Awards.... John Stone (Wed Sep 09 2015 - 14:03:32 CDT)
fftk charge validation fvlieffe (Wed Sep 09 2015 - 04:58:59 CDT)
- Re: fftk charge validation Mayne, Christopher G (Wed Sep 09 2015 - 09:42:24 CDT)
FFTK water interaction Chitrak Gupta (Tue Sep 08 2015 - 10:54:19 CDT)
- Re: FFTK water interaction Mayne, Christopher G (Tue Sep 08 2015 - 12:48:50 CDT)
  - Re: FFTK water interaction Chitrak Gupta (Tue Sep 08 2015 - 14:57:55 CDT)
unable to view .pdb file Raag Saluja (Tue Sep 08 2015 - 08:16:51 CDT)
- Re: unable to view .pdb file John Stone (Tue Sep 08 2015 - 09:51:27 CDT)
  - Re: unable to view .pdb file Raag Saluja (Tue Sep 08 2015 - 10:02:17 CDT)
    - Re: unable to view .pdb file John Stone (Tue Sep 08 2015 - 10:17:49 CDT)
- Re: unable to view .pdb file Akshay Bhatnagar (Tue Sep 08 2015 - 11:17:14 CDT)
Selecting atoms in the RMSD tool Dimitrova, Maria (Thu Sep 03 2015 - 07:34:49 CDT)
Rendering options Eric Smoll (Wed Sep 02 2015 - 15:17:11 CDT)
- Re: Rendering options John Stone (Wed Sep 02 2015 - 15:29:12 CDT)
FFTK initial par file is empty Chitrak Gupta (Wed Sep 02 2015 - 11:05:47 CDT)
- Re: FFTK initial par file is empty Mayne, Christopher G (Wed Sep 02 2015 - 13:37:26 CDT)
  - Re: FFTK initial par file is empty Chitrak Gupta (Wed Sep 02 2015 - 14:59:12 CDT)
    - Re: FFTK initial par file is empty Mayne, Christopher G (Wed Sep 02 2015 - 15:29:28 CDT)
  - Re: FFTK initial par file is empty Mayne, Christopher G (Thu Sep 03 2015 - 11:20:42 CDT)
    - Re: FFTK initial par file is empty Chitrak Gupta (Thu Sep 03 2015 - 19:56:00 CDT)
    - Re: FFTK initial par file is empty Mayne, Christopher G (Thu Sep 03 2015 - 20:07:03 CDT)
ILS on GPU Cluster - Exceeded MAX_BINOFFSETS for CUDA kernel Simon DÃ¼rr (Wed Sep 02 2015 - 09:42:03 CDT)
- Re: ILS on GPU Cluster - Exceeded MAX_BINOFFSETS for CUDA kernel John Stone (Wed Sep 02 2015 - 10:03:38 CDT)
  - Re: ILS on GPU Cluster - Exceeded MAX_BINOFFSETS for CUDA kernel Simon DÃ¼rr (Fri Sep 11 2015 - 09:15:12 CDT)
    - Re: ILS on GPU Cluster - Exceeded MAX_BINOFFSETS for CUDA kernel John Stone (Fri Sep 11 2015 - 11:19:34 CDT)
APPCRASH when loading a big trajectory file (.dcd) into VMD Ern Seang Ong (Tue Sep 01 2015 - 17:49:45 CDT)
- Re: APPCRASH when loading a big trajectory file (.dcd) into VMD Axel Kohlmeyer (Tue Sep 01 2015 - 20:18:06 CDT)
- RE: APPCRASH when loading a big trajectory file (.dcd) into VMD James Kress (Tue Sep 01 2015 - 21:35:54 CDT)
Calculating distances from command line VMD 1.9.2 debra ragland (Tue Sep 01 2015 - 08:08:11 CDT)
Distances from the command line VMD 1.9.2 debra ragland (Tue Sep 01 2015 - 07:49:25 CDT)
- Re: Distances from the command line VMD 1.9.2 Josh Vermaas (Tue Sep 01 2015 - 09:05:18 CDT)
How to close the box of situs electron density map? sunyeping (Mon Aug 31 2015 - 22:18:55 CDT)
- Re: How to close the box of situs electron density map? John Stone (Wed Sep 02 2015 - 11:01:39 CDT)
  - Re: How to close the box of situs electron density map? sunyeping (Sun Sep 06 2015 - 03:36:54 CDT)
Set "center" in script Eric Smoll (Sat Aug 29 2015 - 01:10:04 CDT)
- Re: Set "center" in script Tim Lo (Sat Aug 29 2015 - 01:58:43 CDT)
How to set a common camera state Eric Smoll (Fri Aug 28 2015 - 23:15:22 CDT)
- Re: How to set a common camera state John Stone (Sat Aug 29 2015 - 08:47:09 CDT)
salt bridge cutoff distance LW (Fri Aug 28 2015 - 04:30:00 CDT)
- Re: salt bridge cutoff distance John Stone (Wed Sep 02 2015 - 13:55:30 CDT)
  - Re: salt bridge cutoff distance LW (Wed Sep 02 2015 - 17:27:07 CDT)
why mdff griddx command cannot generate .dx file sunyeping (Fri Aug 28 2015 - 03:46:48 CDT)
NAMD energy Shubhadip Das (Thu Aug 27 2015 - 09:15:34 CDT)
1.9.3 Version Christian Wohlschlager (Thu Aug 27 2015 - 08:22:51 CDT)
- Re: 1.9.3 Version John Stone (Fri Aug 28 2015 - 01:23:04 CDT)
Calculate torsional angle with big_dcd adding a boolean control for pyrimidines and purines selection Mahad Gatti (Wed Aug 26 2015 - 05:41:09 CDT)
- Re: Calculate torsional angle with big_dcd adding a boolean control for pyrimidines and purines selection Josh Vermaas (Wed Aug 26 2015 - 08:04:56 CDT)
  - Re: Calculate torsional angle with big_dcd adding a boolean control for pyrimidines and purines selection Josh Vermaas (Wed Aug 26 2015 - 09:09:01 CDT)
Interactive Optix ray tracing on multiple GPUs? Anders Gabrielsson (Tue Aug 25 2015 - 09:08:04 CDT)
- Re: Interactive Optix ray tracing on multiple GPUs? Anders Gabrielsson (Wed Aug 26 2015 - 10:19:26 CDT)
  - Re: Interactive Optix ray tracing on multiple GPUs? John Stone (Wed Aug 26 2015 - 10:37:03 CDT)
VMD cannot display electron density map å™ä¸šå¹³ (Sun Aug 23 2015 - 13:11:01 CDT)
- Re: VMD cannot display electron density map Tristan Croll (Tue Aug 25 2015 - 03:53:07 CDT)
embedding proteins in membrane: child killed: segmentation violation Atila Petrosian (Sun Aug 23 2015 - 09:59:08 CDT)
- Re: embedding proteins in membrane: child killed: segmentation violation John Stone (Fri Aug 28 2015 - 01:33:32 CDT)
Bader Charge Analysis Ozan Dernek (Fri Aug 21 2015 - 10:05:18 CDT)
- Re: Bader Charge Analysis Axel Kohlmeyer (Fri Aug 21 2015 - 12:05:44 CDT)
removing bonds across periodic boundary in a video Charlesworth, Henry (Thu Aug 20 2015 - 12:44:22 CDT)
- Re: removing bonds across periodic boundary in a video Axel Kohlmeyer (Thu Aug 20 2015 - 14:38:26 CDT)
- Re: removing bonds across periodic boundary in a video Charlesworth, Henry (Fri Aug 21 2015 - 07:49:27 CDT)
ffTK and geometry optimization level Francesco Pietra (Thu Aug 20 2015 - 10:13:52 CDT)
- Re: ffTK and geometry optimization level Mayne, Christopher G (Thu Aug 20 2015 - 12:23:09 CDT)
  - Re: ffTK and geometry optimization level Francesco Pietra (Thu Aug 20 2015 - 12:50:55 CDT)
Namd Plot Plugin Daniela Rivas (Thu Aug 20 2015 - 08:54:58 CDT)
- Re: Namd Plot Plugin Ajasja LjubetiÄ (Thu Aug 20 2015 - 10:37:12 CDT)
  - RE: Namd Plot Plugin Richard Wood (Thu Aug 20 2015 - 12:35:54 CDT)
    - Re: Namd Plot Plugin Dani (Thu Aug 20 2015 - 13:26:33 CDT)
    - Re: Namd Plot Plugin Dani (Thu Aug 20 2015 - 13:27:57 CDT)
Python.h error when compile VMD-1.9.2 sunyeping (Tue Aug 18 2015 - 21:26:54 CDT)
- Re: Python.h error when compile VMD-1.9.2 Josh Vermaas (Wed Aug 19 2015 - 09:29:31 CDT)
How to extract data from NAMD log file for viscosity calculation Ern Seang Ong (Tue Aug 18 2015 - 20:38:57 CDT)
- Re: How to extract data from NAMD log file for viscosity calculation Ashar Malik (Tue Aug 18 2015 - 22:44:28 CDT)
- Re: How to extract data from NAMD log file for viscosity calculation Pawel Kedzierski (Wed Aug 19 2015 - 09:23:22 CDT)
Plot of distance between two atoms vs frame number Stojanoski, Vlatko (Tue Aug 18 2015 - 12:35:48 CDT)
- RE: Plot of distance between two atoms vs frame number Bennion, Brian (Tue Aug 18 2015 - 14:24:08 CDT)
  - Re: Plot of distance between two atoms vs frame number Stojanoski, Vlatko (Tue Aug 18 2015 - 15:21:10 CDT)
- Re: Plot of distance between two atoms vs frame number Prof. Eddie (Tue Aug 18 2015 - 15:26:01 CDT)
(no subject) Ozan Dernek (Tue Aug 18 2015 - 09:31:29 CDT)
- Re: John Stone (Tue Aug 18 2015 - 10:09:40 CDT)
  - Re: Ozan Dernek (Wed Aug 19 2015 - 03:40:08 CDT)
    - Re: John Stone (Wed Aug 19 2015 - 14:39:00 CDT)
Hydrogen bonds plugin for liquid water Gupta, S.S. (Somil) (Tue Aug 18 2015 - 04:34:10 CDT)
paratool Prof. Eddie (Mon Aug 17 2015 - 14:52:20 CDT)
- Re: paratool John Stone (Mon Aug 17 2015 - 23:09:35 CDT)
ffTK problems with Gaussian OPT Francesco Pietra (Sun Aug 16 2015 - 05:43:43 CDT)
- Fwd: ffTK problems with Gaussian OPT Francesco Pietra (Sun Aug 16 2015 - 05:54:24 CDT)
  - Re: Fwd: ffTK problems with Gaussian OPT Mayne, Christopher G (Mon Aug 17 2015 - 14:31:52 CDT)
nvidia cuda mismatch andrea spitaleri (Thu Aug 13 2015 - 10:58:39 CDT)
- Re: nvidia cuda mismatch Josh Vermaas (Thu Aug 13 2015 - 15:27:55 CDT)
  - Re: nvidia cuda mismatch John Stone (Thu Aug 13 2015 - 16:38:06 CDT)
  - Re: nvidia cuda mismatch Andrea Spitaleri (Tue Aug 18 2015 - 04:10:24 CDT)
- RE: nvidia cuda mismatch James Kress (Sat Aug 15 2015 - 15:31:11 CDT)
vmd freezes for certain files on MacOs 10.10.4 Beat Meier (Thu Aug 13 2015 - 02:17:10 CDT)
- Re: vmd freezes for certain files on MacOs 10.10.4 John Stone (Mon Aug 17 2015 - 09:48:46 CDT)
RE: Delete redundant bonds in water molecule Xiaohui She (Wed Aug 12 2015 - 14:25:05 CDT)
Delete redundant bonds in water molecule Xiaohui She (Wed Aug 12 2015 - 11:32:31 CDT)
- Re: Delete redundant bonds in water molecule Axel Kohlmeyer (Wed Aug 12 2015 - 18:27:41 CDT)
Problem with NAMD, fftk and Windows 7 64bits ABEL Stephane 175950 (Wed Aug 12 2015 - 08:17:26 CDT)
rlwrap/ffTK issues with vmd 1.9.2 Francesco Pietra (Wed Aug 12 2015 - 02:49:01 CDT)
- Re: rlwrap/ffTK issues with vmd 1.9.2 Josh Vermaas (Wed Aug 12 2015 - 08:54:41 CDT)
why vmd cannot load situs type file in MDFF? sunyeping (Tue Aug 11 2015 - 10:19:53 CDT)
- Re: why vmd cannot load situs type file in MDFF? Josh Vermaas (Wed Aug 12 2015 - 08:56:53 CDT)
  - Re: why vmd cannot load situs type file in MDFF? Ryan McGreevy (Wed Aug 12 2015 - 10:28:57 CDT)
Merging two structures with duplicate segment names using TCL/Tk Console Ash Johnson (Mon Aug 10 2015 - 19:29:31 CDT)
- Re: Merging two structures with duplicate segment names using TCL/Tk Console Josh Vermaas (Tue Aug 11 2015 - 09:48:47 CDT)
  - RE: Merging two structures with duplicate segment names using TCL/Tk Console Ash Johnson (Thu Aug 13 2015 - 04:29:19 CDT)
Resuming changes in MOLEFACTURE Francesco Pietra (Mon Aug 10 2015 - 12:25:43 CDT)
- Re: Resuming changes in MOLEFACTURE Francesco Pietra (Tue Aug 11 2015 - 03:54:19 CDT)
writing initial coordinates in Amber format Neelanjana Sengupta (Sat Aug 08 2015 - 01:40:04 CDT)
- Re: writing initial coordinates in Amber format Diego Vazquez (Sun Aug 09 2015 - 00:59:17 CDT)
ACS COMP division travel awards John Stone (Fri Aug 07 2015 - 11:35:14 CDT)
Installing VMD on MACOSX 10.10.4 Yosemite Abhishek Bagusetty (Fri Aug 07 2015 - 09:36:19 CDT)
- Re: Installing VMD on MACOSX 10.10.4 Yosemite John Stone (Fri Aug 07 2015 - 21:00:11 CDT)
  - Re: Installing VMD on MACOSX 10.10.4 Yosemite Abhishek Bagusetty (Fri Aug 07 2015 - 21:21:56 CDT)
About mdffi cc Kevin C Chan (Thu Aug 06 2015 - 01:12:27 CDT)
- Re: About mdffi cc Ryan McGreevy (Thu Aug 06 2015 - 16:22:17 CDT)
  - Re: About mdffi cc John Stone (Thu Aug 06 2015 - 16:29:32 CDT)
3dconnexion spacemouse pro and vmd on fedora 21 Bennion, Brian (Wed Aug 05 2015 - 15:02:54 CDT)
- Re: 3dconnexion spacemouse pro and vmd on fedora 21 John Stone (Thu Aug 06 2015 - 00:32:59 CDT)
  - RE: 3dconnexion spacemouse pro and vmd on fedora 21 Bennion, Brian (Thu Aug 06 2015 - 11:36:17 CDT)
Tilting helix in VMD Jessica Sarver (Wed Aug 05 2015 - 14:11:16 CDT)
.mdcrd to .trr conversion problem Vishal Nemaysh (Wed Aug 05 2015 - 02:00:59 CDT)
- Re: .mdcrd to .trr conversion problem Ajasja LjubetiÄ (Wed Aug 05 2015 - 03:35:46 CDT)
- RE: .mdcrd to .trr conversion problem Norman Geist (Wed Aug 05 2015 - 05:12:02 CDT)
VMD movie error Kshatresh Dutta Dubey (Tue Aug 04 2015 - 17:00:51 CDT)
- RE: VMD movie error Norman Geist (Wed Aug 05 2015 - 00:12:33 CDT)
VMD Composite Extension/swrast Error on Centos 6.6 Joseph Baker (Mon Aug 03 2015 - 16:31:41 CDT)
- Re: VMD Composite Extension/swrast Error on Centos 6.6 John Stone (Fri Aug 07 2015 - 21:02:56 CDT)
Exporting Average Structure to .pdb file Kuiper, Ben (Mon Aug 03 2015 - 12:24:08 CDT)
- Re: Exporting Average Structure to .pdb file Josh Vermaas (Mon Aug 03 2015 - 13:09:50 CDT)
Hydrogen bond angle debra ragland (Mon Aug 03 2015 - 11:58:16 CDT)
- RE: Hydrogen bond angle Norman Geist (Tue Aug 04 2015 - 01:29:48 CDT)
Get XST or XSC from NAMDenergy plugin? Aryan Vahedi-Faridi (Sun Aug 02 2015 - 19:30:52 CDT)
setting the view in VMD Jeeno Jose (Sat Aug 01 2015 - 13:23:35 CDT)
- Re: setting the view in VMD Axel Kohlmeyer (Sat Aug 01 2015 - 13:56:30 CDT)
  - Re: setting the view in VMD Jeeno Jose (Sat Aug 01 2015 - 14:39:07 CDT)
Script for recursive file execution debra ragland (Fri Jul 31 2015 - 11:48:10 CDT)
Selective coloring question JeJoon Yeon (Thu Jul 30 2015 - 19:36:27 CDT)
Using Automatic PSF Builder for Novel Residues Brianna McIntosh (Thu Jul 30 2015 - 17:32:56 CDT)
pbc join bondlist Jacob Gissinger (Thu Jul 30 2015 - 16:01:23 CDT)
Unwrap issue, Completely Different Chart Than Expected, Trajectory Compromised Aryan Vahedi-Faridi (Thu Jul 30 2015 - 15:04:12 CDT)
Question regarding selection of atoms JeJoon Yeon (Wed Jul 29 2015 - 09:21:41 CDT)
VMD camera feature request: zoom and tilt Charles McAnany (Mon Jul 27 2015 - 11:59:29 CDT)
- Re: VMD camera feature request: zoom and tilt John Stone (Tue Jul 28 2015 - 12:53:43 CDT)
  - Re: VMD camera feature request: zoom and tilt Charles McAnany (Wed Jul 29 2015 - 12:04:59 CDT)
Re: 64 bit windows VMD Hart, David Blaine (Mon Jul 27 2015 - 11:16:11 CDT)
- Re: 64 bit windows VMD Ajasja LjubetiÄ (Mon Jul 27 2015 - 15:22:07 CDT)
  - Re: 64 bit windows VMD John Stone (Tue Jul 28 2015 - 11:36:22 CDT)
SC'15 Sci viz showcase deadline extension John Stone (Mon Jul 27 2015 - 10:59:14 CDT)
64 bit windows VMD Sam Wallace (Mon Jul 27 2015 - 03:06:40 CDT)
measure contact between com Kevin Chan (Mon Jul 27 2015 - 01:16:45 CDT)
- Re: measure contact between com John Stone (Tue Jul 28 2015 - 23:22:34 CDT)
  - Re: measure contact between com Kevin C Chan (Wed Jul 29 2015 - 23:05:58 CDT)
  - Re: measure contact between com Kevin Chan (Thu Jul 30 2015 - 20:47:09 CDT)
Question about visualization of multiple frame xyz file JeJoon Yeon (Sun Jul 26 2015 - 22:17:10 CDT)
- Re: Question about visualization of multiple frame xyz file Axel Kohlmeyer (Sun Jul 26 2015 - 23:05:42 CDT)
  - Re: Question about visualization of multiple frame xyz file JeJoon Yeon (Mon Jul 27 2015 - 12:16:13 CDT)
    - Re: Question about visualization of multiple frame xyz file Axel Kohlmeyer (Mon Jul 27 2015 - 12:31:11 CDT)
VMD - cannot download James Kress (Sun Jul 26 2015 - 17:40:50 CDT)
- RE: VMD - cannot download James Kress (Sun Jul 26 2015 - 20:31:16 CDT)
Unit cell for clay material Evgeniya Volkova (Sat Jul 25 2015 - 15:55:00 CDT)
- Re: Unit cell for clay material Axel Kohlmeyer (Sat Jul 25 2015 - 17:12:56 CDT)
Questions about the optimization of a molecule with fftk ABEL Stephane 175950 (Fri Jul 24 2015 - 08:31:54 CDT)
- Re: Questions about the optimization of a molecule with fftk Mayne, Christopher G (Fri Jul 24 2015 - 09:34:38 CDT)
Generating PSF for several proteins in one shot Akshay Bhatnagar (Tue Jul 21 2015 - 02:04:36 CDT)
- Re: Generating PSF for several proteins in one shot Ashar Malik (Tue Jul 21 2015 - 02:33:02 CDT)
  - Re: Generating PSF for several proteins in one shot Josh Vermaas (Tue Jul 21 2015 - 13:44:49 CDT)
[jfavre@cscs.ch: SC'15 Scientific Visualization Showcase] John Stone (Mon Jul 20 2015 - 15:35:53 CDT)
tcl plugins Melvyn Drag (Sat Jul 18 2015 - 20:20:22 CDT)
BUG REPORT: Malfunctioning of VMD with Yosemite/ Follow up Yasaman Ghadarghadr (Wed Jul 15 2015 - 14:14:31 CDT)
- Re: BUG REPORT: Malfunctioning of VMD with Yosemite/ Follow up John Stone (Thu Jul 16 2015 - 09:57:33 CDT)
  - Re: BUG REPORT: Malfunctioning of VMD with Yosemite/ Follow up Yasaman Ghadarghadr (Thu Jul 16 2015 - 13:08:30 CDT)
    - Re: BUG REPORT: Malfunctioning of VMD with Yosemite/ Follow up Tianhua Feng (Fri Jul 17 2015 - 16:45:38 CDT)
Modify XYZ reader plugin Christian Leitold (Tue Jul 14 2015 - 11:07:07 CDT)
- Re: Modify XYZ reader plugin Axel Kohlmeyer (Tue Jul 14 2015 - 11:21:27 CDT)
  - Re: Modify XYZ reader plugin Christian Leitold (Tue Jul 14 2015 - 11:25:17 CDT)
fftk autoDetect indices and fvlieffe (Tue Jul 14 2015 - 07:13:10 CDT)
- Re: fftk autoDetect indices and Evandro Semighini (Tue Jul 14 2015 - 07:30:44 CDT)
- Re: fftk autoDetect indices and Mayne, Christopher G (Tue Jul 14 2015 - 09:25:07 CDT)
cvs Christian Wohlschlager (Mon Jul 13 2015 - 02:08:53 CDT)
- Re: cvs Axel Kohlmeyer (Mon Jul 13 2015 - 03:06:18 CDT)
- Re: cvs John Stone (Mon Jul 13 2015 - 09:43:24 CDT)
  - Antw: Re: cvs Christian Wohlschlager (Tue Jul 14 2015 - 01:02:05 CDT)
Choosing an appropriate isovalue for comparing different systems DEBOSTUTI GHOSHDASTIDAR (Sun Jul 12 2015 - 10:37:35 CDT)
- Re: Choosing an appropriate isovalue for comparing different systems John Stone (Tue Jul 14 2015 - 10:14:12 CDT)
recovery -e file name w/in vmd Thomas C. Bishop (Fri Jul 10 2015 - 16:05:26 CDT)
Problem using BigDCD to wrap, unwrap and animate a long MD trajectory KK R (Fri Jul 10 2015 - 14:51:23 CDT)
Re: Welcome to vmd-l Kyle Mills (Fri Jul 10 2015 - 13:08:48 CDT)
- Re: Re: Welcome to vmd-l Josh Vermaas (Fri Jul 10 2015 - 14:09:21 CDT)
Finding RMSD of atoms Mehdi Bagherpour (Fri Jul 10 2015 - 12:41:25 CDT)
- Re: Finding RMSD of atoms Josh Vermaas (Fri Jul 10 2015 - 14:23:56 CDT)
Finding RMSD of atoms Mehdi Bagherpour (Fri Jul 10 2015 - 11:49:16 CDT)
Multiseq display settings Felipe Montecinos (Fri Jul 10 2015 - 11:28:23 CDT)
- RE: Multiseq display settings Lai, Jonathan (Fri Jul 10 2015 - 12:57:10 CDT)
  - Re: Multiseq display settings Felipe Montecinos (Fri Jul 10 2015 - 13:16:57 CDT)
    - Re: Multiseq display settings Felipe Montecinos (Mon May 02 2016 - 09:49:21 CDT)
Primary structure, Jinasena Hewage (Fri Jul 10 2015 - 10:45:06 CDT)
- Re: Primary structure, Ashar Malik (Fri Jul 10 2015 - 11:21:09 CDT)
- RE: Primary structure, Lai, Jonathan (Fri Jul 10 2015 - 11:39:26 CDT)
  - Re: Primary structure, Jinasena Hewage (Fri Jul 10 2015 - 12:53:45 CDT)
a question regarding the signalproc package Ana Celia Vila Verde (Thu Jul 09 2015 - 10:34:08 CDT)
- Re: a question regarding the signalproc package John Stone (Tue Jul 14 2015 - 10:20:04 CDT)
  - Re: a question regarding the signalproc package Axel Kohlmeyer (Tue Jul 14 2015 - 11:45:56 CDT)
script rotation of system with graphics Eric Smoll (Wed Jul 08 2015 - 19:17:50 CDT)
- Re: script rotation of system with graphics Josh Vermaas (Thu Jul 09 2015 - 02:41:30 CDT)
Using BigDCD to wrap, unwrap and animate a long MD trajectory KK R (Wed Jul 08 2015 - 12:52:47 CDT)
- Re: Using BigDCD to wrap, unwrap and animate a long MD trajectory John Stone (Tue Jul 14 2015 - 10:26:04 CDT)
  - Re: Using BigDCD to wrap, unwrap and animate a long MD trajectory KK R (Wed Jul 15 2015 - 11:30:02 CDT)
write psf is generating an error Life Sciences Inc (Wed Jul 08 2015 - 11:59:30 CDT)
- Re: write psf is generating an error John Stone (Tue Jul 14 2015 - 10:23:36 CDT)
  - Re: write psf is generating an error Life Sciences Inc (Tue Jul 14 2015 - 10:27:48 CDT)
  - Re: write psf is generating an error Axel Kohlmeyer (Tue Jul 14 2015 - 11:09:18 CDT)
Text size in the VMD at high-resolutions Miroslav Krepl (Wed Jul 08 2015 - 11:14:36 CDT)
- Re: Text size in the VMD at high-resolutions John Stone (Thu Jul 09 2015 - 23:20:13 CDT)
  - Re: Text size in the VMD at high-resolutions Miroslav Krepl (Fri Jul 10 2015 - 16:29:49 CDT)
creating psf file Mai Aamer (Tue Jul 07 2015 - 16:10:29 CDT)
- Re: creating psf file John Stone (Tue Jul 14 2015 - 10:57:08 CDT)
VMD 1.9.1 and OS X 10.10 - display freezes Sampath, Janani (Tue Jul 07 2015 - 13:38:55 CDT)
- Re: VMD 1.9.1 and OS X 10.10 - display freezes zhenxing wang (Wed Jul 08 2015 - 11:04:46 CDT)
Volume accessed by a molecule during the MD simulation mish (Tue Jul 07 2015 - 12:12:29 CDT)
- Re: Volume accessed by a molecule during the MD simulation John Stone (Tue Jul 14 2015 - 10:56:12 CDT)
TachyonLOptiXInternal antialiasing Parker de Waal (Mon Jul 06 2015 - 22:44:45 CDT)
Sodium within distance Parker de Waal (Mon Jul 06 2015 - 21:56:39 CDT)
- AW: Sodium within distance Daniel Möller (Tue Jul 07 2015 - 03:47:08 CDT)
  - Re: AW: Sodium within distance Thomas C. Bishop (Wed Jul 08 2015 - 09:51:10 CDT)
reading in trajectory file causes VMD to crash Richard Wood (Mon Jul 06 2015 - 19:52:11 CDT)
- Re: reading in trajectory file causes VMD to crash Axel Kohlmeyer (Mon Jul 06 2015 - 20:12:10 CDT)
  - RE: reading in trajectory file causes VMD to crash Richard Wood (Mon Jul 06 2015 - 20:14:20 CDT)
Building Plugins to work with Mac Builds Hart, David Blaine (Mon Jul 06 2015 - 11:56:30 CDT)
- Re: Building Plugins to work with Mac Builds John Stone (Mon Jul 06 2015 - 16:42:34 CDT)
  - Re: Building Plugins to work with Mac Builds Hart, David Blaine (Mon Jul 06 2015 - 17:26:13 CDT)
molecule selection along an axis anu chandra (Mon Jul 06 2015 - 10:18:17 CDT)
- Re: molecule selection along an axis Axel Kohlmeyer (Mon Jul 06 2015 - 11:46:08 CDT)
should commercial user pay for VMD Albert (Mon Jul 06 2015 - 08:48:50 CDT)
- Re: should commercial user pay for VMD John Stone (Mon Jul 06 2015 - 09:39:18 CDT)
  - Re: should commercial user pay for VMD Albert (Mon Jul 06 2015 - 09:45:23 CDT)
Energy based coloring of residues Atreya Dey (Mon Jul 06 2015 - 06:28:54 CDT)
- Re: Energy based coloring of residues John Stone (Mon Jul 06 2015 - 16:46:03 CDT)
HIS Residue Jinasena Hewage (Fri Jul 03 2015 - 14:08:04 CDT)
- Re: HIS Residue zoran (Fri Jul 03 2015 - 14:56:43 CDT)
  - Re: HIS Residue Jinasena Hewage (Fri Jul 03 2015 - 15:03:41 CDT)
pdb and topology files for DNA Mohsen Farshad (Fri Jul 03 2015 - 12:01:54 CDT)
- Re: pdb and topology files for DNA Ashar Malik (Fri Jul 03 2015 - 13:18:23 CDT)
Using bigdcd for an already written script Monika Madhavi (Fri Jul 03 2015 - 05:39:57 CDT)
- RE: Using bigdcd for an already written script Morgan, Brittany (Mon Jul 06 2015 - 07:43:15 CDT)
Error- Periodic cell Jinasena Hewage (Thu Jul 02 2015 - 10:48:18 CDT)
- Re: Error- Periodic cell Ashar Malik (Thu Jul 02 2015 - 11:13:29 CDT)
- Re: Error- Periodic cell Axel Kohlmeyer (Thu Jul 02 2015 - 11:11:06 CDT)
polyhedra / based on atom selection Huinink, H.P. (Thu Jul 02 2015 - 04:31:52 CDT)
Dihedral fiiting - MME - optimum fit Mohan maruthi sena (Wed Jul 01 2015 - 12:39:31 CDT)
VMD users that have Oculus DK2 headsets? John Stone (Wed Jul 01 2015 - 11:06:44 CDT)
VMD and VRPN (7.33) connection - LINUX TUBIANA Thibault CNRS (Mon Jun 29 2015 - 10:09:52 CDT)
VMD MEMBPLUGIN : MEMBRANE THICKNESS Life Sciences Inc (Mon Jun 29 2015 - 04:47:36 CDT)
- Re: VMD MEMBPLUGIN : MEMBRANE THICKNESS Axel Kohlmeyer (Mon Jun 29 2015 - 05:21:13 CDT)
Removing all non polar hydrogens Francesco Pietra (Fri Jun 26 2015 - 12:57:00 CDT)
- Re: Removing all non polar hydrogens Josh Vermaas (Fri Jun 26 2015 - 14:55:56 CDT)
  - Re: Removing all non polar hydrogens Francesco Pietra (Sat Jun 27 2015 - 01:32:59 CDT)
    - Fwd: Removing all non polar hydrogens Francesco Pietra (Sat Jun 27 2015 - 01:46:05 CDT)
    - Re: Fwd: Removing all non polar hydrogens Josh Vermaas (Sat Jun 27 2015 - 19:42:45 CDT)
Re: FFTK charge optimization - COLP Mayne, Christopher G (Fri Jun 26 2015 - 10:51:22 CDT)
PBC tool does not read center from a xsc Kevin C Chan (Thu Jun 25 2015 - 11:42:00 CDT)
- Re: PBC tool does not read center from a xsc Axel Kohlmeyer (Thu Jun 25 2015 - 12:41:36 CDT)
Viewing gromacs .xtc trajectory 'Error reading timestep, file does not match format' Vidyalakshmi CM (Thu Jun 25 2015 - 08:29:13 CDT)
- Re: Viewing gromacs .xtc trajectory 'Error reading timestep, file does not match format' Axel Kohlmeyer (Thu Jun 25 2015 - 08:56:29 CDT)
  - Re: Viewing gromacs .xtc trajectory 'Error reading timestep, file does not match format' Vidyalakshmi CM (Thu Jun 25 2015 - 09:37:36 CDT)
Later protein diffusion through membrane--PBC tools problem Marawan Hussien (Wed Jun 24 2015 - 15:51:57 CDT)
- Re: Later protein diffusion through membrane--PBC tools problem Josh Vermaas (Wed Jun 24 2015 - 16:46:52 CDT)
Drawing extended arrow to show direction vector on VMD Bharat Sharma (Tue Jun 23 2015 - 11:45:18 CDT)
- Re: Drawing extended arrow to show direction vector on VMD Axel Kohlmeyer (Tue Jun 23 2015 - 12:12:10 CDT)
- Re: Drawing extended arrow to show direction vector on VMD Josh Vermaas (Tue Jun 23 2015 - 12:34:31 CDT)
  - Re: Drawing extended arrow to show direction vector on VMD Bharat Sharma (Tue Jun 23 2015 - 13:41:25 CDT)
    - Re: Drawing extended arrow to show direction vector on VMD Axel Kohlmeyer (Tue Jun 23 2015 - 13:51:34 CDT)
Problem with topotools for residue >10k Kin Leung CHU (Tue Jun 23 2015 - 05:16:53 CDT)
- Re: Problem with topotools for residue >10k Axel Kohlmeyer (Tue Jun 23 2015 - 06:43:51 CDT)
Colouring atoms according to their q4 or q6 values Kannan Ridings (Tue Jun 23 2015 - 01:12:31 CDT)
- Re: Colouring atoms according to their q4 or q6 values Axel Kohlmeyer (Tue Jun 23 2015 - 06:53:10 CDT)
pbc tools Jacob Gissinger (Mon Jun 22 2015 - 11:20:28 CDT)
Re: PBC unwrap a membrane Kevin C Chan (Sun Jun 21 2015 - 03:55:15 CDT)
PBC unwrap a membrane Kevin C Chan (Sun Jun 21 2015 - 02:56:21 CDT)
Visualizing and counting broken bonds in VMD Mercer, Brian S. (Fri Jun 19 2015 - 13:43:41 CDT)
- Re: Visualizing and counting broken bonds in VMD Josh Vermaas (Fri Jun 19 2015 - 14:55:13 CDT)
  - RE: Visualizing and counting broken bonds in VMD Mercer, Brian S. (Fri Jun 19 2015 - 15:53:28 CDT)
  - Re: Visualizing and counting broken bonds in VMD Axel Kohlmeyer (Fri Jun 19 2015 - 16:11:54 CDT)
    - RE: Visualizing and counting broken bonds in VMD Mercer, Brian S. (Mon Jun 22 2015 - 10:14:28 CDT)
- Re: Visualizing and counting broken bonds in VMD Axel Kohlmeyer (Fri Jun 19 2015 - 16:03:03 CDT)
PME Electrostatics Error Rohit Goswami (Fri Jun 19 2015 - 05:36:35 CDT)
- Re: PME Electrostatics Error John Stone (Fri Jun 19 2015 - 08:42:11 CDT)
  - Re: PME Electrostatics Error Rohit Goswami (Fri Jun 19 2015 - 09:08:50 CDT)
how to create psf of cyclodextrin in vmd sadia tanweer (Fri Jun 19 2015 - 03:19:01 CDT)
Getting VMD to talk to VRPN on Windows 7 Sean Seyler (Thu Jun 18 2015 - 16:48:48 CDT)
- Re: Getting VMD to talk to VRPN on Windows 7 John Stone (Fri Jun 19 2015 - 08:45:38 CDT)
  - Re: Getting VMD to talk to VRPN on Windows 7 Sean Seyler (Wed Jul 29 2015 - 18:23:35 CDT)
differentiate between nitroso and oxime atomselections Bennion, Brian (Wed Jun 17 2015 - 18:55:27 CDT)
- Re: differentiate between nitroso and oxime atomselections Axel Kohlmeyer (Wed Jun 17 2015 - 19:34:09 CDT)
  - RE: differentiate between nitroso and oxime atomselections Bennion, Brian (Thu Jun 18 2015 - 11:03:48 CDT)
Query on GPI-anchor proteins Aditya Padhi (Tue Jun 16 2015 - 14:03:15 CDT)
Second Announcement: â€˜Hands Onâ€™ Workshop on Computational Biophysics (Berkeley, CA, Aug 3-7, 2015) Lela Vukovic (Tue Jun 16 2015 - 12:04:27 CDT)
minimum value of index numbers Mehdi Bagherpour (Tue Jun 16 2015 - 11:01:18 CDT)
- Re: minimum value of index numbers Axel Kohlmeyer (Tue Jun 16 2015 - 13:08:04 CDT)
- RE: minimum value of index numbers Joaquim Rui de Castro Rodrigues (Tue Jun 16 2015 - 12:56:15 CDT)
Load trajectory file in .sim format Daniela Rivas (Tue Jun 16 2015 - 09:02:13 CDT)
- Re: Load trajectory file in .sim format Axel Kohlmeyer (Tue Jun 16 2015 - 09:38:18 CDT)
  - Re: Load trajectory file in .sim format Daniela Rivas (Tue Jun 16 2015 - 09:46:19 CDT)
Merging multiple PDB files BALCZIAK, LOUIS (Mon Jun 15 2015 - 13:24:49 CDT)
- Re: Merging multiple PDB files Axel Kohlmeyer (Mon Jun 15 2015 - 14:49:29 CDT)
- Re: Merging multiple PDB files Josh Vermaas (Mon Jun 15 2015 - 15:03:16 CDT)
Generating psf for uranyl ion Sakinah Ellickson (Mon Jun 15 2015 - 10:55:08 CDT)
- Re: Generating psf for uranyl ion Axel Kohlmeyer (Mon Jun 15 2015 - 11:10:14 CDT)
- Re: Generating psf for uranyl ion Josh Vermaas (Mon Jun 15 2015 - 11:28:14 CDT)
annoying bug in 1.9.2 Maxim Paliy (Mon Jun 15 2015 - 07:43:35 CDT)
- Re: annoying bug in 1.9.2 Axel Kohlmeyer (Mon Jun 15 2015 - 08:07:38 CDT)
NetCDF type is missing Alessandro Mariani (Mon Jun 15 2015 - 07:31:59 CDT)
- Re: NetCDF type is missing Axel Kohlmeyer (Mon Jun 15 2015 - 07:58:46 CDT)
Announcement: Workshop on Simulation Based Drug Discovery (San Diego, CA, Sept 21-25, 2015) Lela Vukovic (Fri Jun 12 2015 - 21:06:22 CDT)
Water molecules Jinasena Hewage (Fri Jun 12 2015 - 15:51:20 CDT)
- Re: Water molecules Axel Kohlmeyer (Fri Jun 12 2015 - 17:16:42 CDT)
  - Re: Water molecules Jinasena Hewage (Sat Jun 13 2015 - 16:11:14 CDT)
Re: namd-l: FFTK - error Mayne, Christopher G (Fri Jun 12 2015 - 11:52:09 CDT)
- Re: namd-l: FFTK - error Mohan maruthi sena (Fri Jun 12 2015 - 23:21:09 CDT)
- Re: namd-l: FFTK - error Mayne, Christopher G (Mon Jun 15 2015 - 10:17:01 CDT)
Forcing FFTK to treat aminos as planar Aaron Larsen (Fri Jun 12 2015 - 08:03:25 CDT)
- Re: Forcing FFTK to treat aminos as planar Mayne, Christopher G (Fri Jun 12 2015 - 10:18:00 CDT)
  - Re: Forcing FFTK to treat aminos as planar Aaron Larsen (Thu Jun 18 2015 - 14:27:55 CDT)
    - Re: Forcing FFTK to treat aminos as planar Mayne, Christopher G (Thu Jun 18 2015 - 14:37:31 CDT)
    - Re: Forcing FFTK to treat aminos as planar Aaron Larsen (Thu Jun 18 2015 - 14:57:16 CDT)
Per Residue Interaction Energy from Desmond MD simulations Daniel Moore (Fri Jun 12 2015 - 04:54:02 CDT)
- Re: Per Residue Interaction Energy from Desmond MD simulations Axel Kohlmeyer (Fri Jun 12 2015 - 05:57:23 CDT)
vmd error xMDFF CPMAS Chen (Thu Jun 11 2015 - 14:34:51 CDT)
- Re: vmd error xMDFF John Stone (Tue Jun 16 2015 - 15:11:49 CDT)
  - Re: vmd error xMDFF CPMAS Chen (Tue Jun 16 2015 - 15:49:26 CDT)
  - Re: vmd error xMDFF CPMAS Chen (Thu Jun 25 2015 - 15:44:09 CDT)
unwap/wrap failure in recomposing splitted system from periodic cells Francesco Pietra (Thu Jun 11 2015 - 12:24:23 CDT)
- Re: unwap/wrap failure in recomposing splitted system from periodic cells Josh Vermaas (Thu Jun 11 2015 - 14:31:39 CDT)
  - Re: unwap/wrap failure in recomposing splitted system from periodic cells Francesco Pietra (Fri Jun 12 2015 - 02:33:33 CDT)
problem with output format Mehdi Bagherpour (Thu Jun 11 2015 - 05:56:18 CDT)
- Re: problem with output format Felipe Merino (Thu Jun 11 2015 - 06:50:13 CDT)
- Re: problem with output format karthik kumar (Thu Jun 11 2015 - 06:46:51 CDT)
finding distance of atoms Mehdi Bagherpour (Wed Jun 10 2015 - 12:12:36 CDT)
- Re: finding distance of atoms Axel Kohlmeyer (Wed Jun 10 2015 - 13:01:03 CDT)
Splitting homotetramer subunits Francesco Pietra (Tue Jun 09 2015 - 06:04:37 CDT)
- Re: Splitting homotetramer subunits Felipe Merino (Tue Jun 09 2015 - 10:10:30 CDT)
  - Re: Splitting homotetramer subunits Francesco Pietra (Wed Jun 10 2015 - 02:24:57 CDT)
    - Re: Splitting homotetramer subunits Felipe Merino (Wed Jun 10 2015 - 02:50:54 CDT)
Dynamic molecular connectivity Eric Smoll (Fri Jun 05 2015 - 22:31:53 CDT)
- Re: Dynamic molecular connectivity Axel Kohlmeyer (Sat Jun 06 2015 - 13:28:17 CDT)
  - Re: Dynamic molecular connectivity Eric Smoll (Sat Jun 06 2015 - 14:55:07 CDT)
    - Re: Dynamic molecular connectivity Axel Kohlmeyer (Sat Jun 06 2015 - 15:51:20 CDT)
H.bond - VMD SaeeD PourasaD (Fri Jun 05 2015 - 01:04:40 CDT)
- Re: H.bond - VMD Axel Kohlmeyer (Fri Jun 05 2015 - 02:04:34 CDT)
  - Re: H.bond - VMD Axel Kohlmeyer (Fri Jun 05 2015 - 08:29:59 CDT)
AW: IR Spectroscopy plugin questions Daniel MÃ¶ller (Thu Jun 04 2015 - 13:51:07 CDT)
AW: IR Spectroscopy plugin questions Daniel MÃ¶ller (Thu Jun 04 2015 - 12:57:00 CDT)
Comparing distance.tcl/bigdcd.tcl with resid/CA vs index Francesco Pietra (Thu Jun 04 2015 - 09:32:47 CDT)
- Re: Comparing distance.tcl/bigdcd.tcl with resid/CA vs index Josh Vermaas (Thu Jun 04 2015 - 10:46:12 CDT)
  - Re: Comparing distance.tcl/bigdcd.tcl with resid/CA vs index Francesco Pietra (Thu Jun 04 2015 - 12:00:24 CDT)
IR Spectroscopy plugin questions Amira Yu (Wed Jun 03 2015 - 17:39:49 CDT)
- Re: IR Spectroscopy plugin questions Josh Vermaas (Wed Jun 03 2015 - 18:33:48 CDT)
  - Re: IR Spectroscopy plugin questions Amira Yu (Wed Jun 03 2015 - 20:42:41 CDT)
    - AW: IR Spectroscopy plugin questions Daniel MÃ¶ller (Thu Jun 04 2015 - 05:35:50 CDT)
PSF file generation lecan (Wed Jun 03 2015 - 15:03:34 CDT)
- Re: PSF file generation John Stone (Thu Jun 04 2015 - 19:18:46 CDT)
bigdcd for distance problems Francesco Pietra (Wed Jun 03 2015 - 12:08:44 CDT)
- Re: bigdcd for distance problems Josh Vermaas (Wed Jun 03 2015 - 14:03:58 CDT)
  - Re: bigdcd for distance problems Francesco Pietra (Wed Jun 03 2015 - 16:04:13 CDT)
playing legos with peptide segments Neelanjana Sengupta (Wed Jun 03 2015 - 10:14:16 CDT)
- Re: playing legos with peptide segments Thomas C. Bishop (Wed Jun 03 2015 - 13:55:43 CDT)
  - Re: playing legos with peptide segments Neelanjana Sengupta (Sun Jun 07 2015 - 15:48:40 CDT)
Questions about outputting an image with specified atom colors Xiaohui She (Tue Jun 02 2015 - 09:34:19 CDT)
- Re: Questions about outputting an image with specified atom colors John Stone (Tue Jun 09 2015 - 16:19:29 CDT)
Failure to run tcl script at the mainframe Francesco Pietra (Sat May 30 2015 - 10:19:32 CDT)
- Re: Failure to run tcl script at the mainframe John Stone (Sat May 30 2015 - 10:41:21 CDT)
  - Re: Failure to run tcl script at the mainframe Francesco Pietra (Sat May 30 2015 - 12:30:29 CDT)
    - Re: Failure to run tcl script at the mainframe John Stone (Sun May 31 2015 - 17:51:52 CDT)
    - Re: Failure to run tcl script at the mainframe Francesco Pietra (Mon Jun 01 2015 - 01:49:30 CDT)
(no subject) Francesco Pietra (Fri May 29 2015 - 09:35:57 CDT)
- RE: Bennion, Brian (Fri May 29 2015 - 10:48:54 CDT)
- Re: Josh Vermaas (Fri May 29 2015 - 10:58:07 CDT)
  - Re: Francesco Pietra (Fri May 29 2015 - 12:30:43 CDT)
Modification of terminal N-amino and C-carboxyl of peptide Sourav Ray (Thu May 28 2015 - 05:13:17 CDT)
- Re: Modification of terminal N-amino and C-carboxyl of peptide Josh Vermaas (Fri May 29 2015 - 10:56:45 CDT)
  - Re: Modification of terminal N-amino and C-carboxyl of peptide Sourav Ray (Fri May 29 2015 - 11:10:47 CDT)
Re: Alpha-RMSD Jevgenij Raskatov (Wed May 27 2015 - 20:25:27 CDT)
- Re: Re: Alpha-RMSD Ashar Malik (Wed May 27 2015 - 21:54:20 CDT)
  - Re: Re: Alpha-RMSD Ashar Malik (Thu May 28 2015 - 17:14:24 CDT)
Re-numbering resID after psfgen Kevin C Chan (Wed May 27 2015 - 00:18:58 CDT)
- Re: Re-numbering resID after psfgen Axel Kohlmeyer (Wed May 27 2015 - 01:05:52 CDT)
  - Re: Re-numbering resID after psfgen Kevin C Chan (Wed May 27 2015 - 04:39:15 CDT)
Density Profile Tool: Is the selection updated as the frame is changed? Shane.OMahony (Tue May 26 2015 - 15:11:09 CDT)
- Re: Density Profile Tool: Is the selection updated as the frame is changed? Axel Kohlmeyer (Wed May 27 2015 - 22:37:02 CDT)
Protein Builder terminus Sourav Ray (Mon May 25 2015 - 02:02:31 CDT)
- Re: Protein Builder terminus Josh Vermaas (Tue May 26 2015 - 11:21:41 CDT)
  - Re: Protein Builder terminus Sourav Ray (Tue May 26 2015 - 11:32:06 CDT)
where can I find the parameter file for chlorophenols? ¶¡êÏ (Sun May 24 2015 - 21:43:04 CDT)
Creating boxes of different water models Monika Madhavi (Sun May 24 2015 - 02:17:21 CDT)
- Re: Creating boxes of different water models Axel Kohlmeyer (Sun May 24 2015 - 04:06:30 CDT)
Error while merging structures Sanghamitra Debroy (Sat May 23 2015 - 04:10:08 CDT)
- Re: Error while merging structures Axel Kohlmeyer (Sun May 24 2015 - 03:58:34 CDT)
  - Re: Error while merging structures Sanghamitra Debroy (Sun May 24 2015 - 07:18:42 CDT)
    - Re: Error while merging structures Axel Kohlmeyer (Sun May 24 2015 - 07:36:55 CDT)
Re: FFTK-optimization error Mayne, Christopher G (Fri May 22 2015 - 10:21:44 CDT)
How to find distance between n-terminal c-alpha and c-terminal c-alpha. Seera Suryanarayana (Wed May 20 2015 - 05:29:47 CDT)
- Re: How to find distance between n-terminal c-alpha and c-terminal c-alpha. Evandro Semighini (Wed May 20 2015 - 08:29:26 CDT)
Orienting molecule along principal axes Sourav Ray (Wed May 20 2015 - 02:00:55 CDT)
- Re: Orienting molecule along principal axes Axel Kohlmeyer (Wed May 20 2015 - 03:39:57 CDT)
  - Re: Orienting molecule along principal axes Sourav Ray (Wed May 20 2015 - 03:59:56 CDT)
How to super impose NMR structures Seera Suryanarayana (Wed May 20 2015 - 01:55:44 CDT)
- Re: How to super impose NMR structures Ajasja LjubetiÄ (Wed May 20 2015 - 02:21:42 CDT)
Announcement: â€˜Hands Onâ€™ Workshop on Computational Biophysics (Berkeley, CA, Aug 3-7, 2015) Lela Vukovic (Wed May 20 2015 - 00:06:46 CDT)
- Re: namd-l: Announcement: 'Hands On' Workshop on Computational Biophysics (Berkeley, CA, Aug 3-7, 2015) Sourav Ray (Wed May 20 2015 - 00:33:00 CDT)
Questions regarding fftk and Gaussian Evandro Semighini (Tue May 19 2015 - 08:06:47 CDT)
- RE: Questions regarding fftk and Gaussian Bennion, Brian (Tue May 19 2015 - 10:51:51 CDT)
  - Re: Questions regarding fftk and Gaussian Evandro Semighini (Tue May 19 2015 - 12:45:53 CDT)
very high vdw and electrostatic energy for bulk urea molecules Subrata Paul (Tue May 19 2015 - 01:04:43 CDT)
How to continue the calculation of NAMD in case of power failure? ¶¡êÏ (Sun May 17 2015 - 20:28:31 CDT)
- Re: How to continue the calculation of NAMD in case of power failure? Ashar Malik (Sun May 17 2015 - 21:13:43 CDT)
- RE: How to continue the calculation of NAMD in case of power failure? Norman Geist (Mon May 18 2015 - 02:56:39 CDT)
Error in NAMD energy plugin of VMD Debashis Kundu (Fri May 15 2015 - 08:40:45 CDT)
- Re: Error in NAMD energy plugin of VMD John Stone (Fri May 15 2015 - 11:24:28 CDT)
Running 64-bit Linux VMD in VMWare VM on Windows 8.1 64-bit Host Machine Justin (Fri May 15 2015 - 04:16:16 CDT)
- Re: Running 64-bit Linux VMD in VMWare VM on Windows 8.1 64-bit Host Machine Matic Kisovec (Fri May 15 2015 - 10:53:33 CDT)
- Re: Running 64-bit Linux VMD in VMWare VM on Windows 8.1 64-bit Host Machine John Stone (Sat May 16 2015 - 13:51:48 CDT)
  - RE: Running 64-bit Linux VMD in VMWare VM on Windows 8.1 64-bit Host Machine Norman Geist (Mon May 18 2015 - 02:47:21 CDT)
How can I swap specific atoms for all frames of xyz file? JeJoon Yeon (Wed May 13 2015 - 12:53:27 CDT)
- Re: How can I swap specific atoms for all frames of xyz file? Maxim Belkin (Wed May 13 2015 - 13:07:04 CDT)
  - Re: How can I swap specific atoms for all frames of xyz file? JeJoon Yeon (Wed May 13 2015 - 13:11:06 CDT)
    - Re: How can I swap specific atoms for all frames of xyz file? Maxim Belkin (Wed May 13 2015 - 13:50:36 CDT)
    - Re: How can I swap specific atoms for all frames of xyz file? JeJoon Yeon (Wed May 13 2015 - 16:11:48 CDT)
  - Re: How can I swap specific atoms for all frames of xyz file? Josh Vermaas (Wed May 13 2015 - 13:44:50 CDT)
Is there currently support for loading large PDBx or PDBML files (e.g. 4YBB)? Lai, Jonathan (Wed May 13 2015 - 11:55:36 CDT)
- Re: Is there currently support for loading large PDBx or PDBML files (e.g. 4YBB)? John Stone (Wed May 13 2015 - 12:06:36 CDT)
Limit to total number of atoms in PSF? Jeeno Jose (Wed May 13 2015 - 01:38:25 CDT)
- Re: Limit to total number of atoms in PSF? John Stone (Wed May 13 2015 - 01:49:00 CDT)
  - Re: Limit to total number of atoms in PSF? Jeeno Jose (Wed May 13 2015 - 03:12:52 CDT)
template script for cavity volume Francesco Pietra (Tue May 12 2015 - 13:06:29 CDT)
Using topotools with no VMD display Michael Doig (Tue May 12 2015 - 07:35:33 CDT)
- Re: Using topotools with no VMD display Axel Kohlmeyer (Tue May 12 2015 - 08:07:24 CDT)
Couldn't load the trajectory on to vmd Seera Suryanarayana (Tue May 12 2015 - 03:34:21 CDT)
- Re: Couldn't load the trajectory on to vmd Lutz Maibaum (Tue May 12 2015 - 13:40:07 CDT)
Why the 4ake-target_autopsf.situs can not be generated in MDFF tutorial? sunyeping (Mon May 11 2015 - 02:33:43 CDT)
- Re: Why the 4ake-target_autopsf.situs can not be generated in MDFF tutorial? Ryan McGreevy (Fri May 29 2015 - 14:18:19 CDT)
where are the files provided with MDFF TUTORIAL? sunyeping (Sun May 10 2015 - 22:12:03 CDT)
- Re: where are the files provided with MDFF TUTORIAL? Fotis Baltoumas (Mon May 11 2015 - 01:23:30 CDT)
School on Molecular Dynamics and Enhanced Sampling Methods @ Temple University July 6-10, 2015 Axel Kohlmeyer (Fri May 08 2015 - 11:29:01 CDT)
how to set the coordinates of carbon nanotube? ¶¡êÏ (Fri May 08 2015 - 01:30:17 CDT)
- Re: how to set the coordinates of carbon nanotube? karthik kumar (Fri May 08 2015 - 02:02:15 CDT)
- Re: how to set the coordinates of carbon nanotube? Maxim Belkin (Fri May 08 2015 - 01:59:49 CDT)
Re: AW: Problem with assignation of secondary structure in VMD Matic Kisovec (Thu May 07 2015 - 00:41:07 CDT)
- Re: AW: Problem with assignation of secondary structure in VMD Stefan Doerr (Thu May 07 2015 - 04:34:02 CDT)
  - Re: AW: Problem with assignation of secondary structure in VMD Matic Kisovec (Thu May 07 2015 - 07:48:28 CDT)
OPLS force-field in NAMD AnkiReddy katha (Thu May 07 2015 - 02:12:03 CDT)
VMD for MacBook Pro -- NetCDF Gabrielle Garcia (Wed May 06 2015 - 13:44:05 CDT)
- Re: VMD for MacBook Pro -- NetCDF Axel Kohlmeyer (Wed May 06 2015 - 14:53:00 CDT)
  - Re: VMD for MacBook Pro -- NetCDF Gabrielle Garcia (Wed May 06 2015 - 15:12:09 CDT)
  - Re: VMD for MacBook Pro -- NetCDF Gabrielle Garcia (Wed May 06 2015 - 16:14:03 CDT)
Problem with assignation of secondary structure in VMD Matic Kisovec (Wed May 06 2015 - 06:29:20 CDT)
Announcement: â€˜Hands Onâ€™ Workshop on Computational Biophysics (Odense, Denmark, Oct 12-16, 2015) Lela Vukovic (Wed May 06 2015 - 01:39:55 CDT)
How to create the psf of an aggregation of molecules with VMD? ¶¡êÏ (Tue May 05 2015 - 06:48:39 CDT)
- Re: How to create the psf of an aggregation of molecules with VMD? Axel Kohlmeyer (Tue May 05 2015 - 07:24:10 CDT)
How to create an aggregation of molecules with VMD? ¶¡êÏ (Mon May 04 2015 - 22:12:05 CDT)
- Re: How to create an aggregation of molecules with VMD? Ivan Gregoretti (Mon May 04 2015 - 22:55:05 CDT)
  - AW: How to create an aggregation of molecules with VMD? Daniel MÃ¶ller (Tue May 05 2015 - 02:13:30 CDT)
    - Re: How to create an aggregation of molecules with VMD? Axel Kohlmeyer (Tue May 05 2015 - 07:20:27 CDT)
FFTk: donor water escape during optimization Michetti Davide (Mon May 04 2015 - 08:49:46 CDT)
- Re: FFTk: donor water escape during optimization Mayne, Christopher G (Mon May 04 2015 - 11:38:43 CDT)
  - Re: FFTk: donor water escape during optimization Michetti Davide (Tue May 05 2015 - 03:48:42 CDT)
    - Re: FFTk: donor water escape during optimization Mayne, Christopher G (Tue May 05 2015 - 09:41:16 CDT)
Error on fftk while optimizing bonded parameters Hyunjin Kim (Sun May 03 2015 - 02:55:11 CDT)
- Re: Error on fftk while optimizing bonded parameters Mayne, Christopher G (Mon May 04 2015 - 09:07:09 CDT)
  - Re: Error on fftk while optimizing bonded parameters Mayne, Christopher G (Mon May 04 2015 - 11:27:06 CDT)
Problems in running AutoIMD Ern Seang Ong (Fri May 01 2015 - 00:49:39 CDT)
- Re: Problems in running AutoIMD John Stone (Thu May 07 2015 - 23:12:40 CDT)
  - RE: Problems in running AutoIMD Ern Seang Ong (Sat May 09 2015 - 00:08:44 CDT)
RDF in big trejectory Ondrej Kroutil (Thu Apr 30 2015 - 06:04:23 CDT)
dielectric constant for ELEC energy in VMD namdenergy tool Subrata Paul (Tue Apr 28 2015 - 05:03:37 CDT)
- Re: dielectric constant for ELEC energy in VMD namdenergy tool Axel Kohlmeyer (Tue Apr 28 2015 - 16:34:47 CDT)
Setting up a truncation cutoff fro volumetric data Miguel Caro (Tue Apr 28 2015 - 04:03:52 CDT)
- Re: Setting up a truncation cutoff fro volumetric data Ryan McGreevy (Tue Apr 28 2015 - 10:06:28 CDT)
  - Re: Setting up a truncation cutoff fro volumetric data Axel Kohlmeyer (Tue Apr 28 2015 - 10:41:55 CDT)
    - RE: Setting up a truncation cutoff fro volumetric data Caro Miguel (Tue Apr 28 2015 - 11:05:05 CDT)
using the colvar module in VMD within a tcl loop through trajectory frames Vlad Cojocaru (Mon Apr 27 2015 - 09:27:02 CDT)
- Re: using the colvar module in VMD within a tcl loop through trajectory frames Josh Vermaas (Mon Apr 27 2015 - 10:58:33 CDT)
  - Re: using the colvar module in VMD within a tcl loop through trajectory frames Vlad Cojocaru (Mon Apr 27 2015 - 11:24:46 CDT)
follow-up of "new VMD plugin for H5MD file format" Pierre de Buyl (Thu Apr 23 2015 - 06:56:29 CDT)
Dumping the coordinates of single frame karthik kumar (Wed Apr 22 2015 - 05:01:04 CDT)
- Re: Dumping the coordinates of single frame karthik kumar (Wed Apr 22 2015 - 05:02:58 CDT)
fftk water interaction questions Bennion, Brian (Mon Apr 20 2015 - 14:18:45 CDT)
- Re: fftk water interaction questions Pawel Kedzierski (Tue Apr 21 2015 - 03:04:32 CDT)
  - RE: fftk water interaction questions Bennion, Brian (Tue Apr 21 2015 - 16:09:46 CDT)
Error saying "too many open files" Monika Madhavi (Mon Apr 20 2015 - 01:29:34 CDT)
- Re: Error saying "too many open files" John Stone (Mon Apr 20 2015 - 01:45:18 CDT)
  - Re: Error saying "too many open files" Monika Madhavi (Mon Apr 20 2015 - 01:56:32 CDT)
    - Re: Error saying "too many open files" Ashar Malik (Mon Apr 20 2015 - 02:33:57 CDT)
- Re: Error saying "too many open files" Ashar Malik (Mon Apr 20 2015 - 01:56:39 CDT)
XTC to DCD conversion rajan kumar (Thu Apr 16 2015 - 13:41:24 CDT)
- Re: XTC to DCD conversion John Stone (Fri Apr 17 2015 - 16:37:51 CDT)
  - Re: XTC to DCD conversion rajan kumar (Sat Apr 18 2015 - 03:33:16 CDT)
measure sasa of a complex (CNT and protein) Aryan Vahedi (Thu Apr 16 2015 - 10:58:38 CDT)
- RE: measure sasa of a complex (CNT and protein) Joaquim Rui de Castro Rodrigues (Thu Apr 16 2015 - 12:23:09 CDT)
  - Re: measure sasa of a complex (CNT and protein) Josh Vermaas (Thu Apr 16 2015 - 13:05:25 CDT)
Valbond and NAMD zoran (Thu Apr 16 2015 - 07:11:37 CDT)
- Re: Valbond and NAMD JÃ©rÃ´me HÃ©nin (Thu Apr 16 2015 - 09:21:25 CDT)
  - Re: Valbond and NAMD zoran (Thu Apr 16 2015 - 09:37:42 CDT)
CentOS 6.4 crashed right after starting vmd ASHISH BIHANI (Thu Apr 16 2015 - 00:57:51 CDT)
- Re: CentOS 6.4 crashed right after starting vmd John Stone (Thu Apr 16 2015 - 11:33:02 CDT)
Drawing a vector for each particle's velocity Hojjat Behmadi (Tue Apr 14 2015 - 13:04:42 CDT)
- Re: Drawing a vector for each particle's velocity John Stone (Tue Apr 21 2015 - 15:32:33 CDT)
velocity arrow and calculation Hojjat Behmadi (Tue Apr 14 2015 - 13:02:01 CDT)
Assigning colors to atom names Lutz Maibaum (Mon Apr 13 2015 - 19:09:18 CDT)
Updated VMD 1.9.2. Gromacs plugins posted for download John Stone (Mon Apr 13 2015 - 16:36:25 CDT)
- Re: Updated VMD 1.9.2. Gromacs plugins posted for download andrea spitaleri (Tue Apr 14 2015 - 01:46:02 CDT)
reg list of non standard residues. surya narayanan chandrasekaran (Sat Apr 11 2015 - 16:57:05 CDT)
- Re: reg list of non standard residues. Axel Kohlmeyer (Sat Apr 11 2015 - 18:03:49 CDT)
Read CHARMM VDW radii into VMD Gianluca Interlandi (Sat Apr 11 2015 - 02:22:42 CDT)
- Re: Read CHARMM VDW radii into VMD John Stone (Sat Apr 11 2015 - 12:47:02 CDT)
MacOS X Yosemite 10.2.2 workaround for people to try... John Stone (Thu Apr 09 2015 - 21:16:22 CDT)
Immediate Postdoctoral Position Opening Marawan Hussien (Thu Apr 09 2015 - 18:10:32 CDT)
- Immediate PhD Opening Computational Structural Biology Of Membrane Proteins Marawan Hussien (Thu Apr 09 2015 - 19:18:53 CDT)
measure energy Gianluca Interlandi (Thu Apr 09 2015 - 17:39:49 CDT)
- Re: measure energy Gianluca Interlandi (Thu Apr 09 2015 - 17:46:00 CDT)
- Re: measure energy John Stone (Thu Apr 09 2015 - 21:02:03 CDT)
  - Re: measure energy Gianluca Interlandi (Thu Apr 09 2015 - 23:51:42 CDT)
measure sasa not consistent Gianluca Interlandi (Thu Apr 09 2015 - 16:17:18 CDT)
- Re: measure sasa not consistent John Stone (Thu Apr 09 2015 - 16:33:37 CDT)
  - Re: measure sasa not consistent Gianluca Interlandi (Thu Apr 09 2015 - 16:52:40 CDT)
new VMD plugin for H5MD file format Jonas Landsgesell (Thu Apr 09 2015 - 15:27:50 CDT)
- Re: new VMD plugin for H5MD file format Axel Kohlmeyer (Thu Apr 09 2015 - 15:50:37 CDT)
  - Re: new VMD plugin for H5MD file format John Stone (Thu Apr 09 2015 - 16:02:35 CDT)
new VMD plugin for H5MD file format Jonas Landsgesell (Thu Apr 09 2015 - 15:25:52 CDT)
XYZ to psf file Bharat Sharma (Thu Apr 09 2015 - 09:43:10 CDT)
- Re: XYZ to psf file John Stone (Thu Apr 09 2015 - 11:49:16 CDT)
  - Re: XYZ to psf file Vasiliy Triandafilidi (Thu Apr 09 2015 - 19:25:44 CDT)
    - Re: XYZ to psf file Bharat Sharma (Thu Apr 09 2015 - 20:01:46 CDT)
crash with 1.9.2 and not with 1.9.1 andrea spitaleri (Thu Apr 09 2015 - 07:14:52 CDT)
- Re: crash with 1.9.2 and not with 1.9.1 Axel Kohlmeyer (Thu Apr 09 2015 - 07:44:43 CDT)
  - Re: crash with 1.9.2 and not with 1.9.1 andrea spitaleri (Thu Apr 09 2015 - 08:14:50 CDT)
VMD text mode on MAC OS Bharat Sharma (Wed Apr 08 2015 - 18:14:17 CDT)
- Re: VMD text mode on MAC OS Vasiliy Triandafilidi (Thu Apr 09 2015 - 02:18:46 CDT)
  - Re: VMD text mode on MAC OS John Stone (Thu Apr 09 2015 - 09:58:10 CDT)
    - Re: VMD text mode on MAC OS Vasiliy Triandafilidi (Thu Apr 09 2015 - 16:41:13 CDT)
    - Re: VMD text mode on MAC OS Bharat Sharma (Fri Apr 10 2015 - 11:10:50 CDT)
Adding groups Neelanjana Sengupta (Wed Apr 08 2015 - 09:01:41 CDT)
- Re: Adding groups Tim Lo (Wed Apr 08 2015 - 09:34:22 CDT)
new VMD plugin for H5MD file format Jonas Landsgesell (Wed Apr 08 2015 - 08:33:41 CDT)
- Re: new VMD plugin for H5MD file format John Stone (Wed Apr 08 2015 - 13:25:02 CDT)
compiling VMD 1.9.2 source with tcl 8.6 Vlad Cojocaru (Tue Apr 07 2015 - 05:23:35 CDT)
- Re: compiling VMD 1.9.2 source with tcl 8.6 Vlad Cojocaru (Tue Apr 07 2015 - 05:40:33 CDT)
- Re: compiling VMD 1.9.2 source with tcl 8.6 Axel Kohlmeyer (Tue Apr 07 2015 - 05:57:58 CDT)
using namdstats.tcl oguz gurbulak (Sun Apr 05 2015 - 16:54:50 CDT)
- Re: using namdstats.tcl John Stone (Mon Apr 06 2015 - 10:17:46 CDT)
  - Re: using namdstats.tcl oguz gurbulak (Wed Apr 08 2015 - 01:50:47 CDT)
periodic boundary conditions displaying Ming Tang (Sun Apr 05 2015 - 03:58:31 CDT)
- Re: periodic boundary conditions displaying John Stone (Mon Apr 06 2015 - 10:24:36 CDT)
Writing Lammps data file Benjamin Cowen (Sat Apr 04 2015 - 21:46:30 CDT)
- Re: Writing Lammps data file Axel Kohlmeyer (Sat Apr 04 2015 - 22:51:09 CDT)
How to populate lib/ directory when compiling Michael Lamparski (Fri Apr 03 2015 - 15:48:15 CDT)
- Re: How to populate lib/ directory when compiling Josh Vermaas (Fri Apr 03 2015 - 16:22:44 CDT)
  - RE: How to populate lib/ directory when compiling Strahs, Dr. Daniel Bernard (Sat Apr 04 2015 - 10:52:45 CDT)
- Re: How to populate lib/ directory when compiling John Stone (Fri Apr 03 2015 - 22:12:02 CDT)
Residues within a specified distance across all trajectories time steps Aryan Vahedi (Fri Apr 03 2015 - 11:24:56 CDT)
- Re: Residues within a specified distance across all trajectories time steps John Stone (Mon Apr 06 2015 - 10:59:53 CDT)
  - Re: Residues within a specified distance across all trajectories time steps Aryan Vahedi (Mon Apr 06 2015 - 13:34:57 CDT)
    - Re: Residues within a specified distance across all trajectories time steps Josh Vermaas (Mon Apr 06 2015 - 15:49:34 CDT)
    - Re: Residues within a specified distance across all trajectories time steps Maxim Belkin (Mon Apr 06 2015 - 15:49:59 CDT)
Vmd Opengl display do not show anything Denis Zhu (Thu Apr 02 2015 - 09:25:13 CDT)
- Re: Vmd Opengl display do not show anything John Stone (Thu Apr 02 2015 - 11:17:06 CDT)
  - Re: Vmd Opengl display do not show anything deniszhu1991 (Thu Apr 02 2015 - 13:14:35 CDT)
Resid and residue atomselect bug Stefan Doerr (Thu Apr 02 2015 - 03:41:16 CDT)
- Re: Resid and residue atomselect bug Axel Kohlmeyer (Thu Apr 02 2015 - 06:54:55 CDT)
  - Re: Resid and residue atomselect bug Stefan Doerr (Thu Apr 02 2015 - 07:08:33 CDT)
  - Re: Resid and residue atomselect bug Axel Kohlmeyer (Thu May 21 2015 - 08:09:00 CDT)
Questions with Solvation with TIP4P Water Model Kin Leung CHU (Thu Apr 02 2015 - 01:58:01 CDT)
- Re: Questions with Solvation with TIP4P Water Model John Stone (Thu Apr 02 2015 - 11:15:28 CDT)
  - Re: Questions with Solvation with TIP4P Water Model Brian Radak (Thu Apr 02 2015 - 14:21:15 CDT)
Calculating residence time M K (Wed Apr 01 2015 - 23:08:33 CDT)
- Re: Calculating residence time Stefan Doerr (Thu Apr 02 2015 - 02:37:04 CDT)
  - Re: Calculating residence time M K (Fri Apr 03 2015 - 02:49:45 CDT)
fftk bonded parameter optimization Chaya Stern (Wed Apr 01 2015 - 15:57:28 CDT)
- Re: fftk bonded parameter optimization Mayne, Christopher G (Wed Apr 01 2015 - 16:34:32 CDT)
Optimizing an inter-residue distance measurement Charles McAnany (Wed Apr 01 2015 - 14:42:37 CDT)
- Re: Optimizing an inter-residue distance measurement Josh Vermaas (Wed Apr 01 2015 - 15:51:35 CDT)
segv in vmd upon opening a file Burlen Loring (Tue Mar 31 2015 - 16:20:44 CDT)
- Re: segv in vmd upon opening a file John Stone (Tue Mar 31 2015 - 19:56:43 CDT)
  - Re: segv in vmd upon opening a file Burlen Loring (Wed Apr 01 2015 - 03:23:28 CDT)
save coordinates Ducasse Laurent (Mon Mar 30 2015 - 09:00:31 CDT)
- Re: save coordinates John Stone (Mon Mar 30 2015 - 17:32:16 CDT)
about the diffusion & msd plugin M K (Mon Mar 30 2015 - 01:57:12 CDT)
- Re: about the diffusion & msd plugin Mayne, Christopher G (Mon Mar 30 2015 - 09:30:13 CDT)
namdenergy pluding error Subrata Paul (Mon Mar 30 2015 - 00:26:54 CDT)
- Re: namdenergy pluding error Mayne, Christopher G (Mon Mar 30 2015 - 09:26:26 CDT)
  - Re: namdenergy pluding error Mayne, Christopher G (Mon Mar 30 2015 - 13:30:36 CDT)
    - Re: namdenergy pluding error Subrata Paul (Mon Mar 30 2015 - 13:39:02 CDT)
The charge of glycine mutations in Mutator is not equal to zero Jian Dai (Sun Mar 29 2015 - 07:28:47 CDT)
flip the sheet using transaxis command Mohan maruthi sena (Sat Mar 28 2015 - 22:37:04 CDT)
- Re: flip the sheet using transaxis command Ashar Malik (Sat Mar 28 2015 - 23:30:46 CDT)
  - Re: flip the sheet using transaxis command Ashar Malik (Sun Mar 29 2015 - 01:29:38 CDT)
Q=B0startup.command=A1=B1_can=A1=AFt_be?= opened because CoreServicesUIAgent is not allowed to open documents in Terminal. Ãç¼ÒÔ¶ (Fri Mar 27 2015 - 15:33:20 CDT)
- Re: ??startup.command?? can??t be opened because CoreServicesUIAgent is not allowed to open documents in Terminal. John Stone (Mon Mar 30 2015 - 17:08:23 CDT)
  - Re:Re: ??startup.command?? can??t be opened because CoreServicesUIAgent is not allowed to open documents in Terminal. è‹—å®¶è¿œ (Wed Apr 01 2015 - 15:13:24 CDT)
    - Re: ??startup.command?? can??t be opened because CoreServicesUIAgent is not allowed to open documents in Terminal. Maxim Belkin (Mon Apr 06 2015 - 13:29:18 CDT)
(no subject) Jevgenij Raskatov (Fri Mar 27 2015 - 11:43:31 CDT)
- Re: Maxim Belkin (Fri Mar 27 2015 - 11:55:05 CDT)
  - Re: Ajasja LjubetiÄ (Fri Mar 27 2015 - 12:38:49 CDT)
    - Re: Maxim Belkin (Fri Mar 27 2015 - 13:26:01 CDT)
VMD 1.9.3 alpha Matic Kisovec (Fri Mar 27 2015 - 07:58:47 CDT)
- RE: VMD 1.9.3 alpha James Kress (Fri Mar 27 2015 - 09:23:23 CDT)
  - Re: VMD 1.9.3 alpha John Stone (Mon Mar 30 2015 - 17:11:36 CDT)
- Re: VMD 1.9.3 alpha John Stone (Mon Mar 30 2015 - 16:59:10 CDT)
MSD calculation - Memory saving. Bharat Sharma (Fri Mar 27 2015 - 07:33:56 CDT)
- Re: MSD calculation - Memory saving. Felipe Merino (Fri Mar 27 2015 - 08:30:05 CDT)
- Re: MSD calculation - Memory saving. Josh Vermaas (Fri Mar 27 2015 - 08:49:36 CDT)
  - Re: MSD calculation - Memory saving. Bharat Sharma (Fri Mar 27 2015 - 11:10:26 CDT)
Problem with generating psf and pdb files of metalloprotein made up of two fragments zoran (Thu Mar 26 2015 - 13:45:59 CDT)
Colour coordinating atoms in a trajectory by Coordination Number Samuel Jobbins (Thu Mar 26 2015 - 10:57:51 CDT)
- Re: Colour coordinating atoms in a trajectory by Coordination Number Josh Vermaas (Thu Mar 26 2015 - 12:12:29 CDT)
  - Fw: Colour coordinating atoms in a trajectory by Coordination Number Samuel Jobbins (Mon Mar 30 2015 - 10:13:00 CDT)
- Re: Colour coordinating atoms in a trajectory by Coordination Number Axel Kohlmeyer (Thu Mar 26 2015 - 12:08:48 CDT)
Script to impose coordinates from separate file onto equivalent selection of atoms Sam Wallace (Thu Mar 26 2015 - 07:21:43 CDT)
- Re: Script to impose coordinates from separate file onto equivalent selection of atoms Josh Vermaas (Thu Mar 26 2015 - 08:27:33 CDT)
  - Re: Script to impose coordinates from separate file onto equivalent selection of atoms zoran (Thu Mar 26 2015 - 10:59:07 CDT)
- Re: Script to impose coordinates from separate file onto equivalent selection of atoms Martin, Erik W (Thu Mar 26 2015 - 12:53:29 CDT)
FFTK: Running optimizations in batch? Amira Yu (Wed Mar 25 2015 - 22:09:15 CDT)
- Re: FFTK: Running optimizations in batch? Mayne, Christopher G (Wed Mar 25 2015 - 23:38:03 CDT)
How to visualize the moving periodic boundaries in VMD Yihua Zhou (Wed Mar 25 2015 - 16:15:26 CDT)
- Re: How to visualize the moving periodic boundaries in VMD Axel Kohlmeyer (Wed Mar 25 2015 - 20:07:42 CDT)
"color by mass" - change default colors Maria Sander (Wed Mar 25 2015 - 15:09:56 CDT)
- Re: "color by mass" - change default colors Axel Kohlmeyer (Wed Mar 25 2015 - 15:42:32 CDT)
namdenergy Subrata Paul (Wed Mar 25 2015 - 13:21:07 CDT)
Visualizing H-bonds between two segnames or chains Dolan, Michael A. (NIH/NIAID) [C] (Wed Mar 25 2015 - 10:30:07 CDT)
- Re: Visualizing H-bonds between two segnames or chains Stefan Doerr (Wed Mar 25 2015 - 10:57:36 CDT)
  - Re: Visualizing H-bonds between two segnames or chains Josh Vermaas (Wed Mar 25 2015 - 11:22:30 CDT)
    - Re: Visualizing H-bonds between two segnames or chains Axel Kohlmeyer (Wed Mar 25 2015 - 12:43:28 CDT)
Periodic Tab with PDB input Viswanath Pasumarthi (Wed Mar 25 2015 - 08:06:54 CDT)
- Re: Periodic Tab with PDB input Axel Kohlmeyer (Wed Mar 25 2015 - 08:59:25 CDT)
  - Re: Periodic Tab with PDB input Josh Vermaas (Wed Mar 25 2015 - 09:48:04 CDT)
Running TCL scripts (textmode) on a Server Stephan Grein (Wed Mar 25 2015 - 06:00:58 CDT)
- Re: Running TCL scripts (textmode) on a Server Stephan Grein (Wed Mar 25 2015 - 06:45:04 CDT)
- Re: Running TCL scripts (textmode) on a Server karthik kumar (Wed Mar 25 2015 - 06:48:34 CDT)
- Re: Running TCL scripts (textmode) on a Server Michail Palaiokostas Avramidis (Wed Mar 25 2015 - 06:57:57 CDT)
- RE: Running TCL scripts (textmode) on a Server Joaquim Rui de Castro Rodrigues (Wed Mar 25 2015 - 07:12:38 CDT)
- RE: Running TCL scripts (textmode) on a Server Morgan, Brittany (Wed Mar 25 2015 - 07:20:38 CDT)
  - Re: Running TCL scripts (textmode) on a Server Stephan Grein (Wed Mar 25 2015 - 10:56:52 CDT)
    - Re: Running TCL scripts (textmode) on a Server Axel Kohlmeyer (Wed Mar 25 2015 - 11:21:03 CDT)
Re: Running VMD in user folder on Windows (bug fix?) Pawel Kedzierski (Wed Mar 25 2015 - 04:33:10 CDT)
- Re: Running VMD in user folder on Windows (bug fix?) Ajasja LjubetiÄ (Wed Mar 25 2015 - 05:03:52 CDT)
  - Re: Running VMD in user folder on Windows (bug fix?) Pawel Kedzierski (Wed Mar 25 2015 - 10:20:20 CDT)
  - Re: Running VMD in user folder on Windows (bug fix?) Pawel Kedzierski (Tue Mar 31 2015 - 04:09:21 CDT)
Running VMD in user folder on Windows (bug fix?) Pawel Kedzierski (Wed Mar 25 2015 - 03:50:29 CDT)
Coloring of basins Maria Ivanova (Tue Mar 24 2015 - 19:48:10 CDT)
- Re: Coloring of basins John Stone (Mon Apr 06 2015 - 11:36:37 CDT)
How to run VMD text mode on Windows 7 Bharat Sharma (Tue Mar 24 2015 - 19:33:47 CDT)
- Re: How to run VMD text mode on Windows 7 Ashar Malik (Tue Mar 24 2015 - 23:32:54 CDT)
- Re: How to run VMD text mode on Windows 7 Ashar Malik (Wed Mar 25 2015 - 02:03:26 CDT)
Announcement: â€˜Hands Onâ€™ Workshop on Computational Biophysics (Lake Tahoe, CA, Aug 3-7, 2015) Lela Vukovic (Tue Mar 24 2015 - 15:51:28 CDT)
GPU Programming workshop @ ICTP: deadline extended for participants not requiring visa and financial support Axel Kohlmeyer (Tue Mar 24 2015 - 14:17:22 CDT)
vmd-I: Using the MergeMultiFramesPDB code Akshata Rudrapatna (Sat Mar 21 2015 - 17:06:42 CDT)
- Re: vmd-I: Using the MergeMultiFramesPDB code John Stone (Fri Apr 10 2015 - 01:55:52 CDT)
fftk bonded and dihedral optimization question Chaya Stern (Fri Mar 20 2015 - 09:13:01 CDT)
- Re: fftk bonded and dihedral optimization question Tim Lo (Fri Mar 20 2015 - 10:36:27 CDT)
Recent martini top+par+cgc files Sourav Ray (Thu Mar 19 2015 - 06:34:03 CDT)
Align a trajectory Kevin C Chan (Thu Mar 19 2015 - 07:35:06 CDT)
- Re: Align a trajectory Ryan McGreevy (Thu Mar 19 2015 - 10:29:00 CDT)
- Re: Align a trajectory Axel Kohlmeyer (Thu Mar 19 2015 - 10:08:57 CDT)
Counting water transition through a channel nicolas martin (Thu Mar 19 2015 - 03:04:26 CDT)
- Re: Counting water transition through a channel Adelman, Joshua Lev (Thu Mar 19 2015 - 08:29:51 CDT)
  - Re: Counting water transition through a channel nicolas martin (Thu Mar 19 2015 - 09:29:20 CDT)
Total volume of ligand calculation in vmd mish (Tue Mar 17 2015 - 11:10:28 CDT)
Coarse-graining a retro protein Sourav Ray (Tue Mar 17 2015 - 01:25:46 CDT)
selected atoms James Lord (Mon Mar 16 2015 - 15:56:28 CDT)
- Re: selected atoms James Lord (Mon Mar 16 2015 - 16:03:50 CDT)
Atom order in VMD Arjun Sharma (Sat Mar 14 2015 - 17:50:42 CDT)
- Re: Atom order in VMD Maxim Belkin (Sat Mar 14 2015 - 19:21:08 CDT)
Fwd: Segmentation fault (core dump) Nima Soltani (Fri Mar 13 2015 - 16:00:30 CDT)
- Re: Fwd: Segmentation fault (core dump) John Stone (Fri Mar 13 2015 - 16:14:13 CDT)
PBC Plugin Kevin C Chan (Wed Mar 11 2015 - 10:09:09 CDT)
- Re: PBC Plugin Josh Vermaas (Wed Mar 11 2015 - 11:07:36 CDT)
writing a new plugin Albert Solernou (Mon Mar 09 2015 - 10:11:26 CDT)
- Re: writing a new plugin John Stone (Mon Mar 09 2015 - 13:00:45 CDT)
  - Re: writing a new plugin Albert Solernou (Tue Mar 10 2015 - 05:53:09 CDT)
TopoTools and box information in LAMMPS data Ondrej Marsalek (Sun Mar 08 2015 - 23:28:28 CDT)
- Re: TopoTools and box information in LAMMPS data Axel Kohlmeyer (Mon Mar 09 2015 - 01:12:52 CDT)
  - Re: TopoTools and box information in LAMMPS data Ondrej Marsalek (Mon Mar 09 2015 - 02:43:29 CDT)
    - Re: TopoTools and box information in LAMMPS data Axel Kohlmeyer (Mon Mar 09 2015 - 03:22:53 CDT)
How to write coordinates to a pdb without replacing existing entries Monika Madhavi (Sun Mar 08 2015 - 09:33:03 CDT)
- RE: How to write coordinates to a pdb without replacing existing entries Joaquim Rui de Castro Rodrigues (Sun Mar 08 2015 - 11:41:18 CDT)
  - RE: How to write coordinates to a pdb without replacing existing entries Monika Madhavi (Sun Mar 08 2015 - 12:17:16 CDT)
How to select a particular water molecule from a water box Monika Madhavi (Sat Mar 07 2015 - 01:19:45 CST)
(no subject) Jevgenij Raskatov (Fri Mar 06 2015 - 14:26:49 CST)
- Re: Maxim Belkin (Fri Mar 06 2015 - 14:47:05 CST)
(no subject) Jevgenij Raskatov (Fri Mar 06 2015 - 14:01:48 CST)
Re: vmd error saying "no atom selection" Monika Madhavi (Fri Mar 06 2015 - 08:04:17 CST)
Oculus Rift Christian Wohlschlager (Fri Mar 06 2015 - 04:21:55 CST)
- Re: Oculus Rift Dudo (Fri Mar 06 2015 - 04:47:03 CST)
  - Re: Oculus Rift John Stone (Fri Mar 06 2015 - 08:35:53 CST)
vmd error saying "no atom selection" Monika Madhavi (Fri Mar 06 2015 - 02:56:46 CST)
Residue label moves upon rendering James Lord (Wed Mar 04 2015 - 19:55:05 CST)
- Re: Residue label moves upon rendering John Stone (Thu Mar 05 2015 - 15:25:54 CST)
Announcement: â€˜Hands Onâ€™ Workshop on Computational Biophysics (Pittsburgh, PA, June 1-5, 2015) Lela Vukovic (Wed Mar 04 2015 - 13:08:28 CST)
Using Multiseq for aligning a structure and a sequence Arijit Ghosh (Wed Mar 04 2015 - 00:56:40 CST)
Render as Object or 3DS file Tom.Verhelst_at_ucb.com (Mon Mar 02 2015 - 06:01:09 CST)
- Re: Render as Object or 3DS file John Stone (Mon Mar 02 2015 - 11:25:19 CST)
  - RE: Render as Object or 3DS file Tom.Verhelst_at_ucb.com (Tue Mar 03 2015 - 11:13:25 CST)
Aligning portions of proteins Anjela Manandhar (Sun Mar 01 2015 - 20:06:02 CST)
movie making Maryam Kowsar (Sat Feb 28 2015 - 12:04:00 CST)
- Re: movie making Josh Vermaas (Sat Feb 28 2015 - 13:13:49 CST)
Moving making with short trajectories anu chandra (Fri Feb 27 2015 - 14:24:59 CST)
- Re: Moving making with short trajectories John Stone (Fri Feb 27 2015 - 14:31:28 CST)
  - Re: Moving making with short trajectories Maxim Belkin (Fri Feb 27 2015 - 14:42:10 CST)
  - Re: Moving making with short trajectories anu chandra (Sat Feb 28 2015 - 11:30:52 CST)
Nvidia GPU driver not detected with VMD anu chandra (Fri Feb 27 2015 - 04:31:00 CST)
- RE: Nvidia GPU driver not detected with VMD Norman Geist (Fri Feb 27 2015 - 07:29:06 CST)
- Re: Nvidia GPU driver not detected with VMD John Stone (Fri Feb 27 2015 - 07:29:56 CST)
  - Re: Nvidia GPU driver not detected with VMD anu chandra (Fri Feb 27 2015 - 07:58:43 CST)
Problem creating tetramer from a monomer Arijit Ghosh (Thu Feb 26 2015 - 23:03:23 CST)
- Re: Problem creating tetramer from a monomer Fotis Baltoumas (Fri Feb 27 2015 - 02:41:47 CST)
velocity IO with psfgen? Brian Radak (Thu Feb 26 2015 - 09:41:04 CST)
- Re: velocity IO with psfgen? John Stone (Thu Feb 26 2015 - 10:24:36 CST)
- Re: namd-l: velocity IO with psfgen? Ajasja LjubetiÄ (Thu Feb 26 2015 - 10:37:55 CST)
  - Re: namd-l: velocity IO with psfgen? Brian Radak (Thu Feb 26 2015 - 10:56:57 CST)
(no subject) Jevgenij Raskatov (Wed Feb 25 2015 - 21:07:32 CST)
- Re: M K (Wed Feb 25 2015 - 21:43:06 CST)
selecting all atoms within a given coordinate range Monika Madhavi (Mon Feb 23 2015 - 20:46:52 CST)
camera navigator question Nuno Sousa Cerqueira (Mon Feb 23 2015 - 16:42:16 CST)
- Re: camera navigator question John Stone (Thu Feb 26 2015 - 14:13:24 CST)
Hydration Shell RDF -- VMD Nomenclature Needed Phelan Jr., Frederick R. Dr. (Mon Feb 23 2015 - 15:31:03 CST)
- Re: Hydration Shell RDF -- VMD Nomenclature Needed Jim Parker (Mon Mar 02 2015 - 21:20:19 CST)
(no subject) Jevgenij Raskatov (Mon Feb 23 2015 - 10:27:01 CST)
- Re: Ashar Malik (Mon Feb 23 2015 - 15:57:27 CST)
  - Re: Martin, Erik W (Mon Feb 23 2015 - 17:38:36 CST)
  - Re: Josh Vermaas (Mon Feb 23 2015 - 17:15:49 CST)
- Re: Tristan Croll (Mon Feb 23 2015 - 17:43:10 CST)
adding additional atoms to psf and dcd Vlad Cojocaru (Sat Feb 21 2015 - 03:59:33 CST)
- Re: adding additional atoms to psf and dcd Josh Vermaas (Sat Feb 21 2015 - 14:29:49 CST)
  - Re: adding additional atoms to psf and dcd Vlad Cojocaru (Mon Feb 23 2015 - 04:15:44 CST)
topotools addbond and retypeimpropers commands Hugo Santos Silva (Thu Feb 19 2015 - 19:22:44 CST)
- Re: topotools addbond and retypeimpropers commands Axel Kohlmeyer (Thu Feb 19 2015 - 21:47:12 CST)
  - Re: topotools addbond and retypeimpropers commands Axel Kohlmeyer (Thu Feb 19 2015 - 22:20:36 CST)
    - Re: topotools addbond and retypeimpropers commands Hugo Santos Silva (Sat Feb 21 2015 - 15:25:49 CST)
OpenGL Display transparent jing liang (Thu Feb 19 2015 - 18:11:46 CST)
- Re: OpenGL Display transparent John Stone (Thu Feb 26 2015 - 15:22:50 CST)
  - Re: OpenGL Display transparent John Stone (Tue Mar 03 2015 - 10:00:26 CST)
(no subject) Jevgenij Raskatov (Thu Feb 19 2015 - 16:31:31 CST)
- Re: Ashar Malik (Thu Feb 19 2015 - 17:48:43 CST)
script for displaying multiple frames jing liang (Thu Feb 19 2015 - 07:26:17 CST)
- Re: script for displaying multiple frames Stefan Doerr (Thu Feb 19 2015 - 07:57:12 CST)
- RE: script for displaying multiple frames James Kress (Thu Feb 19 2015 - 12:23:51 CST)
- Re: script for displaying multiple frames Maxim Belkin (Thu Feb 19 2015 - 15:10:19 CST)
(no subject) Jevgenij Raskatov (Wed Feb 18 2015 - 16:11:18 CST)
- Re: Ashar Malik (Wed Feb 18 2015 - 16:48:31 CST)
FFTK scan torsions question Elena Lilkova (Tue Feb 17 2015 - 07:46:06 CST)
- Re: FFTK scan torsions question Josh Vermaas (Tue Feb 17 2015 - 08:50:02 CST)
- Re: FFTK scan torsions question Mayne, Christopher G (Tue Feb 17 2015 - 09:14:49 CST)
  - Re: FFTK scan torsions question Elena Lilkova (Tue Feb 17 2015 - 10:07:10 CST)
Bonding energies between two atom selections Viswanath Pasumarthi (Tue Feb 17 2015 - 05:12:56 CST)
- Re: Bonding energies between two atom selections Ashar Malik (Tue Feb 17 2015 - 05:56:18 CST)
MDFF plugin calculating ccc Kevin C Chan (Mon Feb 16 2015 - 21:19:19 CST)
- Re: MDFF plugin calculating ccc Ryan McGreevy (Tue Feb 17 2015 - 10:19:48 CST)
  - MDFF plugin calculating ccc Kevin C Chan (Tue Feb 17 2015 - 11:04:40 CST)
On the behavior of "graphics material" Norman Geist (Mon Feb 16 2015 - 05:44:43 CST)
- RE: On the behavior of "graphics material" Norman Geist (Mon Feb 16 2015 - 05:48:33 CST)
Why NAMD??? a general question M K (Sun Feb 15 2015 - 05:49:19 CST)
- Re: Why NAMD??? a general question Akshata Rudrapatna (Sun Feb 15 2015 - 13:01:52 CST)
Extracting coordinates from DCD file to a single PDB file Sourav Ray (Fri Feb 13 2015 - 04:09:36 CST)
- Re: Extracting coordinates from DCD file to a single PDB file Maxim Belkin (Fri Feb 13 2015 - 05:33:27 CST)
vmd command not found Seera Suryanarayana (Fri Feb 13 2015 - 03:56:16 CST)
- Re: vmd command not found Josh Vermaas (Fri Feb 13 2015 - 08:10:20 CST)
Feature request: read environment to set FreeVR lib, include paths Stock, Mark (Thu Feb 12 2015 - 17:54:02 CST)
- Re: Feature request: read environment to set FreeVR lib, include paths John Stone (Fri Feb 13 2015 - 08:58:05 CST)
  - FW: Feature request: read environment to set FreeVR lib, include paths Stock, Mark (Fri Feb 13 2015 - 12:07:56 CST)
color gradient based on the sequence Hyun (Thu Feb 12 2015 - 13:41:01 CST)
- Re: color gradient based on the sequence John Stone (Thu Feb 12 2015 - 16:02:40 CST)
  - Re: color gradient based on the sequence Hyun (Thu Feb 12 2015 - 17:15:10 CST)
Change VDW scaling in CPK drawing method Damien Serres (Thu Feb 12 2015 - 11:03:52 CST)
- Re: Change VDW scaling in CPK drawing method John Stone (Thu Feb 12 2015 - 11:38:18 CST)
- Re: Change VDW scaling in CPK drawing method Josh Vermaas (Thu Feb 12 2015 - 11:54:22 CST)
  - RE: Change VDW scaling in CPK drawing method Norman Geist (Fri Feb 13 2015 - 01:47:34 CST)
Mac issue Michael Patzschke (Thu Feb 12 2015 - 09:08:12 CST)
- Re: Mac issue John Stone (Thu Feb 12 2015 - 10:04:25 CST)
  - Re: Mac issue Michael Patzschke (Thu Feb 12 2015 - 10:48:30 CST)
how to select a particular molecule Monika Madhavi (Thu Feb 12 2015 - 00:56:21 CST)
- Re: how to select a particular molecule Mike Makowski (Thu Feb 12 2015 - 02:28:35 CST)
- RE: how to select a particular molecule Norman Geist (Thu Feb 12 2015 - 02:35:21 CST)
- Re: how to select a particular molecule Tristan Croll (Thu Feb 12 2015 - 03:23:33 CST)
  - Re: how to select a particular molecule Monika Madhavi (Thu Feb 12 2015 - 19:29:53 CST)
Fwd: NAMDEnergy fails to locate supporting files Ashar Malik (Thu Feb 12 2015 - 00:48:48 CST)
VMD Tcl Getting first index from residue number Bharat Sharma (Wed Feb 11 2015 - 12:14:21 CST)
- Re: VMD Tcl Getting first index from residue number Josh Vermaas (Wed Feb 11 2015 - 18:30:25 CST)
Handful of rendering issues Tristan Croll (Wed Feb 11 2015 - 05:15:19 CST)
- RE: Handful of rendering issues Norman Geist (Wed Feb 11 2015 - 09:32:35 CST)
  - Re: Handful of rendering issues John Stone (Wed Feb 11 2015 - 10:21:09 CST)
- Re: Handful of rendering issues Maxim Belkin (Wed Feb 11 2015 - 09:52:15 CST)
- Re: Handful of rendering issues John Stone (Wed Feb 11 2015 - 10:12:44 CST)
  - Re: Handful of rendering issues Tristan Croll (Wed Feb 11 2015 - 15:07:43 CST)
    - Re: Handful of rendering issues Maxim Belkin (Wed Feb 11 2015 - 15:16:16 CST)
    - Re: Handful of rendering issues Tristan Croll (Wed Feb 11 2015 - 15:28:20 CST)
GBIS in NAMD 2.10 CUDA with IMD Tristan Croll (Wed Feb 11 2015 - 04:18:11 CST)
- Re: GBIS in NAMD 2.10 CUDA with IMD John Stone (Wed Feb 11 2015 - 10:03:39 CST)
FFTK charge optimization of one charge group Elena Lilkova (Tue Feb 10 2015 - 08:08:18 CST)
- Re: FFTK charge optimization of one charge group Elena Lilkova (Tue Feb 10 2015 - 08:36:35 CST)
  - Re: Re: FFTK charge optimization of one charge group Mayne, Christopher G (Tue Feb 10 2015 - 15:27:35 CST)
To delete some atoms via VMD Majid Shahbabaei (Tue Feb 10 2015 - 03:26:48 CST)
- Fwd: To delete some atoms via VMD Majid Shahbabaei (Tue Feb 10 2015 - 05:28:31 CST)
  - Re: Fwd: To delete some atoms via VMD John Stone (Tue Feb 10 2015 - 09:59:49 CST)
    - Re: Fwd: To delete some atoms via VMD Majid Shahbabaei (Tue Feb 10 2015 - 21:51:56 CST)
    - Re: Fwd: To delete some atoms via VMD Axel Kohlmeyer (Tue Feb 10 2015 - 22:34:17 CST)
topo guessatom Ben Hanson (Mon Feb 09 2015 - 12:03:14 CST)
- Re: topo guessatom Axel Kohlmeyer (Mon Feb 09 2015 - 12:37:07 CST)
  - Re: topo guessatom Axel Kohlmeyer (Mon Feb 09 2015 - 13:07:10 CST)
VMD secondary structure Stride bug Stefan Doerr (Mon Feb 09 2015 - 10:53:10 CST)
- RE: VMD secondary structure Stride bug Morgan, Brittany (Fri Feb 13 2015 - 09:17:54 CST)
  - Re: VMD secondary structure Stride bug Stefan Doerr (Fri Feb 13 2015 - 09:25:12 CST)
Cross-correlation coefficient calculated MDFF package Kevin C Chan (Mon Feb 09 2015 - 06:47:21 CST)
- Re: Cross-correlation coefficient calculated MDFF package Ryan McGreevy (Mon Feb 09 2015 - 10:36:55 CST)
NAMDEnergy fails to locate supporting files Viswanath Pasumarthi (Mon Feb 09 2015 - 06:32:15 CST)
- Re: NAMDEnergy fails to locate supporting files Fotis Baltoumas (Mon Feb 09 2015 - 06:53:41 CST)
Select Residues Ardavan Mehdizadeh (Mon Feb 09 2015 - 00:46:16 CST)
- Re: Select Residues M K (Mon Feb 09 2015 - 02:30:44 CST)
remove vmd package in centos Marzieh Dehghan (Sun Feb 08 2015 - 08:07:59 CST)
- Re: remove vmd package in centos John Stone (Mon Feb 09 2015 - 11:15:59 CST)
Beta testers wanted for modified AutoPSF Tristan Croll (Sun Feb 08 2015 - 01:57:33 CST)
(no subject) Jevgenij Raskatov (Sat Feb 07 2015 - 19:45:14 CST)
Re: namd-l: Analysis plugins for Martini Coarse Grained protein simulations Fotis Baltoumas (Sat Feb 07 2015 - 05:25:50 CST)
ACS COMP Division awards for Fall 2015 National Meeting in Boston Carlos Simmerling (Thu Feb 05 2015 - 10:55:09 CST)
Problem by removing vmd 1.9.1 and installing 1.9.2. Majid Shahbabaei (Thu Feb 05 2015 - 05:32:16 CST)
- Re: Problem by removing vmd 1.9.1 and installing 1.9.2. Khuong Truong Gia (Thu Feb 05 2015 - 05:56:15 CST)
- RE: Problem by removing vmd 1.9.1 and installing 1.9.2. Norman Geist (Thu Feb 05 2015 - 06:46:40 CST)
Putting different peptide chains (spaced apart) in a single .xbgf file Sourav Ray (Wed Feb 04 2015 - 05:25:19 CST)
- Re: Putting different peptide chains (spaced apart) in a single .xbgf file Tristan Croll (Sun Feb 08 2015 - 14:57:01 CST)
  - RE: Putting different peptide chains (spaced apart) in a single .xbgf file Richard Wood (Sun Feb 08 2015 - 19:11:52 CST)
    - Re: Putting different peptide chains (spaced apart) in a single .xbgf file Tristan Croll (Sun Feb 08 2015 - 19:30:28 CST)
    - Re: Putting different peptide chains (spaced apart) in a single .xbgf file Sourav Ray (Mon Feb 09 2015 - 02:28:54 CST)
LAST CALL: Free Energy Workshop, MÃ¼nster, March 9-11, 2015 Vlad Cojocaru (Tue Feb 03 2015 - 14:35:02 CST)
Recognizing Chlorine atoms in VMD Debasish Mandal (Tue Feb 03 2015 - 13:56:20 CST)
- Re: Recognizing Chlorine atoms in VMD John Stone (Mon Feb 09 2015 - 15:28:59 CST)
Selecting structure closest to average Jonathan Booth (Tue Feb 03 2015 - 10:46:38 CST)
- Re: Selecting structure closest to average Axel Kohlmeyer (Tue Feb 03 2015 - 11:55:55 CST)
namd2.exe has stopped working - NAMDEnergy Viswanath Pasumarthi (Tue Feb 03 2015 - 01:28:13 CST)
- Re: namd2.exe has stopped working - NAMDEnergy Pawel Kedzierski (Tue Feb 03 2015 - 03:23:32 CST)
  - Re: namd2.exe has stopped working - NAMDEnergy Viswanath Pasumarthi (Tue Feb 03 2015 - 04:07:45 CST)
    - Re: namd2.exe has stopped working - NAMDEnergy Pawel Kedzierski (Tue Feb 03 2015 - 05:02:37 CST)
- AW: namd2.exe has stopped working - NAMDEnergy Daniel Möller (Tue Feb 03 2015 - 06:21:10 CST)
(no subject) Jevgenij Raskatov (Mon Feb 02 2015 - 20:15:45 CST)
- Re: Josh Vermaas (Tue Feb 03 2015 - 09:21:06 CST)
vmd-I: Fatal Error: Unable to Open CHARMM Parameter File Akshata Rudrapatna (Mon Feb 02 2015 - 19:44:56 CST)
- AW: vmd-I: Fatal Error: Unable to Open CHARMM Parameter File Daniel MÃ¶ller (Tue Feb 03 2015 - 04:02:56 CST)
  - RE: vmd-I: Fatal Error: Unable to Open CHARMM Parameter File Norman Geist (Tue Feb 03 2015 - 06:17:36 CST)
    - RE: vmd-I: Fatal Error: Unable to Open CHARMM Parameter File Akshata Rudrapatna (Tue Feb 03 2015 - 08:26:31 CST)
Unit Cell PDB of Copper JAVAD NOROOZI (Mon Feb 02 2015 - 17:04:35 CST)
- Re: Unit Cell PDB of Copper Axel Kohlmeyer (Mon Feb 02 2015 - 17:53:34 CST)
  - Re: Unit Cell PDB of Copper M K (Mon Feb 02 2015 - 20:29:56 CST)
movie maker extension Eric Smoll (Mon Feb 02 2015 - 15:55:23 CST)
- RE: movie maker extension Norman Geist (Tue Feb 03 2015 - 01:49:42 CST)
questions about "new" posssible features Daniel Möller (Mon Feb 02 2015 - 05:29:17 CST)
BUG: vmd-1.9.2 final Representations GUI Norman Geist (Mon Feb 02 2015 - 03:52:52 CST)
- RE: BUG: vmd-1.9.2 final Representations GUI Norman Geist (Mon Feb 02 2015 - 05:30:42 CST)
  - Re: BUG: vmd-1.9.2 final Representations GUI Maxim Belkin (Mon Feb 02 2015 - 05:39:53 CST)
  - RE: BUG: vmd-1.9.2 final Representations GUI Norman Geist (Wed Feb 11 2015 - 01:38:08 CST)
plot secondary structure of protein along trajectory. Vy Phan (Mon Feb 02 2015 - 01:20:50 CST)
- RE: plot secondary structure of protein along trajectory. Norman Geist (Mon Feb 02 2015 - 03:39:04 CST)
rms alignment in VMD Gianluca Interlandi (Fri Jan 30 2015 - 14:27:10 CST)
- Re: rms alignment in VMD John Stone (Mon Feb 09 2015 - 15:44:04 CST)
quick tcl question with vmd/psfgen Brian Radak (Thu Jan 29 2015 - 12:30:47 CST)
- Re: quick tcl question with vmd/psfgen JC Gumbart (Thu Jan 29 2015 - 13:06:04 CST)
- Re: quick tcl question with vmd/psfgen Axel Kohlmeyer (Thu Jan 29 2015 - 13:33:20 CST)
  - Re: quick tcl question with vmd/psfgen Brian Radak (Thu Jan 29 2015 - 13:49:00 CST)
    - Re: quick tcl question with vmd/psfgen Axel Kohlmeyer (Thu Jan 29 2015 - 13:56:45 CST)
    - Re: quick tcl question with vmd/psfgen Brian Radak (Thu Jan 29 2015 - 14:04:08 CST)
- Re: quick tcl question with vmd/psfgen Josh Vermaas (Thu Jan 29 2015 - 13:42:33 CST)
Fwd: To delete some angles via VMD Majid Shahbabaei (Wed Jan 28 2015 - 23:09:54 CST)
- Re: Fwd: To delete some angles via VMD Axel Kohlmeyer (Thu Jan 29 2015 - 06:45:34 CST)
VMD Segmentation fault (core dumped) Matic Kisovec (Wed Jan 28 2015 - 09:53:11 CST)
- Re: VMD Segmentation fault (core dumped) John Stone (Wed Jan 28 2015 - 10:04:03 CST)
  - Re: VMD Segmentation fault (core dumped) Axel Kohlmeyer (Wed Jan 28 2015 - 10:52:58 CST)
    - Re: VMD Segmentation fault (core dumped) Matic Kisovec (Thu Jan 29 2015 - 05:51:02 CST)
    - Re: VMD Segmentation fault (core dumped) John Stone (Thu Jan 29 2015 - 10:06:01 CST)
- Re: VMD Segmentation fault (core dumped) Axel Kohlmeyer (Wed Jan 28 2015 - 10:44:10 CST)
Re-centering protein molecule Sourav Ray (Wed Jan 28 2015 - 05:14:56 CST)
- AW: Re-centering protein molecule Norman Geist (Wed Jan 28 2015 - 07:26:42 CST)
making self-adjustable high resolution images M K (Wed Jan 28 2015 - 04:47:26 CST)
- AW: making self-adjustable high resolution images Norman Geist (Wed Jan 28 2015 - 06:24:51 CST)
  - Re: making self-adjustable high resolution images John Stone (Wed Jan 28 2015 - 09:49:29 CST)
- Re: making self-adjustable high resolution images Axel Kohlmeyer (Wed Jan 28 2015 - 07:13:19 CST)
  - Re: making self-adjustable high resolution images Ajasja LjubetiÄ (Wed Jan 28 2015 - 07:56:14 CST)
  - RE: making self-adjustable high resolution images James Kress (Wed Jan 28 2015 - 10:46:09 CST)
    - Re: making self-adjustable high resolution images John Stone (Wed Jan 28 2015 - 11:12:44 CST)
    - Re: making self-adjustable high resolution images Axel Kohlmeyer (Wed Jan 28 2015 - 11:34:59 CST)
catdcd 5.1 not working from VMD terminal Michail Palaiokostas Avramidis (Tue Jan 27 2015 - 09:20:46 CST)
Hbond calculation - periodic atoms Bharat Sharma (Mon Jan 26 2015 - 18:59:58 CST)
- Re: Hbond calculation - periodic atoms Axel Kohlmeyer (Mon Jan 26 2015 - 20:50:46 CST)
Exposed area of a particular residue from dehydrated trajectory Charles McAnany (Sun Jan 25 2015 - 23:31:38 CST)
- Re: Exposed area of a particular residue from dehydrated trajectory Josh Vermaas (Mon Jan 26 2015 - 11:30:46 CST)
Hbond per residue Antonija TomiÄ‡ (Sun Jan 25 2015 - 03:56:19 CST)
- Re: Hbond per residue Maxim Belkin (Sun Jan 25 2015 - 06:24:13 CST)
  - Re: Hbond per residue Antonija TomiÄ‡ (Mon Jan 26 2015 - 03:08:07 CST)
    - Re: Hbond per residue Maxim Belkin (Mon Jan 26 2015 - 07:30:47 CST)
Does topo readlammpsdata automatically detect bonds? Dhritiman Talukdar (Sat Jan 24 2015 - 09:23:00 CST)
- Re: Does topo readlammpsdata automatically detect bonds? M K (Thu Jan 29 2015 - 19:16:23 CST)
  - Re: Does topo readlammpsdata automatically detect bonds? Axel Kohlmeyer (Thu Jan 29 2015 - 20:31:31 CST)
    - Re: Does topo readlammpsdata automatically detect bonds? Dhritiman Talukdar (Fri Jan 30 2015 - 03:21:48 CST)
Output of topo getbondlist to text file from VMD Dhritiman Talukdar (Fri Jan 23 2015 - 14:38:50 CST)
- Re: Output of topo getbondlist to text file from VMD Axel Kohlmeyer (Fri Jan 23 2015 - 15:05:04 CST)
  - Re: Output of topo getbondlist to text file from VMD Dhritiman Talukdar (Sat Jan 24 2015 - 09:21:04 CST)
within command Bennion, Brian (Fri Jan 23 2015 - 14:31:44 CST)
within command Thomas C. Bishop (Fri Jan 23 2015 - 13:04:10 CST)
- Re: within command Axel Kohlmeyer (Fri Jan 23 2015 - 14:05:27 CST)
  - Re: within command Maxim Belkin (Fri Jan 23 2015 - 14:44:27 CST)
VMD killed despite using $sel delete and unset sel MannyEful E (Thu Jan 22 2015 - 23:18:10 CST)
- Re: VMD killed despite using $sel delete and unset sel John Stone (Fri Jan 23 2015 - 00:20:52 CST)
  - Re: VMD killed despite using $sel delete and unset sel John Stone (Fri Jan 23 2015 - 11:39:51 CST)
  - Re: VMD killed despite using $sel delete and unset sel John Stone (Fri Jan 23 2015 - 23:25:25 CST)
Problem with FFTK in VMD 1.9.2 Dawid das (Thu Jan 22 2015 - 07:41:31 CST)
- Re: Problem with FFTK in VMD 1.9.2 Mayne, Christopher G (Thu Jan 22 2015 - 09:32:41 CST)
TachyonL-OptiX not shown in renderer list Alexandre Suman de Araujo (Thu Jan 22 2015 - 04:56:22 CST)
- Re: TachyonL-OptiX not shown in renderer list Josh Vermaas (Thu Jan 22 2015 - 08:00:34 CST)
  - Re: TachyonL-OptiX not shown in renderer list John Stone (Thu Jan 22 2015 - 08:58:05 CST)
tcl script for averaging a parameter along length Nima Nouri (Thu Jan 22 2015 - 03:40:31 CST)
- AW: tcl script for averaging a parameter along length Norman Geist (Thu Jan 22 2015 - 06:11:42 CST)
ion visualization in VMD JhonY. I. (Wed Jan 21 2015 - 21:47:30 CST)
- Re: ion visualization in VMD Pawel Kedzierski (Thu Jan 22 2015 - 02:53:57 CST)
- AW: ion visualization in VMD Norman Geist (Thu Jan 22 2015 - 03:34:26 CST)
  - Re: AW: ion visualization in VMD andrea spitaleri (Thu Jan 22 2015 - 04:30:00 CST)
nvidia optimus problem for 1.9.2 Albert (Wed Jan 21 2015 - 12:05:14 CST)
Error in disulfide bond identification in AutoPSF Tristan Croll (Tue Jan 20 2015 - 23:15:12 CST)
vmd-1: Colors in Representations Tab Akshata Rudrapatna (Tue Jan 20 2015 - 16:09:28 CST)
- Re: vmd-1: Colors in Representations Tab Josh Vermaas (Tue Jan 20 2015 - 17:02:57 CST)
vmd-1: Creating movies in VMD Akshata Rudrapatna (Tue Jan 20 2015 - 14:57:14 CST)
- Re: vmd-1: Creating movies in VMD Axel Kohlmeyer (Tue Jan 20 2015 - 15:26:13 CST)
  - Re: vmd-1: Creating movies in VMD Akshata Rudrapatna (Tue Jan 20 2015 - 15:53:44 CST)
The quality of movie made by VMD sunyeping (Sun Jan 18 2015 - 21:45:31 CST)
- AW: The quality of movie made by VMD Norman Geist (Mon Jan 19 2015 - 02:41:23 CST)
coloring scheme in "VolumeSlice" Walter Huang (Sat Jan 17 2015 - 21:08:02 CST)
- AW: coloring scheme in "VolumeSlice" Norman Geist (Mon Jan 19 2015 - 02:34:06 CST)
Re: Is a PDB file hiding something ??? Ashar Malik (Sat Jan 17 2015 - 05:01:53 CST)
- Re: Is a PDB file hiding something ??? Michail Palaiokostas Avramidis (Sat Jan 17 2015 - 05:57:07 CST)
  - Re: Is a PDB file hiding something ??? Axel Kohlmeyer (Sat Jan 17 2015 - 08:39:19 CST)
  - Re: Is a PDB file hiding something ??? Josh Vermaas (Sat Jan 17 2015 - 09:18:02 CST)
    - Re: Is a PDB file hiding something ??? Ashar Malik (Sat Jan 17 2015 - 21:14:19 CST)
Is a PDB file hiding something ??? Ashar Malik (Sat Jan 17 2015 - 00:27:13 CST)
Can I load NetCDF trajectories from AMBER in VMD on a Windows machine? Emilio Lence (Fri Jan 16 2015 - 06:12:54 CST)
- Re: Can I load NetCDF trajectories from AMBER in VMD on a Windows machine? Axel Kohlmeyer (Sat Jan 17 2015 - 17:11:07 CST)
VMD not working with Yosemite nupur bansal (Thu Jan 15 2015 - 20:38:54 CST)
- Re: VMD not working with Yosemite John Stone (Fri Apr 10 2015 - 16:07:30 CDT)
namdenergy plugin, selection field Bahaa Mostafa (Wed Jan 14 2015 - 23:56:13 CST)
using topotools: error in identifying atoms and dihedrals Nathan K Houtz (Wed Jan 14 2015 - 16:18:42 CST)
- Re: using topotools: error in identifying atoms and dihedrals Axel Kohlmeyer (Thu Jan 15 2015 - 05:10:10 CST)
Running CUDA on a laptop Tristan Croll (Tue Jan 13 2015 - 18:29:59 CST)
- Re: Running CUDA on a laptop Tristan Croll (Tue Jan 13 2015 - 19:14:31 CST)
- Re: Running CUDA on a laptop Jeremiah Babcock (Thu Jan 15 2015 - 22:59:18 CST)
Why does dipole moment depends so strongly on constraints? Dawid das (Tue Jan 13 2015 - 08:57:53 CST)
Build a customized alpha helix using Molefacture by command Jian Dai (Tue Jan 13 2015 - 08:23:01 CST)
- Re: Build a customized alpha helix using Molefacture by command Thomas C. Bishop (Tue Jan 13 2015 - 10:36:11 CST)
Re: Feature Request: Stride on vmd commandline startup Axel Kohlmeyer (Tue Jan 13 2015 - 08:18:01 CST)
- AW: Feature Request: Stride on vmd commandline startup Norman Geist (Wed Jan 14 2015 - 02:23:12 CST)
Feature Request: Stride on vmd commandline startup Norman Geist (Tue Jan 13 2015 - 07:44:31 CST)
atomselection by wildcard and distance exclusion Bennion, Brian (Mon Jan 12 2015 - 18:57:52 CST)
- FW: atomselection by wildcard and distance exclusion Bennion, Brian (Mon Jan 12 2015 - 23:12:58 CST)
  - Re: FW: atomselection by wildcard and distance exclusion John Stone (Mon Jan 12 2015 - 23:25:20 CST)
Re: Problem with the display panel John Stone (Mon Jan 12 2015 - 10:25:56 CST)
Re: Fwd: VMD 1.9.2 released! John Stone (Mon Jan 12 2015 - 10:37:35 CST)
- Re: Fwd: VMD 1.9.2 released! Axel Kohlmeyer (Mon Jan 12 2015 - 11:10:34 CST)
  - Re: Fwd: VMD 1.9.2 released! John Stone (Mon Jan 12 2015 - 11:35:35 CST)
- Re: Fwd: VMD 1.9.2 released! Josh Vermaas (Mon Jan 12 2015 - 11:40:34 CST)
  - AW: Fwd: VMD 1.9.2 released! Norman Geist (Tue Jan 13 2015 - 01:16:34 CST)
Reading chemical bonds by VMD from AMBER parm7 files Francesco Pietra (Sat Jan 10 2015 - 12:12:07 CST)
- Re: Reading chemical bonds by VMD from AMBER parm7 files John Stone (Wed Jan 14 2015 - 10:44:32 CST)
  - Re: Reading chemical bonds by VMD from AMBER parm7 files Francesco Pietra (Wed Jan 21 2015 - 11:52:10 CST)
Fwd: namd-l: Free Energy Workshop, MÃ¼nster, March 9-11, 2015 Ana Celia Vila Verde (Fri Jan 09 2015 - 06:34:01 CST)
Fwd: namd-l: Free Energy Workshop, MÃ¼nster, March 9-11, 2015 Ana Celia Vila Verde (Fri Jan 09 2015 - 03:35:00 CST)
Free Energy Workshop, MÃ¼nster, March 9-11, 2015 Vlad Cojocaru (Fri Jan 09 2015 - 03:20:14 CST)
write bonding/connectivity to file Eric Smoll (Thu Jan 08 2015 - 15:49:09 CST)
- Re: write bonding/connectivity to file Josh Vermaas (Thu Jan 08 2015 - 16:45:32 CST)
- Re: write bonding/connectivity to file Axel Kohlmeyer (Thu Jan 08 2015 - 16:57:40 CST)
RE: VMD TkConsole command Sanjib Chowdhury (Thu Jan 08 2015 - 10:27:51 CST)
- AW: VMD TkConsole command Daniel Möller (Thu Jan 08 2015 - 14:14:11 CST)
  - RE: VMD TkConsole command Sanjib Chowdhury (Thu Jan 08 2015 - 15:22:31 CST)
AW: VMD TkConsole command Norman Geist (Thu Jan 08 2015 - 09:17:15 CST)
VMD TkConsole command Sanjib Chowdhury (Wed Jan 07 2015 - 18:53:29 CST)
- AW: VMD TkConsole command Norman Geist (Thu Jan 08 2015 - 03:00:37 CST)
Troubles with VMD 1.9.2 recognizing TclTk 8.6 St. John, Alexander V. (MU-Student) (Wed Jan 07 2015 - 16:34:53 CST)
- Re: Troubles with VMD 1.9.2 recognizing TclTk 8.6 John Stone (Wed Jan 07 2015 - 16:46:53 CST)
  - Re: Troubles with VMD 1.9.2 recognizing TclTk 8.6 John Stone (Mon Jan 12 2015 - 10:30:50 CST)
Announcement: Hands-On Workshop On Computational Biophysics Danielle Chandler (Wed Jan 07 2015 - 12:30:34 CST)
Problem with Kinetic Energy of Atomselection JAVAD NOROOZI (Wed Jan 07 2015 - 00:48:34 CST)
- AW: Problem with Kinetic Energy of Atomselection Norman Geist (Wed Jan 07 2015 - 02:58:12 CST)
Change bond per atom limit of VMD Dhritiman Talukdar (Tue Jan 06 2015 - 09:36:52 CST)
- Re: Change bond per atom limit of VMD John Stone (Tue Jan 06 2015 - 10:23:47 CST)
  - Re: Change bond per atom limit of VMD Dhritiman Talukdar (Wed Jan 07 2015 - 14:53:49 CST)
- Re: Change bond per atom limit of VMD Axel Kohlmeyer (Tue Jan 06 2015 - 10:24:19 CST)
  - Re: Change bond per atom limit of VMD Dhritiman Talukdar (Tue Jan 06 2015 - 12:15:21 CST)
Large angle force constants with FFTK Elena Lilkova (Tue Jan 06 2015 - 07:32:57 CST)
- Re: Large angle force constants with FFTK Mayne, Christopher G (Wed Jan 07 2015 - 09:52:14 CST)
add/remove bonds between different types of atoms DanLiu (Mon Jan 05 2015 - 05:20:07 CST)
- Re: add/remove bonds between different types of atoms Ashar Malik (Mon Jan 05 2015 - 08:27:03 CST)
  - Re: add/remove bonds between different types of atoms John Stone (Tue Jan 06 2015 - 13:27:50 CST)
Display Problem with VMD in Mac OS Q=96zer_Duman?= (Sat Jan 03 2015 - 10:32:29 CST)
show water around a residue for all the frames of the MD trajectory Sunyeping (Sat Jan 03 2015 - 09:13:16 CST)
- Re: show water around a residue for all the frames of the MD trajectory Josh Vermaas (Mon Jan 05 2015 - 10:49:39 CST)
psf gen: missing atoms for bonds Mihaela Drenscko (Wed Dec 31 2014 - 10:17:49 CST)
REï¼š a script to count the frames in which some water molecules interact with selected protein atoms sunyeping (Tue Dec 30 2014 - 19:13:35 CST)
VMD 1.9.2 released! John Stone (Tue Dec 30 2014 - 13:47:29 CST)
- Re: VMD 1.9.2 released! Francesco Pietra (Wed Dec 31 2014 - 09:17:55 CST)
a script to count the frames in which some water molecules interact with selected protein atoms sunyeping (Tue Dec 30 2014 - 00:39:04 CST)
- RE: a script to count the frames in which some water molecules interact with selected protein atoms Bennion, Brian (Tue Dec 30 2014 - 10:25:41 CST)
ç”å¤ï¼š the usage of measure bond sunyeping (Mon Dec 29 2014 - 20:01:36 CST)
How to constrain a atom Sindrila Dutta Banik (Mon Dec 29 2014 - 10:19:13 CST)
- AW: How to constrain a atom Norman Geist (Mon Jan 05 2015 - 00:54:35 CST)
the usage of measure bond sunyeping (Mon Dec 29 2014 - 01:23:18 CST)
- Re: the usage of measure bond Josh Vermaas (Mon Dec 29 2014 - 06:14:52 CST)
- AW: the usage of measure bond Norman Geist (Mon Jan 05 2015 - 00:50:46 CST)
  - Re: AW: the usage of measure bond Sunyeping (Mon Jan 05 2015 - 01:31:39 CST)
density profile install Kazem Sepehrinia (Fri Dec 26 2014 - 10:14:19 CST)
ribbon rendering errors Rebecca Taylor (Thu Dec 25 2014 - 23:15:15 CST)
- Re: ribbon rendering errors Josh Vermaas (Fri Dec 26 2014 - 07:20:29 CST)
  - Re: ribbon rendering errors Rebecca Taylor (Mon Dec 29 2014 - 11:08:21 CST)
1.9.2 beta2 doesn't pop up window Albert (Thu Dec 25 2014 - 05:34:25 CST)
ç”å¤ï¼š non-bonded interactions sunyeping (Thu Dec 25 2014 - 03:46:36 CST)
non-bonded interactions Bahaa Mostafa (Wed Dec 24 2014 - 02:54:43 CST)
- Re: non-bonded interactions Ashar Malik (Wed Dec 24 2014 - 06:43:07 CST)
  - Re: non-bonded interactions Bahaa Mostafa (Wed Dec 24 2014 - 23:42:56 CST)
IR Spectral Density Calculator Plugin Ramin Ekhteiari (Tue Dec 23 2014 - 02:31:01 CST)
VMD 1.9.2 beta 2 posted for download... John Stone (Mon Dec 22 2014 - 21:03:04 CST)
- Re: VMD 1.9.2 beta 2 posted for download... Sujata Roy (Tue Dec 23 2014 - 05:41:12 CST)
Graphic window does not refresh Alessandro Mariani (Mon Dec 22 2014 - 20:04:41 CST)
Graphic window does not refresh Alessandro Mariani (Sun Dec 21 2014 - 13:19:41 CST)
- Re: Graphic window does not refresh John Stone (Sun Dec 21 2014 - 13:29:21 CST)
  - Re: Graphic window does not refresh Alessandro Mariani (Sun Dec 21 2014 - 15:28:47 CST)
    - Re: Graphic window does not refresh John Stone (Mon Dec 22 2014 - 20:03:35 CST)
  - Re: Graphic window does not refresh Alessandro Mariani (Mon Dec 22 2014 - 19:58:34 CST)
- Re: Graphic window does not refresh John Stone (Mon Dec 22 2014 - 20:04:22 CST)
Problem to generate solvent box Sindrila Dutta Banik (Fri Dec 19 2014 - 06:27:01 CST)
AW: AW: namd-l: FATAL ERROR: seek failed while writing DCD file: No such file or directory Norman Geist (Fri Dec 19 2014 - 02:45:26 CST)
- Re: AW: AW: namd-l: FATAL ERROR: seek failed while writing DCD file: No such file or directory John Stone (Fri Dec 19 2014 - 12:10:47 CST)
Topotools: Lammps data file for protein Hemant Gangwar (Thu Dec 18 2014 - 11:35:03 CST)
- Re: Topotools: Lammps data file for protein Axel Kohlmeyer (Thu Dec 18 2014 - 12:05:48 CST)
Announcement: Hands-On Workshop On Computational Biophysics Danielle Chandler (Wed Dec 17 2014 - 10:24:49 CST)
VMD crashing when loading prmtop files alex lin (Tue Dec 16 2014 - 17:37:58 CST)
- AW: VMD crashing when loading prmtop files Norman Geist (Wed Dec 17 2014 - 04:03:32 CST)
  - Re: VMD crashing when loading prmtop files John Stone (Wed Dec 17 2014 - 08:49:19 CST)
- Re: VMD crashing when loading prmtop files Hannes Loeffler (Wed Dec 17 2014 - 04:30:27 CST)
get the coordinate of the mouse arrow Xinqiang Ding (Tue Dec 16 2014 - 17:11:48 CST)
- Re: get the coordinate of the mouse arrow Ivan Moncayo (Tue Dec 16 2014 - 17:50:27 CST)
- Re: get the coordinate of the mouse arrow John Stone (Tue Dec 16 2014 - 20:23:25 CST)
  - Re: get the coordinate of the mouse arrow Xinqiang Ding (Tue Dec 16 2014 - 20:32:58 CST)
    - Re: get the coordinate of the mouse arrow John Stone (Wed Dec 17 2014 - 10:21:36 CST)
- Re: get the coordinate of the mouse arrow Maxim Belkin (Wed Dec 17 2014 - 01:30:56 CST)
Molspace volume calculation failed Albert (Tue Dec 16 2014 - 02:48:53 CST)
FFTK work's with molecules containing new atom types zoran (Mon Dec 15 2014 - 17:57:28 CST)
- Re: FFTK work's with molecules containing new atom types Francesco Pietra (Tue Dec 16 2014 - 01:21:43 CST)
  - Re: Re: FFTK work's with molecules containing new atom types zoran (Tue Dec 16 2014 - 09:42:00 CST)
    - Re: Re: FFTK work's with molecules containing new atom types Francesco Pietra (Tue Dec 16 2014 - 09:56:42 CST)
Question Eric Smoll (Mon Dec 15 2014 - 14:20:04 CST)
- AW: Question Norman Geist (Tue Dec 16 2014 - 04:03:18 CST)
need help for tcl script Kshatresh Dutta Dubey (Sun Dec 14 2014 - 10:02:14 CST)
- Re: need help for tcl script Ashar Malik (Sun Dec 14 2014 - 14:38:33 CST)
- Re: need help for tcl script Josh Vermaas (Sun Dec 14 2014 - 14:35:14 CST)
  - Re: need help for tcl script Kshatresh Dutta Dubey (Sun Dec 14 2014 - 14:52:54 CST)
Network View plugin Vlad Cojocaru (Sat Dec 13 2014 - 06:40:55 CST)
- Re: Network View plugin Vlad Cojocaru (Sat Dec 13 2014 - 07:11:42 CST)
FFTK most probably doesn't work with molecules containing new atom types zoran (Sat Dec 13 2014 - 06:50:49 CST)
- Re: FFTK most probably doesn't work with molecules containing new atom types Josh Vermaas (Sat Dec 13 2014 - 13:54:38 CST)
- Re: FFTK most probably doesn't work with molecules containing new atom types Axel Kohlmeyer (Sat Dec 13 2014 - 15:15:52 CST)
  - Re: FFTK most probably doesn't work with molecules containing new atom types Francesco Pietra (Sat Dec 13 2014 - 16:44:12 CST)
molefacture doesn't recognize lower-case letters nealec (Fri Dec 12 2014 - 20:23:24 CST)
- Re: molefacture doesn't recognize lower-case letters John Stone (Tue Apr 21 2015 - 04:06:30 CDT)
molefacture builds leucine with a nearly linear CA-CB-CG angle nealec (Fri Dec 12 2014 - 20:22:47 CST)
Using the chirality and cispeptide plugins with "vmd -dispdev text" nealec (Fri Dec 12 2014 - 20:17:09 CST)
- Re: Using the chirality and cispeptide plugins with "vmd -dispdev text" John Stone (Fri Dec 12 2014 - 20:33:04 CST)
  - Re: Using the chirality and cispeptide plugins with "vmd -dispdev text" nealec (Fri Dec 12 2014 - 23:55:20 CST)
VMD with 3D TV Smolin, Nikolai (Fri Dec 12 2014 - 10:09:43 CST)
- AW: VMD with 3D TV Norman Geist (Mon Dec 15 2014 - 01:43:12 CST)
  - Re: VMD with 3D TV John Stone (Mon Dec 15 2014 - 08:25:00 CST)
    - Re: VMD with 3D TV John Stone (Mon Feb 09 2015 - 11:26:12 CST)
    - Re: VMD with 3D TV John Stone (Mon Apr 13 2015 - 16:14:14 CDT)
  - Re: VMD with 3D TV John Stone (Wed Dec 17 2014 - 10:12:18 CST)
Small bugfix for NAMD Plot Pawel Kedzierski (Fri Dec 12 2014 - 02:35:54 CST)
- Re: Small bugfix for NAMD Plot John Stone (Fri Dec 12 2014 - 10:48:19 CST)
  - Re: Small bugfix for NAMD Plot Pawel Kedzierski (Sat Dec 13 2014 - 03:33:28 CST)
VMD/IMD problems on MacOS Yosemite Dimitrov, Alex (Fri Dec 12 2014 - 00:38:53 CST)
- Re: VMD/IMD problems on MacOS Yosemite John Stone (Fri Dec 12 2014 - 10:27:32 CST)
- Re: VMD/IMD problems on MacOS Yosemite John Stone (Fri Dec 12 2014 - 16:03:07 CST)
format I should use if I have different total number of atoms for each timesteps Jun-Chieh Wang (Thu Dec 11 2014 - 19:47:04 CST)
- Re: format I should use if I have different total number of atoms for each timesteps Ashar Malik (Thu Dec 11 2014 - 20:58:14 CST)
  - AW: format I should use if I have different total number of atoms for each timesteps Norman Geist (Fri Dec 12 2014 - 02:43:08 CST)
- Re: format I should use if I have different total number of atoms for each timesteps Pawel Kedzierski (Fri Dec 12 2014 - 02:32:05 CST)
tcl and vmd Eric Smoll (Thu Dec 11 2014 - 16:43:18 CST)
- Re: tcl and vmd Ashar Malik (Thu Dec 11 2014 - 18:01:48 CST)
- Re: tcl and vmd Axel Kohlmeyer (Fri Dec 12 2014 - 05:20:29 CST)
adding solvation box Kshatresh Dutta Dubey (Thu Dec 11 2014 - 09:53:24 CST)
- Re: adding solvation box Ashar Malik (Thu Dec 11 2014 - 15:05:14 CST)
fftk-bonded-opt problem zoran (Thu Dec 11 2014 - 03:30:25 CST)
Fwd: How find water mediated hydrogen bond Mehdi Bagherpour (Wed Dec 10 2014 - 16:33:25 CST)
- Re: Fwd: How find water mediated hydrogen bond Josh Vermaas (Wed Dec 10 2014 - 17:57:40 CST)
  - Re: Fwd: How find water mediated hydrogen bond M K (Tue Dec 16 2014 - 01:26:40 CST)
- Re: Fwd: How find water mediated hydrogen bond Axel Kohlmeyer (Wed Dec 10 2014 - 18:06:44 CST)
How find water mediated hydrogen bond Mehdi Bagherpour (Wed Dec 10 2014 - 09:40:58 CST)
- Re: How find water mediated hydrogen bond Axel Kohlmeyer (Wed Dec 10 2014 - 10:27:34 CST)
- Re: How find water mediated hydrogen bond zoran (Thu Dec 11 2014 - 06:26:39 CST)
Select phi, psi dihedrals with TopoTools George Patargias (Wed Dec 10 2014 - 08:12:25 CST)
- Re: Select phi, psi dihedrals with TopoTools Axel Kohlmeyer (Wed Dec 10 2014 - 08:46:14 CST)
  - Re: Select phi, psi dihedrals with TopoTools George Patargias (Wed Jan 21 2015 - 11:38:00 CST)
    - Re: Select phi, psi dihedrals with TopoTools Axel Kohlmeyer (Wed Jan 21 2015 - 12:18:50 CST)
vmd and yosemite gergely.gyimesi_at_ibmm.unibe.ch (Wed Dec 10 2014 - 02:38:55 CST)
- Re: vmd and yosemite gergely.gyimesi_at_ibmm.unibe.ch (Wed Dec 10 2014 - 03:18:22 CST)
  - Re: vmd and yosemite John Stone (Fri Dec 12 2014 - 15:48:57 CST)
How to save particular md frames by VMD Seera Suryanarayana (Tue Dec 09 2014 - 23:25:38 CST)
- Re: How to save particular md frames by VMD Ashar Malik (Wed Dec 10 2014 - 00:17:59 CST)
A query about the deletion of Hydrogen and re-adding them by psfgen Kshatresh Dutta Dubey (Tue Dec 09 2014 - 09:39:10 CST)
- Re: A query about the deletion of Hydrogen and re-adding them by psfgen Ashar Malik (Tue Dec 09 2014 - 16:50:08 CST)
  - Re: A query about the deletion of Hydrogen and re-adding them by psfgen Kshatresh Dutta Dubey (Tue Dec 09 2014 - 17:23:07 CST)
    - Re: A query about the deletion of Hydrogen and re-adding them by psfgen Ashar Malik (Tue Dec 09 2014 - 19:44:20 CST)
fftk problem - opt_bonded zoran (Mon Dec 08 2014 - 06:39:38 CST)
- Re: fftk problem - opt_bonded Mayne, Christopher G (Mon Dec 08 2014 - 08:28:13 CST)
H-Bonds not shown when loading by topo readlammpsdata M K (Sun Dec 07 2014 - 21:51:37 CST)
- Re: H-Bonds not shown when loading by topo readlammpsdata John Stone (Sun Dec 07 2014 - 22:08:43 CST)
  - Re: H-Bonds not shown when loading by topo readlammpsdata M K (Sun Dec 07 2014 - 22:34:02 CST)
    - AW: H-Bonds not shown when loading by topo readlammpsdata Norman Geist (Mon Dec 08 2014 - 01:49:11 CST)
Density of water box in solvate 1.5 plugin ~ 0.9 g/cc Jim Parker (Fri Dec 05 2014 - 07:29:22 CST)
- RE: Density of water box in solvate 1.5 plugin ~ 0.9 g/cc Richard Wood (Fri Dec 05 2014 - 08:58:47 CST)
  - Re: Density of water box in solvate 1.5 plugin ~ 0.9 g/cc Jim Parker (Fri Dec 05 2014 - 15:33:06 CST)
    - Re: Density of water box in solvate 1.5 plugin ~ 0.9 g/cc Jim Parker (Sat Dec 13 2014 - 15:02:17 CST)
Problem with 'measure energy elect' command in VMD Sujata Roy (Thu Dec 04 2014 - 23:17:53 CST)
- Re: Problem with 'measure energy elect' command in VMD Ashar Malik (Fri Dec 05 2014 - 00:03:26 CST)
  - Re: Problem with 'measure energy elect' command in VMD Sujata Roy (Sun Dec 07 2014 - 22:26:43 CST)
Fwd: How can I get the path of the TOP molecule in the tcl console? Ashar Malik (Thu Dec 04 2014 - 22:15:51 CST)
How can I get the path of the TOP molecule in the tcl console? Mohammad Khalkhali (Thu Dec 04 2014 - 19:25:50 CST)
- Re: How can I get the path of the TOP molecule in the tcl console? Cun Zhang (Thu Dec 04 2014 - 20:20:00 CST)
  - Re: How can I get the path of the TOP molecule in the tcl console? Cun Zhang (Thu Dec 04 2014 - 20:58:18 CST)
Topotools not changing psf Morgan, Brittany (Thu Dec 04 2014 - 12:00:21 CST)
- Re: Topotools not changing psf Axel Kohlmeyer (Thu Dec 04 2014 - 12:45:12 CST)
- Re: Topotools not changing psf Josh Vermaas (Thu Dec 04 2014 - 13:12:20 CST)
  - RE: Topotools not changing psf Morgan, Brittany (Thu Dec 04 2014 - 14:08:26 CST)
    - Re: Topotools not changing psf Axel Kohlmeyer (Thu Dec 04 2014 - 14:53:13 CST)
getting extra number of input file at the charge optimization phase/ ffTK Zeinab Emami (Wed Dec 03 2014 - 07:04:38 CST)
- Re: getting extra number of input file at the charge optimization phase/ ffTK Mayne, Christopher G (Wed Dec 03 2014 - 15:58:46 CST)
XOpenIM failed (failed to find CUDA devices) Vlad Cojocaru (Wed Dec 03 2014 - 06:47:01 CST)
- Re: XOpenIM failed (failed to find CUDA devices) John Stone (Wed Dec 03 2014 - 10:26:57 CST)
  - Re: XOpenIM failed (failed to find CUDA devices) John Stone (Wed Dec 03 2014 - 10:38:11 CST)
  - Re: XOpenIM failed (failed to find CUDA devices) Vlad Cojocaru (Wed Dec 03 2014 - 12:27:55 CST)
Regarding RMSD Seera Suryanarayana (Wed Dec 03 2014 - 00:53:03 CST)
- Re: Regarding RMSD Ashar Malik (Wed Dec 03 2014 - 01:13:42 CST)
How to find rmsd of energy minimized structure of protein Seera Suryanarayana (Tue Dec 02 2014 - 23:24:46 CST)
- Re: How to find rmsd of energy minimized structure of protein Abhijit Muley (Wed Dec 03 2014 - 00:10:12 CST)
- Re: How to find rmsd of energy minimized structure of protein Ashar Malik (Wed Dec 03 2014 - 00:27:32 CST)
query about the force field toolkit Kshatresh Dutta Dubey (Tue Dec 02 2014 - 02:56:45 CST)
- Re: query about the force field toolkit Ajasja LjubetiÄ (Tue Dec 02 2014 - 03:58:11 CST)
paratool/forcefield tool error Kshatresh Dutta Dubey (Mon Dec 01 2014 - 08:16:07 CST)
- Re: paratool/forcefield tool error Mayne, Christopher G (Tue Dec 02 2014 - 14:24:51 CST)
AW: Antw: AW: Oculus Rift DK2 Norman Geist (Mon Dec 01 2014 - 03:15:36 CST)
- AW: Antw: AW: Oculus Rift DK2 Christian Wohlschlager (Wed Dec 10 2014 - 04:49:00 CST)
program errors Albert (Sun Nov 30 2014 - 02:32:36 CST)
- AW: program errors Norman Geist (Mon Dec 01 2014 - 02:09:08 CST)
- Re: program errors John Stone (Wed Dec 03 2014 - 15:11:44 CST)
  - Re: program errors Albert (Wed Dec 03 2014 - 15:24:52 CST)
    - Re: program errors John Stone (Wed Dec 03 2014 - 15:30:09 CST)
Building structure Brittany Boykin (Sat Nov 29 2014 - 14:38:49 CST)
Building zeolite cage Abu Naser (Fri Nov 28 2014 - 07:08:00 CST)
How to make solid surfaces work with non-orthorhombic cells Miguel Caro (Fri Nov 28 2014 - 04:02:43 CST)
- AW: How to make solid surfaces work with non-orthorhombic cells Norman Geist (Fri Nov 28 2014 - 05:49:09 CST)
- Re: How to make solid surfaces work with non-orthorhombic cells Axel Kohlmeyer (Fri Nov 28 2014 - 07:04:17 CST)
  - Re: How to make solid surfaces work with non-orthorhombic cells Miguel Caro (Fri Nov 28 2014 - 10:00:59 CST)
Oculus Rift DK2 Christian Wohlschlager (Fri Nov 28 2014 - 03:47:14 CST)
- AW: Oculus Rift DK2 Norman Geist (Fri Nov 28 2014 - 05:33:58 CST)
Announcement: User defined movie animation Norman Geist (Fri Nov 28 2014 - 01:04:06 CST)
- Re: Announcement: User defined movie animation Emmanuel, Alaina (Fri Nov 28 2014 - 10:58:51 CST)
"measure bond" vs veclength Gianluca Interlandi (Wed Nov 26 2014 - 18:06:03 CST)
- Re: "measure bond" vs veclength John Stone (Wed Nov 26 2014 - 23:45:10 CST)
  - Re: "measure bond" vs veclength Gianluca Interlandi (Wed Nov 26 2014 - 23:55:47 CST)
    - Re: "measure bond" vs veclength John Stone (Wed Nov 26 2014 - 23:58:13 CST)
Any interest in VMD supporting mirror reflections w/ ray tracing? John Stone (Wed Nov 26 2014 - 13:49:51 CST)
- AW: Any interest in VMD supporting mirror reflections w/ ray tracing? Norman Geist (Thu Nov 27 2014 - 10:31:26 CST)
  - Re: Any interest in VMD supporting mirror reflections w/ ray tracing? Maxim Belkin (Thu Nov 27 2014 - 21:27:45 CST)
  - AW: Any interest in VMD supporting mirror reflections w/ ray tracing? Daniel Möller (Fri Nov 28 2014 - 06:53:01 CST)
    - Re: Any interest in VMD supporting mirror reflections w/ ray tracing? John Stone (Fri Nov 28 2014 - 17:30:44 CST)
Fwd: Problem with merging structures!( psfgen) Warning: failed to set coordinate for atom AU0 AU:1 A) Rangeen Othman (Wed Nov 26 2014 - 11:09:20 CST)
- Re: Problem with merging structures!( psfgen) Warning: failed to set coordinate for atom AU0 AU:1 A) Axel Kohlmeyer (Wed Nov 26 2014 - 11:25:44 CST)
  - Re: Problem with merging structures!( psfgen) Warning: failed to set coordinate for atom AU0 AU:1 A) Rangeen Othman (Wed Nov 26 2014 - 12:15:03 CST)
Problem with merging structures!( psfgen) Warning: failed to set coordinate for atom AU0 AU:1 A) Rangeen Othman (Wed Nov 26 2014 - 09:36:57 CST)
- Re: Problem with merging structures!( psfgen) Warning: failed to set coordinate for atom AU0 AU:1 A) Axel Kohlmeyer (Wed Nov 26 2014 - 10:13:20 CST)
Problem with merging structures!( psfgen) Warning: failed to set coordinate for atom AU0 AU:1 A) Rangeen Othman (Wed Nov 26 2014 - 09:20:10 CST)
A box of amino acids Kevin C Chan (Mon Nov 24 2014 - 10:08:52 CST)
- Re: A box of amino acids Axel Kohlmeyer (Mon Nov 24 2014 - 10:40:31 CST)
- Re: A box of amino acids Ajasja LjubetiÄ (Mon Nov 24 2014 - 10:54:04 CST)
  - RE: A box of amino acids Richard Wood (Mon Nov 24 2014 - 12:48:33 CST)
Tachyon Optix BUG vmd-1.9.2beta1 Norman Geist (Mon Nov 24 2014 - 05:12:59 CST)
- Re: Tachyon Optix BUG vmd-1.9.2beta1 John Stone (Mon Nov 24 2014 - 09:02:46 CST)
question about CUDA-enabled maryam atabay (Mon Nov 24 2014 - 03:08:43 CST)
- Re: question about CUDA-enabled Ashar Malik (Mon Nov 24 2014 - 03:45:07 CST)
Problem with incomplete ring in HIS Seera Suryanarayana (Mon Nov 24 2014 - 00:01:39 CST)
velocity or force of water molecules sunyeping (Sun Nov 23 2014 - 19:29:50 CST)
- Re: velocity or force of water molecules John Stone (Wed Nov 26 2014 - 16:51:32 CST)
  - Re: velocity or force of water molecules Ashar Malik (Wed Nov 26 2014 - 17:31:30 CST)
truncated atom types after merge Mihaela Drenscko (Sun Nov 23 2014 - 17:06:34 CST)
- Re: truncated atom types after merge Josh Vermaas (Mon Nov 24 2014 - 16:47:27 CST)
Misleading failure of VMD with charge/CGenFF from waterbox Francesco Pietra (Sun Nov 23 2014 - 03:21:38 CST)
problems with in text mode towards pdf and pdb files Francesco Pietra (Fri Nov 21 2014 - 09:09:52 CST)
- Re: namd-l: problems with in text mode towards pdf and pdb files Jim Phillips (Fri Nov 21 2014 - 09:29:35 CST)
  - Re: namd-l: problems with in text mode towards pdf and pdb files Francesco Pietra (Fri Nov 21 2014 - 09:39:56 CST)
create psf file without hydrogens Revthi Sanker (Thu Nov 20 2014 - 12:26:13 CST)
- Re: create psf file without hydrogens Josh Vermaas (Thu Nov 20 2014 - 13:55:24 CST)
  - Re: create psf file without hydrogens Revthi Sanker (Fri Nov 21 2014 - 03:23:41 CST)
Using "orient" - Vectors reversing direction? Meander Myself (Thu Nov 20 2014 - 09:26:27 CST)
Fixing the rotation of complex during trajectory visualization Kshatresh Dutta Dubey (Wed Nov 19 2014 - 06:09:27 CST)
- Re: Fixing the rotation of complex during trajectory visualization Ashar Malik (Wed Nov 19 2014 - 06:54:59 CST)
  - Re: Fixing the rotation of complex during trajectory visualization MannyEful E (Wed Nov 19 2014 - 08:18:25 CST)
(no subject) MannyEful E (Tue Nov 18 2014 - 07:40:29 CST)
- Re: Ajasja LjubetiÄ (Tue Nov 18 2014 - 08:24:59 CST)
  - Re: MannyEful E (Tue Nov 18 2014 - 09:14:12 CST)
- Re: Maxim Belkin (Tue Nov 18 2014 - 10:05:44 CST)
  - Re: MannyEful E (Tue Nov 18 2014 - 10:15:51 CST)
psfgen: no element symbol in pdb when occupancy zero Francesco Pietra (Fri Nov 14 2014 - 04:00:01 CST)
- Re: psfgen: no element symbol in pdb when occupancy zero Francesco Pietra (Fri Nov 14 2014 - 11:07:45 CST)
plotchart problem Albert (Thu Nov 13 2014 - 03:11:24 CST)
"Dynamic" gofr Ondrej Kroutil (Wed Nov 12 2014 - 17:52:22 CST)
How to calculate MSD on VMD Bharat Sharma (Wed Nov 12 2014 - 12:38:19 CST)
- Re: How to calculate MSD on VMD Bharat Sharma (Wed Nov 12 2014 - 13:52:55 CST)
  - Re: How to calculate MSD on VMD M K (Wed Nov 12 2014 - 17:54:44 CST)
cartoon of alpha carbon trace Knapp Bernhard (Wed Nov 12 2014 - 08:00:27 CST)
- Re: cartoon of alpha carbon trace John Stone (Wed Nov 12 2014 - 10:35:55 CST)
  - Re: cartoon of alpha carbon trace Knapp Bernhard (Thu Nov 13 2014 - 05:39:06 CST)
    - Re: cartoon of alpha carbon trace John Stone (Thu Nov 13 2014 - 11:31:45 CST)
    - Re: cartoon of alpha carbon trace Knapp Bernhard (Fri Nov 14 2014 - 10:24:32 CST)
FFTK-Opt.Bonded-empty string error_VMD1.9.2Beta SEZEN VATANSEVER (Wed Nov 12 2014 - 04:40:59 CST)
- Re: FFTK-Opt.Bonded-empty string error_VMD1.9.2Beta Ashar Malik (Wed Nov 12 2014 - 06:51:52 CST)
  - Re: FFTK-Opt.Bonded-empty string error_VMD1.9.2Beta Mayne, Christopher G (Wed Nov 12 2014 - 08:04:11 CST)
    - Re: FFTK-Opt.Bonded-empty string error_VMD1.9.2Beta Zeinab Emami (Wed Nov 12 2014 - 13:08:47 CST)
    - Re: FFTK-Opt.Bonded-empty string error_VMD1.9.2Beta Mayne, Christopher G (Mon Nov 17 2014 - 13:43:48 CST)
  - Re: FFTK-Opt.Bonded-empty string error_VMD1.9.2Beta SEZEN VATANSEVER (Thu Nov 20 2014 - 06:23:43 CST)
    - Re: FFTK-Opt.Bonded-empty string error_VMD1.9.2Beta Mayne, Christopher G (Wed Nov 26 2014 - 02:44:58 CST)
    - Re: FFTK-Opt.Bonded-empty string error_VMD1.9.2Beta Mayne, Christopher G (Thu Dec 04 2014 - 16:53:13 CST)
Query about the NAMD user forum Kshatresh Dutta Dubey (Wed Nov 12 2014 - 03:27:12 CST)
- Re: Query about the NAMD user forum Ajasja LjubetiÄ (Wed Nov 12 2014 - 04:12:23 CST)
Displaying Colors Kraemer, Tobias (Mon Nov 10 2014 - 07:04:58 CST)
- Re: Displaying Colors John Stone (Mon Nov 10 2014 - 09:14:52 CST)
  - Re: Displaying Colors John Stone (Wed Nov 12 2014 - 10:45:38 CST)
unable to create OpenGL window. Seera Suryanarayana (Mon Nov 10 2014 - 00:41:14 CST)
- Re: unable to create OpenGL window. John Stone (Mon Nov 10 2014 - 00:58:23 CST)
can't use arrow key in vmd -disp text mode Xinqiang Ding (Sat Nov 08 2014 - 16:46:28 CST)
- RE: can't use arrow key in vmd -disp text mode Joaquim Rui de Castro Rodrigues (Sat Nov 08 2014 - 18:24:19 CST)
  - Re: can't use arrow key in vmd -disp text mode Xinqiang Ding (Sun Nov 09 2014 - 11:00:14 CST)
- Re: can't use arrow key in vmd -disp text mode Axel Kohlmeyer (Sat Nov 08 2014 - 18:19:50 CST)
can we visualize sos file? Albert (Sat Nov 08 2014 - 10:18:08 CST)
- Re: can we visualize sos file? John Stone (Wed Nov 12 2014 - 22:42:24 CST)
ffTK: COLP (Charge Optimization Log Plotter) Zeinab Emami (Sat Nov 08 2014 - 10:07:14 CST)
- Re: ffTK: COLP (Charge Optimization Log Plotter) Mayne, Christopher G (Sat Nov 08 2014 - 11:14:15 CST)
Charge Optimization error: error deleting "base-wat.pdb": permission denied Zeinab Emami (Sat Nov 08 2014 - 07:40:24 CST)
- Re: Charge Optimization error: error deleting "base-wat.pdb": permission denied Mayne, Christopher G (Sat Nov 08 2014 - 10:11:49 CST)
  - Re: Charge Optimization error: error deleting "base-wat.pdb": permission denied Zeinab Emami (Sat Nov 08 2014 - 10:30:55 CST)
    - Re: Charge Optimization error: error deleting "base-wat.pdb": permission denied Mayne, Christopher G (Sat Nov 08 2014 - 11:29:31 CST)
  - Re: Re: Charge Optimization error: error deleting "base-wat.pdb": permission denied Ashar Malik (Sat Nov 08 2014 - 10:46:00 CST)
    - Re: Re: Charge Optimization error: error deleting "base-wat.pdb": permission denied Zeinab Emami (Sat Nov 08 2014 - 15:28:08 CST)
Problem in fink install netpbm for Movie Making M K (Fri Nov 07 2014 - 22:55:07 CST)
- Re: Problem in fink install netpbm for Movie Making John Stone (Wed Nov 12 2014 - 22:49:06 CST)
  - Re: Problem in fink install netpbm for Movie Making M K (Mon Dec 22 2014 - 21:19:58 CST)
ffTK problem: OPT.Charges Zeinab Emami (Fri Nov 07 2014 - 09:14:15 CST)
- Re: ffTK problem: OPT.Charges Mayne, Christopher G (Fri Nov 07 2014 - 10:51:57 CST)
  - Re: namd-l: Re: ffTK problem: OPT.Charges Zeinab Emami (Fri Nov 07 2014 - 11:13:04 CST)
Problems with reading Amber NetCDF restart files Giuseppe La Rosa (Fri Nov 07 2014 - 07:51:26 CST)
- Re: Problems with reading Amber NetCDF restart files John Stone (Thu Nov 13 2014 - 11:43:28 CST)
topology file for polystyrene Mihaela Drenscko (Thu Nov 06 2014 - 19:10:52 CST)
FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OE Mihaela Drenscko (Thu Nov 06 2014 - 12:47:34 CST)
- Re: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OE Axel Kohlmeyer (Thu Nov 06 2014 - 22:23:45 CST)
Rotate exchanges y and z axes? Miguel Caro (Wed Nov 05 2014 - 04:53:08 CST)
- Re: Rotate exchanges y and z axes? jing xia (Wed Nov 05 2014 - 19:53:16 CST)
- Re: Rotate exchanges y and z axes? John Stone (Wed Nov 05 2014 - 21:07:12 CST)
  - RE: Rotate exchanges y and z axes? Caro Miguel (Thu Nov 06 2014 - 02:29:03 CST)
how to have residues list and properties in vmd James Lord (Wed Nov 05 2014 - 03:20:58 CST)
Antw: Stereo Mode User Defined Christian Wohlschlager (Wed Nov 05 2014 - 02:08:34 CST)
Stereo Mode User Defined Christian Wohlschlager (Wed Nov 05 2014 - 02:06:10 CST)
Fwd: namd-l: Why RDF increases as r increase instead of constant Nifeng Guo hui (Sun Nov 02 2014 - 16:01:29 CST)
- Re: Fwd: namd-l: Why RDF increases as r increase instead of constant Tim Lo (Sun Nov 02 2014 - 19:19:57 CST)
  - Re: Fwd: namd-l: Why RDF increases as r increase instead of constant Nifeng Guo hui (Sun Nov 02 2014 - 22:19:43 CST)
psfgen N-terminal patches Chaya Stern (Fri Oct 31 2014 - 14:08:07 CDT)
- Re: psfgen N-terminal patches Ashar Malik (Fri Oct 31 2014 - 15:37:42 CDT)
  - Re: psfgen N-terminal patches Ashar Malik (Fri Oct 31 2014 - 16:05:54 CDT)
- Re: psfgen N-terminal patches Josh Vermaas (Fri Oct 31 2014 - 16:41:52 CDT)
  - Re: psfgen N-terminal patches Chaya Stern (Mon Nov 03 2014 - 11:17:08 CST)
can VMD render movies in stereo quad-buffered mode? Jose Borreguero (Fri Oct 31 2014 - 13:11:58 CDT)
- Re: can VMD render movies in stereo quad-buffered mode? John Stone (Fri Oct 31 2014 - 14:48:09 CDT)
Re: Need testers: VMD 1.9.2 w/ interactive GPU ray tracing w/ AO, depth of field, etc. John Stone (Fri Oct 31 2014 - 11:31:36 CDT)
Problem with VMD 1.9.1 and OS X 10.10 (OpenGL display freezing on reading PDB coordinates) Nick Fisher (Fri Oct 31 2014 - 10:51:09 CDT)
- Re: Problem with VMD 1.9.1 and OS X 10.10 (OpenGL display freezing on reading PDB coordinates) John Stone (Fri Oct 31 2014 - 11:22:29 CDT)
  - Re: Problem with VMD 1.9.1 and OS X 10.10 (OpenGL display freezing on reading PDB coordinates) John Stone (Fri Oct 31 2014 - 14:51:38 CDT)
  - Re: Problem with VMD 1.9.1 and OS X 10.10 (OpenGL display freezing on reading PDB coordinates) John Stone (Tue Jan 27 2015 - 12:36:31 CST)
Graphics card suitable for VMD Afroditi Maria Zaki (Fri Oct 31 2014 - 09:46:10 CDT)
- Re: Graphics card suitable for VMD Dudo (Fri Oct 31 2014 - 10:38:30 CDT)
  - Re: Graphics card suitable for VMD Josh Vermaas (Fri Oct 31 2014 - 13:35:02 CDT)
    - Re: Graphics card suitable for VMD John Stone (Fri Oct 31 2014 - 14:45:04 CDT)
    - Re: Graphics card suitable for VMD Gianluca Interlandi (Fri Oct 31 2014 - 15:59:46 CDT)
- Interactive Display of Molecular Orbitals Douglas Houston (Fri Oct 31 2014 - 11:05:24 CDT)
  - Re: Interactive Display of Molecular Orbitals John Stone (Mon Nov 03 2014 - 12:35:40 CST)
Oculus Rift Christian Wohlschlager (Fri Oct 31 2014 - 06:51:43 CDT)
- Re: Oculus Rift Basheer Subei (Sun Nov 02 2014 - 15:26:31 CST)
Need testers: VMD 1.9.2 w/ interactive GPU ray tracing w/ AO, depth of field, etc. John Stone (Thu Oct 30 2014 - 11:33:12 CDT)
- Re: Need testers: VMD 1.9.2 w/ interactive GPU ray tracing w/ AO, depth of field, etc. John Stone (Thu Nov 13 2014 - 00:21:33 CST)
  - AW: Re: Need testers: VMD 1.9.2 w/ interactive GPU ray tracing w/ AO, depth of field, etc. Norman Geist (Wed Nov 26 2014 - 02:32:21 CST)
Dynamic atomselect Ondrej Kroutil (Thu Oct 30 2014 - 08:49:09 CDT)
- Re: Dynamic atomselect Josh Vermaas (Thu Oct 30 2014 - 09:55:16 CDT)
  - Re: Dynamic atomselect Ondrej Kroutil (Thu Oct 30 2014 - 11:07:02 CDT)
- Re: Dynamic atomselect Micha³ Jakub Kañski (Thu Oct 30 2014 - 11:49:36 CDT)
essential dynamics visualization in VMD Vlad Cojocaru (Thu Oct 30 2014 - 04:38:51 CDT)
- Re: essential dynamics visualization in VMD John Stone (Thu Oct 30 2014 - 08:41:05 CDT)
  - Re: essential dynamics visualization in VMD Vlad Cojocaru (Thu Oct 30 2014 - 09:15:20 CDT)
install the third part plugins sunyeping (Wed Oct 29 2014 - 12:26:59 CDT)
BUG(s): vmd-1.9.2b Norman Geist (Wed Oct 29 2014 - 04:10:16 CDT)
- Re: BUG(s): vmd-1.9.2b John Stone (Thu Oct 30 2014 - 08:50:21 CDT)
  - AW: BUG(s): vmd-1.9.2b Norman Geist (Thu Oct 30 2014 - 09:25:36 CDT)
removing water inside the nanotube Asis Jana (Tue Oct 28 2014 - 11:19:42 CDT)
- Re: removing water inside the nanotube Ajasja LjubetiÄ (Tue Oct 28 2014 - 11:54:41 CDT)
  - Re: removing water inside the nanotube Asis Jana (Tue Oct 28 2014 - 23:24:57 CDT)
    - Re: removing water inside the nanotube Ashar Malik (Wed Oct 29 2014 - 03:54:03 CDT)
    - Re: removing water inside the nanotube Ajasja LjubetiÄ (Wed Oct 29 2014 - 05:07:28 CDT)
ParseFEP in text mode Gianluca Interlandi (Mon Oct 27 2014 - 21:19:54 CDT)
VMD with Cuda 6.5, Mac OS X 10.10 McNutt, Nick (Mon Oct 27 2014 - 17:14:25 CDT)
- Re: VMD with Cuda 6.5, Mac OS X 10.10 John Stone (Mon Oct 27 2014 - 23:19:43 CDT)
AW: AW: AW: VMD warnings Norman Geist (Mon Oct 27 2014 - 03:05:14 CDT)
AW: AW: VMD warnings Norman Geist (Fri Oct 24 2014 - 13:01:27 CDT)
(no subject) Rangeen Othman (Fri Oct 24 2014 - 06:39:03 CDT)
vmd-l incoming mails become Spam Ashar Malik (Fri Oct 24 2014 - 06:20:43 CDT)
- Re: vmd-l incoming mails become Spam Axel Kohlmeyer (Fri Oct 24 2014 - 06:48:24 CDT)
  - Re: vmd-l incoming mails become Spam Maxim Belkin (Fri Oct 24 2014 - 06:56:54 CDT)
    - Re: vmd-l incoming mails become Spam Ashar Malik (Fri Oct 24 2014 - 07:04:41 CDT)
  - Re: vmd-l incoming mails become Spam Ashar Malik (Fri Oct 24 2014 - 07:00:24 CDT)
VMD warnings amirhossein taghavi (Fri Oct 24 2014 - 01:58:41 CDT)
- AW: VMD warnings Norman Geist (Fri Oct 24 2014 - 05:05:16 CDT)
converting a .cif file into a vmd readable format, how? Jonathan Gough (Thu Oct 23 2014 - 11:58:07 CDT)
- Re: converting a .cif file into a vmd readable format, how? Ryan McGreevy (Thu Oct 23 2014 - 12:45:44 CDT)
  - Re: converting a .cif file into a vmd readable format, how? Jonathan Gough (Thu Oct 23 2014 - 12:52:51 CDT)
    - Re: converting a .cif file into a vmd readable format, how? Ryan McGreevy (Thu Oct 23 2014 - 13:01:11 CDT)
Extensions menu empty Woodson, Michael (Thu Oct 23 2014 - 10:27:54 CDT)
- Re: Extensions menu empty Josh Vermaas (Thu Oct 23 2014 - 12:13:23 CDT)
  - RE: Extensions menu empty Woodson, Michael (Thu Oct 23 2014 - 13:15:05 CDT)
Tachyon-Optix failure when SSH X11 Norman Geist (Thu Oct 23 2014 - 10:01:31 CDT)
- Re: Tachyon-Optix failure when SSH X11 John Stone (Thu Oct 23 2014 - 10:29:43 CDT)
  - AW: Tachyon-Optix failure when SSH X11 Norman Geist (Thu Oct 23 2014 - 10:48:28 CDT)
- Re: Tachyon-Optix failure when SSH X11 Maxim Belkin (Thu Oct 23 2014 - 10:34:22 CDT)
Syntax of the "within [distance] of" command Meander Myself (Wed Oct 22 2014 - 13:01:55 CDT)
- Re: Syntax of the "within [distance] of" command Maxim Belkin (Wed Oct 22 2014 - 15:26:05 CDT)
compile VMD with cuda 6.5.14 Vlad Cojocaru (Wed Oct 22 2014 - 09:39:04 CDT)
- Re: compile VMD with cuda 6.5.14 John Stone (Wed Oct 22 2014 - 11:28:35 CDT)
  - Re: compile VMD with cuda 6.5.14 Vlad Cojocaru (Thu Oct 23 2014 - 04:47:31 CDT)
    - Re: compile VMD with cuda 6.5.14 Vlad Cojocaru (Thu Oct 23 2014 - 05:33:43 CDT)
Gaussian run for ffTK: Solvation needed? Zeinab Emami (Wed Oct 22 2014 - 09:00:53 CDT)
- Re: Gaussian run for ffTK: Solvation needed? Mayne, Christopher G (Wed Oct 22 2014 - 09:14:49 CDT)
Python text interpreter in VMD Woodson, Michael (Tue Oct 21 2014 - 10:13:18 CDT)
- Re: Python text interpreter in VMD Josh Vermaas (Tue Oct 21 2014 - 11:53:38 CDT)
  - RE: Python text interpreter in VMD Woodson, Michael (Tue Oct 21 2014 - 14:07:25 CDT)
    - Re: Python text interpreter in VMD Josh Vermaas (Tue Oct 21 2014 - 15:10:10 CDT)
namd-l: Re: ffTK problem: initial parameter file is void of atoms! Zeinab Emami (Mon Oct 20 2014 - 11:34:17 CDT)
- Re: namd-l: Re: ffTK problem: initial parameter file is void of atoms! Zeinab Emami (Mon Oct 20 2014 - 12:44:19 CDT)
  - Re: namd-l: Re: ffTK problem: initial parameter file is void of atoms! Mayne, Christopher G (Mon Oct 20 2014 - 13:05:04 CDT)
- Re: namd-l: Re: ffTK problem: initial parameter file is void of atoms! Zeinab Emami (Mon Oct 20 2014 - 14:14:23 CDT)
  - Re: namd-l: Re: ffTK problem: initial parameter file is void of atoms! Zeinab Emami (Mon Oct 20 2014 - 14:15:16 CDT)
  - Re: namd-l: Re: ffTK problem: initial parameter file is void of atoms! Mayne, Christopher G (Mon Oct 20 2014 - 14:19:29 CDT)
    - Re: namd-l: Re: ffTK problem: initial parameter file is void of atoms! Zeinab Emami (Mon Oct 20 2014 - 14:27:30 CDT)
Selecting one half of a residue based CG lipid bilayer Meander Myself (Thu Oct 16 2014 - 21:01:58 CDT)
- RE: Selecting one half of a residue based CG lipid bilayer Tristan Croll (Fri Oct 17 2014 - 00:57:34 CDT)
Re: Issue rendering cylinders in povray John Stone (Thu Oct 16 2014 - 15:57:32 CDT)
VRPN support for the Windows VMD 1.9.1 George Patargias (Thu Oct 16 2014 - 09:27:53 CDT)
- Re: VRPN support for the Windows VMD 1.9.1 John Stone (Thu Oct 16 2014 - 15:40:32 CDT)
  - Re: VRPN support for the Windows VMD 1.9.1 George Patargias (Fri Oct 17 2014 - 02:45:52 CDT)
  - Re: VRPN support for the Windows VMD 1.9.1 George Patargias (Mon Oct 20 2014 - 09:15:34 CDT)
"graphics top line" and "render POV3" Eric Smoll (Wed Oct 15 2014 - 21:46:05 CDT)
- Re: "graphics top line" and "render POV3" John Stone (Wed Oct 15 2014 - 22:03:09 CDT)
  - Re: "graphics top line" and "render POV3" Eric Smoll (Wed Oct 15 2014 - 22:25:37 CDT)
VMD with Falcon George Patargias (Wed Oct 15 2014 - 10:07:29 CDT)
- Re: VMD with Falcon John Stone (Wed Oct 15 2014 - 10:22:21 CDT)
  - Re: VMD with Falcon George Patargias (Wed Oct 15 2014 - 10:34:41 CDT)
GTP and GDP parameter files Anjela Manandhar (Wed Oct 15 2014 - 10:02:23 CDT)
- Re: GTP and GDP parameter files Josh Vermaas (Wed Oct 15 2014 - 14:04:06 CDT)
  - RE: GTP and GDP parameter files Tristan Croll (Wed Oct 15 2014 - 17:45:30 CDT)
  - Re: GTP and GDP parameter files Anjela Manandhar (Mon Dec 01 2014 - 15:00:59 CST)
- Re: GTP and GDP parameter files andrea (Wed Oct 15 2014 - 15:38:14 CDT)
Scale the molecule spandu K (Wed Oct 15 2014 - 03:21:57 CDT)
- AW: Scale the molecule Norman Geist (Wed Oct 15 2014 - 05:25:25 CDT)
Transparency rendering by Tachyon Kevin C Chan (Sun Oct 12 2014 - 23:39:05 CDT)
- AW: Transparency rendering by Tachyon Norman Geist (Mon Oct 13 2014 - 01:52:28 CDT)
Displaying residue name in simulation movie James Lord (Sun Oct 12 2014 - 22:04:36 CDT)
- Fwd: Displaying residue name in simulation movie James Lord (Sun Oct 12 2014 - 22:11:16 CDT)
- Re: Displaying residue name in simulation movie Josh Vermaas (Mon Oct 13 2014 - 09:15:38 CDT)
set tcl/tk variable from "get resname" command mason H (Fri Oct 10 2014 - 12:58:47 CDT)
- Re: set tcl/tk variable from "get resname" command Maxim Belkin (Fri Oct 10 2014 - 13:12:45 CDT)
Successful VMD win64 Compile Nima Nouri (Thu Oct 09 2014 - 16:48:15 CDT)
Error while calculating rotational angle Aiswarya (Thu Oct 09 2014 - 13:32:55 CDT)
- RE: Error while calculating rotational angle Bennion, Brian (Thu Oct 09 2014 - 15:09:58 CDT)
- Re: Error while calculating rotational angle Josh Vermaas (Thu Oct 09 2014 - 15:31:13 CDT)
  - Re: Error while calculating rotational angle Aiswarya Pawar (Thu Oct 09 2014 - 22:51:41 CDT)
    - Re: Error while calculating rotational angle Tristan Croll (Fri Oct 10 2014 - 00:38:50 CDT)
    - Re: Error while calculating rotational angle Josh Vermaas (Fri Oct 10 2014 - 08:19:20 CDT)
How to remove particular residues and then view "ramachandran plot" in VMD Devanand T (Thu Oct 09 2014 - 04:44:06 CDT)
- AW: How to remove particular residues and then view "ramachandran plot" in VMD Norman Geist (Thu Oct 09 2014 - 07:05:14 CDT)
- Re: How to remove particular residues and then view "ramachandran plot" in VMD Björn Forsberg (Thu Oct 09 2014 - 07:50:41 CDT)
Visualizing two different data sets in the isosurface mode DEBOSTUTI GHOSHDASTIDAR (Thu Oct 09 2014 - 02:24:39 CDT)
- Re: Visualizing two different data sets in the isosurface mode John Stone (Fri Oct 10 2014 - 10:07:02 CDT)
  - Re: Visualizing two different data sets in the isosurface mode DEBOSTUTI GHOSHDASTIDAR (Sat Oct 11 2014 - 00:31:44 CDT)
VMD plugins not available without gui BjÃ¶rn Forsberg (Wed Oct 08 2014 - 03:37:23 CDT)
- Re: VMD plugins not available without gui Ashar Malik (Wed Oct 08 2014 - 04:13:33 CDT)
Announcement: Hands-On Workshop On Computational Biophysics Danielle Chandler (Tue Oct 07 2014 - 11:30:00 CDT)
Haptic interface options Tristan Croll (Mon Oct 06 2014 - 20:00:28 CDT)
- Re: Haptic interface options Axel Kohlmeyer (Tue Oct 07 2014 - 12:00:37 CDT)
  - Re: Haptic interface options Tristan Croll (Tue Oct 07 2014 - 14:23:17 CDT)
Fwd: VMD Compile problem Nima Nouri (Mon Oct 06 2014 - 16:51:59 CDT)
psfgen not parsing toppar_all36_lipid_detergent.str Chaya Stern (Mon Oct 06 2014 - 15:01:48 CDT)
- Re: psfgen not parsing toppar_all36_lipid_detergent.str Josh Vermaas (Mon Oct 06 2014 - 16:09:00 CDT)
  - Re: psfgen not parsing toppar_all36_lipid_detergent.str Chaya Stern (Mon Oct 06 2014 - 16:25:30 CDT)
log colorscale Eric Smoll (Sun Oct 05 2014 - 15:28:58 CDT)
- Re: log colorscale Axel Kohlmeyer (Sun Oct 05 2014 - 16:09:50 CDT)
- Re: log colorscale Tristan Croll (Mon Oct 06 2014 - 03:12:31 CDT)
  - AW: log colorscale Norman Geist (Mon Oct 06 2014 - 05:25:26 CDT)
Compiling VMD for Windows 64bit Nima Nouri (Fri Oct 03 2014 - 15:08:15 CDT)
- Re: Compiling VMD for Windows 64bit John Stone (Fri Oct 03 2014 - 15:47:50 CDT)
  - Re: Compiling VMD for Windows 64bit Nima Nouri (Sun Oct 05 2014 - 07:46:47 CDT)
    - Re: Compiling VMD for Windows 64bit Nima Nouri (Sun Oct 05 2014 - 07:56:08 CDT)
    - Re: Compiling VMD for Windows 64bit Nima Nouri (Sun Oct 05 2014 - 11:07:33 CDT)
creating an index file for POPC in water Mihaela Drenscko (Fri Oct 03 2014 - 13:57:31 CDT)
- Re: creating an index file for POPC in water Fotis Baltoumas (Fri Oct 03 2014 - 15:24:52 CDT)
topotools question regarding ordering of bonds, angles, etc in output. Dave Schall (Fri Oct 03 2014 - 11:08:27 CDT)
- Re: topotools question regarding ordering of bonds, angles, etc in output. Josh Vermaas (Fri Oct 03 2014 - 12:21:34 CDT)
  - Re: topotools question regarding ordering of bonds, angles, etc in output. Axel Kohlmeyer (Fri Oct 03 2014 - 13:16:37 CDT)
    - Re: topotools question regarding ordering of bonds, angles, etc in output. Dave Schall (Fri Oct 03 2014 - 13:25:27 CDT)
    - Re: topotools question regarding ordering of bonds, angles, etc in output. Axel Kohlmeyer (Fri Oct 03 2014 - 14:32:48 CDT)
- Re: topotools question regarding ordering of bonds, angles, etc in output. Axel Kohlmeyer (Fri Oct 03 2014 - 12:44:53 CDT)
  - Re: topotools question regarding ordering of bonds, angles, etc in output. Dave Schall (Fri Oct 03 2014 - 12:51:22 CDT)
calculate structure of protein Rangeen Othman (Fri Oct 03 2014 - 06:45:21 CDT)
- Re: calculate structure of protein Ashar Malik (Fri Oct 03 2014 - 07:18:08 CDT)
Fwd: making psf files Zeinab Emami (Thu Oct 02 2014 - 11:45:27 CDT)
- Re: making psf files Zeinab Emami (Thu Oct 02 2014 - 11:48:49 CDT)
- RE: making psf files Richard Wood (Thu Oct 02 2014 - 13:03:28 CDT)
making psf files M Karim (Wed Oct 01 2014 - 07:53:14 CDT)
- Re: making psf files John Stone (Wed Oct 01 2014 - 08:02:49 CDT)
Creating multiple views from same trajectory file for movie generation Michael Doig (Wed Oct 01 2014 - 07:25:04 CDT)
- Re: Creating multiple views from same trajectory file for movie generation John Stone (Wed Oct 01 2014 - 07:43:22 CDT)
  - Re: Creating multiple views from same trajectory file for movie generation Michael Doig (Fri Oct 03 2014 - 05:45:02 CDT)
- Re: Creating multiple views from same trajectory file for movie generation Felipe Merino (Wed Oct 01 2014 - 08:36:35 CDT)
Reg: Peptide dimer Amit Jaiswal (Wed Oct 01 2014 - 03:42:30 CDT)
- Re: Reg: Peptide dimer Ajasja LjubetiÄ (Wed Oct 01 2014 - 04:45:43 CDT)
  - RE: Reg: Peptide dimer Richard Wood (Wed Oct 01 2014 - 05:54:59 CDT)
    - Re: Reg: Peptide dimer Tim Lo (Wed Oct 01 2014 - 06:49:33 CDT)
    - Re: Reg: Peptide dimer Amit Jaiswal (Wed Oct 01 2014 - 23:12:13 CDT)
NetworkView -- Averaging SEPARATE contact.dat files? mason H (Tue Sep 30 2014 - 20:22:31 CDT)
- Re: NetworkView -- Averaging SEPARATE contact.dat files? Anurag Sethi (Tue Oct 07 2014 - 11:16:31 CDT)
NetworkView - Path lengths mason H (Tue Sep 30 2014 - 19:39:53 CDT)
- Re: NetworkView - Path lengths Anurag Sethi (Tue Oct 07 2014 - 11:12:52 CDT)
Tk script PaweÅ‚ Wolski (Tue Sep 30 2014 - 09:54:26 CDT)
- Re: Tk script Maxim Belkin (Tue Sep 30 2014 - 10:11:23 CDT)
- Re: Tk script Axel Kohlmeyer (Tue Sep 30 2014 - 11:08:27 CDT)
  - Re: Tk script PaweÅ‚ Wolski (Tue Sep 30 2014 - 13:08:50 CDT)
Stray PME grid Vy Phan (Tue Sep 30 2014 - 09:39:12 CDT)
- Re: Stray PME grid Mayne, Christopher G (Tue Sep 30 2014 - 12:26:28 CDT)
Problem with ViewChangeRender Mikhail Suyetin (Tue Sep 30 2014 - 09:07:18 CDT)
- Re: Problem with ViewChangeRender Mikhail Suyetin (Wed Oct 01 2014 - 08:20:58 CDT)
  - Re: Problem with ViewChangeRender John Stone (Wed Oct 01 2014 - 13:27:59 CDT)
Reg: Peptide dimer Amit Jaiswal (Tue Sep 30 2014 - 06:18:14 CDT)
- AW: Reg: Peptide dimer Norman Geist (Tue Sep 30 2014 - 08:49:55 CDT)
Protein went out of the Box Vy Phan (Mon Sep 29 2014 - 08:09:02 CDT)
- Re: Protein went out of the Box Ana Celia Vila Verde (Mon Sep 29 2014 - 09:21:18 CDT)
  - Re: Protein went out of the Box M K (Mon Mar 02 2015 - 02:06:24 CST)
    - RE: Protein went out of the Box Norman Geist (Mon Mar 02 2015 - 02:15:16 CST)
- Re: Protein went out of the Box Josh Vermaas (Mon Sep 29 2014 - 09:14:02 CDT)
  - Re: Protein went out of the Box M K (Tue Nov 11 2014 - 18:12:50 CST)
how to make the structures in the movie look better ALIYUN (Mon Sep 29 2014 - 05:06:14 CDT)
- AW: how to make the structures in the movie look better Norman Geist (Mon Sep 29 2014 - 07:58:00 CDT)
  - Re: AW: how to make the structures in the movie look better Felipe Merino (Mon Sep 29 2014 - 09:28:49 CDT)
    - Re: AW: how to make the structures in the movie look better SebastiÃ¡n GutiÃ©rrez (Mon Oct 20 2014 - 15:10:32 CDT)
- Re: how to make the structures in the movie look better Axel Kohlmeyer (Mon Sep 29 2014 - 08:55:27 CDT)
color by Name PaweÅ‚ Wolski (Mon Sep 29 2014 - 04:10:04 CDT)
Writepdb all frames of DCD to same file using command line Mike Makowski (Sun Sep 28 2014 - 21:41:06 CDT)
"OpenGL Display" and "VMD Main" windows; size and location on launch Eric Smoll (Sun Sep 28 2014 - 15:06:37 CDT)
- Re: "OpenGL Display" and "VMD Main" windows; size and location on launch John Stone (Sun Sep 28 2014 - 15:16:37 CDT)
  - Re: "OpenGL Display" and "VMD Main" windows; size and location on launch Eric Smoll (Sun Sep 28 2014 - 15:27:09 CDT)
    - AW: "OpenGL Display" and "VMD Main" windows; size and location on launch Norman Geist (Mon Sep 29 2014 - 00:49:34 CDT)
    - Re: "OpenGL Display" and "VMD Main" windows; size and location on launch Mayne, Christopher G (Mon Sep 29 2014 - 09:12:59 CDT)
Is there a way to view .Hin files in VMD Ganesh Kamath (Fri Sep 26 2014 - 12:38:17 CDT)
- Re: Is there a way to view .Hin files in VMD John Stone (Sat Sep 27 2014 - 23:35:58 CDT)
VMD 1.9.2 b1 OptiX Tachyon Error Stober, Spencer T (Fri Sep 26 2014 - 09:40:07 CDT)
- Re: VMD 1.9.2 b1 OptiX Tachyon Error John Stone (Fri Sep 26 2014 - 09:55:36 CDT)
  - RE: VMD 1.9.2 b1 OptiX Tachyon Error Stober, Spencer T (Fri Sep 26 2014 - 10:35:07 CDT)
Problem with TIP3 angles during phosphorylation Thierry Oscar Wambo (Fri Sep 26 2014 - 08:04:18 CDT)
- TclBC of an asymmetric system Thierry Oscar Wambo (Wed Apr 22 2015 - 12:56:27 CDT)
select a group of atoms/distance measurement amirhossein taghavi (Fri Sep 26 2014 - 07:59:17 CDT)
- Re: select a group of atoms/distance measurement Maxim Belkin (Fri Sep 26 2014 - 11:30:58 CDT)
create bonds with uniform pairwise cut off radius for XYZ trajectories. khannan krishna (Fri Sep 26 2014 - 00:48:04 CDT)
- Re: create bonds with uniform pairwise cut off radius for XYZ trajectories. Axel Kohlmeyer (Fri Sep 26 2014 - 03:59:32 CDT)
  - Re: create bonds with uniform pairwise cut off radius for XYZ trajectories. khannan krishna (Fri Sep 26 2014 - 05:05:52 CDT)
Labels for part of a trajectory Thomas Sexton (Thu Sep 25 2014 - 10:28:10 CDT)
- Re: Labels for part of a trajectory Josh Vermaas (Thu Sep 25 2014 - 11:29:14 CDT)
  - Re: Labels for part of a trajectory M Karim (Thu Sep 25 2014 - 18:38:45 CDT)
Atom Selection Rectangle Parker de Waal (Tue Sep 23 2014 - 20:27:08 CDT)
- Re: Atom Selection Rectangle John Stone (Tue Sep 23 2014 - 21:00:29 CDT)
  - Re: Atom Selection Rectangle Parker de Waal (Tue Sep 23 2014 - 21:49:32 CDT)
Resname CHARMM to NAMD Thierry Oscar Wambo (Mon Sep 22 2014 - 22:58:32 CDT)
- Re: Resname CHARMM to NAMD Ashar Malik (Mon Sep 22 2014 - 23:50:14 CDT)
- Re: Resname CHARMM to NAMD Josh Vermaas (Tue Sep 23 2014 - 09:28:30 CDT)
  - Re: Resname CHARMM to NAMD Thierry Oscar Wambo (Tue Sep 23 2014 - 10:57:53 CDT)
Selecting atoms based on the charges M Karim (Mon Sep 22 2014 - 21:25:44 CDT)
- Re: Selecting atoms based on the charges Josh Vermaas (Tue Sep 23 2014 - 09:08:07 CDT)
  - Re: Selecting atoms based on the charges Maxim Belkin (Tue Sep 23 2014 - 09:38:09 CDT)
CatDCD on Windows Ashar Malik (Mon Sep 22 2014 - 18:07:48 CDT)
- Re: CatDCD on Windows Josh Vermaas (Mon Sep 22 2014 - 19:08:55 CDT)
  - Re: CatDCD on Windows Ashar Malik (Mon Sep 22 2014 - 19:35:07 CDT)
Re: namd-l: Problem with running namdenergy plugin from text interface Josh Vermaas (Mon Sep 22 2014 - 15:09:10 CDT)
draw geometrical objects on specific frames Bin Liu (Mon Sep 22 2014 - 11:44:59 CDT)
- Re: draw geometrical objects on specific frames John Stone (Thu Sep 25 2014 - 09:34:30 CDT)
Solvate Plugin: Why "Rotate to minimize volume" along 2 instead of 3 axes? Sebastian Stolzenberg (Mon Sep 22 2014 - 09:59:35 CDT)
- Solvate Plugin: Why "Rotate to minimize volume" along 2 instead of 3 axes? Sebastian Stolzenberg (Mon Sep 22 2014 - 10:22:13 CDT)
- Re: Solvate Plugin: Why "Rotate to minimize volume" along 2 instead of 3 axes? Josh Vermaas (Mon Sep 22 2014 - 10:58:56 CDT)
- Re: Solvate Plugin: Why "Rotate to minimize volume" along 2 instead of 3 axes? John Stone (Mon Sep 22 2014 - 11:33:40 CDT)
merging several pdbs in one file Aref Takiden (Mon Sep 22 2014 - 07:55:53 CDT)
- Re: merging several pdbs in one file Maxim Belkin (Mon Sep 22 2014 - 13:04:37 CDT)
  - Re: merging several pdbs in one file Maxim Belkin (Tue Sep 23 2014 - 06:23:31 CDT)
    - RE: merging several pdbs in one file Tristan Croll (Tue Sep 23 2014 - 19:13:08 CDT)
  - Re: merging several pdbs in one file Aref Takiden (Fri Sep 26 2014 - 02:55:30 CDT)
- Re: merging several pdbs in one file Dennis N Bromley (Mon Sep 22 2014 - 12:52:59 CDT)
using vmd to apply symmetry operators part 2 Bennion, Brian (Thu Sep 18 2014 - 17:21:43 CDT)
- Re: using vmd to apply symmetry operators part 2 Tristan Croll (Sat Sep 20 2014 - 03:17:42 CDT)
measure hbonds in VMD tcl script Vasumathi Velachi (Fri Sep 19 2014 - 04:34:21 CDT)
- Re: measure hbonds in VMD tcl script Ana Celia Vila Verde (Fri Sep 19 2014 - 05:57:45 CDT)
  - Re: measure hbonds in VMD tcl script Vasumathi Velachi (Fri Sep 19 2014 - 06:10:48 CDT)
- Re: measure hbonds in VMD tcl script Ana Celia Vila Verde (Fri Sep 19 2014 - 06:31:36 CDT)
Carbon Nanotube Interaction with Protein Simulation NAMD VMD Aryan Vahedi-Faridi (Thu Sep 18 2014 - 14:44:34 CDT)
- Re: Carbon Nanotube Interaction with Protein Simulation NAMD VMD Tim Lo (Thu Sep 18 2014 - 20:19:10 CDT)
gofr not full PBC length Casey Johnson (Wed Sep 17 2014 - 18:45:23 CDT)
- Re: gofr not full PBC length Axel Kohlmeyer (Wed Sep 17 2014 - 22:47:25 CDT)
graphics command displays shapes of unusual sizes Lane Votapka (Wed Sep 17 2014 - 17:43:55 CDT)
- Re: graphics command displays shapes of unusual sizes Axel Kohlmeyer (Wed Sep 17 2014 - 22:49:48 CDT)
Clusters help Alessandro Mariani (Wed Sep 17 2014 - 03:57:10 CDT)
- Re: Clusters help Axel Kohlmeyer (Wed Sep 17 2014 - 04:41:59 CDT)
  - Re: Clusters help Axel Kohlmeyer (Wed Sep 17 2014 - 05:53:48 CDT)
Constraining two sets of atoms Natnael Doilicho (Mon Sep 15 2014 - 18:21:45 CDT)
- Re: Constraining two sets of atoms Josh Vermaas (Mon Sep 15 2014 - 19:41:49 CDT)
Modify bond label. Dawid das (Mon Sep 15 2014 - 10:01:01 CDT)
- Re: Modify bond label. John Stone (Thu Sep 18 2014 - 16:46:07 CDT)
question about hbonds in vmd tutorial Version 1.9.2beta1 maryam atabay (Mon Sep 15 2014 - 01:45:26 CDT)
- Re: question about hbonds in vmd tutorial Version 1.9.2beta1 Josh Vermaas (Mon Sep 15 2014 - 12:10:47 CDT)
question about hbonds in vmd tutorial Version 1.9.2beta1 maryam atabay (Mon Sep 15 2014 - 01:37:59 CDT)
question about hbonds in vmd tutorial Version 1.9.2beta1 maryam atabay (Mon Sep 15 2014 - 00:46:31 CDT)
VMD 1.9.2 beta 1 posted for download... John Stone (Sat Sep 13 2014 - 00:03:12 CDT)
- RE: VMD 1.9.2 beta 1 posted for download... Tristan Croll (Wed Sep 17 2014 - 02:02:55 CDT)
  - Re: VMD 1.9.2 beta 1 posted for download... John Stone (Wed Sep 17 2014 - 08:24:44 CDT)
ACS COMP Division travel awards for Spring 2015 National Meeting in Denver Carlos Simmerling (Fri Sep 12 2014 - 09:42:32 CDT)
problems with tachyon David Muramatsu (Fri Sep 12 2014 - 04:46:39 CDT)
- Re: problems with tachyon John Stone (Fri Sep 12 2014 - 08:08:12 CDT)
  - Re: problems with tachyon Josh Vermaas (Fri Sep 12 2014 - 09:01:12 CDT)
Re: FFTK: Opt Bonded error Mayne, Christopher G (Thu Sep 11 2014 - 11:17:17 CDT)
Half of a dimer out of the box in a simulation Luis Agullo (Wed Sep 10 2014 - 14:49:13 CDT)
- Re: Half of a dimer out of the box in a simulation Josh Vermaas (Wed Sep 10 2014 - 15:44:26 CDT)
  - Re: Half of a dimer out of the box in a simulation Luis Agullo (Fri Sep 12 2014 - 12:29:04 CDT)
velocities in trr Eric Smoll (Wed Sep 10 2014 - 14:28:56 CDT)
- Re: velocities in trr John Stone (Wed Sep 10 2014 - 14:45:09 CDT)
  - Re: velocities in trr Eric Smoll (Wed Sep 10 2014 - 15:03:39 CDT)
    - Re: velocities in trr John Stone (Wed Sep 10 2014 - 15:25:12 CDT)
    - Re: velocities in trr Axel Kohlmeyer (Wed Sep 10 2014 - 15:43:58 CDT)
vmd in windows 8 (64bite) Boshra Moradi (Tue Sep 09 2014 - 12:47:23 CDT)
- Re: vmd in windows 8 (64bite) Ajasja LjubetiÄ (Tue Sep 09 2014 - 13:36:57 CDT)
  - Re: vmd in windows 8 (64bite) Nagarajan C (Tue Sep 09 2014 - 14:30:07 CDT)
NAMD energy on dihedrals Joyce Yang (Tue Sep 09 2014 - 10:38:00 CDT)
Unable to read corrupted binary DCD trajectory file Viswanath Pasumarthi (Mon Sep 08 2014 - 09:03:50 CDT)
- Re: Unable to read corrupted binary DCD trajectory file John Stone (Mon Sep 08 2014 - 10:00:13 CDT)
  - Re: Unable to read corrupted binary DCD trajectory file Viswanath Pasumarthi (Mon Sep 08 2014 - 10:01:07 CDT)
- Re: Unable to read corrupted binary DCD trajectory file Josh Vermaas (Mon Sep 08 2014 - 10:15:23 CDT)
  - Re: Unable to read corrupted binary DCD trajectory file Viswanath Pasumarthi (Mon Sep 08 2014 - 14:05:10 CDT)
    - Re: Unable to read corrupted binary DCD trajectory file Josh Vermaas (Mon Sep 08 2014 - 14:23:00 CDT)
    - Re: Unable to read corrupted binary DCD trajectory file John Stone (Mon Sep 08 2014 - 16:13:11 CDT)
Etiquette, please. Ivan Gregoretti (Mon Sep 08 2014 - 07:58:34 CDT)
- Re: Etiquette, please. Ivan Gregoretti (Mon Sep 08 2014 - 10:17:21 CDT)
Overlaying multiple files in VMD ankit agrawal (Mon Sep 08 2014 - 00:13:59 CDT)
- Re: Overlaying multiple files in VMD John Stone (Mon Sep 08 2014 - 10:03:10 CDT)
  - Re: Overlaying multiple files in VMD ankit agrawal (Mon Sep 08 2014 - 11:52:42 CDT)
update selection used in "animate write" Eric Smoll (Sun Sep 07 2014 - 23:43:05 CDT)
- Re: update selection used in "animate write" Axel Kohlmeyer (Mon Sep 08 2014 - 00:34:10 CDT)
- Re: update selection used in "animate write" John Stone (Mon Sep 08 2014 - 09:55:55 CDT)
Selection along line in 3D Eric Smoll (Sat Sep 06 2014 - 01:40:10 CDT)
- Re: Selection along line in 3D Ana Celia Vila Verde (Sat Sep 06 2014 - 03:39:38 CDT)
  - Re: Selection along line in 3D Josh Vermaas (Sat Sep 06 2014 - 11:53:40 CDT)
  - Re: Selection along line in 3D Josh Vermaas (Sun Sep 07 2014 - 12:22:46 CDT)
RE: Fwd: fixed atoms_creating psf with out change in pdb Tristan Croll (Sat Sep 06 2014 - 00:10:59 CDT)
actual simulation time for a frame Dominik Bottländer (Thu Sep 04 2014 - 10:12:22 CDT)
- Re: actual simulation time for a frame Axel Kohlmeyer (Thu Sep 04 2014 - 10:51:44 CDT)
  - Re: actual simulation time for a frame John Stone (Thu Sep 04 2014 - 11:10:30 CDT)
  - Re: actual simulation time for a frame Dominik Bottländer (Sat Sep 06 2014 - 01:36:43 CDT)
Fwd: fixed atoms_creating psf with out change in pdb Boshra Moradi (Wed Sep 03 2014 - 21:13:08 CDT)
- Re: Fwd: fixed atoms_creating psf with out change in pdb Tristan Croll (Thu Sep 04 2014 - 07:09:58 CDT)
Possible malfunctioning of VMD with Yosemite? Davide Mercadante (Wed Sep 03 2014 - 14:37:39 CDT)
- Re: BUG REPORT: Malfunctioning of VMD with Yosemite? Davide Mercadante (Thu Sep 04 2014 - 07:08:57 CDT)
  - Re: BUG REPORT: Malfunctioning of VMD with Yosemite? Axel Kohlmeyer (Thu Sep 04 2014 - 07:45:04 CDT)
  - Re: BUG REPORT: Malfunctioning of VMD with Yosemite? John Stone (Thu Sep 04 2014 - 09:53:43 CDT)
    - Re: BUG REPORT: Malfunctioning of VMD with Yosemite? Davide Mercadante (Thu Sep 04 2014 - 17:32:21 CDT)
    - Re: BUG REPORT: Malfunctioning of VMD with Yosemite? John Stone (Fri Sep 05 2014 - 10:05:28 CDT)
Making trajectory movie last longer. Dawid das (Wed Sep 03 2014 - 08:33:37 CDT)
- Re: Making trajectory movie last longer. andrea (Wed Sep 03 2014 - 09:38:21 CDT)
  - RE: Making trajectory movie last longer. Richard Wood (Wed Sep 03 2014 - 10:42:24 CDT)
- Re: Making trajectory movie last longer. Axel Kohlmeyer (Wed Sep 03 2014 - 09:25:13 CDT)
  - Re: Making trajectory movie last longer. Josh Vermaas (Wed Sep 03 2014 - 13:50:03 CDT)
Dynamical Network Analysis (Network View) -- Please help mason H (Mon Sep 01 2014 - 13:27:25 CDT)
- Re: Dynamical Network Analysis (Network View) -- Please help Anurag Sethi (Mon Sep 01 2014 - 14:05:21 CDT)
How to get all bond angles and bond distances for all atoms in sheet Pavan Miriyala (Mon Sep 01 2014 - 07:36:34 CDT)
- Re: How to get all bond angles and bond distances for all atoms in sheet Axel Kohlmeyer (Mon Sep 01 2014 - 08:19:05 CDT)
  - Re: How to get all bond angles and bond distances for all atoms in sheet Pavan Miriyala (Tue Sep 02 2014 - 07:11:05 CDT)
reï¼šç”å¤ï¼š c_top2psf.pl sunyeping (Sun Aug 31 2014 - 10:33:48 CDT)
- Re: ç”å¤ï¼š c_top2psf.pl Axel Kohlmeyer (Sun Aug 31 2014 - 10:38:00 CDT)
Network View -- how to Load Network from command line mason H (Sat Aug 30 2014 - 20:03:09 CDT)
- Re: Network View -- how to Load Network from command line mason H (Tue Sep 02 2014 - 08:14:15 CDT)
entropy calculation by g_anaeig sunyeping (Sat Aug 30 2014 - 10:19:03 CDT)
- Re: entropy calculation by g_anaeig Axel Kohlmeyer (Sat Aug 30 2014 - 11:22:28 CDT)
c_top2psf.pl sunyeping (Sat Aug 30 2014 - 10:14:02 CDT)
- Re: c_top2psf.pl Axel Kohlmeyer (Sat Aug 30 2014 - 11:21:33 CDT)
Calling VMD from Linux Cluster Gonzalez, Aaron (Fri Aug 29 2014 - 12:34:02 CDT)
- Re: Calling VMD from Linux Cluster John Stone (Fri Aug 29 2014 - 17:20:47 CDT)
VMD and FreeVR Michael Krause (Fri Aug 29 2014 - 08:43:46 CDT)
- Re: VMD and FreeVR John Stone (Fri Aug 29 2014 - 17:18:36 CDT)
  - Re: VMD and FreeVR Michael Krause (Fri Sep 12 2014 - 02:40:13 CDT)
    - Re: VMD and FreeVR John Stone (Thu Sep 18 2014 - 16:42:17 CDT)
APBS: ELEC values Jean-Patrick Francoia (Thu Aug 28 2014 - 16:35:56 CDT)
- Re: APBS: ELEC values John Stone (Thu Aug 28 2014 - 16:42:54 CDT)
APBS: uncharged molecule Jean-Patrick Francoia (Thu Aug 28 2014 - 15:00:58 CDT)
- Re: APBS: uncharged molecule John Stone (Thu Aug 28 2014 - 15:31:34 CDT)
  - Re: APBS: uncharged molecule Jean-Patrick Francoia (Thu Aug 28 2014 - 15:32:57 CDT)
    - Re: APBS: uncharged molecule John Stone (Thu Aug 28 2014 - 15:40:44 CDT)
    - Re: APBS: uncharged molecule Jean-Patrick Francoia (Thu Aug 28 2014 - 16:13:29 CDT)
Save position of entire molecule and draw it later Ebert Maximilian (Thu Aug 28 2014 - 10:37:34 CDT)
- Re: Save position of entire molecule and draw it later John Stone (Thu Aug 28 2014 - 13:25:19 CDT)
  - Re: Save position of entire molecule and draw it later Ebert Maximilian (Thu Aug 28 2014 - 13:58:58 CDT)
    - Re: Save position of entire molecule and draw it later John Stone (Thu Aug 28 2014 - 14:14:45 CDT)
Re: Accessible volume around an atom Dudo (Thu Aug 28 2014 - 04:55:01 CDT)
- strange behavior of render command Philippe Bopp (Thu Aug 28 2014 - 10:57:33 CDT)
  - Re: strange behavior of render command John Stone (Thu Aug 28 2014 - 11:30:37 CDT)
  - Re: strange behavior of render command Josh Vermaas (Thu Aug 28 2014 - 11:48:42 CDT)
Dynamical Network Analysis -- Question on Nodes and Restrictions mason H (Wed Aug 27 2014 - 21:38:53 CDT)
building amino acid modification Bennion, Brian (Wed Aug 27 2014 - 18:00:26 CDT)
Different colouring of the same molecule. Dawid das (Wed Aug 27 2014 - 13:37:20 CDT)
- Re: Different colouring of the same molecule. John Stone (Thu Aug 28 2014 - 14:16:13 CDT)
Accessible volume around an atom Ebert Maximilian (Wed Aug 27 2014 - 13:22:29 CDT)
- AW: Accessible volume around an atom Norman Geist (Thu Aug 28 2014 - 03:41:21 CDT)
- Re: Accessible volume around an atom John Stone (Thu Aug 28 2014 - 13:22:56 CDT)
Announcement: Hands-On Workshop On Computational Biophysics Danielle Chandler (Wed Aug 27 2014 - 13:04:56 CDT)
The dreaded VMD / Mac OS 10.9 problems John Grime (Wed Aug 27 2014 - 12:39:50 CDT)
Remote visualisation inconsistency Cara Kreck (Wed Aug 27 2014 - 11:37:39 CDT)
- Re: Remote visualisation inconsistency John Stone (Wed Aug 27 2014 - 11:56:20 CDT)
  - RE: Remote visualisation inconsistency Cara Kreck (Thu Aug 28 2014 - 02:33:13 CDT)
The dreaded VMD / Mac OS 10.9 problems John Grime (Wed Aug 27 2014 - 10:57:24 CDT)
- Re: The dreaded VMD / Mac OS 10.9 problems John Stone (Wed Aug 27 2014 - 11:37:50 CDT)
  - Re: The dreaded VMD / Mac OS 10.9 problems John Stone (Thu Aug 28 2014 - 13:06:53 CDT)
Dynamical Network Analysis (NetworkView): Changing contact cutoff values for edges Fotis Baltoumas (Tue Aug 26 2014 - 10:39:47 CDT)
- Re: Dynamical Network Analysis (NetworkView): Changing contact cutoff values for edges Kirby Vandivort (Tue Aug 26 2014 - 10:53:27 CDT)
  - Re: Dynamical Network Analysis (NetworkView): Changing contact cutoff values for edges Fotis Baltoumas (Tue Aug 26 2014 - 11:01:55 CDT)
Minor bug report in VMD 1.9.1 Tristan Croll (Mon Aug 25 2014 - 22:23:37 CDT)
- Re: Minor bug report in VMD 1.9.1 John Stone (Tue Aug 26 2014 - 10:10:17 CDT)
How does saltbr calculate distance? Dawid das (Sat Aug 23 2014 - 13:55:48 CDT)
- RE: How does saltbr calculate distance? Tristan Croll (Sun Aug 24 2014 - 01:28:22 CDT)
VMD 1.9.1 installation Annika Wittenbecher (Fri Aug 22 2014 - 01:59:24 CDT)
- Re: VMD 1.9.1 installation Axel Kohlmeyer (Fri Aug 22 2014 - 03:43:18 CDT)
Tachyon transparency and depth cueing Tristan Croll (Thu Aug 21 2014 - 02:15:24 CDT)
- AW: Tachyon transparency and depth cueing Norman Geist (Thu Aug 21 2014 - 04:42:53 CDT)
  - Re: AW: Tachyon transparency and depth cueing Tristan Croll (Thu Aug 21 2014 - 05:15:30 CDT)
    - Re: AW: Tachyon transparency and depth cueing John Stone (Thu Aug 21 2014 - 08:34:40 CDT)
    - RE: AW: Tachyon transparency and depth cueing Tristan Croll (Thu Aug 21 2014 - 18:33:44 CDT)
Need compile options for text-only version of VMD Jim Parker (Wed Aug 20 2014 - 16:09:15 CDT)
- Re: Need compile options for text-only version of VMD Jim Parker (Wed Aug 20 2014 - 16:17:16 CDT)
  - Re: Re: Need compile options for text-only version of VMD John Stone (Wed Aug 20 2014 - 16:27:30 CDT)
vmd without OpenGL window Eric Smoll (Wed Aug 20 2014 - 13:41:57 CDT)
- Re: vmd without OpenGL window Maxim Belkin (Wed Aug 20 2014 - 13:46:58 CDT)
How can i connect molecules? RafaÅ‚ GÄ…sior (Wed Aug 20 2014 - 10:26:19 CDT)
- Re: How can i connect molecules? Salomon Turgman Cohen (Wed Aug 20 2014 - 13:19:32 CDT)
can we delete in command line? Albert (Wed Aug 20 2014 - 04:29:42 CDT)
- Re: can we delete in command line? John Stone (Wed Aug 20 2014 - 08:34:33 CDT)
- Re: can we delete in command line? Abhijit Muley (Wed Aug 20 2014 - 09:09:27 CDT)
how to bind peripheral membrane protein to the membrane sunyeping (Tue Aug 19 2014 - 23:24:14 CDT)
Making an extensive search of PDB Diego Granados (Tue Aug 19 2014 - 18:21:25 CDT)
- Re: Making an extensive search of PDB Josh Vermaas (Tue Aug 19 2014 - 19:30:45 CDT)
vmd hangs at creating CUDA pool Bennion, Brian (Tue Aug 19 2014 - 11:11:17 CDT)
- Re: vmd hangs at creating CUDA pool John Stone (Tue Aug 19 2014 - 11:34:16 CDT)
  - RE: vmd hangs at creating CUDA pool Bennion, Brian (Tue Aug 19 2014 - 11:41:12 CDT)
autoionize with polyatomic ions Bennion, Brian (Mon Aug 18 2014 - 16:06:29 CDT)
Parameter and Topology File UPDATE. Ashar Malik (Fri Aug 15 2014 - 21:23:48 CDT)
- Re: Parameter and Topology File UPDATE. Maxim Belkin (Sat Aug 16 2014 - 02:13:03 CDT)
  - Re: Parameter and Topology File UPDATE. Maxim Belkin (Sat Aug 16 2014 - 03:33:34 CDT)
  - Re: Parameter and Topology File UPDATE. Maxim Belkin (Sat Aug 16 2014 - 04:29:29 CDT)
Labeling atoms by index Andrew DeYoung (Fri Aug 15 2014 - 16:46:00 CDT)
- Re: Labeling atoms by index Maxim Belkin (Sat Aug 16 2014 - 02:48:51 CDT)
  - Re: Labeling atoms by index Maxim Belkin (Sat Aug 16 2014 - 03:36:23 CDT)
  - Re: Labeling atoms by index Maxim Belkin (Sat Aug 16 2014 - 03:49:18 CDT)
ammonium sulfate ions in system Bennion, Brian (Fri Aug 15 2014 - 15:51:52 CDT)
Autoi::sod2pot problem in "Modeling Nanopores for Sequencing DNA" tutorial Basheer Subei (Fri Aug 15 2014 - 13:45:20 CDT)
- Re: Autoi::sod2pot problem in "Modeling Nanopores for Sequencing DNA" tutorial Maxim Belkin (Fri Aug 15 2014 - 13:54:08 CDT)
  - Re: Autoi::sod2pot problem in "Modeling Nanopores for Sequencing DNA" tutorial Basheer Subei (Fri Aug 15 2014 - 14:07:12 CDT)
Units used by Volmap Tool Alexandre Suman de Araujo (Fri Aug 15 2014 - 12:54:58 CDT)
- Re: Units used by Volmap Tool Maxim Belkin (Fri Aug 15 2014 - 16:27:11 CDT)
Psf format Bashir (Sat Aug 16 2014 - 12:28:49 CDT)
python 2.7 probelms Chris Knorowski (Thu Aug 14 2014 - 15:52:40 CDT)
- Re: python 2.7 probelms Josh Vermaas (Thu Aug 14 2014 - 20:48:22 CDT)
  - Re: python 2.7 probelms Chris Knorowski (Fri Aug 15 2014 - 16:05:50 CDT)
    - Re: python 2.7 probelms John Stone (Fri Aug 15 2014 - 16:21:12 CDT)
    - Re: python 2.7 probelms Josh Vermaas (Fri Aug 15 2014 - 16:28:42 CDT)
Extension crashes Anoop Krishnan (Thu Aug 14 2014 - 06:49:57 CDT)
- Re: Extension crashes John Stone (Tue Aug 19 2014 - 15:26:22 CDT)
  - Re: Extension crashes Anoop Krishnan (Tue Aug 19 2014 - 23:51:35 CDT)
Ssrestraints error Kevin C Chan (Thu Aug 14 2014 - 06:21:21 CDT)
- RE: Ssrestraints error Tristan Croll (Sun Aug 17 2014 - 21:50:01 CDT)
  - Re: Ssrestraints error Kevin C Chan (Sun Aug 17 2014 - 23:16:09 CDT)
Reading PSF files with longer than 4-letter atom types Alexander Balaeff (Wed Aug 13 2014 - 10:59:22 CDT)
- Re: Reading PSF files with longer than 4-letter atom types Josh Vermaas (Wed Aug 13 2014 - 11:55:16 CDT)
  - Re: Reading PSF files with longer than 4-letter atom types John Stone (Wed Aug 13 2014 - 12:21:27 CDT)
    - Re: Reading PSF files with longer than 4-letter atom types Alexander Balaeff (Wed Aug 13 2014 - 13:12:06 CDT)
  - Re: Reading PSF files with longer than 4-letter atom types Mayne, Christopher G (Wed Aug 13 2014 - 12:57:38 CDT)
    - Re: Reading PSF files with longer than 4-letter atom types Mayne, Christopher G (Wed Aug 13 2014 - 14:36:47 CDT)
writing improper dihedral in topotools, Ali Alizadeh (Tue Aug 12 2014 - 16:31:15 CDT)
- Re: writing improper dihedral in topotools, Axel Kohlmeyer (Tue Aug 12 2014 - 17:36:31 CDT)
  - Re: writing improper dihedral in topotools, Ali Alizadeh (Wed Aug 13 2014 - 00:33:51 CDT)
Announcement: Hands-On Workshop On Computational Biophysics Danielle Chandler (Tue Aug 12 2014 - 09:30:56 CDT)
Re: Tcl scripting - Coloring residues by frame along trajectory MaurÃcio Menegatti Rigo (Tue Aug 12 2014 - 08:31:12 CDT)
Rendering snapshots DEBOSTUTI GHOSHDASTIDAR (Tue Aug 12 2014 - 08:23:50 CDT)
- Re: Rendering snapshots John Stone (Tue Aug 12 2014 - 10:11:46 CDT)
  - Re: Rendering snapshots DEBOSTUTI GHOSHDASTIDAR (Wed Aug 13 2014 - 00:06:32 CDT)
- AW: Rendering snapshots Norman Geist (Tue Aug 12 2014 - 10:57:54 CDT)
averaged structure Natal Kanaan (Tue Aug 12 2014 - 06:30:30 CDT)
- Re: averaged structure Josh Vermaas (Tue Aug 12 2014 - 09:36:49 CDT)
  - Re: averaged structure John Stone (Tue Aug 12 2014 - 10:05:56 CDT)
  - Re: averaged structure Natal Kanaan (Tue Aug 12 2014 - 11:42:05 CDT)
mol new [from memory] Thomas C. Bishop (Mon Aug 11 2014 - 11:59:51 CDT)
- Re: mol new [from memory] Axel Kohlmeyer (Mon Aug 11 2014 - 12:36:16 CDT)
  - Re: mol new [from memory] SOLVED Thomas C. Bishop (Mon Aug 11 2014 - 12:39:26 CDT)
- Re: mol new [from memory] Maxim Belkin (Mon Aug 11 2014 - 12:34:51 CDT)
renumbering water molecules Natal Kanaan (Mon Aug 11 2014 - 11:41:36 CDT)
MDFF simulations Luba Simhaev (Mon Aug 11 2014 - 04:22:31 CDT)
- Re: MDFF simulations Ryan McGreevy (Mon Aug 11 2014 - 12:24:26 CDT)
- RE: MDFF simulations Tristan Croll (Mon Aug 11 2014 - 20:13:42 CDT)
  - Re: MDFF simulations Ryan McGreevy (Mon Aug 11 2014 - 21:09:34 CDT)
visualizing janus particles in VMD Gamot, Ritchie (Sat Aug 09 2014 - 13:24:42 CDT)
- Re: visualizing janus particles in VMD Axel Kohlmeyer (Sat Aug 09 2014 - 19:05:25 CDT)
  - RE: visualizing janus particles in VMD Gamot, Ritchie (Mon Aug 11 2014 - 04:54:30 CDT)
    - Re: visualizing janus particles in VMD Axel Kohlmeyer (Mon Aug 11 2014 - 07:04:31 CDT)
Tcl scripting - Coloring residues by frame along trajectory MaurÃcio Menegatti Rigo (Fri Aug 08 2014 - 13:12:31 CDT)
- AW: Tcl scripting - Coloring residues by frame along trajectory Norman Geist (Mon Aug 11 2014 - 00:29:19 CDT)
Using more than 9 atom types for coloring method and visualizing half of a structure Fikret Aydin (Fri Aug 08 2014 - 12:58:12 CDT)
- Re: Using more than 9 atom types for coloring method and visualizing half of a structure Josh Vermaas (Fri Aug 08 2014 - 15:23:20 CDT)
To the developers: TCL implementation of autofit zoom Norman Geist (Fri Aug 08 2014 - 07:11:32 CDT)
- Re: To the developers: TCL implementation of autofit zoom Josh Vermaas (Fri Aug 08 2014 - 08:41:56 CDT)
  - Re: To the developers: TCL implementation of autofit zoom JÃ©rÃ´me HÃ©nin (Fri Aug 08 2014 - 09:05:20 CDT)
  - AW: To the developers: TCL implementation of autofit zoom Norman Geist (Mon Aug 11 2014 - 00:24:13 CDT)
- Re: To the developers: TCL implementation of autofit zoom John Stone (Fri Aug 08 2014 - 10:58:51 CDT)
  - AW: To the developers: TCL implementation of autofit zoom Norman Geist (Mon Aug 11 2014 - 00:22:42 CDT)
  - AW: To the developers: TCL implementation of autofit zoom Norman Geist (Mon Aug 11 2014 - 05:04:29 CDT)
Re: To the developers: Get current zoom value (scale) JÃ©rÃ´me HÃ©nin (Fri Aug 08 2014 - 03:49:23 CDT)
- AW: To the developers: Get current zoom value (scale) Norman Geist (Fri Aug 08 2014 - 05:05:13 CDT)
To the developers: Get current zoom value (scale) Norman Geist (Fri Aug 08 2014 - 01:27:45 CDT)
- Re: To the developers: Get current zoom value (scale) Mayne, Christopher G (Fri Aug 08 2014 - 09:15:50 CDT)
  - Re: To the developers: Get current zoom value (scale) Mayne, Christopher G (Fri Aug 08 2014 - 10:10:43 CDT)
vmd nearclip setting different from that used in povray render Eric Smoll (Wed Aug 06 2014 - 16:52:02 CDT)
- Re: vmd nearclip setting different from that used in povray render John Stone (Tue Aug 19 2014 - 15:38:51 CDT)
Problem with RBCG tutorial! Rangeen Othman (Wed Aug 06 2014 - 06:30:20 CDT)
- Re: Problem with RBCG tutorial! Kirby Vandivort (Wed Aug 06 2014 - 10:06:00 CDT)
Problem with RBCG tutorial! Rangeen Othman (Wed Aug 06 2014 - 05:21:51 CDT)
Feature suggestion: "glow" representation Tristan Croll (Wed Aug 06 2014 - 01:49:00 CDT)
- Re: Feature suggestion: "glow" representation Josh Vermaas (Wed Aug 06 2014 - 09:21:04 CDT)
  - Re: Feature suggestion: "glow" representation John Stone (Wed Aug 06 2014 - 09:50:09 CDT)
Cardiolipin residue names changed by vmd Rose, Stuart Wallace (Tue Aug 05 2014 - 19:30:02 CDT)
Does the VMD Linux 64-bit version perform better than the Windows 32-bit when visualizing large molecules? Can Ali Tomruk (Tue Aug 05 2014 - 16:45:31 CDT)
- Re: Does the VMD Linux 64-bit version perform better than the Windows 32-bit when visualizing large molecules? John Stone (Tue Aug 05 2014 - 21:05:56 CDT)
- AW: Does the VMD Linux 64-bit version perform better than the Windows 32-bit when visualizing large molecules? Norman Geist (Wed Aug 06 2014 - 00:35:18 CDT)
Vmd problem in display of surface in Md movie ( Gromacs trajectory) rama david (Tue Aug 05 2014 - 10:05:58 CDT)
- Re: Vmd problem in display of surface in Md movie ( Gromacs trajectory) Josh Vermaas (Tue Aug 05 2014 - 10:59:23 CDT)
automatic extraction of RMSD values of the heavy atoms of residues from NAMD output? Andras Borosy (Tue Aug 05 2014 - 03:10:51 CDT)
Running ABF to seperate DNA strands Charles Whidborne (Mon Aug 04 2014 - 19:40:28 CDT)
- Re: Running ABF to seperate DNA strands Axel Kohlmeyer (Mon Aug 04 2014 - 20:35:35 CDT)
Running ABF to separate DNA strands Charles Whidborne (Mon Aug 04 2014 - 19:36:33 CDT)
Is VMD available to control the movie made by movie maker Xiaohui She (Mon Aug 04 2014 - 16:44:44 CDT)
- Re: Is VMD available to control the movie made by movie maker Axel Kohlmeyer (Mon Aug 04 2014 - 17:24:14 CDT)
CG definition of POPS Steven Neumann (Sun Aug 03 2014 - 23:31:23 CDT)
Reï¼š display water sunyeping (Sun Aug 03 2014 - 20:41:20 CDT)
- Re: Reï¼š display water Josh Vermaas (Mon Aug 04 2014 - 08:58:10 CDT)
display water sunyeping (Sun Aug 03 2014 - 02:06:44 CDT)
- Re: display water Josh Vermaas (Sun Aug 03 2014 - 07:25:55 CDT)
ParseFEP Error Foster, Clay A. (Thu Jul 31 2014 - 17:44:45 CDT)
color scale definitions with more than three colors? Brian Radak (Thu Jul 31 2014 - 12:38:49 CDT)
- Re: color scale definitions with more than three colors? John Stone (Thu Jul 31 2014 - 12:58:37 CDT)
- Re: color scale definitions with more than three colors? Axel Kohlmeyer (Thu Jul 31 2014 - 13:19:31 CDT)
VMD error Kshatresh Dutta Dubey (Thu Jul 31 2014 - 05:56:41 CDT)
- Re: VMD error Ivan Gregoretti (Thu Jul 31 2014 - 07:31:04 CDT)
  - Re: VMD error Ivan Gregoretti (Thu Jul 31 2014 - 07:49:34 CDT)
drop off in IO speed for bigdcd analysis Mayne, Christopher G (Wed Jul 30 2014 - 21:20:53 CDT)
- Re: drop off in IO speed for bigdcd analysis Josh Vermaas (Thu Jul 31 2014 - 09:43:50 CDT)
- Re: drop off in IO speed for bigdcd analysis John Stone (Thu Jul 31 2014 - 10:02:02 CDT)
  - Re: drop off in IO speed for bigdcd analysis Mayne, Christopher G (Thu Jul 31 2014 - 10:26:00 CDT)
AutoPSF error Kukol, Andreas (Wed Jul 30 2014 - 05:12:20 CDT)
- Re: AutoPSF error Moumita Saharay (Wed Jul 30 2014 - 06:06:53 CDT)
  - RE: AutoPSF error Tristan Croll (Thu Jul 31 2014 - 20:27:43 CDT)
Accelerated MD (aMD) Ramin Ekhteiari (Sat Jul 26 2014 - 06:06:25 CDT)
membrane lipid involvement of cholesterol Ramin Ekhteiari (Sat Jul 26 2014 - 03:14:38 CDT)
- RE: membrane lipid involvement of cholesterol Richard Wood (Sat Jul 26 2014 - 06:26:59 CDT)
  - RE: membrane lipid involvement of cholesterol Richard Wood (Sat Jul 26 2014 - 09:07:57 CDT)
Does VMD 1.8.6 support SMP under IRIX? tyrrell t (Fri Jul 25 2014 - 22:25:46 CDT)
- Re: Does VMD 1.8.6 support SMP under IRIX? John Stone (Fri Sep 19 2014 - 23:54:59 CDT)
loading multiple trajectories with stride command in the terminal George Gerogiokas (Fri Jul 25 2014 - 08:27:36 CDT)
- Re: loading multiple trajectories with stride command in the terminal Axel Kohlmeyer (Fri Jul 25 2014 - 10:42:57 CDT)
export trajectory all frames coordinates to numpy array Bachir Aoun (Thu Jul 24 2014 - 13:58:49 CDT)
- Re: export trajectory all frames coordinates to numpy array Axel Kohlmeyer (Thu Jul 24 2014 - 14:37:31 CDT)
- Re: export trajectory all frames coordinates to numpy array Ajasja LjubetiÄ (Thu Jul 24 2014 - 14:59:45 CDT)
  - Re: export trajectory all frames coordinates to numpy array Bachir Aoun (Thu Jul 24 2014 - 16:33:06 CDT)
NVT system: constant energy, small DCD file size ZEINAB EMAMI (Thu Jul 24 2014 - 06:42:49 CDT)
Self-Assemble Monolayer Natnael Doilicho (Wed Jul 23 2014 - 17:22:16 CDT)
.obj Oddity Darrell Kuykendall (Wed Jul 23 2014 - 15:30:19 CDT)
- Re: .obj Oddity John Stone (Thu Jul 24 2014 - 09:37:08 CDT)
  - Re: .obj Oddity Darrell Kuykendall (Thu Jul 24 2014 - 10:00:20 CDT)
    - Re: .obj Oddity John Stone (Thu Jul 24 2014 - 10:19:22 CDT)
    - Re: .obj Oddity Darrell Kuykendall (Thu Jul 24 2014 - 13:57:16 CDT)
Topo Tools for triclinic system karthik kumar (Wed Jul 23 2014 - 03:16:25 CDT)
- Re: Topo Tools for triclinic system Axel Kohlmeyer (Wed Jul 23 2014 - 07:04:10 CDT)
Creating data file for triclinic system Bonakala Satyanarayana (Wed Jul 23 2014 - 01:40:58 CDT)
- Re: Creating data file for triclinic system Axel Kohlmeyer (Wed Jul 23 2014 - 07:03:17 CDT)
MDFF for multiple subunits Anjela Manandhar (Mon Jul 21 2014 - 14:05:34 CDT)
- Re: MDFF for multiple subunits Ryan McGreevy (Mon Jul 21 2014 - 14:49:55 CDT)
  - Re: MDFF for multiple subunits Ryan McGreevy (Wed Jul 23 2014 - 14:37:01 CDT)
vmd-1.9.1 linux installation problem Weiping Liu (Sun Jul 20 2014 - 20:43:54 CDT)
- Re: vmd-1.9.1 linux installation problem Bashir Fotouhi (Mon Jul 21 2014 - 02:23:59 CDT)
  - Re: vmd-1.9.1 linux installation problem Josh Vermaas (Mon Jul 21 2014 - 08:13:35 CDT)
  - Re: vmd-1.9.1 linux installation problem Weiping Liu (Mon Jul 21 2014 - 11:32:08 CDT)
merge structure of two pdb files Marzieh Dehghan (Sun Jul 20 2014 - 15:31:26 CDT)
VMD Quantum Chemistry Visualization Darrell Kuykendall (Sat Jul 19 2014 - 12:38:28 CDT)
- Re: VMD Quantum Chemistry Visualization Mayne, Christopher G (Mon Jul 21 2014 - 10:32:34 CDT)
  - Re: VMD Quantum Chemistry Visualization John Stone (Mon Jul 21 2014 - 10:46:14 CDT)
  - Re: VMD Quantum Chemistry Visualization Darrell Kuykendall (Mon Jul 21 2014 - 10:46:55 CDT)
How to adjust different atom size separately Xiaohui She (Fri Jul 18 2014 - 11:02:32 CDT)
- Re: How to adjust different atom size separately Axel Kohlmeyer (Fri Jul 18 2014 - 11:31:27 CDT)
  - Re: How to adjust different atom size separately Xiaohui She (Mon Jul 21 2014 - 10:46:27 CDT)
- Re: How to adjust different atom size separately Maxim Belkin (Fri Jul 18 2014 - 11:32:26 CDT)
School on Molecular Dynamics with NAMD and LAMMPS in Philadelphia, August 18-22 2014 Axel Kohlmeyer (Thu Jul 17 2014 - 14:48:17 CDT)
hbonds Mary Varughese (Tue Jul 15 2014 - 04:51:50 CDT)
- Re: hbonds Ana Celia Vila Verde (Tue Jul 15 2014 - 06:56:42 CDT)
Graphene Bashir Fotouhi (Sat Jul 12 2014 - 04:55:12 CDT)
Subtract structure to a trajectory Marco Gerolin (Thu Jul 10 2014 - 09:06:29 CDT)
- Re: Subtract structure to a trajectory Josh Vermaas (Thu Jul 10 2014 - 10:01:15 CDT)
  - Re: Subtract structure to a trajectory Josh Vermaas (Thu Jul 10 2014 - 10:54:09 CDT)
- Re: Subtract structure to a trajectory Axel Kohlmeyer (Thu Jul 10 2014 - 10:51:23 CDT)
pdb animation Nuno Sousa Cerqueira (Thu Jul 10 2014 - 07:24:47 CDT)
- RE: pdb animation Richard Wood (Thu Jul 10 2014 - 08:31:54 CDT)
  - RE: pdb animation Nuno Sousa Cerqueira (Thu Jul 10 2014 - 08:33:19 CDT)
- Re: pdb animation Maxim Belkin (Thu Jul 10 2014 - 08:53:21 CDT)
  - Re: pdb animation Nuno Sousa Cerqueira (Thu Jul 10 2014 - 08:56:02 CDT)
origin in VMD Chetan Mahajan (Wed Jul 09 2014 - 20:48:53 CDT)
- Re: origin in VMD Josh Vermaas (Thu Jul 10 2014 - 09:58:17 CDT)
  - Re: origin in VMD Chetan Mahajan (Thu Jul 10 2014 - 12:18:34 CDT)
How to contribute to VMD? Vlastimil ZÃma (Wed Jul 09 2014 - 06:35:03 CDT)
- Re: How to contribute to VMD? Nuno Sousa Cerqueira (Wed Jul 09 2014 - 07:10:36 CDT)
  - Re: How to contribute to VMD? John Stone (Thu Jul 24 2014 - 10:51:34 CDT)
- Re: How to contribute to VMD? Axel Kohlmeyer (Wed Jul 09 2014 - 10:15:29 CDT)
  - Re: How to contribute to VMD? Vlastimil ZÃma (Wed Jul 09 2014 - 12:29:27 CDT)
    - Re: How to contribute to VMD? Axel Kohlmeyer (Wed Jul 09 2014 - 13:01:10 CDT)
    - Re: How to contribute to VMD? Josh Vermaas (Wed Jul 09 2014 - 13:33:15 CDT)
VMD 1.9.2a39_64 segmentation fault MacOS Mark Wistey (Tue Jul 08 2014 - 18:28:09 CDT)
- Re: VMD 1.9.2a39_64 segmentation fault MacOS Maxim Belkin (Tue Jul 08 2014 - 18:48:09 CDT)
  - Re: VMD 1.9.2a39_64 segmentation fault MacOS Mark Wistey (Tue Jul 08 2014 - 19:05:07 CDT)
- Re: VMD 1.9.2a39_64 segmentation fault MacOS John Stone (Wed Jul 09 2014 - 15:50:21 CDT)
secondary structure calculation at certain frame Anjela Manandhar (Tue Jul 08 2014 - 12:32:50 CDT)
- AW: secondary structure calculation at certain frame Norman Geist (Wed Jul 09 2014 - 02:26:45 CDT)
tcl script Mihaela Drenscko (Tue Jul 08 2014 - 09:27:06 CDT)
- Re: tcl script Josh Vermaas (Tue Jul 08 2014 - 11:27:51 CDT)
NAMD energy plugin - dielectric constant Ramin Ekhteiari (Mon Jul 07 2014 - 14:59:42 CDT)
obtain a list of residue numbers kirtana S (Mon Jul 07 2014 - 12:11:40 CDT)
- Re: obtain a list of residue numbers Maxim Belkin (Mon Jul 07 2014 - 12:19:59 CDT)
  - AW: obtain a list of residue numbers Norman Geist (Tue Jul 08 2014 - 00:03:24 CDT)
    - Re: AW: obtain a list of residue numbers Thomas C. Bishop (Tue Jul 08 2014 - 09:59:41 CDT)
residue within x of <geometric centre> Gurunath Katagi (Fri Jul 04 2014 - 09:48:48 CDT)
- Re: residue within x of <geometric centre> Josh Vermaas (Sun Jul 06 2014 - 16:02:34 CDT)
  - Re: residue within x of <geometric centre> Yi Wang, PhD (Sun Jul 06 2014 - 17:58:04 CDT)
Fwd: Visualizing the displacement vector karthik kumar (Fri Jul 04 2014 - 09:28:07 CDT)
- Re: Fwd: Visualizing the displacement vector Axel Kohlmeyer (Fri Jul 04 2014 - 10:47:12 CDT)
  - Re: Fwd: Visualizing the displacement vector Axel Kohlmeyer (Fri Jul 04 2014 - 10:50:03 CDT)
    - Re: Fwd: Visualizing the displacement vector Adam Goler (Fri Jul 04 2014 - 11:18:10 CDT)
CL Christian Wohlschlager (Fri Jul 04 2014 - 06:13:43 CDT)
- Re: CL Axel Kohlmeyer (Fri Jul 04 2014 - 10:47:12 CDT)
Temporary Files for STRIDE Inaccessible on Windows 8 Chris Ing (Thu Jul 03 2014 - 16:08:03 CDT)
- Re: Temporary Files for STRIDE Inaccessible on Windows 8 John Stone (Thu Jul 24 2014 - 12:47:57 CDT)
salt bridge sunyeping (Wed Jul 02 2014 - 09:18:47 CDT)
salt bridge sunyeping (Wed Jul 02 2014 - 08:41:15 CDT)
Combining PDB/PSF of Protein and CNT Adam Kells (Wed Jul 02 2014 - 04:15:55 CDT)
- Re: Combining PDB/PSF of Protein and CNT Ajasja LjubetiÄ (Wed Jul 02 2014 - 07:03:26 CDT)
Re: namd-l: Re: NAMD energy calculation Ramin Ekhteiari (Tue Jul 01 2014 - 12:07:47 CDT)
REï¼š select all residues in a molecule sunyeping (Mon Jun 30 2014 - 02:10:45 CDT)
- AW: REï¼š select all residues in a molecule Norman Geist (Mon Jun 30 2014 - 02:48:45 CDT)
select all residues in a molecule sunyeping (Sat Jun 28 2014 - 21:45:16 CDT)
- Re: select all residues in a molecule Maxim Belkin (Sat Jun 28 2014 - 23:58:27 CDT)
- AW: select all residues in a molecule Norman Geist (Mon Jun 30 2014 - 00:19:07 CDT)
Select the residue which comprises the atom with index Ebert Maximilian (Fri Jun 27 2014 - 11:08:22 CDT)
- Re: Select the residue which comprises the atom with index Maxim Belkin (Fri Jun 27 2014 - 11:29:36 CDT)
  - Re: Select the residue which comprises the atom with index Ebert Maximilian (Fri Jun 27 2014 - 12:14:46 CDT)
    - Re: Select the residue which comprises the atom with index Maxim Belkin (Fri Jun 27 2014 - 12:27:07 CDT)
Which function for animate speed Samuele Salis (Fri Jun 27 2014 - 04:38:36 CDT)
- Re: Which function for animate speed Rohan Mehta (Fri Jun 27 2014 - 05:39:53 CDT)
- Re: Which function for animate speed Josh Vermaas (Fri Jun 27 2014 - 10:52:24 CDT)
  - Re: Which function for animate speed Samuele Salis (Fri Jun 27 2014 - 13:29:14 CDT)
tachyon renderer syntax Tristan Croll (Thu Jun 26 2014 - 23:12:33 CDT)
- Re: tachyon renderer syntax Josh Vermaas (Fri Jun 27 2014 - 10:37:00 CDT)
  - Re: tachyon renderer syntax Tristan Croll (Fri Jun 27 2014 - 18:54:57 CDT)
    - Re: tachyon renderer syntax Axel Kohlmeyer (Fri Jun 27 2014 - 22:07:49 CDT)
    - Re: tachyon renderer syntax Tristan Croll (Sat Jun 28 2014 - 06:28:46 CDT)
what is the center of rotation for the transformation matrix obtained by "measure fit" command? James Chen (Thu Jun 26 2014 - 16:27:43 CDT)
- Re: what is the center of rotation for the transformation matrix obtained by "measure fit" command? Josh Vermaas (Fri Jun 27 2014 - 10:15:58 CDT)
running a C code in VMD Rohan Mehta (Thu Jun 26 2014 - 04:38:40 CDT)
- Re: running a C code in VMD Ajasja LjubetiÄ (Thu Jun 26 2014 - 05:25:30 CDT)
- Re: running a C code in VMD Shailesh Pandey (Thu Jun 26 2014 - 05:59:44 CDT)
  - Re: running a C code in VMD Axel Kohlmeyer (Thu Jun 26 2014 - 06:43:17 CDT)
    - Re: running a C code in VMD Rohan Mehta (Thu Jun 26 2014 - 23:18:36 CDT)
NAMD energy calculation Ramin Ekhteiari (Wed Jun 25 2014 - 11:45:33 CDT)
- Re: NAMD energy calculation John Stone (Mon Jun 30 2014 - 22:59:28 CDT)
sscache with bigdcd Puspita Halder (Wed Jun 25 2014 - 08:23:56 CDT)
- Re: sscache with bigdcd Jeremiah Babcock (Wed Jun 25 2014 - 19:07:37 CDT)
  - Re: sscache with bigdcd Puspita Halder (Thu Jun 26 2014 - 09:15:40 CDT)
    - Re: sscache with bigdcd Maxim Belkin (Thu Jun 26 2014 - 09:43:23 CDT)
    - Re: sscache with bigdcd Puspita Halder (Fri Jun 27 2014 - 00:35:33 CDT)
tcl script causes VMD crash... Alberto Sergio Garay (Wed Jun 25 2014 - 07:55:08 CDT)
- Re: tcl script causes VMD crash... John Stone (Mon Jun 30 2014 - 22:35:40 CDT)
any way to rotate and translate with mouse without changing modes? Carlos Simmerling (Tue Jun 24 2014 - 13:17:52 CDT)
- Re: any way to rotate and translate with mouse without changing modes? Ajasja LjubetiÄ (Tue Jun 24 2014 - 15:37:39 CDT)
  - Re: any way to rotate and translate with mouse without changing modes? Carlos Simmerling (Wed Jun 25 2014 - 09:30:48 CDT)
Minor bug/annoyance: AutoPSF and acetylated CHARMM glycans Tristan Croll (Sat Jun 21 2014 - 19:13:31 CDT)
- Re: Minor bug/annoyance: AutoPSF and acetylated CHARMM glycans Tristan Croll (Mon Jun 23 2014 - 15:48:01 CDT)
Cannot start VMD in background from a script Jim (Sat Jun 21 2014 - 11:08:51 CDT)
- AW: Cannot start VMD in background from a script Norman Geist (Mon Jun 23 2014 - 03:29:50 CDT)
- Re: Cannot start VMD in background from a script John Stone (Mon Jun 23 2014 - 09:51:14 CDT)
Boron nitride preparation khannan krishna (Sat Jun 21 2014 - 01:08:27 CDT)
- Re: Boron nitride preparation Axel Kohlmeyer (Sat Jun 21 2014 - 03:31:23 CDT)
  - Re: Boron nitride preparation khannan krishna (Sat Jun 21 2014 - 04:28:29 CDT)
    - Re: Boron nitride preparation khannan krishna (Sat Jun 21 2014 - 08:50:17 CDT)
    - Re: Boron nitride preparation Axel Kohlmeyer (Sat Jun 21 2014 - 09:26:48 CDT)
Preparation of Boron nitride using Carbon nanotube builder khannan krishna (Tue Jun 17 2014 - 22:56:24 CDT)
Compute angle between 2 principal axis Revthi Sanker (Tue Jun 17 2014 - 00:57:58 CDT)
- Fwd: Compute angle between 2 principal axis Revthi Sanker (Sat Jun 21 2014 - 00:07:50 CDT)
regarding .vmdrc file Monoj Mon Kalita (Mon Jun 16 2014 - 20:53:54 CDT)
- Re: regarding .vmdrc file Axel Kohlmeyer (Tue Jun 17 2014 - 01:02:54 CDT)
  - Re: regarding .vmdrc file Josh Vermaas (Tue Jun 17 2014 - 02:10:24 CDT)
    - Re: regarding .vmdrc file Monoj Mon Kalita (Tue Jun 17 2014 - 03:47:44 CDT)
.vmdrc file Monoj Mon Kalita (Mon Jun 16 2014 - 10:06:57 CDT)
rmsdtt, itrajcomp and other plugins open sourced in github Luis Gracia (Mon Jun 16 2014 - 09:13:22 CDT)
- Re: rmsdtt, itrajcomp and other plugins open sourced in github Francesco Pietra (Tue Jun 17 2014 - 00:26:45 CDT)
- RE: rmsdtt, itrajcomp and other plugins open sourced in github Tristan Croll (Tue Jun 17 2014 - 01:17:05 CDT)
Visualizing Salt Bridges Mitul Saha (Sat Jun 14 2014 - 19:33:44 CDT)
- Re: Visualizing Salt Bridges John Stone (Mon Jun 30 2014 - 22:42:45 CDT)
Fake Guru Hamid Arabnia and bogus WORLDCOMP and CSCI jermy23_at_hushmail.com (Sat Jun 14 2014 - 08:29:47 CDT)
Building Boron Nitride khannan krishna (Fri Jun 13 2014 - 00:23:03 CDT)
Viewing SASA points through draw command-problem Vasumathi Velachi (Thu Jun 12 2014 - 11:33:04 CDT)
- Re: Viewing SASA points through draw command-problem Axel Kohlmeyer (Thu Jun 12 2014 - 12:16:20 CDT)
- RE: Viewing SASA points through draw command-problem Joaquim Rui de Castro Rodrigues (Thu Jun 12 2014 - 12:36:46 CDT)
  - RE: Viewing SASA points through draw command-problem Vasumathi Velachi (Fri Jun 13 2014 - 04:28:16 CDT)
substrate moving out of the box Revthi Sanker (Mon Jun 09 2014 - 06:31:11 CDT)
- Re: substrate moving out of the box Subbarao Kanchi (Mon Jun 09 2014 - 07:28:40 CDT)
analyzing gromacs trajectories with VMD sunyeping (Sat Jun 07 2014 - 04:47:59 CDT)
- Re: analyzing gromacs trajectories with VMD Axel Kohlmeyer (Sat Jun 07 2014 - 05:36:12 CDT)
Trouble with visual representations while loading a dcd. Diego Granados (Thu Jun 05 2014 - 11:34:52 CDT)
- Re: Trouble with visual representations while loading a dcd. Maxim Belkin (Thu Jun 05 2014 - 11:55:56 CDT)
Re: namd-l: NAMD energy plugin Ramin Ekhteiari (Wed Jun 04 2014 - 13:55:23 CDT)
NAMD energy plugin Ramin Ekhteiari (Wed Jun 04 2014 - 12:45:36 CDT)
- Re: NAMD energy plugin Josh Vermaas (Wed Jun 04 2014 - 13:54:51 CDT)
membrane generation question Richard Wood (Tue Jun 03 2014 - 11:35:35 CDT)
- Re: membrane generation question Josh Vermaas (Tue Jun 03 2014 - 13:32:21 CDT)
Unwrap visualization Ivan Moncayo (Fri May 30 2014 - 16:17:32 CDT)
Re: Hydrogen bond occupancy bharat gupta (Thu May 29 2014 - 20:55:55 CDT)
- Re: Re: Hydrogen bond occupancy John Stone (Thu May 29 2014 - 21:18:48 CDT)
  - Re: Re: Hydrogen bond occupancy bharat gupta (Thu May 29 2014 - 21:23:18 CDT)
Calculating RMSF for a lot of trajectories Ricard Argelaguet (Thu May 29 2014 - 11:22:18 CDT)
- Re: Calculating RMSF for a lot of trajectories Axel Kohlmeyer (Thu May 29 2014 - 11:59:26 CDT)
- Re: Calculating RMSF for a lot of trajectories Josh Vermaas (Thu May 29 2014 - 13:22:25 CDT)
psfgen-reading residues above 10 thousand Vasumathi Velachi (Thu May 29 2014 - 05:13:26 CDT)
- Re: psfgen-reading residues above 10 thousand Josh Vermaas (Thu May 29 2014 - 08:46:30 CDT)
  - Re: psfgen-reading residues above 10 thousand Vasumathi Velachi (Fri May 30 2014 - 04:25:01 CDT)
    - Re: psfgen-reading residues above 10 thousand Josh Vermaas (Fri May 30 2014 - 07:08:27 CDT)
    - Re: psfgen-reading residues above 10 thousand Tristan Croll (Fri May 30 2014 - 15:33:52 CDT)
CUDA errors for graphics card in Linux Matthew J. Comstock (Wed May 28 2014 - 14:06:23 CDT)
- Re: CUDA errors for graphics card in Linux John Stone (Wed May 28 2014 - 14:33:45 CDT)
  - Re: CUDA errors for graphics card in Linux John Stone (Wed May 28 2014 - 14:35:00 CDT)
    - Re: CUDA errors for graphics card in Linux Matthew J. Comstock (Wed May 28 2014 - 16:07:29 CDT)
    - Re: CUDA errors for graphics card in Linux John Stone (Wed May 28 2014 - 16:09:48 CDT)
Re: Help with RDF calculation Axel Kohlmeyer (Wed May 28 2014 - 13:45:51 CDT)
- Re: Re: Help with RDF calculation Mike Makowski (Wed May 28 2014 - 15:44:26 CDT)
  - Re: Re: Help with RDF calculation Axel Kohlmeyer (Wed May 28 2014 - 15:55:45 CDT)
Re: Rapid and accurate parameterization of new molecules in CHARMM Mayne, Christopher G (Wed May 28 2014 - 08:17:56 CDT)
snapshot including molecules in a distance interval Ali Alizadeh (Mon May 26 2014 - 05:55:37 CDT)
Re: Help request regarding PBCTOOLs plugin in vmd Olaf Lenz (Mon May 26 2014 - 02:38:58 CDT)
when will 1.9.2 be released? Albert (Sun May 25 2014 - 12:12:31 CDT)
Distance measurement and PBC Ozgun Kirker (Student) (Fri May 23 2014 - 21:30:17 CDT)
- Re: Distance measurement and PBC Olaf Lenz (Sun May 25 2014 - 05:41:59 CDT)
Re: pbc wrap -center com Olaf Lenz (Thu May 22 2014 - 05:45:00 CDT)
- AW: pbc wrap -center com Norman Geist (Thu May 22 2014 - 06:10:23 CDT)
- Re: pbc wrap -center com Olaf Lenz (Sun May 25 2014 - 06:04:35 CDT)
  - AW: pbc wrap -center com Norman Geist (Mon May 26 2014 - 02:20:27 CDT)
pbc wrap -center com Norman Geist (Thu May 22 2014 - 04:43:39 CDT)
Periodic boundaries and long bonds Olaf Lenz (Thu May 22 2014 - 01:17:51 CDT)
Ask VMD scripts Vy Phan (Tue May 20 2014 - 22:52:08 CDT)
- Re: Ask VMD scripts Nuno Sousa Cerqueira (Wed May 21 2014 - 03:17:07 CDT)
How to delete unwanted atoms from PSF Sadegh Faramarzi Ganjabad (Tue May 20 2014 - 22:40:59 CDT)
Select atoms within certain distance of vertical symmetry axis Bryan Roessler (Tue May 20 2014 - 16:25:26 CDT)
- Re: Select atoms within certain distance of vertical symmetry axis Josh Vermaas (Tue May 20 2014 - 17:39:09 CDT)
REï¼š REï¼š proper enviroment for the VMD namdenergy plugin sunyeping (Mon May 19 2014 - 16:40:05 CDT)
- Re: RE??? RE??? proper enviroment for the VMD namdenergy plugin John Stone (Tue May 20 2014 - 10:12:50 CDT)
REï¼š REï¼š proper enviroment for the VMD namdenergy plugin sunyeping (Mon May 19 2014 - 16:39:49 CDT)
REï¼š proper enviroment for the VMD namdenergy plugin sunyeping (Sun May 18 2014 - 12:00:10 CDT)
- Re: REï¼š proper enviroment for the VMD namdenergy plugin Josh Vermaas (Sun May 18 2014 - 16:11:45 CDT)
proper enviroment for the VMD namdenergy plugin sunyeping (Sun May 18 2014 - 00:30:00 CDT)
- Re: proper enviroment for the VMD namdenergy plugin Axel Kohlmeyer (Sun May 18 2014 - 08:08:19 CDT)
Workshop on Very Large System Simulation, Urbana, IL, August 11-15, 2014 David Brandon (Sat May 17 2014 - 18:26:44 CDT)
3-d printing of vmd scenes Bennion, Brian (Fri May 16 2014 - 12:49:05 CDT)
- Re: 3-d printing of vmd scenes John Stone (Fri May 16 2014 - 14:11:06 CDT)
  - Re: 3-d printing of vmd scenes Hurt, Darrell (NIH/NIAID) [E] (Mon May 19 2014 - 09:49:56 CDT)
Unable to use VMD1.9.1 binary (no CUDA) on Mac OSX 10.9.3 Leah Isseroff Bendavid (Thu May 15 2014 - 20:58:40 CDT)
- Re: Unable to use VMD1.9.1 binary (no CUDA) on Mac OSX 10.9.3 Joshua Skootsky (Thu May 15 2014 - 21:51:17 CDT)
- Re: Unable to use VMD1.9.1 binary (no CUDA) on Mac OSX 10.9.3 John Stone (Fri May 16 2014 - 10:04:00 CDT)
  - Re: Unable to use VMD1.9.1 binary (no CUDA) on Mac OSX 10.9.3 Maxim Belkin (Fri May 16 2014 - 10:56:34 CDT)
    - Re: Unable to use VMD1.9.1 binary (no CUDA) on Mac OSX 10.9.3 John Stone (Fri May 16 2014 - 11:27:50 CDT)
    - Re: Unable to use VMD1.9.1 binary (no CUDA) on Mac OSX 10.9.3 Leah Isseroff Bendavid (Fri May 16 2014 - 11:55:33 CDT)
Using bigdcd Ozgun Kirker (Student) (Thu May 15 2014 - 18:40:57 CDT)
- Re: Using bigdcd Joshua Skootsky (Thu May 15 2014 - 19:55:26 CDT)
default representations for multiple molecules Bokas George (Thu May 15 2014 - 16:48:54 CDT)
- Re: default representations for multiple molecules Axel Kohlmeyer (Thu May 15 2014 - 17:30:12 CDT)
  - Re: default representations for multiple molecules Bokas George (Thu May 15 2014 - 17:58:52 CDT)
    - Re: default representations for multiple molecules Axel Kohlmeyer (Thu May 15 2014 - 18:06:53 CDT)
    - Re: default representations for multiple molecules Bokas George (Thu May 15 2014 - 18:31:47 CDT)
- Re: default representations for multiple molecules Josh Vermaas (Thu May 15 2014 - 17:49:51 CDT)
- RE: default representations for multiple molecules Bennion, Brian (Thu May 15 2014 - 17:48:54 CDT)
file output issue Karl Lundquist (Thu May 15 2014 - 14:13:58 CDT)
- Re: file output issue John Stone (Fri May 16 2014 - 10:15:20 CDT)
  - Re: file output issue Karl Lundquist (Mon May 19 2014 - 11:15:28 CDT)
mutating a residue Research Jubilant (Wed May 14 2014 - 22:28:39 CDT)
(no subject) Mahesh Chandrasekhar Gandikota (Wed May 14 2014 - 09:59:40 CDT)
- Re: Re: John Stone (Fri May 16 2014 - 11:33:40 CDT)
NAMD-GPU Ramin Ekhteiari (Wed May 14 2014 - 07:19:10 CDT)
- Re: namd-l: NAMD-GPU Axel Kohlmeyer (Wed May 14 2014 - 07:51:37 CDT)
multiplying maps in non-orthogonal coordinates Tristan Croll (Tue May 13 2014 - 20:42:57 CDT)
- RE: multiplying maps in non-orthogonal coordinates Tristan Croll (Tue May 13 2014 - 21:26:14 CDT)
(no subject) Ed Robertson (Tue May 13 2014 - 04:48:54 CDT)
Space between protein and simulaton cell boundaries ramin_ekh_at_REMOVE_yahoo.com (Sun May 11 2014 - 09:30:33 CDT)
Problem with amorphous silicon dioxide: Inorganic builder Pavan Miriyala (Sun May 11 2014 - 08:53:30 CDT)
- Re: Problem with amorphous silicon dioxide: Inorganic builder Axel Kohlmeyer (Sun May 11 2014 - 09:44:42 CDT)
  - Re: Problem with amorphous silicon dioxide: Inorganic builder Pavan Miriyala (Sun May 11 2014 - 23:37:19 CDT)
    - Re: Problem with amorphous silicon dioxide: Inorganic builder Pavan Miriyala (Mon May 12 2014 - 00:59:46 CDT)
    - Re: Problem with amorphous silicon dioxide: Inorganic builder Axel Kohlmeyer (Mon May 12 2014 - 03:58:17 CDT)
Trajectory from multiple .gro files John Brown (Sat May 10 2014 - 06:49:42 CDT)
- Re: Trajectory from multiple .gro files Josh Vermaas (Mon May 12 2014 - 09:40:55 CDT)
  - RE: Trajectory from multiple .gro files Tristan Croll (Mon May 12 2014 - 23:56:08 CDT)
select two segment in structure sunyeping (Thu May 08 2014 - 11:36:28 CDT)
Re: [apbs-users] Missing library on mac Fateme Sadat Emami (Wed May 07 2014 - 14:45:22 CDT)
Trouble Recognizing Peptide Sequence Shyam Saladi (Wed May 07 2014 - 00:45:46 CDT)
- Re: Trouble Recognizing Peptide Sequence John Stone (Fri May 16 2014 - 14:36:08 CDT)
  - Re: Trouble Recognizing Peptide Sequence Shyam Saladi (Fri May 16 2014 - 15:47:59 CDT)
APBS plugin - lib error Fateme Sadat Emami (Tue May 06 2014 - 20:59:58 CDT)
- Re: APBS plugin - lib error John Stone (Thu May 22 2014 - 19:24:31 CDT)
choosing an optimal workstation video card for VMD Erik Nordgren (Tue May 06 2014 - 11:08:40 CDT)
- Re: choosing an optimal workstation video card for VMD Axel Kohlmeyer (Tue May 06 2014 - 12:58:13 CDT)
- Re: choosing an optimal workstation video card for VMD Josh Vermaas (Tue May 06 2014 - 12:48:05 CDT)
- Re: choosing an optimal workstation video card for VMD John Stone (Tue May 06 2014 - 16:01:20 CDT)
  - Re: choosing an optimal workstation video card for VMD Jeremiah Babcock (Tue May 06 2014 - 21:58:36 CDT)
Add bond across boundaries Passerone, Daniele (Tue May 06 2014 - 08:25:54 CDT)
- Re: Add bond across boundaries Axel Kohlmeyer (Tue May 06 2014 - 09:15:13 CDT)
  - R: Re: Add bond across boundaries Passerone, Daniele (Tue May 06 2014 - 09:58:19 CDT)
    - Re: Re: Add bond across boundaries Axel Kohlmeyer (Tue May 06 2014 - 10:06:39 CDT)
Empirical force fields: release new version of RED Server Dev/PyRED FyD (Mon May 05 2014 - 06:07:18 CDT)
number of water molecules within 5 angstroms of the ligand Ramin Ekhteiari (Mon May 05 2014 - 03:47:17 CDT)
- AW: number of water molecules within 5 angstroms of the ligand Norman Geist (Mon May 05 2014 - 05:16:47 CDT)
- AW: number of water molecules within 5 angstroms of the ligand Norman Geist (Mon May 05 2014 - 05:09:05 CDT)
- Re: number of water molecules within 5 angstroms of the ligand Axel Kohlmeyer (Mon May 05 2014 - 05:30:00 CDT)
  - Re: number of water molecules within 5 angstroms of the ligand Ramin Ekhteiari (Mon May 05 2014 - 13:03:34 CDT)
  - Re: number of water molecules within 5 angstroms of the ligand Joshua Skootsky (Wed May 07 2014 - 07:22:04 CDT)
    - AW: number of water molecules within 5 angstroms of the ligand Norman Geist (Wed May 07 2014 - 07:47:46 CDT)
Patch to connect monomers code Rawan Al Nsour (Sun May 04 2014 - 12:15:12 CDT)
Water visualization de Waal, Parker (Wed Apr 30 2014 - 20:46:31 CDT)
- Re: Water visualization John Stone (Wed Apr 30 2014 - 22:07:48 CDT)
Re: [lammps-users] Regarding rdf from VMD extensions+lammps Axel Kohlmeyer (Tue Apr 29 2014 - 13:37:43 CDT)
Visualize a SMILES string Jean-Patrick Francoia (Tue Apr 29 2014 - 07:49:11 CDT)
- Re: Visualize a SMILES string Axel Kohlmeyer (Tue Apr 29 2014 - 08:54:50 CDT)
- AW: Visualize a SMILES string Norman Geist (Tue Apr 29 2014 - 10:01:56 CDT)
writing out a new dcd file Ramin Ekhteiari (Tue Apr 29 2014 - 06:07:48 CDT)
- Re: writing out a new dcd file Axel Kohlmeyer (Tue Apr 29 2014 - 06:50:35 CDT)
- Re: writing out a new dcd file AnkiReddy katha (Tue Apr 29 2014 - 08:57:17 CDT)
surface charge calculations Fateme Sadat Emami (Fri Apr 25 2014 - 13:28:40 CDT)
- Re: surface charge calculations Ajasja LjubetiÄ (Fri Apr 25 2014 - 15:55:48 CDT)
AW: measure Hbond and orient (with vec {0 0 1}) of a selected molecule Norman Geist (Fri Apr 25 2014 - 06:36:35 CDT)
- Re: measure Hbond and orient (with vec {0 0 1}) of a selected molecule JC Gumbart (Fri Apr 25 2014 - 15:27:30 CDT)
AW: measure Hbond and orient (with vec {0 0 1}) of a selected molecule Norman Geist (Fri Apr 25 2014 - 05:39:11 CDT)
AW: measure Hbond and orient (with vec {0 0 1}) of a selected molecule Norman Geist (Fri Apr 25 2014 - 02:49:20 CDT)
measure Hbond and orient (with vec {0 0 1}) of a selected molecule HongTham (Thu Apr 24 2014 - 19:51:51 CDT)
- AW: measure Hbond and orient (with vec {0 0 1}) of a selected molecule Norman Geist (Fri Apr 25 2014 - 01:13:38 CDT)
ligand-protein bonds representation Jeremías Corradi (Tue Apr 22 2014 - 08:36:14 CDT)
- Re: ligand-protein bonds representation Axel Kohlmeyer (Tue Apr 22 2014 - 09:50:52 CDT)
  - Re: ligand-protein bonds representation JeremÃas Corradi (Tue Apr 22 2014 - 10:08:58 CDT)
    - Re: ligand-protein bonds representation Axel Kohlmeyer (Tue Apr 22 2014 - 10:53:19 CDT)
selection manager Nuno Sousa Cerqueira (Tue Apr 22 2014 - 05:44:00 CDT)
- Re: selection manager Ajasja LjubetiÄ (Tue Apr 22 2014 - 06:38:16 CDT)
  - Re: selection manager Nuno Sousa Cerqueira (Wed Apr 23 2014 - 04:16:08 CDT)
alchemical transformations Chiara Cardelli (Sun Apr 20 2014 - 13:19:41 CDT)
- Re: alchemical transformations Fotis Baltoumas (Mon Apr 21 2014 - 03:36:26 CDT)
  - Re: alchemical transformations Chiara Cardelli (Mon Apr 21 2014 - 04:21:58 CDT)
printf in tcl script Martin, Erik W (Fri Apr 18 2014 - 17:05:09 CDT)
- Re: printf in tcl script Josh Vermaas (Fri Apr 18 2014 - 17:49:32 CDT)
- Re: printf in tcl script Mayne, Christopher G (Fri Apr 18 2014 - 18:42:33 CDT)
Workshop on GPU Programming for Molecular Modeling, in Urbana, Illinois, July 22-24, 2014 David Brandon (Fri Apr 18 2014 - 16:42:16 CDT)
automate pdb processing Martin, Erik W (Thu Apr 17 2014 - 16:32:13 CDT)
code precision problem Jeremiah Babcock (Wed Apr 16 2014 - 15:06:15 CDT)
- AW: code precision problem Norman Geist (Thu Apr 17 2014 - 01:29:04 CDT)
- Re: code precision problem JC Gumbart (Thu Apr 17 2014 - 12:48:05 CDT)
  - Re: code precision problem Jeremiah Babcock (Mon Apr 21 2014 - 12:32:30 CDT)
convert AMBER format file to CHARMM format file or NAMD format file Norge Cruz HernÃ¡ndez (Wed Apr 16 2014 - 13:24:26 CDT)
- Re: convert AMBER format file to CHARMM format file or NAMD format file Josh Vermaas (Wed Apr 16 2014 - 14:29:44 CDT)
  - Re: convert AMBER format file to CHARMM format file or NAMD format file Norge Cruz HernÃ¡ndez (Thu Apr 17 2014 - 10:08:29 CDT)
    - Re: convert AMBER format file to CHARMM format file or NAMD format file Josh Vermaas (Thu Apr 17 2014 - 10:27:43 CDT)
    - Re: convert AMBER format file to CHARMM format file or NAMD format file Axel Kohlmeyer (Thu Apr 17 2014 - 11:03:49 CDT)
- Re: convert AMBER format file to CHARMM format file or NAMD format file Axel Kohlmeyer (Wed Apr 16 2014 - 14:55:58 CDT)
How do i merge files with mergemols Ashish .Chauniyal (Wed Apr 16 2014 - 10:07:00 CDT)
- Re: How do i merge files with mergemols Josh Vermaas (Wed Apr 16 2014 - 11:04:15 CDT)
  - Re: How do i merge files with mergemols Ashish .Chauniyal (Fri Apr 25 2014 - 06:14:22 CDT)
How to output formed dynamic bonds in VMD Mingchao Wang (Wed Apr 16 2014 - 00:01:20 CDT)
- Re: How to output formed dynamic bonds in VMD Axel Kohlmeyer (Wed Apr 16 2014 - 00:40:16 CDT)
get resname from resid sunyeping (Tue Apr 15 2014 - 04:18:38 CDT)
- AW: get resname from resid Norman Geist (Tue Apr 15 2014 - 06:30:32 CDT)
Matal binding protein prediction 3d Recep adýyaman (Tue Apr 15 2014 - 03:49:01 CDT)
- Re: Matal binding protein prediction 3d Ajasja LjubetiÄ (Tue Apr 15 2014 - 05:22:11 CDT)
Altering extrabonds force constant during MD Bryan Roessler (Mon Apr 14 2014 - 16:11:28 CDT)
- Re: Altering extrabonds force constant during MD Axel Kohlmeyer (Mon Apr 14 2014 - 16:56:59 CDT)
  - Re: Altering extrabonds force constant during MD Bryan Roessler (Tue Apr 15 2014 - 09:52:18 CDT)
No native HOOMD xml support for Windows? Joshua Dempster (Mon Apr 14 2014 - 11:10:51 CDT)
- Re: No native HOOMD xml support for Windows? Axel Kohlmeyer (Mon Apr 14 2014 - 12:06:42 CDT)
Changing the Font size of the XYZ Logo Mehdi Eftekhari (Fri Apr 11 2014 - 10:48:37 CDT)
- Re: Changing the Font size of the XYZ Logo Maxim Belkin (Fri Apr 11 2014 - 11:05:35 CDT)
  - Re: Changing the Font size of the XYZ Logo Mehdi Eftekhari (Fri Apr 11 2014 - 12:00:25 CDT)
    - Re: Changing the Font size of the XYZ Logo Axel Kohlmeyer (Fri Apr 11 2014 - 12:45:51 CDT)
how to control the superposition (measure fit) ? Vlad Cojocaru (Fri Apr 11 2014 - 07:16:17 CDT)
- AW: how to control the superposition (measure fit) ? Norman Geist (Fri Apr 11 2014 - 09:20:06 CDT)
  - Re: AW: how to control the superposition (measure fit) ? Vlad Cojocaru (Sat Apr 12 2014 - 05:49:13 CDT)
- Re: how to control the superposition (measure fit) ? Josh Vermaas (Fri Apr 11 2014 - 09:28:15 CDT)
  - Re: how to control the superposition (measure fit) ? Josh Vermaas (Fri Apr 11 2014 - 10:29:18 CDT)
  - Re: how to control the superposition (measure fit) ? Josh Vermaas (Sat Apr 12 2014 - 09:37:43 CDT)
    - Re: how to control the superposition (measure fit) ? Vlad Cojocaru (Sun Apr 13 2014 - 07:28:33 CDT)
Re: namd-l: MMPBSA Energy Calculations using VMD (Post-Processing) Fotis Baltoumas (Thu Apr 10 2014 - 10:09:00 CDT)
manually generate PSF for small molecules Adam Goler (Wed Apr 09 2014 - 20:04:56 CDT)
hiding or disabling some of the atom types Mehdi Eftekhari (Wed Apr 09 2014 - 15:45:31 CDT)
- Re: hiding or disabling some of the atom types Axel Kohlmeyer (Wed Apr 09 2014 - 16:20:34 CDT)
problem with movie generation Carlos Simmerling (Wed Apr 09 2014 - 10:31:51 CDT)
- Re: problem with movie generation John Stone (Wed Apr 09 2014 - 10:48:46 CDT)
  - Re: problem with movie generation Carlos Simmerling (Wed Apr 09 2014 - 11:16:53 CDT)
Changing colors during a dynamics Luca Bellarosa (Wed Apr 09 2014 - 09:29:21 CDT)
- Re: Changing colors during a dynamics Axel Kohlmeyer (Wed Apr 09 2014 - 10:15:02 CDT)
  - Re: Changing colors during a dynamics Luca Bellarosa (Tue Apr 22 2014 - 10:43:46 CDT)
psf file with D-proline Gurunath Katagi (Wed Apr 09 2014 - 01:18:35 CDT)
problem displaying CPK Misraim Enrique Gurrola Acosta (Tue Apr 08 2014 - 21:04:12 CDT)
posting from Yahoo addresses disabled Jim Phillips (Tue Apr 08 2014 - 17:45:46 CDT)
- Re: posting from Yahoo addresses disabled Jim Phillips (Wed Apr 09 2014 - 17:10:06 CDT)
problem with 'atomselect' command Ashish .Chauniyal (Tue Apr 08 2014 - 12:23:05 CDT)
- Re: problem with 'atomselect' command Axel Kohlmeyer (Tue Apr 08 2014 - 13:23:22 CDT)
FFTK: bond and angle parameters denilson_at_dqi.ufla.br (Mon Apr 07 2014 - 14:42:28 CDT)
- Re: FFTK: bond and angle parameters Mayne, Christopher G (Wed Apr 16 2014 - 09:44:19 CDT)
Minimal VMD Jacob Durrant (Mon Apr 07 2014 - 14:42:47 CDT)
- Re: Minimal VMD John Stone (Mon Apr 07 2014 - 15:23:42 CDT)
REï¼š Re: REï¼š visualize gromacs trajectory in vmd sunyeping (Mon Apr 07 2014 - 06:52:55 CDT)
Feature request: capturing tool location and steering forces in IMD trajectory Tristan Croll (Mon Apr 07 2014 - 00:45:51 CDT)
- Re: Feature request: capturing tool location and steering forces in IMD trajectory Axel Kohlmeyer (Mon Apr 07 2014 - 01:23:09 CDT)
  - Re: Feature request: capturing tool location and steering forces in IMD trajectory Tristan Croll (Mon Apr 07 2014 - 03:29:31 CDT)
  - Re: Feature request: capturing tool location and steering forces in IMD trajectory John Stone (Fri May 16 2014 - 14:20:10 CDT)
    - Re: Feature request: capturing tool location and steering forces in IMD trajectory Tristan Croll (Fri May 16 2014 - 16:27:01 CDT)
    - Re: Feature request: capturing tool location and steering forces in IMD trajectory John Stone (Mon May 19 2014 - 14:54:39 CDT)
Movie Smoothing error Maria Pikoula (Sun Apr 06 2014 - 08:36:15 CDT)
- Re: Movie Smoothing error Maxim Belkin (Mon Apr 07 2014 - 10:50:58 CDT)
Dynamical bond rendering Caro Miguel (Sat Apr 05 2014 - 01:36:34 CDT)
- Re: Dynamical bond rendering Axel Kohlmeyer (Sat Apr 05 2014 - 02:35:50 CDT)
SHAKE or RATTLE algorithm Ramin Ekhteiari (Fri Apr 04 2014 - 15:08:04 CDT)
VMD color by user Zhencheng Ren (Fri Apr 04 2014 - 14:24:53 CDT)
ffTk user feature request Jim Parker (Fri Apr 04 2014 - 05:58:57 CDT)
- Re: ffTk user feature request John Stone (Fri Apr 04 2014 - 09:26:32 CDT)
  - Re: ffTk user feature request Mayne, Christopher G (Fri Apr 04 2014 - 10:40:13 CDT)
    - Re: ffTk user feature request Maxim Belkin (Fri Apr 04 2014 - 11:05:19 CDT)
ffTK generated Gaussian file puts "atoms too close" and Gaussian fails to run Jim Parker (Fri Apr 04 2014 - 05:42:33 CDT)
- Re: ffTK generated Gaussian file puts "atoms too close" and Gaussian fails to run Mayne, Christopher G (Fri Apr 04 2014 - 11:08:13 CDT)
  - Re: ffTK generated Gaussian file puts "atoms too close" and Gaussian fails to run Jim Parker (Fri Apr 04 2014 - 14:32:24 CDT)
GPU-accelerated ionization Tristan Croll (Thu Apr 03 2014 - 20:05:50 CDT)
- Re: GPU-accelerated ionization John Stone (Wed Apr 09 2014 - 11:31:41 CDT)
writing velocities from VMD Marcela Madrid (Thu Apr 03 2014 - 19:31:10 CDT)
- AW: writing velocities from VMD Norman Geist (Fri Apr 04 2014 - 02:44:48 CDT)
- Re: writing velocities from VMD Axel Kohlmeyer (Fri Apr 04 2014 - 06:36:30 CDT)
  - AW: writing velocities from VMD Norman Geist (Mon Apr 07 2014 - 01:56:05 CDT)
    - Re: writing velocities from VMD John Stone (Wed Apr 09 2014 - 11:35:28 CDT)
Gaussian Log File problem Hay, Stuart (Thu Apr 03 2014 - 12:35:55 CDT)
- Re: Gaussian Log File problem Mayne, Christopher G (Thu Apr 03 2014 - 22:15:04 CDT)
Comparing Structures with Multiseq and Qres Donald Karr (Thu Apr 03 2014 - 10:33:55 CDT)
- Re: Comparing Structures with Multiseq and Qres Anurag Sethi (Mon Apr 07 2014 - 19:37:48 CDT)
  - Re: Comparing Structures with Multiseq and Qres Anurag Sethi (Wed Apr 16 2014 - 10:41:02 CDT)
HOW MAKE CROSS CO-RELATION MATRIX rajan kumar (Thu Apr 03 2014 - 04:06:55 CDT)
Visualizing volume slice from PME electrostatics Riccardo Innocenti Malini (Thu Apr 03 2014 - 03:40:28 CDT)
- Re: Visualizing volume slice from PME electrostatics John Stone (Thu Apr 03 2014 - 10:51:58 CDT)
BUG? Hbond rep brakes RowInterleaved Stereo VMD 1.9.2a35 Norman Geist (Thu Apr 03 2014 - 02:17:38 CDT)
- Re: BUG? Hbond rep brakes RowInterleaved Stereo VMD 1.9.2a35 John Stone (Wed Apr 09 2014 - 14:15:43 CDT)
  - Re: BUG? Hbond rep brakes RowInterleaved Stereo VMD 1.9.2a35 John Stone (Fri May 16 2014 - 14:31:17 CDT)
    - AW: BUG? Hbond rep brakes RowInterleaved Stereo VMD 1.9.2a35 Norman Geist (Mon May 19 2014 - 02:33:46 CDT)
    - Re: BUG? Hbond rep brakes RowInterleaved Stereo VMD 1.9.2a35 John Stone (Mon May 19 2014 - 11:28:07 CDT)
secondary structure inconsistency Charles Greenberg (Wed Apr 02 2014 - 12:39:33 CDT)
- AW: secondary structure inconsistency Norman Geist (Thu Apr 03 2014 - 00:40:31 CDT)
- Re: secondary structure inconsistency John Stone (Thu Apr 03 2014 - 11:03:39 CDT)
  - Re: secondary structure inconsistency Charles Greenberg (Thu Apr 03 2014 - 12:48:16 CDT)
REï¼š visualize gromacs trajectory in vmd sunyeping (Wed Apr 02 2014 - 10:40:07 CDT)
- Re: REï¼š visualize gromacs trajectory in vmd Felipe Merino (Wed Apr 02 2014 - 10:47:30 CDT)
"Hands-on" Workshop on Computational Biophysics at Lake Tahoe, August 4-8, 2014 David Brandon (Tue Apr 01 2014 - 16:23:08 CDT)
visualize gromacs trajectory in vmd sunyeping (Tue Apr 01 2014 - 10:43:41 CDT)
generatei psf file for a dimer protein Ramin Ekhteiari (Tue Apr 01 2014 - 08:24:33 CDT)
- Re: generatei psf file for a dimer protein Josh Vermaas (Tue Apr 01 2014 - 09:30:24 CDT)
set view along an chosen axis wei gao (Mon Mar 31 2014 - 15:44:07 CDT)
- Re: set view along an chosen axis Maxim Belkin (Mon Mar 31 2014 - 15:55:49 CDT)
Assigning different temperatures in the same simulaiton Jhonatam Cordeiro Rodrigues (Mon Mar 31 2014 - 08:25:06 CDT)
- AW: Assigning different temperatures in the same simulaiton Norman Geist (Tue Apr 01 2014 - 00:07:02 CDT)
- AW: Assigning different temperatures in the same simulaiton Norman Geist (Tue Apr 01 2014 - 00:21:03 CDT)
Fwd: Align specific residues of two structures Hailin Huang (Mon Mar 31 2014 - 02:07:44 CDT)
Align specific residues of two structures Hailin Huang (Fri Mar 28 2014 - 15:37:37 CDT)
- Re: Align specific residues of two structures Ivan Gregoretti (Fri Mar 28 2014 - 16:57:16 CDT)
  - AW: Align specific residues of two structures Norman Geist (Mon Mar 31 2014 - 00:35:37 CDT)
TCL scripting question: how to make a list of atomselections persistent? Tristan Croll (Thu Mar 27 2014 - 19:04:22 CDT)
- AW: TCL scripting question: how to make a list of atomselections persistent? Norman Geist (Fri Mar 28 2014 - 03:00:02 CDT)
  - Re: AW: TCL scripting question: how to make a list of atomselections persistent? Tristan Croll (Fri Mar 28 2014 - 03:45:22 CDT)
    - Re: AW: TCL scripting question: how to make a list of atomselections persistent? Ivan Gregoretti (Fri Mar 28 2014 - 09:06:56 CDT)
    - RE: AW: TCL scripting question: how to make a list of atomselections persistent? Tristan Croll (Fri Mar 28 2014 - 23:19:50 CDT)
- AW: TCL scripting question: how to make a list of atomselections persistent? Norman Geist (Fri Mar 28 2014 - 03:02:24 CDT)
selecting every nth residue in a protein Research Jubilant (Thu Mar 27 2014 - 15:29:06 CDT)
- Re: selecting every nth residue in a protein Axel Kohlmeyer (Thu Mar 27 2014 - 17:34:30 CDT)
  - Re: selecting every nth residue in a protein Ajasja LjubetiÄ (Thu Mar 27 2014 - 18:20:55 CDT)
atomselect across two different molids Ravinder Abrol (Thu Mar 27 2014 - 15:15:42 CDT)
cant find output file from tachyon render. Semeraro, B David (Thu Mar 27 2014 - 08:50:56 CDT)
- Re: cant find output file from tachyon render. Massimiliano Porrini (Thu Mar 27 2014 - 11:51:33 CDT)
  - RE: cant find output file from tachyon render. Semeraro, B David (Thu Mar 27 2014 - 12:07:45 CDT)
Multiple proteins in MDFF? Lyman K Monroe (Tue Mar 25 2014 - 20:59:49 CDT)
- Re: Multiple proteins in MDFF? Ryan McGreevy (Wed Mar 26 2014 - 11:25:55 CDT)
multiple proteins Lyman K Monroe (Tue Mar 25 2014 - 20:58:41 CDT)
topo writelammpsdata: size limitation? Laurent Joly (Sun Mar 23 2014 - 18:11:29 CDT)
impropers dropped when using psfgen Michael F. Harrach (Fri Mar 21 2014 - 11:36:31 CDT)
- Re: impropers dropped when using psfgen Josh Vermaas (Fri Mar 21 2014 - 14:18:07 CDT)
- Re: impropers dropped when using psfgen Michael F. Harrach (Mon Mar 24 2014 - 03:48:36 CDT)
  - Re: Re: impropers dropped when using psfgen Josh Vermaas (Mon Mar 24 2014 - 11:13:55 CDT)
problem for VMD extension_radial pair distribution function_truncation Ming-Tsung Lee (Fri Mar 21 2014 - 10:23:22 CDT)
- Re: problem for VMD extension_radial pair distribution function_truncation Axel Kohlmeyer (Fri Mar 21 2014 - 11:08:28 CDT)
- Re: problem for VMD extension_radial pair distribution function_truncation Philippe Bopp (Fri Mar 21 2014 - 12:21:38 CDT)
Re: Writing DCD from modified coordinates Ivan Gregoretti (Fri Mar 21 2014 - 07:31:32 CDT)
- Re: Writing DCD from modified coordinates Adam Goler (Fri Mar 21 2014 - 12:21:16 CDT)
  - Re: Writing DCD from modified coordinates JÃ©rÃ´me HÃ©nin (Fri Mar 21 2014 - 13:04:58 CDT)
Writing DCD from modified coordinates Adam Goler (Thu Mar 20 2014 - 23:59:33 CDT)
- AW: Writing DCD from modified coordinates Norman Geist (Fri Mar 21 2014 - 02:51:25 CDT)
Broken link to MacKerell parameterization tutorial Jim Parker (Thu Mar 20 2014 - 14:26:40 CDT)
- Re: Broken link to MacKerell parameterization tutorial John Stone (Thu Mar 20 2014 - 15:22:11 CDT)
  - Re: Broken link to MacKerell parameterization tutorial JC Gumbart (Thu Mar 20 2014 - 20:12:22 CDT)
    - Re: Broken link to MacKerell parameterization tutorial Jim Parker (Fri Mar 21 2014 - 06:28:03 CDT)
Some useful scripts for people using CHARMM-36 glycans Tristan Croll (Thu Mar 20 2014 - 01:20:29 CDT)
wrapping option in namd Research Jubilant (Wed Mar 19 2014 - 21:34:57 CDT)
- Re: namd-l: wrapping option in namd Ivan Gregoretti (Wed Mar 19 2014 - 21:58:30 CDT)
  - Re: Re: namd-l: wrapping option in namd Research Jubilant (Wed Mar 19 2014 - 22:38:16 CDT)
Writing dcd/pdb file of selection from NAMD velocity dcd file Chola Regmi (Wed Mar 19 2014 - 16:29:06 CDT)
- Re: Writing dcd/pdb file of selection from NAMD velocity dcd file Josh Vermaas (Wed Mar 19 2014 - 17:35:41 CDT)
  - Re: Writing dcd/pdb file of selection from NAMD velocity dcd file Chola Regmi (Wed Mar 19 2014 - 19:36:55 CDT)
XRD from a structure Fatemesadat Emami (Wed Mar 19 2014 - 16:01:03 CDT)
psfgen, adding residues with command "residue" Ivan Gregoretti (Wed Mar 19 2014 - 13:07:42 CDT)
- Re: psfgen, adding residues with command "residue" Josh Vermaas (Wed Mar 19 2014 - 14:01:37 CDT)
  - Re: psfgen, adding residues with command "residue" Ivan Gregoretti (Wed Mar 19 2014 - 17:58:24 CDT)
Get num. of residues spandu K (Wed Mar 19 2014 - 01:38:44 CDT)
- Re: Get num. of residues Axel Kohlmeyer (Wed Mar 19 2014 - 02:34:23 CDT)
- AW: Get num. of residues Norman Geist (Wed Mar 19 2014 - 03:56:12 CDT)
psfgen and Alternate location indicator Ivan Gregoretti (Tue Mar 18 2014 - 13:53:18 CDT)
- Re: psfgen and Alternate location indicator John Stone (Tue Mar 18 2014 - 17:12:43 CDT)
  - Re: psfgen and Alternate location indicator Ivan Gregoretti (Wed Mar 19 2014 - 08:44:01 CDT)
Error : Lammps-data file error after merging two structures. Pavan Miriyala (Tue Mar 18 2014 - 10:47:37 CDT)
REï¼š removing water from dcd file sunyeping (Tue Mar 18 2014 - 08:13:31 CDT)
removing water from dcd file Ramin Ekhteiari (Tue Mar 18 2014 - 08:01:41 CDT)
- Re: removing water from dcd file Axel Kohlmeyer (Tue Mar 18 2014 - 08:55:15 CDT)
- Re: removing water from dcd file Adam Goler (Tue Mar 18 2014 - 09:09:38 CDT)
- Re: removing water from dcd file amin_at_imtech.res.in (Tue Mar 18 2014 - 12:03:26 CDT)
Unwrapping a trajectory with H2O Kipp Johnson (Mon Mar 17 2014 - 18:08:45 CDT)
- Re: Unwrapping a trajectory with H2O Axel Kohlmeyer (Tue Mar 18 2014 - 01:10:34 CDT)
  - Re: Unwrapping a trajectory with H2O Axel Kohlmeyer (Fri Mar 21 2014 - 15:23:29 CDT)
Custom Visualization of Atom Properties Change with Color Nima Nouri (Sun Mar 16 2014 - 16:59:58 CDT)
adding new colors Leonhard Henkes (Thu Mar 13 2014 - 09:21:57 CDT)
SURF error Shomesankar Bhunia (Wed Mar 12 2014 - 05:17:40 CDT)
- Re: SURF error John Stone (Wed Mar 12 2014 - 12:16:09 CDT)
radial pair distribution function Adam Goler (Tue Mar 11 2014 - 20:03:55 CDT)
- Re: radial pair distribution function Josh Vermaas (Tue Mar 11 2014 - 22:00:13 CDT)
  - Re: radial pair distribution function Adam Goler (Tue Mar 11 2014 - 23:55:56 CDT)
    - Re: radial pair distribution function Axel Kohlmeyer (Wed Mar 12 2014 - 00:35:52 CDT)
    - Re: radial pair distribution function Adam Goler (Wed Mar 12 2014 - 13:02:04 CDT)
Segmentation fault Simon Etter (Tue Mar 11 2014 - 07:31:17 CDT)
- Re: Segmentation fault John Stone (Tue Mar 11 2014 - 10:10:44 CDT)
  - Re: Segmentation fault Simon Etter (Tue Mar 11 2014 - 10:21:07 CDT)
- RE: Segmentation fault Cosseddu, Salvatore (Tue Mar 11 2014 - 10:00:30 CDT)
  - RE: Segmentation fault Cosseddu, Salvatore (Tue Mar 11 2014 - 10:02:52 CDT)
Call for participation: ISQBP Meeting, Telluride 15-19.06.2014 Vlad Cojocaru (Mon Mar 10 2014 - 11:38:42 CDT)
Fedora 20 x86_64 + ibus + sazanami fonts + GNOME => VMD 1.9.1 crashes René Genz (Sun Mar 09 2014 - 08:51:55 CDT)
- Re: Fedora 20 x86_64 + ibus + sazanami fonts + GNOME => VMD 1.9.1 crashes John Stone (Sun Mar 09 2014 - 09:25:50 CDT)
  - Re: Fedora 20 x86_64 + ibus + sazanami fonts + GNOME => VMD 1.9.1 crashes René Genz (Mon Mar 10 2014 - 14:15:23 CDT)
  - Re: Fedora 20 x86_64 + ibus + sazanami fonts + GNOME => VMD 1.9.1 crashes René Genz (Mon Mar 10 2014 - 14:07:40 CDT)
Changing bond numbers T K (Sun Mar 09 2014 - 00:52:22 CST)
- Re: Changing bond numbers Axel Kohlmeyer (Sun Mar 09 2014 - 03:37:28 CDT)
  - Re: Changing bond numbers T K (Thu Mar 20 2014 - 10:05:53 CDT)
    - Re: Changing bond numbers Axel Kohlmeyer (Thu Mar 20 2014 - 11:58:09 CDT)
Velocity storing in VMD Maria Pikoula (Sat Mar 08 2014 - 05:51:44 CST)
- Re: Velocity storing in VMD Maxim Belkin (Sat Mar 08 2014 - 10:50:07 CST)
  - Re: Velocity storing in VMD Maria Pikoula (Sat Mar 08 2014 - 18:52:56 CST)
  - Re: Velocity storing in VMD Maria Pikoula (Sat Mar 08 2014 - 18:52:56 CST)
distance selection Antonio Tilocca (Fri Mar 07 2014 - 10:41:43 CST)
- Re: distance selection Josh Vermaas (Fri Mar 07 2014 - 14:19:02 CST)
VMD within emacs Cosseddu, Salvatore (Thu Mar 06 2014 - 11:17:53 CST)
- VMD within emacs Cosseddu, Salvatore (Thu Mar 06 2014 - 11:21:28 CST)
How to delete atoms in graphene sheet Pavan Miriyala (Wed Mar 05 2014 - 10:21:29 CST)
- Re: How to delete atoms in graphene sheet Maxim Belkin (Wed Mar 05 2014 - 10:53:29 CST)
Compile VMD saeed (Wed Mar 05 2014 - 09:52:59 CST)
- Re: Compile VMD John Stone (Wed Mar 05 2014 - 10:33:35 CST)
  - Re: Compile VMD saeed (Thu Mar 06 2014 - 06:37:06 CST)
Generalisation of chirality plugin to handle chiral bonds spanning residues Tristan Croll (Wed Mar 05 2014 - 05:48:46 CST)
Mutate Residue Extension Daou, Joseph A (Tue Mar 04 2014 - 14:25:38 CST)
- Re: Mutate Residue Extension Josh Vermaas (Tue Mar 04 2014 - 15:39:16 CST)
  - RE: Mutate Residue Extension Daou, Joseph A (Tue Mar 04 2014 - 19:53:37 CST)
    - Re: Mutate Residue Extension Josh Vermaas (Tue Mar 04 2014 - 20:28:34 CST)
Writing new coordinates to file. Dawid das (Mon Mar 03 2014 - 15:25:14 CST)
- Re: Writing new coordinates to file. Maxim Belkin (Mon Mar 03 2014 - 15:49:00 CST)
  - Re: Writing new coordinates to file. Josh Vermaas (Tue Mar 04 2014 - 13:01:17 CST)
  - Re: Writing new coordinates to file. Josh Vermaas (Tue Mar 04 2014 - 13:27:36 CST)
- Re: Writing new coordinates to file. Maxim Belkin (Mon Mar 03 2014 - 15:37:36 CST)
- Re: Writing new coordinates to file. Axel Kohlmeyer (Mon Mar 03 2014 - 16:04:14 CST)
- Re: Writing new coordinates to file. Josh Vermaas (Mon Mar 03 2014 - 16:27:05 CST)
rlwrap: No match. Subbarao Kanchi (Mon Mar 03 2014 - 07:34:17 CST)
- Re: rlwrap: No match. Axel Kohlmeyer (Mon Mar 03 2014 - 08:15:26 CST)
  - Re: rlwrap: No match. Subbarao Kanchi (Mon Mar 03 2014 - 08:24:55 CST)
Issues using VMD 1.91. with CUDA on Mac OSX 10.9.1 Phillips, Carolyn L. (Sun Mar 02 2014 - 14:42:31 CST)
- Re: Issues using VMD 1.91. with CUDA on Mac OSX 10.9.1 Axel Kohlmeyer (Sun Mar 02 2014 - 15:20:48 CST)
Drawing circles and tooltips. Lee-Ping Wang (Fri Feb 28 2014 - 08:58:35 CST)
- Re: Drawing circles and tooltips. Benjamin Kaduk (Fri Feb 28 2014 - 21:57:36 CST)
  - Re: Drawing circles and tooltips. Lee-Ping Wang (Fri Feb 28 2014 - 23:03:01 CST)
    - Re: Drawing circles and tooltips. Benjamin Kaduk (Fri Feb 28 2014 - 23:22:48 CST)
    - Re: Drawing circles and tooltips. Lee-Ping Wang (Sat Mar 01 2014 - 17:38:38 CST)
  - Re: Drawing circles and tooltips. Lee-Ping Wang (Fri Feb 28 2014 - 22:58:59 CST)
- Re: Drawing circles and tooltips. John Stone (Mon Mar 03 2014 - 10:22:46 CST)
  - Re: Drawing circles and tooltips. Lee-Ping Wang (Tue Mar 04 2014 - 11:52:59 CST)
    - RE: Drawing circles and tooltips. Lee-Ping Wang (Tue Mar 11 2014 - 13:30:02 CDT)
charges optimisation of a cationic molecule with ffTK Massimiliano Porrini (Fri Feb 28 2014 - 05:18:51 CST)
- Re: charges optimisation of a cationic molecule with ffTK JC Gumbart (Mon Mar 03 2014 - 00:06:04 CST)
  - Re: charges optimisation of a cationic molecule with ffTK Massimiliano Porrini (Mon Mar 03 2014 - 03:45:21 CST)
isosurfaces with non-orthorhombic unit cells using cube file Karen Chan (Thu Feb 27 2014 - 17:54:03 CST)
- Re: isosurfaces with non-orthorhombic unit cells using cube file John Stone (Thu Feb 27 2014 - 18:50:19 CST)
Compiling 64bit VMD Nima Nouri (Wed Feb 26 2014 - 03:15:31 CST)
issue(s) with ffTK of vmd-1.9.2a35 Massimiliano Porrini (Tue Feb 25 2014 - 16:18:25 CST)
- Re: issue(s) with ffTK of vmd-1.9.2a35 Mayne, Christopher G (Tue Feb 25 2014 - 17:08:14 CST)
- Re: issue(s) with ffTK of vmd-1.9.2a35 Tim Lo (Tue Feb 25 2014 - 19:38:52 CST)
  - Re: issue(s) with ffTK of vmd-1.9.2a35 Mayne, Christopher G (Wed Feb 26 2014 - 12:57:44 CST)
Nanostructure Plugin from TCL Script Michail Palaiokostas Avramidis (Tue Feb 25 2014 - 11:41:32 CST)
- Re: Nanostructure Plugin from TCL Script Maxim Belkin (Tue Feb 25 2014 - 12:15:49 CST)
  - RE: Nanostructure Plugin from TCL Script Michail Palaiokostas Avramidis (Tue Feb 25 2014 - 12:35:11 CST)
Failed to compile VMD 1.9.2 on OSX 10.9 Zhenquan Hu (Tue Feb 25 2014 - 10:19:01 CST)
- Re: Failed to compile VMD 1.9.2 on OSX 10.9 John Stone (Wed Mar 05 2014 - 22:51:25 CST)
  - Re: Failed to compile VMD 1.9.2 on OSX 10.9 Zhenquan Hu (Thu Mar 06 2014 - 15:34:53 CST)
    - Re: Failed to compile VMD 1.9.2 on OSX 10.9 John Stone (Thu Mar 06 2014 - 15:42:06 CST)
    - Re: Failed to compile VMD 1.9.2 on OSX 10.9 Zhenquan Hu (Thu Mar 06 2014 - 16:43:55 CST)
Update Plugin DanLiu (Tue Feb 25 2014 - 05:18:07 CST)
- Re: Update Plugin Axel Kohlmeyer (Tue Feb 25 2014 - 05:56:22 CST)
  - Re: Update Plugin DanLiu (Tue Feb 25 2014 - 06:42:05 CST)
- Re: Update Plugin Olaf Lenz (Tue Feb 25 2014 - 06:28:57 CST)
  - Re: Update Plugin DanLiu (Tue Feb 25 2014 - 06:35:34 CST)
    - Re: Update Plugin Axel Kohlmeyer (Tue Feb 25 2014 - 06:54:45 CST)
Re: psfgen and unknown residue types Ivan Gregoretti (Sun Feb 23 2014 - 17:39:13 CST)
- RE: psfgen and unknown residue types Tristan Croll (Sun Feb 23 2014 - 17:48:04 CST)
- RE: psfgen and unknown residue types Tristan Croll (Sun Feb 23 2014 - 18:13:23 CST)
  - Re: psfgen and unknown residue types Ivan Gregoretti (Sun Feb 23 2014 - 18:56:42 CST)
psfgen and unknown residue types Ivan Gregoretti (Sat Feb 22 2014 - 17:29:35 CST)
Oculus Rift support in VMD? Mirco Wahab (Sat Feb 22 2014 - 03:40:21 CST)
- Re: Oculus Rift support in VMD? John Stone (Sat Feb 22 2014 - 11:16:05 CST)
Atom selection to identify residues that clash Jacob Durrant (Fri Feb 21 2014 - 21:56:32 CST)
- Re: Atom selection to identify residues that clash Mike Makowski (Sat Feb 22 2014 - 00:05:19 CST)
  - Re: Atom selection to identify residues that clash Josh Vermaas (Tue Feb 25 2014 - 21:44:09 CST)
    - Re: Atom selection to identify residues that clash Jacob Durrant (Tue Feb 25 2014 - 23:49:38 CST)
- Re: Atom selection to identify residues that clash Josh Vermaas (Sat Feb 22 2014 - 17:49:43 CST)
importing topology file from PRODRG chandrakala gowda (Fri Feb 21 2014 - 10:48:00 CST)
manually change secondary structure Beat Meier (Fri Feb 21 2014 - 07:46:02 CST)
- Re: manually change secondary structure John Stone (Fri Feb 21 2014 - 10:08:16 CST)
- AW: manually change secondary structure Norman Geist (Mon Feb 24 2014 - 00:06:29 CST)
- custom color on surface plot Beat Meier (Thu Apr 10 2014 - 09:09:05 CDT)
  - Re: custom color on surface plot Axel Kohlmeyer (Thu Apr 10 2014 - 09:57:41 CDT)
Security problem? Olaf Lenz (Wed Feb 19 2014 - 06:01:26 CST)
- RE: Security problem? Cosseddu, Salvatore (Wed Feb 19 2014 - 08:24:26 CST)
  - Re: Security problem? Olaf Lenz (Wed Feb 19 2014 - 08:30:59 CST)
    - RE: Security problem? Cosseddu, Salvatore (Wed Feb 19 2014 - 08:38:02 CST)
- Re: Security problem? John Stone (Wed Feb 19 2014 - 09:16:06 CST)
  - RE: Security problem? Cosseddu, Salvatore (Thu Feb 20 2014 - 10:37:07 CST)
    - RE: Security problem? Cosseddu, Salvatore (Thu Feb 20 2014 - 10:44:37 CST)
  - Re: Security problem? Olaf Lenz (Fri Feb 21 2014 - 02:46:04 CST)
    - Re: Security problem? Olaf Lenz (Fri Feb 21 2014 - 03:20:39 CST)
    - Re: Security problem? John Stone (Fri Feb 21 2014 - 10:01:15 CST)
coordinates: visual and in-file Chetan Mahajan (Tue Feb 18 2014 - 19:18:14 CST)
- Re: coordinates: visual and in-file Josh Vermaas (Wed Feb 19 2014 - 00:18:03 CST)
ACS COMP Division student and junior faculty awards for Fall 2014 meeting in San Francisco Carlos Simmerling (Tue Feb 18 2014 - 15:30:45 CST)
Extracting complex of protein-ligand+water from every frame of DCD trajectory KK R (Tue Feb 18 2014 - 13:30:19 CST)
- Re: Extracting complex of protein-ligand+water from every frame of DCD trajectory. . Martin, Erik W (Tue Feb 18 2014 - 14:50:23 CST)
Bounced VMD-L postings... John Stone (Tue Feb 18 2014 - 13:17:04 CST)
- Re: Bounced VMD-L postings... Maxim Belkin (Tue Feb 18 2014 - 13:26:22 CST)
Webinar on VMD's use of GPUs to accelerate MD visualization and analysis John Stone (Mon Feb 17 2014 - 16:15:03 CST)
- Re: Webinar on VMD's use of GPUs to accelerate MD visualization and analysis Ali Alizadeh (Mon Feb 24 2014 - 02:00:02 CST)
  - Re: Webinar on VMD's use of GPUs to accelerate MD visualization and analysis John Stone (Mon Feb 24 2014 - 08:57:40 CST)
    - Re: Webinar on VMD's use of GPUs to accelerate MD visualization and analysis Ali Alizadeh (Mon Feb 24 2014 - 10:07:36 CST)
Pruning defunct users and bouncing email accounts from VMD-L... John Stone (Mon Feb 17 2014 - 10:24:16 CST)
help with stereo viz on new samsung "3D" LCD and quadro card Carlos Simmerling (Fri Feb 14 2014 - 13:25:25 CST)
- Re: help with stereo viz on new samsung "3D" LCD and quadro card John Stone (Mon Feb 17 2014 - 11:53:45 CST)
  - Re: help with stereo viz on new samsung "3D" LCD and quadro card Carlos Simmerling (Tue Feb 18 2014 - 07:06:04 CST)
How upgrade a molfile plugin? Arham Amouie (Sun Feb 16 2014 - 12:28:17 CST)
- Re: How upgrade a molfile plugin? Axel Kohlmeyer (Sun Feb 16 2014 - 13:54:46 CST)
Tachyon question Andrew DeYoung (Sun Feb 16 2014 - 09:48:37 CST)
- Re: Tachyon question Axel Kohlmeyer (Sun Feb 16 2014 - 10:39:41 CST)
- Re: Tachyon question John Stone (Mon Feb 17 2014 - 09:43:44 CST)
AW: namd-l: Solvation in non standard solvent Norman Geist (Fri Feb 14 2014 - 06:47:51 CST)
- Re: AW: namd-l: Solvation in non standard solvent Tim Lo (Fri Feb 14 2014 - 09:23:50 CST)
  - Re: AW: namd-l: Solvation in non standard solvent Josh Vermaas (Fri Feb 14 2014 - 12:41:36 CST)
deleting trajectory paths Research Jubilant (Wed Feb 12 2014 - 19:31:53 CST)
- Re: deleting trajectory paths Axel Kohlmeyer (Wed Feb 12 2014 - 20:45:14 CST)
Modulus atom selection Jacob Durrant (Wed Feb 12 2014 - 14:37:09 CST)
- Re: Modulus atom selection Axel Kohlmeyer (Wed Feb 12 2014 - 17:01:55 CST)
- Re: Modulus atom selection Josh Vermaas (Wed Feb 12 2014 - 17:16:06 CST)
  - Re: Modulus atom selection Jacob Durrant (Sat Feb 15 2014 - 02:19:12 CST)
    - Re: Modulus atom selection John Stone (Mon Feb 17 2014 - 10:33:02 CST)
    - Re: Modulus atom selection Jacob Durrant (Mon Feb 17 2014 - 13:30:56 CST)
Simplest file format that includes atom color? Arham Amouie (Wed Feb 12 2014 - 13:28:44 CST)
- AW: Simplest file format that includes atom color? Norman Geist (Thu Feb 13 2014 - 00:20:11 CST)
  - Re: AW: Simplest file format that includes atom color? Arham Amouie (Thu Feb 13 2014 - 02:51:07 CST)
    - AW: AW: Simplest file format that includes atom color? Norman Geist (Thu Feb 13 2014 - 03:28:18 CST)
    - Re: AW: AW: Simplest file format that includes atom color? Philippe Bopp (Thu Feb 13 2014 - 06:34:59 CST)
  - Re: AW: Simplest file format that includes atom color? Olaf Lenz (Thu Feb 13 2014 - 04:42:45 CST)
- Re: Simplest file format that includes atom color? Olaf Lenz (Thu Feb 13 2014 - 02:18:39 CST)
(no subject) Arham Amouie (Wed Feb 12 2014 - 13:22:40 CST)
Installation of VMD topotools Jeeno Jose (Tue Feb 11 2014 - 11:22:07 CST)
- Re: Installation of VMD topotools Axel Kohlmeyer (Tue Feb 11 2014 - 13:05:06 CST)
reg extracting coordinates for first water shell. surya narayanan chandrasekaran (Tue Feb 11 2014 - 06:52:31 CST)
- AW: reg extracting coordinates for first water shell. Norman Geist (Tue Feb 11 2014 - 09:38:29 CST)
VMD can't read 1OXY Boris Steipe (Mon Feb 10 2014 - 21:16:55 CST)
- Re: VMD can't read 1OXY Axel Kohlmeyer (Mon Feb 10 2014 - 22:20:25 CST)
  - Re: VMD can't read 1OXY Boris Steipe (Tue Feb 11 2014 - 09:51:10 CST)
  - Re: VMD can't read 1OXY Josh Vermaas (Tue Feb 11 2014 - 09:42:22 CST)
- Re: VMD can't read 1OXY Maxim Belkin (Tue Feb 11 2014 - 09:31:47 CST)
Do I need a "professional" graphics card? Charles McAnany (Sun Feb 09 2014 - 13:29:41 CST)
- Re: Do I need a "professional" graphics card? John Stone (Sun Feb 09 2014 - 13:41:14 CST)
  - AW: Do I need a "professional" graphics card? Norman Geist (Mon Feb 10 2014 - 01:43:22 CST)
- AW: Do I need a "professional" graphics card? Norman Geist (Mon Feb 10 2014 - 01:38:00 CST)
Script commands that control the display of periodic images Eric Smoll (Sat Feb 08 2014 - 21:46:40 CST)
- Re: Script commands that control the display of periodic images Axel Kohlmeyer (Sat Feb 08 2014 - 22:52:38 CST)
Minor bug: clash between Multiseq representations and AutoIMD Tristan Croll (Sat Feb 08 2014 - 18:40:16 CST)
Calculating density for a molecule Research Jubilant (Fri Feb 07 2014 - 11:36:41 CST)
measure dihedral angle for all the loaded pdb files chandrakala gowda (Fri Feb 07 2014 - 10:08:55 CST)
- Re: measure dihedral angle for all the loaded pdb files Maxim Belkin (Fri Feb 07 2014 - 10:23:00 CST)
  - Re: measure dihedral angle for all the loaded pdb files chandrakala gowda (Fri Feb 07 2014 - 14:48:28 CST)
- Re: measure dihedral angle for all the loaded pdb files Axel Kohlmeyer (Fri Feb 07 2014 - 11:07:01 CST)
loading .xtc file Chetan Mahajan (Thu Feb 06 2014 - 20:18:25 CST)
- Re: loading .xtc file Axel Kohlmeyer (Thu Feb 06 2014 - 21:17:52 CST)
- Re: loading .xtc file Christopher Gutnajer (Thu Feb 06 2014 - 22:37:14 CST)
FFTK: Error when optimizing charges Shane.OMahony (Thu Feb 06 2014 - 08:10:00 CST)
- Re: FFTK: Error when optimizing charges Mayne, Christopher G (Thu Feb 06 2014 - 09:29:04 CST)
  - Re: FFTK: Error when optimizing charges Mayne, Christopher G (Thu Feb 06 2014 - 11:51:34 CST)
porcupine plot Revthi Sanker (Wed Feb 05 2014 - 08:05:55 CST)
- Re: porcupine plot Benjamin Hall (Wed Apr 02 2008 - 17:30:49 CDT)
  - Re: Re: porcupine plot John Stone (Wed Apr 02 2008 - 23:41:12 CDT)
    - Re: Re: porcupine plot Benjamin Hall (Thu Apr 03 2008 - 12:00:11 CDT)
- Re: porcupine plot Axel Kohlmeyer (Wed Feb 05 2014 - 09:13:31 CST)
  - Re: porcupine plot Ban Arn (Wed Feb 05 2014 - 10:19:39 CST)
How do you construct a .cgc file that actually works? Freda Lim (IHPC) (Wed Feb 05 2014 - 00:12:20 CST)
- Re: How do you construct a .cgc file that actually works? Kirby Vandivort (Wed Feb 05 2014 - 17:19:26 CST)
  - RE: How do you construct a .cgc file that actually works? Freda Lim (IHPC) (Thu Feb 06 2014 - 04:25:14 CST)
    - Re: How do you construct a .cgc file that actually works? John Stone (Thu Feb 06 2014 - 09:59:23 CST)
Query on introducing a protein Aditya Padhi (Tue Feb 04 2014 - 23:12:10 CST)
Re: SScache performance; fast secondary structure assignment Axel Kohlmeyer (Tue Feb 04 2014 - 07:44:58 CST)
- AW: SScache performance; fast secondary structure assignment Norman Geist (Tue Feb 04 2014 - 08:00:29 CST)
- Re: SScache performance; fast secondary structure assignment John Stone (Tue Feb 04 2014 - 09:00:55 CST)
- Re: SScache performance; fast secondary structure assignment John Stone (Tue Feb 04 2014 - 10:13:51 CST)
  - Re: SScache performance; fast secondary structure assignment Ajasja LjubetiÄ (Tue Feb 04 2014 - 14:58:37 CST)
SScache performance; fast secondary structure assignment Norman Geist (Tue Feb 04 2014 - 06:40:26 CST)
Loading molfileplugins without modifying vmd install Daniel Russel (Mon Feb 03 2014 - 16:04:55 CST)
- Re: Loading molfileplugins without modifying vmd install John Stone (Mon Feb 03 2014 - 16:52:16 CST)
  - Re: Loading molfileplugins without modifying vmd install Daniel Russel (Tue Feb 04 2014 - 10:13:28 CST)
AW: wrapper for VMD to read compressed .xz files Norman Geist (Mon Feb 03 2014 - 01:01:49 CST)
triple bond parametrization Tim Lo (Fri Jan 31 2014 - 20:11:55 CST)
- Re: triple bond parametrization Mayne, Christopher G (Sat Feb 01 2014 - 19:02:18 CST)
  - Re: triple bond parametrization Mayne, Christopher G (Sat Feb 01 2014 - 20:00:03 CST)
  - Re: triple bond parametrization Mayne, Christopher G (Sat Feb 01 2014 - 22:44:14 CST)
wrapper for VMD to read compressed .xz files Bennion, Brian (Fri Jan 31 2014 - 16:33:18 CST)
- Re: wrapper for VMD to read compressed .xz files John Stone (Fri Jan 31 2014 - 16:43:14 CST)
  - Re: wrapper for VMD to read compressed .xz files Axel Kohlmeyer (Fri Jan 31 2014 - 17:48:58 CST)
    - AW: wrapper for VMD to read compressed .xz files Norman Geist (Sat Feb 01 2014 - 15:06:26 CST)
Re: self-diffusion coefficient from RMSD Ali Alizadeh (Thu Jan 30 2014 - 06:57:55 CST)
- RE: self-diffusion coefficient from RMSD . Juita (Fri Jan 31 2014 - 00:55:55 CST)
  - Re: self-diffusion coefficient from RMSD Ali Alizadeh (Fri Jan 31 2014 - 12:45:41 CST)
- Re: self-diffusion coefficient from RMSD Josh Vermaas (Mon Feb 03 2014 - 19:04:56 CST)
  - Re: self-diffusion coefficient from RMSD Dudo (Mon Feb 03 2014 - 21:44:29 CST)
Adding a keyword to mol addfile Tristan Croll (Wed Jan 29 2014 - 22:39:41 CST)
- RE: Adding a keyword to mol addfile Joaquim Rui de Castro Rodrigues (Thu Jan 30 2014 - 08:23:09 CST)
- Re: Adding a keyword to mol addfile Maxim Belkin (Thu Jan 30 2014 - 09:58:25 CST)
  - RE: Adding a keyword to mol addfile Tristan Croll (Thu Jan 30 2014 - 15:07:21 CST)
VMD crash on large DCD files. Villalain Boullon, Jose (Wed Jan 29 2014 - 12:46:18 CST)
- Re: VMD crash on large DCD files. Josh Vermaas (Wed Jan 29 2014 - 14:50:06 CST)
  - AW: VMD crash on large DCD files. Norman Geist (Thu Jan 30 2014 - 02:17:24 CST)
    - Re: VMD crash on large DCD files. John Stone (Thu Jan 30 2014 - 10:25:06 CST)
  - Re: VMD crash on large DCD files. Ajasja LjubetiÄ (Thu Jan 30 2014 - 03:34:27 CST)
background color Fateme Sadat Emami (Mon Jan 27 2014 - 11:08:58 CST)
- Re: background color John Stone (Mon Jan 27 2014 - 11:33:17 CST)
- Re: background color Maxim Belkin (Mon Jan 27 2014 - 11:41:11 CST)
psfgen error for Argon atoms Arash Azari (Sun Jan 26 2014 - 15:06:16 CST)
- Re: psfgen error for Argon atoms Josh Vermaas (Sun Jan 26 2014 - 16:29:06 CST)
  - Re: psfgen error for Argon atoms Arash Azari (Mon Jan 27 2014 - 00:51:37 CST)
RE: namd-l: How to solvate a protein using C36 and not C27 Tristan Croll (Sat Jan 25 2014 - 23:07:30 CST)
- RE: namd-l: How to solvate a protein using C36 and not C27 Tristan Croll (Sat Jan 25 2014 - 23:24:34 CST)
Upgrade CUDA5.5 driver and vmd doesn't work anymore Damiano Buratto (Fri Jan 24 2014 - 10:09:36 CST)
- Re: Upgrade CUDA5.5 driver and vmd doesn't work anymore John Stone (Fri Jan 24 2014 - 13:55:35 CST)
  - Re: Upgrade CUDA5.5 driver and vmd doesn't work anymore Damiano Buratto (Mon Jan 27 2014 - 04:26:04 CST)
Crash with molfile plugin when doing "Load data into molecule" Daniel Russel (Thu Jan 23 2014 - 23:23:06 CST)
- Re: Crash with molfile plugin when doing "Load data into molecule" Axel Kohlmeyer (Fri Jan 24 2014 - 05:26:53 CST)
FATAL ERROR: UNABLE TO FIND DIHEDRAL PARAMETERS FOR NH3 CT1 CT2A CT2 (ATOMS 1 5 7 10) Allen, Caley R (Thu Jan 23 2014 - 13:37:06 CST)
- Re: FATAL ERROR: UNABLE TO FIND DIHEDRAL PARAMETERS FOR NH3 CT1 CT2A CT2 (ATOMS 1 5 7 10) Josh Vermaas (Thu Jan 23 2014 - 15:12:34 CST)
  - Re: FATAL ERROR: UNABLE TO FIND DIHEDRAL PARAMETERS FOR NH3 CT1 CT2A CT2 (ATOMS 1 5 7 10) Allen, Caley R (Thu Jan 23 2014 - 16:00:54 CST)
- RE: FATAL ERROR: UNABLE TO FIND DIHEDRAL PARAMETERS FOR NH3 CT1 CT2A CT2 (ATOMS 1 5 7 10) Tristan Croll (Fri Jan 24 2014 - 02:49:22 CST)
  - Re: FATAL ERROR: UNABLE TO FIND DIHEDRAL PARAMETERS FOR NH3 CT1 CT2A CT2 (ATOMS 1 5 7 10) Allen, Caley R (Mon Jan 27 2014 - 12:32:45 CST)
3D texture mapping Nicola De Mitri (Thu Jan 23 2014 - 04:07:49 CST)
Creating a Regular Structure Fatemesadat Emami (Wed Jan 22 2014 - 17:38:31 CST)
- Re: Creating a Regular Structure Maxim Belkin (Wed Jan 22 2014 - 17:48:18 CST)
  - Re: Creating a Regular Structure Fatemesadat Emami (Wed Jan 22 2014 - 17:59:10 CST)
  - Re: Creating a Regular Structure Fatemesadat Emami (Wed Jan 22 2014 - 18:03:05 CST)
    - Re: Creating a Regular Structure Maxim Belkin (Wed Jan 22 2014 - 18:06:39 CST)
VMD text mode commands Subbarao Kanchi (Wed Jan 22 2014 - 13:29:55 CST)
- Re: VMD text mode commands Maxim Belkin (Wed Jan 22 2014 - 14:02:35 CST)
  - Re: VMD text mode commands Subbarao Kanchi (Wed Jan 22 2014 - 14:21:08 CST)
- RE: VMD text mode commands Cosseddu, Salvatore (Wed Jan 22 2014 - 16:06:13 CST)
select and save every X atom Steven Neumann (Tue Jan 21 2014 - 15:01:19 CST)
- Re: select and save every X atom Axel Kohlmeyer (Tue Jan 21 2014 - 15:55:02 CST)
- Re: select and save every X atom Josh Vermaas (Tue Jan 21 2014 - 16:16:13 CST)
misleading documentation for -res switch in MDFF plugin Tristan Croll (Mon Jan 20 2014 - 19:50:35 CST)
Question about measure cluster manali_at_bioinfo.net.in (Mon Jan 20 2014 - 05:43:39 CST)
Question about measure cluster manali_at_bioinfo.net.in (Mon Jan 20 2014 - 05:43:39 CST)
- Re: Question about measure cluster Axel Kohlmeyer (Mon Jan 20 2014 - 06:48:35 CST)
  - Re: Question about measure cluster Axel Kohlmeyer (Mon Jan 20 2014 - 09:18:45 CST)
    - Re: Question about measure cluster manali_at_bioinfo.net.in (Mon Jan 20 2014 - 10:17:39 CST)
    - Re: Question about measure cluster Axel Kohlmeyer (Mon Jan 20 2014 - 10:39:45 CST)
Bond order cut-off value Sanjib Chowdhury (Thu Jan 16 2014 - 16:53:54 CST)
- Re: Bond order cut-off value John Stone (Thu Jan 16 2014 - 17:01:41 CST)
  - Re: Bond order cut-off value John Stone (Fri Jan 17 2014 - 11:06:26 CST)
- Re: Bond order cut-off value Axel Kohlmeyer (Thu Jan 16 2014 - 19:35:23 CST)
DCD is not detected as protein but single pdbs are? Michael LeVine (Wed Jan 15 2014 - 19:45:48 CST)
merging multiple structures Martin, Erik W (Wed Jan 15 2014 - 12:49:32 CST)
- Re: merging multiple structures Josh Vermaas (Wed Jan 15 2014 - 14:08:56 CST)
- Re: merging multiple structures Axel Kohlmeyer (Wed Jan 15 2014 - 14:45:38 CST)
PDMS with VMD Buddhika Jayasena (Tue Jan 14 2014 - 16:07:07 CST)
RDF calculation . Juita (Mon Jan 13 2014 - 18:27:09 CST)
- Re: RDF calculation Axel Kohlmeyer (Mon Jan 13 2014 - 19:43:21 CST)
  - self-diffusion coefficient from RMSD . Juita (Thu Jan 30 2014 - 03:21:45 CST)
    - Re: self-diffusion coefficient from RMSD Josh Vermaas (Thu Jan 30 2014 - 08:12:14 CST)
centering problem in salvation box Ramin Ekhteiari (Fri Jan 10 2014 - 12:01:22 CST)
- Re: centering problem in salvation box John Stone (Tue Jan 14 2014 - 09:45:43 CST)
strange problems adding extra bonds to interactive simulations Tristan Croll (Thu Jan 09 2014 - 20:03:39 CST)
- Re: strange problems adding extra bonds to interactive simulations Axel Kohlmeyer (Thu Jan 09 2014 - 21:50:21 CST)
  - RE: strange problems adding extra bonds to interactive simulations Tristan Croll (Thu Jan 09 2014 - 22:25:24 CST)
    - Re: strange problems adding extra bonds to interactive simulations John Stone (Fri Jan 10 2014 - 09:33:58 CST)
    - Re: strange problems adding extra bonds to interactive simulations Ryan McGreevy (Fri Jan 10 2014 - 10:06:47 CST)
  - Re: strange problems adding extra bonds to interactive simulations Ryan McGreevy (Thu Jan 16 2014 - 13:22:47 CST)
    - RE: strange problems adding extra bonds to interactive simulations Tristan Croll (Thu Jan 16 2014 - 14:57:31 CST)
Display APBS on Solvent Accessible Surface Ricardo O. S. Soares (Thu Jan 09 2014 - 15:12:41 CST)
- Re: Display APBS on Solvent Accessible Surface John Stone (Thu Jan 09 2014 - 16:01:14 CST)
- Re: Display APBS on Solvent Accessible Surface Josh Vermaas (Thu Jan 09 2014 - 16:36:59 CST)
  - Re: Display APBS on Solvent Accessible Surface Ricardo O. S. Soares (Fri Jan 10 2014 - 08:42:05 CST)
    - Re: Display APBS on Solvent Accessible Surface John Stone (Tue Jan 14 2014 - 09:43:03 CST)
    - Re: Display APBS on Solvent Accessible Surface Ricardo O. S. Soares (Thu Jan 16 2014 - 07:55:14 CST)
Viscosity calculation Yan Shen (Thu Jan 09 2014 - 13:19:25 CST)
Surface Area Calculation flavio seixas (Tue Jan 07 2014 - 12:40:57 CST)
- Re: Surface Area Calculation Ajasja LjubetiÄ (Tue Jan 07 2014 - 14:04:19 CST)
- Re: Surface Area Calculation Josh Vermaas (Tue Jan 07 2014 - 14:22:10 CST)
  - Re: Surface Area Calculation flavio seixas (Wed Jan 08 2014 - 06:40:10 CST)
RDF Normalization Mike Makowski (Mon Jan 06 2014 - 15:14:21 CST)
- Re: RDF Normalization Axel Kohlmeyer (Mon Jan 06 2014 - 16:23:10 CST)
- Re: RDF Normalization Axel Kohlmeyer (Wed Jan 08 2014 - 20:28:28 CST)
citing SODIUM program Shyno Mathew (Sat Jan 04 2014 - 10:45:36 CST)
- Re: citing SODIUM program John Stone (Tue Jan 14 2014 - 09:19:27 CST)
measure command in vmd ÂÀ¿µ½Ü (Fri Jan 03 2014 - 21:03:43 CST)
- Re: measure command in vmd John Stone (Tue Jan 14 2014 - 09:47:50 CST)
Issues with tachyon internal renderer Tyler Smith (Fri Jan 03 2014 - 14:19:36 CST)
- RE: Issues with tachyon internal renderer Ryan Hoffman (Fri Jan 03 2014 - 16:07:52 CST)
  - RE: Issues with tachyon internal renderer Ryan Hoffman (Fri Jan 03 2014 - 16:32:14 CST)
- Re: Issues with tachyon internal renderer Josh Vermaas (Fri Jan 03 2014 - 16:13:15 CST)
  - Re: Issues with tachyon internal renderer Tyler Smith (Fri Jan 03 2014 - 18:43:13 CST)
  - Re: Issues with tachyon internal renderer Tyler Smith (Fri Jan 03 2014 - 19:02:57 CST)
cgtools Gurunath Katagi (Wed Jan 01 2014 - 04:08:07 CST)
why tutorial cannot be played? Albert (Fri Dec 27 2013 - 14:32:17 CST)
- Re: why tutorial cannot be played? Axel Kohlmeyer (Fri Dec 27 2013 - 15:19:55 CST)
  - Re: why tutorial cannot be played? Albert (Fri Dec 27 2013 - 15:51:08 CST)
    - Re: why tutorial cannot be played? John Stone (Tue Jan 14 2014 - 09:58:53 CST)
- Re: why tutorial cannot be played? chandrakala gowda (Fri Dec 27 2013 - 16:16:40 CST)
setup path to write Jorgen Simonsen (Fri Dec 27 2013 - 13:38:32 CST)
- Re: setup path to write John Stone (Tue Jan 14 2014 - 11:00:25 CST)
VMD's NAMD GUI Douglas Houston (Tue Dec 24 2013 - 06:13:24 CST)
- Re: VMD's NAMD GUI Axel Kohlmeyer (Wed Dec 25 2013 - 02:58:43 CST)
  - Re: VMD's NAMD GUI Douglas Houston (Sun Dec 29 2013 - 03:39:02 CST)
    - Re: VMD's NAMD GUI Axel Kohlmeyer (Sun Dec 29 2013 - 03:47:35 CST)
constructing a .tpr Rasoul Nasiri (Tue Dec 24 2013 - 02:30:03 CST)
- Re: constructing a .tpr Axel Kohlmeyer (Tue Dec 24 2013 - 04:29:10 CST)
  - Re: constructing a .tpr Axel Kohlmeyer (Tue Dec 24 2013 - 05:49:49 CST)
    - Re: constructing a .tpr Rasoul Nasiri (Tue Dec 24 2013 - 11:42:25 CST)
    - Re: constructing a .tpr Axel Kohlmeyer (Tue Dec 24 2013 - 12:04:09 CST)
Problem while installing VMD indu purushothaman (Tue Dec 24 2013 - 01:18:38 CST)
- Re: Problem while installing VMD Axel Kohlmeyer (Wed Dec 25 2013 - 03:02:35 CST)
- Re: Problem while installing VMD John Stone (Tue Jan 14 2014 - 11:05:04 CST)
How to generate a PDB file of the protein containing one phosphoserine Sunita Patel (Sat Dec 21 2013 - 06:42:12 CST)
- 'percent' symbol syntax in .conf file? Ryan Hoffman (Sat Dec 21 2013 - 09:49:40 CST)
  - Re: 'percent' symbol syntax in .conf file? Maxim Belkin (Sat Dec 21 2013 - 18:10:36 CST)
    - Re: 'percent' symbol syntax in .conf file? John Stone (Tue Jan 14 2014 - 11:08:13 CST)
Regarding calculating principal Axis Vectors using VMD ssaurabh_at_physics.iisc.ernet.in (Fri Dec 20 2013 - 14:09:28 CST)
- Re: Regarding calculating principal Axis Vectors using VMD John Stone (Fri Dec 20 2013 - 16:03:08 CST)
VMD on Blue Waters Avisek Das (Fri Dec 20 2013 - 11:55:25 CST)
- Re: VMD on Blue Waters John Stone (Fri Dec 20 2013 - 12:11:35 CST)
  - Re: VMD on Blue Waters Avisek Das (Fri Dec 20 2013 - 12:32:48 CST)
slice image Tomek Wlodarski (Tue Dec 17 2013 - 11:09:38 CST)
- Re: slice image Thomas C Bishop (Tue Dec 17 2013 - 20:24:26 CST)
- Re: slice image John Stone (Fri Dec 20 2013 - 12:28:35 CST)
(no subject) jeevan gc (Mon Dec 16 2013 - 17:00:04 CST)
- Re: John Stone (Fri Dec 20 2013 - 16:01:20 CST)
Define bond length Lee, Sa (Mon Dec 16 2013 - 11:41:38 CST)
- Re: Define bond length Axel Kohlmeyer (Mon Dec 16 2013 - 12:37:37 CST)
  - Re: Define bond length John Stone (Mon Dec 16 2013 - 15:17:17 CST)
Convert RNA to DNA Iman Jeddi (Sat Dec 14 2013 - 11:54:12 CST)
Unit of RMSF calculated by measure HIRA BATOOL (Sat Dec 14 2013 - 05:30:17 CST)
- Re: Unit of RMSF calculated by measure Josh Vermaas (Mon Dec 16 2013 - 09:29:33 CST)
HBonds representation draws bonds with atoms (Hs) not included in the selection Camilo Andrés Jimenez Cruz (Fri Dec 13 2013 - 09:35:37 CST)
- Re: HBonds representation draws bonds with atoms (Hs) not included in the selection Camilo Andrés Jimenez Cruz (Fri Dec 13 2013 - 13:20:07 CST)
changing chain id and pdb generating Ramin Ekhteiari (Thu Dec 12 2013 - 03:06:36 CST)
- AW: changing chain id and pdb generating Norman Geist (Thu Dec 12 2013 - 06:55:01 CST)
- Re: changing chain id and pdb generating John Stone (Fri Dec 20 2013 - 17:06:46 CST)
AMD vs. nvidia support JÃ©rÃ´me HÃ©nin (Wed Dec 11 2013 - 11:31:12 CST)
- RE: AMD vs. nvidia support Bennion, Brian (Wed Dec 11 2013 - 12:50:36 CST)
- Re: AMD vs. nvidia support Axel Kohlmeyer (Thu Dec 12 2013 - 00:04:44 CST)
  - Re: AMD vs. nvidia support Bogdan Costescu (Thu Dec 12 2013 - 04:16:48 CST)
    - Re: AMD vs. nvidia support Axel Kohlmeyer (Thu Dec 12 2013 - 04:32:46 CST)
generated pdb file via vmd Ramin Ekhteiari (Wed Dec 11 2013 - 04:26:39 CST)
- Re: generated pdb file via vmd Axel Kohlmeyer (Wed Dec 11 2013 - 07:21:06 CST)
  - Re: generated pdb file via vmd flavio seixas (Thu Dec 12 2013 - 16:22:45 CST)
AW: AW: AW: vmd-1.9.1 broken after upgrade to Ubuntu 13.10 Norman Geist (Wed Dec 11 2013 - 01:06:44 CST)
- Re: AW: AW: vmd-1.9.1 broken after upgrade to Ubuntu 13.10 John Stone (Wed Dec 11 2013 - 01:10:51 CST)
how can we improve it in VMD? Albert (Tue Dec 10 2013 - 01:55:04 CST)
- Re: how can we improve it in VMD? Axel Kohlmeyer (Tue Dec 10 2013 - 04:03:40 CST)
- AW: how can we improve it in VMD? Norman Geist (Tue Dec 10 2013 - 08:13:44 CST)
- Re: how can we improve it in VMD? John Stone (Tue Dec 10 2013 - 10:06:07 CST)
AW: AW: vmd-1.9.1 broken after upgrade to Ubuntu 13.10 Norman Geist (Tue Dec 10 2013 - 00:57:37 CST)
Re: Change transparency along a trajectory Axel Kohlmeyer (Mon Dec 09 2013 - 08:13:35 CST)
Atomic trajectory to COM trajectory, Ali Alizadeh (Mon Dec 09 2013 - 07:09:30 CST)
- Re: Atomic trajectory to COM trajectory, Axel Kohlmeyer (Mon Dec 09 2013 - 08:32:15 CST)
  - Re: Atomic trajectory to COM trajectory, Ali Alizadeh (Mon Dec 09 2013 - 09:55:58 CST)
Change transparency along a trajectory Gaetano Calabró (Mon Dec 09 2013 - 05:55:12 CST)
- AW: Change transparency along a trajectory Norman Geist (Mon Dec 09 2013 - 08:58:33 CST)
AW: AW: hydrogen bond criteria Norman Geist (Fri Dec 06 2013 - 01:14:33 CST)
- Re: AW: AW: hydrogen bond criteria Hamid (Fri Dec 06 2013 - 13:42:53 CST)
Fwd: dcd file uploading problem Subbusinger N (Thu Dec 05 2013 - 21:59:32 CST)
- Re: Fwd: dcd file uploading problem Axel Kohlmeyer (Thu Dec 05 2013 - 22:56:17 CST)
hydrogen bond criteria Alexandre PERRET (Thu Dec 05 2013 - 04:31:55 CST)
- AW: hydrogen bond criteria Norman Geist (Thu Dec 05 2013 - 07:10:21 CST)
Combination of bigdcd.tcl and topotools plugin Sofya Lushchekina (Wed Dec 04 2013 - 10:34:47 CST)
line DanLiu (Tue Nov 19 2013 - 02:01:37 CST)
- Re: line Suresh (Wed Dec 04 2013 - 03:52:50 CST)
  - Re: line DanLiu (Wed Nov 20 2013 - 11:13:17 CST)
REï¼š Re: REï¼š hydrogen bond cutoff value sunyeping (Tue Dec 03 2013 - 06:57:20 CST)
Dowser installation trouble James Marsh (Tue Dec 03 2013 - 03:09:29 CST)
- Re: Dowser installation trouble John Stone (Tue Jan 14 2014 - 17:10:22 CST)
REï¼š hydrogen bond cutoff value sunyeping (Tue Dec 03 2013 - 01:45:26 CST)
- Re: RE£º hydrogen bond cutoff value Axel Kohlmeyer (Tue Dec 03 2013 - 01:48:13 CST)
  - Re: Re: REï¼š hydrogen bond cutoff value chandrakala gowda (Tue Dec 03 2013 - 07:40:29 CST)
- REï¼š hydrogen bond cutoff value Boris Steipe (Tue Dec 03 2013 - 08:31:52 CST)
hydrogen bond cutoff value sunyeping (Mon Dec 02 2013 - 21:37:00 CST)
- Re: hydrogen bond cutoff value Axel Kohlmeyer (Mon Dec 02 2013 - 23:31:28 CST)
Domain Error while using ParseFEP plugin Shyno Mathew (Mon Dec 02 2013 - 11:42:37 CST)
- Re: Domain Error while using ParseFEP plugin Josh Vermaas (Tue Dec 03 2013 - 10:08:48 CST)
  - Re: Domain Error while using ParseFEP plugin John Stone (Tue Dec 03 2013 - 10:46:15 CST)
vmd display problem Andy Lam (Sat Nov 30 2013 - 19:22:27 CST)
- Re: vmd display problem John Stone (Fri Dec 20 2013 - 17:31:17 CST)
atoms selection/special characters Fatemesadat Emami (Fri Nov 29 2013 - 18:13:17 CST)
- Re: atoms selection/special characters Axel Kohlmeyer (Fri Nov 29 2013 - 19:17:08 CST)
  - Re: atoms selection/special characters Axel Kohlmeyer (Fri Nov 29 2013 - 20:43:33 CST)
Why are all carbon atoms lumped into C in the Name category in the colors dialog? Andrew DeYoung (Fri Nov 29 2013 - 11:37:41 CST)
- Re: Why are all carbon atoms lumped into C in the Name category in the colors dialog? Axel Kohlmeyer (Fri Nov 29 2013 - 19:13:50 CST)
loading pdb files from multiple directories chandrakala gowda (Fri Nov 29 2013 - 04:43:37 CST)
- Re: loading pdb files from multiple directories Axel Kohlmeyer (Fri Nov 29 2013 - 05:59:58 CST)
  - Re: loading pdb files from multiple directories chandrakala gowda (Fri Nov 29 2013 - 06:14:51 CST)
- Re: loading pdb files from multiple directories Ajasja LjubetiÄ (Fri Nov 29 2013 - 06:39:48 CST)
script to draw lines between labelled atoms david MARTROU (Wed Nov 27 2013 - 07:30:07 CST)
script to draw lines between labelled atoms david MARTROU (Wed Nov 27 2013 - 05:26:21 CST)
Centering water molecules Mihaela Drenscko (Tue Nov 26 2013 - 18:26:51 CST)
- Re: Centering water molecules John Stone (Tue Nov 26 2013 - 19:04:21 CST)
  - Re: Centering water molecules Mihaela Drenscko (Wed Nov 27 2013 - 06:56:17 CST)
Speeding up the VDW drawing method and Tachyon rendering process Andrews, Casey (Tue Nov 26 2013 - 17:53:02 CST)
- Re: Speeding up the VDW drawing method and Tachyon rendering process John Stone (Tue Nov 26 2013 - 19:02:31 CST)
  - RE: Speeding up the VDW drawing method and Tachyon rendering process Andrews, Casey (Wed Nov 27 2013 - 12:28:22 CST)
vmd-1.9.1 broken after upgrade to Ubuntu 13.10 Robert Wohlhueter (Tue Nov 26 2013 - 16:15:53 CST)
- Re: vmd-1.9.1 broken after upgrade to Ubuntu 13.10 John Stone (Tue Nov 26 2013 - 17:03:22 CST)
- Re: vmd-1.9.1 broken after upgrade to Ubuntu 13.10 Josh Vermaas (Tue Nov 26 2013 - 18:42:09 CST)
  - Re: vmd-1.9.1 broken after upgrade to Ubuntu 13.10 John Stone (Tue Nov 26 2013 - 19:08:09 CST)
RMSD for non-pdb file. Dawid das (Tue Nov 26 2013 - 08:07:48 CST)
- Re: RMSD for non-pdb file. John Stone (Tue Nov 26 2013 - 11:11:15 CST)
ugly font in linux/xubuntu-13.10 Spitaleri Andrea (Sat Nov 23 2013 - 02:56:18 CST)
- Re: ugly font in linux/xubuntu-13.10 Axel Kohlmeyer (Sat Nov 23 2013 - 04:10:08 CST)
Mapping Gaussian electrostatic potential to electron density with cube files David Slochower (Fri Nov 22 2013 - 12:56:35 CST)
- Re: Mapping Gaussian electrostatic potential to electron density with cube files John Stone (Fri Nov 22 2013 - 13:19:10 CST)
  - Re: Mapping Gaussian electrostatic potential to electron density with cube files David Slochower (Fri Nov 22 2013 - 17:46:21 CST)
- Re: Mapping Gaussian electrostatic potential to electron density with cube files Clark II, Jeffrey Keith (Fri Mar 14 2014 - 14:29:06 CDT)
  - Re: Re: Mapping Gaussian electrostatic potential to electron density with cube files John Stone (Mon Mar 17 2014 - 19:37:54 CDT)
New empirical force field tools: Release of R.E.D. Server Dev./R.E.D. Python FyD (Fri Nov 22 2013 - 04:18:53 CST)
pre residues and ligands interaction Ramin Ekhteiari (Thu Nov 21 2013 - 06:48:15 CST)
- Re: namd-l: pre residues and ligands interaction Axel Kohlmeyer (Thu Nov 21 2013 - 06:55:04 CST)
windows usage question Thomas C. Bishop (Tue Nov 19 2013 - 12:26:47 CST)
- Re: windows usage question Ahmet Bakan (Wed Nov 20 2013 - 10:14:41 CST)
issues rendering images Tyler Smith (Mon Nov 18 2013 - 18:40:48 CST)
- Re: issues rendering images John Stone (Mon Nov 18 2013 - 18:56:45 CST)
Ramachandran plot question Thomas Albers (Mon Nov 18 2013 - 11:47:07 CST)
- Re: Ramachandran plot question John Stone (Mon Nov 18 2013 - 12:05:30 CST)
segmentation fault error when trying to add bonds to Si3N4 crystal in vmd Mehdi Bakhshi (Sat Nov 16 2013 - 23:37:46 CST)
- Re: segmentation fault error when trying to add bonds to Si3N4 crystal in vmd John Stone (Mon Nov 18 2013 - 12:15:49 CST)
  - Re: segmentation fault error when trying to add bonds to Si3N4 crystal in vmd Mehdi Bakhshi (Mon Nov 18 2013 - 15:00:54 CST)
    - Re: segmentation fault error when trying to add bonds to Si3N4 crystal in vmd John Stone (Fri Nov 22 2013 - 23:26:12 CST)
Error when opening the VMD.exe (Window 8) Thiau Fu Ang (Thu Nov 14 2013 - 22:51:06 CST)
- Re: Error when opening the VMD.exe (Window 8) John Stone (Fri Nov 15 2013 - 17:24:43 CST)
  - Re: Error when opening the VMD.exe (Window 8) Thiau Fu Ang (Fri Nov 15 2013 - 23:43:51 CST)
H-atoms placed at the end in PDB file Biswa Ranjan Meher (Thu Nov 14 2013 - 17:15:15 CST)
- Re: H-atoms placed at the end in PDB file John Stone (Fri Nov 22 2013 - 23:38:10 CST)
BN nanostructure builder Upamanyu Ray (Thu Nov 14 2013 - 15:54:42 CST)
issue with ppmtompeg movie making Louis Smith (Thu Nov 14 2013 - 11:41:07 CST)
- Re: issue with ppmtompeg movie making Josh Vermaas (Thu Nov 14 2013 - 13:16:36 CST)
"measure symmetry" and SymmetryTools fail to find simple symmetry FX (Thu Nov 14 2013 - 10:42:58 CST)
- Re: "measure symmetry" and SymmetryTools fail to find simple symmetry FX (Sat Nov 16 2013 - 15:58:20 CST)
  - Re: "measure symmetry" and SymmetryTools fail to find simple symmetry FX (Wed Nov 20 2013 - 18:00:44 CST)
Tachyon generation of dat files only Shomesankar Bhunia (Thu Nov 14 2013 - 08:04:40 CST)
- Re: Tachyon generation of dat files only Axel Kohlmeyer (Thu Nov 14 2013 - 08:59:48 CST)
- Re: Tachyon generation of dat files only John Stone (Thu Nov 14 2013 - 08:32:41 CST)
  - Re: Tachyon generation of dat files only Shomesankar Bhunia (Thu Nov 14 2013 - 08:43:55 CST)
    - Re: Tachyon generation of dat files only John Stone (Thu Nov 14 2013 - 08:49:04 CST)
    - Re: Tachyon generation of dat files only Shomesankar Bhunia (Thu Nov 14 2013 - 08:53:52 CST)
Trace Frame in "Draw Multiple Frames"-Representations Norman Geist (Thu Nov 14 2013 - 04:17:53 CST)
- Re: Trace Frame in "Draw Multiple Frames"-Representations John Stone (Thu Nov 14 2013 - 08:40:26 CST)
VMD closes upon loading a gromacs xtc file jayant james (Wed Nov 13 2013 - 20:55:46 CST)
- Re: VMD closes upon loading a gromacs xtc file John Stone (Fri Nov 22 2013 - 23:54:10 CST)
Re: Depicting hydrogen bonds between water and residues bharat gupta (Mon Nov 11 2013 - 20:24:59 CST)
- Re: Re: Depicting hydrogen bonds between water and residues Josh Vermaas (Tue Nov 12 2013 - 08:42:11 CST)
periodic images with xyz coordinates Chris Knorowski (Mon Nov 11 2013 - 16:09:50 CST)
- Re: periodic images with xyz coordinates John Stone (Mon Nov 11 2013 - 16:25:59 CST)
Problems with large solvation boxes John Grime (Mon Nov 11 2013 - 09:04:24 CST)
- Re: Problems with large solvation boxes Josh Vermaas (Mon Nov 11 2013 - 15:55:34 CST)
  - Re: Problems with large solvation boxes Juan R. Perilla (Thu Nov 21 2013 - 17:12:21 CST)
- Re: Problems with large solvation boxes John Stone (Fri Nov 15 2013 - 16:17:25 CST)
creating high quality movie in VMD Shomesankar Bhunia (Sat Nov 09 2013 - 12:57:10 CST)
- Re: creating high quality movie in VMD John Stone (Sat Nov 09 2013 - 17:39:20 CST)
  - Re: creating high quality movie in VMD Shomesankar Bhunia (Mon Nov 11 2013 - 07:04:45 CST)
Re: [philippebopp@yahoo.com: PME calculations] Jim Phillips (Fri Nov 08 2013 - 12:47:05 CST)
Running Multiseq Operations in Text-Only Mode Dennis N (Thu Nov 07 2013 - 16:53:42 CST)
Interactive MD and Tcl Leonhard Henkes (Thu Nov 07 2013 - 15:37:50 CST)
- Re: Interactive MD and Tcl Axel Kohlmeyer (Thu Nov 07 2013 - 16:34:13 CST)
- Re: Interactive MD and Tcl Stephanie Teich-McGoldrick (Thu Nov 07 2013 - 17:12:41 CST)
problem with trr file Alexandre PERRET (Thu Nov 07 2013 - 09:31:15 CST)
- Re: problem with trr file John Stone (Thu Nov 07 2013 - 14:50:18 CST)
  - Re: problem with trr file Alexandre PERRET (Fri Nov 08 2013 - 01:43:41 CST)
Rmsd Subbusinger N (Thu Nov 07 2013 - 00:25:37 CST)
- Re: Rmsd John Stone (Sat Nov 23 2013 - 00:36:08 CST)
installing netpbm Tom Haxton (Wed Nov 06 2013 - 16:34:18 CST)
- Re: installing netpbm John Stone (Sat Nov 23 2013 - 00:05:51 CST)
Structure summary in output file Anurag Sharma (Wed Nov 06 2013 - 12:11:55 CST)
- Re: Structure summary in output file John Stone (Fri Nov 08 2013 - 17:51:02 CST)
PME calculations Philippe Bopp (Wed Nov 06 2013 - 10:50:37 CST)
ramachandran plot Marzieh Dehghan (Wed Nov 06 2013 - 09:31:15 CST)
- Re: ramachandran plot John Stone (Wed Nov 06 2013 - 10:37:51 CST)
APBS Output file missing or unreadable Ahmet yýldýrým (Wed Nov 06 2013 - 07:05:09 CST)
- Re: APBS Output file missing or unreadable John Stone (Wed Nov 06 2013 - 10:31:14 CST)
  - Re: APBS Output file missing or unreadable Ahmet yýldýrým (Thu Nov 07 2013 - 03:11:40 CST)
APBS electrostatics: Output file missing or unreadable. Ahmet yýldýrým (Wed Nov 06 2013 - 05:57:40 CST)
MM-PBSA calculation Ramin Ekhteiari (Wed Nov 06 2013 - 02:56:43 CST)
- R: MM-PBSA calculation Spitaleri Andrea (Fri Nov 08 2013 - 01:09:33 CST)
  - Re: R: MM-PBSA calculation Hannes Loeffler (Fri Nov 08 2013 - 03:27:34 CST)
    - R: R: MM-PBSA calculation Spitaleri Andrea (Fri Nov 08 2013 - 04:50:40 CST)
genetaring psf file for HEME ( hemoglobin) Ramin Ekhteiari (Tue Nov 05 2013 - 03:15:07 CST)
- Re: genetaring psf file for HEME ( hemoglobin) Ajasja LjubetiÄ (Tue Nov 05 2013 - 04:30:53 CST)
VolMap Occupancy Anne Laustsen (Tue Nov 05 2013 - 03:04:48 CST)
- Re: VolMap Occupancy John Stone (Sat Nov 23 2013 - 00:39:53 CST)
measuring angles between principal axes through multiple frames Jeremiah Babcock (Mon Nov 04 2013 - 21:55:13 CST)
- RE: measuring angles between principal axes through multiple frames Joaquim Rui de Castro Rodrigues (Tue Nov 05 2013 - 03:46:17 CST)
  - Re: measuring angles between principal axes through multiple frames Jeremiah Babcock (Tue Nov 05 2013 - 10:24:27 CST)
generate parameter and topology file Ramin Ekhteiari (Mon Nov 04 2013 - 13:51:29 CST)
- Re: generate parameter and topology file Josh Vermaas (Mon Nov 04 2013 - 16:35:20 CST)
Fwd: Re: Volmap bharat gupta (Mon Nov 04 2013 - 07:47:29 CST)
- Re: Re: Volmap Axel Kohlmeyer (Mon Nov 04 2013 - 08:51:50 CST)
Re: Newbie question - Labeling a residue bharat gupta (Mon Nov 04 2013 - 06:07:47 CST)
- Re: Re: Newbie question - Labeling a residue Axel Kohlmeyer (Mon Nov 04 2013 - 07:21:25 CST)
  - Re: Re: Newbie question - Labeling a residue bharat gupta (Mon Nov 04 2013 - 07:23:35 CST)
    - Re: Re: Newbie question - Labeling a residue Axel Kohlmeyer (Mon Nov 04 2013 - 08:21:26 CST)
  - Re: Re: Newbie question - Labeling a residue Axel Kohlmeyer (Mon Nov 04 2013 - 07:23:52 CST)
Re: Volmap bharat gupta (Mon Nov 04 2013 - 04:49:34 CST)
- Fwd: Re: Volmap bharat gupta (Mon Nov 04 2013 - 05:42:17 CST)
- Re: Re: Volmap Axel Kohlmeyer (Mon Nov 04 2013 - 06:24:14 CST)
- Re: Volmap bharat gupta (Mon Nov 04 2013 - 06:41:42 CST)
  - Re: Re: Volmap Axel Kohlmeyer (Mon Nov 04 2013 - 07:31:29 CST)
The radius of sphere representing an atom shown as vdw sunyeping (Sun Nov 03 2013 - 19:58:02 CST)
- Re: The radius of sphere representing an atom shown as vdw Axel Kohlmeyer (Mon Nov 04 2013 - 00:50:49 CST)
- Re: The radius of sphere representing an atom shown as vdw Olaf Lenz (Mon Nov 04 2013 - 01:39:53 CST)
sugar cluster analysis Subrata Paul (Sat Nov 02 2013 - 00:14:14 CDT)
- Re: sugar cluster analysis Axel Kohlmeyer (Sat Nov 02 2013 - 01:27:01 CDT)
Problems with external Tachyon Renderer Bryan Roessler (Fri Nov 01 2013 - 21:02:34 CDT)
- Re: Problems with external Tachyon Renderer Axel Kohlmeyer (Sat Nov 02 2013 - 01:21:02 CDT)
How to prevent psfgen from adding atoms Pete Kekenes-Huskey (Fri Nov 01 2013 - 11:23:22 CDT)
- Re: How to prevent psfgen from adding atoms Josh Vermaas (Fri Nov 01 2013 - 13:01:03 CDT)
  - Re: How to prevent psfgen from adding atoms Pete Kekenes-Huskey (Mon Nov 04 2013 - 15:42:49 CST)
volume analysis in vmd Revthi Sanker (Wed Oct 30 2013 - 03:44:54 CDT)
- Re: volume analysis in vmd John Stone (Thu Oct 31 2013 - 10:05:24 CDT)
  - Re: volume analysis in vmd Axel Kohlmeyer (Thu Oct 31 2013 - 11:00:24 CDT)
    - Re: volume analysis in vmd Dudo (Thu Oct 31 2013 - 12:48:46 CDT)
    - Re: volume analysis in vmd Dudo (Mon Nov 04 2013 - 11:02:04 CST)
fftk optimization of bonded parameters + Error: missing close-bracket AnkiReddy katha (Wed Oct 30 2013 - 03:08:57 CDT)
- Re: fftk optimization of bonded parameters + Error: missing close-bracket Mayne, Christopher G (Wed Oct 30 2013 - 07:42:33 CDT)
  - Re: fftk optimization of bonded parameters + Error: missing close-bracket AnkiReddy katha (Thu Oct 31 2013 - 03:20:50 CDT)
Creating custom molecule in VMD scripting Luká¹ Pravda (Tue Oct 29 2013 - 04:40:29 CDT)
- Re: Creating custom molecule in VMD scripting Axel Kohlmeyer (Tue Oct 29 2013 - 05:36:28 CDT)
- RE: Creating custom molecule in VMD scripting Joaquim Rui de Castro Rodrigues (Tue Oct 29 2013 - 06:45:08 CDT)
Hydrogen Bond Calculation in VMD for DNA in VMD Himanshu Joshi (Tue Oct 29 2013 - 02:16:11 CDT)
- Re: Hydrogen Bond Calculation in VMD for DNA in VMD Josh Vermaas (Tue Oct 29 2013 - 09:57:38 CDT)
namdenergy pugin for interaction energy Jana, Suvamay (Mon Oct 28 2013 - 13:02:40 CDT)
- Re: namdenergy pugin for interaction energy John Stone (Thu Oct 31 2013 - 10:03:26 CDT)
How to address two different geometries for same atom in PDB? Sung M Hong (Fri Oct 25 2013 - 19:17:49 CDT)
- Re: How to address two different geometries for same atom in PDB? John Stone (Fri Oct 25 2013 - 20:52:32 CDT)
NVIDIA GeForce GT 750M and CUDA Ebert Maximilian (Fri Oct 25 2013 - 15:06:36 CDT)
- RE : NVIDIA GeForce GT 750M and CUDA Andrei Tudor (Sat Oct 26 2013 - 10:26:38 CDT)
  - Re: NVIDIA GeForce GT 750M and CUDA Ebert Maximilian (Sat Oct 26 2013 - 10:49:33 CDT)
    - RE : NVIDIA GeForce GT 750M and CUDA Andrei Tudor (Sat Oct 26 2013 - 11:32:18 CDT)
    - Re: Re: NVIDIA GeForce GT 750M and CUDA John Stone (Sat Oct 26 2013 - 11:56:56 CDT)
isto variable in gofr Lorenzo Gontrani (Thu Oct 24 2013 - 12:35:13 CDT)
Problem with using FFKT to optimize bonded parameters Shane O Mahony (Wed Oct 23 2013 - 09:29:46 CDT)
- Re: Problem with using FFKT to optimize bonded parameters John Stone (Wed Oct 23 2013 - 09:49:42 CDT)
  - Re: Problem with using FFKT to optimize bonded parameters Shane O Mahony (Wed Oct 23 2013 - 10:03:37 CDT)
Cluster plug Ramin Ekhteiari (Tue Oct 22 2013 - 15:39:48 CDT)
- Re: Cluster plug Axel Kohlmeyer (Tue Oct 22 2013 - 16:55:40 CDT)
- Re: Cluster plug John Stone (Wed Oct 23 2013 - 10:15:57 CDT)
loading trajectory Ramin Ekhteiari (Tue Oct 22 2013 - 04:24:26 CDT)
- Re: loading trajectory Axel Kohlmeyer (Tue Oct 22 2013 - 05:32:03 CDT)
- AW: loading trajectory Norman Geist (Tue Oct 22 2013 - 10:31:56 CDT)
Re: fftk-charges rodolfo gonzalez (Mon Oct 21 2013 - 01:57:55 CDT)
- AW: fftk-charges Norman Geist (Mon Oct 21 2013 - 07:59:53 CDT)
- Re: fftk-charges rodolfo gonzalez (Mon Oct 21 2013 - 10:43:01 CDT)
  - Re: fftk-charges Josh Vermaas (Mon Oct 21 2013 - 14:50:44 CDT)
fftk-charges rodolfo gonzalez (Sun Oct 20 2013 - 10:00:50 CDT)
Volarea Himanshu Joshi (Fri Oct 18 2013 - 07:44:40 CDT)
- Re: Volarea João Ribeiro (Fri Oct 18 2013 - 08:44:54 CDT)
  - Re: Volarea Himanshu Joshi (Fri Oct 18 2013 - 12:09:06 CDT)
  - Re: Volarea Himanshu Joshi (Mon Oct 21 2013 - 07:17:05 CDT)
- Re: Volarea Axel Kohlmeyer (Fri Oct 18 2013 - 08:35:35 CDT)
topotools question Vikas Varshney (Thu Oct 17 2013 - 15:34:42 CDT)
- Re: topotools question Axel Kohlmeyer (Thu Oct 17 2013 - 16:57:57 CDT)
  - Re: topotools question Vikas Varshney (Fri Oct 18 2013 - 08:53:23 CDT)
FFTK, pyrrolidine parametrization bonded parameters- issue with Hessian AnkiReddy katha (Thu Oct 17 2013 - 02:44:02 CDT)
- RE: FFTK, pyrrolidine parametrization bonded parameters- issue with Hessian JC Gumbart (Thu Oct 17 2013 - 06:32:24 CDT)
- Re: FFTK, pyrrolidine parametrization bonded parameters- issue with Hessian JC Gumbart (Fri Oct 18 2013 - 13:28:42 CDT)
  - Re: FFTK, pyrrolidine parametrization bonded parameters- issue with Hessian AnkiReddy katha (Tue Oct 22 2013 - 06:59:59 CDT)
    - Re: FFTK, pyrrolidine parametrization bonded parameters- issue with Hessian JC Gumbart (Tue Oct 22 2013 - 10:23:45 CDT)
writepsf method of atomselect objects generates bad atom types Jim Parker (Wed Oct 16 2013 - 13:20:30 CDT)
- Re: writepsf method of atomselect objects generates bad atom types JÃ©rÃ´me HÃ©nin (Wed Oct 16 2013 - 14:34:23 CDT)
- Re: writepsf method of atomselect objects generates bad atom types Josh Vermaas (Wed Oct 16 2013 - 14:37:33 CDT)
  - Re: writepsf method of atomselect objects generates bad atom types Jim Parker (Wed Oct 16 2013 - 18:25:32 CDT)
how shall we fill in clipped molecules? Albert (Wed Oct 16 2013 - 09:08:10 CDT)
- Re: how shall we fill in clipped molecules? John Stone (Wed Oct 16 2013 - 09:49:30 CDT)
  - Re: how shall we fill in clipped molecules? Albert (Wed Oct 16 2013 - 09:57:36 CDT)
Dowser-plugin with RNA Behrmann, Elmar (Wed Oct 16 2013 - 07:36:12 CDT)
visualization of el. potential Petr Jerabek (Mon Oct 14 2013 - 07:44:32 CDT)
- Re: visualization of el. potential John Stone (Mon Oct 14 2013 - 10:13:28 CDT)
  - Re: visualization of el. potential Petr Jerabek (Mon Oct 14 2013 - 14:06:22 CDT)
BUG Report -> Draw multiple frames Norman Geist (Fri Oct 11 2013 - 02:41:25 CDT)
- Re: BUG Report -> Draw multiple frames John Stone (Fri Oct 11 2013 - 08:34:49 CDT)
- RE: BUG Report -> Draw multiple frames Tristan Croll (Sun Oct 13 2013 - 18:53:22 CDT)
  - Re: BUG Report -> Draw multiple frames John Stone (Fri Nov 08 2013 - 16:58:23 CST)
Compiling VMD from source John Grime (Thu Oct 10 2013 - 16:29:04 CDT)
embed a protein that includes a ligand into the membrane Ramin Ekhteiari (Thu Oct 10 2013 - 12:38:11 CDT)
- Re: embed a protein that includes a ligand into the membrane John Stone (Thu Oct 10 2013 - 22:24:05 CDT)
- Re: embed a protein that includes a ligand into the membrane Suresh (Thu Oct 10 2013 - 23:36:02 CDT)
namdenergy plugin for Amber simulations Nupur Bansal (Thu Oct 10 2013 - 12:25:00 CDT)
- namdenergy plugin for Amber simulations Nupur Bansal (Mon Oct 28 2013 - 11:06:07 CDT)
Installing VMD with PYTHON support A. Gomez-Sicilia (Thu Oct 10 2013 - 07:09:29 CDT)
- Re: Installing VMD with PYTHON support Axel Kohlmeyer (Thu Oct 10 2013 - 08:05:12 CDT)
  - Re: Installing VMD with PYTHON support A. Gomez-Sicilia (Thu Oct 10 2013 - 08:11:03 CDT)
    - Re: Installing VMD with PYTHON support Axel Kohlmeyer (Thu Oct 10 2013 - 08:17:40 CDT)
  - Re: Installing VMD with PYTHON support John Stone (Thu Oct 10 2013 - 08:59:07 CDT)
VMD graphical representations: a few bugs Tristan Croll (Thu Oct 10 2013 - 00:50:06 CDT)
psfgen forces to apply terminils to peptide Wanzhi Qiu (Thu Oct 10 2013 - 00:11:40 CDT)
- Re: psfgen forces to apply terminils to peptide Tristan Croll (Thu Oct 10 2013 - 03:49:56 CDT)
  - Re: psfgen forces to apply terminils to peptide Wanzhi Qiu (Fri Oct 11 2013 - 03:36:09 CDT)
clipping plane Chris Knorowski (Wed Oct 09 2013 - 14:25:45 CDT)
- Re: clipping plane Axel Kohlmeyer (Wed Oct 09 2013 - 15:19:52 CDT)
  - Re: clipping plane Chris Knorowski (Wed Oct 09 2013 - 15:44:53 CDT)
create and operate a point in space sunyeping (Wed Oct 09 2013 - 05:15:44 CDT)
- Re: create and operate a point in space Axel Kohlmeyer (Wed Oct 09 2013 - 06:29:51 CDT)
Finding particles that are close Olaf Lenz (Tue Oct 08 2013 - 03:31:45 CDT)
- Re: Finding particles that are close Axel Kohlmeyer (Tue Oct 08 2013 - 04:21:45 CDT)
- Re: Finding particles that are close John Stone (Tue Oct 08 2013 - 08:51:36 CDT)
  - RE: Finding particles that are close Bennion, Brian (Tue Oct 08 2013 - 10:24:22 CDT)
    - Re: Finding particles that are close Chris Knorowski (Tue Oct 08 2013 - 16:05:38 CDT)
    - Re: Finding particles that are close John Stone (Tue Oct 08 2013 - 16:43:34 CDT)
- Re: Finding particles that are close Olaf Lenz (Wed Oct 09 2013 - 02:37:07 CDT)
  - Re: Finding particles that are close John Stone (Wed Oct 09 2013 - 09:50:22 CDT)
No timestep available for 'within' search! Nupur Bansal (Mon Oct 07 2013 - 15:28:04 CDT)
- Re: No timestep available for 'within' search! John Stone (Mon Oct 07 2013 - 15:38:17 CDT)
  - Re: No timestep available for 'within' search! Nupur Bansal (Mon Oct 07 2013 - 15:42:15 CDT)
    - Re: No timestep available for 'within' search! John Stone (Mon Oct 07 2013 - 16:46:15 CDT)
How to calculate tetrahedral order parameter ? Subrata Paul (Sat Oct 05 2013 - 00:07:03 CDT)
- viewing bond between two hydrogens on a water molecule Ramin Ekhteiari (Mon Oct 07 2013 - 06:23:19 CDT)
  - Re: viewing bond between two hydrogens on a water molecule John Stone (Mon Oct 07 2013 - 09:37:35 CDT)
    - Re: viewing bond between two hydrogens on a water molecule Axel Kohlmeyer (Mon Oct 07 2013 - 10:25:03 CDT)
namdenergy fulldirect Prof. Eddie (Fri Oct 04 2013 - 14:02:30 CDT)
- Re: namdenergy fulldirect Josh Vermaas (Fri Oct 04 2013 - 16:04:40 CDT)
GLSL rendering problems on MAC OS 10.8.5 (Intel Graphics Card) Vani Vemparala (Thu Oct 03 2013 - 23:30:59 CDT)
- Re: GLSL rendering problems on MAC OS 10.8.5 (Intel Graphics Card) Axel Kohlmeyer (Fri Oct 04 2013 - 00:33:13 CDT)
  - Re: GLSL rendering problems on MAC OS 10.8.5 (Intel Graphics Card) John Stone (Mon Oct 07 2013 - 12:07:21 CDT)
Measuring angle between two domains? Peterson J (Thu Oct 03 2013 - 10:40:50 CDT)
- Re: Measuring angle between two domains? Axel Kohlmeyer (Thu Oct 03 2013 - 11:37:49 CDT)
  - Re: Measuring angle between two domains? Thomas C. Bishop (Thu Oct 03 2013 - 12:42:02 CDT)
Creating very large solvation boxes John Grime (Wed Oct 02 2013 - 16:45:14 CDT)
- Re: Creating very large solvation boxes Josh Vermaas (Wed Oct 02 2013 - 19:47:40 CDT)
  - RE: Creating very large solvation boxes John Grime (Thu Oct 03 2013 - 07:36:44 CDT)
    - Re: Creating very large solvation boxes Ajasja LjubetiÄ (Thu Oct 03 2013 - 09:06:37 CDT)
convert dcd file to xyz Huong Vu (Wed Oct 02 2013 - 12:21:04 CDT)
- Re: convert dcd file to xyz John Stone (Wed Oct 02 2013 - 12:48:06 CDT)
- Re: convert dcd file to xyz Axel Kohlmeyer (Wed Oct 02 2013 - 13:13:18 CDT)
- Re: convert dcd file to xyz Josh Vermaas (Wed Oct 02 2013 - 13:24:13 CDT)
ffTK dihedral fitting question and cmap derivation Daniel Klose (Wed Oct 02 2013 - 03:24:38 CDT)
- Re: ffTK dihedral fitting question and cmap derivation Mayne, Christopher G (Wed Oct 02 2013 - 08:04:29 CDT)
- Re: ffTK dihedral fitting question and cmap derivation Josh Vermaas (Wed Oct 02 2013 - 09:00:54 CDT)
custom residue ribbon/cartoon representation issue Do Yong Kim (Tue Oct 01 2013 - 10:59:08 CDT)
How to diagnose SpaceNavigator not working with VMD? FX (Tue Oct 01 2013 - 07:02:56 CDT)
- Re: How to diagnose SpaceNavigator not working with VMD? John Stone (Wed Oct 02 2013 - 14:12:01 CDT)
  - Re: How to diagnose SpaceNavigator not working with VMD? FX (Thu Oct 03 2013 - 03:35:00 CDT)
Re: µªÎ`: How to show section contour of volumetric data Axel Kohlmeyer (Tue Oct 01 2013 - 02:58:10 CDT)
- ´ð¸´: ´ð¸´: How to show section contour of volumetric data CHEN, Chi (Tue Oct 01 2013 - 03:08:42 CDT)
How to show section contour of volumetric data CHEN, Chi (Mon Sep 30 2013 - 20:57:24 CDT)
- Re: How to show section contour of volumetric data Axel Kohlmeyer (Tue Oct 01 2013 - 02:21:04 CDT)
RE: get resisue names from atom index number sunyeping (Mon Sep 30 2013 - 02:56:04 CDT)
- Re: get resisue names from atom index number Axel Kohlmeyer (Mon Sep 30 2013 - 03:20:01 CDT)
- Re: RE: get resisue names from atom index number Josh Vermaas (Mon Sep 30 2013 - 10:10:17 CDT)
Force field tool kit - missing close brackets-vmd version 1.9.2 Mohan maruthi sena (Mon Sep 30 2013 - 01:40:41 CDT)
- Re: Force field tool kit - missing close brackets-vmd version 1.9.2 Axel Kohlmeyer (Mon Sep 30 2013 - 02:47:21 CDT)
need your hep about IR Spectrum Plugin Hamid (Sun Sep 29 2013 - 07:26:56 CDT)
- Re: need your hep about IR Spectrum Plugin Axel Kohlmeyer (Sun Sep 29 2013 - 09:31:10 CDT)
get resisue names from atom index number sunyeping (Sun Sep 29 2013 - 01:33:09 CDT)
- Re: get resisue names from atom index number Axel Kohlmeyer (Sun Sep 29 2013 - 09:27:28 CDT)
User defined command order Stephanie Teich-McGoldrick (Fri Sep 27 2013 - 19:42:43 CDT)
- Re: User defined command order Axel Kohlmeyer (Sat Sep 28 2013 - 04:27:12 CDT)
  - Re: User defined command order Stephanie Teich-McGoldrick (Mon Sep 30 2013 - 22:08:53 CDT)
Running the ParseFEP Plugin from the Command Line David Huggins (Thu Sep 26 2013 - 11:14:59 CDT)
rendering Luciano Pinho (Thu Sep 26 2013 - 07:01:49 CDT)
- Re: rendering Axel Kohlmeyer (Thu Sep 26 2013 - 15:13:03 CDT)
- Re: rendering John Stone (Fri Sep 27 2013 - 13:30:02 CDT)
non-orthorhombic PBCs Jaap Kroes (Wed Sep 25 2013 - 20:14:39 CDT)
- Re: non-orthorhombic PBCs Axel Kohlmeyer (Thu Sep 26 2013 - 00:56:36 CDT)
  - Re: non-orthorhombic PBCs Jaap Kroes (Thu Sep 26 2013 - 04:10:58 CDT)
VMD script Marzieh Dehghan (Wed Sep 25 2013 - 07:30:05 CDT)
Re: Making a trajectory movie from frames. Dawid das (Tue Sep 24 2013 - 11:04:38 CDT)
- Re: Making a trajectory movie from frames. Axel Kohlmeyer (Tue Sep 24 2013 - 11:10:33 CDT)
Re: HBonds from Desmond Trajectory JC Gumbart (Tue Sep 24 2013 - 10:35:31 CDT)
Incompatible cubefiles (G09revD.01 cubegen) Ari Turpeinen (Tue Sep 24 2013 - 01:20:18 CDT)
- Re: Incompatible cubefiles (G09revD.01 cubegen) Axel Kohlmeyer (Tue Sep 24 2013 - 02:37:55 CDT)
  - Re: Incompatible cubefiles (G09revD.01 cubegen) Ari Turpeinen (Tue Sep 24 2013 - 03:23:51 CDT)
draw a time bar for a trajectory Davide Mercadante (Mon Sep 23 2013 - 09:53:24 CDT)
- Re: draw a time bar for a trajectory Axel Kohlmeyer (Mon Sep 23 2013 - 11:13:35 CDT)
  - Re: draw a time bar for a trajectory Davide Mercadante (Tue Sep 24 2013 - 01:28:58 CDT)
VMD freezing up when left alone Tristan Croll (Sun Sep 22 2013 - 18:34:46 CDT)
- Re: VMD freezing up when left alone John Stone (Sun Sep 22 2013 - 20:34:01 CDT)
  - Re: VMD freezing up when left alone Tristan Croll (Sun Sep 22 2013 - 20:43:05 CDT)
water cluster analysis? Subrata Paul (Sun Sep 22 2013 - 08:50:33 CDT)
- Re: water cluster analysis? Axel Kohlmeyer (Sun Sep 22 2013 - 10:27:02 CDT)
  - Re: water cluster analysis? Axel Kohlmeyer (Sun Sep 22 2013 - 13:55:35 CDT)
water interaction - force field kit vmd - Mohan maruthi sena (Sat Sep 21 2013 - 14:23:58 CDT)
- Re: water interaction - force field kit vmd - Mayne, Christopher G (Mon Sep 23 2013 - 07:35:25 CDT)
Creating very large solvation boxes John Grime (Fri Sep 20 2013 - 12:12:45 CDT)
to set VMDFORCECPUCOUNT upayan baul (Fri Sep 20 2013 - 09:04:30 CDT)
- Re: to set VMDFORCECPUCOUNT Christopher MacDermaid (Fri Sep 20 2013 - 11:08:56 CDT)
- Re: to set VMDFORCECPUCOUNT Gianluca Interlandi (Fri Sep 20 2013 - 12:50:16 CDT)
  - Re: to set VMDFORCECPUCOUNT upayan baul (Sat Sep 21 2013 - 00:27:22 CDT)
ehrenfest dynamics surya narayanan chandrasekaran (Fri Sep 20 2013 - 04:58:06 CDT)
force field tool kit - error in the step of tutorial charges optimization 2-using vmd1.9.1 Mohan maruthi sena (Thu Sep 19 2013 - 03:38:09 CDT)
- Re: force field tool kit - error in the step of tutorial charges optimization 2-using vmd1.9.1 Mohan maruthi sena (Thu Sep 19 2013 - 04:52:34 CDT)
- Re: force field tool kit - error in the step of tutorial charges optimization 2-using vmd1.9.1 Mayne, Christopher G (Thu Sep 19 2013 - 08:14:38 CDT)
Open VMD from a remote host Gianluca Interlandi (Wed Sep 18 2013 - 13:43:49 CDT)
- Re: Open VMD from a remote host John Stone (Wed Sep 18 2013 - 13:53:55 CDT)
- Re: Open VMD from a remote host Axel Kohlmeyer (Wed Sep 18 2013 - 14:48:11 CDT)
  - Re: Open VMD from a remote host Gianluca Interlandi (Wed Sep 18 2013 - 15:33:38 CDT)
Buffer Overflow in "label add" in VMD Christopher MacDermaid (Wed Sep 18 2013 - 10:19:26 CDT)
remove hydrogen atoms from psf file Yunjie Zhao (Wed Sep 18 2013 - 01:57:38 CDT)
- Re: remove hydrogen atoms from psf file Axel Kohlmeyer (Wed Sep 18 2013 - 03:22:51 CDT)
  - Re: remove hydrogen atoms from psf file Yunjie Zhao (Wed Sep 18 2013 - 08:30:59 CDT)
    - Re: remove hydrogen atoms from psf file Yunjie Zhao (Wed Sep 18 2013 - 08:32:07 CDT)
    - Re: remove hydrogen atoms from psf file Axel Kohlmeyer (Wed Sep 18 2013 - 09:48:34 CDT)
â˜… vmd-l@ks.uiuc.edu., Parth left a message for you Hot or Not (Mon Sep 16 2013 - 22:51:51 CDT)
show_replicas.vmd can't find basesel Francesco Pietra (Mon Sep 16 2013 - 12:49:15 CDT)
- Re: show_replicas.vmd can't find basesel John Stone (Tue Sep 17 2013 - 00:03:53 CDT)
  - Re: show_replicas.vmd can't find basesel Francesco Pietra (Tue Sep 17 2013 - 02:31:30 CDT)
data analysis script help Martin, Erik W (Mon Sep 16 2013 - 11:51:15 CDT)
- Re: data analysis script help Axel Kohlmeyer (Tue Sep 17 2013 - 08:18:57 CDT)
Certain combinations of X-server and X-client do not allow VMD to start Clarinet (Mon Sep 16 2013 - 09:40:08 CDT)
- Re: Certain combinations of X-server and X-client do not allow VMD to start John Stone (Mon Sep 16 2013 - 23:56:11 CDT)
  - Re: Certain combinations of X-server and X-client do not allow VMD to start Jiri Polach (Tue Sep 17 2013 - 08:02:23 CDT)
- AW: Certain combinations of X-server and X-client do not allow VMD to start Norman Geist (Tue Sep 17 2013 - 05:23:26 CDT)
regd arrangment of atom types in psf and par from fftk surya narayanan chandrasekaran (Sun Sep 15 2013 - 13:27:53 CDT)
- Re: regd arrangment of atom types in psf and par from fftk Josh Vermaas (Sun Sep 15 2013 - 17:04:51 CDT)
calculating total energy rasti_at_ut.ac.ir (Sun Sep 15 2013 - 03:17:42 CDT)
- AW: calculating total energy Norman Geist (Mon Sep 16 2013 - 01:44:38 CDT)
- Re: calculating total energy John Stone (Tue Sep 17 2013 - 00:08:49 CDT)
Hbonds color in VMD Research Jubilant (Fri Sep 13 2013 - 12:38:17 CDT)
- cannot find PSF and PDB Rejwan (Sun Sep 15 2013 - 13:04:14 CDT)
  - Re: cannot find PSF and PDB John Stone (Mon Sep 16 2013 - 23:59:51 CDT)
- Re: Hbonds color in VMD Josh Vermaas (Sun Sep 15 2013 - 17:11:27 CDT)
  - Re: Hbonds color in VMD Josh Vermaas (Mon Sep 16 2013 - 10:34:05 CDT)
vmd in Debian Johannes Schauer (Thu Sep 12 2013 - 07:18:32 CDT)
- Re: vmd in Debian Benjamin Kaduk (Thu Sep 12 2013 - 18:19:33 CDT)
- Re: vmd in Debian John Stone (Tue Sep 17 2013 - 11:05:14 CDT)
  - Re: vmd in Debian Johannes Schauer (Mon Oct 07 2013 - 02:11:37 CDT)
    - Re: vmd in Debian John Stone (Mon Oct 07 2013 - 09:08:35 CDT)
(no subject) Ignacio Irurzun (Wed Sep 11 2013 - 13:50:22 CDT)
searching for contact atomh sunyeping (Wed Sep 11 2013 - 01:35:13 CDT)
reg FFTK surya narayanan chandrasekaran (Tue Sep 10 2013 - 14:12:27 CDT)
- Re: reg FFTK Mayne, Christopher G (Tue Sep 10 2013 - 16:23:10 CDT)
Problems uploading new molecule Daniel.Mulvihill (Tue Sep 10 2013 - 10:22:20 CDT)
- Re: Problems uploading new molecule Axel Kohlmeyer (Wed Sep 11 2013 - 04:02:51 CDT)
  - RE: Problems uploading new molecule Daniel.Mulvihill (Wed Sep 11 2013 - 05:11:56 CDT)
monitoring of aromatic interactions? Cecilia Lindgren (Tue Sep 10 2013 - 07:25:46 CDT)
Problem with VMD's depth cueing and 3DConnexion SpaceNavigator Christian Mücksch (Tue Sep 10 2013 - 07:11:21 CDT)
- Re: Problem with VMD's depth cueing and 3DConnexion SpaceNavigator Axel Kohlmeyer (Tue Sep 10 2013 - 08:03:49 CDT)
  - Re: Problem with VMD's depth cueing and 3DConnexion SpaceNavigator Christian Mücksch (Tue Sep 10 2013 - 08:20:16 CDT)
    - Re: Problem with VMD's depth cueing and 3DConnexion SpaceNavigator John Stone (Tue Sep 17 2013 - 10:40:22 CDT)
    - Re: Problem with VMD's depth cueing and 3DConnexion SpaceNavigator Christian Mücksch (Tue Sep 17 2013 - 12:19:56 CDT)
tetrahedral order parameter Subrata Paul (Tue Sep 10 2013 - 01:12:51 CDT)
cispeptide and chirality extrab options Tristan Croll (Mon Sep 09 2013 - 04:15:06 CDT)
Error: Maximum number of bonds exceeded Orsolya Karácsony (Sat Sep 07 2013 - 13:30:21 CDT)
water cluster size analysis Subrata Paul (Fri Sep 06 2013 - 07:14:47 CDT)
- Re: water cluster size analysis Axel Kohlmeyer (Fri Sep 06 2013 - 08:16:06 CDT)
Autobond Criterion Oliver Stenning (Fri Sep 06 2013 - 03:52:40 CDT)
- Re: Autobond Criterion Axel Kohlmeyer (Fri Sep 06 2013 - 05:09:23 CDT)
- mol2 file format & displaying atom connectivities FyD (Fri Sep 06 2013 - 06:35:52 CDT)
  - Re: mol2 file format & displaying atom connectivities Axel Kohlmeyer (Fri Sep 06 2013 - 07:43:12 CDT)
    - Re: mol2 file format & displaying atom connectivities FyD (Fri Sep 06 2013 - 08:55:42 CDT)
Add a gap in my simulation Ali Alizadeh (Thu Sep 05 2013 - 11:40:46 CDT)
- Re: Add a gap in my simulation Axel Kohlmeyer (Thu Sep 05 2013 - 13:38:51 CDT)
  - Re: Add a gap in my simulation Ali Alizadeh (Thu Sep 05 2013 - 14:41:00 CDT)
    - Re: Add a gap in my simulation Axel Kohlmeyer (Thu Sep 05 2013 - 14:42:28 CDT)
Add a gap in my simulation Ali Alizadeh (Thu Sep 05 2013 - 11:36:54 CDT)
calculation of angular distribution function Subrata Paul (Thu Sep 05 2013 - 09:32:12 CDT)
Re: AW: how to enable multiple core rendering? Albert (Thu Sep 05 2013 - 04:02:10 CDT)
- Re: AW: how to enable multiple core rendering? John Stone (Thu Sep 05 2013 - 09:43:18 CDT)
tachyon batch render in parallel Anne Dara Bowen (Wed Sep 04 2013 - 10:51:22 CDT)
- Re: tachyon batch render in parallel John Stone (Wed Sep 04 2013 - 11:06:58 CDT)
  - Re: tachyon batch render in parallel John Stone (Wed Aug 13 2014 - 13:16:23 CDT)
Puckering Parameters mish (Wed Sep 04 2013 - 07:49:44 CDT)
- Re: Puckering Parameters Payne, Christina M (Wed Sep 04 2013 - 12:43:56 CDT)
how to enable multiple core rendering? Albert (Wed Sep 04 2013 - 03:05:15 CDT)
- Re: how to enable multiple core rendering? John Stone (Thu Sep 05 2013 - 09:39:50 CDT)
Increasing number of digits Dawid das (Tue Sep 03 2013 - 09:31:00 CDT)
- Re: Increasing number of digits John Stone (Fri Sep 06 2013 - 17:24:19 CDT)
- RE: Increasing number of digits Martin, Erik W (Fri Sep 06 2013 - 19:32:42 CDT)
Error with show_replicas.vmd Francesco Pietra (Tue Sep 03 2013 - 04:44:55 CDT)
- Re: Error with show_replicas.vmd John Stone (Tue Sep 03 2013 - 10:57:26 CDT)
atom selection from multiple molecules Oliver Schillinger (Mon Sep 02 2013 - 10:17:06 CDT)
- Re: atom selection from multiple molecules Axel Kohlmeyer (Mon Sep 02 2013 - 11:13:31 CDT)
psf file Marzieh Dehghan (Sat Aug 31 2013 - 07:42:26 CDT)
- Re: psf file Axel Kohlmeyer (Sat Aug 31 2013 - 09:00:12 CDT)
Question regarding color schemes on crystals and grain boundaries Roger A Larson (Fri Aug 30 2013 - 16:13:13 CDT)
- Re: Question regarding color schemes on crystals and grain boundaries Axel Kohlmeyer (Sat Aug 31 2013 - 06:37:12 CDT)
SangbaeLee: question about pbc wrap Lee, Sangbae (Thu Aug 29 2013 - 13:12:21 CDT)
Energy contribution analysis eneas_at_usal.es (Wed Aug 28 2013 - 05:42:43 CDT)
.VMD state file does not load properly Hamed Mortazavi (Wed Aug 28 2013 - 03:43:30 CDT)
- Re: .VMD state file does not load properly Axel Kohlmeyer (Wed Aug 28 2013 - 04:52:20 CDT)
  - Re: .VMD state file does not load properly Hamed Mortazavi (Wed Aug 28 2013 - 04:58:32 CDT)
making patch rasti_at_ut.ac.ir (Tue Aug 27 2013 - 18:41:06 CDT)
Installation Problem Vinícius Aguiar (Tue Aug 27 2013 - 15:25:15 CDT)
Problem in buried surface area calculation m r (Tue Aug 27 2013 - 08:35:55 CDT)
- Re: Problem in buried surface area calculation John Stone (Tue Aug 27 2013 - 10:33:21 CDT)
- RE: Problem in buried surface area calculation Joaquim Rui de Castro Rodrigues (Tue Aug 27 2013 - 10:39:46 CDT)
- Re: Problem in buried surface area calculation Josh Vermaas (Tue Aug 27 2013 - 10:34:32 CDT)
MOLEFACTURE with more than 200 atoms Francesco Pietra (Tue Aug 27 2013 - 05:24:23 CDT)
compiling VMD -- confused failure Cook, Rich (Mon Aug 26 2013 - 20:15:07 CDT)
- RE: compiling VMD -- confused failure Strahs, Dr. Daniel Bernard (Mon Aug 26 2013 - 22:03:56 CDT)
- Re: compiling VMD -- confused failure John Stone (Tue Aug 27 2013 - 10:29:49 CDT)
  - Re: compiling VMD -- confused failure Cook, Rich (Tue Aug 27 2013 - 13:31:05 CDT)
trouble compiling/setting up VMD Cook, Rich (Mon Aug 26 2013 - 18:44:26 CDT)
- Re: trouble compiling/setting up VMD Axel Kohlmeyer (Mon Aug 26 2013 - 19:57:36 CDT)
  - Re: trouble compiling/setting up VMD Cook, Rich (Mon Aug 26 2013 - 20:06:20 CDT)
problem with ptch ... rasti (Mon Aug 26 2013 - 15:23:34 CDT)
Segmentation fault (core dumped) Yubo Fan (Mon Aug 26 2013 - 13:33:57 CDT)
- Re: Segmentation fault (core dumped) John Stone (Tue Aug 27 2013 - 11:31:32 CDT)
movie making in vmd chin chun (Mon Aug 26 2013 - 13:29:20 CDT)
- Re: movie making in vmd Peter Murphy (Mon Aug 26 2013 - 14:24:36 CDT)
  - Re: movie making in vmd Sumit Kumar (Mon Aug 26 2013 - 15:16:13 CDT)
reg FFTK BOND opt surya narayanan chandrasekaran (Mon Aug 26 2013 - 10:16:02 CDT)
- Re: reg FFTK BOND opt Mayne, Christopher G (Tue Sep 03 2013 - 09:35:50 CDT)
  - Re: reg FFTK BOND opt surya narayanan chandrasekaran (Tue Sep 03 2013 - 11:54:26 CDT)
    - Re: reg FFTK BOND opt Mayne, Christopher G (Tue Sep 03 2013 - 11:57:54 CDT)
    - Re: reg FFTK BOND opt Mayne, Christopher G (Wed Sep 04 2013 - 08:32:32 CDT)
matching part of two models Francesco Pietra (Mon Aug 26 2013 - 01:47:33 CDT)
- Fwd: matching part of two models Francesco Pietra (Mon Aug 26 2013 - 03:46:55 CDT)
problem with building psf file rasti (Sun Aug 25 2013 - 14:52:40 CDT)
- Re: problem with building psf file Josh Vermaas (Sun Aug 25 2013 - 16:34:44 CDT)
  - Re: problem with building psf file Josh Vermaas (Mon Aug 26 2013 - 12:17:44 CDT)
  - Re: problem with building psf file Josh Vermaas (Mon Aug 26 2013 - 15:38:04 CDT)
Quality of color scale bar when creating images for publication Holger Scheib (Sat Aug 24 2013 - 02:44:47 CDT)
- Re: Quality of color scale bar when creating images for publication John Stone (Tue Aug 27 2013 - 11:36:54 CDT)
VMD script Marzieh Dehghan (Sat Aug 24 2013 - 00:54:37 CDT)
Computational Biophysics Workshop using NAMD and VMD, November 18-22, 2013, Urbana, Illinois, USA David Brandon (Fri Aug 23 2013 - 14:15:11 CDT)
generation of psf of phenol Asaf Farhi (Thu Aug 22 2013 - 11:42:14 CDT)
- RE: generation of psf of phenol Tristan Croll (Thu Aug 22 2013 - 21:21:03 CDT)
Re: problem with using parameterization tool of VMD Suresh (Thu Aug 22 2013 - 08:39:06 CDT)
problem with using parameterization tool of VMD rasti (Thu Aug 22 2013 - 04:07:36 CDT)
unable to load .xtc files on VMD 1.8.7 Holden Ranz (Wed Aug 21 2013 - 16:18:50 CDT)
- Re: unable to load .xtc files on VMD 1.8.7 Axel Kohlmeyer (Wed Aug 21 2013 - 19:46:26 CDT)
- Re: unable to load .xtc files on VMD 1.8.7 Collins Nganou (Thu Aug 22 2013 - 08:05:12 CDT)
measure gofr for finding hydration shells Martin, Erik W (Mon Aug 19 2013 - 16:54:13 CDT)
A question with dipwatch.tcl script in VMD Ganesh Kamath (Sat Aug 17 2013 - 14:10:52 CDT)
- Re: A question with dipwatch.tcl script in VMD Boris Steipe (Sat Aug 17 2013 - 16:58:12 CDT)
  - Re: A question with dipwatch.tcl script in VMD Ganesh Kamath (Sat Aug 17 2013 - 20:32:42 CDT)
    - Re: A question with dipwatch.tcl script in VMD John Stone (Mon Aug 19 2013 - 10:45:40 CDT)
how to use measure cluster and clustering plugin of VMD? sunyeping (Fri Aug 16 2013 - 01:39:39 CDT)
- Re: how to use measure cluster and clustering plugin of VMD? Axel Kohlmeyer (Fri Aug 16 2013 - 08:33:48 CDT)
Question related to circular membrane snoze pa (Thu Aug 15 2013 - 16:26:28 CDT)
- Re: Question related to circular membrane John Stone (Fri Aug 16 2013 - 10:58:56 CDT)
STAMP Multiseq Eli Alster (Tue Aug 13 2013 - 11:40:32 CDT)
- Re: STAMP Multiseq Kirby Vandivort (Tue Aug 13 2013 - 12:03:49 CDT)
  - Re: STAMP Multiseq Anurag Sethi (Tue Aug 13 2013 - 13:46:42 CDT)
Re: Urgent---documents uploaded for you John Stone (Tue Aug 13 2013 - 11:35:55 CDT)
Vmd visualizing occupancy maps Andrei Tudor (Tue Aug 13 2013 - 10:21:14 CDT)
- Re: Vmd visualizing occupancy maps John Stone (Tue Aug 13 2013 - 11:17:29 CDT)
dihedral angle distribution Collins Nganou (Tue Aug 13 2013 - 08:36:47 CDT)
RE : namd-l: AW: Occupancy maps Andrei Tudor (Mon Aug 12 2013 - 10:40:27 CDT)
nonbond and covalent bond Marzieh Dehghan (Sun Aug 11 2013 - 06:53:38 CDT)
everything grey with glsl Gordon Wells (Sat Aug 10 2013 - 12:39:42 CDT)
- Re: everything grey with glsl Axel Kohlmeyer (Sat Aug 10 2013 - 13:57:18 CDT)
  - Re: everything grey with glsl Gordon Wells (Sat Aug 10 2013 - 14:08:40 CDT)
Fwd: adding calcium atom to the nmr structure Mahendra B Thapa (Fri Aug 09 2013 - 18:38:33 CDT)
gofr CUDA in script Martin, Erik W (Fri Aug 09 2013 - 17:12:07 CDT)
- Re: gofr CUDA in script Josh Vermaas (Fri Aug 09 2013 - 19:38:37 CDT)
  - Re: gofr CUDA in script Salvador H-V (Fri Aug 09 2013 - 22:59:27 CDT)
Occupancy maps Andrei Tudor (Fri Aug 09 2013 - 11:27:25 CDT)
cmd line FFK surya narayanan chandrasekaran (Fri Aug 09 2013 - 08:00:12 CDT)
- Re: cmd line FFK Mayne, Christopher G (Fri Aug 09 2013 - 11:26:52 CDT)
Fwd: APBS on each frame PANAGIOTA KYRIAKOU (Thu Aug 08 2013 - 14:56:39 CDT)
- Re: Fwd: APBS on each frame Davide Mercadante (Thu Aug 08 2013 - 16:08:12 CDT)
  - Re: Fwd: APBS on each frame -> ON FLY ANALYSIS Thomas C. Bishop (Fri Aug 09 2013 - 09:30:32 CDT)
Considering special bonds not all of bonds, Ali Alizadeh (Wed Aug 07 2013 - 08:03:40 CDT)
- Re: Considering special bonds not all of bonds, Axel Kohlmeyer (Wed Aug 07 2013 - 09:10:43 CDT)
  - Re: Considering special bonds not all of bonds, Ali Alizadeh (Wed Aug 07 2013 - 12:42:56 CDT)
VMD Mutate to nonstandard amino acid residue George Omolloh (Tue Aug 06 2013 - 15:06:26 CDT)
- Re: VMD Mutate to nonstandard amino acid residue Josh Vermaas (Tue Aug 06 2013 - 17:45:18 CDT)
NAMDGUI Li, Haiqing (Tue Aug 06 2013 - 13:29:54 CDT)
about the wrap and unwrap by pbc plugin Kong, Ren (Tue Aug 06 2013 - 11:06:41 CDT)
Loading new molecule without changing view? Marc van der Kamp (Tue Aug 06 2013 - 04:49:07 CDT)
- Re: Loading new molecule without changing view? Axel Kohlmeyer (Tue Aug 06 2013 - 06:09:49 CDT)
  - Re: Loading new molecule without changing view? Marc van der Kamp (Tue Aug 06 2013 - 06:24:24 CDT)
    - Re: Loading new molecule without changing view? Axel Kohlmeyer (Tue Aug 06 2013 - 07:33:01 CDT)
- Re: Loading new molecule without changing view? Mayne, Christopher G (Tue Aug 06 2013 - 06:41:49 CDT)
extracting grid points from an isosurface Georgios Gerogiokas (Tue Aug 06 2013 - 03:44:15 CDT)
- Re: extracting grid points from an isosurface Axel Kohlmeyer (Tue Aug 06 2013 - 06:05:11 CDT)
  - Re: extracting grid points from an isosurface John Stone (Tue Aug 06 2013 - 09:51:49 CDT)
Animations using VMD: Sumit Kumar (Mon Aug 05 2013 - 19:00:03 CDT)
- Re: Animations using VMD: Axel Kohlmeyer (Tue Aug 06 2013 - 06:02:42 CDT)
- Re: Animations using VMD: Vikas Varshney (Tue Aug 06 2013 - 06:41:35 CDT)
Regarding FFTK option surya narayanan chandrasekaran (Mon Aug 05 2013 - 12:06:32 CDT)
- Re: Regarding FFTK option Mayne, Christopher G (Mon Aug 05 2013 - 15:41:40 CDT)
Re: X11 on Mac 10.8 Valentina Erastova (Mon Aug 05 2013 - 09:50:05 CDT)
Display CCP4 density map around selection only Jim (Sun Aug 04 2013 - 18:51:08 CDT)
- Re: Display CCP4 density map around selection only Ryan McGreevy (Sun Aug 04 2013 - 20:14:57 CDT)
- Re: Display CCP4 density map around selection only Axel Kohlmeyer (Sun Aug 04 2013 - 23:11:02 CDT)
Bond error Benjamin Cowen (Fri Aug 02 2013 - 15:25:37 CDT)
- Re: Bond error Axel Kohlmeyer (Sat Aug 03 2013 - 15:03:40 CDT)
  - Re: Bond error Benjamin Cowen (Sat Aug 03 2013 - 16:07:17 CDT)
Segmentation fault (core dumped) Hailin Huang (Thu Aug 01 2013 - 15:03:59 CDT)
- Re: Segmentation fault (core dumped) Josh Vermaas (Thu Aug 01 2013 - 16:52:19 CDT)
Area per lipid for tubular micellae Vita Duka (Thu Aug 01 2013 - 08:10:10 CDT)
- Re: Area per lipid for tubular micellae Jeffrey Potoff (Thu Aug 01 2013 - 11:26:58 CDT)
  - Re: Area per lipid for tubular micellae Nuno Sousa Cerqueira (Thu Aug 01 2013 - 18:29:57 CDT)
BUG in VMD dx reader plugin Norman Geist (Thu Aug 01 2013 - 03:43:07 CDT)
Re: Problems when using specden package in VMD Axel Kohlmeyer (Thu Aug 01 2013 - 01:59:16 CDT)
- Re: Problems when using specden package in VMD Axel Kohlmeyer (Thu Aug 01 2013 - 02:19:44 CDT)
Problems when using specden package in VMD Mingchao Wang (Thu Aug 01 2013 - 00:19:16 CDT)
- Re: Problems when using specden package in VMD Axel Kohlmeyer (Thu Aug 01 2013 - 01:36:01 CDT)
- Re: Problems when using specden package in VMD John Stone (Thu Aug 01 2013 - 09:49:49 CDT)
bypassing MolFrac step surya narayanan chandrasekaran (Wed Jul 31 2013 - 05:50:57 CDT)
- Re: bypassing MolFrac step Mayne, Christopher G (Wed Jul 31 2013 - 09:35:13 CDT)
  - RE: bypassing MolFrac step Upadhyay, Him [him.upadhyay_at_ndsu.edu] (Wed Jul 31 2013 - 11:45:23 CDT)
    - Re: bypassing MolFrac step Mayne, Christopher G (Wed Jul 31 2013 - 11:53:04 CDT)
    - RE: bypassing MolFrac step Upadhyay, Him [him.upadhyay_at_ndsu.edu] (Wed Jul 31 2013 - 12:02:36 CDT)
Leap Motion Olaf Lenz (Tue Jul 30 2013 - 03:19:38 CDT)
- Re: Leap Motion Axel Kohlmeyer (Tue Jul 30 2013 - 04:13:53 CDT)
Replica exchange, colvars & harmonic restraints Andrei Tudor (Mon Jul 29 2013 - 11:14:01 CDT)
- RE : Replica exchange, colvars & harmonic restraints Andrei Tudor (Mon Jul 29 2013 - 13:22:45 CDT)
problems wrapping waters using PBC tools Markus Dahlgren (Mon Jul 29 2013 - 10:02:46 CDT)
- Re: problems wrapping waters using PBC tools Olaf Lenz (Tue Jul 30 2013 - 03:43:42 CDT)
Re: How to import .lammpstrj files using LAMMPS plugin Axel Kohlmeyer (Mon Jul 29 2013 - 01:17:40 CDT)
How to import .lammpstrj files using LAMMPS plugin Mingchao Wang (Mon Jul 29 2013 - 00:13:26 CDT)
SOLVED Fwd: Merge structures coordinate failure Francesco Pietra (Sun Jul 28 2013 - 05:06:14 CDT)
Error in merging manipulated graphene sheet (generate with VMD and manipulate with Hyperchem) with protein v.satarifard (Sun Jul 28 2013 - 03:22:20 CDT)
remove vmd in ubuntu v.satarifard (Sun Jul 28 2013 - 02:52:17 CDT)
- Re: remove vmd in ubuntu Olaf Lenz (Mon Jul 29 2013 - 01:50:58 CDT)
  - Re: remove vmd in ubuntu v.satarifard (Mon Jul 29 2013 - 09:43:51 CDT)
Problem with autoionize plugin and long atomtypes Thomas Albers (Sat Jul 27 2013 - 16:37:19 CDT)
- RE: Problem with autoionize plugin and long atomtypes Tristan Croll (Sun Jul 28 2013 - 18:54:19 CDT)
  - Re: Problem with autoionize plugin and long atomtypes Thomas Albers (Mon Jul 29 2013 - 10:47:11 CDT)
Merge structures coordinate failure Francesco Pietra (Sat Jul 27 2013 - 13:04:11 CDT)
VMD with Python on MacOSX 10.7.5 Payne, Christina M (Fri Jul 26 2013 - 11:52:24 CDT)
Re: autoionize error in vmd Revthi Sanker (Fri Jul 26 2013 - 09:53:30 CDT)
- Re: autoionize error in vmd Rajan Vatassery (Fri Jul 26 2013 - 12:55:36 CDT)
- Re: Re: autoionize error in vmd Tristan Croll (Sat Jul 27 2013 - 15:27:25 CDT)
FFTK question regarding dihedral fitting Daniel Klose (Fri Jul 26 2013 - 01:29:14 CDT)
- Re: FFTK question regarding dihedral fitting Mayne, Christopher G (Fri Jul 26 2013 - 02:56:21 CDT)
new VMD plugin for reading LAMMPS dumps with variable number of atoms Axel Kohlmeyer (Thu Jul 25 2013 - 07:43:34 CDT)
Muhammad Radifar Muhammad Radifar (Wed Jul 24 2013 - 11:58:37 CDT)
FFTK partial charges against water Francesco Pietra (Wed Jul 24 2013 - 08:32:42 CDT)
catdcd a vmd extension? R. Charbel MAROUN (Tue Jul 23 2013 - 12:09:30 CDT)
- Re: catdcd a vmd extension? Axel Kohlmeyer (Tue Jul 23 2013 - 13:09:00 CDT)
catdcd -first R. Charbel MAROUN (Tue Jul 23 2013 - 09:30:01 CDT)
- Re: catdcd -first Salvatore Mario Cosseddu (Wed Jul 24 2013 - 05:33:12 CDT)
Mutator plugin error Thomas Christott (Tue Jul 23 2013 - 05:54:51 CDT)
- RE: Mutator plugin error Thomas Christott (Mon Jul 29 2013 - 02:47:01 CDT)
FFTK scan torsions aromatics Francesco Pietra (Tue Jul 23 2013 - 02:14:14 CDT)
- Fwd: FFTK scan torsions aromatics Francesco Pietra (Tue Jul 23 2013 - 03:12:05 CDT)
- Re: FFTK scan torsions aromatics Christian Jorgensen (Fri Dec 06 2013 - 11:12:48 CST)
  - Re: Re: FFTK scan torsions aromatics Mayne, Christopher G (Fri Dec 06 2013 - 14:27:18 CST)
FFTK scan torsions MP2 vs RHF Francesco Pietra (Mon Jul 22 2013 - 11:24:55 CDT)
- Re: FFTK scan torsions MP2 vs RHF Mayne, Christopher G (Wed Jul 24 2013 - 04:22:18 CDT)
regarding FFTK improper angle surya narayanan chandrasekaran (Mon Jul 22 2013 - 11:08:37 CDT)
unusual bond warning during psf building melis.yildirim_at_boun.edu.tr (Mon Jul 22 2013 - 09:19:51 CDT)
Re: density of system Axel Kohlmeyer (Sun Jul 21 2013 - 16:08:49 CDT)
density of system chin chun (Sun Jul 21 2013 - 14:46:30 CDT)
Dynamic number of atoms visualization amit kunte (Sat Jul 20 2013 - 05:36:19 CDT)
- Re: Dynamic number of atoms visualization Axel Kohlmeyer (Sat Jul 20 2013 - 06:42:50 CDT)
  - Re: Dynamic number of atoms visualization amit kunte (Sat Jul 20 2013 - 07:31:42 CDT)
    - Re: Dynamic number of atoms visualization Axel Kohlmeyer (Sat Jul 20 2013 - 07:46:18 CDT)
simulating proteins with missing resdiues melis.yildirim_at_boun.edu.tr (Fri Jul 19 2013 - 11:01:49 CDT)
- Re: simulating proteins with missing resdiues Axel Kohlmeyer (Fri Jul 19 2013 - 11:56:29 CDT)
charge re-optimization Darre Castell, Leonardo (Fri Jul 19 2013 - 08:10:47 CDT)
- Re: charge re-optimization Mayne, Christopher G (Fri Jul 19 2013 - 10:08:36 CDT)
  - RE: charge re-optimization Darre Castell, Leonardo (Fri Jul 19 2013 - 10:13:47 CDT)
combine .pdb files to make movie Sarah MohammadiNejad (Fri Jul 19 2013 - 06:35:57 CDT)
- Re: combine .pdb files to make movie Axel Kohlmeyer (Fri Jul 19 2013 - 07:25:37 CDT)
  - Re: combine .pdb files to make movie Sarah MohammadiNejad (Fri Jul 19 2013 - 07:53:01 CDT)
CatDCD windows binaries Axel Kohlmeyer (Fri Jul 19 2013 - 04:56:00 CDT)
How can I easily show ball and stick residues across all molecules and representations? Dennis N Bromley (Thu Jul 18 2013 - 17:07:51 CDT)
- Re: How can I easily show ball and stick residues across all molecules and representations? Josh Vermaas (Thu Jul 18 2013 - 19:48:04 CDT)
- RE: How can I easily show ball and stick residues across all molecules and representations? Tristan Croll (Thu Jul 18 2013 - 20:18:40 CDT)
  - Re: How can I easily show ball and stick residues across all molecules and representations? John Stone (Thu Jul 18 2013 - 21:43:02 CDT)
FFTK about Water Interaction Francesco Pietra (Thu Jul 18 2013 - 11:18:21 CDT)
- Fwd: FFTK about Water Interaction Francesco Pietra (Fri Jul 19 2013 - 11:50:29 CDT)
VTF Bailey, Steven (Thu Jul 18 2013 - 08:35:28 CDT)
- Re: VTF Olaf Lenz (Thu Jul 18 2013 - 10:10:48 CDT)
- Re: VTF Olaf Lenz (Mon Feb 03 2014 - 12:09:13 CST)
WG: VMD mismatch between CUDA runtime and GPU driver Greipel.Joachim_at_mh-hannover.de (Thu Jul 18 2013 - 02:24:18 CDT)
- Re: WG: VMD mismatch between CUDA runtime and GPU driver John Stone (Thu Jul 18 2013 - 10:28:47 CDT)
  - AW: WG: VMD mismatch between CUDA runtime and GPU driver Greipel.Joachim_at_mh-hannover.de (Fri Jul 19 2013 - 01:04:54 CDT)
VMD mismatch between CUDA runtime and GPU driver Greipel.Joachim_at_mh-hannover.de (Thu Jul 18 2013 - 02:01:31 CDT)
- Re: VMD mismatch between CUDA runtime and GPU driver Axel Kohlmeyer (Thu Jul 18 2013 - 03:31:33 CDT)
charmm36 and charmm27 together with namd? Francesco Pietra (Thu Jul 18 2013 - 01:54:35 CDT)
- Re: charmm36 and charmm27 together with namd? JC Gumbart (Thu Jul 18 2013 - 09:00:37 CDT)
RE: Re: problems about atoms display in certain region sunnytov (Thu Jul 18 2013 - 01:07:21 CDT)
Re: problems about atoms display in certain region Axel Kohlmeyer (Wed Jul 17 2013 - 23:04:53 CDT)
FFTK and CGenFF Francesco Pietra (Wed Jul 17 2013 - 10:14:04 CDT)
- Fwd: FFTK and CGenFF Francesco Pietra (Wed Jul 17 2013 - 12:48:36 CDT)
  - Re: FFTK and CGenFF Mayne, Christopher G (Wed Jul 17 2013 - 15:27:27 CDT)
- Re: FFTK and CGenFF Mayne, Christopher G (Wed Jul 17 2013 - 14:54:00 CDT)
script for size distribution niladri patra (Tue Jul 16 2013 - 10:53:29 CDT)
- Re: script for size distribution Axel Kohlmeyer (Wed Jul 17 2013 - 02:26:41 CDT)
Center a trajectory Andrei Tudor (Tue Jul 16 2013 - 09:18:15 CDT)
- Re: Center a trajectory Ajasja LjubetiÄ (Tue Jul 16 2013 - 10:57:40 CDT)
  - Re: Center a trajectory Ajasja LjubetiÄ (Tue Jul 16 2013 - 11:27:16 CDT)
- Re: Center a trajectory Cathy Kelly (Tue Jul 16 2013 - 11:15:03 CDT)
Combine volmap occupancy maps Andrei Tudor (Mon Jul 15 2013 - 14:44:54 CDT)
- Re: Combine volmap occupancy maps Axel Kohlmeyer (Wed Jul 17 2013 - 02:31:04 CDT)
  - Re: Combine volmap occupancy maps John Stone (Wed Jul 17 2013 - 09:50:33 CDT)
logging in vmd Verwandlung Die (Sun Jul 14 2013 - 22:32:40 CDT)
- Re: logging in vmd Axel Kohlmeyer (Sun Jul 14 2013 - 23:31:32 CDT)
  - Re: logging in vmd Axel Kohlmeyer (Mon Jul 15 2013 - 01:31:47 CDT)
    - Re: logging in vmd Verwandlung Die (Tue Jul 30 2013 - 06:18:08 CDT)
    - Re: logging in vmd Axel Kohlmeyer (Tue Jul 30 2013 - 07:28:33 CDT)
membrane in xplor format Francesco Pietra (Fri Jul 12 2013 - 05:14:50 CDT)
- Re: membrane in xplor format Francesco Pietra (Fri Jul 12 2013 - 09:39:55 CDT)
autoionization error in VMD melis.yildirim_at_boun.edu.tr (Fri Jul 12 2013 - 03:21:25 CDT)
- Re: autoionization error in VMD Ajasja LjubetiÄ (Fri Jul 12 2013 - 04:53:34 CDT)
How to change resolution default setting? ÕÅÏàÐÛ (Thu Jul 11 2013 - 09:02:35 CDT)
Movies in VMD Hunter Brown (Wed Jul 10 2013 - 13:22:41 CDT)
- Re: Movies in VMD Josh Vermaas (Wed Jul 10 2013 - 15:01:07 CDT)
  - Re: Movies in VMD John Stone (Wed Jul 10 2013 - 15:30:32 CDT)
Error during Water interaction data generation using gaussian following ffTK screencast Peterson J (Wed Jul 10 2013 - 12:03:45 CDT)
- Re: Error during Water interaction data generation using gaussian following ffTK screencast Mayne, Christopher G (Wed Jul 10 2013 - 14:19:40 CDT)
Water interaction generation step in ffTK Peterson J (Tue Jul 09 2013 - 14:59:47 CDT)
- Re: Water interaction generation step in ffTK Josh Vermaas (Tue Jul 09 2013 - 16:02:24 CDT)
manipulation of atomselections Bennion, Brian (Fri Jul 05 2013 - 15:54:16 CDT)
- Re: manipulation of atomselections Axel Kohlmeyer (Fri Jul 05 2013 - 17:00:17 CDT)
  - RE: manipulation of atomselections Bennion, Brian (Fri Jul 05 2013 - 17:27:28 CDT)
- Re: manipulation of atomselections Josh Vermaas (Fri Jul 05 2013 - 17:12:43 CDT)
center of mass Jorgen Simonsen (Fri Jul 05 2013 - 11:25:55 CDT)
- Re: center of mass JÃ©rÃ´me HÃ©nin (Fri Jul 05 2013 - 12:17:28 CDT)
two Molecules in one pdb and psf Christian Wohlschlager (Fri Jul 05 2013 - 04:37:21 CDT)
- Re: two Molecules in one pdb and psf Axel Kohlmeyer (Fri Jul 05 2013 - 07:14:28 CDT)
dihedrals in ffTK Darre Castell, Leonardo (Thu Jul 04 2013 - 06:56:16 CDT)
- Re: dihedrals in ffTK Mayne, Christopher G (Thu Jul 04 2013 - 13:17:54 CDT)
FW: Dynamical network analysis-NetworkView Ciara McCormack (Thu Jul 04 2013 - 04:17:14 CDT)
- Re: FW: Dynamical network analysis-NetworkView Kirby Vandivort (Tue Jul 09 2013 - 11:29:29 CDT)
Trouble with the mergepdbs.tcl script Hunter Brown (Wed Jul 03 2013 - 09:56:51 CDT)
- Re: Trouble with the mergepdbs.tcl script Axel Kohlmeyer (Wed Jul 03 2013 - 10:46:47 CDT)
Merge Structur Christian Wohlschlager (Wed Jul 03 2013 - 08:52:00 CDT)
- Re: Merge Structur Axel Kohlmeyer (Wed Jul 03 2013 - 10:01:48 CDT)
atom indices from x y z coordinates Gurunath Katagi (Wed Jul 03 2013 - 03:00:15 CDT)
- Re: atom indices from x y z coordinates Axel Kohlmeyer (Wed Jul 03 2013 - 03:56:14 CDT)
Macromolecule? Benjamin Cowen (Tue Jul 02 2013 - 18:38:55 CDT)
- Re: Macromolecule? John Stone (Tue Jul 09 2013 - 13:03:46 CDT)
Announcement about Faraday Discussion on Molecular Simulation and Visualization - call for abstracts deadline 22 July 2013 Marc Baaden (Tue Jul 02 2013 - 15:00:02 CDT)
secondary structure works on linux, it doesn't work on Mac in certain structures Juan Felipe Ortiz (Tue Jul 02 2013 - 11:24:06 CDT)
- RE: secondary structure works on linux, it doesn't work on Mac in certain structures Tristan Croll (Wed Jul 03 2013 - 23:50:03 CDT)
  - RE: secondary structure works on linux, it doesn't work on Mac in certain structures Juan Felipe Ortiz (Sun Jul 07 2013 - 18:26:14 CDT)
  - Re: RE: secondary structure works on linux, it doesn't work on Mac in certain structures John Stone (Mon Jul 08 2013 - 15:16:20 CDT)
reg interaction energy surya narayanan chandrasekaran (Tue Jul 02 2013 - 11:08:33 CDT)
- Re: reg interaction energy Mayne, Christopher G (Mon Jul 08 2013 - 15:00:28 CDT)
Use AMBER files in CG-builder Nathaniel Eagan (Mon Jul 01 2013 - 16:21:14 CDT)
- Re: Use AMBER files in CG-builder John Stone (Tue Jul 09 2013 - 16:32:44 CDT)
Box boundaries displaying Michele Formica (Mon Jul 01 2013 - 10:21:54 CDT)
- Re: Box boundaries displaying Michele Formica (Mon Jul 01 2013 - 10:36:57 CDT)
  - Re: Box boundaries displaying Michele Formica (Mon Jul 01 2013 - 10:40:03 CDT)
- Re: Box boundaries displaying Axel Kohlmeyer (Mon Jul 01 2013 - 11:08:23 CDT)
- Re: Box boundaries displaying Olaf Lenz (Mon Jul 01 2013 - 12:46:00 CDT)
  - Re: Box boundaries displaying Ramin Ekhteiari (Tue Jul 02 2013 - 02:14:36 CDT)
VMD 1.9.1 namdenergy plugin problem with GPU acceleration Alessandro Mascioni (Sun Jun 30 2013 - 15:42:38 CDT)
- Re: VMD 1.9.1 namdenergy plugin problem with GPU acceleration John Stone (Tue Jul 09 2013 - 13:45:47 CDT)
  - Re: VMD 1.9.1 namdenergy plugin problem with GPU acceleration Jim Phillips (Tue Jul 09 2013 - 13:57:02 CDT)
    - Re: VMD 1.9.1 namdenergy plugin problem with GPU acceleration John Stone (Tue Jul 09 2013 - 14:02:01 CDT)
3d pdf Roberto Gaspari (Sun Jun 30 2013 - 14:47:25 CDT)
- Re: 3d pdf John Stone (Tue Jul 09 2013 - 13:43:25 CDT)
auto ionise error Revthi Sanker (Sat Jun 29 2013 - 07:53:03 CDT)
- Re: auto ionise error John Stone (Tue Jul 09 2013 - 13:40:47 CDT)
  - Re: auto ionise error Ajasja LjubetiÄ (Tue Jul 09 2013 - 14:25:25 CDT)
VMD shows there's a H-BOND between Carbon and Hydrogen? Hovakim Grabski (Sat Jun 29 2013 - 05:47:02 CDT)
Reusing the psf file Peterson J (Fri Jun 28 2013 - 22:06:56 CDT)
- Re: Reusing the psf file Axel Kohlmeyer (Sat Jun 29 2013 - 02:06:10 CDT)
setting bonds so that they are saved in DMS format output Christopher Neale (Fri Jun 28 2013 - 21:26:40 CDT)
- Re: setting bonds so that they are saved in DMS format output Axel Kohlmeyer (Fri Jun 28 2013 - 22:23:31 CDT)
Coarse Graining Cholesterol with VMD's cg builder Christopher Gutnajer (Fri Jun 28 2013 - 15:12:48 CDT)
- Re: Coarse Graining Cholesterol with VMD's cg builder Kirby Vandivort (Tue Jul 09 2013 - 13:14:18 CDT)
  - Re: Coarse Graining Cholesterol with VMD's cg builder Christopher Gutnajer (Tue Jul 09 2013 - 22:30:01 CDT)
ureybradley and impropers in ffTK Darre Castell, Leonardo (Fri Jun 28 2013 - 11:52:21 CDT)
- Re: ureybradley and impropers in ffTK JC Gumbart (Sat Jun 29 2013 - 07:55:40 CDT)
  - RE: ureybradley and impropers in ffTK Darre Castell, Leonardo (Sat Jun 29 2013 - 08:01:38 CDT)
Change in color of residue rama david (Fri Jun 28 2013 - 09:59:29 CDT)
- Re: Change in color of residue Ramin Ekhteiari (Fri Jun 28 2013 - 13:09:32 CDT)
calculating distance between center of mass of two set of residues Peterson J (Thu Jun 27 2013 - 13:06:44 CDT)
- Re: calculating distance between center of mass of two set of residues Josh Vermaas (Thu Jun 27 2013 - 14:29:11 CDT)
Visualise variable atoms amit kunte (Thu Jun 27 2013 - 01:34:09 CDT)
- Re: Visualise variable atoms Axel Kohlmeyer (Thu Jun 27 2013 - 02:52:57 CDT)
variable atoms visualization amit kunte (Wed Jun 26 2013 - 23:28:17 CDT)
- Re: variable atoms visualization Axel Kohlmeyer (Thu Jun 27 2013 - 01:15:49 CDT)
can't read "::vmd_pick_event": no such variable Alex Richards (Wed Jun 26 2013 - 11:13:33 CDT)
Problems with MDFF tutorial Catalin Buiu (Tue Jun 25 2013 - 16:27:02 CDT)
- Re: Problems with MDFF tutorial Ryan McGreevy (Wed Jun 26 2013 - 11:00:40 CDT)
  - Re: Problems with MDFF tutorial Catalin Buiu (Wed Jun 26 2013 - 11:28:46 CDT)
    - Re: Problems with MDFF tutorial Ryan McGreevy (Thu Jun 27 2013 - 12:41:52 CDT)
    - Re: Problems with MDFF tutorial Catalin Buiu (Thu Jun 27 2013 - 12:44:36 CDT)
load speed of dcds Thomas C. Bishop (Tue Jun 25 2013 - 12:22:23 CDT)
- RE: load speed of dcds Jonathan Phillips (Tue Jun 25 2013 - 15:09:53 CDT)
  - Re: load speed of dcds Thomas C. Bishop (Tue Jun 25 2013 - 17:09:01 CDT)
    - Re: load speed of dcds Josh Vermaas (Tue Jun 25 2013 - 21:11:01 CDT)
    - RE: load speed of dcds Jonathan Phillips (Wed Jun 26 2013 - 06:45:28 CDT)
  - Re: load speed of dcds John Stone (Wed Jun 26 2013 - 09:26:04 CDT)
    - Re: load speed of dcds Thomas C. Bishop (Wed Jun 26 2013 - 11:19:15 CDT)
    - Re: load speed of dcds John Stone (Wed Jun 26 2013 - 11:45:46 CDT)
question concerning measure gofr Philippe Bopp (Tue Jun 25 2013 - 11:14:51 CDT)
- Re: question concerning measure gofr Axel Kohlmeyer (Tue Jun 25 2013 - 12:01:22 CDT)
Desmond Trajectory Alignment for Timeline Analysis Pedley, Anthony M (Tue Jun 25 2013 - 09:15:33 CDT)
How to save 2 gro file in 1 gro file? leila karami (Sun Jun 23 2013 - 09:34:10 CDT)
- Re: How to save 2 gro file in 1 gro file? Axel Kohlmeyer (Sun Jun 23 2013 - 12:22:58 CDT)
How to save 2 gro file in 1 gro file? leila karami (Sun Jun 23 2013 - 08:08:12 CDT)
- Re: How to save 2 gro file in 1 gro file? Axel Kohlmeyer (Sun Jun 23 2013 - 09:08:14 CDT)
Query regarding getting intial configuration of laponite clay!! Siddharth Subramanian (Sat Jun 22 2013 - 12:19:33 CDT)
Re: multiseq Ramin Ekhteiari (Fri Jun 21 2013 - 08:24:23 CDT)
multiseq Ramin Ekhteiari (Fri Jun 21 2013 - 03:13:06 CDT)
Fw: PSF not generating flavio seixas (Thu Jun 20 2013 - 11:25:52 CDT)
Basic question about improper Wenhao Liu (Tue Jun 18 2013 - 18:29:38 CDT)
fftk Opt. Charges Prof. Eddie (Tue Jun 18 2013 - 16:47:25 CDT)
- RE: fftk Opt. Charges Bennion, Brian (Tue Jun 18 2013 - 17:47:56 CDT)
  - Re: fftk Opt. Charges Prof. Eddie (Wed Jun 19 2013 - 08:50:47 CDT)
PSF not generating Nathan Li (Tue Jun 18 2013 - 12:53:27 CDT)
- Re: PSF not generating flavio seixas (Tue Jun 18 2013 - 17:58:17 CDT)
AutoIMD with Periodic Boundary Conditions Robert Johnson (Tue Jun 18 2013 - 11:43:13 CDT)
Atom Selection & List Generation Alex Richards (Mon Jun 17 2013 - 16:32:12 CDT)
- Re: Atom Selection & List Generation Josh Vermaas (Mon Jun 17 2013 - 18:37:43 CDT)
  - Re: Atom Selection & List Generation Alex Richards (Tue Jun 18 2013 - 15:31:54 CDT)
Generating .top and .crd using VMD manikanthan bhavaraju (Mon Jun 17 2013 - 10:18:25 CDT)
periodic boxes Jonathan Phillips (Fri Jun 14 2013 - 16:53:33 CDT)
graphics: not enough parameters Chavent Mathieu (Fri Jun 14 2013 - 12:56:24 CDT)
- Re: graphics: not enough parameters Axel Kohlmeyer (Sat Jun 15 2013 - 16:39:42 CDT)
namdenergy non-bonded question Prof. Eddie (Fri Jun 14 2013 - 11:45:14 CDT)
How to read the output of ParseFEP Ramie (Fri Jun 14 2013 - 07:58:04 CDT)
Query regarding merging structures in vmd!! Siddharth Subramanian (Fri Jun 14 2013 - 04:52:55 CDT)
variable particle size Solen (Thu Jun 13 2013 - 23:01:19 CDT)
- Re: variable particle size Axel Kohlmeyer (Fri Jun 14 2013 - 00:21:33 CDT)
  - Re: variable particle size Solen (Sat Jun 29 2013 - 09:57:20 CDT)
    - Re: variable particle size Axel Kohlmeyer (Sat Jun 29 2013 - 09:59:54 CDT)
- Re: variable particle size Olaf Lenz (Tue Jun 18 2013 - 01:55:17 CDT)
Problem with writepsf and CGenFF long atomtypes Alexandre Suman de Araujo (Thu Jun 13 2013 - 12:57:30 CDT)
- Re: Problem with writepsf and CGenFF long atomtypes John Stone (Thu Jun 13 2013 - 13:12:44 CDT)
  - Re: Problem with writepsf and CGenFF long atomtypes Alexandre Suman de Araujo (Thu Jun 13 2013 - 13:25:44 CDT)
    - Re: Problem with writepsf and CGenFF long atomtypes John Stone (Thu Jun 13 2013 - 13:28:15 CDT)
- Re: Problem with writepsf and CGenFF long atomtypes Josh Vermaas (Thu Jun 13 2013 - 14:16:46 CDT)
error: too many open files Ludovic (Wed Jun 12 2013 - 19:14:35 CDT)
- Re: error: too many open files John Stone (Wed Jun 12 2013 - 21:03:55 CDT)
  - Re: error: too many open files Ludovic (Tue Jun 18 2013 - 09:31:14 CDT)
- Re: error: too many open files Axel Kohlmeyer (Wed Jun 12 2013 - 21:22:53 CDT)
protein order parameter Thomas Schmidt (Wed Jun 12 2013 - 15:39:01 CDT)
(no subject) Thomas Schmidt (Wed Jun 12 2013 - 15:37:37 CDT)
Workshop on GPU Programming for Molecular Modeling, August 2-4, 2013, in Urbana, Illinois David Brandon (Wed Jun 12 2013 - 11:03:08 CDT)
Re: protein schematic representaton francesco oteri (Wed Jun 12 2013 - 09:24:32 CDT)
multiple vector in smd yp sun (Mon Jun 10 2013 - 22:34:44 CDT)
- Re: multiple vector in smd Axel Kohlmeyer (Mon Jun 10 2013 - 23:55:51 CDT)
protein schematic representaton francesco oteri (Mon Jun 10 2013 - 13:23:17 CDT)
- Fw: protein schematic representaton hamid mosaddeghi (Wed Jun 12 2013 - 04:29:22 CDT)
  - Re: Fw: protein schematic representaton Axel Kohlmeyer (Wed Jun 12 2013 - 05:33:17 CDT)
best method for showing metal nanoparticle and protein in vmd hamid mosaddeghi (Fri Jun 07 2013 - 04:24:15 CDT)
- Re: best method for showing metal nanoparticle and protein in vmd Axel Kohlmeyer (Sat Jun 08 2013 - 12:48:45 CDT)
charge exceed the range between Low bound and High bound in ffTK charge optimization Wenhao Liu (Thu Jun 06 2013 - 21:58:35 CDT)
- RE: charge exceed the range between Low bound and High bound in ffTK charge optimization JC Gumbart (Fri Jun 07 2013 - 07:40:49 CDT)
  - Re: charge exceed the range between Low bound and High bound in ffTK charge optimization Wenhao Liu (Fri Jun 07 2013 - 09:16:14 CDT)
  - Re: charge exceed the range between Low bound and High bound in ffTK charge optimization Mayne, Christopher G (Fri Jun 07 2013 - 09:29:16 CDT)
    - Re: charge exceed the range between Low bound and High bound in ffTK charge optimization Wenhao Liu (Fri Jun 07 2013 - 10:00:43 CDT)
Calculation of no. of turns, pitch in DNA Anurag Sharma (Wed Jun 05 2013 - 17:04:45 CDT)
- Calculation of no. of turns, pitch in DNA Anurag Sharma (Wed Jun 12 2013 - 13:49:04 CDT)
Dihedrals Ali Alizadeh (Wed Jun 05 2013 - 07:48:14 CDT)
- Re: Dihedrals Axel Kohlmeyer (Wed Jun 05 2013 - 09:03:00 CDT)
  - Re: Dihedrals Ali Alizadeh (Wed Jun 05 2013 - 09:28:19 CDT)
Change atom color dynamically. amit kunte (Wed Jun 05 2013 - 02:12:49 CDT)
- Re: Change atom color dynamically. Axel Kohlmeyer (Wed Jun 05 2013 - 03:14:02 CDT)
Compare "measure rgyr" to SAXS Martin, Erik W (Tue Jun 04 2013 - 14:37:28 CDT)
Re: molfracture force field Prof. Eddie (Tue Jun 04 2013 - 07:12:11 CDT)
- Re: molfracture force field Mayne, Christopher G (Tue Jun 04 2013 - 09:12:59 CDT)
  - Re: molfracture force field JC Gumbart (Tue Jun 04 2013 - 11:25:10 CDT)
Which Linux distribution works best with Quadro cards? Alexander Balaeff (Tue Jun 04 2013 - 01:39:26 CDT)
- Re: Which Linux distribution works best with Quadro cards? Joshua Anderson (Tue Jun 04 2013 - 06:40:06 CDT)
  - Re: Which Linux distribution works best with Quadro cards? John Hodrien (Tue Jun 04 2013 - 08:40:47 CDT)
Bond Labels - Issue with Rendering Peter Murphy (Mon Jun 03 2013 - 12:12:04 CDT)
Showing bonds created with"bond" command of LEaP Francesco Pietra (Mon Jun 03 2013 - 09:42:28 CDT)
Calculation of VAF using signalproc plugin Mingchao Wang (Mon Jun 03 2013 - 00:33:25 CDT)
- Re: Calculation of VAF using signalproc plugin Axel Kohlmeyer (Mon Jun 03 2013 - 03:16:35 CDT)
  - Re: Calculation of VAF using signalproc plugin Mingchao Wang (Tue Jun 04 2013 - 21:04:40 CDT)
    - Re: Calculation of VAF using signalproc plugin Axel Kohlmeyer (Wed Jun 05 2013 - 00:40:52 CDT)
not work "selection atoms" for trajectory of dl_poly hamid mosaddeghi (Sat Jun 01 2013 - 09:55:06 CDT)
- Re: not work "selection atoms" for trajectory of dl_poly Axel Kohlmeyer (Sat Jun 01 2013 - 11:05:38 CDT)
- Re: not work "selection atoms" for trajectory of dl_poly Salomon Turgman Cohen (Sun Jun 02 2013 - 18:51:48 CDT)
  - Fw: not work "selection atoms" for trajectory of dl_poly hamid mosaddeghi (Mon Jun 03 2013 - 00:07:38 CDT)
How to place the origin point at the position of an atom? WuChaofu (Fri May 31 2013 - 02:14:00 CDT)
- Re: How to place the origin point at the position of an atom? Axel Kohlmeyer (Fri May 31 2013 - 03:11:16 CDT)
save waters around ligand trajectory updated Laura Lopez Munoz (Fri May 31 2013 - 01:17:12 CDT)
What is revbonds in cgtools.tcl? WuChaofu (Thu May 30 2013 - 08:16:44 CDT)
- Re: What is revbonds in cgtools.tcl? Kirby Vandivort (Thu Jun 13 2013 - 09:24:54 CDT)
molfracture force field Prof. Eddie (Wed May 29 2013 - 15:32:57 CDT)
MDFF difficulties with mdff sim command Martin Jones (Wed May 29 2013 - 09:24:44 CDT)
- Re: MDFF difficulties with mdff sim command Ryan McGreevy (Wed May 29 2013 - 14:32:53 CDT)
autopsf Prof. Eddie (Tue May 28 2013 - 14:43:16 CDT)
- Re: autopsf Jiawei Xu (Tue May 28 2013 - 15:45:46 CDT)
  - Re: autopsf Prof. Eddie (Tue May 28 2013 - 16:27:32 CDT)
    - Re: autopsf Josh Vermaas (Wed May 29 2013 - 07:52:53 CDT)
    - Re: autopsf Prof. Eddie (Wed May 29 2013 - 08:56:48 CDT)
file format of VMD Reza Md. (Tue May 28 2013 - 09:19:19 CDT)
- Re: file format of VMD John Stone (Wed May 29 2013 - 09:13:27 CDT)
regarding FFTK surya narayanan chandrasekaran (Mon May 27 2013 - 11:02:39 CDT)
- RE: regarding FFTK Bennion, Brian (Tue May 28 2013 - 11:09:20 CDT)
- Re: regarding FFTK Mayne, Christopher G (Tue May 28 2013 - 12:13:33 CDT)
How to characterize and change the tacticity of polymer chain WuChaofu (Mon May 27 2013 - 04:44:12 CDT)
why does VMD load dcd file so slowly? yp sun (Sat May 25 2013 - 20:40:46 CDT)
- Re: why does VMD load dcd file so slowly? Axel Kohlmeyer (Sun May 26 2013 - 01:24:16 CDT)
  - å›žå¤ï¼š why does VMD load dcd file so slowly? yp sun (Sun May 26 2013 - 04:00:43 CDT)
VMD crashes on opening large cube files VandeVondele Joost (Sat May 25 2013 - 11:38:14 CDT)
- Re: VMD crashes on opening large cube files John Stone (Tue May 28 2013 - 09:36:26 CDT)
RE: MDFF difficulties with mdff sim command Martin Jones (Fri May 24 2013 - 14:02:50 CDT)
- Re: MDFF difficulties with mdff sim command Ryan McGreevy (Fri May 24 2013 - 14:37:23 CDT)
  - RE: MDFF difficulties with mdff sim command Martin Jones (Fri May 24 2013 - 14:57:25 CDT)
    - Re: MDFF difficulties with mdff sim command Ryan McGreevy (Fri May 24 2013 - 15:10:27 CDT)
    - RE: MDFF difficulties with mdff sim command Martin Jones (Fri May 24 2013 - 15:28:46 CDT)
MDFF difficulties with mdff sim command Martin Jones (Fri May 24 2013 - 12:55:05 CDT)
Remove overlapping solvent molecules Michele Formica (Thu May 23 2013 - 07:40:44 CDT)
- Re: Remove overlapping solvent molecules Axel Kohlmeyer (Thu May 23 2013 - 08:37:09 CDT)
starting vmd in current working directory Bennion, Brian (Wed May 22 2013 - 11:59:28 CDT)
- Re: starting vmd in current working directory John Stone (Wed May 22 2013 - 12:06:50 CDT)
Suggestions on parameterizing a ligand to simulate in NAMD Peterson J (Mon May 20 2013 - 13:03:57 CDT)
- RE: Suggestions on parameterizing a ligand to simulate in NAMD Bennion, Brian (Mon May 20 2013 - 14:15:26 CDT)
- Re: Suggestions on parameterizing a ligand to simulate in NAMD Jiawei Xu (Mon May 20 2013 - 14:11:50 CDT)
- Re: Suggestions on parameterizing a ligand to simulate in NAMD Mayne, Christopher G (Mon May 20 2013 - 14:32:42 CDT)
  - Re: namd-l: Re: Suggestions on parameterizing a ligand to simulate in NAMD Peterson J (Mon May 20 2013 - 23:48:48 CDT)
Obtain solvent-accessible surface vertices Filip Persson (Mon May 20 2013 - 10:47:47 CDT)
- Re: Obtain solvent-accessible surface vertices John Stone (Mon May 20 2013 - 13:26:25 CDT)
please remove me from the list Denis Davydov (Fri May 17 2013 - 04:40:56 CDT)
Formatting labels in script PaweÅ‚ KÄ™dzierski (Fri May 17 2013 - 04:17:59 CDT)
- Re: Formatting labels in script Axel Kohlmeyer (Fri May 17 2013 - 05:22:43 CDT)
  - Re: Formatting labels in script PaweÅ‚ KÄ™dzierski (Fri May 17 2013 - 09:03:40 CDT)
- Re: Formatting labels in script Jim Parker (Fri Aug 23 2013 - 06:02:26 CDT)
  - Re: Formatting labels in script Jim Parker (Fri Aug 23 2013 - 06:30:11 CDT)
dynamical network analysis on GROMACS trajectories Payman Pirzadeh (Thu May 16 2013 - 14:46:23 CDT)
building VMD with opnempi support Vlad Cojocaru (Thu May 16 2013 - 11:00:43 CDT)
- Re: building VMD with opnempi support John Stone (Thu May 16 2013 - 15:52:41 CDT)
error in merging two structures Anurag Sharma (Wed May 15 2013 - 18:38:58 CDT)
- error in merging two structures Anurag Sharma (Mon May 20 2013 - 12:38:18 CDT)
  - Re: error in merging two structures John Stone (Wed May 22 2013 - 10:24:02 CDT)
paratool and g09 Prof. Eddie (Wed May 15 2013 - 16:13:29 CDT)
- Re: paratool and g09 Mayne, Christopher G (Thu May 16 2013 - 09:21:57 CDT)
Error when compiling plugins: tcl.h not found Daniel LÃ©vesque (Tue May 14 2013 - 11:37:47 CDT)
- Re: Error when compiling plugins: tcl.h not found Axel Kohlmeyer (Tue May 14 2013 - 12:48:29 CDT)
- Re: Error when compiling plugins: tcl.h not found Josh Vermaas (Tue May 14 2013 - 12:38:42 CDT)
  - Re: Error when compiling plugins: tcl.h not found John Stone (Tue May 14 2013 - 13:09:19 CDT)
  - Re: Error when compiling plugins: tcl.h not found Daniel LÃ©vesque (Tue May 14 2013 - 13:51:46 CDT)
dynamic cross correlation map Prof. Eddie (Tue May 14 2013 - 11:12:26 CDT)
- RE: dynamic cross correlation map Mark Cunningham (Wed May 15 2013 - 10:58:17 CDT)
  - Re: dynamic cross correlation map Prof. Eddie (Thu May 16 2013 - 09:29:32 CDT)
visualizing dynamic charge Dave Schall (Mon May 13 2013 - 15:20:24 CDT)
- Re: visualizing dynamic charge Axel Kohlmeyer (Tue May 14 2013 - 02:38:00 CDT)
  - Re: visualizing dynamic charge Dave Schall (Tue May 14 2013 - 11:47:07 CDT)
    - Re: visualizing dynamic charge Axel Kohlmeyer (Tue May 14 2013 - 11:59:37 CDT)
    - Re: visualizing dynamic charge John Stone (Tue May 14 2013 - 13:11:16 CDT)
hide/display VMD graphics primitives Chavent Mathieu (Fri May 10 2013 - 12:09:52 CDT)
- Re: hide/display VMD graphics primitives Mayne, Christopher G (Fri May 10 2013 - 14:39:14 CDT)
  - Re: hide/display VMD graphics primitives Chavent Mathieu (Sun May 12 2013 - 08:50:49 CDT)
molinfo top get filename, dialogue vs. "mol new" Christopher MacDermaid (Thu May 09 2013 - 08:30:13 CDT)
- Re: molinfo top get filename, dialogue vs. "mol new" Axel Kohlmeyer (Thu May 09 2013 - 09:21:27 CDT)
  - Re: molinfo top get filename, dialogue vs. "mol new" Christopher MacDermaid (Thu May 09 2013 - 10:32:35 CDT)
- Re: molinfo top get filename, dialogue vs. "mol new" Mayne, Christopher G (Thu May 09 2013 - 09:52:08 CDT)
  - Re: molinfo top get filename, dialogue vs. "mol new" Christopher MacDermaid (Thu May 09 2013 - 10:36:54 CDT)
convert pdb file from angstorm to nm units Nandigana, Vishal Venkata Raghave (Tue May 07 2013 - 22:47:24 CDT)
convert pdb file from angstorm to nm units Nandigana, Vishal Venkata Raghave (Tue May 07 2013 - 13:55:18 CDT)
- Re: convert pdb file from angstorm to nm units John Stone (Tue May 07 2013 - 14:38:47 CDT)
  - Re: convert pdb file from angstorm to nm units Josh Vermaas (Tue May 07 2013 - 17:26:52 CDT)
- Re: convert pdb file from angstorm to nm units Josh Vermaas (Tue May 07 2013 - 15:09:09 CDT)
  - RE: convert pdb file from angstorm to nm units Nandigana, Vishal Venkata Raghave (Wed May 08 2013 - 12:06:29 CDT)
    - Re: convert pdb file from angstorm to nm units John Stone (Thu May 09 2013 - 10:35:21 CDT)
ABF tutorial: Methane-Hydration water going -> Water in gas phase? Maximilian Ebert (Fri May 03 2013 - 21:13:38 CDT)
- RE: ABF tutorial: Methane-Hydration water going -> Water in gas phase? JC Gumbart (Sat May 04 2013 - 00:29:25 CDT)
  - Re: ABF tutorial: Methane-Hydration water going -> Water in gas phase? Maximilian Ebert (Sat May 04 2013 - 08:32:23 CDT)
    - RE: ABF tutorial: Methane-Hydration water going -> Water in gas phase? JC Gumbart (Sat May 04 2013 - 08:36:41 CDT)
problem/NVIDIA 3D vision/VMD/Windows 7 Pro 64-bit/GeForce GTX680 Ming-Tsung Lee (Fri May 03 2013 - 20:59:37 CDT)
- Re: problem/NVIDIA 3D vision/VMD/Windows 7 Pro 64-bit/GeForce GTX680 John Stone (Wed May 22 2013 - 10:47:15 CDT)
  - Re: problem/NVIDIA 3D vision/VMD/Windows 7 Pro 64-bit/GeForce GTX680 Ming-Tsung Lee (Wed May 22 2013 - 11:11:57 CDT)
    - Re: problem/NVIDIA 3D vision/VMD/Windows 7 Pro 64-bit/GeForce GTX680 John Stone (Wed May 22 2013 - 11:22:03 CDT)
ABF tutorial: Methane-Hydration water going -> Water in gas phase? Maximilian Ebert (Fri May 03 2013 - 20:49:33 CDT)
Question about FFTK charge optimization procedure to CGENFF modeling Alexandre Suman de Araujo (Fri May 03 2013 - 15:40:41 CDT)
- Re: Question about FFTK charge optimization procedure to CGENFF modeling Mayne, Christopher G (Sat May 04 2013 - 09:37:11 CDT)
  - Re: Question about FFTK charge optimization procedure to CGENFF modeling Alexandre Suman de Araujo (Tue May 14 2013 - 08:12:10 CDT)
Re: Fwd: VMD Crash with Ubuntu 12.04 LTS and NVidia 310.44 driver. DENILSON FERREIRA DE OLIVEIRA (Fri May 03 2013 - 13:36:24 CDT)
- Re: Fwd: VMD Crash with Ubuntu 12.04 LTS and NVidia 310.44 driver. Francesco Pietra (Sat May 04 2013 - 01:37:42 CDT)
- Re: Fwd: VMD Crash with Ubuntu 12.04 LTS and NVidia 310.44 driver. Aric Newton (Sun May 05 2013 - 10:32:15 CDT)
  - Re: Fwd: VMD Crash with Ubuntu 12.04 LTS and NVidia 310.44 driver. John Stone (Tue May 07 2013 - 08:19:15 CDT)
Step 6 ffTK ligand calculation. aravind chandrasekaran (Thu May 02 2013 - 10:26:06 CDT)
- Re: Step 6 ffTK ligand calculation. Mayne, Christopher G (Thu May 02 2013 - 13:51:37 CDT)
  - Re: Step 6 ffTK ligand calculation. Mayne, Christopher G (Fri May 03 2013 - 09:04:09 CDT)
  - Re: Step 6 ffTK ligand calculation. Mayne, Christopher G (Sat May 04 2013 - 08:16:36 CDT)
    - Re: Step 6 ffTK ligand calculation. aravind chandrasekaran (Mon May 06 2013 - 00:31:09 CDT)
    - Re: Step 6 ffTK ligand calculation. Mayne, Christopher G (Mon May 06 2013 - 07:57:36 CDT)
VMD Crash with Ubuntu 12.04 LTS and NVidia 310.44 driver. Aric Newton (Thu May 02 2013 - 06:17:49 CDT)
Unable to find bond parameters for NOH P4 (ATOMS 292 294) Ð¤¸»¹ó (Thu May 02 2013 - 04:14:35 CDT)
- Re: Unable to find bond parameters for NOH P4 (ATOMS 292 294) Aaron Oakley (Thu May 02 2013 - 18:50:39 CDT)
how do I show spheres that are rotating around their centre Das, Debasish (Wed May 01 2013 - 17:33:38 CDT)
- Re: how do I show spheres that are rotating around their centre John Stone (Fri May 03 2013 - 16:10:31 CDT)
cannot ionize coarse-grained system Ð¤¸»¹ó (Wed May 01 2013 - 14:25:37 CDT)
- Re: cannot ionize coarse-grained system Josh Vermaas (Wed May 01 2013 - 15:40:40 CDT)
  - Re: cannot ionize coarse-grained system John Stone (Fri May 03 2013 - 15:45:09 CDT)
Tiled display setup John Hodrien (Tue Apr 30 2013 - 03:08:06 CDT)
- Re: Tiled display setup John Stone (Fri May 03 2013 - 15:43:02 CDT)
OpenGL problem Avisek Das (Mon Apr 29 2013 - 11:04:36 CDT)
- Re: OpenGL problem John Stone (Fri May 03 2013 - 17:24:53 CDT)
FFTK - Step -3 missing log file. aravind chandrasekaran (Sun Apr 28 2013 - 10:54:59 CDT)
- Re: FFTK - Step -3 missing log file. Mayne, Christopher G (Sun Apr 28 2013 - 11:47:16 CDT)
water in crystal yp sun (Sat Apr 27 2013 - 19:43:24 CDT)
How to get improper dihedral list Wenhao Liu (Sat Apr 27 2013 - 15:39:56 CDT)
- Re: How to get improper dihedral list Mayne, Christopher G (Sat Apr 27 2013 - 20:34:13 CDT)
  - Re: How to get improper dihedral list Wenhao Liu (Sat Apr 27 2013 - 21:14:03 CDT)
"transparent" material not working Martin, Erik W (Fri Apr 26 2013 - 15:57:12 CDT)
- Re: "transparent" material not working John Stone (Sun Apr 28 2013 - 15:28:16 CDT)
  - Re: "transparent" material not working sollebac (Wed May 01 2013 - 13:19:30 CDT)
    - Re: "transparent" material not working John Stone (Thu May 02 2013 - 00:49:01 CDT)
number of atoms changes on loading .cms file Nidhi Jatana (Fri Apr 26 2013 - 02:04:09 CDT)
- Re: number of atoms changes on loading .cms file Axel Kohlmeyer (Fri Apr 26 2013 - 02:50:10 CDT)
Detecting Custom "h-bonds" Salomon Turgman Cohen (Thu Apr 25 2013 - 13:13:57 CDT)
- Re: Detecting Custom "h-bonds" Josh Vermaas (Thu Apr 25 2013 - 14:51:15 CDT)
  - Re: Detecting Custom "h-bonds" Salomon Turgman Cohen (Thu Apr 25 2013 - 17:15:20 CDT)
(no subject) Lorenzo Gontrani (Wed Apr 24 2013 - 16:51:59 CDT)
- Re: Mayne, Christopher G (Wed Apr 24 2013 - 18:02:10 CDT)
  - Re: JÃ©rÃ´me HÃ©nin (Thu Apr 25 2013 - 04:29:27 CDT)
criteria for hydrogen bonds. Kristine Manibog (Tue Apr 23 2013 - 19:39:17 CDT)
VMD: Mutator --> ASP to ASN problems Peter Murphy (Tue Apr 23 2013 - 13:40:57 CDT)
- Re: VMD: Mutator --> ASP to ASN problems Ajasja LjubetiÄ (Tue Apr 23 2013 - 14:29:06 CDT)
  - Re: VMD: Mutator --> ASP to ASN problems Ajasja LjubetiÄ (Tue Apr 23 2013 - 16:22:47 CDT)
- Re: VMD: Mutator --> ASP to ASN problems Peter Murphy (Tue Apr 23 2013 - 13:30:46 CDT)
Re: dock LW (Tue Apr 23 2013 - 03:40:47 CDT)
- Re: Re: dock Axel Kohlmeyer (Tue Apr 23 2013 - 04:22:26 CDT)
problem in saving the output Sindrila Dutta Banik (Tue Apr 23 2013 - 02:22:13 CDT)
- Re: problem in saving the output Axel Kohlmeyer (Tue Apr 23 2013 - 03:17:05 CDT)
mol options first and last Andrew Petersen (Mon Apr 22 2013 - 13:59:06 CDT)
- Re: mol options first and last Axel Kohlmeyer (Mon Apr 22 2013 - 14:44:47 CDT)
problem of pbc command Albert (Mon Apr 22 2013 - 01:39:37 CDT)
- Re: problem of pbc command Olaf Lenz (Mon Apr 22 2013 - 02:40:32 CDT)
- Re: problem of pbc command Axel Kohlmeyer (Mon Apr 22 2013 - 02:48:33 CDT)
- Re: problem of pbc command John Stone (Mon Apr 22 2013 - 02:29:26 CDT)
  - Re: problem of pbc command Albert (Mon Apr 22 2013 - 02:34:36 CDT)
how to calculate binding free energy and contribution of individual residue? yp sun (Sun Apr 21 2013 - 21:40:19 CDT)
- Re: how to calculate binding free energy and contribution of individual residue? Axel Kohlmeyer (Mon Apr 22 2013 - 03:35:20 CDT)
HEME acting unplanar Yarrow Madrona (Sun Apr 21 2013 - 17:49:21 CDT)
- Re: HEME acting unplanar Axel Kohlmeyer (Mon Apr 22 2013 - 04:48:09 CDT)
  - Re: HEME acting unplanar Yarrow Madrona (Mon Apr 22 2013 - 14:10:18 CDT)
    - Re: HEME acting unplanar PaweÅ‚ KÄ™dzierski (Tue Apr 23 2013 - 03:13:08 CDT)
how to write pbc option in python? Albert (Sun Apr 21 2013 - 11:50:19 CDT)
- Re: how to write pbc option in python? Olaf Lenz (Mon Apr 22 2013 - 02:00:37 CDT)
  - Re: how to write pbc option in python? Axel Kohlmeyer (Mon Apr 22 2013 - 02:50:40 CDT)
    - Re: how to write pbc option in python? Caio S. Souza (Mon Apr 22 2013 - 10:03:32 CDT)
ellipsoidal particles farrokh yousefi (Sun Apr 21 2013 - 10:33:18 CDT)
- Re: ellipsoidal particles Olaf Lenz (Mon Apr 22 2013 - 01:44:15 CDT)
  - Re: ellipsoidal particles farrokh yousefi (Mon Apr 22 2013 - 02:28:15 CDT)
  - Re: ellipsoidal particles Axel Kohlmeyer (Mon Apr 22 2013 - 02:42:08 CDT)
(no subject) Rob (Sun Apr 21 2013 - 06:10:17 CDT)
(no subject) Ganesh Shahane (Sun Apr 21 2013 - 02:10:12 CDT)
- Re: Jeffrey Potoff (Sun Apr 21 2013 - 13:24:20 CDT)
VMD crashes KDE at startup Felix Rausch (Fri Apr 19 2013 - 06:41:40 CDT)
- Re: VMD crashes KDE at startup denilson_at_dqi.ufla.br (Fri Apr 19 2013 - 09:27:08 CDT)
  - Re: VMD crashes KDE at startup John Stone (Fri Apr 19 2013 - 10:57:29 CDT)
    - Re: VMD crashes KDE at startup denilson_at_dqi.ufla.br (Fri Apr 19 2013 - 11:48:56 CDT)
  - Re: VMD crashes KDE at startup denilson_at_dqi.ufla.br (Fri Apr 19 2013 - 14:17:48 CDT)
pdb -arge magnitude coordinates Mohan maruthi sena (Fri Apr 19 2013 - 00:34:56 CDT)
- Re: pdb -arge magnitude coordinates Axel Kohlmeyer (Sat Apr 20 2013 - 12:57:38 CDT)
how vmd return actual vector for given atom Steven Neumann (Thu Apr 18 2013 - 10:36:50 CDT)
- Re: how vmd return actual vector for given atom Axel Kohlmeyer (Thu Apr 18 2013 - 11:47:28 CDT)
  - Re: how vmd return actual vector for given atom Steven Neumann (Tue Apr 23 2013 - 06:43:25 CDT)
    - Re: how vmd return actual vector for given atom Josh Vermaas (Tue Apr 23 2013 - 10:21:03 CDT)
Computing the transformation_matrix for best fit alignment of structures LW (Wed Apr 17 2013 - 22:54:18 CDT)
- Re: Computing the transformation_matrix for best fit alignment of structures John Stone (Thu Apr 18 2013 - 01:22:21 CDT)
  - Re: Computing the transformation_matrix for best fit alignment of structures LW (Thu Apr 18 2013 - 02:22:48 CDT)
No bonds in the generated psf file Anurag Sharma (Wed Apr 17 2013 - 14:54:35 CDT)
- Re: No bonds in the generated psf file Josh Vermaas (Wed Apr 17 2013 - 17:34:14 CDT)
  - Re: No bonds in the generated psf file Anurag Sharma (Wed Apr 17 2013 - 17:52:16 CDT)
FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE toppar_water_ions.str LINE=*set nat ?NATC* Research Jubilant (Wed Apr 17 2013 - 12:51:08 CDT)
- Re: FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE toppar_water_ions.str LINE=*set nat ?NATC* Mayne, Christopher G (Wed Apr 17 2013 - 14:11:45 CDT)
- Re: FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE toppar_water_ions.str LINE=*set nat ?NATC* Jeffrey Potoff (Wed Apr 17 2013 - 15:16:06 CDT)
  - Re: FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE toppar_water_ions.str LINE=*set nat ?NATC* Research Jubilant (Wed Apr 17 2013 - 16:54:08 CDT)
command line rep creation Martin, Erik W (Wed Apr 17 2013 - 11:14:26 CDT)
- Re: command line rep creation Salomon Turgman Cohen (Wed Apr 17 2013 - 12:43:08 CDT)
SASA Algorithm? Esra Bozkurt (Wed Apr 17 2013 - 11:04:24 CDT)
- Re: SASA Algorithm? John Stone (Wed May 22 2013 - 11:08:40 CDT)
build unit cells and supercells for VASP §õ¤å¤Z (Wed Apr 17 2013 - 10:03:30 CDT)
Is it necessary to set up more than 1 hydrogen bonding for one Acceptor in Water Int. in ffTK Wenhao Liu (Wed Apr 17 2013 - 01:53:12 CDT)
- Re: Is it necessary to set up more than 1 hydrogen bonding for one Acceptor in Water Int. in ffTK Mayne, Christopher G (Wed Apr 17 2013 - 08:00:26 CDT)
  - Re: Is it necessary to set up more than 1 hydrogen bonding for one Acceptor in Water Int. in ffTK Wenhao Liu (Wed Apr 17 2013 - 09:17:23 CDT)
    - Re: Is it necessary to set up more than 1 hydrogen bonding for one Acceptor in Water Int. in ffTK Mayne, Christopher G (Wed Apr 17 2013 - 09:52:43 CDT)
  - Re: Is it necessary to set up more than 1 hydrogen bonding for one Acceptor in Water Int. in ffTK Mayne, Christopher G (Wed Apr 17 2013 - 12:26:35 CDT)
VMD water box vs. CHARMM Yarrow Madrona (Tue Apr 16 2013 - 18:21:20 CDT)
- Re: VMD water box vs. CHARMM Yarrow Madrona (Wed Apr 17 2013 - 08:56:54 CDT)
Save trr using command line Steven Neumann (Tue Apr 16 2013 - 05:31:18 CDT)
problem about displaying hbond in periodic box yi (Tue Apr 16 2013 - 04:22:06 CDT)
- Re: problem about displaying hbond in periodic box Axel Kohlmeyer (Tue Apr 16 2013 - 04:41:53 CDT)
fftk - Opt-charges Carolina Penhavel de souza (Mon Apr 15 2013 - 09:40:26 CDT)
- Re: fftk - Opt-charges Mayne, Christopher G (Mon Apr 15 2013 - 11:54:54 CDT)
Mouse-Add/Remove Bonds DanLiu (Mon Apr 15 2013 - 07:04:24 CDT)
- Re: Mouse-Add/Remove Bonds John Stone (Mon Apr 15 2013 - 10:11:28 CDT)
  - Re: Mouse-Add/Remove Bonds DanLiu (Mon Apr 15 2013 - 11:32:58 CDT)
Improper parameters for CNT Anurag Sharma (Sun Apr 14 2013 - 16:30:59 CDT)
- Re: Improper parameters for CNT Josh Vermaas (Sun Apr 14 2013 - 17:38:37 CDT)
  - Re: Improper parameters for CNT Anurag Sharma (Sun Apr 14 2013 - 18:20:09 CDT)
- Re: Improper parameters for CNT Axel Kohlmeyer (Mon Apr 15 2013 - 03:17:05 CDT)
VMD, Paratool ³Âº½Ñà (Fri Apr 12 2013 - 15:40:20 CDT)
- RE: VMD, Paratool JC Gumbart (Sat Apr 13 2013 - 08:08:17 CDT)
average structure generation from trajectory Sindrila Dutta Banik (Thu Apr 11 2013 - 02:00:10 CDT)
- Re: average structure generation from trajectory Axel Kohlmeyer (Thu Apr 11 2013 - 03:16:30 CDT)
put the water box in a grid and traverse for the atoms in each grid Gurunath Katagi (Thu Apr 11 2013 - 01:53:45 CDT)
- Re: put the water box in a grid and traverse for the atoms in each grid Axel Kohlmeyer (Thu Apr 11 2013 - 03:20:26 CDT)
parameters for PE100 chain? kerexen_at_gmail.com (Wed Apr 10 2013 - 10:41:22 CDT)
- RE: parameters for PE100 chain? Bennion, Brian (Wed Apr 10 2013 - 11:56:31 CDT)
- Re: parameters for PE100 chain? Mayne, Christopher G (Wed Apr 10 2013 - 12:36:23 CDT)
Placing a peptide between two points Mohan maruthi sena (Wed Apr 10 2013 - 02:47:31 CDT)
- Re: Placing a peptide between two points Axel Kohlmeyer (Thu Apr 11 2013 - 00:41:14 CDT)
  - Re: Placing a peptide between two points Mohan maruthi sena (Fri Apr 12 2013 - 10:48:44 CDT)
fftk source code Francesco Pietra (Wed Apr 10 2013 - 01:05:13 CDT)
- Re: fftk source code Axel Kohlmeyer (Wed Apr 10 2013 - 03:08:35 CDT)
- Re: fftk source code Mayne, Christopher G (Wed Apr 10 2013 - 13:14:50 CDT)
is there a way to measure the long axis of a protein or angle between domains in VMD Kristine Manibog (Wed Apr 10 2013 - 00:54:46 CDT)
- Re: is there a way to measure the long axis of a protein or angle between domains in VMD Axel Kohlmeyer (Wed Apr 10 2013 - 03:35:46 CDT)
Writing povray files from a VMD trajectory Gordon S Freeman (Tue Apr 09 2013 - 14:32:07 CDT)
- Re: Writing povray files from a VMD trajectory John Stone (Tue Apr 09 2013 - 14:56:55 CDT)
  - Re: Writing povray files from a VMD trajectory Axel Kohlmeyer (Tue Apr 09 2013 - 15:16:47 CDT)
Re: how to convert dcd to pdbs in command line Yarrow Madrona (Mon Apr 08 2013 - 18:42:49 CDT)
- RE: how to convert dcd to pdbs in command line peter.schmidtke_at_fr.netgrs.com (Tue Apr 09 2013 - 01:12:20 CDT)
  - Re: how to convert dcd to pdbs in command line Josh Vermaas (Tue Apr 09 2013 - 09:25:07 CDT)
- Re: how to convert dcd to pdbs in command line Anthony Cruz Balberdi (Tue Apr 09 2013 - 10:00:24 CDT)
Disable autobonds for LAMMPS trajectory file John Michael Alex Grime (Mon Apr 08 2013 - 17:26:12 CDT)
Merge Protein/Small Molecule psf/pdb Zachary E Tibbs (Mon Apr 08 2013 - 16:54:52 CDT)
- Re: Merge Protein/Small Molecule psf/pdb Josh Vermaas (Mon Apr 08 2013 - 18:18:59 CDT)
Concatenate translated pdb's in to one pdb file- Writepdb is giving error Mohan maruthi sena (Mon Apr 08 2013 - 06:27:15 CDT)
moving center of protien to another new center x,y,z Mohan maruthi sena (Sun Apr 07 2013 - 10:31:03 CDT)
- Re: moving center of protien to another new center x,y,z Axel Kohlmeyer (Sun Apr 07 2013 - 11:17:13 CDT)
Moving center of protein to another center x,y,z Mohan maruthi sena (Sun Apr 07 2013 - 10:28:52 CDT)
how to visualize water movement over trajectory Yarrow Madrona (Sat Apr 06 2013 - 20:46:00 CDT)
- Re: how to visualize water movement over trajectory amin_at_imtech.res.in (Sun Apr 07 2013 - 02:12:49 CDT)
- Re: how to visualize water movement over trajectory PaweÅ‚ KÄ™dzierski (Sun Apr 07 2013 - 10:30:22 CDT)
  - Re: how to visualize water movement over trajectory Yarrow Madrona (Sun Apr 07 2013 - 13:27:04 CDT)
Kshatresh Dutta, let's connect on LinkedIn shiyong liu (Sat Apr 06 2013 - 00:06:13 CDT)
Solvate with a define number of water molecule Yann Fichou (Thu Apr 04 2013 - 12:54:22 CDT)
- Re: Solvate with a define number of water molecule Pawel Kedzierski (Fri Apr 05 2013 - 05:32:38 CDT)
complex buried area Felipe Merino (Wed Apr 03 2013 - 11:07:38 CDT)
- Re: complex buried area Josh Vermaas (Wed Apr 03 2013 - 12:58:51 CDT)
fftk - Opt. Torsion Carolina Penhavel de souza (Tue Apr 02 2013 - 17:53:54 CDT)
Quick wrapping JÃ©rÃ´me HÃ©nin (Tue Apr 02 2013 - 10:05:11 CDT)
- Re: Quick wrapping John Stone (Wed Apr 03 2013 - 16:02:29 CDT)
  - Re: Quick wrapping Thomas C. Bishop (Thu Apr 04 2013 - 07:37:44 CDT)
    - Re: Quick wrapping JÃ©rÃ´me HÃ©nin (Thu Apr 04 2013 - 08:31:49 CDT)
How to build a coiled alpha-helix shixin yang (Tue Apr 02 2013 - 09:23:44 CDT)
- Re: How to build a coiled alpha-helix Christopher MacDermaid (Tue Apr 02 2013 - 10:18:44 CDT)
generate nanotube other than CNT Sundararajan Natarajan (Tue Apr 02 2013 - 06:26:43 CDT)
- Re: generate nanotube other than CNT Axel Kohlmeyer (Tue Apr 02 2013 - 07:20:55 CDT)
  - Re: generate nanotube other than CNT Sundararajan Natarajan (Tue Apr 02 2013 - 14:06:48 CDT)
Issue in Cal. Bonded and Scan Torsion in fftk Win Liu (Mon Apr 01 2013 - 22:11:35 CDT)
- Re: Issue in Cal. Bonded and Scan Torsion in fftk JC Gumbart (Mon Apr 01 2013 - 22:51:27 CDT)
  - Re: Issue in Cal. Bonded and Scan Torsion in fftk Win Liu (Mon Apr 01 2013 - 23:23:15 CDT)
  - Re: Issue in Cal. Bonded and Scan Torsion in fftk John Stone (Tue Apr 09 2013 - 10:28:43 CDT)
Exported POSCAR does not match original Steve Jensen (Mon Apr 01 2013 - 17:12:37 CDT)
CGTools with pdb and top files WuChaofu (Mon Apr 01 2013 - 02:55:13 CDT)
- Re: CGTools with pdb and top files Dong Luo (Mon Apr 01 2013 - 10:39:56 CDT)
  - RE: CGTools with pdb and top files WuChaofu (Mon Apr 01 2013 - 17:52:08 CDT)
    - Re: CGTools with pdb and top files Dong Luo (Tue Apr 02 2013 - 11:29:46 CDT)
  - RE: CGTools with pdb and top files WuChaofu (Mon Apr 01 2013 - 23:59:51 CDT)
    - Re: CGTools with pdb and top files Kirby Vandivort (Tue Apr 02 2013 - 16:36:47 CDT)
Disable display resetview Crosskey, Mark William (Sun Mar 31 2013 - 22:38:11 CDT)
- Re: Disable display resetview John Stone (Wed Apr 03 2013 - 15:52:20 CDT)
  - Re: Disable display resetview Axel Kohlmeyer (Thu Apr 04 2013 - 02:17:46 CDT)
  - Re: Disable display resetview Ahmet Bakan (Thu Apr 04 2013 - 08:38:56 CDT)
FFTK bond optimization +idlepoll request Francesco Pietra (Sun Mar 31 2013 - 13:14:38 CDT)
- Re: FFTK bond optimization +idlepoll request JC Gumbart (Sun Mar 31 2013 - 14:13:41 CDT)
- Re: FFTK bond optimization +idlepoll request Josh Vermaas (Sun Mar 31 2013 - 14:14:42 CDT)
  - Re: FFTK bond optimization +idlepoll request Francesco Pietra (Mon Apr 01 2013 - 00:39:22 CDT)
    - RE: FFTK bond optimization +idlepoll request JC Gumbart (Mon Apr 01 2013 - 00:45:20 CDT)
Re: One same issue happened as before in fftk Win Liu (Sun Mar 31 2013 - 11:37:19 CDT)
- Re: One same issue happened as before in fftk Win Liu (Sun Mar 31 2013 - 14:24:18 CDT)
- Re: One same issue happened as before in fftk Win Liu (Sun Mar 31 2013 - 16:24:38 CDT)
- Re: One same issue happened as before in fftk Win Liu (Sun Mar 31 2013 - 19:59:03 CDT)
One same issue happened as before in fftk Win Liu (Sat Mar 30 2013 - 21:00:47 CDT)
bug in xsfplugin [patch included] Roberto Guerra (Sat Mar 30 2013 - 19:55:43 CDT)
- Re: bug in xsfplugin [patch included] John Stone (Wed Apr 03 2013 - 15:56:28 CDT)
  - Re: bug in xsfplugin [patch included] Axel Kohlmeyer (Thu Apr 11 2013 - 08:18:59 CDT)
transparent option sollebac (Fri Mar 29 2013 - 02:55:20 CDT)
- Re: transparent option John Stone (Fri Mar 29 2013 - 09:48:35 CDT)
  - Re: transparent option sollebac (Fri Mar 29 2013 - 12:23:14 CDT)
Re: vmd-I: remove water, protein from a dcd Axel Kohlmeyer (Thu Mar 28 2013 - 17:42:06 CDT)
- Re: vmd-I: remove water, protein from a dcd Yarrow Madrona (Thu Mar 28 2013 - 17:46:17 CDT)
  - Re: vmd-I: remove water, protein from a dcd John Stone (Thu Mar 28 2013 - 18:07:01 CDT)
How to strip atoms from dcd in command line Yarrow Madrona (Thu Mar 28 2013 - 16:37:45 CDT)
vmd-I: remove water, protein from a dcd Yarrow Madrona (Thu Mar 28 2013 - 15:45:02 CDT)
- Re: vmd-I: remove water, protein from a dcd Mert Gür (Thu Mar 28 2013 - 18:27:13 CDT)
  - Re: vmd-I: remove water, protein from a dcd Yarrow Madrona (Thu Mar 28 2013 - 19:36:48 CDT)
    - Re: vmd-I: remove water, protein from a dcd Mert Gür (Thu Mar 28 2013 - 20:50:23 CDT)
Error with NAMD Energy Anurag Sharma (Thu Mar 28 2013 - 15:25:11 CDT)
- Re: Error with NAMD Energy Josh Vermaas (Thu Mar 28 2013 - 16:57:04 CDT)
  - Re: Error with NAMD Energy Anurag Sharma (Thu Mar 28 2013 - 17:06:58 CDT)
    - Re: Error with NAMD Energy Josh Vermaas (Thu Mar 28 2013 - 17:19:01 CDT)
    - Re: Error with NAMD Energy JC Gumbart (Thu Mar 28 2013 - 18:27:44 CDT)
Is there a script to calculate root-mean-square thermal displacement Z.Y.Qiu (Thu Mar 28 2013 - 07:51:31 CDT)
FFTK Update Parameter File with Optimized Parameters - fails? PaweÅ‚ KÄ™dzierski (Thu Mar 28 2013 - 06:26:15 CDT)
- Re: FFTK Update Parameter File with Optimized Parameters - fails? Mayne, Christopher G (Thu Mar 28 2013 - 08:03:11 CDT)
  - Re: FFTK... and now gaussian version or QMtool problem PaweÅ‚ KÄ™dzierski (Thu Mar 28 2013 - 09:25:50 CDT)
Computational Electrostatics for Biological Applications (CEBA'13) July 01-03, 2013 - Genova - Italy Walter Rocchia (Wed Mar 27 2013 - 17:49:09 CDT)
Hotkeys don't work Aaron Taudt (Wed Mar 27 2013 - 03:50:41 CDT)
FFTK Atom types Francesco Pietra (Wed Mar 27 2013 - 02:21:13 CDT)
- Fwd: FFTK Atom types Francesco Pietra (Wed Mar 27 2013 - 03:34:30 CDT)
  - RE: FFTK Atom types JC Gumbart (Wed Mar 27 2013 - 08:00:01 CDT)
    - Re: FFTK Atom types Francesco Pietra (Wed Mar 27 2013 - 10:54:21 CDT)
  - Re: FFTK Atom types Mayne, Christopher G (Wed Mar 27 2013 - 08:24:31 CDT)
- Re: FFTK Atom types Mayne, Christopher G (Wed Mar 27 2013 - 08:06:05 CDT)
making the Orient plugin available in VMD Research Jubilant (Tue Mar 26 2013 - 17:30:20 CDT)
- Re: making the Orient plugin available in VMD John Stone (Fri Mar 29 2013 - 10:41:07 CDT)
Re: problems aligning two simillar structures Yarrow Madrona (Tue Mar 26 2013 - 14:19:48 CDT)
- Re: problems aligning two simillar structures John Stone (Tue Mar 26 2013 - 14:59:27 CDT)
- Re: problems aligning two simillar structures Yarrow Madrona (Tue Mar 26 2013 - 17:38:11 CDT)
  - Re: problems aligning two simillar structures John Stone (Tue Mar 26 2013 - 17:39:30 CDT)
problems aligning two simillar structures Yarrow Madrona (Tue Mar 26 2013 - 14:10:38 CDT)
- Re: problems aligning two simillar structures Josh Vermaas (Tue Mar 26 2013 - 15:16:46 CDT)
  - Re: problems aligning two simillar structures Yarrow Madrona (Tue Mar 26 2013 - 17:35:44 CDT)
- Re: problems aligning two simillar structures Ishwar Hosamani (Tue Mar 26 2013 - 16:21:43 CDT)
  - Re: problems aligning two simillar structures Boris Steipe (Tue Mar 26 2013 - 20:07:40 CDT)
FFTK plugin, Water Inter issue Francesco Pietra (Tue Mar 26 2013 - 12:15:00 CDT)
- Fwd: FFTK plugin, Water Inter issue Francesco Pietra (Tue Mar 26 2013 - 12:20:12 CDT)
  - Re: Fwd: FFTK plugin, Water Inter issue Josh Vermaas (Tue Mar 26 2013 - 13:48:40 CDT)
  - Re: Fwd: FFTK plugin, Water Inter issue Mayne, Christopher G (Tue Mar 26 2013 - 14:29:29 CDT)
How to generate average structure from trajectory using VMD Sindrila Dutta Banik (Tue Mar 26 2013 - 07:13:00 CDT)
- Re: How to generate average structure from trajectory using VMD Axel Kohlmeyer (Tue Mar 26 2013 - 08:06:15 CDT)
RE: Theory of backmapping of CGTools WuChaofu (Mon Mar 25 2013 - 19:04:21 CDT)
- Re: Theory of backmapping of CGTools John Stone (Tue Mar 26 2013 - 10:01:37 CDT)
Theory of backmapping of CGTools WuChaofu (Mon Mar 25 2013 - 07:06:07 CDT)
- Re: Theory of backmapping of CGTools Kirby Vandivort (Mon Mar 25 2013 - 15:37:55 CDT)
Tethering, or restraining, part of a molecule during MD playback John Keller (Mon Mar 25 2013 - 00:14:44 CDT)
- Re: Tethering, or restraining, part of a molecule during MD playback Axel Kohlmeyer (Mon Mar 25 2013 - 01:42:46 CDT)
Aminoacid selection Juan Antonio Raygoza Garay (Sun Mar 24 2013 - 16:51:02 CDT)
- Re: Aminoacid selection Mert Gür (Sun Mar 24 2013 - 17:54:42 CDT)
Morse potentail with charmm 27 Francesco Pietra (Sun Mar 24 2013 - 11:04:56 CDT)
Re: vmd-l digest V1 #2344 Amit Jaiswal (Sun Mar 24 2013 - 02:26:04 CDT)
- Re: hydrogen bonds John Stone (Mon Mar 25 2013 - 15:30:42 CDT)
Topo tools: can't use non-numeric string as operand of "+" Ivan Moncayo (Fri Mar 22 2013 - 08:36:15 CDT)
- Re: Topo tools: can't use non-numeric string as operand of "+" Axel Kohlmeyer (Fri Mar 22 2013 - 09:35:19 CDT)
protein secondary structure Juan Antonio Raygoza Garay (Thu Mar 21 2013 - 16:42:25 CDT)
- Re: protein secondary structure Jack Bulat (Thu Mar 21 2013 - 18:34:37 CDT)
  - Re: protein secondary structure Juan Antonio Raygoza Garay (Thu Mar 21 2013 - 19:54:27 CDT)
    - Re: protein secondary structure John Stone (Wed Mar 27 2013 - 14:54:02 CDT)
VMD 1.9.1 for 64-bit Windows Jernej Zidar (Tue Mar 19 2013 - 21:18:11 CDT)
- Re: VMD 1.9.1 for 64-bit Windows Ajasja LjubetiÄ (Wed Mar 20 2013 - 08:12:34 CDT)
  - Re: VMD 1.9.1 for 64-bit Windows John Stone (Thu Mar 21 2013 - 11:12:02 CDT)
phantom omni linux install Thomas C. Bishop (Tue Mar 19 2013 - 11:28:14 CDT)
- Re: phantom omni linux install: Phantom OMNI HOWTO Thomas C. Bishop (Wed Mar 20 2013 - 12:52:17 CDT)
  - Re: phantom omni linux install: Phantom OMNI HOWTO John Stone (Thu Mar 21 2013 - 11:00:46 CDT)
- Re: phantom omni linux install John Stone (Thu Mar 21 2013 - 10:57:58 CDT)
How to save a snapshot from the trajectory in amber restrt formate Sindrila Dutta Banik (Tue Mar 19 2013 - 02:47:39 CDT)
delete segments from dcd file yp sun (Tue Mar 19 2013 - 01:12:22 CDT)
- Re: delete segments from dcd file Axel Kohlmeyer (Tue Mar 19 2013 - 02:13:32 CDT)
gofr between center of mass of a functional group and solvent AnkiReddy katha (Tue Mar 19 2013 - 00:52:52 CDT)
- Re: gofr between center of mass of a functional group and solvent Yi Wang, PhD (Tue Mar 19 2013 - 01:37:54 CDT)
- Re: gofr between center of mass of a functional group and solvent Axel Kohlmeyer (Tue Mar 19 2013 - 02:17:00 CDT)
Amorphous Structure code or builder for non-programmer Rawan Al Nsour (Mon Mar 18 2013 - 15:20:05 CDT)
cp: cannot stat `../LINUXAMD64/vmd_LINUXAMD64': No such file or directory §õ¤å¤Z (Mon Mar 18 2013 - 09:16:44 CDT)
- Re: cp: cannot stat `../LINUXAMD64/vmd_LINUXAMD64': No such file or directory Axel Kohlmeyer (Mon Mar 18 2013 - 11:00:26 CDT)
atomselect within a loop Yohann Morille (Mon Mar 18 2013 - 06:17:15 CDT)
- Re: atomselect within a loop Josh Vermaas (Mon Mar 18 2013 - 13:29:23 CDT)
membrane protein embedding Ramin Ekhteiari (Wed Mar 13 2013 - 14:32:57 CDT)
Fit function Joseph Geraci (Wed Mar 13 2013 - 14:00:55 CDT)
using cionize Shyno Mathew (Tue Mar 12 2013 - 17:44:55 CDT)
Calculating rdfs without the VMD gui Salvador H-V (Tue Mar 12 2013 - 14:42:57 CDT)
- Re: Calculating rdfs without the VMD gui JÃ©rÃ´me HÃ©nin (Wed Mar 13 2013 - 02:36:42 CDT)
  - Re: Calculating rdfs without the VMD gui Salvador H-V (Wed Mar 13 2013 - 10:37:39 CDT)
problem related to generation of average structure from trajectory Sindrila Dutta Banik (Tue Mar 12 2013 - 14:06:20 CDT)
namdenergy: different results for single vs multiple frames Joshua Adelman (Tue Mar 12 2013 - 11:53:01 CDT)
- Re: namdenergy: different results for single vs multiple frames John Stone (Tue Mar 12 2013 - 14:29:02 CDT)
  - Re: namdenergy: different results for single vs multiple frames Joshua Adelman (Tue Mar 12 2013 - 14:42:25 CDT)
clear altloc field Martin, Erik W (Mon Mar 11 2013 - 16:49:47 CDT)
- color problem with tachyon Rejwan (Tue Mar 12 2013 - 10:36:40 CDT)
  - Re: color problem with tachyon John Stone (Tue Mar 12 2013 - 14:21:40 CDT)
- Re: clear altloc field John Stone (Tue Mar 12 2013 - 14:50:37 CDT)
dx file format Edward Lyman (Mon Mar 11 2013 - 16:41:46 CDT)
- Re: dx file format Edward Lyman (Mon Mar 11 2013 - 20:23:55 CDT)
  - Re: dx file format Axel Kohlmeyer (Mon Mar 11 2013 - 23:30:27 CDT)
    - Re: dx file format Edward Lyman (Tue Mar 12 2013 - 10:35:06 CDT)
~Tawhid Ezaz~ Tawhid Ezaz (Mon Mar 11 2013 - 14:57:41 CDT)
VMD-L Mailing List: Velocity autocorrelation and spatial distribution functions David Smith (Sun Mar 10 2013 - 14:33:17 CDT)
'Hands-on' Workshop on Computational Biophysics using VMD, NAMD, and ProDy, June 10-14, 2013 in Pittsburgh, PA David Brandon (Fri Mar 08 2013 - 12:22:27 CST)
Tachyon Renderer and Multiple Representations Salomon Turgman Cohen (Fri Mar 08 2013 - 09:27:21 CST)
(no subject) Jessica Padden (Thu Mar 07 2013 - 13:05:49 CST)
Installation Tolga Akiner (Thu Mar 07 2013 - 10:17:37 CST)
- Re: Installation John Stone (Thu Mar 07 2013 - 10:34:17 CST)
  - Re: Installation tolga.akiner (Fri Mar 08 2013 - 01:11:10 CST)
Slow display with nVidia GeForce 9400GT and 3xx drivers on Linux Bogdan Costescu (Tue Mar 05 2013 - 14:01:21 CST)
- Re: Slow display with nVidia GeForce 9400GT and 3xx drivers on Linux John Stone (Tue Mar 05 2013 - 15:27:41 CST)
  - Re: Slow display with nVidia GeForce 9400GT and 3xx drivers on Linux Bogdan Costescu (Fri Mar 08 2013 - 11:56:12 CST)
Radial pair distribution function Bharath K. Srikanth (Fri Mar 01 2013 - 03:05:58 CST)
- Re: Radial pair distribution function John Stone (Fri Mar 01 2013 - 09:25:13 CST)
- Re: Radial pair distribution function Josh Vermaas (Fri Mar 01 2013 - 09:49:31 CST)
- Re: Radial pair distribution function Axel Kohlmeyer (Fri Mar 01 2013 - 09:39:35 CST)
gofr with PBC Khanal Rabi (Thu Feb 28 2013 - 19:19:06 CST)
- Re: gofr with PBC Axel Kohlmeyer (Fri Mar 01 2013 - 09:34:00 CST)
Amorphous Structure code or builder Rawan Al Nsour (Thu Feb 28 2013 - 14:47:14 CST)
lammps charge data, adding bond Erik (Wed Feb 27 2013 - 19:50:07 CST)
About PLUMED with NAMD VMD Francesco Pietra (Wed Feb 27 2013 - 02:16:28 CST)
- Re: About PLUMED with NAMD VMD John Stone (Wed Feb 27 2013 - 10:10:48 CST)
  - Re: About PLUMED with NAMD VMD andrea spitaleri (Thu Feb 28 2013 - 02:46:34 CST)
Problem related to the save trajectory] Sindrila Dutta Banik (Wed Feb 27 2013 - 00:35:46 CST)
- Re: Problem related to the save trajectory] John Stone (Wed Feb 27 2013 - 10:07:46 CST)
definition of single word "protein" selection Bennion, Brian (Tue Feb 26 2013 - 17:00:39 CST)
- Re: definition of single word "protein" selection John Stone (Wed Feb 27 2013 - 10:18:49 CST)
  - RE: definition of single word "protein" selection Bennion, Brian (Wed Feb 27 2013 - 10:22:55 CST)
    - Re: definition of single word "protein" selection John Stone (Wed Feb 27 2013 - 10:28:52 CST)
Load a molecule in a function without output and slow Tcl gui console Maximilian Ebert (Tue Feb 26 2013 - 15:52:38 CST)
- Re: Load a molecule in a function without output and slow Tcl gui console John Stone (Tue Feb 26 2013 - 16:16:53 CST)
  - Re: Load a molecule in a function without output and slow Tcl gui console Maximilian Ebert (Tue Feb 26 2013 - 16:35:54 CST)
VMD crashes with malloc error Fahimeh Baftizadeh (Tue Feb 26 2013 - 12:42:59 CST)
- Re: VMD crashes with malloc error John Stone (Tue Feb 26 2013 - 13:12:52 CST)
  - Re: VMD crashes with malloc error Fahimeh Baftizadeh (Wed Feb 27 2013 - 10:19:02 CST)
ParseFEP plugin error Bernandie Jean (Tue Feb 26 2013 - 12:11:13 CST)
- Re: ParseFEP plugin error John Stone (Tue Feb 26 2013 - 13:14:18 CST)
Displaying Flat Cross-Sections Using Surface Representation Robert Johnson (Tue Feb 26 2013 - 11:59:28 CST)
- Re: Displaying Flat Cross-Sections Using Surface Representation Mayne, Christopher G (Tue Feb 26 2013 - 12:58:11 CST)
  - Re: Displaying Flat Cross-Sections Using Surface Representation John Stone (Tue Feb 26 2013 - 13:06:47 CST)
VMD Tutorial Help Nance, Sierra (Tue Feb 26 2013 - 09:07:41 CST)
- Re: VMD Tutorial Help John Stone (Tue Feb 26 2013 - 09:51:56 CST)
- Re: VMD Tutorial Help Joshua Adelman (Tue Feb 26 2013 - 10:48:28 CST)
trajectory conversion: dcd to trr to xtc manali_at_bioinfo.net.in (Tue Feb 26 2013 - 03:59:34 CST)
- Re: trajectory conversion: dcd to trr to xtc John Stone (Tue Feb 26 2013 - 08:30:15 CST)
Can I calculate B-factor using VMD Sindrila Dutta Banik (Tue Feb 26 2013 - 01:19:10 CST)
- Re: Can I calculate B-factor using VMD John Stone (Wed Feb 27 2013 - 10:22:00 CST)
  - Re: Can I calculate B-factor using VMD Maximilian Ebert (Wed Feb 27 2013 - 15:54:51 CST)
conversion from CHARMM27 psf to charmm36 with psfgen? Edward Lyman (Mon Feb 25 2013 - 08:37:12 CST)
gofr with periodic boundary condition in vasp trajectory Khanal Rabi (Sun Feb 24 2013 - 19:08:17 CST)
spectrum simulation francesco oteri (Sun Feb 24 2013 - 14:57:13 CST)
Different output of Saltbridge calculation between Saltbridge plugin and Timeline Priyabrata Panigrahi (Sat Feb 23 2013 - 02:21:14 CST)
measure fit rotation matrix convention Daniel Klose (Fri Feb 22 2013 - 10:16:23 CST)
- Re: measure fit rotation matrix convention John Stone (Mon Feb 25 2013 - 15:11:51 CST)
  - Re: measure fit rotation matrix convention Daniel Klose (Tue Feb 26 2013 - 04:43:23 CST)
setting up the grid for periodic coulomb volmap calc Edward Lyman (Fri Feb 22 2013 - 09:19:43 CST)
- Re: setting up the grid for periodic coulomb volmap calc John Stone (Mon Feb 25 2013 - 15:03:27 CST)
  - Re: setting up the grid for periodic coulomb volmap calc Edward Lyman (Mon Feb 25 2013 - 15:20:43 CST)
  - Re: setting up the grid for periodic coulomb volmap calc David Hardy (Mon Feb 25 2013 - 15:21:52 CST)
FPR monitor+glasses Marcel UJI (IMAP) (Fri Feb 22 2013 - 07:13:42 CST)
- Re: FPR monitor+glasses Axel Kohlmeyer (Fri Feb 22 2013 - 08:18:12 CST)
  - Re: FPR monitor+glasses John Stone (Mon Feb 25 2013 - 16:36:54 CST)
about visualization in VMD hamid mosaddeghi (Thu Feb 21 2013 - 05:32:12 CST)
- Re: about visualization in VMD Axel Kohlmeyer (Thu Feb 21 2013 - 06:41:45 CST)
Atom serial numbers in array format Marzieh Alishahi (Thu Feb 21 2013 - 03:26:33 CST)
- Re: Atom serial numbers in array format Axel Kohlmeyer (Thu Feb 21 2013 - 04:43:08 CST)
  - Re: Atom serial numbers in array format Marzieh Alishahi (Thu Feb 21 2013 - 05:30:58 CST)
    - Re: Atom serial numbers in array format Axel Kohlmeyer (Thu Feb 21 2013 - 06:38:45 CST)
edit pdb file hamid mosaddeghi (Wed Feb 20 2013 - 18:03:13 CST)
- Re: edit pdb file Josh Vermaas (Wed Feb 20 2013 - 19:27:45 CST)
How to save coordinates of periodic systems skolev_at_mnet.bg (Wed Feb 20 2013 - 08:31:15 CST)
- Re: How to save coordinates of periodic systems Axel Kohlmeyer (Wed Feb 20 2013 - 09:34:47 CST)
Measuring the order parameter Rawan Al Nsour (Tue Feb 19 2013 - 11:59:31 CST)
select by residue Jorgen Simonsen (Mon Feb 18 2013 - 11:45:55 CST)
- Re: select by residue Josh Vermaas (Mon Feb 18 2013 - 12:58:36 CST)
Surface won't close Sabine Reisser (Mon Feb 18 2013 - 09:45:38 CST)
- Re: Surface won't close John Stone (Mon Feb 18 2013 - 09:54:24 CST)
  - Re: Surface won't close Walter Rocchia (Mon Feb 18 2013 - 12:21:12 CST)
- Re: Surface won't close Axel Kohlmeyer (Mon Feb 18 2013 - 10:37:26 CST)
Spring script not working Davide Mercadante (Mon Feb 18 2013 - 07:26:13 CST)
- Re: Spring script not working Axel Kohlmeyer (Mon Feb 18 2013 - 08:57:09 CST)
- Re: Spring script not working Josh Vermaas (Mon Feb 18 2013 - 09:11:48 CST)
  - Re: Spring script not working Davide Mercadante (Mon Feb 18 2013 - 09:17:25 CST)
Problem related to the save trajectory Sindrila Dutta Banik (Mon Feb 18 2013 - 00:56:07 CST)
- Re: Problem related to the save trajectory Ajasja LjubetiÄ (Mon Feb 18 2013 - 01:46:49 CST)
  - Re: Problem related to the save trajectory Axel Kohlmeyer (Mon Feb 18 2013 - 02:31:13 CST)
- Re: Problem related to the save trajectory Bjørnar Jensen (Mon Feb 18 2013 - 02:04:47 CST)
  - Re: Problem related to the save trajectory Axel Kohlmeyer (Mon Feb 18 2013 - 03:44:27 CST)
    - Re: Problem related to the save trajectory Bjørnar Jensen (Mon Feb 18 2013 - 04:27:33 CST)
- Re: Problem related to the save trajectory Axel Kohlmeyer (Mon Feb 18 2013 - 02:15:10 CST)
porcupine plot - dynatraj server missing NG HUI WEN (Mon Feb 18 2013 - 00:18:29 CST)
- Re: porcupine plot - dynatraj server missing John Stone (Mon Feb 18 2013 - 10:00:22 CST)
SSRestraints missing some beta sheets Charles Greenberg (Fri Feb 15 2013 - 18:57:14 CST)
Licorice in transparent surface visualisation Sabine Reisser (Fri Feb 15 2013 - 08:57:40 CST)
- Re: Licorice in transparent surface visualisation Axel Kohlmeyer (Fri Feb 15 2013 - 09:43:11 CST)
  - Re: Licorice in transparent surface visualisation Sabine Reisser (Fri Feb 15 2013 - 09:58:06 CST)
modeling rGO without ReaxFF David Cohen-Tanugi (Fri Feb 15 2013 - 08:53:15 CST)
residency times continued Magnus Andersson (Fri Feb 15 2013 - 07:12:04 CST)
making time lapse video Do Yong Kim (Thu Feb 14 2013 - 15:06:06 CST)
- Re: making time lapse video Josh Vermaas (Fri Feb 15 2013 - 09:03:28 CST)
Dynamic bonds for amorphous silicon carbide? Dave Schall (Thu Feb 14 2013 - 13:52:07 CST)
- Re: Dynamic bonds for amorphous silicon carbide? Bjørnar Jensen (Fri Feb 15 2013 - 04:09:18 CST)
  - Re: Dynamic bonds for amorphous silicon carbide? Axel Kohlmeyer (Fri Feb 15 2013 - 05:20:31 CST)
psfread error Mohammad Elgamacy (Wed Feb 13 2013 - 08:55:03 CST)
- Re: psfread error Salvatore Mario Cosseddu (Thu Feb 14 2013 - 09:28:49 CST)
vmd1.9.2 alpha on windows/Mac valeria.losasso_at_stfc.ac.uk (Tue Feb 12 2013 - 10:42:01 CST)
- FW: vmd1.9.2 alpha on windows/Mac valeria.losasso_at_stfc.ac.uk (Tue Feb 12 2013 - 10:45:28 CST)
- Re: vmd1.9.2 alpha on windows/Mac John Stone (Thu Feb 14 2013 - 10:32:58 CST)
  - RE: vmd1.9.2 alpha on windows/Mac valeria.losasso_at_stfc.ac.uk (Fri Mar 15 2013 - 05:11:23 CDT)
- Re: vmd1.9.2 alpha on windows/Mac John Stone (Mon Feb 25 2013 - 15:15:13 CST)
How to display a selection from the Tk console Raul Araya (Tue Feb 12 2013 - 08:59:33 CST)
- Re: How to display a selection from the Tk console Bjørnar Jensen (Tue Feb 12 2013 - 09:59:56 CST)
VMD for Windows with VRPN option Stefano Ugolini (Tue Feb 12 2013 - 08:04:51 CST)
- Re: VMD for Windows with VRPN option John Stone (Fri Feb 15 2013 - 09:46:16 CST)
  - Re: VMD for Windows with VRPN option Stefano Ugolini (Fri Feb 15 2013 - 10:44:01 CST)
  - Re: VMD for Windows with VRPN option Stefano Ugolini (Wed Feb 20 2013 - 09:55:19 CST)
Command not found Error Allison Rossetto (Mon Feb 11 2013 - 16:02:50 CST)
- Re: Command not found Error John Stone (Thu Feb 14 2013 - 11:05:31 CST)
  - Re: Command not found Error Allison Rossetto (Thu Feb 14 2013 - 11:55:58 CST)
    - Re: Command not found Error PaweÅ‚ KÄ™dzierski (Fri Feb 15 2013 - 02:03:46 CST)
draw structure with xyz coordinates DanLiu (Mon Feb 11 2013 - 09:46:48 CST)
- Re: draw structure with xyz coordinates Axel Kohlmeyer (Mon Feb 11 2013 - 11:06:47 CST)
- Re: draw structure with xyz coordinates Heather Mayes (Mon Feb 11 2013 - 16:40:22 CST)
  - Re: draw structure with xyz coordinates DanLiu (Tue Feb 12 2013 - 02:09:37 CST)
non-bonded residue-residue namdEnergy question Prof. Eddie (Mon Feb 11 2013 - 08:51:38 CST)
problem with g(r) Ali Alizadeh (Sat Feb 09 2013 - 08:29:46 CST)
- Re: problem with g(r) Jeffrey Potoff (Sat Feb 09 2013 - 19:10:54 CST)
  - Re: problem with g(r) Ali Alizadeh (Sun Feb 10 2013 - 03:01:41 CST)
- Re: problem with g(r) Ramin Ekhteiari (Sun Feb 10 2013 - 03:51:47 CST)
differing particle numbers in each frame Gavin Melaugh (Fri Feb 08 2013 - 06:55:05 CST)
- Re: differing particle numbers in each frame Axel Kohlmeyer (Fri Feb 08 2013 - 07:53:07 CST)
  - Re: differing particle numbers in each frame Axel Kohlmeyer (Tue Apr 23 2013 - 05:58:58 CDT)
- Re: differing particle numbers in each frame Jeffrey Potoff (Fri Feb 08 2013 - 09:56:22 CST)
- Re: differing particle numbers in each frame Olaf Lenz (Fri Feb 08 2013 - 10:01:15 CST)
Head Tracking for Desktop VR Displays using the WiiRemote and VMD Ajasja LjubetiÄ (Thu Feb 07 2013 - 15:48:00 CST)
- Re: Head Tracking for Desktop VR Displays using the WiiRemote and VMD John Stone (Tue Feb 26 2013 - 15:25:03 CST)
isosurface for non-orthorhombic cells Torsten Kerber (Thu Feb 07 2013 - 08:55:52 CST)
- Re: isosurface for non-orthorhombic cells John Stone (Thu Feb 07 2013 - 09:05:29 CST)
  - Re: isosurface for non-orthorhombic cells John Stone (Wed Feb 27 2013 - 16:35:03 CST)
Colouring rings in paperchain gargiulo (Wed Feb 06 2013 - 09:04:01 CST)
- Re: Colouring rings in paperchain John Stone (Tue Feb 26 2013 - 16:19:28 CST)
  - Re: Colouring rings in paperchain gargiulo (Wed Feb 27 2013 - 02:52:53 CST)
same problem Albert (Tue Feb 05 2013 - 12:31:29 CST)
Unable to re-install vmd Soumya Lipsa Rath (Mon Feb 04 2013 - 00:01:33 CST)
- Re: Unable to re-install vmd Axel Kohlmeyer (Mon Feb 04 2013 - 11:43:50 CST)
delet a frame from dcd file yp sun (Sat Feb 02 2013 - 19:59:51 CST)
- Re: delet a frame from dcd file John Stone (Tue Feb 26 2013 - 16:47:17 CST)
making movies in vmd Payman Pirzadeh (Fri Feb 01 2013 - 01:53:05 CST)
- Re: making movies in vmd Axel Kohlmeyer (Fri Feb 01 2013 - 02:46:25 CST)
Problem in loading the trajectories Soumya Lipsa Rath (Thu Jan 31 2013 - 22:35:29 CST)
Removing an installed Plug-in aneesh cna (Thu Jan 31 2013 - 00:26:49 CST)
- Re: Removing an installed Plug-in John Stone (Thu Jan 31 2013 - 09:19:19 CST)
PYTHONPATH Word too long francesco oteri (Tue Jan 29 2013 - 09:56:21 CST)
- Re: PYTHONPATH Word too long John Stone (Tue Jan 29 2013 - 10:56:02 CST)
how to configure VMD plugin location? Albert (Tue Jan 29 2013 - 01:35:26 CST)
- Re: how to configure VMD plugin location? Axel Kohlmeyer (Tue Jan 29 2013 - 02:32:45 CST)
  - Re: how to configure VMD plugin location? Albert (Tue Jan 29 2013 - 04:02:00 CST)
    - Re: how to configure VMD plugin location? Axel Kohlmeyer (Tue Jan 29 2013 - 04:08:18 CST)
    - Re: how to configure VMD plugin location? Albert (Tue Jan 29 2013 - 04:43:59 CST)
NameError: name 'AtomSel' is not defined Albert (Mon Jan 28 2013 - 11:38:16 CST)
- Re: NameError: name 'AtomSel' is not defined Josh Vermaas (Mon Jan 28 2013 - 14:12:43 CST)
  - Re: NameError: name 'AtomSel' is not defined Albert (Tue Jan 29 2013 - 01:12:23 CST)
- Re: NameError: name 'AtomSel' is not defined Caio S. Souza (Mon Jan 28 2013 - 13:40:45 CST)
Extracting Entropies and Enthalpies With The ParseFEP Plugin Using SOS or BAR David Huggins (Fri Jan 25 2013 - 07:41:58 CST)
- Re: Extracting Entropies and Enthalpies With The ParseFEP Plugin Using SOS or BAR JÃ©rÃ´me HÃ©nin (Sat Jan 26 2013 - 11:43:59 CST)
cannot open vmd ragesh c (Fri Jan 25 2013 - 00:22:50 CST)
- Re: cannot open vmd Axel Kohlmeyer (Fri Jan 25 2013 - 02:28:15 CST)
plugin path problem Albert (Thu Jan 24 2013 - 12:33:04 CST)
How to split large DCD file snoze pa (Thu Jan 24 2013 - 10:50:27 CST)
- Re: How to split large DCD file John Stone (Thu Jan 24 2013 - 10:56:39 CST)
Re: namd-l: Assigning Partial Charges to FE in Active Site Superoxide Dismutase. JC Gumbart (Wed Jan 23 2013 - 14:26:59 CST)
- Re: Re: namd-l: Assigning Partial Charges to FE in Active Site Superoxide Dismutase. John Stone (Thu Jan 24 2013 - 10:54:14 CST)
compiling stopped without any obvious erros Albert (Wed Jan 23 2013 - 13:00:41 CST)
- Re: compiling stopped without any obvious erros John Stone (Wed Jan 23 2013 - 14:13:57 CST)
  - Re: compiling stopped without any obvious erros Albert (Thu Jan 24 2013 - 01:16:17 CST)
  - Re: compiling stopped without any obvious erros Albert (Thu Jan 24 2013 - 10:40:55 CST)
another tachyon problem Albert (Wed Jan 23 2013 - 11:15:04 CST)
- Re: another tachyon problem John Stone (Wed Jan 23 2013 - 11:40:49 CST)
  - Re: another tachyon problem Albert (Wed Jan 23 2013 - 11:41:52 CST)
    - Re: another tachyon problem John Stone (Wed Jan 23 2013 - 12:10:08 CST)
tc.h problem Albert (Wed Jan 23 2013 - 10:50:27 CST)
- Re: tc.h problem John Stone (Wed Jan 23 2013 - 11:35:05 CST)
Dynamic bond representations Peitong Duan (Tue Jan 22 2013 - 16:44:02 CST)
- Re: Dynamic bond representations Josh Vermaas (Tue Jan 22 2013 - 18:18:52 CST)
  - Re: Dynamic bond representations Heather Mayes (Tue Jan 22 2013 - 19:27:14 CST)
Fwd: namd-l: About "add solvation" Francesco Pietra (Mon Jan 21 2013 - 03:49:06 CST)
fftk charge optimization option ehsan zahedinejad (Sat Jan 19 2013 - 19:12:06 CST)
- Re: fftk charge optimization option JC Gumbart (Sun Jan 20 2013 - 13:16:33 CST)
tachyon configuration failed Albert (Sat Jan 19 2013 - 11:52:07 CST)
- Re: tachyon configuration failed Albert (Sat Jan 19 2013 - 11:53:19 CST)
  - Re: Re: tachyon configuration failed John Stone (Tue Jan 22 2013 - 11:11:39 CST)
ied with VMD 1.9.1 Antonija Tomiæ (Fri Jan 18 2013 - 09:03:05 CST)
- RE: ied with VMD 1.9.1 hannes.loeffler_at_stfc.ac.uk (Fri Jan 18 2013 - 12:35:19 CST)
about inorganic builder and define variable hamid mosaddeghi (Thu Jan 17 2013 - 16:19:23 CST)
- Re: about inorganic builder and define variable Marzieh Alishahi (Fri Jan 18 2013 - 00:51:15 CST)
  - Fw: about inorganic builder and define variable hamid mosaddeghi (Fri Jan 18 2013 - 03:16:37 CST)
- Re: about inorganic builder and define variable Axel Kohlmeyer (Fri Jan 18 2013 - 04:27:40 CST)
  - Fw: about inorganic builder and define variable hamid mosaddeghi (Fri Jan 18 2013 - 04:53:21 CST)
VMD-1.9.1 and TC/TK-8.6 break analysis g(r) and IR Spectral Density Calculator Benj FitzPatrick (Thu Jan 17 2013 - 14:47:11 CST)
- Re: VMD-1.9.1 and TC/TK-8.6 break analysis g(r) and IR Spectral Density Calculator John Stone (Tue Feb 26 2013 - 16:04:09 CST)
  - Re: VMD-1.9.1 and TC/TK-8.6 break analysis g(r) and IR Spectral Density Calculator Benj FitzPatrick (Wed Feb 27 2013 - 17:32:20 CST)
    - Re: VMD-1.9.1 and TC/TK-8.6 break analysis g(r) and IR Spectral Density Calculator John Stone (Wed Feb 27 2013 - 17:54:18 CST)
  - Re: VMD-1.9.1 and TC/TK-8.6 break analysis g(r) and IR Spectral Density Calculator John Stone (Thu Feb 28 2013 - 15:13:10 CST)
RE: Editing in Molefacture plugin by importing pdb file Him Bandhu Upadhyay (Thu Jan 17 2013 - 11:49:41 CST)
Editing in Molefacture plugin by importing pdb file Him Bandhu Upadhyay (Thu Jan 17 2013 - 10:36:52 CST)
Martini RBCG denilson_at_dqi.ufla.br (Wed Jan 16 2013 - 12:18:00 CST)
ssrestraints for determining the secondary structure of large protein complex Yujie Wu (Wed Jan 16 2013 - 05:51:36 CST)
Variable number of steps in run command? David Cohen-Tanugi (Tue Jan 15 2013 - 10:30:55 CST)
CG- CNT hamid mosaddeghi (Sat Jan 12 2013 - 06:05:02 CST)
- Re: CG- CNT Axel Kohlmeyer (Sat Jan 12 2013 - 10:02:04 CST)
displaying charge distribution mpincu (Fri Jan 11 2013 - 15:28:51 CST)
- Re: displaying charge distribution BjÃ¸rnar Jensen (Mon Jan 14 2013 - 01:53:38 CST)
write new dcd after duplicating periodic images? Fatemesadat Emami (Fri Jan 11 2013 - 15:12:35 CST)
periodic images in the hydrogen bond tool Fatemesadat Emami (Fri Jan 11 2013 - 14:15:37 CST)
Autoionize error in VMD Shaherin Basith (Fri Jan 11 2013 - 02:06:22 CST)
- Re: Autoionize error in VMD Jiawei Xu (Fri Jan 11 2013 - 11:28:46 CST)
  - Re: Autoionize error in VMD Rajan Vatassery (Fri Jan 11 2013 - 14:05:47 CST)
Potential memory consumption bug in VMD 1.9.1 John Jumper (Thu Jan 10 2013 - 21:08:22 CST)
- Re: Potential memory consumption bug in VMD 1.9.1 John Stone (Sat Jan 12 2013 - 06:18:10 CST)
Error in loading large trajectories Esam Tolba (Thu Jan 10 2013 - 15:56:15 CST)
- Re: Error in loading large trajectories Jiawei Xu (Thu Jan 10 2013 - 17:26:53 CST)
- Re: Error in loading large trajectories John Stone (Sat Jan 12 2013 - 06:23:55 CST)
VMD read wrong charges if the atom type is longer than 5 characters in PSF file Jiawei Xu (Thu Jan 10 2013 - 11:30:40 CST)
Regarding fit_angle.tcl script Chola Regmi (Thu Jan 10 2013 - 10:45:59 CST)
- Re: Regarding fit_angle.tcl script Chola Regmi (Fri Jan 11 2013 - 22:19:58 CST)
  - Re: Regarding fit_angle.tcl script Grace Brannigan (Sat Jan 12 2013 - 01:01:27 CST)
    - Re: Regarding fit_angle.tcl script Chola Regmi (Sat Jan 12 2013 - 10:23:01 CST)
rgyr from big DCD Steven Neumann (Mon Jan 07 2013 - 05:49:58 CST)
- Re: rgyr from big DCD lloyd riggs (Mon Jan 07 2013 - 15:27:37 CST)
  - Re: rgyr from big DCD PaweÅ‚ KÄ™dzierski (Tue Jan 08 2013 - 03:29:58 CST)
RE: Stride update in every frame of a trajectory? peter.schmidtke_at_fr.netgrs.com (Mon Jan 07 2013 - 03:03:13 CST)
Stride update in every frame of a trajectory? Martin, Erik W (Sat Jan 05 2013 - 10:57:17 CST)
how to plot per-atom field variable Wei Gao (Sat Jan 05 2013 - 10:42:53 CST)
- RE: how to plot per-atom field variable peter.schmidtke_at_fr.netgrs.com (Mon Jan 07 2013 - 02:56:30 CST)
  - Re: how to plot per-atom field variable Wei Gao (Mon Jan 07 2013 - 14:51:11 CST)
    - Re: how to plot per-atom field variable Wei Gao (Mon Jan 07 2013 - 17:20:48 CST)
tcl script for vmd troubleshooting Martin, Erik W (Fri Jan 04 2013 - 11:17:30 CST)
- Re: tcl script for vmd troubleshooting. . Martin, Erik W (Fri Jan 04 2013 - 14:05:14 CST)
  - Re: tcl script for vmd troubleshooting. . JC Gumbart (Fri Jan 04 2013 - 16:48:37 CST)
FW: 3D-Connexion Space Navigator for Macosx Passerone, Daniele (Fri Jan 04 2013 - 00:47:42 CST)
How to read every second frame with bigdcd Jiawei Xu (Thu Jan 03 2013 - 11:33:31 CST)
- Re: How to read every second frame with bigdcd Axel Kohlmeyer (Thu Jan 03 2013 - 12:33:40 CST)
  - Re: How to read every second frame with bigdcd Jiawei Xu (Fri Jan 04 2013 - 08:00:40 CST)
'Abort file I/O' key not working aneesh cna (Fri Dec 28 2012 - 04:59:56 CST)
- Re: 'Abort file I/O' key not working John Stone (Wed Jan 02 2013 - 14:37:00 CST)
  - Re: 'Abort file I/O' key not working aneesh cna (Wed Jan 02 2013 - 23:52:45 CST)
  - GPU acceleration Martin, Erik W (Thu Jan 03 2013 - 08:20:27 CST)
    - Re: GPU acceleration John Stone (Thu Jan 03 2013 - 09:57:05 CST)
about atomselect command Marzieh Alishahi (Mon Dec 24 2012 - 09:13:08 CST)
- Re: about atomselect command Caio S. Souza (Mon Dec 24 2012 - 11:17:24 CST)
  - Re: about atomselect command Marzieh Alishahi (Mon Dec 24 2012 - 11:32:49 CST)
python simple script Adrian Jasiñski (Fri Dec 21 2012 - 04:52:41 CST)
- Re: python simple script Jack Bulat (Fri Dec 21 2012 - 09:12:22 CST)
- Re: python simple script Jack Bulat (Mon Dec 24 2012 - 12:13:29 CST)
VMD not displaying represenations by line maria goranovic (Thu Dec 20 2012 - 04:48:03 CST)
- Re: VMD not displaying represenations by line John Stone (Thu Dec 20 2012 - 09:49:40 CST)
  - Re: VMD not displaying represenations by line maria goranovic (Thu Dec 20 2012 - 09:53:05 CST)
Tachyon does not capture the dark colors! Fatemesadat Emami (Wed Dec 19 2012 - 13:25:20 CST)
- Re: Tachyon does not capture the dark colors! John Stone (Wed Dec 19 2012 - 13:54:04 CST)
Real-time Representation Changes During Interactive MD Chris Ing (Wed Dec 19 2012 - 11:36:22 CST)
- Re: Real-time Representation Changes During Interactive MD John Stone (Thu Dec 20 2012 - 09:56:01 CST)
  - Re: Real-time Representation Changes During Interactive MD Chris Ing (Thu Jan 03 2013 - 18:14:29 CST)
vmd 1.9.2a11macx86_64 on OSX 10.8 Raul Araya (Wed Dec 19 2012 - 07:28:33 CST)
Gromacs index file Ignacio Fernández Galván (Wed Dec 19 2012 - 03:01:58 CST)
- Re: Gromacs index file Axel Kohlmeyer (Wed Dec 19 2012 - 03:52:49 CST)
- Re: Gromacs index file poker_at_physics.usyd.edu.au (Wed Dec 19 2012 - 06:04:23 CST)
  - Re: Gromacs index file Jeremy Lucid (Wed Dec 19 2012 - 06:59:37 CST)
problem of selection Albert (Wed Dec 19 2012 - 02:52:30 CST)
- Re: problem of selection Caio S. Souza (Wed Dec 19 2012 - 07:30:38 CST)
Update atom labels each frame Sandeep Kumar Reddy (Wed Dec 19 2012 - 00:42:18 CST)
How to get the coordinate of periodic images anyy zsj (Tue Dec 18 2012 - 23:58:53 CST)
- Re: How to get the coordinate of periodic images Axel Kohlmeyer (Sat Dec 22 2012 - 09:50:51 CST)
VMD 1.9.1 src // GCC 4.7.0 - Error compiling plugins directory Adam Brenner (Tue Dec 18 2012 - 19:32:00 CST)
- Re: VMD 1.9.1 src // GCC 4.7.0 - Error compiling plugins directory John Stone (Tue Dec 18 2012 - 20:13:52 CST)
  - Re: VMD 1.9.1 src // GCC 4.7.0 - Error compiling plugins directory Adam Brenner (Tue Dec 18 2012 - 20:17:43 CST)
    - Re: VMD 1.9.1 src // GCC 4.7.0 - Error compiling plugins directory John Stone (Tue Dec 18 2012 - 20:25:42 CST)
    - Re: VMD 1.9.1 src // GCC 4.7.0 - Error compiling plugins directory Adam Brenner (Tue Dec 18 2012 - 20:27:25 CST)
can vmd add protons to particular atoms? yp sun (Tue Dec 18 2012 - 00:43:01 CST)
combine.tcl yp sun (Mon Dec 17 2012 - 08:52:24 CST)
- Re: combine.tcl Axel Kohlmeyer (Mon Dec 17 2012 - 10:30:47 CST)
delete of some molecules mohammad agha (Fri Dec 14 2012 - 23:42:56 CST)
- Re: delete of some molecules Axel Kohlmeyer (Sat Dec 15 2012 - 01:10:25 CST)
visualizing multiframe trajectory simultaneously with multimolecule Bennion, Brian (Thu Dec 13 2012 - 11:46:18 CST)
- Re: visualizing multiframe trajectory simultaneously with multimolecule Axel Kohlmeyer (Thu Dec 13 2012 - 12:53:11 CST)
  - RE: visualizing multiframe trajectory simultaneously with multimolecule Bennion, Brian (Fri Dec 14 2012 - 17:06:03 CST)
problem with ascribing data to the user field Pawel Siuda (Thu Dec 13 2012 - 04:48:58 CST)
- Re: problem with ascribing data to the user field Axel Kohlmeyer (Thu Dec 13 2012 - 06:30:54 CST)
Re: visualizing certain sanpshots on top of each other Suresh (Mon Dec 10 2012 - 22:27:04 CST)
visualizing certain sanpshots on top of each other Fatemesadat Emami (Mon Dec 10 2012 - 13:23:23 CST)
VMD : Force Field Toolkit : Help Esra Bozkurt (Mon Dec 10 2012 - 13:21:06 CST)
- Re: VMD : Force Field Toolkit : Help JC Gumbart (Mon Dec 10 2012 - 17:50:06 CST)
VMD 1.9.1 core dumps (CentOS-5 x86_64) nvidia drivers: 304.64/4x GTX 680 Tru Huynh (Mon Dec 10 2012 - 09:14:43 CST)
- Re: VMD 1.9.1 core dumps (CentOS-5 x86_64) nvidia drivers: 304.64/4x GTX 680 Tru Huynh (Mon Dec 10 2012 - 09:19:55 CST)
  - Re: Re: VMD 1.9.1 core dumps (CentOS-5 x86_64) nvidia drivers: 304.64/4x GTX 680 John Stone (Mon Dec 10 2012 - 11:40:11 CST)
- Re: VMD 1.9.1 core dumps (CentOS-5 x86_64) nvidia drivers: 304.64/4x GTX 680 Axel Kohlmeyer (Mon Dec 10 2012 - 10:22:49 CST)
  - Re: VMD 1.9.1 core dumps (CentOS-5 x86_64) nvidia drivers: 304.64/4x GTX 680 Tru Huynh (Mon Dec 10 2012 - 15:46:45 CST)
Getting volumetric map from old Insight file into VMD-readable format Tristan Croll (Sun Dec 09 2012 - 22:36:44 CST)
VMD-CUDA crash on Mac OSX 10.8.2 James Conway (Thu Dec 06 2012 - 12:35:11 CST)
Coloring lots of Groups Doran Bennett (Thu Dec 06 2012 - 10:25:06 CST)
- Re: Coloring lots of Groups Benjamin Kaduk (Thu Dec 06 2012 - 13:48:37 CST)
invalid command name "dict" mohammad agha (Thu Dec 06 2012 - 01:26:01 CST)
- Re: invalid command name "dict" Axel Kohlmeyer (Thu Dec 06 2012 - 02:29:59 CST)
  - uninstall of previous version mohammad agha (Thu Dec 06 2012 - 02:40:20 CST)
    - Re: uninstall of previous version Axel Kohlmeyer (Thu Dec 06 2012 - 03:44:21 CST)
    - Re: uninstall of previous version mohammad agha (Thu Dec 06 2012 - 05:19:08 CST)
error while loading shared libraries: libcudart.so.4 MichaÅ‚ Kadlof (Wed Dec 05 2012 - 19:25:26 CST)
Default XML format Tim Moore (Wed Dec 05 2012 - 09:55:15 CST)
- Re: Default XML format Axel Kohlmeyer (Fri Dec 07 2012 - 14:10:03 CST)
Use Movie Maker Plugin in Script Aaron Taudt (Wed Dec 05 2012 - 08:40:46 CST)
- Re: Use Movie Maker Plugin in Script Axel Kohlmeyer (Thu Dec 06 2012 - 07:02:33 CST)
  - Re: Use Movie Maker Plugin in Script John Stone (Thu Dec 06 2012 - 10:00:15 CST)
  - Re: Use Movie Maker Plugin in Script John Stone (Mon Dec 10 2012 - 11:45:42 CST)
vmd invalid connection error when launched Huixi Violet Zhang (Tue Dec 04 2012 - 14:48:01 CST)
Full-Screen display Sabine Reisser (Tue Dec 04 2012 - 06:54:47 CST)
- Re: Full-Screen display Axel Kohlmeyer (Tue Dec 04 2012 - 08:54:23 CST)
  - Re: Full-Screen display Axel Kohlmeyer (Tue Dec 04 2012 - 09:47:31 CST)
    - RE: Full-Screen display Grzegorz Wieczorek (Wed Dec 05 2012 - 08:24:33 CST)
A problem about atomselect command in a script Z.Y.Qiu (Mon Dec 03 2012 - 22:53:30 CST)
- Re: A problem about atomselect command in a script Axel Kohlmeyer (Tue Dec 04 2012 - 02:32:54 CST)
use volmap tool for probability density map Liyu Jin (Leo) (Sat Dec 01 2012 - 07:56:30 CST)
- Re: use volmap tool for probability density map John Stone (Sat Dec 01 2012 - 22:36:22 CST)
unable to load cartoon represention of my peptide Shubhadip Das (Sat Dec 01 2012 - 01:49:23 CST)
- Re: unable to load cartoon represention of my peptide John Stone (Sat Dec 01 2012 - 22:32:47 CST)
cant open .car file Erik (Fri Nov 30 2012 - 12:25:30 CST)
- Re: cant open .car file John Stone (Sat Dec 01 2012 - 22:41:24 CST)
  - Re: cant open .car file Erik (Mon Dec 03 2012 - 21:28:30 CST)
Question regarding dihedral fitting using fftk ehsan zahedinejad (Fri Nov 30 2012 - 00:23:42 CST)
- Re: Question regarding dihedral fitting using fftk Mayne, Christopher G (Fri Nov 30 2012 - 09:15:08 CST)
  - Re: Question regarding dihedral fitting using fftk Erik (Fri Nov 30 2012 - 12:24:42 CST)
delete the most recent atomselect? Fatemesadat Emami (Thu Nov 29 2012 - 14:21:23 CST)
- Re: delete the most recent atomselect? Axel Kohlmeyer (Thu Nov 29 2012 - 15:42:33 CST)
- RDF Ramin Ekhteiari (Fri Nov 30 2012 - 12:34:13 CST)
  - Re: RDF Axel Kohlmeyer (Fri Nov 30 2012 - 13:34:45 CST)
    - Re: RDF Philippe Bopp / temporary (Mon Dec 03 2012 - 06:56:54 CST)
Setting up a Phantom Omni for use with VMD on CentOS 6 Ray, William (Thu Nov 29 2012 - 12:22:23 CST)
- Re: Setting up a Phantom Omni for use with VMD on CentOS 6 John Stone (Sat Dec 01 2012 - 23:20:06 CST)
How do I make sure the normals value of trinorms? javacfish (Wed Nov 28 2012 - 14:21:16 CST)
- Re: How do I make sure the normals value of trinorms? Pawel Kedzierski (Thu Nov 29 2012 - 06:34:21 CST)
- Re: How do I make sure the normals value of trinorms? Axel Kohlmeyer (Thu Nov 29 2012 - 08:36:17 CST)
not very helpful documentation Philippe Bopp / temporary (Wed Nov 28 2012 - 09:02:28 CST)
- Re: not very helpful documentation Axel Kohlmeyer (Wed Nov 28 2012 - 10:40:12 CST)
- RE: not very helpful documentation Joaquim Rui de Castro Rodrigues (Wed Nov 28 2012 - 10:50:30 CST)
  - RE: not very helpful documentation Philippe Bopp / temporary (Wed Nov 28 2012 - 10:58:32 CST)
(no subject) Mustafa Tekpinar (Tue Nov 27 2012 - 15:00:55 CST)
- Re: Axel Kohlmeyer (Tue Nov 27 2012 - 16:06:29 CST)
- Re: Mert Gür (Tue Nov 27 2012 - 16:13:21 CST)
update selection every frame not working Pawel Siuda (Mon Nov 26 2012 - 15:41:15 CST)
- Re: update selection every frame not working John Stone (Mon Nov 26 2012 - 15:51:14 CST)
  - Re: update selection every frame not working Pawel Siuda (Wed Nov 28 2012 - 08:42:11 CST)
compiled failed Albert (Mon Nov 26 2012 - 12:16:28 CST)
- Re: compiled failed Axel Kohlmeyer (Mon Nov 26 2012 - 15:41:09 CST)
Coarse Grained - angle/bond parameters Steven Neumann (Mon Nov 26 2012 - 10:20:33 CST)
python script failed Albert (Mon Nov 26 2012 - 04:44:12 CST)
- Re: python script failed Axel Kohlmeyer (Mon Nov 26 2012 - 05:52:09 CST)
- Re: python script failed Caio S. Souza (Mon Nov 26 2012 - 07:15:14 CST)
3D-Connexion Space Navigator for Macosx Passerone, Daniele (Wed Nov 21 2012 - 04:35:43 CST)
- Re: 3D-Connexion Space Navigator for Macosx John Stone (Sat Dec 01 2012 - 23:50:34 CST)
Hole program for vmd hole tcl script Ban Arn (Tue Nov 20 2012 - 08:59:20 CST)
- Re: Hole program for vmd hole tcl script John Stone (Tue Nov 20 2012 - 10:54:38 CST)
  - RE: Hole program for vmd hole tcl script Bennion, Brian (Tue Nov 20 2012 - 12:14:30 CST)
Drawing Method: Lines does not display anything Clarinet (Tue Nov 20 2012 - 08:04:09 CST)
- Re: Drawing Method: Lines does not display anything John Stone (Tue Nov 20 2012 - 10:51:39 CST)
  - Re: Drawing Method: Lines does not display anything Clarinet (Wed Nov 21 2012 - 07:03:03 CST)
    - Re: Drawing Method: Lines does not display anything John Stone (Sat Dec 01 2012 - 23:44:11 CST)
How to calculate the Hydrogen bond strengh Ð¤¸»¹ó (Tue Nov 20 2012 - 06:10:22 CST)
- Re: How to calculate the Hydrogen bond strengh Ajasja LjubetiÄ (Tue Nov 20 2012 - 07:05:53 CST)
  - RE: How to calculate the Hydrogen bond strengh. . Martin, Erik W (Wed Nov 21 2012 - 08:58:11 CST)
[Solved]RE: molfile_plugins makefile errors Bennion, Brian (Mon Nov 19 2012 - 18:09:11 CST)
Structural Change of DNA satya kumar (Mon Nov 19 2012 - 17:50:42 CST)
VMD can't display new PDB secondary structure properly (pyMol, jMol can) Larry Guy (Mon Nov 19 2012 - 16:00:29 CST)
- RE: VMD can't display new PDB secondary structure properly (pyMol, jMol can) Bennion, Brian (Mon Nov 19 2012 - 17:30:19 CST)
- Re: VMD can't display new PDB secondary structure properly (pyMol, jMol can) John Stone (Mon Nov 19 2012 - 18:18:10 CST)
  - RE: VMD can't display new PDB secondary structure properly ( pyMol, jMol can). . Martin, Erik W (Mon Nov 19 2012 - 20:37:26 CST)
Error in RATTLE algorithm Stefan Franzen (Mon Nov 19 2012 - 15:38:05 CST)
molfile_plugins makefile errors Bennion, Brian (Mon Nov 19 2012 - 15:24:33 CST)
building plugins fails on tcl based plugins Bennion, Brian (Mon Nov 19 2012 - 14:59:18 CST)
(no subject) Gert Peters (Sun Nov 18 2012 - 12:50:32 CST)
how to measure the distance of two atoms in 1000 conformations? Ð¤¸»¹ó (Sat Nov 17 2012 - 07:33:39 CST)
- Re: how to measure the distance of two atoms in 1000 conformations? BjÃ¸rnar Jensen (Mon Nov 19 2012 - 07:05:21 CST)
  - Re: how to measure the distance of two atoms in 1000 conformations? Thomas Evangelidis (Mon Nov 19 2012 - 09:04:07 CST)
creating SiO2 device with Inorganic Builder Marzieh Alishahi (Sat Nov 17 2012 - 02:36:22 CST)
Typo in my previous e-mail subject. It's: "VMD" very slow on a 8400M GS laptop.... Pietro Amodeo (Sat Nov 17 2012 - 02:18:12 CST)
MD very slow on a 8400M GS laptop (but not on a GT230M one) after NVidia driver update to 304.64 or 310.14 Pietro Amodeo (Fri Nov 16 2012 - 13:44:51 CST)
- Re: MD very slow on a 8400M GS laptop (but not on a GT230M one) after NVidia driver update to 304.64 or 310.14 John Stone (Sun Nov 18 2012 - 22:25:27 CST)
  - Re: MD very slow on a 8400M GS laptop (but not on a GT230M one) after NVidia driver update to 304.64 or 310.14 Pietro Amodeo (Mon Nov 19 2012 - 10:25:33 CST)
How to label the chains in a multimer Ð¤¸»¹ó (Fri Nov 16 2012 - 09:00:21 CST)
- Re: How to label the chains in a multimer Boris Steipe (Fri Nov 16 2012 - 13:50:34 CST)
how to delete one peptide from dimer Ð¤¸»¹ó (Thu Nov 15 2012 - 07:26:22 CST)
- Re: how to delete one peptide from dimer Boris Steipe (Thu Nov 15 2012 - 09:59:37 CST)
pbc box problem Albert (Thu Nov 15 2012 - 01:37:27 CST)
- Re: pbc box problem Axel Kohlmeyer (Thu Nov 15 2012 - 02:45:25 CST)
RE: acylated and amidated parameters. Bennion, Brian (Wed Nov 14 2012 - 11:52:05 CST)
periodicity and bonds Celia Bremer (Wed Nov 14 2012 - 10:23:18 CST)
tc.h error while compiling vmd Bennion, Brian (Tue Nov 13 2012 - 16:00:27 CST)
- Re: tc.h error while compiling vmd John Stone (Wed Nov 14 2012 - 21:59:01 CST)
Installation error with rlwrap Matthew Barlow (Tue Nov 13 2012 - 13:41:55 CST)
- Re: Installation error with rlwrap John Stone (Sun Dec 02 2012 - 00:21:25 CST)
calculate HBOND George Lai (Mon Nov 12 2012 - 19:48:50 CST)
- RE: calculate HBOND Martin, Erik W (Mon Nov 12 2012 - 22:04:11 CST)
  - Re: calculate HBOND George Lai (Tue Nov 13 2012 - 12:54:23 CST)
    - Re: calculate HBOND Martin, Erik W (Tue Nov 13 2012 - 14:21:26 CST)
psfgen generating incorrect dihedrals Sasha Perkins (Thu Nov 08 2012 - 16:40:39 CST)
- Re: psfgen generating incorrect dihedrals JC Gumbart (Fri Nov 09 2012 - 04:12:47 CST)
test VMD mailist post Erik Winardi (Thu Nov 08 2012 - 14:42:36 CST)
Units of bond distance in vmd siladitya mukherjee (Thu Nov 08 2012 - 11:04:06 CST)
- Re: Units of bond distance in vmd Axel Kohlmeyer (Thu Nov 08 2012 - 12:20:34 CST)
  - Re: Units of bond distance in vmd siladitya mukherjee (Thu Nov 08 2012 - 12:22:16 CST)
vmd cause linux system freezes randomly Kasra Fattah (Wed Nov 07 2012 - 19:18:01 CST)
- Re: vmd cause linux system freezes randomly Kasra Fattah (Wed Nov 07 2012 - 23:03:50 CST)
dihedral energy using namdenergy -regd Rajitha Tatikonda (Wed Nov 07 2012 - 06:52:20 CST)
periodic images of molecule containing custom graphics rocfo (Wed Nov 07 2012 - 05:31:46 CST)
- Re: periodic images of molecule containing custom graphics Axel Kohlmeyer (Wed Nov 07 2012 - 06:37:38 CST)
vmd crashes during gromacs trr loading Roberto Gaspari (Wed Nov 07 2012 - 02:05:11 CST)
- Re: vmd crashes during gromacs trr loading Axel Kohlmeyer (Wed Nov 07 2012 - 03:14:28 CST)
- Re: vmd crashes during gromacs trr loading Bogdan Costescu (Wed Nov 07 2012 - 04:51:37 CST)
  - Re: vmd crashes during gromacs trr loading Roberto Gaspari (Thu Nov 08 2012 - 05:11:19 CST)
3rd party tools- vmd Ban Arn (Tue Nov 06 2012 - 11:46:59 CST)
- Re: 3rd party tools- vmd Axel Kohlmeyer (Tue Nov 06 2012 - 13:42:13 CST)
Solvating protein in water sucrose solution amin_at_imtech.res.in (Tue Nov 06 2012 - 11:01:17 CST)
- Re: Solvating protein in water sucrose solution Ajasja LjubetiÄ (Tue Nov 06 2012 - 13:39:07 CST)
  - Re: Solvating protein in water sucrose solution amin_at_imtech.res.in (Tue Nov 06 2012 - 22:18:43 CST)
- Re: Solvating protein in water sucrose solution Axel Kohlmeyer (Tue Nov 06 2012 - 13:47:56 CST)
Workshop on Scientific Software Development at ICTP in Trieste Axel Kohlmeyer (Thu Nov 01 2012 - 09:39:46 CDT)
Re: control the spacing between the dashes in the hydrogen bonding between two atoms mahesh gudem (Tue Oct 30 2012 - 07:48:21 CDT)
- Re: Re: control the spacing between the dashes in the hydrogen bonding between two atoms Axel Kohlmeyer (Tue Oct 30 2012 - 08:59:22 CDT)
Command line representation Aronica, Pietro (Mon Oct 29 2012 - 06:57:30 CDT)
- Re: Command line representation Axel Kohlmeyer (Mon Oct 29 2012 - 07:51:16 CDT)
Colouring by velocity component in VMD Michael Doig (Mon Oct 29 2012 - 05:20:27 CDT)
- Re: Colouring by velocity component in VMD Axel Kohlmeyer (Mon Oct 29 2012 - 07:18:10 CDT)
IMD with Novint Falcon George Patargias (Fri Oct 26 2012 - 06:01:47 CDT)
- Re: IMD with Novint Falcon Axel Kohlmeyer (Fri Oct 26 2012 - 08:22:00 CDT)
  - Re: IMD with Novint Falcon George Patargias (Tue Oct 30 2012 - 05:57:26 CDT)
    - Re: IMD with Novint Falcon Axel Kohlmeyer (Tue Oct 30 2012 - 08:10:18 CDT)
    - Re: IMD with Novint Falcon George Patargias (Thu Nov 01 2012 - 03:26:28 CDT)
  - Re: IMD with Novint Falcon George Patargias (Fri Jan 18 2013 - 10:08:17 CST)
how to extract a frame in a binary coordinate restart file format for NAMD ? Jose Borreguero (Wed Oct 24 2012 - 14:13:37 CDT)
- Re: how to extract a frame in a binary coordinate restart file format for NAMD ? John Stone (Fri Oct 26 2012 - 10:34:23 CDT)
Secondary structure analysis ngpntm_at_gmail.com (Wed Oct 24 2012 - 05:44:33 CDT)
- RE: Secondary structure analysis Bennion, Brian (Wed Oct 24 2012 - 14:32:32 CDT)
Error in reading data file prakhar gupta (Tue Oct 23 2012 - 08:50:50 CDT)
- Re: Error in reading data file Axel Kohlmeyer (Tue Oct 23 2012 - 09:56:49 CDT)
  - Re: Error in reading data file prakhar gupta (Tue Oct 23 2012 - 10:05:29 CDT)
    - Re: Error in reading data file Axel Kohlmeyer (Tue Oct 23 2012 - 10:08:15 CDT)
- Re: Error in reading data file John Stone (Tue Oct 23 2012 - 11:52:06 CDT)
  - Re: Error in reading data file prakhar gupta (Tue Oct 23 2012 - 12:10:45 CDT)
Units reported by VMD SASA ??? Germán Andrés Miño (Mon Oct 22 2012 - 19:06:35 CDT)
Re: Re: how to make separate molecule whole? Axel Kohlmeyer (Sun Oct 21 2012 - 23:20:57 CDT)
Re: how to make separate molecule whole? Axel Kohlmeyer (Sun Oct 21 2012 - 11:06:32 CDT)
Visualizing phonon displacement patterns from axsf format forces? Ijäs Mari (Sun Oct 21 2012 - 01:46:49 CDT)
- Re: Visualizing phonon displacement patterns from axsf format forces? Axel Kohlmeyer (Sun Oct 21 2012 - 02:49:55 CDT)
calculate end-to-end distance with trajectory files Eric Lovejoy (Sat Oct 20 2012 - 16:44:13 CDT)
- Re: calculate end-to-end distance with trajectory files John Stone (Mon Oct 22 2012 - 10:49:01 CDT)
VMD (and NAMD) fail to read simple AMBER prmtop file (and it's not the SCEE and SCNB flags) Jose Borreguero (Sat Oct 20 2012 - 15:57:16 CDT)
- Re: VMD (and NAMD) fail to read simple AMBER prmtop file (and it's not the SCEE and SCNB flags) Thomas Evangelidis (Mon Oct 22 2012 - 06:15:49 CDT)
Selecting waters between two given distances from a particular point Sajeewa Pemasinghe (Fri Oct 19 2012 - 21:13:57 CDT)
- Re: Selecting waters between two given distances from a particular point Bjørnar Jensen (Sat Oct 20 2012 - 04:34:26 CDT)
Application Error message during dihedral optimization using FFTK Him Bandhu Upadhyay (Thu Oct 18 2012 - 21:53:45 CDT)
- Re: Application Error message during dihedral optimization using FFTK Mayne, Christopher G (Fri Oct 19 2012 - 07:34:49 CDT)
  - RE: Application Error message during dihedral optimization using FFTK Him Bandhu Upadhyay (Fri Oct 19 2012 - 08:48:47 CDT)
how to put command line arguments in tcl script Vikas Varshney (Thu Oct 18 2012 - 14:30:52 CDT)
- Re: how to put command line arguments in tcl script Axel Kohlmeyer (Thu Oct 18 2012 - 15:42:14 CDT)
duplicating an equilibrated system with psfgen Gianluca Lattanzi (Wed Oct 17 2012 - 11:11:09 CDT)
Graphic card Han Hu (Wed Oct 17 2012 - 08:27:40 CDT)
- Re: Graphic card Axel Kohlmeyer (Wed Oct 17 2012 - 09:34:06 CDT)
postdoc position available JC Gumbart (Tue Oct 16 2012 - 00:47:41 CDT)
pick center with tcl text command Yi Shang (Mon Oct 15 2012 - 11:59:59 CDT)
coloring atoms based on max bond length; Need help with bond retrieval Vikas Varshney (Mon Oct 15 2012 - 10:53:26 CDT)
- Re: coloring atoms based on max bond length; Need help with bond retrieval Axel Kohlmeyer (Mon Oct 15 2012 - 14:12:33 CDT)
  - Re: coloring atoms based on max bond length; Need help with bond retrieval Vikas Varshney (Tue Oct 16 2012 - 10:11:24 CDT)
VRPN driver for Novint Falcon haptic device available - Looking for Testers Marcos Ackel (Sun Oct 14 2012 - 12:31:59 CDT)
- Re: VRPN driver for Novint Falcon haptic device available - Looking for Testers Axel Kohlmeyer (Sun Oct 14 2012 - 13:31:12 CDT)
  - Re: VRPN driver for Novint Falcon haptic device available - Looking for Testers Marcos Ackel (Wed Oct 17 2012 - 20:58:31 CDT)
problem of VMD-1.91 in MacOS10.8 Albert (Sat Oct 13 2012 - 11:09:44 CDT)
secondary structure calculations Bennion, Brian (Thu Oct 11 2012 - 18:16:25 CDT)
- Re: secondary structure calculations Mayne, Christopher G (Thu Oct 11 2012 - 19:37:59 CDT)
  - RE: secondary structure calculations Joaquim Rui de Castro Rodrigues (Fri Oct 12 2012 - 07:30:52 CDT)
  - RE: secondary structure calculations Bennion, Brian (Fri Oct 12 2012 - 11:27:25 CDT)
    - RE: secondary structure calculations Joaquim Rui de Castro Rodrigues (Sat Oct 13 2012 - 14:38:36 CDT)
    - RE: secondary structure calculations Bennion, Brian (Sat Oct 13 2012 - 23:03:19 CDT)
Error message -" cannot find NAMD binary files" during parameterization using FFTK plugin. Him Bandhu Upadhyay (Thu Oct 11 2012 - 12:41:59 CDT)
- Re: Error message -" cannot find NAMD binary files" during parameterization using FFTK plugin. Mayne, Christopher G (Thu Oct 11 2012 - 13:09:21 CDT)
  - RE: Error message -" cannot find NAMD binary files" during parameterization using FFTK plugin. Him Bandhu Upadhyay (Thu Oct 11 2012 - 14:43:10 CDT)
    - Re: Error message -" cannot find NAMD binary files" during parameterization using FFTK plugin. Mayne, Christopher G (Thu Oct 11 2012 - 14:55:38 CDT)
    - RE: Error message -" cannot find NAMD binary files" during parameterization using FFTK plugin. Him Bandhu Upadhyay (Thu Oct 11 2012 - 15:02:16 CDT)
Problem in invoking VMD P A Deshpande (Mon Oct 08 2012 - 10:27:00 CDT)
- Re: Problem in invoking VMD John Stone (Mon Oct 08 2012 - 10:41:08 CDT)
Heat mapper Esam Tolba (Mon Oct 08 2012 - 05:53:04 CDT)
- Re: Heat mapper John Stone (Mon Oct 08 2012 - 12:57:08 CDT)
  - Re: Heat mapper Barry Isralewitz (Mon Oct 08 2012 - 13:09:39 CDT)
  - max mice for IMD Thomas C. Bishop (Tue Oct 09 2012 - 16:16:18 CDT)
    - Re: max mice for IMD John Stone (Tue Oct 09 2012 - 22:19:10 CDT)
VMD on Mac OS X, converter problem DanLiu (Mon Oct 08 2012 - 02:44:56 CDT)
- Re: VMD on Mac OS X, converter problem Joshua D. Moore (Mon Oct 08 2012 - 10:39:31 CDT)
Coloring bonds in VMD Mingchao Wang (Mon Oct 08 2012 - 01:24:21 CDT)
- Re: Coloring bonds in VMD John Stone (Mon Oct 08 2012 - 12:42:49 CDT)
Script for reading Gaussian 09 MD file? John Keller (Fri Oct 05 2012 - 17:06:49 CDT)
- Re: Script for reading Gaussian 09 MD file? John Stone (Wed Oct 10 2012 - 14:40:45 CDT)
  - Re: Script for reading Gaussian 09 MD file? John Keller (Wed Oct 10 2012 - 14:50:00 CDT)
    - Re: Script for reading Gaussian 09 MD file? John Stone (Wed Oct 10 2012 - 14:53:19 CDT)
    - Re: Script for reading Gaussian 09 MD file? Mayne, Christopher G (Wed Oct 10 2012 - 15:57:55 CDT)
Visualizing DNA Damage satya kumar (Fri Oct 05 2012 - 14:40:05 CDT)
Lennard-Jones parameters of rubidium Abolfazl Bayat (Fri Oct 05 2012 - 10:44:19 CDT)
adding 3rdparty plugins in VMD-1.9.1 Ban Arn (Fri Oct 05 2012 - 07:00:11 CDT)
- Re: adding 3rdparty plugins in VMD-1.9.1 John Stone (Wed Oct 10 2012 - 11:14:27 CDT)
Heat mapper Esam Tolba (Thu Oct 04 2012 - 16:42:25 CDT)
- Re: Heat mapper Suresh (Thu Oct 04 2012 - 22:53:22 CDT)
Rendering "draw text" in Povray Joshua D. Moore (Thu Oct 04 2012 - 12:12:32 CDT)
- Re: Rendering "draw text" in Povray Joshua D. Moore (Thu Oct 04 2012 - 15:49:15 CDT)
  - Re: Rendering "draw text" in Povray John Stone (Thu Oct 04 2012 - 23:26:00 CDT)
Persistent troubles with tk fonts Vlastimil ZÃma (Thu Oct 04 2012 - 04:07:03 CDT)
- Re: Persistent troubles with tk fonts John Stone (Fri Oct 05 2012 - 09:08:05 CDT)
  - Re: Persistent troubles with tk fonts Vlastimil Zíma (Fri Oct 05 2012 - 12:07:49 CDT)
  - Re: Persistent troubles with tk fonts John Stone (Mon Feb 09 2015 - 15:32:56 CST)
Fw: VMD compile on windows (where is windows.h?) Marcos Ackel (Wed Oct 03 2012 - 13:48:45 CDT)
compiling VMD with gcc 4.7 Vlad Cojocaru (Wed Oct 03 2012 - 09:37:45 CDT)
- Re: compiling VMD with gcc 4.7 John Stone (Wed Oct 03 2012 - 14:03:36 CDT)
  - Re: compiling VMD with gcc 4.7 Vlad Cojocaru (Wed Oct 03 2012 - 14:08:55 CDT)
- Re: compiling VMD with gcc 4.7 Axel Kohlmeyer (Thu Oct 04 2012 - 08:30:36 CDT)
  - Re: compiling VMD with gcc 4.7 Vlad Cojocaru (Thu Oct 04 2012 - 08:41:51 CDT)
    - Re: Re: compiling VMD with gcc 4.7 lloyd riggs (Thu Oct 04 2012 - 10:49:33 CDT)
    - Re: Re: compiling VMD with gcc 4.7 Vlad Cojocaru (Thu Oct 04 2012 - 13:25:24 CDT)
VMD compile on windows (where is windows.h?) Marcos Ackel (Tue Oct 02 2012 - 15:17:48 CDT)
- Re: VMD compile on windows (where is windows.h?) John Stone (Tue Oct 02 2012 - 15:33:52 CDT)
  - Re: VMD compile on windows (where is windows.h?) Marcos Ackel (Tue Oct 02 2012 - 16:38:18 CDT)
    - Re: VMD compile on windows (where is windows.h?) John Stone (Tue Oct 02 2012 - 16:59:47 CDT)
regarding representations, resolution and length of trajectory movies Derya Meral (Tue Oct 02 2012 - 13:00:54 CDT)
- Re: regarding representations, resolution and length of trajectory movies John Stone (Tue Oct 02 2012 - 14:55:31 CDT)
Lennard-Jones parameters Abolfazl Bayat (Tue Oct 02 2012 - 10:28:38 CDT)
question about fftk Carolina Penhavel de souza (Tue Oct 02 2012 - 08:26:12 CDT)
- Re: question about fftk ehsan zahedinejad (Tue Oct 02 2012 - 11:05:35 CDT)
  - RE: question about fftk Him Bandhu Upadhyay (Tue Oct 02 2012 - 14:16:53 CDT)
  - Re: question about fftk John Stone (Wed Oct 03 2012 - 13:57:11 CDT)
writing Gaussian input files in FFTK ..... Him Bandhu Upadhyay (Mon Oct 01 2012 - 12:40:44 CDT)
Fwd: RE:psfgen and CG lloyd riggs (Mon Oct 01 2012 - 12:10:05 CDT)
RE:psfgen and CG lloyd riggs (Mon Oct 01 2012 - 11:39:43 CDT)
- Re: RE:psfgen and CG John Stone (Mon Oct 01 2012 - 12:33:19 CDT)
Solvated outside the box Steven Neumann (Mon Oct 01 2012 - 02:58:44 CDT)
- Re: Solvated outside the box Olaf Lenz (Mon Oct 01 2012 - 04:19:32 CDT)
  - Re: Solvated outside the box Steven Neumann (Mon Oct 01 2012 - 05:56:33 CDT)
    - Re: Solvated outside the box Olaf Lenz (Mon Oct 01 2012 - 06:24:05 CDT)
    - Re: Solvated outside the box Steven Neumann (Mon Oct 01 2012 - 06:29:23 CDT)
Support for Retina displays? FX (Sun Sep 30 2012 - 05:40:23 CDT)
- Re: Support for Retina displays? John Stone (Sun Sep 30 2012 - 11:11:54 CDT)
Radius of gyration from Big DCD flavio seixas (Thu Sep 27 2012 - 14:08:31 CDT)
- Re: Radius of gyration from Big DCD Bjørnar Jensen (Fri Sep 28 2012 - 05:35:53 CDT)
  - Re: Radius of gyration from Big DCD flavio seixas (Fri Sep 28 2012 - 08:07:27 CDT)
Color atoms Ivan Moncayo (Thu Sep 27 2012 - 11:59:32 CDT)
- Re: Color atoms Andrew Jewett (Sun Sep 30 2012 - 03:00:13 CDT)
  - Re: Color atoms John Stone (Sun Sep 30 2012 - 16:49:19 CDT)
    - Re: Color atoms Joshua Anderson (Mon Oct 01 2012 - 06:31:58 CDT)
IMD and AutoIMD bug when releasing forces on residues? William Ray (Thu Sep 27 2012 - 09:57:52 CDT)
- Re: IMD and AutoIMD bug when releasing forces on residues? John Stone (Thu Sep 27 2012 - 10:15:08 CDT)
  - Re: IMD and AutoIMD bug when releasing forces on residues? William Ray (Thu Sep 27 2012 - 10:51:44 CDT)
  - Re: IMD and AutoIMD bug when releasing forces on residues? William Ray (Thu Sep 27 2012 - 13:09:55 CDT)
    - Re: IMD and AutoIMD bug when releasing forces on residues? William Ray (Thu Sep 27 2012 - 13:29:49 CDT)
Re: Get objects from precompiled VMD? Axel Kohlmeyer (Thu Sep 27 2012 - 06:11:16 CDT)
Get objects from precompiled VMD? Sabine Reisser (Thu Sep 27 2012 - 04:32:01 CDT)
- Re: Get objects from precompiled VMD? John Stone (Thu Sep 27 2012 - 09:49:32 CDT)
High Bound charge values missing during charge optimization in FFTK Him Bandhu Upadhyay (Wed Sep 26 2012 - 22:32:44 CDT)
- Re: High Bound charge values missing during charge optimization in FFTK Mayne, Christopher G (Thu Sep 27 2012 - 11:15:31 CDT)
  - Re: High Bound charge values missing during charge optimization in FFTK Him Bandhu Upadhyay (Fri Sep 28 2012 - 09:42:57 CDT)
Convergence of the Gram-Charlier expansion Ali Khanlarkhani (Wed Sep 26 2012 - 10:36:37 CDT)
- Convergence of the Gram-Charlier expansion Ali Khanlarkhani (Wed Sep 26 2012 - 15:24:20 CDT)
  - Convergence of the Gram-Charlier expansion Ali Khanlarkhani (Wed Sep 26 2012 - 15:25:54 CDT)
    - Re: Convergence of the Gram-Charlier expansion John Stone (Wed Oct 10 2012 - 15:05:48 CDT)
Big DCD file help flavio seixas (Tue Sep 25 2012 - 10:16:29 CDT)
- Re: Big DCD file help Axel Kohlmeyer (Tue Sep 25 2012 - 11:10:26 CDT)
- RE: Big DCD file help Bennion, Brian (Tue Sep 25 2012 - 11:43:52 CDT)
  - RE: Big DCD file help flavio seixas (Tue Sep 25 2012 - 11:56:05 CDT)
Big DCD file flavio seixas (Tue Sep 25 2012 - 07:37:40 CDT)
Lammps simulation Ivan Moncayo (Mon Sep 24 2012 - 11:39:06 CDT)
- Re: Lammps simulation Axel Kohlmeyer (Mon Sep 24 2012 - 12:47:11 CDT)
  - Re: Lammps simulation Ivan Moncayo (Mon Sep 24 2012 - 13:02:51 CDT)
Linking Error on Mac OS X Stephen Herbein (Mon Sep 24 2012 - 10:45:25 CDT)
- Re: Linking Error on Mac OS X John Stone (Mon Sep 24 2012 - 15:03:56 CDT)
Printing accessible hydrophobic surface area Sabine Reisser (Mon Sep 24 2012 - 09:41:04 CDT)
Extracting chi angles / Saving coordinate with a script Jon (Mon Sep 24 2012 - 03:56:59 CDT)
Getting trajectories from DCD files? Venkata Mandala (Sun Sep 23 2012 - 13:48:30 CDT)
- RE: Getting trajectories from DCD files? Maria Antonieta Sanchez Farran (Sun Sep 23 2012 - 15:04:58 CDT)
  - RE: RE: Getting trajectories from DCD files?. . Martin, Erik W (Sun Sep 23 2012 - 18:18:10 CDT)
- Re: Getting trajectories from DCD files? Joshua Adelman (Sun Sep 23 2012 - 19:01:42 CDT)
changing name of N and C term residues Martin, Erik W (Fri Sep 21 2012 - 10:23:12 CDT)
- RE: changing name of N and C term residues Joaquim Rui de Castro Rodrigues (Fri Sep 21 2012 - 13:04:59 CDT)
Re: VMD in Linux, assigning a variable using awk Axel Kohlmeyer (Thu Sep 20 2012 - 14:40:52 CDT)
- Re: VMD in Linux, assigning a variable using awk Joshua D. Moore (Thu Sep 20 2012 - 14:56:41 CDT)
VMD in Linux, assigning a variable using awk Joshua D. Moore (Thu Sep 20 2012 - 13:44:04 CDT)
- RE: VMD in Linux, assigning a variable using awk Peter Lai (Thu Sep 20 2012 - 16:23:13 CDT)
Use of topotools kirtana S (Thu Sep 20 2012 - 00:13:47 CDT)
- Re: Use of topotools Axel Kohlmeyer (Thu Sep 20 2012 - 07:50:35 CDT)
Name selections Prof. Eddie (Wed Sep 19 2012 - 13:23:33 CDT)
- Re: Name selections Peter C. Lai (Wed Sep 19 2012 - 18:50:55 CDT)
Color code the structure by RMSF values Esam Tolba (Wed Sep 19 2012 - 11:40:26 CDT)
- Re: Color code the structure by RMSF values John Stone (Wed Sep 19 2012 - 12:09:56 CDT)
compiling vmd with g++-4.6 on ubuntu Sandeep Gupta (Wed Sep 19 2012 - 06:45:55 CDT)
- Re: compiling vmd with g++-4.6 on ubuntu John Stone (Wed Sep 19 2012 - 11:08:34 CDT)
  - Re: compiling vmd with g++-4.6 on ubuntu Sandeep Gupta (Wed Sep 19 2012 - 11:45:46 CDT)
    - Re: compiling vmd with g++-4.6 on ubuntu John Stone (Wed Sep 19 2012 - 12:06:22 CDT)
  - Re: compiling vmd with g++-4.6 on ubuntu Caio Silva Souza (Wed Sep 19 2012 - 12:30:53 CDT)
Reading trajectories from FMO-MD run Rasoul Nasiri (Wed Sep 19 2012 - 05:00:20 CDT)
- Re: Reading trajectories from FMO-MD run John Stone (Thu Sep 20 2012 - 14:43:26 CDT)
How to create strong bond between atoms in VMD ragesh c (Wed Sep 19 2012 - 04:24:38 CDT)
How to create strong bond between atoms in VMD ragesh c (Wed Sep 19 2012 - 04:22:41 CDT)
- Re: How to create strong bond between atoms in VMD Axel Kohlmeyer (Thu Sep 20 2012 - 07:03:07 CDT)
Q-chem MD output with VMD? John Keller (Wed Sep 19 2012 - 01:53:38 CDT)
- Re: Q-chem MD output with VMD? Benjamin Kaduk (Wed Sep 19 2012 - 09:07:18 CDT)
  - Re: Q-chem MD output with VMD? John Stone (Wed Sep 19 2012 - 10:50:54 CDT)
Hello hanif mahboobi (Tue Sep 18 2012 - 18:41:20 CDT)
- Re: Hello rainy908_at_yahoo.com (Wed Sep 12 2012 - 15:49:24 CDT)
(no subject) ragesh c (Tue Sep 18 2012 - 12:22:58 CDT)
Using Tools (grab, tug, etc) Marcos Ackel (Mon Sep 17 2012 - 13:53:51 CDT)
- Re: Using Tools (grab, tug, etc) John Stone (Tue Sep 18 2012 - 14:40:12 CDT)
APBS location in vmdrc ? Sabine Reisser (Mon Sep 17 2012 - 10:51:52 CDT)
- Re: APBS location in vmdrc ? John Stone (Thu Sep 20 2012 - 14:35:24 CDT)
  - Re: APBS location in vmdrc ? Sabine Reisser (Mon Sep 24 2012 - 09:14:11 CDT)
VMD_waterbox Shomesankar Bhunia (Sun Sep 16 2012 - 23:23:59 CDT)
How to disable CUDA in VMD 1.9.1? Joakim Swedberg (Sun Sep 16 2012 - 21:48:38 CDT)
- Re: How to disable CUDA in VMD 1.9.1? John Stone (Mon Sep 17 2012 - 10:21:06 CDT)
Invitation to connect on LinkedIn gorka lasso via LinkedIn (Sat Sep 15 2012 - 12:05:12 CDT)
Determining the Size of my Molecule Marc Gordon (Sat Sep 15 2012 - 07:15:28 CDT)
- RE: Determining the Size of my Molecule. . Martin, Erik W (Sat Sep 15 2012 - 10:29:06 CDT)
  - RE: Determining the Size of my Molecule. . Rajan Vatassery (Sat Sep 15 2012 - 16:43:08 CDT)
  - Re: Determining the Size of my Molecule. . Marc Gordon (Sun Sep 16 2012 - 05:21:29 CDT)
    - Re: Determining the Size of my Molecule. . Axel Kohlmeyer (Sun Sep 16 2012 - 17:10:21 CDT)
ERROR) Unable to change color name Teich-McGoldrick, Stephanie (Fri Sep 14 2012 - 16:40:04 CDT)
- Re: ERROR) Unable to change color name John Stone (Fri Sep 14 2012 - 16:46:10 CDT)
  - Re: [EXTERNAL] Re: ERROR) Unable to change color name Teich-McGoldrick, Stephanie (Fri Sep 14 2012 - 16:51:36 CDT)
    - Re: [EXTERNAL] Re: ERROR) Unable to change color name John Stone (Fri Sep 14 2012 - 17:44:44 CDT)
    - Re: [EXTERNAL] Re: ERROR) Unable to change color name Teich-McGoldrick, Stephanie (Fri Sep 14 2012 - 20:01:04 CDT)
Hello rainy908_at_yahoo.com (Fri Sep 14 2012 - 04:17:41 CDT)
Hi rainy908_at_yahoo.com (Fri Sep 14 2012 - 02:48:50 CDT)
- Re: Hi Garf (Fri Nov 05 2004 - 15:29:42 CST)
- Re: Hi rainy908_at_yahoo.com (Wed Sep 12 2012 - 05:13:32 CDT)
- Re: Hi rainy908_at_yahoo.com (Fri Sep 14 2012 - 01:53:34 CDT)
problem showing lammps dump files luoyuan Q (Thu Sep 13 2012 - 21:18:29 CDT)
- Re: problem showing lammps dump files Joshua D. Moore (Fri Sep 14 2012 - 13:36:44 CDT)
Duplicate option in fftk ehsan zahedinejad (Thu Sep 13 2012 - 18:53:39 CDT)
- Re: Duplicate option in fftk Mayne, Christopher G (Thu Sep 13 2012 - 19:58:48 CDT)
(no subject) rainy908_at_yahoo.com (Wed Sep 12 2012 - 23:43:19 CDT)
problem loading LAMMPS trajectory using VMD Li, Yanfei (Wed Sep 12 2012 - 22:50:20 CDT)
- Re: problem loading LAMMPS trajectory using VMD Axel Kohlmeyer (Thu Sep 13 2012 - 02:23:08 CDT)
(no subject) rainy908_at_yahoo.com (Wed Sep 12 2012 - 14:05:37 CDT)
(no subject) rainy908 (Wed Sep 12 2012 - 11:55:53 CDT)
- (no subject) Dudo (Wed Sep 12 2012 - 13:17:08 CDT)
MDFF and implicit solvent Gorka Lasso (Wed Sep 12 2012 - 10:54:01 CDT)
- Re: MDFF and implicit solvent Chris Harrison (Wed Sep 12 2012 - 12:03:45 CDT)
  - Re: MDFF and implicit solvent Gorka Lasso (Thu Sep 13 2012 - 02:40:08 CDT)
  - Re: MDFF and implicit solvent Gorka Lasso (Thu Sep 13 2012 - 03:19:42 CDT)
(no subject) rainy908_at_yahoo.com (Tue Sep 11 2012 - 23:53:20 CDT)
tutorial BIO MED (Tue Sep 11 2012 - 03:53:07 CDT)
- Re: tutorial Chris Harrison (Tue Sep 11 2012 - 04:41:16 CDT)
- Re: tutorial Ajasja LjubetiÄ (Tue Sep 11 2012 - 04:54:37 CDT)
- tutorial 2 BIO MED (Thu Sep 13 2012 - 03:12:30 CDT)
  - Re: tutorial 2 Axel Kohlmeyer (Thu Sep 13 2012 - 04:18:16 CDT)
Protein line chain in water spehere Steven Neumann (Mon Sep 10 2012 - 09:45:42 CDT)
SpaceNavigator: How can I grab a molecule? MVACKEL (Sat Sep 08 2012 - 08:59:35 CDT)
Question about generating a .js file Ganesh Kamath (Fri Sep 07 2012 - 09:57:39 CDT)
- Re: Question about generating a .js file John Stone (Thu Sep 20 2012 - 17:08:11 CDT)
  - Re: Question about generating a .js file Ganesh Kamath (Thu Sep 20 2012 - 17:25:29 CDT)
APBS automation with VMD Martin, Erik W (Fri Sep 07 2012 - 09:41:54 CDT)
- Re: APBS automation with VMD John Stone (Thu Sep 20 2012 - 15:57:24 CDT)
How to use the Grab (or Tug) Tool Marcos Ackel (Wed Sep 05 2012 - 14:10:09 CDT)
Largest published IMD (interactive simulation) examples? Marc Baaden (Tue Sep 04 2012 - 12:02:10 CDT)
- Re: Largest published IMD (interactive simulation) examples? Thomas C. Bishop (Tue Sep 04 2012 - 13:19:51 CDT)
- Re: Largest published IMD (interactive simulation) examples? John Stone (Tue Sep 04 2012 - 14:11:09 CDT)
Invitation to connect on LinkedIn Violina Sharma via LinkedIn (Tue Sep 04 2012 - 09:05:40 CDT)
a basic question on binding energy Ð¤¸»¹ó (Mon Sep 03 2012 - 08:51:01 CDT)
Question about reflecting wall in NAMD Ganesh Kamath (Fri Aug 31 2012 - 09:21:29 CDT)
- Re: Question about reflecting wall in NAMD Axel Kohlmeyer (Fri Aug 31 2012 - 10:17:55 CDT)
NAMD 2.8 and PLUMED 1.3 candy deck (Thu Aug 30 2012 - 07:23:27 CDT)
- Re: NAMD 2.8 and PLUMED 1.3 Chris Harrison (Thu Aug 30 2012 - 08:21:55 CDT)
Text-mode VMD David Minh (Wed Aug 29 2012 - 13:17:18 CDT)
- Re: Text-mode VMD John Stone (Wed Aug 29 2012 - 14:26:40 CDT)
  - Re: Text-mode VMD John Stone (Thu Sep 20 2012 - 16:31:17 CDT)
Question regarding FEP parameters snoze pa (Wed Aug 29 2012 - 13:05:15 CDT)
- Re: namd-l: Question regarding FEP parameters snoze pa (Wed Aug 29 2012 - 13:47:31 CDT)
  - Re: namd-l: Question regarding FEP parameters Chris Harrison (Wed Aug 29 2012 - 15:32:52 CDT)
pbc wrap question Daniel Klose (Mon Aug 27 2012 - 03:22:04 CDT)
Possible handle leak in 'measure gofr' VMD 1.9.1 Windows (no cuda) Sam Wallace (Sun Aug 26 2012 - 06:52:39 CDT)
- Re: Possible handle leak in 'measure gofr' VMD 1.9.1 Windows (no cuda) Axel Kohlmeyer (Sun Aug 26 2012 - 08:05:00 CDT)
  - Re: Possible handle leak in 'measure gofr' VMD 1.9.1 Windows (no cuda) Sam Wallace (Sun Aug 26 2012 - 09:02:36 CDT)
    - Re: Possible handle leak in 'measure gofr' VMD 1.9.1 Windows (no cuda) Axel Kohlmeyer (Sun Aug 26 2012 - 10:44:48 CDT)
    - Re: Possible handle leak in 'measure gofr' VMD 1.9.1 Windows (no cuda) Sam Wallace (Sun Aug 26 2012 - 21:27:07 CDT)
  - Re: Possible handle leak in 'measure gofr' VMD 1.9.1 Windows (no cuda) Sam Wallace (Sun Aug 26 2012 - 09:33:24 CDT)
- Re: Possible handle leak in 'measure gofr' VMD 1.9.1 Windows (no cuda) John Stone (Sun Aug 26 2012 - 21:33:39 CDT)
  - Re: Possible handle leak in 'measure gofr' VMD 1.9.1 Windows (no cuda) Sam Wallace (Tue Aug 28 2012 - 00:54:21 CDT)
    - Re: Possible handle leak in 'measure gofr' VMD 1.9.1 Windows (no cuda) John Stone (Fri Sep 21 2012 - 16:53:06 CDT)
    - Re: Possible handle leak in 'measure gofr' VMD 1.9.1 Windows (no cuda) Sam Wallace (Fri Sep 21 2012 - 19:14:00 CDT)
Regarding the latest VMD 1.9.2.alpha builds from BioCoRE Him Bandhu Upadhyay (Thu Aug 23 2012 - 21:01:05 CDT)
- Re: Regarding the latest VMD 1.9.2.alpha builds from BioCoRE Wang Yi (Thu Aug 23 2012 - 21:57:27 CDT)
  - Re: Regarding the latest VMD 1.9.2.alpha builds from BioCoRE Chris Harrison (Thu Aug 23 2012 - 22:34:20 CDT)
  - Re: Regarding the latest VMD 1.9.2.alpha builds from BioCoRE John Stone (Fri Sep 21 2012 - 16:45:40 CDT)
- Re: Regarding the latest VMD 1.9.2.alpha builds from BioCoRE Chris Harrison (Thu Aug 23 2012 - 22:00:46 CDT)
shift the molecules via VMD oguz gurbulak (Thu Aug 23 2012 - 05:11:18 CDT)
- Re: shift the molecules via VMD John Stone (Thu Aug 23 2012 - 09:43:37 CDT)
RDF COM Bhanita Sharma (Thu Aug 23 2012 - 00:28:56 CDT)
- Re: RDF COM Axel Kohlmeyer (Thu Aug 23 2012 - 02:47:02 CDT)
- re: RDF COM Sam Wallace (Tue Aug 28 2012 - 01:35:19 CDT)
Error while running NAMD after using patch in psfgen Ganesh Kamath (Wed Aug 22 2012 - 15:16:14 CDT)
obtaining the axis of a helix vitalini_at_zedat.fu-berlin.de (Wed Aug 22 2012 - 10:21:23 CDT)
- Re: obtaining the axis of a helix John Stone (Tue Aug 28 2012 - 16:13:09 CDT)
VolMap Tool coulombmsm - with periodic boundary conditions Bjørnar Jensen (Wed Aug 22 2012 - 06:19:08 CDT)
- Re: VolMap Tool coulombmsm - with periodic boundary conditions Bjørnar Jensen (Wed Aug 22 2012 - 07:40:24 CDT)
  - Re: VolMap Tool coulombmsm - with periodic boundary conditions John Stone (Wed Aug 22 2012 - 09:31:49 CDT)
(no subject) ragesh c (Wed Aug 22 2012 - 05:18:37 CDT)
- (no subject) Axel Kohlmeyer (Wed Aug 22 2012 - 06:17:50 CDT)
- (no subject) Leandro Martínez (Wed Aug 22 2012 - 11:04:55 CDT)
The err happens when movie maker Renderer POV-Ray javacfish (Wed Aug 22 2012 - 04:01:23 CDT)
- Re: The err happens when movie maker Renderer POV-Ray Axel Kohlmeyer (Wed Aug 22 2012 - 04:58:30 CDT)
  - Re: The err happens when movie maker Renderer POV-Ray javacfish (Thu Aug 23 2012 - 04:04:15 CDT)
    - Re: The err happens when movie maker Renderer POV-Ray Axel Kohlmeyer (Thu Aug 23 2012 - 04:07:30 CDT)
beta column in a multiseq sequences alignment Pablo Villalobos Navarro (Tue Aug 21 2012 - 18:21:07 CDT)
Error building VMD plugins from CVS 21.08.2012 Vlad Cojocaru (Tue Aug 21 2012 - 11:06:01 CDT)
- Re: Error building VMD plugins from CVS 21.08.2012 John Stone (Tue Aug 21 2012 - 12:02:06 CDT)
- Re: Error building VMD plugins from CVS 21.08.2012 Vlad Cojocaru (Wed Aug 22 2012 - 04:41:21 CDT)
  - Re: Re: Error building VMD plugins from CVS 21.08.2012 John Stone (Wed Aug 22 2012 - 09:34:30 CDT)
main menu rests to top molecule after each double click in a list of molecules Vlad Cojocaru (Tue Aug 21 2012 - 10:14:38 CDT)
- Re: main menu rests to top molecule after each double click in a list of molecules John Stone (Tue Aug 21 2012 - 10:22:05 CDT)
- Re: main menu rests to top molecule after each double click in a list of molecules Vlad Cojocaru (Tue Aug 21 2012 - 10:17:12 CDT)
writing a psf with bonds Joaquim Rui de Castro Rodrigues (Mon Aug 20 2012 - 14:13:34 CDT)
- Re: writing a psf with bonds Axel Kohlmeyer (Mon Aug 20 2012 - 15:15:31 CDT)
FLTK fonts GUIXA GONZALEZ, RAMON (Sun Aug 19 2012 - 09:26:24 CDT)
- Re: FLTK fonts John Stone (Mon Aug 20 2012 - 10:57:24 CDT)
  - Re: FLTK fonts John Stone (Mon Aug 20 2012 - 16:43:36 CDT)
CHARMM36 topology files, AutoPSF and DNA Law, Yu Kay (Fri Aug 17 2012 - 10:20:26 CDT)
- Re: CHARMM36 topology files, AutoPSF and DNA JC Gumbart (Fri Aug 17 2012 - 13:57:45 CDT)
- Re: CHARMM36 topology files, AutoPSF and DNA Suresh (Fri Aug 17 2012 - 23:30:41 CDT)
  - Re: CHARMM36 topology files, AutoPSF and DNA Law, Yu Kay (Fri Aug 17 2012 - 23:32:24 CDT)
multiple residues with same resid and problem with solvation using VMD AnkiReddy katha (Fri Aug 17 2012 - 06:36:59 CDT)
- RE: multiple residues with same resid and problem with solvation using VMD simao.pereira_at_di3.units.it (Fri Aug 17 2012 - 09:26:43 CDT)
select grafted chains in nanoparticle simao.pereira_at_di3.units.it (Thu Aug 16 2012 - 11:04:47 CDT)
- Re: select grafted chains in nanoparticle John Stone (Fri Aug 17 2012 - 10:24:19 CDT)
  - RE: select grafted chains in nanoparticle simao.pereira_at_di3.units.it (Fri Aug 17 2012 - 14:21:59 CDT)
    - Re: select grafted chains in nanoparticle John Stone (Mon Aug 20 2012 - 10:44:50 CDT)
how to get interaction energy bond.james (Wed Aug 15 2012 - 07:50:11 CDT)
- Re: how to get interaction energy Axel Kohlmeyer (Wed Aug 15 2012 - 08:37:02 CDT)
how to get interaction energy bond.james (Wed Aug 15 2012 - 06:04:29 CDT)
- Re: how to get interaction energy Axel Kohlmeyer (Wed Aug 15 2012 - 06:53:16 CDT)
Cartesian coordinates to polar coordinates Ganesh Kamath (Tue Aug 14 2012 - 17:20:30 CDT)
- Re: Cartesian coordinates to polar coordinates Axel Kohlmeyer (Wed Aug 15 2012 - 01:50:57 CDT)
VMD 1.9.1 on Macosx Snow Leopard: items greyed out Passerone, Daniele (Tue Aug 14 2012 - 04:14:17 CDT)
- Re: VMD 1.9.1 on Macosx Snow Leopard: items greyed out John Stone (Tue Aug 14 2012 - 09:10:05 CDT)
  - Re: VMD 1.9.1 on Macosx Snow Leopard: items greyed out John Stone (Tue Aug 14 2012 - 09:30:05 CDT)
creating a modified pdb/psf file Sean T Kigerl (Tue Aug 14 2012 - 00:43:26 CDT)
- Re: creating a modified pdb/psf file Monika Madhavi (Tue Aug 14 2012 - 07:11:33 CDT)
- Re: creating a modified pdb/psf file Axel Kohlmeyer (Tue Aug 14 2012 - 07:25:42 CDT)
Failure getting correct charge on the system Francesco Pietra (Mon Aug 13 2012 - 02:34:56 CDT)
- Re: Failure getting correct charge on the system Axel Kohlmeyer (Mon Aug 13 2012 - 03:37:08 CDT)
  - Re: Failure getting correct charge on the system Francesco Pietra (Mon Aug 13 2012 - 04:38:46 CDT)
    - Re: Failure getting correct charge on the system Axel Kohlmeyer (Mon Aug 13 2012 - 04:45:16 CDT)
    - Re: Failure getting correct charge on the system Francesco Pietra (Mon Aug 13 2012 - 05:13:41 CDT)
pleaseme help how to build Metal ion topology file conneted aramice Malkhasian (Sat Aug 11 2012 - 01:50:05 CDT)
long bonds in surface structure is not shown in vmd !? Fatemesadat Emami (Fri Aug 10 2012 - 19:28:42 CDT)
- Re: long bonds in surface structure is not shown in vmd !? Axel Kohlmeyer (Sat Aug 11 2012 - 23:28:48 CDT)
how add new plugin to vmd hamid mosaddeghi (Fri Aug 10 2012 - 15:17:20 CDT)
- Re: how add new plugin to vmd Axel Kohlmeyer (Fri Aug 10 2012 - 16:27:00 CDT)
- Re: how add new plugin to vmd hamid mosaddeghi (Sat Aug 11 2012 - 06:54:30 CDT)
  - Re: Re: how add new plugin to vmd Axel Kohlmeyer (Sat Aug 11 2012 - 08:10:46 CDT)
    - Re: Re: how add new plugin to vmd hamid mosaddeghi (Sat Aug 11 2012 - 10:36:29 CDT)
    - Re: Re: how add new plugin to vmd Axel Kohlmeyer (Sat Aug 11 2012 - 17:23:25 CDT)
RMSF plugin to share flavio seixas (Fri Aug 10 2012 - 11:37:42 CDT)
SASA Algorithm?? Jeremy Lucid (Fri Aug 10 2012 - 04:46:27 CDT)
- Re: SASA Algorithm?? Axel Kohlmeyer (Fri Aug 10 2012 - 06:42:54 CDT)
convert dcd to coordinate, each frame, conserving the identity fabrizio.benedetti_at_unil.ch (Fri Aug 10 2012 - 02:23:30 CDT)
- Re: convert dcd to coordinate, each frame, conserving the identity Axel Kohlmeyer (Fri Aug 10 2012 - 03:13:23 CDT)
Convert CHARMM psf to X-PLOR Monika Madhavi (Fri Aug 10 2012 - 01:04:08 CDT)
- Re: Convert CHARMM psf to X-PLOR John Stone (Fri Aug 10 2012 - 09:29:08 CDT)
  - Re: Convert CHARMM psf to X-PLOR Monika Madhavi (Fri Aug 10 2012 - 10:19:15 CDT)
  - Re: Convert CHARMM psf to X-PLOR Axel Kohlmeyer (Fri Aug 10 2012 - 10:43:03 CDT)
how to write topology for Metal in protein aramice Malkhasian (Thu Aug 09 2012 - 17:28:33 CDT)
- Re: how to write topology for Metal in protein Axel Kohlmeyer (Fri Aug 10 2012 - 02:07:38 CDT)
B-factor plugin flavio seixas (Thu Aug 09 2012 - 14:13:26 CDT)
- Re: B-factor plugin Wang Yi (Thu Aug 09 2012 - 15:00:42 CDT)
  - Re: B-factor plugin Axel Kohlmeyer (Thu Aug 09 2012 - 15:50:47 CDT)
Selecting based on parameters from another file Nate Hurley (Thu Aug 09 2012 - 11:22:02 CDT)
- Re: Selecting based on parameters from another file Axel Kohlmeyer (Fri Aug 10 2012 - 02:08:02 CDT)
- Re: Selecting based on parameters from another file Ana Celia Vila Verde (Fri Aug 10 2012 - 02:23:27 CDT)
unique residue names Jim Kress (Thu Aug 09 2012 - 10:47:33 CDT)
topology file for metal in the protein aramice Malkhasian (Thu Aug 09 2012 - 10:12:43 CDT)
- Re: topology file for metal in the protein Ana Celia Vila Verde (Fri Aug 10 2012 - 02:30:51 CDT)
unique residue names Jim Kress (Thu Aug 09 2012 - 09:55:42 CDT)
- Re: unique residue names Axel Kohlmeyer (Thu Aug 09 2012 - 11:12:39 CDT)
  - RE: unique residue names Jim Kress (Thu Aug 09 2012 - 13:26:28 CDT)
Showing frame number on display? Bryan Roessler (Wed Aug 08 2012 - 12:04:58 CDT)
- Re: Showing frame number on display? Peter C. Lai (Wed Aug 08 2012 - 16:35:41 CDT)
- Re: Showing frame number on display? John Stone (Wed Aug 08 2012 - 16:43:00 CDT)
- Re: Showing frame number on display? Peter C. Lai (Wed Aug 08 2012 - 16:49:54 CDT)
  - Re: Showing frame number on display? John Stone (Wed Aug 08 2012 - 16:57:18 CDT)
    - Re: Showing frame number on display? Bryan Roessler (Thu Aug 09 2012 - 11:12:02 CDT)
3D projectors compatible with VMD. Diego Gomes (Tue Aug 07 2012 - 20:43:23 CDT)
- Re: 3D projectors compatible with VMD. John Stone (Wed Aug 08 2012 - 09:49:41 CDT)
Creating surfaces with desired lengths- Inorganic Builder Monika Madhavi (Mon Aug 06 2012 - 23:26:37 CDT)
ESPResSo Summer School Olaf Lenz (Mon Aug 06 2012 - 09:10:22 CDT)
connect a spring between all the atoms present in pdb structure SONY kaur (Sat Aug 04 2012 - 04:31:42 CDT)
- Re: namd-l: connect a spring between all the atoms present in pdb structure Axel Kohlmeyer (Sat Aug 04 2012 - 13:21:27 CDT)
- Re: connect a spring between all the atoms present in pdb structure Axel Kohlmeyer (Sat Aug 04 2012 - 13:20:05 CDT)
Re: namd-l: How to create psf for graphene Monika Madhavi (Sat Aug 04 2012 - 01:04:24 CDT)
- Re: namd-l: How to create psf for graphene Axel Kohlmeyer (Sat Aug 04 2012 - 13:28:04 CDT)
problem with polygon file conversion to pdb Oliver Schmetzer (Fri Aug 03 2012 - 11:33:21 CDT)
- Re: problem with polygon file conversion to pdb John Stone (Fri Aug 03 2012 - 13:47:17 CDT)
Setting molecule ColorID to values greater than 32 Nate Hurley (Thu Aug 02 2012 - 13:36:02 CDT)
- Re: Setting molecule ColorID to values greater than 32 John Stone (Thu Aug 02 2012 - 14:01:18 CDT)
- Re: Setting molecule ColorID to values greater than 32 Dudo (Fri Aug 03 2012 - 09:07:56 CDT)
Creating psf file for graphene sheet Monika Madhavi (Thu Aug 02 2012 - 04:10:07 CDT)
(no subject) DUCHER Roland (Thu Aug 02 2012 - 04:09:33 CDT)
- Re: Axel Kohlmeyer (Thu Aug 02 2012 - 05:11:39 CDT)
missing terminal residues while generating side chain atoms by psfgen MeiShan Lin (Wed Aug 01 2012 - 13:36:51 CDT)
- Re: missing terminal residues while generating side chain atoms by psfgen Jernej Zidar (Thu Aug 02 2012 - 04:31:10 CDT)
how to generate .pdb file of graphene in VMD(nanotube builder) ragesh c (Wed Aug 01 2012 - 04:45:23 CDT)
- Re: how to generate .pdb file of graphene in VMD(nanotube builder) Axel Kohlmeyer (Wed Aug 01 2012 - 06:20:08 CDT)
VMD 1.9.1 python interpreter Carolyn Phillips (Tue Jul 31 2012 - 18:54:23 CDT)
- Re: VMD 1.9.1 python interpreter Carolyn Phillips (Tue Jul 31 2012 - 19:00:26 CDT)
  - Re: Re: VMD 1.9.1 python interpreter John Stone (Tue Jul 31 2012 - 19:45:06 CDT)
Loop through atoms in a molecule Gamot, Ritchie (Tue Jul 31 2012 - 06:51:52 CDT)
- Re: Loop through atoms in a molecule John Stone (Tue Jul 31 2012 - 11:57:29 CDT)
SpaceNavigator on Win7 64 bit James Ryley (Mon Jul 30 2012 - 20:53:14 CDT)
- Re: SpaceNavigator on Win7 64 bit John Stone (Tue Jul 31 2012 - 11:44:32 CDT)
  - RE: SpaceNavigator on Win7 64 bit James Ryley (Tue Jul 31 2012 - 12:25:12 CDT)
Question about H-bond plugin flavio seixas (Mon Jul 30 2012 - 15:36:06 CDT)
Representation Selections Joshua Engelman (Mon Jul 30 2012 - 14:47:57 CDT)
- Re: Representation Selections John Stone (Mon Jul 30 2012 - 15:03:54 CDT)
Minor error in VMD PSF parser for atom charges Tristan Croll (Sat Jul 28 2012 - 19:53:08 CDT)
- Re: Minor error in VMD PSF parser for atom charges John Stone (Mon Jul 30 2012 - 16:25:35 CDT)
  - Re: Minor error in VMD PSF parser for atom charges Tristan Croll (Mon Jul 30 2012 - 17:32:45 CDT)
RE: possible problem with graphics rep gui under with large numbers of molecules Bennion, Brian (Fri Jul 27 2012 - 12:41:51 CDT)
- Re: possible problem with graphics rep gui under with large numbers of molecules John Stone (Fri Jul 27 2012 - 12:50:45 CDT)
APBS plugin requires molecule renaming after drag and drop loading of .pqr file Christopher Neale (Thu Jul 26 2012 - 21:03:35 CDT)
- Re: APBS plugin requires molecule renaming after drag and drop loading of .pqr file John Stone (Fri Jul 27 2012 - 11:34:13 CDT)
VMD compilation 64 bits Ivan Moncayo (Wed Jul 25 2012 - 12:03:49 CDT)
- Re: VMD compilation 64 bits John Stone (Wed Jul 25 2012 - 15:09:03 CDT)
  - Re: VMD compilation 64 bits Ivan Moncayo (Wed Jul 25 2012 - 16:22:47 CDT)
Dowser files and manual Sebastián Gutiérrez (Tue Jul 24 2012 - 18:50:37 CDT)
- Re: Dowser files and manual John Stone (Tue Jul 24 2012 - 23:19:26 CDT)
attaching an arbitrary surface molecule to a nanopore Sean T Kigerl (Tue Jul 24 2012 - 14:25:06 CDT)
Search options within mailing list Monika Madhavi (Tue Jul 24 2012 - 13:22:02 CDT)
- Re: Search options within mailing list John Stone (Tue Jul 24 2012 - 13:36:38 CDT)
- Re: Search options within mailing list Jan-Philip Gehrcke (Tue Jul 24 2012 - 14:19:11 CDT)
Charmm FF parameter file for 2-hydroxypyridine Him Bandhu Upadhyay (Tue Jul 24 2012 - 13:10:30 CDT)
- Re: Charmm FF parameter file for 2-hydroxypyridine Mayne, Christopher G (Tue Jul 24 2012 - 13:52:23 CDT)
Re: FW: difficulty in viewing AMBER mdcrd files Mahendra B Thapa (Tue Jul 24 2012 - 12:38:00 CDT)
- Re: FW: difficulty in viewing AMBER mdcrd files Thomas C. Bishop (Tue Jul 24 2012 - 15:24:15 CDT)
  - Re: FW: difficulty in viewing AMBER mdcrd files John Stone (Tue Jul 24 2012 - 15:36:01 CDT)
    - Re: FW: difficulty in viewing AMBER mdcrd files Brian Radak (Wed Jul 25 2012 - 08:45:38 CDT)
    - Re: FW: difficulty in viewing AMBER mdcrd files Thomas C. Bishop (Wed Jul 25 2012 - 11:40:35 CDT)
Question about Drude polarizable model Ganesh Kamath (Tue Jul 24 2012 - 11:19:03 CDT)
- Re: Question about Drude polarizable model John Stone (Tue Jul 24 2012 - 11:36:44 CDT)
  - Re: Question about Drude polarizable model David Hardy (Tue Jul 24 2012 - 12:19:41 CDT)
(no subject) Monika Madhavi (Tue Jul 24 2012 - 10:20:54 CDT)
- Re: John Stone (Tue Jul 24 2012 - 11:56:10 CDT)
iOS support? Samuel Schlachter (Tue Jul 24 2012 - 09:59:51 CDT)
- Re: iOS support? John Stone (Tue Jul 24 2012 - 10:08:14 CDT)
Scripting API: are arguments to representation types documented somewhere? Jan-Philip Gehrcke (Tue Jul 24 2012 - 07:58:04 CDT)
- Re: Scripting API: are arguments to representation types documented somewhere? Jan-Philip Gehrcke (Mon Aug 20 2012 - 06:24:17 CDT)
  - Re: Scripting API: are arguments to representation types documented somewhere? Axel Kohlmeyer (Mon Aug 20 2012 - 07:15:52 CDT)
  - Re: Scripting API: are arguments to representation types documented somewhere? Ajasja LjubetiÄ (Mon Aug 20 2012 - 07:34:55 CDT)
(no subject) Monika Madhavi (Tue Jul 24 2012 - 07:53:40 CDT)
- Re: Axel Kohlmeyer (Tue Jul 24 2012 - 11:10:42 CDT)
molefacture selection Reza Khalkhali (Tue Jul 24 2012 - 07:44:50 CDT)
- Re: molefacture selection John Stone (Tue Jul 24 2012 - 10:13:43 CDT)
Generating PSF for 1JNO.pdb chain A Ramin Ekhteiari (Tue Jul 24 2012 - 06:57:42 CDT)
converting Desmond trajectory and energy file to gromacs Nidhi Jatana (Tue Jul 24 2012 - 04:53:48 CDT)
- Re: converting Desmond trajectory and energy file to gromacs Axel Kohlmeyer (Tue Jul 24 2012 - 06:22:00 CDT)
vmd 1.9.1 Centos oguz gurbulak (Tue Jul 24 2012 - 04:12:29 CDT)
- Re: vmd 1.9.1 Centos John Stone (Tue Jul 24 2012 - 10:02:13 CDT)
  - Re: vmd 1.9.1 Centos oguz gurbulak (Wed Jul 25 2012 - 02:04:08 CDT)
VolMap. mass weighted densities raunest (Tue Jul 24 2012 - 04:05:43 CDT)
- Re: VolMap. mass weighted densities John Stone (Tue Jul 24 2012 - 10:26:00 CDT)
(no subject) Monika Madhavi (Mon Jul 23 2012 - 13:51:19 CDT)
- Re: John Stone (Mon Jul 23 2012 - 15:59:09 CDT)
(no subject) Monika Madhavi (Mon Jul 23 2012 - 09:04:15 CDT)
- Re: Axel Kohlmeyer (Mon Jul 23 2012 - 12:46:16 CDT)
Problem with Reading GROMACS file in VMD satya kumar (Sun Jul 22 2012 - 22:06:42 CDT)
- Re: Problem with Reading GROMACS file in VMD Axel Kohlmeyer (Sun Jul 22 2012 - 23:46:35 CDT)
  - Re: Problem with Reading GROMACS file in VMD satya kumar (Mon Jul 23 2012 - 12:24:20 CDT)
Python plans Caio Silva Souza (Sat Jul 21 2012 - 18:47:13 CDT)
- Re: Python plans John Stone (Tue Jul 24 2012 - 11:48:52 CDT)
  - Re: Python plans Olaf Lenz (Wed Jul 25 2012 - 03:07:49 CDT)
  - Re: Python plans John Stone (Wed Aug 01 2012 - 10:46:26 CDT)
RE: Joining DCD files with overlapping frames amin_at_imtech.res.in (Fri Jul 20 2012 - 05:21:58 CDT)
RE: Joining DCD files with overlapping frames. JC Gumbart (Fri Jul 20 2012 - 01:40:50 CDT)
- RE: Joining DCD files with overlapping frames. amin_at_imtech.res.in (Fri Jul 20 2012 - 08:53:47 CDT)
Joining DCD files with overlapping frames. amin_at_imtech.res.in (Thu Jul 19 2012 - 21:53:08 CDT)
- Re: Joining DCD files with overlapping frames. JC Gumbart (Fri Jul 20 2012 - 00:05:33 CDT)
VMD's superposition algorithm Víctor (Thu Jul 19 2012 - 05:06:29 CDT)
- Re: VMD's superposition algorithm Axel Kohlmeyer (Thu Jul 19 2012 - 06:55:12 CDT)
  - Re: VMD's superposition algorithm Víctor (Thu Jul 19 2012 - 07:17:54 CDT)
    - Re: VMD's superposition algorithm Axel Kohlmeyer (Thu Jul 19 2012 - 07:28:09 CDT)
    - Re: VMD's superposition algorithm Víctor (Thu Jul 19 2012 - 07:41:45 CDT)
constant velocity for carbon nanotubes bond.james (Wed Jul 18 2012 - 21:38:48 CDT)
- Re: constant velocity for carbon nanotubes Axel Kohlmeyer (Thu Jul 19 2012 - 02:15:07 CDT)
namdEnergy doesn't run on clusters Wang Yi (Tue Jul 17 2012 - 22:28:06 CDT)
- Re: namdEnergy doesn't run on clusters John Stone (Wed Jul 18 2012 - 09:46:30 CDT)
periodic bonds in vmd Fatemesadat Emami (Tue Jul 17 2012 - 13:10:59 CDT)
- Re: periodic bonds in vmd Olaf Lenz (Tue Jul 17 2012 - 14:15:45 CDT)
- Re: periodic bonds in vmd Axel Kohlmeyer (Tue Jul 17 2012 - 14:27:39 CDT)
  - periodic bonds in vmd Fatemesadat Emami (Tue Jul 17 2012 - 14:38:41 CDT)
H-H dynamic bonds DESPIAU-PUJO Emilie UJF (Tue Jul 17 2012 - 09:58:31 CDT)
- Re: H-H dynamic bonds Axel Kohlmeyer (Tue Jul 17 2012 - 11:22:07 CDT)
IMD selections Thomas C. Bishop (Mon Jul 16 2012 - 10:25:05 CDT)
- Re: IMD selections Axel Kohlmeyer (Mon Jul 16 2012 - 11:25:49 CDT)
  - Re: IMD selections John Stone (Mon Jul 16 2012 - 11:44:02 CDT)
    - Re: IMD selections Thomas C. Bishop (Mon Jul 16 2012 - 13:16:32 CDT)
problem generating psf file Ginger Emel (Fri Jul 13 2012 - 11:22:50 CDT)
- Re: problem generating psf file John Stone (Wed Jul 18 2012 - 10:56:45 CDT)
how to change color of the one type of atom niaz poorgholami (Fri Jul 13 2012 - 08:15:42 CDT)
- Re: how to change color of the one type of atom Axel Kohlmeyer (Fri Jul 13 2012 - 09:05:31 CDT)
Building a beta barrel using a beta hairpin Diego Granados (Thu Jul 12 2012 - 17:27:43 CDT)
Re: namd-l: Re: vmd installation problem Axel Kohlmeyer (Thu Jul 12 2012 - 01:53:15 CDT)
- Re: namd-l: Re: vmd installation problem Jernej Zidar (Thu Jul 12 2012 - 01:23:25 CDT)
vmd installation problem oguz gurbulak (Wed Jul 11 2012 - 09:54:16 CDT)
- Re: vmd installation problem John Stone (Wed Jul 11 2012 - 09:59:27 CDT)
  - Re: vmd installation problem oguz gurbulak (Thu Jul 12 2012 - 02:43:58 CDT)
    - Re: vmd installation problem Axel Kohlmeyer (Thu Jul 12 2012 - 03:52:04 CDT)
fftk: domain error: argument not in valid range Ð¤¸»¹ó (Tue Jul 10 2012 - 03:30:31 CDT)
- Re: fftk: domain error: argument not in valid range Mayne, Christopher G (Tue Jul 10 2012 - 08:57:56 CDT)
psfgen, mutate, and multiple chains Andrea Kirkpatrick (Mon Jul 09 2012 - 17:31:35 CDT)
'Hands-On' Workshop on Computational Biophysics using VMD and NAMD, October 22-26, 2012 in Urbana, Illinois David Brandon (Mon Jul 09 2012 - 14:32:25 CDT)
Distance constraints satya kumar (Fri Jul 06 2012 - 18:34:20 CDT)
- Re: Distance constraints Axel Kohlmeyer (Fri Jul 06 2012 - 23:05:45 CDT)
  - Re: Distance constraints Suresh (Fri Jul 06 2012 - 23:33:01 CDT)
  - Re: Distance constraints satya kumar (Mon Jul 09 2012 - 08:15:51 CDT)
Secondary Structure Issue Sarah Richards (Fri Jul 06 2012 - 08:16:04 CDT)
- Re: Secondary Structure Issue John Stone (Thu Jul 12 2012 - 10:24:08 CDT)
  - Re: Secondary Structure Issue John Stone (Wed Jul 18 2012 - 09:57:28 CDT)
Building unit cell from asymmetric unit Sebastián Gutiérrez (Wed Jul 04 2012 - 17:16:32 CDT)
- Re: Building unit cell from asymmetric unit Axel Kohlmeyer (Thu Jul 05 2012 - 01:50:28 CDT)
  - Re: Building unit cell from asymmetric unit Sebastián Gutiérrez (Thu Jul 05 2012 - 11:33:43 CDT)
about analysis plugin oguz gurbulak (Wed Jul 04 2012 - 09:40:30 CDT)
- Re: about analysis plugin Axel Kohlmeyer (Wed Jul 04 2012 - 11:09:07 CDT)
  - Re: about analysis plugin oguz gurbulak (Fri Jul 06 2012 - 01:39:08 CDT)
    - Re: about analysis plugin John Stone (Thu Jul 12 2012 - 10:29:05 CDT)
Problem with psfgen and Drude Polarizable Force Field Roman Shevchuk (Wed Jul 04 2012 - 06:42:06 CDT)
3D visualization options on Linux boxes Vikas Varshney (Tue Jul 03 2012 - 11:37:48 CDT)
- Re: 3D visualization options on Linux boxes John Stone (Tue Jul 03 2012 - 12:01:10 CDT)
  - Re: 3D visualization options on Linux boxes Vikas Varshney (Tue Jul 03 2012 - 12:33:27 CDT)
    - Re: 3D visualization options on Linux boxes Vikas Varshney (Thu Jul 05 2012 - 09:35:17 CDT)
    - Re: 3D visualization options on Linux boxes John Stone (Thu Jul 05 2012 - 11:39:49 CDT)
3d space navigator and MacosX-vmd Passerone, Daniele (Mon Jul 02 2012 - 22:08:28 CDT)
- Re: 3d space navigator and MacosX-vmd Passerone, Daniele (Fri Jul 06 2012 - 07:01:20 CDT)
  - Re: 3d space navigator and MacosX-vmd John Stone (Tue Jul 10 2012 - 10:04:52 CDT)
Problem with tachyon Fatemesadat Emami (Mon Jul 02 2012 - 16:25:43 CDT)
- Re: Problem with tachyon John Stone (Mon Jul 02 2012 - 16:38:30 CDT)
difficulty in viewing AMBER mdcrd files Mahendra B Thapa (Mon Jul 02 2012 - 11:56:43 CDT)
- Re: difficulty in viewing AMBER mdcrd files Axel Kohlmeyer (Mon Jul 02 2012 - 12:56:46 CDT)
- Re: difficulty in viewing AMBER mdcrd files John Stone (Mon Jul 02 2012 - 15:22:10 CDT)
  - Re: difficulty in viewing AMBER mdcrd files Thomas C. Bishop (Sat Jul 07 2012 - 09:56:37 CDT)
volmap Áõ½ð·å (Sun Jul 01 2012 - 09:01:33 CDT)
remove a selection in vmd? Fatemesadat Emami (Sat Jun 30 2012 - 21:50:36 CDT)
- Re: remove a selection in vmd? Wang Yi (Sun Jul 01 2012 - 00:09:54 CDT)
pore radius measurement Raul Araya (Fri Jun 29 2012 - 13:50:00 CDT)
- Re: pore radius measurement John Stone (Thu Jul 12 2012 - 10:34:38 CDT)
VMD selection: change atom size across various frames Wolf Dapp (Fri Jun 29 2012 - 08:57:04 CDT)
- Re: VMD selection: change atom size across various frames Axel Kohlmeyer (Fri Jun 29 2012 - 10:26:27 CDT)
  - Re: VMD selection: change atom size across various frames Wolf Dapp (Mon Jul 02 2012 - 03:25:22 CDT)
    - Re: VMD selection: change atom size across various frames Axel Kohlmeyer (Mon Jul 02 2012 - 05:10:50 CDT)
bug of VMD Albert (Fri Jun 29 2012 - 03:40:15 CDT)
- Re: bug of VMD John Stone (Thu Jul 12 2012 - 10:37:18 CDT)
problem with pbc wrap Dian Jiao (Thu Jun 28 2012 - 13:46:00 CDT)
- Re: problem with pbc wrap Axel Kohlmeyer (Thu Jun 28 2012 - 17:09:09 CDT)
Isosurfaces and volume slices FX (Thu Jun 28 2012 - 08:22:29 CDT)
- Re: Isosurfaces and volume slices John Stone (Thu Jul 12 2012 - 10:42:53 CDT)
DX potential files Abolfazl Bayat (Thu Jun 28 2012 - 04:10:23 CDT)
- Re: DX potential files John Stone (Thu Jul 12 2012 - 10:45:37 CDT)
- Re: DX potential files raunest (Tue Jul 24 2012 - 03:35:37 CDT)
  - Re: Re: DX potential files John Stone (Tue Jul 24 2012 - 10:33:23 CDT)
Building a membrane Vince Cho (Wed Jun 27 2012 - 23:03:54 CDT)
- Re: Building a membrane Sebastián Gutiérrez (Tue Jul 03 2012 - 11:31:41 CDT)
  - Re: Building a membrane Vince Cho (Tue Jul 03 2012 - 12:44:39 CDT)
    - Re: Building a membrane Sebastián Gutiérrez (Wed Jul 04 2012 - 17:40:32 CDT)
how to calculate water density in the 'hole'? Albert (Wed Jun 27 2012 - 13:26:01 CDT)
- Re: how to calculate water density in the 'hole'? fariba taghavi (Thu Jun 28 2012 - 01:09:05 CDT)
  - Re: how to calculate water density in the 'hole'? meisam valizadeh kiamahalleh (Thu Jun 28 2012 - 05:38:45 CDT)
    - Re: how to calculate water density in the 'hole'? Albert (Thu Jun 28 2012 - 07:18:11 CDT)
    - Re: how to calculate water density in the 'hole'? fariba taghavi (Sat Jun 30 2012 - 10:36:44 CDT)
Python script to fix autoionize issues related to long atom type names Evgeny Bulat (Tue Jun 26 2012 - 16:42:37 CDT)
- Re: Python script to fix autoionize issues related to long atom type names Thomas C. Bishop (Wed Jun 27 2012 - 08:24:30 CDT)
TkConsole functions Fatemesadat Emami (Tue Jun 26 2012 - 14:38:16 CDT)
- Script for Lipid Order Parameter Ricardo Soares (Wed Jun 27 2012 - 13:58:58 CDT)
computing potential using pmepot Abolfazl Bayat (Mon Jun 25 2012 - 11:16:49 CDT)
Force Field ToolKit and QM codes other than Gaussian MOHAMMAD JAVAD AGHAEI (Mon Jun 25 2012 - 02:05:41 CDT)
- Re: Force Field ToolKit and QM codes other than Gaussian Axel Kohlmeyer (Mon Jun 25 2012 - 05:07:47 CDT)
dump to vmd Ramin Ekhteiari (Sun Jun 24 2012 - 04:19:57 CDT)
- Re: dump to vmd Axel Kohlmeyer (Sun Jun 24 2012 - 06:44:01 CDT)
Running ProcupinePlot script Ban Arn (Fri Jun 22 2012 - 10:01:38 CDT)
- Re: Running ProcupinePlot script John Stone (Fri Jun 22 2012 - 11:44:18 CDT)
  - Re: Running ProcupinePlot script Ban Arn (Fri Jun 22 2012 - 11:53:33 CDT)
patch SAM in psfgen flavio seixas (Fri Jun 22 2012 - 09:37:17 CDT)
- Re: patch SAM in psfgen JC Gumbart (Fri Jun 22 2012 - 23:35:14 CDT)
  - Re: patch SAM in psfgen flavio seixas (Sat Jun 23 2012 - 14:13:14 CDT)
generating psf files for bicarbonate Traci Clymer (Fri Jun 22 2012 - 09:13:36 CDT)
- Re: generating psf files for bicarbonate flavio seixas (Fri Jun 22 2012 - 13:21:35 CDT)
- Re: generating psf files for bicarbonate JC Gumbart (Fri Jun 22 2012 - 23:32:42 CDT)
VMD NMWiz plugin Ban Arn (Thu Jun 21 2012 - 11:16:08 CDT)
Workshop for Computational Chemistry and Physics MARK PLUMMER (Wed Jun 20 2012 - 15:20:40 CDT)
changing font size Shyno Mathew (Tue Jun 19 2012 - 16:44:13 CDT)
- Re: changing font size John Stone (Thu Jun 21 2012 - 10:10:31 CDT)
  - Re: changing font size Shyno Mathew (Thu Jun 21 2012 - 10:18:05 CDT)
Bond angle distribution Prof. Eddie (Tue Jun 19 2012 - 13:49:33 CDT)
- Re: Bond angle distribution Wang Yi (Tue Jun 19 2012 - 15:13:48 CDT)
PMEpot plugin Abolfazl Bayat (Tue Jun 19 2012 - 11:43:42 CDT)
- Re: PMEpot plugin Axel Kohlmeyer (Tue Jun 19 2012 - 13:06:38 CDT)
  - Re: PMEpot plugin Bryan Roessler (Wed Jun 20 2012 - 17:03:25 CDT)
Getting the internal coordinates table Ajasja LjubetiÄ (Mon Jun 18 2012 - 04:11:03 CDT)
- Re: Getting the internal coordinates table JC Gumbart (Mon Jun 18 2012 - 17:05:56 CDT)
  - Re: Getting the internal coordinates table Mayne, Christopher G (Mon Jun 18 2012 - 22:07:28 CDT)
    - Re: Getting the internal coordinates table Ajasja LjubetiÄ (Tue Jun 19 2012 - 04:06:50 CDT)
fix the viewing angles XY (Mon Jun 18 2012 - 00:29:56 CDT)
- Re: fix the viewing angles Axel Kohlmeyer (Mon Jun 18 2012 - 06:27:10 CDT)
Changing the color of atoms of a particular name Andrew DeYoung (Sat Jun 16 2012 - 18:50:47 CDT)
- Re: Changing the color of atoms of a particular name Axel Kohlmeyer (Sun Jun 17 2012 - 06:45:40 CDT)
SBCG Bond/Angle Parameter Extraction Files Tye Dwight Martin (Fri Jun 15 2012 - 17:28:59 CDT)
difference in angles and dihedral between psf files Raul Araya (Thu Jun 14 2012 - 10:02:58 CDT)
scripting bond labeling Prof. Eddie (Wed Jun 13 2012 - 16:44:18 CDT)
- Re: scripting bond labeling Axel Kohlmeyer (Wed Jun 13 2012 - 17:47:25 CDT)
  - Re: scripting bond labeling Prof. Eddie (Sat Jun 30 2012 - 09:29:50 CDT)
    - Re: scripting bond labeling Axel Kohlmeyer (Sat Jun 30 2012 - 10:32:04 CDT)
VMD for rectifying oxygen atoms ? Marc Hömberger (Wed Jun 13 2012 - 09:53:31 CDT)
VMD 1.9 installation on linux Shyno Mathew (Wed Jun 13 2012 - 08:09:43 CDT)
- Re: VMD 1.9 installation on linux Axel Kohlmeyer (Wed Jun 13 2012 - 09:00:11 CDT)
- Re: VMD 1.9 installation on linux bsnmrem-obj_at_yahoo.com (Wed Jun 13 2012 - 19:18:47 CDT)
  - Re: VMD 1.9 installation on linux Axel Kohlmeyer (Wed Jun 13 2012 - 20:06:28 CDT)
    - Re: VMD 1.9 installation on linux Shyno Mathew (Thu Jun 14 2012 - 11:17:52 CDT)
Problems with analysis tools INPE (Ingrid Viveka Pettersson) (Wed Jun 13 2012 - 07:05:30 CDT)
- Re: Problems with analysis tools Axel Kohlmeyer (Wed Jun 13 2012 - 08:08:17 CDT)
  - Re: Problems with analysis tools Axel Kohlmeyer (Wed Jun 13 2012 - 08:11:41 CDT)
Using psfgen with long atom names (How to prepare PDB file?) Ajasja LjubetiÄ (Wed Jun 13 2012 - 05:33:27 CDT)
- Re: Using psfgen with long atom names (How to prepare PDB file?) Ajasja LjubetiÄ (Wed Jun 13 2012 - 05:41:27 CDT)
- Re: Using psfgen with long atom names (How to prepare PDB file?) Vincent Leroux (Wed Jun 13 2012 - 10:08:18 CDT)
The "gopython" is wrong on the Lunux VMD1.9.1 javacfish (Wed Jun 13 2012 - 01:21:59 CDT)
- Re: The "gopython" is wrong on the Lunux VMD1.9.1 Axel Kohlmeyer (Wed Jun 13 2012 - 05:50:48 CDT)
  - Re: The "gopython" is wrong on the Lunux VMD1.9.1 javacfish (Thu Jun 14 2012 - 07:27:59 CDT)
    - Re: The "gopython" is wrong on the Lunux VMD1.9.1 Axel Kohlmeyer (Thu Jun 14 2012 - 07:48:04 CDT)
    - Re: The "gopython" is wrong on the Lunux VMD1.9.1 Ajasja LjubetiÄ (Thu Jun 14 2012 - 08:29:40 CDT)
wrapall visualization Prof. Eddie (Tue Jun 12 2012 - 12:03:39 CDT)
Workshop - Computational Molecular Physics of Non-Bonded Bio-Molecular Interactions MARK PLUMMER (Mon Jun 11 2012 - 17:16:47 CDT)
(no subject) Francesco Pietra (Sun Jun 10 2012 - 12:45:22 CDT)
hbond Subrata Paul (Sat Jun 09 2012 - 06:27:34 CDT)
Finding the Number of Chains Present via Scripting Nate Hurley (Fri Jun 08 2012 - 11:19:12 CDT)
- Re: Finding the Number of Chains Present via Scripting Axel Kohlmeyer (Fri Jun 08 2012 - 12:10:36 CDT)
- Re: Finding the Number of Chains Present via Scripting harish vashisth (Fri Jun 08 2012 - 12:49:18 CDT)
unwrapping long trajectories Edward Lyman (Fri Jun 08 2012 - 10:09:48 CDT)
- Re: unwrapping long trajectories Jérôme Hénin (Mon Jun 11 2012 - 09:54:00 CDT)
  - Re: unwrapping long trajectories Edward Lyman (Mon Jun 11 2012 - 18:05:32 CDT)
problem vmd python Tom King (Wed Jun 06 2012 - 08:20:09 CDT)
- Re: problem vmd python John Stone (Thu Jun 07 2012 - 15:13:07 CDT)
namd/vmd support to GTX-6## series Francesco Pietra (Wed Jun 06 2012 - 03:43:38 CDT)
- Re: namd/vmd support to GTX-6## series John Stone (Wed Jun 06 2012 - 09:13:01 CDT)
  - Re: namd/vmd support to GTX-6## series Francesco Pietra (Thu Jun 21 2012 - 12:36:27 CDT)
VMD Psfgen issue Evgeny Bulat (Tue Jun 05 2012 - 12:55:53 CDT)
Changing alphanumeric atom naming scheme to numeric Bryan Roessler (Tue Jun 05 2012 - 12:07:15 CDT)
- Re: Changing alphanumeric atom naming scheme to numeric John Stone (Tue Jun 05 2012 - 13:05:38 CDT)
  - Re: Changing alphanumeric atom naming scheme to numeric Bryan Roessler (Wed Jun 06 2012 - 09:47:44 CDT)
    - Re: Changing alphanumeric atom naming scheme to numeric John Stone (Wed Jun 06 2012 - 12:07:11 CDT)
    - Re: Changing alphanumeric atom naming scheme to numeric Peter C. Lai (Wed Jun 06 2012 - 14:21:46 CDT)
Segmentation fault (core dumped) arun kumar (Tue Jun 05 2012 - 09:01:03 CDT)
- Re: Segmentation fault (core dumped) John Stone (Tue Jun 05 2012 - 09:38:28 CDT)
  - Re: Segmentation fault (core dumped) Axel Kohlmeyer (Wed Jun 06 2012 - 08:19:58 CDT)
  - Re: Segmentation fault (core dumped) arun kumar (Thu Jun 07 2012 - 07:45:30 CDT)
    - Re: Segmentation fault (core dumped) Axel Kohlmeyer (Thu Jun 07 2012 - 08:42:51 CDT)
    - Re: Segmentation fault (core dumped) arun kumar (Fri Jun 08 2012 - 05:17:48 CDT)
- Re: Segmentation fault (core dumped) Axel Kohlmeyer (Tue Jun 05 2012 - 10:09:48 CDT)
FFTK VMD plugin issue (arising from VECSCALE TCL issues of either NAMD or VMD ?) Francesco Pietra (Tue Jun 05 2012 - 02:16:40 CDT)
- Re: FFTK VMD plugin issue (arising from VECSCALE TCL issues of either NAMD or VMD ?) JC Gumbart (Tue Jun 05 2012 - 09:22:10 CDT)
  - Re: namd-l: Re: FFTK VMD plugin issue (arising from VECSCALE TCL issues of either NAMD or VMD ?) Francesco Pietra (Tue Jun 05 2012 - 12:54:05 CDT)
    - Re: namd-l: Re: FFTK VMD plugin issue (arising from VECSCALE TCL issues of either NAMD or VMD ?) Mayne, Christopher G (Tue Jun 05 2012 - 13:27:13 CDT)
Workshop In Aspen Colorado - MARK PLUMMER (Mon Jun 04 2012 - 15:15:32 CDT)
FFTK OptCharges Francesco Pietra (Mon Jun 04 2012 - 04:10:40 CDT)
- Re: FFTK OptCharges Mayne, Christopher G (Mon Jun 04 2012 - 09:41:59 CDT)
  - Re: Re: FFTK OptCharges Francesco Pietra (Mon Jun 04 2012 - 13:28:23 CDT)
    - Re: Re: FFTK OptCharges Mayne, Christopher G (Mon Jun 04 2012 - 13:45:14 CDT)
Strange results when visualizing .trr trajectory patrick wintrode (Sat Jun 02 2012 - 11:41:04 CDT)
- Re: Strange results when visualizing .trr trajectory Axel Kohlmeyer (Sat Jun 02 2012 - 12:38:42 CDT)
- Re: Strange results when visualizing .trr trajectory Anurag Sethi (Sat Jun 02 2012 - 12:36:14 CDT)
Re: hbonds vs time JC Gumbart (Thu May 31 2012 - 15:09:06 CDT)
(no subject) Marc Charendoff (Thu May 31 2012 - 12:09:44 CDT)
hbonds vs time Subrata Paul (Thu May 31 2012 - 10:40:13 CDT)
- RE: hbonds vs time JC Gumbart (Thu May 31 2012 - 11:04:48 CDT)
Drawing an ellipsoid bsnmrem-obj_at_yahoo.com (Thu May 31 2012 - 08:44:33 CDT)
- Re: Drawing an ellipsoid Axel Kohlmeyer (Thu May 31 2012 - 10:35:17 CDT)
  - Re: Drawing an ellipsoid bsnmrem-obj_at_yahoo.com (Thu May 31 2012 - 16:03:53 CDT)
    - Re: Drawing an ellipsoid Axel Kohlmeyer (Thu May 31 2012 - 21:14:54 CDT)
    - Re: Drawing an ellipsoid John Stone (Thu Jun 07 2012 - 15:11:19 CDT)
VMD membrane builder P.-L. Chau (Thu May 31 2012 - 07:03:34 CDT)
- Re: VMD membrane builder JC Gumbart (Thu May 31 2012 - 16:20:22 CDT)
- Re: VMD membrane builder Peter C. Lai (Thu May 31 2012 - 18:59:35 CDT)
Problem in making IMD connection prakhar gupta (Thu May 31 2012 - 05:57:27 CDT)
- Re: Problem in making IMD connection Axel Kohlmeyer (Thu May 31 2012 - 07:14:35 CDT)
anybody interested in running VMD in parallel (without recompiling)? Axel Kohlmeyer (Wed May 30 2012 - 19:40:45 CDT)
questions for trajectory analysis oguz gurbulak (Wed May 30 2012 - 01:44:59 CDT)
- Re: questions for trajectory analysis Andrew Jewett (Wed May 30 2012 - 15:41:25 CDT)
  - RE: questions for trajectory analysis Jim Kress (Wed May 30 2012 - 20:01:18 CDT)
    - Re: questions for trajectory analysis PaweÅ‚ KÄ™dzierski (Thu May 31 2012 - 03:07:51 CDT)
Quick Surf Representation Getting Cutoff when Rendering with Tachyon Robert Johnson (Tue May 29 2012 - 14:11:52 CDT)
- Re: Quick Surf Representation Getting Cutoff when Rendering with Tachyon John Stone (Tue May 29 2012 - 16:08:16 CDT)
  - Re: Quick Surf Representation Getting Cutoff when Rendering with Tachyon Robert Johnson (Tue May 29 2012 - 16:11:59 CDT)
Flickering display when running remotely Clarinet (Tue May 29 2012 - 10:43:52 CDT)
- Re: Flickering display when running remotely John Stone (Tue May 29 2012 - 11:01:26 CDT)
- Re: Flickering display when running remotely Peter C. Lai (Tue May 29 2012 - 12:51:51 CDT)
  - Re: Flickering display when running remotely Clarinet (Wed May 30 2012 - 04:37:58 CDT)
FFTK for adjusting partial charge only Francesco Pietra (Tue May 29 2012 - 10:29:53 CDT)
- RE: FFTK for adjusting partial charge only JC Gumbart (Tue May 29 2012 - 11:08:02 CDT)
VMD 1.9.1 becomes unresponsive Jim Kress (Sat May 26 2012 - 15:47:08 CDT)
- Re: VMD 1.9.1 becomes unresponsive John Stone (Tue May 29 2012 - 11:16:40 CDT)
Another thought related to drawing dipole moment vectors Andrew DeYoung (Sat May 26 2012 - 12:27:53 CDT)
- Re: Another thought related to drawing dipole moment vectors Wang Yi (Sat May 26 2012 - 14:27:25 CDT)
  - RE: Another thought related to drawing dipole moment vectors Andrew DeYoung (Sat May 26 2012 - 16:14:52 CDT)
- Re: Another thought related to drawing dipole moment vectors Axel Kohlmeyer (Sat May 26 2012 - 16:22:55 CDT)
- Re: Another thought related to drawing dipole moment vectors Bogdan Costescu (Sun May 27 2012 - 07:10:12 CDT)
Using Dipole Moment Watcher with Gromacs configurations and trajectories Andrew DeYoung (Sat May 26 2012 - 12:20:09 CDT)
- Re: Using Dipole Moment Watcher with Gromacs configurations and trajectories Axel Kohlmeyer (Sat May 26 2012 - 16:19:26 CDT)
Re: vmd ATI card John Stone (Fri May 25 2012 - 13:05:20 CDT)
Movie making with smoothed trajectories Jim Kress (Thu May 24 2012 - 11:02:18 CDT)
- Re: Movie making with smoothed trajectories Axel Kohlmeyer (Thu May 24 2012 - 12:03:04 CDT)
  - RE: Movie making with smoothed trajectories Jim Kress (Thu May 24 2012 - 13:38:23 CDT)
TR: VMD atomselect with cartesian reference peter.schmidtke_at_fr.netgrs.com (Thu May 24 2012 - 08:16:55 CDT)
- Re: TR: VMD atomselect with cartesian reference Axel Kohlmeyer (Thu May 24 2012 - 09:13:04 CDT)
  - Re: TR: VMD atomselect with cartesian reference PaweÅ‚ KÄ™dzierski (Thu May 24 2012 - 12:45:08 CDT)
    - RE: TR: VMD atomselect with cartesian reference peter.schmidtke_at_fr.netgrs.com (Wed May 30 2012 - 02:00:24 CDT)
    - Re: TR: VMD atomselect with cartesian reference Wang Yi (Wed May 30 2012 - 08:56:42 CDT)
Hydrogen bond energy calculation Aditya Padhi (Wed May 23 2012 - 22:56:10 CDT)
7th Industrial Fluid Properties Simulation Challenge Joshua D. Moore (Wed May 23 2012 - 11:22:23 CDT)
Regarding the Use of STL Files as Boundary Features Phelan Jr, Frederick R. Dr. (Wed May 23 2012 - 11:05:46 CDT)
- Re: Regarding the Use of STL Files as Boundary Features John Stone (Thu May 24 2012 - 10:32:08 CDT)
pbc-box mohammad agha (Wed May 23 2012 - 10:31:08 CDT)
vmd on Ubuntu: tcl howto Eros Albertazzi (Wed May 23 2012 - 05:37:57 CDT)
- Re: vmd on Ubuntu: tcl howto Axel Kohlmeyer (Wed May 23 2012 - 07:09:28 CDT)
- Re: vmd on Ubuntu: tcl howto John Stone (Thu May 24 2012 - 10:45:46 CDT)
Aspen Center for Physics 2013 Workshop MARK PLUMMER (Tue May 22 2012 - 14:58:42 CDT)
Polymer Building in VMD Gkourmpis, Thomas (Tue May 22 2012 - 08:21:12 CDT)
Fw: pbc-box mohammad agha (Mon May 21 2012 - 23:30:38 CDT)
- Re: Fw: pbc-box Olaf Lenz (Tue May 22 2012 - 02:42:45 CDT)
  - pbc-box mohammad agha (Tue May 22 2012 - 08:10:30 CDT)
    - Re: pbc-box Olaf Lenz (Wed May 23 2012 - 01:31:41 CDT)
RMSF and bigdcd Raul Araya (Mon May 21 2012 - 09:39:45 CDT)
- Re: RMSF and bigdcd John Stone (Tue May 22 2012 - 18:02:31 CDT)
  - Re: RMSF and bigdcd Axel Kohlmeyer (Tue May 22 2012 - 18:53:22 CDT)
    - Re: RMSF and bigdcd John Stone (Fri May 25 2012 - 14:34:03 CDT)
FFTK plugin: in which order should the components be run? Francesco Pietra (Mon May 21 2012 - 04:20:58 CDT)
- Re: FFTK plugin: in which order should the components be run? Wang Yi (Mon May 21 2012 - 08:47:10 CDT)
- Re: FFTK plugin: in which order should the components be run? Mayne, Christopher G (Tue May 22 2012 - 11:00:41 CDT)
pbc-box mohammad agha (Sat May 19 2012 - 08:02:59 CDT)
cg_bonds.tcl mohammad agha (Sat May 19 2012 - 00:32:37 CDT)
- Re: cg_bonds.tcl Ajasja LjubetiÄ (Sat May 19 2012 - 15:07:20 CDT)
  - cg_bonds.tcl mohammad agha (Sat May 19 2012 - 15:56:00 CDT)
libGLU.so missing? Fatemesadat Emami (Fri May 18 2012 - 18:55:21 CDT)
- Re: libGLU.so missing? Axel Kohlmeyer (Fri May 18 2012 - 19:53:59 CDT)
Waters enclosed in internal cavities Wendy González (Fri May 18 2012 - 04:46:53 CDT)
- Re: Waters enclosed in internal cavities Vivek Sharma (Fri May 18 2012 - 06:23:52 CDT)
- Re: Waters enclosed in internal cavities Vlad Cojocaru (Fri May 18 2012 - 06:26:55 CDT)
file splitting P.-L. Chau (Thu May 17 2012 - 03:19:50 CDT)
- Re: file splitting Axel Kohlmeyer (Thu May 17 2012 - 07:34:47 CDT)
  - Re: file splitting P.-L. Chau (Thu May 17 2012 - 07:42:58 CDT)
    - Re: file splitting Grace Brannigan (Thu May 17 2012 - 10:40:25 CDT)
    - Re: file splitting Axel Kohlmeyer (Thu May 17 2012 - 11:11:00 CDT)
how to calculate PBC box volume in VMD? Albert (Thu May 17 2012 - 01:26:36 CDT)
- Re: how to calculate PBC box volume in VMD? Ajasja LjubetiÄ (Thu May 17 2012 - 02:25:15 CDT)
- Re: how to calculate PBC box volume in VMD? Axel Kohlmeyer (Thu May 17 2012 - 02:31:06 CDT)
Docking protein-protein vladanstefanovic_at_kg.ac.rs (Wed May 16 2012 - 16:08:22 CDT)
panel missing! Reza Khalkhali (Wed May 16 2012 - 10:49:51 CDT)
- Re: panel missing! Axel Kohlmeyer (Wed May 16 2012 - 12:23:18 CDT)
  - Re: panel missing! Reza Khalkhali (Thu May 17 2012 - 03:51:38 CDT)
    - Re: panel missing! Axel Kohlmeyer (Thu May 17 2012 - 10:16:40 CDT)
Getting PSF in right format from .gro file Donovan B.T. (Wed May 16 2012 - 08:54:59 CDT)
Making only a subset of atoms transparent (or otherwise non-emphasized) Andrew DeYoung (Tue May 15 2012 - 12:49:22 CDT)
- Re: Making only a subset of atoms transparent (or otherwise non-emphasized) Wang Yi (Tue May 15 2012 - 13:44:17 CDT)
- Re: Making only a subset of atoms transparent (or otherwise non-emphasized) Axel Kohlmeyer (Tue May 15 2012 - 13:38:17 CDT)
APBS for small molecules jcorradi_at_criba.edu.ar (Sun May 13 2012 - 22:00:08 CDT)
- Re: APBS for small molecules Axel Kohlmeyer (Tue May 15 2012 - 00:41:56 CDT)
  - Re: APBS for small molecules jcorradi_at_criba.edu.ar (Tue May 15 2012 - 08:28:28 CDT)
Suggestion for measure cluster Jérôme Hénin (Fri May 11 2012 - 04:32:39 CDT)
- Re: Suggestion for measure cluster Jérôme Hénin (Fri May 11 2012 - 04:35:07 CDT)
Loop for Andrés Morales (Thu May 10 2012 - 18:40:58 CDT)
- Re: Loop for Axel Kohlmeyer (Thu May 10 2012 - 20:00:51 CDT)
- RE: Loop for Bennion, Brian (Thu May 10 2012 - 21:17:27 CDT)
  - Re: Loop for Axel Kohlmeyer (Thu May 10 2012 - 22:06:41 CDT)
VMD1.9.1 is crashing my system mpincu (Thu May 10 2012 - 16:24:27 CDT)
- Re: VMD1.9.1 is crashing my system John Stone (Thu May 10 2012 - 16:38:09 CDT)
- Re: VMD1.9.1 is crashing my system Axel Kohlmeyer (Thu May 10 2012 - 17:19:50 CDT)
- Re: VMD1.9.1 is crashing my system Mirco Wahab (Fri May 11 2012 - 11:19:38 CDT)
  - Re: VMD1.9.1 is crashing my system Gianluca Interlandi (Fri May 11 2012 - 16:58:47 CDT)
Clustering plugin updated to v2.0 Luis Gracia (Thu May 10 2012 - 12:54:20 CDT)
PBC missed in Amber MD Albert (Thu May 10 2012 - 02:53:00 CDT)
- Re: PBC missed in Amber MD Axel Kohlmeyer (Thu May 10 2012 - 09:05:04 CDT)
  - Re: PBC missed in Amber MD Axel Kohlmeyer (Thu May 10 2012 - 13:43:31 CDT)
flashing the VMD mohammad agha (Thu May 10 2012 - 02:00:37 CDT)
- Re: flashing the VMD Wang Yi (Thu May 10 2012 - 09:57:19 CDT)
  - Re: flashing the VMD Axel Kohlmeyer (Thu May 10 2012 - 10:49:11 CDT)
    - Re: flashing the VMD Wang Yi (Thu May 10 2012 - 11:17:11 CDT)
  - flashing the VMD mohammad agha (Sat May 19 2012 - 02:49:39 CDT)
flashing the VMD mohammad agha (Thu May 10 2012 - 01:56:22 CDT)
- Re: flashing the VMD Axel Kohlmeyer (Thu May 10 2012 - 08:41:00 CDT)
New crystallography plugin Dan Michael O. HeggÃ¸ (Wed May 09 2012 - 17:33:04 CDT)
New crystallography plugin Dan Michael O. HeggÃ¸ (Wed May 09 2012 - 16:31:33 CDT)
Add-H for crystallization water only Francesco Pietra (Wed May 09 2012 - 15:08:09 CDT)
flashing the VMD mohammad agha (Wed May 09 2012 - 12:26:10 CDT)
flashing the VMD mohammad agha (Wed May 09 2012 - 11:16:02 CDT)
flashing the VMD mohammad agha (Tue May 08 2012 - 14:52:53 CDT)
- Re: flashing the VMD Axel Kohlmeyer (Tue May 08 2012 - 16:26:26 CDT)
  - flashing the VMD mohammad agha (Wed May 09 2012 - 10:00:54 CDT)
counting specific atom types winardi, erik (Tue May 08 2012 - 08:37:01 CDT)
- Re: counting specific atom types Ana Celia Vila Verde (Tue May 08 2012 - 09:31:23 CDT)
- Re: counting specific atom types Axel Kohlmeyer (Tue May 08 2012 - 09:24:20 CDT)
diffusion coefficient plug-in in VMD fariba taghavi (Tue May 08 2012 - 07:06:31 CDT)
- Re: diffusion coefficient plug-in in VMD Axel Kohlmeyer (Tue May 08 2012 - 08:12:35 CDT)
  - Re: diffusion coefficient plug-in in VMD fariba taghavi (Tue May 08 2012 - 09:14:54 CDT)
- Re: diffusion coefficient plug-in in VMD Ana Celia Vila Verde (Tue May 08 2012 - 11:17:41 CDT)
flashing the VMD mohammad agha (Tue May 08 2012 - 05:18:04 CDT)
- Re: flashing the VMD Wang Yi (Tue May 08 2012 - 08:19:43 CDT)
  - Re: flashing the VMD Axel Kohlmeyer (Tue May 08 2012 - 09:09:27 CDT)
  - Re: flashing the VMD Gianluca Interlandi (Tue May 08 2012 - 11:23:06 CDT)
    - flashing the VMD mohammad agha (Tue May 08 2012 - 15:32:31 CDT)
    - Re: flashing the VMD Axel Kohlmeyer (Tue May 08 2012 - 16:22:57 CDT)
flasshing the VMD mohammad agha (Mon May 07 2012 - 21:13:43 CDT)
- Re: flasshing the VMD Axel Kohlmeyer (Mon May 07 2012 - 22:10:30 CDT)
  - flasshing the VMD mohammad agha (Mon May 07 2012 - 22:25:58 CDT)
    - Re: flasshing the VMD Axel Kohlmeyer (Tue May 08 2012 - 08:16:53 CDT)
strange coloring Wei Chen (Mon May 07 2012 - 15:17:21 CDT)
- Re: strange coloring John Stone (Mon May 07 2012 - 15:39:26 CDT)
  - Re: strange coloring Wei Chen (Mon May 07 2012 - 15:54:51 CDT)
    - Re: strange coloring John Stone (Mon May 07 2012 - 16:19:34 CDT)
    - Re: strange coloring Wei Chen (Mon May 07 2012 - 16:44:19 CDT)
- Re: strange coloring Axel Kohlmeyer (Mon May 07 2012 - 16:05:49 CDT)
.trr files slow to load patrick wintrode (Mon May 07 2012 - 12:00:19 CDT)
- Re: .trr files slow to load John Stone (Mon May 07 2012 - 12:40:13 CDT)
- Re: .trr files slow to load Axel Kohlmeyer (Mon May 07 2012 - 12:55:52 CDT)
what's the Letter in figure caption meaning of TIME-LINE 2nd structure present? Albert (Mon May 07 2012 - 10:07:43 CDT)
- Re: what's the Letter in figure caption meaning of TIME-LINE 2nd structure present? santhu kumar (Mon May 07 2012 - 11:10:40 CDT)
  - Re: what's the Letter in figure caption meaning of TIME-LINE 2nd structure present? Barry Isralewitz (Mon May 07 2012 - 12:32:42 CDT)
Fwd: VMD Stereo does not work Quadbufferd Christian Wohlschlager (Mon May 07 2012 - 02:46:23 CDT)
- Re: Fwd: VMD Stereo does not work Quadbufferd John Stone (Mon May 07 2012 - 03:03:38 CDT)
  - Re: Fwd: VMD Stereo does not work Quadbufferd Christian Wohlschlager (Fri May 11 2012 - 03:45:12 CDT)
    - RE: Fwd: VMD Stereo does not work Quadbufferd Mark Cunningham (Fri May 11 2012 - 09:54:45 CDT)
%-sign shortcut for mouse->force->atom not working Christopher Neale (Sun May 06 2012 - 12:21:38 CDT)
- Re: %-sign shortcut for mouse->force->atom not working Axel Kohlmeyer (Sun May 06 2012 - 14:01:37 CDT)
Save/restore display parameters Jérôme Hénin (Fri May 04 2012 - 09:51:28 CDT)
- Re: Save/restore display parameters John Stone (Mon May 07 2012 - 10:40:59 CDT)
gromacs trajectory file ahmet yýldýrým (Thu May 03 2012 - 01:49:13 CDT)
- Re: gromacs trajectory file amin_at_imtech.res.in (Thu May 03 2012 - 02:51:23 CDT)
N-methylated amino acid topologies Joakim Swedberg (Wed May 02 2012 - 19:20:41 CDT)
Free software for building peptide meisam valizadeh kiamahalleh (Wed May 02 2012 - 01:34:20 CDT)
- Re: Free software for building peptide Thomas Evangelidis (Wed May 02 2012 - 04:01:09 CDT)
- Re: Free software for building peptide amin_at_imtech.res.in (Wed May 02 2012 - 04:06:30 CDT)
- Re: Free software for building peptide sajad falsafi (Wed May 02 2012 - 06:56:14 CDT)
Problem with moving protein for all frames gökçe ayþe güven (Tue May 01 2012 - 16:14:24 CDT)
- Re: Problem with moving protein for all frames Axel Kohlmeyer (Tue May 01 2012 - 17:04:37 CDT)
- Re: Problem with moving protein for all frames Jeffrey Potoff (Tue May 01 2012 - 19:53:12 CDT)
Make "Load all at once" the default? Adding representations? Heather Mayes (Tue May 01 2012 - 15:45:39 CDT)
- Re: Make "Load all at once" the default? Adding representations? Axel Kohlmeyer (Tue May 01 2012 - 16:54:49 CDT)
  - Re: Make "Load all at once" the default? Adding representations? Heather Mayes (Tue May 01 2012 - 17:18:41 CDT)
    - Re: Make "Load all at once" the default? Adding representations? Axel Kohlmeyer (Tue May 01 2012 - 19:13:11 CDT)
    - Re: Make "Load all at once" the default? Adding representations? Heather Mayes (Wed May 02 2012 - 15:50:28 CDT)
helical content script Ban Arn (Tue May 01 2012 - 05:55:51 CDT)
- Re: helical content script francesco oteri (Tue May 01 2012 - 07:09:03 CDT)
- Re: helical content script Axel Kohlmeyer (Tue May 01 2012 - 07:28:05 CDT)
  - Re: helical content script Ban Arn (Tue May 01 2012 - 09:23:52 CDT)
visualization of HOMO&LUMO in vmd leila karami (Tue May 01 2012 - 04:26:06 CDT)
- Re: visualization of HOMO&LUMO in vmd Axel Kohlmeyer (Tue May 01 2012 - 07:31:29 CDT)
3D density in the specific part of the simulation box fariba taghavi (Tue May 01 2012 - 00:48:35 CDT)
- Re: 3D density in the specific part of the simulation box Axel Kohlmeyer (Tue May 01 2012 - 07:34:55 CDT)
In-Residence Training at the Theoretical & Computational Biophysics Group, July 16-27, 2012 TCBG Workshop (Mon Apr 30 2012 - 17:02:14 CDT)
how to use the AutoIMD "Tool control" panel. Christopher Neale (Mon Apr 30 2012 - 11:28:19 CDT)
- Re: how to use the AutoIMD "Tool control" panel. Axel Kohlmeyer (Mon Apr 30 2012 - 12:34:07 CDT)
  - Re: how to use the AutoIMD "Tool control" panel. Thomas C. Bishop (Mon Apr 30 2012 - 13:52:14 CDT)
writing pair/bond/angle/dihedral information for lammps input winardi, erik (Sun Apr 29 2012 - 17:17:14 CDT)
- Re: writing pair/bond/angle/dihedral information for lammps input Axel Kohlmeyer (Sun Apr 29 2012 - 18:18:24 CDT)
  - Re: writing pair/bond/angle/dihedral information for lammps input winardi, erik (Sun Apr 29 2012 - 23:21:01 CDT)
    - Re: writing pair/bond/angle/dihedral information for lammps input Axel Kohlmeyer (Sun Apr 29 2012 - 23:52:25 CDT)
Force Field ToolKit - Angles DENILSON FERREIRA DE OLIVEIRA (Sun Apr 29 2012 - 14:39:52 CDT)
- RE: Force Field ToolKit - Angles JC Gumbart (Sun Apr 29 2012 - 14:57:33 CDT)
  - RE: Force Field ToolKit - Angles Mayne, Christopher G (Sun Apr 29 2012 - 16:28:16 CDT)
  - RE: Force Field ToolKit - Angles DENILSON FERREIRA DE OLIVEIRA (Sun Apr 29 2012 - 19:29:33 CDT)
Force Field Toolkit: scaling, weight etc DENILSON FERREIRA DE OLIVEIRA (Sun Apr 29 2012 - 06:37:04 CDT)
- Re: Force Field Toolkit: scaling, weight etc Mayne, Christopher G (Sun Apr 29 2012 - 16:13:30 CDT)
  - Re: Force Field Toolkit: scaling, weight etc DENILSON FERREIRA DE OLIVEIRA (Sun Apr 29 2012 - 18:11:56 CDT)
measure gofr script Emiliano Ippoliti (Sat Apr 28 2012 - 08:51:58 CDT)
- Re: measure gofr script Axel Kohlmeyer (Sat Apr 28 2012 - 10:11:58 CDT)
  - Re: measure gofr script Emiliano Ippoliti (Sat Apr 28 2012 - 11:17:00 CDT)
    - Re: measure gofr script Axel Kohlmeyer (Sat Apr 28 2012 - 12:33:09 CDT)
water mean residence time jampani srinivas (Fri Apr 27 2012 - 17:23:53 CDT)
- Re: water mean residence time Axel Kohlmeyer (Fri Apr 27 2012 - 18:30:21 CDT)
PSF generation for proteins with isopeptide bonds Zack Scholl (Thu Apr 26 2012 - 19:57:48 CDT)
VMD Stereo not work Christian Wohlschlager (Thu Apr 26 2012 - 08:32:48 CDT)
Problem with generating psf using CGENFF amin_at_imtech.res.in (Thu Apr 26 2012 - 04:42:40 CDT)
- Re: Problem with generating psf using CGENFF Chris Harrison (Thu Apr 26 2012 - 06:23:08 CDT)
  - Re: Problem with generating psf using CGENFF amin_at_imtech.res.in (Thu Apr 26 2012 - 11:37:56 CDT)
- Re:Problem with generating psf using CGENFF amin_at_imtech.res.in (Fri Apr 27 2012 - 22:35:16 CDT)
  - RE: Re:Problem with generating psf using CGENFF Bennion, Brian (Mon Apr 30 2012 - 13:26:00 CDT)
- Re:Problem with generating psf using CGENFF amin_at_imtech.res.in (Fri Apr 27 2012 - 22:46:21 CDT)
VMD Question: How to build a polymer in VMD? Gkourmpis, Thomas (Thu Apr 26 2012 - 03:51:45 CDT)
how to center protein? Chirag Vora (Tue Apr 24 2012 - 00:04:09 CDT)
- Re: how to center protein? Hitesh Patel (Tue Apr 24 2012 - 11:34:00 CDT)
H-H dynamic bonds Q=A3ukasz_Pi=EAko=B6=22?= (Mon Apr 23 2012 - 17:21:42 CDT)
- Re: H-H dynamic bonds Axel Kohlmeyer (Mon Apr 23 2012 - 18:10:58 CDT)
Hydrophobic mismatch script Ban Arn (Mon Apr 23 2012 - 04:08:28 CDT)
- Re: Hydrophobic mismatch script francesco oteri (Mon Apr 23 2012 - 05:17:13 CDT)
  - Re: Hydrophobic mismatch script Ban Arn (Mon Apr 23 2012 - 05:29:34 CDT)
  - Re: Hydrophobic mismatch script kanchi subbarao rao (Mon Apr 23 2012 - 06:11:24 CDT)
Movie Plugin Engelman, Joshua (Sat Apr 21 2012 - 15:54:54 CDT)
- Re: Movie Plugin Engelman, Joshua (Sat Apr 21 2012 - 16:50:59 CDT)
  - Re: Re: Movie Plugin Axel Kohlmeyer (Sun Apr 22 2012 - 12:32:41 CDT)
- Re: Movie Plugin John Stone (Mon Apr 23 2012 - 15:52:40 CDT)
  - Re: Movie Plugin Engelman, Joshua (Mon Apr 23 2012 - 16:32:01 CDT)
openGL x,y position Mayne, Christopher G (Sat Apr 21 2012 - 14:01:51 CDT)
- Re: openGL x,y position Axel Kohlmeyer (Sun Apr 22 2012 - 21:46:14 CDT)
  - Re: openGL x,y position Mayne, Christopher G (Sun Apr 22 2012 - 22:08:59 CDT)
HOOMD problems Engelman, Joshua (Fri Apr 20 2012 - 15:35:52 CDT)
- Re: HOOMD problems John Stone (Fri Apr 20 2012 - 15:51:16 CDT)
  - Re: HOOMD problems Axel Kohlmeyer (Fri Apr 20 2012 - 20:19:43 CDT)
- Re: HOOMD problems Axel Kohlmeyer (Fri Apr 20 2012 - 16:37:56 CDT)
stereo images for publication Vlad Cojocaru (Fri Apr 20 2012 - 09:59:21 CDT)
- Re: stereo images for publication Vlad Cojocaru (Fri Apr 20 2012 - 10:04:39 CDT)
Anaglyph stereo with other colors Luis M. Sánchez (Fri Apr 20 2012 - 08:09:19 CDT)
- Re: Anaglyph stereo with other colors John Stone (Fri Apr 20 2012 - 17:27:39 CDT)
  - Re: Anaglyph stereo with other colors flavio seixas (Sat Apr 21 2012 - 13:36:01 CDT)
gofr limit, Kirkwood-Buff integrals Ivan Vyalov (Fri Apr 20 2012 - 05:43:18 CDT)
- Re: gofr limit, Kirkwood-Buff integrals Axel Kohlmeyer (Fri Apr 20 2012 - 14:11:28 CDT)
  - Re: gofr limit, Kirkwood-Buff integrals Ivan Vyalov (Fri Apr 20 2012 - 14:49:21 CDT)
    - Re: gofr limit, Kirkwood-Buff integrals Axel Kohlmeyer (Fri Apr 20 2012 - 17:50:26 CDT)
    - Re: gofr limit, Kirkwood-Buff integrals Ivan Vyalov (Sat Apr 21 2012 - 14:13:37 CDT)
AutoPSF Donovan B.T. (Fri Apr 20 2012 - 04:29:53 CDT)
Re: Thickness of bilayer script Andrés Morales (Thu Apr 19 2012 - 20:58:35 CDT)
- Re: Re: Thickness of bilayer script Ban Arn (Fri Apr 20 2012 - 05:30:38 CDT)
segmentation fault with NAMDenergy amin_at_imtech.res.in (Thu Apr 19 2012 - 20:12:53 CDT)
- Re: segmentation fault with NAMDenergy John Stone (Thu Apr 19 2012 - 20:59:32 CDT)
Problem with hydration script Bryan Roessler (Thu Apr 19 2012 - 13:17:39 CDT)
- RE: Problem with hydration script Bennion, Brian (Thu Apr 19 2012 - 14:32:53 CDT)
- RE: Problem with hydration script Joaquim Rui de Castro Rodrigues (Thu Apr 19 2012 - 14:23:33 CDT)
  - Re: Problem with hydration script Bryan Roessler (Thu Apr 19 2012 - 15:17:35 CDT)
Valence bond force field in NAMD Ganesh Kamath (Thu Apr 19 2012 - 09:26:35 CDT)
- Re: Valence bond force field in NAMD Axel Kohlmeyer (Thu Apr 19 2012 - 12:53:26 CDT)
Units of Isovalue Slider in Isovalue Drawing Method Andrew DeYoung (Wed Apr 18 2012 - 20:08:53 CDT)
- Re: Units of Isovalue Slider in Isovalue Drawing Method John Stone (Wed Apr 18 2012 - 20:49:08 CDT)
  - RE: Units of Isovalue Slider in Isovalue Drawing Method Andrew DeYoung (Wed Apr 18 2012 - 20:52:13 CDT)
- Re: Units of Isovalue Slider in Isovalue Drawing Method Axel Kohlmeyer (Wed Apr 18 2012 - 21:10:24 CDT)
Average pocket size? patrick wintrode (Wed Apr 18 2012 - 11:45:04 CDT)
- Re: Average pocket size? Thomas Evangelidis (Wed Apr 18 2012 - 13:51:11 CDT)
Saving coordinates that meet selection criteria for each frame Ben Rodriguez (Tue Apr 17 2012 - 18:28:43 CDT)
- Re: Saving coordinates that meet selection criteria for each frame Axel Kohlmeyer (Tue Apr 17 2012 - 19:20:56 CDT)
- Re: Saving coordinates that meet selection criteria for each frame Wang Yi (Tue Apr 17 2012 - 19:23:15 CDT)
Misfunction of some plugins if compiled Vlastimil ZÃma (Tue Apr 17 2012 - 12:28:10 CDT)
- Re: Misfunction of some plugins if compiled Axel Kohlmeyer (Wed Apr 18 2012 - 21:18:53 CDT)
Saving of pdb-trajectory in NMR-like format James Starlight (Tue Apr 17 2012 - 09:21:40 CDT)
Using Measure SASA in NAMD Simulation Ajith Rathnaweera Rajapaksha Mudalige (Mon Apr 16 2012 - 18:54:32 CDT)
- Re: Using Measure SASA in NAMD Simulation John Stone (Mon Apr 16 2012 - 23:39:24 CDT)
lipid order parameter Ban Arn (Mon Apr 16 2012 - 05:16:31 CDT)
- Re: lipid order parameter John Stone (Tue Apr 17 2012 - 00:01:18 CDT)
align electron density map onto simulated structure (with different center) Magnus Andersson (Sun Apr 15 2012 - 18:42:21 CDT)
- Re: align electron density map onto simulated structure (with different center) John Stone (Tue Apr 17 2012 - 00:13:31 CDT)
Dynamical Network Analysis programs gncommunities and subopt elena ermakova (Sat Apr 14 2012 - 01:40:33 CDT)
Is it possible to save the position and angle of the camera for future VMD sessions? Andrew DeYoung (Fri Apr 13 2012 - 13:07:20 CDT)
- Re: Is it possible to save the position and angle of the camera for future VMD sessions? Axel Kohlmeyer (Fri Apr 13 2012 - 18:57:22 CDT)
Default representation style in command line Paulo E. Abreu (Fri Apr 13 2012 - 06:10:43 CDT)
- Re: Default representation style in command line Nuno Sousa Cerqueira (Fri Apr 13 2012 - 07:08:18 CDT)
- Re: Default representation style in command line Axel Kohlmeyer (Fri Apr 13 2012 - 07:21:39 CDT)
(no subject) rainy908_at_yahoo.com (Thu Apr 12 2012 - 20:54:30 CDT)
Drawing a high resolution transparent or translucent sphere Andrew DeYoung (Wed Apr 11 2012 - 20:37:20 CDT)
- Re: Drawing a high resolution transparent or translucent sphere John Stone (Wed Apr 11 2012 - 21:26:58 CDT)
- Re: Drawing a high resolution transparent or translucent sphere Axel Kohlmeyer (Wed Apr 11 2012 - 23:45:18 CDT)
saving dcd file different if by script or by interactive mode Jose Borreguero (Tue Apr 10 2012 - 17:32:11 CDT)
- Re: saving dcd file different if by script or by interactive mode Axel Kohlmeyer (Tue Apr 10 2012 - 18:16:03 CDT)
  - Re: saving dcd file different if by script or by interactive mode Jose Borreguero (Tue Apr 10 2012 - 18:23:01 CDT)
- RE: saving dcd file different if by script or by interactive mode Kei Sit (Tue Apr 10 2012 - 19:24:56 CDT)
topotools writelammps data winardi, erik (Tue Apr 10 2012 - 17:24:48 CDT)
- Re: topotools writelammps data Axel Kohlmeyer (Tue Apr 10 2012 - 18:15:16 CDT)
Problems with for loop Andrés Morales (Tue Apr 10 2012 - 11:43:10 CDT)
- Re: Problems with for loop John Stone (Tue Apr 10 2012 - 14:15:07 CDT)
VMD QUESTION( Movie making ) james Fernandez (Mon Apr 09 2012 - 16:49:21 CDT)
- Re: VMD QUESTION( Movie making ) Axel Kohlmeyer (Mon Apr 09 2012 - 17:45:21 CDT)
- Re: VMD QUESTION( Movie making ) John Stone (Mon Apr 09 2012 - 19:22:11 CDT)
Average angle between the lipid dipole vector and the bilayer normal. Andrés Morales (Mon Apr 09 2012 - 12:45:44 CDT)
- Average angle between the lipid dipole vector and the bilayer normal. Andrés Morales (Mon Apr 09 2012 - 12:55:17 CDT)
- Re: Average angle between the lipid dipole vector and the bilayer normal. John Stone (Wed Apr 11 2012 - 14:06:52 CDT)
  - Re: Average angle between the lipid dipole vector and the bilayer normal. Andrés Morales (Wed Apr 11 2012 - 16:43:01 CDT)
Re: problems with MDFF Gregorio Fernandez (Mon Apr 09 2012 - 06:21:33 CDT)
IMD - remove forces on mouse release jonathan KHAO (Sun Apr 08 2012 - 13:05:45 CDT)
- Re: IMD - remove forces on mouse release Axel Kohlmeyer (Sun Apr 08 2012 - 14:12:19 CDT)
  - Re: IMD - remove forces on mouse release jonathan KHAO (Sun Apr 08 2012 - 15:50:44 CDT)
Mac OS compilation… what could be going wrongQ?= FX (Sun Apr 08 2012 - 12:03:42 CDT)
- Re: Mac OS compilation? what could be going wrong? John Stone (Mon Apr 09 2012 - 10:11:17 CDT)
  - Re: Mac OS compilation? what could be going wrong? FX (Mon Apr 09 2012 - 14:06:06 CDT)
an old question Albert (Sat Apr 07 2012 - 00:28:29 CDT)
- Re: an old question John Stone (Mon Apr 09 2012 - 10:30:33 CDT)
  - Re: an old question Albert (Mon Apr 09 2012 - 23:36:16 CDT)
problems with MDFF Gregorio Fernandez (Fri Apr 06 2012 - 02:42:22 CDT)
Lipid order paramaeter script Ban Arn (Thu Apr 05 2012 - 04:35:52 CDT)
Regarding saving data snoze pa (Wed Apr 04 2012 - 12:21:39 CDT)
- Re: Regarding saving data John Stone (Wed Apr 04 2012 - 15:10:03 CDT)
using min. image. conven. for transport properties Papan S (Wed Apr 04 2012 - 08:16:00 CDT)
- Re: using min. image. conven. for transport properties Axel Kohlmeyer (Wed Apr 04 2012 - 09:13:37 CDT)
  - Re: using min. image. conven. for transport properties Papan S (Wed Apr 04 2012 - 23:06:18 CDT)
Auto Bead Display Size using topotools Phelan Jr, Frederick R. Dr. (Mon Apr 02 2012 - 14:50:47 CDT)
- Re: Auto Bead Display Size using topotools Axel Kohlmeyer (Mon Apr 02 2012 - 15:59:06 CDT)
python error? Albert (Mon Apr 02 2012 - 11:28:14 CDT)
- Re: python error? Axel Kohlmeyer (Mon Apr 02 2012 - 13:48:02 CDT)
  - Re: python error? Albert (Mon Apr 02 2012 - 14:17:08 CDT)
psfgen tyrosine anion-Fe bond Francesco Pietra (Sun Apr 01 2012 - 09:53:13 CDT)
- Re: namd-l: psfgen tyrosine anion-Fe bond Francesco Pietra (Sun Apr 01 2012 - 12:03:17 CDT)
  - Re: namd-l: psfgen tyrosine anion-Fe bond Francesco Pietra (Sun Apr 01 2012 - 12:14:27 CDT)
FW: How to set VMD_Plugin_path? a a (Sat Mar 31 2012 - 23:25:30 CDT)
- Re: FW: How to set VMD_Plugin_path? John Stone (Mon Apr 02 2012 - 10:58:28 CDT)
Printing Coordinates with Tcl/Tk Mr Bernard Ramos (Fri Mar 30 2012 - 12:16:00 CDT)
- Re: Printing Coordinates with Tcl/Tk Axel Kohlmeyer (Fri Mar 30 2012 - 13:38:57 CDT)
Plotting of Co-ordinates on VMD james Fernandez (Fri Mar 30 2012 - 11:37:07 CDT)
- Re: Plotting of Co-ordinates on VMD Axel Kohlmeyer (Fri Mar 30 2012 - 12:49:51 CDT)
- Re: Plotting of Co-ordinates on VMD Jeffrey Potoff (Fri Mar 30 2012 - 14:04:27 CDT)
  - Re: Plotting of Co-ordinates on VMD Barry Isralewitz (Fri Mar 30 2012 - 14:25:06 CDT)
bondsrecalc question Denis Davydov (Fri Mar 30 2012 - 11:10:14 CDT)
- Re: bondsrecalc question Axel Kohlmeyer (Fri Mar 30 2012 - 12:46:52 CDT)
Dynamically displaying the length of hydrogen bonds Andrew DeYoung (Fri Mar 30 2012 - 10:30:08 CDT)
- Re: Dynamically displaying the length of hydrogen bonds Wang Yi (Fri Mar 30 2012 - 11:24:22 CDT)
  - RE: Dynamically displaying the length of hydrogen bonds Andrew DeYoung (Fri Mar 30 2012 - 11:54:56 CDT)
    - Re: Dynamically displaying the length of hydrogen bonds Axel Kohlmeyer (Fri Mar 30 2012 - 12:44:35 CDT)
RE: Is there any way to stop the display of bonds for bonded atoms on opposite sides of a periodic boundary without unwrapping? Phelan Jr, Frederick R. Dr. (Thu Mar 29 2012 - 15:32:59 CDT)
- Re: Is there any way to stop the display of bonds for bonded atoms on opposite sides of a periodic boundary without unwrapping? Axel Kohlmeyer (Fri Mar 30 2012 - 08:13:09 CDT)
Is there any way to stop the display of bonds for bonded atoms on opposite sides of a periodic boundary without unwrapping? Phelan Jr, Frederick R. Dr. (Thu Mar 29 2012 - 14:31:58 CDT)
- Re: Is there any way to stop the display of bonds for bonded atoms on opposite sides of a periodic boundary without unwrapping? John Stone (Thu Mar 29 2012 - 14:44:28 CDT)
Possible MPI code problem (and fix) Christoph Willing (Thu Mar 29 2012 - 07:30:12 CDT)
- Re: Possible MPI code problem (and fix) John Stone (Thu Mar 29 2012 - 09:58:15 CDT)
kill source'd tcl script Philippe Bopp / temporary (Wed Mar 28 2012 - 03:37:12 CDT)
- RE: kill source'd tcl script Mikkel Vestergaard (Wed Mar 28 2012 - 04:41:15 CDT)
  - Re: kill source'd tcl script Axel Kohlmeyer (Wed Mar 28 2012 - 08:50:02 CDT)
Can't set graphics window position to 0,0 Christoph Willing (Tue Mar 27 2012 - 18:17:10 CDT)
- Re: Can't set graphics window position to 0,0 John Stone (Thu Mar 29 2012 - 10:20:27 CDT)
secondary structure calculation Ban Arn (Tue Mar 27 2012 - 11:55:24 CDT)
- Re: secondary structure calculation Barry Isralewitz (Tue Mar 27 2012 - 12:44:38 CDT)
- Re: secondary structure calculation Axel Kohlmeyer (Tue Mar 27 2012 - 15:26:26 CDT)
  - Re: secondary structure calculation Ban Arn (Wed Mar 28 2012 - 04:47:27 CDT)
    - Re: secondary structure calculation Ban Arn (Thu Mar 29 2012 - 05:05:38 CDT)
    - Re: secondary structure calculation Axel Kohlmeyer (Thu Mar 29 2012 - 08:01:38 CDT)
COORDINATES extraction of molecule's centers of mass VladanStefanovic_at_kg.ac.rs (Tue Mar 27 2012 - 01:37:23 CDT)
- Re: COORDINATES extraction of molecule's centers of mass John Stone (Wed Mar 28 2012 - 11:40:54 CDT)
autopsf: can't read "logfilename" Francesco Pietra (Sat Mar 24 2012 - 11:46:15 CDT)
- Re: autopsf: can't read "logfilename" John Stone (Thu Mar 29 2012 - 10:44:28 CDT)
(no subject) rainy908_at_yahoo.com (Fri Mar 23 2012 - 07:55:48 CDT)
(no subject) rainy908_at_yahoo.com (Thu Mar 22 2012 - 17:42:38 CDT)
(no subject) rainy908_at_yahoo.com (Thu Mar 22 2012 - 15:06:33 CDT)
adding patches via autopsf Bennion, Brian (Wed Mar 21 2012 - 11:34:47 CDT)
starting tkcon mbcx7sa3_at_zedat.fu-berlin.de (Wed Mar 21 2012 - 10:17:30 CDT)
- Re: starting tkcon John Stone (Wed Mar 21 2012 - 11:09:16 CDT)
  - Re: starting tkcon mbcx7sa3_at_zedat.fu-berlin.de (Wed Mar 21 2012 - 17:34:10 CDT)
- Re: starting tkcon Axel Kohlmeyer (Wed Mar 21 2012 - 11:20:36 CDT)
- Re: starting tkcon Olaf Lenz (Wed Mar 21 2012 - 11:56:20 CDT)
solvent radius setyanto md (Tue Mar 20 2012 - 01:03:29 CDT)
lib/stride/README Benjamin Kaduk (Mon Mar 19 2012 - 21:57:22 CDT)
- Re: lib/stride/README Ajasja LjubetiÄ (Tue Mar 20 2012 - 02:39:29 CDT)
  - Re: lib/stride/README John Stone (Wed Mar 21 2012 - 11:13:32 CDT)
plugins/hesstrans/Makefile recurses on CXXFLAGS Benjamin Kaduk (Mon Mar 19 2012 - 21:42:36 CDT)
- Re: plugins/hesstrans/Makefile recurses on CXXFLAGS John Stone (Wed Mar 21 2012 - 11:15:38 CDT)
Define "color Element" through rgb values Roger Nadler (Mon Mar 19 2012 - 11:47:14 CDT)
- Re: Define "color Element" through rgb values Axel Kohlmeyer (Mon Mar 19 2012 - 12:55:31 CDT)
- Re: Define "color Element" through rgb values John Stone (Wed Mar 21 2012 - 11:34:24 CDT)
  - Re: Define "color Element" through rgb values Roger Nadler (Wed Mar 21 2012 - 12:20:50 CDT)
bond cutoff Zhuyi Xue (Mon Mar 19 2012 - 08:45:34 CDT)
- Re: bond cutoff John Stone (Wed Mar 21 2012 - 11:29:49 CDT)
RMSD George Tzotzos (Sun Mar 18 2012 - 06:47:36 CDT)
- Re: RMSD John Stone (Sun Mar 18 2012 - 12:26:39 CDT)
- Re: RMSD Alexander Balaeff (Sun Mar 18 2012 - 12:59:28 CDT)
turns, using Stride Neelanjana Sengupta (Sat Mar 17 2012 - 02:03:52 CDT)
- Re: turns, using Stride John Stone (Wed Mar 21 2012 - 13:12:45 CDT)
Simulations with alpha methylated amino acids amin_at_imtech.res.in (Wed Mar 14 2012 - 20:17:04 CDT)
writepdb, wrong lines in output Francois Martz (Wed Mar 14 2012 - 12:15:22 CDT)
- Re: writepdb, wrong lines in output John Stone (Wed Mar 14 2012 - 12:31:18 CDT)
  - Re: writepdb, wrong lines in output Francois Martz (Thu Mar 15 2012 - 04:51:54 CDT)
Desmond Trajectory Files on the fly in VMD Hitesh Patel (Tue Mar 13 2012 - 05:13:34 CDT)
- Re: Desmond Trajectory Files on the fly in VMD Axel Kohlmeyer (Tue Mar 13 2012 - 08:56:45 CDT)
tutorial on inorganic builder setyanto md (Tue Mar 13 2012 - 03:56:35 CDT)
- Re: tutorial on inorganic builder John Stone (Tue Mar 13 2012 - 14:52:28 CDT)
load propka3.1 results error Albert (Mon Mar 12 2012 - 15:24:37 CDT)
- Re: load propka3.1 results error John Stone (Mon Mar 12 2012 - 15:36:25 CDT)
  - Re: load propka3.1 results error Albert (Mon Mar 12 2012 - 15:40:12 CDT)
how to configure PROPKA3 in VMD 1.91? Albert (Mon Mar 12 2012 - 15:11:39 CDT)
Drawing the simulation box from a Gromacs trajectory Andrew DeYoung (Mon Mar 12 2012 - 12:43:23 CDT)
- Re: Drawing the simulation box from a Gromacs trajectory Axel Kohlmeyer (Mon Mar 12 2012 - 14:30:23 CDT)
Force field toolkit (ffTK) - problem of reading Gaussian log file Wang Yi (Sat Mar 10 2012 - 13:58:20 CST)
- Re: Force field toolkit (ffTK) - problem of reading Gaussian log file Wang Yi (Sat Mar 10 2012 - 15:14:20 CST)
- Re: Force field toolkit (ffTK) - problem of reading Gaussian log file Mayne, Christopher G (Sat Mar 10 2012 - 15:44:06 CST)
Re: get avg ca distance Ana Celia Vila Verde (Fri Mar 09 2012 - 02:10:56 CST)
- Re: get avg ca distance Murpholino Peligro (Fri Mar 09 2012 - 11:09:08 CST)
VMD Display Error - Detected X11 'Composite' extension Shalabh Maroo (Thu Mar 08 2012 - 17:53:05 CST)
- Re: VMD Display Error - Detected X11 'Composite' extension Gianluca Interlandi (Thu Mar 08 2012 - 20:55:14 CST)
- Re: VMD Display Error - Detected X11 'Composite' extension Axel Kohlmeyer (Thu Mar 08 2012 - 21:06:08 CST)
  - Re: VMD Display Error - Detected X11 'Composite' extension John Stone (Thu Mar 08 2012 - 22:29:26 CST)
    - Re: VMD Display Error - Detected X11 'Composite' extension Shalabh Maroo (Fri Mar 09 2012 - 10:50:14 CST)
get avg ca distance Murpholino Peligro (Thu Mar 08 2012 - 15:33:19 CST)
positively charged portion of the protein surface Thomas Evangelidis (Thu Mar 08 2012 - 06:23:20 CST)
Re: [AMBER] Viewing with VMD bonds set by the "bond" command Francesco Pietra (Thu Mar 08 2012 - 03:48:48 CST)
- Re: [AMBER] Viewing with VMD bonds set by the "bond" command Francesco Pietra (Thu Mar 08 2012 - 12:27:58 CST)
  - Fwd: Re: [AMBER] Viewing with VMD bonds set by the "bond" command Francesco Pietra (Fri Mar 09 2012 - 01:39:17 CST)
    - Re: Re: Viewing with VMD bonds set by the "bond" command FyD (Fri Mar 09 2012 - 12:10:27 CST)
namd2 unable to find bond. Dave Arias (NelsonDa) (Wed Mar 07 2012 - 14:58:39 CST)
Memory used by VMD is much less than installed Meyer-Almes, Franz-Josef, Prof. Dr. (Wed Mar 07 2012 - 05:03:08 CST)
- Re: Memory used by VMD is much less than installed Axel Kohlmeyer (Wed Mar 07 2012 - 06:34:44 CST)
- Re: Memory used by VMD is much less than installed Ajasja LjubetiÄ (Wed Mar 07 2012 - 07:11:22 CST)
- Re: Memory used by VMD is much less than installed PaweÅ‚ KÄ™dzierski (Wed Mar 07 2012 - 08:15:54 CST)
rmsf to b-factor conversion abinayar_at_imsc.res.in (Wed Mar 07 2012 - 04:06:29 CST)
Individual components of RMSD? patrick wintrode (Tue Mar 06 2012 - 11:36:44 CST)
- Re: Individual components of RMSD? Andrew Jewett (Tue Mar 06 2012 - 20:31:31 CST)
  - Re: Individual components of RMSD? John Stone (Thu Mar 08 2012 - 12:15:47 CST)
    - Re: Individual components of RMSD? Axel Kohlmeyer (Thu Mar 08 2012 - 13:07:49 CST)
make movies with user-defined script lam nguyen (Mon Mar 05 2012 - 12:49:00 CST)
- Re: make movies with user-defined script John Stone (Thu Mar 08 2012 - 12:12:06 CST)
  - Re: make movies with user-defined script lam nguyen (Fri Mar 09 2012 - 12:10:05 CST)
information regarding tcl script for cell volume changing with each frame siladitya mukherjee (Sat Mar 03 2012 - 13:50:09 CST)
- Re: information regarding tcl script for cell volume changing with each frame Axel Kohlmeyer (Sat Mar 03 2012 - 14:45:14 CST)
  - Re: information regarding tcl script for cell volume changing with each frame siladitya mukherjee (Sat Mar 03 2012 - 16:18:07 CST)
    - Re: information regarding tcl script for cell volume changing with each frame Axel Kohlmeyer (Sat Mar 03 2012 - 17:25:43 CST)
Bug in VMD main? Ahmet Bakan (Sat Mar 03 2012 - 12:25:05 CST)
- Re: Bug in VMD main? John Stone (Sat Mar 03 2012 - 12:37:43 CST)
Re: Using VMD to plot coordination number of solvated ion v/s time Ana Celia Vila Verde (Fri Mar 02 2012 - 10:15:23 CST)
- Re: Using VMD to plot coordination number of solvated ion v/s time skolev_at_mnet.bg (Fri Mar 02 2012 - 12:33:57 CST)
Using VMD to plot coordination number of solvated ion v/s time skolev_at_mnet.bg (Fri Mar 02 2012 - 09:33:07 CST)
exporting marching cubes data from QuickSurf Zhe Wu (Thu Mar 01 2012 - 21:40:11 CST)
- Re: exporting marching cubes data from QuickSurf John Stone (Thu Mar 01 2012 - 22:18:48 CST)
  - RE: exporting marching cubes data from QuickSurf Zhe Wu (Fri Mar 02 2012 - 15:04:18 CST)
Calculating RDF from xyz file siladitya mukherjee (Thu Mar 01 2012 - 16:38:54 CST)
- Re: Calculating RDF from xyz file Axel Kohlmeyer (Thu Mar 01 2012 - 17:36:46 CST)
measure sasa Aaron Oakley (Wed Feb 29 2012 - 17:50:08 CST)
- Re: measure sasa John Stone (Thu Mar 01 2012 - 10:06:21 CST)
how to place a membrane protein with OPM ? Albert (Wed Feb 29 2012 - 15:33:44 CST)
- Re: how to place a membrane protein with OPM ? Andrew Jewett (Wed Feb 29 2012 - 19:24:10 CST)
  - Re: how to place a membrane protein with OPM ? Albert (Wed Feb 29 2012 - 23:54:35 CST)
- Re: how to place a membrane protein with OPM ? Chris Harrison (Wed Feb 29 2012 - 21:35:28 CST)
  - Re: how to place a membrane protein with OPM ? Chris Harrison (Wed Feb 29 2012 - 21:36:32 CST)
  - Re: how to place a membrane protein with OPM ? Albert (Wed Feb 29 2012 - 23:54:00 CST)
    - Re: how to place a membrane protein with OPM ? Chris Harrison (Thu Mar 01 2012 - 00:13:58 CST)
Adsorption VMD Tcl script error vladanstefanovic_at_kg.ac.rs (Wed Feb 29 2012 - 13:51:58 CST)
- Re: Adsorption VMD Tcl script error John Stone (Wed Feb 29 2012 - 14:05:21 CST)
  - Re: Adsorption VMD Tcl script error Ajasja LjubetiÄ (Wed Feb 29 2012 - 16:09:59 CST)
    - Re: Adsorption VMD Tcl script error Axel Kohlmeyer (Wed Feb 29 2012 - 16:56:31 CST)
Lipid order parameters Ganesh Kamath (Mon Feb 27 2012 - 14:21:13 CST)
Problems with PSFGEN Dave Arias (NelsonDa) (Mon Feb 27 2012 - 13:18:07 CST)
Plugins use after compilation question Anthony Cruz Balberdi (Mon Feb 27 2012 - 12:38:01 CST)
- Re: Plugins use after compilation question Axel Kohlmeyer (Mon Feb 27 2012 - 13:30:49 CST)
How to change the python include and linkage path in configure script Haw-Zan Goh (Mon Feb 27 2012 - 12:15:06 CST)
- Re: How to change the python include and linkage path in configure script Axel Kohlmeyer (Mon Feb 27 2012 - 13:33:18 CST)
From Vmd to lammps data file Dimitrios Mantzalis (Mon Feb 27 2012 - 06:55:34 CST)
- Re: From Vmd to lammps data file Axel Kohlmeyer (Mon Feb 27 2012 - 08:07:24 CST)
  - Re: From Vmd to lammps data file Dimitrios Mantzalis (Mon Feb 27 2012 - 09:07:05 CST)
    - Re: From Vmd to lammps data file Axel Kohlmeyer (Mon Feb 27 2012 - 09:19:31 CST)
possible memory leak with pbc wrap Ana Celia Vila Verde (Fri Feb 24 2012 - 09:16:59 CST)
- Re: possible memory leak with pbc wrap John Stone (Tue Feb 28 2012 - 14:20:14 CST)
Input selection as xyz co-ordinates Ban Arn (Wed Feb 22 2012 - 09:09:33 CST)
- Re: Input selection as xyz co-ordinates John Stone (Wed Feb 22 2012 - 22:43:52 CST)
Release of the R.E.D.-III.5 tools FyD (Wed Feb 22 2012 - 05:00:23 CST)
Secondary structure assignment Zhuyi Xue (Tue Feb 21 2012 - 21:24:14 CST)
- Re: Secondary structure assignment Peter C. Lai (Wed Feb 22 2012 - 00:31:39 CST)
- Re: Secondary structure assignment sajad falsafi (Wed Feb 22 2012 - 01:39:07 CST)
[request] Best practices for rendering frames and making movies Diego Enry Barreto Gomes (Tue Feb 21 2012 - 17:22:56 CST)
- Re: [request] Best practices for rendering frames and making movies Axel Kohlmeyer (Tue Feb 21 2012 - 18:29:19 CST)
  - mono2poly question Joseph Bylund (Sun Feb 26 2012 - 23:24:00 CST)
- Re: [request] Best practices for rendering frames and making movies John Stone (Wed Feb 22 2012 - 11:12:27 CST)
SASA -tcl script Ban Arn (Tue Feb 21 2012 - 12:36:07 CST)
- Re: SASA -tcl script John Stone (Tue Feb 21 2012 - 14:31:09 CST)
incorrect number of coordinates in .dcd file error abinayar_at_imsc.res.in (Tue Feb 21 2012 - 00:53:08 CST)
- Re: incorrect number of coordinates in .dcd file error Ajasja LjubetiÄ (Tue Feb 21 2012 - 02:17:37 CST)
how to add spring between two atoms SONY kaur (Mon Feb 20 2012 - 13:05:40 CST)
- Re: how to add spring between two atoms John Stone (Mon Feb 20 2012 - 13:17:23 CST)
.xyz bond winardi, erik (Mon Feb 20 2012 - 05:15:05 CST)
- Re: .xyz bond Axel Kohlmeyer (Mon Feb 20 2012 - 06:07:02 CST)
Distance between center of mass of two amino acid residues. mish (Sun Feb 19 2012 - 10:27:45 CST)
- Re: Distance between center of mass of two amino acid residues. Axel Kohlmeyer (Sun Feb 19 2012 - 11:37:25 CST)
- R: Distance between center of mass of two amino acid residues. Cosseddu, Salvatore (Sun Feb 19 2012 - 13:50:37 CST)
  - Re: Distance between center of mass of two amino acid residues. Axel Kohlmeyer (Sun Feb 19 2012 - 14:43:17 CST)
quicksurf and PBC Philippe Bopp / temporary (Sat Feb 18 2012 - 09:45:48 CST)
- Re: quicksurf and PBC Axel Kohlmeyer (Sat Feb 18 2012 - 10:57:01 CST)
- Re: quicksurf and PBC John Stone (Sat Feb 18 2012 - 11:14:25 CST)
About FFTP with transition metal complexes Francesco Pietra (Sat Feb 18 2012 - 00:23:01 CST)
- Re: About FFTP with transition metal complexes Mayne, Christopher G (Sat Feb 18 2012 - 15:39:58 CST)
  - RE: Re: About FFTP with transition metal complexes JC Gumbart (Sat Feb 18 2012 - 16:39:55 CST)
    - Re: Re: About FFTP with transition metal complexes Francesco Pietra (Wed Feb 29 2012 - 05:52:03 CST)
    - Re: Re: About FFTP with transition metal complexes JC Gumbart (Wed Feb 29 2012 - 20:36:18 CST)
trajector@VMD Turgay Cakmak (Fri Feb 17 2012 - 08:54:15 CST)
- Re: trajector@VMD Axel Kohlmeyer (Fri Feb 17 2012 - 09:38:26 CST)
  - Re: trajector@VMD John Stone (Fri Feb 17 2012 - 10:17:12 CST)
append glow lights to a VMD/Tachyon scene Filip Persson (Fri Feb 17 2012 - 03:11:53 CST)
- Re: append glow lights to a VMD/Tachyon scene Axel Kohlmeyer (Fri Feb 17 2012 - 08:11:53 CST)
pdb reader/writer appears to corrupt pdb output Bennion, Brian (Thu Feb 16 2012 - 14:49:06 CST)
- Re: pdb reader/writer appears to corrupt pdb output John Stone (Thu Feb 16 2012 - 15:51:08 CST)
  - RE: pdb reader/writer appears to corrupt pdb output Bennion, Brian (Thu Feb 16 2012 - 16:04:27 CST)
    - Re: pdb reader/writer appears to corrupt pdb output John Stone (Thu Feb 16 2012 - 16:21:53 CST)
Membrane and box with PBC Ricardo Soares (Thu Feb 16 2012 - 12:28:06 CST)
Create multiple tcl interpreter child instances within VMD to run several scripts at once Salvatore Mario Cosseddu (Thu Feb 16 2012 - 11:23:15 CST)
- Re: Create multiple tcl interpreter child instances within VMD to run several scripts at once John Stone (Thu Feb 16 2012 - 11:40:11 CST)
  - Re: Create multiple tcl interpreter child instances within VMD to run several scripts at once Salvatore Mario Cosseddu (Thu Feb 16 2012 - 11:49:55 CST)
    - Re: Create multiple tcl interpreter child instances within VMD to run several scripts at once John Stone (Thu Feb 16 2012 - 11:52:15 CST)
    - Re: Create multiple tcl interpreter child instances within VMD to run several scripts at once Salvatore Mario Cosseddu (Thu Feb 16 2012 - 12:04:17 CST)
- Re: Create multiple tcl interpreter child instances within VMD to run several scripts at once Axel Kohlmeyer (Thu Feb 16 2012 - 12:46:48 CST)
quick-surf and throb Philippe Bopp / temporary (Thu Feb 16 2012 - 03:55:32 CST)
- Re: quick-surf and throb John Stone (Thu Feb 16 2012 - 09:40:44 CST)
Re: [Stefan_Franzen@ncsu.edu: Patch for deoxy and dideoxy nucleotides] Jim Phillips (Wed Feb 15 2012 - 10:24:11 CST)
ERROR) Tcl startup error: Can't find a usable init.tcl in the following directories: Urszula Uciechowska (Wed Feb 15 2012 - 07:59:30 CST)
installation error Urszula Uciechowska (Wed Feb 15 2012 - 03:28:59 CST)
ERROR) Tcl startup error: Can't find a usable init.tcl in the following directories: Urszula Uciechowska (Wed Feb 15 2012 - 01:48:52 CST)
- Re: ERROR) Tcl startup error: Can't find a usable init.tcl in the following directories: John Stone (Wed Feb 15 2012 - 10:08:38 CST)
Hbonds Analysis Aric Newton (Tue Feb 14 2012 - 14:22:27 CST)
- Re: Hbonds Analysis Axel Kohlmeyer (Tue Feb 14 2012 - 15:36:13 CST)
  - Re: Hbonds Analysis John Stone (Wed Feb 15 2012 - 10:13:18 CST)
Timestep Molybdos Kirkimpolakis (Mon Feb 13 2012 - 15:53:15 CST)
- Re: Timestep Axel Kohlmeyer (Mon Feb 13 2012 - 16:57:22 CST)
radial distribution funtion Paymon Pirzadeh (Mon Feb 13 2012 - 15:21:25 CST)
- Re: radial distribution funtion Axel Kohlmeyer (Mon Feb 13 2012 - 16:21:16 CST)
  - Re: radial distribution funtion Paymon Pirzadeh (Mon Feb 13 2012 - 21:43:54 CST)
    - Re: radial distribution funtion Axel Kohlmeyer (Mon Feb 13 2012 - 21:59:32 CST)
Spatial (angular) distribution function David Cohen-Tanugi (Mon Feb 13 2012 - 13:38:11 CST)
- Re: Spatial (angular) distribution function John Stone (Wed Feb 15 2012 - 10:17:06 CST)
Patch for deoxy and dideoxy nucleotides Stefan Franzen (Mon Feb 13 2012 - 09:31:12 CST)
Problem with VMD 1.9.1 (CUDA) on Snow Leopard Christian Mücksch (Mon Feb 13 2012 - 05:02:54 CST)
- Re: Problem with VMD 1.9.1 (CUDA) on Snow Leopard John Stone (Tue Feb 14 2012 - 11:52:24 CST)
Meadionize lecan (Sun Feb 12 2012 - 21:05:15 CST)
- RE: Meadionize Mark Cunningham (Mon Feb 13 2012 - 09:15:18 CST)
PROPKA doesn't work in recent VMD1.9.1 Albert (Sun Feb 12 2012 - 05:25:14 CST)
- Re: PROPKA doesn't work in recent VMD1.9.1 Axel Kohlmeyer (Sun Feb 12 2012 - 09:47:21 CST)
problem with catdcd Albert (Sun Feb 12 2012 - 02:23:40 CST)
- RE: problem with catdcd JC Gumbart (Sun Feb 12 2012 - 08:21:18 CST)
  - Re: problem with catdcd Albert (Sun Feb 12 2012 - 08:24:29 CST)
    - RE: problem with catdcd JC Gumbart (Sun Feb 12 2012 - 08:34:56 CST)
- Re: problem with catdcd Joshua Adelman (Sun Feb 12 2012 - 08:38:22 CST)
charges in VMD 1.9 vs. VMD 1.8.7 Philippe Bopp / temporary (Fri Feb 10 2012 - 07:43:17 CST)
- Re: charges in VMD 1.9 vs. VMD 1.8.7 Axel Kohlmeyer (Fri Feb 10 2012 - 08:38:12 CST)
Stand-alone VMD ? R. Charbel Maroun (Fri Feb 10 2012 - 05:26:38 CST)
- Re: Stand-alone VMD ? Ajasja LjubetiÄ (Fri Feb 10 2012 - 07:29:36 CST)
  - Re: Stand-alone VMD ? R. Charbel Maroun (Fri Feb 10 2012 - 09:25:21 CST)
  - Re: Stand-alone VMD ? R. Charbel Maroun (Mon Feb 13 2012 - 05:58:52 CST)
    - Re: Stand-alone VMD ? Salvatore Mario Cosseddu (Mon Feb 13 2012 - 08:03:43 CST)
- Re: Stand-alone VMD ? Salvatore Mario Cosseddu (Fri Feb 10 2012 - 08:49:55 CST)
- RE: Stand-alone VMD ? Yamada, Masako (GE Global Research) (Fri Feb 10 2012 - 09:41:49 CST)
multiseq doesn't respond to ctrl key correctly charles sun (Thu Feb 09 2012 - 22:58:45 CST)
- Re: multiseq doesn't respond to ctrl key correctly Kirby Vandivort (Fri Feb 10 2012 - 10:19:22 CST)
radial distribution function Paymon Pirzadeh (Thu Feb 09 2012 - 20:15:15 CST)
- Re: radial distribution function Axel Kohlmeyer (Thu Feb 09 2012 - 21:09:54 CST)
change of font lecan (Thu Feb 09 2012 - 20:01:17 CST)
- Re: change of font John Stone (Fri Feb 10 2012 - 09:04:57 CST)
- Re: change of font Salvatore Mario Cosseddu (Fri Feb 10 2012 - 09:12:46 CST)
Source Command MARK PLUMMER (Thu Feb 09 2012 - 10:06:42 CST)
Source Command MARK PLUMMER (Thu Feb 09 2012 - 09:53:36 CST)
- Re: Source Command Salvatore Mario Cosseddu (Thu Feb 09 2012 - 13:42:10 CST)
Use of coarse grain plugin kirtana S (Wed Feb 08 2012 - 17:35:26 CST)
- Re: Use of coarse grain plugin Dudo (Wed Feb 08 2012 - 18:47:01 CST)
- Re: Use of coarse grain plugin Kirby Vandivort (Tue Feb 28 2012 - 16:53:50 CST)
VMD Contact map through time Zack Scholl (Wed Feb 08 2012 - 16:09:04 CST)
- Re: VMD Contact map through time Barry Isralewitz (Wed Feb 08 2012 - 16:47:22 CST)
charge visualization niladri patra (Tue Feb 07 2012 - 18:41:37 CST)
- Re: charge visualization Axel Kohlmeyer (Tue Feb 07 2012 - 19:49:17 CST)
Use variable in atomselect command Brian Kim (Tue Feb 07 2012 - 15:16:17 CST)
- Re: Use variable in atomselect command Axel Kohlmeyer (Tue Feb 07 2012 - 16:15:55 CST)
  - Re: Use variable in atomselect command Brian Kim (Tue Feb 07 2012 - 16:40:24 CST)
  - Re: Use variable in atomselect command Brian Kim (Tue Feb 07 2012 - 19:11:27 CST)
NAMDenergy plugin_VMD_van der Waal interactions Bruno Luís Pinto de Oliveira (Tue Feb 07 2012 - 09:20:23 CST)
- NAMDenergy plugin_VMD_van der Waal interactions Bruno Luís Pinto de Oliveira (Wed Feb 08 2012 - 10:05:41 CST)
  - NAMDenergy plugin_VMD_van der Waal interactions Bruno Luís Pinto de Oliveira (Wed Feb 08 2012 - 12:40:57 CST)
Configure VMD while GROMACS Installation Hitesh Patel (Tue Feb 07 2012 - 03:39:30 CST)
- Re: Configure VMD while GROMACS Installation Axel Kohlmeyer (Tue Feb 07 2012 - 05:52:22 CST)
testing vmd1.9.1 Bennion, Brian (Mon Feb 06 2012 - 18:19:19 CST)
- Re: testing vmd1.9.1 John Stone (Wed Feb 08 2012 - 13:34:10 CST)
Tcl script error Ban Arn (Mon Feb 06 2012 - 10:50:14 CST)
- Re: Tcl script error John Stone (Mon Feb 06 2012 - 10:58:26 CST)
  - Re: Tcl script error Ban Arn (Mon Feb 06 2012 - 11:12:12 CST)
    - Re: Tcl script error John Stone (Mon Feb 06 2012 - 11:23:05 CST)
    - Re: Tcl script error Ban Arn (Mon Feb 06 2012 - 11:28:12 CST)
  - Re: Tcl script error Axel Kohlmeyer (Mon Feb 06 2012 - 11:54:35 CST)
- Re: Tcl script error Axel Kohlmeyer (Mon Feb 06 2012 - 11:46:43 CST)
PSFGEN and Reading Bonds from PDB Files Rajan Vatassery (Sun Feb 05 2012 - 14:13:43 CST)
- Re: PSFGEN and Reading Bonds from PDB Files Axel Kohlmeyer (Sun Feb 05 2012 - 15:36:29 CST)
- Re: PSFGEN and Reading Bonds from PDB Files Chris Harrison (Sun Feb 05 2012 - 15:45:19 CST)
- Re: PSFGEN and Reading Bonds from PDB Files flavio seixas (Sun Feb 05 2012 - 18:24:40 CST)
- Re: PSFGEN and Reading Bonds from PDB Files Rajan Vatassery (Mon Feb 06 2012 - 11:02:14 CST)
  - Re: PSFGEN and Reading Bonds from PDB Files Axel Kohlmeyer (Mon Feb 06 2012 - 11:52:27 CST)
ffTK in the just released VMD 1.9.1 JC Gumbart (Sat Feb 04 2012 - 15:04:05 CST)
Announce: VMD 1.9.1 released John Stone (Sat Feb 04 2012 - 14:25:58 CST)
- The spheres become oval, getting close to the screen borders Cosseddu, Salvatore (Sun Feb 05 2012 - 09:53:57 CST)
  - Re: The spheres become oval, getting close to the screen borders John Stone (Sun Feb 05 2012 - 10:44:57 CST)
    - RE: The spheres become oval, getting close to the screen borders Cosseddu, Salvatore (Sun Feb 05 2012 - 11:43:11 CST)
  - Re: The spheres become oval, getting close to the screen borders Axel Kohlmeyer (Sun Feb 05 2012 - 11:07:34 CST)
create images in vmd oguz gurbulak (Fri Feb 03 2012 - 05:34:54 CST)
- create images in vmd oguz gurbulak (Fri Feb 03 2012 - 06:21:28 CST)
- Re: create images in vmd Axel Kohlmeyer (Fri Feb 03 2012 - 06:34:53 CST)
how to display the full molecule when use "within" option? Albert (Fri Feb 03 2012 - 05:31:10 CST)
- Re: how to display the full molecule when use "within" option? Ajasja LjubetiÄ (Fri Feb 03 2012 - 06:21:29 CST)
- Re: how to display the full molecule when use "within" option? Axel Kohlmeyer (Fri Feb 03 2012 - 06:32:34 CST)
floating error - tcl script Ban Arn (Fri Feb 03 2012 - 04:51:11 CST)
Error while running steered MD script Ban Arn (Thu Feb 02 2012 - 10:24:18 CST)
- Re: Error while running steered MD script John Stone (Thu Feb 02 2012 - 17:10:01 CST)
  - Re: Error while running steered MD script Ban Arn (Thu Feb 02 2012 - 17:29:02 CST)
    - Re: Error while running steered MD script John Stone (Thu Feb 02 2012 - 18:18:20 CST)
    - Re: Error while running steered MD script Ban Arn (Fri Feb 03 2012 - 03:07:34 CST)
how to measure residues' chi angle in VMD? Albert (Thu Feb 02 2012 - 03:34:27 CST)
how to merge two PDB trajectories? Albert (Wed Feb 01 2012 - 23:34:31 CST)
- Re: how to merge two PDB trajectories? John Stone (Wed Feb 01 2012 - 23:40:45 CST)
is it possible to enable GPU rendering? Albert (Wed Feb 01 2012 - 14:04:02 CST)
- Re: is it possible to enable GPU rendering? John Stone (Wed Feb 01 2012 - 14:12:47 CST)
Save coor coordinates as pdb R. Charbel Maroun (Wed Feb 01 2012 - 12:26:31 CST)
- Re: Save coor coordinates as pdb John Stone (Wed Feb 01 2012 - 13:53:58 CST)
Gromacs analysis tools for Namd output PAUL NEWMAN (Wed Feb 01 2012 - 11:41:40 CST)
- Re: namd-l: Gromacs analysis tools for Namd output Axel Kohlmeyer (Wed Feb 01 2012 - 11:48:47 CST)
- Re: Gromacs analysis tools for Namd output John Stone (Wed Feb 01 2012 - 11:47:43 CST)
- RE: Gromacs analysis tools for Namd output Kei Sit (Wed Feb 01 2012 - 17:33:01 CST)
Re: RE : PCA of desmond trajectories Hitesh Patel (Wed Feb 01 2012 - 10:26:44 CST)
- Re: RE : PCA of desmond trajectories John Stone (Wed Feb 01 2012 - 10:41:58 CST)
Unusual visualisations Ben Hall (Wed Feb 01 2012 - 09:54:01 CST)
- Re: Unusual visualisations John Stone (Wed Feb 01 2012 - 10:50:30 CST)
  - Re: Unusual visualisations John Stone (Wed Feb 01 2012 - 16:11:07 CST)
PCA of desmond trajectories Hitesh Patel (Wed Feb 01 2012 - 09:29:15 CST)
Rmsd script with arguments Mustafa Tekpinar (Tue Jan 31 2012 - 13:48:40 CST)
- Re: Rmsd script with arguments Axel Kohlmeyer (Tue Jan 31 2012 - 15:55:06 CST)
  - Re: Rmsd script with arguments Mustafa Tekpinar (Wed Feb 01 2012 - 13:38:34 CST)
Quantitative meaning of volmap isosurface Ben Hall (Tue Jan 31 2012 - 06:01:20 CST)
- Re: Quantitative meaning of volmap isosurface Axel Kohlmeyer (Tue Jan 31 2012 - 07:25:02 CST)
  - Re: Quantitative meaning of volmap isosurface Benjamin Hall (Tue Jan 31 2012 - 07:32:50 CST)
how to fix structural alignment pdbs thereal sisterdot (Tue Jan 31 2012 - 03:04:52 CST)
- Re: how to fix structural alignment pdbs Axel Kohlmeyer (Tue Jan 31 2012 - 07:22:44 CST)
how to configure Tachyon image render size? Albert (Mon Jan 30 2012 - 11:52:02 CST)
- Re: how to configure Tachyon image render size? Jeffrey Potoff (Mon Jan 30 2012 - 14:14:09 CST)
  - Re: how to configure Tachyon image render size? Axel Kohlmeyer (Mon Jan 30 2012 - 15:46:42 CST)
NewRibbons/NewCartoon problem due to missing CUDA ? thereal sisterdot (Mon Jan 30 2012 - 05:27:33 CST)
- Re: NewRibbons/NewCartoon problem due to missing CUDA ? Axel Kohlmeyer (Tue Jan 31 2012 - 07:18:10 CST)
  - Re: NewRibbons/NewCartoon problem due to missing CUDA ? Ajasja LjubetiÄ (Tue Jan 31 2012 - 08:32:01 CST)
- Re: NewRibbons/NewCartoon problem due to missing CUDA ? John Stone (Tue Jan 31 2012 - 15:47:00 CST)
- Re: NewRibbons/NewCartoon problem due to missing CUDA ? thereal sisterdot (Thu Feb 02 2012 - 05:49:34 CST)
  - Re: NewRibbons/NewCartoon problem due to missing CUDA ? Axel Kohlmeyer (Thu Feb 02 2012 - 07:52:24 CST)
Calculation of ligand displacement Vs time Ban Arn (Mon Jan 30 2012 - 03:53:27 CST)
problem with new plugin installation. Albert (Sat Jan 28 2012 - 01:18:14 CST)
- problem with new plugin installation. Albert (Sat Jan 28 2012 - 08:08:16 CST)
  - Re: problem with new plugin installation. Axel Kohlmeyer (Sat Jan 28 2012 - 10:33:50 CST)
    - Re: problem with new plugin installation. John Stone (Sat Jan 28 2012 - 11:25:14 CST)
Cutting a sphere with a specified radius along a trajectory Mustafa Tekpinar (Fri Jan 27 2012 - 16:26:29 CST)
- Re: Cutting a sphere with a specified radius along a trajectory John Stone (Fri Jan 27 2012 - 17:17:43 CST)
- Re: Cutting a sphere with a specified radius along a trajectory Axel Kohlmeyer (Fri Jan 27 2012 - 17:24:23 CST)
Re: how to enlarge the menu font? Albert (Fri Jan 27 2012 - 01:33:48 CST)
- Re: how to enlarge the menu font? John Stone (Fri Jan 27 2012 - 01:42:20 CST)
how to enlarge the menu font? Albert (Fri Jan 27 2012 - 00:18:36 CST)
- Re: how to enlarge the menu font? Ajasja LjubetiÄ (Fri Jan 27 2012 - 01:29:11 CST)
Viewing "other" data as a trajectory plays J. Nathan Scott (Thu Jan 26 2012 - 11:40:08 CST)
- Re: Viewing "other" data as a trajectory plays John Stone (Thu Jan 26 2012 - 12:19:32 CST)
  - Re: Viewing "other" data as a trajectory plays J. Nathan Scott (Thu Jan 26 2012 - 13:07:28 CST)
package ::struct::set not available Ana Celia Vila Verde (Thu Jan 26 2012 - 08:36:56 CST)
- Re: package ::struct::set not available Axel Kohlmeyer (Thu Jan 26 2012 - 09:40:06 CST)
VMD 1.9.1 beta 2 to be posted tonight... John Stone (Wed Jan 25 2012 - 16:08:28 CST)
- Re: VMD 1.9.1 beta 2 to be posted tonight... John Stone (Wed Jan 25 2012 - 19:35:42 CST)
  - Re: VMD 1.9.1 beta 2 to be posted tonight... Ajasja LjubetiÄ (Thu Jan 26 2012 - 03:04:29 CST)
unit cell volume is zero jeela keel (Wed Jan 25 2012 - 15:56:40 CST)
- Re: unit cell volume is zero Axel Kohlmeyer (Wed Jan 25 2012 - 16:03:04 CST)
  - Re: Re: unit cell volume is zero jeela keel (Wed Jan 25 2012 - 16:59:19 CST)
- Re: unit cell volume is zero John Stone (Wed Jan 25 2012 - 16:03:35 CST)
Looking for nice example images for VMD 1.9.1 release page... John Stone (Wed Jan 25 2012 - 14:29:39 CST)
- Re: Looking for nice example images for VMD 1.9.1 release page... Toni Giorgino (Fri Jan 27 2012 - 16:38:04 CST)
  - Re: Looking for nice example images for VMD 1.9.1 release page... John Stone (Fri Jan 27 2012 - 17:10:57 CST)
atomselect counting jeela keel (Wed Jan 25 2012 - 08:39:47 CST)
- Re: atomselect counting Axel Kohlmeyer (Wed Jan 25 2012 - 09:12:16 CST)
  - Re: Re: atomselect counting jeela keel (Wed Jan 25 2012 - 13:48:18 CST)
    - Re: Re: atomselect counting Axel Kohlmeyer (Wed Jan 25 2012 - 14:46:05 CST)
    - Re: Re: atomselect counting Peter C. Lai (Wed Jan 25 2012 - 16:51:49 CST)
- Re: atomselect counting Bryan Roessler (Thu Feb 02 2012 - 13:20:38 CST)
Topotools - limit to size of system it can be used for? Michael Doig (Tue Jan 24 2012 - 05:48:04 CST)
- Re: Topotools - limit to size of system it can be used for? Axel Kohlmeyer (Tue Jan 24 2012 - 07:13:27 CST)
ImportError: cannot import name AtomSel Wim R. Cardoen (Mon Jan 23 2012 - 15:36:19 CST)
- Re: ImportError: cannot import name AtomSel Axel Kohlmeyer (Mon Jan 23 2012 - 16:33:29 CST)
- Re: ImportError: cannot import name AtomSel John Stone (Mon Jan 23 2012 - 16:35:53 CST)
  - Re: ImportError: cannot import name AtomSel Wim R. Cardoen (Tue Jan 24 2012 - 11:26:23 CST)
Calling all DCD files in a directory sequentially using CatDCD Bryan Roessler (Mon Jan 23 2012 - 15:11:34 CST)
- Re: Calling all DCD files in a directory sequentially using CatDCD John Stone (Mon Jan 23 2012 - 15:24:51 CST)
  - Re: Calling all DCD files in a directory sequentially using CatDCD Bryan Roessler (Mon Jan 23 2012 - 16:15:48 CST)
    - Re: Calling all DCD files in a directory sequentially using CatDCD Bryan Roessler (Mon Jan 23 2012 - 18:24:07 CST)
    - RE: Calling all DCD files in a directory sequentially using CatDCD Cosseddu, Salvatore (Tue Jan 24 2012 - 03:47:29 CST)
script to modify cysteines with spinlabel Anna Kuznetsova (Mon Jan 23 2012 - 14:55:50 CST)
- Re: script to modify cysteines with spinlabel Ajasja LjubetiÄ (Tue Jan 24 2012 - 13:35:22 CST)
VMD and Centos 6 Irene Newhouse (Sat Jan 21 2012 - 22:49:47 CST)
- Re: VMD and Centos 6 Axel Kohlmeyer (Sun Jan 22 2012 - 10:19:06 CST)
  - RE: VMD and Centos 6 Irene Newhouse (Sun Jan 22 2012 - 14:39:16 CST)
    - RE: VMD and Centos 6 Irene Newhouse (Sun Jan 22 2012 - 16:17:15 CST)
ERROR) measure gofr: bad frame range given. max jeela keel (Fri Jan 20 2012 - 14:43:13 CST)
- Re: ERROR) measure gofr: bad frame range given. max jeela keel (Mon Jan 23 2012 - 08:09:54 CST)
  - Re: ERROR) measure gofr: bad frame range given. max Axel Kohlmeyer (Mon Jan 23 2012 - 09:29:37 CST)
is it possible to hide ONLY non-polar hydrogens? Albert (Fri Jan 20 2012 - 03:54:32 CST)
- Re: is it possible to hide ONLY non-polar hydrogens? Ajasja LjubetiÄ (Fri Jan 20 2012 - 04:49:36 CST)
- Re: is it possible to hide ONLY non-polar hydrogens? poker_at_physics.usyd.edu.au (Fri Jan 20 2012 - 16:41:14 CST)
(no subject) vaneeta bala (Fri Jan 20 2012 - 01:11:06 CST)
ionic radii of sodium and chloride Zumot, Elia Nabil (Thu Jan 19 2012 - 20:12:38 CST)
- Re: ionic radii of sodium and chloride Axel Kohlmeyer (Thu Jan 19 2012 - 21:12:49 CST)
  - RE: ionic radii of sodium and chloride Zumot, Elia Nabil (Fri Jan 20 2012 - 10:57:19 CST)
  - Re: ionic radii of sodium and chloride Alexander Balaeff (Fri Jan 20 2012 - 13:59:55 CST)
Generating a psf file using VMD Ganesh Kamath (Thu Jan 19 2012 - 16:56:47 CST)
- Re: Generating a psf file using VMD Axel Kohlmeyer (Thu Jan 19 2012 - 17:55:01 CST)
- Re: Generating a psf file using VMD John Stone (Mon Jan 23 2012 - 10:58:38 CST)
rendering question Alex Angerhofer (Thu Jan 19 2012 - 10:56:59 CST)
- Re: rendering question John Stone (Thu Jan 19 2012 - 11:31:20 CST)
- Re: rendering question Axel Kohlmeyer (Thu Jan 19 2012 - 11:55:22 CST)
Use "Metal complexes/FeS-clusters" in VMD paratool Jiajian Li (Wed Jan 18 2012 - 16:01:10 CST)
- Re: Use "Metal complexes/FeS-clusters" in VMD paratool John Stone (Wed Feb 01 2012 - 23:21:49 CST)
Haptic devices for IMD gpat_at_bioacademy.gr (Wed Jan 18 2012 - 09:56:21 CST)
- Re: Haptic devices for IMD John Stone (Wed Jan 18 2012 - 10:57:05 CST)
- Re: Haptic devices for IMD Axel Kohlmeyer (Wed Jan 18 2012 - 11:24:19 CST)
  - Re: Haptic devices for IMD gpat_at_bioacademy.gr (Fri Jan 20 2012 - 05:01:35 CST)
- Re: Haptic devices for IMD Marc Baaden (Wed Jan 18 2012 - 12:27:55 CST)
New "surf" calculations in VMD 1.9.1 beta FX (Wed Jan 18 2012 - 06:12:08 CST)
- Re: New "surf" calculations in VMD 1.9.1 beta Ajasja LjubetiÄ (Wed Jan 18 2012 - 07:17:32 CST)
- Re: New "surf" calculations in VMD 1.9.1 beta Axel Kohlmeyer (Wed Jan 18 2012 - 08:00:54 CST)
- Re: New "surf" calculations in VMD 1.9.1 beta John Stone (Wed Jan 18 2012 - 11:01:13 CST)
Using threads in VMD's tcl Víctor (Tue Jan 17 2012 - 10:04:57 CST)
- Re: Using threads in VMD's tcl Axel Kohlmeyer (Tue Jan 17 2012 - 11:05:20 CST)
- Re: Using threads in VMD's tcl Ajasja LjubetiÄ (Tue Jan 17 2012 - 12:40:13 CST)
  - Re: Using threads in VMD's tcl Víctor (Tue Jan 17 2012 - 16:03:38 CST)
    - Re: Using threads in VMD's tcl Axel Kohlmeyer (Tue Jan 17 2012 - 17:17:25 CST)
    - Re: Using threads in VMD's tcl Víctor (Tue Jan 17 2012 - 17:19:48 CST)
Question regarding HBond analysis Ganesh Kamath (Mon Jan 16 2012 - 17:05:19 CST)
- Re: Question regarding HBond analysis Axel Kohlmeyer (Mon Jan 16 2012 - 18:13:55 CST)
  - Fwd: Question regarding HBond analysis Ganesh Kamath (Tue Jan 17 2012 - 12:26:01 CST)
    - Re: Question regarding HBond analysis Axel Kohlmeyer (Tue Jan 17 2012 - 13:19:21 CST)
using vmd to apply symmetry transformations Bennion, Brian (Fri Jan 13 2012 - 09:21:39 CST)
- Re: using vmd to apply symmetry transformations John Stone (Fri Jan 13 2012 - 10:58:08 CST)
  - RE: using vmd to apply symmetry transformations Bennion, Brian (Fri Jan 13 2012 - 11:06:27 CST)
Yet another python question: how to run a python script from the vmd console ? maria goranovic (Fri Jan 13 2012 - 05:04:16 CST)
- Re: Yet another python question: how to run a python script from the vmd console ? John Stone (Wed Feb 01 2012 - 23:33:46 CST)
precompiled python libraries still work for vmd 1.9 maria goranovic (Fri Jan 13 2012 - 04:50:12 CST)
- Re: precompiled python libraries still work for vmd 1.9 John Stone (Fri Jan 13 2012 - 11:24:56 CST)
using fit_angle.py over a trajectory maria goranovic (Fri Jan 13 2012 - 03:36:26 CST)
Problems in setting up low pH systems Sheng, Zi-Zhang (Wed Jan 11 2012 - 10:03:10 CST)
- Re: Problems in setting up low pH systems Sheng, Zi-Zhang (Wed Jan 11 2012 - 20:26:49 CST)
  - Re: Problems in setting up low pH systems Axel Kohlmeyer (Wed Jan 11 2012 - 21:26:28 CST)
camera position and scale Arham Amouie (Mon Jan 09 2012 - 08:09:46 CST)
- Re: camera position and scale John Stone (Wed Feb 01 2012 - 23:18:23 CST)
Implicit Ligand Sampling-molecule rotation issue Aaron Oakley (Sun Jan 08 2012 - 18:30:08 CST)
- Re: Implicit Ligand Sampling-molecule rotation issue Jérôme Hénin (Mon Jan 09 2012 - 05:11:19 CST)
vmd-density-profile subrata paul (Sat Jan 07 2012 - 07:11:26 CST)
- Re: vmd-density-profile Axel Kohlmeyer (Sat Jan 07 2012 - 10:23:44 CST)
  - Re: vmd-density-profile Toni Giorgino (Mon Jan 09 2012 - 05:30:22 CST)
method for user-defined coloring JhonY. I. (Fri Jan 06 2012 - 11:53:37 CST)
- Re: method for user-defined coloring Axel Kohlmeyer (Fri Jan 06 2012 - 12:44:15 CST)
Coloring by RMSD during trajectory Joseph Bylund (Fri Jan 06 2012 - 11:40:27 CST)
- Re: Coloring by RMSD during trajectory John Stone (Wed Feb 01 2012 - 23:14:38 CST)
  - Re: Coloring by RMSD during trajectory Joseph Bylund (Wed Feb 01 2012 - 23:49:19 CST)
    - Re: Coloring by RMSD during trajectory John Stone (Thu Feb 02 2012 - 00:00:15 CST)
vmd 1.9.1 beta - quicksurf rendering artifacts Ajasja LjubetiÄ (Wed Jan 04 2012 - 05:08:18 CST)
- Re: vmd 1.9.1 beta - quicksurf rendering artifacts Ajasja LjubetiÄ (Wed Jan 04 2012 - 05:28:06 CST)
  - Re: Re: vmd 1.9.1 beta - quicksurf rendering artifacts John Stone (Wed Jan 04 2012 - 09:28:23 CST)
    - Re: Re: vmd 1.9.1 beta - quicksurf rendering artifacts Ajasja LjubetiÄ (Wed Jan 04 2012 - 13:52:28 CST)
    - Re: Re: vmd 1.9.1 beta - quicksurf rendering artifacts John Stone (Thu Jan 05 2012 - 14:08:48 CST)
select whole residues Peter C. Lai (Tue Jan 03 2012 - 17:50:00 CST)
- Re: select whole residues Chris Harrison (Tue Jan 03 2012 - 18:37:13 CST)
- Re: select whole residues Axel Kohlmeyer (Tue Jan 03 2012 - 18:39:05 CST)
represent water molecules oguz gurbulak (Mon Jan 02 2012 - 05:48:41 CST)
- water molecules oguz gurbulak (Mon Jan 02 2012 - 07:49:12 CST)
- Re: represent water molecules Dudo (Mon Jan 02 2012 - 08:49:57 CST)
  - Re: represent water molecules oguz gurbulak (Tue Jan 03 2012 - 03:09:43 CST)
- Re: represent water molecules Axel Kohlmeyer (Mon Jan 02 2012 - 11:42:41 CST)
  - Re: represent water molecules oguz gurbulak (Mon Jan 02 2012 - 13:07:45 CST)
    - Re: represent water molecules Axel Kohlmeyer (Mon Jan 02 2012 - 13:19:41 CST)
external field application sarah k (Sun Jan 01 2012 - 03:57:21 CST)
- Re: external field application Axel Kohlmeyer (Sun Jan 01 2012 - 11:11:24 CST)
  - Re: external field application sarah k (Mon Jan 02 2012 - 06:22:10 CST)
    - Re: external field application Axel Kohlmeyer (Mon Jan 02 2012 - 12:21:06 CST)
CUDA driver for Mac OS X 10.7 on Late 2008 13 inch Macbook with NVIDA GeForce 9400M 256 MB ? Joshua D. Moore (Fri Dec 30 2011 - 19:07:05 CST)
- Re: CUDA driver for Mac OS X 10.7 on Late 2008 13 inch Macbook with NVIDA GeForce 9400M 256 MB ? Joshua D. Moore (Fri Dec 30 2011 - 19:30:45 CST)
  - Re: Re: CUDA driver for Mac OS X 10.7 on Late 2008 13 inch Macbook with NVIDA GeForce 9400M 256 MB ? John Stone (Thu Jan 05 2012 - 15:14:17 CST)
VMD 1.9.1 beta 1 posted for download... John Stone (Fri Dec 30 2011 - 01:02:15 CST)
- Re: VMD 1.9.1 beta 1 posted for download... Bjoern Olausson (Tue Jan 03 2012 - 01:32:26 CST)
  - Re: VMD 1.9.1 beta 1 (RMSDTT bug) John Stone (Tue Jan 03 2012 - 10:11:29 CST)
  - Re: VMD 1.9.1 beta 1 posted for download... FX (Thu Jan 05 2012 - 15:28:58 CST)
- out-of-core visualization of large trajectories Marc Baaden (Tue Jan 17 2012 - 12:08:31 CST)
  - Re: out-of-core visualization of large trajectories John Stone (Tue Jan 17 2012 - 12:19:40 CST)
using xtc file to generate pdb's J. Matthew Franklin (Tue Dec 27 2011 - 15:38:23 CST)
- Re: using xtc file to generate pdb's Axel Kohlmeyer (Tue Dec 27 2011 - 17:32:59 CST)
- Re: using xtc file to generate pdb's Bogdan Costescu (Wed Dec 28 2011 - 07:01:39 CST)
paratool CHARMM style charges Adrian Jasiñski (Tue Dec 27 2011 - 08:24:49 CST)
- Re: paratool CHARMM style charges Axel Kohlmeyer (Tue Dec 27 2011 - 09:46:32 CST)
- Re: paratool CHARMM style charges Jeffrey Potoff (Tue Dec 27 2011 - 13:55:04 CST)
problem generating NAD Magnus Andersson (Fri Dec 23 2011 - 13:37:19 CST)
- Re: problem generating NAD flavio seixas (Fri Dec 23 2011 - 17:42:12 CST)
Parse Fep plugin error Joseph Antoine Garate (Fri Dec 23 2011 - 08:27:39 CST)
Change Color Scale Joshua D. Moore (Wed Dec 21 2011 - 13:57:10 CST)
- Re: Change Color Scale John Stone (Wed Dec 21 2011 - 15:09:09 CST)
  - Re: Change Color Scale Joshua D. Moore (Wed Dec 21 2011 - 15:49:50 CST)
- Re: Change Color Scale Axel Kohlmeyer (Wed Dec 21 2011 - 15:04:07 CST)
Ionization Yu Zhou (Tue Dec 20 2011 - 21:23:41 CST)
- Re: Ionization Axel Kohlmeyer (Wed Dec 21 2011 - 08:25:16 CST)
Hbond analysis George Tzotzos (Tue Dec 20 2011 - 13:46:38 CST)
- Recall: Hbond analysis message George Tzotzos (Tue Dec 20 2011 - 13:52:02 CST)
Protein-ligand contact flavio seixas (Tue Dec 20 2011 - 08:10:15 CST)
- Re: Protein-ligand contact Dong Luo (Wed Dec 21 2011 - 11:13:26 CST)
  - Re: Protein-ligand contact flavio seixas (Mon Apr 30 2012 - 18:29:17 CDT)
I: vmd on windows Sergio Decherchi (Tue Dec 20 2011 - 07:48:55 CST)
- Re: I: vmd on windows Sergio Decherchi (Tue Dec 20 2011 - 16:18:14 CST)
  - Re: I: vmd on windows John Stone (Thu Dec 29 2011 - 22:21:19 CST)
Re: About open file .pdbqt in VMD software John Stone (Mon Dec 19 2011 - 17:29:30 CST)
VMD on Windows64 Mirco Wahab (Mon Dec 19 2011 - 16:51:45 CST)
- Re: VMD on Windows64 John Stone (Mon Dec 19 2011 - 16:57:52 CST)
VMD stereo for NVidia Quadro 5000? Alexander Balaeff (Mon Dec 19 2011 - 12:07:18 CST)
- Re: VMD stereo for NVidia Quadro 5000? John Stone (Mon Dec 19 2011 - 17:23:53 CST)
Assign velocities so I can color by velocity Joshua D. Moore (Mon Dec 19 2011 - 10:48:36 CST)
- Re: Assign velocities so I can color by velocity Alexander Balaeff (Mon Dec 19 2011 - 11:37:36 CST)
- Re: Assign velocities so I can color by velocity Axel Kohlmeyer (Mon Dec 19 2011 - 12:05:45 CST)
  - Re: Assign velocities so I can color by velocity Joshua D. Moore (Mon Dec 19 2011 - 12:26:57 CST)
    - Re: Assign velocities so I can color by velocity Axel Kohlmeyer (Mon Dec 19 2011 - 12:32:34 CST)
    - Re: Assign velocities so I can color by velocity Joshua D. Moore (Mon Dec 19 2011 - 20:54:02 CST)
vmd-l DynamicBond between two given type of atoms Salvatore Mario Cosseddu (Mon Dec 19 2011 - 10:44:17 CST)
- Re: vmd-l DynamicBond between two given type of atoms Axel Kohlmeyer (Mon Dec 19 2011 - 12:08:37 CST)
  - Re: vmd-l DynamicBond between two given type of atoms Salvatore Mario Cosseddu (Mon Dec 19 2011 - 14:27:53 CST)
  - Re: vmd-l DynamicBond between two given type of atoms PaweÅ‚ KÄ™dzierski (Mon Dec 19 2011 - 14:42:33 CST)
    - Re: vmd-l DynamicBond between two given type of atoms Salvatore Mario Cosseddu (Mon Dec 19 2011 - 15:16:03 CST)
    - Re: vmd-l DynamicBond between two given type of atoms John Stone (Mon Dec 19 2011 - 17:21:29 CST)
vmd ligand fluctuation analysis Ban Arn (Fri Dec 16 2011 - 09:28:41 CST)
vmd on windows Sergio Decherchi (Fri Dec 16 2011 - 09:16:42 CST)
- Re: vmd on windows John Stone (Mon Dec 19 2011 - 17:26:39 CST)
Multiple Stream Files: What Order? Bryan Roessler (Wed Dec 14 2011 - 11:20:25 CST)
Solvating with Nonaqueous Solvent Rajan Vatassery (Tue Dec 13 2011 - 12:46:50 CST)
- Re: Solvating with Nonaqueous Solvent Axel Kohlmeyer (Tue Dec 13 2011 - 14:16:12 CST)
  - Re: Solvating with Nonaqueous Solvent Rajan Vatassery (Thu Dec 15 2011 - 16:30:47 CST)
    - Re: Solvating with Nonaqueous Solvent Axel Kohlmeyer (Thu Dec 15 2011 - 16:38:26 CST)
    - Re: Solvating with Nonaqueous Solvent Rajan Vatassery (Thu Dec 15 2011 - 16:58:43 CST)
package MDEnergy menica dibenedetto (Tue Dec 13 2011 - 12:13:02 CST)
- Re: package MDEnergy Axel Kohlmeyer (Tue Dec 13 2011 - 13:44:01 CST)
Povray renders labels always centered Bjoern Olausson (Mon Dec 12 2011 - 01:37:04 CST)
- Re: Povray renders labels always centered Axel Kohlmeyer (Mon Dec 12 2011 - 10:08:49 CST)
  - Re: Povray renders labels always centered Bjoern Olausson (Tue Dec 13 2011 - 09:31:52 CST)
    - Re: Povray renders labels always centered John Stone (Fri Dec 23 2011 - 17:39:06 CST)
Re: VMD and 3D visualization problems with Nvidia Quadro 4000 Karel Berka (Sat Dec 10 2011 - 15:29:36 CST)
- Re: Re: VMD and 3D visualization problems with Nvidia Quadro 4000 John Stone (Tue Jan 10 2012 - 14:43:54 CST)
  - Re: Re: VMD and 3D visualization problems with Nvidia Quadro 4000 Karel Berka (Wed Jan 11 2012 - 10:43:13 CST)
get Ramachadran plot using textmode Gurunath Katagi (Fri Dec 09 2011 - 22:00:28 CST)
- Re: get Ramachadran plot using textmode John Stone (Fri Dec 23 2011 - 17:46:46 CST)
Tachyon render problem Töre Han Balta (Fri Dec 09 2011 - 02:45:09 CST)
- Re: Tachyon render problem Ajasja LjubetiÄ (Fri Dec 09 2011 - 08:22:26 CST)
  - Re: Tachyon render problem Axel Kohlmeyer (Sun Dec 11 2011 - 18:09:43 CST)
  - Re: Tachyon render problem Töre Han Balta (Sun Dec 11 2011 - 18:24:40 CST)
- Re: Tachyon render problem Axel Kohlmeyer (Fri Dec 09 2011 - 09:55:22 CST)
RE: TCL strangeness Gianluca Interlandi (Thu Dec 08 2011 - 20:27:28 CST)
Tip to start VMD with external terminal Gianluca Interlandi (Thu Dec 08 2011 - 16:06:27 CST)
- TCL strangeness Gianluca Interlandi (Thu Dec 08 2011 - 18:09:20 CST)
  - Re: TCL strangeness Ben Roberts (Thu Dec 08 2011 - 20:07:16 CST)
    - Re: TCL strangeness Ben Roberts (Thu Dec 08 2011 - 21:17:45 CST)
    - Re: TCL strangeness Axel Kohlmeyer (Thu Dec 08 2011 - 22:37:16 CST)
to use tcl script in command line Sangita Kachhap (Thu Dec 08 2011 - 04:14:59 CST)
- Re: to use tcl script in command line Joshua Adelman (Thu Dec 08 2011 - 07:32:08 CST)
- Re: to use tcl script in command line Anthony Rey (Thu Dec 08 2011 - 07:38:04 CST)
- Re: to use tcl script in command line Chris Harrison (Thu Dec 08 2011 - 08:30:37 CST)
Coloring particular atom with particular index Töre Han Balta (Wed Dec 07 2011 - 11:51:00 CST)
- Re: Coloring particular atom with particular index Ajasja LjubetiÄ (Wed Dec 07 2011 - 12:57:42 CST)
- Re: Coloring particular atom with particular index Töre Han Balta (Thu Dec 08 2011 - 16:15:26 CST)
Analyzing a 10ns simulation on Mac aborts Anthony Rey (Tue Dec 06 2011 - 23:25:17 CST)
- Re: Analyzing a 10ns simulation on Mac aborts Peter C. Lai (Wed Dec 07 2011 - 01:47:12 CST)
- Re: Analyzing a 10ns simulation on Mac aborts John Stone (Thu Dec 29 2011 - 22:49:32 CST)
Script for Angular Distribution Function? David Cohen-Tanugi (Tue Dec 06 2011 - 09:45:36 CST)
- Re: Script for Angular Distribution Function? Dudo (Tue Dec 06 2011 - 10:30:41 CST)
  - Re: Script for Angular Distribution Function? Axel Kohlmeyer (Wed Dec 07 2011 - 10:48:47 CST)
mmView - a tool for mmCIF exploration Daniel Svozil (Tue Dec 06 2011 - 05:38:03 CST)
topology and parameter files for H2 and O2 Yungok Ihm (Tue Dec 06 2011 - 03:52:31 CST)
- Re: topology and parameter files for H2 and O2 Axel Kohlmeyer (Tue Dec 06 2011 - 07:46:33 CST)
- Re: topology and parameter files for H2 and O2 flavio seixas (Wed Dec 07 2011 - 13:49:51 CST)
Binding site similarity Ban Arn (Mon Dec 05 2011 - 09:51:55 CST)
Improve OFF plugin: handle colors FX (Mon Dec 05 2011 - 07:20:06 CST)
- Re: Improve OFF plugin: handle colors John Stone (Wed Dec 07 2011 - 00:56:19 CST)
Rendering long and high-quality movies from VMD David Cohen-Tanugi (Sun Dec 04 2011 - 21:35:40 CST)
- Re: Rendering long and high-quality movies from VMD Axel Kohlmeyer (Sun Dec 04 2011 - 23:19:35 CST)
  - Re: Rendering long and high-quality movies from VMD Axel Kohlmeyer (Sun Dec 04 2011 - 23:27:48 CST)
    - Re: Rendering long and high-quality movies from VMD Bjoern Olausson (Wed Dec 07 2011 - 10:58:01 CST)
Re: out-of-order writegmx with topotools 1.2 Axel Kohlmeyer (Sat Dec 03 2011 - 18:18:38 CST)
- Re: out-of-order writegmx with topotools 1.2 Axel Kohlmeyer (Mon Dec 05 2011 - 00:07:18 CST)
Viewing System of Molecules where coordinates are in text file. Joey Vella (Thu Dec 01 2011 - 20:43:45 CST)
- Re: Viewing System of Molecules where coordinates are in text file. Axel Kohlmeyer (Thu Dec 01 2011 - 22:28:12 CST)
How to disable CUDA in VMD-1.9? Joaim Swedberg (Wed Nov 30 2011 - 20:29:48 CST)
- Re: How to disable CUDA in VMD-1.9? John Stone (Wed Nov 30 2011 - 21:18:23 CST)
- RE: How to disable CUDA in VMD-1.9? Ismail, Mohd F. (Wed Nov 30 2011 - 22:31:31 CST)
Reading the SMD information form the log file Molybdos Kirkimpolakis (Wed Nov 30 2011 - 14:54:45 CST)
- Re: Reading the SMD information form the log file Molybdos Kirkimpolakis (Fri Dec 02 2011 - 10:34:27 CST)
  - Re: Reading the SMD information form the log file Chris Harrison (Fri Dec 02 2011 - 11:37:38 CST)
Get the camera position SAPAY Nicolas 232321 (Wed Nov 30 2011 - 10:20:52 CST)
- RE : Get the camera position SAPAY Nicolas 232321 (Thu Dec 01 2011 - 04:22:34 CST)
Re: simulation bharat gupta (Wed Nov 30 2011 - 05:50:56 CST)
convertind dcd to xyz file siladitya mukherjee (Tue Nov 29 2011 - 16:39:22 CST)
- Re: convertind dcd to xyz file Axel Kohlmeyer (Tue Nov 29 2011 - 17:43:05 CST)
- Re: convertind dcd to xyz file Thomas Bishop (Mon Dec 05 2011 - 08:54:11 CST)
Save pdb with original numbering Ricardo Soares (Tue Nov 29 2011 - 05:47:33 CST)
- Re: Save pdb with original numbering John Stone (Tue Nov 29 2011 - 10:25:22 CST)
  - Re: Save pdb with original numbering Ricardo Soares (Tue Nov 29 2011 - 13:25:16 CST)
    - Re: Save pdb with original numbering Peter C. Lai (Tue Nov 29 2011 - 17:22:35 CST)
    - Re: Save pdb with original numbering Ricardo Soares (Tue Nov 29 2011 - 18:58:56 CST)
- Re: Save pdb with original numbering Dong Luo (Tue Nov 29 2011 - 10:12:44 CST)
Can Catdcd Write Out Periodic Cell Size Information? Tessa Young (Mon Nov 28 2011 - 01:20:31 CST)
- Re: Can Catdcd Write Out Periodic Cell Size Information? Pablo M. De Biase (Mon Nov 28 2011 - 10:39:55 CST)
  - Re: Can Catdcd Write Out Periodic Cell Size Information? Jeffrey Potoff (Mon Nov 28 2011 - 16:30:08 CST)
- Re: Can Catdcd Write Out Periodic Cell Size Information? Axel Kohlmeyer (Mon Nov 28 2011 - 11:45:47 CST)
  - Re: Can Catdcd Write Out Periodic Cell Size Information? Jeffrey Potoff (Mon Nov 28 2011 - 15:00:35 CST)
vmd solvate Pavan Ghatty (Sun Nov 27 2011 - 13:56:17 CST)
- Re: vmd solvate Axel Kohlmeyer (Sun Nov 27 2011 - 15:00:26 CST)
tcl script Ban Arn (Fri Nov 25 2011 - 12:16:47 CST)
- Re: tcl script Axel Kohlmeyer (Fri Nov 25 2011 - 13:16:32 CST)
- Re: tcl script Thomas Evangelidis (Fri Nov 25 2011 - 13:51:07 CST)
  - Re: tcl script Axel Kohlmeyer (Fri Nov 25 2011 - 14:52:32 CST)
average structure script flavio seixas (Fri Nov 25 2011 - 09:52:40 CST)
- Re: average structure script Ajasja LjubetiÄ (Fri Nov 25 2011 - 11:09:59 CST)
- Re: average structure script Toni Giorgino (Fri Nov 25 2011 - 11:21:28 CST)
q4md-forcefieldtools.org announcement FyD (Fri Nov 25 2011 - 07:33:39 CST)
VMD never finishes reading vis. state file, stalls and hoggs CPU Bjoern Olausson (Fri Nov 25 2011 - 00:51:07 CST)
- Re: VMD never finishes reading vis. state file, stalls and hoggs CPU Ajasja LjubetiÄ (Fri Nov 25 2011 - 05:05:32 CST)
  - Re: VMD never finishes reading vis. state file, stalls and hoggs CPU Bjoern Olausson (Fri Nov 25 2011 - 05:36:26 CST)
- Re: VMD never finishes reading vis. state file, stalls and hoggs CPU Axel Kohlmeyer (Fri Nov 25 2011 - 09:38:01 CST)
  - Re: VMD never finishes reading vis. state file, stalls and hoggs CPU Bjoern Olausson (Mon Nov 28 2011 - 02:54:17 CST)
POPE CHARMM36 generations error. mail gromacs (Thu Nov 24 2011 - 13:13:02 CST)
- Re: POPE CHARMM36 generations error. Axel Kohlmeyer (Thu Nov 24 2011 - 14:46:47 CST)
how to convert Desmond trajectories into PDB in text mode? mail gromacs (Thu Nov 24 2011 - 13:09:40 CST)
- Re: how to convert Desmond trajectories into PDB in text mode? Axel Kohlmeyer (Thu Nov 24 2011 - 14:48:44 CST)
How to save Automatic psf builder script flavio seixas (Thu Nov 24 2011 - 12:03:15 CST)
- Re: How to save Automatic psf builder script Axel Kohlmeyer (Thu Nov 24 2011 - 14:45:59 CST)
VMD STRIDE not functional after operating system upgrade Vlad Cojocaru (Thu Nov 24 2011 - 08:50:40 CST)
- Re: VMD STRIDE not functional after operating system upgrade John Stone (Wed Nov 30 2011 - 10:24:22 CST)
  - Re: VMD STRIDE not functional after operating system upgrade Vlad Cojocaru (Wed Nov 30 2011 - 11:15:15 CST)
Change coordinates Andrés Morales (Thu Nov 24 2011 - 02:14:02 CST)
- Re: Change coordinates sajad falsafi (Thu Nov 24 2011 - 06:51:44 CST)
  - Re: Change coordinates Andrés Morales (Thu Nov 24 2011 - 10:38:15 CST)
    - Re: Change coordinates Axel Kohlmeyer (Thu Nov 24 2011 - 14:42:53 CST)
Translocate molecule within a box rainy908 (Wed Nov 23 2011 - 19:51:03 CST)
- Re: Translocate molecule within a box harish vashisth (Wed Nov 23 2011 - 21:43:13 CST)
clip plane and cpk / VdW Philippe Bopp / temporary (Wed Nov 23 2011 - 04:48:33 CST)
- Re: clip plane and cpk / VdW John Stone (Wed Nov 23 2011 - 09:22:43 CST)
  - Re: clip plane and cpk / VdW BIN ZHANG (Wed Nov 23 2011 - 11:25:22 CST)
    - Re: clip plane and cpk / VdW Philippe Bopp / temporary (Thu Nov 24 2011 - 09:58:54 CST)
- Re: clip plane and cpk / VdW PaweÅ‚ KÄ™dzierski (Thu Nov 24 2011 - 02:52:32 CST)
- Re: clip plane and cpk / VdW Pawel Kedzierski (Thu Nov 24 2011 - 02:52:49 CST)
Rebuilding psf file Siew Wen Leong (Wed Nov 23 2011 - 04:45:38 CST)
Spam from my email hanif mahboobi (Wed Nov 23 2011 - 03:38:19 CST)
(no subject) hanif mahboobi (Tue Nov 22 2011 - 21:55:31 CST)
(no subject) hanif mahboobi (Tue Nov 22 2011 - 18:19:50 CST)
Radial distribution function in VMD Chirag Vora (Tue Nov 22 2011 - 12:01:52 CST)
bash scripts quits after few frames Jorgen Simonsen (Tue Nov 22 2011 - 03:55:02 CST)
- Re: bash scripts quits after few frames Axel Kohlmeyer (Tue Nov 22 2011 - 06:20:24 CST)
- Re: bash scripts quits after few frames Jérôme Hénin (Tue Nov 22 2011 - 06:32:43 CST)
VMD and R Thomas Bishop (Mon Nov 21 2011 - 14:42:44 CST)
compile VMD 1.9 with FLTK 1.3 Vlad Cojocaru (Mon Nov 21 2011 - 06:37:19 CST)
- Re: compile VMD 1.9 with FLTK 1.3 Vlad Cojocaru (Mon Nov 21 2011 - 07:45:24 CST)
- Re: compile VMD 1.9 with FLTK 1.3 Axel Kohlmeyer (Mon Nov 21 2011 - 08:37:31 CST)
movie out of principal component analysis maria goranovic (Mon Nov 21 2011 - 04:35:44 CST)
- Re: movie out of principal component analysis Davide Provasi (Mon Nov 21 2011 - 12:37:44 CST)
  - Re: movie out of principal component analysis maria goranovic (Tue Nov 22 2011 - 06:04:46 CST)
'Hands-On' Workshop on Computational Biophysics using VMD and NAMD, February 11-15, 2012 in Urbana, Illinois David Brandon (Thu Nov 17 2011 - 13:53:59 CST)
Installation problems with VMD 1.9 PaulW (Thu Nov 17 2011 - 07:17:44 CST)
- Re: Installation problems with VMD 1.9 John Stone (Fri Nov 18 2011 - 11:24:03 CST)
  - Re: Installation problems with VMD 1.9 Paul Anderson (Fri Nov 18 2011 - 12:51:34 CST)
Patching Glu/N-terminus peptide bond type bond Joaim Swedberg (Wed Nov 16 2011 - 17:41:38 CST)
- RE: Patching Glu/N-terminus peptide bond type bond Tristan Croll (Thu Nov 17 2011 - 01:02:52 CST)
Maximum length of an extended peptide? Aaron Oakley (Tue Nov 15 2011 - 17:53:14 CST)
- Re: Maximum length of an extended peptide? Axel Kohlmeyer (Tue Nov 15 2011 - 19:55:57 CST)
  - Re: Maximum length of an extended peptide? Boris Steipe (Tue Nov 15 2011 - 22:29:42 CST)
- Re: Maximum length of an extended peptide? Chris Harrison (Tue Nov 15 2011 - 20:07:24 CST)
- Re: Maximum length of an extended peptide? Aaron Oakley (Tue Nov 15 2011 - 20:58:20 CST)
  - Re: Maximum length of an extended peptide? Anurag Sethi (Tue Nov 15 2011 - 21:57:44 CST)
  - Re: Maximum length of an extended peptide? Axel Kohlmeyer (Tue Nov 15 2011 - 22:57:45 CST)
Mac OS X 64 bit Issues Andrew Fenley (Tue Nov 15 2011 - 15:00:56 CST)
- Re: Mac OS X 64 bit Issues Andrew Fenley (Tue Nov 15 2011 - 17:47:41 CST)
VMD slows down at multiple windows lam nguyen (Mon Nov 14 2011 - 16:51:46 CST)
- Re: VMD slows down at multiple windows Ajasja LjubetiÄ (Tue Nov 15 2011 - 03:08:28 CST)
  - Re: VMD slows down at multiple windows lam nguyen (Wed Nov 16 2011 - 22:20:54 CST)
- Re: VMD slows down at multiple windows John Stone (Wed Nov 16 2011 - 12:56:18 CST)
  - Re: VMD slows down at multiple windows Tristan Croll (Wed Nov 16 2011 - 19:26:21 CST)
  - Re: VMD slows down at multiple windows lam nguyen (Wed Nov 16 2011 - 22:30:03 CST)
pbc wrap Hitesh Patel (Mon Nov 14 2011 - 08:48:42 CST)
- Re: pbc wrap Axel Kohlmeyer (Mon Nov 14 2011 - 09:57:06 CST)
  - Re: pbc wrap Hitesh Patel (Mon Nov 14 2011 - 10:17:12 CST)
    - Re: pbc wrap Hitesh Patel (Mon Nov 14 2011 - 11:09:41 CST)
- Re: pbc wrap Olaf Lenz (Mon Nov 14 2011 - 09:57:04 CST)
(no subject) niaz poorgholami (Fri Nov 11 2011 - 22:02:25 CST)
Volume Slice + Coloring by volume problem in MacOsx (REPOST) Passerone, Daniele (Fri Nov 11 2011 - 15:06:27 CST)
- Re: Volume Slice + Coloring by volume problem in MacOsx (REPOST) John Stone (Fri Nov 11 2011 - 15:14:37 CST)
how to place polymers on carbon nanotube surface niaz poorgholami (Fri Nov 11 2011 - 12:31:47 CST)
- Re: how to place polymers on carbon nanotube surface John Stone (Fri Nov 11 2011 - 12:51:11 CST)
  - Re: how to place polymers on carbon nanotube surface niaz poorgholami (Fri Nov 11 2011 - 13:21:24 CST)
- Re: how to place polymers on carbon nanotube surface Axel Kohlmeyer (Fri Nov 11 2011 - 13:27:35 CST)
Save "Visulaization State" from within Tk Console Bjoern Olausson (Fri Nov 11 2011 - 07:41:18 CST)
- Re: Save "Visulaization State" from within Tk Console Bjoern Olausson (Fri Nov 11 2011 - 07:48:03 CST)
  - Re: Re: Save "Visulaization State" from within Tk Console Axel Kohlmeyer (Fri Nov 11 2011 - 08:57:13 CST)
    - Re: Re: Save "Visulaization State" from within Tk Console Bjoern Olausson (Mon Nov 14 2011 - 01:17:02 CST)
- Re: Save "Visulaization State" from within Tk Console Axel Kohlmeyer (Fri Nov 11 2011 - 08:41:38 CST)
- Re: Save "Visulaization State" from within Tk Console John Stone (Fri Nov 11 2011 - 09:20:43 CST)
UPDATE OCCUPANCY Jordi Faraudo (Fri Nov 11 2011 - 06:04:50 CST)
- Re: UPDATE OCCUPANCY Axel Kohlmeyer (Fri Nov 11 2011 - 07:34:53 CST)
- Re: UPDATE OCCUPANCY John Stone (Fri Nov 11 2011 - 09:22:49 CST)
RMSD Tool failes with MOL ID > 999 Bjoern Olausson (Fri Nov 11 2011 - 05:52:11 CST)
- Re: RMSD Tool failes with MOL ID > 999 John Stone (Fri Nov 11 2011 - 09:48:57 CST)
  - Re: RMSD Tool failes with MOL ID > 999 Bjoern Olausson (Tue Nov 15 2011 - 02:38:34 CST)
Couldn't locate ppmtompeg Rabab Toubar (Thu Nov 10 2011 - 14:57:58 CST)
- Re: Couldn't locate ppmtompeg Magnus Andersson (Thu Nov 10 2011 - 16:03:41 CST)
- Re: Couldn't locate ppmtompeg Axel Kohlmeyer (Thu Nov 10 2011 - 15:47:31 CST)
installing and running VMD on Windows 64-bit Rabab Toubar (Thu Nov 10 2011 - 09:17:54 CST)
- Re: installing and running VMD on Windows 64-bit John Stone (Thu Nov 10 2011 - 10:05:29 CST)
  - Re: installing and running VMD on Windows 64-bit Rabab Toubar (Thu Nov 10 2011 - 15:08:05 CST)
    - Re: installing and running VMD on Windows 64-bit John Stone (Fri Nov 11 2011 - 09:32:51 CST)
- Re: installing and running VMD on Windows 64-bit Dennis N Bromley (Thu Nov 10 2011 - 12:12:43 CST)
pbwithin selection arash azari (Thu Nov 10 2011 - 07:58:28 CST)
- Re: pbwithin selection Axel Kohlmeyer (Thu Nov 10 2011 - 09:27:47 CST)
Adding an atom to existing trajectory (to enable RDF from centre of mass of a selection) Sam Wallace (Wed Nov 09 2011 - 16:38:39 CST)
- Re: Adding an atom to existing trajectory (to enable RDF from centre of mass of a selection) John Stone (Fri Nov 11 2011 - 10:06:58 CST)
  - Re: Adding an atom to existing trajectory (to enable RDF from centre of mass of a selection) Sam Wallace (Sun Nov 13 2011 - 04:58:37 CST)
How to parse very large trajectories? Aleksandr Kivenson (Wed Nov 09 2011 - 14:41:55 CST)
- Re: How to parse very large trajectories? Axel Kohlmeyer (Wed Nov 09 2011 - 15:44:30 CST)
- Re: How to parse very large trajectories? Bogdan Costescu (Thu Nov 10 2011 - 08:20:41 CST)
Suppress "Info)" messages Bjoern Olausson (Mon Nov 07 2011 - 11:56:06 CST)
- Re: Suppress "Info)" messages John Stone (Mon Nov 07 2011 - 12:34:07 CST)
  - Re: Suppress "Info)" messages Bjoern Olausson (Mon Nov 07 2011 - 13:15:59 CST)
- Re: Suppress "Info)" messages Axel Kohlmeyer (Mon Nov 07 2011 - 13:15:19 CST)
  - Re: Suppress "Info)" messages Bjoern Olausson (Mon Nov 07 2011 - 18:26:50 CST)
tcl procedure to set data Casey Johnson (Sun Nov 06 2011 - 19:26:25 CST)
- Re: tcl procedure to set data Axel Kohlmeyer (Sun Nov 06 2011 - 20:31:00 CST)
blank output sarah k (Sun Nov 06 2011 - 09:34:39 CST)
- Re: blank output John Stone (Mon Nov 07 2011 - 12:43:57 CST)
lipid bilayer thickness Andrés Morales (Sun Nov 06 2011 - 00:07:36 CDT)
- Re: lipid bilayer thickness Axel Kohlmeyer (Sun Nov 06 2011 - 06:14:50 CST)
tkinter load problem in VMD Gianluca Interlandi (Sun Nov 06 2011 - 00:04:42 CDT)
- Re: tkinter load problem in VMD Gianluca Interlandi (Sun Nov 06 2011 - 00:13:41 CDT)
  - Re: Re: tkinter load problem in VMD John Stone (Sun Nov 06 2011 - 00:24:39 CDT)
Batch image creation Juan Antonio Raygoza Garay (Fri Nov 04 2011 - 16:59:57 CDT)
- Re: Batch image creation Axel Kohlmeyer (Fri Nov 04 2011 - 18:07:41 CDT)
Secondary structure elements in VMD Rabab Toubar (Fri Nov 04 2011 - 16:03:26 CDT)
- Re: Secondary structure elements in VMD harish vashisth (Fri Nov 04 2011 - 19:37:43 CDT)
  - Re: Secondary structure elements in VMD Rabab Toubar (Sat Nov 05 2011 - 00:38:29 CDT)
- Re: Secondary structure elements in VMD Ajasja LjubetiÄ (Sat Nov 05 2011 - 03:00:01 CDT)
find avgstruct hamze rahimi (Fri Nov 04 2011 - 04:30:38 CDT)
- Re: find avgstruct Ajasja LjubetiÄ (Fri Nov 04 2011 - 06:03:16 CDT)
- Re: find avgstruct Axel Kohlmeyer (Fri Nov 04 2011 - 07:29:32 CDT)
Volume Slice + Coloring by volume problem in MacOsx Passerone, Daniele (Fri Nov 04 2011 - 00:31:15 CDT)
- Re: Volume Slice + Coloring by volume problem in MacOsx John Stone (Fri Nov 11 2011 - 10:12:57 CST)
How to understand the occupancy? lina (Thu Nov 03 2011 - 09:06:06 CDT)
- Re: How to understand the occupancy? Dong Luo (Fri Nov 04 2011 - 14:42:09 CDT)
radius of gyration ban arn (Wed Nov 02 2011 - 14:41:09 CDT)
- Re: radius of gyration Axel Kohlmeyer (Wed Nov 02 2011 - 15:49:19 CDT)
  - Re: radius of gyration ban arn (Wed Nov 02 2011 - 16:02:45 CDT)
- Re: radius of gyration Ajasja LjubetiÄ (Wed Nov 02 2011 - 16:14:59 CDT)
Re: namd-l: selection of cholesterol molecules Chris Harrison (Wed Nov 02 2011 - 00:06:35 CDT)
Use of RBCG to convert multiple frames from atomistic trajectory to Coarse grained rohan uttarwar (Tue Nov 01 2011 - 16:17:08 CDT)
- Re: Use of RBCG to convert multiple frames from atomistic trajectory to Coarse grained Axel Kohlmeyer (Tue Nov 01 2011 - 17:09:50 CDT)
Finding resname without using atomselect? Casey Johnson (Tue Nov 01 2011 - 15:46:28 CDT)
- Re: Finding resname without using atomselect? Axel Kohlmeyer (Tue Nov 01 2011 - 16:50:51 CDT)
- RE: Finding resname without using atomselect? Cosseddu, Salvatore (Tue Nov 01 2011 - 18:35:22 CDT)
  - RE: Finding resname without using atomselect? Cosseddu, Salvatore (Tue Nov 01 2011 - 18:48:29 CDT)
graphical representation kirtana S (Tue Nov 01 2011 - 12:21:29 CDT)
- Re: graphical representation John Stone (Mon Nov 07 2011 - 13:29:43 CST)
rlwrap problem on Frank Barry (Tue Nov 01 2011 - 10:50:26 CDT)
- Re: rlwrap problem on Joshua A. Anderson (Tue Nov 01 2011 - 13:46:10 CDT)
- Re: rlwrap problem on Gianluca Interlandi (Tue Nov 01 2011 - 14:14:51 CDT)
  - Re: rlwrap problem on Gianluca Interlandi (Tue Nov 01 2011 - 14:15:49 CDT)
    - Re: rlwrap problem on Frank Barry (Tue Nov 08 2011 - 14:34:21 CST)
    - Re: rlwrap problem on sajad falsafi (Wed Nov 09 2011 - 02:53:43 CST)
- Re: rlwrap problem on John Stone (Fri Nov 11 2011 - 09:26:24 CST)
- Re: rlwrap problem on Pablo De Biase (Tue Nov 22 2011 - 13:38:58 CST)
  - Re: Re: rlwrap problem on Cun Zhang (Thu Nov 24 2011 - 07:07:11 CST)
H-bond distance measurement Aditya Padhi (Tue Nov 01 2011 - 03:53:57 CDT)
VRPN-ICMS conflict with NVidia driver Tristan Croll (Tue Nov 01 2011 - 02:16:14 CDT)
- Re: VRPN-ICMS conflict with NVidia driver Axel Kohlmeyer (Tue Nov 01 2011 - 08:15:36 CDT)
  - RE: VRPN-ICMS conflict with NVidia driver Tristan Croll (Tue Nov 01 2011 - 19:03:55 CDT)
selection matziast_at_med.uth.gr (Mon Oct 31 2011 - 13:39:43 CDT)
- Re: selection John Stone (Mon Oct 31 2011 - 14:39:13 CDT)
  - Re: selection matziast_at_med.uth.gr (Mon Oct 31 2011 - 15:50:58 CDT)
  - haptic devices VMD/NAMD/IMD Thomas Bishop (Mon Oct 31 2011 - 15:52:48 CDT)
Dynamic lines Bogdan Costescu (Mon Oct 31 2011 - 13:21:59 CDT)
- Re: Dynamic lines Axel Kohlmeyer (Mon Oct 31 2011 - 14:32:47 CDT)
  - Re: Dynamic lines John Stone (Mon Oct 31 2011 - 16:18:33 CDT)
    - Re: Dynamic lines Bogdan Costescu (Wed Nov 02 2011 - 13:42:01 CDT)
    - Re: Dynamic lines John Stone (Wed Nov 02 2011 - 14:12:35 CDT)
selection matziast_at_med.uth.gr (Mon Oct 31 2011 - 12:45:50 CDT)
- Re: selection Chris Harrison (Mon Oct 31 2011 - 15:13:57 CDT)
  - Re: selection matziast_at_med.uth.gr (Mon Oct 31 2011 - 15:57:03 CDT)
move ligand around the protin Steven Neumann (Mon Oct 31 2011 - 10:46:07 CDT)
- Re: move ligand around the protin Chris Harrison (Mon Oct 31 2011 - 11:54:43 CDT)
Feedback wanted from Linux VMD users with ATI/AMD graphics chipsets John Stone (Mon Oct 31 2011 - 10:12:15 CDT)
- Re: Feedback wanted from Linux VMD users with ATI/AMD graphics chipsets Andrew Jewett (Thu Nov 03 2011 - 15:56:37 CDT)
  - Re: Feedback wanted from Linux VMD users with ATI/AMD graphics chipsets Andrew Jewett (Thu Nov 03 2011 - 16:07:46 CDT)
  - Re: Feedback wanted from Linux VMD users with ATI/AMD graphics chipsets John Stone (Fri Nov 11 2011 - 10:19:21 CST)
Hi all, Bo HÃ¸jen Justesen (Mon Oct 31 2011 - 05:47:22 CDT)
- Re: Hi all, John Stone (Mon Oct 31 2011 - 16:10:14 CDT)
Run a variable through VMD Tk/Tcl console .vmdrc file Anthony Rey (Sun Oct 30 2011 - 06:55:06 CDT)
- Re: Run a variable through VMD Tk/Tcl console .vmdrc file Axel Kohlmeyer (Sun Oct 30 2011 - 10:04:09 CDT)
  - Re: Run a variable through VMD Tk/Tcl console .vmdrc file Anthony Rey (Mon Oct 31 2011 - 02:09:42 CDT)
- Re: Run a variable through VMD Tk/Tcl console .vmdrc file Chris Harrison (Sun Oct 30 2011 - 10:28:37 CDT)
Run a variable through VMD Tk/Tcl console /// .vmdrc file Anthony Rey (Sun Oct 30 2011 - 06:14:22 CDT)
About the syntax in Autopsf - Add Patch for PRES PLIG Francesco Pietra (Sun Oct 30 2011 - 03:28:27 CDT)
- Re: About the syntax in Autopsf - Add Patch for PRES PLIG Francesco Pietra (Sun Oct 30 2011 - 10:34:43 CDT)
Structure preparation via VMD James Starlight (Sat Oct 29 2011 - 07:29:33 CDT)
- Re: Structure preparation via VMD Gianluca Interlandi (Sat Oct 29 2011 - 10:55:28 CDT)
Problem with Movie Maker Carolyn Phillips (Fri Oct 28 2011 - 17:41:12 CDT)
- Re: Problem with Movie Maker Carolyn Phillips (Sat Oct 29 2011 - 11:38:10 CDT)
- Re: Problem with Movie Maker John Stone (Mon Oct 31 2011 - 09:54:03 CDT)
Installing CATDCD on a Mac Michael LeVine (Fri Oct 28 2011 - 14:55:14 CDT)
- Re: Installing CATDCD on a Mac John Stone (Fri Oct 28 2011 - 16:21:43 CDT)
VMD crashes. Diego Javier Alonso de Armiño (Fri Oct 28 2011 - 10:22:19 CDT)
- Re: VMD crashes. John Stone (Fri Oct 28 2011 - 10:44:02 CDT)
Adding a three letter residue name to VMD's protein recognition J. Nathan Scott (Thu Oct 27 2011 - 13:13:09 CDT)
- Re: Adding a three letter residue name to VMD's protein recognition John Stone (Fri Nov 11 2011 - 12:24:10 CST)
Is it possible to automatically label all bonds? Mike Wykes (Thu Oct 27 2011 - 11:43:18 CDT)
- Re: Is it possible to automatically label all bonds? Axel Kohlmeyer (Thu Oct 27 2011 - 12:42:02 CDT)
  - Re: Is it possible to automatically label all bonds? Mike Wykes (Mon Oct 31 2011 - 07:09:55 CDT)
    - Re: Is it possible to automatically label all bonds? Axel Kohlmeyer (Mon Oct 31 2011 - 08:10:08 CDT)
- Re: Is it possible to automatically label all bonds? John Stone (Thu Oct 27 2011 - 12:42:54 CDT)
Visualizing Timeline (tml) data w/o having to load trajectories Bryan Roessler (Thu Oct 27 2011 - 11:34:40 CDT)
- Re: Visualizing Timeline (tml) data w/o having to load trajectories Barry Isralewitz (Thu Oct 27 2011 - 13:25:08 CDT)
average pdb from dcd file hamze rahimi (Thu Oct 27 2011 - 07:39:53 CDT)
- Re: average pdb from dcd file Bjoern Olausson (Thu Oct 27 2011 - 09:54:06 CDT)
- Re: average pdb from dcd file sajad falsafi (Thu Oct 27 2011 - 11:40:38 CDT)
Xenon binding site free energies Aaron Oakley (Thu Oct 27 2011 - 01:30:23 CDT)
Problem vmd 1.9 plus Cave Christian Wohlschlager (Thu Oct 27 2011 - 01:12:09 CDT)
- Re: Problem vmd 1.9 plus Cave John Stone (Thu Oct 27 2011 - 01:29:42 CDT)
  - Re: Problem vmd 1.9 plus Cave Christian Wohlschlager (Fri Oct 28 2011 - 04:23:30 CDT)
Compiling vmd 1.9 plugins Matt Fioravante (Wed Oct 26 2011 - 12:55:22 CDT)
- Re: Compiling vmd 1.9 plugins Andrew Jewett (Wed Oct 26 2011 - 16:44:48 CDT)
- Re: Compiling vmd 1.9 plugins John Stone (Wed Oct 26 2011 - 17:03:49 CDT)
Selecting Atoms within a Volume, Manipulating Volumetric Data Michael LeVine (Sun Oct 23 2011 - 14:24:20 CDT)
- Re: Selecting Atoms within a Volume, Manipulating Volumetric Data Axel Kohlmeyer (Tue Oct 25 2011 - 08:03:13 CDT)
- Re: Selecting Atoms within a Volume, Manipulating Volumetric Data John Stone (Wed Oct 26 2011 - 21:43:49 CDT)
Calculating parameters in lipid bilayers Andrés Morales (Thu Oct 20 2011 - 22:04:03 CDT)
Thinkpad X120e with Linux and VMD Gianluca Interlandi (Thu Oct 20 2011 - 19:48:32 CDT)
- Re: Thinkpad X120e with Linux and VMD John Stone (Fri Oct 28 2011 - 14:28:21 CDT)
coloring bonds on the same segments differently from those between segments lam nguyen (Thu Oct 20 2011 - 19:07:42 CDT)
- Re: coloring bonds on the same segments differently from those between segments Axel Kohlmeyer (Thu Oct 20 2011 - 20:10:23 CDT)
  - Re: coloring bonds on the same segments differently from those between segments lam nguyen (Fri Oct 21 2011 - 17:06:35 CDT)
- Re: coloring bonds on the same segments differently from those between segments Joseph Bylund (Thu Oct 20 2011 - 20:13:59 CDT)
superimposing groups of three atoms bio lab (Thu Oct 20 2011 - 06:25:46 CDT)
- Re: superimposing groups of three atoms JC Gumbart (Fri Oct 21 2011 - 06:53:28 CDT)
  - Re: superimposing groups of three atoms bio lab (Fri Oct 21 2011 - 12:10:51 CDT)
    - Re: superimposing groups of three atoms Axel Kohlmeyer (Fri Oct 21 2011 - 13:07:16 CDT)
calculation hydrogen bond. subrata paul (Thu Oct 20 2011 - 02:19:04 CDT)
- Fwd: calculation hydrogen bond. subrata paul (Thu Oct 20 2011 - 22:57:17 CDT)
- Re: calculation hydrogen bond. JC Gumbart (Fri Oct 21 2011 - 06:55:18 CDT)
area per lipid Andrés Morales (Thu Oct 20 2011 - 01:12:14 CDT)
Error running IED Manish (Tue Oct 18 2011 - 13:39:09 CDT)
- RE: Error running IED Manish (Tue Oct 18 2011 - 14:33:15 CDT)
angle calculation trajectory Peyman Z.Moghadam (Tue Oct 18 2011 - 12:28:16 CDT)
- Re: angle calculation trajectory Axel Kohlmeyer (Tue Oct 18 2011 - 13:22:15 CDT)
  - Fw: angle calculation trajectory sajad falsafi (Wed Oct 19 2011 - 01:11:39 CDT)
atomselect and macro Molybdos Kirkimpolakis (Sat Oct 15 2011 - 15:34:59 CDT)
- Re: atomselect and macro Axel Kohlmeyer (Sat Oct 15 2011 - 17:33:49 CDT)
  - Re: atomselect and macro Molybdos Kirkimpolakis (Mon Oct 17 2011 - 00:11:05 CDT)
Error running IED with VMD Manish (Fri Oct 14 2011 - 08:47:17 CDT)
- Re: Error running IED with VMD Axel Kohlmeyer (Fri Oct 14 2011 - 10:09:16 CDT)
hbond analysis subrata paul (Fri Oct 14 2011 - 04:11:46 CDT)
- Re: hbond analysis sajad falsafi (Fri Oct 14 2011 - 08:06:08 CDT)
- Re: hbond analysis Jernej Zidar (Fri Oct 14 2011 - 08:19:22 CDT)
Installing VMD on Debian Linux James Starlight (Fri Oct 14 2011 - 01:51:01 CDT)
- Re: Installing VMD on Debian Linux Axel Kohlmeyer (Fri Oct 14 2011 - 07:47:38 CDT)
- Re: Installing VMD on Debian Linux Cun Zhang (Tue Oct 25 2011 - 03:53:49 CDT)
Using two color scales in one scene Robert Johnson (Thu Oct 13 2011 - 14:23:02 CDT)
- Re: Using two color scales in one scene John Stone (Thu Oct 13 2011 - 14:33:52 CDT)
How to select whole residues when at least one atom is within a specific distance Michael LeVine (Thu Oct 13 2011 - 12:48:43 CDT)
- Re: How to select whole residues when at least one atom is within a specific distance John Stone (Thu Oct 13 2011 - 14:32:26 CDT)
- Re: How to select whole residues when at least one atom is within a specific distance Axel Kohlmeyer (Thu Oct 13 2011 - 14:37:24 CDT)
  - Re: How to select whole residues when at least one atom is within a specific distance Michael LeVine (Thu Oct 13 2011 - 16:57:26 CDT)
topotools kirtana S (Wed Oct 12 2011 - 15:45:13 CDT)
- Re: topotools Axel Kohlmeyer (Wed Oct 12 2011 - 16:46:59 CDT)
  - Re: topotools kirtana S (Thu Nov 10 2011 - 23:49:47 CST)
Uniform Distribution of drug molecules in water meisam valizadeh kiamahalleh (Wed Oct 12 2011 - 09:35:03 CDT)
Re: query about "ViewChangeRender" plugin harish vashisth (Tue Oct 11 2011 - 10:42:09 CDT)
query about "ViewChangeRender" plugin harish vashisth (Mon Oct 10 2011 - 17:04:45 CDT)
amber traj to pqr - radii error Jesper Soerensen (Mon Oct 10 2011 - 12:42:30 CDT)
- Re: amber traj to pqr - radii error Axel Kohlmeyer (Mon Oct 10 2011 - 13:40:51 CDT)
  - Re: Re: amber traj to pqr - radii error Jesper Soerensen (Mon Oct 10 2011 - 15:41:54 CDT)
    - Re: Re: amber traj to pqr - radii error John Stone (Thu Oct 13 2011 - 10:25:45 CDT)
    - Re: AMBER prmtop and traj to pqr - radii error Jesper Soerensen (Mon Oct 17 2011 - 18:58:53 CDT)
alignment problem Markus K. Dahlgren (Mon Oct 10 2011 - 10:29:40 CDT)
centering problem in trajectory tool Markus K. Dahlgren (Mon Oct 10 2011 - 08:59:11 CDT)
- RE: centering problem in trajectory tool Zumot, Elia Nabil (Mon Oct 10 2011 - 11:19:48 CDT)
  - RE: centering problem in trajectory tool Markus K. Dahlgren (Mon Oct 10 2011 - 15:09:35 CDT)
Re: VMD fails to start/stalls/crashes on AMD workstation with Quadro FX 3800 Vlad Cojocaru (Fri Oct 07 2011 - 07:50:19 CDT)
(no subject) denilson_at_dqi.ufla.br (Thu Oct 06 2011 - 15:12:44 CDT)
- Re: John Stone (Thu Oct 13 2011 - 10:33:26 CDT)
RMSD vs RMSF Rabab Toubar (Thu Oct 06 2011 - 14:22:09 CDT)
- Re: RMSD vs RMSF Francesco Oteri (Thu Oct 06 2011 - 15:37:05 CDT)
water bridged H-bond calculation Hitesh Patel (Thu Oct 06 2011 - 07:17:26 CDT)
Solvating hexagonal unit cell Leandro Barros da Silva (Wed Oct 05 2011 - 13:00:27 CDT)
- Re: Solvating hexagonal unit cell Jérôme Hénin (Thu Oct 06 2011 - 06:15:48 CDT)
VMD fails to start/stalls/crashes on AMD workstation with Quadro FX 3800 Vlad Cojocaru (Wed Oct 05 2011 - 06:47:08 CDT)
unable to load Amber trajectories to visualize-Coordinate I/O rate 0 frames/sec, 0 MB/sec, 32.4 sec -Please help hongphuc nguyen (Wed Oct 05 2011 - 03:30:58 CDT)
Fw: denilson_at_dqi.ufla.br (Mon Oct 03 2011 - 11:18:01 CDT)
(no subject) denilson_at_dqi.ufla.br (Mon Oct 03 2011 - 08:56:08 CDT)
solvent_box_type lara lara (Sat Oct 01 2011 - 08:13:43 CDT)
GPU choice for large systems Dmitry Osolodkin (Sat Oct 01 2011 - 06:39:16 CDT)
- Re: GPU choice for large systems Axel Kohlmeyer (Sat Oct 01 2011 - 07:58:19 CDT)
  - Re: GPU choice for large systems Dmitry Osolodkin (Sat Oct 01 2011 - 08:37:43 CDT)
  - Re: GPU choice for large systems John Stone (Sat Oct 01 2011 - 21:20:18 CDT)
    - Re: GPU choice for large systems Axel Kohlmeyer (Sun Oct 02 2011 - 14:34:39 CDT)
    - Re: GPU choice for large systems John Stone (Sun Oct 02 2011 - 23:02:20 CDT)
methanol_solvent box lara lara (Sat Oct 01 2011 - 05:45:32 CDT)
- Re: methanol_solvent box Axel Kohlmeyer (Sat Oct 01 2011 - 07:08:44 CDT)
  - Re: methanol_solvent box lara lara (Sat Oct 01 2011 - 07:17:27 CDT)
    - Re: methanol_solvent box Axel Kohlmeyer (Sat Oct 01 2011 - 08:31:05 CDT)
mutator plugin generates extra bond for tip3 Burgess, Don E (Fri Sep 30 2011 - 11:49:26 CDT)
H Bond Plug-in Questions Alex Hahn (Thu Sep 29 2011 - 11:53:13 CDT)
- Re: H Bond Plug-in Questions JC Gumbart (Thu Sep 29 2011 - 12:46:25 CDT)
VMD meets Andy Warhol/Campbell's Soup on display wall Thomas Bishop (Wed Sep 28 2011 - 18:43:14 CDT)
- Re: VMD meets Andy Warhol/Campbell's Soup on display wall Axel Kohlmeyer (Wed Sep 28 2011 - 19:46:03 CDT)
  - Re: VMD meets Andy Warhol/Campbell's Soup on display wall Christian Wohlschlager (Thu Sep 29 2011 - 01:18:13 CDT)
  - Re: VMD meets Andy Warhol/Campbell's Soup on display wall Thomas Bishop (Thu Sep 29 2011 - 08:15:59 CDT)
    - Re: VMD meets Andy Warhol/Campbell's Soup on display wall Axel Kohlmeyer (Thu Sep 29 2011 - 08:22:26 CDT)
    - Re: VMD meets Andy Warhol/Campbell's Soup on display wall John Stone (Fri Sep 30 2011 - 12:22:48 CDT)
- Re: VMD meets Andy Warhol/Campbell's Soup on display wall John Stone (Fri Sep 30 2011 - 12:19:23 CDT)
VMD with LAMMPS trjaectory - help? jgrime_at_uchicago.edu (Wed Sep 28 2011 - 18:20:36 CDT)
- Re: VMD with LAMMPS trjaectory - help? Axel Kohlmeyer (Wed Sep 28 2011 - 19:27:16 CDT)
  - Re: VMD with LAMMPS trjaectory - help? jgrime_at_uchicago.edu (Thu Sep 29 2011 - 09:49:32 CDT)
    - Re: VMD with LAMMPS trjaectory - help? Axel Kohlmeyer (Thu Sep 29 2011 - 10:08:37 CDT)
vmd topotools 1.2 error oguz gurbulak (Wed Sep 28 2011 - 09:05:17 CDT)
- Re: vmd topotools 1.2 error Axel Kohlmeyer (Wed Sep 28 2011 - 10:01:43 CDT)
- Re: vmd topotools 1.2 oguz gurbulak (Thu Sep 29 2011 - 06:15:12 CDT)
  - Re: Re: vmd topotools 1.2 Axel Kohlmeyer (Thu Sep 29 2011 - 08:16:39 CDT)
vmd topotools 1.2 error oguz gurbulak (Wed Sep 28 2011 - 06:41:37 CDT)
- vmd topotools 1.2 error oguz gurbulak (Wed Sep 28 2011 - 08:21:55 CDT)
- Re: vmd topotools 1.2 error Axel Kohlmeyer (Wed Sep 28 2011 - 09:06:59 CDT)
Re: question on "Recompile VMD with larger index types" Axel Kohlmeyer (Wed Sep 28 2011 - 05:44:13 CDT)
Re: Selecting a laptop for VMD and NAMD PaweÅ‚ KÄ™dzierski (Wed Sep 28 2011 - 04:07:30 CDT)
question on "Recompile VMD with larger index types" JhonY. I. (Wed Sep 28 2011 - 00:50:33 CDT)
- Re: question on "Recompile VMD with larger index types" PaweÅ‚ KÄ™dzierski (Wed Sep 28 2011 - 08:17:35 CDT)
Associating .crd file extension with COR Plugin Vadim Patsalo (Tue Sep 27 2011 - 21:08:31 CDT)
- Re: Associating .crd file extension with COR Plugin Jernej Zidar (Tue Sep 27 2011 - 22:34:53 CDT)
- Re: Associating .crd file extension with COR Plugin Axel Kohlmeyer (Wed Sep 28 2011 - 08:51:38 CDT)
connectivity in RBCG file(pdb extension) ANURAG JHA (Tue Sep 27 2011 - 18:46:20 CDT)
Associating .crd file extension with COR Plugin. Vadim Patsalo (Tue Sep 27 2011 - 16:58:50 CDT)
problem of exceeding max atom number JhonY. I. (Tue Sep 27 2011 - 12:51:43 CDT)
- Re: problem of exceeding max atom number John Stone (Tue Sep 27 2011 - 13:24:22 CDT)
- Re: problem of exceeding max atom number Axel Kohlmeyer (Tue Sep 27 2011 - 13:41:45 CDT)
Re: Selecting a laptop for VMD and NAMD (was: CUDA cores seen by VMD on GT540M) PaweÅ‚ KÄ™dzierski (Tue Sep 27 2011 - 09:29:31 CDT)
- Re: Re: Selecting a laptop for VMD and NAMD (was: CUDA cores seen by VMD on GT540M) Axel Kohlmeyer (Tue Sep 27 2011 - 10:36:20 CDT)
convert .coor to pdb matziast_at_med.uth.gr (Mon Sep 26 2011 - 06:08:24 CDT)
- Re: convert .coor to pdb Axel Kohlmeyer (Mon Sep 26 2011 - 07:04:11 CDT)
- RE: convert .coor to pdb Zumot, Elia Nabil (Mon Sep 26 2011 - 08:08:59 CDT)
  - Re: convert .coor to pdb Joshua D. Moore (Mon Sep 26 2011 - 09:12:09 CDT)
RDF related problems siladitya mukherjee (Sat Sep 24 2011 - 15:17:37 CDT)
- Re: RDF related problems Axel Kohlmeyer (Sat Sep 24 2011 - 16:19:21 CDT)
Epsilon, Rmin for copper ions Francesco Pietra (Sat Sep 24 2011 - 03:55:34 CDT)
Fwd: Copper ions paratool Francesco Pietra (Fri Sep 23 2011 - 10:12:04 CDT)
Fwd: Saved project and paratool Francesco Pietra (Fri Sep 23 2011 - 06:00:05 CDT)
stream files and paratool Francesco Pietra (Fri Sep 23 2011 - 03:10:52 CDT)
Locked files in Windows 7 Ignacio Fernández Galván (Thu Sep 22 2011 - 06:08:13 CDT)
- Re: Locked files in Windows 7 Ajasja LjubetiÄ (Thu Sep 22 2011 - 07:17:55 CDT)
  - Re: Locked files in Windows 7 Ignacio FernÃ¡ndez GalvÃ¡n (Thu Sep 22 2011 - 11:48:23 CDT)
- Re: Locked files in Windows 7 Axel Kohlmeyer (Thu Sep 22 2011 - 07:49:47 CDT)
Quick TCl scripting question Anthony Rey (Wed Sep 21 2011 - 22:49:02 CDT)
- Re: Quick TCl scripting question Tim Travers (Wed Sep 21 2011 - 23:57:14 CDT)
  - Re: Quick TCl scripting question Anthony Rey (Thu Sep 22 2011 - 00:02:54 CDT)
redirecting to output kirtana S (Wed Sep 21 2011 - 13:31:52 CDT)
- RE: redirecting to output Kei Sit (Thu Sep 22 2011 - 00:32:53 CDT)
- Re: redirecting to output John Stone (Thu Sep 22 2011 - 01:42:26 CDT)
radial pair distribution problems aiswarya pawar (Wed Sep 21 2011 - 01:27:50 CDT)
- Re: radial pair distribution problems John Stone (Wed Sep 21 2011 - 11:22:33 CDT)
NetCDF plugin Alexandr Kornev (Tue Sep 20 2011 - 17:55:59 CDT)
- Re: NetCDF plugin Axel Kohlmeyer (Tue Sep 20 2011 - 18:59:11 CDT)
extra characters kirtana S (Tue Sep 20 2011 - 10:54:07 CDT)
Problem with measuring dihedrals Jernej Zidar (Tue Sep 20 2011 - 03:47:24 CDT)
- Re: Problem with measuring dihedrals Ajasja LjubetiÄ (Tue Sep 20 2011 - 04:54:54 CDT)
  - Re: Problem with measuring dihedrals Jernej Zidar (Tue Sep 20 2011 - 05:28:57 CDT)
- Re: Problem with measuring dihedrals Axel Kohlmeyer (Tue Sep 20 2011 - 04:55:10 CDT)
Problem building POPE membrane with plugin using CHARMM36 Maggie Pruitt (Mon Sep 19 2011 - 12:19:41 CDT)
- Re: Problem building POPE membrane with plugin using CHARMM36 John Stone (Wed Sep 21 2011 - 11:32:57 CDT)
  - RE: Problem building POPE membrane with plugin using CHARMM36 JC Gumbart (Wed Sep 21 2011 - 11:44:00 CDT)
RMSD heatmapper -plugin Anssi Nurminen (Mon Sep 19 2011 - 12:03:51 CDT)
- Re: RMSD heatmapper -plugin Axel Kohlmeyer (Mon Sep 19 2011 - 12:49:40 CDT)
- Re: RMSD heatmapper -plugin John Stone (Mon Sep 19 2011 - 14:03:52 CDT)
select each element of array kirtana S (Mon Sep 19 2011 - 11:11:59 CDT)
- Re: select each element of array Axel Kohlmeyer (Mon Sep 19 2011 - 12:10:44 CDT)
  - Re: select each element of array kirtana S (Mon Sep 19 2011 - 17:31:43 CDT)
Adding water in protein madhumita das (Mon Sep 19 2011 - 06:01:15 CDT)
- Re: Adding water in protein Axel Kohlmeyer (Mon Sep 19 2011 - 07:01:15 CDT)
bug in Hbond Option hamid mosaddeghi (Mon Sep 19 2011 - 00:37:41 CDT)
- Re: bug in Hbond Option Axel Kohlmeyer (Mon Sep 19 2011 - 06:51:38 CDT)
topotools readvarxyz puroorava annapaneni (Sun Sep 18 2011 - 12:22:58 CDT)
- Re: topotools readvarxyz Axel Kohlmeyer (Mon Sep 19 2011 - 07:03:25 CDT)
Creating a fragment of the given protein Trung Nguyen Duc (Sun Sep 18 2011 - 11:43:18 CDT)
- Re: Creating a fragment of the given protein JC Gumbart (Mon Sep 19 2011 - 01:56:14 CDT)
fonts for paratool Francesco Pietra (Sun Sep 18 2011 - 09:11:38 CDT)
- Re: fonts for paratool John Stone (Thu Sep 22 2011 - 01:31:07 CDT)
I can't not see my post in Archive list hongphuc nguyen (Sat Sep 17 2011 - 22:52:58 CDT)
- Re: I can't not see my post in Archive list John Stone (Sat Sep 17 2011 - 23:42:43 CDT)
units on the volmap tool Raul Araya (Sat Sep 17 2011 - 00:26:04 CDT)
color with name Yamei (Fri Sep 16 2011 - 11:56:03 CDT)
- Re: color with name John Stone (Fri Sep 16 2011 - 13:32:39 CDT)
  - Re: color with name Andrew Fenley (Fri Sep 16 2011 - 16:11:17 CDT)
A bug about "trans" command KM Tu (Fri Sep 16 2011 - 10:33:49 CDT)
- Re: A bug about "trans" command John Stone (Wed Sep 21 2011 - 11:06:17 CDT)
Clustering MD trajectories Vijay Vammi (Fri Sep 16 2011 - 08:13:49 CDT)
- Re: Clustering MD trajectories Hurt, Darrell (NIH/NIAID) [E] (Fri Sep 16 2011 - 10:17:54 CDT)
  - Re: Clustering MD trajectories Vijay Vammi (Fri Sep 16 2011 - 10:39:40 CDT)
  - Re: Clustering MD trajectories Vijay Vammi (Fri Sep 16 2011 - 14:52:47 CDT)
calculate the solvent molecule within a cut off from protein aiswarya pawar (Thu Sep 15 2011 - 05:36:25 CDT)
Cionize Christian Wohlschlager (Thu Sep 15 2011 - 01:12:16 CDT)
- Re: Cionize John Stone (Fri Sep 16 2011 - 13:48:43 CDT)
LINK or PACTH command in VMD snoze pa (Wed Sep 14 2011 - 11:48:53 CDT)
- Re: LINK or PACTH command in VMD Axel Kohlmeyer (Wed Sep 14 2011 - 13:38:40 CDT)
  - Re: LINK or PACTH command in VMD snoze pa (Wed Sep 14 2011 - 15:56:13 CDT)
Does Paratool support CgenFF? Alexandre Suman de Araujo (Wed Sep 14 2011 - 07:22:33 CDT)
- Re: Does Paratool support CgenFF? Axel Kohlmeyer (Wed Sep 14 2011 - 09:37:26 CDT)
- Re: Does Paratool support CgenFF? John Stone (Wed Sep 14 2011 - 10:10:31 CDT)
  - Re: Does Paratool support CgenFF? JC Gumbart (Thu Sep 15 2011 - 01:31:32 CDT)
Showing and Calculating the amount of water molecules inside carbon nanotube meisam valizadeh kiamahalleh (Tue Sep 13 2011 - 22:23:13 CDT)
- Re: Showing and Calculating the amount of water molecules inside carbon nanotube Axel Kohlmeyer (Tue Sep 13 2011 - 23:54:39 CDT)
2011 VMD User Survey results are posted... John Stone (Tue Sep 13 2011 - 15:26:21 CDT)
RDF calculation for production steps siladitya mukherjee (Tue Sep 13 2011 - 15:15:53 CDT)
- Re: RDF calculation for production steps Axel Kohlmeyer (Tue Sep 13 2011 - 23:51:17 CDT)
  - RE: RDF calculation for production steps Goldsmith, Jacob (Thu Sep 15 2011 - 08:25:20 CDT)
    - RE: RDF calculation for production steps Axel Kohlmeyer (Thu Sep 15 2011 - 10:38:16 CDT)
    - Re: RDF calculation for production steps Dudo (Thu Sep 15 2011 - 15:23:15 CDT)
Bug in 'source' command or in for loop? dwds gerge (Tue Sep 13 2011 - 12:06:10 CDT)
- Re: Bug in 'source' command or in for loop? John Stone (Tue Sep 13 2011 - 13:52:43 CDT)
- re: Bug in 'source' command or in for loop? dwds gerge (Tue Sep 13 2011 - 19:37:08 CDT)
  - Re: re: Bug in 'source' command or in for loop? John Stone (Fri Sep 16 2011 - 14:03:38 CDT)
Showing and Calculating the amount of water molecules inside carbon nanotube meisam valizadeh kiamahalleh (Mon Sep 12 2011 - 22:18:48 CDT)
- Re: Showing and Calculating the amount of water molecules inside carbon nanotube John Stone (Fri Sep 16 2011 - 13:59:40 CDT)
linux issues Vivek Ranjan (Mon Sep 12 2011 - 11:01:25 CDT)
- Re: linux issues John Stone (Mon Sep 12 2011 - 11:22:06 CDT)
- Re: linux issues Axel Kohlmeyer (Mon Sep 12 2011 - 12:03:04 CDT)
- RE: linux issues Bennion, Brian (Mon Sep 12 2011 - 12:25:34 CDT)
Displaying residues on chain A within X of chain B Irene Newhouse (Fri Sep 09 2011 - 16:19:18 CDT)
- Re: Displaying residues on chain A within X of chain B Axel Kohlmeyer (Fri Sep 09 2011 - 17:51:33 CDT)
  - RE: Displaying residues on chain A within X of chain B Irene Newhouse (Fri Sep 09 2011 - 19:54:51 CDT)
    - Re: Displaying residues on chain A within X of chain B Axel Kohlmeyer (Fri Sep 09 2011 - 20:27:25 CDT)
    - RE: Displaying residues on chain A within X of chain B Irene Newhouse (Sat Sep 10 2011 - 00:49:34 CDT)
- RE: Displaying residues on chain A within X of chain B Mark Cunningham (Fri Sep 09 2011 - 20:40:36 CDT)
  - RE: Displaying residues on chain A within X of chain B Irene Newhouse (Sat Sep 10 2011 - 00:33:25 CDT)
cionize Christian Wohlschlager (Fri Sep 09 2011 - 02:10:28 CDT)
output values in my script kirtana S (Thu Sep 08 2011 - 17:38:04 CDT)
- Re: output values in my script Axel Kohlmeyer (Thu Sep 08 2011 - 19:51:54 CDT)
Visualization of FEP simulation Bruno Luís Pinto de Oliveira (Thu Sep 08 2011 - 12:38:41 CDT)
- Visualization of FEP simulation Bruno Luís Pinto de Oliveira (Thu Sep 08 2011 - 13:24:32 CDT)
  - Visualization of FEP simulation Bruno Luís Pinto de Oliveira (Wed Oct 19 2011 - 09:04:06 CDT)
Fwd: Pdb file generation,bad water removal and coordinates of psf. madhumita das (Wed Sep 07 2011 - 20:24:47 CDT)
Visualizing Trajectory file: .pdb or .xyz winardi, erik (Wed Sep 07 2011 - 13:49:06 CDT)
- Re: Visualizing Trajectory file: .pdb or .xyz Axel Kohlmeyer (Wed Sep 07 2011 - 14:55:10 CDT)
  - Re: Visualizing Trajectory file: .pdb or .xyz winardi, erik (Wed Sep 07 2011 - 18:02:19 CDT)
    - Re: Visualizing Trajectory file: .pdb or .xyz Axel Kohlmeyer (Wed Sep 07 2011 - 18:11:44 CDT)
autoionize Jacopo Sgrignani (Wed Sep 07 2011 - 09:00:02 CDT)
draw intersection volume between two spheres Filip Persson (Wed Sep 07 2011 - 08:30:33 CDT)
- Re: draw intersection volume between two spheres Axel Kohlmeyer (Wed Sep 07 2011 - 10:35:43 CDT)
TK console problem J. Matthew Franklin (Tue Sep 06 2011 - 22:40:26 CDT)
- Re: TK console problem John Stone (Wed Sep 07 2011 - 10:50:41 CDT)
  - Re: TK console problem J. Matthew Franklin (Sat Sep 10 2011 - 17:46:38 CDT)
    - Re: TK console problem John Stone (Sun Sep 11 2011 - 12:06:56 CDT)
    - Re: TK console problem J. Matthew Franklin (Wed Sep 14 2011 - 20:38:38 CDT)
VMD align to principal axis kirtana S (Tue Sep 06 2011 - 22:06:04 CDT)
- Re: VMD align to principal axis Axel Kohlmeyer (Tue Sep 06 2011 - 23:31:11 CDT)
  - Re: VMD align to principal axis kirtana S (Wed Sep 07 2011 - 13:47:51 CDT)
Count waters inside a specified box Manish (Tue Sep 06 2011 - 11:11:40 CDT)
- Re: Count waters inside a specified box Jérôme Hénin (Wed Sep 07 2011 - 06:18:06 CDT)
  - RE: Count waters inside a specified box Manish (Wed Sep 07 2011 - 09:19:55 CDT)
define water cavity using atom selection in graphical representations window Filip Persson (Tue Sep 06 2011 - 03:08:20 CDT)
- Re: define water cavity using atom selection in graphical representations window Hitesh Patel (Tue Sep 06 2011 - 04:20:35 CDT)
  - Re: define water cavity using atom selection in graphical representations window Axel Kohlmeyer (Tue Sep 06 2011 - 05:31:23 CDT)
  - RE: define water cavity using atom selection in graphical representations window Mark Cunningham (Tue Sep 06 2011 - 07:35:23 CDT)
    - Re: define water cavity using atom selection in graphical representations window Axel Kohlmeyer (Tue Sep 06 2011 - 09:28:45 CDT)
- Re: define water cavity using atom selection in graphical representations window Axel Kohlmeyer (Tue Sep 06 2011 - 05:11:00 CDT)
plugin kirtana S (Mon Sep 05 2011 - 13:38:47 CDT)
- Re: plugin Axel Kohlmeyer (Mon Sep 05 2011 - 14:37:19 CDT)
Density Profile in VMD oguz gurbulak (Mon Sep 05 2011 - 02:37:37 CDT)
- Re: Density Profile in VMD Axel Kohlmeyer (Mon Sep 05 2011 - 08:39:31 CDT)
How to read pdbqt file? Chirag Vora (Sat Sep 03 2011 - 14:57:01 CDT)
- Re: How to read pdbqt file? Axel Kohlmeyer (Sat Sep 03 2011 - 15:53:58 CDT)
- Re: How to read pdbqt file? Balazs Jojart (Sun Sep 04 2011 - 01:41:08 CDT)
Re: namd-l: SASA of PBD files sajad falsafi (Sat Sep 03 2011 - 14:38:17 CDT)
Radial distribution function Kartheek (Sat Sep 03 2011 - 10:10:03 CDT)
Radial distribution function Kartheek (Sat Sep 03 2011 - 05:33:50 CDT)
- Radial distribution function Kartheek (Sat Sep 03 2011 - 06:32:58 CDT)
  - Radial distribution function Kartheek (Sat Sep 03 2011 - 07:18:46 CDT)
Re: Movie maker in VMD siladitya mukherjee (Thu Sep 01 2011 - 13:04:58 CDT)
- Re: Movie maker in VMD siladitya mukherjee (Fri Sep 02 2011 - 11:12:21 CDT)
  - Re: Movie maker in VMD Axel Kohlmeyer (Fri Sep 02 2011 - 12:14:32 CDT)
    - Re: Movie maker in VMD siladitya mukherjee (Fri Sep 02 2011 - 12:41:02 CDT)
Movie maker in VMD siladitya mukherjee (Thu Sep 01 2011 - 11:11:15 CDT)
Invitation to connect on LinkedIn Hideya Nakamura via LinkedIn (Wed Aug 31 2011 - 19:22:00 CDT)
Fw: Hbond in VMD hamid mosaddeghi (Wed Aug 31 2011 - 12:29:01 CDT)
- Fw: Hbond in VMD hamid mosaddeghi (Wed Aug 31 2011 - 12:28:09 CDT)
  - Re: Fw: Hbond in VMD Axel Kohlmeyer (Wed Aug 31 2011 - 13:16:11 CDT)
- Re: Fw: Hbond in VMD Axel Kohlmeyer (Wed Aug 31 2011 - 13:27:21 CDT)
- Fw: Fw: Hbond in VMD hamid mosaddeghi (Wed Aug 31 2011 - 14:50:19 CDT)
  - Re: Fw: Fw: Hbond in VMD Axel Kohlmeyer (Wed Aug 31 2011 - 15:56:52 CDT)
Saving ionized.psf from add ions plug in of VMD Andrea Holfelder (Wed Aug 31 2011 - 10:35:45 CDT)
- Re: Saving ionized.psf from add ions plug in of VMD Axel Kohlmeyer (Wed Aug 31 2011 - 11:34:08 CDT)
  - Re: Saving ionized.psf from add ions plug in of VMD Andrea Holfelder (Wed Aug 31 2011 - 14:27:04 CDT)
pdb naming convention to get ribbon representation Casey Johnson (Wed Aug 31 2011 - 09:08:11 CDT)
- Re: pdb naming convention to get ribbon representation John Stone (Thu Sep 01 2011 - 07:59:26 CDT)
CUDA cores seen by VMD on GT540M Pawe³ Kêdzierski (Wed Aug 31 2011 - 09:02:09 CDT)
- Re: CUDA cores seen by VMD on GT540M Axel Kohlmeyer (Wed Aug 31 2011 - 10:17:39 CDT)
- Re: CUDA cores seen by VMD on GT540M John Stone (Wed Aug 31 2011 - 10:19:39 CDT)
  - Re: CUDA cores seen by VMD on GT540M PaweÅ‚ KÄ™dzierski (Thu Sep 01 2011 - 08:07:26 CDT)
Hbond in VMD hamid mosaddeghi (Wed Aug 31 2011 - 03:12:47 CDT)
- Re: Hbond in VMD Axel Kohlmeyer (Wed Aug 31 2011 - 07:45:45 CDT)
  - Re: Hbond in VMD hamid mosaddeghi (Fri Sep 02 2011 - 05:46:16 CDT)
Re: Fw: Lammps Output data format Axel Kohlmeyer (Tue Aug 30 2011 - 12:45:15 CDT)
VMD display residues ban arn (Tue Aug 30 2011 - 12:14:35 CDT)
- Re: VMD display residues Axel Kohlmeyer (Tue Aug 30 2011 - 13:19:46 CDT)
  - Re: VMD display residues ban arn (Wed Aug 31 2011 - 04:28:35 CDT)
    - Re: VMD display residues Axel Kohlmeyer (Wed Aug 31 2011 - 06:22:04 CDT)
Hbonds for a specific frame Hitesh Patel (Tue Aug 30 2011 - 11:47:23 CDT)
- Fw: Hbonds for a specific frame hamid mosaddeghi (Wed Aug 31 2011 - 01:23:37 CDT)
VMD movie ban arn (Tue Aug 30 2011 - 10:31:58 CDT)
- Re: VMD movie Axel Kohlmeyer (Tue Aug 30 2011 - 11:28:37 CDT)
  - Re: VMD movie ban arn (Tue Aug 30 2011 - 12:10:26 CDT)
    - Re: VMD movie Axel Kohlmeyer (Tue Aug 30 2011 - 12:22:29 CDT)
- Re: VMD movie John Stone (Tue Aug 30 2011 - 11:25:30 CDT)
Depletion of few atoms makkuva Ram vivek (Mon Aug 29 2011 - 22:16:16 CDT)
loading a trajectory where particles aren't conservd Chris Knorowski (Mon Aug 29 2011 - 16:35:28 CDT)
- Re: loading a trajectory where particles aren't conservd Axel Kohlmeyer (Mon Aug 29 2011 - 17:26:22 CDT)
  - Re: loading a trajectory where particles aren't conservd Chris Knorowski (Wed Aug 31 2011 - 15:35:04 CDT)
    - Re: loading a trajectory where particles aren't conservd Axel Kohlmeyer (Wed Aug 31 2011 - 15:42:14 CDT)
Lammps Output data format winardi, erik (Mon Aug 29 2011 - 12:20:31 CDT)
- Re: Lammps Output data format Axel Kohlmeyer (Mon Aug 29 2011 - 13:20:02 CDT)
  - Re: Lammps Output data format winardi, erik (Tue Aug 30 2011 - 10:44:49 CDT)
  - Re: Lammps Output data format Axel Kohlmeyer (Tue Aug 30 2011 - 10:54:19 CDT)
3d viz? Dave Schall (Mon Aug 29 2011 - 09:28:34 CDT)
- Re: 3d viz? Axel Kohlmeyer (Mon Aug 29 2011 - 10:37:24 CDT)
  - Re: 3d viz? Dave Schall (Mon Aug 29 2011 - 13:53:05 CDT)
    - Re: 3d viz? Dave Schall (Mon Aug 29 2011 - 14:45:17 CDT)
Water in binding site ban arn (Mon Aug 29 2011 - 04:47:53 CDT)
Represent custom peptide as ribbon? Casey Johnson (Sat Aug 27 2011 - 09:24:07 CDT)
vmd does not run on the VNC client peng liu (Thu Aug 25 2011 - 21:15:15 CDT)
- Re: vmd does not run on the VNC client John Stone (Thu Aug 25 2011 - 21:27:07 CDT)
  - Re: Re: vmd does not run on the VNC client superdirac (Thu Aug 25 2011 - 22:33:55 CDT)
    - Re: Re: vmd does not run on the VNC client John Stone (Thu Aug 25 2011 - 22:40:57 CDT)
    - Re: Re: Re: vmd does not run on the VNC client superdirac (Thu Aug 25 2011 - 22:54:48 CDT)
Fwd: Re: namd-l: How to evaluate the area per lipid and thickness of the lipid bilayer in a membrane-protein system? Vlad Cojocaru (Thu Aug 25 2011 - 02:14:15 CDT)
- Re: Fwd: Re: namd-l: How to evaluate the area per lipid and thickness of the lipid bilayer in a membrane-protein system? Toni Giorgino (Thu Aug 25 2011 - 07:24:55 CDT)
Text in line with line Nuno Sousa Cerqueira (Wed Aug 24 2011 - 21:21:52 CDT)
how to load Orient package in VMD Jiao, Dian NMN (-EXP) (Wed Aug 24 2011 - 15:24:42 CDT)
- Re: how to load Orient package in VMD Axel Kohlmeyer (Wed Aug 24 2011 - 16:47:49 CDT)
  - Re: how to load Orient package in VMD Jiao, Dian NMN (-EXP) (Wed Aug 24 2011 - 16:55:23 CDT)
    - Re: how to load Orient package in VMD Axel Kohlmeyer (Wed Aug 24 2011 - 16:57:50 CDT)
Initial configuration reorientation Anna (Wed Aug 24 2011 - 11:48:38 CDT)
- Fwd: Initial configuration reorientation Anna (Wed Aug 24 2011 - 12:34:11 CDT)
  - Mailing list problems Anna (Wed Aug 24 2011 - 14:53:46 CDT)
- Re: Initial configuration reorientation John Stone (Wed Aug 24 2011 - 12:43:52 CDT)
convert pdb format to normal pdb format hamze rahimi (Wed Aug 24 2011 - 04:48:09 CDT)
- Re: convert pdb format to normal pdb format Bjoern Olausson (Wed Aug 24 2011 - 06:10:45 CDT)
extrabonds Ling Wu (Tue Aug 23 2011 - 16:13:53 CDT)
- Re: extrabonds John Stone (Tue Aug 23 2011 - 17:05:37 CDT)
  - Re: extrabonds Ling Wu (Wed Aug 24 2011 - 10:08:41 CDT)
    - Re: extrabonds John Stone (Wed Aug 24 2011 - 10:21:28 CDT)
RMSD calculator extension George Tzotzos (Tue Aug 23 2011 - 08:59:19 CDT)
- Re: RMSD calculator extension Axel Kohlmeyer (Tue Aug 23 2011 - 09:48:38 CDT)
Problem with psfgen Florian Mrugalla (Tue Aug 23 2011 - 07:41:02 CDT)
- Re: Problem with psfgen Axel Kohlmeyer (Tue Aug 23 2011 - 09:33:39 CDT)
  - Re: Problem with psfgen Florian Mrugalla (Tue Aug 23 2011 - 10:14:24 CDT)
Wrap PBC inside unit cellâ€ Casey Johnson (Mon Aug 22 2011 - 17:54:41 CDT)
- Re: Wrap PBC inside unit cellâ€ Nima Nouri (Mon Aug 22 2011 - 18:56:25 CDT)
  - Re: Re: Wrap PBC inside unit cellâ€ Axel Kohlmeyer (Tue Aug 23 2011 - 09:27:20 CDT)
- Re: Wrap PBC inside unit cellâ€ Axel Kohlmeyer (Tue Aug 23 2011 - 09:26:09 CDT)
Fwd: Dowser plugin: Error message George Tzotzos (Mon Aug 22 2011 - 16:34:31 CDT)
- Re: Fwd: Dowser plugin: Error message John Stone (Tue Aug 23 2011 - 12:39:44 CDT)
how to put two identical proteins in a same water sphere? juan jesus sanchez sanchez (Mon Aug 22 2011 - 13:06:12 CDT)
DNA hairpin Shesh Nath (Sat Aug 20 2011 - 01:19:04 CDT)
- Re: DNA hairpin Jernej Zidar (Sat Aug 20 2011 - 02:39:31 CDT)
- Re: DNA hairpin Anna (Sat Aug 20 2011 - 04:30:52 CDT)
  - Re: DNA hairpin Shesh Nath (Sat Aug 20 2011 - 04:41:20 CDT)
    - Re: DNA hairpin Chirag Vora (Sun Aug 21 2011 - 11:49:44 CDT)
changing origin of rotation (NOT center of mass) Michael Daily (Fri Aug 19 2011 - 13:41:06 CDT)
Turning Label Info output off in vmd console Sebastián Gutiérrez (Thu Aug 18 2011 - 18:14:06 CDT)
- Re: Turning Label Info output off in vmd console Axel Kohlmeyer (Thu Aug 18 2011 - 19:28:04 CDT)
  - Re: Turning Label Info output off in vmd console Sebastián Gutiérrez (Fri Aug 19 2011 - 15:21:02 CDT)
    - Re: Turning Label Info output off in vmd console Axel Kohlmeyer (Fri Aug 19 2011 - 18:14:30 CDT)
How can I draw secondary structures if I only have the carbon alpha coordinates Mert Gür (Thu Aug 18 2011 - 10:01:00 CDT)
- Re: How can I draw secondary structures if I only have the carbon alpha coordinates John Stone (Thu Aug 18 2011 - 11:48:01 CDT)
  - Re: How can I draw secondary structures if I only have the carbon alpha coordinates Mert Gür (Thu Aug 18 2011 - 12:20:30 CDT)
- Re: How can I draw secondary structures if I only have the carbon alpha coordinates Tim Travers (Thu Aug 18 2011 - 12:26:14 CDT)
converting coarse grained POPC membranes to atomistic representation (AMBER, GAFF) Vlad Cojocaru (Thu Aug 18 2011 - 07:06:32 CDT)
CatDcd Windows Version NAMITA BHADRA (Wed Aug 17 2011 - 23:52:28 CDT)
how to rename a representation in vmd maria goranovic (Wed Aug 17 2011 - 04:18:42 CDT)
- Re: how to rename a representation in vmd Ajasja LjubetiÄ (Wed Aug 17 2011 - 05:11:31 CDT)
changing label format with some arithmetic maria goranovic (Wed Aug 17 2011 - 04:05:19 CDT)
- Re: changing label format with some arithmetic Axel Kohlmeyer (Wed Aug 17 2011 - 10:13:09 CDT)
Intel HD3000 versus ATI Mobility Radeon 6310 Gianluca Interlandi (Wed Aug 17 2011 - 00:09:01 CDT)
- Re: Intel HD3000 versus ATI Mobility Radeon 6310 John Stone (Wed Aug 17 2011 - 00:50:43 CDT)
MMTools Chathurika Abeyrathne (Tue Aug 16 2011 - 20:03:45 CDT)
- Re: namd-l: MMTools Axel Kohlmeyer (Wed Aug 17 2011 - 10:15:50 CDT)
  - Re: Re: namd-l: MMTools Chathurika Abeyrathne (Wed Aug 17 2011 - 19:02:46 CDT)
    - Re: Re: namd-l: MMTools Axel Kohlmeyer (Wed Aug 17 2011 - 20:28:28 CDT)
    - Re: Re: namd-l: MMTools Chathurika Abeyrathne (Wed Aug 17 2011 - 21:07:21 CDT)
Spaceball navigator - making movies Michael Doig (Tue Aug 16 2011 - 06:16:42 CDT)
- Re: Spaceball navigator - making movies John Stone (Tue Aug 16 2011 - 10:16:56 CDT)
  - Re: Spaceball navigator - making movies Michael Doig (Wed Aug 17 2011 - 03:58:38 CDT)
visualizing unrealistic bonds Moeed (Mon Aug 15 2011 - 11:09:51 CDT)
- Re: visualizing unrealistic bonds John Stone (Mon Aug 15 2011 - 11:21:02 CDT)
  - Re: visualizing unrealistic bonds Moeed (Tue Aug 23 2011 - 05:49:22 CDT)
    - Re: visualizing unrealistic bonds John Stone (Tue Aug 23 2011 - 09:06:23 CDT)
    - Re: visualizing unrealistic bonds Axel Kohlmeyer (Tue Aug 23 2011 - 09:30:52 CDT)
  - Re: visualizing unrealistic bonds Axel Kohlmeyer (Tue Aug 23 2011 - 10:18:00 CDT)
- Re: visualizing unrealistic bonds Axel Kohlmeyer (Mon Aug 15 2011 - 12:07:13 CDT)
- Re: visualizing unrealistic bonds Magnus Andersson (Mon Aug 15 2011 - 14:26:08 CDT)
Re: Solvating a Protein in VMD using NON STANDARD SOLVENT Babban Mia (Sat Aug 13 2011 - 07:10:18 CDT)
- Re: Re: Solvating a Protein in VMD using NON STANDARD SOLVENT Axel Kohlmeyer (Sat Aug 13 2011 - 08:22:08 CDT)
  - Re: Re: Solvating a Protein in VMD using NON STANDARD SOLVENT Babban Mia (Sat Aug 13 2011 - 08:42:09 CDT)
Maria Tziastoudi matziast_at_med.uth.gr (Sat Aug 13 2011 - 05:29:29 CDT)
.COOR TO PDB FILE Babban Mia (Sat Aug 13 2011 - 01:11:48 CDT)
- Re: namd-l: .COOR TO PDB FILE JC Gumbart (Sat Aug 13 2011 - 01:29:04 CDT)
Implicit Patch for Nucleic Acids? Stefan Franzen (Fri Aug 12 2011 - 13:46:24 CDT)
Orienting a Protein Kapil Amarnath (Fri Aug 12 2011 - 11:19:31 CDT)
- Re: Orienting a Protein Balazs Jojart (Fri Aug 12 2011 - 18:57:22 CDT)
  - Re: Orienting a Protein Kapil Amarnath (Sun Aug 14 2011 - 13:30:09 CDT)
how to wrap a protein with periodic waters Thomas Evangelidis (Fri Aug 12 2011 - 10:19:47 CDT)
- Re: how to wrap a protein with periodic waters Olaf Lenz (Mon Aug 15 2011 - 02:43:51 CDT)
Maria Tziastoudi matziast_at_med.uth.gr (Fri Aug 12 2011 - 04:29:38 CDT)
- Re: Maria Tziastoudi John Stone (Fri Aug 12 2011 - 09:39:51 CDT)
rmsf hamze rahimi (Fri Aug 12 2011 - 01:32:44 CDT)
- Re: rmsf Nima Nouri (Fri Aug 12 2011 - 02:20:23 CDT)
- Re: rmsf Axel Kohlmeyer (Fri Aug 12 2011 - 03:52:10 CDT)
package require help hamze rahimi (Fri Aug 12 2011 - 01:31:22 CDT)
- Re: package require help Axel Kohlmeyer (Fri Aug 12 2011 - 03:51:27 CDT)
- Re: package require help sajad falsafi (Fri Aug 12 2011 - 04:05:33 CDT)
Vmd Problem Sara baretller (Thu Aug 11 2011 - 15:49:08 CDT)
- Re: Vmd Problem Axel Kohlmeyer (Thu Aug 11 2011 - 16:35:56 CDT)
- Re: Vmd Problem John Stone (Thu Aug 11 2011 - 16:36:50 CDT)
  - Re: Vmd Problem Sara baretller (Thu Aug 11 2011 - 16:42:32 CDT)
    - Re: Vmd Problem John Stone (Thu Aug 11 2011 - 16:51:38 CDT)
- Timeline plugin Ada Zhan (Thu Aug 11 2011 - 19:12:01 CDT)
Update selection every frame command Guenegou, Guillaume [ORDFR] (Thu Aug 11 2011 - 04:56:11 CDT)
- Re: Update selection every frame command Axel Kohlmeyer (Thu Aug 11 2011 - 07:23:04 CDT)
Change Path to Povray Moritz Münsterberg (Thu Aug 11 2011 - 03:34:59 CDT)
- Re: Change Path to Povray John Stone (Thu Aug 11 2011 - 10:30:15 CDT)
Molefacture - VMD agreement Marc Charendoff (Wed Aug 10 2011 - 23:10:27 CDT)
- Re: Molefacture - VMD agreement Axel Kohlmeyer (Thu Aug 11 2011 - 00:14:01 CDT)
  - Re: Molefacture - VMD agreement Jernej Zidar (Thu Aug 11 2011 - 01:41:08 CDT)
Solvation in VMD using Non Standard Solvent System Babban Mia (Wed Aug 10 2011 - 07:35:32 CDT)
- Re: namd-l: Solvation in VMD using Non Standard Solvent System Axel Kohlmeyer (Wed Aug 10 2011 - 07:47:35 CDT)
Long atom types from CGenFF causing charge problems Anna Whitney (Tue Aug 09 2011 - 16:01:09 CDT)
- Re: Long atom types from CGenFF causing charge problems JC Gumbart (Tue Aug 09 2011 - 17:42:32 CDT)
  - Re: Long atom types from CGenFF causing charge problems John Stone (Tue Aug 09 2011 - 22:19:02 CDT)
    - RE: Long atom types from CGenFF causing charge problems JC Gumbart (Tue Aug 09 2011 - 23:52:22 CDT)
TCL and Plugins Mark Suhovecky (Tue Aug 09 2011 - 12:23:41 CDT)
- TCL and Plugins Mark Suhovecky (Tue Aug 09 2011 - 12:43:22 CDT)
  - Re: TCL and Plugins John Stone (Tue Aug 09 2011 - 13:45:32 CDT)
- Re: TCL and Plugins Axel Kohlmeyer (Tue Aug 09 2011 - 13:48:48 CDT)
measure dihedral and improper angles matziast_at_med.uth.gr (Tue Aug 09 2011 - 11:02:57 CDT)
Command line for thickness parameter Guenegou, Guillaume [ORDFR] (Tue Aug 09 2011 - 06:00:29 CDT)
Solvate a Protein for Explicit Solvent MD Babban Mia (Tue Aug 09 2011 - 04:16:03 CDT)
Command line for thickness parameter Guenegou, Guillaume [ORDFR] (Tue Aug 09 2011 - 03:46:46 CDT)
- Re: Command line for thickness parameter Cun Zhang (Tue Aug 09 2011 - 07:56:27 CDT)
How to cionize DNA? example needed! Bikan Tan (Mon Aug 08 2011 - 18:59:19 CDT)
Vmd molecule rotation and translation Anna (Mon Aug 08 2011 - 18:41:49 CDT)
- Fwd: Vmd molecule rotation and translation Anna (Mon Aug 08 2011 - 19:45:53 CDT)
- Re: Vmd molecule rotation and translation Cun Zhang (Mon Aug 08 2011 - 21:34:01 CDT)
  - Re: Vmd molecule rotation and translation Anna (Tue Aug 09 2011 - 01:27:37 CDT)
script KIRTANA S (Mon Aug 08 2011 - 16:09:45 CDT)
- Re: script Axel Kohlmeyer (Mon Aug 08 2011 - 22:37:15 CDT)
vmd Shesh Nath (Sat Aug 06 2011 - 02:04:59 CDT)
- Re: vmd sajad falsafi (Sat Aug 06 2011 - 05:55:14 CDT)
xtc plugin writing ability Francesco Oteri (Fri Aug 05 2011 - 07:39:59 CDT)
- Re: xtc plugin writing ability Axel Kohlmeyer (Fri Aug 05 2011 - 09:09:00 CDT)
specden - IR spectral density calculator plugin Kukol, Andreas (Thu Aug 04 2011 - 03:25:17 CDT)
- Re: specden - IR spectral density calculator plugin Axel Kohlmeyer (Thu Aug 04 2011 - 13:49:06 CDT)
problem to render .cms file AB (Thu Aug 04 2011 - 02:11:34 CDT)
- Re: problem to render .cms file John Stone (Fri Aug 05 2011 - 16:12:31 CDT)
making movie Moeed (Wed Aug 03 2011 - 20:56:47 CDT)
- Re: making movie John Stone (Fri Aug 05 2011 - 16:13:28 CDT)
  - Re: making movie Moeed (Tue Aug 23 2011 - 05:55:37 CDT)
.car or .xyz output winardi, erik (Wed Aug 03 2011 - 19:39:47 CDT)
- Re: .car or .xyz output John Stone (Fri Aug 05 2011 - 16:15:47 CDT)
Fwd: hbond analysis subrata paul (Wed Aug 03 2011 - 07:41:05 CDT)
- Re: Fwd: hbond analysis John Stone (Fri Aug 05 2011 - 16:28:17 CDT)
viewing dcd files Vivek Ranjan (Tue Aug 02 2011 - 19:51:37 CDT)
- RE: viewing dcd files Ismail, Mohd F. (Tue Aug 02 2011 - 23:49:04 CDT)
- Re: viewing dcd files Axel Kohlmeyer (Thu Aug 04 2011 - 13:44:33 CDT)
Problems running VMD-CUDA with GNU-Linux Francesco Pietra (Tue Aug 02 2011 - 16:52:01 CDT)
selection of sugars with VMD Molybdos Kirkimpolakis (Tue Aug 02 2011 - 14:11:49 CDT)
- Re: selection of sugars with VMD John Stone (Tue Aug 02 2011 - 17:09:34 CDT)
vmd 1.9 sur doesn't work AB (Tue Aug 02 2011 - 13:58:43 CDT)
VMD User Survey coming to your email inbox soon.... John Stone (Tue Aug 02 2011 - 10:19:24 CDT)
about psf file generation safron saif (Mon Aug 01 2011 - 07:22:08 CDT)
- Re: about psf file generation sajad falsafi (Tue Aug 02 2011 - 02:12:54 CDT)
  - Re: about psf file generation Axel Kohlmeyer (Tue Aug 02 2011 - 07:43:29 CDT)
moveby command hanif mahboobi (Sun Jul 31 2011 - 06:13:57 CDT)
- Re: moveby command Axel Kohlmeyer (Sun Jul 31 2011 - 09:50:29 CDT)
a file for commands of console JhonY. I. (Sat Jul 30 2011 - 08:55:14 CDT)
- Re: a file for commands of console Ajasja LjubetiÄ (Sat Jul 30 2011 - 09:40:23 CDT)
  - Re: a file for commands of console Nima Nouri (Sat Jul 30 2011 - 11:56:58 CDT)
different number of atoms in each frame of the trajectory file Debasis Sengupta (Fri Jul 29 2011 - 16:58:34 CDT)
- Re: different number of atoms in each frame of the trajectory file Axel Kohlmeyer (Fri Jul 29 2011 - 18:05:32 CDT)
'Hands-On' Workshop on Computational Biophysics using VMD and NAMD, October 17-21, 2011, Bremen, Germany David Brandon (Fri Jul 29 2011 - 14:15:06 CDT)
PDB manipulation nahren manuel (Fri Jul 29 2011 - 09:44:38 CDT)
- Re: PDB manipulation John Stone (Fri Aug 05 2011 - 16:35:52 CDT)
  - Re: PDB manipulation nahren manuel (Wed Aug 31 2011 - 05:07:03 CDT)
Nvidia quadro Fx1300 problem Federico Filomia (Fri Jul 29 2011 - 03:55:25 CDT)
- Re: Nvidia quadro Fx1300 problem John Stone (Fri Jul 29 2011 - 09:57:18 CDT)
  - Re: Nvidia quadro Fx1300 problem Federico Filomia (Mon Aug 01 2011 - 02:25:42 CDT)
- Re: Nvidia quadro Fx1300 problem Axel Kohlmeyer (Fri Jul 29 2011 - 10:39:19 CDT)
converting .dx volumetric data to 2D isocontour Raul Araya (Thu Jul 28 2011 - 12:31:37 CDT)
- Re: converting .dx volumetric data to 2D isocontour John Stone (Tue Aug 02 2011 - 16:53:16 CDT)
creating chiral molecules Peyman Z.Moghadam (Thu Jul 28 2011 - 04:21:16 CDT)
- Re: creating chiral molecules Ajasja LjubetiÄ (Thu Jul 28 2011 - 05:09:29 CDT)
How to save image in SVG format? ºÎØ¹»Ô (Tue Jul 26 2011 - 00:48:28 CDT)
- Re: How to save image in SVG format? Axel Kohlmeyer (Tue Jul 26 2011 - 01:36:14 CDT)
loading saved state from command line Erik Nordgren (Mon Jul 25 2011 - 19:12:03 CDT)
- Re: loading saved state from command line Erik Nordgren (Mon Jul 25 2011 - 19:28:30 CDT)
- Re: loading saved state from command line Ajasja LjubetiÄ (Tue Jul 26 2011 - 01:47:56 CDT)
Question about eval Pavan Ghatty (Mon Jul 25 2011 - 13:51:53 CDT)
- Re: Question about eval Axel Kohlmeyer (Mon Jul 25 2011 - 14:33:37 CDT)
  - Re: Question about eval Pavan Ghatty (Tue Jul 26 2011 - 08:45:56 CDT)
  - Re: Question about eval Pavan Ghatty (Tue Jul 26 2011 - 11:14:15 CDT)
    - Re: Question about eval John Stone (Tue Jul 26 2011 - 11:40:45 CDT)
Understand a script Sara baretller (Mon Jul 25 2011 - 08:35:51 CDT)
- Re: Understand a script Bjoern Olausson (Mon Jul 25 2011 - 10:05:59 CDT)
  - Re: Understand a script Axel Kohlmeyer (Mon Jul 25 2011 - 10:50:47 CDT)
- Re: Understand a script Axel Kohlmeyer (Mon Jul 25 2011 - 10:23:31 CDT)
  - Re: Understand a script Ajasja LjubetiÄ (Tue Jul 26 2011 - 03:54:58 CDT)
- Re: Understand a script Paul VanAllsburg (Mon Jul 25 2011 - 10:58:51 CDT)
Re: namd-l: how to generate transparent figures? BIN ZHANG (Sun Jul 24 2011 - 11:31:04 CDT)
- Re: namd-l: how to generate transparent figures? Axel Kohlmeyer (Mon Jul 25 2011 - 03:48:10 CDT)
- Re: Re: namd-l: how to generate transparent figures? Dudo (Mon Jul 25 2011 - 05:13:50 CDT)
  - Re: Re: namd-l: how to generate transparent figures? Jérôme Hénin (Mon Jul 25 2011 - 07:19:40 CDT)
cyclic peptides Alisha \ (Fri Jul 22 2011 - 13:09:55 CDT)
SOLVED: Failure to run namd-cuda with gtx-470 Francesco Pietra (Fri Jul 22 2011 - 09:56:34 CDT)
ViewChangerRender (VCR) plug-in Nuno Sousa Cerqueira (Thu Jul 21 2011 - 11:53:32 CDT)
Novint Falcon in VMD - help with setup Filip Persson (Wed Jul 20 2011 - 05:12:44 CDT)
MDFF problem hamze rahimi (Tue Jul 19 2011 - 23:13:05 CDT)
about docking with VMD Hui WEI (Tue Jul 19 2011 - 16:37:36 CDT)
- Re: about docking with VMD Cristina Rodríguez (Tue Jul 19 2011 - 17:34:25 CDT)
- Re: about docking with VMD Nuno Sousa Cerqueira (Wed Jul 20 2011 - 10:32:41 CDT)
Mutating a residue to a nonstandard amino acid Alisha \ (Tue Jul 19 2011 - 16:14:56 CDT)
- Re: Mutating a residue to a nonstandard amino acid Ajasja LjubetiÄ (Wed Jul 20 2011 - 16:57:49 CDT)
AMBER coordinates with periodic box Guenegou, Guillaume [ORDFR] (Tue Jul 19 2011 - 08:18:44 CDT)
- Re: AMBER coordinates with periodic box John Stone (Wed Jul 20 2011 - 13:41:23 CDT)
shades of licorice representation maria goranovic (Tue Jul 19 2011 - 07:53:52 CDT)
- Re: shades of licorice representation Axel Kohlmeyer (Tue Jul 19 2011 - 08:44:13 CDT)
  - Re: shades of licorice representation maria goranovic (Tue Jul 19 2011 - 08:52:19 CDT)
    - Re: shades of licorice representation Axel Kohlmeyer (Tue Jul 19 2011 - 10:02:52 CDT)
- Re: shades of licorice representation Boris Steipe (Tue Jul 19 2011 - 10:10:01 CDT)
- RE: shades of licorice representation Mark Cunningham (Tue Jul 19 2011 - 11:53:54 CDT)
  - Re: shades of licorice representation Hurt, Darrell (NIH/NIAID) [E] (Tue Jul 19 2011 - 14:24:42 CDT)
- Re: shades of licorice representation Sébastien Légaré (Wed Oct 09 2013 - 23:42:09 CDT)
RE.: Re: VMD and MDFF: ssrestraints package error message under Windows Nicolas Coudray (Mon Jul 18 2011 - 14:46:13 CDT)
how to change working directory of VMD? Esam Tolba (Mon Jul 18 2011 - 14:02:17 CDT)
- Re: how to change working directory of VMD? sajad falsafi (Tue Jul 19 2011 - 14:02:57 CDT)
  - Re: how to change working directory of VMD? Esam Tolba (Tue Jul 19 2011 - 18:16:29 CDT)
    - Re: how to change working directory of VMD? Nima Nouri (Wed Jul 20 2011 - 05:42:55 CDT)
script KIRTANA S (Mon Jul 18 2011 - 13:20:52 CDT)
Hydration dynamics:Phrase selection problem in vmd Kartheek (Mon Jul 18 2011 - 07:09:02 CDT)
- Re: Hydration dynamics:Phrase selection problem in vmd Axel Kohlmeyer (Mon Jul 18 2011 - 09:40:28 CDT)
zinc-finger protein simulation hamze rahimi (Mon Jul 18 2011 - 06:55:08 CDT)
calculate atom distance between two chain hamze rahimi (Mon Jul 18 2011 - 06:31:04 CDT)
- Re: calculate atom distance between two chain John Stone (Mon Jul 18 2011 - 09:57:59 CDT)
Problem of installing VMD 1.8.3 on Fedora14 Tatyana Sysoeva (Sun Jul 17 2011 - 15:42:28 CDT)
- Re: Problem of installing VMD 1.8.3 on Fedora14 Axel Kohlmeyer (Sun Jul 17 2011 - 16:52:34 CDT)
autoionize adds too many ions Edward Lyman (Fri Jul 15 2011 - 14:34:48 CDT)
- Re: autoionize adds too many ions Leonardo Trabuco (Wed Jul 20 2011 - 09:41:03 CDT)
  - RE: autoionize adds too many ions JC Gumbart (Wed Jul 20 2011 - 10:20:35 CDT)
    - Re: autoionize adds too many ions Leonardo Trabuco (Wed Jul 20 2011 - 10:30:02 CDT)
  - RE: autoionize adds too many ions Goldsmith, Jacob (Wed Jul 20 2011 - 12:10:28 CDT)
angle between two domains connected at a hinge maria goranovic (Fri Jul 15 2011 - 08:35:52 CDT)
- Re: angle between two domains connected at a hinge sajad falsafi (Fri Jul 15 2011 - 11:51:28 CDT)
hi kanchi subbarao rao (Fri Jul 15 2011 - 04:43:19 CDT)
Initial configurations / topology for LAMMPS molecular dynamics (Thu Jul 14 2011 - 15:22:41 CDT)
- Re: [lammps-users] Initial configurations / topology for LAMMPS Axel Kohlmeyer (Thu Jul 14 2011 - 15:29:08 CDT)
  - Re: [lammps-users] Initial configurations / topology for LAMMPS Anna (Thu Jul 14 2011 - 17:17:56 CDT)
Implicit Ligand Sampling Jacopo Sgrignani (Thu Jul 14 2011 - 14:50:21 CDT)
Implicit Ligand Sampling Jacopo Sgrignani (Thu Jul 14 2011 - 11:05:37 CDT)
How to change the VMD working Directory Esam Tolba (Thu Jul 14 2011 - 09:10:17 CDT)
- Re: How to change the VMD working Directory Axel Kohlmeyer (Thu Jul 14 2011 - 09:58:26 CDT)
Add user output to DCD trajectories Nima Nouri (Thu Jul 14 2011 - 05:18:29 CDT)
- Re: Add user output to DCD trajectories Axel Kohlmeyer (Thu Jul 14 2011 - 09:23:45 CDT)
  - Re: Add user output to DCD trajectories Nima Nouri (Thu Jul 21 2011 - 18:41:05 CDT)
script KIRTANA S (Tue Jul 12 2011 - 11:12:41 CDT)
- Re: script Ajasja LjubetiÄ (Tue Jul 12 2011 - 12:08:12 CDT)
- Re: script Axel Kohlmeyer (Tue Jul 12 2011 - 11:58:55 CDT)
  - Re: script Ajasja LjubetiÄ (Tue Jul 12 2011 - 13:01:26 CDT)
Retrieving Cremer-Pople parameters Mr Bernard Ramos (Tue Jul 12 2011 - 07:40:05 CDT)
- Re: Retrieving Cremer-Pople parameters Axel Kohlmeyer (Tue Jul 12 2011 - 09:03:56 CDT)
  - Re: Retrieving Cremer-Pople parameters John Stone (Tue Jul 12 2011 - 09:13:36 CDT)
    - Re: Retrieving Cremer-Pople parameters Payne, Christy (Tue Jul 12 2011 - 10:32:24 CDT)
  - Re: Retrieving Cremer-Pople parameters Payne, Christy (Tue Jul 12 2011 - 10:31:26 CDT)
stereo anaglyph rendering thiru pathi (Sun Jul 10 2011 - 01:47:59 CDT)
- Re: stereo anaglyph rendering Axel Kohlmeyer (Sun Jul 10 2011 - 05:36:00 CDT)
  - Re: stereo anaglyph rendering thiru pathi (Sun Jul 10 2011 - 07:18:29 CDT)
    - Re: stereo anaglyph rendering John Stone (Sun Jul 10 2011 - 22:17:20 CDT)
PBCwrap tools Simulation Biology (Sat Jul 09 2011 - 17:48:29 CDT)
- Re: PBCwrap tools Axel Kohlmeyer (Sat Jul 09 2011 - 18:33:24 CDT)
  - Re: PBCwrap tools Molybdos Kirkimpolakis (Sun Jul 10 2011 - 00:17:29 CDT)
Does this work with VMD: Nvidia 3DVision Glasses + SyncMaster 2233RZ + GTX 580 + Win7? Ajasja LjubetiÄ (Sat Jul 09 2011 - 17:06:19 CDT)
- Re: Does this work with VMD: Nvidia 3DVision Glasses + SyncMaster 2233RZ + GTX 580 + Win7? John Stone (Sat Jul 09 2011 - 22:20:20 CDT)
import selection in array for script KIRTANA S (Fri Jul 08 2011 - 14:37:11 CDT)
- Re: import selection in array for script Axel Kohlmeyer (Fri Jul 08 2011 - 15:04:46 CDT)
  - Re: import selection in array for script KIRTANA S (Fri Jul 08 2011 - 15:36:50 CDT)
    - Re: import selection in array for script John Stone (Tue Jul 12 2011 - 13:04:43 CDT)
Quadro FX1800 , Stereo and VMD Vlad Cojocaru (Fri Jul 08 2011 - 09:25:33 CDT)
- Re: Quadro FX1800 , Stereo and VMD John Stone (Fri Jul 08 2011 - 10:41:12 CDT)
  - Re: Quadro FX1800 , Stereo and VMD Vlad Cojocaru (Fri Jul 08 2011 - 11:26:17 CDT)
    - RE: Quadro FX1800 , Stereo and VMD Jacob Story (Fri Jul 08 2011 - 13:35:44 CDT)
- RE: Quadro FX1800 , Stereo and VMD Jacob Story (Fri Jul 08 2011 - 11:23:30 CDT)
how to draw different set of points for different frames in a trajectory my script does not work maria goranovic (Fri Jul 08 2011 - 07:59:10 CDT)
- Re: how to draw different set of points for different frames in a trajectory my script does not work Axel Kohlmeyer (Fri Jul 08 2011 - 08:31:17 CDT)
  - Re: how to draw different set of points for different frames in a trajectory my script does not work maria goranovic (Fri Jul 08 2011 - 09:56:14 CDT)
Pucker parameters Payne, Christy (Thu Jul 07 2011 - 14:35:18 CDT)
- Re: Pucker parameters John Stone (Tue Jul 12 2011 - 12:53:39 CDT)
Salt brigde Christian Wohlschlager (Thu Jul 07 2011 - 01:06:51 CDT)
- Re: Salt brigde John Stone (Thu Jul 07 2011 - 13:01:56 CDT)
  - Re: Salt brigde Jérôme Hénin (Thu Jul 07 2011 - 15:32:27 CDT)
script KIRTANA S (Wed Jul 06 2011 - 17:04:29 CDT)
- Re: script Axel Kohlmeyer (Wed Jul 06 2011 - 19:01:31 CDT)
On Cremer-Pople ring puckering Mr Bernard Ramos (Wed Jul 06 2011 - 14:13:05 CDT)
VMD and MDFF: ssrestraints package error message under Windows Nicolas Coudray (Wed Jul 06 2011 - 13:55:21 CDT)
- Re: VMD and MDFF: ssrestraints package error message under Windows Leonardo Trabuco (Fri Jul 08 2011 - 03:07:06 CDT)
Problem with for loop. Sara baretller (Wed Jul 06 2011 - 09:38:20 CDT)
- Re: Problem with for loop. Sara baretller (Wed Jul 06 2011 - 10:04:01 CDT)
  - Re: Re: Problem with for loop. Axel Kohlmeyer (Wed Jul 06 2011 - 10:57:44 CDT)
  - RE: Re: Problem with for loop. Mark Cunningham (Wed Jul 06 2011 - 12:34:36 CDT)
- Re: Problem with for loop. Axel Kohlmeyer (Wed Jul 06 2011 - 10:26:10 CDT)
  - Re: Problem with for loop. Sara baretller (Fri Jul 08 2011 - 09:52:16 CDT)
average radius of cavity over many frames from hole maria goranovic (Wed Jul 06 2011 - 02:28:49 CDT)
Distance between atoms in frame snoze pa (Tue Jul 05 2011 - 18:12:31 CDT)
- Re: Distance between atoms in frame snoze pa (Tue Jul 05 2011 - 19:12:47 CDT)
  - Re: Distance between atoms in frame Axel Kohlmeyer (Tue Jul 05 2011 - 20:10:04 CDT)
    - Re: Distance between atoms in frame sajad falsafi (Wed Jul 06 2011 - 05:56:58 CDT)
    - Re: Distance between atoms in frame snoze pa (Wed Jul 06 2011 - 09:53:32 CDT)
- RE: Distance between atoms in frame Mark Cunningham (Tue Jul 05 2011 - 21:09:24 CDT)
qpt_conv command of Hole is interactive, how to automate it for multiple frames? maria goranovic (Tue Jul 05 2011 - 10:05:55 CDT)
- Re: qpt_conv command of Hole is interactive, how to automate it for multiple frames? maria goranovic (Thu Jul 07 2011 - 05:21:00 CDT)
  - Re: qpt_conv command of Hole is interactive, how to automate it for multiple frames? John Stone (Tue Jul 12 2011 - 13:08:13 CDT)
    - Re: qpt_conv command of Hole is interactive, how to automate it for multiple frames? maria goranovic (Tue Jul 12 2011 - 14:22:35 CDT)
File as video safron saif (Tue Jul 05 2011 - 00:02:36 CDT)
- Re: File as video sajad falsafi (Tue Jul 05 2011 - 03:25:15 CDT)
- Re: File as video Bjoern Olausson (Tue Jul 05 2011 - 03:33:13 CDT)
New Multi-platform Surface and volume Calculator João Ribeiro (Mon Jul 04 2011 - 16:06:53 CDT)
Computer hangs on trying to launch VMD CUDA Francesco Pietra (Mon Jul 04 2011 - 02:19:02 CDT)
- Re: Computer hangs on trying to launch VMD CUDA John Stone (Tue Jul 05 2011 - 14:01:24 CDT)
  - Re: Computer hangs on trying to launch VMD CUDA Axel Kohlmeyer (Tue Jul 05 2011 - 15:08:03 CDT)
contacts and pbc Jesper Sørensen (Sun Jul 03 2011 - 08:39:02 CDT)
- Re: contacts and pbc Axel Kohlmeyer (Sun Jul 03 2011 - 11:21:39 CDT)
  - RE: contacts and pbc Jesper Sørensen (Sun Jul 03 2011 - 11:30:43 CDT)
    - Re: contacts and pbc John Stone (Tue Jul 05 2011 - 13:59:28 CDT)
    - RE: contacts and pbc Jesper Sørensen (Wed Jul 06 2011 - 03:30:37 CDT)
Patchlet for MacOS 32/64-bit compilation FX (Sat Jul 02 2011 - 05:13:21 CDT)
A patch for OFF import and a question about representation of surfaces FX (Sat Jul 02 2011 - 05:08:08 CDT)
- Re: A patch for OFF import and a question about representation of surfaces John Stone (Tue Jul 12 2011 - 13:22:54 CDT)
Problem with loop. it s not going to the next peptide Sara baretller (Fri Jul 01 2011 - 13:13:14 CDT)
- Re: Problem with loop. it s not going to the next peptide Sara baretller (Fri Jul 01 2011 - 16:35:28 CDT)
  - Re: Problem with loop. it s not going to the next peptide Axel Kohlmeyer (Fri Jul 01 2011 - 17:06:25 CDT)
catdcd and velocity dcd file arash azari (Fri Jul 01 2011 - 10:06:11 CDT)
- Re: catdcd and velocity dcd file Axel Kohlmeyer (Fri Jul 01 2011 - 10:45:16 CDT)
VMD scripting: Perform PBCwrap+fitframes on several dcd files Filip Persson (Fri Jul 01 2011 - 08:03:26 CDT)
VMD atom NUMER problem snoze pa (Wed Jun 29 2011 - 15:07:27 CDT)
- Re: VMD atom NUMER problem John Stone (Wed Jun 29 2011 - 15:21:41 CDT)
  - Re: VMD atom NUMER problem snoze pa (Wed Jun 29 2011 - 15:24:44 CDT)
    - Re: VMD atom NUMER problem John Stone (Wed Jun 29 2011 - 17:25:42 CDT)
H-bond analysis Rupashree Shyama Ray (Wed Jun 29 2011 - 09:15:50 CDT)
About psf file safron saif (Wed Jun 29 2011 - 04:02:57 CDT)
- Re: About psf file Axel Kohlmeyer (Wed Jun 29 2011 - 08:31:02 CDT)
Installation problem -Solvate mohan maruthi sena (Tue Jun 28 2011 - 23:06:58 CDT)
- Re: Installation problem -Solvate Axel Kohlmeyer (Wed Jun 29 2011 - 05:25:15 CDT)
Normalization of RDFs in gofr plugin gaborekt_at_duq.edu (Tue Jun 28 2011 - 12:34:37 CDT)
- Re: Normalization of RDFs in gofr plugin Axel Kohlmeyer (Tue Jun 28 2011 - 13:06:49 CDT)
  - Re: Normalization of RDFs in gofr plugin gaborekt_at_duq.edu (Tue Jun 28 2011 - 16:05:59 CDT)
Bond between two hydrogen atoms Debasis Sengupta (Tue Jun 28 2011 - 12:23:05 CDT)
- Re: Bond between two hydrogen atoms Axel Kohlmeyer (Tue Jun 28 2011 - 12:56:11 CDT)
Changing representations on a per-atom per-timestep basis J. Nathan Scott (Tue Jun 28 2011 - 11:34:19 CDT)
- Re: Changing representations on a per-atom per-timestep basis Axel Kohlmeyer (Tue Jun 28 2011 - 12:14:19 CDT)
- Re: Changing representations on a per-atom per-timestep basis Ajasja LjubetiÄ (Tue Jun 28 2011 - 12:48:11 CDT)
Total Dipole Moment Chathurika Abeyrathne (Tue Jun 28 2011 - 04:48:54 CDT)
- Re: Total Dipole Moment Axel Kohlmeyer (Tue Jun 28 2011 - 09:48:33 CDT)
  - Re: Total Dipole Moment Chathurika Abeyrathne (Tue Jun 28 2011 - 19:56:41 CDT)
VMD-I: rsmd calculation nataliaperez_at_infomed.sld.cu (Mon Jun 27 2011 - 14:57:41 CDT)
- Re: VMD-I: rsmd calculation Axel Kohlmeyer (Tue Jun 28 2011 - 09:53:26 CDT)
VMD-I: nataliaperez_at_infomed.sld.cu (Mon Jun 27 2011 - 11:21:02 CDT)
best fit lines through two selections per each molecule ( I have 80 molecules) and the angle with another vector for each molecule Sara Biocomputation (Mon Jun 27 2011 - 10:39:30 CDT)
- Re: best fit lines through two selections per each molecule ( I have 80 molecules) and the angle with another vector for each molecule Sara Biocomputation (Mon Jun 27 2011 - 10:44:48 CDT)
  - Re: Re: best fit lines through two selections per each molecule ( I have 80 molecules) and the angle with another vector for each molecule Axel Kohlmeyer (Tue Jun 28 2011 - 09:55:40 CDT)
color trajectory using specific values rather than color scale Brian Puchala (Mon Jun 27 2011 - 09:55:05 CDT)
- Re: color trajectory using specific values rather than color scale Axel Kohlmeyer (Mon Jun 27 2011 - 10:32:51 CDT)
  - Re: color trajectory using specific values rather than color scale John Stone (Mon Jun 27 2011 - 10:42:31 CDT)
- Re: color trajectory using specific values rather than color scale Jérôme Hénin (Mon Jun 27 2011 - 11:20:41 CDT)
- Re: color trajectory using specific values rather than color scale Joshua A. Anderson (Mon Jun 27 2011 - 11:50:44 CDT)
Molefacture: creating model helices Neelanjana Sengupta (Mon Jun 27 2011 - 06:31:03 CDT)
- Re: Molefacture: creating model helices Ajasja LjubetiÄ (Mon Jun 27 2011 - 07:10:23 CDT)
protein-water RDF divya nayar (Mon Jun 27 2011 - 01:15:21 CDT)
- Re: protein-water RDF Ajasja LjubetiÄ (Mon Jun 27 2011 - 03:05:03 CDT)
- Re: protein-water RDF Axel Kohlmeyer (Mon Jun 27 2011 - 09:08:35 CDT)
not to display atoms in certain region pouyan farzinpor (Fri Jun 24 2011 - 14:53:03 CDT)
- Re: not to display atoms in certain region John Stone (Fri Jun 24 2011 - 15:01:06 CDT)
  - Re: not to display atoms in certain region pouyan farzinpor (Fri Jun 24 2011 - 15:29:11 CDT)
    - Re: not to display atoms in certain region John Stone (Fri Jun 24 2011 - 15:45:31 CDT)
    - Re: not to display atoms in certain region Axel Kohlmeyer (Fri Jun 24 2011 - 16:09:33 CDT)
align axes Adrian Roitberg (Wed Jun 22 2011 - 14:17:50 CDT)
- Re: align axes Axel Kohlmeyer (Thu Jun 23 2011 - 13:42:44 CDT)
  - Re: align axes Toni Giorgino (Thu Jun 23 2011 - 14:50:14 CDT)
VMD not working on MacOS X 10.6.7 Daniel Aiello (Thu Jun 23 2011 - 12:26:20 CDT)
- Re: VMD not working on MacOS X 10.6.7 John Stone (Thu Jun 23 2011 - 12:37:18 CDT)
volume of hydration shells divya nayar (Thu Jun 23 2011 - 06:12:35 CDT)
- Re: volume of hydration shells Boris Steipe (Thu Jun 23 2011 - 09:00:10 CDT)
hydration shell volume divya nayar (Thu Jun 23 2011 - 01:43:55 CDT)
finding water around protein divya nayar (Wed Jun 22 2011 - 23:55:35 CDT)
can not compile VMD plugin hongphuc nguyen (Wed Jun 22 2011 - 22:15:55 CDT)
- Re: can not compile VMD plugin hongphuc nguyen (Wed Jun 22 2011 - 22:48:34 CDT)
Dividing the water in groups like WAT1; WAT2; WAT3 PAUL NEWMAN (Wed Jun 22 2011 - 20:41:32 CDT)
APBS installation problem Sangita Kachhap (Wed Jun 22 2011 - 12:44:34 CDT)
APBS installation problem Sangita Kachhap (Wed Jun 22 2011 - 11:23:19 CDT)
- Re: APBS installation problem Axel Kohlmeyer (Wed Jun 22 2011 - 13:17:30 CDT)
Rotating a non-coordinate file Reza Salari (Wed Jun 22 2011 - 04:45:53 CDT)
- Re: Rotating a non-coordinate file Axel Kohlmeyer (Wed Jun 22 2011 - 05:56:04 CDT)
  - Re: Rotating a non-coordinate file Reza Salari (Wed Jun 22 2011 - 12:50:10 CDT)
Reading PSF with extended atom types Gianluca Interlandi (Wed Jun 22 2011 - 00:05:18 CDT)
problem in launching vmd kaustubh joshi (Tue Jun 21 2011 - 07:21:17 CDT)
- Re: problem in launching vmd John Stone (Tue Jun 21 2011 - 08:57:50 CDT)
can not import Hessian/charge from single point calculation hongphuc nguyen (Tue Jun 21 2011 - 03:14:15 CDT)
- RE: can not import Hessian/charge from single point calculation Bennion, Brian (Tue Jun 21 2011 - 12:04:46 CDT)
  - RE: can not import Hessian/charge from single point calculation Bennion, Brian (Wed Jun 22 2011 - 12:55:36 CDT)
mutate amino acid hamze rahimi (Sun Jun 19 2011 - 02:25:05 CDT)
how to get pqr format file with catdcd jnsong (Sat Jun 18 2011 - 01:25:15 CDT)
- Re: how to get pqr format file with catdcd John Stone (Mon Jun 20 2011 - 15:34:01 CDT)
  - Re: how to get pqr format file with catdcd jnsong (Mon Jun 20 2011 - 22:00:33 CDT)
    - Re: how to get pqr format file with catdcd John Stone (Tue Jun 21 2011 - 09:10:16 CDT)
    - Re: how to get pqr format file with catdcd jnsong (Wed Jun 22 2011 - 02:22:59 CDT)
Re: Fwd: "cuda error cudastreamcreate", Francesco Pietra (Fri Jun 17 2011 - 00:50:05 CDT)
- Re: Re: Fwd: "cuda error cudastreamcreate", John Stone (Fri Jun 17 2011 - 01:22:50 CDT)
  - Re: Re: Fwd: "cuda error cudastreamcreate", Francesco Pietra (Fri Jun 17 2011 - 02:36:49 CDT)
invisible files in windows Michael Zimmermann (Wed Jun 15 2011 - 16:57:39 CDT)
- Re: invisible files in windows Axel Kohlmeyer (Wed Jun 15 2011 - 17:37:36 CDT)
- Re: invisible files in windows Denny Bromley (Wed Jun 15 2011 - 20:41:57 CDT)
  - Re: invisible files in windows Ajasja LjubetiÄ (Thu Jun 16 2011 - 02:27:34 CDT)
    - Question about "orient" script Masaki UNNO (Thu Jun 16 2011 - 04:33:51 CDT)
    - Re: Question about "orient" script John Stone (Tue Jun 21 2011 - 13:15:44 CDT)
rdf for specific group of atoms Rupashree Shyama Ray (Wed Jun 15 2011 - 08:29:29 CDT)
- Re: rdf for specific group of atoms Axel Kohlmeyer (Wed Jun 15 2011 - 09:14:46 CDT)
water is forming bonds between hydrogens PAUL NEWMAN (Wed Jun 15 2011 - 00:25:46 CDT)
- Re: water is forming bonds between hydrogens Magnus Andersson (Wed Jun 15 2011 - 10:01:55 CDT)
- Re: water is forming bonds between hydrogens Axel Kohlmeyer (Wed Jun 15 2011 - 10:38:26 CDT)
water is forming bonds between oxigens PAUL NEWMAN (Wed Jun 15 2011 - 00:01:37 CDT)
color sidechains differently Magnus Andersson (Tue Jun 14 2011 - 21:30:10 CDT)
- Re: color sidechains differently Axel Kohlmeyer (Tue Jun 14 2011 - 22:21:07 CDT)
Invitation to connect on LinkedIn Iman Salehinia via LinkedIn (Tue Jun 14 2011 - 18:31:13 CDT)
Vmd vs QUANTA Sajad Ahrari (Tue Jun 14 2011 - 01:46:38 CDT)
Vmd vs QUANTA Sajad Ahrari (Mon Jun 13 2011 - 23:59:04 CDT)
- Re: Vmd vs QUANTA Axel Kohlmeyer (Tue Jun 14 2011 - 04:55:11 CDT)
VolMap Tool Question Joe Janicki (Mon Jun 13 2011 - 13:36:18 CDT)
- Re: VolMap Tool Question Axel Kohlmeyer (Mon Jun 13 2011 - 14:31:47 CDT)
showperiodic - not self? Jesper Sørensen (Mon Jun 13 2011 - 12:14:44 CDT)
- Re: showperiodic - not self? Axel Kohlmeyer (Mon Jun 13 2011 - 12:51:04 CDT)
cropping the missing residues from other PDB file Joyce Tan (Mon Jun 13 2011 - 09:37:14 CDT)
- Re: cropping the missing residues from other PDB file sarah k (Mon Jun 13 2011 - 10:19:05 CDT)
Using VMD/NAMD to construct Cyclodextrins using Chamm topologies Sam Wallace (Sun Jun 12 2011 - 21:34:17 CDT)
simulation in Nitrogen box sarah k (Sat Jun 11 2011 - 09:12:39 CDT)
- Re: simulation in Nitrogen box Axel Kohlmeyer (Sat Jun 11 2011 - 10:21:45 CDT)
  - Re: simulation in Nitrogen box sarah k (Sun Jun 12 2011 - 05:57:46 CDT)
    - Re: simulation in Nitrogen box PaweÅ‚ KÄ™dzierski (Sun Jun 12 2011 - 08:59:40 CDT)
create surface of overlapping VdW volume Dow Hurst (Fri Jun 10 2011 - 18:17:50 CDT)
- Re: create surface of overlapping VdW volume Dow Hurst (Sat Jun 11 2011 - 11:08:43 CDT)
Selecting multiple ranges Seibold, Stephen (Fri Jun 10 2011 - 09:28:48 CDT)
- Re: Selecting multiple ranges John Stone (Fri Jun 10 2011 - 09:43:48 CDT)
  - RE: Selecting multiple ranges Seibold, Stephen (Fri Jun 10 2011 - 10:05:21 CDT)
- Re: Selecting multiple ranges Salvatore Mario Cosseddu (Fri Jun 10 2011 - 11:20:21 CDT)
Problem using rotate command in a script ...(2) Alberto Sergio Garay (Fri Jun 10 2011 - 07:10:05 CDT)
Problem using rotate command in a script ...(2) Alberto Sergio Garay (Thu Jun 09 2011 - 13:11:01 CDT)
- Re: Problem using rotate command in a script ...(2) John Stone (Fri Jun 10 2011 - 09:40:45 CDT)
Problem using rotate command in a script .... Alberto Sergio Garay (Thu Jun 09 2011 - 09:36:33 CDT)
- Re: Problem using rotate command in a script .... John Stone (Thu Jun 09 2011 - 10:53:17 CDT)
Adding missing residues Joyce Tan (Thu Jun 09 2011 - 01:50:05 CDT)
Tracing distances among atoms in a MD simulation DCM CA (Wed Jun 08 2011 - 20:57:17 CDT)
- Re: Tracing distances among atoms in a MD simulation Jérôme Hénin (Thu Jun 09 2011 - 02:25:23 CDT)
parameterization tool Bennion, Brian (Wed Jun 08 2011 - 16:14:31 CDT)
- Add solvation box tool Dong Luo (Thu Jun 09 2011 - 09:46:33 CDT)
- Re: parameterization tool sajad falsafi (Thu Jun 09 2011 - 11:40:57 CDT)
  - RE: parameterization tool Bennion, Brian (Thu Jun 09 2011 - 11:52:29 CDT)
xy diagonal Magnus Andersson (Wed Jun 08 2011 - 12:29:30 CDT)
- Re: xy diagonal Davide Provasi (Wed Jun 08 2011 - 13:23:40 CDT)
Problem using rotate in a script .... Alberto Sergio Garay (Wed Jun 08 2011 - 10:33:49 CDT)
VMD on Intel core i3 + Ubuntu masci002_at_umn.edu (Tue Jun 07 2011 - 19:03:26 CDT)
- Re: VMD on Intel core i3 + Ubuntu John Stone (Tue Jun 07 2011 - 19:31:07 CDT)
  - Re: VMD on Intel core i3 + Ubuntu John Stone (Tue Jun 07 2011 - 22:48:47 CDT)
    - Re: VMD on Intel core i3 + Ubuntu masci002_at_umn.edu (Wed Jun 08 2011 - 18:34:55 CDT)
Problem with Starting vmd after Debian System Upgrade Angelo Rossi (Tue Jun 07 2011 - 11:26:06 CDT)
- Re: Problem with Starting vmd after Debian System Upgrade Axel Kohlmeyer (Tue Jun 07 2011 - 12:19:42 CDT)
  - Re: Problem with Starting vmd after Debian System Upgrade Angelo R. Rossi (Wed Jun 08 2011 - 07:27:05 CDT)
VMD moviemaker KK Sahu (Tue Jun 07 2011 - 05:22:34 CDT)
saving dcd with less frames Joyce Tan (Tue Jun 07 2011 - 04:39:35 CDT)
- Re: saving dcd with less frames Axel Kohlmeyer (Tue Jun 07 2011 - 05:08:17 CDT)
- Re: saving dcd with less frames Bjoern Olausson (Tue Jun 07 2011 - 05:27:58 CDT)
VMD does not exit after running closest.tcl script in combination with bigdcd maria goranovic (Tue Jun 07 2011 - 04:01:34 CDT)
- Re: VMD does not exit after running closest.tcl script in combination with bigdcd Ajasja LjubetiÄ (Tue Jun 07 2011 - 09:02:10 CDT)
  - Re: VMD does not exit after running closest.tcl script in combination with bigdcd Ajasja LjubetiÄ (Tue Jun 07 2011 - 09:07:08 CDT)
Dipole Moment Monitoring Sally Fisher (Mon Jun 06 2011 - 21:10:57 CDT)
- Re: Dipole Moment Monitoring Axel Kohlmeyer (Mon Jun 06 2011 - 21:45:08 CDT)
topotools {.top} for Gromacs {.tpr} generation Lalit (Mon Jun 06 2011 - 18:19:21 CDT)
- Re: topotools {.top} for Gromacs {.tpr} generation Axel Kohlmeyer (Mon Jun 06 2011 - 18:26:46 CDT)
- Re: topotools {.top} for Gromacs {.tpr} generation Axel Kohlmeyer (Mon Jun 06 2011 - 19:14:57 CDT)
  - Re: topotools {.top} for Gromacs {.tpr} generation Lalit (Tue Jun 07 2011 - 15:12:29 CDT)
    - Re: topotools {.top} for Gromacs {.tpr} generation Axel Kohlmeyer (Tue Jun 07 2011 - 15:24:30 CDT)
Superimposition problem Qmer_AN?= (Mon Jun 06 2011 - 12:30:04 CDT)
Tachyon post-render commands under Win-XP Daniel Holloway (Mon Jun 06 2011 - 08:50:17 CDT)
- Re: Tachyon post-render commands under Win-XP Axel Kohlmeyer (Mon Jun 06 2011 - 09:25:14 CDT)
- Re: Tachyon post-render commands under Win-XP Ajasja LjubetiÄ (Mon Jun 06 2011 - 09:32:09 CDT)
  - Re: Tachyon post-render commands under Win-XP Daniel Holloway (Tue Jun 07 2011 - 05:07:42 CDT)
Fw: how do I show contacts with XXX angstroms between a protein and a ligand? sajad falsafi (Sun Jun 05 2011 - 08:06:56 CDT)
how do I show contacts with XXX angstroms between a protein and a ligand? Dennis N Bromley (Fri Jun 03 2011 - 22:27:58 CDT)
- Re: how do I show contacts with XXX angstroms between a protein and a ligand? sajad falsafi (Sat Jun 04 2011 - 08:26:14 CDT)
  - Re: how do I show contacts with XXX angstroms between a protein and a ligand? Dennis N Bromley (Sat Jun 04 2011 - 12:14:40 CDT)
  - Re: how do I show contacts with XXX angstroms between a protein and a ligand? sajad falsafi (Tue Jun 07 2011 - 04:55:18 CDT)
- Re: how do I show contacts with XXX angstroms between a protein and a ligand? Craig Knox (Mon Jun 06 2011 - 11:33:42 CDT)
questions about RBCG ½¹±ª (Fri Jun 03 2011 - 21:27:17 CDT)
submit VMD_SS script sajad falsafi (Fri Jun 03 2011 - 11:35:20 CDT)
Invitation to connect on LinkedIn Lucas FernÃ¡ndez Seivane via LinkedIn (Fri Jun 03 2011 - 02:30:33 CDT)
submit VMD_SS script sajad falsafi (Fri Jun 03 2011 - 00:59:22 CDT)
installation trouble Michael Zimmermann (Thu Jun 02 2011 - 23:00:40 CDT)
- Re: installation trouble John Stone (Thu Jun 02 2011 - 23:11:53 CDT)
  - Re: installation trouble Michael Zimmermann (Fri Jun 03 2011 - 09:38:46 CDT)
For loops decelerate Benjamin Hall (Thu Jun 02 2011 - 03:39:02 CDT)
- Re: For loops decelerate Axel Kohlmeyer (Thu Jun 02 2011 - 06:27:04 CDT)
  - Re: For loops decelerate Benjamin Hall (Fri Jun 03 2011 - 11:23:25 CDT)
  - Re: For loops decelerate John Stone (Mon Jun 06 2011 - 13:47:41 CDT)
    - Re: For loops decelerate Benjamin Hall (Mon Jun 06 2011 - 16:28:31 CDT)
    - Re: For loops decelerate Axel Kohlmeyer (Mon Jun 06 2011 - 16:36:31 CDT)
charge information for the PMEpot plugin Raul Araya (Wed Jun 01 2011 - 11:48:07 CDT)
- Re: charge information for the PMEpot plugin Axel Kohlmeyer (Wed Jun 01 2011 - 12:25:04 CDT)
.gro format to .pqr format Mona Habibi (Wed Jun 01 2011 - 10:17:20 CDT)
- Re: .gro format to .pqr format Axel Kohlmeyer (Wed Jun 01 2011 - 10:52:24 CDT)
Compiling plugins without netcdf Guido Polles (Wed Jun 01 2011 - 10:09:24 CDT)
- Re: Compiling plugins without netcdf John Stone (Wed Jun 01 2011 - 10:15:46 CDT)
  - Re: Compiling plugins without netcdf Guido Polles (Wed Jun 01 2011 - 12:59:50 CDT)
Re: [lammps-users] using topotools to view lammps output Axel Kohlmeyer (Wed Jun 01 2011 - 08:48:04 CDT)
Invitation to connect on LinkedIn masoud Kazemi via LinkedIn (Wed Jun 01 2011 - 07:55:20 CDT)
problem with bigdcd rmsd calculaton output Bian Li (Mon May 30 2011 - 22:22:48 CDT)
- Re: problem with bigdcd rmsd calculaton output Axel Kohlmeyer (Mon May 30 2011 - 23:16:30 CDT)
Issue with NAMD/VMD tutorial Matthew Bick (Mon May 30 2011 - 12:32:29 CDT)
- Re: Issue with NAMD/VMD tutorial Axel Kohlmeyer (Mon May 30 2011 - 13:15:58 CDT)
  - Re: Issue with NAMD/VMD tutorial Matthew Bick (Mon May 30 2011 - 14:03:30 CDT)
    - Re: Issue with NAMD/VMD tutorial Axel Kohlmeyer (Mon May 30 2011 - 14:49:19 CDT)
Save Coordinates for Multiple Loads Qmer_AN?= (Sun May 29 2011 - 09:14:25 CDT)
- Re: Save Coordinates for Multiple Loads Axel Kohlmeyer (Sun May 29 2011 - 10:17:22 CDT)
- Re: Save Coordinates for Multiple Loads Vlad Cojocaru (Sun May 29 2011 - 14:53:11 CDT)
  - Re: Save Coordinates for Multiple Loads Vlad Cojocaru (Mon May 30 2011 - 00:33:50 CDT)
Protein cavities BRAULIO VALDEBENITO MATURANA (Sat May 28 2011 - 23:26:02 CDT)
- Re: Protein cavities Axel Kohlmeyer (Sun May 29 2011 - 03:17:08 CDT)
  - Re: Protein cavities Francesco Oteri (Sun May 29 2011 - 07:09:59 CDT)
  - Re: Protein cavities BRAULIO VALDEBENITO MATURANA (Sun May 29 2011 - 16:42:33 CDT)
    - Re: Protein cavities Axel Kohlmeyer (Sun May 29 2011 - 17:31:44 CDT)
use variable in atomselect dhacademic (Fri May 27 2011 - 14:55:26 CDT)
- Re: use variable in atomselect Ajasja LjubetiÄ (Fri May 27 2011 - 16:28:34 CDT)
  - Re: use variable in atomselect Axel Kohlmeyer (Fri May 27 2011 - 17:05:16 CDT)
    - Re: use variable in atomselect Ajasja LjubetiÄ (Sat May 28 2011 - 02:24:03 CDT)
creating psf file seda demirci (Fri May 27 2011 - 10:13:05 CDT)
- Re: creating psf file John Stone (Fri May 27 2011 - 14:37:59 CDT)
Protein cavities BRAULIO FAVIÁN VALDEBENITO MATURANA (Thu May 26 2011 - 12:41:48 CDT)
- Re: Protein cavities John Stone (Fri May 27 2011 - 14:47:03 CDT)
  - RE: Protein cavities Irene Newhouse (Fri May 27 2011 - 16:52:50 CDT)
tips for an annoying aliasing task? Edward Lyman (Thu May 26 2011 - 10:33:27 CDT)
- RE: tips for an annoying aliasing task? Cosseddu, Salvatore (Thu May 26 2011 - 15:51:49 CDT)
  - Re: tips for an annoying aliasing task? Salvatore Mario Cosseddu (Fri May 27 2011 - 04:20:55 CDT)
measure fit - wrong alignment Eduardo Oliveira (Thu May 26 2011 - 05:56:40 CDT)
- Re: measure fit - wrong alignment Jérôme Hénin (Thu May 26 2011 - 07:43:12 CDT)
  - Re: measure fit - wrong alignment Axel Kohlmeyer (Thu May 26 2011 - 13:17:43 CDT)
surface of an atomic property Anna Amat (Wed May 25 2011 - 11:44:38 CDT)
- Re: surface of an atomic property Axel Kohlmeyer (Wed May 25 2011 - 14:01:44 CDT)
3Dconnexion SpaceNavigator (OS X) Hans Martin Senn (Wed May 25 2011 - 11:37:51 CDT)
- Re: 3Dconnexion SpaceNavigator (OS X) John Stone (Fri May 27 2011 - 14:54:34 CDT)
surface from a generic atomic property Anna Amat (Wed May 25 2011 - 11:15:11 CDT)
pbctools plugin & protein-bound ligand Irene Newhouse (Tue May 24 2011 - 14:36:12 CDT)
- Re: pbctools plugin & protein-bound ligand Olaf Lenz (Wed May 25 2011 - 02:01:11 CDT)
  - RE: pbctools plugin & protein-bound ligand Irene Newhouse (Wed May 25 2011 - 14:59:59 CDT)
trying to combine closewater.tcl with bigdcd.tcl error frame 3 out of range for molecule 0 maria goranovic (Tue May 24 2011 - 08:39:08 CDT)
- Re: trying to combine closewater.tcl with bigdcd.tcl error frame 3 out of range for molecule 0 Ajasja LjubetiÄ (Tue May 24 2011 - 09:48:15 CDT)
  - Re: trying to combine closewater.tcl with bigdcd.tcl error frame 3 out of range for molecule 0 maria goranovic (Tue May 24 2011 - 11:19:26 CDT)
size for render Kevin Knoops (Tue May 24 2011 - 06:01:15 CDT)
- Re: size for render Bjoern Olausson (Tue May 24 2011 - 06:34:49 CDT)
  - RE: size for render Jesper Sørensen (Tue May 24 2011 - 07:24:03 CDT)
- Re: size for render Axel Kohlmeyer (Tue May 24 2011 - 06:47:25 CDT)
vmd calculating wrong number of frames in xtc file using molinfo numframes ? maria goranovic (Mon May 23 2011 - 10:13:08 CDT)
- Re: vmd calculating wrong number of frames in xtc file using molinfo numframes ? Axel Kohlmeyer (Mon May 23 2011 - 11:11:52 CDT)
  - Re: vmd calculating wrong number of frames in xtc file using molinfo numframes ? maria goranovic (Tue May 24 2011 - 04:45:55 CDT)
- APBS plugin, created file pot-PE0.dx Ricardo Oliveira dos Santos Soares (Mon May 23 2011 - 14:55:00 CDT)
  - Re: APBS plugin, created file pot-PE0.dx John Stone (Mon May 23 2011 - 15:12:51 CDT)
    - Re: APBS plugin, created file pot-PE0.dx Ricardo Oliveira dos Santos Soares (Tue May 24 2011 - 13:39:56 CDT)
    - Re: APBS plugin, created file pot-PE0.dx John Stone (Fri May 27 2011 - 14:43:04 CDT)
problem in overlapping atoms Parul tew (Sun May 22 2011 - 05:01:31 CDT)
- problem in overlapping atoms Parul tew (Sun May 22 2011 - 05:02:18 CDT)
  - Re: problem in overlapping atoms Ajasja LjubetiÄ (Sun May 22 2011 - 05:52:14 CDT)
Non-cuda version of VMD on Linux? Ismail, Mohd F. (Sat May 21 2011 - 22:02:01 CDT)
- Re: Non-cuda version of VMD on Linux? John Stone (Sat May 21 2011 - 22:22:42 CDT)
  - RE: Non-cuda version of VMD on Linux? Ismail, Mohd F. (Sun May 22 2011 - 02:22:23 CDT)
    - Re: Non-cuda version of VMD on Linux? Axel Kohlmeyer (Sun May 22 2011 - 05:17:34 CDT)
color atom by stress Shaorui Yang (Sat May 21 2011 - 15:23:48 CDT)
- Re: color atom by stress Axel Kohlmeyer (Sat May 21 2011 - 16:25:18 CDT)
  - Re: color atom by stress Shaorui Yang (Sat May 21 2011 - 21:10:17 CDT)
    - Re: color atom by stress John Stone (Sat May 21 2011 - 22:55:46 CDT)
move volume file Lane Votapka (Fri May 20 2011 - 17:11:49 CDT)
- Re: move volume file Lane Votapka (Wed May 25 2011 - 13:17:26 CDT)
  - Mean value of el. potential ? Marek Maly (Wed May 25 2011 - 17:59:42 CDT)
antechamber for Windows Keith Battle (Fri May 20 2011 - 12:48:21 CDT)
- Re: antechamber for Windows John Stone (Fri May 27 2011 - 15:16:20 CDT)
Displaying protein AND ligand from an amber trajectory George Tzotzos (Fri May 20 2011 - 08:31:17 CDT)
- Re: Displaying protein AND ligand from an amber trajectory Axel Kohlmeyer (Fri May 20 2011 - 09:07:14 CDT)
- Re: Displaying protein AND ligand from an amber trajectory Ajasja LjubetiÄ (Fri May 20 2011 - 09:11:24 CDT)
  - Re: Displaying protein AND ligand from an amber trajectory George Tzotzos (Fri May 20 2011 - 09:16:14 CDT)
pbc unwrap not complete Nicola Giacche' (Fri May 20 2011 - 08:05:40 CDT)
- Re: pbc unwrap not complete Olaf Lenz (Mon May 23 2011 - 04:57:38 CDT)
  - Re: pbc unwrap not complete Nicola Giacche' (Tue May 24 2011 - 09:42:19 CDT)
Problems with APBS calculations Ramon Garduno-Juarez (Thu May 19 2011 - 20:51:53 CDT)
- Re: Problems with APBS calculations Chris Harrison (Thu May 19 2011 - 21:37:36 CDT)
  - Re: Problems with APBS calculations Ramon Garduno-Juarez (Fri May 20 2011 - 12:18:48 CDT)
Aligning two proteins of varying atom numbers ban arn (Thu May 19 2011 - 10:43:10 CDT)
- Re: Aligning two proteins of varying atom numbers Axel Kohlmeyer (Thu May 19 2011 - 11:17:37 CDT)
- Re: Aligning two proteins of varying atom numbers Joseph Bylund (Thu May 19 2011 - 11:31:52 CDT)
  - Re: Aligning two proteins of varying atom numbers ban arn (Thu May 19 2011 - 11:37:40 CDT)
indentified particular water molecule Sangita Kachhap (Thu May 19 2011 - 07:24:03 CDT)
aligning multiple trajectories to a single .pdb file andrew ritchie (Wed May 18 2011 - 13:30:54 CDT)
problem merging two identical proteins juan jesus sanchez sanchez (Wed May 18 2011 - 12:32:09 CDT)
reading .vel files and .veldcd files Mao Mao (Wed May 18 2011 - 10:50:46 CDT)
run and close vmd with bash script? Jorgen Simonsen (Wed May 18 2011 - 07:04:26 CDT)
- Re: run and close vmd with bash script? Axel Kohlmeyer (Wed May 18 2011 - 08:23:49 CDT)
  - Re: run and close vmd with bash script? Salvatore Mario Cosseddu (Wed May 18 2011 - 10:10:22 CDT)
    - Re: run and close vmd with bash script? Axel Kohlmeyer (Wed May 18 2011 - 10:42:53 CDT)
    - Re: run and close vmd with bash script? Salvatore Mario Cosseddu (Wed May 18 2011 - 11:21:35 CDT)
hi to all kanchi subbarao rao (Tue May 17 2011 - 11:34:04 CDT)
- Re: hi to all Ajasja LjubetiÄ (Tue May 17 2011 - 12:27:50 CDT)
- Re: hi to all Salvatore Mario Cosseddu (Tue May 17 2011 - 15:06:51 CDT)
- Re: hi to all Bjoern Olausson (Thu May 19 2011 - 04:15:26 CDT)
Tkcon on at startup Qmer_AN?= (Tue May 17 2011 - 11:00:19 CDT)
- Re: Tkcon on at startup John Stone (Tue May 17 2011 - 11:07:55 CDT)
Do psf generated by psfgen and psf produced by "$sel writepsf" function in VMD have different impact on MD simulation using NAMD? jnsong (Tue May 17 2011 - 08:54:54 CDT)
- Re: Do psf generated by psfgen and psf produced by "$sel writepsf" function in VMD have different impact on MD simulation using NAMD? Axel Kohlmeyer (Tue May 17 2011 - 09:44:26 CDT)
  - Re: Do psf generated by psfgen and psf produced by "$sel writepsf" function in VMD have different impact on MD simulation using NAMD? jnsong (Tue May 17 2011 - 21:42:42 CDT)
- Re: Do psf generated by psfgen and psf produced by "$sel writepsf" function in VMD have different impact on MD simulation using NAMD? John Stone (Tue May 17 2011 - 10:09:55 CDT)
  - Re: Do psf generated by psfgen and psf produced by "$sel writepsf" function in VMD have different impact on MD simulation using NAMD? jnsong (Tue May 17 2011 - 21:32:52 CDT)
convert prmtop to psf Jorgen Simonsen (Tue May 17 2011 - 04:17:33 CDT)
- Re: convert prmtop to psf Axel Kohlmeyer (Tue May 17 2011 - 05:56:15 CDT)
Re: error in movie generator Esam Tolba (Tue May 17 2011 - 03:57:06 CDT)
- Re: error in movie generator John Stone (Tue May 17 2011 - 10:11:16 CDT)
  - RE: error in movie generator Phelan Jr, Frederick R. Dr. (Thu Jun 02 2011 - 08:44:38 CDT)
velocity profile Mao Mao (Mon May 16 2011 - 10:45:55 CDT)
error in movie generator Esam Tolba (Mon May 16 2011 - 10:01:27 CDT)
sharing atoms beyza bilgic (Mon May 16 2011 - 08:52:33 CDT)
- Re: sharing atoms Axel Kohlmeyer (Mon May 16 2011 - 09:43:13 CDT)
Secondary Structure Disappears after Molecule Move Qmer_AN?= (Mon May 16 2011 - 05:45:21 CDT)
- Re: Secondary Structure Disappears after Molecule Move John Stone (Mon May 16 2011 - 10:30:25 CDT)
pbc wrap cnu gromacs (Fri May 13 2011 - 13:50:30 CDT)
- Re: pbc wrap Olaf Lenz (Mon May 16 2011 - 03:14:25 CDT)
PhD position in Computational Structural Biology at MPI Muenster Vlad Cojocaru (Fri May 13 2011 - 04:49:14 CDT)
- AW: PhD position in Computational Structural Biology at MPI Muenster Prskalo, Alen-Pilip (Fri May 13 2011 - 06:26:56 CDT)
  - Re: PhD position in Computational Structural Biology at MPI Muenster Ajasja LjubetiÄ (Fri May 13 2011 - 07:04:26 CDT)
  - Re: PhD position in Computational Structural Biology at MPI Muenster Wendy González (Fri May 13 2011 - 07:54:29 CDT)
Compiling plugins without netcdf support returns an error. Cosseddu, Salvatore (Thu May 12 2011 - 13:28:48 CDT)
- Compiling plugins without netcdf support returns an error. Cosseddu, Salvatore (Thu May 12 2011 - 15:12:32 CDT)
  - Re: Compiling plugins without netcdf support returns an error. Axel Kohlmeyer (Thu May 12 2011 - 15:56:52 CDT)
  - Re: Compiling plugins without netcdf support returns an error. John Stone (Thu May 12 2011 - 15:58:12 CDT)
Large positive non-integer charge Grant Schauer (Thu May 12 2011 - 13:16:46 CDT)
- Re: Large positive non-integer charge Axel Kohlmeyer (Thu May 12 2011 - 13:56:44 CDT)
  - Re: Large positive non-integer charge John Stone (Thu May 12 2011 - 14:00:30 CDT)
Atom ID/Color change with timesteps Adkins, Laura R (Wed May 11 2011 - 19:17:05 CDT)
- Re: Atom ID/Color change with timesteps Axel Kohlmeyer (Wed May 11 2011 - 19:58:38 CDT)
  - Re: Atom ID/Color change with timesteps Axel Kohlmeyer (Thu May 12 2011 - 13:54:23 CDT)
    - RE: Atom ID/Color change with timesteps Adkins, Laura R (Thu May 12 2011 - 16:04:26 CDT)
    - RE: Atom ID/Color change with timesteps Axel Kohlmeyer (Thu May 12 2011 - 16:21:21 CDT)
May 18th, Late abstract submission deadline for 3Dsig Structural Bioinformatics & Computational Biophysics 3D SIG (Wed May 11 2011 - 16:57:22 CDT)
command for volume slice? Jennifer Williams (Wed May 11 2011 - 08:16:25 CDT)
- Re: command for volume slice? Olaf Lenz (Wed May 11 2011 - 09:11:32 CDT)
- Re: command for volume slice? John Stone (Wed May 11 2011 - 11:02:12 CDT)
changing the color of Sn atom beyza bilgic (Wed May 11 2011 - 06:12:50 CDT)
- RE: changing the color of Sn atom Goldsmith, Jacob (Wed May 11 2011 - 08:45:50 CDT)
- Re: changing the color of Sn atom Axel Kohlmeyer (Wed May 11 2011 - 08:37:46 CDT)
- RE: changing the color of Sn atom Mark Cunningham (Wed May 11 2011 - 09:34:41 CDT)
changing the color of Sn atom Beyza Bilgiç (Wed May 11 2011 - 05:24:31 CDT)
to change color of Sn atom Beyza Bilgiç (Wed May 11 2011 - 04:33:51 CDT)
to change color of Sn atom Beyza Bilgiç (Wed May 11 2011 - 04:28:07 CDT)
save coordinate POSCAR Haijun (Tue May 10 2011 - 12:56:09 CDT)
- Re: save coordinate POSCAR Axel Kohlmeyer (Tue May 10 2011 - 13:30:03 CDT)
  - Re: save coordinate POSCAR Axel Kohlmeyer (Tue May 10 2011 - 13:50:39 CDT)
    - Re: save coordinate POSCAR Haijun (Tue May 10 2011 - 13:58:07 CDT)
apbs with vmd, no output Asmaa Elsheshiny (Tue May 10 2011 - 12:14:08 CDT)
- Re: apbs with vmd, no output John Stone (Tue May 10 2011 - 15:09:39 CDT)
  - Re: apbs with vmd, no output John Stone (Thu Jun 02 2011 - 09:44:03 CDT)
bad window parameter -- SOLVED Robert Wohlhueter (Tue May 10 2011 - 10:16:48 CDT)
Calculating RMSD on two sets of points Carolyn Phillips (Tue May 10 2011 - 09:57:25 CDT)
- Re: Calculating RMSD on two sets of points Carolyn Phillips (Tue May 10 2011 - 10:13:56 CDT)
  - Re: Re: Calculating RMSD on two sets of points Axel Kohlmeyer (Tue May 10 2011 - 10:43:51 CDT)
bad window parameter Robert Wohlhueter (Tue May 10 2011 - 09:27:34 CDT)
- Re: bad window parameter Axel Kohlmeyer (Tue May 10 2011 - 10:39:44 CDT)
trajectory of water within 5 A of protein maria goranovic (Tue May 10 2011 - 02:27:58 CDT)
- Re: trajectory of water within 5 A of protein Jernej Zidar (Tue May 10 2011 - 03:09:38 CDT)
  - RE: trajectory of water within 5 A of protein Aaron Oakley (Tue May 10 2011 - 05:47:47 CDT)
    - Re: trajectory of water within 5 A of protein Neelanjana Sengupta (Tue May 10 2011 - 07:03:55 CDT)
- Re: trajectory of water within 5 A of protein Eduard Schreiner (Tue May 10 2011 - 09:51:13 CDT)
  - Re: trajectory of water within 5 A of protein Emmanuel Baribefe Naziga (Tue May 10 2011 - 10:26:52 CDT)
    - Re: trajectory of water within 5 A of protein maria goranovic (Thu May 12 2011 - 02:31:16 CDT)
SASA calculation Aditya Padhi (Mon May 09 2011 - 05:26:36 CDT)
plotting spin density Olesya Haze (Thu May 05 2011 - 18:17:50 CDT)
- Re: plotting spin density Axel Kohlmeyer (Thu May 05 2011 - 22:45:20 CDT)
CAVE and Flystick control David Joiner (Wed May 04 2011 - 14:52:34 CDT)
- Re: CAVE and Flystick control John Stone (Wed May 04 2011 - 15:15:20 CDT)
  - Re: CAVE and Flystick control John Stone (Fri May 27 2011 - 14:41:03 CDT)
Fwd: molefacture "force tetrahedral" failure: SOLVED with chimera-vmd Francesco Pietra (Wed May 04 2011 - 02:45:21 CDT)
molefacture "force tetrahedral" failure Francesco Pietra (Wed May 04 2011 - 01:33:01 CDT)
- Re: molefacture "force tetrahedral" failure Peter Freddolino (Wed May 04 2011 - 19:31:24 CDT)
Visualization of coarse grained molecule with coarse_grain.tcl Paolo Conflitti (Tue May 03 2011 - 10:10:41 CDT)
RE: SASA calculation using periodic images? Jesper Sørensen (Tue May 03 2011 - 08:38:29 CDT)
- Re: SASA calculation using periodic images? Edward Lyman (Tue May 03 2011 - 09:34:57 CDT)
  - RE: SASA calculation using periodic images? Jesper Sørensen (Thu May 05 2011 - 07:27:34 CDT)
SASA calculation using periodic images? Jesper SÃ¸rensen (Tue May 03 2011 - 06:14:31 CDT)
- RE: SASA calculation using periodic images? Jesper SÃ¸rensen (Tue May 03 2011 - 06:50:35 CDT)
- Re: SASA calculation using periodic images? Axel Kohlmeyer (Tue May 03 2011 - 07:10:56 CDT)
Cartoons and secondary structure prediction Francisco José Taberner Sanchis (Tue May 03 2011 - 05:51:24 CDT)
- Re: Cartoons and secondary structure prediction Axel Kohlmeyer (Tue May 03 2011 - 07:05:39 CDT)
Problem with cartoon and secondary structure Francisco José Taberner Sanchis (Tue May 03 2011 - 05:13:18 CDT)
Fwd: Problem with cartoon and secondary structure Francisco José Taberner Sanchis (Tue May 03 2011 - 03:26:18 CDT)
Generate psf file for cyclic peptide Tu.Le_at_csiro.au (Mon May 02 2011 - 22:33:01 CDT)
desmond trajectory plugin Davide Provasi (Mon May 02 2011 - 10:40:30 CDT)
- Re: desmond trajectory plugin John Stone (Wed May 04 2011 - 22:36:41 CDT)
VMD Movie Generator problem with "Image smoothing" set Bjoern Olausson (Mon May 02 2011 - 06:26:54 CDT)
VMD- Ra Measurement Saurav Goel (Sun May 01 2011 - 19:43:28 CDT)
Reconstruction of XST data from DCD data B.M.B. Vanschouwen (Sun May 01 2011 - 19:29:03 CDT)
- Re: Reconstruction of XST data from DCD data Axel Kohlmeyer (Sun May 01 2011 - 20:15:06 CDT)
X & Y co-ordinate data ban arn (Sun May 01 2011 - 11:27:39 CDT)
- Re: X & Y co-ordinate data Axel Kohlmeyer (Sun May 01 2011 - 12:12:09 CDT)
question regarding H-bond calculation juzer stationwala (Sun May 01 2011 - 10:31:55 CDT)
- RE: question regarding H-bond calculation JC Gumbart (Sun May 01 2011 - 11:29:18 CDT)
- Re: question regarding H-bond calculation Axel Kohlmeyer (Sun May 01 2011 - 11:32:09 CDT)
Save molecule in pdb format Moutusi Manna (Sat Apr 30 2011 - 01:43:55 CDT)
- Re: Save molecule in pdb format Ajasja LjubetiÄ (Sat Apr 30 2011 - 02:29:35 CDT)
- Re: Save molecule in pdb format Peter C. Lai (Sat Apr 30 2011 - 04:34:27 CDT)
- Re: Save molecule in pdb format Axel Kohlmeyer (Sat Apr 30 2011 - 04:42:15 CDT)
  - Re: Save molecule in pdb format Peter C. Lai (Sat Apr 30 2011 - 13:50:01 CDT)
Questions about trajectory files obtained from LAMMPS Molecular dynamics with Reax Force field DreamCatcher (Fri Apr 29 2011 - 07:48:18 CDT)
- Re: Questions about trajectory files obtained from LAMMPS Molecular dynamics with Reax Force field Axel Kohlmeyer (Fri Apr 29 2011 - 08:36:01 CDT)
hello kanchi subbarao rao (Fri Apr 29 2011 - 05:58:05 CDT)
- Re: hello Eduard Schreiner (Fri Apr 29 2011 - 06:40:50 CDT)
request to know about bonds in between carbon atoms in carbon nanotubes safron saif (Fri Apr 29 2011 - 03:54:53 CDT)
coloring by gradient Rodolfo Pereyra (Thu Apr 28 2011 - 15:36:51 CDT)
HOW TO PARAMETRIZE A LIGAND shome sankar bhunia (Thu Apr 28 2011 - 04:53:12 CDT)
- Re: HOW TO PARAMETRIZE A LIGAND Markus K. Dahlgren (Thu Apr 28 2011 - 08:24:52 CDT)
  - Re: HOW TO PARAMETRIZE A LIGAND Diego Enry (Thu Apr 28 2011 - 10:20:02 CDT)
hello kanchi subbarao rao (Thu Apr 28 2011 - 01:38:36 CDT)
- Re: hello Axel Kohlmeyer (Thu Apr 28 2011 - 10:01:18 CDT)
running plugin from the command line Sara Nichols (Wed Apr 27 2011 - 14:49:33 CDT)
- Re: running plugin from the command line Axel Kohlmeyer (Wed Apr 27 2011 - 15:34:10 CDT)
  - Re: running plugin from the command line Leonardo Trabuco (Thu Apr 28 2011 - 11:12:06 CDT)
    - Re: running plugin from the command line Sara Nichols (Thu Apr 28 2011 - 11:28:43 CDT)
making a movie Moeed (Tue Apr 26 2011 - 17:58:06 CDT)
- Re: making a movie Axel Kohlmeyer (Tue Apr 26 2011 - 18:36:48 CDT)
RE: RE: New NAMD version 2011-03-03 uses Ada Zhan (Fri Apr 22 2011 - 16:04:52 CDT)
RE: New NAMD version 2011-03-03 uses Ada Zhan (Fri Apr 22 2011 - 13:35:30 CDT)
- ParseFEP_domain error Ada Zhan (Fri Apr 22 2011 - 14:50:57 CDT)
  - Re: ParseFEP_domain error John Stone (Tue Apr 26 2011 - 10:50:18 CDT)
    - RE: ParseFEP_domain error Ada Zhan (Tue Apr 26 2011 - 15:02:24 CDT)
psfgen: error processing bonds Edward Lyman (Fri Apr 22 2011 - 10:03:30 CDT)
- Re: psfgen: error processing bonds John Stone (Tue Apr 26 2011 - 10:53:05 CDT)
  - Re: psfgen: error processing bonds Jim Phillips (Tue Apr 26 2011 - 11:43:56 CDT)
  - Re: psfgen: error processing bonds Jim Phillips (Tue Apr 26 2011 - 14:21:01 CDT)
fit dcd is not converging mohan maruthi sena (Thu Apr 21 2011 - 04:10:07 CDT)
- Re: fit dcd is not converging John Stone (Thu Apr 21 2011 - 10:22:10 CDT)
  - Re: fit dcd is not converging mohan maruthi sena (Thu Apr 21 2011 - 10:48:33 CDT)
  - Re: fit dcd is not converging mohan maruthi sena (Thu Apr 21 2011 - 10:37:31 CDT)
Installation/Upgrade Error Phelan Jr., Frederick R. Dr. (Wed Apr 20 2011 - 15:57:49 CDT)
- Re: Installation/Upgrade Error John Stone (Wed Apr 20 2011 - 16:05:38 CDT)
  - RE: Installation/Upgrade Error Phelan Jr., Frederick R. Dr. (Wed Apr 20 2011 - 16:48:08 CDT)
RE: Generating Topo Bond Data from LAMMPS Data File Phelan Jr., Frederick R. Dr. (Wed Apr 20 2011 - 15:30:52 CDT)
Generating Topo Bond Data from LAMMPS Data File Phelan Jr., Frederick R. Dr. (Wed Apr 20 2011 - 10:23:29 CDT)
- Re: Generating Topo Bond Data from LAMMPS Data File Axel Kohlmeyer (Wed Apr 20 2011 - 11:17:34 CDT)
generating .xsc files using periodic information Neelanjana Sengupta (Wed Apr 20 2011 - 07:06:04 CDT)
- Re: generating .xsc files using periodic information John Stone (Tue Apr 26 2011 - 11:02:48 CDT)
  - Re: generating .xsc files using periodic information Axel Kohlmeyer (Tue Apr 26 2011 - 11:31:28 CDT)
Simple Question regarding psf generation Christian Wohlschlager (Tue Apr 19 2011 - 08:09:15 CDT)
- Re: Simple Question regarding psf generation Axel Kohlmeyer (Tue Apr 19 2011 - 09:24:57 CDT)
- Re: Simple Question regarding psf generation Gianluca Interlandi (Tue Apr 19 2011 - 11:05:21 CDT)
waters selection agustina_at_cabm.rutgers.edu (Mon Apr 18 2011 - 15:49:09 CDT)
- Re: waters selection John Stone (Mon Apr 18 2011 - 15:58:07 CDT)
- Re: waters selection Axel Kohlmeyer (Mon Apr 18 2011 - 16:20:51 CDT)
mdf molfile plugin reader atom_type bug Craig Knox (Mon Apr 18 2011 - 13:03:51 CDT)
- Re: mdf molfile plugin reader atom_type bug John Stone (Mon Apr 18 2011 - 16:14:00 CDT)
  - Re: mdf molfile plugin reader atom_type bug Craig Knox (Tue Apr 19 2011 - 13:44:42 CDT)
compiling on LINUXAMD64 problem ZHAO Lina (Sun Apr 17 2011 - 00:14:59 CDT)
- Re: compiling on LINUXAMD64 problem Axel Kohlmeyer (Sun Apr 17 2011 - 03:26:32 CDT)
  - Re: compiling on LINUXAMD64 problem ZHAO Lina (Sun Apr 17 2011 - 06:50:47 CDT)
Re: Res: webpdb load problem John Stone (Fri Apr 15 2011 - 15:51:38 CDT)
- Res: Res: webpdb load problem tiago sobreira (Mon Apr 18 2011 - 10:00:13 CDT)
3Dsig 2011: Structural Bioinformatics & Computational Biophysics, Vienna, 15-16 July 2011 (abstract deadline May 1st) 3D SIG (Fri Apr 15 2011 - 14:38:03 CDT)
Replica Exchange alamng_at_uci.edu (Fri Apr 15 2011 - 02:35:05 CDT)
- Re: Replica Exchange Olaf Lenz (Fri Apr 15 2011 - 04:18:17 CDT)
Question about SASA Sebastian Maximilian Wilhelm (Thu Apr 14 2011 - 10:31:34 CDT)
- Re: Question about SASA John Stone (Fri Apr 15 2011 - 16:03:05 CDT)
Re: using vmd to view gromacs trajectory bharat gupta (Thu Apr 14 2011 - 10:20:29 CDT)
- Re: Re: using vmd to view gromacs trajectory Axel Kohlmeyer (Thu Apr 14 2011 - 11:43:36 CDT)
Recent Geforce Cuda GPU cards(GT 440, GTX 560ti) Burgess, Don E (Wed Apr 13 2011 - 11:26:02 CDT)
- Re: Recent Geforce Cuda GPU cards(GT 440, GTX 560ti) John Stone (Wed Apr 13 2011 - 12:57:44 CDT)
X3DOM sphere resolution Joshua A. Anderson (Wed Apr 13 2011 - 07:09:37 CDT)
- Re: X3DOM sphere resolution John Stone (Wed Apr 13 2011 - 09:49:34 CDT)
  - Re: X3DOM sphere resolution John Stone (Wed Apr 13 2011 - 10:02:38 CDT)
webpdb load problem tiago sobreira (Tue Apr 12 2011 - 13:48:29 CDT)
- Re: webpdb load problem John Stone (Tue Apr 12 2011 - 14:09:33 CDT)
moving rotational center to display center Joseph Bylund (Tue Apr 12 2011 - 12:01:27 CDT)
NMWiz - a new VMD plugin Ahmet Bakan (Tue Apr 12 2011 - 11:51:36 CDT)
Tcl plugin development and debugging Anssi Nurminen (Tue Apr 12 2011 - 06:14:36 CDT)
- Re: Tcl plugin development and debugging John Stone (Tue Apr 12 2011 - 09:04:37 CDT)
  - Re: Tcl plugin development and debugging Anssi Nurminen (Tue Apr 12 2011 - 09:33:01 CDT)
trajectory generation using gaussian cube files Vamsee Voora (Mon Apr 11 2011 - 15:53:33 CDT)
- Re: trajectory generation using gaussian cube files Axel Kohlmeyer (Mon Apr 11 2011 - 16:47:48 CDT)
box vectores in .trr leila karami (Sat Apr 09 2011 - 08:44:04 CDT)
- Re: box vectores in .trr Axel Kohlmeyer (Sat Apr 09 2011 - 15:17:23 CDT)
- Re: box vectores in .trr Matt Watkins (Sat Apr 09 2011 - 17:47:06 CDT)
measuring the orientation of a small a-helix Raul Araya (Wed Apr 06 2011 - 16:23:29 CDT)
electrostatic potential maps. Raul Araya (Wed Apr 06 2011 - 13:13:58 CDT)
- Re: electrostatic potential maps. John Stone (Wed Apr 06 2011 - 16:23:13 CDT)
  - Re: electrostatic potential maps. John Stone (Wed Apr 06 2011 - 16:39:41 CDT)
  - Re: electrostatic potential maps. Guanglei Cui (Wed Jun 08 2011 - 10:56:40 CDT)
2D Contour plot ban arn (Wed Apr 06 2011 - 05:06:09 CDT)
vectors box in .trr file leila karami (Wed Apr 06 2011 - 02:49:24 CDT)
Transparent image render problem after vmd 1.9 version Bongkeun Kim (Wed Apr 06 2011 - 01:22:21 CDT)
- Re: Transparent image render problem after vmd 1.9 version John Stone (Wed Apr 06 2011 - 09:55:32 CDT)
  - Re: Transparent image render problem after vmd 1.9 version Bongkeun Kim (Wed Apr 06 2011 - 11:51:43 CDT)
recenter Mark M Huntress (Sun Apr 03 2011 - 16:34:17 CDT)
- Re: recenter Olaf Lenz (Mon Apr 04 2011 - 02:11:25 CDT)
  - RE: recenter Mark M Huntress (Mon Apr 04 2011 - 15:04:17 CDT)
    - Re: recenter Olaf Lenz (Tue Apr 05 2011 - 02:29:57 CDT)
Fwd: (my) problems using molefacture dihedral Francesco Pietra (Sun Apr 03 2011 - 09:14:44 CDT)
problem on rmsdtt masoud kazemi (Sun Apr 03 2011 - 08:52:22 CDT)
Fwd: (my) problems using molefacture dihedral Francesco Pietra (Sun Apr 03 2011 - 08:49:53 CDT)
(my) problems using molefacture dihedral Francesco Pietra (Sat Apr 02 2011 - 15:36:21 CDT)
- Re: (my) problems using molefacture dihedral Peter Freddolino (Sat Apr 02 2011 - 19:05:13 CDT)
Water Models Chathurika Abeyrathne (Sat Apr 02 2011 - 02:43:29 CDT)
- Re: Water Models Axel Kohlmeyer (Sat Apr 02 2011 - 05:34:38 CDT)
How to create bonds in VMD? Saketh Bharadwaja (Fri Apr 01 2011 - 11:07:21 CDT)
- Re: How to create bonds in VMD? Axel Kohlmeyer (Fri Apr 01 2011 - 11:59:54 CDT)
script problem Mark M Huntress (Thu Mar 31 2011 - 15:32:33 CDT)
- Re: script problem John Stone (Thu Mar 31 2011 - 15:39:01 CDT)
Rotating and saving coordinates of a copy of molecule alongwith original molecule Sujata Sovani (Thu Mar 31 2011 - 13:18:54 CDT)
- RE: Rotating and saving coordinates of a copy of molecule alongwith original molecule Cosseddu, Salvatore (Thu Mar 31 2011 - 16:59:32 CDT)
Reverse Mapping of RBCG Model Sibel Cakan (Wed Mar 30 2011 - 07:39:51 CDT)
- Re: Reverse Mapping of RBCG Model Peter Freddolino (Thu Mar 31 2011 - 11:10:35 CDT)
  - Re: Reverse Mapping of RBCG Model Vlad Cojocaru (Thu Mar 31 2011 - 12:39:17 CDT)
    - Re: Reverse Mapping of RBCG Model Peter Freddolino (Thu Mar 31 2011 - 21:46:14 CDT)
  - Re: Reverse Mapping of RBCG Model Peter Freddolino (Thu Mar 31 2011 - 21:44:25 CDT)
viewing trajectory Moeed (Tue Mar 29 2011 - 18:44:43 CDT)
- Re: viewing trajectory Axel Kohlmeyer (Tue Mar 29 2011 - 19:32:41 CDT)
how to mark regions in Multiseq Irene Newhouse (Mon Mar 28 2011 - 19:35:31 CDT)
- Re: how to mark regions in Multiseq Kirby Vandivort (Tue Mar 29 2011 - 10:13:48 CDT)
Generate a PSF file for small, simple molecules THANH NGUYEN (Mon Mar 28 2011 - 19:11:42 CDT)
- Re: Generate a PSF file for small, simple molecules John Stone (Thu Mar 31 2011 - 14:59:37 CDT)
  - Re: Generate a PSF file for small, simple molecules THANH NGUYEN (Thu Mar 31 2011 - 17:46:44 CDT)
    - Re: Generate a PSF file for small, simple molecules Ajasja LjubetiÄ (Fri Apr 01 2011 - 02:15:51 CDT)
phi-psi plot Ramya Narasimhan (Mon Mar 28 2011 - 05:29:01 CDT)
- Re: phi-psi plot Ajasja LjubetiÄ (Mon Mar 28 2011 - 08:08:32 CDT)
Selecting atoms based on 'type' with LAMMPS + PSF Taco de Wolff (Mon Mar 28 2011 - 05:02:10 CDT)
size of box Moeed (Mon Mar 28 2011 - 01:10:54 CDT)
- Re: size of box Ajasja LjubetiÄ (Mon Mar 28 2011 - 02:50:18 CDT)
Invitation to connect on LinkedIn Ma Ming via LinkedIn (Sun Mar 27 2011 - 23:26:07 CDT)
Ma Ming wants to stay in touch on LinkedIn Ma Ming via LinkedIn (Sun Mar 27 2011 - 23:21:55 CDT)
Invitation to connect on LinkedIn ram prasad via LinkedIn (Sun Mar 27 2011 - 12:38:16 CDT)
How to add iond for RBCG model maming10002000 (Sun Mar 27 2011 - 10:23:27 CDT)
How to add ions for RBCG maming10002000 (Sun Mar 27 2011 - 09:56:02 CDT)
- Re: How to add ions for RBCG John Stone (Sun Mar 27 2011 - 23:42:36 CDT)
Software to create 3D PDF documents Petridis, Loukas (Fri Mar 25 2011 - 14:03:03 CDT)
- Re: Software to create 3D PDF documents John Stone (Fri Mar 25 2011 - 22:01:53 CDT)
Save Coordinates Question ... Phelan Jr., Frederick R. Dr. (Fri Mar 25 2011 - 12:34:01 CDT)
Save Coordinates Question ... Phelan Jr., Frederick R. Dr. (Fri Mar 25 2011 - 12:22:50 CDT)
- Re: Save Coordinates Question ... Axel Kohlmeyer (Fri Mar 25 2011 - 13:04:44 CDT)
how to convert X_PLOR to CHARMM? Lisa Brown (Fri Mar 25 2011 - 11:01:26 CDT)
CHARMM parameters for Mn 2+ ion Lisa Brown (Fri Mar 25 2011 - 10:43:45 CDT)
- Re: CHARMM parameters for Mn 2+ ion Jernej Zidar (Fri Mar 25 2011 - 12:57:00 CDT)
  - Re: namd-l: Re: CHARMM parameters for Mn 2+ ion Daniel Aguayo (Fri Mar 25 2011 - 14:45:15 CDT)
NAMDenergy calculation shome sankar bhunia (Fri Mar 25 2011 - 08:28:50 CDT)
measure dipole Donovan B.T. (Thu Mar 24 2011 - 13:07:28 CDT)
- Re: measure dipole Axel Kohlmeyer (Thu Mar 24 2011 - 13:53:10 CDT)
- Re: measure dipole PaweÅ‚ KÄ™dzierski (Fri Mar 25 2011 - 02:55:54 CDT)
  - RE: measure dipole Donovan B.T. (Fri Mar 25 2011 - 08:18:38 CDT)
How can I operate on multiple .pdb structures in a list Anna Kuznetsova (Wed Mar 23 2011 - 18:49:02 CDT)
- Re: How can I operate on multiple .pdb structures in a list Axel Kohlmeyer (Wed Mar 23 2011 - 19:43:49 CDT)
Error starting second VMD Jérôme Hénin (Wed Mar 23 2011 - 09:40:20 CDT)
- Re: Error starting second VMD John Stone (Thu Mar 24 2011 - 21:02:06 CDT)
  - Re: Error starting second VMD Jérôme Hénin (Fri Mar 25 2011 - 04:40:04 CDT)
3Dsig 2011: Structural Bioinformatics & Computational Biophysics, Vienna, 15-16 July 2011 (abstract deadline May 1st). 3D SIG (Wed Mar 23 2011 - 06:15:19 CDT)
Color wheel gradient Jonathan KHAO (Tue Mar 22 2011 - 12:57:08 CDT)
- Re: Color wheel gradient John Stone (Thu Mar 24 2011 - 22:14:38 CDT)
  - Re: Color wheel gradient jonathan (Fri Mar 25 2011 - 09:03:34 CDT)
Fwd: charmmgen to autopsf Francesco Pietra (Tue Mar 22 2011 - 11:03:05 CDT)
- Re: Fwd: charmmgen to autopsf Peter Freddolino (Tue Mar 22 2011 - 11:21:42 CDT)
  - Re: Fwd: charmmgen to autopsf Francesco Pietra (Tue Mar 22 2011 - 13:38:37 CDT)
VMD 1.9 builds on MACOSXX86_64 Joshua A. Anderson (Tue Mar 22 2011 - 08:55:00 CDT)
- Re: VMD 1.9 builds on MACOSXX86_64 John Stone (Thu Mar 24 2011 - 21:56:32 CDT)
  - Re: VMD 1.9 builds on MACOSXX86_64 Joshua A. Anderson (Fri Mar 25 2011 - 12:54:56 CDT)
Fwd: Re: script for projection of c-alpha atom cordinates on xy plane PaweÅ‚ KÄ™dzierski (Tue Mar 22 2011 - 08:19:14 CDT)
How to maximize the VMD display window Yingzhe Liu (Tue Mar 22 2011 - 02:10:48 CDT)
- Re: How to maximize the VMD display window John Stone (Thu Mar 24 2011 - 21:58:27 CDT)
  - Re: How to maximize the VMD display window Yingzhe Liu (Fri Mar 25 2011 - 07:08:06 CDT)
Fwd: charmmgen to autopsf Francesco Pietra (Mon Mar 21 2011 - 07:20:00 CDT)
- Re: Fwd: charmmgen to autopsf Peter Freddolino (Mon Mar 21 2011 - 19:11:35 CDT)
charmmgen to autopsf Francesco Pietra (Mon Mar 21 2011 - 05:12:05 CDT)
- Re: charmmgen to autopsf Peter Freddolino (Mon Mar 21 2011 - 05:48:06 CDT)
  - Re: charmmgen to autopsf Francesco Pietra (Mon Mar 21 2011 - 11:50:13 CDT)
Problem with using bigdcd.tcl jnsong (Sun Mar 20 2011 - 22:38:01 CDT)
- Re: Problem with using bigdcd.tcl Ajasja LjubetiÄ (Mon Mar 21 2011 - 03:36:15 CDT)
  - Re: Problem with using bigdcd.tcl jnsong (Wed Mar 23 2011 - 00:06:00 CDT)
ANALYZING DESMOND OUTPUT IN VMD shome sankar bhunia (Sun Mar 20 2011 - 03:55:58 CDT)
- Re: ANALYZING DESMOND OUTPUT IN VMD Axel Kohlmeyer (Sun Mar 20 2011 - 15:49:12 CDT)
"non-grid" volumetric data Xiaogang Wang (Sat Mar 19 2011 - 01:23:32 CDT)
- Re: "non-grid" volumetric data Axel Kohlmeyer (Sat Mar 19 2011 - 04:32:27 CDT)
  - Re: "non-grid" volumetric data Xiaogang Wang (Sat Mar 19 2011 - 17:15:48 CDT)
    - Re: "non-grid" volumetric data Axel Kohlmeyer (Sat Mar 19 2011 - 17:53:16 CDT)
script for projection of c-alpha atom cordinates on xy plane ban arn (Fri Mar 18 2011 - 12:58:19 CDT)
- Re: script for projection of c-alpha atom cordinates on xy plane Joseph Bylund (Fri Mar 18 2011 - 13:39:37 CDT)
  - Re: script for projection of c-alpha atom cordinates on xy plane Ajasja LjubetiÄ (Fri Mar 18 2011 - 15:23:12 CDT)
- Re: script for projection of c-alpha atom cordinates on xy plane PaweÅ‚ KÄ™dzierski (Fri Mar 18 2011 - 15:17:31 CDT)
  - Re: script for projection of c-alpha atom cordinates on xy plane ban arn (Mon Mar 21 2011 - 10:37:03 CDT)
SV: Authentication error VMD-xplor Robert Dagil (Fri Mar 18 2011 - 10:13:23 CDT)
Authentication error VMD-xplor Robert Dagil (Fri Mar 18 2011 - 07:46:07 CDT)
Hbond rendering issue with VMD 1.9 Nicolas Sapay (Fri Mar 18 2011 - 04:58:27 CDT)
- Re: Hbond rendering issue with VMD 1.9 John Stone (Fri Mar 18 2011 - 13:09:41 CDT)
Molden format plugin Ignacio Fernández Galván (Thu Mar 17 2011 - 11:12:33 CDT)
- Re: Molden format plugin John Stone (Thu Mar 17 2011 - 11:28:24 CDT)
  - Re: Molden format plugin Ignacio Fernández Galván (Thu Mar 17 2011 - 13:33:50 CDT)
- Re: Molden format plugin John Stone (Tue Mar 29 2011 - 10:23:49 CDT)
to block the information appearing during the run Ramya Narasimhan (Thu Mar 17 2011 - 06:14:24 CDT)
- Re: to block the information appearing during the run Ajasja LjubetiÄ (Thu Mar 17 2011 - 08:16:14 CDT)
Re: .pdbqt file type Francesco Pietra (Thu Mar 17 2011 - 02:38:19 CDT)
- Fwd: .pdbqt file type Francesco Pietra (Thu Mar 17 2011 - 05:16:04 CDT)
segid & chain id Francesco Pietra (Thu Mar 17 2011 - 02:27:23 CDT)
- Re: segid & chain id John Stone (Thu Mar 17 2011 - 10:10:25 CDT)
  - Re: segid & chain id Francesco Pietra (Thu Mar 17 2011 - 11:05:17 CDT)
calculation of binding energy vani panguluri (Wed Mar 16 2011 - 23:06:45 CDT)
TCL Callbacks Julia Doh (Wed Mar 16 2011 - 13:45:31 CDT)
- Re: TCL Callbacks John Stone (Thu Mar 17 2011 - 14:11:30 CDT)
  - Re: TCL Callbacks Julia Doh (Wed Mar 30 2011 - 15:33:28 CDT)
    - Re: TCL Callbacks John Stone (Thu Mar 31 2011 - 15:04:15 CDT)
Question about vdW-area Sebastian Maximilian Wilhelm (Wed Mar 16 2011 - 12:40:43 CDT)
pdb file with different number of molecules Peyman Z.Moghadam (Wed Mar 16 2011 - 12:30:53 CDT)
- Re: pdb file with different number of molecules Axel Kohlmeyer (Wed Mar 16 2011 - 13:20:42 CDT)
.pdbqt file type Francesco Pietra (Wed Mar 16 2011 - 12:15:51 CDT)
- Re: .pdbqt file type John Stone (Thu Mar 17 2011 - 09:56:08 CDT)
MSD calculation from VMD RMSD plugin. Ranyere Deyler (Wed Mar 16 2011 - 09:24:54 CDT)
- Re: MSD calculation from VMD RMSD plugin. Axel Kohlmeyer (Wed Mar 16 2011 - 10:54:41 CDT)
  - Re: MSD calculation from VMD RMSD plugin. Ranyere Deyler (Wed Mar 16 2011 - 14:12:45 CDT)
    - Re: MSD calculation from VMD RMSD plugin. Axel Kohlmeyer (Wed Mar 16 2011 - 14:23:30 CDT)
    - Re: MSD calculation from VMD RMSD plugin. Ranyere Deyler (Wed Mar 16 2011 - 14:33:58 CDT)
Problem with using bigdcd.tcl jnsong (Tue Mar 15 2011 - 21:42:10 CDT)
vmd for mac: range in isosurface representation Passerone, Daniele (Tue Mar 15 2011 - 04:34:48 CDT)
- Re: vmd for mac: range in isosurface representation John Stone (Tue Mar 15 2011 - 10:35:28 CDT)
Announce VMD 1.9 released John Stone (Mon Mar 14 2011 - 16:49:37 CDT)
Linkage problem when compiling fortran bindings for VMD molfile plugins Susana Tomasio (Mon Mar 14 2011 - 11:52:49 CDT)
- Re: Linkage problem when compiling fortran bindings for VMD molfile plugins Axel Kohlmeyer (Mon Mar 14 2011 - 13:43:28 CDT)
  - Re: Linkage problem when compiling fortran bindings for VMD molfile plugins Susana Tomasio (Mon Mar 14 2011 - 16:04:51 CDT)
zero box vector leila karami (Sun Mar 13 2011 - 10:14:49 CDT)
- Re: zero box vector Axel Kohlmeyer (Sun Mar 13 2011 - 11:49:26 CDT)
time line leila karami (Sat Mar 12 2011 - 03:19:52 CST)
- Re: time line Barry Isralewitz (Wed Mar 16 2011 - 15:03:45 CDT)
zero box vector leila karami (Sat Mar 12 2011 - 00:50:40 CST)
- Re: zero box vector Axel Kohlmeyer (Sat Mar 12 2011 - 05:20:48 CST)
count CLA number from different frames emiliawu_at_dicp.ac.cn (Sat Mar 12 2011 - 07:16:32 CST)
- Re: count CLA number from different frames JC Gumbart (Fri Mar 11 2011 - 20:47:02 CST)
snow leopard CUDA and VMD 1.9 Passerone, Daniele (Fri Mar 11 2011 - 09:29:30 CST)
- Re: snow leopard CUDA and VMD 1.9 John Stone (Fri Mar 11 2011 - 10:50:41 CST)
  - Re: snow leopard CUDA and VMD 1.9 Passerone, Daniele (Fri Mar 11 2011 - 12:14:55 CST)
tcl script ban arn (Fri Mar 11 2011 - 09:06:00 CST)
- Re: tcl script Ajasja LjubetiÄ (Fri Mar 11 2011 - 10:17:15 CST)
  - Re: tcl script ban arn (Fri Mar 11 2011 - 11:15:51 CST)
    - RE: tcl script Goldsmith, Jacob (Fri Mar 11 2011 - 13:59:36 CST)
    - Re: tcl script Ajasja Ljubetiè (Fri Mar 11 2011 - 14:12:52 CST)
  - Re: tcl script Axel Kohlmeyer (Fri Mar 11 2011 - 11:49:39 CST)
2 Issues in VMD 1.9 beta3 hanif mahboobi (Fri Mar 11 2011 - 06:10:30 CST)
- Re: 2 Issues in VMD 1.9 beta3 Axel Kohlmeyer (Fri Mar 11 2011 - 08:14:02 CST)
problem on making a movie Jun Cheng (Fri Mar 11 2011 - 04:42:34 CST)
- Re: problem on making a movie Axel Kohlmeyer (Fri Mar 11 2011 - 05:58:33 CST)
  - RE: problem on making a movie Goldsmith, Jacob (Fri Mar 11 2011 - 09:20:58 CST)
Not calculate bonds by default. Eric Germaneau (Fri Mar 11 2011 - 07:12:04 CST)
- Re: Not calculate bonds by default. Axel Kohlmeyer (Thu Mar 10 2011 - 19:08:44 CST)
zero box vector leila karami (Thu Mar 10 2011 - 11:27:59 CST)
- Re: zero box vector Axel Kohlmeyer (Thu Mar 10 2011 - 12:37:31 CST)
psf and top Francesco Oteri (Thu Mar 10 2011 - 09:10:05 CST)
- Re: psf and top John Stone (Thu Mar 10 2011 - 09:51:58 CST)
zero box vector leila karami (Thu Mar 10 2011 - 08:04:14 CST)
Triclinic boxes in VMD using the LAMMPS file format Taco de Wolff (Thu Mar 10 2011 - 06:36:22 CST)
- Re: Triclinic boxes in VMD using the LAMMPS file format Olaf Lenz (Thu Mar 10 2011 - 07:44:14 CST)
  - Re: Triclinic boxes in VMD using the LAMMPS file format Axel Kohlmeyer (Thu Mar 10 2011 - 09:44:13 CST)
    - Re: Triclinic boxes in VMD using the LAMMPS file format Taco de Wolff (Thu Mar 10 2011 - 10:46:09 CST)
- Re: Triclinic boxes in VMD using the LAMMPS file format Axel Kohlmeyer (Thu Mar 10 2011 - 08:18:03 CST)
Zero box vector leila karami (Thu Mar 10 2011 - 06:11:56 CST)
- Re: Zero box vector Olaf Lenz (Thu Mar 10 2011 - 07:07:35 CST)
tcl script menica dibenedetto (Wed Mar 09 2011 - 08:32:25 CST)
- Re: tcl script Axel Kohlmeyer (Wed Mar 09 2011 - 09:41:31 CST)
- Re: tcl script JC Gumbart (Wed Mar 09 2011 - 11:55:58 CST)
VMD beta3 windows installer Ajasja LjubetiÄ (Wed Mar 09 2011 - 08:21:46 CST)
- Re: VMD beta3 windows installer John Stone (Wed Mar 09 2011 - 10:43:23 CST)
VMD and Kinect Olaf Lenz (Wed Mar 09 2011 - 05:30:16 CST)
- Re: VMD and Kinect John Stone (Wed Mar 09 2011 - 10:58:04 CST)
  - Re: VMD and Kinect Dudo (Wed Mar 09 2011 - 12:27:40 CST)
Extra bond in TIP3 water Julie Grouleff (Wed Mar 09 2011 - 04:56:53 CST)
- Re: Extra bond in TIP3 water Axel Kohlmeyer (Wed Mar 09 2011 - 06:04:00 CST)
ERROR vani panguluri (Wed Mar 09 2011 - 00:11:59 CST)
- Re: ERROR John Stone (Wed Mar 09 2011 - 00:19:45 CST)
- Re: ERROR Axel Kohlmeyer (Wed Mar 09 2011 - 04:17:56 CST)
how to make default background color to white Sushil Mishra (Tue Mar 08 2011 - 09:11:33 CST)
- Re: how to make default background color to white Manoj Yadav (Tue Mar 08 2011 - 10:13:31 CST)
  - Re: how to make default background color to white Gianluca Interlandi (Tue Mar 08 2011 - 12:13:10 CST)
    - Re: how to make default background color to white Sushil Mishra (Wed Mar 09 2011 - 01:03:47 CST)
    - Re: how to make default background color to white Axel Kohlmeyer (Wed Mar 09 2011 - 04:31:00 CST)
- Re: how to make default background color to white Ajasja LjubetiÄ (Tue Mar 08 2011 - 10:29:54 CST)
- Re: how to make default background color to white Axel Kohlmeyer (Tue Mar 08 2011 - 10:45:40 CST)
measure energy elect vs. NAMDenergy Sebastian Maximilian Wilhelm (Tue Mar 08 2011 - 05:21:10 CST)
- Re: measure energy elect vs. NAMDenergy Axel Kohlmeyer (Tue Mar 08 2011 - 06:23:07 CST)
Fwd: Re: namd-l: hBond colvars and patching Francesco Pietra (Tue Mar 08 2011 - 00:34:36 CST)
VMD 1.9 beta 3 posted for download... John Stone (Mon Mar 07 2011 - 14:53:43 CST)
- Re: VMD 1.9 beta 3 posted for download... Cesar Millan (Mon Mar 07 2011 - 15:47:47 CST)
  - Re: VMD 1.9 beta 3 posted for download... John Stone (Mon Mar 07 2011 - 15:53:04 CST)
  - Re: VMD 1.9 beta 3 posted for download... John Stone (Wed Mar 09 2011 - 11:06:56 CST)
- Re: (Minnesota Supercomputing Institute Install) VMD 1.9 beta 3 posted for download... nlabello (Tue Mar 08 2011 - 16:00:25 CST)
request help about hbond hamid mosaddeghi (Mon Mar 07 2011 - 13:20:13 CST)
Fwd: ACS awards information John Stone (Mon Mar 07 2011 - 10:45:17 CST)
request help about hbond hamid mosaddeghi (Mon Mar 07 2011 - 09:06:20 CST)
Re: namd-l: hBond colvars and patching Francesco Pietra (Mon Mar 07 2011 - 00:12:54 CST)
- Re: Re: namd-l: hBond colvars and patching Peter Freddolino (Mon Mar 07 2011 - 09:19:20 CST)
  - Re: Re: namd-l: hBond colvars and patching Peter Freddolino (Mon Mar 07 2011 - 17:08:23 CST)
hBond colvars and patching Francesco Pietra (Sun Mar 06 2011 - 14:05:47 CST)
Android support Dow Hurst (Sun Mar 06 2011 - 11:24:15 CST)
- Re: Android support Axel Kohlmeyer (Sun Mar 06 2011 - 12:38:38 CST)
- Re: Android support John Stone (Sun Mar 06 2011 - 13:39:44 CST)
  - Re: Android support Dow Hurst (Sun Mar 06 2011 - 13:55:02 CST)
    - Re: Android support John Stone (Sun Mar 06 2011 - 15:28:46 CST)
    - Re: Android support John Stone (Sun Mar 06 2011 - 15:44:09 CST)
hBond component in colvars and patching Francesco Pietra (Sat Mar 05 2011 - 14:38:45 CST)
- Fwd: namd-l: hBond component in colvars and patching Francesco Pietra (Sun Mar 06 2011 - 02:36:10 CST)
view temperature, forces and velocities alberto baldelli (Fri Mar 04 2011 - 09:35:18 CST)
- Re: view temperature, forces and velocities Axel Kohlmeyer (Sat Mar 05 2011 - 12:27:23 CST)
Re: public VMD cvs server John Stone (Fri Mar 04 2011 - 09:13:10 CST)
Bug in VMD? Sujata Sovani (Thu Mar 03 2011 - 12:15:16 CST)
- Re: Bug in VMD? John Stone (Thu Mar 03 2011 - 13:38:58 CST)
capping or patching protein ends Ashlynne Monroe (Thu Mar 03 2011 - 10:40:37 CST)
- Re: capping or patching protein ends Tim Travers (Thu Mar 03 2011 - 11:39:11 CST)
- RE: capping or patching protein ends Mark Cunningham (Thu Mar 03 2011 - 14:32:08 CST)
  - Re: capping or patching protein ends Tim Travers (Thu Mar 03 2011 - 15:13:33 CST)
    - Re: capping or patching protein ends Peter Freddolino (Thu Mar 03 2011 - 17:51:20 CST)
Mutator Plugin Patching Thomas Freeman (Wed Mar 02 2011 - 15:27:21 CST)
- Re: Mutator Plugin Patching JC Gumbart (Wed Mar 02 2011 - 23:48:24 CST)
  - Re: Mutator Plugin Patching Thomas Freeman (Thu Mar 03 2011 - 12:21:01 CST)
Installing VMD 1.8.7 on i686/SL5 David Huggins (Wed Mar 02 2011 - 07:38:14 CST)
- Re: Installing VMD 1.8.7 on i686/SL5 Olaf Lenz (Wed Mar 02 2011 - 08:31:01 CST)
  - Re: Installing VMD 1.8.7 on i686/SL5 David Huggins (Wed Mar 02 2011 - 09:41:34 CST)
    - Re: Installing VMD 1.8.7 on i686/SL5 John Stone (Wed Mar 02 2011 - 10:02:46 CST)
Error in coordinate information of PDB file after merging nabaneeta mukhopadhyay (Wed Mar 02 2011 - 00:50:42 CST)
- Re: Error in coordinate information of PDB file after merging Axel Kohlmeyer (Wed Mar 02 2011 - 10:39:01 CST)
VMD.RC Question Phelan Jr., Frederick R. Dr. (Tue Mar 01 2011 - 14:33:45 CST)
- Re: VMD.RC Question Axel Kohlmeyer (Tue Mar 01 2011 - 16:51:49 CST)
  - Re: VMD.RC Question John Stone (Wed Mar 02 2011 - 12:45:53 CST)
question about the inorganic builder Mao Mao (Tue Mar 01 2011 - 11:30:53 CST)
- Re: question about the inorganic builder Robert Brunner (Tue Mar 01 2011 - 14:15:25 CST)
Compiling Fortran bindings for the VMD molfile plugins Susana Tomasio (Tue Mar 01 2011 - 10:16:18 CST)
- Re: Compiling Fortran bindings for the VMD molfile plugins John Stone (Tue Mar 01 2011 - 10:24:32 CST)
  - Re: Compiling Fortran bindings for the VMD molfile plugins Susana Tomasio (Tue Mar 01 2011 - 10:34:35 CST)
  - Re: Compiling Fortran bindings for the VMD molfile plugins John Stone (Thu Mar 03 2011 - 13:28:03 CST)
VMD 1.9 beta 2 posted for download... John Stone (Mon Feb 28 2011 - 21:44:36 CST)
TCL Related Question Phelan Jr., Frederick R. Dr. (Mon Feb 28 2011 - 21:34:31 CST)
Can paratools really parametrize a structure? Is it really finished? Ranyere Deyler (Mon Feb 28 2011 - 10:55:21 CST)
surf fails with TIP4P water in VMD 1.9b1 chris.neale_at_utoronto.ca (Mon Feb 28 2011 - 10:52:08 CST)
- Re: surf fails with TIP4P water in VMD 1.9b1 John Stone (Mon Feb 28 2011 - 10:57:03 CST)
Drawing Bonds in Periodic structure soumyajyoti haldar (Mon Feb 28 2011 - 10:07:32 CST)
- Re: Drawing Bonds in Periodic structure Olaf Lenz (Tue Mar 01 2011 - 03:06:06 CST)
  - Re: Drawing Bonds in Periodic structure soumyajyoti haldar (Tue Mar 01 2011 - 03:50:36 CST)
ERROR: graphics: color index value '1057' out of range Jervis Chu (Sun Feb 27 2011 - 08:41:00 CST)
- Re2: ERROR: graphics: color index value '1057' out of range Jervis Chu (Sun Feb 27 2011 - 20:43:03 CST)
  - Re: Re2: ERROR: graphics: color index value '1057' out of range John Stone (Sun Feb 27 2011 - 22:03:44 CST)
pot.dx question Robin Varghese (Sat Feb 26 2011 - 15:43:35 CST)
pot.dx file question Robin Varghese (Sat Feb 26 2011 - 15:42:04 CST)
Pot.dx files Robin Varghese (Sat Feb 26 2011 - 15:02:14 CST)
- Re: Pot.dx files Axel Kohlmeyer (Sat Feb 26 2011 - 15:50:57 CST)
  - Re: Pot.dx files Robin Varghese (Sat Feb 26 2011 - 17:18:56 CST)
Server for structural models of the unfolded state of proteins Samy Hamdouche (Fri Feb 25 2011 - 19:03:15 CST)
- Re: Server for structural models of the unfolded state of proteins Axel Kohlmeyer (Fri Feb 25 2011 - 19:48:08 CST)
- Re: Server for structural models of the unfolded state of proteins Joshua Adelman (Fri Feb 25 2011 - 20:53:53 CST)
lindex related question Pavan Ghatty (Fri Feb 25 2011 - 15:09:45 CST)
- Re: lindex related question Axel Kohlmeyer (Fri Feb 25 2011 - 15:49:48 CST)
- Re: lindex related question Axel Kohlmeyer (Fri Feb 25 2011 - 16:11:42 CST)
showing fixed number of frames as the animation Lin, Kan-Ju (Fri Feb 25 2011 - 13:27:26 CST)
- Re: showing fixed number of frames as the animation Jérôme Hénin (Sat Feb 26 2011 - 07:43:45 CST)
  - Re: showing fixed number of frames as the animation Jérôme Hénin (Sat Feb 26 2011 - 08:01:58 CST)
Paratool`s error reading single point calculation. Ranyere Deyler (Fri Feb 25 2011 - 13:24:42 CST)
Adding bonds between many metal atoms Qiang Fu (Fri Feb 25 2011 - 09:48:45 CST)
- Re: Adding bonds between many metal atoms Axel Kohlmeyer (Fri Feb 25 2011 - 10:33:27 CST)
  - Re: Adding bonds between many metal atoms Qiang Fu (Mon Feb 28 2011 - 03:41:34 CST)
Fwd: autopsf-patches C++ error 'expected integer but got "" ""' SOLVED, MY FAULT Francesco Pietra (Fri Feb 25 2011 - 07:59:56 CST)
package psfgen: Failed to set coordinates for C3 Sebastian Maximilian Wilhelm (Fri Feb 25 2011 - 05:30:45 CST)
- Re: package psfgen: Failed to set coordinates for C3 Jérôme Hénin (Fri Feb 25 2011 - 08:55:47 CST)
Intel HD Graphics and VMD Peixi Zhu (Thu Feb 24 2011 - 22:28:40 CST)
- Re: Intel HD Graphics and VMD John Stone (Sun Feb 27 2011 - 23:22:29 CST)
Using the MovieMaker Phelan Jr., Frederick R. Dr. (Thu Feb 24 2011 - 15:52:28 CST)
- Re: Using the MovieMaker Axel Kohlmeyer (Thu Feb 24 2011 - 16:57:19 CST)
- Re: Using the MovieMaker John Stone (Thu Feb 24 2011 - 20:42:33 CST)
Area per lipid snoze pa (Thu Feb 24 2011 - 12:35:30 CST)
vmd1.9beta1 Bennion, Brian (Wed Feb 23 2011 - 14:21:51 CST)
- feature request Francesco Oteri (Wed Feb 23 2011 - 15:37:34 CST)
  - Re: feature request John Stone (Wed Feb 23 2011 - 15:45:48 CST)
- Re: vmd1.9beta1 Peter Freddolino (Wed Feb 23 2011 - 19:30:06 CST)
  - RE: vmd1.9beta1 namdEnergyPlugin Bennion, Brian (Thu Feb 24 2011 - 12:42:02 CST)
RMSF measurement Alex Liu (Wed Feb 23 2011 - 12:51:16 CST)
- Re: RMSF measurement Jérôme Hénin (Thu Feb 24 2011 - 05:47:36 CST)
abuot avpos emiliawu_at_dicp.ac.cn (Thu Feb 24 2011 - 00:57:00 CST)
- Re: abuot avpos John Stone (Wed Feb 23 2011 - 13:02:12 CST)
autopsf-patches C++ error 'expected integer but got "" ""' Francesco Pietra (Wed Feb 23 2011 - 10:21:11 CST)
- Re: autopsf-patches C++ error 'expected integer but got "" ""' John Stone (Wed Feb 23 2011 - 10:34:09 CST)
  - Re: autopsf-patches C++ error 'expected integer but got "" ""' Francesco Pietra (Wed Feb 23 2011 - 10:42:55 CST)
Incorrect results from 'measure dipole -masscenter' Stéphane Pezennec (Wed Feb 23 2011 - 07:24:02 CST)
- Re: Incorrect results from 'measure dipole -masscenter' Axel Kohlmeyer (Wed Feb 23 2011 - 09:12:37 CST)
  - Re: Incorrect results from 'measure dipole -masscenter' Stéphane Pezennec (Wed Feb 23 2011 - 10:30:36 CST)
    - Re: Incorrect results from 'measure dipole -masscenter' John Stone (Wed Feb 23 2011 - 13:55:38 CST)
    - Re: Incorrect results from 'measure dipole -masscenter' Stéphane Pezennec (Thu Feb 24 2011 - 03:05:22 CST)
how to write out the dcd file by vmd python command? mjyang (Mon Feb 21 2011 - 22:40:48 CST)
how to write out the dcd file by vmd python command? mjyang (Mon Feb 21 2011 - 22:09:17 CST)
- Re: how to write out the dcd file by vmd python command? Axel Kohlmeyer (Tue Feb 22 2011 - 07:19:28 CST)
Drawing using variables Phelan Jr., Frederick R. Dr. (Mon Feb 21 2011 - 16:01:52 CST)
- Re: Drawing using variables Axel Kohlmeyer (Mon Feb 21 2011 - 17:14:58 CST)
memory leak 1.8.7 and 1.9b1 Tim Meyer (Mon Feb 21 2011 - 09:13:18 CST)
- Re: memory leak 1.8.7 and 1.9b1 John Stone (Mon Feb 21 2011 - 09:48:08 CST)
- Re: memory leak 1.8.7 and 1.9b1 Axel Kohlmeyer (Mon Feb 21 2011 - 10:10:41 CST)
Application Error while use of Auto PSF Builder Sebastian Wilhelm (Sun Feb 20 2011 - 07:54:35 CST)
- Re: Application Error while use of Auto PSF Builder Axel Kohlmeyer (Sun Feb 20 2011 - 09:42:19 CST)
atoms selection Iman Salehinia (Sat Feb 19 2011 - 16:33:27 CST)
- Re: atoms selection Axel Kohlmeyer (Sun Feb 20 2011 - 12:18:56 CST)
  - Re: atoms selection Jérôme Hénin (Mon Feb 21 2011 - 08:18:04 CST)
ParaTool alamng_at_uci.edu (Sat Feb 19 2011 - 15:43:36 CST)
- Re: ParaTool Axel Kohlmeyer (Sun Feb 20 2011 - 12:25:46 CST)
scripts CGTools menica dibenedetto (Fri Feb 18 2011 - 05:11:05 CST)
- Fwd: scripts CGTools menica dibenedetto (Fri Feb 18 2011 - 06:39:29 CST)
  - Re: scripts CGTools Axel Kohlmeyer (Fri Feb 18 2011 - 07:25:44 CST)
Compiling on Windows David Joiner (Thu Feb 17 2011 - 14:12:44 CST)
- Re: Compiling on Windows John Stone (Thu Feb 17 2011 - 14:40:24 CST)
  - Re: Compiling on Windows David Joiner (Thu Feb 17 2011 - 19:57:13 CST)
VMD Volmap ILS Error & Orient Function larac_at_berkeley.edu (Thu Feb 17 2011 - 12:13:40 CST)
- Re: VMD Volmap ILS Error & Orient Function Axel Kohlmeyer (Thu Feb 17 2011 - 13:54:49 CST)
  - Re: VMD Volmap ILS Error & Orient Function larac_at_berkeley.edu (Fri Feb 18 2011 - 12:10:06 CST)
RE: VMD 1.9 beta 1 posted for download... Julie Grouleff (Thu Feb 17 2011 - 09:21:49 CST)
- Re: VMD 1.9 beta 1 posted for download... John Stone (Thu Feb 17 2011 - 09:36:22 CST)
- Re: VMD 1.9 beta 1 posted for download... Axel Kohlmeyer (Thu Feb 17 2011 - 10:15:08 CST)
Dynamically updating water colors for each frame of a trajectory J. Nathan Scott (Wed Feb 16 2011 - 17:17:28 CST)
- Re: Dynamically updating water colors for each frame of a trajectory Axel Kohlmeyer (Wed Feb 16 2011 - 18:01:35 CST)
- Re: Dynamically updating water colors for each frame of a trajectory Jérôme Hénin (Thu Feb 17 2011 - 04:10:04 CST)
  - Re: Dynamically updating water colors for each frame of a trajectory J. Nathan Scott (Wed Feb 23 2011 - 12:10:38 CST)
PBC & Solvate Tool in VMD Sharlene Denos (Wed Feb 16 2011 - 00:03:36 CST)
- Re: PBC & Solvate Tool in VMD Ajasja LjubetiÄ (Wed Feb 16 2011 - 03:20:25 CST)
- RE: PBC & Solvate Tool in VMD JC Gumbart (Wed Feb 16 2011 - 07:49:41 CST)
  - Re: PBC & Solvate Tool in VMD Sharlene Denos (Wed Feb 16 2011 - 08:37:30 CST)
PBC Option With Solvate Tool Sharlene Denos (Tue Feb 15 2011 - 23:31:00 CST)
VMD 1.9 beta 1 posted for download... John Stone (Tue Feb 15 2011 - 19:26:31 CST)
- Re: VMD 1.9 beta 1 posted for download... John Stone (Wed Feb 16 2011 - 11:21:31 CST)
DOPC membrane snoze pa (Tue Feb 15 2011 - 17:35:24 CST)
- Re: DOPC membrane JC Gumbart (Tue Feb 15 2011 - 19:52:11 CST)
bring z-axis along a new vector dhacademic (Tue Feb 15 2011 - 14:39:04 CST)
- Re: bring z-axis along a new vector Ajasja LjubetiÄ (Wed Feb 16 2011 - 03:00:01 CST)
conflict between VMD and Cygwin Li, Liwei (Mon Feb 14 2011 - 18:02:00 CST)
- Re: conflict between VMD and Cygwin John Stone (Mon Feb 14 2011 - 18:19:52 CST)
setting different bond length for different atom pair Debasis Sengupta (Fri Feb 11 2011 - 12:01:44 CST)
- Re: setting different bond length for different atom pair Axel Kohlmeyer (Fri Feb 11 2011 - 13:00:56 CST)
  - Volmap ILS: Orient function & Invalid VDW parameters Error larac_at_berkeley.edu (Tue Feb 15 2011 - 18:23:57 CST)
  - Re: setting different bond length for different atom pair Debasis Sengupta (Thu Apr 14 2011 - 12:07:56 CDT)
    - Re: setting different bond length for different atom pair John Stone (Fri Apr 15 2011 - 16:24:55 CDT)
Re: only one model is displayed Joyce Tan (Fri Feb 11 2011 - 10:50:31 CST)
- Re: only one model is displayed John Stone (Fri Feb 11 2011 - 12:49:23 CST)
only one model is displayed Joyce Tan (Fri Feb 11 2011 - 09:56:39 CST)
dipole / move (align) Stéphane Pezennec (Fri Feb 11 2011 - 08:25:43 CST)
One more psfgen question Marc Charendoff (Thu Feb 10 2011 - 15:40:14 CST)
how to update the selection in NAMDEnergy juan roman (Tue Feb 08 2011 - 20:02:15 CST)
- Re: how to update the selection in NAMDEnergy Peter Freddolino (Tue Feb 08 2011 - 23:35:00 CST)
Re: Fwd: [multiple topology files and resetpsf] Jim Phillips (Tue Feb 08 2011 - 14:49:48 CST)
psfgen script for VMD 1.8.7 Marc Charendoff (Tue Feb 08 2011 - 12:26:25 CST)
- RE: psfgen script for VMD 1.8.7 Mark Cunningham (Tue Feb 08 2011 - 20:48:50 CST)
multiple topology files and resetpsf Goldsmith, Jacob (Tue Feb 08 2011 - 10:11:54 CST)
- Re: multiple topology files and resetpsf Axel Kohlmeyer (Tue Feb 08 2011 - 16:38:35 CST)
  - RE: multiple topology files and resetpsf Goldsmith, Jacob (Wed Feb 09 2011 - 07:38:42 CST)
Displaying an overlay of multiple structures with VMD B.M.B. Vanschouwen (Tue Feb 08 2011 - 09:19:45 CST)
- Re: Displaying an overlay of multiple structures with VMD John Stone (Tue Feb 08 2011 - 14:22:21 CST)
  - Re: Displaying an overlay of multiple structures with VMD John Stone (Thu Feb 10 2011 - 12:56:22 CST)
- Re: Displaying an overlay of multiple structures with VMD Axel Kohlmeyer (Tue Feb 08 2011 - 16:28:23 CST)
VMD Volmap ILS Error larac_at_berkeley.edu (Mon Feb 07 2011 - 18:23:21 CST)
- Re: VMD Volmap ILS Error Axel Kohlmeyer (Mon Feb 07 2011 - 19:25:54 CST)
  - Re: VMD Volmap ILS Error larac_at_berkeley.edu (Tue Feb 08 2011 - 15:15:48 CST)
    - Re: VMD Volmap ILS Error Axel Kohlmeyer (Tue Feb 08 2011 - 16:25:00 CST)
Multiseq in text mode Ekta Khurana (Mon Feb 07 2011 - 13:11:57 CST)
- Re: Multiseq in text mode Axel Kohlmeyer (Mon Feb 07 2011 - 19:33:48 CST)
- Re: Multiseq in text mode John Stone (Mon Feb 07 2011 - 20:30:11 CST)
  - Re: Multiseq in text mode Ekta Khurana (Mon Feb 07 2011 - 23:33:00 CST)
ERROR while using PSF builder vani panguluri (Mon Feb 07 2011 - 11:29:09 CST)
- Re: ERROR while using PSF builder John Stone (Mon Feb 07 2011 - 20:25:33 CST)
- latest vmd Francesco Oteri (Sat Feb 12 2011 - 18:23:52 CST)
  - Re: latest vmd Axel Kohlmeyer (Sat Feb 12 2011 - 19:06:57 CST)
Helix motions ban arn (Mon Feb 07 2011 - 05:29:31 CST)
- Re: Helix motions Hurt, Darrell (NIH/NIAID) [E] (Mon Feb 07 2011 - 06:54:08 CST)
  - Re: Helix motions ban arn (Wed Feb 09 2011 - 10:50:45 CST)
graphical representations over a number of molecule files Stephen Cox (Sun Feb 06 2011 - 14:38:30 CST)
- Re: graphical representations over a number of molecule files Axel Kohlmeyer (Sun Feb 06 2011 - 15:43:12 CST)
  - Re: graphical representations over a number of molecule files Stephen Cox (Mon Feb 07 2011 - 04:00:48 CST)
  - Re: graphical representations over a number of molecule files Stephen Cox (Mon Mar 07 2011 - 13:28:41 CST)
CA distance command ban arn (Thu Feb 03 2011 - 08:16:14 CST)
Adding missing residues to a protein sriteja mantha (Wed Feb 02 2011 - 23:40:47 CST)
CG_MD temperature Sibel Cakan (Wed Feb 02 2011 - 17:56:12 CST)
- Re: CG_MD temperature BIN ZHANG (Thu Feb 03 2011 - 01:30:15 CST)
a detail about PSFGENv1.4 Seth Tanner (Wed Feb 02 2011 - 12:49:37 CST)
- Re: a detail about PSFGENv1.4 Jim Phillips (Wed Feb 02 2011 - 22:45:23 CST)
Re: USING IED for essential dynamics in VMD bharat gupta (Tue Feb 01 2011 - 18:38:39 CST)
- Re: Re: USING IED for essential dynamics in VMD Axel Kohlmeyer (Tue Feb 01 2011 - 19:34:30 CST)
Installation problem with VMD, Multiseq, and BLAST David Guertin (Tue Feb 01 2011 - 10:49:24 CST)
- Re: Installation problem with VMD, Multiseq, and BLAST Kirby Vandivort (Tue Feb 01 2011 - 11:08:55 CST)
  - Re: Installation problem with VMD, Multiseq, and BLAST David Guertin (Tue Feb 01 2011 - 12:50:04 CST)
Installation problem with VMD, Multiseq, and BLAST David Guertin (Tue Feb 01 2011 - 10:15:48 CST)
water molecule count ban arn (Tue Feb 01 2011 - 08:56:55 CST)
- Re: water molecule count Jérôme Hénin (Tue Feb 01 2011 - 10:12:47 CST)
  - Re: water molecule count ban arn (Tue Feb 01 2011 - 10:25:52 CST)
    - Re: water molecule count Jérôme Hénin (Tue Feb 01 2011 - 11:19:15 CST)
    - Re: water molecule count Axel Kohlmeyer (Tue Feb 01 2011 - 11:33:34 CST)
Side-chain Dihedrals ban arn (Tue Feb 01 2011 - 05:07:19 CST)
- Re: Side-chain Dihedrals Ajasja LjubetiÄ (Tue Feb 01 2011 - 14:46:23 CST)
  - Re: Side-chain Dihedrals Ajasja LjubetiÄ (Tue Feb 01 2011 - 16:13:36 CST)
Re: using IED interface in VMD 1.8.7 windows bharat gupta (Tue Feb 01 2011 - 02:51:45 CST)
How to use VMD script "PorcupinePlot.tcl" B.M.B. Vanschouwen (Mon Jan 31 2011 - 10:46:55 CST)
- Re: How to use VMD script "PorcupinePlot.tcl" Axel Kohlmeyer (Mon Jan 31 2011 - 11:59:50 CST)
vmd draw command for text kaushik lakkaraju (Sun Jan 30 2011 - 12:32:01 CST)
- Re: vmd draw command for text John Stone (Tue Feb 01 2011 - 09:47:07 CST)
CG Builder mohamad rahimi (Sun Jan 30 2011 - 03:31:23 CST)
- Re: CG Builder Axel Kohlmeyer (Sun Jan 30 2011 - 05:53:54 CST)
  - Re: CG Builder mohamad rahimi (Sun Jan 30 2011 - 06:14:03 CST)
    - Re: CG Builder Axel Kohlmeyer (Sun Jan 30 2011 - 08:54:59 CST)
License question Gianluca Interlandi (Sat Jan 29 2011 - 16:19:27 CST)
- Re: License question John Stone (Sat Jan 29 2011 - 19:18:20 CST)
- VMD and Monte Carlo Gianluca Interlandi (Mon Jan 31 2011 - 14:13:24 CST)
Re: Trouble rendering tranparent atoms with Tachyon Ajasja Ljubetiè (Fri Jan 28 2011 - 09:06:11 CST)
- Re: Re: Trouble rendering tranparent atoms with Tachyon Axel Kohlmeyer (Fri Jan 28 2011 - 09:56:06 CST)
  - Re: Re: Trouble rendering tranparent atoms with Tachyon John Stone (Fri Jan 28 2011 - 10:14:26 CST)
    - Re: Re: Trouble rendering tranparent atoms with Tachyon Ajasja LjubetiÄ (Sat Jan 29 2011 - 06:42:06 CST)
illegal stereo mode Nicolas Belloy (Fri Jan 28 2011 - 08:34:28 CST)
- Re: illegal stereo mode John Stone (Fri Jan 28 2011 - 08:55:05 CST)
  - Re: illegal stereo mode Nicolas Belloy (Fri Jan 28 2011 - 08:58:11 CST)
- Re: illegal stereo mode Axel Kohlmeyer (Fri Jan 28 2011 - 09:23:45 CST)
vrml2 output crashes VTK/Paraview Peter C. Lai (Thu Jan 27 2011 - 19:14:25 CST)
- Re: vrml2 output crashes VTK/Paraview Axel Kohlmeyer (Thu Jan 27 2011 - 20:05:25 CST)
- Re: vrml2 output crashes VTK/Paraview John Stone (Thu Jan 27 2011 - 20:09:15 CST)
  - Re: vrml2 output crashes VTK/Paraview Peter C. Lai (Thu Feb 03 2011 - 02:42:17 CST)
    - Re: vrml2 output crashes VTK/Paraview John Stone (Thu Feb 03 2011 - 09:25:00 CST)
RE: How can I add bonds ? Germain Salvato Vallverdu (Thu Jan 27 2011 - 14:31:08 CST)
- RE: How can I add bonds ? Axel Kohlmeyer (Thu Jan 27 2011 - 14:49:19 CST)
  - RE: How can I add bonds ? Germain Salvato Vallverdu (Thu Jan 27 2011 - 15:10:57 CST)
  - RE: How can I add bonds ? Germain Salvato Vallverdu (Thu Jan 27 2011 - 16:38:08 CST)
Warning in the log file candy deck (Thu Jan 27 2011 - 09:28:12 CST)
Slower FPS in dual monitor systems? Ramon Crehuet (Thu Jan 27 2011 - 07:24:03 CST)
- Re: Slower FPS in dual monitor systems? Axel Kohlmeyer (Thu Jan 27 2011 - 08:17:19 CST)
removing all water molecules ahmet yýldýrým (Thu Jan 27 2011 - 06:51:34 CST)
- Re: removing all water molecules Dudo (Thu Jan 27 2011 - 07:40:16 CST)
  - Re: removing all water molecules Dudo (Thu Jan 27 2011 - 08:05:54 CST)
    - Re: removing all water molecules Salvatore Mario Cosseddu (Thu Jan 27 2011 - 10:27:32 CST)
- Re: removing all water molecules Axel Kohlmeyer (Thu Jan 27 2011 - 08:08:27 CST)
- Re: removing all water molecules Ajasja LjubetiÄ (Thu Jan 27 2011 - 07:37:57 CST)
  - Re: removing all water molecules Axel Kohlmeyer (Thu Jan 27 2011 - 08:28:46 CST)
    - Re: removing all water molecules Dudo (Thu Jan 27 2011 - 09:41:49 CST)
- Re: removing all water molecules Joshua Adelman (Thu Jan 27 2011 - 08:24:09 CST)
- Re: removing all water molecules Salvatore Mario Cosseddu (Thu Jan 27 2011 - 09:14:40 CST)
a problem about multiplot superdirac (Wed Jan 26 2011 - 20:01:18 CST)
- Re: a problem about multiplot John Stone (Wed Jan 26 2011 - 20:19:47 CST)
  - Re: a problem about multiplot superdirac (Wed Jan 26 2011 - 21:09:38 CST)
    - Fw: Re: a problem about multiplot superdirac (Wed Jan 26 2011 - 21:43:38 CST)
    - Re: a problem about multiplot Jérôme Hénin (Thu Jan 27 2011 - 04:04:55 CST)
Question regarding g(r) utility Narayanan Veeraraghavan (Wed Jan 26 2011 - 17:30:33 CST)
- Re: Question regarding g(r) utility Axel Kohlmeyer (Wed Jan 26 2011 - 18:35:47 CST)
GLSL with ATI 5750 in Mac OS X 10.6 / 64-bit build Joshua A. Anderson (Wed Jan 26 2011 - 14:17:05 CST)
- Re: GLSL with ATI 5750 in Mac OS X 10.6 / 64-bit build John Stone (Wed Jan 26 2011 - 14:31:53 CST)
  - Re: GLSL with ATI 5750 in Mac OS X 10.6 / 64-bit build Joshua A. Anderson (Thu Jan 27 2011 - 06:35:56 CST)
    - Re: GLSL with ATI 5750 in Mac OS X 10.6 / 64-bit build John Stone (Thu Jan 27 2011 - 13:44:16 CST)
  - Re: GLSL with ATI 5750 in Mac OS X 10.6 / 64-bit build John Stone (Thu Mar 10 2011 - 16:38:33 CST)
a script for angular distribution David Wedner (Wed Jan 26 2011 - 11:41:51 CST)
a script for angular distribution David Wedner (Wed Jan 26 2011 - 10:44:34 CST)
duplicate frames / slow down movie Nicolas Belloy (Tue Jan 25 2011 - 07:50:10 CST)
- Re: duplicate frames / slow down movie Axel Kohlmeyer (Tue Jan 25 2011 - 08:55:42 CST)
Secondary Structure of alkane polymers Manish Agarwal (Mon Jan 24 2011 - 15:43:47 CST)
- Re: Secondary Structure of alkane polymers Axel Kohlmeyer (Mon Jan 24 2011 - 16:42:43 CST)
  - Re: Secondary Structure of alkane polymers Manish Agarwal (Mon Jan 24 2011 - 17:48:07 CST)
    - Re: Secondary Structure of alkane polymers Axel Kohlmeyer (Mon Jan 24 2011 - 21:27:07 CST)
How can I add bonds ? Germain Salvato Vallverdu (Mon Jan 24 2011 - 09:01:39 CST)
- Re: How can I add bonds ? Axel Kohlmeyer (Mon Jan 24 2011 - 09:58:19 CST)
  - Re: How can I add bonds ? Germain Vallverdu (Wed Jan 26 2011 - 08:57:30 CST)
    - Re: How can I add bonds ? Axel Kohlmeyer (Wed Jan 26 2011 - 10:02:42 CST)
draw bond across cell boudary pascal boulet (Thu Jan 20 2011 - 15:47:44 CST)
- Re: draw bond across cell boudary Nima Nouri (Fri Jan 21 2011 - 01:01:23 CST)
question from a tutorial Lisa Brown (Thu Jan 20 2011 - 14:17:29 CST)
- Re: namd-l: question from a tutorial JC Gumbart (Thu Jan 20 2011 - 14:29:23 CST)
Formats supported by animate write file_type Salvatore Mario Cosseddu (Thu Jan 20 2011 - 10:19:42 CST)
Displaying Bead and Bonds Phelan Jr., Frederick R. Dr. (Wed Jan 19 2011 - 13:32:48 CST)
- Re: Displaying Bead and Bonds Axel Kohlmeyer (Wed Jan 19 2011 - 14:30:29 CST)
Problem installing vmd in UBUNTU 10.10 Nima Nouri (Sat Jan 15 2011 - 12:55:17 CST)
- Re: Problem installing vmd in UBUNTU 10.10 John Stone (Sat Jan 15 2011 - 13:15:09 CST)
  - Re: Problem installing vmd in UBUNTU 10.10 Nima Nouri (Sat Jan 15 2011 - 13:18:21 CST)
Where can I download VMD alpha version Nima Nouri (Sat Jan 15 2011 - 09:30:16 CST)
- Re: Where can I download VMD alpha version Axel Kohlmeyer (Sat Jan 15 2011 - 10:45:14 CST)
- Re: Where can I download VMD alpha version Ajasja LjubetiÄ (Sat Jan 15 2011 - 11:05:34 CST)
problem in extracting frame number dhacademic (Thu Jan 13 2011 - 09:45:16 CST)
- Re: problem in extracting frame number John Stone (Thu Jan 13 2011 - 09:53:20 CST)
  - Re: problem in extracting frame number dhacademic (Thu Jan 13 2011 - 13:08:17 CST)
    - Re: problem in extracting frame number Ajasja LjubetiÄ (Thu Jan 13 2011 - 15:46:48 CST)
- Re: problem in extracting frame number Eduard Schreiner (Thu Jan 13 2011 - 10:33:34 CST)
FW: Issues with Paratools and Gaussian Ali, Rejwan (Wed Jan 12 2011 - 11:57:16 CST)
VTF trajectory from coarse grained ESPReSo simulations. Visualization in Windows. Dudo (Wed Jan 12 2011 - 06:41:27 CST)
- Re: VTF trajectory from coarse grained ESPReSo simulations. Visualization in Windows. Axel Kohlmeyer (Wed Jan 12 2011 - 11:40:12 CST)
  - Re: VTF trajectory from coarse grained ESPReSo simulations. Visualization in Windows. Dudo (Wed Jan 12 2011 - 12:16:39 CST)
Truncated octahedron Box francesco oteri (Wed Jan 12 2011 - 04:43:17 CST)
- Re: Truncated octahedron Box Jérôme Hénin (Wed Jan 12 2011 - 10:59:34 CST)
Issues with Paratools and Gaussian Ali, Rejwan (Tue Jan 11 2011 - 14:51:18 CST)
- Re: Issues with Paratools and Gaussian Jacqueline Cawthray (Tue Jan 11 2011 - 17:09:37 CST)
  - Re: Issues with Paratools and Gaussian Aaron Oakley (Tue Jan 11 2011 - 19:57:49 CST)
  - RE: Issues with Paratools and Gaussian Ali, Rejwan (Wed Jan 12 2011 - 11:54:33 CST)
    - RE: Issues with Paratools and Gaussian Ali, Rejwan (Wed Jan 12 2011 - 12:13:54 CST)
    - Re: Issues with Paratools and Gaussian JC Gumbart (Sun Jan 16 2011 - 17:12:10 CST)
namd energy plugin error: toplevel Michela Candotti (Tue Jan 11 2011 - 04:09:14 CST)
- Re: namd energy plugin error: toplevel Axel Kohlmeyer (Tue Jan 11 2011 - 09:22:22 CST)
a guide for installing vmd-1.8.7 on ubuntu10.10 (LINUXAMD64) Andrew Jewett (Mon Jan 10 2011 - 19:56:23 CST)
- Re: a guide for installing vmd-1.8.7 on ubuntu10.10 (LINUXAMD64) Andrew Jewett (Mon Jan 10 2011 - 22:27:39 CST)
pbctools & Desmond trajectory with protein units 'jumping' into other cells Irene Newhouse (Mon Jan 10 2011 - 13:22:26 CST)
volumetric trajectory Fahimeh Baftizadeh (Mon Jan 10 2011 - 04:50:46 CST)
- Re: volumetric trajectory John Stone (Mon Jan 10 2011 - 14:28:55 CST)
  - Re: volumetric trajectory Fahimeh Baftizadeh (Mon Jan 10 2011 - 15:29:46 CST)
vmd with 3d vision Yubo Fan (Fri Jan 07 2011 - 15:35:49 CST)
- Re: vmd with 3d vision Axel Kohlmeyer (Fri Jan 07 2011 - 16:20:40 CST)
  - Re: vmd with 3d vision Yubo Fan (Fri Jan 07 2011 - 16:27:31 CST)
Re: Binary request Axel Kohlmeyer (Fri Jan 07 2011 - 09:01:48 CST)
Binary request Nima Nouri (Fri Jan 07 2011 - 04:19:13 CST)
- Re: Binary request Axel Kohlmeyer (Fri Jan 07 2011 - 08:15:18 CST)
orientation of protein molecule prabhakar g (Wed Jan 05 2011 - 18:12:19 CST)
- Re: orientation of protein molecule Joshua Adelman (Wed Jan 05 2011 - 19:59:46 CST)
- Re: orientation of protein molecule Axel Kohlmeyer (Wed Jan 05 2011 - 19:17:55 CST)
VMD 1.8.7 and lammpsplugin.so error Stephanie Teich-McGoldrick (Wed Jan 05 2011 - 15:14:59 CST)
- Re: VMD 1.8.7 and lammpsplugin.so error Axel Kohlmeyer (Wed Jan 05 2011 - 16:48:16 CST)
  - Re: VMD 1.8.7 and lammpsplugin.so error Stephanie Teich-McGoldrick (Fri Jan 07 2011 - 11:02:33 CST)
Regarding fitframes.tcl pragya.saxena_at_research.iiit.ac.in (Tue Jan 04 2011 - 04:51:39 CST)
- Re: Regarding fitframes.tcl Eduard Schreiner (Tue Jan 04 2011 - 05:31:58 CST)
  - Re: Regarding fitframes.tcl pragya.saxena_at_research.iiit.ac.in (Tue Jan 04 2011 - 06:41:21 CST)
  - Re: Regarding fitframes.tcl pragya.saxena_at_research.iiit.ac.in (Tue Jan 04 2011 - 07:37:45 CST)
    - Re: Regarding fitframes.tcl Eduard Schreiner (Tue Jan 04 2011 - 07:48:33 CST)
How to show dynamic bonds? Jervis Chu (Tue Jan 04 2011 - 01:58:39 CST)
- Re: How to show dynamic bonds? Axel Kohlmeyer (Tue Jan 04 2011 - 09:28:39 CST)
- Re: Re: How to show dynamic bonds? Jervis Chu (Thu Jan 06 2011 - 01:06:18 CST)
  - Re: Re: How to show dynamic bonds? Axel Kohlmeyer (Thu Jan 06 2011 - 08:27:52 CST)
(no subject) Sibel Cakan (Mon Jan 03 2011 - 04:15:23 CST)
- Re: Axel Kohlmeyer (Mon Jan 03 2011 - 05:04:23 CST)
the IR spetra calculation module - from MD trajectory Jun Zhao (Sat Jan 01 2011 - 15:12:48 CST)
- Re: the IR spetra calculation module - from MD trajectory Axel Kohlmeyer (Sat Jan 01 2011 - 16:09:04 CST)
Re: how to make the picture size suitable for the image size in pov file ? Cun Zhang (Fri Dec 31 2010 - 20:08:42 CST)
Running Namd in Window zizi moradi (Fri Dec 31 2010 - 18:34:43 CST)
- Re: Running Namd in Window John Stone (Mon Jan 03 2011 - 13:46:34 CST)
  - Molecular viewer for android or iPhone Gianluca Interlandi (Wed Aug 08 2012 - 12:44:36 CDT)
error in the conversion of dcd to pdb files Ramya Narasimhan (Fri Dec 31 2010 - 04:11:06 CST)
- Re: error in the conversion of dcd to pdb files Axel Kohlmeyer (Fri Dec 31 2010 - 04:54:08 CST)
  - Re: error in the conversion of dcd to pdb files Ramya Narasimhan (Sun Jan 02 2011 - 23:50:43 CST)
    - Re: error in the conversion of dcd to pdb files Axel Kohlmeyer (Mon Jan 03 2011 - 04:58:45 CST)
how to make the picture size suitable for the image size in pov file ? Cun Zhang (Thu Dec 30 2010 - 20:52:14 CST)
Volmap Tool: Angular or spatial correlation function around a center molecule Xijun Wang (Wed Dec 29 2010 - 17:57:56 CST)
- Re: Volmap Tool: Angular or spatial correlation function around a center molecule Axel Kohlmeyer (Thu Dec 30 2010 - 14:53:56 CST)
MOE and NAMD Bharat Kumar (Wed Dec 29 2010 - 09:55:21 CST)
- Re: MOE and NAMD Axel Kohlmeyer (Thu Dec 30 2010 - 14:43:20 CST)
  - Re: MOE and NAMD Bharat Kumar (Thu Dec 30 2010 - 18:31:21 CST)
psfgen or autopsf leila karami (Sun Dec 26 2010 - 08:11:34 CST)
- Re: psfgen or autopsf Axel Kohlmeyer (Sun Dec 26 2010 - 09:25:08 CST)
conversion of gromacs trajectory file (xtc) to amber trajectory file (mdcrd) leila karami (Sat Dec 25 2010 - 09:14:57 CST)
- Re: conversion of gromacs trajectory file (xtc) to amber trajectory file (mdcrd) Axel Kohlmeyer (Sat Dec 25 2010 - 11:20:06 CST)
Bad Length and GLXBadLargeRequest errors Corenflos, Steven (Wed Dec 22 2010 - 15:57:58 CST)
- Re: Bad Length and GLXBadLargeRequest errors Axel Kohlmeyer (Thu Dec 23 2010 - 04:01:03 CST)
Re: regarding counting water molecules Joshua Adelman (Wed Dec 22 2010 - 07:26:33 CST)
consultation about metal_enviroment.tcl ÅÓ´ºÀö (Wed Dec 22 2010 - 03:30:20 CST)
- Re: consultation about metal_enviroment.tcl Dong Luo (Wed Dec 22 2010 - 09:45:19 CST)
"Hands-On" Workshop on Computational Biophysics, March 21-25, 2011, Atlanta, GA, USA David Brandon (Tue Dec 21 2010 - 14:38:16 CST)
rmsd with 2 different structures using serial numbers Lisa Perez (Tue Dec 21 2010 - 13:30:33 CST)
- Re: rmsd with 2 different structures using serial numbers Lisa Perez (Tue Dec 21 2010 - 14:38:48 CST)
  - Re: rmsd with 2 different structures using serial numbers JC Gumbart (Tue Dec 21 2010 - 21:40:43 CST)
    - Re: rmsd with 2 different structures using serial numbers Lisa Perez (Wed Dec 22 2010 - 11:43:28 CST)
    - Re: rmsd with 2 different structures using serial numbers JC Gumbart (Wed Dec 22 2010 - 18:07:46 CST)
autopsf error: failed on end of segment Francesco Pietra (Tue Dec 21 2010 - 11:49:14 CST)
- Fwd: autopsf error: failed on end of segment Francesco Pietra (Wed Dec 22 2010 - 00:50:35 CST)
  - Re: Fwd: autopsf error: failed on end of segment Dong Luo (Wed Dec 22 2010 - 09:51:39 CST)
  - Re: Fwd: autopsf error: failed on end of segment Jim Phillips (Tue Dec 28 2010 - 17:03:41 CST)
    - Re: Fwd: autopsf error: failed on end of segment Peter Freddolino (Tue Dec 28 2010 - 19:01:22 CST)
Installing vmd-1.8.7 on LINUXAMD64 Michael Mwalaba (Tue Dec 21 2010 - 08:01:18 CST)
- Re: Installing vmd-1.8.7 on LINUXAMD64 Axel Kohlmeyer (Tue Dec 21 2010 - 08:49:30 CST)
RMSD and PSF generation Bharat Kumar (Mon Dec 20 2010 - 21:29:48 CST)
- Re: RMSD and PSF generation Hurt, Darrell (NIH/NIAID) [E] (Tue Dec 21 2010 - 11:18:00 CST)
selection of amino acids with certain distance each others leila karami (Sun Dec 19 2010 - 13:00:23 CST)
- Re: selection of amino acids with certain distance each others Axel Kohlmeyer (Sun Dec 19 2010 - 13:59:02 CST)
  - Re: selection of amino acids with certain distance each others Francesco Oteri (Sun Dec 19 2010 - 14:39:53 CST)
- Re: selection of amino acids with certain distance each others Ajasja LjubetiÄ (Sun Dec 19 2010 - 14:07:03 CST)
- Re: selection of amino acids with certain distance each others Joshua Adelman (Sun Dec 19 2010 - 15:00:40 CST)
xterm zaizhi lai (Fri Dec 17 2010 - 18:52:30 CST)
- Re: xterm Axel Kohlmeyer (Sat Dec 18 2010 - 04:42:42 CST)
delete water molecules siddesh southekal (Fri Dec 17 2010 - 07:18:17 CST)
- Re: delete water molecules Ajasja LjubetiÄ (Fri Dec 17 2010 - 08:29:52 CST)
  - Re: delete water molecules Joshua Adelman (Fri Dec 17 2010 - 10:31:41 CST)
    - Re: delete water molecules siddesh southekal (Sat Dec 18 2010 - 08:14:25 CST)
    - Re: delete water molecules Joshua Adelman (Sat Dec 18 2010 - 09:07:59 CST)
Save Atom Selection to DCD David Huggins (Wed Dec 15 2010 - 13:46:16 CST)
- Re: Save Atom Selection to DCD Wei Chen (Wed Dec 15 2010 - 14:55:24 CST)
- Re: Save Atom Selection to DCD Axel Kohlmeyer (Thu Dec 16 2010 - 04:29:53 CST)
why atom positions are reset after readpsf, coordpdb commands? ºÎØ¹»Ô (Wed Dec 15 2010 - 03:37:53 CST)
- Re: why atom positions are reset after readpsf, coordpdb commands? Erik Nordgren (Thu Dec 16 2010 - 13:25:22 CST)
  - Re: why atom positions are reset after readpsf, coordpdb commands? Jim Phillips (Fri Dec 17 2010 - 10:58:39 CST)
problem regarding the MC trajectory Ramya Narasimhan (Wed Dec 15 2010 - 00:41:46 CST)
- Re: problem regarding the MC trajectory John Stone (Wed Dec 15 2010 - 16:25:24 CST)
  - Re: problem regarding the MC trajectory Ramya Narasimhan (Sun Dec 19 2010 - 23:40:19 CST)
Paratool Tutorial Jacqueline Cawthray (Tue Dec 14 2010 - 14:01:59 CST)
Rv: Re: Phonon spectrum and VACF jj mm (Tue Dec 14 2010 - 12:09:38 CST)
- Re: Rv: Re: Phonon spectrum and VACF Axel Kohlmeyer (Tue Dec 14 2010 - 13:08:07 CST)
Adsorption and diffusion candy deck (Tue Dec 14 2010 - 03:38:53 CST)
- Re: Adsorption and diffusion Axel Kohlmeyer (Tue Dec 14 2010 - 04:21:44 CST)
how to measure some constants matziast_at_med.uth.gr (Tue Dec 14 2010 - 03:26:17 CST)
- Re: how to measure some constants Axel Kohlmeyer (Tue Dec 14 2010 - 04:13:41 CST)
load of information on B factor as independent file JhonY. I. (Tue Dec 14 2010 - 00:55:12 CST)
- Re: load of information on B factor as independent file Ajasja LjubetiÄ (Tue Dec 14 2010 - 02:38:42 CST)
- Re: load of information on B factor as independent file Axel Kohlmeyer (Tue Dec 14 2010 - 02:33:54 CST)
HBONDS bug? Nicolas Tilmans (Mon Dec 13 2010 - 15:21:20 CST)
- Re: HBONDS bug? Axel Kohlmeyer (Tue Dec 14 2010 - 02:36:38 CST)
automatic PSF builder leila karami (Mon Dec 13 2010 - 02:22:19 CST)
Using LES with solvated, ionized protein Jacqueline Cawthray (Sun Dec 12 2010 - 18:38:18 CST)
- Re: Using LES with solvated, ionized protein Jim Phillips (Tue Dec 28 2010 - 16:52:12 CST)
automatic PSF builder leila karami (Sun Dec 12 2010 - 08:25:03 CST)
- Re: automatic PSF builder Francesco Oteri (Sun Dec 12 2010 - 10:00:52 CST)
- Re: automatic PSF builder Axel Kohlmeyer (Mon Dec 13 2010 - 04:03:50 CST)
color change on atoms selected using mouse JhonY. I. (Thu Dec 09 2010 - 10:11:35 CST)
- Re: color change on atoms selected using mouse Axel Kohlmeyer (Thu Dec 09 2010 - 11:04:44 CST)
Plotting potential energy Joyce Tan (Thu Dec 09 2010 - 03:36:19 CST)
- Re: Plotting potential energy Axel Kohlmeyer (Thu Dec 09 2010 - 05:27:57 CST)
Phonon spectrum and VACF jj mm (Thu Dec 09 2010 - 03:11:03 CST)
- Re: Phonon spectrum and VACF Axel Kohlmeyer (Thu Dec 09 2010 - 05:26:13 CST)
Rotation about one axis Sweta Iyer (Wed Dec 08 2010 - 19:43:55 CST)
psfgen 1.4.7 and CMAP extended PSF Gianluca Interlandi (Wed Dec 08 2010 - 19:11:17 CST)
Translating protein along one coordinate Sweta Iyer (Tue Dec 07 2010 - 23:18:41 CST)
- Re: Translating protein along one coordinate John Stone (Thu Dec 09 2010 - 16:25:47 CST)
(no subject) Diehl, Alex (NIH/NCI) [V] (Tue Dec 07 2010 - 14:06:41 CST)
(no subject) Olimpia Popko (Tue Dec 07 2010 - 05:08:50 CST)
- Re: Kirby Vandivort (Tue Dec 07 2010 - 11:15:01 CST)
apocynin/1k4u vani panguluri (Mon Dec 06 2010 - 13:50:06 CST)
- Re: apocynin/1k4u John Stone (Tue Dec 07 2010 - 09:23:57 CST)
  - Re: apocynin/1k4u Ajasja LjubetiÄ (Tue Dec 07 2010 - 10:31:25 CST)
Bug in AutoIMD Tristan Croll (Sun Dec 05 2010 - 21:44:48 CST)
- Re: Bug in AutoIMD John Stone (Thu Dec 09 2010 - 16:42:53 CST)
Bug in AutoIMD Tristan Croll (Sun Dec 05 2010 - 19:42:50 CST)
Membrane Protein Tutorial Bharat Kumar (Sat Dec 04 2010 - 01:42:49 CST)
- Re: Membrane Protein Tutorial Bharat Kumar (Sun Dec 05 2010 - 22:40:28 CST)
  - surface representation question Joseph Bylund (Wed Dec 08 2010 - 12:15:02 CST)
- Re: Membrane Protein Tutorial John Stone (Mon Dec 06 2010 - 09:31:05 CST)
Plot the value of the current frame in the Progress Bar for elapsed Time ABEL Stephane 175950 (Thu Dec 02 2010 - 09:51:44 CST)
- Re: Plot the value of the current frame in the Progress Bar for elapsed Time Axel Kohlmeyer (Thu Dec 02 2010 - 10:47:31 CST)
  - RE : Plot the value of the current frame in the Progress Bar for elapsed Time ABEL Stephane 175950 (Thu Dec 02 2010 - 12:15:22 CST)
    - Re: RE : Plot the value of the current frame in the Progress Bar for elapsed Time Axel Kohlmeyer (Thu Dec 02 2010 - 13:44:37 CST)
generating lipid membrane psf file Patrick Fleming (Thu Dec 02 2010 - 07:15:22 CST)
- Re: generating lipid membrane psf file Axel Kohlmeyer (Thu Dec 02 2010 - 10:39:53 CST)
  - Re: generating lipid membrane psf file Ajasja LjubetiÄ (Sat Dec 04 2010 - 14:57:11 CST)
use gelato render with VMD 1.8.7 for movie ABEL Stephane 175950 (Thu Dec 02 2010 - 06:22:36 CST)
- Re: use gelato render with VMD 1.8.7 for movie John Stone (Fri Dec 03 2010 - 11:55:24 CST)
  - RE : use gelato render with VMD 1.8.7 for movie ABEL Stephane 175950 (Fri Dec 03 2010 - 12:18:26 CST)
    - Re: RE Q?= use gelato render with VMD 1.8.7 for movie John Stone (Fri Dec 03 2010 - 14:17:31 CST)
order of atoms in an improper dihedral matziast_at_med.uth.gr (Thu Dec 02 2010 - 04:10:41 CST)
order of atoms in an improper dihedral matziast_at_med.uth.gr (Thu Dec 02 2010 - 03:31:35 CST)
Output of forces Pletezhov Alexandr (Thu Dec 02 2010 - 03:18:26 CST)
- Re: Output of forces Axel Kohlmeyer (Thu Dec 02 2010 - 04:29:05 CST)
Re: namd-l: wrapping problem Ramya Gamini (Wed Dec 01 2010 - 11:37:26 CST)
- Re: namd-l: wrapping problem Ramya Gamini (Wed Dec 01 2010 - 13:45:25 CST)
Plot a time line in the movie made with VMD ABEL Stephane 175950 (Wed Dec 01 2010 - 11:08:39 CST)
- Re: Plot a time line in the movie made with VMD Bogdan Costescu (Wed Dec 01 2010 - 15:44:56 CST)
  - TR : Plot a time line in the movie made with VMD ABEL Stephane 175950 (Thu Dec 02 2010 - 06:48:01 CST)
namdenergy problem Francesco Oteri (Wed Dec 01 2010 - 06:23:23 CST)
- Re: namdenergy problem Peter Freddolino (Wed Dec 01 2010 - 20:35:52 CST)
per-residue alignment Antonija Tomiæ (Wed Dec 01 2010 - 02:24:33 CST)
- Re: per-residue alignment Toni Giorgino (Fri Dec 10 2010 - 09:05:01 CST)
reading of one frame from DCD file JhonY. I. (Tue Nov 30 2010 - 18:13:14 CST)
- Re: reading of one frame from DCD file Eduard Schreiner (Tue Nov 30 2010 - 19:44:55 CST)
reading of one frame from DCD file JhonY. I. (Tue Nov 30 2010 - 18:12:03 CST)
print numerical values in a Ramachandran plot Rebeca García Fandiño (Tue Nov 30 2010 - 17:01:12 CST)
- Re: print numerical values in a Ramachandran plot Ajasja LjubetiÄ (Wed Dec 01 2010 - 01:54:32 CST)
  - RE: print numerical values in a Ramachandran plot Rebeca García Fandiño (Wed Dec 01 2010 - 09:56:45 CST)
  - rotate a selection of a molecule and write rotated coordinates Rebeca García Fandiño (Tue Feb 19 2013 - 08:45:30 CST)
top2psf - bridging_waters.tcl script leila karami (Tue Nov 30 2010 - 00:41:58 CST)
- Time line ABEL Stephane 175950 (Tue Nov 30 2010 - 08:55:05 CST)
- Re: top2psf - bridging_waters.tcl script John Stone (Fri Dec 03 2010 - 12:08:59 CST)
Can VMD build predicted protein structures by homology? Seweryn Bialasiewicz (Mon Nov 29 2010 - 21:43:11 CST)
- Re: Can VMD build predicted protein structures by homology? John Stone (Fri Dec 03 2010 - 12:02:47 CST)
missing fragments in molefacture Irene Newhouse (Mon Nov 29 2010 - 16:08:46 CST)
- Re: missing fragments in molefacture Peter Freddolino (Tue Nov 30 2010 - 19:25:50 CST)
  - RE: missing fragments in molefacture Irene Newhouse (Wed Dec 01 2010 - 00:16:32 CST)
RMSD Question snoze pa (Sun Nov 28 2010 - 11:08:25 CST)
- Re: RMSD Question Germain Salvato Vallverdu (Mon Nov 29 2010 - 02:56:05 CST)
top2psf - bridging_waters.tcl script leila karami (Sat Nov 27 2010 - 06:15:37 CST)
- Re: top2psf - bridging_waters.tcl script John Stone (Mon Nov 29 2010 - 10:32:03 CST)
VASP crystal structure visualisation Germain Salvato Vallverdu (Thu Nov 25 2010 - 08:32:11 CST)
- Re: VASP crystal structure visualisation Ajasja LjubetiÄ (Thu Nov 25 2010 - 14:14:58 CST)
  - Re: VASP crystal structure visualisation Ajasja LjubetiÄ (Thu Nov 25 2010 - 14:57:13 CST)
  - Re: VASP crystal structure visualisation Axel Kohlmeyer (Fri Nov 26 2010 - 16:11:41 CST)
VASP crystal structure visualisation Germain Salvato Vallverdu (Thu Nov 25 2010 - 06:41:35 CST)
- Re: VASP crystal structure visualisation Axel Kohlmeyer (Thu Nov 25 2010 - 17:10:04 CST)
subtlety with PSFGEN - angle/dihedral regeneration Erik Nordgren (Wed Nov 24 2010 - 20:55:06 CST)
average structure/solute and solvent Alex Liu (Wed Nov 24 2010 - 10:19:28 CST)
how to display bond btw backbone atom and sidechain atom ³Ì²ýÀû (Wed Nov 24 2010 - 04:58:37 CST)
- Re: how to display bond btw backbone atom and sidechain atom Axel Kohlmeyer (Wed Nov 24 2010 - 06:07:32 CST)
- Re: how to display bond btw backbone atom and sidechain atom Boris Steipe (Wed Nov 24 2010 - 07:57:41 CST)
Seminars Trainings Christian Wohlschlager (Wed Nov 24 2010 - 02:37:48 CST)
average structure/solute and solvent Alex Liu (Tue Nov 23 2010 - 09:21:31 CST)
radial distribution function from the center of mass David Wedner (Thu Nov 18 2010 - 19:41:56 CST)
- Re: radial distribution function from the center of mass Axel Kohlmeyer (Thu Nov 18 2010 - 20:20:18 CST)
  - Re: radial distribution function from the center of mass Axel Kohlmeyer (Thu Nov 18 2010 - 20:27:55 CST)
.xsf triclinic cell contents Erin L. (Thu Nov 18 2010 - 14:23:06 CST)
- Re: .xsf triclinic cell contents Axel Kohlmeyer (Thu Nov 18 2010 - 15:41:28 CST)
  - Re: .xsf triclinic cell contents Axel Kohlmeyer (Fri Nov 19 2010 - 14:49:31 CST)
does vmd allow change in volume David Wedner (Thu Nov 18 2010 - 12:57:00 CST)
- Re: does vmd allow change in volume Axel Kohlmeyer (Thu Nov 18 2010 - 14:34:29 CST)
tcl script problem using -dispdev text .. Alberto Sergio Garay (Thu Nov 18 2010 - 07:12:46 CST)
- Re: tcl script problem using -dispdev text .. Jérôme Hénin (Thu Nov 18 2010 - 08:07:24 CST)
- Re: tcl script problem using -dispdev text .. Axel Kohlmeyer (Thu Nov 18 2010 - 08:28:41 CST)
  - Re: tcl script problem using -dispdev text .. Alberto Sergio Garay (Fri Nov 19 2010 - 04:33:33 CST)
    - Re: tcl script problem using -dispdev text .. Axel Kohlmeyer (Fri Nov 19 2010 - 06:27:46 CST)
    - Re: tcl script problem using -dispdev text .. John Stone (Fri Nov 19 2010 - 21:40:52 CST)
Test Graphic card performance using VMD as benchmark TRINH Minh Hieu (Thu Nov 18 2010 - 06:18:04 CST)
- Re: Test Graphic card performance using VMD as benchmark Axel Kohlmeyer (Fri Nov 19 2010 - 15:50:23 CST)
Max Characters in Writing Files Michael LeVine (Wed Nov 17 2010 - 15:36:49 CST)
missing operator at _@_in expression "$i _@_$n" ç¨‹æ˜Œåˆ© (Wed Nov 17 2010 - 09:59:16 CST)
- Re: missing operator at _@_in expression "$i _@_$n" Axel Kohlmeyer (Wed Nov 17 2010 - 10:39:07 CST)
  - Re: missing operator at _@_in expression "$i _@_$n" Matt Watkins (Wed Nov 17 2010 - 12:31:51 CST)
atom selection in vmd Alex Liu (Wed Nov 17 2010 - 08:49:55 CST)
- Re: atom selection in vmd Axel Kohlmeyer (Wed Nov 17 2010 - 09:56:35 CST)
  - Re: atom selection in vmd Ignacio Fernández Galván (Wed Nov 17 2010 - 12:30:59 CST)
    - Re: atom selection in vmd Alex Liu (Mon Nov 22 2010 - 16:16:45 CST)
- Re: atom selection in vmd Ajasja LjubetiÄ (Wed Nov 17 2010 - 10:25:55 CST)
Problem With No Atoms In Selection David Huggins (Tue Nov 16 2010 - 14:35:20 CST)
- Re: Problem With No Atoms In Selection John Stone (Tue Nov 16 2010 - 15:33:50 CST)
Re: How to Measure Radius of gyration David Wedner (Tue Nov 16 2010 - 13:24:05 CST)
- Re: How to Measure Radius of gyration John Stone (Tue Nov 16 2010 - 23:33:36 CST)
  - Re: How to Measure Radius of gyration David Wedner (Wed Nov 17 2010 - 18:40:22 CST)
Rendering .dat files created from Movie Maker using Tachyon Truc Kim (Tue Nov 16 2010 - 06:34:12 CST)
- Re: Rendering .dat files created from Movie Maker using Tachyon Axel Kohlmeyer (Tue Nov 16 2010 - 10:43:38 CST)
- Re: Rendering .dat files created from Movie Maker using Tachyon Eduard Schreiner (Tue Nov 16 2010 - 11:25:07 CST)
  - Re: Rendering .dat files created from Movie Maker using Tachyon Truc Kim (Tue Nov 16 2010 - 22:53:54 CST)
    - Re: Rendering .dat files created from Movie Maker using Tachyon Eduard Schreiner (Tue Nov 16 2010 - 23:39:58 CST)
    - Re: Rendering .dat files created from Movie Maker using Tachyon John Stone (Tue Nov 16 2010 - 23:43:17 CST)
Headtracking software Tamás Borsos (Tue Nov 16 2010 - 04:25:04 CST)
- Re: Headtracking software Ajasja LjubetiÄ (Tue Nov 16 2010 - 09:00:27 CST)
  - Re: Headtracking software Axel Kohlmeyer (Tue Nov 16 2010 - 10:48:32 CST)
- Re: Headtracking software Biff Forbush (Tue Nov 16 2010 - 11:01:00 CST)
- Re: Headtracking software Biff Forbush (Tue Nov 16 2010 - 12:37:21 CST)
- Re: Headtracking software John Stone (Tue Nov 16 2010 - 15:23:14 CST)
- PMF vs distance plot from isosurface Aaron Oakley (Tue Dec 14 2010 - 22:17:48 CST)
question on color assignment on trajectories JhonY. I. (Mon Nov 15 2010 - 20:29:49 CST)
- Re: question on color assignment on trajectories Axel Kohlmeyer (Mon Nov 15 2010 - 22:06:45 CST)
Background gradient in image quantrum75 (Mon Nov 15 2010 - 15:45:43 CST)
- Re: Background gradient in image Axel Kohlmeyer (Mon Nov 15 2010 - 16:48:25 CST)
Measure Radius of gyration David Wedner (Mon Nov 15 2010 - 12:31:15 CST)
- Re: Measure Radius of gyration Eduard Schreiner (Mon Nov 15 2010 - 13:47:16 CST)
- Water molecules within a definite radius quantrum75 (Mon Nov 15 2010 - 15:26:18 CST)
  - Re: Water molecules within a definite radius Axel Kohlmeyer (Mon Nov 15 2010 - 16:22:49 CST)
  - Re: Water molecules within a definite radius Joshua Adelman (Mon Nov 15 2010 - 17:06:05 CST)
How to change atom type and make it take effect immediately ï¼Ÿ Cun Zhang (Sat Nov 13 2010 - 08:17:24 CST)
Interactive MD driver/controller software no longer in beta Axel Kohlmeyer (Fri Nov 12 2010 - 09:41:59 CST)
vmd-I:Hbonds nataliaperez_at_infomed.sld.cu (Thu Nov 11 2010 - 10:53:57 CST)
- Re: vmd-I:Hbonds John Stone (Thu Nov 11 2010 - 11:07:55 CST)
vmd-I:Hbonds nataliaperez_at_infomed.sld.cu (Thu Nov 11 2010 - 08:59:11 CST)
POV renderer and volume coloring problem Guido Polles (Thu Nov 11 2010 - 05:33:00 CST)
- Re: POV renderer and volume coloring problem John Stone (Thu Nov 11 2010 - 07:53:50 CST)
Ions conversion from atomic model to coarse grained model ÖÜÎÄ²ý (Wed Nov 10 2010 - 11:41:41 CST)
k3b also launches vmd Francesco Pietra (Wed Nov 10 2010 - 03:05:03 CST)
- Re: k3b also launches vmd John Stone (Wed Nov 10 2010 - 10:47:01 CST)
  - Re: k3b also launches vmd Francesco Pietra (Wed Nov 10 2010 - 13:33:43 CST)
    - Re: k3b also launches vmd Francesco Pietra (Thu Nov 11 2010 - 02:10:36 CST)
dynamic atom selection Stephen Cox (Tue Nov 09 2010 - 07:11:58 CST)
- Re: dynamic atom selection Leonardo Trabuco (Tue Nov 09 2010 - 08:01:15 CST)
  - Re: dynamic atom selection Axel Kohlmeyer (Tue Nov 09 2010 - 11:06:31 CST)
- Re: dynamic atom selection Ajasja LjubetiÄ (Tue Nov 09 2010 - 08:06:58 CST)
- Re: dynamic atom selection Axel Kohlmeyer (Tue Nov 09 2010 - 08:10:49 CST)
- Re: dynamic atom selection Jérôme Hénin (Tue Nov 09 2010 - 08:28:49 CST)
3D protein visualization quantrum75 (Mon Nov 08 2010 - 12:37:50 CST)
- Re: 3D protein visualization Axel Kohlmeyer (Mon Nov 08 2010 - 13:22:50 CST)
  - Re: 3D protein visualization Ajasja LjubetiÄ (Mon Nov 08 2010 - 15:10:33 CST)
  - Re: 3D protein visualization Deepangi Pandit (Mon Nov 08 2010 - 15:59:08 CST)
    - Re: 3D protein visualization John Stone (Mon Nov 08 2010 - 16:33:55 CST)
- Re: 3D protein visualization John Stone (Mon Nov 08 2010 - 16:31:45 CST)
  - Re: 3D protein visualization quantrum75 (Mon Nov 08 2010 - 17:31:55 CST)
    - Re: 3D protein visualization Joseph Bylund (Mon Nov 08 2010 - 18:39:42 CST)
    - Re: 3D protein visualization Ignacio Fernández Galván (Tue Nov 09 2010 - 03:05:03 CST)
Graphics card for VMD, number of atoms, file format Prskalo, Alen-Pilip (Mon Nov 08 2010 - 11:38:22 CST)
- Re: Graphics card for VMD, number of atoms, file format Axel Kohlmeyer (Mon Nov 08 2010 - 12:38:46 CST)
  - RE: Graphics card for VMD, number of atoms, file format Prskalo, Alen-Pilip (Tue Nov 09 2010 - 10:43:08 CST)
    - RE: Graphics card for VMD, number of atoms, file format Axel Kohlmeyer (Tue Nov 09 2010 - 10:51:32 CST)
    - Re: Graphics card for VMD, number of atoms, file format John Stone (Tue Nov 09 2010 - 11:16:54 CST)
- Re: Graphics card for VMD, number of atoms, file format Andrew (Mon Nov 08 2010 - 14:29:07 CST)
Script for counting water molecules aneesh cna (Mon Nov 08 2010 - 07:06:33 CST)
- Re: Script for counting water molecules Joshua Adelman (Mon Nov 08 2010 - 15:26:02 CST)
Building a membrane from a individual surfactant molecule surendra jain (Mon Nov 08 2010 - 06:27:02 CST)
fit.tcl divya nayar (Mon Nov 08 2010 - 03:01:14 CST)
- Re: fit.tcl Bo Liu (Mon Nov 08 2010 - 09:23:24 CST)
VMD: Ability to add terminal carbonyl oxygen Amor San Juan (Sun Nov 07 2010 - 23:32:20 CST)
regarding merging of protein and a ligand vani panguluri (Sat Nov 06 2010 - 15:43:13 CDT)
- Re: regarding merging of protein and a ligand Axel Kohlmeyer (Sat Nov 06 2010 - 16:54:53 CDT)
- Re: regarding merging of protein and a ligand Joshua Adelman (Sat Nov 06 2010 - 18:03:19 CDT)
rgyr calculation problem Branko (Fri Nov 05 2010 - 16:21:05 CDT)
- Re: rgyr calculation problem Axel Kohlmeyer (Fri Nov 05 2010 - 17:09:31 CDT)
DCD write/save with a python script David Huggins (Fri Nov 05 2010 - 14:58:18 CDT)
dtr plugin: does it work for forces traj? Edward Lyman (Fri Nov 05 2010 - 11:03:55 CDT)
- Re: dtr plugin: does it work for forces traj? John Stone (Wed Nov 10 2010 - 13:22:07 CST)
Release of R.E.D. Server 2.0 FyD (Thu Nov 04 2010 - 04:50:36 CDT)
Web Portal NAMD Job Visualisation...possibilities? Heidi Perrett (Wed Nov 03 2010 - 22:15:38 CDT)
- Re: Web Portal NAMD Job Visualisation...possibilities? John Stone (Wed Nov 03 2010 - 22:54:44 CDT)
Regarding merging of two files vani panguluri (Wed Nov 03 2010 - 12:18:16 CDT)
- Re: Regarding merging of two files John Stone (Wed Nov 03 2010 - 13:03:11 CDT)
  - Re: Regarding merging of two files vani panguluri (Wed Nov 03 2010 - 13:30:40 CDT)
    - Re: Regarding merging of two files John Stone (Wed Nov 03 2010 - 13:40:30 CDT)
- Re: Regarding merging of two files Joseph Bylund (Wed Nov 03 2010 - 13:08:21 CDT)
- Re: Regarding merging of two files Joshua Adelman (Wed Nov 03 2010 - 13:44:08 CDT)
Running VMD from the terminal on MacBook Pro Steven S Plotkin (Wed Nov 03 2010 - 08:25:15 CDT)
- Re: Running VMD from the terminal on MacBook Pro Leonardo Trabuco (Wed Nov 03 2010 - 08:37:44 CDT)
  - Re: Running VMD from the terminal on MacBook Pro Steven S Plotkin (Wed Nov 03 2010 - 11:30:51 CDT)
- Re: Running VMD from the terminal on MacBook Pro Shore, Jay (Wed Nov 03 2010 - 10:52:49 CDT)
Asymmetric water molecule Stefan Franzen (Wed Nov 03 2010 - 02:11:22 CDT)
- Re: Asymmetric water molecule Jérôme Hénin (Wed Nov 03 2010 - 05:03:40 CDT)
Text command for isosurface Thomas Steinbrecher (Wed Nov 03 2010 - 01:51:37 CDT)
- Re: Text command for isosurface Leonardo Trabuco (Wed Nov 03 2010 - 02:13:15 CDT)
rmsd divya nayar (Tue Nov 02 2010 - 11:53:26 CDT)
- Re: rmsd Eduard Schreiner (Tue Nov 02 2010 - 13:01:09 CDT)
vmd: Saving output Christian Jorgensen (Mon Nov 01 2010 - 04:30:03 CDT)
- Re: vmd: Saving output Ajasja LjubetiÄ (Mon Nov 01 2010 - 06:00:58 CDT)
VMD text mode/unwrap Parisa Akhski (Sun Oct 31 2010 - 19:53:47 CDT)
- Re: VMD text mode/unwrap Jérôme Hénin (Mon Nov 01 2010 - 05:12:59 CDT)
  - RE: VMD text mode/unwrap Parisa Akhski (Mon Nov 01 2010 - 21:40:11 CDT)
    - Re: VMD text mode/unwrap Axel Kohlmeyer (Tue Nov 02 2010 - 08:43:42 CDT)
Where to download Hbond plugin surendra jain (Sat Oct 30 2010 - 07:52:15 CDT)
- Re: Where to download Hbond plugin Axel Kohlmeyer (Sat Oct 30 2010 - 11:01:01 CDT)
  - Re: Where to download Hbond plugin surendra jain (Sun Oct 31 2010 - 03:27:16 CDT)
    - Re: Where to download Hbond plugin Ajasja LjubetiÄ (Sun Oct 31 2010 - 05:50:10 CDT)
Contour plots for XYZ format Wang Xianqiao (Fri Oct 29 2010 - 23:47:51 CDT)
- Re: Contour plots for XYZ format Axel Kohlmeyer (Sat Oct 30 2010 - 10:56:04 CDT)
  - Re: Contour plots for XYZ format Wang Xianqiao (Sat Oct 30 2010 - 19:02:25 CDT)
    - Re: Contour plots for XYZ format Axel Kohlmeyer (Sat Oct 30 2010 - 19:17:46 CDT)
vmd: Tcl script help Christian Jorgensen (Fri Oct 29 2010 - 14:06:59 CDT)
- Re: vmd: Tcl script help Ajasja LjubetiÄ (Fri Oct 29 2010 - 15:10:54 CDT)
  - Re: vmd: Tcl script help Jérôme Hénin (Sat Oct 30 2010 - 12:47:22 CDT)
namd-I : Constraint failure in RATTLE algorithm for atom 268 surendra jain (Thu Oct 28 2010 - 23:39:30 CDT)
- Re: namd-I : Constraint failure in RATTLE algorithm for atom 268 Ajasja LjubetiÄ (Fri Oct 29 2010 - 01:41:51 CDT)
PBC wrap on hexagonal periodic cells OPC3_at_pitt.edu (Thu Oct 28 2010 - 12:12:51 CDT)
Possible bug in freeing global selections Ajasja LjubetiÄ (Thu Oct 28 2010 - 06:56:02 CDT)
- Re: Possible bug in freeing global selections Ajasja LjubetiÄ (Thu Oct 28 2010 - 08:16:14 CDT)
- Re: Possible bug in freeing global selections Axel Kohlmeyer (Thu Oct 28 2010 - 09:22:13 CDT)
  - Re: Possible bug in freeing global selections Ajasja LjubetiÄ (Thu Oct 28 2010 - 13:05:33 CDT)
    - Re: Possible bug in freeing global selections Axel Kohlmeyer (Thu Oct 28 2010 - 13:11:30 CDT)
    - Re: Possible bug in freeing global selections Ajasja LjubetiÄ (Thu Oct 28 2010 - 17:23:16 CDT)
menus unresponsive in ubuntu 10.10 Andrew Jewett (Thu Oct 28 2010 - 02:42:15 CDT)
- Re: menus unresponsive in ubuntu 10.10 John Stone (Fri Oct 29 2010 - 09:28:23 CDT)
  - Re: menus unresponsive in ubuntu 10.10 Andrew Jewett (Sat Oct 30 2010 - 02:22:06 CDT)
    - Re: menus unresponsive in ubuntu 10.10 Axel Kohlmeyer (Sat Oct 30 2010 - 10:58:17 CDT)
    - Re: menus unresponsive in ubuntu 10.10 Andrew Jewett (Sun Oct 31 2010 - 18:55:33 CDT)
Water mediated hydrogen bond - VMD script ban arn (Tue Oct 26 2010 - 13:31:42 CDT)
Algorithm for RMSD and alignment Ignacio Fernández Galván (Tue Oct 26 2010 - 11:47:18 CDT)
How to delete a residue Kshatresh Dutta Dubey (Tue Oct 26 2010 - 00:51:45 CDT)
- Re: How to delete a residue John Stone (Wed Oct 27 2010 - 12:53:23 CDT)
RDF calculation sarah k (Mon Oct 25 2010 - 10:21:40 CDT)
- Re: RDF calculation Ramya Gamini (Mon Oct 25 2010 - 11:44:58 CDT)
Reading MatStudio/ LAMMPS structures to VMD Aric Newton (Sat Oct 23 2010 - 18:45:06 CDT)
- Re: Reading MatStudio/ LAMMPS structures to VMD Axel Kohlmeyer (Sun Oct 24 2010 - 17:02:38 CDT)
  - Re: Reading MatStudio/ LAMMPS structures to VMD Axel Kohlmeyer (Tue Oct 26 2010 - 09:43:48 CDT)
  - Re: Reading MatStudio/ LAMMPS structures to VMD Aric Newton (Fri Oct 29 2010 - 09:16:30 CDT)
    - Re: Reading MatStudio/ LAMMPS structures to VMD Axel Kohlmeyer (Fri Oct 29 2010 - 11:37:11 CDT)
Adding cadmium into protein Joyce Tan (Wed Oct 20 2010 - 01:55:36 CDT)
- Re: Adding cadmium into protein John Stone (Wed Oct 20 2010 - 10:23:25 CDT)
problem at convert single trajectory frame to pdb Joyce Tan (Tue Oct 19 2010 - 10:36:43 CDT)
- Re: problem at convert single trajectory frame to pdb John Stone (Tue Oct 19 2010 - 10:45:43 CDT)
  - Re: problem at convert single trajectory frame to pdb Joyce Tan (Tue Oct 19 2010 - 11:04:36 CDT)
- Re: problem at convert single trajectory frame to pdb Nicholas Musolino (Tue Oct 19 2010 - 12:10:51 CDT)
Vega ZZ DCD trajectory crashes VMD Ajasja LjubetiÄ (Tue Oct 19 2010 - 09:21:44 CDT)
- Re: Vega ZZ DCD trajectory crashes VMD John Stone (Tue Oct 19 2010 - 10:39:50 CDT)
  - Re: Vega ZZ DCD trajectory crashes VMD John Stone (Tue Oct 19 2010 - 11:07:27 CDT)
- Re: Vega ZZ DCD trajectory crashes VMD Axel Kohlmeyer (Tue Oct 19 2010 - 11:02:34 CDT)
  - Re: Vega ZZ DCD trajectory crashes VMD John Stone (Tue Oct 19 2010 - 11:28:45 CDT)
    - Re: Vega ZZ DCD trajectory crashes VMD Ajasja LjubetiÄ (Tue Oct 19 2010 - 11:56:26 CDT)
    - Re: Vega ZZ DCD trajectory crashes VMD Ajasja LjubetiÄ (Tue Nov 09 2010 - 06:56:26 CST)
Novint Falcon Christian Wohlschlager (Tue Oct 19 2010 - 07:22:21 CDT)
- Re: Novint Falcon Axel Kohlmeyer (Tue Oct 19 2010 - 08:19:49 CDT)
PCA analysis of NAMD dcd files surendra jain (Tue Oct 19 2010 - 04:58:47 CDT)
- Re: PCA analysis of NAMD dcd files Joshua Adelman (Tue Oct 19 2010 - 07:30:16 CDT)
Best way for model post processing? Steve Jensen (Sun Oct 17 2010 - 23:22:14 CDT)
- Re: Best way for model post processing? Axel Kohlmeyer (Mon Oct 18 2010 - 12:11:55 CDT)
Select non-redundant set using struture Qr not working Raul Araya (Sun Oct 17 2010 - 18:52:00 CDT)
- Re: Select non-redundant set using struture Qr not working Kirby Vandivort (Tue Oct 19 2010 - 11:54:26 CDT)
psf format masoumeh ozmaeian (Sun Oct 17 2010 - 02:26:04 CDT)
- Re: psf format Axel Kohlmeyer (Sun Oct 17 2010 - 13:36:34 CDT)
  - Re: psf format masoumeh ozmaeian (Sun Oct 31 2010 - 13:37:18 CDT)
    - Re: psf format Axel Kohlmeyer (Sun Oct 31 2010 - 13:54:12 CDT)
Memory leak with "mol modselect" and index TRINH Minh Hieu (Sat Oct 16 2010 - 20:11:16 CDT)
- Re: Memory leak with "mol modselect" and index Axel Kohlmeyer (Sun Oct 17 2010 - 13:29:22 CDT)
  - Re: Memory leak with "mol modselect" and index TRINH Minh Hieu (Sun Oct 17 2010 - 13:43:40 CDT)
    - Re: Memory leak with "mol modselect" and index John Stone (Sun Oct 17 2010 - 15:52:47 CDT)
test masoumeh ozmaeian (Sat Oct 16 2010 - 14:26:58 CDT)
setenv: Too many arguments Balazs Jojart (Fri Oct 15 2010 - 16:34:52 CDT)
- Re: setenv: Too many arguments John Stone (Fri Oct 15 2010 - 16:42:00 CDT)
  - Re: setenv: Too many arguments Balazs Jojart (Sat Oct 16 2010 - 00:53:21 CDT)
Bond Colors Brooke Dallas (Wed Oct 13 2010 - 08:46:36 CDT)
- Re: Bond Colors Axel Kohlmeyer (Wed Oct 13 2010 - 09:41:00 CDT)
  - Re: Bond Colors Brooke Dallas (Wed Oct 13 2010 - 11:31:16 CDT)
IED 2.02 and VMD 1.8.7 Birgitte Maria Elisabeth Brydsoe (Wed Oct 13 2010 - 08:33:00 CDT)
- Re: IED 2.02 and VMD 1.8.7 Axel Kohlmeyer (Wed Oct 13 2010 - 09:23:19 CDT)
  - Re: IED 2.02 and VMD 1.8.7 Birgitte Maria Elisabeth Brydsoe (Wed Oct 13 2010 - 09:28:13 CDT)
- Re: IED 2.02 and VMD 1.8.7 Hannes Loeffler (Wed Oct 13 2010 - 09:24:33 CDT)
  - Re: IED 2.02 and VMD 1.8.7 Birgitte Maria Elisabeth Brydsoe (Wed Oct 13 2010 - 09:47:39 CDT)
  - Re: IED 2.02 and VMD 1.8.7 Jérôme Hénin (Wed Oct 13 2010 - 16:33:02 CDT)
    - Re: IED 2.02 and VMD 1.8.7 Jérôme Hénin (Wed Nov 03 2010 - 05:44:06 CDT)
    - Re: IED 2.02 and VMD 1.8.7 Vlad Cojocaru (Mon Dec 20 2010 - 09:31:41 CST)
Selecting by X-coordinate Keith Battle (Tue Oct 12 2010 - 17:31:02 CDT)
- Re: Selecting by X-coordinate John Stone (Tue Oct 12 2010 - 17:43:19 CDT)
  - Re: Selecting by X-coordinate Keith Battle (Tue Oct 12 2010 - 18:00:35 CDT)
Real-time ambient occlusion lighting Ajasja LjubetiÄ (Tue Oct 12 2010 - 15:54:00 CDT)
- Re: Real-time ambient occlusion lighting John Stone (Tue Oct 12 2010 - 16:24:42 CDT)
  - Re: Real-time ambient occlusion lighting Boris Steipe (Tue Oct 12 2010 - 19:07:16 CDT)
    - Re: Real-time ambient occlusion lighting John Stone (Tue Oct 12 2010 - 19:58:12 CDT)
  - Re: Real-time ambient occlusion lighting Ajasja LjubetiÄ (Wed Oct 13 2010 - 06:01:01 CDT)
Combined "Within" atom selection jonathan (Mon Oct 11 2010 - 11:59:08 CDT)
- Re: Combined "Within" atom selection John Stone (Tue Oct 12 2010 - 14:59:44 CDT)
How to stop a script (eg : source myscript.tcl) ? TRINH Minh Hieu (Mon Oct 11 2010 - 07:34:31 CDT)
- Re: How to stop a script (eg : source myscript.tcl) ? Axel Kohlmeyer (Mon Oct 11 2010 - 09:23:14 CDT)
  - Re: How to stop a script (eg : source myscript.tcl) ? TRINH Minh Hieu (Tue Oct 12 2010 - 02:20:19 CDT)
    - C-terminus link to side chain amine Al-Ali, Hassan (Tue Oct 12 2010 - 08:33:46 CDT)
Re: psf gen charmm format Hannes Loeffler (Mon Oct 11 2010 - 07:25:58 CDT)
Orientation an rotation of molecules in a movie Daniel Hornburg (Sat Oct 09 2010 - 07:26:21 CDT)
- Re: Orientation an rotation of molecules in a movie John Stone (Tue Oct 12 2010 - 15:04:26 CDT)
Link Patch? Al-Ali, Hassan (Fri Oct 08 2010 - 23:39:15 CDT)
Ubiquitin - patch? Al-Ali, Hassan (Thu Oct 07 2010 - 22:33:23 CDT)
- RE: Ubiquitin - patch? JC Gumbart (Thu Oct 07 2010 - 23:14:10 CDT)
(no subject) Kei Sit (Thu Oct 07 2010 - 21:03:31 CDT)
- RE: JC Gumbart (Thu Oct 07 2010 - 23:19:28 CDT)
patch CT3 and ACE problems in PSFGEN Markus K. Dahlgren (Thu Oct 07 2010 - 15:11:52 CDT)
- Re: patch CT3 and ACE problems in PSFGEN JC Gumbart (Thu Oct 07 2010 - 19:01:15 CDT)
  - Re: patch CT3 and ACE problems in PSFGEN Markus K. Dahlgren (Fri Oct 08 2010 - 11:32:02 CDT)
    - Re: patch CT3 and ACE problems in PSFGEN JC Gumbart (Fri Oct 08 2010 - 19:25:12 CDT)
missing frames in trajectory file Parisa Akhski (Wed Oct 06 2010 - 17:49:29 CDT)
- Re: missing frames in trajectory file John Stone (Tue Oct 12 2010 - 15:28:06 CDT)
  - RE: missing frames in trajectory file Parisa Akhski (Tue Oct 12 2010 - 16:33:12 CDT)
membrane_problem lara lara (Wed Oct 06 2010 - 00:29:39 CDT)
aligning- on top of the bilayer lara lara (Wed Oct 06 2010 - 00:11:00 CDT)
K-linked Ub, ACE patch, and autoPSF Al-Ali, Hassan (Tue Oct 05 2010 - 22:49:42 CDT)
K-linked Ub, ACE patch, and autoPSF Al-Ali, Hassan (Tue Oct 05 2010 - 22:49:37 CDT)
K-linked Ub, ACE patch, and autoPSF Al-Ali, Hassan (Tue Oct 05 2010 - 22:49:34 CDT)
Query regarding RMSD calculcation hirdesh kumar (Tue Oct 05 2010 - 00:50:32 CDT)
- Re: Query regarding RMSD calculcation John Stone (Tue Oct 12 2010 - 15:25:35 CDT)
trouble with measure hbonds Charlotte Siska (Mon Oct 04 2010 - 15:01:36 CDT)
- Re: trouble with measure hbonds Eduard Schreiner (Mon Oct 04 2010 - 15:53:17 CDT)
- Re: trouble with measure hbonds Axel Kohlmeyer (Mon Oct 04 2010 - 16:02:13 CDT)
- RE: trouble with measure hbonds Pat Yee (Mon Oct 04 2010 - 17:09:42 CDT)
  - Re: RE: trouble with measure hbonds charbott_at_gmail.com (Tue Oct 05 2010 - 10:35:14 CDT)
    - Re: RE: trouble with measure hbonds Eduard Schreiner (Tue Oct 05 2010 - 11:33:03 CDT)
Loading DCD Frames in Python David Huggins (Sat Oct 02 2010 - 05:16:05 CDT)
- Re: Loading DCD Frames in Python Cun Zhang (Sun Oct 03 2010 - 00:39:53 CDT)
load-traj for three dimensions Stefan Franzen (Fri Oct 01 2010 - 13:35:55 CDT)
Interaction Energy Using Python David Huggins (Wed Sep 29 2010 - 11:04:25 CDT)
- Re: Interaction Energy Using Python John Stone (Tue Oct 12 2010 - 15:34:49 CDT)
  - Re: Interaction Energy Using Python David Huggins (Wed Oct 13 2010 - 08:48:12 CDT)
    - Re: Interaction Energy Using Python John Stone (Fri Oct 15 2010 - 13:57:51 CDT)
IR Spectra plugin Agarwal, Silvi (Wed Sep 29 2010 - 10:59:59 CDT)
- Re: IR Spectra plugin Axel Kohlmeyer (Wed Sep 29 2010 - 12:03:13 CDT)
Solvent accessible surface area change during MD run hirdesh kumar (Tue Sep 28 2010 - 04:54:14 CDT)
- Re: Solvent accessible surface area change during MD run John Stone (Tue Sep 28 2010 - 10:53:46 CDT)
- Re: Solvent accessible surface area change during MD run Pat Yee (Fri Oct 01 2010 - 19:33:41 CDT)
Check out my photos on Facebook Aneesh Cna (Tue Sep 28 2010 - 04:27:52 CDT)
Water-mediated hydrogen bonds ban arn (Tue Sep 28 2010 - 04:19:30 CDT)
missing atoms yan zhang (Mon Sep 27 2010 - 08:42:07 CDT)
- Re: missing atoms Axel Kohlmeyer (Mon Sep 27 2010 - 10:29:25 CDT)
protein breaks into parts after converting trajectory file to pdb file Joyce Tan (Mon Sep 27 2010 - 04:58:48 CDT)
- Re: protein breaks into parts after converting trajectory file to pdb file Axel Kohlmeyer (Mon Sep 27 2010 - 10:32:58 CDT)
- Re: protein breaks into parts after converting trajectory file to pdb file Cun Zhang (Mon Sep 27 2010 - 20:17:33 CDT)
Experience with Asus Netbook Gianluca Interlandi (Sun Sep 26 2010 - 14:01:40 CDT)
- Re: Experience with Asus Netbook John Stone (Tue Sep 28 2010 - 10:45:08 CDT)
  - Re: Experience with Asus Netbook Thomas C. Bishop (Tue Sep 28 2010 - 14:20:46 CDT)
    - Re: Experience with Asus Netbook Gianluca Interlandi (Tue Sep 28 2010 - 15:19:47 CDT)
- Re: Experience with Asus Netbook TRINH Minh Hieu (Wed Sep 29 2010 - 12:59:46 CDT)
  - Re: Re: Experience with Asus Netbook Gianluca Interlandi (Wed Sep 29 2010 - 15:18:53 CDT)
implicit ligand sampling Marc Zimmer (Sat Sep 25 2010 - 06:26:24 CDT)
Weird bonds in water box/sphere Sujata Sovani (Fri Sep 24 2010 - 18:51:27 CDT)
IED/Tkinter problems Birgitte Maria Elisabeth Brydsoe (Fri Sep 24 2010 - 09:13:43 CDT)
wheris sculptor.tcl Christian Wohlschlager (Fri Sep 24 2010 - 05:39:50 CDT)
about psfgen patch Zhang, Jiong (MU-Student) (Thu Sep 23 2010 - 09:20:39 CDT)
- Re: about psfgen patch Jérôme Hénin (Thu Sep 23 2010 - 11:58:38 CDT)
Clarification on solvent box sizing Ian Stokes-Rees (Wed Sep 22 2010 - 14:42:30 CDT)
write pdbs of selected frames of a trajectory Katherine Parra (Wed Sep 22 2010 - 14:05:58 CDT)
- Re: write pdbs of selected frames of a trajectory Eduard Schreiner (Wed Sep 22 2010 - 15:09:14 CDT)
- Re: write pdbs of selected frames of a trajectory Joshua Adelman (Wed Sep 22 2010 - 15:52:11 CDT)
  - Re: write pdbs of selected frames of a trajectory Jérôme Hénin (Thu Sep 23 2010 - 03:55:43 CDT)
superimpose residues across several protein structures Joyce Tan (Wed Sep 22 2010 - 08:02:18 CDT)
- Re: superimpose residues across several protein structures Eduard Schreiner (Wed Sep 22 2010 - 08:52:20 CDT)
  - Re: superimpose residues across several protein structures Joyce Tan (Wed Sep 22 2010 - 10:20:00 CDT)
- Re: superimpose residues across several protein structures Ajasja LjubetiÄ (Wed Sep 22 2010 - 08:57:04 CDT)
ppmtompeg Carla Jamous (Wed Sep 22 2010 - 07:52:42 CDT)
- Re: ppmtompeg Axel Kohlmeyer (Wed Sep 22 2010 - 10:54:35 CDT)
psf gen charmm format Jorgen Simonsen (Wed Sep 22 2010 - 06:18:45 CDT)
- Re: psf gen charmm format John Stone (Wed Oct 20 2010 - 13:57:18 CDT)
adding a metal ion Joyce Tan (Tue Sep 21 2010 - 20:39:43 CDT)
Hydrogen bonds ban arn (Tue Sep 21 2010 - 11:17:10 CDT)
- Re: Hydrogen bonds Knut Jørgen Bjuland (Wed Sep 22 2010 - 11:19:53 CDT)
movie rendering on MacOS 10.6 Neelanjana Sengupta (Mon Sep 20 2010 - 10:51:59 CDT)
- Re: movie rendering on MacOS 10.6 Toni Giorgino (Tue Sep 21 2010 - 07:13:21 CDT)
ppm files Carla Jamous (Mon Sep 20 2010 - 07:07:52 CDT)
- Re: ppm files John Stone (Mon Sep 20 2010 - 07:32:29 CDT)
  - Re: ppm files Carla Jamous (Mon Sep 20 2010 - 07:36:20 CDT)
    - Re: ppm files John Stone (Mon Sep 20 2010 - 07:39:03 CDT)
    - Re: ppm files Carla Jamous (Tue Sep 21 2010 - 09:50:05 CDT)
vmd can't display Pt-Cl bond ç¨‹æ˜Œåˆ© (Mon Sep 20 2010 - 02:06:38 CDT)
- Re: vmd can't display Pt-Cl bond Ajasja LjubetiÄ (Mon Sep 20 2010 - 03:12:18 CDT)
cg_ionize Sibel Cakan (Sun Sep 19 2010 - 16:37:15 CDT)
- Re: cg_ionize Peter Freddolino (Mon Sep 20 2010 - 20:34:08 CDT)
cg ionization Sibel Cakan (Sun Sep 19 2010 - 15:28:14 CDT)
cg ionization Sibel Cakan (Sun Sep 19 2010 - 15:16:06 CDT)
minimization changed the occupancy of all atoms to zero Parisa Akhski (Fri Sep 17 2010 - 16:17:11 CDT)
- Re: minimization changed the occupancy of all atoms to zero John Stone (Sun Sep 19 2010 - 14:09:41 CDT)
  - RE: minimization changed the occupancy of all atoms to zero Parisa Akhski (Mon Sep 20 2010 - 10:35:35 CDT)
    - Re: minimization changed the occupancy of all atoms to zero John Stone (Mon Sep 20 2010 - 16:37:47 CDT)
vmd_pdb file format Ramasamy, Ellankavi (Fri Sep 17 2010 - 11:43:18 CDT)
- Re: vmd_pdb file format Axel Kohlmeyer (Fri Sep 17 2010 - 12:35:27 CDT)
vmd display water molecules error Cun Zhang (Fri Sep 17 2010 - 02:37:03 CDT)
- Re: vmd display water molecules error John Stone (Sun Sep 19 2010 - 19:46:44 CDT)
  - Re: vmd display water molecules error Cun Zhang (Sun Sep 19 2010 - 20:55:47 CDT)
    - Re: vmd display water molecules error John Stone (Sun Sep 19 2010 - 20:58:44 CDT)
    - Re: vmd display water molecules error Cun Zhang (Sun Sep 19 2010 - 21:16:00 CDT)
bigdcd + salt-bridge analysis Murpholino Peligro (Thu Sep 16 2010 - 15:31:58 CDT)
- Re: bigdcd + salt-bridge analysis John Stone (Sun Sep 19 2010 - 19:39:16 CDT)
maximum trajectory size? Murpholino Peligro (Thu Sep 16 2010 - 15:19:58 CDT)
- Re: maximum trajectory size? Axel Kohlmeyer (Thu Sep 16 2010 - 16:12:11 CDT)
Compatibility with Orcad (PSpice) ? A. M. Carmen Pérez (Thu Sep 16 2010 - 05:06:29 CDT)
- Re: Compatibility with Orcad (PSpice) ? John Stone (Sun Sep 19 2010 - 19:35:12 CDT)
Mouse event listener Gianluca Interlandi (Wed Sep 15 2010 - 16:11:41 CDT)
- Re: Mouse event listener John Stone (Sun Sep 19 2010 - 19:32:23 CDT)
  - Re: Mouse event listener Gianluca Interlandi (Sun Sep 19 2010 - 20:42:36 CDT)
  - Re: Mouse event listener Gianluca Interlandi (Thu Mar 17 2011 - 13:21:42 CDT)
    - Re: Mouse event listener John Stone (Thu Mar 17 2011 - 14:02:14 CDT)
Mouse event listener Gianluca Interlandi (Wed Sep 15 2010 - 15:20:37 CDT)
VMD for windows 64-bit Michel Espinoza-Fonseca (Wed Sep 15 2010 - 14:02:02 CDT)
- Re: VMD for windows 64-bit John Stone (Sun Sep 19 2010 - 16:51:40 CDT)
compile vmd Knut Jørgen Bjuland (Wed Sep 15 2010 - 11:54:17 CDT)
- Re: compile vmd Axel Kohlmeyer (Wed Sep 15 2010 - 13:09:28 CDT)
  - Re: compile vmd Cun Zhang (Thu Sep 16 2010 - 20:25:45 CDT)
    - Re: compile vmd Knut Jørgen Bjuland (Wed Sep 22 2010 - 11:15:13 CDT)
Draw a box cell for a crystal Germain Vallverdu (Wed Sep 15 2010 - 06:43:35 CDT)
- Re: Draw a box cell for a crystal Axel Kohlmeyer (Wed Sep 15 2010 - 08:15:50 CDT)
- Re: Draw a box cell for a crystal Bjoern Olausson (Wed Sep 15 2010 - 08:19:32 CDT)
H-bond life time Nicolas SAPAY (Wed Sep 15 2010 - 03:22:09 CDT)
- Re: H-bond life time Ignacio Fernández Galván (Wed Sep 15 2010 - 07:24:14 CDT)
  - Re: H-bond life time Nicolas SAPAY (Wed Sep 15 2010 - 07:45:06 CDT)
Autoionize question for DNA molecule Parisa Akhski (Tue Sep 14 2010 - 17:45:52 CDT)
- Re: Autoionize question for DNA molecule Peter Freddolino (Tue Sep 14 2010 - 18:55:35 CDT)
  - RE: Autoionize question for DNA molecule Parisa Akhski (Fri Sep 17 2010 - 16:11:50 CDT)
vasp POSCAR plugin Tawhid Ezaz (Tue Sep 14 2010 - 17:36:00 CDT)
- Re: vasp POSCAR plugin John Stone (Sun Sep 19 2010 - 19:26:47 CDT)
Re:vmd_start_problem_in_mac OSX Raman Parkesh (Tue Sep 14 2010 - 12:27:26 CDT)
- Re: Re:vmd_start_problem_in_mac OSX John Stone (Tue Sep 14 2010 - 12:35:46 CDT)
  - Re: Re:vmd_start_problem_in_mac OSX John Stone (Tue Sep 14 2010 - 13:03:43 CDT)
- RE: Re:vmd_start_problem_in_mac OSX Raman Parkesh (Thu Sep 30 2010 - 14:38:38 CDT)
turning on the tcl/tk console in .vmdrc Rosanne Zeiler (Tue Sep 14 2010 - 06:18:13 CDT)
- Re: turning on the tcl/tk console in .vmdrc Ajasja LjubetiÄ (Tue Sep 14 2010 - 07:47:49 CDT)
- Re: turning on the tcl/tk console in .vmdrc Tim Travers (Tue Sep 14 2010 - 07:45:14 CDT)
- Re: turning on the tcl/tk console in .vmdrc Eduard Schreiner (Tue Sep 14 2010 - 07:35:55 CDT)
Error encountered when quitting VMD on the Mac Ben Roberts (Mon Sep 13 2010 - 16:55:53 CDT)
- Re: Error encountered when quitting VMD on the Mac John Stone (Mon Sep 13 2010 - 20:08:36 CDT)
  - Re: Error encountered when quitting VMD on the Mac Ben Roberts (Mon Sep 13 2010 - 21:12:37 CDT)
    - Re: Error encountered when quitting VMD on the Mac Ben Roberts (Wed Oct 13 2010 - 12:39:07 CDT)
GLXBadLargeRequest and BadLength messages Moulton, Steve (Mon Sep 13 2010 - 15:43:32 CDT)
- Re: GLXBadLargeRequest and BadLength messages John Stone (Mon Sep 13 2010 - 16:34:33 CDT)
  - RE: GLXBadLargeRequest and BadLength messages Moulton, Steve (Tue Sep 14 2010 - 11:03:13 CDT)
    - Re: GLXBadLargeRequest and BadLength messages Roland Schulz (Thu Sep 23 2010 - 23:13:03 CDT)
phosphorylation modelling Zhang, Jiong (MU-Student) (Mon Sep 13 2010 - 15:11:49 CDT)
compile windows binary in linux CLEMENTS, ROBERT (Mon Sep 13 2010 - 14:17:51 CDT)
- Re: compile windows binary in linux John Stone (Mon Sep 13 2010 - 14:28:01 CDT)
- Re: compile windows binary in linux Axel Kohlmeyer (Mon Sep 13 2010 - 15:13:13 CDT)
writepdb append Jacopo Sgrignani (Mon Sep 13 2010 - 05:49:20 CDT)
- Re: writepdb append John Stone (Mon Sep 13 2010 - 12:25:47 CDT)
Anaglyph rendering problem Ajasja LjubetiÄ (Mon Sep 13 2010 - 03:50:27 CDT)
- Re: Anaglyph rendering problem John Stone (Mon Sep 13 2010 - 08:43:16 CDT)
  - Re: Anaglyph rendering problem Ajasja LjubetiÄ (Mon Sep 13 2010 - 08:55:39 CDT)
Use of parmtool plugin Christian Wohlschlager (Mon Sep 13 2010 - 01:38:01 CDT)
Visualization problem with aromatic bromo atom? Meyer-Almes, Franz-Josef, Prof. Dr. (Sun Sep 12 2010 - 13:18:46 CDT)
- Re: Visualization problem with aromatic bromo atom? Axel Kohlmeyer (Sun Sep 12 2010 - 14:59:54 CDT)
vmd.ps ³Ì²ýÀû (Sun Sep 12 2010 - 11:14:49 CDT)
(no subject) ³Ì²ýÀû (Sun Sep 12 2010 - 11:12:01 CDT)
- (no subject) Axel Kohlmeyer (Sun Sep 12 2010 - 12:33:25 CDT)
- Re: Rogan Carr (Sun Sep 12 2010 - 18:19:09 CDT)
change residue colors? Fatemesadat Emami (Fri Sep 10 2010 - 14:37:23 CDT)
- Re: change residue colors? John Stone (Mon Sep 13 2010 - 12:42:33 CDT)
Distance lines Patargias, George (Thu Sep 09 2010 - 15:24:38 CDT)
- Re: Distance lines Joseph Bylund (Thu Sep 09 2010 - 16:46:55 CDT)
maximum trajectory size? Patrick Burney (Wed Sep 08 2010 - 19:04:38 CDT)
- Re: maximum trajectory size? John Stone (Wed Sep 08 2010 - 19:58:19 CDT)
  - Re: maximum trajectory size? Joshua A. Anderson (Thu Sep 09 2010 - 06:50:43 CDT)
Loss of VDW upon rendering with POV3 Stefan Oliver (Wed Sep 08 2010 - 14:10:34 CDT)
- Re: Loss of VDW upon rendering with POV3 John Stone (Wed Sep 08 2010 - 14:26:11 CDT)
  - Re: Loss of VDW upon rendering with POV3 John Stone (Wed Sep 08 2010 - 16:08:05 CDT)
two coloring method Tawhid Ezaz (Fri Sep 03 2010 - 17:18:38 CDT)
- Re: two coloring method John Stone (Fri Sep 03 2010 - 18:01:00 CDT)
problem about dowser Chen, Zhihong (chenz2) (Fri Sep 03 2010 - 16:38:05 CDT)
- Re: problem about dowser Leonardo Trabuco (Sat Sep 04 2010 - 04:36:45 CDT)
Matrix based intermediate rotations Bogdan Costescu (Fri Sep 03 2010 - 05:50:40 CDT)
- Re: Matrix based intermediate rotations John Stone (Fri Sep 03 2010 - 10:08:34 CDT)
- Re: Matrix based intermediate rotations Eduardo (Fri Sep 03 2010 - 11:16:26 CDT)
  - Re: Matrix based intermediate rotations Bogdan Costescu (Sat Sep 04 2010 - 05:35:41 CDT)
Symposium on Accelerating Biology jani vinod (Fri Sep 03 2010 - 00:11:03 CDT)
Problem with orient.tcl Salvador H-V (Thu Sep 02 2010 - 12:59:38 CDT)
Best way to bond peptides Sujata Sovani (Wed Sep 01 2010 - 18:30:08 CDT)
Best way to join two PDB fragments by a peptide bond Sujata Sovani (Wed Sep 01 2010 - 17:36:46 CDT)
How to set the default mol style as VDW? Eric Grzelak (Wed Sep 01 2010 - 15:07:49 CDT)
- VMD and named pipes Thomas C. Bishop (Thu Sep 02 2010 - 14:28:55 CDT)
  - Re: VMD and named pipes Bogdan Costescu (Thu Sep 02 2010 - 23:51:23 CDT)
    - Re: VMD and named pipes Thomas C. Bishop (Fri Sep 03 2010 - 13:18:17 CDT)
    - Re: VMD and named pipes Bogdan Costescu (Sat Sep 04 2010 - 05:26:52 CDT)
- Re: How to set the default mol style as VDW? Ajasja LjubetiÄ (Fri Sep 03 2010 - 06:36:08 CDT)
question about Ca-dist.tcl dhacademic (Wed Sep 01 2010 - 10:14:24 CDT)
paratool error Goutham (Tue Aug 31 2010 - 20:02:30 CDT)
vmd paratool - getting GAUSSIAN charges Goutham (Tue Aug 31 2010 - 10:51:48 CDT)
Using Bigdcd with RMSD Trajectory tool in VMD Dan J Martingano (Mon Aug 30 2010 - 14:33:29 CDT)
- Re: Using Bigdcd with RMSD Trajectory tool in VMD Ajasja LjubetiÄ (Tue Aug 31 2010 - 05:42:16 CDT)
creating psf file unni kuttan (Mon Aug 30 2010 - 12:14:15 CDT)
- Re: creating psf file John Stone (Sun Sep 19 2010 - 20:09:03 CDT)
- Re: creating psf file Eduard Schreiner (Sun Sep 19 2010 - 21:39:29 CDT)
  - VMD 1.8.7 terminal window Gianluca Interlandi (Mon Sep 20 2010 - 00:10:26 CDT)
    - Re: VMD 1.8.7 terminal window John Stone (Mon Sep 20 2010 - 00:23:29 CDT)
    - Re: VMD 1.8.7 terminal window Gianluca Interlandi (Sat Sep 25 2010 - 20:02:55 CDT)
Faster secondary structure assignment Jérôme Hénin (Mon Aug 30 2010 - 11:28:45 CDT)
- Re: Faster secondary structure assignment John Stone (Mon Aug 30 2010 - 11:57:25 CDT)
  - Re: Faster secondary structure assignment Jérôme Hénin (Tue Aug 31 2010 - 10:38:49 CDT)
    - Re: Faster secondary structure assignment John Stone (Tue Aug 31 2010 - 10:57:35 CDT)
paratool doan dung (Sun Aug 29 2010 - 10:04:29 CDT)
plugin for Abinit output files Rob (Sat Aug 28 2010 - 03:22:05 CDT)
- Re: plugin for Abinit output files John Stone (Sun Sep 19 2010 - 20:18:56 CDT)
- Re: plugin for Abinit output files Rob (Sun Sep 26 2010 - 23:36:52 CDT)
- Re: plugin for Abinit output files Rob (Sun Sep 26 2010 - 23:45:15 CDT)
  - Re: Re: plugin for Abinit output files John Stone (Sun Oct 17 2010 - 17:54:20 CDT)
RMSD trajectory tool Parisa Akhski (Fri Aug 27 2010 - 13:06:40 CDT)
- Re: RMSD trajectory tool John Stone (Fri Aug 27 2010 - 14:32:05 CDT)
  - RE: RMSD trajectory tool Parisa Akhski (Fri Aug 27 2010 - 15:22:03 CDT)
Hydrogen bond angle hirdesh kumar (Fri Aug 27 2010 - 08:19:29 CDT)
- Re: Hydrogen bond angle Axel Kohlmeyer (Fri Aug 27 2010 - 09:41:22 CDT)
  - Re: Hydrogen bond angle hirdesh kumar (Fri Aug 27 2010 - 23:25:21 CDT)
  - Re: Hydrogen bond angle Karteek Kumar (Tue Aug 04 2015 - 01:59:26 CDT)
BB Trace Rex Palmer (Thu Aug 26 2010 - 14:49:39 CDT)
showing the backbone trace of a cyclic peptide Rex Palmer (Thu Aug 26 2010 - 14:45:33 CDT)
DCD Based on a parameter Pat Yee (Thu Aug 26 2010 - 09:01:51 CDT)
- Re: DCD Based on a parameter Ajasja LjubetiÄ (Thu Aug 26 2010 - 10:12:42 CDT)
  - Re: DCD Based on a parameter Axel Kohlmeyer (Thu Aug 26 2010 - 11:11:07 CDT)
vmd - rendering Ramasamy, Ellankavi (Wed Aug 25 2010 - 09:32:14 CDT)
- Re: vmd - rendering John Stone (Wed Aug 25 2010 - 09:49:28 CDT)
Re: runsqm plugin required but not installed John Stone (Tue Aug 24 2010 - 17:12:24 CDT)
hydrophobic accessible surface area Jorgen Simonsen (Tue Aug 24 2010 - 13:55:20 CDT)
[carlos.simmerling@gmail.com: Re: ACS award information, Oct 15 deadline] John Stone (Tue Aug 24 2010 - 09:48:02 CDT)
Structure won't move after loading trajectory NG HUI WEN (Mon Aug 23 2010 - 19:40:36 CDT)
- Re: Structure won't move after loading trajectory Axel Kohlmeyer (Mon Aug 23 2010 - 20:39:30 CDT)
  - Re: Structure won't move after loading trajectory Tim Travers (Mon Aug 23 2010 - 23:26:00 CDT)
    - RE: Structure won't move after loading trajectory NG HUI WEN (Tue Aug 24 2010 - 00:08:49 CDT)
    - Re: Structure won't move after loading trajectory hirdesh kumar (Tue Aug 24 2010 - 23:38:00 CDT)
converting old LAMMPS ASCII dumps Dan Lussier (Mon Aug 23 2010 - 19:08:01 CDT)
- Re: converting old LAMMPS ASCII dumps Axel Kohlmeyer (Mon Aug 23 2010 - 20:04:32 CDT)
  - Re: converting old LAMMPS ASCII dumps Dan Lussier (Tue Aug 24 2010 - 09:38:11 CDT)
    - Re: converting old LAMMPS ASCII dumps Axel Kohlmeyer (Tue Aug 24 2010 - 09:48:26 CDT)
    - Re: converting old LAMMPS ASCII dumps Dan Lussier (Tue Aug 24 2010 - 12:59:40 CDT)
OSX 10.6 support? Steve Smith (Mon Aug 23 2010 - 15:32:05 CDT)
- Re: OSX 10.6 support? Axel Kohlmeyer (Mon Aug 23 2010 - 17:28:21 CDT)
- Re: OSX 10.6 support? Joshua A. Anderson (Tue Aug 24 2010 - 07:00:36 CDT)
  - Re: OSX 10.6 support? Steve Smith (Tue Aug 24 2010 - 09:39:59 CDT)
Problem with 'unwrap' Sandra Rennebaum (Mon Aug 23 2010 - 03:44:34 CDT)
(no subject) Janani.S (Fri Aug 20 2010 - 22:39:10 CDT)
- Re: Ajasja LjubetiÄ (Sat Aug 21 2010 - 02:14:19 CDT)
  - Re: Edelmiro Moman (Sat Aug 21 2010 - 04:03:35 CDT)
POPC from charmm27 to charmm36 Raul Araya (Fri Aug 20 2010 - 18:43:00 CDT)
RMSF calculation: residue wise hirdesh kumar (Fri Aug 20 2010 - 11:22:55 CDT)
- Re: RMSF calculation: residue wise Axel Kohlmeyer (Fri Aug 20 2010 - 12:13:21 CDT)
- Re: RMSF calculation: residue wise Nicholas Musolino (Fri Aug 20 2010 - 12:46:36 CDT)
  - Re: RMSF calculation: residue wise hirdesh kumar (Fri Aug 20 2010 - 13:30:42 CDT)
    - Re: RMSF calculation: residue wise hirdesh kumar (Sat Aug 21 2010 - 06:03:46 CDT)
(no subject) yan zhang (Fri Aug 20 2010 - 03:54:47 CDT)
- Re: John Stone (Fri Aug 20 2010 - 14:05:26 CDT)
catdcd usage with Desmond trajectory Irene Newhouse (Thu Aug 19 2010 - 16:19:10 CDT)
- Re: catdcd usage with Desmond trajectory John Stone (Thu Aug 19 2010 - 20:32:23 CDT)
  - RE: catdcd usage with Desmond trajectory Irene Newhouse (Thu Aug 19 2010 - 22:26:26 CDT)
    - Re: catdcd usage with Desmond trajectory John Stone (Tue Aug 24 2010 - 16:44:25 CDT)
    - RE: catdcd usage with Desmond trajectory Irene Newhouse (Wed Aug 25 2010 - 15:33:25 CDT)
VMD plus Phantom Christian Wohlschlager (Wed Aug 18 2010 - 11:04:42 CDT)
- Re: VMD plus Phantom John Stone (Wed Aug 18 2010 - 13:11:03 CDT)
- Re: VMD plus Phantom Axel Kohlmeyer (Wed Aug 18 2010 - 14:13:53 CDT)
plugin : membrane builder : "integer value too large to represent" Lepore, Bryan (Wed Aug 18 2010 - 10:21:07 CDT)
- Re: plugin : membrane builder : "integer value too large to represent" John Stone (Wed Aug 18 2010 - 13:07:13 CDT)
  - Re: plugin : membrane builder : "integer value too large to represent" Lepore, Bryan (Wed Aug 18 2010 - 17:40:37 CDT)
Is it possible to load a part of a big xtc file faster... Alberto Sergio Garay (Wed Aug 18 2010 - 09:44:56 CDT)
- Re: Is it possible to load a part of a big xtc file faster... John Stone (Wed Aug 18 2010 - 10:00:08 CDT)
  - Re: Is it possible to load a part of a big xtc file faster... Bogdan Costescu (Wed Aug 18 2010 - 10:50:43 CDT)
PQR parser failure in pqr plugin 0.5 and pqr plugin in latest alpha Knut Jørgen Bjuland (Wed Aug 18 2010 - 09:11:21 CDT)
- Re: PQR parser failure in pqr plugin 0.5 and pqr plugin in latest alpha John Stone (Wed Aug 18 2010 - 13:38:40 CDT)
  - Re: PQR parser failure in pqr plugin 0.5 and pqr plugin in latest alpha John Stone (Wed Aug 18 2010 - 15:30:39 CDT)
    - Re: PQR parser failure in pqr plugin 0.5 and pqr plugin in latest alpha Knut Jørgen Bjuland (Wed Aug 18 2010 - 16:14:53 CDT)
Re: tcl script Cun Zhang (Wed Aug 18 2010 - 03:25:21 CDT)
tcl script deepti nayar (Wed Aug 18 2010 - 01:14:06 CDT)
- Re: tcl script Axel Kohlmeyer (Wed Aug 18 2010 - 04:01:00 CDT)
REMD + RBCG Gregorio Alanislobato (Tue Aug 17 2010 - 16:12:22 CDT)
- Re: REMD + RBCG Peter Freddolino (Tue Aug 17 2010 - 18:14:05 CDT)
  - Re: REMD + RBCG Gregorio Alanislobato (Tue Aug 17 2010 - 18:26:08 CDT)
    - Re: REMD + RBCG Gregorio Alanislobato (Tue Aug 17 2010 - 19:51:10 CDT)
    - Re: REMD + RBCG Peter Freddolino (Wed Aug 18 2010 - 00:30:20 CDT)
RSMD of coarse grained molecules Gregorio Alanislobato (Mon Aug 16 2010 - 12:13:59 CDT)
- Re: RSMD of coarse grained molecules John Stone (Mon Aug 16 2010 - 12:57:59 CDT)
- Re: RSMD of coarse grained molecules Mert Gür (Mon Aug 16 2010 - 13:58:02 CDT)
  - Re: RSMD of coarse grained molecules Gregorio Alanislobato (Mon Aug 16 2010 - 20:29:13 CDT)
workaround for DynamicBonds Georg Spiekermann (Mon Aug 16 2010 - 10:12:10 CDT)
- Re: workaround for DynamicBonds John Stone (Mon Aug 16 2010 - 11:05:28 CDT)
VMD 3D movies rendering Daniel Hornburg (Mon Aug 16 2010 - 05:07:59 CDT)
- Re: VMD 3D movies rendering Axel Kohlmeyer (Mon Aug 16 2010 - 08:40:36 CDT)
  - Re: VMD 3D movies rendering John Stone (Mon Aug 16 2010 - 11:20:00 CDT)
where can I download Tachyon version 0.98.10 ? Cun Zhang (Fri Aug 13 2010 - 23:06:19 CDT)
- Re: where can I download Tachyon version 0.98.10 ? Axel Kohlmeyer (Sat Aug 14 2010 - 08:19:12 CDT)
  - Re: where can I download Tachyon version 0.98.10 ? Cun Zhang (Sun Aug 15 2010 - 08:01:14 CDT)
- Re: where can I download Tachyon version 0.98.10 ? John Stone (Sat Aug 14 2010 - 23:10:51 CDT)
  - Re: where can I download Tachyon version 0.98.10 ? Cun Zhang (Sun Aug 15 2010 - 03:16:45 CDT)
    - Re: where can I download Tachyon version 0.98.10 ? Axel Kohlmeyer (Sun Aug 15 2010 - 04:28:42 CDT)
"Hands-On" Workshop on Computational Biophysics, November 1-5, 2010 & November 29-December 3, 2010 in Urbana, IL TCBG Workshops (Thu Aug 12 2010 - 17:10:53 CDT)
Interpreting a contact map Ian Stokes-Rees (Thu Aug 12 2010 - 16:17:12 CDT)
- Re: Interpreting a contact map John Stone (Thu Aug 12 2010 - 16:33:23 CDT)
  - Re: Interpreting a contact map Ian Stokes-Rees (Fri Aug 13 2010 - 16:11:29 CDT)
VMD questions about animating residue distance lines and contact maps Ian Stokes-Rees (Thu Aug 12 2010 - 15:56:18 CDT)
- Re: VMD questions about animating residue distance lines and contact maps John Stone (Thu Aug 12 2010 - 16:43:46 CDT)
  - Re: VMD questions about animating residue distance lines and contact maps Ian Stokes-Rees (Fri Aug 13 2010 - 10:30:15 CDT)
    - Re: VMD questions about animating residue distance lines and contact maps Axel Kohlmeyer (Fri Aug 13 2010 - 11:12:55 CDT)
    - Re: VMD questions about animating residue distance lines and contact maps John Stone (Fri Aug 13 2010 - 13:03:59 CDT)
Solvent Accessible Surface R. Johnson (Thu Aug 12 2010 - 13:26:48 CDT)
- Re: Solvent Accessible Surface Edward Lyman (Thu Aug 12 2010 - 14:10:25 CDT)
cant connect Novint Falcon with VMD Shawn (Thu Aug 12 2010 - 13:21:56 CDT)
- Re: cant connect Novint Falcon with VMD Axel Kohlmeyer (Thu Aug 12 2010 - 14:22:13 CDT)
  - Re: cant connect Novint Falcon with VMD Shawn (Thu Aug 12 2010 - 14:28:06 CDT)
About Atom Index Order Cun Zhang (Wed Aug 11 2010 - 20:59:08 CDT)
- Re: About Atom Index Order Axel Kohlmeyer (Wed Aug 11 2010 - 22:01:11 CDT)
  - Re: About Atom Index Order Cun Zhang (Thu Aug 12 2010 - 03:52:10 CDT)
Problem Material Studio/VMD candy deck (Wed Aug 11 2010 - 01:49:55 CDT)
- Re: Problem Material Studio/VMD Ajasja LjubetiÄ (Wed Aug 11 2010 - 03:48:44 CDT)
- Re: Problem Material Studio/VMD Axel Kohlmeyer (Wed Aug 11 2010 - 04:26:56 CDT)
  - Re: Problem Material Studio/VMD Vikas Varshney (Wed Aug 11 2010 - 12:54:07 CDT)
- Re: Problem Material Studio/VMD m.raviprasad_at_ndsu.edu (Wed Aug 11 2010 - 12:55:52 CDT)
Solvate plug-in Charles Zhao (Tue Aug 10 2010 - 21:53:22 CDT)
- Re: Solvate plug-in Axel Kohlmeyer (Tue Aug 10 2010 - 23:28:11 CDT)
Writing Python Plugins properly jonathan (Mon Aug 09 2010 - 11:48:25 CDT)
- Re: Writing Python Plugins properly Axel Kohlmeyer (Tue Aug 10 2010 - 21:38:07 CDT)
  - Re: Writing Python Plugins properly jonathan (Wed Aug 11 2010 - 06:54:10 CDT)
input file Agnieszka Sobkiewicz (Mon Aug 09 2010 - 06:41:18 CDT)
- Re: input file John Stone (Wed Aug 18 2010 - 15:00:41 CDT)
ion bead (residue based CG) Demet Akten (Mon Aug 09 2010 - 05:34:26 CDT)
- Re: ion bead (residue based CG) John Stone (Wed Aug 18 2010 - 15:06:39 CDT)
  - Re: ion bead (residue based CG) Peter Freddolino (Wed Aug 18 2010 - 19:16:17 CDT)
Superimpose protein - plot water position - visualize water pathway Marc Zimmer (Sat Aug 07 2010 - 19:51:26 CDT)
- Re: Superimpose protein - plot water position - visualize water pathway Axel Kohlmeyer (Sat Aug 07 2010 - 20:42:05 CDT)
upgrading vmd's nvidia component Bob Wohlhueter (Thu Aug 05 2010 - 16:04:53 CDT)
- Re: upgrading vmd's nvidia component John Stone (Thu Aug 05 2010 - 16:11:09 CDT)
  - Re: upgrading vmd's nvidia component Robert Wohlhueter (Thu Aug 05 2010 - 17:01:20 CDT)
Inserting amino acids to a protein Gregorio Alanislobato (Thu Aug 05 2010 - 14:24:56 CDT)
- Re: Inserting amino acids to a protein Ajasja LjubetiÄ (Fri Aug 06 2010 - 02:40:35 CDT)
NAMD energy plugin politr_at_huji.ac.il (Thu Aug 05 2010 - 07:41:37 CDT)
- Re: NAMD energy plugin Mert Gür (Thu Aug 05 2010 - 08:51:04 CDT)
- Re: NAMD energy plugin Axel Kohlmeyer (Thu Aug 05 2010 - 08:53:18 CDT)
- Re: NAMD energy plugin Nicholas Musolino (Thu Aug 05 2010 - 10:17:23 CDT)
Conversion into POVRay coordinates Nicolas Sapay (Wed Aug 04 2010 - 04:01:20 CDT)
- Re: Conversion into POVRay coordinates John Stone (Thu Aug 05 2010 - 17:06:54 CDT)
  - Re: Conversion into POVRay coordinates Nicolas Sapay (Fri Aug 06 2010 - 08:41:47 CDT)
    - Re: Conversion into POVRay coordinates John Stone (Fri Aug 06 2010 - 09:23:02 CDT)
water molecules shooting during SMD + PDB WRITE ERROR koushik.k (Tue Aug 03 2010 - 06:45:25 CDT)
- Re: water molecules shooting during SMD + PDB WRITE ERROR Nicholas Musolino (Tue Aug 03 2010 - 08:59:00 CDT)
povray rendering help Ramasamy, Ellankavi (Fri Jul 30 2010 - 07:45:31 CDT)
- Re: povray rendering help Axel Kohlmeyer (Fri Jul 30 2010 - 08:41:35 CDT)
2D RMSD matrix plot ban arn (Fri Jul 30 2010 - 05:52:02 CDT)
Focal blur with Tachyon Nicolas Sapay (Fri Jul 30 2010 - 03:13:49 CDT)
- Re: Focal blur with Tachyon Bogdan Costescu (Fri Jul 30 2010 - 04:49:55 CDT)
  - Re: Focal blur with Tachyon John Stone (Thu Aug 05 2010 - 17:09:46 CDT)
surface rendering across X11 windows David Hoover (Thu Jul 29 2010 - 16:15:48 CDT)
- Re: surface rendering across X11 windows John Stone (Mon Aug 02 2010 - 11:34:31 CDT)
script to calculate molecular surface area latha (Wed Jul 28 2010 - 12:46:23 CDT)
Dihedrals Angle ban arn (Wed Jul 28 2010 - 11:43:47 CDT)
- Re: Dihedrals Angle Ajasja LjubetiÄ (Thu Jul 29 2010 - 02:13:30 CDT)
2D rmsd matrix plot for C-alpha atoms ban arn (Wed Jul 28 2010 - 05:50:21 CDT)
- Re: 2D rmsd matrix plot for C-alpha atoms Leonardo Trabuco (Wed Jul 28 2010 - 06:24:53 CDT)
  - Re: 2D rmsd matrix plot for C-alpha atoms ban arn (Wed Jul 28 2010 - 07:45:52 CDT)
"can not find channel named ... Asmaa Elsheshiny (Wed Jul 28 2010 - 04:14:31 CDT)
- Re: "can not find channel named ... Ajasja LjubetiÄ (Wed Jul 28 2010 - 05:04:28 CDT)
- Re: "can not find channel named ... Axel Kohlmeyer (Wed Jul 28 2010 - 06:55:13 CDT)
multiseq/stamp alignment of coiled coil bundle and homo-dimer Ian Stokes-Rees (Tue Jul 27 2010 - 14:37:02 CDT)
- Re: multiseq/stamp alignment of coiled coil bundle and homo-dimer Ian Stokes-Rees (Tue Jul 27 2010 - 16:54:53 CDT)
  - Re: multiseq/stamp alignment of coiled coil bundle and homo-dimer John Stone (Wed Jul 28 2010 - 16:23:51 CDT)
2D rmsd plot for C-alpha atoms ban arn (Tue Jul 27 2010 - 10:55:48 CDT)
- Re: 2D rmsd plot for C-alpha atoms Leonardo Trabuco (Tue Jul 27 2010 - 11:07:03 CDT)
install on Centos - issues Joseph Norris (Fri Jul 23 2010 - 18:48:04 CDT)
- Re: install on Centos - issues John Stone (Wed Jul 28 2010 - 00:01:41 CDT)
VMD XRequest errors Richard Cook (Fri Jul 23 2010 - 18:47:49 CDT)
- Re: VMD XRequest errors John Stone (Tue Jul 27 2010 - 23:58:01 CDT)
  - Re: VMD XRequest errors Richard Cook (Wed Jul 28 2010 - 16:39:08 CDT)
    - RE: VMD XRequest errors Bennion, Brian (Wed Jul 28 2010 - 17:24:33 CDT)
  - Re: VMD XRequest errors Richard Cook (Wed Jul 28 2010 - 20:15:01 CDT)
MDFF Query: how to convert XPLOR style density maps to DX or SITUS format harish vashisth (Fri Jul 23 2010 - 16:28:59 CDT)
- Re: MDFF Query: how to convert XPLOR style density maps to DX or SITUS format Edelmiro Moman (Sat Jul 24 2010 - 03:50:58 CDT)
  - Re: MDFF Query: how to convert XPLOR style density maps to DX or SITUS format harish vashisth (Sat Jul 24 2010 - 11:12:27 CDT)
Extra lines shown in trajectories in VMD Elias Ahadi (Wed Jul 21 2010 - 12:26:08 CDT)
- Re: Extra lines shown in trajectories in VMD John Stone (Wed Jul 21 2010 - 13:08:34 CDT)
PC suitable for visualisation of large systems, maximum namuber of atoms in a .pdb file Prskalo, Alen-Pilip (Wed Jul 21 2010 - 02:40:27 CDT)
- Re: PC suitable for visualisation of large systems, maximum namuber of atoms in a .pdb file Ian Stokes-Rees (Wed Jul 21 2010 - 07:07:51 CDT)
  - Re: PC suitable for visualisation of large systems, maximum namuber of atoms in a .pdb file Axel Kohlmeyer (Wed Jul 21 2010 - 08:11:34 CDT)
  - RE: PC suitable for visualisation of large systems, maximum namuber of atoms in a .pdb file Prskalo, Alen-Pilip (Wed Jul 21 2010 - 08:42:42 CDT)
    - Re: PC suitable for visualisation of large systems, maximum namuber of atoms in a .pdb file Axel Kohlmeyer (Wed Jul 21 2010 - 09:09:19 CDT)
    - Re: PC suitable for visualisation of large systems, maximum namuber of atoms in a .pdb file Ian Stokes-Rees (Wed Jul 21 2010 - 12:20:56 CDT)
compilation of vmd 1.8.7 source Vlad Cojocaru (Tue Jul 20 2010 - 09:22:15 CDT)
- Re: compilation of vmd 1.8.7 source John Stone (Tue Jul 20 2010 - 09:47:22 CDT)
  - trajectory sort by RMSD or other Thomas C. Bishop (Tue Jul 20 2010 - 12:17:14 CDT)
- Re: compilation of vmd 1.8.7 source Ian Stokes-Rees (Tue Jul 20 2010 - 10:07:45 CDT)
  - Re: compilation of vmd 1.8.7 source John Stone (Tue Jul 20 2010 - 10:17:44 CDT)
lowest energy structure Jorgen Simonsen (Mon Jul 19 2010 - 22:52:59 CDT)
VMD failure of RMSD Traj Tool, time index on each rendered frame, and crash Ian Stokes-Rees (Mon Jul 19 2010 - 12:10:16 CDT)
- Re: VMD failure of RMSD Traj Tool, time index on each rendered frame, and crash John Stone (Tue Jul 20 2010 - 10:39:53 CDT)
  - Re: VMD failure of RMSD Traj Tool, time index on each rendered frame, and crash Ian Stokes-Rees (Tue Jul 20 2010 - 11:00:11 CDT)
    - Re: VMD failure of RMSD Traj Tool, time index on each rendered frame, and crash John Stone (Tue Jul 20 2010 - 11:04:44 CDT)
VMD Crashes on Windows Vista when trying to load more than 5000 steps Josiah Zayner (Mon Jul 19 2010 - 09:37:51 CDT)
- Re: VMD Crashes on Windows Vista when trying to load more than 5000 steps John Stone (Mon Jul 19 2010 - 09:55:03 CDT)
Invitation to connect on LinkedIn Deepti Mishra (Mon Jul 19 2010 - 05:57:43 CDT)
Adding other online PDB data bases to VMD Ian Stokes-Rees (Fri Jul 16 2010 - 18:46:31 CDT)
- Re: Adding other online PDB data bases to VMD Axel Kohlmeyer (Fri Jul 16 2010 - 19:58:22 CDT)
  - Re: Adding other online PDB data bases to VMD John Stone (Tue Jul 20 2010 - 10:52:25 CDT)
Cannot find "cionize plugin" in VMD Parisa Akhski (Fri Jul 16 2010 - 14:26:59 CDT)
- Re: Cannot find "cionize plugin" in VMD John Stone (Tue Jul 20 2010 - 09:41:53 CDT)
  - RE: Cannot find "cionize plugin" in VMD Parisa Akhski (Tue Jul 20 2010 - 12:36:32 CDT)
making a movie of an unusual trajectory Edward Lyman (Fri Jul 16 2010 - 11:54:47 CDT)
- Re: making a movie of an unusual trajectory John Stone (Fri Jul 16 2010 - 12:23:01 CDT)
  - Re: making a movie of an unusual trajectory Edward Lyman (Fri Jul 16 2010 - 12:34:06 CDT)
    - Re: making a movie of an unusual trajectory Axel Kohlmeyer (Fri Jul 16 2010 - 13:05:49 CDT)
    - Re: making a movie of an unusual trajectory Edward Lyman (Fri Jul 16 2010 - 13:09:09 CDT)
- Re: making a movie of an unusual trajectory Axel Kohlmeyer (Fri Jul 16 2010 - 12:47:26 CDT)
Building VMD on OS X 10.6 with Python and CUDA support Ian Stokes-Rees (Thu Jul 15 2010 - 22:44:34 CDT)
- Re: Building VMD on OS X 10.6 with Python and CUDA support Ian Stokes-Rees (Fri Jul 16 2010 - 02:24:38 CDT)
  - Re: Building VMD on OS X 10.6 with Python and CUDA support John Stone (Tue Jul 20 2010 - 10:23:56 CDT)
- Re: Building VMD on OS X 10.6 with Python and CUDA support Ian Stokes-Rees (Fri Jul 16 2010 - 02:41:24 CDT)
  - Re: Building VMD on OS X 10.6 with Python and CUDA support John Stone (Tue Jul 20 2010 - 10:22:23 CDT)
Adding Single Residues to a Protein Anwaar Al-Zireeni (Thu Jul 15 2010 - 18:34:56 CDT)
- Re: Adding Single Residues to a Protein John Stone (Tue Jul 20 2010 - 14:59:19 CDT)
locating or creating a .vmdsensors file for windows VMD Jeffrey Sanders (Wed Jul 14 2010 - 12:42:02 CDT)
- Re: locating or creating a .vmdsensors file for windows VMD John Stone (Wed Jul 14 2010 - 12:52:16 CDT)
using tcl variables in representation gui Robert Wohlhueter (Wed Jul 14 2010 - 09:22:09 CDT)
- Re: using tcl variables in representation gui John Stone (Wed Jul 14 2010 - 09:32:33 CDT)
Graphics Representation - Drawing methods puroorava annapaneni (Tue Jul 13 2010 - 17:39:06 CDT)
- Re: Graphics Representation - Drawing methods Axel Kohlmeyer (Tue Jul 13 2010 - 18:08:18 CDT)
Question about vrpn server build for using Phantom with VMD Jeffrey Sanders (Tue Jul 13 2010 - 15:05:58 CDT)
- Re: Question about vrpn server build for using Phantom with VMD John Stone (Tue Jul 13 2010 - 15:13:23 CDT)
Native contacts trajectory tool available Toni Giorgino (Tue Jul 13 2010 - 14:09:49 CDT)
VMD cuda Raul Araya (Mon Jul 12 2010 - 15:59:19 CDT)
- Re: VMD cuda John Stone (Mon Jul 12 2010 - 16:48:39 CDT)
- Re: VMD cuda Axel Kohlmeyer (Mon Jul 12 2010 - 16:50:26 CDT)
  - Re: VMD cuda John Stone (Tue Jul 13 2010 - 14:50:08 CDT)
Autoionize question for DNA molecule Parisa Akhski (Mon Jul 12 2010 - 10:10:11 CDT)
- Re: Autoionize question for DNA molecule Eduard Schreiner (Mon Jul 12 2010 - 11:08:02 CDT)
  - RE: Cionize question for DNA molecule Parisa Akhski (Thu Jul 15 2010 - 11:52:54 CDT)
contact map for Protein-DNA interaction atila petrosian (Mon Jul 12 2010 - 02:19:13 CDT)
- Re: contact map for Protein-DNA interaction Barry Isralewitz (Mon Jul 12 2010 - 13:50:25 CDT)
ILS tool fails Aaron Oakley (Fri Jul 09 2010 - 20:25:38 CDT)
- Re: ILS tool fails John Stone (Tue Jul 13 2010 - 11:39:50 CDT)
DPPC jouko_at_uchicago.edu (Thu Jul 08 2010 - 22:21:25 CDT)
- Re: DPPC Eduard Schreiner (Thu Jul 08 2010 - 23:42:27 CDT)
Modifying amino acid to a non-standard amino acid using VMD (proline to hydroxyproline) Sujata Sovani (Thu Jul 08 2010 - 19:05:55 CDT)
- Re: Modifying amino acid to a non-standard amino acid using VMD (proline to hydroxyproline) Ajasja LjubetiÄ (Fri Jul 09 2010 - 02:33:13 CDT)
Install VMD on intel i5 moacyr comar (Wed Jul 07 2010 - 12:00:18 CDT)
- Re: Install VMD on intel i5 John Stone (Mon Jul 12 2010 - 11:52:30 CDT)
contact map for protein-dna interaction leila karami (Wed Jul 07 2010 - 03:32:51 CDT)
Release of the R.E.D.-III.4 tools FyD (Wed Jul 07 2010 - 02:04:36 CDT)
Selecting basic residues in g(r) GUI Plugin Rabab Toubar (Tue Jul 06 2010 - 10:47:06 CDT)
Autoionize does not neutralize the system Parisa Akhski (Tue Jul 06 2010 - 09:16:20 CDT)
- Re: Autoionize does not neutralize the system Axel Kohlmeyer (Tue Jul 06 2010 - 09:49:19 CDT)
  - Re: Autoionize does not neutralize the system John Stone (Tue Jul 06 2010 - 10:16:43 CDT)
- Re: Autoionize does not neutralize the system John Stone (Tue Jul 06 2010 - 10:42:58 CDT)
  - RE: Autoionize does not neutralize the system Parisa Akhski (Tue Jul 06 2010 - 14:36:20 CDT)
color charmm dcd by kinetic energy Ardy Davari (Mon Jul 05 2010 - 15:59:22 CDT)
- Re: color charmm dcd by kinetic energy Axel Kohlmeyer (Mon Jul 05 2010 - 17:02:53 CDT)
- Re: color charmm dcd by kinetic energy Bjoern Olausson (Tue Jul 06 2010 - 02:51:24 CDT)
  - Re: color charmm dcd by kinetic energy Ardy Davari (Tue Jul 06 2010 - 09:30:27 CDT)
contact map leila karami (Mon Jul 05 2010 - 09:46:04 CDT)
contact map leila karami (Mon Jul 05 2010 - 09:12:47 CDT)
- Re: contact map Axel Kohlmeyer (Mon Jul 05 2010 - 11:47:31 CDT)
contact map leila karami (Mon Jul 05 2010 - 08:33:23 CDT)
Conversion of DCD trajectories to AMBER ones ? Marek Maly (Mon Jul 05 2010 - 05:06:40 CDT)
- Re: Conversion of DCD trajectories to AMBER ones ? Axel Kohlmeyer (Mon Jul 05 2010 - 05:54:16 CDT)
  - Re: Conversion of DCD trajectories to AMBER ones ? Marek Maly (Mon Jul 05 2010 - 09:07:14 CDT)
RGB values... Luis Guillermo Cota Preciado (Thu Jul 01 2010 - 18:10:10 CDT)
- Re: RGB values... Robert Brunner (Fri Jul 02 2010 - 11:07:06 CDT)
- Re: RGB values... John Stone (Sat Jul 03 2010 - 09:12:35 CDT)
Sasa implentation/ algorithm VMD henri mone (Thu Jul 01 2010 - 17:19:06 CDT)
- Re: Sasa implentation/ algorithm VMD John Stone (Sat Jul 03 2010 - 09:14:11 CDT)
  - possible chain select bug on RCSB ".ent" files Thomas C. Bishop (Mon Jul 05 2010 - 09:30:09 CDT)
    - Re: possible chain select bug on RCSB ".ent" files Leonardo Trabuco (Mon Jul 05 2010 - 09:46:18 CDT)
    - Re: possible chain select bug on RCSB ".ent" files Thomas C. Bishop (Mon Jul 05 2010 - 10:08:27 CDT)
Re: Tachyon Rendering with a Surf Representation jamesgiacmo_at_aol.com (Wed Jun 30 2010 - 08:29:39 CDT)
getting python to work Seth Burleigh (Tue Jun 29 2010 - 11:20:09 CDT)
- Re: getting python to work John Stone (Thu Jul 01 2010 - 10:23:41 CDT)
Tachyon Rendering with a Surf Representation jamesgiacmo_at_aol.com (Tue Jun 29 2010 - 10:12:11 CDT)
- Re: Tachyon Rendering with a Surf Representation John Stone (Thu Jul 01 2010 - 10:20:20 CDT)
VMD / Tachyon Questions Andrew (Sun Jun 27 2010 - 19:27:21 CDT)
- Re: VMD / Tachyon Questions John Stone (Thu Jul 01 2010 - 10:58:26 CDT)
  - Re: VMD / Tachyon Questions Andrew (Tue Jul 06 2010 - 17:05:13 CDT)
Re: namd-l: Simulation configuration file not accesible Ajasja LjubetiÄ (Fri Jun 25 2010 - 16:19:34 CDT)
stereo problem with vmd Osmany Guirola Cruz (Fri Jun 25 2010 - 06:58:06 CDT)
- Re: stereo problem with vmd John Stone (Fri Jun 25 2010 - 10:14:20 CDT)
  - Re: stereo problem with vmd Osmany Guirola Cruz (Fri Jun 25 2010 - 12:51:26 CDT)
    - Re: stereo problem with vmd John Stone (Fri Jun 25 2010 - 12:56:34 CDT)
VMD 1.8.7 and NVIDIA 256.35 driver problems (CUDA issue?) ben rodriguez (Thu Jun 24 2010 - 14:29:18 CDT)
- Re: VMD 1.8.7 and NVIDIA 256.35 driver problems (CUDA issue?) John Stone (Thu Jun 24 2010 - 14:58:59 CDT)
Add/Remove Bonds Rabab Toubar (Thu Jun 24 2010 - 12:27:20 CDT)
- Re: Add/Remove Bonds John Stone (Thu Jun 24 2010 - 16:47:36 CDT)
vmd on Microsoft 2000 and Phantom Christian Wohlschlager (Tue Jun 22 2010 - 07:51:03 CDT)
- Re: vmd on Microsoft 2000 and Phantom Axel Kohlmeyer (Tue Jun 22 2010 - 08:48:53 CDT)
- Re: vmd on Microsoft 2000 and Phantom John Stone (Tue Jun 22 2010 - 11:26:18 CDT)
Fwd: convert prmtop to psf Lai zaizhi (Mon Jun 21 2010 - 16:42:10 CDT)
Re: convert prmtop to psf Lai zaizhi (Mon Jun 21 2010 - 16:41:37 CDT)
- Re: Re: convert prmtop to psf John Stone (Mon Jun 21 2010 - 16:56:08 CDT)
- Re: Re: convert prmtop to psf Axel Kohlmeyer (Mon Jun 21 2010 - 17:25:22 CDT)
  - Re: Re: convert prmtop to psf George Madalin Giambasu (Mon Jun 21 2010 - 18:09:28 CDT)
AutoPSF errors Emily Chen (Mon Jun 21 2010 - 14:06:19 CDT)
- Re: AutoPSF errors Peter Freddolino (Mon Jun 21 2010 - 18:42:33 CDT)
  - OpenGL Display slow/freeze Yangyang Shen (Mon Jun 21 2010 - 22:08:11 CDT)
  - Re: AutoPSF errors Peter Freddolino (Tue Jun 22 2010 - 20:16:06 CDT)
Cannot read MSMS data files Jayne Wallace (Mon Jun 21 2010 - 09:12:07 CDT)
- Re: Cannot read MSMS data files John Stone (Mon Jun 21 2010 - 16:00:36 CDT)
  - Re: Cannot read MSMS data files John Stone (Tue Jun 22 2010 - 11:37:48 CDT)
namdenergy: writepdb failed Neelanjana Sengupta (Sun Jun 20 2010 - 06:27:02 CDT)
- Re: namdenergy: writepdb failed Axel Kohlmeyer (Sun Jun 20 2010 - 08:25:03 CDT)
- Re: namdenergy: writepdb failed Peter Freddolino (Sun Jun 20 2010 - 19:09:47 CDT)
structure file for big molecules Moeed (Fri Jun 18 2010 - 21:19:02 CDT)
- Re: structure file for big molecules Axel Kohlmeyer (Sun Jun 20 2010 - 18:55:39 CDT)
- Re: structure file for big molecules Nicholas Musolino (Sun Jun 20 2010 - 20:23:50 CDT)
Hydrophobic interaction ban arn (Fri Jun 18 2010 - 06:53:37 CDT)
- Hydrophobic interaction ban arn (Fri Jun 18 2010 - 07:30:45 CDT)
  - Re: Hydrophobic interaction Nicolas Sapay (Fri Jun 18 2010 - 08:25:09 CDT)
- Re: Hydrophobic interaction Axel Kohlmeyer (Fri Jun 18 2010 - 08:10:23 CDT)
  - Re: Hydrophobic interaction ban arn (Fri Jun 18 2010 - 08:18:23 CDT)
    - Re: Hydrophobic interaction Axel Kohlmeyer (Fri Jun 18 2010 - 08:25:36 CDT)
Hydrophobic interaction ban arn (Fri Jun 18 2010 - 05:59:43 CDT)
- Re: Hydrophobic interaction Nicholas Musolino (Fri Jun 18 2010 - 08:40:44 CDT)
-samples flag of measure sasa Edward Lyman (Thu Jun 17 2010 - 11:47:34 CDT)
- Re: -samples flag of measure sasa John Stone (Fri Jun 18 2010 - 13:10:08 CDT)
  - Re: -samples flag of measure sasa Edward Lyman (Fri Jun 18 2010 - 14:15:10 CDT)
Workshop on GPU Programming for Molecular Modeling, August 6-8, 2010, at the Beckman Institute in Urbana, Illinois TCBG Workshops (Fri Jun 11 2010 - 17:28:26 CDT)
vmd crash at start Bogdan Tarus (Thu Jun 17 2010 - 10:33:35 CDT)
- Re: vmd crash at start John Stone (Thu Jun 17 2010 - 10:41:34 CDT)
  - Re: vmd crash at start Bogdan Tarus (Thu Jun 17 2010 - 12:16:06 CDT)
Invalid command name "His" during Solvation Michael LeVine (Thu Jun 17 2010 - 09:10:52 CDT)
- Re: Invalid command name "His" during Solvation John Stone (Fri Jun 25 2010 - 13:51:18 CDT)
Color by velocity (speed?) Ardy Davari (Wed Jun 16 2010 - 12:04:04 CDT)
- Re: Color by velocity (speed?) Axel Kohlmeyer (Wed Jun 16 2010 - 13:01:21 CDT)
solvate nonstandard patch error Harold Hatch (Wed Jun 16 2010 - 10:42:50 CDT)
- Re: solvate nonstandard patch error Peter Freddolino (Wed Jun 16 2010 - 11:52:23 CDT)
visualize trajectories from lammps parallel results shiziyuan (Tue Jun 15 2010 - 15:44:58 CDT)
- Re: visualize trajectories from lammps parallel results John Stone (Thu Jun 17 2010 - 14:41:03 CDT)
  - Re: visualize trajectories from lammps parallel results Axel Kohlmeyer (Thu Jun 17 2010 - 15:34:31 CDT)
    - Re: visualize trajectories from lammps parallel results shiziyuan (Thu Jun 17 2010 - 15:44:41 CDT)
particular set of xyz coordinates in PDB causes seg fault Daniel Farrell (Tue Jun 15 2010 - 12:16:58 CDT)
- Re: particular set of xyz coordinates in PDB causes seg fault Axel Kohlmeyer (Tue Jun 15 2010 - 12:56:50 CDT)
  - Re: particular set of xyz coordinates in PDB causes seg fault Daniel Farrell (Tue Jun 15 2010 - 13:59:50 CDT)
    - Re: particular set of xyz coordinates in PDB causes seg fault Axel Kohlmeyer (Tue Jun 15 2010 - 15:02:45 CDT)
    - Re: particular set of xyz coordinates in PDB causes seg fault Daniel Farrell (Tue Jun 15 2010 - 15:35:50 CDT)
AutoPSF deleting residues Kelly Leung (Tue Jun 15 2010 - 10:35:38 CDT)
- Re: AutoPSF deleting residues Peter Freddolino (Tue Jun 15 2010 - 20:33:02 CDT)
Re: Grid spacing in mdff Leonardo Trabuco (Tue Jun 15 2010 - 02:54:08 CDT)
Gradient Background Vikas Varshney (Mon Jun 14 2010 - 15:13:26 CDT)
- Re: Gradient Background John Stone (Fri Jun 18 2010 - 15:11:05 CDT)
Change only the CA coordinates in a pdb file via tcl Mert Gür (Mon Jun 14 2010 - 14:26:14 CDT)
- Re: Change only the CA coordinates in a pdb file via tcl John Stone (Mon Jun 14 2010 - 15:12:33 CDT)
  - Re: Change only the CA coordinates in a pdb file via tcl Mert Gür (Mon Jun 14 2010 - 16:24:44 CDT)
- Re: Change only the CA coordinates in a pdb file via tcl genie lfs (Mon Jun 14 2010 - 15:45:07 CDT)
top2psf.tcl Rabab Toubar (Sun Jun 13 2010 - 05:59:28 CDT)
- Re: top2psf.tcl Axel Kohlmeyer (Sun Jun 13 2010 - 07:19:12 CDT)
  - Re: top2psf.tcl Rabab Toubar (Tue Jun 15 2010 - 08:21:19 CDT)
  - Re: top2psf.tcl Rabab Toubar (Tue Jun 15 2010 - 10:14:14 CDT)
Rending to png format using tachyon or otherwise ? maria goranovic (Wed Jun 09 2010 - 09:33:25 CDT)
- Re: Rending to png format using tachyon or otherwise ? John Stone (Wed Jun 09 2010 - 10:06:06 CDT)
  - Re: Rending to png format using tachyon or otherwise ? maria goranovic (Wed Jun 09 2010 - 11:18:13 CDT)
    - Re: Rending to png format using tachyon or otherwise ? Axel Kohlmeyer (Wed Jun 09 2010 - 13:08:57 CDT)
topotools and Partial charges Michael Doig (Wed Jun 09 2010 - 05:25:25 CDT)
- Re: topotools and Partial charges Axel Kohlmeyer (Wed Jun 09 2010 - 11:49:55 CDT)
about vmd solvation plugin David Li (Sat Jun 05 2010 - 18:31:36 CDT)
- Re: about vmd solvation plugin Axel Kohlmeyer (Sat Jun 05 2010 - 19:32:54 CDT)
  - Re: about vmd solvation plugin David Li (Wed Jun 09 2010 - 05:33:10 CDT)
    - Re: about vmd solvation plugin Axel Kohlmeyer (Wed Jun 09 2010 - 07:11:11 CDT)
visualizing small molecule in a trajectory file .trr and .gro using VMD Hassan Shallal (Fri Jun 04 2010 - 22:49:33 CDT)
- Re: visualizing small molecule in a trajectory file .trr and .gro using VMD Joshua Adelman (Sat Jun 05 2010 - 08:16:16 CDT)
Trouble compiling from source - Mac OS X Reid Van Lehn (Fri Jun 04 2010 - 11:36:54 CDT)
- Re: Trouble compiling from source - Mac OS X Axel Kohlmeyer (Fri Jun 04 2010 - 13:11:08 CDT)
- Re: Trouble compiling from source - Mac OS X John Stone (Fri Jun 04 2010 - 17:08:33 CDT)
  - Re: Trouble compiling from source - Mac OS X Reid Van Lehn (Fri Jun 04 2010 - 23:11:38 CDT)
    - Re: Trouble compiling from source - Mac OS X Reid Van Lehn (Fri Jun 04 2010 - 23:36:13 CDT)
    - Re: Trouble compiling from source - Mac OS X Reid Van Lehn (Sun Jun 06 2010 - 14:53:58 CDT)
Retrieving the Cremer-Pople parameters Nicolas Sapay (Fri Jun 04 2010 - 03:46:30 CDT)
- Re: Retrieving the Cremer-Pople parameters John Stone (Fri Jun 04 2010 - 17:03:59 CDT)
  - Re: Retrieving the Cremer-Pople parameters Nicolas Sapay (Mon Jun 07 2010 - 04:05:01 CDT)
Problems with Linux install... Luis Guillermo Cota Preciado (Fri Jun 04 2010 - 02:32:23 CDT)
- Re: Problems with Linux install... John Stone (Fri Jun 04 2010 - 08:37:54 CDT)
  - Re: Problems with Linux install... Luis Guillermo Cota Preciado (Fri Jun 04 2010 - 10:19:01 CDT)
- Re: Problems with Linux install... Luis Guillermo Cota Preciado (Fri Jun 04 2010 - 13:30:30 CDT)
  - Re: Re: Problems with Linux install... Axel Kohlmeyer (Fri Jun 04 2010 - 14:18:40 CDT)
about ".cpmd" format Liu (Thu Jun 03 2010 - 22:31:58 CDT)
- Re: about ".cpmd" format Axel Kohlmeyer (Fri Jun 04 2010 - 00:50:48 CDT)
about paratool Francesco Pietra (Thu Jun 03 2010 - 02:50:05 CDT)
- Re: about paratool Axel Kohlmeyer (Thu Jun 03 2010 - 04:59:08 CDT)
Has anyone done ILS successfully? Irene Newhouse (Wed Jun 02 2010 - 14:39:36 CDT)
CAN ANY ONE HELP ME vani panguluri (Wed Jun 02 2010 - 10:09:08 CDT)
- Re: CAN ANY ONE HELP ME John Stone (Wed Jun 02 2010 - 11:01:15 CDT)
  - Re: CAN ANY ONE HELP ME vani panguluri (Wed Jun 02 2010 - 11:44:33 CDT)
    - Re: CAN ANY ONE HELP ME John Stone (Wed Jun 02 2010 - 12:51:24 CDT)
Interaction Energy ban arn (Wed Jun 02 2010 - 07:29:38 CDT)
- Re: Interaction Energy John Stone (Wed Jun 02 2010 - 11:02:40 CDT)
  - Re: Interaction Energy ban arn (Wed Jun 02 2010 - 11:35:57 CDT)
Visualize intersection of overlapping spheres? Bjoern Olausson (Wed Jun 02 2010 - 06:51:56 CDT)
- Re: Visualize intersection of overlapping spheres? John Stone (Wed Jun 02 2010 - 12:57:04 CDT)
  - Re: Visualize intersection of overlapping spheres? Axel Kohlmeyer (Wed Jun 02 2010 - 13:46:02 CDT)
    - Re: Visualize intersection of overlapping spheres? John Stone (Wed Jun 02 2010 - 13:48:36 CDT)
    - Re: Visualize intersection of overlapping spheres? Bjoern Olausson (Thu Jun 03 2010 - 02:24:02 CDT)
psfgen plugin sriteja mantha (Wed Jun 02 2010 - 05:23:51 CDT)
- Re: psfgen plugin John Stone (Wed Jun 02 2010 - 12:58:54 CDT)
Bug in VMD-1.8.7 multiseq functionality genie lfs (Wed Jun 02 2010 - 04:54:48 CDT)
RMSD Trajectory Tool Philip Peartree (Tue Jun 01 2010 - 20:33:54 CDT)
- Re: RMSD Trajectory Tool Axel Kohlmeyer (Tue Jun 01 2010 - 22:02:36 CDT)
- Re: RMSD Trajectory Tool Thomas C Bishop (Wed Jun 02 2010 - 09:24:13 CDT)
Compiling without graphics Philip Peartree (Tue Jun 01 2010 - 20:31:18 CDT)
- Re: Compiling without graphics John Stone (Tue Jun 01 2010 - 22:06:55 CDT)
- Re: Compiling without graphics Axel Kohlmeyer (Tue Jun 01 2010 - 21:55:58 CDT)
Deleting/modifying specific molecule representations Bob Johnson (Tue Jun 01 2010 - 11:23:58 CDT)
- Re: Deleting/modifying specific molecule representations Ajasja LjubetiÄ (Wed Jun 02 2010 - 11:53:00 CDT)
- Re: Deleting/modifying specific molecule representations John Stone (Fri Jun 18 2010 - 16:20:57 CDT)
Mol2 with Charmm atom types? Edelmiro Moman (Mon May 31 2010 - 04:45:51 CDT)
- Re: Mol2 with Charmm atom types? Peter Freddolino (Tue Jun 01 2010 - 21:11:12 CDT)
Residue Number Assignment by VMD Sally Fisher (Fri May 28 2010 - 07:29:55 CDT)
- Re: Residue Number Assignment by VMD Axel Kohlmeyer (Fri May 28 2010 - 08:24:45 CDT)
  - Re: Residue Number Assignment by VMD: RESID vs RESIDUE Thomas C. Bishop (Fri May 28 2010 - 10:47:05 CDT)
- Re: Residue Number Assignment by VMD John Stone (Fri May 28 2010 - 13:32:38 CDT)
RDF and Coordination Number Amir Hajiahmadi Farmahini (Fri May 28 2010 - 05:40:15 CDT)
- Re: RDF and Coordination Number Axel Kohlmeyer (Fri May 28 2010 - 08:52:10 CDT)
APBS plugin Sladjana Maric (Thu May 27 2010 - 18:16:15 CDT)
- Re: APBS plugin John Stone (Thu Jun 03 2010 - 11:37:06 CDT)
  - Re: APBS plugin Sladjana Maric (Thu Jun 03 2010 - 11:50:33 CDT)
pbc wrap Salvador H-V (Thu May 27 2010 - 17:35:54 CDT)
- Re: pbc wrap Olaf Lenz (Tue Jun 01 2010 - 05:23:05 CDT)
Modelling program that does hydrogen adjust Jennifer Williams (Thu May 27 2010 - 10:21:49 CDT)
- Re: Modelling program that does hydrogen adjust Bjoern Olausson (Fri May 28 2010 - 06:14:24 CDT)
- Re: Modelling program that does hydrogen adjust Axel Kohlmeyer (Fri May 28 2010 - 08:30:34 CDT)
- Slice through molecule Jennifer Williams (Wed May 11 2011 - 06:32:13 CDT)
  - Re: Slice through molecule Axel Kohlmeyer (Wed May 11 2011 - 09:16:40 CDT)
Tcl-wrapped "lightweight plugin" in C++ Jérôme Hénin (Thu May 27 2010 - 07:27:00 CDT)
- Re: Tcl-wrapped "lightweight plugin" in C++ John Stone (Thu May 27 2010 - 22:16:44 CDT)
  - Re: Tcl-wrapped "lightweight plugin" in C++ Jérôme Hénin (Sun May 30 2010 - 04:26:07 CDT)
    - Re: Tcl-wrapped "lightweight plugin" in C++ John Stone (Tue Jun 01 2010 - 11:04:09 CDT)
    - Re: Tcl-wrapped "lightweight plugin" in C++ Jérôme Hénin (Thu Jun 03 2010 - 07:56:51 CDT)
Residue Ordering in Sequence Viewer/MultiSeq Sally Fisher (Wed May 26 2010 - 10:15:20 CDT)
radial distribution function problem Hyun Tae Jung (Wed May 26 2010 - 08:42:48 CDT)
- Re: radial distribution function problem Axel Kohlmeyer (Wed May 26 2010 - 11:26:30 CDT)
Problem with display on Intel graphics card Tim Travers (Tue May 25 2010 - 17:29:09 CDT)
- Re: Problem with display on Intel graphics card John Stone (Wed May 26 2010 - 09:46:45 CDT)
  - Re: Problem with display on Intel graphics card Tim Travers (Wed May 26 2010 - 16:27:01 CDT)
  - Re: Problem with display on Intel graphics card Tim Travers (Wed May 26 2010 - 16:25:03 CDT)
parameter file for CHARMM matziast_at_med.uth.gr (Tue May 25 2010 - 16:03:33 CDT)
monomer transposes boundary box Hugo Gutiérrez de Teran (Tue May 25 2010 - 06:48:04 CDT)
- Re: monomer transposes boundary box Axel Kohlmeyer (Tue May 25 2010 - 08:16:51 CDT)
  - Re: monomer transposes boundary box Hugo Gutierrez de Teran (Tue May 25 2010 - 08:25:37 CDT)
  - Re: monomer transposes boundary box Olaf Lenz (Wed May 26 2010 - 05:10:21 CDT)
Tachyon 0.9.10 and recommende version of cuda? Knut Jørgen Bjuland (Mon May 24 2010 - 05:10:37 CDT)
- Re: Tachyon 0.9.10 and recommende version of cuda? Axel Kohlmeyer (Mon May 24 2010 - 07:45:24 CDT)
LAMMPS Trajectory Moslem Sabouri (Sun May 23 2010 - 04:46:17 CDT)
- Re: LAMMPS Trajectory Axel Kohlmeyer (Sun May 23 2010 - 17:24:08 CDT)
generating PSF file for a small molecule Hassan Shallal (Sun May 23 2010 - 03:53:58 CDT)
- Re: generating PSF file for a small molecule Ranyere Deyler (Sun May 23 2010 - 15:52:11 CDT)
Atom Selection for RDF Amir Hajiahmadi Farmahini (Sat May 22 2010 - 09:19:18 CDT)
- Re: Atom Selection for RDF Axel Kohlmeyer (Sat May 22 2010 - 10:25:06 CDT)
  - Re: Atom Selection for RDF Amir Hajiahmadi Farmahini (Sat May 22 2010 - 12:15:36 CDT)
    - Re: Atom Selection for RDF Axel Kohlmeyer (Sat May 22 2010 - 12:46:48 CDT)
Re: namd-l: Error in running minimization Joshua Adelman (Fri May 21 2010 - 07:56:06 CDT)
Cutting a bond Francesco Pietra (Wed May 19 2010 - 13:52:18 CDT)
- Re: Cutting a bond Axel Kohlmeyer (Wed May 19 2010 - 14:33:01 CDT)
Frames-Movie Salvador H-V (Wed May 19 2010 - 11:54:32 CDT)
- Re: Frames-Movie Vikas Varshney (Wed May 19 2010 - 13:12:58 CDT)
  - Re: Frames-Movie Axel Kohlmeyer (Wed May 19 2010 - 14:39:12 CDT)
Adding an atom to the existing pdb Narasimhan LOGANATHAN (Wed May 19 2010 - 05:18:22 CDT)
- Re: Adding an atom to the existing pdb Axel Kohlmeyer (Wed May 19 2010 - 06:36:59 CDT)
LANG setting needs to be solved in next release.... Rob (Tue May 18 2010 - 19:33:06 CDT)
- Re: LANG setting needs to be solved in next release.... John Stone (Tue May 18 2010 - 22:18:28 CDT)
- Re: LANG setting needs to be solved in next release.... Bogdan Costescu (Wed May 19 2010 - 08:34:38 CDT)
  - Re: LANG setting needs to be solved in next release.... John Stone (Wed May 19 2010 - 08:41:47 CDT)
    - Re: LANG setting needs to be solved in next release.... Bogdan Costescu (Wed May 19 2010 - 09:14:27 CDT)
- Re: LANG setting needs to be solved in next release.... Rob (Thu May 20 2010 - 02:16:43 CDT)
  - Re: Re: LANG setting needs to be solved in next release.... Bogdan Costescu (Thu May 20 2010 - 08:47:06 CDT)
compile error Liu Shiyong (Tue May 18 2010 - 04:40:12 CDT)
- Re: compile error Axel Kohlmeyer (Tue May 18 2010 - 06:27:22 CDT)
adding water box Hao Sun (Mon May 17 2010 - 19:09:57 CDT)
- Re: adding water box John Stone (Tue May 18 2010 - 12:36:24 CDT)
  - Multimodel PDB files with different models (again)? Boris Steipe (Tue May 18 2010 - 16:19:46 CDT)
adding water box Hao Sun (Mon May 17 2010 - 19:09:36 CDT)
Radial distribution function: "y" axis martin klvana (Sun May 16 2010 - 12:39:54 CDT)
- Re: Radial distribution function: "y" axis Axel Kohlmeyer (Sun May 16 2010 - 14:01:26 CDT)
  - Re: Radial distribution function: "y" axis martin klvana (Mon May 17 2010 - 17:05:03 CDT)
    - Re: Radial distribution function: "y" axis Axel Kohlmeyer (Mon May 17 2010 - 17:13:23 CDT)
append pdb politr_at_huji.ac.il (Sun May 16 2010 - 09:48:19 CDT)
- Re: append pdb Axel Kohlmeyer (Sun May 16 2010 - 11:00:52 CDT)
Xrequest in VMD Mantzalis, Dimitrios (Wed May 12 2010 - 06:03:28 CDT)
- Re: Xrequest in VMD Axel Kohlmeyer (Wed May 12 2010 - 06:44:02 CDT)
Recenter membrane bilayer to unit cell Mühlbacher, Markus (Wed May 12 2010 - 03:37:13 CDT)
- Re: Recenter membrane bilayer to unit cell Olaf Lenz (Wed May 12 2010 - 04:55:06 CDT)
Selecting CUDA devices in VMD 1.8.7 Joakim Swedberg (Tue May 11 2010 - 17:49:54 CDT)
- Re: Selecting CUDA devices in VMD 1.8.7 John Stone (Tue May 11 2010 - 19:23:48 CDT)
  - Re: Selecting CUDA devices in VMD 1.8.7 Axel Kohlmeyer (Tue May 11 2010 - 20:08:25 CDT)
    - Re: Selecting CUDA devices in VMD 1.8.7 John Stone (Tue May 11 2010 - 22:07:03 CDT)
  - Re: Selecting CUDA devices in VMD 1.8.7 John Stone (Wed May 26 2010 - 10:39:53 CDT)
- Re: Selecting CUDA devices in VMD 1.8.7 Axel Kohlmeyer (Tue May 11 2010 - 19:19:21 CDT)
units of "measure dipole" Edward Lyman (Tue May 11 2010 - 14:47:45 CDT)
- Re: units of "measure dipole" Axel Kohlmeyer (Tue May 11 2010 - 15:29:59 CDT)
  - Re: units of "measure dipole" Edward Lyman (Tue May 11 2010 - 15:35:56 CDT)
    - Re: units of "measure dipole" Axel Kohlmeyer (Tue May 11 2010 - 15:53:29 CDT)
    - Re: units of "measure dipole" Axel Kohlmeyer (Tue May 11 2010 - 16:23:51 CDT)
Atom movement within a range of Z value muniyamuthu.raviprasad_at_ndsu.edu (Tue May 11 2010 - 14:47:15 CDT)
- Re: namd-l: Atom movement within a range of Z value Axel Kohlmeyer (Tue May 11 2010 - 15:27:44 CDT)
- Re: namd-l: Atom movement within a range of Z value Eduardo Cruz-Chu (Tue May 11 2010 - 15:45:59 CDT)
regarding fit_angle.tcl jani vinod (Tue May 11 2010 - 07:04:20 CDT)
- Re: regarding fit_angle.tcl John Stone (Tue May 18 2010 - 16:02:37 CDT)
  - Re: regarding fit_angle.tcl jani vinod (Tue May 18 2010 - 23:14:46 CDT)
    - Re: regarding fit_angle.tcl John Stone (Tue May 18 2010 - 23:40:16 CDT)
    - Re: regarding fit_angle.tcl jani vinod (Wed May 19 2010 - 01:41:34 CDT)
namd gui problem sarah k (Tue May 11 2010 - 02:29:02 CDT)
- Re: namd gui problem Joshua Adelman (Tue May 11 2010 - 07:26:58 CDT)
  - Re: namd gui problem sarah k (Fri May 14 2010 - 00:16:34 CDT)
LAMMPS trajectory file Anna Ceguerra (Mon May 10 2010 - 21:12:28 CDT)
- Re: LAMMPS trajectory file Axel Kohlmeyer (Mon May 10 2010 - 23:25:23 CDT)
  - Re: LAMMPS trajectory file Anna Ceguerra (Tue May 11 2010 - 03:32:52 CDT)
Creating AVI movies David Poger (Mon May 10 2010 - 07:28:24 CDT)
- Re: Creating AVI movies Axel Kohlmeyer (Mon May 10 2010 - 08:21:13 CDT)
- Re: Creating AVI movies Bjoern Olausson (Mon May 10 2010 - 08:37:58 CDT)
Stereoscopic visualization Emiliano Ippoliti (Sun May 09 2010 - 10:58:46 CDT)
- Re: Stereoscopic visualization Axel Kohlmeyer (Sun May 09 2010 - 11:58:13 CDT)
  - Re: Stereoscopic visualization Emiliano Ippoliti (Sun May 09 2010 - 13:56:59 CDT)
    - Re: Stereoscopic visualization Axel Kohlmeyer (Sun May 09 2010 - 14:12:14 CDT)
- Re: Stereoscopic visualization John Stone (Mon May 10 2010 - 11:47:46 CDT)
  - Re: Stereoscopic visualization Emiliano Ippoliti (Tue May 11 2010 - 02:37:15 CDT)
adding atomselections? Fatemesadat Emami (Sat May 08 2010 - 18:28:48 CDT)
- Re: adding atomselections? Axel Kohlmeyer (Sat May 08 2010 - 19:34:30 CDT)
  - Re: adding atomselections? Fatemesadat Emami (Sat May 08 2010 - 19:42:24 CDT)
- Re: adding atomselections? Nicholas Musolino (Sat May 08 2010 - 20:10:24 CDT)
  - Re: adding atomselections? Fatemesadat Emami (Sat May 08 2010 - 22:15:43 CDT)
How to remove hydrogens from a pdb file? Francesca Ricci-Tam (Thu May 06 2010 - 23:17:19 CDT)
- Re: How to remove hydrogens from a pdb file? Ajasja LjubetiÄ (Fri May 07 2010 - 02:45:30 CDT)
- Re: How to remove hydrogens from a pdb file? Bjoern Olausson (Fri May 07 2010 - 02:41:51 CDT)
G(r) tcl script not including intramolecular correlations Hall, Lisa Michelle (Thu May 06 2010 - 18:12:49 CDT)
- Re: G(r) tcl script not including intramolecular correlations Axel Kohlmeyer (Thu May 06 2010 - 19:46:26 CDT)
  - Re: G(r) tcl script not including intramolecular correlations Hall, Lisa Michelle (Fri May 07 2010 - 10:46:27 CDT)
selecting from different molecules simultaneously Fatemesadat Emami (Wed May 05 2010 - 18:35:26 CDT)
- Re: selecting from different molecules simultaneously Axel Kohlmeyer (Wed May 05 2010 - 21:39:54 CDT)
  - Re: selecting from different molecules simultaneously Axel Kohlmeyer (Thu May 06 2010 - 19:55:33 CDT)
problem with "animate delete all" Wei Chen (Tue May 04 2010 - 17:07:54 CDT)
- Re: problem with "animate delete all" Ajasja LjubetiÄ (Wed May 05 2010 - 02:44:02 CDT)
  - Re: problem with "animate delete all" Wei Chen (Wed May 05 2010 - 13:57:16 CDT)
- Re: problem with "animate delete all" John Stone (Mon May 10 2010 - 16:20:55 CDT)
  - Re: problem with "animate delete all" Wei Chen (Mon May 10 2010 - 17:37:31 CDT)
Re: drawing a length scale on the vmd display maria goranovic (Tue May 04 2010 - 03:56:00 CDT)
drawing a length scale on the vmd display maria goranovic (Tue May 04 2010 - 03:01:07 CDT)
animation with variable number/names of atoms Maxim Paliy. (Mon May 03 2010 - 09:10:58 CDT)
- Re: animation with variable number/names of atoms John Stone (Mon May 03 2010 - 14:46:34 CDT)
  - Re: animation with variable number/names of atoms Axel Kohlmeyer (Mon May 03 2010 - 16:47:05 CDT)
    - Re: animation with variable number/names of atoms Maxim Paliy. (Mon May 03 2010 - 19:05:44 CDT)
  - Re: animation with variable number/names of atoms Axel Kohlmeyer (Tue May 04 2010 - 07:40:37 CDT)
Using RMSD in colvar Stefan Franzen (Mon May 03 2010 - 08:48:10 CDT)
- Re: Using RMSD in colvar John Stone (Mon May 03 2010 - 14:47:55 CDT)
Follow-up to PME question Stefan Franzen (Sun May 02 2010 - 16:54:06 CDT)
Question Regarding PME Set-up Stefan Franzen (Sun May 02 2010 - 16:48:20 CDT)
- Re: Question Regarding PME Set-up John Stone (Mon May 03 2010 - 15:08:32 CDT)
ellipsoidal particles Germain Vallverdu (Sun May 02 2010 - 14:10:43 CDT)
- Re: ellipsoidal particles Axel Kohlmeyer (Sun May 02 2010 - 15:08:54 CDT)
Tachyon? Fatemesadat Emami (Fri Apr 30 2010 - 11:41:25 CDT)
- Re: Tachyon? John Stone (Fri Apr 30 2010 - 12:58:46 CDT)
- Re: Tachyon? John Stone (Fri Apr 30 2010 - 12:48:26 CDT)
choice of VDW radius Nicolas Floquet (Fri Apr 30 2010 - 02:43:58 CDT)
- Re: choice of VDW radius Axel Kohlmeyer (Fri Apr 30 2010 - 08:34:36 CDT)
paratools charmm partial charges Corey Fugate (Thu Apr 29 2010 - 23:30:19 CDT)
- Re: paratools charmm partial charges Axel Kohlmeyer (Fri Apr 30 2010 - 08:38:27 CDT)
  - Re: paratools charmm partial charges Corey Fugate (Mon May 03 2010 - 13:42:02 CDT)
VMD: set light coordinates Nicolas Floquet (Thu Apr 29 2010 - 02:48:16 CDT)
- Re: VMD: set light coordinates John Stone (Thu Apr 29 2010 - 12:10:07 CDT)
Paratools Question Corey Fugate (Wed Apr 28 2010 - 23:17:39 CDT)
- Re: Paratools Question Axel Kohlmeyer (Wed Apr 28 2010 - 23:47:45 CDT)
  - Re: Paratools Question Corey Fugate (Thu Apr 29 2010 - 01:35:23 CDT)
topotools Chenchen Wang (Wed Apr 28 2010 - 00:19:21 CDT)
- Re: topotools Axel Kohlmeyer (Wed Apr 28 2010 - 04:46:11 CDT)
  - Re: topotools Axel Kohlmeyer (Wed Apr 28 2010 - 10:37:36 CDT)
    - Re: topotools Chenchen Wang (Wed Apr 28 2010 - 15:15:38 CDT)
    - Re: topotools Axel Kohlmeyer (Wed Apr 28 2010 - 15:30:47 CDT)
Is nvidia 3D Vision + quadro working in linux ben rodriguez (Tue Apr 27 2010 - 17:16:48 CDT)
- Re: Is nvidia 3D Vision + quadro working in linux Axel Kohlmeyer (Tue Apr 27 2010 - 18:20:38 CDT)
merge structure : It is working muniyamuthu.raviprasad_at_ndsu.edu (Tue Apr 27 2010 - 10:26:45 CDT)
Run Python Scripts in VMD on Mac OS X Burkhard Heil (Tue Apr 27 2010 - 06:52:50 CDT)
- Re: Run Python Scripts in VMD on Mac OS X Axel Kohlmeyer (Tue Apr 27 2010 - 08:38:32 CDT)
representation question Joseph Bylund (Mon Apr 26 2010 - 14:01:40 CDT)
- Re: representation question Axel Kohlmeyer (Mon Apr 26 2010 - 15:09:17 CDT)
Conversion of GAMESS Quantum MD trajectory file Diego Javier Alonso de Armiño (Mon Apr 26 2010 - 13:59:49 CDT)
- Re: Conversion of GAMESS Quantum MD trajectory file Axel Kohlmeyer (Mon Apr 26 2010 - 15:01:16 CDT)
- Re: Conversion of GAMESS Quantum MD trajectory file radak004_at_umn.edu (Mon Apr 26 2010 - 16:38:36 CDT)
merge structure: error processing angles muniyamuthu.raviprasad_at_ndsu.edu (Fri Apr 23 2010 - 17:36:32 CDT)
- Re: merge structure: error processing angles Robert Brunner (Mon Apr 26 2010 - 18:32:44 CDT)
  - Re: merge structure: error processing angles muniyamuthu.raviprasad_at_ndsu.edu (Mon Apr 26 2010 - 18:57:55 CDT)
    - Re: merge structure: error processing angles Robert Brunner (Mon Apr 26 2010 - 19:12:07 CDT)
    - Re: merge structure: error processing angles John Stone (Mon Apr 26 2010 - 19:30:05 CDT)
Symmetry Tool Error (Draw): invalid command name "getargs" and expected integer but got "" Mario Saavedra (Fri Apr 23 2010 - 16:41:06 CDT)
- Re: Symmetry Tool Error (Draw): invalid command name "getargs" and expected integer but got "" John Stone (Wed Apr 28 2010 - 11:13:11 CDT)
  - Re: Symmetry Tool Error (Draw): invalid command name "getargs" and expected integer but got "" Mario Saavedra (Thu Apr 29 2010 - 08:23:42 CDT)
    - Re: Symmetry Tool Error (Draw): invalid command name "getargs" and expected integer but got "" Mario Saavedra (Thu Apr 29 2010 - 13:47:24 CDT)
VRPN driver for Novint Falcon haptic device available - Looking for Testers Axel Kohlmeyer (Fri Apr 23 2010 - 15:59:34 CDT)
Problems with licorice representation when rendering 3D PDF for Power Point Bob Johnson (Thu Apr 22 2010 - 14:56:52 CDT)
- Re: Problems with licorice representation when rendering 3D PDF for Power Point John Stone (Thu Apr 22 2010 - 17:22:33 CDT)
  - Re: Problems with licorice representation when rendering 3D PDF for Power Point Bob Johnson (Fri Apr 23 2010 - 09:59:08 CDT)
    - Re: Problems with licorice representation when rendering 3D PDF for Power Point John Stone (Fri Apr 23 2010 - 12:54:49 CDT)
Coloring atoms based on timeframe range? Bjoern Olausson (Thu Apr 22 2010 - 08:51:34 CDT)
- Re: Coloring atoms based on timeframe range? Joseph Bylund (Thu Apr 22 2010 - 10:04:08 CDT)
  - Re: Coloring atoms based on timeframe range? John Stone (Thu Apr 22 2010 - 10:11:43 CDT)
- Re: Coloring atoms based on timeframe range? Axel Kohlmeyer (Thu Apr 22 2010 - 10:11:05 CDT)
  - Re: Coloring atoms based on timeframe range? Bjoern Olausson (Thu Apr 22 2010 - 10:41:46 CDT)
- Re: Coloring atoms based on timeframe range? Nicholas Musolino (Thu Apr 22 2010 - 10:53:08 CDT)
  - Re: Coloring atoms based on timeframe range? Bjoern Olausson (Fri Apr 23 2010 - 04:01:19 CDT)
Re: namd-l: building a MARTINI bilayer Peter Freddolino (Wed Apr 21 2010 - 13:16:00 CDT)
High quality movies, bmp frames and videomach=poor quality Jennifer Williams (Wed Apr 21 2010 - 05:57:11 CDT)
- Re: High quality movies, bmp frames and videomach=poor quality Bjoern Olausson (Wed Apr 21 2010 - 08:34:00 CDT)
Fwd: High quality movies, bmp frames and videomach=poor quality Jennifer Williams (Wed Apr 21 2010 - 05:56:33 CDT)
Fragments Olaf Lenz (Wed Apr 21 2010 - 03:19:04 CDT)
- Re: Fragments John Stone (Thu Apr 22 2010 - 10:26:59 CDT)
Problem with creation of child fragment in Molefacture Alexandre Suman de Araujo (Tue Apr 20 2010 - 14:04:31 CDT)
- Re: Problem with creation of child fragment in Molefacture Peter Freddolino (Tue Apr 20 2010 - 18:02:23 CDT)
  - Re: Problem with creation of child fragment in Molefacture Alexandre Suman de Araujo (Tue Apr 20 2010 - 20:04:05 CDT)
rmsd trajectory tool question Joseph Bylund (Tue Apr 20 2010 - 13:23:07 CDT)
run_vmd_tmp: Permission denied adil mughal (Tue Apr 20 2010 - 10:37:09 CDT)
- Re: run_vmd_tmp: Permission denied John Stone (Thu Apr 22 2010 - 10:32:35 CDT)
  - Re: run_vmd_tmp: Permission denied adil mughal (Thu Apr 22 2010 - 11:38:37 CDT)
pbc and measure hbond yongpingzeng (Tue Apr 20 2010 - 10:11:38 CDT)
- Re: pbc and measure hbond Nicholas Musolino (Tue Apr 20 2010 - 11:27:39 CDT)
- Re:pbc and measure hbond yongpingzeng (Tue Apr 20 2010 - 23:16:04 CDT)
  - Re:pbc and measure hbond yongpingzeng (Wed Apr 21 2010 - 08:33:43 CDT)
  - Re: Re:pbc and measure hbond Dong Luo (Wed Apr 21 2010 - 10:38:30 CDT)
pbc and measure hbond yongpingzeng (Tue Apr 20 2010 - 10:07:29 CDT)
- Re: pbc and measure hbond John Stone (Thu Apr 22 2010 - 10:30:17 CDT)
vmd does not read pqr file correct, vmd parse chain information incorrect. Knut Jørgen Bjuland (Tue Apr 20 2010 - 09:58:35 CDT)
- Re: vmd does not read pqr file correct, vmd parse chain information incorrect. Axel Kohlmeyer (Tue Apr 20 2010 - 19:18:09 CDT)
vmd does not read pqr file correct, vmd parse chain information incorrect. Knut Jørgen Bjuland (Tue Apr 20 2010 - 09:53:57 CDT)
Re: vmd-l digest V1 #1583 Nicholas Musolino (Sun Apr 18 2010 - 20:14:36 CDT)
Load and change representation? Fatemesadat Emami (Sat Apr 17 2010 - 16:51:53 CDT)
Problem with vmd and pqr file Knut Jørgen Bjuland (Sat Apr 17 2010 - 13:51:13 CDT)
- Re: Problem with vmd and pqr file Rodrigo Silveira (Sat Apr 17 2010 - 14:33:58 CDT)
  - Re: Problem with vmd and pqr file Knut Jørgen Bjuland (Sun Apr 18 2010 - 00:55:54 CDT)
    - Re: Problem with vmd and pqr file Axel Kohlmeyer (Sun Apr 18 2010 - 11:14:01 CDT)
  - Re: Problem with vmd and pqr file Axel Kohlmeyer (Sun Apr 18 2010 - 18:50:33 CDT)
RE : pbc tools in vmd for simulation bharat gupta (Sat Apr 17 2010 - 08:40:16 CDT)
- Re: RE : pbc tools in vmd for simulation Olaf Lenz (Sat Apr 17 2010 - 10:06:32 CDT)
  - Re: RE : pbc tools in vmd for simulation Knut JÃ¸rgen Bjuland (Sun Apr 18 2010 - 00:54:27 CDT)
problem about running chiloo777 777 (Sat Apr 17 2010 - 01:54:41 CDT)
- Re: problem about running John Stone (Thu Apr 22 2010 - 10:36:39 CDT)
Load and change representation? Fatemesadat Emami (Fri Apr 16 2010 - 23:37:32 CDT)
- Re: Load and change representation? Nicholas Musolino (Sun Apr 18 2010 - 12:13:12 CDT)
Resonable visualisation of the molecules inside the periodic box ? Marek Maly (Fri Apr 16 2010 - 09:59:50 CDT)
Colouring atoms named with the same first letter Jennifer Williams (Fri Apr 16 2010 - 08:15:07 CDT)
- Re: Colouring atoms named with the same first letter Joshua Anderson (Fri Apr 16 2010 - 11:09:23 CDT)
  - Re: Colouring atoms named with the same first letter Axel Kohlmeyer (Fri Apr 16 2010 - 12:03:24 CDT)
    - Re: Colouring atoms named with the same first letter Joshua Anderson (Fri Apr 16 2010 - 12:25:47 CDT)
- Re: Colouring atoms named with the same first letter John Stone (Fri Apr 16 2010 - 16:42:22 CDT)
- Re: Colouring atoms named with the same first letter Jennifer Williams (Tue Apr 20 2010 - 10:13:04 CDT)
recognizing TCL variables in a matrix argument Ronald Salesky (Thu Apr 15 2010 - 16:06:56 CDT)
- Re: recognizing TCL variables in a matrix argument Axel Kohlmeyer (Thu Apr 15 2010 - 19:45:15 CDT)
- mol urlload -- this doesn't seem to work in Windows (it does seem to work from Linux) Andrew M. Simms (Fri Apr 16 2010 - 11:30:09 CDT)
  - Re: mol urlload -- this doesn't seem to work in Windows (it does seem to work from Linux) John Stone (Fri Apr 16 2010 - 17:00:15 CDT)
how to download & install QMTool plugin Russell, John Thomas (Wed Apr 14 2010 - 09:33:33 CDT)
- Re: how to download & install QMTool plugin Axel Kohlmeyer (Wed Apr 14 2010 - 10:42:52 CDT)
how to pick certain water molecular from a .mdcrd ÅÓÑ©ÇÛ Pang Xueqin (Tue Apr 13 2010 - 01:37:16 CDT)
- Re: how to pick certain water molecular from a .mdcrd Joseph Bylund (Tue Apr 13 2010 - 05:30:48 CDT)
VMD has problem displaying glsl rendermode Euclid Sun (Mon Apr 12 2010 - 09:04:29 CDT)
- Re: VMD has problem displaying glsl rendermode John Stone (Mon Apr 12 2010 - 09:10:01 CDT)
calculate side-chain dihedral/torsion angles Ajasja LjubetiÄ (Mon Apr 12 2010 - 03:43:25 CDT)
- Re: calculate side-chain dihedral/torsion angles Axel Kohlmeyer (Mon Apr 12 2010 - 05:43:37 CDT)
  - Re: calculate side-chain dihedral/torsion angles Ajasja LjubetiÄ (Mon Apr 12 2010 - 06:38:16 CDT)
Andres Morales sent you a little gift Andres Morales (Sun Apr 11 2010 - 20:33:52 CDT)
DynamicBonding Ziemys, Arturas (Fri Apr 09 2010 - 14:10:56 CDT)
- Re: DynamicBonding Axel Kohlmeyer (Fri Apr 09 2010 - 15:23:38 CDT)
  - RE: DynamicBonding Ziemys, Arturas (Fri Apr 09 2010 - 15:50:58 CDT)
  - RE: DynamicBonding Ziemys, Arturas (Fri Apr 09 2010 - 15:34:09 CDT)
    - Re: DynamicBonding Axel Kohlmeyer (Fri Apr 09 2010 - 15:43:03 CDT)
regarding installation Asfa Ali (Fri Apr 09 2010 - 10:45:45 CDT)
- Re: regarding installation John Stone (Sun Apr 11 2010 - 22:25:56 CDT)
AutoHotkey script for managing VMD windows Ajasja LjubetiÄ (Fri Apr 09 2010 - 07:56:42 CDT)
Turn off initial VMD animation and "menu tkcon on" problem Ajasja LjubetiÄ (Fri Apr 09 2010 - 07:18:57 CDT)
- Re: Turn off initial VMD animation and "menu tkcon on" problem Axel Kohlmeyer (Fri Apr 09 2010 - 08:37:36 CDT)
  - Re: Turn off initial VMD animation and "menu tkcon on" problem Ajasja LjubetiÄ (Fri Apr 09 2010 - 09:12:05 CDT)
build dependency Knut Jørgen Bjuland (Fri Apr 09 2010 - 02:28:48 CDT)
- Re: build dependency Ajasja LjubetiÄ (Fri Apr 09 2010 - 03:43:19 CDT)
- Re: build dependency Axel Kohlmeyer (Fri Apr 09 2010 - 04:37:59 CDT)
question about vmd use Knut Jørgen Bjuland (Fri Apr 09 2010 - 02:26:32 CDT)
- Re: question about vmd use Axel Kohlmeyer (Fri Apr 09 2010 - 04:42:49 CDT)
- Re: question about vmd use Bjoern Olausson (Mon Apr 12 2010 - 06:16:42 CDT)
creating and appending to DCD in VMD Nicholas Musolino (Thu Apr 08 2010 - 15:50:04 CDT)
- Re: creating and appending to DCD in VMD John Stone (Thu Apr 08 2010 - 16:18:41 CDT)
  - Re: creating and appending to DCD in VMD Nicholas Musolino (Thu Apr 08 2010 - 17:04:40 CDT)
Hydrogen bonds plugin obscures charged atoms -- help! Hurt, Darrell (NIH/NIAID) [E] (Thu Apr 08 2010 - 11:48:39 CDT)
- Re: Hydrogen bonds plugin obscures charged atoms -- help! Hurt, Darrell (NIH/NIAID) [E] (Thu Apr 08 2010 - 15:32:18 CDT)
Rotating the current view Muhammet ©smet Töreh Balta (Thu Apr 08 2010 - 11:10:17 CDT)
- Re: Rotating the current view John Stone (Sun Apr 11 2010 - 22:20:06 CDT)
center of unit cell Yinglong Miao (Thu Apr 08 2010 - 10:10:17 CDT)
- Re: center of unit cell Axel Kohlmeyer (Thu Apr 08 2010 - 11:13:45 CDT)
- Re: center of unit cell Bhargava (Thu Apr 08 2010 - 11:10:51 CDT)
problem with IED: 'numpy.ndarray' object has no attribute 'typecode' J. Rui Rodrigues (Wed Apr 07 2010 - 14:01:37 CDT)
Way to change ColorScale Method to single color gradient? Bjoern Olausson (Wed Apr 07 2010 - 03:33:18 CDT)
- Re: Way to change ColorScale Method to single color gradient? Axel Kohlmeyer (Wed Apr 07 2010 - 06:08:23 CDT)
  - Re: Way to change ColorScale Method to single color gradient? Bjoern Olausson (Wed Apr 07 2010 - 08:05:07 CDT)
    - Re: Way to change ColorScale Method to single color gradient? Axel Kohlmeyer (Wed Apr 07 2010 - 08:43:19 CDT)
    - Re: Way to change ColorScale Method to single color gradient? Bjoern Olausson (Thu Apr 08 2010 - 02:18:05 CDT)
problems with hotkeys and "user add key" command Rocchia Walter (Mon Apr 05 2010 - 16:31:03 CDT)
- Re: problems with hotkeys and "user add key" command John Stone (Mon Apr 05 2010 - 16:45:53 CDT)
NAMD energy plugin question Rachel Ruskin (Mon Apr 05 2010 - 12:02:44 CDT)
- Re: NAMD energy plugin question Peter Freddolino (Mon Apr 05 2010 - 20:44:59 CDT)
Generating nanotubes psf file Ranyere Deyler (Mon Apr 05 2010 - 08:58:55 CDT)
- Re: Generating nanotubes psf file Axel Kohlmeyer (Mon Apr 05 2010 - 09:52:55 CDT)
  - Re: Generating nanotubes psf file Ranyere Deyler (Mon Apr 05 2010 - 11:33:46 CDT)
[Help] cross-sections Jervis Chu (Sat Apr 03 2010 - 23:18:54 CDT)
- Re: [Help] cross-sections Axel Kohlmeyer (Sun Apr 04 2010 - 05:27:44 CDT)
RuntimeError: tk.h version (8.4) doesn't match libtk.a version (8.5) J. Rui Rodrigues (Thu Apr 01 2010 - 11:51:06 CDT)
- Re: RuntimeError: tk.h version (8.4) doesn't match libtk.a version (8.5) John Stone (Fri Apr 02 2010 - 00:26:18 CDT)
  - Re: RuntimeError: tk.h version (8.4) doesn't match libtk.a version (8.5) J. Rui Rodrigues (Tue Apr 06 2010 - 08:11:00 CDT)
Extract specific frames from trajectory Cathal Leahy (Thu Apr 01 2010 - 10:40:19 CDT)
- Re: Extract specific frames from trajectory Roman Petrenko (Thu Apr 01 2010 - 17:19:17 CDT)
Creating length dependent coloured bonds in VMD Willie Maddox (Tue Mar 30 2010 - 14:17:33 CDT)
- Re: Creating length dependent coloured bonds in VMD Axel Kohlmeyer (Tue Mar 30 2010 - 15:12:28 CDT)
Creating bonds using VMD Mihir Tungare (Mon Mar 29 2010 - 16:34:21 CDT)
- Re: Creating bonds using VMD John Stone (Sun Apr 11 2010 - 23:07:21 CDT)
(no subject) Irene Newhouse (Mon Mar 29 2010 - 15:12:41 CDT)
can't find file sarah k (Mon Mar 29 2010 - 02:46:20 CDT)
- Re: can't find file John Stone (Mon Mar 29 2010 - 10:11:23 CDT)
  - Re: can't find file sarah k (Sun Apr 04 2010 - 12:02:56 CDT)
VMD 1.8.7 hangs on launch Leif Halvorsen (Fri Mar 26 2010 - 14:37:03 CDT)
- Re: VMD 1.8.7 hangs on launch Marek Maly (Fri Mar 26 2010 - 18:07:55 CDT)
problem with ied and vmd,ImportError: liblapack.so.3: cannot open shared object file: No such file or directory Knut Jørgen Bjuland (Thu Mar 25 2010 - 04:26:35 CDT)
- Re: problem with ied and vmd,ImportError: liblapack.so.3: cannot open shared object file: No such file or directory Axel Kohlmeyer (Thu Mar 25 2010 - 06:01:48 CDT)
  - Re: problem with ied and vmd,ImportError: liblapack.so.3: cannot open shared object file: No such file or directory Knut Jørgen Bjuland (Thu Mar 25 2010 - 09:49:05 CDT)
    - Re: problem with ied and vmd,ImportError: liblapack.so.3: cannot open shared object file: No such file or directory Axel Kohlmeyer (Thu Mar 25 2010 - 10:49:09 CDT)
visualizing trr file gurvisha sandhu (Thu Mar 25 2010 - 03:27:23 CDT)
- Re: visualizing trr file Esteban Gabriel Vega Hissi (Fri Mar 26 2010 - 16:28:57 CDT)
Visualisation of VTF trajectories using VMD under Windows ? Marek Maly (Wed Mar 24 2010 - 05:31:36 CDT)
- Re: Visualisation of VTF trajectories using VMD under Windows ? Olaf Lenz (Wed Mar 24 2010 - 10:19:33 CDT)
solventplugin-Watermodels Salvador H-V (Tue Mar 23 2010 - 13:08:13 CDT)
Wrapping membrane to center of PBC-Box Bjoern Olausson (Tue Mar 23 2010 - 12:06:31 CDT)
implicit solvent politr_at_huji.ac.il (Tue Mar 23 2010 - 09:16:29 CDT)
- Re: implicit solvent Ajasja LjubetiÄ (Tue Mar 23 2010 - 10:57:54 CDT)
- Re: implicit solvent Axel Kohlmeyer (Tue Mar 23 2010 - 12:00:04 CDT)
Fwd: [ACS award information, March 30 deadline] John Stone (Mon Mar 22 2010 - 12:23:45 CDT)
writepdb using selection form different molecules Bernardo Sosa Padilla Araujo (Fri Mar 19 2010 - 23:29:56 CDT)
- Re: writepdb using selection form different molecules John Stone (Mon Mar 22 2010 - 11:05:53 CDT)
  - Re: writepdb using selection form different molecules Axel Kohlmeyer (Mon Mar 22 2010 - 13:16:43 CDT)
    - Re: writepdb using selection form different molecules Bernardo Sosa Padilla Araujo (Mon Mar 22 2010 - 13:25:35 CDT)
Running IMD interactivelly under the shell Nuno Sousa Cerqueira (Thu Mar 18 2010 - 14:18:22 CDT)
- Re: Running IMD interactivelly under the shell John Stone (Thu Mar 18 2010 - 16:16:06 CDT)
- Re: Running IMD interactivelly under the shell Axel Kohlmeyer (Thu Mar 18 2010 - 16:54:42 CDT)
  - Re: Running IMD interactivelly under the shell Nuno Sousa Cerqueira (Thu Mar 18 2010 - 17:50:33 CDT)
    - Re: Running IMD interactivelly under the shell Axel Kohlmeyer (Thu Mar 18 2010 - 17:56:52 CDT)
why electrostatic interaction energy increases with the increase of cutoff using namdenergy Lan Hua (Wed Mar 17 2010 - 21:18:55 CDT)
Selecting AMBER ions Cl- and Na+ using VMD DimitryASuplatov (Wed Mar 17 2010 - 06:42:41 CDT)
- Re: Selecting AMBER ions Cl- and Na+ using VMD Thomas C. Bishop (Wed Mar 17 2010 - 09:22:57 CDT)
- Re: Selecting AMBER ions Cl- and Na+ using VMD Ajasja LjubetiÄ (Wed Mar 17 2010 - 09:31:12 CDT)
- Re: Selecting AMBER ions Cl- and Na+ using VMD Balazs Jojart (Wed Mar 17 2010 - 13:29:27 CDT)
  - was: Selecting Cl- Na; now: redefining key words in VMD Thomas C. Bishop (Wed Mar 17 2010 - 16:38:25 CDT)
    - Re: was: Selecting Cl- Na; now: redefining key words in VMD Axel Kohlmeyer (Wed Mar 17 2010 - 17:20:02 CDT)
Installing VMD Salvador H-V (Tue Mar 16 2010 - 12:26:08 CDT)
- Re: Installing VMD John Stone (Tue Mar 16 2010 - 12:55:29 CDT)
  - Re: Installing VMD Joseph Bylund (Tue Mar 16 2010 - 13:22:27 CDT)
(no subject) Roshan Tasgaonkar (Mon Mar 15 2010 - 18:07:34 CDT)
- Re: Joshua Adelman (Mon Mar 15 2010 - 19:56:04 CDT)
why huge positive vdw energy from namdenergy plugin Lan Hua (Mon Mar 15 2010 - 18:02:56 CDT)
Re: Loading Gaussian Log File into Paratool Kovács, Sándor Ádám (Mon Mar 15 2010 - 16:54:39 CDT)
Aligning Desmond Trajectories again Irene Newhouse (Mon Mar 15 2010 - 15:05:46 CDT)
CGenFF atom types Ziemys, Arturas (Sun Mar 14 2010 - 19:44:53 CDT)
- Re: CGenFF atom types Axel Kohlmeyer (Sun Mar 14 2010 - 21:19:30 CDT)
IMD with Phantom Omni Mark Cunningham (Sun Mar 14 2010 - 14:45:21 CDT)
running ILS under Windows 7 Irene Newhouse (Sat Mar 13 2010 - 22:32:15 CST)
- Re: running ILS under Windows 7 Axel Kohlmeyer (Sun Mar 14 2010 - 14:11:16 CDT)
  - RE: running ILS under Windows 7 Irene Newhouse (Sun Mar 14 2010 - 16:51:20 CDT)
Loading Gaussian Log File into Paratool Will Bricker (Sat Mar 13 2010 - 16:19:08 CST)
Topotools1.0 muniyamuthu.raviprasad_at_ndsu.edu (Sat Mar 13 2010 - 13:04:38 CST)
- Re: Topotools1.0 Axel Kohlmeyer (Sat Mar 13 2010 - 14:03:22 CST)
Problems with VMD installation Fedora 12 64bits Edith Euan (Sat Mar 13 2010 - 00:57:39 CST)
- Re: Problems with VMD installation Fedora 12 64bits John Stone (Sat Mar 13 2010 - 08:50:37 CST)
Patch for Three or More monomers muniyamuthu.raviprasad_at_ndsu.edu (Fri Mar 12 2010 - 10:41:03 CST)
- Re: Patch for Three or More monomers Axel Kohlmeyer (Fri Mar 12 2010 - 11:32:10 CST)
CUDA out of memory Ajasja LjubetiÄ (Fri Mar 12 2010 - 08:22:40 CST)
- Re: CUDA out of memory John Stone (Fri Mar 12 2010 - 09:02:19 CST)
  - Re: CUDA out of memory Ajasja LjubetiÄ (Mon Mar 15 2010 - 04:41:14 CDT)
    - Re: CUDA out of memory John Stone (Mon Mar 15 2010 - 10:20:37 CDT)
Re: WIN64 build Ajasja LjubetiÄ (Fri Mar 12 2010 - 07:46:55 CST)
Re: properly applying patches to create DPPC JC Gumbart (Thu Mar 11 2010 - 17:48:11 CST)
(no subject) Roshan Tasgaonkar (Wed Mar 10 2010 - 22:55:31 CST)
- RE: JC Gumbart (Wed Mar 10 2010 - 23:00:43 CST)
properly applying patches to create DPPC Ronald Salesky (Wed Mar 10 2010 - 18:33:59 CST)
- RE: properly applying patches to create DPPC JC Gumbart (Wed Mar 10 2010 - 22:56:48 CST)
Problems with "animate next" inside for-loops nicholas lee (Wed Mar 10 2010 - 16:41:45 CST)
- Re: Problems with "animate next" inside for-loops Axel Kohlmeyer (Wed Mar 10 2010 - 17:23:04 CST)
Charmm parameters for Polybutylene terephthalate (PBT) muniyamuthu.raviprasad_at_ndsu.edu (Wed Mar 10 2010 - 13:20:38 CST)
- Re: Charmm parameters for Polybutylene terephthalate (PBT) Eduardo (Thu Mar 11 2010 - 01:33:56 CST)
Isosurface wraps in PME Electrostatics calc'n Irene Newhouse (Tue Mar 09 2010 - 14:06:02 CST)
- Re: Isosurface wraps in PME Electrostatics calc'n John Stone (Tue Mar 09 2010 - 14:40:45 CST)
- Re: Isosurface wraps in PME Electrostatics calc'n Axel Kohlmeyer (Tue Mar 09 2010 - 14:59:13 CST)
  - RE: Isosurface wraps in PME Electrostatics calc'n Irene Newhouse (Tue Mar 09 2010 - 15:56:22 CST)
MergeStructs Plugin in text mode Alexandre Suman de Araujo (Tue Mar 09 2010 - 12:24:46 CST)
- Re: MergeStructs Plugin in text mode Axel Kohlmeyer (Tue Mar 09 2010 - 13:24:49 CST)
  - Re: MergeStructs Plugin in text mode Alexandre Suman de Araujo (Wed Mar 10 2010 - 06:03:01 CST)
keyboard-mouse-controlled view for VMDMovie plugin Tibbitt, Jeffrey A. (Tue Mar 09 2010 - 10:27:36 CST)
- Re: keyboard-mouse-controlled view for VMDMovie plugin Kirby Vandivort (Tue Mar 09 2010 - 16:00:47 CST)
Viewing changing beta along a trajectory Thomas Steinbrecher (Tue Mar 09 2010 - 10:26:16 CST)
- Re: Viewing changing beta along a trajectory John Stone (Tue Mar 09 2010 - 10:39:57 CST)
  - Re: Viewing changing beta along a trajectory John Stone (Tue Mar 09 2010 - 10:54:06 CST)
Error vmd and Nvidia Graphik Card Christian Wohlschlager (Tue Mar 09 2010 - 10:19:47 CST)
- Re: Error vmd and Nvidia Graphik Card John Stone (Tue Mar 09 2010 - 10:37:25 CST)
analyzing gromacs trajectory (.trr) with VMD politr_at_huji.ac.il (Tue Mar 09 2010 - 03:48:24 CST)
- Re: analyzing gromacs trajectory (.trr) with VMD Axel Kohlmeyer (Tue Mar 09 2010 - 04:47:13 CST)
Mean atom position Katherine Parra (Mon Mar 08 2010 - 13:04:47 CST)
- Re: Mean atom position John Stone (Mon Mar 08 2010 - 14:34:04 CST)
(no subject) Roshan Tasgaonkar (Mon Mar 08 2010 - 12:21:08 CST)
- Re: Edelmiro Moman (Mon Mar 08 2010 - 14:05:52 CST)
Add a surface to a pdb file Fatemesadat Emami (Mon Mar 08 2010 - 08:59:14 CST)
- Re: Add a surface to a pdb file John Stone (Mon Mar 08 2010 - 09:25:27 CST)
  - Re: Add a surface to a pdb file Fatemesadat Emami (Mon Mar 08 2010 - 09:57:02 CST)
script for area per lipid Demet Akten (Mon Mar 08 2010 - 06:39:16 CST)
- Re: script for area per lipid Ajeeta kaushiki (Tue Mar 09 2010 - 05:04:27 CST)
trajectory_path.tcl queries Francesco Pietra (Sun Mar 07 2010 - 02:55:03 CST)
- Re: trajectory_path.tcl queries Axel Kohlmeyer (Sun Mar 07 2010 - 10:53:39 CST)
- Fwd: trajectory_path.tcl queries Francesco Pietra (Sun Mar 14 2010 - 04:51:02 CDT)
  - Re: Fwd: trajectory_path.tcl queries Axel Kohlmeyer (Sun Mar 14 2010 - 10:10:02 CDT)
Question Regarding User-Defined Trajectories Wallace Dumars (Fri Mar 05 2010 - 15:53:01 CST)
- Re: Question Regarding User-Defined Trajectories John Stone (Mon Mar 08 2010 - 09:37:25 CST)
MDFF plug-in A D (Fri Mar 05 2010 - 15:09:06 CST)
- Re: MDFF plug-in John Stone (Fri Mar 05 2010 - 15:12:10 CST)
STRIDE error: too many atoms in res Nadine Utz (Fri Mar 05 2010 - 10:29:34 CST)
- Re: STRIDE error: too many atoms in res John Stone (Fri Mar 05 2010 - 14:46:07 CST)
VMD-Cones and Povray rendering Olaf Lenz (Fri Mar 05 2010 - 02:31:11 CST)
- Re: VMD-Cones and Povray rendering John Stone (Fri Mar 05 2010 - 08:58:23 CST)
pbc in water count Agarwal, Silvi (Thu Mar 04 2010 - 12:07:37 CST)
- Re: pbc in water count Olaf Lenz (Fri Mar 05 2010 - 01:06:46 CST)
  - RE: pbc in water count Agarwal, Silvi (Sat Mar 06 2010 - 11:52:55 CST)
CUDA issues Filippo Federici (Thu Mar 04 2010 - 01:18:14 CST)
- Re: CUDA issues John Stone (Thu Mar 04 2010 - 08:11:53 CST)
  - Re: CUDA issues Filippo Federici (Thu Mar 04 2010 - 10:29:44 CST)
Finding residues with some distance Neeraj Jagdish Agrawal (Wed Mar 03 2010 - 17:38:33 CST)
- Re: Finding residues with some distance Anurag Sethi (Wed Mar 03 2010 - 18:25:11 CST)
- Re: Finding residues with some distance John Stone (Wed Mar 03 2010 - 22:35:10 CST)
intersurf plugin missing in VMD 1.8.7 ? Bennion, Brian (Wed Mar 03 2010 - 11:11:49 CST)
- Re: intersurf plugin missing in VMD 1.8.7 ? John Stone (Wed Mar 03 2010 - 11:24:15 CST)
Binary VMD buid for Linux, text mode only Benjamin Bouvier (Wed Mar 03 2010 - 09:26:20 CST)
- Re: Binary VMD buid for Linux, text mode only John Stone (Wed Mar 03 2010 - 17:09:42 CST)
display of the atom number beyond 100000 in pdb file YangMingjun (Tue Mar 02 2010 - 20:36:25 CST)
- Re: display of the atom number beyond 100000 in pdb file Dipesh Bhattarai (Tue Mar 02 2010 - 21:41:53 CST)
  - Re: Re: display of the atom number beyond 100000 in pdb file YangMingjun (Wed Mar 03 2010 - 00:52:07 CST)
    - Re: Re: display of the atom number beyond 100000 in pdb file John Stone (Wed Mar 03 2010 - 01:11:27 CST)
3D Connexion - Space Navigator (OSX drivers) Tibbitt, Jeffrey A. (Tue Mar 02 2010 - 20:24:34 CST)
- Re: 3D Connexion - Space Navigator (OSX drivers) John Stone (Wed Mar 03 2010 - 10:34:03 CST)
wrapping dimer units in a Desmond traj Irene Newhouse (Tue Mar 02 2010 - 13:51:25 CST)
- RE: wrapping dimer units in a Desmond traj Irene Newhouse (Thu Mar 18 2010 - 19:43:16 CDT)
Running Python within VMD radak004_at_umn.edu (Tue Mar 02 2010 - 13:07:51 CST)
- Re: Running Python within VMD John Stone (Wed Mar 03 2010 - 10:41:49 CST)
psfgen for protein-RNA complex YangMingjun (Tue Mar 02 2010 - 10:50:13 CST)
- Re: psfgen for protein-RNA complex Schreiner Eduard (Tue Mar 02 2010 - 11:17:42 CST)
measure command problem Bernardo Sosa Padilla Araujo (Mon Mar 01 2010 - 21:44:09 CST)
- Re: measure command problem Bernardo Sosa Padilla Araujo (Tue Mar 02 2010 - 12:33:57 CST)
  - Re: measure command problem Edelmiro Moman (Tue Mar 02 2010 - 13:53:08 CST)
    - Re: measure command problem Bernardo Sosa Padilla Araujo (Tue Mar 02 2010 - 14:15:42 CST)
Generating a PSF for a Non-protien Aziz, John (Mon Mar 01 2010 - 08:27:10 CST)
- Re: Generating a PSF for a Non-protien John Stone (Wed Mar 03 2010 - 10:47:52 CST)
Problem with New cartoon representation Carla Jamous (Mon Mar 01 2010 - 02:37:33 CST)
- Re: Problem with New cartoon representation Axel Kohlmeyer (Mon Mar 01 2010 - 03:33:05 CST)
Hbonds calc with residue not in CHARMm Irene Newhouse (Fri Feb 26 2010 - 14:40:28 CST)
- RE: Hbonds calc with residue not in CHARMm JC Gumbart (Fri Feb 26 2010 - 22:34:42 CST)
  - RE: Hbonds calc with residue not in CHARMm Irene Newhouse (Sat Feb 27 2010 - 11:33:43 CST)
  - RE: Hbonds calc with residue not in CHARMm Irene Newhouse (Thu Mar 04 2010 - 12:52:08 CST)
Rotating user-defined graphics? Reid Van Lehn (Fri Feb 26 2010 - 12:24:43 CST)
- Re: Rotating user-defined graphics? Axel Kohlmeyer (Fri Feb 26 2010 - 13:24:30 CST)
Can anyone help me get the coordinate of the cylinders in the cartoon representation? Chen, Bo (NIH/NIDDK) [F] (Fri Feb 26 2010 - 11:11:42 CST)
- Re: Can anyone help me get the coordinate of the cylinders in the cartoon representation? John Stone (Wed Mar 03 2010 - 10:56:00 CST)
slower trajectory loading when CUDA support is enabled Michel Espinoza-Fonseca (Thu Feb 25 2010 - 14:35:18 CST)
- Re: slower trajectory loading when CUDA support is enabled John Stone (Thu Feb 25 2010 - 15:01:19 CST)
  - RE: slower trajectory loading when CUDA support is enabled Michel Espinoza-Fonseca (Thu Feb 25 2010 - 15:48:00 CST)
    - Re: slower trajectory loading when CUDA support is enabled John Stone (Thu Feb 25 2010 - 15:51:50 CST)
    - RE: slower trajectory loading when CUDA support is enabled Michel Espinoza-Fonseca (Thu Feb 25 2010 - 15:59:32 CST)
VMD Asfa Ali (Thu Feb 25 2010 - 13:18:21 CST)
about command measure dipole matziast_at_med.uth.gr (Wed Feb 24 2010 - 12:37:49 CST)
- Re: about command measure dipole Axel Kohlmeyer (Wed Feb 24 2010 - 13:22:51 CST)
Bigdcd and Namdenergy batch problem Andrea Carotti (Wed Feb 24 2010 - 10:21:34 CST)
- Re: Bigdcd and Namdenergy batch problem John Stone (Thu Feb 25 2010 - 16:46:08 CST)
Regarding coordinates transformation aneesh cna (Wed Feb 24 2010 - 01:04:27 CST)
- Re: Regarding coordinates transformation John Stone (Thu Feb 25 2010 - 16:33:13 CST)
  - Re: Regarding coordinates transformation aneesh cna (Thu Feb 25 2010 - 23:51:15 CST)
a problem in visualizing dump files with vmd Robabeh Moosavi (Tue Feb 23 2010 - 05:43:46 CST)
- Re: a problem in visualizing dump files with vmd Axel Kohlmeyer (Tue Feb 23 2010 - 05:44:27 CST)
VMD water protein anlysis snoze pa (Mon Feb 22 2010 - 15:39:54 CST)
- Re: VMD water protein anlysis John Stone (Mon Feb 22 2010 - 15:45:47 CST)
  - Re: VMD water protein anlysis Roman Petrenko (Mon Feb 22 2010 - 17:28:19 CST)
Probe orientations in ILS Irene Newhouse (Mon Feb 22 2010 - 13:19:56 CST)
- Principle Component Analysis of Protein PDB Structures MUHAMMAD IMTIA SHAFIQ (Mon Feb 22 2010 - 14:03:47 CST)
  - Re: Principle Component Analysis of Protein PDB Structures Benjamin Bouvier (Mon Feb 22 2010 - 14:43:40 CST)
- Re: Probe orientations in ILS John Stone (Mon Feb 22 2010 - 15:41:08 CST)
Mutator plugin console q (Mon Feb 22 2010 - 07:04:50 CST)
- Re: Mutator plugin console John Stone (Thu Feb 25 2010 - 16:53:16 CST)
gradient background not rendered BIN ZHANG (Fri Feb 19 2010 - 16:50:59 CST)
- Re: gradient background not rendered John Stone (Fri Feb 19 2010 - 16:58:46 CST)
Numeric Library of Python for VMD 1.8.7 Yue Yang (Wed Feb 17 2010 - 22:22:27 CST)
- Re: Numeric Library of Python for VMD 1.8.7 Axel Kohlmeyer (Wed Feb 17 2010 - 23:36:39 CST)
  - Re: Numeric Library of Python for VMD 1.8.7 Yue Yang (Thu Feb 18 2010 - 00:08:41 CST)
    - Re: Numeric Library of Python for VMD 1.8.7 John Stone (Thu Feb 18 2010 - 00:11:12 CST)
producing high quality video on Mac Dan Lussier (Wed Feb 17 2010 - 17:51:03 CST)
- Re: producing high quality video on Mac John Stone (Wed Feb 17 2010 - 19:57:08 CST)
- slowing down movie maker Samuel Coulbourn Flores (Wed Feb 17 2010 - 20:20:16 CST)
  - Re: slowing down movie maker John Stone (Wed Feb 17 2010 - 20:43:50 CST)
  - Re: slowing down movie maker Axel Kohlmeyer (Wed Feb 17 2010 - 21:24:14 CST)
2 questions about "measure sasa" Edward Lyman (Wed Feb 17 2010 - 14:40:53 CST)
- Re: 2 questions about "measure sasa" John Stone (Thu Feb 25 2010 - 17:00:31 CST)
  - Re: 2 questions about "measure sasa" Edward Lyman (Thu Feb 25 2010 - 17:05:37 CST)
  - Re: 2 questions about "measure sasa" Edward Lyman (Fri Feb 26 2010 - 13:44:59 CST)
    - Re: 2 questions about "measure sasa" John Stone (Thu Mar 04 2010 - 10:50:11 CST)
creating a povray file gschlau-cohen_at_berkeley.edu (Wed Feb 17 2010 - 10:44:02 CST)
- Re: creating a povray file John Stone (Wed Feb 17 2010 - 10:51:44 CST)
  - Re: creating a povray file gschlau-cohen_at_berkeley.edu (Wed Feb 17 2010 - 15:56:34 CST)
    - Re: creating a povray file John Stone (Wed Feb 17 2010 - 16:07:16 CST)
problem of installing vmd 1.8.7 on Mac osx 10.4.11 Jane Bailey (Wed Feb 17 2010 - 09:35:53 CST)
- Re: problem of installing vmd 1.8.7 on Mac osx 10.4.11 John Stone (Wed Feb 17 2010 - 09:47:58 CST)
- Re: problem of installing vmd 1.8.7 on Mac osx 10.4.11 Benjamin Bouvier (Wed Feb 17 2010 - 10:50:33 CST)
  - Re: problem of installing vmd 1.8.7 on Mac osx 10.4.11 Jane Bailey (Wed Feb 17 2010 - 11:14:55 CST)
    - Re: problem of installing vmd 1.8.7 on Mac osx 10.4.11 John Stone (Wed Feb 17 2010 - 11:55:01 CST)
Porcupine update Carsten Olbrich (Wed Feb 17 2010 - 03:03:27 CST)
How to make Porcupine plots in VMD Surendra Kumar Jain (Tue Feb 16 2010 - 13:28:07 CST)
VMD and Amber coordinates rebeca (Tue Feb 16 2010 - 12:31:52 CST)
- Re: VMD and Amber coordinates John Stone (Tue Feb 16 2010 - 13:12:14 CST)
  - Re: VMD and Amber coordinates rebeca (Tue Feb 16 2010 - 13:35:07 CST)
    - Re: VMD and Amber coordinates rebeca (Tue Feb 16 2010 - 16:44:13 CST)
get view direction Jacob Kirkensgaard (Tue Feb 16 2010 - 03:58:24 CST)
- Re: get view direction Axel Kohlmeyer (Tue Feb 16 2010 - 06:21:23 CST)
- Re: get view direction John Stone (Tue Feb 16 2010 - 10:25:37 CST)
  - Re: get view direction Jacob Kirkensgaard (Tue Feb 16 2010 - 15:21:21 CST)
PSF Generation BIPLAB NANDI (Mon Feb 15 2010 - 23:10:53 CST)
- Re: PSF Generation Rogan Carr (Tue Feb 16 2010 - 09:24:06 CST)
Can't find C-PDB bond parameters Francesco Pietra (Mon Feb 15 2010 - 03:46:29 CST)
- RE: namd-l: Can't find C-PDB bond parameters JC Gumbart (Mon Feb 15 2010 - 08:15:53 CST)
  - Re: namd-l: Can't find C-PDB bond parameters Francesco Pietra (Mon Feb 15 2010 - 11:44:52 CST)
    - Re: namd-l: Can't find C-PDB bond parameters JC Gumbart (Mon Feb 15 2010 - 12:06:41 CST)
running namd2 on Mac PPC cluster Robert Wohlhueter (Sun Feb 14 2010 - 13:13:16 CST)
- Re: running namd2 on Mac PPC cluster Axel Kohlmeyer (Sun Feb 14 2010 - 15:16:22 CST)
CAN'T FIND BOND PARAMETERS FOR BOND C - CPB IN PARAMETER FILES Francesco Pietra (Sun Feb 14 2010 - 10:26:01 CST)
- Re: CAN'T FIND BOND PARAMETERS FOR BOND C - CPB IN PARAMETER FILES Francesco Pietra (Sun Feb 14 2010 - 11:32:57 CST)
  - Re: CAN'T FIND BOND PARAMETERS FOR BOND C - CPB IN PARAMETER FILES snoze pa (Sun Feb 14 2010 - 12:47:04 CST)
top_all22_prot.inp & par_all22_prot.inp geetha9999_at_aol.com (Sun Feb 14 2010 - 09:49:24 CST)
- Re: top_all22_prot.inp & par_all22_prot.inp Axel Kohlmeyer (Sun Feb 14 2010 - 13:06:20 CST)
Retrieving an atom and its coordinates Marc Charendoff (Sat Feb 13 2010 - 16:19:50 CST)
- Re: Retrieving an atom and its coordinates Schreiner Eduard (Sat Feb 13 2010 - 16:35:39 CST)
- Re: Retrieving an atom and its coordinates Axel Kohlmeyer (Sat Feb 13 2010 - 17:20:59 CST)
- Re: Retrieving an atom and its coordinates Roman Petrenko (Sat Feb 13 2010 - 20:14:34 CST)
Mirror reflection Rachel Ruskin (Sat Feb 13 2010 - 01:24:58 CST)
- Re: Mirror reflection John Stone (Sat Feb 13 2010 - 01:32:37 CST)
psfgen generates 0 atom .psf file Ronald Salesky (Fri Feb 12 2010 - 19:41:10 CST)
- Re: psfgen generates 0 atom .psf file Axel Kohlmeyer (Fri Feb 12 2010 - 22:52:25 CST)
- RE: psfgen generates 0 atom .psf file JC Gumbart (Fri Feb 12 2010 - 22:58:35 CST)
X_ChangeProperty error Bennion, Brian (Fri Feb 12 2010 - 14:50:27 CST)
- Re: X_ChangeProperty error John Stone (Mon Feb 15 2010 - 16:18:27 CST)
xyz file and VASP CHGCAR file do not overlap Decai Yu (Fri Feb 12 2010 - 13:29:44 CST)
- Re: xyz file and VASP CHGCAR file do not overlap Axel Kohlmeyer (Fri Feb 12 2010 - 15:00:45 CST)
  - RE: xyz file and VASP CHGCAR file do not overlap Decai Yu (Fri Feb 12 2010 - 15:20:16 CST)
  - Re: xyz file and VASP CHGCAR file do not overlap matt watkins (Fri Feb 12 2010 - 19:54:08 CST)
RMSD trajectory tools Asfa Ali (Fri Feb 12 2010 - 06:16:22 CST)
- Re: RMSD trajectory tools Axel Kohlmeyer (Fri Feb 12 2010 - 07:20:42 CST)
amino acid mutation plugin geetha9999_at_aol.com (Thu Feb 11 2010 - 13:37:08 CST)
how to set PBC for ILS Irene Newhouse (Wed Feb 10 2010 - 16:35:17 CST)
- Re: how to set PBC for ILS John Stone (Wed Feb 10 2010 - 16:43:43 CST)
  - RE: how to set PBC for ILS Irene Newhouse (Wed Feb 10 2010 - 16:53:43 CST)
    - Re: how to set PBC for ILS John Stone (Wed Feb 10 2010 - 16:59:29 CST)
    - RE: how to set PBC for ILS Irene Newhouse (Wed Feb 10 2010 - 17:01:24 CST)
Boolean operators and the new atomsel type Daniel Terry (Wed Feb 10 2010 - 12:30:21 CST)
- Re: Boolean operators and the new atomsel type Axel Kohlmeyer (Wed Feb 10 2010 - 14:35:37 CST)
convert unformatted delphi phi to formatted Jun Cheng (Wed Feb 10 2010 - 10:09:55 CST)
psf file generation.? zubin mehta (Wed Feb 10 2010 - 05:58:45 CST)
- Re: psf file generation.? John Stone (Fri Feb 12 2010 - 00:00:21 CST)
invalid command name 'vmdcon' zubin mehta (Wed Feb 10 2010 - 04:41:01 CST)
- Re: invalid command name 'vmdcon' John Stone (Fri Feb 12 2010 - 00:21:01 CST)
What occupancy at the Hbond plugin mean? Itamar Kass (Tue Feb 09 2010 - 05:15:27 CST)
- Re: What occupancy at the Hbond plugin mean? Dong Luo (Tue Feb 09 2010 - 10:21:29 CST)
how long do ILS runs take? Irene Newhouse (Mon Feb 08 2010 - 14:05:30 CST)
- Re: how long do ILS runs take? John Stone (Mon Feb 08 2010 - 14:48:16 CST)
  - RE: how long do ILS runs take? Irene Newhouse (Mon Feb 08 2010 - 14:56:53 CST)
    - RE: how long do ILS runs take? Irene Newhouse (Mon Feb 08 2010 - 16:51:23 CST)
Converting tracker coordinates to molecule coordinate for selection Dipesh Bhattarai (Mon Feb 08 2010 - 10:57:03 CST)
- Re: Converting tracker coordinates to molecule coordinate for selection John Stone (Fri Feb 12 2010 - 00:26:09 CST)
  - Re: Converting tracker coordinates to molecule coordinate for selection Dipesh Bhattarai (Fri Feb 12 2010 - 09:24:58 CST)
    - Re: Converting tracker coordinates to molecule coordinate for selection John Stone (Fri Feb 12 2010 - 11:32:37 CST)
    - Re: Converting tracker coordinates to molecule coordinate for selection Dipesh Bhattarai (Fri Feb 12 2010 - 11:57:03 CST)
Blank thumbnails and non-working snapshots Christopher McLean (Mon Feb 08 2010 - 09:55:13 CST)
- Re: Blank thumbnails and non-working snapshots Axel Kohlmeyer (Mon Feb 08 2010 - 11:47:35 CST)
  - RE: Blank thumbnails and non-working snapshots Christopher McLean (Tue Feb 09 2010 - 03:47:41 CST)
problem with generating PSF file for guanine based molecule Parisa Akhski (Sun Feb 07 2010 - 11:51:03 CST)
- Re: problem with generating PSF file for guanine based molecule Axel Kohlmeyer (Sun Feb 07 2010 - 14:05:19 CST)
VMD, Tachyon and depth of field Marc Baaden (Sat Feb 06 2010 - 10:07:07 CST)
- Re: VMD, Tachyon and depth of field John Stone (Sat Feb 06 2010 - 11:15:34 CST)
  - Re: VMD, Tachyon and depth of field John Stone (Sat Feb 06 2010 - 15:01:42 CST)
how to do acetylated lysine in VMD Vo Cam Quy (Fri Feb 05 2010 - 14:27:46 CST)
Changing decimal places in a label? Dr. Seth Olsen (Wed Feb 03 2010 - 23:21:12 CST)
- Re: Changing decimal places in a label? John Stone (Thu Feb 04 2010 - 10:48:38 CST)
Trouble building VMD 1.8.7 on Mac OS X Joshua Anderson (Wed Feb 03 2010 - 15:39:52 CST)
- Re: Trouble building VMD 1.8.7 on Mac OS X John Stone (Wed Feb 03 2010 - 15:55:51 CST)
  - Re: Trouble building VMD 1.8.7 on Mac OS X Joshua Anderson (Thu Feb 04 2010 - 07:26:10 CST)
    - Re: Trouble building VMD 1.8.7 on Mac OS X John Stone (Thu Feb 04 2010 - 10:06:33 CST)
  - Re: Trouble building VMD 1.8.7 on Mac OS X Joshua Anderson (Thu Feb 04 2010 - 10:04:53 CST)
    - Re: Trouble building VMD 1.8.7 on Mac OS X John Stone (Thu Feb 04 2010 - 10:14:13 CST)
molecular dipole moment Jelle van Sijl (Wed Feb 03 2010 - 11:21:33 CST)
- Re: molecular dipole moment Axel Kohlmeyer (Thu Feb 04 2010 - 05:11:59 CST)
VMD script: save coordinates problem martin klvana (Mon Feb 01 2010 - 20:25:49 CST)
- Re: VMD script: save coordinates problem Axel Kohlmeyer (Mon Feb 01 2010 - 21:10:15 CST)
running LAMMPS output via VMD Krigel, Igal (Mon Feb 01 2010 - 06:10:56 CST)
- Re: running LAMMPS output via VMD Axel Kohlmeyer (Mon Feb 01 2010 - 07:37:44 CST)
Number of H bond formation in VMD snoze pa (Thu Jan 28 2010 - 17:32:10 CST)
- Re: Number of H bond formation in VMD Axel Kohlmeyer (Fri Jan 29 2010 - 09:18:32 CST)
vmd hbond Calculation snoze pa (Thu Jan 28 2010 - 11:54:45 CST)
import xyz file Naiyin Yu (Tue Jan 26 2010 - 16:51:04 CST)
- Re: import xyz file John Stone (Tue Jan 26 2010 - 20:48:30 CST)
About Paratool Caio Veloso (Tue Jan 26 2010 - 11:21:13 CST)
- Re: About Paratool Axel Kohlmeyer (Wed Jan 27 2010 - 04:48:11 CST)
VMD version 1.8.7 (LINUX OpenGL, CUDA) on UBUNTU 9.10 A D (Mon Jan 25 2010 - 13:50:06 CST)
- Re: VMD version 1.8.7 (LINUX OpenGL, CUDA) on UBUNTU 9.10 Axel Kohlmeyer (Mon Jan 25 2010 - 16:08:58 CST)
  - Re: VMD version 1.8.7 (LINUX OpenGL, CUDA) on UBUNTU 9.10 John Stone (Mon Jan 25 2010 - 16:32:25 CST)
SASA and SESA Khaled Barakat (Sun Jan 24 2010 - 14:44:45 CST)
- Re: SASA and SESA John Stone (Sun Jan 24 2010 - 14:51:08 CST)
  - Re: SASA and SESA Khaled Barakat (Sun Jan 24 2010 - 15:31:59 CST)
    - Re: SASA and SESA John Stone (Sun Jan 24 2010 - 15:47:28 CST)
    - DNA form Taufik Al-Sarraj (Thu Feb 11 2010 - 12:42:19 CST)
- Re: SASA and SESA Eduard Schreiner (Sun Jan 24 2010 - 15:38:54 CST)
Re: VMD installation: Windows OpenGL John Stone (Sun Jan 24 2010 - 13:33:16 CST)
Number of Hydrogen Bonds among Water an Protein Mert Gür (Sun Jan 24 2010 - 13:17:09 CST)
- Re: Number of Hydrogen Bonds among Water an Protein Leonardo Trabuco (Sun Jan 24 2010 - 13:22:31 CST)
  - Re: Number of Hydrogen Bonds among Water an Protein Mert Gür (Sun Jan 24 2010 - 14:00:32 CST)
autopsf needs at least one atom error Ronald Salesky (Sun Jan 24 2010 - 12:43:51 CST)
- Re: autopsf needs at least one atom error Peter Freddolino (Sun Jan 24 2010 - 13:55:07 CST)
  - Re: autopsf needs at least one atom error Ronald Salesky (Sun Jan 24 2010 - 14:09:57 CST)
    - Re: autopsf needs at least one atom error John Stone (Sun Jan 24 2010 - 14:18:22 CST)
autopsf generator need at least one atom error Ronald Salesky (Sun Jan 24 2010 - 12:29:12 CST)
- Re: autopsf generator need at least one atom error John Stone (Sun Jan 24 2010 - 13:51:27 CST)
Graphics card for molecular graphics Edelmiro Moman (Sun Jan 24 2010 - 10:57:42 CST)
- Re: Graphics card for molecular graphics John Stone (Sun Jan 24 2010 - 13:01:36 CST)
- Re: Graphics card for molecular graphics Axel Kohlmeyer (Sun Jan 24 2010 - 13:09:26 CST)
- Re: Graphics card for molecular graphics Edelmiro Moman (Thu Feb 11 2010 - 06:03:47 CST)
SASA and SESA Khaled Barakat (Fri Jan 22 2010 - 20:22:25 CST)
Syntax and capabilities of writetrr Marc Baaden (Fri Jan 22 2010 - 02:43:27 CST)
- Re: Syntax and capabilities of writetrr John Stone (Fri Jan 22 2010 - 10:45:53 CST)
water in a certein box Naiyin Yu (Thu Jan 21 2010 - 17:09:10 CST)
- Re: water in a certein box John Stone (Thu Jan 21 2010 - 23:43:32 CST)
sasa function Bernhard Knapp (Thu Jan 21 2010 - 02:32:31 CST)
- Re: sasa function Deepangi Pandit (Thu Jan 21 2010 - 09:13:45 CST)
- Re: sasa function John Stone (Thu Jan 21 2010 - 14:09:13 CST)
3D glasses with LCD Nicolas Floquet (Wed Jan 20 2010 - 06:52:16 CST)
- Re: 3D glasses with LCD John Stone (Wed Jan 20 2010 - 10:08:24 CST)
Re: namd-l: NAMD ibverbs not working on new cluster Carsten Olbrich (Wed Jan 20 2010 - 06:49:43 CST)
- Re: Re: namd-l: NAMD ibverbs not working on new cluster John Stone (Wed Jan 20 2010 - 12:46:35 CST)
3D Glasses with LCD for VMD Nicolas Floquet (Wed Jan 20 2010 - 06:46:11 CST)
How to display real time when reading trr file? Cun Zhang (Wed Jan 20 2010 - 01:59:20 CST)
How to display real time when reading trr file? Cun Zhang (Wed Jan 20 2010 - 01:59:16 CST)
- Re: How to display real time when reading trr file? Axel Kohlmeyer (Wed Jan 20 2010 - 05:06:06 CST)
3D Stereo : Windows 7, nVIDIA GEFORCE Deepangi Pandit (Tue Jan 19 2010 - 17:32:04 CST)
- Re: 3D Stereo : Windows 7, nVIDIA GEFORCE John Stone (Tue Jan 19 2010 - 17:57:23 CST)
  - Re: 3D Stereo : Windows 7, nVIDIA GEFORCE Deepangi Pandit (Wed Jan 20 2010 - 09:39:38 CST)
visualizing APBS output Irene Newhouse (Tue Jan 19 2010 - 13:31:08 CST)
- Re: visualizing APBS output John Stone (Tue Jan 19 2010 - 13:50:55 CST)
  - RE: visualizing APBS output Irene Newhouse (Tue Jan 19 2010 - 14:21:33 CST)
    - Re: visualizing APBS output John Stone (Tue Jan 19 2010 - 22:07:43 CST)
    - RE: visualizing APBS output Irene Newhouse (Wed Jan 20 2010 - 12:26:48 CST)
Selection tool Narasimhan LOGANATHAN (Tue Jan 19 2010 - 03:06:21 CST)
masure distance trajectory - delete variable Balazs Jojart (Sun Jan 17 2010 - 05:11:07 CST)
- Re: masure distance trajectory - delete variable Axel Kohlmeyer (Sun Jan 17 2010 - 11:54:03 CST)
  - Re: masure distance trajectory - delete variable Balazs Jojart (Sun Jan 17 2010 - 13:20:20 CST)
bad text display in tk console (ubuntu 8.04 VMD 1.8.7 linux 32 bit) Dong Luo (Fri Jan 15 2010 - 11:30:48 CST)
- Re: bad text display in tk console (ubuntu 8.04 VMD 1.8.7 linux 32 bit) John Stone (Fri Jan 15 2010 - 12:01:17 CST)
  - Re: bad text display in tk console (ubuntu 8.04 VMD 1.8.7 linux 32 bit) Dong Luo (Wed Jan 20 2010 - 10:17:57 CST)
  - Re: bad text display in tk console (ubuntu 8.04 VMD 1.8.7 linux 32 bit) John Stone (Wed Jan 20 2010 - 12:24:16 CST)
- Re: bad text display in tk console (ubuntu 8.04 VMD 1.8.7 linux 32 bit) Axel Kohlmeyer (Fri Jan 15 2010 - 12:11:21 CST)
APBS tutorial link broken Irene Newhouse (Thu Jan 14 2010 - 17:01:14 CST)
- Re: APBS tutorial link broken John Stone (Thu Jan 14 2010 - 17:11:56 CST)
labeling bonds between two atoms gurunath katagi (Thu Jan 14 2010 - 12:12:36 CST)
- Re: labeling bonds between two atoms Axel Kohlmeyer (Thu Jan 14 2010 - 17:17:35 CST)
harmonic constraint when equilibrate the system Naiyin Yu (Wed Jan 13 2010 - 21:44:03 CST)
Topotools plugin: guessimpropers? MyLinkka (Wed Jan 13 2010 - 08:28:28 CST)
- Re: Topotools plugin: guessimpropers? Axel Kohlmeyer (Wed Jan 13 2010 - 09:19:16 CST)
  - Re: Topotools plugin: guessimpropers? MyLinkka (Wed Jan 13 2010 - 10:41:18 CST)
HOOMD plugin Benjamin Bouvier (Tue Jan 12 2010 - 11:04:08 CST)
- Re: HOOMD plugin Axel Kohlmeyer (Tue Jan 12 2010 - 13:11:32 CST)
PME isosurface not superimposed on protein Irene Newhouse (Mon Jan 11 2010 - 16:20:50 CST)
- Re: PME isosurface not superimposed on protein Axel Kohlmeyer (Mon Jan 11 2010 - 16:59:59 CST)
  - RE: PME isosurface not superimposed on protein Irene Newhouse (Mon Jan 11 2010 - 17:17:50 CST)
vmdcollab in VMD xaneorat_at_mail.uni-paderborn.de (Mon Jan 11 2010 - 05:19:33 CST)
- Re: vmdcollab in VMD John Stone (Wed Jan 13 2010 - 15:55:01 CST)
Maestro file export Jacob Poehlsgaard (Mon Jan 11 2010 - 03:21:22 CST)
- Re: Maestro file export John Stone (Tue Jan 12 2010 - 16:46:07 CST)
  - Re: Maestro file export Jacob Poehlsgaard (Wed Jan 13 2010 - 09:15:03 CST)
display surface amino acid beads Christine Horejs (Sat Jan 09 2010 - 04:22:34 CST)
- Re: display surface amino acid beads John Stone (Tue Jan 12 2010 - 14:25:28 CST)
obscurity in sbcg tutorial description Francesco Pietra (Sat Jan 09 2010 - 03:37:49 CST)
- Fwd: obscurity in sbcg tutorial description Francesco Pietra (Sat Jan 09 2010 - 16:01:21 CST)
Compiling VMD plugins on Windows? Olaf Lenz (Fri Jan 08 2010 - 09:20:47 CST)
- Re: Compiling VMD plugins on Windows? John Stone (Tue Jan 12 2010 - 10:51:39 CST)
Fwd: Re: allowing negative 'resid' numbers in selection strings Vlad Cojocaru (Fri Jan 08 2010 - 09:10:02 CST)
allowing negative 'resid' numbers in selection strings Vlad Cojocaru (Fri Jan 08 2010 - 07:56:16 CST)
- Re: allowing negative 'resid' numbers in selection strings Axel Kohlmeyer (Fri Jan 08 2010 - 08:49:01 CST)
vmd 1.8.7 getting the terminal free maria goranovic (Fri Jan 08 2010 - 05:20:46 CST)
- Re: vmd 1.8.7 getting the terminal free Axel Kohlmeyer (Fri Jan 08 2010 - 06:25:40 CST)
  - Re: vmd 1.8.7 getting the terminal free Axel Kohlmeyer (Fri Jan 08 2010 - 06:26:43 CST)
    - Re: vmd 1.8.7 getting the terminal free Nuno Sousa Cerqueira (Fri Jan 08 2010 - 07:38:29 CST)
    - Re: vmd 1.8.7 getting the terminal free Axel Kohlmeyer (Fri Jan 08 2010 - 08:03:21 CST)
VMD lammps plugin: a possible bug MyLinkka (Thu Jan 07 2010 - 10:35:57 CST)
- Re: VMD lammps plugin: a possible bug Axel Kohlmeyer (Thu Jan 07 2010 - 12:03:23 CST)
  - Re: VMD lammps plugin: a possible bug Axel Kohlmeyer (Fri Jan 08 2010 - 08:19:15 CST)
VMD hangs up with a file size ~ 1.2 GB ? maria goranovic (Wed Jan 06 2010 - 04:32:30 CST)
- Re: VMD hangs up with a file size ~ 1.2 GB ? Olaf Lenz (Wed Jan 06 2010 - 05:57:47 CST)
  - Re: VMD hangs up with a file size ~ 1.2 GB ? maria goranovic (Wed Jan 06 2010 - 15:58:02 CST)
- Re: VMD hangs up with a file size ~ 1.2 GB ? Axel Kohlmeyer (Wed Jan 06 2010 - 07:41:05 CST)
  - Re: VMD hangs up with a file size ~ 1.2 GB ? maria goranovic (Wed Jan 06 2010 - 08:26:00 CST)
- Re: VMD hangs up with a file size ~ 1.2 GB ? John Stone (Wed Jan 06 2010 - 10:06:34 CST)
CUDA-NAMD hangs -- check the Northbridge temp! Biff Forbush (Tue Jan 05 2010 - 21:51:51 CST)
conflict between VMD and Netbeans IDE on MacOSX Wayne Dawson (Tue Jan 05 2010 - 21:16:58 CST)
- Re: conflict between VMD and Netbeans IDE on MacOSX Robert Brunner (Wed Jan 06 2010 - 11:18:11 CST)
  - Re: conflict between VMD and Netbeans IDE on MacOSX Wayne Dawson (Thu Jan 07 2010 - 06:44:52 CST)
    - Re: conflict between VMD and Netbeans IDE on MacOSX Leonardo Trabuco (Thu Jan 07 2010 - 08:02:37 CST)
    - Re: conflict between VMD and Netbeans IDE on MacOSX John Stone (Tue Jan 12 2010 - 14:13:30 CST)
New Cartoon representation problem Kassem Ghaddar (Tue Jan 05 2010 - 04:09:16 CST)
- retrieving atom indexes from measure contacts Sunita Patel (Tue Jan 05 2010 - 19:56:22 CST)
  - Re: retrieving atom indexes from measure contacts Leonardo Trabuco (Tue Jan 05 2010 - 20:16:54 CST)
- Re: New Cartoon representation problem John Stone (Wed Jan 06 2010 - 12:49:18 CST)
slow visualization using molecular representations with VMD 1.8.7 on mac Matthieu Chavent (Tue Jan 05 2010 - 03:47:17 CST)
- Re: slow visualization using molecular representations with VMD 1.8.7 on mac John Stone (Tue Jan 05 2010 - 08:59:04 CST)
VMD-Xplor interface problem Vitaly Vostrikov (Sun Jan 03 2010 - 20:18:01 CST)
- Re: VMD-Xplor interface problem John Stone (Sun Jan 03 2010 - 21:38:24 CST)
  - Re: VMD-Xplor interface problem Vitaly Vostrikov (Mon Jan 04 2010 - 12:04:14 CST)
    - Re: VMD-Xplor problem Vitaly Vostrikov (Tue Jan 05 2010 - 22:22:12 CST)
Failure of AutoSCFBuilder to recognize all monomers Francesco Pietra (Sun Jan 03 2010 - 04:54:24 CST)
- Fwd: Failure of AutoSCFBuilder to recognize all monomers Francesco Pietra (Sun Jan 03 2010 - 09:24:22 CST)
vmd 1.8.7CUDA/1.8.7/1.8.6 can not start Guo Zhi (Sat Jan 02 2010 - 18:16:54 CST)
- Re: vmd 1.8.7CUDA/1.8.7/1.8.6 can not start John Stone (Sun Jan 03 2010 - 01:56:14 CST)
  - Re: vmd 1.8.7CUDA/1.8.7/1.8.6 can not start Guo Zhi (Sun Jan 03 2010 - 11:41:03 CST)
reply Prathit Chatterjee (Sat Jan 02 2010 - 05:33:04 CST)
- Re: reply John Stone (Sat Jan 02 2010 - 08:53:01 CST)
About the criterion of H bond yongle (Sat Jan 02 2010 - 02:23:18 CST)
- Re: About the criterion of H bond Axel Kohlmeyer (Sat Jan 02 2010 - 03:33:38 CST)
vmd installation in linux Prathit Chatterjee (Fri Jan 01 2010 - 22:08:09 CST)
- Re: vmd installation in linux John Stone (Sat Jan 02 2010 - 01:08:58 CST)
  - Re: vmd installation in linux Ocar Campos (Sat Jan 02 2010 - 06:20:15 CST)
  - Re: vmd installation in linux Prathit Chatterjee (Sun Jan 03 2010 - 04:09:13 CST)
Superposition of Multiple Trajectory Timesteps ÖÜÎÄ²ý (Thu Dec 31 2009 - 05:47:20 CST)
- Re: Superposition of Multiple Trajectory Timesteps Axel Kohlmeyer (Thu Dec 31 2009 - 08:08:03 CST)
  - Re: Re: Superposition of Multiple Trajectory Timesteps Axel Kohlmeyer (Thu Dec 31 2009 - 10:57:08 CST)
sbcg with multimers Francesco Pietra (Wed Dec 30 2009 - 15:22:43 CST)
- Fwd: sbcg with multimers Francesco Pietra (Thu Dec 31 2009 - 04:40:14 CST)
- Re: sbcg with multimers Anton Arkhipov (Sun Jan 17 2010 - 23:37:48 CST)
IMD in VMD Lixia Jin Day (Tue Dec 29 2009 - 17:42:57 CST)
- Re: IMD in VMD Axel Kohlmeyer (Wed Dec 30 2009 - 00:58:00 CST)
  - Re: IMD in VMD John Stone (Wed Dec 30 2009 - 12:55:28 CST)
- Re: IMD in VMD John Stone (Wed Dec 30 2009 - 12:39:10 CST)
UNIT CELL Narasimhan LOGANATHAN (Tue Dec 29 2009 - 09:49:29 CST)
- Re: UNIT CELL Axel Kohlmeyer (Tue Dec 29 2009 - 10:37:59 CST)
  - Re: UNIT CELL Olaf Lenz (Wed Dec 30 2009 - 04:13:59 CST)
PDB file Burak Cankurtaran (Tue Dec 29 2009 - 05:41:23 CST)
- Re: PDB file John Stone (Sun Jan 03 2010 - 02:23:41 CST)
Re: Problem when using VMD Python Library Cun Zhang (Sun Dec 27 2009 - 08:31:04 CST)
Problem when using VMD Python Library Cun Zhang (Fri Dec 25 2009 - 06:03:46 CST)
- Re: Problem when using VMD Python Library John Stone (Wed Dec 30 2009 - 12:46:36 CST)
remove water snoze pa (Wed Dec 23 2009 - 14:44:45 CST)
installation problem Jin Wen (Tue Dec 22 2009 - 17:46:43 CST)
- Re: installation problem Ale Gomez (Tue Dec 22 2009 - 20:54:29 CST)
- Re: installation problem Axel Kohlmeyer (Wed Dec 23 2009 - 02:14:47 CST)
  - Re: installation problem Jin Wen (Wed Dec 23 2009 - 14:13:05 CST)
    - Re: installation problem Axel Kohlmeyer (Wed Dec 23 2009 - 14:30:56 CST)
    - Re: installation problem John Stone (Wed Dec 30 2009 - 12:53:37 CST)
rdf curve gurunath katagi (Tue Dec 22 2009 - 08:17:57 CST)
- Re: rdf curve Axel Kohlmeyer (Tue Dec 22 2009 - 09:08:20 CST)
- vmd 1.8.7 - console window fullscreen gbellesia_at_chem.ucsb.edu (Thu Dec 24 2009 - 16:20:17 CST)
  - Re: vmd 1.8.7 - console window fullscreen Axel Kohlmeyer (Fri Dec 25 2009 - 02:23:27 CST)
superimposed structure leila karami (Sun Dec 20 2009 - 08:46:03 CST)
- Re: superimposed structure Axel Kohlmeyer (Sun Dec 20 2009 - 09:55:04 CST)
superimposed structure leila karami (Sun Dec 20 2009 - 08:07:16 CST)
vmd won't display in lines Gard Nelson (Fri Dec 18 2009 - 16:17:45 CST)
- Re: vmd won't display in lines John Stone (Fri Dec 18 2009 - 16:32:12 CST)
Re: VMD CVS Request for Richard Cook Rich Cook (Thu Dec 17 2009 - 16:45:07 CST)
- Re: Re: VMD CVS Request for Richard Cook John Stone (Thu Dec 17 2009 - 17:03:07 CST)
  - Re: Re: VMD CVS Request for Richard Cook Rich Cook (Thu Dec 17 2009 - 18:05:34 CST)
Re: Request for information John Stone (Thu Dec 17 2009 - 13:29:52 CST)
- Re: Request for information Rich Cook (Thu Dec 17 2009 - 13:58:45 CST)
Fwd: Fwd: Re: namd-l: Fwd: conf file for coarse grained simulation Francesco Pietra (Thu Dec 17 2009 - 02:34:23 CST)
- Fwd: Fwd: Re: namd-l: Fwd: conf file for coarse grained simulation Francesco Pietra (Thu Dec 17 2009 - 12:27:15 CST)
- Re: Fwd: Fwd: Re: namd-l: Fwd: conf file for coarse grained simulation John Stone (Thu Dec 17 2009 - 13:33:34 CST)
Problem generating psf file in psfgen Ranyere Deyler (Wed Dec 16 2009 - 23:24:58 CST)
- Re: Problem generating psf file in psfgen John Stone (Sat Dec 19 2009 - 01:52:07 CST)
Re: Fwd: Re: namd-l: Fwd: conf file for coarse grained simulation Peter Freddolino (Wed Dec 16 2009 - 18:49:13 CST)
Graphical Representations doesn't recognize chain ID z Samuel Coulbourn Flores (Wed Dec 16 2009 - 09:59:47 CST)
- Re: Graphical Representations doesn't recognize chain ID z John Stone (Wed Dec 16 2009 - 10:21:12 CST)
VMD plugin: filenames supposed to have dot in it?!?! Rob (Wed Dec 16 2009 - 01:07:20 CST)
- Re: VMD plugin: filenames supposed to have dot in it?!?! John Stone (Wed Dec 16 2009 - 10:51:29 CST)
- Re: VMD plugin: filenames supposed to have dot in it?!?! Rob (Thu Dec 17 2009 - 18:12:46 CST)
- pbc wrap center on protein Balazs Jojart (Sat Dec 19 2009 - 12:16:22 CST)
  - Re: pbc wrap center on protein Axel Kohlmeyer (Sat Dec 19 2009 - 14:45:59 CST)
    - Re: pbc wrap center on protein Balazs Jojart (Sat Dec 19 2009 - 14:56:22 CST)
  - Re: pbc wrap center on protein Luca Bellucci (Sat Dec 19 2009 - 16:06:12 CST)
VMD plugin for abinit Rob (Tue Dec 15 2009 - 21:47:08 CST)
- Re: VMD plugin for abinit John Stone (Thu Dec 17 2009 - 13:38:12 CST)
how to label the distances using tk console mode YangMingjun (Tue Dec 15 2009 - 19:24:00 CST)
- Re: how to label the distances using tk console mode Eric H. Lee (Tue Dec 15 2009 - 20:09:58 CST)
  - Re: Re: how to label the distances using tk console mode YangMingjun (Tue Dec 15 2009 - 20:39:49 CST)
    - Re: how to label the distances using tk console mode Eric H. Lee (Tue Dec 15 2009 - 20:54:17 CST)
- Re: how to label the distances using tk console mode Schreiner Eduard (Tue Dec 15 2009 - 20:40:02 CST)
VMD on AIX --- successful build, failed execution Rich Cook (Tue Dec 15 2009 - 16:26:00 CST)
- Re: VMD on AIX --- successful build, failed execution John Stone (Wed Dec 16 2009 - 10:56:56 CST)
  - Re: VMD on AIX --- successful build, failed execution Rich Cook (Wed Dec 16 2009 - 14:07:52 CST)
Issues with flickering display using VMD 1.8.7 displaying over X11 to remote Mac Rich Cook (Tue Dec 15 2009 - 15:03:07 CST)
- Re: Issues with flickering display using VMD 1.8.7 displaying over X11 to remote Mac John Stone (Tue Dec 15 2009 - 15:20:01 CST)
  - Re: Issues with flickering display using VMD 1.8.7 displaying over X11 to remote Mac John Stone (Wed Dec 16 2009 - 23:55:15 CST)
    - Re: Issues with flickering display using VMD 1.8.7 displaying over X11 to remote Mac Rich Cook (Thu Dec 17 2009 - 12:52:54 CST)
Graphics card for VMD Berit Hinnemann (Tue Dec 15 2009 - 11:25:25 CST)
- Re: Graphics card for VMD Axel Kohlmeyer (Tue Dec 15 2009 - 12:26:08 CST)
  - Re: Graphics card for VMD Berit Hinnemann (Wed Dec 16 2009 - 07:16:14 CST)
hbonds.tcl selection problem in command-line Nicola Giacche' (Tue Dec 15 2009 - 05:25:01 CST)
- Re: hbonds.tcl selection problem in command-line Axel Kohlmeyer (Tue Dec 15 2009 - 06:17:46 CST)
IDs of representations Carsten Olbrich (Tue Dec 15 2009 - 03:30:54 CST)
- Re: IDs of representations Leonardo Trabuco (Tue Dec 15 2009 - 11:30:26 CST)
Re: namd-l: Fwd: conf file for coarse grained simulation Francesco Pietra (Tue Dec 15 2009 - 02:40:55 CST)
- Re: namd-l: Fwd: conf file for coarse grained simulation Francesco Pietra (Tue Dec 15 2009 - 10:01:30 CST)
- Re: Re: namd-l: Fwd: conf file for coarse grained simulation Peter Freddolino (Tue Dec 15 2009 - 10:45:27 CST)
superimposed structure leila karami (Tue Dec 15 2009 - 00:21:04 CST)
- Re: superimposed structure Joshua Adelman (Tue Dec 15 2009 - 07:15:52 CST)
  - Re: superimposed structure Axel Kohlmeyer (Tue Dec 15 2009 - 09:34:12 CST)
File owner/group settings after installing precompiled VMD. Rob (Mon Dec 14 2009 - 21:13:23 CST)
- Re: File owner/group settings after installing precompiled VMD. John Stone (Thu Dec 17 2009 - 00:24:11 CST)
solvating diferent regions in VMD Ranyere Deyler (Mon Dec 14 2009 - 17:07:38 CST)
PBC + DCD wrap/unwrap Goutham (Mon Dec 14 2009 - 13:37:36 CST)
- Re: PBC + DCD wrap/unwrap Olaf Lenz (Tue Dec 15 2009 - 03:38:55 CST)
Re: namd CG minimization error: unable to find angle parameters for nxg nxx nxg Francesco Pietra (Fri Dec 11 2009 - 09:52:43 CST)
namd CG minimization error: unable to find angle parameters for nxg nxx nxg Francesco Pietra (Thu Dec 10 2009 - 10:27:13 CST)
- Re: namd CG minimization error: unable to find angle parameters for nxg nxx nxg Peter Freddolino (Thu Dec 10 2009 - 15:06:05 CST)
Fwd: Calculation the Surface Area/Volume of a Protein Cavity Nuno Sousa Cerqueira (Thu Dec 10 2009 - 07:13:07 CST)
About "Visualization and Analysis of CPMD data with VMD" tutorial Aurum Bai (Thu Dec 10 2009 - 02:29:22 CST)
- Re: About "Visualization and Analysis of CPMD data with VMD" tutorial Joshua Adelman (Thu Dec 10 2009 - 05:29:17 CST)
Fwd: paratool - parameter generation from gaussian log files Nuno Sousa Cerqueira (Thu Dec 10 2009 - 01:05:51 CST)
Re: vmd 1.8.7 on Intel 64 bit: segmentation fault" Rob (Wed Dec 09 2009 - 22:24:16 CST)
- Re: Re: vmd 1.8.7 on Intel 64 bit: segmentation fault" Bogdan Costescu (Thu Dec 10 2009 - 06:14:34 CST)
- Re: Re: vmd 1.8.7 on Intel 64 bit: segmentation fault" John Stone (Thu Dec 10 2009 - 10:15:06 CST)
paratool - parameter generation from gaussian log files Yu Fang (Wed Dec 09 2009 - 22:17:57 CST)
- Re: paratool - parameter generation from gaussian log files sarah k (Thu Dec 10 2009 - 00:07:06 CST)
  - Re: paratool - parameter generation from gaussian log files Yu Fang (Thu Dec 10 2009 - 05:08:03 CST)
  - Re: paratool - parameter generation from gaussian log files Yu Fang (Mon Dec 14 2009 - 17:41:06 CST)
error in rmsd.tcl for tutorial TAE BUM LEE (Wed Dec 09 2009 - 16:37:42 CST)
- Re: error in rmsd.tcl for tutorial John Stone (Thu Dec 10 2009 - 10:28:16 CST)
  - Re: error in rmsd.tcl for tutorial TAE BUM LEE (Thu Dec 10 2009 - 17:42:04 CST)
    - Re: error in rmsd.tcl for tutorial John Stone (Fri Dec 11 2009 - 16:12:22 CST)
    - Re: error in rmsd.tcl for tutorial TAE BUM LEE (Sun Dec 13 2009 - 12:23:03 CST)
Counting number of water molecules Bernardo Sosa Padilla Araujo (Wed Dec 09 2009 - 16:30:13 CST)
- Re: Counting number of water molecules Axel Kohlmeyer (Wed Dec 09 2009 - 17:32:07 CST)
- Re: Counting number of water molecules Andrew Dalke (Wed Dec 09 2009 - 17:20:43 CST)
  - Re: Counting number of water molecules Bernardo Sosa Padilla Araujo (Thu Dec 10 2009 - 18:48:20 CST)
Re: A VMD script to emulate the Matlab "jet" colorscale John Stone (Wed Dec 09 2009 - 11:48:11 CST)
A VMD script to emulate the Matlab "jet" colorscale John Stone (Tue Dec 08 2009 - 16:49:40 CST)
Restraints on coarse grained model Francesco Pietra (Tue Dec 08 2009 - 13:23:59 CST)
- Fwd: Restraints on coarse grained model Francesco Pietra (Wed Dec 09 2009 - 03:07:36 CST)
  - Re: Restraints on coarse grained model Anton Arkhipov (Wed Dec 09 2009 - 10:58:56 CST)
- Re: Restraints on coarse grained model BIN ZHANG (Wed Dec 09 2009 - 12:07:37 CST)
  - Re: Restraints on coarse grained model Francesco Pietra (Wed Dec 09 2009 - 12:49:28 CST)
    - Re: Restraints on coarse grained model BIN ZHANG (Wed Dec 09 2009 - 13:01:58 CST)
Broken bonds in trajectory due to pbc Jennifer Williams (Tue Dec 08 2009 - 05:41:07 CST)
- Re: Broken bonds in trajectory due to pbc Olaf Lenz (Tue Dec 08 2009 - 07:39:39 CST)
  - Re: Broken bonds in trajectory due to pbc Olaf Lenz (Tue Dec 08 2009 - 13:07:39 CST)
Re: vmd 1.8.7 on Intel 64 bit: segmentation fault (however: 1.8.6 works!) Rob (Tue Dec 08 2009 - 01:03:29 CST)
- Re: Re: vmd 1.8.7 on Intel 64 bit: segmentation fault (however: 1.8.6 works!) John Stone (Tue Dec 08 2009 - 01:17:25 CST)
vmd 1.8.7 on Intel 64 bit: segmentation fault Rob (Mon Dec 07 2009 - 21:25:11 CST)
- Re: vmd 1.8.7 on Intel 64 bit: segmentation fault John Stone (Mon Dec 07 2009 - 21:45:44 CST)
- Re: vmd 1.8.7 on Intel 64 bit: segmentation fault Rob (Tue Dec 08 2009 - 08:05:26 CST)
  - Re: Re: vmd 1.8.7 on Intel 64 bit: segmentation fault John Stone (Tue Dec 08 2009 - 12:34:57 CST)
    - Re: Re: vmd 1.8.7 on Intel 64 bit: segmentation fault Axel Kohlmeyer (Tue Dec 08 2009 - 16:53:15 CST)
- Re: vmd 1.8.7 on Intel 64 bit: segmentation fault Rob (Fri Dec 11 2009 - 08:53:35 CST)
  - Re: Re: vmd 1.8.7 on Intel 64 bit: segmentation fault John Stone (Fri Dec 11 2009 - 14:34:23 CST)
- Re: vmd 1.8.7 on Intel 64 bit: segmentation fault Rob (Sun Dec 13 2009 - 18:33:35 CST)
  - Re: Re: vmd 1.8.7 on Intel 64 bit: segmentation fault Bogdan Costescu (Mon Dec 14 2009 - 06:21:14 CST)
FW: VMD 1.8.7 build with VRPN 7.23 Mark Cunningham (Mon Dec 07 2009 - 14:09:59 CST)
- Re: FW: VMD 1.8.7 build with VRPN 7.23 John Stone (Mon Dec 07 2009 - 14:42:26 CST)
vmd-1.8.7 building from source ->few plugins "package could not be loaded" Tru Huynh (Mon Dec 07 2009 - 09:40:30 CST)
- Re: vmd-1.8.7 building from source ->few plugins "package could not be loaded" John Stone (Mon Dec 07 2009 - 14:43:51 CST)
  - Re: vmd-1.8.7 building from source ->few plugins "package could not be loaded" Tru Huynh (Tue Dec 08 2009 - 14:22:23 CST)
cluster of particles Salvador H-V (Sun Dec 06 2009 - 20:00:39 CST)
porcupine plots for PC1 Dawn (Sun Dec 06 2009 - 13:29:19 CST)
- Re: porcupine plots for PC1 Joshua Adelman (Sun Dec 06 2009 - 15:22:06 CST)
  - Re: porcupine plots for PC1 Joshua Adelman (Mon Dec 07 2009 - 06:49:11 CST)
    - Re: porcupine plots for PC1 Carsten Olbrich (Thu Dec 10 2009 - 04:43:03 CST)
    - Calculation the Surface Area/Volume of a Protein Cavity MUHAMMAD IMTIA SHAFIQ (Thu Dec 10 2009 - 05:24:12 CST)
Fwd: Failure with AutoPSF (PDB has x, y, z zero) Francesco Pietra (Sat Dec 05 2009 - 12:51:22 CST)
- Fwd: Failure with AutoPSF (PDB has x, y, z zero) Francesco Pietra (Sat Dec 05 2009 - 14:25:41 CST)
  - Re: Fwd: Failure with AutoPSF (PDB has x, y, z zero) Peter Freddolino (Sat Dec 05 2009 - 15:40:27 CST)
Failure with AutoPSF (PDB has x, y, z zero) Francesco Pietra (Fri Dec 04 2009 - 12:35:12 CST)
- Re: Failure with AutoPSF (PDB has x, y, z zero) Peter Freddolino (Sat Dec 05 2009 - 08:21:29 CST)
regarding generating movie jani sahil (Fri Dec 04 2009 - 02:49:19 CST)
- Re: regarding generating movie John Stone (Fri Dec 04 2009 - 14:06:51 CST)
  - Re: regarding generating movie jani sahil (Fri Dec 04 2009 - 23:56:42 CST)
RMSD for individual residue for a tetarmer gurunath katagi (Fri Dec 04 2009 - 00:20:03 CST)
- Re: RMSD for individual residue for a tetarmer John Stone (Wed Dec 09 2009 - 00:25:01 CST)
  - Re: RMSD for individual residue for a tetarmer gurunath katagi (Wed Dec 09 2009 - 04:41:11 CST)
Nucleic acid topology file for PSF generation Jim Parker (Thu Dec 03 2009 - 21:56:00 CST)
- Re: Nucleic acid topology file for PSF generation Schreiner Eduard (Thu Dec 03 2009 - 23:01:58 CST)
  - [Solved] Re: Nucleic acid topology file for PSF generation Jim Parker (Fri Dec 04 2009 - 22:13:50 CST)
desmond plugin Nuno Sousa Cerqueira (Thu Dec 03 2009 - 17:43:02 CST)
- Re: desmond plugin John Stone (Fri Dec 04 2009 - 10:43:25 CST)
  - Re: desmond plugin John Stone (Wed Dec 09 2009 - 09:11:33 CST)
- Re: desmond plugin John Stone (Fri Dec 04 2009 - 13:54:38 CST)
  - Re: desmond plugin Nuno Sousa Cerqueira (Fri Dec 04 2009 - 15:07:32 CST)
    - Re: desmond plugin John Stone (Fri Dec 04 2009 - 17:28:31 CST)
desmond plugin Nuno Sousa Cerqueira (Thu Dec 03 2009 - 17:37:51 CST)
in search of lipid files Francesco Pietra (Thu Dec 03 2009 - 16:11:43 CST)
ccp4 in vmd pebblepeddle_at_gmail.com (Wed Dec 02 2009 - 21:55:58 CST)
- Re: ccp4 in vmd John Stone (Wed Dec 02 2009 - 22:41:17 CST)
Drawing cylinder in VMD rainy908_at_yahoo.com (Wed Dec 02 2009 - 17:29:24 CST)
- Re: Drawing cylinder in VMD John Stone (Wed Dec 02 2009 - 17:35:04 CST)
  - Re: Drawing cylinder in VMD rainy908_at_yahoo.com (Wed Dec 02 2009 - 20:22:50 CST)
    - Re: Drawing cylinder in VMD John Stone (Wed Dec 02 2009 - 20:36:13 CST)
- Re: Drawing cylinder in VMD rainy908_at_yahoo.com (Wed Dec 02 2009 - 17:36:00 CST)
CG lipid bilayer vmd 1.8.7 Francesco Pietra (Wed Dec 02 2009 - 12:13:53 CST)
- Re: CG lipid bilayer vmd 1.8.7 BIN ZHANG (Wed Dec 02 2009 - 14:03:58 CST)
  - Re: CG lipid bilayer vmd 1.8.7 BIN ZHANG (Wed Dec 02 2009 - 15:17:05 CST)
  - Re: CG lipid bilayer vmd 1.8.7 Francesco Pietra (Thu Dec 03 2009 - 02:57:24 CST)
    - Re: CG lipid bilayer vmd 1.8.7 Peter Freddolino (Thu Dec 03 2009 - 05:31:58 CST)
- Re: CG lipid bilayer vmd 1.8.7 Anton Arkhipov (Sun Dec 06 2009 - 00:35:46 CST)
  - Re: CG lipid bilayer vmd 1.8.7 Francesco Pietra (Sun Dec 06 2009 - 13:24:06 CST)
coloring by difference in beta factors cubellis_at_unina.it (Tue Dec 01 2009 - 06:25:28 CST)
- Re: coloring by difference in beta factors Axel Kohlmeyer (Tue Dec 01 2009 - 07:30:43 CST)
Cant start IED Thomas Steinbrecher (Tue Dec 01 2009 - 05:00:15 CST)
- Re: Cant start IED Axel Kohlmeyer (Tue Dec 01 2009 - 07:26:44 CST)
building VMD is tricky -please help Rich Cook (Mon Nov 30 2009 - 17:49:23 CST)
- Re: building VMD is tricky -please help Dipesh Bhattarai (Mon Nov 30 2009 - 19:32:09 CST)
  - Re: building VMD is tricky -please help Pieter van 't Hof (Tue Dec 01 2009 - 03:40:05 CST)
- Re: building VMD is tricky -please help John Stone (Tue Dec 01 2009 - 10:05:01 CST)
  - Re: building VMD is tricky -please help Rich Cook (Tue Dec 01 2009 - 13:59:29 CST)
Survey: 3 minutes of your time Pieter van 't Hof (Mon Nov 30 2009 - 07:56:47 CST)
generating .xsc file from .dcd Neelanjana Sengupta (Mon Nov 30 2009 - 04:19:43 CST)
- Re: generating .xsc file from .dcd John Stone (Tue Dec 01 2009 - 10:07:57 CST)
Polyhedra with two selections? Georg Spiekermann (Mon Nov 30 2009 - 04:01:12 CST)
- Re: Polyhedra with two selections? Axel Kohlmeyer (Mon Nov 30 2009 - 05:10:54 CST)
  - Re: Polyhedra with two selections? John Stone (Mon Nov 30 2009 - 09:54:00 CST)
Color by position behavior JT (Sun Nov 29 2009 - 02:59:31 CST)
- Re: Color by position behavior Axel Kohlmeyer (Sun Nov 29 2009 - 03:47:08 CST)
  - Re: Color by position behavior JT (Sun Nov 29 2009 - 08:23:06 CST)
error in rbcg-2007.par file BIN ZHANG (Fri Nov 27 2009 - 13:15:01 CST)
- Re: error in rbcg-2007.par file Peter Freddolino (Fri Nov 27 2009 - 19:27:37 CST)
desmond plug-in error Nuno Sousa Cerqueira (Thu Nov 26 2009 - 11:53:58 CST)
- Re: desmond plug-in error John Stone (Thu Nov 26 2009 - 14:16:26 CST)
  - Re: desmond plug-in error Justin Gullingsrud (Mon Nov 30 2009 - 16:35:13 CST)
    - Re: desmond plug-in error Nuno Sousa Cerqueira (Mon Nov 30 2009 - 18:35:39 CST)
Secondary structure with Timeline Florentina Tofoleanu (Thu Nov 26 2009 - 06:19:15 CST)
- Re: Secondary structure with Timeline John Stone (Tue Dec 01 2009 - 10:53:00 CST)
- Re: Secondary structure with Timeline Florentina Tofoleanu (Tue Dec 01 2009 - 12:18:05 CST)
Hydrogen bonds with different evaluations Florentina Tofoleanu (Thu Nov 26 2009 - 05:16:34 CST)
Move molecule to the origin of coordinate system snoze pa (Wed Nov 25 2009 - 10:49:12 CST)
- Re: Move molecule to the origin of coordinate system John Stone (Wed Nov 25 2009 - 11:22:07 CST)
- Re: Move molecule to the origin of coordinate system Joshua Adelman (Wed Nov 25 2009 - 12:46:13 CST)
GRID maps visualization problems Sergey Samsonov (Tue Nov 24 2009 - 07:50:51 CST)
- Re: GRID maps visualization problems Björn Windshügel (Tue Nov 24 2009 - 12:22:47 CST)
  - Re: GRID maps visualization problems John Stone (Wed Nov 25 2009 - 15:05:30 CST)
GRID maps visualization problems Sergey Samsonov (Tue Nov 24 2009 - 07:35:51 CST)
- Re: GRID maps visualization problems John Stone (Tue Nov 24 2009 - 09:12:30 CST)
aligning trajectories maria goranovic (Tue Nov 24 2009 - 04:22:54 CST)
Using class UIVR Dipesh Bhattarai (Mon Nov 23 2009 - 10:59:57 CST)
- Re: Using class UIVR John Stone (Mon Nov 23 2009 - 17:15:49 CST)
  - Re: Using class UIVR Dipesh Bhattarai (Tue Nov 24 2009 - 10:27:22 CST)
    - Re: Using class UIVR John Stone (Tue Nov 24 2009 - 11:06:52 CST)
VMD 1.8.7 amd64 python libs? Tru Huynh (Mon Nov 23 2009 - 10:30:17 CST)
- Re: VMD 1.8.7 amd64 python libs? John Stone (Mon Nov 23 2009 - 17:30:30 CST)
  - Re: VMD 1.8.7 amd64 python libs? John Stone (Wed Dec 02 2009 - 10:29:56 CST)
  - Re: VMD 1.8.7 amd64 python libs? John Stone (Wed Dec 02 2009 - 11:16:06 CST)
    - Re: VMD 1.8.7 amd64 python libs? Ondrej Marsalek (Wed Dec 02 2009 - 11:22:21 CST)
    - Re: VMD 1.8.7 amd64 python libs? John Stone (Wed Dec 02 2009 - 11:48:41 CST)
Re: namd-l: Re: problems with CG protein-lipidbilayer-water system Francesco Pietra (Sun Nov 22 2009 - 15:32:18 CST)
problems with CG protein-lipidbilayer-water system Francesco Pietra (Sat Nov 21 2009 - 12:00:54 CST)
- Re: problems with CG protein-lipidbilayer-water system Axel Kohlmeyer (Sat Nov 21 2009 - 16:54:04 CST)
- Re: problems with CG protein-lipidbilayer-water system Anton Arkhipov (Mon Nov 23 2009 - 00:51:43 CST)
destroyed molecule sarah k (Sat Nov 21 2009 - 06:57:32 CST)
- Re: destroyed molecule Peter Freddolino (Sat Nov 21 2009 - 08:59:35 CST)
coarse-grained solvate usage Francesco Pietra (Fri Nov 20 2009 - 05:12:35 CST)
- Re: coarse-grained solvate usage Kirby Vandivort (Fri Nov 20 2009 - 12:09:51 CST)
aquire coordinates from the points of the solvent representation Nuno Sousa Cerqueira (Thu Nov 19 2009 - 13:53:40 CST)
- Re: aquire coordinates from the points of the solvent representation Axel Kohlmeyer (Fri Nov 20 2009 - 13:23:11 CST)
  - Re: aquire coordinates from the points of the solvent representation John Stone (Sat Nov 21 2009 - 01:01:15 CST)
solvate error Rebecca Alexander (Thu Nov 19 2009 - 11:48:42 CST)
- Re: solvate error Axel Kohlmeyer (Thu Nov 19 2009 - 12:29:08 CST)
paratool problem sarah k (Wed Nov 18 2009 - 23:43:52 CST)
Is it the bug of VMD1.87_partool? Aurum Bai (Wed Nov 18 2009 - 06:29:56 CST)
xzy format and ResType Christine Horejs (Tue Nov 17 2009 - 14:03:01 CST)
- Re: xzy format and ResType Axel Kohlmeyer (Tue Nov 17 2009 - 14:40:46 CST)
Holo-Bench with VMD and Flystick2 and/or Phantom Carsten Olbrich (Tue Nov 17 2009 - 12:03:56 CST)
- Re: Holo-Bench with VMD and Flystick2 and/or Phantom Dipesh Bhattarai (Tue Nov 17 2009 - 13:04:59 CST)
polymer bead spring model file format Ding, L. (Tue Nov 17 2009 - 11:15:50 CST)
- Re: polymer bead spring model file format Axel Kohlmeyer (Tue Nov 17 2009 - 12:40:49 CST)
  - Re: polymer bead spring model file format Olaf Lenz (Wed Nov 18 2009 - 02:20:38 CST)
    - Re: polymer bead spring model file format Joshua Adelman (Wed Nov 18 2009 - 06:48:36 CST)
Changing Nvidia driver Christian Wohlschlager (Tue Nov 17 2009 - 02:46:23 CST)
VMD video-projection in 3D Nicolas Floquet (Mon Nov 16 2009 - 08:08:49 CST)
- Re: VMD video-projection in 3D John Stone (Mon Nov 16 2009 - 15:22:41 CST)
Error: failed on end of segment with RBCG Francesco Pietra (Sun Nov 15 2009 - 03:18:57 CST)
- Re: Error: failed on end of segment with RBCG Peter Freddolino (Sun Nov 15 2009 - 08:46:47 CST)
Multiseq question Tomek Wlodarski (Sat Nov 14 2009 - 08:02:43 CST)
- Re: Multiseq question John Stone (Mon Nov 16 2009 - 15:28:45 CST)
  - Re: Multiseq question Tomek Wlodarski (Mon Nov 23 2009 - 05:43:14 CST)
    - Re: Multiseq question Boris Steipe (Mon Nov 23 2009 - 09:48:34 CST)
    - Re: Multiseq question Tomek Wlodarski (Tue Nov 24 2009 - 05:17:59 CST)
parent molecule sarah k (Fri Nov 13 2009 - 23:59:28 CST)
- Re: parent molecule Joshua Adelman (Sat Nov 14 2009 - 07:47:23 CST)
  - Re: parent molecule Joshua Adelman (Sun Nov 15 2009 - 07:06:58 CST)
  - Re: parent molecule Joshua Adelman (Wed Nov 18 2009 - 11:43:00 CST)
(no subject) Francesco Pietra (Fri Nov 13 2009 - 03:23:21 CST)
- Re: J. Rui Rodrigues (Fri Nov 13 2009 - 06:13:52 CST)
  - Re: John Stone (Fri Nov 13 2009 - 08:19:04 CST)
version 1.8.7 for amd64 and cg tools Francesco Pietra (Thu Nov 12 2009 - 23:15:31 CST)
- Re: version 1.8.7 for amd64 and cg tools John Stone (Thu Nov 12 2009 - 23:20:18 CST)
  - Re: version 1.8.7 for amd64 and cg tools Francesco Pietra (Fri Nov 13 2009 - 00:02:43 CST)
- Fwd: version 1.8.7 for amd64 and cg tools Francesco Pietra (Thu Nov 12 2009 - 23:33:42 CST)
  - Re: Fwd: version 1.8.7 for amd64 and cg tools John Stone (Thu Nov 12 2009 - 23:40:32 CST)
PBCTools-problem getting unitcell parameters A D (Thu Nov 12 2009 - 19:40:31 CST)
- Re: PBCTools-problem getting unitcell parameters Axel Kohlmeyer (Thu Nov 12 2009 - 20:25:30 CST)
problems displaying newcartoon representation Robert Meklemburg (Thu Nov 12 2009 - 11:17:19 CST)
- Re: problems displaying newcartoon representation John Stone (Thu Nov 12 2009 - 12:24:42 CST)
- Re: problems displaying newcartoon representation Axel Kohlmeyer (Thu Nov 12 2009 - 12:09:16 CST)
  - Re: problems displaying newcartoon representation Joseph Bylund (Thu Nov 12 2009 - 12:43:24 CST)
Stop using directory from previous session J. Rui Rodrigues (Wed Nov 11 2009 - 10:54:01 CST)
- Re: Stop using directory from previous session John Stone (Wed Nov 11 2009 - 11:13:36 CST)
  - Re: Stop using directory from previous session J. Rui Rodrigues (Wed Nov 11 2009 - 11:51:38 CST)
  - Re: Stop using directory from previous session J. Rui Rodrigues (Wed Nov 11 2009 - 11:57:37 CST)
    - Re: Stop using directory from previous session John Stone (Wed Nov 11 2009 - 12:38:08 CST)
vmd bug in ubuntu 9.10 ChoiHeeSung (Wed Nov 11 2009 - 10:53:04 CST)
- Re: vmd bug in ubuntu 9.10 John Stone (Wed Nov 11 2009 - 11:15:09 CST)
- Re: vmd bug in ubuntu 9.10 Ale Gomez (Wed Nov 11 2009 - 17:56:44 CST)
- Re: vmd bug in ubuntu 9.10 Olaf Lenz (Thu Nov 12 2009 - 02:06:03 CST)
  - Re: vmd bug in ubuntu 9.10 Olaf Lenz (Thu Nov 12 2009 - 02:28:14 CST)
bad_alloc error Gustavo Gust (Wed Nov 11 2009 - 09:04:34 CST)
- Re: bad_alloc error John Stone (Wed Nov 11 2009 - 09:20:20 CST)
  - Re: bad_alloc error Gustavo Gust (Wed Nov 11 2009 - 09:58:01 CST)
paratool and fatal error sarah k (Tue Nov 10 2009 - 23:27:33 CST)
Problem with exit button Nuno Sousa Cerqueira (Tue Nov 10 2009 - 04:55:24 CST)
- Re: Problem with exit button John Stone (Tue Nov 10 2009 - 16:33:36 CST)
  - Re: Problem with exit button Nuno Sousa Cerqueira (Tue Nov 10 2009 - 18:14:12 CST)
    - Re: Problem with exit button John Stone (Tue Nov 10 2009 - 18:41:04 CST)
CG Builder Francesco Pietra (Mon Nov 09 2009 - 14:06:44 CST)
- Re: CG Builder Roman Petrenko (Mon Nov 09 2009 - 15:01:26 CST)
plugin for reading (and writing) trajectories with a varying number of atoms Axel Kohlmeyer (Fri Nov 06 2009 - 14:51:02 CST)
Question about Keyboaerd events send from other PC Christian Wohlschlager (Thu Nov 05 2009 - 02:29:36 CST)
- Re: Question about Keyboaerd events send from other PC John Stone (Thu Nov 05 2009 - 08:46:50 CST)
rmsd calculation and plot sarah k (Tue Nov 03 2009 - 23:18:29 CST)
- Re: rmsd calculation and plot John Stone (Tue Nov 10 2009 - 16:25:00 CST)
  - Re: rmsd calculation and plot sarah k (Tue Nov 10 2009 - 23:20:06 CST)
radius of gyration units Bernardo Sosa Padilla Araujo (Tue Nov 03 2009 - 15:08:36 CST)
- Re: radius of gyration units Leonardo Trabuco (Tue Nov 03 2009 - 15:13:19 CST)
  - Re: radius of gyration units Roman Petrenko (Tue Nov 03 2009 - 15:59:54 CST)
Matrix: Warning: no convergence (0.00000000<390.26229858 after 1000 iterations). Bob Johnson (Tue Nov 03 2009 - 14:49:29 CST)
- Re: Matrix: Warning: no convergence (0.00000000<390.26229858 after 1000 iterations). John Stone (Tue Nov 03 2009 - 16:18:43 CST)
Control of aminoacid ionization in VMD Luis Agullo (LAB) (Tue Nov 03 2009 - 04:50:55 CST)
- Re: Control of aminoacid ionization in VMD L. Michel Espinoza-Fonseca (Tue Nov 03 2009 - 05:24:46 CST)
  - Re: Control of aminoacid ionization in VMD Luis Agullo (LAB) (Thu Nov 05 2009 - 02:24:26 CST)
VMD autopsfgen and Mg2+ Luis Agullo (LAB) (Tue Nov 03 2009 - 04:17:59 CST)
- Re: VMD autopsfgen and Mg2+ John Stone (Wed Nov 04 2009 - 09:49:17 CST)
- Re: VMD autopsfgen and Mg2+ Peter Freddolino (Thu Nov 05 2009 - 09:03:44 CST)
running under Shell using VMD Nuno Sousa Cerqueira (Tue Nov 03 2009 - 02:29:30 CST)
- Re: running under Shell using VMD Nicolas Sapay (Tue Nov 03 2009 - 05:07:45 CST)
  - Re: running under Shell using VMD Nuno Sousa Cerqueira (Tue Nov 03 2009 - 07:41:11 CST)
    - Re: running under Shell using VMD John Stone (Tue Nov 03 2009 - 09:11:05 CST)
- Re: running under Shell using VMD Axel Kohlmeyer (Tue Nov 03 2009 - 21:43:33 CST)
memory issues Paymon Pirzadeh (Mon Nov 02 2009 - 12:02:14 CST)
- Re: memory issues John Stone (Mon Nov 02 2009 - 13:50:12 CST)
Using Tcl functions in a C-plugin Olaf Lenz (Mon Nov 02 2009 - 07:29:24 CST)
- Re: Using Tcl functions in a C-plugin John Stone (Mon Nov 02 2009 - 14:08:27 CST)
  - Re: Using Tcl functions in a C-plugin Olaf Lenz (Mon Nov 02 2009 - 14:57:49 CST)
movie rendering Liang, Linus H. (Mon Nov 02 2009 - 07:08:35 CST)
- Re: movie rendering John Stone (Mon Nov 02 2009 - 13:54:09 CST)
dll by c++ cannot be recognized by VMD tk console ? vmd_chcwaaa (Sun Nov 01 2009 - 01:32:42 CDT)
- Re: dll by c++ cannot be recognized by VMD tk console ? John Stone (Mon Nov 02 2009 - 13:57:35 CST)
full version OEM soft chucruz_at_ks.uiuc.edu (Thu Oct 29 2009 - 23:14:25 CDT)
Downloadable version chucruz_at_ks.uiuc.edu (Thu Oct 29 2009 - 02:51:04 CDT)
RBCG bead diameter Christine Horejs (Wed Oct 28 2009 - 11:54:50 CDT)
- Re: RBCG bead diameter Axel Kohlmeyer (Sat Oct 31 2009 - 14:42:05 CDT)
abnormal water surface after nvt and npt for POPC membrane pxq ÅÓÑ©ÇÛ (Tue Oct 27 2009 - 19:57:58 CDT)
- Re: namd-l: abnormal water surface after nvt and npt for POPC membrane Axel Kohlmeyer (Wed Oct 28 2009 - 10:55:16 CDT)
Unable to find Stride output file: /usr/tmp/... Bob Johnson (Tue Oct 27 2009 - 12:22:03 CDT)
- Re: Unable to find Stride output file: /usr/tmp/... John Stone (Tue Oct 27 2009 - 12:37:28 CDT)
  - Re: Unable to find Stride output file: /usr/tmp/... Bob Johnson (Tue Oct 27 2009 - 12:42:06 CDT)
lammpstrj file as pdb Christine Horejs (Tue Oct 27 2009 - 11:50:06 CDT)
- Re: lammpstrj file as pdb John Stone (Tue Oct 27 2009 - 12:06:56 CDT)
  - Re: lammpstrj file as pdb Christine Horejs (Tue Oct 27 2009 - 12:18:15 CDT)
    - Re: lammpstrj file as pdb John Stone (Tue Oct 27 2009 - 12:21:49 CDT)
Tachyon Rendering daniel aguayo (Tue Oct 27 2009 - 10:27:52 CDT)
- Re: Tachyon Rendering Axel Kohlmeyer (Tue Oct 27 2009 - 11:23:48 CDT)
  - Re: Tachyon Rendering John Stone (Tue Oct 27 2009 - 12:05:06 CDT)
    - Re: Tachyon Rendering daniel aguayo (Tue Oct 27 2009 - 14:14:55 CDT)
RBCG Model Katherine Parra (Tue Oct 27 2009 - 09:19:55 CDT)
order parameters for long lipids Raul Araya (Tue Oct 27 2009 - 08:47:38 CDT)
pbwithin and within differences Gustavo Gust (Tue Oct 27 2009 - 06:48:51 CDT)
- Re: pbwithin and within differences Olaf Lenz (Tue Oct 27 2009 - 08:26:08 CDT)
- Re: pbwithin and within differences Roman Petrenko (Tue Oct 27 2009 - 09:09:36 CDT)
Solvate-GUI Problem: Collapses Solvent to Origin Joshua Adelman (Mon Oct 26 2009 - 20:03:37 CDT)
- Re: Solvate-GUI Problem: Collapses Solvent to Origin Peter Freddolino (Mon Oct 26 2009 - 21:31:23 CDT)
using NAMD with SPC water politr_at_huji.ac.il (Mon Oct 26 2009 - 07:48:26 CDT)
- Re: using NAMD with SPC water Axel Kohlmeyer (Mon Oct 26 2009 - 08:48:24 CDT)
  - Re: using NAMD with SPC water L. Michel Espinoza-Fonseca (Mon Oct 26 2009 - 09:40:33 CDT)
unparameterized residue sarah k (Sun Oct 25 2009 - 02:24:21 CDT)
VMD and Intel X3100 GPU Mohd Farid Ismail (Sat Oct 24 2009 - 16:27:38 CDT)
- Re: VMD and Intel X3100 GPU Axel Kohlmeyer (Sat Oct 24 2009 - 17:28:33 CDT)
  - Re: VMD and Intel X3100 GPU Mohd Farid Ismail (Sat Oct 24 2009 - 21:18:49 CDT)
Loading trajectory into Multiseq stephane acoca (Fri Oct 23 2009 - 18:07:02 CDT)
- Re: Loading trajectory into Multiseq John Stone (Mon Oct 26 2009 - 10:22:21 CDT)
Selections based on "bonded to" Schmidt, Mike (Fri Oct 23 2009 - 10:56:00 CDT)
- Re: Selections based on "bonded to" John Stone (Fri Oct 23 2009 - 11:13:51 CDT)
  - Re: Selections based on "bonded to" John Stone (Fri Oct 23 2009 - 13:39:08 CDT)
Bugs ? Representation window does not update new material TRINH Minh Hieu (Fri Oct 23 2009 - 08:57:49 CDT)
- Re: Bugs ? Representation window does not update new material John Stone (Fri Oct 23 2009 - 09:56:47 CDT)
  - Re: Bugs ? Representation window does not update new material TRINH Minh Hieu (Fri Oct 23 2009 - 10:52:39 CDT)
    - Re: Bugs ? Representation window does not update new material John Stone (Fri Oct 23 2009 - 11:06:20 CDT)
Cuda an a cluster ? Christian Wohlschlager (Thu Oct 22 2009 - 02:56:18 CDT)
- Re: Cuda an a cluster ? John Stone (Thu Oct 22 2009 - 11:04:45 CDT)
  - Antw: Re: Cuda an a cluster ? Christian Wohlschlager (Fri Oct 23 2009 - 00:20:59 CDT)
Problem with vmd and ssh -X Thomas Lemmin (Thu Oct 22 2009 - 02:51:44 CDT)
- Re: Problem with vmd and ssh -X Thomas Lemmin (Thu Oct 22 2009 - 06:39:16 CDT)
- Re: Problem with vmd and ssh -X John Stone (Thu Oct 22 2009 - 10:58:34 CDT)
  - Re: Problem with vmd and ssh -X Thomas Lemmin (Fri Oct 23 2009 - 07:22:28 CDT)
    - Re: Problem with vmd and ssh -X John Stone (Fri Oct 23 2009 - 09:52:29 CDT)
Input File Format Arian Arian (Wed Oct 21 2009 - 14:03:01 CDT)
- Re: Input File Format Axel Kohlmeyer (Wed Oct 21 2009 - 14:52:05 CDT)
questions Umesh Ghoshdastider (Wed Oct 21 2009 - 11:56:24 CDT)
- Re: questions Axel Kohlmeyer (Wed Oct 21 2009 - 13:03:57 CDT)
- Re: questions John Stone (Wed Oct 21 2009 - 16:50:06 CDT)
bond connectivity not displayed in VMD Elias Ahadi (Wed Oct 21 2009 - 11:36:39 CDT)
- Re: bond connectivity not displayed in VMD Axel Kohlmeyer (Wed Oct 21 2009 - 12:58:15 CDT)
Atom sorting according to resid andrea carotti (Wed Oct 21 2009 - 10:16:33 CDT)
- Re: Atom sorting according to resid Axel Kohlmeyer (Wed Oct 21 2009 - 11:21:58 CDT)
Direct manipulation of the camera poker_at_physics.usyd.edu.au (Wed Oct 21 2009 - 00:21:57 CDT)
- Re: Direct manipulation of the camera poker_at_physics.usyd.edu.au (Wed Oct 21 2009 - 03:26:59 CDT)
X server is not capable of displaying double RGB images with a Z buffer Ma.Busch (Tue Oct 20 2009 - 04:09:40 CDT)
- Re: X server is not capable of displaying double RGB images with a Z buffer Axel Kohlmeyer (Tue Oct 20 2009 - 10:40:59 CDT)
Translating an atom along a specific direction and saving the pdb files priyodorshi satpati (Tue Oct 20 2009 - 04:08:12 CDT)
- Re: Translating an atom along a specific direction and saving the pdb files John Stone (Tue Oct 20 2009 - 09:39:48 CDT)
  - Re: Translating an atom along a specific direction and saving the pdb files Axel Kohlmeyer (Tue Oct 20 2009 - 10:38:17 CDT)
glycerol AyÅŸe Ã–zlem Aykut (Tue Oct 20 2009 - 03:13:57 CDT)
NAMD can't malloc() error Ronald Salesky (Mon Oct 19 2009 - 12:44:55 CDT)
- Re: NAMD can't malloc() error Axel Kohlmeyer (Mon Oct 19 2009 - 13:29:20 CDT)
Arbitrary values of isosurface aizoon_at_gmx.net (Mon Oct 19 2009 - 06:25:32 CDT)
- Re: Arbitrary values of isosurface Axel Kohlmeyer (Mon Oct 19 2009 - 08:58:17 CDT)
- Re: Arbitrary values of isosurface John Stone (Thu Oct 22 2009 - 17:10:14 CDT)
paratool: unable to load optimized geometry Stanislaw Bobritsky (Mon Oct 19 2009 - 03:21:33 CDT)
- Re: paratool: unable to load optimized geometry Axel Kohlmeyer (Mon Oct 19 2009 - 08:51:46 CDT)
- Re: paratool: unable to load optimized geometry JC Gumbart (Mon Oct 19 2009 - 12:15:56 CDT)
Calculate Free Volume? YingZhe (Sun Oct 18 2009 - 20:07:30 CDT)
- Re: Calculate Free Volume? Axel Kohlmeyer (Mon Oct 19 2009 - 08:59:32 CDT)
Question about running tcl/tk script without graphic interface (vmd option -dispdev none ...) Alberto Sergio Garay (Fri Oct 16 2009 - 17:48:04 CDT)
- Re: Question about running tcl/tk script without graphic interface (vmd option -dispdev none ...) Axel Kohlmeyer (Fri Oct 16 2009 - 18:25:07 CDT)
MDFF sim Problem Joshua Adelman (Fri Oct 16 2009 - 16:20:03 CDT)
- Re: MDFF sim Problem Leonardo Trabuco (Sat Oct 17 2009 - 15:26:03 CDT)
  - Re: MDFF sim Problem Joshua Adelman (Sun Oct 18 2009 - 22:19:28 CDT)
Re: Align membrane Ramya Gamini (Fri Oct 16 2009 - 15:02:57 CDT)
- Re: Align membrane Ale Gomez (Fri Oct 16 2009 - 19:18:41 CDT)
Align membrane Ale Gomez (Fri Oct 16 2009 - 13:24:48 CDT)
vmd mailing list Roman Petrenko (Thu Oct 15 2009 - 17:14:10 CDT)
- Re: vmd mailing list Benjamin Bouvier (Fri Oct 16 2009 - 03:46:43 CDT)
Re: Water Sphere Solvation Peter Murphy (Tue Oct 13 2009 - 16:54:45 CDT)
- Re: Re: Water Sphere Solvation Axel Kohlmeyer (Sun Oct 18 2009 - 09:25:30 CDT)
Problems with selecting atoms for representations Joseph Bylund (Tue Oct 13 2009 - 10:39:52 CDT)
- Re: Problems with selecting atoms for representations Axel Kohlmeyer (Tue Oct 13 2009 - 11:29:09 CDT)
writing gromacs .trr format with nonorthorhomic cells Matt Watkins (Tue Oct 13 2009 - 07:05:27 CDT)
- Re: writing gromacs .trr format with nonorthorhomic cells Axel Kohlmeyer (Tue Oct 13 2009 - 08:59:59 CDT)
  - Re: writing gromacs .trr format with nonorthorhomic cells Matt Watkins (Tue Oct 13 2009 - 11:48:27 CDT)
FW: Disulfide bonds Andres Morales N (Tue Oct 13 2009 - 01:02:30 CDT)
- Re: FW: Disulfide bonds Pavan Ghatty (Mon Oct 19 2009 - 10:55:24 CDT)
Disulfude bonds Andres Morales N (Tue Oct 13 2009 - 01:00:39 CDT)
- Re: Disulfude bonds Schreiner Eduard (Tue Oct 13 2009 - 01:12:23 CDT)
- RE: Disulfude bonds JC Gumbart (Tue Oct 13 2009 - 01:08:13 CDT)
  - RE: Disulfude bonds JC Gumbart (Tue Oct 13 2009 - 01:20:11 CDT)
colour residues Christine Horejs (Mon Oct 12 2009 - 17:58:31 CDT)
- Re: colour residues Eric H. Lee (Mon Oct 12 2009 - 18:26:11 CDT)
  - Re: colour residues Leonardo Trabuco (Mon Oct 12 2009 - 18:56:31 CDT)
- Re: colour residues Axel Kohlmeyer (Mon Oct 12 2009 - 19:05:13 CDT)
  - Re: colour residues Eric H. Lee (Mon Oct 12 2009 - 21:31:18 CDT)
covalently bonded atoms politr_at_huji.ac.il (Mon Oct 12 2009 - 11:11:22 CDT)
- Re: covalently bonded atoms Axel Kohlmeyer (Mon Oct 12 2009 - 12:41:31 CDT)
catdcd Katherine Parra (Mon Oct 12 2009 - 09:59:23 CDT)
- Re: catdcd Axel Kohlmeyer (Mon Oct 12 2009 - 10:43:42 CDT)
  - Re: catdcd John Stone (Fri Oct 23 2009 - 13:44:52 CDT)
- Re: catdcd Eric H. Lee (Mon Oct 12 2009 - 10:05:09 CDT)
format of pdb file Christine Horejs (Mon Oct 12 2009 - 09:04:51 CDT)
- Re: format of pdb file Axel Kohlmeyer (Mon Oct 12 2009 - 10:10:06 CDT)
Load struture form memory Nuno Sousa Cerqueira (Mon Oct 12 2009 - 06:06:47 CDT)
- Re: Load struture form memory Axel Kohlmeyer (Mon Oct 12 2009 - 08:35:22 CDT)
Lipid Membrane Ale Gomez (Sun Oct 11 2009 - 22:58:08 CDT)
- Re: Lipid Membrane Axel Kohlmeyer (Mon Oct 12 2009 - 08:39:20 CDT)
mac tk widgets Nuno Sousa Cerqueira (Sat Oct 10 2009 - 21:13:15 CDT)
- Re: mac tk widgets John Stone (Mon Oct 12 2009 - 15:55:19 CDT)
  - Re: mac tk widgets Nuno Sousa Cerqueira (Mon Oct 12 2009 - 15:58:03 CDT)
VMD 1.8.7 CUDA on Mac OS X 10.6.1 Mengjuei Hsieh (Sat Oct 10 2009 - 18:23:52 CDT)
- Re: VMD 1.8.7 CUDA on Mac OS X 10.6.1 John Stone (Mon Oct 12 2009 - 15:36:23 CDT)
  - Re: VMD 1.8.7 CUDA on Mac OS X 10.6.1 Mengjuei Hsieh (Mon Oct 12 2009 - 19:23:08 CDT)
Parameter file for protein siloxane interactions Nilesh Ingle (Thu Oct 08 2009 - 21:47:14 CDT)
Problem using psfgen and carbohydrate charmm parameters. Alexandre Suman de Araujo (Thu Oct 08 2009 - 16:19:26 CDT)
- Re: Problem using psfgen and carbohydrate charmm parameters. John Stone (Mon Oct 12 2009 - 15:50:56 CDT)
how to display the periodic box in VMD Lan He (Wed Oct 07 2009 - 17:51:41 CDT)
- Re: how to display the periodic box in VMD Axel Kohlmeyer (Wed Oct 07 2009 - 18:39:55 CDT)
  - Re: how to display the periodic box in VMD Olaf Lenz (Thu Oct 08 2009 - 02:03:54 CDT)
CatDCD Desmond Support andrea carotti (Wed Oct 07 2009 - 10:31:53 CDT)
- Re: CatDCD Desmond Support John Stone (Wed Oct 07 2009 - 13:24:00 CDT)
- Re: CatDCD Desmond Support John Stone (Fri Oct 23 2009 - 13:44:15 CDT)
How to generate a monolayer in VMD Nilesh Ingle (Mon Oct 05 2009 - 18:55:37 CDT)
- Re: How to generate a monolayer in VMD Leandro Martínez (Mon Oct 05 2009 - 19:24:44 CDT)
  - Re: How to generate a monolayer in VMD John Stone (Mon Oct 05 2009 - 20:54:03 CDT)
How to translate my diffused protein back to COM? A D (Mon Oct 05 2009 - 18:20:15 CDT)
- Re: How to translate my diffused protein back to COM? Axel Kohlmeyer (Mon Oct 05 2009 - 20:31:13 CDT)
Tracking atoms automatically Nanako Takahashi (Mon Oct 05 2009 - 11:52:37 CDT)
- Re: Tracking atoms automatically Axel Kohlmeyer (Mon Oct 05 2009 - 13:24:17 CDT)
  - Re: Tracking atoms automatically Nanako Takahashi (Tue Oct 06 2009 - 13:03:16 CDT)
distance of two center of mass Nicola Giacche' (Mon Oct 05 2009 - 04:36:37 CDT)
- Re: distance of two center of mass Axel Kohlmeyer (Mon Oct 05 2009 - 06:04:33 CDT)
Breaking a trajectory into separate files with tcl Patrick Redmill (Sun Oct 04 2009 - 21:48:27 CDT)
- Re: Breaking a trajectory into separate files with tcl Schreiner Eduard (Sun Oct 04 2009 - 22:06:21 CDT)
  - Re: Breaking a trajectory into separate files with tcl Axel Kohlmeyer (Mon Oct 05 2009 - 01:41:49 CDT)
    - Re: Breaking a trajectory into separate files with tcl Patrick Redmill (Mon Oct 05 2009 - 05:41:39 CDT)
R.E.D.-III.3 tools release - q4md-forcefieldtools.org FyD (Sun Oct 04 2009 - 09:37:06 CDT)
problem with psfgen Q=C5=CC=C1=CC=CF=D7_=E9=CC=D8=D1?= (Sat Oct 03 2009 - 05:35:24 CDT)
Problems with Stride Martin K. Jones (Fri Oct 02 2009 - 12:18:41 CDT)
- Re: Problems with Stride Axel Kohlmeyer (Fri Oct 02 2009 - 13:06:45 CDT)
  - RE: Problems with Stride Martin K. Jones (Fri Oct 02 2009 - 13:16:54 CDT)
- Re: Problems with Stride John Stone (Fri Oct 02 2009 - 16:22:26 CDT)
Rx for VMD crashing PC? Ronald Salesky (Thu Oct 01 2009 - 21:57:00 CDT)
- Re: Rx for VMD crashing PC? John Stone (Fri Oct 02 2009 - 10:26:13 CDT)
  - Re: Rx for VMD crashing PC? Ronald Salesky (Fri Oct 02 2009 - 11:42:51 CDT)
  - Re: Rx for VMD crashing PC? MyLinkka (Mon Oct 05 2009 - 17:40:16 CDT)
    - Re: Rx for VMD crashing PC? John Stone (Mon Oct 05 2009 - 20:46:10 CDT)
how to load an external file to user field Sun Yicheng (Thu Oct 01 2009 - 10:28:39 CDT)
- Re: how to load an external file to user field Axel Kohlmeyer (Thu Oct 01 2009 - 16:12:41 CDT)
multiseq and fasta files from pdb Vlad Cojocaru (Thu Oct 01 2009 - 04:26:01 CDT)
- Re: multiseq and fasta files from pdb John Stone (Mon Oct 05 2009 - 21:14:10 CDT)
Reading output of quantum packages and plotting orbitals Ignacio Fernández Galván (Wed Sep 30 2009 - 11:57:35 CDT)
- Re: Reading output of quantum packages and plotting orbitals Axel Kohlmeyer (Wed Sep 30 2009 - 17:38:26 CDT)
  - Re: Reading output of quantum packages and plotting orbitals Ignacio Fernández Galván (Fri Oct 02 2009 - 03:01:36 CDT)
namd2.7b1, tip4p, and dummies Edward Lyman (Wed Sep 30 2009 - 01:36:06 CDT)
trace cartoon etc displaying incompletely after alignment Rahul Mahajan (Tue Sep 29 2009 - 21:23:53 CDT)
- Re: trace cartoon etc displaying incompletely after alignment mirandaisbest (Fri Oct 02 2009 - 10:18:56 CDT)
- Re: trace cartoon etc displaying incompletely after alignment Yi Shang (Fri Oct 02 2009 - 10:39:21 CDT)
Representation problem Ahmet Bakan (Mon Sep 28 2009 - 16:22:36 CDT)
- Re: Representation problem John Stone (Mon Sep 28 2009 - 16:34:18 CDT)
  - Re: Representation problem Ahmet Bakan (Tue Sep 29 2009 - 09:42:41 CDT)
    - Re: Representation problem John Stone (Tue Sep 29 2009 - 17:38:21 CDT)
    - Re: Representation problem Ahmet Bakan (Thu Oct 15 2009 - 12:16:26 CDT)
model protein chain not displayed properly Elias Ahadi (Mon Sep 28 2009 - 13:38:32 CDT)
- Re: model protein chain not displayed properly Benjamin Bouvier (Mon Sep 28 2009 - 14:54:09 CDT)
- Re: model protein chain not displayed properly John Stone (Mon Sep 28 2009 - 15:08:22 CDT)
H_Bonds Katherine Parra (Mon Sep 28 2009 - 12:53:21 CDT)
- Re: H_Bonds Axel Kohlmeyer (Mon Sep 28 2009 - 14:16:12 CDT)
Return value of a vector Stephanie Held (Mon Sep 28 2009 - 08:39:27 CDT)
- Re: Return value of a vector Axel Kohlmeyer (Mon Sep 28 2009 - 09:35:25 CDT)
  - Re: Return value of a vector Stephanie Held (Mon Sep 28 2009 - 09:57:08 CDT)
user field Sun Yicheng (Mon Sep 28 2009 - 08:36:34 CDT)
- Re: user field Axel Kohlmeyer (Mon Sep 28 2009 - 09:28:03 CDT)
text timer in vmd animations maria goranovic (Mon Sep 28 2009 - 04:57:16 CDT)
- Re: text timer in vmd animations Axel Kohlmeyer (Mon Sep 28 2009 - 09:30:19 CDT)
  - Re: text timer in vmd animations maria goranovic (Mon Sep 28 2009 - 09:55:02 CDT)
Paratool: QMTool::bondlist error message Sebastian Stolzenberg (Fri Sep 25 2009 - 21:53:27 CDT)
- Re: Paratool: QMTool::bondlist error message John Stone (Fri Sep 25 2009 - 22:09:51 CDT)
Overlaying 2 structures madura_at_duq.edu (Fri Sep 25 2009 - 15:55:05 CDT)
- Re: Overlaying 2 structures John Stone (Fri Sep 25 2009 - 22:17:31 CDT)
ERROR) Error reading bond information. Luca Gelisio (Fri Sep 25 2009 - 05:40:17 CDT)
- Re: ERROR) Error reading bond information. John Stone (Fri Sep 25 2009 - 07:41:11 CDT)
  - Re: ERROR) Error reading bond information. Luca Gelisio (Fri Sep 25 2009 - 09:10:23 CDT)
- Re: ERROR) Error reading bond information. Axel Kohlmeyer (Fri Sep 25 2009 - 07:55:47 CDT)
  - Re: ERROR) Error reading bond information. Luca Gelisio (Fri Sep 25 2009 - 09:03:41 CDT)
Frame creation Andreas Wagenmann (Thu Sep 24 2009 - 09:28:50 CDT)
- Re: Frame creation Axel Kohlmeyer (Thu Sep 24 2009 - 10:13:16 CDT)
  - Re: Frame creation Andreas Wagenmann (Fri Sep 25 2009 - 02:01:27 CDT)
    - Re: Frame creation Axel Kohlmeyer (Fri Sep 25 2009 - 05:14:03 CDT)
- Re: Frame creation John Stone (Thu Sep 24 2009 - 10:02:58 CDT)
problem in reading .nc NETCDF FILE Genform GK (Wed Sep 23 2009 - 23:02:10 CDT)
- Re: problem in reading .nc NETCDF FILE John Stone (Thu Sep 24 2009 - 08:18:59 CDT)
  - Re: problem in reading .nc NETCDF FILE Genform GK (Fri Sep 25 2009 - 00:21:15 CDT)
Web-based Flash/Quicktime 3-D VMD/Tachyon renderings of PDB structures John Stone (Wed Sep 23 2009 - 15:45:30 CDT)
double bonds Taufik Al-Sarraj (Wed Sep 23 2009 - 13:13:12 CDT)
- Re: double bonds John Stone (Wed Sep 23 2009 - 13:17:09 CDT)
trajectory analysis Barry Bickmore (Wed Sep 23 2009 - 11:39:08 CDT)
"Lines" representation does not show Martin Lep¹ík (Wed Sep 23 2009 - 10:49:33 CDT)
- Re: "Lines" representation does not show John Stone (Wed Sep 23 2009 - 11:03:05 CDT)
  - Re: "Lines" representation does not show Martin Lepsik (Thu Sep 24 2009 - 05:16:09 CDT)
atom selection Myunggi Yi (Mon Sep 21 2009 - 13:45:20 CDT)
- Re: atom selection Myunggi Yi (Mon Sep 21 2009 - 13:57:29 CDT)
  - Re: atom selection Myunggi Yi (Mon Sep 21 2009 - 14:02:49 CDT)
    - double bonds Taufik Al-Sarraj (Wed Sep 23 2009 - 12:22:27 CDT)
    - Re: double bonds J. Rui Rodrigues (Thu Sep 24 2009 - 07:22:09 CDT)
- Re: atom selection Axel Kohlmeyer (Mon Sep 21 2009 - 14:22:08 CDT)
[carlos.simmerling@gmail.com: ACS awards application announcements] John Stone (Mon Sep 21 2009 - 12:54:04 CDT)
Resize window from TCL Ondrej Marsalek (Mon Sep 21 2009 - 11:51:46 CDT)
- Re: Resize window from TCL Axel Kohlmeyer (Mon Sep 21 2009 - 13:08:14 CDT)
- Re: Resize window from TCL John Stone (Mon Sep 21 2009 - 12:48:08 CDT)
  - Re: Resize window from TCL Ondrej Marsalek (Mon Sep 21 2009 - 12:52:02 CDT)
automated loading Myunggi Yi (Mon Sep 21 2009 - 10:27:58 CDT)
- Re: automated loading Myunggi Yi (Mon Sep 21 2009 - 11:01:19 CDT)
  - Re: Re: automated loading John Stone (Mon Sep 21 2009 - 11:17:21 CDT)
    - Re: Re: automated loading Myunggi Yi (Mon Sep 21 2009 - 11:53:53 CDT)
- Re: automated loading Axel Kohlmeyer (Mon Sep 21 2009 - 11:18:17 CDT)
problem with density map obtained by volmap Ana Célia Vila Verde (Sun Sep 20 2009 - 08:01:12 CDT)
- Re: problem with density map obtained by volmap Axel Kohlmeyer (Sun Sep 20 2009 - 13:44:03 CDT)
Velocity Auto Correlation Goutham (Fri Sep 18 2009 - 14:53:42 CDT)
- Re: Velocity Auto Correlation Axel Kohlmeyer (Fri Sep 18 2009 - 15:36:45 CDT)
  - Re: Velocity Auto Correlation Goutham (Fri Sep 18 2009 - 15:52:44 CDT)
  - Re: Velocity Auto Correlation Axel Kohlmeyer (Thu Sep 24 2009 - 09:30:33 CDT)
water molecules around proteins Katherine Parra (Fri Sep 18 2009 - 12:04:04 CDT)
- Re: water molecules around proteins Thomas Evangelidis (Sat Sep 19 2009 - 09:04:36 CDT)
  - Re: water molecules around proteins Axel Kohlmeyer (Sat Sep 19 2009 - 09:55:57 CDT)
    - Re: water molecules around proteins Florentina Tofoleanu (Wed Mar 10 2010 - 16:27:37 CST)
    - Re: water molecules around proteins Axel Kohlmeyer (Wed Mar 10 2010 - 17:41:03 CST)
  - Re: water molecules around proteins Axel Kohlmeyer (Thu Mar 11 2010 - 11:51:01 CST)
    - Re: water molecules around proteins Florentina Tofoleanu (Thu Mar 11 2010 - 14:54:57 CST)
    - Re: water molecules around proteins Axel Kohlmeyer (Fri Mar 12 2010 - 09:20:07 CST)
Install VMD binary with CUDA, CUDA card detected but then error "no CUDA-capable device is available" Jim Parker (Thu Sep 17 2009 - 19:33:51 CDT)
- Re: Install VMD binary with CUDA, CUDA card detected but then error "no CUDA-capable device is available" John Stone (Thu Sep 17 2009 - 21:34:36 CDT)
  - Re: Install VMD binary with CUDA, CUDA card detected but then error "no CUDA-capable device is available"--Solved Jim Parker (Sun Oct 11 2009 - 21:31:05 CDT)
    - Re: Install VMD binary with CUDA, CUDA card detected but then error "no CUDA-capable device is available"--Solved John Stone (Sun Oct 11 2009 - 22:43:17 CDT)
Installing Multiseq updates Jeremias Corradi (Thu Sep 17 2009 - 08:42:51 CDT)
- Re: Installing Multiseq updates Kirby Vandivort (Thu Sep 17 2009 - 10:44:07 CDT)
  - Re: Installing Multiseq updates Kirby Vandivort (Thu Sep 17 2009 - 11:54:44 CDT)
  - Re: Installing Multiseq updates Jeremias Corradi (Sat Sep 19 2009 - 11:10:11 CDT)
    - Re: Installing Multiseq updates Jeremias Corradi (Tue Sep 22 2009 - 14:24:43 CDT)
Average structure and NamdEnergy Andres Morales N (Thu Sep 17 2009 - 00:03:36 CDT)
- Re: Average structure and NamdEnergy John Stone (Thu Sep 17 2009 - 11:35:58 CDT)
Install VMD with plugins to NAMD Jim Parker (Wed Sep 16 2009 - 21:44:31 CDT)
- Re: Install VMD with plugins to NAMD John Stone (Wed Sep 16 2009 - 22:04:35 CDT)
  - Re: Install VMD with plugins to NAMD Jim Parker (Wed Sep 16 2009 - 22:53:24 CDT)
DLP Stereo and VR toolkit integration with vmd Simon Su (Wed Sep 16 2009 - 16:04:25 CDT)
- Re: DLP Stereo and VR toolkit integration with vmd John Stone (Wed Sep 16 2009 - 16:10:38 CDT)
  - Re: DLP Stereo and VR toolkit integration with vmd Simon Su (Wed Sep 16 2009 - 16:29:22 CDT)
Average structure and NamdEnergy Andres Morales N (Wed Sep 16 2009 - 14:27:23 CDT)
Reading new amber prmtop formats. Crowley, Michael (Wed Sep 16 2009 - 12:21:42 CDT)
- Re: Reading new amber prmtop formats. Axel Kohlmeyer (Wed Sep 16 2009 - 13:28:37 CDT)
  - Re: Reading new amber prmtop formats. Thomas C. Bishop (Wed Sep 16 2009 - 15:37:17 CDT)
    - Re: Reading new amber prmtop formats. John Stone (Wed Sep 16 2009 - 16:08:07 CDT)
- Re: Reading new amber prmtop formats. John Stone (Wed Sep 16 2009 - 13:46:26 CDT)
- Re: Reading new amber prmtop formats. John Stone (Thu Sep 17 2009 - 12:50:48 CDT)
Re: segid WT100 is longer than 4 characters allowed by psf format Ramya Gamini (Wed Sep 16 2009 - 08:01:57 CDT)
segid WT100 is longer than 4 characters allowed by psf format Luca Gelisio (Wed Sep 16 2009 - 03:34:16 CDT)
PSF for AMBER top + crd files Goutham (Tue Sep 15 2009 - 16:35:23 CDT)
- Re: PSF for AMBER top + crd files John Stone (Tue Sep 15 2009 - 16:56:34 CDT)
- Re: PSF for AMBER top + crd files Axel Kohlmeyer (Tue Sep 15 2009 - 17:10:32 CDT)
rotate dihedral angle Jorgen Simonsen (Mon Sep 14 2009 - 14:08:21 CDT)
- Re: rotate dihedral angle Peter Freddolino (Mon Sep 14 2009 - 21:32:23 CDT)
  - Re: rotate dihedral angle Sebastian Stolzenberg (Wed Sep 16 2009 - 14:21:00 CDT)
CGTools error: atom select: cannot parse selection text... wuxiao (Mon Sep 14 2009 - 08:48:36 CDT)
- Re: CGTools error: atom select: cannot parse selection text... Kirby Vandivort (Mon Sep 14 2009 - 14:16:24 CDT)
  - Re: CGTools error: atom select: cannot parse selection text... Kirby Vandivort (Tue Sep 15 2009 - 11:32:35 CDT)
Segmentation fault on linux Fedora 11 Rob (Sun Sep 13 2009 - 19:16:28 CDT)
- Re: Segmentation fault on linux Fedora 11 John Stone (Mon Sep 14 2009 - 14:08:35 CDT)
  - Re: Segmentation fault on linux Fedora 11 Axel Kohlmeyer (Mon Sep 14 2009 - 14:45:02 CDT)
VMD and NetCDF under Windows Vista 32bit Jan F. Totz (Sun Sep 13 2009 - 01:57:02 CDT)
- Re: VMD and NetCDF under Windows Vista 32bit John Stone (Mon Sep 14 2009 - 14:10:54 CDT)
get coordinates Andres Morales N (Sat Sep 12 2009 - 12:05:35 CDT)
- Re: get coordinates Axel Kohlmeyer (Sat Sep 12 2009 - 13:01:35 CDT)
"measure fit" problem Yi Shang (Wed Sep 09 2009 - 13:31:17 CDT)
- Re: "measure fit" problem John Stone (Wed Sep 09 2009 - 13:34:18 CDT)
Mistakes in the 1.8.7 User guide Myunggi Yi (Wed Sep 09 2009 - 10:18:40 CDT)
- Re: Mistakes in the 1.8.7 User guide Myunggi Yi (Wed Sep 09 2009 - 13:20:21 CDT)
psf for CNT? Ronald Salesky (Wed Sep 09 2009 - 09:55:05 CDT)
- Re: psf for CNT? Axel Kohlmeyer (Wed Sep 09 2009 - 10:46:49 CDT)
Question about PSF generation NAMITA BHADRA (Tue Sep 08 2009 - 23:01:53 CDT)
- Re: Question about PSF generation John Stone (Thu Sep 10 2009 - 11:04:05 CDT)
  - Re: Question about PSF generation NAMITA BHADRA (Sun Sep 20 2009 - 08:50:18 CDT)
    - Re: Question about PSF generation Schreiner Eduard (Sun Sep 20 2009 - 12:04:52 CDT)
    - Re: Question about PSF generation Axel Kohlmeyer (Sun Sep 20 2009 - 13:34:12 CDT)
catdcd in Windows Wei Chen (Tue Sep 08 2009 - 21:44:25 CDT)
- Re: catdcd in Windows John Stone (Wed Sep 09 2009 - 13:38:54 CDT)
(no subject) Roshan Tasgaonkar (Tue Sep 08 2009 - 20:48:01 CDT)
- Re: Roman Petrenko (Wed Sep 09 2009 - 14:09:35 CDT)
  - Re: John Stone (Wed Sep 09 2009 - 14:14:58 CDT)
- Re: John Stone (Wed Sep 09 2009 - 14:14:08 CDT)
How to select a hetatom while get rid of N-term ACE in atomselect Sujata Sovani (Tue Sep 08 2009 - 17:47:43 CDT)
- Re: How to select a hetatom while get rid of N-term ACE in atomselect John Stone (Thu Sep 10 2009 - 10:56:08 CDT)
Main menu not compiled? Pieter van 't Hof (Fri Sep 04 2009 - 09:00:56 CDT)
- Re: Main menu not compiled? John Stone (Fri Sep 04 2009 - 09:27:33 CDT)
RE: namd-l: Re: rmsd matrix Andres Morales N (Thu Sep 03 2009 - 15:00:30 CDT)
rmsd matrix Andres Morales N (Thu Sep 03 2009 - 07:45:06 CDT)
Bond representation of coarse grained molecules BAN,YOUNG MIN (Wed Sep 02 2009 - 16:52:23 CDT)
- Re: Bond representation of coarse grained molecules John Stone (Fri Sep 04 2009 - 09:49:26 CDT)
  - Re: Bond representation of coarse grained molecules Axel Kohlmeyer (Sat Sep 05 2009 - 14:45:59 CDT)
- VMD on Suse 11.1 w/ NVIDIA dies. Bishop, Thomas C (Fri Sep 04 2009 - 17:52:35 CDT)
  - Re: VMD on Suse 11.1 w/ NVIDIA dies. Axel Kohlmeyer (Sat Sep 05 2009 - 14:33:34 CDT)
  - Re: VMD on Suse 11.1 w/ NVIDIA dies. John Stone (Tue Sep 08 2009 - 10:57:12 CDT)
- Re: Bond representation of coarse grained molecules Baofu Qiao (Wed Oct 07 2009 - 02:21:14 CDT)
  - Re: Bond representation of coarse grained molecules Axel Kohlmeyer (Wed Oct 07 2009 - 09:39:42 CDT)
    - Re: Bond representation of coarse grained molecules Sunjoo Lee (Wed Oct 07 2009 - 12:17:12 CDT)
Script error Negar Ashari Astani (Tue Sep 01 2009 - 11:58:32 CDT)
- Re: Script error Axel Kohlmeyer (Tue Sep 01 2009 - 12:55:26 CDT)
VMD on MacOSX 10.6 Snow Leopard: fast Christoph Weber (Mon Aug 31 2009 - 18:31:11 CDT)
- Re: VMD on MacOSX 10.6 Snow Leopard: fast Joshua D. Moore (Mon Aug 31 2009 - 22:20:51 CDT)
  - Re: VMD on MacOSX 10.6 Snow Leopard: fast Christoph Weber (Tue Sep 01 2009 - 13:30:07 CDT)
    - RE: VMD on MacOSX 10.6 Snow Leopard: fast David Poger (Mon Sep 07 2009 - 04:01:48 CDT)
    - Re: VMD on MacOSX 10.6 Snow Leopard: fast John Stone (Mon Sep 07 2009 - 16:31:54 CDT)
3D pdf problem Michael K. Gilson (Mon Aug 31 2009 - 06:24:06 CDT)
- Re: 3D pdf problem John Stone (Mon Aug 31 2009 - 11:51:01 CDT)
  - Re: 3D pdf problem Michael K. Gilson (Mon Aug 31 2009 - 14:36:49 CDT)
    - Re: 3D pdf problem John Stone (Mon Aug 31 2009 - 14:50:33 CDT)
    - Re: 3D pdf problem Michael K. Gilson (Mon Aug 31 2009 - 16:22:55 CDT)
superimpose two proteins with different residue numbers Soumya Lipsa Rath (Mon Aug 31 2009 - 02:55:13 CDT)
- Re: superimpose two proteins with different residue numbers John Stone (Mon Aug 31 2009 - 11:34:03 CDT)
  - label options Taufik Al-Sarraj (Thu Sep 17 2009 - 13:46:29 CDT)
    - Re: label options John Stone (Sun Sep 20 2009 - 15:35:25 CDT)
VMD, MultiSeq, STAMP Damian Loska (Sun Aug 30 2009 - 11:42:14 CDT)
- Re: VMD, MultiSeq, STAMP Kirby Vandivort (Mon Aug 31 2009 - 14:25:30 CDT)
  - Re: VMD, MultiSeq, STAMP John Stone (Mon Aug 31 2009 - 14:37:44 CDT)
User field Urahata (Fri Aug 28 2009 - 10:40:43 CDT)
- Re: User field Axel Kohlmeyer (Fri Aug 28 2009 - 16:14:00 CDT)
viewing MOs Dan thomas Major (Fri Aug 28 2009 - 09:47:34 CDT)
- Re: viewing MOs John Stone (Fri Aug 28 2009 - 09:55:37 CDT)
- Re: viewing MOs Axel Kohlmeyer (Fri Aug 28 2009 - 10:29:57 CDT)
  - Re: viewing MOs saam (Fri Aug 28 2009 - 15:37:59 CDT)
superimposing proteins with non-similar coordinates Mark M Huntress (Wed Aug 26 2009 - 16:17:41 CDT)
- Re: superimposing proteins with non-similar coordinates Schreiner Eduard (Wed Aug 26 2009 - 16:33:39 CDT)
- Re: superimposing proteins with non-similar coordinates John Stone (Wed Aug 26 2009 - 16:31:46 CDT)
- Re: superimposing proteins with non-similar coordinates Christopher MacDermaid (Wed Aug 26 2009 - 17:17:34 CDT)
rotating ligand Steve Seibold (Wed Aug 26 2009 - 14:58:19 CDT)
- Re: rotating ligand Schreiner Eduard (Wed Aug 26 2009 - 15:07:49 CDT)
drawing waterbox Narender Singh Maan (Wed Aug 26 2009 - 09:35:56 CDT)
- Re: drawing waterbox John Stone (Wed Aug 26 2009 - 13:29:10 CDT)
  - Re: drawing waterbox Narender Singh Maan (Thu Aug 27 2009 - 10:14:58 CDT)
    - Re: drawing waterbox John Stone (Thu Aug 27 2009 - 10:29:08 CDT)
    - Re: drawing waterbox BIN ZHANG (Thu Aug 27 2009 - 11:02:46 CDT)
Bond in pbc condition Yew Yong Kin (Wed Aug 26 2009 - 01:46:27 CDT)
- Re: Bond in pbc condition Olaf Lenz (Fri Aug 28 2009 - 04:06:39 CDT)
  - Re: Bond in pbc condition John Stone (Fri Aug 28 2009 - 10:22:06 CDT)
selection for polar hydrogens only poker_at_physics.usyd.edu.au (Tue Aug 25 2009 - 22:13:26 CDT)
- Re: selection for polar hydrogens only Schreiner Eduard (Tue Aug 25 2009 - 22:50:43 CDT)
  - Re: selection for polar hydrogens only poker_at_physics.usyd.edu.au (Wed Aug 26 2009 - 02:05:44 CDT)
tinkerxyz Mark M Huntress (Tue Aug 25 2009 - 19:21:48 CDT)
- Re: tinkerxyz Urahata (Tue Aug 25 2009 - 20:58:41 CDT)
- Re: tinkerxyz Axel Kohlmeyer (Tue Aug 25 2009 - 21:21:28 CDT)
- Re: tinkerxyz Joshua D. Moore (Sat Aug 29 2009 - 02:26:29 CDT)
problem with 1.8.7 installation Barbault Florent (Tue Aug 25 2009 - 04:50:41 CDT)
- Re: problem with 1.8.7 installation Axel Kohlmeyer (Tue Aug 25 2009 - 06:43:51 CDT)
Mac and cmd line Jorgen Simonsen (Mon Aug 24 2009 - 11:58:16 CDT)
- Re: Mac and cmd line Robert Brunner (Mon Aug 24 2009 - 15:02:20 CDT)
  - Re: Mac and cmd line Ben Eisenbraun (Mon Aug 24 2009 - 15:50:58 CDT)
    - Re: Mac and cmd line Jorgen Simonsen (Mon Aug 24 2009 - 17:50:49 CDT)
  - Re: Mac and cmd line JT (Mon Aug 24 2009 - 17:27:44 CDT)
Moving Molecule Steve Seibold (Mon Aug 24 2009 - 10:37:42 CDT)
- Re: Moving Molecule BIN ZHANG (Mon Aug 24 2009 - 11:21:41 CDT)
using VMD 1.8.7 on a Mac Carolyn Phillips (Sun Aug 23 2009 - 15:13:40 CDT)
- Re: using VMD 1.8.7 on a Mac John Stone (Sun Aug 23 2009 - 21:32:18 CDT)
  - Re: using VMD 1.8.7 on a Mac Carolyn Phillips (Mon Aug 24 2009 - 11:33:04 CDT)
Re: NAMD tutorial for Windows problem reading pgn file from vmd tkconsole Eric H. Lee (Fri Aug 21 2009 - 17:13:21 CDT)
NAMD tutorial for Windows problem reading pgn file from vmd tkconsole Carmen Valladares (Fri Aug 21 2009 - 16:26:04 CDT)
- Re: NAMD tutorial for Windows problem reading pgn file from vmd tkconsole John Stone (Fri Aug 21 2009 - 16:30:30 CDT)
- Re: NAMD tutorial for Windows problem reading pgn file from vmd tkconsole Eric H. Lee (Fri Aug 21 2009 - 16:40:52 CDT)
VMD: 1.8.7 win32 opengl runtime error Guanglei Cui (Fri Aug 21 2009 - 09:14:56 CDT)
- Re: VMD: 1.8.7 win32 opengl runtime error John Stone (Fri Aug 21 2009 - 09:56:33 CDT)
  - Re: VMD: 1.8.7 win32 opengl runtime error Guanglei Cui (Fri Aug 21 2009 - 21:48:43 CDT)
    - Re: VMD: 1.8.7 win32 opengl runtime error John Stone (Fri Aug 21 2009 - 21:58:25 CDT)
Force extension from SMD log file snoze pa (Thu Aug 20 2009 - 17:25:20 CDT)
Color bar Iman Salehinia (Thu Aug 20 2009 - 16:46:36 CDT)
- Re: Color bar Axel Kohlmeyer (Thu Aug 20 2009 - 17:28:26 CDT)
Pyhton Mode Peyman Yamin (Thu Aug 20 2009 - 04:49:33 CDT)
- Re: Pyhton Mode Axel Kohlmeyer (Thu Aug 20 2009 - 08:10:51 CDT)
Mutator: Losing Chromophore Carmen Valladares (Wed Aug 19 2009 - 19:14:57 CDT)
Render command not executed Nicolas SAPAY (Wed Aug 19 2009 - 02:22:18 CDT)
- Re: Render command not executed Axel Kohlmeyer (Wed Aug 19 2009 - 04:30:36 CDT)
  - Re: Render command not executed Nicolas SAPAY (Wed Aug 19 2009 - 04:59:45 CDT)
VMD Tracking VRPN Christian Wohlschlager (Wed Aug 19 2009 - 02:01:49 CDT)
Rendering polyhedra with POV-Ray Nicolas SAPAY (Tue Aug 18 2009 - 09:53:10 CDT)
- Re: Rendering polyhedra with POV-Ray John Stone (Tue Aug 18 2009 - 10:23:05 CDT)
  - Re: Rendering polyhedra with POV-Ray Nicolas Sapay (Tue Aug 18 2009 - 10:54:44 CDT)
    - Re: Rendering polyhedra with POV-Ray John Stone (Tue Aug 18 2009 - 10:59:37 CDT)
    - Re: Rendering polyhedra with POV-Ray Nicolas Sapay (Tue Aug 18 2009 - 11:11:35 CDT)
positioning of a compound Steve Seibold (Wed Aug 12 2009 - 14:48:23 CDT)
- Re: positioning of a compound John Stone (Wed Aug 12 2009 - 14:59:04 CDT)
  - RE: positioning of a compound Steve Seibold (Wed Aug 12 2009 - 15:11:00 CDT)
    - Re: positioning of a compound Esteban Gabriel Vega Hissi (Wed Aug 12 2009 - 16:07:37 CDT)
- Re: positioning of a compound jen hsin (Wed Aug 12 2009 - 15:02:15 CDT)
Periodic Bonding Liang, Linus H. (Wed Aug 12 2009 - 08:44:19 CDT)
- Re: Periodic Bonding Axel Kohlmeyer (Wed Aug 12 2009 - 09:42:00 CDT)
  - RE: Periodic Bonding Bishop, Thomas C (Thu Aug 13 2009 - 14:46:24 CDT)
- Re: Periodic Bonding Olaf Lenz (Wed Aug 12 2009 - 10:56:53 CDT)
Turn off the autobond feature in VMD Liang, Linus H. (Wed Aug 12 2009 - 08:27:55 CDT)
- Re: Turn off the autobond feature in VMD John Stone (Wed Aug 12 2009 - 09:58:01 CDT)
- Re: Turn off the autobond feature in VMD Axel Kohlmeyer (Wed Aug 12 2009 - 09:40:08 CDT)
VMD Periodic cells Florentina Tofoleanu (Wed Aug 12 2009 - 07:03:53 CDT)
- Re: VMD Periodic cells Olaf Lenz (Wed Aug 12 2009 - 08:43:09 CDT)
- Re: VMD Periodic cells Olaf Lenz (Wed Aug 12 2009 - 09:06:01 CDT)
CUDA Support Christian Wohlschlager (Wed Aug 12 2009 - 03:09:35 CDT)
- Re: CUDA Support John Stone (Wed Aug 12 2009 - 07:55:30 CDT)
  - Antw: Re: CUDA Support Christian Wohlschlager (Tue Aug 18 2009 - 01:06:27 CDT)
    - Re: Antw: Re: CUDA Support John Stone (Tue Aug 18 2009 - 01:18:10 CDT)
can we control the number and distribution of solvate molecular pxq ÅÓÑ©ÇÛ (Wed Aug 12 2009 - 03:02:33 CDT)
- Re: can we control the number and distribution of solvate molecular John Stone (Wed Aug 12 2009 - 16:14:30 CDT)
Re: namd-l: how to write a command to close vmd in shell script? Benjamin Bouvier (Mon Aug 10 2009 - 03:07:38 CDT)
HRTEM Joshua D. Moore (Fri Aug 07 2009 - 02:20:45 CDT)
- Re: HRTEM John Stone (Fri Aug 07 2009 - 12:22:53 CDT)
How to compile the source of VMD1.8.7 on linux system Aurum Bai (Fri Aug 07 2009 - 00:10:40 CDT)
- Re: How to compile the source of VMD1.8.7 on linux system John Stone (Fri Aug 07 2009 - 00:24:09 CDT)
NEW New Christian Wohlschlager (Thu Aug 06 2009 - 07:44:37 CDT)
- Re: NEW New John Stone (Thu Aug 06 2009 - 10:31:36 CDT)
Cionize on mac cuda daniel aguayo (Wed Aug 05 2009 - 20:29:07 CDT)
- Re: Cionize on mac cuda John Stone (Wed Aug 05 2009 - 20:43:04 CDT)
  - Re: Cionize on mac cuda daniel aguayo (Wed Aug 05 2009 - 20:46:10 CDT)
Announce: VMD 1.8.7 released John Stone (Mon Aug 03 2009 - 14:21:59 CDT)
"mol scaleminmax auto" vs. "mol scaleminmax $min_val $max_val" Nadja Lederer (Mon Aug 03 2009 - 06:21:42 CDT)
Why the win_version of vmd1.86 can not change to python interpreter? Aurum Bai (Sat Aug 01 2009 - 08:21:06 CDT)
- Re: Why the win_version of vmd1.86 can not change to python interpreter? Axel Kohlmeyer (Sat Aug 01 2009 - 09:30:12 CDT)
vmd Linux 64 Christian Wohlschlager (Fri Jul 31 2009 - 03:29:04 CDT)
- Re: vmd Linux 64 Axel Kohlmeyer (Fri Jul 31 2009 - 07:50:20 CDT)
visualization problem Srikanth Dhondi (Thu Jul 30 2009 - 21:58:27 CDT)
- Re: visualization problem Axel Kohlmeyer (Fri Jul 31 2009 - 07:44:29 CDT)
- Re: visualization problem John Stone (Fri Jul 31 2009 - 10:41:30 CDT)
Building polymer psf from monomer topology Alexandre Suman de Araujo (Thu Jul 30 2009 - 14:48:13 CDT)
NAMDEnergy Plugin Andres Morales N (Tue Jul 28 2009 - 00:34:43 CDT)
removed all proton in protein with vmd albert albert (Mon Jul 27 2009 - 01:40:34 CDT)
- Re: removed all proton in protein with vmd Nicolas SAPAY (Mon Jul 27 2009 - 03:36:38 CDT)
PDB COORDINATES Edward P. Manning (Sun Jul 26 2009 - 19:08:28 CDT)
- Re: PDB COORDINATES Axel Kohlmeyer (Sun Jul 26 2009 - 19:59:55 CDT)
Stripping out H20 Jehanzeb Hameed (Sun Jul 26 2009 - 18:24:33 CDT)
- Re: Stripping out H20 Axel Kohlmeyer (Sun Jul 26 2009 - 18:47:33 CDT)
  - Re: Stripping out H20 Axel Kohlmeyer (Sun Jul 26 2009 - 20:09:45 CDT)
File to benchmark a new GPU system luc Renambot (Sun Jul 26 2009 - 16:20:28 CDT)
- Re: File to benchmark a new GPU system Axel Kohlmeyer (Sun Jul 26 2009 - 18:22:59 CDT)
  - Re: File to benchmark a new GPU system luc Renambot (Sun Jul 26 2009 - 18:52:30 CDT)
    - Re: File to benchmark a new GPU system Axel Kohlmeyer (Sun Jul 26 2009 - 20:07:37 CDT)
- Re: File to benchmark a new GPU system John Stone (Mon Jul 27 2009 - 16:39:45 CDT)
order parameter from trajectory Roman Petrenko (Fri Jul 24 2009 - 17:08:50 CDT)
Lovyeou gumbart_at_ks.uiuc.edu (Fri Jul 24 2009 - 09:31:56 CDT)
time-averaged RMSD per residue Dawn (Fri Jul 24 2009 - 08:06:08 CDT)
- Re: time-averaged RMSD per residue Roman Petrenko (Fri Jul 24 2009 - 09:00:08 CDT)
  - Re: time-averaged RMSD per residue Roman Petrenko (Fri Jul 24 2009 - 11:15:02 CDT)
    - Re: time-averaged RMSD per residue Roman Petrenko (Sun Jul 26 2009 - 05:39:19 CDT)
- Re: time-averaged RMSD per residue Axel Kohlmeyer (Fri Jul 24 2009 - 09:19:52 CDT)
question about atomselect and periodic condition Linchen Gong (Fri Jul 24 2009 - 05:44:41 CDT)
- Re: question about atomselect and periodic condition Axel Kohlmeyer (Fri Jul 24 2009 - 09:17:13 CDT)
Hydrogen Bonding energy Goutham (Thu Jul 23 2009 - 20:56:52 CDT)
Loevyou gumbart_at_ks.uiuc.edu (Thu Jul 23 2009 - 16:55:17 CDT)
stereo anaglyph Roman Petrenko (Thu Jul 23 2009 - 16:16:07 CDT)
TkConsole not working Ziemys, Arturas (Thu Jul 23 2009 - 14:45:20 CDT)
- Re: TkConsole not working John Stone (Thu Jul 23 2009 - 14:52:24 CDT)
  - RE: TkConsole not working Ziemys, Arturas (Thu Jul 23 2009 - 14:56:57 CDT)
drawing bond for coarse grained model Sunjoo Lee (Thu Jul 23 2009 - 13:25:46 CDT)
- Re: drawing bond for coarse grained model Axel Kohlmeyer (Thu Jul 23 2009 - 14:06:53 CDT)
Save State Fails Carmen Valladares (Tue Jul 21 2009 - 18:57:00 CDT)
- Re: Save State Fails Leonardo Trabuco (Wed Jul 22 2009 - 00:52:57 CDT)
  - Re: Save State Fails Andrew Dalke (Thu Jul 23 2009 - 13:11:46 CDT)
could not visualize DCD file downloaded from VMD website Yi Shang (Tue Jul 21 2009 - 14:59:04 CDT)
- Re: could not visualize DCD file downloaded from VMD website Yi Shang (Tue Jul 21 2009 - 15:05:51 CDT)
  - Re: could not visualize DCD file downloaded from VMD website Yi Shang (Tue Jul 21 2009 - 15:24:30 CDT)
insert a protein into a membrane Lixia Jin Day (Tue Jul 21 2009 - 13:41:21 CDT)
- Re: insert a protein into a membrane Leonardo Trabuco (Tue Jul 21 2009 - 21:17:29 CDT)
of diet pills, like a racing heart or queasy stomach ltrabuco_at_ks.uiuc.edu (Tue Jul 21 2009 - 09:47:48 CDT)
error using Molecule.save() (vmd python) Michael Kreim (Tue Jul 21 2009 - 06:49:44 CDT)
- Re: error using Molecule.save() (vmd python) Axel Kohlmeyer (Tue Jul 21 2009 - 08:43:21 CDT)
IMD interface for VASP Michael Robbert (Mon Jul 20 2009 - 17:54:36 CDT)
- Re: IMD interface for VASP Axel Kohlmeyer (Mon Jul 20 2009 - 19:03:45 CDT)
need convert when using VMD to make a movie under Mac Yongmei Pan (Mon Jul 20 2009 - 17:49:29 CDT)
- Re: need convert when using VMD to make a movie under Mac Eric H. Lee (Mon Jul 20 2009 - 18:34:53 CDT)
- Re: need convert when using VMD to make a movie under Mac John Stone (Tue Jul 21 2009 - 01:13:44 CDT)
VMD on laptop with ATI Radeon 3650 Ramon Rocha (Mon Jul 20 2009 - 16:00:40 CDT)
- Re: VMD on laptop with ATI Radeon 3650 John Stone (Mon Jul 20 2009 - 16:09:18 CDT)
  - RE: VMD on laptop with ATI Radeon 3650 Mark Cunningham (Tue Jul 21 2009 - 10:00:33 CDT)
Problem: volumetric data coloring fails on AIX5_64 with GXT6500 OpenGL renderer Stanislav Polonsky (Mon Jul 20 2009 - 11:04:25 CDT)
- Re: Problem: volumetric data coloring fails on AIX5_64 with GXT6500 OpenGL renderer John Stone (Mon Jul 20 2009 - 11:29:20 CDT)
  - Re: Problem: volumetric data coloring fails on AIX5_64 with GXT6500 OpenGL renderer Stanislav Polonsky (Mon Jul 20 2009 - 11:40:40 CDT)
- Re: Problem: volumetric data coloring fails on AIX5_64 with GXT6500 OpenGL renderer Axel Kohlmeyer (Mon Jul 20 2009 - 11:36:28 CDT)
Re PSF file generation karthigeyan karthigeyantp (Mon Jul 20 2009 - 07:34:51 CDT)
- Re: Re PSF file generation Axel Kohlmeyer (Mon Jul 20 2009 - 08:49:33 CDT)
VMD 1.8.7 installation problem Ajeeta kaushiki (Mon Jul 20 2009 - 06:55:41 CDT)
- Re: VMD 1.8.7 installation problem Axel Kohlmeyer (Mon Jul 20 2009 - 08:49:00 CDT)
Problem With Psfgen again avl211_at_lehigh.edu (Fri Jul 17 2009 - 13:53:49 CDT)
- Re: Problem With Psfgen again Axel Kohlmeyer (Fri Jul 17 2009 - 14:37:13 CDT)
error after changing of PYTHONPATH variable Michael Kreim (Fri Jul 17 2009 - 07:12:52 CDT)
- Re: error after changing of PYTHONPATH variable Axel Kohlmeyer (Fri Jul 17 2009 - 08:22:13 CDT)
  - Re: error after changing of PYTHONPATH variable Michael Kreim (Fri Jul 17 2009 - 08:51:46 CDT)
    - Re: error after changing of PYTHONPATH variable Axel Kohlmeyer (Fri Jul 17 2009 - 09:16:22 CDT)
File conversion for from Amber to Charmm Yogesh Aher (Fri Jul 17 2009 - 04:34:55 CDT)
- Re: File conversion for from Amber to Charmm Axel Kohlmeyer (Fri Jul 17 2009 - 07:23:35 CDT)
  - Re: File conversion for from Amber to Charmm Axel Kohlmeyer (Fri Jul 17 2009 - 10:14:24 CDT)
    - Re: File conversion for from Amber to Charmm Yogesh Aher (Mon Jul 20 2009 - 07:22:21 CDT)
    - Re: File conversion for from Amber to Charmm Axel Kohlmeyer (Mon Jul 20 2009 - 08:54:41 CDT)
Problems with psfgen avl211_at_lehigh.edu (Thu Jul 16 2009 - 16:06:31 CDT)
- Re: Problems with psfgen Axel Kohlmeyer (Thu Jul 16 2009 - 17:30:59 CDT)
algorithm for command *within* BIN ZHANG (Thu Jul 16 2009 - 11:29:43 CDT)
- Re: algorithm for command *within* John Stone (Thu Jul 16 2009 - 11:32:50 CDT)
  - Re: algorithm for command *within* Thomas Evangelidis (Fri Jul 17 2009 - 03:30:45 CDT)
ied and gypython gurunath katagi (Thu Jul 16 2009 - 02:16:21 CDT)
- Re: ied and gypython Axel Kohlmeyer (Thu Jul 16 2009 - 09:22:39 CDT)
A problem on PBC yzliu (Thu Jul 16 2009 - 02:06:34 CDT)
- Re: A problem on PBC Axel Kohlmeyer (Thu Jul 16 2009 - 11:56:57 CDT)
HETATM records are written as ATOM Thomas Evangelidis (Wed Jul 15 2009 - 16:58:27 CDT)
- Re: HETATM records are written as ATOM Leonardo Trabuco (Wed Jul 15 2009 - 17:32:07 CDT)
Natural WeightL0SS Solution ltrabuco_at_ks.uiuc.edu (Wed Jul 15 2009 - 17:35:35 CDT)
Can I build a structure by VMD? Lixia Jin Day (Wed Jul 15 2009 - 14:29:01 CDT)
- Re: Can I build a structure by VMD? John Stone (Wed Jul 15 2009 - 14:36:56 CDT)
.xst file disagrees with pbctools/.dcd file - what are the limitations of pbctools? Patrick Kiley (Wed Jul 15 2009 - 05:05:01 CDT)
- Re: .xst file disagrees with pbctools/.dcd file - what are the limitations of pbctools? John Stone (Wed Jul 15 2009 - 14:32:57 CDT)
- Re: .xst file disagrees with pbctools/.dcd file - what are the limitations of pbctools? Olaf Lenz (Thu Jul 16 2009 - 01:14:37 CDT)
python and vmd Jorgen Simonsen (Wed Jul 15 2009 - 04:23:12 CDT)
- Re: python and vmd Axel Kohlmeyer (Wed Jul 15 2009 - 07:46:20 CDT)
scan interleaved stereo on Zalman M220W monitor Sinan Arslan (Tue Jul 14 2009 - 13:11:39 CDT)
- Re: scan interleaved stereo on Zalman M220W monitor John Stone (Tue Jul 14 2009 - 13:25:50 CDT)
molecule jumps from one site to the other? uu zhu (Mon Jul 13 2009 - 21:11:52 CDT)
- Re: namd-l: molecule jumps from one site to the other? Eric H. Lee (Mon Jul 13 2009 - 21:33:42 CDT)
getting other variables out of LAMMPS ascii dump files Dan Lussier (Mon Jul 13 2009 - 13:44:23 CDT)
- Re: getting other variables out of LAMMPS ascii dump files Axel Kohlmeyer (Mon Jul 13 2009 - 14:21:03 CDT)
  - Re: getting other variables out of LAMMPS ascii dump files Dan Lussier (Tue Jul 14 2009 - 17:31:57 CDT)
    - Re: getting other variables out of LAMMPS ascii dump files Axel Kohlmeyer (Tue Jul 14 2009 - 18:00:35 CDT)
    - Re: getting other variables out of LAMMPS ascii dump files Dan Lussier (Thu Jul 16 2009 - 04:46:03 CDT)
Be someone whom you have never been before with DrMaxMan ltrabuco_at_ks.uiuc.edu (Mon Jul 13 2009 - 10:30:41 CDT)
Problem: I got a runtime error "CthCreate failed to create fiber!". Chuck (Sun Jul 12 2009 - 03:49:44 CDT)
Need Guidance with pbctools Angelo Rossi (Sat Jul 11 2009 - 13:47:11 CDT)
- Re: Need Guidance with pbctools Olaf Lenz (Sun Jul 12 2009 - 03:00:58 CDT)
  - Re: Need Guidance with pbctools Angelo Rossi (Sun Jul 12 2009 - 08:02:21 CDT)
residue based CG model Xiang Yu (Fri Jul 10 2009 - 09:20:42 CDT)
- Re: residue based CG model Anton Arkhipov (Fri Jul 10 2009 - 10:47:00 CDT)
measure rmsf Alison Grinthal (Fri Jul 10 2009 - 08:31:26 CDT)
- Re: measure rmsf John Stone (Fri Jul 10 2009 - 10:42:33 CDT)
  - Re: measure rmsf Alison Grinthal (Fri Jul 10 2009 - 13:10:14 CDT)
    - Re: measure rmsf John Stone (Fri Jul 10 2009 - 13:31:54 CDT)
- list of residue contacts Alison Grinthal (Wed Sep 23 2009 - 15:02:23 CDT)
A problem on SASA measure yzliu (Fri Jul 10 2009 - 08:12:23 CDT)
- Re: A problem on SASA measure John Stone (Wed Jul 15 2009 - 16:03:25 CDT)
  - make movie w/ VMD in SUSE environment Thomas C. Bishop (Thu Jul 16 2009 - 10:55:57 CDT)
Need GAMESS logfiles for testing VMD's new QM interface saam (Thu Jul 09 2009 - 11:58:08 CDT)
How to make a selection in atomselect using an element in a list? maria goranovic (Wed Jul 08 2009 - 10:39:39 CDT)
- Re: How to make a selection in atomselect using an element in a list? Axel Kohlmeyer (Wed Jul 08 2009 - 11:17:14 CDT)
LES problem Irene Newhouse (Tue Jul 07 2009 - 00:25:20 CDT)
- re: LES problem Irene Newhouse (Tue Jul 07 2009 - 00:28:21 CDT)
Make sure girls notice your package petefred_at_ks.uiuc.edu (Sat Jul 04 2009 - 22:12:43 CDT)
NAMDenergy: problems on changing VMD version/platform Neelanjana Sengupta (Sat Jul 04 2009 - 11:17:44 CDT)
- Re: NAMDenergy: problems on changing VMD version/platform Axel Kohlmeyer (Sat Jul 04 2009 - 11:54:50 CDT)
  - Re: NAMDenergy: problems on changing VMD version/platform Axel Kohlmeyer (Sun Jul 05 2009 - 13:58:50 CDT)
    - Re: NAMDenergy: problems on changing VMD version/platform Neelanjana Sengupta (Mon Jul 06 2009 - 05:17:30 CDT)
GPL compatible PluginMgr/vmddlopen Roland Schulz (Sat Jul 04 2009 - 08:13:37 CDT)
- Re: GPL compatible PluginMgr/vmddlopen John Stone (Sun Jul 05 2009 - 20:14:35 CDT)
  - Re: GPL compatible PluginMgr/vmddlopen Roland Schulz (Mon Jul 06 2009 - 04:19:52 CDT)
    - Re: GPL compatible PluginMgr/vmddlopen John Stone (Mon Jul 06 2009 - 21:45:27 CDT)
    - Re: GPL compatible PluginMgr/vmddlopen Roland Schulz (Wed Jul 08 2009 - 09:56:08 CDT)
Hardware for NAMD / VMD machine Olve Peersen (Fri Jul 03 2009 - 01:26:11 CDT)
- Re: namd-l: Hardware for NAMD / VMD machine Axel Kohlmeyer (Fri Jul 03 2009 - 11:56:08 CDT)
- Re: Hardware for NAMD / VMD machine John Stone (Mon Jul 06 2009 - 11:04:30 CDT)
  - Re: Hardware for NAMD / VMD machine Olve Peersen (Mon Jul 06 2009 - 13:39:53 CDT)
    - Re: namd-l: Re: Hardware for NAMD / VMD machine Axel Kohlmeyer (Mon Jul 06 2009 - 16:46:40 CDT)
Be the largest man around petefred_at_ks.uiuc.edu (Thu Jul 02 2009 - 13:35:37 CDT)
Manunlly Assign Secondary Structure (May Not Be Realistic) John C. H. Chao (Thu Jul 02 2009 - 06:00:07 CDT)
- Re: Manunlly Assign Secondary Structure (May Not Be Realistic) Axel Kohlmeyer (Thu Jul 02 2009 - 14:42:30 CDT)
  - RE: Manunlly Assign Secondary Structure (May Not Be Realistic) John C. H. Chao (Fri Jul 03 2009 - 04:42:10 CDT)
superimposing proteins based on a few residues Irene Newhouse (Wed Jul 01 2009 - 15:59:33 CDT)
- Re: superimposing proteins based on a few residues Axel Kohlmeyer (Wed Jul 01 2009 - 17:13:25 CDT)
Some VMD questions Steve Jensen (Tue Jun 30 2009 - 12:27:01 CDT)
- Re: Some VMD questions Daniel Gaston (Tue Jun 30 2009 - 13:10:14 CDT)
- Re: Some VMD questions Axel Kohlmeyer (Tue Jun 30 2009 - 13:56:02 CDT)
Coloring atoms by a general scalar Heidenreich, Joseph David (Tue Jun 30 2009 - 12:19:29 CDT)
- Re: Coloring atoms by a general scalar Axel Kohlmeyer (Tue Jun 30 2009 - 12:53:26 CDT)
- Re: Coloring atoms by a general scalar Pawel Kedzierski (Wed Jul 01 2009 - 04:27:32 CDT)
  - Re: Coloring atoms by a general scalar Axel Kohlmeyer (Wed Jul 01 2009 - 08:12:52 CDT)
    - RE: Coloring atoms by a general scalar Heidenreich, Joseph David (Thu Jul 02 2009 - 14:17:25 CDT)
Funny tcl/tk script behavior.... Alberto Sergio Garay (Tue Jun 30 2009 - 08:02:57 CDT)
- Re: Funny tcl/tk script behavior.... Axel Kohlmeyer (Tue Jun 30 2009 - 09:48:45 CDT)
  - Re: Funny tcl/tk script behavior.... Alberto Sergio Garay (Tue Jun 30 2009 - 12:08:32 CDT)
atom name can not exceed four characters in pdb and psf? accomp lin (Mon Jun 29 2009 - 21:59:36 CDT)
- Re: atom name can not exceed four characters in pdb and psf? Axel Kohlmeyer (Mon Jun 29 2009 - 22:32:22 CDT)
Packed with Antioxidants . Acai Berry. petefred_at_ks.uiuc.edu (Mon Jun 29 2009 - 21:30:17 CDT)
Oprah certified wieght loss solution Acai.Berri. petefred_at_ks.uiuc.edu (Mon Jun 29 2009 - 19:29:14 CDT)
GPGPU Programming summer school at University of Tennessee, Aug 10-14. Axel Kohlmeyer (Mon Jun 29 2009 - 14:44:15 CDT)
running vmd on computer node BIN ZHANG (Mon Jun 29 2009 - 12:55:08 CDT)
- Re: running vmd on computer node Axel Kohlmeyer (Mon Jun 29 2009 - 13:46:51 CDT)
selection update kumar prashanth (Fri Jun 26 2009 - 08:03:21 CDT)
- Re: selection update John Stone (Fri Jun 26 2009 - 14:26:51 CDT)
Problem using pbc wrap..... Alberto Sergio Garay (Fri Jun 26 2009 - 07:13:44 CDT)
- Re: Problem using pbc wrap..... Olaf Lenz (Fri Jun 26 2009 - 10:06:06 CDT)
  - Re: Problem using pbc wrap..... Alberto Sergio Garay (Fri Jun 26 2009 - 15:01:35 CDT)
    - Re: Problem using pbc wrap..... Olaf Lenz (Sat Jun 27 2009 - 10:44:53 CDT)
Curious about analytical capabilities of VMD Bjoern Olausson (Fri Jun 26 2009 - 03:48:05 CDT)
- Re: Curious about analytical capabilities of VMD Axel Kohlmeyer (Fri Jun 26 2009 - 07:09:06 CDT)
  - Re: Curious about analytical capabilities of VMD Bjoern Olausson (Mon Jun 29 2009 - 05:29:33 CDT)
constant region selection for animation Dan Lussier (Thu Jun 25 2009 - 09:55:00 CDT)
- Re: constant region selection for animation John Stone (Thu Jun 25 2009 - 10:03:21 CDT)
Re: regarding positioning of protein molecule Ramya Gamini (Thu Jun 25 2009 - 01:48:07 CDT)
"no CUDA accelerator devices available", Nvidia GeForce 9600 GT card Low Soo Mei (Wed Jun 24 2009 - 21:44:35 CDT)
- Re: "no CUDA accelerator devices available", Nvidia GeForce 9600 GT card John Stone (Wed Jun 24 2009 - 22:17:52 CDT)
  - Re: "no CUDA accelerator devices available", Nvidia GeForce 9600 GT card Low Soo Mei (Thu Jun 25 2009 - 00:41:15 CDT)
Multimodel PDB files with Different Models? Kevin Wu (Wed Jun 24 2009 - 21:05:30 CDT)
- Re: Multimodel PDB files with Different Models? John Stone (Thu Jun 25 2009 - 13:11:30 CDT)
residue index problem Jianhui Tian (Wed Jun 24 2009 - 15:51:54 CDT)
- Re: residue index problem John Stone (Wed Jun 24 2009 - 16:40:44 CDT)
trace the distance between center of mass of one certain residue and the other Naiyin Yu (Wed Jun 24 2009 - 14:59:14 CDT)
- Re: trace the distance between center of mass of one certain residue and the other John Stone (Wed Jun 24 2009 - 15:34:05 CDT)
Rejecting plugin... Gustavo Seabra (Wed Jun 24 2009 - 14:04:25 CDT)
- Re: Rejecting plugin... Axel Kohlmeyer (Wed Jun 24 2009 - 14:30:15 CDT)
- Re: Rejecting plugin... John Stone (Wed Jun 24 2009 - 14:34:53 CDT)
  - Re: Rejecting plugin... Gustavo Seabra (Wed Jun 24 2009 - 17:53:26 CDT)
vmd error message in Fedora 11 snoze pa (Wed Jun 24 2009 - 11:04:15 CDT)
- Re: vmd error message in Fedora 11 Axel Kohlmeyer (Wed Jun 24 2009 - 12:07:24 CDT)
  - vmd 1.8.7 not spawn new console: feature,bug, or just different? Thomas C. Bishop (Wed Jun 24 2009 - 15:08:07 CDT)
bigdcd v3 available. testers needed. Axel Kohlmeyer (Wed Jun 24 2009 - 09:07:14 CDT)
joystick, win32 simple interface Biff Forbush (Tue Jun 23 2009 - 18:32:57 CDT)
- Re: joystick, win32 simple interface John Stone (Wed Jun 24 2009 - 15:50:18 CDT)
VMD 1.8.7 beta5 probs with NVIDIA Quadro FX3450/4000 graphic card Baumert, Uwe Dr.rer.nat. (Mon Jun 22 2009 - 04:18:54 CDT)
- Re: VMD 1.8.7 beta5 probs with NVIDIA Quadro FX3450/4000 graphic card John Stone (Mon Jun 22 2009 - 09:29:11 CDT)
Plugins: plz add one more conversion to unit_conversion.h Rob (Sun Jun 21 2009 - 21:00:57 CDT)
- Re: Plugins: plz add one more conversion to unit_conversion.h John Stone (Mon Jun 22 2009 - 14:54:33 CDT)
tag heuer rep watch for you; Forest Jefferson (Sat Jun 20 2009 - 05:44:49 CDT)
porsche design is your style; Fletcher Quick (Thu Jun 18 2009 - 14:18:17 CDT)
transformation matrix Thomas Evangelidis (Thu Jun 18 2009 - 02:55:52 CDT)
- Re: transformation matrix JC Gumbart (Thu Jun 18 2009 - 15:15:34 CDT)
  - Re: transformation matrix Thomas Evangelidis (Thu Jun 18 2009 - 15:34:51 CDT)
    - Re: transformation matrix Thomas Evangelidis (Thu Jun 18 2009 - 15:36:13 CDT)
    - Re: transformation matrix John Stone (Thu Jun 18 2009 - 15:39:12 CDT)
"Re: ABINIT plugin ready for testing: can read GEO and DEN files. Rob (Thu Jun 18 2009 - 02:27:08 CDT)
- Re: "Re: ABINIT plugin ready for testing: can read GEO and DEN files. John Stone (Thu Jun 18 2009 - 09:59:46 CDT)
  - Re: "Re: ABINIT plugin ready for testing: can read GEO and DEN files. Axel Kohlmeyer (Thu Jun 18 2009 - 11:13:59 CDT)
Wrong coordinates using guesscoord in psfgen - lipids poker_at_physics.usyd.edu.au (Wed Jun 17 2009 - 02:30:55 CDT)
movie maker Alison Grinthal (Tue Jun 16 2009 - 09:44:48 CDT)
- Re: movie maker John Stone (Tue Jun 16 2009 - 09:59:26 CDT)
- alignment Alison Grinthal (Fri Jun 19 2009 - 09:45:28 CDT)
  - Re: alignment Axel Kohlmeyer (Fri Jun 19 2009 - 10:56:09 CDT)
Molscripts Tomek Wlodarski (Tue Jun 16 2009 - 08:54:22 CDT)
- Re: Molscripts John Stone (Tue Jun 16 2009 - 09:23:24 CDT)
using atomselect to write a set of atoms and not some residue whose residue numbers are in a list maria goranovic (Mon Jun 15 2009 - 10:31:26 CDT)
- Re: using atomselect to write a set of atoms and not some residue whose residue numbers are in a list John Stone (Mon Jun 15 2009 - 10:38:18 CDT)
"Save coordinates..." silently overwrites existing files... Rob (Mon Jun 15 2009 - 10:25:10 CDT)
- Re: "Save coordinates..." silently overwrites existing files... Axel Kohlmeyer (Mon Jun 15 2009 - 11:29:10 CDT)
Memory allocation problem kumar prashanth (Mon Jun 15 2009 - 04:06:49 CDT)
- Re: Memory allocation problem Peter Freddolino (Mon Jun 15 2009 - 09:22:49 CDT)
- Re: Memory allocation problem Axel Kohlmeyer (Mon Jun 15 2009 - 10:00:02 CDT)
psfgen: auto none not working Ruchi Sachdeva (Mon Jun 15 2009 - 03:57:25 CDT)
- Re: psfgen: auto none not working Peter Freddolino (Mon Jun 15 2009 - 06:50:46 CDT)
ABINIT plugin ready for testing: can read GEO and DEN files. Rob (Mon Jun 15 2009 - 01:32:28 CDT)
- Re: ABINIT plugin ready for testing: can read GEO and DEN files. John Stone (Mon Jun 15 2009 - 09:52:21 CDT)
- Re: ABINIT plugin ready for testing: can read GEO and DEN files. Axel Kohlmeyer (Mon Jun 15 2009 - 10:18:34 CDT)
- Re: ABINIT plugin ready for testing: can read GEO and DEN files. Rob (Tue Jun 16 2009 - 03:27:28 CDT)
  - Re: Re: ABINIT plugin ready for testing: can read GEO and DEN files. Axel Kohlmeyer (Tue Jun 16 2009 - 07:31:03 CDT)
- Re: ABINIT plugin ready for testing: can read GEO and DEN files. Rob (Tue Jun 16 2009 - 21:23:22 CDT)
  - Re: Re: ABINIT plugin ready for testing: can read GEO and DEN files. John Stone (Tue Jun 16 2009 - 21:33:31 CDT)
  - Re: Re: ABINIT plugin ready for testing: can read GEO and DEN files. Axel Kohlmeyer (Tue Jun 16 2009 - 22:59:20 CDT)
- Re: ABINIT plugin ready for testing: can read GEO and DEN files. Rob (Wed Jun 17 2009 - 10:59:23 CDT)
  - Re: Re: ABINIT plugin ready for testing: can read GEO and DEN files. John Stone (Wed Jun 17 2009 - 11:33:20 CDT)
  - Re: Re: ABINIT plugin ready for testing: can read GEO and DEN files. Axel Kohlmeyer (Wed Jun 17 2009 - 12:01:30 CDT)
vmdnumpy for IED... Cihan Aydin (Sun Jun 14 2009 - 17:42:36 CDT)
- Re: vmdnumpy for IED... Axel Kohlmeyer (Sun Jun 14 2009 - 18:23:41 CDT)
Ho to save exactly the screen structure? Víctor (Sun Jun 14 2009 - 15:35:55 CDT)
- Re: Ho to save exactly the screen structure? Axel Kohlmeyer (Sun Jun 14 2009 - 16:58:32 CDT)
  - Re: Ho to save exactly the screen structure? Víctor (Mon Jun 15 2009 - 02:21:43 CDT)
Tcl commands and X11 craig bullington (Fri Jun 12 2009 - 11:48:37 CDT)
- Re: Tcl commands and X11 Axel Kohlmeyer (Fri Jun 12 2009 - 13:26:59 CDT)
VMD and X forwarding to MacOS 10.5.7 Benjamin Bouvier (Fri Jun 12 2009 - 09:48:29 CDT)
- Re: VMD and X forwarding to MacOS 10.5.7 John Stone (Fri Jun 12 2009 - 10:02:33 CDT)
  - Re: VMD and X forwarding to MacOS 10.5.7 Benjamin Bouvier (Fri Jun 12 2009 - 10:28:17 CDT)
FW: Unable to render electrostatic potential cube files with most non-HF densities Whiteside, Alexander (Thu Jun 11 2009 - 08:39:21 CDT)
- Re: FW: Unable to render electrostatic potential cube files with most non-HF densities John Stone (Thu Jun 11 2009 - 08:54:59 CDT)
- Re: FW: Unable to render electrostatic potential cube files with most non-HF densities Axel Kohlmeyer (Thu Jun 11 2009 - 09:19:21 CDT)
vmd cannot be launched after successful installation Stefano Meliga (Wed Jun 10 2009 - 10:58:15 CDT)
- Re: vmd cannot be launched after successful installation John Stone (Wed Jun 10 2009 - 11:02:58 CDT)
Transparency settings Bjoern Olausson (Wed Jun 10 2009 - 09:13:13 CDT)
- Re: Transparency settings Axel Kohlmeyer (Wed Jun 10 2009 - 09:38:57 CDT)
- Re: Transparency settings Eric H. Lee (Wed Jun 10 2009 - 09:23:55 CDT)
  - Re: Transparency settings Bjoern Olausson (Wed Jun 10 2009 - 10:29:08 CDT)
NAMDEnergy Andres Morales N (Wed Jun 10 2009 - 08:59:51 CDT)
- Re: NAMDEnergy John Stone (Wed Jun 10 2009 - 09:47:29 CDT)
plugin: can I load volumetric data as frames (i.e. timesteps)? Rob (Wed Jun 10 2009 - 03:11:34 CDT)
- Re: plugin: can I load volumetric data as frames (i.e. timesteps)? John Stone (Wed Jun 10 2009 - 07:24:05 CDT)
  - Re: plugin: can I load volumetric data as frames (i.e. timesteps)? Ondrej Marsalek (Wed Jun 10 2009 - 07:54:05 CDT)
- Re: plugin: can I load volumetric data as frames (i.e. timesteps)? Axel Kohlmeyer (Wed Jun 10 2009 - 08:16:58 CDT)
bonds not created as desired Akemi Matsuno-Yagi (Tue Jun 09 2009 - 13:01:09 CDT)
- Re: bonds not created as desired John Stone (Tue Jun 09 2009 - 14:55:44 CDT)
  - Re: bonds not created as desired Akemi Matsuno-Yagi (Tue Jun 09 2009 - 15:09:25 CDT)
  - namdplot 1.0 Thomas C. Bishop (Wed Jun 10 2009 - 22:14:11 CDT)
    - Re: namdplot 1.0 John Stone (Wed Jun 10 2009 - 23:03:34 CDT)
Re: Cannot load file for SASA analysis Lili Peng (Mon Jun 08 2009 - 20:39:16 CDT)
MSMS installation craig bullington (Mon Jun 08 2009 - 14:27:57 CDT)
- Re: MSMS installation John Stone (Mon Jun 08 2009 - 16:09:42 CDT)
crystal eyes vmd Thomas Lemmin (Mon Jun 08 2009 - 08:16:22 CDT)
- Re: crystal eyes vmd Thomas Lemmin (Mon Jun 08 2009 - 08:21:48 CDT)
  - Re: Re: crystal eyes vmd John Stone (Mon Jun 08 2009 - 08:43:56 CDT)
atom selection Deepti Mishra (Sun Jun 07 2009 - 23:32:43 CDT)
- Re: atom selection Eric H. Lee (Sun Jun 07 2009 - 23:46:39 CDT)
NAMDEnergy Andres Morales N (Sun Jun 07 2009 - 15:24:33 CDT)
- Re: NAMDEnergy Eric H. Lee (Sun Jun 07 2009 - 15:37:30 CDT)
  - Re: NAMDEnergy Peter Freddolino (Sun Jun 07 2009 - 16:41:54 CDT)
NAMDEnergy Andres Morales N (Sun Jun 07 2009 - 15:23:35 CDT)
Building LPS membrane dipti lele (Sun Jun 07 2009 - 00:35:50 CDT)
Vector corresponding to the long axis Navendu bhatnagar (Fri Jun 05 2009 - 17:26:16 CDT)
- Re: Vector corresponding to the long axis Peter Freddolino (Fri Jun 05 2009 - 19:53:16 CDT)
disulphide bond formation gurunath katagi (Fri Jun 05 2009 - 10:14:11 CDT)
- Re: disulphide bond formation Axel Kohlmeyer (Fri Jun 05 2009 - 10:45:12 CDT)
  - psfgen: how to place patches to end of residue definition in pdb file? Sebastian Stolzenberg (Tue Jun 09 2009 - 11:33:41 CDT)
debugging tool for atomselect Axel Kohlmeyer (Thu Jun 04 2009 - 17:05:10 CDT)
Memory Problem with tcl/tk script...(Solved!) Alberto Sergio Garay (Thu Jun 04 2009 - 07:08:19 CDT)
Energy Andres Morales N (Wed Jun 03 2009 - 21:50:41 CDT)
- Re: Energy Axel Kohlmeyer (Wed Jun 03 2009 - 22:29:45 CDT)
- Re: Energy John Stone (Wed Jun 03 2009 - 22:04:04 CDT)
Memory Problem with tcl/tk script...(3) Alberto Sergio Garay (Wed Jun 03 2009 - 14:17:07 CDT)
Memory Problem with tcl/tk script...(2) Alberto Sergio Garay (Wed Jun 03 2009 - 12:54:53 CDT)
- Re: Memory Problem with tcl/tk script...(2) Robert Brunner (Wed Jun 03 2009 - 13:48:49 CDT)
- Re: Memory Problem with tcl/tk script...(2) Axel Kohlmeyer (Wed Jun 03 2009 - 13:57:40 CDT)
vmd 1.8.7 - problems loading vmd state file lucie delemotte (Tue Jun 02 2009 - 10:31:26 CDT)
- Re: vmd 1.8.7 - problems loading vmd state file John Stone (Tue Jun 02 2009 - 10:39:18 CDT)
APBS error : Cannot read output file Navendu bhatnagar (Tue Jun 02 2009 - 09:51:01 CDT)
- Re: APBS error : Cannot read output file John Stone (Tue Jun 02 2009 - 09:55:51 CDT)
VMD HOLE Result Hyundeok Song (Tue Jun 02 2009 - 08:49:20 CDT)
- Re: VMD HOLE Result John Stone (Tue Jun 02 2009 - 09:53:26 CDT)
  - Re: VMD HOLE Result Hyundeok Song (Tue Jun 02 2009 - 14:05:59 CDT)
    - Re: VMD HOLE Result daniel aguayo (Tue Jun 02 2009 - 17:03:26 CDT)
Memory Problem with tcl/tk script... Alberto Sergio Garay (Tue Jun 02 2009 - 07:25:16 CDT)
- Re: Memory Problem with tcl/tk script... Axel Kohlmeyer (Tue Jun 02 2009 - 09:27:22 CDT)
adding atoms to empty molecules Thomas Evangelidis (Mon Jun 01 2009 - 13:47:07 CDT)
- Re: adding atoms to empty molecules Axel Kohlmeyer (Tue Jun 02 2009 - 09:22:43 CDT)
  - Re: adding atoms to empty molecules Thomas Evangelidis (Tue Jun 02 2009 - 15:57:56 CDT)
VMD 1.8.7 Beta 5 -- Possible bug when typing in the VMD menu boxes. JT (Mon Jun 01 2009 - 17:29:07 CDT)
VMD 1.8.7 beta 5 posted for download John Stone (Mon Jun 01 2009 - 16:11:31 CDT)
Accelerating your VMD 1.8.7 calculations with an NVIDIA Tesla GPU Jacob Story (Mon Jun 01 2009 - 09:20:22 CDT)
- Re: Accelerating your VMD 1.8.7 calculations with an NVIDIA Tesla GPU John Stone (Tue Jun 02 2009 - 10:25:36 CDT)
Linking to molfile_plugin libraries David Tanner (Fri May 29 2009 - 13:02:59 CDT)
- Re: Linking to molfile_plugin libraries John Stone (Fri May 29 2009 - 13:07:26 CDT)
  - Re: Linking to molfile_plugin libraries David Tanner (Fri May 29 2009 - 13:18:28 CDT)
    - Re: Linking to molfile_plugin libraries John Stone (Fri May 29 2009 - 13:24:30 CDT)
    - Re: Linking to molfile_plugin libraries David Tanner (Fri May 29 2009 - 13:30:24 CDT)
Macbook and VMD Tk windows madura_at_duq.edu (Fri May 29 2009 - 06:49:08 CDT)
- Re: Macbook and VMD Tk windows Axel Kohlmeyer (Fri May 29 2009 - 08:07:21 CDT)
- Re: Macbook and VMD Tk windows John Stone (Fri May 29 2009 - 09:17:20 CDT)
VMD crash snoze pa (Thu May 28 2009 - 14:45:10 CDT)
- Re: VMD crash John Stone (Thu May 28 2009 - 15:13:22 CDT)
  - statistics in VMD Thomas C. Bishop (Thu May 28 2009 - 19:18:17 CDT)
    - Re: statistics in VMD John Stone (Thu May 28 2009 - 19:25:09 CDT)
  - Re: VMD crash Axel Kohlmeyer (Thu May 28 2009 - 19:05:48 CDT)
    - Re: VMD crash John Stone (Thu May 28 2009 - 19:32:44 CDT)
    - Re: VMD crash Axel Kohlmeyer (Thu May 28 2009 - 19:46:33 CDT)
Re: [lammps-users] LAMMPS to VMD: lmp2vmd tool Axel Kohlmeyer (Thu May 28 2009 - 10:31:42 CDT)
- RE: Re: [lammps-users] LAMMPS to VMD: lmp2vmd tool Chetan Mahajan (Tue Jun 09 2009 - 13:08:16 CDT)
  - RE: Re: [lammps-users] LAMMPS to VMD: lmp2vmd tool Axel Kohlmeyer (Wed Jun 10 2009 - 08:36:44 CDT)
    - RE: Re: [lammps-users] LAMMPS to VMD: lmp2vmd tool Chetan Mahajan (Wed Jun 10 2009 - 10:00:30 CDT)
    - RE: Re: [lammps-users] LAMMPS to VMD: lmp2vmd tool Axel Kohlmeyer (Sat Jun 13 2009 - 17:00:27 CDT)
problem with dispdev KIRTANA S (Wed May 27 2009 - 15:59:41 CDT)
- Re: problem with dispdev John Stone (Wed May 27 2009 - 16:02:38 CDT)
- Re: problem with dispdev Axel Kohlmeyer (Wed May 27 2009 - 16:20:37 CDT)
main window missing? BIN ZHANG (Wed May 27 2009 - 15:17:40 CDT)
- Re: main window missing? John Stone (Wed May 27 2009 - 15:30:21 CDT)
  - Re: main window missing? BIN ZHANG (Wed May 27 2009 - 15:49:40 CDT)
    - Re: main window missing? John Stone (Wed May 27 2009 - 16:00:55 CDT)
    - Re: main window missing? BIN ZHANG (Wed May 27 2009 - 16:36:07 CDT)
- Re: main window missing? Axel Kohlmeyer (Wed May 27 2009 - 16:01:33 CDT)
Need testers for VMD/Tachyon volumetric coloring feature :-) John Stone (Wed May 27 2009 - 14:37:59 CDT)
Angles in psf file KIRTANA S (Tue May 26 2009 - 15:05:20 CDT)
Re: new problem John Stone (Tue May 26 2009 - 11:05:07 CDT)
Heat capacity zizi moradi (Sun May 24 2009 - 16:39:45 CDT)
Isosurface and Fieldlines Not rendered in colour Burak Cankurtaran (Tue May 26 2009 - 00:15:44 CDT)
- Re: Isosurface and Fieldlines Not rendered in colour Axel Kohlmeyer (Tue May 26 2009 - 08:44:49 CDT)
- Re: Isosurface and Fieldlines Not rendered in colour John Stone (Tue May 26 2009 - 02:42:15 CDT)
  - Re: Isosurface and Fieldlines Not rendered in colour Burak Cankurtaran (Tue May 26 2009 - 21:17:36 CDT)
Plugin: molfile_plugin_t filename_extension; problem and bug... Rob (Sun May 24 2009 - 22:39:33 CDT)
- Re: Plugin: molfile_plugin_t filename_extension; problem and bug... Axel Kohlmeyer (Mon May 25 2009 - 09:52:04 CDT)
- Re: Plugin: molfile_plugin_t filename_extension; problem and bug... John Stone (Mon May 25 2009 - 23:28:34 CDT)
VMD crashes in VolumeSlice representation Suman Chakrabarty (Sun May 24 2009 - 13:09:10 CDT)
- Re: VMD crashes in VolumeSlice representation Axel Kohlmeyer (Sun May 24 2009 - 13:49:41 CDT)
- Re: VMD crashes in VolumeSlice representation John Stone (Mon May 25 2009 - 23:20:24 CDT)
Problem in loading data Jae Hyun Park (Sun May 24 2009 - 10:38:24 CDT)
- Re: Problem in loading data Axel Kohlmeyer (Sun May 24 2009 - 11:08:09 CDT)
- Re: Problem in loading data Peter Freddolino (Sun May 24 2009 - 17:53:19 CDT)
"Determine file type" list is far too long... Rob (Sun May 24 2009 - 04:45:30 CDT)
- Re: "Determine file type" list is far too long... Axel Kohlmeyer (Sun May 24 2009 - 08:52:35 CDT)
  - Re: "Determine file type" list is far too long... John Stone (Mon May 25 2009 - 23:09:16 CDT)
- Re: "Determine file type" list is far too long... Axel Kohlmeyer (Sun May 24 2009 - 11:40:33 CDT)
solvent accessible surface area zizi moradi (Sat May 23 2009 - 13:11:19 CDT)
- Re: solvent accessible surface area Peter Freddolino (Sat May 23 2009 - 14:19:37 CDT)
Offset for frame ids in dcd trajectory DimitryASuplatov (Sat May 23 2009 - 11:11:09 CDT)
- Re: Offset for frame ids in dcd trajectory John Stone (Tue May 26 2009 - 15:32:40 CDT)
Operations with MD frames - acquiring time infromation DimitryASuplatov (Sat May 23 2009 - 08:16:37 CDT)
- Re: Operations with MD frames - acquiring time infromation Peter Freddolino (Sat May 23 2009 - 09:09:49 CDT)
  - Re: Operations with MD frames - acquiring time infromation DimitryASuplatov (Sat May 23 2009 - 09:21:49 CDT)
    - Re: Operations with MD frames - acquiring time infromation Peter Freddolino (Sat May 23 2009 - 09:43:28 CDT)
    - Re: Operations with MD frames - acquiring time infromation John Stone (Mon May 25 2009 - 23:44:49 CDT)
Question3 about introducing variables in "mol selection..." Alberto Sergio Garay (Fri May 22 2009 - 16:47:25 CDT)
- Re: Question3 about introducing variables in "mol selection..." Axel Kohlmeyer (Fri May 22 2009 - 17:09:08 CDT)
Question2 about introducing variables in "mol selection..." Alberto Sergio Garay (Fri May 22 2009 - 15:31:51 CDT)
- Re: Question2 about introducing variables in "mol selection..." Axel Kohlmeyer (Fri May 22 2009 - 16:10:24 CDT)
Question about introducing variables in "mol selection..." Alberto Sergio Garay (Fri May 22 2009 - 10:06:54 CDT)
- Re: Question about introducing variables in "mol selection..." Peter Freddolino (Fri May 22 2009 - 10:18:59 CDT)
- Re: Question about introducing variables in "mol selection..." Axel Kohlmeyer (Fri May 22 2009 - 11:34:03 CDT)
abinit plugin for VMD not yet tried? Rob (Fri May 22 2009 - 02:08:15 CDT)
- Re: abinit plugin for VMD not yet tried? Axel Kohlmeyer (Fri May 22 2009 - 10:05:14 CDT)
- Re: abinit plugin for VMD not yet tried? Rob (Sun May 24 2009 - 04:31:17 CDT)
  - Re: Re: abinit plugin for VMD not yet tried? Axel Kohlmeyer (Sun May 24 2009 - 08:38:11 CDT)
- Re: abinit plugin for VMD not yet tried? Rob (Mon May 25 2009 - 02:04:57 CDT)
  - Re: Re: abinit plugin for VMD not yet tried? Axel Kohlmeyer (Mon May 25 2009 - 10:05:30 CDT)
bonds in .psf file KIRTANA S (Thu May 21 2009 - 12:32:35 CDT)
- Re: bonds in .psf file Axel Kohlmeyer (Thu May 21 2009 - 12:48:40 CDT)
angles and dihedrals in .psf file KIRTANA S (Thu May 21 2009 - 10:45:51 CDT)
- Re: angles and dihedrals in .psf file Axel Kohlmeyer (Thu May 21 2009 - 11:28:15 CDT)
RMSF Maria Sanchez (Wed May 20 2009 - 23:14:17 CDT)
- Re: RMSF John Stone (Fri May 22 2009 - 10:57:39 CDT)
pdb file generated not readable by tleap Yi Shang (Wed May 20 2009 - 14:49:26 CDT)
- Re: pdb file generated not readable by tleap Axel Kohlmeyer (Wed May 20 2009 - 16:28:54 CDT)
  - Re: pdb file generated not readable by tleap Myunggi Yi (Fri May 22 2009 - 09:19:36 CDT)
    - Re: pdb file generated not readable by tleap Axel Kohlmeyer (Fri May 22 2009 - 10:08:06 CDT)
Re: Distance between COM for 2 chains for each frame of trajectory Axel Kohlmeyer (Wed May 20 2009 - 14:05:27 CDT)
Distance between COM for 2 chains for each frame of trajectory Florentina Tofoleanu (Wed May 20 2009 - 11:34:18 CDT)
- Re: Distance between COM for 2 chains for each frame of trajectory Axel Kohlmeyer (Wed May 20 2009 - 12:09:39 CDT)
how to load a state from the command line maria goranovic (Wed May 20 2009 - 09:21:13 CDT)
- Re: how to load a state from the command line Axel Kohlmeyer (Wed May 20 2009 - 09:51:47 CDT)
- Re: how to load a state from the command line Ondrej Marsalek (Wed May 20 2009 - 10:18:24 CDT)
VMD 1.8.7b3 and desktop effects on Fedora 10 Nicolas Sapay (Wed May 20 2009 - 07:48:33 CDT)
- Re: VMD 1.8.7b3 and desktop effects on Fedora 10 Axel Kohlmeyer (Wed May 20 2009 - 08:43:16 CDT)
- Re: VMD 1.8.7b3 and desktop effects on Fedora 10 John Stone (Wed May 20 2009 - 20:54:32 CDT)
default colors MyLinkka (Wed May 20 2009 - 07:11:35 CDT)
- Re: default colors Axel Kohlmeyer (Wed May 20 2009 - 09:38:40 CDT)
  - Re: default colors MyLinkka (Wed May 20 2009 - 11:58:57 CDT)
    - Re: default colors Axel Kohlmeyer (Mon May 25 2009 - 16:10:47 CDT)
    - Re: default colors MyLinkka (Tue May 26 2009 - 04:57:50 CDT)
- Re: default colors John Stone (Wed May 20 2009 - 21:11:25 CDT)
- Re: default colors John Stone (Tue May 26 2009 - 17:03:39 CDT)
  - Re: default colors MyLinkka (Fri May 29 2009 - 05:15:26 CDT)
Why is the 'antialias' option is grey? MyLinkka (Wed May 20 2009 - 05:37:47 CDT)
- Re: Why is the 'antialias' option is grey? John Stone (Wed May 20 2009 - 06:58:21 CDT)
  - Re: Why is the 'antialias' option is grey? MyLinkka (Wed May 20 2009 - 07:31:01 CDT)
Request for change in gaussian cube reader Xavier Cartoixa Soler (Tue May 19 2009 - 13:40:37 CDT)
- Re: Request for change in gaussian cube reader Axel Kohlmeyer (Tue May 19 2009 - 14:32:10 CDT)
NVidia GeForce 3D Vision Christoph Weber (Tue May 19 2009 - 12:38:08 CDT)
- Re: NVidia GeForce 3D Vision John Stone (Tue May 19 2009 - 20:28:10 CDT)
Align mistake Andres Morales N (Tue May 19 2009 - 11:14:21 CDT)
- Re: Align mistake John Stone (Tue May 19 2009 - 20:32:52 CDT)
Average strcuture Andres Morales N (Tue May 19 2009 - 08:51:23 CDT)
- Re: Average strcuture jen hsin (Tue May 19 2009 - 09:08:41 CDT)
  - RE: Average strcuture Andres Morales N (Tue May 19 2009 - 10:21:28 CDT)
New vmd Windows version crash MyLinkka (Tue May 19 2009 - 05:14:34 CDT)
- Re: New vmd Windows version crash John Stone (Tue May 19 2009 - 21:02:57 CDT)
Adding two separate pdb files: Lipid Bilayer's with Protein's Lalit (Mon May 18 2009 - 18:07:34 CDT)
- Re: Adding two separate pdb files: Lipid Bilayer's with Protein's David Tanner (Tue May 19 2009 - 11:00:30 CDT)
  - Re: Adding two separate pdb files: Lipid Bilayer's with Protein's Lalit (Wed May 20 2009 - 13:36:56 CDT)
    - Re: Adding two separate pdb files: Lipid Bilayer's with Protein's Axel Kohlmeyer (Wed May 20 2009 - 16:34:45 CDT)
VMD 1.8.7 beta 3 posted for download... John Stone (Mon May 18 2009 - 15:24:21 CDT)
- Re: VMD 1.8.7 beta 3 posted for download... Axel Kohlmeyer (Mon May 18 2009 - 20:29:44 CDT)
  - Re: VMD 1.8.7 beta 3 posted for download... Thomas Evangelidis (Wed May 20 2009 - 23:20:38 CDT)
    - Re: VMD 1.8.7 beta 3 posted for download... Axel Kohlmeyer (Sun May 24 2009 - 19:52:41 CDT)
    - bigdcd are related issues. was: Re: VMD 1.8.7 beta 3 posted for download... Axel Kohlmeyer (Mon May 25 2009 - 11:42:59 CDT)
Model building questions YangMingjun (Mon May 18 2009 - 08:14:38 CDT)
VMD as a python module Ondrej Marsalek (Mon May 18 2009 - 04:45:39 CDT)
- Re: VMD as a python module Axel Kohlmeyer (Mon May 18 2009 - 09:27:16 CDT)
  - Re: VMD as a python module Ondrej Marsalek (Mon May 18 2009 - 11:30:55 CDT)
resolved [Re: vmd / python / f10] Cameron Mura (Sun May 17 2009 - 19:07:47 CDT)
- Re: resolved [Re: vmd / python / f10] John Stone (Mon May 18 2009 - 00:15:06 CDT)
vmd / python / f10 Cameron Mura (Sat May 16 2009 - 18:43:18 CDT)
- Re: vmd / python / f10 John Stone (Sat May 16 2009 - 18:57:24 CDT)
  - Re: vmd / python / f10 Cameron Mura (Sat May 16 2009 - 22:00:29 CDT)
    - Re: vmd / python / f10 Axel Kohlmeyer (Sun May 17 2009 - 08:37:47 CDT)
    - Re: vmd / python / f10 John Stone (Sun May 17 2009 - 12:20:39 CDT)
Change requested in lammps plugin for VMD Gopinath Subramanian (Fri May 15 2009 - 11:42:38 CDT)
- Re: Change requested in lammps plugin for VMD Axel Kohlmeyer (Fri May 15 2009 - 12:32:48 CDT)
adding bonds with the mouse and writing psf Maxim Paliy. (Thu May 14 2009 - 20:01:40 CDT)
- Re: adding bonds with the mouse and writing psf John Stone (Thu May 14 2009 - 20:59:20 CDT)
- Re: adding bonds with the mouse and writing psf Axel Kohlmeyer (Fri May 15 2009 - 10:28:59 CDT)
a small bug in solvate 1.3 Maxim Paliy. (Thu May 14 2009 - 19:06:32 CDT)
- Re: a small bug in solvate 1.3 John Stone (Thu May 14 2009 - 20:45:17 CDT)
solvate v1.3 bug Íõ—² (Thu May 14 2009 - 07:43:23 CDT)
How to color atom by charge loc duong ding (Thu May 14 2009 - 00:46:38 CDT)
- Re: How to color atom by charge Axel Kohlmeyer (Thu May 14 2009 - 07:01:32 CDT)
Translate Andres Morales N (Wed May 13 2009 - 22:25:22 CDT)
- Re: Translate Peter Freddolino (Wed May 13 2009 - 22:41:34 CDT)
Color problem. knowlesc_at_msu.edu (Wed May 13 2009 - 13:55:31 CDT)
- Re: Color problem. John Stone (Wed May 13 2009 - 16:17:12 CDT)
  - Re: Color problem. Axel Kohlmeyer (Wed May 13 2009 - 17:45:44 CDT)
Can bonds radius be controlled by tcl command? accomp lin (Wed May 13 2009 - 03:54:47 CDT)
- Re: Can bonds radius be controlled by tcl command? John Stone (Wed May 13 2009 - 16:19:16 CDT)
  - Re: Can bonds radius be controlled by tcl command? Roman Petrenko (Wed May 13 2009 - 17:09:09 CDT)
    - Re: Can bonds radius be controlled by tcl command? Axel Kohlmeyer (Wed May 13 2009 - 17:55:17 CDT)
VMD 1.8.7 beta 2 posted for download John Stone (Wed May 13 2009 - 14:09:40 CDT)
- namdenergy missing for -dispdev none (vmd 1.8.6) Thomas C. Bishop (Fri May 15 2009 - 12:37:13 CDT)
  - Re: namdenergy missing for -dispdev none (vmd 1.8.6) Peter Freddolino (Fri May 15 2009 - 12:43:50 CDT)
  - Re: namdenergy missing for -dispdev none (vmd 1.8.6) Axel Kohlmeyer (Fri May 15 2009 - 13:27:22 CDT)
Axes Andres Morales N (Wed May 13 2009 - 08:42:45 CDT)
Sphere representaion with radius from pdb field "occupancy" or "temp. fac" Thomas Zauner (Wed May 13 2009 - 05:08:50 CDT)
- Re: Sphere representaion with radius from pdb field "occupancy" or "temp. fac" Axel Kohlmeyer (Wed May 13 2009 - 05:56:32 CDT)
Alignment Andres Morales N (Mon May 11 2009 - 21:44:55 CDT)
selecting waters Mark M Huntress (Mon May 11 2009 - 12:35:10 CDT)
- Re: selecting waters Rogan Carr (Mon May 11 2009 - 12:53:28 CDT)
  - Re: selecting waters cmhartshorn (Mon May 11 2009 - 17:31:55 CDT)
- Re: selecting waters Axel Kohlmeyer (Mon May 11 2009 - 13:11:50 CDT)
calculate charges of the binding site residues with psfgen Thomas Evangelidis (Sat May 09 2009 - 22:54:16 CDT)
- Re: calculate charges of the binding site residues with psfgen Axel Kohlmeyer (Sun May 10 2009 - 07:00:29 CDT)
How to compute excluded volume using volmap? Suman Chakrabarty (Sat May 09 2009 - 14:46:31 CDT)
- Re: How to compute excluded volume using volmap? Suman Chakrabarty (Tue May 12 2009 - 07:53:12 CDT)
  - Re: How to compute excluded volume using volmap? Axel Kohlmeyer (Tue May 12 2009 - 08:47:43 CDT)
Paratool:Problems to load Hessian for charge distribution Sabine Leroch (Fri May 08 2009 - 11:12:05 CDT)
- Re: Paratool:Problems to load Hessian for charge distribution saam (Sat May 09 2009 - 08:06:00 CDT)
volmap question Jian Dai (Fri May 08 2009 - 01:22:22 CDT)
- Re: volmap question John Stone (Fri May 08 2009 - 09:49:33 CDT)
Thiol on gold KIRTANA S (Thu May 07 2009 - 23:57:48 CDT)
- Re: Thiol on gold Axel Kohlmeyer (Fri May 08 2009 - 10:17:49 CDT)
vmd-read data from lammps H Q (Thu May 07 2009 - 20:26:53 CDT)
- Re: vmd-read data from lammps Axel Kohlmeyer (Thu May 07 2009 - 21:22:51 CDT)
namdenergy BIN ZHANG (Thu May 07 2009 - 17:26:23 CDT)
- Re: namdenergy Peter Freddolino (Thu May 07 2009 - 22:45:00 CDT)
  - Re: namdenergy BIN ZHANG (Mon May 11 2009 - 12:29:37 CDT)
    - Re: namdenergy Peter Freddolino (Mon May 11 2009 - 12:37:07 CDT)
BMP snapshot Tawhid Ezaz (Thu May 07 2009 - 14:04:58 CDT)
- Re: BMP snapshot Eric H. Lee (Thu May 07 2009 - 14:26:24 CDT)
- Re: BMP snapshot John Stone (Thu May 07 2009 - 14:24:57 CDT)
Display not updated when using move() from Python in VMD 1.8.6 Pawel Kedzierski (Wed May 06 2009 - 13:50:47 CDT)
- Re: Display not updated when using move() from Python in VMD 1.8.6 Axel Kohlmeyer (Wed May 06 2009 - 18:18:54 CDT)
  - calculate charges of the binding site residues with psfgen Thomas Evangelidis (Wed May 06 2009 - 20:19:54 CDT)
  - Re: Display not updated when using move() from Python in VMD 1.8.6 Pawel Kedzierski (Thu May 07 2009 - 07:31:25 CDT)
memory allocation issue Edward Lyman (Wed May 06 2009 - 13:37:04 CDT)
- Re: memory allocation issue Leonardo Trabuco (Wed May 06 2009 - 13:48:12 CDT)
Postdoc position in computational biophysics and nanotehnology Aleksei Aksimentiev (Tue May 05 2009 - 14:28:20 CDT)
Satellite tobacco mosaic virus images making by VMD ÖÜÎÄ²ý (Tue May 05 2009 - 08:31:33 CDT)
- Re: Satellite tobacco mosaic virus images making by VMD John Stone (Tue May 05 2009 - 09:24:32 CDT)
  - Re: Satellite tobacco mosaic virus images making by VMD ÖÜÎÄ²ý (Tue May 05 2009 - 10:16:45 CDT)
    - Re: Satellite tobacco mosaic virus images making by VMD John Stone (Tue May 05 2009 - 10:28:42 CDT)
    - Re: Satellite tobacco mosaic virus images making by VMD Anton Arkhipov (Tue May 05 2009 - 12:48:10 CDT)
VMD 1.8.7beta1 doesn't close OpenGL window Olaf Lenz (Tue May 05 2009 - 07:53:57 CDT)
- Re: VMD 1.8.7beta1 doesn't close OpenGL window Axel Kohlmeyer (Tue May 05 2009 - 08:26:03 CDT)
  - Re: VMD 1.8.7beta1 doesn't close OpenGL window Olaf Lenz (Tue May 05 2009 - 09:07:35 CDT)
    - Re: VMD 1.8.7beta1 doesn't close OpenGL window John Stone (Tue May 05 2009 - 09:27:10 CDT)
Solvation energies using implicit ligand sampling Richard Daigle (Mon May 04 2009 - 12:21:41 CDT)
- Re: Solvation energies using implicit ligand sampling John Stone (Mon May 04 2009 - 13:49:44 CDT)
  - Re: Solvation energies using implicit ligand sampling Richard Daigle (Mon May 04 2009 - 14:06:22 CDT)
- Re: Solvation energies using implicit ligand sampling saam (Mon May 04 2009 - 14:31:31 CDT)
VMD on Cray/CNL Jim Pfaendtner (Fri May 01 2009 - 01:03:07 CDT)
- Re: VMD on Cray/CNL John Stone (Fri May 01 2009 - 01:20:53 CDT)
  - Re: VMD on Cray/CNL Jim Pfaendtner (Fri May 01 2009 - 07:56:02 CDT)
    - Re: VMD on Cray/CNL John Stone (Fri May 01 2009 - 10:36:23 CDT)
autopfs: unknown atom type error when processing ATP Sasha Buzko (Thu Apr 30 2009 - 16:13:41 CDT)
- Re: autopfs: unknown atom type error when processing ATP Peter Freddolino (Thu Apr 30 2009 - 16:30:30 CDT)
  - Re: autopfs: unknown atom type error when processing ATP Sasha Buzko (Thu Apr 30 2009 - 16:38:51 CDT)
Selection "@myselection" Olaf Lenz (Thu Apr 30 2009 - 04:25:05 CDT)
- Re: Selection "@myselection" John Stone (Tue May 05 2009 - 10:17:57 CDT)
Size of a protein Khaled Barakat (Wed Apr 29 2009 - 16:06:31 CDT)
- Re: Size of a protein John Stone (Wed Apr 29 2009 - 16:15:05 CDT)
- Re: Size of a protein Axel Kohlmeyer (Wed Apr 29 2009 - 16:50:25 CDT)
VMD 1.8.7 beta 1 posted for download... John Stone (Wed Apr 29 2009 - 15:06:27 CDT)
- Re: VMD 1.8.7 beta 1 posted for download... Low Soo Mei (Wed Apr 29 2009 - 22:35:05 CDT)
  - Re: VMD 1.8.7 beta 1 posted for download... John Stone (Wed Apr 29 2009 - 22:38:21 CDT)
- vdna 2.0 for VMD Thomas C. Bishop (Tue May 12 2009 - 15:08:26 CDT)
  - Re: vdna 2.0 for VMD John Stone (Tue May 12 2009 - 16:04:44 CDT)
hydrogen bonds tcl script politr_at_huji.ac.il (Tue Apr 28 2009 - 09:40:12 CDT)
- Re: hydrogen bonds tcl script Axel Kohlmeyer (Tue Apr 28 2009 - 10:17:26 CDT)
Installation issue Hugh Martin (Tue Apr 28 2009 - 08:09:04 CDT)
- Re: Installation issue John Stone (Tue Apr 28 2009 - 09:29:20 CDT)
  - Re: Installation issue Hugh Martin (Tue Apr 28 2009 - 09:39:29 CDT)
Can the CG model built from VMD be used as an Input of NAMD,GROMACS and any other MD program? wuxiao (Tue Apr 28 2009 - 02:52:44 CDT)
- Re: Can the CG model built from VMD be used as an Input of NAMD,GROMACS and any other MD program? Axel Kohlmeyer (Tue Apr 28 2009 - 08:32:24 CDT)
  - Re: Can the CG model built from VMD be used as an Input of NAMD,GROMACS and any other MD program? Anton Arkhipov (Tue Apr 28 2009 - 10:34:04 CDT)
Manipulating dcd using script in VMD DimitryASuplatov (Tue Apr 28 2009 - 01:26:05 CDT)
- Re: Manipulating dcd using script in VMD Eduardo Cruz-Chu (Tue Apr 28 2009 - 01:55:25 CDT)
  - Re: Manipulating dcd using script in VMD David Tanner (Tue Apr 28 2009 - 08:07:24 CDT)
  - Re: Manipulating dcd using script in VMD Axel Kohlmeyer (Tue Apr 28 2009 - 08:24:04 CDT)
Molefacture "namehead" error Sebastián Gutiérrez (Mon Apr 27 2009 - 16:43:10 CDT)
- Re: Molefacture "namehead" error Peter Freddolino (Mon Apr 27 2009 - 20:29:31 CDT)
Calculating system net charge with tcl in VMD DimitryASuplatov (Mon Apr 27 2009 - 04:43:34 CDT)
- Re: Calculating system net charge with tcl in VMD Athanassios Stavrakoudis (Mon Apr 27 2009 - 05:12:18 CDT)
- Re: Calculating system net charge with tcl in VMD Peter Freddolino (Mon Apr 27 2009 - 07:02:18 CDT)
- Re: Calculating system net charge with tcl in VMD Eduardo Cruz-Chu (Mon Apr 27 2009 - 10:50:01 CDT)
Using clustering tool Andres Morales N (Fri Apr 24 2009 - 22:56:48 CDT)
- Re: Using clustering tool John Stone (Sun Apr 26 2009 - 23:10:24 CDT)
iTrajComp plugin. Andres Morales N (Fri Apr 24 2009 - 22:23:45 CDT)
- Re: iTrajComp plugin. John Stone (Sun Apr 26 2009 - 23:09:29 CDT)
graphics for publication YangMingjun (Fri Apr 24 2009 - 10:14:23 CDT)
- Re: graphics for publication Peter Freddolino (Fri Apr 24 2009 - 11:06:57 CDT)
- Re: graphics for publication Axel Kohlmeyer (Fri Apr 24 2009 - 11:26:58 CDT)
Error processing bonds Gianluca Interlandi (Fri Apr 24 2009 - 01:41:07 CDT)
- Re: Error processing bonds John Stone (Fri Apr 24 2009 - 08:03:21 CDT)
- Re: Error processing bonds Axel Kohlmeyer (Fri Apr 24 2009 - 08:42:34 CDT)
  - Re: Error processing bonds Gianluca Interlandi (Fri Apr 24 2009 - 10:15:38 CDT)
  - Re: Error processing bonds Gianluca Interlandi (Fri Apr 24 2009 - 11:12:31 CDT)
    - Re: Error processing bonds Gianluca Interlandi (Fri Apr 24 2009 - 14:09:59 CDT)
local packing density around a chemical group (say, a methyl group or a side chain) Krishnan, Marimuthu (Thu Apr 23 2009 - 10:15:44 CDT)
- Re: local packing density around a chemical group (say, a methyl group or a side chain) Axel Kohlmeyer (Thu Apr 23 2009 - 11:27:20 CDT)
  - RE: local packing density around a chemical group (say, a methyl group or a side chain) Krishnan, Marimuthu (Thu Apr 23 2009 - 12:11:07 CDT)
- Re: local packing density around a chemical group (say, a methyl group or a side chain) Leandro Martínez (Thu Apr 23 2009 - 12:22:38 CDT)
installed plugin won't show up next time accomp lin (Thu Apr 23 2009 - 06:58:38 CDT)
- Re: installed plugin won't show up next time Axel Kohlmeyer (Thu Apr 23 2009 - 08:45:51 CDT)
  - Re: installed plugin won't show up next time accomp lin (Fri Apr 24 2009 - 04:59:22 CDT)
animate read and write A D (Wed Apr 22 2009 - 15:36:00 CDT)
- Re: animate read and write John Stone (Wed Apr 22 2009 - 15:42:24 CDT)
density profiles Raul Araya (Wed Apr 22 2009 - 11:24:31 CDT)
- Re: density profiles BIN ZHANG (Wed Apr 22 2009 - 12:25:59 CDT)
- Re: density profiles Eduardo (Wed Apr 22 2009 - 22:17:42 CDT)
Select atoms using coordinates Max (Wed Apr 22 2009 - 06:09:16 CDT)
- Re: Select atoms using coordinates Rogan Carr (Wed Apr 22 2009 - 11:30:49 CDT)
- Re: Select atoms using coordinates J. Rui Rodrigues (Wed Apr 22 2009 - 13:52:07 CDT)
  - Re: Select atoms using coordinates John Stone (Wed Apr 22 2009 - 14:03:32 CDT)
    - Re: Select atoms using coordinates Max (Thu Apr 23 2009 - 03:15:15 CDT)
    - Re: Select atoms using coordinates Axel Kohlmeyer (Thu Apr 23 2009 - 08:48:57 CDT)
sys.argv, python and VMD Michael Kreim (Wed Apr 22 2009 - 03:50:59 CDT)
- Re: sys.argv, python and VMD Axel Kohlmeyer (Wed Apr 22 2009 - 10:42:58 CDT)
  - Re: sys.argv, python and VMD Michael Kreim (Fri Apr 24 2009 - 08:43:13 CDT)
setbonds BIN ZHANG (Tue Apr 21 2009 - 23:01:35 CDT)
- Re: setbonds John Stone (Tue Apr 21 2009 - 23:44:35 CDT)
  - Re: Re: setbonds zhngbn_at_gmail.com (Tue Apr 21 2009 - 23:48:30 CDT)
    - Re: setbonds Rogan Carr (Wed Apr 22 2009 - 11:29:32 CDT)
    - Re: setbonds BIN ZHANG (Wed Apr 22 2009 - 14:53:11 CDT)
Spaceball and OSX JT (Tue Apr 21 2009 - 12:30:04 CDT)
- Re: Spaceball and OSX John Stone (Tue Apr 21 2009 - 12:34:34 CDT)
  - Re: Spaceball and OSX JT (Tue Apr 21 2009 - 12:53:31 CDT)
    - Re: Spaceball and OSX JT (Tue Apr 21 2009 - 13:15:22 CDT)
    - Re: Spaceball and OSX John Stone (Tue Apr 21 2009 - 13:49:36 CDT)
Secondary Structure Depiction Daniel Gaston (Tue Apr 21 2009 - 09:25:08 CDT)
- Re: Secondary Structure Depiction L. Michel Espinoza-Fonseca (Tue Apr 21 2009 - 10:33:50 CDT)
  - Re: Secondary Structure Depiction Daniel Gaston (Tue Apr 21 2009 - 10:29:03 CDT)
    - Re: Secondary Structure Depiction Axel Kohlmeyer (Tue Apr 21 2009 - 11:23:10 CDT)
    - Re: Secondary Structure Depiction Daniel Gaston (Tue Apr 21 2009 - 12:02:29 CDT)
  - Re: Secondary Structure Depiction George Madalin Giambasu (Tue Apr 21 2009 - 11:12:54 CDT)
    - Re: Secondary Structure Depiction Axel Kohlmeyer (Tue Apr 21 2009 - 14:07:41 CDT)
- Re: Secondary Structure Depiction John Stone (Tue Apr 21 2009 - 10:51:48 CDT)
  - Re: Secondary Structure Depiction Daniel Gaston (Tue Apr 21 2009 - 12:01:08 CDT)
Mol representation using coordinates Max (Tue Apr 21 2009 - 08:50:05 CDT)
- Re: Mol representation using coordinates Rogan Carr (Tue Apr 21 2009 - 09:03:35 CDT)
RMSD-gaps Karne, Sai Harish Babu (Mon Apr 20 2009 - 17:09:51 CDT)
- Re: RMSD-gaps Daniel Gaston (Mon Apr 20 2009 - 18:57:33 CDT)
  - Re: RMSD-gaps Karne, Sai Harish Babu (Mon Apr 20 2009 - 21:04:53 CDT)
Solvent Accessible Surface Area zizi moradi (Sun Apr 19 2009 - 09:01:49 CDT)
- Re: Solvent Accessible Surface Area John Stone (Wed Apr 22 2009 - 14:14:01 CDT)
(no subject) zizi moradi (Sun Apr 19 2009 - 08:55:44 CDT)
Possible bug in vmd 1.8.7 alpha? Cesar Millan (Sat Apr 18 2009 - 00:09:57 CDT)
- Re: Possible bug in vmd 1.8.7 alpha? Axel Kohlmeyer (Sat Apr 18 2009 - 10:15:24 CDT)
- Re: Possible bug in vmd 1.8.7 alpha? John Stone (Sat Apr 18 2009 - 17:02:20 CDT)
coloring by atom type Ryan Pavlovicz (Fri Apr 17 2009 - 15:53:29 CDT)
- Re: coloring by atom type Rogan Carr (Sat Apr 18 2009 - 16:53:39 CDT)
Re: namd-l: display all frames simultaneously Samuel Coulbourn Flores èŠ±å±± (Fri Apr 17 2009 - 11:35:11 CDT)
pbctools on alpha version Dan Lussier (Fri Apr 17 2009 - 09:05:06 CDT)
- Re: pbctools on alpha version Olaf Lenz (Sat Apr 18 2009 - 04:18:50 CDT)
  - Re: pbctools on alpha version Axel Kohlmeyer (Sat Apr 18 2009 - 10:11:47 CDT)
    - Re: pbctools on alpha version Dan Lussier (Wed Apr 22 2009 - 03:46:23 CDT)
    - Re: pbctools on alpha version Olaf Lenz (Wed Apr 22 2009 - 06:14:42 CDT)
psf file for Doxorubicin mishacat_at_udm.ru (Thu Apr 16 2009 - 08:32:14 CDT)
- display all frames simultaneously Samuel Coulbourn Flores èŠ±å±± (Thu Apr 16 2009 - 21:35:59 CDT)
  - Re: display all frames simultaneously Axel Kohlmeyer (Thu Apr 16 2009 - 22:11:12 CDT)
  - Re: display all frames simultaneously Peter Freddolino (Thu Apr 16 2009 - 22:32:26 CDT)
Multiseq error Karne, Sai Harish Babu (Wed Apr 15 2009 - 13:48:18 CDT)
- Re: Multiseq error John Stone (Wed Apr 15 2009 - 13:57:57 CDT)
VRPN & PHANToM Omni Mark Cunningham (Wed Apr 15 2009 - 13:40:03 CDT)
- Re: VRPN & PHANToM Omni John Stone (Wed Apr 15 2009 - 13:59:42 CDT)
Problem in finding the HBonds Manishi Pandey (Wed Apr 15 2009 - 02:50:29 CDT)
- RE: Problem in finding the HBonds Irene Newhouse (Wed Apr 15 2009 - 03:56:52 CDT)
- Re: Problem in finding the HBonds Axel Kohlmeyer (Wed Apr 15 2009 - 07:56:52 CDT)
(no subject) Narasimhan LOGANATHAN (Tue Apr 14 2009 - 04:33:39 CDT)
- Re: Axel Kohlmeyer (Tue Apr 14 2009 - 07:25:54 CDT)
RMSD of a protein shell, from the NAMD traj priyodorshi satpati (Sun Apr 12 2009 - 11:02:13 CDT)
- Re: RMSD of a protein shell, from the NAMD traj John Stone (Sun Apr 26 2009 - 23:59:51 CDT)
within, used with pbcwrap Neelanjana Sengupta (Fri Apr 10 2009 - 06:35:19 CDT)
- Re: within, used with pbcwrap Axel Kohlmeyer (Fri Apr 10 2009 - 09:03:36 CDT)
  - Re: within, used with pbcwrap John Stone (Fri Apr 10 2009 - 09:14:00 CDT)
    - Re: within, used with pbcwrap Neelanjana Sengupta (Sat Apr 11 2009 - 00:49:22 CDT)
    - Re: within, used with pbcwrap John Stone (Sat Apr 11 2009 - 09:36:08 CDT)
- Re: within, used with pbcwrap Olaf Lenz (Sat Apr 11 2009 - 07:15:51 CDT)
install plugin: problems with vmd_install_extension Steve Massard (Fri Apr 10 2009 - 04:35:45 CDT)
- Re: install plugin: problems with vmd_install_extension Axel Kohlmeyer (Fri Apr 10 2009 - 09:10:13 CDT)
  - Re: install plugin: problems with vmd_install_extension Axel Kohlmeyer (Fri Apr 10 2009 - 10:13:57 CDT)
Release of R.E.D. Server FyD (Thu Apr 09 2009 - 03:31:30 CDT)
isosurface saving question YI Zhang (Tue Apr 07 2009 - 20:41:17 CDT)
about TkConsole cong chen (Mon Apr 06 2009 - 23:16:19 CDT)
- Re: about TkConsole Axel Kohlmeyer (Tue Apr 07 2009 - 12:58:48 CDT)
  - Re: about TkConsole cong chen (Tue Apr 07 2009 - 20:04:45 CDT)
    - Re: about TkConsole Axel Kohlmeyer (Tue Apr 07 2009 - 21:32:40 CDT)
  - Re: about TkConsole cong chen (Wed Apr 08 2009 - 07:27:52 CDT)
Any Mac (Intel) users still running 10.4.x??? John Stone (Sun Apr 05 2009 - 10:13:08 CDT)
- Re: Any Mac (Intel) users still running 10.4.x??? John Stone (Mon Apr 06 2009 - 11:34:31 CDT)
OS X intel binary problem Dan Lussier (Sun Apr 05 2009 - 03:02:20 CDT)
- Re: OS X intel binary problem Axel Kohlmeyer (Sun Apr 05 2009 - 09:05:07 CDT)
  - Re: OS X intel binary problem Dan Lussier (Sun Apr 05 2009 - 09:40:26 CDT)
    - Re: OS X intel binary problem Axel Kohlmeyer (Sun Apr 05 2009 - 09:48:37 CDT)
    - Re: OS X intel binary problem John Stone (Sun Apr 05 2009 - 09:48:59 CDT)
(no subject) Crowley, Michael (Sun Apr 05 2009 - 00:48:58 CDT)
- too many bonds Crowley, Michael (Sun Apr 05 2009 - 01:27:03 CDT)
  - Re: too many bonds JT (Sun Apr 05 2009 - 03:06:17 CDT)
    - Re: too many bonds Axel Kohlmeyer (Sun Apr 05 2009 - 08:57:59 CDT)
ligand names Katherine Parra (Fri Apr 03 2009 - 10:35:54 CDT)
- Re: ligand names Peter Freddolino (Fri Apr 03 2009 - 15:54:42 CDT)
questions about the electron density map YI Zhang (Fri Apr 03 2009 - 05:38:54 CDT)
- Re: questions about the electron density map John Stone (Fri Apr 03 2009 - 08:00:39 CDT)
Problem with autoionize ? Kalavera_at_gmx.net (Thu Apr 02 2009 - 08:50:49 CDT)
- Re: Problem with autoionize ? Axel Kohlmeyer (Thu Apr 02 2009 - 09:25:33 CDT)
  - Re: Problem with autoionize ? Kalavera_at_gmx.net (Thu Apr 02 2009 - 09:58:53 CDT)
    - Re: Problem with autoionize ? Axel Kohlmeyer (Thu Apr 02 2009 - 11:46:33 CDT)
H-bonds Bernhard Knapp (Thu Apr 02 2009 - 06:27:25 CDT)
- Re: H-bonds Peter Freddolino (Thu Apr 02 2009 - 09:27:02 CDT)
VMD atomselect Steve Massard (Thu Apr 02 2009 - 05:57:37 CDT)
- Re: VMD atomselect J. Rui Rodrigues (Thu Apr 02 2009 - 07:19:40 CDT)
pairInteraction and NAMDEnergy Goutham (Wed Apr 01 2009 - 17:05:52 CDT)
- Re: pairInteraction and NAMDEnergy Peter Freddolino (Wed Apr 01 2009 - 20:12:19 CDT)
  - Re: pairInteraction and NAMDEnergy Goutham (Wed Apr 01 2009 - 22:43:23 CDT)
    - Re: pairInteraction and NAMDEnergy Peter Freddolino (Wed Apr 01 2009 - 22:49:26 CDT)
    - Re: pairInteraction and NAMDEnergy Goutham (Thu Apr 02 2009 - 11:21:27 CDT)
paratool questions Lisa Brown (Tue Mar 31 2009 - 15:25:00 CDT)
pKa and Temperature in MD Caterina Bernini (Tue Mar 31 2009 - 14:47:39 CDT)
Re: vmd cvs compilation with CUDA fails John Stone (Tue Mar 31 2009 - 14:26:31 CDT)
Re: cvs plugins do not compile because of errors in the sgsmooth.C John Stone (Tue Mar 31 2009 - 13:34:05 CDT)
- RE: cvs plugins do not compile because of errors in the sgsmooth.C Cojocaru,Vlad (Tue Mar 31 2009 - 13:40:47 CDT)
helix axes Alison Grinthal (Tue Mar 31 2009 - 07:34:56 CDT)
- Re: helix axes Thomas C. Bishop (Tue Mar 31 2009 - 09:44:21 CDT)
  - Re: helix axes Peter Freddolino (Tue Mar 31 2009 - 09:51:11 CDT)
  - Re: helix axes Goutham (Tue Mar 31 2009 - 10:30:30 CDT)
- RE: helix axes Wei Huang (Tue Mar 31 2009 - 10:06:20 CDT)
How to add heme to dowser plugin? Irene Newhouse (Mon Mar 30 2009 - 19:27:01 CDT)
- Re: How to add heme to dowser plugin? Axel Kohlmeyer (Mon Mar 30 2009 - 20:24:24 CDT)
  - RE: How to add heme to dowser plugin? Irene Newhouse (Mon Mar 30 2009 - 20:39:59 CDT)
  - RE: How to add heme to dowser plugin? Irene Newhouse (Tue Mar 31 2009 - 16:48:34 CDT)
selection syntax Peter Jones (Mon Mar 30 2009 - 01:54:32 CDT)
- Re: selection syntax Leonardo Trabuco (Mon Mar 30 2009 - 09:10:29 CDT)
- Re: selection syntax Anton Arkhipov (Mon Mar 30 2009 - 09:03:47 CDT)
Graphical representation Francesco Pietra (Sun Mar 29 2009 - 13:59:15 CDT)
- Re: Graphical representation Eric H. Lee (Sun Mar 29 2009 - 14:22:18 CDT)
- Re: Graphical representation Goutham (Sun Mar 29 2009 - 15:01:50 CDT)
Synchronization of statements in tcl script Raluca Mihaela ANDREI (Fri Mar 27 2009 - 12:44:32 CDT)
- Re: Synchronization of statements in tcl script John Stone (Sat Mar 28 2009 - 14:41:52 CDT)
  - Re: Synchronization of statements in tcl script Raluca Mihaela ANDREI (Tue Mar 31 2009 - 02:57:56 CDT)
    - Re: Synchronization of statements in tcl script John Stone (Wed Apr 01 2009 - 00:31:01 CDT)
openGL library Goutham (Thu Mar 26 2009 - 19:48:52 CDT)
- Re: openGL library Axel Kohlmeyer (Thu Mar 26 2009 - 20:20:31 CDT)
  - Re: openGL library Goutham (Fri Mar 27 2009 - 00:32:34 CDT)
  - Re: openGL library John Stone (Tue Mar 31 2009 - 11:38:28 CDT)
- Re: openGL library John Stone (Thu Mar 26 2009 - 21:38:22 CDT)
  - Re: openGL library Goutham (Fri Mar 27 2009 - 01:34:00 CDT)
    - Re: openGL library John Stone (Fri Mar 27 2009 - 07:53:34 CDT)
Searching for Number of Resname Ocar Campos (Thu Mar 26 2009 - 14:51:44 CDT)
- Re: Searching for Number of Resname Giovanni Bellesia (Thu Mar 26 2009 - 15:16:25 CDT)
  - Re: Searching for Number of Resname Ocar Campos (Thu Mar 26 2009 - 15:21:28 CDT)
- Re: Searching for Number of Resname Roman Petrenko (Thu Mar 26 2009 - 15:28:00 CDT)
howto select stain reveal map Francesco Pietra (Thu Mar 26 2009 - 02:30:29 CDT)
- Re: howto select stain reveal map Axel Kohlmeyer (Thu Mar 26 2009 - 06:41:07 CDT)
  - namdenergy: how set "runextcommand"? Sebastian Stolzenberg (Sat Mar 28 2009 - 18:59:33 CDT)
    - Re: namdenergy: how set "runextcommand"? Peter Freddolino (Sat Mar 28 2009 - 19:36:45 CDT)
    - building psf with CMAP, old topology remark entries still in psf Sebastian Stolzenberg (Fri Apr 10 2009 - 18:22:15 CDT)
how to make a mivie by VMD Lan He (Wed Mar 25 2009 - 17:33:41 CDT)
- Re: how to make a mivie by VMD Eric H. Lee (Wed Mar 25 2009 - 17:44:43 CDT)
  - Re: how to make a mivie by VMD Anton Arkhipov (Wed Mar 25 2009 - 18:00:10 CDT)
  - Re: how to make a mivie by VMD Eric H. Lee (Wed Mar 25 2009 - 20:37:16 CDT)
merging atomselection Goutham (Wed Mar 25 2009 - 16:54:33 CDT)
- Re: merging atomselection Axel Kohlmeyer (Wed Mar 25 2009 - 17:20:45 CDT)
- Re: merging atomselection Tomek Wlodarski (Wed Mar 25 2009 - 17:56:49 CDT)
how to block psfgen warning messages Thomas Evangelidis (Wed Mar 25 2009 - 16:11:12 CDT)
- Re: how to block psfgen warning messages Axel Kohlmeyer (Wed Mar 25 2009 - 17:17:19 CDT)
  - Re: how to block psfgen warning messages John Stone (Wed Mar 25 2009 - 23:34:08 CDT)
Rosetta Academic Training Webinar Nir London (Wed Mar 25 2009 - 11:10:34 CDT)
Command line argument Goutham (Wed Mar 25 2009 - 10:12:19 CDT)
- Re: Command line argument Axel Kohlmeyer (Wed Mar 25 2009 - 10:57:22 CDT)
External renderer not rendering colors from volumetric data Höfling Martin (Wed Mar 25 2009 - 08:34:24 CDT)
- Re: External renderer not rendering colors from volumetric data John Stone (Wed Mar 25 2009 - 09:38:18 CDT)
- Re: External renderer not rendering colors from volumetric data Michael Geoffrey Klein (Wed Mar 25 2009 - 09:35:25 CDT)
vmd_plot Francesco Pietra (Wed Mar 25 2009 - 06:16:36 CDT)
- Re: vmd_plot Axel Kohlmeyer (Wed Mar 25 2009 - 07:47:14 CDT)
GTP topology file tiziano gallo cassarino (Fri Mar 20 2009 - 08:54:12 CDT)
- Re: GTP topology file Peter Freddolino (Fri Mar 20 2009 - 12:03:01 CDT)
near clip Leandro Martínez (Fri Mar 20 2009 - 07:48:51 CDT)
- Re: near clip John Stone (Fri Mar 20 2009 - 11:52:39 CDT)
  - Re: near clip Leandro Martínez (Fri Mar 20 2009 - 14:28:53 CDT)
    - Re: near clip John Stone (Fri Mar 20 2009 - 14:53:20 CDT)
    - Re: near clip Schreiner Eduard (Wed Mar 25 2009 - 23:53:49 CDT)
VMD 1.8.7 alpha 62 posted for all mainstream platforms... John Stone (Fri Mar 20 2009 - 03:30:48 CDT)
accessing values for selection keywords Nadja Lederer (Wed Mar 18 2009 - 05:48:43 CDT)
accessing values for selection keywords Nadja Lederer (Wed Mar 18 2009 - 05:25:54 CDT)
building VMD on LINUX Raluca Mihaela ANDREI (Tue Mar 17 2009 - 06:51:51 CDT)
- Re: building VMD on LINUX Axel Kohlmeyer (Tue Mar 17 2009 - 08:58:38 CDT)
- Re: building VMD on LINUX John Stone (Tue Mar 17 2009 - 10:03:16 CDT)
paratool tutorial/ complete user guide Lisa Brown (Mon Mar 16 2009 - 14:43:49 CDT)
VMD needs your vote. Nir London (Mon Mar 16 2009 - 12:21:07 CDT)
Posting messages to VMD-L truncates the empty spaces in lines JT (Sun Mar 15 2009 - 18:58:01 CDT)
- Re: Posting messages to VMD-L truncates the empty spaces in lines John Stone (Mon Mar 16 2009 - 17:49:34 CDT)
  - Re: Posting messages to VMD-L truncates the empty spaces in lines JT (Mon Mar 16 2009 - 20:31:09 CDT)
rlwrap bug in Ubuntu Thomas Evangelidis (Sun Mar 15 2009 - 01:11:30 CDT)
- Re: rlwrap bug in Ubuntu John Stone (Sun Mar 15 2009 - 09:32:06 CDT)
- Re: rlwrap bug in Ubuntu Axel Kohlmeyer (Sun Mar 15 2009 - 09:32:49 CDT)
  - Re: rlwrap bug in Ubuntu John Stone (Sun Mar 15 2009 - 14:20:26 CDT)
    - Re: rlwrap bug in Ubuntu Axel Kohlmeyer (Sun Mar 15 2009 - 15:14:45 CDT)
how to find the sign of the dihedral angle (full message). karthigeyan karthigeyantp (Sat Mar 14 2009 - 00:23:47 CDT)
- Re: how to find the sign of the dihedral angle (full message). JT (Sat Mar 14 2009 - 03:21:33 CDT)
  - Re: Taufik Al-Sarraj (Mon Mar 16 2009 - 17:01:26 CDT)
isosurface from pdb with beta field Peter Varnai (Fri Mar 13 2009 - 16:09:33 CDT)
- Re: isosurface from pdb with beta field Peter Freddolino (Fri Mar 13 2009 - 20:26:06 CDT)
Problem with the script mono2poly.tcl Fabio Trovato (Fri Mar 13 2009 - 11:46:44 CDT)
- Re: Problem with the script mono2poly.tcl John Stone (Fri Mar 13 2009 - 12:36:37 CDT)
  - Re: Problem with the script mono2poly.tcl Fabio Trovato (Sat Mar 14 2009 - 04:56:17 CDT)
    - Re: Problem with the script mono2poly.tcl John Stone (Sun Mar 15 2009 - 14:22:19 CDT)
color update for xyz trajectory Tawhid Ezaz (Thu Mar 12 2009 - 14:52:14 CDT)
- Re: color update for xyz trajectory John Stone (Thu Mar 12 2009 - 14:57:03 CDT)
question of iso-surface in VMD graphical representations HeeSung Choi (Thu Mar 12 2009 - 13:04:01 CDT)
- Re: question of iso-surface in VMD graphical representations John Stone (Thu Mar 12 2009 - 13:17:23 CDT)
  - Re: question of iso-surface in VMD graphical representations HeeSung Choi (Thu Mar 12 2009 - 14:13:42 CDT)
Script problem Christopher Hartshorn (Thu Mar 12 2009 - 03:40:50 CDT)
- Re: Script problem J. Rui Rodrigues (Thu Mar 12 2009 - 06:16:17 CDT)
  - Re: Script problem J. Rui Rodrigues (Thu Mar 12 2009 - 07:01:30 CDT)
- Re: Script problem Peter Freddolino (Thu Mar 12 2009 - 07:07:14 CDT)
pops/popc lipid bilayer Jianping Lin (Wed Mar 11 2009 - 19:32:42 CDT)
How to use " segment " in tcl script. accomp lin (Wed Mar 11 2009 - 01:31:13 CDT)
- Re: How to use " segment " in tcl script. Axel Kohlmeyer (Wed Mar 11 2009 - 10:15:05 CDT)
obj export Raluca Mihaela ANDREI (Tue Mar 10 2009 - 03:27:40 CDT)
- Re: obj export Axel Kohlmeyer (Tue Mar 10 2009 - 09:24:01 CDT)
  - Re: obj export Raluca Mihaela ANDREI (Tue Mar 10 2009 - 10:02:01 CDT)
    - Re: obj export Axel Kohlmeyer (Tue Mar 10 2009 - 10:25:07 CDT)
    - Re: obj export John Stone (Tue Mar 10 2009 - 12:01:10 CDT)
- Re: obj export John Stone (Tue Mar 10 2009 - 21:56:21 CDT)
  - Re: obj export Raluca Mihaela ANDREI (Wed Mar 11 2009 - 10:04:07 CDT)
regarding draw_arrow.tcl Falgun Shah (Mon Mar 09 2009 - 17:55:58 CDT)
- Re: regarding draw_arrow.tcl John Stone (Wed Mar 11 2009 - 10:36:05 CDT)
  - Re: regarding draw_arrow.tcl Axel Kohlmeyer (Wed Mar 11 2009 - 11:30:30 CDT)
  - Re: regarding draw_arrow.tcl Falgun Shah (Fri Mar 13 2009 - 08:56:31 CDT)
(no subject) Leonhard Henkes (Mon Mar 09 2009 - 07:08:32 CDT)
- <please insert a decent subject here next time, thanks> Axel Kohlmeyer (Mon Mar 09 2009 - 12:08:49 CDT)
- selecting ribose atoms? Samuel Coulbourn Flores (Fri May 01 2009 - 18:47:46 CDT)
  - Re: selecting ribose atoms? Axel Kohlmeyer (Fri May 01 2009 - 19:48:34 CDT)
    - Re: selecting ribose atoms? Samuel Coulbourn Flores (Fri May 01 2009 - 19:59:48 CDT)
vmd crashes bo baker (Mon Mar 09 2009 - 04:49:42 CDT)
- Re: vmd crashes John Stone (Mon Mar 09 2009 - 09:36:56 CDT)
  - Re: vmd crashes bo baker (Mon Mar 09 2009 - 19:09:59 CDT)
    - Re: vmd crashes John Stone (Tue Mar 10 2009 - 21:58:40 CDT)
motion correlation map Falgun Shah (Sun Mar 08 2009 - 12:41:18 CDT)
charmm binary ele. pot. Jure Praznikar (Sun Mar 08 2009 - 11:36:47 CDT)
- Re: charmm binary ele. pot. John Stone (Mon Mar 09 2009 - 09:45:56 CDT)
  - Re: charmm binary ele. pot. Axel Kohlmeyer (Mon Mar 09 2009 - 11:57:21 CDT)
  - Re: charmm binary ele. pot. John Stone (Wed Mar 11 2009 - 14:45:06 CDT)
the scripting interface Dawn (Sun Mar 08 2009 - 10:00:19 CDT)
- Re: the scripting interface John Stone (Mon Mar 09 2009 - 09:43:16 CDT)
correlation Dawn (Sun Mar 08 2009 - 03:05:49 CDT)
- Re: correlation Axel Kohlmeyer (Sun Mar 08 2009 - 10:33:03 CDT)
problem with Dowser Irene Newhouse (Sat Mar 07 2009 - 19:50:35 CST)
- Re: problem with Dowser Leonardo Trabuco (Sat Mar 07 2009 - 20:07:47 CST)
- Re: problem with Dowser Axel Kohlmeyer (Sat Mar 07 2009 - 20:18:42 CST)
  - RE: problem with Dowser Irene Newhouse (Sun Mar 08 2009 - 00:55:03 CST)
    - Re: problem with Dowser Leonardo Trabuco (Tue Mar 10 2009 - 22:41:52 CDT)
    - RE: problem with Dowser Irene Newhouse (Wed Mar 11 2009 - 00:59:08 CDT)
Save thousands... no one will know Olivia Reilly (Sat Mar 07 2009 - 11:23:52 CST)
Your C0deine 0rder #247424 Fran Villa (Fri Mar 06 2009 - 19:51:11 CST)
Charm force field for POPS lipid Jianping Lin (Fri Mar 06 2009 - 15:56:34 CST)
Re: adding lipid bilayers Ramya Gamini (Fri Mar 06 2009 - 02:06:17 CST)
- Re: adding lipid bilayers Goutham (Fri Mar 06 2009 - 08:38:25 CST)
adding lipid bilayers Goutham (Fri Mar 06 2009 - 00:46:47 CST)
use of spring tcl script Falgun Shah (Thu Mar 05 2009 - 20:49:30 CST)
Script for calculating hydrogen-bonding energy Jianping Lin (Thu Mar 05 2009 - 19:19:28 CST)
Hydrophobicity Scale Goutham (Thu Mar 05 2009 - 18:58:41 CST)
- Re: Hydrophobicity Scale John Stone (Thu Mar 05 2009 - 19:17:49 CST)
  - Re: Hydrophobicity Scale Goutham (Thu Mar 05 2009 - 19:36:46 CST)
  - Re: Hydrophobicity Scale Ramya Gamini (Thu Mar 05 2009 - 20:20:42 CST)
    - Re: Hydrophobicity Scale Ramya Gamini (Thu Mar 05 2009 - 20:36:34 CST)
Re: selection by residue Marius Retegan (Thu Mar 05 2009 - 08:29:28 CST)
selection by residue Marius Retegan (Thu Mar 05 2009 - 06:47:53 CST)
- Re: selection by residue Nicolas (Thu Mar 05 2009 - 10:34:05 CST)
Seventh European Workshop in Drug Design - Siena Lucilla Angeli (Thu Mar 05 2009 - 06:42:36 CST)
script to resolve trajectory "jumps" on Desmond dynamic Nicola Giacche' (Wed Mar 04 2009 - 10:15:03 CST)
- RE: script to resolve trajectory "jumps" on Desmond dynamic Brittany Morgan (Wed Mar 04 2009 - 11:21:13 CST)
  - RE: script to resolve trajectory "jumps" on Desmond dynamic Nicola Giacche' (Thu Mar 05 2009 - 09:01:08 CST)
    - Re: script to resolve trajectory "jumps" on Desmond dynamic Peter Freddolino (Thu Mar 05 2009 - 10:43:18 CST)
Problem in IMD with Compiled VMD Amr Rizq (Wed Mar 04 2009 - 06:00:58 CST)
- Re: Problem in IMD with Compiled VMD John Stone (Wed Mar 04 2009 - 08:34:37 CST)
  - RE: Problem in IMD with Compiled VMD Amr Rizq (Wed Mar 04 2009 - 08:55:33 CST)
- Re: Problem in IMD with Compiled VMD Axel Kohlmeyer (Wed Mar 04 2009 - 08:55:24 CST)
  - RE: Problem in IMD with Compiled VMD Amr Rizq (Wed Mar 04 2009 - 09:20:20 CST)
OpenGL Window Max (Wed Mar 04 2009 - 05:16:54 CST)
- Re: OpenGL Window Axel Kohlmeyer (Wed Mar 04 2009 - 07:55:24 CST)
How to convert DCD file into Amber trajectory file in vmd Jianping Lin (Tue Mar 03 2009 - 17:30:33 CST)
- Re: How to convert DCD file into Amber trajectory file in vmd John Stone (Tue Mar 03 2009 - 18:35:31 CST)
  - Re: How to convert DCD file into Amber trajectory file in vmd Jianping Lin (Wed Mar 04 2009 - 11:41:14 CST)
displaying residues within 5 A of ligand in vmd Falgun Shah (Tue Mar 03 2009 - 09:53:29 CST)
- Re: displaying residues within 5 A of ligand in vmd John Stone (Tue Mar 03 2009 - 10:25:12 CST)
Outline rendering style with Tachyon Heikki Kasnanen (Tue Mar 03 2009 - 02:20:08 CST)
- Re: Outline rendering style with Tachyon John Stone (Tue Mar 03 2009 - 14:48:32 CST)
- Re: Outline rendering style with Tachyon Nicolas (Tue Mar 03 2009 - 16:04:17 CST)
- Re: Outline rendering style with Tachyon John Stone (Mon May 18 2009 - 14:47:33 CDT)
  - VS: Outline rendering style with Tachyon Heikki Kasnanen (Mon May 18 2009 - 14:50:52 CDT)
rmsd computation in text mode with a reference pdb Monika Sharma (Mon Mar 02 2009 - 01:18:30 CST)
- Re: rmsd computation in text mode with a reference pdb Leonardo Trabuco (Mon Mar 02 2009 - 01:42:38 CST)
select atoms bo baker (Sun Mar 01 2009 - 22:18:42 CST)
- Re: select atoms Joaquim Rui Rodrigues (Mon Mar 02 2009 - 04:57:41 CST)
  - Re: select atoms bo baker (Mon Mar 02 2009 - 18:30:29 CST)
    - Re: select atoms Axel Kohlmeyer (Mon Mar 02 2009 - 20:24:55 CST)
images for publication Falgun Shah (Sun Mar 01 2009 - 15:23:12 CST)
- Re: images for publication John Stone (Tue Mar 03 2009 - 14:51:18 CST)
  - Re: images for publication John Stone (Tue Mar 03 2009 - 23:49:42 CST)
Re: delete residues from trajectory bo baker (Sat Feb 28 2009 - 23:06:17 CST)
paratool: gaussian output error Falgun Shah (Sat Feb 28 2009 - 17:15:25 CST)
delete residues from trajectory bo baker (Sat Feb 28 2009 - 03:46:20 CST)
delete residues from trajectory bo baker (Sat Feb 28 2009 - 03:44:06 CST)
- Re: delete residues from trajectory Schreiner Eduard (Sun Mar 01 2009 - 01:14:53 CST)
vmd error related to opengl FyD (Fri Feb 27 2009 - 18:12:02 CST)
- Re: vmd error related to opengl John Stone (Fri Feb 27 2009 - 18:15:37 CST)
problem while integrating bigdcd into a namespace Thomas Evangelidis (Fri Feb 27 2009 - 16:19:03 CST)
- Re: problem while integrating bigdcd into a namespace John Stone (Thu Mar 05 2009 - 22:36:23 CST)
wrong bonds during loading pdb file(protein plus lipids) Nikolay Simakov (Fri Feb 27 2009 - 16:01:30 CST)
- Re: wrong bonds during loading pdb file(protein plus lipids) John Stone (Fri Feb 27 2009 - 16:23:19 CST)
  - Re: wrong bonds during loading pdb file(protein plus lipids) Nikolay Simakov (Fri Feb 27 2009 - 20:07:52 CST)
(no subject) Irene Newhouse (Fri Feb 27 2009 - 14:08:30 CST)
- Re: Axel Kohlmeyer (Fri Feb 27 2009 - 14:48:42 CST)
  - RE: Irene Newhouse (Tue Mar 03 2009 - 14:55:11 CST)
- Re: John Stone (Fri Feb 27 2009 - 18:03:40 CST)
draw command with different material BIN ZHANG (Thu Feb 26 2009 - 23:31:08 CST)
- Re: draw command with different material John Stone (Thu Feb 26 2009 - 23:46:09 CST)
proline trans to cis Roman Petrenko (Thu Feb 26 2009 - 19:20:07 CST)
Does command "animate delete all" free memory? Fred (Rui FENG) (Thu Feb 26 2009 - 15:00:53 CST)
- Re: Does command "animate delete all" free memory? John Stone (Thu Feb 26 2009 - 15:16:44 CST)
  - Re: Does command "animate delete all" free memory? Fred (Rui FENG) (Thu Feb 26 2009 - 15:57:56 CST)
    - Re: Does command "animate delete all" free memory? John Stone (Thu Feb 26 2009 - 16:48:58 CST)
    - Re: Does command "animate delete all" free memory? Fred (Rui FENG) (Thu Feb 26 2009 - 17:00:49 CST)
Displaying local water molecules throughout trajectory ben rodriguez (Thu Feb 26 2009 - 14:47:26 CST)
- Re: Displaying local water molecules throughout trajectory Axel Kohlmeyer (Thu Feb 26 2009 - 15:20:50 CST)
- Re: Displaying local water molecules throughout trajectory John Stone (Thu Feb 26 2009 - 14:53:56 CST)
Weighted RMS fit bug Jumper, John (Thu Feb 26 2009 - 12:21:15 CST)
- Re: Weighted RMS fit bug John Stone (Thu Feb 26 2009 - 14:25:06 CST)
MM/PBSA in VMD Jianping Lin (Thu Feb 26 2009 - 12:12:46 CST)
- Re: MM/PBSA in VMD L. Michel Espinoza-Fonseca (Fri Feb 27 2009 - 06:49:43 CST)
Help: Installation Problem Lee Amy (Wed Feb 25 2009 - 09:45:12 CST)
- Re: Help: Installation Problem Axel Kohlmeyer (Thu Feb 26 2009 - 10:57:30 CST)
  - Re: Help: Installation Problem Lee Amy (Sat Feb 28 2009 - 05:19:46 CST)
    - Re: Help: Installation Problem Axel Kohlmeyer (Sat Feb 28 2009 - 07:45:27 CST)
    - Re: Help: Installation Problem Lee Amy (Sun Mar 01 2009 - 05:41:39 CST)
to get angle from matrix of rotation around an axis Yinglong Miao (Wed Feb 25 2009 - 14:55:27 CST)
- Re: to get angle from matrix of rotation around an axis John Stone (Wed Feb 25 2009 - 15:37:47 CST)
  - Re: to get angle from matrix of rotation around an axis Yinglong Miao (Wed Feb 25 2009 - 15:45:53 CST)
volmap masks Dan Willenbring (Wed Feb 25 2009 - 14:17:32 CST)
- Re: volmap masks John Stone (Tue Mar 03 2009 - 22:19:47 CST)
embed VMD in web page Xunlei Wu (Wed Feb 25 2009 - 11:21:39 CST)
- Re: embed VMD in web page Axel Kohlmeyer (Wed Feb 25 2009 - 12:03:34 CST)
charm27 forcefield_topology Falgun Shah (Wed Feb 25 2009 - 11:02:02 CST)
- Re: namd-l: charm27 forcefield_topology Peter Freddolino (Wed Feb 25 2009 - 15:09:23 CST)
question about "measure dihed" with COM points Lee, Hwan Kyu (NIH/NHLBI) [E] (Tue Feb 24 2009 - 19:09:27 CST)
- Re: question about "measure dihed" with COM points Axel Kohlmeyer (Tue Feb 24 2009 - 19:51:15 CST)
- Re: question about "measure dihed" with COM points J T (Tue Feb 24 2009 - 21:37:21 CST)
  - RE: question about "measure dihed" with COM points Lee, Hwan Kyu (NIH/NHLBI) [E] (Wed Feb 25 2009 - 12:55:38 CST)
  - RE: question about "measure dihed" with COM points Lee, Hwan Kyu (NIH/NHLBI) [E] (Wed Feb 25 2009 - 13:35:07 CST)
    - Re: question about "measure dihed" with COM points J T (Wed Feb 25 2009 - 14:43:01 CST)
    - Re: question about "measure dihed" with COM points Hwankyu Lee (Wed Feb 25 2009 - 14:55:39 CST)
Test Lee Amy (Tue Feb 24 2009 - 07:48:25 CST)
- Re: Test John Stone (Tue Feb 24 2009 - 08:59:26 CST)
  - Re: Test Katherine Parra (Tue Feb 24 2009 - 10:01:41 CST)
info for computational chemistry awards, please forward Carlos Simmerling (Fri Feb 20 2009 - 10:22:27 CST)
Adding a Water Box Mohamed Seyam (Mon Feb 23 2009 - 17:36:14 CST)
- Re: Adding a Water Box Axel Kohlmeyer (Mon Feb 23 2009 - 19:00:55 CST)
FATAL ERROR: ABNORMAL EOF FOUND - buffer=*0 0* Chuck (Mon Feb 23 2009 - 15:52:05 CST)
Can you show me an example of the .xyz file that is used to calculate the IR spectrum Shuo Li (Mon Feb 23 2009 - 14:05:15 CST)
- Re: Can you show me an example of the .xyz file that is used to calculate the IR spectrum Axel Kohlmeyer (Mon Feb 23 2009 - 14:46:18 CST)
Membrane builder ?'s Christopher Hartshorn (Mon Feb 23 2009 - 13:09:16 CST)
- Re: Membrane builder ?'s John Stone (Tue Feb 24 2009 - 00:06:40 CST)
passing arguments to a vmd script which is executed using play or source mariagoranovic_at_gmail.com (Mon Feb 23 2009 - 04:24:14 CST)
- Re: passing arguments to a vmd script which is executed using play or source Axel Kohlmeyer (Mon Feb 23 2009 - 09:08:58 CST)
  - Re: passing arguments to a vmd script which is executed using play or source maria goranovic (Mon Feb 23 2009 - 09:19:24 CST)
    - Re: passing arguments to a vmd script which is executed using play or source Axel Kohlmeyer (Mon Feb 23 2009 - 10:20:55 CST)
- Re: passing arguments to a vmd script which is executed using play or source Axel Kohlmeyer (Mon Feb 23 2009 - 09:15:44 CST)
multiple colors for a single atom BIN ZHANG (Mon Feb 23 2009 - 00:05:50 CST)
- Re: multiple colors for a single atom John Stone (Mon Feb 23 2009 - 09:06:43 CST)
  - Re: multiple colors for a single atom BIN ZHANG (Mon Feb 23 2009 - 11:55:48 CST)
Is there a way to add custormized representation method to VMD Yang, Shaorui (Sun Feb 22 2009 - 22:42:19 CST)
- Re: Is there a way to add custormized representation method to VMD John Stone (Mon Feb 23 2009 - 15:04:06 CST)
VMD exits immediately after starting on Windows xp Robert Mullen (Sun Feb 22 2009 - 17:35:46 CST)
- Re: VMD exits immediately after starting on Windows xp John Stone (Sun Feb 22 2009 - 17:44:19 CST)
a way to create a nice image politr_at_huji.ac.il (Sat Feb 21 2009 - 08:36:44 CST)
- Re: a way to create a nice image Axel Kohlmeyer (Sat Feb 21 2009 - 11:03:44 CST)
  - Re: a way to create a nice image politr_at_huji.ac.il (Sun Feb 22 2009 - 10:51:35 CST)
  - Re: a way to create a nice image politr_at_huji.ac.il (Sun Feb 22 2009 - 10:52:01 CST)
    - Re: a way to create a nice image Axel Kohlmeyer (Sun Feb 22 2009 - 11:16:17 CST)
transparent background James Rustad (Fri Feb 20 2009 - 13:55:55 CST)
- Re: transparent background Axel Kohlmeyer (Fri Feb 20 2009 - 14:39:17 CST)
  - Re: transparent background John Stone (Fri Feb 20 2009 - 18:14:32 CST)
    - Re: transparent background FX (Fri Feb 20 2009 - 18:52:47 CST)
    - Re: transparent background John Stone (Mon Feb 23 2009 - 15:01:32 CST)
converting trajectory files with catdcd in command line Luciano Costa (Fri Feb 20 2009 - 06:31:00 CST)
- Re: converting trajectory files with catdcd in command line Axel Kohlmeyer (Fri Feb 20 2009 - 08:02:38 CST)
vmd intel compiler prebuild for 64 bit Roman Petrenko (Thu Feb 19 2009 - 19:29:09 CST)
- Re: vmd intel compiler prebuild for 64 bit John Stone (Tue Feb 24 2009 - 00:54:55 CST)
Unrecognized Chains in VMD for tetrameric protein ben rodriguez (Thu Feb 19 2009 - 18:14:55 CST)
- Re: Unrecognized Chains in VMD for tetrameric protein John Stone (Thu Feb 19 2009 - 18:57:54 CST)
SMD question Edward Lyman (Thu Feb 19 2009 - 14:00:32 CST)
"pbcwithin" keyword Thomas Evangelidis (Thu Feb 19 2009 - 09:29:37 CST)
- Re: "pbcwithin" keyword Axel Kohlmeyer (Thu Feb 19 2009 - 11:00:48 CST)
making .psf file based on .gro or .pdb Hideya Nakamura (Tue Feb 17 2009 - 18:19:18 CST)
- Re: making .psf file based on .gro or .pdb John Stone (Tue Feb 17 2009 - 19:04:22 CST)
vmd with cuda1.0 Roman Petrenko (Mon Feb 16 2009 - 21:47:16 CST)
- Re: vmd with cuda1.0 John Stone (Mon Feb 16 2009 - 21:56:04 CST)
  - Re: vmd with cuda1.0 Roman Petrenko (Mon Feb 16 2009 - 22:07:30 CST)
    - Re: vmd with cuda1.0 John Stone (Mon Feb 16 2009 - 22:23:18 CST)
    - Re: vmd with cuda1.0 Roman Petrenko (Mon Feb 16 2009 - 22:25:44 CST)
change cylinder surface properties Peter Varnai (Mon Feb 16 2009 - 11:42:13 CST)
- Re: change cylinder surface properties Axel Kohlmeyer (Mon Feb 16 2009 - 18:29:11 CST)
error messages "*** glibc detected *** free(): invalid pointer" Yinglong Miao (Mon Feb 16 2009 - 11:23:32 CST)
- Re: error messages "*** glibc detected *** free(): invalid pointer" John Stone (Mon Feb 16 2009 - 11:43:44 CST)
  - Re: error messages "*** glibc detected *** free(): invalid pointer" Yinglong Miao (Mon Feb 16 2009 - 11:51:38 CST)
- Re: error messages "*** glibc detected *** free(): invalid pointer" Axel Kohlmeyer (Mon Feb 16 2009 - 12:26:19 CST)
  - Re: error messages "*** glibc detected *** free(): invalid pointer" Yinglong Miao (Mon Feb 16 2009 - 12:44:16 CST)
Cannot read MSMS facet file BIN ZHANG (Sun Feb 15 2009 - 23:54:52 CST)
- Re: Cannot read MSMS facet file John Stone (Mon Feb 16 2009 - 00:27:26 CST)
  - Re: Cannot read MSMS facet file BIN ZHANG (Mon Feb 16 2009 - 17:05:31 CST)
The display windows is out of my screen G.H. Zuo (Sun Feb 15 2009 - 00:21:05 CST)
- Re: The display windows is out of my screen John Stone (Sun Feb 15 2009 - 12:57:36 CST)
  - Re: The display windows is out of my screen G.H. Zuo (Mon Feb 16 2009 - 00:23:10 CST)
about measuring volume of the binding site Falgun Shah (Sat Feb 14 2009 - 15:58:14 CST)
- Re: about measuring volume of the binding site John Stone (Sun Feb 15 2009 - 12:59:15 CST)
- creating videos where the representation changes throughout Brian Kidd (Thu Feb 19 2009 - 23:30:20 CST)
  - Re: creating videos where the representation changes throughout John Stone (Thu Feb 19 2009 - 23:45:17 CST)
Membrane Proteins Tutorial Marcos Sotomayor (Fri Feb 13 2009 - 16:25:15 CST)
Atom distances from trajotory bo baker (Thu Feb 12 2009 - 23:50:21 CST)
- Re: Atom distances from trajotory Peter Freddolino (Fri Feb 13 2009 - 09:33:01 CST)
Problem when labeling atoms on machine with intel X4500HD integreted graphic card Shi, Chuanyin (Thu Feb 12 2009 - 15:25:45 CST)
- Re: Problem when labeling atoms on machine with intel X4500HD integreted graphic card John Stone (Thu Feb 12 2009 - 15:46:21 CST)
installation Fernanda S. (Thu Feb 12 2009 - 13:08:19 CST)
- Re: installation John Stone (Thu Feb 12 2009 - 13:40:02 CST)
  - Re: installation John Stone (Sat Feb 14 2009 - 14:32:53 CST)
  - Re: installation Fernanda S. (Sat Feb 14 2009 - 17:18:57 CST)
- Re: installation Ramon Crehuet (Fri Feb 13 2009 - 05:08:51 CST)
  - No 'xterm' needed for next VMD... Was Re: installation John Stone (Sat Feb 14 2009 - 19:37:26 CST)
Atom distances from trajotory bo baker (Thu Feb 12 2009 - 03:27:20 CST)
- Re: Atom distances from trajotory Peter Freddolino (Thu Feb 12 2009 - 07:40:14 CST)
  - Re: Atom distances from trajotory Peter Freddolino (Sat Feb 14 2009 - 08:01:53 CST)
    - Re: Atom distances from trajotory bo baker (Sat Feb 14 2009 - 17:16:27 CST)
Load multiple files bo baker (Wed Feb 11 2009 - 22:43:35 CST)
- Re: Load multiple files John Stone (Thu Feb 12 2009 - 08:36:11 CST)
  - RE: Load multiple files Bishop, Thomas C (Thu Feb 12 2009 - 11:18:57 CST)
- RE: Load multiple files Andres Morales N (Thu Feb 12 2009 - 08:59:39 CST)
problem Barbault Florent (Wed Feb 11 2009 - 02:41:52 CST)
- Re: problem Axel Kohlmeyer (Wed Feb 11 2009 - 09:01:42 CST)
  - Re: problem Barbault Florent (Fri Feb 13 2009 - 05:24:39 CST)
- Re: problem Paulo E. Abreu (Wed Feb 11 2009 - 11:00:15 CST)
Flow Fields Roland Schulz (Tue Feb 10 2009 - 16:04:23 CST)
- Re: Flow Fields John Stone (Tue Feb 10 2009 - 16:28:08 CST)
- Re: Flow Fields Axel Kohlmeyer (Tue Feb 10 2009 - 16:53:19 CST)
How to specify processors for running VMD on a cluster? Yinglong Miao (Tue Feb 10 2009 - 10:45:27 CST)
- Re: How to specify processors for running VMD on a cluster? Axel Kohlmeyer (Tue Feb 10 2009 - 12:24:58 CST)
  - Re: How to specify processors for running VMD on a cluster? Axel Kohlmeyer (Tue Feb 10 2009 - 15:35:46 CST)
Equivalent Mouse Capabilities to Tracker CAVELib Amr Rizq (Mon Feb 09 2009 - 07:06:26 CST)
- Re: Equivalent Mouse Capabilities to Tracker CAVELib John Stone (Mon Feb 09 2009 - 15:24:34 CST)
multiplot : integration of undrawing command (?) Nadja Lederer (Thu Feb 05 2009 - 05:14:43 CST)
- Re: multiplot : integration of undrawing command (?) Axel Kohlmeyer (Sun Feb 08 2009 - 23:48:49 CST)
"Hands-On" Workshop on Computational Biophysics, July 6-10 and August 10-14, 2009 TCBG Workshop (Thu Feb 05 2009 - 15:52:29 CST)
Take a look at jaxtr! Sudipta Sinha (Sun Feb 08 2009 - 22:20:40 CST)
concatenate protein and 2 ligand files Thomas Evangelidis (Sat Feb 07 2009 - 11:02:30 CST)
- Re: concatenate protein and 2 ligand files John Stone (Mon Feb 09 2009 - 15:17:44 CST)
International opportunity robert (Fri Feb 06 2009 - 11:25:07 CST)
VMD and IED on Windows XP Roland Schmucki (Thu Feb 05 2009 - 20:57:34 CST)
- Re: VMD and IED on Windows XP John Stone (Fri Feb 06 2009 - 12:36:04 CST)
Progress Bar for the Elapsed Time: rendering problem Suman Chakrabarty (Thu Feb 05 2009 - 16:42:20 CST)
- Re: Progress Bar for the Elapsed Time: rendering problem Axel Kohlmeyer (Thu Feb 05 2009 - 17:23:40 CST)
Render alpha-carbon trace as cartoon Patrick Buck (Thu Feb 05 2009 - 13:57:54 CST)
- Re: Render alpha-carbon trace as cartoon John Stone (Fri Feb 06 2009 - 12:23:33 CST)
trajectory path script Katherine Parra (Thu Feb 05 2009 - 11:00:12 CST)
- Re: trajectory path script Axel Kohlmeyer (Thu Feb 05 2009 - 11:39:06 CST)
Atomselect in NAMD GUI bo baker (Thu Feb 05 2009 - 05:02:45 CST)
- Re: Atomselect in NAMD GUI bo baker (Sun Feb 08 2009 - 16:17:15 CST)
  - Re: Atomselect in NAMD GUI John Stone (Mon Feb 09 2009 - 00:06:46 CST)
    - Re: Atomselect in NAMD GUI bo baker (Wed Feb 11 2009 - 16:01:37 CST)
    - Re: Atomselect in NAMD GUI Peter Freddolino (Thu Feb 12 2009 - 06:21:11 CST)
"Sorry, this version VMD was compiled with Python support disabled" Maxim Paliy (Wed Feb 04 2009 - 09:19:49 CST)
- Re: "Sorry, this version VMD was compiled with Python support disabled" John Stone (Wed Feb 04 2009 - 16:31:09 CST)
Apologies Lucas Fernandez Seivane (Tue Feb 03 2009 - 17:34:58 CST)
problem with "measure fit " Leontyev Igor (Tue Feb 03 2009 - 15:51:02 CST)
- Re: problem with "measure fit " John Stone (Mon Feb 09 2009 - 16:41:32 CST)
property iterate over a range (representation / draw style) bonicoli_at_loria.fr (Tue Feb 03 2009 - 11:16:12 CST)
- Re: property iterate over a range (representation / draw style) Axel Kohlmeyer (Tue Feb 03 2009 - 12:10:49 CST)
  - Re: property iterate over a range (representation / draw style) bonicoli_at_loria.fr (Wed Feb 04 2009 - 10:04:40 CST)
rmsd matrix Andres Morales N (Tue Feb 03 2009 - 10:01:28 CST)
- Re: rmsd matrix John Stone (Tue Feb 03 2009 - 10:08:00 CST)
deleting specific residues or atoms maria goranovic (Tue Feb 03 2009 - 09:57:54 CST)
- Re: deleting specific residues or atoms Axel Kohlmeyer (Tue Feb 03 2009 - 10:55:28 CST)
add a new representation style to VMD Vlad Cojocaru (Tue Feb 03 2009 - 08:22:24 CST)
- Re: add a new representation style to VMD John Stone (Tue Feb 03 2009 - 09:02:27 CST)
pictures with frame BIN ZHANG (Tue Feb 03 2009 - 01:40:32 CST)
- Re: pictures with frame Mario Valle (Tue Feb 03 2009 - 02:56:50 CST)
- Re: pictures with frame (corrected) Mario Valle (Tue Feb 03 2009 - 02:58:39 CST)
selecting set of residue Falgun Shah (Mon Feb 02 2009 - 14:44:45 CST)
Bug in molefacture proline residue of official version (1.8.6 LINUXAMD64) Alexandre Suman de Araujo (Mon Feb 02 2009 - 12:51:46 CST)
rmsd matrix Andres Morales N (Mon Feb 02 2009 - 10:59:50 CST)
- Re: rmsd matrix Wei Huang (Mon Feb 02 2009 - 11:08:40 CST)
Link between the electrostatic potential on the surface and the grid.dx generated by APBS Emeline Leproult (Mon Feb 02 2009 - 09:57:02 CST)
- Re: Link between the electrostatic potential on the surface and the grid.dx generated by APBS John Stone (Mon Feb 02 2009 - 10:41:09 CST)
scriptable way to add hydrogens Thomas Evangelidis (Sat Jan 31 2009 - 16:25:16 CST)
- Re: scriptable way to add hydrogens Peter Freddolino (Sat Jan 31 2009 - 16:44:37 CST)
- Re: scriptable way to add hydrogens Axel Kohlmeyer (Sat Jan 31 2009 - 17:35:53 CST)
How to install the inorganicbuilder on Windows vista Hideya Nakamura (Thu Jan 29 2009 - 19:41:45 CST)
- Re: How to install the inorganicbuilder on Windows vista John Stone (Fri Jan 30 2009 - 08:28:04 CST)
Unable to run VMD in graphical mode/ ubuntu 8.10 / Open GL problem Katya Lyakhova (Wed Jan 28 2009 - 09:19:35 CST)
- Re: Unable to run VMD in graphical mode/ ubuntu 8.10 / Open GL problem John Stone (Wed Jan 28 2009 - 09:25:52 CST)
- contactmap for RNA Samuel Coulbourn Flores èŠ±å±± (Wed Jan 28 2009 - 16:44:43 CST)
[patch] potential CUDA acceleration - load-balancing on different CUDA devices Martin Aumüller (Wed Jan 28 2009 - 06:35:19 CST)
- Re: [patch] potential CUDA acceleration - load-balancing on different CUDA devices John Stone (Wed Jan 28 2009 - 08:21:58 CST)
get a PDB file from DCD file Andres Morales N (Tue Jan 27 2009 - 07:58:23 CST)
- Re: get a PDB file from DCD file Axel Kohlmeyer (Tue Jan 27 2009 - 08:42:18 CST)
  - Re: get a PDB file from DCD file JT (Tue Jan 27 2009 - 11:01:41 CST)
- Re: get a PDB file from DCD file John Stone (Tue Jan 27 2009 - 08:44:32 CST)
- Re: get a PDB file from DCD file Benjamin Bouvier (Tue Jan 27 2009 - 09:49:51 CST)
Rosetta Academic Training Workshop Nir London (Tue Jan 27 2009 - 07:05:12 CST)
VMD & NAMD atoms naming convention? Javier Goicochea (Tue Jan 27 2009 - 03:05:09 CST)
- Re: VMD & NAMD atoms naming convention? Axel Kohlmeyer (Tue Jan 27 2009 - 08:35:34 CST)
Note to VMD-L about posting attachments etc... John Stone (Mon Jan 26 2009 - 15:58:53 CST)
Re: (Resend) Re: Breaking Bonds in VMD John Stone (Mon Jan 26 2009 - 15:55:29 CST)
(no subject) Andres Morales N (Mon Jan 26 2009 - 14:37:40 CST)
(no subject) gurunath katagi (Mon Jan 26 2009 - 03:19:30 CST)
- Re: Peter Freddolino (Mon Jan 26 2009 - 06:09:46 CST)
how to set color parameters differently for different molecules Thomas Evangelidis (Sun Jan 25 2009 - 12:09:10 CST)
- Re: how to set color parameters differently for different molecules Axel Kohlmeyer (Sun Jan 25 2009 - 13:18:10 CST)
  - Re: how to set color parameters differently for different molecules Thomas Evangelidis (Thu Jan 29 2009 - 15:34:31 CST)
- Re: how to set color parameters differently for different molecules MQO. Carlos Javier NÃºÃ±ez Aguero (Thu Jan 29 2009 - 19:03:40 CST)
VMD not loading in Suse 11.1 Andrew James Bennett (Fri Jan 23 2009 - 05:43:05 CST)
- Re: VMD not loading in Suse 11.1 Axel Kohlmeyer (Fri Jan 23 2009 - 09:04:18 CST)
Tcl script Leonardo Trabuco (Thu Jan 22 2009 - 00:01:39 CST)
Tcl script varsha gautham (Wed Jan 21 2009 - 22:45:29 CST)
accessing bonds angles dihedrals etc lists after PSF file is read into VMD Maxim Paliy (Wed Jan 21 2009 - 15:29:54 CST)
- Re: accessing bonds angles dihedrals etc lists after PSF file is read into VMD John Stone (Thu Jan 22 2009 - 11:33:21 CST)
  - Re: accessing bonds angles dihedrals etc lists after PSF file is read into VMD Iman Salehinia (Thu Jan 22 2009 - 18:21:59 CST)
Breaking Bonds in VMD nicholas lee (Tue Jan 20 2009 - 10:40:46 CST)
- Re: Breaking Bonds in VMD John Stone (Tue Jan 20 2009 - 10:47:17 CST)
  - Re: Breaking Bonds in VMD nicholas lee (Tue Jan 20 2009 - 15:01:16 CST)
    - Re: Breaking Bonds in VMD John Stone (Tue Jan 20 2009 - 17:26:01 CST)
    - Re: Breaking Bonds in VMD Axel Kohlmeyer (Tue Jan 20 2009 - 17:21:16 CST)
VMD Installation problem on Ubuntu 8.10 maria goranovic (Tue Jan 20 2009 - 08:27:12 CST)
- Re: VMD Installation problem on Ubuntu 8.10 John Stone (Tue Jan 20 2009 - 08:46:05 CST)
  - Re: VMD Installation problem on Ubuntu 8.10 maria goranovic (Tue Jan 20 2009 - 09:10:58 CST)
VMD plugin for Desmond ÖÜÎÄ²ý (Tue Jan 20 2009 - 08:23:13 CST)
- Re: VMD plugin for Desmond John Stone (Tue Jan 20 2009 - 08:42:20 CST)
  - Re: VMD plugin for Desmond ÖÜÎÄ²ý (Tue Jan 20 2009 - 08:58:31 CST)
    - Re: VMD plugin for Desmond John Stone (Tue Jan 20 2009 - 09:34:49 CST)
- Re: VMD plugin for Desmond Axel Kohlmeyer (Tue Jan 20 2009 - 08:58:24 CST)
VMD window transparent in Opensuse 11.1 ATI system Ramon Crehuet (Tue Jan 20 2009 - 06:09:27 CST)
- Re: VMD window transparent in Opensuse 11.1 ATI system John Stone (Tue Jan 20 2009 - 08:44:57 CST)
  - Re: VMD window transparent in Opensuse 11.1 ATI system John Stone (Tue Jan 20 2009 - 10:36:12 CST)
- Re: VMD window transparent in Opensuse 11.1 ATI system Axel Kohlmeyer (Tue Jan 20 2009 - 08:56:12 CST)
Fwd: Tcl script varsha gautham (Tue Jan 20 2009 - 02:11:56 CST)
- Re: Fwd: Tcl script Roman Petrenko (Tue Jan 20 2009 - 06:24:37 CST)
- Re: Fwd: Tcl script Axel Kohlmeyer (Tue Jan 20 2009 - 08:49:21 CST)
Problems with tcl/tk 8.5 Bernd Doser (Tue Jan 20 2009 - 02:08:05 CST)
- Re: Problems with tcl/tk 8.5 John Stone (Tue Jan 20 2009 - 08:51:08 CST)
- Re: Problems with tcl/tk 8.5 Axel Kohlmeyer (Tue Jan 20 2009 - 08:53:02 CST)
Download the newest version of VMD ÖÜÎÄ²ý (Mon Jan 19 2009 - 04:15:52 CST)
- Re: Download the newest version of VMD Carsten Olbrich (Mon Jan 19 2009 - 05:05:08 CST)
- Re: Download the newest version of VMD Axel Kohlmeyer (Mon Jan 19 2009 - 10:09:33 CST)
How to get rid of default patch for NTER and CTER Jianping Lin (Sun Jan 18 2009 - 15:45:34 CST)
- Re: How to get rid of default patch for NTER and CTER Schreiner Eduard (Sun Jan 18 2009 - 19:11:32 CST)
- RE: How to get rid of default patch for NTER and CTER Aaron.Oakley_at_csiro.au (Sun Jan 18 2009 - 19:24:36 CST)
Test builds of VMD 1.8.7 using Tcl/Tk 8.5.x... John Stone (Fri Jan 16 2009 - 15:34:21 CST)
- Re: Test builds of VMD 1.8.7 using Tcl/Tk 8.5.x... Axel Kohlmeyer (Tue Jan 20 2009 - 17:31:19 CST)
XYZ trajectory with different atom types? AA (Fri Jan 16 2009 - 13:21:15 CST)
- Re: XYZ trajectory with different atom types? Axel Kohlmeyer (Fri Jan 16 2009 - 14:00:00 CST)
trans routine Edward Lyman (Fri Jan 16 2009 - 12:49:24 CST)
- Re: trans routine John Stone (Tue Jan 27 2009 - 22:29:29 CST)
Problem with Install bo baker (Fri Jan 16 2009 - 05:12:34 CST)
- Re: Problem with Install Joaquim Rui Rodrigues (Fri Jan 16 2009 - 06:59:15 CST)
ANGLES and DIHEDRALS ... location in VMD code? Javier Goicochea (Fri Jan 16 2009 - 02:17:00 CST)
- Re: ANGLES and DIHEDRALS ... location in VMD code? John Stone (Fri Jan 16 2009 - 09:31:01 CST)
  - Re: ANGLES and DIHEDRALS ... location in VMD code? Javier Goicochea (Mon Feb 02 2009 - 08:33:15 CST)
helicity score? BIN ZHANG (Thu Jan 15 2009 - 23:39:21 CST)
- Re: helicity score? Suman Chakrabarty (Thu Feb 19 2009 - 12:27:25 CST)
  - Re: helicity score? BIN ZHANG (Thu Feb 19 2009 - 15:14:45 CST)
Understanding topology files? Javier Goicochea (Thu Jan 15 2009 - 08:03:50 CST)
- Re: Understanding topology files? Christopher Gillespie (Thu Jan 15 2009 - 09:25:23 CST)
  - Re: Understanding topology files? Javier Goicochea (Thu Jan 15 2009 - 10:11:05 CST)
    - Re: Understanding topology files? Christopher Gillespie (Thu Jan 15 2009 - 10:27:52 CST)
    - Re: Understanding topology files? Javier Goicochea (Thu Jan 15 2009 - 10:32:55 CST)
- Re: Understanding topology files? Axel Kohlmeyer (Thu Jan 15 2009 - 14:06:16 CST)
  - Re: Understanding topology files? Javier Goicochea (Fri Jan 16 2009 - 02:10:19 CST)
loosing color when rendering molecular surface in VMD Michael Klein (Wed Jan 14 2009 - 20:17:23 CST)
- Re: loosing color when rendering molecular surface in VMD John Stone (Wed Jan 14 2009 - 20:50:03 CST)
  - Re: loosing color when rendering molecular surface in VMD Schreiner Eduard (Wed Jan 14 2009 - 20:58:22 CST)
Data fields in vmd Cesar Luis Avila (Wed Jan 14 2009 - 15:02:25 CST)
- Re: Data fields in vmd Axel Kohlmeyer (Wed Jan 14 2009 - 14:56:10 CST)
  - Re: Data fields in vmd Cesar Luis Avila (Thu Jan 15 2009 - 13:27:14 CST)
    - Re: Data fields in vmd Axel Kohlmeyer (Thu Jan 15 2009 - 14:10:26 CST)
- Re: Data fields in vmd John Stone (Thu Jan 15 2009 - 10:34:56 CST)
  - Re: Data fields in vmd Cesar Luis Avila (Thu Jan 15 2009 - 12:33:09 CST)
    - Re: Data fields in vmd John Stone (Thu Jan 15 2009 - 11:38:22 CST)
updating DCD frames in python Michael Kreim (Wed Jan 14 2009 - 09:55:06 CST)
- Re: updating DCD frames in python Axel Kohlmeyer (Wed Jan 14 2009 - 11:11:45 CST)
  - Re: updating DCD frames in python Michael Kreim (Thu Jan 15 2009 - 03:30:55 CST)
building loops riya doreen (Tue Jan 13 2009 - 18:53:09 CST)
- Re: building loops Peter Freddolino (Tue Jan 13 2009 - 19:18:55 CST)
Dobule and triple bonds Max (Tue Jan 13 2009 - 04:32:04 CST)
- Re: Dobule and triple bonds Peter Freddolino (Tue Jan 13 2009 - 09:30:56 CST)
center of mass Alison Grinthal (Mon Jan 12 2009 - 13:51:43 CST)
- Re: center of mass Axel Kohlmeyer (Mon Jan 12 2009 - 14:37:05 CST)
Release of the R.E.D.-III.1 tools FyD (Mon Jan 12 2009 - 05:59:14 CST)
VMD for Linux bo baker (Mon Jan 12 2009 - 05:14:50 CST)
- Re: VMD for Linux Axel Kohlmeyer (Mon Jan 12 2009 - 09:11:00 CST)
: about complexing protein and ligand! Shirin Awasthi (Sun Jan 11 2009 - 22:40:48 CST)
- Re: : about complexing protein and ligand! Axel Kohlmeyer (Mon Jan 12 2009 - 08:54:21 CST)
odd render problems with Vista Irene Newhouse (Sun Jan 11 2009 - 13:26:57 CST)
- Re: odd render problems with Vista Peter Freddolino (Sun Jan 11 2009 - 14:05:18 CST)
  - Re: odd render problems with Vista Axel Kohlmeyer (Sun Jan 11 2009 - 14:37:10 CST)
    - Re: odd render problems with Vista Peter Freddolino (Sun Jan 11 2009 - 14:49:47 CST)
    - RE: odd render problems with Vista Irene Newhouse (Sun Jan 11 2009 - 18:25:25 CST)
  - RE: odd render problems with Vista Irene Newhouse (Sun Jan 11 2009 - 18:21:59 CST)
- Re: odd render problems with Vista Axel Kohlmeyer (Sun Jan 11 2009 - 14:27:58 CST)
- Re: odd render problems with Vista Benjamin Bouvier (Sun Jan 11 2009 - 14:20:04 CST)
  - RE: odd render problems with Vista Irene Newhouse (Sun Jan 11 2009 - 18:20:08 CST)
putting a set of selections in a list or an array A D (Sun Jan 11 2009 - 12:14:08 CST)
- Re: putting a set of selections in a list or an array Axel Kohlmeyer (Sun Jan 11 2009 - 13:53:41 CST)
cube file question Jun Cheng (Fri Jan 09 2009 - 05:12:20 CST)
- Re: cube file question Axel Kohlmeyer (Fri Jan 09 2009 - 08:23:16 CST)
Functional Groups Max (Fri Jan 09 2009 - 04:51:39 CST)
- Re: Functional Groups Axel Kohlmeyer (Fri Jan 09 2009 - 08:16:12 CST)
Calculating acyl chain order parameter profile on phospholipid vesicles Cesar Luis Avila (Thu Jan 08 2009 - 15:43:55 CST)
- Re: Calculating acyl chain order parameter profile on phospholipid vesicles dimka (Tue Jan 13 2009 - 10:28:43 CST)
which model in pdb vill VMD present? Steven W (Wed Jan 07 2009 - 12:21:59 CST)
- Re: which model in pdb vill VMD present? John Stone (Tue Jan 13 2009 - 14:03:58 CST)
measure rmsf - command (step argument) Nadja Lederer (Wed Jan 07 2009 - 05:20:42 CST)
- Re: measure rmsf - command (step argument) Axel Kohlmeyer (Wed Jan 07 2009 - 10:44:18 CST)
Large dcd file jouko_at_berkeley.edu (Tue Jan 06 2009 - 16:31:46 CST)
- Re: Large dcd file Roman Petrenko (Tue Jan 06 2009 - 17:25:03 CST)
  - Re: Large dcd file Axel Kohlmeyer (Tue Jan 06 2009 - 19:04:46 CST)
  - Re: Large dcd file jouko_at_berkeley.edu (Tue Jan 06 2009 - 22:32:51 CST)
- Re: Large dcd file Axel Kohlmeyer (Tue Jan 06 2009 - 19:01:25 CST)
Problems with NewCartoon Cartoon Representations haosheng_at_hec.utah.edu (Tue Jan 06 2009 - 15:39:43 CST)
- Re: Problems with NewCartoon Cartoon Representations Peter Freddolino (Tue Jan 06 2009 - 19:48:47 CST)
eliminate atoms from psf and pdb files caterinabernini_at_unisi.it (Tue Jan 06 2009 - 11:40:15 CST)
- Re: eliminate atoms from psf and pdb files Peter Freddolino (Tue Jan 06 2009 - 11:51:45 CST)
- Re: eliminate atoms from psf and pdb files Axel Kohlmeyer (Tue Jan 06 2009 - 12:33:37 CST)
changing bond color jfgaff_at_ncsu.edu (Tue Jan 06 2009 - 11:39:20 CST)
- Re: changing bond color Peter Freddolino (Tue Jan 06 2009 - 11:50:11 CST)
- Re: changing bond color Axel Kohlmeyer (Tue Jan 06 2009 - 12:30:19 CST)
- Re: changing bond color Ramya Gamini (Tue Jan 06 2009 - 12:27:22 CST)
tcl scripts in parallel in VMD? Maxim Paliy (Tue Jan 06 2009 - 08:14:41 CST)
- Re: tcl scripts in parallel in VMD? Axel Kohlmeyer (Tue Jan 06 2009 - 10:06:25 CST)
a problem on Red Hat Enterprise Linux 5 Seungho Choe (Mon Jan 05 2009 - 10:48:32 CST)
- Re: a problem on Red Hat Enterprise Linux 5 John Stone (Mon Jan 05 2009 - 16:13:40 CST)
  - Re: a problem on Red Hat Enterprise Linux 5 Seungho Choe (Mon Jan 05 2009 - 11:25:16 CST)
list of all the file type keywords for "mol load"? Maxim Paliy (Mon Jan 05 2009 - 10:00:20 CST)
- Re: list of all the file type keywords for "mol load"? Axel Kohlmeyer (Mon Jan 05 2009 - 10:44:03 CST)
Changing the Secondary Structure of a Protein MIke S (Sun Dec 28 2008 - 01:18:23 CST)
- Re: namd-l: Changing the Secondary Structure of a Protein JC Gumbart (Sun Dec 28 2008 - 08:55:03 CST)
- Re: namd-l: Changing the Secondary Structure of a Protein Peter Freddolino (Sun Dec 28 2008 - 08:48:38 CST)
I need a bid trajectory please!!! Thomas Evangelidis (Thu Dec 25 2008 - 16:54:44 CST)
- Re: I need a bid trajectory please!!! Axel Kohlmeyer (Fri Dec 26 2008 - 14:20:38 CST)
  - Re: I need a bid trajectory please!!! Thomas Evangelidis (Fri Dec 26 2008 - 16:01:33 CST)
Space distribution functions aneesh cna (Wed Dec 24 2008 - 23:08:03 CST)
- Re: Space distribution functions Axel Kohlmeyer (Fri Dec 26 2008 - 14:15:58 CST)
beta column format in PDB BIN ZHANG (Wed Dec 24 2008 - 13:41:23 CST)
- Re: beta column format in PDB Axel Kohlmeyer (Wed Dec 24 2008 - 14:33:53 CST)
  - Re: beta column format in PDB BIN ZHANG (Wed Dec 24 2008 - 14:57:47 CST)
    - Re: beta column format in PDB Axel Kohlmeyer (Wed Dec 24 2008 - 15:53:27 CST)
SBCG membrane Dolan, Michael (NIH/NIAID) [C] (Wed Dec 24 2008 - 11:59:25 CST)
- Re: SBCG membrane Anton Arkhipov (Wed Dec 24 2008 - 15:01:38 CST)
difficulties referencing a variable within a namespace Thomas Evangelidis (Sun Dec 21 2008 - 21:00:38 CST)
- Re: difficulties referencing a variable within a namespace Peter Freddolino (Mon Dec 22 2008 - 14:04:35 CST)
Remove PBC Alessandro.Maiorana_at_roma2.infn.it (Sun Dec 21 2008 - 04:09:38 CST)
- Re: Remove PBC Peter Freddolino (Sun Dec 21 2008 - 21:30:56 CST)
- measure the distance between center of molecules Taufik Al-Sarraj (Tue Dec 23 2008 - 11:06:22 CST)
  - Re: measure the distance between center of molecules John Stone (Tue Dec 23 2008 - 11:12:38 CST)
VMD Animation example doesn't work... Alberto Sergio Garay (Fri Dec 19 2008 - 06:52:05 CST)
- Re: VMD Animation example doesn't work... John Stone (Tue Jan 13 2009 - 16:35:01 CST)
CHARMM to AMBER trajectory conversion Peter Jones (Thu Dec 18 2008 - 22:40:53 CST)
- Re: CHARMM to AMBER trajectory conversion Axel Kohlmeyer (Fri Dec 19 2008 - 09:56:01 CST)
known issues with measure hbonds Harindar Keer (Thu Dec 18 2008 - 17:59:34 CST)
- Re: known issues with measure hbonds JC Gumbart (Mon Dec 29 2008 - 09:31:59 CST)
How to get all the angle combinations? BIN ZHANG (Wed Dec 17 2008 - 23:07:16 CST)
- Re: How to get all the angle combinations? John Stone (Mon Dec 22 2008 - 10:37:35 CST)
QM Geometry optimization bo baker (Tue Dec 16 2008 - 23:59:49 CST)
- Re: QM Geometry optimization Peter Freddolino (Wed Dec 17 2008 - 08:57:05 CST)
- Re: QM Geometry optimization Axel Kohlmeyer (Wed Dec 17 2008 - 09:23:33 CST)
  - Re: QM Geometry optimization bo baker (Wed Dec 17 2008 - 12:30:08 CST)
    - Re: QM Geometry optimization Axel Kohlmeyer (Wed Dec 17 2008 - 13:53:09 CST)
VMD Animation example doesn't work... Alberto Sergio Garay (Tue Dec 16 2008 - 04:43:23 CST)
defintion of alpha helix in vmd? Bernhard Knapp (Tue Dec 16 2008 - 03:30:03 CST)
- Re: defintion of alpha helix in vmd? L. Michel Espinoza-Fonseca (Tue Dec 16 2008 - 04:41:47 CST)
haptics device "novint falcon" angel_at_cbuc.cl (Mon Dec 15 2008 - 09:13:31 CST)
- Re: haptics device "novint falcon" John Stone (Mon Dec 15 2008 - 09:26:40 CST)
the exact definition of the keyword "radius" of the atom selection Lan Hua (Sat Dec 13 2008 - 14:10:40 CST)
- Re: the exact definition of the keyword "radius" of the atom selection Axel Kohlmeyer (Sat Dec 13 2008 - 16:37:11 CST)
paratool dont recognize gaussian output angel_at_cbuc.cl (Fri Dec 12 2008 - 10:10:13 CST)
VMD, VRPN, Phantom Desktop Nicholas Labello (Fri Dec 12 2008 - 09:43:19 CST)
- Re: VMD, VRPN, Phantom Desktop John Stone (Tue Jan 13 2009 - 16:36:20 CST)
coloring of an item created by canvas Nadja Lederer (Wed Dec 10 2008 - 04:07:51 CST)
Problem finding center of mass for all the frames ramya narasimhan (Wed Dec 10 2008 - 01:31:38 CST)
- Re: Problem finding center of mass for all the frames Schreiner Eduard (Wed Dec 10 2008 - 01:52:29 CST)
  - Re: Problem finding center of mass for all the frames ramya narasimhan (Wed Dec 10 2008 - 04:26:16 CST)
    - Re: Problem finding center of mass for all the frames Leonardo Trabuco (Wed Dec 10 2008 - 04:34:27 CST)
    - Re: Problem finding center of mass for all the frames ramya narasimhan (Wed Dec 10 2008 - 04:45:35 CST)
How to get number of electrons of an atom in VMD? BIN ZHANG (Mon Dec 08 2008 - 15:31:42 CST)
- Re: How to get number of electrons of an atom in VMD? John Stone (Mon Dec 08 2008 - 15:35:39 CST)
equilibrating a membrane patch Edward Lyman (Mon Dec 08 2008 - 13:25:30 CST)
regarding writemol2 jani sahil (Sat Dec 06 2008 - 00:34:19 CST)
- Re: regarding writemol2 Peter Freddolino (Sat Dec 06 2008 - 19:42:33 CST)
reagsrding writemol2 jani sahil (Fri Dec 05 2008 - 00:11:42 CST)
- Re: reagsrding writemol2 Peter Freddolino (Fri Dec 05 2008 - 09:00:29 CST)
How to generate an index (.ind) file? Anirban Ghosh (Fri Dec 05 2008 - 00:07:49 CST)
- Re: How to generate an index (.ind) file? Carsten Olbrich (Fri Dec 05 2008 - 01:30:17 CST)
- vmd on fedora Taufik Al-Sarraj (Mon Dec 08 2008 - 16:57:24 CST)
  - Re: vmd on fedora John Stone (Mon Dec 08 2008 - 20:34:48 CST)
    - Re: vmd on fedora Taufik Al-Sarraj (Tue Dec 09 2008 - 10:25:37 CST)
    - Re: vmd on fedora John Stone (Tue Dec 09 2008 - 10:34:33 CST)
atom selection aneesh cna (Wed Dec 03 2008 - 05:32:57 CST)
- Re: atom selection Leonardo Trabuco (Wed Dec 03 2008 - 11:10:53 CST)
- Re: atom selection Joaquim Rui Rodrigues (Wed Dec 03 2008 - 11:44:55 CST)
To find the residues on each side of the protein ramya narasimhan (Wed Dec 03 2008 - 02:42:33 CST)
- Re: To find the residues on each side of the protein Axel Kohlmeyer (Wed Dec 03 2008 - 05:17:48 CST)
  - Re: To find the residues on each side of the protein ramya narasimhan (Wed Dec 03 2008 - 22:36:40 CST)
undrawing lines in multiplot? Nadja Lederer (Wed Dec 03 2008 - 02:29:57 CST)
memory leak found Ondrej Marsalek (Tue Dec 02 2008 - 09:08:09 CST)
- Re: memory leak found John Stone (Tue Dec 02 2008 - 09:14:22 CST)
- Re: memory leak found Axel Kohlmeyer (Tue Dec 02 2008 - 11:23:28 CST)
  - Re: memory leak found Ondrej Marsalek (Tue Dec 02 2008 - 12:19:51 CST)
  - Re: memory leak found Ondrej Marsalek (Tue Dec 02 2008 - 12:40:26 CST)
    - Re: memory leak found Axel Kohlmeyer (Tue Dec 02 2008 - 12:58:25 CST)
Rotation of molecules Björn Windshügel (Tue Dec 02 2008 - 08:20:30 CST)
- Re: Rotation of molecules Axel Kohlmeyer (Tue Dec 02 2008 - 11:29:25 CST)
Getting data as vector or matrix Iman Salehinia (Tue Dec 02 2008 - 00:48:29 CST)
Running VMD on Mac OS X Christopher Share (Mon Dec 01 2008 - 23:23:08 CST)
prepare initial structure oguz gurbulak (Mon Dec 01 2008 - 13:52:31 CST)
- Re: prepare initial structure Schreiner Eduard (Mon Dec 01 2008 - 14:16:48 CST)
script that reacts on movement of frameslider in vmd main Nadja Lederer (Mon Dec 01 2008 - 07:41:36 CST)
- Re: script that reacts on movement of frameslider in vmd main Benjamin Bouvier (Mon Dec 01 2008 - 09:28:55 CST)
how to prevent view reset on data load Ondrej Marsalek (Sat Nov 29 2008 - 10:52:45 CST)
- Re: how to prevent view reset on data load Axel Kohlmeyer (Sun Nov 30 2008 - 05:46:45 CST)
  - Re: how to prevent view reset on data load Ondrej Marsalek (Sun Nov 30 2008 - 15:58:56 CST)
transparent or translucent backgrond for images Neelanjana Sengupta (Sat Nov 29 2008 - 06:18:46 CST)
- Re: transparent or translucent backgrond for images Axel Kohlmeyer (Sun Nov 30 2008 - 05:37:01 CST)
total number of donors and acceptors Roman Petrenko (Wed Nov 26 2008 - 18:27:16 CST)
Desmond trajectory conversion to dcd format Dong Xu (Wed Nov 26 2008 - 16:24:57 CST)
- Re: Desmond trajectory conversion to dcd format John Stone (Wed Nov 26 2008 - 16:52:42 CST)
- Re: Desmond trajectory conversion to dcd format dimka (Wed Nov 26 2008 - 17:09:57 CST)
  - Re: Desmond trajectory conversion to dcd format Dong Xu (Wed Nov 26 2008 - 17:15:25 CST)
Other color scales than the predefined ones? Berit Hinnemann (Wed Nov 26 2008 - 07:00:17 CST)
- Re: Other color scales than the predefined ones? Axel Kohlmeyer (Wed Nov 26 2008 - 10:21:02 CST)
  - Re: Other color scales than the predefined ones? Berit Hinnemann (Thu Nov 27 2008 - 03:38:46 CST)
    - Re: Other color scales than the predefined ones? John Stone (Thu Nov 27 2008 - 09:36:40 CST)
Re: bug in comments interpretation of vmd John Stone (Wed Nov 26 2008 - 11:13:49 CST)
Re: multiplot: control reaction for click on datapoints? Nadja Lederer (Wed Nov 26 2008 - 11:12:20 CST)
- Re: multiplot: control reaction for click on datapoints? Nadja Lederer (Wed Nov 26 2008 - 14:00:18 CST)
- Re: multiplot: control reaction for click on datapoints? Nadja Lederer (Thu Nov 27 2008 - 10:09:53 CST)
Other color scales than the predefined ones Berit Hinnemann (Wed Nov 26 2008 - 09:52:23 CST)
tcl fscript or Removeing protein flucutation karthigeyan karthigeyantp (Wed Nov 26 2008 - 05:45:33 CST)
- Re: tcl fscript or Removeing protein flucutation Axel Kohlmeyer (Wed Nov 26 2008 - 10:24:18 CST)
Movie of a xyz trajectory Roberto Gaspari (Wed Nov 26 2008 - 03:09:43 CST)
- Re: Movie of a xyz trajectory Axel Kohlmeyer (Wed Nov 26 2008 - 05:12:34 CST)
- Re: Movie of a xyz trajectory Berit Hinnemann (Wed Nov 26 2008 - 07:03:06 CST)
multiplot: control reaction for click on datapoints? Nadja Lederer (Wed Nov 26 2008 - 02:34:31 CST)
drawing lines Ryan Pavlovicz (Tue Nov 25 2008 - 12:38:31 CST)
- Re: drawing lines Peter Freddolino (Tue Nov 25 2008 - 18:23:12 CST)
unloading volumetric data Ondrej Marsalek (Mon Nov 24 2008 - 10:18:39 CST)
- Re: unloading volumetric data John Stone (Mon Nov 24 2008 - 10:32:14 CST)
  - Re: unloading volumetric data Ondrej Marsalek (Mon Nov 24 2008 - 11:09:35 CST)
CG bead definition BIN ZHANG (Sun Nov 23 2008 - 23:56:12 CST)
- Re: CG bead definition Anton Arkhipov (Mon Nov 24 2008 - 16:43:28 CST)
  - Re: CG bead definition BIN ZHANG (Mon Nov 24 2008 - 18:24:35 CST)
    - Re: CG bead definition Anton Arkhipov (Mon Nov 24 2008 - 18:36:23 CST)
  - Re: CG bead definition Anton Arkhipov (Mon Aug 31 2009 - 23:24:05 CDT)
entropy calculations Roman Petrenko (Fri Nov 21 2008 - 15:23:07 CST)
entropy calculations Roman Petrenko (Fri Nov 21 2008 - 15:16:40 CST)
- Re: entropy calculations L. Michel Espinoza-Fonseca (Fri Nov 21 2008 - 16:05:11 CST)
Calculating volumes enclosed by SAS Ghaleb El Masri (Fri Nov 21 2008 - 14:44:39 CST)
- Re: Calculating volumes enclosed by SAS Deepangi Pandit (Fri Nov 21 2008 - 16:09:12 CST)
need tcl help, please Irene Newhouse (Fri Nov 21 2008 - 12:57:03 CST)
- Re: need tcl help, please Peter Freddolino (Fri Nov 21 2008 - 13:22:04 CST)
  - RE: need tcl help, please Irene Newhouse (Fri Nov 21 2008 - 14:36:07 CST)
view only parts of the loaded volumetric data Vlad Cojocaru (Fri Nov 21 2008 - 04:18:11 CST)
- Re: view only parts of the loaded volumetric data Axel Kohlmeyer (Fri Nov 21 2008 - 05:01:21 CST)
Loading .vel file in VMD dipti lele (Thu Nov 20 2008 - 23:03:42 CST)
- Re: Loading .vel file in VMD Axel Kohlmeyer (Fri Nov 21 2008 - 03:45:39 CST)
  - Re: namd-l: Re: Loading .vel file in VMD Thomas C. Bishop (Fri Nov 21 2008 - 09:11:42 CST)
question Wojciech Rajchel (Thu Nov 20 2008 - 11:08:31 CST)
- Re: question Axel Kohlmeyer (Thu Nov 20 2008 - 11:55:59 CST)
running a script Mark M Huntress (Thu Nov 20 2008 - 10:03:10 CST)
- Re: running a script Axel Kohlmeyer (Thu Nov 20 2008 - 11:54:38 CST)
how to get temperature fluctuations maria goranovic (Thu Nov 20 2008 - 08:36:06 CST)
3D Graphics Jesper Soerensen (Thu Nov 20 2008 - 05:50:51 CST)
- Re: 3D Graphics John Stone (Mon Nov 24 2008 - 10:40:21 CST)
  - Re: 3D Graphics Jesper Soerensen (Tue Nov 25 2008 - 09:41:12 CST)
  - Re: 3D Graphics John Stone (Wed Nov 26 2008 - 11:16:18 CST)
[patch] Autodetection of formats supported by openbabel FX (Thu Nov 20 2008 - 05:07:17 CST)
- Re: [patch] Autodetection of formats supported by openbabel John Stone (Mon Nov 24 2008 - 10:22:47 CST)
  - Re: [patch] Autodetection of formats supported by openbabel FX (Mon Nov 24 2008 - 17:05:26 CST)
H-bond occupancy Irene Newhouse (Wed Nov 19 2008 - 12:23:58 CST)
- Re: H-bond occupancy bharat gupta (Wed May 28 2014 - 03:18:16 CDT)
  - Re: Re: H-bond occupancy JC Gumbart (Wed May 28 2014 - 06:36:31 CDT)
representation ColorID in Tcl David Tanner (Wed Nov 19 2008 - 11:25:42 CST)
- Re: representation ColorID in Tcl Peter Freddolino (Wed Nov 19 2008 - 12:16:07 CST)
- Re: representation ColorID in Tcl Axel Kohlmeyer (Wed Nov 19 2008 - 12:24:51 CST)
IED analysis ÖÜÎÄ²ý (Wed Nov 19 2008 - 02:19:19 CST)
- Re: IED analysis John Stone (Mon Nov 24 2008 - 10:34:42 CST)
Autoionize plugin Rabab Toubar (Tue Nov 18 2008 - 19:40:24 CST)
- RE: Autoionize plugin JC Gumbart (Wed Nov 19 2008 - 00:23:56 CST)
  - Re: Autoionize plugin bo liu (Wed Nov 19 2008 - 08:42:58 CST)
    - Re: Autoionize plugin Rabab Toubar (Wed Nov 19 2008 - 10:07:33 CST)
use configure.options Chen Chen (Mon Nov 17 2008 - 19:34:24 CST)
- Re: use configure.options John Stone (Mon Nov 17 2008 - 20:28:36 CST)
  - Re: use configure.options Chen Chen (Mon Nov 17 2008 - 20:53:14 CST)
    - Re: use configure.options John Stone (Mon Nov 17 2008 - 21:06:12 CST)
    - Re: use configure.options Chen Chen (Mon Nov 17 2008 - 21:37:24 CST)
- Re: use configure.options jani sahil (Mon Nov 17 2008 - 21:27:58 CST)
- Re: use configure.options Anirban Ghosh (Mon Nov 17 2008 - 22:34:14 CST)
General question about the memory usage of VMD tinifcarter_at_gmail.com (Mon Nov 17 2008 - 11:48:00 CST)
- Re: General question about the memory usage of VMD Robert Brunner (Mon Nov 17 2008 - 14:42:45 CST)
- Re: General question about the memory usage of VMD Axel Kohlmeyer (Mon Nov 17 2008 - 14:31:02 CST)
- Re: General question about the memory usage of VMD John Stone (Mon Nov 24 2008 - 11:00:33 CST)
  - Re: General question about the memory usage of VMD gurunath katagi (Mon Jan 26 2009 - 03:10:56 CST)
how to run catdcd from within a proc Thomas Evangelidis (Mon Nov 17 2008 - 10:42:44 CST)
- Re: how to run catdcd from within a proc BIN ZHANG (Mon Nov 17 2008 - 11:25:32 CST)
- Re: how to run catdcd from within a proc Axel Kohlmeyer (Mon Nov 17 2008 - 12:48:52 CST)
Installation problems on openSUSE 10.3 Lawrence Wickert (Sat Nov 15 2008 - 20:22:44 CST)
(no subject) Lawrence Wickert (Sat Nov 15 2008 - 20:19:35 CST)
How to set the default properties of drawing methods? Heikki Kasnanen (Thu Nov 13 2008 - 08:39:43 CST)
- Re: How to set the default properties of drawing methods? John Stone (Thu Nov 13 2008 - 08:45:40 CST)
  - Re: How to set the default properties of drawing methods? no tengo nombre (Thu Nov 13 2008 - 11:55:11 CST)
combine.tcl error Jennifer Brookes (Thu Nov 13 2008 - 04:23:03 CST)
About Hydrogen bond calculation ÖÜÎÄ²ý (Thu Nov 13 2008 - 03:20:03 CST)
wavefront and VMD Sandro Canavezzi de Abreu (Wed Nov 12 2008 - 14:07:36 CST)
- Re: wavefront and VMD John Stone (Fri Nov 14 2008 - 15:46:51 CST)
  - Re: wavefront and VMD Sandro Canavezzi de Abreu (Mon Nov 17 2008 - 07:58:08 CST)
    - Re: wavefront and VMD Axel Kohlmeyer (Mon Nov 17 2008 - 09:12:55 CST)
    - Re: wavefront and VMD Sandro Canavezzi de Abreu (Mon Nov 17 2008 - 11:44:29 CST)
(no subject) Anirban Ghosh (Tue Nov 11 2008 - 07:17:04 CST)
- Re: Peter Freddolino (Tue Nov 11 2008 - 10:30:47 CST)
  - Re: Re: Anirban Ghosh (Tue Nov 11 2008 - 21:59:01 CST)
OpenGL Display max_at_liaad.up.pt (Tue Nov 11 2008 - 04:03:12 CST)
- Re: OpenGL Display John Stone (Tue Nov 11 2008 - 08:05:17 CST)
doubling a membrane Edward Lyman (Mon Nov 10 2008 - 16:42:13 CST)
- Re: doubling a membrane Peter Freddolino (Mon Nov 10 2008 - 17:29:24 CST)
  - Re: doubling a membrane Cesar Luis Avila (Tue Nov 11 2008 - 13:23:33 CST)
  - Re: doubling a membrane Cesar Luis Avila (Tue Nov 11 2008 - 18:44:07 CST)
fasta2pdb Roman Petrenko (Mon Nov 10 2008 - 14:33:24 CST)
- Re: fasta2pdb Eric H. Lee (Mon Nov 10 2008 - 15:16:00 CST)
  - Re: fasta2pdb Peter Freddolino (Mon Nov 10 2008 - 17:30:19 CST)
movie Abu Naser (Sun Nov 09 2008 - 11:06:20 CST)
- Re: movie Axel Kohlmeyer (Sun Nov 09 2008 - 11:56:35 CST)
usage for the patch 5DP (there is no information in the tutorial) OZGE ENGIN (Sat Nov 08 2008 - 03:17:41 CST)
usage for the pacth 5DP (there is no information in the tutorial) OZGE ENGIN (Sat Nov 08 2008 - 03:10:17 CST)
usage for the patch 5DP (there is no information in the tutorial) OZGE ENGIN (Fri Nov 07 2008 - 19:04:35 CST)
load MSMS files into vmd Prevost Martine (Fri Nov 07 2008 - 09:29:34 CST)
- Re: load MSMS files into vmd John Stone (Wed Nov 12 2008 - 09:57:39 CST)
  - Re: load MSMS files into vmd John Stone (Wed Nov 12 2008 - 13:51:23 CST)
Multiple incompatible definitions warning Subramanian Vaitheeswaran (Thu Nov 06 2008 - 11:25:01 CST)
- Re: Multiple incompatible definitions warning Peter Freddolino (Thu Nov 06 2008 - 12:04:06 CST)
RMSD error "Matrix: Warning: no convergence" Maria Sanchez (Thu Nov 06 2008 - 09:16:20 CST)
Sequentially numbering atom names in pdb file Subramanian Vaitheeswaran (Wed Nov 05 2008 - 14:29:24 CST)
- Re: Sequentially numbering atom names in pdb file Robert Brunner (Wed Nov 05 2008 - 16:02:54 CST)
- Re: Sequentially numbering atom names in pdb file Axel Kohlmeyer (Wed Nov 05 2008 - 16:24:57 CST)
CG Map Tool Syntax Error Anirban Ghosh (Wed Nov 05 2008 - 04:48:32 CST)
- Re: CG Map Tool Syntax Error Anton Arkhipov (Wed Nov 05 2008 - 16:16:59 CST)
B factor calculation AyÅŸe Ã–zlem Aykut (Tue Nov 04 2008 - 10:51:24 CST)
- RE: B factor calculation Aaron.Oakley_at_csiro.au (Tue Nov 04 2008 - 16:27:02 CST)
Average position of atom set Christopher Hartshorn (Tue Nov 04 2008 - 09:59:56 CST)
- Re: Average position of atom set Leonardo Trabuco (Tue Nov 04 2008 - 20:11:01 CST)
Psfgen : apply patches Nicolas Floquet (Tue Nov 04 2008 - 06:51:57 CST)
- Re: Psfgen : apply patches Peter Freddolino (Tue Nov 04 2008 - 07:16:07 CST)
conformations of a linker Edward Lyman (Fri Oct 31 2008 - 14:07:08 CDT)
- Re: conformations of a linker Peter Freddolino (Fri Oct 31 2008 - 14:37:34 CDT)
- Re: conformations of a linker Boris Steipe (Fri Oct 31 2008 - 16:39:17 CDT)
[Fwd: problems with manipulating control switches on VMS main menu] Piotr Cieplak (Fri Oct 31 2008 - 12:57:15 CDT)
- Re: [Fwd: problems with manipulating control switches on VMS main menu] Axel Kohlmeyer (Fri Oct 31 2008 - 18:05:46 CDT)
Per-frame 'graphics'? Benjamin Bouvier (Fri Oct 31 2008 - 10:46:03 CDT)
- Re: Per-frame 'graphics'? Rogan Carr (Fri Oct 31 2008 - 11:22:55 CDT)
  - Re: Per-frame 'graphics'? Benjamin Bouvier (Fri Oct 31 2008 - 13:36:24 CDT)
    - Re: Per-frame 'graphics'? Axel Kohlmeyer (Fri Oct 31 2008 - 16:59:44 CDT)
    - Re: Per-frame 'graphics'? John Stone (Sat Nov 01 2008 - 10:12:56 CDT)
VMD crashes on displaying NewRibbons or New Cartoon Jufang Shan (Fri Oct 31 2008 - 10:13:32 CDT)
- Re: VMD crashes on displaying NewRibbons or New Cartoon John Stone (Wed Nov 12 2008 - 09:35:13 CST)
  - Re: VMD crashes on displaying NewRibbons or New Cartoon Jufang Shan (Wed Nov 12 2008 - 20:48:17 CST)
    - Re: VMD crashes on displaying NewRibbons or New Cartoon John Stone (Thu Nov 13 2008 - 08:26:20 CST)
    - Re: VMD crashes on displaying NewRibbons or New Cartoon Thomas C. Bishop (Thu Nov 13 2008 - 08:20:50 CST)
Visualizing multiple molecules max_at_liaad.up.pt (Fri Oct 31 2008 - 07:26:00 CDT)
PMEpot units jirasak wong-ekkabut (Thu Oct 30 2008 - 15:10:05 CDT)
problems with manipulating control switches on VMS main menu Piotr Cieplak (Wed Oct 29 2008 - 19:52:24 CDT)
- Re: problems with manipulating control switches on VMS main menu John Stone (Thu Oct 30 2008 - 02:13:11 CDT)
Render surface colored by electrostatic potential Adam Kraut (Tue Oct 28 2008 - 13:27:52 CDT)
- Re: Render surface colored by electrostatic potential Axel Kohlmeyer (Tue Oct 28 2008 - 14:03:47 CDT)
isosurface question Raluca Mihaela ANDREI (Tue Oct 28 2008 - 12:48:14 CDT)
- Re: isosurface question John Stone (Wed Oct 29 2008 - 04:47:48 CDT)
move matrix definition Edward Lyman (Tue Oct 28 2008 - 11:39:42 CDT)
- Re: move matrix definition Axel Kohlmeyer (Tue Oct 28 2008 - 12:14:13 CDT)
Free Trial of New Toxicity Prediction Software (LD50, MRDD, side effects) is now available Maxim Kholin (Tue Oct 28 2008 - 09:00:25 CDT)
reading multiples molecules. no tengo nombre (Tue Oct 28 2008 - 05:05:19 CDT)
- Re: reading multiples molecules. Benjamin Bouvier (Tue Oct 28 2008 - 06:15:45 CDT)
  - Re: reading multiples molecules. no tengo nombre (Wed Oct 29 2008 - 05:26:09 CDT)
- Re: reading multiples molecules. Axel Kohlmeyer (Tue Oct 28 2008 - 09:20:54 CDT)
  - Re: reading multiples molecules. no tengo nombre (Wed Oct 29 2008 - 04:17:12 CDT)
A question about the namd energy plugin of VMD wayj86 wayj86 (Sun Oct 26 2008 - 08:58:21 CDT)
- Re: A question about the namd energy plugin of VMD Axel Kohlmeyer (Sun Oct 26 2008 - 13:12:06 CDT)
Camera in VMD!!! Iman Salehinia (Fri Oct 24 2008 - 23:10:35 CDT)
- Re: Camera in VMD!!! Schreiner Eduard (Sat Oct 25 2008 - 00:18:58 CDT)
Warning: no convergence in alignment Jianhui Tian (Fri Oct 24 2008 - 17:02:08 CDT)
- Re: Warning: no convergence in alignment Jianhui Tian (Mon Oct 27 2008 - 14:01:21 CDT)
  - Re: Warning: no convergence in alignment John Stone (Mon Oct 27 2008 - 16:35:37 CDT)
PBCtools verison 2.3: how to obtain it? mon_sharma_at_research.iiit.ac.in (Fri Oct 24 2008 - 09:19:37 CDT)
- Re: PBCtools verison 2.3: how to obtain it? Axel Kohlmeyer (Fri Oct 24 2008 - 10:32:16 CDT)
- Re: PBCtools verison 2.3: how to obtain it? Olaf Lenz (Sun Oct 26 2008 - 02:57:17 CDT)
advanced selections (or explicit pair list) for measure gofr ? Maxim Paliy (Fri Oct 24 2008 - 07:48:40 CDT)
- Re: advanced selections (or explicit pair list) for measure gofr ? Axel Kohlmeyer (Fri Oct 24 2008 - 10:31:13 CDT)
independent stereo display Petrica GASCA (Thu Oct 23 2008 - 11:39:07 CDT)
- Re: independent stereo display Axel Kohlmeyer (Thu Oct 23 2008 - 14:15:13 CDT)
create movie from multiple frames Petrica GASCA (Thu Oct 23 2008 - 08:25:17 CDT)
extraction of bound water molecules in a trajectory mon_sharma_at_research.iiit.ac.in (Thu Oct 23 2008 - 04:39:07 CDT)
- Re: extraction of bound water molecules in a trajectory Thomas C. Bishop (Thu Oct 23 2008 - 08:46:59 CDT)
change the radius of atoms Iman Salehinia (Wed Oct 22 2008 - 21:35:36 CDT)
- Re: change the radius of atoms Joaquim Rui Rodrigues (Thu Oct 23 2008 - 05:40:59 CDT)
Multiseq error: 'can't read 'SequenceIDtoMolID(122)': no such element in array' Perreault, Roger Edward (Wed Oct 22 2008 - 20:34:57 CDT)
- Re: Multiseq error: 'can't read 'SequenceIDtoMolID(122)': no such element in array' Elijah Roberts (Wed Oct 22 2008 - 22:24:11 CDT)
Re: A question about the plugin of salt bridge plugin Leonardo Trabuco (Wed Oct 22 2008 - 11:24:09 CDT)
dcd format JONATHAN BLACK (Wed Oct 22 2008 - 04:30:19 CDT)
- RE: dcd format Tibbitt, Jeffrey A. (Wed Oct 22 2008 - 11:56:30 CDT)
  - RE: dcd format Axel Kohlmeyer (Wed Oct 22 2008 - 12:49:56 CDT)
Extract parameters of Shape-based Coarse Graining model from AA simulation dongsheng lei (Wed Oct 22 2008 - 01:54:54 CDT)
- Re: Extract parameters of Shape-based Coarse Graining model from AA simulation Anton Arkhipov (Wed Oct 22 2008 - 10:28:02 CDT)
  - Re: Extract parameters of Shape-based Coarse Graining model from AA simulation dongsheng lei (Thu Oct 23 2008 - 04:46:50 CDT)
convert THR and SER to the phosphorylated forms bo baker (Tue Oct 21 2008 - 19:06:11 CDT)
- Re: convert THR and SER to the phosphorylated forms L. Michel Espinoza-Fonseca (Wed Oct 22 2008 - 04:01:01 CDT)
Querry dipti lele (Tue Oct 21 2008 - 08:42:18 CDT)
fitting structure to map generated by Volmap Tomek Wlodarski (Tue Oct 21 2008 - 07:55:09 CDT)
- Re: fitting structure to map generated by Volmap Axel Kohlmeyer (Tue Oct 21 2008 - 09:01:22 CDT)
  - Re: fitting structure to map generated by Volmap Tomek Wlodarski (Tue Oct 21 2008 - 14:46:15 CDT)
volmap Panagiota Georgoulia (Tue Oct 21 2008 - 06:17:51 CDT)
- Re: volmap Peter Freddolino (Tue Oct 21 2008 - 07:26:23 CDT)
  - volmap Panagiota Georgoulia (Tue Oct 21 2008 - 09:07:35 CDT)
    - Re: volmap Anton Arkhipov (Tue Oct 21 2008 - 10:43:40 CDT)
    - Re: volmap Peter Freddolino (Tue Oct 21 2008 - 10:57:44 CDT)
(no subject) JONATHAN BLACK (Tue Oct 21 2008 - 04:16:29 CDT)
- Re: Peter Freddolino (Tue Oct 21 2008 - 07:21:42 CDT)
Selecting some atoms and changing the color of them Iman Salehinia (Tue Oct 21 2008 - 01:55:03 CDT)
- Re: Selecting some atoms and changing the color of them Peter Freddolino (Tue Oct 21 2008 - 07:24:08 CDT)
animated gif Panagiota Georgoulia (Mon Oct 20 2008 - 06:37:32 CDT)
- Re: animated gif Peter Freddolino (Mon Oct 20 2008 - 07:01:18 CDT)
PSFGEN problem with URA residues Anirban Ghosh (Mon Oct 20 2008 - 06:27:06 CDT)
- Re: PSFGEN problem with URA residues Peter Freddolino (Mon Oct 20 2008 - 06:59:42 CDT)
  - Re: PSFGEN problem with URA residues Anirban Ghosh (Mon Oct 20 2008 - 08:30:49 CDT)
    - Re: PSFGEN problem with URA residues Peter Freddolino (Mon Oct 20 2008 - 09:04:03 CDT)
feature request Tamara Rogers (Sun Oct 19 2008 - 12:38:18 CDT)
- Re: feature request Axel Kohlmeyer (Sun Oct 19 2008 - 13:26:42 CDT)
Improving VMD performance on Linux? nbabcock_at_qis.ucalgary.ca (Sat Oct 18 2008 - 14:06:35 CDT)
- Re: Improving VMD performance on Linux? Benjamin Bouvier (Mon Oct 20 2008 - 06:05:26 CDT)
  - Re: Improving VMD performance on Linux? Leandro Martínez (Mon Oct 20 2008 - 07:22:08 CDT)
  - Re: Improving VMD performance on Linux? Olaf Lenz (Mon Oct 20 2008 - 07:37:58 CDT)
    - Re: Improving VMD performance on Linux? Olaf Lenz (Mon Oct 20 2008 - 07:57:28 CDT)
Out of town until November 1 John Stone (Thu Oct 16 2008 - 15:53:42 CDT)
Catdcd? Christopher Hartshorn (Thu Oct 16 2008 - 11:37:15 CDT)
- Re: Catdcd? Christopher Gillespie (Thu Oct 16 2008 - 12:25:42 CDT)
  - Re: Catdcd? Anirban Ghosh (Mon Oct 20 2008 - 06:31:25 CDT)
- Re: Catdcd? Axel Kohlmeyer (Thu Oct 16 2008 - 13:23:14 CDT)
  - Re: Catdcd? bo liu (Fri Oct 17 2008 - 00:01:59 CDT)
saving trajectories from the command line Jim Pfaendtner (Thu Oct 16 2008 - 07:28:00 CDT)
- Re: saving trajectories from the command line Axel Kohlmeyer (Thu Oct 16 2008 - 09:11:17 CDT)
Problem in text mode Wei Huang (Thu Oct 16 2008 - 00:25:07 CDT)
- Re: Problem in text mode Schreiner Eduard (Thu Oct 16 2008 - 00:41:25 CDT)
  - RE: Problem in text mode Wei Huang (Thu Oct 16 2008 - 00:58:55 CDT)
velocity calculations Ryan Pavlovicz (Wed Oct 15 2008 - 10:18:50 CDT)
- Re: velocity calculations John Stone (Wed Oct 15 2008 - 11:11:02 CDT)
- Re: velocity calculations Axel Kohlmeyer (Wed Oct 15 2008 - 11:20:33 CDT)
  - Re: velocity calculations John Stone (Wed Oct 15 2008 - 12:39:12 CDT)
    - Re: velocity calculations Suman Chakrabarty (Wed Oct 15 2008 - 15:40:04 CDT)
    - Re: velocity calculations John Stone (Wed Oct 15 2008 - 15:58:49 CDT)
Deleting frames / molecules does not free up memory! Benjamin Bouvier (Tue Oct 14 2008 - 10:26:55 CDT)
- Re: Deleting frames / molecules does not free up memory! Axel Kohlmeyer (Tue Oct 14 2008 - 11:13:11 CDT)
  - Re: Deleting frames / molecules does not free up memory! Benjamin Bouvier (Tue Oct 14 2008 - 11:34:44 CDT)
why atomselection "protein" can not choose all the protein atoms with different alternate locations? Lan Hua (Mon Oct 13 2008 - 16:49:07 CDT)
- Re: why atomselection "protein" can not choose all the protein atoms with different alternate locations? Axel Kohlmeyer (Mon Oct 13 2008 - 18:23:35 CDT)
- Re: why atomselection "protein" can not choose all the protein atoms with different alternate locations? John Stone (Tue Oct 14 2008 - 11:43:43 CDT)
  - Re: why atomselection "protein" can not choose all the protein atoms with different alternate locations? Lan Hua (Tue Oct 14 2008 - 11:55:14 CDT)
How to specify color based on dihedral angle? Suman Chakrabarty (Mon Oct 13 2008 - 13:09:53 CDT)
- Re: How to specify color based on dihedral angle? Axel Kohlmeyer (Mon Oct 13 2008 - 14:25:11 CDT)
Windows version: Loading/writing files Neelanjana Sengupta (Mon Oct 13 2008 - 07:53:41 CDT)
- Re: Windows version: Loading/writing files Alexander A. Vakhrushev (Mon Oct 13 2008 - 08:49:21 CDT)
  - Re: Windows version: Loading/writing files bo liu (Mon Oct 13 2008 - 09:50:41 CDT)
CHARMM TO AMBER FORMAT CONVERT Semorale (Sun Oct 12 2008 - 18:20:28 CDT)
- Re: CHARMM TO AMBER FORMAT CONVERT Axel Kohlmeyer (Sun Oct 12 2008 - 19:26:18 CDT)
Error in "measure fit" Stephen Hicks (Sat Oct 11 2008 - 15:05:45 CDT)
- Re: Error in "measure fit" John Stone (Thu Oct 16 2008 - 15:43:17 CDT)
Density distribution plots mahesh naalla (Fri Oct 10 2008 - 15:39:30 CDT)
- Re: Density distribution plots Axel Kohlmeyer (Fri Oct 10 2008 - 16:26:20 CDT)
STRIDE analysis of beta-sheets in VMD Tristan Bereau (Fri Oct 10 2008 - 15:28:33 CDT)
- Re: STRIDE analysis of beta-sheets in VMD Axel Kohlmeyer (Fri Oct 10 2008 - 16:50:59 CDT)
  - intersurf in vmd BIN ZHANG (Sat Oct 11 2008 - 14:58:14 CDT)
    - Re: intersurf in vmd Axel Kohlmeyer (Sat Oct 11 2008 - 18:44:10 CDT)
    - Re: intersurf in vmd John Stone (Tue Oct 14 2008 - 16:44:01 CDT)
Question about the Main Menu window display Alfredo Quevedo (Fri Oct 10 2008 - 14:15:47 CDT)
- Re: Question about the Main Menu window display Axel Kohlmeyer (Fri Oct 10 2008 - 14:47:28 CDT)
  - Re: Question about the Main Menu window display Alfredo Quevedo (Wed Oct 15 2008 - 13:31:58 CDT)
loading python Ryan Pavlovicz (Thu Oct 09 2008 - 15:21:15 CDT)
- Re: loading python Axel Kohlmeyer (Thu Oct 09 2008 - 16:31:13 CDT)
  - Re: loading python Ryan Pavlovicz (Thu Oct 09 2008 - 22:10:44 CDT)
    - Re: loading python Axel Kohlmeyer (Fri Oct 10 2008 - 11:37:28 CDT)
Density distribution plots mahesh naalla (Thu Oct 09 2008 - 13:28:31 CDT)
- Re: Density distribution plots Axel Kohlmeyer (Thu Oct 09 2008 - 14:14:57 CDT)
Povray render cuts litorice,bond,cpk representations schwarz_at_titus.u-strasbg.fr (Thu Oct 09 2008 - 05:14:20 CDT)
Fw: VMD 1.8.6 for UBUNTU 8.04LTS Mamta Mohan (Wed Oct 08 2008 - 20:21:11 CDT)
- Re: Fw: VMD 1.8.6 for UBUNTU 8.04LTS Axel Kohlmeyer (Wed Oct 08 2008 - 20:57:54 CDT)
  - Re: Fw: VMD 1.8.6 for UBUNTU 8.04LTS Alexander A. Vakhrushev (Wed Oct 08 2008 - 23:37:06 CDT)
    - Re: Fw: VMD 1.8.6 for UBUNTU 8.04LTS Mamta Mohan (Thu Oct 09 2008 - 10:55:29 CDT)
pbctools usage Subramanian Vaitheeswaran (Wed Oct 08 2008 - 08:21:10 CDT)
- Re: pbctools usage Axel Kohlmeyer (Wed Oct 08 2008 - 10:23:44 CDT)
How to visualize only parts of a molecular surface schwarz (Wed Oct 08 2008 - 08:11:47 CDT)
- Re: How to visualize only parts of a molecular surface John Stone (Wed Oct 08 2008 - 13:51:19 CDT)
Fullscreen mode in VMD Alexandr Bezginov (Tue Oct 07 2008 - 12:34:59 CDT)
- Re: Fullscreen mode in VMD John Stone (Tue Oct 07 2008 - 12:53:07 CDT)
Vmd on MACOSX awkward msg at startup and error when running Ubq simulation Montoya, Jesus Gerardo Galaz (Mon Oct 06 2008 - 14:58:39 CDT)
- Re: Vmd on MACOSX awkward msg at startup and error when running Ubq simulation John Stone (Mon Oct 06 2008 - 15:57:08 CDT)
lipid tail selection BIN ZHANG (Sun Oct 05 2008 - 01:16:45 CDT)
- Re: lipid tail selection Axel Kohlmeyer (Mon Oct 06 2008 - 09:18:15 CDT)
- Re: lipid tail selection Danielle Chandler (Thu Oct 09 2008 - 14:30:37 CDT)
VMD 1.8.6 for UBUNTU 8.04LTS Mamta Mohan (Fri Oct 03 2008 - 14:03:28 CDT)
- Re: VMD 1.8.6 for UBUNTU 8.04LTS John Stone (Fri Oct 03 2008 - 14:15:18 CDT)
Pairwise RMSD Dong Xu (Fri Oct 03 2008 - 10:10:16 CDT)
- Re: Pairwise RMSD John Stone (Tue Oct 07 2008 - 13:20:12 CDT)
  - Re: Pairwise RMSD Elijah Roberts (Tue Oct 07 2008 - 15:13:16 CDT)
Re: Problems after installation (ubuntu 8.04) Alexander A. Vakhrushev (Fri Oct 03 2008 - 08:43:39 CDT)
- Re: Problems after installation (ubuntu 8.04) John Stone (Fri Oct 03 2008 - 09:49:22 CDT)
  - Re: Problems after installation (ubuntu 8.04) Tomek Wlodarski (Fri Oct 03 2008 - 16:23:41 CDT)
- Re: Problems after installation (ubuntu 8.04) Anirban Ghosh (Sat Oct 04 2008 - 13:04:09 CDT)
Problems after installation (ubuntu 8.04) Tomek Wlodarski (Fri Oct 03 2008 - 07:23:25 CDT)
Problem with creating psf file from structure made by inorganic builder Anneta Tzampazi (Fri Oct 03 2008 - 04:43:19 CDT)
TAB key in vmd terminal BIN ZHANG (Thu Oct 02 2008 - 23:32:00 CDT)
- Re: TAB key in vmd terminal John Stone (Fri Oct 03 2008 - 11:16:26 CDT)
suggested graphic card for Mac Pro Joaquim Rui Rodrigues (Thu Oct 02 2008 - 12:09:32 CDT)
- Re: suggested graphic card for Mac Pro John Stone (Thu Oct 02 2008 - 12:22:39 CDT)
volumetric maps markus.mooslechner_at_chello.at (Thu Oct 02 2008 - 07:18:38 CDT)
volumetric maps markus.mooslechner_at_chello.at (Thu Oct 02 2008 - 07:08:11 CDT)
- Re: volumetric maps Axel Kohlmeyer (Thu Oct 02 2008 - 10:57:45 CDT)
- Re: volumetric maps John Stone (Thu Oct 02 2008 - 12:05:19 CDT)
  - AW: volumetric maps markus.mooslechner_at_orf.at (Fri Oct 03 2008 - 05:11:50 CDT)
Does VMD support cfg file format? zhjjvmd (Wed Oct 01 2008 - 03:52:32 CDT)
- Re: Does VMD support cfg file format? John Stone (Wed Oct 01 2008 - 11:03:05 CDT)
  - Re: Re: Does VMD support cfg file format? zhjjvmd (Wed Oct 01 2008 - 12:00:33 CDT)
- Re: Re: Does VMD support cfg file format? zhjjvmd (Wed Oct 01 2008 - 11:58:06 CDT)
  - Re: Re: Does VMD support cfg file format? John Stone (Wed Oct 01 2008 - 12:57:19 CDT)
atom type Rudra Banerjee (Tue Sep 30 2008 - 23:28:58 CDT)
- Re: atom type Boris Steipe (Wed Oct 01 2008 - 11:37:48 CDT)
  - Re: atom type Rudra Banerjee (Thu Oct 02 2008 - 12:14:25 CDT)
    - Re: atom type Axel Kohlmeyer (Thu Oct 02 2008 - 13:16:47 CDT)
  - Re: atom type Rudra Banerjee (Thu Oct 02 2008 - 22:57:47 CDT)
    - Re: atom type bo liu (Fri Oct 03 2008 - 06:51:22 CDT)
water box Rudra Banerjee (Tue Sep 30 2008 - 03:48:37 CDT)
- Re: water box Alexander A. Vakhrushev (Tue Sep 30 2008 - 04:55:46 CDT)
periodic box image in tcl script Brian Kidd (Mon Sep 29 2008 - 11:27:39 CDT)
- Re: periodic box image in tcl script John Stone (Tue Oct 07 2008 - 13:22:02 CDT)
question about sscache qwang_at_mail.uh.edu (Sun Sep 28 2008 - 19:33:02 CDT)
(no subject) studier_at_life.illinois.edu (Sat Sep 27 2008 - 16:22:10 CDT)
- Re: Axel Kohlmeyer (Sun Sep 28 2008 - 13:15:18 CDT)
question about sscache qwang_at_mail.uh.edu (Fri Sep 26 2008 - 14:00:07 CDT)
- Re: question about sscache Alexander A. Vakhrushev (Fri Sep 26 2008 - 22:41:50 CDT)
  - Re: question about sscache Margaret S. Cheung (Sun Sep 28 2008 - 21:04:56 CDT)
    - Re: question about sscache John Stone (Mon Sep 29 2008 - 10:03:46 CDT)
    - Re: question about sscache qwang_at_mail.uh.edu (Mon Sep 29 2008 - 11:44:35 CDT)
visualisation problem with bonds and PBC Jennifer Williams (Fri Sep 26 2008 - 09:32:42 CDT)
- Re: visualisation problem with bonds and PBC Axel Kohlmeyer (Fri Sep 26 2008 - 11:46:39 CDT)
Atoms numbers in VMD Nd S (Thu Sep 25 2008 - 14:07:30 CDT)
- Re: Atoms numbers in VMD Leandro Martínez (Thu Sep 25 2008 - 14:56:01 CDT)
Creating a cuboid box to fit in atoms Ananyo Bandyopadhyay (Thu Sep 25 2008 - 13:29:15 CDT)
- Re: Creating a cuboid box to fit in atoms Leandro Martínez (Thu Sep 25 2008 - 14:51:00 CDT)
Re: psf file generation: once again Rudra Banerjee (Wed Sep 24 2008 - 23:11:04 CDT)
- Re: psf file generation: once again Rudra Banerjee (Wed Sep 24 2008 - 23:42:22 CDT)
  - Re: psf file generation: once again Peter Freddolino (Thu Sep 25 2008 - 08:12:34 CDT)
psf file generation: once again Rudra Banerjee (Wed Sep 24 2008 - 22:45:49 CDT)
- Re: psf file generation: once again Peter Freddolino (Wed Sep 24 2008 - 23:01:48 CDT)
How to render an image like this one with VMD? Dong Xu (Wed Sep 24 2008 - 20:58:12 CDT)
- Re: How to render an image like this one with VMD? Peter Freddolino (Wed Sep 24 2008 - 21:49:25 CDT)
  - Re: How to render an image like this one with VMD? Anton Arkhipov (Thu Sep 25 2008 - 11:29:20 CDT)
water residence time L. Michel Espinoza-Fonseca (Wed Sep 24 2008 - 15:56:53 CDT)
Re: Help, my molecule is being destroyed John Stone (Wed Sep 24 2008 - 15:46:14 CDT)
Movie maker problem in VMD Ananyo Bandyopadhyay (Wed Sep 24 2008 - 11:11:14 CDT)
- Re: Movie maker problem in VMD L. Michel Espinoza-Fonseca (Wed Sep 24 2008 - 11:56:11 CDT)
weird behavior with RMSD Irene Newhouse (Tue Sep 23 2008 - 16:21:02 CDT)
viewing an embryo markt_at_mskcc.org (Tue Sep 23 2008 - 14:04:41 CDT)
- Re: viewing an embryo Anton Arkhipov (Tue Sep 23 2008 - 14:37:15 CDT)
  - RE: viewing an embryo markt_at_mskcc.org (Tue Sep 23 2008 - 14:54:19 CDT)
    - Re: viewing an embryo Anton Arkhipov (Tue Sep 23 2008 - 15:03:01 CDT)
  - Re: viewing an embryo Axel Kohlmeyer (Tue Sep 23 2008 - 15:10:02 CDT)
- Re: viewing an embryo Leandro Martínez (Tue Sep 23 2008 - 14:48:30 CDT)
Re: namd-l: solvate a molecule Chang, Christopher (Tue Sep 23 2008 - 11:57:58 CDT)
- Re: namd-l: solvate a molecule Rudra Banerjee (Tue Sep 23 2008 - 22:32:53 CDT)
Periodic BC Nd S (Mon Sep 22 2008 - 15:26:20 CDT)
- Re: Periodic BC Olaf Lenz (Tue Sep 23 2008 - 02:47:30 CDT)
solvate a molecule Rudra Banerjee (Sat Sep 20 2008 - 01:08:03 CDT)
- Re: solvate a molecule John Stone (Sat Sep 20 2008 - 02:12:59 CDT)
rotation around phi/psi Roman Petrenko (Fri Sep 19 2008 - 21:05:24 CDT)
- Re: rotation around phi/psi John Stone (Sat Sep 20 2008 - 02:05:49 CDT)
  - Re: rotation around phi/psi Roman Petrenko (Sun Sep 21 2008 - 14:46:00 CDT)
Solvation Box Navdeep (Fri Sep 19 2008 - 16:43:25 CDT)
- Re: Solvation Box Robert Brunner (Tue Sep 23 2008 - 11:32:42 CDT)
  - Re: Solvation Box Leandro Martínez (Tue Sep 23 2008 - 13:20:52 CDT)
Projection of a vector on to another. Katherine Parra (Fri Sep 19 2008 - 13:56:01 CDT)
- Re: Projection of a vector on to another. bo liu (Fri Sep 19 2008 - 23:03:42 CDT)
- Re: Projection of a vector on to another. John Stone (Sat Sep 20 2008 - 02:11:41 CDT)
  - Re: Projection of a vector on to another. bo liu (Sat Sep 20 2008 - 06:09:46 CDT)
running simulation on dual core processor Mamta Mohan (Fri Sep 19 2008 - 10:44:27 CDT)
- Re: running simulation on dual core processor JC Gumbart (Fri Sep 19 2008 - 13:50:27 CDT)
Restarting a simulation $ Langevin Anirban Ghosh (Fri Sep 19 2008 - 07:17:12 CDT)
- Re: Restarting a simulation $ Langevin John Stone (Sat Sep 20 2008 - 02:20:34 CDT)
difficulty in installing VMD on linux. Deepti Mishra (Fri Sep 19 2008 - 05:47:18 CDT)
- Re: difficulty in installing VMD on linux. John Stone (Fri Sep 19 2008 - 15:11:32 CDT)
trouble with running vmd after installation , machine gets hung shiladitya_at_jncasr.ac.in (Fri Sep 19 2008 - 04:30:01 CDT)
- Re: trouble with running vmd after installation , machine gets hung Axel Kohlmeyer (Fri Sep 19 2008 - 06:05:42 CDT)
  - Re: trouble with running vmd after installation , machine gets hung shiladitya_at_jncasr.ac.in (Sat Sep 20 2008 - 23:14:50 CDT)
Error generating psf files Nd S (Thu Sep 18 2008 - 18:55:28 CDT)
- Re: Error generating psf files Peter Freddolino (Thu Sep 18 2008 - 20:18:14 CDT)
  - Re: Error generating psf files Nd S (Thu Sep 18 2008 - 22:05:07 CDT)
Solid Support Problem Christopher Hartshorn (Thu Sep 18 2008 - 13:33:07 CDT)
- Re: Solid Support Problem Peter Freddolino (Thu Sep 18 2008 - 22:10:46 CDT)
Fw: warning during psfgen file Mamta Mohan (Thu Sep 18 2008 - 13:08:29 CDT)
warning during psfgen file Mamta Mohan (Thu Sep 18 2008 - 10:11:33 CDT)
counting gas molecules inside the nanotube mishacat_at_udm.ru (Thu Sep 18 2008 - 06:52:51 CDT)
- Re: counting gas molecules inside the nanotube John Stone (Thu Sep 18 2008 - 11:18:43 CDT)
  - Re: counting gas molecules inside the nanotube Alexander A. Vakhrushev (Thu Sep 18 2008 - 12:11:04 CDT)
    - Re: counting gas molecules inside the nanotube John Stone (Thu Sep 18 2008 - 12:29:34 CDT)
    - Re: namd-l: Re: counting gas molecules inside the nanotube bo liu (Fri Sep 19 2008 - 11:38:19 CDT)
Trouble installing VMD on LINUX machine Gregor Kladnik (Thu Sep 18 2008 - 06:43:14 CDT)
- Re: Trouble installing VMD on LINUX machine John Stone (Thu Sep 18 2008 - 11:06:45 CDT)
  - Re: Trouble installing VMD on LINUX machine SOLVED Gregor Kladnik (Thu Sep 18 2008 - 11:18:40 CDT)
Re: problem with psf file generation Rudra Banerjee (Thu Sep 18 2008 - 03:29:07 CDT)
psfgen problem Rudra Banerjee (Thu Sep 18 2008 - 01:45:55 CDT)
- Re: psfgen problem Peter Freddolino (Thu Sep 18 2008 - 07:18:15 CDT)
  - Re: psfgen problem Rudra Banerjee (Thu Sep 18 2008 - 09:34:14 CDT)
    - Re: psfgen problem L. Michel Espinoza-Fonseca (Thu Sep 18 2008 - 10:13:55 CDT)
  - Re: psfgen problem Rudra Banerjee (Thu Sep 18 2008 - 21:48:08 CDT)
problem with psf file generation Rudra Banerjee (Thu Sep 18 2008 - 01:12:44 CDT)
apbs electrostatics James Haven (Wed Sep 17 2008 - 15:15:08 CDT)
- Re: apbs electrostatics John Stone (Wed Sep 17 2008 - 21:42:28 CDT)
solvation Mamta Mohan (Wed Sep 17 2008 - 13:28:55 CDT)
- Re: solvation John Stone (Wed Sep 17 2008 - 21:46:39 CDT)
simulation image question Mamta Mohan (Wed Sep 17 2008 - 12:42:34 CDT)
- Re: simulation image question John Stone (Wed Sep 17 2008 - 12:57:37 CDT)
problem downloading VMD 1.8.6 source code Lai, Massimo (Wed Sep 17 2008 - 09:59:40 CDT)
- Re: problem downloading VMD 1.8.6 source code John Stone (Wed Sep 17 2008 - 10:40:41 CDT)
  - RE: problem downloading VMD 1.8.6 source code Lai, Massimo (Thu Sep 18 2008 - 04:21:38 CDT)
Interface Propensity bo baker (Wed Sep 17 2008 - 05:56:20 CDT)
- Re: Interface Propensity John Stone (Wed Sep 17 2008 - 21:53:13 CDT)
regarding rotating dihedral jani sahil (Tue Sep 16 2008 - 22:26:17 CDT)
- Re: regarding rotating dihedral John Stone (Wed Sep 17 2008 - 21:58:14 CDT)
  - Re: regarding rotating dihedral Peter Freddolino (Wed Sep 17 2008 - 22:39:40 CDT)
Installing VMD on Fedora Neelanjana Sengupta (Tue Sep 16 2008 - 08:25:54 CDT)
- Re: Installing VMD on Fedora John Stone (Tue Sep 16 2008 - 10:58:40 CDT)
  - Re: Installing VMD on Fedora Neelanjana Sengupta (Wed Sep 17 2008 - 03:32:02 CDT)
    - Re: Installing VMD on Fedora Peter Freddolino (Wed Sep 17 2008 - 07:18:07 CDT)
parallel VMD Benjamin Stauch (Tue Sep 16 2008 - 07:47:16 CDT)
- Re: parallel VMD John Stone (Tue Sep 16 2008 - 13:35:03 CDT)
electrostatic potential Raluca Mihaela ANDREI (Tue Sep 16 2008 - 03:28:02 CDT)
- Re: electrostatic potential John Stone (Tue Sep 16 2008 - 11:01:18 CDT)
  - Re: electrostatic potential Raluca Mihaela ANDREI (Thu Sep 18 2008 - 07:33:00 CDT)
extract centers et radii of beads model Matthieu Chavent (Mon Sep 15 2008 - 13:25:13 CDT)
- Re: extract centers et radii of beads model John Stone (Mon Sep 15 2008 - 16:11:20 CDT)
Fwd: ACS awards John Stone (Mon Sep 15 2008 - 12:53:34 CDT)
Tachyon render and Tcl scripting Shay Amram (Mon Sep 15 2008 - 11:42:00 CDT)
- Re: Tachyon render and Tcl scripting John Stone (Tue Sep 16 2008 - 14:00:06 CDT)
How to ionize a Shape Based CG Model? Anirban Ghosh (Mon Sep 15 2008 - 08:09:07 CDT)
- Re: How to ionize a Shape Based CG Model? Anton Arkhipov (Mon Sep 15 2008 - 09:10:04 CDT)
  - Re: How to ionize a Shape Based CG Model? L. Michel Espinoza-Fonseca (Mon Sep 15 2008 - 10:02:27 CDT)
    - Re: How to ionize a Shape Based CG Model? Anton Arkhipov (Mon Sep 15 2008 - 10:15:23 CDT)
    - Re: How to ionize a Shape Based CG Model? Peter Freddolino (Mon Sep 15 2008 - 10:21:44 CDT)
Alias histidine residue Rabab Toubar (Fri Sep 12 2008 - 23:31:47 CDT)
- Re: Alias histidine residue Axel Kohlmeyer (Sat Sep 13 2008 - 09:09:31 CDT)
  - Re: Alias histidine residue Roman Petrenko (Sat Sep 13 2008 - 22:04:46 CDT)
    - Re: Alias histidine residue Roman Petrenko (Sat Sep 13 2008 - 22:07:46 CDT)
a VMD script similar to "Rahmachandran plot' applicable to nucleic acids ? Maxim Paliy (Fri Sep 12 2008 - 19:14:04 CDT)
problems with VMD under linux/64-bit machine Irene Newhouse (Fri Sep 12 2008 - 15:17:56 CDT)
- Re: problems with VMD under linux/64-bit machine John Stone (Fri Sep 12 2008 - 16:03:48 CDT)
How to use Inorganic Builder Nd S (Fri Sep 12 2008 - 03:19:12 CDT)
- Re: How to use Inorganic Builder Robert Brunner (Fri Sep 12 2008 - 10:19:45 CDT)
Rendering problem lillestolen (Thu Sep 11 2008 - 14:16:29 CDT)
- Re: Rendering problem Axel Kohlmeyer (Fri Sep 12 2008 - 01:25:43 CDT)
- Re: Rendering problem John Stone (Fri Sep 12 2008 - 11:27:01 CDT)
Calculating the torsion angles in nucleic acids mon_sharma_at_research.iiit.ac.in (Thu Sep 11 2008 - 06:40:54 CDT)
- Re: Calculating the torsion angles in nucleic acids Peter Freddolino (Thu Sep 11 2008 - 08:52:36 CDT)
Measure hbonds equivalent in Python interface? Chang, Christopher (Wed Sep 10 2008 - 18:52:43 CDT)
Volume slice: slice color pontes_at_if.usp.br (Wed Sep 10 2008 - 10:31:55 CDT)
- Re: Volume slice: slice color John Stone (Wed Sep 10 2008 - 14:07:04 CDT)
  - Volume slice-I: slice color pontes_at_if.usp.br (Thu Sep 11 2008 - 07:22:07 CDT)
    - Re: Volume slice-I: slice color John Stone (Thu Sep 11 2008 - 11:06:03 CDT)
long bonds Marcelo Carignano (Wed Sep 10 2008 - 07:35:36 CDT)
- Re: long bonds Axel Kohlmeyer (Wed Sep 10 2008 - 10:23:18 CDT)
problems with autopsf & psfgen Irene Newhouse (Tue Sep 09 2008 - 13:50:10 CDT)
- psfgen - loss of disulfide bonds Rabab Toubar (Thu Sep 11 2008 - 21:35:53 CDT)
  - Re: psfgen - loss of disulfide bonds Roman Petrenko (Thu Sep 11 2008 - 22:50:34 CDT)
  - Re: psfgen - loss of disulfide bonds Peter Freddolino (Thu Sep 11 2008 - 22:33:18 CDT)
- Re: problems with autopsf & psfgen JC Gumbart (Fri Sep 12 2008 - 02:51:03 CDT)
How to generate more segments? mishacat_at_udm.ru (Tue Sep 09 2008 - 01:30:05 CDT)
- Re: How to generate more segments? John Stone (Tue Sep 09 2008 - 01:46:41 CDT)
Extensions menu is blank Janet Jacobsen (Mon Sep 08 2008 - 18:46:07 CDT)
- Re: Extensions menu is blank John Stone (Tue Sep 09 2008 - 10:52:00 CDT)
  - Re: Extensions menu is blank Janet Jacobsen (Tue Sep 09 2008 - 12:07:24 CDT)
saving charges snoze pa (Mon Sep 08 2008 - 12:14:15 CDT)
- Re: saving charges Axel Kohlmeyer (Mon Sep 08 2008 - 14:13:46 CDT)
feedback on pc-over-ip technology? Tru Huynh (Mon Sep 08 2008 - 10:40:24 CDT)
- Re: feedback on pc-over-ip technology? John Stone (Mon Sep 08 2008 - 11:07:09 CDT)
Concerning protein rotation Anneta Tzampazi (Mon Sep 08 2008 - 05:22:40 CDT)
- Re: Concerning protein rotation John Stone (Mon Sep 08 2008 - 11:25:47 CDT)
Superimposition: atomselect for reverse topology guillaume.santini_at_free.fr (Sat Sep 06 2008 - 09:34:52 CDT)
- Re: Superimposition: atomselect for reverse topology Axel Kohlmeyer (Sun Sep 07 2008 - 14:09:44 CDT)
  - Re: Superimposition: atomselect for reverse topology John Stone (Mon Sep 08 2008 - 11:16:37 CDT)
generate psf structure Rudra Banerjee (Sat Sep 06 2008 - 04:15:25 CDT)
- Re: generate psf structure Axel Kohlmeyer (Sun Sep 07 2008 - 13:50:39 CDT)
how to draw the bonds in VMD? Alfred Shaohui Zheng (Sat Sep 06 2008 - 03:07:16 CDT)
- Re: how to draw the bonds in VMD? Axel Kohlmeyer (Sun Sep 07 2008 - 13:41:30 CDT)
Protein coordinate rotation ianboru_at_email.arizona.edu (Fri Sep 05 2008 - 12:40:48 CDT)
- Re: Protein coordinate rotation John Stone (Fri Sep 05 2008 - 13:07:55 CDT)
Running without interface Emily Moore (Thu Sep 04 2008 - 11:29:02 CDT)
- Re: Running without interface Axel Kohlmeyer (Thu Sep 04 2008 - 12:06:44 CDT)
DIHE in topology file politr_at_huji.ac.il (Thu Sep 04 2008 - 02:31:52 CDT)
- Re: DIHE in topology file Peter Freddolino (Thu Sep 04 2008 - 07:51:51 CDT)
CONECT Records in .pdb file - bonds not getting plotted Paul T. Bauman (Wed Sep 03 2008 - 10:42:10 CDT)
- Re: CONECT Records in .pdb file - bonds not getting plotted Paul T. Bauman (Wed Sep 03 2008 - 11:53:37 CDT)
  - Re: Re: CONECT Records in .pdb file - bonds not getting plotted John Stone (Wed Sep 03 2008 - 14:01:23 CDT)
newbie issues markus mooslechner (Tue Sep 02 2008 - 13:39:19 CDT)
- Re: newbie issues Axel Kohlmeyer (Tue Sep 02 2008 - 14:10:19 CDT)
pbc join Edward Lyman (Tue Sep 02 2008 - 13:34:46 CDT)
- Re: pbc join Olaf Lenz (Tue Sep 02 2008 - 14:14:17 CDT)
Is position dependent color possible? Suman Chakrabarty (Tue Sep 02 2008 - 12:17:59 CDT)
- Re: Is position dependent color possible? John Stone (Tue Sep 02 2008 - 12:28:06 CDT)
  - Re: Is position dependent color possible? Suman Chakrabarty (Tue Sep 02 2008 - 13:27:02 CDT)
  - Re: Is position dependent color possible? Suman Chakrabarty (Tue Sep 02 2008 - 14:02:55 CDT)
Merge psf and pdb max_at_liaad.up.pt (Tue Sep 02 2008 - 04:28:53 CDT)
- Re: Merge psf and pdb Axel Kohlmeyer (Tue Sep 02 2008 - 08:15:39 CDT)
  - Re: Merge psf and pdb bo liu (Tue Sep 02 2008 - 10:02:26 CDT)
Py_atomsel.C: invalid conversion Chang, Christopher (Fri Aug 29 2008 - 13:01:04 CDT)
- Re: Py_atomsel.C: invalid conversion John Stone (Fri Aug 29 2008 - 13:05:06 CDT)
  - Re: Py_atomsel.C: invalid conversion Chang, Christopher (Tue Sep 02 2008 - 13:59:12 CDT)
algorithm for finding center of mass of the side chains in the protein aneesh cna (Fri Aug 29 2008 - 07:26:26 CDT)
- Re: algorithm for finding center of mass of the side chains in the protein Ramya Gamini (Fri Aug 29 2008 - 14:28:15 CDT)
Calculating pocket volume ben rodriguez (Thu Aug 28 2008 - 16:37:55 CDT)
- Re: Calculating pocket volume Peter Freddolino (Thu Aug 28 2008 - 17:27:44 CDT)
TXT program editor Alejandro Ortega (Thu Aug 28 2008 - 14:43:14 CDT)
- Re: TXT program editor Peter Freddolino (Thu Aug 28 2008 - 15:06:53 CDT)
  - Re: TXT program editor Emily Moore (Thu Aug 28 2008 - 17:09:42 CDT)
- Re: TXT program editor Axel Kohlmeyer (Thu Aug 28 2008 - 15:50:21 CDT)
- Re: TXT program editor Sabuj Pattanayek (Thu Aug 28 2008 - 17:03:11 CDT)
- Re: namd-l: TXT program editor Giovanni Bellesia (Thu Aug 28 2008 - 16:21:03 CDT)
diffusion coefficient from rmsd Rudra Banerjee (Wed Aug 27 2008 - 21:55:28 CDT)
- Re: namd-l: diffusion coefficient from rmsd Axel Kohlmeyer (Wed Aug 27 2008 - 22:39:52 CDT)
  - Re: namd-l: diffusion coefficient from rmsd bo liu (Thu Aug 28 2008 - 01:38:38 CDT)
HOLE PROGRAM Semorale (Wed Aug 27 2008 - 18:23:10 CDT)
- Re: HOLE PROGRAM John Stone (Fri Aug 29 2008 - 02:08:14 CDT)
catDCD Robert Fenwick (Wed Aug 27 2008 - 08:01:38 CDT)
- Re: catDCD John Stone (Wed Aug 27 2008 - 11:58:58 CDT)
  - Re: catDCD Robert Fenwick (Wed Aug 27 2008 - 12:16:14 CDT)
- Re: catDCD Peter Freddolino (Wed Aug 27 2008 - 22:04:10 CDT)
- Re: catDCD John Stone (Fri Aug 29 2008 - 01:45:45 CDT)
segfault using VMD 1.8.6 32-bit Linux and chromium 1.9 Chris Berthiaume (Mon Aug 25 2008 - 20:50:12 CDT)
- Re: segfault using VMD 1.8.6 32-bit Linux and chromium 1.9 John Stone (Mon Aug 25 2008 - 22:45:15 CDT)
  - Re: segfault using VMD 1.8.6 32-bit Linux and chromium 1.9 Chris Berthiaume (Tue Aug 26 2008 - 12:23:11 CDT)
Failure to open PDB files hzf101_at_psu.edu (Mon Aug 25 2008 - 13:12:52 CDT)
- Re: Failure to open PDB files Axel Kohlmeyer (Mon Aug 25 2008 - 14:52:38 CDT)
resid of water that is hydrogen bonded nahren manuel (Mon Aug 25 2008 - 07:35:22 CDT)
- Re: resid of water that is hydrogen bonded Axel Kohlmeyer (Mon Aug 25 2008 - 14:56:41 CDT)
  - again :resid of water that is H bonded nahren manuel (Mon Aug 25 2008 - 21:55:40 CDT)
measure gofr - how is g(r) normalised? Maxim Paliy (Mon Aug 25 2008 - 05:07:37 CDT)
- Re: measure gofr - how is g(r) normalised? Axel Kohlmeyer (Mon Aug 25 2008 - 15:14:35 CDT)
Python callbacks in VMD James E. Magee (Wed Aug 20 2008 - 06:41:52 CDT)
- Re: Python callbacks in VMD John Stone (Wed Aug 20 2008 - 22:59:53 CDT)
Inorganic Builder Plugin max_at_liaad.up.pt (Wed Aug 20 2008 - 04:57:09 CDT)
- Re: Inorganic Builder Plugin John Stone (Wed Aug 20 2008 - 23:01:45 CDT)
- Re: Inorganic Builder Plugin Robert Brunner (Thu Aug 21 2008 - 08:31:19 CDT)
Trouble updating frames in script Emily Moore (Tue Aug 19 2008 - 12:21:11 CDT)
- Re: Trouble updating frames in script Axel Kohlmeyer (Tue Aug 19 2008 - 13:06:44 CDT)
  - Re: Trouble updating frames in script Emily Moore (Tue Aug 19 2008 - 14:23:29 CDT)
    - Re: Trouble updating frames in script Axel Kohlmeyer (Tue Aug 19 2008 - 15:14:42 CDT)
how to call dssp in a script Yuan Feng (Sun Aug 17 2008 - 18:51:56 CDT)
- Re: how to call dssp in a script John Stone (Mon Aug 18 2008 - 11:17:44 CDT)
- Re: how to call dssp in a script Axel Kohlmeyer (Mon Aug 18 2008 - 10:42:14 CDT)
Question about trace vmd_frame(molid) Oren Elrad (Fri Aug 15 2008 - 11:33:02 CDT)
- Re: Question about trace vmd_frame(molid) Axel Kohlmeyer (Fri Aug 15 2008 - 12:12:03 CDT)
  - Re: Question about trace vmd_frame(molid) Oren Elrad (Fri Aug 15 2008 - 13:24:25 CDT)
    - Re: Question about trace vmd_frame(molid) Axel Kohlmeyer (Fri Aug 15 2008 - 13:55:54 CDT)
RMSD SCRIPT Semorale (Fri Aug 15 2008 - 05:12:11 CDT)
- Re: RMSD SCRIPT John Stone (Tue Aug 19 2008 - 01:01:07 CDT)
LAMMPS Trajectory Bond Specification nicholas lee (Thu Aug 14 2008 - 14:25:07 CDT)
- Re: LAMMPS Trajectory Bond Specification Nazanin Samadi (Thu Aug 14 2008 - 15:24:45 CDT)
- Re: LAMMPS Trajectory Bond Specification Axel Kohlmeyer (Thu Aug 14 2008 - 16:24:13 CDT)
axes Nazanin Samadi (Wed Aug 13 2008 - 14:21:06 CDT)
- Re: axes John Stone (Tue Aug 19 2008 - 00:54:31 CDT)
renumbering residues Roman Petrenko (Wed Aug 13 2008 - 13:50:44 CDT)
- Re: renumbering residues John Stone (Wed Aug 13 2008 - 18:00:59 CDT)
label all residues Roman Petrenko (Wed Aug 13 2008 - 10:09:17 CDT)
- Re: label all residues Peter Freddolino (Wed Aug 13 2008 - 10:29:20 CDT)
catDCD- convert DCD format Semorale (Tue Aug 12 2008 - 16:10:27 CDT)
- Re: catDCD- convert DCD format John Stone (Wed Aug 13 2008 - 10:58:21 CDT)
protein-water hydrogen bonds Roman Petrenko (Tue Aug 12 2008 - 10:05:46 CDT)
- Re: protein-water hydrogen bonds Axel Kohlmeyer (Tue Aug 12 2008 - 10:37:45 CDT)
  - Re: protein-water hydrogen bonds Roman Petrenko (Tue Aug 12 2008 - 10:52:32 CDT)
    - Re: protein-water hydrogen bonds Axel Kohlmeyer (Tue Aug 12 2008 - 10:53:35 CDT)
rmsd Shadi Mirzae (Mon Aug 11 2008 - 13:52:14 CDT)
- Re: rmsd John Stone (Tue Aug 19 2008 - 01:02:57 CDT)
problem controlling orientation of the simulation box drawn by pbctools shiladitya_at_jncasr.ac.in (Sun Aug 10 2008 - 10:52:54 CDT)
- Re: problem controlling orientation of the simulation box drawn by pbctools Axel Kohlmeyer (Sun Aug 10 2008 - 11:11:34 CDT)
save selected residues bo baker (Sun Aug 10 2008 - 06:04:37 CDT)
- Re: save selected residues Axel Kohlmeyer (Sun Aug 10 2008 - 09:48:15 CDT)
  - Re: save selected residues bo baker (Mon Aug 11 2008 - 06:31:12 CDT)
    - Re: save selected residues Axel Kohlmeyer (Mon Aug 11 2008 - 11:01:48 CDT)
backbone dihedral angles over trajectory Roman Petrenko (Fri Aug 08 2008 - 17:05:59 CDT)
- Re: backbone dihedral angles over trajectory Giovanni Bellesia (Fri Aug 08 2008 - 17:36:44 CDT)
request ability to append in CatDCD (and NAMD) Andrew Jewett (Fri Aug 08 2008 - 14:15:46 CDT)
- Re: request ability to append in CatDCD (and NAMD) John Stone (Fri Aug 08 2008 - 14:45:52 CDT)
Depth Cueing and dispdev none Oleg Stroganov (Thu Aug 07 2008 - 16:10:36 CDT)
- Re: Depth Cueing and dispdev none John Stone (Mon Aug 11 2008 - 14:13:55 CDT)
  - Re: Depth Cueing and dispdev none Oleg Stroganov (Tue Aug 12 2008 - 18:03:29 CDT)
    - Re: Depth Cueing and dispdev none John Stone (Wed Aug 13 2008 - 09:56:44 CDT)
VMD files to SDF max_at_liaad.up.pt (Thu Aug 07 2008 - 05:20:59 CDT)
- Re: VMD files to SDF John Stone (Thu Aug 07 2008 - 12:52:48 CDT)
Problems with Newcartoon representation Cesar Luis Avila (Wed Aug 06 2008 - 11:17:58 CDT)
- Re: Problems with Newcartoon representation John Stone (Wed Aug 06 2008 - 11:33:28 CDT)
  - Re: Problems with Newcartoon representation John Stone (Wed Aug 06 2008 - 13:38:00 CDT)
    - Re: Problems with Newcartoon representation Cesar Luis Avila (Wed Aug 06 2008 - 14:28:00 CDT)
NAMDENERGY crashing repeatedly Chandra Ramananjara (Tue Aug 05 2008 - 09:27:12 CDT)
- Re: NAMDENERGY crashing repeatedly Peter Freddolino (Tue Aug 05 2008 - 16:26:52 CDT)
  - Re: NAMDENERGY crashing repeatedly Chandra Ramananjara (Tue Aug 05 2008 - 18:49:40 CDT)
How to reduce memory usage of a script? David Poger (Mon Aug 04 2008 - 20:31:10 CDT)
- Re: How to reduce memory usage of a script? John Stone (Mon Aug 04 2008 - 21:44:48 CDT)
  - Re: How to reduce memory usage of a script? David Poger (Tue Aug 05 2008 - 00:24:10 CDT)
    - Re: How to reduce memory usage of a script? John Stone (Tue Aug 05 2008 - 00:36:59 CDT)
    - Re: How to reduce memory usage of a script? David Poger (Tue Aug 05 2008 - 02:18:05 CDT)
How to embed 3-D image into powerpoint Claw Isthelaw (Mon Aug 04 2008 - 15:15:33 CDT)
- Re: How to embed 3-D image into powerpoint Axel Kohlmeyer (Mon Aug 04 2008 - 15:57:41 CDT)
- Re: How to embed 3-D image into powerpoint John Stone (Tue Aug 05 2008 - 14:17:47 CDT)
suggested video card for linux Burcin Temel (Mon Aug 04 2008 - 07:32:03 CDT)
- Re: suggested video card for linux John Stone (Mon Aug 04 2008 - 11:24:47 CDT)
  - Re: suggested video card for linux Burcin Temel (Mon Aug 11 2008 - 12:13:06 CDT)
SURF and broken surface Vivek Sharma (Fri Aug 01 2008 - 23:16:14 CDT)
- Re: SURF and broken surface John Stone (Fri Aug 01 2008 - 23:28:04 CDT)
ionize with VMD a TOP file rebeca_at_mmb.pcb.ub.es (Fri Aug 01 2008 - 07:14:40 CDT)
- Re: ionize with VMD a TOP file Axel Kohlmeyer (Fri Aug 01 2008 - 09:28:58 CDT)
vmd-rmsd-color-tool Bernhard Knapp (Fri Aug 01 2008 - 02:27:48 CDT)
- Re: vmd-rmsd-color-tool Axel Kohlmeyer (Fri Aug 01 2008 - 09:27:35 CDT)
Re: namdenergy and simulation with amber ff Alan (Fri Aug 01 2008 - 02:05:23 CDT)
- Re: Re: namdenergy and simulation with amber ff Peter Freddolino (Fri Aug 01 2008 - 08:24:36 CDT)
  - Re: Re: namdenergy and simulation with amber ff Peter Freddolino (Mon Aug 04 2008 - 11:50:31 CDT)
problem using pbc wrap: broken molecule Jianhui Tian (Thu Jul 31 2008 - 20:32:47 CDT)
- Re: problem using pbc wrap: broken molecule Peter Freddolino (Fri Aug 01 2008 - 10:14:47 CDT)
  - Re: problem using pbc wrap: broken molecule Jianhui Tian (Fri Aug 01 2008 - 10:52:45 CDT)
    - Re: problem using pbc wrap: broken molecule Peter Freddolino (Fri Aug 01 2008 - 15:24:51 CDT)
    - Re: problem using pbc wrap: broken molecule Axel Kohlmeyer (Fri Aug 01 2008 - 16:29:59 CDT)
- Re: problem using pbc wrap: broken molecule Axel Kohlmeyer (Fri Aug 01 2008 - 10:00:18 CDT)
Gromacs reading: Why scaling?? Nicolas Bigaouette (Thu Jul 31 2008 - 18:33:26 CDT)
- Re: Gromacs reading: Why scaling?? Axel Kohlmeyer (Thu Jul 31 2008 - 19:11:11 CDT)
  - Re: Gromacs reading: Why scaling?? Nicolas Bigaouette (Thu Jul 31 2008 - 19:21:12 CDT)
    - Re: Gromacs reading: Why scaling?? Axel Kohlmeyer (Thu Jul 31 2008 - 19:51:10 CDT)
- Re: Gromacs reading: Why scaling?? Nicolas (Thu Jul 31 2008 - 19:32:16 CDT)
VMD crasch Lixia Jin Day (Thu Jul 31 2008 - 15:58:28 CDT)
- Re: VMD crasch Eric H. Lee (Thu Jul 31 2008 - 16:11:33 CDT)
  - Re: VMD crasch John Stone (Thu Jul 31 2008 - 17:00:22 CDT)
VMD with amber rst7 and parm7 files Alan (Thu Jul 31 2008 - 03:26:33 CDT)
- Re: VMD with amber rst7 and parm7 files Axel Kohlmeyer (Thu Jul 31 2008 - 09:02:29 CDT)
Hot repl1ca w4tches from 2008 Villa Tory Mohr (Wed Jul 30 2008 - 21:06:33 CDT)
How to disable automatic view rotations? Roman Petrenko (Wed Jul 30 2008 - 13:08:31 CDT)
- Re: How to disable automatic view rotations? John Stone (Wed Jul 30 2008 - 14:34:15 CDT)
  - Re: How to disable automatic view rotations? Roman Petrenko (Wed Jul 30 2008 - 15:37:41 CDT)
    - Re: How to disable automatic view rotations? John Stone (Wed Jul 30 2008 - 15:50:09 CDT)
  - Re: How to disable automatic view rotations? John Stone (Wed Jul 30 2008 - 15:47:05 CDT)
g(r) Rudra Banerjee (Wed Jul 30 2008 - 12:13:40 CDT)
- Re: g(r) Axel Kohlmeyer (Wed Jul 30 2008 - 14:31:55 CDT)
  - Re: g(r) Rudra Banerjee (Thu Jul 31 2008 - 00:46:01 CDT)
    - Re: g(r) Axel Kohlmeyer (Thu Jul 31 2008 - 08:57:34 CDT)
3DConnexion SpaceNavigator in 1.8.7alpha30 on OS X Benjamin Bouvier (Wed Jul 30 2008 - 09:37:32 CDT)
- Re: 3DConnexion SpaceNavigator in 1.8.7alpha30 on OS X John Stone (Wed Jul 30 2008 - 10:25:53 CDT)
  - Re: 3DConnexion SpaceNavigator in 1.8.7alpha30 on OS X Benjamin Bouvier (Wed Jul 30 2008 - 10:36:17 CDT)
    - Re: 3DConnexion SpaceNavigator in 1.8.7alpha30 on OS X John Stone (Wed Jul 30 2008 - 10:38:41 CDT)
- Vmd on Fedora 9 Al-Ali, Hassan (Wed Jul 30 2008 - 11:43:28 CDT)
  - Re: Vmd on Fedora 9 Axel Kohlmeyer (Wed Jul 30 2008 - 12:18:11 CDT)
tcl script problem with "atomselect' combined with "measure fit ...order" Loison Claire (Tue Jul 29 2008 - 09:16:36 CDT)
- Re: tcl script problem with "atomselect' combined with "measure fit ...order" Roman Petrenko (Tue Jul 29 2008 - 15:26:13 CDT)
Query Kaur, Tarandeep (Tue Jul 29 2008 - 07:55:49 CDT)
- Re: Query John Stone (Tue Jul 29 2008 - 13:13:24 CDT)
Multiseq refusing to load a structure due to taxonomy problem Robison, Keith (Tue Jul 29 2008 - 08:22:24 CDT)
- Re: Multiseq refusing to load a structure due to taxonomy problem Elijah Roberts (Tue Jul 29 2008 - 13:17:04 CDT)
  - RE: Multiseq refusing to load a structure due to taxonomy problem Robison, Keith (Tue Jul 29 2008 - 13:32:19 CDT)
periodic boundary conditions (yes, i read the tutorials) Roman Petrenko (Mon Jul 28 2008 - 19:46:09 CDT)
- Re: periodic boundary conditions (yes, i read the tutorials) Roman Petrenko (Mon Jul 28 2008 - 19:50:12 CDT)
  - Re: Re: periodic boundary conditions (yes, i read the tutorials) Axel Kohlmeyer (Mon Jul 28 2008 - 20:44:41 CDT)
  - Re: Re: periodic boundary conditions (yes, i read the tutorials) Balazs Jojart (Tue Jul 29 2008 - 01:21:17 CDT)
    - Re: Re: periodic boundary conditions (yes, i read the tutorials) John Stone (Tue Jul 29 2008 - 13:22:57 CDT)
solvating protein, fixed residue Rudra Banerjee (Mon Jul 28 2008 - 13:01:56 CDT)
- Re: solvating protein, fixed residue Axel Kohlmeyer (Mon Jul 28 2008 - 13:52:42 CDT)
water box...density!!! Rudra Banerjee (Mon Jul 28 2008 - 05:02:55 CDT)
- Re: water box...density!!! Christopher Gillespie (Mon Jul 28 2008 - 09:43:47 CDT)
solvation and box size Sue Legge (Mon Jul 28 2008 - 01:25:43 CDT)
- Re: solvation and box size Roman Petrenko (Mon Jul 28 2008 - 06:52:08 CDT)
- Re: solvation and box size Axel Kohlmeyer (Mon Jul 28 2008 - 06:30:07 CDT)
- Re: solvation and box size Christopher Gillespie (Mon Jul 28 2008 - 07:33:37 CDT)
translation/transformation Roman Petrenko (Sat Jul 26 2008 - 23:31:36 CDT)
- Re: translation/transformation Schreiner Eduard (Sun Jul 27 2008 - 01:52:20 CDT)
  - Re: translation/transformation Schreiner Eduard (Sun Jul 27 2008 - 02:16:58 CDT)
    - Re: translation/transformation Roman Petrenko (Sun Jul 27 2008 - 04:09:35 CDT)
how to create dityrosine links Roman Petrenko (Sat Jul 26 2008 - 17:47:52 CDT)
- Re: how to create dityrosine links JC Gumbart (Sat Jul 26 2008 - 20:21:14 CDT)
  - Re: how to create dityrosine links Roman Petrenko (Sun Jul 27 2008 - 04:14:20 CDT)
Python for OS X Hans Martin Senn (Fri Jul 25 2008 - 10:19:38 CDT)
- Re: Python for OS X Axel Kohlmeyer (Sat Jul 26 2008 - 12:56:18 CDT)
- Re: Python for OS X John Stone (Tue Jul 29 2008 - 14:09:57 CDT)
question about using namdenergy.tcl with vmd -dispdev text -e *.tcl Margaret S. Cheung (Fri Jul 25 2008 - 08:38:20 CDT)
- Re: question about using namdenergy.tcl with vmd -dispdev text -e *.tcl Peter Freddolino (Fri Jul 25 2008 - 17:31:16 CDT)
  - Re: question about using namdenergy.tcl with vmd -dispdev text -e *.tcl Margaret.Cheung_at_mail.uh.edu (Fri Jul 25 2008 - 18:41:40 CDT)
Slow mail deliver for next day or so... John Stone (Fri Jul 25 2008 - 15:15:09 CDT)
membrane plugin | lipid structures Jufang Shan (Fri Jul 25 2008 - 11:50:18 CDT)
- RE: membrane plugin | lipid structures JC Gumbart (Sun Jul 27 2008 - 23:36:37 CDT)
Get your w4tch now Villa Joan Winslow (Thu Jul 24 2008 - 04:40:10 CDT)
questions relating to VolMapTool bo liu (Wed Jul 23 2008 - 02:35:18 CDT)
- Re: questions relating to VolMapTool Axel Kohlmeyer (Wed Jul 23 2008 - 06:30:55 CDT)
rdf for big systems Valeria Molinero (Tue Jul 22 2008 - 16:23:04 CDT)
- Re: rdf for big systems Axel Kohlmeyer (Tue Jul 22 2008 - 17:06:30 CDT)
  - Re: rdf for big systems Valeria Molinero (Tue Jul 22 2008 - 18:58:25 CDT)
    - Re: rdf for big systems Axel Kohlmeyer (Tue Jul 22 2008 - 19:09:09 CDT)
    - Re: rdf for big systems John Stone (Thu Jul 31 2008 - 13:00:35 CDT)
  - Re: rdf for big systems John Stone (Wed Aug 06 2008 - 11:24:27 CDT)
vecsub command Katherine Parra (Tue Jul 22 2008 - 11:03:42 CDT)
- Re: vecsub command Schreiner Eduard (Tue Jul 22 2008 - 11:40:13 CDT)
- Re: vecsub command Axel Kohlmeyer (Tue Jul 22 2008 - 11:48:31 CDT)
Selecting the sides of a benzene ring Ignacio Fernández Galván (Tue Jul 22 2008 - 06:30:21 CDT)
- Re: Selecting the sides of a benzene ring Eduardo Cruz-Chu (Tue Jul 22 2008 - 11:21:42 CDT)
  - Re: Selecting the sides of a benzene ring Ignacio Fernández Galván (Wed Jul 23 2008 - 02:39:23 CDT)
- Re: Selecting the sides of a benzene ring Schreiner Eduard (Tue Jul 22 2008 - 11:01:39 CDT)
- Re: Selecting the sides of a benzene ring Axel Kohlmeyer (Tue Jul 22 2008 - 11:45:54 CDT)
Problem to find the number of frames of a trajectory David Poger (Mon Jul 21 2008 - 20:19:01 CDT)
- Re: Problem to find the number of frames of a trajectory John Stone (Mon Jul 21 2008 - 23:50:56 CDT)
  - Re: Problem to find the number of frames of a trajectory David Poger (Mon Jul 21 2008 - 23:58:48 CDT)
    - Re: Problem to find the number of frames of a trajectory John Stone (Tue Jul 22 2008 - 00:50:30 CDT)
  - Re: Problem to find the number of frames of a trajectory John Stone (Tue Jul 22 2008 - 10:15:00 CDT)
Periodic image and transformation matrix Cesar Avila (Mon Jul 21 2008 - 19:20:06 CDT)
- Re: Periodic image and transformation matrix Axel Kohlmeyer (Mon Jul 21 2008 - 19:50:24 CDT)
Missing angles and dihedrals Rene Prieto (Mon Jul 21 2008 - 18:25:52 CDT)
- Re: Missing angles and dihedrals Schreiner Eduard (Mon Jul 21 2008 - 19:04:44 CDT)
- Re: Missing angles and dihedrals Axel Kohlmeyer (Mon Jul 21 2008 - 19:31:48 CDT)
You can s4ve 80% Villa Norberto Martinez (Mon Jul 21 2008 - 01:18:56 CDT)
Selecting atoms that have real SASA greater than 0, Not using "Surface" Christopher Gillespie (Sun Jul 20 2008 - 16:28:04 CDT)
- Re: Selecting atoms that have real SASA greater than 0, Not using "Surface" Schreiner Eduard (Sun Jul 20 2008 - 22:03:40 CDT)
- Re: Selecting atoms that have real SASA greater than 0, Not using "Surface" John Stone (Mon Jul 21 2008 - 10:22:51 CDT)
  - Re: Selecting atoms that have real SASA greater than 0, Not using "Surface" Christopher Gillespie (Tue Jul 29 2008 - 18:39:14 CDT)
    - Re: Selecting atoms that have real SASA greater than 0, Not using "Surface" Axel Kohlmeyer (Tue Jul 29 2008 - 20:40:30 CDT)
Parametrization of hydrogen sulfide Raul Araya (Fri Jul 18 2008 - 17:54:45 CDT)
real coordinates Maria Sanchez Farran (Thu Jul 17 2008 - 21:40:46 CDT)
- Re: real coordinates Axel Kohlmeyer (Fri Jul 18 2008 - 12:08:25 CDT)
vmd MacOSX using dispdev Brian Kidd (Thu Jul 17 2008 - 18:08:03 CDT)
- Re: vmd MacOSX using dispdev John Stone (Thu Jul 17 2008 - 22:12:18 CDT)
- Re: vmd MacOSX using dispdev Kevin DeMarco (Fri Jul 18 2008 - 13:33:09 CDT)
- Re: vmd MacOSX using dispdev Giovanni Bellesia (Fri Jul 18 2008 - 16:00:00 CDT)
autopsf from console brosbam_at_berkeley.edu (Thu Jul 17 2008 - 12:23:21 CDT)
- Re: autopsf from console Peter Freddolino (Thu Jul 17 2008 - 12:52:33 CDT)
VMD Does not start on my MacBook Dr. Seth Olsen (Wed Jul 16 2008 - 21:15:57 CDT)
- Re: VMD Does not start on my MacBook John Stone (Thu Jul 17 2008 - 15:39:55 CDT)
Tetrahedral representation FX (Wed Jul 16 2008 - 17:20:22 CDT)
- Re: Tetrahedral representation Axel Kohlmeyer (Wed Jul 16 2008 - 18:24:09 CDT)
  - Re: Tetrahedral representation FX (Thu Jul 17 2008 - 06:19:09 CDT)
    - Re: Tetrahedral representation John Stone (Thu Jul 17 2008 - 16:14:35 CDT)
- Re: Tetrahedral representation John Stone (Wed Aug 13 2008 - 13:07:04 CDT)
- Re: Tetrahedral representation John Stone (Wed Aug 13 2008 - 18:14:03 CDT)
Error message in VMD console when I try to switch to Python mode. Katherine Parra (Wed Jul 16 2008 - 13:16:28 CDT)
- Re: Error message in VMD console when I try to switch to Python mode. John Stone (Wed Jul 16 2008 - 13:28:55 CDT)
  - Re: Error message in VMD console when I try to switch to Python mode. Katherine Parra (Wed Jul 16 2008 - 14:06:06 CDT)
Creating a VMD movie from a Tcl script Samir Unni (Wed Jul 16 2008 - 09:32:37 CDT)
- Re: Creating a VMD movie from a Tcl script John Stone (Thu Jul 17 2008 - 17:02:05 CDT)
Problem writing trajectory to "crd" (Amber) format? Ian (Wed Jul 16 2008 - 04:43:24 CDT)
- Re: Problem writing trajectory to "crd" (Amber) format? Axel Kohlmeyer (Wed Jul 16 2008 - 09:31:59 CDT)
- Re: Problem writing trajectory to "crd" (Amber) format? John Stone (Tue Jul 22 2008 - 14:01:32 CDT)
Fwd: memory overflow problem of Tcl scripting when dealing with trajectories(sorry for cross mailing...) bo liu (Wed Jul 16 2008 - 03:18:43 CDT)
- Re: Fwd: memory overflow problem of Tcl scripting when dealing with trajectories(sorry for cross mailing...) Peter Freddolino (Wed Jul 16 2008 - 07:20:26 CDT)
problem with correct visualization of residues L. Michel Espinoza-Fonseca (Tue Jul 15 2008 - 12:50:58 CDT)
- Re: problem with correct visualization of residues John Stone (Tue Jul 15 2008 - 13:04:18 CDT)
  - Re: problem with correct visualization of residues L. Michel Espinoza-Fonseca (Tue Jul 15 2008 - 13:08:55 CDT)
- Re: problem with correct visualization of residues Axel Kohlmeyer (Tue Jul 15 2008 - 13:21:57 CDT)
pick atom id script Abu Naser (Fri Jul 11 2008 - 06:07:05 CDT)
- Re: pick atom id script Axel Kohlmeyer (Fri Jul 11 2008 - 09:37:49 CDT)
- Re: pick atom id script David Tanner (Fri Jul 11 2008 - 09:32:53 CDT)
purple bacteria and psfgen brosbam_at_berkeley.edu (Tue Jul 15 2008 - 12:37:30 CDT)
- Re: purple bacteria and psfgen John Stone (Wed Jul 16 2008 - 02:50:49 CDT)
Fwd: PDB Bonds versus "distance" bonds Sergey Ivanov (Tue Jul 15 2008 - 10:49:43 CDT)
- Re: Fwd: PDB Bonds versus "distance" bonds Axel Kohlmeyer (Tue Jul 15 2008 - 11:20:53 CDT)
  - Re: Fwd: PDB Bonds versus "distance" bonds John Stone (Tue Jul 15 2008 - 13:00:42 CDT)
    - Re: Fwd: PDB Bonds versus "distance" bonds Sergey Ivanov (Thu Jul 17 2008 - 08:14:39 CDT)
    - Re: Fwd: PDB Bonds versus "distance" bonds John Stone (Thu Jul 17 2008 - 09:24:55 CDT)
Visualizing History file from DL_POLY mahesh naalla (Mon Jul 14 2008 - 11:43:43 CDT)
- Re: Visualizing History file from DL_POLY John Stone (Tue Jul 15 2008 - 10:39:33 CDT)
tachyon rendering on black background figure Lixia Jin Day (Fri Jul 11 2008 - 13:06:30 CDT)
- Re: tachyon rendering on black background figure John Stone (Wed Jul 16 2008 - 01:46:53 CDT)
  - Re: tachyon rendering on black background figure John Stone (Thu Jul 17 2008 - 16:31:06 CDT)
QR factorization for structural alignment Dong Xu (Thu Jul 10 2008 - 17:30:39 CDT)
- Re: QR factorization for structural alignment Leonardo Trabuco (Fri Jul 11 2008 - 01:51:51 CDT)
(no subject) Abu Naser (Thu Jul 10 2008 - 10:43:17 CDT)
- Re: Kirby Vandivort (Thu Jul 10 2008 - 11:05:33 CDT)
  - RE: Abu Naser (Thu Jul 10 2008 - 11:23:19 CDT)
building an uncoming sulfide bridge Jim Pfaendtner (Thu Jul 10 2008 - 08:56:32 CDT)
- Re: building an uncoming sulfide bridge JC Gumbart (Thu Jul 10 2008 - 11:17:46 CDT)
contour plots Aaron.Oakley_at_csiro.au (Wed Jul 09 2008 - 22:50:54 CDT)
- Re: contour plots Peter Freddolino (Thu Jul 10 2008 - 00:27:41 CDT)
- Re: contour plots Giovanni Bellesia (Thu Jul 10 2008 - 01:09:36 CDT)
- Re: contour plots Subramanian Vaitheeswaran (Thu Jul 10 2008 - 10:02:58 CDT)
- Re: contour plots Alexandre A. Vakhrouchev (Mon Jul 21 2008 - 02:25:51 CDT)
Inorganic Builder Plugin Renata KWIECIEN (Wed Jul 09 2008 - 02:56:17 CDT)
- Re: Inorganic Builder Plugin Robert Brunner (Wed Jul 09 2008 - 10:38:27 CDT)
I'm back.. John Stone (Tue Jul 08 2008 - 16:24:12 CDT)
measure forces applied on VMD S.K. Ghosh (Mon Jul 07 2008 - 16:18:17 CDT)
- Re: measure forces applied in VMD S.K. Ghosh (Tue Jul 08 2008 - 20:11:19 CDT)
  - Re: measure forces applied in VMD John Stone (Fri Jul 11 2008 - 10:48:11 CDT)
trajectory to xyz file. Katherine Parra (Mon Jul 07 2008 - 13:16:30 CDT)
- Re: trajectory to xyz file. Christopher Gillespie (Mon Jul 07 2008 - 14:44:12 CDT)
- Re: trajectory to xyz file. Axel Kohlmeyer (Mon Jul 07 2008 - 15:11:30 CDT)
Newbie Questions Paul Dennis Simonson (Sun Jul 06 2008 - 21:15:13 CDT)
- Re: Newbie Questions Peter Freddolino (Sun Jul 06 2008 - 22:06:53 CDT)
QR factorization for structural alignment Dong Xu (Sat Jul 05 2008 - 17:06:29 CDT)
Maximum velocities Alejandro Ortega (Thu Jul 03 2008 - 16:03:13 CDT)
- Re: Maximum velocities Eric H. Lee (Thu Jul 03 2008 - 16:17:54 CDT)
Dihedrale angles in VMD Jorgen Simonsen (Thu Jul 03 2008 - 07:43:07 CDT)
- Re: Dihedrale angles in VMD Axel Kohlmeyer (Thu Jul 03 2008 - 12:24:16 CDT)
Loading Problem hirdesh kumar (Thu Jul 03 2008 - 06:27:44 CDT)
- Re: Loading Problem Axel Kohlmeyer (Thu Jul 03 2008 - 12:28:18 CDT)
- Re: Loading Problem John Stone (Fri Jul 11 2008 - 10:54:39 CDT)
ResdueType and hydrophobicity scale Giovanni Bellesia (Wed Jul 02 2008 - 18:16:29 CDT)
- Re: ResdueType and hydrophobicity scale John Stone (Wed Jul 16 2008 - 01:59:34 CDT)
  - Re: ResdueType and hydrophobicity scale Giovanni Bellesia (Wed Jul 16 2008 - 02:13:46 CDT)
    - Re: ResdueType and hydrophobicity scale John Stone (Wed Jul 16 2008 - 02:47:41 CDT)
    - Re: ResdueType and hydrophobicity scale Andrew Dalke (Wed Jul 16 2008 - 05:45:13 CDT)
The maximal size which can be displayed by VMD? Fred (Rui FENG) (Wed Jul 02 2008 - 16:06:18 CDT)
- Re: The maximal size which can be displayed by VMD? Axel Kohlmeyer (Wed Jul 02 2008 - 16:36:57 CDT)
  - Re: The maximal size which can be displayed by VMD? Fred (Rui FENG) (Wed Jul 02 2008 - 20:55:07 CDT)
VMD Mutator, which side chain rotamer? S. Jamal Rahi (Wed Jul 02 2008 - 07:30:32 CDT)
- Re: VMD Mutator, which side chain rotamer? Peter Freddolino (Wed Jul 02 2008 - 07:52:43 CDT)
VMD Mutator, which side chain rotamer? S. Jamal Rahi (Wed Jul 02 2008 - 07:20:52 CDT)
VMDMODULATERIBBON or sausage representation Tim Meyer (Tue Jul 01 2008 - 13:38:28 CDT)
- Re: VMDMODULATERIBBON or sausage representation Axel Kohlmeyer (Tue Jul 01 2008 - 14:07:42 CDT)
rmsd per residue Alberto Sergio Garay (Tue Jul 01 2008 - 05:36:46 CDT)
rmsd per residue Michal Kolinski (Mon Jun 30 2008 - 10:19:40 CDT)
- Re: rmsd per residue Eric H. Lee (Mon Jun 30 2008 - 14:42:18 CDT)
Error using namdstat.tcl script S.K. Ghosh (Mon Jun 30 2008 - 10:51:20 CDT)
- Re: Error using namdstat.tcl script Axel Kohlmeyer (Mon Jun 30 2008 - 11:42:26 CDT)
Mac OSX crash with bus error/segmentation fault upon loading pdb/dcd James Irving (Sun Jun 29 2008 - 21:14:14 CDT)
- Re: Mac OSX crash with bus error/segmentation fault upon loading pdb/dcd Axel Kohlmeyer (Mon Jun 30 2008 - 13:17:20 CDT)
  - Re: Mac OSX crash with bus error/segmentation fault upon loading pdb/dcd James Irving (Mon Jun 30 2008 - 18:10:13 CDT)
- Re: Mac OSX crash with bus error/segmentation fault upon loading pdb/dcd Kevin DeMarco (Mon Jun 30 2008 - 18:50:24 CDT)
  - Re: Mac OSX crash with bus error/segmentation fault upon loading pdb/dcd James Irving (Mon Jun 30 2008 - 20:03:44 CDT)
Problem of Movie Maker Plugin lei wang (Sat Jun 28 2008 - 05:41:29 CDT)
- Re: Problem of Movie Maker Plugin Axel Kohlmeyer (Sat Jun 28 2008 - 11:19:02 CDT)
mutate by D-residues... Yasser Almeida Hernández (Fri Jun 27 2008 - 16:45:00 CDT)
- Re: mutate by D-residues... Axel Kohlmeyer (Fri Jun 27 2008 - 20:47:58 CDT)
mutate by D-residues... Yasser Almeida Hernández (Fri Jun 27 2008 - 16:44:25 CDT)
select cylindrical slab dimka (Fri Jun 27 2008 - 12:08:41 CDT)
- Re: select cylindrical slab Peter Freddolino (Fri Jun 27 2008 - 12:34:01 CDT)
- Re: select cylindrical slab Axel Kohlmeyer (Fri Jun 27 2008 - 12:51:26 CDT)
Compiling from source on Mac OS X 10.5 Marylou Kunkle (Fri Jun 27 2008 - 11:12:37 CDT)
- Re: Compiling from source on Mac OS X 10.5 Marylou Kunkle (Fri Jun 27 2008 - 13:29:37 CDT)
  - Re: Compiling from source on Mac OS X 10.5 Axel Kohlmeyer (Fri Jun 27 2008 - 14:23:44 CDT)
- Re: Compiling from source on Mac OS X 10.5 Axel Kohlmeyer (Fri Jun 27 2008 - 13:54:36 CDT)
- Re: Compiling from source on Mac OS X 10.5 John Stone (Thu Jul 17 2008 - 17:04:38 CDT)
vmd shuts itself down A D (Thu Jun 26 2008 - 19:20:58 CDT)
- Re: vmd shuts itself down Axel Kohlmeyer (Fri Jun 27 2008 - 09:23:12 CDT)
how to make a movie of 2 or more trajectories parth singh (Thu Jun 26 2008 - 15:59:08 CDT)
- Re: how to make a movie of 2 or more trajectories Axel Kohlmeyer (Fri Jun 27 2008 - 20:57:18 CDT)
How to delete anwanted waters in a special area ? Leonhard Henkes (Wed Jun 25 2008 - 07:31:10 CDT)
- Re: How to delete anwanted waters in a special area ? Axel Kohlmeyer (Wed Jun 25 2008 - 11:51:29 CDT)
On solvate plugin S.K. Ghosh (Mon Jun 23 2008 - 07:22:06 CDT)
On solvate plugin S.K. Ghosh (Mon Jun 23 2008 - 07:23:00 CDT)
- Re: On solvate plugin Bhargava (Mon Jun 23 2008 - 09:14:05 CDT)
How to visualize iron and chlorine properly. wangyong_at_dicp.ac.cn (Mon Jun 23 2008 - 19:44:35 CDT)
- Re: How to visualize iron and chlorine properly. Axel Kohlmeyer (Mon Jun 23 2008 - 10:13:41 CDT)
- Re: How to visualize iron and chlorine properly. Ignacio Fernández Galván (Tue Jun 24 2008 - 03:25:40 CDT)
Inquiry concerning the plugin "Inorganic builder" Anneta Tzampazi (Mon Jun 23 2008 - 05:23:46 CDT)
- Re: Inquiry concerning the plugin "Inorganic builder" Axel Kohlmeyer (Mon Jun 23 2008 - 10:11:04 CDT)
how to export into postscript with MultiPlot in tcl mode? Sebastian Stolzenberg (Sun Jun 22 2008 - 19:01:53 CDT)
- Re: how to export into postscript with MultiPlot in tcl mode? Axel Kohlmeyer (Mon Jun 23 2008 - 10:03:21 CDT)
- Re: how to export into postscript with MultiPlot in tcl mode? Johannes Müllegger (Mon Jun 23 2008 - 11:23:24 CDT)
vmd/vista32b/zalman M220 stereo? Michael Galloway (Fri Jun 20 2008 - 16:03:46 CDT)
- Re: vmd/vista32b/zalman M220 stereo? Sabuj Pattanayek (Fri Jun 20 2008 - 19:18:59 CDT)
- Re: vmd/vista32b/zalman M220 stereo? Michael Galloway (Mon Jun 23 2008 - 10:17:32 CDT)
  - Making a water-only sphere S.K. Ghosh (Mon Jun 23 2008 - 14:21:08 CDT)
enantiomers Ed Lowe (Fri Jun 20 2008 - 08:38:06 CDT)
- Re: enantiomers L. Michel Espinoza-Fonseca (Fri Jun 20 2008 - 09:10:31 CDT)
Volume slice color scale Ignacio Fernández Galván (Fri Jun 20 2008 - 04:15:39 CDT)
SpaceNavigator test builds (last note before I go offline!) John Stone (Fri Jun 20 2008 - 02:04:50 CDT)
Away from VMD-L/email until July 8th... John Stone (Thu Jun 19 2008 - 19:50:06 CDT)
- Re: Away from VMD-L/email until July 8th... Alexandre A. Vakhrouchev (Thu Jun 19 2008 - 21:09:17 CDT)
- Re: Away from VMD-L/email until July 8th... daniel aguayo (Fri Jun 20 2008 - 16:27:34 CDT)
Discrepancy between colours when coloured by timestep and Tachyon rendered Tim Carpenter (Thu Jun 19 2008 - 12:48:40 CDT)
- Re: Discrepancy between colours when coloured by timestep and Tachyon rendered John Stone (Thu Jun 19 2008 - 13:02:04 CDT)
  - Re: Discrepancy between colours when coloured by timestep and Tachyon rendered John Stone (Thu Jun 19 2008 - 13:05:52 CDT)
Print and save DLPOLY HISTORY plots mahesh naalla (Thu Jun 19 2008 - 12:15:50 CDT)
- Re: Print and save DLPOLY HISTORY plots John Stone (Thu Jun 19 2008 - 13:05:02 CDT)
  - Re: Print and save DLPOLY HISTORY plots mahesh naalla (Thu Jun 19 2008 - 14:08:17 CDT)
    - Re: Print and save DLPOLY HISTORY plots John Stone (Thu Jun 19 2008 - 23:48:06 CDT)
displaying hydrogen bonds when hydrogens are not available Y. U. Sasidhar (Thu Jun 19 2008 - 07:34:23 CDT)
- Re: displaying hydrogen bonds when hydrogens are not available Axel Kohlmeyer (Thu Jun 19 2008 - 09:31:53 CDT)
- Re: displaying hydrogen bonds when hydrogens are not available Eric H. Lee (Thu Jun 19 2008 - 09:46:51 CDT)
Labelling Coordinates (not Atoms) Anthony Ivetac (Wed Jun 18 2008 - 17:52:09 CDT)
- Re: Labelling Coordinates (not Atoms) Axel Kohlmeyer (Wed Jun 18 2008 - 18:43:57 CDT)
- Re: Labelling Coordinates (not Atoms) Anthony Ivetac (Wed Jun 18 2008 - 21:32:03 CDT)
IED Vahdati N. (Wed Jun 18 2008 - 10:26:37 CDT)
PSF works in NAMD but not in VMD Esben A. Gad (Wed Jun 18 2008 - 03:17:04 CDT)
- Re: PSF works in NAMD but not in VMD Peter Freddolino (Wed Jun 18 2008 - 06:53:50 CDT)
- Re: PSF works in NAMD but not in VMD Esben A. Gad (Fri Jun 20 2008 - 06:05:22 CDT)
specify a rtf file when generating a psf file. Nicolas Sapay (Tue Jun 17 2008 - 13:46:22 CDT)
- Re: specify a rtf file when generating a psf file. Peter Freddolino (Tue Jun 17 2008 - 14:32:13 CDT)
- Re: specify a rtf file when generating a psf file. Axel Kohlmeyer (Tue Jun 17 2008 - 14:50:55 CDT)
  - Re: specify a rtf file when generating a psf file. Nicolas Sapay (Tue Jun 17 2008 - 15:28:34 CDT)
render "color by volume" Gerald Mathias (Tue Jun 17 2008 - 13:27:15 CDT)
- Re: render "color by volume" Axel Kohlmeyer (Tue Jun 17 2008 - 14:51:28 CDT)
- Re: render "color by volume" Nicolas Sapay (Tue Jun 17 2008 - 17:11:45 CDT)
  - Re: render "color by volume" Axel Kohlmeyer (Tue Jun 17 2008 - 18:34:28 CDT)
opening gromacs .gro file gives warning messsage and does not display the molecule jake wernik (Mon Jun 16 2008 - 20:19:52 CDT)
- Re: opening gromacs .gro file gives warning messsage and does not display the molecule Axel Kohlmeyer (Tue Jun 17 2008 - 09:11:03 CDT)
- Re: opening gromacs .gro file gives warning messsage and does not display the molecule Nicolas Sapay (Tue Jun 17 2008 - 13:51:36 CDT)
Drawing a line between two atoms Marx Gomes Van der Linden (Mon Jun 16 2008 - 17:10:12 CDT)
Question: Too many arguments Leonhard Henkes (Mon Jun 16 2008 - 08:24:15 CDT)
- Re: Question: Too many arguments Axel Kohlmeyer (Mon Jun 16 2008 - 09:45:36 CDT)
problem with namdstats.tcl sudipta sinha (Sun Jun 15 2008 - 01:51:11 CDT)
Electrostatic - PMEpot daniel aguayo (Fri Jun 13 2008 - 12:23:22 CDT)
- Re: Electrostatic - PMEpot Leonardo Trabuco (Fri Jun 13 2008 - 13:13:00 CDT)
  - Re: Electrostatic - PMEpot daniel aguayo (Mon Jun 16 2008 - 09:02:08 CDT)
About occupancy volume maps Ignacio Fernández Galván (Fri Jun 13 2008 - 05:40:17 CDT)
- Re: About occupancy volume maps John Stone (Thu Jun 19 2008 - 00:38:25 CDT)
  - Re: About occupancy volume maps Ignacio Fernández Galván (Thu Jun 19 2008 - 02:43:11 CDT)
    - Re: About occupancy volume maps Axel Kohlmeyer (Thu Jun 19 2008 - 05:20:24 CDT)
User defined charges with PMEpot Nicolas Sapay (Thu Jun 12 2008 - 18:24:57 CDT)
- Re: User defined charges with PMEpot Axel Kohlmeyer (Thu Jun 12 2008 - 22:24:15 CDT)
  - Re: User defined charges with PMEpot Nicolas (Thu Jun 12 2008 - 23:08:24 CDT)
    - Re: User defined charges with PMEpot Axel Kohlmeyer (Fri Jun 13 2008 - 07:34:42 CDT)
Re: vmd-l digest V1 #1086 Ibrahim Moustafa (Wed Jun 11 2008 - 11:27:48 CDT)
import QM single point calculation Tim Werner (Wed Jun 11 2008 - 04:27:02 CDT)
problem loading trajectory in VMD under windows XP Aaron.Oakley_at_csiro.au (Tue Jun 10 2008 - 18:41:24 CDT)
- Re: problem loading trajectory in VMD under windows XP Axel Kohlmeyer (Tue Jun 10 2008 - 20:21:24 CDT)
- Re: problem loading trajectory in VMD under windows XP John Stone (Wed Jun 11 2008 - 01:37:58 CDT)
Spring quality watches offer Estela Gibbs (Tue Jun 10 2008 - 18:50:16 CDT)
Image rendering using pov-ray Dong Xu (Mon Jun 09 2008 - 20:35:55 CDT)
- Re: Image rendering using pov-ray Axel Kohlmeyer (Mon Jun 09 2008 - 21:30:35 CDT)
- Re: Image rendering using pov-ray Axel Kohlmeyer (Mon Jun 09 2008 - 21:34:57 CDT)
  - Re: Image rendering using pov-ray Dong Xu (Thu Jun 12 2008 - 21:31:03 CDT)
psf generation of circular proteins Rabab Toubar (Sun Jun 08 2008 - 09:36:00 CDT)
- IED on MacOSX 10.3.9 Peter Jones (Tue Jun 10 2008 - 05:54:54 CDT)
  - Re: IED on MacOSX 10.3.9 Axel Kohlmeyer (Tue Jun 10 2008 - 07:03:30 CDT)
- Re: psf generation of circular proteins John Stone (Wed Jun 11 2008 - 10:18:02 CDT)
  - Re: psf generation of circular proteins Rabab Toubar (Wed Jun 11 2008 - 13:30:05 CDT)
    - Re: psf generation of circular proteins John Stone (Thu Jun 12 2008 - 00:22:46 CDT)
Dipole moment? Alexandre A. Vakhrouchev (Sat Jun 07 2008 - 07:21:55 CDT)
- Re: Dipole moment? Axel Kohlmeyer (Sat Jun 07 2008 - 12:47:19 CDT)
  - Re: Dipole moment? Alexandre A. Vakhrouchev (Sat Jun 07 2008 - 13:25:40 CDT)
  - Re: Dipole moment? Ignacio Fernández Galván (Tue Jul 15 2008 - 09:52:07 CDT)
Total list of Tcl features Alexandre A. Vakhrouchev (Sat Jun 07 2008 - 00:15:05 CDT)
- Re: Total list of Tcl features John Stone (Sat Jun 07 2008 - 00:35:26 CDT)
  - Re: Total list of Tcl features Alexandre A. Vakhrouchev (Sat Jun 07 2008 - 01:14:37 CDT)
- Re: Total list of Tcl features Axel Kohlmeyer (Sat Jun 07 2008 - 09:41:05 CDT)
  - Re: Total list of Tcl features Alexandre A. Vakhrouchev (Sat Jun 07 2008 - 10:31:31 CDT)
    - Re: Total list of Tcl features Axel Kohlmeyer (Sat Jun 07 2008 - 10:21:27 CDT)
Watches for him, her and you Penny Boyle (Fri Jun 06 2008 - 19:47:03 CDT)
Solvation Katherine Parra (Fri Jun 06 2008 - 08:56:31 CDT)
- Re: Solvation Axel Kohlmeyer (Fri Jun 06 2008 - 09:04:27 CDT)
Solvation of a molecule Katherine Parra (Thu Jun 05 2008 - 08:15:41 CDT)
speed of movie gurpreet singh (Thu Jun 05 2008 - 05:40:55 CDT)
- Re: speed of movie Mario Valle (Thu Jun 05 2008 - 07:01:28 CDT)
- Re: speed of movie Axel Kohlmeyer (Sun Jul 13 2008 - 15:49:02 CDT)
Long file paths in Mac OS 10.5.3 Kevin DeMarco (Wed Jun 04 2008 - 15:24:51 CDT)
- Re: Long file paths in Mac OS 10.5.3 John Stone (Wed Jun 04 2008 - 16:27:03 CDT)
  - Re: Long file paths in Mac OS 10.5.3 Kevin DeMarco (Wed Jun 04 2008 - 16:43:32 CDT)
    - Re: Long file paths in Mac OS 10.5.3 John Stone (Wed Jun 04 2008 - 16:52:10 CDT)
- Re: Long file paths in Mac OS 10.5.3 Axel Kohlmeyer (Wed Jun 04 2008 - 16:17:25 CDT)
  - Re: Long file paths in Mac OS 10.5.3 Kevin DeMarco (Wed Jun 04 2008 - 18:30:19 CDT)
psf file Katherine Parra (Tue Jun 03 2008 - 11:47:43 CDT)
- Re: psf file JC Gumbart (Tue Jun 03 2008 - 15:24:36 CDT)
Batch mode on Mac OS 10.5.3 Benjamin Hall (Tue Jun 03 2008 - 05:16:52 CDT)
- Re: Batch mode on Mac OS 10.5.3 John Stone (Tue Jun 03 2008 - 11:10:18 CDT)
- Re: Batch mode on Mac OS 10.5.3 Dan Wright (Tue Jun 03 2008 - 11:24:22 CDT)
  - Re: Batch mode on Mac OS 10.5.3 Benjamin Hall (Wed Jun 04 2008 - 08:26:23 CDT)
- Re: Batch mode on Mac OS 10.5.3 Robert Brunner (Tue Jun 03 2008 - 12:34:02 CDT)
Create atom selection from list of integers Claw Isthelaw (Mon Jun 02 2008 - 11:01:49 CDT)
- Re: Create atom selection from list of integers Axel Kohlmeyer (Mon Jun 02 2008 - 11:08:16 CDT)
- Re: Create atom selection from list of integers Leonardo Trabuco (Mon Jun 02 2008 - 11:15:58 CDT)
  - Re: Create atom selection from list of integers Leonardo Trabuco (Mon Jun 02 2008 - 11:51:09 CDT)
- Re: Create atom selection from list of integers Joaquim Rui Rodrigues (Mon Jun 02 2008 - 12:10:28 CDT)
  - RE: Create atom selection from list of integers Claw Isthelaw (Mon Jun 02 2008 - 13:10:12 CDT)
Postdoc position available... John Stone (Sat May 31 2008 - 01:06:59 CDT)
measure hbonds problem politr_at_huji.ac.il (Fri May 30 2008 - 10:59:28 CDT)
- Re: measure hbonds problem Peter Freddolino (Fri May 30 2008 - 15:00:52 CDT)
  - Re: measure hbonds problem politr_at_huji.ac.il (Sun Jun 01 2008 - 06:27:48 CDT)
hydrogen bonds politr_at_huji.ac.il (Fri May 30 2008 - 06:05:12 CDT)
silly rmsd script doesn' t work ... andrea spitaleri (Fri May 30 2008 - 07:17:16 CDT)
- Re: silly rmsd script doesn' t work ... Peter Freddolino (Fri May 30 2008 - 08:44:00 CDT)
- Re: silly rmsd script doesn' t work ... Axel Kohlmeyer (Fri May 30 2008 - 07:49:45 CDT)
  - Re: silly rmsd script doesn' t work ... andrea spitaleri (Fri May 30 2008 - 08:28:40 CDT)
preriodic box problem Matthieu Chavent (Fri May 30 2008 - 04:12:31 CDT)
- Re: preriodic box problem L. Michel Espinoza-Fonseca (Fri May 30 2008 - 05:20:24 CDT)
  - Re: preriodic box problem Matthieu Chavent (Fri May 30 2008 - 10:40:00 CDT)
    - Re: preriodic box problem Olaf Lenz (Sat May 31 2008 - 06:20:06 CDT)
Exceeded maximum number of bonds Demian Riccardi (Thu May 29 2008 - 13:18:09 CDT)
- Re: Exceeded maximum number of bonds Axel Kohlmeyer (Thu May 29 2008 - 13:54:24 CDT)
vmd_init Paul Schlesinger (Wed May 28 2008 - 18:25:38 CDT)
- Re: vmd_init John Stone (Fri Jun 20 2008 - 00:11:41 CDT)
Re: [lammps-users] MDAnalysis (slightly OT) Axel Kohlmeyer (Tue May 27 2008 - 12:54:41 CDT)
errors with using surf and MSMS representations Yinglong Miao (Tue May 27 2008 - 14:53:54 CDT)
- Re: errors with using surf and MSMS representations John Stone (Tue May 27 2008 - 15:12:35 CDT)
  - Re: errors with using surf and MSMS representations John Stone (Tue May 27 2008 - 16:13:41 CDT)
    - Re: errors with using surf and MSMS representations Yinglong Miao (Tue May 27 2008 - 17:11:54 CDT)
IMD per TCL Stephan Frickenhaus (Tue May 27 2008 - 02:06:34 CDT)
- Re: IMD per TCL Axel Kohlmeyer (Tue May 27 2008 - 04:39:51 CDT)
- Re: IMD per TCL John Stone (Fri Jun 20 2008 - 00:15:33 CDT)
Label on Movie Wei Huang (Mon May 26 2008 - 10:26:30 CDT)
- Re: Label on Movie Axel Kohlmeyer (Mon May 26 2008 - 12:02:08 CDT)
  - Re: Label on Movie Wei Huang (Mon May 26 2008 - 14:21:22 CDT)
    - Re: Label on Movie Axel Kohlmeyer (Mon May 26 2008 - 14:06:52 CDT)
mass weighted rms fit Dong Xu (Sun May 25 2008 - 11:14:47 CDT)
- Re: mass weighted rms fit Axel Kohlmeyer (Sun May 25 2008 - 11:20:56 CDT)
How to discard certain atoms politr_at_huji.ac.il (Sun May 25 2008 - 05:50:43 CDT)
- Re: How to discard certain atoms Axel Kohlmeyer (Sun May 25 2008 - 07:59:23 CDT)
Measure gofr with large DCD files (Possibly use bigdcd ???) Christopher Gillespie (Fri May 23 2008 - 18:43:22 CDT)
- Re: Measure gofr with large DCD files (Possibly use bigdcd ???) Axel Kohlmeyer (Fri May 23 2008 - 18:59:33 CDT)
Movies using Cygwin's ImageMagick? Gustavo Seabra (Thu May 22 2008 - 09:18:45 CDT)
- Re: Movies using Cygwin's ImageMagick? Axel Kohlmeyer (Thu May 22 2008 - 09:33:30 CDT)
Crystal water INPE (Ingrid Viveka Pettersson) (Thu May 22 2008 - 04:32:59 CDT)
- Re: Crystal water Axel Kohlmeyer (Thu May 22 2008 - 05:23:24 CDT)
scale trajectory coords Peter Jones (Wed May 21 2008 - 22:28:35 CDT)
- Re: scale trajectory coords Axel Kohlmeyer (Wed May 21 2008 - 22:58:01 CDT)
(no subject) paquotau_at_loria.fr (Wed May 21 2008 - 08:12:51 CDT)
- Re: your mail Axel Kohlmeyer (Wed May 21 2008 - 09:17:12 CDT)
Several molecules paquotau_at_loria.fr (Tue May 20 2008 - 10:17:18 CDT)
- Re: Several molecules John Stone (Tue May 20 2008 - 10:21:03 CDT)
Using NAMD Energy Plugin S.K. Ghosh (Tue May 20 2008 - 07:18:35 CDT)
- Re: Using NAMD Energy Plugin Peter Freddolino (Tue May 20 2008 - 08:12:50 CDT)
  - save NAMD plot as a picture S.K. Ghosh (Thu Jun 19 2008 - 14:00:30 CDT)
    - Re: save NAMD plot as a picture John Stone (Thu Jun 19 2008 - 23:51:06 CDT)
- Re: Using NAMD Energy Plugin Axel Kohlmeyer (Tue May 20 2008 - 07:42:39 CDT)
plot residues without hydrogen atoms ABEL Stephane 175950 (Tue May 20 2008 - 07:02:41 CDT)
- Re: plot residues without hydrogen atoms Axel Kohlmeyer (Tue May 20 2008 - 07:40:19 CDT)
- Re: plot residues without hydrogen atoms Peter Freddolino (Tue May 20 2008 - 08:13:32 CDT)
  - RE : plot residues without hydrogen atoms ABEL Stephane 175950 (Tue May 20 2008 - 11:11:46 CDT)
Re: [vmd_chcwaaa@yahoo.com.cn: about measure dihedral angle] Jan Saam (Fri May 16 2008 - 18:15:51 CDT)
Color of bond betwen atoms with different colors Alberto Torres (Fri May 16 2008 - 15:35:40 CDT)
- Re: Color of bond betwen atoms with different colors Axel Kohlmeyer (Fri May 16 2008 - 16:35:50 CDT)
Slow tcl/tk script for trajectory analysis Alberto Sergio Garay (Fri May 16 2008 - 14:34:40 CDT)
- Re: Slow tcl/tk script for trajectory analysis John Stone (Fri May 16 2008 - 14:45:49 CDT)
- Re: Slow tcl/tk script for trajectory analysis Axel Kohlmeyer (Fri May 16 2008 - 14:46:11 CDT)
- Re: Slow tcl/tk script for trajectory analysis Jian Zou (Fri May 16 2008 - 15:23:46 CDT)
Draw in a new layer problems Nuno Sousa Cerqueira (Fri May 16 2008 - 08:36:58 CDT)
- Re: Draw in a new layer problems Peter Freddolino (Fri May 16 2008 - 09:09:43 CDT)
- Re: Draw in a new layer problems Axel Kohlmeyer (Fri May 16 2008 - 10:48:12 CDT)
How to calculate the volume of a molecule using vmd? Khaled Barakat (Thu May 15 2008 - 22:17:36 CDT)
- Re: How to calculate the volume of a molecule using vmd? John Stone (Thu May 15 2008 - 23:39:45 CDT)
Truncated Octahedron for VMD and NAMD simulation Yinglong Miao (Thu May 15 2008 - 14:31:48 CDT)
- Re: namd-l: Truncated Octahedron for VMD and NAMD simulation George Madalin Giambasu (Thu May 15 2008 - 15:23:51 CDT)
  - Re: Re: namd-l: Truncated Octahedron for VMD and NAMD simulation Vlad Cojocaru (Fri May 16 2008 - 03:29:41 CDT)
    - Re: Re: namd-l: Truncated Octahedron for VMD and NAMD simulation Yinglong Miao (Fri May 16 2008 - 09:42:20 CDT)
    - Re: Re: namd-l: Truncated Octahedron for VMD and NAMDsimulation Bishop, Thomas C (Fri May 16 2008 - 13:39:16 CDT)
Info regarding residue based CG simulation anshudx_at_indiatimes.com (Thu May 15 2008 - 13:04:11 CDT)
Re: namd-l: Energy plot script Subramanian Vaitheeswaran (Thu May 15 2008 - 07:28:20 CDT)
- Re: namd-l: Energy plot script bo liu (Thu May 15 2008 - 13:00:23 CDT)
Energy plot script Alexandre A. Vakhrouchev (Wed May 14 2008 - 22:11:19 CDT)
Individual atoms trajectory Alexandre A. Vakhrouchev (Wed May 14 2008 - 00:34:38 CDT)
- Re: Individual atoms trajectory John Stone (Thu May 15 2008 - 23:42:40 CDT)
  - Re: Individual atoms trajectory Alexandre A. Vakhrouchev (Fri May 16 2008 - 01:08:22 CDT)
    - Re: Individual atoms trajectory John Stone (Fri May 16 2008 - 01:33:59 CDT)
    - Re: Individual atoms trajectory Alexandre A. Vakhrouchev (Fri May 16 2008 - 02:08:59 CDT)
membrane builder ffavela_at_fis.cinvestav.mx (Tue May 13 2008 - 17:30:57 CDT)
- Re: membrane builder Axel Kohlmeyer (Tue May 13 2008 - 17:31:47 CDT)
Bond lengths from PDB and PSF Andrew Huang (Mon May 12 2008 - 16:36:18 CDT)
- Re: Bond lengths from PDB and PSF Axel Kohlmeyer (Mon May 12 2008 - 17:32:55 CDT)
coloring according to charge of residues OZGE ENGIN (Mon May 12 2008 - 10:05:33 CDT)
- Re: coloring according to charge of residues Giovanni Bellesia (Mon May 12 2008 - 10:58:45 CDT)
'within' command in VMD Neelanjana Sengupta (Sun May 11 2008 - 02:04:57 CDT)
- Re: 'within' command in VMD Axel Kohlmeyer (Sun May 11 2008 - 03:35:53 CDT)
- Re: 'within' command in VMD John Stone (Sun May 11 2008 - 10:54:53 CDT)
  - Re: 'within' command in VMD Neelanjana Sengupta (Sun May 11 2008 - 12:35:35 CDT)
    - Re: 'within' command in VMD John Stone (Sun May 11 2008 - 13:12:48 CDT)
    - Re: 'within' command in VMD Axel Kohlmeyer (Sun May 11 2008 - 13:22:18 CDT)
Recompile VMD with larger index types Alexandre A. Vakhrouchev (Sat May 10 2008 - 07:36:43 CDT)
- Re: Recompile VMD with larger index types John Stone (Sat May 10 2008 - 10:24:43 CDT)
  - Re: Recompile VMD with larger index types Axel Kohlmeyer (Sat May 10 2008 - 10:19:36 CDT)
- Re: Recompile VMD with larger index types John Stone (Mon Jun 11 2018 - 10:10:57 CDT)
Charge State Confusion MIke S (Thu May 08 2008 - 22:17:33 CDT)
- Re: Charge State Confusion John Stone (Thu May 08 2008 - 22:55:36 CDT)
  - Re: Charge State Confusion MIke S (Fri May 09 2008 - 00:45:39 CDT)
about measure dihedral angle cong chen (Thu May 08 2008 - 20:53:08 CDT)
measure sasa gives different results on different platforms Jufang Shan (Wed May 07 2008 - 15:52:47 CDT)
- Re: measure sasa gives different results on different platforms John Stone (Wed May 07 2008 - 16:59:55 CDT)
  - Re: measure sasa gives different results on different platforms Jufang Shan (Wed May 07 2008 - 23:04:19 CDT)
bigdcd v2.0 testers needed... Axel Kohlmeyer (Wed May 07 2008 - 15:21:47 CDT)
running vmd as pbs job zhenlong li (Tue May 06 2008 - 14:40:44 CDT)
- Re: running vmd as pbs job John Stone (Fri May 09 2008 - 02:29:22 CDT)
  - Re: running vmd as pbs job zhenlong li (Fri May 09 2008 - 08:34:41 CDT)
Writepdb with Solvation Box Alejandro Ortega (Tue May 06 2008 - 12:50:23 CDT)
- Re: Writepdb with Solvation Box Axel Kohlmeyer (Tue May 06 2008 - 13:25:34 CDT)
NAMDENERGY: function of 'cutoff' parameter when -pme option is enabled Ghalib Bello (Mon May 05 2008 - 23:02:45 CDT)
- Re: namd-l: NAMDENERGY: function of 'cutoff' parameter when -pme option is enabled Peter Freddolino (Tue May 06 2008 - 00:37:54 CDT)
question related to rmsd snoze pa (Mon May 05 2008 - 15:03:07 CDT)
- Re: namd-l: question related to rmsd JC Gumbart (Mon May 05 2008 - 16:19:47 CDT)
Vmd too slow on Suse10.x cgji (Mon May 05 2008 - 08:20:47 CDT)
- Re: Vmd too slow on Suse10.x Olaf Lenz (Mon May 05 2008 - 09:01:51 CDT)
- Re: Vmd too slow on Suse10.x John Stone (Mon May 05 2008 - 09:42:31 CDT)
The discreet replica store Greta Bush (Mon May 05 2008 - 01:28:30 CDT)
about writepdb cong chen (Mon May 05 2008 - 00:08:53 CDT)
- RE: about writepdb JC Gumbart (Mon May 05 2008 - 00:18:00 CDT)
Get one of these awesome replicas Rolando Carlson (Sun May 04 2008 - 12:10:27 CDT)
Replica watches make great gifts Edwina Grove (Sun May 04 2008 - 01:24:11 CDT)
The affordable watch alternative Ariel Mitchell (Fri May 02 2008 - 20:35:12 CDT)
a common list problem Thomas C. Bishop (Fri May 02 2008 - 10:28:30 CDT)
- Re: a common list problem John Stone (Fri May 02 2008 - 10:39:04 CDT)
Get one of these awesome replicas Melanie Mcmahon (Fri May 02 2008 - 01:05:03 CDT)
Rendering electrostatic surface potentials using Tachyon Jason Winget (Thu May 01 2008 - 15:39:31 CDT)
- Re: Rendering electrostatic surface potentials using Tachyon John Stone (Thu May 01 2008 - 21:56:13 CDT)
- Re: Rendering electrostatic surface potentials using Tachyon JT (Thu Apr 09 2009 - 15:14:41 CDT)
  - Re: Re: Rendering electrostatic surface potentials using Tachyon John Stone (Fri Apr 10 2009 - 10:22:45 CDT)
One of a kind replicas Richard Stone (Thu May 01 2008 - 11:18:31 CDT)
Watches made to impress Clinton Sylvester (Thu May 01 2008 - 10:40:03 CDT)
Measuring fit exclusively in 1 plane Benjamin Hall (Thu May 01 2008 - 04:59:04 CDT)
- Re: Measuring fit exclusively in 1 plane John Stone (Thu May 01 2008 - 21:54:14 CDT)
Why get an original watch? Leticia Larkin (Wed Apr 30 2008 - 20:14:01 CDT)
Impressive Glashutte timepieces! Lorena Shipley (Wed Apr 30 2008 - 08:35:35 CDT)
Spring quality watches offer Bertie Earl (Tue Apr 29 2008 - 19:30:10 CDT)
creating psf from pgn S.K. Ghosh (Tue Apr 29 2008 - 13:42:45 CDT)
- Re: creating psf from pgn John Stone (Tue Apr 29 2008 - 16:09:24 CDT)
Beginner with cyclic peptide Gao, Fan, Ph.D. (Tue Apr 29 2008 - 11:25:34 CDT)
- Re: Beginner with cyclic peptide Peter Freddolino (Tue Apr 29 2008 - 11:44:04 CDT)
Rolex replica is a ultimate gift Jimmie Corona (Tue Apr 29 2008 - 08:25:38 CDT)
clarification to "problem using pbc wrap" politr_at_huji.ac.il (Tue Apr 29 2008 - 06:43:23 CDT)
problem using pbc wrap politr_at_huji.ac.il (Tue Apr 29 2008 - 05:52:09 CDT)
(no subject) politr_at_huji.ac.il (Tue Apr 29 2008 - 05:49:41 CDT)
- Re: problem using pbc wrap Axel Kohlmeyer (Tue Apr 29 2008 - 06:49:20 CDT)
Spring quality watches offer Bryce Vang (Mon Apr 28 2008 - 12:56:22 CDT)
Hot replica watches from 2008 Rudy Puckett (Sun Apr 27 2008 - 14:53:15 CDT)
Re: namd-l: How to play molecule trajectory with VMD? Regina Politi (Sun Apr 27 2008 - 07:15:22 CDT)
Replica watch is a perfect gift Christian Courtney (Sun Apr 27 2008 - 04:18:34 CDT)
Replica watch is a perfect gift Murray Dyer (Sat Apr 26 2008 - 17:18:11 CDT)
Can not enter text in VMD plugin window Dong Xu (Fri Apr 25 2008 - 21:21:16 CDT)
- Re: Can not enter text in VMD plugin window Axel Kohlmeyer (Fri Apr 25 2008 - 21:52:12 CDT)
- Re: Can not enter text in VMD plugin window John Stone (Fri Apr 25 2008 - 21:53:05 CDT)
  - Re: Can not enter text in VMD plugin window Dong Xu (Sat Apr 26 2008 - 00:10:04 CDT)
Eigen values of Moment of Intertia Tensor greddy1_at_umd.edu (Fri Apr 25 2008 - 15:12:19 CDT)
Eigen values of Moment of Intertia Tensor greddy1_at_umd.edu (Fri Apr 25 2008 - 10:19:52 CDT)
You can save 80% Arturo Fernandez (Fri Apr 25 2008 - 05:58:21 CDT)
Get one of these awesome replicas Jerry Kiser (Thu Apr 24 2008 - 18:45:18 CDT)
problem with "within" command of VMD politr_at_huji.ac.il (Thu Apr 24 2008 - 08:22:23 CDT)
- Re: problem with "within" command of VMD Axel Kohlmeyer (Thu Apr 24 2008 - 08:43:19 CDT)
viewing pca output Bala subramanian (Thu Apr 24 2008 - 08:09:43 CDT)
- Re: viewing pca output John Stone (Thu May 01 2008 - 22:38:31 CDT)
  - Re: viewing pca output Bala subramanian (Fri May 02 2008 - 06:16:00 CDT)
    - Re: viewing pca output John Stone (Fri May 02 2008 - 16:36:51 CDT)
Inexpensive Louis Vuitton bags Buford Granger (Thu Apr 24 2008 - 09:03:05 CDT)
resolution screen in Linux andrea spitaleri (Thu Apr 24 2008 - 07:33:24 CDT)
- Re: resolution screen in Linux Axel Kohlmeyer (Thu Apr 24 2008 - 08:15:59 CDT)
- Re: resolution screen in Linux John Stone (Thu Apr 24 2008 - 08:46:50 CDT)
  - Re: resolution screen in Linux andrea spitaleri (Mon Apr 28 2008 - 02:54:15 CDT)
how to identify DNA-protein interaction interface BERGY (Thu Apr 24 2008 - 05:42:53 CDT)
- Re: how to identify DNA-protein interaction interface Thomas C. Bishop (Thu Apr 24 2008 - 09:40:50 CDT)
problem while running VMD politr_at_huji.ac.il (Thu Apr 24 2008 - 03:31:22 CDT)
problem while running VMD Regina Politi (Thu Apr 24 2008 - 03:30:19 CDT)
- Re: problem while running VMD John Stone (Thu Apr 24 2008 - 09:20:17 CDT)
One of a kind replicas Erin Ziegler (Wed Apr 23 2008 - 21:53:24 CDT)
Rendering Labels with Tachyon Anthony Ivetac (Wed Apr 23 2008 - 18:18:33 CDT)
- Re: Rendering Labels with Tachyon John Stone (Wed Apr 23 2008 - 19:36:49 CDT)
  - Re: Rendering Labels with Tachyon Anthony Ivetac (Thu Apr 24 2008 - 11:58:52 CDT)
Get your watch now Helena Slater (Wed Apr 23 2008 - 12:17:13 CDT)
measure distance politr_at_huji.ac.il (Wed Apr 23 2008 - 09:02:41 CDT)
- Re: measure distance Axel Kohlmeyer (Wed Apr 23 2008 - 09:04:00 CDT)
- Re: measure distance Jian Zou (Wed Apr 23 2008 - 09:45:58 CDT)
memorry problem politr_at_huji.ac.il (Wed Apr 23 2008 - 06:48:53 CDT)
- Re: memorry problem Axel Kohlmeyer (Wed Apr 23 2008 - 06:58:42 CDT)
  - Re: memorry problem Axel Kohlmeyer (Fri May 02 2008 - 15:04:02 CDT)
bug in the g(r) evaluation? cipitaua_at_gmail.com (Tue Apr 22 2008 - 09:30:37 CDT)
- Re: bug in the g(r) evaluation? Axel Kohlmeyer (Tue Apr 22 2008 - 10:10:35 CDT)
  - Re: bug in the g(r) evaluation? cipitaua_at_gmail.com (Tue Apr 22 2008 - 11:06:14 CDT)
    - Re: bug in the g(r) evaluation? Axel Kohlmeyer (Tue Apr 22 2008 - 14:32:07 CDT)
    - Re: bug in the g(r) evaluation? cipitaua_at_gmail.com (Wed Apr 23 2008 - 07:50:12 CDT)
alignment problem. trying to align new lipid to bilayer, but lipid always has wrong direction? maria goranovic (Tue Apr 22 2008 - 07:02:42 CDT)
One of a kind replicas Jane Mayberry (Mon Apr 21 2008 - 07:16:11 CDT)
Tag Heuer replicas better than originals Errol Lusk (Sun Apr 20 2008 - 18:30:56 CDT)
Tag Heuer replicas better than originals Corine Brady (Sun Apr 20 2008 - 07:33:41 CDT)
Tag Heuer replicas better than originals Mona Gomes (Sat Apr 19 2008 - 17:17:44 CDT)
warnings during plugin build Cojocaru,Vlad (Sat Apr 19 2008 - 09:09:32 CDT)
- Re: warnings during plugin build Axel Kohlmeyer (Sat Apr 19 2008 - 09:21:04 CDT)
  - RE: warnings during plugin build Cojocaru,Vlad (Sat Apr 19 2008 - 13:34:22 CDT)
  - Re: warnings during plugin build John Stone (Sat Apr 19 2008 - 14:29:46 CDT)
- Re: warnings during plugin build John Stone (Sat Apr 19 2008 - 14:46:06 CDT)
  - RE: warnings during plugin build Cojocaru,Vlad (Sat Apr 19 2008 - 17:53:58 CDT)
Take a look at the latest replica watches Lillie Lyons (Sat Apr 19 2008 - 07:00:53 CDT)
Spring quality watches offer Weldon Sylvester (Fri Apr 18 2008 - 18:29:29 CDT)
RMSD between two structures without the same number of atoms Aurelie.DeLuca_at_sanofi-aventis.com (Fri Apr 18 2008 - 08:08:39 CDT)
- Re: RMSD between two structures without the same number of atoms Axel Kohlmeyer (Fri Apr 18 2008 - 09:20:29 CDT)
You can save 80% Annabelle Posey (Thu Apr 17 2008 - 17:58:17 CDT)
PPMTOMPEG Quality Anthony Ivetac (Thu Apr 17 2008 - 14:40:15 CDT)
- Re: PPMTOMPEG Quality John Stone (Thu Apr 17 2008 - 16:38:16 CDT)
- Re: PPMTOMPEG Quality Axel Kohlmeyer (Thu Apr 17 2008 - 16:23:34 CDT)
Compiled version for MacOSX with non-standard options Delalande (Thu Apr 17 2008 - 08:37:14 CDT)
- Re: Compiled version for MacOSX with non-standard options John Stone (Thu Apr 17 2008 - 13:15:46 CDT)
  - Re: Compiled version for MacOSX with non-standard options Marc Baaden (Fri Apr 18 2008 - 08:36:25 CDT)
Replica watch is a perfect gift Deanna Fleming (Thu Apr 17 2008 - 05:25:56 CDT)
measure hbonds between protein and water - problem with periodic boundary conditions Ana Vila Verde (Thu Apr 17 2008 - 02:54:08 CDT)
- Re: measure hbonds between protein and water - problem with periodic boundary conditions Olaf Lenz (Thu Apr 17 2008 - 04:32:34 CDT)
  - Re: measure hbonds between protein and water - problem with periodic boundary conditions Axel Kohlmeyer (Thu Apr 17 2008 - 04:52:29 CDT)
    - Re: measure hbonds between protein and water - problem with periodic boundary conditions Olaf Lenz (Thu Apr 17 2008 - 05:19:52 CDT)
    - Re: measure hbonds between protein and water - problem with periodic boundary conditions Ana Vila Verde (Thu Apr 17 2008 - 05:54:50 CDT)
atomselect cong chen (Wed Apr 16 2008 - 19:58:18 CDT)
- Re: atomselect Jian Zou (Thu Apr 17 2008 - 09:06:48 CDT)
- Re: atomselect Axel Kohlmeyer (Thu Apr 17 2008 - 11:07:27 CDT)
Trajectory title Alessandro Cembran (Wed Apr 16 2008 - 07:53:47 CDT)
- Re: Trajectory title Axel Kohlmeyer (Wed Apr 16 2008 - 11:06:05 CDT)
You and a Rolex watch Tisha Engle (Wed Apr 16 2008 - 05:16:24 CDT)
Timer in VMD Lili Peng (Tue Apr 15 2008 - 16:59:28 CDT)
- Re: Timer in VMD Axel Kohlmeyer (Tue Apr 15 2008 - 18:58:46 CDT)
  - Re: Timer in VMD Lili Peng (Tue Apr 15 2008 - 21:52:22 CDT)
You and a Rolex watch Althea Lake (Tue Apr 15 2008 - 17:12:00 CDT)
Example tutorial snoze pa (Mon Apr 14 2008 - 18:38:03 CDT)
catDCD Raul Araya (Mon Apr 14 2008 - 12:01:41 CDT)
- RE: catDCD Richard Swenson (Mon Apr 14 2008 - 13:28:19 CDT)
- Re: catDCD Axel Kohlmeyer (Mon Apr 14 2008 - 12:08:34 CDT)
Spring quality watches offer Grace Clay (Mon Apr 14 2008 - 11:47:27 CDT)
topology files L/D form Jorgen Simonsen (Mon Apr 14 2008 - 04:50:08 CDT)
- Re: topology files L/D form Peter Freddolino (Mon Apr 14 2008 - 10:26:40 CDT)
  - Re: topology files L/D form Jorgen Simonsen (Mon Apr 14 2008 - 12:55:11 CDT)
    - Re: topology files L/D form Peter Freddolino (Mon Apr 14 2008 - 13:13:10 CDT)
15% off on two watches Lora Burgos (Mon Apr 14 2008 - 00:35:59 CDT)
compilation with python 2.5 and file permissions from the CVS repository Cojocaru,Vlad (Sun Apr 13 2008 - 12:24:52 CDT)
- Re: compilation with python 2.5 and file permissions from the CVS repository Axel Kohlmeyer (Sun Apr 13 2008 - 12:58:26 CDT)
  - RE: compilation with python 2.5 and file permissions from the CVS repository Cojocaru,Vlad (Sun Apr 13 2008 - 14:50:44 CDT)
Inexpensive Louis Vuitton bags Royce Rosa (Sat Apr 12 2008 - 18:57:58 CDT)
change residue name and write a trajectory file L. Michel Espinoza-Fonseca (Thu Apr 10 2008 - 17:02:13 CDT)
- Re: change residue name and write a trajectory file Axel Kohlmeyer (Thu Apr 10 2008 - 18:19:12 CDT)
Using namdenergy in batch mode to compute dihedral energies Irene Newhouse (Thu Apr 10 2008 - 15:15:36 CDT)
- Re: Using namdenergy in batch mode to compute dihedral energies Peter Freddolino (Thu Apr 10 2008 - 17:05:18 CDT)
  - RE: Using namdenergy in batch mode to compute dihedral energies Irene Newhouse (Thu Apr 10 2008 - 21:17:08 CDT)
Join tens of thousands of LUCKY winners today........ Mel Weston (Thu Apr 10 2008 - 05:48:03 CDT)
Play at the world's leading online casino..... Bobbie Horton (Thu Apr 10 2008 - 01:28:24 CDT)
The safest and most secure Online casino in the world....... Marian Clifton (Wed Apr 09 2008 - 18:55:11 CDT)
Visualization in 3-D using NVIDIA quaddro Himanshu Khandelia (Wed Apr 09 2008 - 05:27:18 CDT)
- Re: Visualization in 3-D using NVIDIA quaddro John Stone (Wed Apr 09 2008 - 10:28:10 CDT)
Play at the world's leading online casino..... Ned Roy (Wed Apr 09 2008 - 01:14:11 CDT)
Displaying nearest images using PBCTools Subramanian Vaitheeswaran (Tue Apr 08 2008 - 15:49:03 CDT)
- Re: Displaying nearest images using PBCTools Olaf Lenz (Wed Apr 09 2008 - 03:06:08 CDT)
some questions about the RDF plugin Raul Araya (Mon Apr 07 2008 - 15:23:32 CDT)
- Re: some questions about the RDF plugin Axel Kohlmeyer (Mon Apr 07 2008 - 15:32:29 CDT)
  - Re: some questions about the RDF plugin Axel Kohlmeyer (Mon Apr 07 2008 - 16:01:54 CDT)
How to circumvent: FATAL ERROR: Periodic cell has become too small for original patch grid! Maxim Paliy (Mon Apr 07 2008 - 12:36:24 CDT)
psfgen 999 waters resname X column Low Soo Mei (Mon Apr 07 2008 - 05:31:52 CDT)
- Re: psfgen 999 waters resname X column John Stone (Mon Apr 07 2008 - 11:54:54 CDT)
  - Re: psfgen 999 waters resname X column Low Soo Mei (Mon Apr 07 2008 - 21:02:37 CDT)
Insall Problem VMD Linux 1.8.6 Part II! Peter Hains (Sun Apr 06 2008 - 23:07:55 CDT)
- Re: Insall Problem VMD Linux 1.8.6 Part II! John Stone (Sun Apr 06 2008 - 23:23:31 CDT)
  - Re: Insall Problem VMD Linux 1.8.6 Part II! Peter Freddolino (Sun Apr 06 2008 - 23:31:25 CDT)
- Re: Insall Problem VMD Linux 1.8.6 Part II! Axel Kohlmeyer (Sun Apr 06 2008 - 23:50:58 CDT)
- Re: Insall Problem VMD Linux 1.8.6 Part II! John Stone (Sun Apr 06 2008 - 23:48:11 CDT)
Install problem VMD Linux 1.8.6 Peter Hains (Sun Apr 06 2008 - 19:19:15 CDT)
- Re: Install problem VMD Linux 1.8.6 John Stone (Sun Apr 06 2008 - 20:15:31 CDT)
- Re: Install problem VMD Linux 1.8.6 Axel Kohlmeyer (Sun Apr 06 2008 - 20:21:11 CDT)
About Tcl command zhjjvmd (Sat Apr 05 2008 - 20:58:15 CDT)
- Re: About Tcl command Axel Kohlmeyer (Sun Apr 06 2008 - 00:58:40 CDT)
  - Re: Re: About Tcl command zhjjvmd (Sun Apr 06 2008 - 01:17:54 CDT)
How to read specific DCD frames directly in Fortran? Yinglong Miao (Sat Apr 05 2008 - 13:21:53 CDT)
- Re: How to read specific DCD frames directly in Fortran? Peter Freddolino (Sat Apr 05 2008 - 13:38:39 CDT)
- Re: How to read specific DCD frames directly in Fortran? John Stone (Sat Apr 05 2008 - 13:43:21 CDT)
- Re: How to read specific DCD frames directly in Fortran? Axel Kohlmeyer (Sat Apr 05 2008 - 18:08:23 CDT)
  - Re: How to read specific DCD frames directly in Fortran? Leandro Martínez (Sun Apr 06 2008 - 02:25:45 CDT)
    - Re: How to read specific DCD frames directly in Fortran? Yinglong Miao (Sun Apr 06 2008 - 10:51:40 CDT)
how to render higher resolution figures for publication? Lixia Jin Day (Fri Apr 04 2008 - 16:27:04 CDT)
- Re: how to render higher resolution figures for publication? John Stone (Fri Apr 04 2008 - 16:36:05 CDT)
  - Re: how to render higher resolution figures for publication? Lixia Jin Day (Fri Apr 04 2008 - 17:42:08 CDT)
Topology file Alejandro Ortega (Fri Apr 04 2008 - 11:24:14 CDT)
- Re: Topology file Axel Kohlmeyer (Fri Apr 04 2008 - 11:52:27 CDT)
0ne of a kind repl1cas Sandy Anderson (Thu Apr 03 2008 - 08:19:31 CDT)
You can s4ve 80% Sherman Sherman (Wed Apr 02 2008 - 10:10:22 CDT)
Cannot perform RMSD analysis Maria Sanchez Farran (Wed Apr 02 2008 - 07:49:55 CDT)
- Re: Cannot perform RMSD analysis John Stone (Wed Apr 02 2008 - 23:53:41 CDT)
April promo on w4tches Randell Lund (Mon Mar 31 2008 - 22:03:54 CDT)
render Dongsheng Zhang (Mon Mar 31 2008 - 15:51:35 CDT)
- Re: render John Stone (Tue Apr 01 2008 - 14:14:12 CDT)
  - Re: render Dongsheng Zhang (Tue Apr 01 2008 - 14:22:17 CDT)
    - Re: render John Stone (Thu Apr 03 2008 - 00:24:30 CDT)
using cvs under Windows XP Ben Chern (Mon Mar 31 2008 - 08:31:31 CDT)
- Re: using cvs under Windows XP Axel Kohlmeyer (Mon Mar 31 2008 - 09:37:54 CDT)
  - Re: using cvs under Windows XP Ben Chern (Mon Mar 31 2008 - 10:21:11 CDT)
Compiling VMD under Windows XP Ben Chern (Mon Mar 31 2008 - 04:13:38 CDT)
- Re: Compiling VMD under Windows XP John Stone (Mon Mar 31 2008 - 10:29:59 CDT)
  - Re: Compiling VMD under Windows XP Ben Chern (Mon Mar 31 2008 - 21:39:41 CDT)
porcupine plot SWAPNA (Mon Mar 31 2008 - 01:06:36 CDT)
- Re: porcupine plot John Stone (Mon Mar 31 2008 - 01:22:18 CDT)
  - Re: porcupine plot Oliver Beckstein (Wed Apr 02 2008 - 16:46:40 CDT)
- Re: porcupine plot Axel Kohlmeyer (Mon Mar 31 2008 - 04:01:53 CDT)
NAMDenergy: how to override a FATAL ERROR Neelanjana Sengupta (Sun Mar 30 2008 - 14:50:29 CDT)
- Re: NAMDenergy: how to override a FATAL ERROR Peter Freddolino (Sun Mar 30 2008 - 15:02:58 CDT)
  - Re: NAMDenergy: how to override a FATAL ERROR Neelanjana Sengupta (Sun Mar 30 2008 - 15:51:45 CDT)
    - Re: NAMDenergy: how to override a FATAL ERROR Peter Freddolino (Sun Mar 30 2008 - 16:02:30 CDT)
  - Re: NAMDenergy: how to override a FATAL ERROR Peter Freddolino (Tue Apr 01 2008 - 10:55:05 CDT)
Problems with PDB file format in VMD cong chen (Thu Mar 27 2008 - 18:55:38 CDT)
- Re: Problems with PDB file format in VMD Axel Kohlmeyer (Thu Mar 27 2008 - 20:42:45 CDT)
Tcl 8.5.x in upcoming versions of VMD... John Stone (Thu Mar 27 2008 - 17:19:47 CDT)
- Re: Tcl 8.5.x in upcoming versions of VMD... Axel Kohlmeyer (Thu Mar 27 2008 - 17:32:20 CDT)
  - Re: Tcl 8.5.x in upcoming versions of VMD... John Stone (Thu Mar 27 2008 - 18:11:20 CDT)
    - Re: Tcl 8.5.x in upcoming versions of VMD... Axel Kohlmeyer (Thu Mar 27 2008 - 18:14:23 CDT)
Test VMD with CUDA support for Linux and MacOS X 10.5.2... John Stone (Thu Mar 27 2008 - 17:13:15 CDT)
Selection "within x of something" is not updated throughout DCD trajectory? Maxim Paliy (Thu Mar 27 2008 - 13:59:25 CDT)
- Re: Selection "within x of something" is not updated throughout DCD trajectory? John Stone (Thu Mar 27 2008 - 14:04:35 CDT)
How to see the original Origin (0,0,0, coordinate) of a system Utpal Sarkar (Thu Mar 27 2008 - 11:20:03 CDT)
- Re: How to see the original Origin (0,0,0, coordinate) of a system Axel Kohlmeyer (Thu Mar 27 2008 - 11:57:58 CDT)
- Re: How to see the original Origin (0,0,0, coordinate) of a system Adrian Kaats (Thu Mar 27 2008 - 15:56:52 CDT)
- Re: How to see the original Origin (0,0,0, coordinate) of a system John Stone (Thu Mar 27 2008 - 16:51:44 CDT)
Can VMD show the interactions between different structure part? Ben Chern (Wed Mar 26 2008 - 22:20:57 CDT)
- Re: Can VMD show the interactions between different structure part? Axel Kohlmeyer (Wed Mar 26 2008 - 23:19:40 CDT)
  - Re: Can VMD show the interactions between different structure part? Ben Chern (Thu Mar 27 2008 - 06:35:56 CDT)
    - Re: Can VMD show the interactions between different structure part? Axel Kohlmeyer (Thu Mar 27 2008 - 06:43:41 CDT)
    - Re: Can VMD show the interactions between different structure part? Ben Chern (Thu Mar 27 2008 - 20:26:13 CDT)
problem with pbc Matt Watkins (Wed Mar 26 2008 - 16:20:55 CDT)
- Re: problem with pbc Axel Kohlmeyer (Wed Mar 26 2008 - 16:38:07 CDT)
  - Re: problem with pbc Matt Watkins (Wed Mar 26 2008 - 17:07:58 CDT)
Can we get secondary structure from PDB files? Ben Chern (Wed Mar 26 2008 - 04:02:04 CDT)
- Re: Can we get secondary structure from PDB files? Axel Kohlmeyer (Wed Mar 26 2008 - 06:15:42 CDT)
  - Re: Can we get secondary structure from PDB files? Ben Chern (Wed Mar 26 2008 - 20:44:00 CDT)
    - Re: Can we get secondary structure from PDB files? John Stone (Wed Mar 26 2008 - 21:26:46 CDT)
    - Re: Can we get secondary structure from PDB files? Ben Chern (Wed Mar 26 2008 - 22:12:12 CDT)
time correlation function Krishnan, Marimuthu (Tue Mar 25 2008 - 22:44:40 CDT)
- Re: time correlation function Axel Kohlmeyer (Tue Mar 25 2008 - 22:56:27 CDT)
- Re: time correlation function David A. Case (Thu Mar 27 2008 - 16:35:11 CDT)
  - Re: time correlation function John Stone (Thu Mar 27 2008 - 17:08:08 CDT)
Test cong chen (Tue Mar 25 2008 - 18:39:50 CDT)
- Re: Test John Stone (Tue Mar 25 2008 - 21:59:05 CDT)
VMD tutorial for working with solid crystals Minhaj (Tue Mar 25 2008 - 03:33:19 CDT)
- Re: VMD tutorial for working with solid crystals Axel Kohlmeyer (Tue Mar 25 2008 - 13:38:06 CDT)
script to read dcd frame-at-a-time & write a selection Irene Newhouse (Mon Mar 24 2008 - 17:16:39 CDT)
- Re: script to read dcd frame-at-a-time & write a selection Axel Kohlmeyer (Mon Mar 24 2008 - 17:43:28 CDT)
  - RE: script to read dcd frame-at-a-time & write a selection Irene Newhouse (Mon Mar 24 2008 - 19:26:00 CDT)
Loading a PDB file with different atom counts in models Adrian Kaats (Fri Mar 21 2008 - 09:19:35 CDT)
- Re: Loading a PDB file with different atom counts in models John Stone (Mon Mar 24 2008 - 23:31:20 CDT)
  - Re: Loading a PDB file with different atom counts in models Adrian Kaats (Tue Mar 25 2008 - 07:41:38 CDT)
atoms with changing colors Simone Melchionna (Thu Mar 20 2008 - 16:50:50 CDT)
- Re: atoms with changing colors Axel Kohlmeyer (Thu Mar 20 2008 - 17:05:53 CDT)
- Re: atoms with changing colors John Stone (Thu Mar 20 2008 - 17:03:47 CDT)
atomselect protein Adrian Kaats (Thu Mar 20 2008 - 16:39:54 CDT)
- Re: atomselect protein John Stone (Thu Mar 20 2008 - 16:48:27 CDT)
old VMD post - RE: measuring distances in vmd tkon Simpson, Lisa M (Thu Mar 20 2008 - 12:38:36 CDT)
- Re: old VMD post - RE: measuring distances in vmd tkon L. Michel Espinoza-Fonseca (Thu Mar 20 2008 - 13:35:33 CDT)
  - Re: old VMD post - RE: measuring distances in vmd tkon L. Michel Espinoza-Fonseca (Thu Mar 20 2008 - 13:46:21 CDT)
GPU test machine Michael Di Domenico (Thu Mar 20 2008 - 11:04:59 CDT)
- Re: GPU test machine John Stone (Thu Mar 20 2008 - 11:25:09 CDT)
  - Re: GPU test machine Michael Di Domenico (Thu Mar 20 2008 - 15:29:41 CDT)
running ca-dist.tcl Simpson, Lisa M (Thu Mar 20 2008 - 08:57:47 CDT)
- Re: running ca-dist.tcl L. Michel Espinoza-Fonseca (Thu Mar 20 2008 - 10:38:50 CDT)
RMSD calc SENTHIL KUMAR (Thu Mar 20 2008 - 01:11:02 CDT)
- Re: RMSD calc Axel Kohlmeyer (Thu Mar 20 2008 - 05:37:31 CDT)
Build a VMD forum? Stanley, Yemin Shi (Wed Mar 19 2008 - 15:49:08 CDT)
- Re: Build a VMD forum? Axel Kohlmeyer (Wed Mar 19 2008 - 16:08:27 CDT)
  - Calculating the Tilt Angle of a non-helical peptide Arneh Babakhani (Wed Mar 19 2008 - 20:24:38 CDT)
Radial Density Jennifer Williams (Wed Mar 19 2008 - 11:12:56 CDT)
- Re: Radial Density Axel Kohlmeyer (Wed Mar 19 2008 - 11:48:49 CDT)
dipole Alessio Alexiadis (Wed Mar 19 2008 - 06:54:21 CDT)
- Re: dipole Axel Kohlmeyer (Wed Mar 19 2008 - 07:32:17 CDT)
Display bond breaking Stanley, Yemin Shi (Tue Mar 18 2008 - 22:17:50 CDT)
- Re: Display bond breaking Axel Kohlmeyer (Tue Mar 18 2008 - 22:25:27 CDT)
DLPOLY HISTORY FILE in VMD Utpal Sarkar (Tue Mar 18 2008 - 11:08:29 CDT)
- Re: DLPOLY HISTORY FILE in VMD Axel Kohlmeyer (Tue Mar 18 2008 - 11:23:31 CDT)
Re-create Figures in VMD Images and Movies Tutorial Dong Xu (Mon Mar 17 2008 - 16:17:57 CDT)
- Re: Re-create Figures in VMD Images and Movies Tutorial John Stone (Sun Mar 30 2008 - 15:51:16 CDT)
closewater.tcl Irene Newhouse (Mon Mar 17 2008 - 14:48:37 CDT)
- Re: closewater.tcl L. Michel Espinoza-Fonseca (Mon Mar 17 2008 - 15:41:14 CDT)
  - RE: closewater.tcl Irene Newhouse (Mon Mar 17 2008 - 15:50:03 CDT)
    - RE: closewater.tcl Axel Kohlmeyer (Mon Mar 17 2008 - 16:02:02 CDT)
    - RE: closewater.tcl Irene Newhouse (Mon Mar 17 2008 - 18:59:24 CDT)
GLSL lost Ignacio Fernández Galván (Mon Mar 17 2008 - 12:17:21 CDT)
- Re: GLSL lost Axel Kohlmeyer (Mon Mar 17 2008 - 13:59:35 CDT)
  - Re: GLSL lost Ignacio Fernández Galván (Tue Mar 18 2008 - 04:59:41 CDT)
different numbers of frames even though... Christopher Stiles (Fri Mar 14 2008 - 01:49:53 CDT)
- Re: different numbers of frames even though... Axel Kohlmeyer (Fri Mar 14 2008 - 09:49:00 CDT)
  - RE: different numbers of frames even though... Christopher Stiles (Fri Mar 14 2008 - 10:59:50 CDT)
    - RE: different numbers of frames even though... Axel Kohlmeyer (Fri Mar 14 2008 - 13:05:03 CDT)
ramaplot ramya narasimhan (Fri Mar 14 2008 - 00:46:30 CDT)
- Re: ramaplot Axel Kohlmeyer (Fri Mar 14 2008 - 09:37:41 CDT)
Does VMD support to draw a velocity field diagram? Fred (Rui FENG) (Thu Mar 13 2008 - 16:26:13 CDT)
- Re: Does VMD support to draw a velocity field diagram? Axel Kohlmeyer (Thu Mar 13 2008 - 18:03:54 CDT)
Diffusion Constant joy tehrani (Wed Mar 12 2008 - 17:44:52 CDT)
- Re: Diffusion Constant Axel Kohlmeyer (Tue Mar 18 2008 - 22:59:53 CDT)
  - Re: Diffusion Constant Massimo Lai (Wed Mar 19 2008 - 06:09:44 CDT)
    - Re: Diffusion Constant Axel Kohlmeyer (Wed Mar 19 2008 - 06:09:56 CDT)
Re: about paratool saam (Tue Mar 11 2008 - 11:56:45 CDT)
Paratools problem with Gaussian Output Nicolas Floquet (Tue Mar 11 2008 - 02:39:05 CDT)
- Re: Paratools problem with Gaussian Output Jan Saam (Tue Mar 11 2008 - 05:40:06 CDT)
Using namdenergy without cutoffs? poker_at_physics.usyd.edu.au (Tue Mar 11 2008 - 01:09:20 CDT)
- Re: Using namdenergy without cutoffs? Peter Freddolino (Tue Mar 11 2008 - 07:45:44 CDT)
  - Re: Using namdenergy without cutoffs? poker_at_physics.usyd.edu.au (Tue Mar 11 2008 - 20:05:46 CDT)
problem with gopython Carolyn Phillips (Mon Mar 10 2008 - 22:32:05 CDT)
- Re: problem with gopython John Stone (Tue Mar 11 2008 - 10:06:47 CDT)
snapshot not compatible with -dispdev text? Emmanuel Levy (Mon Mar 10 2008 - 17:08:02 CDT)
- Re: snapshot not compatible with -dispdev text? Axel Kohlmeyer (Mon Mar 10 2008 - 17:35:52 CDT)
  - Re: snapshot not compatible with -dispdev text? Emmanuel Levy (Mon Mar 10 2008 - 18:19:49 CDT)
- Re: snapshot not compatible with -dispdev text? John Stone (Mon Mar 10 2008 - 17:46:22 CDT)
Solvent accessible surface area calculation L. Michel Espinoza-Fonseca (Mon Mar 10 2008 - 14:41:08 CDT)
Automatically zoom so that the protein fill the display Emmanuel Levy (Mon Mar 10 2008 - 13:21:46 CDT)
- Re: Automatically zoom so that the protein fill the display Axel Kohlmeyer (Mon Mar 10 2008 - 13:50:50 CDT)
  - Re: Automatically zoom so that the protein fill the display Emmanuel Levy (Mon Mar 10 2008 - 14:28:30 CDT)
    - Re: Automatically zoom so that the protein fill the display John Stone (Mon Mar 10 2008 - 14:36:02 CDT)
    - Re: Automatically zoom so that the protein fill the display Emmanuel Levy (Mon Mar 10 2008 - 15:03:40 CDT)
  - Re: Automatically zoom so that the protein fill the display John Stone (Mon Mar 10 2008 - 14:17:27 CDT)
    - Re: Automatically zoom so that the protein fill the display Emmanuel Levy (Mon Mar 10 2008 - 14:30:51 CDT)
pbc join Dongsheng Zhang (Sun Mar 09 2008 - 22:44:32 CDT)
- Re: pbc join Axel Kohlmeyer (Sun Mar 09 2008 - 23:57:35 CDT)
- Re: pbc join Olaf Lenz (Mon Mar 10 2008 - 01:49:46 CDT)
radial density over one frame Christopher Stiles (Sun Mar 09 2008 - 14:55:51 CDT)
- Re: radial density over one frame Axel Kohlmeyer (Sun Mar 09 2008 - 15:49:17 CDT)
compile problem for VMD1.8.6: OpenGLRenderer.C Dan Strahs (Sat Mar 08 2008 - 20:17:23 CST)
- Re: compile problem for VMD1.8.6: OpenGLRenderer.C Axel Kohlmeyer (Sat Mar 08 2008 - 20:51:50 CST)
calculate volume Dong Xu (Fri Mar 07 2008 - 21:20:40 CST)
- Re: calculate volume John Stone (Fri Mar 07 2008 - 22:20:45 CST)
  - Re: calculate volume Dong Xu (Fri Mar 07 2008 - 22:46:28 CST)
    - Re: calculate volume John Stone (Sat Mar 08 2008 - 00:01:06 CST)
    - Re: calculate volume Dong Xu (Sat Mar 08 2008 - 11:09:36 CST)
- Re: calculate volume Axel Kohlmeyer (Sat Mar 08 2008 - 12:29:19 CST)
  - Re: calculate volume Dong Xu (Sat Mar 08 2008 - 17:28:39 CST)
    - Re: calculate volume John Stone (Sat Mar 08 2008 - 19:03:06 CST)
DCD file Alejandro Ortega (Fri Mar 07 2008 - 12:07:23 CST)
- Re: DCD file Yinglong Miao (Fri Mar 07 2008 - 14:43:37 CST)
how to make smooth movies ? maria goranovic (Fri Mar 07 2008 - 07:13:53 CST)
- Re: how to make smooth movies ? John Stone (Fri Mar 07 2008 - 10:52:15 CST)
- Re: how to make smooth movies ? Axel Kohlmeyer (Fri Mar 07 2008 - 10:40:59 CST)
Using RMSDTT in a script and aligning volume data Ignacio Fernández Galván (Fri Mar 07 2008 - 03:35:55 CST)
- Re: Using RMSDTT in a script and aligning volume data Axel Kohlmeyer (Fri Mar 07 2008 - 10:23:46 CST)
H2 bond distances calculation n displaying image SENTHIL KUMAR (Thu Mar 06 2008 - 22:07:18 CST)
- Re: H2 bond distances calculation n displaying image Axel Kohlmeyer (Fri Mar 07 2008 - 10:16:05 CST)
RMSD trajectory Tool joy tehrani (Thu Mar 06 2008 - 06:45:35 CST)
- Re: RMSD trajectory Tool Axel Kohlmeyer (Thu Mar 06 2008 - 07:48:05 CST)
VMD 3D stereo hardware Alba Colet Subirachs (Thu Mar 06 2008 - 03:16:25 CST)
- Re: VMD 3D stereo hardware John Stone (Thu Mar 06 2008 - 10:25:46 CST)
complete residues within Leandro Martínez (Thu Mar 06 2008 - 02:20:59 CST)
- Re: complete residues within jrui_at_ci.uc.pt (Thu Mar 06 2008 - 03:02:28 CST)
  - Re: complete residues within Leandro Martínez (Thu Mar 06 2008 - 03:06:48 CST)
- Re: complete residues within Olaf Lenz (Thu Mar 06 2008 - 03:28:08 CST)
- Re: complete residues within Alberto Perez (Thu Mar 06 2008 - 04:38:02 CST)
TCL/VMD problem Corenflos, Steven Charles (Wed Mar 05 2008 - 11:59:20 CST)
- Re: TCL/VMD problem John Stone (Wed Mar 05 2008 - 12:25:42 CST)
radial distribution function and number integrals Giovanni Bellesia (Wed Mar 05 2008 - 11:45:31 CST)
- Re: radial distribution function and number integrals Axel Kohlmeyer (Wed Mar 05 2008 - 12:45:36 CST)
  - Re: radial distribution function and number integrals Giovanni Bellesia (Wed Mar 05 2008 - 13:21:01 CST)
running vmd in parallel Michael Kreim (Wed Mar 05 2008 - 11:13:10 CST)
- Re: running vmd in parallel John Stone (Wed Mar 05 2008 - 12:31:35 CST)
- Re: running vmd in parallel Axel Kohlmeyer (Wed Mar 05 2008 - 12:37:02 CST)
What's the main reason of the structure or function of a protein? Fei Chen (Wed Mar 05 2008 - 07:53:18 CST)
- Re: What's the main reason of the structure or function of a protein? Andrew Dalke (Wed Mar 05 2008 - 16:32:42 CST)
  - Re: What's the main reason of the structure or function of a protein? Fei Chen (Wed Mar 05 2008 - 19:48:49 CST)
    - Re: What's the main reason of the structure or function of a protein? Andrew Dalke (Thu Mar 06 2008 - 00:25:03 CST)
about paratool laura (Wed Mar 05 2008 - 02:33:41 CST)
Visualizing trajectory with changing atoms Suman Chakrabarty (Tue Mar 04 2008 - 15:19:58 CST)
- Re: Visualizing trajectory with changing atoms John Stone (Tue Mar 04 2008 - 15:26:04 CST)
VMD languaje information Alba Colet Subirachs (Tue Mar 04 2008 - 10:24:09 CST)
- Re: VMD languaje information Axel Kohlmeyer (Tue Mar 04 2008 - 11:57:08 CST)
  - Re: VMD languaje information Andrew Dalke (Tue Mar 04 2008 - 14:44:16 CST)
    - Re: VMD languaje information L. Michel Espinoza-Fonseca (Tue Mar 04 2008 - 15:48:41 CST)
- Re: VMD languaje information John Stone (Tue Mar 04 2008 - 13:53:24 CST)
- Re: VMD languaje information L. Michel Espinoza-Fonseca (Tue Mar 04 2008 - 14:54:36 CST)
[carlos.simmerling@gmail.com: ACS awards] John Stone (Mon Mar 03 2008 - 20:11:56 CST)
VS: average area per lipid Bo Højen Justensen (Mon Mar 03 2008 - 15:10:09 CST)
average area per lipid Stephen Dutz (Mon Mar 03 2008 - 11:14:11 CST)
- RE: average area per lipid Stephen Dutz (Mon Mar 03 2008 - 16:06:44 CST)
  - SV: average area per lipid Bo Højen Justensen (Tue Mar 04 2008 - 02:33:11 CST)
missing basic tutorials for VMD scripting? massimo camarda (Sat Mar 01 2008 - 03:02:49 CST)
- Re: missing basic tutorials for VMD scripting? Axel Kohlmeyer (Sat Mar 01 2008 - 06:49:32 CST)
- Re: missing basic tutorials for VMD scripting? John Stone (Mon Mar 03 2008 - 10:57:10 CST)
unusual bond between the cysteine and arginine residue during the simulation OZGE ENGIN (Fri Feb 29 2008 - 13:30:01 CST)
- Re: unusual bond between the cysteine and arginine residue during the simulation John Stone (Fri Feb 29 2008 - 13:58:08 CST)
- Re: unusual bond between the cysteine and arginine residue during the simulation Axel Kohlmeyer (Fri Feb 29 2008 - 13:47:55 CST)
  - Re: Re: unusual bond between the cysteine and arginine residue during the simulation OZGE ENGIN (Fri Feb 29 2008 - 15:01:10 CST)
    - Re: Re: unusual bond between the cysteine and arginine residue during the simulation John Stone (Fri Feb 29 2008 - 15:06:49 CST)
no convergence in align Jorgen Simonsen (Fri Feb 29 2008 - 07:03:18 CST)
- Re: no convergence in align Axel Kohlmeyer (Fri Feb 29 2008 - 09:25:23 CST)
  - Re: no convergence in align John Stone (Fri Feb 29 2008 - 11:07:38 CST)
    - Re: no convergence in align Jorgen Simonsen (Fri Feb 29 2008 - 12:15:49 CST)
    - Re: no convergence in align John Stone (Fri Feb 29 2008 - 12:39:20 CST)
- Re: no convergence in align John Stone (Fri Feb 29 2008 - 10:05:34 CST)
Re: Cluster plugin and Gromacs g_cluster OZGE ENGIN (Wed Feb 27 2008 - 07:21:15 CST)
periodic images for trajectory Jennifer Williams (Wed Feb 27 2008 - 04:18:56 CST)
- Re: periodic images for trajectory Axel Kohlmeyer (Wed Feb 27 2008 - 05:07:04 CST)
- Re: periodic images for trajectory Olaf Lenz (Wed Feb 27 2008 - 04:59:30 CST)
Compute force between two atoms Chen Fei (Tue Feb 26 2008 - 20:28:22 CST)
- Re: Compute force between two atoms Axel Kohlmeyer (Tue Feb 26 2008 - 21:42:48 CST)
more on lammps and VMD coordinates Arienti, Marco UTRC (Tue Feb 26 2008 - 11:18:37 CST)
- Re: more on lammps and VMD coordinates Axel Kohlmeyer (Tue Feb 26 2008 - 12:08:13 CST)
control drawing method Myunggi Yi (Mon Feb 25 2008 - 13:26:33 CST)
- Re: control drawing method Axel Kohlmeyer (Mon Feb 25 2008 - 14:51:57 CST)
How to get rubber-like surface with Tachyon renderer Alexander Metz (Mon Feb 25 2008 - 09:37:02 CST)
- Re: How to get rubber-like surface with Tachyon renderer Axel Kohlmeyer (Mon Feb 25 2008 - 10:13:33 CST)
  - Re: How to get rubber-like surface with Tachyon renderer Axel Kohlmeyer (Mon Feb 25 2008 - 11:21:09 CST)
- Re: How to get rubber-like surface with Tachyon renderer John Stone (Mon Feb 25 2008 - 11:33:21 CST)
specify the bonds between the atoms massimo camarda (Mon Feb 25 2008 - 01:48:52 CST)
- classify and compute the forces between two atoms ChenFei (Mon Feb 25 2008 - 06:38:58 CST)
  - Re: classify and compute the forces between two atoms Axel Kohlmeyer (Mon Feb 25 2008 - 10:08:44 CST)
    - ´ð¸´: classify and compute the forces between two atoms ChenFei (Tue Feb 26 2008 - 01:10:29 CST)
- Re: specify the bonds between the atoms John Stone (Fri Feb 29 2008 - 14:04:44 CST)
measure binding site SASA Dong Xu (Sun Feb 24 2008 - 12:38:49 CST)
Changing a structure of macromolecule with VMD fouchni_at_uni-osnabrueck.de (Sun Feb 24 2008 - 08:38:44 CST)
- Re: Changing a structure of macromolecule with VMD Peter Freddolino (Sun Feb 24 2008 - 09:27:34 CST)
- Re: Changing a structure of macromolecule with VMD Axel Kohlmeyer (Sun Feb 24 2008 - 11:36:04 CST)
visualizing disulphide bonds OZGE ENGIN (Sun Feb 24 2008 - 04:31:18 CST)
- Re: visualizing disulphide bonds Axel Kohlmeyer (Sun Feb 24 2008 - 06:21:41 CST)
Ramachandran plot tcl script Anthony Samiotakis (Sat Feb 23 2008 - 15:54:50 CST)
- Re: Ramachandran plot tcl script Axel Kohlmeyer (Sat Feb 23 2008 - 17:17:38 CST)
vmd snapshots without display Thomas C. Bishop (Fri Feb 22 2008 - 10:59:50 CST)
- Re: vmd snapshots without display John Stone (Fri Feb 22 2008 - 11:33:36 CST)
- Re: vmd snapshots without display Axel Kohlmeyer (Fri Feb 22 2008 - 11:41:19 CST)
Residue replacement question] fouchni_at_uni-osnabrueck.de (Fri Feb 22 2008 - 04:20:04 CST)
- Re: Residue replacement question] Axel Kohlmeyer (Sat Feb 23 2008 - 17:29:35 CST)
movie generation without runtime frame show massimo camarda (Fri Feb 22 2008 - 04:15:58 CST)
- Re: movie generation without runtime frame show Axel Kohlmeyer (Fri Feb 22 2008 - 06:54:42 CST)
monitor helicity change Jufang Shan (Thu Feb 21 2008 - 19:06:14 CST)
- Re: monitor helicity change Axel Kohlmeyer (Thu Feb 21 2008 - 22:40:02 CST)
  - Re: monitor helicity change Jufang Shan (Fri Feb 22 2008 - 11:40:52 CST)
    - Re: Re: monitor helicity change OZGE ENGIN (Fri Feb 22 2008 - 01:58:26 CST)
    - Re: Re: monitor helicity change Jufang Shan (Fri Feb 22 2008 - 11:37:55 CST)
defining bonds Thomas C. Bishop (Thu Feb 21 2008 - 14:47:15 CST)
- Re: defining bonds Axel Kohlmeyer (Thu Feb 21 2008 - 15:17:50 CST)
VASP CHGCAR Wesley Smith (Thu Feb 21 2008 - 14:12:05 CST)
- Re: VASP CHGCAR Axel Kohlmeyer (Thu Feb 21 2008 - 15:35:07 CST)
  - Re: VASP CHGCAR Wesley Smith (Thu Feb 21 2008 - 17:10:28 CST)
couldn't fork child process: not enough memory jrui_at_ci.uc.pt (Thu Feb 21 2008 - 13:47:06 CST)
- Re: couldn't fork child process: not enough memory Axel Kohlmeyer (Thu Feb 21 2008 - 15:28:16 CST)
  - Re: couldn't fork child process: not enough memory jrui_at_ci.uc.pt (Fri Feb 22 2008 - 05:13:16 CST)
    - Re: couldn't fork child process: not enough memory Peter Freddolino (Fri Feb 22 2008 - 06:48:23 CST)
    - Re: couldn't fork child process: not enough memory jrui_at_ci.uc.pt (Fri Feb 22 2008 - 08:41:54 CST)
- Re: couldn't fork child process: not enough memory John Stone (Thu Feb 21 2008 - 15:39:30 CST)
couldn't open "c:/multiseq-406080740227.start.domain": invalid argument Maurice O'Connell (Thu Feb 21 2008 - 12:30:26 CST)
gromacs trajectory files maria goranovic (Thu Feb 21 2008 - 04:18:17 CST)
- Re: gromacs trajectory files Axel Kohlmeyer (Thu Feb 21 2008 - 06:58:52 CST)
Selection in VMD Graphical representation Pavan Ghatty (Wed Feb 20 2008 - 10:22:03 CST)
- Re: Selection in VMD Graphical representation Axel Kohlmeyer (Wed Feb 20 2008 - 12:05:29 CST)
  - Re: Selection in VMD Graphical representation John Stone (Wed Feb 20 2008 - 13:32:03 CST)
Residue replacement question fouchni_at_uni-osnabrueck.de (Wed Feb 20 2008 - 04:15:33 CST)
spacial distribution function L. Michel Espinoza-Fonseca (Tue Feb 19 2008 - 18:52:15 CST)
- Fwd: spacial distribution function L. Michel Espinoza-Fonseca (Tue Feb 19 2008 - 18:54:53 CST)
- Re: spacial distribution function L. Michel Espinoza-Fonseca (Tue Feb 19 2008 - 19:48:02 CST)
how to set molinfo from python Jorgen Simonsen (Tue Feb 19 2008 - 02:03:16 CST)
- Re: how to set molinfo from python Axel Kohlmeyer (Tue Feb 19 2008 - 10:49:17 CST)
tcl script memory problem - NOT in atomselect Johannes Müllegger (Mon Feb 18 2008 - 21:45:42 CST)
- Re: tcl script memory problem - NOT in atomselect Axel Kohlmeyer (Tue Feb 19 2008 - 07:35:20 CST)
  - Re: tcl script memory problem - NOT in atomselect Johannes Müllegger (Tue Feb 19 2008 - 11:19:04 CST)
change axes name massimo camarda (Mon Feb 18 2008 - 11:57:35 CST)
- Re: change axes name John Stone (Tue Feb 19 2008 - 10:59:23 CST)
VMD limitation for loading large trajectory file Dong Xu (Fri Feb 15 2008 - 16:48:45 CST)
- Re: VMD limitation for loading large trajectory file John Stone (Fri Feb 15 2008 - 17:03:15 CST)
- Re: VMD limitation for loading large trajectory file Axel Kohlmeyer (Fri Feb 15 2008 - 17:00:40 CST)
Unable to see VDW , CPK representations Arnab Chakrabarty (Fri Feb 15 2008 - 16:25:23 CST)
- Re: Unable to see VDW , CPK representations John Stone (Fri Feb 15 2008 - 16:42:15 CST)
- Re: Unable to see VDW , CPK representations Axel Kohlmeyer (Fri Feb 15 2008 - 16:51:34 CST)
  - Re: Unable to see VDW , CPK representations Arnab Chakrabarty (Sat Feb 16 2008 - 17:51:04 CST)
    - Re: Unable to see VDW , CPK representations John Stone (Thu Feb 21 2008 - 11:34:53 CST)
display of periodic DCD information Thomas C. Bishop (Thu Feb 14 2008 - 14:15:15 CST)
- Re: display of periodic DCD information Olaf Lenz (Thu Feb 14 2008 - 16:05:32 CST)
  - Re: display of periodic DCD information Olaf Lenz (Thu Feb 14 2008 - 16:08:46 CST)
  - Re: display of periodic DCD information/PBCTOOL Thomas C. Bishop (Fri Feb 15 2008 - 11:44:24 CST)
    - Re: display of periodic DCD information/PBCTOOL Axel Kohlmeyer (Fri Feb 15 2008 - 12:22:40 CST)
- Re: display of periodic DCD information John Stone (Thu Feb 14 2008 - 16:34:22 CST)
Volume data formats Ignacio Fernández Galván (Thu Feb 14 2008 - 11:58:40 CST)
- Re: Volume data formats John Stone (Thu Feb 14 2008 - 12:10:26 CST)
- Re: Volume data formats Wesley Smith (Thu Feb 14 2008 - 12:37:16 CST)
- Re: Volume data formats Axel Kohlmeyer (Thu Feb 14 2008 - 12:23:56 CST)
rmsd different from rmsd implemented in VMD Jorgen Simonsen (Wed Feb 13 2008 - 10:18:19 CST)
- RE: rmsd different from rmsd implemented in VMD JC Gumbart (Wed Feb 13 2008 - 10:58:13 CST)
- Re: rmsd different from rmsd implemented in VMD Thomas C. Bishop (Thu Feb 14 2008 - 08:19:08 CST)
PSFGEN::: ERROR: failed on end of segment Dibyadeep Paul (Wed Feb 13 2008 - 03:38:14 CST)
Improved VMD performance on MacOSX 10.5.2 Christoph Weber (Tue Feb 12 2008 - 16:51:14 CST)
- Re: Improved VMD performance on MacOSX 10.5.2 John Stone (Tue Feb 12 2008 - 18:26:09 CST)
FieldLines Mary Karpen (Tue Feb 12 2008 - 07:34:42 CST)
- Re: FieldLines Axel Kohlmeyer (Tue Feb 12 2008 - 09:53:36 CST)
- Re: FieldLines John Stone (Wed Feb 13 2008 - 14:34:04 CST)
variables from VMD to psfgen Thomas C. Bishop (Mon Feb 11 2008 - 17:28:12 CST)
- Re: variables from VMD to psfgen L. Michel Espinoza-Fonseca (Mon Feb 11 2008 - 18:22:49 CST)
measure SASA L. Michel Espinoza-Fonseca (Sun Feb 10 2008 - 17:48:12 CST)
namd energy plugin L. Michel Espinoza-Fonseca (Sun Feb 10 2008 - 15:44:04 CST)
- Re: namd energy plugin Peter Freddolino (Sun Feb 10 2008 - 15:55:50 CST)
  - Re: namd energy plugin L. Michel Espinoza-Fonseca (Sun Feb 10 2008 - 16:10:36 CST)
the script do not update the frame number for secondary structure analysis OZGE ENGIN (Sun Feb 10 2008 - 05:18:46 CST)
- Re: the script do not update the frame number for secondary structure analysis jrui_at_ci.uc.pt (Mon Feb 11 2008 - 03:10:25 CST)
  - Re: Re: the script do not update the frame number for secondary structure analysis OZGE ENGIN (Mon Feb 11 2008 - 04:01:15 CST)
the script do not update the frame for secondary structure analysis OZGE ENGIN (Sun Feb 10 2008 - 04:13:03 CST)
- Re: the script do not update the frame for secondary structure analysis Nuno Loureiro Ferreira (Mon Feb 11 2008 - 03:03:19 CST)
  - Re: the script do not update the frame for secondary structure analysis poker_at_physics.usyd.edu.au (Mon Feb 11 2008 - 18:51:32 CST)
ssrecalc output for the whole trajectory OZGE ENGIN (Sat Feb 09 2008 - 08:28:02 CST)
output of the ssrecalc command OZGE ENGIN (Fri Feb 08 2008 - 14:01:45 CST)
- Re: output of the ssrecalc command jrui_at_ci.uc.pt (Sat Feb 09 2008 - 04:50:46 CST)
  - Re: Re: output of the ssrecalc command OZGE ENGIN (Sat Feb 09 2008 - 06:39:27 CST)
installation problem vmd 1.8.6 on fedora 3 kinshuk_at_chem.iitb.ac.in (Fri Feb 08 2008 - 00:15:50 CST)
- Re: installation problem vmd 1.8.6 on fedora 3 John Stone (Fri Feb 08 2008 - 11:27:28 CST)
  - Re: installation problem vmd 1.8.6 on fedora 3 Bertrand P. S. Russell (Sat Feb 09 2008 - 05:22:24 CST)
    - Re: installation problem vmd 1.8.6 on fedora 3 Axel Kohlmeyer (Sat Feb 09 2008 - 07:57:27 CST)
heuristic bond computation Tony Sheh (Thu Feb 07 2008 - 21:58:15 CST)
- Re: heuristic bond computation Axel Kohlmeyer (Thu Feb 07 2008 - 22:16:18 CST)
- Re: heuristic bond computation John Stone (Thu Feb 07 2008 - 22:37:45 CST)
  - Re: heuristic bond computation Olaf Lenz (Fri Feb 08 2008 - 01:33:37 CST)
    - Re: heuristic bond computation Axel Kohlmeyer (Fri Feb 08 2008 - 08:03:31 CST)
SASA calculation (protein + small molecules) Manali Mehendale (Thu Feb 07 2008 - 14:45:37 CST)
- Re: SASA calculation (protein + small molecules) Dong Xu (Sun Feb 24 2008 - 20:42:44 CST)
  - Re: SASA calculation (protein + small molecules) John Stone (Fri Feb 29 2008 - 13:11:37 CST)
merge pdb Lucie Huynh (Wed Feb 06 2008 - 10:29:58 CST)
- Re: merge pdb Axel Kohlmeyer (Wed Feb 06 2008 - 10:41:43 CST)
vmd maxAtom C L Freeman (Wed Feb 06 2008 - 10:10:30 CST)
- Re: vmd maxAtom Axel Kohlmeyer (Wed Feb 06 2008 - 10:47:56 CST)
  - Re: vmd maxAtom C L Freeman (Thu Feb 07 2008 - 04:53:30 CST)
    - Re: vmd maxAtom Axel Kohlmeyer (Thu Feb 07 2008 - 05:58:14 CST)
help with animate read command Jim Pfaendtner (Tue Feb 05 2008 - 11:26:47 CST)
- Re: help with animate read command John Stone (Tue Feb 05 2008 - 13:48:02 CST)
  - Re: animate read command Jim Pfaendtner (Tue Feb 05 2008 - 13:55:29 CST)
    - Re: animate read command John Stone (Tue Feb 05 2008 - 14:16:00 CST)
namd help? Corenflos, Steven Charles (Tue Feb 05 2008 - 12:15:47 CST)
- Re: namd help? Axel Kohlmeyer (Tue Feb 05 2008 - 12:54:36 CST)
About Cluster Plug-in OZGE ENGIN (Tue Feb 05 2008 - 09:05:00 CST)
- Re: About Cluster Plug-in John Stone (Tue Feb 05 2008 - 09:45:23 CST)
Displaying Counter Alongside Animation Adrian Koh (Tue Feb 05 2008 - 00:20:36 CST)
- Re: Displaying Counter Alongside Animation Axel Kohlmeyer (Tue Feb 05 2008 - 03:23:44 CST)
- RE: Displaying Counter alongside animation Adrian Koh (Mon Feb 11 2008 - 03:08:44 CST)
VMD, NAMDenergy & AMBER parameters Irene Newhouse (Mon Feb 04 2008 - 17:23:37 CST)
- Re: VMD, NAMDenergy & AMBER parameters Peter Freddolino (Tue Feb 05 2008 - 06:51:37 CST)
  - RE: VMD, NAMDenergy & AMBER parameters Irene Newhouse (Tue Feb 05 2008 - 12:46:40 CST)
To create Tetramer Swarna Patra (Mon Feb 04 2008 - 16:42:52 CST)
- RE: To create Tetramer Irene Newhouse (Mon Feb 04 2008 - 17:56:41 CST)
- Re: To create Tetramer John Stone (Tue Feb 05 2008 - 09:55:43 CST)
Question about geometrical figures Felix Rodrigues Gulias (Fri Feb 01 2008 - 11:03:42 CST)
- Re: Question about geometrical figures Axel Kohlmeyer (Fri Feb 01 2008 - 11:28:35 CST)
question about 'measure bond' MW Van der Kamp, School of Chemistry (Fri Feb 01 2008 - 09:21:20 CST)
- Re: question about 'measure bond' Axel Kohlmeyer (Fri Feb 01 2008 - 09:46:30 CST)
Rdf from a specific point Robert Coridan (Fri Feb 01 2008 - 06:12:42 CST)
- Re: Rdf from a specific point Axel Kohlmeyer (Fri Feb 01 2008 - 08:55:39 CST)
  - Re: Rdf from a specific point Robert Coridan (Fri Feb 01 2008 - 11:48:19 CST)
    - Re: Rdf from a specific point Axel Kohlmeyer (Fri Feb 01 2008 - 11:48:12 CST)
animation of an atom diffusion inside a bulk crystal massimo camarda (Fri Feb 01 2008 - 02:27:59 CST)
- Re: animation of an atom diffusion inside a bulk crystal Axel Kohlmeyer (Fri Feb 01 2008 - 05:01:33 CST)
sausage view of NMR ensembles dimka (Thu Jan 31 2008 - 23:10:59 CST)
- Re: sausage view of NMR ensembles John Stone (Thu Jan 31 2008 - 23:31:36 CST)
Percentage Helicity calculation in VMD aneesh cna (Thu Jan 31 2008 - 22:54:53 CST)
- Re: Percentage Helicity calculation in VMD Axel Kohlmeyer (Thu Jan 31 2008 - 23:37:28 CST)
  - Re: Percentage Helicity calculation in VMD aneesh cna (Fri Feb 01 2008 - 03:18:53 CST)
    - Re: Percentage Helicity calculation in VMD Peter Freddolino (Sat Feb 02 2008 - 08:42:40 CST)
    - Re: Percentage Helicity calculation in VMD John Stone (Sat Feb 02 2008 - 15:30:18 CST)
problems with MDenergy Irene Newhouse (Wed Jan 30 2008 - 15:06:49 CST)
Mutate nucleotides Maurizio Olla (Tue Jan 29 2008 - 23:51:05 CST)
Sasa script in python returns "Runtime error" Per Jr. Greisen (Tue Jan 29 2008 - 09:53:59 CST)
- Re: Sasa script in python returns "Runtime error" Axel Kohlmeyer (Tue Jan 29 2008 - 11:19:17 CST)
  - Re: Sasa script in python returns "Runtime error" Axel Kohlmeyer (Wed Jan 30 2008 - 09:01:21 CST)
(no subject) mbyr8097_at_mail.usyd.edu.au (Mon Jan 28 2008 - 19:02:49 CST)
- Re: your mail Axel Kohlmeyer (Mon Jan 28 2008 - 19:36:38 CST)
'gopython' Tkinter and Numeric Python error brmorgan_at_clarku.edu (Mon Jan 28 2008 - 09:55:36 CST)
- Re: 'gopython' Tkinter and Numeric Python error John Stone (Wed Jan 30 2008 - 10:29:49 CST)
(no subject) Steve Seibold (Mon Jan 28 2008 - 08:39:37 CST)
- Re: Peter Freddolino (Mon Jan 28 2008 - 08:56:39 CST)
where is the "move" procedure in the toturial Justin JEONG (Sun Jan 27 2008 - 16:32:03 CST)
- Re: where is the "move" procedure in the toturial Axel Kohlmeyer (Mon Jan 28 2008 - 09:08:25 CST)
VMD 1.8.6, XTC format on Mac OS X 10.5.1 Tony Sheh (Sat Jan 26 2008 - 11:56:01 CST)
- Re: VMD 1.8.6, XTC format on Mac OS X 10.5.1 Axel Kohlmeyer (Sat Jan 26 2008 - 13:29:35 CST)
  - Re: VMD 1.8.6, XTC format on Mac OS X 10.5.1 Christoph Weber (Sat Jan 26 2008 - 16:59:17 CST)
re: script hangs when use full dcd file Irene Newhouse (Fri Jan 25 2008 - 14:14:53 CST)
- Re: re: script hangs when use full dcd file John Stone (Fri Jan 25 2008 - 14:32:42 CST)
  - RE: re: script hangs when use full dcd file Irene Newhouse (Fri Jan 25 2008 - 14:56:47 CST)
problem with timeline plugin aneesh cna (Fri Jan 25 2008 - 00:12:17 CST)
- Re: problem with timeline plugin John Stone (Fri Jan 25 2008 - 00:17:48 CST)
MSVC Projects Corrupt and Missing Wesley Smith (Thu Jan 24 2008 - 22:18:09 CST)
- Re: MSVC Projects Corrupt and Missing Axel Kohlmeyer (Thu Jan 24 2008 - 22:42:47 CST)
  - Re: MSVC Projects Corrupt and Missing Wesley Smith (Thu Jan 24 2008 - 22:53:58 CST)
- Re: MSVC Projects Corrupt and Missing John Stone (Thu Jan 24 2008 - 22:45:18 CST)
  - Re: MSVC Projects Corrupt and Missing Wesley Smith (Thu Jan 24 2008 - 22:56:03 CST)
Can VMD visualize forces? Yinglong Miao (Thu Jan 24 2008 - 17:16:14 CST)
- Re: Can VMD visualize forces? John Stone (Thu Jan 24 2008 - 18:01:20 CST)
  - Re: Can VMD visualize forces? Thomas C. Bishop (Fri Jan 25 2008 - 09:44:29 CST)
problems with a script Irene Newhouse (Thu Jan 24 2008 - 16:39:40 CST)
- Re: problems with a script John Stone (Fri Jan 25 2008 - 00:15:14 CST)
preserving atom index or hexadecimal residue numbers after writepdb Vlad Cojocaru (Thu Jan 24 2008 - 04:44:40 CST)
- Re: preserving atom index or hexadecimal residue numbers after writepdb John Stone (Fri Jan 25 2008 - 00:12:56 CST)
minimization command Sourmaidou, Damiani (Wed Jan 23 2008 - 12:35:49 CST)
proximity of residues Francesco Pietra (Wed Jan 23 2008 - 01:40:51 CST)
- Re: proximity of residues Axel Kohlmeyer (Wed Jan 23 2008 - 03:49:49 CST)
  - Re: proximity of residues L. Michel Espinoza-Fonseca (Wed Jan 23 2008 - 04:21:01 CST)
delatom "no segment..." Lucie Huynh (Tue Jan 22 2008 - 05:10:00 CST)
- Re: delatom "no segment..." Axel Kohlmeyer (Tue Jan 22 2008 - 05:49:32 CST)
- Question about autopsf Lucas Fernández Seivane (Tue Jan 22 2008 - 13:39:06 CST)
  - Re: Question about autopsf Peter Freddolino (Tue Jan 22 2008 - 14:26:25 CST)
    - Re: Question about autopsf Lucas Fernández Seivane (Tue Jan 22 2008 - 16:07:50 CST)
    - Re: Question about autopsf Peter Freddolino (Tue Jan 22 2008 - 20:00:40 CST)
Inconsistencies in NAMD simulations Chandra Ramananjara (Tue Jan 22 2008 - 02:49:53 CST)
local urea concentration L. Michel Espinoza-Fonseca (Mon Jan 21 2008 - 11:17:14 CST)
- Re: local urea concentration L. Michel Espinoza-Fonseca (Mon Jan 21 2008 - 12:05:32 CST)
SSE from the protein sequence Lu Lin (Mon Jan 21 2008 - 09:11:49 CST)
- Re: SSE from the protein sequence Axel Kohlmeyer (Mon Jan 21 2008 - 09:53:10 CST)
  - Re: SSE from the protein sequence Peter Freddolino (Mon Jan 21 2008 - 10:09:48 CST)
    - Re: SSE from the protein sequence L. Michel Espinoza-Fonseca (Mon Jan 21 2008 - 10:51:11 CST)
problem with sidechian representation gurpreet singh (Mon Jan 21 2008 - 00:02:37 CST)
- Re: problem with sidechian representation jrui_at_ci.uc.pt (Mon Jan 21 2008 - 04:28:00 CST)
VMD drawing Wesley Smith (Sun Jan 20 2008 - 15:51:06 CST)
- Re: VMD drawing John Stone (Sun Jan 20 2008 - 20:59:51 CST)
  - Re: VMD drawing Wesley Smith (Sun Jan 20 2008 - 21:08:27 CST)
Error in changing on screen options of VMD Monika Sharma (Fri Jan 18 2008 - 07:45:07 CST)
- Re: Error in changing on screen options of VMD John Stone (Sun Jan 20 2008 - 22:54:33 CST)
problem with time line plugin in VMD ABEL Stephane 175950 (Fri Jan 18 2008 - 03:36:30 CST)
- Re: problem with time line plugin in VMD John Stone (Sun Jan 20 2008 - 22:55:40 CST)
error in loading psf file generated from lammps data file. Dongsheng Zhang (Thu Jan 17 2008 - 16:23:27 CST)
- Re: error in loading psf file generated from lammps data file. John Stone (Sun Jan 20 2008 - 20:46:28 CST)
MSMS plugin for windows Lu Lin (Thu Jan 17 2008 - 08:35:55 CST)
- Re: MSMS plugin for windows L. Michel Espinoza-Fonseca (Thu Jan 17 2008 - 09:26:26 CST)
  - Re: MSMS plugin for windows Lu Lin (Thu Jan 17 2008 - 11:47:52 CST)
    - Re: MSMS plugin for windows John Stone (Thu Jan 17 2008 - 12:56:24 CST)
    - Re: MSMS plugin for windows Lu Lin (Fri Jan 18 2008 - 03:09:13 CST)
Could not locate 'dowser' (Program not found message box) Stanley, Yemin Shi (Thu Jan 17 2008 - 07:31:22 CST)
- Re: Could not locate 'dowser' (Program not found message box) John Stone (Thu Jan 17 2008 - 10:43:25 CST)
C NH1 C minimization error Sourmaidou, Damiani (Thu Jan 17 2008 - 06:43:18 CST)
RMSD with protein ligand Francesco Pietra (Thu Jan 17 2008 - 00:49:37 CST)
- Re: RMSD with protein ligand Luis Gracia (Thu Jan 17 2008 - 10:26:44 CST)
  - Re: RMSD with protein ligand Francesco Pietra (Thu Jan 17 2008 - 11:11:35 CST)
    - Re: RMSD with protein ligand Luis Gracia (Thu Jan 17 2008 - 14:45:04 CST)
visualizing a simple polymer chain via VMD Sergey Mkrtchyan (Wed Jan 16 2008 - 11:48:16 CST)
- Re: visualizing a simple polymer chain via VMD Axel Kohlmeyer (Wed Jan 16 2008 - 12:26:08 CST)
  - Re: visualizing a simple polymer chain via VMD Sergey Mkrtchyan (Wed Jan 16 2008 - 12:39:31 CST)
    - Re: visualizing a simple polymer chain via VMD Axel Kohlmeyer (Wed Jan 16 2008 - 12:58:17 CST)
    - Re: visualizing a simple polymer chain via VMD Sergey Mkrtchyan (Wed Jan 16 2008 - 13:53:09 CST)
  - Re: visualizing a simple polymer chain via VMD Sergey Mkrtchyan (Thu Jan 17 2008 - 16:31:07 CST)
- Re: visualizing a simple polymer chain via VMD Olaf Lenz (Thu Jan 17 2008 - 01:24:34 CST)
  - Re: visualizing a simple polymer chain via VMD Sergey Mkrtchyan (Thu Jan 17 2008 - 13:25:29 CST)
replace molecule? Lucie Huynh (Wed Jan 16 2008 - 03:09:39 CST)
- Re: replace molecule? Axel Kohlmeyer (Wed Jan 16 2008 - 11:02:32 CST)
problem rendering NewCartoon with tachyon MW Van der Kamp, School of Chemistry (Tue Jan 15 2008 - 03:03:27 CST)
- Re: problem rendering NewCartoon with tachyon John Stone (Tue Jan 15 2008 - 12:44:31 CST)
  - Re: problem rendering NewCartoon with tachyon MW Van der Kamp, School of Chemistry (Wed Jan 16 2008 - 03:09:04 CST)
How to calculate end-to-end distance in VMD? Lili Peng (Mon Jan 14 2008 - 16:37:33 CST)
- Re: How to calculate end-to-end distance in VMD? Peter Freddolino (Tue Jan 15 2008 - 10:30:10 CST)
how to load a molecule in pdb format and save in mol2 format in batch mode Sridhar Acharya (Mon Jan 14 2008 - 01:32:33 CST)
- Re: how to load a molecule in pdb format and save in mol2 format in batch mode Axel Kohlmeyer (Mon Jan 14 2008 - 03:39:58 CST)
Video Card for VMD, 2D or 3D Stanley, Yemin Shi (Fri Jan 11 2008 - 18:30:59 CST)
- Re: Video Card for VMD, 2D or 3D John Stone (Sat Jan 12 2008 - 00:11:53 CST)
Export VMD graphics to POV-Ray Igor Schapiro (Fri Jan 11 2008 - 08:22:13 CST)
- Re: Export VMD graphics to POV-Ray Axel Kohlmeyer (Fri Jan 11 2008 - 11:59:04 CST)
measure contacts script L. Michel Espinoza-Fonseca (Fri Jan 11 2008 - 05:57:10 CST)
- Re: measure contacts script John Stone (Sat Jan 12 2008 - 00:23:09 CST)
POV-Ray 3.6; VMD Movie Maker; Continuous Render (UNCLASSIFIED) Paul, Kristian (Cont, ARL/WMRD) (Thu Jan 10 2008 - 12:16:16 CST)
- Re: POV-Ray 3.6; VMD Movie Maker; Continuous Render (UNCLASSIFIED) Igor Schapiro (Fri Jan 11 2008 - 07:23:57 CST)
PBC Nazanin Samadi (Thu Jan 10 2008 - 07:19:20 CST)
- Re: PBC Olaf Lenz (Mon Jan 14 2008 - 03:51:10 CST)
problem with superimposing two proteins aneesh cna (Thu Jan 10 2008 - 05:33:21 CST)
- Re: problem with superimposing two proteins Elijah Roberts (Thu Jan 10 2008 - 17:09:37 CST)
- Re: problem with superimposing two proteins Dmitry Lupyan (Fri Jan 11 2008 - 15:26:38 CST)
Is there any way to diagonalize a 3x3 matrix in VMD,.......... Sergio (Wed Jan 09 2008 - 13:18:05 CST)
- Re: Is there any way to diagonalize a 3x3 matrix in VMD,.......... Axel Kohlmeyer (Wed Jan 09 2008 - 14:54:33 CST)
Re: Link atoms snoze pa (Wed Jan 09 2008 - 10:23:31 CST)
- Re: Link atoms John Stone (Wed Jan 09 2008 - 22:51:46 CST)
  - Re: Link atoms snoze pa (Thu Jan 10 2008 - 10:45:28 CST)
connectivity problem rams rams (Wed Jan 09 2008 - 08:57:48 CST)
- Re: connectivity problem Axel Kohlmeyer (Wed Jan 09 2008 - 10:09:35 CST)
Link atoms snoze pa (Tue Jan 08 2008 - 18:10:11 CST)
NAMDEnergy problem Lixia Jin Day (Tue Jan 08 2008 - 14:30:29 CST)
- Re: NAMDEnergy problem Peter Freddolino (Tue Jan 08 2008 - 14:52:46 CST)
How to choose part of the volume data for isosurface visualization? Yinglong Miao (Tue Jan 08 2008 - 10:41:02 CST)
- Re: How to choose part of the volume data for isosurface visualization? Axel Kohlmeyer (Tue Jan 08 2008 - 11:37:29 CST)
VMD intallation Satyan Sharma (Mon Jan 07 2008 - 12:52:39 CST)
- Re: VMD intallation John Stone (Mon Jan 07 2008 - 15:33:25 CST)
Re: X_ChangeProperty: BadValue (integer parameter out of range for operation) 0x40 Brian Bennion (Mon Jan 07 2008 - 10:58:36 CST)
- Re: X_ChangeProperty: BadValue (integer parameter out of range for operation) 0x40 John Stone (Tue Jan 08 2008 - 14:09:56 CST)
X_ChangeProperty: BadValue (integer parameter out of range for operation) 0x40 Guanglei Cui (Mon Jan 07 2008 - 08:35:14 CST)
- Re: X_ChangeProperty: BadValue (integer parameter out of range for operation) 0x40 John Stone (Tue Jan 08 2008 - 14:10:41 CST)
  - Re: X_ChangeProperty: BadValue (integer parameter out of range for operation) 0x40 Guanglei Cui (Tue Jan 08 2008 - 14:40:43 CST)
Phantom Omni Haptic Device Martin Held (Sun Jan 06 2008 - 15:00:47 CST)
- Re: Phantom Omni Haptic Device John Stone (Mon Jan 07 2008 - 01:49:31 CST)
Cluster analysis Francesco Pietra (Sun Jan 06 2008 - 04:27:19 CST)
- Re: Cluster analysis John Stone (Mon Jan 07 2008 - 01:59:40 CST)
  - Re: Cluster analysis Francesco Pietra (Mon Jan 07 2008 - 04:35:30 CST)
VMD-L membership pruning, more anti-spam measures.. John Stone (Sat Jan 05 2008 - 00:26:40 CST)
vmd error message snoze pa (Fri Jan 04 2008 - 12:59:00 CST)
- Re: vmd error message John Stone (Fri Jan 04 2008 - 13:01:37 CST)
VMD-L post spam blocking, rescued messages from the last 30 days... John Stone (Fri Jan 04 2008 - 12:33:38 CST)
- (UNCLASSIFIED) Paul, Kristian (Cont, ARL/WMRD) (Fri Jan 04 2008 - 13:22:28 CST)
  - Re: (UNCLASSIFIED) John Stone (Fri Jan 04 2008 - 13:29:49 CST)
VMD movie from XYZ coordinate if file has two type of atoms Anil Kumar (Sun Dec 09 2007 - 22:12:58 CST)
- Re: VMD movie from XYZ coordinate if file has two type of atoms John Stone (Fri Jan 04 2008 - 12:38:08 CST)
resolving side chain clashes jayant_jacques (Thu Dec 13 2007 - 14:05:10 CST)
namd-l: Creating topology for carbon nanotube / any new structure prateeksha s (Tue Dec 18 2007 - 23:10:42 CST)
VMD on Linux Suse SCIPIONI Roberto (Wed Dec 19 2007 - 01:21:21 CST)
- VMD on Linux Suse SCIPIONI Roberto (Wed Dec 19 2007 - 01:26:44 CST)
  - Re: VMD on Linux Suse John Stone (Wed Dec 19 2007 - 01:34:42 CST)
- Re: VMD on Linux Suse John Stone (Fri Jan 04 2008 - 12:35:27 CST)
replication of bilayer Chanda.Jnanojjal_at_edam.uhp-nancy.fr (Wed Dec 26 2007 - 04:08:00 CST)
- Re: replication of bilayer John Stone (Fri Jan 04 2008 - 12:42:10 CST)
- RE: replication of bilayer Richard Swenson (Fri Jan 04 2008 - 17:07:16 CST)
installation on suse linux 10.3 s lal badshah (Wed Dec 26 2007 - 23:28:27 CST)
- Re: installation on suse linux 10.3 John Stone (Fri Jan 04 2008 - 12:39:02 CST)
Hydrogens in vmd snoze pa (Thu Jan 03 2008 - 14:08:31 CST)
- Re: Hydrogens in vmd Peter Freddolino (Thu Jan 03 2008 - 14:25:05 CST)
  - Re: Hydrogens in vmd L. Michel Espinoza-Fonseca (Thu Jan 03 2008 - 15:17:54 CST)
- Re: Hydrogens in vmd John Stone (Thu Jan 03 2008 - 14:26:16 CST)
  - Re: Hydrogens in vmd snoze pa (Thu Jan 03 2008 - 15:30:40 CST)
Question about Gromacs box size in VMD..... Sergio Garay (Thu Jan 03 2008 - 07:27:37 CST)
- Re: Question about Gromacs box size in VMD..... Axel Kohlmeyer (Thu Jan 03 2008 - 08:24:07 CST)
- Re: Question about Gromacs box size in VMD..... Olaf Lenz (Thu Jan 03 2008 - 08:38:47 CST)
freevr tool transformation Ahmed Nawar (Thu Jan 03 2008 - 00:28:31 CST)
- Re: freevr tool transformation John Stone (Thu Jan 03 2008 - 01:12:44 CST)
select atoms between molecules Sampo Karkola (Wed Jan 02 2008 - 06:13:39 CST)
- Re: select atoms between molecules Axel Kohlmeyer (Wed Jan 02 2008 - 11:46:13 CST)
  - Re: select atoms between molecules Karol Kaszuba (Wed Jan 02 2008 - 15:47:34 CST)
- Re: select atoms between molecules Karol Kaszuba (Wed Jan 02 2008 - 13:10:04 CST)
Selecting water molecules within 5 ang in a trajectory( generated by amber). naga raju (Wed Dec 26 2007 - 01:01:50 CST)
- Re: Selecting water molecules within 5 ang in a trajectory( generated by amber). Thomas Evangelidis (Wed Dec 26 2007 - 09:49:31 CST)
  - Re: Selecting water molecules within 5 ang in a trajectory( generated by amber). Axel Kohlmeyer (Wed Dec 26 2007 - 14:12:05 CST)
  - Re: Selecting water molecules within 5 ang in a trajectory( generated by amber). naga raju (Sat Dec 29 2007 - 00:02:12 CST)
saltbr plugging problem: too many open files Amaury Pupo Meriño (Fri Dec 21 2007 - 09:31:07 CST)
- Re: saltbr plugging problem: too many open files Leonardo Trabuco (Fri Dec 21 2007 - 14:35:16 CST)
Viewing molden grid files Ignacio Fernández Galván (Fri Dec 21 2007 - 03:14:46 CST)
- Re: Viewing molden grid files John Stone (Fri Jan 04 2008 - 13:06:22 CST)
parameter tool tutorial snoze pa (Thu Dec 20 2007 - 17:15:15 CST)
- Re: parameter tool tutorial Jan Saam (Thu Dec 20 2007 - 17:50:00 CST)
vmd QMtool snoze pa (Thu Dec 20 2007 - 16:53:34 CST)
- Re: vmd QMtool Jan Saam (Thu Dec 20 2007 - 17:18:10 CST)
measure hbonds Narender Singh Maan (Mon Dec 17 2007 - 14:52:39 CST)
- Re: measure hbonds poker_at_physics.usyd.edu.au (Mon Dec 17 2007 - 19:03:50 CST)
Increasing MAXATOMBONDS? Oliver Beckstein (Mon Dec 17 2007 - 13:37:42 CST)
- Re: Increasing MAXATOMBONDS? John Stone (Tue Dec 18 2007 - 12:56:55 CST)
  - Re: Increasing MAXATOMBONDS? Oliver Beckstein (Tue Dec 18 2007 - 16:05:02 CST)
OpenSuSE 10.3: ppmtompeg and MovieMaker plugin Dow Hurst DPHURST (Fri Dec 14 2007 - 12:14:46 CST)
display bonds Dongsheng Zhang (Fri Dec 14 2007 - 08:52:24 CST)
- Re: display bonds John Stone (Wed Dec 19 2007 - 14:02:49 CST)
add Mg2+ Lixia Jin Day (Thu Dec 13 2007 - 11:19:06 CST)
- Re: add Mg2+ John Stone (Wed Dec 19 2007 - 14:09:30 CST)
  - Re: add Mg2+ Lixia Jin Day (Wed Dec 19 2007 - 15:27:04 CST)
calculation of alpha helical content L. Michel Espinoza-Fonseca (Tue Dec 11 2007 - 10:29:24 CST)
- Re: calculation of alpha helical content Peter Freddolino (Tue Dec 11 2007 - 10:39:05 CST)
  - Re: calculation of alpha helical content L. Michel Espinoza-Fonseca (Tue Dec 11 2007 - 11:18:14 CST)
    - Re: calculation of alpha helical content Peter Freddolino (Tue Dec 11 2007 - 12:05:04 CST)
VMD movie from XYZ coordinate if file has two type of atoms] Anil Kumar (Tue Dec 11 2007 - 04:20:07 CST)
- Re: VMD movie from XYZ coordinate if file has two type of atoms] Eduard Schreiner (Tue Dec 11 2007 - 07:49:44 CST)
  - Re: VMD movie from XYZ coordinate if file has two type of atoms] Anil Kumar (Tue Dec 11 2007 - 21:00:58 CST)
    - Re: VMD movie from XYZ coordinate if file has two type of atoms] Axel Kohlmeyer (Tue Dec 11 2007 - 21:50:14 CST)
    - Re: VMD movie from XYZ coordinate if file has two type of atoms] Anil Kumar (Wed Dec 12 2007 - 01:48:06 CST)
VMD movie from XYZ coordinate if file has two type of atoms Anil Kumar (Mon Dec 10 2007 - 22:43:49 CST)
- Re: VMD movie from XYZ coordinate if file has two type of atoms Eduard Schreiner (Tue Dec 11 2007 - 02:36:07 CST)
Re: helical construction Harish Lnu (Mon Dec 10 2007 - 13:16:39 CST)
- Re: helical construction Harish Lnu (Mon Dec 10 2007 - 15:31:31 CST)
helical construction Harish Lnu (Mon Dec 10 2007 - 10:58:16 CST)
- Re: helical construction Sanghyun Park (Mon Dec 10 2007 - 13:05:40 CST)
- Re: helical construction Axel Kohlmeyer (Mon Dec 10 2007 - 15:26:30 CST)
delatom usage - no such segment? Stephen M. Dutz (Sun Dec 09 2007 - 19:05:37 CST)
- Re: delatom usage - no such segment? Jim Phillips (Mon Dec 17 2007 - 11:50:12 CST)
problem with the new cartoon representation mode OZGE ENGIN (Sat Dec 08 2007 - 13:42:12 CST)
- Re: problem with the new cartoon representation mode Axel Kohlmeyer (Sat Dec 08 2007 - 14:37:00 CST)
  - Re: Re: problem with the new cartoon representation mode OZGE ENGIN (Sat Dec 08 2007 - 15:36:37 CST)
    - Re: Re: problem with the new cartoon representation mode Axel Kohlmeyer (Sat Dec 08 2007 - 16:08:22 CST)
    - Re: Re: Re: problem with the new cartoon representation mode OZGE ENGIN (Sat Dec 08 2007 - 16:53:51 CST)
how to transform the coordinate of the atom using vmd Shulin Zhuang (Fri Dec 07 2007 - 14:01:51 CST)
- Re: how to transform the coordinate of the atom using vmd John Stone (Fri Dec 07 2007 - 15:02:21 CST)
Finding the length of multiple small molecules Manali Mehendale (Fri Dec 07 2007 - 13:15:59 CST)
- Re: Finding the length of multiple small molecules Axel Kohlmeyer (Fri Dec 07 2007 - 14:19:47 CST)
  - Re: Finding the length of multiple small molecules Manali Mehendale (Sat Dec 08 2007 - 15:09:47 CST)
    - Re: Finding the length of multiple small molecules Axel Kohlmeyer (Sat Dec 08 2007 - 16:03:07 CST)
drawing trajectory of a molecule L. Michel Espinoza-Fonseca (Fri Dec 07 2007 - 08:30:04 CST)
- Re: drawing trajectory of a molecule Axel Kohlmeyer (Fri Dec 07 2007 - 09:20:28 CST)
  - Re: drawing trajectory of a molecule L. Michel Espinoza-Fonseca (Fri Dec 07 2007 - 09:29:56 CST)
  - Re: drawing trajectory of a molecule L. Michel Espinoza-Fonseca (Fri Dec 07 2007 - 09:40:51 CST)
Making movies in VMD Lili Peng (Wed Dec 05 2007 - 18:32:44 CST)
- Re: Making movies in VMD Axel Kohlmeyer (Wed Dec 05 2007 - 19:16:40 CST)
  - Re: Making movies in VMD Lili Peng (Wed Dec 05 2007 - 19:27:32 CST)
    - Re: Making movies in VMD Axel Kohlmeyer (Wed Dec 05 2007 - 19:45:54 CST)
    - Re: Making movies in VMD Lili Peng (Wed Dec 05 2007 - 19:59:48 CST)
- Re: Making movies in VMD John Stone (Thu Dec 06 2007 - 12:34:37 CST)
  - RE: Making movies in VMD (UNCLASSIFIED) Balu, Radhakrishnan (Cont, ARL/WMRD) (Thu Dec 06 2007 - 15:28:03 CST)
    - Re: Making movies in VMD (UNCLASSIFIED) John Stone (Thu Dec 06 2007 - 16:11:00 CST)
Rainbow color scheme for VolumeSlice / Volume Xavier Cartoixa Soler (Tue Dec 04 2007 - 05:41:36 CST)
- Re: Rainbow color scheme for VolumeSlice / Volume John Stone (Tue Dec 04 2007 - 18:03:05 CST)
Fwd: Re: Paratool in VMD Syed Tarique Moin (Tue Dec 04 2007 - 05:18:08 CST)
FreeVR wand Ahmed Nawar (Tue Dec 04 2007 - 03:42:13 CST)
- Re: FreeVR wand John Stone (Tue Dec 04 2007 - 18:00:55 CST)
applying forces on a protein in VMD Peter Schellenberg (Tue Dec 04 2007 - 02:05:58 CST)
- Re: applying forces on a protein in VMD John Stone (Wed Dec 05 2007 - 00:58:14 CST)
Membrane POPC Francesco Pietra (Sat Dec 01 2007 - 17:07:50 CST)
- Render Snapshot from the Tcl console (jpg gif format) Arneh Babakhani (Sun Dec 02 2007 - 15:02:52 CST)
  - Re: Render Snapshot from the Tcl console (jpg gif format) L. Michel Espinoza-Fonseca (Sun Dec 02 2007 - 17:58:31 CST)
  - Re: Render Snapshot from the Tcl console (jpg gif format) John Stone (Sun Dec 02 2007 - 19:53:20 CST)
    - Re: Render Snapshot from the Tcl console (jpg gif format) Arneh Babakhani (Sun Dec 02 2007 - 20:45:38 CST)
Multiseq Wendy González (Fri Nov 30 2007 - 15:57:18 CST)
- Re: Multiseq John Stone (Sun Dec 02 2007 - 22:57:53 CST)
  - QM_plugin_force_constants Karol Kaszuba (Mon Dec 03 2007 - 06:41:24 CST)
  - Re: Multiseq Wendy González (Mon Dec 03 2007 - 07:11:24 CST)
psfgen delatom usage Stephen M. Dutz (Fri Nov 30 2007 - 15:36:18 CST)
Timeline viewer Neelanjana Sengupta (Fri Nov 30 2007 - 09:50:33 CST)
- Re: Timeline viewer Axel Kohlmeyer (Fri Nov 30 2007 - 15:31:56 CST)
  - Re: Timeline viewer Neelanjana Sengupta (Fri Nov 30 2007 - 19:29:49 CST)
How to display Chain name in Labels TRINH Minh Hieu (Fri Nov 30 2007 - 07:33:57 CST)
- Re: How to display Chain name in Labels John Stone (Thu Dec 06 2007 - 23:53:32 CST)
Command to change background to gradient TRINH Minh hieu (Fri Nov 30 2007 - 04:55:27 CST)
- Re: Command to change background to gradient Axel Kohlmeyer (Fri Nov 30 2007 - 06:15:44 CST)
SpaceNavigator Carsten Olbrich (Thu Nov 29 2007 - 11:23:01 CST)
- Re: SpaceNavigator John Stone (Thu Nov 29 2007 - 12:16:55 CST)
  - Re: SpaceNavigator Carsten Olbrich (Fri Nov 30 2007 - 10:16:46 CST)
- Re: SpaceNavigator John Stone (Wed Jun 11 2008 - 02:53:39 CDT)
Water within the minmax of protein Pavan Ghatty (Thu Nov 29 2007 - 09:17:51 CST)
- Re: Water within the minmax of protein John Stone (Thu Nov 29 2007 - 10:30:54 CST)
  - Re: Water within the minmax of protein Thomas Evangelidis (Thu Nov 29 2007 - 18:50:42 CST)
    - Re: Water within the minmax of protein Pavan Ghatty (Thu Nov 29 2007 - 21:08:06 CST)
    - Re: Water within the minmax of protein Thomas Evangelidis (Fri Nov 30 2007 - 09:14:11 CST)
problem with saving changed coordinates in a new state TaoJin (Wed Nov 28 2007 - 23:14:11 CST)
- Re: problem with saving changed coordinates in a new state Eduard Schreiner (Thu Nov 29 2007 - 02:24:56 CST)
Intersurf and interface residues Vincent Wolowski (Tue Nov 27 2007 - 13:34:40 CST)
- Re: Intersurf and interface residues John Stone (Tue Nov 27 2007 - 13:53:24 CST)
  - Re: Intersurf and interface residues Vincent Wolowski (Thu Nov 29 2007 - 03:30:37 CST)
    - Re: Intersurf and interface residues Axel Kohlmeyer (Thu Nov 29 2007 - 04:08:08 CST)
(UNCLASSIFIED) Balu, Radhakrishnan (Cont, ARL/WMRD) (Tue Nov 27 2007 - 09:18:18 CST)
gaussinan_log_file_error_can't use empty string as operand of "/" Karol Kaszuba (Tue Nov 27 2007 - 03:28:04 CST)
Paratools Syed Tarique Moin (Tue Nov 27 2007 - 03:06:27 CST)
(no subject) Syed Tarique Moin (Mon Nov 26 2007 - 06:25:08 CST)
difference for solvating a protein in long box suing or not using Molecule Dimensions Shulin Zhuang (Sun Nov 25 2007 - 16:43:40 CST)
Delete overlapping residues Francesco Pietra (Sat Nov 24 2007 - 10:50:32 CST)
- Re: Delete overlapping residues Axel Kohlmeyer (Sat Nov 24 2007 - 17:30:22 CST)
Hydrophobicity plots in VMD aneesh cna (Sat Nov 24 2007 - 00:33:38 CST)
- Re: Hydrophobicity plots in VMD Peter Freddolino (Sat Nov 24 2007 - 08:36:20 CST)
  - Re: Hydrophobicity plots in VMD aneesh cna (Sat Nov 24 2007 - 22:50:51 CST)
- Re: Hydrophobicity plots in VMD Avell Diroll (Tue Nov 27 2007 - 03:22:21 CST)
cave Ahmed Nawar (Thu Nov 22 2007 - 06:09:24 CST)
- Re: cave John Stone (Thu Nov 22 2007 - 10:21:30 CST)
  - RE: cave Ahmed Nawar (Sun Nov 25 2007 - 09:06:37 CST)
solvate crashes Irene Newhouse (Thu Nov 22 2007 - 04:02:33 CST)
- Re: solvate crashes L. Michel Espinoza-Fonseca (Thu Nov 22 2007 - 05:45:12 CST)
  - RE: solvate crashes Irene Newhouse (Thu Nov 22 2007 - 14:25:46 CST)
problem with loading trajectories in timline plugin aneesh cna (Thu Nov 22 2007 - 00:24:00 CST)
- Re: problem with loading trajectories in timline plugin John Stone (Thu Nov 22 2007 - 00:35:09 CST)
  - Re: problem with loading trajectories in timline plugin Rogan Carr (Sun Nov 25 2007 - 16:01:54 CST)
Re: analysing big trajectories (fwd) John Stone (Tue Nov 20 2007 - 17:30:59 CST)
- Re: analysing big trajectories (fwd) L. Michel Espinoza-Fonseca (Tue Nov 20 2007 - 18:03:25 CST)
  - Re: analysing big trajectories (fwd) John Stone (Tue Nov 20 2007 - 18:32:23 CST)
    - Re: analysing big trajectories (fwd) L. Michel Espinoza-Fonseca (Tue Nov 20 2007 - 18:39:03 CST)
    - Re: analysing big trajectories (fwd) Oliver Beckstein (Wed Nov 21 2007 - 19:05:14 CST)
Trying to get VMD to run locally while logged into a remote machine Daniel Beaman (Tue Nov 20 2007 - 16:04:57 CST)
- Re: Trying to get VMD to run locally while logged into a remote machine John Stone (Tue Nov 20 2007 - 17:24:36 CST)
- Re: Trying to get VMD to run locally while logged into a remote machine Axel Kohlmeyer (Wed Nov 21 2007 - 16:35:50 CST)
  - Re: Trying to get VMD to run locally while logged into a remote machine Daniel Beaman (Mon Nov 26 2007 - 17:27:48 CST)
analysing big trajectories Oliver Beckstein (Tue Nov 20 2007 - 14:28:45 CST)
- Re: analysing big trajectories John Stone (Tue Nov 20 2007 - 14:41:35 CST)
  - Re: analysing big trajectories John Stone (Tue Nov 20 2007 - 16:26:34 CST)
  - Re: analysing big trajectories Thomas Evangelidis (Tue Nov 20 2007 - 18:09:26 CST)
    - Re: analysing big trajectories Oliver Beckstein (Wed Nov 21 2007 - 19:13:32 CST)
Potential map animation, help! Cesar Millan (Tue Nov 20 2007 - 12:40:59 CST)
- Re: Potential map animation, help! John Stone (Tue Nov 20 2007 - 13:05:25 CST)
Calculate density Jianhui Tian (Mon Nov 19 2007 - 15:21:20 CST)
- Re: Calculate density Axel Kohlmeyer (Wed Nov 21 2007 - 14:20:15 CST)
vmd 1.8.6 doesn't run on Fedora Core 7 EMT64 Pascale Geysermans (Fri Nov 16 2007 - 09:37:50 CST)
- Re: vmd 1.8.6 doesn't run on Fedora Core 7 EMT64 Axel Kohlmeyer (Fri Nov 16 2007 - 23:56:37 CST)
re: installed vmd_LINUXIA64 but recieve error : /usr/local/vmd/vmd_LINUX: command not found James.Beavis_at_csiro.au (Wed Nov 14 2007 - 19:28:02 CST)
- Re: installed vmd_LINUXIA64 but recieve error : /usr/local/vmd/vmd_LINUX: command not found Axel Kohlmeyer (Wed Nov 14 2007 - 20:34:06 CST)
combine.tcl membrane plugin Francesco Pietra (Wed Nov 14 2007 - 12:05:12 CST)
- Re: combine.tcl membrane plugin Axel Kohlmeyer (Wed Nov 14 2007 - 20:40:06 CST)
  - Re: combine.tcl membrane plugin Francesco Pietra (Thu Nov 15 2007 - 03:15:33 CST)
OpenGL Display Christopher Stiles (Tue Nov 13 2007 - 23:33:32 CST)
- Re: OpenGL Display Axel Kohlmeyer (Wed Nov 14 2007 - 04:09:40 CST)
  - RE: OpenGL Display Christopher Stiles (Wed Nov 14 2007 - 07:14:17 CST)
    - RE: OpenGL Display Axel Kohlmeyer (Wed Nov 14 2007 - 23:53:07 CST)
installed vmd_LINUXIA64 but recieve error : /usr/local/vmd/vmd_LINUX: command not found James.Beavis_at_csiro.au (Tue Nov 13 2007 - 21:47:43 CST)
- Re: installed vmd_LINUXIA64 but recieve error : /usr/local/vmd/vmd_LINUX: command not found Axel Kohlmeyer (Tue Nov 13 2007 - 23:50:04 CST)
Dynamic bonds and H2 molecules. David Schall (Tue Nov 13 2007 - 11:17:30 CST)
- Re: Dynamic bonds and H2 molecules. Axel Kohlmeyer (Wed Nov 14 2007 - 04:07:00 CST)
stride binaries for windows XP OS aneesh cna (Mon Nov 12 2007 - 23:21:34 CST)
- Re: stride binaries for windows XP OS Axel Kohlmeyer (Tue Nov 13 2007 - 02:27:33 CST)
- Re: stride binaries for windows XP OS John Stone (Tue Nov 13 2007 - 10:18:59 CST)
problem with colouring the surface with electroststic potential aneesh cna (Mon Nov 12 2007 - 23:15:25 CST)
- Re: problem with colouring the surface with electroststic potential Axel Kohlmeyer (Tue Nov 13 2007 - 02:15:54 CST)
  - Re: problem with colouring the surface with electroststic potential John Stone (Wed Nov 14 2007 - 11:19:27 CST)
- Re: problem with colouring the surface with electroststic potential John Stone (Tue Nov 13 2007 - 10:09:17 CST)
problems with atomselect: missing selection Philipp Schön (Mon Nov 12 2007 - 05:23:32 CST)
- Re: problems with atomselect: missing selection Axel Kohlmeyer (Mon Nov 12 2007 - 06:38:01 CST)
POPS topology file lucie huynh (Mon Nov 12 2007 - 03:55:04 CST)
Generatin PSF for alkanes Santanu Chatterjee (Sat Nov 10 2007 - 22:38:55 CST)
- Re: Generatin PSF for alkanes Axel Kohlmeyer (Sun Nov 11 2007 - 00:54:50 CST)
- Re: Generatin PSF for alkanes Peter Freddolino (Sun Nov 11 2007 - 11:02:52 CST)
merging two pdb files Dibyadeep Paul (Thu Nov 08 2007 - 06:06:19 CST)
- Re: merging two pdb files Axel Kohlmeyer (Thu Nov 08 2007 - 06:39:05 CST)
  - Re: merging two pdb files Dibyadeep Paul (Thu Nov 08 2007 - 08:24:18 CST)
    - Re: merging two pdb files Axel Kohlmeyer (Thu Nov 08 2007 - 21:55:17 CST)
    - RE: merging two pdb files Richard Swenson (Fri Nov 09 2007 - 09:20:55 CST)
  - Re: merging two pdb files Francesco Pietra (Thu Nov 08 2007 - 11:48:23 CST)
    - Re: merging two pdb files Axel Kohlmeyer (Thu Nov 08 2007 - 21:50:10 CST)
molfile reader plugin woes Olaf Lenz (Thu Nov 08 2007 - 02:31:42 CST)
- Re: molfile reader plugin woes John Stone (Thu Nov 08 2007 - 07:24:35 CST)
- Re: molfile reader plugin woes Axel Kohlmeyer (Thu Nov 08 2007 - 06:44:28 CST)
VMD/NAMD at SC2007 John Stone (Wed Nov 07 2007 - 21:41:57 CST)
question about ionization Anatoliy (Wed Nov 07 2007 - 12:10:12 CST)
- Re: question about ionization John Stone (Wed Nov 07 2007 - 20:17:54 CST)
Out of office until Nov. 16 John Stone (Wed Nov 07 2007 - 11:57:55 CST)
merge pbd psf files (update) Alessio Alexiadis (Wed Nov 07 2007 - 07:47:48 CST)
combine together two PBD/PSF files Alessio Alexiadis (Wed Nov 07 2007 - 07:38:42 CST)
- Re: combine together two PBD/PSF files Dr. Luis Rosales Leon (Wed Nov 07 2007 - 18:50:50 CST)
vmd command delay jiwu liu (Mon Nov 05 2007 - 16:55:50 CST)
- Re: vmd command delay John Stone (Mon Nov 05 2007 - 17:31:24 CST)
  - Re: vmd command delay jiwu liu (Tue Nov 06 2007 - 20:02:27 CST)
    - Re: vmd command delay John Stone (Wed Nov 21 2007 - 13:26:48 CST)
    - Re: vmd command delay Oliver Beckstein (Wed Nov 21 2007 - 20:27:41 CST)
Download vmd for 64-bit Intel Itanium FyD (Mon Nov 05 2007 - 15:00:36 CST)
- Re: Download vmd for 64-bit Intel Itanium John Stone (Mon Nov 05 2007 - 16:55:20 CST)
question about water sphere script Anatoliy (Mon Nov 05 2007 - 11:21:54 CST)
Alignment Zhaochuan Shen (Thu Nov 01 2007 - 16:52:12 CDT)
- Re: Alignment John Stone (Sat Nov 03 2007 - 23:30:57 CDT)
  - Re: Alignment John Stone (Sun Nov 04 2007 - 13:53:06 CST)
    - changing dihedral angles in molefacture Samuel Coulbourn Flores (Mon Nov 05 2007 - 02:42:48 CST)
    - Re: changing dihedral angles in molefacture Peter Freddolino (Mon Nov 05 2007 - 07:11:28 CST)
  - Re: Alignment Zhaochuan Shen (Mon Nov 05 2007 - 11:41:52 CST)
problem with protein RMSD calculation due to incomplete wrapping of both peptide chains Maria Bagonis (Thu Nov 01 2007 - 16:11:04 CDT)
- Re: problem with protein RMSD calculation due to incomplete wrapping of both peptide chains John Stone (Thu Nov 01 2007 - 17:39:14 CDT)
  - Re: problem with protein RMSD calculation due to incomplete wrapping of both peptide chains Maria Bagonis (Mon Nov 05 2007 - 18:23:08 CST)
cloning a molecule dimka (Thu Nov 01 2007 - 13:46:44 CDT)
- Re: cloning a molecule John Stone (Fri Nov 02 2007 - 14:22:26 CDT)
  - Re: cloning a molecule Axel Kohlmeyer (Mon Nov 05 2007 - 00:35:27 CST)
  - Re: cloning a molecule Thomas C. Bishop (Mon Nov 05 2007 - 21:27:01 CST)
TMD in NAMD: cannot reach target lily jin (Thu Nov 01 2007 - 13:13:23 CDT)
vmd ubuntu crash jacopo.sgrignani_at_unifi.it (Thu Nov 01 2007 - 11:45:04 CDT)
- Re: vmd ubuntu crash John Stone (Thu Nov 01 2007 - 12:32:57 CDT)
aligning protein based on one helix of protein maria goranovic (Wed Oct 31 2007 - 08:48:29 CDT)
- Re: aligning protein based on one helix of protein maria goranovic (Wed Oct 31 2007 - 13:14:12 CDT)
  - Re: aligning protein based on one helix of protein John Stone (Wed Oct 31 2007 - 17:25:50 CDT)
    - easy way to adjust dihedral angles? Samuel Flores (Thu Nov 01 2007 - 13:58:13 CDT)
    - Re: easy way to adjust dihedral angles? Peter Freddolino (Fri Nov 02 2007 - 14:29:14 CDT)
CMYK Adrian Roitberg (Tue Oct 30 2007 - 16:08:37 CDT)
- Re: CMYK John Stone (Tue Oct 30 2007 - 17:49:30 CDT)
  - Re: CMYK Ignacio Fernández Galván (Wed Oct 31 2007 - 06:28:02 CDT)
Re: namd-l: NAMDEnergy lily jin (Tue Oct 30 2007 - 12:34:43 CDT)
NAMDEnergy lily jin (Tue Oct 30 2007 - 12:00:57 CDT)
- Re: namd-l: NAMDEnergy Peter Freddolino (Tue Oct 30 2007 - 12:20:16 CDT)
Re: rna topology and parameters for rna Per Jr. Greisen (Sun Oct 28 2007 - 04:56:03 CDT)
- Re: rna topology and parameters for rna Samuel Flores (Mon Oct 29 2007 - 01:14:01 CDT)
  - Re: rna topology and parameters for rna Per Jr. Greisen (Mon Oct 29 2007 - 01:55:01 CDT)
  - RE: rna topology and parameters for rna Brittany Morgan (Mon Oct 29 2007 - 08:20:16 CDT)
how to display dcd file written with catdcd using an index file Irene Newhouse (Fri Oct 26 2007 - 14:08:44 CDT)
- Re: how to display dcd file written with catdcd using an index file John Stone (Fri Oct 26 2007 - 15:50:55 CDT)
  - Force field atom types FyD (Sun Oct 28 2007 - 05:23:11 CDT)
    - Re: Force field atom types Peter Freddolino (Sun Oct 28 2007 - 10:25:28 CDT)
  - RE: how to display dcd file written with catdcd using an index file Irene Newhouse (Tue Oct 30 2007 - 13:30:26 CDT)
periodic box manipulation Vlad Cojocaru (Fri Oct 26 2007 - 07:39:58 CDT)
- Re: periodic box manipulation (solution) Vlad Cojocaru (Fri Oct 26 2007 - 09:04:03 CDT)
installation of APBS plug-in in VMD 1.8.6 Lhee, SangMoon (Thu Oct 25 2007 - 21:14:47 CDT)
- Re: installation of APBS plug-in in VMD 1.8.6 John Stone (Thu Oct 25 2007 - 21:29:12 CDT)
Writing in NAMD binary format in VMD from TCl/Tk console? poker_at_physics.usyd.edu.au (Tue Oct 23 2007 - 20:33:05 CDT)
- Re: Writing in NAMD binary format in VMD from TCl/Tk console? John Stone (Wed Oct 24 2007 - 17:24:52 CDT)
superposition of two complex according to the same inhibitor Emilia Wu (Mon Oct 22 2007 - 21:42:59 CDT)
- Re: superposition of two complex according to the same inhibitor Eduard Schreiner (Tue Oct 23 2007 - 01:05:26 CDT)
FW: VMD & OpenGL GLX Extension Meij, Henk (Mon Oct 22 2007 - 14:55:42 CDT)
- Re: FW: VMD & OpenGL GLX Extension John Stone (Wed Oct 24 2007 - 17:36:21 CDT)
status of psfgen support for CHARMM psf format Dow Hurst DPHURST (Mon Oct 22 2007 - 09:37:30 CDT)
- Re: status of psfgen support for CHARMM psf format John Stone (Tue Oct 30 2007 - 22:57:31 CDT)
Color by Volume on an Intel 945GM Jeffry D Madura (Sat Oct 20 2007 - 14:42:07 CDT)
- Re: Color by Volume on an Intel 945GM Axel Kohlmeyer (Sat Oct 20 2007 - 15:44:39 CDT)
  - RE: Color by Volume on an Intel 945GM Jeffry D Madura (Sat Oct 20 2007 - 16:22:42 CDT)
    - Re: Color by Volume on an Intel 945GM John Stone (Mon Oct 22 2007 - 10:34:50 CDT)
how to remove chain id ? Sanghyun Park (Fri Oct 19 2007 - 21:57:10 CDT)
- Re: how to remove chain id ? Axel Kohlmeyer (Sat Oct 20 2007 - 08:33:05 CDT)
  - Re: how to remove chain id ? Sanghyun Park (Sat Oct 20 2007 - 11:42:45 CDT)
    - Re: how to remove chain id ? Axel Kohlmeyer (Sat Oct 20 2007 - 14:00:02 CDT)
    - Re: how to remove chain id ? Sanghyun Park (Sat Oct 20 2007 - 14:39:03 CDT)
Extracting IR spectra from trajectories Cesar Luis Avila (Fri Oct 19 2007 - 10:08:45 CDT)
- Re: Extracting IR spectra from trajectories Axel Kohlmeyer (Fri Oct 19 2007 - 15:30:50 CDT)
Problem with bigdcd Vishal Kopardé (Fri Oct 19 2007 - 09:03:24 CDT)
- Re: Problem with bigdcd John Stone (Fri Oct 19 2007 - 11:01:24 CDT)
  - Re: Problem with bigdcd Vishal Kopardé (Fri Oct 19 2007 - 11:16:25 CDT)
- Re: Problem with bigdcd Himanshu Khandelia (Fri Oct 19 2007 - 12:25:56 CDT)
APBS dx colors depend on order of molec files loaded??? Chari, Ravi (Thu Oct 18 2007 - 14:52:48 CDT)
- Re: APBS dx colors depend on order of molec files loaded??? John Stone (Thu Oct 18 2007 - 15:08:21 CDT)
RE: multiple attempts before vmd starts up ZT Yew (Thu Oct 18 2007 - 07:03:23 CDT)
multiple attempts before vmd starts up ZT Yew (Wed Oct 17 2007 - 20:25:55 CDT)
- Re: multiple attempts before vmd starts up John Stone (Wed Oct 17 2007 - 20:34:41 CDT)
  - Re: multiple attempts before vmd starts up Boris Steipe (Thu Oct 18 2007 - 00:07:55 CDT)
    - Re: multiple attempts before vmd starts up klsale (Thu Oct 18 2007 - 13:35:36 CDT)
    - Re: multiple attempts before vmd starts up Boris Steipe (Thu Oct 18 2007 - 13:47:21 CDT)
(no subject) ZT Yew (Wed Oct 17 2007 - 18:26:24 CDT)
Exelent quality watch Landon Beaver (Wed Oct 17 2007 - 17:56:35 CDT)
H- bond emra Heshmati (Wed Oct 17 2007 - 12:16:47 CDT)
Is catdcd running on Windows? Philipp Schön (Wed Oct 17 2007 - 03:45:54 CDT)
- Re: Is catdcd running on Windows? Axel Kohlmeyer (Wed Oct 17 2007 - 06:34:45 CDT)
- Re: Is catdcd running on Windows? John Stone (Wed Oct 17 2007 - 21:15:39 CDT)
Problem vmd1.8.5 & vmd1.8.6 on a mac-pro running ubuntu ZT Yew (Tue Oct 16 2007 - 10:13:22 CDT)
- Re: Problem vmd1.8.5 & vmd1.8.6 on a mac-pro running ubuntu John Stone (Tue Oct 16 2007 - 10:19:21 CDT)
  - RE: Problem vmd1.8.5 & vmd1.8.6 on a mac-pro running ubuntu ZT Yew (Tue Oct 16 2007 - 10:55:34 CDT)
Error with stride Per Jr. Greisen (Tue Oct 16 2007 - 09:01:21 CDT)
- Re: Error with stride John Stone (Tue Oct 16 2007 - 09:27:10 CDT)
bonds across periodic boundaries Barry Bickmore (Tue Oct 16 2007 - 08:53:09 CDT)
- Re: bonds across periodic boundaries John Stone (Tue Oct 16 2007 - 09:22:46 CDT)
Strange behaviour of MSMS Ezequiel Quintana Morales (Tue Oct 16 2007 - 07:33:07 CDT)
- Re: Strange behaviour of MSMS John Stone (Tue Oct 16 2007 - 09:20:37 CDT)
Re: residue selection (water molecule within 5 ang. to protein in simulation) kinshuk_at_chem.iitb.ac.in (Mon Oct 15 2007 - 23:54:21 CDT)
- Re: residue selection (water molecule within 5 ang. to protein in simulation) John Stone (Tue Oct 16 2007 - 10:57:29 CDT)
Problems Opening Large .dx File Corenflos, Steven Charles (Mon Oct 15 2007 - 11:30:04 CDT)
- Re: Problems Opening Large .dx File John Stone (Mon Oct 15 2007 - 15:26:55 CDT)
- Re: Problems Opening Large .dx File Axel Kohlmeyer (Mon Oct 15 2007 - 15:56:28 CDT)
  - RE: Problems Opening Large .dx File Corenflos, Steven Charles (Wed Oct 17 2007 - 17:09:54 CDT)
    - Re: Problems Opening Large .dx File John Stone (Wed Oct 17 2007 - 17:28:37 CDT)
Generating parameter file for Cl2- Per Jr. Greisen (Mon Oct 15 2007 - 10:39:36 CDT)
- Re: Generating parameter file for Cl2- John Stone (Mon Oct 15 2007 - 15:22:08 CDT)
setting unit cell dimensions bbickmore_at_comcast.net (Sun Oct 14 2007 - 23:07:50 CDT)
- Re: setting unit cell dimensions Olaf Lenz (Mon Oct 15 2007 - 02:43:47 CDT)
- Re: setting unit cell dimensions Axel Kohlmeyer (Mon Oct 15 2007 - 03:54:49 CDT)
combine.tcl error Francesco Pietra (Sun Oct 14 2007 - 03:23:23 CDT)
- Re: combine.tcl error John Stone (Wed Oct 17 2007 - 22:11:59 CDT)
residue selection (water molecule within 5 ang. to protein in simulation) kinshuk_at_chem.iitb.ac.in (Sun Oct 14 2007 - 02:21:32 CDT)
- Re: residue selection (water molecule within 5 ang. to protein in simulation) Neelanjana Sengupta (Sun Oct 14 2007 - 08:05:40 CDT)
Small molecules Amit (Fri Oct 12 2007 - 18:02:51 CDT)
- Re: Small molecules L. Michel Espinoza-Fonseca (Fri Oct 12 2007 - 18:44:00 CDT)
  - Re: Small molecules Peter Freddolino (Sat Oct 13 2007 - 17:25:13 CDT)
- Re: Small molecules Jay Shore (Sun Oct 14 2007 - 22:42:42 CDT)
residue selection Giovanni Bellesia (Fri Oct 12 2007 - 14:19:32 CDT)
- Re: residue selection Peter Freddolino (Fri Oct 12 2007 - 14:24:18 CDT)
  - Re: residue selection Giovanni Bellesia (Fri Oct 12 2007 - 14:28:29 CDT)
    - Re: residue selection Peter Freddolino (Fri Oct 12 2007 - 14:27:49 CDT)
VMD access using XWIN32 or X-Deep Deepangi Pandit (Fri Oct 12 2007 - 13:20:01 CDT)
- Re: VMD access using XWIN32 or X-Deep Axel Kohlmeyer (Fri Oct 12 2007 - 14:08:30 CDT)
- Re: VMD access using XWIN32 or X-Deep John Stone (Fri Oct 12 2007 - 15:34:12 CDT)
  - Re: VMD access using XWIN32 or X-Deep Mario Valle (Fri Oct 12 2007 - 22:50:54 CDT)
Fixing the View in a Movie carlos_at_avalon.umaryland.edu (Fri Oct 12 2007 - 11:44:45 CDT)
- Re: Fixing the View in a Movie John Stone (Fri Oct 12 2007 - 16:14:14 CDT)
VMD access using XWIN32 or X-Deep Deepangi Pandit (Fri Oct 12 2007 - 11:35:52 CDT)
RMSD Trajectory Tool Zhaochuan Shen (Wed Oct 10 2007 - 13:09:22 CDT)
- Re: RMSD Trajectory Tool John Stone (Wed Oct 17 2007 - 21:56:39 CDT)
Re: namd-l: Molecule drifts and high average RMSD per residue Peter Freddolino (Tue Oct 09 2007 - 09:45:23 CDT)
- Re: Re: namd-l: Molecule drifts and high average RMSD per residue Peter Freddolino (Tue Oct 09 2007 - 09:51:07 CDT)
- Re: namd-l: Molecule drifts and high average RMSD per residue Peter Freddolino (Tue Oct 09 2007 - 09:58:06 CDT)
Rotate a box with pcb Matteo Guglielmi (Tue Oct 09 2007 - 07:02:34 CDT)
- Re: Rotate a box with pcb John Stone (Wed Oct 17 2007 - 22:24:58 CDT)
  - Re: Rotate a box with pcb Jan Saam (Thu Oct 18 2007 - 01:14:31 CDT)
    - Re: Rotate a box with pcb Matteo Guglielmi (Thu Oct 18 2007 - 14:07:16 CDT)
Re: You are right. That's the problem. Axel Kohlmeyer (Mon Oct 08 2007 - 12:10:07 CDT)
Normal VMD crashed when pdb load but Debug mode works weilin Zhang (Mon Oct 08 2007 - 09:45:50 CDT)
- Re: Normal VMD crashed when pdb load but Debug mode works John Stone (Mon Oct 08 2007 - 11:48:43 CDT)
- Re: Normal VMD crashed when pdb load but Debug mode works Axel Kohlmeyer (Mon Oct 08 2007 - 11:41:09 CDT)
the representation of within 10 angstrom of a specific point Emilia Wu (Sun Oct 07 2007 - 22:01:08 CDT)
- Re: the representation of within 10 angstrom of a specific point Axel Kohlmeyer (Sun Oct 07 2007 - 23:48:36 CDT)
Cube Files - proportion of the electron density Jay Shore (Sun Oct 07 2007 - 15:50:40 CDT)
- Re: Cube Files - proportion of the electron density Axel Kohlmeyer (Sun Oct 07 2007 - 18:14:00 CDT)
  - Re: Cube Files - proportion of the electron density Jay Shore (Tue Oct 09 2007 - 14:10:35 CDT)
    - Re: Cube Files - proportion of the electron density John Stone (Tue Oct 09 2007 - 14:38:06 CDT)
    - Re: Cube Files - proportion of the electron density Axel Kohlmeyer (Tue Oct 09 2007 - 16:40:25 CDT)
NAMDENERGY analysis Narender Singh Maan (Thu Oct 04 2007 - 13:34:16 CDT)
- Re: NAMDENERGY analysis Peter Freddolino (Thu Oct 04 2007 - 14:18:05 CDT)
  - Re: NAMDENERGY analysis Peter Freddolino (Thu Oct 04 2007 - 14:28:18 CDT)
- Re: NAMDENERGY analysis Axel Kohlmeyer (Thu Oct 04 2007 - 15:34:32 CDT)
How to put metal ion into my protein Shulin Zhuang (Wed Oct 03 2007 - 22:29:40 CDT)
no transparency on newest iMacs Christoph Weber (Wed Oct 03 2007 - 19:05:21 CDT)
- Re: no transparency on newest iMacs John Stone (Wed Oct 03 2007 - 19:12:40 CDT)
  - Re: no transparency on newest iMacs Christoph Weber (Thu Oct 04 2007 - 15:56:56 CDT)
    - Re: no transparency on newest iMacs John Stone (Fri Oct 05 2007 - 01:35:41 CDT)
Re: Installation and running on VMD on Debian Testing System Brian Bennion (Wed Oct 03 2007 - 09:51:54 CDT)
- Re: Installation and running on VMD on Debian Testing System Lorenzo Isella (Wed Oct 03 2007 - 17:50:04 CDT)
creating nonstandard solvent lucie huynh (Wed Oct 03 2007 - 07:53:21 CDT)
- Re: creating nonstandard solvent Peter Freddolino (Wed Oct 03 2007 - 08:23:07 CDT)
- Re: creating nonstandard solvent Leandro Martínez (Wed Oct 03 2007 - 08:35:19 CDT)
  - Re: creating nonstandard solvent Nicolas Belloy (Fri Oct 05 2007 - 09:16:30 CDT)
    - Re: creating nonstandard solvent Peter Freddolino (Fri Oct 05 2007 - 10:01:12 CDT)
  - Setting number of water molecules for the given box dimension jestin mandumpal (Thu Oct 18 2007 - 22:01:57 CDT)
- Re: creating nonstandard solvent Peter Freddolino (Wed Oct 03 2007 - 08:19:30 CDT)
Installation and running on VMD on Debian Testing System Lorenzo Isella (Wed Oct 03 2007 - 07:48:08 CDT)
- Re: Installation and running on VMD on Debian Testing System Dan Wright (Wed Oct 03 2007 - 12:05:38 CDT)
- Re: Installation and running on VMD on Debian Testing System Axel Kohlmeyer (Wed Oct 03 2007 - 12:42:25 CDT)
time step Alessio Alexiadis (Wed Oct 03 2007 - 07:44:13 CDT)
- Re: time step John Stone (Thu Oct 04 2007 - 23:39:34 CDT)
  - Re: time step nmichaud_at_jhu.edu (Fri Oct 05 2007 - 07:23:38 CDT)
hbonds (how to count) Alessio Alexiadis (Wed Oct 03 2007 - 03:28:52 CDT)
- Re: hbonds (how to count) Axel Kohlmeyer (Wed Oct 03 2007 - 06:29:53 CDT)
namdenergy problem Narender Singh Maan (Tue Oct 02 2007 - 14:53:47 CDT)
- Re: namdenergy problem Peter Freddolino (Tue Oct 02 2007 - 18:14:14 CDT)
  - Re: namdenergy problem Peter Freddolino (Tue Oct 02 2007 - 18:55:14 CDT)
query regarding membrane building kalyan chaitanya (Sat Sep 29 2007 - 09:41:14 CDT)
- Re: query regarding membrane building L. Michel Espinoza-Fonseca (Sat Sep 29 2007 - 14:05:01 CDT)
  - Re: query regarding membrane building kalyan chaitanya (Sat Sep 29 2007 - 22:58:45 CDT)
util Peter Freddolino (Fri Sep 28 2007 - 16:39:56 CDT)
- Re: util Peter Freddolino (Fri Sep 28 2007 - 16:46:40 CDT)
Storing multiple values in the user field Bob Johnson (Fri Sep 28 2007 - 16:15:05 CDT)
- Re: Storing multiple values in the user field John Stone (Fri Sep 28 2007 - 16:25:34 CDT)
  - Re: Storing multiple values in the user field John Stone (Fri Sep 28 2007 - 17:12:51 CDT)
- Re: Storing multiple values in the user field Axel Kohlmeyer (Fri Sep 28 2007 - 16:17:09 CDT)
video memory and volumetric data Jim Fonseca (Fri Sep 28 2007 - 15:15:02 CDT)
- Re: video memory and volumetric data John Stone (Fri Sep 28 2007 - 16:19:41 CDT)
behavior of "mol addfile first/last" with non-integer frame numbers Axel Kohlmeyer (Thu Sep 27 2007 - 19:35:40 CDT)
- Re: behavior of "mol addfile first/last" with non-integer frame numbers John Stone (Fri Sep 28 2007 - 13:37:49 CDT)
Charlie Buy your loved one Hermes Dick Medrano (Thu Sep 27 2007 - 20:39:34 CDT)
vmd files between linux and windows Sampo Karkola (Thu Sep 27 2007 - 07:52:16 CDT)
- Re: vmd files between linux and windows John Stone (Thu Sep 27 2007 - 10:19:30 CDT)
  - Re: vmd files between linux and windows Sampo Karkola (Mon Oct 01 2007 - 01:51:11 CDT)
atom index number Naser, Md Abu (Thu Sep 27 2007 - 01:28:29 CDT)
- Re: atom index number Axel Kohlmeyer (Thu Sep 27 2007 - 02:42:42 CDT)
How can I get .xyzr file or .xyzrn file? ChenFei (Wed Sep 26 2007 - 02:27:51 CDT)
- Re: How can I get .xyzr file or .xyzrn file? John Stone (Wed Sep 26 2007 - 16:38:04 CDT)
topology file in /linux/src/vmd-1.8.6/plugins/noarch/tcl/readcharmmtop1.0/top_all27_prot_lipid_na.inp Dhiraj Srivastava (Tue Sep 25 2007 - 19:00:30 CDT)
- Re: topology file in /linux/src/vmd-1.8.6/plugins/noarch/tcl/readcharmmtop1.0/top_all27_prot_lipid_na.inp Dhiraj Srivastava (Tue Sep 25 2007 - 19:33:14 CDT)
  - Re: Re: topology file in /linux/src/vmd-1.8.6/plugins/noarch/tcl/readcharmmtop1.0/top_all27_prot_lipid_na.inp Peter Freddolino (Tue Sep 25 2007 - 21:05:12 CDT)
- Re: topology file in /linux/src/vmd-1.8.6/plugins/noarch/tcl/readcharmmtop1.0/top_all27_prot_lipid_na.inp L. Michel Espinoza-Fonseca (Tue Sep 25 2007 - 19:33:46 CDT)
RE: Can't execvp vmd_SOLARISX86 Austin Small (Tue Sep 25 2007 - 16:14:16 CDT)
MultiSeq on the windows vista OS Lhee, SangMoon (Mon Sep 24 2007 - 13:30:25 CDT)
- Re: MultiSeq on the windows vista OS Alexandr Isayev (Mon Sep 24 2007 - 14:25:00 CDT)
Can't execvp vmd_SOLARISX86 Austin Small (Sun Sep 23 2007 - 23:42:50 CDT)
- Re: Can't execvp vmd_SOLARISX86 John Stone (Sun Sep 23 2007 - 21:49:23 CDT)
residue selection: conflict between resid and residue Nicolas Sapay (Fri Sep 21 2007 - 13:22:45 CDT)
- Re: residue selection: conflict between resid and residue Axel Kohlmeyer (Fri Sep 21 2007 - 13:15:29 CDT)
  - Re: residue selection: conflict between resid and residue Nicolas Sapay (Fri Sep 21 2007 - 15:14:23 CDT)
Create a PSF Andrea.Cristiani_at_pharm.unige.ch (Fri Sep 21 2007 - 04:16:37 CDT)
- Re: Create a PSF Èùìáò Åõáããåëéäçò (Fri Sep 21 2007 - 06:12:49 CDT)
  - Re: Create a PSF Peter Freddolino (Fri Sep 21 2007 - 07:27:34 CDT)
- Re: Create a PSF Peter Freddolino (Fri Sep 21 2007 - 06:57:23 CDT)
output of distances between atoms or coordinates INPE (Ingrid Viveka Pettersson) (Thu Sep 20 2007 - 08:27:39 CDT)
- Re: output of distances between atoms or coordinates Axel Kohlmeyer (Thu Sep 20 2007 - 10:20:08 CDT)
Problem generating PSF file for decalanine...any help? Santanu Chatterjee (Wed Sep 19 2007 - 18:24:38 CDT)
Problem generating PSF file for decalanine...any help? Santanu Chatterjee (Wed Sep 19 2007 - 18:20:58 CDT)
sidechain correlated motions L. Michel Espinoza-Fonseca (Wed Sep 19 2007 - 17:18:04 CDT)
- Re: sidechain correlated motions Axel Kohlmeyer (Thu Sep 20 2007 - 09:42:59 CDT)
  - Re: sidechain correlated motions L. Michel Espinoza-Fonseca (Fri Sep 21 2007 - 10:41:21 CDT)
smooting structure Myunggi Yi (Wed Sep 19 2007 - 11:38:23 CDT)
- Re: smooting structure John Stone (Wed Sep 19 2007 - 11:57:16 CDT)
  - Re: smooting structure Myunggi Yi (Wed Sep 19 2007 - 12:59:12 CDT)
Residue highlighting in MD Traj M kutty (Wed Sep 19 2007 - 03:15:09 CDT)
- Re: Residue highlighting in MD Traj Nuno Loureiro Ferreira (Wed Sep 19 2007 - 05:05:01 CDT)
  - Re: Residue highlighting in MD Traj Nuno Loureiro Ferreira (Fri Sep 28 2007 - 03:45:32 CDT)
passive stereo projection using a Mac Jeff Hoch (Tue Sep 18 2007 - 12:18:15 CDT)
change the representation of certain atoms which pass a geometric criterion during a movie maria goranovic (Tue Sep 18 2007 - 08:21:45 CDT)
- Re: change the representation of certain atoms which pass a geometric criterion during a movie Axel Kohlmeyer (Tue Sep 18 2007 - 08:34:29 CDT)
  - Time series for SASA calculation: PARMINDER MANKOO (Wed Sep 26 2007 - 13:40:12 CDT)
    - Re: Time series for SASA calculation: Axel Kohlmeyer (Wed Sep 26 2007 - 20:01:35 CDT)
Re: osx startup script John Stone (Mon Sep 17 2007 - 15:34:55 CDT)
problem with timeline plugin aneesh cna (Mon Sep 17 2007 - 05:33:29 CDT)
problems with ADP vanadate Daniel Kennedy (Sun Sep 16 2007 - 11:12:09 CDT)
VMD text mode version Myunggi Yi (Fri Sep 14 2007 - 10:10:58 CDT)
- Re: VMD text mode version Axel Kohlmeyer (Fri Sep 14 2007 - 10:09:50 CDT)
"truncate_trajectory" a new plugin Èùìáò Åõáããåëéäçò (Fri Sep 14 2007 - 10:01:23 CDT)
Questions abt VMD plugins Audrey Salazar (Fri Sep 14 2007 - 08:59:48 CDT)
- Re: Questions abt VMD plugins Axel Kohlmeyer (Fri Sep 14 2007 - 10:06:06 CDT)
secondary structure colors in timeline plugin cristiana.carellialinovi_at_rm.unicatt.it (Fri Sep 14 2007 - 07:51:31 CDT)
- Re: secondary structure colors in timeline plugin Axel Kohlmeyer (Fri Sep 14 2007 - 07:46:50 CDT)
Generating water transparency around a protein Jeffry D Madura (Fri Sep 14 2007 - 06:31:14 CDT)
- Re: Generating water transparency around a protein Peter Freddolino (Fri Sep 14 2007 - 07:18:45 CDT)
VMD on Playstation 3 Jeffry D Madura (Fri Sep 14 2007 - 06:30:58 CDT)
- Re: VMD on Playstation 3 Axel Kohlmeyer (Fri Sep 14 2007 - 07:39:16 CDT)
secondary structure colors in timeline plugin cristiana.carellialinovi_at_rm.unicatt.it (Fri Sep 14 2007 - 06:24:30 CDT)
Problems with a multiple orbital cube file Dr. Seth Olsen (Fri Sep 14 2007 - 01:49:38 CDT)
- Re: Problems with a multiple orbital cube file Axel Kohlmeyer (Fri Sep 14 2007 - 07:32:14 CDT)
VMD Images and Movies Tutorial: Working With Trajectories Roland Schmucki (Thu Sep 13 2007 - 03:32:05 CDT)
- Re: VMD Images and Movies Tutorial: Working With Trajectories Axel Kohlmeyer (Thu Sep 13 2007 - 09:04:08 CDT)
Re: program finishes before bigdcd is executed completely Èùìáò Åõáããåëéäçò (Tue Sep 11 2007 - 13:56:32 CDT)
- Re: program finishes before bigdcd is executed completely Leonardo Trabuco (Tue Sep 11 2007 - 14:51:11 CDT)
  - Re: program finishes before bigdcd is executed completely Èùìáò Åõáããåëéäçò (Tue Sep 11 2007 - 17:26:12 CDT)
program finishes before bigdcd is ececuted completely Èùìáò Åõáããåëéäçò (Mon Sep 10 2007 - 14:57:11 CDT)
- Re: program finishes before bigdcd is ececuted completely Leonardo Trabuco (Mon Sep 10 2007 - 16:50:39 CDT)
  - Re: program finishes before bigdcd is ececuted completely Èùìáò Åõáããåëéäçò (Tue Sep 11 2007 - 06:19:53 CDT)
    - Re: program finishes before bigdcd is ececuted completely Leonardo Trabuco (Tue Sep 11 2007 - 08:22:11 CDT)
    - Re: program finishes before bigdcd is ececuted completely Èùìáò Åõáããåëéäçò (Tue Sep 11 2007 - 10:07:23 CDT)
polymer molecule orientation parameter Catherine Tweedie (Mon Sep 10 2007 - 13:45:11 CDT)
changing the tilt angle of a peptide embedded in a membrane L. Michel Espinoza-Fonseca (Mon Sep 10 2007 - 13:08:38 CDT)
changing the tile angle of a peptide embedded in a membrane L. Michel Espinoza-Fonseca (Mon Sep 10 2007 - 12:57:13 CDT)
- Re: changing the tile angle of a peptide embedded in a membrane John Stone (Mon Sep 10 2007 - 13:09:39 CDT)
- Re: changing the tile angle of a peptide embedded in a membrane L. Michel Espinoza-Fonseca (Mon Sep 10 2007 - 13:05:36 CDT)
problem regarding timeline aneesh cna (Mon Sep 10 2007 - 10:54:01 CDT)
Re: namd-l: STRIDE Algorithm L. Michel Espinoza-Fonseca (Mon Sep 10 2007 - 10:43:56 CDT)
GLSL rendering mode is NOT available Roland Schmucki (Mon Sep 10 2007 - 07:04:48 CDT)
- Re: GLSL rendering mode is NOT available Axel Kohlmeyer (Mon Sep 10 2007 - 09:28:37 CDT)
- Re: GLSL rendering mode is NOT available John Stone (Mon Sep 10 2007 - 10:32:37 CDT)
Further angle question jo hanna (Sat Sep 08 2007 - 09:16:15 CDT)
- Re: Further angle question Axel Kohlmeyer (Sat Sep 08 2007 - 20:37:28 CDT)
vmdbasename: Undefined variable Austin Small (Sat Sep 08 2007 - 12:13:41 CDT)
- Re: vmdbasename: Undefined variable Axel Kohlmeyer (Sat Sep 08 2007 - 20:39:56 CDT)
- Re: vmdbasename: Undefined variable John Stone (Sat Sep 08 2007 - 22:24:02 CDT)
Computing angles jo hanna (Fri Sep 07 2007 - 17:18:33 CDT)
- Re: Computing angles Axel Kohlmeyer (Fri Sep 07 2007 - 17:27:26 CDT)
Fwd: peptide builder L. Michel Espinoza-Fonseca (Fri Sep 07 2007 - 11:35:39 CDT)
- Re: Fwd: peptide builder Peter Freddolino (Fri Sep 07 2007 - 11:36:45 CDT)
is it possible to skip frame when using bigdcd maria goranovic (Fri Sep 07 2007 - 03:47:05 CDT)
- Re: is it possible to skip frame when using bigdcd Axel Kohlmeyer (Fri Sep 07 2007 - 07:56:23 CDT)
- Re: is it possible to skip frame when using bigdcd John Stone (Fri Sep 07 2007 - 12:38:26 CDT)
  - Re: is it possible to skip frame when using bigdcd maria goranovic (Mon Sep 10 2007 - 04:17:44 CDT)
Averaging volmaps Cesar Luis Avila (Thu Sep 06 2007 - 10:11:36 CDT)
the console window is automatically closed without any error messages Hu Zhonghan (Thu Sep 06 2007 - 10:05:15 CDT)
- Re: the console window is automatically closed without any error messages John Stone (Thu Sep 06 2007 - 10:52:49 CDT)
  - Re: the console window is automatically closed without any error messages Hu Zhonghan (Thu Sep 06 2007 - 12:31:54 CDT)
    - Re: the console window is automatically closed without any error messages John Stone (Thu Sep 06 2007 - 12:36:44 CDT)
    - Re: the console window is automatically closed without any error messages Axel Kohlmeyer (Thu Sep 06 2007 - 12:50:08 CDT)
PMEpot + bigDCD ? Cesar Luis Avila (Wed Sep 05 2007 - 15:08:00 CDT)
Solvate package brmorgan_at_clarku.edu (Wed Sep 05 2007 - 13:02:03 CDT)
- Re: Solvate package Axel Kohlmeyer (Wed Sep 05 2007 - 14:05:45 CDT)
Rebuilding lipid from headgroup coordinates only using psfgen, some atoms put on origin maria goranovic (Wed Sep 05 2007 - 11:05:12 CDT)
- Re: Rebuilding lipid from headgroup coordinates only using psfgen, some atoms put on origin Jim Phillips (Sat Sep 08 2007 - 21:56:51 CDT)
advanced python console Gianluca Santarossa (Tue Sep 04 2007 - 09:17:45 CDT)
- Re: advanced python console Axel Kohlmeyer (Tue Sep 04 2007 - 09:18:34 CDT)
regular expression in Tcl Èùìáò Åõáããåëéäçò (Tue Sep 04 2007 - 06:13:56 CDT)
- Re: regular expression in Tcl Axel Kohlmeyer (Tue Sep 04 2007 - 09:12:58 CDT)
Your Zoc0r 0rder #46390 Vito Ashley (Tue Sep 04 2007 - 03:20:14 CDT)
Stylish repl1ca w4tches from famous brands Susan Langston (Tue Sep 04 2007 - 03:16:35 CDT)
Delightsome Cart1er w4tches at Prest1ge Repl1cas Carson Cope (Fri Aug 31 2007 - 13:58:34 CDT)
Your Val1um 0rder #799563 Eliza Wray (Fri Aug 31 2007 - 10:02:23 CDT)
How to solvate a protein in a large water sphere Shulin Zhuang (Fri Aug 31 2007 - 03:44:50 CDT)
- Re: How to solvate a protein in a large water sphere Peter Freddolino (Fri Aug 31 2007 - 08:16:08 CDT)
Problem with saving coordinate bo baker (Thu Aug 30 2007 - 22:44:57 CDT)
- Re: Problem with saving coordinate Axel Kohlmeyer (Fri Aug 31 2007 - 00:17:25 CDT)
  - Re: Problem with saving coordinate bo baker (Fri Aug 31 2007 - 01:55:26 CDT)
solvation Francesco Pietra (Thu Aug 30 2007 - 15:05:59 CDT)
RE: VMD analysis using NAMD plot Richard Swenson (Wed Aug 29 2007 - 10:42:59 CDT)
VMD analysis using NAMD plot Philipp Schön (Wed Aug 29 2007 - 05:47:01 CDT)
- Re: VMD analysis using NAMD plot John Stone (Wed Aug 29 2007 - 11:03:24 CDT)
- RE: VMD analysis using NAMD plot Richard Swenson (Wed Aug 29 2007 - 10:40:28 CDT)
dcd file error dimka (Tue Aug 28 2007 - 17:50:52 CDT)
- Re: dcd file error John Stone (Wed Aug 29 2007 - 00:08:39 CDT)
numbonds Eduard Schreiner (Tue Aug 28 2007 - 10:54:20 CDT)
- Re: numbonds Axel Kohlmeyer (Tue Aug 28 2007 - 12:05:46 CDT)
Delightful repl1ca w4tches at Prest1ge Repl1cas Kenton Webster (Tue Aug 28 2007 - 09:33:17 CDT)
Re: Your Pharm4cy 0rder #530152 Susanna Crowe (Tue Aug 28 2007 - 05:22:21 CDT)
TIP5P jestin mandumpal (Sun Aug 26 2007 - 23:41:03 CDT)
coordinates with get command Nuno Loureiro Ferreira (Sat Aug 25 2007 - 18:10:02 CDT)
- Re: coordinates with get command John Stone (Sat Aug 25 2007 - 23:04:51 CDT)
  - Re: coordinates with get command Nuno Loureiro Ferreira (Sat Aug 25 2007 - 23:27:28 CDT)
Prest1ge Repl1cas ravishing repl1ca w4tches for you Liliana Dawson (Sat Aug 25 2007 - 12:24:44 CDT)
No prescr1ption? No problem! Buford Greene (Sat Aug 25 2007 - 09:27:00 CDT)
changing the order of atom selections / alignment issue Jim Pfaendtner (Fri Aug 24 2007 - 17:58:51 CDT)
- Re: changing the order of atom selections / alignment issue Leonardo Trabuco (Sat Aug 25 2007 - 01:31:45 CDT)
  - Re: changing the order of atom selections / alignment issue Jim Pfaendtner (Mon Aug 27 2007 - 10:58:31 CDT)
    - Re: changing the order of atom selections / alignment issue Leonardo Trabuco (Mon Aug 27 2007 - 11:07:47 CDT)
vmd-1.8.6 fails with python-2.5 Jeffrey Gardner (Fri Aug 24 2007 - 17:20:51 CDT)
measure imprp - input order of atoms Johannes Müllegger (Fri Aug 24 2007 - 14:51:00 CDT)
- Re: measure imprp - input order of atoms Jan Saam (Mon Aug 27 2007 - 03:30:41 CDT)
atomselection in order Myunggi Yi (Thu Aug 23 2007 - 22:19:35 CDT)
- Re: atomselection in order Leonardo Trabuco (Thu Aug 23 2007 - 23:24:09 CDT)
  - Re: atomselection in order Thomas C. Bishop (Mon Aug 27 2007 - 09:34:15 CDT)
    - Re: atomselection in order John Stone (Mon Aug 27 2007 - 14:57:12 CDT)
  - Re: atomselection in order Myunggi Yi (Tue Aug 28 2007 - 08:29:03 CDT)
Aggregation analysis zhenlong li (Thu Aug 23 2007 - 10:07:49 CDT)
- Re: Aggregation analysis John Stone (Wed Aug 29 2007 - 00:21:48 CDT)
Selection within VMD Mark Zottola (Wed Aug 22 2007 - 14:28:53 CDT)
- Re: Selection within VMD John Stone (Wed Aug 22 2007 - 15:04:15 CDT)
- Re: Selection within VMD Olaf Lenz (Wed Aug 22 2007 - 15:36:09 CDT)
- Re: Selection within VMD Axel Kohlmeyer (Wed Aug 22 2007 - 14:12:59 CDT)
Re: FYI: 1.8.6 runs full GLSL on AMD64 John Stone (Wed Aug 22 2007 - 13:40:37 CDT)
- Re: FYI: 1.8.6 runs full GLSL on AMD64 John Stone (Wed Aug 22 2007 - 22:55:06 CDT)
automating graphic representations Jim Pfaendtner (Wed Aug 22 2007 - 13:37:41 CDT)
- Re: automating graphic representations John Stone (Wed Aug 22 2007 - 13:44:19 CDT)
- Re: automating graphic representations Axel Kohlmeyer (Wed Aug 22 2007 - 13:33:03 CDT)
  - Re: automating graphic representations Jim Pfaendtner (Fri Aug 24 2007 - 13:55:00 CDT)
    - Re: automating graphic representations Axel Kohlmeyer (Fri Aug 24 2007 - 13:08:44 CDT)
W4tches from simple to luxurious at Prest1ge Repl1cas Douglas Dahl (Wed Aug 22 2007 - 13:49:57 CDT)
The only med1cation for we1ght l0ss that does work Mayra Underwood (Wed Aug 22 2007 - 13:03:07 CDT)
VMD w/ amber parm7, segnames/chains etc... Thomas C. Bishop (Wed Aug 22 2007 - 09:30:57 CDT)
- Re: VMD w/ amber parm7, segnames/chains etc... John Stone (Wed Aug 22 2007 - 13:54:14 CDT)
Selecting the N-closest Waters J T (Tue Aug 21 2007 - 12:40:19 CDT)
- Re: Selecting the N-closest Waters Nuno Loureiro Ferreira (Tue Aug 21 2007 - 15:55:13 CDT)
  - Re: Selecting the N-closest Waters J T (Tue Aug 21 2007 - 16:10:03 CDT)
- Re: Selecting the N-closest Waters Claw Isthelaw (Mon Jun 02 2008 - 13:25:51 CDT)
How to load packages from tcllib into VMD Cesar Luis Avila (Mon Aug 20 2007 - 14:59:49 CDT)
- Re: How to load packages from tcllib into VMD Axel Kohlmeyer (Mon Aug 20 2007 - 18:43:53 CDT)
  - Re: How to load packages from tcllib into VMD Cesar Luis Avila (Mon Aug 20 2007 - 17:22:53 CDT)
    - Re: How to load packages from tcllib into VMD Axel Kohlmeyer (Tue Aug 21 2007 - 08:13:00 CDT)
VMD crashes during the execution of a computational intensive TCL script Èùìáò Åõáããåëéäçò (Mon Aug 20 2007 - 16:25:33 CDT)
- Re: VMD crashes during the execution of a computational intensive TCL script John Stone (Mon Aug 20 2007 - 16:41:17 CDT)
residue missed by psfgen Daniel Kennedy (Mon Aug 20 2007 - 12:09:05 CDT)
- Re: residue missed by psfgen Peter Freddolino (Mon Aug 20 2007 - 16:48:00 CDT)
No prescr1ption? No problem! Ferdinand Benton (Sun Aug 19 2007 - 10:50:20 CDT)
Luxurious costume repl1ca w4tches at lowest prices Marvin Allen (Sun Aug 19 2007 - 08:30:41 CDT)
Need help sleeping? Read this! Kendra Baker (Thu Aug 16 2007 - 20:39:47 CDT)
Prest1ge Repl1cas your source for high-quality w4tches Lula Miner (Thu Aug 16 2007 - 19:21:55 CDT)
NAMD energy plugin Cesar Luis Avila (Wed Aug 15 2007 - 08:22:59 CDT)
- Re: NAMD energy plugin Peter Freddolino (Wed Aug 15 2007 - 11:50:55 CDT)
  - Re: NAMD energy plugin Cesar Luis Avila (Wed Aug 15 2007 - 11:15:17 CDT)
Very peculiar problem with bigdcd if not running interactively (post moved over from namd forum) maria goranovic (Wed Aug 15 2007 - 04:09:32 CDT)
- Re: Very peculiar problem with bigdcd if not running interactively (post moved over from namd forum) Axel Kohlmeyer (Wed Aug 15 2007 - 10:47:46 CDT)
- Re: Very peculiar problem with bigdcd if not running interactively (post moved over from namd forum) Gordon Wells (Mon Aug 20 2007 - 04:49:51 CDT)
Installing VMD to work with MSMS Audrey Salazar (Tue Aug 14 2007 - 11:07:38 CDT)
- Re: Installing VMD to work with MSMS Axel Kohlmeyer (Tue Aug 14 2007 - 11:31:49 CDT)
- Re: Installing VMD to work with MSMS John Stone (Tue Aug 14 2007 - 12:23:16 CDT)
- Re: Installing VMD to work with MSMS Audrey Salazar (Tue Aug 14 2007 - 13:42:35 CDT)
Archived Spam in the VMD-L Mailing List Audrey Salazar (Tue Aug 14 2007 - 10:00:30 CDT)
- Re: Archived Spam in the VMD-L Mailing List John Stone (Tue Aug 14 2007 - 10:07:37 CDT)
  - Re: Archived Spam in the VMD-L Mailing List John Stone (Tue Aug 14 2007 - 10:13:27 CDT)
Increasing use of RAM even if I put unset/delete for selections! Due to use of arrays? Philipp Schön (Tue Aug 14 2007 - 05:28:13 CDT)
- Re: Increasing use of RAM even if I put unset/delete for selections! Due to use of arrays? John Stone (Tue Aug 14 2007 - 12:14:38 CDT)
printing timeline window with axes hodak_at_chips.ncsu.edu (Mon Aug 13 2007 - 22:07:27 CDT)
- Re: printing timeline window with axes John Stone (Tue Aug 14 2007 - 14:50:19 CDT)
Re: help with badwater script Jim Pfaendtner (Mon Aug 13 2007 - 18:38:12 CDT)
- Re: Re: help with badwater script Axel Kohlmeyer (Mon Aug 13 2007 - 19:08:30 CDT)
  - Re: Re: help with badwater script Jim Pfaendtner (Tue Aug 14 2007 - 15:29:12 CDT)
new machine problems. Fred Moore (Mon Aug 13 2007 - 17:58:46 CDT)
- Re: new machine problems. John Stone (Tue Aug 14 2007 - 14:49:09 CDT)
create psf and dcd from pdb Èùìáò Åõáããåëéäçò (Mon Aug 13 2007 - 16:26:27 CDT)
- Re: create psf and dcd from pdb Peter Freddolino (Mon Aug 13 2007 - 17:35:01 CDT)
  - Re: create psf and dcd from pdb Èùìáò Åõáããåëéäçò (Tue Aug 14 2007 - 10:25:15 CDT)
    - Re: create psf and dcd from pdb Peter Freddolino (Tue Aug 14 2007 - 10:56:07 CDT)
problem regarding stride aneesh cna (Mon Aug 13 2007 - 05:31:32 CDT)
problem regarding stride aneesh cna (Mon Aug 13 2007 - 00:58:09 CDT)
- Re: problem regarding stride Axel Kohlmeyer (Mon Aug 13 2007 - 11:06:48 CDT)
VMD plugin error src/webpdbplugin.c AustinSmall_at_comcast.net (Sun Aug 12 2007 - 18:08:17 CDT)
- Re: VMD plugin error src/webpdbplugin.c Axel Kohlmeyer (Sun Aug 12 2007 - 18:06:37 CDT)
chime vs vmd Francesco Pietra (Sun Aug 12 2007 - 11:11:05 CDT)
- Re: chime vs vmd John Stone (Mon Aug 13 2007 - 11:49:24 CDT)
- Re: chime vs vmd Peter Schellenberg (Tue Aug 14 2007 - 05:37:55 CDT)
RE: plotting on Mac Claw Isthelaw (Sat Aug 11 2007 - 19:53:35 CDT)
Reference for SASA Patrick Redmill (Sat Aug 11 2007 - 17:48:03 CDT)
- Re: Reference for SASA John Stone (Tue Aug 14 2007 - 15:38:20 CDT)
Re: gmake invalid option --c install AustinSmall_at_comcast.net (Sat Aug 11 2007 - 12:52:32 CDT)
- Re: gmake invalid option --c install Axel Kohlmeyer (Sat Aug 11 2007 - 13:46:01 CDT)
gmake invalid option --c install AustinSmall_at_comcast.net (Sat Aug 11 2007 - 10:47:45 CDT)
- Re: gmake invalid option --c install Axel Kohlmeyer (Sat Aug 11 2007 - 11:38:48 CDT)
RE: bilayer thickness in simulation of POPC membranes Cojocaru,Vlad (Sat Aug 11 2007 - 10:08:28 CDT)
- RE: bilayer thickness in simulation of POPC membranes Axel Kohlmeyer (Sat Aug 11 2007 - 11:33:51 CDT)
  - RE: bilayer thickness in simulation of POPC membranes Cojocaru,Vlad (Sun Aug 12 2007 - 02:54:44 CDT)
    - Re: bilayer thickness in simulation of POPC membranes Olaf Lenz (Sun Aug 12 2007 - 04:00:41 CDT)
  - Running a vmd tcl script in the background Arneh Babakhani (Mon Aug 13 2007 - 19:05:20 CDT)
    - Re: Running a vmd tcl script in the background Axel Kohlmeyer (Mon Aug 13 2007 - 19:11:53 CDT)
Adjusting R/S configuration Francesco Pietra (Sat Aug 11 2007 - 02:21:47 CDT)
- Re: Adjusting R/S configuration Peter Freddolino (Sat Aug 11 2007 - 08:43:09 CDT)
problem regarding stride gurpreet singh (Sat Aug 11 2007 - 01:44:25 CDT)
- Re: problem regarding stride Axel Kohlmeyer (Sat Aug 11 2007 - 12:51:55 CDT)
povray problem: degenerate cylinder revisited Robin L Hayes (Fri Aug 10 2007 - 17:22:37 CDT)
- Re: povray problem: degenerate cylinder revisited John Stone (Tue Aug 14 2007 - 15:42:08 CDT)
Color a protein based on a property Naresh (Fri Aug 10 2007 - 14:13:42 CDT)
- Re: Color a protein based on a property John Stone (Fri Aug 10 2007 - 15:09:49 CDT)
dcd reading routines nmichaud_at_jhu.edu (Fri Aug 10 2007 - 13:12:15 CDT)
- Re: dcd reading routines John Stone (Fri Aug 10 2007 - 13:15:37 CDT)
bilayer thickness in simulation of POPC membranes Vlad Cojocaru (Fri Aug 10 2007 - 10:56:41 CDT)
- Re: namd-l: bilayer thickness in simulation of POPC membranes maria goranovic (Mon Aug 13 2007 - 07:55:48 CDT)
  - Re: Re: namd-l: bilayer thickness in simulation of POPC membranes maria goranovic (Mon Aug 13 2007 - 09:16:09 CDT)
how to make user input during runtime of a tcl program using TkConsole? Philipp Schön (Fri Aug 10 2007 - 10:14:46 CDT)
- Re: how to make user input during runtime of a tcl program using TkConsole? John Stone (Fri Aug 10 2007 - 10:25:55 CDT)
  - Re: how to make user input during runtime of a tcl program using TkConsole? Axel Kohlmeyer (Fri Aug 10 2007 - 10:20:47 CDT)
mutate residue xzhao_at_uiuc.edu (Thu Aug 09 2007 - 21:02:15 CDT)
- Re: mutate residue Peter Freddolino (Thu Aug 09 2007 - 21:29:10 CDT)
What does Stride need to draw SS? Jim Pfaendtner (Thu Aug 09 2007 - 16:49:58 CDT)
- Re: What does Stride need to draw SS? John Stone (Thu Aug 09 2007 - 17:36:23 CDT)
package require Tcl 8.5 => ::tcl::mathfunc:: Philipp Schön (Thu Aug 09 2007 - 10:56:09 CDT)
- Re: package require Tcl 8.5 => ::tcl::mathfunc:: John Stone (Thu Aug 09 2007 - 11:01:09 CDT)
  - Re: package require Tcl 8.5 => ::tcl::mathfunc:: John Stone (Thu Aug 09 2007 - 11:04:00 CDT)
radial density Christopher Stiles (Thu Aug 09 2007 - 09:11:55 CDT)
- Re: radial density Olaf Lenz (Thu Aug 09 2007 - 10:19:22 CDT)
- Re: radial density Axel Kohlmeyer (Thu Aug 09 2007 - 09:23:39 CDT)
Monte Carlo conformational search Daniel Kennedy (Wed Aug 08 2007 - 11:23:54 CDT)
- Re: Monte Carlo conformational search L. Michel Espinoza-Fonseca (Thu Aug 09 2007 - 07:58:19 CDT)
Writing MolFile plugin for CIF Ondrej Sramek (Wed Aug 08 2007 - 06:12:03 CDT)
- Re: Writing MolFile plugin for CIF Axel Kohlmeyer (Wed Aug 08 2007 - 09:40:14 CDT)
- Re: Writing MolFile plugin for CIF John Stone (Wed Aug 08 2007 - 12:24:57 CDT)
VMD acts too slow Roland Schmucki (Tue Aug 07 2007 - 20:38:49 CDT)
- Re: VMD acts too slow John Stone (Tue Aug 07 2007 - 21:03:37 CDT)
CNT Analysis Christopher Stiles (Tue Aug 07 2007 - 08:41:31 CDT)
- Re: CNT Analysis Axel Kohlmeyer (Tue Aug 07 2007 - 08:54:06 CDT)
  - RE: CNT Analysis Christopher Stiles (Tue Aug 07 2007 - 10:12:13 CDT)
a problem with installation (to generate the Makefile ) Panichakorn Jaiyong (Mon Aug 06 2007 - 23:52:26 CDT)
- Re: a problem with installation (to generate the Makefile ) John Stone (Mon Aug 06 2007 - 23:56:38 CDT)
- Re: a problem with installation (to generate the Makefile ) Axel Kohlmeyer (Tue Aug 07 2007 - 08:15:36 CDT)
VMD plugins error AustinSmall_at_comcast.net (Mon Aug 06 2007 - 22:18:52 CDT)
- Re: VMD plugins error John Stone (Mon Aug 06 2007 - 23:59:51 CDT)
within and exwithin macro Èùìáò Åõáããåëéäçò (Mon Aug 06 2007 - 16:52:34 CDT)
- Re: within and exwithin macro John Stone (Tue Aug 07 2007 - 00:06:53 CDT)
  - Re: within and exwithin macro Èùìáò Åõáããåëéäçò (Tue Aug 07 2007 - 08:34:14 CDT)
    - Re: within and exwithin macro Axel Kohlmeyer (Tue Aug 07 2007 - 08:46:49 CDT)
    - Re: within and exwithin macro nmichaud_at_jhu.edu (Tue Aug 07 2007 - 11:54:20 CDT)
  - Re: within and exwithin macro Axel Kohlmeyer (Tue Aug 07 2007 - 08:26:18 CDT)
    - Re: within and exwithin macro Èùìáò Åõáããåëéäçò (Tue Aug 07 2007 - 15:52:50 CDT)
    - Re: within and exwithin macro Axel Kohlmeyer (Tue Aug 07 2007 - 15:18:02 CDT)
Automatic PSF Builder Help Audrey Salazar (Mon Aug 06 2007 - 11:16:12 CDT)
- Re: Automatic PSF Builder Help Peter Freddolino (Mon Aug 06 2007 - 11:46:46 CDT)
  - Re: Automatic PSF Builder Help Peter Freddolino (Mon Aug 06 2007 - 12:45:09 CDT)
    - Re: Automatic PSF Builder Help Audrey Salazar (Mon Aug 06 2007 - 14:27:52 CDT)
    - Re: Automatic PSF Builder Help Peter Freddolino (Mon Aug 06 2007 - 15:59:17 CDT)
  - Re: Automatic PSF Builder Help Audrey Salazar (Mon Aug 06 2007 - 14:47:08 CDT)
- Re: Automatic PSF Builder Help Axel Kohlmeyer (Mon Aug 06 2007 - 11:29:16 CDT)
Loading files into already-running version of VMD from command prompt Victor Albert (Sat Aug 04 2007 - 16:04:16 CDT)
- Re: Loading files into already-running version of VMD from command prompt Axel Kohlmeyer (Sat Aug 04 2007 - 16:04:31 CDT)
chloroform box Francesco Pietra (Sat Aug 04 2007 - 00:52:20 CDT)
- Re: chloroform box Peter Freddolino (Sat Aug 04 2007 - 08:00:48 CDT)
  - Re: chloroform box Francesco Pietra (Sat Aug 04 2007 - 09:08:41 CDT)
Corrupt cpmd-vmd.pdf File? rossi_at_york.cuny.edu (Fri Aug 03 2007 - 05:46:07 CDT)
- Re: Corrupt cpmd-vmd.pdf File? Axel Kohlmeyer (Thu Aug 09 2007 - 16:39:02 CDT)
  - Re: Corrupt cpmd-vmd.pdf File? rossi_at_york.cuny.edu (Mon Aug 20 2007 - 20:03:02 CDT)
Corrupt cpmd-vmd.pdf File? rossi_at_york.cuny.edu (Fri Aug 03 2007 - 05:42:54 CDT)
How to calculate the C alpha RMSD from NAMD trajectory Shulin Zhuang (Fri Aug 03 2007 - 02:31:22 CDT)
- Re: namd-l: How to calculate the C alpha RMSD from NAMD trajectory L. Michel Espinoza-Fonseca (Fri Aug 03 2007 - 02:59:02 CDT)
- Re: How to calculate the C alpha RMSD from NAMD trajectory John Stone (Fri Aug 03 2007 - 10:58:13 CDT)
save state fails Vlad Cojocaru (Thu Aug 02 2007 - 10:09:12 CDT)
- save state fails Vlad Cojocaru (Thu Aug 02 2007 - 10:20:03 CDT)
- Re: save state fails Axel Kohlmeyer (Thu Aug 02 2007 - 10:40:25 CDT)
  - RE: save state fails Cojocaru,Vlad (Thu Aug 02 2007 - 13:41:29 CDT)
eigen values Myunggi Yi (Wed Aug 01 2007 - 14:36:00 CDT)
- Re: eigen values Axel Kohlmeyer (Thu Aug 02 2007 - 11:51:00 CDT)
- electrostatic energy emra Heshmati (Wed Aug 15 2007 - 08:20:16 CDT)
  - Re: electrostatic energy Peter Freddolino (Wed Aug 15 2007 - 09:07:39 CDT)
ViewMaster and rendering Paula Marcela Petrone (Wed Aug 01 2007 - 10:00:34 CDT)
- Re: ViewMaster and rendering Justin Gullingsrud (Thu Aug 02 2007 - 19:13:55 CDT)
question about measure contacts Rachel (Tue Jul 31 2007 - 08:42:57 CDT)
- Re: question about measure contacts Rachel (Thu Aug 02 2007 - 12:31:33 CDT)
  - Re: question about measure contacts Justin Gullingsrud (Thu Aug 02 2007 - 15:16:01 CDT)
coloring selected chains and residues karan uppal (Mon Jul 30 2007 - 18:58:05 CDT)
- Re: coloring selected chains and residues Axel Kohlmeyer (Mon Jul 30 2007 - 19:00:55 CDT)
Problems to load Gaussian .log file in Paratool Alexandre Suman de Araujo (Mon Jul 30 2007 - 13:05:56 CDT)
- Re: Problems to load Gaussian .log file in Paratool Jan Saam (Tue Jul 31 2007 - 11:05:34 CDT)
Tachyon doesn't take into account ColorID Henry Yuen (Mon Jul 30 2007 - 12:54:13 CDT)
- Re: Tachyon doesn't take into account ColorID John Stone (Mon Jul 30 2007 - 14:32:22 CDT)
- Re: Tachyon doesn't take into account ColorID Axel Kohlmeyer (Mon Jul 30 2007 - 14:17:13 CDT)
adding urea to a protein-water system L. Michel Espinoza-Fonseca (Mon Jul 30 2007 - 05:05:46 CDT)
PBC problem in gofr sfrickenhaus (Mon Jul 30 2007 - 04:53:40 CDT)
- Re: PBC problem in gofr Axel Kohlmeyer (Mon Jul 30 2007 - 08:57:10 CDT)
RE: problem with rmsd-fullthrottle Irene Newhouse (Sat Jul 28 2007 - 15:02:54 CDT)
can't add packages karan uppal (Sat Jul 28 2007 - 12:59:37 CDT)
- Re: can't add packages Axel Kohlmeyer (Sat Jul 28 2007 - 17:32:46 CDT)
orientation of hexahedrons parallelepipeds unit cells relative to x,y axes Èùìáò Åõáããåëéäçò (Sat Jul 28 2007 - 09:03:23 CDT)
- Re: orientation of hexahedrons parallelepipeds unit cells relative to x,y axes Axel Kohlmeyer (Sat Jul 28 2007 - 17:24:08 CDT)
problem with rmsd-fullthrottle Irene Newhouse (Fri Jul 27 2007 - 15:16:54 CDT)
- RE: problem with rmsd-fullthrottle JC Gumbart (Sat Jul 28 2007 - 15:36:02 CDT)
Wrap only whole molecules zhenlong li (Fri Jul 27 2007 - 13:00:54 CDT)
- Re: Wrap only whole molecules Axel Kohlmeyer (Fri Jul 27 2007 - 13:26:06 CDT)
- Re: Wrap only whole molecules Jim Phillips (Fri Jul 27 2007 - 16:48:26 CDT)
dssp in vmd (II) pascal.baillod_at_epfl.ch (Fri Jul 27 2007 - 05:04:54 CDT)
- Re: dssp in vmd (II) John Stone (Fri Jul 27 2007 - 12:42:49 CDT)
RE: puzzling psfgen problem with deleted atoms coming back Irene Newhouse (Thu Jul 26 2007 - 17:40:01 CDT)
- Deleting bonds based on length Arneh Babakhani (Thu Jul 26 2007 - 23:41:11 CDT)
  - Re: Deleting bonds based on length Olaf Lenz (Fri Jul 27 2007 - 01:28:09 CDT)
    - Re: Deleting bonds based on length Arneh Babakhani (Fri Jul 27 2007 - 07:58:41 CDT)
- VMD-L moderation fully automatic from now on.... John Stone (Mon Jul 30 2007 - 14:46:47 CDT)
RE: residue_rmsd.tcl Irene Newhouse (Thu Jul 26 2007 - 16:17:46 CDT)
- Re: residue_rmsd.tcl John Stone (Thu Jul 26 2007 - 16:20:50 CDT)
- RE: residue_rmsd.tcl Irene Newhouse (Thu Jul 26 2007 - 16:29:55 CDT)
installation errors with src/hesstrans_wrap.C AustinSmall_at_comcast.net (Thu Jul 26 2007 - 16:16:39 CDT)
- Re: installation errors with src/hesstrans_wrap.C John Stone (Thu Jul 26 2007 - 16:23:47 CDT)
puzzling psfgen problem with deleted atoms coming back Irene Newhouse (Fri Jul 13 2007 - 16:47:05 CDT)
(no subject) AustinSmall_at_comcast.net (Thu Jul 26 2007 - 16:06:23 CDT)
badwater script - help Jim Pfaendtner (Thu Jul 26 2007 - 15:18:48 CDT)
- Re: badwater script - help John Stone (Thu Jul 26 2007 - 16:28:08 CDT)
residue_rmsd.tcl Irene Newhouse (Thu Jul 26 2007 - 12:37:51 CDT)
- Re: residue_rmsd.tcl John Stone (Thu Jul 26 2007 - 12:42:11 CDT)
python and C++ extensions karan uppal (Thu Jul 26 2007 - 11:19:06 CDT)
- Re: python and C++ extensions John Stone (Thu Jul 26 2007 - 16:40:47 CDT)
- Re: python and C++ extensions Jim Phillips (Fri Jul 27 2007 - 16:56:00 CDT)
deposition simulation from lammps Kathleen Barron (Thu Jul 26 2007 - 11:04:33 CDT)
- Re: deposition simulation from lammps Axel Kohlmeyer (Thu Jul 26 2007 - 12:53:39 CDT)
Rotation matrix translatin vector vmd Hazai Eszter (Thu Jul 26 2007 - 05:37:23 CDT)
- Re: Rotation matrix translatin vector vmd Peter Freddolino (Thu Jul 26 2007 - 07:26:09 CDT)
nonstandard solvate + cyclic peptides in explicit DMSO box + gofr sfrickenhaus (Thu Jul 26 2007 - 04:45:13 CDT)
- Re: nonstandard solvate + cyclic peptides in explicit DMSO box + gofr Peter Freddolino (Thu Jul 26 2007 - 07:41:24 CDT)
- Re: nonstandard solvate + cyclic peptides in explicit DMSO box + gofr John Stone (Thu Jul 26 2007 - 11:33:52 CDT)
- Re: nonstandard solvate + cyclic peptides in explicit DMSO box + gofr Axel Kohlmeyer (Thu Jul 26 2007 - 11:48:08 CDT)
Boundry Dimensions for Solvation Vijaya Brahma (Thu Jul 26 2007 - 04:25:03 CDT)
- Re: Boundry Dimensions for Solvation Axel Kohlmeyer (Thu Jul 26 2007 - 11:41:04 CDT)
Re: ntermolecular atomselection Nuno Loureiro Ferreira (Thu Jul 26 2007 - 03:23:25 CDT)
ntermolecular atomselection Robert Wohlhueter (Thu Jul 26 2007 - 00:27:38 CDT)
- Re: ntermolecular atomselection Axel Kohlmeyer (Thu Jul 26 2007 - 11:35:46 CDT)
Boundry Dimensions for Solvation Vijaya Brahma (Wed Jul 25 2007 - 23:56:13 CDT)
vmd multiple residue snoze pa (Wed Jul 25 2007 - 14:42:05 CDT)
- Re: vmd multiple residue snoze pa (Wed Jul 25 2007 - 16:29:16 CDT)
  - Re: vmd multiple residue snoze pa (Wed Jul 25 2007 - 16:37:24 CDT)
vmd residue position snoze pa (Wed Jul 25 2007 - 14:29:51 CDT)
- Re: vmd residue position snoze pa (Wed Jul 25 2007 - 14:54:16 CDT)
- Re: vmd residue position John Stone (Thu Jul 26 2007 - 11:29:58 CDT)
  - Re: vmd residue position Peter Freddolino (Thu Jul 26 2007 - 14:38:42 CDT)
how to run VMD on IBM machines Rachel (Wed Jul 25 2007 - 11:11:34 CDT)
- Re: how to run VMD on IBM machines Axel Kohlmeyer (Wed Jul 25 2007 - 11:04:02 CDT)
  - Re: how to run VMD on IBM machines John Stone (Wed Jul 25 2007 - 13:02:32 CDT)
how to wrap trajectory into truncated octahedral box Rachel (Wed Jul 25 2007 - 10:51:54 CDT)
- Re: how to wrap trajectory into truncated octahedral box Olaf Lenz (Wed Jul 25 2007 - 12:39:39 CDT)
  - Re: how to wrap trajectory into truncated octahedral box sally cii (Thu Jul 26 2007 - 07:03:51 CDT)
    - Re: how to wrap trajectory into truncated octahedral box Olaf Lenz (Thu Jul 26 2007 - 09:20:03 CDT)
    - Re: how to wrap trajectory into truncated octahedral box Axel Kohlmeyer (Thu Jul 26 2007 - 11:50:43 CDT)
- Re: how to wrap trajectory into truncated octahedral box David A. Case (Mon Jul 30 2007 - 11:30:15 CDT)
Calculating volumetric data for a molecule Cesar Luis Avila (Tue Jul 24 2007 - 17:30:43 CDT)
- Re: Calculating volumetric data for a molecule John Stone (Tue Jul 24 2007 - 23:10:06 CDT)
NAMDEnergy virginia miguel (Tue Jul 24 2007 - 13:18:37 CDT)
- Re: NAMDEnergy Peter Freddolino (Tue Jul 24 2007 - 13:26:29 CDT)
frame number input in tcl and direct mol graph display update (II) pascal.baillod_at_epfl.ch (Tue Jul 24 2007 - 09:36:35 CDT)
- Re: frame number input in tcl and direct mol graph display update (II) John Stone (Thu Jul 26 2007 - 16:25:21 CDT)
  - Re: frame number input in tcl and direct mol graph display update (II) pascal.baillod_at_epfl.ch (Fri Jul 27 2007 - 04:56:24 CDT)
    - Re: frame number input in tcl and direct mol graph display update (II) John Stone (Fri Jul 27 2007 - 12:40:35 CDT)
    - Re: frame number input in tcl and direct mol graph display update (II) Axel Kohlmeyer (Fri Jul 27 2007 - 13:56:05 CDT)
how to select atoms according to b-factor Rachel (Mon Jul 23 2007 - 07:37:05 CDT)
- Re: how to select atoms according to b-factor Peter Freddolino (Mon Jul 23 2007 - 09:17:30 CDT)
saltbr# vs. frames hori koshii (Mon Jul 23 2007 - 06:50:10 CDT)
- Re: saltbr# vs. frames Leonardo Trabuco (Mon Jul 23 2007 - 10:28:01 CDT)
  - Re: saltbr# vs. frames Leonardo Trabuco (Mon Jul 23 2007 - 10:32:46 CDT)
Autopsf snoze pa (Fri Jul 20 2007 - 12:42:18 CDT)
- Re: Autopsf Peter Freddolino (Fri Jul 20 2007 - 13:59:56 CDT)
Parameter snoze pa (Fri Jul 20 2007 - 12:03:12 CDT)
- Re: namd-l: Parameter Leonardo Trabuco (Fri Jul 20 2007 - 13:21:40 CDT)
  - Re: namd-l: Parameter snoze pa (Fri Jul 20 2007 - 14:49:18 CDT)
what's the unit for color scale data range? Insight II (Thu Jul 19 2007 - 15:09:17 CDT)
- Re: what's the unit for color scale data range? Leonardo Trabuco (Thu Jul 19 2007 - 15:35:27 CDT)
  - Reading a pdbqt file (generated from AutoDock) Arneh Babakhani (Thu Jul 19 2007 - 18:01:01 CDT)
- Re: what's the unit for color scale data range? John Stone (Fri Jul 20 2007 - 11:23:46 CDT)
Writing out .dcd for discontinous frames Neelanjana Sengupta (Thu Jul 19 2007 - 00:09:36 CDT)
- Re: Writing out .dcd for discontinous frames Nuno Loureiro Ferreira (Thu Jul 19 2007 - 03:47:18 CDT)
- Re: Writing out .dcd for discontinous frames Axel Kohlmeyer (Thu Jul 19 2007 - 06:14:19 CDT)
Setting modstyle volumeslice options via tk console Cesar Luis Avila (Wed Jul 18 2007 - 15:16:20 CDT)
- Re: Setting modstyle volumeslice options via tk console Axel Kohlmeyer (Wed Jul 18 2007 - 16:27:47 CDT)
Re: Making a selection from another selection Arneh Babakhani (Tue Jul 17 2007 - 20:35:19 CDT)
water sphere? Daniel Kennedy (Tue Jul 17 2007 - 16:40:57 CDT)
- Making a selection from another selection Arneh Babakhani (Tue Jul 17 2007 - 20:02:49 CDT)
  - Re: Making a selection from another selection Peter Freddolino (Tue Jul 17 2007 - 20:14:40 CDT)
Regarding APBS calculation in VMD naga raju (Tue Jul 17 2007 - 07:39:06 CDT)
- Re: Regarding APBS calculation in VMD Axel Kohlmeyer (Tue Jul 17 2007 - 07:43:04 CDT)
TkCon problem luca.dallaglio2_at_studio.unibo.it (Mon Jul 16 2007 - 02:15:29 CDT)
- Re: TkCon problem John Stone (Mon Jul 16 2007 - 15:39:23 CDT)
atoms deleted in patch try to come back Irene Newhouse (Sun Jul 15 2007 - 01:01:48 CDT)
- RE: atoms deleted in patch try to come back JC Gumbart (Sun Jul 15 2007 - 02:02:18 CDT)
Language definitions - \usepackage{listings} Nuno Loureiro Ferreira (Sat Jul 14 2007 - 10:47:57 CDT)
- Re: Language definitions - \usepackage{listings} John Stone (Mon Jul 16 2007 - 11:58:29 CDT)
  - Re: Language definitions - \usepackage{listings} Nuno Loureiro Ferreira (Mon Jul 16 2007 - 12:19:59 CDT)
  - Re: Language definitions - \usepackage{listings} Nuno Loureiro Ferreira (Tue Jul 17 2007 - 07:35:17 CDT)
    - Re: Language definitions - \usepackage{listings} Axel Kohlmeyer (Tue Jul 17 2007 - 07:11:54 CDT)
    - Re: Language definitions - \usepackage{listings} Nuno Loureiro Ferreira (Tue Jul 17 2007 - 10:26:20 CDT)
RDF calculations Fred Moore (Fri Jul 13 2007 - 15:16:40 CDT)
- Re: RDF calculations Axel Kohlmeyer (Fri Jul 13 2007 - 17:38:35 CDT)
how to save a list in a file sally cii (Fri Jul 13 2007 - 12:02:02 CDT)
- Re: how to save a list in a file Axel Kohlmeyer (Fri Jul 13 2007 - 13:04:16 CDT)
- Re: how to save a list in a file Nuno Loureiro Ferreira (Sat Jul 14 2007 - 11:49:29 CDT)
  - Re: how to save a list in a file sally cii (Mon Jul 16 2007 - 07:12:14 CDT)
Problem with namdstats.tcl in TkCon luca.dallaglio2_at_studio.unibo.it (Fri Jul 13 2007 - 03:12:03 CDT)
electron density map is shifted? Gunnar Schroeder (Thu Jul 12 2007 - 19:14:01 CDT)
- Re: electron density map is shifted? John Stone (Thu Jul 12 2007 - 22:28:21 CDT)
  - Re: electron density map is shifted? John Stone (Thu Aug 09 2007 - 14:57:55 CDT)
Electron microscopy surface with VMD? Emmanuel Levy (Thu Jul 12 2007 - 16:37:18 CDT)
- Re: Electron microscopy surface with VMD? John Stone (Thu Jul 12 2007 - 16:57:22 CDT)
error - with unknown atom type +CA shyamala (Thu Jul 12 2007 - 13:02:04 CDT)
- Re: error - with unknown atom type +CA Peter Freddolino (Thu Jul 12 2007 - 21:56:32 CDT)
frame number input in tcl and direct mol graph display update pascal.baillod_at_epfl.ch (Thu Jul 12 2007 - 09:35:45 CDT)
- Re: frame number input in tcl and direct mol graph display update Axel Kohlmeyer (Thu Jul 12 2007 - 10:03:43 CDT)
exporting xyz file Bhaskar Jyoti Borah (Thu Jul 12 2007 - 01:38:58 CDT)
- Re: exporting xyz file Axel Kohlmeyer (Thu Jul 12 2007 - 09:58:32 CDT)
  - Re: exporting xyz file Bhaskar Jyoti Borah (Thu Jul 12 2007 - 11:19:25 CDT)
    - Re: exporting xyz file Axel Kohlmeyer (Thu Jul 12 2007 - 10:37:40 CDT)
shifting of the origin Bhaskar Jyoti Borah (Tue Jul 10 2007 - 23:49:15 CDT)
- Re: shifting of the origin Axel Kohlmeyer (Wed Jul 11 2007 - 09:22:41 CDT)
  - Re: shifting of the origin Bhaskar Jyoti Borah (Wed Jul 11 2007 - 11:24:15 CDT)
displaying velocity from dlpoly history Stern, Julie (Tue Jul 10 2007 - 14:52:37 CDT)
- Re: displaying velocity from dlpoly history Peter Freddolino (Tue Jul 10 2007 - 15:22:13 CDT)
- Re: displaying velocity from dlpoly history Axel Kohlmeyer (Tue Jul 10 2007 - 15:07:16 CDT)
atomselect sally cii (Tue Jul 10 2007 - 03:03:23 CDT)
- Re: atomselect Olaf Lenz (Tue Jul 10 2007 - 03:52:46 CDT)
  - Re: atomselect sally cii (Tue Jul 10 2007 - 05:41:42 CDT)
- Re: atomselect Eduard Schreiner (Tue Jul 10 2007 - 09:23:23 CDT)
RE: some principles for building a topology file? Irene Newhouse (Mon Jul 09 2007 - 22:45:09 CDT)
some principles for building a topology file? Irene Newhouse (Mon Jul 09 2007 - 15:27:01 CDT)
- Re: some principles for building a topology file? Peter Freddolino (Mon Jul 09 2007 - 21:14:31 CDT)
Using multiple CPUS SeongJun Heo (Mon Jul 09 2007 - 14:20:14 CDT)
- Re: Using multiple CPUS Axel Kohlmeyer (Mon Jul 09 2007 - 14:12:00 CDT)
  - Re: Using multiple CPUS John Stone (Tue Jul 10 2007 - 20:26:32 CDT)
need help Bhaskar Jyoti Borah (Mon Jul 09 2007 - 05:25:50 CDT)
- Re: need help Axel Kohlmeyer (Mon Jul 09 2007 - 09:25:03 CDT)
  - Re: need help Bhaskar Jyoti Borah (Tue Jul 10 2007 - 01:19:58 CDT)
CAVE & Vmd Christian Wohlschlager (Fri Jul 06 2007 - 02:06:54 CDT)
- Re: CAVE & Vmd John Stone (Tue Jul 17 2007 - 11:46:13 CDT)
  - Antw: Re: CAVE & Vmd Christian Wohlschlager (Wed Jul 25 2007 - 08:21:27 CDT)
    - Re: Antw: Re: CAVE & Vmd John Stone (Thu Jul 26 2007 - 16:06:00 CDT)
    - Re: Antw: Re: CAVE & Vmd Christian Wohlschlager (Fri Jul 27 2007 - 01:45:45 CDT)
RMSD of different molecules hori koshii (Thu Jul 05 2007 - 20:50:56 CDT)
- Re: RMSD of different molecules Peter Freddolino (Fri Jul 06 2007 - 01:50:49 CDT)
  - Re: RMSD of different molecules Leonardo Trabuco (Fri Jul 06 2007 - 10:10:10 CDT)
command line dcd to trr? hori koshii (Thu Jul 05 2007 - 20:46:14 CDT)
- Re: command line dcd to trr? Axel Kohlmeyer (Fri Jul 06 2007 - 08:26:37 CDT)
calculation limit of gofr? Philipp Schön (Thu Jul 05 2007 - 10:16:00 CDT)
- Re: calculation limit of gofr? Axel Kohlmeyer (Thu Jul 05 2007 - 09:47:43 CDT)
Video card query Ignacio Fernández Galván (Thu Jul 05 2007 - 02:34:12 CDT)
- Re: Video card query Axel Kohlmeyer (Thu Jul 05 2007 - 09:42:37 CDT)
  - Re: Video card query Peter Freddolino (Thu Jul 05 2007 - 12:41:59 CDT)
Broken tube drawing method? Claw Isthelaw (Thu Jul 05 2007 - 00:17:37 CDT)
- Re: Broken tube drawing method? Axel Kohlmeyer (Thu Jul 05 2007 - 09:24:39 CDT)
VRPN, phantom and VMD... Dr. Luis Rosales Leon (Wed Jul 04 2007 - 17:12:38 CDT)
- Re: VRPN, phantom and VMD... John Stone (Mon Jul 16 2007 - 16:11:10 CDT)
vmd crashes on startup Arnab Mukherjee (Wed Jul 04 2007 - 16:11:36 CDT)
- Re: vmd crashes on startup Axel Kohlmeyer (Wed Jul 04 2007 - 15:55:33 CDT)
How to display boundary crossing bonds? Zhimin Xiong (Tue Jul 03 2007 - 23:58:00 CDT)
- Re: How to display boundary crossing bonds? Axel Kohlmeyer (Wed Jul 04 2007 - 11:51:57 CDT)
ACE and NH2 ÁèáíÜóéïò Óôáõñáêïýäçò (Tue Jul 03 2007 - 16:37:43 CDT)
- Re: ACE and NH2 Peter Freddolino (Tue Jul 03 2007 - 16:46:26 CDT)
developing plugins to vmd in python shourabh rawat (Tue Jul 03 2007 - 01:12:22 CDT)
- Re: developing plugins to vmd in python Axel Kohlmeyer (Tue Jul 03 2007 - 09:25:33 CDT)
Display bond between fragment and protein residue Mackay Steffensen (Mon Jul 02 2007 - 12:24:47 CDT)
VTF file Jakob Petersen (Sun Jul 01 2007 - 13:56:58 CDT)
- Re: VTF file Olaf Lenz (Mon Jul 02 2007 - 02:53:38 CDT)
Fwd: atom serial number Francesco Pietra (Sun Jul 01 2007 - 02:59:07 CDT)
atom serial number Francesco Pietra (Sun Jul 01 2007 - 02:33:20 CDT)
- Re: atom serial number Peter Freddolino (Sun Jul 01 2007 - 13:40:52 CDT)
RMSF calculation question: Parminder Mankoo (Sat Jun 30 2007 - 19:09:18 CDT)
- Re: RMSF calculation question: Leonardo Trabuco (Sat Jun 30 2007 - 20:14:56 CDT)
  - Re: RMSF calculation question: Parminder Mankoo (Sat Jun 30 2007 - 22:06:43 CDT)
trouble saving the state of two proteins Charlotte J Siska (Fri Jun 29 2007 - 12:45:27 CDT)
- Re: trouble saving the state of two proteins Peter Freddolino (Fri Jun 29 2007 - 12:48:33 CDT)
  - Re: trouble saving the state of two proteins Peter Freddolino (Fri Jun 29 2007 - 15:31:51 CDT)
how to calculate hydrogen bond? lily jin (Fri Jun 29 2007 - 12:21:54 CDT)
- Re: how to calculate hydrogen bond? Axel Kohlmeyer (Sun Jul 01 2007 - 21:34:56 CDT)
Hydrogen and Water Molecules. Yu Liu (Wed Jun 27 2007 - 11:13:40 CDT)
Away until July 12, self-help encouraged! John Stone (Thu Jun 28 2007 - 17:22:36 CDT)
vmd and amber Francesco Pietra (Thu Jun 28 2007 - 16:08:37 CDT)
- Re: vmd and amber Axel Kohlmeyer (Thu Jun 28 2007 - 16:14:49 CDT)
get charge lily jin (Thu Jun 28 2007 - 12:56:46 CDT)
- Re: get charge John Stone (Thu Jun 28 2007 - 13:07:51 CDT)
- Re: get charge Axel Kohlmeyer (Thu Jun 28 2007 - 12:27:43 CDT)
generate surface figure Zhenwei Lu (Thu Jun 28 2007 - 11:54:31 CDT)
- Re: generate surface figure Axel Kohlmeyer (Thu Jun 28 2007 - 12:25:30 CDT)
glycerol box amit dong (Thu Jun 28 2007 - 11:14:12 CDT)
- Re: glycerol box Peter Freddolino (Thu Jun 28 2007 - 12:00:13 CDT)
Amber patches for Auto PSF generator Bob Johnson (Wed Jun 27 2007 - 11:55:44 CDT)
- Re: Amber patches for Auto PSF generator Peter Freddolino (Wed Jun 27 2007 - 12:04:09 CDT)
error while generating a tetramer using transformation matrix Ruchi Sachdeva (Wed Jun 27 2007 - 01:15:28 CDT)
- Re: error while generating a tetramer using transformation matrix Himanshu Khandelia (Wed Jun 27 2007 - 04:00:50 CDT)
angle between protein domains: PARMINDER MANKOO (Tue Jun 26 2007 - 15:46:02 CDT)
help on making stereo diagram Zhenwei Lu (Tue Jun 26 2007 - 15:25:59 CDT)
- Re: help on making stereo diagram John Stone (Tue Jun 26 2007 - 15:46:56 CDT)
parallel capabilities Jana Black (Tue Jun 26 2007 - 14:27:38 CDT)
- Re: parallel capabilities John Stone (Tue Jun 26 2007 - 14:56:29 CDT)
  - Re: parallel capabilities Axel Kohlmeyer (Tue Jun 26 2007 - 16:24:22 CDT)
    - Re: parallel capabilities John Stone (Tue Jun 26 2007 - 18:06:07 CDT)
- Re: parallel capabilities L. Michel Espinoza-Fonseca (Tue Jun 26 2007 - 15:16:58 CDT)
- Re: parallel capabilities Axel Kohlmeyer (Tue Jun 26 2007 - 14:14:27 CDT)
question about ligand volmap Rachel (Tue Jun 26 2007 - 10:56:34 CDT)
- Re: question about ligand volmap Jordi Cohen (Wed Jun 27 2007 - 11:29:31 CDT)
redefining macros vs. update of selections Axel Kohlmeyer (Mon Jun 25 2007 - 19:28:53 CDT)
- Re: redefining macros vs. update of selections John Stone (Tue Jun 26 2007 - 14:52:31 CDT)
! Obtain degrees from Prestigious non-accredite dUniversities 1(484)993-7152 Marty (Sat Jun 23 2007 - 01:45:28 CDT)
Using VMD just to plot some coordinates from a mathematical/geometrical model Arneh Babakhani (Fri Jun 22 2007 - 17:51:35 CDT)
- Re: Using VMD just to plot some coordinates from a mathematical/geometrical model John Stone (Fri Jun 22 2007 - 17:51:59 CDT)
  - Re: Using VMD just to plot some coordinates from a mathematical/geometrical model Arneh Babakhani (Fri Jun 22 2007 - 20:04:40 CDT)
Loading up PDB files in absolute coordinates Arneh Babakhani (Fri Jun 22 2007 - 13:10:06 CDT)
- Re: Loading up PDB files in absolute coordinates John Stone (Fri Jun 22 2007 - 13:24:30 CDT)
  - Re: Loading up PDB files in absolute coordinates Arneh Babakhani (Fri Jun 22 2007 - 13:50:59 CDT)
Text/Labels on ray tracing external renderer Petrica GASCA (Fri Jun 22 2007 - 09:28:57 CDT)
- Re: Text/Labels on ray tracing external renderer John Stone (Fri Jun 22 2007 - 13:03:41 CDT)
  - Re: Text/Labels on ray tracing external renderer Axel Kohlmeyer (Fri Jun 22 2007 - 14:26:00 CDT)
Rotate dx map Cesar Luis Avila (Thu Jun 21 2007 - 10:03:50 CDT)
- Re: Rotate dx map John Stone (Fri Jun 22 2007 - 17:25:56 CDT)
center scaling and rotation Tim Meyer (Thu Jun 21 2007 - 09:35:40 CDT)
- Re: center scaling and rotation John Stone (Fri Jun 22 2007 - 17:25:01 CDT)
Changing Beta values for each frame of a trajectory.. Arun Krishnan (Wed Jun 20 2007 - 22:08:17 CDT)
- Re: Changing Beta values for each frame of a trajectory.. John Stone (Wed Jun 20 2007 - 22:50:19 CDT)
  - Re: Changing Beta values for each frame of a trajectory.. Arun Krishnan (Wed Jun 20 2007 - 23:39:21 CDT)
volmap commands Lutz Maibaum (Wed Jun 20 2007 - 20:35:15 CDT)
- Re: volmap commands Jordi Cohen (Wed Jun 20 2007 - 21:56:08 CDT)
  - Re: volmap commands Lutz Maibaum (Wed Jun 20 2007 - 23:19:01 CDT)
Fw: namd-l-outgoing2@halifax.ks.uiuc.edu lily jin (Wed Jun 20 2007 - 15:25:56 CDT)
Mail System Error - Returned Mail The Post Office (Wed Jun 20 2007 - 12:17:09 CDT)
Re: atomselection Luis Rosales (Wed Jun 20 2007 - 10:14:56 CDT)
atomselection Kevser Göçmen Topal (Wed Jun 20 2007 - 02:27:50 CDT)
Box dimensions Jennie Thomas (Tue Jun 19 2007 - 17:59:53 CDT)
- Re: Box dimensions John Stone (Tue Jun 19 2007 - 18:03:34 CDT)
  - Re: Box dimensions Jennie Thomas (Tue Jun 19 2007 - 18:28:12 CDT)
    - Re: Box dimensions John Stone (Wed Jun 20 2007 - 10:55:34 CDT)
- Script to rendering ANISOU records in VMD Aaron Oakley (Tue Jun 19 2007 - 21:22:51 CDT)
  - Re: Script to rendering ANISOU records in VMD Axel Kohlmeyer (Tue Jun 19 2007 - 22:08:55 CDT)
atomsel: writepdb failed for vmd 1.8.6 Margaret S. Cheung (Tue Jun 19 2007 - 16:16:24 CDT)
- Re: atomsel: writepdb failed for vmd 1.8.6 John Stone (Tue Jun 19 2007 - 17:21:01 CDT)
adding residue at start or end Zhenwei Lu (Tue Jun 19 2007 - 10:58:30 CDT)
- Re: adding residue at start or end Peter Freddolino (Tue Jun 19 2007 - 12:41:10 CDT)
VMD for PPC64 SLES9? Mike Hanby (Tue Jun 19 2007 - 10:19:26 CDT)
- Re: VMD for PPC64 SLES9? John Stone (Tue Jun 19 2007 - 10:49:49 CDT)
  - RE: VMD for PPC64 SLES9? Mike Hanby (Tue Jun 19 2007 - 11:53:44 CDT)
Tracking bond length changes in a simulation Adilah Hussien (Tue Jun 19 2007 - 04:33:22 CDT)
- Re: Tracking bond length changes in a simulation John Stone (Tue Jun 19 2007 - 10:53:00 CDT)
VMD 1.8.6 Not Responding! Vijaya Brahma (Sun Jun 17 2007 - 23:59:06 CDT)
- Re: VMD 1.8.6 Not Responding! Axel Kohlmeyer (Mon Jun 18 2007 - 09:49:47 CDT)
- Re: VMD 1.8.6 Not Responding! John Stone (Mon Jun 18 2007 - 16:04:51 CDT)
  - VMD 1.8.6 Not Responding! Vijaya Brahma (Wed Jun 20 2007 - 23:31:27 CDT)
Solvate 1.2 problem option -ion luca.dallaglio2_at_studio.unibo.it (Thu Jun 14 2007 - 07:02:39 CDT)
- Re: Solvate 1.2 problem option -ion John Stone (Fri Jun 15 2007 - 16:12:51 CDT)
atom position update for reference atom list Philipp Schoen1 (Wed Jun 13 2007 - 08:28:30 CDT)
- Re: atom position update for reference atom list John Stone (Mon Jun 18 2007 - 16:43:13 CDT)
superposition lily jin (Tue Jun 12 2007 - 12:05:20 CDT)
- Re: superposition John Stone (Tue Jun 12 2007 - 15:30:23 CDT)
PME plugin Cesar Luis Avila (Tue Jun 12 2007 - 11:18:47 CDT)
- Re: PME plugin Cesar Luis Avila (Tue Jun 12 2007 - 11:22:26 CDT)
  - Re: Re: PME plugin John Stone (Tue Jun 12 2007 - 16:48:54 CDT)
PSFGEN:buiding an uncharged protein luca.dallaglio2_at_studio.unibo.it (Tue Jun 12 2007 - 02:55:14 CDT)
Paratool Add/Edit Internal Coordinates window Francesco Pietra (Tue Jun 12 2007 - 00:29:05 CDT)
Question about rendering across multiple frames Prashanth Athri (Mon Jun 11 2007 - 13:51:29 CDT)
- Re: Question about rendering across multiple frames John Stone (Mon Jun 11 2007 - 15:33:26 CDT)
Re: Paratool Window Jan Saam (Mon Jun 11 2007 - 14:22:00 CDT)
- Re: Paratool Window L. Michel Espinoza-Fonseca (Mon Jun 11 2007 - 14:52:14 CDT)
  - Paratool Reference (was Re: Paratool Window) Jan Saam (Fri Jun 15 2007 - 11:11:10 CDT)
script for atom collisions Kailee (Mon Jun 11 2007 - 12:10:30 CDT)
- Re: script for atom collisions John Stone (Mon Jun 11 2007 - 15:35:55 CDT)
  - Re: script for atom collisions Kailee (Tue Jun 12 2007 - 08:58:36 CDT)
    - Re: script for atom collisions John Stone (Wed Jun 13 2007 - 03:01:10 CDT)
    - Re: script for atom collisions Kailee (Fri Jun 15 2007 - 12:21:13 CDT)
Paratool Window Vivek Sharma (Mon Jun 11 2007 - 08:48:07 CDT)
Nearest neighbor selection Richard Swenson (Mon Jun 11 2007 - 10:23:57 CDT)
- Re: Nearest neighbor selection John Stone (Tue Jun 12 2007 - 10:36:02 CDT)
  - Re: Nearest neighbor selection Richard Swenson (Tue Jun 12 2007 - 15:23:31 CDT)
vmd visualization and CMAP run problem Moumita Maiti (Mon Jun 11 2007 - 00:52:23 CDT)
- Re: vmd visualization and CMAP run problem John Stone (Wed Jun 13 2007 - 03:04:49 CDT)
  - Re: vmd visualization and CMAP run problem Moumita Maiti (Wed Jun 13 2007 - 04:05:25 CDT)
    - Re: vmd visualization and CMAP run problem John Stone (Mon Jun 18 2007 - 16:47:26 CDT)
    - Re: vmd visualization and CMAP run problem John Stone (Mon Jun 18 2007 - 16:59:19 CDT)
use animatepdbs.tcl to include APBS potential maps Cesar Millan (Sat Jun 09 2007 - 22:48:02 CDT)
- Re: use animatepdbs.tcl to include APBS potential maps Axel Kohlmeyer (Sun Jun 10 2007 - 15:00:58 CDT)
  - Re: use animatepdbs.tcl to include APBS potential maps Cesar Millan (Sun Jun 10 2007 - 22:09:27 CDT)
    - Re: use animatepdbs.tcl to include APBS potential maps Axel Kohlmeyer (Mon Jun 11 2007 - 11:22:01 CDT)
rmsd calculation for RNA Moumita Maiti (Fri Jun 08 2007 - 11:48:58 CDT)
Help with Tcl script Manali Mehendale (Fri Jun 08 2007 - 11:09:56 CDT)
- Re: Help with Tcl script John Stone (Wed Jun 13 2007 - 03:23:27 CDT)
- Re: Help with Tcl script Jan Saam (Wed Jun 13 2007 - 04:00:03 CDT)
Simple TCL/Tk question Pavan Ghatty (Fri Jun 08 2007 - 11:04:10 CDT)
- Re: Simple TCL/Tk question Peter Freddolino (Fri Jun 08 2007 - 11:37:06 CDT)
- Re: Simple TCL/Tk question Robert Brunner (Fri Jun 08 2007 - 14:55:20 CDT)
problem when drawing a cylinder Zhimin Xiong (Fri Jun 08 2007 - 03:27:28 CDT)
- Re: problem when drawing a cylinder Olaf Lenz (Fri Jun 08 2007 - 04:01:40 CDT)
Python Module Harry Bullen (Thu Jun 07 2007 - 13:00:41 CDT)
- Re: Python Module Axel Kohlmeyer (Thu Jun 07 2007 - 17:50:14 CDT)
  - Re: Python Module Justin Gullingsrud (Fri Jun 08 2007 - 09:43:50 CDT)
    - Re: Python Module John Stone (Fri Jun 08 2007 - 10:38:01 CDT)
    - Re: Python Module Harry Bullen (Fri Jun 08 2007 - 11:03:39 CDT)
  - Re: Python Module Harry Bullen (Fri Jun 08 2007 - 08:40:36 CDT)
    - Re: Python Module Axel Kohlmeyer (Fri Jun 08 2007 - 08:35:04 CDT)
RENDER ISSUES Claire Zerafa (Thu Jun 07 2007 - 08:48:17 CDT)
- RE: RENDER ISSUES JC Gumbart (Thu Jun 07 2007 - 09:07:34 CDT)
rendering problems Claire Zerafa (Thu Jun 07 2007 - 09:37:13 CDT)
traj not visualized but pdb is visualized Lambert van Eijck (Thu Jun 07 2007 - 04:44:49 CDT)
- Re: traj not visualized but pdb is visualized Axel Kohlmeyer (Thu Jun 07 2007 - 08:29:33 CDT)
  - Re: traj not visualized but pdb is visualized Lambert van Eijck (Thu Jun 07 2007 - 09:55:57 CDT)
.xyz file, namelist index too large error Erkan Tuzel (Wed Jun 06 2007 - 19:39:48 CDT)
- Re: .xyz file, namelist index too large error Axel Kohlmeyer (Wed Jun 06 2007 - 19:00:56 CDT)
- Re: .xyz file, namelist index too large error John Stone (Thu Jun 07 2007 - 11:11:43 CDT)
how to visualize Charmm generated files ThuZar Lwin (Wed Jun 06 2007 - 16:38:54 CDT)
- Re: how to visualize Charmm generated files Alessandro Cembran (Wed Jun 06 2007 - 18:15:41 CDT)
release memory in TCL lily jin (Wed Jun 06 2007 - 14:44:13 CDT)
- Re: release memory in TCL Axel Kohlmeyer (Wed Jun 06 2007 - 16:35:17 CDT)
  - Re: release memory in TCL lily jin (Thu Jun 07 2007 - 11:46:11 CDT)
- Re: release memory in TCL Jerome Henin (Wed Jun 06 2007 - 17:47:26 CDT)
changing certain dihedral angles while keeping rest of molecule fixed Himanshu Khandelia (Wed Jun 06 2007 - 04:37:01 CDT)
- Re: changing certain dihedral angles while keeping rest of molecule fixed Peter Freddolino (Wed Jun 06 2007 - 09:24:18 CDT)
  - Re: changing certain dihedral angles while keeping rest of molecule fixed Himanshu Khandelia (Wed Jun 06 2007 - 10:02:54 CDT)
    - Re: changing certain dihedral angles while keeping rest of molecule fixed Peter Freddolino (Wed Jun 06 2007 - 10:41:54 CDT)
Duplicate VMD-L emails... John Stone (Tue Jun 05 2007 - 13:11:26 CDT)
Fwd: vmd installation Linux Debian i386 Francesco Pietra (Tue Jun 05 2007 - 12:55:05 CDT)
- Re: Fwd: vmd installation Linux Debian i386 John Stone (Tue Jun 05 2007 - 13:02:26 CDT)
  - Re: Fwd: vmd installation Linux Debian i386 Francesco Pietra (Tue Jun 05 2007 - 17:47:06 CDT)
What is the influence of PBC on measure bond? Philipp Schoen1 (Tue Jun 05 2007 - 09:30:03 CDT)
- Re: What is the influence of PBC on measure bond? John Stone (Tue Jun 05 2007 - 10:12:00 CDT)
VMD-Main window doesn't load after change in .vmdrc Grant Schauer (Mon Jun 04 2007 - 20:22:55 CDT)
- Re: VMD-Main window doesn't load after change in .vmdrc John Stone (Mon Jun 04 2007 - 20:59:37 CDT)
  - Re: VMD-Main window doesn't load after change in .vmdrc Grant Schauer (Mon Jun 04 2007 - 22:20:30 CDT)
- Re: VMD-Main window doesn't load after change in .vmdrc Axel Kohlmeyer (Mon Jun 04 2007 - 20:12:25 CDT)
list in TCL lily jin (Mon Jun 04 2007 - 18:47:16 CDT)
- Re: list in TCL John Stone (Mon Jun 04 2007 - 19:36:42 CDT)
- Re: list in TCL Giovanni Bellesia (Mon Jun 04 2007 - 19:39:37 CDT)
- Re: list in TCL JC Gumbart (Mon Jun 04 2007 - 19:41:42 CDT)
- Re: list in TCL Cesar Luis Avila (Mon Jun 04 2007 - 20:07:33 CDT)
labeling for movie title xiaoqin huang (Mon Jun 04 2007 - 13:21:54 CDT)
- Re: labeling for movie title John Stone (Mon Jun 04 2007 - 16:04:21 CDT)
removing water molecules Atila Iamarino (Mon Jun 04 2007 - 13:21:33 CDT)
- Re: removing water molecules John Stone (Mon Jun 04 2007 - 15:31:53 CDT)
load state and alignments Stern, Julie (Mon Jun 04 2007 - 10:56:36 CDT)
- Re: load state and alignments John Stone (Mon Jun 04 2007 - 14:41:21 CDT)
Distance measurement via measure bond Philipp Schoen1 (Mon Jun 04 2007 - 10:32:02 CDT)
- Re: Distance measurement via measure bond Axel Kohlmeyer (Mon Jun 04 2007 - 10:26:18 CDT)
- Re: Distance measurement via measure bond John Stone (Mon Jun 04 2007 - 14:36:31 CDT)
parameters file of POPC SMAHANE CHALABI (Mon Jun 04 2007 - 09:22:30 CDT)
- Re: parameters file of POPC Axel Kohlmeyer (Mon Jun 04 2007 - 09:17:02 CDT)
Installing VMD 1.8.6 Philipp Schoen1 (Mon Jun 04 2007 - 07:54:24 CDT)
- Re: Installing VMD 1.8.6 Olaf Lenz (Mon Jun 04 2007 - 08:54:21 CDT)
- Re: Installing VMD 1.8.6 Axel Kohlmeyer (Mon Jun 04 2007 - 08:03:30 CDT)
- Re: Installing VMD 1.8.6 John Stone (Mon Jun 04 2007 - 13:09:42 CDT)
  - Re: Installing VMD 1.8.6 Francesco Pietra (Mon Jun 04 2007 - 16:14:29 CDT)
Atom names, RES-IDS...!!! Raul Araya (Fri Jun 01 2007 - 23:55:33 CDT)
- Re: Atom names, RES-IDS...!!! JC Gumbart (Mon Jun 04 2007 - 18:18:45 CDT)
Re: CCL: show ruler in VMD John Stone (Fri Jun 01 2007 - 14:11:07 CDT)
self-coeeficient diffusion nicolas.floquet_at_univ-reims.fr (Fri Jun 01 2007 - 07:41:27 CDT)
Using VolMap tool for charge density visualization Bob Johnson (Fri Jun 01 2007 - 09:59:47 CDT)
Order Parameter Script for changing bilayer normal Richard Swenson (Fri Jun 01 2007 - 09:21:07 CDT)
Using regular expressions on tcl atomselection Cesar Luis Avila (Thu May 31 2007 - 17:45:32 CDT)
- Re: Using regular expressions on tcl atomselection Leonardo Trabuco (Thu May 31 2007 - 18:01:55 CDT)
- Re: Using regular expressions on tcl atomselection Axel Kohlmeyer (Thu May 31 2007 - 17:17:25 CDT)
Electron density profile Cesar Luis Avila (Thu May 31 2007 - 11:30:29 CDT)
lipid Scd order parameter for a large bilayer (1440 lipids) with a changing bilayer normal (ie. bilayer undulations) Richard Swenson (Wed May 30 2007 - 14:15:13 CDT)
- Re: lipid Scd order parameter for a large bilayer (1440 lipids) with a changing bilayer normal (ie. bilayer undulations) Axel Kohlmeyer (Wed May 30 2007 - 14:14:08 CDT)
  - Re: lipid Scd order parameter for a large bilayer (1440 lipids) with a changing bilayer normal (ie. bilayer undulations) Cesar Luis Avila (Wed May 30 2007 - 20:36:09 CDT)
- Re: lipid Scd order parameter for a large bilayer (1440 lipids) with a changing bilayer normal (ie. bilayer undulations) Cesar Luis Avila (Wed Jun 06 2007 - 10:55:19 CDT)
  - Mac OSX TK console issues Marc Baaden (Fri Jun 15 2007 - 09:21:51 CDT)
    - Re: Mac OSX TK console issues Brian Kidd (Fri Jun 15 2007 - 14:57:16 CDT)
    - Re: Mac OSX TK console issues John Stone (Fri Jun 15 2007 - 15:42:52 CDT)
pqr files---- Raul Araya (Tue May 29 2007 - 16:46:49 CDT)
- Re: pqr files---- Axel Kohlmeyer (Tue May 29 2007 - 18:49:38 CDT)
overlay Alison Grinthal (Tue May 29 2007 - 15:58:18 CDT)
- Re: overlay Peter Freddolino (Tue May 29 2007 - 16:20:56 CDT)
  - Re: overlay Marcos Sotomayor (Thu May 31 2007 - 01:29:50 CDT)
- plotting on Mac Alison Grinthal (Fri Aug 10 2007 - 14:50:11 CDT)
  - Re: plotting on Mac John Stone (Fri Aug 10 2007 - 15:11:43 CDT)
Reading in a MOL2 file Mark Zottola (Tue May 29 2007 - 11:31:44 CDT)
- Re: Reading in a MOL2 file Peter Freddolino (Tue May 29 2007 - 12:16:16 CDT)
- Color Scale Data Range Weiqiang Wang (Tue May 29 2007 - 17:08:16 CDT)
  - Re: Color Scale Data Range Weiqiang Wang (Tue May 29 2007 - 17:46:31 CDT)
colomb map in volmap tool Raul Araya (Mon May 28 2007 - 17:03:10 CDT)
- Re: colomb map in volmap tool John Stone (Mon May 28 2007 - 17:17:23 CDT)
overlay Alison Grinthal (Mon May 28 2007 - 06:45:38 CDT)
ligand parametrization Karol Kaszuba (Mon May 28 2007 - 10:57:05 CDT)
- Re: ligand parametrization John Stone (Mon May 28 2007 - 16:12:02 CDT)
  - PSF_and_PDB_file_of_LIGAND Karol Kaszuba (Fri Jun 01 2007 - 05:29:53 CDT)
    - Re: PSF_and_PDB_file_of_LIGAND Peter Freddolino (Fri Jun 01 2007 - 11:00:26 CDT)
- Re: ligand parametrization Jan Saam (Mon May 28 2007 - 18:51:57 CDT)
Problem with bondsrecalc Philippe Roche (Mon May 28 2007 - 11:29:47 CDT)
Problem with bondsrecalc Philippe Roche (Mon May 28 2007 - 11:33:07 CDT)
- Re: Problem with bondsrecalc Axel Kohlmeyer (Mon May 28 2007 - 13:17:22 CDT)
  - Re: Problem with bondsrecalc John Stone (Mon May 28 2007 - 15:38:50 CDT)
RE: Installation Error Involving TLC Claw Isthelaw (Sun May 27 2007 - 22:37:30 CDT)
- Re: Installation Error Involving TLC John Stone (Mon May 28 2007 - 15:35:26 CDT)
  - Re: Installation Error Involving TLC Axel Kohlmeyer (Mon May 28 2007 - 15:36:40 CDT)
help on trajectory density map Kailee (Sun May 27 2007 - 12:54:12 CDT)
- Re: help on trajectory density map Axel Kohlmeyer (Mon May 28 2007 - 10:40:12 CDT)
- Re: help on trajectory density map John Stone (Mon May 28 2007 - 15:34:23 CDT)
  - Re: help on trajectory density map Kailee (Tue May 29 2007 - 07:43:46 CDT)
    - Re: help on trajectory density map John Stone (Tue May 29 2007 - 10:07:15 CDT)
tkconsole and intel macs Dan Gordon (Sun May 27 2007 - 20:32:11 CDT)
- Re: tkconsole and intel macs Dan Gordon (Tue May 29 2007 - 19:21:03 CDT)
Fwd: Linux installation issue Francesco Pietra (Sat May 26 2007 - 09:57:40 CDT)
- Re: Fwd: Linux installation issue Axel Kohlmeyer (Sat May 26 2007 - 15:41:24 CDT)
  - Re: Fwd: Linux installation issue Francesco Pietra (Sun May 27 2007 - 02:44:32 CDT)
    - Re: Fwd: Linux installation issue Axel Kohlmeyer (Tue Jun 05 2007 - 10:00:17 CDT)
Fwd: Linux installation issue Francesco Pietra (Sat May 26 2007 - 09:47:51 CDT)
- Re: Fwd: Linux installation issue Axel Kohlmeyer (Sat May 26 2007 - 15:36:40 CDT)
Linux installation issue Francesco Pietra (Sat May 26 2007 - 09:38:53 CDT)
- Re: Linux installation issue Axel Kohlmeyer (Sat May 26 2007 - 15:32:59 CDT)
problem with installing VMD on a LINUX cluster Yinglong Miao (Fri May 25 2007 - 16:59:11 CDT)
- Re: problem with installing VMD on a LINUX cluster Axel Kohlmeyer (Fri May 25 2007 - 17:00:20 CDT)
  - Re: problem with installing VMD on a LINUX cluster John Stone (Wed May 30 2007 - 16:34:37 CDT)
- Re: problem with installing VMD on a LINUX cluster John Stone (Mon May 28 2007 - 15:43:50 CDT)
  - RE: problem with installing VMD on a LINUX cluster Yinglong Miao (Mon May 28 2007 - 22:54:54 CDT)
Installation Error Involving TLC Jana Black (Fri May 25 2007 - 13:44:00 CDT)
- Re: Installation Error Involving TLC Peter Freddolino (Fri May 25 2007 - 14:02:32 CDT)
- Re: Installation Error Involving TLC Axel Kohlmeyer (Fri May 25 2007 - 13:23:11 CDT)
travelling... John Stone (Fri May 25 2007 - 11:00:52 CDT)
selecting complete residues within perticular distance. naga raju (Fri May 25 2007 - 02:33:28 CDT)
- Re: selecting complete residues within perticular distance. Cesar Luis Avila (Sun May 27 2007 - 16:06:29 CDT)
  - Re: selecting complete residues within perticular distance. Peter Freddolino (Sun May 27 2007 - 18:09:46 CDT)
    - Re: selecting complete residues within perticular distance. Cesar Luis Avila (Mon May 28 2007 - 14:04:32 CDT)
    - Re: selecting complete residues within perticular distance. Peter Freddolino (Mon May 28 2007 - 15:58:26 CDT)
(no subject) Lechuga, Javier (Fri May 25 2007 - 08:10:27 CDT)
- Re: Axel Kohlmeyer (Fri May 25 2007 - 11:00:48 CDT)
regarding selecting complete residues within a distance naga raju (Fri May 25 2007 - 04:43:49 CDT)
- Re: regarding selecting complete residues within a distance Eduard Schreiner (Fri May 25 2007 - 07:41:48 CDT)
fortran/tcl Luca Bellucci (Fri May 25 2007 - 03:13:54 CDT)
- Re: fortran/tcl Axel Kohlmeyer (Fri May 25 2007 - 10:55:50 CDT)
non-standard residue Stern, Julie (Thu May 24 2007 - 21:15:31 CDT)
- Re: non-standard residue Nathan C. Rockwell (Fri May 25 2007 - 11:20:57 CDT)
- Re: non-standard residue John Stone (Mon May 28 2007 - 15:50:41 CDT)
How to use remote GLSL rendering capabilities? Cesar Luis Avila (Thu May 24 2007 - 18:02:43 CDT)
- Re: How to use remote GLSL rendering capabilities? Axel Kohlmeyer (Thu May 24 2007 - 17:38:36 CDT)
  - Re: How to use remote GLSL rendering capabilities? Cesar Luis Avila (Sun May 27 2007 - 16:05:03 CDT)
VMD installation Francesco Pietra (Thu May 24 2007 - 16:04:29 CDT)
- Re: VMD installation Axel Kohlmeyer (Thu May 24 2007 - 16:13:53 CDT)
Adjusting perspective Cesar Luis Avila (Thu May 24 2007 - 11:33:40 CDT)
- Re: Adjusting perspective John Stone (Mon May 28 2007 - 15:57:51 CDT)
Displaying the periodic box ... Stéphane Téletchéa (Thu May 24 2007 - 09:54:25 CDT)
- Re: Displaying the periodic box ... Axel Kohlmeyer (Thu May 24 2007 - 09:19:44 CDT)
- Re: Displaying the periodic box ... Alexandr Isayev (Thu May 24 2007 - 10:59:08 CDT)
- Re: Displaying the periodic box ... Eduard Schreiner (Thu May 24 2007 - 12:39:40 CDT)
paratool/gaff Francesco Pietra (Thu May 24 2007 - 01:14:37 CDT)
- Re: paratool/gaff Jan Saam (Thu May 24 2007 - 02:26:44 CDT)
  - Re: paratool/gaff Francesco Pietra (Thu May 24 2007 - 02:48:06 CDT)
  - Re: paratool/gaff Francesco Pietra (Wed Jun 06 2007 - 10:07:13 CDT)
questions about developing a plugin Yinglong Miao (Wed May 23 2007 - 15:21:11 CDT)
- Re: questions about developing a plugin Axel Kohlmeyer (Wed May 23 2007 - 16:19:17 CDT)
  - Re: questions about developing a plugin Peter Freddolino (Wed May 23 2007 - 19:18:48 CDT)
  - Re: questions about developing a plugin Yinglong Miao (Wed May 23 2007 - 22:20:39 CDT)
Automatic loading of mol2 files FyD (Wed May 23 2007 - 10:42:17 CDT)
- Re: Automatic loading of mol2 files Peter Freddolino (Wed May 23 2007 - 10:52:12 CDT)
About paratool Francesco Pietra (Wed May 23 2007 - 09:38:40 CDT)
calculating b-factors from trajectories gozorows_at_uci.edu (Tue May 22 2007 - 17:53:27 CDT)
- Re: calculating b-factors from trajectories Leandro Martínez (Tue May 22 2007 - 20:57:01 CDT)
- Re: calculating b-factors from trajectories Brian Bennion (Wed May 23 2007 - 10:34:57 CDT)
  - Re: calculating b-factors from trajectories gozorows_at_uci.edu (Wed May 23 2007 - 14:00:53 CDT)
    - Move labels Arneh Babakhani (Wed May 23 2007 - 16:21:33 CDT)
    - Re: Move labels Himanshu Khandelia (Thu May 24 2007 - 06:19:25 CDT)
Customized radii Manali Joshi (Tue May 22 2007 - 13:04:27 CDT)
- Re: Customized radii Axel Kohlmeyer (Tue May 22 2007 - 12:56:58 CDT)
RE: Automatically shutting down VMD after NAMD terminates IMD connection Claw Isthelaw (Sun May 20 2007 - 16:20:30 CDT)
vmd movies in powerpoint Richard Casey (Sun May 20 2007 - 06:01:02 CDT)
- RE: vmd movies in powerpoint Syma Khalid (Sun May 20 2007 - 06:22:04 CDT)
- Re: vmd movies in powerpoint Axel Kohlmeyer (Sun May 20 2007 - 12:23:32 CDT)
Automatically shutting down VMD after NAMD terminates IMD connection Claw Isthelaw (Sat May 19 2007 - 13:23:42 CDT)
- Re: Automatically shutting down VMD after NAMD terminates IMD connection John Stone (Sun May 20 2007 - 13:13:04 CDT)
volmap command and masks Marc Baaden (Fri May 18 2007 - 17:01:20 CDT)
- Re: volmap command and masks John Stone (Sun May 20 2007 - 13:16:38 CDT)
  - atomselection question Brian Kidd (Tue May 22 2007 - 18:55:55 CDT)
    - Re: atomselection question Peter Freddolino (Tue May 22 2007 - 19:29:53 CDT)
Re: custom db in Multiseq John Eargle (Fri May 18 2007 - 11:32:51 CDT)
- Re: custom db in Multiseq Armen Nalian (Fri May 18 2007 - 12:29:41 CDT)
  - Re: custom db in Multiseq Elijah Roberts (Tue May 22 2007 - 16:01:53 CDT)
- Re: custom db in Multiseq John Eargle (Fri May 18 2007 - 14:02:09 CDT)
help on writing a tcl script Kailee (Fri May 18 2007 - 10:57:58 CDT)
- Re: help on writing a tcl script Axel Kohlmeyer (Fri May 18 2007 - 11:22:27 CDT)
  - Re: help on writing a tcl script Axel Kohlmeyer (Sat May 19 2007 - 12:28:29 CDT)
Need help about hbond and saltbridge s104fendy (Fri May 18 2007 - 03:07:05 CDT)
- Re: Need help about hbond and saltbridge Leonardo Trabuco (Sat May 19 2007 - 17:14:18 CDT)
the error of the plugin QMTool in read gaussian output file mashaojienuaa (Fri May 18 2007 - 01:08:09 CDT)
- Re: the error of the plugin QMTool in read gaussian output file John Stone (Fri May 18 2007 - 16:56:20 CDT)
custom db in Multiseq Armen Nalian (Thu May 17 2007 - 18:48:01 CDT)
Questions on VMD Mark Zottola (Thu May 17 2007 - 16:44:10 CDT)
- Re: Questions on VMD Axel Kohlmeyer (Thu May 17 2007 - 16:32:05 CDT)
  - Re: Questions on VMD Kramer Campen (Thu May 17 2007 - 17:45:28 CDT)
inserting protein into membrane baxy (Thu May 17 2007 - 08:39:58 CDT)
- Re: inserting protein into membrane John Stone (Fri May 18 2007 - 16:21:10 CDT)
unreadable prmtop's and reference memory error? Stern, Julie (Thu May 17 2007 - 11:47:04 CDT)
- Re: unreadable prmtop's and reference memory error? John Stone (Thu May 17 2007 - 12:21:26 CDT)
(no subject) Lechuga, Javier (Thu May 17 2007 - 09:40:07 CDT)
- Re: Peter Freddolino (Thu May 17 2007 - 11:21:41 CDT)
Tachyon renderer zsinkala_at_mtsu.edu (Wed May 16 2007 - 23:03:14 CDT)
- Re: Tachyon renderer Alexandr Isayev (Wed May 16 2007 - 23:40:54 CDT)
how to make a movie using Principal Component Analysis gadde suneetha (Wed May 16 2007 - 20:02:48 CDT)
- Re: how to make a movie using Principal Component Analysis Axel Kohlmeyer (Wed May 16 2007 - 20:16:00 CDT)
NOC 3.0 is released chenmengen (Wed May 16 2007 - 14:01:37 CDT)
question about making movies Kailee (Wed May 16 2007 - 11:49:50 CDT)
- Re: question about making movies Axel Kohlmeyer (Wed May 16 2007 - 13:39:13 CDT)
- Re: question about making movies John Stone (Wed May 16 2007 - 14:44:17 CDT)
  - labeling for movie title xiaoqin huang (Mon Jun 04 2007 - 11:43:13 CDT)
absolute C.O.M motion calculation script: help hl332_at_drexel.edu (Wed May 16 2007 - 11:06:45 CDT)
- Re: absolute C.O.M motion calculation script: help John Stone (Fri May 18 2007 - 16:54:42 CDT)
How to add two parallel confinement wall Zhimin Xiong (Wed May 16 2007 - 04:27:04 CDT)
- Re: How to add two parallel confinement wall Peter Freddolino (Wed May 16 2007 - 07:34:31 CDT)
  - Re: How to add two parallel confinement wall Zhimin Xiong (Thu May 17 2007 - 09:41:48 CDT)
help for modification into a small tcl script hl332_at_drexel.edu (Tue May 15 2007 - 10:32:17 CDT)
how to use measure hbonds to calculate occupancy of all hbonds in simulation? lnubiofox (Tue May 15 2007 - 09:21:33 CDT)
- Re: namd-l: how to use measure hbonds to calculate occupancy of all hbonds in simulation? Dong Luo (Tue May 15 2007 - 18:27:01 CDT)
  - Re: namd-l: how to use measure hbonds to calculate occupancy of all hbonds in simulation? lnubiofox (Wed May 16 2007 - 09:57:51 CDT)
  - Re: namd-l: how to use measure hbonds to calculate occupancy of all hbonds in simulation? Dong Luo (Wed May 16 2007 - 11:44:01 CDT)
a gas box SMAHANE CHALABI (Tue May 15 2007 - 06:10:05 CDT)
- Re: a gas box Axel Kohlmeyer (Tue May 15 2007 - 08:22:16 CDT)
RNA Adrian Roitberg (Mon May 14 2007 - 14:25:03 CDT)
- Re: RNA George Madalin Giambasu (Mon May 14 2007 - 15:40:29 CDT)
AutoIMD on vmd 1.8.6 IRIX.... Luis Rosales (Fri May 11 2007 - 19:48:16 CDT)
- Re: AutoIMD on vmd 1.8.6 IRIX.... John Stone (Mon May 14 2007 - 12:52:34 CDT)
how to caculate the hydrogen bonds occupancy? lnubiofox (Sun May 13 2007 - 09:38:37 CDT)
- Re: how to caculate the hydrogen bonds occupancy? Axel Kohlmeyer (Sun May 13 2007 - 14:46:04 CDT)
An remark on PoV output Szymon Zietkiewicz (Sat May 12 2007 - 06:45:01 CDT)
- Re: An remark on PoV output John Stone (Mon May 14 2007 - 12:57:26 CDT)
  - Re: An remark on PoV output dstrahs_at_pace.edu (Mon May 14 2007 - 17:52:17 CDT)
Fast routines for distance evaluations using PBC. Arturas Ziemys (Fri May 11 2007 - 11:52:49 CDT)
- Re: Fast routines for distance evaluations using PBC. John Stone (Fri May 11 2007 - 13:15:27 CDT)
  - Re: Fast routines for distance evaluations using PBC. John Stone (Fri May 11 2007 - 13:46:39 CDT)
show atom number in xyz file Petrica GASCA (Fri May 11 2007 - 06:49:10 CDT)
- Re: show atom number in xyz file John Stone (Fri May 11 2007 - 11:06:17 CDT)
  - Re: show atom number in xyz file Petrica GASCA (Tue May 22 2007 - 04:32:36 CDT)
    - Re: show atom number in xyz file Axel Kohlmeyer (Tue May 22 2007 - 07:33:34 CDT)
    - Re: show atom number in xyz file JC Gumbart (Tue May 22 2007 - 11:59:35 CDT)
  - Re: show atom number in xyz file Petrica GASCA (Wed Jun 06 2007 - 10:24:47 CDT)
    - Re: show atom number in xyz file John Stone (Wed Jun 13 2007 - 02:52:12 CDT)
files for air SMAHANE CHALABI (Fri May 11 2007 - 04:01:27 CDT)
- Re: files for air Axel Kohlmeyer (Fri May 11 2007 - 07:46:23 CDT)
RMSD fitting for molecules adsorbed to surfaces Bob Johnson (Thu May 10 2007 - 16:12:09 CDT)
a air box SMAHANE CHALABI (Thu May 10 2007 - 08:38:15 CDT)
- Re: a air box Axel Kohlmeyer (Thu May 10 2007 - 09:22:45 CDT)
- Re: a air box Peter Freddolino (Thu May 10 2007 - 10:25:46 CDT)
Consider fluctuating volume for density Philipp Schoen1 (Thu May 10 2007 - 05:16:57 CDT)
- Re: Consider fluctuating volume for density Axel Kohlmeyer (Thu May 10 2007 - 09:45:04 CDT)
Fwd: vmd first installation Francesco Pietra (Wed May 09 2007 - 16:59:08 CDT)
- Re: Fwd: vmd first installation Axel Kohlmeyer (Wed May 09 2007 - 16:41:10 CDT)
  - Re: Fwd: vmd first installation Francesco Pietra (Fri May 11 2007 - 02:50:29 CDT)
Problem loading pdb file on VMD ren (Wed May 09 2007 - 02:10:48 CDT)
- Re: Problem loading pdb file on VMD John Stone (Wed May 09 2007 - 02:48:42 CDT)
  - Re: Problem loading pdb file on VMD Mario Valle (Wed May 09 2007 - 03:52:33 CDT)
    - Re: Problem loading pdb file on VMD Axel Kohlmeyer (Wed May 09 2007 - 07:38:54 CDT)
  - Re: Problem loading pdb file on VMD ren (Wed May 09 2007 - 04:46:42 CDT)
- Re: Problem loading pdb file on VMD Axel Kohlmeyer (Wed May 09 2007 - 07:37:56 CDT)
pbcunwrap, DL_POLY v 3 Joshua D. Moore (Wed May 09 2007 - 01:37:14 CDT)
- Re: pbcunwrap, DL_POLY v 3 Axel Kohlmeyer (Wed May 09 2007 - 07:42:23 CDT)
- Re: pbcunwrap, DL_POLY v 3 Olaf Lenz (Wed May 09 2007 - 08:52:55 CDT)
  - Re: pbcunwrap, DL_POLY v 3 Joshua D. Moore (Wed May 09 2007 - 11:27:29 CDT)
    - Re: pbcunwrap, DL_POLY v 3 Olaf Lenz (Wed May 09 2007 - 23:50:34 CDT)
vmd first installation Francesco Pietra (Wed May 09 2007 - 01:24:48 CDT)
drawing a membrane dimka (Tue May 08 2007 - 15:10:03 CDT)
- Re: drawing a membrane John Stone (Tue May 08 2007 - 16:34:02 CDT)
SASA measurements Michael S. Marlow (Tue May 08 2007 - 11:17:12 CDT)
- Re: SASA measurements John Stone (Tue May 08 2007 - 14:00:49 CDT)
installing MSMS on OS X 10.4.9 (Intel) Ralph Jimenez (Mon May 07 2007 - 21:37:38 CDT)
- Re: installing MSMS on OS X 10.4.9 (Intel) John Stone (Mon May 07 2007 - 21:44:39 CDT)
  - Re: installing MSMS on OS X 10.4.9 (Intel) Ralph Jimenez (Tue May 08 2007 - 12:12:33 CDT)
autoPSF with a POPC membrane Stephen M. Dutz (Mon May 07 2007 - 19:37:25 CDT)
- Re: autoPSF with a POPC membrane Peter Freddolino (Mon May 07 2007 - 20:40:47 CDT)
  - Re: autoPSF with a POPC membrane Peter Freddolino (Tue May 08 2007 - 18:19:12 CDT)
color by frame? andrea spitaleri (Mon May 07 2007 - 04:58:40 CDT)
- Re: color by frame? Axel Kohlmeyer (Mon May 07 2007 - 08:47:16 CDT)
  - Re: color by frame? John Stone (Mon May 07 2007 - 10:09:23 CDT)
problem using bigdcd.tcl script does not run beyond the first frame no error reported Himanshu Khandelia (Mon May 07 2007 - 04:42:10 CDT)
- Re: problem using bigdcd.tcl script does not run beyond the first frame no error reported Axel Kohlmeyer (Mon May 07 2007 - 08:36:50 CDT)
  - Re: problem using bigdcd.tcl script does not run beyond the first frame no error reported Himanshu Khandelia (Mon May 07 2007 - 10:25:56 CDT)
How to align a protein normal to lipid bilayer nur avneet (Sun May 06 2007 - 23:29:45 CDT)
- Re: How to align a protein normal to lipid bilayer John Stone (Sun May 06 2007 - 23:49:40 CDT)
measure hbonds lanhua (Fri May 04 2007 - 20:57:35 CDT)
nonbond interaction energy lanhua (Fri May 04 2007 - 12:14:55 CDT)
- Re: nonbond interaction energy Peter Freddolino (Fri May 04 2007 - 13:23:48 CDT)
How to align a protein normal to lipid bilayer nur avneet (Fri May 04 2007 - 06:33:55 CDT)
- Re: How to align a protein normal to lipid bilayer Axel Kohlmeyer (Fri May 04 2007 - 08:53:30 CDT)
- Re: How to align a protein normal to lipid bilayer Stéphane Téletchéa (Mon May 07 2007 - 03:44:36 CDT)
Contribution of selected atoms to surface Brian Smith (Fri May 04 2007 - 03:12:57 CDT)
- Re: Contribution of selected atoms to surface Peter Freddolino (Fri May 04 2007 - 10:13:41 CDT)
Reading additional atom properties Lutz Maibaum (Thu May 03 2007 - 20:07:12 CDT)
- Re: Reading additional atom properties John Stone (Tue May 15 2007 - 13:12:34 CDT)
  - Re: Reading additional atom properties Lutz Maibaum (Tue May 15 2007 - 20:46:25 CDT)
Re: loop in loop - found it lily jin (Thu May 03 2007 - 18:49:47 CDT)
loop in loop lily jin (Thu May 03 2007 - 18:41:04 CDT)
(no subject) lanhua (Thu May 03 2007 - 16:30:24 CDT)
- Re: Axel Kohlmeyer (Thu May 03 2007 - 17:00:48 CDT)
vmd-1:how to merge two proteins (receptor & ligand) kong.winter (Thu May 03 2007 - 16:06:20 CDT)
- Re: vmd-1:how to merge two proteins (receptor & ligand) Axel Kohlmeyer (Thu May 03 2007 - 16:01:46 CDT)
measure Hbond lily jin (Thu May 03 2007 - 14:06:19 CDT)
- Re: measure Hbond Peter Freddolino (Thu May 03 2007 - 14:10:21 CDT)
dumb movie maker question Nichols A. Romero (Thu May 03 2007 - 10:32:26 CDT)
- Re: dumb movie maker question Axel Kohlmeyer (Thu May 03 2007 - 10:16:10 CDT)
a water box containing only the absorbent heads of SMAHANE CHALABI (Thu May 03 2007 - 03:11:45 CDT)
- Re: a water box containing only the absorbent heads of Axel Kohlmeyer (Thu May 03 2007 - 07:44:05 CDT)
rms fitting problem Myunggi Yi (Wed May 02 2007 - 16:34:04 CDT)
- Re: rms fitting problem Peter Freddolino (Wed May 02 2007 - 20:21:47 CDT)
vmd 1.8.6 on MacOS X, with python support, anyone? Jan Rychter (Mon Apr 30 2007 - 05:39:33 CDT)
- Re: vmd 1.8.6 on MacOS X, with python support, anyone? John Stone (Tue May 01 2007 - 12:35:50 CDT)
  - Re: vmd 1.8.6 on MacOS X, with python support, anyone? Jan Rychter (Tue May 01 2007 - 14:29:46 CDT)
    - JMV Samuel Flores (Sat May 12 2007 - 19:31:09 CDT)
    - Re: JMV John Stone (Mon May 14 2007 - 12:51:15 CDT)
Visualization and reading problems Marcelo Puiatti (Fri Apr 27 2007 - 18:12:44 CDT)
- Re: Visualization and reading problems Axel Kohlmeyer (Sun Apr 29 2007 - 13:41:54 CDT)
increase light under depth cueing Vlad Cojocaru (Sat Apr 28 2007 - 17:46:59 CDT)
- Re: increase light under depth cueing Axel Kohlmeyer (Sat Apr 28 2007 - 17:45:36 CDT)
  - Re: increase light under depth cueing Olaf Lenz (Sun Apr 29 2007 - 03:31:34 CDT)
    - Re: increase light under depth cueing Axel Kohlmeyer (Sun Apr 29 2007 - 12:43:19 CDT)
    - RE: increase light under depth cueing Cojocaru,Vlad (Sun Apr 29 2007 - 15:12:54 CDT)
Problem with periodic condition Jianhui Tian (Fri Apr 27 2007 - 13:33:26 CDT)
- Re: Problem with periodic condition Axel Kohlmeyer (Fri Apr 27 2007 - 14:42:33 CDT)
- Re: Problem with periodic condition Olaf Lenz (Sat Apr 28 2007 - 13:27:51 CDT)
  - Re: Problem with periodic condition Charles Cleveland (Sat Apr 28 2007 - 16:02:55 CDT)
    - Re: Problem with periodic condition Olaf Lenz (Sat Apr 28 2007 - 17:14:20 CDT)
    - Re: Problem with periodic condition Axel Kohlmeyer (Sat Apr 28 2007 - 16:15:06 CDT)
  - Re: Problem with periodic condition Jianhui Tian (Mon Apr 30 2007 - 15:57:30 CDT)
    - Re: Problem with periodic condition Axel Kohlmeyer (Mon Apr 30 2007 - 15:47:12 CDT)
Dynamic 'Determine file type' list in main menu !?! Rob (Fri Apr 27 2007 - 01:14:37 CDT)
- Re: Dynamic 'Determine file type' list in main menu !?! Axel Kohlmeyer (Fri Apr 27 2007 - 09:02:09 CDT)
- Re: Dynamic 'Determine file type' list in main menu !?! John Stone (Tue May 01 2007 - 12:38:46 CDT)
vmd problem: session ended Hugh Ferrel Bowen (Thu Apr 26 2007 - 08:46:01 CDT)
- Re: vmd problem: session ended John Stone (Tue May 01 2007 - 12:50:19 CDT)
DOWSER: child process exited abnormally Robert Selwyne (Thu Apr 26 2007 - 06:57:03 CDT)
- Re: DOWSER: child process exited abnormally Leonardo Trabuco (Thu Apr 26 2007 - 11:27:53 CDT)
Fixed number of solvatation water Andrea Cristiani (Wed Apr 25 2007 - 04:56:41 CDT)
GLSL rendering problems (??) Nichols A. Romero (Tue Apr 24 2007 - 15:40:57 CDT)
- Re: GLSL rendering problems (??) John Stone (Tue Apr 24 2007 - 15:52:30 CDT)
  - Re: GLSL rendering problems (??) Nichols A. Romero (Tue Apr 24 2007 - 16:00:20 CDT)
One Year written repl1ca w4tches warranty Kari Maher (Tue Apr 24 2007 - 15:10:17 CDT)
Re: Your Val1um 0rder #63504 Donnie Skinner (Tue Apr 24 2007 - 13:01:46 CDT)
H-bonds amit dong (Tue Apr 24 2007 - 10:58:13 CDT)
- Re: H-bonds Axel Kohlmeyer (Tue Apr 24 2007 - 11:28:31 CDT)
how to reset a timed out connection Amarda Shehu (Tue Apr 24 2007 - 09:23:44 CDT)
- Re: how to reset a timed out connection John Stone (Tue Apr 24 2007 - 11:27:22 CDT)
  - Re: how to reset a timed out connection John Stone (Tue Apr 24 2007 - 13:44:13 CDT)
    - Re: how to reset a timed out connection Amarda Shehu (Tue Apr 24 2007 - 13:55:24 CDT)
    - Re: how to reset a timed out connection John Stone (Tue Apr 24 2007 - 14:57:41 CDT)
selecting atoms Nichols A. Romero (Tue Apr 24 2007 - 09:55:36 CDT)
- Re: selecting atoms Peter Freddolino (Tue Apr 24 2007 - 10:10:41 CDT)
Variable number of atoms in xyz file Ignacio Fernández Galván (Tue Apr 24 2007 - 02:58:20 CDT)
- Re: Variable number of atoms in xyz file Peter Freddolino (Tue Apr 24 2007 - 10:04:40 CDT)
- Re: Variable number of atoms in xyz file Axel Kohlmeyer (Tue Apr 24 2007 - 09:21:45 CDT)
Cheap 3D Glasses Gustavo Seabra (Mon Apr 23 2007 - 18:07:07 CDT)
- Re: Cheap 3D Glasses John Stone (Tue Apr 24 2007 - 14:26:11 CDT)
Your Pharm4cy 0rder #2299650 Mary Rudd (Mon Apr 23 2007 - 17:50:29 CDT)
W4tches from simple to luxurious at Prest1ge Repl1cas Dominique Compton (Mon Apr 23 2007 - 17:51:51 CDT)
About openning a file to write in callback function preeda (Mon Apr 23 2007 - 12:07:59 CDT)
- Re: About openning a file to write in callback function Axel Kohlmeyer (Mon Apr 23 2007 - 14:00:35 CDT)
tcl code atomselect problem in analysis Jianhui Tian (Mon Apr 23 2007 - 09:24:48 CDT)
- Re: tcl code atomselect problem in analysis Peter Freddolino (Mon Apr 23 2007 - 10:10:20 CDT)
  - Re: tcl code atomselect problem in analysis Jianhui Tian (Mon Apr 23 2007 - 10:32:12 CDT)
    - Re: tcl code atomselect problem in analysis Peter Freddolino (Mon Apr 23 2007 - 10:57:10 CDT)
- Re: tcl code atomselect problem in analysis John Stone (Mon Apr 23 2007 - 11:12:07 CDT)
Your Pharm4cy 0rder #3747312 Andres Bynum (Sat Apr 21 2007 - 19:50:21 CDT)
Misunderstanding about SASA Patrick Redmill (Sat Apr 21 2007 - 10:14:19 CDT)
- Re: Misunderstanding about SASA Axel Kohlmeyer (Sat Apr 21 2007 - 17:31:53 CDT)
Reliable w4tches for everyone at Prest1ge Repl1cas Michele Garrett (Sat Apr 21 2007 - 10:20:56 CDT)
Your V1agra 0rder #18671 Willie Bray (Sat Apr 21 2007 - 02:54:52 CDT)
Famous repl1ca w4tches r0lex Cartier Bvlgari Shari Chin (Fri Apr 20 2007 - 23:08:24 CDT)
Re: Your Val1um 0rder #6578980 Owen Lindsay (Fri Apr 20 2007 - 22:11:49 CDT)
How to visualize phi maps calculated with delphi V. 4 Cesar Luis Avila (Fri Apr 20 2007 - 18:36:48 CDT)
- Re: How to visualize phi maps calculated with delphi V. 4 John Stone (Fri Apr 20 2007 - 21:07:01 CDT)
  - Re: How to visualize phi maps calculated with delphi V. 4 Cesar Avila (Sat Apr 21 2007 - 20:05:42 CDT)
  - Re: How to visualize phi maps calculated with delphi V. 4 John Stone (Mon Apr 23 2007 - 14:55:59 CDT)
process and plot matrix data Vlad Cojocaru (Fri Apr 20 2007 - 04:28:12 CDT)
- Re: process and plot matrix data John Stone (Fri Apr 20 2007 - 14:47:44 CDT)
Announcement: QM/MM Workshop Axel Kohlmeyer (Thu Apr 19 2007 - 09:14:50 CDT)
tcl variable withing variable name Vlad Cojocaru (Thu Apr 19 2007 - 07:58:27 CDT)
- Re: tcl variable withing variable name Axel Kohlmeyer (Thu Apr 19 2007 - 08:30:34 CDT)
  - Re: tcl variable withing variable name Vlad Cojocaru (Thu Apr 19 2007 - 11:13:21 CDT)
- Re: tcl variable withing variable name Peter Freddolino (Thu Apr 19 2007 - 09:38:53 CDT)
- RE: tcl variable withing variable name Ana Celia Araujo Vila Verde (Thu Apr 19 2007 - 10:29:43 CDT)
How to get the whole H2O molecule in a domain? Philipp Schoen1 (Wed Apr 18 2007 - 11:55:03 CDT)
- Re: How to get the whole H2O molecule in a domain? Peter Freddolino (Wed Apr 18 2007 - 12:07:52 CDT)
  - Re: How to get the whole H2O molecule in a domain? Peter Freddolino (Wed Apr 18 2007 - 12:10:13 CDT)
secondary_struct script alexandra.marques_at_fc.up.pt (Wed Apr 18 2007 - 11:28:43 CDT)
- Re: secondary_struct script John Stone (Wed Apr 18 2007 - 12:48:36 CDT)
vmd can't start up after being installed in linux lanhua (Tue Apr 17 2007 - 23:22:13 CDT)
- Re: vmd can't start up after being installed in linux John Stone (Tue Apr 17 2007 - 22:50:39 CDT)
- Re: vmd can't start up after being installed in linux Axel Kohlmeyer (Tue Apr 17 2007 - 22:01:27 CDT)
- Re: vmd can't start up after being installed in linux Cesar Luis Avila (Wed Apr 18 2007 - 10:54:40 CDT)
  - Re: vmd can't start up after being installed in linux John Stone (Wed Apr 18 2007 - 11:03:04 CDT)
    - Re: vmd can't start up after being installed in linux Cesar Luis Avila (Wed Apr 18 2007 - 13:23:21 CDT)
    - Re: vmd can't start up after being installed in linux John Stone (Wed Apr 18 2007 - 16:14:32 CDT)
hexagonal box dimka (Tue Apr 17 2007 - 12:11:09 CDT)
assignment of "measure contacts" output to tcl variables Vlad Cojocaru (Tue Apr 17 2007 - 07:25:19 CDT)
- Re: assignment of "measure contacts" output to tcl variables Vlad Cojocaru (Tue Apr 17 2007 - 09:50:49 CDT)
RE: "which files to make a spatial grid?" => Bug for list command? Philipp Schoen1 (Tue Apr 17 2007 - 07:03:46 CDT)
- Re: RE: "which files to make a spatial grid?" => Bug for list command? Axel Kohlmeyer (Tue Apr 17 2007 - 07:25:11 CDT)
- Re: RE: "which files to make a spatial grid?" => Bug for list command? John Stone (Tue Apr 17 2007 - 13:11:52 CDT)
Strange characters using writemol2 (vmd 1.8.5) Cesar Luis Avila (Mon Apr 16 2007 - 18:32:28 CDT)
- Re: Strange characters using writemol2 (vmd 1.8.5) John Stone (Mon Apr 16 2007 - 18:39:17 CDT)
  - Re: Strange characters using writemol2 (vmd 1.8.5) Cesar Luis Avila (Mon Apr 16 2007 - 20:06:58 CDT)
Tinker trajectory file Esther Brugger (Mon Apr 16 2007 - 16:47:00 CDT)
- Re: Tinker trajectory file John Stone (Mon Apr 16 2007 - 18:27:52 CDT)
  - How can i obtain a force and trajectory data of a PHANTOM in IMD simulation preeda (Tue Apr 17 2007 - 09:44:30 CDT)
how to solvate a molecule with cubic periodic boundary box? Margaret S. Cheung (Mon Apr 16 2007 - 15:46:48 CDT)
- Re: how to solvate a molecule with cubic periodic boundary box? Leonardo Trabuco (Mon Apr 16 2007 - 16:56:15 CDT)
Saving mol2 file Atila Iamarino (Mon Apr 16 2007 - 12:36:00 CDT)
- Re: Saving mol2 file Peter Freddolino (Mon Apr 16 2007 - 12:48:18 CDT)
  - Re: Saving mol2 file Atila Iamarino (Wed Apr 18 2007 - 10:50:57 CDT)
    - Re: Saving mol2 file Peter Freddolino (Wed Apr 18 2007 - 11:00:26 CDT)
hbond questions Miguel Ferreira (Mon Apr 16 2007 - 10:10:03 CDT)
VMD for Windows 64bits Lechuga, Javier (Mon Apr 16 2007 - 10:11:34 CDT)
- Re: VMD for Windows 64bits John Stone (Mon Apr 16 2007 - 11:01:48 CDT)
which files to make a spatial grid? Philipp Schoen1 (Mon Apr 16 2007 - 07:39:44 CDT)
- Re: which files to make a spatial grid? Axel Kohlmeyer (Mon Apr 16 2007 - 19:46:08 CDT)
writing coordinates of a selection only Myunggi Yi (Sun Apr 15 2007 - 20:51:19 CDT)
- Re: writing coordinates of a selection only Axel Kohlmeyer (Mon Apr 16 2007 - 18:42:26 CDT)
Release of the R.E.D.-III tools FyD (Sun Apr 15 2007 - 05:22:35 CDT)
Where is the memory leakage? Guo Zhi (Sun Apr 15 2007 - 00:54:48 CDT)
- Re: Where is the memory leakage? John Stone (Sun Apr 15 2007 - 01:14:52 CDT)
  - Re: Where is the memory leakage? Guo Zhi (Sun Apr 15 2007 - 01:45:32 CDT)
winvmd error during calculation lanhua (Fri Apr 13 2007 - 23:17:54 CDT)
- Re: winvmd error during calculation John Stone (Sat Apr 14 2007 - 00:50:21 CDT)
- Re: winvmd error during calculation Axel Kohlmeyer (Sat Apr 14 2007 - 09:10:39 CDT)
GLSL rendering in VMD 1.8.6 Luis Rosales (Fri Apr 13 2007 - 20:18:23 CDT)
- Re: GLSL rendering in VMD 1.8.6 John Stone (Fri Apr 13 2007 - 22:09:35 CDT)
  - Re: GLSL rendering in VMD 1.8.6 Luis Rosales (Mon Apr 16 2007 - 17:40:35 CDT)
    - Re: GLSL rendering in VMD 1.8.6 John Stone (Tue Apr 17 2007 - 14:43:58 CDT)
.xyz to .dcd using catdcd Ekta Khurana (Fri Apr 13 2007 - 16:08:51 CDT)
- Re: .xyz to .dcd using catdcd Peter Freddolino (Fri Apr 13 2007 - 21:26:57 CDT)
  - Re: .xyz to .dcd using catdcd Ekta Khurana (Mon Apr 16 2007 - 14:34:47 CDT)
contact map (over all frames) amit dong (Fri Apr 13 2007 - 15:53:24 CDT)
- Re: contact map (over all frames) Peter Freddolino (Fri Apr 13 2007 - 21:25:24 CDT)
compile a plugin source code dbg (Fri Apr 13 2007 - 06:29:59 CDT)
VMD installation dbg (Fri Apr 13 2007 - 01:09:54 CDT)
- Re: VMD installation John Stone (Fri Apr 13 2007 - 10:38:45 CDT)
- Re: VMD installation Axel Kohlmeyer (Fri Apr 13 2007 - 09:40:07 CDT)
- Re: VMD installation George Madalin Giambasu (Fri Apr 13 2007 - 11:39:50 CDT)
sasa Myunggi Yi (Wed Apr 11 2007 - 21:42:25 CDT)
- Re: sasa Myunggi Yi (Thu Apr 12 2007 - 10:02:14 CDT)
  - Re: sasa John Stone (Thu Apr 12 2007 - 15:08:32 CDT)
  - Re: sasa John Stone (Tue Apr 17 2007 - 13:15:22 CDT)
mismatch between phi and pdb files Michael Widmann (Tue Apr 10 2007 - 03:07:52 CDT)
- Re: mismatch between phi and pdb files John Stone (Tue Apr 10 2007 - 08:34:19 CDT)
If I want to modify measure.C, what should I do? lanhua (Mon Apr 09 2007 - 15:59:18 CDT)
- Re: If I want to modify measure.C, what should I do? John Stone (Mon Apr 09 2007 - 16:52:50 CDT)
I'm sorry ... please ignore the junk !! Vlad Cojocaru (Mon Apr 09 2007 - 05:50:54 CDT)
Vlad has Tagged you! :) Vlad Cojocaru (Mon Apr 09 2007 - 05:06:39 CDT)
VMD 1.8.6 GLSL problem daniel aguayo (Mon Apr 09 2007 - 01:08:04 CDT)
- Re: VMD 1.8.6 GLSL problem John Stone (Mon Apr 09 2007 - 01:15:44 CDT)
  - Re: VMD 1.8.6 GLSL problem daniel aguayo (Tue Apr 10 2007 - 01:21:34 CDT)
1.8.6 install for Windows OpenGL (Microsoft Windows 2000/XP/Vista (32-bit) using OpenGL) Charles Cleveland (Sun Apr 08 2007 - 08:05:00 CDT)
- Re: 1.8.6 install for Windows OpenGL (Microsoft Windows 2000/XP/Vista (32-bit) using OpenGL) John Stone (Sun Apr 08 2007 - 11:26:33 CDT)
Announce: VMD 1.8.6 Released! John Stone (Sun Apr 08 2007 - 00:51:52 CDT)
GLSL rendering problems Nichols A. Romero (Thu Apr 05 2007 - 14:41:22 CDT)
- Re: GLSL rendering problems John Stone (Thu Apr 05 2007 - 14:55:13 CDT)
  - Re: GLSL rendering problems Nichols A. Romero (Thu Apr 05 2007 - 15:07:14 CDT)
    - Re: GLSL rendering problems John Stone (Thu Apr 05 2007 - 15:34:03 CDT)
Problem with Reading Binary ccp4 File Generated by CHARMM rossi_at_york.cuny.edu (Thu Apr 05 2007 - 11:32:02 CDT)
- Re: Problem with Reading Binary ccp4 File Generated by CHARMM John Stone (Thu Apr 05 2007 - 12:22:23 CDT)
  - Re: Problem with Reading Binary ccp4 File Generated by CHARMM Leonardo Trabuco (Thu Apr 05 2007 - 14:55:07 CDT)
    - Re: Problem with Reading Binary ccp4 File Generated by CHARMM rossi_at_york.cuny.edu (Thu Apr 05 2007 - 18:56:08 CDT)
how to connect chains using psfgen Philipp Schoen1 (Wed Apr 04 2007 - 09:49:10 CDT)
- Re: how to connect chains using psfgen Peter Freddolino (Wed Apr 04 2007 - 11:20:30 CDT)
using Grace instead of Multiplot Vlad Cojocaru (Wed Apr 04 2007 - 05:04:36 CDT)
- Re: using Grace instead of Multiplot John Stone (Wed Apr 04 2007 - 12:13:45 CDT)
surface max_density error Jim Fonseca (Tue Apr 03 2007 - 11:25:49 CDT)
- Re: surface max_density error John Stone (Tue Apr 03 2007 - 12:31:16 CDT)
  - Re: surface max_density error Jim Fonseca (Tue Apr 03 2007 - 15:38:41 CDT)
problem using NAMD trajectory in charmm 32-bit, 64-bit etc. (yes, I posted this on charmm lists too) namd vmd (Tue Apr 03 2007 - 07:49:45 CDT)
- Re: problem using NAMD trajectory in charmm 32-bit, 64-bit etc. (yes, I posted this on charmm lists too) Axel Kohlmeyer (Tue Apr 03 2007 - 09:20:25 CDT)
VMD for Win32 API based PC CAVE Michal Husak (Mon Apr 02 2007 - 08:00:34 CDT)
- Re: VMD for Win32 API based PC CAVE Martijn Kragtwijk (Mon Apr 02 2007 - 10:56:26 CDT)
  - Re: VMD for Win32 API based PC CAVE John Stone (Mon Apr 02 2007 - 11:57:45 CDT)
- Re: VMD for Win32 API based PC CAVE John Stone (Mon Apr 02 2007 - 11:55:34 CDT)
How do I overlap that specific nucletide between a protein and RNA? zhangh1_at_umbc.edu (Sat Mar 31 2007 - 08:43:07 CDT)
- Re: How do I overlap that specific nucletide between a protein and RNA? John Stone (Sun Apr 01 2007 - 23:07:46 CDT)
problem during movie making gadde suneetha (Fri Mar 30 2007 - 07:44:48 CDT)
Can anyone help me out with this script Jianhui Tian (Fri Mar 30 2007 - 14:49:45 CDT)
- Re: Can anyone help me out with this script John Stone (Sat Mar 31 2007 - 00:05:17 CDT)
  - Re: Can anyone help me out with this script Jianhui Tian (Sat Mar 31 2007 - 19:50:43 CDT)
    - Re: Can anyone help me out with this script John Stone (Sun Apr 01 2007 - 23:03:24 CDT)
'SURF' representation problem hl332_at_drexel.edu (Thu Mar 29 2007 - 16:04:02 CDT)
- Re: 'SURF' representation problem John Stone (Thu Mar 29 2007 - 16:10:43 CDT)
  - Re: 'SURF' representation problem hl332_at_drexel.edu (Thu Mar 29 2007 - 18:09:43 CDT)
python pro.align() Per Jr. Greisen (Thu Mar 29 2007 - 12:27:21 CDT)
- Re: python pro.align() John Stone (Thu Mar 29 2007 - 16:22:23 CDT)
dcd header information missing Nichols A. Romero (Thu Mar 29 2007 - 10:21:31 CDT)
- Re: dcd header information missing John Stone (Thu Mar 29 2007 - 11:03:17 CDT)
  - Re: dcd header information missing Nichols A. Romero (Sat Mar 31 2007 - 18:11:30 CDT)
Moving volume data with molecule Avell Diroll (Thu Mar 29 2007 - 10:05:40 CDT)
- Re: Moving volume data with molecule John Stone (Thu Mar 29 2007 - 11:31:05 CDT)
  - Re: Moving volume data with molecule Avell Diroll (Thu Mar 29 2007 - 11:59:01 CDT)
how to view the dynamics in power point presentation gadde suneetha (Thu Mar 29 2007 - 06:25:29 CDT)
- Re: how to view the dynamics in power point presentation John Stone (Thu Mar 29 2007 - 11:43:52 CDT)
assigning variable names using a for loop namd vmd (Thu Mar 29 2007 - 03:21:45 CDT)
- Re: assigning variable names using a for loop Olaf Lenz (Thu Mar 29 2007 - 04:38:08 CDT)
doubts in movie making using vmd. gadde suneetha (Wed Mar 28 2007 - 19:05:05 CDT)
- Re: doubts in movie making using vmd. Axel Kohlmeyer (Wed Mar 28 2007 - 21:47:12 CDT)
  - Re: doubts in movie making using vmd. John Stone (Wed Mar 28 2007 - 21:52:17 CDT)
New VMD 1.8.6b15 installer for Windows XP x64... John Stone (Wed Mar 28 2007 - 18:17:29 CDT)
[vmd-l] Graduate assistanship in Bioinformatics at NCSA Gloria Rendon (Wed Mar 28 2007 - 17:45:25 CDT)
ion 'channel axis' Adrian Kaats (Wed Mar 28 2007 - 15:55:17 CDT)
Re: GAMESS plugin bus error Ralph Jimenez (Wed Mar 28 2007 - 15:11:17 CDT)
How to make a movie in VMD using principle component analysis gadde suneetha (Wed Mar 28 2007 - 07:42:56 CDT)
- Re: How to make a movie in VMD using principle component analysis John Stone (Wed Mar 28 2007 - 14:43:14 CDT)
write trajectory of selected atoms namd vmd (Wed Mar 28 2007 - 09:51:28 CDT)
- Re: write trajectory of selected atoms Peter Freddolino (Wed Mar 28 2007 - 10:03:01 CDT)
  - Re: write trajectory of selected atoms Peter Freddolino (Wed Mar 28 2007 - 10:04:03 CDT)
Plugin Issue James Keener (Wed Mar 28 2007 - 09:45:18 CDT)
- Re: Plugin Issue John Stone (Wed Mar 28 2007 - 11:13:06 CDT)
  - Re: Plugin Issue John Stone (Sat Mar 31 2007 - 00:19:20 CDT)
- Re: Plugin Issue Luis Gracia (Wed Mar 28 2007 - 13:14:40 CDT)
FW: rdf using gui syma (Tue Mar 27 2007 - 16:49:06 CDT)
rdf using gui syma (Tue Mar 27 2007 - 16:18:57 CDT)
- Re: rdf using gui Axel Kohlmeyer (Tue Mar 27 2007 - 16:44:09 CDT)
  - vmd in ubuntu on mac mini Syma Khalid (Sat Dec 29 2007 - 13:48:45 CST)
    - Re: vmd in ubuntu on mac mini John Stone (Fri Jan 04 2008 - 12:40:13 CST)
dynamic bonding Zheng Hu (Tue Mar 27 2007 - 14:21:02 CDT)
- Re: dynamic bonding John Stone (Tue Mar 27 2007 - 15:39:26 CDT)
- Re: dynamic bonding Axel Kohlmeyer (Tue Mar 27 2007 - 15:48:22 CDT)
representation selection funnies Fred Moore (Tue Mar 27 2007 - 14:06:21 CDT)
- Re: representation selection funnies John Stone (Tue Mar 27 2007 - 14:25:01 CDT)
  - Re: representation selection funnies John Stone (Wed Mar 28 2007 - 22:25:26 CDT)
problem creating psf lucie huynh (Tue Mar 27 2007 - 09:54:08 CDT)
- Re: problem creating psf John Stone (Tue Mar 27 2007 - 10:34:31 CDT)
  - Re: problem creating psf lucie huynh (Wed Mar 28 2007 - 03:59:47 CDT)
    - Re: problem creating psf John Stone (Wed Mar 28 2007 - 22:27:50 CDT)
    - Re: problem creating psf lucie huynh (Thu Mar 29 2007 - 03:24:01 CDT)
- Re: problem creating psf Peter Freddolino (Tue Mar 27 2007 - 10:45:00 CDT)
hbond calculation alexandra.marques_at_fc.up.pt (Mon Mar 26 2007 - 15:49:19 CDT)
- Re: hbond calculation Peter Freddolino (Mon Mar 26 2007 - 16:00:10 CDT)
PBCTools Plugin Zheng Hu (Mon Mar 26 2007 - 15:14:50 CDT)
- Re: PBCTools Plugin John Stone (Mon Mar 26 2007 - 15:56:23 CDT)
mol load and mol addfile Jianhui Tian (Mon Mar 26 2007 - 15:43:20 CDT)
- Re: mol load and mol addfile Axel Kohlmeyer (Mon Mar 26 2007 - 16:33:51 CDT)
hbond analysis jacopo.sgrignani_at_unifi.it (Sat Mar 24 2007 - 11:03:24 CDT)
- Re: hbond analysis John Stone (Sat Mar 24 2007 - 11:13:25 CDT)
can't read pdb file Mary Lowe (Fri Mar 23 2007 - 21:40:18 CDT)
- Re: can't read pdb file John Stone (Sat Mar 24 2007 - 00:52:55 CDT)
  - Re: can't read pdb file Mary Lowe (Sun Mar 25 2007 - 08:26:31 CDT)
windows version of VMD Zheng Hu (Fri Mar 23 2007 - 16:35:29 CDT)
- Re: windows version of VMD John Stone (Fri Mar 23 2007 - 17:17:31 CDT)
  - Re: windows version of VMD zsinkala_at_mtsu.edu (Mon Mar 26 2007 - 07:21:19 CDT)
    - Re: windows version of VMD John Stone (Mon Mar 26 2007 - 11:57:37 CDT)
- Re: windows version of VMD Zheng Hu (Sat Mar 24 2007 - 16:39:43 CDT)
  - Re: Re: windows version of VMD John Stone (Sat Mar 24 2007 - 17:06:09 CDT)
- Re: windows version of VMD Zheng Hu (Sat Mar 24 2007 - 17:03:27 CDT)
  - Re: Re: windows version of VMD John Stone (Sat Mar 24 2007 - 17:11:33 CDT)
- Re: windows version of VMD Zheng Hu (Sun Mar 25 2007 - 15:19:48 CDT)
  - Re: Re: windows version of VMD Axel Kohlmeyer (Sun Mar 25 2007 - 16:46:41 CDT)
- Re: windows version of VMD Zheng Hu (Mon Apr 09 2007 - 00:20:11 CDT)
  - Re: Re: windows version of VMD John Stone (Mon Apr 09 2007 - 01:01:35 CDT)
hbond jacopo.sgrignani_at_unifi.it (Fri Mar 23 2007 - 13:29:57 CDT)
- Re: hbond John Stone (Fri Mar 23 2007 - 14:08:04 CDT)
script to visualize NMR constrains? Marcela Madrid (Fri Mar 23 2007 - 13:45:46 CDT)
- Re: script to visualize NMR constrains? John Stone (Fri Mar 23 2007 - 14:06:02 CDT)
coloring names Fred Moore (Fri Mar 23 2007 - 13:24:37 CDT)
- Re: coloring names John Stone (Fri Mar 23 2007 - 14:01:05 CDT)
Draw a circle Abi Ghanem josephine (Fri Mar 23 2007 - 09:47:12 CDT)
- Re: Draw a circle John Stone (Fri Mar 23 2007 - 10:25:36 CDT)
visualizing NMR constrains Marcela Madrid (Thu Mar 22 2007 - 17:14:37 CDT)
- Re: visualizing NMR constrains John Stone (Thu Mar 22 2007 - 21:06:20 CDT)
- Re: visualizing NMR constrains Nuno Loureiro Ferreira (Fri Mar 23 2007 - 09:29:41 CDT)
colors Luc Moulinier (Thu Mar 22 2007 - 03:55:26 CDT)
- Re: colors John Stone (Thu Mar 22 2007 - 10:00:06 CDT)
How to superimpose trajectories Kailee (Wed Mar 21 2007 - 09:14:33 CDT)
- Re: How to superimpose trajectories John Stone (Wed Mar 21 2007 - 15:26:20 CDT)
  - Re: How to superimpose trajectories John Stone (Wed Mar 21 2007 - 15:33:56 CDT)
    - Re: How to superimpose trajectories Kailee (Thu Mar 22 2007 - 10:04:44 CDT)
    - Re: How to superimpose trajectories John Stone (Thu Mar 22 2007 - 10:46:08 CDT)
Replica exchange molecular dynamics (REMD) Arindam Ganguly (Tue Mar 20 2007 - 21:22:15 CDT)
- Re: Replica exchange molecular dynamics (REMD) Peter Freddolino (Tue Mar 20 2007 - 22:02:58 CDT)
graphic update Myunggi Yi (Tue Mar 20 2007 - 20:09:06 CDT)
- Re: graphic update John Stone (Tue Mar 20 2007 - 20:40:09 CDT)
  - Re: graphic update Myunggi Yi (Tue Mar 20 2007 - 20:43:59 CDT)
    - Re: graphic update Myunggi Yi (Tue Mar 20 2007 - 22:08:32 CDT)
    - Re: graphic update John Stone (Tue Mar 20 2007 - 22:33:34 CDT)
Any way to output contact map data Guo Zhi (Tue Mar 20 2007 - 09:18:03 CDT)
- Re: Any way to output contact map data John Stone (Wed Mar 21 2007 - 01:42:15 CDT)
  - Re: Any way to output contact map data Guo Zhi (Wed Mar 21 2007 - 03:32:37 CDT)
  - Re: Any way to output contact map data Luis Gracia (Wed Mar 21 2007 - 11:12:32 CDT)
calculating distance between center of geometry/mass of methyl hydrogens for all residue pairs Zu Thur Yew (Mon Mar 19 2007 - 18:48:41 CDT)
Scripting problem with h-bond listing Sanjeev (Sun Mar 18 2007 - 01:30:53 CDT)
- Re: Scripting problem with h-bond listing John Stone (Sun Mar 18 2007 - 01:54:15 CDT)
  - Re: Re: Scripting problem with h-bond listing Sanjeev (Sun Mar 18 2007 - 14:16:42 CDT)
    - Re: Re: Scripting problem with h-bond listing Axel Kohlmeyer (Sun Mar 18 2007 - 15:03:09 CDT)
    - Re: Re: Re: Scripting problem with h-bond listing Sanjeev (Mon Mar 19 2007 - 04:36:05 CDT)
question about gofr lanhua (Sat Mar 17 2007 - 14:30:31 CDT)
- Re: question about gofr Axel Kohlmeyer (Sat Mar 17 2007 - 15:48:44 CDT)
Question about overlaying structures Kara Di Giorgio (Thu Mar 15 2007 - 21:16:26 CDT)
- Re: Question about overlaying structures John Stone (Thu Mar 15 2007 - 22:16:12 CDT)
  - Need helps about connecting phantom with VMD through VRPN preeda (Mon Mar 19 2007 - 09:30:43 CDT)
    - Re: Need helps about connecting phantom with VMD through VRPN John Stone (Mon Mar 19 2007 - 10:08:54 CDT)
  - Re: Question about overlaying structures Kara Di Giorgio (Tue Mar 27 2007 - 12:30:06 CDT)
    - Re: Question about overlaying structures John Stone (Tue Mar 27 2007 - 13:06:33 CDT)
OmpF biological unit Adrian Kaats (Thu Mar 15 2007 - 18:58:17 CDT)
- Re: OmpF biological unit John Stone (Mon Mar 19 2007 - 11:29:09 CDT)
export Ramachandran datas Jianhui Tian (Thu Mar 15 2007 - 16:16:21 CDT)
- Re: export Ramachandran datas John Stone (Thu Mar 15 2007 - 16:23:28 CDT)
  - Re: export Ramachandran datas Jianhui Tian (Thu Mar 15 2007 - 17:11:27 CDT)
Scripts to unwrap PBC from REMD trajectory Bob Johnson (Thu Mar 15 2007 - 16:08:50 CDT)
- Re: Scripts to unwrap PBC from REMD trajectory Olaf Lenz (Fri Mar 16 2007 - 02:52:57 CDT)
- Re: Scripts to unwrap PBC from REMD trajectory Olaf Lenz (Fri Mar 16 2007 - 03:57:59 CDT)
  - Re: Scripts to unwrap PBC from REMD trajectory Bob Johnson (Fri Mar 16 2007 - 09:05:18 CDT)
AutoPSF lily jin (Thu Mar 15 2007 - 15:23:32 CDT)
- Re: AutoPSF Peter Freddolino (Thu Mar 15 2007 - 15:29:05 CDT)
Average structure Per Jr. Greisen (Thu Mar 15 2007 - 14:14:20 CDT)
- Re: Average structure Peter Freddolino (Thu Mar 15 2007 - 14:39:21 CDT)
manually creating frames for VMD yalini.pathy_at_yale.edu (Wed Mar 14 2007 - 17:11:58 CDT)
- Re: manually creating frames for VMD Peter Freddolino (Wed Mar 14 2007 - 20:46:49 CDT)
Measuring specific distances over a trajectory Patrick Wintrode (Wed Mar 14 2007 - 16:06:30 CDT)
- Re: Measuring specific distances over a trajectory John Stone (Wed Mar 14 2007 - 16:56:18 CDT)
molecule orientation in saved state Subramanian Vaitheeswaran (Wed Mar 14 2007 - 12:21:53 CDT)
- Re: molecule orientation in saved state John Stone (Thu Mar 15 2007 - 13:40:07 CDT)
how to set atom index Guo Zhi (Wed Mar 14 2007 - 10:33:57 CDT)
- Re: how to set atom index John Stone (Thu Mar 15 2007 - 13:20:12 CDT)
  - Re: how to set atom index Guo Zhi (Thu Mar 15 2007 - 19:51:04 CDT)
VMD 1.8.6b binaries for win32? Jacob Poehlsgaard (Wed Mar 14 2007 - 10:14:45 CDT)
- Re: VMD 1.8.6b binaries for win32? John Stone (Wed Mar 14 2007 - 17:08:48 CDT)
  - Re: VMD 1.8.6b binaries for win32? John Stone (Thu Mar 15 2007 - 18:48:14 CDT)
Calculate End-End distance for DCD Jianhui Tian (Tue Mar 13 2007 - 15:17:00 CDT)
- RE: Calculate End-End distance for DCD Ana Celia Araujo Vila Verde (Tue Mar 13 2007 - 16:17:48 CDT)
Problems running APBS Per Jr. Greisen (Tue Mar 13 2007 - 13:32:04 CDT)
- Re: Problems running APBS John Stone (Tue Mar 13 2007 - 13:44:45 CDT)
  - Re: Problems running APBS John Stone (Tue Mar 13 2007 - 14:32:22 CDT)
NAMD Energy - Hexagonal Cell Alessandro Cembran (Mon Mar 12 2007 - 18:10:14 CDT)
- Re: NAMD Energy - Hexagonal Cell John Stone (Thu Mar 15 2007 - 14:03:48 CDT)
ed and vmd Nadine Utz (Abt. Koslowski) (Mon Mar 12 2007 - 12:58:49 CDT)
- Re: ed and vmd John Stone (Mon Mar 12 2007 - 17:23:24 CDT)
vmd on core 2 duo matteus.lindgren_at_chem.umu.se (Mon Mar 12 2007 - 03:26:30 CDT)
- Re: vmd on core 2 duo John Stone (Mon Mar 12 2007 - 09:21:47 CDT)
How to specify the orientation of the molecule zhangh1_at_umbc.edu (Sun Mar 11 2007 - 19:39:45 CDT)
- Re: How to specify the orientation of the molecule John Stone (Mon Mar 12 2007 - 20:44:34 CDT)
  - Re: How to specify the orientation of the molecule zhangh1_at_umbc.edu (Tue Mar 13 2007 - 10:23:37 CDT)
Movie Maker: How to specify use of trajectory in the movie script file Shatadal Ghosh (Sat Mar 10 2007 - 01:43:42 CST)
- Re: Movie Maker: How to specify use of trajectory in the movie script file John Stone (Mon Mar 12 2007 - 20:56:51 CDT)
VolumeSlices Pawel Wielgus (Fri Mar 09 2007 - 09:27:17 CST)
- Re: VolumeSlices John Stone (Fri Mar 09 2007 - 09:42:39 CST)
  - Re: VolumeSlices Pawel Wielgus (Fri Mar 09 2007 - 09:54:26 CST)
- Re: VolumeSlices Pawel Wielgus (Tue Mar 13 2007 - 08:07:38 CDT)
  - Re: Re: VolumeSlices John Stone (Tue Mar 13 2007 - 10:21:19 CDT)
VMD_orient pkmukher (Thu Mar 08 2007 - 21:36:49 CST)
- Re: VMD_orient John Stone (Fri Mar 23 2007 - 14:30:22 CDT)
Memory problems with Multiseq Marcelo Puiatti (Thu Mar 08 2007 - 17:21:27 CST)
- Re: Memory problems with Multiseq John Stone (Thu Mar 08 2007 - 17:38:50 CST)
VMD Rex Palmer (Thu Mar 08 2007 - 05:29:14 CST)
- Re: VMD John Stone (Sun Mar 11 2007 - 18:49:02 CDT)
OpenGL problem Rene Salmon (Tue Mar 06 2007 - 16:03:19 CST)
- Re: OpenGL problem John Stone (Tue Mar 06 2007 - 16:17:15 CST)
DCD for windows lily jin (Tue Mar 06 2007 - 15:25:40 CST)
- Re: DCD for windows John Stone (Tue Mar 06 2007 - 16:20:27 CST)
  - Re: DCD for windows John Stone (Mon Mar 12 2007 - 01:15:22 CDT)
- Re: namd-l: DCD for windows Gianluca Interlandi (Tue Mar 06 2007 - 17:32:09 CST)
Locating channel using hole Subramanian Vaitheeswaran (Tue Mar 06 2007 - 12:11:23 CST)
- Re: Locating channel using hole John Stone (Tue Mar 06 2007 - 12:43:42 CST)
  - Re: Locating channel using hole daniel aguayo (Tue Mar 06 2007 - 14:28:24 CST)
  - Re: Locating channel using hole John Stone (Wed Mar 07 2007 - 13:26:41 CST)
unusual residue type problem.. hl332_at_drexel.edu (Tue Mar 06 2007 - 11:38:08 CST)
- Re: unusual residue type problem.. John Stone (Tue Mar 06 2007 - 12:52:25 CST)
  - Re: unusual residue type problem.. hl332_at_drexel.edu (Tue Mar 06 2007 - 14:24:17 CST)
    - Re: unusual residue type problem.. John Stone (Wed Mar 07 2007 - 13:34:35 CST)
Re: Where to find cholesterol ester in PDB format Peter Engelhardt (Tue Mar 06 2007 - 03:56:26 CST)
Configuration file Rita Cassia (Tue Mar 06 2007 - 06:37:47 CST)
- Re: Configuration file John Stone (Tue Mar 06 2007 - 10:02:47 CST)
BPS Meeting @ Baltimore bora erdemli (Mon Mar 05 2007 - 19:16:40 CST)
- Re: BPS Meeting @ Baltimore Peter Freddolino (Thu Mar 08 2007 - 07:07:25 CST)
  - Re: BPS Meeting @ Baltimore L. Michel Espinoza-Fonseca (Thu Mar 08 2007 - 09:40:16 CST)
read the pdb file using VMD Esther Brugger (Mon Mar 05 2007 - 17:00:36 CST)
- Re: read the pdb file using VMD Axel Kohlmeyer (Tue Mar 06 2007 - 01:30:16 CST)
  - Re: read the pdb file using VMD Avell Diroll (Wed Mar 07 2007 - 17:39:38 CST)
vmd core dump on IRIX Rene Salmon (Mon Mar 05 2007 - 16:16:01 CST)
- Re: vmd core dump on IRIX John Stone (Mon Mar 05 2007 - 16:30:10 CST)
- Re: vmd core dump on IRIX Rene Salmon (Tue Mar 06 2007 - 10:18:18 CST)
reading charmm files Grazia Daminelli (Mon Mar 05 2007 - 07:48:22 CST)
- Re: reading charmm files Axel Kohlmeyer (Mon Mar 05 2007 - 08:27:12 CST)
- Re: reading charmm files George Madalin Giambasu (Mon Mar 05 2007 - 08:57:11 CST)
  - Re: reading charmm files Axel Kohlmeyer (Mon Mar 05 2007 - 11:56:34 CST)
New Molecule (or Load Data) resets viewpoint of Display. Why? Rob (Sun Mar 04 2007 - 21:27:14 CST)
- Re: New Molecule (or Load Data) resets viewpoint of Display. Why? Axel Kohlmeyer (Mon Mar 05 2007 - 05:24:25 CST)
- Re: New Molecule (or Load Data) resets viewpoint of Display. Why? John Stone (Mon Mar 05 2007 - 17:06:29 CST)
- Re: New Molecule (or Load Data) resets viewpoint of Display. Why? Rob (Tue Mar 06 2007 - 03:28:56 CST)
  - Re: Re: New Molecule (or Load Data) resets viewpoint of Display. Why? John Stone (Wed Mar 07 2007 - 16:41:04 CST)
E-D stereo glasses aneamtu_at_iasi.mednet.ro (Sat Mar 03 2007 - 04:44:51 CST)
- Re: E-D stereo glasses John Stone (Sat Mar 03 2007 - 14:09:22 CST)
Compiling VMD from source on SDSC Datastar (AIX 5.2) Philip Blood (Fri Mar 02 2007 - 17:09:25 CST)
- Re: Compiling VMD from source on SDSC Datastar (AIX 5.2) John Stone (Fri Mar 02 2007 - 17:15:22 CST)
  - Re: Compiling VMD from source on SDSC Datastar (AIX 5.2) Philip Blood (Fri Mar 02 2007 - 18:14:23 CST)
vmd/gaussian cubes Adrian Roitberg (Fri Mar 02 2007 - 10:11:08 CST)
- Re: vmd/gaussian cubes Axel Kohlmeyer (Fri Mar 02 2007 - 11:48:20 CST)
Calculating dipole moment of protein Per Jr. Greisen (Fri Mar 02 2007 - 06:26:23 CST)
- Re: Calculating dipole moment of protein Axel Kohlmeyer (Fri Mar 02 2007 - 07:41:25 CST)
Updating atomselection from frame to frame Jawahar Neelankatan (Fri Mar 02 2007 - 06:19:38 CST)
- Re: Updating atomselection from frame to frame Cesar Luis Avila (Fri Mar 02 2007 - 07:32:01 CST)
  - Re: Updating atomselection from frame to frame Axel Kohlmeyer (Fri Mar 02 2007 - 08:27:07 CST)
    - Re: Updating atomselection from frame to frame Cesar Luis Avila (Fri Mar 02 2007 - 08:59:48 CST)
- Re: Updating atomselection from frame to frame Axel Kohlmeyer (Fri Mar 02 2007 - 07:32:00 CST)
  - Re: Atomselection in NAMDENERGY Jawahar Neelankatan (Fri Mar 02 2007 - 08:09:27 CST)
    - Re: Atomselection in NAMDENERGY Axel Kohlmeyer (Fri Mar 02 2007 - 08:31:54 CST)
Colouring Atoms according to the centro-symmetric parameter Epiphaniou, Nicholas (Thu Mar 01 2007 - 12:59:00 CST)
- Re: Colouring Atoms according to the centro-symmetric parameter Axel Kohlmeyer (Thu Mar 01 2007 - 13:45:36 CST)
Transform pdb files in psf files using VMD Inês Sousa (Thu Mar 01 2007 - 04:35:44 CST)
- Re: Transform pdb files in psf files using VMD Peter Freddolino (Thu Mar 01 2007 - 09:27:28 CST)
- Re: Transform pdb files in psf files using VMD Peter Freddolino (Thu Mar 01 2007 - 15:05:51 CST)
convert tcl to python Per Jr. Greisen (Thu Mar 01 2007 - 05:54:18 CST)
- Re: convert tcl to python Peter Freddolino (Thu Mar 01 2007 - 09:28:55 CST)
calculation of free energy between lipid membrane and protein Shulin Zhuang (Thu Mar 01 2007 - 00:17:25 CST)
- Re: calculation of free energy between lipid membrane and protein Shulin Zhuang (Thu Mar 01 2007 - 01:11:10 CST)
  - Re: calculation of free energy between lipid membrane and protein Axel Kohlmeyer (Thu Mar 01 2007 - 11:40:00 CST)
Delete Volume Maps via Script Bob Johnson (Wed Feb 28 2007 - 18:36:43 CST)
- Re: Delete Volume Maps via Script John Stone (Tue Mar 06 2007 - 14:47:07 CST)
morph christopher (Wed Feb 28 2007 - 16:18:48 CST)
- Re: morph John Stone (Wed Mar 07 2007 - 16:43:29 CST)
count variable number of molecules Alexandr Isayev (Wed Feb 28 2007 - 14:23:11 CST)
- Re: count variable number of molecules John Stone (Wed Mar 07 2007 - 16:45:56 CST)
multiple dx frames Jim Fonseca (Wed Feb 28 2007 - 13:49:12 CST)
- Re: multiple dx frames Leonardo Trabuco (Wed Feb 28 2007 - 14:16:32 CST)
- Re: multiple dx frames Axel Kohlmeyer (Wed Feb 28 2007 - 14:42:34 CST)
  - Re: multiple dx frames Leonardo Trabuco (Wed Feb 28 2007 - 14:51:16 CST)
Calculate VolMap for every frame by a script Bob Johnson (Tue Feb 27 2007 - 16:21:12 CST)
- Re: Calculate VolMap for every frame by a script Axel Kohlmeyer (Tue Feb 27 2007 - 17:25:16 CST)
VMD open GL Display problem Ayþe Özlem Sezerman (Tue Feb 27 2007 - 06:52:19 CST)
- Re: VMD open GL Display problem L. Michel Espinoza-Fonseca (Tue Feb 27 2007 - 10:06:26 CST)
  - Re: VMD open GL Display problem christopher (Tue Feb 27 2007 - 10:52:51 CST)
    - Re: VMD open GL Display problem John Stone (Tue Feb 27 2007 - 11:20:36 CST)
    - Re: VMD open GL Display problem Axel Kohlmeyer (Tue Feb 27 2007 - 11:43:12 CST)
Cave and usr keys defined in tcl Christian Wohlschlager (Tue Feb 27 2007 - 05:46:38 CST)
- Re: Cave and usr keys defined in tcl John Stone (Wed Feb 28 2007 - 00:00:22 CST)
rmsf calculations bora erdemli (Tue Feb 27 2007 - 01:42:25 CST)
- Re: rmsf calculations L. Michel Espinoza-Fonseca (Tue Feb 27 2007 - 05:51:47 CST)
bug report in VMD 1.8.5 Nichols A. Romero (Mon Feb 26 2007 - 16:24:53 CST)
- Re: bug report in VMD 1.8.5 Nichols A. Romero (Mon Feb 26 2007 - 16:28:41 CST)
  - Re: Re: bug report in VMD 1.8.5 John Stone (Mon Feb 26 2007 - 16:41:14 CST)
  - Re: Re: bug report in VMD 1.8.5 Axel Kohlmeyer (Mon Feb 26 2007 - 17:26:38 CST)
- Re: bug report in VMD 1.8.5 Jerome Henin (Mon Feb 26 2007 - 19:32:29 CST)
lipid headgroup analysis syma (Mon Feb 26 2007 - 04:38:35 CST)
Tracing VMD variables Olaf Lenz (Mon Feb 26 2007 - 08:10:03 CST)
- Re: Tracing VMD variables John Stone (Tue Feb 27 2007 - 13:31:21 CST)
  - Re: Tracing VMD variables Olaf Lenz (Wed Feb 28 2007 - 00:30:35 CST)
IC from paratool Grazia Daminelli (Mon Feb 26 2007 - 02:35:27 CST)
- Re: IC from paratool Jan Saam (Fri Mar 02 2007 - 12:41:59 CST)
Question about RDF of VMD Jianhui Tian (Sat Feb 24 2007 - 20:33:13 CST)
- Re: Question about RDF of VMD Axel Kohlmeyer (Sat Feb 24 2007 - 21:25:14 CST)
"get {x y z}" returns single value Ivan Degtyarenko (Fri Feb 23 2007 - 10:18:16 CST)
- Re: "get {x y z}" returns single value Axel Kohlmeyer (Fri Feb 23 2007 - 11:10:04 CST)
- Re: "get {x y z}" returns single value Olaf Lenz (Fri Feb 23 2007 - 11:16:30 CST)
transparent background in vmd Omololu (Fri Feb 23 2007 - 10:11:24 CST)
- Re: transparent background in vmd Axel Kohlmeyer (Fri Feb 23 2007 - 10:49:56 CST)
Number of Frames in VMD Rita Cassia (Fri Feb 23 2007 - 07:48:39 CST)
- Re: Number of Frames in VMD Axel Kohlmeyer (Fri Feb 23 2007 - 09:05:15 CST)
Same pdb file, different image Hai-Jun Su (Thu Feb 22 2007 - 22:11:27 CST)
- Re: Same pdb file, different image Leonardo Trabuco (Thu Feb 22 2007 - 23:44:37 CST)
- Re: Same pdb file, different image hamdi (Fri Feb 23 2007 - 03:02:57 CST)
cube file: coordinates rotated Yaser Khan (Wed Feb 21 2007 - 20:05:32 CST)
- Re: cube file: coordinates rotated Axel Kohlmeyer (Thu Feb 22 2007 - 09:07:28 CST)
(no subject) Stephen M. Dutz (Wed Feb 21 2007 - 15:40:45 CST)
Nanopore simulation subhasish chatterjee (Tue Feb 20 2007 - 21:58:54 CST)
- Re: namd-l: Nanopore simulation Mark Abraham (Tue Feb 20 2007 - 22:14:46 CST)
  - Re: Re: namd-l: Nanopore simulation subhasish chatterjee (Tue Feb 20 2007 - 23:54:32 CST)
  - Re: Re: namd-l: Nanopore simulation subhasish chatterjee (Wed Feb 21 2007 - 00:00:07 CST)
    - Re: Re: namd-l: Nanopore simulation Axel Kohlmeyer (Wed Feb 21 2007 - 12:06:08 CST)
    - Re: Re: namd-l: Nanopore simulation subhasish chatterjee (Wed Feb 21 2007 - 22:58:18 CST)
superimposing two structures and getting the coordinates bertrand russell (Tue Feb 20 2007 - 11:52:03 CST)
- Re: superimposing two structures and getting the coordinates Cesar Luis Avila (Tue Feb 20 2007 - 12:43:52 CST)
  - Re: superimposing two structures and getting the coordinates John Stone (Tue Feb 20 2007 - 12:56:53 CST)
    - Re: superimposing two structures and getting the coordinates Brian Bennion (Tue Feb 20 2007 - 14:44:17 CST)
    - Re: superimposing two structures and getting the coordinates Cesar Luis Avila (Tue Feb 20 2007 - 14:52:36 CST)
Isosurface rendering Avell Diroll (Tue Feb 20 2007 - 08:52:35 CST)
- Re: Isosurface rendering John Stone (Tue Feb 20 2007 - 10:44:36 CST)
  - Re: Isosurface rendering John Stone (Tue Feb 20 2007 - 12:53:21 CST)
Fwd: generating COORDINATE FILES PREETA DATTA (Tue Feb 20 2007 - 07:22:53 CST)
generating PREETA DATTA (Tue Feb 20 2007 - 07:19:13 CST)
- Re: generating Axel Kohlmeyer (Tue Feb 20 2007 - 09:05:44 CST)
  - Re: generating PREETA DATTA (Tue Feb 20 2007 - 14:30:11 CST)
    - Re: generating Axel Kohlmeyer (Tue Feb 20 2007 - 14:45:27 CST)
a question about paratool Javaria Ahmad (Tue Feb 20 2007 - 06:35:52 CST)
- Re: a question about paratool Jan Saam (Thu Feb 22 2007 - 18:43:57 CST)
syntax error in com file Javaria Ahmad (Tue Feb 20 2007 - 06:15:49 CST)
PC-gamess Per Jr. Greisen (Tue Feb 20 2007 - 05:02:45 CST)
- Re: PC-gamess Ran Friedman (Tue Feb 20 2007 - 08:33:27 CST)
  - Re: PC-gamess Ran Friedman (Tue Feb 20 2007 - 11:24:32 CST)
- Re: PC-gamess John Stone (Tue Feb 20 2007 - 10:55:57 CST)
Anyone have cyclic structures I can use for testing? John Stone (Tue Feb 20 2007 - 01:28:29 CST)
- generating COORDINATE FILES PREETA DATTA (Tue Feb 20 2007 - 05:48:41 CST)
Files closing/Memory issues in VMD Alexander Balaeff (Mon Feb 19 2007 - 14:03:54 CST)
- Re: Files closing/Memory issues in VMD John Stone (Mon Feb 19 2007 - 17:30:16 CST)
Research Position Openings Mike Smith (Sun Feb 18 2007 - 03:45:19 CST)
hbonds problem alexandra.marques_at_fc.up.pt (Sat Feb 17 2007 - 17:52:45 CST)
- Re: hbonds problem JC Gumbart (Sat Feb 17 2007 - 19:57:17 CST)
Strange MOL2 export Mario Valle (Sat Feb 17 2007 - 12:21:42 CST)
- Re: Strange MOL2 export Peter Freddolino (Sat Feb 17 2007 - 15:36:45 CST)
  - Re: Strange MOL2 export Mario Valle (Mon Feb 19 2007 - 09:12:33 CST)
    - Re: Strange MOL2 export Peter Freddolino (Mon Feb 19 2007 - 09:55:24 CST)
Small annoyance with tachion Mario Valle (Sat Feb 17 2007 - 11:34:46 CST)
- Re: Small annoyance with tachion John Stone (Sat Feb 17 2007 - 12:22:25 CST)
- Re: Small annoyance with tachion John Stone (Sun Feb 18 2007 - 20:45:22 CST)
- Re: Small annoyance with tachion John Stone (Wed Feb 21 2007 - 17:27:18 CST)
  - Re: Small annoyance with tachion Mario Valle (Mon Feb 26 2007 - 22:19:28 CST)
  - Re: Small annoyance with tachion Mario Valle (Tue Feb 27 2007 - 03:30:35 CST)
stereo view Osmany Guirola Cruz (Fri Feb 16 2007 - 14:06:43 CST)
- Re: stereo view John Stone (Fri Feb 16 2007 - 17:53:08 CST)
building bilayer with DOPC or other lipids PREETA DATTA (Fri Feb 16 2007 - 04:29:41 CST)
Measure atoms volume on VMD Cesar Luis Avila (Thu Feb 15 2007 - 15:27:53 CST)
- Re: Measure atoms volume on VMD John Stone (Thu Feb 15 2007 - 23:02:17 CST)
3D grid data to 2D contour? Ivan Degtyarenko (Thu Feb 15 2007 - 15:04:05 CST)
- Re: 3D grid data to 2D contour? John Stone (Tue Feb 20 2007 - 02:04:57 CST)
problem with autopsf L. Michel Espinoza-Fonseca (Thu Feb 15 2007 - 07:44:18 CST)
- Re: problem with autopsf Peter Freddolino (Thu Feb 15 2007 - 08:11:49 CST)
  - Re: problem with autopsf L. Michel Espinoza-Fonseca (Thu Feb 15 2007 - 08:16:06 CST)
    - Re: problem with autopsf Peter Freddolino (Thu Feb 15 2007 - 08:20:20 CST)
TCl question: preventing STDOUT namd vmd (Thu Feb 15 2007 - 05:59:50 CST)
- Re: TCl question: preventing STDOUT Axel Kohlmeyer (Thu Feb 15 2007 - 06:37:36 CST)
aligning one molecule s.schweizer_at_dkfz-heidelberg.de (Wed Feb 14 2007 - 08:47:41 CST)
- Re: aligning one molecule Himanshu Khandelia (Wed Feb 14 2007 - 17:30:18 CST)
Bug in the tcl script greddy1_at_umd.edu (Tue Feb 13 2007 - 13:18:58 CST)
- Re: Bug in the tcl script John Stone (Thu Feb 15 2007 - 22:44:32 CST)
GL window offset problem christopher (Mon Feb 12 2007 - 15:09:55 CST)
- Re: GL window offset problem John Stone (Thu Feb 15 2007 - 13:05:37 CST)
average structure dimka (Mon Feb 12 2007 - 13:42:33 CST)
- Re: average structure Eduard Schreiner (Tue Feb 13 2007 - 06:52:21 CST)
aligning molecules with different number of atoms namd vmd (Mon Feb 12 2007 - 11:53:49 CST)
- Re: aligning molecules with different number of atoms JC Gumbart (Mon Feb 12 2007 - 11:58:12 CST)
  - Re: aligning molecules with different number of atoms John Stone (Mon Feb 12 2007 - 12:01:58 CST)
  - Re: aligning molecules with different number of atoms Leandro Martínez (Mon Feb 12 2007 - 12:39:29 CST)
- Re: aligning molecules with different number of atoms Leonardo Trabuco (Mon Feb 12 2007 - 12:05:28 CST)
ionize (big, big, big system!) L. Michel Espinoza-Fonseca (Mon Feb 12 2007 - 10:58:32 CST)
- Re: ionize (big, big, big system!) Peter Freddolino (Mon Feb 12 2007 - 11:07:50 CST)
  - Re: ionize (big, big, big system!) L. Michel Espinoza-Fonseca (Mon Feb 12 2007 - 11:19:57 CST)
atomselection: number of residues namd vmd (Sun Feb 11 2007 - 06:35:17 CST)
- Re: atomselection: number of residues Leonardo Trabuco (Sun Feb 11 2007 - 11:59:23 CST)
  - Re: atomselection: number of residues Peter Freddolino (Sun Feb 11 2007 - 12:11:09 CST)
  - RE: atomselection: number of residues JC Gumbart (Sun Feb 11 2007 - 12:16:11 CST)
- Re: atomselection: number of residues Axel Kohlmeyer (Sun Feb 11 2007 - 13:41:08 CST)
hot keys & save state Yaser Khan (Sun Feb 11 2007 - 03:01:40 CST)
- Re: hot keys & save state Axel Kohlmeyer (Sun Feb 11 2007 - 13:06:08 CST)
VMD-1.8.5: GLSL & NVidia troubles + fixed previous Spaceball problem Pietro Amodeo (Sat Feb 10 2007 - 05:59:42 CST)
- Re: VMD-1.8.5: GLSL & NVidia troubles + fixed previous Spaceball problem John Stone (Sat Feb 10 2007 - 23:58:18 CST)
  - Re: VMD-1.8.5: GLSL & NVidia troubles + fixed previous Spaceball problem Pietro Amodeo (Sun Feb 11 2007 - 06:22:46 CST)
- Re: VMD-1.8.5: GLSL & NVidia troubles + fixed previous Spaceball problem Axel Kohlmeyer (Sun Feb 11 2007 - 12:51:06 CST)
Bug in the Tcl script greddy1_at_umd.edu (Fri Feb 09 2007 - 19:51:24 CST)
load in multiple files once Hai-Jun Su (Fri Feb 09 2007 - 15:53:18 CST)
- Re: load in multiple files once Axel Kohlmeyer (Fri Feb 09 2007 - 16:30:00 CST)
question about rotations Adrian Roitberg (Fri Feb 09 2007 - 08:33:34 CST)
- Re: question about rotations John Stone (Fri Feb 09 2007 - 18:02:33 CST)
Changing the display window size in a script Ignacio Fernández Galván (Fri Feb 09 2007 - 02:37:02 CST)
- Re: Changing the display window size in a script John Stone (Fri Feb 09 2007 - 03:06:28 CST)
How to save the snapshot of my protein? bertrand russell (Fri Feb 09 2007 - 01:24:54 CST)
- Re: How to save the snapshot of my protein? John Stone (Fri Feb 09 2007 - 02:59:19 CST)
  - Re: How to save the snapshot of my protein? bertrand russell (Fri Feb 09 2007 - 03:58:53 CST)
  - Re: How to save the snapshot of my protein? Kateryna Miroshnychenko (Fri Feb 09 2007 - 09:21:23 CST)
Assigning Color Codes for stress/force in .xyz trajectory files Adrian Koh (Fri Feb 09 2007 - 00:08:26 CST)
- Re: Assigning Color Codes for stress/force in .xyz trajectory files John Stone (Fri Feb 09 2007 - 02:56:59 CST)
- Re: Assigning Color Codes for stress/force in .xyz trajectory files Peter Freddolino (Fri Feb 09 2007 - 07:57:09 CST)
  - Re: Assigning Color Codes for stress/force in .xyz trajectory files Peter Freddolino (Fri Feb 09 2007 - 10:48:49 CST)
Making interactive 3-D PDF files using VMD 1.8.6 beta 7 John Stone (Thu Feb 08 2007 - 18:11:53 CST)
H-Bond in VMD Esther Brugger (Thu Feb 08 2007 - 10:48:38 CST)
viewpoint Levin, Andrew Michael (Thu Feb 08 2007 - 09:17:48 CST)
- Re: viewpoint John Stone (Thu Feb 08 2007 - 12:54:27 CST)
viewpoint Levin, Andrew Michael (Thu Feb 08 2007 - 09:19:16 CST)
viewpoint Levin, Andrew Michael (Thu Feb 08 2007 - 09:18:01 CST)
- Saving work in VMD--this seems ridiculously difficult! wolfinbm_at_uci.edu (Thu Feb 08 2007 - 16:09:52 CST)
surface area emra Heshmati (Wed Feb 07 2007 - 22:40:56 CST)
- Re: surface area Lubos Vrbka (Thu Feb 08 2007 - 06:16:59 CST)
stride failed Tsu-Fan Cheng (Wed Feb 07 2007 - 15:23:08 CST)
- Re: stride failed John Stone (Fri Feb 09 2007 - 02:24:12 CST)
file "top_all22_prot.inp" Hai-Jun Su (Tue Feb 06 2007 - 20:26:53 CST)
- Re: file "top_all22_prot.inp" Axel Kohlmeyer (Wed Feb 07 2007 - 09:49:39 CST)
H-Bond display in VMD Esther Brugger (Tue Feb 06 2007 - 12:41:47 CST)
- Re: H-Bond display in VMD John Stone (Thu Feb 08 2007 - 12:37:03 CST)
splitting segments namd vmd (Tue Feb 06 2007 - 11:06:15 CST)
- Re: splitting segments Peter Freddolino (Tue Feb 06 2007 - 11:12:11 CST)
Re: about CHARMM electrostatic potential ivana adamovic (Mon Feb 05 2007 - 14:44:51 CST)
- Re: about CHARMM electrostatic potential John Stone (Mon Feb 05 2007 - 14:47:51 CST)
  - Re: about CHARMM electrostatic potential ivana adamovic (Mon Feb 05 2007 - 14:54:15 CST)
indented atomselect variables namd vmd (Mon Feb 05 2007 - 14:30:48 CST)
- Re: indented atomselect variables John Stone (Mon Feb 05 2007 - 14:45:44 CST)
too large an area/lipid in POPE bilayers using membrane plugin Himanshu Khandelia (Mon Feb 05 2007 - 11:50:04 CST)
- Re: namd-l: too large an area/lipid in POPE bilayers using membrane plugin Richard Law (Mon Feb 05 2007 - 12:49:07 CST)
  - Re: Re: namd-l: too large an area/lipid in POPE bilayers using membrane plugin John Stone (Mon Feb 05 2007 - 14:52:48 CST)
rendering time bars or other vmd added graphics with povray Vlad Cojocaru (Mon Feb 05 2007 - 10:58:48 CST)
- Re: rendering time bars or other vmd added graphics with povray Alexandr Isayev (Mon Feb 05 2007 - 11:23:12 CST)
  - Re: rendering time bars or other vmd added graphics with povray Vlad Cojocaru (Mon Feb 05 2007 - 11:31:50 CST)
about CHARMM electrostaic potential ivana adamovic (Mon Feb 05 2007 - 09:46:47 CST)
- Re: about CHARMM electrostaic potential John Stone (Mon Feb 05 2007 - 11:03:04 CST)
  - Re: about CHARMM electrostaic potential ivana adamovic (Mon Feb 05 2007 - 11:56:35 CST)
volume slices Jim Fonseca (Sun Feb 04 2007 - 14:32:11 CST)
- Re: volume slices John Stone (Sun Feb 04 2007 - 15:09:52 CST)
  - Saving mutli-molecule structures in VMD (e.g., for building membranes) wolfinbm_at_uci.edu (Sun Feb 04 2007 - 22:20:41 CST)
    - Re: Saving mutli-molecule structures in VMD (e.g., for building membranes) Cesar Luis Avila (Mon Feb 05 2007 - 09:11:38 CST)
    - Re: Saving mutli-molecule structures in VMD (e.g., for building membranes) Axel Kohlmeyer (Mon Feb 05 2007 - 12:09:15 CST)
cartoon problems (encore) christopher (Sat Feb 03 2007 - 15:29:56 CST)
- Re: cartoon problems (encore) John Stone (Sat Feb 03 2007 - 15:39:17 CST)
Units for Measure Dipole Kim Gunnerson (Fri Feb 02 2007 - 16:51:16 CST)
- Re: Units for Measure Dipole Axel Kohlmeyer (Fri Feb 02 2007 - 18:28:15 CST)
  - Re: Units for Measure Dipole John Stone (Mon Feb 05 2007 - 10:32:40 CST)
Atomselect on several molecules Veronika Brazdova (Fri Feb 02 2007 - 10:04:22 CST)
- Re: Atomselect on several molecules Axel Kohlmeyer (Fri Feb 02 2007 - 11:19:06 CST)
  - Re: Atomselect on several molecules Veronika Brazdova (Fri Feb 02 2007 - 12:57:25 CST)
    - Re: Atomselect on several molecules Axel Kohlmeyer (Fri Feb 02 2007 - 13:36:13 CST)
    - Re: Atomselect on several molecules Veronika Brazdova (Mon Feb 05 2007 - 10:11:23 CST)
Using "membrane package" with different lipid molecules Lechuga, Javier (Fri Feb 02 2007 - 09:18:06 CST)
- Re: Using "membrane package" with different lipid molecules Peter Freddolino (Fri Feb 02 2007 - 09:37:01 CST)
creating gif animation with povray Vlad Cojocaru (Fri Feb 02 2007 - 04:09:12 CST)
- Re: creating gif animation with povray John Stone (Sat Feb 03 2007 - 00:54:16 CST)
  - Re: creating gif animation with povray Vlad Cojocaru (Mon Feb 05 2007 - 03:48:54 CST)
    - Re: creating gif animation with povray John Stone (Mon Feb 05 2007 - 09:56:28 CST)
VMD performance on Vista Christoph Weber (Thu Feb 01 2007 - 16:23:58 CST)
- Re: VMD performance on Vista John Stone (Thu Feb 01 2007 - 17:10:47 CST)
sending arguments to tcl _at_huji.ac.il (Thu Feb 01 2007 - 13:39:20 CST)
- Re: sending arguments to tcl John Stone (Thu Feb 01 2007 - 14:56:00 CST)
- Re: sending arguments to tcl Axel Kohlmeyer (Thu Feb 01 2007 - 15:55:30 CST)
- Re: sending arguments to tcl John Stone (Thu Feb 01 2007 - 16:53:24 CST)
  - Re: sending arguments to tcl _at_huji.ac.il (Sun Feb 04 2007 - 02:21:02 CST)
addition on CHARMM electrostatic pot. ivana adamovic (Thu Feb 01 2007 - 13:42:08 CST)
- Re: addition on CHARMM electrostatic pot. John Stone (Thu Feb 01 2007 - 17:27:36 CST)
- Re: addition on CHARMM electrostatic pot. ivana adamovic (Fri Feb 02 2007 - 09:11:44 CST)
CHARMM electrostatic potential ivana adamovic (Thu Feb 01 2007 - 13:17:21 CST)
CHARMM electrostatic potential ivana adamovic (Thu Feb 01 2007 - 08:28:20 CST)
- Re: CHARMM electrostatic potential John Stone (Thu Feb 01 2007 - 11:16:38 CST)
  - Error while running scripts: terminate called after throwing an instance of 'std::bad_alloc' Arneh Babakhani (Fri Feb 02 2007 - 16:16:04 CST)
VMD error messages on intel iMac Craig C. Martens (Wed Jan 31 2007 - 23:32:32 CST)
- Re: VMD error messages on intel iMac John Stone (Thu Feb 01 2007 - 16:02:46 CST)
uNABLE TO OPEN VMD ON WINDOWS 2K Caio Julio Martins Veloso (Wed Jan 31 2007 - 21:38:03 CST)
- Re: uNABLE TO OPEN VMD ON WINDOWS 2K John Stone (Wed Jan 31 2007 - 21:32:47 CST)
  - RES: uNABLE TO OPEN VMD ON WINDOWS 2K Caio Julio Martins Veloso (Thu Feb 01 2007 - 06:54:03 CST)
    - Re: RES: uNABLE TO OPEN VMD ON WINDOWS 2K John Stone (Thu Feb 01 2007 - 11:05:32 CST)
animate write of a selection in Linux version of VMD Pawel Weronski (Wed Jan 31 2007 - 15:54:25 CST)
- Re: animate write of a selection in Linux version of VMD John Stone (Wed Jan 31 2007 - 16:10:46 CST)
  - Re: animate write of a selection in Linux version of VMD Pawel Weronski (Wed Jan 31 2007 - 16:24:02 CST)
DNA and low pH Gaurav Sharma (Wed Jan 31 2007 - 15:06:46 CST)
- Re: DNA and low pH Peter Freddolino (Wed Jan 31 2007 - 19:51:26 CST)
Volume Slice Adrian Roitberg (Wed Jan 31 2007 - 15:07:45 CST)
- Re: Volume Slice John Stone (Wed Jan 31 2007 - 15:59:36 CST)
About CHARMM electrostaic potential map ivana adamovic (Wed Jan 31 2007 - 09:26:19 CST)
- Re: About CHARMM electrostaic potential map John Stone (Wed Jan 31 2007 - 13:37:30 CST)
  - Re: About CHARMM electrostaic potential map ivana adamovic (Wed Jan 31 2007 - 14:30:11 CST)
Announce: New VMD Images and Movies tutorial posted online... John Stone (Wed Jan 31 2007 - 00:23:46 CST)
Delete frames in a script Ran Friedman (Tue Jan 30 2007 - 06:12:14 CST)
- RE: Delete frames in a script Ana Celia Araujo Vila Verde (Tue Jan 30 2007 - 10:08:50 CST)
Compute the angle between a vector and the largest inertia axis Prevost Martine (Tue Jan 30 2007 - 04:15:03 CST)
- Re: Compute the angle between a vector and the largest inertia axis Axel Kohlmeyer (Tue Jan 30 2007 - 11:16:32 CST)
Re: Add transparent plane to molecular Rob (Tue Jan 30 2007 - 09:05:36 CST)
Add transparent plane to molecular structure Rob (Mon Jan 29 2007 - 20:57:38 CST)
- Re: Add transparent plane to molecular structure Axel Kohlmeyer (Mon Jan 29 2007 - 21:31:50 CST)
- Re: Add transparent plane to molecular structure Rob (Tue Jan 30 2007 - 03:12:21 CST)
  - Re: Re: Add transparent plane to molecular structure Axel Kohlmeyer (Tue Jan 30 2007 - 11:04:27 CST)
Python development Mikolai Fajer (Mon Jan 29 2007 - 16:39:00 CST)
- Re: Python development John Stone (Tue Jan 30 2007 - 16:49:23 CST)
  - Re: Python development Dr. Seth Olsen (Tue Jan 30 2007 - 19:51:12 CST)
  - Re: Python development Mikolai Fajer (Tue Jan 30 2007 - 21:27:05 CST)
    - Re: Python development Vasiliy S. Znamenskiy (Wed Jan 31 2007 - 07:15:13 CST)
an old...old..old..question Tsu-Fan Cheng (Mon Jan 29 2007 - 16:24:16 CST)
- Re: an old...old..old..question Axel Kohlmeyer (Mon Jan 29 2007 - 18:33:14 CST)
smd analysis Narender Singh Maan (Mon Jan 29 2007 - 14:47:02 CST)
GLSL error Dow Hurst DPHURST (Mon Jan 29 2007 - 14:40:14 CST)
- Re: GLSL error John Stone (Mon Jan 29 2007 - 15:22:50 CST)
  - Re: GLSL error Dow Hurst DPHURST (Tue Jan 30 2007 - 11:08:22 CST)
Skip frames in writing shorter trajectory Neelanjana Sengupta (Mon Jan 29 2007 - 11:56:10 CST)
- Re: Skip frames in writing shorter trajectory Leonardo Trabuco (Mon Jan 29 2007 - 14:26:09 CST)
Re: Regarding paratool, assign atom types Jan Saam (Mon Jan 29 2007 - 10:56:30 CST)
- RE: Regarding paratool, assign atom types Javaria Ahmed (Mon Jan 29 2007 - 16:22:17 CST)
  - Re: RE: Regarding paratool, assign atom types Jan Saam (Wed Jan 31 2007 - 14:30:55 CST)
Pls help, Q abt PDB->PSF Stanley, Yemin Shi (Sat Jan 27 2007 - 21:55:02 CST)
- Re: Pls help, Q abt PDB->PSF Peter Freddolino (Sun Jan 28 2007 - 00:38:29 CST)
[vmd] K3b bug? christopher (Sat Jan 27 2007 - 07:12:57 CST)
- Re: [vmd] K3b bug? Peter Freddolino (Sat Jan 27 2007 - 07:59:55 CST)
  - Re: [vmd] K3b bug? Peter Freddolino (Sat Jan 27 2007 - 08:26:32 CST)
    - Re: [vmd] K3b bug? christopher (Sat Jan 27 2007 - 09:15:58 CST)
draw line Narender Singh Maan (Fri Jan 26 2007 - 17:01:14 CST)
- Re: draw line John Stone (Fri Jan 26 2007 - 17:16:22 CST)
history in tcl/tk script Rita Cassia (Fri Jan 26 2007 - 06:22:32 CST)
- Re: history in tcl/tk script Axel Kohlmeyer (Fri Jan 26 2007 - 10:39:02 CST)
  - Re: history in tcl/tk script Axel Kohlmeyer (Mon Jan 29 2007 - 09:12:13 CST)
wildcards in atomselect command Himanshu Khandelia (Fri Jan 26 2007 - 05:47:02 CST)
- Re: wildcards in atomselect command Axel Kohlmeyer (Fri Jan 26 2007 - 10:03:14 CST)
- Re: wildcards in atomselect command Eduard Schreiner (Fri Jan 26 2007 - 10:13:27 CST)
How can I find the rotation matrix information? Myunggi Yi (Thu Jan 25 2007 - 16:11:12 CST)
(no subject) Prevost Martine (Thu Jan 25 2007 - 04:41:37 CST)
Error when compiling Plugins from source code Epiphaniou, Nicholas (Thu Jan 25 2007 - 04:57:09 CST)
- Re: Error when compiling Plugins from source code John Stone (Thu Jan 25 2007 - 14:49:56 CST)
Installing VMD on a PC Trinh Vo (Wed Jan 24 2007 - 18:58:06 CST)
- Re: Installing VMD on a PC Axel Kohlmeyer (Wed Jan 24 2007 - 19:49:17 CST)
- Re: Installing VMD on a PC John Stone (Thu Jan 25 2007 - 01:03:19 CST)
Molefacture error Javaria Ahmed (Wed Jan 24 2007 - 17:01:09 CST)
- Re: Molefacture error Peter Freddolino (Wed Jan 24 2007 - 17:28:14 CST)
Regarding paratool Javaria Ahmed (Wed Jan 24 2007 - 16:18:01 CST)
- Re: Regarding paratool John Stone (Fri Jan 26 2007 - 02:10:24 CST)
  - Re: Regarding paratool Jan Saam (Wed Jan 31 2007 - 14:14:01 CST)
- Re: Regarding paratool Jan Saam (Mon Jan 29 2007 - 11:00:14 CST)
question on spin density Robert fiske (Wed Jan 24 2007 - 14:00:32 CST)
- Re: question on spin density Axel Kohlmeyer (Wed Jan 24 2007 - 17:14:53 CST)
RE: measure XYZ dimensions of a system Akshay Patny (Wed Jan 24 2007 - 12:47:47 CST)
- RE: measure XYZ dimensions of a system Axel Kohlmeyer (Wed Jan 24 2007 - 13:52:43 CST)
measure XYZ dimensions of a system Akshay Patny (Wed Jan 24 2007 - 10:47:00 CST)
- Re: measure XYZ dimensions of a system Axel Kohlmeyer (Wed Jan 24 2007 - 12:13:42 CST)
vector Vivek Sharma (Wed Jan 24 2007 - 04:14:28 CST)
- Re: vector Axel Kohlmeyer (Wed Jan 24 2007 - 10:26:55 CST)
- Re: vector John Stone (Wed Jan 24 2007 - 12:19:36 CST)
how to run membrane.tcl from user-defined location ? Himanshu Khandelia (Wed Jan 24 2007 - 05:54:51 CST)
- Re: how to run membrane.tcl from user-defined location ? John Stone (Thu Jan 25 2007 - 02:01:12 CST)
Getting (or changing) molinfo matrices Jancsó István (Wed Jan 24 2007 - 03:49:28 CST)
- Re: Getting (or changing) molinfo matrices John Stone (Wed Jan 24 2007 - 12:05:08 CST)
  - Re: Getting (or changing) molinfo matrices Jancsó István (Thu Jan 25 2007 - 02:29:55 CST)
    - Re: Getting (or changing) molinfo matrices John Stone (Fri Jan 26 2007 - 02:07:34 CST)
[Fwd: pdb from trajectory] some clarification _at_huji.ac.il (Tue Jan 23 2007 - 09:41:49 CST)
- Re: [Fwd: pdb from trajectory] some clarification Peter Freddolino (Tue Jan 23 2007 - 10:10:59 CST)
- Re: [Fwd: pdb from trajectory] some clarification John Stone (Tue Jan 23 2007 - 13:45:07 CST)
  - Re: [Fwd: pdb from trajectory] some clarification _at_huji.ac.il (Wed Jan 24 2007 - 04:37:40 CST)
    - Re: [Fwd: pdb from trajectory] some clarification Peter Freddolino (Wed Jan 24 2007 - 07:55:05 CST)
pdb from trajectory _at_huji.ac.il (Tue Jan 23 2007 - 09:16:29 CST)
hingefind Shirley Li (Mon Jan 22 2007 - 18:54:11 CST)
- Re: hingefind JC Gumbart (Mon Jan 22 2007 - 19:20:59 CST)
  - Re: hingefind li19104 (Tue Jan 23 2007 - 10:27:33 CST)
    - RE: hingefind JC Gumbart (Tue Jan 23 2007 - 10:53:39 CST)
    - Re: hingefind Axel Kohlmeyer (Tue Jan 23 2007 - 11:23:17 CST)
- Re: hingefind Axel Kohlmeyer (Mon Jan 22 2007 - 19:27:05 CST)
- NAMD trajectories in VMD Samuel Flores (Fri Oct 26 2007 - 11:51:26 CDT)
  - Re: NAMD trajectories in VMD Axel Kohlmeyer (Fri Oct 26 2007 - 12:22:32 CDT)
    - rna topology and parameters for rna Samuel Flores (Sun Oct 28 2007 - 03:23:39 CDT)
Converting Files with VMD mr.ibid_at_gmail.com (Sat Jan 20 2007 - 04:33:56 CST)
- Re: Converting Files with VMD John Stone (Tue Jan 23 2007 - 17:47:54 CST)
CGTools Plugin Ugur Akgun (Fri Jan 19 2007 - 13:59:31 CST)
- Re: CGTools Plugin Peter Freddolino (Sat Jan 20 2007 - 11:17:00 CST)
rotation to align Himanshu Khandelia (Fri Jan 19 2007 - 05:41:31 CST)
- RE: rotation to align Ana Celia Araujo Vila Verde (Fri Jan 19 2007 - 07:59:55 CST)
H-bond energy amit dong (Thu Jan 18 2007 - 18:13:11 CST)
- Re: H-bond energy Peter Freddolino (Thu Jan 18 2007 - 18:23:24 CST)
  - Re: H-bond energy Himanshu Khandelia (Fri Jan 19 2007 - 07:41:54 CST)
    - Re: H-bond energy Peter Freddolino (Fri Jan 19 2007 - 07:51:34 CST)
Solvent accessibility with sasa Peter Hains (Thu Jan 18 2007 - 15:34:16 CST)
- Re: Solvent accessibility with sasa John Stone (Thu Jan 18 2007 - 16:33:52 CST)
renumbering residues after deletion of atoms Himanshu Khandelia (Thu Jan 18 2007 - 09:55:07 CST)
- Re: renumbering residues after deletion of atoms Axel Kohlmeyer (Thu Jan 18 2007 - 11:51:48 CST)
Large Molecule in CAVE Enviroment Christian Wohlschlager (Thu Jan 18 2007 - 01:35:06 CST)
- Re: Large Molecule in CAVE Enviroment John Stone (Thu Jan 18 2007 - 01:59:41 CST)
Tk console issues Eric Peterson (Wed Jan 17 2007 - 15:48:58 CST)
- Re: Tk console issues John Stone (Wed Jan 17 2007 - 15:59:16 CST)
Loading DCD files Vishal Kopardé (Wed Jan 17 2007 - 13:19:27 CST)
- Re: Loading DCD files John Stone (Wed Jan 17 2007 - 14:06:00 CST)
VMD quits Vishal Kopardé (Wed Jan 17 2007 - 12:50:07 CST)
- Re: VMD quits John Stone (Wed Jan 17 2007 - 12:59:16 CST)
how to read in a multi-segment psf/pdb pair into vmd Himanshu Khandelia (Wed Jan 17 2007 - 05:49:13 CST)
How to change title of display window? Rob (Wed Jan 17 2007 - 01:13:23 CST)
- Re: How to change title of display window? John Stone (Wed Jan 17 2007 - 01:27:52 CST)
- Re: How to change title of display window? JT (Sun Jan 25 2009 - 20:09:35 CST)
  - Re: Re: How to change title of display window? Axel Kohlmeyer (Sun Jan 25 2009 - 21:08:18 CST)
VMD forks to background; can I disable this? Rob (Wed Jan 17 2007 - 00:33:27 CST)
- Re: VMD forks to background; can I disable this? John Stone (Wed Jan 17 2007 - 01:27:08 CST)
  - problem writing correct format psf file from vmd tk-console Himanshu Khandelia (Wed Jan 17 2007 - 05:43:06 CST)
    - Re: problem writing correct format psf file from vmd tk-console John Stone (Wed Jan 17 2007 - 12:26:48 CST)
MSMS on Windows Peter Hains (Tue Jan 16 2007 - 23:21:52 CST)
- Re: MSMS on Windows John Stone (Wed Jan 17 2007 - 01:35:38 CST)
loading molecules with increasing number of backbone atoms in VMD wurl (Tue Jan 16 2007 - 19:39:42 CST)
- Re: loading molecules with increasing number of backbone atoms in VMD John Stone (Wed Jan 17 2007 - 12:05:37 CST)
scripts in windows version wurl (Tue Jan 16 2007 - 19:31:40 CST)
- Re: scripts in windows version John Stone (Wed Jan 17 2007 - 12:01:20 CST)
  - Re: scripts in windows version Axel Kohlmeyer (Wed Jan 17 2007 - 14:47:48 CST)
    - Re: scripts in windows version John Stone (Wed Jan 17 2007 - 15:08:24 CST)
Free Webinar: Vendor Neutral Intro to Data Mining for Absolute Beginners, January 26, 2007 Lisa Solomon (Mon Jan 15 2007 - 22:55:13 CST)
script to load dcds from Replica Exchange simulations by Temperature Ana Celia Araujo Vila Verde (Mon Jan 15 2007 - 17:30:44 CST)
Windows/Cannot generate .dx file! Georgios Villias (Mon Jan 15 2007 - 10:12:43 CST)
- Re: Windows/Cannot generate .dx file! L. Michel Espinoza-Fonseca (Mon Jan 15 2007 - 11:24:43 CST)
  - Re: Windows/Cannot generate .dx file! John Stone (Wed Jan 17 2007 - 14:16:35 CST)
VMD scene information Eric Peterson (Wed Jan 10 2007 - 12:23:29 CST)
- Re: VMD scene information John Stone (Wed Jan 10 2007 - 12:55:53 CST)
  - Re: VMD scene information Eric Peterson (Wed Jan 10 2007 - 17:19:39 CST)
    - Re: VMD scene information John Stone (Wed Jan 10 2007 - 20:01:32 CST)
  - Re: VMD scene information John Stone (Thu Jan 11 2007 - 15:15:22 CST)
plot the box margins wurl (Wed Jan 10 2007 - 02:40:35 CST)
- Re: plot the box margins Olaf Lenz (Wed Jan 10 2007 - 03:11:40 CST)
changing frame Myunggi Yi (Tue Jan 09 2007 - 22:15:11 CST)
- RE: changing frame JC Gumbart (Tue Jan 09 2007 - 23:55:16 CST)
Re: Antw: Re: Unaligned access to ... John Stone (Tue Jan 09 2007 - 14:18:54 CST)
Why does lipid move out of water box Nitin Bhardwaj (Tue Jan 09 2007 - 11:29:24 CST)
- Re: Why does lipid move out of water box Axel Kohlmeyer (Tue Jan 09 2007 - 14:13:08 CST)
[Fwd: Re: create new topology file for new molecule] Peter Freddolino (Tue Jan 09 2007 - 11:11:04 CST)
- Re: [Fwd: Re: create new topology file for new molecule] _at_huji.ac.il (Wed Jan 10 2007 - 03:01:50 CST)
  - Re: [Fwd: Re: create new topology file for new molecule] Axel Kohlmeyer (Wed Jan 10 2007 - 08:39:17 CST)
  - Re: [Fwd: Re: create new topology file for new molecule] Peter Freddolino (Wed Jan 10 2007 - 08:51:29 CST)
create new topology file for new molecule _at_huji.ac.il (Tue Jan 09 2007 - 10:06:25 CST)
Grab tool: picking problems Martijn Kragtwijk (Tue Jan 09 2007 - 09:55:52 CST)
- Re: Grab tool: picking problems John Stone (Tue Jan 09 2007 - 14:25:54 CST)
question about setting variables in a loop Brian Kidd (Mon Jan 08 2007 - 22:01:12 CST)
- Re: question about setting variables in a loop Peter Freddolino (Tue Jan 09 2007 - 09:49:21 CST)
sasa by residue alexandra.marques_at_fc.up.pt (Mon Jan 08 2007 - 19:01:04 CST)
- Re: sasa by residue Peter Freddolino (Tue Jan 09 2007 - 10:02:00 CST)
  - Re: sasa by residue alexandra.marques_at_fc.up.pt (Thu Jan 11 2007 - 13:42:07 CST)
    - Re: sasa by residue Peter Freddolino (Thu Jan 11 2007 - 22:33:55 CST)
Anyone have catdcd-4.0 for BlueGene? Joshua D. Moore (Mon Jan 08 2007 - 15:34:09 CST)
- Re: Anyone have catdcd-4.0 for BlueGene? John Stone (Mon Jan 08 2007 - 15:41:10 CST)
- Re: Anyone have catdcd-4.0 for BlueGene? Axel Kohlmeyer (Mon Jan 08 2007 - 16:36:38 CST)
how to use 'lreplace' of 2D array? Myunggi Yi (Mon Jan 08 2007 - 11:58:26 CST)
Problem with a tcl script: probable memory overload Leonardo Sepulveda Durán (Mon Jan 08 2007 - 09:05:01 CST)
- Re: Problem with a tcl script: probable memory overload Marcos Sotomayor (Mon Jan 08 2007 - 09:53:34 CST)
  - Re: Problem with a tcl script: probable memory overload Leonardo Sepulveda Durán (Mon Jan 08 2007 - 10:22:25 CST)
Unaligned access to ... Christian Wohlschlager (Mon Jan 08 2007 - 02:57:56 CST)
- Re: Unaligned access to ... John Stone (Mon Jan 08 2007 - 11:09:42 CST)
- Re: Unaligned access to ... Axel Kohlmeyer (Mon Jan 08 2007 - 19:10:39 CST)
error message using gofr OMAR NABEEL ALY DEMERDASH (Fri Jan 05 2007 - 16:03:12 CST)
- Re: error message using gofr Axel Kohlmeyer (Fri Jan 05 2007 - 18:09:22 CST)
- Re: error message using gofr John Stone (Mon Jan 08 2007 - 11:29:56 CST)
  - Re: error message using gofr OMAR NABEEL ALY DEMERDASH (Mon Jan 08 2007 - 15:17:42 CST)
"Not all atoms have unique coordinates" Nitin Bhardwaj (Fri Jan 05 2007 - 12:31:18 CST)
Save coordinates from MD simulation Per Jr. Greisen (Thu Jan 04 2007 - 10:55:34 CST)
- Re: Save coordinates from MD simulation Axel Kohlmeyer (Thu Jan 04 2007 - 11:46:39 CST)
Removing water in tcl Cesar Luis Avila (Thu Jan 04 2007 - 10:23:15 CST)
- Re: Removing water in tcl nunolf_at_ci.uc.pt (Thu Jan 04 2007 - 11:03:59 CST)
  - Re: Removing water in tcl Cesar Luis Avila (Thu Jan 04 2007 - 16:13:49 CST)
    - Re: Removing water in tcl John Stone (Thu Jan 04 2007 - 16:38:59 CST)
    - Re: Removing water in tcl JC Gumbart (Fri Jan 05 2007 - 00:13:53 CST)
using namdenergy with amber prmtop file Nitin Bhardwaj (Wed Jan 03 2007 - 18:06:20 CST)
- Re: using namdenergy with amber prmtop file Peter Freddolino (Wed Jan 03 2007 - 20:09:29 CST)
  - Re: using namdenergy with amber prmtop file Nitin Bhardwaj (Thu Jan 04 2007 - 13:02:06 CST)
    - Re: using namdenergy with amber prmtop file Peter Freddolino (Thu Jan 04 2007 - 13:05:19 CST)
Re: Fwd: Writing pdb without chain identifier John Stone (Wed Jan 03 2007 - 10:31:05 CST)
Re: Vizualization Problem while opening DX file John Stone (Wed Jan 03 2007 - 10:03:25 CST)
Install and Configure Problems christopher (Wed Jan 03 2007 - 08:57:14 CST)
- Re: Install and Configure Problems Axel Kohlmeyer (Wed Jan 03 2007 - 09:43:38 CST)
Load last frame of dcd on TKconsole (how?) hori koshii (Sat Dec 30 2006 - 19:20:00 CST)
- Re: Load last frame of dcd on TKconsole (how?) Peter Freddolino (Sun Dec 31 2006 - 08:15:01 CST)
Re: PET force field & topolgy files wolfinbm_at_uci.edu (Wed Dec 27 2006 - 17:24:59 CST)
RE: (); [Fwd: PET force field & topolgy files etc.] wolfinbm_at_uci.edu (Wed Dec 27 2006 - 14:23:22 CST)
- Re: (); [Fwd: PET force field & topolgy files etc.] Peter Freddolino (Thu Dec 28 2006 - 15:46:31 CST)
Writing pdb without chain identifier Cesar Luis Avila (Tue Dec 26 2006 - 14:49:45 CST)
- Re: Writing pdb without chain identifier Marcos Sotomayor (Tue Dec 26 2006 - 15:03:23 CST)
  - Re: Writing pdb without chain identifier Cesar Luis Avila (Tue Dec 26 2006 - 17:16:51 CST)
recenter peptide in PBC _at_huji.ac.il (Tue Dec 26 2006 - 04:54:20 CST)
- Re: recenter peptide in PBC John Stone (Wed Jan 03 2007 - 10:38:43 CST)
box information amber crdbox Myunggi Yi (Fri Dec 22 2006 - 17:24:19 CST)
- Re: box information amber crdbox John Stone (Wed Jan 03 2007 - 10:23:46 CST)
  - Re: box information amber crdbox Myunggi Yi (Fri Jan 05 2007 - 10:44:42 CST)
vmd questions _at_huji.ac.il (Thu Dec 21 2006 - 05:09:59 CST)
- Re: vmd questions John Stone (Wed Jan 03 2007 - 13:05:34 CST)
Re: Trying to Build a Membrane w/conical pore out of PET (polyethylene terephthalate) wolfinbm_at_uci.edu (Fri Dec 22 2006 - 14:29:56 CST)
- Re: Trying to Build a Membrane w/conical pore out of PET (polyethylene terephthalate) Peter Freddolino (Sat Dec 23 2006 - 01:02:19 CST)
  - Re: Trying to Build a Membrane w/conical pore out of PET (polyethylene terephthalate) wolfinbm_at_uci.edu (Sun Dec 24 2006 - 13:07:28 CST)
- Re: Trying to Build a Membrane w/conical pore out of PET (polyethylene terephthalate) wolfinbm_at_uci.edu (Sun Dec 24 2006 - 14:35:08 CST)
  - Re: Trying to Build a Membrane w/conical pore out of PET (polyethylene terephthalate) Peter Freddolino (Mon Dec 25 2006 - 11:38:07 CST)
    - I have working PETE xbgf file, now how to combine into membrane? wolfinbm_at_uci.edu (Wed Dec 27 2006 - 11:34:11 CST)
    - Re: I have working PETE xbgf file, now how to combine into membrane? Peter Freddolino (Wed Dec 27 2006 - 13:21:27 CST)
Trying to Build a Membrane w/conical pore out of PET (polyethylene terephthalate) wolfinbm_at_uci.edu (Fri Dec 22 2006 - 12:48:36 CST)
- Re: Trying to Build a Membrane w/conical pore out of PET (polyethylene terephthalate) Peter Freddolino (Fri Dec 22 2006 - 13:19:24 CST)
  - Re: Trying to Build a Membrane w/conical pore out of PET (polyethylene terephthalate) wolfinbm_at_uci.edu (Fri Dec 22 2006 - 14:05:36 CST)
Voicemail from Pavan Ghatty (5 seconds) pavan.vmd_at_gmail.com (Thu Dec 21 2006 - 18:17:51 CST)
pdb file Rita Cassia (Thu Dec 21 2006 - 05:53:15 CST)
- Re: pdb file nunolf_at_ci.uc.pt (Thu Dec 21 2006 - 08:49:55 CST)
  - Re: pdb file nunolf_at_ci.uc.pt (Thu Dec 21 2006 - 14:22:10 CST)
VMD 1.8.5 installed. The graphics flashed and disappeared after installation. Margaret S. Cheung (Wed Dec 20 2006 - 12:00:11 CST)
- Re: VMD 1.8.5 installed. The graphics flashed and disappeared after installation. Peter Freddolino (Tue Dec 19 2006 - 13:30:20 CST)
  - Re: VMD 1.8.5 installed. The graphics flashed and disappeared after installation. Margaret S. Cheung (Thu Dec 21 2006 - 08:04:38 CST)
    - Re: VMD 1.8.5 installed. The graphics flashed and disappeared after installation. Peter Freddolino (Wed Dec 20 2006 - 10:08:49 CST)
- Re: VMD 1.8.5 installed. The graphics flashed and disappeared after installation. Axel Kohlmeyer (Tue Dec 19 2006 - 14:15:00 CST)
  - Re: VMD 1.8.5 installed. The graphics flashed and disappeared after installation. Margaret S. Cheung (Fri Dec 22 2006 - 12:15:25 CST)
    - Re: VMD 1.8.5 installed. The graphics flashed and disappeared after installation. Margaret S. Cheung (Sat Dec 23 2006 - 11:00:18 CST)
average z-coordinate of a selection Nitin Bhardwaj (Tue Dec 19 2006 - 10:54:29 CST)
- Re: average z-coordinate of a selection Nitin Bhardwaj (Tue Dec 19 2006 - 11:08:42 CST)
VMD using CygWin? Christer Svanberg (Tue Dec 19 2006 - 07:29:15 CST)
- Re: VMD using CygWin? Jerome Henin (Tue Dec 19 2006 - 12:05:02 CST)
- Re: VMD using CygWin? Justin Gullingsrud (Wed Dec 20 2006 - 08:42:13 CST)
Stride Neelanjana Sengupta (Mon Dec 18 2006 - 23:14:22 CST)
- Re: Stride John Stone (Tue Dec 19 2006 - 01:00:24 CST)
- Re: Stride Karsten SUHRE (Tue Dec 19 2006 - 02:05:13 CST)
md simulation of a protein and a ligand Robert Kretschmer (Mon Dec 18 2006 - 12:55:20 CST)
CAVE Sensor Question Christian Wohlschlager (Mon Dec 18 2006 - 01:28:53 CST)
- Re: CAVE Sensor Question John Stone (Tue Dec 19 2006 - 01:10:20 CST)
VMD email support next two weeks John Stone (Sun Dec 17 2006 - 21:19:42 CST)
- Re: VMD email support next two weeks Christoph Weber (Mon Dec 18 2006 - 18:10:13 CST)
  - Re: VMD email support next two weeks Olaf Lenz (Tue Dec 19 2006 - 01:04:21 CST)
    - Re: VMD email support next two weeks John Stone (Tue Dec 19 2006 - 01:17:02 CST)
How to let vmd do secondary structure judgement for each frame and render it on play movie? Guo Zhi (Fri Dec 15 2006 - 22:47:23 CST)
- Re: How to let vmd do secondary structure judgement for each frame and render it on play movie? John Stone (Fri Dec 15 2006 - 23:44:27 CST)
  - Re: How to let vmd do secondary structure judgement for each frame and render it on play movie? Guo Zhi (Sat Dec 16 2006 - 00:31:00 CST)
    - Re: How to let vmd do secondary structure judgement for each frame and render it on play movie? John Stone (Sat Dec 16 2006 - 02:30:04 CST)
    - Re: How to let vmd do secondary structure judgement for each frame and render it on play movie? Guo Zhi (Sat Dec 16 2006 - 02:59:41 CST)
Re: "cartoon" failing to show secondary structure--more info Kenley Barrett (Fri Dec 15 2006 - 12:39:54 CST)
- Re: "cartoon" failing to show secondary structure--more info John Stone (Fri Dec 15 2006 - 14:08:59 CST)
moveby command in vmd Nuno Ricardo Loureiro Ferreira (Fri Dec 15 2006 - 10:42:36 CST)
moveby command in vmd Mohamed Osman (Fri Dec 15 2006 - 09:36:43 CST)
- Re: moveby command in vmd John Stone (Fri Dec 15 2006 - 10:35:57 CST)
  - Re: moveby command in vmd Mohamed Osman (Fri Dec 15 2006 - 12:05:43 CST)
"cartoon" failing to show secondary structure Kenley Barrett (Thu Dec 14 2006 - 18:31:09 CST)
- Re: "cartoon" failing to show secondary structure John Stone (Fri Dec 15 2006 - 11:13:05 CST)
  - Re: "cartoon" failing to show secondary structure Kenley Barrett (Fri Dec 15 2006 - 11:27:30 CST)
vmd-xplor installation Lei Shi (Thu Dec 14 2006 - 18:16:38 CST)
- Re: vmd-xplor installation Charles_at_Schwieters.org (Thu Dec 14 2006 - 18:56:28 CST)
electrostatic potential ivana adamovic (Wed Dec 13 2006 - 14:15:09 CST)
- Re: electrostatic potential Axel Kohlmeyer (Wed Dec 13 2006 - 15:11:27 CST)
- Re: electrostatic potential John Stone (Wed Dec 13 2006 - 15:56:25 CST)
How to make movie with .crd files? bertrand russell (Wed Dec 13 2006 - 02:36:23 CST)
- Re: How to make movie with .crd files? Nuno Ricardo Loureiro Ferreira (Wed Dec 13 2006 - 03:31:54 CST)
  - Re: How to make movie with .crd files? Nuno Ricardo Loureiro Ferreira (Fri Dec 15 2006 - 03:51:01 CST)
Diffusion constant Myunggi Yi (Tue Dec 12 2006 - 17:26:22 CST)
- Re: Diffusion constant Myunggi Yi (Tue Dec 12 2006 - 19:12:35 CST)
  - Re: Diffusion constant Myunggi Yi (Tue Dec 12 2006 - 19:22:23 CST)
Correlation Functions Juan Diaz (Tue Dec 12 2006 - 14:39:52 CST)
- Re: Correlation Functions Neelanjana Sengupta (Tue Dec 12 2006 - 14:39:13 CST)
Correlation Functions Juan Diaz (Tue Dec 12 2006 - 13:29:49 CST)
Question about RMSD calculator Kara Di Giorgio (Tue Dec 12 2006 - 13:16:32 CST)
- Re: Question about RMSD calculator John Stone (Tue Dec 12 2006 - 13:50:47 CST)
- Re: Question about RMSD calculator Dan Wright (Tue Dec 12 2006 - 16:20:58 CST)
Calculating changes Per Jr. Greisen (Tue Dec 12 2006 - 12:56:37 CST)
- Re: Calculating changes Peter Freddolino (Tue Dec 12 2006 - 14:07:18 CST)
Thank you for you answere the folowing is the .vmdsensor file Christian Wohlschlager (Tue Dec 12 2006 - 06:06:52 CST)
CAVE Question Christian Wohlschlager (Mon Dec 11 2006 - 00:28:12 CST)
- Re: CAVE Question John Stone (Mon Dec 11 2006 - 10:21:12 CST)
Details of .psf format Paul T. Bauman (Fri Dec 08 2006 - 14:52:09 CST)
- Re: Details of .psf format Marcos Sotomayor (Fri Dec 08 2006 - 14:56:45 CST)
  - Re: Details of .psf format Peter Freddolino (Fri Dec 08 2006 - 15:19:26 CST)
    - Re: Details of .psf format Paul T. Bauman (Fri Dec 08 2006 - 15:24:48 CST)
Best fit plane axis Myunggi Yi (Fri Dec 08 2006 - 12:23:58 CST)
- Re: Best fit plane axis Amarda Shehu (Fri Dec 08 2006 - 14:21:19 CST)
  - RE: Best fit plane axis Jayendra Balasubramanian (Fri Dec 08 2006 - 14:52:31 CST)
Unable to compile plugins on MACOSXX86 Olaf Lenz (Fri Dec 08 2006 - 07:27:11 CST)
- Problem solved (was: Re: Unable to compile plugins on MACOSXX86) Olaf Lenz (Fri Dec 08 2006 - 10:56:44 CST)
Diffusion coefficient Nicolas Floquet (Fri Dec 08 2006 - 04:24:27 CST)
diffusion coefficient Nicolas Floquet (Fri Dec 08 2006 - 04:21:48 CST)
- Re: diffusion coefficient Ivan Degtyarenko (Fri Dec 08 2006 - 05:44:58 CST)
problem/bug? calling hbonds within a loop over the residues (tcl) Nels Thorsteinson (Thu Dec 07 2006 - 17:31:01 CST)
- Re: problem/bug? calling hbonds within a loop over the residues (tcl) Jerome Henin (Fri Dec 08 2006 - 10:08:32 CST)
drawing helices from partial aminoacids Streutker, J (Thu Dec 07 2006 - 04:40:24 CST)
- Re: drawing helices from partial aminoacids John Stone (Thu Dec 07 2006 - 11:04:39 CST)
Getting coordinates Myunggi Yi (Tue Dec 05 2006 - 15:47:20 CST)
- Re: Getting coordinates Axel Kohlmeyer (Tue Dec 05 2006 - 16:37:00 CST)
generating psf file for a lipid: vmd looking for c-term and n-term ? Mohamed Osman (Tue Dec 05 2006 - 15:45:45 CST)
- Re: generating psf file for a lipid: vmd looking for c-term and n-term ? Peter Freddolino (Tue Dec 05 2006 - 15:57:09 CST)
polyethylene topology Arturas Ziemys (Tue Dec 05 2006 - 12:05:57 CST)
[Fwd: Re: Installing VMD 1.8.5 pon ubuntu linux] Ran Friedman (Mon Dec 04 2006 - 12:58:06 CST)
duration of video mpeg Andres Palencia (Sat Dec 02 2006 - 11:39:04 CST)
- Re: duration of video mpeg Axel Kohlmeyer (Sun Dec 03 2006 - 09:39:28 CST)
  - Re: duration of video mpeg Andres Palencia (Sun Dec 03 2006 - 13:07:28 CST)
Installing VMD 1.8.5 pon ubuntu linux Ran Friedman (Fri Dec 01 2006 - 07:04:02 CST)
- Re: Installing VMD 1.8.5 pon ubuntu linux John Stone (Fri Dec 01 2006 - 10:41:00 CST)
  - Re: Installing VMD 1.8.5 pon ubuntu linux Ran Friedman (Mon Dec 04 2006 - 03:24:43 CST)
    - Re: Installing VMD 1.8.5 pon ubuntu linux John Stone (Mon Dec 04 2006 - 15:33:19 CST)
    - Re: Installing VMD 1.8.5 pon ubuntu linux Ran Friedman (Tue Dec 05 2006 - 09:32:07 CST)
problem with near clip hkhandel_at_memphys.sdu.dk (Fri Dec 01 2006 - 09:26:29 CST)
- Re: problem with near clip John Stone (Fri Dec 01 2006 - 10:49:26 CST)
problems with large structures hkhandel_at_memphys.sdu.dk (Fri Dec 01 2006 - 09:24:57 CST)
- Re: problems with large structures John Stone (Fri Dec 01 2006 - 10:30:29 CST)
R/S asymmetric carbon FyD (Fri Dec 01 2006 - 04:02:39 CST)
draw hydrophobic contact gcmc jie (Thu Nov 30 2006 - 13:41:10 CST)
- Re: draw hydrophobic contact Nuno Ricardo Loureiro Ferreira (Thu Nov 30 2006 - 15:11:28 CST)
  - Re: draw hydrophobic contact Nuno Ricardo Loureiro Ferreira (Sat Dec 02 2006 - 03:18:05 CST)
Poor man's stereolithography Morizono, Hiroki (Thu Nov 30 2006 - 09:07:51 CST)
- Re: Poor man's stereolithography John Stone (Thu Nov 30 2006 - 10:42:08 CST)
- RE: Poor man's stereolithography Samuel C Flores (Thu Nov 30 2006 - 12:37:04 CST)
coloring residues with VMD christopher (Wed Nov 29 2006 - 14:41:37 CST)
- Re: coloring residues with VMD John Stone (Wed Nov 29 2006 - 14:55:07 CST)
ZN2 vs MG? Samuel C Flores (Wed Nov 29 2006 - 12:27:50 CST)
- Re: ZN2 vs MG? John Stone (Wed Nov 29 2006 - 14:14:33 CST)
Help for the CAVE Christian Wohlschlager (Wed Nov 29 2006 - 08:19:11 CST)
radius of the curvature ivana adamovic (Tue Nov 28 2006 - 14:33:01 CST)
- Re: radius of the curvature Axel Kohlmeyer (Tue Nov 28 2006 - 16:08:29 CST)
  - RE: radius of the curvature Samuel C Flores (Wed Nov 29 2006 - 12:16:50 CST)
    - RE: radius of the curvature Axel Kohlmeyer (Wed Nov 29 2006 - 12:31:59 CST)
High res stl files Frederick Sachs (Tue Nov 28 2006 - 13:47:11 CST)
- Re: High res stl files John Stone (Tue Nov 28 2006 - 14:09:03 CST)
Read dcd file error using vmd1.8.5 for windows Shaojie Ma (Mon Nov 27 2006 - 21:49:46 CST)
- Re: Read dcd file error using vmd1.8.5 for windows John Stone (Mon Nov 27 2006 - 22:21:59 CST)
  - Re: Read dcd file error using vmd1.8.5 for windows Shaojie Ma (Tue Nov 28 2006 - 00:41:53 CST)
    - Re: Read dcd file error using vmd1.8.5 for windows John Stone (Wed Nov 29 2006 - 15:04:27 CST)
CAve Question Christian Wohlschlager (Mon Nov 27 2006 - 02:39:04 CST)
- Re: CAve Question John Stone (Mon Nov 27 2006 - 14:50:57 CST)
  - Re: CAve Question Axel Kohlmeyer (Mon Nov 27 2006 - 18:47:22 CST)
  - Antw: Re: CAve Question Christian Wohlschlager (Tue Nov 28 2006 - 08:16:48 CST)
Shutter glasses on VMD Cesar Avila (Sat Nov 25 2006 - 12:14:00 CST)
- Re: Shutter glasses on VMD Robert Kretschmer (Sat Nov 25 2006 - 15:07:10 CST)
  - Re: Shutter glasses on VMD Cesar Avila (Sun Nov 26 2006 - 16:28:10 CST)
    - Re: Shutter glasses on VMD Robert Kretschmer (Tue Nov 28 2006 - 01:51:31 CST)
    - Re: Shutter glasses on VMD John Stone (Wed Nov 29 2006 - 15:19:25 CST)
Atomselect in loops Alexandre A. Vakhrouchev (Fri Nov 24 2006 - 03:50:34 CST)
- Re: Atomselect in loops Lubos Vrbka (Fri Nov 24 2006 - 07:46:14 CST)
VMD 1.8.3 works ok for 64-bit windows, but not VMD 1.8.5 Adrian Koh (Thu Nov 23 2006 - 22:07:27 CST)
- Re: VMD 1.8.3 works ok for 64-bit windows, but not VMD 1.8.5 Adrian Koh (Thu Nov 23 2006 - 23:31:49 CST)
- Re: VMD 1.8.3 works ok for 64-bit windows, but not VMD 1.8.5 John Stone (Fri Nov 24 2006 - 00:56:36 CST)
movie making ivana adamovic (Thu Nov 23 2006 - 14:22:10 CST)
- Re: movie making Axel Kohlmeyer (Thu Nov 23 2006 - 15:36:32 CST)
Installing VMD Windows version on 64-bit Windows Environment Adrian Koh (Tue Nov 21 2006 - 21:30:01 CST)
- Re: Installing VMD Windows version on 64-bit Windows Environment Axel Kohlmeyer (Wed Nov 22 2006 - 09:19:03 CST)
- Re: Installing VMD Windows version on 64-bit Windows Environment Peter Freddolino (Wed Nov 22 2006 - 10:52:07 CST)
- Re: Installing VMD Windows version on 64-bit Windows Environment John Stone (Wed Nov 22 2006 - 11:50:36 CST)
- Re: Installing VMD Windows version on 64-bit Windows Environment John Stone (Thu Dec 14 2006 - 14:41:09 CST)
vector summation Myunggi Yi (Tue Nov 21 2006 - 16:38:54 CST)
- Re: vector summation Axel Kohlmeyer (Wed Nov 22 2006 - 09:13:45 CST)
combine.tcl annalisa_at_biotec.tu-dresden.de (Tue Nov 21 2006 - 15:06:50 CST)
- Re: combine.tcl John Stone (Wed Nov 22 2006 - 12:12:14 CST)
Running a script using text mode Myunggi Yi (Tue Nov 21 2006 - 09:47:43 CST)
- Re: Running a script using text mode John Stone (Tue Nov 21 2006 - 10:31:11 CST)
Writing a trajectory - with box information Jennie Thomas (Mon Nov 20 2006 - 22:09:12 CST)
- Re: Writing a trajectory - with box information John Stone (Mon Nov 20 2006 - 22:46:26 CST)
  - Re: Writing a trajectory - with box information John Stone (Tue Nov 21 2006 - 11:21:20 CST)
trajectory from separate frames Narender Singh Maan (Mon Nov 20 2006 - 17:14:22 CST)
- Re: trajectory from separate frames John Stone (Mon Nov 20 2006 - 20:57:38 CST)
VMD 1.8.6 test versions available, feedback requested... John Stone (Mon Nov 20 2006 - 15:26:33 CST)
Problem rendering NewCartoon Sathyapriya R (Fri Nov 17 2006 - 12:03:52 CST)
- Re:Problem rendering NewCartoon nunolf_at_ci.uc.pt (Fri Nov 17 2006 - 12:43:03 CST)
  - Re: Re:Problem rendering NewCartoon John Stone (Fri Nov 17 2006 - 13:37:26 CST)
- Re: Problem rendering NewCartoon John Stone (Fri Nov 17 2006 - 12:50:31 CST)
  - movie for Openoffice Nguyen Hoang Phuong (Fri Nov 17 2006 - 15:40:34 CST)
    - Re: movie for Openoffice John Stone (Fri Nov 17 2006 - 15:55:00 CST)
    - Re: movie for Openoffice Jeffrey A Tibbitt (Fri Nov 17 2006 - 18:36:30 CST)
changing the representation of a vector L. Michel Espinoza-Fonseca (Fri Nov 17 2006 - 10:09:55 CST)
- Re: changing the representation of a vector Peter Freddolino (Fri Nov 17 2006 - 10:36:11 CST)
- Re: changing the representation of a vector Axel Kohlmeyer (Fri Nov 17 2006 - 11:02:42 CST)
Change properties of representations - batch mode nunolf_at_ci.uc.pt (Fri Nov 17 2006 - 09:48:18 CST)
- Re: Change properties of representations - batch mode Peter Freddolino (Fri Nov 17 2006 - 10:38:07 CST)
- Re: Change properties of representations - batch mode Axel Kohlmeyer (Fri Nov 17 2006 - 10:47:02 CST)
  - Re: Change properties of representations - batch mode John Stone (Fri Nov 17 2006 - 11:13:05 CST)
VMD 'guesses' no. of frames? Neelanjana Sengupta (Thu Nov 16 2006 - 21:15:38 CST)
- Re: VMD 'guesses' no. of frames? John Stone (Thu Nov 16 2006 - 21:27:53 CST)
  - Re: VMD 'guesses' no. of frames? Neelanjana Sengupta (Thu Nov 16 2006 - 21:44:14 CST)
how to extract atom information? Myunggi Yi (Thu Nov 16 2006 - 19:07:49 CST)
- Re: how to extract atom information? Axel Kohlmeyer (Thu Nov 16 2006 - 20:08:01 CST)
- Re: how to extract atom information? Neelanjana Sengupta (Thu Nov 16 2006 - 20:44:11 CST)
  - Re: how to extract atom information? Axel Kohlmeyer (Thu Nov 16 2006 - 21:32:41 CST)
Color surfaces by electrostatic potential Mihaly Mezei (Thu Nov 16 2006 - 17:06:06 CST)
- Re: Color surfaces by electrostatic potential John Stone (Thu Nov 16 2006 - 17:18:24 CST)
VMD 1.8.5 plugin update 1 posted... John Stone (Wed Nov 15 2006 - 17:12:58 CST)
Paratool problem daniel aguayo (Wed Nov 15 2006 - 13:29:58 CST)
- Re: Paratool problem John Stone (Wed Nov 15 2006 - 15:54:55 CST)
PSF files append!! CSM USP (Wed Nov 15 2006 - 13:06:06 CST)
- Re: PSF files append!! John Stone (Fri Nov 17 2006 - 16:33:52 CST)
Sequences and BLAST searching Baxy (Wed Nov 15 2006 - 06:51:22 CST)
Sequences and BLAST searching Baxy (Wed Nov 15 2006 - 06:47:08 CST)
- Re: Sequences and BLAST searching Elijah Roberts (Wed Nov 15 2006 - 12:05:57 CST)
Elastic Properties Jennifer A Carvajal (Tue Nov 14 2006 - 14:51:13 CST)
- Re: Elastic Properties John Stone (Wed Nov 15 2006 - 18:07:44 CST)
Beginner's problem John Young (Tue Nov 14 2006 - 11:20:01 CST)
- Re: Beginner's problem Alexandr Isayev (Tue Nov 14 2006 - 12:01:36 CST)
giant spike in rmsd curve Nels Thorsteinson (Mon Nov 13 2006 - 13:36:14 CST)
- Re: giant spike in rmsd curve Peter Freddolino (Mon Nov 13 2006 - 15:37:46 CST)
Normal mode analysis in VMD Vani Krishna (Sun Nov 12 2006 - 22:00:20 CST)
python alexandra.marques_at_fc.up.pt (Sun Nov 12 2006 - 11:23:39 CST)
- Re: python John Stone (Mon Nov 13 2006 - 10:35:02 CST)
Plotting Number of Hbonds and % Helicity with Time Adelene Sim (Sat Nov 11 2006 - 18:11:22 CST)
- Re: Plotting Number of Hbonds and % Helicity with Time Axel Kohlmeyer (Sat Nov 11 2006 - 18:57:25 CST)
Command line troubles Pavan Ghatty (Sat Nov 11 2006 - 16:11:46 CST)
- Re: Command line troubles Axel Kohlmeyer (Sat Nov 11 2006 - 17:48:00 CST)
VMD installation problem Andres Palencia (Fri Nov 10 2006 - 10:38:41 CST)
- Re: VMD installation problem Axel Kohlmeyer (Fri Nov 10 2006 - 11:19:24 CST)
Is there a way to validate a structure Javaria Ahmed (Thu Nov 09 2006 - 07:41:10 CST)
VMD 1.8.5 startup Chang, Christopher (Wed Nov 08 2006 - 14:56:37 CST)
- Re: VMD 1.8.5 startup Jacob Poehlsgaard (Thu Nov 09 2006 - 02:04:51 CST)
  - Re: VMD 1.8.5 startup dan wright (Thu Nov 09 2006 - 07:47:03 CST)
    - RE: VMD 1.8.5 startup Chang, Christopher (Thu Nov 09 2006 - 14:20:16 CST)
FEP Energy very high: Mutual exclusion of atoms Nitin Bhardwaj (Tue Nov 07 2006 - 17:29:49 CST)
Dynamic selection of residues on a trajectory amit_at_mbu.iisc.ernet.in (Tue Nov 07 2006 - 11:07:13 CST)
Dynamic selection of residues on a trajectory amit_at_mbu.iisc.ernet.in (Tue Nov 07 2006 - 10:45:19 CST)
gamess plungin for PC Gamess mashaojie163 (Tue Nov 07 2006 - 01:00:58 CST)
- Re: gamess plungin for PC Gamess John Stone (Tue Nov 07 2006 - 15:34:33 CST)
VMD - unable to create OpenGL bertrand russell (Tue Nov 07 2006 - 03:31:29 CST)
- Re: VMD - unable to create OpenGL Axel Kohlmeyer (Tue Nov 07 2006 - 08:37:37 CST)
How to delete selected atoms from a molecule Javaria Ahmed (Mon Nov 06 2006 - 07:22:54 CST)
- Re: How to delete selected atoms from a molecule Axel Kohlmeyer (Mon Nov 06 2006 - 09:30:58 CST)
Connecting a phantom with NAMD and VMD preeda (Mon Nov 06 2006 - 00:39:36 CST)
- Re: Connecting a phantom with NAMD and VMD John Stone (Tue Nov 07 2006 - 16:40:45 CST)
Bigdcd - get coordinates from file Per Jr. Greisen (Sun Nov 05 2006 - 05:56:34 CST)
- Re: Bigdcd - get coordinates from file Peter Freddolino (Sun Nov 05 2006 - 07:47:42 CST)
How to align two peptide molecules Sunita Patel (Fri Nov 03 2006 - 10:14:20 CST)
- Re: How to align two peptide molecules Leonardo Trabuco (Fri Nov 03 2006 - 14:17:55 CST)
.pdb file from XMD 04215287d_at_polyu.edu.hk (Thu Nov 02 2006 - 08:39:44 CST)
- Re: .pdb file from XMD Alexandr Isayev (Thu Nov 02 2006 - 09:18:20 CST)
  - Re: .pdb file from XMD John Stone (Thu Nov 02 2006 - 10:45:49 CST)
IED individual eigenvectors/movie nadiav_at_soton.ac.uk (Thu Nov 02 2006 - 05:04:05 CST)
- Re: IED individual eigenvectors/movie Vlad Cojocaru (Thu Nov 02 2006 - 05:40:08 CST)
  - Re: IED individual eigenvectors/movie John Stone (Thu Nov 02 2006 - 11:27:52 CST)
Re: problem for saving as jpg file Esther Brugger (Wed Nov 01 2006 - 10:51:27 CST)
problem for saving as jpg file Esther Brugger (Wed Nov 01 2006 - 09:51:17 CST)
installation problem Esther Brugger (Tue Oct 31 2006 - 17:59:07 CST)
- Re: installation problem Axel Kohlmeyer (Tue Oct 31 2006 - 18:32:13 CST)
- Re: installation problem John Stone (Tue Oct 31 2006 - 19:49:04 CST)
  - Re: installation problem Esther Brugger (Wed Nov 01 2006 - 08:59:39 CST)
VMD 1.8.4 support for AMBER binary trajectory files Kenley Barrett (Tue Oct 31 2006 - 17:47:05 CST)
- Re: VMD 1.8.4 support for AMBER binary trajectory files John Stone (Tue Oct 31 2006 - 19:52:15 CST)
Selection of residues in a trajectory amit_at_mbu.iisc.ernet.in (Tue Oct 31 2006 - 13:50:23 CST)
VMD - ATI video card nunolf_at_ci.uc.pt (Tue Oct 31 2006 - 13:01:24 CST)
- Re: VMD - ATI video card Axel Kohlmeyer (Tue Oct 31 2006 - 13:47:10 CST)
Displaying biological unit revisited Adrian Kaats (Tue Oct 31 2006 - 12:22:19 CST)
- Re: Displaying biological unit revisited John Stone (Wed Nov 01 2006 - 16:32:29 CST)
  - Re: Displaying biological unit revisited Adrian Kaats (Thu Nov 02 2006 - 14:23:41 CST)
    - Re: Displaying biological unit revisited John Stone (Tue Nov 07 2006 - 17:08:12 CST)
autopsf errors in vmd1.8.5 Brian Bennion (Mon Oct 30 2006 - 12:09:54 CST)
- Re: autopsf errors in vmd1.8.5 Peter Freddolino (Mon Oct 30 2006 - 12:18:43 CST)
Reading box info. from PQR file Bob Johnson (Mon Oct 30 2006 - 10:02:43 CST)
- Re: Reading box info. from PQR file Axel Kohlmeyer (Mon Oct 30 2006 - 10:54:13 CST)
  - Re: Reading box info. from PQR file John Stone (Tue Nov 07 2006 - 17:05:14 CST)
coloring HIE, HIP, HID: sorry ... I got it Vlad Cojocaru (Mon Oct 30 2006 - 07:12:12 CST)
changing default colors for resname HIE HID HIP Vlad Cojocaru (Mon Oct 30 2006 - 06:45:42 CST)
VMD - ATI video card nunolf_at_ci.uc.pt (Fri Oct 27 2006 - 12:32:36 CDT)
- Re: VMD - ATI video card John Stone (Fri Oct 27 2006 - 12:44:14 CDT)
xterm problem?? Patrycja (Fri Oct 27 2006 - 09:31:11 CDT)
- Re: xterm problem?? John Stone (Fri Oct 27 2006 - 11:39:50 CDT)
- Re: xterm problem?? Jerome Henin (Fri Oct 27 2006 - 13:56:32 CDT)
VMD trajectory/structure/coordinate format Olaf Lenz (Thu Oct 26 2006 - 07:28:52 CDT)
VMD not working with a Matrox Graphic Card nunolf_at_ci.uc.pt (Thu Oct 26 2006 - 11:09:03 CDT)
- Re: VMD not working with a Matrox Graphic Card John Stone (Thu Oct 26 2006 - 11:22:24 CDT)
Re: how to select the problematic residues(atoms) Jacob Poehlsgaard (Thu Oct 26 2006 - 07:00:55 CDT)
how to select the problematic residues(atoms) Rachel (Thu Oct 26 2006 - 05:53:14 CDT)
Re: How to get the coordinates of periodic image! John Stone (Wed Oct 25 2006 - 13:55:20 CDT)
- Re: Re: How to get the coordinates of periodic image! Neelanjana Sengupta (Wed Oct 25 2006 - 19:33:52 CDT)
problem about "mol load psf md.pdf pdb md.pdb" Qiao Baofu (Wed Oct 25 2006 - 04:31:31 CDT)
- Re: problem about "mol load psf md.pdf pdb md.pdb" Axel Kohlmeyer (Wed Oct 25 2006 - 06:19:41 CDT)
- Re: problem about "mol load psf md.pdf pdb md.pdb" John Stone (Fri Oct 27 2006 - 13:21:31 CDT)
external force Al-Rawi, Ahlam (Tue Oct 24 2006 - 11:41:54 CDT)
- Re: external force John Stone (Tue Oct 24 2006 - 13:11:11 CDT)
EIGENVECTOR ANALYSIS Tim Meyer (Tue Oct 24 2006 - 08:25:47 CDT)
- Re: EIGENVECTOR ANALYSIS John Stone (Wed Oct 25 2006 - 12:40:57 CDT)
Error installing VMD 1.8.5. Lechuga, Javier (Mon Oct 23 2006 - 02:29:06 CDT)
- Re: Error installing VMD 1.8.5. John Stone (Mon Oct 23 2006 - 12:13:35 CDT)
.psf for porphyrin javier.vallejos_at_correo.usach.cl (Sat Oct 21 2006 - 18:11:19 CDT)
Starting VMD at Command Line in OSX Jeffrey A Tibbitt (Sat Oct 21 2006 - 13:07:20 CDT)
- Re: Starting VMD at Command Line in OSX Christian Fufezan (Sat Oct 28 2006 - 13:38:10 CDT)
adding selections Myunggi Yi (Fri Oct 20 2006 - 13:04:21 CDT)
- Re: adding selections Axel Kohlmeyer (Fri Oct 20 2006 - 14:03:56 CDT)
Nvidia graphics card with VMD Berit Hinnemann (Fri Oct 20 2006 - 07:13:42 CDT)
CPK Graphical Representation Jawahar Neelankatan (Fri Oct 20 2006 - 05:57:20 CDT)
- Re: CPK Graphical Representation Axel Kohlmeyer (Fri Oct 20 2006 - 10:40:46 CDT)
  - Re: CPK Graphical Representation Axel Kohlmeyer (Fri Oct 20 2006 - 11:48:23 CDT)
    - Re: CPK Graphical Representation Jawahar Neelankatan (Fri Oct 20 2006 - 19:05:49 CDT)
- Re: CPK Graphical Representation Alexandr Isayev (Fri Oct 20 2006 - 11:48:40 CDT)
How to use vector calculation ??? Myunggi Yi (Thu Oct 19 2006 - 22:30:48 CDT)
- Re: How to use vector calculation ??? Axel Kohlmeyer (Fri Oct 20 2006 - 10:45:11 CDT)
retrieving the center of mass for each frame of trajectory Vlad Cojocaru (Wed Oct 18 2006 - 12:35:14 CDT)
- Re: retrieving the center of mass for each frame of trajectory John Stone (Wed Oct 18 2006 - 12:58:30 CDT)
update of atom selection at each step for trajectories Tim Meyer (Wed Oct 18 2006 - 11:21:36 CDT)
- Re: update of atom selection at each step for trajectories Axel Kohlmeyer (Wed Oct 18 2006 - 12:09:04 CDT)
measure fit sufficient for alignment prior to RMSD? Paul R Brenner (Wed Oct 18 2006 - 10:08:49 CDT)
electrostatic map render problem Matthieu.Chavent_at_edam.uhp-nancy.fr (Wed Oct 18 2006 - 09:36:14 CDT)
- Re: electrostatic map render problem Axel Kohlmeyer (Wed Oct 18 2006 - 11:56:21 CDT)
Using VMDPLUGIN_register_tcl Miller, Patrick (Wed Oct 18 2006 - 09:24:21 CDT)
- Re: Using VMDPLUGIN_register_tcl Axel Kohlmeyer (Wed Oct 18 2006 - 11:52:36 CDT)
- Re: Using VMDPLUGIN_register_tcl Axel Kohlmeyer (Wed Oct 18 2006 - 11:49:55 CDT)
- Re: Using VMDPLUGIN_register_tcl John Stone (Wed Oct 18 2006 - 13:14:01 CDT)
differentiating solvent molecules...... bertrand russell (Tue Oct 17 2006 - 12:44:28 CDT)
- Re: differentiating solvent molecules...... John Stone (Tue Oct 17 2006 - 12:57:41 CDT)
- Re: differentiating solvent molecules...... JC Gumbart (Tue Oct 17 2006 - 12:59:21 CDT)
RPM spec file Andrew Gormanly (Tue Oct 17 2006 - 08:03:45 CDT)
- Re: RPM spec file Axel Kohlmeyer (Tue Oct 17 2006 - 11:04:37 CDT)
Free Linux Cluster-Building Workshop - 30 Nov 2006 - 01 Dec 2006 Tim Skirvin (Mon Oct 16 2006 - 12:34:13 CDT)
VMD 1.8.5 on Mac OSX Panther Neelanjana Sengupta (Mon Oct 16 2006 - 08:32:06 CDT)
Volumetric data: Periodic expansion does not work; why? Rob (Thu Oct 12 2006 - 23:24:26 CDT)
- Re: Volumetric data: Periodic expansion does not work; why? Axel Kohlmeyer (Fri Oct 13 2006 - 11:15:36 CDT)
- Re: Volumetric data: Periodic expansion does not work; why? John Stone (Fri Oct 13 2006 - 13:55:15 CDT)
- Re: Volumetric data: Periodic expansion does not work; why? Rob (Tue Oct 17 2006 - 02:17:26 CDT)
  - Re: Re: Volumetric data: Periodic expansion does not work; why? Axel Kohlmeyer (Tue Oct 17 2006 - 11:08:49 CDT)
- Re: Volumetric data: Periodic expansion does not work; why? Rob (Tue Oct 17 2006 - 21:02:42 CDT)
Test build of CHARMM PBEQ electrostatics map reader plugin John Stone (Thu Oct 12 2006 - 16:10:49 CDT)
IED Ran Friedman (Thu Oct 12 2006 - 08:23:42 CDT)
- Re: IED John Stone (Thu Oct 12 2006 - 15:28:12 CDT)
Python on Intel Mac? Michael Lerner (Thu Oct 12 2006 - 13:25:01 CDT)
- Re: Python on Intel Mac? John Stone (Thu Oct 12 2006 - 15:37:31 CDT)
  - Re: Python on Intel Mac? Michael Lerner (Thu Oct 12 2006 - 17:15:53 CDT)
    - Re: Python on Intel Mac? John Stone (Fri Oct 13 2006 - 14:12:10 CDT)
movie Pijush Ghosh (Wed Oct 11 2006 - 17:36:40 CDT)
- Re: movie John Stone (Wed Oct 11 2006 - 18:25:14 CDT)
- Re: movie Alexandr Isayev (Wed Oct 11 2006 - 18:46:16 CDT)
  - RE: movie Pijush Ghosh (Wed Oct 11 2006 - 19:38:21 CDT)
gofr Arturas Ziemys (Wed Oct 11 2006 - 13:22:54 CDT)
- Re: gofr Axel Kohlmeyer (Wed Oct 11 2006 - 14:46:15 CDT)
HBonds Representation Dallas B. Warren (Tue Oct 10 2006 - 23:04:35 CDT)
- Re: HBonds Representation John Stone (Fri Oct 13 2006 - 15:00:33 CDT)
  - deleting at vmd console Dallas B. Warren (Thu Feb 15 2007 - 22:23:01 CST)
    - Re: deleting at vmd console John Stone (Thu Feb 15 2007 - 22:39:08 CST)
Missing main menu Stefan Gerlach (Mon Oct 09 2006 - 13:12:52 CDT)
- Re: Missing main menu Axel Kohlmeyer (Mon Oct 09 2006 - 13:56:52 CDT)
  - Re: Missing main menu Stefan Gerlach (Tue Oct 10 2006 - 04:03:10 CDT)
Exporting a protein surface into a mesh (plain text file) Emmanuel Levy (Mon Oct 09 2006 - 11:59:57 CDT)
- Re: Exporting a protein surface into a mesh (plain text file) John Stone (Mon Oct 09 2006 - 12:18:33 CDT)
Access to bond information inside a VMD plugin... Miller, Patrick (Mon Oct 09 2006 - 11:19:54 CDT)
- Re: Access to bond information inside a VMD plugin... Axel Kohlmeyer (Mon Oct 09 2006 - 12:14:55 CDT)
Re: Re: pbc: relation of orthonormalizing; cart. coords; rotation matrices. Neelanjana Sengupta (Mon Oct 09 2006 - 09:48:49 CDT)
- Re: Re: pbc: relation of orthonormalizing; cart. coords; rotation matrices. Olaf Lenz (Mon Oct 09 2006 - 09:58:55 CDT)
Question about measure gofr Jennie Thomas (Fri Oct 06 2006 - 12:02:43 CDT)
- Re: Question about measure gofr Axel Kohlmeyer (Fri Oct 06 2006 - 12:54:58 CDT)
  - Re: Question about measure gofr Jennie Thomas (Fri Oct 06 2006 - 15:36:16 CDT)
cutting short a DMPC bilayer in VMD Akshay Patny (Thu Oct 05 2006 - 21:23:43 CDT)
- Re: cutting short a DMPC bilayer in VMD Jerome Henin (Sat Oct 07 2006 - 11:33:03 CDT)
trace to newcartoon inconsistent display problem Ravinder Abrol (Thu Oct 05 2006 - 15:20:28 CDT)
- Re: trace to newcartoon inconsistent display problem John Stone (Fri Oct 06 2006 - 14:37:55 CDT)
  - Re: trace to newcartoon inconsistent display problem Ravinder Abrol (Fri Oct 06 2006 - 17:57:57 CDT)
    - Re: trace to newcartoon inconsistent display problem John Stone (Fri Oct 06 2006 - 18:06:51 CDT)
pbc: relation of orthonormalizing; cart. coords; rotation matrices. Neelanjana Sengupta (Thu Oct 05 2006 - 11:55:17 CDT)
- Re: pbc: relation of orthonormalizing; cart. coords; rotation matrices. Neelanjana Sengupta (Thu Oct 05 2006 - 12:17:57 CDT)
adding new atoms to a molecule from a script Enzo Vitale (Thu Oct 05 2006 - 05:20:55 CDT)
- Re: adding new atoms to a molecule from a script Eduard Schreiner (Thu Oct 05 2006 - 08:20:54 CDT)
VMD PDB to LEAP Readable PDB Akshay Patny (Wed Oct 04 2006 - 20:09:14 CDT)
- Re: VMD PDB to LEAP Readable PDB John Stone (Fri Oct 06 2006 - 14:59:36 CDT)
no main window with ATI openGL Loison Claire (Wed Oct 04 2006 - 05:15:04 CDT)
- Re: no main window with ATI openGL Olaf Lenz (Wed Oct 04 2006 - 08:11:02 CDT)
- Re: no main window with ATI openGL Eduard Schreiner (Wed Oct 04 2006 - 08:05:37 CDT)
problem viewing cube files Dr. Seth Olsen (Tue Oct 03 2006 - 21:10:33 CDT)
- Re: problem viewing cube files Axel Kohlmeyer (Wed Oct 04 2006 - 08:26:45 CDT)
  - Re: problem viewing cube files Dr. Seth Olsen (Thu Oct 05 2006 - 03:32:34 CDT)
    - Re: problem viewing cube files Axel Kohlmeyer (Thu Oct 05 2006 - 10:51:17 CDT)
    - Re: problem viewing cube files John Stone (Fri Oct 06 2006 - 14:54:06 CDT)
Changing Text Style Dr. Seth Olsen (Tue Oct 03 2006 - 21:52:35 CDT)
- Re: Changing Text Style John Stone (Wed Oct 04 2006 - 00:10:36 CDT)
Selecting Atomnumber Jeffrey A Tibbitt (Tue Oct 03 2006 - 21:15:19 CDT)
- Re: Selecting Atomnumber John Stone (Wed Oct 04 2006 - 00:06:25 CDT)
Hbond donor-acceptor distances Vlad Cojocaru (Tue Oct 03 2006 - 14:49:40 CDT)
- Re: Hbond donor-acceptor distances Eduard Schreiner (Wed Oct 04 2006 - 06:15:38 CDT)
save coordinates after moving them. Cesar Millan (Tue Oct 03 2006 - 14:02:41 CDT)
- Re: save coordinates after moving them. John Stone (Tue Oct 03 2006 - 14:35:50 CDT)
  - Re: save coordinates after moving them. Cesar Millan (Tue Oct 03 2006 - 15:32:17 CDT)
    - Re: save coordinates after moving them. John Stone (Wed Oct 04 2006 - 00:12:59 CDT)
    - Re: save coordinates after moving them. Cesar Millan (Wed Oct 04 2006 - 15:35:33 CDT)
PME units Francesco Iori (Tue Oct 03 2006 - 11:36:54 CDT)
- Re: PME units Jim Phillips (Tue Oct 03 2006 - 14:47:35 CDT)
- Re: PME units Cesar Luis Avila (Tue Oct 03 2006 - 15:05:17 CDT)
problem running pgn script file Shenoy, Sukesh (Tue Oct 03 2006 - 10:37:04 CDT)
- Re: problem running pgn script file Peter Freddolino (Tue Oct 03 2006 - 11:07:52 CDT)
- Re: problem running pgn script file Axel Kohlmeyer (Tue Oct 03 2006 - 11:11:45 CDT)
Does volume coloring require GLSL rendering? Robin L Hayes (Mon Oct 02 2006 - 19:26:24 CDT)
- Re: Does volume coloring require GLSL rendering? John Stone (Tue Oct 03 2006 - 14:27:52 CDT)
Possible bug in LAMMPS plugin Lutz Maibaum (Mon Oct 02 2006 - 15:10:43 CDT)
- Re: Possible bug in LAMMPS plugin Lutz Maibaum (Tue Oct 03 2006 - 11:49:23 CDT)
  - Re: Possible bug in LAMMPS plugin John Stone (Wed Oct 04 2006 - 00:24:11 CDT)
Connectivity lost when loading second pdb MW Van der Kamp, School of Chemistry (Mon Oct 02 2006 - 11:06:33 CDT)
- Re: Connectivity lost when loading second pdb John Stone (Tue Oct 03 2006 - 00:38:41 CDT)
  - Re: Connectivity lost when loading second pdb MW Van der Kamp, School of Chemistry (Tue Oct 03 2006 - 04:29:20 CDT)
    - Re: Connectivity lost when loading second pdb Axel Kohlmeyer (Tue Oct 03 2006 - 08:07:39 CDT)
    - Re: Connectivity lost when loading second pdb MW Van der Kamp, School of Chemistry (Tue Oct 03 2006 - 11:31:59 CDT)
top2psf script olga hrydziuszko (Mon Oct 02 2006 - 09:08:29 CDT)
- Re: top2psf script John Stone (Tue Oct 03 2006 - 23:42:25 CDT)
Error on DNA Mario Valle (Mon Oct 02 2006 - 02:59:08 CDT)
- Re: Error on DNA John Stone (Tue Oct 03 2006 - 23:52:24 CDT)
  - Re: Error on DNA Mario Valle (Wed Oct 04 2006 - 00:31:50 CDT)
STRIDE for a trajectory in text mode tnels_at_sfu.ca (Fri Sep 29 2006 - 15:29:02 CDT)
- Re: STRIDE for a trajectory in text mode Jerome Henin (Sun Oct 01 2006 - 23:53:13 CDT)
How to build a pseudo pore? Cesar Millan (Sat Sep 30 2006 - 11:36:15 CDT)
Color by volume Jay Shore (Fri Sep 29 2006 - 11:54:42 CDT)
- Re: Color by volume Peter Freddolino (Sat Sep 30 2006 - 10:41:09 CDT)
problem loading dcd file Shenoy, Sukesh (Fri Sep 29 2006 - 11:43:03 CDT)
- Re: problem loading dcd file Peter Freddolino (Sat Sep 30 2006 - 09:15:20 CDT)
  - Re: problem loading dcd file John Stone (Sun Oct 01 2006 - 21:36:44 CDT)
lammps trajectory Tamara Rogers (Fri Sep 29 2006 - 04:04:33 CDT)
- Re: lammps trajectory John Stone (Wed Oct 04 2006 - 00:19:00 CDT)
Adding bonds in a script Ignacio Fernández Galván (Thu Sep 28 2006 - 04:08:08 CDT)
- Using namdplot from the command line Nicolas SAPAY (Thu Sep 28 2006 - 12:41:03 CDT)
  - Re: Using namdplot from the command line JC Gumbart (Thu Sep 28 2006 - 14:05:03 CDT)
problem using saltbr plugin in text mode tnels_at_sfu.ca (Wed Sep 27 2006 - 13:33:43 CDT)
- Re: problem using saltbr plugin in text mode Axel Kohlmeyer (Wed Sep 27 2006 - 14:00:28 CDT)
VMD Prompt Jeffrey A Tibbitt (Wed Sep 27 2006 - 12:23:40 CDT)
- Re: VMD Prompt Axel Kohlmeyer (Wed Sep 27 2006 - 13:20:46 CDT)
VMD Installation Help bertrand russell (Tue Sep 26 2006 - 12:05:26 CDT)
- Re: VMD Installation Help John Stone (Tue Sep 26 2006 - 12:55:52 CDT)
HBonds criterion François-Xavier Coudert (Tue Sep 26 2006 - 11:18:22 CDT)
- Re: HBonds criterion Peter Freddolino (Tue Sep 26 2006 - 12:24:46 CDT)
  - Re: HBonds criterion FX Coudert (Tue Sep 26 2006 - 14:38:39 CDT)
GRASP plugin for VMD Vineet Pande (Tue Sep 26 2006 - 11:14:31 CDT)
- Re: GRASP plugin for VMD John Stone (Tue Sep 26 2006 - 12:52:06 CDT)
measure angle between three points in space Ivan Degtyarenko (Sun Sep 24 2006 - 04:17:52 CDT)
- Re: measure angle between three points in space Axel Kohlmeyer (Sun Sep 24 2006 - 10:40:06 CDT)
visualizing charges Gustavo Seabra (Fri Sep 22 2006 - 13:37:34 CDT)
- Re: visualizing charges Axel Kohlmeyer (Fri Sep 22 2006 - 14:18:16 CDT)
  - Re: visualizing charges FyD (Sat Sep 23 2006 - 01:37:06 CDT)
1.8.5: VASP plugin not correct Rob (Thu Sep 21 2006 - 22:15:06 CDT)
- Re: 1.8.5: VASP plugin not correct John Stone (Fri Sep 22 2006 - 12:36:44 CDT)
  - Re: 1.8.5: VASP plugin not correct Rob (Mon Sep 25 2006 - 05:45:15 CDT)
How to hide graphics molecules in a python script? Dr. Seth Olsen (Thu Sep 21 2006 - 20:44:28 CDT)
What unit system does VMD use? Dr. Seth Olsen (Thu Sep 21 2006 - 19:21:09 CDT)
- Re: What unit system does VMD use? Axel Kohlmeyer (Thu Sep 21 2006 - 19:41:58 CDT)
  - Re: What unit system does VMD use? Dr. Seth Olsen (Thu Sep 21 2006 - 21:25:09 CDT)
  - Re: What unit system does VMD use? Axel Kohlmeyer (Mon Sep 25 2006 - 12:00:07 CDT)
Paratool Problem Darrell Kuykendall (Thu Sep 21 2006 - 13:50:01 CDT)
- Re: Paratool Problem Jan Saam (Thu Sep 21 2006 - 14:24:58 CDT)
- Re: Paratool Problem Axel Kohlmeyer (Thu Sep 21 2006 - 14:42:15 CDT)
  - Re: Paratool Problem Darrell Kuykendall (Thu Sep 21 2006 - 10:55:20 CDT)
    - Re: Paratool Problem Jan Saam (Thu Sep 21 2006 - 17:21:29 CDT)
Solvate Plug-In -b Boundary variable Akshay Patny (Thu Sep 21 2006 - 10:18:10 CDT)
Precompiled 1.8.5 for Linux-IA64 installs with wrong flags in lib directory? Rob (Wed Sep 20 2006 - 23:53:31 CDT)
- Re: Precompiled 1.8.5 for Linux-IA64 installs with wrong flags in lib directory? John Stone (Thu Sep 21 2006 - 05:53:47 CDT)
which POPC Bilayer is better to start? Akshay Patny (Wed Sep 20 2006 - 16:40:07 CDT)
VMD won't make mpg out of my trajectory Kenley Barrett (Wed Sep 20 2006 - 13:38:19 CDT)
- Re: VMD won't make mpg out of my trajectory John Stone (Wed Sep 20 2006 - 13:47:03 CDT)
- Re: VMD won't make mpg out of my trajectory Axel Kohlmeyer (Wed Sep 20 2006 - 14:00:56 CDT)
  - Re: VMD won't make mpg out of my trajectory Kenley Barrett (Wed Sep 20 2006 - 14:48:59 CDT)
    - Re: VMD won't make mpg out of my trajectory Axel Kohlmeyer (Wed Sep 20 2006 - 15:12:13 CDT)
    - Re: VMD won't make mpg out of my trajectory John Stone (Wed Sep 20 2006 - 15:17:46 CDT)
problem with tcl script in text mode tnels_at_sfu.ca (Wed Sep 20 2006 - 12:47:01 CDT)
- Re: problem with tcl script in text mode Nuno Ricardo Loureiro Ferreira (Wed Sep 20 2006 - 13:28:55 CDT)
GPCR-Membrane Issue Akshay Patny (Wed Sep 20 2006 - 12:29:49 CDT)
problem with tcl script in text mode tnels_at_sfu.ca (Wed Sep 20 2006 - 12:14:08 CDT)
- Re: problem with tcl script in text mode Jerome Henin (Wed Sep 20 2006 - 14:43:29 CDT)
ribbons representation for RNA in vmd 1.8.5 Vlad Cojocaru (Wed Sep 20 2006 - 09:06:43 CDT)
- Re: ribbons representation for RNA in vmd 1.8.5 John Stone (Wed Sep 20 2006 - 13:56:33 CDT)
  - Re: ribbons representation for RNA in vmd 1.8.5 John Stone (Mon Nov 06 2006 - 17:26:32 CST)
Computer for 3D visualization Berit Hinnemann (Wed Sep 20 2006 - 04:45:58 CDT)
- Re: Computer for 3D visualization John Stone (Thu Sep 21 2006 - 05:51:23 CDT)
importing VMD python modules from external interpreterr Dr. Seth Olsen (Tue Sep 19 2006 - 22:19:02 CDT)
- Re: importing VMD python modules from external interpreterr John Stone (Tue Sep 19 2006 - 22:49:20 CDT)
  - Re: importing VMD python modules from external interpreterr Dr. Seth Olsen (Wed Sep 20 2006 - 01:44:24 CDT)
    - Re: importing VMD python modules from external interpreterr John Stone (Thu Sep 21 2006 - 05:41:32 CDT)
measure bond length? Ivan Degtyarenko (Tue Sep 19 2006 - 11:32:05 CDT)
- Re: measure bond length? Axel Kohlmeyer (Tue Sep 19 2006 - 12:03:23 CDT)
rmsf andrea spitaleri (Tue Sep 19 2006 - 10:40:15 CDT)
- Re: rmsf Axel Kohlmeyer (Tue Sep 19 2006 - 11:07:26 CDT)
psf for protein Al-Rawi, Ahlam (Mon Sep 18 2006 - 17:24:27 CDT)
- Re: psf for protein JC Gumbart (Tue Sep 19 2006 - 10:43:53 CDT)
Centering GPCR onto Lipid Bilayer Akshay Patny (Mon Sep 18 2006 - 14:28:35 CDT)
- Re: Centering GPCR onto Lipid Bilayer Ting Wang (Tue Sep 19 2006 - 13:28:40 CDT)
  - RE: Centering GPCR onto Lipid Bilayer Akshay Patny (Tue Sep 19 2006 - 16:19:59 CDT)
modelling phosphorylation Dani Süveges (Mon Sep 18 2006 - 04:45:55 CDT)
- Re: modelling phosphorylation L. Michel Espinoza-Fonseca (Mon Sep 18 2006 - 09:45:03 CDT)
FW: Membrane PlugIn issue Akshay Patny (Sat Sep 16 2006 - 14:20:23 CDT)
problem with -args in text mode tnels_at_sfu.ca (Fri Sep 15 2006 - 19:38:07 CDT)
- Re: problem with -args in text mode Axel Kohlmeyer (Fri Sep 15 2006 - 23:34:41 CDT)
  - Re: problem with -args in text mode Axel Kohlmeyer (Mon Sep 18 2006 - 14:19:28 CDT)
no subject tnels_at_sfu.ca (Fri Sep 15 2006 - 20:18:21 CDT)
- Re: no subject dimka (Mon Sep 18 2006 - 13:50:55 CDT)
how to build an atomistic protein from a low resolution data. Margaret Shun Cheung (Fri Sep 15 2006 - 11:38:56 CDT)
- Re: how to build an atomistic protein from a low resolution data. JC Gumbart (Fri Sep 15 2006 - 19:41:23 CDT)
  - Re: how to build an atomistic protein from a low resolution data. Peter Freddolino (Fri Sep 15 2006 - 20:06:54 CDT)
    - Re: how to build an atomistic protein from a low resolution data. Margaret S. Cheung (Fri Sep 15 2006 - 20:08:41 CDT)
manually defining bonds, setting atom colors Robert Hoy (Thu Sep 14 2006 - 16:10:52 CDT)
- Re: manually defining bonds, setting atom colors Axel Kohlmeyer (Thu Sep 14 2006 - 16:39:36 CDT)
DPPC Bilayer Size Akshay Patny (Thu Sep 14 2006 - 13:49:06 CDT)
- Re: DPPC Bilayer Size Ting Wang (Thu Sep 14 2006 - 17:27:55 CDT)
  - Re: DPPC Bilayer Size L. Michel Espinoza-Fonseca (Thu Sep 14 2006 - 18:11:28 CDT)
    - Re: DPPC Bilayer Size Axel Kohlmeyer (Thu Sep 14 2006 - 18:26:45 CDT)
  - RE: DPPC Bilayer Size Akshay Patny (Fri Sep 15 2006 - 12:07:51 CDT)
    - Re: DPPC Bilayer Size JC Gumbart (Fri Sep 15 2006 - 19:46:30 CDT)
Finding residues involved in Hbonds. Nitin Bhardwaj (Thu Sep 14 2006 - 11:16:21 CDT)
- Re: Finding residues involved in Hbonds. Axel Kohlmeyer (Thu Sep 14 2006 - 13:12:56 CDT)
problem in visualizing gaussian log file Francesca Mocci (Thu Sep 14 2006 - 05:41:51 CDT)
- Re: problem in visualizing gaussian log file Jan Saam (Thu Sep 14 2006 - 08:09:09 CDT)
  - Re: problem in visualizing gaussian log file Francesca Mocci (Thu Sep 14 2006 - 09:26:43 CDT)
    - Re: problem in visualizing gaussian log file dimka (Thu Sep 14 2006 - 13:13:33 CDT)
    - Re: problem in visualizing gaussian log file John Stone (Thu Sep 14 2006 - 13:21:22 CDT)
puts format lily jin (Wed Sep 13 2006 - 15:22:27 CDT)
- Re: puts format Alexandr Isayev (Wed Sep 13 2006 - 16:18:04 CDT)
  - Re: puts format Axel Kohlmeyer (Wed Sep 13 2006 - 16:43:31 CDT)
- Re: puts format John Stone (Wed Sep 13 2006 - 16:27:34 CDT)
- Re: puts format Jerome Henin (Wed Sep 13 2006 - 18:01:21 CDT)
rdf plugin in vmd 1.85 dimka (Wed Sep 13 2006 - 14:08:29 CDT)
- Re: rdf plugin in vmd 1.85 Axel Kohlmeyer (Wed Sep 13 2006 - 14:24:10 CDT)
antialiasing Wen Li (Wed Sep 13 2006 - 13:36:53 CDT)
- Re: antialiasing Axel Kohlmeyer (Wed Sep 13 2006 - 13:56:38 CDT)
  - Re: antialiasing Wen Li (Wed Sep 13 2006 - 14:00:02 CDT)
    - Re: antialiasing John Stone (Wed Sep 13 2006 - 14:07:44 CDT)
    - Re: antialiasing Axel Kohlmeyer (Wed Sep 13 2006 - 14:10:30 CDT)
drawing of direction vectors for conformational transition Zu Thur Yew (Wed Sep 13 2006 - 11:52:45 CDT)
- Re: drawing of direction vectors for conformational transition Axel Kohlmeyer (Wed Sep 13 2006 - 14:18:03 CDT)
  - Re: drawing of direction vectors for conformational transition Charles McCallum (Thu Sep 14 2006 - 10:42:06 CDT)
    - Re: drawing of direction vectors for conformational transition Axel Kohlmeyer (Thu Sep 14 2006 - 11:25:47 CDT)
- Re: drawing of direction vectors for conformational transition Peter Freddolino (Wed Sep 13 2006 - 17:34:34 CDT)
NuVision glasses Grischa Meyer (Mon Sep 11 2006 - 19:41:25 CDT)
rmsd fitting Myunggi Yi (Mon Sep 11 2006 - 20:30:13 CDT)
- Re: rmsd fitting Luis Gracia (Tue Sep 12 2006 - 02:03:30 CDT)
how to run a plugin from the command line? Johannes Müllegger (Mon Sep 11 2006 - 18:25:03 CDT)
- Re: how to run a plugin from the command line? John Stone (Mon Sep 11 2006 - 23:34:01 CDT)
Recentering the box on target molecule and wraping Arturas Ziemys (Mon Sep 11 2006 - 10:39:55 CDT)
- Re: namd-l: Recentering the box on target molecule and wraping Jerome Henin (Mon Sep 11 2006 - 12:05:04 CDT)
RE: How to produce a graph as the one attached, using VMD? Jiapu.Zhang_at_csiro.au (Sun Sep 10 2006 - 23:49:37 CDT)
- Re: How to produce a graph as the one attached, using VMD? Jian Zou (Mon Sep 11 2006 - 00:15:55 CDT)
Graphics cards David Chalmers (Sun Sep 10 2006 - 23:11:58 CDT)
- Re: Graphics cards John Stone (Mon Sep 11 2006 - 11:34:32 CDT)
How to produce a graph as the one attached, using VMD? Jiapu.Zhang_at_csiro.au (Sun Sep 10 2006 - 21:32:20 CDT)
- Re: How to produce a graph as the one attached, using VMD? Jian Zou (Sun Sep 10 2006 - 22:55:52 CDT)
Opening DCD file >2GB Lechuga, Javier (Sun Sep 10 2006 - 13:35:52 CDT)
- Re: Opening DCD file >2GB Peter Freddolino (Sun Sep 10 2006 - 15:23:31 CDT)
saving charges in the B column L. Michel Espinoza-Fonseca (Fri Sep 08 2006 - 18:53:11 CDT)
- Re: saving charges in the B column Axel Kohlmeyer (Fri Sep 08 2006 - 19:27:52 CDT)
- Re: saving charges in the B column Leonardo Trabuco (Sat Sep 09 2006 - 18:09:38 CDT)
protein embedding membrane javier.vallejos_at_correo.usach.cl (Fri Sep 08 2006 - 18:06:50 CDT)
protein in membrane javier.vallejos_at_correo.usach.cl (Fri Sep 08 2006 - 17:35:27 CDT)
- Re: protein in membrane Axel Kohlmeyer (Fri Sep 08 2006 - 18:12:02 CDT)
- Re: protein in membrane Ting Wang (Tue Sep 12 2006 - 13:58:07 CDT)
  - RE: protein in membrane Akshay Patny (Tue Sep 12 2006 - 15:45:31 CDT)
Ramachandran Map of 2 pdbs Rathinavelan, Thenmalarchelvi (Fri Sep 08 2006 - 12:43:32 CDT)
- Re: Ramachandran Map of 2 pdbs John Stone (Fri Sep 08 2006 - 13:13:23 CDT)
- Re: Ramachandran Map of 2 pdbs Justin Gullingsrud (Fri Sep 08 2006 - 14:50:35 CDT)
dipole moment L. Michel Espinoza-Fonseca (Fri Sep 08 2006 - 11:46:59 CDT)
- Re: dipole moment Axel Kohlmeyer (Fri Sep 08 2006 - 12:10:54 CDT)
- Re: dipole moment Axel Kohlmeyer (Fri Sep 08 2006 - 12:13:29 CDT)
- Re: dipole moment - corrigendum! Jan Saam (Fri Sep 08 2006 - 12:18:15 CDT)
- Re: dipole moment Jan Saam (Fri Sep 08 2006 - 12:17:26 CDT)
How to use bigdcd in vmd batch mode? Hamsa Priya Mohana sundaram (Fri Sep 08 2006 - 09:44:45 CDT)
- Re: How to use bigdcd in vmd batch mode? Axel Kohlmeyer (Fri Sep 08 2006 - 12:04:35 CDT)
  - Re: How to use bigdcd in vmd batch mode? John Stone (Fri Sep 08 2006 - 16:32:18 CDT)
Labels not appearing with "load state" Ignacio Fernández Galván (Fri Sep 08 2006 - 07:59:07 CDT)
- Re: Labels not appearing with "load state" John Stone (Sun Sep 10 2006 - 01:36:13 CDT)
  - Re: Labels not appearing with "load state" Ignacio Fernández Galván (Mon Sep 11 2006 - 02:28:23 CDT)
IED, output from nmode (amber) nadiav_at_soton.ac.uk (Fri Sep 08 2006 - 07:55:42 CDT)
- Re: IED, output from nmode (amber) David A. Case (Tue Sep 12 2006 - 10:18:35 CDT)
Min. Image Convention after Translation & Rotation Neelanjana Sengupta (Thu Sep 07 2006 - 17:53:22 CDT)
- Re: Min. Image Convention after Translation & Rotation Axel Kohlmeyer (Thu Sep 07 2006 - 20:08:45 CDT)
  - Re: Min. Image Convention after Translation & Rotation Neelanjana Sengupta (Fri Sep 08 2006 - 13:01:13 CDT)
    - Re: Min. Image Convention after Translation & Rotation Axel Kohlmeyer (Fri Sep 08 2006 - 14:00:58 CDT)
  - Re: Min. Image Convention after Translation & Rotation Neelanjana Sengupta (Mon Oct 02 2006 - 12:14:44 CDT)
pass variables from the shell to VMD Christian Fufezan (Thu Sep 07 2006 - 10:54:05 CDT)
- Re: pass variables from the shell to VMD Axel Kohlmeyer (Thu Sep 07 2006 - 11:51:01 CDT)
- Re: pass variables from the shell to VMD dimka (Thu Sep 07 2006 - 12:09:32 CDT)
Win64 version Dan Strahs (Wed Sep 06 2006 - 14:51:10 CDT)
- Re: Win64 version John Stone (Wed Sep 06 2006 - 15:10:46 CDT)
slicing pinisetty dinesh (Wed Sep 06 2006 - 11:29:48 CDT)
- Re: slicing Axel Kohlmeyer (Wed Sep 06 2006 - 11:46:23 CDT)
dynamical list of atoms Silvina Matysiak (Wed Sep 06 2006 - 10:02:25 CDT)
- Re: dynamical list of atoms Axel Kohlmeyer (Wed Sep 06 2006 - 10:54:30 CDT)
- Re: dynamical list of atoms John Stone (Wed Sep 06 2006 - 11:01:29 CDT)
Matrix inverse Neelanjana Sengupta (Tue Sep 05 2006 - 17:38:23 CDT)
- Re: Matrix inverse Jan Saam (Tue Sep 05 2006 - 18:13:58 CDT)
- Re: Matrix inverse Axel Kohlmeyer (Tue Sep 05 2006 - 18:18:10 CDT)
  - Re: Matrix inverse Neelanjana Sengupta (Tue Sep 05 2006 - 18:26:31 CDT)
    - Re: Matrix inverse Axel Kohlmeyer (Tue Sep 05 2006 - 18:39:22 CDT)
  - TCL wrapper for linear algebra package in VMD Jan Saam (Tue Sep 05 2006 - 19:12:07 CDT)
- Re: Matrix inverse Justin Gullingsrud (Tue Sep 05 2006 - 18:39:37 CDT)
Warning: poorly guessed coordinates using PsfGen Lechuga, Javier (Tue Sep 05 2006 - 10:23:35 CDT)
- Re: Warning: poorly guessed coordinates using PsfGen Axel Kohlmeyer (Tue Sep 05 2006 - 10:53:35 CDT)
- imposing period boundary conditions in a simulation with a crystal Ana Celia Araujo Vila Verde (Tue Sep 05 2006 - 11:13:06 CDT)
  - Re: imposing period boundary conditions in a simulation with a crystal Axel Kohlmeyer (Tue Sep 05 2006 - 12:00:19 CDT)
    - RE: imposing period boundary conditions in a simulation with a crystal Ana Celia Araujo Vila Verde (Wed Sep 06 2006 - 08:31:59 CDT)
    - Re: imposing period boundary conditions in a simulation with a crystal Axel Kohlmeyer (Wed Sep 06 2006 - 09:23:39 CDT)
radial pair distribution function: molecule/water? Ivan Degtyarenko (Mon Sep 04 2006 - 11:31:35 CDT)
- Re: radial pair distribution function: molecule/water? Axel Kohlmeyer (Mon Sep 04 2006 - 12:14:28 CDT)
different number of atoms in different frames of a trajectory Enzo Vitale (Mon Sep 04 2006 - 11:09:33 CDT)
- Re: different number of atoms in different frames of a trajectory John Stone (Mon Sep 04 2006 - 22:46:01 CDT)
qsub (torque/maui) and vmd Gordon Wells (Mon Sep 04 2006 - 08:25:54 CDT)
- Re: qsub (torque/maui) and vmd Neelanjana Sengupta (Mon Sep 04 2006 - 09:02:16 CDT)
  - Re: qsub (torque/maui) and vmd Gordon Wells (Mon Sep 04 2006 - 09:31:33 CDT)
- Re: qsub (torque/maui) and vmd Axel Kohlmeyer (Mon Sep 04 2006 - 11:18:05 CDT)
  - Re: qsub (torque/maui) and vmd Gordon Wells (Mon Sep 04 2006 - 13:01:42 CDT)
    - Re: qsub (torque/maui) and vmd Axel Kohlmeyer (Mon Sep 04 2006 - 14:00:38 CDT)
CoordinateTransformation Neelanjana Sengupta (Sun Sep 03 2006 - 15:34:48 CDT)
- Re: namd-l: CoordinateTransformation Jerome Henin (Sun Sep 03 2006 - 17:54:17 CDT)
CoordinateTransformation Neelanjana Sengupta (Sun Sep 03 2006 - 15:29:56 CDT)
- CoordinateTransformation Neelanjana Sengupta (Sun Sep 03 2006 - 15:33:32 CDT)
  - Re: CoordinateTransformation B.D Allen (Sun Sep 03 2006 - 20:38:38 CDT)
  - Re: CoordinateTransformation Jim Phillips (Sun Sep 03 2006 - 21:59:46 CDT)
Re: namd-l: electric field Peter Freddolino (Sun Sep 03 2006 - 08:10:10 CDT)
electric field Ekta Khurana (Sat Sep 02 2006 - 20:21:23 CDT)
Angles and dihedral generation Cesar Luis Avila (Fri Sep 01 2006 - 20:02:36 CDT)
- Re: Angles and dihedral generation Jim Phillips (Sat Sep 02 2006 - 15:25:12 CDT)
  - Re: namd-l: Re: Angles and dihedral generation Cesar Luis Avila (Mon Sep 04 2006 - 10:00:35 CDT)
    - Re: namd-l: Re: Angles and dihedral generation Jim Phillips (Mon Sep 04 2006 - 16:44:44 CDT)
    - Re: namd-l: Re: Angles and dihedral generation Cesar Luis Avila (Tue Sep 05 2006 - 08:15:18 CDT)
looking for VMD draw scripts. Axel Kohlmeyer (Fri Sep 01 2006 - 15:34:59 CDT)
- Re: looking for VMD draw scripts. Jan Saam (Fri Sep 01 2006 - 15:59:13 CDT)
  - Re: looking for VMD draw scripts. John Stone (Fri Sep 01 2006 - 16:07:38 CDT)
Where did I put those angles? Cesar Luis Avila (Thu Aug 31 2006 - 17:16:01 CDT)
- Re: Where did I put those angles? Axel Kohlmeyer (Thu Aug 31 2006 - 17:51:43 CDT)
  - Re: Where did I put those angles? John Stone (Thu Aug 31 2006 - 17:57:18 CDT)
    - Re: Where did I put those angles? Cesar Luis Avila (Thu Aug 31 2006 - 19:17:14 CDT)
  - Re: Where did I put those angles? Marcos Sotomayor (Thu Aug 31 2006 - 18:02:11 CDT)
NAMD 2.6 released Jim Phillips (Thu Aug 31 2006 - 17:13:40 CDT)
problem with vecsub, help with Tcl Script Leonardo Sepulveda Durán (Thu Aug 31 2006 - 12:25:29 CDT)
- Re: problem with vecsub, help with Tcl Script Axel Kohlmeyer (Thu Aug 31 2006 - 12:59:32 CDT)
output file format alexandra.marques_at_fc.up.pt (Thu Aug 31 2006 - 10:20:14 CDT)
- Re: output file format Axel Kohlmeyer (Thu Aug 31 2006 - 10:52:13 CDT)
  - Re: output file format alexandra.marques_at_fc.up.pt (Fri Sep 01 2006 - 14:20:35 CDT)
    - Re: output file format Axel Kohlmeyer (Fri Sep 01 2006 - 15:01:50 CDT)
Paratool problem daniel aguayo (Wed Aug 30 2006 - 18:35:36 CDT)
- Re: Paratool problem Jan Saam (Thu Aug 31 2006 - 04:02:13 CDT)
  - Re: Paratool problem John Stone (Mon Nov 20 2006 - 13:45:11 CST)
Installing VMFD in kubuntu.............. bertrand russell (Wed Aug 30 2006 - 10:59:37 CDT)
- Re: Installing VMFD in kubuntu.............. Peter Freddolino (Wed Aug 30 2006 - 11:12:27 CDT)
- Re: Installing VMFD in kubuntu.............. Mustafa Burak Boz (Wed Aug 30 2006 - 11:36:49 CDT)
VMD runtime error Lechuga, Javier (Wed Aug 30 2006 - 06:11:47 CDT)
- Re: VMD runtime error Peter Freddolino (Wed Aug 30 2006 - 07:06:21 CDT)
Réf. : Re: VMD1.8.5 : multiseq db l.spitzer_at_fr.fournierpharma.com (Wed Aug 30 2006 - 03:06:55 CDT)
Counting H-bonds from a dcd file Nitin Bhardwaj (Tue Aug 29 2006 - 17:06:21 CDT)
- Re: Counting H-bonds from a dcd file Axel Kohlmeyer (Tue Aug 29 2006 - 17:42:56 CDT)
  - Re: Counting H-bonds from a dcd file Nitin Bhardwaj (Tue Aug 29 2006 - 18:15:56 CDT)
    - Re: Counting H-bonds from a dcd file Axel Kohlmeyer (Tue Aug 29 2006 - 19:16:19 CDT)
question about visualization Sandra Bennun Serrano (Tue Aug 29 2006 - 12:44:58 CDT)
- Re: question about visualization John Stone (Tue Aug 29 2006 - 12:58:40 CDT)
Réf. : Re: Réf. : Re: vmd-l : VMD1.8.5 : multiseq db l.spitzer_at_fr.fournierpharma.com (Tue Aug 29 2006 - 11:18:08 CDT)
- Re: VMD1.8.5 : multiseq db Elijah Roberts (Tue Aug 29 2006 - 12:20:04 CDT)
  - Re: VMD1.8.5 : multiseq db John Stone (Tue Aug 29 2006 - 12:55:03 CDT)
  - Re: VMD1.8.5 : multiseq db Martin Grana (Thu Aug 31 2006 - 03:21:36 CDT)
Réf. : Re: vmd-l : VMD1.8.5 : multiseq db l.spitzer_at_fr.fournierpharma.com (Tue Aug 29 2006 - 09:48:11 CDT)
- Re: Réf. : Re: vmd-l : VMD1.8.5 : multiseq db Elijah Roberts (Tue Aug 29 2006 - 10:45:09 CDT)
loading gzipped trajectories into vmd Vlad Cojocaru (Tue Aug 29 2006 - 08:24:03 CDT)
- Re: loading gzipped trajectories into vmd Bogdan Costescu (Tue Aug 29 2006 - 09:38:42 CDT)
- Re: loading gzipped trajectories into vmd Axel Kohlmeyer (Tue Aug 29 2006 - 11:09:10 CDT)
vmd-l : VMD1.8.5 : multiseq db l.spitzer_at_fr.fournierpharma.com (Tue Aug 29 2006 - 03:29:44 CDT)
- Re: vmd-l : VMD1.8.5 : multiseq db Elijah Roberts (Tue Aug 29 2006 - 09:08:40 CDT)
Dynamic bond calculation Ignacio Fernández Galván (Tue Aug 29 2006 - 02:49:30 CDT)
- Re: Dynamic bond calculation John Stone (Tue Aug 29 2006 - 14:27:46 CDT)
A error of " transforming dcd into pdb " wang (Tue Aug 29 2006 - 01:27:52 CDT)
- Re: A error of " transforming dcd into pdb " Leonardo Trabuco (Tue Aug 29 2006 - 02:02:52 CDT)
- Re: A error of " transforming dcd into pdb " dimka (Tue Aug 29 2006 - 02:37:14 CDT)
  - Re: A error of " transforming dcd into pdb " dimka (Tue Aug 29 2006 - 02:41:47 CDT)
- Re: A error of " transforming dcd into pdb " Eduard Schreiner (Tue Aug 29 2006 - 04:46:24 CDT)
  - Re: A error of " transforming dcd into pdb " Leonardo Trabuco (Tue Aug 29 2006 - 10:48:36 CDT)
psfgen woes... Pavan Ghatty (Mon Aug 28 2006 - 16:00:42 CDT)
- Re: psfgen woes... Peter Freddolino (Mon Aug 28 2006 - 16:11:11 CDT)
Help with psfgen Pavan Ghatty (Mon Aug 28 2006 - 08:09:46 CDT)
Problem with vmdsphere.frag shader Mario Valle (Mon Aug 28 2006 - 09:00:52 CDT)
- Re: Problem with vmdsphere.frag shader John Stone (Mon Aug 28 2006 - 11:44:38 CDT)
  - Re: Problem with vmdsphere.frag shader John Stone (Mon Aug 28 2006 - 11:58:37 CDT)
    - Re: Problem with vmdsphere.frag shader Axel Kohlmeyer (Mon Aug 28 2006 - 12:32:16 CDT)
GLSL failure in VMD 1.8.5, Nvidia 6200 card Guo Zhi (Mon Aug 28 2006 - 08:57:39 CDT)
- Re: GLSL failure in VMD 1.8.5, Nvidia 6200 card John Stone (Mon Aug 28 2006 - 11:37:48 CDT)
  - Re: GLSL failure in VMD 1.8.5, Nvidia 6200 card Guo Zhi (Mon Aug 28 2006 - 21:02:46 CDT)
water numbering alexandra.marques_at_fc.up.pt (Mon Aug 28 2006 - 06:50:33 CDT)
- Re: water numbering alexandra.marques_at_fc.up.pt (Mon Aug 28 2006 - 10:52:03 CDT)
- Re: water numbering John Stone (Mon Aug 28 2006 - 11:28:06 CDT)
autoionize behaviour on big systems L. Michel Espinoza-Fonseca (Mon Aug 28 2006 - 00:44:24 CDT)
- Re: autoionize behaviour on big systems John Stone (Mon Aug 28 2006 - 00:59:33 CDT)
  - Re: autoionize behaviour on big systems L. Michel Espinoza-Fonseca (Mon Aug 28 2006 - 01:12:18 CDT)
    - Re: Re: autoionize behaviour on big systems John Stone (Mon Aug 28 2006 - 01:21:49 CDT)
Announce: VMD 1.8.5 Released! John Stone (Fri Aug 25 2006 - 23:51:22 CDT)
removing structures from a psf&pdb Thomas Caulfield (Fri Aug 25 2006 - 15:58:40 CDT)
- RE: removing structures from a psf&pdb JC Gumbart (Mon Aug 28 2006 - 00:56:18 CDT)
- Re: removing structures from a psf&pdb Marcos Sotomayor (Mon Aug 28 2006 - 10:55:50 CDT)
Heme psfgen issue sseefeld_at_uwm.edu (Fri Aug 25 2006 - 00:33:10 CDT)
Text Editor Got Me. . . Marc Charendoff (Thu Aug 24 2006 - 19:48:11 CDT)
- gyration radius for a trajectory alexandra.marques_at_fc.up.pt (Fri Aug 25 2006 - 05:38:06 CDT)
  - Re: gyration radius for a trajectory Axel Kohlmeyer (Fri Aug 25 2006 - 09:40:54 CDT)
animated gif option in VMD for Windows. Ravinder Abrol (Thu Aug 24 2006 - 14:14:58 CDT)
- Re: animated gif option in VMD for Windows. Axel Kohlmeyer (Thu Aug 24 2006 - 14:45:53 CDT)
  - Re: animated gif option in VMD for Windows. John Stone (Thu Aug 24 2006 - 15:00:01 CDT)
Unexpected End-of-file? Marc Charendoff (Wed Aug 23 2006 - 20:23:52 CDT)
- Re: Unexpected End-of-file? Axel Kohlmeyer (Wed Aug 23 2006 - 23:59:52 CDT)
  - Re: Unexpected End-of-file? John Stone (Thu Aug 24 2006 - 00:44:22 CDT)
    - RE: Unexpected End-of-file? Dallas B. Warren (Thu Aug 24 2006 - 17:38:28 CDT)
spikes in trajectory, problem with the alignment of frames Johannes Müllegger (Wed Aug 23 2006 - 19:25:58 CDT)
- Re: spikes in trajectory, problem with the alignment of frames John Stone (Wed Aug 23 2006 - 22:27:52 CDT)
  - Re: spikes in trajectory, problem with the alignment of frames Johannes Müllegger (Thu Aug 24 2006 - 13:50:20 CDT)
    - Re: spikes in trajectory, problem with the alignment of frames Luis Gracia (Thu Aug 24 2006 - 14:08:48 CDT)
Problem with cellBasisVector 1, 2 and 3 Pavan Ghatty (Wed Aug 23 2006 - 08:55:04 CDT)
- Re: Problem with cellBasisVector 1, 2 and 3 Peter Freddolino (Wed Aug 23 2006 - 09:32:39 CDT)
PRODRG generated .gro file Marc Charendoff (Tue Aug 22 2006 - 21:03:41 CDT)
- Re: PRODRG generated .gro file Axel Kohlmeyer (Tue Aug 22 2006 - 21:51:42 CDT)
VMD and IED for Tiger? ybomble (Tue Aug 22 2006 - 19:54:17 CDT)
- Re: VMD and IED for Tiger? John Stone (Tue Aug 22 2006 - 20:17:45 CDT)
problems with autoionize L. Michel Espinoza-Fonseca (Tue Aug 22 2006 - 17:36:39 CDT)
- Re: problems with autoionize John Stone (Tue Aug 22 2006 - 17:45:34 CDT)
  - Re: problems with autoionize L. Michel Espinoza-Fonseca (Tue Aug 22 2006 - 17:55:02 CDT)
- Re: problems with autoionize Axel Kohlmeyer (Tue Aug 22 2006 - 18:10:54 CDT)
  - Re: problems with autoionize John Stone (Tue Aug 22 2006 - 19:02:12 CDT)
    - Re: problems with autoionize L. Michel Espinoza-Fonseca (Tue Aug 22 2006 - 19:16:29 CDT)
- Re: problems with autoionize John Stone (Tue Aug 22 2006 - 20:56:03 CDT)
  - Re: problems with autoionize L. Michel Espinoza-Fonseca (Tue Aug 22 2006 - 21:18:06 CDT)
charmm toppology : internal coordinates Arturas Ziemys (Tue Aug 22 2006 - 16:39:00 CDT)
psfgen probs Shenoy, Sukesh (Tue Aug 22 2006 - 10:03:41 CDT)
- Re: psfgen probs Peter Freddolino (Tue Aug 22 2006 - 10:12:45 CDT)
(no subject) Lechuga, Javier (Tue Aug 22 2006 - 06:12:20 CDT)
- Re: Peter Freddolino (Tue Aug 22 2006 - 07:36:35 CDT)
- Re: Axel Kohlmeyer (Tue Aug 22 2006 - 07:46:27 CDT)
  - Re: morten østergaard jensen (Tue Aug 22 2006 - 10:02:19 CDT)
corrigendum: error when solvating a system L. Michel Espinoza-Fonseca (Mon Aug 21 2006 - 20:51:54 CDT)
error when solvating a system L. Michel Espinoza-Fonseca (Mon Aug 21 2006 - 20:49:27 CDT)
psfgen problems? Shenoy, Sukesh (Mon Aug 21 2006 - 17:41:52 CDT)
- Re: psfgen problems? Charles McCallum (Tue Aug 22 2006 - 12:41:51 CDT)
[Fwd: Re: Help with "move" command] Peter Freddolino (Mon Aug 21 2006 - 14:40:50 CDT)
Help with "move" command Pavan Ghatty (Mon Aug 21 2006 - 11:52:50 CDT)
- Display Grasp potential map in VMD Wei Liu (Wed Jul 25 2007 - 16:15:14 CDT)
  - Re: Display Grasp potential map in VMD John Stone (Thu Jul 26 2007 - 16:16:27 CDT)
changing the name of a residue L. Michel Espinoza-Fonseca (Mon Aug 21 2006 - 10:23:21 CDT)
- Re: changing the name of a residue John Stone (Mon Aug 21 2006 - 10:37:59 CDT)
md trajectory: centering/h-bonb residence/coordination number Ivan Degtyarenko (Mon Aug 21 2006 - 08:26:44 CDT)
- Re: md trajectory: centering/h-bonb residence/coordination number John Stone (Mon Aug 21 2006 - 11:02:49 CDT)
- Re: md trajectory: centering/h-bonb residence/coordination number Eduard Schreiner (Mon Aug 21 2006 - 12:09:34 CDT)
NAMD 2.6b2 released Jim Phillips (Sun Aug 20 2006 - 15:43:38 CDT)
large mdcrd files alexandra.marques_at_fc.up.pt (Sun Aug 20 2006 - 07:56:30 CDT)
- Re: large mdcrd files Lubos Vrbka (Sun Aug 20 2006 - 11:27:19 CDT)
- Re: large mdcrd files John Stone (Sun Aug 20 2006 - 14:09:50 CDT)
segment name limit with solvate and psfgen Thomas Caulfield (Sat Aug 19 2006 - 22:35:55 CDT)
- Re: segment name limit with solvate and psfgen Leonardo Trabuco (Sat Aug 19 2006 - 23:03:40 CDT)
- Re: segment name limit with solvate and psfgen L. Michel Espinoza-Fonseca (Sat Aug 19 2006 - 23:30:06 CDT)
RealD (Stereographics) E2SGI emitter on Quadro 3450? Sabuj Pattanayek (Fri Aug 18 2006 - 20:25:24 CDT)
- Re: RealD (Stereographics) E2SGI emitter on Quadro 3450? John Stone (Fri Aug 18 2006 - 22:33:36 CDT)
load MSMS face file into VMD Yongcheng Zhou (Fri Aug 18 2006 - 15:54:13 CDT)
- Re: load MSMS face file into VMD John Stone (Fri Aug 18 2006 - 16:24:55 CDT)
small query... hl332_at_drexel.edu (Fri Aug 18 2006 - 11:17:25 CDT)
- Re: small query... Leonardo Trabuco (Fri Aug 18 2006 - 15:25:34 CDT)
Fwd: Crystal eyes stereo on un supported Mac G5 GeForce FX5200 Dan White (Fri Aug 18 2006 - 09:15:23 CDT)
- Re: Fwd: Crystal eyes stereo on un supported Mac G5 GeForce FX5200 John Stone (Fri Aug 18 2006 - 11:42:34 CDT)
reading cmap wih vmd L. Michel Espinoza-Fonseca (Thu Aug 17 2006 - 19:17:26 CDT)
- Re: reading cmap wih vmd John Stone (Thu Aug 17 2006 - 23:43:50 CDT)
  - Re: reading cmap wih vmd Charles McCallum (Fri Aug 18 2006 - 10:23:57 CDT)
Load angel (Thu Aug 17 2006 - 13:14:06 CDT)
- Re: Load John Stone (Thu Aug 17 2006 - 14:04:21 CDT)
- Re: Load Axel Kohlmeyer (Thu Aug 17 2006 - 14:12:56 CDT)
Question About Tcl variables Leonardo Sepulveda Durán (Wed Aug 16 2006 - 16:41:46 CDT)
- Re: Question About Tcl variables Axel Kohlmeyer (Wed Aug 16 2006 - 19:36:28 CDT)
rendering transparent objects Ivan Degtyarenko (Wed Aug 16 2006 - 15:34:35 CDT)
- Re: rendering transparent objects John Stone (Wed Aug 16 2006 - 15:43:57 CDT)
  - Re: rendering transparent objects Ivan Degtyarenko (Wed Aug 16 2006 - 16:32:57 CDT)
  - Re: rendering transparent objects Ivan Degtyarenko (Wed Aug 16 2006 - 16:50:44 CDT)
RE: stereo on LCD display = pipe dream? Warren DeLano (Wed Aug 16 2006 - 15:11:39 CDT)
stereo on LCD display = pipe dream? Jeff Hoch (Wed Aug 16 2006 - 13:46:04 CDT)
- Re: stereo on LCD display = pipe dream? John Stone (Wed Aug 16 2006 - 14:02:24 CDT)
minimum distance b/w two atoms Narender Singh Maan (Tue Aug 15 2006 - 18:05:30 CDT)
- Re: minimum distance b/w two atoms John Stone (Tue Aug 15 2006 - 18:21:12 CDT)
Manipulation on loaded MSMS surface Arturas Ziemys (Tue Aug 15 2006 - 16:19:18 CDT)
- Re: Manipulation on loaded MSMS surface John Stone (Wed Aug 16 2006 - 23:26:54 CDT)
unique opportunity - 20% discount for the EuroQSAR 2006 andras.borosy_at_givaudan.com (Tue Aug 15 2006 - 10:54:04 CDT)
VMD 1.8.5 beta 7 test version posted John Stone (Sun Aug 13 2006 - 17:49:32 CDT)
Re: NAMD minimization error JC Gumbart (Sat Aug 12 2006 - 17:29:49 CDT)
- Re: NAMD minimization error sseefeld_at_uwm.edu (Sat Aug 12 2006 - 18:45:17 CDT)
  - Re: NAMD minimization error Leonardo Trabuco (Sat Aug 12 2006 - 18:52:49 CDT)
- Re: NAMD minimization error sseefeld_at_uwm.edu (Tue Aug 15 2006 - 10:01:28 CDT)
color: negative values Zu Thur Yew (Sat Aug 12 2006 - 14:30:37 CDT)
- Re: color: negative values John Stone (Sat Aug 12 2006 - 14:50:14 CDT)
NAMD minimization error sseefeld_at_uwm.edu (Sat Aug 12 2006 - 11:50:42 CDT)
- RE: NAMD minimization error JC Gumbart (Sat Aug 12 2006 - 12:02:28 CDT)
Installation of VMD on Mandriva Linux 2006 Wei Liu (Sat Aug 12 2006 - 13:23:58 CDT)
- Re: Installation of VMD on Mandriva Linux 2006 John Stone (Sat Aug 12 2006 - 10:40:12 CDT)
  - Re: Installation of VMD on Mandriva Linux 2006 Wei Liu (Sat Aug 12 2006 - 18:52:07 CDT)
    - Re: Installation of VMD on Mandriva Linux 2006 John Stone (Sat Aug 12 2006 - 13:34:42 CDT)
right alignment for numbers in color bar Yongcheng Zhou (Fri Aug 11 2006 - 18:38:38 CDT)
- Re: right alignment for numbers in color bar John Stone (Fri Aug 11 2006 - 23:15:27 CDT)
  - Re: right alignment for numbers in color bar John Stone (Sat Aug 12 2006 - 00:15:58 CDT)
    - Re: right alignment for numbers in color bar John Stone (Sat Aug 12 2006 - 03:42:53 CDT)
Axes dilema griadi_at_utalca.cl (Fri Aug 11 2006 - 18:11:07 CDT)
- Re: Axes dilema John Stone (Fri Aug 11 2006 - 22:27:58 CDT)
favorite VMD material settings? John Stone (Fri Aug 11 2006 - 14:47:18 CDT)
Alignment Python Per Jr. Greisen (Fri Aug 11 2006 - 05:19:15 CDT)
test versions of VMD 1.8.5 -DLPOLY Javier Sacristan (Thu Aug 10 2006 - 11:44:43 CDT)
- Re: test versions of VMD 1.8.5 -DLPOLY John Stone (Thu Aug 10 2006 - 11:51:38 CDT)
Compiling VMD with full OpenGL Marc Baaden (Thu Aug 10 2006 - 07:21:10 CDT)
- Re: Compiling VMD with full OpenGL John Stone (Thu Aug 10 2006 - 11:09:35 CDT)
  - Re: Compiling VMD with full OpenGL Marc Baaden (Thu Aug 10 2006 - 16:35:36 CDT)
    - Re: Compiling VMD with full OpenGL John Stone (Thu Aug 10 2006 - 17:08:48 CDT)
visualization code Hai-Jun Su (Wed Aug 09 2006 - 22:31:00 CDT)
- Re: visualization code John Stone (Wed Aug 09 2006 - 22:45:06 CDT)
- Re: visualization code Axel Kohlmeyer (Thu Aug 10 2006 - 00:00:11 CDT)
making movie from GROMACS trajectory Arindam Ganguly (Wed Aug 09 2006 - 18:05:36 CDT)
- Re: making movie from GROMACS trajectory John Stone (Wed Aug 09 2006 - 20:27:25 CDT)
  - Re: making movie from GROMACS trajectory Arindam Ganguly (Thu Aug 17 2006 - 15:43:43 CDT)
SASA calculation for a trajectory Gaurav Sharma (Tue Aug 08 2006 - 20:50:32 CDT)
- Re: SASA calculation for a trajectory L. Michel Espinoza-Fonseca (Tue Aug 08 2006 - 21:31:51 CDT)
(no subject) Hai-Jun Su (Tue Aug 08 2006 - 10:30:27 CDT)
- Re: John Stone (Tue Aug 08 2006 - 11:08:08 CDT)
Which VMD executible to use? Jeffrey A Tibbitt (Tue Aug 08 2006 - 10:06:44 CDT)
- Re: Which VMD executible to use? Axel Kohlmeyer (Tue Aug 08 2006 - 10:54:22 CDT)
water model used for the waterbox in VMD Vlad Cojocaru (Tue Aug 08 2006 - 08:32:07 CDT)
- Re: water model used for the waterbox in VMD Axel Kohlmeyer (Tue Aug 08 2006 - 09:22:13 CDT)
RE: No stereo display support in Windows Vista... Warren DeLano (Mon Aug 07 2006 - 22:06:10 CDT)
- Re: No stereo display support in Windows Vista... John Stone (Mon Aug 07 2006 - 23:38:02 CDT)
  - Re: No stereo display support in Windows Vista... Marc Baaden (Tue Aug 08 2006 - 02:11:28 CDT)
    - Re: No stereo display support in Windows Vista... John Stone (Tue Aug 08 2006 - 11:26:07 CDT)
No stereo display support in Windows Vista... John Stone (Mon Aug 07 2006 - 12:52:00 CDT)
To display only certain regions of the .dx map in VMD Shirley Li (Mon Aug 07 2006 - 12:01:05 CDT)
- Re: To display only certain regions of the .dx map in VMD Axel Kohlmeyer (Mon Aug 07 2006 - 13:35:43 CDT)
  - Re: To display only certain regions of the .dx map in VMD Shirley Li (Fri Aug 11 2006 - 09:26:11 CDT)
loading trajectory file Arturas Ziemys (Mon Aug 07 2006 - 11:38:34 CDT)
- Re: loading trajectory file John Stone (Mon Aug 07 2006 - 11:46:34 CDT)
  - Periodic builder? andras.borosy_at_givaudan.com (Tue Aug 08 2006 - 07:26:51 CDT)
    - Re: Periodic builder? John Stone (Wed Aug 09 2006 - 13:36:16 CDT)
Atom selection based on arbitrary columns in the pdb file Shatadal Ghosh (Sat Aug 05 2006 - 11:04:57 CDT)
- Re: Atom selection based on arbitrary columns in the pdb file Axel Kohlmeyer (Sat Aug 05 2006 - 12:05:51 CDT)
  - Re: Atom selection based on arbitrary columns in the pdb file Peter Freddolino (Sat Aug 05 2006 - 15:17:21 CDT)
VASP plugins Jennifer Lardge (Thu Aug 03 2006 - 07:21:42 CDT)
- Re: VASP plugins Axel Kohlmeyer (Thu Aug 03 2006 - 09:42:01 CDT)
Cannot run IED! :( Peng Tao (Wed Aug 02 2006 - 21:13:04 CDT)
- Re: Cannot run IED! :( John Stone (Wed Aug 02 2006 - 21:53:55 CDT)
2006 VMD user survey in progress John Stone (Wed Aug 02 2006 - 18:05:13 CDT)
about maximum number of atoms L. Michel Espinoza-Fonseca (Wed Aug 02 2006 - 15:25:41 CDT)
- Re: about maximum number of atoms John Stone (Wed Aug 02 2006 - 15:39:50 CDT)
  - Re: about maximum number of atoms L. Michel Espinoza-Fonseca (Wed Aug 02 2006 - 16:41:16 CDT)
- Re: about maximum number of atoms Brian Bennion (Wed Aug 02 2006 - 17:55:28 CDT)
rendering..... Viswanadham Sridhara (Mon Jul 31 2006 - 14:39:51 CDT)
- Re: rendering..... John Stone (Mon Jul 31 2006 - 17:39:15 CDT)
  - Re: rendering..... Viswanadham Sridhara (Mon Jul 31 2006 - 17:41:26 CDT)
- Re: rendering..... Axel Kohlmeyer (Mon Jul 31 2006 - 17:58:57 CDT)
Altering Definition of Molecular Coloring Method Adrian Koh (Mon Jul 31 2006 - 05:08:56 CDT)
- Re: Altering Definition of Molecular Coloring Method Peter Freddolino (Mon Jul 31 2006 - 09:05:16 CDT)
  - Re: Altering Definition of Molecular Coloring Method Adrian Koh (Mon Jul 31 2006 - 23:18:19 CDT)
    - Re: Altering Definition of Molecular Coloring Method Axel Kohlmeyer (Tue Aug 01 2006 - 07:29:44 CDT)
Latest list of VMD citations John Stone (Wed Jul 26 2006 - 15:58:09 CDT)
where is option "Image Smoothing"? Hu Zhongqiao (Wed Jul 26 2006 - 00:30:07 CDT)
- Re: where is option "Image Smoothing"? Axel Kohlmeyer (Wed Jul 26 2006 - 06:31:32 CDT)
DL_POLY output files Viswanadham Sridhara (Tue Jul 25 2006 - 15:31:08 CDT)
- Re: DL_POLY output files John Stone (Tue Jul 25 2006 - 15:59:58 CDT)
trajectory file format Jonathan Ashar (Tue Jul 25 2006 - 12:31:00 CDT)
- Re: trajectory file format John Stone (Tue Jul 25 2006 - 12:39:40 CDT)
Unable to ionize a solvated structure using autoionization Jose Dinto (Mon Jul 24 2006 - 09:56:41 CDT)
- Re: Unable to ionize a solvated structure using autoionization John Stone (Mon Jul 24 2006 - 11:59:11 CDT)
Rendering surfaces from PLT files Sergio Urahata (Sat Jul 22 2006 - 16:50:02 CDT)
- Re: Rendering surfaces from PLT files Axel Kohlmeyer (Sun Jul 23 2006 - 00:30:08 CDT)
  - Re: Rendering surfaces from PLT files Sergio Urahata (Mon Jul 24 2006 - 11:28:07 CDT)
some parameters for TIP3P Margaret Shun Cheung (Fri Jul 21 2006 - 14:48:33 CDT)
- Re: some parameters for TIP3P Giovanni Bellesia (Fri Jul 21 2006 - 16:34:57 CDT)
  - Re: some parameters for TIP3P Margaret Shun Cheung (Fri Jul 21 2006 - 16:42:29 CDT)
    - Re: some parameters for TIP3P Axel Kohlmeyer (Fri Jul 21 2006 - 18:25:19 CDT)
- Re: some parameters for TIP3P Justin Gullingsrud (Fri Jul 21 2006 - 16:36:53 CDT)
- Re: some parameters for TIP3P Axel Kohlmeyer (Fri Jul 21 2006 - 16:38:07 CDT)
vmd-l digest V1 #579 vmd-l digest (Mon Jul 17 2006 - 15:51:45 CDT)
- RE: vmd-l digest V1 #579 Mark Harder (Wed Jul 19 2006 - 21:09:08 CDT)
  - Re: RE: vmd-l digest V1 #579 Christoph Weber (Thu Jul 20 2006 - 17:19:08 CDT)
AMBER9 netcdf trajectory loading Fabian Boes (Fri Jul 21 2006 - 08:00:30 CDT)
- Re: AMBER9 netcdf trajectory loading John Stone (Wed Jul 26 2006 - 13:27:37 CDT)
temp autocorrelation Swarna Patra (Fri Jul 21 2006 - 00:56:37 CDT)
psf for already hydrogen-added structure hori koshii (Thu Jul 20 2006 - 15:09:14 CDT)
- Re: psf for already hydrogen-added structure Peter Freddolino (Thu Jul 20 2006 - 20:22:05 CDT)
NAMD unit cell data Peter Jones (Thu Jul 20 2006 - 00:43:24 CDT)
Mesa rendering Olaf Lenz (Thu Jul 20 2006 - 07:56:26 CDT)
- Re: Mesa rendering Axel Kohlmeyer (Thu Jul 20 2006 - 08:27:31 CDT)
RE: Atomselection for negative values Chang, Christopher (Wed Jul 19 2006 - 17:46:15 CDT)
Atomselection for negative values Chang, Christopher (Wed Jul 19 2006 - 16:18:39 CDT)
- Re: Atomselection for negative values John Stone (Wed Jul 19 2006 - 17:03:14 CDT)
"Unable to create OpenGL window" César Dp (Tue Jul 18 2006 - 15:20:55 CDT)
- Re: "Unable to create OpenGL window" Axel Kohlmeyer (Tue Jul 18 2006 - 15:41:35 CDT)
Reading Amber .crd files campen_at_geosc.psu.edu (Tue Jul 18 2006 - 12:25:17 CDT)
- Re: Reading Amber .crd files John Stone (Tue Jul 18 2006 - 12:38:26 CDT)
Reading Amber .prd and PARM files into VMD campen_at_geosc.psu.edu (Tue Jul 18 2006 - 08:32:37 CDT)
- Re: Reading Amber .prd and PARM files into VMD John Stone (Tue Jul 18 2006 - 12:37:27 CDT)
revised VMD tutorial Christoph Weber (Fri Jul 14 2006 - 19:03:44 CDT)
Selecting the "n" closest waters Gustavo Seabra (Thu Jul 13 2006 - 12:39:31 CDT)
- Re: Selecting the "n" closest waters John Stone (Thu Jul 13 2006 - 15:58:49 CDT)
  - Re: Selecting the "n" closest waters Gustavo Seabra (Thu Jul 13 2006 - 16:39:59 CDT)
    - Re: Selecting the "n" closest waters John Stone (Thu Jul 13 2006 - 16:53:32 CDT)
    - Re: Selecting the "n" closest waters Gustavo Seabra (Thu Jul 13 2006 - 16:59:58 CDT)
Anyone using ATI X1600? Yu Zhou (Thu Jul 13 2006 - 07:39:59 CDT)
- Re: Anyone using ATI X1600? John Stone (Thu Jul 13 2006 - 10:42:38 CDT)
  - Re: Anyone using ATI X1600? Christoph Weber (Fri Jul 14 2006 - 18:35:35 CDT)
  - Re: Anyone using ATI X1600? John Stone (Mon Jul 17 2006 - 11:17:25 CDT)
    - Re: Anyone using ATI X1600? Christoph Weber (Mon Jul 17 2006 - 16:18:00 CDT)
water selection Vlad Cojocaru (Thu Jul 13 2006 - 04:09:17 CDT)
- Re: water selection Vlad Cojocaru (Thu Jul 13 2006 - 04:44:31 CDT)
  - Re: water selection John Stone (Thu Jul 13 2006 - 10:46:37 CDT)
- Re: water selection Mgr. Lubos Vrbka (Thu Jul 13 2006 - 07:37:58 CDT)
  - Re: water selection John Stone (Thu Jul 13 2006 - 10:47:11 CDT)
residue no. greater than 9999 in pdb files created with VMD Vlad Cojocaru (Wed Jul 12 2006 - 10:56:16 CDT)
- Re: residue no. greater than 9999 in pdb files created with VMD John Stone (Wed Jul 12 2006 - 11:16:21 CDT)
  - Re: residue no. greater than 9999 in pdb files created with VMD Axel Kohlmeyer (Wed Jul 12 2006 - 11:42:42 CDT)
    - Re: residue no. greater than 9999 in pdb files created with VMD Vlad Cojocaru (Thu Jul 13 2006 - 03:57:28 CDT)
- Re: residue no. greater than 9999 in pdb files created with VMD JC Gumbart (Wed Jul 12 2006 - 11:24:34 CDT)
third time..can someone help!! hl332_at_drexel.edu (Tue Jul 11 2006 - 22:09:41 CDT)
- Re: third time..can someone help!! Peter Freddolino (Tue Jul 11 2006 - 23:45:30 CDT)
  - Re: third time..can someone help!! Peter Freddolino (Wed Jul 12 2006 - 01:57:31 CDT)
Feature request: output to Blender 3D modelling software Ralph Jimenez (Tue Jul 11 2006 - 10:32:31 CDT)
- Re: Feature request: output to Blender 3D modelling software John Stone (Tue Jul 11 2006 - 11:06:43 CDT)
  - Re: Feature request: output to Blender 3D modelling software Ralph Jimenez (Tue Jul 11 2006 - 14:19:30 CDT)
    - Re: Feature request: output to Blender 3D modelling software John Stone (Tue Jul 11 2006 - 16:18:23 CDT)
  - Re: Feature request: output to Blender 3D modelling software John Stone (Wed Jul 12 2006 - 00:07:45 CDT)
- Re: Feature request: output to Blender 3D modelling software Sabuj Pattanayek (Tue Jul 11 2006 - 13:19:33 CDT)
please, give me a tip Yuri Nedialkov (Tue Jul 11 2006 - 10:02:20 CDT)
- Re: please, give me a tip Leonardo Trabuco (Tue Jul 11 2006 - 11:05:57 CDT)
  - Re: please, give me a tip Axel Kohlmeyer (Tue Jul 11 2006 - 11:24:20 CDT)
lammps and vmd H Q (Mon Jul 10 2006 - 22:04:20 CDT)
- Re: lammps and vmd Axel Kohlmeyer (Tue Jul 11 2006 - 11:21:19 CDT)
Please, help Yuri Nedialkov (Mon Jul 10 2006 - 13:48:35 CDT)
- Re: Please, help Peter Freddolino (Mon Jul 10 2006 - 17:14:17 CDT)
updating display of atoms in contact Ting Wang (Mon Jul 10 2006 - 16:39:59 CDT)
- Re: updating display of atoms in contact Leonardo Trabuco (Mon Jul 10 2006 - 16:55:02 CDT)
- Re: updating display of atoms in contact Sergio Urahata (Mon Jul 10 2006 - 17:06:30 CDT)
Biometric Case Study Presentations Available (no charge), data mining and predictive modeling Lisa Solomon (Mon Jul 10 2006 - 12:22:37 CDT)
autoionize plugin.. hl332_at_drexel.edu (Mon Jul 10 2006 - 11:38:16 CDT)
namdenergy plugin Chandra Ramananjara (Sun Jul 09 2006 - 23:47:10 CDT)
- Re: namdenergy plugin Peter Freddolino (Mon Jul 10 2006 - 00:02:33 CDT)
  - Re: namdenergy plugin Peter Freddolino (Mon Jul 10 2006 - 00:08:12 CDT)
residue list of within ? distance Ting Wang (Thu Jul 06 2006 - 16:46:44 CDT)
- Re: residue list of within ? distance John Stone (Thu Jul 06 2006 - 16:52:59 CDT)
Queries on making polymer Naser, Md Abu (Thu Jul 06 2006 - 14:42:49 CDT)
- Re: Queries on making polymer John Stone (Fri Jul 07 2006 - 13:37:40 CDT)
VMD selection options and local density maps Urahata (Thu Jul 06 2006 - 14:39:22 CDT)
- Re: VMD selection options and local density maps John Stone (Fri Jul 07 2006 - 13:49:27 CDT)
VMD selection options and local density maps Urahata (Thu Jul 06 2006 - 13:06:53 CDT)
Missing atom error while atoms exist in pdb Rima Chaudhuri (Thu Jul 06 2006 - 11:05:50 CDT)
- Re: Missing atom error while atoms exist in pdb Peter Freddolino (Thu Jul 06 2006 - 11:27:45 CDT)
- Re: Missing atom error while atoms exist in pdb Peter Freddolino (Thu Jul 06 2006 - 11:33:04 CDT)
  - Re: Missing atom error while atoms exist in pdb Rima Chaudhuri (Thu Jul 06 2006 - 11:46:46 CDT)
    - Re: Missing atom error while atoms exist in pdb Peter Freddolino (Thu Jul 06 2006 - 13:12:39 CDT)
xyz animation Jayendra Balasubramanian (Thu Jul 06 2006 - 11:00:52 CDT)
- Re: xyz animation John Stone (Thu Jul 06 2006 - 12:56:46 CDT)
  - Re: xyz animation James Rustad (Thu Jul 06 2006 - 13:19:21 CDT)
VMD as background job on multiprocessor machine doesn't work? Jan Saam (Wed Jul 05 2006 - 19:46:13 CDT)
- Re: VMD as background job on multiprocessor machine doesn't work? John Stone (Thu Jul 06 2006 - 13:00:57 CDT)
pdb file reading error Rima Chaudhuri (Wed Jul 05 2006 - 12:16:59 CDT)
3Dconnexion SpaceTraveler works Eugen Leitl (Wed Jul 05 2006 - 08:21:00 CDT)
- Re: 3Dconnexion SpaceTraveler works John Stone (Thu Jul 06 2006 - 13:21:22 CDT)
  - Re: 3Dconnexion SpaceTraveler works Eugen Leitl (Fri Jul 14 2006 - 03:43:21 CDT)
3Dconnexion SpaceTraveler works Eugen Leitl (Wed Jul 05 2006 - 07:54:46 CDT)
Movie Maker in VMD Adrian Koh (Wed Jul 05 2006 - 04:30:49 CDT)
- Re: Movie Maker in VMD Alexandr Isayev (Wed Jul 05 2006 - 10:27:02 CDT)
  - Re: Movie Maker in VMD kohsj_at_ihpc.a-star.edu.sg (Wed Jul 05 2006 - 12:01:00 CDT)
  - Re: Movie Maker in VMD Josh Vermaas (Thu Jun 18 2020 - 20:54:48 CDT)
how to prevent molecule jump around Dongsheng Zhang (Wed Jul 05 2006 - 00:35:41 CDT)
- Re: how to prevent molecule jump around John Stone (Thu Jul 06 2006 - 13:19:08 CDT)
debug Vivek Sharma (Tue Jul 04 2006 - 01:07:20 CDT)
- Re: debug John Stone (Tue Jul 04 2006 - 22:43:57 CDT)
Trajectory Analysis Javad Azadi (Tue Jul 04 2006 - 11:14:36 CDT)
- Re: Trajectory Analysis John Stone (Tue Jul 04 2006 - 22:56:28 CDT)
Renaming Molecule Names in existing .xyz trajectory files Adrian Koh (Tue Jul 04 2006 - 01:44:28 CDT)
- Re: Renaming Molecule Names in existing .xyz trajectory files John Stone (Tue Jul 04 2006 - 22:37:09 CDT)
  - Re: Renaming Molecule Names in existing .xyz trajectory files Adrian Koh (Tue Jul 04 2006 - 23:07:57 CDT)
    - Re: Renaming Molecule Names in existing .xyz trajectory files John Stone (Tue Jul 04 2006 - 23:11:56 CDT)
movies on a mac Mark Lorch (Mon Jul 03 2006 - 10:13:49 CDT)
- Re: movies on a mac Axel Kohlmeyer (Mon Jul 03 2006 - 11:30:24 CDT)
Volume slices of Gaussian Cube Files: Color scale Berit Hinnemann (Thu Jun 29 2006 - 13:42:05 CDT)
- Re: Volume slices of Gaussian Cube Files: Color scale Axel Kohlmeyer (Thu Jun 29 2006 - 17:50:24 CDT)
Correlated motion Leyla Celik (Wed Jun 28 2006 - 11:19:27 CDT)
- Re: Correlated motion Axel Kohlmeyer (Wed Jun 28 2006 - 14:51:52 CDT)
How to color the atoms based on the stress Zhenyu Yang (Wed Jun 28 2006 - 02:17:09 CDT)
- Re: How to color the atoms based on the stress Axel Kohlmeyer (Wed Jun 28 2006 - 05:46:21 CDT)
coordinate translation ziemys_at_ecr6.ohio-state.edu (Tue Jun 27 2006 - 11:04:28 CDT)
- Re: coordinate translation John Stone (Tue Jun 27 2006 - 16:57:41 CDT)
VMD performance bottlenecks Sacerdoti, Federico (Tue Jun 27 2006 - 09:24:16 CDT)
- Re: VMD performance bottlenecks John Stone (Tue Jun 27 2006 - 17:00:26 CDT)
VMD crashed due to: vmd_LINUXAMD64: indirect_vertex_array.c:659: emit_DrawArrays_old: Assertion `elements_per_request >= count' failed Brett Pemberton (Tue Jun 27 2006 - 00:52:41 CDT)
- Re: VMD crashed due to: vmd_LINUXAMD64: indirect_vertex_array.c:659: emit_DrawArrays_old: Assertion `elements_per_request >= count' failed John Stone (Tue Jun 27 2006 - 17:15:03 CDT)
  - Re: VMD crashed due to: vmd_LINUXAMD64: indirect_vertex_array.c:659: emit_DrawArrays_old: Assertion `elements_per_request >= count' failed Brett Pemberton (Tue Jun 27 2006 - 18:57:15 CDT)
Tcl commands on Mac Oliver Inderwildi (Mon Jun 26 2006 - 17:51:15 CDT)
- Re: Tcl commands on Mac John Stone (Mon Jun 26 2006 - 18:01:55 CDT)
  - Re: Tcl commands on Mac Axel Kohlmeyer (Mon Jun 26 2006 - 18:32:57 CDT)
bonds forming during simulation Sandeep Prakash (Mon Jun 26 2006 - 12:59:50 CDT)
- Re: bonds forming during simulation John Stone (Mon Jun 26 2006 - 14:48:11 CDT)
to create simply a box of water molecules. Margaret Shun Cheung (Sat Jun 24 2006 - 19:46:11 CDT)
GLSL Compile Error (VMD 1.8.4, Nvidia Driver 8762) Hans Martin Senn (Mon Jun 26 2006 - 03:01:03 CDT)
- Re: GLSL Compile Error (VMD 1.8.4, Nvidia Driver 8762) Axel Kohlmeyer (Mon Jun 26 2006 - 06:28:22 CDT)
- Re: GLSL Compile Error (VMD 1.8.4, Nvidia Driver 8762) Hans Martin Senn (Mon Jun 26 2006 - 10:32:49 CDT)
  - Re: GLSL Compile Error (VMD 1.8.4, Nvidia Driver 8762) John Stone (Mon Jun 26 2006 - 11:22:48 CDT)
bond information in psf file Xu (Sat Jun 24 2006 - 20:51:27 CDT)
- Re: bond information in psf file Axel Kohlmeyer (Sat Jun 24 2006 - 22:51:13 CDT)
water box... ivana adamovic (Sat Jun 24 2006 - 08:37:57 CDT)
- Re: water box... Charles McCallum (Sat Jun 24 2006 - 18:24:16 CDT)
- Re: water box... John Stone (Mon Jun 26 2006 - 17:32:45 CDT)
- Re: water box... sstappa_at_uwm.edu (Thu Jul 06 2006 - 19:59:31 CDT)
a question about "measure fit" dwang_at_cs.kent.edu (Thu Jun 22 2006 - 20:36:59 CDT)
- Re: a question about "measure fit" John Stone (Fri Jun 23 2006 - 11:13:26 CDT)
problem with measure command Ana Celia Araujo Vila Verde (Fri Jun 23 2006 - 10:22:49 CDT)
- Re: problem with measure command John Stone (Fri Jun 23 2006 - 10:34:03 CDT)
  - Re: problem with measure command Ana Celia Araujo Vila Verde (Fri Jun 23 2006 - 11:02:14 CDT)
    - Re: problem with measure command John Stone (Fri Jun 23 2006 - 11:09:00 CDT)
psfgen Marcela Madrid (Thu Jun 22 2006 - 15:28:23 CDT)
- Re: psfgen John Stone (Thu Jun 22 2006 - 15:45:15 CDT)
- RE:psfgen lloyd riggs (Fri Sep 28 2012 - 08:49:12 CDT)
Is there any script to analyze radius gyration, center of mass of namd traj file dcd? Youyong Li (Thu Jun 22 2006 - 08:23:47 CDT)
- Re: Is there any script to analyze radius gyration, center of mass of namd traj file dcd? John Stone (Thu Jun 22 2006 - 14:07:45 CDT)
- Re: Is there any script to analyze radius gyration, center of mass of namd traj file dcd? Giovanni Bellesia (Thu Jun 22 2006 - 16:19:33 CDT)
error message occurred in RMSD Trajectory Tool Margaret Shun Cheung (Thu Jun 22 2006 - 11:28:10 CDT)
- Re: error message occurred in RMSD Trajectory Tool John Stone (Thu Jun 22 2006 - 13:53:37 CDT)
  - Re: error message occurred in RMSD Trajectory Tool John Stone (Thu Jun 22 2006 - 14:36:46 CDT)
    - Re: error message occurred in RMSD Trajectory Tool Margaret Shun Cheung (Thu Jun 22 2006 - 14:56:36 CDT)
error using Namdenergy Chandra Ramananjara (Wed Jun 21 2006 - 15:04:19 CDT)
- Re: error using Namdenergy Peter Freddolino (Wed Jun 21 2006 - 17:17:17 CDT)
  - Re: error using Namdenergy Chandra Ramananjara (Wed Jun 21 2006 - 19:55:01 CDT)
- .vmdrc Brian Kidd (Wed Jun 21 2006 - 18:26:48 CDT)
  - Re: .vmdrc John Stone (Thu Jun 22 2006 - 15:17:31 CDT)
(no subject) Hai-Jun Su (Wed Jun 21 2006 - 12:22:29 CDT)
- Re: John Stone (Wed Jun 21 2006 - 13:21:42 CDT)
Average Structure and RMSD griadi_at_utalca.cl (Wed Jun 21 2006 - 11:28:33 CDT)
- Re: Average Structure and RMSD John Stone (Wed Jun 21 2006 - 13:29:44 CDT)
align and superimpose crd structures. Margaret Shun Cheung (Wed Jun 21 2006 - 09:12:37 CDT)
- Re: align and superimpose crd structures. John Stone (Wed Jun 21 2006 - 13:32:33 CDT)
  - Re: align and superimpose crd structures. John Stone (Wed Jun 21 2006 - 13:34:48 CDT)
    - Re: align and superimpose crd structures. Margaret Shun Cheung (Wed Jun 21 2006 - 13:47:56 CDT)
  - Re: align and superimpose crd structures. Margaret Shun Cheung (Wed Jun 21 2006 - 17:02:10 CDT)
    - Re: align and superimpose crd structures. John Stone (Wed Jun 21 2006 - 17:03:38 CDT)
    - Re: align and superimpose crd structures. Margaret Shun Cheung (Wed Jun 21 2006 - 17:16:41 CDT)
RMSF ? ziemys_at_ecr6.ohio-state.edu (Tue Jun 20 2006 - 15:33:32 CDT)
- Re: RMSF ? John Stone (Tue Jun 20 2006 - 16:13:57 CDT)
  - Re: RMSF ? Brian Bennion (Wed Jun 21 2006 - 10:10:08 CDT)
Making a Movie Joanne Hanna (Tue Jun 20 2006 - 09:38:06 CDT)
- Re: Making a Movie Karsten SUHRE (Tue Jun 20 2006 - 12:46:06 CDT)
- Re: Making a Movie Alexandr Isayev (Tue Jun 20 2006 - 13:07:45 CDT)
- Re: Making a Movie John Stone (Tue Jun 20 2006 - 16:21:31 CDT)
Compiling problem angel (Mon Jun 19 2006 - 14:23:04 CDT)
- Re: Compiling problem John Stone (Mon Jun 19 2006 - 14:46:57 CDT)
VMD crashed due to: vmd_LINUXAMD64: indirect_vertex_array.c:659: emit_DrawArrays_old: Assertion `elements_per_request >= count' failed Jinhua Zhang (Mon Jun 19 2006 - 13:28:18 CDT)
- Re: VMD crashed due to: vmd_LINUXAMD64: indirect_vertex_array.c:659: emit_DrawArrays_old: Assertion `elements_per_request >= count' failed John Stone (Mon Jun 19 2006 - 14:43:06 CDT)
Re: vmd display problem Dongsheng Zhang (Mon Jun 19 2006 - 13:17:23 CDT)
Compilation propblem angel (Mon Jun 19 2006 - 12:26:52 CDT)
- Re: Compilation propblem John Stone (Mon Jun 19 2006 - 13:19:16 CDT)
vmd display problem Dongsheng Zhang (Sun Jun 18 2006 - 22:04:53 CDT)
the python library error in VMD when do IED Shulin Zhuang (Thu Jun 15 2006 - 20:40:23 CDT)
- Re: the python library error in VMD when do IED Shulin Zhuang (Thu Jun 15 2006 - 20:55:56 CDT)
- Re: the python library error in VMD when do IED John Stone (Mon Jun 19 2006 - 15:55:13 CDT)
  - Re: the python library error in VMD when do IED Shulin Zhuang (Tue Jun 20 2006 - 01:35:20 CDT)
problem in minimization while running Moumita Maiti (Thu Jun 15 2006 - 15:59:50 CDT)
- Re: problem in minimization while running Peter Freddolino (Thu Jun 15 2006 - 16:06:09 CDT)
psfgen: last CTER does not work Morad Alawneh (Thu Jun 15 2006 - 14:30:14 CDT)
- Re: psfgen: last CTER does not work Peter Freddolino (Thu Jun 15 2006 - 14:35:02 CDT)
error Autoimd Juan de Dios Lopez Castro (Thu Jun 15 2006 - 04:04:02 CDT)
- Re: error Autoimd John Stone (Thu Jun 15 2006 - 15:38:23 CDT)
  - pdbalias not working Samuel C Flores (Thu Jun 15 2006 - 21:42:06 CDT)
    - Re: pdbalias not working John Stone (Wed Jun 21 2006 - 13:55:41 CDT)
    - RE: pdbalias not working Samuel C Flores (Wed Jun 21 2006 - 14:12:41 CDT)
- Re: error Autoimd John Stone (Wed Jun 21 2006 - 14:24:27 CDT)
user-defined movie Ting Wang (Wed Jun 14 2006 - 16:44:22 CDT)
- Re: user-defined movie John Stone (Wed Jun 14 2006 - 16:58:09 CDT)
how to change paramters in making movie Dongsheng Zhang (Wed Jun 14 2006 - 12:33:09 CDT)
- Re: how to change paramters in making movie John Stone (Wed Jun 14 2006 - 13:45:14 CDT)
the patching problem in psfgen Moumita Maiti (Wed Jun 14 2006 - 06:13:20 CDT)
- Re: namd-l: the patching problem in psfgen Leonardo G. Trabuco (Wed Jun 14 2006 - 13:09:36 CDT)
RMSD of not fitted region Ting Wang (Mon Jun 12 2006 - 19:24:02 CDT)
- Re: RMSD of not fitted region John Stone (Tue Jun 13 2006 - 11:17:07 CDT)
fading rep scripts Brian Bennion (Mon Jun 12 2006 - 16:41:38 CDT)
- Re: fading rep scripts John Stone (Mon Jun 12 2006 - 17:43:59 CDT)
(no subject) Zara Sands (Mon Jun 12 2006 - 06:36:34 CDT)
- Re: (no subject) John Stone (Tue Jun 13 2006 - 11:47:30 CDT)
missing" Number of frames to render" in VMD window movie generator pkb bioinfo (Mon Jun 12 2006 - 05:39:40 CDT)
- Re: missing" Number of frames to render" in VMD window movie generator John Stone (Tue Jun 13 2006 - 11:51:15 CDT)
python - writes frames to pdb files Per Jr. Greisen (Sat Jun 10 2006 - 06:19:11 CDT)
- Re: python - writes frames to pdb files John Stone (Tue Jun 13 2006 - 15:51:24 CDT)
animate with varying atom numbers Rene (Fri Jun 09 2006 - 12:53:59 CDT)
- Re: animate with varying atom numbers Axel Kohlmeyer (Sat Jun 10 2006 - 04:55:47 CDT)
RMSD Calculator Tamal Banerjee (Thu Jun 08 2006 - 08:37:43 CDT)
- Re: RMSD Calculator Luis Gracia (Thu Jun 08 2006 - 12:56:02 CDT)
membrane plugin (IRIX version) lothar esser (Wed Jun 07 2006 - 14:26:28 CDT)
- Re: membrane plugin (IRIX version) John Stone (Wed Jun 07 2006 - 14:42:43 CDT)
- color protein based on an event during a trajectory Brian Kidd (Wed Jun 07 2006 - 21:33:39 CDT)
  - Re: color protein based on an event during a trajectory Leonardo G. Trabuco (Wed Jun 07 2006 - 22:14:41 CDT)
  - Re: color protein based on an event during a trajectory Axel Kohlmeyer (Wed Jun 07 2006 - 23:24:40 CDT)
where's the download link for one specific plugin? JunJun Liu (Wed Jun 07 2006 - 12:26:41 CDT)
- Re: where's the download link for one specific plugin? Peter Freddolino (Wed Jun 07 2006 - 13:27:36 CDT)
Simple one-liner? Gustavo Seabra (Wed Jun 07 2006 - 10:56:02 CDT)
- Re: Simple one-liner? Peter Freddolino (Wed Jun 07 2006 - 10:59:49 CDT)
- Re: Simple one-liner? John Stone (Wed Jun 07 2006 - 11:11:23 CDT)
  - Re: Simple one-liner? Gustavo Seabra (Wed Jun 07 2006 - 12:24:03 CDT)
problem with installation Yuan Zhang (Wed Jun 07 2006 - 10:27:51 CDT)
- Re: problem with installation John Stone (Wed Jun 07 2006 - 11:02:06 CDT)
  - Re: problem with installation John Stone (Wed Jun 07 2006 - 11:32:52 CDT)
how to make movies from HISTORY file Come On (Tue Jun 06 2006 - 13:11:55 CDT)
- Re: how to make movies from HISTORY file John Stone (Tue Jun 06 2006 - 13:20:32 CDT)
  - Re: how to make movies from HISTORY file Come On (Wed Jun 07 2006 - 04:20:15 CDT)
    - Re: how to make movies from HISTORY file Axel Kohlmeyer (Wed Jun 07 2006 - 07:01:03 CDT)
(no subject) Sam Ansari (Tue Jun 06 2006 - 06:13:16 CDT)
- Re: John Stone (Tue Jun 06 2006 - 12:59:57 CDT)
  - Re: snoze pa (Tue Jun 06 2006 - 17:47:34 CDT)
Qtight=22?= selection ziemys_at_ecr6.ohio-state.edu (Mon Jun 05 2006 - 15:36:37 CDT)
- Re: "tight" selection John Stone (Tue Jun 06 2006 - 13:14:42 CDT)
vmd in fedora core 5 saravana prakash (Sun Jun 04 2006 - 07:39:16 CDT)
- Re: vmd in fedora core 5 John Stone (Mon Jun 05 2006 - 10:32:15 CDT)
Small molecules alignment with VMD Alexe Bojovschi (Sun Jun 04 2006 - 23:16:47 CDT)
- Re: Small molecules alignment with VMD John Stone (Mon Jun 05 2006 - 10:34:29 CDT)
- Re: Small molecules alignment with VMD L. Michel Espinoza-Fonseca (Mon Jun 05 2006 - 10:52:23 CDT)
Calculating RMSF plots without using scripts!!! Robert Selwyne (Mon Jun 05 2006 - 03:36:54 CDT)
the patch between segments for multiple chains molecule. Moumita Maiti (Fri Jun 02 2006 - 12:14:58 CDT)
- Re: namd-l: the patch between segments for multiple chains molecule. Leonardo G. Trabuco (Fri Jun 02 2006 - 13:09:23 CDT)
  - Re: namd-l: the patch between segments for multiple chains molecule. Moumita Maiti (Wed Jun 14 2006 - 06:21:09 CDT)
  - Re: namd-l: the patch between segments for multiple chains molecule. Leonardo G. Trabuco (Wed Jun 14 2006 - 12:57:42 CDT)
vmd 1.8.5 L. Michel Espinoza-Fonseca (Fri Jun 02 2006 - 12:14:46 CDT)
- Re: vmd 1.8.5 John Stone (Fri Jun 02 2006 - 12:24:19 CDT)
psf generation Moumita Maiti (Fri Jun 02 2006 - 11:56:17 CDT)
- Re: psf generation Leonardo G. Trabuco (Fri Jun 02 2006 - 13:22:41 CDT)
How to show 3D images in the display window of VMD ikek70 (Fri Jun 02 2006 - 11:15:20 CDT)
- Re: How to show 3D images in the display window of VMD John Stone (Fri Jun 02 2006 - 12:27:14 CDT)
Incomplete Display Vineet Pande (Fri Jun 02 2006 - 09:17:51 CDT)
- Re: Incomplete Display Leonardo G. Trabuco (Fri Jun 02 2006 - 13:24:25 CDT)
  - Re: Incomplete Display Vineet Pande (Sat Jun 03 2006 - 10:58:02 CDT)
Global Command to load 200 pdb files, without using script files Robert Selwyne (Fri Jun 02 2006 - 08:47:35 CDT)
- Re: Global Command to load 200 pdb files, without using script files Luis Gracia (Fri Jun 02 2006 - 11:35:53 CDT)
- Re: Global Command to load 200 pdb files, without using script files John Stone (Fri Jun 02 2006 - 11:52:30 CDT)
Problems with APBS Compatibility Vyom Sharma (Thu Jun 01 2006 - 17:34:04 CDT)
- Re: Problems with APBS Compatibility John Stone (Thu Jun 01 2006 - 18:01:15 CDT)
  - Re: Problems with APBS Compatibility Vyom Sharma (Thu Jun 01 2006 - 21:19:19 CDT)
    - Re: Problems with APBS Compatibility John Stone (Fri Jun 02 2006 - 13:40:55 CDT)
error. Autoimd Juan de Dios Lopez Castro (Thu Jun 01 2006 - 05:21:51 CDT)
- Re: error. Autoimd John Stone (Thu Jun 01 2006 - 12:46:38 CDT)
file bigger than 2GB snoze pa (Thu Jun 01 2006 - 10:35:04 CDT)
- Re: file bigger than 2GB John Stone (Thu Jun 01 2006 - 12:44:28 CDT)
simple plugin ikek70 (Wed May 31 2006 - 15:35:53 CDT)
- Re: simple plugin John Stone (Wed May 31 2006 - 16:25:08 CDT)
- Re: simple plugin John Stone (Thu Jun 01 2006 - 14:02:50 CDT)
NewCartoon and mol2 files David Chalmers (Wed May 31 2006 - 06:11:33 CDT)
- Re: NewCartoon and mol2 files John Stone (Wed May 31 2006 - 10:55:47 CDT)
  - Re: NewCartoon and mol2 files John Stone (Thu Jun 01 2006 - 12:36:29 CDT)
AMD64 vmd installation problems simon whitehead (Wed May 31 2006 - 04:41:36 CDT)
- Re: AMD64 vmd installation problems John Stone (Wed May 31 2006 - 10:38:54 CDT)
secondary structure assignment L. Michel Espinoza-Fonseca (Tue May 30 2006 - 16:53:51 CDT)
- Re: secondary structure assignment John Stone (Tue May 30 2006 - 17:01:24 CDT)
PDB CONECT Mihaly Mezei (Tue May 30 2006 - 15:26:36 CDT)
- Re: PDB CONECT John Stone (Tue May 30 2006 - 15:37:41 CDT)
contact between 2 residues L. Michel Espinoza-Fonseca (Tue May 30 2006 - 14:03:06 CDT)
- Re: contact between 2 residues John Stone (Tue May 30 2006 - 14:27:24 CDT)
disulphide bond Naser, Md Abu (Tue May 30 2006 - 13:09:43 CDT)
- Re: disulphide bond Peter Freddolino (Tue May 30 2006 - 13:38:20 CDT)
catDCD 4.0 and xplor Peter Jones (Mon May 29 2006 - 23:23:10 CDT)
- Re: catDCD 4.0 and xplor John Stone (Tue May 30 2006 - 15:41:02 CDT)
how to save a structure after alignment? Guo Zhi (Sun May 28 2006 - 04:33:44 CDT)
- Re: how to save a structure after alignment? John Stone (Tue May 30 2006 - 17:32:24 CDT)
paratool ? Monique Laberge (Fri May 26 2006 - 19:19:35 CDT)
- Re: paratool ? John Stone (Fri May 26 2006 - 21:16:21 CDT)
Re: (ç‘žæ˜Ÿæç¤º-æ¤é‚®ä»¶å¯èƒ½æ˜¯åžƒåœ¾é‚®ä»¶)Re: gamess plugin error when using symmetry operations mashaojienuaa (Fri May 26 2006 - 20:49:03 CDT)
vmd on opteron Leandro Martínez (Fri May 26 2006 - 15:01:30 CDT)
- Re: vmd on opteron John Stone (Fri May 26 2006 - 15:12:12 CDT)
  - Re: vmd on opteron Leandro Martínez (Fri May 26 2006 - 15:20:54 CDT)
extended xyz Ioana Cozmuta (Fri May 26 2006 - 10:57:03 CDT)
- Re: extended xyz John Stone (Wed May 31 2006 - 16:38:03 CDT)
  - Re: extended xyz John Stone (Wed May 31 2006 - 16:42:07 CDT)
number of frames in pdb file? Samuel Flores (Thu May 25 2006 - 20:08:23 CDT)
- never mind .. got it Samuel Flores (Thu May 25 2006 - 21:02:47 CDT)
- Re: number of frames in pdb file? andrea spitaleri (Fri May 26 2006 - 03:01:41 CDT)
Re: the crystal structure of gold: questions about making the psf and about visualization in VMD; John Stone (Thu May 25 2006 - 14:48:50 CDT)
VolMap use !! Xavier Periole (Thu May 25 2006 - 13:07:42 CDT)
something about simulation of small molecules in NAMD q=CF=20=B3=C2?= (Thu May 25 2006 - 05:02:31 CDT)
- Re: something about simulation of small molecules in NAMD John Stone (Thu May 25 2006 - 14:20:40 CDT)
Fw: (ÈðÐÇÌáÊ¾-´ËÓÊ¼þ¿ÉÄÜÊÇÀ¬»øÓÊ¼þ)Re: gamess plugin error when using symmetry operations mashaojienuaa (Thu May 25 2006 - 01:56:08 CDT)
- Re: Fw: (ÈðÐÇÌáÊ¾-´ËÓÊ¼þ¿ÉÄÜÊÇÀ¬»øÓÊ¼þ)Re: vmd-lQ?= gamess plugin error when using symmetry operations John Stone (Thu May 25 2006 - 14:17:20 CDT)
color by charge (can colors be changed?) Jeffrey A Tibbitt (Thu May 25 2006 - 01:14:37 CDT)
- Re: color by charge (can colors be changed?) Axel Kohlmeyer (Thu May 25 2006 - 05:02:29 CDT)
RE: change default drawing and coloring method Habib.Alehossein_at_csiro.au (Wed May 24 2006 - 22:52:36 CDT)
- RE: change default drawing and coloring method Axel Kohlmeyer (Thu May 25 2006 - 05:06:12 CDT)
Compilation angel (Wed May 24 2006 - 17:44:39 CDT)
- Re: Compilation Axel Kohlmeyer (Thu May 25 2006 - 05:20:42 CDT)
- Re: Compilation John Stone (Thu May 25 2006 - 14:24:57 CDT)
- Re: Compilation John Stone (Thu May 25 2006 - 14:31:03 CDT)
  - Re: Compilation John Stone (Thu May 25 2006 - 14:35:31 CDT)
data file extensions Kurt Smith (Wed May 24 2006 - 11:41:21 CDT)
- Re: data file extensions John Stone (Wed May 24 2006 - 13:04:16 CDT)
rmsf Leyla Celik (Wed May 24 2006 - 06:07:55 CDT)
- Re: rmsf John Stone (Thu May 25 2006 - 14:54:21 CDT)
  - RE: rmsf Samuel Flores (Thu May 25 2006 - 20:02:44 CDT)
xyz files into dcd trajectory Ioana Cozmuta (Tue May 23 2006 - 18:55:51 CDT)
- Re: xyz files into dcd trajectory John Stone (Wed May 24 2006 - 13:00:34 CDT)
  - Re: xyz files into dcd trajectory Ioana Cozmuta (Wed May 24 2006 - 15:38:54 CDT)
the crystal structure of gold: questions about making the psf and about visualization in VMD; update Ana Celia Araujo Vila Verde (Tue May 23 2006 - 14:47:00 CDT)
- Re: the crystal structure of gold: questions about making the psf and about visualization in VMD; update John Stone (Tue May 23 2006 - 14:56:30 CDT)
installation problem: InstallShield ganderle_at_optonline.net (Tue May 23 2006 - 14:26:50 CDT)
- Re: installation problem: InstallShield John Stone (Tue May 23 2006 - 14:39:44 CDT)
How to make bold font? Gustavo Seabra (Tue May 23 2006 - 13:40:02 CDT)
- Re: How to make bold font? John Stone (Tue May 23 2006 - 13:59:41 CDT)
  - Re: How to make bold font? Dow Hurst DPHURST (Thu Jun 01 2006 - 09:12:20 CDT)
    - Re: How to make bold font? John Stone (Thu Jun 01 2006 - 15:28:27 CDT)
    - Re: How to make bold font? Robert Brunner (Thu Jun 01 2006 - 23:04:12 CDT)
the crystal structure of gold: questions about making the psf and about visualization in VMD Ana Celia Araujo Vila Verde (Tue May 23 2006 - 11:36:54 CDT)
gamess plugin error when using symmetry operations mashaojienuaa (Tue May 23 2006 - 10:02:36 CDT)
- Re: gamess plugin error when using symmetry operations John Stone (Tue May 23 2006 - 13:02:30 CDT)
change default drawing and coloring method Christian Fufezan (Mon May 22 2006 - 19:08:17 CDT)
- Re: change default drawing and coloring method Axel Kohlmeyer (Mon May 22 2006 - 23:29:51 CDT)
  - Re: change default drawing and coloring method Ch. Fufezan (Tue May 23 2006 - 09:26:52 CDT)
  - Re: change default drawing and coloring method Jian Zou (Tue May 23 2006 - 22:16:49 CDT)
    - Re: change default drawing and coloring method John Stone (Wed May 24 2006 - 16:28:51 CDT)
    - Re: change default drawing and coloring method Jian Zou (Wed May 24 2006 - 20:44:06 CDT)
Gaussian Cube file with VMD Berit Hinnemann (Mon May 22 2006 - 18:29:12 CDT)
- Re: Gaussian Cube file with VMD Axel Kohlmeyer (Mon May 22 2006 - 23:25:18 CDT)
  - RE: Gaussian Cube file with VMD Berit Hinnemann (Tue May 23 2006 - 11:00:36 CDT)
    - Re: Gaussian Cube file with VMD John Stone (Tue May 23 2006 - 13:14:29 CDT)
    - RE: Gaussian Cube file with VMD Axel Kohlmeyer (Tue May 23 2006 - 15:34:04 CDT)
split snoze pa (Mon May 22 2006 - 14:43:32 CDT)
RE: Solutions for stereo - is CRT technology dead? Warren DeLano (Mon May 22 2006 - 12:34:56 CDT)
Stereo VMD on Mac G5 Kim, Kwiseon (Mon May 22 2006 - 12:05:23 CDT)
- Re: Stereo VMD on Mac G5 John Stone (Mon May 22 2006 - 16:13:42 CDT)
Solutions for stereo - is CRT technology dead? Marc Baaden (Mon May 22 2006 - 04:33:17 CDT)
- Re: Solutions for stereo - is CRT technology dead? Bogdan Costescu (Mon May 22 2006 - 06:27:49 CDT)
  - Re: Solutions for stereo - is CRT technology dead? Benjamin Goldsteen (Mon May 22 2006 - 11:15:44 CDT)
- Re: Solutions for stereo - is CRT technology dead? Eugen Leitl (Mon May 22 2006 - 07:03:57 CDT)
- Re: Solutions for stereo - is CRT technology dead? John Stone (Mon May 22 2006 - 10:54:02 CDT)
redhat linux vmd a a (Mon May 22 2006 - 03:51:59 CDT)
- Re: redhat linux vmd John Stone (Mon May 22 2006 - 16:19:39 CDT)
  - Re: redhat linux vmd a a (Mon May 22 2006 - 21:18:43 CDT)
    - Re: redhat linux vmd John Stone (Tue May 23 2006 - 13:09:02 CDT)
- Segmentation fault when trying to load GROMACS trajectories Arneh Babakhani (Mon Jun 12 2006 - 11:47:06 CDT)
  - Re: Segmentation fault when trying to load GROMACS trajectories John Stone (Mon Jun 12 2006 - 13:42:26 CDT)
    - Re: Segmentation fault when trying to load GROMACS trajectories Arneh Babakhani (Mon Jun 12 2006 - 14:10:19 CDT)
gamess plugin error when using symmetry operations mashaojienuaa (Sun May 21 2006 - 21:12:20 CDT)
scrolling up in vmd console Kenley Barrett (Sun May 21 2006 - 13:37:04 CDT)
- Re: scrolling up in vmd console John Stone (Mon May 22 2006 - 15:18:01 CDT)
how to enable the vmd cachemode in .vmdrc? Guo Zhi (Sun May 21 2006 - 02:25:38 CDT)
- Re: how to enable the vmd cachemode in .vmdrc? John Stone (Mon May 22 2006 - 15:15:57 CDT)
How do I change details of a drawing style using the text interface? Dr. Seth Olsen (Fri May 19 2006 - 21:52:05 CDT)
- Re: How do I change details of a drawing style using the text interface? John Stone (Mon May 22 2006 - 17:52:31 CDT)
Plugin compilation problem angel (Thu May 18 2006 - 17:41:16 CDT)
- Re: Plugin compilation problem John Stone (Thu May 18 2006 - 17:57:48 CDT)
reporting various NVidia driver bugs... John Stone (Thu May 18 2006 - 16:14:43 CDT)
water molecules in residue interaction genie lfs (Thu May 18 2006 - 06:12:53 CDT)
- Re: water molecules in residue interaction John Stone (Fri May 19 2006 - 11:50:07 CDT)
reading DLPoly VMD 1.8.4 Javier Sacristan (Wed May 17 2006 - 17:55:26 CDT)
- Re: reading DLPoly VMD 1.8.4 John Stone (Thu May 18 2006 - 11:42:17 CDT)
  - Re: reading DLPoly VMD 1.8.4 Mgr. Lubos Vrbka (Thu May 18 2006 - 14:40:41 CDT)
    - Re: reading DLPoly VMD 1.8.4 John Stone (Fri May 19 2006 - 15:28:44 CDT)
    - Re: reading DLPoly VMD 1.8.4 Mgr. Lubos Vrbka (Sat May 20 2006 - 04:24:10 CDT)
How to make a disulphide bond lily jin (Tue May 16 2006 - 13:02:51 CDT)
- Re: How to make a disulphide bond John Stone (Tue May 16 2006 - 13:12:42 CDT)
- Re: namd-l: How to make a disulphide bond Charles Danko (Tue May 16 2006 - 13:47:37 CDT)
Multiple data files on command line does not seem to work Rob (Mon May 15 2006 - 22:36:09 CDT)
- Re: Multiple data files on command line does not seem to work John Stone (Tue May 16 2006 - 10:58:05 CDT)
measure avpos ziemys_at_ecr6.ohio-state.edu (Mon May 15 2006 - 14:43:28 CDT)
- Re: measure avpos Luis Gracia (Mon May 15 2006 - 17:53:28 CDT)
Plugin compilation angel (Fri May 12 2006 - 16:19:47 CDT)
- Re: Plugin compilation John Stone (Mon May 15 2006 - 12:13:49 CDT)
  - Re: Plugin compilation Axel Kohlmeyer (Mon May 15 2006 - 13:07:50 CDT)
NAMD support for MNDO semi-empirical model Chandra Ramananjara (Mon May 15 2006 - 10:34:07 CDT)
skip frames in dcd file=> no effect? M. Emal Alekozai (Mon May 15 2006 - 06:58:09 CDT)
- Re: skip frames in dcd file=> no effect? Leonardo G. Trabuco (Mon May 15 2006 - 07:50:50 CDT)
  - Re: skip frames in dcd file=> no effect? Marc Q. Ma (Mon May 15 2006 - 09:19:14 CDT)
    - Re: skip frames in dcd file=> no effect? Leonardo G. Trabuco (Mon May 15 2006 - 09:27:47 CDT)
    - Re: skip frames in dcd file=> no effect? Peter Freddolino (Mon May 15 2006 - 09:35:43 CDT)
- Re: skip frames in dcd file=> no effect? M. Emal Alekozai (Thu May 18 2006 - 06:34:08 CDT)
secondary structure assignment Melquiond (Sun May 14 2006 - 15:34:43 CDT)
- Re: secondary structure assignment Axel Kohlmeyer (Mon May 15 2006 - 04:52:05 CDT)
  - Re: secondary structure assignment Melquiond (Mon Jul 17 2006 - 09:23:03 CDT)
Gamepads and VMD (and MacOSX and ForceFeedback) Marc Baaden (Fri May 12 2006 - 10:13:46 CDT)
- Re: Gamepads and VMD (and MacOSX and ForceFeedback) John Stone (Mon May 15 2006 - 12:04:35 CDT)
ati interlace mode Osmany guirola Cruz (Fri May 12 2006 - 12:12:42 CDT)
- Re: ati interlace mode John Stone (Mon May 15 2006 - 12:01:50 CDT)
  - Re: ati interlace mode Osmany guirola Cruz (Mon May 15 2006 - 10:03:44 CDT)
wraping two chains from a simulation L. Michel Espinoza-Fonseca (Fri May 12 2006 - 02:40:59 CDT)
- Re: wraping two chains from a simulation John Stone (Mon May 15 2006 - 12:39:30 CDT)
psfgen for lipid Ting Wang (Thu May 11 2006 - 15:09:07 CDT)
bug in membrane plugin Ting Wang (Thu May 11 2006 - 13:47:11 CDT)
- high resolution images Samuel Flores (Thu May 11 2006 - 17:41:12 CDT)
  - Re: high resolution images Axel Kohlmeyer (Thu May 11 2006 - 18:18:10 CDT)
    - Axel RE: high resolution images Samuel Flores (Fri May 19 2006 - 15:15:12 CDT)
    - Re: Axel RE: high resolution images John Stone (Fri May 19 2006 - 15:30:13 CDT)
- Re: bug in membrane plugin John Stone (Mon May 15 2006 - 12:33:29 CDT)
  - Re: bug in membrane plugin Axel Kohlmeyer (Mon May 15 2006 - 13:44:00 CDT)
  - Re: bug in membrane plugin Ting Wang (Wed May 17 2006 - 13:52:21 CDT)
renderman output? Ralph Jimenez (Wed May 10 2006 - 15:50:47 CDT)
- Re: renderman output? Axel Kohlmeyer (Wed May 10 2006 - 19:37:19 CDT)
How to select water near a certain residue if it is outside of the water box? TZU-LAN YEH (Wed May 10 2006 - 00:11:26 CDT)
- Re: How to select water near a certain residue if it is outside of the water box? Eduard Schreiner (Wed May 10 2006 - 04:22:34 CDT)
  - Re: How to select water near a certain residue if it is outside of the water box? TZU-LAN YEH (Sat May 13 2006 - 11:04:20 CDT)
    - Re: How to select water near a certain residue if it is outside of the water box? Axel Kohlmeyer (Sat May 13 2006 - 18:11:27 CDT)
- Re: How to select water near a certain residue if it is outside of the water box? Mgr. Lubos Vrbka (Wed May 10 2006 - 05:52:32 CDT)
Display the electrostatic character (delphimap) on the structure file Eric Hajjar (Tue May 09 2006 - 05:18:37 CDT)
- Re: Display the electrostatic character (delphimap) on the structure file John Stone (Tue May 09 2006 - 09:25:09 CDT)
  - Re: Display the electrostatic character (delphimap) on the structure file Eric Hajjar (Thu May 11 2006 - 01:18:54 CDT)
How to access the subset after 'fit' and 'move' ? ziemys_at_ecr6.ohio-state.edu (Mon May 08 2006 - 09:50:55 CDT)
- Re: How to access the subset after 'fit' and 'move' ? John Stone (Mon May 08 2006 - 18:21:19 CDT)
(no subject) ziemys_at_ecr6.ohio-state.edu (Mon May 08 2006 - 09:41:21 CDT)
How to pick up the lost periodic information? Guo Zhi (Sun May 07 2006 - 10:32:16 CDT)
- Fwd: How to pick up the lost periodic information? Guo Zhi (Mon May 08 2006 - 09:04:46 CDT)
  - Re: Fwd: How to pick up the lost periodic information? Axel Kohlmeyer (Mon May 08 2006 - 11:46:49 CDT)
New test version posted... John Stone (Fri May 05 2006 - 19:39:47 CDT)
writing charmm psf files MW Van der Kamp, School of Chemistry (Fri May 05 2006 - 09:02:37 CDT)
- Re: writing charmm psf files John Stone (Fri May 05 2006 - 09:42:18 CDT)
  - Re: writing charmm psf files MW Van der Kamp, School of Chemistry (Fri May 05 2006 - 09:50:23 CDT)
    - Re: writing charmm psf files John Stone (Fri May 05 2006 - 10:00:11 CDT)
povray problem: degenerate cylinder Amadeu (Fri May 05 2006 - 07:09:51 CDT)
- Re: povray problem: degenerate cylinder John Stone (Fri May 05 2006 - 09:38:02 CDT)
  - Re: povray problem: degenerate cylinder Amadeu (Fri May 05 2006 - 09:48:43 CDT)
script for multiple structure superimposition? Shirley Li (Thu May 04 2006 - 16:48:33 CDT)
- Re: script for multiple structure superimposition? John Stone (Thu May 04 2006 - 16:58:04 CDT)
plotting x y z data Prof. Y. U. Sasidhar (Thu May 04 2006 - 02:14:38 CDT)
- Re: plotting x y z data Axel Kohlmeyer (Thu May 04 2006 - 07:01:39 CDT)
  - Re: plotting x y z data Prof. Y. U. Sasidhar (Thu May 04 2006 - 07:12:57 CDT)
- Re: plotting x y z data Luis Gracia (Thu May 04 2006 - 08:14:27 CDT)
selecting frames from trajectory Raul Araya Secchi (Wed May 03 2006 - 16:19:21 CDT)
- Re: selecting frames from trajectory John Stone (Wed May 03 2006 - 17:52:21 CDT)
  - Re: selecting frames from trajectory John Stone (Wed May 03 2006 - 18:12:04 CDT)
- Re: selecting frames from trajectory Luis Gracia (Wed May 03 2006 - 19:17:09 CDT)
missing cell length on DCD ziemys_at_ecr6.ohio-state.edu (Wed May 03 2006 - 14:04:48 CDT)
- Re: missing cell length on DCD John Stone (Wed May 03 2006 - 14:15:13 CDT)
- Re: missing cell length on DCD Èùìáò Åõáããåëéäçò (Sat Jul 14 2007 - 11:32:17 CDT)
  - Re: Re: missing cell length on DCD Axel Kohlmeyer (Sat Jul 14 2007 - 11:42:08 CDT)
Water and protein Al-Rawi, Ahlam (Wed May 03 2006 - 13:40:44 CDT)
- Re: Water and protein John Stone (Wed May 03 2006 - 14:16:50 CDT)
Using RMSD without loading all structures? Gustavo Seabra (Wed May 03 2006 - 11:55:25 CDT)
- Re: Using RMSD without loading all structures? John Stone (Wed May 03 2006 - 12:38:43 CDT)
  - Re: Using RMSD without loading all structures? Gustavo Seabra (Wed May 03 2006 - 13:12:40 CDT)
dlpoly history files in vmd 1.8.4 Mgr. Lubos Vrbka (Wed May 03 2006 - 02:26:50 CDT)
- Re: dlpoly history files in vmd 1.8.4 John Stone (Wed May 03 2006 - 10:24:15 CDT)
  - Re: dlpoly history files in vmd 1.8.4 Mgr. Lubos Vrbka (Wed May 03 2006 - 14:24:57 CDT)
search path and naming conventions for custom TCL scripts Enzo Vitale (Wed May 03 2006 - 09:13:42 CDT)
- Re: search path and naming conventions for custom TCL scripts John Stone (Wed May 03 2006 - 10:12:03 CDT)
- Re: search path and naming conventions for custom TCL scripts Axel Kohlmeyer (Wed May 03 2006 - 10:29:29 CDT)
- Re: search path and naming conventions for custom TCL scripts Eduard Schreiner (Wed May 03 2006 - 12:35:15 CDT)
cavity/pocket representation Wei Fu (Linda) (Tue May 02 2006 - 13:50:38 CDT)
- Re: cavity/pocket representation John Stone (Tue May 02 2006 - 13:05:12 CDT)
- Re: cavity/pocket representation Ran Friedman (Thu May 04 2006 - 03:17:24 CDT)
  - Re: cavity/pocket representation Luis Guillermo Cota Preciado (Thu May 04 2006 - 12:48:53 CDT)
PSFGEN NAD spilts up in 3 Per Jr. Greisen (Tue May 02 2006 - 10:42:29 CDT)
ppmtompeg James Rustad (Tue May 02 2006 - 10:39:45 CDT)
- Re: ppmtompeg John Stone (Tue May 02 2006 - 10:48:16 CDT)
saving coordinates of expanded cell James Rustad (Tue May 02 2006 - 10:36:26 CDT)
- Re: saving coordinates of expanded cell John Stone (Tue May 02 2006 - 10:44:20 CDT)
OFF drawing method Leandro Martínez (Tue May 02 2006 - 09:53:19 CDT)
- Re: OFF drawing method John Stone (Tue May 02 2006 - 10:07:49 CDT)
  - Re: OFF drawing method Leandro Martínez (Tue May 02 2006 - 10:10:45 CDT)
coordinates of an atom Enzo Vitale (Tue May 02 2006 - 09:39:10 CDT)
- Re: coordinates of an atom John Stone (Tue May 02 2006 - 10:13:23 CDT)
  - Re: coordinates of an atom Axel Kohlmeyer (Tue May 02 2006 - 11:22:22 CDT)
    - Re: coordinates of an atom John Stone (Tue May 02 2006 - 11:22:37 CDT)
adding hydrogen atoms Naser, Md Abu (Tue May 02 2006 - 09:20:34 CDT)
- Re: adding hydrogen atoms Peter Freddolino (Tue May 02 2006 - 13:00:10 CDT)
Compile of OpenGL shader vmdsphere failed Marc Petitmermet (Tue May 02 2006 - 05:45:03 CDT)
- Re: Compile of OpenGL shader vmdsphere failed John Stone (Tue May 02 2006 - 10:26:41 CDT)
Playing part of a trajectory using TCL David Chalmers (Tue May 02 2006 - 05:30:37 CDT)
- Re: Playing part of a trajectory using TCL John Stone (Wed May 03 2006 - 18:06:12 CDT)
one residue rmsd snoze pa (Mon May 01 2006 - 17:49:02 CDT)
- Re: one residue rmsd John Stone (Tue May 02 2006 - 11:00:59 CDT)
loading amber topology L. Michel Espinoza-Fonseca (Mon May 01 2006 - 13:43:12 CDT)
- Re: loading amber topology John Stone (Mon May 01 2006 - 14:10:18 CDT)
Re: vmd-l digest V1 #514 Fred de Lamotte (Sat Apr 29 2006 - 08:43:56 CDT)
VMD on LINUX with CAVELib ELENA S SLOBOUNOV (Fri Apr 28 2006 - 16:25:13 CDT)
- Re: VMD on LINUX with CAVELib John Stone (Sun Apr 30 2006 - 00:32:53 CDT)
hiding and renaming of graphical objects Enzo Vitale (Fri Apr 28 2006 - 11:54:30 CDT)
- Re: hiding and renaming of graphical objects Axel Kohlmeyer (Fri Apr 28 2006 - 12:32:59 CDT)
  - Re: hiding and renaming of graphical objects John Stone (Fri Apr 28 2006 - 12:45:21 CDT)
OpenGL Programmable Shading not available. Vlad Cojocaru (Fri Apr 28 2006 - 08:52:49 CDT)
- Re: OpenGL Programmable Shading not available. John Stone (Fri Apr 28 2006 - 10:11:21 CDT)
Salt bridges Nuno R. L. Ferreira (Thu Apr 27 2006 - 09:14:32 CDT)
Problems with mouse programming in VMD Chang Hu (Wed Apr 26 2006 - 23:19:57 CDT)
- Re: Problems with mouse programming in VMD John Stone (Thu Apr 27 2006 - 11:52:55 CDT)
  - Re: Problems with mouse programming in VMD Chang Hu (Thu Apr 27 2006 - 12:36:23 CDT)
two references- I got them, thank you! Ioana Cozmuta (Wed Apr 26 2006 - 16:15:11 CDT)
two references Ioana Cozmuta (Wed Apr 26 2006 - 15:18:28 CDT)
Compiling problem angel (Wed Apr 26 2006 - 14:59:31 CDT)
- Re: Compiling problem John Stone (Wed Apr 26 2006 - 15:06:11 CDT)
fedora core 5 and VMD 1.8.4 Brian Kidd (Tue Apr 25 2006 - 18:37:32 CDT)
- Re: fedora core 5 and VMD 1.8.4 John Stone (Tue Apr 25 2006 - 19:20:27 CDT)
  - Re: fedora core 5 and VMD 1.8.4 Brian Kidd (Tue Apr 25 2006 - 20:06:50 CDT)
truncated octahedron from AMBER Kenley Barrett (Tue Apr 25 2006 - 13:05:06 CDT)
- Re: truncated octahedron from AMBER John Stone (Tue Apr 25 2006 - 13:51:41 CDT)
Problem with VMD 1.8.4 on Mac OS X 10.4.6 PPC Matteo Dal Peraro (Tue Apr 25 2006 - 10:22:54 CDT)
- Re: Problem with VMD 1.8.4 on Mac OS X 10.4.6 PPC John Stone (Tue Apr 25 2006 - 10:29:38 CDT)
- Re: Problem with VMD 1.8.4 on Mac OS X 10.4.6 PPC Robert Brunner (Tue Apr 25 2006 - 13:07:00 CDT)
tcl question Mgr. Lubos Vrbka (Tue Apr 25 2006 - 03:31:16 CDT)
- Re: tcl question John Stone (Tue Apr 25 2006 - 10:15:55 CDT)
  - Re: tcl question Mgr. Lubos Vrbka (Wed Apr 26 2006 - 06:29:48 CDT)
Movie for Trajectory analysis Tamal Banerjee (Tue Apr 25 2006 - 00:09:17 CDT)
- Re: Movie for Trajectory analysis John Stone (Tue Apr 25 2006 - 10:41:00 CDT)
Problem with wait daniel aguayo (Mon Apr 24 2006 - 20:39:19 CDT)
- Re: Problem with wait John Stone (Tue Apr 25 2006 - 12:59:07 CDT)
  - Re: Problem with wait daniel aguayo (Tue Apr 25 2006 - 14:43:21 CDT)
Updated "Hull" source code for delaunay script... John Stone (Mon Apr 24 2006 - 20:11:50 CDT)
rendering high resolution images Al Courey (Mon Apr 24 2006 - 16:19:52 CDT)
- Re: rendering high resolution images John Stone (Mon Apr 24 2006 - 16:30:38 CDT)
tcl logging and plugins Jeffrey A Tibbitt (Mon Apr 24 2006 - 13:58:01 CDT)
- Re: tcl logging and plugins John Stone (Mon Apr 24 2006 - 14:07:26 CDT)
[Fwd: Re: bad angels] Peter Freddolino (Mon Apr 24 2006 - 10:15:42 CDT)
bad angels genie lfs (Mon Apr 24 2006 - 05:06:32 CDT)
RE: polynucleotide builder Jacob Pøhlsgaard (Mon Apr 24 2006 - 04:31:54 CDT)
core dump Praveen Madala (Mon Apr 24 2006 - 03:14:15 CDT)
- Re: core dump John Stone (Mon Apr 24 2006 - 03:45:08 CDT)
polynucleotide builder Jean Richelle (Sun Apr 23 2006 - 17:05:17 CDT)
- Re: polynucleotide builder L. Michel Espinoza-Fonseca (Mon Apr 24 2006 - 02:15:31 CDT)
peptide builder John Robinson (Fri Apr 21 2006 - 15:19:01 CDT)
- Re: peptide builder Leandro Martínez (Sat Apr 22 2006 - 12:21:04 CDT)
  - Re: peptide builder dimka (Sat Apr 22 2006 - 14:58:34 CDT)
    - Re: peptide builder Leandro Martínez (Sat Apr 22 2006 - 16:07:56 CDT)
  - Re: peptide builder Arneh Babakhani (Fri Sep 07 2007 - 10:50:23 CDT)
    - Re: peptide builder L. Michel Espinoza-Fonseca (Fri Sep 07 2007 - 11:26:41 CDT)
questions for 1.8.4 Nathan C. Rockwell (Fri Apr 21 2006 - 14:32:16 CDT)
- Re: questions for 1.8.4 John Stone (Fri Apr 21 2006 - 14:52:32 CDT)
  - Re: questions for 1.8.4 Nathan C. Rockwell (Fri Apr 21 2006 - 15:08:00 CDT)
    - Re: questions for 1.8.4 John Stone (Tue Apr 25 2006 - 10:49:28 CDT)
VMD's Python/Tcl - importing libraries ziemys_at_ecr6.ohio-state.edu (Fri Apr 21 2006 - 10:45:08 CDT)
- Re: VMD's Python/Tcl - importing libraries John Stone (Fri Apr 21 2006 - 11:48:07 CDT)
Apologizes for "How to select some sugar atoms" Jean Richelle (Fri Apr 21 2006 - 00:23:40 CDT)
question Maria Konstantakaki (Thu Apr 20 2006 - 10:38:20 CDT)
- Re: question Stéphane Teletchéa (Fri Apr 21 2006 - 03:54:28 CDT)
How to select some sugar atoms Jean Richelle (Thu Apr 20 2006 - 11:37:28 CDT)
Python libs posted for VMD 1.8.4 users... John Stone (Wed Apr 19 2006 - 20:33:15 CDT)
rms and align strucs andrea spitaleri (Wed Apr 19 2006 - 06:05:50 CDT)
- Re: rms and align strucs Peter Freddolino (Wed Apr 19 2006 - 12:02:46 CDT)
Unknown residue type ZN Per Jr. Greisen (Tue Apr 18 2006 - 08:22:33 CDT)
- Re: Unknown residue type ZN Peter Freddolino (Tue Apr 18 2006 - 09:33:19 CDT)
vmd 1.8.4 on Fedora Core 5 Marc Petitmermet (Tue Apr 18 2006 - 06:13:18 CDT)
- Re: vmd 1.8.4 on Fedora Core 5 Marc Petitmermet (Tue Apr 18 2006 - 11:21:39 CDT)
  - contact map lig-pro andrea spitaleri (Wed Apr 19 2006 - 05:37:23 CDT)
    - Re: contact map lig-pro John Stone (Wed Apr 19 2006 - 17:46:14 CDT)
Generating psfgen of multimeric protein complex Per Jr. Greisen (Tue Apr 18 2006 - 04:35:50 CDT)
- Re: Generating psfgen of multimeric protein complex Peter Freddolino (Tue Apr 18 2006 - 09:29:09 CDT)
Announce: VMD 1.8.4 Released!! John Stone (Mon Apr 17 2006 - 11:37:34 CDT)
How to deal with this sugar residues though psfgen? q=E2=BA=E9=C3=F7?= (Mon Apr 17 2006 - 06:22:22 CDT)
breaking the DCD file Rima Chaudhuri (Sun Apr 16 2006 - 16:01:52 CDT)
- Re: breaking the DCD file John Stone (Sun Apr 16 2006 - 17:12:32 CDT)
- Re: breaking the DCD file Peter Freddolino (Sun Apr 16 2006 - 17:23:42 CDT)
vmd 1.8a21 Dan Fishelovitch (Sun Apr 16 2006 - 10:02:34 CDT)
- Re: vmd 1.8a21 John Stone (Sun Apr 16 2006 - 13:05:59 CDT)
  - Re: vmd 1.8a21 John Stone (Sun Apr 16 2006 - 17:06:07 CDT)
- Re: vmd 1.8a21 Mgr. Lubos Vrbka (Sun Apr 16 2006 - 15:31:57 CDT)
Multiple residues at same position snoze pa (Sun Apr 16 2006 - 02:01:35 CDT)
- Re: Multiple residues at same position Peter Freddolino (Sun Apr 16 2006 - 08:38:30 CDT)
VMD-L: how to select water molecules between two residues in a trajectory. Margaret Shun Cheung (Sat Apr 15 2006 - 16:54:25 CDT)
- Re: VMD-L: how to select water molecules between two residues in a trajectory. John Stone (Sat Apr 15 2006 - 17:17:16 CDT)
  - Re: VMD-L: how to select water molecules between two residues in a trajectory. Margaret Shun Cheung (Sat Apr 15 2006 - 19:15:26 CDT)
- Re: VMD-L: how to select water molecules between two residues in a trajectory. Axel Kohlmeyer (Sat Apr 15 2006 - 20:31:11 CDT)
  - Re: VMD-L: how to select water molecules between two residues in a trajectory. Margaret Shun Cheung (Mon Apr 17 2006 - 09:38:54 CDT)
Generating PSF for 1JNO.pdb chain A Lin (Fri Apr 14 2006 - 10:29:07 CDT)
- Re: namd-l: Generating PSF for 1JNO.pdb chain A snoze pa (Fri Apr 14 2006 - 11:40:34 CDT)
write output pdb for lots of different selections Vlad Cojocaru (Thu Apr 13 2006 - 11:48:08 CDT)
- Re: write output pdb for lots of different selections Peter Freddolino (Thu Apr 13 2006 - 12:04:25 CDT)
python ziemys_at_ecr6.ohio-state.edu (Thu Apr 13 2006 - 08:15:01 CDT)
- Re: python John Stone (Thu Apr 13 2006 - 23:01:06 CDT)
merging two pdbs??? genie lfs (Thu Apr 13 2006 - 01:26:36 CDT)
- Re: merging two pdbs??? John Stone (Thu Apr 13 2006 - 01:37:20 CDT)
  - Re: merging two pdbs??? genie lfs (Thu Apr 13 2006 - 02:36:54 CDT)
a question about ribbon representation yzhou_at_chem.umn.edu (Wed Apr 12 2006 - 15:07:27 CDT)
- Re: a question about ribbon representation John Stone (Wed Apr 12 2006 - 16:04:05 CDT)
(xterm: Command not found) error Jorge Hernandez Fernandez (Wed Apr 12 2006 - 14:14:58 CDT)
- Re: (xterm: Command not found) error John Stone (Wed Apr 12 2006 - 14:29:07 CDT)
python math library Grischa Meyer (Tue Apr 11 2006 - 23:50:22 CDT)
- Re: python math library Justin Gullingsrud (Wed Apr 12 2006 - 19:02:22 CDT)
  - Re: python math library John Stone (Wed Apr 12 2006 - 21:25:37 CDT)
VMD-L: how to rotate the molecule so the long axis will be aligned to Z Margaret Shun Cheung (Tue Apr 11 2006 - 20:13:21 CDT)
- Re: VMD-L: how to rotate the molecule so the long axis will be aligned to Z Peter Freddolino (Wed Apr 12 2006 - 11:37:27 CDT)
  - Re: VMD-L: how to rotate the molecule so the long axis will be aligned to Z Margaret Shun Cheung (Wed Apr 12 2006 - 11:48:45 CDT)
    - Re: VMD-L: how to rotate the molecule so the long axis will be aligned to Z Peter Freddolino (Wed Apr 12 2006 - 12:16:30 CDT)
    - Re: VMD-L: how to rotate the molecule so the long axis will be aligned to Z Margaret Shun Cheung (Wed Apr 12 2006 - 13:30:05 CDT)
reconstructing PMF Ioana Cozmuta (Tue Apr 11 2006 - 16:57:02 CDT)
selection in different pcb images dimka (Tue Apr 11 2006 - 15:02:37 CDT)
- Re: selection in different pcb images John Stone (Thu Apr 13 2006 - 00:09:46 CDT)
RMSD Anuradha Mittal (Tue Apr 11 2006 - 13:47:06 CDT)
- Re: RMSD Peter Freddolino (Tue Apr 11 2006 - 13:57:58 CDT)
  - Re: RMSD Anuradha Mittal (Wed Apr 12 2006 - 09:24:45 CDT)
GLSL rendermode now OK on Linux with NVidia 8756 driver version Pietro Amodeo (Tue Apr 11 2006 - 12:24:49 CDT)
- Re: GLSL rendermode now OK on Linux with NVidia 8756 driver version John Stone (Tue Apr 11 2006 - 12:28:43 CDT)
  - Re: GLSL rendermode now OK on Linux with NVidia 8756 driver version Pietro Amodeo (Tue Apr 11 2006 - 13:52:48 CDT)
distances Kenley Barrett (Tue Apr 11 2006 - 11:19:41 CDT)
- Re: distances Axel Kohlmeyer (Tue Apr 11 2006 - 14:11:13 CDT)
need HELP with psf file Praveen Madala (Mon Apr 10 2006 - 22:23:30 CDT)
- Re: need HELP with psf file John Stone (Mon Apr 10 2006 - 23:55:53 CDT)
multiple peptides simulation Noriaki Okimoto (Mon Apr 10 2006 - 14:14:18 CDT)
libcprts.so.6 not found by VMD on RedHat EL3 (ia64). guy.baudoux_at_gskbio.com (Mon Apr 10 2006 - 08:31:38 CDT)
- Re: libcprts.so.6 not found by VMD on RedHat EL3 (ia64). John Stone (Mon Apr 10 2006 - 10:20:52 CDT)
  - Re: libcprts.so.6 not found by VMD on RedHat EL3 (ia64). Bogdan Costescu (Mon Apr 10 2006 - 11:23:46 CDT)
How to measure of radius of molecules? Taeho Kim (Mon Apr 10 2006 - 03:29:18 CDT)
making movie with move on each frame... Ravinder Abrol (Fri Apr 07 2006 - 21:26:52 CDT)
- Re: making movie with move on each frame... John Stone (Mon Apr 10 2006 - 11:33:37 CDT)
  - Re: making movie with move on each frame... Ravinder Abrol (Thu Apr 13 2006 - 06:32:50 CDT)
    - Re: making movie with move on each frame... John Stone (Thu Apr 13 2006 - 10:00:51 CDT)
    - Re: making movie with move on each frame... Ravinder Abrol (Thu Apr 13 2006 - 14:07:31 CDT)
a name quesiton lily jin (Fri Apr 07 2006 - 11:19:41 CDT)
- Re: namd-l: a name quesiton Leonardo G. Trabuco (Sat Apr 08 2006 - 13:15:56 CDT)
parameter file for DAD Yu Wang (Fri Apr 07 2006 - 09:18:55 CDT)
HELP Praveen Madala (Thu Apr 06 2006 - 18:26:23 CDT)
- Re: HELP Peter Freddolino (Fri Apr 07 2006 - 01:02:43 CDT)
proto-HEME parameters Cesar Millan (Thu Apr 06 2006 - 17:05:56 CDT)
RNA first residue vvenditti_at_biochem.wisc.edu (Thu Apr 06 2006 - 14:20:33 CDT)
- Re: RNA first residue John Stone (Thu Apr 06 2006 - 14:29:42 CDT)
dummy atoms and FEP Raul Araya Secchi (Thu Apr 06 2006 - 11:32:32 CDT)
- Re: dummy atoms and FEP Peter Freddolino (Thu Apr 06 2006 - 11:45:26 CDT)
STL rendering Jean Richelle (Thu Apr 06 2006 - 09:39:53 CDT)
- Re: STL rendering John Stone (Thu Apr 06 2006 - 09:45:01 CDT)
how to plot waters h-bonded to a protein? J. Juraszek (Thu Apr 06 2006 - 08:57:08 CDT)
- Re: how to plot waters h-bonded to a protein? John Stone (Thu Apr 06 2006 - 09:42:00 CDT)
- Re: how to plot waters h-bonded to a protein? Eduard Schreiner (Thu Apr 06 2006 - 12:09:19 CDT)
NAMD to Amber AYTUG TUNCEL (Thu Apr 06 2006 - 08:46:10 CDT)
- Re: NAMD to Amber John Stone (Thu Apr 06 2006 - 09:49:39 CDT)
download pdb files from PDB with vmd 1.8.4b10 Vlad Cojocaru (Thu Apr 06 2006 - 03:55:16 CDT)
- Re: download pdb files from PDB with vmd 1.8.4b10 John Stone (Thu Apr 06 2006 - 09:36:28 CDT)
RE: python Numeric library problem Sacerdoti, Federico (Wed Apr 05 2006 - 20:16:44 CDT)
- Re: python Numeric library problem John Stone (Wed Apr 05 2006 - 20:21:52 CDT)
membrane loading xiaoqin huang (Wed Apr 05 2006 - 14:25:12 CDT)
- Re: membrane loading John Stone (Wed Apr 05 2006 - 14:32:38 CDT)
  - Re: membrane loading xiaoqin huang (Wed Apr 05 2006 - 17:05:39 CDT)
graphic representation ivana adamovic (Wed Apr 05 2006 - 12:24:48 CDT)
- Re: graphic representation John Stone (Wed Apr 05 2006 - 12:29:09 CDT)
- Re: graphic representation John Stone (Wed Apr 05 2006 - 13:33:31 CDT)
  - Re: Re: graphic representation ivana adamovic (Wed Apr 05 2006 - 15:06:18 CDT)
SURF -rendering problem M.S.Vijayabaskar (Wed Apr 05 2006 - 04:44:55 CDT)
- Re: SURF -rendering problem John Stone (Wed Apr 05 2006 - 12:32:49 CDT)
  - Re: SURF -rendering problem John Stone (Thu Apr 06 2006 - 00:01:55 CDT)
dict command andrea spitaleri (Wed Apr 05 2006 - 09:44:50 CDT)
- Re: dict command John Stone (Wed Apr 05 2006 - 10:11:08 CDT)
  - Re: dict command andrea spitaleri (Thu Apr 06 2006 - 02:43:21 CDT)
    - Re: dict command John Stone (Thu Apr 06 2006 - 09:55:36 CDT)
warning from psfgen: poorly guessed coordinates... Margaret Shun Cheung (Tue Apr 04 2006 - 17:17:17 CDT)
- Re: warning from psfgen: poorly guessed coordinates... John Stone (Wed Apr 05 2006 - 20:47:40 CDT)
  - Re: warning from psfgen: poorly guessed coordinates... Margaret Shun Cheung (Wed Apr 05 2006 - 20:49:30 CDT)
- Re: warning from psfgen: poorly guessed coordinates... Leonardo G. Trabuco (Wed Apr 05 2006 - 22:08:02 CDT)
box information dimka (Tue Apr 04 2006 - 17:18:30 CDT)
- Re: box information John Stone (Tue Apr 04 2006 - 17:27:17 CDT)
question about psfgen Margaret Shun Cheung (Tue Apr 04 2006 - 16:23:25 CDT)
- Re: question about psfgen John Stone (Wed Apr 05 2006 - 22:57:32 CDT)
  - Re: question about psfgen Marcos Sotomayor (Thu Apr 06 2006 - 00:02:47 CDT)
ied on vmd L. Michel Espinoza-Fonseca (Tue Apr 04 2006 - 16:11:30 CDT)
- Re: ied on vmd John Stone (Tue Apr 04 2006 - 16:41:02 CDT)
MacBookPro and VMD version ivana adamovic (Tue Apr 04 2006 - 13:39:38 CDT)
- Re: MacBookPro and VMD version John Stone (Tue Apr 04 2006 - 14:23:50 CDT)
  - Re: MacBookPro and VMD version Christoph Weber (Wed Apr 05 2006 - 14:10:08 CDT)
    - Re: MacBookPro and VMD version John Stone (Sun Apr 16 2006 - 02:14:50 CDT)
python Numeric library problem Sacerdoti, Federico (Tue Apr 04 2006 - 11:11:16 CDT)
- Re: python Numeric library problem John Stone (Tue Apr 04 2006 - 16:00:09 CDT)
  - Re: python Numeric library problem Geoff Wood (Mon Sep 24 2007 - 15:05:54 CDT)
    - Re: Re: python Numeric library problem John Stone (Fri Sep 28 2007 - 14:35:25 CDT)
alternative display mode of HBonds Jean Richelle (Tue Apr 04 2006 - 09:51:18 CDT)
- Re: alternative display mode of HBonds John Stone (Tue Apr 04 2006 - 14:46:46 CDT)
latest beta nVidia driver for Windows looks good so far... John Stone (Mon Apr 03 2006 - 20:00:50 CDT)
- Re: latest beta nVidia driver for Windows looks good so far... snoze pa (Tue Apr 04 2006 - 00:18:22 CDT)
  - Re: latest beta nVidia driver for Windows looks good so far... Eugen Leitl (Tue Apr 04 2006 - 02:04:43 CDT)
    - Fix for SELinux breaking VMD on FC5 John Stone (Tue Apr 04 2006 - 11:28:38 CDT)
WARNING: Coordinates will be rotated to comply ... Peter Hamm (Mon Apr 03 2006 - 08:01:57 CDT)
- Re: WARNING: Coordinates will be rotated to comply ... Axel Kohlmeyer (Tue Apr 04 2006 - 14:26:01 CDT)
question on vmd installation Shen (Mon Apr 03 2006 - 13:27:38 CDT)
- Re: question on vmd installation John Stone (Mon Apr 03 2006 - 11:18:45 CDT)
  - Re: question on vmd installation Shen (Tue Apr 04 2006 - 05:57:12 CDT)
    - Re: question on vmd installation John Stone (Tue Apr 04 2006 - 14:43:58 CDT)
  - Re: question on vmd installation Shen (Wed Apr 05 2006 - 03:51:30 CDT)
error during creat .psf file Taeho Kim (Mon Apr 03 2006 - 03:16:01 CDT)
- Re: error during creat .psf file John Stone (Wed Apr 05 2006 - 21:47:21 CDT)
  - Re: error during creat .psf file John Stone (Wed Apr 05 2006 - 23:14:27 CDT)
Re: vmd visualization problems with circular proteins John Stone (Sun Apr 02 2006 - 18:13:06 CDT)
about viewing charge density jun (Sun Apr 02 2006 - 14:00:58 CDT)
- Re: about viewing charge density John Stone (Sun Apr 02 2006 - 14:37:46 CDT)
How to add some small peptides to a water box randomly ? q=E2=BA=E9=C3=F7?= (Sun Apr 02 2006 - 09:57:26 CDT)
- Re: How to add some small peptides to a water box randomly ? Leandro Martínez (Sun Apr 02 2006 - 10:37:38 CDT)
  - Re: How to add some small peptides to a water box randomly ? q=E2=BA=E9=C3=F7?= (Sun Apr 02 2006 - 21:00:57 CDT)
Compiling problem angel (Fri Mar 31 2006 - 15:57:47 CST)
- Re: Compiling problem John Stone (Fri Mar 31 2006 - 16:13:07 CST)
how to show biological unit coordiates from PDB using VMD? Margaret Shun Cheung (Fri Mar 31 2006 - 14:33:51 CST)
- Re: how to show biological unit coordiates from PDB using VMD? John Stone (Fri Mar 31 2006 - 15:52:08 CST)
Re: stereo enabler Dan White (Fri Mar 31 2006 - 03:08:21 CST)
- Re: Re: stereo enabler John Stone (Wed Aug 16 2006 - 16:21:44 CDT)
Re: Stereo on non supported G5 Dan White (Fri Mar 31 2006 - 02:12:42 CST)
RE: rmsd-fullthrottle.tcl problem Turman, Cheri M (Wed Mar 29 2006 - 20:25:40 CST)
- RE: rmsd-fullthrottle.tcl problem Marcos Sotomayor (Wed Mar 29 2006 - 20:43:18 CST)
  - Re: rmsd-fullthrottle.tcl problem snoze pa (Thu Mar 30 2006 - 18:27:08 CST)
rmsd-fullthrottle.tcl problem Turman, Cheri M (Wed Mar 29 2006 - 19:34:29 CST)
- Re: rmsd-fullthrottle.tcl problem Marcos Sotomayor (Wed Mar 29 2006 - 19:49:32 CST)
- script to change representaiton Harindar Keer (Thu Mar 30 2006 - 16:37:49 CST)
  - Re: script to change representaiton John Stone (Thu Mar 30 2006 - 17:24:24 CST)
    - Re: script to change representaiton John Stone (Thu Mar 30 2006 - 17:55:05 CST)
Re: namd-l: bulk density in RDF.tcl griadi_at_utalca.cl (Wed Mar 29 2006 - 16:55:07 CST)
strange vdw representation behavior Mgr. Lubos Vrbka (Wed Mar 29 2006 - 14:08:57 CST)
- Re: strange vdw representation behavior John Stone (Wed Mar 29 2006 - 14:18:50 CST)
stereo on MacG5 Dan White (Wed Mar 29 2006 - 12:36:16 CST)
- Re: stereo on MacG5 John Stone (Wed Mar 29 2006 - 12:48:05 CST)
  - Re: stereo on MacG5 with Nvidia GeForce FX 5200 Dan White (Wed Mar 29 2006 - 14:15:45 CST)
    - Re: stereo on MacG5 with Nvidia GeForce FX 5200 John Stone (Wed Mar 29 2006 - 14:20:57 CST)
    - Re: stereo on MacG5 with Nvidia GeForce FX 5200 Robert Brunner (Wed Mar 29 2006 - 16:44:12 CST)
RE: Stereo on MacG5 (single processor) for VMD, Chimera UCSF etc. Warren DeLano (Wed Mar 29 2006 - 11:54:16 CST)
- RE: Stereo on MacG5 (single processor) for VMD, Chimera UCSF etc. Warren DeLano (Wed Mar 29 2006 - 14:52:16 CST)
- RE: Stereo on MacG5 (single processor) for VMD, Chimera UCSF etc. Kim, Kwiseon (Wed Mar 29 2006 - 15:47:24 CST)
Genrating psf Per Jr. Greisen (Wed Mar 29 2006 - 10:50:38 CST)
Re: script for cutting box John Stone (Wed Mar 29 2006 - 09:48:05 CST)
- Re: script for cutting box John Stone (Wed Mar 29 2006 - 10:24:32 CST)
Stereo on MacG5 (single processor) for VMD, Chimera UCSF etc. Peter Engelhardt (Tue Mar 28 2006 - 23:53:56 CST)
- Re: Stereo on MacG5 (single processor) for VMD, Chimera UCSF etc. John Stone (Wed Mar 29 2006 - 10:19:06 CST)
  - Re: Stereo on MacG5 (single processor) for VMD, Chimera UCSF etc. Marc Baaden (Wed Mar 29 2006 - 14:15:19 CST)
    - Re: Stereo on MacG5 (single processor) for VMD, Chimera UCSF etc. John Stone (Wed Mar 29 2006 - 14:23:25 CST)
parameter files lily jin (Tue Mar 28 2006 - 14:13:39 CST)
- Re: parameter files Peter Freddolino (Tue Mar 28 2006 - 14:31:59 CST)
problem with vmd Beniamino Sciacca (Tue Mar 28 2006 - 13:44:37 CST)
- Re: problem with vmd John Stone (Tue Mar 28 2006 - 14:06:30 CST)
  - Re: problem with vmd Shulin Zhuang (Tue Mar 28 2006 - 20:13:46 CST)
  - Re: problem with vmd Super Sayan (Wed Mar 29 2006 - 00:41:43 CST)
input file for PO3 lily jin (Tue Mar 28 2006 - 11:02:34 CST)
Re: namd-l: Re: boubt about consistency of measures John Stone (Mon Mar 27 2006 - 21:37:55 CST)
Some errors angel (Mon Mar 27 2006 - 18:51:51 CST)
- Re: Some errors John Stone (Mon Mar 27 2006 - 19:09:30 CST)
why the same operation vary so large Shulin Zhuang (Mon Mar 27 2006 - 08:31:20 CST)
- Re: why the same operation vary so large Peter Freddolino (Mon Mar 27 2006 - 09:41:24 CST)
problem with viewing gromacs xtc files in vmd hayagreevan R (Mon Mar 27 2006 - 05:30:22 CST)
- Re: problem with viewing gromacs xtc files in vmd Nuno R. L. Ferreira (Mon Mar 27 2006 - 09:16:54 CST)
- Re: problem with viewing gromacs xtc files in vmd John Stone (Mon Mar 27 2006 - 10:12:51 CST)
minimize during FEP & OS-FEP Raul Araya Secchi (Fri Mar 24 2006 - 10:49:09 CST)
Tcl scripting within NAMD configuration file Chandra Ramananjara (Fri Mar 24 2006 - 09:26:18 CST)
error in psfgen file Rima Chaudhuri (Thu Mar 23 2006 - 20:20:10 CST)
- Re: error in psfgen file Marcos Sotomayor (Thu Mar 23 2006 - 22:13:15 CST)
Possible error in aligning/computing RMSD of 2 molecules with three or two atoms Visvaldas Kairys (Thu Mar 23 2006 - 13:38:09 CST)
- Re: Possible error in aligning/computing RMSD of 2 molecules with three or two atoms Jan Saam (Thu Mar 23 2006 - 15:30:53 CST)
  - Re: Possible error in aligning/computing RMSD of 2 molecules with three or two atoms John Stone (Thu Mar 23 2006 - 15:55:38 CST)
    - Re: Possible error in aligning/computing RMSD of 2 molecules with three or two atoms Jan Saam (Thu Mar 23 2006 - 16:11:55 CST)
    - Re: Possible error in aligning/computing RMSD of 2 molecules with three or two atoms Jan Saam (Thu Mar 23 2006 - 16:17:29 CST)
- Re: Possible error in aligning/computing RMSD of 2 molecules with three or two atoms Brian Bennion (Thu Mar 23 2006 - 17:22:15 CST)
  - Re: Possible error in aligning/computing RMSD of 2 molecules with three or two atoms Jan Saam (Thu Mar 23 2006 - 18:36:28 CST)
  - Re: Possible error in aligning/computing RMSD of 2 molecules with three or two atoms Visvaldas Kairys (Fri Mar 24 2006 - 03:45:51 CST)
Big trr trajectory Anthony Cruz (Thu Mar 23 2006 - 13:27:17 CST)
- Re: Big trr trajectory John Stone (Thu Mar 23 2006 - 10:28:14 CST)
TCL scripting within NAMD Configuration File Chandra Ramananjara (Thu Mar 23 2006 - 09:12:56 CST)
boubt about consistency of measures Sergio Anis (Thu Mar 23 2006 - 08:19:52 CST)
- Re: boubt about consistency of measures John Stone (Mon Mar 27 2006 - 00:47:16 CST)
extracting values from a dx file L. Michel Espinoza-Fonseca (Thu Mar 23 2006 - 07:45:35 CST)
- Re: extracting values from a dx file Axel Kohlmeyer (Thu Mar 23 2006 - 20:22:21 CST)
  - Re: extracting values from a dx file John Stone (Mon Mar 27 2006 - 00:00:48 CST)
force over selection Ioana Cozmuta (Wed Mar 22 2006 - 23:51:46 CST)
- Re: force over selection John Stone (Thu Mar 23 2006 - 10:26:50 CST)
solvation Anuradha Mittal (Wed Mar 22 2006 - 17:38:38 CST)
energy calculation in VMD lily jin (Wed Mar 22 2006 - 16:41:45 CST)
- Re: energy calculation in VMD John Stone (Wed Mar 22 2006 - 16:48:08 CST)
Something about loading LAMMPS trace file q=CF=20=B3=C2?= (Wed Mar 22 2006 - 01:45:23 CST)
Something about loading LAMMPS trace file q=CF=20=B3=C2?= (Wed Mar 22 2006 - 01:45:12 CST)
- Re: Something about loading LAMMPS trace file John Stone (Wed Mar 22 2006 - 01:55:19 CST)
euler angles pinisetty dinesh (Tue Mar 21 2006 - 19:07:47 CST)
- Re: euler angles John Stone (Wed Mar 22 2006 - 13:30:55 CST)
what is wrong with this script? lily jin (Tue Mar 21 2006 - 16:25:12 CST)
- Re: what is wrong with this script? Sergio Anis (Tue Mar 21 2006 - 18:52:51 CST)
  - Re: what is wrong with this script? Jérôme Hénin (Wed Mar 22 2006 - 01:31:13 CST)
distance tween two atoms lily jin (Tue Mar 21 2006 - 15:42:18 CST)
- Re: distance tween two atoms John Stone (Wed Mar 22 2006 - 16:55:45 CST)
movie quality degradation Wang, Yangzhou (Tue Mar 21 2006 - 10:50:45 CST)
- Re: movie quality degradation John Stone (Thu Mar 23 2006 - 11:51:41 CST)
  - Re: Generating PSF for 1JNO.pdb chain A Lin (Fri Mar 24 2006 - 08:29:01 CST)
Re: pdb - generation Florian Haberl (Tue Mar 21 2006 - 09:06:57 CST)
about the psfgen of vmd Shulin Zhuang (Tue Mar 21 2006 - 08:46:28 CST)
- Re: about the psfgen of vmd John Stone (Tue Mar 21 2006 - 10:37:14 CST)
pdb - generation Osmany guirola Cruz (Tue Mar 21 2006 - 06:39:31 CST)
- Re: pdb - generation John Stone (Tue Mar 21 2006 - 10:16:00 CST)
sausage nmr ensemble spitaleri.andrea_at_hsr.it (Tue Mar 21 2006 - 04:09:48 CST)
- Re: sausage nmr ensemble John Stone (Tue Mar 21 2006 - 09:50:08 CST)
  - Re: sausage nmr ensemble spitaleri.andrea_at_hsr.it (Tue Mar 21 2006 - 10:09:48 CST)
    - Re: sausage nmr ensemble John Stone (Tue Mar 21 2006 - 10:34:01 CST)
VMD Command Pijush Ghosh (Tue Mar 21 2006 - 00:00:42 CST)
- Re: VMD Command John Stone (Tue Mar 21 2006 - 01:17:36 CST)
- Re: VMD Command dimka (Tue Mar 21 2006 - 01:20:06 CST)
- Re: namd-l: VMD Command Viswanadham Sridhara (Tue Mar 21 2006 - 12:31:23 CST)
autoionize "error procesing bonds" George M Giambasu (Mon Mar 20 2006 - 16:50:28 CST)
- Re: autoionize "error procesing bonds" John Stone (Wed Mar 22 2006 - 16:58:16 CST)
Re: namd-l: what does "patch" mean? dimka (Sun Mar 19 2006 - 23:33:21 CST)
Re: (ÈðÐÇÌáÊ¾-´ËÓÊ¼þ¿ÉÄÜÊÇÀ¬»øÓÊ¼þ)Re: namd-l: error in membrane producing mashaojienuaa (Sun Mar 19 2006 - 20:19:40 CST)
- Re: Re: namd-l: error in membrane producing John Stone (Thu Apr 13 2006 - 01:21:39 CDT)
Poor Hydrogen Placement in AutoPSF Brian Bennion (Fri Mar 17 2006 - 16:39:15 CST)
- Re: Poor Hydrogen Placement in AutoPSF Peter Freddolino (Sun Mar 19 2006 - 14:51:49 CST)
  - Re: Poor Hydrogen Placement in AutoPSF Brian Bennion (Mon Mar 20 2006 - 10:27:52 CST)
Problem with gopython Ludovic Pétain (Fri Mar 17 2006 - 07:19:11 CST)
- Re: Problem with gopython John Stone (Fri Mar 17 2006 - 11:17:33 CST)
  - Re: Problem with gopython Peter Freddolino (Fri Mar 17 2006 - 11:42:12 CST)
VMD 1.8.4b12 test version, Wiki / BioCoRE public area John Stone (Thu Mar 16 2006 - 16:44:57 CST)
error loading dcd file on Windows XP Jindal Shah (Thu Mar 16 2006 - 15:18:24 CST)
- Re: error loading dcd file on Windows XP John Stone (Thu Mar 16 2006 - 15:30:43 CST)
  - Re: error loading dcd file on Windows XP Jindal Shah (Thu Mar 16 2006 - 18:44:30 CST)
    - Re: error loading dcd file on Windows XP John Stone (Fri Mar 17 2006 - 16:28:17 CST)
    - Re: error loading dcd file on Windows XP Jindal Shah (Fri Mar 17 2006 - 16:36:58 CST)
large selection Ioana Cozmuta (Tue Mar 14 2006 - 18:00:27 CST)
- Re: large selection John Stone (Tue Mar 14 2006 - 18:05:29 CST)
  - Re: large selection Ioana Cozmuta (Tue Mar 14 2006 - 18:17:46 CST)
    - Re: large selection John Stone (Wed Mar 15 2006 - 10:13:58 CST)
    - Re: large selection Ioana Cozmuta (Wed Mar 15 2006 - 23:33:46 CST)
Strange GLSL rendering Mario Valle (Tue Mar 14 2006 - 06:07:53 CST)
- Re: Strange GLSL rendering John Stone (Tue Mar 14 2006 - 10:20:11 CST)
- Re: Strange GLSL rendering Axel Kohlmeyer (Tue Mar 14 2006 - 09:12:33 CST)
cartoon selection Viswanadham Sridhara (Mon Mar 13 2006 - 13:02:53 CST)
- Re: cartoon selection John Stone (Tue Mar 14 2006 - 00:27:38 CST)
contact map definition Jindal Shah (Mon Mar 13 2006 - 11:21:20 CST)
- Re: contact map definition John Stone (Mon Mar 13 2006 - 11:34:02 CST)
- Re: contact map definition Vlad Cojocaru (Mon Mar 13 2006 - 11:53:22 CST)
- Re: contact map definition dimka (Mon Mar 13 2006 - 12:03:18 CST)
changing colours isosurface L. Michel Espinoza-Fonseca (Mon Mar 13 2006 - 10:44:23 CST)
- Re: changing colours isosurface John Stone (Mon Mar 13 2006 - 11:17:08 CST)
Re: OSX quad buffered stereo possible on older G5 with GeForce FX5200! Dan White (Mon Mar 13 2006 - 08:17:46 CST)
user field memory demand Leandro Martínez (Mon Mar 13 2006 - 08:10:16 CST)
- Re: user field memory demand John Stone (Mon Mar 13 2006 - 10:24:21 CST)
  - Re: user field memory demand Leandro Martínez (Mon Mar 13 2006 - 10:29:42 CST)
- Re: user field memory demand Jérôme Hénin (Mon Mar 13 2006 - 11:02:36 CST)
IMD with linux VMD client and IBM namd server Marc Baaden (Mon Mar 13 2006 - 07:29:36 CST)
- Re: IMD with linux VMD client and IBM namd server John Stone (Mon Mar 13 2006 - 10:31:24 CST)
changing the color of subset of representation Jeffrey Tseng (Sun Mar 12 2006 - 14:52:15 CST)
- Re: changing the color of subset of representation John Stone (Mon Mar 13 2006 - 11:41:19 CST)
  - Re: changing the color of subset of representation Jeffrey Tseng (Mon Mar 13 2006 - 14:12:09 CST)
Convert an ascii matrix to an image Nuno R. L. Ferreira (Sat Mar 11 2006 - 13:05:10 CST)
- Re: Convert an ascii matrix to an image Nicolas Sapay (Mon Mar 13 2006 - 04:34:22 CST)
- Re: Convert an ascii matrix to an image Jérôme Hénin (Mon Mar 13 2006 - 07:33:11 CST)
- Re: Convert an ascii matrix to an image John Stone (Mon Mar 13 2006 - 10:18:17 CST)
- Re: Convert an ascii matrix to an image Axel Kohlmeyer (Sat Mar 11 2006 - 16:25:18 CST)
  - Re: Convert an ascii matrix to an image Nuno R. L. Ferreira (Mon Mar 13 2006 - 11:47:04 CST)
    - Re: Convert an ascii matrix to an image Jérôme Hénin (Mon Mar 13 2006 - 15:22:11 CST)
VMD script lily jin (Fri Mar 10 2006 - 13:41:03 CST)
- Re: VMD script John Stone (Fri Mar 10 2006 - 13:47:47 CST)
- Re: VMD script Mario Valle (Sun Mar 12 2006 - 00:43:26 CST)
electrostatic potential maps in vmd Andrei A Golosov (Fri Mar 10 2006 - 10:52:14 CST)
- Re: electrostatic potential maps in vmd John Stone (Fri Mar 10 2006 - 11:24:47 CST)
  - Re: electrostatic potential maps in vmd Andrei A Golosov (Fri Mar 10 2006 - 12:17:50 CST)
RE: namd-l: Aligning structures EPF $Esben Peter Friis$ (Fri Mar 10 2006 - 01:34:40 CST)
selecting protein + water shell L. Michel Espinoza-Fonseca (Fri Mar 10 2006 - 09:43:34 CST)
- Re: selecting protein + water shell Marcos Sotomayor (Fri Mar 10 2006 - 10:00:13 CST)
  - Re: selecting protein + water shell L. Michel Espinoza-Fonseca (Fri Mar 10 2006 - 10:02:32 CST)
radial distribution L. Michel Espinoza-Fonseca (Fri Mar 10 2006 - 08:10:56 CST)
- Re: radial distribution Peter Freddolino (Fri Mar 10 2006 - 10:52:38 CST)
RE: namd-l: is possible to remove the waterbox before running VMD Wolbach, Jeffrey P $WOLBACH$ (Thu Mar 09 2006 - 13:45:20 CST)
is possible to remove the waterbox before running VMD lily jin (Thu Mar 09 2006 - 10:34:02 CST)
- Re: is possible to remove the waterbox before running VMD John Stone (Thu Mar 09 2006 - 10:39:27 CST)
  - Re: is possible to remove the waterbox before running VMD John Stone (Thu Mar 09 2006 - 10:40:39 CST)
- Re: namd-l: is possible to remove the waterbox before running VMD Sterling Paramore (Thu Mar 09 2006 - 11:50:08 CST)
  - Re: namd-l: is possible to remove the waterbox before running VMD Michael.Grabe_at_ucsf.edu (Thu Mar 09 2006 - 12:29:00 CST)
- Re: namd-l: is possible to remove the waterbox before running VMD griadi_at_utalca.cl (Thu Mar 09 2006 - 12:56:38 CST)
  - Aligning structures Richard Wood (Thu Mar 09 2006 - 21:20:45 CST)
a display problem lily jin (Thu Mar 09 2006 - 10:22:57 CST)
- Re: a display problem John Stone (Thu Mar 09 2006 - 10:33:27 CST)
- Re: namd-l: a display problem L. Michel Espinoza-Fonseca (Thu Mar 09 2006 - 10:53:08 CST)
nVidia Quadro FX1400 Stereo Clone Mode Paul Van Allsburg (Wed Mar 08 2006 - 13:01:31 CST)
- Re: nVidia Quadro FX1400 Stereo Clone Mode John Stone (Wed Mar 08 2006 - 13:35:48 CST)
About VMD compile in win32 mustapha.hamdi_at_ensi-bourges.fr (Wed Mar 08 2006 - 12:04:29 CST)
- Re: About VMD compile in win32 John Stone (Wed Mar 08 2006 - 11:18:25 CST)
Analysis Anthony Cruz (Wed Mar 08 2006 - 13:37:21 CST)
- Re: Analysis John Stone (Wed Mar 08 2006 - 10:55:49 CST)
  - Re: Analysis Anthony Cruz (Mon Mar 20 2006 - 12:33:53 CST)
  - Re: Analysis Anthony Cruz (Thu Mar 23 2006 - 10:20:13 CST)
energy minimization of a trajectory with vmd+namd L. Michel Espinoza-Fonseca (Wed Mar 08 2006 - 08:41:37 CST)
- Re: energy minimization of a trajectory with vmd+namd John Stone (Wed Mar 08 2006 - 09:39:30 CST)
  - Re: energy minimization of a trajectory with vmd+namd Peter Freddolino (Wed Mar 08 2006 - 10:02:25 CST)
drawing a truncated octahedron Vlad Cojocaru (Wed Mar 08 2006 - 05:26:06 CST)
- Re: drawing a truncated octahedron John Stone (Fri Mar 10 2006 - 18:40:17 CST)
  - Re: drawing a truncated octahedron Vlad Cojocaru (Mon Mar 13 2006 - 04:07:17 CST)
Atom name label FyD (Wed Mar 08 2006 - 04:26:17 CST)
- Re: Atom name label John Stone (Wed Mar 08 2006 - 09:42:02 CST)
change default bond cutoff distance Weiqiang Wang (Tue Mar 07 2006 - 03:25:53 CST)
- Re: change default bond cutoff distance John Stone (Tue Mar 07 2006 - 10:55:23 CST)
  - Re: change default bond cutoff distance Weiqiang Wang (Tue Mar 07 2006 - 15:12:42 CST)
pbc and vmd L. Michel Espinoza-Fonseca (Sun Mar 05 2006 - 18:06:50 CST)
- Re: pbc and vmd griadi_at_utalca.cl (Mon Mar 06 2006 - 09:23:09 CST)
  - Re: Re: pbc and vmd Nicolas Sapay (Mon Mar 06 2006 - 10:52:23 CST)
- Re: pbc and vmd Axel Kohlmeyer (Mon Mar 06 2006 - 01:01:20 CST)
  - Re: pbc and vmd L. Michel Espinoza-Fonseca (Tue Mar 07 2006 - 07:11:21 CST)
- Re: pbc and vmd John Stone (Mon Mar 06 2006 - 19:20:18 CST)
manipulate DLPOLY HISTORY files Javier Sacristan (Fri Mar 03 2006 - 15:43:37 CST)
- Re: manipulate DLPOLY HISTORY files John Stone (Mon Mar 06 2006 - 19:14:18 CST)
Summing volumetric data within a sub-volume of a simulation cell Joshua Speidel (Thu Mar 02 2006 - 17:41:23 CST)
- Re: Summing volumetric data within a sub-volume of a simulation cell John Stone (Thu Apr 06 2006 - 00:05:04 CDT)
(no subject) Naser, Md Abu (Wed Mar 01 2006 - 14:17:10 CST)
- Re: John Stone (Wed Mar 01 2006 - 14:56:46 CST)
shutter glasses with VMD Hannes Barsch (Wed Mar 01 2006 - 10:33:40 CST)
- Re: shutter glasses with VMD Bogdan Costescu (Thu Mar 02 2006 - 07:05:36 CST)
selection of atoms on INSIDE protein ziemys_at_ecr6.ohio-state.edu (Tue Feb 28 2006 - 18:50:00 CST)
- Re: selection of atoms on INSIDE protein John Stone (Wed Mar 01 2006 - 16:44:04 CST)
  - Re: selection of atoms on INSIDE protein Anthony Cruz (Mon Mar 06 2006 - 10:20:08 CST)
  - Re: selection of atoms on INSIDE protein Anthony Cruz (Mon Mar 06 2006 - 11:26:12 CST)
Q:selection of atoms on the surface of a molecule kovzany_at_go.com (Tue Feb 28 2006 - 17:22:13 CST)
- Re: Q:selection of atoms on the surface of a molecule John Stone (Tue Feb 28 2006 - 17:35:00 CST)
  - Re: Q:selection of atoms on the surface of a molecule Mgr. Lubos Vrbka (Wed Mar 01 2006 - 00:44:11 CST)
question about electrostatic potential maps ivana adamovic (Mon Feb 27 2006 - 12:19:48 CST)
- Re: question about electrostatic potential maps John Stone (Mon Feb 27 2006 - 16:06:56 CST)
- Re: question about electrostatic potential maps Vlad Cojocaru (Tue Feb 28 2006 - 04:12:02 CST)
  - Re: question about electrostatic potential maps ivana adamovic (Tue Feb 28 2006 - 09:48:47 CST)
converting pdb to xtc L. Michel Espinoza-Fonseca (Mon Feb 27 2006 - 10:17:42 CST)
- Re: converting pdb to xtc Nuno R. L. Ferreira (Mon Feb 27 2006 - 10:50:16 CST)
  - Re: converting pdb to xtc John Stone (Mon Feb 27 2006 - 11:13:22 CST)
    - Re: converting pdb to xtc L. Michel Espinoza-Fonseca (Mon Feb 27 2006 - 14:20:04 CST)
color scale data range Vlad Cojocaru (Mon Feb 27 2006 - 05:28:18 CST)
color scale data range Vlad Cojocaru (Mon Feb 27 2006 - 05:25:43 CST)
- Re: color scale data range Axel Kohlmeyer (Mon Feb 27 2006 - 08:20:34 CST)
Warning) Unusual bond between residues 25 and 26 Nuno R. L. Ferreira (Sat Feb 25 2006 - 11:42:49 CST)
- Re: Warning) Unusual bond between residues 25 and 26 Nuno R. L. Ferreira (Mon Feb 27 2006 - 09:25:57 CST)
  - Re: Warning) Unusual bond between residues 25 and 26 John Stone (Mon Feb 27 2006 - 16:25:38 CST)
  - Re: Warning) Unusual bond between residues 25 and 26 John Stone (Thu Apr 13 2006 - 01:34:09 CDT)
Atomselection problem Manali Joshi (Fri Feb 24 2006 - 16:54:12 CST)
- Re: Atomselection problem John Stone (Fri Feb 24 2006 - 17:07:48 CST)
representation using COM Anthony Cruz (Fri Feb 24 2006 - 16:53:27 CST)
- Re: representation using COM John Stone (Fri Feb 24 2006 - 13:56:40 CST)
Re: Mapping electronic potential to surface Xifang Wang (Thu Feb 23 2006 - 19:42:50 CST)
- Re: Mapping electronic potential to surface John Stone (Fri Feb 24 2006 - 13:08:51 CST)
- Re: Mapping electronic potential to surface Axel Kohlmeyer (Thu Feb 23 2006 - 22:47:20 CST)
loading a trajectory using bigdcd and job launched on a PBS server Nicolas Sapay (Thu Feb 23 2006 - 15:05:09 CST)
- Re: loading a trajectory using bigdcd and job launched on a PBS server John Stone (Thu Feb 23 2006 - 16:31:10 CST)
  - Re: loading a trajectory using bigdcd and job launched on a PBS server nsapay_at_ibcp.fr (Thu Feb 23 2006 - 16:59:07 CST)
isplay script that displays a system in the original pbc cell snoze pa (Thu Feb 23 2006 - 13:47:52 CST)
- Re: isplay script that displays a system in the original pbc cell John Stone (Thu Feb 23 2006 - 13:50:49 CST)
  - Re: isplay script that displays a system in the original pbc cell snoze pa (Mon Feb 27 2006 - 11:30:08 CST)
    - Re: isplay script that displays a system in the original pbc cell John Stone (Mon Feb 27 2006 - 16:11:07 CST)
Tachyon and text rendering Vlad Cojocaru (Thu Feb 23 2006 - 13:08:44 CST)
- Re: Tachyon and text rendering Bogdan Costescu (Thu Feb 23 2006 - 14:37:56 CST)
- Re: Tachyon and text rendering Jérôme Hénin (Thu Feb 23 2006 - 17:04:47 CST)
load multiple CRD trajectories into a PDB file Thereza Soares (Thu Feb 23 2006 - 11:26:14 CST)
- Re: load multiple CRD trajectories into a PDB file John Stone (Thu Feb 23 2006 - 11:42:24 CST)
Moving domains in VMD Francis Reyes (Thu Feb 23 2006 - 09:08:45 CST)
- Re: Moving domains in VMD John Stone (Thu Feb 23 2006 - 11:46:13 CST)
very large pdb file Jack Gundrum (Thu Feb 23 2006 - 11:09:39 CST)
- Re: very large pdb file John Stone (Thu Feb 23 2006 - 11:26:34 CST)
  - Re: very large pdb file Nuno R. L. Ferreira (Thu Feb 23 2006 - 11:51:45 CST)
  - Re: very large pdb file Jack Gundrum (Thu Feb 23 2006 - 12:13:24 CST)
render text in VMD with Tachyon Vlad Cojocaru (Thu Feb 23 2006 - 09:07:54 CST)
- Re: render text in VMD with Tachyon John Stone (Thu Feb 23 2006 - 12:39:51 CST)
Mapping electronic potential to surface Xifang Wang (Wed Feb 22 2006 - 21:36:16 CST)
- Re: Mapping electronic potential to surface Axel Kohlmeyer (Thu Feb 23 2006 - 00:55:53 CST)
- Re: Mapping electronic potential to surface John Stone (Thu Feb 23 2006 - 11:48:47 CST)
restart simulation with NAMD lily jin (Wed Feb 22 2006 - 14:01:30 CST)
- Re: restart simulation with NAMD Nuno R. L. Ferreira (Thu Feb 23 2006 - 05:02:23 CST)
How to display a periodic image using TCL commands? Nicolas Sapay (Wed Feb 22 2006 - 11:08:28 CST)
- Re: How to display a periodic image using TCL commands? John Stone (Wed Feb 22 2006 - 11:11:23 CST)
VMD /w >2GB RAM on Windows XP, and Windows XP x64 64-bit version... John Stone (Wed Feb 22 2006 - 10:51:19 CST)
RE: problem with script to get RMSD-solved Ana Celia Araujo Vila Verde (Tue Feb 21 2006 - 10:53:16 CST)
- Re: problem with script to get RMSD-solved Nuno R. L. Ferreira (Tue Feb 21 2006 - 11:41:30 CST)
read_next_timestep(...) Marco Kalweit (Tue Feb 21 2006 - 07:08:40 CST)
- Re: read_next_timestep(...) John Stone (Tue Feb 21 2006 - 09:53:55 CST)
Problem installation on RedHat Fan,Huajun (Mon Feb 20 2006 - 21:18:32 CST)
- Re: Problem installation on RedHat Mgr. Lubos Vrbka (Tue Feb 21 2006 - 00:43:11 CST)
- Re: Problem installation on RedHat Axel Kohlmeyer (Tue Feb 21 2006 - 01:10:52 CST)
Problem with Hg, H Younes Ansari (Sun Feb 19 2006 - 12:38:20 CST)
- Re: Problem with Hg, H John Stone (Mon Feb 20 2006 - 18:41:22 CST)
  - Re: Problem with Hg, H Younes Ansari (Wed May 10 2006 - 04:09:57 CDT)
- Re: Problem with Hg, H Axel Kohlmeyer (Mon Feb 20 2006 - 19:13:49 CST)
vmd 1.8.b does not start up Prashanth Athri (Thu Feb 16 2006 - 17:59:50 CST)
- Re: vmd 1.8.b does not start up Axel Kohlmeyer (Thu Feb 16 2006 - 22:11:29 CST)
RE: problem with script to get RMSD Ana Celia Araujo Vila Verde (Thu Feb 16 2006 - 15:49:23 CST)
- Re: problem with script to get RMSD Nuno R. L. Ferreira (Fri Feb 17 2006 - 03:50:45 CST)
- RE: problem with script to get RMSD Ana Celia Araujo Vila Verde (Fri Feb 17 2006 - 08:41:20 CST)
- RE: problem with script to get RMSD Ana Celia Araujo Vila Verde (Fri Feb 17 2006 - 14:10:10 CST)
problem with script to get RMSD Ana Celia Araujo Vila Verde (Thu Feb 16 2006 - 13:31:28 CST)
- Re: problem with script to get RMSD John Stone (Thu Feb 16 2006 - 13:41:21 CST)
catdcd.LINUX lily jin (Thu Feb 16 2006 - 13:24:16 CST)
- Re: catdcd.LINUX John Stone (Thu Feb 16 2006 - 13:32:27 CST)
  - Re: catdcd.LINUX John Stone (Thu Feb 16 2006 - 14:17:03 CST)
How can i use the catdcd plugin with the VMD windows version? lily jin (Thu Feb 16 2006 - 13:19:50 CST)
- Re: How can i use the catdcd plugin with the VMD windows version? John Stone (Thu Feb 16 2006 - 13:42:30 CST)
Selections in periodic boxes Ignacio Fernández Galván (Thu Feb 16 2006 - 05:24:07 CST)
- Re: Selections in periodic boxes Nicolas Sapay (Mon Mar 06 2006 - 09:13:38 CST)
fortran bindings for molfile library Axel Kohlmeyer (Wed Feb 15 2006 - 09:31:54 CST)
- Re: fortran bindings for molfile library John Stone (Wed Feb 15 2006 - 10:22:04 CST)
PDB Parser cannot interpret ^M ? Francis Reyes (Tue Feb 14 2006 - 22:53:06 CST)
- Re: PDB Parser cannot interpret ^M ? John Stone (Wed Feb 15 2006 - 11:29:03 CST)
RE: PSF tools in windows and long paths Jacob Pøhlsgaard (Wed Feb 15 2006 - 02:51:06 CST)
- Re: PSF tools in windows and long paths Peter Freddolino (Wed Feb 15 2006 - 10:34:21 CST)
moving an atom in VMD lily jin (Tue Feb 14 2006 - 11:15:13 CST)
- Re: moving an atom in VMD John Stone (Tue Feb 14 2006 - 19:58:28 CST)
PSF tools in windows and long paths Jacob Pøhlsgaard (Tue Feb 14 2006 - 03:47:34 CST)
- Re: PSF tools in windows and long paths L. Michel Espinoza-Fonseca (Tue Feb 14 2006 - 04:38:34 CST)
- Re: PSF tools in windows and long paths John Stone (Tue Feb 14 2006 - 16:11:54 CST)
Writing a pdb file with header information Palmer, Teresa (Mon Feb 13 2006 - 16:57:04 CST)
- Re: Writing a pdb file with header information Nuno R. L. Ferreira (Tue Feb 14 2006 - 04:42:50 CST)
  - Installation of VMD-1.8.4b11 binary + IED-2.02 on RH9 Martinek Tamas (Tue Feb 14 2006 - 08:58:15 CST)
Free Cluster-Building Workshops - 16-17 Mar 2006, 20-21 Apr 2006 Tim Skirvin (Mon Feb 13 2006 - 13:33:09 CST)
Loading structures into sequence alignment extension? Francis Reyes (Mon Feb 13 2006 - 11:31:40 CST)
- Re: Loading structures into sequence alignment extension? Elijah Roberts (Mon Feb 13 2006 - 14:03:28 CST)
tcl-reading files Anna Modzelewska (Mon Feb 13 2006 - 07:35:26 CST)
- Re: tcl-reading files Nuno R. L. Ferreira (Mon Feb 13 2006 - 08:10:20 CST)
  - Re: tcl-reading files Anna Modzelewska (Mon Feb 13 2006 - 08:52:19 CST)
- Re: tcl-reading files andrea spitaleri (Mon Feb 13 2006 - 08:42:49 CST)
number of waters around a protein L. Michel Espinoza-Fonseca (Mon Feb 13 2006 - 06:05:23 CST)
$64k/yr hpc post-doc@lanl Kevin Y. Sanbonmatsu (Sun Feb 12 2006 - 19:05:34 CST)
test - 0123456789abcdefghijklnmopqrstuvwxyz Kevin Y. Sanbonmatsu (Sun Feb 12 2006 - 16:17:28 CST)
Problem with VMD 'animate' command Chandra Ramananjara (Sun Feb 12 2006 - 10:12:36 CST)
- Re: Problem with VMD 'animate' command John Stone (Sun Feb 12 2006 - 16:02:36 CST)
  - Re: Problem with VMD 'animate' command Axel Kohlmeyer (Sun Feb 12 2006 - 20:00:46 CST)
    - Re: Problem with VMD 'animate' command Chandra Ramananjara (Mon Feb 13 2006 - 01:37:31 CST)
    - Re: Problem with VMD 'animate' command John Stone (Tue Feb 14 2006 - 10:32:20 CST)
VMD Plugin update for Windows problem Mikolai Fajer (Sat Feb 11 2006 - 07:58:21 CST)
- Re: VMD Plugin update for Windows problem John Stone (Sun Feb 12 2006 - 16:21:09 CST)
RE: VMD 1.8.4 beta 11 test version available Warren DeLano (Fri Feb 10 2006 - 19:12:14 CST)
- Re: VMD 1.8.4 beta 11 test version available John Stone (Fri Feb 10 2006 - 19:12:57 CST)
using paratool L. Michel Espinoza-Fonseca (Fri Feb 10 2006 - 17:45:32 CST)
- Re: using paratool Jan Saam (Fri Feb 10 2006 - 18:06:31 CST)
VMD 1.8.4 beta 11 test version available John Stone (Fri Feb 10 2006 - 17:20:47 CST)
- Re: VMD 1.8.4 beta 11 test version available L. Michel Espinoza-Fonseca (Fri Feb 10 2006 - 17:43:07 CST)
  - Re: VMD 1.8.4 beta 11 test version available John Stone (Fri Feb 10 2006 - 17:50:44 CST)
  - Re: VMD 1.8.4 beta 11 test version available Jan Saam (Fri Feb 10 2006 - 18:29:34 CST)
water box lily jin (Fri Feb 10 2006 - 17:07:13 CST)
- Re: water box John Stone (Sun Feb 12 2006 - 16:33:58 CST)
  - Re: water box Alexander A. Vakhrushev (Tue Sep 30 2008 - 09:24:43 CDT)
AtomSel with object index (Python scripting) ziemys_at_ecr6.ohio-state.edu (Fri Feb 10 2006 - 13:04:07 CST)
- Re: AtomSel with object index (Python scripting) John Stone (Fri Feb 10 2006 - 13:26:44 CST)
batchmode use of "labels" functions? Brian Bennion (Fri Feb 10 2006 - 11:59:32 CST)
- Re: batchmode use of "labels" functions? John Stone (Fri Feb 10 2006 - 12:50:40 CST)
VTK with VMD Rahul Sampath (Thu Feb 09 2006 - 21:15:27 CST)
- Re: VTK with VMD John Stone (Fri Feb 10 2006 - 13:52:53 CST)
uncompress files in tcl script Joseph Fernandez (Thu Feb 09 2006 - 09:55:05 CST)
- Re: uncompress files in tcl script Nuno R. L. Ferreira (Thu Feb 09 2006 - 10:28:22 CST)
- Re: uncompress files in tcl script Axel Kohlmeyer (Thu Feb 09 2006 - 12:20:44 CST)
  - Re: uncompress files in tcl script Joseph Fernandez (Thu Feb 09 2006 - 14:56:51 CST)
vmd-1.8.4b10/Linux amd64 only libstdc++.so.6 dependancy Tru Huynh (Tue Feb 07 2006 - 08:16:05 CST)
- Re: vmd-1.8.4b10/Linux amd64 only libstdc++.so.6 dependancy John Stone (Wed Feb 08 2006 - 17:48:25 CST)
  - Re: vmd-1.8.4b10/Linux amd64 only libstdc++.so.6 dependancy Dan Wright (Wed Feb 08 2006 - 22:26:53 CST)
  - Re: vmd-1.8.4b10/Linux amd64 only libstdc++.so.6 dependancy Tru Huynh (Thu Feb 09 2006 - 09:13:52 CST)
trajectory2 bizoniusz_at_o2.pl (Mon Feb 06 2006 - 14:55:20 CST)
- Re: trajectory2 John Stone (Mon Feb 06 2006 - 18:08:01 CST)
Tcl scripting Nuno R. L. Ferreira (Mon Feb 06 2006 - 13:13:06 CST)
- Re: Tcl scripting Mario Valle (Mon Feb 06 2006 - 22:46:08 CST)
  - Re: Tcl scripting daniel aguayo (Tue Feb 07 2006 - 17:34:22 CST)
    - Re: Tcl scripting Dan Wright (Wed Feb 08 2006 - 12:14:41 CST)
- Re: Tcl scripting John Stone (Wed Feb 08 2006 - 17:34:53 CST)
  - Re: Tcl scripting Nuno R. L. Ferreira (Thu Feb 09 2006 - 03:07:25 CST)
trajectory bizoniusz_at_o2.pl (Mon Feb 06 2006 - 12:02:27 CST)
- Re: trajectory John Stone (Mon Feb 06 2006 - 12:44:13 CST)
OpenGL Shading Program is not available griadi_at_utalca.cl (Fri Feb 03 2006 - 20:39:37 CST)
- Re: OpenGL Shading Program is not available John Stone (Wed Feb 08 2006 - 18:04:21 CST)
Looking for x86 Mac testers... John Stone (Fri Feb 03 2006 - 19:55:57 CST)
compose pdb Osmany Guirola Cruz (Fri Feb 03 2006 - 12:37:47 CST)
- Re: compose pdb John Stone (Fri Feb 03 2006 - 12:42:49 CST)
Moving molecules with Spaceball or with a Tool Marc Baaden (Fri Feb 03 2006 - 11:50:15 CST)
- Re: Moving molecules with Spaceball or with a Tool John Stone (Wed Feb 08 2006 - 18:06:43 CST)
analysis script causes vmd to crash Eliud Oloo (Thu Feb 02 2006 - 19:26:35 CST)
- Re: analysis script causes vmd to crash Axel Kohlmeyer (Thu Feb 02 2006 - 22:03:15 CST)
Problems with Spaceball 4000FLX Pietro Amodeo (Thu Feb 02 2006 - 15:04:58 CST)
- Re: Problems with Spaceball 4000FLX John Stone (Thu Feb 02 2006 - 17:31:45 CST)
vmdtext on Mac OS X dimka (Thu Feb 02 2006 - 13:54:32 CST)
- Re: vmdtext on Mac OS X John Stone (Thu Feb 02 2006 - 17:34:43 CST)
  - Re: vmdtext on Mac OS X dimka (Thu Feb 02 2006 - 18:25:08 CST)
    - Re: vmdtext on Mac OS X John Stone (Fri Feb 03 2006 - 17:19:37 CST)
RE: a question about dcd files Ana Celia Vila Verde (Thu Feb 02 2006 - 08:32:35 CST)
external ??? Damien Touraine (Thu Feb 02 2006 - 09:45:11 CST)
- Re: external ??? John Stone (Thu Feb 02 2006 - 10:06:02 CST)
installing problem python 2.2.2 for ied on amd64 Florian Haberl (Thu Feb 02 2006 - 08:50:36 CST)
- Re: installing problem python 2.2.2 for ied on amd64 John Stone (Thu Feb 02 2006 - 17:51:13 CST)
RE: printing to a file from a procedure to get RMSD Ana Celia Araujo Vila Verde (Thu Feb 02 2006 - 08:35:30 CST)
stereo with vmd Osmany Guirola Cruz (Wed Feb 01 2006 - 16:53:32 CST)
- Re: stereo with vmd John Stone (Wed Feb 01 2006 - 17:06:00 CST)
a question about dcd files Ana Celia Vila Verde (Wed Feb 01 2006 - 13:53:39 CST)
- Re: a question about dcd files John Stone (Wed Feb 01 2006 - 14:29:15 CST)
dublicated residue name in PDB/PSF ziemys_at_ecr6.ohio-state.edu (Wed Feb 01 2006 - 09:15:37 CST)
- Re: dublicated residue name in PDB/PSF daniel aguayo (Wed Feb 01 2006 - 12:24:16 CST)
printing to a file from a procedure to get RMSD Ana Celia Araujo Vila Verde (Tue Jan 31 2006 - 10:28:37 CST)
- Re: printing to a file from a procedure to get RMSD John Stone (Tue Jan 31 2006 - 10:43:23 CST)
- Re: printing to a file from a procedure to get RMSD Jérôme Hénin (Tue Jan 31 2006 - 12:57:09 CST)
opendx and vmd Guanglei Cui (Sat Jan 28 2006 - 21:30:52 CST)
- Re: opendx and vmd John Stone (Mon Jan 30 2006 - 14:43:39 CST)
ntdll.dll problem when changing drawing methods Paul Van Allsburg (Mon Jan 30 2006 - 14:06:54 CST)
- Re: ntdll.dll problem when changing drawing methods John Stone (Mon Jan 30 2006 - 16:32:10 CST)
  - Re: ntdll.dll problem when changing drawing methods Paul Van Allsburg (Tue Jan 31 2006 - 10:53:24 CST)
vmd installation on the server andrea spitaleri (Mon Jan 30 2006 - 09:31:46 CST)
- Re: vmd installation on the server John Stone (Mon Jan 30 2006 - 10:08:37 CST)
  - Re: vmd installation on the server andrea spitaleri (Tue Jan 31 2006 - 03:25:19 CST)
    - Re: vmd installation on the server John Stone (Tue Jan 31 2006 - 13:41:55 CST)
grid Pavel Macek (Mon Jan 30 2006 - 06:30:07 CST)
- Re: grid Vlad Cojocaru (Mon Jan 30 2006 - 07:15:56 CST)
  - Re: grid John Stone (Mon Jan 30 2006 - 10:15:29 CST)
timeline - write canvas to ps Nuno R. L. Ferreira (Sat Jan 28 2006 - 07:54:14 CST)
- Re: timeline - write canvas to ps John Stone (Mon Jan 30 2006 - 16:28:10 CST)
installing vmd on IBM AIX 5 mrg28_at_drexel.edu (Fri Jan 27 2006 - 15:22:45 CST)
- Re: installing vmd on IBM AIX 5 John Stone (Fri Jan 27 2006 - 15:58:53 CST)
Message from Chaitanya Krishna Chaitanya Krishna (Fri Jan 27 2006 - 08:17:50 CST)
An APBS problem Zhiyong Zhang (Thu Jan 26 2006 - 20:38:15 CST)
- Re: An APBS problem John Stone (Fri Jan 27 2006 - 13:56:03 CST)
Re: Question: Cannot input hostname (LINUXAMD64.opengl) John Stone (Thu Jan 26 2006 - 14:24:30 CST)
- Re: Question: Cannot input hostname (LINUXAMD64.opengl) Hideki Hatanaka (Fri Jan 27 2006 - 10:42:52 CST)
IED-plugin Nadia Vahdati (Thu Jan 26 2006 - 04:46:40 CST)
- Re: IED-plugin John Stone (Thu Jan 26 2006 - 12:45:52 CST)
Re: vmd movie ppmtompeg Dan White (Thu Jan 26 2006 - 01:42:09 CST)
distances on a isosurface plot Marco Neves (Wed Jan 25 2006 - 12:28:09 CST)
- Re: distances on a isosurface plot John Stone (Thu Jan 26 2006 - 14:21:37 CST)
Can't load a large dcd? Vineet Pande (Wed Jan 25 2006 - 06:21:53 CST)
- Re: Can't load a large dcd? John Stone (Wed Jan 25 2006 - 10:23:36 CST)
  - Re: Can't load a large dcd? Vineet Pande (Thu Jan 26 2006 - 01:33:19 CST)
- Re: Can't load a large dcd? Axel Kohlmeyer (Wed Jan 25 2006 - 10:52:41 CST)
vmd plugins / external programs Nuno R. L. Ferreira (Wed Jan 25 2006 - 04:11:09 CST)
- Re: vmd plugins / external programs John Stone (Thu Jan 26 2006 - 13:54:06 CST)
Changing Graphical Representations Adrian Koh (Wed Jan 25 2006 - 00:15:54 CST)
- Re: Changing Graphical Representations Axel Kohlmeyer (Wed Jan 25 2006 - 06:53:15 CST)
  - Re: Changing Graphical Representations John Stone (Thu Jan 26 2006 - 14:03:29 CST)
Generating more than 100,000 water molecules Jindal Shah (Tue Jan 24 2006 - 15:06:15 CST)
- Re: Generating more than 100,000 water molecules John Stone (Tue Jan 24 2006 - 15:26:18 CST)
vmdmovie (ppmtompeg) doesn't work Jackson Gois (Tue Jan 24 2006 - 12:40:43 CST)
- Re: vmdmovie (ppmtompeg) doesn't work John Stone (Tue Jan 24 2006 - 12:50:56 CST)
problem with APBS pqr generation... Ravinder Abrol (Mon Jan 23 2006 - 20:26:17 CST)
- Re: problem with APBS pqr generation... John Stone (Tue Jan 24 2006 - 11:21:16 CST)
error loading pdb files Dean Appling (Tue Jan 24 2006 - 08:59:08 CST)
- Re: error loading pdb files John Stone (Tue Jan 24 2006 - 10:09:12 CST)
  - Re: error loading pdb files John Stone (Tue Jan 24 2006 - 11:13:39 CST)
Adding New Color Definitions to Color Form Adrian Koh (Tue Jan 24 2006 - 03:08:48 CST)
- Re: Adding New Color Definitions to Color Form John Stone (Tue Jan 24 2006 - 10:11:21 CST)
Re: [jrodgers78@gmail.com: outputing secondary structure from timeline] Barry Isralewitz (Mon Jan 23 2006 - 15:16:42 CST)
pytjhon John M. Robinson (Mon Jan 23 2006 - 14:06:12 CST)
- Re: pytjhon John Stone (Tue Jan 24 2006 - 11:25:06 CST)
large DCD file "appears to contain no timesteps" Linghao Zhong (Mon Jan 23 2006 - 13:15:47 CST)
- Re: large DCD file "appears to contain no timesteps" John Stone (Mon Jan 23 2006 - 13:28:49 CST)
outputing secondary structure from timeline Jocelyn Rodgers (Mon Jan 23 2006 - 10:29:30 CST)
64 bit NAMD on AIX and CatDCD Joshua D. Moore (Sat Jan 21 2006 - 13:22:11 CST)
- Re: 64 bit NAMD on AIX and CatDCD John Stone (Mon Jan 23 2006 - 13:21:14 CST)
rod-like shapes Craig Knox (Fri Jan 20 2006 - 16:49:21 CST)
- Re: rod-like shapes John Stone (Fri Jan 20 2006 - 17:05:26 CST)
Re: X-PLOR EDM files (from AMBER) John Stone (Fri Jan 20 2006 - 14:27:39 CST)
- Re: X-PLOR EDM files (from AMBER) Vlad Cojocaru (Wed Feb 01 2006 - 09:05:37 CST)
loading X-PLOR grids created with ptraj Vlad Cojocaru (Fri Jan 20 2006 - 03:59:35 CST)
- Re: loading X-PLOR grids created with ptraj John Stone (Fri Jan 20 2006 - 10:05:01 CST)
Changing Default Settings for VMD Main Window Adrian Koh (Thu Jan 19 2006 - 05:08:23 CST)
- Re: Changing Default Settings for VMD Main Window Axel Kohlmeyer (Thu Jan 19 2006 - 08:02:47 CST)
General query on MD Lin (Wed Jan 18 2006 - 23:31:06 CST)
- Re: General query on MD Peter Freddolino (Fri Jan 20 2006 - 09:06:49 CST)
Secondary Structure Stays at the last frame h9826299_at_hkusua.hku.hk (Wed Jan 18 2006 - 15:22:41 CST)
- Re: Secondary Structure Stays at the last frame John Stone (Wed Jan 18 2006 - 16:04:52 CST)
  - Re: Secondary Structure Stays at the last frame h9826299_at_hkusua.hku.hk (Wed Jan 18 2006 - 16:19:52 CST)
measure hbonds question Mgr. Lubos Vrbka (Wed Jan 18 2006 - 10:13:29 CST)
- Re: measure hbonds question John Stone (Fri Jan 20 2006 - 15:02:37 CST)
  - Re: measure hbonds question Mgr. Lubos Vrbka (Fri Jan 20 2006 - 15:19:54 CST)
creating periodic images of an atom Mgr. Lubos Vrbka (Wed Jan 18 2006 - 08:08:41 CST)
- Re: creating periodic images of an atom John Stone (Wed Jan 18 2006 - 17:08:27 CST)
  - Re: creating periodic images of an atom Mgr. Lubos Vrbka (Thu Jan 19 2006 - 01:58:15 CST)
    - Re: creating periodic images of an atom John Stone (Fri Jan 20 2006 - 14:39:57 CST)
    - Re: creating periodic images of an atom Mgr. Lubos Vrbka (Mon Jan 23 2006 - 08:22:43 CST)
PSF file Jindal Shah (Tue Jan 17 2006 - 13:21:49 CST)
trouble with autopsf Lin (Tue Jan 17 2006 - 09:54:05 CST)
- Re: trouble with autopsf Peter Freddolino (Tue Jan 17 2006 - 09:57:46 CST)
[vmd] max number of molecules on mac James Rustad (Mon Jan 16 2006 - 22:27:30 CST)
- Re: [vmd] max number of molecules on mac Axel Kohlmeyer (Tue Jan 17 2006 - 06:32:23 CST)
  - Re: [vmd] max number of molecules on mac James Rustad (Tue Jan 17 2006 - 09:55:22 CST)
    - Re: [vmd] max number of molecules on mac John Stone (Tue Jan 17 2006 - 10:06:26 CST)
opengl not found Gavin Seddon (Mon Jan 16 2006 - 10:00:14 CST)
- Re: opengl not found John Stone (Tue Jan 17 2006 - 10:49:40 CST)
get values from openDx grid format daniel aguayo (Mon Jan 16 2006 - 19:25:57 CST)
- Re: get values from openDx grid format John Stone (Tue Jan 17 2006 - 10:46:10 CST)
  - Re: get values from openDx grid format daniel aguayo (Wed Jan 18 2006 - 12:45:07 CST)
Release of RESP ESP charge DDatabase FyD (Mon Jan 16 2006 - 10:06:08 CST)
get values from openDx grid format daniel aguayo (Sun Jan 15 2006 - 19:33:45 CST)
- Re: get values from openDx grid format daniel aguayo (Mon Jan 16 2006 - 19:00:34 CST)
maximum number of molecules James Rustad (Fri Jan 13 2006 - 13:27:06 CST)
- Re: maximum number of molecules John Stone (Fri Jan 13 2006 - 13:36:39 CST)
Re: transoffset command Nuno R. L. Ferreira (Thu Jan 12 2006 - 12:05:55 CST)
generating a huge number of water molecules Morad Alawneh (Thu Jan 12 2006 - 12:11:19 CST)
- Re: generating a huge number of water molecules John Stone (Thu Jan 19 2006 - 14:40:22 CST)
  - Problem with biotin autopsf Lin (Thu Jan 19 2006 - 22:17:02 CST)
    - Re: Problem with biotin autopsf Peter Freddolino (Fri Jan 20 2006 - 09:14:56 CST)
transoffset command Nuno R. L. Ferreira (Thu Jan 12 2006 - 10:49:05 CST)
script no reading correct number of frames syma (Thu Jan 12 2006 - 10:03:02 CST)
- Re: script no reading correct number of frames John Stone (Thu Jan 12 2006 - 10:07:41 CST)
mpeg1 movie output makes 0Kb file - any one know why? Dan White (Thu Jan 12 2006 - 08:13:42 CST)
- Re: mpeg1 movie output makes 0Kb file - any one know why? John Stone (Thu Jan 12 2006 - 09:57:17 CST)
  - Re: mpeg1 movie output makes 0Kb file - any one know why? Dan White (Thu Jan 12 2006 - 10:42:38 CST)
    - Re: mpeg1 movie output makes 0Kb file - any one know why? John Stone (Thu Jan 12 2006 - 10:57:11 CST)
    - Re: mpeg1 movie output makes 0Kb file - any one know why? John Stone (Thu Jan 12 2006 - 10:58:22 CST)
Trouble installing VMD Jon Savian (Tue Jan 10 2006 - 17:54:34 CST)
- Re: Trouble installing VMD Axel Kohlmeyer (Tue Jan 10 2006 - 23:37:14 CST)
secondary structure's display - problem Anna Modzelewska (Tue Jan 10 2006 - 10:29:43 CST)
- Re: secondary structure's display - problem Vlad Cojocaru (Tue Jan 10 2006 - 11:08:43 CST)
  - Re: secondary structure's display - problem Anna Modzelewska (Wed Jan 11 2006 - 09:03:28 CST)
High CPU usage with vmd-1.8.4b6 (99.9 %CPU ...) while using the FPS indicator Stéphane Teletchéa (Tue Jan 10 2006 - 09:37:04 CST)
- Re: High CPU usage with vmd-1.8.4b6 (99.9 %CPU ...) while using the FPS indicator John Stone (Tue Jan 10 2006 - 09:54:52 CST)
  - Re: High CPU usage with vmd-1.8.4b6 (99.9 %CPU ...) while using the FPS indicator Stéphane Teletchéa (Tue Jan 10 2006 - 10:08:22 CST)
How to display text on helices ? Stéphane Teletchéa (Mon Jan 09 2006 - 11:45:17 CST)
- Re: How to display text on helices ? John Stone (Mon Jan 09 2006 - 11:50:38 CST)
  - Re: How to display text on helices ? Stéphane Teletchéa (Tue Jan 10 2006 - 08:47:37 CST)
    - Re: How to display text on helices ? Stéphane Teletchéa (Wed Jan 11 2006 - 02:49:16 CST)
    - Re: How to display text on helices ? John Stone (Wed Jan 11 2006 - 12:58:00 CST)
Re: namd-l: Turning off forces in VMD Marc Baaden (Mon Jan 09 2006 - 01:01:03 CST)
loading a new molecule without changing the view Benjamin SCHWARZ (Fri Jan 06 2006 - 08:01:05 CST)
- Re: loading a new molecule without changing the view Axel Kohlmeyer (Fri Jan 06 2006 - 14:05:40 CST)
animate transparency Yu Chen (Thu Jan 05 2006 - 15:07:37 CST)
- Re: animate transparency Axel Kohlmeyer (Fri Jan 06 2006 - 07:07:43 CST)
problem with generating movie from pdb files Sergey Krishtal (Thu Jan 05 2006 - 04:19:38 CST)
- Re: problem with generating movie from pdb files John Stone (Mon Jan 09 2006 - 17:08:46 CST)
Text/Labels on ray tracing externer render Xiangyun Qiu (Wed Jan 04 2006 - 21:53:13 CST)
VMD 1.8.4 beta 7 posted for testers... John Stone (Wed Jan 04 2006 - 19:19:35 CST)
psfgen problem Morad Alawneh (Wed Jan 04 2006 - 17:34:46 CST)
Help on MD animation with VMD yuhl (Tue Jan 03 2006 - 17:41:07 CST)
- Re: Help on MD animation with VMD John Stone (Wed Jan 04 2006 - 18:24:15 CST)
question about script for drawing dipole moment for helix jz7_at_duke.edu (Tue Jan 03 2006 - 17:39:32 CST)
- Re: question about script for drawing dipole moment for helix John Stone (Mon Jan 09 2006 - 11:08:54 CST)
installing IED on an sgi Denise Teotico (Tue Jan 03 2006 - 17:35:07 CST)
CMAP problem Morad Alawneh (Tue Jan 03 2006 - 13:45:41 CST)
- Re: CMAP problem John Stone (Tue Jan 03 2006 - 14:05:32 CST)
installing IED on vmd on windows Denise G Teotico (Tue Jan 03 2006 - 10:06:51 CST)
- Re: installing IED on vmd on windows John Stone (Tue Jan 03 2006 - 10:25:13 CST)
changing default sec struct colors sheldonp_at_sas.upenn.edu (Mon Jan 02 2006 - 10:18:21 CST)
- Re: changing default sec struct colors Axel Kohlmeyer (Mon Jan 02 2006 - 16:12:46 CST)
pdb structure off the web sheldonp_at_sas.upenn.edu (Mon Jan 02 2006 - 10:00:06 CST)
- Re: pdb structure off the web John Stone (Tue Jan 03 2006 - 10:06:25 CST)
Building a sphere of atoms around a chosen atom Chaitanya Krishna A (Mon Jan 02 2006 - 08:01:49 CST)
- Re: Building a sphere of atoms around a chosen atom Axel Kohlmeyer (Tue Jan 03 2006 - 05:03:53 CST)
installation problem on solaris 9 deepti sethi (Sat Dec 31 2005 - 03:57:55 CST)
- Re: installation problem on solaris 9 Axel Kohlmeyer (Sat Dec 31 2005 - 09:42:53 CST)
- Re: installation problem on solaris 9 John Stone (Tue Jan 03 2006 - 10:31:44 CST)
POPC lipid parameters reference Ravinder Abrol (Wed Dec 28 2005 - 15:47:31 CST)
- Re: POPC lipid parameters reference Taeho Kim (Mon Jan 02 2006 - 09:41:55 CST)
  - Re: POPC lipid parameters reference Ravinder Abrol (Mon Jan 02 2006 - 18:46:45 CST)
problem in using "Automatic PSF Builder" Li Anbang (Tue Dec 27 2005 - 06:51:50 CST)
- Re: problem in using "Automatic PSF Builder" John Stone (Wed Dec 28 2005 - 14:42:36 CST)
- Re: problem in using "Automatic PSF Builder" John Stone (Mon Jan 09 2006 - 11:17:12 CST)
Re: VMD 1.8.4 beta 6 posted on the web... John Stone (Mon Dec 26 2005 - 11:59:43 CST)
RE: default directory Michel Espinoza-Fonseca (Mon Dec 26 2005 - 10:25:01 CST)
default directory Li Anbang (Mon Dec 26 2005 - 09:49:39 CST)
RMSF value of a group of atoms h9826299_at_hkusua.hku.hk (Fri Dec 23 2005 - 12:02:16 CST)
- Re: RMSF value of a group of atoms John Stone (Mon Jan 09 2006 - 11:34:46 CST)
Loading a pdb traj in VMD 1.8.4 beta 6 h9826299_at_hkusua.hku.hk (Fri Dec 23 2005 - 09:18:30 CST)
- Re: Loading a pdb traj in VMD 1.8.4 beta 6 John Stone (Wed Dec 28 2005 - 14:38:11 CST)
Charmm expanded coordinate file format? Joshua Speidel (Thu Dec 22 2005 - 19:30:51 CST)
- Re: Charmm expanded coordinate file format? John Stone (Mon Dec 26 2005 - 12:02:31 CST)
VMD 1.8.4 beta 6 posted on the web... John Stone (Thu Dec 22 2005 - 16:46:43 CST)
ati radeon 9200 Osmany Guirola Cruz (Thu Dec 22 2005 - 10:00:07 CST)
- Re: ati radeon 9200 John Stone (Thu Dec 22 2005 - 10:18:17 CST)
  - Re: ati radeon 9200 Osmany Guirola Cruz (Thu Dec 22 2005 - 14:58:33 CST)
RE: how to use APBS Michel Espinoza-Fonseca (Wed Dec 21 2005 - 12:32:36 CST)
- Re: how to use APBS John Stone (Thu Dec 22 2005 - 16:49:37 CST)
  - Re: how to use APBS John Stone (Mon Jan 09 2006 - 16:38:24 CST)
how to use APBS lily jin (Wed Dec 21 2005 - 12:14:47 CST)
FYI: vmd & vrpn v7.0b5 Marc Baaden (Wed Dec 21 2005 - 05:25:11 CST)
- Re: FYI: vmd & vrpn v7.0b5 John Stone (Wed Dec 21 2005 - 09:57:26 CST)
breaking a big dcd file Nitin Bhardwaj (Tue Dec 20 2005 - 16:09:40 CST)
- Re: breaking a big dcd file John Stone (Tue Dec 20 2005 - 16:28:31 CST)
  - Re: breaking a big dcd file Nitin Bhardwaj (Tue Dec 20 2005 - 16:48:08 CST)
  - Re: breaking a big dcd file Kim Gunnerson (Wed Jan 11 2006 - 13:41:49 CST)
    - Re: Re: breaking a big dcd file John Stone (Wed Jan 11 2006 - 16:23:26 CST)
- Re: breaking a big dcd file Axel Kohlmeyer (Tue Dec 20 2005 - 18:58:28 CST)
Video card compatibility Michael T. Davis (Tue Dec 20 2005 - 14:34:29 CST)
- Re: Video card compatibility John Stone (Tue Dec 20 2005 - 14:54:02 CST)
- Re: Video card compatibility Stéphane Teletchéa (Wed Dec 21 2005 - 07:56:24 CST)
RMSD or RMSF value Anthony Cruz (Tue Dec 20 2005 - 13:17:32 CST)
Error in running VMD on AMD64-bit machine (Fedora Core 4) Cheng, Kelvin (Mon Dec 19 2005 - 16:36:55 CST)
- Re: Error in running VMD on AMD64-bit machine (Fedora Core 4) John Stone (Mon Dec 19 2005 - 16:54:21 CST)
message in the console Cojocaru,Vlad (Sun Dec 18 2005 - 13:42:18 CST)
- Re: message in the console John Stone (Mon Dec 19 2005 - 11:47:36 CST)
  - Re: message in the console Axel Kohlmeyer (Mon Dec 19 2005 - 14:59:27 CST)
how to measure the distance between centroids Michel Espinoza-Fonseca (Fri Dec 16 2005 - 13:37:07 CST)
- Re: how to measure the distance between centroids John Stone (Mon Dec 19 2005 - 16:51:29 CST)
question about "then: then/endif not found" in the start VMD. Cheng Luo, Ph.D. (Fri Dec 16 2005 - 11:52:18 CST)
- Re: question about "then: then/endif not found" in the start VMD. John Stone (Fri Dec 16 2005 - 13:17:28 CST)
vmd and xmgrace Vlad Cojocaru (Fri Dec 16 2005 - 09:24:58 CST)
- Re: vmd and xmgrace John Stone (Mon Dec 19 2005 - 17:13:10 CST)
  - Re: vmd and xmgrace John Stone (Mon Dec 19 2005 - 17:24:32 CST)
regarding 1ORQ.pdb Viswanadham Sridhara (Thu Dec 15 2005 - 14:37:17 CST)
vmd-xplor and noe call andrea spitaleri (Thu Dec 15 2005 - 05:16:58 CST)
- Re: vmd-xplor and noe call John Stone (Thu Dec 15 2005 - 09:51:52 CST)
  - contact map [Re: vmd-xplor and noe call ] andrea spitaleri (Thu Dec 15 2005 - 10:13:30 CST)
Calculation of RMSF h9826299_at_hkusua.hku.hk (Wed Dec 14 2005 - 17:10:28 CST)
- Re: Calculation of RMSF John Stone (Wed Dec 14 2005 - 18:45:30 CST)
- Re: Calculation of RMSF John Stone (Mon Dec 19 2005 - 17:21:51 CST)
RMSD problem on 1.8.4a22 (Linux OpenGL) Stéphane Teletchéa (Wed Dec 14 2005 - 06:05:11 CST)
- Re: RMSD problem on 1.8.4a22 (Linux OpenGL) John Stone (Wed Dec 14 2005 - 12:48:00 CST)
  - Re: RMSD problem on 1.8.4a22 (Linux OpenGL) Stéphane Teletchéa (Thu Dec 15 2005 - 03:54:08 CST)
  - Re: RMSD problem on 1.8.4a22 (Linux OpenGL) Dow Hurst DPHURST (Thu Dec 15 2005 - 09:15:09 CST)
    - Re: RMSD problem on 1.8.4a22 (Linux OpenGL) Stéphane Teletchéa (Thu Dec 15 2005 - 11:59:52 CST)
VMD 1.8.4 hangs on AMD64 Peter Carlsson (Tue Dec 13 2005 - 11:48:48 CST)
- Re: VMD 1.8.4 hangs on AMD64 John Stone (Tue Dec 13 2005 - 13:28:18 CST)
  - Re: VMD 1.8.4 hangs on AMD64 Peter Carlsson (Tue Dec 13 2005 - 15:38:22 CST)
cross correlation in VMD Simon Whitehead (Mon Dec 12 2005 - 12:19:30 CST)
compilation from source: make error message Vlad Cojocaru (Mon Dec 12 2005 - 03:59:36 CST)
- Re: compilation from source: make error message Bogdan Costescu (Mon Dec 12 2005 - 06:04:24 CST)
- Re: compilation from source: make error message John Stone (Mon Dec 12 2005 - 10:02:59 CST)
- Re: compilation from source: make error message Cojocaru,Vlad (Mon Dec 12 2005 - 15:06:08 CST)
  - Re: Re: compilation from source: make error message John Stone (Mon Dec 12 2005 - 15:36:49 CST)
lags on VDW Aleksander Debinski (Mon Dec 12 2005 - 03:54:33 CST)
- Re: lags on VDW John Stone (Mon Dec 12 2005 - 10:44:09 CST)
coloring trajectory depending on coordination number Mgr. Lubos Vrbka (Fri Dec 09 2005 - 10:41:37 CST)
- Re: coloring trajectory depending on coordination number John Stone (Fri Dec 09 2005 - 10:57:18 CST)
  - Re: coloring trajectory depending on coordination number Mgr. Lubos Vrbka (Sun Dec 18 2005 - 08:24:02 CST)
  - Re: coloring trajectory depending on coordination number Mgr. Lubos Vrbka (Thu Apr 27 2006 - 05:06:46 CDT)
compilation: forgot to say about Python Vlad Cojocaru (Fri Dec 09 2005 - 08:06:39 CST)
compilation from source: first attempt failed Vlad Cojocaru (Fri Dec 09 2005 - 08:01:34 CST)
- Re: compilation from source: first attempt failed John Stone (Fri Dec 09 2005 - 09:46:08 CST)
- Re: compilation from source: first attempt failed Bogdan Costescu (Fri Dec 09 2005 - 10:30:07 CST)
fedora core 4 install problem Michal Kolinski (Fri Dec 09 2005 - 05:06:24 CST)
- Re: fedora core 4 install problem John Stone (Fri Dec 09 2005 - 09:49:22 CST)
  - Re: fedora core 4 install problem Michal Kolinski (Mon Dec 12 2005 - 05:06:08 CST)
animate error handling Jérôme Hénin (Fri Dec 09 2005 - 05:04:52 CST)
- Re: animate error handling John Stone (Fri Dec 09 2005 - 09:50:32 CST)
spaceballs, etc. Eugen Leitl (Thu Dec 08 2005 - 16:33:53 CST)
- Re: spaceballs, etc. John Stone (Thu Dec 08 2005 - 16:39:36 CST)
  - Re: spaceballs, etc. Eugen Leitl (Fri Dec 09 2005 - 03:26:35 CST)
    - Re: spaceballs, etc. John Stone (Fri Dec 09 2005 - 09:54:11 CST)
sorry John .. I found them Cojocaru,Vlad (Thu Dec 08 2005 - 15:07:07 CST)
- Re: sorry John .. I found them John Stone (Thu Dec 08 2005 - 15:16:30 CST)
plugin source tree Cojocaru,Vlad (Thu Dec 08 2005 - 14:57:46 CST)
- Re: plugin source tree John Stone (Thu Dec 08 2005 - 15:15:35 CST)
babel compilation error Cojocaru,Vlad (Thu Dec 08 2005 - 14:26:38 CST)
- Re: babel compilation error John Stone (Thu Dec 08 2005 - 14:30:13 CST)
- Re: babel compilation error Bogdan Costescu (Fri Dec 09 2005 - 10:04:22 CST)
  - Re: babel compilation error John Stone (Fri Dec 09 2005 - 10:10:20 CST)
  - Re: babel compilation error Eugen Leitl (Fri Dec 09 2005 - 11:30:24 CST)
    - Re: babel compilation error John Stone (Fri Dec 09 2005 - 12:59:39 CST)
PBC and H-bond detection Jérôme Hénin (Thu Dec 08 2005 - 09:03:57 CST)
- Re: PBC and H-bond detection John Stone (Thu Dec 08 2005 - 13:40:13 CST)
Clipping plane tool and export Paul D. Jones (Wed Dec 07 2005 - 12:58:40 CST)
- Re: Clipping plane tool and export John Stone (Wed Dec 07 2005 - 13:17:20 CST)
Two questions: MacOS X and Raster3D output Mamoru Yamanishi (Wed Dec 07 2005 - 12:28:32 CST)
- Re: Two questions: MacOS X and Raster3D output John Stone (Thu Dec 08 2005 - 16:45:16 CST)
APBS plugin Anthony Cruz (Wed Dec 07 2005 - 14:06:06 CST)
- Re: APBS plugin Mamoru Yamanishi (Wed Dec 07 2005 - 14:18:48 CST)
- Re: APBS plugin John Stone (Wed Dec 07 2005 - 17:08:21 CST)
  - Re: APBS plugin Mamoru Yamanishi (Wed Dec 07 2005 - 21:48:56 CST)
    - Re: APBS plugin John Stone (Thu Dec 08 2005 - 10:14:01 CST)
    - Re: APBS plugin Nathan C. Rockwell (Thu Dec 08 2005 - 15:17:48 CST)
  - Re: APBS plugin Anthony Cruz (Thu Dec 08 2005 - 14:07:37 CST)
    - Re: APBS plugin John Stone (Thu Dec 08 2005 - 11:16:19 CST)
Protein volume and cavityes Anthony Cruz (Wed Dec 07 2005 - 13:01:53 CST)
- Re: Protein volume and cavityes John Stone (Wed Dec 07 2005 - 10:05:27 CST)
  - Re: Protein volume and cavityes spitaleri.andrea_at_hsr.it (Wed Dec 07 2005 - 16:32:33 CST)
- Re: Protein volume and cavityes Ran Friedman (Wed Dec 07 2005 - 11:44:25 CST)
compiling vmd from source--will that solve ied issue? Vlad Cojocaru (Wed Dec 07 2005 - 09:16:31 CST)
- Re: compiling vmd from source--will that solve ied issue? John Stone (Wed Dec 07 2005 - 10:01:13 CST)
colorid Luc Moulinier (Wed Dec 07 2005 - 07:27:35 CST)
- Re: colorid John Stone (Wed Dec 07 2005 - 10:17:58 CST)
Problem in linking (with TCL included in webpdbplugin.c) Do_Ba Duc (Tue Dec 06 2005 - 20:55:11 CST)
- Re: Problem in linking (with TCL included in webpdbplugin.c) John Stone (Wed Dec 07 2005 - 10:47:51 CST)
Problem with webpdgplugin-s.o and TCL while linking Do_Ba Duc (Tue Dec 06 2005 - 19:42:55 CST)
python: it doesnt work Cojocaru,Vlad (Tue Dec 06 2005 - 16:34:13 CST)
H-Bonds Paul D. Jones (Tue Dec 06 2005 - 15:18:31 CST)
- Re: H-Bonds John Stone (Tue Dec 06 2005 - 16:34:22 CST)
Python libraries for vmd: _tkinter was not enabled in Modules/Setup Cojocaru,Vlad (Tue Dec 06 2005 - 14:45:55 CST)
coloring method Guanglei Cui (Tue Dec 06 2005 - 12:48:55 CST)
- Re: coloring method John Stone (Tue Dec 06 2005 - 16:40:15 CST)
RE: dihedral angles Michel Espinoza-Fonseca (Mon Dec 05 2005 - 17:28:28 CST)
dihedral angles Narender Singh Maan (Mon Dec 05 2005 - 16:04:20 CST)
- Re: dihedral angles Eduard Schreiner (Tue Dec 06 2005 - 09:35:22 CST)
RE: MSMS problem Cojocaru,Vlad (Mon Dec 05 2005 - 13:36:33 CST)
- Re: MSMS problem John Stone (Mon Dec 05 2005 - 13:56:07 CST)
  - Re: MSMS problem Bogdan Costescu (Tue Dec 06 2005 - 11:31:53 CST)
Fwd: Re: VMD installation on Mac Stephen Walch (Mon Dec 05 2005 - 11:04:26 CST)
- Re: Fwd: Re: VMD installation on Mac John Stone (Mon Dec 05 2005 - 14:02:54 CST)
discriminate aromatic ring face andrea spitaleri (Mon Dec 05 2005 - 09:54:38 CST)
- RE: discriminate aromatic ring face Michel Espinoza-Fonseca (Mon Dec 05 2005 - 10:45:47 CST)
Installation problem. Taeho Kim (Sun Dec 04 2005 - 22:31:24 CST)
- Re: Installation problem. John Stone (Mon Dec 05 2005 - 14:07:23 CST)
the same old IED problem Cojocaru,Vlad (Sun Dec 04 2005 - 14:01:07 CST)
MSMS problem Cojocaru,Vlad (Sun Dec 04 2005 - 06:05:43 CST)
- Re: MSMS problem Bogdan Costescu (Mon Dec 05 2005 - 13:21:19 CST)
MSMS problem Cojocaru,Vlad (Sat Dec 03 2005 - 02:40:29 CST)
Delphi binary phi map problem Mengjuei Hsieh (Thu Dec 01 2005 - 17:10:03 CST)
- Re: Delphi binary phi map problem John Stone (Thu Dec 01 2005 - 17:26:20 CST)
  - Re: Delphi binary phi map problem Mengjuei Hsieh (Fri Dec 02 2005 - 18:11:30 CST)
macros and variables Anthony Cruz (Thu Dec 01 2005 - 15:09:07 CST)
- Re: macros and variables John Stone (Thu Dec 01 2005 - 14:34:46 CST)
Tachyon rendering Vlad Cojocaru (Thu Dec 01 2005 - 07:01:22 CST)
- Re: Tachyon rendering John Stone (Thu Dec 01 2005 - 10:01:03 CST)
calling scripts from the command line Galip Gurkan Yardimci (Thu Dec 01 2005 - 04:36:45 CST)
- Re: calling scripts from the command line John Stone (Thu Dec 08 2005 - 18:12:26 CST)
hbonds count Michel Espinoza-Fonseca (Wed Nov 30 2005 - 06:34:26 CST)
- Re: hbonds count J. Rui Rodrigues (Wed Nov 30 2005 - 07:28:41 CST)
- Re: hbonds count Axel Kohlmeyer (Wed Nov 30 2005 - 09:22:16 CST)
  - visualizing charmm trajectories? Samuel Flores (Wed Nov 30 2005 - 17:37:16 CST)
    - Re: visualizing charmm trajectories? John Stone (Wed Nov 30 2005 - 17:44:05 CST)
RE: Video Card Michel Espinoza-Fonseca (Wed Nov 30 2005 - 03:12:48 CST)
MSMS of selection's contribution to total surface Eden Duthie (Tue Nov 29 2005 - 18:10:05 CST)
- Re: MSMS of selection's contribution to total surface John Stone (Wed Nov 30 2005 - 10:15:45 CST)
superposition of molecules Marcela Madrid (Tue Nov 29 2005 - 16:15:26 CST)
- Re: superposition of molecules John Stone (Thu Dec 01 2005 - 15:05:17 CST)
Video Card Jindal Shah (Tue Nov 29 2005 - 10:24:35 CST)
- Re: Video Card Jerome Henin (Tue Nov 29 2005 - 14:00:55 CST)
  - Re: Video Card Mgr. Lubos Vrbka (Wed Nov 30 2005 - 01:12:51 CST)
- Re: Video Card Karsten Suhre (Wed Nov 30 2005 - 02:02:33 CST)
How to efficiently update a surface Mario Valle (Tue Nov 29 2005 - 10:08:21 CST)
- Re: How to efficiently update a surface Justin Gullingsrud (Tue Nov 29 2005 - 11:25:10 CST)
- Re: How to efficiently update a surface Axel Kohlmeyer (Tue Nov 29 2005 - 13:11:17 CST)
  - Re: How to efficiently update a surface Mario Valle (Wed Nov 30 2005 - 04:01:49 CST)
    - Re: How to efficiently update a surface John Stone (Thu Dec 01 2005 - 15:06:44 CST)
vmd-1.83's crash upon pdb load Martin Grana (Tue Nov 29 2005 - 06:25:57 CST)
- Re: vmd-1.83's crash upon pdb load John Stone (Thu Dec 01 2005 - 15:45:26 CST)
Changing colors ed mendez (Sun Nov 27 2005 - 06:30:51 CST)
- Re: Changing colors Axel Kohlmeyer (Mon Nov 28 2005 - 14:56:54 CST)
Quite confused with Movie Maker Yinghong (Fri Nov 25 2005 - 18:30:09 CST)
- Re: Quite confused with Movie Maker John Stone (Thu Dec 08 2005 - 18:17:02 CST)
Bad performance of VMD Jernej Zidar (Wed Nov 23 2005 - 09:40:53 CST)
- Re: Bad performance of VMD John Stone (Mon Nov 28 2005 - 11:16:13 CST)
  - Re: Bad performance of VMD Jernej Zidar (Wed Nov 30 2005 - 04:41:24 CST)
    - Re: Bad performance of VMD John Stone (Fri Dec 02 2005 - 13:03:20 CST)
s-s bond in vmd not visualized andrea spitaleri (Tue Nov 22 2005 - 07:03:52 CST)
- Re: s-s bond in vmd not visualized JC Gumbart (Wed Nov 23 2005 - 13:43:35 CST)
- Re: s-s bond in vmd not visualized Axel Kohlmeyer (Wed Nov 23 2005 - 11:31:57 CST)
  - Re: s-s bond in vmd not visualized andrea spitaleri (Wed Nov 23 2005 - 03:05:39 CST)
- Re: s-s bond in vmd not visualized John Stone (Mon Nov 28 2005 - 11:21:49 CST)
  - Re: s-s bond in vmd not visualized andrea spitaleri (Tue Nov 29 2005 - 03:22:52 CST)
RE: psfgen error: MOLECULE DESTROYED BY FATAL ERROR Michel Espinoza-Fonseca (Tue Nov 22 2005 - 16:47:42 CST)
- RE: psfgen error: MOLECULE DESTROYED BY FATAL ERROR Michel Espinoza-Fonseca (Tue Nov 22 2005 - 18:12:31 CST)
Re: psfgen error: MOLECULE DESTROYED BY FATAL ERROR Sergio Anis (Tue Nov 22 2005 - 15:58:42 CST)
VMD input devices for USB-only Macs ? Marc Baaden (Tue Nov 22 2005 - 13:17:54 CST)
- Re: VMD input devices for USB-only Macs ? John Stone (Tue Nov 22 2005 - 13:22:58 CST)
psfgen error: MOLECULE DESTROYED BY FATAL ERROR Ana Celia Araujo Vila Verde (Tue Nov 22 2005 - 13:13:15 CST)
RE: Uncharged terminal ends? Michel Espinoza-Fonseca (Tue Nov 22 2005 - 03:57:06 CST)
- RE: Uncharged terminal ends? hodak_at_chips.ncsu.edu (Tue Nov 22 2005 - 04:00:00 CST)
- RE: Uncharged terminal ends? Michel Espinoza-Fonseca (Tue Nov 22 2005 - 04:18:27 CST)
  - RE: Uncharged terminal ends? hodak_at_chips.ncsu.edu (Tue Nov 22 2005 - 04:16:55 CST)
- RE: Uncharged terminal ends? Michel Espinoza-Fonseca (Tue Nov 22 2005 - 04:32:02 CST)
  - RE: Uncharged terminal ends? hodak_at_chips.ncsu.edu (Tue Nov 22 2005 - 04:40:25 CST)
- RE: Uncharged terminal ends? Michel Espinoza-Fonseca (Tue Nov 22 2005 - 04:57:18 CST)
  - RE: Uncharged terminal ends? hodak_at_chips.ncsu.edu (Tue Nov 22 2005 - 05:13:43 CST)
- RE: Uncharged terminal ends? Michel Espinoza-Fonseca (Tue Nov 22 2005 - 06:44:36 CST)
- RE: Uncharged terminal ends? Michel Espinoza-Fonseca (Tue Nov 29 2005 - 04:46:38 CST)
Loading files all at once time to create movie Jindal Shah (Mon Nov 21 2005 - 12:43:48 CST)
- Re: Loading files all at once time to create movie John Stone (Mon Nov 21 2005 - 14:59:51 CST)
python Irina Tuszynska (Mon Nov 21 2005 - 11:37:17 CST)
Uncharged terminal ends? hodak_at_chips.ncsu.edu (Fri Nov 18 2005 - 17:41:13 CST)
- Re: Uncharged terminal ends? Justin Gullingsrud (Sun Nov 20 2005 - 15:12:11 CST)
  - Re: Uncharged terminal ends? hodak_at_chips.ncsu.edu (Mon Nov 21 2005 - 02:19:10 CST)
    - Re: Uncharged terminal ends? Justin Gullingsrud (Mon Nov 21 2005 - 11:49:19 CST)
    - Re: Uncharged terminal ends? hodak_at_chips.ncsu.edu (Tue Nov 22 2005 - 03:18:06 CST)
STRIDE error dimka (Fri Nov 18 2005 - 13:41:02 CST)
- Re: STRIDE error John Stone (Fri Nov 18 2005 - 13:52:17 CST)
  - Re: STRIDE error dimka (Fri Nov 18 2005 - 14:50:04 CST)
Réf. : Re: calculate rmsd in a loop:feedback [sorry if you get it twice] l.spitzer_at_fr.fournierpharma.com (Fri Nov 18 2005 - 04:48:26 CST)
Use VMD Graphics Primitives to Construct Stilized Cyclodextrins rossi_at_york.cuny.edu (Thu Nov 17 2005 - 16:31:01 CST)
- Re: Use VMD Graphics Primitives to Construct Stilized Cyclodextrins John Stone (Fri Nov 18 2005 - 11:06:36 CST)
visualizing charge density in vmd Michel Espinoza-Fonseca (Thu Nov 17 2005 - 09:48:14 CST)
- Re: visualizing charge density in vmd John Stone (Thu Nov 17 2005 - 15:06:18 CST)
Use VMD Primitives to Construct Stilized Cyclodextrins rossi_at_york.cuny.edu (Thu Nov 17 2005 - 07:14:02 CST)
Réf. : Re: Réf. : calculate rmsd in a loop:feedback [sorry if you get it twice] l.spitzer_at_fr.fournierpharma.com (Thu Nov 17 2005 - 04:50:45 CST)
Réf. : calculate rmsd in a loop:feedback [sorry if you get it twice] l.spitzer_at_fr.fournierpharma.com (Thu Nov 17 2005 - 03:52:05 CST)
- Re: Réf. : calculate rmsd in a loop:feedback [sorry if you get it twice] andrea spitaleri (Thu Nov 17 2005 - 04:14:01 CST)
  - Re: Re: Réf. : calculate rmsd in a loop:feedback [sorry if you get it twice] Nuno R. L. Ferreira (Thu Nov 17 2005 - 04:34:44 CST)
- Re: Réf. : calculate rmsd in a loop:feedback [sorry if you get it twice] Nuno R. L. Ferreira (Thu Nov 17 2005 - 04:14:40 CST)
RE: Appending to DCD file with "animate write" Chang, Christopher (Wed Nov 16 2005 - 13:42:36 CST)
- Re: Appending to DCD file with "animate write" John Stone (Wed Nov 16 2005 - 15:01:02 CST)
- RE: Appending to DCD file with "animate write" Chang, Christopher (Wed Nov 16 2005 - 17:05:41 CST)
Appending to DCD file with "animate write" Chang, Christopher (Wed Nov 16 2005 - 13:11:30 CST)
load two or more molecuoles at one time baogen duan (Tue Nov 15 2005 - 21:42:53 CST)
- Re: load two or more molecuoles at one time Axel Kohlmeyer (Wed Nov 16 2005 - 16:21:35 CST)
- calculate rmsd in a loop:feedback [sorry if you get it twice] andrea spitaleri (Thu Nov 17 2005 - 02:50:19 CST)
STRIDE doesnt recognize unusual protein residue Vlad Cojocaru (Wed Nov 16 2005 - 05:14:47 CST)
- Re: STRIDE doesnt recognize unusual protein residue John Stone (Wed Nov 16 2005 - 15:39:11 CST)
  - Re: STRIDE doesnt recognize unusual protein residue Vlad Cojocaru (Fri Nov 18 2005 - 04:57:08 CST)
    - Re: STRIDE doesnt recognize unusual protein residue John Stone (Fri Nov 18 2005 - 09:59:16 CST)
    - Re: STRIDE doesnt recognize unusual protein residue Vlad Cojocaru (Fri Nov 18 2005 - 10:51:09 CST)
Method to measure DNA perterbation Kara Di Giorgio (Tue Nov 15 2005 - 19:43:35 CST)
- RE: Method to measure DNA perterbation syma (Wed Nov 16 2005 - 02:28:14 CST)
Problem with Dell Workstation Kamil Tamiola (Tue Nov 15 2005 - 13:42:00 CST)
- Re: Problem with Dell Workstation John Stone (Tue Nov 15 2005 - 17:51:36 CST)
How do I share trajectory visualizations with other systems? Kara Di Giorgio (Mon Nov 14 2005 - 21:15:19 CST)
- Re: How do I share trajectory visualizations with other systems? Marc Q. Ma (Tue Nov 15 2005 - 06:50:29 CST)
Calculating minimal distance between two groups eladp_at_hplus.tau.ac.il (Mon Nov 14 2005 - 10:02:59 CST)
convert PDB file to CRD? Zhen Qin (Fri Nov 11 2005 - 17:49:21 CST)
- Re: convert PDB file to CRD? Wei Chen (Mon Nov 14 2005 - 11:13:18 CST)
- Re: convert PDB file to CRD? John Stone (Mon Nov 14 2005 - 11:47:48 CST)
illegal mouse mode Axel Kohlmeyer (Fri Nov 11 2005 - 13:33:13 CST)
- Re: illegal mouse mode Dan Wright (Fri Nov 11 2005 - 17:00:07 CST)
- Re: illegal mouse mode John Stone (Tue Nov 15 2005 - 11:24:07 CST)
Error, Tk option requires Tcl zhurx (Fri Nov 11 2005 - 00:14:00 CST)
- Re: Error, Tk option requires Tcl John Stone (Fri Nov 11 2005 - 13:55:05 CST)
psfgen vs. x-plor Craig Maloney (Tue Nov 08 2005 - 20:01:52 CST)
- Re: psfgen vs. x-plor Axel Kohlmeyer (Wed Nov 09 2005 - 02:12:36 CST)
problem generating a psf of a solvated system using VMD Leonardo Sepulveda Durán (Tue Nov 08 2005 - 18:54:18 CST)
mol files Osmany Guirola Cruz (Tue Nov 08 2005 - 14:26:47 CST)
- Re: mol files John Stone (Tue Nov 08 2005 - 14:35:16 CST)
Updating color_scale_bar_new.tcl JOSE MANUEL ROMO HERRERA (Tue Nov 08 2005 - 13:19:08 CST)
L/R lighting discrepancy Bram Stolk (Tue Nov 08 2005 - 10:44:39 CST)
- Re: L/R lighting discrepancy John Stone (Tue Nov 08 2005 - 10:55:57 CST)
  - Re: L/R lighting discrepancy Bram Stolk (Tue Nov 08 2005 - 14:01:25 CST)
explicit secondary structure William Sheffler (Tue Nov 08 2005 - 00:21:29 CST)
- Re: explicit secondary structure John Stone (Tue Nov 08 2005 - 09:55:11 CST)
graphics card William Sheffler (Tue Nov 08 2005 - 00:17:18 CST)
- Re: graphics card John Stone (Tue Nov 08 2005 - 09:56:57 CST)
IRIX6 build from CVS Bram Stolk (Tue Nov 08 2005 - 03:28:25 CST)
- Re: IRIX6 build from CVS Axel Kohlmeyer (Tue Nov 08 2005 - 07:01:51 CST)
  - Re: IRIX6 build from CVS Bram Stolk (Tue Nov 08 2005 - 10:20:10 CST)
- Re: IRIX6 build from CVS Dan Wright (Tue Nov 08 2005 - 10:14:45 CST)
Lipid area dimka (Mon Nov 07 2005 - 13:10:20 CST)
visualizing CCP4 maps in VMD Vlad Cojocaru (Mon Nov 07 2005 - 11:44:00 CST)
- Re: visualizing CCP4 maps in VMD Eric Johnson (Mon Nov 07 2005 - 14:51:57 CST)
- Re: visualizing CCP4 maps in VMD John Stone (Mon Nov 07 2005 - 15:22:40 CST)
error when solvating protein/vmd1.8.4a22 Anna Modzelewska (Mon Nov 07 2005 - 07:31:59 CST)
- Re: error when solvating protein/vmd1.8.4a22 John Stone (Tue Nov 08 2005 - 10:00:58 CST)
  - Re: error when solvating protein/vmd1.8.4a22 amodzelewska_at_iimcb.gov.pl (Tue Nov 08 2005 - 08:44:30 CST)
    - Re: error when solvating protein/vmd1.8.4a22 John Stone (Tue Nov 08 2005 - 15:24:57 CST)
Problems with Terminal and 1.8.4.a22 under OSX (Tiger 10.4.3) kamilt_at_ibmb.uni.wroc.pl (Sun Nov 06 2005 - 16:08:34 CST)
- Re: Problems with Terminal and 1.8.4.a22 under OSX (Tiger 10.4.3) John Stone (Tue Nov 08 2005 - 10:04:01 CST)
increase size membrane andrea spitaleri (Fri Nov 04 2005 - 02:58:43 CST)
- Re: increase size membrane John Stone (Tue Nov 08 2005 - 15:13:33 CST)
indexing water molecules VISWANADHA SRIDHARA (Thu Nov 03 2005 - 16:21:15 CST)
- Re: indexing water molecules John Stone (Thu Nov 03 2005 - 16:43:59 CST)
help with modifying script syma (Wed Nov 02 2005 - 11:47:48 CST)
- Re: help with modifying script Philip Fowler (Mon Nov 07 2005 - 03:05:48 CST)
intermediate states of a morph Yu Chen (Wed Nov 02 2005 - 10:20:24 CST)
- Re: intermediate states of a morph John Stone (Wed Nov 02 2005 - 14:17:44 CST)
saving macros Anna Modzelewska (Wed Nov 02 2005 - 05:35:09 CST)
- Re: saving macros Axel Kohlmeyer (Wed Nov 02 2005 - 08:43:58 CST)
python can't find math module Craig Maloney (Tue Nov 01 2005 - 15:50:10 CST)
superimposing Beth Ashbridge (Tue Nov 01 2005 - 08:03:15 CST)
add a new file to vmd1.8.3 on linux(FC4) baogen duan (Sun Oct 30 2005 - 21:50:22 CST)
- Re: add a new file to vmd1.8.3 on linux(FC4) John Stone (Tue Nov 01 2005 - 15:09:30 CST)
changing the default representation for the sequence viewer Vlad Cojocaru (Mon Oct 31 2005 - 05:20:48 CST)
- Re: changing the default representation for the sequence viewer John Stone (Mon Oct 31 2005 - 16:25:10 CST)
Re: How to rotate a molecule spitaleri.andrea_at_hsr.it (Sun Oct 30 2005 - 03:12:04 CST)
How to rotate a molecule Yang Zhenyu (Sat Oct 29 2005 - 23:32:01 CDT)
How to change the colour of isosurface Yang Zhenyu (Sat Oct 29 2005 - 06:42:13 CDT)
- Re: How to change the colour of isosurface John Stone (Mon Oct 31 2005 - 17:29:09 CST)
[selection problem] When I choose all not 'solvent', one residue is gone?v1.8.3 Stanley Lan (Fri Oct 28 2005 - 11:47:06 CDT)
add a new file type to VMD on linux(FC4) baogen duan (Thu Oct 27 2005 - 22:32:59 CDT)
- Re: add a new file type to VMD on linux(FC4) John Stone (Fri Oct 28 2005 - 09:55:51 CDT)
  - Re: add a new file type to VMD on linux(FC4) John Stone (Fri Oct 28 2005 - 10:24:32 CDT)
MacOS 10.4 problems Craig Maloney (Fri Oct 28 2005 - 00:13:25 CDT)
- Re: MacOS 10.4 problems John Stone (Fri Oct 28 2005 - 09:43:13 CDT)
structural alignment Shachi Gosavi (Thu Oct 27 2005 - 17:01:42 CDT)
- Re: structural alignment John Stone (Fri Oct 28 2005 - 10:43:27 CDT)
Re: removing waters (gramicidin example) Charles McCallum (Thu Oct 27 2005 - 15:46:22 CDT)
- Re: removing waters (gramicidin example) Charles McCallum (Thu Oct 27 2005 - 15:26:01 CDT)
removing waters (gramicidin example) Charles McCallum (Thu Oct 27 2005 - 12:57:46 CDT)
writepsf error... Ravinder Abrol (Thu Oct 27 2005 - 06:07:50 CDT)
- Re: writepsf error... John Stone (Thu Oct 27 2005 - 13:15:39 CDT)
  - Re: writepsf error... Ravinder Abrol (Thu Oct 27 2005 - 16:33:25 CDT)
Réf. : Re: Réf. : Re: visualization of DX map l.spitzer_at_fr.fournierpharma.com (Thu Oct 27 2005 - 03:22:04 CDT)
- Re: Réf. : Re: Réf. : Re: visualization of DX map John Stone (Thu Oct 27 2005 - 11:27:13 CDT)
tcl/python and readline not working Craig Maloney (Wed Oct 26 2005 - 17:48:27 CDT)
- Re: tcl/python and readline not working Robert Brunner (Thu Oct 27 2005 - 11:09:25 CDT)
  - Re: tcl/python and readline not working Craig Maloney (Fri Oct 28 2005 - 00:05:47 CDT)
    - Re: tcl/python and readline not working John Stone (Fri Oct 28 2005 - 09:45:49 CDT)
core API? Craig Maloney (Wed Oct 26 2005 - 13:46:38 CDT)
- Re: core API? John Stone (Wed Oct 26 2005 - 14:28:43 CDT)
making bonds myself Craig Maloney (Tue Oct 25 2005 - 19:16:32 CDT)
- Re: making bonds myself JC Gumbart (Tue Oct 25 2005 - 19:32:08 CDT)
  - Re: making bonds myself Craig Maloney (Tue Oct 25 2005 - 20:05:04 CDT)
    - Re: making bonds myself JC Gumbart (Tue Oct 25 2005 - 22:34:13 CDT)
- Helix display Scott Thibault (Wed Oct 26 2005 - 09:55:10 CDT)
  - Re: Helix display John Stone (Wed Oct 26 2005 - 10:04:26 CDT)
Does Vmd support GUI and rendering separate Terry Jordan (Tue Oct 25 2005 - 14:26:06 CDT)
- Re: Does Vmd support GUI and rendering separate John Stone (Tue Oct 25 2005 - 15:09:00 CDT)
  - Re: Does Vmd support GUI and rendering separate Terry Jordan (Thu Oct 27 2005 - 09:26:10 CDT)
    - Re: Does Vmd support GUI and rendering separate John Stone (Thu Oct 27 2005 - 13:43:42 CDT)
Ask the Cluster Expert Nick I (Tue Oct 25 2005 - 11:45:59 CDT)
Réf. : Re: visualization of DX map l.spitzer_at_fr.fournierpharma.com (Tue Oct 25 2005 - 02:28:43 CDT)
- Re: RéfQ?= : Re: visualization of DX map John Stone (Wed Oct 26 2005 - 17:37:51 CDT)
RE: problem with writepdb Chang, Christopher (Mon Oct 24 2005 - 11:15:22 CDT)
- Re: problem with writepdb John Stone (Mon Oct 24 2005 - 13:10:24 CDT)
visualization of DX map l.spitzer_at_fr.fournierpharma.com (Mon Oct 24 2005 - 10:38:40 CDT)
- Re: visualization of DX map John Stone (Mon Oct 24 2005 - 13:15:07 CDT)
nvidia drivers and 64bit OS VMD/PYMOL asimplefunguy_at_netscape.net (Mon Oct 24 2005 - 09:10:23 CDT)
- Re: nvidia drivers and 64bit OS VMD/PYMOL John Stone (Mon Oct 24 2005 - 13:18:36 CDT)
VMD display size and position Jeffrey Tseng (Sun Oct 23 2005 - 11:55:57 CDT)
- Re: VMD display size and position John Stone (Mon Oct 24 2005 - 17:08:36 CDT)
trouble with autopsf rob zehr (Sat Oct 22 2005 - 08:27:12 CDT)
- Re: trouble with autopsf Peter Freddolino (Sat Oct 22 2005 - 17:35:21 CDT)
  - RE: trouble with autopsf Armen Nalian (Sun Oct 23 2005 - 23:36:09 CDT)
vmd@ks.uiuc.edu,johns@ks.uiuc.edu pinisetty dinesh (Fri Oct 21 2005 - 14:20:45 CDT)
- Re: vmd@ks.uiuc.edu,johns@ks.uiuc.edu John Stone (Fri Oct 21 2005 - 14:26:27 CDT)
Creating bond between two atoms Nitin Bhardwaj (Fri Oct 21 2005 - 12:05:09 CDT)
- Re: Creating bond between two atoms John Stone (Fri Oct 21 2005 - 12:32:44 CDT)
  - Re: Creating bond between two atoms Sergio Anis (Fri Oct 21 2005 - 13:27:36 CDT)
  - Re: Creating bond between two atoms Nitin Bhardwaj (Fri Oct 21 2005 - 13:33:00 CDT)
    - Re: Creating bond between two atoms John Stone (Mon Oct 24 2005 - 17:20:52 CDT)
    - Re: Creating bond between two atoms Nitin Bhardwaj (Tue Oct 25 2005 - 16:09:00 CDT)
RE: Loading multiple molecules in one step / "Apply changes automatically" Michel Espinoza-Fonseca (Fri Oct 21 2005 - 10:29:40 CDT)
- RE: Loading multiple molecules in one step / "Apply changes automatically" Michel Espinoza-Fonseca (Fri Oct 21 2005 - 10:46:46 CDT)
- RE: Loading multiple molecules in one step / "Apply changes automatically" Chang, Christopher (Fri Oct 21 2005 - 11:15:40 CDT)
VMD testers for ATI+Linux automatic driver workaround... John Stone (Thu Oct 20 2005 - 14:56:41 CDT)
Starting v1.8.4a20 vs. v1.8.2a22 Stephen P. Molar, Ph.D. (Thu Oct 20 2005 - 14:07:53 CDT)
- Re: Starting v1.8.4a20 vs. v1.8.2a22 John Stone (Thu Oct 20 2005 - 14:14:56 CDT)
  - Re: Starting v1.8.4a20 vs. v1.8.2a22 Stephen P. Molar, Ph.D. (Thu Oct 20 2005 - 15:05:26 CDT)
RE: Warning: add bond failed in patch ACE Chang, Christopher (Thu Oct 20 2005 - 11:41:43 CDT)
Joystick, VMD and vrpn on Linux Luis Rosales (Wed Oct 19 2005 - 20:50:46 CDT)
- Re: Joystick, VMD and vrpn on Linux John Stone (Thu Oct 20 2005 - 14:25:17 CDT)
  - Re: Joystick, VMD and vrpn on Linux Luis Rosales (Fri Oct 21 2005 - 18:46:37 CDT)
Warning: add bond failed in patch ACE Per Jr. Greisen (Thu Oct 20 2005 - 09:35:44 CDT)
Compiling CATDCD and VMD plugins on AIX5.2 Fiona Reid (Thu Oct 20 2005 - 04:13:27 CDT)
- Re: Compiling CATDCD and VMD plugins on AIX5.2 Fiona Reid (Thu Oct 20 2005 - 10:44:32 CDT)
Mac Stereo 3D Displays & Equipment Jim Phillips (Wed Oct 19 2005 - 18:29:39 CDT)
- solid color clipping plane - render with "scratches" Arturas (Tue Oct 25 2005 - 04:49:45 CDT)
  - Re: solid color clipping plane - render with "scratches" John Stone (Tue Oct 25 2005 - 14:08:51 CDT)
can VMD show artificial bond info? jiwu liu (Wed Oct 19 2005 - 18:04:31 CDT)
- Re: can VMD show artificial bond info? John Stone (Wed Oct 19 2005 - 18:52:46 CDT)
new macs out Eugen Leitl (Wed Oct 19 2005 - 15:10:22 CDT)
- Re: new macs out John Stone (Wed Oct 19 2005 - 15:36:58 CDT)
dots per inch? Kelvin Luther (Wed Oct 19 2005 - 14:01:18 CDT)
- Re: dots per inch? John Stone (Wed Oct 19 2005 - 14:56:23 CDT)
  - RE: dots per inch? Chang, Christopher (Wed Oct 19 2005 - 15:26:46 CDT)
- Re: dots per inch? Dan Strahs (Wed Oct 19 2005 - 16:46:02 CDT)
vmd crashes on startup Dr Gavin Seddon (Wed Oct 19 2005 - 07:40:54 CDT)
- Re: vmd crashes on startup John Stone (Wed Oct 19 2005 - 09:35:08 CDT)
Measuring distance during a trajectory Per Jr. Greisen (Tue Oct 18 2005 - 14:59:42 CDT)
- Re: Measuring distance during a trajectory John Stone (Wed Oct 19 2005 - 16:55:17 CDT)
Reference to SASA calculation in VMD Basak Isin (Tue Oct 18 2005 - 10:12:24 CDT)
- Re: Reference to SASA calculation in VMD John Stone (Thu Oct 20 2005 - 15:20:13 CDT)
How to get a membran.psf from membrane.pdb? Weidong Xin (Tue Oct 18 2005 - 03:42:58 CDT)
- Re: How to get a membran.psf from membrane.pdb? John Stone (Mon Oct 24 2005 - 17:23:55 CDT)
Cannot load Gromos96 trajectory file (attached) Stanley Lan (Mon Oct 17 2005 - 16:26:17 CDT)
- Re: Cannot load Gromos96 trajectory file (attached) John Stone (Mon Oct 17 2005 - 17:11:32 CDT)
  - Re: Cannot load Gromos96 trajectory file (attached) Axel Kohlmeyer (Mon Oct 17 2005 - 19:37:14 CDT)
- problem with writepdb Samuel Flores (Mon Oct 17 2005 - 19:16:33 CDT)
  - Re: problem with writepdb JC Gumbart (Mon Oct 17 2005 - 19:25:49 CDT)
    - problem with writepdb Samuel Flores (Mon Oct 24 2005 - 07:00:04 CDT)
    - Re: problem with writepdb Jim Phillips (Mon Oct 24 2005 - 17:33:23 CDT)
The usual problem with IED Simone Lorenzi (Mon Oct 17 2005 - 13:28:43 CDT)
- Re: The usual problem with IED John Stone (Mon Oct 17 2005 - 17:13:35 CDT)
- Re: The usual problem with IED John Stone (Mon Oct 24 2005 - 17:30:48 CDT)
rdf.tcl one more time bizoniusz_at_o2.pl (Mon Oct 17 2005 - 10:19:28 CDT)
- Re: rdf.tcl one more time John Stone (Mon Oct 17 2005 - 17:20:20 CDT)
gamess plugin error of vmd 1.8.4a22 on windows mashaojie163 (Mon Oct 17 2005 - 06:53:53 CDT)
- Re: gamess plugin error of vmd 1.8.4a22 on windows mashaojie163 (Sat Oct 15 2005 - 01:20:40 CDT)
  - Re: Re: gamess plugin error of vmd 1.8.4a22 on windows John Stone (Mon Oct 17 2005 - 15:03:37 CDT)
- Re: gamess plugin error of vmd 1.8.4a22 on windows John Stone (Fri Oct 28 2005 - 12:04:37 CDT)
IED problem update: IED works only with vmd 1.8.2 Vlad Cojocaru (Mon Oct 17 2005 - 05:21:28 CDT)
- Re: IED problem update: IED works only with vmd 1.8.2 John Stone (Mon Oct 17 2005 - 17:27:23 CDT)
Test version of 1.8.4 posted for Situs users and others... John Stone (Fri Oct 14 2005 - 16:15:43 CDT)
how to make IED work? Vlad Cojocaru (Fri Oct 14 2005 - 14:33:56 CDT)
(no subject) Naser, Md Abu (Fri Oct 14 2005 - 14:12:44 CDT)
- Re: John Stone (Fri Oct 14 2005 - 14:46:53 CDT)
vmd & python Vlad Cojocaru (Fri Oct 14 2005 - 13:15:40 CDT)
- Re: vmd & python John Stone (Fri Oct 14 2005 - 14:50:24 CDT)
PSC WORKSHOP: COMPUTATIONAL BIOPHYSICS WORKSHOP Troy Wymore (Fri Oct 14 2005 - 13:13:15 CDT)
RDF.tcl bizoniusz_at_o2.pl (Fri Oct 14 2005 - 07:02:26 CDT)
- Re: RDF.tcl John Stone (Fri Oct 14 2005 - 15:18:53 CDT)
- Re: RDF.tcl griadi_at_utalca.cl (Fri Jul 28 2006 - 17:01:24 CDT)
  - Re: Re: RDF.tcl Axel Kohlmeyer (Fri Jul 28 2006 - 17:28:49 CDT)
RE: What's wrong with my VMD Dallas B. Warren (Thu Oct 13 2005 - 21:02:12 CDT)
- RE: What's wrong with my VMD Luis Rosales (Fri Oct 14 2005 - 00:42:19 CDT)
matrix transforms of volume objects Dan Strahs (Thu Oct 13 2005 - 20:18:06 CDT)
- Re: matrix transforms of volume objects John Stone (Fri Oct 14 2005 - 15:36:51 CDT)
Classroom Stereo projection Paul Van Allsburg (Thu Oct 13 2005 - 15:16:20 CDT)
- Re: Classroom Stereo projection John Stone (Fri Oct 14 2005 - 15:45:29 CDT)
  - Re: Classroom Stereo projection Paul Van Allsburg (Mon Oct 17 2005 - 08:42:01 CDT)
Interpolation in internal space Jerry Parks (Thu Oct 13 2005 - 10:21:32 CDT)
- poorly get coordinates Samuel Flores (Thu Oct 13 2005 - 13:17:42 CDT)
  - Re: poorly get coordinates JC Gumbart (Thu Oct 13 2005 - 13:43:01 CDT)
- Re: Interpolation in internal space John Stone (Fri Oct 14 2005 - 15:55:29 CDT)
What's wrong with my VMD Yang Zhenyu (Thu Oct 13 2005 - 09:13:59 CDT)
- Re: What's wrong with my VMD John Stone (Fri Oct 14 2005 - 15:51:06 CDT)
IED with VMD 1.8.3 on Debian Vlad Cojocaru (Thu Oct 13 2005 - 07:50:52 CDT)
making a movie Hyonseok Hwang (Thu Oct 13 2005 - 00:13:21 CDT)
- Re: making a movie Axel Kohlmeyer (Thu Oct 13 2005 - 10:49:25 CDT)
RE: Show a movie from one static structure to another in VMD? Dallas B. Warren (Wed Oct 12 2005 - 19:51:36 CDT)
clipplane Linda (Wed Oct 12 2005 - 19:10:35 CDT)
- Re: clipplane John Stone (Fri Oct 14 2005 - 15:58:31 CDT)
- Warining when generating psf file phoenix (Sun Oct 16 2005 - 03:12:12 CDT)
  - Re: Warining when generating psf file Jim Phillips (Wed Oct 19 2005 - 18:15:26 CDT)
RE: puzzling writepdb error Chang, Christopher (Wed Oct 12 2005 - 17:58:33 CDT)
Show a movie from one static structure to another in VMD? Mingliang Tan (Wed Oct 12 2005 - 12:58:55 CDT)
- puzzling writepdb error Samuel Flores (Wed Oct 12 2005 - 16:12:26 CDT)
  - Re: puzzling writepdb error John Stone (Wed Oct 12 2005 - 16:58:24 CDT)
- Re: Show a movie from one static structure to another in VMD? John Stone (Wed Oct 12 2005 - 17:01:22 CDT)
binning data for each frame and coordinate syma (Wed Oct 12 2005 - 04:35:45 CDT)
- Re: binning data for each frame and coordinate Axel Kohlmeyer (Wed Oct 12 2005 - 13:34:37 CDT)
  - modifying mk3drame.tcl syma (Wed Oct 19 2005 - 04:39:12 CDT)
Can vmd do symmetry operation? mashaojie163 (Tue Oct 11 2005 - 21:49:00 CDT)
- Re: Can vmd do symmetry operation? John Stone (Wed Oct 12 2005 - 17:03:56 CDT)
  - extract euler angles from transformation matrix? Samuel Flores (Tue Dec 13 2005 - 15:43:03 CST)
    - Re: extract euler angles from transformation matrix? John Stone (Wed Dec 14 2005 - 10:11:34 CST)
vmd-xplor griadi_at_utalca.cl (Tue Oct 11 2005 - 18:45:46 CDT)
- Re: vmd-xplor John Stone (Wed Oct 12 2005 - 17:08:14 CDT)
rendering problems Turman, Cheri M (Tue Oct 11 2005 - 11:51:37 CDT)
- Re: rendering problems John Stone (Tue Oct 11 2005 - 20:12:57 CDT)
about new vmd on windows mashaojie163 (Tue Oct 11 2005 - 04:11:24 CDT)
using scrpt making movies in Windows Xinyu(cindy) Li (Mon Oct 10 2005 - 10:02:11 CDT)
- Re: using scrpt making movies in Windows John Stone (Mon Oct 10 2005 - 10:10:58 CDT)
getting centre of mass of contacts syma (Mon Oct 10 2005 - 07:13:39 CDT)
- Re: getting centre of mass of contacts John Stone (Mon Oct 10 2005 - 10:30:20 CDT)
Hello! baogen duan (Sat Oct 08 2005 - 05:54:54 CDT)
- Re: Hello! John Stone (Mon Oct 10 2005 - 10:08:13 CDT)
how can I combine several selection into one selection by TCL mashaojie163 (Fri Oct 07 2005 - 22:09:24 CDT)
- Re: how can I combine several selection into one selection by TCL John Stone (Mon Oct 10 2005 - 10:38:37 CDT)
VMD scripting Shirley Li (Thu Oct 06 2005 - 14:37:50 CDT)
- Re: VMD scripting Peter Freddolino (Thu Oct 06 2005 - 14:43:15 CDT)
  - Re: VMD scripting (Thank you) Shirley Li (Thu Oct 06 2005 - 15:55:17 CDT)
overlapping two structures Peter Schellenberg (Thu Oct 06 2005 - 08:37:24 CDT)
- Re: overlapping two structures Peter Freddolino (Fri Oct 07 2005 - 11:20:25 CDT)
- Re: overlapping two structures John Stone (Mon Oct 10 2005 - 10:52:00 CDT)
RMSF calculation Michel Espinoza-Fonseca (Thu Oct 06 2005 - 08:23:00 CDT)
- Re: RMSF calculation JC Gumbart (Thu Oct 06 2005 - 14:51:53 CDT)
large output XYZ file > 2 Gio? (Re: [biosimgrid-team] Re: DCD to XYZ conversion) Kaihsu Tai (Thu Oct 06 2005 - 05:43:14 CDT)
- Re: large output XYZ file > 2 Gio? (Re: [biosimgrid-team] Re: DCD to XYZ conversion) John Stone (Mon Oct 10 2005 - 14:53:09 CDT)
new coordinates Anna Karawajczyk (Thu Oct 06 2005 - 02:57:55 CDT)
- Re: new coordinates Eduard Schreiner (Thu Oct 06 2005 - 06:18:01 CDT)
new coordinates Anna Karawajczyk (Thu Oct 06 2005 - 02:35:09 CDT)
dynamically changing label... Ravinder Abrol (Thu Oct 06 2005 - 02:27:26 CDT)
- Re: dynamically changing label... John Stone (Mon Oct 10 2005 - 14:54:18 CDT)
  - Re: dynamically changing label... Ravinder Abrol (Mon Oct 10 2005 - 16:12:52 CDT)
    - Re: dynamically changing label... John Stone (Mon Oct 10 2005 - 16:15:02 CDT)
how can I combine several selection into one selection by TCL mashaojie163 (Wed Oct 05 2005 - 21:55:49 CDT)
TCL: centering molecule into middle of display after translation pascal.baillod_at_epfl.ch (Wed Oct 05 2005 - 12:13:53 CDT)
- Re: TCL: centering molecule into middle of display after translation John Stone (Wed Oct 12 2005 - 17:54:13 CDT)
changing cpk shere scale in TCL pascal.baillod_at_epfl.ch (Wed Oct 05 2005 - 12:07:15 CDT)
- Re: changing cpk shere scale in TCL JC Gumbart (Wed Oct 05 2005 - 13:38:59 CDT)
  - Re: changing cpk shere scale in TCL John Stone (Wed Oct 05 2005 - 14:47:45 CDT)
Export problem Licorice to STL Kevin Smith (Mon Oct 03 2005 - 10:50:53 CDT)
- Re: Export problem Licorice to STL John Stone (Mon Oct 03 2005 - 11:13:07 CDT)
  - Re: Export problem Licorice to STL Kevin Smith (Mon Oct 03 2005 - 13:16:07 CDT)
centering the molecule Jeffrey Tseng (Sun Oct 02 2005 - 17:53:00 CDT)
- Re: centering the molecule John Stone (Mon Oct 03 2005 - 16:32:10 CDT)
RE: How can I compile win32-vmd Michel Espinoza-Fonseca (Sun Oct 02 2005 - 05:33:45 CDT)
How can I compile win32-vmd mashaojie163 (Sun Oct 02 2005 - 00:18:11 CDT)
- Re: How can I compile win32-vmd John Stone (Mon Oct 03 2005 - 11:15:01 CDT)
  - Re: How can I compile win32-vmd mashaojie163 (Mon Oct 03 2005 - 20:16:15 CDT)
  - Re: How can I compile win32-vmd mashaojie163 (Wed Oct 05 2005 - 22:26:27 CDT)
    - Re: How can I compile win32-vmd John Stone (Tue Oct 11 2005 - 17:03:21 CDT)
Re: RMSD of dihedrals Charles McCallum (Fri Sep 30 2005 - 09:14:55 CDT)
- passing parameters to a tcl script Samuel Flores (Sat Oct 01 2005 - 11:42:51 CDT)
  - Re: passing parameters to a tcl script Justin Gullingsrud (Sat Oct 01 2005 - 15:26:00 CDT)
- Re: RMSD of dihedrals Luis Gracia (Fri Sep 30 2005 - 15:07:22 CDT)
RMSD of dihedrals Charles McCallum (Thu Sep 29 2005 - 15:58:07 CDT)
Display alternative atom locations using vmd Wang, Yangzhou (Thu Sep 29 2005 - 13:35:47 CDT)
- Re: Display alternative atom locations using vmd John Stone (Thu Sep 29 2005 - 14:03:29 CDT)
about gamess plugin mashaojienuaa (Thu Sep 29 2005 - 01:40:50 CDT)
- Re: about gamess plugin John Stone (Thu Sep 29 2005 - 10:59:51 CDT)
fancy representations for lipids? nsapay_at_ibcp.fr (Wed Sep 28 2005 - 18:22:51 CDT)
- Re: fancy representations for lipids? John Stone (Mon Oct 03 2005 - 11:45:35 CDT)
  - Re: fancy representations for lipids? Mauricio Carrillo Tripp (Mon Oct 03 2005 - 14:23:04 CDT)
Potential map display in VMD (GRASP) Anton B. Guliaev (Wed Sep 28 2005 - 18:33:59 CDT)
- Re: Potential map display in VMD (GRASP) John Stone (Thu Sep 29 2005 - 00:19:00 CDT)
- Re: Potential map display in VMD (GRASP) John Stone (Mon Oct 03 2005 - 13:57:10 CDT)
Clip Adrian turjanski (Wed Sep 28 2005 - 20:49:04 CDT)
- Re: Clip John Stone (Thu Sep 29 2005 - 00:22:12 CDT)
RE: visualizing an atomselect Chang, Christopher (Wed Sep 28 2005 - 18:38:29 CDT)
RE: tcl command to save structure to file? Chang, Christopher (Wed Sep 28 2005 - 18:30:16 CDT)
visualizing an atomselect Turman, Cheri M (Wed Sep 28 2005 - 17:25:32 CDT)
- Re: visualizing an atomselect Sergio Anis (Wed Sep 28 2005 - 20:54:35 CDT)
Changing the title in the viewer window Palmer, Teresa (Wed Sep 28 2005 - 12:16:55 CDT)
- Re: Changing the title in the viewer window John Stone (Mon Oct 03 2005 - 11:43:03 CDT)
Can VMD add other organic solvent into system? weikai (Wed Sep 28 2005 - 02:51:38 CDT)
Re: vmd that works with ati/linux John Stone (Tue Sep 27 2005 - 21:18:03 CDT)
- Re: ???UNSURE??? Re: vmd that works with ati/linux Praedor Atrebates (Wed Sep 28 2005 - 07:15:28 CDT)
  - tcl command to save structure to file? Samuel Flores (Wed Sep 28 2005 - 14:05:20 CDT)
- Re: ???UNSURE??? Re: vmd that works with ati/linux Praedor Atrebates (Wed Sep 28 2005 - 16:43:14 CDT)
  - Re: ???UNSURE??? Re: vmd that works with ati/linux John Stone (Thu Sep 29 2005 - 00:24:22 CDT)
write pdb and psf with missing segments in original pdb file Baoqiang Cao (Tue Sep 27 2005 - 21:10:07 CDT)
COR format and first residue Chang, Christopher (Tue Sep 27 2005 - 18:31:32 CDT)
(no subject) Yifat Brill (Tue Sep 27 2005 - 07:03:33 CDT)
- Re: your mail John Stone (Tue Sep 27 2005 - 09:51:37 CDT)
ptraj Michel Espinoza-Fonseca (Tue Sep 27 2005 - 06:24:50 CDT)
- Re: ptraj John Stone (Tue Sep 27 2005 - 09:57:34 CDT)
- Re: namd-l: ptraj Nicolas Sapay (Tue Sep 27 2005 - 10:03:18 CDT)
Hello! baogen duan (Mon Sep 26 2005 - 08:52:05 CDT)
- Re: Hello! John Stone (Mon Sep 26 2005 - 11:56:43 CDT)
position of protein respect to membrane andrea spitaleri (Mon Sep 26 2005 - 09:35:10 CDT)
- Re: position of protein respect to membrane John Stone (Mon Sep 26 2005 - 10:26:59 CDT)
  - Re: position of protein respect to membrane andrea spitaleri (Tue Sep 27 2005 - 03:41:35 CDT)
  - Re: position of protein respect to membrane andrea spitaleri (Tue Sep 27 2005 - 04:00:31 CDT)
Can VMD add other solvent except water in system? weikai (Mon Sep 26 2005 - 03:17:42 CDT)
- Re: Can VMD add other solvent except water in system? Joshua D. Moore (Mon Sep 26 2005 - 06:21:38 CDT)
  - Re: Can VMD add other solvent except water in system? Leonardo Sepulveda Durán (Mon Sep 26 2005 - 10:59:58 CDT)
- Re: Can VMD add other solvent except water in system? John Stone (Mon Sep 26 2005 - 10:12:51 CDT)
Problem building vmd 1.8.3 and destroyed usable 1.8.2 version Dr. Seth Olsen (Mon Sep 26 2005 - 00:28:22 CDT)
- Re: Problem building vmd 1.8.3 and destroyed usable 1.8.2 version John Stone (Mon Sep 26 2005 - 10:09:15 CDT)
vmd crashes upon load of pdb Praedor Atrebates (Fri Sep 23 2005 - 13:30:56 CDT)
- Re: vmd crashes upon load of pdb John Stone (Fri Sep 23 2005 - 13:44:07 CDT)
  - Re: ???UNSURE??? Re: vmd crashes upon load of pdb Praedor Atrebates (Fri Sep 23 2005 - 14:30:03 CDT)
gopython tcickovs_at_nd.edu (Fri Sep 23 2005 - 10:36:36 CDT)
- Re: gopython John Stone (Sat Sep 24 2005 - 00:00:33 CDT)
  - Re: gopython John Stone (Sat Sep 24 2005 - 22:36:07 CDT)
tachyon rendering and background color Nicolas Sapay (Fri Sep 23 2005 - 07:20:07 CDT)
- Re: tachyon rendering and background color John Stone (Fri Sep 23 2005 - 09:50:19 CDT)
  - Re: tachyon rendering and background color John Stone (Fri Sep 23 2005 - 17:03:03 CDT)
RE: How to build a crystal structure from a pdb file ? Dallas B. Warren (Wed Sep 21 2005 - 18:20:02 CDT)
[Fwd: Re: Lipid Order Parameter] Nicolas Sapay (Wed Sep 21 2005 - 13:29:06 CDT)
Import gromos output file into VMD without format conversion? Stanley Lan (Wed Sep 21 2005 - 09:37:35 CDT)
- Re: Import gromos output file into VMD without format conversion? John Stone (Wed Sep 21 2005 - 10:20:02 CDT)
  - Re: Import gromos output file into VMD without format conversion? Mauricio Carrillo Tripp (Wed Sep 21 2005 - 12:51:04 CDT)
  - Re: Import gromos output file into VMD without format conversion? Nathan C. Rockwell (Wed Sep 21 2005 - 14:17:10 CDT)
    - Re: Import gromos output file into VMD without format conversion? John Stone (Wed Sep 21 2005 - 14:27:45 CDT)
- Re: Import gromos output file into VMD without format conversion? Axel Kohlmeyer (Thu Sep 22 2005 - 07:32:55 CDT)
calculating lipid order parameters Philip Fowler (Wed Sep 21 2005 - 07:54:59 CDT)
RE: problem with coloring surface by electrostatic potential Dallas B. Warren (Tue Sep 20 2005 - 20:54:12 CDT)
- Re: problem with coloring surface by electrostatic potential Eugen Leitl (Wed Sep 21 2005 - 03:50:47 CDT)
How to build a crystal structure from a pdb file ? Chunhu Tan (Tue Sep 20 2005 - 19:43:41 CDT)
- Re: How to build a crystal structure from a pdb file ? John Stone (Wed Sep 21 2005 - 13:37:21 CDT)
  - Re: How to build a crystal structure from a pdb file ? Karsten Suhre (Thu Sep 22 2005 - 02:07:16 CDT)
Lipid Order Parameter Saladino, Alex (Tue Sep 20 2005 - 16:21:30 CDT)
- Re: Lipid Order Parameter Nicolas Sapay (Wed Sep 21 2005 - 02:44:45 CDT)
- Re: Lipid Order Parameter Sebastian Stolzenberg (Sat Nov 07 2009 - 16:48:29 CST)
  - Re: Lipid Order Parameter Sebastian Stolzenberg (Sat Nov 07 2009 - 16:49:42 CST)
problem with coloring surface by electrostatic potential Dan Strahs (Tue Sep 20 2005 - 11:13:58 CDT)
- Re: problem with coloring surface by electrostatic potential John Stone (Tue Sep 20 2005 - 11:29:30 CDT)
- Re: problem with coloring surface by electrostatic potential Axel Kohlmeyer (Tue Sep 20 2005 - 14:17:54 CDT)
  - Re: problem with coloring surface by electrostatic potential John Stone (Tue Sep 20 2005 - 14:34:02 CDT)
secondary structure assingnment Michel Espinoza-Fonseca (Tue Sep 20 2005 - 07:22:07 CDT)
- Re: secondary structure assingnment John Stone (Tue Sep 20 2005 - 10:14:22 CDT)
map files Demetrios Braddock (Mon Sep 19 2005 - 19:41:39 CDT)
- Re: map files John Stone (Wed Sep 21 2005 - 13:22:07 CDT)
molecules drifted away from the focus.... Margaret Shun Cheung (Sun Sep 18 2005 - 15:11:45 CDT)
- Re: molecules drifted away from the focus.... John Stone (Mon Sep 19 2005 - 15:05:17 CDT)
  - Re: molecules drifted away from the focus.... Margaret Shun Cheung (Mon Sep 19 2005 - 15:08:15 CDT)
    - Re: molecules drifted away from the focus.... John Stone (Mon Sep 19 2005 - 15:13:15 CDT)
keywords to access surface? Dan Strahs (Fri Sep 16 2005 - 19:44:53 CDT)
- Re: keywords to access surface? John Stone (Fri Sep 16 2005 - 21:03:41 CDT)
  - Re: keywords to access surface? Daniel Strahs (Sun Sep 18 2005 - 18:39:00 CDT)
    - Re: keywords to access surface? John Stone (Mon Sep 19 2005 - 10:19:59 CDT)
screen size Jeffrey Tseng (Fri Sep 16 2005 - 18:09:39 CDT)
- Re: screen size John Stone (Fri Sep 16 2005 - 21:08:55 CDT)
  - Re: screen size Jeffrey Tseng (Sat Sep 17 2005 - 09:47:31 CDT)
    - screen size Jeffrey Tseng (Sat Sep 17 2005 - 10:12:41 CDT)
    - Re: screen size John Stone (Mon Sep 19 2005 - 10:41:28 CDT)
Generating an average structure from a trajectory Kara Di Giorgio (Fri Sep 16 2005 - 13:01:34 CDT)
- Re: Generating an average structure from a trajectory John Stone (Fri Sep 16 2005 - 15:38:06 CDT)
- Re: Generating an average structure from a trajectory Luis Gracia (Fri Sep 16 2005 - 16:24:51 CDT)
- Re: Generating an average structure from a trajectory Brian Bennion (Fri Sep 16 2005 - 18:22:43 CDT)
visualization of ghemical figure haider abbas (Fri Sep 16 2005 - 04:29:37 CDT)
- Re: visualization of ghemical figure John Stone (Fri Sep 16 2005 - 10:30:01 CDT)
.grd and .srf vivek sharma (Fri Sep 16 2005 - 01:52:45 CDT)
- Re: .grd and .srf John Stone (Fri Sep 16 2005 - 10:25:47 CDT)
  - Re: .grd and .srf John Stone (Fri Sep 16 2005 - 16:08:13 CDT)
    - Re: .grd and .srf John Stone (Fri Sep 16 2005 - 16:37:21 CDT)
  - Re: .grd and .srf vivek sharma (Mon Sep 19 2005 - 00:09:52 CDT)
(no subject) Demetrios Braddock (Thu Sep 15 2005 - 18:40:47 CDT)
- Re: your mail John Stone (Fri Sep 16 2005 - 11:19:00 CDT)
Sybyl trajectory jim_at_wellyes.com (Thu Sep 15 2005 - 14:10:23 CDT)
PSC WORKSHOP: COMPUTATIONAL BIOPHYSICS WORKSHOP Troy Wymore (Thu Sep 15 2005 - 11:15:13 CDT)
several coor files from dcd file Ya.Shashel (Thu Sep 15 2005 - 06:18:23 CDT)
- Re: several coor files from dcd file John Stone (Thu Sep 15 2005 - 10:54:59 CDT)
Zooming with Tcl? Scott Thibault (Thu Sep 15 2005 - 08:31:08 CDT)
- Re: Zooming with Tcl? John Stone (Thu Sep 15 2005 - 10:50:31 CDT)
RE: Left Right eye stereo flip in Crystal Eyes Chang, Christopher (Wed Sep 14 2005 - 15:18:37 CDT)
RE: DCD file format Chang, Christopher (Wed Sep 14 2005 - 14:27:47 CDT)
Left Right eye stereo flip in Crystal Eyes Jill Vickery (Wed Sep 14 2005 - 14:04:52 CDT)
- Re: Left Right eye stereo flip in Crystal Eyes John Stone (Thu Sep 15 2005 - 11:09:35 CDT)
DCD file format Tatyana Kuznetsova (Wed Sep 14 2005 - 09:09:06 CDT)
- Re: DCD file format John Stone (Thu Sep 15 2005 - 11:07:50 CDT)
  - Re: DCD file format Tatyana Kuznetsova (Fri Sep 16 2005 - 05:58:44 CDT)
several cmds to read structure and trajectory files Jian Zou (Wed Sep 14 2005 - 08:19:33 CDT)
- Re: several cmds to read structure and trajectory files John Stone (Thu Sep 15 2005 - 11:19:43 CDT)
Ployhedra in VMD Jen-Chang Chen (Wed Sep 14 2005 - 03:58:30 CDT)
- Re: Ployhedra in VMD John Stone (Thu Sep 15 2005 - 11:11:25 CDT)
  - Re: Ployhedra in VMD Jen-Chang Chen (Mon Sep 26 2005 - 07:56:53 CDT)
    - Re: Ployhedra in VMD John Stone (Mon Sep 26 2005 - 18:20:28 CDT)
RE: problem rendering traj file with tachyon Chang, Christopher (Tue Sep 13 2005 - 16:19:22 CDT)
problem rendering traj file with tachyon Carlos Simmerling (Tue Sep 13 2005 - 10:47:03 CDT)
- Re: problem rendering traj file with tachyon John Stone (Thu Sep 15 2005 - 11:46:54 CDT)
dcd tools dimka (Mon Sep 12 2005 - 20:34:20 CDT)
- RE: dcd tools JC Gumbart (Mon Sep 12 2005 - 21:11:58 CDT)
  - RE: dcd tools Chang, Christopher (Tue Sep 13 2005 - 10:20:35 CDT)
- writing pdb Sergio Anis (Mon Sep 12 2005 - 22:07:04 CDT)
  - Re: writing pdb Leonardo Sepulveda Durán (Tue Sep 13 2005 - 11:50:04 CDT)
use phantom with VMD Hai-Jun Su (Sun Sep 11 2005 - 11:22:44 CDT)
- use phantom with VMD Hai-Jun Su (Tue Sep 13 2005 - 14:39:37 CDT)
  - Re: use phantom with VMD John Stone (Thu Sep 15 2005 - 11:45:30 CDT)
RMSD of identical pdbs not zero Robin Bush (Fri Sep 09 2005 - 12:57:24 CDT)
- Re: RMSD of identical pdbs not zero Dan Wright (Tue Sep 13 2005 - 09:30:02 CDT)
  - Re: RMSD of identical pdbs not zero Robin Bush (Wed Sep 14 2005 - 07:50:56 CDT)
index VISWANADHA SRIDHARA (Thu Sep 08 2005 - 10:29:54 CDT)
- Re: index John Stone (Thu Sep 08 2005 - 10:39:34 CDT)
  - Re: index John Stone (Thu Sep 08 2005 - 10:54:50 CDT)
    - Re: index Viswanadham Sridhara (Thu Sep 08 2005 - 10:59:27 CDT)
    - Re: index Viswanadham Sridhara (Thu Nov 03 2005 - 16:11:54 CST)
Reading arrays in VMD VISWANADHA SRIDHARA (Thu Sep 08 2005 - 03:38:02 CDT)
- Re: Reading arrays in VMD JC Gumbart (Thu Sep 08 2005 - 11:37:27 CDT)
Trying to get Crystal Eyes to work on VMD with Twin View confirguation...Fixed myself Kim Taylor (Wed Sep 07 2005 - 19:57:15 CDT)
Trying to get Crystal Eyes to work on VMD with Twin View confirguation Kim Taylor (Wed Sep 07 2005 - 19:35:24 CDT)
Fw: visualising bonds in vmd Claire Zerafa (Wed Sep 07 2005 - 16:02:25 CDT)
- Re: Fw: visualising bonds in vmd John Stone (Wed Sep 07 2005 - 16:11:13 CDT)
Analyzing pdb files remotely with VMD installed locally Jindal Shah (Wed Sep 07 2005 - 11:25:50 CDT)
- Re: Analyzing pdb files remotely with VMD installed locally John Stone (Wed Sep 07 2005 - 11:33:09 CDT)
  - RE: Analyzing pdb files remotely with VMD installed locally Michel Espinoza-Fonseca (Wed Sep 07 2005 - 11:48:02 CDT)
  - Re: Analyzing pdb files remotely with VMD installed locally Jindal Shah (Wed Sep 07 2005 - 11:54:00 CDT)
    - Re: Analyzing pdb files remotely with VMD installed locally John Stone (Wed Sep 07 2005 - 16:14:26 CDT)
    - Re: Analyzing pdb files remotely with VMD installed locally Jindal Shah (Wed Sep 07 2005 - 20:09:32 CDT)
visualising bonds in vmd Claire Zerafa (Wed Sep 07 2005 - 08:00:31 CDT)
CAVE Hai-Jun Su (Tue Sep 06 2005 - 23:20:07 CDT)
- Re: CAVE John Stone (Tue Sep 06 2005 - 23:32:18 CDT)
  - RE: CAVE Hai-Jun Su (Wed Sep 07 2005 - 10:30:05 CDT)
  - RE: CAVE Hai-Jun Su (Wed Sep 07 2005 - 15:35:10 CDT)
    - Re: CAVE John Stone (Wed Sep 07 2005 - 15:47:10 CDT)
- Re: CAVE Dan Strahs (Wed Sep 07 2005 - 08:59:22 CDT)
Re: VMD crashes with FX440 and RH Entreprise 4.0 Dow Hurst DPHURST (Tue Sep 06 2005 - 13:10:51 CDT)
- Re: VMD crashes with FX440 and RH Entreprise 4.0 John Stone (Tue Sep 06 2005 - 13:13:31 CDT)
Dihedral angle calculations for alanine dipeptide Jindal Shah (Tue Sep 06 2005 - 12:36:42 CDT)
VMD crashes with FX440 and RH Entreprise 4.0 Joseph Fernandez (Tue Sep 06 2005 - 09:52:07 CDT)
- Re: VMD crashes with FX440 and RH Entreprise 4.0 John Stone (Tue Sep 06 2005 - 09:56:05 CDT)
- Re: VMD crashes with FX440 and RH Entreprise 4.0 John Stone (Tue Sep 06 2005 - 11:13:08 CDT)
IED2.02 Problem xzp02_at_mails.tsinghua.edu.cn (Tue Sep 06 2005 - 07:27:16 CDT)
- Re: IED2.02 Problem John Stone (Tue Sep 06 2005 - 09:38:58 CDT)
script Sergio Anis (Tue Sep 06 2005 - 07:11:50 CDT)
- Re: namd-l: script LEWYN LI (Tue Sep 06 2005 - 11:12:35 CDT)
- Re: namd-l: script Luis Gracia (Tue Sep 06 2005 - 13:21:40 CDT)
  - Modified DNA bases PDB files Shahid Qamar (Wed Sep 07 2005 - 14:00:54 CDT)
how to start vmd with "menu tkcon on"? Jian Zou (Tue Sep 06 2005 - 02:37:37 CDT)
- Re: how to start vmd with "menu tkcon on"? Jan Saam (Tue Sep 06 2005 - 03:05:36 CDT)
  - Re: how to start vmd with "menu tkcon on"? Jian Zou (Tue Sep 06 2005 - 09:55:50 CDT)
    - Re: how to start vmd with "menu tkcon on"? John Stone (Tue Sep 06 2005 - 09:58:37 CDT)
- Re: how to start vmd with "menu tkcon on"? John Stone (Tue Sep 06 2005 - 09:36:23 CDT)
help: i can not type words in hostname textbox in imd ÕÅ Îª (Mon Sep 05 2005 - 10:36:56 CDT)
- Re: help: i can not type words in hostname textbox in imd John Stone (Mon Sep 05 2005 - 13:28:53 CDT)
  - Re: help: i can not type words in hostname textbox in imd ÕÅ Îª (Wed Sep 07 2005 - 01:36:29 CDT)
  - Re: help: i can not type words in hostname textbox in imd ÕÅ Îª (Wed Sep 07 2005 - 02:00:28 CDT)
when i use imd connect in vmd,i can not type words in hostname textbox ÕÅ Îª (Mon Sep 05 2005 - 10:22:54 CDT)
TkCon History bybaker_at_itsa.ucsf.edu (Mon Sep 05 2005 - 03:20:56 CDT)
- Re: TkCon History q=E2=BA=E9=C3=F7?= (Mon Sep 05 2005 - 10:50:55 CDT)
  - Re: TkCon History John Stone (Mon Sep 05 2005 - 13:36:28 CDT)
- Re: TkCon History John Stone (Mon Sep 05 2005 - 13:38:22 CDT)
Sybyl trajectory Josef Scheiber (Mon Sep 05 2005 - 01:56:04 CDT)
- Re: Sybyl trajectory John Stone (Mon Sep 05 2005 - 13:41:23 CDT)
  - Re: Sybyl trajectory Josef Scheiber (Tue Sep 06 2005 - 05:38:38 CDT)
    - Re: Sybyl trajectory John Stone (Tue Sep 06 2005 - 09:43:23 CDT)
X error Adrian turjanski (Sun Sep 04 2005 - 16:00:59 CDT)
- Re: X error John Stone (Mon Sep 05 2005 - 13:44:20 CDT)
Re: crash on ubuntu linux Sabuj Pattanayek (Sun Sep 04 2005 - 13:32:25 CDT)
Re: vmdtext & Window bybaker_at_itsa.ucsf.edu (Sat Sep 03 2005 - 22:06:14 CDT)
- RE: Re: vmdtext & Window JC Gumbart (Sun Sep 04 2005 - 02:08:01 CDT)
Re: vmdtext and .cshrc. Jacinto S. (Sat Sep 03 2005 - 14:37:29 CDT)
crash on ubuntu linux Jay McAliley (Sat Sep 03 2005 - 11:41:59 CDT)
vmdtext and .cshrc. bybaker_at_itsa.ucsf.edu (Fri Sep 02 2005 - 21:09:25 CDT)
counting selected atoms---selection time series Daniel Barsky (Wed Aug 31 2005 - 12:57:32 CDT)
- Re: counting selected atoms---selection time series Axel Kohlmeyer (Thu Sep 01 2005 - 01:16:43 CDT)
- Re: counting selected atoms---selection time series Jérôme Hénin (Thu Sep 01 2005 - 02:05:32 CDT)
Help with running IED in VMD Kristina Woods (Tue Aug 30 2005 - 19:38:30 CDT)
plugin problem bybaker_at_itsa.ucsf.edu (Tue Aug 30 2005 - 01:17:45 CDT)
- Re: plugin problem John Stone (Tue Aug 30 2005 - 10:14:13 CDT)
Error in visualizing the 5 prime end of DNA strand Bob Johnson (Mon Aug 29 2005 - 10:56:06 CDT)
Problems with AMBER trajectories (MOVIE!) and crd-files Matthias Negri (Mon Aug 29 2005 - 04:19:19 CDT)
- Re: Problems with AMBER trajectories (MOVIE!) and crd-files John Stone (Mon Aug 29 2005 - 09:43:30 CDT)
  - Re: Problems with AMBER trajectories (MOVIE!) and crd-files Matthias Negri (Tue Aug 30 2005 - 06:53:28 CDT)
    - Re: Problems with AMBER trajectories (MOVIE!) and crd-files John Stone (Tue Aug 30 2005 - 10:15:22 CDT)
    - Re: Problems with AMBER trajectories (MOVIE!) and crd-files Axel Kohlmeyer (Tue Aug 30 2005 - 13:43:29 CDT)
Making good trayectory movies Leonardo Sepulveda Durán (Sun Aug 28 2005 - 18:44:52 CDT)
- Re: Making good trayectory movies John Stone (Tue Aug 30 2005 - 13:36:37 CDT)
Re: Using VMD to overlay structures (Mikolai Fajer) Peter Schellenberg (Sun Aug 28 2005 - 05:28:29 CDT)
Problems with VMD in Federa 4 (x86_64) Adrian turjanski (Sat Aug 27 2005 - 17:22:00 CDT)
- Re: Problems with VMD in Federa 4 (x86_64) John Stone (Sat Aug 27 2005 - 22:30:18 CDT)
coloring surface by volume Dan Strahs (Fri Aug 26 2005 - 20:05:55 CDT)
- Re: coloring surface by volume John Stone (Fri Sep 02 2005 - 17:12:18 CDT)
RE: Read support for CHARMM binary coordinate file? Chang, Christopher (Thu Aug 25 2005 - 17:59:55 CDT)
a problem using python in vmd Kristina Woods (Thu Aug 25 2005 - 10:56:15 CDT)
molecule.write() Guanglei Cui (Thu Aug 25 2005 - 10:19:55 CDT)
- Re: molecule.write() John Stone (Thu Aug 25 2005 - 10:42:40 CDT)
MSMS calculations floquet_at_icsn.cnrs-gif.fr (Thu Aug 25 2005 - 03:52:29 CDT)
- Re: MSMS calculations John Stone (Thu Aug 25 2005 - 18:10:50 CDT)
eTimeBanker Bill Pay Service Bankf of the West (Wed Aug 24 2005 - 11:02:50 CDT)
No bonds Jindal Shah (Wed Aug 24 2005 - 10:06:09 CDT)
- Re: No bonds John Stone (Wed Aug 24 2005 - 10:21:05 CDT)
  - Re: No bonds Jindal Shah (Wed Aug 24 2005 - 11:35:11 CDT)
    - Re: No bonds John Stone (Thu Aug 25 2005 - 18:11:57 CDT)
Read support for CHARMM binary coordinate file? Chang, Christopher (Tue Aug 23 2005 - 17:28:31 CDT)
- Re: Read support for CHARMM binary coordinate file? John Stone (Thu Aug 25 2005 - 17:44:57 CDT)
Intersurf & MAC OSX 10.3 William A. Shelton (Tue Aug 23 2005 - 15:28:16 CDT)
- Re: Intersurf & MAC OSX 10.3 John Stone (Tue Aug 23 2005 - 15:45:28 CDT)
  - Re: Intersurf & MAC OSX 10.3 Sabuj Pattanayek (Tue Aug 23 2005 - 19:40:30 CDT)
    - Re: Intersurf & MAC OSX 10.3 John Stone (Thu Aug 25 2005 - 17:35:11 CDT)
protein-lipids v z coordinate syma (Tue Aug 23 2005 - 12:06:27 CDT)
- Re: protein-lipids v z coordinate John Stone (Tue Aug 23 2005 - 12:58:50 CDT)
PME values floquet_at_icsn.cnrs-gif.fr (Tue Aug 23 2005 - 09:38:16 CDT)
- Re: PME values Jim Phillips (Wed Aug 24 2005 - 15:27:43 CDT)
Plugins update floquet_at_icsn.cnrs-gif.fr (Tue Aug 23 2005 - 04:00:39 CDT)
- Re: Plugins update John Stone (Tue Aug 23 2005 - 09:41:09 CDT)
Secondary Structure Color Definitions Mark Formaneck (Sun Aug 21 2005 - 19:17:11 CDT)
- Re: Secondary Structure Color Definitions John Stone (Mon Aug 22 2005 - 11:00:12 CDT)
  - Re: Secondary Structure Color Definitions Mark Formaneck (Mon Aug 22 2005 - 12:55:06 CDT)
RE: small figures Dallas B. Warren (Sun Aug 21 2005 - 18:51:33 CDT)
- RE: small figures Mark Formaneck (Sun Aug 21 2005 - 20:11:50 CDT)
VMD fails to run Bob Johnson (Sat Aug 20 2005 - 21:43:55 CDT)
- Re: VMD fails to run Axel Kohlmeyer (Sun Aug 21 2005 - 06:05:53 CDT)
  - Replacing DPPC with DPPS Viswanadham Sridhara (Sun Aug 21 2005 - 12:24:54 CDT)
    - RE: Replacing DPPC with DPPS JC Gumbart (Mon Aug 22 2005 - 00:32:39 CDT)
- Re: VMD fails to run John Stone (Mon Aug 22 2005 - 01:37:12 CDT)
  - Re: VMD fails to run Sabuj Pattanayek (Mon Aug 22 2005 - 11:17:58 CDT)
Using VMD to overlay structures Kara Di Giorgio (Fri Aug 19 2005 - 16:26:32 CDT)
- Re: Using VMD to overlay structures John Stone (Mon Aug 22 2005 - 11:11:44 CDT)
  - Re: Using VMD to overlay structures Kara Di Giorgio (Mon Aug 22 2005 - 14:11:22 CDT)
    - Re: Using VMD to overlay structures Mikolai Fajer (Thu Aug 25 2005 - 07:09:33 CDT)
catdcd vs readdcd.h error checking Brian Bennion (Fri Aug 19 2005 - 11:53:55 CDT)
- Re: catdcd vs readdcd.h error checking Justin Gullingsrud (Fri Aug 19 2005 - 18:56:52 CDT)
  - Re: catdcd vs readdcd.h error checking Brian Bennion (Sat Aug 20 2005 - 11:22:16 CDT)
small figures Anna Karawajczyk (Fri Aug 19 2005 - 07:47:30 CDT)
- Re: small figures JC Gumbart (Fri Aug 19 2005 - 12:01:43 CDT)
setting different colors Jaime Sanchez (Thu Aug 18 2005 - 23:33:32 CDT)
- Re: setting different colors Justin Gullingsrud (Sun Aug 21 2005 - 15:55:04 CDT)
Periodic boundary conditions Bob Johnson (Thu Aug 18 2005 - 12:00:19 CDT)
- Re: Periodic boundary conditions Justin Gullingsrud (Thu Aug 18 2005 - 13:43:38 CDT)
Adjacent surface? paul d jones (Thu Aug 18 2005 - 07:54:31 CDT)
- Re: Adjacent surface? Brian Bennion (Thu Aug 18 2005 - 14:24:07 CDT)
- Re: Adjacent surface? John Stone (Mon Aug 22 2005 - 11:05:33 CDT)
moving by angle and measuring angle Shahid Qamar (Wed Aug 17 2005 - 18:01:10 CDT)
Selecting residues by number Mihaly Mezei (Wed Aug 17 2005 - 17:46:13 CDT)
- Re: Selecting residues by number John Stone (Wed Aug 17 2005 - 18:14:32 CDT)
  - Re: Selecting residues by number John Stone (Wed Aug 17 2005 - 18:45:02 CDT)
    - Re: Selecting residues by number John Stone (Wed Aug 17 2005 - 18:51:45 CDT)
New BioCoRE server released Robert Brunner (Wed Aug 17 2005 - 11:59:52 CDT)
overlaying more than 2 molecules Vlad Cojocaru (Wed Aug 17 2005 - 11:31:15 CDT)
- RE: overlaying more than 2 molecules Blake Charlebois (Wed Aug 17 2005 - 12:57:30 CDT)
RMSD question L. Michel Espinoza-Fonseca (Wed Aug 17 2005 - 06:44:24 CDT)
scripts for binding free energy calculation using SMD and Jarzynski's equality Marc Q. Ma (Wed Aug 17 2005 - 09:45:12 CDT)
- Script for calculating energy of a water molecule Jindal Shah (Wed Aug 17 2005 - 11:41:23 CDT)
  - Re: Script for calculating energy of a water molecule John Stone (Wed Aug 17 2005 - 14:32:41 CDT)
    - Re: Script for calculating energy of a water molecule Jindal Shah (Wed Aug 17 2005 - 17:07:12 CDT)
dssp in vmd pascal.baillod_at_epfl.ch (Wed Aug 17 2005 - 02:15:11 CDT)
- Re: dssp in vmd John Stone (Wed Aug 17 2005 - 14:39:51 CDT)
RMSD question Jerry Parks (Tue Aug 16 2005 - 17:08:59 CDT)
- Re: RMSD question Giovanni Bellesia (Wed Aug 17 2005 - 06:04:38 CDT)
- Re: RMSD question Luis Gracia (Tue Aug 16 2005 - 20:20:00 CDT)
What applications are the cest? Nick I (Mon Aug 15 2005 - 15:01:29 CDT)
- Re: What applications are the cest? Nick I (Tue Oct 25 2005 - 11:43:17 CDT)
area of protein cross sections dimka (Mon Aug 15 2005 - 14:29:38 CDT)
Problem with DNA bonds Bob Johnson (Mon Aug 15 2005 - 13:54:28 CDT)
- Re: Problem with DNA bonds John Stone (Mon Aug 15 2005 - 14:05:54 CDT)
Visualizing an infinite carbon nanotube Bob Johnson (Mon Aug 15 2005 - 13:23:44 CDT)
- Re: Visualizing an infinite carbon nanotube John Stone (Mon Aug 15 2005 - 14:07:42 CDT)
RE: help with BIOMT Chang, Christopher (Fri Aug 12 2005 - 14:57:51 CDT)
help with BIOMT Steve Ding (Thu Aug 11 2005 - 18:10:13 CDT)
- Re: help with BIOMT John Stone (Fri Aug 12 2005 - 14:04:21 CDT)
- Re: help with BIOMT Brian Bennion (Fri Aug 12 2005 - 15:52:25 CDT)
creating movie files Jaime Sanchez (Fri Aug 12 2005 - 08:34:15 CDT)
- Re: creating movie files John Stone (Fri Aug 12 2005 - 10:58:16 CDT)
Backbone representation of RNA Peter Schellenberg (Fri Aug 12 2005 - 01:40:44 CDT)
- Re: Backbone representation of RNA John Stone (Fri Aug 12 2005 - 10:55:56 CDT)
RE: vmd with no x Chang, Christopher (Thu Aug 11 2005 - 18:00:33 CDT)
vmd with no x Guanglei Cui (Thu Aug 11 2005 - 16:35:37 CDT)
- Re: vmd with no x John Stone (Thu Aug 11 2005 - 16:42:59 CDT)
all within selection Guanglei Cui (Thu Aug 11 2005 - 10:55:39 CDT)
- Re: all within selection John Stone (Thu Aug 11 2005 - 11:56:29 CDT)
  - Re: all within selection Guanglei Cui (Thu Aug 11 2005 - 12:32:32 CDT)
File size limits Jayendra Balasubramanian (Thu Aug 11 2005 - 09:53:44 CDT)
- Re: File size limits John Stone (Thu Aug 11 2005 - 09:57:11 CDT)
Question about .vmdsensors configuration leepersonpp (Thu Aug 11 2005 - 05:47:19 CDT)
- Re: Question about .vmdsensors configuration John Stone (Thu Aug 11 2005 - 09:48:32 CDT)
100% of CPU usage griadi_at_utalca.cl (Wed Aug 10 2005 - 18:46:46 CDT)
- Re: 100% of CPU usage John Stone (Thu Aug 11 2005 - 09:46:14 CDT)
  - Re: 100% of CPU usage John Stone (Wed Sep 07 2005 - 22:22:16 CDT)
VMD-1.8.3 installation erRor griadi_at_utalca.cl (Wed Aug 10 2005 - 14:07:57 CDT)
- Re: VMD-1.8.3 installation erRor John Stone (Wed Aug 10 2005 - 14:22:15 CDT)
  - Re: VMD-1.8.3 installation erRor griadi_at_utalca.cl (Wed Aug 10 2005 - 18:29:12 CDT)
using VMD with LAMMPS Jaime Sanchez (Wed Aug 10 2005 - 13:59:40 CDT)
- Re: using VMD with LAMMPS John Stone (Wed Aug 10 2005 - 14:24:22 CDT)
display hexagonal periodic system dimka (Wed Aug 10 2005 - 12:38:54 CDT)
- Re: display hexagonal periodic system Justin Gullingsrud (Wed Aug 10 2005 - 19:21:02 CDT)
RE: Atom renumbering in DCD file Chang, Christopher (Tue Aug 09 2005 - 14:15:03 CDT)
output secondary structure assignment into a file Ting Wang (Tue Aug 09 2005 - 03:50:11 CDT)
- Re: output secondary structure assignment into a file John Stone (Thu Aug 11 2005 - 14:33:06 CDT)
Atom renumbering in DCD file Chang, Christopher (Mon Aug 08 2005 - 18:48:33 CDT)
- Re: Atom renumbering in DCD file John Stone (Mon Aug 08 2005 - 19:08:03 CDT)
- Re: Atom renumbering in DCD file Justin Gullingsrud (Tue Aug 09 2005 - 13:30:08 CDT)
Draw Bonds Bob Johnson (Mon Aug 08 2005 - 10:42:13 CDT)
- Re: Draw Bonds Joshua D. Moore (Mon Aug 08 2005 - 14:48:05 CDT)
- Re: Draw Bonds John Stone (Mon Aug 08 2005 - 18:48:11 CDT)
SASA Irena Tuszyska (Mon Aug 08 2005 - 04:17:17 CDT)
- Re: SASA John Stone (Mon Aug 08 2005 - 19:19:47 CDT)
RE: dihedral angles cleaned up Alexei Podtelezhnikov (Fri Aug 05 2005 - 17:47:13 CDT)
volume from VMD and NAMD different? Brian Bennion (Fri Aug 05 2005 - 16:12:34 CDT)
- Re: namd-l: volume from VMD and NAMD different? Jim Phillips (Fri Aug 05 2005 - 17:34:45 CDT)
  - Re: namd-l: volume from VMD and NAMD different? Brian Bennion (Fri Aug 05 2005 - 17:38:27 CDT)
    - Re: namd-l: volume from VMD and NAMD different? Jim Phillips (Fri Aug 05 2005 - 17:46:25 CDT)
Video card driver Bob Johnson (Thu Aug 04 2005 - 13:56:44 CDT)
- Re: Video card driver John Stone (Thu Aug 04 2005 - 14:12:49 CDT)
- Re: Video card driver Brian Bennion (Thu Aug 04 2005 - 17:05:05 CDT)
dihedral angles cleaned up! Alexei Podtelezhnikov (Thu Aug 04 2005 - 11:19:31 CDT)
wrapping and extra points in gromacs trajectories Mgr. Lubos Vrbka (Thu Aug 04 2005 - 10:59:44 CDT)
- Re: wrapping and extra points in gromacs trajectories John Stone (Fri Aug 05 2005 - 14:44:06 CDT)
dihedral angles cleaned up Alexei Podtelezhnikov (Thu Aug 04 2005 - 10:09:38 CDT)
- Re: dihedral angles cleaned up John Stone (Thu Aug 04 2005 - 11:08:08 CDT)
PDB to STL help needed Kevin Smith (Wed Aug 03 2005 - 09:23:02 CDT)
- Re: PDB to STL help needed John Stone (Wed Aug 03 2005 - 12:59:09 CDT)
  - Re: PDB to STL help needed John Stone (Tue Sep 06 2005 - 11:15:01 CDT)
Re: more precision in inverse trig functions vivek sharma (Wed Aug 03 2005 - 00:33:17 CDT)
NAMD 2.6b1 Released Jim Phillips (Tue Aug 02 2005 - 12:31:02 CDT)
Nanotube Simulations Gaurav Sharma (Tue Aug 02 2005 - 08:51:14 CDT)
- Re: Nanotube Simulations John Stone (Tue Aug 02 2005 - 12:34:58 CDT)
  - Re: Nanotube Simulations Gaurav Sharma (Tue Aug 02 2005 - 13:56:15 CDT)
- RE: namd-l: Nanotube Simulations Jason Lee (Tue Aug 02 2005 - 14:23:32 CDT)
rotate atomic coordinates? Samuel Flores (Sun Jul 31 2005 - 14:58:36 CDT)
- weird atomselect problem Samuel Flores (Sun Jul 31 2005 - 19:37:36 CDT)
  - Re: weird atomselect problem Dan Wright (Mon Aug 01 2005 - 08:56:56 CDT)
    - RE: weird atomselect problem Samuel Flores (Mon Aug 01 2005 - 11:48:07 CDT)
    - Re: weird atomselect problem Dan Wright (Mon Aug 01 2005 - 15:19:03 CDT)
  - Re: weird atomselect problem John Stone (Mon Aug 01 2005 - 14:31:20 CDT)
- Re: rotate atomic coordinates? John Stone (Mon Aug 01 2005 - 14:32:54 CDT)
CMYK images ioana_at_pegasus.arc.nasa.gov (Thu Jul 28 2005 - 21:13:08 CDT)
- Re: CMYK images John Stone (Fri Jul 29 2005 - 18:21:28 CDT)
  - Re: CMYK images Dow Hurst DPHURST (Fri Jul 29 2005 - 19:51:30 CDT)
  - Re: CMYK images Dow Hurst DPHURST (Fri Jul 29 2005 - 19:54:46 CDT)
    - RE: CMYK images Samuel Flores (Sat Jul 30 2005 - 16:42:40 CDT)
    - trig functions in vmd Samuel Flores (Sat Jul 30 2005 - 20:08:16 CDT)
sun server with graphics card sankari thirumal (Wed Jul 27 2005 - 23:24:29 CDT)
- Re: sun server with graphics card John Stone (Thu Jul 28 2005 - 10:05:16 CDT)
Why vmd can't connect vrpn server in windows xp? leepersonpp (Wed Jul 27 2005 - 21:55:01 CDT)
- Re: Why vmd can't connect vrpn server in windows xp? John Stone (Thu Jul 28 2005 - 12:49:48 CDT)
FC4 stereo problems Cameron Mura (Wed Jul 27 2005 - 18:03:58 CDT)
- Re: FC4 stereo problems John Stone (Wed Jul 27 2005 - 18:59:05 CDT)
  - Re: FC4 stereo problems John Stone (Thu Jul 28 2005 - 12:55:24 CDT)
H-H bond in solvate Jorge Pikunic (Wed Jul 27 2005 - 14:25:09 CDT)
tcl syntax problem Ramon Crehuet (Wed Jul 27 2005 - 11:18:53 CDT)
- Re: tcl syntax problem John Stone (Wed Jul 27 2005 - 11:47:32 CDT)
  - Re: tcl syntax problem Axel Kohlmeyer (Wed Jul 27 2005 - 15:09:23 CDT)
RE: SAS values for a residue Michel Espinoza-Fonseca (Wed Jul 27 2005 - 10:22:41 CDT)
SAS values for a residue Andrea Carotti (Wed Jul 27 2005 - 07:58:45 CDT)
- Re: SAS values for a residue John Stone (Wed Jul 27 2005 - 10:30:31 CDT)
  - Re: SAS values for a residue Mgr. Lubos Vrbka (Thu Jul 28 2005 - 05:00:35 CDT)
How to configure the joystick in VMD of linux version? leepersonpp (Tue Jul 26 2005 - 21:48:58 CDT)
residue numbering TCL versus PDB ioana_at_pegasus.arc.nasa.gov (Tue Jul 26 2005 - 20:32:08 CDT)
- Re: residue numbering TCL versus PDB Axel Kohlmeyer (Wed Jul 27 2005 - 07:36:48 CDT)
  - Re: residue numbering TCL versus PDB Axel Kohlmeyer (Fri Jul 29 2005 - 02:13:59 CDT)
Visualizing Delphi output Vani Krishna (Tue Jul 26 2005 - 09:50:41 CDT)
- Re: Visualizing Delphi output John Stone (Tue Jul 26 2005 - 10:11:45 CDT)
vmd-vrpn in windowsXP leepersonpp (Tue Jul 26 2005 - 05:25:24 CDT)
- Re: vmd-vrpn in windowsXP John Stone (Tue Jul 26 2005 - 09:57:35 CDT)
Changing atom order in DCD structures? Chang, Christopher (Mon Jul 25 2005 - 15:42:45 CDT)
White background Shirley Hui (Mon Jul 25 2005 - 13:08:28 CDT)
- Re: White background John Stone (Mon Jul 25 2005 - 13:13:30 CDT)
- Re: White background Joshua D. Moore (Mon Jul 25 2005 - 17:03:08 CDT)
VMD running slow Jindal Shah (Mon Jul 25 2005 - 12:20:58 CDT)
- Re: VMD running slow John Stone (Mon Jul 25 2005 - 12:44:08 CDT)
  - Re: VMD running slow Jindal Shah (Mon Jul 25 2005 - 12:58:51 CDT)
    - Re: VMD running slow John Stone (Mon Jul 25 2005 - 13:06:13 CDT)
    - Re: VMD running slow Jindal Shah (Mon Jul 25 2005 - 14:02:11 CDT)
- Re: VMD running slow Axel Kohlmeyer (Mon Jul 25 2005 - 15:18:27 CDT)
Altering water sphere and charmm type shgnwgn_at_eden.rutgers.edu (Mon Jul 25 2005 - 10:50:50 CDT)
problem about hotkey for vmd-1.8.3 windows version Jian Zou (Mon Jul 25 2005 - 09:44:12 CDT)
- Re: problem about hotkey for vmd-1.8.3 windows version John Stone (Mon Jul 25 2005 - 12:49:18 CDT)
  - Re: problem about hotkey for vmd-1.8.3 windows version Jian Zou (Mon Jul 25 2005 - 20:47:00 CDT)
Coloring by BETA not updating per frame David Kingsbury (Sat Jul 23 2005 - 11:16:09 CDT)
- Re: Coloring by BETA not updating per frame Axel Kohlmeyer (Sun Jul 24 2005 - 02:29:44 CDT)
  - Re: Coloring by BETA not updating per frame David Kingsbury (Sun Jul 24 2005 - 20:45:47 CDT)
    - Re: Coloring by BETA not updating per frame David Kingsbury (Sun Jul 24 2005 - 23:39:25 CDT)
Re: namd-l: catdcd and dcdunitcell Joshua D. Moore (Fri Jul 22 2005 - 16:04:00 CDT)
- Re: Re: namd-l: catdcd and dcdunitcell John Stone (Mon Jul 25 2005 - 13:50:03 CDT)
  - Re: Re: namd-l: catdcd and dcdunitcell Joshua D. Moore (Mon Jul 25 2005 - 14:16:16 CDT)
RE: Representing disulfide bonds when using psfgen Chang, Christopher (Thu Jul 21 2005 - 12:39:06 CDT)
- RE: Representing disulfide bonds when using psfgen Paul R Brenner (Thu Jul 21 2005 - 13:26:53 CDT)
Representing disulfide bonds when using psfgen Paul R Brenner (Thu Jul 21 2005 - 11:15:30 CDT)
- Re: Representing disulfide bonds when using psfgen Wei Chen (Thu Jul 21 2005 - 12:48:58 CDT)
ied - again Nuno R. L. Ferreira (Tue Jul 19 2005 - 13:41:57 CDT)
measuring rotation of protein about an axis Vani Krishna (Tue Jul 19 2005 - 10:07:37 CDT)
- RE: measuring rotation of protein about an axis Blake Charlebois (Tue Jul 19 2005 - 11:28:59 CDT)
Fitting trajectory frames to another molecule klsale (Mon Jul 18 2005 - 18:49:15 CDT)
- Re: Fitting trajectory frames to another molecule Justin Gullingsrud (Mon Jul 18 2005 - 20:22:51 CDT)
(no subject) Sale, Kenneth L (Mon Jul 18 2005 - 14:48:01 CDT)
- RE: Blake Charlebois (Mon Jul 18 2005 - 16:26:56 CDT)
PDB Files for Carbon Nanotubes Gaurav Sharma (Sun Jul 17 2005 - 17:22:55 CDT)
VMD + linux (64) + Flock of Birds Elena Slobounov (Fri Jul 15 2005 - 16:06:24 CDT)
- Re: VMD + linux (64) + Flock of Birds John Stone (Tue Jul 19 2005 - 16:32:46 CDT)
  - Re: VMD + linux (64) + Flock of Birds John Stone (Mon Jul 25 2005 - 15:11:19 CDT)
quality rendering Herbert Georg (Wed Jul 13 2005 - 15:27:44 CDT)
- Re: quality rendering Eduard Schreiner (Thu Jul 14 2005 - 01:46:46 CDT)
VMD & FC 4.0 FyD (Wed Jul 13 2005 - 14:42:37 CDT)
- Re: VMD & FC 4.0 Jerry Ebalunode (Wed Jul 13 2005 - 15:02:05 CDT)
  - Re: VMD & FC 4.0 FyD (Wed Jul 13 2005 - 15:56:59 CDT)
- Re: VMD & FC 4.0 B.D Allen (Wed Jul 13 2005 - 16:30:12 CDT)
catdcd Francesco Iori (Wed Jul 13 2005 - 04:05:40 CDT)
- Re: catdcd J. Rui Rodrigues (Wed Jul 13 2005 - 10:14:57 CDT)
vmd mpg movies not working in office 2000 Brian Bennion (Tue Jul 12 2005 - 17:36:52 CDT)
- Re: vmd mpg movies not working in office 2000 John Stone (Tue Jul 12 2005 - 17:49:35 CDT)
- Re: vmd mpg movies not working in office 2000 Jerry Ebalunode (Tue Jul 12 2005 - 18:33:19 CDT)
- Re: vmd mpg movies not working in office 2000 Jerry Ebalunode (Tue Jul 12 2005 - 18:33:49 CDT)
  - Re: vmd mpg movies not working in office 2000 John Stone (Tue Jul 12 2005 - 19:18:32 CDT)
display Gaussian cube file Jiabo Li (Tue Jul 12 2005 - 11:24:56 CDT)
- Re: display Gaussian cube file John Stone (Tue Jul 12 2005 - 13:05:46 CDT)
- Re: display Gaussian cube file Eduard Schreiner (Wed Jul 13 2005 - 04:05:27 CDT)
wrong bond drawing with pdb files Peter Schellenberg (Tue Jul 12 2005 - 02:36:11 CDT)
- Re: wrong bond drawing with pdb files Eduard Schreiner (Tue Jul 12 2005 - 11:01:24 CDT)
- Re: wrong bond drawing with pdb files John Stone (Tue Jul 12 2005 - 17:37:23 CDT)
- Re: wrong bond drawing with pdb files Peter Schellenberg (Wed Jul 13 2005 - 03:02:52 CDT)
  - Re: Re: wrong bond drawing with pdb files John Stone (Wed Jul 13 2005 - 10:04:22 CDT)
SPC/E Water Model and RigidBonds Joshua D. Moore (Fri Jul 08 2005 - 15:46:41 CDT)
changing occupancy for bunch of PDB file Shahid Qamar (Fri Jul 08 2005 - 13:48:44 CDT)
- Re: changing occupancy for bunch of PDB file John Stone (Fri Jul 08 2005 - 13:58:44 CDT)
problems to launch VMD 1.83 in MAC os x tiger Miguel Valvano (Fri Jul 08 2005 - 11:20:35 CDT)
- Re: problems to launch VMD 1.83 in MAC os x tiger John Stone (Fri Jul 08 2005 - 12:48:39 CDT)
- Re: problems to launch VMD 1.83 in MAC os x tiger Robert Brunner (Fri Jul 08 2005 - 15:17:02 CDT)
Error when running ied.py Joseph Fernandez (Fri Jul 08 2005 - 09:50:59 CDT)
TCL for adding bonds? Chang, Christopher (Thu Jul 07 2005 - 11:30:21 CDT)
- Re: TCL for adding bonds? Jérôme Hénin (Fri Jul 08 2005 - 02:58:31 CDT)
- Re: TCL for adding bonds? Eduard Schreiner (Fri Jul 08 2005 - 03:26:15 CDT)
- Re: TCL for adding bonds? peter.schellenberg_at_ipht-jena.de (Sun Jul 10 2005 - 05:59:27 CDT)
RE: psfgen and DNA Chang, Christopher (Thu Jul 07 2005 - 10:54:42 CDT)
psfgen and DNA Meunier, Vincent (Wed Jul 06 2005 - 20:46:39 CDT)
IndexError in ied Kateryna Miroshnychenko (Wed Jul 06 2005 - 11:27:11 CDT)
- Re: IndexError in ied John Stone (Wed Jul 06 2005 - 12:46:23 CDT)
  - Re: IndexError in ied Kateryna Miroshnychenko (Thu Jul 07 2005 - 02:23:06 CDT)
  - Re: IndexError in ied Kateryna Miroshnychenko (Tue Jul 12 2005 - 08:22:39 CDT)
Grasp plugin... Luis Rosales (Tue Jul 05 2005 - 20:17:12 CDT)
- Re: Grasp plugin... John Stone (Wed Jul 06 2005 - 10:14:05 CDT)
  - Re: Grasp plugin... Luis Rosales (Wed Jul 06 2005 - 19:19:25 CDT)
geometric location of amino acids in proteins sankari thirumal (Wed Jul 06 2005 - 00:04:10 CDT)
- Re: geometric location of amino acids in proteins John Stone (Tue Jul 12 2005 - 17:59:40 CDT)
RE: applying 6dof input forces wmsmith (Tue Jul 05 2005 - 17:10:09 CDT)
- RE: applying 6dof input forces wmsmith (Mon Jul 11 2005 - 12:03:52 CDT)
applying 6dof input forces Charles Moad (Tue Jul 05 2005 - 16:13:02 CDT)
dmpc membrane Swarna Patra (Mon Jul 04 2005 - 20:17:43 CDT)
a suggestion and query on command usage cbala_at_igib.res.in (Fri Jul 01 2005 - 08:08:57 CDT)
- Re: a suggestion and query on command usage Eduard Schreiner (Sat Jul 02 2005 - 10:01:53 CDT)
- Re: a suggestion and query on command usage John Stone (Tue Jul 05 2005 - 10:06:10 CDT)
Viewing an SDF file in VMD Brian Dotson (Thu Jun 30 2005 - 07:54:31 CDT)
- Re: Viewing an SDF file in VMD John Stone (Thu Jun 30 2005 - 13:38:44 CDT)
can't see all frames in XYZ file Valere Chen (Wed Jun 29 2005 - 14:42:50 CDT)
- Re: can't see all frames in XYZ file John Stone (Thu Jun 30 2005 - 14:03:37 CDT)
Movie frame rendering Peter Holm (Wed Jun 29 2005 - 11:06:50 CDT)
auto none /psfgen vivek sharma (Wed Jun 29 2005 - 07:31:23 CDT)
- Re: auto none /psfgen Jim Phillips (Thu Jun 30 2005 - 10:40:34 CDT)
  - exclude residues John (Thu Jun 30 2005 - 11:42:09 CDT)
hydrogen bond energy shgnwgn_at_eden.rutgers.edu (Tue Jun 28 2005 - 10:50:25 CDT)
- Re: hydrogen bond energy John Stone (Tue Jun 28 2005 - 11:09:04 CDT)
Re: sball.h not found Luis Rosales (Sat Jun 25 2005 - 21:31:01 CDT)
MSMS Peter Holm (Mon Jun 27 2005 - 07:19:22 CDT)
- Re: MSMS John Stone (Mon Jun 27 2005 - 10:01:45 CDT)
  - Re: MSMS Peter Holm (Mon Jun 27 2005 - 10:37:57 CDT)
Display shuts down on startup Peter Holm (Mon Jun 27 2005 - 05:36:50 CDT)
- Re: Display shuts down on startup QS=2E_Teletch=E9a=22?= (Mon Jun 27 2005 - 06:55:45 CDT)
  - Re: Display shuts down on startup Peter Holm (Mon Jun 27 2005 - 07:07:07 CDT)
    - Re: Display shuts down on startup QS=2E_Teletch=E9a=22?= (Mon Jun 27 2005 - 07:33:36 CDT)
- Re: Display shuts down on startup John Stone (Mon Jun 27 2005 - 09:52:56 CDT)
- Re: Display shuts down on startup Peter Holm (Tue Jun 28 2005 - 07:05:04 CDT)
  - Re: Re: Display shuts down on startup John Stone (Tue Jun 28 2005 - 15:35:12 CDT)
    - Re: Re: Display shuts down on startup Stefano Piana (Tue Jun 28 2005 - 20:37:15 CDT)
    - Re: Re: Display shuts down on startup Peter Holm (Wed Jun 29 2005 - 02:37:37 CDT)
Tcl script and plugin Jay Lee (Sat Jun 25 2005 - 15:00:13 CDT)
- Re: Tcl script and plugin Marcos Sotomayor (Sat Jun 25 2005 - 17:37:37 CDT)
sball.h not found Ignacio Rodriguez Fernandez (Sat Jun 25 2005 - 08:47:16 CDT)
Updating COLOURS for atoms master mendez (Sat Jun 25 2005 - 02:24:08 CDT)
- Re: Updating COLOURS for atoms John Stone (Tue Jun 28 2005 - 19:26:28 CDT)
Re: Adding Salt to a system Ioana Cozmuta (Wed Jun 22 2005 - 20:59:47 CDT)
do not compute/draw bonds? Ivan Degtyarenko (Thu Jun 23 2005 - 08:36:33 CDT)
- Re: do not compute/draw bonds? Axel Kohlmeyer (Thu Jun 23 2005 - 12:26:44 CDT)
  - Re: do not compute/draw bonds? John Stone (Fri Jun 24 2005 - 11:02:38 CDT)
phi and psi information matteo.pennestri_at_virgilio.it (Thu Jun 23 2005 - 00:55:54 CDT)
- Re: phi and psi information nordgren_at_sas.upenn.edu (Thu Jun 23 2005 - 04:02:50 CDT)
- Re: phi and psi information Axel Kohlmeyer (Thu Jun 23 2005 - 04:09:59 CDT)
visualising protein dynamics Claire Zerafa (Wed Jun 22 2005 - 12:39:55 CDT)
- Re: visualising protein dynamics John Stone (Wed Jun 22 2005 - 14:03:03 CDT)
  - Re: visualising protein dynamics Adrian Roitberg (Wed Jun 22 2005 - 16:57:47 CDT)
Nvidia update 1.0-7664 success for VMD-1.8.3 Dow Hurst DPHURST (Tue Jun 21 2005 - 16:49:37 CDT)
VMD 1.8.4 test builds, 32-bit and 64-bit AIX5... John Stone (Tue Jun 21 2005 - 14:46:32 CDT)
- Re: VMD 1.8.4 test builds, 32-bit and 64-bit AIX5... Ioana Cozmuta (Tue Jun 21 2005 - 17:47:24 CDT)
  - Re: VMD 1.8.4 test builds, 32-bit and 64-bit AIX5... John Stone (Tue Jun 21 2005 - 17:50:56 CDT)
test email Dow Hurst DPHURST (Tue Jun 21 2005 - 14:32:05 CDT)
Test version of VMD 1.8.4 for Linux/IA64 (SGI Prism, Altix, etc..) John Stone (Tue Jun 21 2005 - 13:51:51 CDT)
- Re: Test version of VMD 1.8.4 for Linux/IA64 (SGI Prism, Altix, etc..) Oliver Otto (Wed Jun 22 2005 - 05:34:37 CDT)
  - Re: Test version of VMD 1.8.4 for Linux/IA64 (SGI Prism, Altix, etc..) John Stone (Wed Jun 22 2005 - 10:58:38 CDT)
  - Re: Test version of VMD 1.8.4 for Linux/IA64 (SGI Prism, Altix, etc..) John Stone (Wed Jun 22 2005 - 13:34:51 CDT)
Create a new color category Dow Hurst DPHURST (Tue Jun 21 2005 - 12:25:52 CDT)
- Re: Create a new color category John Stone (Tue Jun 21 2005 - 15:52:39 CDT)
  - Re: Create a new color category John Stone (Wed Jun 22 2005 - 14:19:38 CDT)
Creating a demo - updating the OpenGL window Palmer, Teresa (Mon Jun 20 2005 - 14:30:22 CDT)
- Re: Creating a demo - updating the OpenGL window John Stone (Mon Jun 20 2005 - 14:40:54 CDT)
IMD question wmsmith (Mon Jun 20 2005 - 13:38:18 CDT)
- Re: IMD question John Stone (Tue Jun 21 2005 - 15:48:42 CDT)
Rotating cube files Mikolai Fajer (Mon Jun 20 2005 - 12:44:26 CDT)
- Re: Rotating cube files John Stone (Mon Jun 20 2005 - 17:35:43 CDT)
Script for automated selection Andrea Carotti (Mon Jun 20 2005 - 09:38:51 CDT)
- RE: Script for automated selection Blake Charlebois (Mon Jun 20 2005 - 12:28:39 CDT)
- Re: Script for automated selection Axel Kohlmeyer (Mon Jun 20 2005 - 12:58:41 CDT)
  - Re: Script for automated selection Andrea Carotti (Wed Jun 22 2005 - 03:28:54 CDT)
autoimd on windows Anna Modzelewska (Mon Jun 20 2005 - 06:40:29 CDT)
- Re: autoimd on windows John Stone (Tue Jun 21 2005 - 15:43:11 CDT)
  - Re: autoimd on windows Anna Modzelewska (Wed Jun 22 2005 - 05:29:52 CDT)
  - Re: autoimd on windows Anna Modzelewska (Wed Jun 22 2005 - 11:51:22 CDT)
VMD for SGI Altix/Prism, IBM AIX5, etc.. Oliver Otto (Mon Jun 20 2005 - 06:16:01 CDT)
- Re: VMD for SGI Altix/Prism, IBM AIX5, etc.. John Stone (Mon Jun 20 2005 - 09:58:17 CDT)
Fwd: Re: vmd version for solaris 8 Justin (Sat Jun 18 2005 - 11:19:32 CDT)
vmd version for solaris 8 Justin (Fri Jun 17 2005 - 16:29:48 CDT)
- Re: vmd version for solaris 8 John Stone (Fri Jun 17 2005 - 16:33:05 CDT)
  - Re: vmd version for solaris 8 Justin (Mon Jun 20 2005 - 09:54:14 CDT)
Strange VMD output Chang, Christopher (Fri Jun 17 2005 - 15:02:57 CDT)
- Re: Strange VMD output John Stone (Tue Jun 21 2005 - 16:01:12 CDT)
Mesa libs + Mac OS X + HW stereo + vmd Dr. Mick Knaggs (Fri Jun 17 2005 - 14:28:30 CDT)
- Re: Mesa libs + Mac OS X + HW stereo + vmd John Stone (Fri Jun 17 2005 - 17:20:52 CDT)
size of output graphics Samuel Flores (Fri Jun 17 2005 - 11:41:37 CDT)
render question Samuel Flores (Fri Jun 17 2005 - 10:43:49 CDT)
- Re: render question John Stone (Fri Jun 17 2005 - 17:42:27 CDT)
vmd load molecule problem Claire Zerafa (Fri Jun 17 2005 - 06:30:29 CDT)
- Re: vmd load molecule problem John Stone (Fri Jun 17 2005 - 17:39:48 CDT)
RE: namd-l: tcl question Blake Charlebois (Thu Jun 16 2005 - 22:32:39 CDT)
Render to Tachyon Internal in a Tcl script Yalini (Tue Jun 14 2005 - 19:52:56 CDT)
- Re: Render to Tachyon Internal in a Tcl script Eduard Schreiner (Thu Jun 16 2005 - 01:41:30 CDT)
autoimd error Anna Modzelewska (Wed Jun 15 2005 - 09:35:01 CDT)
- Re: autoimd error Jordi Cohen (Wed Jun 15 2005 - 13:13:25 CDT)
RE: Combine Drawing Methods - Cartoon and Disulfide Bonds Chang, Christopher (Tue Jun 14 2005 - 18:43:48 CDT)
Combine Drawing Methods - Cartoon and Disulfide Bonds Paul R Brenner (Tue Jun 14 2005 - 17:00:12 CDT)
(no subject) Simon Whitehead (Tue Jun 14 2005 - 05:34:53 CDT)
- Re: John Stone (Tue Jun 21 2005 - 17:23:53 CDT)
VMD on Debian Linux Urgent Nara Dashdorj (Sat Jun 11 2005 - 20:12:41 CDT)
- Re: VMD on Debian Linux Urgent John Stone (Mon Jun 13 2005 - 13:27:04 CDT)
  - Re: VMD on Debian Linux Urgent Luis Gracia (Mon Jun 13 2005 - 16:18:00 CDT)
psfgen deleting water molecules shgnwgn_at_eden.rutgers.edu (Mon Jun 13 2005 - 09:37:55 CDT)
- Re: psfgen deleting water molecules Jim Phillips (Fri Jun 24 2005 - 15:51:37 CDT)
Solvate with LES (Locally Enhanced Sampling) pdb does not work Marcin Wojciechowski (Thu Jun 09 2005 - 04:52:29 CDT)
- Re: Solvate with LES (Locally Enhanced Sampling) pdb does not work Jim Phillips (Thu Jun 09 2005 - 13:41:38 CDT)
Selection basing on the number of hydrogen bonds Tatyana Kuznetsova (Thu Jun 09 2005 - 02:30:14 CDT)
Query Tamal Banerjee (Thu Jun 09 2005 - 01:34:58 CDT)
- Re: Query Wei Chen (Thu Jun 09 2005 - 13:54:59 CDT)
multiple automated calls to NAMD nordgren_at_sas.upenn.edu (Wed Jun 08 2005 - 20:57:56 CDT)
- Re: multiple automated calls to NAMD Axel Kohlmeyer (Thu Jun 09 2005 - 02:38:35 CDT)
  - Re: namd-l: Re: multiple automated calls to NAMD nordgren_at_sas.upenn.edu (Thu Jun 09 2005 - 21:56:31 CDT)
RE: Problems with Psf using Charmm format, solvate and autoionize Chang, Christopher (Wed Jun 08 2005 - 15:12:41 CDT)
- RE: Problems with Psf using Charmm format, solvate and autoionize Jim Phillips (Thu Jun 09 2005 - 14:02:18 CDT)
memory problem p4_Globmemsize shgnwgn_at_eden.rutgers.edu (Wed Jun 08 2005 - 14:50:48 CDT)
- Re: memory problem p4_Globmemsize John Stone (Wed Jun 08 2005 - 16:05:04 CDT)
Problems with Psf using Charmm format, solvate and autoionize Leonardo Sepulveda Durán (Wed Jun 08 2005 - 12:55:21 CDT)
Membrane plugin error? rwiese_at_unr.edu (Wed Jun 08 2005 - 12:37:14 CDT)
- Re: Membrane plugin error? John Stone (Wed Jun 08 2005 - 13:24:00 CDT)
  - Re: Membrane plugin error? rwiese_at_unr.edu (Wed Jun 08 2005 - 14:04:49 CDT)
ATI crashes, use of setenv VMD_EXCL_GL_EXTENSIONS Dr. Peter Schellenberg (Mon Jun 06 2005 - 02:28:21 CDT)
RE: creating scripts Chang, Christopher (Fri Jun 03 2005 - 17:50:51 CDT)
creating scripts Mark A. Hallman (Fri Jun 03 2005 - 16:00:54 CDT)
installation of vmd 1.8.3 Dmitry Osolodkin (Fri Jun 03 2005 - 11:49:21 CDT)
- Re: installation of vmd 1.8.3 John Stone (Fri Jun 03 2005 - 14:02:11 CDT)
  - Re: installation of vmd 1.8.3 Dmitry Osolodkin (Mon Jun 06 2005 - 05:57:34 CDT)
about gamess plugin mashaojie163 (Thu Jun 02 2005 - 20:50:59 CDT)
- Re: about gamess plugin John Stone (Mon Jun 06 2005 - 12:49:20 CDT)
Re: [PyMOL] nVidia Driver 7664 for Linux sabuj pattanayek (Thu Jun 02 2005 - 13:57:54 CDT)
- Re: Re: [PyMOL] nVidia Driver 7664 for Linux John Stone (Thu Jun 02 2005 - 15:12:06 CDT)
nVidia Driver 7664 for Linux Warren DeLano (Thu Jun 02 2005 - 11:41:38 CDT)
- Re: nVidia Driver 7664 for Linux John Stone (Thu Jun 02 2005 - 13:27:02 CDT)
Error message disappears before I can read it! Robert Coridan (Thu Jun 02 2005 - 11:21:35 CDT)
- Re: Error message disappears before I can read it! John Stone (Thu Jun 02 2005 - 12:56:48 CDT)
  - Re: Error message disappears before I can read it! Robert Coridan (Thu Jun 02 2005 - 13:51:29 CDT)
Change representation default from lines to points Prasad S Garimella (Thu Jun 02 2005 - 09:56:16 CDT)
- Re: Change representation default from lines to points Axel Kohlmeyer (Thu Jun 02 2005 - 10:08:24 CDT)
Eye position / camera position Breght Boschker (Thu Jun 02 2005 - 05:27:49 CDT)
- Re: Eye position / camera position John Stone (Thu Jun 09 2005 - 16:51:33 CDT)
vmd installation with Mesa installed in a non-standard location Jing (Wed Jun 01 2005 - 23:53:37 CDT)
- Re: vmd installation with Mesa installed in a non-standard location John Stone (Thu Jun 02 2005 - 17:05:50 CDT)
  - Re: vmd installation with Mesa installed in a non-standard location Luis Rosales (Thu Jun 02 2005 - 18:56:19 CDT)
  - Re: vmd installation with Mesa installed in a non-standard location Jing (Thu Jun 02 2005 - 23:00:34 CDT)
contact map Anuradha Mittal (Wed Jun 01 2005 - 14:56:06 CDT)
- Re: contact map Luis Gracia (Wed Jun 01 2005 - 18:13:39 CDT)
how to write out the coordinates of center of mass of a particular residue Xiongce Zhao (Wed Jun 01 2005 - 12:36:45 CDT)
- RE: how to write out the coordinates of center of mass of a particularresidue Blake Charlebois (Wed Jun 01 2005 - 21:39:49 CDT)
  - RE: how to write out the coordinates of center of mass of a particularresidue Ekta Khurana (Thu Jun 02 2005 - 10:12:00 CDT)
loading amber file cbala_at_igib.res.in (Tue May 31 2005 - 01:05:45 CDT)
- Re: loading amber file Axel Kohlmeyer (Wed Jun 01 2005 - 01:32:33 CDT)
Self Assembled Monolayer Daniel Schwaab (Tue May 31 2005 - 09:48:06 CDT)
Any way for comparing two structures?? Dmitry Osolodkin (Tue May 31 2005 - 09:11:07 CDT)
Any way for comparing two structures?? Dmitry Osolodkin (Tue May 31 2005 - 08:58:29 CDT)
- RE: Any way for comparing two structures?? Blake Charlebois (Tue May 31 2005 - 10:50:32 CDT)
  - Re: Any way for comparing two structures?? Luis Gracia (Tue May 31 2005 - 14:07:45 CDT)
how to study the effect of mutation in vmd sankari thirumal (Sun May 29 2005 - 23:15:33 CDT)
molfile plugin and the NetCDF file format Lars Bruno Hansen (Thu May 26 2005 - 06:21:16 CDT)
- Re: molfile plugin and the NetCDF file format John Stone (Thu May 26 2005 - 09:49:31 CDT)
lipid definition dimka (Wed May 25 2005 - 10:55:04 CDT)
- Re: lipid definition John Stone (Thu May 26 2005 - 10:17:55 CDT)
  - Re: lipid definition Jim Phillips (Thu May 26 2005 - 13:11:08 CDT)
plugins compilation problem - gcc switches Mgr. Lubos Vrbka (Wed May 25 2005 - 09:19:25 CDT)
- Re: plugins compilation problem - gcc switches John Stone (Wed May 25 2005 - 10:26:12 CDT)
bad resolution and too slow on mandrake 10.0 matteo.pennestri_at_virgilio.it (Wed May 25 2005 - 02:00:01 CDT)
- Re: bad resolution and too slow on mandrake 10.0 Cetin Baloglu (Wed May 25 2005 - 04:04:55 CDT)
  - Re: bad resolution and too slow on mandrake 10.0 Jorge Hernandez Fernandez (Fri May 27 2005 - 14:50:09 CDT)
    - Re: bad resolution and too slow on mandrake 10.0 John Stone (Fri May 27 2005 - 15:00:06 CDT)
- Re: bad resolution and too slow on mandrake 10.0 Olga Kravchenko (Wed May 25 2005 - 05:00:28 CDT)
  - Re: bad resolution and too slow on mandrake 10.0 matteo.pennestri_at_virgilio.it (Sun May 29 2005 - 12:37:42 CDT)
an inconsistance between psf file and coor file after equilibration Baoqiang Cao (Sun May 22 2005 - 22:28:16 CDT)
- Re: an inconsistance between psf file and coor file after equilibration John Stone (Tue May 24 2005 - 11:12:22 CDT)
Volume coloring problems Hernán Alonso (Tue May 24 2005 - 03:44:48 CDT)
- Re: Volume coloring problems John Stone (Tue May 24 2005 - 09:06:33 CDT)
Compiling VMD: Trouble with DispCmds.C Luis Rosales (Fri May 20 2005 - 22:28:18 CDT)
- Re: Compiling VMD: Trouble with DispCmds.C John Stone (Mon May 23 2005 - 10:04:27 CDT)
  - Re: Compiling VMD: Trouble with DispCmds.C Luis Rosales (Tue May 24 2005 - 17:36:32 CDT)
Adding a logo to a screenshot Palmer, Teresa (Fri May 20 2005 - 15:12:55 CDT)
- Re: Adding a logo to a screenshot John Stone (Fri May 20 2005 - 15:28:47 CDT)
  - Calculate the area of overlap? Brian Kidd (Sat May 21 2005 - 02:01:04 CDT)
    - Re: Calculate the area of overlap? John Stone (Mon May 23 2005 - 10:22:28 CDT)
Python interface (was: Accessing TCL through Python interface) Daniel B. Faken (Fri May 20 2005 - 08:34:00 CDT)
- Re: Python interface (was: Accessing TCL through Python interface) Justin Gullingsrud (Fri May 20 2005 - 14:30:06 CDT)
Adding Salt to a system Thomas C. Bishop (Thu May 19 2005 - 10:09:26 CDT)
ied.py : tk.h version (8.3) doesn't match libtk.a version (8.4) IBC strbio (Wed May 18 2005 - 05:38:02 CDT)
- Re: ied.py : tk.h version (8.3) doesn't match libtk.a version (8.4) John Stone (Wed May 18 2005 - 13:34:10 CDT)
Hydration Cetin Baloglu (Wed May 18 2005 - 03:44:34 CDT)
- Re: Hydration John Stone (Wed May 18 2005 - 13:36:52 CDT)
VMD does not run on MacOS X 10.4 Tiger Suckjoon JUN (Mon May 16 2005 - 19:09:51 CDT)
- Re: VMD does not run on MacOS X 10.4 Tiger John Stone (Mon May 16 2005 - 19:41:03 CDT)
  - Re: VMD does not run on MacOS X 10.4 Tiger Fred de Lamotte (Tue May 17 2005 - 01:38:52 CDT)
- Re: VMD does not run on MacOS X 10.4 Tiger Robert Brunner (Mon May 16 2005 - 22:11:18 CDT)
  - Re: VMD does not run on MacOS X 10.4 Tiger Suckjoon JUN (Tue May 17 2005 - 03:03:54 CDT)
skipping frames in hbonding script YOLANDA SMALL (Sun May 15 2005 - 11:39:03 CDT)
Accessing TCL through Python interface Daniel B. Faken (Sat May 14 2005 - 15:09:35 CDT)
Open diff pdbs with diff # of atoms? Prasad S Garimella (Fri May 13 2005 - 17:02:51 CDT)
- Re: Open diff pdbs with diff # of atoms? Axel Kohlmeyer (Sat May 14 2005 - 02:04:23 CDT)
Total charge query? Chang, Christopher (Fri May 13 2005 - 13:32:20 CDT)
- RE: Total charge query? Blake Charlebois (Fri May 13 2005 - 17:28:41 CDT)
Buried Surface Area Matthew Wilce (Fri May 13 2005 - 09:33:36 CDT)
- Re: Buried Surface Area John Stone (Fri May 13 2005 - 09:52:30 CDT)
RE: What is missing when using VMDSIMPLEGRAPHICS 1? Dallas B. Warren (Fri May 13 2005 - 02:07:05 CDT)
- Re: What is missing when using VMDSIMPLEGRAPHICS 1? John Stone (Fri May 13 2005 - 02:30:27 CDT)
- RE: What is missing when using VMDSIMPLEGRAPHICS 1? Dallas B. Warren (Fri May 13 2005 - 21:31:43 CDT)
What is missing when using VMDSIMPLEGRAPHICS 1? Dallas B. Warren (Thu May 12 2005 - 23:13:20 CDT)
- Re: What is missing when using VMDSIMPLEGRAPHICS 1? John Stone (Fri May 13 2005 - 01:18:00 CDT)
how can I read volume data in spider-format Michael Radermacher (Thu May 12 2005 - 19:50:10 CDT)
- Re: how can I read volume data in spider-format John Stone (Thu May 12 2005 - 20:09:06 CDT)
creating psf with trimethoprim Charles Moad (Wed May 11 2005 - 21:38:14 CDT)
VMD crash on athlon64 with licorice representation Carlos Simmerling (Wed May 11 2005 - 08:13:25 CDT)
- Re: VMD crash on athlon64 with licorice representation John Stone (Wed May 11 2005 - 10:28:18 CDT)
  - Re: VMD crash on athlon64 with licorice representation Carlos Simmerling (Wed May 11 2005 - 10:34:22 CDT)
Ramachandran plot Ekta Khurana (Mon May 09 2005 - 18:00:46 CDT)
- Re: Ramachandran plot Charles McCallum (Tue May 10 2005 - 22:56:14 CDT)
how to delete atoms from the command line? Nicolas Sapay (Tue May 10 2005 - 07:30:50 CDT)
- Re: how to delete atoms from the command line? John Stone (Tue May 10 2005 - 09:58:51 CDT)
  - Re: how to delete atoms from the command line? Nicolas Sapay (Tue May 10 2005 - 09:59:30 CDT)
  - PSFGEN vs. VMD nordgren_at_sas.upenn.edu (Wed May 11 2005 - 05:01:37 CDT)
radius of gyration Cetin Baloglu (Tue May 10 2005 - 09:47:59 CDT)
- Re: radius of gyration John Stone (Tue May 10 2005 - 10:16:01 CDT)
IMDEnergies from python Charles Moad (Mon May 09 2005 - 22:51:43 CDT)
RE: Rama plot Michel Espinoza-Fonseca (Mon May 09 2005 - 18:27:12 CDT)
- RE: Rama plot Ekta Khurana (Mon May 09 2005 - 18:34:48 CDT)
  - RE: Rama plot Axel Kohlmeyer (Tue May 10 2005 - 01:53:57 CDT)
- RE: Rama plot Ekta Khurana (Tue May 10 2005 - 11:31:27 CDT)
Rama plot Ekta Khurana (Mon May 09 2005 - 18:07:40 CDT)
select within distance range YOLANDA SMALL (Mon May 09 2005 - 16:23:24 CDT)
- Re: select within distance range John Stone (Tue May 10 2005 - 10:36:24 CDT)
  - Re: select within distance range YOLANDA SMALL (Tue May 10 2005 - 12:44:12 CDT)
    - Re: select within distance range John Stone (Tue May 10 2005 - 13:18:13 CDT)
Head tracking with VRPN and VMD Oliver Wenisch (Mon May 09 2005 - 09:57:43 CDT)
- Re: Head tracking with VRPN and VMD John Stone (Mon May 09 2005 - 10:07:04 CDT)
Plugins... Luis Rosales (Fri May 06 2005 - 19:31:11 CDT)
- Re: Plugins... John Stone (Sat May 07 2005 - 11:31:35 CDT)
GNU-Darwin rides Tiger, packages back on-line proclus_at_gnu-darwin.org (Fri May 06 2005 - 11:05:55 CDT)
How to determine distribution of the orientation of a molecule Raj Gupta (Thu May 05 2005 - 07:31:56 CDT)
- Re: How to determine distribution of the orientation of a molecule John Stone (Thu May 05 2005 - 10:05:16 CDT)
  - writing DCD files nordgren_at_sas.upenn.edu (Fri May 06 2005 - 03:54:18 CDT)
rmsf calculation Michel Espinoza-Fonseca (Tue May 03 2005 - 15:58:43 CDT)
- Re: rmsf calculation Wei Chen (Wed May 04 2005 - 10:18:10 CDT)
Error Encountered in making vmdmovie Adrian Koh (Tue May 03 2005 - 02:42:00 CDT)
- Re: Error Encountered in making vmdmovie John Stone (Tue May 03 2005 - 09:59:45 CDT)
VMD crash on PDB read Stefano Piana (Mon May 02 2005 - 04:38:25 CDT)
- Re: VMD crash on PDB read John Stone (Mon May 02 2005 - 09:54:50 CDT)
compiling VMD 1.8.3 Stefano Piana (Mon May 02 2005 - 05:17:34 CDT)
- Re: compiling VMD 1.8.3 John Stone (Mon May 02 2005 - 09:56:44 CDT)
align two molecules with index Zhenyu Lu (Thu Apr 28 2005 - 17:42:23 CDT)
Updated APBS plugin for VMD available for testing... John Stone (Thu Apr 28 2005 - 14:15:00 CDT)
Problem with "bigdcd" Leyla Celik (Thu Apr 28 2005 - 09:53:18 CDT)
- Re: Problem with "bigdcd" John Stone (Thu Apr 28 2005 - 09:58:49 CDT)
  - Re: Problem with "bigdcd" Leyla Celik (Thu Apr 28 2005 - 12:12:36 CDT)
- Re: Problem with "bigdcd" Brian Bennion (Thu Apr 28 2005 - 12:33:59 CDT)
RE: color the surface with electrostatic potential value Michel Espinoza-Fonseca (Wed Apr 27 2005 - 18:02:31 CDT)
- RE: color the surface with electrostatic potential value Axel Kohlmeyer (Thu Apr 28 2005 - 01:12:24 CDT)
color the surface with electrostatic potential value Yongcheng Zhou (Wed Apr 27 2005 - 17:12:29 CDT)
wrap ions Brian Kidd (Wed Apr 27 2005 - 11:39:35 CDT)
RE: Solvate plugin Luis Rosales (Wed Apr 27 2005 - 04:12:08 CDT)
Re:Re:missing bond problem haider abbas (Wed Apr 27 2005 - 06:28:03 CDT)
- Re: Re:Re:missing bond problem Axel Kohlmeyer (Wed Apr 27 2005 - 10:01:50 CDT)
Solvate plugin Huaer XC (Wed Apr 27 2005 - 01:28:28 CDT)
RMSD calculation Simon Whitehead (Mon Apr 25 2005 - 06:17:35 CDT)
- Re: RMSD calculation Luis Gracia (Mon Apr 25 2005 - 19:29:21 CDT)
bond missimg haider abbas (Mon Apr 25 2005 - 05:25:19 CDT)
- Re: bond missimg Axel Kohlmeyer (Mon Apr 25 2005 - 08:47:20 CDT)
- Re: bond missimg Eduard Schreiner (Mon Apr 25 2005 - 08:58:44 CDT)
Color bar in VMD Dan Wright (Fri Apr 22 2005 - 16:23:36 CDT)
dcd large files, charmm-VMD Kos (Thu Apr 21 2005 - 20:29:21 CDT)
- Re: dcd large files, charmm-VMD Bogdan Costescu (Fri Apr 22 2005 - 08:09:11 CDT)
- Re: dcd large files, charmm-VMD Marc Q. Ma (Fri Apr 22 2005 - 09:15:17 CDT)
  - Re: dcd large files, charmm-VMD John Stone (Fri Apr 22 2005 - 10:21:17 CDT)
    - Re: dcd large files, charmm-VMD Marc Q. Ma (Fri Apr 22 2005 - 10:44:25 CDT)
  - Re: dcd large files, charmm-VMD Axel Kohlmeyer (Fri Apr 22 2005 - 11:53:25 CDT)
- Re: dcd large files, charmm-VMD John Stone (Fri Apr 22 2005 - 10:33:21 CDT)
console in vmd-1.8.3 amd64 is blank (like white text on white background) so I can't see any output messages Sabuj Pattanayek (Thu Apr 21 2005 - 17:19:57 CDT)
- Re: console in vmd-1.8.3 amd64 is blank (like white text on white background) so I can't see any output messages John Stone (Thu Apr 21 2005 - 17:22:44 CDT)
  - Re: console in vmd-1.8.3 amd64 is blank (like white text on white background) so I can't see any output messages Sabuj Pattanayek (Thu Apr 21 2005 - 17:32:55 CDT)
  - Re: console in vmd-1.8.3 amd64 is blank (like white text on white background) so I can't see any output messages Pattanayek, Sabuj (Tue Jun 07 2005 - 11:57:52 CDT)
Sphere size Kurt Smith (Wed Apr 20 2005 - 17:18:45 CDT)
- Re: Sphere size John Stone (Wed Apr 20 2005 - 17:30:30 CDT)
  - Re: Sphere size Kurt Smith (Thu Apr 21 2005 - 15:04:39 CDT)
    - Re: Sphere size John Stone (Fri Apr 22 2005 - 18:08:27 CDT)
    - Re: Sphere size Axel Kohlmeyer (Sat Apr 23 2005 - 06:22:25 CDT)
RE: representation_problem Chang, Christopher (Wed Apr 20 2005 - 16:34:14 CDT)
- Re: representation_problem John Stone (Thu Apr 21 2005 - 16:40:07 CDT)
RE: compiling VMD on mac Michel Espinoza-Fonseca (Wed Apr 20 2005 - 14:53:05 CDT)
compiling VMD on mac William Sheffler (Wed Apr 20 2005 - 14:32:05 CDT)
- Re: compiling VMD on mac John Stone (Wed Apr 20 2005 - 14:57:42 CDT)
  - Re: compiling VMD on mac Hirsh Nanda (Tue Apr 26 2005 - 14:17:32 CDT)
    - Re: compiling VMD on mac John Stone (Tue Apr 26 2005 - 14:25:13 CDT)
    - Re: compiling VMD on mac John Stone (Tue Apr 26 2005 - 17:13:36 CDT)
representation_problem Wei Chen (Wed Apr 20 2005 - 14:21:21 CDT)
Enabling a menu on the top level Palmer, Teresa (Wed Apr 20 2005 - 11:17:43 CDT)
- Re: Enabling a menu on the top level John Stone (Wed Apr 20 2005 - 15:43:27 CDT)
Off Topic: Small Molecule Modeling Paul Daniel Jones (Wed Apr 20 2005 - 11:00:21 CDT)
Interactive Simulations, ligand size limits.... Luis Rosales (Tue Apr 19 2005 - 22:51:52 CDT)
- Re: Interactive Simulations, ligand size limits.... John Stone (Wed Apr 20 2005 - 16:12:20 CDT)
Normal mode analysis David Poger (Tue Apr 19 2005 - 08:02:57 CDT)
- Re: Normal mode analysis John Stone (Tue Apr 19 2005 - 16:45:19 CDT)
Setting the speed of rotation Palmer, Teresa (Mon Apr 18 2005 - 11:27:26 CDT)
- Re: Setting the speed of rotation John Stone (Tue Apr 19 2005 - 10:28:58 CDT)
loading two dcd files in VMD Jorge Pikunic (Mon Apr 18 2005 - 10:40:51 CDT)
- Re: loading two dcd files in VMD Luis Gracia (Mon Apr 18 2005 - 13:47:19 CDT)
compressed trajectory support Mgr. Lubos Vrbka (Mon Apr 18 2005 - 07:13:10 CDT)
- Re: compressed trajectory support Bogdan Costescu (Mon Apr 18 2005 - 09:20:00 CDT)
  - Re: compressed trajectory support Mgr. Lubos Vrbka (Mon Apr 18 2005 - 09:46:40 CDT)
    - Re: compressed trajectory support Bogdan Costescu (Mon Apr 18 2005 - 09:57:14 CDT)
    - Re: compressed trajectory support Mgr. Lubos Vrbka (Mon Apr 18 2005 - 10:08:41 CDT)
  - Re: compressed trajectory support Axel Kohlmeyer (Mon Apr 18 2005 - 12:47:01 CDT)
    - Re: compressed trajectory support Mgr. Lubos Vrbka (Tue Apr 19 2005 - 01:04:57 CDT)
- Re: compressed trajectory support Axel Kohlmeyer (Mon Apr 18 2005 - 10:38:14 CDT)
  - Re: compressed trajectory support Mgr. Lubos Vrbka (Mon Apr 18 2005 - 10:48:02 CDT)
RE: criteria for detecting hydrogen bonds Michel Espinoza-Fonseca (Sun Apr 17 2005 - 19:41:29 CDT)
"Draw" different things in different frames Kiniu Wong (Sat Apr 16 2005 - 20:16:02 CDT)
- Re: "Draw" different things in different frames Axel Kohlmeyer (Sun Apr 17 2005 - 03:07:11 CDT)
about tcl program and run tcl script in namd Gino (Sat Apr 16 2005 - 01:31:23 CDT)
- Re: about tcl program and run tcl script in namd Justin Gullingsrud (Sat Apr 16 2005 - 16:42:52 CDT)
AMBER pbsa electrostatic potential map Mengjuei Hsieh (Fri Apr 15 2005 - 20:09:09 CDT)
- Re: AMBER pbsa electrostatic potential map John Stone (Mon Apr 18 2005 - 10:13:39 CDT)
a question about get the coordinates in vector form M SH (Fri Apr 15 2005 - 13:31:45 CDT)
- Re: a question about get the coordinates in vector form Eugen Leitl (Fri Apr 15 2005 - 15:45:24 CDT)
- Re: a question about get the coordinates in vector form Axel Kohlmeyer (Fri Apr 15 2005 - 16:19:25 CDT)
Basic membrane plugin questions Meyer, Douglas K $UMC-Student$ (Fri Apr 15 2005 - 11:20:56 CDT)
- Re: Basic membrane plugin questions John Stone (Tue Apr 19 2005 - 18:42:53 CDT)
wrong bond and bond breaking Hyonseok Hwang (Fri Apr 15 2005 - 11:14:43 CDT)
- Re: wrong bond and bond breaking John Stone (Fri Apr 15 2005 - 11:46:09 CDT)
  - Re: wrong bond and bond breaking Hyonseok Hwang (Fri Apr 15 2005 - 12:24:00 CDT)
    - Re: wrong bond and bond breaking Shahid Qamar (Fri Apr 15 2005 - 13:19:24 CDT)
UHBD-grids Alexander Spaar (Fri Apr 15 2005 - 04:12:57 CDT)
- Re: UHBD-grids Luis Rosales (Fri Apr 15 2005 - 17:40:27 CDT)
Adding color scale bar on the screen Jay Lee (Thu Apr 14 2005 - 18:50:22 CDT)
- Re: Adding color scale bar on the screen John Stone (Thu Apr 14 2005 - 20:36:53 CDT)
MSMS on linux and Draw Multiple Frames in VMD 1.8.3 Dr. Daniel James White PhD (Thu Apr 14 2005 - 09:17:40 CDT)
- Re: MSMS on linux and Draw Multiple Frames in VMD 1.8.3 John Stone (Thu Apr 14 2005 - 10:27:58 CDT)
CA-CA distances in a trayectory Nuno R. L. Ferreira (Thu Apr 14 2005 - 03:29:03 CDT)
Customizing VMD Sessions Adrian Koh (Thu Apr 14 2005 - 02:49:19 CDT)
- Re: Customizing VMD Sessions Axel Kohlmeyer (Thu Apr 14 2005 - 05:39:38 CDT)
  - Re: Customizing VMD Sessions Adrian Koh (Thu Apr 14 2005 - 06:03:41 CDT)
    - Re: Customizing VMD Sessions Axel Kohlmeyer (Thu Apr 14 2005 - 08:45:00 CDT)
    - Re: Customizing VMD Sessions John Stone (Thu Apr 14 2005 - 09:46:01 CDT)
- Re: Customizing VMD Sessions Olaf Lenz (Thu Apr 14 2005 - 05:39:22 CDT)
CA-CA distances in a trayectory Michel Espinoza-Fonseca (Wed Apr 13 2005 - 18:31:10 CDT)
- Re: CA-CA distances in a trayectory Axel Kohlmeyer (Thu Apr 14 2005 - 09:07:57 CDT)
- Re: CA-CA distances in a trayectory Luis Gracia (Thu Apr 14 2005 - 12:18:00 CDT)
  - Re: CA-CA distances in a trayectory Luis Gracia (Thu Apr 14 2005 - 15:44:45 CDT)
RE: rmsd and angle between the two domains Luis Rosales (Tue Apr 12 2005 - 23:51:55 CDT)
dihedral & g(r) Kos (Tue Apr 12 2005 - 15:16:55 CDT)
- Re: dihedral & g(r) Mgr. Lubos Vrbka (Wed Apr 13 2005 - 00:52:34 CDT)
- Re: dihedral & g(r) John Stone (Wed Apr 13 2005 - 09:34:13 CDT)
rmsd and angle between the two domains venkataraman kabaleeswaran (Tue Apr 12 2005 - 12:31:42 CDT)
bonding across periodic boundary Glenn Johnson (Tue Apr 12 2005 - 12:14:53 CDT)
- Re: bonding across periodic boundary Jim Phillips (Tue Apr 12 2005 - 13:02:10 CDT)
mpg image speed Chaitanya Krishna A (Tue Apr 12 2005 - 09:06:44 CDT)
vmdcavemem.... Luis Rosales (Mon Apr 11 2005 - 21:19:03 CDT)
- Re: vmdcavemem.... John Stone (Tue Apr 12 2005 - 09:16:34 CDT)
RE: how to creat a file containing only one potassium ion Michel Espinoza-Fonseca (Mon Apr 11 2005 - 16:08:26 CDT)
how to creat a file containing only one potassium ion M SH (Mon Apr 11 2005 - 14:50:27 CDT)
hbond Anuradha Mittal (Mon Apr 11 2005 - 12:24:05 CDT)
RE: mpg image speed Chang, Christopher (Mon Apr 11 2005 - 11:20:24 CDT)
- Re: mpg image speed Charles Moad (Mon Apr 11 2005 - 14:23:08 CDT)
density Swarna Patra (Sun Apr 10 2005 - 20:25:43 CDT)
Converting graphics to a pdb's coord system Charles Moad (Sun Apr 10 2005 - 19:13:31 CDT)
- Converting graphics to a pdb's coord system Charles Moad (Tue Apr 12 2005 - 08:52:12 CDT)
- Re: Converting graphics to a pdb's coord system John Stone (Wed Apr 13 2005 - 17:29:33 CDT)
  - Re: Converting graphics to a pdb's coord system Charles Moad (Wed Apr 13 2005 - 18:40:54 CDT)
    - Re: Converting graphics to a pdb's coord system John Stone (Thu Apr 14 2005 - 16:23:19 CDT)
    - Re: Converting graphics to a pdb's coord system Charles Moad (Thu Apr 14 2005 - 20:08:24 CDT)
only vmd console matteo.pennestri_at_virgilio.it (Sun Apr 10 2005 - 08:43:26 CDT)
- Re: only vmd console Huaer XC (Sun Apr 10 2005 - 16:40:31 CDT)
  - Re: only vmd console John Stone (Mon Apr 11 2005 - 00:30:13 CDT)
- Re: only vmd console John Stone (Mon Apr 11 2005 - 00:29:17 CDT)
mpg image speed Chaitanya Krishna A (Sun Apr 10 2005 - 01:01:08 CDT)
- Re: mpg image speed Marc Q. Ma (Mon Apr 11 2005 - 08:41:56 CDT)
mpg image speed Chaitanya Krishna A (Sun Apr 10 2005 - 00:04:34 CDT)
Opening amber files in VMD Simon Whitehead (Fri Apr 08 2005 - 10:14:51 CDT)
- Re: Opening amber files in VMD John Stone (Fri Apr 08 2005 - 13:57:01 CDT)
RE: How to remove "Lable" Chang, Christopher (Thu Apr 07 2005 - 17:39:55 CDT)
makemovie errors (povray) -- VMD 1.8.3 on MacOS 10.3.8 Suckjoon JUN (Thu Apr 07 2005 - 15:00:51 CDT)
- Re: makemovie errors (povray) -- VMD 1.8.3 on MacOS 10.3.8 John Stone (Thu Apr 07 2005 - 15:31:50 CDT)
  - Re: makemovie errors (povray) -- VMD 1.8.3 on MacOS 10.3.8 Suckjoon JUN (Fri Apr 08 2005 - 04:17:52 CDT)
    - Re: makemovie errors (povray) -- VMD 1.8.3 on MacOS 10.3.8 John Stone (Fri Apr 08 2005 - 14:38:30 CDT)
How to remove "Lable" Huaer XC (Thu Apr 07 2005 - 14:46:38 CDT)
FYI: cause of a common Windows VMD install error message... John Stone (Thu Apr 07 2005 - 13:01:43 CDT)
mpg image speed Chaitanya Krishna A (Thu Apr 07 2005 - 04:08:54 CDT)
- Re: mpg image speed Mauricio Carrillo Tripp (Thu Apr 07 2005 - 08:39:14 CDT)
pairwise rmsds in rmsdtt cvs1.9 Luis Gracia (Wed Apr 06 2005 - 16:15:48 CDT)
capturing box dimensions from amber coordinate files jbaucom_at_unity.ncsu.edu (Wed Apr 06 2005 - 12:39:08 CDT)
- Re: capturing box dimensions from amber coordinate files John Stone (Wed Apr 06 2005 - 13:33:12 CDT)
Choice of a Linux machine for VMD and high-end computing Karsten Suhre (Wed Apr 06 2005 - 11:09:58 CDT)
- Re: Choice of a Linux machine for VMD and high-end computing John Stone (Wed Apr 06 2005 - 11:27:54 CDT)
- Re: Choice of a Linux machine for VMD and high-end computing Sabuj Pattanayek (Wed Apr 06 2005 - 15:39:19 CDT)
  - Re: Choice of a Linux machine for VMD and high-end computing John Stone (Wed Apr 06 2005 - 16:01:34 CDT)
    - Re: Choice of a Linux machine for VMD and high-end computing Karsten Suhre (Fri Apr 08 2005 - 07:34:04 CDT)
- Re: Choice of a Linux machine for VMD and high-end computing Benjamin Goldsteen (Wed Apr 06 2005 - 16:58:07 CDT)
solvate numbering problems Christina Payne (Wed Apr 06 2005 - 11:05:39 CDT)
- Re: solvate numbering problems John Stone (Wed Apr 06 2005 - 11:14:38 CDT)
Displaying simulations and rotations Palmer, Teresa (Wed Apr 06 2005 - 11:03:11 CDT)
- Re: Displaying simulations and rotations John Stone (Wed Apr 06 2005 - 11:23:09 CDT)
- Re: Displaying simulations and rotations Mauricio Carrillo Tripp (Wed Apr 06 2005 - 15:00:54 CDT)
Install VMD on Mandrake Linux huaer_at_myway.com (Wed Apr 06 2005 - 10:37:34 CDT)
- Re: Install VMD on Mandrake Linux John Stone (Wed Apr 06 2005 - 10:59:38 CDT)
  - Re: Install VMD on Mandrake Linux huaer_at_myway.com (Wed Apr 06 2005 - 11:06:26 CDT)
add water on the top of protein border Xiaoqing Wang (Wed Apr 06 2005 - 09:20:24 CDT)
(no subject) ËïÍ¢ (Wed Apr 06 2005 - 08:58:13 CDT)
- Re: John Stone (Wed Apr 06 2005 - 15:05:52 CDT)
  - Re: Jim Phillips (Thu Apr 07 2005 - 11:10:45 CDT)
rmsd Anuradha Mittal (Tue Apr 05 2005 - 11:24:28 CDT)
- Re: rmsd John Stone (Tue Apr 05 2005 - 17:17:10 CDT)
- Re: rmsd Luis Gracia (Wed Apr 06 2005 - 16:02:58 CDT)
VMD and Cyclotides... Luis Rosales (Mon Apr 04 2005 - 20:05:33 CDT)
- Re: VMD and Cyclotides... Luis Gracia (Mon Apr 04 2005 - 22:08:24 CDT)
  - RE: VMD and Cyclotides... Luis Rosales (Tue Apr 05 2005 - 02:47:11 CDT)
    - Re: VMD and Cyclotides... Luis Gracia (Tue Apr 05 2005 - 12:56:59 CDT)
    - RE: VMD and Cyclotides... Luis Rosales (Tue Apr 05 2005 - 17:01:21 CDT)
- Re: VMD and Cyclotides... Andrew Dalke (Tue Apr 05 2005 - 02:59:29 CDT)
  - Re: VMD and Cyclotides... John Stone (Tue Apr 05 2005 - 12:54:48 CDT)
dynamic coloring Leonor Cruzeiro (Mon Apr 04 2005 - 11:22:02 CDT)
- Re: dynamic coloring John Stone (Wed Apr 06 2005 - 13:49:01 CDT)
GLSL or Clip plane Jerry Ebalunode (Sat Apr 02 2005 - 17:44:02 CST)
- Re: GLSL or Clip plane John Stone (Mon Apr 04 2005 - 10:23:44 CDT)
Re: vmd movie maker Axel Kohlmeyer (Sun Apr 03 2005 - 03:11:22 CDT)
- Re: vmd movie maker huaer_at_myway.com (Wed Apr 06 2005 - 00:27:28 CDT)
vmd movie maker huaer_at_myway.com (Sat Apr 02 2005 - 17:35:30 CST)
- Re: vmd movie maker John Stone (Tue Apr 05 2005 - 18:37:47 CDT)
VMD causing xorg crash Jernej Zidar (Fri Apr 01 2005 - 16:04:12 CST)
- Re: VMD causing xorg crash John Stone (Fri Apr 01 2005 - 16:23:11 CST)
Re: [PyMOL] NVidia [7174] Drivers & Nuccyl Sabuj Pattanayek (Fri Apr 01 2005 - 14:24:34 CST)
ATI radeon x300 jerry xu (Fri Apr 01 2005 - 12:42:59 CST)
- Re: ATI radeon x300 John Stone (Fri Apr 01 2005 - 14:06:16 CST)
superimpose RNA backbones gtg991m_at_mail.gatech.edu (Fri Apr 01 2005 - 11:17:21 CST)
- Re: superimpose RNA backbones Luis Gracia (Fri Apr 01 2005 - 14:11:32 CST)
- Re: superimpose RNA backbones John Stone (Tue Apr 05 2005 - 19:00:45 CDT)
Errors compiling VMD on 1.8.3 on Solaris x86 Koo Kee Kiat (Fri Apr 01 2005 - 00:17:45 CST)
- Re: Errors compiling VMD on 1.8.3 on Solaris x86 John Stone (Fri Apr 01 2005 - 18:10:36 CST)
  - Re: Errors compiling VMD on 1.8.3 on Solaris x86 John Stone (Fri Apr 01 2005 - 18:20:20 CST)
about adding ions to an ion channel pore Xiaoqing Wang (Thu Mar 31 2005 - 20:59:36 CST)
- Re: about adding ions to an ion channel pore Axel Kohlmeyer (Fri Apr 01 2005 - 01:46:50 CST)
fglrx driver workaround? Alec Robertson (Thu Mar 31 2005 - 09:53:21 CST)
- Re: fglrx driver workaround? John Stone (Thu Mar 31 2005 - 10:12:55 CST)
  - Re: fglrx driver workaround? Alec Robertson (Thu Mar 31 2005 - 10:18:45 CST)
- Re: fglrx driver workaround? Gyimesi Gergely (Sun May 15 2005 - 10:16:08 CDT)
  - Re: Re: fglrx driver workaround? John Stone (Mon May 16 2005 - 19:51:04 CDT)
conformational alignment Wen Li (Wed Mar 30 2005 - 15:21:26 CST)
- Re: conformational alignment John Stone (Wed Mar 30 2005 - 15:30:26 CST)
  - Re: conformational alignment Wen Li (Thu Mar 31 2005 - 10:24:18 CST)
- Re: namd-l: conformational alignment Giovanni Bellesia (Wed Mar 30 2005 - 16:40:36 CST)
Maximum numbers of atoms Nicolas CHARVIN (Wed Mar 30 2005 - 01:54:37 CST)
- Re: Maximum numbers of atoms Axel Kohlmeyer (Wed Mar 30 2005 - 05:06:49 CST)
  - Re: Maximum numbers of atoms John Stone (Wed Mar 30 2005 - 16:08:25 CST)
  - Re: Maximum numbers of atoms Nicolas CHARVIN (Mon Apr 04 2005 - 05:31:31 CDT)
- Re: Maximum numbers of atoms John Stone (Wed Mar 30 2005 - 10:03:16 CST)
NOC (current version 1.5.2.10) a new, free program for protein structure model-building, visualization, validation and analysis Chenmengen (Tue Mar 29 2005 - 19:07:52 CST)
displaying double, triple bonds Stern, Julie (Tue Mar 29 2005 - 14:56:57 CST)
- Re: displaying double, triple bonds Andrew Dalke (Tue Mar 29 2005 - 17:05:33 CST)
- Re: displaying double, triple bonds John Stone (Thu Aug 11 2005 - 15:41:31 CDT)
Knowing the euler angles from a particular orientation Nitin Bhardwaj (Tue Mar 29 2005 - 13:18:20 CST)
vmd 1.8.3 mac OS-X dlpoly history file nicholas blake (Tue Mar 29 2005 - 12:49:17 CST)
- Re: vmd 1.8.3 mac OS-X dlpoly history file John Stone (Tue Mar 29 2005 - 12:55:06 CST)
Python, numpy, and so on .... Nuno R. L. Ferreira (Tue Mar 29 2005 - 05:42:23 CST)
- Re: Python, numpy, and so on .... John Stone (Tue Mar 29 2005 - 13:54:50 CST)
Problem with the Graphics Command Nitin Bhardwaj (Mon Mar 28 2005 - 18:56:16 CST)
- RE: Problem with the Graphics Command Luis Rosales (Mon Mar 28 2005 - 21:23:07 CST)
Knowing the euler angles from a particular orientation. Nitin Bhardwaj (Mon Mar 28 2005 - 18:41:25 CST)
snapshots to pdb Michel Espinoza-Fonseca (Mon Mar 28 2005 - 14:12:21 CST)
- Re: snapshots to pdb John Stone (Thu Mar 31 2005 - 13:02:42 CST)
Molecular Display component Alexandre Suman de Araujo (Mon Mar 28 2005 - 10:56:17 CST)
vmd and k3b Paul D. Jones (Mon Mar 28 2005 - 11:11:34 CST)
- Re: vmd and k3b John Stone (Mon Mar 28 2005 - 11:50:07 CST)
winvmd error Paul Schlesinger (Mon Mar 21 2005 - 12:09:17 CST)
- Re: winvmd error John Stone (Mon Mar 28 2005 - 10:24:50 CST)
Biomolecular Simulations Meeting Bordeaux, 2&3 Sept. 2005 Biomolecular Simulations Congress 2005 (Tue Mar 22 2005 - 08:19:24 CST)
resid le 250 Haibo Yu (Wed Mar 23 2005 - 16:22:15 CST)
- Re: resid le 250 John Stone (Mon Mar 28 2005 - 13:08:57 CST)
vmd and Re: [PyMOL] pymol crashes with new [7167] nvidia driver Sabuj Pattanayek (Sat Mar 26 2005 - 16:42:42 CST)
- Re: vmd and Re: [PyMOL] pymol crashes with new [7167] nvidia driver Sabuj Pattanayek (Sat Mar 26 2005 - 16:45:31 CST)
- Re: vmd and Re: [PyMOL] pymol crashes with new [7167] nvidia driver John Stone (Mon Mar 28 2005 - 09:10:09 CST)
  - Re: vmd and Re: [PyMOL] pymol crashes with new [7167] nvidia driver Sabuj Pattanayek (Tue Mar 29 2005 - 11:11:54 CST)
TCL atomselect bug Josh Ward (Thu Mar 24 2005 - 15:49:44 CST)
- Re: TCL atomselect bug John Stone (Mon Mar 28 2005 - 11:58:17 CST)
# of waters limit dimka (Tue Mar 22 2005 - 15:19:51 CST)
- Re: # of waters limit Justin Gullingsrud (Tue Mar 22 2005 - 18:09:26 CST)
GRD file format Keith Refson (Tue Mar 22 2005 - 09:57:02 CST)
- Re: GRD file format Axel Kohlmeyer (Tue Mar 22 2005 - 13:15:35 CST)
- Re: GRD file format Justin Gullingsrud (Tue Mar 22 2005 - 11:44:16 CST)
  - Re: GRD file format Keith Refson (Tue Mar 22 2005 - 12:30:46 CST)
    - Re: GRD file format Axel Kohlmeyer (Wed Mar 23 2005 - 01:33:31 CST)
    - Re: GRD file format Justin Gullingsrud (Tue Mar 22 2005 - 13:24:26 CST)
New Sharp 3D Notebook Available with Linux Eugen Leitl (Tue Mar 22 2005 - 05:35:19 CST)
vmd installation in rehdat7.3 Priti Hansia (Mon Mar 21 2005 - 22:40:59 CST)
- Re: vmd installation in rehdat7.3 Axel Kohlmeyer (Tue Mar 22 2005 - 02:01:52 CST)
Re: VMD does not start on Mac OS 10.3.8 (problem was solved) Tomo Hayashi (Sat Mar 19 2005 - 20:38:24 CST)
Out of town until 3/28/2005... John Stone (Fri Mar 18 2005 - 10:54:25 CST)
Can vmd select residues in radius of 3.5 to a specific residue? scopio (Fri Mar 18 2005 - 05:52:43 CST)
- Re: Can vmd select residues in radius of 3.5 to a specific residue? J. Rui Rodrigues (Fri Mar 18 2005 - 06:21:08 CST)
- Re: Can vmd select residues in radius of 3.5 to a specific residue? Marc Q. Ma (Fri Mar 18 2005 - 07:59:59 CST)
- Re: Can vmd select residues in radius of 3.5 to a specific residue? John Stone (Fri Mar 18 2005 - 08:16:15 CST)
May I use my own radii? Chunhu Tan (Thu Mar 17 2005 - 16:17:49 CST)
- Re: May I use my own radii? Dallas Warren (Thu Mar 17 2005 - 19:00:58 CST)
- Re: May I use my own radii? John Stone (Thu Mar 17 2005 - 21:37:13 CST)
install 1.8.3 on RHEL4 HuiZhe Li (Thu Mar 17 2005 - 13:23:15 CST)
- Re: install 1.8.3 on RHEL4 John Stone (Thu Mar 17 2005 - 14:05:45 CST)
  - Re: install 1.8.3 on RHEL4 HuiZhe Li (Fri Mar 18 2005 - 02:51:05 CST)
  - Re: install 1.8.3 on RHEL4 HuiZhe Li (Fri Mar 18 2005 - 03:00:00 CST)
- Re: install 1.8.3 on RHEL4 Dallas Warren (Thu Mar 17 2005 - 16:16:25 CST)
Mac OS X problems with 1.8.3 nicholas blake (Wed Mar 16 2005 - 17:25:10 CST)
- Re: Mac OS X problems with 1.8.3 John Stone (Thu Mar 17 2005 - 09:55:26 CST)
  - Re: Mac OS X problems with 1.8.3 nicholas blake (Thu Mar 17 2005 - 13:27:03 CST)
Bio-Image summer school in Paris this year Marc Baaden (Wed Mar 16 2005 - 05:45:47 CST)
IMD, basic questions... Luis Rosales (Tue Mar 15 2005 - 19:01:29 CST)
set a different beta field for each frame of trajectory Vlad Cojocaru (Tue Mar 15 2005 - 08:02:02 CST)
- Re: set a different beta field for each frame of trajectory John Stone (Tue Mar 15 2005 - 10:03:49 CST)
VMD does not start on Mac OS 10.3.8 Tomo Hayashi (Tue Mar 15 2005 - 03:42:51 CST)
- Re: VMD does not start on Mac OS 10.3.8 John Stone (Fri Mar 18 2005 - 13:48:18 CST)
- Re: VMD does not start on Mac OS 10.3.8 Charles McCallum (Fri Mar 18 2005 - 17:07:22 CST)
  - Re: VMD does not start on Mac OS 10.3.8 Tomo Hayashi (Fri Mar 18 2005 - 23:41:48 CST)
LAMMPS Vizualization Frederick R. Phelan Jr. (Mon Mar 14 2005 - 10:21:52 CST)
- Re: LAMMPS Vizualization John Stone (Mon Mar 14 2005 - 13:33:36 CST)
  - Re: LAMMPS Vizualization John Stone (Mon Mar 14 2005 - 15:14:04 CST)
    - Re: LAMMPS Vizualization Frederick R. Phelan Jr. (Mon Mar 14 2005 - 17:26:48 CST)
Python, Numeric, and Mac OS X problem Eric Brown (Mon Mar 14 2005 - 06:14:29 CST)
- Re: Python, Numeric, and Mac OS X problem Florian Haberl (Mon Mar 14 2005 - 06:47:10 CST)
  - Re: Python, Numeric, and Mac OS X problem John Stone (Fri Mar 18 2005 - 12:05:51 CST)
- Re: Python, Numeric, and Mac OS X problem Jacinto S. (Fri Aug 26 2005 - 13:32:50 CDT)
Python, Numeric, and Mac OS X problem Eric Brown (Mon Mar 14 2005 - 05:18:08 CST)
Building plugins with Borland Bcc32 Nicolas CHARVIN (Mon Mar 14 2005 - 04:41:04 CST)
- Re: Building plugins with Borland Bcc32 John Stone (Mon Mar 14 2005 - 09:47:35 CST)
  - Re: Building plugins with Borland Bcc32 Nicolas CHARVIN (Tue Mar 15 2005 - 11:30:14 CST)
Re: psfgen failure Leyla Celik (Mon Mar 14 2005 - 04:13:13 CST)
psfgen failure Leyla Celik (Mon Mar 14 2005 - 02:17:17 CST)
viewing .brix maps Assa Sittner (Sun Mar 13 2005 - 04:58:03 CST)
- Re: viewing .brix maps John Stone (Mon Mar 14 2005 - 13:08:22 CST)
limit on segment atom number in solvate and autoionize Philip Blood (Fri Mar 11 2005 - 11:52:41 CST)
- RE: limit on segment atom number in solvate and autoionize Philip Blood (Fri Mar 11 2005 - 13:18:22 CST)
  - Re: limit on segment atom number in solvate and autoionize John Stone (Fri Mar 11 2005 - 13:38:23 CST)
    - RE: limit on segment atom number in solvate and autoionize Philip Blood (Fri Mar 11 2005 - 13:44:45 CST)
    - Re: limit on segment atom number in solvate and autoionize John Stone (Fri Mar 11 2005 - 15:13:12 CST)
drawing the edges of a non-rectangular box Andre Farias de Moura (Fri Mar 11 2005 - 06:17:46 CST)
- Re: drawing the edges of a non-rectangular box Eduard Schreiner (Fri Mar 11 2005 - 13:02:50 CST)
keeping original coordinates in trajectory David A. Horita (Wed Mar 09 2005 - 14:27:28 CST)
- Re: keeping original coordinates in trajectory John Stone (Thu Mar 10 2005 - 10:56:41 CST)
Intersurf plugin Nuno R. L. Ferreira (Wed Mar 09 2005 - 13:07:01 CST)
init.tcl startup problem with vmd 1.8.3 (but 1.8.2 works) Sabuj Pattanayek (Wed Mar 09 2005 - 12:41:13 CST)
- Re: init.tcl startup problem with vmd 1.8.3 (but 1.8.2 works) John Stone (Wed Mar 09 2005 - 12:45:19 CST)
  - Re: init.tcl startup problem with vmd 1.8.3 (but 1.8.2 works) Sabuj Pattanayek (Wed Mar 09 2005 - 12:53:36 CST)
problem with DPPC topology Alexis Salas (Tue Mar 08 2005 - 14:29:43 CST)
"Hands-On" Workshop on Computational Biophysics David Brandon (Tue Mar 08 2005 - 11:54:35 CST)
Joystick on Linux Jyh-Shyong Ho (Mon Mar 07 2005 - 23:26:25 CST)
RE: Display only side chains Chang, Christopher (Mon Mar 07 2005 - 17:40:24 CST)
Re: Display only side chains Peter Holm (Mon Mar 07 2005 - 16:21:02 CST)
- Re: Display only side chains Peter Holm (Mon Mar 07 2005 - 17:04:25 CST)
Display only side chains Peter Holm (Mon Mar 07 2005 - 15:42:40 CST)
- Re: Display only side chains Luis Rosales (Mon Mar 07 2005 - 17:36:29 CST)
  - Re: Display only side chains John Stone (Mon Mar 07 2005 - 16:46:47 CST)
    - Re: Display only side chains Justin Gullingsrud (Tue Mar 08 2005 - 10:33:32 CST)
- Re: Display only side chains Jérôme Hénin (Mon Mar 07 2005 - 18:59:42 CST)
Intersurf plugin Nuno R. L. Ferreira (Sat Mar 05 2005 - 07:27:53 CST)
- Re: Intersurf plugin John Stone (Sun Mar 06 2005 - 21:35:26 CST)
  - Re: Intersurf plugin Nuno R. L. Ferreira (Mon Mar 07 2005 - 07:40:35 CST)
  - Re: Intersurf plugin Nuno R. L. Ferreira (Wed Mar 09 2005 - 09:32:51 CST)
coloring way in a volume slice YAMAZAKI Takeshi (Fri Mar 04 2005 - 18:26:33 CST)
- Re: coloring way in a volume slice John Stone (Sun Mar 06 2005 - 21:36:34 CST)
  - Re: coloring way in a volume slice John Stone (Fri Mar 11 2005 - 17:17:37 CST)
Problem starting VMD with Fedora Core3 olivier Walker (Fri Mar 04 2005 - 09:10:15 CST)
- Re: Problem starting VMD with Fedora Core3 John Stone (Fri Mar 04 2005 - 09:30:05 CST)
ResType Color Seiichiro Tanizaki (Thu Mar 03 2005 - 14:49:39 CST)
RUNNING VMD Claire Zerafa (Thu Mar 03 2005 - 12:42:35 CST)
- Re: RUNNING VMD John Stone (Thu Mar 03 2005 - 13:53:11 CST)
AutoIMD on VMD 1.8.3 Luis Rosales (Wed Mar 02 2005 - 20:24:46 CST)
- Re: AutoIMD on VMD 1.8.3 John Stone (Thu Mar 03 2005 - 10:42:24 CST)
hbonds time series syma khalid (Thu Mar 03 2005 - 09:33:34 CST)
- Re: hbonds time series John Stone (Thu Mar 03 2005 - 14:28:24 CST)
[bigdcd.tcl] How to stream output to file Sascha Tayefeh (Thu Mar 03 2005 - 04:20:38 CST)
- Re: [bigdcd.tcl] How to stream output to file Justin Gullingsrud (Thu Mar 03 2005 - 10:33:45 CST)
VMD 1.8.2 and 1.8.3 fail on MacOS X after upgrade to 10.3.8 Michael Feig (Wed Mar 02 2005 - 09:12:52 CST)
- Re: VMD 1.8.2 and 1.8.3 fail on MacOS X after upgrade to 10.3.8 Robert Brunner (Wed Mar 02 2005 - 10:36:54 CST)
- Re: VMD 1.8.2 and 1.8.3 fail on MacOS X after upgrade to 10.3.8 Alexander Peyser (Wed Mar 02 2005 - 12:45:30 CST)
error message from IED Vlad Cojocaru (Wed Mar 02 2005 - 08:55:06 CST)
- Re: error message from IED John Stone (Wed Mar 02 2005 - 10:02:54 CST)
problem with IED on VMD 1.8.3 Vlad Cojocaru (Wed Mar 02 2005 - 08:51:59 CST)
Problem using ied.py Stef (Tue Mar 01 2005 - 08:54:24 CST)
- Re: Problem using ied.py John Stone (Thu Mar 03 2005 - 15:22:48 CST)
  - Re: Problem using ied.py Jim Nettles (Thu Mar 03 2005 - 16:45:44 CST)
- Re: Problem using ied.py John Stone (Fri Mar 18 2005 - 12:16:30 CST)
Is it possible to select a sub-trajectory specificities. Stef (Tue Mar 01 2005 - 08:58:50 CST)
- Re: Is it possible to select a sub-trajectory specificities. Eduard Schreiner (Wed Mar 02 2005 - 05:18:30 CST)
  - Re: Is it possible to select a sub-trajectory specificities. Stef (Thu Mar 03 2005 - 04:37:05 CST)
Volumeslice doesn't work in 1.8.3 Paul Tangney (Mon Feb 28 2005 - 13:55:17 CST)
- Re: Volumeslice doesn't work in 1.8.3 John Stone (Mon Feb 28 2005 - 14:08:52 CST)
  - Re: Volumeslice doesn't work in 1.8.3 John Stone (Mon Feb 28 2005 - 15:35:00 CST)
surface residues of protein Mgr. Lubos Vrbka (Mon Feb 28 2005 - 07:42:52 CST)
- Re: surface residues of protein John Stone (Mon Feb 28 2005 - 10:17:54 CST)
Apple hardware configuration fabrizio cleri (Fri Feb 25 2005 - 05:29:24 CST)
- Re: Apple hardware configuration fabrizio cleri (Sat Feb 26 2005 - 02:32:42 CST)
  - Re: Apple hardware configuration John Stone (Mon Feb 28 2005 - 10:48:25 CST)
- Re: Apple hardware configuration John Stone (Thu Mar 03 2005 - 15:46:17 CST)
Other glasses with CE emitters? cmorton_at_medstv.unimelb.edu.au (Thu Feb 24 2005 - 17:20:58 CST)
printing real 3D model using z-printer Hui-Hsu Tsai (Thu Feb 24 2005 - 14:38:04 CST)
- Re: printing real 3D model using z-printer John Stone (Thu Feb 24 2005 - 16:28:37 CST)
Is it possible to write CHARMM crd file from VMD? Leyla Celik (Thu Feb 24 2005 - 13:31:03 CST)
- Re: Is it possible to write CHARMM crd file from VMD? John Stone (Thu Feb 24 2005 - 17:42:46 CST)
  - Re: Is it possible to write CHARMM crd file from VMD? Leyla Celik (Tue Mar 01 2005 - 04:35:27 CST)
    - Re: Is it possible to write CHARMM crd file from VMD? John Stone (Thu Mar 03 2005 - 15:27:01 CST)
(no subject) matteo.pennestri_at_virgilio.it (Thu Feb 24 2005 - 09:11:19 CST)
- Re: your mail John Stone (Thu Feb 24 2005 - 10:03:15 CST)
RNA polymerase docking on DNA Lady L. Gutierrez (Wed Feb 23 2005 - 18:54:11 CST)
- Re: RNA polymerase docking on DNA Jérôme Hénin (Thu Feb 24 2005 - 02:04:50 CST)
- Re: RNA polymerase docking on DNA Luis Rosales (Wed Feb 23 2005 - 22:55:20 CST)
potential surface matteo.pennestri_at_virgilio.it (Wed Feb 23 2005 - 16:35:00 CST)
- Re: potential surface John Stone (Wed Feb 23 2005 - 16:46:15 CST)
question of PBC Margaret Shun Cheung (Wed Feb 23 2005 - 09:42:45 CST)
- Re: question of PBC Marc Q. Ma (Wed Feb 23 2005 - 11:45:36 CST)
(no subject) matteo.pennestri_at_virgilio.it (Wed Feb 23 2005 - 04:44:47 CST)
- Re: your mail John Stone (Wed Feb 23 2005 - 10:56:05 CST)
User colors and povray apeyser_at_newssun.med.miami.edu (Tue Feb 22 2005 - 13:34:47 CST)
- Re: User colors and povray John Stone (Wed Feb 23 2005 - 15:15:17 CST)
  - Re: User colors and povray apeyser_at_newssun.med.miami.edu (Wed Feb 23 2005 - 15:45:26 CST)
    - Re: User colors and povray John Stone (Wed Feb 23 2005 - 15:54:48 CST)
  - Re: User colors and povray Alexander Peyser (Wed Feb 23 2005 - 16:01:19 CST)
LAMMPS reader Kooser, Ara S (Tue Feb 22 2005 - 10:58:25 CST)
- Re: LAMMPS reader John Stone (Wed Feb 23 2005 - 15:38:34 CST)
Volumeslice in arbitrary plane Jérôme Hénin (Tue Feb 22 2005 - 10:13:28 CST)
- Re: Volumeslice in arbitrary plane John Stone (Wed Feb 23 2005 - 11:07:42 CST)
VMD, NAMD and Interactive Essential Dynamics (IED) Philip Fowler (Tue Feb 22 2005 - 10:06:55 CST)
- Re: VMD, NAMD and Interactive Essential Dynamics (IED) Justin Gullingsrud (Tue Feb 22 2005 - 13:22:26 CST)
  - Re: VMD, NAMD and Interactive Essential Dynamics (IED) Axel Kohlmeyer (Wed Feb 23 2005 - 14:29:22 CST)
    - Re: VMD, NAMD and Interactive Essential Dynamics (IED) Glenn Johnson (Mon Mar 21 2005 - 10:39:00 CST)
    - Re: VMD, NAMD and Interactive Essential Dynamics (IED) Axel Kohlmeyer (Mon Mar 21 2005 - 12:22:52 CST)
  - Re: VMD, NAMD and Interactive Essential Dynamics (IED) Glenn Johnson (Mon Mar 21 2005 - 12:08:26 CST)
- VMD and Interactive Essential Dynamics (IED) Shatadal Ghosh (Tue Mar 22 2005 - 00:22:05 CST)
  - Re: VMD and Interactive Essential Dynamics (IED) Justin Gullingsrud (Tue Mar 22 2005 - 11:40:52 CST)
displaying many frames with periodic images Philip Blood (Mon Feb 21 2005 - 10:49:51 CST)
- Re: displaying many frames with periodic images John Stone (Mon Feb 21 2005 - 11:30:01 CST)
VMD object exported to Pymol Peter Holm (Mon Feb 21 2005 - 07:47:52 CST)
- Re: VMD object exported to Pymol John Stone (Mon Feb 21 2005 - 11:58:32 CST)
  - Re: VMD object exported to Pymol John Stone (Wed Feb 23 2005 - 13:44:32 CST)
  - Re: VMD object exported to Pymol John Stone (Wed Feb 23 2005 - 16:19:17 CST)
RE: Tracking system configuration Luis Rosales (Fri Feb 18 2005 - 20:21:43 CST)
vmd 1.8.3 on my mac fabri (Sat Feb 19 2005 - 03:21:14 CST)
- Re: vmd 1.8.3 on my mac Ebrahim Mayat (Sun Feb 20 2005 - 08:42:49 CST)
- Re: vmd 1.8.3 on my mac John Stone (Sun Feb 20 2005 - 22:37:43 CST)
RE: vmdmovie plugin Chang, Christopher (Fri Feb 18 2005 - 15:21:59 CST)
(no subject) James Stevens (Fri Feb 18 2005 - 14:24:19 CST)
- Re: John Stone (Mon Feb 21 2005 - 12:05:33 CST)
vmdmovie plugin Marc Q. Ma (Fri Feb 18 2005 - 10:31:09 CST)
- Re: vmdmovie plugin John Stone (Fri Feb 18 2005 - 10:41:06 CST)
Call to Stride program failed Jérôme Hénin (Fri Feb 18 2005 - 09:42:27 CST)
- Re: Call to Stride program failed John Stone (Fri Feb 18 2005 - 09:49:33 CST)
  - Re: Call to Stride program failed Jérôme Hénin (Fri Feb 18 2005 - 10:05:37 CST)
    - Re: Call to Stride program failed John Stone (Fri Feb 18 2005 - 10:35:00 CST)
mmtools Swarna Patra (Thu Feb 17 2005 - 23:32:55 CST)
(no subject) Francis Reyes (Thu Feb 17 2005 - 16:33:15 CST)
- Re: John Stone (Thu Feb 17 2005 - 16:42:44 CST)
  - Re: John Stone (Mon Feb 28 2005 - 10:13:25 CST)
Keyboard mapping incorrect for OS X Francis Reyes (Thu Feb 17 2005 - 13:50:00 CST)
- Re: Keyboard mapping incorrect for OS X John Stone (Thu Feb 17 2005 - 14:42:32 CST)
  - Re: Keyboard mapping incorrect for OS X Dan Wright (Thu Feb 17 2005 - 21:48:21 CST)
smoothed trajectory Nicolas Sapay (Thu Feb 17 2005 - 10:06:41 CST)
- Re: smoothed trajectory Jan Saam (Thu Feb 17 2005 - 11:52:30 CST)
  - Re: smoothed trajectory Nicolas Sapay (Fri Feb 18 2005 - 02:45:07 CST)
- Re: smoothed trajectory Jérôme Hénin (Thu Feb 17 2005 - 13:59:19 CST)
Re: APBS error Vlad Cojocaru (Thu Feb 17 2005 - 08:24:07 CST)
Can't compile VMD 1.8.3: Tachyon 0.97 needed Sangwoo Shim (Thu Feb 17 2005 - 01:54:04 CST)
- Re: Can't compile VMD 1.8.3: Tachyon 0.97 needed John Stone (Thu Feb 17 2005 - 09:48:00 CST)
  - Re: Can't compile VMD 1.8.3: Tachyon 0.97 needed Sangwoo Shim (Fri Mar 18 2005 - 03:49:33 CST)
    - Re: Can't compile VMD 1.8.3: Tachyon 0.97 needed John Stone (Fri Mar 18 2005 - 09:42:22 CST)
determining vdw, elec, and others Brian Kidd (Wed Feb 16 2005 - 23:09:12 CST)
- Re: determining vdw, elec, and others Axel Kohlmeyer (Thu Feb 17 2005 - 03:43:21 CST)
- Re: determining vdw, elec, and others Jan Saam (Thu Feb 17 2005 - 16:00:00 CST)
APBS error Armen Nalian (Wed Feb 16 2005 - 18:58:54 CST)
Tachyon does not render surfaces colored by EP Vlad Cojocaru (Wed Feb 16 2005 - 04:19:59 CST)
- Re: Tachyon does not render surfaces colored by EP John Stone (Wed Feb 16 2005 - 09:38:47 CST)
- Re: Tachyon does not render surfaces colored by EP Jérôme Hénin (Wed Feb 16 2005 - 09:53:02 CST)
  - Re: Tachyon does not render surfaces colored by EP John Stone (Wed Feb 16 2005 - 10:03:35 CST)
Defining Bonds in .xyz file format Adrian Koh (Wed Feb 16 2005 - 02:29:09 CST)
- Re: Defining Bonds in .xyz file format Axel Kohlmeyer (Wed Feb 16 2005 - 06:09:46 CST)
Announce: VMD 1.8.3 released!! John Stone (Wed Feb 16 2005 - 00:09:04 CST)
Unprotonating GLU, ASP Gaurav Sharma (Tue Feb 15 2005 - 10:42:06 CST)
- Re: Unprotonating GLU, ASP Luis Rosales (Tue Feb 15 2005 - 18:16:00 CST)
  - Re: Unprotonating GLU, ASP Gaurav Sharma (Tue Feb 15 2005 - 17:13:16 CST)
    - Re: Unprotonating GLU, ASP Luis Rosales (Tue Feb 15 2005 - 20:29:32 CST)
How to image molecules back into a PBC box? Xiongce Zhao (Tue Feb 15 2005 - 09:09:33 CST)
- Re: How to image molecules back into a PBC box? Olaf Lenz (Wed Feb 16 2005 - 03:08:15 CST)
- Re: How to image molecules back into a PBC box? Axel Kohlmeyer (Wed Feb 16 2005 - 06:02:17 CST)
Tracking system configuration??? Luis Rosales (Mon Feb 14 2005 - 21:36:03 CST)
- Re: Tracking system configuration??? John Stone (Thu Feb 17 2005 - 16:13:26 CST)
PBC atom selection and contacts Mgr. Lubos Vrbka (Mon Feb 14 2005 - 10:29:45 CST)
- Re: PBC atom selection and contacts John Stone (Mon Feb 14 2005 - 11:29:42 CST)
  - Re: PBC atom selection and contacts Mgr. Lubos Vrbka (Wed Feb 16 2005 - 09:32:53 CST)
    - Re: PBC atom selection and contacts John Stone (Thu Feb 17 2005 - 14:29:25 CST)
slowing the movie animation Sunita Patel (Sun Feb 13 2005 - 09:52:50 CST)
- Re: slowing the movie animation Axel Kohlmeyer (Mon Feb 14 2005 - 03:45:59 CST)
  - Re: slowing the movie animation Luis Rosales (Mon Feb 14 2005 - 23:08:44 CST)
protein peptide alignment. matteo.pennestri_at_virgilio.it (Sat Feb 12 2005 - 12:30:51 CST)
- Re: protein peptide alignment. Peter Freddolino (Sat Feb 12 2005 - 13:23:01 CST)
- Re: protein peptide alignment. Luis Gracia (Tue Feb 22 2005 - 00:20:10 CST)
RE: window size Chang, Christopher (Thu Feb 10 2005 - 17:07:31 CST)
Stereo 3D by the Numbers Warren DeLano (Thu Feb 10 2005 - 16:50:44 CST)
- Re: Stereo 3D by the Numbers John Stone (Thu Feb 17 2005 - 16:47:20 CST)
Align protein with different number of aminoacid matteo.pennestri_at_virgilio.it (Thu Feb 10 2005 - 16:42:50 CST)
- Re: Align protein with different number of aminoacid Eduard Schreiner (Fri Feb 11 2005 - 04:42:24 CST)
- Re: Align protein with different number of aminoacid Luis Gracia (Thu Feb 10 2005 - 22:35:16 CST)
window size Guanglei Cui (Thu Feb 10 2005 - 15:10:21 CST)
- Re: window size John Stone (Thu Feb 10 2005 - 15:23:39 CST)
PBC atom selection and contacts Lubos Vrbka (Thu Feb 10 2005 - 03:13:44 CST)
Micelles... Luis Rosales (Wed Feb 09 2005 - 23:06:16 CST)
Distance calculation in TkConsole Leyla Celik (Thu Feb 10 2005 - 04:33:43 CST)
- Re: Distance calculation in TkConsole Axel Kohlmeyer (Thu Feb 10 2005 - 07:44:33 CST)
- Re: Distance calculation in TkConsole Giovanni Bellesia (Thu Feb 10 2005 - 08:00:15 CST)
problem vivek sharma (Wed Feb 09 2005 - 06:57:43 CST)
- Re: problem John Stone (Wed Feb 09 2005 - 10:05:25 CST)
atom fitting in non-PDB order James Melville (Mon Feb 07 2005 - 21:27:47 CST)
Surface accesible area w/v1.8.3beta Edward Patrick Obrien (Mon Feb 07 2005 - 11:26:16 CST)
- Re: Surface accesible area w/v1.8.3beta John Stone (Mon Feb 07 2005 - 11:39:06 CST)
  - Re: Surface accesible area w/v1.8.3beta John Stone (Mon Feb 07 2005 - 11:53:12 CST)
SMD Ekta Khurana (Mon Feb 07 2005 - 10:28:24 CST)
- Re: SMD John Stone (Mon Feb 07 2005 - 10:33:32 CST)
- Re: SMD Marc Q. Ma (Mon Feb 07 2005 - 12:24:04 CST)
- Re: SMD Giovanni Bellesia (Mon Feb 07 2005 - 13:19:24 CST)
  - Re: SMD Ekta Khurana (Mon Feb 07 2005 - 13:57:23 CST)
volume shading in 1.8.3b1 ? Oliver Beckstein (Mon Feb 07 2005 - 10:03:34 CST)
- Re: volume shading in 1.8.3b1 ? John Stone (Mon Feb 07 2005 - 10:07:46 CST)
  - Re: volume shading in 1.8.3b1 ? Oliver Beckstein (Mon Feb 07 2005 - 10:58:50 CST)
    - Re: volume shading in 1.8.3b1 ? John Stone (Mon Feb 07 2005 - 11:56:58 CST)
    - Re: volume shading in 1.8.3b1 ? Axel Kohlmeyer (Mon Feb 07 2005 - 14:27:53 CST)
  - Re: volume shading in 1.8.3b1 ? Oliver Beckstein (Tue Feb 08 2005 - 15:28:30 CST)
IED and output of labels Vlad Cojocaru (Mon Feb 07 2005 - 08:55:35 CST)
vrml2 export without PROTO? Raymond de Vries (Mon Feb 07 2005 - 04:45:09 CST)
- Re: vrml2 export without PROTO? John Stone (Mon Feb 07 2005 - 10:03:35 CST)
  - Re: vrml2 export without PROTO? Raymond de Vries (Tue Feb 08 2005 - 04:43:40 CST)
    - Re: vrml2 export without PROTO? John Stone (Tue Feb 08 2005 - 10:15:41 CST)
    - Re: vrml2 export without PROTO? Raymond de Vries (Tue Feb 08 2005 - 10:59:26 CST)
Calling Python hackers.... John Stone (Fri Feb 04 2005 - 14:56:59 CST)
- Re: Calling Python hackers.... Justin Gullingsrud (Fri Feb 04 2005 - 17:50:58 CST)
  - Re: Calling Python hackers.... John Stone (Sun Feb 06 2005 - 20:00:30 CST)
- Re: Calling Python hackers.... Charles_at_Schwieters.org (Tue Feb 08 2005 - 11:11:21 CST)
  - Re: Calling Python hackers.... John Stone (Tue Feb 08 2005 - 14:00:36 CST)
RE: installation of VIDEOMACH, how to point to the location of the files Chang, Christopher (Fri Feb 04 2005 - 13:49:17 CST)
- RE: installation of VIDEOMACH, how to point to the location of the files Dieter Blaas (Sun Feb 06 2005 - 16:23:26 CST)
installation of VIDEOMACH, how to point to the location of the files Dieter Blaas (Fri Feb 04 2005 - 04:37:07 CST)
- Re: installation of VIDEOMACH, how to point to the location of the files John Stone (Fri Feb 04 2005 - 09:57:09 CST)
  - Re: installation of VIDEOMACH, how to point to the location of the files Dieter Blaas (Fri Feb 04 2005 - 10:22:34 CST)
  - Re: installation of VIDEOMACH, how to point to the location of the files John Stone (Fri Feb 04 2005 - 14:31:15 CST)
openGL error vijay_at_mbu.iisc.ernet.in (Fri Feb 04 2005 - 00:46:00 CST)
- Re: openGL error John Stone (Fri Feb 04 2005 - 09:55:38 CST)
Selected angles during build? Chang, Christopher (Thu Feb 03 2005 - 15:38:04 CST)
multiple alignment tool Klaus Hoffmeier (Thu Feb 03 2005 - 10:59:10 CST)
- Re: multiple alignment tool John Stone (Thu Feb 03 2005 - 14:22:49 CST)
multiple alignment tool Klaus Hoffmeier (Thu Feb 03 2005 - 10:30:52 CST)
- Re: multiple alignment tool Dan Wright (Fri Feb 04 2005 - 16:23:32 CST)
solvent mixture Ekta Khurana (Wed Feb 02 2005 - 20:44:48 CST)
dummy atom ? mbb (Wed Feb 02 2005 - 09:50:21 CST)
- Re: dummy atom ? John Stone (Wed Feb 02 2005 - 09:59:34 CST)
prefferential adsorption analysis Lubos Vrbka (Wed Feb 02 2005 - 06:51:46 CST)
- Re: prefferential adsorption analysis Justin Gullingsrud (Wed Feb 02 2005 - 11:41:19 CST)
  - Re: prefferential adsorption analysis Lubos Vrbka (Thu Feb 03 2005 - 07:52:00 CST)
RE: Crosseye stereo image rendering Wang, Yangzhou (Tue Feb 01 2005 - 16:43:24 CST)
Crosseye stereo image rendering Wang, Yangzhou (Tue Feb 01 2005 - 15:06:07 CST)
- Re: Crosseye stereo image rendering John Stone (Tue Feb 01 2005 - 15:32:03 CST)
- Re: Crosseye stereo image rendering John Kerrigan (Tue Feb 01 2005 - 18:20:27 CST)
Vibration Noriaki Okimoto (Tue Feb 01 2005 - 12:29:21 CST)
- Re: Vibration John Stone (Tue Feb 01 2005 - 12:57:20 CST)
variable atom count in XYZ multiframe trajectory Pascal Boulet (Tue Feb 01 2005 - 10:55:36 CST)
- Re: variable atom count in XYZ multiframe trajectory John Stone (Tue Feb 01 2005 - 11:12:55 CST)
- Re: variable atom count in XYZ multiframe trajectory Axel Kohlmeyer (Tue Feb 01 2005 - 13:59:08 CST)
AutoIMD and fixedatoms Luis Rosales (Mon Jan 31 2005 - 21:47:12 CST)
- Re: AutoIMD and fixedatoms Jordi Cohen (Tue Feb 01 2005 - 12:32:38 CST)
VMD vs. BALLview? Olaf Lenz (Tue Feb 01 2005 - 01:45:03 CST)
Outputing Dihedral Indexes for key structures (backbone, alpha-helix, etc...) Paul R Brenner (Mon Jan 31 2005 - 22:11:28 CST)
- Re: Outputing Dihedral Indexes for key structures (backbone, alpha-helix, etc...) Jan Saam (Tue Feb 01 2005 - 00:01:29 CST)
  - Re: Outputing Dihedral Indexes for key structures (backbone, alpha-helix, etc...) Paul R Brenner (Tue Feb 01 2005 - 13:59:55 CST)
  - Re: Outputing Dihedral Indexes for key structures (backbone, alpha-helix, etc...) Paul R Brenner (Tue Feb 01 2005 - 21:47:38 CST)
    - Re: Outputing Dihedral Indexes for key structures (backbone, alpha-helix, etc...) John Stone (Wed Feb 02 2005 - 10:08:07 CST)
Matrix in VMD Jeffery (Mon Jan 31 2005 - 14:18:02 CST)
- Re: Matrix in VMD John Stone (Mon Jan 31 2005 - 14:18:17 CST)
  - Re: Matrix in VMD Jeffery (Mon Jan 31 2005 - 14:59:52 CST)
making animations Jay Lee (Sat Jan 29 2005 - 17:57:05 CST)
- Re: making animations John Stone (Mon Jan 31 2005 - 13:21:05 CST)
molecular orientation li (Fri Jan 28 2005 - 21:10:26 CST)
- Re: molecular orientation John Stone (Mon Jan 31 2005 - 13:40:42 CST)
How do I use the plugin to read the DLPOLY HISTORY file? Low, John (Fri Jan 28 2005 - 15:38:03 CST)
- Re: How do I use the plugin to read the DLPOLY HISTORY file? John Stone (Fri Jan 28 2005 - 15:50:45 CST)
Display on a Graphic Cluster Luis Rosales (Fri Jan 28 2005 - 15:23:51 CST)
- Re: Display on a Graphic Cluster John Stone (Fri Jan 28 2005 - 13:55:58 CST)
  - Re: Display on a Graphic Cluster Luis Rosales (Fri Jan 28 2005 - 17:54:15 CST)
measure hbonds YOLANDA SMALL (Thu Jan 27 2005 - 18:41:27 CST)
- Re: measure hbonds bora erdemli (Fri Jan 28 2005 - 06:38:12 CST)
  - RE: measure hbonds syma khalid (Fri Jan 28 2005 - 07:09:27 CST)
vmd and hull syma khalid (Thu Jan 27 2005 - 06:36:09 CST)
- Re: vmd and hull John Stone (Thu Jan 27 2005 - 11:16:40 CST)
  - RE: vmd and hull syma khalid (Thu Jan 27 2005 - 11:27:03 CST)
sidechain atomselection Daniel Han (Wed Jan 26 2005 - 18:53:55 CST)
- Re: sidechain atomselection John Stone (Thu Jan 27 2005 - 16:39:24 CST)
  - Re: sidechain atomselection Johannes Müllegger (Mon Sep 25 2006 - 13:10:48 CDT)
    - Re: Re: sidechain atomselection John Stone (Mon Sep 25 2006 - 22:55:10 CDT)
vmdmovie command line Stuart Murdock (Wed Jan 26 2005 - 16:42:11 CST)
- Re: vmdmovie command line John Stone (Mon Jan 31 2005 - 13:35:36 CST)
parm7 plugin Guanglei Cui (Wed Jan 26 2005 - 10:00:13 CST)
- Re: parm7 plugin John Stone (Wed Jan 26 2005 - 10:12:00 CST)
  - Re: parm7 plugin Guanglei Cui (Wed Jan 26 2005 - 11:06:21 CST)
- Re: parm7 plugin Florian Haberl (Wed Jan 26 2005 - 10:27:24 CST)
VMD and CPMD rschurhammer_at_chimie.u-strasbg.fr (Wed Jan 26 2005 - 04:47:23 CST)
- Re: VMD and CPMD Eduard Schreiner (Wed Jan 26 2005 - 08:56:00 CST)
script for mapping the electrostatic potential from APBS on surfaces Vlad Cojocaru (Wed Jan 26 2005 - 03:58:37 CST)
- Re: script for mapping the electrostatic potential from APBS on surfaces John Stone (Wed Jan 26 2005 - 09:38:50 CST)
  - Re: script for mapping the electrostatic potential from APBS on surfaces Vlad Cojocaru (Wed Jan 26 2005 - 10:01:02 CST)
APBS data visualization Vlad Cojocaru (Tue Jan 25 2005 - 13:08:23 CST)
APBS Plugin Vlad Cojocaru (Tue Jan 25 2005 - 09:36:11 CST)
- Re: APBS Plugin John Stone (Tue Jan 25 2005 - 11:22:53 CST)
which nForce to use? Eugen Leitl (Tue Jan 25 2005 - 03:23:18 CST)
- Re: which nForce to use? John Stone (Tue Jan 25 2005 - 12:54:35 CST)
Auto IMD Luis Rosales (Mon Jan 24 2005 - 14:12:45 CST)
- Re: Auto IMD Jordi Cohen (Mon Jan 24 2005 - 14:27:49 CST)
Grasp output view format! N. Chitra (Mon Jan 24 2005 - 12:28:50 CST)
Grasp file format for VMD!! N. Chitra (Mon Jan 24 2005 - 12:22:53 CST)
- Re: Grasp file format for VMD!! John Stone (Mon Jan 24 2005 - 17:26:08 CST)
HOW TO: visualization of electron density maps Dieter Blaas (Mon Jan 24 2005 - 04:28:00 CST)
- Re: HOW TO: visualization of electron density maps John Stone (Mon Jan 24 2005 - 14:31:33 CST)
- Re: HOW TO: visualization of electron density maps Dallas Warren (Mon Jan 24 2005 - 15:34:41 CST)
How to compute the angles li (Sun Jan 23 2005 - 23:08:08 CST)
unwrapping 'wrapping' DCd files Vani Krishna (Fri Jan 21 2005 - 23:44:07 CST)
- Re: unwrapping 'wrapping' DCd files John Stone (Mon Jan 24 2005 - 14:22:45 CST)
python or Tcl/Tk Guanglei Cui (Fri Jan 21 2005 - 12:48:12 CST)
- Re: python or Tcl/Tk John Stone (Fri Jan 21 2005 - 17:27:24 CST)
dynamic coloring Jay Lee (Fri Jan 21 2005 - 12:36:39 CST)
- Re: dynamic coloring John Stone (Fri Jan 21 2005 - 17:26:46 CST)
python or tcl/tk Guanglei Cui (Fri Jan 21 2005 - 11:03:32 CST)
Updates in rmsdtt (Excel) and cluster (Xcluster) plugins Luis Gracia (Fri Jan 21 2005 - 00:22:42 CST)
Closing filehandles in vmd tcl script Ben Roberts (Thu Jan 20 2005 - 21:05:51 CST)
- Re: Closing filehandles in vmd tcl script Justin Gullingsrud (Fri Jan 21 2005 - 01:28:42 CST)
constraints Swarna Patra (Thu Jan 20 2005 - 20:49:49 CST)
trio and osX vuissoz jean-marc (Thu Jan 20 2005 - 14:23:43 CST)
- Re: trio and osX John Stone (Thu Feb 03 2005 - 18:22:19 CST)
model export Paul D. Jones (Wed Jan 19 2005 - 13:33:04 CST)
- Re: model export John Stone (Wed Jan 19 2005 - 16:48:59 CST)
how to display PDB with MODEL card Sichun Yang (Tue Jan 18 2005 - 22:29:20 CST)
- Re: how to display PDB with MODEL card John Stone (Fri Jan 21 2005 - 17:32:35 CST)
Hbonds counting script li (Tue Jan 18 2005 - 01:06:58 CST)
PBS script for LINUX cluster Swarna Patra (Sun Jan 16 2005 - 20:03:04 CST)
- Re: PBS script for LINUX cluster Brian Bennion (Tue Jan 18 2005 - 10:25:05 CST)
  - Re: PBS script for LINUX cluster Florian Haberl (Wed Jan 19 2005 - 02:56:39 CST)
Autoionize / SODIUM Blake Charlebois (Sun Jan 16 2005 - 12:14:04 CST)
- Re: Autoionize / SODIUM John Stone (Fri Jan 21 2005 - 17:30:29 CST)
  - RE: Autoionize / SODIUM Blake Charlebois (Mon Jan 24 2005 - 17:04:58 CST)
last call for early registrations for "Horizons2005" Vlad Cojocaru (Fri Jan 14 2005 - 07:19:00 CST)
RE: 3D/stereo hardware recommendations wanted!!! Mads Nørregaard-Madsen (Fri Jan 14 2005 - 05:09:54 CST)
3D/stereo hardware recommendations wanted!!! Thomas Hedegaard Pedersen (Fri Jan 14 2005 - 02:41:13 CST)
- Re: 3D/stereo hardware recommendations wanted!!! Bogdan Costescu (Fri Jan 14 2005 - 04:51:45 CST)
- Re: 3D/stereo hardware recommendations wanted!!! John Stone (Fri Jan 14 2005 - 11:29:36 CST)
Stereo-3D in a Window: Not in MacOS X Tiger?!! Warren DeLano (Thu Jan 13 2005 - 19:58:50 CST)
- Stereo 3D matters to me John Stone (Fri Jan 14 2005 - 10:02:50 CST)
stereo for XP and Linux Michal Kolinski (Wed Jan 12 2005 - 11:22:57 CST)
- Re: stereo for XP and Linux John Stone (Wed Jan 12 2005 - 11:30:18 CST)
  - Re: stereo for XP and Linux Benjamin Goldsteen (Wed Jan 12 2005 - 18:04:44 CST)
Deleting atomselect selections for proper memory management pbrenne1_at_nd.edu (Wed Jan 12 2005 - 08:56:43 CST)
- Re: Deleting atomselect selections for proper memory management John Stone (Wed Jan 12 2005 - 10:22:00 CST)
- Re: Deleting atomselect selections for proper memory management Justin Gullingsrud (Wed Jan 12 2005 - 11:08:15 CST)
  - Re: Deleting atomselect selections for proper memory management pbrenne1_at_nd.edu (Wed Jan 12 2005 - 13:10:44 CST)
Fwd: linux FC3 VMD vs insightII conflict Dr. Daniel James White PhD (Wed Jan 12 2005 - 06:36:57 CST)
- Re: Fwd: linux FC3 VMD vs insightII conflict John Stone (Wed Jan 12 2005 - 10:20:08 CST)
- Re: Fwd: linux FC3 VMD vs insightII conflict Bogdan Costescu (Wed Jan 12 2005 - 11:08:45 CST)
angle between two vectors Ekta Khurana (Tue Jan 11 2005 - 18:56:54 CST)
- Re: angle between two vectors John Stone (Tue Jan 11 2005 - 19:05:43 CST)
- Re: angle between two vectors Luis Gracia (Wed Jan 12 2005 - 12:31:58 CST)
Python and numpy Florian Haberl (Tue Jan 11 2005 - 07:31:37 CST)
pmf calculation Swarna Patra (Mon Jan 10 2005 - 19:29:24 CST)
Possible values for "select_method"? Chang, Christopher (Mon Jan 10 2005 - 16:48:27 CST)
- Re: Possible values for "select_method"? John Stone (Mon Jan 10 2005 - 17:01:31 CST)
vmd exit tcl callback Luis Gracia (Mon Jan 10 2005 - 11:43:43 CST)
- Re: vmd exit tcl callback John Stone (Tue Jan 11 2005 - 15:41:03 CST)
VMD and windows Florian Haberl (Mon Jan 10 2005 - 01:37:40 CST)
- Re: VMD and windows John Stone (Mon Jan 10 2005 - 18:02:41 CST)
Periodic box display feature suggestion Marc Baaden (Sat Jan 08 2005 - 12:41:13 CST)
- Re: Periodic box display feature suggestion Axel Kohlmeyer (Mon Jan 10 2005 - 15:00:47 CST)
ATOM or HETATM record Joseph E. Curtis (Fri Jan 07 2005 - 16:46:16 CST)
Cluster Analysis given a dcd trajectory pbrenne1_at_nd.edu (Fri Jan 07 2005 - 15:58:41 CST)
- Re: Cluster Analysis given a dcd trajectory Axel Kohlmeyer (Sat Jan 08 2005 - 13:28:55 CST)
  - Re: Cluster Analysis given a dcd trajectory pbrenne1_at_nd.edu (Sun Jan 09 2005 - 13:25:16 CST)
  - special instructions in psfgen for circular proteins? Amarda Shehu (Thu Mar 30 2006 - 16:50:02 CST)
    - Re: special instructions in psfgen for circular proteins? John Stone (Sun Apr 02 2006 - 20:14:28 CDT)
- Re: Cluster Analysis given a dcd trajectory lug2002_at_med.cornell.edu (Fri Jan 07 2005 - 23:41:14 CST)
atom index starting at 0 pl (Fri Jan 07 2005 - 09:47:00 CST)
- Re: atom index starting at 0 John Stone (Fri Jan 07 2005 - 16:10:41 CST)
  - Re: atom index starting at 0 Andrew Dalke (Fri Jan 07 2005 - 17:36:50 CST)
    - Re: atom index starting at 0 John Stone (Mon Jan 10 2005 - 18:38:51 CST)
    - Re: atom index starting at 0 John Stone (Thu Aug 11 2005 - 16:19:57 CDT)
vmd not starting up on Fedora core 3 linux , nVidia quadro 980 XGL, nVidia 6629 driver Dr. Daniel James White PhD (Thu Jan 06 2005 - 05:27:34 CST)
- Re: vmd not starting up on Fedora core 3 linux , nVidia quadro 980 XGL, nVidia 6629 driver Axel Kohlmeyer (Thu Jan 06 2005 - 09:42:26 CST)
  - Re: vmd not starting up on Fedora core 3 linux , nVidia quadro 980 XGL, nVidia 6629 driver John Stone (Thu Jan 06 2005 - 17:28:14 CST)
  - vmd not starting up on Fedora core 3 linux , nVidia quadro 980 XGL, nVidia 6629 driver Dr. Daniel James White PhD (Fri Jan 07 2005 - 02:15:08 CST)
- Re: vmd not starting up on Fedora core 3 linux , nVidia quadro 980 XGL, nVidia 6629 driver Dr. Daniel James White PhD (Mon Jan 10 2005 - 01:20:31 CST)
  - Re: Re: vmd not starting up on Fedora core 3 linux , nVidia quadro 980 XGL, nVidia 6629 driver John Stone (Mon Jan 10 2005 - 18:05:54 CST)
- Re: vmd not starting up on Fedora core 3 linux , nVidia quadro 980 XGL, nVidia 6629 driver Dr. Daniel James White PhD (Tue Jan 11 2005 - 07:42:45 CST)
  - Re: Re: vmd not starting up on Fedora core 3 linux , nVidia quadro 980 XGL, nVidia 6629 driver Axel Kohlmeyer (Tue Jan 11 2005 - 10:50:57 CST)
can I combine several dcd files into one dcd file? mashaojie163 (Wed Jan 05 2005 - 08:55:14 CST)
- Re: can I combine several dcd files into one dcd file? Justin Gullingsrud (Wed Jan 05 2005 - 10:30:56 CST)
- Re: can I combine several dcd files into one dcd file? John E. Kerrigan (Wed Jan 05 2005 - 12:52:38 CST)
how to represent H-bonds between chain A and chain B using VMD Uday Chippada (Tue Jan 04 2005 - 17:02:42 CST)
- Re: how to represent H-bonds between chain A and chain B using VMD Axel Kohlmeyer (Wed Jan 05 2005 - 02:29:52 CST)
  - Re: how to represent H-bonds between chain A and chain B using VMD Justin Gullingsrud (Wed Jan 05 2005 - 10:29:51 CST)
dcd file appears to contain no timesteps mashaojie163 (Tue Jan 04 2005 - 02:58:38 CST)
- Re: dcd file appears to contain no timesteps John Stone (Tue Jan 04 2005 - 10:18:52 CST)
pdb files VISWANADHA SRIDHARA (Mon Jan 03 2005 - 18:19:04 CST)
- Re: pdb files Axel Kohlmeyer (Tue Jan 04 2005 - 01:33:53 CST)
- Re: pdb files John Stone (Tue Jan 04 2005 - 10:23:26 CST)
merge Osmany Guirola Cruz (Mon Jan 03 2005 - 11:26:46 CST)
- Re: merge John Stone (Mon Jan 03 2005 - 16:20:51 CST)
(no subject) dtp3+_at_pitt.edu (Mon Jan 03 2005 - 14:33:55 CST)
- Re: your mail John Stone (Mon Jan 03 2005 - 15:15:20 CST)
  - Re: Re: your mail Axel Kohlmeyer (Tue Jan 04 2005 - 01:25:10 CST)
    - RE: Re: Re: your mail dtp3+_at_pitt.edu (Tue Jan 04 2005 - 13:12:57 CST)
Drawing oriented cylinders Jake . (Wed Dec 29 2004 - 14:16:10 CST)
- Re: Drawing oriented cylinders John Stone (Wed Dec 29 2004 - 18:04:17 CST)
about vmd yoongho (Wed Dec 29 2004 - 06:58:51 CST)
- Re: about vmd John Stone (Wed Dec 29 2004 - 18:07:49 CST)
VMD and Remote X-Servers Greipel.Joachim_at_MH-Hannover.DE (Tue Dec 28 2004 - 08:39:32 CST)
- Re: VMD and Remote X-Servers John Stone (Tue Dec 28 2004 - 10:56:26 CST)
  - nvidia quadro, linux_x86, and performance difference w/nvidia drivers 1.0.5336 vs anything newer or older on VMD 1.8.2 Sabuj Pattanayek (Tue Jan 04 2005 - 16:06:39 CST)
ERROR) Failed to create Surf atom radii input file dieter blaas (Tue Dec 28 2004 - 04:14:50 CST)
- Re: ERROR) Failed to create Surf atom radii input file Axel Kohlmeyer (Tue Dec 28 2004 - 08:37:37 CST)
  - Re: ERROR) Failed to create Surf atom radii input file dieter blaas (Tue Dec 28 2004 - 10:02:40 CST)
    - Re: ERROR) Failed to create Surf atom radii input file Axel Kohlmeyer (Tue Dec 28 2004 - 10:14:27 CST)
    - Re: ERROR) Failed to create Surf atom radii input file John Stone (Tue Dec 28 2004 - 10:46:02 CST)
  - Re: ERROR) Failed to create Surf atom radii input file dieter blaas (Wed Dec 29 2004 - 02:42:54 CST)
    - Re: ERROR) Failed to create Surf atom radii input file John Stone (Wed Dec 29 2004 - 18:14:08 CST)
- Re: ERROR) Failed to create Surf atom radii input file Brian Bennion (Tue Dec 28 2004 - 11:16:46 CST)
Stereo on an SGI Octane2 using Crystal Eyes Jill Vickery (Mon Dec 27 2004 - 12:50:09 CST)
- Re: Stereo on an SGI Octane2 using Crystal Eyes John Stone (Tue Dec 28 2004 - 11:23:35 CST)
torsions = NaN ? nordgren_at_sas.upenn.edu (Mon Dec 20 2004 - 18:23:07 CST)
- Re: torsions = NaN ? John Stone (Tue Dec 21 2004 - 10:14:12 CST)
handling electron density maps (.mrc and .map files) Amarda Shehu (Sat Dec 18 2004 - 15:29:30 CST)
- Re: handling electron density maps (.mrc and .map files) Jim Nettles (Sat Dec 18 2004 - 18:20:39 CST)
  - criteria for detecting hydrogen bonds Amarda Shehu (Sun Apr 17 2005 - 18:14:21 CDT)
  - understanding NOE restraints Amarda Shehu (Mon May 02 2005 - 18:56:34 CDT)
    - Re: understanding NOE restraints Charles_at_Schwieters.org (Tue May 03 2005 - 05:52:56 CDT)
- Re: handling electron density maps (.mrc and .map files) hinsen_at_dsm-mail.saclay.cea.fr (Sun Dec 19 2004 - 03:04:09 CST)
RMSD for non-continous residues Srinivasan Madabushi (Fri Dec 17 2004 - 18:24:44 CST)
VMD on Linux RH9 with ATI's fglrx-4.3.0-3.14.6 1280x1024@100Hz dumping core ... any helpful advice :>? chris.harwell_at_pharma.novartis.com (Fri Dec 17 2004 - 15:27:21 CST)
- Re: VMD on Linux RH9 with ATI's fglrx-4.3.0-3.14.6 1280x1024@100Hz dumping core ... any helpful advice :>? John Stone (Tue Dec 21 2004 - 10:22:46 CST)
MD: Water network analysis + visualization Sanjeev B.S. (Fri Dec 17 2004 - 12:21:33 CST)
- Re: MD: Water network analysis + visualization sanjeev_at_mbu.iisc.ernet.in (Tue Mar 22 2005 - 08:02:07 CST)
turning Info output off in vmd console? pl (Fri Dec 17 2004 - 06:44:03 CST)
- Re: turning Info output off in vmd console? John Stone (Fri Dec 17 2004 - 10:32:39 CST)
VMD for ALTIX ioana_at_pegasus.arc.nasa.gov (Thu Dec 16 2004 - 19:25:51 CST)
- Re: VMD for ALTIX John Stone (Fri Dec 17 2004 - 10:31:05 CST)
  - Re: VMD for ALTIX Philip Fowler (Thu May 05 2005 - 11:04:18 CDT)
    - Re: VMD for ALTIX John Stone (Thu May 05 2005 - 13:11:16 CDT)
    - VMD for SGI Altix/Prism, IBM AIX5, etc.. John Stone (Wed May 25 2005 - 15:48:27 CDT)
VMDNUMPY and OS X (Panther) Joseph E. Curtis (Thu Dec 16 2004 - 15:40:16 CST)
- Re: VMDNUMPY and OS X (Panther) John Stone (Thu Dec 16 2004 - 16:22:12 CST)
DynamicBonds representation Lars Bruno Hansen (Thu Dec 16 2004 - 08:58:39 CST)
- Re: DynamicBonds representation Axel Kohlmeyer (Thu Dec 16 2004 - 13:04:27 CST)
  - Re: DynamicBonds representation John Stone (Thu Dec 16 2004 - 13:33:13 CST)
Nanotech Ventures 2005 - Tokyo & California NSTI Nanotech Ventures (Thu Dec 16 2004 - 00:50:00 CST)
VMD plugin: Membrane: POPG Vani Krishna (Wed Dec 15 2004 - 20:58:57 CST)
- Re: VMD plugin: Membrane: POPG John Stone (Thu Dec 16 2004 - 13:35:23 CST)
Screen corruption Sylvain EDALEINE (Wed Dec 15 2004 - 04:16:22 CST)
- Re: Screen corruption John Stone (Wed Dec 15 2004 - 08:57:05 CST)
Autoionize plugin problem Gaurav Sharma (Tue Dec 14 2004 - 12:52:03 CST)
- Re: Autoionize plugin problem John Stone (Thu Dec 16 2004 - 11:30:21 CST)
Multiple Sequence Alignment Extension Klaus Hoffmeier (Tue Dec 14 2004 - 08:06:22 CST)
- Re: Multiple Sequence Alignment Extension John Stone (Tue Dec 14 2004 - 08:55:41 CST)
(no subject) Eunice Ramirez Melendez (Mon Dec 13 2004 - 19:20:55 CST)
- Re: Brian Bennion (Tue Dec 14 2004 - 12:47:07 CST)
Re: [linux-elitists] ATI Radeon support (fwd from deejoe@raccoon.com) Eugen Leitl (Tue Dec 14 2004 - 03:33:02 CST)
Virtual Reality and VMD Enrico Santori (Tue Dec 14 2004 - 02:31:00 CST)
- Re: Virtual Reality and VMD John Stone (Tue Dec 14 2004 - 09:10:30 CST)
  - Re: Virtual Reality and VMD Enrico Santori (Tue Dec 14 2004 - 09:32:30 CST)
  - Re: Virtual Reality and VMD Eugen Leitl (Tue Dec 14 2004 - 10:41:33 CST)
    - Re: Virtual Reality and VMD John Stone (Tue Dec 14 2004 - 10:45:45 CST)
CAVE on OS X Ebrahim Mayat (Mon Dec 13 2004 - 02:57:27 CST)
- Re: CAVE on OS X John Stone (Tue Dec 14 2004 - 09:44:54 CST)
How to use solvate add water in amber crd/parm files? Îº¿ (Thu Dec 09 2004 - 20:34:12 CST)
- Re: How to use solvate add water in amber crd/parm files? John Stone (Fri Dec 10 2004 - 02:22:22 CST)
Solvent accessible surface area Vani Krishna (Wed Dec 08 2004 - 18:07:55 CST)
- Re: Solvent accessible surface area John Stone (Wed Dec 08 2004 - 22:51:02 CST)
  - Solvent accessible area/Radii definition Vani Krishna (Thu Dec 09 2004 - 10:20:37 CST)
    - Re: Solvent accessible area/Radii definition John Stone (Thu Dec 16 2004 - 13:55:00 CST)
    - Re: Solvent accessible area/Radii definition Hui-Hsu Tsai (Thu Dec 16 2004 - 15:44:26 CST)
Problem with the move command to rotate a molecule Nitin Bhardwaj (Wed Dec 08 2004 - 16:06:50 CST)
- Re: Problem with the move command to rotate a molecule James C. Patterson (Wed Dec 08 2004 - 16:15:43 CST)
Rotating a molecule around its center of mass... Nitin Bhardwaj (Wed Dec 08 2004 - 12:40:21 CST)
- Re: Rotating a molecule around its center of mass... Nitin Bhardwaj (Wed Dec 08 2004 - 12:43:35 CST)
Re: Thanks :) Garf (Wed Dec 08 2004 - 10:02:08 CST)
bond distance across different proteins Stern, Julie (Tue Dec 07 2004 - 14:56:59 CST)
Tube representation of alpha carbons Matthew Geballe (Tue Dec 07 2004 - 14:29:43 CST)
- Re: Tube representation of alpha carbons Andrew Dalke (Tue Dec 07 2004 - 19:46:58 CST)
  - Re: Tube representation of alpha carbons Matthew Thomas Geballe (Tue Dec 07 2004 - 20:43:11 CST)
- Re: Tube representation of alpha carbons Marc Q. Ma (Wed Dec 08 2004 - 07:44:55 CST)
problem Nvidia and vmd Sylvain EDALEINE (Mon Dec 06 2004 - 11:02:14 CST)
- Re: problem Nvidia and vmd John Stone (Mon Dec 06 2004 - 11:14:26 CST)
  - Re: problem Nvidia and vmd Jérôme Hénin (Mon Dec 06 2004 - 15:49:35 CST)
VMD 1.8.3 beta 1 available for testing/feedback John Stone (Sun Dec 05 2004 - 22:44:56 CST)
- Re: VMD 1.8.3 beta 1 available for testing/feedback Jerry Ebalunode (Mon Dec 06 2004 - 11:56:12 CST)
  - Re: VMD 1.8.3 beta 1 available for testing/feedback John Stone (Mon Dec 06 2004 - 12:42:59 CST)
Calculating and drawing symmetry axes Eugene Valkov (Thu Dec 02 2004 - 13:37:14 CST)
VMD compatibility with graphics card Eric Hajjar (Thu Dec 02 2004 - 03:27:08 CST)
- Re: VMD compatibility with graphics card John Stone (Thu Dec 02 2004 - 09:55:55 CST)
Difficulties using Crystal Eyes 3 Christian Simon (Thu Dec 02 2004 - 09:00:05 CST)
- Re: Difficulties using Crystal Eyes 3 John Stone (Thu Dec 02 2004 - 09:51:12 CST)
  - Re: Difficulties using Crystal Eyes 3 John Stone (Thu Dec 02 2004 - 12:54:23 CST)
    - Re: Difficulties using Crystal Eyes 3 Jim Nettles (Thu Dec 02 2004 - 14:09:58 CST)
    - Re: Difficulties using Crystal Eyes 3 Christian Simon (Mon Dec 06 2004 - 10:20:59 CST)
solvate problem vivek sharma (Wed Dec 01 2004 - 11:58:46 CST)
- Re: solvate problem John Stone (Mon Dec 06 2004 - 09:42:54 CST)
  - Re: solvate problem vivek sharma (Tue Dec 07 2004 - 06:23:38 CST)
  - Re: solvate problem vsharma (Tue Dec 07 2004 - 08:26:00 CST)
distribution analysis Lubos Vrbka (Wed Dec 01 2004 - 09:25:53 CST)
- Re: distribution analysis Jerry Ebalunode (Wed Dec 01 2004 - 10:00:26 CST)
- Re: distribution analysis John Stone (Wed Dec 01 2004 - 10:02:22 CST)
  - Re: distribution analysis Lubos Vrbka (Wed Dec 01 2004 - 10:29:25 CST)
    - Re: distribution analysis John Stone (Wed Dec 01 2004 - 10:43:51 CST)
  - Re: distribution analysis Lubos Vrbka (Tue Dec 07 2004 - 02:23:05 CST)
Problems with Mac OSX VMD and certain PDB files bozell, joe (Wed Nov 24 2004 - 12:34:47 CST)
- Re: Problems with Mac OSX VMD and certain PDB files John Stone (Wed Nov 24 2004 - 13:26:50 CST)
Povray & color gradients Tatyana I. Igumenova (Wed Nov 24 2004 - 11:28:45 CST)
- RE: Povray & color gradients Luis Rosales (Wed Nov 24 2004 - 16:35:55 CST)
  - Re: Povray & color gradients John Stone (Mon Nov 29 2004 - 00:31:16 CST)
Chloroform Solvent Box Harindar Keer (Tue Nov 23 2004 - 11:17:45 CST)
Label using TCL Ekta Khurana (Mon Nov 22 2004 - 18:43:28 CST)
- Re: Label using TCL John Stone (Mon Nov 22 2004 - 21:16:10 CST)
obtaining lists of bond, angle, and dihedral interactions Philip Blood (Fri Nov 19 2004 - 17:21:44 CST)
- Re: obtaining lists of bond, angle, and dihedral interactions John Stone (Mon Nov 22 2004 - 21:11:43 CST)
Tcl startup error on 3X3 tiled display ladyg30_at_eden.rutgers.edu (Fri Nov 19 2004 - 13:00:32 CST)
- Re: Tcl startup error on 3X3 tiled display John Stone (Fri Nov 19 2004 - 13:05:31 CST)
measure fit alignment problems Gavin Murphy (Thu Nov 18 2004 - 22:37:35 CST)
- Re: measure fit alignment problems John Stone (Fri Nov 19 2004 - 10:24:35 CST)
- Re: measure fit alignment problems Luis Gracia (Fri Nov 19 2004 - 15:03:37 CST)
  - MSMS variable Luis Rosales (Tue Nov 23 2004 - 18:52:35 CST)
Re: namd-l: Writing pdb file.. easier way? Jérôme Hénin (Thu Nov 18 2004 - 17:28:36 CST)
- Re: namd-l: Writing pdb file.. easier way? griadi_at_utalca.cl (Tue Nov 23 2004 - 12:44:03 CST)
- Re: Re: namd-l: Writing pdb file.. easier way? Justin Gullingsrud (Tue Nov 23 2004 - 14:45:15 CST)
Re: Move molecule John Stone (Thu Nov 18 2004 - 14:26:51 CST)
- Re: Move molecule Uday Chippada (Thu Nov 18 2004 - 14:53:49 CST)
- Updating selections.... Luis Rosales (Thu Nov 18 2004 - 18:41:21 CST)
  - Re: Updating selections.... John Stone (Thu Nov 18 2004 - 18:47:11 CST)
(no subject) Paul Whitford (Wed Nov 17 2004 - 19:01:11 CST)
- Re: Charles McCallum (Wed Nov 17 2004 - 22:21:11 CST)
- Re: your mail John Stone (Thu Nov 18 2004 - 10:11:18 CST)
  - Re: your mail Paul Whitford (Thu Nov 18 2004 - 17:12:28 CST)
Drawing Vectors Anthony Ivetac (Tue Nov 16 2004 - 08:53:35 CST)
- Re: Drawing Vectors John Stone (Wed Nov 17 2004 - 10:23:17 CST)
  - Re: Drawing Vectors John Stone (Thu Nov 18 2004 - 17:06:08 CST)
Fwd: Re: putting Lipid layers around a protein Florian Haberl (Tue Nov 16 2004 - 03:32:41 CST)
Electrostatic potential mapping Patti Schaefer (Mon Nov 15 2004 - 15:28:15 CST)
- Re: Electrostatic potential mapping John Stone (Mon Nov 15 2004 - 15:40:21 CST)
Re: putting Lipid layers around a protein li (Mon Nov 15 2004 - 00:42:15 CST)
putting Lipid layers around a protein Nitin Bhardwaj (Sun Nov 14 2004 - 19:20:22 CST)
Solvate and VMD on OS X Eric Peterson (Fri Nov 12 2004 - 20:20:28 CST)
- Re: Solvate and VMD on OS X Justin Gullingsrud (Sat Nov 13 2004 - 12:25:45 CST)
Where should I put script file? Chung, Dong Hoon (Fri Nov 12 2004 - 14:02:09 CST)
- Re: Where should I put script file? Jérôme Hénin (Fri Nov 12 2004 - 17:10:07 CST)
loading limits Stern, Julie (Fri Nov 12 2004 - 07:52:24 CST)
- Re: loading limits John Stone (Fri Nov 12 2004 - 10:36:00 CST)
VMD newbie question Laura Lucan (Thu Nov 11 2004 - 16:18:34 CST)
- Re: VMD newbie question Luis Gracia (Thu Nov 11 2004 - 19:24:46 CST)
  - Re: VMD newbie question Laura Lucan (Thu Nov 11 2004 - 22:04:01 CST)
LAMMPS visualization tsirk (Thu Nov 11 2004 - 15:02:42 CST)
- Re: LAMMPS visualization John Stone (Thu Nov 11 2004 - 15:13:14 CST)
- Re: LAMMPS visualization Jim Shepherd (Thu Nov 11 2004 - 17:30:26 CST)
- Re: LAMMPS visualization Akiyama, Jotaro (Thu Nov 11 2004 - 18:27:15 CST)
RE: Conversion of trajectory files Kooser, Ara S (Wed Nov 10 2004 - 10:11:32 CST)
Apologies Adrain Koh (Wed Nov 10 2004 - 04:12:55 CST)
Conversion of trajectory files Adrain Koh (Tue Nov 09 2004 - 21:43:52 CST)
- Re: Conversion of trajectory files Ernesto E. Di Iorio (Wed Nov 10 2004 - 04:23:19 CST)
writepdb and list problem pl (Tue Nov 09 2004 - 05:52:51 CST)
- Re: writepdb and list problem John Stone (Thu Nov 11 2004 - 10:39:11 CST)
  - Re: writepdb and list problem- Resolved but still... pl (Fri Nov 12 2004 - 07:59:48 CST)
- Re: writepdb and list problem Justin Gullingsrud (Thu Nov 11 2004 - 11:57:24 CST)
getbonds for H-bonds request pl (Mon Nov 08 2004 - 08:10:57 CST)
- Re: getbonds for H-bonds request Axel Kohlmeyer (Mon Nov 08 2004 - 13:31:35 CST)
bridging_waters.tcl error and usage pl (Mon Nov 08 2004 - 05:18:21 CST)
- Re: bridging_waters.tcl error and usage Justin Gullingsrud (Mon Nov 08 2004 - 12:51:05 CST)
  - Re: bridging_waters.tcl error and usage Justin Gullingsrud (Mon Nov 08 2004 - 13:04:00 CST)
Coloring by type? Akiyama, Jotaro (Mon Nov 08 2004 - 03:06:34 CST)
- Re: Coloring by type? John Stone (Thu Nov 11 2004 - 10:57:55 CST)
  - Re: Coloring by type? Akiyama, Jotaro (Thu Nov 11 2004 - 18:56:02 CST)
    - Re: Coloring by type? John Stone (Thu Nov 11 2004 - 21:51:00 CST)
    - Re: Coloring by type? Akiyama, Jotaro (Fri Nov 12 2004 - 02:45:10 CST)
Fwd: Re: Any methods for real stereo viewing with Mac and OsX Peter Engelhardt (Sat Nov 06 2004 - 16:51:32 CST)
plot color scale for volume slice YAMAZAKI Takeshi (Sat Nov 06 2004 - 16:12:28 CST)
- Re: plot color scale for volume slice John Stone (Sun Nov 07 2004 - 21:02:23 CST)
Any methods for real stereo viewing with Mac and OsX Peter Engelhardt (Sat Nov 06 2004 - 13:19:33 CST)
- Re: Any methods for real stereo viewing with Mac and OsX John Stone (Sat Nov 06 2004 - 12:41:30 CST)
Selection of atoms and bond specific to MD snapshot Sanjeev B.S. (Sat Nov 06 2004 - 10:58:40 CST)
- Re: Selection of atoms and bond specific to MD snapshot Axel Kohlmeyer (Sat Nov 06 2004 - 15:12:35 CST)
Converting .txt trajectory files to VMD compatible format Adrain Koh (Fri Nov 05 2004 - 04:43:40 CST)
- Re: Converting .txt trajectory files to VMD compatible format John Stone (Fri Nov 05 2004 - 11:25:08 CST)
  - Re: Converting .txt trajectory files to VMD compatible format Adrain Koh (Tue Nov 09 2004 - 21:40:18 CST)
  - Re: Converting .txt trajectory files to VMD compatible format John Stone (Wed Nov 17 2004 - 11:20:27 CST)
Display of H-bonded waters only pl (Wed Nov 03 2004 - 10:04:29 CST)
linux installation MERIC AYSE OVACIK (Wed Nov 03 2004 - 03:57:20 CST)
- Re: linux installation John Stone (Wed Nov 03 2004 - 10:02:40 CST)
trajectory loading ioana_at_pegasus.arc.nasa.gov (Mon Nov 01 2004 - 22:07:43 CST)
- Re: trajectory loading John Stone (Tue Nov 02 2004 - 09:31:44 CST)
  - Re: trajectory loading ioana_at_pegasus.arc.nasa.gov (Tue Nov 02 2004 - 17:42:20 CST)
question on ion size Hyonseok Hwang (Mon Nov 01 2004 - 17:53:29 CST)
- Re: question on ion size John Stone (Mon Nov 01 2004 - 18:09:26 CST)
structure superimposition Shirley Li (Sat Oct 30 2004 - 23:18:33 CDT)
web script Osmany Guirola Cruz (Fri Oct 29 2004 - 16:20:05 CDT)
- Re: web script John Stone (Fri Oct 29 2004 - 19:08:40 CDT)
  - Re: web script Osmany Guirola Cruz (Mon Nov 01 2004 - 06:49:53 CST)
VMD scripting questions Peter Bazeley (Fri Oct 29 2004 - 04:48:11 CDT)
- Re: VMD scripting questions Axel Kohlmeyer (Fri Oct 29 2004 - 08:26:48 CDT)
Re: Thank you! Garf (Fri Oct 29 2004 - 04:13:47 CDT)
Error psfgen Surendra Negi (Thu Oct 28 2004 - 20:07:14 CDT)
Install VMD on Window XP bybaker_at_itsa.ucsf.edu (Thu Oct 28 2004 - 22:19:46 CDT)
Install VMD on Window XP bybaker_at_itsa.ucsf.edu (Thu Oct 28 2004 - 22:17:59 CDT)
- Re: Install VMD on Window XP John Stone (Fri Oct 29 2004 - 15:34:06 CDT)
BOND CP2 - CT2 IN PARAMETER FILES bora erdemli (Thu Oct 28 2004 - 16:42:09 CDT)
multistructure XYZ Herbert Georg (Thu Oct 28 2004 - 14:52:58 CDT)
- Re: multistructure XYZ John Stone (Thu Oct 28 2004 - 16:19:47 CDT)
vmd customization angelo vargas (Thu Oct 28 2004 - 03:57:25 CDT)
- Re: vmd customization Axel Kohlmeyer (Thu Oct 28 2004 - 07:30:57 CDT)
Question about using psfgen on protein 4HVP jin (Tue Oct 26 2004 - 11:39:16 CDT)
- Re: Question about using psfgen on protein 4HVP Brian Bennion (Tue Oct 26 2004 - 15:02:51 CDT)
- Re: Question about using psfgen on protein 4HVP Justin Gullingsrud (Tue Oct 26 2004 - 18:46:21 CDT)
psfgen and xplor topology Marc Q. Ma (Mon Oct 25 2004 - 15:08:03 CDT)
- Re: psfgen and xplor topology Charles McCallum (Mon Oct 25 2004 - 22:33:48 CDT)
  - Re: psfgen and xplor topology Marc Q. Ma (Tue Oct 26 2004 - 08:17:25 CDT)
  - Re: psfgen and xplor topology Jerry Xu (Tue Oct 26 2004 - 15:16:26 CDT)
"same as" failing? Luis Gracia (Mon Oct 25 2004 - 13:42:37 CDT)
- Re: "same as" failing? John Stone (Mon Oct 25 2004 - 13:49:14 CDT)
  - Re: "same as" failing? Luis Gracia (Mon Oct 25 2004 - 14:45:54 CDT)
question about electrostatic map visualizing Cristina (Sat Sep 04 2004 - 11:02:47 CDT)
- Re: question about electrostatic map visualizing John Stone (Mon Oct 25 2004 - 13:27:12 CDT)
  - Re: question about electrostatic map visualizing Cristina (Tue Oct 26 2004 - 13:00:13 CDT)
Problems with povray Dominique Vlieghe (Mon Oct 25 2004 - 07:13:11 CDT)
- Re: Problems with povray John Stone (Mon Oct 25 2004 - 13:15:43 CDT)
- RE: Problems with povray Luis Rosales (Mon Oct 25 2004 - 13:47:59 CDT)
  - Re: Problems with povray John Stone (Mon Oct 25 2004 - 14:01:21 CDT)
    - RE: Problems with povray Luis Rosales (Tue Oct 26 2004 - 15:11:53 CDT)
    - Re: Problems with povray John Stone (Tue Oct 26 2004 - 15:20:48 CDT)
error while loading shared libraries: libGLU.so.1 Cheri M Turman (Thu Oct 21 2004 - 13:24:12 CDT)
- Re: error while loading shared libraries: libGLU.so.1 John Stone (Thu Oct 21 2004 - 13:35:23 CDT)
- Re: error while loading shared libraries: libGLU.so.1 John Stone (Thu Oct 21 2004 - 15:20:33 CDT)
python2.3 and vmd Lars Bruno Hansen (Thu Oct 21 2004 - 08:41:42 CDT)
- Re: python2.3 and vmd John Stone (Thu Oct 21 2004 - 10:56:29 CDT)
- Re: python2.3 and vmd Lars Bruno Hansen (Thu Oct 28 2004 - 05:04:06 CDT)
  - Re: python2.3 and vmd Justin Gullingsrud (Fri Oct 29 2004 - 00:23:29 CDT)
    - Re: python2.3 and vmd Lars Bruno Hansen (Fri Oct 29 2004 - 02:05:38 CDT)
Re: xyz file John Stone (Wed Oct 20 2004 - 17:49:01 CDT)
trajectory file with xyz mbb (Wed Oct 20 2004 - 15:56:26 CDT)
- Re: trajectory file with xyz John Stone (Fri Oct 22 2004 - 10:47:36 CDT)
International PhD Symppozium "DECODING NATURE: HIERARCHY OF INTERACTIONS" Vlad Cojocaru (Wed Oct 20 2004 - 11:10:43 CDT)
selection of 2 molecules Volodymyr Zloy (Wed Oct 20 2004 - 08:25:16 CDT)
- Re: selection of 2 molecules John Stone (Wed Oct 20 2004 - 14:32:47 CDT)
save states with relative directory structure Marc Q. Ma (Wed Oct 20 2004 - 08:00:23 CDT)
- Re: save states with relative directory structure John Stone (Wed Oct 20 2004 - 09:40:09 CDT)
- Re: save states with relative directory structure Axel Kohlmeyer (Wed Oct 20 2004 - 11:15:27 CDT)
xyz pinisetty dinesh (Tue Oct 19 2004 - 18:18:11 CDT)
- Re: xyz John Stone (Tue Oct 19 2004 - 18:41:03 CDT)
change color from script S.G.Falkovich (Wed Oct 13 2004 - 04:27:06 CDT)
- Re: change color from script John Stone (Fri Oct 15 2004 - 10:44:47 CDT)
  - outputing xyz coordinates of selection Amarda Shehu (Sat Oct 23 2004 - 14:58:21 CDT)
    - Re: outputing xyz coordinates of selection John Stone (Mon Oct 25 2004 - 13:25:50 CDT)
RE: VMD on Linux Fedora Core 2 EPF $Esben Peter Friis$ (Wed Oct 13 2004 - 10:20:43 CDT)
- Re: VMD on Linux Fedora Core 2 Eugen Leitl (Fri Oct 15 2004 - 01:24:29 CDT)
Changing the rotation and centering matrix of a molecule CHAUMONT Alain (Wed Oct 13 2004 - 10:39:48 CDT)
- Re: Changing the rotation and centering matrix of a molecule Justin Gullingsrud (Wed Oct 13 2004 - 13:29:24 CDT)
VMD on Linux Fedora Core 2 Fernandez-Alonso, F (Felix) (Wed Oct 13 2004 - 06:53:05 CDT)
- Re: VMD on Linux Fedora Core 2 Y U Sasidhar (Wed Oct 13 2004 - 08:46:24 CDT)
- Re: VMD on Linux Fedora Core 2 Bogdan Costescu (Wed Oct 13 2004 - 09:11:15 CDT)
  - Re: VMD on Linux Fedora Core 2 Eugen Leitl (Wed Oct 13 2004 - 11:28:18 CDT)
- Re: VMD on Linux Fedora Core 2 Brian Bennion (Wed Oct 13 2004 - 12:26:39 CDT)
- RE: VMD on Linux Fedora Core 2 Luis Rosales (Wed Oct 13 2004 - 17:10:31 CDT)
- Re: VMD on Linux Fedora Core 2 John Stone (Thu Oct 14 2004 - 21:30:29 CDT)
Changing color of a given atom Hess, Bret (Mon Oct 11 2004 - 18:31:03 CDT)
- Re: Changing color of a given atom Axel Kohlmeyer (Wed Oct 13 2004 - 00:52:36 CDT)
Specifying distances for bond cutoffs? Hess, Bret (Mon Oct 11 2004 - 18:24:06 CDT)
- Re: Specifying distances for bond cutoffs? Axel Kohlmeyer (Wed Oct 13 2004 - 00:46:39 CDT)
Re: namd-l: counterion software mashaojie163 (Mon Oct 11 2004 - 01:30:48 CDT)
problem_1 vivek sharma (Sat Oct 09 2004 - 01:16:55 CDT)
RE: measure fit error?? mdcooper (Fri Oct 08 2004 - 17:35:37 CDT)
- Re: measure fit error?? Justin Gullingsrud (Sat Oct 09 2004 - 00:41:49 CDT)
PSFGEN problem mdcooper (Fri Oct 08 2004 - 15:54:58 CDT)
- Re: PSFGEN problem Brian Bennion (Fri Oct 08 2004 - 21:58:07 CDT)
CMAP and psfgen Jorge Pikunic (Fri Oct 08 2004 - 12:38:47 CDT)
- Re: CMAP and psfgen Justin Gullingsrud (Fri Oct 08 2004 - 14:57:48 CDT)
problem vivek sharma (Fri Oct 08 2004 - 09:01:52 CDT)
- Re: problem J. Rui Rodrigues (Fri Oct 08 2004 - 10:18:30 CDT)
- Re: problem Jorge Pikunic (Fri Oct 08 2004 - 10:29:25 CDT)
- Re: problem Luis Gracia (Fri Oct 08 2004 - 12:53:03 CDT)
measure fit error?? mashaojie163 (Fri Oct 08 2004 - 07:28:20 CDT)
- Re: measure fit error?? bora erdemli (Fri Oct 08 2004 - 12:29:22 CDT)
  - Re: measure fit error?? Justin Gullingsrud (Fri Oct 08 2004 - 14:26:10 CDT)
RE: amd64/nvidiaFX1100/linux crash David A. Horita (Tue Oct 05 2004 - 17:19:49 CDT)
amd64/nvidiaFX1100/linux crash David A. Horita (Tue Oct 05 2004 - 16:00:07 CDT)
- Re: amd64/nvidiaFX1100/linux crash John Stone (Tue Oct 05 2004 - 16:50:30 CDT)
dihedral angles at the ends Meric Ayse Ovacik (Sat Oct 02 2004 - 06:42:20 CDT)
- Re: dihedral angles at the ends Brian Bennion (Tue Oct 05 2004 - 11:44:53 CDT)
only show some HBonds ioana_at_pegasus.arc.nasa.gov (Fri Oct 01 2004 - 20:59:35 CDT)
- Re: only show some HBonds Sanjeev B.S. (Sat Oct 02 2004 - 00:20:11 CDT)
docking Adam Kubach (Wed Sep 29 2004 - 20:20:38 CDT)
- Re: docking John Stone (Wed Sep 29 2004 - 20:33:05 CDT)
  - AutoIMD Luis Rosales (Wed Oct 06 2004 - 02:50:02 CDT)
Feature request: modify several representations at the same time Luis Gracia (Wed Sep 29 2004 - 15:37:06 CDT)
Writing pdb files for trajectory frames Raymond C. Fort Jr. (Wed Sep 29 2004 - 15:18:41 CDT)
- Re: Writing pdb files for trajectory frames John Stone (Wed Sep 29 2004 - 15:22:49 CDT)
Can we fix the position of two atoms while minimization? Shahid Qamar (Wed Sep 29 2004 - 10:39:50 CDT)
- Re: Can we fix the position of two atoms while minimization? John Stone (Wed Sep 29 2004 - 12:40:52 CDT)
problem in autoionize bora erdemli (Wed Sep 29 2004 - 08:43:05 CDT)
- Re: problem in autoionize John Stone (Wed Sep 29 2004 - 09:37:19 CDT)
  - Re: problem in autoionize bora erdemli (Thu Sep 30 2004 - 01:38:51 CDT)
How does VMD predict alpha helices Scott Pendley (Tue Sep 28 2004 - 12:18:11 CDT)
- Re: How does VMD predict alpha helices John Stone (Tue Sep 28 2004 - 12:26:09 CDT)
Defining graphics colors hinsen_at_llb.saclay.cea.fr (Tue Sep 28 2004 - 12:15:05 CDT)
- Re: Defining graphics colors John Stone (Tue Sep 28 2004 - 12:31:28 CDT)
  - Re: Defining graphics colors hinsen_at_llb.saclay.cea.fr (Wed Sep 29 2004 - 03:45:18 CDT)
  - Re: Defining graphics colors hinsen_at_llb.saclay.cea.fr (Thu Sep 30 2004 - 03:34:26 CDT)
    - Re: Defining graphics colors John Stone (Thu Sep 30 2004 - 14:09:38 CDT)
    - Re: Defining graphics colors John Stone (Mon Oct 25 2004 - 14:33:57 CDT)
Phosphate mass Manuel Rueda (Tue Sep 28 2004 - 08:43:52 CDT)
Phosphate mass Manuel Rueda (Tue Sep 28 2004 - 07:55:44 CDT)
- Re: Phosphate mass John Stone (Tue Sep 28 2004 - 09:55:29 CDT)
rmsd calculation and alignment bora erdemli (Tue Sep 28 2004 - 07:28:15 CDT)
- Re: rmsd calculation and alignment mashaojie163 (Tue Sep 28 2004 - 10:46:15 CDT)
- Re: rmsd calculation and alignment lug2002_at_med.cornell.edu (Tue Sep 28 2004 - 11:27:10 CDT)
measure fit error?? mashaojie163 (Mon Sep 27 2004 - 23:12:22 CDT)
tkcon problem with my vmd dong (Mon Sep 27 2004 - 12:07:50 CDT)
- Re: tkcon problem with my vmd John Stone (Mon Sep 27 2004 - 13:21:24 CDT)
  - ´ð¸´: tkcon problem with my vmd dong (Tue Sep 28 2004 - 01:54:33 CDT)
Python error Vlad Cojocaru (Mon Sep 27 2004 - 12:33:47 CDT)
- Re: Python error John Stone (Mon Sep 27 2004 - 13:49:25 CDT)
how can I get hole program mashaojie163 (Sat Sep 25 2004 - 19:34:17 CDT)
- Re: how can I get hole program John Stone (Tue Sep 28 2004 - 14:59:18 CDT)
  - Re: how can I get hole program mashaojie163 (Tue Sep 28 2004 - 20:01:30 CDT)
    - Re: how can I get hole program John Stone (Wed Sep 29 2004 - 10:08:01 CDT)
  - Re: how can I get hole program mashaojie163 (Wed Sep 29 2004 - 20:06:05 CDT)
IMD Plugin Errors Shirley Hui (Sat Feb 21 2004 - 21:18:12 CST)
- Re: IMD Plugin Errors John Stone (Tue Sep 28 2004 - 15:01:04 CDT)
Flexible Water molecules Shirley Hui (Sat Feb 21 2004 - 17:54:00 CST)
- Re: Flexible Water molecules Jim Phillips (Fri Sep 24 2004 - 19:02:37 CDT)
Problems with PSFGEN in Simulation of Water Permeation through nanotubes David L. Azevedo (Fri Sep 24 2004 - 08:52:13 CDT)
Updating atom names/types in xyz-files Pär Olsson (Fri Sep 24 2004 - 02:24:29 CDT)
- Re: Updating atom names/types in xyz-files John Stone (Fri Sep 24 2004 - 10:57:41 CDT)
How do I set the color scale for beta? Brian Smith (Fri Sep 24 2004 - 01:43:31 CDT)
- Re: How do I set the color scale for beta? John Stone (Fri Sep 24 2004 - 10:06:15 CDT)
Hydrogen bond representation and cut off distance Uday Chippada (Thu Sep 23 2004 - 13:53:51 CDT)
- Re: Hydrogen bond representation and cut off distance John Stone (Fri Sep 24 2004 - 10:51:02 CDT)
quitting VMD mdcooper (Thu Sep 23 2004 - 12:55:09 CDT)
- Re: quitting VMD John Stone (Thu Sep 23 2004 - 13:22:48 CDT)
question about rendering images cpao_at_Princeton.EDU (Wed Sep 22 2004 - 16:54:38 CDT)
- Re: question about rendering images John Stone (Wed Sep 22 2004 - 17:07:11 CDT)
displaying neighboring residues Stern, Julie (Wed Sep 22 2004 - 11:54:26 CDT)
- Re: displaying neighboring residues John Stone (Wed Sep 22 2004 - 12:36:51 CDT)
superimposing frames Amarda Shehu (Wed Sep 22 2004 - 10:51:57 CDT)
- Re: superimposing frames John Stone (Wed Sep 22 2004 - 11:15:19 CDT)
  - Re: superimposing frames Amarda Shehu (Wed Sep 22 2004 - 12:16:56 CDT)
  - Re: superimposing frames Luis Gracia (Wed Sep 22 2004 - 14:23:04 CDT)
problems with vecdist in accepting variables Jerry Ebalunode (Tue Sep 21 2004 - 04:38:01 CDT)
- Re: problems with vecdist in accepting variables Justin Gullingsrud (Tue Sep 21 2004 - 12:43:23 CDT)
  - Re: problems with vecdist in accepting variables Jerry Ebalunode (Tue Sep 21 2004 - 11:27:15 CDT)
    - Re: problems with vecdist in accepting variables John Stone (Tue Sep 21 2004 - 16:40:26 CDT)
Phantom and VMD Adam Kubach (Mon Sep 20 2004 - 15:18:18 CDT)
- Re: Phantom and VMD John Stone (Mon Sep 20 2004 - 15:58:40 CDT)
BUG with MODEL card in PDB file Nicholson, James D Mr ARO (Mon Sep 20 2004 - 15:34:41 CDT)
- Re: BUG with MODEL card in PDB file John Stone (Mon Sep 20 2004 - 15:39:29 CDT)
  - Re: BUG with MODEL card in PDB file John Stone (Mon Sep 20 2004 - 16:02:12 CDT)
(no subject) mdcooper (Mon Sep 20 2004 - 13:14:02 CDT)
- Re: John Stone (Mon Sep 20 2004 - 13:26:17 CDT)
how to make a snapshot that... Margaret Shun Cheung (Mon Sep 20 2004 - 11:09:59 CDT)
- Re: how to make a snapshot that... John Stone (Mon Sep 20 2004 - 13:23:14 CDT)
  - Re: how to make a snapshot that... Margaret Shun Cheung (Mon Sep 20 2004 - 14:46:29 CDT)
  - Re: how to make a snapshot that... Margaret Shun Cheung (Fri Sep 24 2004 - 10:48:09 CDT)
    - Re: how to make a snapshot that... John Stone (Mon Sep 27 2004 - 09:29:40 CDT)
Quadro 750 XGL problem Sylvain EDALEINE (Mon Sep 20 2004 - 09:38:22 CDT)
- Re: Quadro 750 XGL problem John Stone (Mon Sep 20 2004 - 09:44:11 CDT)
  - Re: Quadro 750 XGL problem John Stone (Tue Sep 21 2004 - 09:56:16 CDT)
Sharp 3D stereo monitors Mads Nørregaard-Madsen (Mon Sep 20 2004 - 06:11:02 CDT)
- Re: Sharp 3D stereo monitors John Stone (Mon Sep 20 2004 - 09:04:07 CDT)
measuring h-bonds Alicia Hopkins (Sun Sep 19 2004 - 08:42:12 CDT)
- Re: measuring h-bonds Marcos Sotomayor (Sun Sep 19 2004 - 14:08:04 CDT)
MSMS under Windows Oleg V. Stroganov (Sun Sep 19 2004 - 06:33:40 CDT)
- Re: MSMS under Windows John Stone (Mon Sep 20 2004 - 15:37:30 CDT)
measuring h-bonds Alicia Hopkins (Thu Sep 16 2004 - 09:24:33 CDT)
- Re: measuring h-bonds Axel Kohlmeyer (Fri Sep 17 2004 - 01:16:45 CDT)
Away from email until Sunday... John Stone (Wed Sep 15 2004 - 17:48:55 CDT)
Getting started with VMD/freeVR plbrown_at_cs.duke.edu (Wed Sep 15 2004 - 08:14:08 CDT)
- Re: Getting started with VMD/freeVR John Stone (Wed Sep 15 2004 - 13:20:03 CDT)
New Athlon64/Opteron AMD64/EMT64 test version... John Stone (Tue Sep 14 2004 - 16:49:29 CDT)
- Re: New Athlon64/Opteron AMD64/EMT64 test version... Jerry Ebalunode (Tue Sep 14 2004 - 13:48:44 CDT)
  - Re: New Athlon64/Opteron AMD64/EMT64 test version... John Stone (Tue Sep 14 2004 - 21:35:21 CDT)
Counting number of hydrogen bonds in the representation Uday K. Chippada (Tue Sep 14 2004 - 16:38:20 CDT)
- RE: Counting number of hydrogen bonds in the representation Ahmet Bakan (Wed Sep 15 2004 - 03:39:56 CDT)
  - Re: Counting number of hydrogen bonds in the representation Justin Gullingsrud (Wed Sep 15 2004 - 07:30:39 CDT)
    - RE: Counting number of hydrogen bonds in the representation Ahmet Bakan (Wed Sep 15 2004 - 07:44:29 CDT)
    - Re: RE: Counting number of hydrogen bonds in the representation Uday K. Chippada (Wed Sep 15 2004 - 13:21:59 CDT)
Solvate Shirley Hui (Tue Sep 14 2004 - 08:16:14 CDT)
- Re: Solvate John Stone (Wed Sep 15 2004 - 13:23:15 CDT)
Default resource file (.vmdrc) Gustavo Mercier (Mon Sep 13 2004 - 15:41:02 CDT)
- Re: Default resource file (.vmdrc) John Stone (Mon Sep 13 2004 - 15:59:23 CDT)
error python effekri_at_infinito.it (Mon Sep 13 2004 - 02:18:25 CDT)
- Re: error python John Stone (Mon Sep 13 2004 - 10:02:20 CDT)
measuring h-bond distances Alicia Hopkins (Sat Sep 11 2004 - 12:01:58 CDT)
- Re: measuring h-bond distances Axel Kohlmeyer (Sun Sep 12 2004 - 06:18:27 CDT)
Compiling NAMD from SRC: Tungsten@NCSA Vani Krishna (Fri Sep 10 2004 - 19:54:55 CDT)
- Re: Compiling NAMD from SRC: Tungsten@NCSA John Stone (Fri Sep 10 2004 - 20:16:25 CDT)
dynamic bonds question?? David Schall (Thu Sep 09 2004 - 16:20:47 CDT)
- Re: dynamic bonds question?? John Stone (Thu Sep 09 2004 - 17:38:07 CDT)
Changing the atom species during animation Oliver Lanning (Wed Sep 08 2004 - 02:59:11 CDT)
- Re: Changing the atom species during animation John Stone (Wed Sep 15 2004 - 17:56:07 CDT)
problem with memory S.G.Falkovich (Tue Sep 07 2004 - 04:58:35 CDT)
- Re: problem with memory John Stone (Tue Sep 07 2004 - 10:05:00 CDT)
torsion angle bora erdemli (Mon Sep 06 2004 - 06:18:22 CDT)
- Re: torsion angle Axel Kohlmeyer (Mon Sep 06 2004 - 09:28:52 CDT)
Euro QSAR 2004 Ahmet Bakan (Sun Sep 05 2004 - 15:42:27 CDT)
new user: how to load output file Paul Christopher Millett (Sun Sep 05 2004 - 12:04:40 CDT)
- Re: new user: how to load output file John Stone (Tue Sep 07 2004 - 16:27:38 CDT)
thanks pinisetty dinesh (Fri Sep 03 2004 - 15:19:23 CDT)
- Re: thanks John Stone (Fri Sep 03 2004 - 16:26:44 CDT)
SMD: Group of atoms COM fixed? Vani Krishna (Thu Sep 02 2004 - 20:58:44 CDT)
VMD-VRPN-PHANTOM problem ? Gaurav Sharma (Thu Sep 02 2004 - 02:47:24 CDT)
- Re: VMD-VRPN-PHANTOM problem ? John Stone (Thu Sep 02 2004 - 01:32:22 CDT)
  - Re: VMD-VRPN-PHANTOM problem ? Marc Baaden (Thu Sep 02 2004 - 05:00:44 CDT)
    - Re: VMD-VRPN-PHANTOM problem ? John Stone (Thu Sep 02 2004 - 09:50:23 CDT)
    - Re: VMD-VRPN-PHANTOM problem ? Marc Baaden (Thu Sep 02 2004 - 09:59:58 CDT)
  - Align a PORTION of several structures Shirley Li (Wed Oct 13 2004 - 18:05:01 CDT)
    - Re: Align a PORTION of several structures Justin Gullingsrud (Thu Oct 14 2004 - 09:54:45 CDT)
    - Re: Align a PORTION of several structures Shirley Li (Fri Oct 15 2004 - 09:33:00 CDT)
RE: xyz-file loading Kooser, Ara S (Wed Sep 01 2004 - 15:32:50 CDT)
xyz-file loading pinisetty dinesh (Wed Sep 01 2004 - 12:50:06 CDT)
- Re: xyz-file loading John Stone (Wed Sep 01 2004 - 13:14:24 CDT)
Extensions question Troy Wymore (Wed Sep 01 2004 - 11:28:31 CDT)
- Re: Extensions question John Stone (Wed Sep 01 2004 - 13:45:20 CDT)
g03 output and editing features for VMD Vlad Cojocaru (Mon Aug 30 2004 - 11:03:41 CDT)
- Re: g03 output and editing features for VMD John Stone (Mon Aug 30 2004 - 11:18:25 CDT)
Protonated GLU/ASP in PSF generation Vani Krishna (Sun Aug 29 2004 - 16:23:00 CDT)
- Re: Protonated GLU/ASP in PSF generation Justin Gullingsrud (Sun Aug 29 2004 - 21:01:52 CDT)
VRML2 export and viewpoints Marc Baaden (Sun Aug 29 2004 - 05:37:28 CDT)
- Re: VRML2 export and viewpoints John Stone (Tue Aug 31 2004 - 15:06:35 CDT)
  - Re: VRML2 export and viewpoints Marc Baaden (Tue Aug 31 2004 - 16:36:05 CDT)
convert DCD files to GROMACS .XTC format Vani Krishna (Sat Aug 28 2004 - 17:43:11 CDT)
- Re: convert DCD files to GROMACS .XTC format John Stone (Tue Aug 31 2004 - 15:11:09 CDT)
Fullerene coordinates #WONG CHEE HOW# (Fri Aug 27 2004 - 03:50:03 CDT)
- Re: Fullerene coordinates lothar esser (Fri Aug 27 2004 - 08:21:41 CDT)
Area per lipid Saladino, Alex (Thu Aug 26 2004 - 11:00:55 CDT)
Installation on vmd-1.8 on mandrake10 Priti Hansia (Thu Aug 26 2004 - 10:47:22 CDT)
- rmsd problem bora erdemli (Thu Aug 26 2004 - 14:10:05 CDT)
  - Re: rmsd problem John Stone (Tue Aug 31 2004 - 15:11:47 CDT)
    - rmsd problem,script and version bora erdemli (Fri Sep 03 2004 - 00:23:42 CDT)
- Re: Installation on vmd-1.8 on mandrake10 John Stone (Thu Aug 26 2004 - 14:09:52 CDT)
  - Re: Installation on vmd-1.8 on mandrake10 Priti Hansia (Thu Aug 26 2004 - 23:06:11 CDT)
VMD on NetBSD Lubos Vrbka (Thu Aug 26 2004 - 04:28:53 CDT)
- Re: VMD on NetBSD John Stone (Thu Aug 26 2004 - 14:07:43 CDT)
  - Re: VMD on NetBSD John Stone (Fri Aug 27 2004 - 17:21:39 CDT)
RE: namd-l: cff91 force field in namd + A Question Ahmet Bakan (Wed Aug 25 2004 - 10:53:59 CDT)
ATI fglrx 3.11 drivers for Radeon 8500 LE with linux 2.6 kernel, quad buffered stereo on sony G520??? Dr. Daniel James White PhD (Wed Aug 25 2004 - 03:44:24 CDT)
- Re: ATI fglrx 3.11 drivers for Radeon 8500 LE with linux 2.6 kernel, quad buffered stereo on sony G520??? John Stone (Wed Aug 25 2004 - 09:23:09 CDT)
Weird lighting in CAVE by way of Jeroen Akershoek (Wed Aug 25 2004 - 03:24:00 CDT)
- Re: Weird lighting in CAVE John Stone (Thu Aug 26 2004 - 14:16:51 CDT)
RMSDTT plugin Luis Gracia (Tue Aug 24 2004 - 17:21:35 CDT)
Gaussian03 output Vlad Cojocaru (Tue Aug 24 2004 - 10:09:27 CDT)
center of mass position Andre Farias de Moura (Tue Aug 24 2004 - 07:07:24 CDT)
- Re: center of mass position John Stone (Tue Aug 24 2004 - 10:03:40 CDT)
  - to get SURFACE CHARGE DISTRIBUTION of protein Shirley Li (Tue Aug 24 2004 - 13:12:51 CDT)
    - Re: to get SURFACE CHARGE DISTRIBUTION of protein John Stone (Tue Aug 31 2004 - 15:35:15 CDT)
problem vivek sharma (Tue Aug 24 2004 - 08:46:56 CDT)
- Re: problem John Stone (Tue Aug 24 2004 - 09:33:01 CDT)
  - Re: problem vivek sharma (Wed Feb 09 2005 - 23:50:37 CST)
Molscript Eckhart Guthöhrlein (Tue Aug 24 2004 - 06:16:30 CDT)
- Re: Molscript John Stone (Tue Aug 24 2004 - 09:41:23 CDT)
  - Re: Molscript Eckhart Guthöhrlein (Wed Aug 25 2004 - 04:05:04 CDT)
no main window Eckhart Guthöhrlein (Tue Aug 24 2004 - 06:11:06 CDT)
- Re: no main window J. Rui Rodrigues (Tue Aug 24 2004 - 06:21:44 CDT)
  - Re: no main window John Stone (Tue Aug 24 2004 - 09:18:44 CDT)
    - Re: no main window Eckhart Guthöhrlein (Tue Aug 24 2004 - 09:25:07 CDT)
Periodic display problem Keith Refson (Tue Aug 24 2004 - 05:34:31 CDT)
- Re: Periodic display problem John Stone (Tue Aug 24 2004 - 09:29:15 CDT)
  - Re: Periodic display problem John Stone (Tue Aug 24 2004 - 12:44:43 CDT)
    - Re: Periodic display problem Axel Kohlmeyer (Wed Aug 25 2004 - 01:52:26 CDT)
    - Re: Periodic display problem John Stone (Wed Aug 25 2004 - 10:18:51 CDT)
  - Re: Periodic display problem John Stone (Thu Aug 26 2004 - 14:04:59 CDT)
- Re: Periodic display problem Axel Kohlmeyer (Tue Aug 24 2004 - 09:56:02 CDT)
  - Re: Periodic display problem John Stone (Tue Aug 24 2004 - 10:13:25 CDT)
How to select water molecules within certain distance from a protein Sekwan Oh (Tue Aug 24 2004 - 03:44:57 CDT)
- Re: How to select water molecules within certain distance from a protein John Stone (Fri Aug 27 2004 - 15:27:01 CDT)
python callbacks Travis DePuy (Mon Aug 23 2004 - 16:56:25 CDT)
- Re: python callbacks John Stone (Tue Aug 31 2004 - 15:26:21 CDT)
vmd port on FreeBSD Stephen Montgomery-Smith (Sat Aug 21 2004 - 12:20:52 CDT)
- Re: vmd port on FreeBSD Osmany Guirola Cruz (Mon Aug 23 2004 - 09:36:35 CDT)
  - Re: vmd port on FreeBSD Stephen Montgomery-Smith (Mon Aug 23 2004 - 09:49:31 CDT)
    - Re: vmd port on FreeBSD Osmany Guirola Cruz (Mon Aug 23 2004 - 10:42:03 CDT)
Installer problem Peter Freddolino (Sat Aug 21 2004 - 09:55:02 CDT)
- Re: Installer problem John Stone (Sat Aug 21 2004 - 12:20:36 CDT)
Activation energy Alexis Salas (Thu Aug 19 2004 - 13:33:36 CDT)
VMD too slow on my Linux system preethi_at_bu.edu (Thu Aug 19 2004 - 11:33:48 CDT)
- Re: VMD too slow on my Linux system John Stone (Fri Aug 20 2004 - 14:06:23 CDT)
  - Re: VMD too slow on my Linux system preethi_at_bu.edu (Mon Aug 23 2004 - 09:34:38 CDT)
makefile not generated from configure rossi_at_york.cuny.edu (Wed Aug 18 2004 - 19:05:15 CDT)
- Re: makefile not generated from configure Brian Bennion (Thu Aug 19 2004 - 12:24:13 CDT)
  - Re: makefile not generated from configure rossi_at_york.cuny.edu (Thu Aug 19 2004 - 14:12:29 CDT)
monitoring h bonds bora erdemli (Wed Aug 18 2004 - 08:59:56 CDT)
- Re: monitoring h bonds John Stone (Mon Aug 23 2004 - 14:03:01 CDT)
  - Re: monitoring h bonds bora erdemli (Tue Aug 24 2004 - 06:52:50 CDT)
    - Re: monitoring h bonds John Stone (Tue Aug 24 2004 - 09:58:04 CDT)
multiple entry mol2 file Jerry Ebalunode (Tue Aug 17 2004 - 07:15:05 CDT)
- Re: multiple entry mol2 file John Stone (Tue Aug 17 2004 - 12:56:43 CDT)
  - Re: multiple entry mol2 file John Stone (Wed Sep 15 2004 - 16:45:38 CDT)
Plugins and did I compile VMD correctly? Stephen Montgomery-Smith (Thu Aug 12 2004 - 11:05:49 CDT)
- Re: Plugins and did I compile VMD correctly? John Stone (Thu Aug 12 2004 - 16:14:01 CDT)
  - Re: Plugins and did I compile VMD correctly? Stephen Montgomery-Smith (Thu Aug 12 2004 - 16:51:42 CDT)
    - Re: Plugins and did I compile VMD correctly? John Stone (Thu Aug 12 2004 - 18:13:01 CDT)
    - FreeBSD port Stephen Montgomery-Smith (Thu Aug 12 2004 - 23:20:56 CDT)
Windows XP SP2 and some OpenGL drivers.... John Stone (Wed Aug 11 2004 - 15:35:03 CDT)
VolumeSlice matteo (Tue Aug 10 2004 - 16:29:47 CDT)
- Re: VolumeSlice John Stone (Tue Aug 10 2004 - 16:41:24 CDT)
analysis scripts: VMD text /batch mode Vani Krishna (Tue Aug 10 2004 - 11:46:12 CDT)
- Re: analysis scripts: VMD text /batch mode John Stone (Tue Aug 10 2004 - 13:03:22 CDT)
- Re: analysis scripts: VMD text /batch mode Justin Gullingsrud (Tue Aug 10 2004 - 13:31:01 CDT)
VideoMach/personable Label/label by ResName Shirley Li (Mon Aug 09 2004 - 14:53:32 CDT)
- Re: VideoMach/personable Label/label by ResName John Stone (Mon Aug 09 2004 - 16:10:23 CDT)
  - Re: VideoMach/personable Label/label by ResName Shirley Li (Mon Aug 09 2004 - 21:03:33 CDT)
    - Re: VideoMach/personable Label/label by ResName John Stone (Mon Aug 09 2004 - 23:27:28 CDT)
translating a molecule Marcela Madrid (Sat Aug 07 2004 - 15:00:31 CDT)
- Re: translating a molecule John Stone (Mon Aug 09 2004 - 10:11:45 CDT)
Changing the label for resname Sunita Patel (Mon Aug 09 2004 - 09:44:03 CDT)
- Re: Changing the label for resname John Stone (Mon Aug 09 2004 - 16:06:46 CDT)
molecular surface/multiple trajectory files/the speed in animation Shirley Li (Sun Aug 08 2004 - 19:26:56 CDT)
- Re: molecular surface/multiple trajectory files/the speed in animation John Stone (Mon Aug 09 2004 - 16:17:12 CDT)
  - Re: molecular surface/multiple trajectory files/the speed in animation Shirley Li (Mon Aug 09 2004 - 20:51:00 CDT)
Trajectory Files Travis DePuy (Fri Aug 06 2004 - 18:03:32 CDT)
- Re: Trajectory Files Axel Kohlmeyer (Sun Aug 08 2004 - 13:36:35 CDT)
- Re: Trajectory Files John Stone (Mon Aug 09 2004 - 10:08:36 CDT)
CVS access is back online... John Stone (Fri Aug 06 2004 - 10:12:15 CDT)
- Re: CVS access is back online... Jerry Ebalunode (Fri Aug 06 2004 - 06:53:15 CDT)
  - Re: CVS access is back online... John Stone (Fri Aug 06 2004 - 16:08:41 CDT)
How to Solvate protiens in any other solvent Shahid Qamar (Tue Aug 03 2004 - 17:19:53 CDT)
- Re: How to Solvate protiens in any other solvent John Stone (Wed Aug 04 2004 - 17:11:26 CDT)
Solvating with TIP4 or SPC Alexis Salas (Tue Aug 03 2004 - 16:01:03 CDT)
- Re: Solvating with TIP4 or SPC Brian Bennion (Wed Aug 04 2004 - 10:43:19 CDT)
TIP3 by TIP4 Alexis Salas (Tue Aug 03 2004 - 13:57:40 CDT)
progports, new project vmd-l_at_spider.med.jhmi.edu (Tue Aug 03 2004 - 11:02:09 CDT)
Nightly VMD web updates running again... John Stone (Tue Aug 03 2004 - 10:20:37 CDT)
Loading a script Prasad S Garimella (Mon Aug 02 2004 - 17:21:31 CDT)
- Re: Loading a script John Stone (Mon Aug 02 2004 - 17:48:04 CDT)
CVS root directory not found Jerry Ebalunode (Mon Aug 02 2004 - 10:57:47 CDT)
- Re: CVS root directory not found John Stone (Mon Aug 02 2004 - 16:10:27 CDT)
readable files pinisetty dinesh (Mon Aug 02 2004 - 14:47:58 CDT)
- Re: readable files John Stone (Mon Aug 02 2004 - 15:50:33 CDT)
- Re: readable files J. Rui Rodrigues (Mon Aug 02 2004 - 15:58:29 CDT)
How i can changue the charge of my protein Alexis Salas (Mon Aug 02 2004 - 13:13:06 CDT)
- Re: How i can changue the charge of my protein Justin Gullingsrud (Mon Aug 02 2004 - 16:06:43 CDT)
Error in modifying and concatenating two pdb files into one [plz Help!] Sekwan Oh (Fri Jul 30 2004 - 20:30:22 CDT)
- Re: Error in modifying and concatenating two pdb files into one [plz Help!] John Stone (Mon Aug 02 2004 - 09:59:02 CDT)
How to enable Python on Windows XP Ahmet Bakan (Fri Jul 30 2004 - 16:30:09 CDT)
- Re: How to enable Python on Windows XP DePuy (Sat Jul 31 2004 - 17:12:20 CDT)
- Re: How to enable Python on Windows XP John Stone (Mon Aug 02 2004 - 10:00:44 CDT)
1.8.3 Daniel B. Faken (Fri Jul 30 2004 - 09:36:52 CDT)
- Re: 1.8.3 John Stone (Fri Jul 30 2004 - 14:33:35 CDT)
tcl: wait for exec Luis Gracia (Thu Jul 29 2004 - 19:09:04 CDT)
- Re: tcl: wait for exec John Stone (Thu Jul 29 2004 - 21:50:46 CDT)
  - Re: tcl: wait for exec Luis Gracia (Fri Jul 30 2004 - 14:26:52 CDT)
shake vs. rigidbonds Sheldon Park (Thu Jul 29 2004 - 14:29:12 CDT)
GLXBadLargeRequest Ryan Golhar (Thu Jul 29 2004 - 13:52:35 CDT)
- Re: GLXBadLargeRequest John Stone (Thu Jul 29 2004 - 14:03:00 CDT)
  - RE: GLXBadLargeRequest Ryan Golhar (Thu Jul 29 2004 - 14:20:06 CDT)
    - Re: GLXBadLargeRequest John Stone (Thu Jul 29 2004 - 18:14:05 CDT)
(no subject) Karunesh Arora (Thu Jul 29 2004 - 10:09:40 CDT)
- Re: your mail Jim Phillips (Thu Jul 29 2004 - 10:45:14 CDT)
- Re: your mail John Stone (Thu Jul 29 2004 - 10:46:44 CDT)
stereo with GForce video board Anna Modzelewska (Thu Jul 29 2004 - 04:20:31 CDT)
- Re: stereo with GForce video board John Stone (Thu Jul 29 2004 - 10:58:05 CDT)
Compiling VMD Ryan Golhar (Wed Jul 28 2004 - 21:20:12 CDT)
- Re: Compiling VMD John Stone (Thu Jul 29 2004 - 10:49:14 CDT)
angles pinisetty dinesh (Wed Jul 28 2004 - 21:11:12 CDT)
- Re: angles John Stone (Thu Jul 29 2004 - 10:53:38 CDT)
python callback!!!! Anand Kaushal (Wed Jul 28 2004 - 16:19:15 CDT)
XYZ file to video John M. Kolinski (Wed Jul 28 2004 - 08:26:10 CDT)
- Re: XYZ file to video John Stone (Wed Jul 28 2004 - 08:42:17 CDT)
movie showing loop movement Min Wu (Wed Jul 28 2004 - 01:54:51 CDT)
- Re: movie showing loop movement Sanjeev B.S. (Wed Jul 28 2004 - 03:20:43 CDT)
  - Re: movie showing loop movement Min Wu (Wed Jul 28 2004 - 17:57:37 CDT)
    - Re: movie showing loop movement John Stone (Thu Jul 29 2004 - 18:15:03 CDT)
  - Re: movie showing loop movement Karsten Suhre (Thu Jul 29 2004 - 01:43:24 CDT)
Tachyon Internal Rendering Anthony Ivetac (Mon Jul 26 2004 - 08:34:05 CDT)
- Re: Tachyon Internal Rendering John Stone (Mon Jul 26 2004 - 09:41:27 CDT)
  - Rendering Harindar Keer (Thu Jul 29 2004 - 17:49:51 CDT)
    - Re: Rendering John Stone (Thu Jul 29 2004 - 17:54:11 CDT)
Extensions to the selection language Olaf Lenz (Thu Jul 22 2004 - 11:08:38 CDT)
loading compressed trajectory files Vlad Cojocaru (Wed Jul 21 2004 - 05:49:17 CDT)
mol clipplane very slow Simon Latapie (Wed Jul 21 2004 - 02:03:44 CDT)
- Re: mol clipplane very slow John Stone (Wed Jul 21 2004 - 09:50:13 CDT)
reading structure *.xyz Luciano (Tue Jul 20 2004 - 13:57:30 CDT)
- Re: reading structure *.xyz Axel Kohlmeyer (Tue Jul 20 2004 - 17:39:02 CDT)
loading .gz trajectory files Vlad Cojocaru (Tue Jul 20 2004 - 12:56:38 CDT)
- Re: loading .gz trajectory files Axel Kohlmeyer (Tue Jul 20 2004 - 17:12:47 CDT)
Unit cell coordinates and radial distribution functions Ben Roberts (Mon Jul 19 2004 - 21:12:38 CDT)
- Re: Unit cell coordinates and radial distribution functions Axel Kohlmeyer (Tue Jul 20 2004 - 01:29:03 CDT)
  - Re: Unit cell coordinates and radial distribution functions Ben Roberts (Thu Jul 22 2004 - 20:27:18 CDT)
VMD slowdown on MacOS X 10.3.4 Lance Pickens (Mon Jul 19 2004 - 20:29:31 CDT)
- Re: VMD slowdown on MacOS X 10.3.4 John Stone (Tue Jul 20 2004 - 11:01:54 CDT)
  - Re: VMD slowdown on MacOS X 10.3.4 Lance Pickens (Tue Jul 20 2004 - 14:20:24 CDT)
    - Re: VMD slowdown on MacOS X 10.3.4 John Stone (Wed Jul 21 2004 - 10:31:29 CDT)
molecular dynamics problems vlad.chindea_at_pharmatech.ro (Mon Jul 19 2004 - 15:45:48 CDT)
- Re: molecular dynamics problems nettles (Mon Jul 19 2004 - 16:01:02 CDT)
Axes are not rotated? Olaf Lenz (Mon Jul 19 2004 - 10:12:29 CDT)
- Re: Axes are not rotated? John Stone (Mon Jul 19 2004 - 10:22:44 CDT)
  - Re: Axes are not rotated? Olaf Lenz (Thu Jul 22 2004 - 10:50:06 CDT)
FPS indicator color Olaf Lenz (Mon Jul 19 2004 - 10:06:55 CDT)
- Re: FPS indicator color John Stone (Mon Jul 19 2004 - 10:16:20 CDT)
  - Re: FPS indicator color John Stone (Mon Jul 19 2004 - 11:35:36 CDT)
    - Re: FPS indicator color Olaf Lenz (Tue Jul 20 2004 - 12:06:03 CDT)
    - Re: FPS indicator color John Stone (Wed Jul 21 2004 - 11:12:48 CDT)
visualization of electroly solvation shells Axel Kohlmeyer (Mon Jul 19 2004 - 04:09:34 CDT)
Picking atoms Olaf Lenz (Fri Jul 16 2004 - 10:06:46 CDT)
- Picking atoms: romoving or changing the position of atoms Albert Sun (Sun Jul 18 2004 - 09:17:00 CDT)
  - Re: Picking atoms: romoving or changing the position of atoms Olaf Lenz (Mon Jul 19 2004 - 03:44:44 CDT)
"Selection not understood" Olaf Lenz (Fri Jul 16 2004 - 09:47:04 CDT)
- Re: "Selection not understood" John Stone (Fri Jul 16 2004 - 13:18:59 CDT)
File Reader Plugin Issues Olaf Lenz (Fri Jul 16 2004 - 09:40:33 CDT)
- Re: File Reader Plugin Issues John Stone (Fri Jul 16 2004 - 10:31:22 CDT)
  - Re: File Reader Plugin Issues Olaf Lenz (Mon Jul 19 2004 - 06:14:29 CDT)
Default radii and colors Olaf Lenz (Fri Jul 16 2004 - 09:21:03 CDT)
- Re: Default radii and colors John Stone (Fri Jul 16 2004 - 10:12:01 CDT)
Box of non-polar solvent Raymond C. Fort Jr. (Fri Jul 16 2004 - 09:17:23 CDT)
- Re: Box of non-polar solvent John Stone (Fri Jul 16 2004 - 10:36:28 CDT)
  - Re: Box of non-polar solvent Brian Bennion (Fri Jul 16 2004 - 13:13:01 CDT)
  - Re: Box of non-polar solvent Brian Bennion (Fri Jul 16 2004 - 13:35:28 CDT)
- Re: Box of non-polar solvent Axel Kohlmeyer (Fri Jul 16 2004 - 11:59:45 CDT)
How to read out .vel file from charmm xzp02_at_mails.tsinghua.edu.cn (Fri Jul 16 2004 - 00:00:18 CDT)
problems loading dcd files Patti Schaefer (Thu Jul 15 2004 - 13:55:18 CDT)
- Re: problems loading dcd files John Stone (Thu Jul 15 2004 - 13:58:24 CDT)
vmd psfgen problem with CHARMM Jerry Xu (Thu Jul 15 2004 - 10:28:15 CDT)
- Re: vmd psfgen problem with CHARMM John Stone (Thu Jul 15 2004 - 10:58:58 CDT)
- Re: vmd psfgen problem with CHARMM Bogdan Costescu (Thu Jul 15 2004 - 12:41:16 CDT)
Elliptic molecules Leonid Paramonov (Thu Jul 15 2004 - 07:10:01 CDT)
- Re: Elliptic molecules Olaf Lenz (Thu Jul 15 2004 - 09:56:21 CDT)
  - Re: Elliptic molecules John Stone (Thu Jul 15 2004 - 10:40:55 CDT)
- Re: Elliptic molecules Erik Abrahamsson (Tue Jun 30 2009 - 18:25:41 CDT)
nvidia 6106 kernel drivers and opengl Jerry Ebalunode (Tue Jul 13 2004 - 20:00:21 CDT)
- Re: nvidia 6106 kernel drivers and opengl John Stone (Tue Jul 13 2004 - 21:00:36 CDT)
Updated Bonding Connectivity each frame Kenneth Smith (Tue Jul 13 2004 - 08:27:07 CDT)
- Re: Updated Bonding Connectivity each frame John Stone (Tue Jul 13 2004 - 10:15:33 CDT)
- Re: Updated Bonding Connectivity each frame Axel Kohlmeyer (Tue Jul 13 2004 - 15:28:17 CDT)
Re: [MMTK] Visualization to an image file (fwd from hinsen@cnrs-orleans.fr) Eugen Leitl (Mon Jul 12 2004 - 08:36:58 CDT)
polar surface area with VMD! Ramesh Sistla (Mon Jul 12 2004 - 13:22:48 CDT)
- Re: polar surface area with VMD! John Stone (Mon Jul 12 2004 - 10:10:04 CDT)
Re: coloring.tlc script John Stone (Fri Jul 09 2004 - 16:48:29 CDT)
element Si Peter Deák (Fri Jul 09 2004 - 06:59:03 CDT)
- Re: element Si Axel Kohlmeyer (Fri Jul 09 2004 - 12:11:46 CDT)
RE: vmd 1.8.3a7 no longer works after installing NVIDIA dr iver x86_64 -1.0-6106 Zampighi, Lorenzo (Thu Jul 08 2004 - 17:10:24 CDT)
- Re: vmd 1.8.3a7 no longer works after installing NVIDIA dr iver x86_64 -1.0-6106 John Stone (Thu Jul 08 2004 - 17:21:15 CDT)
vmd 1.8.3a7 no longer works after installing NVIDIA driver x86_64 -1.0-6106 Zampighi, Lorenzo (Thu Jul 08 2004 - 16:31:27 CDT)
- Re: vmd 1.8.3a7 no longer works after installing NVIDIA driver x86_64 -1.0-6106 John Stone (Thu Jul 08 2004 - 16:41:06 CDT)
New and updated VMD plugins posted (update 4, 7/8/2004) John Stone (Thu Jul 08 2004 - 11:08:11 CDT)
Isosurface and stepsize Simon Latapie (Thu Jul 08 2004 - 04:30:34 CDT)
- Re: Isosurface and stepsize John Stone (Fri Jul 09 2004 - 13:09:09 CDT)
I can not load mdcrd file after simulation with sander Valodymyr Nechyporuk-Zloy (Tue Jul 06 2004 - 15:44:57 CDT)
- Re: I can not load mdcrd file after simulation with sander John Stone (Wed Jul 07 2004 - 14:16:33 CDT)
periodic display and space group and VMD Pawel Sikorski (Tue Jul 06 2004 - 09:24:40 CDT)
- Re: periodic display and space group and VMD John Stone (Tue Jul 06 2004 - 10:28:43 CDT)
  - Re: periodic display and space group and VMD Axel Kohlmeyer (Tue Jul 06 2004 - 14:18:34 CDT)
problem with MSMS and VMD james tomomi macdonald (Mon Jul 05 2004 - 11:29:29 CDT)
- Re: problem with MSMS and VMD John Stone (Mon Jul 05 2004 - 14:18:33 CDT)
  - Re: problem with MSMS and VMD james tomomi macdonald (Mon Jul 05 2004 - 16:02:12 CDT)
CONECT in pdb files Travis DePuy (Fri Jul 02 2004 - 14:45:10 CDT)
- Re: CONECT in pdb files Brian Bennion (Fri Jul 02 2004 - 18:01:58 CDT)
- Re: CONECT in pdb files John Stone (Mon Jul 05 2004 - 14:16:13 CDT)
mol clipplane Jiancong Xu (Fri Jul 02 2004 - 14:48:26 CDT)
- Re: mol clipplane John Stone (Mon Jul 05 2004 - 14:12:41 CDT)
autostereograms in VMD? Karsten Suhre (Fri Jul 02 2004 - 02:42:11 CDT)
- Re: autostereograms in VMD? John Stone (Mon Jul 05 2004 - 13:52:38 CDT)
suggested citation vs. pubmed entry Craig Shepherd (Thu Jul 01 2004 - 13:18:58 CDT)
(no subject) ying xiong (Thu Jul 01 2004 - 05:57:28 CDT)
- Re: John Stone (Mon Jul 05 2004 - 14:31:03 CDT)
suggested citation versus pubmed entry Craig Shepherd (Wed Jun 30 2004 - 19:00:19 CDT)
- Re: suggested citation versus pubmed entry John Stone (Mon Jul 05 2004 - 13:58:31 CDT)
(no subject) Sardiu, Mihaela (NIH/NLM/NCBI) (Wed Jun 30 2004 - 17:28:42 CDT)
- Re: John Stone (Mon Jul 05 2004 - 13:57:46 CDT)
  - width for triangle Harindar Keer (Tue Jul 06 2004 - 20:41:58 CDT)
    - Re: width for triangle Axel Kohlmeyer (Wed Jul 07 2004 - 09:06:32 CDT)
(no subject) Sardiu, Mihaela (NIH/NLM/NCBI) (Wed Jun 30 2004 - 17:08:09 CDT)
- Re: John Stone (Wed Jun 30 2004 - 17:16:57 CDT)
Gone until July 6th. John Stone (Wed Jun 30 2004 - 15:59:08 CDT)
Recent VMD-L mails, etc.. John Stone (Wed Jun 30 2004 - 13:40:21 CDT)
(no subject) Heshe Peshkin (Tue Jun 29 2004 - 14:58:01 CDT)
drawing a plane vivek sharma (Tue Jun 29 2004 - 09:30:00 CDT)
- Re: drawing a plane John Stone (Tue Jun 29 2004 - 13:45:14 CDT)
PBCWrap for Gromacs? Xu Zhiping (Tue Jun 29 2004 - 07:19:33 CDT)
- Re: PBCWrap for Gromacs? John Stone (Tue Jun 29 2004 - 13:52:45 CDT)
wrapping DCD files Vani Krishna (Mon Jun 28 2004 - 14:25:24 CDT)
- Re: wrapping DCD files John Stone (Mon Jun 28 2004 - 15:25:39 CDT)
  - PBCwrap: wrapping DCD files Vani Krishna (Mon Jun 28 2004 - 22:03:45 CDT)
    - Re: PBCwrap: wrapping DCD files John Stone (Tue Jun 29 2004 - 13:20:48 CDT)
shifting the origin of the box Vani Krishna (Mon Jun 28 2004 - 13:38:17 CDT)
- Re: shifting the origin of the box John Stone (Mon Jun 28 2004 - 15:24:24 CDT)
isosurface question Randall Hall (Mon Jun 28 2004 - 10:14:20 CDT)
- Re: isosurface question John Stone (Mon Jun 28 2004 - 15:11:03 CDT)
  - Re: isosurface question John Stone (Wed Jun 30 2004 - 13:04:29 CDT)
- Re: isosurface question John Stone (Tue Aug 10 2004 - 16:38:23 CDT)
VMD/NAMD downloads, web site status John Stone (Fri Jun 25 2004 - 17:16:37 CDT)
Transparency rendering Simon Latapie (Fri Jun 25 2004 - 03:28:22 CDT)
- Re: Transparency rendering John Stone (Fri Jun 25 2004 - 18:03:15 CDT)
Average coordinates Ahmet Bakan (Thu Jun 24 2004 - 13:51:12 CDT)
- Re: Average coordinates Axel Kohlmeyer (Thu Jun 24 2004 - 23:48:36 CDT)
Making movies balas002_at_bama.ua.edu (Tue Jun 22 2004 - 16:15:27 CDT)
- Re: Making movies John Stone (Tue Jun 22 2004 - 16:49:18 CDT)
RE: incompatibility between VMD & NAMD for reading Amber crd files Kamp, Marc vander (Tue Jun 22 2004 - 04:20:16 CDT)
- Re: incompatibility between VMD & NAMD for reading Amber crd files David A. Case (Wed Jun 23 2004 - 12:39:42 CDT)
Re: thank you! John Stone (Mon Jun 21 2004 - 13:33:18 CDT)
incompatibility between VMD & NAMD for reading Amber crd files Kamp, Marc vander (Mon Jun 21 2004 - 07:33:11 CDT)
- Re: incompatibility between VMD & NAMD for reading Amber crd files John Stone (Mon Jun 21 2004 - 09:58:31 CDT)
  - Re: incompatibility between VMD & NAMD for reading Amber crd files John Stone (Mon Jun 21 2004 - 14:53:13 CDT)
Re: namd-l: recentering protein in the waterbox Gianluca Interlandi (Fri Jun 18 2004 - 18:16:35 CDT)
Test version of VMD for flaky graphics boards/drivers John Stone (Fri Jun 18 2004 - 15:53:18 CDT)
visualizing trr files Nitin Rathore (Fri Jun 18 2004 - 10:03:37 CDT)
- Re: visualizing trr files John Stone (Fri Jun 18 2004 - 10:24:54 CDT)
  - Re: visualizing trr files Axel Kohlmeyer (Fri Jun 18 2004 - 13:46:13 CDT)
opening VMD on OSX tom keyes (Thu Jun 17 2004 - 13:32:48 CDT)
- Re: opening VMD on OSX John Stone (Fri Jun 18 2004 - 11:08:59 CDT)
  - Re: opening VMD on OSX tom keyes (Sat Jun 19 2004 - 16:30:47 CDT)
problem with tool command Simon Latapie (Wed Jun 16 2004 - 09:38:26 CDT)
- Re: problem with tool command John Stone (Wed Jun 16 2004 - 10:12:50 CDT)
word too long Hua Wong (Wed Jun 16 2004 - 03:40:48 CDT)
- Re: word too long John Stone (Wed Jun 16 2004 - 09:08:08 CDT)
Vmd 1.8.1 or 1.8.2 on Linux not starting text interpreter Romaric David (Wed Jun 16 2004 - 05:02:23 CDT)
- Re: Vmd 1.8.1 or 1.8.2 on Linux not starting text interpreter John Stone (Wed Jun 16 2004 - 09:26:33 CDT)
  - Re: Vmd 1.8.1 or 1.8.2 on Linux not starting text interpreter Romaric David (Wed Jun 16 2004 - 11:56:18 CDT)
base plane not being filled in for terminal adenines in ribbons/new ribbons Pattanayek, Sabuj (Mon Jun 14 2004 - 13:30:18 CDT)
- Re: base plane not being filled in for terminal adenines in ribbons/new ribbons John Stone (Tue Jun 15 2004 - 14:38:30 CDT)
Inserting missing residues Michael Chen (Sat Jun 12 2004 - 16:49:35 CDT)
Need a few testers for Linux version of VMD 1.8.3... John Stone (Fri Jun 11 2004 - 10:33:55 CDT)
- Re: Need a few testers for Linux version of VMD 1.8.3... Jerry Ebalunode (Fri Jun 11 2004 - 09:56:51 CDT)
  - Re: Need a few testers for Linux version of VMD 1.8.3... John Stone (Fri Jun 11 2004 - 11:10:15 CDT)
- Re: Need a few testers for Linux version of VMD 1.8.3... Luca Mollica (Fri Jun 11 2004 - 12:08:15 CDT)
- Re: Need a few testers for Linux version of VMD 1.8.3... Axel Kohlmeyer (Fri Jun 11 2004 - 15:17:13 CDT)
Re: [PyMOL] enable direct rendering DRI on fedora core 2 Jack Howarth (Fri Jun 11 2004 - 07:22:35 CDT)
enable direct rendering DRI on fedora core 2 Dr. Daniel James White PhD (Fri Jun 11 2004 - 06:50:34 CDT)
"measure fit" inaccuracy? Jérôme Hénin (Fri Jun 11 2004 - 02:48:49 CDT)
- Re: "measure fit" inaccuracy? John Stone (Fri Jun 11 2004 - 09:04:43 CDT)
  - Re: "measure fit" inaccuracy? Jérôme Hénin (Fri Jun 11 2004 - 09:34:45 CDT)
- Re: "measure fit" inaccuracy? Justin Gullingsrud (Fri Jun 11 2004 - 10:07:54 CDT)
  - Re: "measure fit" inaccuracy? John Stone (Fri Jun 11 2004 - 10:16:03 CDT)
rmsd option in timeline Marta Murcia (Thu Jun 10 2004 - 12:19:54 CDT)
- Re: rmsd option in timeline John Stone (Fri Jun 11 2004 - 09:20:50 CDT)
xyz file format Justyna Jaroniec (Wed Jun 09 2004 - 13:54:17 CDT)
- Re: xyz file format John Stone (Wed Jun 09 2004 - 14:06:24 CDT)
- Re: xyz file format John Stone (Fri Jun 11 2004 - 09:16:53 CDT)
vmd-1.8.2, Spaceball and FC2 Cesar Delgado (Mon Jun 07 2004 - 13:54:36 CDT)
- Re: vmd-1.8.2, Spaceball and FC2 John Stone (Mon Jun 07 2004 - 14:21:20 CDT)
vmdnumpy ? nettles (Thu Jun 03 2004 - 18:02:19 CDT)
- Re: vmdnumpy ? (IED 2.0 on MacOS X /w VMD 1.8.2) John Stone (Fri Jun 11 2004 - 14:33:34 CDT)
  - Re: vmdnumpy ? (IED 2.0 on MacOS X /w VMD 1.8.2) nettles (Fri Jun 11 2004 - 15:29:15 CDT)
    - Re: vmdnumpy ? (IED 2.0 on MacOS X /w VMD 1.8.2) John Stone (Fri Jun 11 2004 - 16:28:44 CDT)
    - Re: vmdnumpy ? (IED 2.0 on MacOS X /w VMD 1.8.2) John Stone (Tue Jun 15 2004 - 13:45:47 CDT)
- Visualising Helix Dipole Moment Anthony Ivetac (Mon Jul 19 2004 - 05:25:54 CDT)
Little problem with VolumeSlice Simon Latapie (Thu Jun 03 2004 - 09:16:02 CDT)
- Re: Little problem with VolumeSlice John Stone (Thu Jun 03 2004 - 15:28:50 CDT)
display of electron density maps Karsten Suhre (Thu Jun 03 2004 - 07:53:20 CDT)
- Re: display of electron density maps Eamon Caddigan (Thu Jun 03 2004 - 11:33:00 CDT)
- Re: display of electron density maps Axel Kohlmeyer (Thu Jun 03 2004 - 11:50:29 CDT)
CUBIC box of system Raghunadha Reddy Burri (Thu Jun 03 2004 - 03:24:54 CDT)
- Re: CUBIC box of system Axel Kohlmeyer (Thu Jun 03 2004 - 07:22:09 CDT)
  - Re: CUBIC box of system Ran Friedman (Thu Jun 03 2004 - 14:56:23 CDT)
    - Re: CUBIC box of system Axel Kohlmeyer (Thu Jun 03 2004 - 12:44:37 CDT)
Van der Waal's radii of atoms Vani Krishna (Wed Jun 02 2004 - 20:24:47 CDT)
- Re: Van der Waal's radii of atoms Andrew Dalke (Wed Jun 02 2004 - 23:21:30 CDT)
  - Re: Van der Waal's radii of atoms John Stone (Thu Jun 03 2004 - 17:00:32 CDT)
vmd and Konqueror web browser under Suse 9? Gustavo Mercier (Mon May 31 2004 - 08:20:28 CDT)
- Re: vmd and Konqueror web browser under Suse 9? John Stone (Mon May 31 2004 - 12:28:35 CDT)
Animate the "beta" field emmanuel.levy1_at_free.fr (Sat May 29 2004 - 14:05:16 CDT)
- Re: Animate the "beta" field John Stone (Mon Jun 21 2004 - 14:17:38 CDT)
Pore volume/radius in protein bundles Vani Krishna (Thu May 27 2004 - 11:57:34 CDT)
- Re: Pore volume/radius in protein bundles John Stone (Fri May 28 2004 - 19:10:15 CDT)
Help about Contact Map plugin. Still puzzled by atom selection. Hua Wong (Thu May 27 2004 - 04:05:56 CDT)
- Re: Help about Contact Map plugin. Still puzzled by atom selection. Eamon Caddigan (Thu May 27 2004 - 17:48:01 CDT)
vmd1.8.2 on laptop Ramesh K. Sistla (Thu May 27 2004 - 07:34:39 CDT)
- Re: vmd1.8.2 on laptop John Stone (Thu May 27 2004 - 10:31:55 CDT)
Torsional Angles Ahmet Bakan (Wed May 26 2004 - 13:52:53 CDT)
- RE: Torsional Angles Ahmet Bakan (Sun May 30 2004 - 19:41:49 CDT)
  - Re: Torsional Angles John Stone (Mon May 31 2004 - 12:44:40 CDT)
    - RE: Torsional Angles Ahmet Bakan (Mon May 31 2004 - 15:54:52 CDT)
- Re: Torsional Angles John Stone (Mon May 31 2004 - 12:40:22 CDT)
animating an iso-surface Randall Hall (Wed May 26 2004 - 13:18:03 CDT)
- Re: animating an iso-surface Axel Kohlmeyer (Wed May 26 2004 - 15:48:49 CDT)
draw lines Osmany Guirola Cruz (Tue May 25 2004 - 13:02:36 CDT)
- Re: draw lines Axel Kohlmeyer (Wed May 26 2004 - 01:01:05 CDT)
  - Re: draw lines Osmany Guirola Cruz (Wed May 26 2004 - 07:36:13 CDT)
    - Re: draw lines John Stone (Mon Jun 21 2004 - 14:02:54 CDT)
copying parts of an atomselect selection Travis DePuy (Tue May 25 2004 - 07:10:54 CDT)
movies on mac os x (panther) James Rustad (Mon May 24 2004 - 15:30:19 CDT)
- Re: movies on mac os x (panther) Mengjuei Hsieh (Mon May 24 2004 - 18:23:44 CDT)
Iso-surfaces, VolumeSlices and tracing with VMD 1.8.2 B.D Allen (Mon May 24 2004 - 10:09:22 CDT)
- Re: Iso-surfaces, VolumeSlices and tracing with VMD 1.8.2 Axel Kohlmeyer (Mon May 24 2004 - 12:44:03 CDT)
Non-protein Multiple-Frame File Anthony Ivetac (Mon May 24 2004 - 06:44:54 CDT)
- Re: Non-protein Multiple-Frame File Axel Kohlmeyer (Mon May 24 2004 - 08:59:05 CDT)
labeling a residue Han Choe (Mon May 24 2004 - 03:57:42 CDT)
- Re: labeling a residue John Stone (Mon Jun 21 2004 - 13:59:02 CDT)
RE: How to read i8(64 bit) .crd file with 32 bit VMD EPF (Esben Peter Friis) (Sun May 23 2004 - 15:31:55 CDT)
- Re: How to read i8(64 bit) .crd file with 32 bit VMD John Stone (Sun May 23 2004 - 15:40:35 CDT)
- RE: How to read i8(64 bit) trajectory (.dcd) file with 32 bit VMD ILJA Khavrutskii (Sun May 23 2004 - 18:51:25 CDT)
  - RE: How to read i8(64 bit) trajectory (.dcd) file with 32 bit VMD Bogdan Costescu (Mon May 24 2004 - 03:32:12 CDT)
- RE: How to read i8(64 bit) .dcd file with 32 bit VMD Bogdan Costescu (Mon May 24 2004 - 03:24:33 CDT)
How to read i8(64 bit) .crd file with 32 bit VMD ILJA Khavrutskii (Sat May 22 2004 - 12:07:23 CDT)
- Re: How to read i8(64 bit) .crd file with 32 bit VMD John Stone (Sat May 22 2004 - 19:45:39 CDT)
VMD-1.8.2 OpenGL Shader Extns. and Chromium Stewart Dickson (Wed May 19 2004 - 15:44:24 CDT)
- Re: VMD-1.8.2 OpenGL Shader Extns. and Chromium John Stone (Wed May 19 2004 - 23:47:05 CDT)
changing the representation of all loaded molecules Elif Ozkirimli (Wed May 19 2004 - 14:32:02 CDT)
- Re: changing the representation of all loaded molecules Axel Kohlmeyer (Thu May 20 2004 - 02:34:14 CDT)
  - Re: changing the representation of all loaded molecules Elif Ozkirimli (Thu May 20 2004 - 08:55:25 CDT)
  - Re: changing the representation of all loaded molecules John Stone (Thu May 20 2004 - 09:13:35 CDT)
    - Re: changing the representation of all loaded molecules Axel Kohlmeyer (Thu May 20 2004 - 13:35:08 CDT)
- Re: changing the representation of all loaded molecules Jim Phillips (Thu May 20 2004 - 15:38:37 CDT)
  - Re: changing the representation of all loaded molecules Elif Ozkirimli (Wed May 26 2004 - 13:32:28 CDT)
Dynamic selection of residues in a trajectory Sanjeev B.S. (Wed May 19 2004 - 04:34:24 CDT)
- Re: Dynamic selection of residues in a trajectory Axel Kohlmeyer (Wed May 19 2004 - 08:45:05 CDT)
  - Re: Dynamic selection of residues in a trajectory Sanjeev B.S. (Wed May 19 2004 - 08:53:36 CDT)
python disabled (still?) Travis DePuy (Tue May 18 2004 - 10:49:17 CDT)
python disabled (still?) Travis DePuy (Tue May 18 2004 - 10:49:17 CDT)
- Re: python disabled (still?) John Stone (Sat May 22 2004 - 00:31:39 CDT)
Help about Contact Map plugin Hua Wong (Tue May 18 2004 - 07:23:24 CDT)
- Re: Help about Contact Map plugin John Stone (Sat May 22 2004 - 00:25:19 CDT)
displaying tube/ribbon with varying diameter ? Marc Baaden (Tue May 18 2004 - 05:26:26 CDT)
- Re: displaying tube/ribbon with varying diameter ? John Stone (Tue May 18 2004 - 08:56:09 CDT)
analysis of energy with water excluded from dcd file li (Mon May 17 2004 - 01:28:40 CDT)
- Re: analysis of energy with water excluded from dcd file John Stone (Sun May 23 2004 - 15:46:26 CDT)
some visualization challenges Axel Kohlmeyer (Sun May 16 2004 - 14:03:11 CDT)
- Re: some visualization challenges John Stone (Sun May 16 2004 - 20:25:59 CDT)
  - Re: some visualization challenges Axel Kohlmeyer (Mon May 17 2004 - 15:07:43 CDT)
    - Re: some visualization challenges John Stone (Tue May 18 2004 - 00:58:22 CDT)
  - Re: some visualization challenges John Stone (Tue May 18 2004 - 09:21:44 CDT)
autoionize script amodzelewska_at_dns.iimcb.gov.pl (Sun May 16 2004 - 13:21:58 CDT)
dcd to coor files Amit Paliwal (Fri May 14 2004 - 15:18:26 CDT)
- Re: dcd to coor files John Stone (Sat May 15 2004 - 14:08:20 CDT)
Confidential Ibrahim Dunga (Fri May 14 2004 - 07:37:05 CDT)
unit of force using Haptic during IMD Harit Jani (Fri May 14 2004 - 01:34:02 CDT)
- Re: unit of force using Haptic during IMD John Stone (Fri May 14 2004 - 10:33:10 CDT)
high resolution ps or eps picture wei (Wed May 12 2004 - 14:25:21 CDT)
- Re: high resolution ps or eps picture John Stone (Wed May 12 2004 - 20:26:54 CDT)
  - Re: dihedral angles for a lot of identical molecules tatyana_at_fi.uib.no (Thu Jun 17 2004 - 04:32:29 CDT)
- Re: high resolution ps or eps picture Gadi Oron (Thu May 13 2004 - 04:48:55 CDT)
tkCon window - how to make font bigger? Olya Kravchenko (Tue May 11 2004 - 14:16:29 CDT)
- Re: tkCon window - how to make font bigger? John Stone (Wed May 12 2004 - 14:24:24 CDT)
Compile from Source Crashes 5/11/04 Stewart Dickson (Tue May 11 2004 - 09:51:09 CDT)
- Re: Compile from Source Crashes 5/11/04 Brian Bennion (Tue May 11 2004 - 11:22:20 CDT)
  - Re: Compile from Source Crashes 5/11/04 Brian Bennion (Tue May 11 2004 - 16:26:33 CDT)
- Re: Compile from Source Crashes 5/11/04 John Stone (Wed May 12 2004 - 18:41:32 CDT)
RE: change location of temporay file storage (Win2k Dieter Blaas (Tue May 11 2004 - 08:20:31 CDT)
Surface rendering crashes PC Dieter Blaas (Tue May 11 2004 - 08:13:20 CDT)
- Re: Surface rendering crashes PC Axel Kohlmeyer (Tue May 11 2004 - 10:05:08 CDT)
  - Re: Surface rendering crashes PC John Stone (Tue May 11 2004 - 13:10:40 CDT)
Surface - upper limit for number of coordinates? dieter blaas (Tue May 11 2004 - 07:08:31 CDT)
Surface - upper limit for number of coordinates? dieter blaas (Tue May 11 2004 - 07:10:36 CDT)
- Re: Surface - upper limit for number of coordinates? John Stone (Tue May 11 2004 - 10:06:48 CDT)
  - Re: Surface - upper limit for number of coordinates? Marc Baaden (Tue May 11 2004 - 16:10:22 CDT)
    - Re: Surface - upper limit for number of coordinates? John Stone (Wed May 12 2004 - 14:18:15 CDT)
How to make VMD to work with Phantom Haptic Device Fung Wai Keung (Tue May 11 2004 - 06:29:24 CDT)
- Re: How to make VMD to work with Phantom Haptic Device John Stone (Tue May 11 2004 - 09:41:54 CDT)
vmd 1.8.2 - slow on linux Olya Kravchenko (Mon May 10 2004 - 16:35:36 CDT)
- Re: vmd 1.8.2 - slow on linux John Stone (Tue May 11 2004 - 09:01:06 CDT)
  - Re: vmd 1.8.2 - slow on linux Olya Kravchenko (Tue May 11 2004 - 13:21:22 CDT)
  - Re: vmd 1.8.2 - slow on linux Olya Kravchenko (Tue May 11 2004 - 16:44:27 CDT)
    - Re: vmd 1.8.2 - slow on linux Bogdan Costescu (Wed May 12 2004 - 07:26:11 CDT)
    - Re: slow vmd - it works now!!! Olya Kravchenko (Wed May 12 2004 - 16:03:49 CDT)
RE: trouble loading dcd files Olga Kravchenko (Sun May 09 2004 - 03:30:27 CDT)
- Re: RE: trouble loading dcd files AMIT PALIWAL (Sun May 09 2004 - 09:53:07 CDT)
trouble loading dcd files AMIT PALIWAL (Sat May 08 2004 - 23:43:13 CDT)
- Re: trouble loading dcd files John Stone (Sun May 09 2004 - 08:24:25 CDT)
  - Re: trouble loading dcd files AMIT PALIWAL (Sun May 09 2004 - 09:48:37 CDT)
Stereo on Mac OX 10.3.3 Jill Vickery (Thu May 06 2004 - 16:50:27 CDT)
- Re: Stereo on Mac OX 10.3.3 John Stone (Thu May 06 2004 - 21:53:39 CDT)
measuring distances in vmd tkon Jerry Ebalunode (Thu May 06 2004 - 15:18:00 CDT)
- RE: measuring distances in vmd tkon Ahmet Bakan (Thu May 06 2004 - 17:45:21 CDT)
how to look for overlaps? Olya Kravchenko (Thu May 06 2004 - 14:55:05 CDT)
- Re: how to look for overlaps? John Stone (Thu May 06 2004 - 21:51:27 CDT)
core when using some features of vmd-xplor Pilar Saiz Vela (Thu May 06 2004 - 13:10:48 CDT)
- Re: core when using some features of vmd-xplor Charles_at_Schwieters.org (Thu May 06 2004 - 16:03:01 CDT)
- Re: core when using some features of vmd-xplor John Stone (Thu May 06 2004 - 16:45:02 CDT)
VMD: Potential Energy Calculation Shirley Hui (Wed May 05 2004 - 23:28:49 CDT)
- Re: VMD: Potential Energy Calculation John Stone (Thu May 06 2004 - 10:15:39 CDT)
  - Re: VMD: Potential Energy Calculation Dominique Vlieghe (Fri May 07 2004 - 09:25:39 CDT)
Missing bonds Min Chin Chai (Wed May 05 2004 - 17:28:28 CDT)
- Re: Missing bonds Karsten Suhre (Thu May 06 2004 - 01:44:52 CDT)
ATI 3.7.6 driver bugs (and VMD..) John Stone (Wed May 05 2004 - 16:46:01 CDT)
- Rotating and translating molecules .. Dallas Warren (Tue Jan 18 2005 - 19:15:56 CST)
  - Re: Rotating and translating molecules .. Justin Gullingsrud (Tue Jan 18 2005 - 20:56:22 CST)
- Catching error info before it shuts down ... Dallas Warren (Thu Feb 17 2005 - 23:41:08 CST)
variable atom number and dynamic bonds Cosmin ROMAN (Wed May 05 2004 - 10:55:19 CDT)
- Re: variable atom number and dynamic bonds Axel Kohlmeyer (Wed May 05 2004 - 13:22:24 CDT)
  - Re: variable atom number and dynamic bonds John Stone (Wed May 05 2004 - 15:49:55 CDT)
Coloring with an XYZ file Edward J. Smiley Jr. (Tue May 04 2004 - 15:25:50 CDT)
- Re: Coloring with an XYZ file Axel Kohlmeyer (Wed May 05 2004 - 01:28:00 CDT)
- Re: Coloring with an XYZ file John Stone (Wed May 05 2004 - 01:18:01 CDT)
Include HETATM into *.psf file Davit Hakobyan (Mon May 03 2004 - 14:04:32 CDT)
- Re: Include HETATM into *.psf file Tim Isgro (Wed May 05 2004 - 17:24:12 CDT)
  - Re: Include HETATM into *.psf file Davit Hakobyan (Thu May 06 2004 - 01:05:11 CDT)
Selection problem on TkCon Ahmet Bakan (Sun May 02 2004 - 19:55:43 CDT)
- Re: Selection problem on TkCon Justin Gullingsrud (Mon May 03 2004 - 03:35:50 CDT)
  - RE: Selection problem on TkCon Ahmet Bakan (Mon May 03 2004 - 05:56:25 CDT)
dcd files generated with catdcd Giovanni (Fri Apr 30 2004 - 04:11:00 CDT)
- Re: namd-l: dcd files generated with catdcd J. Rui Rodrigues (Fri Apr 30 2004 - 10:51:27 CDT)
  - Re: Re: namd-l: dcd files generated with catdcd John Stone (Fri Apr 30 2004 - 12:47:59 CDT)
    - Re: Re: namd-l: dcd files generated with catdcd Giovanni (Fri Apr 30 2004 - 13:08:33 CDT)
    - Re: Re: namd-l: dcd files generated with catdcd J. Rui Rodrigues (Fri Apr 30 2004 - 14:02:49 CDT)
script problem Ioana Cozmuta (Thu Apr 29 2004 - 23:09:49 CDT)
- Re: script problem John Stone (Fri Apr 30 2004 - 16:02:12 CDT)
problems with Autoimd on mac os x ( panther ) Arieana Moore (Thu Apr 29 2004 - 19:02:09 CDT)
- Re: problems with Autoimd on mac os x ( panther ) Mike McCallum (Thu Apr 29 2004 - 22:02:26 CDT)
Fwd: MOE discussion Mike McCallum (Wed Apr 28 2004 - 23:11:43 CDT)
MOE discussion Mike McCallum (Wed Apr 28 2004 - 14:43:22 CDT)
- RE: MOE discussion Ahmet Bakan (Wed Apr 28 2004 - 17:26:07 CDT)
- Re: MOE discussion John Stone (Wed Apr 28 2004 - 17:03:31 CDT)
Amber periodic images Xiang, Tian-Xiang (Wed Apr 28 2004 - 10:25:09 CDT)
- Re: Amber periodic images John Stone (Thu Apr 29 2004 - 10:56:26 CDT)
  - Re: Amber periodic images Jim Shepherd (Thu Apr 29 2004 - 13:41:23 CDT)
    - Re: Amber periodic images John Stone (Thu Apr 29 2004 - 13:49:52 CDT)
    - Re: Amber periodic images John Stone (Thu Apr 29 2004 - 13:52:17 CDT)
Heteroatom entries Mithun Mitra (Tue Apr 27 2004 - 10:17:00 CDT)
coloring selection Ioana Cozmuta (Mon Apr 26 2004 - 15:19:25 CDT)
- Re: coloring selection John Stone (Mon Apr 26 2004 - 18:27:50 CDT)
Bond display and Periodic Boxes Jim Shepherd (Mon Apr 26 2004 - 14:19:02 CDT)
- Re: Bond display and Periodic Boxes John Stone (Mon Apr 26 2004 - 17:51:03 CDT)
compile catdcd.c Sichun Yang (Fri Apr 23 2004 - 18:38:56 CDT)
- Re: compile catdcd.c Sichun Yang (Fri Apr 23 2004 - 19:06:04 CDT)
(no subject) Andrew Watts (Fri Apr 23 2004 - 15:26:37 CDT)
- Re: John Stone (Sat Apr 24 2004 - 15:41:39 CDT)
cartoon representation of 1crn BETTLER Emmanuel (Fri Apr 23 2004 - 11:25:46 CDT)
Help in VMD Sunando Datta (Wed Apr 21 2004 - 22:04:07 CDT)
- Re: Help in VMD John Stone (Thu Apr 22 2004 - 10:29:50 CDT)
Amber trajectory loading Xiang, Tian-Xiang (Wed Apr 21 2004 - 10:03:48 CDT)
- Re: Amber trajectory loading John Stone (Wed Apr 21 2004 - 13:22:49 CDT)
error with top2psf davide\.ruffoni (Wed Apr 21 2004 - 06:04:51 CDT)
- Re: error with top2psf John Stone (Wed Apr 21 2004 - 13:40:22 CDT)
  - Re: error with top2psf Axel Kohlmeyer (Wed Apr 21 2004 - 15:47:17 CDT)
  - Re: error with top2psf Marc Baaden (Thu Apr 22 2004 - 02:52:23 CDT)
Rendering of screen/display different Dallas Warren (Wed Apr 21 2004 - 00:36:12 CDT)
- Re: Rendering of screen/display different Eamon Caddigan (Wed Apr 21 2004 - 10:24:16 CDT)
  - Re: Rendering of screen/display different Dallas Warren (Mon Apr 26 2004 - 20:45:57 CDT)
- Re: Rendering of screen/display different John Stone (Wed Apr 21 2004 - 10:51:57 CDT)
  - Re: Rendering of screen/display different Dallas Warren (Wed Apr 21 2004 - 16:40:10 CDT)
Rendering of screen/display different Dallas Warren (Wed Apr 21 2004 - 00:36:56 CDT)
python 2.3 Ramon Crehuet (Tue Apr 20 2004 - 11:39:32 CDT)
- Re: python 2.3 John Stone (Tue Apr 20 2004 - 15:02:25 CDT)
Updated plugins for VMD 1.8.2 John Stone (Mon Apr 19 2004 - 10:34:55 CDT)
Re: VMD Bug ? John Stone (Mon Apr 19 2004 - 09:38:36 CDT)
top2psf davide\.ruffoni (Mon Apr 19 2004 - 09:29:55 CDT)
- Re: top2psf John Stone (Mon Apr 19 2004 - 11:51:14 CDT)
xyz plugin Lubos Vrbka (Mon Apr 19 2004 - 09:16:46 CDT)
- Re: xyz plugin John Stone (Mon Apr 19 2004 - 11:49:49 CDT)
  - Re: xyz plugin Axel Kohlmeyer (Tue Apr 20 2004 - 01:55:15 CDT)
  - Re: xyz plugin Lubos Vrbka (Tue Apr 20 2004 - 04:19:14 CDT)
    - Re: xyz plugin John Stone (Tue Apr 20 2004 - 09:37:19 CDT)
Required Assistance for VMD zaheer qasmi (Sat Apr 17 2004 - 09:16:34 CDT)
- Re: Required Assistance for VMD John Stone (Sun Apr 18 2004 - 12:19:19 CDT)
Looking for assistance on vmd Dr. Zaheer-ul-Haq Qasmi (Sat Apr 17 2004 - 11:45:53 CDT)
(no subject) Yang Yang (Fri Apr 16 2004 - 21:59:41 CDT)
vmd linux binary / native build on netbsd Lubos Vrbka (Fri Apr 16 2004 - 11:58:44 CDT)
- Re: vmd linux binary / native build on netbsd Brian Bennion (Fri Apr 16 2004 - 13:12:13 CDT)
  - Re: vmd linux binary / native build on netbsd Lubos Vrbka (Mon Apr 19 2004 - 10:52:07 CDT)
    - Re: vmd linux binary / native build on netbsd Brian Bennion (Mon Apr 19 2004 - 12:25:21 CDT)
    - Re: vmd linux binary / native build on netbsd John Stone (Mon Apr 19 2004 - 17:08:18 CDT)
Webpdb crashing Josh Ward (Fri Apr 16 2004 - 09:24:41 CDT)
- Re: Webpdb crashing Brian Bennion (Fri Apr 16 2004 - 11:22:50 CDT)
  - Re: Webpdb crashing Josh Ward (Fri Apr 16 2004 - 11:43:18 CDT)
- Re: Webpdb crashing John Stone (Fri Apr 16 2004 - 13:27:44 CDT)
(no subject) Yang Yang (Thu Apr 15 2004 - 13:19:11 CDT)
- Re: your mail John Stone (Thu Apr 15 2004 - 16:24:29 CDT)
  - a question in using PSFGEN Yang Yang (Mon Apr 26 2004 - 21:55:45 CDT)
    - Re: a question in using PSFGEN Jim Phillips (Tue Apr 27 2004 - 11:04:31 CDT)
- Re: No Subject Gadi Oron (Sun Apr 18 2004 - 03:50:37 CDT)
move molecule using tcl li (Thu Apr 15 2004 - 01:46:00 CDT)
- Re: move molecule using tcl John Stone (Sun Apr 18 2004 - 19:24:40 CDT)
Memory leak using "moveby" command inside a loop Artem Mamonov (Wed Apr 14 2004 - 21:34:20 CDT)
- Re: Memory leak using "moveby" command inside a loop Justin Gullingsrud (Thu Apr 15 2004 - 13:22:08 CDT)
How to save trajectory using Tcl commands? Chen Yongzhi (Wed Apr 14 2004 - 19:28:11 CDT)
- Re: How to save trajectory using Tcl commands? Tim Isgro (Wed Apr 14 2004 - 22:49:55 CDT)
  - Re: How to save trajectory using Tcl commands? Tim Isgro (Thu Apr 15 2004 - 17:54:15 CDT)
- Re: How to save trajectory using Tcl commands? Justin Gullingsrud (Thu Apr 15 2004 - 14:05:59 CDT)
RE: Viewing MD trajectories Kooser, Ara S (Tue Apr 13 2004 - 15:46:35 CDT)
RE: file type specification question Kooser, Ara S (Tue Apr 13 2004 - 15:04:55 CDT)
- RE: file type specification question Kooser, Ara S (Tue Apr 13 2004 - 16:08:35 CDT)
- Re: file type specification question John Stone (Tue Apr 13 2004 - 16:05:56 CDT)
- RE: file type specification question Kooser, Ara S (Fri Apr 16 2004 - 10:50:39 CDT)
  - Re: file type specification question John Stone (Sun Apr 18 2004 - 19:44:40 CDT)
  - Re: file type specification question John Stone (Mon Apr 19 2004 - 18:06:03 CDT)
RE: xyz aluminium connectivity questions Kooser, Ara S (Tue Apr 13 2004 - 09:42:10 CDT)
- Re: xyz aluminium connectivity questions Lubos Vrbka (Tue Apr 13 2004 - 09:59:52 CDT)
  - Re: xyz aluminium connectivity questions Axel Kohlmeyer (Tue Apr 13 2004 - 11:27:30 CDT)
    - Re: xyz aluminium connectivity questions John Stone (Tue Apr 13 2004 - 13:42:52 CDT)
- RE: xyz aluminium connectivity questions Kooser, Ara S (Tue Apr 13 2004 - 10:14:28 CDT)
  - Re: xyz aluminium connectivity questions Lubos Vrbka (Tue Apr 13 2004 - 10:29:07 CDT)
xyz aluminium connectivity questions Lubos Vrbka (Tue Apr 13 2004 - 09:01:56 CDT)
- could not make avi file Albert Sun (Tue Apr 13 2004 - 10:58:49 CDT)
  - Re: could not make avi file John Stone (Tue Apr 13 2004 - 13:33:33 CDT)
(no subject) Ajith Gunaratne (Sun Apr 11 2004 - 23:36:05 CDT)
- Re: John Stone (Mon Apr 12 2004 - 21:59:15 CDT)
center selection problem Mike McCallum (Sat Apr 10 2004 - 00:17:26 CDT)
- Re: center selection problem Justin Gullingsrud (Sat Apr 10 2004 - 13:48:19 CDT)
Viewing MD trajectories Jayendra Balasubramanian (Fri Apr 09 2004 - 16:46:48 CDT)
- Re: Viewing MD trajectories John Stone (Fri Apr 09 2004 - 20:12:46 CDT)
  - Re: Viewing MD trajectories Jayendra Balasubramanian (Tue Apr 13 2004 - 15:02:27 CDT)
    - Re: Viewing MD trajectories John Stone (Tue Apr 13 2004 - 15:12:08 CDT)
  - Re: Viewing MD trajectories John Stone (Tue Apr 13 2004 - 15:59:32 CDT)
making ps files Ioana Cozmuta (Thu Apr 08 2004 - 14:55:34 CDT)
- Re: making ps files John Stone (Thu Apr 08 2004 - 17:41:29 CDT)
  - Re: making ps files Ioana Cozmuta (Fri Apr 09 2004 - 17:10:14 CDT)
- Re: making ps files Mike McCallum (Thu Apr 08 2004 - 17:40:16 CDT)
- Re: making ps files Jerry Ebalunode (Fri Apr 09 2004 - 11:19:08 CDT)
  - Re: making ps files T Luchko (Fri Apr 09 2004 - 14:57:43 CDT)
mapping delphi potential maps on surfaces Miguel Ortiz Lombardía (Thu Apr 08 2004 - 04:03:00 CDT)
- Re: mapping delphi potential maps on surfaces John Stone (Thu Apr 08 2004 - 16:48:43 CDT)
  - Re: mapping delphi potential maps on surfaces John Stone (Thu Apr 08 2004 - 17:49:37 CDT)
Typing Au(111) surface Kooser, Ara S (Wed Apr 07 2004 - 15:41:25 CDT)
- Re: Typing Au(111) surface John Stone (Thu Apr 08 2004 - 16:50:46 CDT)
  - Re: Typing Au(111) surface John Stone (Fri Apr 09 2004 - 10:00:14 CDT)
file type specification question Lubos Vrbka (Wed Apr 07 2004 - 11:12:56 CDT)
- Re: file type specification question John Stone (Wed Apr 07 2004 - 15:32:42 CDT)
  - Re: file type specification question John Stone (Thu Apr 08 2004 - 16:53:04 CDT)
    - Re: file type specification question Lubos Vrbka (Fri Apr 09 2004 - 09:35:19 CDT)
    - Re: file type specification question John Stone (Tue Apr 13 2004 - 14:23:17 CDT)
  - Re: file type specification question Kooser, Ara S (Fri Apr 09 2004 - 10:37:32 CDT)
drawing poligons Vlad Cojocaru (Tue Apr 06 2004 - 06:39:54 CDT)
- Re: drawing poligons John Stone (Tue Apr 06 2004 - 09:57:04 CDT)
question about the definition of secondary motiffs weiz (Mon Apr 05 2004 - 19:44:44 CDT)
- Re: question about the definition of secondary motiffs John Stone (Thu Apr 08 2004 - 16:57:13 CDT)
how to make whole biological unit / virus capsid from pdb BIOMT records Dr. Daniel James White PhD (Mon Apr 05 2004 - 10:35:06 CDT)
- Re: how to make whole biological unit / virus capsid from pdb BIOMT records John Stone (Mon Apr 05 2004 - 14:11:45 CDT)
  - Re: how to make whole biological unit / virus capsid from pdb BIOMT records Dr. Daniel James White PhD (Tue Apr 06 2004 - 04:12:58 CDT)
  - Re: how to make whole biological unit / virus capsid from pdb BIOMT records John Stone (Sun Apr 18 2004 - 19:29:30 CDT)
TCL string operation Ahmet Bakan (Sat Apr 03 2004 - 07:48:40 CST)
- Re: TCL string operation Justin Gullingsrud (Sat Apr 03 2004 - 09:27:12 CST)
- Re: TCL string operation Jérôme Hénin (Sat Apr 03 2004 - 10:10:56 CST)
startup failure Cheri M Turman (Fri Apr 02 2004 - 15:29:00 CST)
- Re: startup failure John Stone (Fri Apr 02 2004 - 19:19:28 CST)
Adding Atoms in Colors Menu Alexandre Suman de Araujo (Fri Apr 02 2004 - 03:33:52 CST)
- Re: Adding Atoms in Colors Menu Justin Gullingsrud (Fri Apr 02 2004 - 10:18:01 CST)
VMD shows bad structure with 'line' type Arturas (Fri Apr 02 2004 - 06:27:38 CST)
- Re: VMD shows bad structure with 'line' type John Stone (Fri Apr 02 2004 - 10:36:41 CST)
startup errors and variations of installation Cheri M Turman (Thu Apr 01 2004 - 14:43:58 CST)
startup failure Cheri M Turman (Thu Apr 01 2004 - 14:24:14 CST)
- Re: startup failure John Stone (Thu Apr 01 2004 - 17:33:35 CST)
  - Re: startup failure Cheri M Turman (Mon Apr 05 2004 - 12:47:54 CDT)
animating drawn objects Vlad Cojocaru (Thu Apr 01 2004 - 10:20:56 CST)
- Re: animating drawn objects John Stone (Thu Apr 01 2004 - 13:26:17 CST)
sorry...I got it!!! Vlad Cojocaru (Thu Apr 01 2004 - 10:07:47 CST)
draw command Vlad Cojocaru (Thu Apr 01 2004 - 09:30:13 CST)
- Re: draw command Justin Gullingsrud (Thu Apr 01 2004 - 11:17:30 CST)
about dynamical change color of atoms Emmanouil_Bambakopoulos (Thu Apr 01 2004 - 09:35:40 CST)
- Re: about dynamical change color of atoms John Stone (Thu Apr 01 2004 - 12:57:33 CST)
how to save coordinates after moving molecule in VMD? li (Wed Mar 31 2004 - 21:42:44 CST)
- Re: how to save coordinates after moving molecule in VMD? Gadi Oron (Thu Apr 01 2004 - 07:48:21 CST)
  - Re: how to save coordinates after moving molecule in VMD? John Stone (Thu Apr 01 2004 - 11:08:11 CST)
- Re: how to save coordinates after moving molecule in VMD? John Stone (Thu Apr 01 2004 - 10:40:51 CST)
Centering of the view on one atom CHAUMONT Alain (Wed Mar 31 2004 - 09:42:09 CST)
- Re: Centering of the view on one atom Axel Kohlmeyer (Wed Mar 31 2004 - 14:12:51 CST)
  - Re: configure do nothing in Linux (???) - thank you ! Arturas (Thu Apr 01 2004 - 03:23:39 CST)
configure do nothing in Linux(???) Arturas (Wed Mar 31 2004 - 09:27:36 CST)
- Re: configure do nothing in Linux(???) John Stone (Wed Mar 31 2004 - 10:20:28 CST)
- Re: configure do nothing in Linux(???) Jérôme Hénin (Wed Mar 31 2004 - 11:20:51 CST)
configure do nothing (Linux) Arturas (Wed Mar 31 2004 - 09:22:54 CST)
- Re: configure do nothing (Linux) Mike McCallum (Wed Mar 31 2004 - 10:44:25 CST)
- Re: configure do nothing (Linux) Juan Alfredo Freites (Wed Mar 31 2004 - 12:04:28 CST)
  - JMV Chris Upton (Wed Mar 31 2004 - 13:30:08 CST)
    - Re: JMV Robert Brunner (Wed Mar 31 2004 - 16:36:17 CST)
VECSUB function Satyavani Vemparala (Tue Mar 30 2004 - 16:44:03 CST)
- Re: VECSUB function Justin Gullingsrud (Tue Mar 30 2004 - 17:53:44 CST)
Atom typing Kooser, Ara S (Tue Mar 30 2004 - 12:24:30 CST)
- Re: Atom typing Justin Gullingsrud (Tue Mar 30 2004 - 14:59:54 CST)
Stereo projection ? Marc Baaden (Mon Mar 29 2004 - 15:56:37 CST)
- Re: Stereo projection ? John Stone (Mon Mar 29 2004 - 19:44:51 CST)
Molecular ruler ? Marc Baaden (Mon Mar 29 2004 - 14:44:03 CST)
- Re: Molecular ruler ? John Stone (Tue Mar 30 2004 - 11:28:00 CST)
  - Re: Molecular ruler ? John Stone (Tue Mar 30 2004 - 15:18:25 CST)
re :psfgen question li (Fri Mar 26 2004 - 01:00:28 CST)
psfgen question li (Thu Mar 25 2004 - 03:48:27 CST)
- Re: psfgen question Brian Bennion (Thu Mar 25 2004 - 11:42:45 CST)
New and updated plugins for VMD 1.8.2 posted John Stone (Wed Mar 24 2004 - 15:17:29 CST)
xyz to psf Kooser, Ara S (Wed Mar 24 2004 - 11:22:42 CST)
- Re: xyz to psf John Stone (Wed Mar 24 2004 - 15:47:03 CST)
residence time Ioana Cozmuta (Tue Mar 23 2004 - 21:51:10 CST)
- Re: residence time John Stone (Wed Mar 24 2004 - 16:01:07 CST)
To many bonds error. Kooser, Ara S (Tue Mar 23 2004 - 13:45:15 CST)
.cshrc error prevents VMD working on OSX10.3.3??? or something else??? Dr. Daniel James White PhD (Tue Mar 23 2004 - 03:36:59 CST)
- Re: .cshrc error prevents VMD working on OSX10.3.3??? or something else??? John Stone (Tue Mar 23 2004 - 10:54:22 CST)
VMD1.82 version with MacOS10.3.3 DO NOT WORK Peter Engelhardt (Mon Mar 22 2004 - 02:22:03 CST)
- Re: VMD1.82 version with MacOS10.3.3 DO NOT WORK Paul Fons (Mon Mar 22 2004 - 06:07:16 CST)
  - Re: VMD1.82 version with MacOS10.3.3 DO NOT WORK John Stone (Mon Mar 22 2004 - 10:03:24 CST)
  - Re: VMD1.82 version with MacOS10.3.3 DO NOT WORK Mike McCallum (Mon Mar 22 2004 - 10:40:53 CST)
- Re: VMD1.82 version with MacOS10.3.3 DO NOT WORK John Stone (Mon Mar 22 2004 - 09:50:25 CST)
  - Re: VMD1.82 version with MacOS10.3.3 Problem solved Peter Engelhardt (Tue Mar 23 2004 - 02:18:27 CST)
    - Re: VMD1.82 version with MacOS10.3.3 Problem solved John Stone (Tue Mar 23 2004 - 09:48:35 CST)
Copying a selection Adam Marcus (Mon Mar 22 2004 - 01:04:29 CST)
- Re: Copying a selection Philip Fowler (Mon Mar 22 2004 - 02:42:02 CST)
- Re: Copying a selection Axel Kohlmeyer (Mon Mar 22 2004 - 12:56:30 CST)
Re: about average structure Jan Saam (Sun Mar 21 2004 - 05:16:00 CST)
coloring method User Cosmin ROMAN (Sun Mar 21 2004 - 09:05:23 CST)
- Re: coloring method User John Stone (Mon Mar 22 2004 - 11:18:35 CST)
  - Re: coloring method User Cosmin ROMAN (Mon Mar 22 2004 - 11:56:03 CST)
    - Re: coloring method User John Stone (Mon Mar 22 2004 - 11:45:35 CST)
Periodic Images Joshua A. Speidel (Fri Mar 19 2004 - 14:10:07 CST)
- Re: Periodic Images John Stone (Mon Mar 22 2004 - 11:40:42 CST)
again about average strutcure li (Tue Mar 18 2008 - 17:31:26 CDT)
Black & white VMD in CAVE? Jeroen Akershoek (Thu Mar 18 2004 - 00:28:34 CST)
- Re: Black & white VMD in CAVE? John Stone (Thu Mar 18 2004 - 11:02:10 CST)
VMD-L digests available John Stone (Wed Mar 17 2004 - 18:01:56 CST)
Fwd: Digest Dr. Daniel James White PhD (Wed Mar 17 2004 - 03:32:00 CST)
get average structure from dcd file? li (Mon Mar 17 2008 - 16:24:47 CDT)
- Re: get average structure from dcd file? Philip Fowler (Wed Mar 17 2004 - 03:31:58 CST)
dcd with fixed atoms Luis Gracia (Wed Mar 17 2004 - 00:39:28 CST)
- Re: dcd with fixed atoms John Stone (Wed Mar 17 2004 - 10:13:00 CST)
  - Re: dcd with fixed atoms Bogdan Costescu (Wed Mar 17 2004 - 13:05:14 CST)
- Re: dcd with fixed atoms John Stone (Thu Mar 18 2004 - 19:31:16 CST)
HOLE output visualization Saladino, Alex (Tue Mar 16 2004 - 16:35:12 CST)
- Re: HOLE output visualization Oliver Beckstein (Wed Mar 17 2004 - 04:45:45 CST)
- Re: HOLE output visualization John Stone (Mon Mar 22 2004 - 10:16:37 CST)
Fwd: Announce: STRAP John Stone (Tue Mar 16 2004 - 16:06:47 CST)
density profile Ekta Khurana (Tue Mar 16 2004 - 14:57:36 CST)
- Re: density profile Justin Gullingsrud (Tue Mar 16 2004 - 16:36:08 CST)
- Re: density profile John Stone (Tue Mar 16 2004 - 18:49:27 CST)
digest form Dr. Daniel James White PhD (Tue Mar 16 2004 - 03:34:05 CST)
- Re: digest form John Stone (Tue Mar 16 2004 - 10:09:07 CST)
  - Re: digest form Bogdan Costescu (Wed Mar 17 2004 - 05:10:43 CST)
    - Re: digest form John Stone (Wed Mar 17 2004 - 10:06:24 CST)
loading PDB+PSF Kurt Smith (Tue Mar 16 2004 - 03:01:10 CST)
- Re: loading PDB+PSF John Stone (Tue Mar 16 2004 - 09:55:55 CST)
  - Re: loading PDB+PSF John Stone (Tue Mar 16 2004 - 12:46:46 CST)
- Re: loading PDB+PSF Brian Bennion (Tue Mar 16 2004 - 11:00:18 CST)
Suggestions on sending VMD bug reports/questions, etc... John Stone (Mon Mar 15 2004 - 14:09:51 CST)
msms and vmd on amd athlon64. Jerry Ebalunode (Mon Mar 15 2004 - 12:49:18 CST)
- Re: msms and vmd on amd athlon64. John Stone (Mon Mar 15 2004 - 12:58:52 CST)
  - Re: msms and vmd on amd athlon64. Michel Sanner (Fri Mar 19 2004 - 18:05:30 CST)
    - Re: Re: msms and vmd on amd athlon64. John Stone (Mon Mar 22 2004 - 11:21:55 CST)
- Re: msms and vmd on amd athlon64. Benjamin Goldsteen (Mon Mar 15 2004 - 14:18:16 CST)
Sine Cosine Ahmet Bakan (Sat Mar 13 2004 - 18:06:04 CST)
- Re: Sine Cosine Jérôme Hénin (Sun Mar 14 2004 - 04:32:26 CST)
  - Re: Sine Cosine Justin Gullingsrud (Sun Mar 14 2004 - 11:02:12 CST)
RE: Rotatind a chain (some further Qs) Ahmet Bakan (Fri Mar 12 2004 - 13:43:41 CST)
- Re: Rotatind a chain (some further Qs) John Stone (Mon Mar 15 2004 - 13:49:01 CST)
msms and socketPort Jerry Ebalunode (Fri Mar 12 2004 - 07:11:43 CST)
- Re: msms and socketPort John Stone (Fri Mar 12 2004 - 10:11:26 CST)
  - Re: msms and socketPort Jerry Ebalunode (Fri Mar 12 2004 - 15:49:28 CST)
    - Re: msms and socketPort John Stone (Fri Mar 12 2004 - 17:06:36 CST)
RE: is VMD compatible with NVIDIA 3D stereo drivers ? Kim, Kwiseon (Fri Mar 12 2004 - 09:50:07 CST)
- RE: is VMD compatible with NVIDIA 3D stereo drivers ? Kim, Kwiseon (Fri Mar 12 2004 - 11:01:29 CST)
Rotatind a chainn Ahmet Bakan (Fri Mar 12 2004 - 08:59:09 CST)
- Re: Rotatind a chainn John Stone (Fri Mar 12 2004 - 12:46:47 CST)
is VMD compatible with NVIDIA 3D stereo drivers ? BETTLER Emmanuel (Fri Mar 12 2004 - 08:47:12 CST)
- Re: is VMD compatible with NVIDIA 3D stereo drivers ? John Stone (Fri Mar 12 2004 - 10:56:37 CST)
change location of temporay file storage (Win2k) dieter blaas (Thu Mar 11 2004 - 23:55:32 CST)
- Re: change location of temporay file storage (Win2k) John Stone (Mon Mar 15 2004 - 13:53:02 CST)
  - Re: change location of temporay file storage (Win2k) dieter blaas (Mon May 10 2004 - 23:59:18 CDT)
VMD as command line interface Vlad Cojocaru (Thu Mar 11 2004 - 07:33:52 CST)
- Re: VMD as command line interface Justin Gullingsrud (Thu Mar 11 2004 - 09:25:32 CST)
- Re: VMD as command line interface John Stone (Thu Mar 11 2004 - 09:59:51 CST)
- Re: VMD as command line interface Brian Bennion (Thu Mar 11 2004 - 10:24:31 CST)
Coloring based on POS DongHoon Chung (Thu Mar 11 2004 - 03:11:40 CST)
- Re: Coloring based on POS Justin Gullingsrud (Thu Mar 11 2004 - 08:23:31 CST)
- Re: Coloring based on POS Justin Gullingsrud (Thu Mar 11 2004 - 08:18:16 CST)
- Re: Coloring based on POS John Stone (Thu Mar 11 2004 - 10:16:19 CST)
Solvate Package Satyavani Vemparala (Wed Mar 10 2004 - 18:23:33 CST)
- Re: Solvate Package John Stone (Mon Mar 15 2004 - 13:55:29 CST)
- Re: Solvate Package Brian Bennion (Wed Mar 17 2004 - 11:39:15 CST)
gromos96 files Franca Fraternali (Wed Mar 10 2004 - 04:55:47 CST)
- Re: gromos96 files John Stone (Wed Mar 10 2004 - 15:56:08 CST)
  - Re: gromos96 files Franca Fraternali (Thu Mar 11 2004 - 03:47:43 CST)
    - Re: gromos96 files John Stone (Thu Mar 11 2004 - 14:35:03 CST)
coloring of trajectory Florian Barth (Wed Mar 10 2004 - 07:10:27 CST)
- Re: coloring of trajectory John Stone (Wed Mar 10 2004 - 11:19:55 CST)
  - Re: coloring of trajectory Florian Barth (Thu Mar 11 2004 - 11:56:38 CST)
  - Re: coloring of trajectory John Stone (Thu Mar 11 2004 - 14:29:47 CST)
gziped files Diss Romain (Mon Mar 08 2004 - 10:00:49 CST)
- rotating a representation Harindar Keer (Mon Mar 08 2004 - 14:04:10 CST)
  - Re: rotating a representation John Stone (Mon Mar 08 2004 - 16:38:18 CST)
  - Re: rotating a representation Dallas Warren (Mon Mar 08 2004 - 15:39:53 CST)
- Re: gziped files John Stone (Mon Mar 08 2004 - 14:33:41 CST)
  - Re: gziped files Axel Kohlmeyer (Tue Mar 09 2004 - 06:19:39 CST)
    - Re: gziped files Brian Bennion (Tue Mar 09 2004 - 11:08:55 CST)
Problems with RMSD Maik Götte (Mon Mar 08 2004 - 09:20:56 CST)
- Re: Problems with RMSD John Stone (Mon Mar 08 2004 - 17:31:26 CST)
numeric python Dmitry Kovalsky (Mon Mar 08 2004 - 05:01:39 CST)
- Re: numeric python John Stone (Mon Mar 08 2004 - 10:17:18 CST)
- Re: numeric python Brian Bennion (Mon Mar 08 2004 - 10:07:17 CST)
- Re: numeric python Justin Gullingsrud (Mon Mar 08 2004 - 09:49:27 CST)
hydrophobic surface area calculation Markus Laub (Mon Mar 08 2004 - 05:01:59 CST)
- Re: hydrophobic surface area calculation John Stone (Mon Mar 08 2004 - 17:38:54 CST)
How to make VMD work with Phantom haptic device? Fung Wai Keung (Mon Mar 08 2004 - 01:51:40 CST)
- Re: How to make VMD work with Phantom haptic device? John Stone (Mon Mar 08 2004 - 10:14:42 CST)
  - Re: How to make VMD work with Phantom haptic device? John Stone (Tue Mar 16 2004 - 10:33:33 CST)
- Formation of a gold layer lmfok_at_acae.cuhk.edu.hk (Mon Mar 08 2004 - 20:41:33 CST)
  - Re: Formation of a gold layer John Stone (Tue Mar 16 2004 - 10:24:23 CST)
(no subject) Jerry Ebalunode (Fri Mar 05 2004 - 23:09:07 CST)
- Re: your mail John Stone (Sat Mar 06 2004 - 13:05:07 CST)
- Re: your mail John Stone (Mon Mar 08 2004 - 17:20:52 CST)
  - Re: your mail athlon 64/opteron VMD Jerry Ebalunode (Mon Mar 08 2004 - 17:34:48 CST)
    - Re: your mail athlon 64/opteron VMD John Stone (Mon Mar 08 2004 - 17:41:17 CST)
unusual bonds Satyavani Vemparala (Sat Mar 06 2004 - 04:31:27 CST)
- Re: unusual bonds John Stone (Mon Mar 08 2004 - 17:28:46 CST)
athlon64 version of vmd Jerry Ebalunode (Fri Mar 05 2004 - 13:08:52 CST)
- Re: athlon64 version of vmd Brian Bennion (Fri Mar 05 2004 - 16:30:57 CST)
- Re: athlon64 version of vmd John Stone (Fri Mar 05 2004 - 17:39:47 CST)
COR plugin for SGI Josh Ward (Fri Mar 05 2004 - 08:27:57 CST)
- Updated plugins for VMD 1.8.x John Stone (Fri Mar 05 2004 - 13:23:45 CST)
color problem with Ati Fire GL E1 Luis Gracia (Wed Mar 03 2004 - 16:45:19 CST)
- Re: color problem with Ati Fire GL E1 John Stone (Wed Mar 03 2004 - 21:02:04 CST)
- Re: color problem with Ati Fire GL E1 Benjamin Goldsteen (Wed Mar 03 2004 - 22:23:31 CST)
  - Re: color problem with Ati Fire GL E1 Luis Gracia (Fri Mar 05 2004 - 19:50:20 CST)
  - Re: color problem with Ati Fire GL E1 Luis Gracia (Fri Mar 05 2004 - 19:46:32 CST)
Non-serious query Sanjeev B.S. (Wed Mar 03 2004 - 09:54:34 CST)
- Re: Non-serious query Brian Bennion (Wed Mar 03 2004 - 11:23:33 CST)
  - Re: Non-serious query Sanjeev B.S. (Wed Mar 03 2004 - 11:29:29 CST)
- Re: Non-serious query Jérôme Hénin (Wed Mar 03 2004 - 12:03:13 CST)
- Re: Non-serious query John Stone (Wed Mar 03 2004 - 13:20:30 CST)
  - Re: Non-serious query Sanjeev B.S. (Thu Mar 04 2004 - 00:11:31 CST)
    - Re: Non-serious query John Stone (Thu Mar 04 2004 - 10:54:22 CST)
    - RE: Non-serious query DongHoon Chung (Thu Mar 04 2004 - 18:16:23 CST)
Using VMD for non-atomic simulations? Olaf Lenz (Wed Mar 03 2004 - 03:51:39 CST)
- Re: Using VMD for non-atomic simulations? Nguyen Hoang Phuong (Wed Mar 03 2004 - 06:21:57 CST)
- Re: Using VMD for non-atomic simulations? John Stone (Wed Mar 03 2004 - 10:03:13 CST)
Color error on loading Josh Ward (Tue Mar 02 2004 - 14:30:51 CST)
- Re: Color error on loading John Stone (Tue Mar 02 2004 - 17:24:45 CST)
  - Re: Color error on loading Olaf Lenz (Wed Mar 03 2004 - 03:12:02 CST)
    - Re: Color error on loading John Stone (Wed Mar 03 2004 - 09:58:20 CST)
RE: Using VMD with Chromium Brian Dotson (Tue Mar 02 2004 - 06:12:42 CST)
- Re: Using VMD with Chromium John Stone (Tue Mar 02 2004 - 09:56:59 CST)
passive stereo setup on linux Joe Zhou (Mon Mar 01 2004 - 16:18:06 CST)
- Re: passive stereo setup on linux John Stone (Mon Mar 01 2004 - 18:54:17 CST)
  - Re: passive stereo setup on linux Joe Zhou (Tue Mar 02 2004 - 12:28:17 CST)
- Re: passive stereo setup on linux John Stone (Mon Mar 01 2004 - 18:53:27 CST)
Using VMD with Chromium Brian Dotson (Mon Mar 01 2004 - 06:59:34 CST)
- Re: Using VMD with Chromium John Stone (Mon Mar 01 2004 - 09:51:04 CST)
  - Re: Using VMD with Chromium Cesar Delgado (Tue Mar 02 2004 - 19:26:22 CST)
  - Re: Using VMD with Chromium Brian Dotson (Wed Mar 03 2004 - 07:22:01 CST)
- RE: Using VMD with Chromium Stewart Dickson (Wed May 19 2004 - 11:22:54 CDT)
waters within hydrophobic pore of protein Satyavani Vemparala (Sun Feb 29 2004 - 10:45:49 CST)
- Re: waters within hydrophobic pore of protein Axel Kohlmeyer (Mon Mar 01 2004 - 02:20:19 CST)
  - Re: waters within hydrophobic pore of protein Justin Gullingsrud (Mon Mar 01 2004 - 03:35:20 CST)
I've tried latest vmd but still problems with mdcrd/crd/rst parser Teletchéa Stéphane (Fri Feb 27 2004 - 12:19:56 CST)
- Re: I've tried latest vmd but still problems with mdcrd/crd/rst parser John Stone (Fri Feb 27 2004 - 14:07:28 CST)
RE: atomselect within Wagener, M. (Markus) (Fri Feb 27 2004 - 04:39:48 CST)
Hydrogen Bond Energy Sichun Yang (Wed Feb 25 2004 - 12:31:45 CST)
- Re: Hydrogen Bond Energy Axel Kohlmeyer (Thu Feb 26 2004 - 03:46:52 CST)
atomselect within Wagener, M. (Markus) (Wed Feb 25 2004 - 08:23:37 CST)
- Re: atomselect within John Stone (Wed Feb 25 2004 - 13:28:37 CST)
finding charges and diameters Shuaib Shahid (Wed Feb 25 2004 - 03:21:52 CST)
finding charges and diameters Shuaib Shahid (Tue Feb 24 2004 - 11:20:27 CST)
entropy calculations Ioana Cozmuta (Mon Feb 23 2004 - 17:41:54 CST)
Test version of VMD 1.8.3 for Linux on AMD x86_64 (Athlon64 / Opteron) available... John Stone (Mon Feb 23 2004 - 14:14:33 CST)
APBS Plugin for VMD Eamon Caddigan (Mon Feb 23 2004 - 14:14:33 CST)
vmd on ppc (G4) apeyser_at_newssun.med.miami.edu (Mon Feb 23 2004 - 14:07:25 CST)
- Re: vmd on ppc (G4) John Stone (Mon Feb 23 2004 - 16:30:39 CST)
add a new color Vlad Cojocaru (Sun Feb 22 2004 - 12:51:11 CST)
- Re: add a new color John Stone (Mon Feb 23 2004 - 11:07:41 CST)
Rama plot Ioana Cozmuta (Fri Feb 20 2004 - 19:48:17 CST)
- Re: Rama plot John Stone (Mon Feb 23 2004 - 10:58:56 CST)
Compiling vmd for ppc linux apeyser_at_newssun.med.miami.edu (Fri Feb 20 2004 - 13:55:41 CST)
- Re: Compiling vmd for ppc linux John Stone (Fri Feb 20 2004 - 16:23:33 CST)
Compiling vmd for ppc linux apeyser_at_newssun.med.miami.edu (Fri Feb 20 2004 - 13:46:50 CST)
save psf Ekta Khurana (Thu Feb 19 2004 - 16:44:16 CST)
Stationary labels; delays ("wait") in scripts Hoch,Jeffrey (Thu Feb 19 2004 - 06:40:59 CST)
- Re: Stationary labels; delays ("wait") in scripts John Stone (Mon Feb 23 2004 - 13:18:57 CST)
adding bonds between segments Streiff, John H. (Tue Feb 17 2004 - 14:20:24 CST)
- Re: adding bonds between segments Justin Gullingsrud (Thu Feb 19 2004 - 12:28:52 CST)
adding waters only in top of lipid Satyavani Vemparala (Tue Feb 17 2004 - 12:15:55 CST)
- Re: adding waters only in top of lipid Justin Gullingsrud (Thu Feb 19 2004 - 12:30:36 CST)
Customizing vdw radius Marcin Krol (Tue Feb 17 2004 - 03:57:21 CST)
- Re: Customizing vdw radius John Stone (Tue Feb 17 2004 - 10:32:22 CST)
veclength Juan Alfredo Freites (Mon Feb 16 2004 - 21:54:55 CST)
- Re: veclength John Stone (Mon Feb 16 2004 - 23:56:13 CST)
  - Re: veclength Justin Gullingsrud (Thu Feb 19 2004 - 12:45:52 CST)
ca contact map Y U Sasidhar (Mon Feb 16 2004 - 20:36:06 CST)
- Re: ca contact map John Stone (Tue Feb 17 2004 - 10:40:01 CST)
(no subject) B $B6Q (Mon Feb 16 2004 - 19:44:43 CST)
- Re: your mail John Stone (Mon Feb 16 2004 - 22:19:55 CST)
VMD-L downtime Feb 18/19... John Stone (Mon Feb 16 2004 - 15:21:14 CST)
repitition of residue numbers in LIPIDS Satyavani Vemparala (Mon Feb 16 2004 - 15:18:49 CST)
- Re: repitition of residue numbers in LIPIDS John Stone (Mon Feb 16 2004 - 17:45:08 CST)
- Re: repitition of residue numbers in LIPIDS Jim Phillips (Mon Feb 16 2004 - 17:55:50 CST)
  - Re: repitition of residue numbers in LIPIDS Satyavani Vemparala (Tue Feb 17 2004 - 16:48:51 CST)
    - Re: repitition of residue numbers in LIPIDS Jim Phillips (Tue Feb 17 2004 - 17:14:42 CST)
duplicate atom coordinates in PDB files Streiff, John H. (Mon Feb 16 2004 - 11:57:51 CST)
- Re: duplicate atom coordinates in PDB files John Stone (Mon Feb 16 2004 - 15:10:06 CST)
For Users of VMD Yojana Joshi (Mon Feb 16 2004 - 09:58:50 CST)
RE: removing residues/fragments from the system Kim, Kwiseon (Sun Feb 15 2004 - 09:09:07 CST)
removing residues/fragments from the system Satyavani Vemparala (Sat Feb 14 2004 - 21:00:02 CST)
- RE:removing residues/fragments from the system Streiff, John H. (Tue Feb 17 2004 - 10:15:37 CST)
missing RMSD tool in extensions menu Sergio E. Wong (Fri Feb 13 2004 - 18:22:42 CST)
- Re: missing RMSD tool in extensions menu John Stone (Sat Feb 14 2004 - 01:28:56 CST)
RE: removing surrounding water molecules Kim, Kwiseon (Fri Feb 13 2004 - 16:51:33 CST)
removing surrounding water molecules Bamidele Adisa (Fri Feb 13 2004 - 16:03:15 CST)
- Re: removing surrounding water molecules Brian Bennion (Fri Feb 13 2004 - 16:53:24 CST)
- Re: removing surrounding water molecules John Stone (Fri Feb 13 2004 - 17:40:24 CST)
- Re: removing surrounding water molecules p.w.fowler_at_qmul.ac.uk (Fri Feb 13 2004 - 17:04:08 CST)
Some pdb file contains many frames : How Can I retrieve all in a frame... piriboy (Thu Feb 12 2004 - 18:50:30 CST)
- Re: Some pdb file contains many frames : How Can I retrieve all in a frame... John Stone (Fri Feb 13 2004 - 11:31:34 CST)
- Re: Some pdb file contains many frames : How Can I retrieve all in a frame... John Stone (Mon Feb 16 2004 - 11:50:58 CST)
- Re: Some pdb file contains many frames : How Can I retrieve all in a frame... John Stone (Mon Feb 16 2004 - 17:25:36 CST)
stripping off oxygen groups Ross J. Toedte (Thu Feb 12 2004 - 14:31:39 CST)
- Re: stripping off oxygen groups John Stone (Thu Feb 12 2004 - 16:49:01 CST)
Where can I read the specifications on molecular file formats? Hess, Bret (Wed Feb 11 2004 - 22:46:17 CST)
- Re: Where can I read the specifications on molecular file formats? John Stone (Thu Feb 12 2004 - 00:51:08 CST)
solvating lipid bilayers Satyavani Vemparala (Wed Feb 11 2004 - 20:30:38 CST)
- Re: solvating lipid bilayers John Stone (Thu Feb 12 2004 - 17:17:19 CST)
any body else have VMD problems with Linux + ATI FireGL X1-256p + fglrx-glc22-4.3.0-3.7.0 chris.harwell_at_pharma.novartis.com (Wed Feb 11 2004 - 16:16:46 CST)
- Re: any body else have VMD problems with Linux + ATI FireGL X1-256p + fglrx-glc22-4.3.0-3.7.0 Dallas Warren (Wed Feb 11 2004 - 17:14:28 CST)
  - Re: any body else have VMD problems with Linux + ATI FireGL X1-256p + fglrx-glc22-4.3.0-3.7.0 John Stone (Wed Feb 11 2004 - 20:02:26 CST)
- Re: any body else have VMD problems with Linux + ATI FireGL X1-256p + fglrx-glc22-4.3.0-3.7.0 John Stone (Wed Feb 11 2004 - 18:33:51 CST)
attempting to source a script Kristy L. Mardis (Wed Feb 11 2004 - 15:51:17 CST)
- Re: attempting to source a script Brian Bennion (Wed Feb 11 2004 - 16:49:41 CST)
- Re: attempting to source a script Tim Isgro (Wed Feb 11 2004 - 18:50:04 CST)
  - Re: attempting to source a script Andrew Dalke (Thu Feb 12 2004 - 08:41:46 CST)
    - Re: attempting to source a script Tim Isgro (Thu Feb 12 2004 - 13:58:28 CST)
- Re: attempting to source a script Oliver Beckstein (Wed Feb 11 2004 - 18:05:24 CST)
- Re: attempting to source a script John Stone (Wed Feb 11 2004 - 18:39:41 CST)
xyz files and VMD 1.8.2 Samartha G. Anekal (Wed Feb 11 2004 - 12:32:22 CST)
- Re: xyz files and VMD 1.8.2 John Stone (Wed Feb 11 2004 - 18:49:54 CST)
New stage? Jeff Hoch (Tue Feb 10 2004 - 08:30:02 CST)
- Re: New stage? John Stone (Wed Feb 11 2004 - 18:57:25 CST)
experience using VMD with 3-D printers? Karsten Suhre (Mon Feb 09 2004 - 08:30:25 CST)
- Re: experience using VMD with 3-D printers? John Stone (Mon Feb 09 2004 - 10:49:31 CST)
  - Re: experience using VMD with 3-D printers? Karsten Suhre (Tue Feb 10 2004 - 06:50:59 CST)
  - Apple VMD not showing gro file properly barrett (Tue Feb 10 2004 - 07:56:50 CST)
tcl question Vlad Cojocaru (Sat Feb 07 2004 - 06:47:17 CST)
- Re: tcl question Axel Kohlmeyer (Sat Feb 07 2004 - 08:13:33 CST)
- Re: tcl question Juan Alfredo Freites (Sat Feb 07 2004 - 12:28:18 CST)
Spatial Distributionb Functions CHAUMONT Alain (Thu Feb 05 2004 - 03:01:46 CST)
- Re: Spatial Distributionb Functions Axel Kohlmeyer (Thu Feb 05 2004 - 04:12:31 CST)
- Re: Spatial Distributionb Functions Oliver Beckstein (Thu Feb 05 2004 - 12:35:41 CST)
Densities for protein and ligand Jim Nettles (Wed Feb 04 2004 - 11:52:31 CST)
- Re: Densities for protein and ligand John Stone (Fri Feb 06 2004 - 13:56:17 CST)
random graphics outages on startup Oliver Beckstein (Wed Feb 04 2004 - 08:06:33 CST)
- Re: random graphics outages on startup Bogdan Costescu (Wed Feb 04 2004 - 10:47:59 CST)
  - Re: random graphics outages on startup Oliver Beckstein (Thu Feb 05 2004 - 12:23:42 CST)
- Re: random graphics outages on startup John Stone (Wed Feb 04 2004 - 10:42:19 CST)
Helical King Angle Saladino, Alex (Mon Feb 02 2004 - 16:41:45 CST)
- Re: Helical King Angle Mike McCallum (Wed Feb 04 2004 - 11:07:39 CST)
amidated C-terminus and pyroglutamate Han Choe (Sat Jan 31 2004 - 04:01:05 CST)
fwd [Re: Does VMD support LES simulations?] John Stone (Fri Jan 30 2004 - 13:10:34 CST)
test Vlad Cojocaru (Fri Jan 30 2004 - 07:36:53 CST)
- VMD-L mail delivery rate... was Re: test John Stone (Fri Jan 30 2004 - 10:02:45 CST)
  - Sorry ... the test was because of ..... Vlad Cojocaru (Fri Jan 30 2004 - 10:07:15 CST)
a question Vlad Cojocaru (Fri Jan 30 2004 - 07:29:38 CST)
Error loading .cor files from CHARMM using dcd Tjaart de Beer (Fri Jan 30 2004 - 06:58:22 CST)
- Re: Error loading .cor files from CHARMM using dcd John Stone (Wed Feb 04 2004 - 13:02:45 CST)
Recognition of backbone in 5'-end Sanjeev B.S. (Fri Jan 30 2004 - 05:40:46 CST)
few colors in new ribbons representation - raytrace output Charles_at_Schwieters.org (Thu Jan 29 2004 - 17:40:15 CST)
- Re: few colors in new ribbons representation - raytrace output John Stone (Thu Jan 29 2004 - 20:21:53 CST)
  - Re: few colors in new ribbons representation - raytrace output Charles_at_Schwieters.org (Thu Jan 29 2004 - 21:31:23 CST)
    - Re: few colors in new ribbons representation - raytrace output John Stone (Fri Jan 30 2004 - 00:57:40 CST)
- Re: few colors in new ribbons representation - raytrace output John Stone (Sat Jan 31 2004 - 16:47:43 CST)
Does VMD support LES simulations? Vlad Cojocaru (Thu Jan 29 2004 - 11:17:28 CST)
- Re: Does VMD support LES simulations? John Stone (Fri Jan 30 2004 - 01:26:48 CST)
an arrow for a dipole Marcelo A. Carignano (Wed Jan 28 2004 - 13:30:41 CST)
- Re: an arrow for a dipole John Stone (Wed Jan 28 2004 - 18:26:45 CST)
Perspective Ratio Problems Matt Elder (Wed Jan 28 2004 - 12:41:54 CST)
- Re: Perspective Ratio Problems John Stone (Wed Jan 28 2004 - 14:59:21 CST)
Helical Tilt Angle Saladino, Alex (Wed Jan 28 2004 - 08:31:56 CST)
- Re: Helical Tilt Angle Justin Gullingsrud (Wed Jan 28 2004 - 11:23:15 CST)
surf for mac Yusu Wang (Mon Jan 26 2004 - 14:23:42 CST)
- Re: surf for mac John Stone (Mon Jan 26 2004 - 16:38:59 CST)
  - Re: surf for mac Yusu Wang (Tue Jan 27 2004 - 00:21:30 CST)
    - Re: surf for mac John Stone (Tue Jan 27 2004 - 15:32:11 CST)
    - Re: surf for mac Yusu Wang (Tue Jan 27 2004 - 19:26:16 CST)
patch in psfgen - ionic interaction and hydrogen bond Han Choe (Sun Jan 25 2004 - 20:42:50 CST)
- Re: patch in psfgen - ionic interaction and hydrogen bond Jim Phillips (Mon Jan 26 2004 - 17:41:55 CST)
OpenGL library loading Steven F. Killen (Thu Jan 22 2004 - 13:34:26 CST)
- Re: OpenGL library loading John Stone (Thu Jan 22 2004 - 16:13:37 CST)
  - Re: OpenGL library loading Steven F. Killen (Tue Jan 27 2004 - 11:26:51 CST)
    - Re: OpenGL library loading John Stone (Tue Jan 27 2004 - 13:04:08 CST)
  - Re: OpenGL library loading John Stone (Tue Jan 27 2004 - 15:20:56 CST)
    - Re: OpenGL library loading Steven F. Killen (Tue Jan 27 2004 - 16:23:35 CST)
    - Re: OpenGL library loading John Stone (Tue Jan 27 2004 - 16:31:56 CST)
Problems with graphics.color function under VMD's python interpreter Manuel Melle-Franco (Tue Jan 20 2004 - 10:20:55 CST)
- Re: Problems with graphics.color function under VMD's python interpreter John Stone (Fri Feb 13 2004 - 17:43:27 CST)
How to install VMD on AIX5 OpenGL server Dai Ling (Tue Jan 20 2004 - 04:52:47 CST)
- Re: How to install VMD on AIX5 OpenGL server John Stone (Tue Jan 20 2004 - 10:44:30 CST)
  - Re: How to install VMD on AIX5 OpenGL server John Stone (Wed Feb 04 2004 - 13:06:43 CST)
about frame moggces_at_rx.mc.ntu.edu.tw (Mon Jan 19 2004 - 20:17:40 CST)
- Re: about frame John Stone (Tue Jan 20 2004 - 10:50:37 CST)
docking in VMD Han Choe (Mon Jan 19 2004 - 06:03:48 CST)
- Re: docking in VMD John Stone (Mon Jan 19 2004 - 07:54:36 CST)
  - RE: docking in VMD Han Choe (Tue Jan 20 2004 - 01:24:57 CST)
multiple id's himanshu chandola (Mon Jan 19 2004 - 15:44:29 CST)
- Re: multiple id's Jim Phillips (Mon Jan 19 2004 - 06:50:12 CST)
Hi phubbard_at_post.its.mcw.edu (Sun Jan 18 2004 - 22:09:47 CST)
- Re: Hi John Stone (Sun Jan 18 2004 - 23:44:30 CST)
Hybond calulator and display Jerry Ebalunode (Fri Jan 16 2004 - 12:24:30 CST)
- Re: Hybond calulator and display John Stone (Fri Jan 16 2004 - 13:07:09 CST)
solvate function zhilei chen (Sat Jan 10 2004 - 12:18:53 CST)
- Re: solvate function John Stone (Sat Jan 10 2004 - 17:33:36 CST)
Re: New version very slow? Fixed also... Patrick Ladam (Fri Jan 09 2004 - 09:19:40 CST)
Question about Python and Mac osx simon stockes (Thu Jan 08 2004 - 17:06:00 CST)
- Re: Question about Python and Mac osx John Stone (Sat Jan 10 2004 - 17:32:00 CST)
RE: PBC Mauricio C. Tripp (Tue Jan 06 2004 - 13:32:31 CST)
- Re: PBC Axel Kohlmeyer (Tue Jan 06 2004 - 16:49:44 CST)
  - Re: PBC John Stone (Tue Jan 06 2004 - 18:27:10 CST)
- Re: PBC John Stone (Tue Jan 06 2004 - 18:25:44 CST)
PBC Mauricio C. Tripp (Tue Jan 06 2004 - 10:25:51 CST)
- Re: PBC Axel Kohlmeyer (Tue Jan 06 2004 - 12:19:50 CST)
VMD 1.8.2 on MacOS 10.3 Ghislain Deslongchamps (Mon Jan 05 2004 - 19:32:22 CST)
- Re: VMD 1.8.2 on MacOS 10.3 John Stone (Tue Jan 06 2004 - 01:30:26 CST)
RE: dcd reading error Mauricio C. Tripp (Fri Jan 02 2004 - 14:27:06 CST)
- Re: dcd reading error John Stone (Fri Jan 02 2004 - 14:34:07 CST)
- RE: dcd reading error Mauricio C. Tripp (Fri Jan 02 2004 - 13:58:44 CST)
- RE: dcd reading error Mauricio C. Tripp (Fri Jan 02 2004 - 13:48:06 CST)
- RE: dcd reading error Bogdan Costescu (Sat Jan 03 2004 - 10:07:49 CST)
  - Re: dcd reading error John Stone (Sat Jan 03 2004 - 21:35:03 CST)
dcd reading error Mauricio C. Tripp (Fri Jan 02 2004 - 11:23:08 CST)
- Re: dcd reading error John Stone (Fri Jan 02 2004 - 13:05:17 CST)
Cartoon representation for large molecules Aurore Zyto (Wed Dec 31 2003 - 15:43:11 CST)
- Re: Cartoon representation for large molecules Gadi Oron (Thu Jan 01 2004 - 03:52:04 CST)
- Re: Cartoon representation for large molecules John Stone (Fri Jan 02 2004 - 13:29:32 CST)
vmd and msms for mac Jerry Ebalunode (Mon Dec 22 2003 - 09:15:05 CST)
- Re: vmd and msms for mac John Stone (Mon Dec 22 2003 - 11:29:25 CST)
Announce: CPMD VMD visualization tutorial Axel Kohlmeyer (Thu Dec 18 2003 - 13:25:56 CST)
graphics display works sometimes Luis Gracia (Tue Dec 16 2003 - 21:42:44 CST)
- Re: graphics display works sometimes John Stone (Tue Dec 16 2003 - 23:07:43 CST)
movie making in batch mode barrett (Tue Dec 16 2003 - 10:07:33 CST)
- Re: movie making in batch mode John Stone (Tue Dec 16 2003 - 20:47:04 CST)
  - RE: movie making in batch mode barrett (Fri Feb 06 2004 - 04:57:01 CST)
CHARMM CRD files: COR plugin Josh Ward (Fri Dec 12 2003 - 14:52:22 CST)
- Re: CHARMM CRD files: COR plugin John Stone (Tue Dec 16 2003 - 21:02:57 CST)
topology and parameter files ? Harit Jani (Thu Dec 11 2003 - 18:09:52 CST)
ACTC Triangle Consolidation Tyler Luchko (Thu Dec 11 2003 - 16:37:33 CST)
- Re: ACTC Triangle Consolidation John Stone (Fri Dec 12 2003 - 10:06:50 CST)
  - Re: ACTC Triangle Consolidation Tyler Luchko (Fri Dec 12 2003 - 12:24:06 CST)
    - Re: ACTC Triangle Consolidation John Stone (Fri Dec 12 2003 - 14:32:00 CST)
Different number of atoms trajectory frames Manuel Melle-Franco (Thu Dec 11 2003 - 05:14:04 CST)
- Re: Different number of atoms trajectory frames John Stone (Thu Dec 11 2003 - 10:12:35 CST)
  - Re: Different number of atoms trajectory frames John Stone (Thu Dec 11 2003 - 10:41:34 CST)
.psf and .params files for IMD Harit Jani (Wed Dec 10 2003 - 19:08:02 CST)
- Re: .psf and .params files for IMD John Stone (Thu Dec 11 2003 - 10:15:30 CST)
Re: New version very slow?... me too John Stone (Wed Dec 10 2003 - 09:49:14 CST)
New version very slow? Dallas Warren (Tue Dec 09 2003 - 19:45:09 CST)
- Re: New version very slow? John Stone (Wed Dec 10 2003 - 00:07:59 CST)
  - Re: New version very slow? Dallas Warren (Wed Dec 10 2003 - 22:21:49 CST)
  - Re: New version very slow? Dallas Warren (Thu Dec 11 2003 - 00:53:38 CST)
    - Re: New version very slow? Dallas Warren (Thu Jan 08 2004 - 20:17:17 CST)
(no subject) Ioana Cozmuta (Mon Dec 08 2003 - 18:10:49 CST)
- Re: your mail John Stone (Mon Dec 08 2003 - 23:58:26 CST)
  - Re: Re: your mail Marc Baaden (Tue Dec 09 2003 - 10:54:28 CST)
stride error Tyler Luchko (Mon Dec 08 2003 - 12:36:03 CST)
- Re: stride error John Stone (Wed Dec 10 2003 - 00:42:08 CST)
remote display Juan Alfredo Freites (Sat Dec 06 2003 - 23:16:38 CST)
- Re: remote display John Stone (Thu Dec 11 2003 - 10:39:01 CST)
  - Re: remote display Juan Alfredo Freites (Thu Dec 11 2003 - 12:28:18 CST)
autoionize Lei Guo (Fri Dec 05 2003 - 17:36:26 CST)
Announce: VMD 1.8.2 released!! John Stone (Fri Dec 05 2003 - 14:53:13 CST)
xplor vs. charmm PSF files / psfgen Mike McCallum (Thu Dec 04 2003 - 00:05:25 CST)
- Re: xplor vs. charmm PSF files / psfgen Justin Gullingsrud (Thu Dec 04 2003 - 01:17:52 CST)
vmd crashes after startup... Luis Guillermo Cota Preciado (Wed Dec 03 2003 - 15:51:57 CST)
- Re: vmd crashes after startup... John Stone (Wed Dec 03 2003 - 18:44:26 CST)
  - Re: vmd crashes after startup... Benjamin Goldsteen (Wed Dec 03 2003 - 22:46:17 CST)
Stride problems in XP.... Jorge Hernanez Fernandez (Tue Dec 02 2003 - 11:52:19 CST)
- Re: Stride problems in XP.... John Stone (Tue Dec 02 2003 - 13:41:03 CST)
periodic box lines Anna Modzelewska (Mon Dec 01 2003 - 06:50:05 CST)
- Re: periodic box lines John Stone (Mon Dec 01 2003 - 12:43:36 CST)
Fwd: Re: graphics card Benjamin Goldsteen (Sun Nov 30 2003 - 19:02:23 CST)
Background colour Derek Ng (Sat Nov 29 2003 - 23:38:26 CST)
- Re: Background colour Jérôme Hénin (Sun Nov 30 2003 - 03:39:16 CST)
  - graphics card Nguyen Hoang Phuong (Sun Nov 30 2003 - 09:41:16 CST)
    - Re: graphics card Jérôme Hénin (Sun Nov 30 2003 - 11:18:29 CST)
draw multiple frames Karunesh Arora (Fri Nov 28 2003 - 21:30:03 CST)
- Re: draw multiple frames John Stone (Mon Dec 01 2003 - 12:16:16 CST)
1.8.2beta Mike McCallum (Tue Nov 25 2003 - 16:38:38 CST)
plt plugin found Oliver Beckstein (Tue Nov 25 2003 - 09:33:14 CST)
plt plugin missing (?) Oliver Beckstein (Tue Nov 25 2003 - 09:14:51 CST)
vmdmovie in OS X.3 Dmitry A Kondrashov (Mon Nov 24 2003 - 16:42:10 CST)
- Re: vmdmovie in OS X.3 John Stone (Mon Nov 24 2003 - 18:51:01 CST)
  - Re: vmdmovie in OS X.3 John Stone (Tue Nov 25 2003 - 15:51:28 CST)
- Re: vmdmovie in OS X.3 Robert Brunner (Mon Nov 24 2003 - 19:15:34 CST)
- Re: vmdmovie in OS X.3 Robert Brunner (Mon Nov 24 2003 - 19:26:44 CST)
  - Re: vmdmovie in OS X.3 John Stone (Mon Nov 24 2003 - 21:07:12 CST)
Molecular Simulation using PHANToM Haptic Harit Jani (Mon Nov 24 2003 - 16:36:01 CST)
- Re: Molecular Simulation using PHANToM Haptic Jim Phillips (Mon Nov 24 2003 - 18:24:47 CST)
about command readpdb? Li Qiang (Mon Nov 24 2003 - 09:12:11 CST)
- Re: about command readpdb? John Stone (Mon Nov 24 2003 - 14:14:21 CST)
MSMS probe radius and CHARMM VDW radii Tyler Luchko (Sun Nov 23 2003 - 16:18:10 CST)
- Re: MSMS probe radius and CHARMM VDW radii John Stone (Mon Dec 01 2003 - 15:37:46 CST)
rmsd from VMD Madhuri Agashe (Sun Nov 23 2003 - 13:34:32 CST)
- Re: rmsd from VMD Tim Isgro (Mon Nov 24 2003 - 15:46:21 CST)
Matching electron density map and PDB Keith Refson (Sat Nov 22 2003 - 11:16:30 CST)
- Re: Matching electron density map and PDB John Stone (Mon Dec 01 2003 - 17:27:09 CST)
  - Re: Matching electron density map and PDB Keith Refson (Tue Dec 02 2003 - 03:43:41 CST)
AMBER (old ?) nucleic acids names not recognised Teletchéa Stéphane (Fri Nov 21 2003 - 03:57:04 CST)
New version of CatDCD available Justin Gullingsrud (Thu Nov 20 2003 - 15:36:57 CST)
antialiasing problem ailong (Thu Nov 20 2003 - 12:54:22 CST)
- Re: antialiasing problem Eamon Caddigan (Thu Nov 20 2003 - 15:15:00 CST)
about resid moggces (Thu Nov 20 2003 - 11:16:17 CST)
- Re: about resid Justin Gullingsrud (Thu Nov 20 2003 - 12:16:35 CST)
Parameter-Topology-Repository Jan Saam (Wed Nov 19 2003 - 11:56:41 CST)
- Re: namd-l: LYC Parameter-Topology ? Harindar Keer (Wed Nov 19 2003 - 13:01:55 CST)
Rodlike mixture nabil Khalil (Wed Nov 19 2003 - 07:02:47 CST)
- Re: Rodlike mixture John Stone (Wed Nov 19 2003 - 10:27:33 CST)
(no subject) Alexandre Vakhrouchev (Wed Nov 19 2003 - 02:11:14 CST)
- Re: Eugen Leitl (Wed Nov 19 2003 - 04:13:28 CST)
  - Re: John Stone (Wed Nov 19 2003 - 10:22:01 CST)
(no subject) Dongsheng Zhang (Tue Nov 18 2003 - 17:24:20 CST)
- Re: John Stone (Wed Nov 19 2003 - 10:36:55 CST)
Updated VMD-L archive page... John Stone (Tue Nov 18 2003 - 13:10:07 CST)
Naming in XmGrace Teletchéa Stéphane (Tue Nov 18 2003 - 07:03:10 CST)
- Re: Naming in XmGrace himanshu chandola (Tue Nov 18 2003 - 20:09:09 CST)
- Re: Naming in XmGrace John Stone (Tue Nov 18 2003 - 10:05:04 CST)
  - Re: Naming in XmGrace Teletchéa Stéphane (Tue Nov 18 2003 - 10:39:08 CST)
Reading in unit cell David Chalmers (Mon Nov 17 2003 - 17:45:13 CST)
- Re: Reading in unit cell Justin Gullingsrud (Mon Nov 17 2003 - 22:15:14 CST)
subscribe and questions Albert Sun (Fri Nov 14 2003 - 13:06:34 CST)
- Re: subscribe and questions John Stone (Fri Nov 14 2003 - 14:45:33 CST)
send data on demand using IMD? Jan Saam (Thu Nov 13 2003 - 11:59:10 CST)
- Re: send data on demand using IMD? John Stone (Fri Nov 14 2003 - 10:24:05 CST)
I am sorry Tauna Rignall (Wed Nov 12 2003 - 11:25:31 CST)
"nucleic" selection Vlad Cojocaru (Wed Nov 12 2003 - 10:45:47 CST)
- Re: "nucleic" selection Andrew Dalke (Wed Nov 12 2003 - 13:29:15 CST)
"nucleic" selection Vlad Cojocaru (Wed Nov 12 2003 - 09:17:56 CST)
"nucleic" selection Vlad Cojocaru (Wed Nov 12 2003 - 04:55:26 CST)
Re: Highlighting nearest atom ? (wrt to a tool) (fwd from eugen@leitl.org) Eugen Leitl (Wed Nov 12 2003 - 04:51:06 CST)
RE: POV-Ray Felix Frolow (Wed Nov 12 2003 - 01:57:42 CST)
uninitialized coordinates himanshu chandola (Tue Nov 11 2003 - 17:58:45 CST)
- Re: uninitialized coordinates Jim Phillips (Tue Nov 11 2003 - 17:26:02 CST)
unit cell Juan Alfredo Freites (Mon Nov 10 2003 - 14:43:42 CST)
- Re: unit cell John Stone (Mon Nov 10 2003 - 16:44:22 CST)
  - Re: unit cell Y U Sasidhar (Mon Nov 10 2003 - 21:25:08 CST)
    - Re: unit cell John Stone (Wed Nov 12 2003 - 17:21:32 CST)
- x-plor map file and readedm Francesca Mocci (Tue Nov 11 2003 - 09:11:11 CST)
  - Re: x-plor map file and readedm John Stone (Tue Nov 11 2003 - 10:56:28 CST)
    - Re: x-plor map file and readedm Francesca Mocci (Wed Nov 12 2003 - 05:47:26 CST)
    - Re: x-plor map file and readedm John Stone (Tue Nov 18 2003 - 14:54:13 CST)
POV-Ray Tauna Rignall (Fri Nov 07 2003 - 14:42:13 CST)
- Re: POV-Ray John Stone (Mon Nov 10 2003 - 13:17:30 CST)
  - Re: POV-Ray Tauna Rignall (Tue Nov 11 2003 - 11:19:33 CST)
    - Re: POV-Ray Alexandre Vakhrouchev (Wed Nov 12 2003 - 03:33:03 CST)
    - Re: POV-Ray John Stone (Wed Nov 12 2003 - 17:23:27 CST)
Parameter/topology repository Jan Saam (Fri Nov 07 2003 - 06:05:15 CST)
- Re: Parameter/topology repository Mike McCallum (Fri Nov 07 2003 - 10:45:16 CST)
running vmd in batch mode Ioana Cozmuta (Thu Nov 06 2003 - 15:46:19 CST)
- Re: running vmd in batch mode John Stone (Thu Nov 06 2003 - 17:28:49 CST)
  - Re: running vmd in batch mode Ioana Cozmuta (Thu Nov 06 2003 - 19:19:30 CST)
    - Re: running vmd in batch mode John Stone (Thu Nov 06 2003 - 19:26:27 CST)
(no subject) Alexandre Vakhrouchev (Thu Nov 06 2003 - 06:43:18 CST)
- Re: John Stone (Thu Nov 06 2003 - 09:26:23 CST)
VMD and Mandrake Linux 9.1 Alexandre Vakhrouchev (Thu Nov 06 2003 - 02:59:04 CST)
- Re: VMD and Mandrake Linux 9.1 John Stone (Thu Nov 06 2003 - 15:34:46 CST)
- Re: VMD and Mandrake Linux 9.1 Teletchéa Stéphane (Fri Nov 07 2003 - 06:08:23 CST)
bigdcd Ioana Cozmuta (Wed Nov 05 2003 - 17:00:40 CST)
- Re: bigdcd Brian Bennion (Wed Nov 05 2003 - 17:52:38 CST)
  - Re: namd-l: Re: bigdcd Ioana Cozmuta (Wed Nov 05 2003 - 18:29:25 CST)
bigdcd Ioana Cozmuta (Tue Nov 04 2003 - 19:52:51 CST)
installation problem Laura De Luca (Tue Nov 04 2003 - 04:59:38 CST)
- Re: installation problem Brian Bennion (Tue Nov 04 2003 - 10:16:20 CST)
  - Re: installation problem John Stone (Wed Dec 30 2009 - 13:18:54 CST)
- Re: installation problem John Stone (Tue Nov 04 2003 - 10:47:44 CST)
Re: making movie on Mac OSX taeho.kim_at_utoronto.ca (Mon Nov 03 2003 - 21:52:13 CST)
- Re: Re: making movie on Mac OSX John Stone (Tue Nov 04 2003 - 13:16:25 CST)
stereo projection, Mac Jeff Hoch (Mon Nov 03 2003 - 15:19:56 CST)
- Re: stereo projection, Mac John Stone (Mon Nov 03 2003 - 17:00:12 CST)
Re: loading MD trajectories Luca Mollica (Mon Nov 03 2003 - 10:33:22 CST)
- Re: Re: loading MD trajectories John Stone (Tue Nov 04 2003 - 13:18:33 CST)
VMD and chromium Dave Pugmire (Fri Oct 31 2003 - 14:00:56 CST)
- Re: VMD and chromium John Stone (Fri Oct 31 2003 - 16:14:52 CST)
  - Re: VMD and chromium Dave Pugmire (Fri Oct 31 2003 - 17:56:43 CST)
    - Re: VMD and chromium John Stone (Mon Nov 03 2003 - 15:47:03 CST)
    - Re: VMD and chromium Dave Pugmire (Mon Nov 03 2003 - 16:39:55 CST)
accessing VMD help Fernandez-Alonso, F (Felix) (Fri Oct 31 2003 - 07:42:15 CST)
- RE: accessing VMD help John Robert Kitchin (Fri Oct 31 2003 - 09:22:10 CST)
- Re: accessing VMD help Brian Bennion (Fri Oct 31 2003 - 10:14:42 CST)
- Re: accessing VMD help Robert Campbell (Fri Oct 31 2003 - 09:51:53 CST)
secondary structure update Jérôme Hénin (Fri Oct 31 2003 - 07:37:31 CST)
- Re: secondary structure update james tomomi macdonald (Fri Oct 31 2003 - 09:44:09 CST)
- Re: secondary structure update John Stone (Fri Oct 31 2003 - 09:45:07 CST)
- Re: secondary structure update Brian Bennion (Fri Oct 31 2003 - 10:12:40 CST)
Radeon FireGL drivers crash VMD Lucas Watkins (Thu Oct 30 2003 - 06:53:47 CST)
- Re: Radeon FireGL drivers crash VMD Jérôme Hénin (Fri Oct 31 2003 - 04:38:39 CST)
  - Re: Radeon FireGL drivers crash VMD John Stone (Fri Oct 31 2003 - 09:47:36 CST)
- Re: Radeon FireGL drivers crash VMD John Stone (Fri Oct 31 2003 - 09:41:48 CST)
SMD: constant velocity or force pulling? Ioana Cozmuta (Thu Oct 30 2003 - 21:02:54 CST)
Updated plugins for VMD 1.8.1... John Stone (Thu Oct 30 2003 - 14:46:09 CST)
- stereo problem and VMD 1.8.2beta5 Marc Baaden (Tue Nov 11 2003 - 14:13:49 CST)
  - Re: stereo problem and VMD 1.8.2beta5 John Stone (Tue Nov 11 2003 - 15:36:04 CST)
Running VTK from VMD's python Lars Bruno Hansen (Thu Oct 30 2003 - 08:21:43 CST)
- Re: Running VTK from VMD's python Justin Gullingsrud (Thu Oct 30 2003 - 09:29:46 CST)
- Re: Running VTK from VMD's python John Stone (Thu Oct 30 2003 - 10:42:15 CST)
  - Re: Running VTK from VMD's python Lars Bruno Hansen (Thu Oct 30 2003 - 11:15:23 CST)
coloring by charge suzie.k.hight.1 (Wed Oct 29 2003 - 00:26:42 CST)
- Re: coloring by charge John Stone (Wed Oct 29 2003 - 13:46:01 CST)
Measuring distances between two sets of atoms in a dcd file Rudesh Toofanny (Tue Oct 28 2003 - 10:32:51 CST)
- Re: Measuring distances between two sets of atoms in a dcd file John Stone (Tue Oct 28 2003 - 14:18:12 CST)
aminoacid mutation Ioana Cozmuta (Mon Oct 27 2003 - 18:23:58 CST)
- Re: aminoacid mutation Y U Sasidhar (Mon Oct 27 2003 - 22:25:00 CST)
- Re: aminoacid mutation Brian Bennion (Tue Oct 28 2003 - 10:22:38 CST)
  - Re: aminoacid mutation Justin Gullingsrud (Tue Oct 28 2003 - 10:55:42 CST)
- Re: aminoacid mutation Jim Phillips (Tue Oct 28 2003 - 11:08:05 CST)
How to improve the running of VMD with data on remote servers Fred Salsbury (Mon Oct 27 2003 - 17:52:47 CST)
- Re: How to improve the running of VMD with data on remote servers John Stone (Tue Oct 28 2003 - 08:57:08 CST)
  - Re: How to improve the running of VMD with data on remote servers Robert Campbell (Thu Oct 30 2003 - 11:37:37 CST)
    - Re: How to improve the running of VMD with data on remote servers John Stone (Thu Oct 30 2003 - 13:26:15 CST)
getting ramachandran plots with VMD Madhuri Agashe (Mon Oct 27 2003 - 12:26:36 CST)
- Re: getting ramachandran plots with VMD John Stone (Mon Oct 27 2003 - 15:50:51 CST)
- Re: getting ramachandran plots with VMD Jérôme Hénin (Mon Oct 27 2003 - 15:47:06 CST)
VMD 1.8.1 MacOSX running very slow on new G4 1 GHz Powerbook Dafydd Jones (Thu Oct 23 2003 - 07:00:38 CDT)
- Re: VMD 1.8.1 MacOSX running very slow on new G4 1 GHz Powerbook John Stone (Thu Oct 23 2003 - 09:46:37 CDT)
- Re: VMD 1.8.1 MacOSX running very slow on new G4 1 GHz Powerbook Charles McCallum (Thu Oct 23 2003 - 13:12:39 CDT)
  - Re: VMD 1.8.1 MacOSX running very slow on new G4 1 GHz Powerbook John Stone (Thu Oct 23 2003 - 16:14:49 CDT)
  - Re: VMD 1.8.1 MacOSX running very slow on new G4 1 GHz Powerbook Benjamin Goldsteen (Sun Nov 09 2003 - 20:49:02 CST)
    - Re: VMD 1.8.1 MacOSX running very slow on new G4 1 GHz Powerbook John Stone (Mon Nov 10 2003 - 11:13:26 CST)
VMD and Chromium Cesar Delgado (Wed Oct 22 2003 - 18:13:57 CDT)
- Re: VMD and Chromium John Stone (Thu Oct 23 2003 - 02:32:50 CDT)
VMD and XP Jorge Pikunic (Wed Oct 22 2003 - 14:40:23 CDT)
- Re: VMD and XP John Stone (Wed Oct 22 2003 - 17:35:10 CDT)
  - Re: VMD and XP John Stone (Thu Oct 23 2003 - 09:47:29 CDT)
Calculating angles between subunits Markus Laub (Wed Oct 22 2003 - 07:37:44 CDT)
- Re: Calculating angles between subunits John Stone (Fri Oct 24 2003 - 19:11:25 CDT)
  - Re: Calculating angles between subunits John Stone (Thu Nov 06 2003 - 16:10:35 CST)
Re: ribbon representation :: VRML John Stone (Tue Oct 21 2003 - 15:43:26 CDT)
Viewing Amber6 trajectory with VMD 1.8.1 Amrit Kalra (Mon Oct 20 2003 - 01:21:03 CDT)
- Re: Viewing Amber6 trajectory with VMD 1.8.1 John Stone (Fri Oct 24 2003 - 19:05:32 CDT)
Bond drawing questino Paul Fons (Tue Oct 21 2003 - 01:52:22 CDT)
- Re: Bond drawing questino John Stone (Fri Oct 24 2003 - 18:51:59 CDT)
mousing problem under OS X Charles McCallum (Fri Oct 17 2003 - 23:25:46 CDT)
- Re: mousing problem under OS X John Stone (Tue Oct 21 2003 - 15:57:22 CDT)
ribbon representation Darui Xu (Fri Oct 17 2003 - 11:28:31 CDT)
- Re: ribbon representation John Stone (Fri Oct 17 2003 - 18:14:17 CDT)
(no subject) J. Rui Rodrigues (Fri Oct 17 2003 - 11:46:41 CDT)
show hbonds tscheng_at_ic.sunysb.edu (Thu Oct 16 2003 - 20:37:06 CDT)
- Re: show hbonds John Stone (Fri Oct 17 2003 - 18:16:47 CDT)
vmd 1.8.1 Ioana Cozmuta (Wed Oct 15 2003 - 18:54:58 CDT)
- Re: vmd 1.8.1 John Stone (Tue Oct 21 2003 - 15:54:51 CDT)
DCD unit cell data Erica Smith (Wed Oct 15 2003 - 15:45:51 CDT)
- Re: DCD unit cell data Ioana Cozmuta (Wed Oct 15 2003 - 16:40:18 CDT)
- Re: DCD unit cell data Axel Kohlmeyer (Thu Oct 16 2003 - 04:59:29 CDT)
loading crd files into VMD Madhuri Agashe (Wed Oct 15 2003 - 14:21:21 CDT)
- Re: loading crd files into VMD Ioana Cozmuta (Wed Oct 15 2003 - 15:48:51 CDT)
- Re: loading crd files into VMD John Stone (Wed Oct 15 2003 - 17:00:12 CDT)
vmd 1.8 Linux mesa on RedHat Miguel (Tue Oct 14 2003 - 13:24:56 CDT)
- Re: vmd 1.8 Linux mesa on RedHat james tomomi macdonald (Tue Oct 14 2003 - 13:53:53 CDT)
  - Re: vmd 1.8 Linux mesa on RedHat Miguel (Tue Oct 14 2003 - 15:12:42 CDT)
    - Re: vmd 1.8 Linux mesa on RedHat Oliver Beckstein (Tue Oct 14 2003 - 17:44:42 CDT)
- Re: vmd 1.8 Linux mesa on RedHat Jérôme Hénin (Tue Oct 14 2003 - 17:23:03 CDT)
- Re: vmd 1.8 Linux mesa on RedHat John Stone (Tue Oct 14 2003 - 15:45:51 CDT)
  - Re: vmd 1.8 Linux mesa on RedHat Miguel (Tue Oct 14 2003 - 16:26:15 CDT)
VMD performance on Mac OSX, 10.2.8 taeho.kim_at_utoronto.ca (Tue Oct 14 2003 - 13:11:26 CDT)
- Re: VMD performance on Mac OSX, 10.2.8 John Stone (Tue Oct 14 2003 - 15:43:18 CDT)
  - Re: VMD performance on Mac OSX, 10.2.8 taeho.kim_at_utoronto.ca (Wed Oct 15 2003 - 13:58:45 CDT)
    - Re: VMD performance on Mac OSX, 10.2.8 John Stone (Wed Oct 15 2003 - 14:36:32 CDT)
- Re: VMD performance on Mac OSX, 10.2.8 John Stone (Wed Oct 15 2003 - 13:24:02 CDT)
  - Re: VMD performance on Mac OSX, 10.2.8 Miguel (Wed Oct 15 2003 - 14:34:55 CDT)
Compiling VMD on IRIX 6.5 redux steve_at_beefeater.darkorb.net (Thu Oct 09 2003 - 11:24:13 CDT)
- Re: Compiling VMD on IRIX 6.5 redux John Stone (Tue Oct 14 2003 - 15:25:49 CDT)
  - Re: Compiling VMD on IRIX 6.5 redux steve_at_beefeater.darkorb.net (Wed Oct 15 2003 - 12:15:07 CDT)
RE: vmd information Izrailev, Sergei (Thu Oct 09 2003 - 09:03:14 CDT)
vmd information Ioana Cozmuta (Wed Oct 08 2003 - 20:12:20 CDT)
- Re: vmd information John Stone (Wed Oct 08 2003 - 22:45:18 CDT)
Problem Fixed Raymond C. Fort Jr. (Wed Oct 08 2003 - 09:26:51 CDT)
- Setting default viewing window location in XP Dallas Warren (Mon Oct 13 2003 - 19:40:48 CDT)
  - Re: Setting default viewing window location in XP John Stone (Tue Oct 14 2003 - 11:03:04 CDT)
NAMD-L mailing list Jim Phillips (Tue Oct 07 2003 - 15:15:41 CDT)
VDW radii in input files Ran Friedman (Tue Oct 07 2003 - 10:47:50 CDT)
- Re: VDW radii in input files John Stone (Tue Oct 07 2003 - 15:35:08 CDT)
  - Re: VDW radii in input files Ran Friedman (Wed Oct 08 2003 - 03:13:43 CDT)
    - Re: VDW radii in input files John Stone (Fri Oct 24 2003 - 19:27:32 CDT)
- Re: VDW radii in input files John Stone (Tue Oct 07 2003 - 15:42:28 CDT)
[kwiseon_kim@nrel.gov: RE: NVIDIA Quadro - CrystalEyes - Windows] John Stone (Mon Oct 06 2003 - 17:39:34 CDT)
opdating the selection during trajectory Vlad Cojocaru (Mon Oct 06 2003 - 07:20:38 CDT)
- Re: opdating the selection during trajectory Justin Gullingsrud (Mon Oct 06 2003 - 09:24:48 CDT)
Feature request: PBC from CHARMM DCD files Tyler Luchko (Thu Oct 02 2003 - 13:08:27 CDT)
- Re: Feature request: PBC from CHARMM DCD files John Stone (Thu Oct 02 2003 - 16:49:14 CDT)
HBonds J. Rui Rodrigues (Wed Oct 01 2003 - 17:16:37 CDT)
- Re: HBonds John Stone (Thu Oct 02 2003 - 14:55:14 CDT)
python support and pipes in vmd John R. Kitchin (Tue Sep 30 2003 - 13:52:00 CDT)
- Re: python support and pipes in vmd John Stone (Tue Sep 30 2003 - 16:05:49 CDT)
- Re: python support and pipes in vmd Justin Gullingsrud (Tue Sep 30 2003 - 16:48:47 CDT)
RE: File format of DCD Trajectory file Izrailev, Sergei (Tue Sep 30 2003 - 11:21:35 CDT)
nvidia driver Alan Wilter Sousa da Silva (Tue Sep 30 2003 - 09:30:48 CDT)
- Re: nvidia driver John Stone (Tue Sep 30 2003 - 10:04:21 CDT)
  - Re: nvidia driver John Stone (Wed Oct 01 2003 - 14:08:32 CDT)
RE: NVIDIA Quadro - CrystalEyes - Linux EPF (Esben Peter Friis) (Tue Sep 30 2003 - 09:27:56 CDT)
- Re: NVIDIA Quadro - CrystalEyes - Linux Jérôme Hénin (Tue Sep 30 2003 - 09:39:35 CDT)
- RE: NVIDIA Quadro - CrystalEyes - Linux EPF (Esben Peter Friis) (Tue Sep 30 2003 - 08:45:41 CDT)
  - Re: NVIDIA Quadro - CrystalEyes - Linux Jérôme Hénin (Tue Sep 30 2003 - 09:13:20 CDT)
    - Re: NVIDIA Quadro - CrystalEyes - Linux John Stone (Tue Sep 30 2003 - 11:03:20 CDT)
NVIDIA Quadro - CrystalEyes - Linux Jérôme Hénin (Tue Sep 30 2003 - 08:20:52 CDT)
Python's future in VMD Patrick Ladam (Tue Sep 30 2003 - 05:58:23 CDT)
- Re: Python's future in VMD Alfredo Valles (Tue Sep 30 2003 - 08:01:05 CDT)
  - Re: Python's future in VMD John Stone (Tue Sep 30 2003 - 10:14:34 CDT)
    - Re: Python's future in VMD Andrew Dalke (Tue Sep 30 2003 - 12:19:46 CDT)
    - RE: Python's future in VMD Warren L. DeLano (Tue Sep 30 2003 - 20:38:19 CDT)
- Re: Python's future in VMD Alan Wilter Sousa da Silva (Tue Sep 30 2003 - 07:48:28 CDT)
  - Re: Python's future in VMD John Stone (Tue Sep 30 2003 - 12:30:15 CDT)
convert pdb to psf FOK LO MING (Tue Sep 30 2003 - 03:54:34 CDT)
- Re: convert pdb to psf Jim Phillips (Tue Sep 30 2003 - 12:48:26 CDT)
vizualization of modes $B:,>k(J $B6Q(J (Tue Sep 30 2003 - 03:31:55 CDT)
- Re: vizualization of modes John Stone (Tue Sep 30 2003 - 10:17:49 CDT)
- Re: vizualization of modes Nguyen Hoang Phuong (Tue Sep 30 2003 - 10:12:03 CDT)
NAMD 2.5 Released Jim Phillips (Mon Sep 29 2003 - 14:02:48 CDT)
File format of DCD Trajectory file FUNG WAI KEUNG (Mon Sep 29 2003 - 01:10:13 CDT)
- Re: File format of DCD Trajectory file John Stone (Mon Sep 29 2003 - 10:53:21 CDT)
Mac OS X -dispdev options Tobias Mandrup Johansen (Thu Sep 25 2003 - 04:12:27 CDT)
- Re: Mac OS X -dispdev options John Stone (Thu Sep 25 2003 - 11:25:57 CDT)
vmd script library Karunesh Arora (Wed Sep 24 2003 - 14:08:35 CDT)
- Re: vmd script library John Stone (Thu Sep 25 2003 - 14:31:54 CDT)
text mode to calculate Internal Energy Sichun Yang (Wed Sep 24 2003 - 11:48:34 CDT)
- Re: text mode to calculate Internal Energy John Stone (Wed Sep 24 2003 - 13:39:30 CDT)
vrml Darui Xu (Wed Sep 24 2003 - 11:19:37 CDT)
- Re: vrml John Stone (Wed Sep 24 2003 - 13:12:14 CDT)
keyframe animations Ross J. Toedte (Tue Sep 23 2003 - 07:04:25 CDT)
- Re: keyframe animations John Stone (Tue Sep 23 2003 - 10:53:08 CDT)
water sphere srinivasa murthy (Tue Sep 23 2003 - 01:40:10 CDT)
- Re: water sphere John Stone (Tue Sep 23 2003 - 10:04:39 CDT)
  - Re: water sphere srinivasa murthy (Wed Sep 24 2003 - 08:54:13 CDT)
    - Re: water sphere John Stone (Wed Sep 24 2003 - 13:16:05 CDT)
    - Re: water sphere srinivasa murthy (Fri Sep 26 2003 - 00:18:41 CDT)
  - Re: water sphere srinivasa murthy (Tue Oct 07 2003 - 10:14:38 CDT)
NAMD 2.5b3 Released Jim Phillips (Fri Sep 19 2003 - 18:02:58 CDT)
spacemice Philip Fowler (Fri Sep 19 2003 - 11:09:11 CDT)
- Re: spacemice John Stone (Tue Sep 23 2003 - 13:25:41 CDT)
showing all vmd output Lubos Vrbka (Thu Sep 18 2003 - 13:09:57 CDT)
- Re: showing all vmd output John Stone (Thu Sep 18 2003 - 15:59:55 CDT)
- Re: showing all vmd output Justin Gullingsrud (Thu Sep 18 2003 - 16:36:33 CDT)
Drawing of bonds while trajectory animation. Hiroyuki Maeshima (Thu Sep 18 2003 - 07:53:17 CDT)
- Re: Drawing of bonds while trajectory animation. John Stone (Thu Sep 18 2003 - 14:09:30 CDT)
(no subject) Tsu-Fan Cheng (Wed Sep 17 2003 - 22:02:23 CDT)
Re: making movie with snapshot - bogus images John Stone (Wed Sep 17 2003 - 16:20:20 CDT)
VMD, CAVEs and pointing devices Philip Fowler (Wed Sep 17 2003 - 12:05:07 CDT)
- Re: VMD, CAVEs and pointing devices John Stone (Wed Sep 17 2003 - 13:53:56 CDT)
vmd 1.8.2b3 (September 16, 2003) on freebsd Tsu-Fan Cheng (Tue Sep 16 2003 - 22:00:19 CDT)
- Re: vmd 1.8.2b3 (September 16, 2003) on freebsd Brian Bennion (Tue Sep 16 2003 - 23:05:07 CDT)
- Re: vmd 1.8.2b3 (September 16, 2003) on freebsd John Stone (Wed Sep 17 2003 - 00:16:02 CDT)
AtomLexer/lex.yy.c error Jeroen Akershoek (Tue Sep 16 2003 - 05:38:11 CDT)
- Re: AtomLexer/lex.yy.c error Brian Bennion (Tue Sep 16 2003 - 10:06:33 CDT)
  - Re: AtomLexer/lex.yy.c error Jeroen Akershoek (Tue Sep 16 2003 - 10:28:20 CDT)
NAMD 2.5b2 Released Jim Phillips (Mon Sep 15 2003 - 19:53:01 CDT)
Systematic VMD crash above critical size Jérôme Hénin (Mon Sep 15 2003 - 09:04:01 CDT)
- Re: Systematic VMD crash above critical size John Stone (Mon Sep 15 2003 - 10:21:50 CDT)
  - Re: Systematic VMD crash above critical size John Stone (Mon Sep 15 2003 - 10:37:10 CDT)
updating cartoon representation in trajectory Matthew C. Lee (Sun Sep 14 2003 - 00:27:52 CDT)
- Re: updating cartoon representation in trajectory John Stone (Sun Sep 14 2003 - 11:00:11 CDT)
"Distributed Cavelib" VMD port Romaric David (Fri Sep 12 2003 - 09:01:33 CDT)
- Re: "Distributed Cavelib" VMD port John Stone (Fri Sep 12 2003 - 11:15:00 CDT)
trio program Nguyen Hoang Phuong (Fri Sep 12 2003 - 08:19:38 CDT)
- Re: trio program John Stone (Fri Sep 12 2003 - 10:12:57 CDT)
  - Re: trio program Brian Bennion (Fri Sep 12 2003 - 11:00:17 CDT)
    - Re: trio program Nguyen Hoang Phuong (Tue Sep 16 2003 - 02:22:36 CDT)
    - Re: trio program Brian Bennion (Tue Sep 16 2003 - 10:17:13 CDT)
Compute B-factor from MD run Aaron Oakley (Fri Sep 12 2003 - 03:02:42 CDT)
loading trj file Ioana Cozmuta (Thu Sep 11 2003 - 18:06:47 CDT)
- Re: loading trj file Brian Bennion (Fri Sep 12 2003 - 09:59:35 CDT)
  - Re: loading trj file Ioana Cozmuta (Fri Sep 12 2003 - 13:58:28 CDT)
    - Re: loading trj file John Stone (Fri Sep 12 2003 - 15:16:48 CDT)
periodic woes Scott Stagg (Thu Sep 11 2003 - 15:07:33 CDT)
- Re: periodic woes Lubos Vrbka (Thu Sep 11 2003 - 16:34:59 CDT)
- Re: periodic woes Jan Saam (Fri Sep 12 2003 - 04:42:09 CDT)
Re: static text John Stone (Thu Sep 11 2003 - 13:06:06 CDT)
saving bond-length information Karsten Suhre (Thu Sep 11 2003 - 04:51:47 CDT)
- Re: saving bond-length information Axel Kohlmeyer (Thu Sep 11 2003 - 06:36:48 CDT)
OpenGLExtensions.C compile problem Dave Humbird (Wed Sep 10 2003 - 18:52:59 CDT)
- Re: OpenGLExtensions.C compile problem John Stone (Thu Sep 11 2003 - 10:12:19 CDT)
  - Re: OpenGLExtensions.C compile problem John Stone (Sun Sep 14 2003 - 14:44:31 CDT)
Reading large traj file error or how to divide a large traj file into parts? Peng Tao (Wed Sep 10 2003 - 14:15:43 CDT)
- Re: Reading large traj file error or how to divide a large traj file into parts? John Stone (Wed Sep 10 2003 - 14:56:18 CDT)
  - Re: Reading large traj file error or how to divide a large traj file into parts? Peng Tao (Wed Sep 10 2003 - 15:12:44 CDT)
    - Re: Reading large traj file error or how to divide a large traj file into parts? John Stone (Wed Sep 10 2003 - 16:07:34 CDT)
numerical output for SURF? suzie.k.hight.1 (Wed Sep 10 2003 - 13:24:15 CDT)
- Re: numerical output for SURF? John Stone (Wed Sep 10 2003 - 15:42:33 CDT)
Backspace not functionning in console Patrick Ladam (Wed Sep 10 2003 - 07:07:05 CDT)
- Re: Backspace not functionning in console John Stone (Wed Sep 10 2003 - 10:07:34 CDT)
  - Re: Backspace not functionning in console John Stone (Thu Sep 11 2003 - 10:04:29 CDT)
python: packages not found also...(FIXED, thanks John) Patrick Ladam (Tue Sep 09 2003 - 05:14:14 CDT)
Reg: General question! Shantipriya Tenneti (Mon Sep 08 2003 - 11:26:39 CDT)
How to measure cross angles between helices Matthew C. Lee (Fri Sep 05 2003 - 13:57:42 CDT)
question about selection Ioana Cozmuta (Thu Sep 04 2003 - 17:10:41 CDT)
- Re: question about selection Andrew Dalke (Thu Sep 04 2003 - 18:57:00 CDT)
python: packages not found also...(repost) Patrick Ladam (Thu Sep 04 2003 - 07:28:17 CDT)
- Re: python: packages not found also...(repost) John Stone (Tue Sep 09 2003 - 02:10:39 CDT)
Re: hardware stereo with nVidia card John Stone (Wed Sep 03 2003 - 22:44:38 CDT)
- Re: Re: hardware stereo with nVidia card Mads Nørregaard-Madsen (Thu Sep 04 2003 - 02:26:56 CDT)
simple question Ioana Cozmuta (Tue Sep 02 2003 - 19:05:41 CDT)
- Re: simple question Justin Gullingsrud (Tue Sep 02 2003 - 19:35:05 CDT)
- Re: simple question Andrew Dalke (Tue Sep 02 2003 - 19:40:49 CDT)
- Re: simple question John Stone (Wed Sep 03 2003 - 22:39:14 CDT)
NMR module in VMD ? Patrick Ladam (Tue Sep 02 2003 - 05:00:41 CDT)
python: packages not found also... Patrick Ladam (Tue Sep 02 2003 - 04:44:33 CDT)
- RE: python: packages not found also... barrett (Mon Sep 08 2003 - 05:44:12 CDT)
Re: ATI radeon 8500 and Linux quad buffered stereo Dr. Daniel James White PhD (Tue Sep 02 2003 - 03:09:28 CDT)
protein/carbohydrate Aaron Oakley (Tue Sep 02 2003 - 03:07:53 CDT)
NAMD constant pressure/temp advice David Chalmers (Mon Sep 01 2003 - 03:06:35 CDT)
drawing objects Karunesh Arora (Sat Aug 30 2003 - 08:37:22 CDT)
- Re: drawing objects John Stone (Tue Sep 09 2003 - 02:20:35 CDT)
need urgent help Ioana Cozmuta (Thu Aug 28 2003 - 13:04:30 CDT)
- Re: need urgent help Justin Gullingsrud (Fri Aug 29 2003 - 23:04:00 CDT)
  - Re: need urgent help Ioana Cozmuta (Fri Aug 29 2003 - 23:24:44 CDT)
    - Re: need urgent help Justin Gullingsrud (Sat Aug 30 2003 - 19:30:56 CDT)
VMD support -- Out of town until Sept. 9th John Stone (Wed Aug 27 2003 - 11:02:20 CDT)
Graphics workstation and Xenon problems with VMD? Fred Salsbury (Tue Aug 26 2003 - 19:49:41 CDT)
- Re: Graphics workstation and Xenon problems with VMD? John Stone (Wed Aug 27 2003 - 00:26:11 CDT)
  - Re: Graphics workstation and Xenon problems with VMD? Fred Salsbury (Wed Aug 27 2003 - 06:22:05 CDT)
  - Re: Graphics workstation and Xenon problems with VMD? Axel Kohlmeyer (Wed Aug 27 2003 - 10:19:44 CDT)
    - Re: Graphics workstation and Xenon problems with VMD? Fred Salsbury (Wed Aug 27 2003 - 13:24:11 CDT)
    - Re: Graphics workstation and Xenon problems with VMD? John Stone (Wed Aug 27 2003 - 13:39:17 CDT)
linux mesa binaries no longer available? Lubos Vrbka (Tue Aug 26 2003 - 12:20:31 CDT)
- Re: linux mesa binaries no longer available? John Stone (Tue Aug 26 2003 - 14:13:11 CDT)
More Script Problems Raymond C. Fort Jr. (Tue Aug 26 2003 - 09:12:25 CDT)
- Re: More Script Problems John Stone (Tue Aug 26 2003 - 09:31:24 CDT)
  - Re: More Script Problems John Stone (Tue Aug 26 2003 - 13:32:18 CDT)
truncated octahedron box in namd carles ferrer (Tue Aug 26 2003 - 17:58:28 CDT)
support for multi-frame XYZ files? jsu_at_its.caltech.edu (Mon Aug 25 2003 - 23:59:50 CDT)
- Re: support for multi-frame XYZ files? John Stone (Tue Aug 26 2003 - 00:13:35 CDT)
psfgen Oded Kleifeld (Mon Aug 25 2003 - 19:50:26 CDT)
reading/writing Ioana Cozmuta (Mon Aug 25 2003 - 18:24:27 CDT)
- Re: reading/writing John Stone (Mon Aug 25 2003 - 19:11:16 CDT)
  - Re: reading/writing Ioana Cozmuta (Mon Aug 25 2003 - 19:29:55 CDT)
    - Re: reading/writing John Stone (Thu Aug 28 2003 - 15:38:18 CDT)
  - Re: reading/writing John Stone (Thu Aug 28 2003 - 19:58:15 CDT)
    - Re: reading/writing Ioana Cozmuta (Thu Aug 28 2003 - 20:10:53 CDT)
Using Solvate Script Raymond C. Fort Jr. (Mon Aug 25 2003 - 13:30:31 CDT)
- Re: Using Solvate Script John Stone (Mon Aug 25 2003 - 13:27:45 CDT)
Re: truncated octahedron box in namd (fwd) John Stone (Mon Aug 25 2003 - 10:24:18 CDT)
colors changed in animation yifat b (Mon Aug 25 2003 - 10:00:41 CDT)
- Re: colors changed in animation John Stone (Mon Aug 25 2003 - 10:32:47 CDT)
  - Re: colors changed in animation yifat b (Tue Aug 26 2003 - 05:25:18 CDT)
python question Alfredo Valles (Sat Aug 23 2003 - 09:41:37 CDT)
- Re: python question Justin Gullingsrud (Sat Aug 23 2003 - 21:34:10 CDT)
  - python question 2 Alfredo Valles (Mon Aug 25 2003 - 04:02:10 CDT)
    - Re: python question 2 Justin Gullingsrud (Mon Aug 25 2003 - 10:09:54 CDT)
hi Alfredo Valles (Sat Aug 23 2003 - 06:15:08 CDT)
Re: VMD print out John Stone (Thu Aug 14 2003 - 22:15:42 CDT)
re-centering view/rotation axes Charles McCallum (Mon Aug 11 2003 - 17:03:37 CDT)
protein/carbohydrate Aaron Oakley (Fri Aug 08 2003 - 22:48:54 CDT)
configuring vmd w/ browser on OS X Charles McCallum (Fri Aug 08 2003 - 21:49:16 CDT)
- Re: configuring vmd w/ browser on OS X John Stone (Mon Aug 11 2003 - 11:22:14 CDT)
rgb to mpg Ioana Cozmuta (Fri Aug 08 2003 - 18:20:49 CDT)
- Re: rgb to mpg John Stone (Fri Aug 08 2003 - 18:34:46 CDT)
  - Re: rgb to mpg Ioana Cozmuta (Fri Aug 08 2003 - 18:56:30 CDT)
trajectory animation usign PBC Ioana Cozmuta (Wed Aug 06 2003 - 17:33:45 CDT)
- Re: trajectory animation usign PBC Justin Gullingsrud (Wed Aug 06 2003 - 18:04:39 CDT)
Pressure and Gpressure output in NAMD Vlad Cojocaru (Wed Aug 06 2003 - 10:40:55 CDT)
- Re: Pressure and Gpressure output in NAMD Jim Phillips (Wed Aug 06 2003 - 15:23:41 CDT)
python: cannot find library barrett (Wed Aug 06 2003 - 04:53:06 CDT)
- Re: python: cannot find library John Stone (Wed Aug 06 2003 - 11:02:24 CDT)
  - RE: python: cannot find library barrett (Thu Aug 07 2003 - 03:28:12 CDT)
    - Re: python: cannot find library Justin Gullingsrud (Thu Aug 07 2003 - 09:40:55 CDT)
- Re: python: cannot find library Justin Gullingsrud (Wed Aug 06 2003 - 11:16:12 CDT)
  - Re: python: cannot find library Justin Gullingsrud (Wed Aug 06 2003 - 11:18:20 CDT)
Bondlength information! Ramesh K. Sistla (Wed Aug 06 2003 - 02:54:34 CDT)
- Re: Bondlength information! John Stone (Wed Aug 06 2003 - 11:04:57 CDT)
error when making a movie Ioana Cozmuta (Tue Aug 05 2003 - 18:04:15 CDT)
- Re: error when making a movie John Stone (Tue Aug 05 2003 - 21:59:45 CDT)
  - Re: error when making a movie Ioana Cozmuta (Tue Aug 05 2003 - 22:32:21 CDT)
Re: movie making Charles McCallum (Tue Aug 05 2003 - 16:05:53 CDT)
- Re: movie making Josh Vermaas (Sat Feb 28 2015 - 14:41:41 CST)
movie making Ioana Cozmuta (Tue Aug 05 2003 - 14:09:54 CDT)
Vmd -dispdev text under OS X Ken Sale (Mon Aug 04 2003 - 20:04:25 CDT)
- Re: Vmd -dispdev text under OS X John Stone (Mon Aug 04 2003 - 20:13:47 CDT)
Re: problems compiling vmd (1.8.1) John Stone (Mon Aug 04 2003 - 14:34:24 CDT)
Re: Re: CCL:NAMD failure on Berendsen pressure scheme Ioana Cozmuta (Thu Jul 31 2003 - 13:03:24 CDT)
NAMD failure on Berendsen pressure scheme Vlad Cojocaru (Wed Jul 30 2003 - 07:53:39 CDT)
- Re: CCL:NAMD failure on Berendsen pressure scheme Ioana Cozmuta (Wed Jul 30 2003 - 11:51:49 CDT)
Periodic images J. Rui Rodrigues (Tue Jul 29 2003 - 11:43:23 CDT)
- Re: Periodic images Justin Gullingsrud (Tue Jul 29 2003 - 11:38:15 CDT)
Amber prmtop/inpcrd files Anshul Shah (Mon Jul 28 2003 - 15:45:05 CDT)
- Re: Amber prmtop/inpcrd files Anshul Shah (Mon Jul 28 2003 - 17:17:29 CDT)
  - Re: Amber prmtop/inpcrd files John Stone (Thu Jul 31 2003 - 11:44:38 CDT)
  - Re: Amber prmtop/inpcrd files John Stone (Thu Aug 28 2003 - 15:46:52 CDT)
- Re: Amber prmtop/inpcrd files Teletchéa Stéphane (Thu Jul 31 2003 - 12:49:27 CDT)
  - Re: Amber prmtop/inpcrd files caldwell_at_heimdal.compchem.ucsf.edu (Thu Jul 31 2003 - 14:22:12 CDT)
    - Re: Amber prmtop/inpcrd files Teletchéa Stéphane (Thu Jul 31 2003 - 15:44:32 CDT)
    - Re: Amber prmtop/inpcrd files John Stone (Thu Jul 31 2003 - 18:01:25 CDT)
namd restraints question Vlad Cojocaru (Mon Jul 28 2003 - 14:54:28 CDT)
Re: maillist Vlad Cojocaru (Sun Jul 27 2003 - 14:34:03 CDT)
- Re: Re: maillist Justin Gullingsrud (Sun Jul 27 2003 - 23:58:21 CDT)
Reg: No. of Frames Shantipriya Tenneti (Sun Jul 27 2003 - 02:11:09 CDT)
- Re: Reg: No. of Frames Axel Kohlmeyer (Mon Jul 28 2003 - 02:13:51 CDT)
  - Re: Reg: No. of Frames Shantipriya Tenneti (Mon Jul 28 2003 - 13:04:31 CDT)
    - Re: Reg: No. of Frames Axel Kohlmeyer (Mon Jul 28 2003 - 13:33:51 CDT)
    - Re: Reg: No. of Frames Justin Gullingsrud (Mon Jul 28 2003 - 13:40:12 CDT)
Some improvements for 1.8.2 Teletchéa Stéphane (Fri Jul 25 2003 - 19:55:17 CDT)
- Re: Some improvements for 1.8.2 Andrew Dalke (Fri Jul 25 2003 - 20:18:57 CDT)
- Re: Some improvements for 1.8.2 John Stone (Fri Jul 25 2003 - 20:37:46 CDT)
  - Re: Some improvements for 1.8.2 Teletchéa Stéphane (Fri Jul 25 2003 - 21:06:37 CDT)
- Re: Some improvements for 1.8.2 Hannes Loeffler (Fri Jul 25 2003 - 20:58:52 CDT)
  - Re: Some improvements for 1.8.2 Justin Gullingsrud (Sat Jul 26 2003 - 16:08:56 CDT)
selection Ioana Cozmuta (Fri Jul 25 2003 - 17:38:46 CDT)
- Re: selection Andrew Dalke (Fri Jul 25 2003 - 18:22:25 CDT)
  - Re: selection matziast_at_med.uth.gr (Mon Oct 31 2011 - 16:23:38 CDT)
volume slice problem Giovanni Settanni (Fri Jul 25 2003 - 06:04:38 CDT)
- Re: volume slice problem John Stone (Fri Jul 25 2003 - 10:12:03 CDT)
VMD at Siggraph next week... John Stone (Thu Jul 24 2003 - 14:18:17 CDT)
New VMD CVS tree location, update your aliases... John Stone (Wed Jul 23 2003 - 14:23:55 CDT)
compile VMD on freebsd 4.8 Tsu-Fan Cheng (Wed Jul 23 2003 - 14:23:12 CDT)
- Re: compile VMD on freebsd 4.8 John Stone (Wed Jul 23 2003 - 14:27:04 CDT)
  - Re: compile VMD on freebsd 4.8 Tsu-Fan Cheng (Wed Jul 23 2003 - 14:43:26 CDT)
- Re: compile VMD on freebsd 4.8 brad noyes (Tue Sep 09 2003 - 16:43:10 CDT)
  - Re: compile VMD on freebsd 4.8 John Stone (Tue Sep 09 2003 - 19:43:33 CDT)
    - Re: compile VMD on freebsd 4.8 brad noyes (Tue Sep 09 2003 - 21:05:44 CDT)
New VMD-L subject lines... John Stone (Tue Jul 22 2003 - 16:53:05 CDT)
STL files alarcon_at_lncc.br (Thu Jul 17 2003 - 11:07:02 CDT)
- Re: STL files John Stone (Thu Jul 17 2003 - 11:21:22 CDT)
  - Re: STL files Dieter Krachtus (Fri Aug 08 2003 - 09:04:45 CDT)
superposition Oscar Moran (Thu Jul 17 2003 - 06:53:53 CDT)
- Re: superposition John Stone (Thu Jul 17 2003 - 09:48:20 CDT)
- Re: superposition John Stone (Thu Jul 17 2003 - 19:55:49 CDT)
Labels (atom type, partial charge) Bartek Dobrzelecki (Thu Jul 17 2003 - 06:00:22 CDT)
- Re: Labels (atom type, partial charge) John Stone (Thu Jul 17 2003 - 20:14:25 CDT)
question Ioana Cozmuta (Tue Jul 15 2003 - 16:22:42 CDT)
- Re: question John Stone (Tue Jul 15 2003 - 16:33:13 CDT)
  - Re: question Ioana Cozmuta (Tue Jul 15 2003 - 16:58:45 CDT)
    - Re: question John Stone (Tue Jul 15 2003 - 17:08:58 CDT)
VMD and doubleprecision trajectories Luca Mollica (Tue Jul 15 2003 - 07:30:44 CDT)
- Re: VMD and doubleprecision trajectories John Stone (Tue Jul 15 2003 - 09:48:44 CDT)
render to png, and ppm Brad Noyes (Sun Jul 13 2003 - 20:47:15 CDT)
Reg: BABEL Shantipriya Tenneti (Sun Jul 13 2003 - 15:30:20 CDT)
Reg:Babel Shantipriya Tenneti (Sun Jul 13 2003 - 14:57:10 CDT)
Problem with Vmd on SGI + Cavelib Romaric David (Fri Jul 11 2003 - 06:37:10 CDT)
- Re: Problem with Vmd on SGI + Cavelib John Stone (Fri Jul 11 2003 - 12:59:49 CDT)
- Re: Problem with Vmd on SGI + Cavelib Romaric David (Sat Jul 12 2003 - 06:20:52 CDT)
  - Re: Problem with Vmd on SGI + Cavelib John Stone (Tue Jul 15 2003 - 23:33:55 CDT)
    - Re: Problem with Vmd on SGI + Cavelib Romaric David (Wed Jul 16 2003 - 08:22:29 CDT)
    - Re: Problem with Vmd on SGI + Cavelib John Stone (Wed Jul 16 2003 - 16:34:45 CDT)
animate delete Hannes Loeffler (Fri Jul 11 2003 - 01:37:45 CDT)
- Re: animate delete John Stone (Fri Jul 11 2003 - 10:20:11 CDT)
fitting Vlad Cojocaru (Thu Jul 10 2003 - 07:13:07 CDT)
- Re: fitting Justin Gullingsrud (Thu Jul 10 2003 - 09:20:41 CDT)
VMD Georgios Scheiner-Bobis (Tue Jul 08 2003 - 03:39:38 CDT)
- Re: VMD John Stone (Tue Jul 08 2003 - 10:44:23 CDT)
Re: print results to file John Stone (Mon Jul 07 2003 - 18:16:26 CDT)
Note about VMD 1.8.1 on on MacOS X 10.1.x.... John Stone (Mon Jul 07 2003 - 17:20:21 CDT)
segid and geometry script Dominique Vlieghe (Wed Jun 25 2003 - 08:51:52 CDT)
- Re: segid and geometry script Jan Saam (Wed Jun 25 2003 - 18:33:35 CDT)
- Re: segid and geometry script Jan Saam (Wed Jun 25 2003 - 18:42:52 CDT)
(no subject) Gemma Kinsella (Tue Jun 24 2003 - 10:11:04 CDT)
(no subject) Gemma Kinsella (Tue Jun 24 2003 - 10:07:26 CDT)
- Re: your mail John Stone (Tue Jun 24 2003 - 10:18:33 CDT)
question on resname Ioana Cozmuta (Mon Jun 23 2003 - 16:16:02 CDT)
- Re: question on resname John Stone (Tue Jun 24 2003 - 10:31:10 CDT)
  - Re: question on resname Ioana Cozmuta (Tue Jul 22 2003 - 21:03:56 CDT)
    - Re: Re: question on resname Justin Gullingsrud (Tue Jul 22 2003 - 21:13:50 CDT)
    - Re: Re: question on resname Ioana Cozmuta (Tue Jul 22 2003 - 21:17:10 CDT)
Simple potential energy calculations in VMD Dominique Vlieghe (Mon Jun 23 2003 - 10:34:45 CDT)
- Re: Simple potential energy calculations in VMD Jan Saam (Mon Jun 23 2003 - 19:19:47 CDT)
Re: .XYZ File format (DL_POLY conversion) John Stone (Mon Jun 23 2003 - 09:37:34 CDT)
.XYZ File format Shantipriya Tenneti (Fri Jun 20 2003 - 18:04:42 CDT)
- Re: .XYZ File format Ramesh K. Sistla (Mon Jun 23 2003 - 06:10:30 CDT)
Bond Lengths Timothy W Suen (Fri Jun 20 2003 - 08:54:25 CDT)
- Re: Bond Lengths John Stone (Fri Jun 20 2003 - 09:55:54 CDT)
Visualizing CURVES output Vlad Cojocaru (Fri Jun 20 2003 - 05:08:12 CDT)
- Re: Visualizing CURVES output Teletchéa Stéphane (Fri Jun 20 2003 - 06:36:12 CDT)
- Re: Visualizing CURVES output John Stone (Fri Jun 20 2003 - 15:11:25 CDT)
coloring method: user Jan Saam (Fri Jun 20 2003 - 06:56:26 CDT)
- Re: coloring method: user John Stone (Fri Jun 20 2003 - 10:03:15 CDT)
coloring waters caldwell_at_heimdal.compchem.ucsf.edu (Thu Jun 19 2003 - 12:51:05 CDT)
- Re: coloring waters Sanjeev B.S. (Thu Jun 19 2003 - 14:55:14 CDT)
  - Re: coloring waters caldwell_at_heimdal.compchem.ucsf.edu (Thu Jun 19 2003 - 18:25:04 CDT)
    - Re: coloring waters John Stone (Thu Jun 19 2003 - 19:50:02 CDT)
    - Re: coloring waters caldwell_at_heimdal.compchem.ucsf.edu (Fri Jun 20 2003 - 12:06:32 CDT)
Re: MacOSX VMD errors. (solved) John Stone (Wed Jun 18 2003 - 12:57:00 CDT)
New User of VMD Shantipriya Tenneti (Wed Jun 18 2003 - 12:37:09 CDT)
- Re: New User of VMD John Stone (Wed Jun 18 2003 - 13:43:53 CDT)
quicktime/mpeg movies Peter Tieleman (Wed Jun 18 2003 - 10:51:56 CDT)
- Re: quicktime/mpeg movies John Stone (Wed Jun 18 2003 - 11:21:53 CDT)
  - Re: quicktime/mpeg movies Bogdan Costescu (Fri Jun 20 2003 - 14:30:24 CDT)
    - Re: quicktime/mpeg movies John Stone (Fri Jun 20 2003 - 14:59:37 CDT)
MacOSX VMD errors. Kelvin Chu (Wed Jun 18 2003 - 10:37:55 CDT)
- Re: MacOSX VMD errors. John Stone (Wed Jun 18 2003 - 10:55:19 CDT)
Re: VMD & NAMD John Stone (Wed Jun 18 2003 - 10:09:35 CDT)
amber trajectory Oscar Moran (Wed Jun 18 2003 - 03:17:58 CDT)
- Re: amber trajectory John Stone (Wed Jun 18 2003 - 09:55:39 CDT)
PLT file format? Dallas Warren (Wed Jun 18 2003 - 01:55:31 CDT)
- Re: PLT file format? John Stone (Thu Jun 19 2003 - 11:03:28 CDT)
  - Re: PLT file format? Dallas Warren (Thu Jun 19 2003 - 16:39:43 CDT)
- Re: PLT file format? John Stone (Tue Jun 24 2003 - 10:46:43 CDT)
- Re: PLT file format? John Stone (Thu Jul 03 2003 - 13:58:53 CDT)
  - Re: PLT file format? Dallas Warren (Tue Jul 15 2003 - 17:58:30 CDT)
    - Re: PLT file format? John Stone (Tue Jul 15 2003 - 23:16:39 CDT)
Colouring #WONG CHEE HOW# (Wed Jun 18 2003 - 01:02:39 CDT)
- Re: Colouring Justin Gullingsrud (Wed Jun 18 2003 - 09:22:42 CDT)
opengl window resize hangs on linux/nvidia Mikko Huhtala (Tue Jun 17 2003 - 03:01:44 CDT)
- Re: opengl window resize hangs on linux/nvidia John Stone (Tue Jun 17 2003 - 15:32:29 CDT)
osX anti aliasing and rendering speed / window size on linux Dr. Daniel James White PhD (Mon Jun 16 2003 - 04:45:54 CDT)
- Re: osX anti aliasing and rendering speed / window size on linux John Stone (Mon Jun 16 2003 - 10:11:33 CDT)
  - Re: osX anti aliasing and rendering speed / window size on linux John Stone (Mon Jun 16 2003 - 11:26:06 CDT)
Announce: VMD 1.8.1 released!! John Stone (Sun Jun 15 2003 - 15:38:19 CDT)
- Re: Announce: VMD 1.8.1 released!! MengJuei Hsieh (Sun Jun 15 2003 - 22:47:23 CDT)
  - Re: Announce: VMD 1.8.1 released!! John Stone (Sun Jun 15 2003 - 23:37:12 CDT)
MSMS and VMD: vertices discripancy Sanjeev B.S. (Sat Jun 14 2003 - 14:32:38 CDT)
- Re: MSMS and VMD: vertices discripancy John Stone (Mon Jun 16 2003 - 18:48:56 CDT)
  - Re: MSMS and VMD: vertices discripancy Sanjeev B.S. (Tue Jun 17 2003 - 12:24:00 CDT)
- Re: MSMS and VMD: vertices discripancy John Stone (Thu Jul 03 2003 - 14:37:27 CDT)
stereo glasses and VMD Sanjeev B.S. (Thu Jun 12 2003 - 12:47:56 CDT)
- Re: stereo glasses and VMD John Stone (Thu Jun 12 2003 - 15:26:17 CDT)
NAMD IMD large protein model Dr. Daniel James White PhD (Thu Jun 12 2003 - 08:51:23 CDT)
- Re: NAMD IMD large protein model Marc Baaden (Thu Jun 12 2003 - 10:23:38 CDT)
  - Re: NAMD IMD large protein model Jim Phillips (Thu Jun 12 2003 - 11:32:45 CDT)
    - Re: NAMD IMD large protein model Marc Baaden (Fri Jun 13 2003 - 05:35:45 CDT)
    - Re: NAMD IMD large protein model John Stone (Fri Jun 13 2003 - 15:53:15 CDT)
double image for one eye with crystal eyes stereo Dr. Daniel James White PhD (Thu Jun 12 2003 - 08:38:37 CDT)
- Re: double image for one eye with crystal eyes stereo Bogdan Costescu (Thu Jun 12 2003 - 09:34:36 CDT)
  - Re: double image for one eye with crystal eyes stereo Dr. Daniel James White PhD (Thu Jun 12 2003 - 09:48:30 CDT)
- Re: double image for one eye with crystal eyes stereo John Stone (Thu Jun 12 2003 - 10:11:43 CDT)
  - Re: double image for one eye with crystal eyes stereo Bogdan Costescu (Thu Jun 12 2003 - 11:02:01 CDT)
    - Re: double image for one eye with crystal eyes stereo John Stone (Thu Jun 12 2003 - 11:24:51 CDT)
  - Re: double image for one eye with crystal eyes stereo Dr. Daniel James White PhD (Fri Jun 13 2003 - 03:38:01 CDT)
    - Re: double image for one eye with crystal eyes stereo John Stone (Fri Jun 13 2003 - 10:04:58 CDT)
Re: VMD Error! (fwd) R.Sathyapriya (Wed Jun 11 2003 - 10:10:31 CDT)
- Re: VMD Error! (fwd) John Stone (Wed Jun 11 2003 - 09:44:48 CDT)
  - Re: VMD Error! (fwd) R.Sathyapriya (Thu Jun 12 2003 - 00:33:35 CDT)
helix axis for A-RNA Vlad Cojocaru (Tue Jun 10 2003 - 07:25:09 CDT)
- Re: helix axis for A-RNA Teletchéa Stéphane (Tue Jun 10 2003 - 08:11:35 CDT)
VMD Error! Ramesh K. Sistla (Tue Jun 10 2003 - 02:02:02 CDT)
- Re: VMD Error! Teletchéa Stéphane (Tue Jun 10 2003 - 01:40:55 CDT)
  - Re: VMD Error! Ramesh K. Sistla (Tue Jun 10 2003 - 02:33:56 CDT)
    - Re: VMD Error! Teletchéa Stéphane (Tue Jun 10 2003 - 02:06:50 CDT)
psfgen error with alias residue Dr. Daniel James White PhD (Mon Jun 09 2003 - 08:48:32 CDT)
- Re: psfgen error with alias residue Jim Phillips (Mon Jun 09 2003 - 09:33:06 CDT)
GeForce FX5800 and VMD 1.8.1 Joost Van Durme (Thu Jun 05 2003 - 12:19:59 CDT)
VMD and Situs Suzanne Brewerton (Thu Jun 05 2003 - 04:53:33 CDT)
- Re: VMD and Situs John Stone (Thu Jun 05 2003 - 09:10:21 CDT)
distance to solvent accessible surface Greg Moore (Wed Jun 04 2003 - 15:29:42 CDT)
- Re: distance to solvent accessible surface John Stone (Wed Jun 04 2003 - 16:23:06 CDT)
Re: Format of the axes John Stone (Wed Jun 04 2003 - 14:22:20 CDT)
Dihedral angle calculation! Thomas Hedegaard Pedersen (Wed Jun 04 2003 - 10:58:36 CDT)
- Re: Dihedral angle calculation! John Stone (Wed Jun 04 2003 - 11:32:15 CDT)
- Re: Dihedral angle calculation! Jan Saam (Wed Jun 04 2003 - 11:37:41 CDT)
  - Re: Dihedral angle calculation! Justin Gullingsrud (Wed Jun 04 2003 - 12:29:43 CDT)
- Re: Dihedral angle calculation! Justin Gullingsrud (Wed Jun 04 2003 - 12:08:32 CDT)
- Re: Dihedral angle calculation! Jan Saam (Wed Jun 04 2003 - 16:54:02 CDT)
Situs Suzanne Brewerton (Wed Jun 04 2003 - 09:22:23 CDT)
- RE: Situs Zampighi, Lorenzo (Wed Jun 04 2003 - 13:46:54 CDT)
  - Re: Situs John Stone (Wed Jun 04 2003 - 14:03:56 CDT)
  - RE: Situs Suzanne Brewerton (Thu Jun 05 2003 - 03:44:51 CDT)
- Re: Situs John Stone (Wed Jun 04 2003 - 13:52:49 CDT)
- Re: Situs John Stone (Wed Jun 04 2003 - 17:36:45 CDT)
Re: tubes John Stone (Tue Jun 03 2003 - 13:41:23 CDT)
cartoon representation Tyler Luchko (Fri May 30 2003 - 15:21:40 CDT)
- Re: cartoon representation John Stone (Fri May 30 2003 - 15:46:30 CDT)
trajectory_path Tatyana Kuznetsova (Fri May 30 2003 - 09:25:51 CDT)
- Re: trajectory_path John Stone (Fri May 30 2003 - 10:19:55 CDT)
Missing bonds noel.oboyle2_at_mail.dcu.ie (Fri May 30 2003 - 09:14:49 CDT)
- Re: Missing bonds John Stone (Fri May 30 2003 - 10:03:34 CDT)
Rotating dihedrals Patrick Ladam (Fri May 30 2003 - 05:09:43 CDT)
- Re: Rotating dihedrals John Stone (Fri May 30 2003 - 15:16:18 CDT)
- Re: Rotating dihedrals John Stone (Fri May 30 2003 - 16:04:54 CDT)
problem in loading dcd file? Ioana Cozmuta (Thu May 29 2003 - 19:53:40 CDT)
- Re: problem in loading dcd file? John Stone (Fri May 30 2003 - 10:29:32 CDT)
  - Re: problem in loading dcd file? Ioana Cozmuta (Fri May 30 2003 - 15:56:08 CDT)
    - Re: problem in loading dcd file? John Stone (Fri May 30 2003 - 16:02:50 CDT)
    - Re: problem in loading dcd file? Ioana Cozmuta (Fri May 30 2003 - 19:15:14 CDT)
load multiple pdb files simultaneously J. Zheng (Wed May 28 2003 - 18:29:13 CDT)
- Re: load multiple pdb files simultaneously John Stone (Wed May 28 2003 - 19:28:34 CDT)
Re: advice for a PCI video card on redhat John Stone (Wed May 28 2003 - 15:49:07 CDT)
Re: 3-d visualization John Stone (Wed May 28 2003 - 12:29:25 CDT)
stereo Oscar Moran (Wed May 28 2003 - 12:24:47 CDT)
- Re: stereo Alan Wilter Sousa da Silva (Wed May 28 2003 - 13:02:00 CDT)
about shape order parameter Emmanuel Vamvakopoulos (Sat May 24 2003 - 07:12:07 CDT)
center command Ioana Cozmuta (Fri May 23 2003 - 17:02:51 CDT)
implicit casting brad noyes (Fri May 23 2003 - 15:14:27 CDT)
- Re: implicit casting John Stone (Fri May 23 2003 - 15:20:51 CDT)
  - Re: implicit casting brad noyes (Fri May 23 2003 - 15:25:40 CDT)
VMD 1.8.1 beta 8 posted... John Stone (Fri May 23 2003 - 00:28:04 CDT)
- Support Contours? Dallas Warren (Wed Jun 11 2003 - 17:16:09 CDT)
  - Re: Support Contours? John Stone (Fri Jun 13 2003 - 09:53:49 CDT)
    - Re: Support Contours? Dallas Warren (Tue Jun 17 2003 - 21:28:26 CDT)
compiling/porting vmd brad noyes (Thu May 22 2003 - 22:23:25 CDT)
- Re: compiling/porting vmd John Stone (Thu May 22 2003 - 23:03:06 CDT)
  - Re: compiling/porting vmd brad noyes (Fri May 23 2003 - 01:30:18 CDT)
Wrapping atoms around unit cell boundaries John Stone (Thu May 22 2003 - 10:14:18 CDT)
(no subject) Dongsheng Zhang (Wed May 21 2003 - 23:13:52 CDT)
- Re: your mail John Stone (Thu May 22 2003 - 23:18:11 CDT)
VMD 1.8.1 beta 7 posted.. John Stone (Tue May 20 2003 - 18:21:42 CDT)
Molecular dynamics order parameters David Chalmers (Tue May 20 2003 - 06:47:18 CDT)
- Re: Molecular dynamics order parameters Justin Gullingsrud (Tue May 20 2003 - 13:03:29 CDT)
- Re: Molecular dynamics order parameters Joe Huang (Tue May 20 2003 - 17:41:59 CDT)
- Re: Molecular dynamics order parameters Dallas Warren (Tue May 20 2003 - 16:58:09 CDT)
Temperature/Beta factor coloring MengJuei Hsieh (Tue May 20 2003 - 02:00:26 CDT)
VMD 1.8.1 beta 6 posted... John Stone (Mon May 19 2003 - 18:13:55 CDT)
- Re: VMD 1.8.1 beta 6 posted... John Stone (Mon May 19 2003 - 18:15:09 CDT)
Sequence Menu For Nucleic Acids Patrick Ladam (Mon May 19 2003 - 08:55:45 CDT)
Re: VMD mods for the CAVE John Stone (Fri May 16 2003 - 10:11:15 CDT)
VMD 1.8.1 beta 5 posted for testing... John Stone (Thu May 15 2003 - 17:35:00 CDT)
- Graphics Cards Dallas Warren (Sun May 18 2003 - 17:55:37 CDT)
  - Re: Graphics Cards John Stone (Mon May 19 2003 - 12:27:54 CDT)
    - Re: Graphics Cards Dallas Warren (Mon May 19 2003 - 17:06:30 CDT)
    - Re: Graphics Cards John Stone (Tue May 20 2003 - 10:55:24 CDT)
Re: solute + solvent temperature? John Stone (Thu May 15 2003 - 16:19:58 CDT)
- Re: solute + solvent temperature? Ioana Cozmuta (Thu May 15 2003 - 18:00:23 CDT)
  - Re: solute + solvent temperature? Charles McCallum (Fri May 16 2003 - 01:04:12 CDT)
- Re: solute + solvent temperature? John Stone (Fri May 16 2003 - 10:00:27 CDT)
VMD 1.8 on Windows2000 to crash when executing simple scripts Jos Aerts (Thu May 15 2003 - 07:10:50 CDT)
- Re: VMD 1.8 on Windows2000 to crash when executing simple scripts John Stone (Thu May 15 2003 - 17:52:44 CDT)
Where is the Tracker Menu Stephen P. Molnar, Ph.D. (Tue May 13 2003 - 18:46:22 CDT)
- Re: Where is the Tracker Menu John Stone (Tue May 13 2003 - 21:15:17 CDT)
VMD 1.8.1 beta 4 posted... John Stone (Mon May 12 2003 - 15:25:22 CDT)
- Re: VMD 1.8.1 beta 4 posted... John Stone (Mon May 12 2003 - 18:59:46 CDT)
changing atom number in animation yifat b (Mon May 12 2003 - 04:50:17 CDT)
- Re: changing atom number in animation John Stone (Mon May 12 2003 - 11:07:32 CDT)
  - Re: changing atom number in animation yifat b (Thu May 15 2003 - 05:01:06 CDT)
    - Re: changing atom number in animation John Stone (Thu May 15 2003 - 16:21:24 CDT)
Plugins Problem with 1.8.1b2 Patrick Ladam (Mon May 12 2003 - 04:08:14 CDT)
- Re: Plugins Problem with 1.8.1b2 John Stone (Mon May 12 2003 - 11:03:23 CDT)
Is it possible to read a discover trajectory into VMD? Knut Teigen (Sat May 10 2003 - 09:11:23 CDT)
- Re: Is it possible to read a discover trajectory into VMD? John Stone (Mon May 12 2003 - 15:37:44 CDT)
vmdmovie on OS X current Charles McCallum (Fri May 09 2003 - 02:22:23 CDT)
- Re: vmdmovie on OS X current John Stone (Fri May 09 2003 - 09:48:56 CDT)
about superimposing by VMD Hu, Xiaohua (Wed May 07 2003 - 13:36:47 CDT)
- Re: about superimposing by VMD John Stone (Fri May 09 2003 - 10:46:46 CDT)
Re: Wavefront output of VMD John Stone (Wed May 07 2003 - 11:09:12 CDT)
VMD on Solaris 2.x doesn't compile Prabhakar Reddy Gudla (Fri May 02 2003 - 00:45:53 CDT)
- Re: VMD on Solaris 2.x doesn't compile John Stone (Fri May 02 2003 - 09:52:53 CDT)
- Re: VMD on Solaris 2.x doesn't compile John Stone (Fri May 02 2003 - 13:08:22 CDT)
  - new color scale Rukman Hertadi (Tue May 06 2003 - 00:44:46 CDT)
    - Re: new color scale John Stone (Tue May 06 2003 - 13:06:01 CDT)
Save_state and Load_state Jill Vickery (Thu May 01 2003 - 12:05:00 CDT)
- Re: Save_state and Load_state John Stone (Fri May 02 2003 - 10:04:44 CDT)
cursor size/shape in pick mode Mads Nørregaard-Madsen (Thu May 01 2003 - 03:43:32 CDT)
- Re: cursor size/shape in pick mode John Stone (Thu May 01 2003 - 08:30:57 CDT)
- RE: cursor size/shape in pick mode Mads Nørregaard-Madsen (Fri May 02 2003 - 12:04:45 CDT)
Memory problems using the "move" command inside a loop! Thomas Hedegaard Pedersen (Wed Apr 30 2003 - 09:28:01 CDT)
- Re: Memory problems using the "move" command inside a loop! John Stone (Wed Apr 30 2003 - 10:05:19 CDT)
- Re: Memory problems using the "move" command inside a loop! Justin Gullingsrud (Wed Apr 30 2003 - 17:56:32 CDT)
  - Re: Memory problems using the "move" command inside a loop! Joe Huang (Fri May 02 2003 - 16:23:54 CDT)
    - Re: Memory problems using the "move" command inside a loop! John Stone (Fri May 02 2003 - 15:30:39 CDT)
configuration file Ioana Cozmuta (Tue Apr 29 2003 - 19:41:47 CDT)
problem with labels Lubos Vrbka (Tue Apr 29 2003 - 08:36:05 CDT)
- Re: problem with labels John Stone (Tue Apr 29 2003 - 13:07:30 CDT)
- Re: problem with labels John Stone (Tue Apr 29 2003 - 13:36:00 CDT)
  - Re: problem with labels Lubos Vrbka (Tue Apr 29 2003 - 16:09:38 CDT)
    - Re: problem with labels John Stone (Tue Apr 29 2003 - 17:53:40 CDT)
VMD on redhat9 Michele Seeber (Tue Apr 29 2003 - 03:31:40 CDT)
- Re: VMD on redhat9 John Stone (Tue Apr 29 2003 - 13:41:30 CDT)
  - Re: VMD on redhat9 Michele Seeber (Wed Apr 30 2003 - 03:19:25 CDT)
Text-line command for Graphics? Changbong Hyeon (Fri Apr 25 2003 - 16:00:40 CDT)
- Re: Text-line command for Graphics? John Stone (Fri Apr 25 2003 - 16:05:46 CDT)
DCD file format? Changbong Hyeon (Fri Apr 25 2003 - 15:50:23 CDT)
- Re: DCD file format? John Stone (Fri Apr 25 2003 - 16:02:00 CDT)
- Re: DCD file format? John Stone (Fri Apr 25 2003 - 17:40:04 CDT)
unit cell information Ioana Cozmuta (Fri Apr 25 2003 - 15:34:41 CDT)
- Re: unit cell information Ioana Cozmuta (Fri Apr 25 2003 - 15:46:35 CDT)
- Re: unit cell information John Stone (Fri Apr 25 2003 - 17:28:48 CDT)
- Re: unit cell information Justin Gullingsrud (Mon Apr 28 2003 - 12:07:46 CDT)
installation problems with Redhat 9 james tomomi macdonald (Wed Apr 23 2003 - 13:15:22 CDT)
- Re: installation problems with Redhat 9 John Stone (Wed Apr 23 2003 - 13:27:57 CDT)
  - Re: installation problems with Redhat 9 james tomomi macdonald (Wed Apr 23 2003 - 13:53:11 CDT)
Movie Script Rukman Hertadi (Wed Apr 23 2003 - 04:27:43 CDT)
- Re: Movie Script John Stone (Wed Apr 23 2003 - 09:48:40 CDT)
Updating colors Paul Tangney (Tue Apr 22 2003 - 20:44:35 CDT)
- Re: Updating colors John Stone (Wed Apr 23 2003 - 15:01:05 CDT)
- Re: Updating colors John Stone (Wed Apr 23 2003 - 15:24:57 CDT)
- Re: Updating colors John Stone (Wed Apr 23 2003 - 15:30:28 CDT)
VMD 1.8.1 beta 2 available for testing.... John Stone (Tue Apr 22 2003 - 15:25:05 CDT)
question about periodicity Ioana Cozmuta (Mon Apr 21 2003 - 13:38:49 CDT)
- Re: question about periodicity John Stone (Tue Apr 22 2003 - 13:57:56 CDT)
Re: Memory problems with XP John Stone (Mon Apr 21 2003 - 11:31:59 CDT)
Fwd: FW: centering selection on screen John Stone (Thu Apr 17 2003 - 12:38:35 CDT)
centering seection on screen Lubos Vrbka (Thu Apr 17 2003 - 05:28:46 CDT)
- Re: centering seection on screen B. Bennion (Thu Apr 17 2003 - 09:50:32 CDT)
  - Re: centering seection on screen Lubos Vrbka (Thu Apr 17 2003 - 10:38:25 CDT)
trace P atoms in RNA Yongmei Wang (Wed Apr 16 2003 - 17:08:15 CDT)
Some comments about stereo with nvidia cards & shutter glasses Marc Baaden (Tue Apr 15 2003 - 03:03:31 CDT)
- Re: Some comments about stereo with nvidia cards & shutter glasses Michael Redmond (Tue Apr 22 2003 - 17:15:22 CDT)
  - Re: Some comments about stereo with nvidia cards & shutter glasses Marc Baaden (Wed Apr 30 2003 - 02:43:58 CDT)
a few questions on uninstall, labels, rasmol,seq window Y U Sasidhar (Fri Apr 11 2003 - 00:07:51 CDT)
- Re: a few questions on uninstall, labels, rasmol,seq window John Stone (Fri Apr 11 2003 - 14:49:49 CDT)
water box Ioana Cozmuta (Thu Apr 10 2003 - 19:00:42 CDT)
- Re: water box John Stone (Thu Apr 10 2003 - 19:30:22 CDT)
  - Re: water box Ioana Cozmuta (Thu Apr 10 2003 - 19:52:25 CDT)
    - Re: water box John Stone (Fri Apr 11 2003 - 14:55:44 CDT)
  - Re: water box Ioana Cozmuta (Thu Apr 10 2003 - 20:05:39 CDT)
    - Re: water box John Stone (Fri Apr 11 2003 - 14:56:41 CDT)
plotting wave functions Ioana Cozmuta (Thu Apr 10 2003 - 18:45:23 CDT)
- Re: plotting wave functions John Stone (Thu Apr 10 2003 - 19:27:36 CDT)
(no subject) silvya (Thu Apr 10 2003 - 17:55:11 CDT)
Error compiling trio Patrick Ladam (Wed Apr 09 2003 - 10:18:56 CDT)
- Re: Error compiling trio John Stone (Wed Apr 09 2003 - 10:08:53 CDT)
Metal-Metal distance chandran karunakaran (Tue Apr 08 2003 - 17:26:13 CDT)
- Re: Metal-Metal distance John Stone (Tue Apr 08 2003 - 17:42:22 CDT)
Drawing bonds to metals Stephen Koch (Tue Apr 08 2003 - 15:37:08 CDT)
- Re: Drawing bonds to metals John Stone (Tue Apr 08 2003 - 17:10:39 CDT)
gamepad on linux? Dr. Daniel James White PhD (Wed Apr 02 2003 - 10:52:15 CST)
- Re: gamepad on linux? John Stone (Wed Apr 02 2003 - 11:15:44 CST)
support for truncated octahedron Ioana Cozmuta (Tue Apr 01 2003 - 17:39:04 CST)
(no subject) Markus Laub (Mon Mar 31 2003 - 06:31:44 CST)
- Re: your mail John Stone (Mon Mar 31 2003 - 10:09:49 CST)
animation question Randall Hall (Thu Mar 27 2003 - 12:37:35 CST)
- Re: animation question John Stone (Thu Mar 27 2003 - 22:51:57 CST)
- RE: animation question #WONG CHEE HOW# (Fri Mar 28 2003 - 00:10:24 CST)
Unit cell information in python and IMD interface code Lars Bruno Hansen (Thu Mar 27 2003 - 09:26:57 CST)
- Re: Unit cell information in python and IMD interface code Justin Gullingsrud (Fri Mar 28 2003 - 12:03:31 CST)
- Re: Unit cell information in python and IMD interface code Justin Gullingsrud (Mon Mar 31 2003 - 12:12:22 CST)
  - IMD interface code and endianness Marc Baaden (Wed May 28 2003 - 13:36:18 CDT)
Problem with stride, surf and tachyon in Windows2000 J. Rui Rodrigues (Wed Mar 26 2003 - 11:47:03 CST)
- Re: Problem with stride, surf and tachyon in Windows2000 John Stone (Wed Mar 26 2003 - 13:42:54 CST)
- Re: Problem with stride, surf and tachyon in Windows2000 John Stone (Fri Mar 28 2003 - 15:37:49 CST)
Compilation issues with tcl.h Paul Darwen (Tue Mar 25 2003 - 21:36:27 CST)
- Re: Compilation issues with tcl.h John Stone (Tue Mar 25 2003 - 22:33:02 CST)
Solvate 1.1.1 chandran karunakaran (Tue Mar 25 2003 - 13:05:23 CST)
drawing bonds Lubos Vrbka (Tue Mar 25 2003 - 09:27:05 CST)
- Re: drawing bonds John Stone (Tue Mar 25 2003 - 09:36:38 CST)
- Re: drawing bonds Justin Gullingsrud (Tue Mar 25 2003 - 09:40:19 CST)
Distance, angle chandran karunakaran (Sat Mar 22 2003 - 15:09:10 CST)
- Re: Distance, angle John Stone (Mon Mar 24 2003 - 10:27:52 CST)
Re: mouse-move-rep in VMD 1.8 John Stone (Fri Mar 21 2003 - 16:44:59 CST)
Can't import python math module Scott Stagg (Fri Mar 21 2003 - 10:16:14 CST)
- Re: Can't import python math module John Stone (Mon Mar 24 2003 - 10:47:19 CST)
  - python: error importing packages Lars Bruno Hansen (Wed Apr 02 2003 - 06:22:56 CST)
    - Re: python: error importing packages John Stone (Tue Apr 08 2003 - 10:56:41 CDT)
PBC - setting box size Dallas Warren (Thu Mar 20 2003 - 20:43:35 CST)
- Re: PBC - setting box size John Stone (Thu Mar 20 2003 - 21:58:52 CST)
(no subject) chandran karunakaran (Thu Mar 20 2003 - 13:56:44 CST)
(no subject) chandran karunakaran (Thu Mar 20 2003 - 13:55:13 CST)
- Re: your mail John Stone (Thu Mar 20 2003 - 14:01:56 CST)
getting heavy atom contacts B. Bennion (Thu Mar 20 2003 - 12:40:59 CST)
Memory problems with TCL scripts in VMD. Joe Huang (Thu Mar 20 2003 - 13:02:48 CST)
- Re: Memory problems with TCL scripts in VMD. John Stone (Fri Mar 21 2003 - 16:36:02 CST)
  - Re: Memory problems with TCL scripts in VMD. Justin Gullingsrud (Fri Mar 21 2003 - 17:53:51 CST)
Missing vmdplugin.h in VMD source code Paul Darwen (Wed Mar 19 2003 - 22:35:22 CST)
- Color code Rukman Hertadi (Thu Mar 20 2003 - 01:42:37 CST)
  - Re: Color code Justin Gullingsrud (Thu Mar 20 2003 - 10:29:29 CST)
- Re: Missing vmdplugin.h in VMD source code John Stone (Fri Mar 21 2003 - 16:31:34 CST)
atomselect B. Bennion (Tue Mar 18 2003 - 16:03:05 CST)
- Re: atomselect Justin Gullingsrud (Tue Mar 18 2003 - 16:19:36 CST)
- Re: atomselect Justin Gullingsrud (Tue Mar 18 2003 - 16:52:12 CST)
AMBER parmfiles Patrick Ladam (Mon Mar 17 2003 - 05:24:31 CST)
- Re: AMBER parmfiles John Stone (Mon Mar 17 2003 - 10:06:11 CST)
Re: atom velocity arrows John Stone (Wed Mar 12 2003 - 13:45:21 CST)
- Re: atom velocity arrows John Stone (Wed Mar 12 2003 - 15:24:31 CST)
Trasperent images Sanjeev B.S. (Mon Mar 10 2003 - 22:18:43 CST)
- bond connectivity for different frames Lars Bruno Hansen (Tue Mar 11 2003 - 10:16:38 CST)
  - Re: bond connectivity for different frames John Stone (Tue Mar 11 2003 - 10:26:52 CST)
- Re: Trasperent images John Stone (Wed Mar 12 2003 - 13:53:32 CST)
Massive Inventory Clearance Sale on DTI 2D/3D 18.1" Flat Panel Displays! Mike Doolin (Fri Mar 07 2003 - 18:43:27 CST)
msms question... Lubos Vrbka (Fri Mar 07 2003 - 07:48:17 CST)
- Re: msms question... John Stone (Fri Mar 07 2003 - 09:40:43 CST)
  - Re: msms question... Lubos Vrbka (Fri Mar 07 2003 - 11:04:44 CST)
    - Re: msms question... John Stone (Fri Mar 07 2003 - 17:00:41 CST)
question on Force Ioana Cozmuta (Thu Mar 06 2003 - 21:59:48 CST)
- Re: question on Force John Stone (Wed Mar 12 2003 - 14:27:54 CST)
  - Re: question on Force Ioana Cozmuta (Wed Mar 12 2003 - 14:36:26 CST)
    - Re: question on Force John Stone (Wed Mar 12 2003 - 17:18:12 CST)
Re: Backspace and delete John Stone (Thu Mar 06 2003 - 18:46:50 CST)
volume problems Klaus Kramer (Thu Mar 06 2003 - 12:56:57 CST)
- Re: volume problems John Stone (Thu Mar 06 2003 - 13:42:53 CST)
two molecules Matt Whorton (Thu Mar 06 2003 - 12:20:32 CST)
- Re: two molecules John Stone (Thu Mar 06 2003 - 12:30:12 CST)
  - Re: two molecules Sichun Yang (Thu Mar 06 2003 - 14:33:17 CST)
    - Re: two molecules John Stone (Thu Mar 06 2003 - 14:38:49 CST)
problems with the Surf... Lubos Vrbka (Thu Mar 06 2003 - 10:00:38 CST)
- Re: problems with the Surf... John Stone (Thu Mar 06 2003 - 10:07:23 CST)
- Re: problems with the Surf... John Stone (Thu Mar 06 2003 - 10:18:30 CST)
  - Re: problems with the Surf... Lubos Vrbka (Thu Mar 06 2003 - 10:36:08 CST)
- Re: problems with the Surf... John Stone (Fri Mar 14 2003 - 11:09:15 CST)
residue labels in vmd Jim Caldwell (Wed Mar 05 2003 - 18:59:03 CST)
- Re: residue labels in vmd John Stone (Thu Mar 06 2003 - 10:05:37 CST)
'topology' command crashes vmd 1.8 (LINUX) Patrick Ladam (Wed Mar 05 2003 - 06:22:43 CST)
- Re: 'topology' command crashes vmd 1.8 (LINUX) John Stone (Wed Mar 05 2003 - 09:57:56 CST)
CatDCD Question Saladino, Alex (Tue Mar 04 2003 - 11:51:10 CST)
trajectory/movie Ioana Cozmuta (Mon Mar 03 2003 - 17:13:55 CST)
trajectory movie Ioana Cozmuta (Mon Mar 03 2003 - 17:11:02 CST)
Suggested graphic card :: LINUX Joseph Edward Curtis (Mon Mar 03 2003 - 10:07:19 CST)
- Re: Suggested graphic card :: LINUX John Stone (Mon Mar 03 2003 - 10:51:31 CST)
  - Re: Suggested graphic card :: LINUX Tru Huynh (Tue Mar 04 2003 - 05:47:59 CST)
- Re: Suggested graphic card :: LINUX Dr. Daniel James White PhD (Tue Mar 04 2003 - 02:31:52 CST)
Re: Protein Reorientation Gemma Kinsella (Mon Mar 03 2003 - 08:39:51 CST)
- Re: Protein Reorientation John Stone (Thu Mar 06 2003 - 10:52:52 CST)
same view in VMD and Molscript Eckhart Guthöhrlein (Tue Feb 25 2003 - 10:22:10 CST)
- Re: same view in VMD and Molscript John Stone (Tue Feb 25 2003 - 15:08:47 CST)
multiple cells representation Ioana Cozmuta (Mon Feb 24 2003 - 19:19:32 CST)
- Re: multiple cells representation Justin Gullingsrud (Mon Feb 24 2003 - 20:31:07 CST)
  - Re: multiple cells representation John Stone (Mon Feb 24 2003 - 22:04:47 CST)
Problems loading shared object, vmd1.8 linux mesa binaries Christopher D. Wassman (Sun Feb 23 2003 - 21:59:24 CST)
- Re: Problems loading shared object, vmd1.8 linux mesa binaries John Stone (Mon Feb 24 2003 - 11:28:14 CST)
  - Re: Problems loading shared object, vmd1.8 linux mesa binaries Christopher D. Wassman (Tue Feb 25 2003 - 01:49:09 CST)
Updating colors at each trajectory step Paul Tangney (Sun Feb 23 2003 - 20:34:51 CST)
- Re: Updating colors at each trajectory step John Stone (Mon Feb 24 2003 - 10:49:00 CST)
making movie SGI Ioana Cozmuta (Fri Feb 21 2003 - 15:28:16 CST)
- Re: making movie SGI John Stone (Fri Feb 21 2003 - 15:37:25 CST)
Quick question about 3-letter codes for positive residues Paul Darwen (Wed Feb 19 2003 - 01:58:36 CST)
- Re: Quick question about 3-letter codes for positive residues Justin Gullingsrud (Wed Feb 19 2003 - 09:16:52 CST)
Announce: Updated VMD 1.8 plugins available John Stone (Fri Feb 14 2003 - 16:47:39 CST)
Fwd: Postdoctoral position available in Molecular Modeling John Stone (Fri Feb 14 2003 - 13:27:31 CST)
aligntool Ioana Cozmuta (Thu Feb 13 2003 - 17:43:44 CST)
- Re: aligntool Barry Isralewitz (Thu Feb 13 2003 - 19:33:38 CST)
New user questions Michele Andrews - Contractor (Thu Feb 13 2003 - 11:11:16 CST)
- Re: New user questions Justin Gullingsrud (Thu Feb 13 2003 - 12:29:00 CST)
  - Re: New user questions John Stone (Thu Feb 13 2003 - 13:54:00 CST)
- Re: New user questions Michele Andrews - Contractor (Thu Feb 13 2003 - 14:52:35 CST)
remote_ctl.tcl: VMD's stdout -> socket ? Oliver Beckstein (Wed Feb 12 2003 - 16:10:04 CST)
- Re: remote_ctl.tcl: VMD's stdout -> socket ? Justin Gullingsrud (Wed Feb 12 2003 - 16:43:19 CST)
  - Re: remote_ctl.tcl: VMD's stdout -> socket ? Justin Gullingsrud (Wed Feb 12 2003 - 16:46:36 CST)
    - Re: remote_ctl.tcl: VMD's stdout -> socket ? Oliver Beckstein (Wed Feb 12 2003 - 17:22:38 CST)
rna pdb file Ioana Cozmuta (Wed Feb 12 2003 - 16:03:29 CST)
- Re: rna pdb file John Stone (Wed Feb 12 2003 - 16:08:55 CST)
  - Re: rna pdb file Ioana Cozmuta (Wed Feb 12 2003 - 16:52:32 CST)
    - Re: rna pdb file John Stone (Thu Feb 13 2003 - 14:13:58 CST)
plug-in for multiple frame xyz files Luca UvA (Mon Feb 10 2003 - 04:17:08 CST)
- Re: plug-in for multiple frame xyz files John Stone (Mon Feb 10 2003 - 14:32:39 CST)
Making VMD movies Sanjeev B.S. (Sun Feb 09 2003 - 23:06:00 CST)
- Re: Making VMD movies John Stone (Sun Feb 09 2003 - 23:05:20 CST)
  - Re: Making VMD movies Sanjeev B.S. (Sun Feb 09 2003 - 23:41:57 CST)
install of new VMD 1.8 Yongmei Wang (Thu Feb 06 2003 - 15:56:44 CST)
- Re: install of new VMD 1.8 John Stone (Thu Feb 06 2003 - 17:27:38 CST)
[tripp@fis.unam.mx: Re: Pls help me to render files with only traces of proteins!] John Stone (Thu Feb 06 2003 - 13:55:43 CST)
different colors Luca UvA (Thu Feb 06 2003 - 05:04:21 CST)
Pls help me to render files with only traces of proteins! Margaret Cheung (Wed Feb 05 2003 - 19:06:41 CST)
- Re: Pls help me to render files with only traces of proteins! John Stone (Wed Feb 05 2003 - 19:28:31 CST)
  - Re: Pls help me to render files with only traces of proteins! Margaret Cheung (Wed Feb 05 2003 - 19:48:33 CST)
- Re: Pls help me to render files with only traces of proteins! Mauricio Carrillo Tripp (Thu Feb 06 2003 - 08:06:38 CST)
PNY Quadro4 980XGL Card Jill Vickery (Wed Feb 05 2003 - 11:47:55 CST)
- Re: PNY Quadro4 980XGL Card John Stone (Wed Feb 05 2003 - 12:40:35 CST)
VMD 1.8 problems with AMBER parm and crd file Yongmei Wang (Tue Feb 04 2003 - 14:57:18 CST)
- Re: VMD 1.8 problems with AMBER parm and crd file John Stone (Tue Feb 04 2003 - 15:00:55 CST)
- Re: VMD 1.8 problems with AMBER parm and crd file John Stone (Tue Feb 04 2003 - 15:29:38 CST)
  - Re: VMD 1.8 problems with AMBER parm and crd file Lubos Vrbka (Wed Feb 05 2003 - 02:21:25 CST)
remote control (fifo/socket) ? Oliver Beckstein (Tue Feb 04 2003 - 09:58:54 CST)
- Re: remote control (fifo/socket) ? John Stone (Tue Feb 04 2003 - 10:08:06 CST)
python: readline support Oliver Beckstein (Tue Feb 04 2003 - 09:47:13 CST)
- Compiling VMD-1.8 as a loadable python module Lars Bruno Hansen (Thu Feb 06 2003 - 06:15:02 CST)
  - Re: Compiling VMD-1.8 as a loadable python module Justin Gullingsrud (Thu Feb 06 2003 - 10:55:14 CST)
    - Python callbacks Lars Bruno Hansen (Mon Feb 10 2003 - 04:03:58 CST)
    - Re: Python callbacks Justin Gullingsrud (Mon Feb 10 2003 - 10:47:37 CST)
python: packages not found Oliver Beckstein (Tue Feb 04 2003 - 09:45:46 CST)
- Re: python: packages not found Justin Gullingsrud (Tue Feb 04 2003 - 10:50:35 CST)
different colors Luca UvA (Tue Feb 04 2003 - 04:50:40 CST)
- Re: different colors John Stone (Tue Feb 04 2003 - 10:01:19 CST)
Bugfix: new save_state.tcl for VMD 1.8 installations... John Stone (Fri Jan 31 2003 - 14:02:44 CST)
SASA Rukman Hertadi (Fri Jan 31 2003 - 03:59:16 CST)
- Re: SASA John Stone (Fri Jan 31 2003 - 10:24:41 CST)
Re: save_state John Stone (Thu Jan 30 2003 - 13:28:24 CST)
Re: [PyMOL] 3D on linux (fwd) Eugen Leitl (Thu Jan 30 2003 - 09:40:15 CST)
mol volume J. Rui Rodrigues (Wed Jan 29 2003 - 10:17:30 CST)
- Re: mol volume John Stone (Wed Jan 29 2003 - 13:51:23 CST)
initial run by vmd on loading a trajectory Dr. Y. U. Sasidhar (Tue Jan 28 2003 - 22:58:17 CST)
- Re: initial run by vmd on loading a trajectory Mikko Huhtala (Wed Jan 29 2003 - 02:28:56 CST)
- Re: initial run by vmd on loading a trajectory Justin Gullingsrud (Wed Jan 29 2003 - 09:07:29 CST)
  - Re: initial run by vmd on loading a trajectory Dr. Y. U. Sasidhar (Thu Jan 30 2003 - 05:32:53 CST)
FYI: (for OSX version) a document about shell script and applescript MengJuei Hsieh (Tue Jan 28 2003 - 17:13:41 CST)
compiling vmd... Lubos Vrbka (Tue Jan 28 2003 - 04:54:00 CST)
- Re: compiling vmd... John Stone (Tue Jan 28 2003 - 09:39:36 CST)
- Re: compiling vmd... B. Bennion (Tue Jan 28 2003 - 10:09:33 CST)
hard ware stereo Y. U. Sasidhar (Sun Jan 26 2003 - 08:48:18 CST)
- Re: hard ware stereo MJR (Sun Jan 26 2003 - 21:14:35 CST)
- Re: hard ware stereo Dr. Daniel James White PhD (Mon Jan 27 2003 - 04:14:09 CST)
Stereo mode on NVidia/Win2000 Michael Redmond (Fri Jan 24 2003 - 09:29:55 CST)
- Re: Stereo mode on NVidia/Win2000 John Stone (Fri Jan 24 2003 - 10:20:10 CST)
  - Wait command in Win2000 Michael Redmond (Fri Apr 11 2003 - 15:43:13 CDT)
- RE: Stereo mode on NVidia/Win2000 DeLano, Warren (Fri Jan 24 2003 - 13:44:14 CST)
  - Re: Stereo mode on NVidia/Win2000 John Stone (Fri Jan 24 2003 - 14:01:55 CST)
- RE: Stereo mode on NVidia/Win2000 Michael Redmond (Fri Jan 24 2003 - 13:54:26 CST)
  - Re: Stereo mode on NVidia/Win2000 John Stone (Fri Jan 24 2003 - 14:18:32 CST)
cylindrical water Rukman Hertadi (Fri Jan 24 2003 - 04:22:28 CST)
[jrui@ci.uc.pt: Re: visualizing Delphi output (electrostatic potential)] John Stone (Thu Jan 23 2003 - 14:37:36 CST)
visualizing Delphi output (electrostatic potential) Vlad Cojocaru (Thu Jan 23 2003 - 10:08:51 CST)
- Re: visualizing Delphi output (electrostatic potential) John Stone (Thu Jan 23 2003 - 10:23:09 CST)
2 more quick questions phubbard_at_post.its.mcw.edu (Wed Jan 22 2003 - 17:53:54 CST)
- Re: 2 more quick questions John Stone (Wed Jan 22 2003 - 18:18:30 CST)
  - [OT] pdb files with lots of residues gianluca santarossa (Thu Jan 30 2003 - 09:10:23 CST)
    - Re: [OT] pdb files with lots of residues Jim Phillips (Thu Jan 30 2003 - 09:21:37 CST)
    - Re: [OT] pdb files with lots of residues Justin Gullingsrud (Thu Jan 30 2003 - 09:45:07 CST)
Surfaces/Cavities phubbard_at_post.its.mcw.edu (Wed Jan 22 2003 - 14:01:37 CST)
- Re: Surfaces/Cavities John Stone (Wed Jan 22 2003 - 14:16:49 CST)
  - Re: Surfaces/Cavities phubbard_at_post.its.mcw.edu (Wed Jan 22 2003 - 14:45:36 CST)
- RE: Surfaces/Cavities Liu, Zhanwu (Wed Jan 22 2003 - 15:37:35 CST)
  - RE: Surfaces/Cavities phubbard_at_post.its.mcw.edu (Wed Jan 22 2003 - 16:04:25 CST)
- Re: Surfaces/Cavities Alan Wilter Sousa da Silva (Thu Jan 23 2003 - 06:21:18 CST)
aligntool docs?... Joshua Speidel (Tue Jan 21 2003 - 15:03:36 CST)
- Re: aligntool docs?... John Stone (Tue Jan 21 2003 - 15:36:56 CST)
bug? Ioana Cozmuta (Fri Jan 17 2003 - 22:08:41 CST)
20 colors for 20 amino acids! Dr Nick (Fri Jan 17 2003 - 11:23:28 CST)
- Re: 20 colors for 20 amino acids! John Stone (Wed Jan 22 2003 - 10:13:30 CST)
Cl ions Ioana Cozmuta (Thu Jan 16 2003 - 21:05:34 CST)
- Re: Cl ions Justin Gullingsrud (Thu Jan 16 2003 - 23:26:37 CST)
SHAKE/namd Ioana Cozmuta (Thu Jan 16 2003 - 20:20:05 CST)
- Re: SHAKE/namd John Stone (Thu Jan 16 2003 - 20:54:37 CST)
- Re: SHAKE/namd Justin Gullingsrud (Thu Jan 16 2003 - 23:23:33 CST)
pdb files in VMD/NAMD TUTORIAL Ioana Cozmuta (Wed Jan 15 2003 - 21:52:27 CST)
- Re: pdb files in VMD/NAMD TUTORIAL John Stone (Thu Jan 16 2003 - 15:11:53 CST)
SCRIPT directory... Sanjeev B.S. (Wed Jan 15 2003 - 11:46:56 CST)
- Re: SCRIPT directory... John Stone (Wed Jan 15 2003 - 11:47:47 CST)
- Re: SCRIPT directory... gianluca santarossa (Thu Jan 16 2003 - 04:10:48 CST)
solvate option in vmd Ioana Cozmuta (Tue Jan 14 2003 - 20:05:46 CST)
- Re: solvate option in vmd John Stone (Wed Jan 15 2003 - 10:29:36 CST)
Maximum number of atoms/bonds #WONG CHEE HOW# (Tue Jan 14 2003 - 19:04:54 CST)
- Re: Maximum number of atoms/bonds John Stone (Wed Jan 15 2003 - 10:33:03 CST)
[ARitger@nvidia.com: Re: problems with stereo display on NVIDIA Quadro4 750 XGL] John Stone (Tue Jan 14 2003 - 13:07:58 CST)
movie from amber traj eric hu (Tue Jan 14 2003 - 12:46:38 CST)
- Re: movie from amber traj John Stone (Tue Jan 14 2003 - 13:02:30 CST)
problems with stereo display on NVIDIA Quadro4 750 XGL Karsten Suhre (Tue Jan 14 2003 - 02:12:49 CST)
stereo display on NVIDIA Quadro4 750 XGL Karsten Suhre (Tue Jan 07 2003 - 05:32:22 CST)
- Re: stereo display on NVIDIA Quadro4 750 XGL John Stone (Tue Jan 07 2003 - 09:42:35 CST)
  - Re: stereo display on NVIDIA Quadro4 750 XGL Magnus Kreth (Mon Jan 13 2003 - 09:32:28 CST)
    - Re: stereo display on NVIDIA Quadro4 750 XGL John Stone (Mon Jan 13 2003 - 17:14:06 CST)
- Re: stereo display on NVIDIA Quadro4 750 XGL John Stone (Wed Mar 12 2003 - 15:01:15 CST)
Cylindrical water box Liu, Zhanwu (Fri Jan 03 2003 - 08:49:53 CST)
hydrophobicity on the Connolly surface Denys Bashtovyy (Thu Jan 02 2003 - 07:04:10 CST)
- Re: hydrophobicity on the Connolly surface John Stone (Thu Jan 02 2003 - 10:33:33 CST)
VMD Representation (addition) Sichun Yang (Sun Dec 29 2002 - 15:16:32 CST)
- Re: VMD Representation (addition) Justin Gullingsrud (Sun Dec 29 2002 - 19:22:03 CST)
VMD Representation Sichun Yang (Sun Dec 29 2002 - 14:55:12 CST)
creating spherical water droplet Rukman Hertadi (Thu Dec 26 2002 - 19:41:52 CST)
- Re: creating spherical water droplet Justin Gullingsrud (Fri Dec 27 2002 - 09:46:09 CST)
Stereo VMD jwc_at_itsa.ucsf.edu (Tue Dec 24 2002 - 18:24:51 CST)
- Re: Stereo VMD MengJuei Hsieh (Thu Dec 26 2002 - 03:26:35 CST)
- Re: Stereo VMD jwc_at_itsa.ucsf.edu (Thu Dec 26 2002 - 11:32:16 CST)
  - Re: Stereo VMD John Stone (Thu Dec 26 2002 - 15:40:43 CST)
STL format file - rendering alarcon_at_lncc.br (Thu Dec 19 2002 - 13:39:20 CST)
- Re: STL format file - rendering John Stone (Thu Dec 19 2002 - 15:34:41 CST)
water model Ioana Cozmuta (Wed Dec 18 2002 - 19:56:03 CST)
- Re: water model Justin Gullingsrud (Wed Dec 18 2002 - 21:59:12 CST)
vmd version 1.8 Ioana Cozmuta (Wed Dec 18 2002 - 14:42:20 CST)
- Re: vmd version 1.8 John Stone (Wed Dec 18 2002 - 14:46:11 CST)
amber trajectory Ioana Cozmuta (Tue Dec 17 2002 - 23:15:55 CST)
- Re: amber trajectory John Stone (Tue Dec 17 2002 - 23:44:51 CST)
rendering from VMD Marcela Madrid (Tue Dec 17 2002 - 13:58:57 CST)
- Re: rendering from VMD B. Bennion (Tue Dec 17 2002 - 14:36:07 CST)
  - Re: rendering from VMD Marcela Madrid (Tue Dec 17 2002 - 15:53:41 CST)
    - Re: rendering from VMD B. Bennion (Tue Dec 17 2002 - 15:56:45 CST)
surface problems Tyler Luchko (Mon Dec 16 2002 - 18:48:45 CST)
- Re: surface problems John Stone (Wed Dec 18 2002 - 09:11:52 CST)
BioCoRE Release: New Features Robert Brunner (Mon Dec 16 2002 - 17:04:02 CST)
Building VMD on windows 2000 B. Bennion (Mon Dec 16 2002 - 15:35:51 CST)
saving a tiff file Marcela Madrid (Mon Dec 16 2002 - 15:01:30 CST)
- Re: saving a tiff file John Stone (Mon Dec 16 2002 - 17:43:51 CST)
  - Re: saving a tiff file Robert Brunner (Mon Dec 16 2002 - 20:01:02 CST)
- Re: saving a tiff file John Stone (Tue Dec 17 2002 - 16:36:56 CST)
  - Re: saving a tiff file Dr. Daniel James White PhD (Wed Dec 18 2002 - 05:16:45 CST)
pdb format Ioana Cozmuta (Fri Dec 13 2002 - 20:23:17 CST)
- Re: pdb format Justin Gullingsrud (Sun Dec 15 2002 - 23:07:05 CST)
smoothing from the command line Vlad Cojocaru (Fri Dec 13 2002 - 08:55:17 CST)
- Re: smoothing from the command line Justin Gullingsrud (Sun Dec 15 2002 - 23:20:12 CST)
Re: Loading multiple PDB files in VMD 1.8 John Stone (Tue Dec 10 2002 - 18:02:39 CST)
Loading XYZ trajectory file #WONG CHEE HOW# (Mon Dec 09 2002 - 19:17:00 CST)
- Re: Loading XYZ trajectory file John Stone (Tue Dec 10 2002 - 12:39:23 CST)
Tachyon VMD and MPI Cesar Delgado (Mon Dec 09 2002 - 18:25:19 CST)
- Re: Tachyon VMD and MPI John Stone (Mon Dec 09 2002 - 18:47:57 CST)
- Re: Tachyon VMD and MPI John Stone (Tue Jan 21 2003 - 15:44:11 CST)
Empty Extension menu on OSX Pascal Mercier (Mon Dec 09 2002 - 17:24:52 CST)
- Re: Empty Extension menu on OSX John Stone (Mon Dec 09 2002 - 17:35:32 CST)
Announce: VMD 1.8 is available! John Stone (Mon Dec 09 2002 - 15:22:28 CST)
interatomic distances Vlad Cojocaru (Mon Dec 09 2002 - 07:59:30 CST)
- Re: interatomic distances Justin Gullingsrud (Mon Dec 09 2002 - 14:33:43 CST)
Re: 3D printing John Stone (Fri Dec 06 2002 - 16:17:24 CST)
rotate a molecule eric hu (Thu Dec 05 2002 - 17:09:28 CST)
- Re: rotate a molecule John Stone (Thu Dec 05 2002 - 17:12:33 CST)
converting Vlad Cojocaru (Wed Dec 04 2002 - 16:04:06 CST)
- Re: converting John Stone (Wed Dec 04 2002 - 16:16:22 CST)
Fitting simple geometric objects to a molecule ? Marc Baaden (Mon Dec 02 2002 - 04:59:11 CST)
- Re: Fitting simple geometric objects to a molecule ? Justin Gullingsrud (Mon Dec 02 2002 - 09:19:55 CST)
hbonds during trajectorywith vmd 1.8beta Vlad Cojocaru (Mon Dec 02 2002 - 03:05:44 CST)
- Re: hbonds during trajectorywith vmd 1.8beta Justin Gullingsrud (Mon Dec 02 2002 - 09:15:20 CST)
  - Re: hbonds during trajectorywith vmd 1.8beta Vlad Cojocaru (Tue Dec 03 2002 - 04:05:59 CST)
Fwd: GROMOS to AMBER and reverse John Stone (Fri Nov 29 2002 - 23:23:53 CST)
dti monitor linux Peter Tieleman (Fri Nov 29 2002 - 15:12:58 CST)
- Re: dti monitor linux John Stone (Fri Nov 29 2002 - 15:58:59 CST)
can VMD display a box? Minerva Gonzalez (Thu Nov 28 2002 - 12:23:15 CST)
- Re: can VMD display a box? Marc Baaden (Thu Nov 28 2002 - 07:26:05 CST)
polar coordinates Peter VARNAI (Wed Nov 27 2002 - 11:52:10 CST)
- Re: polar coordinates John Stone (Wed Nov 27 2002 - 12:34:10 CST)
unix -vmd Ioana Cozmuta (Tue Nov 26 2002 - 17:29:25 CST)
- Re: unix -vmd John Stone (Tue Nov 26 2002 - 17:39:34 CST)
VMD 1.8 beta 6 Unix binaries available... John Stone (Tue Nov 26 2002 - 16:16:16 CST)
Raytracing with tachyon/povray because of pb with raster3d Marc Baaden (Tue Nov 26 2002 - 10:47:22 CST)
- Re: Raytracing with tachyon/povray because of pb with raster3d John Stone (Tue Nov 26 2002 - 11:17:33 CST)
- Re: Raytracing with tachyon/povray because of pb with raster3d Bogdan Costescu (Tue Nov 26 2002 - 11:41:38 CST)
  - Re: Raytracing with tachyon/povray because of pb with raster3d Marc Baaden (Tue Nov 26 2002 - 12:02:51 CST)
    - Re: Raytracing with tachyon/povray because of pb with raster3d Bogdan Costescu (Tue Nov 26 2002 - 12:58:40 CST)
- Re: Raytracing with tachyon/povray because of pb with raster3d John Stone (Tue Nov 26 2002 - 13:11:26 CST)
  - Re: Raytracing with tachyon/povray because of pb with raster3d John Stone (Tue Nov 26 2002 - 13:34:38 CST)
breaking the last bond when loading Vlad Cojocaru (Tue Nov 26 2002 - 07:24:59 CST)
- Re: breaking the last bond when loading John Stone (Tue Nov 26 2002 - 09:34:35 CST)
- Re: breaking the last bond when loading John Stone (Tue Nov 26 2002 - 11:06:20 CST)
speed prob Sanjeev B.S. (Tue Nov 26 2002 - 03:14:14 CST)
beta version Sanjeev B.S. (Tue Nov 26 2002 - 01:35:28 CST)
Using Magellan Spacemouse with VMD srtlscao (Mon Nov 25 2002 - 08:38:46 CST)
- Re: Using Magellan Spacemouse with VMD John Stone (Tue Nov 26 2002 - 14:49:38 CST)
A very minor question on the MacOS X native bundle version MengJuei Hsieh (Fri Nov 22 2002 - 19:53:57 CST)
- Re: A very minor question on the MacOS X native bundle version John Stone (Sun Nov 24 2002 - 20:43:06 CST)
  - Re: A very minor question on the MacOS X native bundle version MengJuei Hsieh (Wed Nov 27 2002 - 01:28:08 CST)
New AMBER 7 file reader plugin, testers needed :-) John Stone (Wed Nov 20 2002 - 13:23:32 CST)
- Re: New AMBER 7 file reader plugin, testers needed :-) MengJuei Hsieh (Fri Nov 22 2002 - 19:58:10 CST)
- draw a vector Nguyen Hoang Phuong (Thu Nov 28 2002 - 07:59:56 CST)
  - Re: draw a vector John Stone (Sat Nov 30 2002 - 15:17:39 CST)
VMD 1.8 beta 2 available for testing! John Stone (Mon Nov 18 2002 - 17:01:35 CST)
MacOS X window resizing fix... John Stone (Mon Nov 18 2002 - 00:21:53 CST)
Maintaining original coordinates from PDB ? Marc Baaden (Sun Nov 17 2002 - 14:52:15 CST)
- Re: Maintaining original coordinates from PDB ? John Stone (Mon Nov 18 2002 - 09:54:24 CST)
avoiding distance based bond search when reading a PDB file Christophe Guilbert (Thu Nov 14 2002 - 14:31:17 CST)
- Re: avoiding distance based bond search when reading a PDB file John Stone (Thu Nov 14 2002 - 15:25:53 CST)
CRD problems and CRD to DCD conversion Mark Zottola - Contractor (Wed Nov 13 2002 - 14:59:33 CST)
- Re: CRD problems and CRD to DCD conversion John Stone (Wed Nov 13 2002 - 15:06:39 CST)
- Re: CRD problems and CRD to DCD conversion B. Bennion (Wed Nov 13 2002 - 15:48:57 CST)
- Re: CRD problems and CRD to DCD conversion Mark Zottola - Contractor (Wed Nov 13 2002 - 16:04:39 CST)
cartoon representation stefano ricagno (Wed Nov 13 2002 - 06:27:33 CST)
- Re: cartoon representation John Stone (Thu Nov 14 2002 - 16:02:48 CST)
  - Re: cartoon representation Robert Campbell (Fri Nov 15 2002 - 09:58:02 CST)
    - Re: cartoon representation John Stone (Fri Nov 15 2002 - 09:58:43 CST)
mpeg movie from trajectory Vlad Cojocaru (Wed Nov 13 2002 - 04:39:26 CST)
- Re: mpeg movie from trajectory Stéphane Teletchéa (Wed Nov 13 2002 - 06:21:04 CST)
- Re: mpeg movie from trajectory John Stone (Wed Nov 13 2002 - 09:38:49 CST)
- Re: mpeg movie from trajectory John Stone (Wed Nov 13 2002 - 09:40:41 CST)
How to add atoms to a molecule? Paul Darwen (Tue Nov 12 2002 - 22:39:53 CST)
- Re: How to add atoms to a molecule? John Stone (Mon Nov 18 2002 - 00:35:43 CST)
Problems with color #WONG CHEE HOW# (Mon Nov 11 2002 - 09:52:17 CST)
- Re: Problems with color John Stone (Mon Nov 11 2002 - 10:07:57 CST)
alignment and rmsd fit Marcela Madrid (Fri Nov 08 2002 - 16:16:38 CST)
- Re: alignment and rmsd fit John Stone (Fri Nov 08 2002 - 17:00:06 CST)
Stereo quality and Save State Problems Jill Vickery (Fri Nov 08 2002 - 14:07:46 CST)
- Re: Stereo quality and Save State Problems John Stone (Fri Nov 08 2002 - 14:36:04 CST)
sources Dmitry Kovalsky (Fri Nov 08 2002 - 06:39:40 CST)
- Re: sources John Stone (Fri Nov 08 2002 - 11:36:08 CST)
Beta color of atoms #WONG CHEE HOW# (Thu Nov 07 2002 - 19:57:26 CST)
- Re: Beta color of atoms John Stone (Fri Nov 08 2002 - 11:38:47 CST)
[mjd@dti3d.com: Re: VMD 1.8 alpha 29 available for testing!] John Stone (Thu Nov 07 2002 - 15:11:38 CST)
animation with PDBs Ross J. Toedte (Thu Nov 07 2002 - 10:10:09 CST)
- Re: animation with PDBs John Stone (Thu Nov 07 2002 - 10:33:26 CST)
Labels 'springs' in labels form Stéphane Teletchéa (Wed Nov 06 2002 - 07:44:24 CST)
- Re: Labels 'springs' in labels form John Stone (Fri Nov 08 2002 - 17:33:21 CST)
No stereo mode in vmd -dispdev none ?? Marc Baaden (Wed Nov 06 2002 - 07:15:03 CST)
- Re: No stereo mode in vmd -dispdev none ?? John Stone (Thu Nov 07 2002 - 16:46:02 CST)
Postdoctoral positions in Australia Brendan O'Malley (Wed Nov 06 2002 - 04:55:13 CST)
Re: Display size in VMD 1.8a29 for OS X John Stone (Tue Nov 05 2002 - 10:41:46 CST)
Re: command args to MSMS in VMD John Stone (Tue Nov 05 2002 - 10:27:26 CST)
vmd runs slowly on vmware jen ramus (Mon Nov 04 2002 - 17:05:14 CST)
- Re: vmd runs slowly on vmware John Stone (Mon Nov 04 2002 - 18:31:54 CST)
- Re: vmd runs slowly on vmware MengJuei Hsieh (Mon Nov 04 2002 - 18:51:35 CST)
AMBER6 format MengJuei Hsieh (Mon Nov 04 2002 - 14:39:52 CST)
- Re: AMBER6 format John Stone (Mon Nov 04 2002 - 14:56:12 CST)
  - Re: AMBER6 format MengJuei Hsieh (Mon Nov 04 2002 - 17:22:44 CST)
- Re: AMBER6 format John Stone (Mon Nov 18 2002 - 00:20:19 CST)
- Re: AMBER6 format MengJuei Hsieh (Tue Nov 19 2002 - 16:02:55 CST)
VMD 1.8 alpha 29 available for testing! John Stone (Fri Nov 01 2002 - 17:52:09 CST)
- RE: VMD 1.8 alpha 29 available for testing! #WONG CHEE HOW# (Fri Nov 01 2002 - 22:47:01 CST)
  - Re: VMD 1.8 alpha 29 available for testing! John Stone (Sat Nov 02 2002 - 00:25:51 CST)
- RE: VMD 1.8 alpha 29 available for testing! #WONG CHEE HOW# (Fri Nov 01 2002 - 22:48:10 CST)
- Re: VMD 1.8 alpha 29 available for testing! Marc Baaden (Mon Nov 04 2002 - 10:41:30 CST)
  - Re: VMD 1.8 alpha 29 available for testing! John Stone (Mon Nov 04 2002 - 10:51:34 CST)
- Re: VMD 1.8 alpha 29 available for testing! John Stone (Wed Nov 06 2002 - 14:40:16 CST)
Coloring of atoms/molecules #WONG CHEE HOW# (Thu Oct 31 2002 - 23:24:13 CST)
- Re: Coloring of atoms/molecules John Stone (Fri Nov 01 2002 - 21:18:42 CST)
A vmd bug 1.8a28 Stéphane Teletchéa (Thu Oct 31 2002 - 08:01:34 CST)
carnal output trajectory Vlad Cojocaru (Wed Oct 30 2002 - 07:25:36 CST)
- Re: carnal output trajectory Stéphane Teletchéa (Wed Oct 30 2002 - 07:50:19 CST)
- Re: carnal output trajectory Sanjeev B.S. (Wed Oct 30 2002 - 07:50:45 CST)
Unable to use short loabels Stéphane Teletchéa (Wed Oct 30 2002 - 03:50:01 CST)
- Re: Unable to use short loabels John Stone (Wed Oct 30 2002 - 10:14:14 CST)
helices in coil B. Bennion (Tue Oct 29 2002 - 18:24:13 CST)
- Re: helices in coil John Stone (Wed Oct 30 2002 - 10:48:47 CST)
  - Re: helices in coil Justin Gullingsrud (Wed Oct 30 2002 - 10:57:34 CST)
Gromacs file formats gro, xtc and trr Marc Baaden (Tue Oct 29 2002 - 15:59:38 CST)
- Re: Gromacs file formats gro, xtc and trr John Stone (Tue Oct 29 2002 - 16:14:37 CST)
positioning a protein with trans etc. Marc Baaden (Tue Oct 29 2002 - 12:59:56 CST)
- Re: positioning a protein with trans etc. John Stone (Tue Oct 29 2002 - 15:56:18 CST)
  - Re: positioning a protein with trans etc. Marc Baaden (Wed Oct 30 2002 - 05:33:26 CST)
- Re: positioning a protein with trans etc. Marc Baaden (Tue Oct 29 2002 - 16:02:55 CST)
  - Re: positioning a protein with trans etc. Stéphane Teletchéa (Wed Oct 30 2002 - 02:26:36 CST)
reference about structure Vlad Cojocaru (Tue Oct 29 2002 - 04:34:57 CST)
- Re: reference about structure John Stone (Tue Oct 29 2002 - 09:49:31 CST)
vmd checking socket in tcl jen ramus (Mon Oct 28 2002 - 19:30:04 CST)
- Re: vmd checking socket in tcl John Stone (Mon Oct 28 2002 - 19:46:12 CST)
  - hydrogen bonding Y. U. Sasidhar (Mon Oct 28 2002 - 21:52:48 CST)
    - Re: hydrogen bonding John Stone (Wed Oct 30 2002 - 10:37:02 CST)
    - Re: hydrogen bonding Justin Gullingsrud (Wed Oct 30 2002 - 10:54:13 CST)
rms dumping in a file Vlad Cojocaru (Mon Oct 28 2002 - 05:16:41 CST)
- Re: rms dumping in a file John Stone (Mon Oct 28 2002 - 10:34:44 CST)
Feature request for vmd 1.8 Stéphane Teletchéa (Mon Oct 28 2002 - 04:10:55 CST)
- Re: Feature request for vmd 1.8 Justin Gullingsrud (Mon Oct 28 2002 - 09:53:56 CST)
- Another feature request for vmd 1.8 David Chalmers (Mon Oct 28 2002 - 20:02:15 CST)
  - Re: Another feature request for vmd 1.8 John Stone (Wed Oct 30 2002 - 10:41:11 CST)
carnal output trajectory Vlad Cojocaru (Fri Oct 25 2002 - 04:50:55 CDT)
core dump when launching vmd1.8a21 Margaret Cheung (Thu Oct 24 2002 - 19:49:42 CDT)
- Re: core dump when launching vmd1.8a21 John Stone (Thu Oct 24 2002 - 19:55:21 CDT)
- Re: core dump when launching vmd1.8a21 B. Bennion (Thu Oct 24 2002 - 20:30:05 CDT)
  - Re: core dump when launching vmd1.8a21 Margaret Cheung (Thu Oct 24 2002 - 20:31:28 CDT)
    - Re: core dump when launching vmd1.8a21 John Stone (Thu Oct 24 2002 - 20:36:16 CDT)
    - Re: core dump when launching vmd1.8a21 Margaret Cheung (Thu Oct 24 2002 - 21:05:30 CDT)
carnal output trajectory Vlad Cojocaru (Thu Oct 24 2002 - 15:07:35 CDT)
- Re: carnal output trajectory Margaret Cheung (Thu Oct 24 2002 - 15:57:50 CDT)
Vmd console window colors in Irix 6.5 Ken Sale (Thu Oct 24 2002 - 13:47:03 CDT)
- Re: Vmd console window colors in Irix 6.5 John Stone (Thu Oct 24 2002 - 14:31:47 CDT)
Antialiasing ? Marc Baaden (Wed Oct 23 2002 - 08:45:22 CDT)
- Re: Antialiasing ? John Stone (Wed Oct 23 2002 - 10:07:15 CDT)
  - Re: Antialiasing ? Stéphane Teletchéa (Thu Oct 24 2002 - 02:16:35 CDT)
question on prmtop & prmcrd from leap (amber) Sichun Yang (Fri Oct 18 2002 - 16:17:46 CDT)
- Re: question on prmtop & prmcrd from leap (amber) B. Bennion (Fri Oct 18 2002 - 18:13:43 CDT)
question on prmtop & prmcrd from leap (amber) Sichun Yang (Fri Oct 18 2002 - 16:15:15 CDT)
solvate documentation. Gadi Oron (Thu Oct 17 2002 - 07:05:06 CDT)
RMS fits Tara Sprules (Wed Oct 16 2002 - 17:34:09 CDT)
- Re: RMS fits Dean Johnson (Fri Oct 18 2002 - 23:04:11 CDT)
XTC files in 1.8a21 Dmitry Kovalsky (Wed Oct 16 2002 - 04:08:30 CDT)
- Re: XTC files in 1.8a21 John Stone (Wed Oct 16 2002 - 10:22:41 CDT)
load molecule made by amber7. Margaret Cheung (Fri Oct 11 2002 - 20:10:35 CDT)
- Re: load molecule made by amber7. John Stone (Tue Oct 15 2002 - 15:52:00 CDT)
  - Re: load molecule made by amber7. Margaret Cheung (Tue Oct 15 2002 - 16:14:57 CDT)
MacOSX and the solvate package Evan Thompson (Fri Oct 11 2002 - 20:02:59 CDT)
- Re: MacOSX and the solvate package John Stone (Fri Oct 11 2002 - 22:48:14 CDT)
molden xyz movie eric hu (Thu Oct 10 2002 - 17:57:13 CDT)
- Re: molden xyz movie B. Bennion (Thu Oct 10 2002 - 18:22:59 CDT)
  - Re: molden xyz movie eric hu (Thu Oct 10 2002 - 20:27:11 CDT)
    - Re: molden xyz movie B. Bennion (Fri Oct 11 2002 - 00:40:52 CDT)
Windows XP refresh rate bug/stereo, information page John Stone (Tue Oct 08 2002 - 17:25:08 CDT)
Hydrophobicity Markus Laub (Sat Oct 05 2002 - 17:42:20 CDT)
- Re: Hydrophobicity Justin Gullingsrud (Sun Oct 06 2002 - 13:37:35 CDT)
VDW radii ran friedman (Thu Oct 03 2002 - 09:33:30 CDT)
- Re: VDW radii John Stone (Thu Oct 03 2002 - 09:39:22 CDT)
"Pick item mode" inactive in OSX bundle ? Christian Simon (Thu Oct 03 2002 - 07:44:53 CDT)
- Re: "Pick item mode" inactive in OSX bundle ? John Stone (Thu Oct 03 2002 - 08:47:32 CDT)
H-bond plotting Liu, Zhanwu (Wed Oct 02 2002 - 09:54:38 CDT)
quick help jmp17_at_duke.edu (Wed Oct 02 2002 - 00:48:31 CDT)
- Re: quick help John Stone (Wed Oct 02 2002 - 00:54:33 CDT)
Re: VRML2.0 John Stone (Tue Oct 01 2002 - 10:05:37 CDT)
VMD 1.8a28 bundle for MacOS X 10.2 available... John Stone (Thu Sep 26 2002 - 18:19:18 CDT)
- Re: VMD 1.8a28 bundle for MacOS X 10.2 available... MengJuei Hsieh (Fri Sep 27 2002 - 04:18:46 CDT)
- Re: VMD 1.8a28 bundle for MacOS X 10.2 available... Mauricio Carrillo Tripp (Fri Sep 27 2002 - 19:22:30 CDT)
  - Re: VMD 1.8a28 bundle for MacOS X 10.2 available... Justin Gullingsrud (Fri Sep 27 2002 - 19:35:05 CDT)
Fwd: superimposing molecules John Stone (Tue Sep 24 2002 - 14:23:24 CDT)
Re: multiple structure PDB files John Stone (Tue Sep 24 2002 - 14:19:01 CDT)
- Re: multiple structure PDB files Stéphane Teletchéa (Wed Sep 25 2002 - 03:17:31 CDT)
Save state miss some parameters ! Stéphane Teletchéa (Tue Sep 24 2002 - 06:55:50 CDT)
- Re: Save state miss some parameters ! John Stone (Tue Sep 24 2002 - 09:36:49 CDT)
Menu is missing? Jeroen Akershoek (Tue Sep 24 2002 - 03:31:16 CDT)
- Re: Menu is missing? John Stone (Tue Sep 24 2002 - 11:09:51 CDT)
How to select the interacting atoms between two molecules in two different pdb files Tran Trung Tran (Mon Sep 23 2002 - 19:23:46 CDT)
- Re: How to select the interacting atoms between two molecules in two different pdb files John Stone (Tue Sep 24 2002 - 15:30:25 CDT)
Re: Native OSX VMD version for 10.2 John Stone (Mon Sep 23 2002 - 15:22:38 CDT)
- Re: Native OSX VMD version for 10.2 John Stone (Wed Oct 02 2002 - 13:18:51 CDT)
CDROM/Windows/Linux Surjit Dixit (Thu Sep 19 2002 - 14:35:46 CDT)
- Re: CDROM/Windows/Linux John Stone (Thu Sep 19 2002 - 15:16:54 CDT)
  - Re: CDROM/Windows/Linux Stéphane Teletchéa (Fri Sep 20 2002 - 04:24:12 CDT)
    - Re: CDROM/Windows/Linux Surjit Dixit (Fri Sep 20 2002 - 07:29:47 CDT)
Yes Another HPUX problem Tobias Mandrup Johansen (Thu Sep 19 2002 - 10:04:42 CDT)
- Re: Yes Another HPUX problem Justin Gullingsrud (Thu Sep 19 2002 - 10:37:08 CDT)
How to show the strain energies of each atom #WONG CHEE HOW# (Thu Sep 19 2002 - 02:36:27 CDT)
- Re: How to show the strain energies of each atom John Stone (Thu Sep 26 2002 - 16:38:08 CDT)
VMD 1.7.1 on HPUX in text mode Tobias Mandrup Johansen (Tue Sep 17 2002 - 08:57:27 CDT)
- Re: VMD 1.7.1 on HPUX in text mode John Stone (Tue Sep 17 2002 - 09:31:01 CDT)
  - Re: VMD 1.7.1 on HPUX in text mode Tobias Mandrup Johansen (Wed Sep 18 2002 - 02:38:57 CDT)
Is vmd working in float environment ? Stéphane Teletchéa (Tue Sep 17 2002 - 08:20:13 CDT)
- Re: Is vmd working in float environment ? John Stone (Tue Sep 17 2002 - 09:37:14 CDT)
Drawing atom - atom bonds Yves Frapart (Mon Sep 16 2002 - 11:08:13 CDT)
- Re: Drawing atom - atom bonds Justin Gullingsrud (Mon Sep 16 2002 - 09:44:49 CDT)
Centre of gravity for movies Mark Hilge (Fri Sep 13 2002 - 12:21:14 CDT)
- Re: Centre of gravity for movies John Stone (Tue Sep 17 2002 - 11:25:07 CDT)
Surface calculation Markus Laub (Thu Sep 12 2002 - 11:05:54 CDT)
Surface calculation Markus Laub (Thu Sep 12 2002 - 11:05:54 CDT)
- Re: Surface calculation John Stone (Mon Sep 16 2002 - 11:04:51 CDT)
vrml output Yifei Kong (Wed Sep 11 2002 - 21:04:15 CDT)
- Re: vrml output John Stone (Mon Sep 16 2002 - 16:02:31 CDT)
High-Res and Eye 3D glasses and SynthaGram Monitors Jill Vickery (Wed Sep 11 2002 - 13:53:44 CDT)
- RE: High-Res and Eye 3D glasses and SynthaGram Monitors Mads Nørregaard-Madsen (Wed Sep 11 2002 - 16:21:37 CDT)
- Re: High-Res and Eye 3D glasses and SynthaGram Monitors John Stone (Wed Sep 11 2002 - 17:22:56 CDT)
just a test Vlad Cojocaru (Wed Sep 11 2002 - 08:40:47 CDT)
vmd and catdcd Liu, Zhanwu (Fri Sep 06 2002 - 12:43:22 CDT)
- Re: vmd and catdcd John Stone (Fri Sep 06 2002 - 14:04:13 CDT)
Trouble with tcl script (puts command) J. Rui Rodrigues (Thu Sep 05 2002 - 13:42:20 CDT)
- Re: Trouble with tcl script (puts command) John Stone (Thu Sep 05 2002 - 14:00:11 CDT)
VMD 1.7.1 on HPUX Tobias Mandrup Johansen (Thu Sep 05 2002 - 05:41:31 CDT)
- Re: VMD 1.7.1 on HPUX John Stone (Thu Sep 05 2002 - 14:02:38 CDT)
assigning variables for representations Vlad Cojocaru (Wed Sep 04 2002 - 07:10:40 CDT)
- Re: assigning variables for representations John Stone (Thu Sep 05 2002 - 13:53:27 CDT)
All that I never took the time to ask about VMD ... Marc Baaden (Sat Aug 31 2002 - 07:14:29 CDT)
- Re: All that I never took the time to ask about VMD ... John Stone (Fri Sep 06 2002 - 14:51:50 CDT)
People having plugin troubles, READ THIS John Stone (Fri Aug 30 2002 - 13:54:55 CDT)
VMD and CHARMm format Nicolas Foloppe (Fri Aug 30 2002 - 04:54:19 CDT)
- Re: VMD and CHARMm format John Stone (Fri Sep 06 2002 - 15:39:07 CDT)
Getting history and file completion to work in vmd console ? Marc Baaden (Fri Aug 30 2002 - 04:02:47 CDT)
- Re: Getting history and file completion to work in vmd console ? Justin Gullingsrud (Fri Aug 30 2002 - 08:37:04 CDT)
- Re: Getting history and file completion to work in vmd console ? Paul Grayson (Fri Aug 30 2002 - 09:36:22 CDT)
  - Re: Getting history and file completion to work in vmd console ? Marc Baaden (Fri Aug 30 2002 - 09:48:28 CDT)
    - Re: Getting history and file completion to work in vmd console ? Paul Grayson (Fri Aug 30 2002 - 10:01:50 CDT)
- Re: Getting history and file completion to work in vmd console ? John Stone (Fri Aug 30 2002 - 09:58:28 CDT)
from points to a surface ? Marc Baaden (Wed Aug 28 2002 - 03:03:48 CDT)
- Re: from points to a surface ? John Stone (Wed Aug 28 2002 - 15:05:35 CDT)
  - Re: from points to a surface ? Marc Baaden (Wed Aug 28 2002 - 16:35:10 CDT)
Stereo on Linux: Eyes3D Premium + Nvidia Pawel Kedzierski (Tue Aug 27 2002 - 23:49:49 CDT)
- Re: Stereo on Linux: Eyes3D Premium + Nvidia John Stone (Wed Aug 28 2002 - 14:58:20 CDT)
- Re: Stereo on Linux: Eyes3D Premium + Nvidia John Stone (Thu Aug 29 2002 - 09:40:40 CDT)
Problem with VMD 1.8a21 under MacOS X 10.2 Jeffrey D. Hartgerink (Tue Aug 27 2002 - 12:32:44 CDT)
- Re: Problem with VMD 1.8a21 under MacOS X 10.2 John Stone (Tue Aug 27 2002 - 12:53:55 CDT)
stereo on linux: DTI monitors? Peter Tieleman (Sat Aug 24 2002 - 00:12:23 CDT)
- Re: stereo on linux: DTI monitors? Johannes von Langen (Mon Aug 26 2002 - 02:57:32 CDT)
- Re: stereo on linux: DTI monitors? John Stone (Mon Aug 26 2002 - 11:10:48 CDT)
- RE: stereo on linux: DTI monitors? Mads Nørregaard-Madsen (Tue Aug 27 2002 - 03:38:14 CDT)
- Re: stereo on linux: DTI monitors? Alexander Farley (Sun Sep 08 2002 - 09:36:48 CDT)
Secondary structure Mark Hilge (Fri Aug 23 2002 - 09:18:52 CDT)
- Re: Secondary structure Justin Gullingsrud (Fri Aug 23 2002 - 09:49:03 CDT)
- Re: Secondary structure Robert Campbell (Fri Aug 23 2002 - 12:13:44 CDT)
ftp failed Hitoshi Nejo (Fri Aug 23 2002 - 02:14:23 CDT)
- Re: ftp failed John Stone (Mon Aug 26 2002 - 10:58:43 CDT)
- Re: ftp failed $B:,>k(J $B6Q(J (Tue Aug 27 2002 - 02:35:49 CDT)
  - Re: ftp failed John Stone (Wed Aug 28 2002 - 15:28:00 CDT)
- Re: ftp failed $B:,>k(J $B6Q(J (Thu Aug 29 2002 - 03:21:12 CDT)
reading cube files Vlad Cojocaru (Thu Aug 22 2002 - 10:58:09 CDT)
- Re: reading cube files John Stone (Thu Aug 22 2002 - 11:34:29 CDT)
  - springs Nguyen Hoang Phuong (Wed Sep 04 2002 - 07:20:00 CDT)
    - Re: springs John Stone (Thu Sep 05 2002 - 13:58:50 CDT)
SPACEBALLS Jill Vickery (Wed Aug 21 2002 - 17:19:08 CDT)
- Re: SPACEBALLS John Stone (Wed Aug 21 2002 - 17:39:15 CDT)
  - Re: SPACEBALLS .. in Europe ? Marc Baaden (Thu Aug 22 2002 - 03:23:49 CDT)
    - Re: SPACEBALLS .. in Europe ? Surjit Dixit (Thu Aug 22 2002 - 08:02:47 CDT)
    - Re: SPACEBALLS .. in Europe ? John Stone (Thu Aug 22 2002 - 09:50:12 CDT)
save Vlad Cojocaru (Tue Aug 20 2002 - 06:15:02 CDT)
- Re: save John Stone (Tue Aug 20 2002 - 17:23:26 CDT)
SURF_BIN and psfgen missing? Jeroen Akershoek (Mon Aug 19 2002 - 03:33:41 CDT)
- Re: SURF_BIN and psfgen missing? John Stone (Mon Aug 19 2002 - 09:45:59 CDT)
Charge coloring and Stereo hot keys Jill Vickery (Fri Aug 16 2002 - 17:48:55 CDT)
- Re: Charge coloring and Stereo hot keys John Stone (Mon Aug 19 2002 - 10:29:48 CDT)
movie maker plugin doesn't load Dr. Dan White (Fri Aug 16 2002 - 10:54:22 CDT)
- Re: movie maker plugin doesn't load Justin Gullingsrud (Fri Aug 16 2002 - 11:07:18 CDT)
Saving two molecules into one PDB file Reinhard Klement (Fri Aug 16 2002 - 09:41:54 CDT)
- Re: Saving two molecules into one PDB file John Stone (Fri Aug 16 2002 - 13:44:32 CDT)
the same problem Vlad Cojocaru (Fri Aug 16 2002 - 04:33:55 CDT)
- Re: the same problem Justin Gullingsrud (Fri Aug 16 2002 - 08:56:28 CDT)
selection question Vlad Cojocaru (Thu Aug 15 2002 - 07:28:58 CDT)
- Re: selection question Justin Gullingsrud (Thu Aug 15 2002 - 08:51:05 CDT)
Separate graphical objects? Pawel Kedzierski (Wed Aug 14 2002 - 23:40:31 CDT)
- Re: Separate graphical objects? Justin Gullingsrud (Thu Aug 15 2002 - 16:05:55 CDT)
  - Re: Separate graphical objects? Pawel Kedzierski (Sat Aug 17 2002 - 11:36:24 CDT)
    - Re: Separate graphical objects? Justin Gullingsrud (Sat Aug 17 2002 - 12:01:07 CDT)
[Contribute] transparent MacOS X icon for VMD MengJuei Hsieh (Wed Aug 14 2002 - 19:15:49 CDT)
- Re: [Contribute] transparent MacOS X icon for VMD John Stone (Thu Aug 15 2002 - 17:08:44 CDT)
  - Re: [Contribute] transparent MacOS X icon for VMD MengJuei Hsieh (Fri Aug 16 2002 - 20:54:41 CDT)
    - Re: [Contribute] transparent MacOS X icon for VMD John Stone (Mon Aug 19 2002 - 11:47:21 CDT)
VMD and rendering packages Marc Baaden (Wed Aug 14 2002 - 11:01:13 CDT)
- Re: VMD and rendering packages John Stone (Wed Aug 14 2002 - 11:30:51 CDT)
rmsd problem Vlad Cojocaru (Wed Aug 14 2002 - 10:46:48 CDT)
- Re: rmsd problem John Stone (Wed Aug 14 2002 - 11:35:17 CDT)
  - Re: rmsd problem John Stone (Mon Aug 19 2002 - 11:42:08 CDT)
Phantom on Sgi? Kenneth Ayers (Wed Aug 14 2002 - 08:41:13 CDT)
- Re: Phantom on Sgi? John Stone (Wed Aug 14 2002 - 10:16:58 CDT)
Cannot start CAVE display Pawel Kedzierski (Tue Aug 13 2002 - 15:20:17 CDT)
- Re: Cannot start CAVE display John Stone (Tue Aug 13 2002 - 15:15:27 CDT)
- Re: Cannot start CAVE display Pawel Kedzierski (Thu Aug 15 2002 - 23:00:42 CDT)
  - Re: Cannot start CAVE display John Stone (Fri Aug 16 2002 - 11:32:42 CDT)
Windows XP and Eye3D glasses Jill Vickery (Tue Aug 13 2002 - 11:53:48 CDT)
- Re: Windows XP and Eye3D glasses John Stone (Tue Aug 13 2002 - 15:29:37 CDT)
- Re: Windows XP and Eye3D glasses John Stone (Tue Aug 13 2002 - 17:01:37 CDT)
Joysticks for VMD on Windows XP Jill Vickery (Mon Aug 12 2002 - 17:46:29 CDT)
- Re: Joysticks for VMD on Windows XP John Stone (Mon Aug 12 2002 - 18:49:35 CDT)
index Sanjeev B.S. (Fri Aug 09 2002 - 02:28:45 CDT)
Couldn't open required GL library J. Rui Rodrigues (Thu Aug 08 2002 - 18:48:37 CDT)
- Re: Couldn't open required GL library John Stone (Fri Aug 09 2002 - 15:32:33 CDT)
- Re: Couldn't open required GL library John Stone (Fri Aug 16 2002 - 14:40:18 CDT)
- Re: Couldn't open required GL library John Stone (Fri Aug 16 2002 - 15:13:30 CDT)
Gromacs XTC reader broken in 1.8beta version Marc Baaden (Thu Aug 08 2002 - 10:34:56 CDT)
- Re: Gromacs XTC reader broken in 1.8beta version John Stone (Thu Aug 08 2002 - 12:46:19 CDT)
VMD with stereo on RedHat Linux Steve Chen (Wed Aug 07 2002 - 18:49:27 CDT)
- Re: VMD with stereo on RedHat Linux John Stone (Wed Aug 07 2002 - 21:14:55 CDT)
  - Re: VMD with stereo on RedHat Linux John Stone (Wed Aug 07 2002 - 21:17:15 CDT)
Question about dihedral angles in VMD. Joe Huang (Wed Aug 07 2002 - 15:01:06 CDT)
- Re: Question about dihedral angles in VMD. Justin Gullingsrud (Wed Aug 07 2002 - 15:29:38 CDT)
Structural Biology Software Database updated... John Stone (Tue Aug 06 2002 - 10:24:14 CDT)
Problem with stride Troy Wymore (Mon Aug 05 2002 - 11:54:21 CDT)
- Re: Problem with stride John Stone (Mon Aug 05 2002 - 12:30:56 CDT)
  - Re: Problem with stride Troy Wymore (Mon Aug 05 2002 - 13:01:58 CDT)
namd callback command Will Sheffler (Mon Aug 05 2002 - 03:51:14 CDT)
Projection on plane Raj Gupta (Fri Aug 02 2002 - 10:41:38 CDT)
- Re: Projection on plane John Stone (Fri Aug 02 2002 - 10:48:41 CDT)
Chromium Cesar Delgado (Thu Aug 01 2002 - 15:16:31 CDT)
- Re: Chromium John Stone (Thu Aug 01 2002 - 15:48:34 CDT)
- Re: Chromium Cesar Delgado (Thu Aug 01 2002 - 16:07:40 CDT)
  - Re: Chromium John Stone (Thu Aug 01 2002 - 16:15:00 CDT)
- Re: Chromium Cesar Delgado (Thu Aug 01 2002 - 16:21:54 CDT)
  - Re: Chromium John Stone (Mon Aug 05 2002 - 14:33:57 CDT)
- Re: Chromium Cesar Delgado (Mon Aug 05 2002 - 16:19:09 CDT)
- Re: Chromium Alexander Farley (Sun Sep 08 2002 - 09:44:58 CDT)
vmdmovie problem mimurra3 (Thu Aug 01 2002 - 14:07:25 CDT)
- Re: vmdmovie problem John Stone (Thu Aug 01 2002 - 20:00:51 CDT)
  - Re: vmdmovie problem Michael Murray (Thu Aug 01 2002 - 23:52:26 CDT)
    - Re: vmdmovie problem John Stone (Thu Aug 01 2002 - 23:53:24 CDT)
- Re: vmdmovie problem John Stone (Fri Aug 09 2002 - 17:00:08 CDT)
delete bonds in TIP3P Pascal Bonnet (Wed Jul 31 2002 - 06:52:07 CDT)
- Re: delete bonds in TIP3P John Stone (Wed Jul 31 2002 - 08:12:28 CDT)
Re: white background John Stone (Mon Jul 29 2002 - 11:01:12 CDT)
charmm vs amber Tommy Wang (Mon Jul 29 2002 - 07:01:07 CDT)
delete bonds in TIP3P water model Pascal Bonnet (Sat Jul 27 2002 - 05:51:49 CDT)
More Linux woes Cesar Delgado (Fri Jul 26 2002 - 16:08:10 CDT)
- Re: More Linux woes John Stone (Mon Jul 29 2002 - 13:42:58 CDT)
Linux compile error Cesar Delgado (Fri Jul 26 2002 - 15:47:34 CDT)
- Re: Linux compile error John Stone (Mon Jul 29 2002 - 13:46:08 CDT)
Problem with VMD on linux with Xig solved Russell Poyner (Wed Jul 24 2002 - 13:18:43 CDT)
problem connecting namd/vmd using charmrun/charmd Will Sheffler (Thu Jul 25 2002 - 13:19:23 CDT)
- Re: problem connecting namd/vmd using charmrun/charmd Will Sheffler (Thu Jul 25 2002 - 13:58:39 CDT)
2D projection Stéphane Teletchéa (Thu Jul 25 2002 - 08:12:15 CDT)
- Re: 2D projection John Stone (Fri Jul 26 2002 - 09:40:38 CDT)
  - Re: 2D projection Paul Grayson (Fri Jul 26 2002 - 10:11:58 CDT)
No sequence tool for DNA Stéphane Teletchéa (Mon Jul 22 2002 - 04:53:57 CDT)
- Re: No sequence tool for DNA John Stone (Tue Jul 23 2002 - 22:01:06 CDT)
bonds in graphical representation Marcela Madrid (Sat Jul 20 2002 - 15:20:08 CDT)
- Re: bonds in graphical representation John Stone (Tue Jul 23 2002 - 22:10:19 CDT)
  - conect2psf Andrew Dalke (Tue Jul 23 2002 - 23:35:06 CDT)
    - Re: conect2psf Eugen Leitl (Wed Jul 24 2002 - 04:14:53 CDT)
    - Re: conect2psf Andrew Dalke (Wed Jul 24 2002 - 04:51:04 CDT)
tracker coordinate calibration Will Sheffler (Fri Jul 19 2002 - 23:43:53 CDT)
- Re: tracker coordinate calibration John Stone (Sat Jul 20 2002 - 00:58:51 CDT)
Linux/Intel configuration for processing large trajectory file Liu, Zhanwu (Fri Jul 19 2002 - 17:18:10 CDT)
- Re: Linux/Intel configuration for processing large trajectory file Johannes von Langen (Mon Jul 22 2002 - 05:26:19 CDT)
[gcarter@circular.dna.caltech.edu: Re: Stereoglasses Linux] John Stone (Fri Jul 19 2002 - 13:37:11 CDT)
VMD 1.8 alpha 21 available for testing! John Stone (Thu Jul 18 2002 - 19:49:09 CDT)
Re: Windows vs. Linux John Stone (Wed Jul 17 2002 - 09:43:32 CDT)
icon in LABEL Pascal Bonnet (Wed Jul 17 2002 - 08:17:58 CDT)
- Re: icon in LABEL John Stone (Wed Jul 17 2002 - 10:10:03 CDT)
problem reading AMBER7 parm file Jeff Ames (Wed Jul 17 2002 - 01:51:49 CDT)
- Re: problem reading AMBER7 parm file John Stone (Wed Jul 17 2002 - 09:55:15 CDT)
- Re: problem reading AMBER7 parm file John Stone (Wed Jul 17 2002 - 10:23:08 CDT)
vmd python availability on other platforms jen ramus (Tue Jul 16 2002 - 22:31:07 CDT)
- Re: vmd python availability on other platforms John Stone (Wed Jul 17 2002 - 15:13:46 CDT)
Re: plugin problems John Stone (Tue Jul 16 2002 - 14:45:39 CDT)
vmd on mac 9.1 eric hu (Tue Jul 16 2002 - 13:39:14 CDT)
- Re: vmd on mac 9.1 John Stone (Tue Jul 16 2002 - 14:05:06 CDT)
  - Re: vmd on mac 9.1 eric hu (Wed Jul 17 2002 - 11:00:35 CDT)
- Re: vmd on mac 9.1 MengJuei Hsieh (Tue Jul 16 2002 - 15:56:54 CDT)
Not able to read a restart file from AMBER Stéphane Teletchéa (Mon Jul 15 2002 - 06:17:26 CDT)
- Re: Not able to read a restart file from AMBER MengJuei Hsieh (Mon Jul 15 2002 - 15:48:53 CDT)
VMD and Trackers Brendan O'Malley (Sun Jul 14 2002 - 19:22:45 CDT)
- Re: VMD and Trackers John Stone (Tue Jul 16 2002 - 14:39:12 CDT)
- Re: VMD and Trackers John Stone (Tue Jul 16 2002 - 15:04:35 CDT)
Adding labels, etc. Sanjeev B.S. (Sun Jul 14 2002 - 05:40:26 CDT)
- Re: Adding labels, etc. Justin Gullingsrud (Sun Jul 14 2002 - 12:25:20 CDT)
New VMD 1.8 alpha 20 MacOS X native OpenGL test version... John Stone (Sat Jul 13 2002 - 22:39:49 CDT)
VMD / Eye3D stereo works on Mac G4... John Stone (Fri Jul 12 2002 - 13:18:21 CDT)
VMD stereo with Radeon 8500 and crystal eyes on Xig Xserver Dr. Dan White (Fri Jul 12 2002 - 08:10:32 CDT)
Problem installing on linux Russell Poyner (Thu Jul 11 2002 - 16:16:18 CDT)
- Re: Problem installing on linux John Stone (Fri Jul 12 2002 - 11:38:09 CDT)
  - Re: Problem installing on linux Russell Poyner (Fri Jul 12 2002 - 12:43:03 CDT)
    - Re: Problem installing on linux John Stone (Fri Jul 12 2002 - 14:24:12 CDT)
Compressed files Stéphane Teletchéa (Thu Jul 11 2002 - 03:17:41 CDT)
- Re: Compressed files John Stone (Thu Jul 11 2002 - 10:26:13 CDT)
residue rotation within single pdb file B. Bennion (Sun Jul 07 2002 - 02:27:32 CDT)
- Re: residue rotation within single pdb file Justin Gullingsrud (Sun Jul 07 2002 - 11:21:13 CDT)
MacOSX bundle Chris Upton (Sat Jul 06 2002 - 00:16:13 CDT)
- Re: MacOSX bundle John Stone (Sat Jul 06 2002 - 18:08:10 CDT)
JMV Molecular Viewer Support within BioCoRE Robert Brunner (Wed Jul 03 2002 - 16:19:02 CDT)
MacOS X VMD 1.8 alpha 16 "bundle" test version... John Stone (Wed Jul 03 2002 - 14:47:59 CDT)
- Re: MacOS X VMD 1.8 alpha 16 "bundle" test version... MengJuei Hsieh (Wed Jul 03 2002 - 17:22:36 CDT)
- Re: MacOS X VMD 1.8 alpha 16 "bundle" test version... Holger Frauenrath (Thu Jul 04 2002 - 11:11:11 CDT)
  - Re: MacOS X VMD 1.8 alpha 16 "bundle" test version... John Stone (Tue Jul 09 2002 - 14:05:23 CDT)
problem with bitmap rendering sjcav_at_aros.net (Wed Jul 03 2002 - 05:35:56 CDT)
- Re: problem with bitmap rendering John Stone (Wed Jul 03 2002 - 09:24:14 CDT)
resolution for previous message sjcav_at_aros.net (Wed Jul 03 2002 - 05:30:00 CDT)
VMD 1.8 alpha 16 MacOSX depends on xterm MengJuei Hsieh (Mon Jul 01 2002 - 14:34:29 CDT)
- Re: VMD 1.8 alpha 16 MacOSX depends on xterm John Stone (Mon Jul 01 2002 - 14:36:44 CDT)
- Re: VMD 1.8 alpha 16 MacOSX depends on xterm John Stone (Mon Jul 01 2002 - 21:55:40 CDT)
Issue with wildcat 3 cards Will Sheffler (Mon Jul 01 2002 - 14:13:09 CDT)
- Re: Issue with wildcat 3 cards John Stone (Mon Jul 01 2002 - 14:34:08 CDT)
  - RE: Issue with wildcat 3 cards Mads Norregaard-Madsen (Mon Jul 01 2002 - 18:37:15 CDT)
Q: Compiling VMD on IRIX 6.5 ran friedman (Mon Jul 01 2002 - 09:07:30 CDT)
- Re: Q: Compiling VMD on IRIX 6.5 John Stone (Mon Jul 01 2002 - 09:27:10 CDT)
follow-up to previous message sjcav_at_aros.net (Sat Jun 29 2002 - 03:56:13 CDT)
VMD not working anymore sjcav_at_aros.net (Sat Jun 29 2002 - 01:26:26 CDT)
Simple format for animation Mario Schubert (Fri Jun 28 2002 - 07:19:31 CDT)
- Re: Simple format for animation John Stone (Wed Jul 03 2002 - 19:45:33 CDT)
- Re: Simple format for animation John Stone (Wed Jul 17 2002 - 15:08:14 CDT)
Mac OSX version Chris Upton (Tue Jun 25 2002 - 12:18:47 CDT)
- Re: Mac OSX version John Stone (Tue Jun 25 2002 - 12:49:54 CDT)
RMSD (Re-send of James Cavenaugh's bounced mail) John Stone (Tue Jun 25 2002 - 10:50:33 CDT)
viewing insight trajectories with vmd Bjoern Windshuegel (Tue Jun 25 2002 - 01:29:15 CDT)
- Re: viewing insight trajectories with vmd John Stone (Tue Jun 25 2002 - 15:15:22 CDT)
Re: VMD 1.8 alpha 16, publically available ... Christian Simon (Mon Jun 24 2002 - 13:43:23 CDT)
MacOS native version resource attach info... John Stone (Mon Jun 24 2002 - 11:46:10 CDT)
- Re: MacOS native version resource attach info... tom keyes (Tue Jun 25 2002 - 10:44:22 CDT)
  - Re: MacOS native version resource attach info... John Stone (Tue Jun 25 2002 - 11:02:08 CDT)
vmd1.8a16 - no stereo on linux any more Johannes von Langen (Mon Jun 24 2002 - 06:47:02 CDT)
- Re: vmd1.8a16 - no stereo on linux any more John Stone (Mon Jun 24 2002 - 10:28:07 CDT)
- Re: vmd1.8a16 - no stereo on linux any more John Stone (Mon Jun 24 2002 - 11:35:41 CDT)
Unable to generate surface Sanjeev B.S. (Sun Jun 23 2002 - 21:40:32 CDT)
- Re: Unable to generate surface John Stone (Mon Jun 24 2002 - 11:33:52 CDT)
animation from files with different numbers of atoms Jennifer Young (Sat Jun 22 2002 - 16:21:01 CDT)
- Re: animation from files with different numbers of atoms Justin Gullingsrud (Sat Jun 22 2002 - 17:07:56 CDT)
animations with molecular surfaces Will Sheffler (Sat Jun 22 2002 - 02:32:12 CDT)
- Re: animations with molecular surfaces John Stone (Mon Jun 24 2002 - 14:17:12 CDT)
VMD 1.8 alpha 16, publically available for testing.... John Stone (Fri Jun 21 2002 - 16:14:14 CDT)
- image jumps Y U Sasidhar (Sat Jun 22 2002 - 00:03:46 CDT)
  - Re: image jumps John Stone (Tue Jun 25 2002 - 15:00:36 CDT)
No 'Primary File Type' in Load menu (v1.8a10 on MacOSX) Christian Simon (Thu Jun 20 2002 - 08:01:20 CDT)
- Re: No 'Primary File Type' in Load menu (v1.8a10 on MacOSX) John Stone (Thu Jun 20 2002 - 10:12:40 CDT)
Re: moving objects John Stone (Mon Jun 17 2002 - 13:40:21 CDT)
Tracking devices and VMD Brendan O'Malley (Mon Jun 17 2002 - 04:15:07 CDT)
- Re: Tracking devices and VMD John Stone (Mon Jun 17 2002 - 11:38:55 CDT)
vdw radii Sanjeev B.S. (Thu Jun 13 2002 - 04:51:42 CDT)
vmd-1.8a10; psfgen; AMBER-trajectories; strange bondlengths Johannes von Langen (Tue Jun 11 2002 - 03:17:31 CDT)
- Re: vmd-1.8a10; psfgen; AMBER-trajectories; strange bondlengths John Stone (Wed Jun 12 2002 - 01:18:34 CDT)
MANDRAKE and VMD Dmitry Kovalsky (Sun Jun 09 2002 - 03:35:45 CDT)
TK script problem Wuwei Liang (Fri Jun 07 2002 - 12:11:13 CDT)
- Re: TK script problem Justin Gullingsrud (Fri Jun 07 2002 - 09:32:02 CDT)
psfgen crashes VMD jrui_at_ci.uc.pt (Thu Jun 06 2002 - 19:55:28 CDT)
- vibration Nguyen Hoang Phuong (Fri Jun 07 2002 - 10:13:54 CDT)
  - Re: vibration John Stone (Fri Jun 07 2002 - 11:32:21 CDT)
- Re: psfgen crashes VMD John Stone (Fri Jun 07 2002 - 11:44:41 CDT)
Problem with instalation process jrui_at_ci.uc.pt (Thu Jun 06 2002 - 19:03:09 CDT)
- Re: Problem with instalation process John Stone (Fri Jun 07 2002 - 11:42:32 CDT)
- Re: Problem with instalation process John Stone (Fri Jun 07 2002 - 14:08:57 CDT)
- Re: Problem with instalation process John Stone (Fri Jun 07 2002 - 14:30:28 CDT)
Plugin testing B. Bennion (Thu Jun 06 2002 - 12:07:05 CDT)
Mandrake and VMD Dmitry Kovalsky (Thu Jun 06 2002 - 04:22:15 CDT)
- Re: Mandrake and VMD John Stone (Thu Jun 06 2002 - 09:55:07 CDT)
haptic interfaces Will Sheffler (Thu Jun 06 2002 - 00:11:34 CDT)
- Re: haptic interfaces John Stone (Thu Jun 06 2002 - 00:24:19 CDT)
  - Re: haptic interfaces && namd on clusters Will Sheffler (Thu Jun 06 2002 - 01:27:25 CDT)
    - Re: haptic interfaces && namd on clusters John Stone (Thu Jun 06 2002 - 01:41:32 CDT)
Mac Titanium video card Christian Simon (Wed Jun 05 2002 - 17:06:20 CDT)
- Re: Mac Titanium video card John Stone (Sat Jun 08 2002 - 23:45:47 CDT)
  - Re: Re: Mac Titanium video card Christian Simon (Mon Jun 10 2002 - 07:45:42 CDT)
Default parameters for image renderers Reinhard Klement (Wed Jun 05 2002 - 04:20:15 CDT)
- Re: Default parameters for image renderers John Stone (Sat Jun 08 2002 - 22:24:24 CDT)
problem with amber 6 restart files (parm and rst) Raik Grunberg (Tue Jun 04 2002 - 04:08:40 CDT)
- Re: problem with amber 6 restart files (parm and rst) Stéphane Teletchéa (Tue Jun 04 2002 - 06:39:20 CDT)
- Re: problem with amber 6 restart files (parm and rst) Johannes von Langen (Tue Jun 11 2002 - 03:57:29 CDT)
compilation problem using vmd1.8 alpha Tommy Wang (Thu May 30 2002 - 19:52:15 CDT)
- Re: compilation problem using vmd1.8 alpha John Stone (Thu May 30 2002 - 20:11:30 CDT)
MSD Storr, Mark (Wed May 29 2002 - 10:43:53 CDT)
- Re: MSD Paul Grayson (Wed May 29 2002 - 11:03:40 CDT)
- Re: MSD Hannes Loeffler (Thu May 30 2002 - 01:29:13 CDT)
fiiting Vlad Cojocaru (Mon May 27 2002 - 09:30:59 CDT)
- Re: fiiting Justin Gullingsrud (Mon May 27 2002 - 10:24:14 CDT)
- Re: fiiting Justin Gullingsrud (Mon May 27 2002 - 12:25:44 CDT)
VMD 1.8 alpha 10, publically available for testing.... John Stone (Fri May 24 2002 - 16:20:54 CDT)
Metal_Envornment Script Storr, Mark (Fri May 24 2002 - 11:38:00 CDT)
- Re: Metal_Envornment Script John Stone (Fri May 24 2002 - 12:02:42 CDT)
  - Re: Metal_Envornment Script John Stone (Fri May 24 2002 - 12:05:19 CDT)
- Re: Metal_Envornment Script John Stone (Fri May 24 2002 - 15:40:24 CDT)
Babel and Windows Storr, Mark (Tue May 21 2002 - 08:22:37 CDT)
atoms filter? Wuwei Liang (Thu May 16 2002 - 13:03:35 CDT)
- Re: atoms filter? John Stone (Thu May 16 2002 - 10:09:07 CDT)
Main window (button bars) does not start Akemi Yagi (Tue May 14 2002 - 10:02:18 CDT)
- Re: Main window (button bars) does not start John Stone (Tue May 14 2002 - 10:11:44 CDT)
Write DCD Storr, Mark (Tue May 14 2002 - 09:51:06 CDT)
- Re: Write DCD Justin Gullingsrud (Tue May 14 2002 - 10:03:16 CDT)
transparency tripp_at_fis.unam.mx (Fri May 10 2002 - 11:46:01 CDT)
- Re: transparency John Stone (Fri May 10 2002 - 12:57:52 CDT)
  - Re: transparency Todd J. Furlong (Mon May 13 2002 - 11:20:57 CDT)
compilation error Tommy Wang (Fri May 10 2002 - 07:52:24 CDT)
- Re: compilation error Todd J. Furlong (Fri May 10 2002 - 10:13:56 CDT)
- Re: compilation error John Stone (Fri May 10 2002 - 10:31:05 CDT)
VMD 1.7.1 Ross J. Toedte (Thu May 09 2002 - 13:57:02 CDT)
- Re: VMD 1.7.1 John Stone (Thu May 09 2002 - 14:28:43 CDT)
Animating Trajectories/NAMD Output files Storr, Mark (Tue May 07 2002 - 13:06:43 CDT)
- Re: Animating Trajectories/NAMD Output files Barry Isralewitz (Tue May 07 2002 - 22:15:21 CDT)
- Re: Animating Trajectories/NAMD Output files Barry Isralewitz (Wed May 08 2002 - 11:01:26 CDT)
- RE: Animating Trajectories/NAMD Output files Storr, Mark (Wed May 08 2002 - 11:16:23 CDT)
  - Re: Animating Trajectories/NAMD Output files Barry Isralewitz (Wed May 08 2002 - 11:37:05 CDT)
RDFs etc Storr, Mark (Mon May 06 2002 - 11:18:54 CDT)
Re: RDFs, TCFs etc. John Stone (Mon May 06 2002 - 10:15:14 CDT)
Regular Expression problem with $ jen ramus (Tue Apr 30 2002 - 20:24:52 CDT)
- Re: Regular Expression problem with $ Andrew Dalke (Tue Apr 30 2002 - 20:38:10 CDT)
Reading GOLD .sdf output files Todd J. Furlong (Tue Apr 30 2002 - 09:09:03 CDT)
About drawing bonds. Luca UvA (Wed Apr 24 2002 - 08:07:32 CDT)
- Re: About drawing bonds. John Stone (Wed Apr 24 2002 - 10:11:10 CDT)
color by resid Tran Trung Tran (Mon Apr 22 2002 - 23:31:52 CDT)
- Re: color by resid Don Havelberg (Tue Apr 23 2002 - 02:02:23 CDT)
  - RE: color by resid Tran Trung Tran (Tue Apr 23 2002 - 18:28:57 CDT)
    - Re: color by resid John Stone (Thu Apr 25 2002 - 14:02:30 CDT)
    - Animate data Nguyen Hoang Phuong (Fri Apr 26 2002 - 12:31:38 CDT)
Re: GnuPlot works! John Stone (Mon Apr 22 2002 - 17:09:31 CDT)
- Re: GnuPlot works! Joe Huang (Mon Apr 22 2002 - 18:10:45 CDT)
Graphics card & Accelerator Sanjeev B.S. (Fri Apr 19 2002 - 02:58:22 CDT)
- Re: Graphics card & Accelerator Stéphane Teletchéa (Fri Apr 19 2002 - 06:15:18 CDT)
How to plot the data created by VMD analysis script - difference_matrix? Joe Huang (Thu Apr 18 2002 - 14:22:40 CDT)
- Re: How to plot the data created by VMD analysis script - difference_matrix? John Stone (Mon Apr 22 2002 - 14:48:19 CDT)
  - Re: How to plot the data created by VMD analysis script - difference_matrix? Sanjeev B.S. (Mon Apr 22 2002 - 21:34:51 CDT)
pdb naming convention Adrian E. Roitberg (Wed Apr 17 2002 - 07:59:32 CDT)
- Re: pdb naming convention Justin Gullingsrud (Wed Apr 17 2002 - 10:26:39 CDT)
stl Patricia Soto (Wed Apr 17 2002 - 05:08:20 CDT)
- Re: stl John Stone (Wed Apr 17 2002 - 08:52:40 CDT)
about graphics accelaration Emanuel Vamvakopoulos (Fri Apr 12 2002 - 11:36:49 CDT)
- Re: about graphics accelaration John Stone (Fri Apr 12 2002 - 12:27:41 CDT)
  - Re: about graphics accelaration Stéphane Teletchéa (Mon Apr 15 2002 - 03:22:03 CDT)
  - Re: about graphics accelaration Stéphane Teletchéa (Wed May 15 2002 - 10:47:04 CDT)
    - Re: about graphics accelaration John Stone (Wed May 15 2002 - 11:21:56 CDT)
    - my solution to the freezing problem. Tommy Wang (Wed May 15 2002 - 20:32:30 CDT)
VMD 1.7.1 in CAVE? Todd J. Furlong (Fri Apr 12 2002 - 07:57:05 CDT)
- Re: VMD 1.7.1 in CAVE? John Stone (Fri Apr 12 2002 - 09:28:46 CDT)
Re: Linking with FLTK 1.1.0b12 John Stone (Tue Apr 09 2002 - 16:01:55 CDT)
- Re: Linking with FLTK 1.1.0b12 Justin Gullingsrud (Tue Apr 09 2002 - 16:43:48 CDT)
Which drawing method is used in the picture? Anna Aagaard (Tue Apr 09 2002 - 14:40:17 CDT)
- Re: Which drawing method is used in the picture? John Stone (Tue Apr 09 2002 - 15:01:03 CDT)
  - Re: Which drawing method is used in the picture? Alan Wilter Sousa da Silva (Wed Apr 10 2002 - 10:20:05 CDT)
- Re: Which drawing method is used in the picture? Andrew Dalke (Tue Apr 09 2002 - 15:04:19 CDT)
  - Re: Which drawing method is used in the picture? John Stone (Tue Apr 09 2002 - 15:50:12 CDT)
Animation Paul Hubbard (Tue Apr 09 2002 - 14:12:49 CDT)
- Re: Animation John Stone (Tue Apr 09 2002 - 14:24:36 CDT)
  - Re: Animation Justin Gullingsrud (Tue Apr 09 2002 - 14:36:36 CDT)
    - Re: Animation Paul Hubbard (Tue Apr 09 2002 - 15:09:40 CDT)
- RE: Animation John Stone (Wed Apr 10 2002 - 09:18:24 CDT)
Re: Electron Density Map Display John Stone (Tue Apr 09 2002 - 13:02:21 CDT)
Fixing CAVE Functionality Todd J. Furlong (Tue Apr 09 2002 - 10:27:49 CDT)
Geforce 3 DRI crashes Mikko Huhtala (Tue Apr 09 2002 - 08:37:11 CDT)
- Re: Geforce 3 DRI crashes John Stone (Tue Apr 09 2002 - 09:57:55 CDT)
  - Re: Geforce 3 DRI crashes Stéphane Teletchéa (Wed Apr 10 2002 - 04:10:21 CDT)
- Re: Geforce 3 DRI crashes John Stone (Tue Apr 09 2002 - 13:07:18 CDT)
Announce: new vmdmovie script available... John Stone (Mon Apr 08 2002 - 22:23:01 CDT)
draw text or title in pov Peter Varnai (Thu Apr 04 2002 - 10:04:03 CST)
- Re: draw text or title in pov John Stone (Thu Apr 04 2002 - 21:56:25 CST)
strange bond Nguyen Hoang Phuong (Wed Apr 03 2002 - 05:24:16 CST)
- Re: strange bond John Stone (Wed Apr 03 2002 - 09:48:14 CST)
  - Re: strange bond Nguyen Hoang Phuong (Wed Apr 03 2002 - 10:20:54 CST)
orthographic views and size Marc Baaden (Wed Apr 03 2002 - 03:43:28 CST)
- Re: orthographic views and size John Stone (Wed Apr 03 2002 - 09:53:30 CST)
picture/resid color Peter Varnai (Tue Apr 02 2002 - 11:11:36 CST)
- Re: picture/resid color John Stone (Tue Apr 02 2002 - 11:18:55 CST)
  - resid color Peter VARNAI (Wed Apr 03 2002 - 12:00:09 CST)
    - Re: resid color John Stone (Wed Apr 03 2002 - 12:40:29 CST)
Exceeded maximum number of bonds (8) Lu Yang (Sun Mar 31 2002 - 13:19:55 CST)
- Re: Exceeded maximum number of bonds (8) John Stone (Sun Mar 31 2002 - 16:38:11 CST)
Resolution of movie? Troy Wymore (Tue Mar 26 2002 - 17:02:43 CST)
- Re: Resolution of movie? John Stone (Tue Mar 26 2002 - 18:00:20 CST)
python create graphics molecule Don Havelberg (Tue Mar 26 2002 - 07:10:25 CST)
- Re: python create graphics molecule Justin Gullingsrud (Tue Mar 26 2002 - 10:15:03 CST)
  - Re: python create graphics molecule Don Havelberg (Tue Mar 26 2002 - 17:16:00 CST)
  - Re: python create graphics molecule Don Havelberg (Tue Mar 26 2002 - 17:19:02 CST)
single residue mutation Yunfeng Hu (Fri Mar 22 2002 - 14:36:54 CST)
RE: Help on script Liu, Zhanwu (Fri Mar 22 2002 - 14:16:53 CST)
- Re: Help on script Christian Simon (Mon Mar 25 2002 - 08:06:27 CST)
- RE: Help on script Liu, Zhanwu (Mon Mar 25 2002 - 11:09:49 CST)
drawing bonds with vmd/python interface Sonja M. Schwarzl (Fri Mar 22 2002 - 09:36:46 CST)
- Re: drawing bonds with vmd/python interface Justin Gullingsrud (Fri Mar 22 2002 - 11:55:45 CST)
Re: Help on script John Stone (Thu Mar 21 2002 - 22:55:31 CST)
record changed {x y z} Yufang Wang (Wed Mar 20 2002 - 10:50:02 CST)
- Re: record changed {x y z} Paul Grayson (Wed Mar 20 2002 - 13:31:50 CST)
graph button on label form Yufang Wang (Sun Mar 17 2002 - 15:03:41 CST)
- Re: graph button on label form John Stone (Mon Mar 18 2002 - 15:23:35 CST)
smooth movie Sanjeev B.S. (Sat Mar 16 2002 - 11:24:39 CST)
- Re: smooth movie John Stone (Sat Mar 16 2002 - 11:57:54 CST)
Re: Best hardware for 3d. John Stone (Fri Mar 15 2002 - 10:06:09 CST)
Loading trajectory frames - bug ? Tcl-equivalent ? Marc Baaden (Fri Mar 15 2002 - 06:27:54 CST)
- Re: Loading trajectory frames - bug ? Tcl-equivalent ? John Stone (Fri Mar 15 2002 - 20:01:41 CST)
how vmd calculate dihedral angle Yufang Wang (Fri Mar 15 2002 - 00:07:15 CST)
- Re: how vmd calculate dihedral angle John Stone (Fri Mar 15 2002 - 10:18:23 CST)
boolean operators in graphics Sanjeev B.S. (Thu Mar 14 2002 - 22:11:11 CST)
- Re: boolean operators in graphics Andrew Dalke (Thu Mar 14 2002 - 22:32:38 CST)
- Re: boolean operators in graphics John Stone (Thu Mar 14 2002 - 22:39:09 CST)
New version of VMD movie script/plugin available John Stone (Wed Mar 13 2002 - 00:04:10 CST)
- Re: New version of VMD movie script/plugin available Alan Wilter Sousa da Silva (Wed Mar 13 2002 - 07:58:33 CST)
  - Re: New version of VMD movie script/plugin available John Stone (Wed Mar 13 2002 - 09:34:12 CST)
- Re: New version of VMD movie script/plugin available Adrian E. Roitberg (Wed Mar 13 2002 - 07:22:32 CST)
  - Re: New version of VMD movie script/plugin available John Stone (Wed Mar 13 2002 - 10:34:28 CST)
- Re: New version of VMD movie script/plugin available John Stone (Wed Mar 13 2002 - 12:21:54 CST)
atom coloring Dominik Horinek (Mon Mar 11 2002 - 17:59:30 CST)
- Re: atom coloring Paul Grayson (Tue Mar 12 2002 - 14:33:29 CST)
  - RE: atom coloring Laurence F. Wood (Tue Mar 12 2002 - 16:39:37 CST)
  - Molscript Alan Wilter Sousa da Silva (Wed Mar 13 2002 - 07:32:50 CST)
    - Re: Molscript John Stone (Wed Mar 13 2002 - 09:31:36 CST)
NAMD 2.4 Released Jim Phillips (Mon Mar 11 2002 - 14:24:39 CST)
Can any of you help me out in building VMD pls Kiran, Kotresh (Fri Mar 08 2002 - 05:48:35 CST)
- Re: Can any of you help me out in building VMD pls John Stone (Fri Mar 08 2002 - 09:47:04 CST)
- Re: Can any of you help me out in building VMD pls John Stone (Mon Mar 11 2002 - 00:11:44 CST)
create new colors Fei Xu (Thu Mar 07 2002 - 10:49:25 CST)
- Re: create new colors Justin Gullingsrud (Fri Mar 08 2002 - 11:39:58 CST)
selection and coloring Fei Xu (Mon Mar 04 2002 - 10:06:35 CST)
- Re: selection and coloring John Stone (Tue Mar 05 2002 - 10:35:48 CST)
how to color one residue with two or three different colors? Margaret Cheung (Sat Mar 02 2002 - 20:03:45 CST)
- Re: how to color one residue with two or three different colors? John Stone (Mon Mar 04 2002 - 15:48:37 CST)
fwd (Re: coloring method) John Stone (Fri Mar 01 2002 - 15:01:54 CST)
coloring method Fei Xu (Thu Feb 28 2002 - 15:44:11 CST)
Removing perspective projection at startup Stéphane Teletchéa (Thu Feb 28 2002 - 07:11:37 CST)
- Re: Removing perspective projection at startup John Stone (Thu Feb 28 2002 - 09:41:57 CST)
  - Re: Removing perspective projection at startup Stéphane Teletchéa (Fri Mar 01 2002 - 03:12:43 CST)
- Re: Removing perspective projection at startup Alan Wilter Sousa da Silva (Thu Feb 28 2002 - 12:27:47 CST)
  - Re: Removing perspective projection at startup Justin Gullingsrud (Thu Feb 28 2002 - 11:19:35 CST)
Access to Python libraries from Mandrake8.1 jen ramus (Wed Feb 27 2002 - 19:08:08 CST)
- Re: Access to Python libraries from Mandrake8.1 John Stone (Thu Feb 28 2002 - 09:59:42 CST)
  - Re: Access to Python libraries from Mandrake8.1 Justin Gullingsrud (Sun Mar 03 2002 - 03:16:34 CST)
Upcoming NAMD Workshop Jim Phillips (Tue Feb 26 2002 - 15:24:32 CST)
Plotting elect. pot. surface Alan Wilter Sousa da Silva (Mon Feb 25 2002 - 12:15:52 CST)
- Re: Plotting elect. pot. surface John Stone (Mon Feb 25 2002 - 11:27:53 CST)
  - Re: Plotting elect. pot. surface Alan Wilter Sousa da Silva (Mon Feb 25 2002 - 14:40:57 CST)
- Re: Plotting elect. pot. surface Alan Wilter Sousa da Silva (Wed Mar 13 2002 - 08:05:14 CST)
VMD: EDM and Gaussian "Cube" reader scripts available John Stone (Fri Feb 22 2002 - 15:25:18 CST)
NAMD 2.4b2 Release Announcement Jim Phillips (Fri Feb 22 2002 - 12:56:35 CST)
AtomSel and Graphics Fei Xu (Fri Feb 22 2002 - 11:26:51 CST)
- Re: AtomSel and Graphics John Stone (Fri Feb 22 2002 - 16:07:07 CST)
- Re: AtomSel and Graphics Justin Gullingsrud (Sat Feb 23 2002 - 16:53:21 CST)
Using Python Sam Ansari (Fri Feb 22 2002 - 07:59:02 CST)
- Re: Using Python John Stone (Fri Feb 22 2002 - 12:59:19 CST)
Loading new molecules into VMD from an application jen ramus (Wed Feb 20 2002 - 17:25:44 CST)
- Re: Loading new molecules into VMD from an application Paul Grayson (Wed Feb 20 2002 - 19:59:54 CST)
- Re: Loading new molecules into VMD from an application John Stone (Wed Feb 20 2002 - 20:48:56 CST)
Re: animated colors, trajectories, etc.. John Stone (Tue Feb 19 2002 - 18:41:02 CST)
VMD CVS and build procedure changes... John Stone (Tue Feb 19 2002 - 18:15:06 CST)
python script of atomsel expression Fei Xu (Tue Feb 19 2002 - 09:42:25 CST)
- Re: python script of atomsel expression Justin Gullingsrud (Tue Feb 19 2002 - 10:47:58 CST)
Radial distribution function script (fwd) John Stone (Thu Feb 07 2002 - 21:29:50 CST)
Announce: VMD 1.7.2 (Windows-only GUI update) is available John Stone (Wed Feb 06 2002 - 19:07:55 CST)
Python: radius always 1 for cylinder and cones Fredrik Sjunnesson (Wed Feb 06 2002 - 16:04:13 CST)
- Re: Python: radius always 1 for cylinder and cones Justin Gullingsrud (Wed Feb 06 2002 - 17:03:55 CST)
NVidia GeForce issues on PCs (article URL) John Stone (Tue Feb 05 2002 - 14:25:30 CST)
Nothing happens with Window's install Keith Oxenrider (Tue Feb 05 2002 - 11:25:23 CST)
- Re: Nothing happens with Window's install John Stone (Tue Feb 05 2002 - 11:33:43 CST)
- Re: Nothing happens with Window's install John Stone (Tue Feb 05 2002 - 12:50:45 CST)
van der Waals volume Markus Laub (Mon Feb 04 2002 - 12:49:02 CST)
- Re: van der Waals volume John Stone (Tue Feb 05 2002 - 19:29:42 CST)
VMD/Eye3d/Linux/Nvidia question Troy Wymore (Fri Feb 01 2002 - 15:58:56 CST)
- Re: VMD/Eye3d/Linux/Nvidia question John Stone (Fri Feb 01 2002 - 16:23:25 CST)
Main window off top of screen Keith Oxenrider (Fri Feb 01 2002 - 10:57:58 CST)
- Re: Main window off top of screen John Stone (Fri Feb 01 2002 - 11:02:17 CST)
python disabled Alexey Kozlenkov (Wed Jan 30 2002 - 14:53:54 CST)
- Re: python disabled Justin Gullingsrud (Wed Jan 30 2002 - 14:51:03 CST)
NAMD 2.4b1 released Jim Phillips (Mon Jan 28 2002 - 16:44:30 CST)
bond length Vlad Cojocaru (Mon Jan 28 2002 - 05:26:27 CST)
- Re: bond length Justin Gullingsrud (Mon Jan 28 2002 - 11:32:36 CST)
Drawing electron density surfaces (from cube files) Francesco Gervasio (Fri Jan 25 2002 - 07:01:41 CST)
- Re: Drawing electron density surfaces (from cube files) John Stone (Thu Jan 31 2002 - 15:36:29 CST)
Re: seeing ions John Stone (Thu Jan 24 2002 - 13:23:46 CST)
vmdmovie Stéphane Teletchéa (Thu Jan 24 2002 - 11:47:23 CST)
- Re: vmdmovie John Stone (Thu Jan 24 2002 - 12:41:36 CST)
Volumetric Data Formats for VMD Reinhard Klement (Thu Jan 24 2002 - 09:02:33 CST)
- Re: Volumetric Data Formats for VMD John Stone (Thu Jan 24 2002 - 09:51:44 CST)
display panel only showed 1/4 of its area on the screen. Margaret Cheung (Sun Jan 20 2002 - 12:45:26 CST)
- Re: display panel only showed 1/4 of its area on the screen. John Stone (Sun Jan 20 2002 - 13:25:32 CST)
  - Re: display panel only showed 1/4 of its area on the screen. Margaret Cheung (Mon Jan 21 2002 - 01:40:58 CST)
- Re: display panel only showed 1/4 of its area on the screen. Jim Phillips (Sun Jan 20 2002 - 13:59:26 CST)
Stereo in linux/oxygen gvx1/xig driver Boaz Shaanan (Sat Jan 19 2002 - 06:35:50 CST)
- Re: Stereo in linux/oxygen gvx1/xig driver John Stone (Wed Jan 23 2002 - 19:49:00 CST)
  - Re: Stereo in linux/oxygen gvx1/xig driver Boaz Shaanan (Thu Jan 24 2002 - 03:30:25 CST)
- Re: Stereo in linux/oxygen gvx1/xig driver John Stone (Thu Jan 24 2002 - 12:53:41 CST)
Re: up arrow for previous commands John Stone (Fri Jan 18 2002 - 11:03:39 CST)
- Re: up arrow for previous commands (with the command attached) Paul Grayson (Fri Jan 18 2002 - 13:42:54 CST)
  - Re: up arrow for previous commands (with the command attached) Justin Gullingsrud (Sat Jan 19 2002 - 01:46:17 CST)
cavetracker Derek R. Ploor (Wed Jan 16 2002 - 15:00:31 CST)
- Re: cavetracker John Stone (Fri Jan 18 2002 - 01:32:48 CST)
Test release of VMD movie maker John Stone (Wed Jan 16 2002 - 11:38:14 CST)
- Re: Test release of VMD movie maker Margaret Cheung (Thu Mar 21 2002 - 22:34:58 CST)
  - Re: Test release of VMD movie maker John Stone (Thu Mar 21 2002 - 22:59:10 CST)
immersadesk Adrian E. Roitberg (Tue Apr 16 2002 - 09:06:25 CDT)
- Re: immersadesk John Stone (Fri Jan 18 2002 - 01:27:40 CST)
  - vmd-1.7.1 installation problems Wuwei Liang (Wed Jan 23 2002 - 12:41:52 CST)
    - Re: vmd-1.7.1 installation problems John Stone (Wed Jan 23 2002 - 09:47:04 CST)
2 questions Sanjeev B.S. (Mon Jan 07 2002 - 02:43:18 CST)
- Re: 2 questions Justin Gullingsrud (Wed Jan 09 2002 - 11:23:07 CST)
High-end PC graphics boards for VMD... John Stone (Fri Jan 04 2002 - 17:23:23 CST)
OpenGL cards for workstations Justin Gullingsrud (Fri Jan 04 2002 - 17:05:36 CST)
Announce: VMD 1.7.1 released! John Stone (Sun Dec 23 2001 - 22:53:26 CST)
Pictures Sanjeev B.S. (Fri Dec 21 2001 - 10:55:12 CST)
- Re: Pictures John Stone (Fri Dec 21 2001 - 11:08:48 CST)
3D visualization Stephen Koch (Thu Dec 20 2001 - 13:39:17 CST)
- Re: 3D visualization John Stone (Thu Dec 20 2001 - 14:09:12 CST)
  - Re: 3D visualization John Stone (Thu Dec 20 2001 - 14:16:33 CST)
rotating two superposed molecules Marcela Madrid (Sun Dec 16 2001 - 14:44:44 CST)
- Re: rotating two superposed molecules Justin Gullingsrud (Sun Dec 16 2001 - 16:36:58 CST)
NAMD problem (ReceiveDatagram: recv: Resource temporarily unavailable:) Reuter Nathalie (Wed Dec 12 2001 - 11:20:53 CST)
secondary structure Nikolai Smolin (Tue Dec 11 2001 - 07:45:20 CST)
- Re: secondary structure Barry Isralewitz (Tue Dec 11 2001 - 11:46:33 CST)
Announce: Struc. Bio. Software DB updates John Stone (Thu Dec 06 2001 - 11:21:57 CST)
Announce: VMD 1.7.1b1 test version is available... John Stone (Wed Dec 05 2001 - 21:14:37 CST)
- Re: Announce: VMD 1.7.1b1 test version is available... John Stone (Sat Dec 22 2001 - 21:56:00 CST)
'wrap' any kind of solvent Reuter Nathalie (Mon Dec 03 2001 - 03:20:45 CST)
- Re: 'wrap' any kind of solvent Jim Phillips (Mon Dec 03 2001 - 11:14:50 CST)
(no subject) César Filipe Barbosa Ribeiro (Sun Dec 02 2001 - 13:50:44 CST)
- Re: your mail John Stone (Tue Dec 04 2001 - 01:55:14 CST)
save config & RMSD not functioning nepenthes_at_vplaces.net (Thu Nov 29 2001 - 01:28:10 CST)
- Re: save config & RMSD not functioning John Stone (Thu Nov 29 2001 - 11:26:24 CST)
- crystallographic symmetry tool Daniel Barsky (Wed Dec 05 2001 - 19:11:35 CST)
opengl libraries B. Bennion (Mon Nov 26 2001 - 12:23:49 CST)
- Re: opengl libraries John Stone (Mon Nov 26 2001 - 12:32:53 CST)
  - Re: opengl libraries John Stone (Tue Nov 27 2001 - 15:04:55 CST)
compiling problems B. Bennion (Mon Nov 26 2001 - 11:35:50 CST)
- Re: compiling problems Justin Gullingsrud (Mon Nov 26 2001 - 13:24:55 CST)
VMD Spaceball and Magellan/SpaceMouse support for Windows... John Stone (Tue Nov 20 2001 - 15:02:06 CST)
Waiting for files to load in VMD Justin Gullingsrud (Fri Nov 09 2001 - 11:14:28 CST)
Re: making a movie of trajectory file animation Barry Isralewitz (Thu Nov 08 2001 - 15:51:55 CST)
more animating trajectories tom keyes (Wed Oct 31 2001 - 17:24:04 CST)
- Re: more animating trajectories John Stone (Thu Nov 01 2001 - 13:13:47 CST)
- Re: more animating trajectories tom keyes (Sun Nov 04 2001 - 09:02:35 CST)
  - Re: more animating trajectories John Stone (Sun Nov 04 2001 - 11:02:59 CST)
Announce: JMV version 0.7 is available! John Stone (Tue Oct 30 2001 - 16:15:33 CST)
- Re: Announce: JMV version 0.7 is available! John Stone (Fri Nov 02 2001 - 15:30:28 CST)
Making UIobjects B. Bennion (Thu Oct 25 2001 - 11:13:27 CDT)
- Re: Making UIobjects Justin Gullingsrud (Thu Oct 25 2001 - 11:46:02 CDT)
VMD freezes KDE under Linux Redhat 7.1 Raik Grunberg (Wed Oct 24 2001 - 07:22:06 CDT)
- RE: VMD freezes KDE under Linux Redhat 7.1 Laurence Wood (Wed Oct 24 2001 - 15:25:30 CDT)
  - Re: VMD freezes KDE under Linux Redhat 7.1 Stephane (Thu Oct 25 2001 - 09:16:30 CDT)
Superimposing two frames Sanjeev B.S. (Mon Oct 22 2001 - 01:54:50 CDT)
- Re: Superimposing two frames John Stone (Mon Oct 22 2001 - 10:41:36 CDT)
  - Re: Superimposing two frames Sanjeev B.S. (Mon Oct 22 2001 - 13:05:20 CDT)
- Re: Superimposing two frames Andrew Dalke (Tue Oct 30 2001 - 16:12:03 CST)
more animation Tom Keyes (Sun Oct 07 2001 - 17:17:23 CDT)
movie under Windows Nikolai Smolin (Fri Oct 05 2001 - 04:07:00 CDT)
- Re: movie under Windows John Stone (Fri Oct 05 2001 - 16:40:32 CDT)
SMP, coord transform, cpu usage Robert Matthew Fesinmeyer (Wed Oct 03 2001 - 17:42:01 CDT)
- Re: SMP, coord transform, cpu usage John Stone (Fri Oct 05 2001 - 14:40:30 CDT)
  - Re: SMP, coord transform, cpu usage R. M. Fesinmeyer (Sat Oct 06 2001 - 22:57:14 CDT)
    - Re: SMP, coord transform, cpu usage John Stone (Mon Oct 08 2001 - 10:11:18 CDT)
new user animation question tom keyes (Wed Oct 03 2001 - 16:37:49 CDT)
- Re: new user animation question B. Bennion (Thu Oct 04 2001 - 00:47:08 CDT)
- Re: new user animation question tom keyes (Thu Oct 04 2001 - 09:44:41 CDT)
  - Re: new user animation question B. Bennion (Thu Oct 04 2001 - 10:37:32 CDT)
  - Re: new user animation question John Stone (Fri Oct 05 2001 - 12:49:10 CDT)
    - Re: new user animation question Mauricio Carrillo Tripp (Tue Oct 09 2001 - 20:01:20 CDT)
- Re: new user animation question tom keyes (Thu Oct 04 2001 - 13:01:01 CDT)
VMD 1.7.1 pre-alpha, volume visualization, new stereo modes, etc. John Stone (Thu Aug 30 2001 - 23:29:56 CDT)
memory problems Dr. Paul Fons (Sat Aug 25 2001 - 19:54:48 CDT)
- Re: memory problems Justin Gullingsrud (Sat Aug 25 2001 - 21:51:25 CDT)
Programming problem (making bonds) Dr. Paul Fons (Sat Aug 25 2001 - 19:51:09 CDT)
diplaying multiple frames from DCD file diane lynch (Fri Aug 24 2001 - 15:11:20 CDT)
Making movies of trajectories Troy Wymore (Thu Aug 23 2001 - 13:14:34 CDT)
- Re: Making movies of trajectories John Stone (Thu Aug 30 2001 - 21:49:52 CDT)
problem with RMSD script Elizabeth K. White (Wed Aug 15 2001 - 15:03:11 CDT)
- Re: problem with RMSD script John Stone (Fri Aug 17 2001 - 14:00:10 CDT)
- Re: problem with RMSD script Justin Gullingsrud (Sun Aug 19 2001 - 18:48:02 CDT)
VMD 1.7 AIX and MacOS X distributions updated... John Stone (Wed Aug 08 2001 - 00:57:16 CDT)
Work around and problem with 1.7 for MacOS X Tyler Heibeck (Mon Aug 06 2001 - 15:17:57 CDT)
- Re: Work around and problem with 1.7 for MacOS X John Stone (Tue Aug 07 2001 - 21:35:41 CDT)
  - Re: Work around and problem with 1.7 for MacOS X Tyler Heibeck (Wed Aug 08 2001 - 11:30:20 CDT)
raster3d Yunfeng Hu (Thu Aug 02 2001 - 19:11:28 CDT)
- Re: raster3d John Stone (Thu Aug 02 2001 - 19:13:49 CDT)
NAMD 2.3 Release Announcement Jim Phillips (Thu Aug 02 2001 - 14:36:22 CDT)
Announce: VMD 1.7 Released!! John Stone (Thu Aug 02 2001 - 14:26:09 CDT)
fixing a molecule Mauricio Carrillo-Tripp (Mon Jul 30 2001 - 17:08:39 CDT)
- Re: fixing a molecule John Stone (Mon Jul 30 2001 - 20:40:28 CDT)
- Re: fixing a molecule Jeff Taylor (Tue Jul 31 2001 - 10:19:39 CDT)
- Re: fixing a molecule Barry Isralewitz (Wed Aug 01 2001 - 17:40:06 CDT)
Announce: VMD 1.7b2 is available! John Stone (Wed Jul 25 2001 - 10:12:11 CDT)
(fwd) Re: Dialboxes John Stone (Mon Jul 23 2001 - 10:00:55 CDT)
(fwd) vmd 1.7b1 sequence window disappeares John Stone (Mon Jul 23 2001 - 09:59:20 CDT)
3 simple questions from a newbie Alexey Kozlenkov (Mon Jul 23 2001 - 07:01:43 CDT)
- Re: 3 simple questions from a newbie Justin Gullingsrud (Mon Jul 23 2001 - 12:34:16 CDT)
Dialboxes Craig Morton (Sun Jul 22 2001 - 21:36:49 CDT)
- Re: Dialboxes John Stone (Sun Jul 22 2001 - 23:58:19 CDT)
(forwarded) cylinder drawing bug in 1.7b1 on NT? John Stone (Fri Jul 20 2001 - 10:20:06 CDT)
(forwarded) Modifying a Tcl script John Stone (Fri Jul 20 2001 - 10:17:04 CDT)
Announce: VMD 1.7b1 is available! John Stone (Tue Jul 10 2001 - 18:15:45 CDT)
Coloring mols by carbon only Niklas.Blomberg_at_astrazeneca.com (Mon Jul 09 2001 - 04:09:32 CDT)
- Re: Coloring mols by carbon only John Stone (Mon Jul 09 2001 - 10:53:28 CDT)
follow up Jeff Taylor (Mon Jun 04 2001 - 15:30:35 CDT)
- Re: follow up John Stone (Mon Jun 04 2001 - 15:47:29 CDT)
Can a script change the projection? Jeff Taylor (Mon Jun 04 2001 - 15:04:53 CDT)
Coloring Sections of Peptides B. Bennion (Wed May 16 2001 - 15:26:01 CDT)
- Re: Coloring Sections of Peptides Justin Gullingsrud (Wed May 16 2001 - 15:58:26 CDT)
hyperchem files Mauricio Carrillo Tripp (Thu May 10 2001 - 10:22:44 CDT)
- RE: hyperchem files Laurence F. Wood (Thu May 10 2001 - 14:11:24 CDT)
free sample!!! your1word_at_yahoo.com (Wed May 09 2001 - 07:18:35 CDT)
- Re: free sample!!! Ali Deyhim (Wed May 09 2001 - 10:35:13 CDT)
Surface slices Timm Essigke (Tue May 08 2001 - 07:44:28 CDT)
- Re: Surface slices John Stone (Fri May 11 2001 - 13:08:34 CDT)
VMD 1.6.1 IRIX6_64 startup script fix John Stone (Thu May 03 2001 - 11:16:05 CDT)
1.6.1 hotkey problem Ben Cornett (Wed May 02 2001 - 13:05:47 CDT)
- Re: 1.6.1 hotkey problem Justin Gullingsrud (Wed May 02 2001 - 15:18:40 CDT)
bond length definition Mauricio Carrillo Tripp (Tue Apr 24 2001 - 13:40:17 CDT)
- Re: bond length definition Aitor Gonzalez (Wed Apr 25 2001 - 04:41:32 CDT)
- Re: bond length definition John Stone (Wed Apr 25 2001 - 13:39:35 CDT)
Announce: VMD 1.6.1 Released! John Stone (Tue Apr 24 2001 - 10:03:39 CDT)
Sorry! Forgot to include the name of the molecule M. Arent (Sun Apr 22 2001 - 15:32:22 CDT)
- Re: Sorry! Forgot to include the name of the molecule Justin Gullingsrud (Sun Apr 22 2001 - 15:44:57 CDT)
  - Re: Sorry! Forgot to include the name of the molecule Sergei Izrailev (Mon Apr 23 2001 - 13:23:21 CDT)
Some newbie questions Arent, Michael (Fri Apr 20 2001 - 08:44:27 CDT)
- Re: Some newbie questions B. Bennion (Fri Apr 20 2001 - 10:40:20 CDT)
- Re: Some newbie questions John Stone (Sun Apr 22 2001 - 16:17:35 CDT)
TIS SARL promotions AVRIL N°1 TIS SARL (Fri Apr 13 2001 - 01:09:39 CDT)
need help - hardware stereo on a Windows PC Kristian Mueller (Thu Apr 12 2001 - 11:41:36 CDT)
- Re: need help - hardware stereo on a Windows PC John Stone (Fri Apr 13 2001 - 00:21:10 CDT)
Card for VMD with OpenGL & Linux Dominik Horinek (Mon Apr 09 2001 - 16:38:40 CDT)
- Re: Card for VMD with OpenGL & Linux John Stone (Mon Apr 09 2001 - 16:46:34 CDT)
  - Re: Card for VMD with OpenGL & Linux Dominik Horinek (Mon Apr 09 2001 - 17:09:45 CDT)
    - Re: Card for VMD with OpenGL & Linux John Stone (Wed Apr 11 2001 - 01:31:59 CDT)
New Release: Planetsweep Revolutionizes Internet Browsing cyclone_at_team.planetsweep.com (Mon Apr 09 2001 - 13:13:23 CDT)
animation and reps B. Bennion (Sat Mar 31 2001 - 01:40:43 CST)
- Re: animation and reps John Stone (Sat Mar 31 2001 - 11:02:23 CST)
  - Re: animation and reps Justin Gullingsrud (Wed Apr 04 2001 - 14:15:19 CDT)
    - Re: animation and reps Aitor Gonzalez (Mon Apr 09 2001 - 08:17:52 CDT)
ANN: BioCoRE now includes remote job submission biocore_at_ks.uiuc.edu (Fri Mar 30 2001 - 13:26:32 CST)
python vmd interface Aitor Gonzalez (Thu Mar 29 2001 - 08:57:32 CST)
- Re: python vmd interface Justin Gullingsrud (Thu Mar 29 2001 - 11:53:11 CST)
NVidia OpenGL HOWTO for Linux users... John Stone (Tue Mar 27 2001 - 01:01:37 CST)
Scripts to color amino acids based on given properties Y Xu (Wed Mar 21 2001 - 08:22:31 CST)
rasmol script Yunfeng Hu (Tue Mar 20 2001 - 19:36:24 CST)
- Re: rasmol script Andrew Dalke (Tue Mar 20 2001 - 22:45:49 CST)
group selection Yunfeng Hu (Mon Mar 19 2001 - 21:33:01 CST)
- Re: group selection Justin Gullingsrud (Thu Mar 22 2001 - 12:32:23 CST)
- Re: group selection Justin Gullingsrud (Fri Mar 23 2001 - 09:38:46 CST)
python loop Aitor Gonzalez (Fri Mar 16 2001 - 04:40:38 CST)
- Re: python loop Justin Gullingsrud (Fri Mar 16 2001 - 12:23:18 CST)
  - Re: python loop Aitor Gonzalez (Fri Mar 16 2001 - 12:39:34 CST)
Announce: VMD 1.6.1a3 is available John Stone (Mon Mar 12 2001 - 17:46:34 CST)
switching off the location axes Aitor Gonzalez (Fri Mar 09 2001 - 02:48:53 CST)
- Re: switching off the location axes John Stone (Fri Mar 09 2001 - 02:51:46 CST)
  - Re: switching off the location axes Aitor Gonzalez (Fri Mar 09 2001 - 03:10:03 CST)
  - Re: switching off the location axes Jim Phillips (Fri Mar 09 2001 - 09:39:39 CST)
Molecule rotation B. Bennion (Thu Mar 08 2001 - 12:16:46 CST)
- Re: Molecule rotation Justin Gullingsrud (Thu Mar 08 2001 - 12:32:15 CST)
- Re: Molecule rotation Charles.Schwieters_at_nih.gov (Thu Mar 08 2001 - 12:54:04 CST)
caculate the RMSD of 10 DNA Kuen Phon Wu (Wed Mar 07 2001 - 22:50:24 CST)
- Re: caculate the RMSD of 10 DNA Justin Gullingsrud (Wed Mar 07 2001 - 23:16:30 CST)
Bug in VMD-1.6 (linux, GL) Timm Essigke (Mon Mar 05 2001 - 16:21:53 CST)
- Re: Bug in VMD-1.6 (linux, GL) John Stone (Fri Mar 09 2001 - 00:25:26 CST)
Announce: VMD 1.6.1a2 is available John Stone (Mon Mar 05 2001 - 15:17:19 CST)
How can I change the wireframe look Jeff Taylor (Thu Mar 01 2001 - 14:12:50 CST)
- Re: How can I change the wireframe look John Stone (Thu Mar 01 2001 - 14:21:30 CST)
NAMD 2.3b1 Release Jim Phillips (Fri Feb 23 2001 - 11:01:55 CST)
Announce: VMD Users Image Gallery John Stone (Thu Feb 22 2001 - 13:43:31 CST)
Stereoscopic rendering on Linux Timm Essigke (Wed Feb 21 2001 - 10:41:56 CST)
- Re: Stereoscopic rendering on Linux John Stone (Wed Feb 21 2001 - 11:00:57 CST)
TkCon, an alternative VMD console... John Stone (Mon Feb 19 2001 - 15:07:16 CST)
a question cojocaru vlad (Mon Feb 05 2001 - 10:24:40 CST)
- Re: a question John Stone (Tue Feb 06 2001 - 09:55:21 CST)
Re: vmd, linux & dri (fwd) Bob Milius (Fri Jan 12 2001 - 19:29:20 CST)
- Re: vmd, linux & dri (fwd) Bob Milius (Fri Jan 12 2001 - 19:39:34 CST)
  - Re: vmd, linux & dri (fwd) Justin Gullingsrud (Fri Jan 12 2001 - 20:57:12 CST)
vmd, linux & dri Robert Milius (Fri Jan 12 2001 - 16:41:52 CST)
- Re: vmd, linux & dri John Stone (Fri Jan 12 2001 - 17:44:29 CST)
- Re:vmd, linux & dri Angelo R. Rossi (Tue Feb 13 2001 - 08:20:42 CST)
  - Re: vmd, linux & dri John Stone (Tue Feb 13 2001 - 10:06:46 CST)
Announce: Structural Biology Software Database John Stone (Thu Jan 04 2001 - 14:04:34 CST)
Announce: ZoomSeq -- sequence browser for VMD Barry Isralewitz (Thu Dec 28 2000 - 14:54:20 CST)
Announce: VMD 1.6 Released John Stone (Fri Dec 22 2000 - 17:17:04 CST)
Q: MO visualisation Christoph Hagedorn (Thu Dec 14 2000 - 11:35:39 CST)
update sec. structure in animation, sscache Raik Gruenberg (Mon Dec 11 2000 - 10:40:13 CST)
VMD Python binaries available for testing Justin Gullingsrud (Fri Dec 08 2000 - 14:08:55 CST)
files Zachariah Sinkala (Fri Dec 08 2000 - 11:50:31 CST)
- Re: files John Stone (Fri Dec 08 2000 - 12:40:43 CST)
- Re: files Lars Burgdorf (Fri Dec 08 2000 - 13:57:33 CST)
making a movie with a serie of pdb's Aitor Gonzalez (Thu Dec 07 2000 - 06:51:07 CST)
- Re: making a movie with a serie of pdb's John Stone (Thu Dec 07 2000 - 09:51:36 CST)
  - Re: making a movie with a serie of pdb's Aitor Gonzalez (Fri Dec 08 2000 - 05:26:00 CST)
VMD + MSMS + WinNT ee_at_post.harvard.edu (Thu Nov 30 2000 - 15:27:31 CST)
- Re: VMD + MSMS + WinNT John Stone (Thu Nov 30 2000 - 21:20:53 CST)
Announce: MDTools update John Stone (Thu Nov 30 2000 - 14:51:44 CST)
VMD stereo (Win/SGI) and graphics accelerators... John Stone (Wed Nov 29 2000 - 11:29:57 CST)
Measuring cluster size Madhavan Poyyapakkam (Wed Nov 22 2000 - 20:46:59 CST)
Announcing MDSalon! Jim Phillips (Tue Nov 21 2000 - 15:15:21 CST)
Announce: VMD 1.6a4 is available John Stone (Tue Nov 21 2000 - 00:19:42 CST)
- VMD 1.6a4 core dumps. Kim Branson (Thu Nov 23 2000 - 19:35:00 CST)
  - Re: VMD 1.6a4 core dumps. John Stone (Thu Nov 23 2000 - 19:45:08 CST)
    - Re: VMD 1.6a4 core dumps. Kim Branson (Thu Nov 23 2000 - 21:45:20 CST)
rending softwares for win98 Eric Hu (Thu Nov 16 2000 - 17:26:20 CST)
- Re: rending softwares for win98 John Stone (Fri Nov 17 2000 - 01:42:17 CST)
Using VMD on Redhat 7.0 John Stone (Wed Nov 15 2000 - 11:29:07 CST)
2000 VMD Survey Report is up John Stone (Mon Nov 13 2000 - 18:08:44 CST)
vmd stereo Brendan O'Malley (Sun Oct 29 2000 - 19:27:16 CST)
- Re: vmd stereo John Stone (Mon Oct 30 2000 - 01:04:12 CST)
Re: CCL:program for viewing MD Barry Isralewitz (Mon Oct 23 2000 - 11:55:02 CDT)
Selection Deepak Singh (Tue Oct 17 2000 - 11:08:51 CDT)
- Re: Selection Sergei Izrailev (Tue Oct 17 2000 - 11:28:18 CDT)
  - Re: Selection Deepak Singh (Tue Oct 17 2000 - 11:31:12 CDT)
    - Re: Selection John Stone (Tue Oct 17 2000 - 11:42:30 CDT)
    - Re: Selection Deepak Singh (Tue Oct 17 2000 - 11:51:33 CDT)
VMD Script Library pages updated... John Stone (Fri Oct 13 2000 - 14:39:38 CDT)
Ca-dist script Troy Wymore (Thu Oct 12 2000 - 13:36:59 CDT)
- Re: Ca-dist script Justin Gullingsrud (Fri Oct 13 2000 - 13:29:23 CDT)
problem compiling on redhat 7.0 John Duff (Sat Oct 07 2000 - 00:57:48 CDT)
- Re: problem compiling on redhat 7.0 Justin Gullingsrud (Sat Oct 07 2000 - 11:03:30 CDT)
  - Re: problem compiling on redhat 7.0 John Duff (Sun Oct 08 2000 - 14:52:46 CDT)
- Re: problem compiling on redhat 7.0 John Stone (Sun Oct 08 2000 - 22:49:58 CDT)
Announce: VMD 1.6a3 is available John Stone (Fri Oct 06 2000 - 14:37:27 CDT)
MSMS 2.5.3 is available for VMD users!! John Stone (Fri Oct 06 2000 - 09:25:38 CDT)
Using VMD to edit dynamics output David Chalmers (Sun Oct 01 2000 - 22:47:14 CDT)
- Re: Using VMD to edit dynamics output Justin Gullingsrud (Mon Oct 02 2000 - 00:22:25 CDT)
  - Re: Using VMD to edit dynamics output Barry Isralewitz (Mon Oct 02 2000 - 01:07:39 CDT)
NAMD 2.2 Release Announcement Jim Phillips (Fri Sep 29 2000 - 18:32:22 CDT)
several questions, Bettler Emmanuel (Tue Sep 26 2000 - 07:01:11 CDT)
- Re: several questions, John Stone (Thu Oct 05 2000 - 16:43:57 CDT)
a few questions about VMD Eric Hu (Wed Sep 20 2000 - 17:49:07 CDT)
- Re: a few questions about VMD John Stone (Wed Sep 20 2000 - 19:55:26 CDT)
- Re: a few questions about VMD Eric Hu (Fri Sep 22 2000 - 16:31:06 CDT)
  - Re: a few questions about VMD John Stone (Fri Sep 22 2000 - 16:34:17 CDT)
Building VMD under Windows 2000 Laurence F. Wood (Sun Sep 17 2000 - 19:42:28 CDT)
- Re: Building VMD under Windows 2000 John Stone (Mon Sep 18 2000 - 09:53:51 CDT)
parallel rendering across clusters? John Duff (Fri Sep 15 2000 - 16:16:16 CDT)
- Re: parallel rendering across clusters? John Stone (Fri Sep 15 2000 - 18:18:53 CDT)
msms 2.5 and vmd? Robert Milius (Thu Sep 14 2000 - 13:09:41 CDT)
- Re: msms 2.5 and vmd? John Stone (Thu Sep 14 2000 - 13:25:48 CDT)
Announce: VMD 1.6a2 is available John Stone (Thu Sep 14 2000 - 02:38:08 CDT)
File Selector in VMD1.6a1 Surjit Dixit (Wed Sep 13 2000 - 12:03:45 CDT)
- Re: File Selector in VMD1.6a1 John Stone (Wed Sep 13 2000 - 23:15:21 CDT)
viewing CHARMM trajectory Surjit Dixit (Mon Sep 11 2000 - 13:54:16 CDT)
- Re: viewing CHARMM trajectory Ernesto Moreno (Tue Sep 12 2000 - 09:37:47 CDT)
  - Re: viewing CHARMM trajectory John Stone (Wed Sep 13 2000 - 22:33:09 CDT)
- Re: viewing CHARMM trajectory John Stone (Wed Sep 13 2000 - 22:30:44 CDT)
Inspired Internet Business Opportunity! jo333_4_at_lawrence-lca.co.uk (Wed Sep 06 2000 - 13:38:24 CDT)
NAMD 2.2b1 Release Announcement Jim Phillips (Tue Sep 05 2000 - 17:39:24 CDT)
removing unwanted residues B. Bennion (Thu Aug 31 2000 - 11:57:00 CDT)
- Re: removing unwanted residues Justin Gullingsrud (Thu Aug 31 2000 - 12:03:21 CDT)
hbond calculations B. Bennion (Tue Aug 29 2000 - 10:49:16 CDT)
- Re: hbond calculations Justin Gullingsrud (Tue Aug 29 2000 - 14:18:45 CDT)
animation spezia_at_caspur.it (Tue Aug 29 2000 - 09:26:07 CDT)
- Re: animation John Stone (Wed Aug 30 2000 - 11:06:03 CDT)
  - Re: animation B. Bennion (Wed Aug 30 2000 - 11:47:25 CDT)
- Re: animation Simon Hogg (Wed Aug 30 2000 - 19:13:17 CDT)
Announce: VMD 1.6a1 is available John Stone (Thu Aug 24 2000 - 18:43:53 CDT)
- Re: Announce: VMD 1.6a1 is available Kim Branson (Sun Aug 27 2000 - 23:13:24 CDT)
incorrect tube, trace and ribbon drawings Lars Burgdorf (Mon Aug 21 2000 - 08:15:42 CDT)
- Re: incorrect tube, trace and ribbon drawings Justin Gullingsrud (Mon Aug 21 2000 - 13:32:52 CDT)
vmd on redhat6.2 and elsa gladiac Kim Branson (Tue Aug 15 2000 - 21:32:06 CDT)
- Re: vmd on redhat6.2 and elsa gladiac John Stone (Tue Aug 15 2000 - 22:11:05 CDT)
Bond information Timm Essigke (Fri Aug 04 2000 - 11:09:44 CDT)
- Re: Bond information Justin Gullingsrud (Fri Aug 04 2000 - 12:11:21 CDT)
RMSD calculation/fit doesn't work? Timm Essigke (Thu Aug 03 2000 - 13:17:18 CDT)
- Re: RMSD calculation/fit doesn't work? John Stone (Mon Aug 14 2000 - 18:58:34 CDT)
  - Re: RMSD calculation/fit doesn't work? Timm Essigke (Tue Aug 15 2000 - 07:47:51 CDT)
loading molecule from command line Mauricio Carrillo Tripp (Fri Jul 28 2000 - 14:42:56 CDT)
- Re: loading molecule from command line John Stone (Fri Jul 28 2000 - 15:11:02 CDT)
PDB file output B. Bennion (Tue Jul 25 2000 - 11:59:40 CDT)
- Re: PDB file output Sergei Izrailev (Tue Jul 25 2000 - 12:26:18 CDT)
  - Re: PDB file output Justin Gullingsrud (Tue Jul 25 2000 - 12:22:38 CDT)
Re: OpenGL, rendering spheres Tim Freeman (Thu Jul 20 2000 - 07:40:33 CDT)
Erro compiling vmd and or fltk mark knapp (Sun Jul 16 2000 - 13:37:04 CDT)
- Re: Erro compiling vmd and or fltk John Stone (Sun Jul 16 2000 - 14:12:10 CDT)
Spheres with OpenGL (was Re: linux graphics adapters?) Tim Freeman (Sun Jul 16 2000 - 12:05:02 CDT)
- Re: Spheres with OpenGL (was Re: linux graphics adapters?) John Stone (Sun Jul 16 2000 - 14:06:08 CDT)
- Re: Spheres with OpenGL (was Re: linux graphics adapters?) Andrew Dalke (Sun Jul 16 2000 - 20:54:55 CDT)
linux graphics adapters? Michael Galloway (Thu Jul 13 2000 - 06:57:25 CDT)
- Re: linux graphics adapters? Guy Coates (Thu Jul 13 2000 - 07:05:42 CDT)
  - nvidia woes. Kim Branson (Mon Sep 11 2000 - 21:10:28 CDT)
    - Re: nvidia woes. John Stone (Tue Sep 12 2000 - 11:04:08 CDT)
- Re: linux graphics adapters? John Stone (Thu Jul 13 2000 - 10:10:48 CDT)
  - Re: linux graphics adapters? Michael Galloway (Thu Jul 13 2000 - 12:36:28 CDT)
    - Re: linux graphics adapters? John Stone (Thu Jul 13 2000 - 12:50:58 CDT)
    - Re: linux graphics adapters? David E. Jones (Thu Jul 13 2000 - 14:43:06 CDT)
VMD 1.5 is available! John Stone (Wed Jun 28 2000 - 15:46:17 CDT)
DCD command-line options Timm Essigke (Tue Jun 27 2000 - 11:55:16 CDT)
- Re: DCD command-line options John Stone (Wed Jun 28 2000 - 11:05:34 CDT)
VMD runs on the T3E! Justin Gullingsrud (Sat Jun 24 2000 - 22:37:13 CDT)
Pretty Picture Paul Hubbard (Wed Jun 21 2000 - 16:15:59 CDT)
- Re: Pretty Picture erik vogan (Wed Jun 21 2000 - 22:24:30 CDT)
- Re: Pretty Picture Justin Gullingsrud (Fri Jun 23 2000 - 12:18:47 CDT)
stereo postscript rendering Charles_at_Schwieters.org (Tue Jun 20 2000 - 08:04:27 CDT)
vmd/namd connection in linux Kim Foster (Thu Jun 15 2000 - 15:58:08 CDT)
- Re: vmd/namd connection in linux Justin Gullingsrud (Thu Jun 15 2000 - 17:05:51 CDT)
VMD command line Windows98 Heiko Carstens (Thu Jun 15 2000 - 03:28:38 CDT)
- Re: VMD command line Windows98 John Stone (Sun Jun 18 2000 - 10:59:25 CDT)
VMD and GRASP Qu.II Paul Hubbard (Wed Jun 14 2000 - 15:16:23 CDT)
- Re: VMD and GRASP Qu.II Andrew Dalke (Thu Jun 15 2000 - 04:23:39 CDT)
  - Re: VMD and GRASP Qu.II Lothar Esser (Thu Jun 15 2000 - 09:09:52 CDT)
    - Re: VMD and GRASP Qu.II Paul Hubbard (Thu Jun 15 2000 - 10:08:22 CDT)
    - Re: VMD and GRASP Qu.II Lothar Esser (Thu Jun 15 2000 - 10:33:42 CDT)
  - Re: VMD and GRASP Qu.II Scott W. Sides (Thu Jun 15 2000 - 10:14:14 CDT)
Please unsubscribe me from VMD mailing list Scott W. Sides (Wed Jun 14 2000 - 11:39:20 CDT)
GRASP files Andrew Hall (Wed Jun 14 2000 - 10:17:27 CDT)
- Re: GRASP files Paul Hubbard (Wed Jun 14 2000 - 11:10:34 CDT)
- Re: GRASP files Justin Gullingsrud (Wed Jun 14 2000 - 14:37:01 CDT)
Problems with VMD 1.5b1 and XFree4/DRI OpenGL under linux Miguel Teodoro (Tue Jun 13 2000 - 18:39:48 CDT)
- Re: Problems with VMD 1.5b1 and XFree4/DRI OpenGL under linux John Stone (Mon Jun 26 2000 - 15:57:45 CDT)
- Re: Problems with VMD 1.5b1 and XFree4/DRI OpenGL under linux Miguel Teodoro (Thu Jun 29 2000 - 11:37:34 CDT)
  - Re: Problems with VMD 1.5b1 and XFree4/DRI OpenGL under linux John Stone (Thu Jun 29 2000 - 15:12:53 CDT)
(No Subject) prachi singh (Mon Jun 05 2000 - 08:26:51 CDT)
- Re: Prachi Singh's mail Barry Isralewitz (Mon Jun 05 2000 - 16:19:59 CDT)
- Re: Prachi Singh's mail Daniel Barsky (Mon Jun 05 2000 - 16:35:06 CDT)
File patterns Luis Gracia (Tue May 30 2000 - 09:58:38 CDT)
- Re: File patterns Justin Gullingsrud (Tue May 30 2000 - 14:00:15 CDT)
Re: POV failure 2nd try Keith Refson (Fri May 26 2000 - 13:09:04 CDT)
- Re: POV failure 2nd try John Stone (Fri May 26 2000 - 13:24:42 CDT)
POV render fails 2nd time Keith Refson (Fri May 26 2000 - 13:00:39 CDT)
- Re: POV render fails 2nd time David Norris (Fri May 26 2000 - 15:15:51 CDT)
More than 99999 atoms? Keith Refson (Fri May 26 2000 - 06:24:38 CDT)
- Re: More than 99999 atoms? David Norris (Fri May 26 2000 - 09:51:19 CDT)
- Re: More than 99999 atoms? Dr Nicolas Le Novere (Mon May 29 2000 - 08:04:29 CDT)
VMD 1.5b1 is available! John Stone (Thu May 25 2000 - 14:18:24 CDT)
using trackers Kimberly Ann Foster (Tue May 23 2000 - 16:09:40 CDT)
- Re: using trackers John Stone (Wed May 24 2000 - 09:54:10 CDT)
cns files Matthew Wilce (Sun May 21 2000 - 05:28:05 CDT)
VMD on XFree86 4.0 /w hardware acceleration... John Stone (Fri May 19 2000 - 18:22:39 CDT)
- Re: VMD on XFree86 4.0 /w hardware acceleration... John Stone (Thu May 25 2000 - 22:14:34 CDT)
graphing a dihedral Deepak Singh (Sat May 13 2000 - 20:48:31 CDT)
- Re: graphing a dihedral Justin Gullingsrud (Sun May 14 2000 - 17:07:30 CDT)
Remote control of VMD on SGI-NT mixture Andrew Hall (Wed Apr 26 2000 - 11:11:50 CDT)
Mouse behavior in VMD Justin Gullingsrud (Mon Apr 24 2000 - 10:16:12 CDT)
problem with vmd/namd connection on linux John Duff (Tue Apr 18 2000 - 17:35:03 CDT)
- Re: problem with vmd/namd connection on linux John Stone (Tue Apr 18 2000 - 18:49:25 CDT)
  - Re: problem with vmd/namd connection on linux John Duff (Wed Apr 19 2000 - 10:25:46 CDT)
VMD 1.5a2 is available... John Stone (Thu Apr 06 2000 - 17:50:42 CDT)
surface in raster3d Dr Nicolas Le Novere (Thu Apr 06 2000 - 07:18:30 CDT)
- Re: surface in raster3d John Stone (Thu Apr 06 2000 - 10:42:51 CDT)
MSMS help Andrew Hall (Mon Apr 03 2000 - 15:04:30 CDT)
- Re: MSMS help John Stone (Mon Apr 03 2000 - 15:19:25 CDT)
membrane modeling Kemikal Kid Kolby (Sat Mar 25 2000 - 18:17:52 CST)
- Re: membrane modeling Peter Tieleman (Sat Mar 25 2000 - 18:43:50 CST)
- membrane modeling Eugene Leitl (Sat Mar 25 2000 - 19:03:56 CST)
Real Cash, Real Profit....Believe it !!! cashprofit3_at_address.com (Tue Mar 21 2000 - 00:09:55 CST)
Re: Stereo on Linux? John Stone (Fri Mar 17 2000 - 16:18:09 CST)
VMD 1.5a1 is available... John Stone (Fri Mar 17 2000 - 10:01:47 CST)
MSMS in VMD Xiao-Ping Zhang (Fri Mar 17 2000 - 07:53:22 CST)
- Re: MSMS in VMD John Stone (Fri Mar 17 2000 - 09:16:16 CST)
  - Re: MSMS in VMD Xiao-Ping Zhang (Fri Mar 17 2000 - 08:28:32 CST)
  - Re: MSMS in VMD Xiao-Ping Zhang (Sat Mar 18 2000 - 14:00:37 CST)
- Re: MSMS in VMD Andrew Dalke (Wed Oct 15 1997 - 00:30:42 CDT)
ANNOUNCEMENT: BioCoRe Robert Brunner (Fri Mar 03 2000 - 10:22:28 CST)
Re: Graphics algorithm II (fwd) Vieri Di Paola (Wed Mar 01 2000 - 11:03:48 CST)
Graphics algorithm (fwd) Vieri Di Paola (Wed Mar 01 2000 - 04:30:58 CST)
- Re: Graphics algorithm (fwd) John Stone (Wed Mar 01 2000 - 09:30:42 CST)
  - Re: Graphics algorithm (fwd) Vieri Di Paola (Wed Mar 01 2000 - 10:41:41 CST)
Graphics algorithm Vieri Di Paola (Wed Mar 01 2000 - 03:59:15 CST)
B-factor Plot Paul Hubbard (Mon Feb 28 2000 - 17:06:33 CST)
Remote Control Timm Essigke (Mon Feb 21 2000 - 12:12:44 CST)
AD:Family Reunion T Shirts & More hifiber7_at_compuserve.com (Sat Feb 19 2000 - 11:12:59 CST)
msms & vmd Robert Milius (Fri Feb 18 2000 - 11:51:29 CST)
- Re: msms & vmd John Stone (Fri Feb 18 2000 - 12:11:25 CST)
Setting colors Timm Essigke (Thu Feb 17 2000 - 16:04:33 CST)
- Re: Setting colors Justin Gullingsrud (Fri Feb 18 2000 - 10:25:50 CST)
SGI O2 stereo problems Bogdan Costescu (Tue Feb 15 2000 - 13:33:15 CST)
- Re: SGI O2 stereo problems Bogdan Costescu (Wed Mar 08 2000 - 14:43:38 CST)
  - Re: SGI O2 stereo problems John Stone (Wed Mar 08 2000 - 15:04:34 CST)
    - Re: SGI O2 stereo problems Bogdan Costescu (Thu Mar 09 2000 - 08:00:27 CST)
    - Re: SGI O2 stereo problems Ben Cornett (Thu Mar 09 2000 - 12:13:20 CST)
AD:Family Reunion T Shirts & More hifiber7_at_compuserve.com (Sat Feb 12 2000 - 02:20:20 CST)
script for generating stereo postscript images Charles_at_Schwieters.org (Fri Feb 11 2000 - 14:53:32 CST)
- Re: script for generating stereo postscript images John Stone (Fri Feb 11 2000 - 15:55:06 CST)
NVIDIA, SGI and VA Linux To Bring Graphics Standard To Desktop Linux Market Eugene Leitl (Wed Jan 19 2000 - 19:21:19 CST)
Stereo on SGI Indigo2? - Linux? Timm Essigke (Sat Jan 15 2000 - 10:11:49 CST)
- Stereo on SGI Indigo2? - Linux? Eugene Leitl (Sat Jan 15 2000 - 19:35:26 CST)
- Re: Stereo on SGI Indigo2? - Linux? John Stone (Wed Jan 19 2000 - 11:09:23 CST)
6DOF controllers Eugene Leitl (Sat Jan 08 2000 - 20:42:01 CST)
- Re: 6DOF controllers John Stone (Sat Jan 08 2000 - 21:23:23 CST)
VMD 1.4 Released (long) John Stone (Fri Jan 07 2000 - 17:59:02 CST)
Announce: VMD 1.4 beta 4 John Stone (Wed Dec 22 1999 - 16:40:53 CST)
Superimposing two molecules in VMD Gitte Iversen (Mon Nov 29 1999 - 02:38:09 CST)
Pegasus Technologies FreeD drivers? Eugene Leitl (Fri Nov 26 1999 - 19:39:54 CST)
- Re: Pegasus Technologies FreeD drivers? John Stone (Wed Dec 08 1999 - 10:08:33 CST)
  - Re: Pegasus Technologies FreeD drivers? Eugene Leitl (Wed Dec 08 1999 - 15:05:42 CST)
Gromacs trajectories in VMD Gitte Iversen (Mon Nov 22 1999 - 01:22:02 CST)
Announce: VMD 1.4 beta 3 John Stone (Thu Nov 18 1999 - 16:08:16 CST)
VMD working on Linux i386 w/ Mesa & Nvidia doug irvine (Wed Nov 17 1999 - 14:19:21 CST)
output Deepak Singh (Sun Nov 14 1999 - 19:48:57 CST)
- Re: output John Stone (Mon Nov 15 1999 - 10:40:20 CST)
question Deepak Singh (Sun Nov 14 1999 - 17:00:26 CST)
- Re: question John Stone (Mon Nov 15 1999 - 09:16:50 CST)
font size Deepak Singh (Fri Nov 12 1999 - 13:38:53 CST)
Announce: VMD at Super Computing 99 Kirby Vandivort (Thu Nov 11 1999 - 16:32:51 CST)
Announce: VMD 1.4 beta 2 John Stone (Tue Nov 09 1999 - 15:19:35 CST)
rmsd crashes vmd Kevin Sanbonmatsu (Thu Nov 04 1999 - 21:02:26 CST)
- Re: rmsd crashes vmd John Stone (Sat Nov 06 1999 - 00:17:28 CST)
- Re: rmsd crashes vmd 1.3 John Stone (Tue Nov 09 1999 - 21:59:58 CST)
SGI problem! Emmanuel Vamvakopoulos (Fri Oct 29 1999 - 07:57:27 CDT)
Problems with Charmm dcd Guy Coates (Wed Oct 27 1999 - 07:24:17 CDT)
- Re: Problems with Charmm dcd John Stone (Wed Oct 27 1999 - 09:23:35 CDT)
windows 98/ vmd14a2.exe & vmd14b1.exe francy_at_mvcch3.unica.it (Fri Oct 22 1999 - 12:52:43 CDT)
- Re: windows 98/ vmd14a2.exe & vmd14b1.exe John Stone (Fri Oct 22 1999 - 13:12:52 CDT)
- Re: windows 98/ vmd14a2.exe & vmd14b1.exe John Stone (Tue Oct 26 1999 - 15:35:34 CDT)
SEGMENT ID Deepak Singh (Tue Oct 19 1999 - 23:45:46 CDT)
- Re: SEGMENT ID John Stone (Fri Oct 22 1999 - 09:21:01 CDT)
  - Re: SEGMENT ID Deepak Singh (Fri Oct 22 1999 - 09:30:09 CDT)
Announce: VMD 1.4 beta 1 John Stone (Mon Oct 04 1999 - 17:07:49 CDT)
New VMD development pages John Stone (Mon Sep 27 1999 - 10:42:25 CDT)
VMD and 3Dfx Glide Massimiliano Stengel (Mon Aug 30 1999 - 06:31:33 CDT)
- Re: VMD and 3Dfx Glide John Stone (Mon Aug 30 1999 - 09:36:38 CDT)
how is dcd trajectory format ! Emmanuel Vamvakopoulos (Fri Aug 27 1999 - 14:18:04 CDT)
VMD 1.4 Alpha 5 (Windows+Unix) is available. John Stone (Tue Aug 17 1999 - 00:55:58 CDT)
VMD 1.4 Alpha 4 (Windows) is available. John Stone (Mon Aug 09 1999 - 17:00:50 CDT)
VMD 1.4 Alpha 3 (Windows+Unix) is available. John Stone (Tue Jul 27 1999 - 15:37:46 CDT)
VMD 1.4 Alpha 2 (Windows) is available. John Stone (Fri Jun 18 1999 - 16:24:12 CDT)
No Display when running vmd 1.3 Dr. David Gregory (Thu May 27 1999 - 14:53:51 CDT)
- Re: No Display when running vmd 1.3 Charles Schwieters (Thu May 27 1999 - 16:03:58 CDT)
- Re: No Display when running vmd 1.3 John Stone (Thu May 27 1999 - 16:00:02 CDT)
  - Re: No Display when running vmd 1.3 Dr. David Gregory (Fri May 28 1999 - 08:31:57 CDT)
1999 VMD User Survey Report John Stone (Mon May 24 1999 - 15:21:56 CDT)
VMD 1.4 Alpha 1 (Windows) is available. John Stone (Wed May 19 1999 - 17:21:47 CDT)
vmd and color Robert Milius (Thu Apr 22 1999 - 15:56:17 CDT)
- Re: vmd and color Sergei Izrailev (Fri Apr 23 1999 - 10:50:40 CDT)
translations with fixed and unfixed molecules Charles Schwieters (Mon Apr 12 1999 - 16:27:28 CDT)
- Re: translations with fixed and unfixed molecules Justin Gullingsrud (Tue Apr 13 1999 - 13:37:00 CDT)
- Re: translations with fixed and unfixed molecules Andrew Dalke (Thu Apr 15 1999 - 23:18:33 CDT)
VMD 1.3 Release John Stone (Mon Apr 05 1999 - 16:46:35 CDT)
moving molecules and getting the new positions Charles Schwieters (Tue Mar 30 1999 - 15:57:19 CST)
- Re: moving molecules and getting the new positions Andrew Dalke (Tue Mar 30 1999 - 18:50:35 CST)
questions about MSMS and H-bonds Axel Berg (Fri Mar 05 1999 - 06:38:48 CST)
- Re: questions about MSMS and H-bonds Andrew Dalke (Fri Mar 05 1999 - 14:54:07 CST)
- Re: questions about MSMS and H-bonds Andrew Dalke (Fri Mar 05 1999 - 15:04:39 CST)
1.3b2 Keith Refson (Wed Mar 03 1999 - 11:51:13 CST)
- Re: 1.3b2 John Stone (Wed Mar 03 1999 - 12:23:29 CST)
  - Re: 1.3b2 robert austin (Sun Mar 21 1999 - 16:31:34 CST)
VMD 1.3 Beta 2 release ... ¶¬ John Stone (Wed Feb 24 1999 - 13:38:37 CST)
VMD 1.3 Beta 1 release ... John Stone (Wed Feb 17 1999 - 02:08:02 CST)
Stereo on SGI Octane 250HMz R10000, IRIX 6.5 Kim Vilbour Andersen (Fri Feb 12 1999 - 09:20:16 CST)
- Re: Stereo on SGI Octane 250HMz R10000, IRIX 6.5 John Stone (Fri Feb 12 1999 - 09:30:37 CST)
  - Re: Stereo on SGI Octane 250HMz R10000, IRIX 6.5 Kim Vilbour Andersen (Mon Feb 15 1999 - 05:21:17 CST)
    - Re: Stereo on SGI Octane 250HMz R10000, IRIX 6.5 John Stone (Wed Feb 17 1999 - 00:43:56 CST)
Visualizing volumetric data with Situs and VMD Willy Wriggers (Mon Feb 01 1999 - 16:55:29 CST)
VMD 1.3 Alpha 2 release... John Stone (Mon Jan 25 1999 - 20:57:45 CST)
extracting distances David Horita (Wed Dec 09 1998 - 17:00:54 CST)
- Re: extracting distances Andrew Dalke (Thu Dec 10 1998 - 20:06:25 CST)
convex hull and VMD Andrew Dalke (Mon Sep 28 1998 - 17:31:10 CDT)
- Re: convex hull and VMD John Stone (Mon Sep 28 1998 - 17:05:51 CDT)
Transparent graphics Siegmar Kardinal (Sun Sep 13 1998 - 11:00:44 CDT)
- Re: Transparent graphics Andrew Dalke (Fri Sep 18 1998 - 12:32:30 CDT)
  - Re: Transparent graphics John Stone (Fri Sep 18 1998 - 11:17:16 CDT)
99 Toyotas as low as 2% over invoice accutone_at_atlsky.com (Sat Sep 05 1998 - 19:10:53 CDT)
calculation of RMS values Christoph Schneider (Wed Aug 19 1998 - 04:05:51 CDT)
- Re: calculation of RMS values Andrew Dalke (Wed Aug 19 1998 - 13:49:12 CDT)
VMDTECH: CONECTing atoms Andrew Dalke (Fri Aug 14 1998 - 17:16:26 CDT)
- VMDTECH: CONECTing atoms Keith Refson (Mon Aug 24 1998 - 09:28:47 CDT)
  - Re: VMDTECH: CONECTing atoms Andrew Dalke (Mon Aug 24 1998 - 15:01:05 CDT)
VMD 1.2 port to MkLinux/LinuxPPC Tom Pollard (Mon Aug 10 1998 - 01:00:23 CDT)
measuring torsion angles Christoph Schneider (Mon Jun 29 1998 - 03:08:48 CDT)
VMD 1.2b3 is available! John Stone (Fri Jun 26 1998 - 12:57:17 CDT)
problems with MSMS Patric Beuthen (Fri Jun 26 1998 - 08:38:12 CDT)
- Re: problems with MSMS John Stone (Sat Aug 15 1998 - 22:00:51 CDT)
VMD 1.2b2 Linux & MSMS ... . (Sun May 17 1998 - 08:55:16 CDT)
- RE: VMD 1.2b2 Linux & MSMS ... Ivo Hofacker (Wed May 20 1998 - 04:56:29 CDT)
VMD 1.2b2 is now available!!! Sergei Izrailev (Tue May 12 1998 - 18:29:10 CDT)
new version of VMD Sergei Izrailev (Thu Apr 30 1998 - 18:59:15 CDT)
dihedral angles Stephane Spieser (Wed Apr 22 1998 - 09:09:34 CDT)
Babel and VMD aldo jongejan (Tue Mar 03 1998 - 11:05:07 CST)
- Re: Babel and VMD Neil Henson T-12 (Tue Mar 03 1998 - 12:12:27 CST)
The pdb format of vmd Dayong He (Thu Jan 22 1998 - 11:01:58 CST)
- Re: The pdb format of vmd Andrew Dalke (Thu Jan 22 1998 - 12:02:32 CST)
Surface plots s.hogg_at_ic.ac.uk (Tue Jan 20 1998 - 10:50:04 CST)
protein surface and volume code Andrew Dalke (Wed Jan 14 1998 - 22:17:10 CST)
VMD on a DEC? s.hogg_at_ic.ac.uk (Wed Jan 14 1998 - 07:15:56 CST)
- Re: VMD on a DEC? Andrew Dalke (Wed Jan 14 1998 - 22:07:30 CST)
FYI:Re: CCL:md rookie update (fwd) root (Thu Jan 08 1998 - 12:44:37 CST)
FYI:CCL:md rookie update (fwd) root (Thu Jan 08 1998 - 12:42:37 CST)
FYI:Re: CCL:md rookie update (fwd) root (Thu Jan 08 1998 - 12:41:39 CST)
FYI:Re: CCL:md rookie update (fwd) root (Thu Jan 08 1998 - 12:41:23 CST)
Re: CCL:md rookie update Konrad Hinsen (Thu Jan 08 1998 - 06:50:36 CST)
other-endian dcd problem also when trajectory obtained over network? root (Mon Dec 29 1997 - 09:19:31 CST)
RE: stereo mode problems with vmd on IRIX6.2 Thomas Ehmer (Mon Dec 29 1997 - 07:34:06 CST)
problem with getting started. Rainer Fink (Fri Dec 19 1997 - 12:32:29 CST)
- Re: problem with getting started. Andrew Dalke (Sun Dec 21 1997 - 11:47:00 CST)
DCD architecture dependence Jason Gans (Mon Dec 08 1997 - 08:58:10 CST)
unable to animate alanine.dcd root (Sat Dec 06 1997 - 07:26:43 CST)
- Re: unable to animate alanine.dcd Barry Isralewitz (Sat Dec 06 1997 - 07:30:28 CST)
  - Re: unable to animate alanine.dcd root (Sat Dec 06 1997 - 08:08:16 CST)
- Re: unable to animate alanine.dcd Andrew Dalke (Sun Dec 07 1997 - 23:16:55 CST)
- Re: unable to animate alanine.dcd root (Mon Dec 08 1997 - 03:41:44 CST)
- Re: unable to animate alanine.dcd Andrew Dalke (Mon Dec 08 1997 - 13:34:06 CST)
molecular representation: new lead generation software SciFarma (Tue Dec 02 1997 - 02:53:25 CST)
- Re: molecular representation: new lead generation software root (Tue Dec 02 1997 - 06:18:33 CST)
- Re: molecular representation: new lead generation software Salvatore Guccione (Wed Dec 03 1997 - 05:19:07 CST)
- Re: molecular representation: new lead generation software Salvatore Guccione (Thu Dec 04 1997 - 04:43:51 CST)
  - Re: molecular representation: new lead generation software root (Fri Dec 05 1997 - 05:08:29 CST)
FIX:Re: difficulties with starting vmd (fwd) root (Mon Dec 01 1997 - 09:25:02 CST)
difficulties with starting vmd root (Sat Nov 29 1997 - 07:38:28 CST)
Release Date for v.1.2 ?? Simon Hogg (Thu Nov 20 1997 - 17:35:06 CST)
stereo mode problems with vmd on IRIX 6.2 matt_at_clarkeconsulting.com (Thu Nov 20 1997 - 18:14:21 CST)
drawing spheres Nithin Rai (Tue Nov 18 1997 - 11:34:14 CST)
- Re: drawing spheres Andrew Dalke (Wed Nov 19 1997 - 08:03:35 CST)
MSMS in VMD Axel Berg (Tue Oct 14 1997 - 07:58:11 CDT)
reading minimalised pdb files Nithin Rai (Tue Oct 07 1997 - 04:12:06 CDT)
- Re: reading minimalised pdb files Andrew Dalke (Tue Oct 07 1997 - 04:34:33 CDT)
- tcl script for writinging modified pdb co-ordinates Nithin Rai (Thu Dec 04 1997 - 16:13:22 CST)
  - Re: tcl script for writinging modified pdb co-ordinates Andrew Dalke (Thu Dec 04 1997 - 18:41:03 CST)
VMD & PoV files Mensur (Mon Oct 06 1997 - 19:34:47 CDT)
- Re: VMD & PoV files Andrew Dalke (Wed Oct 08 1997 - 12:12:54 CDT)
H-bonds Christoph Schneider (Mon Oct 06 1997 - 12:02:13 CDT)
rock around the clock? Christoph Schneider (Mon Oct 06 1997 - 11:02:46 CDT)
- Re: rock around the clock? Ivo Hofacker (Mon Oct 06 1997 - 21:25:08 CDT)
Problems with vmd under Linux Simon Hogg (Thu Jul 31 1997 - 05:53:01 CDT)
New VMD User's Guide available Sergei Izrailev (Tue Jul 29 1997 - 13:08:25 CDT)
- Re: New VMD User's Guide available Sergei Izrailev (Wed Jul 30 1997 - 15:33:32 CDT)
Exporting VMD images to Alias Andrew Dalke (Thu Jul 24 1997 - 14:28:40 CDT)
Latest Linux News? s.hogg_at_ic.ac.uk (Fri Jul 04 1997 - 13:58:40 CDT)
[VMDTECH] Working with colors Sergei Izrailev (Tue Jul 01 1997 - 20:21:43 CDT)
[VMDTECH] Hingefind Sergei Izrailev (Wed Jun 11 1997 - 16:45:17 CDT)
- Re: [VMDTECH] Hingefind Willy Wriggers (Wed Jun 11 1997 - 16:57:22 CDT)
residue-residue distances and atom selection bug Andrew Dalke (Tue Jun 10 1997 - 13:05:11 CDT)
[VMD TECH] Tracing VMD Variables (Part II) Jeff Ulrich (Wed Apr 30 1997 - 17:42:04 CDT)
- Re: [VMD TECH] Tracing VMD Variables (Part II) Alexander Balaeff (Thu May 01 1997 - 16:29:52 CDT)
VMD with Babel and chemical2vmd Kiraly Andras (Mon Apr 21 1997 - 18:35:26 CDT)
- Re: VMD with Babel and chemical2vmd Stefan Grzybek (Tue Apr 22 1997 - 01:31:41 CDT)
- Re: VMD with Babel and chemical2vmd Kiraly Andras (Tue Apr 22 1997 - 13:58:15 CDT)
[VMDTECH] Schedule Change Andrew Dalke (Fri Apr 18 1997 - 18:07:35 CDT)
Run time error on Max Impact Brian Corrie (Wed Apr 16 1997 - 01:16:40 CDT)
[VMDTECH] Smoothing Animations Andrew Dalke (Sun Apr 13 1997 - 01:28:43 CDT)
Error in Linux cheol_at_rccd.snu.ac.kr (Wed Apr 09 1997 - 05:51:13 CDT)
Segmentation error! Cheol Soon Lee (Wed Apr 09 1997 - 05:47:56 CDT)
Segmentation error! Cheol Soon Lee (Wed Apr 09 1997 - 05:46:34 CDT)
- Re: Segmentation error! Andrew Dalke (Wed Apr 09 1997 - 10:46:36 CDT)
[VMDTECH] Tracing Atom Picks Andrew Dalke (Fri Apr 04 1997 - 18:27:57 CST)
[VMDTECH] Morphing Andrew Dalke (Fri Mar 28 1997 - 12:14:17 CST)
Two (small) VMD 1.2b1 bugs Andrew Dalke (Wed Mar 26 1997 - 13:55:16 CST)
building VMD on SGI IRIX 6.x Joseph Landman (Wed Mar 26 1997 - 11:55:35 CST)
[VMDTECH] VMD 1.2b1 is now available Andrew Dalke (Tue Mar 25 1997 - 02:09:57 CST)
- Re: [VMDTECH] VMD 1.2b1 is now available Andrew Dalke (Tue Mar 25 1997 - 03:03:32 CST)
[VMDTECH] Drawing Methods, Part II Andrew Dalke (Fri Mar 14 1997 - 16:40:47 CST)
Wavefront obj output David E. Jones (Wed Mar 12 1997 - 13:40:03 CST)
- Re: Wavefront obj output Andrew Dalke (Wed Mar 12 1997 - 15:19:48 CST)
[VMDTECH] Drawing Methods, Part I Andrew Dalke (Fri Mar 07 1997 - 16:22:57 CST)
VMD now uses Tcl 7.6 Andrew Dalke (Wed Mar 05 1997 - 22:47:42 CST)
Updated VMD Script Library Jeff Ulrich (Wed Mar 05 1997 - 10:57:03 CST)
H-bonds? Andrea Bernini (Wed Mar 05 1997 - 06:36:47 CST)
- Re: H-bonds? Andrew Dalke (Wed Mar 05 1997 - 09:37:55 CST)
why does VMD quit automatically? Qiang Liu (Tue Mar 04 1997 - 18:04:36 CST)
- Re: why does VMD quit automatically? Andrew Dalke (Wed Mar 05 1997 - 08:58:34 CST)
- Re: why does VMD quit automatically? Andrew Dalke (Wed Mar 05 1997 - 11:50:27 CST)
[VMDTECH] Secondary Structure Andrew Dalke (Fri Feb 28 1997 - 16:38:21 CST)
[VMDTECH] Small things Andrew Dalke (Fri Feb 21 1997 - 13:02:34 CST)
VMD workshop material Andrew Dalke (Tue Feb 18 1997 - 17:43:13 CST)
[VMDTECH] Making Movies Andrew Dalke (Fri Feb 14 1997 - 12:56:27 CST)
[VMDTECH] RMSD and best-fit alignments Andrew Dalke (Fri Feb 07 1997 - 14:37:24 CST)
[Tech] Customizing VMD: hot keys and popup menus Andrew Dalke (Fri Jan 31 1997 - 12:10:02 CST)
Re: textures in VMD and rayshade scripts Andrew Dalke (Mon Jan 27 1997 - 15:42:15 CST)
- VMD only read 58 frames from XYZ file Keith Refson (Wed Nov 05 1997 - 06:42:17 CST)
[Tech] Colors in VMD Andrew Dalke (Fri Jan 24 1997 - 11:44:45 CST)
- Re: [Tech] Colors in VMD Chris Upton (Fri Jan 24 1997 - 11:55:13 CST)
- Re: [Tech] Colors in VMD Andrew Dalke (Fri Jan 24 1997 - 15:24:38 CST)
Mailing List John Hondroulis (Wed Jan 08 1997 - 14:30:26 CST)
Special Christmas binary Andrew Dalke (Fri Dec 20 1996 - 04:01:38 CST)
Welcome to VMD-L! Andrew Dalke (Thu Dec 19 1996 - 11:40:38 CST)
- Re: Welcome to VMD-L! T. Chyau Liang, Ph.D. (Wed Jan 08 1997 - 15:05:28 CST)

Last message date: Mon Oct 21 2024 - 06:24:29 CDT
Archived on: Tue Oct 22 2024 - 02:17:47 CDT

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