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NAMD-L: By Thread

By Thread

8255 messages sorted by: [ author ] [ date ] [ subject ] [ attachment ]
About this archive

Starting: Mon Sep 08 2003 - 09:54:14 CDT
Ending: Fri Aug 29 2008 - 23:11:11 CDT

Trouble with params file when trying to perform basic dynamics with alanine. Diego Alejandro Vargas (Fri Aug 29 2008 - 23:11:03 CDT)
nvidia and namd Jorgen Simonsen (Fri Aug 29 2008 - 10:21:17 CDT)
- Re: nvidia and namd Chris Harrison (Fri Aug 29 2008 - 12:07:53 CDT)
NPT enzemble and ABF Jorgen Simonsen (Fri Aug 29 2008 - 07:07:39 CDT)
TXT program editor Alejandro Ortega (Thu Aug 28 2008 - 14:43:14 CDT)
- Re: vmd-l: TXT program editor Peter Freddolino (Thu Aug 28 2008 - 15:06:53 CDT)
- Re: vmd-l: TXT program editor Axel Kohlmeyer (Thu Aug 28 2008 - 15:50:21 CDT)
- Re: TXT program editor Giovanni Bellesia (Thu Aug 28 2008 - 16:21:03 CDT)
- Re: vmd-l: TXT program editor Sabuj Pattanayek (Thu Aug 28 2008 - 17:03:11 CDT)
NAMD compilation / TACC Ranger Arturas Ziemys (Thu Aug 28 2008 - 11:25:14 CDT)
- Re: NAMD compilation / TACC Ranger Axel Kohlmeyer (Thu Aug 28 2008 - 14:12:36 CDT)
PME questions Lam T Nguyen (Thu Aug 28 2008 - 10:58:54 CDT)
- Explicit Membrane Protein Simulations in NAMD/VMD Shultz, Jack (Thu Aug 28 2008 - 12:25:23 CDT)
  - Re: Explicit Membrane Protein Simulations in NAMD/VMD Jerome Henin (Thu Aug 28 2008 - 14:57:07 CDT)
    - RE: Explicit Membrane Protein Simulations in NAMD/VMD Shultz, Jack (Thu Aug 28 2008 - 15:07:24 CDT)
    - Re: Explicit Membrane Protein Simulations in NAMD/VMD Richard Law (Thu Aug 28 2008 - 15:40:10 CDT)
- Re: PME questions Gianluca Interlandi (Thu Aug 28 2008 - 12:39:31 CDT)
diffusion coefficient from rmsd Rudra Banerjee (Wed Aug 27 2008 - 21:55:28 CDT)
- Re: diffusion coefficient from rmsd Axel Kohlmeyer (Wed Aug 27 2008 - 22:39:52 CDT)
  - Re: diffusion coefficient from rmsd bo liu (Thu Aug 28 2008 - 01:38:38 CDT)
corrupt DCD file Forbes, Jeff (NIH/NIAMS) [E] (Wed Aug 27 2008 - 16:54:07 CDT)
- Re: corrupt DCD file Axel Kohlmeyer (Wed Aug 27 2008 - 18:56:20 CDT)
Struggling with the compilation of NAMD 2.6 on a PBS Cluster with LAM/MPI Frank Thommen (Wed Aug 27 2008 - 11:41:08 CDT)
- Re: Struggling with the compilation of NAMD 2.6 on a PBS Cluster with LAM/MPI Axel Kohlmeyer (Wed Aug 27 2008 - 12:12:00 CDT)
  - Re: Struggling with the compilation of NAMD 2.6 on a PBS Cluster with LAM/MPI Frank Thommen (Thu Aug 28 2008 - 12:21:56 CDT)
- Re: Struggling with the compilation of NAMD 2.6 on a PBS Cluster with LAM/MPI Christopher Gillespie (Wed Aug 27 2008 - 12:49:31 CDT)
  - Re: Struggling with the compilation of NAMD 2.6 on a PBS Cluster with LAM/MPI Frank Thommen (Thu Aug 28 2008 - 12:22:57 CDT)
Fe-S cluster topology parameters jose correa (Wed Aug 27 2008 - 09:20:58 CDT)
- Re: Fe-S cluster topology parameters Chang, Christopher (Wed Aug 27 2008 - 11:51:45 CDT)
change in box geometry for simulation of pure water maria goranovic (Wed Aug 27 2008 - 07:48:12 CDT)
- Re: change in box geometry for simulation of pure water Peter Freddolino (Wed Aug 27 2008 - 22:58:07 CDT)
  - Re: change in box geometry for simulation of pure water maria goranovic (Thu Aug 28 2008 - 02:11:31 CDT)
- Re: change in box geometry for simulation of pure water Chris Harrison (Wed Aug 27 2008 - 21:23:22 CDT)
  - Re: change in box geometry for simulation of pure water Axel Kohlmeyer (Thu Aug 28 2008 - 14:06:47 CDT)
error with calling exec: child process exited abnormally Yinglong Miao (Tue Aug 26 2008 - 10:37:25 CDT)
- Re: error with calling exec: child process exited abnormally Peter Freddolino (Tue Aug 26 2008 - 14:38:52 CDT)
  - Re: error with calling exec: child process exited abnormally Yinglong Miao (Tue Aug 26 2008 - 16:22:21 CDT)
van der walls-understanding problem Rudra Banerjee (Tue Aug 26 2008 - 09:50:31 CDT)
- Re: van der walls-understanding problem Schreiner Eduard (Tue Aug 26 2008 - 10:05:28 CDT)
- Re: van der walls-understanding problem Peter Freddolino (Tue Aug 26 2008 - 10:08:24 CDT)
running precompiled NAMD with multiple processors Neelanjana Sengupta (Tue Aug 26 2008 - 01:04:57 CDT)
- Re: running precompiled NAMD with multiple processors Axel Kohlmeyer (Tue Aug 26 2008 - 09:41:49 CDT)
Re: How to write gradual heating config file Hyundeok Song (Mon Aug 25 2008 - 19:30:26 CDT)
How to write gradual heating config file Audrey Salazar (Mon Aug 25 2008 - 17:41:59 CDT)
- Re: How to write gradual heating config file Audrey Salazar (Mon Aug 25 2008 - 18:23:41 CDT)
NAMD COMPILATION ERROR Semorale (Mon Aug 25 2008 - 08:43:13 CDT)
Why turning on 'pressureProfile' make NAMD get into sleep? loligo huang (Sun Aug 24 2008 - 21:49:55 CDT)
- Re: Why turning on 'pressureProfile' make NAMD get into sleep? Huang (Thu Aug 28 2008 - 08:20:15 CDT)
  - basic question about drawing methods Subhashis Biswas (Thu Aug 28 2008 - 10:25:16 CDT)
    - Re: basic question about drawing methods Ramya Gamini (Thu Aug 28 2008 - 11:55:16 CDT)
  - Re: Why turning on 'pressureProfile' make NAMD get into sleep? Huang (Fri Aug 29 2008 - 08:33:57 CDT)
How does NAMD count atoms in PDB files? Corenflos, Steven Charles (Thu Aug 21 2008 - 16:15:18 CDT)
parallel execution speedup Roman Petrenko (Thu Aug 21 2008 - 15:51:57 CDT)
- Re: parallel execution speedup Joshua Adelman (Thu Aug 21 2008 - 16:26:06 CDT)
  - Re: parallel execution speedup Eric H. Lee (Thu Aug 21 2008 - 16:31:32 CDT)
    - Re: parallel execution speedup bo liu (Thu Aug 28 2008 - 01:51:29 CDT)
storing velocity data of a NVE simulation sudipta sinha (Thu Aug 21 2008 - 11:32:37 CDT)
- Re: storing velocity data of a NVE simulation David Hardy (Thu Aug 21 2008 - 11:47:26 CDT)
SMD more than once JARROD EDWARD CHARLES NICKEL (Wed Aug 20 2008 - 14:24:17 CDT)
- Re: SMD more than once Eric H. Lee (Wed Aug 20 2008 - 14:39:37 CDT)
- Re: SMD more than once Gungor Ozer (Wed Aug 20 2008 - 23:40:58 CDT)
about force fields oguz gurbulak (Tue Aug 19 2008 - 09:54:14 CDT)
bad exclusion error - searching remedies Arturas Ziemys (Mon Aug 18 2008 - 18:12:48 CDT)
Benchmark calculation rebeca_at_mmb.pcb.ub.es (Thu Aug 14 2008 - 12:36:55 CDT)
Problem in energy conservation in NVE ensemble with 1fs timestep tinni sona (Thu Aug 14 2008 - 11:34:43 CDT)
- Re: Problem in energy conservation in NVE ensemble with 1fs timestep Peter Freddolino (Thu Aug 14 2008 - 11:40:32 CDT)
Problem in energy conservation in NVE ensemble with 1fs timestep tinni sona (Thu Aug 14 2008 - 11:27:18 CDT)
Problems with TMD could not be solved with the CVS version Robert Schulz (Thu Aug 14 2008 - 10:06:44 CDT)
- Re: Problems with TMD could not be solved with the CVS version Peter Freddolino (Thu Aug 14 2008 - 11:41:26 CDT)
TMD and TclForces Gianluca Interlandi (Thu Aug 14 2008 - 01:35:21 CDT)
- Re: TMD and TclForces Peter Freddolino (Fri Aug 15 2008 - 07:53:23 CDT)
  - Re: TMD and TclForces Gianluca Interlandi (Fri Aug 15 2008 - 12:14:06 CDT)
FATAL ERROR: Patch needed for tuple is missing rebeca_at_mmb.pcb.ub.es (Wed Aug 13 2008 - 17:31:27 CDT)
Dihedral angle calculation over the trajectories sunita gupta (Wed Aug 13 2008 - 10:17:14 CDT)
- Re: Dihedral angle calculation over the trajectories Peter Freddolino (Wed Aug 13 2008 - 10:24:59 CDT)
TclForces and wrapping Gianluca Interlandi (Wed Aug 13 2008 - 03:05:43 CDT)
namd: 64 p job runs; 128 p job fails why? Sangamesh B (Tue Aug 12 2008 - 12:27:18 CDT)
128 core namd job fails to run Sangamesh B (Tue Aug 12 2008 - 10:14:03 CDT)
SMD forces Roman Petrenko (Mon Aug 11 2008 - 17:38:18 CDT)
SMD force units Roman Petrenko (Mon Aug 11 2008 - 17:33:25 CDT)
- Re: SMD force units Eric H. Lee (Mon Aug 11 2008 - 17:46:15 CDT)
  - Re: SMD force units Eric H. Lee (Mon Aug 11 2008 - 17:50:30 CDT)
namd mpi version with smp Vlad Cojocaru (Mon Aug 11 2008 - 05:22:18 CDT)
- Re: namd mpi version with smp Philip Peartree (Mon Aug 11 2008 - 08:35:41 CDT)
torsion potentials for phi/psi angles in CHARMM force field? Roman Petrenko (Sat Aug 09 2008 - 14:52:55 CDT)
Rv: Value 99999999.9999 during minimization Eduardo Tejera (Fri Aug 08 2008 - 14:50:45 CDT)
Turn off H-bonding on select residues dora guzman (Fri Aug 08 2008 - 13:21:35 CDT)
Value 99999999.9999 during minimization rebeca_at_mmb.pcb.ub.es (Fri Aug 08 2008 - 03:16:57 CDT)
- Re: Value 99999999.9999 during minimization Schreiner Eduard (Fri Aug 08 2008 - 03:44:12 CDT)
restartfreq question.... Dr. Luis Rosales León (Thu Aug 07 2008 - 16:31:54 CDT)
- Re: restartfreq question.... JC Gumbart (Fri Aug 08 2008 - 13:25:56 CDT)
Average Velocity and How to choose Right Alias abhijit ramachandran (Thu Aug 07 2008 - 16:13:06 CDT)
build smp version of namd with intel 10.1 Vlad Cojocaru (Thu Aug 07 2008 - 10:44:02 CDT)
- Re: build smp version of namd with intel 10.1 Axel Kohlmeyer (Thu Aug 07 2008 - 12:08:34 CDT)
- Re: build smp version of namd with intel 10.1 Gengbin Zheng (Thu Aug 07 2008 - 10:49:00 CDT)
  - Re: build smp version of namd with intel 10.1 Vlad Cojocaru (Fri Aug 08 2008 - 05:18:42 CDT)
Abnormal EOF found - buffer Rene Prieto (Thu Aug 07 2008 - 00:46:37 CDT)
- Re: Abnormal EOF found - buffer David Tanner (Fri Aug 08 2008 - 10:14:21 CDT)
  - Re: Abnormal EOF found - buffer Rene Prieto (Sun Aug 10 2008 - 09:37:47 CDT)
NAMD crashed with TclForce turned on Chi-Cheng Chiu (Wed Aug 06 2008 - 16:10:01 CDT)
- Re: NAMD crashed with TclForce turned on Axel Kohlmeyer (Wed Aug 06 2008 - 17:20:55 CDT)
  - Re: NAMD crashed with TclForce turned on Chi-Cheng Chiu (Thu Aug 07 2008 - 11:17:16 CDT)
  - Re: NAMD crashed with TclForce turned on Chi-Cheng Chiu (Wed Aug 13 2008 - 10:33:36 CDT)
- Re: NAMD crashed with TclForce turned on Vlad Cojocaru (Thu Aug 07 2008 - 03:05:30 CDT)
Problems with the charge (membrane simulation) rebeca_at_mmb.pcb.ub.es (Wed Aug 06 2008 - 13:18:34 CDT)
- RE: Problems with the charge (membrane simulation) JC Gumbart (Fri Aug 08 2008 - 10:04:54 CDT)
Warning in log file tinni sona (Wed Aug 06 2008 - 06:23:50 CDT)
- Re: Warning in log file Axel Kohlmeyer (Wed Aug 06 2008 - 11:17:34 CDT)
[Fwd: Notice:Re: Re: segmentation fault when running ABF] Vlad Cojocaru (Wed Aug 06 2008 - 05:15:19 CDT)
- Re: [Fwd: Notice:Re: Re: segmentation fault when running ABF] Axel Kohlmeyer (Wed Aug 06 2008 - 11:15:06 CDT)
Error with Shape Based CG Model Anirban Ghosh (Wed Aug 06 2008 - 05:04:27 CDT)
- Re: Error with Shape Based CG Model Anton Arkhipov (Wed Aug 06 2008 - 11:39:38 CDT)
membrane using OPLS force field rebeca_at_mmb.pcb.ub.es (Tue Aug 05 2008 - 07:48:45 CDT)
- Re: unwanted bonds in .pdb file while using molefacture Subhashis Biswas (Wed Aug 06 2008 - 14:23:23 CDT)
  - Re: Re: unwanted bonds in .pdb file while using molefacture José (Wed Aug 06 2008 - 15:40:45 CDT)
Some question about Target MD Yang Gao (Tue Aug 05 2008 - 10:40:10 CDT)
segmentation fault when running ABF Vlad Cojocaru (Tue Aug 05 2008 - 10:20:32 CDT)
- Re: segmentation fault when running ABF Vlad Cojocaru (Tue Aug 05 2008 - 10:34:48 CDT)
  - Re: Re: segmentation fault when running ABF Axel Kohlmeyer (Tue Aug 05 2008 - 12:13:56 CDT)
Zinc-NAMD parameters jose correa (Mon Aug 04 2008 - 14:14:13 CDT)
- Re: Zinc-NAMD parameters L. Michel Espinoza-Fonseca (Mon Aug 04 2008 - 15:05:45 CDT)
how do you debug tcl scripts in vmd ? Andriy Volynets (Mon Aug 04 2008 - 12:12:18 CDT)
compilation of the CVS code Vlad Cojocaru (Mon Aug 04 2008 - 01:46:11 CDT)
- Re: compilation of the CVS code Vlad Cojocaru (Mon Aug 04 2008 - 01:53:41 CDT)
- Re: compilation of the CVS code Peter Freddolino (Mon Aug 04 2008 - 07:36:20 CDT)
  - Re: compilation of the CVS code Peter Freddolino (Mon Aug 04 2008 - 09:22:00 CDT)
    - Re: compilation of the CVS code Vlad Cojocaru (Mon Aug 04 2008 - 10:02:03 CDT)
TMD + temperature/pressure coupling Gianluca Interlandi (Sat Aug 02 2008 - 17:04:31 CDT)
Impropers in histidine residues Marc Baaden (Sat Aug 02 2008 - 03:56:17 CDT)
- Re: Impropers in histidine residues Jerome Henin (Wed Aug 06 2008 - 16:54:15 CDT)
psf-generation. yambem soniya (Thu Jul 31 2008 - 16:57:08 CDT)
- Re: psf-generation. Peter Freddolino (Fri Aug 01 2008 - 00:06:19 CDT)
  - Can this be modelled in NAMD S.K. Ghosh (Fri Aug 01 2008 - 11:38:38 CDT)
coord file output minus solvation box brosbam_at_berkeley.edu (Wed Jul 30 2008 - 18:21:18 CDT)
- Re: coord file output minus solvation box Joshua Adelman (Thu Jul 31 2008 - 12:05:08 CDT)
SMD in water Roman Petrenko (Thu Jul 31 2008 - 06:22:43 CDT)
- Re: SMD in water Axel Kohlmeyer (Thu Jul 31 2008 - 09:16:01 CDT)
  - Re: SMD in water Roman Petrenko (Thu Jul 31 2008 - 12:34:26 CDT)
    - Re: SMD in water Marcos Sotomayor (Thu Jul 31 2008 - 13:01:12 CDT)
build charm++ and namd Vlad Cojocaru (Thu Jul 31 2008 - 05:06:44 CDT)
- Re: build charm++ and namd Vlad Cojocaru (Thu Jul 31 2008 - 06:46:31 CDT)
  - Re: Re: build charm++ and namd Peter Freddolino (Thu Jul 31 2008 - 07:38:31 CDT)
    - Re: Re: build charm++ and namd Vlad Cojocaru (Thu Jul 31 2008 - 07:57:36 CDT)
    - Re: Re: build charm++ and namd Peter Freddolino (Thu Jul 31 2008 - 08:39:07 CDT)
g(r) Rudra Banerjee (Thu Jul 31 2008 - 00:39:47 CDT)
- Re: g(r) Alexandre A. Vakhrouchev (Thu Jul 31 2008 - 01:10:05 CDT)
  - Re: g(r) Rudra Banerjee (Thu Jul 31 2008 - 01:51:17 CDT)
- Re: g(r) Philip Fowler (Thu Jul 31 2008 - 02:29:47 CDT)
output .coor minus solvation box brosbam_at_berkeley.edu (Wed Jul 30 2008 - 18:27:01 CDT)
- Re: output .coor minus solvation box Peter Freddolino (Wed Jul 30 2008 - 23:45:25 CDT)
phosphate (PO4) topology Dr. Luis Rosales León (Wed Jul 30 2008 - 17:37:19 CDT)
- Re: phosphate (PO4) topology Victor Ovchinnikov (Wed Jul 30 2008 - 21:34:31 CDT)
namdenergy and amber trajectory Alessandro Nascimento (Wed Jul 30 2008 - 10:06:27 CDT)
namd linked to tcl8.5 Vlad Cojocaru (Wed Jul 30 2008 - 09:58:23 CDT)
- Re: namd linked to tcl8.5 Axel Kohlmeyer (Wed Jul 30 2008 - 10:20:55 CDT)
Does anyone have a sample tcl file for counting H-bonds Yang Gao (Wed Jul 30 2008 - 09:33:18 CDT)
namdenergy and amber trajectory Alessandro Nascimento (Tue Jul 29 2008 - 14:58:56 CDT)
- Re: namdenergy and amber trajectory V.Ovchinnikov (Tue Jul 29 2008 - 17:30:53 CDT)
- Re: namdenergy and amber trajectory Peter Freddolino (Wed Jul 30 2008 - 00:46:57 CDT)
DNA pdb file xing jing (Tue Jul 29 2008 - 15:16:16 CDT)
recenter atom and remove rotation (translation) Lam T Nguyen (Tue Jul 29 2008 - 12:28:11 CDT)
- Re: recenter atom and remove rotation (translation) Roman Petrenko (Tue Jul 29 2008 - 15:58:03 CDT)
Running CGMD using NAMD Anirban Ghosh (Mon Jul 28 2008 - 23:46:54 CDT)
- Re: Running CGMD using NAMD Peter Freddolino (Tue Jul 29 2008 - 11:39:54 CDT)
PME fails no matter what Roman Petrenko (Mon Jul 28 2008 - 23:29:54 CDT)
- Re: PME fails no matter what Joshua Adelman (Mon Jul 28 2008 - 23:50:19 CDT)
  - Re: PME fails no matter what Roman Petrenko (Tue Jul 29 2008 - 00:17:41 CDT)
    - Re: PME fails no matter what Axel Kohlmeyer (Tue Jul 29 2008 - 03:18:21 CDT)
- Re: PME fails no matter what Peter Freddolino (Tue Jul 29 2008 - 11:38:20 CDT)
  - Re: PME fails no matter what Joshua Adelman (Tue Jul 29 2008 - 12:00:11 CDT)
    - Re: PME fails no matter what David Hardy (Tue Jul 29 2008 - 12:39:04 CDT)
    - Re: PME fails no matter what Roman Petrenko (Fri Aug 01 2008 - 18:02:03 CDT)
  - Re: PME fails no matter what Gianluca Interlandi (Tue Jul 29 2008 - 14:41:50 CDT)
fixed residue Rudra Banerjee (Mon Jul 28 2008 - 22:49:36 CDT)
- Re: fixed residue Roman Petrenko (Mon Jul 28 2008 - 23:36:45 CDT)
  - Re: fixed residue Roman Petrenko (Mon Jul 28 2008 - 23:38:10 CDT)
- Re: fixed residue Joshua Adelman (Mon Jul 28 2008 - 23:16:41 CDT)
- Re: fixed residue Gianluca Interlandi (Tue Jul 29 2008 - 01:03:40 CDT)
ABF simulations Raul Araya (Mon Jul 28 2008 - 14:45:46 CDT)
- Re: ABF simulations Chris Chipot (Tue Jul 29 2008 - 09:55:41 CDT)
ubuntu reads my psf as an audio file patrick wintrode (Mon Jul 28 2008 - 13:29:17 CDT)
- Re: ubuntu reads my psf as an audio file Axel Kohlmeyer (Mon Jul 28 2008 - 13:58:34 CDT)
how to run namd in cluster Anupam Nath Jha (Sun Jul 27 2008 - 13:23:22 CDT)
TMD + harmonic restraints Gianluca Interlandi (Sat Jul 26 2008 - 16:17:42 CDT)
Different dcd files for minimize and MD Lam T Nguyen (Fri Jul 25 2008 - 07:50:38 CDT)
Different dcd files for minimize and MD Lam T Nguyen (Thu Jul 24 2008 - 15:20:17 CDT)
NAMD + TMD on Abe Gianluca Interlandi (Thu Jul 24 2008 - 23:05:38 CDT)
- Re: NAMD + TMD on Abe Peter Freddolino (Fri Jul 25 2008 - 09:21:05 CDT)
  - Re: NAMD + TMD on Abe Gianluca Interlandi (Fri Jul 25 2008 - 12:58:08 CDT)
    - Re: NAMD + TMD on Abe Peter Freddolino (Fri Jul 25 2008 - 14:55:13 CDT)
Appending dcd when restarting a simulation pellegrini (Thu Jul 24 2008 - 03:17:02 CDT)
- Re: Appending dcd when restarting a simulation Axel Kohlmeyer (Thu Jul 24 2008 - 08:52:56 CDT)
- Re: Appending dcd when restarting a simulation Eric H. Lee (Thu Jul 24 2008 - 08:58:21 CDT)
- PME and infinite polymer Arturas Ziemys (Thu Jul 24 2008 - 20:59:33 CDT)
  - Re: PME and infinite polymer Peter Freddolino (Fri Jul 25 2008 - 09:23:28 CDT)
  - Re: PME and infinite polymer Axel Kohlmeyer (Fri Jul 25 2008 - 08:24:30 CDT)
    - Re: PME and infinite polymer Arturas Ziemys (Fri Jul 25 2008 - 09:26:53 CDT)
virtual and heavy hydrogens in NAMD rebeca_at_mmb.pcb.ub.es (Wed Jul 23 2008 - 09:22:12 CDT)
Protonation of nucleic acid phosphates in CHARMM for use in NAMD Hughtendo Martin (Tue Jul 22 2008 - 08:43:09 CDT)
MD problems jose correa (Sun Jul 20 2008 - 21:37:13 CDT)
- Re: MD problems Schreiner Eduard (Sun Jul 20 2008 - 22:13:47 CDT)
CHARMM parameters for H2S Raul Araya (Fri Jul 18 2008 - 17:51:50 CDT)
- Re: CHARMM parameters for H2S Jeffrey J. Potoff (Sat Jul 19 2008 - 22:34:21 CDT)
ERROR(S) IN THE CONFIGURATION FILE when running on a cluster. Lam T Nguyen (Fri Jul 18 2008 - 13:32:14 CDT)
- Re: ERROR(S) IN THE CONFIGURATION FILE when running on a cluster. Joaquim Rui Rodrigues (Fri Jul 18 2008 - 14:17:43 CDT)
- Re: ERROR(S) IN THE CONFIGURATION FILE when running on a cluster. Axel Kohlmeyer (Fri Jul 18 2008 - 14:18:02 CDT)
how to generate psf file using the AMBER topology file tinni sona (Fri Jul 18 2008 - 05:38:45 CDT)
- Re: how to generate psf file using the AMBER topology file Axel Kohlmeyer (Fri Jul 18 2008 - 12:09:48 CDT)
- Re: how to generate psf file using the AMBER topology file Peter Freddolino (Fri Jul 18 2008 - 15:30:45 CDT)
Problem while installing NAMD Karan Maroo (Thu Jul 17 2008 - 04:06:17 CDT)
Re: vmd-l: Fwd: memory overflow problem of Tcl scripting when dealing with trajectories(sorry for cross mailing...) Peter Freddolino (Wed Jul 16 2008 - 07:20:26 CDT)
memory overflow problem of Tcl scripting when dealing with trajectories bo liu (Wed Jul 16 2008 - 03:16:31 CDT)
- Re: memory overflow problem of Tcl scripting when dealing with trajectories Chris Harrison (Sun Jul 20 2008 - 15:21:16 CDT)
LangevinTemp and KE calculation E. Prabhu Raman (Tue Jul 15 2008 - 18:25:49 CDT)
- Re: LangevinTemp and KE calculation Peter Freddolino (Wed Jul 16 2008 - 06:53:01 CDT)
  - Re: LangevinTemp and KE calculation E. Prabhu Raman (Wed Jul 16 2008 - 12:56:22 CDT)
  - Constraining center of mass of monomers S.K. Ghosh (Wed Jul 16 2008 - 17:45:57 CDT)
Error in NAMD Time Steps Hsing Pao (Tue Jul 15 2008 - 14:29:36 CDT)
NAMD Timestep Hsing Pao (Mon Jul 14 2008 - 19:11:59 CDT)
trajectories jfgaff_at_ncsu.edu (Mon Jul 14 2008 - 13:38:39 CDT)
- Re: trajectories Schreiner Eduard (Mon Jul 14 2008 - 14:53:52 CDT)
- Re: trajectories Jerome Henin (Mon Jul 14 2008 - 14:45:23 CDT)
- Re: trajectories Anton Arkhipov (Mon Jul 14 2008 - 14:58:14 CDT)
NAMD OUTPUT Semorale (Sun Jul 13 2008 - 15:37:14 CDT)
- Re: NAMD OUTPUT Jerome Henin (Sun Jul 13 2008 - 16:37:39 CDT)
  - Re: NAMD OUTPUT Ramya Gamini (Sun Jul 13 2008 - 17:14:48 CDT)
cannot find -lsrfftw... collect2: ld returned 1 exit status Anupam Nath Jha (Sun Jul 13 2008 - 12:59:09 CDT)
- Re: cannot find -lsrfftw... collect2: ld returned 1 exit status Axel Kohlmeyer (Sun Jul 13 2008 - 15:54:54 CDT)
DNA simulation by NAMD sudipta sinha (Sun Jul 13 2008 - 06:07:20 CDT)
minimization and MD in one configuration file? NGUYEN LAM (Sat Jul 12 2008 - 10:46:38 CDT)
- RE: minimization and MD in one configuration file? JC Gumbart (Sat Jul 12 2008 - 13:13:52 CDT)
installation of charm-6.0 in ia-64 cluster machine Anupam Nath Jha (Fri Jul 11 2008 - 06:49:34 CDT)
- Re: installation of charm-6.0 in ia-64 cluster machine Peter Freddolino (Fri Jul 11 2008 - 12:23:30 CDT)
Hi,Thank you! Peter Murphy (Fri Jul 11 2008 - 03:46:57 CDT)
Hi,Thank you! Peter Murphy (Fri Jul 11 2008 - 03:35:29 CDT)
use of charmm27 & NPT ensemble for lipid bilayer simulation Ruchi Sachdeva (Fri Jul 11 2008 - 00:26:17 CDT)
- Re: use of charmm27 & NPT ensemble for lipid bilayer simulation JC Gumbart (Sat Jul 12 2008 - 22:07:00 CDT)
  - Re: use of charmm27 & NPT ensemble for lipid bilayer simulation Ruchi Sachdeva (Sun Jul 13 2008 - 23:09:57 CDT)
NAMD on blue gene BG/P Andrew Emerson (Thu Jul 10 2008 - 05:46:36 CDT)
- Re: NAMD on blue gene BG/P George Madalin Giambasu (Thu Jul 10 2008 - 17:00:50 CDT)
  - Re: NAMD on blue gene BG/P Andrew Emerson (Fri Jul 11 2008 - 05:44:16 CDT)
    - Re: NAMD on blue gene BG/P George Madalin Giambasu (Fri Jul 11 2008 - 10:17:27 CDT)
alkane-silicon_dioxide simulation Raul Araya Secchi (Thu Jul 10 2008 - 15:18:06 CDT)
- Re: alkane-silicon_dioxide simulation Eduardo Cruz-Chu (Thu Jul 10 2008 - 15:46:25 CDT)
WCA Particle Dave Rogers (Wed Jul 09 2008 - 21:45:48 CDT)
- Re: WCA Particle Peter Freddolino (Thu Jul 10 2008 - 11:25:51 CDT)
  - Re: WCA Particle Giovanni Bellesia (Thu Jul 10 2008 - 16:07:25 CDT)
    - Re: WCA Particle Joshua D. Moore (Wed Aug 06 2008 - 09:48:45 CDT)
TMD SIMULATION - RMSD DOUBT Semorale (Tue Jul 08 2008 - 20:05:37 CDT)
- Re: TMD SIMULATION - RMSD DOUBT Joshua Adelman (Tue Jul 08 2008 - 22:04:51 CDT)
  - Re: TMD SIMULATION - RMSD DOUBT Semorale (Wed Jul 09 2008 - 10:30:34 CDT)
Interaction energy abhijit ramachandran (Tue Jul 08 2008 - 15:57:47 CDT)
- Re: Interaction energy Peter Freddolino (Tue Jul 08 2008 - 21:07:10 CDT)
Maximum Velocities Alejandro Ortega (Tue Jul 08 2008 - 13:20:33 CDT)
- Re: Maximum Velocities Eric H. Lee (Tue Jul 08 2008 - 13:50:51 CDT)
- Re: Maximum Velocities Chris Harrison (Tue Jul 08 2008 - 15:33:19 CDT)
Re: NAMD 2.7 Claw Isthelaw (Tue Jul 08 2008 - 00:30:52 CDT)
unsubscribe namd-l Richard Swenson (Mon Jul 07 2008 - 14:36:39 CDT)
relating to NAMD Energy Plugin scripting bo liu (Sun Jul 06 2008 - 23:19:44 CDT)
- Re: relating to NAMD Energy Plugin scripting Peter Freddolino (Mon Jul 07 2008 - 12:47:25 CDT)
Implementation of TCL script in NAMD .conf file sudipta sinha (Sat Jul 05 2008 - 00:18:25 CDT)
- Re: Implementation of TCL script in NAMD .conf file Benjamin Bouvier (Mon Jul 07 2008 - 04:34:54 CDT)
won't launch on linux ubuntu cluster for a parallel run LinJia Qi (Fri Jul 04 2008 - 21:23:45 CDT)
won't launch on linux ubuntu cluster for a parallel run accomp lin (Fri Jul 04 2008 - 12:21:18 CDT)
- Re: won't launch on linux ubuntu cluster for a parallel run Peter Freddolino (Fri Jul 04 2008 - 22:34:03 CDT)
ABF Method Bonnie A Merchant (Wed Jul 02 2008 - 09:19:39 CDT)
- drop in Temp from NVT to NVE S.K. Ghosh (Wed Jul 02 2008 - 10:18:41 CDT)
  - Re: drop in Temp from NVT to NVE Peter Freddolino (Wed Jul 02 2008 - 10:49:15 CDT)
- Re: ABF Method Eric H. Lee (Wed Jul 02 2008 - 10:45:15 CDT)
- Re: ABF Method digenova (Thu Jul 03 2008 - 08:52:29 CDT)
Topology cartoon of proteins DEEPESH AGARWAL (Wed Jul 02 2008 - 06:13:59 CDT)
Avoiding alpha-helix distortions Valeria Losasso (Wed Jul 02 2008 - 03:38:20 CDT)
- Re: Avoiding alpha-helix distortions Peter Freddolino (Wed Jul 02 2008 - 07:59:15 CDT)
  - Re: Avoiding alpha-helix distortions Eric H. Lee (Wed Jul 02 2008 - 10:41:01 CDT)
Heat flux along CNT Andy Shelley (Tue Jul 01 2008 - 14:13:36 CDT)
2 dimension PBC politr_at_huji.ac.il (Tue Jul 01 2008 - 07:15:29 CDT)
palmytoilated Balazs JOJART (Mon Jun 30 2008 - 07:09:03 CDT)
NAMD 2.7? L. Michel Espinoza-Fonseca (Mon Jun 30 2008 - 06:42:59 CDT)
- Re: NAMD 2.7? Peter Freddolino (Mon Jun 30 2008 - 14:40:39 CDT)
  - Re: NAMD 2.7? Jerome Henin (Mon Jun 30 2008 - 15:52:29 CDT)
- Re: NAMD 2.7? Chris Harrison (Mon Jun 30 2008 - 12:54:29 CDT)
  - Re: NAMD 2.7? L. Michel Espinoza-Fonseca (Mon Jun 30 2008 - 14:15:38 CDT)
    - Re: NAMD 2.7? Davide Branduardi (Tue Jul 01 2008 - 02:04:26 CDT)
    - RE: NAMD 2.7? Branduardi Davide (Wed Jul 02 2008 - 02:14:27 CDT)
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carbohydrates: CHARMM versus AMBER Gianluca Interlandi (Fri Jun 27 2008 - 17:16:26 CDT)
- RE: carbohydrates: CHARMM versus AMBER Matthew Tessier (Wed Jul 02 2008 - 08:02:24 CDT)
carbohydrates: CHARMM versus AMBER Gianluca Interlandi (Fri Jun 27 2008 - 14:16:08 CDT)
- Re: carbohydrates: CHARMM versus AMBER L. Michel Espinoza-Fonseca (Fri Jun 27 2008 - 17:44:41 CDT)
Problem in making cyclic peptide Narang, Pooja, Ph.D. (Fri Jun 27 2008 - 15:24:38 CDT)
- Re: Problem in making cyclic peptide JC Gumbart (Fri Jun 27 2008 - 16:01:27 CDT)
- Re: Problem in making cyclic peptide Peter Freddolino (Fri Jun 27 2008 - 16:11:21 CDT)
Re: Running minimization, heating and FEP simulation within the same configuration file. Floris Buelens (Thu Jun 26 2008 - 02:46:41 CDT)
- Re: Running minimization, heating and FEP simulation within the same configuration file. Jawahar Neelankatan (Thu Jun 26 2008 - 21:44:25 CDT)
Cannot spot error in namd config file Claw Isthelaw (Thu Jun 26 2008 - 10:41:53 CDT)
Re: Output of forces. Osman Yogurtcu (Thu Jun 26 2008 - 02:30:25 CDT)
- Re: Output of forces. Hidekazu WATANABE (Fri Jun 27 2008 - 04:11:56 CDT)
Output of forces. Hidekazu WATANABE (Thu Jun 26 2008 - 00:26:51 CDT)
, Build your vocab (word power)-Get emails daily Fr.ee Deepesh (Thu Jun 26 2008 - 00:02:52 CDT)
MD for phospho-aspartate using NAMD sunita gupta (Wed Jun 25 2008 - 03:37:51 CDT)
Running minimization, heating and FEP simulation within the same configuration file. Jawahar Neelankatan (Tue Jun 24 2008 - 20:28:21 CDT)
charmrun not found Diego Alejandro Vargas (Tue Jun 24 2008 - 21:59:24 CDT)
- Re: charmrun not found Alexandre A. Vakhrouchev (Tue Jun 24 2008 - 22:50:45 CDT)
Problem regarding psfgen haosheng_at_hec.utah.edu (Tue Jun 24 2008 - 18:03:08 CDT)
- Re: Problem regarding psfgen Peter Freddolino (Tue Jun 24 2008 - 21:18:33 CDT)
problem with executing MPI program in NAMD simulation Yinglong Miao (Mon Jun 23 2008 - 17:12:56 CDT)
Incorrect PSF file for min.pme Eva Nong (Mon Jun 23 2008 - 15:32:58 CDT)
- Re: Incorrect PSF file for min.pme Peter Freddolino (Tue Jun 24 2008 - 10:37:34 CDT)
Dihedral scan in NAMD? Kamilla Kopec (Mon Jun 23 2008 - 10:06:30 CDT)
- Re: Dihedral scan in NAMD? L. Michel Espinoza-Fonseca (Mon Jun 23 2008 - 10:47:07 CDT)
  - Re: Dihedral scan in NAMD? Chris Chipot (Mon Jun 23 2008 - 15:21:57 CDT)
    - Re: Dihedral scan in NAMD? L. Michel Espinoza-Fonseca (Tue Jun 24 2008 - 02:23:53 CDT)
- Re: Dihedral scan in NAMD? Peter Freddolino (Mon Jun 23 2008 - 15:02:14 CDT)
psf file Christine Horejs DI (Mon Jun 23 2008 - 06:22:48 CDT)
- Re: psf file Peter Freddolino (Mon Jun 23 2008 - 06:54:08 CDT)
Impressive Glashutte timepieces Becky Peoples (Sat Jun 21 2008 - 22:17:24 CDT)
creation and equilibration of a monolayer creston . (Fri Jun 20 2008 - 16:01:06 CDT)
Typical maximization steps S.K. Ghosh (Fri Jun 20 2008 - 14:05:36 CDT)
- Re: Typical maximization steps JC Gumbart (Fri Jun 20 2008 - 21:23:44 CDT)
error messages with "reinitvels" Yinglong Miao (Fri Jun 20 2008 - 13:56:25 CDT)
mutate G->U? paco ty (Fri Jun 20 2008 - 11:16:13 CDT)
Large MD simulations and atom number limits with NAMD Andrew Thomas (Fri Jun 20 2008 - 09:53:50 CDT)
- Re: Large MD simulations and atom number limits with NAMD Peter Freddolino (Mon Jun 30 2008 - 14:43:08 CDT)
(no subject) Ariovaldo de Souza Junior (Fri Jun 20 2008 - 05:27:36 CDT)
problem compiling NAMD2.6 in a MacOSX-PPC Andrea Diaz (Thu Jun 19 2008 - 10:15:27 CDT)
Force Calibration Interaction abhijit ramachandran (Thu Jun 19 2008 - 17:31:57 CDT)
problem compiling NAMD2.6 in a MacOSX-PPC Andrea Diaz (Thu Jun 19 2008 - 16:30:57 CDT)
- Re: problem compiling NAMD2.6 in a MacOSX-PPC Peter Freddolino (Fri Jun 20 2008 - 08:16:56 CDT)
Simulation with non-periodic boundary condition S.K. Ghosh (Thu Jun 19 2008 - 13:36:50 CDT)
- Re: Simulation with non-periodic boundary condition Victor Ovchinnikov (Thu Jun 19 2008 - 15:15:47 CDT)
NVT simulation by NAMD sudipta sinha (Thu Jun 19 2008 - 08:06:50 CDT)
Time step is incompatible in the NAMD DCD file analyzed with CHARMM twshen (Wed Jun 18 2008 - 14:07:02 CDT)
amber parameters for congo red Shaheen Ahmed (Wed Jun 18 2008 - 15:29:22 CDT)
- Re: amber parameters for congo red L. Michel Espinoza-Fonseca (Wed Jun 18 2008 - 16:07:30 CDT)
  - Re: amber parameters for congo red Shaheen Ahmed (Thu Jun 19 2008 - 02:19:08 CDT)
    - Re: amber parameters for congo red L. Michel Espinoza-Fonseca (Thu Jun 19 2008 - 04:07:31 CDT)
Time step is incompatible in the NAMD DCD file analyzed with CHARMM tw shen (Wed Jun 18 2008 - 14:42:32 CDT)
- Re: Time step is incompatible in the NAMD DCD file analyzed with CHARMM Victor Ovchinnikov (Wed Jun 18 2008 - 16:35:42 CDT)
Time Step is Incompatible in the NAMD DCD Analyzed with CHARMM twshen (Wed Jun 18 2008 - 12:28:22 CDT)
Trouble in energy minimization with warning to increase cutoff Eva Nong (Tue Jun 17 2008 - 18:57:49 CDT)
- Re: Trouble in energy minimization with warning to increase cutoff Peter Freddolino (Wed Jun 18 2008 - 00:01:29 CDT)
2D periodic boundary condn & PME Harindar Keer (Tue Jun 17 2008 - 14:12:28 CDT)
Simulation stalled at startup Sean Law (Mon Jun 16 2008 - 11:01:06 CDT)
Problem with .conf file of NAMD sudipta sinha (Mon Jun 16 2008 - 06:30:57 CDT)
NAMD & CUDA, still in development ? Michael Heymann (Mon Jun 16 2008 - 06:40:24 CDT)
- Re: NAMD & CUDA, still in development ? Peter Freddolino (Tue Jun 17 2008 - 14:43:55 CDT)
NAMD log file analysis script problem (namdstats.tcl) sudipta sinha (Sat Jun 14 2008 - 13:39:32 CDT)
- Re: NAMD log file analysis script problem (namdstats.tcl) Demet Akten (Sun Jun 15 2008 - 03:35:49 CDT)
  - Re: NAMD log file analysis script problem (namdstats.tcl) Axel Kohlmeyer (Sun Jun 15 2008 - 13:09:50 CDT)
Charmm is not free so how to learn it abhijit ramachandran (Fri Jun 13 2008 - 15:01:50 CDT)
- Re: Charmm is not free so how to learn it Philip Peartree (Sun Jun 15 2008 - 09:38:02 CDT)
  - Re: Charmm is not free so how to learn it jfgaff_at_ncsu.edu (Sun Jun 15 2008 - 18:51:19 CDT)
use of 'measure hbonds' DEEPESH AGARWAL (Thu Jun 12 2008 - 23:54:34 CDT)
- Re: use of 'measure hbonds' Axel Kohlmeyer (Fri Jun 13 2008 - 07:43:12 CDT)
Seeking suggestions to decide on realistic configuration values S.K. Ghosh (Thu Jun 12 2008 - 14:40:27 CDT)
Language Used and Elementary doubts abhijit ramachandran (Thu Jun 12 2008 - 00:08:27 CDT)
- Re: Language Used and Elementary doubts Alexandre A. Vakhrouchev (Thu Jun 12 2008 - 12:15:43 CDT)
- Re: Language Used and Elementary doubts Peter Freddolino (Thu Jun 12 2008 - 12:26:50 CDT)
use of 'measure hbonds' DEEPESH AGARWAL (Thu Jun 12 2008 - 06:03:06 CDT)
- Re: use of 'measure hbonds' mon_sharma_at_research.iiit.ac.in (Thu Jun 12 2008 - 11:08:12 CDT)
ApoB structure Alexandre A. Vakhrouchev (Thu Jun 12 2008 - 01:12:02 CDT)
paramter snoze pa (Wed Jun 11 2008 - 17:44:10 CDT)
- Re: paramter JC Gumbart (Wed Jun 11 2008 - 21:08:26 CDT)
  - Re: paramter snoze pa (Thu Jun 12 2008 - 16:16:21 CDT)
  - Re: paramter snoze pa (Fri Jun 13 2008 - 10:37:55 CDT)
Velocity scaling and thermostatting both at a time sudipta sinha (Wed Jun 11 2008 - 13:36:46 CDT)
- Re: Velocity scaling and thermostatting both at a time Jerome Henin (Wed Jun 11 2008 - 17:37:24 CDT)
April promo on watches Priscilla Dahl (Tue Jun 10 2008 - 16:41:36 CDT)
Replica or Original? Terrence Hare (Tue Jun 10 2008 - 07:43:09 CDT)
Classic timepieces replicas Cole Cox (Mon Jun 09 2008 - 19:10:25 CDT)
- Re: Classic timepieces replicas Alexandre A. Vakhrouchev (Tue Jun 10 2008 - 04:41:40 CDT)
  - Re: Classic timepieces replicas Axel Kohlmeyer (Tue Jun 10 2008 - 04:37:57 CDT)
capping of end residues sudipta sinha (Mon Jun 09 2008 - 23:55:56 CDT)
psgfen patch Hatley, Jade M (Mon Jun 09 2008 - 12:05:15 CDT)
- Re: psgfen patch Peter Freddolino (Mon Jun 09 2008 - 23:09:06 CDT)
Re: Which conformation is more proper for the SMD Shulin Zhuang (Mon Jun 09 2008 - 13:21:57 CDT)
- Re: Which conformation is more proper for the SMD Eric H. Lee (Mon Jun 09 2008 - 13:47:27 CDT)
Inexpensive IWC watches Janie Sweeney (Mon Jun 09 2008 - 12:47:28 CDT)
Which conformation is more proper for the SMD Shulin Zhuang (Mon Jun 09 2008 - 11:43:56 CDT)
FW: Hydroxylysine parameters Elham Hamed (Mon Jun 09 2008 - 10:53:08 CDT)
Temperature rescaling and reassignment parameters sudipta sinha (Mon Jun 09 2008 - 10:04:24 CDT)
- Re: Temperature rescaling and reassignment parameters Alexandre A. Vakhrouchev (Mon Jun 09 2008 - 23:20:38 CDT)
  - Re: Temperature rescaling and reassignment parameters sudipta sinha (Mon Jun 09 2008 - 23:46:29 CDT)
    - Re: Temperature rescaling and reassignment parameters Alexandre A. Vakhrouchev (Tue Jun 10 2008 - 04:53:44 CDT)
    - Re: Temperature rescaling and reassignment parameters sudipta sinha (Tue Jun 10 2008 - 05:35:03 CDT)
Correctness of Simulation Results Rahul (Mon Jun 09 2008 - 09:16:13 CDT)
- Re: Correctness of Simulation Results Axel Kohlmeyer (Mon Jun 09 2008 - 12:03:06 CDT)
  - Re: Correctness of Simulation Results Rahul (Tue Jun 10 2008 - 10:15:56 CDT)
    - Re: Correctness of Simulation Results Peter Freddolino (Tue Jun 10 2008 - 11:45:03 CDT)
Temperature rescaling and reassignment parameters sudipta sinha (Mon Jun 09 2008 - 05:14:59 CDT)
Different Hbonds values on different machines using same script for same trajectories sunita gupta (Mon Jun 09 2008 - 02:29:57 CDT)
- Re: Different Hbonds values on different machines using same script for same trajectories John Stone (Tue Jun 10 2008 - 00:18:07 CDT)
- Re: Different Hbonds values on different machines using same script for same trajectories John Stone (Wed Jun 11 2008 - 03:11:11 CDT)
NAMD compilation on linux cluster sudipta sinha (Sun Jun 08 2008 - 10:55:36 CDT)
- Re: NAMD compilation on linux cluster Axel Kohlmeyer (Sun Jun 08 2008 - 11:32:26 CDT)
PME and r-RESPA issue in NAMD sudipta sinha (Sat Jun 07 2008 - 07:05:37 CDT)
- Re: PME and r-RESPA issue in NAMD Axel Kohlmeyer (Sat Jun 07 2008 - 09:50:59 CDT)
  - Re: PME and r-RESPA issue in NAMD Thomas C. Bishop (Fri Jun 20 2008 - 09:56:25 CDT)
output area JARROD EDWARD CHARLES NICKEL (Thu Jun 05 2008 - 15:26:49 CDT)
- Re: output area JC Gumbart (Thu Jun 05 2008 - 17:35:17 CDT)
free enrgy calculations - an additional information politr_at_huji.ac.il (Wed Jun 04 2008 - 07:07:01 CDT)
Multiple successive addforce calls Benjamin Bouvier (Thu Jun 05 2008 - 08:18:16 CDT)
- Re: Multiple successive addforce calls Benjamin Bouvier (Thu Jun 05 2008 - 12:35:31 CDT)
  - Re: Multiple successive addforce calls Gungor Ozer (Thu Jun 05 2008 - 13:53:12 CDT)
  - Re: Multiple successive addforce calls Peter Freddolino (Thu Jun 05 2008 - 14:02:46 CDT)
    - Re: Multiple successive addforce calls Benjamin Bouvier (Thu Jun 05 2008 - 15:05:40 CDT)
    - Re: Multiple successive addforce calls Peter Freddolino (Thu Jun 05 2008 - 15:25:31 CDT)
NAMD in water vs in vacuum Yang Gao (Thu Jun 05 2008 - 09:54:48 CDT)
Bond energy become Zero!!! Ming (Thu Jun 05 2008 - 04:17:01 CDT)
- Re: Bond energy become Zero!!! Peter Freddolino (Thu Jun 05 2008 - 08:25:55 CDT)
steepest descent technique DEEPESH AGARWAL (Thu Jun 05 2008 - 00:53:30 CDT)
- Re: steepest descent technique Peter Freddolino (Thu Jun 05 2008 - 08:32:43 CDT)
free energy calculations politr_at_huji.ac.il (Wed Jun 04 2008 - 05:34:01 CDT)
- Re: free energy calculations Eric H. Lee (Wed Jun 04 2008 - 11:28:13 CDT)
- Problem with TclBC when run in more than one processor fett_at_vtr.net (Wed Jun 04 2008 - 12:08:57 CDT)
  - Re: Problem with TclBC when run in more than one processor Peter Freddolino (Thu Jun 05 2008 - 08:36:51 CDT)
  - Re: Problem with TclBC when run in more than one processor Alexandre A. Vakhrouchev (Wed Jun 04 2008 - 22:52:43 CDT)
- Re: free energy calculations Peter Freddolino (Wed Jun 04 2008 - 11:52:02 CDT)
Thank you for your advices feng jack (Tue Jun 03 2008 - 11:15:41 CDT)
Postdoctoral Position in Scientific Computing David Brandon (Mon Jun 02 2008 - 15:08:45 CDT)
Average energy in NAMD feng jack (Sun Jun 01 2008 - 16:31:16 CDT)
- Re: Average energy in NAMD JC Gumbart (Sun Jun 01 2008 - 18:06:29 CDT)
  - Re: Average energy in NAMD Axel Kohlmeyer (Sun Jun 01 2008 - 19:22:51 CDT)
    - Re: Average energy in NAMD JC Gumbart (Sun Jun 01 2008 - 21:02:40 CDT)
- Re: Average energy in NAMD Axel Kohlmeyer (Sun Jun 01 2008 - 16:51:15 CDT)
Mindboggling Problem Related To NAMD2 Code Rahul (Sun Jun 01 2008 - 04:19:13 CDT)
- Re: Mindboggling Problem Related To NAMD2 Code Axel Kohlmeyer (Sun Jun 01 2008 - 08:01:34 CDT)
- Re: Mindboggling Problem Related To NAMD2 Code Peter Freddolino (Sun Jun 01 2008 - 09:56:21 CDT)
  - Re: Mindboggling Problem Related To NAMD2 Code Graham Jenkins (Mon Jun 02 2008 - 17:43:27 CDT)
(no subject) feng jack (Fri May 30 2008 - 16:04:44 CDT)
Building Namd on a linux cluster. Khaled Barakat (Thu May 29 2008 - 21:39:53 CDT)
- Re: Building Namd on a linux cluster. Alexandre A. Vakhrouchev (Fri May 30 2008 - 00:38:25 CDT)
  - Re: Building Namd on a linux cluster. Khaled Barakat (Fri May 30 2008 - 14:32:09 CDT)
    - Re: Building Namd on a linux cluster. Axel Kohlmeyer (Fri May 30 2008 - 14:41:27 CDT)
  - Re: Building Namd on a linux cluster. Khaled Barakat (Fri May 30 2008 - 19:30:23 CDT)
    - Re: Building Namd on a linux cluster. Axel Kohlmeyer (Fri May 30 2008 - 19:25:00 CDT)
- Re: Building Namd on a linux cluster. Axel Kohlmeyer (Fri May 30 2008 - 07:38:12 CDT)
aromatic-aromatic interaction ramya narasimhan (Thu May 29 2008 - 00:20:43 CDT)
- Re: aromatic-aromatic interaction L. Michel Espinoza-Fonseca (Fri May 30 2008 - 06:57:51 CDT)
benchmarking of NAMD: sustained performance (TF) satya work (Wed May 28 2008 - 22:47:30 CDT)
- Re: benchmarking of NAMD: sustained performance (TF) Philip Peartree (Thu May 29 2008 - 04:35:50 CDT)
- Re: benchmarking of NAMD: sustained performance (TF) Axel Kohlmeyer (Thu May 29 2008 - 09:05:40 CDT)
constraintScaling - FOR LOOP Semorale (Wed May 28 2008 - 20:29:23 CDT)
- Re: constraintScaling - FOR LOOP Peter Freddolino (Fri May 30 2008 - 08:30:07 CDT)
dihedral force constant jfgaff_at_ncsu.edu (Tue May 27 2008 - 18:38:06 CDT)
- Re: dihedral force constant Jerome Henin (Tue May 27 2008 - 20:38:40 CDT)
charmm parameter and topology files me00109_at_cc.uoi.gr (Tue May 27 2008 - 10:17:52 CDT)
- Re: charmm parameter and topology files Jerome Henin (Tue May 27 2008 - 11:20:30 CDT)
NAMD trajectory format Konrad Hinsen (Tue May 27 2008 - 02:41:29 CDT)
- Re: NAMD trajectory format Axel Kohlmeyer (Tue May 27 2008 - 05:27:04 CDT)
  - Re: NAMD trajectory format Konrad Hinsen (Wed May 28 2008 - 07:35:17 CDT)
Charm++ compilation sudipta sinha (Tue May 27 2008 - 01:51:12 CDT)
dihedral restraints "on-the-fly"? Sebastian Stolzenberg (Mon May 26 2008 - 19:40:32 CDT)
- Re: dihedral restraints "on-the-fly"? JC Gumbart (Mon May 26 2008 - 22:06:46 CDT)
- changing dcd output file DURING run? Sebastian Stolzenberg (Thu May 29 2008 - 12:49:36 CDT)
harmonic restraint between two atoms Esben A. Gad (Mon May 26 2008 - 03:55:16 CDT)
- Re: harmonic restraint between two atoms Leonardo Trabuco (Mon May 26 2008 - 11:34:27 CDT)
  - Re: harmonic restraint between two atoms Leonardo Trabuco (Mon May 26 2008 - 12:01:15 CDT)
PROTEIN VACUUM MINIMIZATION ERROR Semorale (Sat May 24 2008 - 10:24:47 CDT)
- Re: PROTEIN VACUUM MINIMIZATION ERROR Peter Freddolino (Sat May 24 2008 - 20:46:34 CDT)
REMD Khaled Barakat (Sat May 24 2008 - 02:58:54 CDT)
- Re: REMD Peter Freddolino (Sat May 24 2008 - 09:01:10 CDT)
  - Re: REMD Khaled Barakat (Sat May 24 2008 - 15:02:00 CDT)
    - Re: REMD Peter Freddolino (Sat May 24 2008 - 20:45:00 CDT)
  - Re: REMD Khaled Barakat (Sun May 25 2008 - 18:43:11 CDT)
Error Parsing Config File MIke S (Sat May 24 2008 - 00:01:43 CDT)
- Re: Error Parsing Config File Alexandre A. Vakhrouchev (Sat May 24 2008 - 03:06:29 CDT)
  - Re: Error Parsing Config File MIke S (Mon May 26 2008 - 15:46:19 CDT)
Acceptable pressure values Fabio Zegarra (Fri May 23 2008 - 17:24:22 CDT)
- Re: Acceptable pressure values Peter Freddolino (Sat May 24 2008 - 09:27:24 CDT)
  - Re: Acceptable pressure values Fabio Zegarra (Mon May 26 2008 - 19:32:21 CDT)
    - Re: Acceptable pressure values Peter Freddolino (Tue May 27 2008 - 14:33:00 CDT)
ABF:reversibility and number of samples Luca Bellucci (Fri May 23 2008 - 07:33:27 CDT)
- Re: ABF:reversibility and number of samples Chris Chipot (Fri May 23 2008 - 10:43:59 CDT)
  - Re: ABF:reversibility and number of samples Luca (Fri May 23 2008 - 14:26:03 CDT)
  - Re: ABF:reversibility and number of samples Subramanian Vaitheeswaran (Fri May 23 2008 - 16:55:53 CDT)
    - Re: ABF:reversibility and number of samples Jerome Henin (Fri May 23 2008 - 17:21:35 CDT)
- Re: ABF:reversibility and number of samples Jerome Henin (Fri May 23 2008 - 12:15:11 CDT)
  - Re: ABF:reversibility and number of samples Eric Cyr (Fri May 23 2008 - 15:11:29 CDT)
a question about equilibrium taojinwuhan_at_sohu.com (Wed May 21 2008 - 20:32:14 CDT)
- Re: a question about equilibrium Joshua Adelman (Wed May 21 2008 - 21:07:35 CDT)
Applying weak harmonic force between two proteins greddy1_at_umd.edu (Wed May 21 2008 - 11:12:18 CDT)
- Re: Applying weak harmonic force between two proteins Joshua Adelman (Wed May 21 2008 - 11:42:15 CDT)
  - Re: Applying weak harmonic force between two proteins Floris Buelens (Thu May 22 2008 - 09:06:57 CDT)
scaling the interaction energy Krishnan, Marimuthu (Wed May 21 2008 - 07:21:20 CDT)
Unable to edit files in NAMD folder. Alexandre A. Vakhrouchev (Wed May 21 2008 - 03:37:52 CDT)
- Re: Unable to edit files in NAMD folder. Low Soo Mei (Wed May 21 2008 - 05:40:21 CDT)
Unable to edit files in NAMD folder. Diego Alejandro Vargas (Tue May 20 2008 - 23:39:51 CDT)
- Re: Unable to edit files in NAMD folder. Diego Alejandro Vargas (Thu May 22 2008 - 13:31:59 CDT)
running namd with condor emir mahmut bahsi (Mon May 19 2008 - 15:42:38 CDT)
CFP: 3rd Annual CMM Workshop on QM/MM Simulations CMM QM/MM Workshop (Mon May 19 2008 - 13:43:55 CDT)
minimization of the squared gradient Krishnan, Marimuthu (Mon May 19 2008 - 01:53:05 CDT)
- Re: minimization of the squared gradient Peter Freddolino (Mon May 19 2008 - 06:40:33 CDT)
  - RE: minimization of the squared gradient Krishnan, Marimuthu (Mon May 19 2008 - 08:56:31 CDT)
  - Re: minimization of the squared gradient Victor Ovchinnikov (Mon May 19 2008 - 10:24:28 CDT)
scaling the interaction energy Krishnan, Marimuthu (Mon May 19 2008 - 01:41:53 CDT)
pair interaction Osman Yogurtcu (Fri May 16 2008 - 13:34:21 CDT)
- Re: pair interaction Osman Yogurtcu (Sat May 17 2008 - 05:54:14 CDT)
Re: vmd-l: Re: Truncated Octahedron for VMD and NAMD simulation Vlad Cojocaru (Fri May 16 2008 - 09:51:44 CDT)
Truncated Octahedron for VMD and NAMD simulation Yinglong Miao (Thu May 15 2008 - 14:31:48 CDT)
- Re: Truncated Octahedron for VMD and NAMD simulation George Madalin Giambasu (Thu May 15 2008 - 15:23:51 CDT)
Error: transport retry exceeded error Alexandre A. Vakhrouchev (Thu May 15 2008 - 13:41:21 CDT)
- Re: Error: transport retry exceeded error Axel Kohlmeyer (Fri May 16 2008 - 10:49:46 CDT)
  - Re: Error: transport retry exceeded error Alexandre A. Vakhrouchev (Sat May 17 2008 - 00:03:03 CDT)
    - Re: Error: transport retry exceeded error Axel Kohlmeyer (Sat May 17 2008 - 15:37:12 CDT)
NVE ENSEMBLE Semorale (Thu May 15 2008 - 10:24:21 CDT)
- Re: NVE ENSEMBLE Vlad Cojocaru (Fri May 16 2008 - 03:36:38 CDT)
  - Simulation of Thiolated Biotin-Streptavidin on Gold S.K. Ghosh (Tue May 20 2008 - 07:11:36 CDT)
Re: Energy plot script Subramanian Vaitheeswaran (Thu May 15 2008 - 07:28:20 CDT)
- Re: Energy plot script bo liu (Thu May 15 2008 - 13:00:23 CDT)
Energy plot script Alexandre A. Vakhrouchev (Wed May 14 2008 - 22:11:19 CDT)
how to prepare *.paramas file Kalyan chaitanya (Tue May 13 2008 - 17:48:54 CDT)
S-OXY CYSTEINE parameter snoze pa (Tue May 13 2008 - 13:53:57 CDT)
- Re: S-OXY CYSTEINE parameter snoze pa (Mon Jun 09 2008 - 16:19:38 CDT)
NAMD electrostatics no cutoff or switching Alvaro Foletti (Tue May 13 2008 - 12:44:01 CDT)
- Re: NAMD electrostatics no cutoff or switching Peter Freddolino (Tue May 13 2008 - 21:25:30 CDT)
ZINC parameter surendra negi (Tue May 13 2008 - 12:22:47 CDT)
- Re: ZINC parameter Jerome Henin (Tue May 13 2008 - 14:57:48 CDT)
DCD file size Alexandre A. Vakhrouchev (Mon May 12 2008 - 14:19:57 CDT)
- Re: DCD file size JC Gumbart (Mon May 12 2008 - 15:08:48 CDT)
  - Re: DCD file size Alexandre A. Vakhrouchev (Mon May 12 2008 - 21:50:25 CDT)
    - Re: DCD file size Peter Freddolino (Mon May 12 2008 - 21:56:26 CDT)
    - Re: DCD file size Joshua D. Moore (Tue May 13 2008 - 01:39:57 CDT)
puase MD integration to communicate between jobs Floris Buelens (Sun May 11 2008 - 12:31:50 CDT)
Run NPT ensemble simulation with sphericalBC? Yinglong Miao (Fri May 09 2008 - 13:37:04 CDT)
2 pdb files Christine Horejs DI (Fri May 09 2008 - 06:58:01 CDT)
- Re: 2 pdb files Peter Freddolino (Fri May 09 2008 - 07:15:00 CDT)
spermine force field bqluan (Thu May 08 2008 - 18:47:54 CDT)
spermine force field bqluan (Thu May 08 2008 - 17:24:01 CDT)
Trajectory file formats & structural alignment Wei Huang (Thu May 08 2008 - 15:46:13 CDT)
- Re: Trajectory file formats & structural alignment Giovanni Bellesia (Thu May 08 2008 - 18:00:18 CDT)
  - Re: Trajectory file formats & structural alignment Wei Huang (Tue May 13 2008 - 21:57:01 CDT)
    - RE: Trajectory file formats & structural alignment JC Gumbart (Wed May 14 2008 - 00:15:17 CDT)
running NAMD with ranger@tacc Lei Shi (Wed May 07 2008 - 13:08:50 CDT)
- Re: running NAMD with ranger@tacc Peter Freddolino (Wed May 07 2008 - 13:23:36 CDT)
recalculating energy using dcd file gurvisha_at_leadinvent.com (Wed May 07 2008 - 09:19:14 CDT)
- Re: recalculating energy using dcd file JC Gumbart (Wed May 07 2008 - 17:08:16 CDT)
pbc Ahlam Al-Rawi (Tue May 06 2008 - 18:41:33 CDT)
Negative Pressure Fabio Zegarra (Tue May 06 2008 - 15:44:53 CDT)
- Re: Negative Pressure Vlad Cojocaru (Wed May 07 2008 - 09:39:02 CDT)
Question about a shift in rmsd using fixedatom off snoze pa (Tue May 06 2008 - 11:47:45 CDT)
NAMDENERGY: function of 'cutoff' parameter when -pme option is enabled Ghalib Bello (Mon May 05 2008 - 23:02:45 CDT)
- Re: NAMDENERGY: function of 'cutoff' parameter when -pme option is enabled Peter Freddolino (Tue May 06 2008 - 00:37:54 CDT)
Re: BOUNCE namd-l@ks.uiuc.edu: Message too long (>40000 chars) snoze pa (Mon May 05 2008 - 16:49:43 CDT)
- Re: Re: BOUNCE namd-l@ks.uiuc.edu: Message too long (>40000 chars) snoze pa (Tue May 06 2008 - 10:20:47 CDT)
question related to rmsd snoze pa (Mon May 05 2008 - 15:03:07 CDT)
- Re: question related to rmsd JC Gumbart (Mon May 05 2008 - 16:19:47 CDT)
  - Re: question related to rmsd snoze pa (Mon May 05 2008 - 16:35:21 CDT)
    - Re: question related to rmsd JC Gumbart (Mon May 05 2008 - 17:58:43 CDT)
help with calcforces Prabhakar Bhimalapuram (Fri May 02 2008 - 13:32:22 CDT)
error on installing ImageMagick Hero (Thu May 01 2008 - 13:54:57 CDT)
- Re: error on installing ImageMagick Peter Freddolino (Thu May 01 2008 - 14:02:39 CDT)
- Re: error on installing ImageMagick Richard Law (Thu May 01 2008 - 14:53:37 CDT)
electrostatics NAMD vs CHARMM Arturas Ziemys (Thu May 01 2008 - 11:29:49 CDT)
langevin dynamics and random seeds Peter Freddolino (Thu May 01 2008 - 11:44:40 CDT)
How to save the animation movie into files? Hero (Thu May 01 2008 - 01:48:35 CDT)
- Re: How to save the animation movie into files? Jianhui Tian (Thu May 01 2008 - 09:16:50 CDT)
compilaton error Swarna Patra (Wed Apr 30 2008 - 23:32:45 CDT)
- Re: compilaton error Leonardo Trabuco (Thu May 01 2008 - 11:32:22 CDT)
  - Re: compilaton error Swarna Patra (Thu May 01 2008 - 20:04:47 CDT)
Running NAMD on cluster sudipta sinha (Wed Apr 30 2008 - 04:41:53 CDT)
- Re: Running NAMD on cluster Philip Peartree (Wed Apr 30 2008 - 07:21:28 CDT)
Neutral arginine patch in topology file. Alexandre F. G. (Tue Apr 29 2008 - 16:45:29 CDT)
- RE: Neutral arginine patch in topology file. JC Gumbart (Thu May 01 2008 - 00:15:28 CDT)
NAMD on a remote UNIX and VMD on local Windows - does this work? S.K. Ghosh (Tue Apr 29 2008 - 13:40:29 CDT)
- Re: NAMD on a remote UNIX and VMD on local Windows - does this work? Tao Wu (Tue Apr 29 2008 - 15:49:57 CDT)
NAMD on a remote UNIX and VMD on local Windows - does this work? S.K. Ghosh (Tue Apr 29 2008 - 13:31:34 CDT)
velocity units in .vel file Neelanjana Sengupta (Mon Apr 28 2008 - 15:21:06 CDT)
- Re: velocity units in .vel file Joshua D. Moore (Mon Apr 28 2008 - 17:47:48 CDT)
How to save the animation movie into files? Hero (Mon Apr 28 2008 - 00:23:49 CDT)
- Re: How to save the animation movie into files? Low Soo Mei (Mon Apr 28 2008 - 00:51:37 CDT)
A question about restaints force. Yang Gao (Fri Apr 25 2008 - 11:28:20 CDT)
q=D8=B8=B4=A3=BA=20Re:=20=20nodelist=20being=20ignore?= d during paralleling cong chen (Sun Apr 27 2008 - 21:50:34 CDT)
How to save vmd figures to jpg or tiff? Hero (Sun Apr 27 2008 - 16:18:35 CDT)
help with TCL forces script Jim Pfaendtner (Sun Apr 27 2008 - 05:47:30 CDT)
nodelist being ignored during paralleling cong chen (Sat Apr 26 2008 - 22:24:17 CDT)
How to play molecule trajectory with VMD? Hero (Sat Apr 26 2008 - 20:00:52 CDT)
tracing not available with CMK_OPTIMIZE! Semorale (Sat Apr 26 2008 - 16:26:13 CDT)
How to run namd2 on ubuntu linux? Hero (Sat Apr 26 2008 - 14:45:01 CDT)
- Re: How to run namd2 on ubuntu linux? Leandro Martínez (Sat Apr 26 2008 - 16:10:35 CDT)
Re: install VMD on Ubuntu Hero (Sat Apr 26 2008 - 14:38:19 CDT)
install VMD on Ubuntu Hero (Sat Apr 26 2008 - 14:09:39 CDT)
- Re: install VMD on Ubuntu Low Soo Mei (Sat Apr 26 2008 - 14:25:32 CDT)
Configurations-Statistical Mechanics Mert Gür (Sat Apr 26 2008 - 13:00:08 CDT)
How to install VMD and NAMD on Ubuntu? Hero (Sat Apr 26 2008 - 12:55:17 CDT)
FEP triangular bracket average Mert Gür (Sat Apr 26 2008 - 05:56:26 CDT)
- Re: FEP triangular bracket average Jerome Henin (Sat Apr 26 2008 - 11:30:37 CDT)
  - Re: FEP triangular bracket average Mert Gür (Sat Apr 26 2008 - 13:14:29 CDT)
    - Re: FEP triangular bracket average Jerome Henin (Sat Apr 26 2008 - 13:54:31 CDT)
    - Re: FEP triangular bracket average Mert Gür (Sat Apr 26 2008 - 15:26:21 CDT)
install NAMD on Ubuntu Hero (Fri Apr 25 2008 - 23:46:07 CDT)
- Re: install NAMD on Ubuntu Alexandre A. Vakhrouchev (Sat Apr 26 2008 - 01:12:30 CDT)
A question about restaints force. Yang Gao (Fri Apr 25 2008 - 15:23:01 CDT)
- Re: A question about restaints force. Gungor Ozer (Fri Apr 25 2008 - 16:17:13 CDT)
  - Re: A question about restaints force. Victor Ovchinnikov (Fri Apr 25 2008 - 17:48:40 CDT)
Time factor Alexandre A. Vakhrouchev (Thu Apr 24 2008 - 23:16:04 CDT)
TMD AND RIGIDBONDS Samuel Morales (Wed Apr 23 2008 - 20:50:43 CDT)
compiling namd: cannot find -lmodulecommlib Corenflos, Steven Charles (Wed Apr 23 2008 - 14:42:18 CDT)
reversing constant velocity SMD Jeff Forbes (Wed Apr 23 2008 - 14:36:16 CDT)
- Re: reversing constant velocity SMD Peter Freddolino (Thu Apr 24 2008 - 08:24:55 CDT)
VMD-NAMD-commands Vivek Sharma (Fri Apr 18 2008 - 23:06:12 CDT)
- Re: VMD-NAMD-commands Alexandre A. Vakhrouchev (Sat Apr 19 2008 - 00:16:08 CDT)
- Re: VMD-NAMD-commands Peter Freddolino (Sun Apr 20 2008 - 20:20:27 CDT)
  - Re: VMD-NAMD-commands Vivek Sharma (Sun Apr 20 2008 - 21:06:36 CDT)
Format of Binary Restart and Output Coordinate and Velocity Files Joshua D. Moore (Fri Apr 18 2008 - 19:34:20 CDT)
RE: Reading and writing Binary Restart or Output files with Fortran Joshua D. Moore (Fri Apr 18 2008 - 19:25:55 CDT)
- Re: RE: Reading and writing Binary Restart or Output files with Fortran V.Ovchinnikov (Sat Apr 19 2008 - 10:40:46 CDT)
  - Re: RE: Reading and writing Binary Restart or Output files with Fortran Leandro Martínez (Sat Apr 19 2008 - 12:51:58 CDT)
    - Re: RE: Reading and writing Binary Restart or Output files with Fortran V.Ovchinnikov (Sat Apr 19 2008 - 16:10:32 CDT)
question on ABF L. Michel Espinoza-Fonseca (Fri Apr 18 2008 - 18:40:08 CDT)
- Re: question on ABF Jerome Henin (Fri Apr 18 2008 - 22:14:45 CDT)
  - Re: question on ABF Chris Chipot (Mon Apr 21 2008 - 07:01:39 CDT)
    - Re: question on ABF L. Michel Espinoza-Fonseca (Mon May 05 2008 - 09:16:44 CDT)
  - RE: question on ABF Xu, Jiancong (Mon Apr 21 2008 - 10:35:16 CDT)
What does "cellOrigin" really mean? bo liu (Fri Apr 18 2008 - 09:38:56 CDT)
- What does "cellOrigin" really mean? bo liu (Wed Apr 23 2008 - 05:48:45 CDT)
  - Re: What does "cellOrigin" really mean? Alexandre A. Vakhrouchev (Wed Apr 23 2008 - 08:36:51 CDT)
Multiple Different Harmonic Restraint Defitions Joshua Adelman (Thu Apr 17 2008 - 20:13:23 CDT)
2 molecule pair interactions Arturas Ziemys (Wed Apr 16 2008 - 16:26:27 CDT)
- Re: 2 molecule pair interactions Peter Freddolino (Wed Apr 16 2008 - 17:11:52 CDT)
  - Re: 2 molecule pair interactions Ben Chern (Wed Apr 16 2008 - 23:49:33 CDT)
Which namd on amd64? Corenflos, Steven Charles (Tue Apr 15 2008 - 15:26:25 CDT)
- Re: Which namd on amd64? V.Ovchinnikov (Tue Apr 15 2008 - 17:19:43 CDT)
binary install question winsvern_at_isu.edu (Tue Apr 15 2008 - 15:23:29 CDT)
How to write different DCD files for separate MD runs in one simulation? Yinglong Miao (Tue Apr 15 2008 - 13:55:14 CDT)
- Re: How to write different DCD files for separate MD runs in one simulation? Peter Freddolino (Tue Apr 15 2008 - 14:07:03 CDT)
- Re: How to write different DCD files for separate MD runs in one simulation? V.Ovchinnikov (Tue Apr 15 2008 - 15:14:20 CDT)
  - Re: How to write different DCD files for separate MD runs in one simulation? Peter Freddolino (Tue Apr 15 2008 - 15:34:11 CDT)
    - Re: How to write different DCD files for separate MD runs in one simulation? V.Ovchinnikov (Tue Apr 15 2008 - 15:52:07 CDT)
    - Re: How to write different DCD files for separate MD runs in one simulation? Yinglong Miao (Tue Apr 15 2008 - 16:22:18 CDT)
Electrostatics cutoff with PME Gianluca Interlandi (Tue Apr 15 2008 - 13:01:48 CDT)
- Re: Electrostatics cutoff with PME L. Michel Espinoza-Fonseca (Tue Apr 15 2008 - 14:00:03 CDT)
  - Re: Electrostatics cutoff with PME Christopher Gillespie (Tue Apr 15 2008 - 15:21:06 CDT)
- Re: Electrostatics cutoff with PME Peter Freddolino (Tue Apr 15 2008 - 14:31:35 CDT)
temperature stepping during heating Low Soo Mei (Tue Apr 15 2008 - 05:21:43 CDT)
- Re: temperature stepping during heating JC Gumbart (Thu Apr 17 2008 - 16:35:13 CDT)
  - Re: temperature stepping during heating Low Soo Mei (Thu Apr 17 2008 - 21:14:34 CDT)
    - Re: temperature stepping during heating Low Soo Mei (Fri Apr 18 2008 - 04:00:41 CDT)
Problem with NAMD crashing without warning or error messages Jacob Durrant (Mon Apr 14 2008 - 20:36:25 CDT)
help regarding NAMD equilibration snoze pa (Mon Apr 14 2008 - 18:11:46 CDT)
- Re: help regarding NAMD equilibration Low Soo Mei (Tue Apr 15 2008 - 01:05:25 CDT)
  - Re: help regarding NAMD equilibration snoze pa (Tue Apr 15 2008 - 10:39:54 CDT)
  - Re: help regarding NAMD equilibration Dr. Luis Rosales León (Tue Apr 15 2008 - 12:39:24 CDT)
NAMD CVS RUN ERROR Samuel Morales (Mon Apr 14 2008 - 16:13:31 CDT)
rmsd_RNA_DNA sripad chandan (Mon Apr 14 2008 - 05:27:45 CDT)
restarting ABF simulation Luca Bellucci (Mon Apr 14 2008 - 04:14:19 CDT)
- Re: restarting ABF simulation Jerome Henin (Mon Apr 14 2008 - 06:43:40 CDT)
problem with VMD installation- libstdc++.so.5 => not found steve_at_phas.ubc.ca (Sat Apr 12 2008 - 22:03:05 CDT)
- Re: problem with VMD installation- libstdc++.so.