VMD-L Mailing List

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About this archive

Starting: Thu Dec 19 1996 - 11:40:41 CST
Ending: Thu May 25 2023 - 02:29:30 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)
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)

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