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NAMD-L: By Thread

By Thread

3203 messages sorted by: [ author ] [ date ] [ subject ] [ attachment ]
About this archive

Starting: Sat Jan 01 2011 - 12:21:40 CST
Ending: Fri May 25 2012 - 14:53:54 CDT

AW: AW: Generating force field for novel molecules Norman Geist (Fri May 25 2012 - 00:56:07 CDT)
- Re: AW: AW: Generating force field for novel molecules Sajad Falsafi-Zadeh (Fri May 25 2012 - 01:50:35 CDT)
  - Re: AW: AW: Generating force field for novel molecules Axel Kohlmeyer (Fri May 25 2012 - 05:44:42 CDT)
- Re: AW: AW: Generating force field for novel molecules Jeffrey Potoff (Fri May 25 2012 - 09:34:11 CDT)
- Re: AW: AW: Generating force field for novel molecules Mayne, Christopher G (Fri May 25 2012 - 12:07:43 CDT)
queries about "Tclforces" utility in NAMD harish vashisth (Fri May 25 2012 - 00:06:28 CDT)
- AW: queries about "Tclforces" utility in NAMD Norman Geist (Fri May 25 2012 - 01:11:47 CDT)
- Re: queries about "Tclforces" utility in NAMD Jérôme Hénin (Fri May 25 2012 - 02:48:01 CDT)
  - Re: queries about "Tclforces" utility in NAMD Axel Kohlmeyer (Fri May 25 2012 - 05:54:27 CDT)
    - Re: queries about "Tclforces" utility in NAMD harish vashisth (Fri May 25 2012 - 09:57:43 CDT)
  - Re: queries about "Tclforces" utility in NAMD harish vashisth (Fri May 25 2012 - 10:06:39 CDT)
Advertisement Workshop Aspen Center for Physics MARK PLUMMER (Thu May 24 2012 - 16:04:35 CDT)
Simultaneous calculation on CPU-only nodes and CPU/GPU node (with or without rCUDA) Benjamin Merget (Thu May 24 2012 - 04:51:06 CDT)
- AW: Simultaneous calculation on CPU-only nodes and CPU/GPU node (with or without rCUDA) Norman Geist (Fri May 25 2012 - 01:10:17 CDT)
- Re: Simultaneous calculation on CPU-only nodes and CPU/GPU node (with or without rCUDA) Axel Kohlmeyer (Fri May 25 2012 - 05:39:37 CDT)
hbonds colvar component Vlad Cojocaru (Thu May 24 2012 - 02:13:29 CDT)
- Re: hbonds colvar component Giacomo Fiorin (Thu May 24 2012 - 08:58:04 CDT)
  - Re: hbonds colvar component Vlad Cojocaru (Thu May 24 2012 - 09:47:45 CDT)
    - Re: hbonds colvar component Giacomo Fiorin (Thu May 24 2012 - 10:12:51 CDT)
protein folding by simulated annealing method Puspita Halder (Thu May 24 2012 - 00:01:25 CDT)
Issues with 'Gyration' in Colvars module Shaon Chakrabarti (Wed May 23 2012 - 14:48:35 CDT)
- Re: Issues with 'Gyration' in Colvars module Aron Broom (Wed May 23 2012 - 14:56:49 CDT)
  - Re: Issues with 'Gyration' in Colvars module Giacomo Fiorin (Wed May 23 2012 - 15:27:51 CDT)
(no subject) Puspita Halder (Wed May 23 2012 - 07:45:48 CDT)
Generating force field for novel molecules MOHAMMAD JAVAD AGHAEI (Wed May 23 2012 - 03:16:36 CDT)
- AW: Generating force field for novel molecules Norman Geist (Thu May 24 2012 - 00:15:11 CDT)
TMD output format Payne, Christy (Mon May 21 2012 - 10:00:24 CDT)
- Re: TMD output format JC Gumbart (Mon May 21 2012 - 11:34:17 CDT)
Parameters for Cesium Burgess, Don E (Thu May 17 2012 - 11:43:44 CDT)
FEP - Dynamic charges John Baker (Tue May 15 2012 - 12:38:59 CDT)
- AW: FEP - Dynamic charges Norman Geist (Wed May 16 2012 - 00:48:20 CDT)
- Re: FEP - Dynamic charges Jérôme Hénin (Wed May 16 2012 - 03:03:54 CDT)
MDFF for protein complex Hamze Rahimi (Mon May 14 2012 - 09:22:42 CDT)
- MDFF for huge trajectories Samuel Flores (Wed May 16 2012 - 14:31:53 CDT)
  - Re: MDFF for huge trajectories Ajasja LjubetiÄ (Wed May 16 2012 - 16:36:41 CDT)
    - Re: MDFF for huge trajectories Samuel Flores (Wed May 16 2012 - 17:20:29 CDT)
    - Re: MDFF for huge trajectories Samuel Flores (Wed May 16 2012 - 17:54:56 CDT)
five 'ERROR' in the log file of NAMD2.9 ypg (Sun May 13 2012 - 02:15:27 CDT)
- RE: five 'ERROR' in the log file of NAMD2.9 JC Gumbart (Sun May 13 2012 - 08:23:53 CDT)
- RE: five 'ERROR' in the log file of NAMD2.9 ypg (Sun May 13 2012 - 09:13:49 CDT)
Problem with Methane-Methane PMF Shaon Chakrabarti (Fri May 11 2012 - 16:08:23 CDT)
- Re: Problem with Methane-Methane PMF Aron Broom (Fri May 11 2012 - 16:38:03 CDT)
- Re: Problem with Methane-Methane PMF Giacomo Fiorin (Fri May 11 2012 - 16:40:03 CDT)
  - Re: Problem with Methane-Methane PMF Shaon Chakrabarti (Sat May 12 2012 - 13:46:01 CDT)
Atomic Radii for GB Implicit Solvent Aron Broom (Fri May 11 2012 - 14:40:12 CDT)
fixed bond length Mortaza Aghtar (Fri May 11 2012 - 10:51:01 CDT)
- Re: fixed bond length Ajasja LjubetiÄ (Fri May 11 2012 - 11:06:35 CDT)
  - Re: fixed bond length Mortaza Aghtar (Fri May 11 2012 - 11:29:12 CDT)
    - Re: fixed bond length Aron Broom (Fri May 11 2012 - 13:25:14 CDT)
    - AW: fixed bond length Norman Geist (Mon May 14 2012 - 01:23:05 CDT)
Multicore executable error Caitlin Scott (Wed May 09 2012 - 13:05:20 CDT)
- Re: Multicore executable error Chris Harrison (Wed May 09 2012 - 16:21:02 CDT)
Fwd: AW: stereo-chemical inversion during MD Gordon Wells (Wed May 09 2012 - 10:04:04 CDT)
Fwd: Re: AW: stereo-chemical inversion during MD Branko (Tue May 08 2012 - 03:26:25 CDT)
- Re: Re: AW: stereo-chemical inversion during MD Axel Kohlmeyer (Tue May 08 2012 - 08:33:03 CDT)
  - Re: AW: stereo-chemical inversion during MD Branko (Tue May 08 2012 - 10:51:46 CDT)
Fwd: stereo-chemical inversion during MD Francesco Pietra (Tue May 08 2012 - 01:59:49 CDT)
stereo-chemical inversion during MD Gordon Wells (Mon May 07 2012 - 12:01:24 CDT)
- AW: stereo-chemical inversion during MD Norman Geist (Tue May 08 2012 - 01:01:05 CDT)
  - Re: AW: stereo-chemical inversion during MD Branko (Tue May 08 2012 - 15:03:08 CDT)
- Re: stereo-chemical inversion during MD Branko (Tue May 08 2012 - 04:53:27 CDT)
Specific colvar component needed. Germán Andrés Miño (Mon May 07 2012 - 10:55:14 CDT)
- Re: Specific colvar component needed. Aron Broom (Mon May 07 2012 - 11:02:30 CDT)
  - Re: Specific colvar component needed. Giacomo Fiorin (Mon May 07 2012 - 11:05:41 CDT)
Hole Buddhadev Maiti (Fri May 04 2012 - 22:47:27 CDT)
Fwd: Re: charmrun setup Branko (Sat May 05 2012 - 13:37:05 CDT)
- AW: Re: charmrun setup Norman Geist (Mon May 07 2012 - 00:49:22 CDT)
charmrun setup Pedro Armando Ojeda May (Sat May 05 2012 - 13:14:12 CDT)
Applying TclBC script every x steps Error Maria Pikoula (Fri May 04 2012 - 16:46:03 CDT)
Concerning Restarting Multiple Walkers MetaDynamics Aron Broom (Fri May 04 2012 - 15:52:41 CDT)
- Re: Concerning Restarting Multiple Walkers MetaDynamics Aron Broom (Fri May 04 2012 - 15:54:28 CDT)
  - Re: Re: Concerning Restarting Multiple Walkers MetaDynamics Giacomo Fiorin (Fri May 04 2012 - 16:30:26 CDT)
    - Re: Re: Concerning Restarting Multiple Walkers MetaDynamics Aron Broom (Fri May 04 2012 - 16:33:39 CDT)
A question about the CHARMM force field Hall McDull (Fri May 04 2012 - 03:32:30 CDT)
- A question about the CHARMM force field Hall McDull (Fri May 04 2012 - 07:33:48 CDT)
  - Re: A question about the CHARMM force field Axel Kohlmeyer (Fri May 04 2012 - 08:12:26 CDT)
Umbrella sampling-reliability of results Parisa Akhski (Fri May 04 2012 - 09:20:17 CDT)
- Re: Umbrella sampling-reliability of results Aron Broom (Fri May 04 2012 - 09:41:35 CDT)
Periodic cell has become too small lecan (Fri May 04 2012 - 00:19:38 CDT)
forces saved in forcedcd Xiaohu Li (Thu May 03 2012 - 15:43:50 CDT)
- Re: forces saved in forcedcd Chris Harrison (Thu May 03 2012 - 18:42:19 CDT)
  - Re: forces saved in forcedcd Xiaohu Li (Thu May 03 2012 - 19:51:36 CDT)
NAMD 2.9 released Jim Phillips (Thu May 03 2012 - 10:27:09 CDT)
Need help preventing hydration of the lipid-protein interface in my system Syed Kashif Zafar (Thu May 03 2012 - 05:48:48 CDT)
- Re: Need help preventing hydration of the lipid-protein interface in my system Chris Harrison (Thu May 03 2012 - 18:31:50 CDT)
a question about ensemble Albert (Thu May 03 2012 - 01:04:58 CDT)
tclBC incorrect output P.-L. Chau (Wed May 02 2012 - 22:18:21 CDT)
- AW: tclBC incorrect output Norman Geist (Thu May 03 2012 - 00:55:58 CDT)
  - Re: AW: tclBC incorrect output P.-L. Chau (Thu May 03 2012 - 01:44:17 CDT)
Question about targetsNumSteps in ColVar Wang Yi (Wed May 02 2012 - 08:52:26 CDT)
- Re: Question about targetsNumSteps in ColVar Giacomo Fiorin (Wed May 02 2012 - 11:38:18 CDT)
  - Re: Question about targetsNumSteps in ColVar Wang Yi (Wed May 02 2012 - 11:54:20 CDT)
    - Re: Question about targetsNumSteps in ColVar Giacomo Fiorin (Wed May 02 2012 - 11:57:34 CDT)
    - Re: Question about targetsNumSteps in ColVar Wang Yi (Wed May 02 2012 - 12:05:16 CDT)
ion placement method vs total energy of the system raghav singh (Mon Apr 30 2012 - 10:25:42 CDT)
- Re: ion placement method vs total energy of the system Anurag Sethi (Mon Apr 30 2012 - 10:36:59 CDT)
non integral charges raghav singh (Mon Apr 30 2012 - 08:06:15 CDT)
- Re: non integral charges Branko (Mon Apr 30 2012 - 08:24:29 CDT)
nucleic acids - total charge raghav singh (Mon Apr 30 2012 - 04:55:38 CDT)
- Re: nucleic acids - total charge Boyang Wang (Tue May 01 2012 - 02:50:35 CDT)
  - Re: nucleic acids - total charge Axel Kohlmeyer (Tue May 01 2012 - 07:37:18 CDT)
- Re: nucleic acids - total charge JC Gumbart (Tue May 01 2012 - 10:48:19 CDT)
  - Re: nucleic acids - total charge Raghav (Tue May 01 2012 - 11:18:22 CDT)
    - Re: nucleic acids - total charge JC Gumbart (Tue May 01 2012 - 11:34:48 CDT)
AW: AW: Set up NPT simulation in cubic PBC-box Norman Geist (Mon Apr 30 2012 - 00:29:21 CDT)
AW: AW: Set up NPT simulation in cubic PBC-box Norman Geist (Mon Apr 30 2012 - 00:21:02 CDT)
non integer total charge raghav singh (Sat Apr 28 2012 - 21:16:02 CDT)
- Re: non integer total charge Chris Harrison (Sat Apr 28 2012 - 21:23:42 CDT)
fwd: sara (Fri Apr 27 2012 - 21:51:50 CDT)
fwd: sara (Fri Apr 27 2012 - 21:51:49 CDT)
Go model in NAMD? Bin Zhang (Thu Apr 26 2012 - 16:52:26 CDT)
Set up NPT simulation in cubic PBC-box Xi Cheng (Thu Apr 26 2012 - 16:22:33 CDT)
- AW: Set up NPT simulation in cubic PBC-box Norman Geist (Fri Apr 27 2012 - 00:42:29 CDT)
  - Re: AW: Set up NPT simulation in cubic PBC-box Xi Cheng (Fri Apr 27 2012 - 10:22:56 CDT)
  - Re: AW: Set up NPT simulation in cubic PBC-box Aron Broom (Mon Apr 30 2012 - 01:40:35 CDT)
- Re: Set up NPT simulation in cubic PBC-box Axel Kohlmeyer (Fri Apr 27 2012 - 10:54:15 CDT)
  - Re: Set up NPT simulation in cubic PBC-box Xi Cheng (Fri Apr 27 2012 - 11:08:42 CDT)
    - Re: Set up NPT simulation in cubic PBC-box Axel Kohlmeyer (Fri Apr 27 2012 - 11:11:30 CDT)
GPCR MD Tutorial Anirban Ghosh (Thu Apr 26 2012 - 04:18:08 CDT)
constant pulling velocity in SMD Jiao, Dian NMN (-EXP) (Wed Apr 25 2012 - 14:41:06 CDT)
- Re: constant pulling velocity in SMD Axel Kohlmeyer (Wed Apr 25 2012 - 17:16:15 CDT)
- constant pulling velocity in SMD Jiao, Dian NMN (-EXP) (Thu Apr 26 2012 - 11:33:07 CDT)
  - Re: constant pulling velocity in SMD JC Gumbart (Thu Apr 26 2012 - 18:15:42 CDT)
About error in .pgn error in vmd cmd prompt Vidhya Sankar (Wed Apr 25 2012 - 03:00:33 CDT)
In-Residence Training at the Theoretical & Computational Biophysics Group, July 16-27, 2012 TCBG Workshop (Tue Apr 24 2012 - 14:06:22 CDT)
- Martini parameter files Chiara Cosenza unina (Thu Apr 26 2012 - 04:45:18 CDT)
FEP using amber topologies felmerino_at_uchile.cl (Mon Apr 23 2012 - 17:46:17 CDT)
Question about GPUs hardware. Cesar Millan (Mon Apr 23 2012 - 17:32:01 CDT)
- Re: Question about GPUs hardware. Aron Broom (Mon Apr 23 2012 - 17:57:56 CDT)
  - Re: Question about GPUs hardware. Aron Broom (Mon Apr 23 2012 - 19:51:44 CDT)
  - AW: Question about GPUs hardware. Norman Geist (Tue Apr 24 2012 - 01:11:01 CDT)
FEP difficulties between two ion species Jeremy Parlin (Mon Apr 23 2012 - 16:38:31 CDT)
- Re: FEP difficulties between two ion species Jérôme Hénin (Tue Apr 24 2012 - 07:19:45 CDT)
  - Re: FEP difficulties between two ion species Niklaus Johner (Fri May 18 2012 - 09:13:06 CDT)
    - Re: FEP difficulties between two ion species Jérôme Hénin (Sat May 19 2012 - 15:11:55 CDT)
    - Re: FEP difficulties between two ion species Jérôme Hénin (Wed May 23 2012 - 13:21:26 CDT)
AW: vmd-l: segmentation fault with NAMDenergy Norman Geist (Mon Apr 23 2012 - 00:52:17 CDT)
AW: problem with gpu namd 2.9b3 Norman Geist (Mon Apr 23 2012 - 00:45:58 CDT)
- Re: problem with gpu namd 2.9b3 Peter Jones (Mon Apr 23 2012 - 01:00:11 CDT)
(no subject) Taruna Gupta (Sun Apr 22 2012 - 12:37:42 CDT)
- Re: Axel Kohlmeyer (Sun Apr 22 2012 - 12:49:15 CDT)
  - Re: Aron Broom (Sun Apr 22 2012 - 16:07:24 CDT)
Simulation Using Both NAMD and VMD Ajith Rathnaweera Rajapaksha Mudalige (Fri Apr 20 2012 - 17:05:28 CDT)
- Re: Simulation Using Both NAMD and VMD Axel Kohlmeyer (Fri Apr 20 2012 - 17:10:30 CDT)
  - Re: Simulation Using Both NAMD and VMD Aron Broom (Fri Apr 20 2012 - 17:30:14 CDT)
Bug with BOUNDARY energy in postprocessing? David Minh (Fri Apr 20 2012 - 13:03:31 CDT)
- Re: Bug with BOUNDARY energy in postprocessing? David Minh (Fri Apr 20 2012 - 13:10:29 CDT)
  - Re: Re: Bug with BOUNDARY energy in postprocessing? Chris Harrison (Fri Apr 20 2012 - 19:41:37 CDT)
Re: problem with gpu namd 2.9b3 Aron Broom (Fri Apr 20 2012 - 09:25:40 CDT)
What is the means of system-min.conf in the Residue-Based Coarse tutorial? javacfish (Fri Apr 20 2012 - 01:17:57 CDT)
- Re: What is the means of system-min.conf in the Residue-Based Coarse tutorial? Ramya Gamini (Fri Apr 20 2012 - 14:32:41 CDT)
segmentation fault with NAMDenergy amin_at_imtech.res.in (Thu Apr 19 2012 - 10:19:55 CDT)
- AW: segmentation fault with NAMDenergy Norman Geist (Fri Apr 20 2012 - 01:00:23 CDT)
problem with gpu namd 2.9b3 Peter Jones (Thu Apr 19 2012 - 04:30:42 CDT)
- AW: problem with gpu namd 2.9b3 Norman Geist (Fri Apr 20 2012 - 00:45:50 CDT)
Using Measure SASA in NAMD Simulations Ajith Rathnaweera Rajapaksha Mudalige (Mon Apr 16 2012 - 20:22:28 CDT)
- Re: Using Measure SASA in NAMD Simulations Aron Broom (Tue Apr 17 2012 - 02:02:16 CDT)
Amber topology felmerino_at_uchile.cl (Mon Apr 16 2012 - 16:13:54 CDT)
creating a protonated cytidine entry raghav singh (Mon Apr 16 2012 - 06:35:15 CDT)
psfgen warnings Vidhya Sankar (Sun Apr 15 2012 - 01:27:14 CDT)
- Re: psfgen warnings Syed Kashif Zafar (Sun Apr 15 2012 - 23:28:49 CDT)
- RE: psfgen warnings hannes.loeffler_at_stfc.ac.uk (Mon Apr 16 2012 - 02:35:35 CDT)
Abouf Psfgen error Syed Kashif Zafar (Sat Apr 14 2012 - 14:50:37 CDT)
About psfgen error Vidhya Sankar (Sat Apr 14 2012 - 11:15:01 CDT)
namd and x-plor Hasan haska (Sat Apr 14 2012 - 06:19:57 CDT)
- Re: namd and x-plor Jernej Zidar (Sat Apr 14 2012 - 08:16:08 CDT)
About error during creation of psf file Vidhya Sankar (Sat Apr 14 2012 - 01:28:27 CDT)
- Re: About error during creation of psf file flavio seixas (Thu Apr 19 2012 - 13:48:42 CDT)
(no subject) Vidhya Sankar (Sat Apr 14 2012 - 01:26:21 CDT)
- (no subject) Hannes Loeffler (Mon Apr 16 2012 - 03:34:41 CDT)
- (no subject) David Rogers (Wed Apr 18 2012 - 23:21:43 CDT)
about molecular axis Namd Namd (Wed Apr 11 2012 - 05:40:30 CDT)
fatal error running namd on Mac Jiao, Dian NMN (-EXP) (Tue Apr 10 2012 - 17:53:54 CDT)
- Re: fatal error running namd on Mac Aron Broom (Tue Apr 10 2012 - 18:04:25 CDT)
  - Re: fatal error running namd on Mac JC Gumbart (Tue Apr 10 2012 - 20:25:46 CDT)
  - Re: fatal error running namd on Mac johan strumpfer (Tue Apr 10 2012 - 19:05:26 CDT)
Importing a DCD into Mathematica Ajasja LjubetiÄ (Tue Apr 10 2012 - 14:58:30 CDT)
- Re: Importing a DCD into Mathematica Branko (Tue Apr 10 2012 - 15:09:51 CDT)
  - Re: Importing a DCD into Mathematica Ajasja LjubetiÄ (Tue Apr 10 2012 - 16:38:24 CDT)
User-defined forces in NAMD Ali Ghaffaari (Tue Apr 10 2012 - 06:38:13 CDT)
- Re: User-defined forces in NAMD Axel Kohlmeyer (Tue Apr 10 2012 - 07:16:18 CDT)
  - Re: User-defined forces in NAMD Ehsan Ban (Tue Apr 10 2012 - 11:55:30 CDT)
FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE AUC Kiarash Hosseini (Tue Apr 10 2012 - 04:24:10 CDT)
NAMD 2.9b3 colvars oddity Aron Broom (Mon Apr 09 2012 - 20:48:32 CDT)
- Re: NAMD 2.9b3 colvars oddity Giacomo Fiorin (Tue Apr 10 2012 - 16:54:39 CDT)
how to generate psf for membrane+protein Jiao, Dian NMN (-EXP) (Mon Apr 09 2012 - 18:16:59 CDT)
Nonzero BOUNDARY ENERGY without periodic boundary conditions David Minh (Mon Apr 09 2012 - 12:36:25 CDT)
- Re: Nonzero BOUNDARY ENERGY without periodic boundary conditions JC Gumbart (Mon Apr 09 2012 - 18:27:33 CDT)
  - Re: Nonzero BOUNDARY ENERGY without periodic boundary conditions David Minh (Tue Apr 10 2012 - 08:35:37 CDT)
Galilean Invariant Thermostat Ismail, Mohd F. (Sun Apr 08 2012 - 18:26:38 CDT)
- Re: Galilean Invariant Thermostat Jérôme Hénin (Mon Apr 09 2012 - 04:43:37 CDT)
Sufficiently large values for 'firsttimestep' can lead to immediate simulation abort. Nikolaos Glykos (Sun Apr 08 2012 - 12:25:15 CDT)
- Re: Sufficiently large values for 'firsttimestep' can lead to immediate simulation abort. Axel Kohlmeyer (Sun Apr 08 2012 - 12:38:10 CDT)
  - Re: Sufficiently large values for 'firsttimestep' can lead to immediate simulation abort. Nikolaos Glykos (Sun Apr 08 2012 - 13:08:59 CDT)
Re: NAMD 2.9b2-cuda does not scale well compared to NAMD 2.8 (solved) Thomas Albers (Sat Apr 07 2012 - 16:44:35 CDT)
- Re: Re: NAMD 2.9b2-cuda does not scale well compared to NAMD 2.8 (solved) Jim Phillips (Fri Apr 27 2012 - 14:10:20 CDT)
  - Re: Re: NAMD 2.9b2-cuda does not scale well compared to NAMD 2.8 (solved) Thomas Albers (Sun Apr 29 2012 - 08:33:54 CDT)
NAMD 2.9b3 released Jim Phillips (Fri Apr 06 2012 - 08:38:23 CDT)
multicore versus net-linux Gianluca Interlandi (Thu Apr 05 2012 - 20:04:57 CDT)
- Re: multicore versus net-linux Jim Phillips (Thu Apr 05 2012 - 22:40:09 CDT)
  - AW: multicore versus net-linux Norman Geist (Wed Apr 11 2012 - 01:05:33 CDT)
  - Re: multicore versus net-linux Chris Harrison (Fri Apr 20 2012 - 19:46:56 CDT)
DCD Buddhadev Maiti (Thu Apr 05 2012 - 15:44:43 CDT)
- Re: DCD Gianluca Interlandi (Thu Apr 05 2012 - 16:04:41 CDT)
  - RE: DCD Buddhadev Maiti (Thu Apr 05 2012 - 16:22:52 CDT)
  - Re: DCD Ernesto Vargas (Thu Apr 05 2012 - 16:21:19 CDT)
changing harmonic restraints (colvars) Jon Phillips (Thu Apr 05 2012 - 06:52:46 CDT)
- Re: changing harmonic restraints (colvars) Aron Broom (Thu Apr 05 2012 - 10:01:16 CDT)
  - Re: changing harmonic restraints (colvars) Jérôme Hénin (Thu Apr 05 2012 - 11:17:56 CDT)
Re: Line minimizerfailure because of IMPR? Francesco Pietra (Thu Apr 05 2012 - 03:57:03 CDT)
AW: Line minimizerfailure because of IMPR? Norman Geist (Thu Apr 05 2012 - 03:24:12 CDT)
Fwd: Line minimizerfailure because of IMPR? Francesco Pietra (Thu Apr 05 2012 - 03:02:14 CDT)
- Fwd: Line minimizerfailure because of IMPR? Francesco Pietra (Thu Apr 05 2012 - 03:10:59 CDT)
- AW: Line minimizerfailure because of IMPR? Norman Geist (Thu Apr 05 2012 - 03:28:14 CDT)
how to edit restart.coor Jiao, Dian NMN (-EXP) (Wed Apr 04 2012 - 17:29:26 CDT)
- Re: how to edit restart.coor Aron Broom (Wed Apr 04 2012 - 17:47:52 CDT)
  - Re: [EXTERNAL] Re: how to edit restart.coor Jiao, Dian NMN (-EXP) (Wed Apr 04 2012 - 17:56:38 CDT)
  - AW: how to edit restart.coor Norman Geist (Thu Apr 05 2012 - 01:18:58 CDT)
MetaDynamics in 2.9b2 Question Aron Broom (Wed Apr 04 2012 - 14:54:39 CDT)
- Re: MetaDynamics in 2.9b2 Question Giacomo Fiorin (Wed Apr 04 2012 - 19:32:41 CDT)
  - Re: MetaDynamics in 2.9b2 Question Aron Broom (Wed Apr 04 2012 - 20:24:56 CDT)
CUDA problem? Albert (Wed Apr 04 2012 - 14:02:49 CDT)
- CUDA problem with 2.9b2 Albert (Thu Apr 05 2012 - 00:51:05 CDT)
- AW: CUDA problem? Norman Geist (Thu Apr 05 2012 - 01:12:24 CDT)
  - Re: AW: CUDA problem? Albert (Thu Apr 05 2012 - 01:15:52 CDT)
Line minimizerfailure because of IMPR? Francesco Pietra (Wed Apr 04 2012 - 10:01:45 CDT)
- AW: Line minimizerfailure because of IMPR? Norman Geist (Thu Apr 05 2012 - 01:08:31 CDT)
mdff energy calculation snoze pa (Mon Apr 02 2012 - 10:56:28 CDT)
Protonated nucleotides Zack Scholl (Mon Apr 02 2012 - 07:49:53 CDT)
- Re: Protonated nucleotides johan strumpfer (Mon Apr 02 2012 - 11:15:50 CDT)
  - Re: Protonated nucleotides Aksimentiev, Oleksii (Mon Apr 02 2012 - 13:45:27 CDT)
    - Re: Protonated nucleotides Zack Scholl (Wed Apr 04 2012 - 16:02:22 CDT)
psfgen tyrosine anion-Fe bond Francesco Pietra (Sun Apr 01 2012 - 09:53:13 CDT)
- Re: psfgen tyrosine anion-Fe bond Francesco Pietra (Sun Apr 01 2012 - 12:03:17 CDT)
  - Re: psfgen tyrosine anion-Fe bond Francesco Pietra (Sun Apr 01 2012 - 12:14:27 CDT)
NAMD 2.9b2-cuda does not scale well compared to NAMD 2.8 Thomas Albers (Sat Mar 31 2012 - 18:00:06 CDT)
- Re: NAMD 2.9b2-cuda does not scale well compared to NAMD 2.8 Nicholas M Glykos (Sun Apr 01 2012 - 03:41:08 CDT)
Bug in SASA for alanin example John Jumper (Fri Mar 30 2012 - 15:10:44 CDT)
Dielectric constant for MDFF of a membrane protein. Raul Araya (Fri Mar 30 2012 - 09:18:22 CDT)
- Re: Dielectric constant for MDFF of a membrane protein. JC Gumbart (Fri Mar 30 2012 - 13:55:56 CDT)
Compiling NAMD_2.9b2_Source with GCC 4.7.0 Fabien Archambault (Fri Mar 30 2012 - 08:25:18 CDT)
- Re: Compiling NAMD_2.9b2_Source with GCC 4.7.0 Axel Kohlmeyer (Fri Mar 30 2012 - 08:32:19 CDT)
- Re: Compiling NAMD_2.9b2_Source with GCC 4.7.0 Jim Phillips (Fri Mar 30 2012 - 10:21:21 CDT)
CHARMM-GUI running error for ligand Hannes Loeffler (Fri Mar 30 2012 - 05:39:17 CDT)
CHARMM-GUI running error for ligand Albert (Fri Mar 30 2012 - 02:37:10 CDT)
- Re: CHARMM-GUI running error for ligand Chiara Cosenza unina (Fri Mar 30 2012 - 05:05:58 CDT)
  - Re: CHARMM-GUI running error for ligand Albert (Fri Mar 30 2012 - 05:27:35 CDT)
  - Re: CHARMM-GUI running error for ligand Albert (Fri Mar 30 2012 - 05:48:12 CDT)
    - Re: CHARMM-GUI running error for ligand Hannes Loeffler (Fri Mar 30 2012 - 05:50:58 CDT)
The simplest pair list generation scheme anaome_at_fundp.ac.be (Thu Mar 29 2012 - 14:01:45 CDT)
PDB sugar unit residue name Massimiliano Porrini (Thu Mar 29 2012 - 06:03:40 CDT)
- Re: PDB sugar unit residue name Aron Broom (Thu Mar 29 2012 - 07:52:20 CDT)
- Re: PDB sugar unit residue name Michelle Kuttel (Thu Mar 29 2012 - 09:30:25 CDT)
  - Re: PDB sugar unit residue name Olgun Guvench (Thu Mar 29 2012 - 11:14:52 CDT)
GBIS and thermostats Gianluca Interlandi (Wed Mar 28 2012 - 21:48:40 CDT)
output nonbonded and bonded terms separately chris liopiri (Wed Mar 28 2012 - 04:59:36 CDT)
collective variable component -- eigenvector usage chang (Tue Mar 27 2012 - 19:46:04 CDT)
- Re: collective variable component -- eigenvector usage Giacomo Fiorin (Tue Mar 27 2012 - 21:13:00 CDT)
NAMD 2.9b2 released Jim Phillips (Tue Mar 27 2012 - 15:17:30 CDT)
2.9b1 crashes Francesco Pietra (Tue Mar 27 2012 - 09:56:15 CDT)
- Re: 2.9b1 crashes Chris Harrison (Tue Mar 27 2012 - 10:15:36 CDT)
  - Re: 2.9b1 crashes Chris Harrison (Tue Mar 27 2012 - 20:33:25 CDT)
  - Re: 2.9b1 crashes Chris Harrison (Wed Mar 28 2012 - 15:41:39 CDT)
Re: How to Get Bonded Pair Force Calculation with NAMD Ehsan Ban (Tue Mar 27 2012 - 09:01:04 CDT)
- AW: How to Get Bonded Pair Force Calculation with NAMD Norman Geist (Wed Mar 28 2012 - 01:11:34 CDT)
AW: AW: conf file question Norman Geist (Mon Mar 26 2012 - 00:39:38 CDT)
How to Get Bonded Pair Force Calculation with NAMD Ehsan Ban (Mon Mar 26 2012 - 07:41:01 CDT)
- AW: How to Get Bonded Pair Force Calculation with NAMD Norman Geist (Tue Mar 27 2012 - 01:16:10 CDT)
accelMD parameter choice Grant Schauer (Sat Mar 24 2012 - 17:08:55 CDT)
- Re: accelMD parameter choice Chris Harrison (Sat Mar 24 2012 - 17:23:50 CDT)
AW: conf file question Norman Geist (Fri Mar 23 2012 - 06:09:41 CDT)
Nonbonded 3-body potential Xavier Bidault (Fri Mar 23 2012 - 05:44:59 CDT)
- Re: Nonbonded 3-body potential Axel Kohlmeyer (Fri Mar 23 2012 - 06:39:52 CDT)
Umbrella sampling with hbond Payne, Christy (Thu Mar 22 2012 - 19:05:24 CDT)
- Re: Umbrella sampling with hbond Giacomo Fiorin (Sat Mar 24 2012 - 12:52:17 CDT)
NAMD 2.9b1 crashes during minimization Francesco Pietra (Thu Mar 22 2012 - 10:28:04 CDT)
- AW: NAMD 2.9b1 crashes during minimization Norman Geist (Fri Mar 23 2012 - 01:58:15 CDT)
Glycosaminoglycan sulfate group with CHARMM Massimiliano Porrini (Thu Mar 22 2012 - 10:09:03 CDT)
- AW: Glycosaminoglycan sulfate group with CHARMM Norman Geist (Fri Mar 23 2012 - 01:48:05 CDT)
- Re: Glycosaminoglycan sulfate group with CHARMM Michelle Kuttel (Fri Mar 23 2012 - 02:20:29 CDT)
  - Re: Glycosaminoglycan sulfate group with CHARMM Massimiliano Porrini (Wed Mar 28 2012 - 12:18:08 CDT)
    - AW: Glycosaminoglycan sulfate group with CHARMM Norman Geist (Thu Mar 29 2012 - 00:58:54 CDT)
problem with paramters? Albert (Thu Mar 22 2012 - 00:25:27 CDT)
- AW: problem with paramters? Norman Geist (Thu Mar 22 2012 - 02:08:44 CDT)
conf file question Molecular Dynamics (Wed Mar 21 2012 - 04:19:57 CDT)
- AW: conf file question Norman Geist (Wed Mar 21 2012 - 10:27:19 CDT)
2.9b1 and GPU accelerated GB implicit solvent Aron Broom (Tue Mar 20 2012 - 23:16:57 CDT)
- Re: 2.9b1 and GPU accelerated GB implicit solvent David Tanner (Wed Mar 21 2012 - 12:41:23 CDT)
NAMD 2.9b1 released Jim Phillips (Tue Mar 20 2012 - 20:35:59 CDT)
will Jaguar enough for NAMD partial charge? Albert (Tue Mar 20 2012 - 02:18:54 CDT)
Collective variable on COM instead of COG poker_at_physics.usyd.edu.au (Mon Mar 19 2012 - 20:47:53 CDT)
- Re: Collective variable on COM instead of COG Jérôme Hénin (Tue Mar 20 2012 - 08:14:04 CDT)
Linux-x86_64-CUDA version 2.8 on CentOS-5 x86_64 non local user issue? Tru Huynh (Mon Mar 19 2012 - 18:31:40 CDT)
- AW: Linux-x86_64-CUDA version 2.8 on CentOS-5 x86_64 non local user issue? Norman Geist (Tue Mar 20 2012 - 01:36:34 CDT)
  - Re: Linux-x86_64-CUDA version 2.8 on CentOS-5 x86_64 non local user issue? Tru Huynh (Tue Mar 20 2012 - 08:32:49 CDT)
DNA system and PH control raghav singh (Mon Mar 19 2012 - 12:42:31 CDT)
- Re: DNA system and PH control Aron Broom (Mon Mar 19 2012 - 12:54:11 CDT)
SMD under NPT ensemble raghav singh (Mon Mar 19 2012 - 10:12:17 CDT)
- Re: SMD under NPT ensemble Wang Yi (Mon Mar 19 2012 - 10:20:07 CDT)
  - Re: SMD under NPT ensemble johan strumpfer (Mon Mar 19 2012 - 11:28:25 CDT)
is it possible to strip the restrain linearly? Albert (Mon Mar 19 2012 - 08:29:00 CDT)
- Re: is it possible to strip the restrain linearly? Axel Kohlmeyer (Mon Mar 19 2012 - 08:37:10 CDT)
  - Re: is it possible to strip the restrain linearly? Albert (Mon Mar 19 2012 - 10:33:09 CDT)
    - Re: is it possible to strip the restrain linearly? Jérôme Hénin (Mon Mar 19 2012 - 11:33:16 CDT)
FEP tutorial-my molecule doesn't show up in VMD Alisha \ (Mon Mar 19 2012 - 01:20:44 CDT)
- Re: FEP tutorial-my molecule doesn't show up in VMD Chris Harrison (Mon Mar 19 2012 - 01:40:57 CDT)
  - Re: FEP tutorial-my molecule doesn't show up in VMD Alisha \ (Mon Mar 19 2012 - 01:56:38 CDT)
Tyrosine ligand at Fe(II) Francesco Pietra (Sun Mar 18 2012 - 11:34:57 CDT)
what does .inp do from CHARMM GUI? Albert (Sun Mar 18 2012 - 07:19:22 CDT)
- Re: what does .inp do from CHARMM GUI? Bjoern Olausson (Mon Mar 19 2012 - 07:42:46 CDT)
jobs failed Albert (Sat Mar 17 2012 - 14:33:19 CDT)
- Re: jobs failed Axel Kohlmeyer (Sat Mar 17 2012 - 14:52:17 CDT)
Simulations with alpha methylated amino acids amin_at_imtech.res.in (Fri Mar 16 2012 - 20:23:33 CDT)
NAMD on Bluegene Thomas Lemmin (Fri Mar 16 2012 - 12:39:16 CDT)
- Re: NAMD on Bluegene Axel Kohlmeyer (Sat Mar 17 2012 - 15:27:40 CDT)
ABF - coordNum collective variable Adam Skelton (Thu Mar 15 2012 - 15:27:07 CDT)
- Re: ABF - coordNum collective variable Giacomo Fiorin (Fri Mar 16 2012 - 10:59:38 CDT)
  - Re: ABF - coordNum collective variable Jérôme Hénin (Mon Mar 19 2012 - 10:47:45 CDT)
External electric field using Grid Mohammad Jomah Ibraheem Ali Abu Saude (mbusaude) (Thu Mar 15 2012 - 14:47:12 CDT)
selecting multiple fixed atom in SMD raghav singh (Thu Mar 15 2012 - 11:47:30 CDT)
Announcement: Large biomolecule benchmark report Hannes Loeffler (Thu Mar 15 2012 - 07:51:36 CDT)
restart a simulation upayan baul (Thu Mar 15 2012 - 07:20:42 CDT)
- Re: restart a simulation Aron Broom (Thu Mar 15 2012 - 09:19:20 CDT)
- AW: restart a simulation Norman Geist (Fri Mar 16 2012 - 02:01:34 CDT)
Apply two Different eFeild on the same Direction Mohammad Jomah Ibraheem Ali Abu Saude (mbusaude) (Thu Mar 15 2012 - 02:34:46 CDT)
center of mass movement removal throughout simulation? Markus K. Dahlgren (Mon Mar 12 2012 - 18:53:53 CDT)
- AW: center of mass movement removal throughout simulation? Norman Geist (Tue Mar 13 2012 - 01:32:45 CDT)
- AW: center of mass movement removal throughout simulation? Norman Geist (Tue Mar 13 2012 - 01:36:16 CDT)
  - Re: AW: center of mass movement removal throughout simulation? Markus K. Dahlgren (Tue Mar 13 2012 - 09:50:37 CDT)
    - Re: AW: center of mass movement removal throughout simulation? Aron Broom (Tue Mar 13 2012 - 11:30:38 CDT)
    - AW: AW: center of mass movement removal throughout simulation? Norman Geist (Wed Mar 14 2012 - 01:49:39 CDT)
Regarding Installing NAMD in Ubuntu amit majhi (Mon Mar 12 2012 - 11:44:48 CDT)
- Re: Regarding Installing NAMD in Ubuntu Axel Kohlmeyer (Mon Mar 12 2012 - 11:52:53 CDT)
Fw: forough askari (Sun Mar 11 2012 - 11:54:25 CDT)
Fwd: SOLVED, however multiple CUDA efficiency? Francesco Pietra (Sun Mar 11 2012 - 11:36:55 CDT)
CUDA error 0 attaching to node Francesco Pietra (Fri Mar 09 2012 - 09:12:19 CST)
- Fwd: CUDA error 0 attaching to node Francesco Pietra (Sat Mar 10 2012 - 00:32:08 CST)
  - Fwd: CUDA error 0 attaching to node Francesco Pietra (Sun Mar 11 2012 - 10:28:04 CDT)
is zeroMomentum safe in a steered MD simulation? Jose Borreguero (Fri Mar 09 2012 - 09:08:41 CST)
Compiling NAMD Marcel UJI (IMAP) (Fri Mar 09 2012 - 06:49:34 CST)
Missing angle parameters in the ffTK ¼¿ëÀÏ (Fri Mar 09 2012 - 01:38:08 CST)
- Re: Missing angle parameters in the ffTK Mayne, Christopher G (Fri Mar 09 2012 - 09:17:06 CST)
Compiling NAMD on NICS Kraken Alexander Predeus (Thu Mar 08 2012 - 22:39:05 CST)
- Re: Compiling NAMD on NICS Kraken Jernej Zidar (Thu Mar 08 2012 - 23:42:09 CST)
  - Re: Compiling NAMD on NICS Kraken Alexander Predeus (Fri Mar 09 2012 - 11:45:11 CST)
TclForces clearconfig cancels addforce calls? Niklaus Johner (Thu Mar 08 2012 - 15:32:39 CST)
Metadynamics Problems Aron Broom (Wed Mar 07 2012 - 17:13:23 CST)
- Re: Metadynamics Problems Axel Kohlmeyer (Wed Mar 07 2012 - 17:22:46 CST)
  - Re: Metadynamics Problems Aron Broom (Wed Mar 07 2012 - 17:29:38 CST)
geometry deformation lecan (Wed Mar 07 2012 - 15:10:27 CST)
- Re: geometry deformation Grace Brannigan (Wed Mar 07 2012 - 15:45:36 CST)
charmm param ... wrong charges raghav singh (Wed Mar 07 2012 - 08:44:50 CST)
- Re: charmm param ... wrong charges Cristhian Boetsch (Thu Mar 08 2012 - 12:49:35 CST)
  - Re: charmm param ... wrong charges Aron Broom (Thu Mar 08 2012 - 13:27:49 CST)
    - Re: charmm param ... wrong charges Raghav (Thu Mar 08 2012 - 17:31:24 CST)
    - Re: charmm param ... wrong charges Aron Broom (Thu Mar 08 2012 - 18:58:01 CST)
How to set protonation states of certain atom in DNA with namd/vmd raghav singh (Wed Mar 07 2012 - 07:15:55 CST)
how to calculate the box size mjyang (Tue Mar 06 2012 - 01:48:45 CST)
- Re: how to calculate the box size Aron Broom (Tue Mar 06 2012 - 08:44:57 CST)
  - Re: how to calculate the box size Axel Kohlmeyer (Tue Mar 06 2012 - 08:52:59 CST)
- Re: how to calculate the box size Cristhian Boetsch (Tue Mar 06 2012 - 10:48:30 CST)
  - AW: how to calculate the box size Norman Geist (Wed Mar 07 2012 - 01:01:31 CST)
    - RE: how to calculate the box size mjyang (Wed Mar 07 2012 - 01:27:17 CST)
Replica exchange and multiple time-stepping Niklaus Johner (Mon Mar 05 2012 - 10:19:10 CST)
Constant Pull Velocity ishiikai08_at_yahoo.co.jp (Mon Mar 05 2012 - 09:11:28 CST)
- Re: Constant Pull Velocity Wang Yi (Mon Mar 05 2012 - 09:59:28 CST)
  - Re:Re: Constant Pull Velocity ishiikai08_at_yahoo.co.jp (Mon Mar 05 2012 - 21:39:29 CST)
SMD-DNA : ABNORMAL EOF FOUND - buffer=*END* raghav singh (Mon Mar 05 2012 - 08:12:33 CST)
- Re: SMD-DNA : ABNORMAL EOF FOUND - buffer=*END* Aron Broom (Mon Mar 05 2012 - 08:31:31 CST)
- Re: SMD-DNA : ABNORMAL EOF FOUND - buffer=*END* Chris Harrison (Mon Mar 05 2012 - 09:11:54 CST)
system splitted lecan (Fri Mar 02 2012 - 06:54:50 CST)
- Re: system splitted Aron Broom (Fri Mar 02 2012 - 09:21:12 CST)
  - AW: system splitted Norman Geist (Mon Mar 05 2012 - 00:59:23 CST)
Internal Unit system Niklaus Johner (Thu Mar 01 2012 - 11:21:53 CST)
- Re: Internal Unit system Ajasja LjubetiÄ (Thu Mar 01 2012 - 12:14:21 CST)
  - Re: Internal Unit system Niklaus Johner (Thu Mar 01 2012 - 14:52:24 CST)
    - Re: Internal Unit system Victor Ovchinnikov (Thu Mar 01 2012 - 15:16:00 CST)
SHAKE Tolerance and Performance Aron Broom (Thu Mar 01 2012 - 01:04:28 CST)
- Re: SHAKE Tolerance and Performance Nicholas M Glykos (Thu Mar 01 2012 - 03:16:05 CST)
Protein ligand simulation Tutorial sai nitin (Wed Feb 29 2012 - 06:47:38 CST)
- Re: Protein ligand simulation Tutorial Chris Chipot (Wed Feb 29 2012 - 08:07:08 CST)
- Re: Protein ligand simulation Tutorial poker_at_physics.usyd.edu.au (Wed Feb 29 2012 - 17:01:06 CST)
drude water simulation bug ? radial distrubuion function Sergey (Wed Feb 29 2012 - 01:22:30 CST)
problem with installing NAMD in Linux Red Hat rukman kesh (Wed Feb 29 2012 - 00:40:12 CST)
- Re: problem with installing NAMD in Linux Red Hat Chris Harrison (Thu Mar 01 2012 - 00:17:28 CST)
  - Re: problem with installing NAMD in Linux Red Hat rukman kesh (Mon Mar 05 2012 - 01:39:38 CST)
rigidBonds water and langevinHydrogen off are INCOMPATIBLE when using a solute with hdyrogens Aron Broom (Tue Feb 28 2012 - 21:58:25 CST)
- Re: rigidBonds water and langevinHydrogen off (no problem!) JC Gumbart (Thu Mar 01 2012 - 12:49:09 CST)
  - Re: rigidBonds water and langevinHydrogen off (no problem!) Aron Broom (Thu Mar 01 2012 - 13:27:59 CST)
- Re: rigidBonds water and langevinHydrogen off are INCOMPATIBLE when using a solute with hdyrogens Jim Phillips (Thu Mar 01 2012 - 14:47:48 CST)
  - Re: rigidBonds water and langevinHydrogen off are INCOMPATIBLE when using a solute with hdyrogens Aron Broom (Thu Mar 01 2012 - 15:06:29 CST)
    - Re: rigidBonds water and langevinHydrogen off are INCOMPATIBLE when using a solute with hdyrogens Aron Broom (Fri Mar 02 2012 - 10:51:16 CST)
drude water simulation bug ? Sergey (Tue Feb 28 2012 - 14:35:26 CST)
Drug design issue. Boyang Wang (Tue Feb 28 2012 - 02:08:07 CST)
- Re: Drug design issue. Branko (Tue Feb 28 2012 - 05:39:26 CST)
R: restart file Chiara.cosenza (Sat Feb 25 2012 - 09:16:29 CST)
- Re: R: restart file Nicholas M Glykos (Sat Feb 25 2012 - 09:38:27 CST)
  - Re: R: restart file Aron Broom (Sat Feb 25 2012 - 11:00:24 CST)
restart file Namd Namd (Sat Feb 25 2012 - 07:31:18 CST)
- Re: restart file Aron Broom (Sat Feb 25 2012 - 08:43:56 CST)
Re: Consistent temperature increase in CUDA runs Aron Broom (Fri Feb 24 2012 - 14:49:28 CST)
- Re: Consistent temperature increase in CUDA runs Aron Broom (Fri Feb 24 2012 - 19:53:08 CST)
  - AW: Consistent temperature increase in CUDA runs Norman Geist (Mon Feb 27 2012 - 00:28:03 CST)
    - Re: AW: Consistent temperature increase in CUDA runs Axel Kohlmeyer (Tue Feb 28 2012 - 06:14:18 CST)
    - Re: AW: Consistent temperature increase in CUDA runs Nicholas M Glykos (Tue Feb 28 2012 - 08:40:29 CST)
- Re: Consistent temperature increase in CUDA runs Aron Broom (Mon Feb 27 2012 - 08:31:46 CST)
  - AW: Consistent temperature increase in CUDA runs Norman Geist (Tue Feb 28 2012 - 00:19:29 CST)
regarding ion concentration in implicit solvent Prathit Chatterjee (Fri Feb 24 2012 - 05:19:51 CST)
- Re: regarding ion concentration in implicit solvent Prathit Chatterjee (Wed Feb 29 2012 - 08:04:08 CST)
  - Re: regarding ion concentration in implicit solvent Nicholas M Glykos (Wed Feb 29 2012 - 08:29:40 CST)
  - Re: regarding ion concentration in implicit solvent Aron Broom (Wed Feb 29 2012 - 08:31:53 CST)
Consistent temperature increase in CUDA runs Norman Geist (Fri Feb 24 2012 - 00:51:38 CST)
what restraint can I use to prevent membrane diffusion on the Z-axis? Jose Borreguero (Wed Feb 22 2012 - 14:07:30 CST)
- Re: what restraint can I use to prevent membrane diffusion on the Z-axis? Chris Harrison (Sat Feb 25 2012 - 11:59:43 CST)
  - Re: what restraint can I use to prevent membrane diffusion on the Z-axis? kanchi subbarao rao (Sun Feb 26 2012 - 10:39:42 CST)
  - Re: what restraint can I use to prevent membrane diffusion on the Z-axis? kanchi subbarao rao (Tue Feb 28 2012 - 11:58:49 CST)
Error in NAMD 2.8 function Sereda, Yuriy Vladimirovich (Wed Feb 22 2012 - 11:02:09 CST)
- Re: Error in NAMD 2.8 function Chris Harrison (Thu Mar 01 2012 - 00:25:22 CST)
Re: Keep PBC box size in Z-direction constant? Bjoern Olausson (Wed Feb 22 2012 - 03:36:42 CST)
- Release of the R.E.D.-III.5 tools FyD (Wed Feb 22 2012 - 05:00:23 CST)
AW: Keep PBC box size in Z-direction constant? Norman Geist (Wed Feb 22 2012 - 00:24:02 CST)
Keep PBC box size in Z-direction constant? Bjoern Olausson (Mon Feb 20 2012 - 06:37:05 CST)
- AW: Keep PBC box size in Z-direction constant? Norman Geist (Tue Feb 21 2012 - 00:27:45 CST)
FW: vmd-l: Stand-alone VMD ? Mark Cunningham (Thu Feb 16 2012 - 15:45:55 CST)
Re: Possible bug or inconvenience Chris Harrison (Wed Feb 15 2012 - 15:12:03 CST)
RMSD metadynamics simone bardwell (Wed Feb 15 2012 - 13:25:16 CST)
- Re: RMSD metadynamics Giacomo Fiorin (Wed Feb 15 2012 - 13:48:50 CST)
  - Re: RMSD metadynamics simone bardwell (Wed Feb 15 2012 - 15:59:20 CST)
    - Re: RMSD metadynamics Giacomo Fiorin (Wed Feb 15 2012 - 16:38:03 CST)
    - Re: RMSD metadynamics Jérôme Hénin (Thu Feb 16 2012 - 02:39:04 CST)
how can i demonstrate that a chain-like molecule within a membrane. superdirac (Wed Feb 15 2012 - 07:19:36 CST)
- Re: how can i demonstrate that a chain-like molecule within a membrane. Chris Chipot (Wed Feb 15 2012 - 07:27:44 CST)
Possible bug or inconvenience Norman Geist (Wed Feb 15 2012 - 04:06:34 CST)
Graphene pdb/psf files cannot be read by psfgen Wanzhi Qiu (Wed Feb 15 2012 - 01:14:04 CST)
- Re: Graphene pdb/psf files cannot be read by psfgen Cruz-Chu Eduardo Roberto (Wed Feb 15 2012 - 05:06:31 CST)
  - Re: Graphene pdb/psf files cannot be read by psfgen kanchi subbarao rao (Wed Feb 15 2012 - 08:11:10 CST)
  - Re: Graphene pdb/psf files cannot be read by psfgen Wanzhi Qiu (Wed Feb 15 2012 - 20:06:01 CST)
martini force field Swarna M Patra (Tue Feb 14 2012 - 21:41:19 CST)
- Re: martini force field Chris Harrison (Wed Feb 15 2012 - 15:02:28 CST)
  - Re: martini force field Chris Harrison (Wed Feb 15 2012 - 15:09:45 CST)
Regarding thermostats felmerino_at_uchile.cl (Mon Feb 13 2012 - 09:21:33 CST)
- Re: Regarding thermostats Gianluca Interlandi (Mon Feb 13 2012 - 09:59:18 CST)
- Re: Regarding thermostats Marcos Sotomayor (Thu Feb 23 2012 - 16:37:03 CST)
where is psf develop in ffTK ¼¿ëÀÏ (Mon Feb 13 2012 - 06:55:37 CST)
- Re: where is psf develop in ffTK Chris Harrison (Wed Feb 15 2012 - 15:21:27 CST)
2CPU+1GPU vs 1CPU+2GPU Marcel UJI (IMAP) (Mon Feb 13 2012 - 05:21:18 CST)
- Re: 2CPU+1GPU vs 1CPU+2GPU Nicholas M Glykos (Mon Feb 13 2012 - 05:44:59 CST)
  - Re: 2CPU+1GPU vs 1CPU+2GPU Aron Broom (Mon Feb 13 2012 - 08:26:30 CST)
how to understand vdwForceSwitching Liqun Zhang (Sat Feb 11 2012 - 17:09:48 CST)
- Re: how to understand vdwForceSwitching Chris Harrison (Wed Feb 15 2012 - 15:50:33 CST)
parameter file for POPC (RBCG model) Swarna M Patra (Thu Feb 09 2012 - 22:29:21 CST)
RBCG-configuration file Swarna M Patra (Thu Feb 09 2012 - 05:53:15 CST)
Re: Copper ion moving out of the protein towards bulk solvent poker_at_physics.usyd.edu.au (Wed Feb 08 2012 - 18:24:50 CST)
How to calculate surface tension properly Bjoern Olausson (Wed Feb 08 2012 - 07:59:15 CST)
Copper ion moving out of the protein towards bulk solvent SUBHA KALYAANAMOORTHY (Tue Feb 07 2012 - 19:16:26 CST)
crossing the border by protein/ion complex Maria Bykhovskaia (Tue Feb 07 2012 - 17:16:30 CST)
- Re: crossing the border by protein/ion complex Axel Kohlmeyer (Tue Feb 07 2012 - 17:33:08 CST)
  - AW: crossing the border by protein/ion complex Norman Geist (Wed Feb 08 2012 - 00:54:30 CST)
Ewald contribution to pressure profile only working on single core Bjoern Olausson (Tue Feb 07 2012 - 06:59:43 CST)
Question about "Free Energy of Conformational Change Calculations" Shen, Han (Mon Feb 06 2012 - 11:03:44 CST)
- Re: Question about "Free Energy of Conformational Change Calculations" Giacomo Fiorin (Mon Feb 06 2012 - 11:13:21 CST)
gurukatagi@gmail.com Gurunath Katagi (Mon Feb 06 2012 - 10:37:49 CST)
- Re: gurukatagi@gmail.com Ajasja LjubetiÄ (Mon Feb 06 2012 - 11:05:26 CST)
  - Re: gurukatagi@gmail.com Aron Broom (Mon Feb 06 2012 - 12:09:08 CST)
  - Re: gurukatagi@gmail.com Gurunath Katagi (Wed Feb 22 2012 - 11:22:01 CST)
ffTK in the just released VMD 1.9.1 JC Gumbart (Sat Feb 04 2012 - 15:04:05 CST)
- AW: ffTK in the just released VMD 1.9.1 Norman Geist (Mon Feb 06 2012 - 01:04:05 CST)
  - RE: ffTK in the just released VMD 1.9.1 JC Gumbart (Mon Feb 06 2012 - 01:15:52 CST)
Hard sphere potential M.Raviprasad (Thu Feb 02 2012 - 20:20:14 CST)
- Re: Hard sphere potential Axel Kohlmeyer (Thu Feb 02 2012 - 20:56:09 CST)
  - RE: Hard sphere potential M.Raviprasad (Thu Feb 02 2012 - 22:18:23 CST)
    - Re: Hard sphere potential Axel Kohlmeyer (Thu Feb 02 2012 - 22:41:22 CST)
one question about gtp flipping in namd simulation Liqun Zhang (Thu Feb 02 2012 - 13:42:27 CST)
- Re: one question about gtp flipping in namd simulation Chris Harrison (Thu Feb 02 2012 - 13:49:56 CST)
RMSD collective variable - Different atons to align and to calculate RMSD Paulo Cesar Telles de Souza (Thu Feb 02 2012 - 12:19:10 CST)
- Re: RMSD collective variable - Different atons to align and to calculate RMSD Giacomo Fiorin (Thu Feb 02 2012 - 13:52:49 CST)
- Re: RMSD collective variable - Different atons to align and to calculate RMSD Chris Harrison (Thu Feb 02 2012 - 13:54:55 CST)
  - Re: RMSD collective variable - Different atons to align and to calculate RMSD Jérôme Hénin (Thu Feb 02 2012 - 15:40:47 CST)
- Re: RMSD collective variable - Different atons to align and to calculate RMSD Davide Branduardi (Thu Feb 02 2012 - 14:27:18 CST)
NAMDenergy plugin_van der Waal interactions Bruno Luís Pinto de Oliveira (Thu Feb 02 2012 - 11:06:20 CST)
- Re: NAMDenergy plugin_van der Waal interactions Chris Harrison (Wed Feb 15 2012 - 15:27:12 CST)
  - RE: NAMDenergy plugin_van der Waal interactions Bruno Luís Pinto de Oliveira (Mon Feb 20 2012 - 07:01:14 CST)
Energy minimization of membrane R. Charbel Maroun (Thu Feb 02 2012 - 06:37:42 CST)
- Re: Energy minimization of membrane Boyang Wang (Thu Feb 02 2012 - 23:31:28 CST)
  - AW: Energy minimization of membrane Norman Geist (Fri Feb 03 2012 - 01:14:50 CST)
rigidBonds water option Hasan haska (Thu Feb 02 2012 - 01:48:22 CST)
- Re: rigidBonds water option Chris Harrison (Thu Feb 02 2012 - 14:02:37 CST)
Gromacs analysis tools for Namd output PAUL NEWMAN (Wed Feb 01 2012 - 11:41:40 CST)
- Re: vmd-l: Gromacs analysis tools for Namd output John Stone (Wed Feb 01 2012 - 11:47:43 CST)
- Re: Gromacs analysis tools for Namd output Axel Kohlmeyer (Wed Feb 01 2012 - 11:48:47 CST)
- RE: vmd-l: Gromacs analysis tools for Namd output Kei Sit (Wed Feb 01 2012 - 17:33:01 CST)
Analysis of FEP output file sudipta (Tue Jan 31 2012 - 11:41:33 CST)
- Re: Analysis of FEP output file Chris Harrison (Wed Feb 15 2012 - 15:29:59 CST)
  - Re: Analysis of FEP output file Chris Chipot (Thu Feb 16 2012 - 07:35:12 CST)
Trouble using rotateReference, centerRefrence and refPositionsGroup in the colvar module Ajasja LjubetiÄ (Tue Jan 31 2012 - 08:30:05 CST)
- Re: Trouble using rotateReference, centerRefrence and refPositionsGroup in the colvar module Giacomo Fiorin (Tue Jan 31 2012 - 12:28:24 CST)
  - Re: Trouble using rotateReference, centerRefrence and refPositionsGroup in the colvar module Ajasja LjubetiÄ (Wed Feb 01 2012 - 03:44:26 CST)
Fwd: Madhulika Gupta (Mon Jan 30 2012 - 22:10:37 CST)
problem to analyze the output of FEP file using vmd plugin sudipta (Mon Jan 30 2012 - 15:58:41 CST)
Installing NAMD on a 64-bit linux (NVIDIA CUDA) Shyno Mathew (Mon Jan 30 2012 - 12:15:15 CST)
- Re: Installing NAMD on a 64-bit linux (NVIDIA CUDA) Axel Kohlmeyer (Mon Jan 30 2012 - 12:24:40 CST)
  - AW: Installing NAMD on a 64-bit linux (NVIDIA CUDA) Norman Geist (Tue Jan 31 2012 - 00:53:47 CST)
Alchemical free-energy methods and electroneutrality Thomas Albers (Sat Jan 28 2012 - 13:35:27 CST)
- Re: Alchemical free-energy methods and electroneutrality Rajan Vatassery (Sat Jan 28 2012 - 15:31:18 CST)
- RE: Alchemical free-energy methods and electroneutrality JC Gumbart (Sat Jan 28 2012 - 15:47:54 CST)
Output of thermodynamic integration Kei-ichi Okazaki (Fri Jan 27 2012 - 18:16:47 CST)
- Re: Output of thermodynamic integration Jérôme Hénin (Sat Jan 28 2012 - 04:25:19 CST)
  - RE: Output of thermodynamic integration Okazaki, Keiichi (NIH/NIDDK) [F] (Sat Jan 28 2012 - 10:31:35 CST)
(no subject) Madhulika Gupta (Tue Jan 24 2012 - 23:08:52 CST)
- Re: Ajasja LjubetiÄ (Wed Jan 25 2012 - 12:05:49 CST)
NAMD on ranger.tacc Jesper Sørensen (Mon Jan 23 2012 - 10:28:33 CST)
- Re: NAMD on ranger.tacc George M Giambasu (Mon Jan 23 2012 - 11:26:26 CST)
  - Re: NAMD on ranger.tacc Jesper Sørensen (Tue Jan 24 2012 - 11:46:11 CST)
    - Re: NAMD on ranger.tacc George M Giambasu (Tue Jan 24 2012 - 12:22:42 CST)
    - Re: NAMD on ranger.tacc Jesper Sørensen (Tue Jan 24 2012 - 14:35:39 CST)
Umbrella sampling using dihedral angle Buddhadev Maiti (Sun Jan 22 2012 - 22:17:25 CST)
- Re: Umbrella sampling using dihedral angle Giacomo Fiorin (Tue Jan 24 2012 - 09:38:30 CST)
- Re: Umbrella sampling using dihedral angle Giacomo Fiorin (Tue Jan 24 2012 - 11:21:34 CST)
(no subject) Basak Isin (Mon Jan 23 2012 - 01:16:45 CST)
Harmonic Constrain like MMFP in CHARMM Vahid Mirjalili (Fri Jan 20 2012 - 17:52:14 CST)
- Re: Harmonic Constrain like MMFP in CHARMM Giacomo Fiorin (Fri Jan 20 2012 - 18:42:26 CST)
  - Re: Harmonic Constrain like MMFP in CHARMM Vahid Mirjalili (Fri Jan 20 2012 - 19:41:28 CST)
    - Re: Harmonic Constrain like MMFP in CHARMM Giacomo Fiorin (Sat Jan 21 2012 - 01:24:14 CST)
    - Re: Harmonic Constrain like MMFP in CHARMM Vahid Mirjalili (Mon Jan 23 2012 - 14:56:55 CST)
  - Re: Harmonic Constrain like MMFP in CHARMM Giacomo Fiorin (Tue Jan 24 2012 - 09:40:08 CST)
Using TCLforces to rescale force(s) on particular atom(s) --- loadtotalforces, addforce and previous/current timestep issue Gungor Ozer (Thu Jan 19 2012 - 11:44:29 CST)
- Re: Using TCLforces to rescale force(s) on particular atom(s) --- loadtotalforces, addforce and previous/current timestep issue Giacomo Fiorin (Thu Jan 19 2012 - 11:56:00 CST)
- Re: Using TCLforces to rescale force(s) on particular atom(s) --- loadtotalforces, addforce and previous/current timestep issue Boyang Wang (Thu Jan 19 2012 - 17:45:41 CST)
RE: spinAngle Giacomo Fiorin (Wed Jan 18 2012 - 13:06:47 CST)
Re: spinAngle Giacomo Fiorin (Wed Jan 18 2012 - 12:32:32 CST)
- Re: spinAngle Giacomo Fiorin (Wed Jan 18 2012 - 13:41:27 CST)
  - RE: spinAngle Buddhadev Maiti (Wed Jan 18 2012 - 16:28:58 CST)
    - Re: spinAngle Giacomo Fiorin (Wed Jan 18 2012 - 16:34:18 CST)
    - Re: Re: spinAngle Ajasja LjubetiÄ (Thu Jan 19 2012 - 05:13:15 CST)
namd question in parameter conversion Liqun Zhang (Wed Jan 18 2012 - 10:27:12 CST)
- Re: namd question in parameter conversion Aron Broom (Wed Jan 18 2012 - 12:35:01 CST)
- Re: namd question in parameter conversion Boyang Wang (Thu Jan 19 2012 - 02:08:46 CST)
questions regarding ABF sampling in a DMPC bilayer Ajasja LjubetiÄ (Wed Jan 18 2012 - 08:12:20 CST)
- Re: questions regarding ABF sampling in a DMPC bilayer Jérôme Hénin (Wed Jan 18 2012 - 12:00:28 CST)
  - Re: questions regarding ABF sampling in a DMPC bilayer felmerino_at_uchile.cl (Wed Jan 18 2012 - 12:27:31 CST)
    - Re: questions regarding ABF sampling in a DMPC bilayer Giacomo Fiorin (Wed Jan 18 2012 - 13:13:50 CST)
  - Re: questions regarding ABF sampling in a DMPC bilayer Ajasja LjubetiÄ (Fri Jan 27 2012 - 08:03:54 CST)
    - Re: questions regarding ABF sampling in a DMPC bilayer Jérôme Hénin (Fri Jan 27 2012 - 09:10:44 CST)
    - Re: questions regarding ABF sampling in a DMPC bilayer Ajasja LjubetiÄ (Mon Jan 30 2012 - 06:49:52 CST)
- Re: questions regarding ABF sampling in a DMPC bilayer Giacomo Fiorin (Wed Jan 18 2012 - 12:05:02 CST)
question about NPT oguz gurbulak (Wed Jan 18 2012 - 02:06:19 CST)
- RE: question about NPT JC Gumbart (Wed Jan 18 2012 - 12:36:43 CST)
- Re: question about NPT Boyang Wang (Thu Jan 19 2012 - 02:16:03 CST)
  - Re: question about NPT oguz gurbulak (Thu Jan 19 2012 - 03:51:42 CST)
    - Re: question about NPT Boyang Wang (Thu Jan 19 2012 - 04:03:21 CST)
  - Re: question about NPT Axel Kohlmeyer (Thu Jan 19 2012 - 05:14:04 CST)
target pressure value Namd Namd (Tue Jan 17 2012 - 06:30:20 CST)
- target pressure value Namd Namd (Tue Jan 17 2012 - 06:32:45 CST)
  - Re: target pressure value Ajasja LjubetiÄ (Tue Jan 17 2012 - 07:03:36 CST)
Problems in setting up low pH systems Sheng, Zi-Zhang (Wed Jan 11 2012 - 09:43:31 CST)
- Re: Problems in setting up low pH systems Giacomo Fiorin (Wed Jan 11 2012 - 10:03:34 CST)
surfaceTensionTarget - Surface Tension per interface or per bilayer Jon Fuller (Wed Jan 11 2012 - 04:25:24 CST)
- Re: surfaceTensionTarget - Surface Tension per interface or per bilayer Boyang Wang (Wed Jan 11 2012 - 08:30:17 CST)
  - Re: surfaceTensionTarget - Surface Tension per interface or per bilayer Jérôme Hénin (Wed Jan 11 2012 - 09:18:39 CST)
how does namd handle violations of the minimum image convention? Ana Celia Vila Verde (Mon Jan 09 2012 - 05:32:32 CST)
- Re: how does namd handle violations of the minimum image convention? Boyang Wang (Tue Jan 10 2012 - 21:45:04 CST)
Re: incompatibility between NAMD and amber topology files Osman, Roman (Tue Jan 10 2012 - 15:33:43 CST)
ERROR: 0031-250 task 0: Terminated Gurunath Katagi (Mon Jan 09 2012 - 23:42:53 CST)
incompatibility between NAMD and amber topology files Osman, Roman (Mon Jan 09 2012 - 16:13:24 CST)
ATTENTION: 0031-408 4 tasks allocated by LoadLeveler, continuing Gurunath Katagi (Tue Jan 10 2012 - 14:03:03 CST)
- RE: ATTENTION: 0031-408 4 tasks allocated by LoadLeveler, continuing Bennion, Brian (Tue Jan 10 2012 - 14:18:06 CST)
- Re: ATTENTION: 0031-408 4 tasks allocated by LoadLeveler, continuing Axel Kohlmeyer (Tue Jan 10 2012 - 14:21:26 CST)
Problem with parameter file in Pair Interaction Calculation M Mahjour (Mon Jan 09 2012 - 05:47:20 CST)
- Re: Problem with parameter file in Pair Interaction Calculation Boyang Wang (Mon Jan 09 2012 - 08:27:02 CST)
  - AW: Problem with parameter file in Pair Interaction Calculation Norman Geist (Tue Jan 10 2012 - 00:41:23 CST)
    - Re: AW: Problem with parameter file in Pair Interaction Calculation Kovacs, Sandor (Tue Jan 10 2012 - 01:14:04 CST)
    - Re: AW: Problem with parameter file in Pair Interaction Calculation M Mahjour (Tue Jan 10 2012 - 10:48:33 CST)
can TMD alignment prior to force calculation be turned off? Michael Zimmermann (Sun Jan 08 2012 - 15:04:15 CST)
- Re: can TMD alignment prior to force calculation be turned off? Axel Kohlmeyer (Sun Jan 08 2012 - 15:19:55 CST)
  - Re: can TMD alignment prior to force calculation be turned off? Michael Zimmermann (Sun Jan 08 2012 - 17:03:41 CST)
    - Re: can TMD alignment prior to force calculation be turned off? Jérôme Hénin (Sun Jan 08 2012 - 17:18:28 CST)
Problem with parameter file in Pair Interaction Calculation M Mahjour (Sun Jan 08 2012 - 00:14:50 CST)
IB fabrics Thomas Bishop (Fri Jan 06 2012 - 11:42:53 CST)
- Re: IB fabrics Axel Kohlmeyer (Fri Jan 06 2012 - 11:58:14 CST)
  - RE: IB fabrics Bennion, Brian (Fri Jan 06 2012 - 12:39:04 CST)
ABF simulation Tugba Nogay (Fri Jan 06 2012 - 10:53:36 CST)
- Re: ABF simulation Jérôme Hénin (Sat Jan 07 2012 - 05:16:24 CST)
Problem running NAMD 2.8 with ibverbs Moritz Schlarb (Fri Jan 06 2012 - 09:29:18 CST)
- Re: Problem running NAMD 2.8 with ibverbs Moritz Schlarb (Fri Jan 06 2012 - 09:41:49 CST)
  - AW: Problem running NAMD 2.8 with ibverbs Norman Geist (Mon Jan 09 2012 - 00:32:06 CST)
    - Re: Problem running NAMD 2.8 with ibverbs Moritz Schlarb (Wed Jan 11 2012 - 04:20:57 CST)
    - AW: Problem running NAMD 2.8 with ibverbs Norman Geist (Thu Jan 12 2012 - 07:34:31 CST)
TIP5P simulation Mallajosyula, Sairam (Thu Jan 05 2012 - 21:41:05 CST)
- Re: TIP5P simulation Axel Kohlmeyer (Thu Jan 05 2012 - 21:59:12 CST)
  - RE: TIP5P simulation Mallajosyula, Sairam (Fri Jan 06 2012 - 09:58:54 CST)
Problem with NVE simulation gaborekt_at_duq.edu (Thu Jan 05 2012 - 15:42:10 CST)
- Re: Problem with NVE simulation Axel Kohlmeyer (Thu Jan 05 2012 - 16:48:47 CST)
TIP4P force field Udaysankar Midya (Tue Jan 03 2012 - 21:46:52 CST)
- Re: TIP4P force field Boyang Wang (Tue Jan 03 2012 - 22:33:07 CST)
Re: Replica Exchange Discrete Molecular Dynamics for structure based models bharat gupta (Tue Jan 03 2012 - 00:48:16 CST)
water molecules oguz gurbulak (Mon Jan 02 2012 - 06:04:08 CST)
- Re: water molecules Nicholas M Glykos (Mon Jan 02 2012 - 07:35:19 CST)
  - Re: water molecules Boyang Wang (Tue Jan 03 2012 - 02:51:56 CST)
    - Re: water molecules oguz gurbulak (Tue Jan 03 2012 - 03:08:58 CST)
- AW: water molecules Norman Geist (Tue Jan 03 2012 - 00:34:15 CST)
(no subject) ÐìÖÓºÓ (Mon Jan 02 2012 - 03:03:31 CST)
GPRESSURE becomes nan in TIP4P simulation Udaysankar Midya (Sat Dec 31 2011 - 05:23:35 CST)
tabulatd potentials Arturas (Thu Dec 29 2011 - 13:09:17 CST)
- Re: tabulatd potentials Arturas (Thu Dec 29 2011 - 14:11:43 CST)
Coarse-Graining MD don't work perfect as expected ÐìÖÓºÓ (Thu Dec 29 2011 - 00:50:31 CST)
- Re: Coarse-Graining MD don't work perfect as expected Boyang Wang (Fri Dec 30 2011 - 03:57:44 CST)
scaling Neelanjana Sengupta (Wed Dec 28 2011 - 22:56:45 CST)
- Re: scaling Boyang Wang (Fri Dec 30 2011 - 03:56:03 CST)
  - AW: scaling Norman Geist (Mon Jan 02 2012 - 00:44:13 CST)
Fwd: about md in npt Boyang Wang (Wed Dec 28 2011 - 02:54:01 CST)
about md in npt Hasan haska (Wed Dec 28 2011 - 02:18:30 CST)
- Re: about md in npt Joshua Adelman (Wed Dec 28 2011 - 07:55:02 CST)
equilibrate the system in NPT Hasan haska (Mon Dec 26 2011 - 13:57:37 CST)
Parse Fep plugin error Joseph Antoine Garate (Fri Dec 23 2011 - 08:27:39 CST)
- Re: vmd-l: Parse Fep plugin error John Stone (Fri Dec 23 2011 - 10:47:56 CST)
collective variable calculation from dcd file Giovanni Bellesia (Wed Dec 21 2011 - 14:44:47 CST)
- Re: collective variable calculation from dcd file Branko (Wed Dec 21 2011 - 15:15:06 CST)
  - Re: collective variable calculation from dcd file Giovanni Bellesia (Wed Dec 21 2011 - 15:20:27 CST)
    - Re: collective variable calculation from dcd file Branko (Wed Dec 21 2011 - 15:38:39 CST)
- Re: collective variable calculation from dcd file Jérôme Hénin (Thu Dec 22 2011 - 05:20:15 CST)
AW: glycosaminoglycan with GLYCAM06 in amber format Norman Geist (Wed Dec 21 2011 - 00:54:50 CST)
- Re: AW: glycosaminoglycan with GLYCAM06 in amber format felmerino_at_uchile.cl (Wed Dec 21 2011 - 12:44:08 CST)
  - Re: AW: glycosaminoglycan with GLYCAM06 in amber format Massimiliano Porrini (Thu Dec 22 2011 - 11:12:10 CST)
AW: glycosaminoglycan with GLYCAM06 in amber format Norman Geist (Tue Dec 20 2011 - 06:45:32 CST)
coordNum colvar with dummyAtom Ernesto Vargas (Mon Dec 19 2011 - 18:56:40 CST)
- Re: coordNum colvar with dummyAtom Giacomo Fiorin (Thu Dec 22 2011 - 17:41:20 CST)
Re: Generating .tpr file using NAMD files rajitha tatikonda (Mon Dec 19 2011 - 00:32:56 CST)
- Re: Re: Generating .tpr file using NAMD files Axel Kohlmeyer (Mon Dec 19 2011 - 11:59:35 CST)
- Re: Re: Generating .tpr file using NAMD files Jeffrey Potoff (Mon Dec 19 2011 - 12:05:56 CST)
Re: glycosaminoglycan with GLYCAM06 in amber format Massimiliano Porrini (Mon Dec 19 2011 - 05:04:40 CST)
- AW: glycosaminoglycan with GLYCAM06 in amber format Norman Geist (Mon Dec 19 2011 - 07:35:58 CST)
- Re: glycosaminoglycan with GLYCAM06 in amber format Lachele Foley (Lists) (Tue Dec 20 2011 - 08:53:59 CST)
  - Re: glycosaminoglycan with GLYCAM06 in amber format Massimiliano Porrini (Tue Dec 20 2011 - 09:46:18 CST)
    - AW: glycosaminoglycan with GLYCAM06 in amber format Norman Geist (Wed Dec 21 2011 - 00:51:03 CST)
- Re: glycosaminoglycan with GLYCAM06 in amber format Massimiliano Porrini (Tue Dec 20 2011 - 08:55:58 CST)
Sticking TIP4P water molecules AMBER Norman Geist (Mon Dec 19 2011 - 04:33:25 CST)
- Re: Sticking TIP4P water molecules AMBER Nicholas M Glykos (Mon Dec 19 2011 - 04:58:13 CST)
  - Re: Sticking TIP4P water molecules AMBER George M Giambasu (Mon Dec 19 2011 - 10:16:56 CST)
    - AW: Sticking TIP4P water molecules AMBER Norman Geist (Tue Dec 20 2011 - 00:33:08 CST)
Fwd: Generating .tpr file using NAMD files rajitha rajeshwar (Mon Dec 19 2011 - 03:05:34 CST)
glycosaminoglycan with GLYCAM06 in amber format Massimiliano Porrini (Sun Dec 18 2011 - 10:44:48 CST)
- AW: glycosaminoglycan with GLYCAM06 in amber format Norman Geist (Mon Dec 19 2011 - 00:45:19 CST)
Interfaces in NAMD Hasan haska (Sat Dec 17 2011 - 14:20:25 CST)
New physical understanding. Boyang Wang (Fri Dec 16 2011 - 00:39:27 CST)
- Re: New physical understanding. Axel Kohlmeyer (Fri Dec 16 2011 - 05:47:48 CST)
  - Re: New physical understanding. Boyang Wang (Fri Dec 16 2011 - 06:56:42 CST)
Umbrella sampling-NAMD Parisa Akhski (Thu Dec 15 2011 - 09:24:36 CST)
- Re: Umbrella sampling-NAMD Jérôme Hénin (Thu Dec 15 2011 - 11:07:04 CST)
- Re: Umbrella sampling-NAMD Aron Broom (Thu Dec 15 2011 - 11:11:04 CST)
  - RE: Umbrella sampling-NAMD Parisa Akhski (Thu Dec 15 2011 - 12:51:57 CST)
cell size Hasan haska (Tue Dec 13 2011 - 08:10:49 CST)
- Re: cell size Axel Kohlmeyer (Tue Dec 13 2011 - 08:21:18 CST)
  - Re: cell size Hasan haska (Tue Dec 13 2011 - 09:47:50 CST)
tclforces and extrabonds Jian Dai (Mon Dec 12 2011 - 10:13:16 CST)
- Re: tclforces and extrabonds Aron Broom (Mon Dec 12 2011 - 11:30:36 CST)
- Re: tclforces and extrabonds Jérôme Hénin (Mon Dec 12 2011 - 11:30:47 CST)
correlation functions Molecular Dynamics (Sat Dec 10 2011 - 05:18:50 CST)
- Re: correlation functions Aron Broom (Sat Dec 10 2011 - 08:54:56 CST)
  - Re: correlation functions Boyang Wang (Sat Dec 10 2011 - 18:03:53 CST)
    - Re: correlation functions Thomas Bishop (Mon Dec 12 2011 - 07:54:06 CST)
MMTools for analysis Namd Namd (Sat Dec 10 2011 - 05:07:19 CST)
- Re: MMTools for analysis Branko (Sat Dec 10 2011 - 10:21:06 CST)
Peptide planarity Dihedral angle restraints Vijay Vammi (Thu Dec 08 2011 - 20:07:12 CST)
- Re: Peptide planarity Dihedral angle restraints Boyang Wang (Thu Dec 08 2011 - 20:17:02 CST)
  - Re: Peptide planarity Dihedral angle restraints Aron Broom (Thu Dec 08 2011 - 21:11:20 CST)
    - Re: Peptide planarity Dihedral angle restraints Vijay Vammi (Thu Dec 08 2011 - 21:20:23 CST)
    - AW: Peptide planarity Dihedral angle restraints Norman Geist (Fri Dec 09 2011 - 00:18:47 CST)
- Re: Peptide planarity Dihedral angle restraints Chris Harrison (Fri Dec 09 2011 - 00:27:29 CST)
  - Re: Peptide planarity Dihedral angle restraints Vijay Vammi (Fri Dec 09 2011 - 00:47:00 CST)
NAMD FEP - Bad Hydrogen group size John Baker (Wed Dec 07 2011 - 05:38:11 CST)
- Re: NAMD FEP - Bad Hydrogen group size Jérôme Hénin (Wed Dec 07 2011 - 06:54:01 CST)
stochastical boundary conditions in NAMD mjyang (Tue Dec 06 2011 - 19:24:17 CST)
- AW: stochastical boundary conditions in NAMD Norman Geist (Wed Dec 07 2011 - 00:38:58 CST)
- Re: stochastical boundary conditions in NAMD Jérôme Hénin (Wed Dec 07 2011 - 04:39:41 CST)
Re: xplor-formated parameters Chris Harrison (Tue Dec 06 2011 - 12:41:05 CST)
Thermodynamic integration questions pepe barrientos (Tue Dec 06 2011 - 10:39:38 CST)
mmView - a tool for mmCIF exploration Daniel Svozil (Tue Dec 06 2011 - 05:38:35 CST)
Calculation of distance traveled by an atom M.Raviprasad (Mon Dec 05 2011 - 14:54:27 CST)
- Re: Calculation of distance traveled by an atom Axel Kohlmeyer (Mon Dec 05 2011 - 17:36:58 CST)
  - RE: Calculation of distance traveled by an atom M.Raviprasad (Mon Dec 05 2011 - 23:11:19 CST)
    - Re: Calculation of distance traveled by an atom Axel Kohlmeyer (Mon Dec 05 2011 - 23:22:53 CST)
    - Re: Calculation of distance traveled by an atom Aron Broom (Tue Dec 06 2011 - 02:43:34 CST)
- Re: Calculation of distance traveled by an atom Aron Broom (Mon Dec 05 2011 - 17:38:33 CST)
  - RE: Calculation of distance traveled by an atom M.Raviprasad (Mon Dec 05 2011 - 23:19:54 CST)
AW: installing namd on ibm cluster (powerpc) Norman Geist (Mon Dec 05 2011 - 03:30:48 CST)
AW: installing namd on ibm cluster (powerpc) Norman Geist (Mon Dec 05 2011 - 00:29:43 CST)
Coulomb 1-4 interactions oguz gurbulak (Fri Dec 02 2011 - 10:11:24 CST)
- Re: Coulomb 1-4 interactions Axel Kohlmeyer (Fri Dec 02 2011 - 10:21:36 CST)
cpu-gpu vs cpu Francesco Pietra (Tue Nov 29 2011 - 00:44:10 CST)
- Re: cpu-gpu vs cpu Axel Kohlmeyer (Tue Nov 29 2011 - 07:41:51 CST)
  - Re: cpu-gpu vs cpu Nicholas M Glykos (Tue Nov 29 2011 - 09:28:34 CST)
    - Re: cpu-gpu vs cpu Axel Kohlmeyer (Tue Nov 29 2011 - 10:19:50 CST)
paper/articule on colvars module Leonardo Herrera (Mon Nov 28 2011 - 19:35:37 CST)
- Re: paper/articule on colvars module Giacomo Fiorin (Tue Nov 29 2011 - 01:12:39 CST)
  - Re: paper/articule on colvars module Leonardo Herrera (Tue Nov 29 2011 - 13:59:02 CST)
- Re: paper/articule on colvars module Branko (Tue Nov 29 2011 - 04:16:42 CST)
help in a FEP restart? Bruno Luís Pinto de Oliveira (Sat Nov 26 2011 - 10:15:13 CST)
- Re: help in a FEP restart? Chris Chipot (Sat Nov 26 2011 - 10:51:57 CST)
charmrun constantly hanging jani vinod (Fri Nov 25 2011 - 00:59:35 CST)
- Re: charmrun constantly hanging Axel Kohlmeyer (Fri Nov 25 2011 - 08:27:08 CST)
  - Re: charmrun constantly hanging jani vinod (Sat Nov 26 2011 - 01:06:22 CST)
    - Re: charmrun constantly hanging Axel Kohlmeyer (Sat Nov 26 2011 - 10:06:22 CST)
equilibrate water molecules Hasan haska (Thu Nov 24 2011 - 01:43:38 CST)
AW: AW: AW: AW: namd-ibverbs fails to start Norman Geist (Thu Nov 24 2011 - 00:15:52 CST)
HEME and Cystein instead of His Raul Araya (Wed Nov 23 2011 - 13:10:36 CST)
- Re: HEME and Cystein instead of His Aron Broom (Wed Nov 23 2011 - 14:02:42 CST)
  - Re: HEME and Cystein instead of His Raul Araya (Wed Nov 23 2011 - 14:25:37 CST)
- RE: HEME and Cystein instead of His Bruno Luís Pinto de Oliveira (Wed Nov 23 2011 - 14:33:39 CST)
Is it possible to print out the force of one specific atom? Wenhao Liu (Wed Nov 23 2011 - 08:29:23 CST)
- Re: Is it possible to print out the force of one specific atom? Michelle Kuttel (Wed Nov 23 2011 - 08:45:22 CST)
  - Re: Is it possible to print out the force of one specific atom? Wenhao Liu (Wed Nov 23 2011 - 08:59:10 CST)
    - Re: Is it possible to print out the force of one specific atom? Ehsan Ban (Wed Nov 23 2011 - 15:45:49 CST)
Re: Predicting the binding affinity and anion bharat gupta (Wed Nov 23 2011 - 07:23:29 CST)
- Re: Re: Predicting the binding affinity and anion Axel Kohlmeyer (Wed Nov 23 2011 - 07:37:19 CST)
- Re: Re: Predicting the binding affinity and anion Aron Broom (Wed Nov 23 2011 - 12:46:33 CST)
AW: AW: Norman Geist (Wed Nov 23 2011 - 01:00:42 CST)
AW: AW: Norman Geist (Wed Nov 23 2011 - 00:59:15 CST)
- AW: AW: Norman Geist (Wed Nov 23 2011 - 01:25:12 CST)
AW: AW: AW: namd-ibverbs fails to start Norman Geist (Wed Nov 23 2011 - 00:09:41 CST)
OpenCL and AMD GPUs Aron Broom (Tue Nov 22 2011 - 22:04:13 CST)
- Re: OpenCL and AMD GPUs Nicholas M Glykos (Wed Nov 23 2011 - 01:01:20 CST)
- Re: OpenCL and AMD GPUs Axel Kohlmeyer (Wed Nov 23 2011 - 05:07:52 CST)
  - Re: OpenCL and AMD GPUs Aron Broom (Wed Nov 23 2011 - 09:06:13 CST)
(no subject) Chandra Ramananjara (Tue Nov 22 2011 - 12:31:08 CST)
- AW: Norman Geist (Wed Nov 23 2011 - 00:01:50 CST)
Re: AW: namd-ibverbs fails to start Axel Kohlmeyer (Tue Nov 22 2011 - 08:02:12 CST)
- AW: AW: namd-ibverbs fails to start Norman Geist (Wed Nov 23 2011 - 00:16:28 CST)
(no subject) Chandra Ramananjara (Tue Nov 22 2011 - 06:53:15 CST)
- (no subject) Gabriel Jara (Tue Nov 22 2011 - 06:59:12 CST)
namd force field Molecular Dynamics (Tue Nov 22 2011 - 06:21:16 CST)
- Re: namd force field Axel Kohlmeyer (Tue Nov 22 2011 - 08:05:08 CST)
  - Re: namd force field felmerino_at_uchile.cl (Tue Nov 22 2011 - 12:14:28 CST)
AW: AW: namd-ibverbs fails to start Norman Geist (Tue Nov 22 2011 - 00:49:46 CST)
AW: AW: namd-ibverbs fails to start Norman Geist (Tue Nov 22 2011 - 00:47:00 CST)
Segmentation violation with adaptive tempering. Nicholas M Glykos (Sun Nov 20 2011 - 05:13:02 CST)
- Re: Segmentation violation with adaptive tempering. johan strumpfer (Mon Nov 21 2011 - 12:04:38 CST)
  - Re: Segmentation violation with adaptive tempering. Nicholas M Glykos (Mon Nov 21 2011 - 12:11:45 CST)
    - Re: Segmentation violation with adaptive tempering. johan strumpfer (Mon Nov 21 2011 - 12:20:28 CST)
Scaled forces, colvars and harmonic con/restraints Michelle Kuttel (Mon Nov 21 2011 - 04:45:39 CST)
- Re: Scaled forces, colvars and harmonic con/restraints Michelle Kuttel (Wed Nov 23 2011 - 08:16:58 CST)
  - Re: Scaled forces, colvars and harmonic con/restraints Giacomo Fiorin (Wed Nov 23 2011 - 09:28:50 CST)
intermittent non-execution of NAMD on tesla P.-L. Chau (Mon Nov 21 2011 - 04:09:04 CST)
fullSamples in ABF: applied at restart? Neelanjana Sengupta (Sun Nov 20 2011 - 22:14:15 CST)
- fullSamples in ABF: applied at restart? Neelanjana Sengupta (Sun Nov 20 2011 - 22:19:00 CST)
  - Re: fullSamples in ABF: applied at restart? Jérôme Hénin (Mon Nov 21 2011 - 02:10:10 CST)
    - Re: fullSamples in ABF: applied at restart? Neelanjana Sengupta (Mon Nov 21 2011 - 02:51:55 CST)
    - Re: fullSamples in ABF: applied at restart? Jérôme Hénin (Mon Nov 21 2011 - 04:11:06 CST)
problem regarding charmm parameter file of carbon nano tube kanchi subbarao rao (Sun Nov 20 2011 - 16:43:01 CST)
- Fwd: problem regarding charmm parameter file of carbon nano tube kanchi subbarao rao (Mon Nov 21 2011 - 05:07:50 CST)
- Re: problem regarding charmm parameter file of carbon nano tube kanchi subbarao rao (Mon Nov 21 2011 - 09:52:36 CST)
Fwd: restrain on COM Swarna M Patra (Fri Nov 18 2011 - 23:33:09 CST)
- Re: Fwd: restrain on COM Jérôme Hénin (Sat Nov 19 2011 - 10:48:41 CST)
namd-ibverbs fails to start David Hemmendinger (Fri Nov 18 2011 - 21:39:20 CST)
'Hands-On' Workshop on Computational Biophysics using VMD and NAMD, February 11-15, 2012 in Urbana, Illinois David Brandon (Thu Nov 17 2011 - 13:46:56 CST)
Umbrella sampling Parisa Akhski (Wed Nov 16 2011 - 15:12:17 CST)
- Re: Umbrella sampling koushik.k (Wed Nov 16 2011 - 22:18:59 CST)
  - Re: Umbrella sampling Jérôme Hénin (Thu Nov 17 2011 - 03:29:23 CST)
Resend - ERROR: Atoms moving too fast; Nikhil Kumar Mittal (Fri Nov 11 2011 - 19:56:39 CST)
- RE: Resend - ERROR: Atoms moving too fast; Nikhil Kumar Mittal (Fri Nov 11 2011 - 20:02:51 CST)
ERROR: Atoms moving too fast; Nikhil Kumar Mittal (Fri Nov 11 2011 - 12:10:52 CST)
- Re: ERROR: Atoms moving too fast; Chris Harrison (Fri Nov 11 2011 - 13:03:52 CST)
Steered dynamics Jacopo Sgrignani (Fri Nov 11 2011 - 04:56:32 CST)
- RE: Steered dynamics JC Gumbart (Sat Nov 12 2011 - 01:18:06 CST)
improper angle Marco Sant (Fri Nov 11 2011 - 02:34:42 CST)
- Re: improper angle johan strumpfer (Fri Nov 11 2011 - 06:21:38 CST)
  - RE: improper angle JC Gumbart (Sat Nov 12 2011 - 01:14:09 CST)
Assertion failed in file @ KRAKEN PAUL NEWMAN (Wed Nov 09 2011 - 10:07:07 CST)
- Re: Assertion failed in file @ KRAKEN Axel Kohlmeyer (Wed Nov 09 2011 - 11:00:04 CST)
  - two NAMD questions Richard Wood (Wed Nov 09 2011 - 22:31:18 CST)
    - Re: two NAMD questions sajad falsafi (Wed Nov 09 2011 - 23:16:18 CST)
PLUMED release 1.3 available Massimiliano Bonomi (Wed Nov 09 2011 - 09:05:09 CST)
Pressure Problems, Excessively High Readings Rajan Vatassery (Tue Nov 08 2011 - 20:43:10 CST)
- Re: Pressure Problems, Excessively High Readings Jeffrey Potoff (Wed Nov 09 2011 - 04:02:30 CST)
- Re: Pressure Problems, Excessively High Readings johan strumpfer (Tue Nov 08 2011 - 21:13:23 CST)
  - Re: Pressure Problems, Excessively High Readings Rajan Vatassery (Mon Nov 14 2011 - 01:14:41 CST)
Low global exclusion count matziast_at_med.uth.gr (Tue Nov 08 2011 - 04:23:47 CST)
Extra bonds-ABF Parisa Akhski (Mon Nov 07 2011 - 10:53:18 CST)
- Re: Extra bonds-ABF Giacomo Fiorin (Mon Nov 07 2011 - 11:01:22 CST)
dextran and or poly-D-glucosamine topology Raul Araya (Fri Nov 04 2011 - 16:58:34 CDT)
membrane simulation at high Temp Jiao, Dian NMN (-EXP) (Fri Nov 04 2011 - 16:50:20 CDT)
- Re: membrane simulation at high Temp Giacomo Fiorin (Fri Nov 04 2011 - 16:56:12 CDT)
  - Re: membrane simulation at high Temp Jiao, Dian NMN (-EXP) (Fri Nov 04 2011 - 17:38:56 CDT)
Running NAMD CUDA Steven Cox (Fri Nov 04 2011 - 15:06:31 CDT)
- Re: Running NAMD CUDA Axel Kohlmeyer (Fri Nov 04 2011 - 15:16:45 CDT)
AW: Reading files for multiple threaded simulations Norman Geist (Fri Nov 04 2011 - 02:28:50 CDT)
(no subject) Gurunath Katagi (Thu Nov 03 2011 - 03:01:19 CDT)
(no subject) Gurunath Katagi (Thu Nov 03 2011 - 03:00:22 CDT)
Re: Reading files for multiple threaded simulations Chris Harrison (Wed Nov 02 2011 - 01:57:36 CDT)
- Re: Reading files for multiple threaded simulations Yi He (Wed Nov 02 2011 - 11:00:11 CDT)
  - AW: Reading files for multiple threaded simulations Norman Geist (Thu Nov 03 2011 - 02:26:05 CDT)
selection of cholesterol molecules Swarna M Patra (Tue Nov 01 2011 - 23:54:06 CDT)
- Re: selection of cholesterol molecules Chris Harrison (Wed Nov 02 2011 - 00:06:35 CDT)
Use of RBCG to convert multiple frames from atomistic trajectory to Coarse grained rohan uttarwar (Tue Nov 01 2011 - 13:13:20 CDT)
- Re: Use of RBCG to convert multiple frames from atomistic trajectory to Coarse grained Axel Kohlmeyer (Tue Nov 01 2011 - 14:59:27 CDT)
Reading files for multiple threaded simulations Yi He (Tue Nov 01 2011 - 12:16:52 CDT)
- AW: Reading files for multiple threaded simulations Norman Geist (Wed Nov 02 2011 - 01:45:32 CDT)
Cluster on commodity hardware Thomas Albers (Mon Oct 31 2011 - 12:37:30 CDT)
(no subject) Buddhadev Maiti (Fri Oct 28 2011 - 22:14:30 CDT)
- Re: Chris Harrison (Mon Oct 31 2011 - 15:24:19 CDT)
minimization and gradient trend Francesco Pietra (Mon Oct 31 2011 - 03:57:10 CDT)
installing namd on ibm cluster (powerpc) Gurunath Katagi (Fri Oct 28 2011 - 15:14:02 CDT)
- Re: installing namd on ibm cluster (powerpc) Chris Harrison (Fri Oct 28 2011 - 17:35:07 CDT)
question about namd simulation on protein in tip4p water box Liqun Zhang (Fri Oct 28 2011 - 13:14:36 CDT)
- Re: question about namd simulation on protein in tip4p water box Chris Harrison (Fri Oct 28 2011 - 13:43:51 CDT)
ForceConstant in Umbrella Sampling Buddhadev Maiti (Fri Oct 28 2011 - 12:38:24 CDT)
- Re: ForceConstant in Umbrella Sampling Chris Harrison (Fri Oct 28 2011 - 18:10:40 CDT)
NAMD on KRAKEN PAUL NEWMAN (Fri Oct 28 2011 - 02:04:00 CDT)
- Re: NAMD on KRAKEN Axel Kohlmeyer (Fri Oct 28 2011 - 04:43:59 CDT)
  - Re: NAMD on KRAKEN PAUL NEWMAN (Fri Oct 28 2011 - 07:55:01 CDT)
    - Re: NAMD on KRAKEN Axel Kohlmeyer (Fri Oct 28 2011 - 08:03:35 CDT)
Carma v.1.1 released. Nicholas M Glykos (Thu Oct 27 2011 - 12:54:24 CDT)
PME and net charge in the system Salvatore Mario Cosseddu (Thu Oct 27 2011 - 12:00:12 CDT)
- Re: PME and net charge in the system Chris Harrison (Thu Oct 27 2011 - 12:12:46 CDT)
  - Re: PME and net charge in the system Salvatore Mario Cosseddu (Thu Oct 27 2011 - 12:20:26 CDT)
Evaluated heat capacities via NAMD are larger than experimental values Mert Gür (Wed Oct 26 2011 - 13:44:35 CDT)
- Re: Evaluated heat capacities via NAMD are larger than experimental values Jun Zhang (Wed Oct 26 2011 - 19:00:18 CDT)
Error with "namd" Bob Masong (Wed Oct 26 2011 - 00:01:21 CDT)
- AW: Error with "namd" Norman Geist (Wed Oct 26 2011 - 02:05:17 CDT)
Accelerated Molecular Dynamics Vijay Vammi (Tue Oct 25 2011 - 16:11:54 CDT)
- Re: Accelerated Molecular Dynamics Yi Wang (Tue Oct 25 2011 - 18:03:33 CDT)
  - Re: Accelerated Molecular Dynamics Vijay Vammi (Tue Oct 25 2011 - 21:04:49 CDT)
    - Re: Accelerated Molecular Dynamics Vijay Vammi (Tue Oct 25 2011 - 23:45:32 CDT)
    - Re: Accelerated Molecular Dynamics Vijay Vammi (Wed Nov 02 2011 - 20:42:07 CDT)
PMF jafar azamat (Tue Oct 25 2011 - 06:52:28 CDT)
- Re: PMF Axel Kohlmeyer (Tue Oct 25 2011 - 07:23:21 CDT)
different velocities problem Hasan haska (Tue Oct 25 2011 - 01:28:22 CDT)
- Re: different velocities problem Jérôme Hénin (Tue Oct 25 2011 - 02:10:14 CDT)
Error with ubqp.pdb in NAMD tutorial Bob Masong (Mon Oct 24 2011 - 22:43:46 CDT)
- Re: Error with ubqp.pdb in NAMD tutorial Jens K. Munk (Tue Oct 25 2011 - 02:10:22 CDT)
What is the proper value of TMDk in TMD simulations? å¸¸å§—ç‡• (Sun Oct 23 2011 - 23:21:19 CDT)
- Re: What is the proper value of TMDk in TMD simulations? Jérôme Hénin (Mon Oct 24 2011 - 03:02:43 CDT)
  - Re: What is the proper value of TMDk in TMD simulations? Gianluca Interlandi (Mon Oct 24 2011 - 11:03:37 CDT)
FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CT2 CT1 CT2 (ATOMS 107 98 100) Jens K. Munk (Sun Oct 23 2011 - 14:39:24 CDT)
- Re: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CT2 CT1 CT2 (ATOMS 107 98 100) Jernej Zidar (Sun Oct 23 2011 - 19:45:56 CDT)
- Re: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CT2 CT1 CT2 (ATOMS 107 98 100) johan strumpfer (Sun Oct 23 2011 - 16:42:07 CDT)
GBIS and hydrophobic term, in replay to Jerome and David discussion Branko (Sun Oct 23 2011 - 09:36:17 CDT)
- Re: GBIS and hydrophobic term, in replay to Jerome and David discussion Jérôme Hénin (Sun Oct 23 2011 - 09:43:08 CDT)
  - Re: GBIS and hydrophobic term, in replay to Jerome and David discussion Branko (Sun Oct 23 2011 - 09:55:27 CDT)
* CGtool force field * HAMID - (Sat Oct 22 2011 - 12:00:19 CDT)
- Re: * CGtool force field * Axel Kohlmeyer (Sat Oct 22 2011 - 12:47:47 CDT)
  - Re: * CGtool force field * HAMID - (Sat Oct 22 2011 - 14:11:14 CDT)
    - Re: * CGtool force field * Axel Kohlmeyer (Sat Oct 22 2011 - 14:36:38 CDT)
- Re: * CGtool force field * Chris Harrison (Sat Oct 22 2011 - 17:02:37 CDT)
  - Re: * CGtool force field * HAMID - (Sun Oct 23 2011 - 03:09:03 CDT)
    - Re: * CGtool force field * Axel Kohlmeyer (Sun Oct 23 2011 - 16:16:47 CDT)
    - Re: * CGtool force field * HAMID - (Wed Oct 26 2011 - 08:47:39 CDT)
About "alchDecouple" in FEP wenhao_at_uchicago.edu (Sat Oct 22 2011 - 10:47:14 CDT)
- Re: About "alchDecouple" in FEP Jérôme Hénin (Sat Oct 22 2011 - 11:51:27 CDT)
  - Re: About "alchDecouple" in FEP wenhao_at_uchicago.edu (Sun Oct 23 2011 - 07:47:26 CDT)
Problems Bionanotechnology Tutorial Salvador H-V (Fri Oct 21 2011 - 22:19:01 CDT)
cellBasisvectors/.xsc fixing/colvars while running amber ff Francesco Pietra (Fri Oct 21 2011 - 13:13:57 CDT)
- Re: cellBasisvectors/.xsc fixing/colvars while running amber ff Giacomo Fiorin (Fri Oct 21 2011 - 17:06:43 CDT)
Error with tclBC to induce shear flow KONG Xian (Thu Oct 20 2011 - 20:59:42 CDT)
coloring method in VMD lam nguyen (Thu Oct 20 2011 - 18:19:14 CDT)
- Re: coloring method in VMD Axel Kohlmeyer (Thu Oct 20 2011 - 18:21:30 CDT)
RBCG electrostatic term HAMID - (Thu Oct 20 2011 - 12:43:33 CDT)
rigid body Dimitrios Tragoudaras (Thu Oct 20 2011 - 12:33:45 CDT)
Sampling schemes with FEP Patargias, George (Thu Oct 20 2011 - 08:13:19 CDT)
- Re: Sampling schemes with FEP Chris Chipot (Thu Oct 20 2011 - 09:16:34 CDT)
how to visualize an alchemical FEP transformation?? Bruno Luís Pinto de Oliveira (Thu Oct 20 2011 - 06:27:47 CDT)
- Re: how to visualize an alchemical FEP transformation?? Axel Kohlmeyer (Thu Oct 20 2011 - 09:02:34 CDT)
  - RE: how to visualize an alchemical FEP transformation?? Bruno Luís Pinto de Oliveira (Thu Oct 20 2011 - 13:28:13 CDT)
TClforce Swarna M Patra (Thu Oct 20 2011 - 03:11:01 CDT)
- Re: TClforce harish vashisth (Thu Oct 20 2011 - 12:29:14 CDT)
- Re: TClforce poker_at_physics.usyd.edu.au (Thu Oct 20 2011 - 21:22:25 CDT)
fftw libraries for ppc Gurunath Katagi (Wed Oct 19 2011 - 22:04:42 CDT)
Using CHARMM Compatible Amber Parameters Ehsan Ban (Wed Oct 19 2011 - 20:10:30 CDT)
- Re: Using CHARMM Compatible Amber Parameters Jernej Zidar (Wed Oct 19 2011 - 20:22:46 CDT)
  - Re: Using CHARMM Compatible Amber Parameters johan strumpfer (Wed Oct 19 2011 - 22:57:48 CDT)
- Re: Using CHARMM Compatible Amber Parameters Axel Kohlmeyer (Thu Oct 20 2011 - 11:34:33 CDT)
  - Re: Using CHARMM Compatible Amber Parameters Ehsan Ban (Sun Oct 23 2011 - 12:57:03 CDT)
Multiple dihedral parameters in X-PLOR format Joe Yelk (Tue Oct 18 2011 - 17:46:57 CDT)
Question about silver nanoparticle simulation Yao Xiao (Wed Oct 19 2011 - 08:37:23 CDT)
- Re: Question about silver nanoparticle simulation Axel Kohlmeyer (Wed Oct 19 2011 - 09:26:27 CDT)
Running AMBER FF with NAMD 2.8-CUDA Francesco Pietra (Wed Oct 19 2011 - 08:14:59 CDT)
- Re: Running AMBER FF with NAMD 2.8-CUDA Nicholas M Glykos (Wed Oct 19 2011 - 08:37:15 CDT)
  - Re: Running AMBER FF with NAMD 2.8-CUDA Francesco Pietra (Wed Oct 19 2011 - 09:23:32 CDT)
    - Re: Running AMBER FF with NAMD 2.8-CUDA Nicholas M Glykos (Wed Oct 19 2011 - 10:06:08 CDT)
Area per lipid error Andres Morales N (Mon Oct 17 2011 - 21:12:33 CDT)
tclforces- tcl extension written in c and built with swig Eva Gonzalez Noya (Mon Oct 17 2011 - 18:30:33 CDT)
- Re: tclforces- tcl extension written in c and built with swig Axel Kohlmeyer (Mon Oct 17 2011 - 18:43:08 CDT)
- Re: tclforces- tcl extension written in c and built with swig Chris Harrison (Mon Oct 17 2011 - 18:46:36 CDT)
membrane moving up in simulation box kanchi subbarao rao (Mon Oct 17 2011 - 01:09:17 CDT)
- Re: membrane moving up in simulation box Marcos Sotomayor (Mon Oct 17 2011 - 01:58:17 CDT)
RE: Hello imran.1.618_at_gmail.com (Sat Oct 15 2011 - 00:32:59 CDT)
Re: what is wrong with this pdb to simulate with NAMD raghav singh (Fri Oct 14 2011 - 12:04:20 CDT)
rigid bonds Francesco Pietra (Fri Oct 14 2011 - 09:24:41 CDT)
- Re: rigid bonds Axel Kohlmeyer (Fri Oct 14 2011 - 09:27:34 CDT)
- Fwd: rigid bonds Francesco Pietra (Fri Oct 14 2011 - 09:44:14 CDT)
RBCG water HAMID - (Thu Oct 13 2011 - 17:45:14 CDT)
unit of force constant for dihedral angle restrain with extrabonds command Ling Wu (Thu Oct 13 2011 - 15:43:13 CDT)
Restarting protein system simulation using different ligand Kevin Kastner (Thu Oct 13 2011 - 12:22:41 CDT)
- Re: Restarting protein system simulation using different ligand Chris Harrison (Sun Oct 16 2011 - 18:41:55 CDT)
Re: iron sulphur cluster parametrization francesco oteri (Thu Oct 13 2011 - 09:03:43 CDT)
membrane moving up in simulation box kanchi subbarao rao (Thu Oct 13 2011 - 01:54:32 CDT)
- Fwd: membrane moving up in simulation box kanchi subbarao rao (Thu Oct 13 2011 - 04:54:15 CDT)
  - Fwd: membrane moving up in simulation box kanchi subbarao rao (Thu Oct 13 2011 - 06:26:12 CDT)
Boundary potential of colvar alpha not working? Yun Luo (Wed Oct 12 2011 - 09:34:27 CDT)
- Re: Boundary potential of colvar alpha not working? Jérôme Hénin (Thu Oct 13 2011 - 07:14:53 CDT)
  - Re: Boundary potential of colvar alpha not working? Yun Luo (Thu Oct 13 2011 - 08:21:15 CDT)
rsh not working Neelanjana Sengupta (Tue Oct 11 2011 - 00:58:27 CDT)
- Re: rsh not working Matteo Rotter (Tue Oct 11 2011 - 13:37:26 CDT)
  - Re: rsh not working Neelanjana Sengupta (Wed Oct 12 2011 - 02:29:16 CDT)
    - Re: rsh not working Chris Harrison (Wed Oct 12 2011 - 10:08:27 CDT)
Questions Kevin Littrell (Mon Oct 10 2011 - 21:20:37 CDT)
- Re: Questions Joshua Adelman (Mon Oct 10 2011 - 21:54:49 CDT)
PBC Wrap + TMD Gianluca Interlandi (Mon Oct 10 2011 - 14:02:58 CDT)
GBIS and hydrophobic solvation Jérôme Hénin (Mon Oct 10 2011 - 07:24:50 CDT)
- Re: GBIS and hydrophobic solvation Branko (Mon Oct 10 2011 - 10:11:42 CDT)
  - Re: GBIS and hydrophobic solvation David Tanner (Thu Oct 13 2011 - 13:40:32 CDT)
install NAMD 2.8 v Namd Namd (Mon Oct 10 2011 - 05:50:53 CDT)
Force Vector Between Two Atoms Ehsan Ban (Fri Oct 07 2011 - 17:14:02 CDT)
- RE: Force Vector Between Two Atoms Bruno Luís Pinto de Oliveira (Sat Oct 08 2011 - 04:25:40 CDT)
  - Re: Force Vector Between Two Atoms Ehsan Ban (Mon Oct 10 2011 - 01:19:55 CDT)
namd log file Namd Namd (Fri Oct 07 2011 - 07:20:02 CDT)
- Re: namd log file Jian Liu (Fri Oct 07 2011 - 19:14:39 CDT)
Re: Minimization doesn't stop when converged Boyang Wang (Fri Oct 07 2011 - 03:56:01 CDT)
- AW: Minimization doesn't stop when converged Norman Geist (Fri Oct 07 2011 - 04:54:47 CDT)
- Re: Minimization doesn't stop when converged Jérôme Hénin (Fri Oct 07 2011 - 05:27:13 CDT)
- Re: Minimization doesn't stop when converged Boyang Wang (Sat Oct 08 2011 - 01:25:24 CDT)
Minimization doesn't stop when converged Norman Geist (Fri Oct 07 2011 - 03:48:36 CDT)
iron sulphur cluster parametrization francesco oteri (Thu Oct 06 2011 - 09:24:31 CDT)
Compiled Windows HPC version. Chewning, Joseph (Tue Oct 04 2011 - 07:04:31 CDT)
Restart from anywhere in DCD trajectory Zack Scholl (Mon Oct 03 2011 - 13:19:41 CDT)
- Re: Restart from anywhere in DCD trajectory johan strumpfer (Mon Oct 03 2011 - 17:16:57 CDT)
How to write a dcd in fortran? lam nguyen (Mon Oct 03 2011 - 13:21:36 CDT)
- Re: How to write a dcd in fortran? Axel Kohlmeyer (Mon Oct 03 2011 - 13:26:54 CDT)
  - Re: How to write a dcd in fortran? lam nguyen (Mon Oct 03 2011 - 14:07:47 CDT)
Help in reverse Free Energy perturbation - hysteresis Bruno Luís Pinto de Oliveira (Mon Oct 03 2011 - 05:24:58 CDT)
- Re: Help in reverse Free Energy perturbation - hysteresis Jérôme Hénin (Mon Oct 03 2011 - 06:49:46 CDT)
  - Re: Help in reverse Free Energy perturbation - hysteresis Chris Chipot (Mon Oct 03 2011 - 07:05:16 CDT)
    - RE: Help in reverse Free Energy perturbation - hysteresis Bruno Luís Pinto de Oliveira (Tue Oct 04 2011 - 14:29:34 CDT)
    - Re: Help in reverse Free Energy perturbation - hysteresis Chris Chipot (Wed Oct 05 2011 - 01:10:24 CDT)
script for equilibration matziast_at_med.uth.gr (Sun Oct 02 2011 - 04:19:19 CDT)
- AW: script for equilibration Norman Geist (Tue Oct 04 2011 - 00:18:04 CDT)
refphrasing of the question for equilibration script matziast_at_med.uth.gr (Fri Sep 30 2011 - 04:16:27 CDT)
refphrasing of the question for equilibration script matziast_at_med.uth.gr (Fri Sep 30 2011 - 03:43:13 CDT)
- Re: refphrasing of the question for equilibration script Jernej Zidar (Fri Sep 30 2011 - 03:50:35 CDT)
Periodic cell has become too small for original patch grid!â€ Andres Morales N (Thu Sep 29 2011 - 23:52:39 CDT)
- Re: Periodic cell has become too small for original patch grid!â€ Axel Kohlmeyer (Fri Sep 30 2011 - 08:06:26 CDT)
an important question for equilibration script matziast_at_med.uth.gr (Thu Sep 29 2011 - 15:44:58 CDT)
- Re: an important question for equilibration script Jernej Zidar (Thu Sep 29 2011 - 18:42:58 CDT)
Dangling Bonds? atsuiai_at_aim.com (Wed Sep 28 2011 - 17:35:12 CDT)
- Re: Dangling Bonds? Axel Kohlmeyer (Wed Sep 28 2011 - 17:58:18 CDT)
- Re: Dangling Bonds? atsuiai_at_aim.com (Thu Sep 29 2011 - 06:23:55 CDT)
- Re: Dangling Bonds? atsuiai_at_aim.com (Thu Sep 29 2011 - 08:45:39 CDT)
TMD and binary coordinate files Bryan Roessler (Wed Sep 28 2011 - 16:40:49 CDT)
ABF with Alpha colvar can't be used on supercomputer? Yun Luo (Wed Sep 28 2011 - 15:38:02 CDT)
- Re: ABF with Alpha colvar can't be used on supercomputer? JC Gumbart (Thu Sep 29 2011 - 01:05:53 CDT)
  - Re: ABF with Alpha colvar can't be used on supercomputer? Jérôme Hénin (Thu Sep 29 2011 - 05:04:42 CDT)
Problem with NAMD2.8 & prmtop files made with AMBER11/AmberTools1.5 Irene Newhouse (Wed Sep 28 2011 - 15:40:24 CDT)
- Re: Problem with NAMD2.8 & prmtop files made with AMBER11/AmberTools1.5 George Madalin Giambasu (Wed Sep 28 2011 - 19:04:22 CDT)
CUDA compiled code for Windows HPC Chewning, Joseph (Wed Sep 28 2011 - 14:52:29 CDT)
restraining residues in NAMD Haydee Valdes (Wed Sep 28 2011 - 10:59:20 CDT)
- Re: restraining residues in NAMD flavio seixas (Wed Sep 28 2011 - 17:32:27 CDT)
  - Re: restraining residues in NAMD johan strumpfer (Wed Sep 28 2011 - 19:44:34 CDT)
membrane simulation and mobility of lipids - blocking ion channel Jorgen Simonsen (Wed Sep 28 2011 - 09:07:50 CDT)
- Re: membrane simulation and mobility of lipids - blocking ion channel HAMID - (Thu Sep 29 2011 - 04:33:48 CDT)
  - Re: membrane simulation and mobility of lipids - blocking ion channel HAMID - (Thu Sep 29 2011 - 04:57:10 CDT)
Trouble running NAMD on win7 Haque-Student,STW, Farhadul (Sun Sep 25 2011 - 23:44:14 CDT)
- Re: Trouble running NAMD on win7 Ajasja LjubetiÄ (Mon Sep 26 2011 - 03:09:19 CDT)
- Re: Trouble running NAMD on win7 Jernej Zidar (Mon Sep 26 2011 - 03:42:19 CDT)
colvar and tclForces with CUDA Jiyong Park (Sun Sep 25 2011 - 02:02:29 CDT)
Epsilon, Rmin for copper ions Francesco Pietra (Sat Sep 24 2011 - 03:55:34 CDT)
how to use variables in colvar configuration file Ling Wu (Fri Sep 23 2011 - 12:26:08 CDT)
- Re: how to use variables in colvar configuration file Jérôme Hénin (Fri Sep 23 2011 - 13:23:55 CDT)
Fwd: Solved stream files and paratool Francesco Pietra (Fri Sep 23 2011 - 10:13:06 CDT)
velocity information Molecular Dynamics (Fri Sep 23 2011 - 08:20:29 CDT)
stream files and paratool Francesco Pietra (Fri Sep 23 2011 - 03:10:52 CDT)
Help in FEP backward/reverse calculation Bruno Luís Pinto de Oliveira (Thu Sep 22 2011 - 14:36:38 CDT)
- Re: Help in FEP backward/reverse calculation Jérôme Hénin (Fri Sep 23 2011 - 03:22:52 CDT)
namd 2.8 new feature Hasan haska (Thu Sep 22 2011 - 08:37:27 CDT)
ABF & distanceZ projection axis more HAMID - (Thu Sep 22 2011 - 03:05:07 CDT)
- Re: ABF & distanceZ projection axis more Jérôme Hénin (Thu Sep 22 2011 - 04:33:02 CDT)
  - Re: ABF & distanceZ projection axis more HAMID - (Thu Sep 22 2011 - 05:36:32 CDT)
force question Hasan haska (Thu Sep 22 2011 - 02:50:18 CDT)
- Re: force question Jérôme Hénin (Thu Sep 22 2011 - 04:32:45 CDT)
  - Re: force question Ehsan Ban (Thu Sep 22 2011 - 05:18:34 CDT)
  - Re: force question Hasan haska (Thu Sep 22 2011 - 05:36:47 CDT)
save the last frame as a pdb file using dcd file Namd Namd (Thu Sep 22 2011 - 02:02:53 CDT)
- Re: save the last frame as a pdb file using dcd file HAMID - (Thu Sep 22 2011 - 03:08:25 CDT)
- Re: save the last frame as a pdb file using dcd file Nicholas M Glykos (Thu Sep 22 2011 - 03:10:21 CDT)
- AW: save the last frame as a pdb file using dcd file Norman Geist (Thu Sep 22 2011 - 03:15:43 CDT)
  - Re : AW: save the last frame as a pdb file using dcd file Namd Namd (Thu Sep 22 2011 - 03:33:05 CDT)
    - AW: AW: save the last frame as a pdb file using dcd file Norman Geist (Thu Sep 22 2011 - 04:33:07 CDT)
Quick TCl scripting question Anthony Rey (Wed Sep 21 2011 - 20:57:07 CDT)
- Re: Quick TCl scripting question Axel Kohlmeyer (Wed Sep 21 2011 - 21:09:50 CDT)
ABF & distanceZ projection axis HAMID - (Wed Sep 21 2011 - 16:15:45 CDT)
- Re: ABF & distanceZ projection axis Giacomo Fiorin (Wed Sep 21 2011 - 19:22:36 CDT)
  - Re: ABF & distanceZ projection axis HAMID - (Thu Sep 22 2011 - 01:20:02 CDT)
ABF results interpretation HAMID - (Wed Sep 21 2011 - 10:22:38 CDT)
Re: ABF question Jérôme Hénin (Wed Sep 21 2011 - 07:01:50 CDT)
membrane system ipsita basu (Wed Sep 21 2011 - 01:30:00 CDT)
- Re: membrane system Jérôme Hénin (Wed Sep 21 2011 - 02:44:42 CDT)
  - Re: membrane system Jérôme Hénin (Wed Sep 21 2011 - 03:47:16 CDT)
  - Re: membrane system Bjoern Olausson (Thu Sep 22 2011 - 03:10:00 CDT)
- Re: membrane system Bjoern Olausson (Wed Sep 21 2011 - 05:02:08 CDT)
NAMD running on windows HPC question Chewning, Joseph (Tue Sep 20 2011 - 07:58:43 CDT)
- Re: NAMD running on windows HPC question Nikolaos Glykos (Tue Sep 20 2011 - 08:23:34 CDT)
- Re: NAMD running on windows HPC question johan strumpfer (Tue Sep 20 2011 - 08:30:51 CDT)
  - RE: NAMD running on windows HPC question Chewning, Joseph (Tue Sep 20 2011 - 08:34:51 CDT)
    - Re: NAMD running on windows HPC question johan strumpfer (Tue Sep 20 2011 - 08:46:51 CDT)
    - Re: NAMD running on windows HPC question Axel Kohlmeyer (Tue Sep 20 2011 - 11:27:23 CDT)
NOE Jacopo Sgrignani (Tue Sep 20 2011 - 07:27:09 CDT)
- Re: NOE Jérôme Hénin (Tue Sep 20 2011 - 08:17:30 CDT)
Re: Fwd: Re : Setting up a membrane simulation Bjoern Olausson (Tue Sep 20 2011 - 04:27:23 CDT)
- Re: Fwd: Re : Setting up a membrane simulation Bjoern Olausson (Tue Sep 20 2011 - 05:43:30 CDT)
Heating in NPT Pellegrini Eric (Mon Sep 19 2011 - 07:44:04 CDT)
Infiniband and commodity hardware Thomas Albers (Sat Sep 17 2011 - 14:59:20 CDT)
- Re: Infiniband and commodity hardware Axel Kohlmeyer (Sun Sep 18 2011 - 02:38:48 CDT)
- AW: Infiniband and commodity hardware Norman Geist (Mon Sep 19 2011 - 01:03:41 CDT)
phosphorilated serine Branko (Sat Sep 17 2011 - 11:01:42 CDT)
Setting up a membrane simulation Pellegrini Eric (Fri Sep 16 2011 - 02:52:05 CDT)
- Re: Setting up a membrane simulation Bjoern Olausson (Fri Sep 16 2011 - 07:13:56 CDT)
  - Re : Setting up a membrane simulation Pellegrini Eric (Mon Sep 19 2011 - 02:09:58 CDT)
Invitation to connect on LinkedIn Ahlam Al-Rawi (Thu Sep 15 2011 - 16:11:12 CDT)
SMD Jacopo Sgrignani (Thu Sep 15 2011 - 07:12:26 CDT)
- Re: SMD Leandro Martínez (Thu Sep 15 2011 - 07:21:15 CDT)
Na ion, Cl ion in TIP4P divya nayar (Thu Sep 15 2011 - 02:42:54 CDT)
time step and total simulation time in conf file Namd Namd (Wed Sep 14 2011 - 09:41:00 CDT)
- Re: time step and total simulation time in conf file Jérôme Hénin (Wed Sep 14 2011 - 10:53:43 CDT)
Constraint failure during equalibration Jiao, Dian NMN (-EXP) (Tue Sep 13 2011 - 12:45:50 CDT)
- Constraint failure during equalibration Jiao, Dian NMN (-EXP) (Tue Sep 13 2011 - 12:55:22 CDT)
- AW: Constraint failure during equalibration Norman Geist (Wed Sep 14 2011 - 00:31:59 CDT)
Differences between ABF and metadynamics Alex (Tue Sep 13 2011 - 05:13:34 CDT)
- Re: Differences between ABF and metadynamics Jérôme Hénin (Tue Sep 13 2011 - 05:43:39 CDT)
  - Re: Differences between ABF and metadynamics Jérôme Hénin (Tue Sep 13 2011 - 08:45:17 CDT)
question about Distance XY Song, Hyundeok (songhk) (Mon Sep 12 2011 - 23:27:05 CDT)
- Re: question about Distance XY Jérôme Hénin (Tue Sep 13 2011 - 02:50:13 CDT)
  - RE: question about Distance XY Song, Hyundeok (songhk) (Tue Sep 13 2011 - 09:10:07 CDT)
Unsubscribe Gmail (Mon Sep 12 2011 - 14:33:58 CDT)
SMD Jacopo Sgrignani (Mon Sep 12 2011 - 02:53:30 CDT)
- Re: SMD Ajasja LjubetiÄ (Mon Sep 12 2011 - 04:07:52 CDT)
restraint with colvars mocule Ling Wu (Sun Sep 11 2011 - 16:25:39 CDT)
- Re: restraint with colvars mocule Jérôme Hénin (Mon Sep 12 2011 - 04:48:33 CDT)
  - Re: restraint with colvars mocule Ling Wu (Mon Sep 12 2011 - 09:53:21 CDT)
    - Re: restraint with colvars mocule Jérôme Hénin (Mon Sep 12 2011 - 10:08:47 CDT)
    - Re: restraint with colvars mocule Giacomo Fiorin (Mon Sep 12 2011 - 11:23:57 CDT)
Nice paper on MD Simulations pawan raghav (Sat Sep 10 2011 - 13:37:00 CDT)
difference between run and minimize snoze pa (Fri Sep 09 2011 - 16:01:55 CDT)
- Re: difference between run and minimize snoze pa (Wed Sep 14 2011 - 10:02:03 CDT)
  - Re: difference between run and minimize snoze pa (Wed Sep 14 2011 - 10:05:56 CDT)
TopoTools for tpr file Hasan haska (Fri Sep 09 2011 - 09:01:44 CDT)
- Re: TopoTools for tpr file Axel Kohlmeyer (Fri Sep 09 2011 - 10:44:42 CDT)
- Re: TopoTools for tpr file Daniel Aguayo (Fri Sep 09 2011 - 10:46:33 CDT)
- Re: TopoTools for tpr file Jeffrey Potoff (Fri Sep 09 2011 - 11:09:22 CDT)
can we run FEP calculation in water sphere? wenhao_at_uchicago.edu (Fri Sep 09 2011 - 03:21:01 CDT)
RE: Temperature during membrane equilibration Andres Morales N (Thu Sep 08 2011 - 18:33:47 CDT)
- Re: Temperature during membrane equilibration Erik Nordgren (Fri Sep 09 2011 - 11:17:53 CDT)
  - RE: Temperature during membrane equilibration Andres Morales N (Fri Sep 09 2011 - 20:57:36 CDT)
help in FEP calculations : analysis/confirmation of results Bruno Luís Pinto de Oliveira (Thu Sep 08 2011 - 13:59:23 CDT)
Temperature during membrane equilibration Andres Morales N (Wed Sep 07 2011 - 23:57:10 CDT)
Bonds are too long after simulation Anthony Rey (Wed Sep 07 2011 - 10:32:11 CDT)
- Re: Bonds are too long after simulation Markus K. Dahlgren (Wed Sep 07 2011 - 12:54:16 CDT)
  - Re: Bonds are too long after simulation Anthony Rey (Wed Sep 07 2011 - 22:48:37 CDT)
- Re: Bonds are too long after simulation flavio seixas (Wed Sep 07 2011 - 13:10:13 CDT)
- Re: Bonds are too long after simulation Axel Kohlmeyer (Wed Sep 07 2011 - 13:18:26 CDT)
namd2_ti.pl Modification of non-creatable array value attempted, subscript -49999 Pete Kekenes-Huskey (Tue Sep 06 2011 - 17:22:26 CDT)
mean square displacement Molecular Dynamics (Mon Sep 05 2011 - 08:15:28 CDT)
- Re: mean square displacement Ajasja LjubetiÄ (Mon Sep 05 2011 - 08:22:55 CDT)
- Re: mean square displacement Axel Kohlmeyer (Mon Sep 05 2011 - 08:42:03 CDT)
Density Profile in VMD oguz gurbulak (Mon Sep 05 2011 - 02:30:50 CDT)
Patch at AutoPsfBuilder flavio seixas (Sun Sep 04 2011 - 14:17:38 CDT)
POPC membrane model in pH 4 zhjpan_at_mail.ustc.edu.cn (Sat Sep 03 2011 - 09:36:58 CDT)
- Re: POPC membrane model in pH 4 Axel Kohlmeyer (Sat Sep 03 2011 - 09:50:08 CDT)
  - Re: Re: POPC membrane model in pH 4 zhjpan_at_mail.ustc.edu.cn (Sat Sep 03 2011 - 10:12:06 CDT)
Hints for building namd2.8 on charm++ ibverbs layer? Bennion, Brian (Fri Sep 02 2011 - 18:06:15 CDT)
(solved) charmrun: ssh_exchange_identification: Connection closed by remote host Leandro Martínez (Fri Sep 02 2011 - 14:44:24 CDT)
Pressure Calculation Priyan Amaras (Fri Sep 02 2011 - 12:43:25 CDT)
Component distanceZ-ABF Parisa Akhski (Fri Sep 02 2011 - 11:21:56 CDT)
- Re: Component distanceZ-ABF Jérôme Hénin (Fri Sep 02 2011 - 16:19:53 CDT)
  - RE: Component distanceZ-ABF Parisa Akhski (Mon Sep 05 2011 - 09:42:17 CDT)
Namd-I: A question about constant force pulling of a group of atoms Ye Yang (Thu Sep 01 2011 - 10:16:18 CDT)
help in FEP calculations_binding free energy difference between 2 inhibitors Bruno Luís Pinto de Oliveira (Thu Sep 01 2011 - 10:04:41 CDT)
- help in FEP calculations_binding free energy difference between 2 inhibitors Bruno Luís Pinto de Oliveira (Mon Sep 05 2011 - 13:08:58 CDT)
  - Re: help in FEP calculations_binding free energy difference between 2 inhibitors Chirag Vora (Mon Sep 05 2011 - 16:36:04 CDT)
Margin Value in NAMD Andrea Holfelder (Wed Aug 31 2011 - 21:42:05 CDT)
- Re: Margin Value in NAMD johan strumpfer (Wed Aug 31 2011 - 22:56:39 CDT)
  - Re: Margin Value in NAMD Andrea Holfelder (Wed Aug 31 2011 - 23:57:36 CDT)
    - Re: Margin Value in NAMD johan strumpfer (Thu Sep 01 2011 - 00:35:30 CDT)
  - Re: Margin Value in NAMD Andrea Holfelder (Thu Sep 01 2011 - 03:09:09 CDT)
Keeping rigidBonds during Minimization David Huggins (Wed Aug 31 2011 - 19:05:05 CDT)
- Re: Keeping rigidBonds during Minimization David Huggins (Mon Sep 12 2011 - 12:20:28 CDT)
  - Re: Keeping rigidBonds during Minimization Jérôme Hénin (Mon Sep 12 2011 - 18:09:58 CDT)
Dock a metal ion into a peptide/protein Andrea Holfelder (Wed Aug 31 2011 - 14:29:39 CDT)
- Re: Dock a metal ion into a peptide/protein Branko (Wed Aug 31 2011 - 15:28:17 CDT)
  - Re: Dock a metal ion into a peptide/protein Andrea Holfelder (Wed Aug 31 2011 - 21:51:27 CDT)
    - Re: Dock a metal ion into a peptide/protein Branko (Thu Sep 01 2011 - 04:09:16 CDT)
HETATM vs ATOM in .pdb file Andrea Holfelder (Wed Aug 31 2011 - 04:56:35 CDT)
- Re: HETATM vs ATOM in .pdb file Axel Kohlmeyer (Wed Aug 31 2011 - 06:16:16 CDT)
- Re: HETATM vs ATOM in .pdb file Bjoern Olausson (Wed Aug 31 2011 - 06:20:55 CDT)
about extrabonds restrain Ling Wu (Mon Aug 29 2011 - 16:22:53 CDT)
- AW: about extrabonds restrain Norman Geist (Tue Aug 30 2011 - 01:18:37 CDT)
  - Re: AW: about extrabonds restrain Ling Wu (Tue Aug 30 2011 - 07:58:25 CDT)
    - AW: AW: about extrabonds restrain Norman Geist (Wed Aug 31 2011 - 00:05:47 CDT)
- Re: about extrabonds restrain Axel Kohlmeyer (Tue Aug 30 2011 - 08:06:04 CDT)
- Re: about extrabonds restrain JC Gumbart (Tue Aug 30 2011 - 08:41:35 CDT)
FATAL ERROR: Low global exclusion count! System unstable or pairlistdist or cutoff too small. Massimiliano Porrini (Mon Aug 29 2011 - 09:36:55 CDT)
- Re: FATAL ERROR: Low global exclusion count! System unstable or pairlistdist or cutoff too small. Chris Harrison (Mon Aug 29 2011 - 11:50:00 CDT)
  - Re: FATAL ERROR: Low global exclusion count! System unstable or pairlistdist or cutoff too small. Massimiliano Porrini (Mon Aug 29 2011 - 14:26:06 CDT)
    - Re: FATAL ERROR: Low global exclusion count! System unstable or pairlistdist or cutoff too small. Chris Harrison (Mon Aug 29 2011 - 19:35:42 CDT)
    - Re: FATAL ERROR: Low global exclusion count! System unstable or pairlistdist or cutoff too small. Chris Harrison (Mon Aug 29 2011 - 20:07:33 CDT)
colvar restrain of water in lipid system Ling Wu (Mon Aug 29 2011 - 09:13:58 CDT)
- Re: colvar restrain of water in lipid system Giacomo Fiorin (Mon Aug 29 2011 - 09:36:39 CDT)
  - Re: colvar restrain of water in lipid system Ling Wu (Mon Aug 29 2011 - 09:55:45 CDT)
    - Re: colvar restrain of water in lipid system Giacomo Fiorin (Mon Aug 29 2011 - 11:06:44 CDT)
    - Re: colvar restrain of water in lipid system Jérôme Hénin (Mon Aug 29 2011 - 11:17:47 CDT)
Using 'Alignment to principal axes ' Andres Morales N (Mon Aug 29 2011 - 00:38:44 CDT)
RNA simulation Juan Antonio Raygoza Garay (Fri Aug 26 2011 - 15:38:38 CDT)
- Re: RNA simulation Chris Harrison (Mon Aug 29 2011 - 19:23:07 CDT)
colvar restrain of water in lipid system Ling Wu (Fri Aug 26 2011 - 14:44:21 CDT)
dummyAtom-ABF Parisa Akhski (Fri Aug 26 2011 - 09:57:13 CDT)
- Re: dummyAtom-ABF Jérôme Hénin (Fri Aug 26 2011 - 10:32:20 CDT)
combining metadynamics simulations Giovanni Bellesia (Fri Aug 26 2011 - 08:40:29 CDT)
- Re: combining metadynamics simulations Giacomo Fiorin (Fri Aug 26 2011 - 09:18:01 CDT)
Heating /Equilibration Babban Mia (Fri Aug 26 2011 - 05:20:23 CDT)
- Re: Heating /Equilibration Axel Kohlmeyer (Fri Aug 26 2011 - 08:16:29 CDT)
SMD-extension MOhan maruthi sena (Fri Aug 26 2011 - 05:18:25 CDT)
- Re: SMD-extension Axel Kohlmeyer (Fri Aug 26 2011 - 08:20:28 CDT)
  - Re: SMD-extension Ehsan Ban (Fri Aug 26 2011 - 08:36:10 CDT)
- Re: SMD-extension johan strumpfer (Fri Aug 26 2011 - 07:26:18 CDT)
About Columb energy of 2 ions in Vacuum wenhao_at_uchicago.edu (Thu Aug 25 2011 - 18:02:04 CDT)
- RE: About Columb energy of 2 ions in Vacuum JC Gumbart (Fri Aug 26 2011 - 01:37:05 CDT)
  - RE: About Columb energy of 2 ions in Vacuum wenhao_at_uchicago.edu (Fri Aug 26 2011 - 02:30:48 CDT)
    - Re: About Columb energy of 2 ions in Vacuum Jérôme Hénin (Fri Aug 26 2011 - 04:30:54 CDT)
How to evaluate the area per lipid and thickness of the lipid bilayer in a membrane-protein system? ÕÅÓÂ (Thu Aug 25 2011 - 01:32:33 CDT)
- Re: How to evaluate the area per lipid and thickness of the lipid bilayer in a membrane-protein system? Boyang Wang (Thu Aug 25 2011 - 01:41:51 CDT)
  - Re: Re: How to evaluate the area per lipid and thickness of the lipid bilayer in a membrane-protein system? å¼ å‹‡ (Thu Aug 25 2011 - 02:26:50 CDT)
    - Re: Re: How to evaluate the area per lipid and thickness of the lipid bilayer in a membrane-protein system? Boyang Wang (Thu Aug 25 2011 - 02:32:01 CDT)
- Re: How to evaluate the area per lipid and thickness of the lipid bilayer in a membrane-protein system? Salvador H-V (Thu Aug 25 2011 - 11:12:49 CDT)
SWM4-NDP Simulation David Huggins (Wed Aug 24 2011 - 14:49:33 CDT)
- Re: SWM4-NDP Simulation David Hardy (Wed Aug 24 2011 - 18:49:22 CDT)
convert pdb format to normal pdb format hamze rahimi (Wed Aug 24 2011 - 04:48:09 CDT)
- Re: convert pdb format to normal pdb format flavio seixas (Wed Aug 24 2011 - 18:05:18 CDT)
Heating /Equilibration Babban Mia (Wed Aug 24 2011 - 02:56:37 CDT)
About Columb energy of 2 ions in Vacuum wenhao_at_uchicago.edu (Tue Aug 23 2011 - 17:28:04 CDT)
- Re: About Columb energy of 2 ions in Vacuum Edward Lyman (Tue Aug 23 2011 - 19:47:25 CDT)
  - Re: About Columb energy of 2 ions in Vacuum wenhao_at_uchicago.edu (Tue Aug 23 2011 - 22:30:29 CDT)
  - Re: About Columb energy of 2 ions in Vacuum wenhao_at_uchicago.edu (Tue Aug 23 2011 - 22:32:08 CDT)
Memory leak patch Andy Somogyi (Tue Aug 23 2011 - 09:20:09 CDT)
Logfile flooded with "The last position output [...]" when IMDon is used. Bjoern Olausson (Tue Aug 23 2011 - 04:32:47 CDT)
'firsttimestep' treated as signed integer ? Nicholas M Glykos (Mon Aug 22 2011 - 12:01:26 CDT)
Ib version and nodelist Neelanjana Sengupta (Mon Aug 22 2011 - 00:36:09 CDT)
- AW: Ib version and nodelist Norman Geist (Mon Aug 22 2011 - 00:50:56 CDT)
distanceXY colvar-ABF Parisa Akhski (Sun Aug 21 2011 - 09:05:16 CDT)
- Re: distanceXY colvar-ABF Giacomo Fiorin (Sun Aug 21 2011 - 12:28:07 CDT)
SASA of PBD files Andrea Holfelder (Sat Aug 20 2011 - 04:11:25 CDT)
- Re: SASA of PBD files David Tanner (Thu Aug 25 2011 - 08:47:31 CDT)
CUDA on GPU Cluster Arvind Kannan (Fri Aug 19 2011 - 17:31:06 CDT)
- AW: CUDA on GPU Cluster Norman Geist (Mon Aug 22 2011 - 00:47:16 CDT)
PBB File Format/Setup for PBC Anna James (Fri Aug 19 2011 - 07:24:11 CDT)
- Re: PBB File Format/Setup for PBC johan strumpfer (Fri Aug 19 2011 - 17:41:04 CDT)
remove translation of protein under spherical boundary conditions kakali sen (Fri Aug 19 2011 - 04:39:24 CDT)
Restarting MD (Disabling Checklist) Babban Mia (Thu Aug 18 2011 - 10:58:55 CDT)
- Re: Restarting MD (Disabling Checklist) Babban Mia (Fri Aug 19 2011 - 06:50:04 CDT)
  - Re: Restarting MD (Disabling Checklist) Joshua Adelman (Fri Aug 19 2011 - 07:18:17 CDT)
Re: Multinode NAMD CUDA GPU Selection Axel Kohlmeyer (Thu Aug 18 2011 - 10:39:18 CDT)
- AW: Multinode NAMD CUDA GPU Selection Norman Geist (Fri Aug 19 2011 - 00:22:56 CDT)
  - Re: AW: Multinode NAMD CUDA GPU Selection Axel Kohlmeyer (Fri Aug 19 2011 - 06:33:28 CDT)
- AW: Multinode NAMD CUDA GPU Selection Norman Geist (Fri Aug 19 2011 - 00:53:31 CDT)
Heating in NAMD Babban Mia (Thu Aug 18 2011 - 10:13:08 CDT)
- Re: Heating in NAMD Erik Nordgren (Fri Aug 19 2011 - 12:52:31 CDT)
  - Re: Heating in NAMD Babban Mia (Sat Aug 20 2011 - 05:37:53 CDT)
    - Re: Heating in NAMD Babban Mia (Sun Aug 21 2011 - 06:06:25 CDT)
Relationship between High temperature and the boiling point of water albus hawking (Wed Aug 17 2011 - 13:29:56 CDT)
- Re: Relationship between High temperature and the boiling point of water Jeffrey Potoff (Thu Aug 18 2011 - 09:22:36 CDT)
(no subject) Andrea Holfelder (Thu Aug 18 2011 - 04:59:05 CDT)
- (no subject) David Rogers (Mon Aug 22 2011 - 20:25:04 CDT)
- (no subject) Axel Kohlmeyer (Tue Aug 23 2011 - 09:37:15 CDT)
RHDO lattice as a PBC unit Cell in NAMD Andrea Holfelder (Thu Aug 18 2011 - 04:59:59 CDT)
Multinode NAMD CUDA GPU Selection Norman Geist (Thu Aug 18 2011 - 01:25:00 CDT)
differences in multiprocessor energy minimization results Markus Metz (Wed Aug 17 2011 - 11:44:19 CDT)
Relative RMSD constraint jiyong (Wed Aug 17 2011 - 02:00:57 CDT)
- Re: Relative RMSD constraint Alexander Predeus (Wed Aug 17 2011 - 02:31:56 CDT)
Truncated octahedron - unwrapping the trajectory etc Alexander Predeus (Tue Aug 16 2011 - 21:46:22 CDT)
MMTools Chathurika Abeyrathne (Tue Aug 16 2011 - 20:03:45 CDT)
- Re: MMTools Axel Kohlmeyer (Wed Aug 17 2011 - 10:15:50 CDT)
  - Re: vmd-l: Re: MMTools Chathurika Abeyrathne (Wed Aug 17 2011 - 19:02:46 CDT)
low dielectric constants in GBIS Branko (Tue Aug 16 2011 - 15:41:04 CDT)
Generalized Born calcs Thomas Bishop (Tue Aug 16 2011 - 14:53:17 CDT)
PME Grid Settings and its significance relative to a cutoff value Andrea Holfelder (Tue Aug 16 2011 - 15:07:14 CDT)
- Re: PME Grid Settings and its significance relative to a cutoff value Erik Nordgren (Fri Aug 19 2011 - 12:38:34 CDT)
  - Re: PME Grid Settings and its significance relative to a cutoff value Axel Kohlmeyer (Fri Aug 19 2011 - 13:05:26 CDT)
Namd / gromacs Sara baretller (Tue Aug 16 2011 - 09:17:41 CDT)
(no subject) Anna James (Tue Aug 16 2011 - 08:38:14 CDT)
- Re: Axel Kohlmeyer (Tue Aug 16 2011 - 08:43:00 CDT)
  - RE: Anna James (Tue Aug 16 2011 - 08:48:51 CDT)
  - RE: Anna James (Tue Aug 16 2011 - 09:20:49 CDT)
Re: AW: Letzte Hilfe Bjoern Olausson (Tue Aug 16 2011 - 06:17:36 CDT)
convergence and stability of simulation Jorgen Simonsen (Mon Aug 15 2011 - 14:08:29 CDT)
AW: Letzte Hilfe Norman Geist (Mon Aug 15 2011 - 07:16:39 CDT)
AW: Batch Mode MD simulation Script for NAMD Norman Geist (Mon Aug 15 2011 - 00:29:43 CDT)
Denaturation via increased temperature Bjoern Olausson (Mon Aug 15 2011 - 04:11:06 CDT)
- Re: Denaturation via increased temperature Bjoern Olausson (Mon Aug 15 2011 - 04:31:25 CDT)
- Re: Denaturation via increased temperature Jernej Zidar (Mon Aug 15 2011 - 04:38:55 CDT)
  - Re: Denaturation via increased temperature Bjoern Olausson (Mon Aug 15 2011 - 06:11:17 CDT)
Lingand Unbinding using SMD Jacopo Sgrignani (Mon Aug 15 2011 - 02:19:17 CDT)
- Re: Lingand Unbinding using SMD Jian Liu (Mon Aug 15 2011 - 03:28:37 CDT)
Re: Moving an atom 1A0 in one timestep then running MD for 10,000 timesteps while holding that one atom fixed Ehsan Ban (Mon Aug 15 2011 - 00:01:22 CDT)
Periodic Boundary Condition for a 630 Amino Acid Protein Babban Mia (Sun Aug 14 2011 - 08:15:28 CDT)
- Re: Periodic Boundary Condition for a 630 Amino Acid Protein Joshua Adelman (Sun Aug 14 2011 - 08:46:11 CDT)
  - Re: Periodic Boundary Condition for a 630 Amino Acid Protein Babban Mia (Sun Aug 14 2011 - 09:19:18 CDT)
MD condition hamze rahimi (Sun Aug 14 2011 - 05:02:36 CDT)
.COOR TO PDB FILE Babban Mia (Sat Aug 13 2011 - 01:11:48 CDT)
- Re: .COOR TO PDB FILE JC Gumbart (Sat Aug 13 2011 - 01:29:04 CDT)
- Re: .COOR TO PDB FILE Ehsan Ban (Sat Aug 13 2011 - 02:47:27 CDT)
- AW: .COOR TO PDB FILE Norman Geist (Mon Aug 15 2011 - 00:34:58 CDT)
Re: Batch Mode MD simulation Script for NAMD Babban Mia (Fri Aug 12 2011 - 05:46:32 CDT)
- Re: Batch Mode MD simulation Script for NAMD Jeffrey Potoff (Fri Aug 12 2011 - 06:45:12 CDT)
  - Re: Batch Mode MD simulation Script for NAMD Axel Kohlmeyer (Fri Aug 12 2011 - 07:53:13 CDT)
    - Re: Batch Mode MD simulation Script for NAMD Jernej Zidar (Fri Aug 12 2011 - 08:03:21 CDT)
- AW: Batch Mode MD simulation Script for NAMD Norman Geist (Fri Aug 12 2011 - 07:02:29 CDT)
- Re: Batch Mode MD simulation Script for NAMD Babban Mia (Fri Aug 12 2011 - 12:06:28 CDT)
  - Re: Batch Mode MD simulation Script for NAMD Babban Mia (Fri Aug 12 2011 - 12:59:45 CDT)
  - RE: Batch Mode MD simulation Script for NAMD Ismail, Mohd F. (Fri Aug 12 2011 - 13:07:59 CDT)
Batch Mode MD simulation Script for NAMD Babban Mia (Thu Aug 11 2011 - 18:56:19 CDT)
- AW: Batch Mode MD simulation Script for NAMD Norman Geist (Fri Aug 12 2011 - 00:47:19 CDT)
Mixed TIP3/TIP4 Waters Keith Battle (Thu Aug 11 2011 - 06:29:18 CDT)
- Re: Mixed TIP3/TIP4 Waters Jernej Zidar (Thu Aug 11 2011 - 07:28:29 CDT)
image centering problem ipsita basu (Thu Aug 11 2011 - 00:41:20 CDT)
sodium ion in water divya nayar (Thu Aug 11 2011 - 00:17:27 CDT)
- Re: sodium ion in water Axel Kohlmeyer (Thu Aug 11 2011 - 00:36:08 CDT)
Re: Topology file for ethanol Babban Mia (Wed Aug 10 2011 - 23:35:37 CDT)
Topology file for ethanol Babban Mia (Wed Aug 10 2011 - 22:58:19 CDT)
Solvation in VMD using Non Standard Solvent System Babban Mia (Wed Aug 10 2011 - 07:35:32 CDT)
- Re: Solvation in VMD using Non Standard Solvent System Axel Kohlmeyer (Wed Aug 10 2011 - 07:47:35 CDT)
Compiling Namd on MAC with Cuda Stan Skafidas (Wed Aug 10 2011 - 07:16:49 CDT)
Custom CHARMM forcefield usage problem Jernej Zidar (Tue Aug 09 2011 - 23:12:04 CDT)
- Re: Custom CHARMM forcefield usage problem Jernej Zidar (Tue Aug 09 2011 - 23:47:30 CDT)
  - RE: Custom CHARMM forcefield usage problem JC Gumbart (Wed Aug 10 2011 - 00:00:55 CDT)
Fwd: Re: Explicit Solvent Sytem (40% Ethanol + 60% Water) Branko (Tue Aug 09 2011 - 13:29:52 CDT)
Blue Waters Andy Somogyi (Tue Aug 09 2011 - 10:18:49 CDT)
Re: Explicit Solvent Sytem (40% Ethanol + 60% Water) Babban Mia (Tue Aug 09 2011 - 09:42:26 CDT)
- RE: Explicit Solvent Sytem (40% Ethanol + 60% Water) Ismail, Mohd F. (Tue Aug 09 2011 - 13:02:19 CDT)
  - Re: Explicit Solvent Sytem (40% Ethanol + 60% Water) Babban Mia (Wed Aug 10 2011 - 04:49:20 CDT)
minimization problem Narasimhan LOGANATHAN (Tue Aug 09 2011 - 07:00:28 CDT)
- Re: minimization problem Jeffrey Potoff (Tue Aug 09 2011 - 07:16:08 CDT)
  - Re: minimization problem Narasimhan LOGANATHAN (Tue Aug 09 2011 - 08:21:37 CDT)
Explicit Solvent Sytem (40% Ethanol + 60% Water) Babban Mia (Tue Aug 09 2011 - 01:20:20 CDT)
patch becoming too small Jorgen Simonsen (Tue Aug 09 2011 - 01:14:33 CDT)
- AW: patch becoming too small Norman Geist (Tue Aug 09 2011 - 02:41:19 CDT)
Lipid bilayer equilibration: Periodic cell has become too small for original patch grid! Andres Morales N (Sun Aug 07 2011 - 21:00:38 CDT)
- Re: Lipid bilayer equilibration: Periodic cell has become too small for original patch grid! Bjoern Olausson (Mon Aug 08 2011 - 02:57:08 CDT)
  - RE: Lipid bilayer equilibration: Periodic cell has become too small for original patch grid! Andres Morales N (Mon Aug 08 2011 - 17:20:56 CDT)
    - Re: Lipid bilayer equilibration: Periodic cell has become too small for original patch grid! Bjoern Olausson (Wed Aug 10 2011 - 02:49:01 CDT)
- Re: Lipid bilayer equilibration: Periodic cell has become too small for original patch grid! flavio seixas (Mon Aug 08 2011 - 21:12:24 CDT)
- Re: Lipid bilayer equilibration: Periodic cell has become too small for original patch grid! Jeffrey Potoff (Mon Aug 08 2011 - 21:12:39 CDT)
NAMD on PS3 Ali Khanlarkhani (Sat Aug 06 2011 - 11:02:22 CDT)
- Re: NAMD on PS3 Andy Somogyi (Sat Aug 06 2011 - 13:16:20 CDT)
nvidia cuda driver version Francesco Pietra (Fri Aug 05 2011 - 08:44:44 CDT)
- AW: nvidia cuda driver version Norman Geist (Mon Aug 08 2011 - 00:04:40 CDT)
Minimization is taking a lot of computing time. Kartheek (Fri Aug 05 2011 - 04:53:42 CDT)
- AW: Minimization is taking a lot of computing time. Norman Geist (Fri Aug 05 2011 - 05:54:49 CDT)
- Minimization is taking a lot of computing time. Kartheek (Tue Aug 09 2011 - 06:06:57 CDT)
  - Re: Minimization is taking a lot of computing time. Branko (Tue Aug 09 2011 - 12:42:17 CDT)
  - AW: Minimization is taking a lot of computing time. Norman Geist (Wed Aug 10 2011 - 00:44:55 CDT)
    - RE: Minimization is taking a lot of computing time. JC Gumbart (Wed Aug 10 2011 - 00:52:16 CDT)
    - AW: Minimization is taking a lot of computing time. Norman Geist (Wed Aug 10 2011 - 01:21:10 CDT)
GBIS on GPU? Danny Xu (Thu Aug 04 2011 - 11:51:57 CDT)
error: expected floating-point number but got Shen, Han (Thu Aug 04 2011 - 10:21:32 CDT)
- Re: error: expected floating-point number but got Axel Kohlmeyer (Thu Aug 04 2011 - 10:29:08 CDT)
online guide for using amber ff in NAMD George Madalin Giambasu (Wed Aug 03 2011 - 11:18:10 CDT)
Re: [ppl] Regarding Compiling in Redhat linux. Phil Miller (Wed Aug 03 2011 - 09:30:01 CDT)
Re: Namd-I: namd compiling problem Ye Yang (Wed Aug 03 2011 - 10:46:13 CDT)
- AW: Namd-I: namd compiling problem Norman Geist (Thu Aug 04 2011 - 00:33:59 CDT)
Namd-I: namd compiling problem Ye Yang (Tue Aug 02 2011 - 22:28:05 CDT)
- AW: Namd-I: namd compiling problem Norman Geist (Wed Aug 03 2011 - 00:23:52 CDT)
RE: System net charge Andres Morales N (Tue Aug 02 2011 - 19:20:38 CDT)
- Re: System net charge Cruz-Chu Eduardo Roberto (Thu Aug 04 2011 - 03:28:45 CDT)
  - RE: System net charge Andres Morales N (Thu Aug 04 2011 - 23:43:11 CDT)
Re: [ppl] Compliling NAMD in RedHat Phil Miller (Tue Aug 02 2011 - 10:10:18 CDT)
Pair interaction and thermo integration Courtney Taylor (Mon Aug 01 2011 - 09:32:38 CDT)
Temperature bath Chathurika Abeyrathne (Mon Aug 01 2011 - 02:20:15 CDT)
'Hands-On' Workshop on Computational Biophysics using VMD and NAMD, October 17-21, 2011, Bremen, Germany David Brandon (Fri Jul 29 2011 - 14:13:05 CDT)
Moving an atom 1A0 in one timestep then running MD for 10,000 timesteps while holding that one atom fixed Ehsan Ban (Fri Jul 29 2011 - 12:40:27 CDT)
namd-I: cionize problem in vmd Ye Yang (Fri Jul 29 2011 - 11:17:10 CDT)
- Re: namd-I: cionize problem in vmd Axel Kohlmeyer (Fri Jul 29 2011 - 11:23:56 CDT)
  - Re: namd-I: cionize problem in vmd Ye Yang (Mon Aug 01 2011 - 11:36:26 CDT)
Dividing a 2D ABF simulations into regions (on nodes with different speeds) Ajasja LjubetiÄ (Fri Jul 29 2011 - 04:44:38 CDT)
- Re: Dividing a 2D ABF simulations into regions (on nodes with different speeds) Axel Kohlmeyer (Fri Jul 29 2011 - 08:34:33 CDT)
  - Re: Dividing a 2D ABF simulations into regions (on nodes with different speeds) Ajasja LjubetiÄ (Fri Jul 29 2011 - 11:56:17 CDT)
About fastest CUDA cards Francesco Pietra (Fri Jul 29 2011 - 04:09:37 CDT)
about D amino acid AB (Fri Jul 29 2011 - 03:50:16 CDT)
- Re: about D amino acid Eduard Schreiner (Fri Jul 29 2011 - 04:27:39 CDT)
System net charge Andres Morales N (Fri Jul 29 2011 - 03:25:11 CDT)
RE: DPPC membrane Andres Morales N (Fri Jul 29 2011 - 03:16:50 CDT)
"Constraint failure in RATTLE algorithm" when restart FEP Dong Luo (Thu Jul 28 2011 - 12:21:28 CDT)
- Re: "Constraint failure in RATTLE algorithm" when restart FEP Dong Luo (Fri Jul 29 2011 - 14:36:44 CDT)
  - Re: "Constraint failure in RATTLE algorithm" when restart FEP Dong Luo (Mon Aug 01 2011 - 10:50:27 CDT)
NAMD energy plugin politr_at_fh.huji.ac.il (Thu Jul 28 2011 - 04:22:42 CDT)
DPPC membrane Andres Morales N (Thu Jul 28 2011 - 01:29:36 CDT)
- Re: DPPC membrane Ajasja LjubetiÄ (Thu Jul 28 2011 - 05:21:10 CDT)
Quartz modelling Nikita Vakula (Thu Jul 28 2011 - 00:46:05 CDT)
- Re: Quartz modelling Cruz-Chu Eduardo Roberto (Thu Jul 28 2011 - 03:20:53 CDT)
Trp-cage folding simulation divya nayar (Thu Jul 28 2011 - 00:09:07 CDT)
colvars, discontinuous rotation JC Gumbart (Wed Jul 27 2011 - 20:41:30 CDT)
- Re: colvars, discontinuous rotation Giacomo Fiorin (Wed Jul 27 2011 - 21:20:41 CDT)
  - Re: colvars, discontinuous rotation JC Gumbart (Wed Jul 27 2011 - 23:27:23 CDT)
Setting integrator parameters for ABF Ajasja LjubetiÄ (Wed Jul 27 2011 - 12:49:24 CDT)
- Re: Setting integrator parameters for ABF Giacomo Fiorin (Wed Jul 27 2011 - 13:12:46 CDT)
  - Re: Setting integrator parameters for ABF Ajasja LjubetiÄ (Wed Jul 27 2011 - 14:01:31 CDT)
    - Re: Setting integrator parameters for ABF Giacomo Fiorin (Wed Jul 27 2011 - 14:10:17 CDT)
    - water sphere plus dielectric esmael (Wed Jul 27 2011 - 14:11:20 CDT)
nitrogen in namd Marco Sant (Wed Jul 27 2011 - 04:47:15 CDT)
- Re: nitrogen in namd Jim Phillips (Wed Jul 27 2011 - 15:07:25 CDT)
  - Re: nitrogen in namd Marco Sant (Sun Jul 31 2011 - 05:47:18 CDT)
- Re: nitrogen in namd Erik Nordgren (Wed Jul 27 2011 - 14:49:04 CDT)
  - Re: nitrogen in namd Jeffrey Potoff (Wed Jul 27 2011 - 15:51:57 CDT)
    - Re: nitrogen in namd Jim Phillips (Thu Jul 28 2011 - 11:57:05 CDT)
using colvars for bending modulus? JC Gumbart (Tue Jul 26 2011 - 15:43:50 CDT)
- Re: using colvars for bending modulus? Jérôme Hénin (Wed Jul 27 2011 - 01:29:59 CDT)
  - RE: using colvars for bending modulus? JC Gumbart (Wed Jul 27 2011 - 01:40:24 CDT)
    - Re: using colvars for bending modulus? Jérôme Hénin (Wed Jul 27 2011 - 03:12:33 CDT)
NAMD 2.8 on Cray XE6 segfaulting Tim Robinson (Tue Jul 26 2011 - 05:46:01 CDT)
- Re: NAMD 2.8 on Cray XE6 segfaulting Jim Phillips (Tue Jul 26 2011 - 11:05:30 CDT)
  - Re: NAMD 2.8 on Cray XE6 segfaulting Jim Phillips (Tue Jul 26 2011 - 11:58:34 CDT)
    - Re: NAMD 2.8 on Cray XE6 segfaulting Jim Phillips (Tue Jul 26 2011 - 16:14:34 CDT)
NAMD 2.8 job submission script for queenbee cnu gromacs (Mon Jul 25 2011 - 18:29:51 CDT)
- Re: NAMD 2.8 job submission script for queenbee Jim Phillips (Tue Jul 26 2011 - 11:13:57 CDT)
- Re: NAMD 2.8 job submission script for queenbee: ManyJobs Thomas Bishop (Tue Jul 26 2011 - 08:46:29 CDT)
Segmentation Faults on Mac OS X Lion Arvind Kannan (Mon Jul 25 2011 - 16:48:21 CDT)
- RE: Segmentation Faults on Mac OS X Lion Jesper Sørensen (Tue Jul 26 2011 - 03:40:33 CDT)
- Re: Segmentation Faults on Mac OS X Lion Jim Phillips (Tue Jul 26 2011 - 15:46:30 CDT)
Segmentation Faults on Mac OS X Lion Arvind Kannan (Mon Jul 25 2011 - 16:39:31 CDT)
is there any difference between non-constrained equilibrium and normal MD production? AB (Mon Jul 25 2011 - 13:04:35 CDT)
combining thermodynamic integration with replica exchange in NAMD Hugh Heldenbrand (Mon Jul 25 2011 - 10:05:50 CDT)
how to generate transparent figures? AB (Sat Jul 23 2011 - 09:59:07 CDT)
- Re: how to generate transparent figures? Nicholas M Glykos (Sat Jul 23 2011 - 10:47:54 CDT)
- Re: how to generate transparent figures? Bjoern Olausson (Mon Jul 25 2011 - 04:04:58 CDT)
SOLVED: Failure to run namd-cuda with gtx-470 Francesco Pietra (Fri Jul 22 2011 - 09:56:34 CDT)
Controlling fans on a GTX 560 ti Ajasja LjubetiÄ (Fri Jul 22 2011 - 05:24:26 CDT)
- Re: Controlling fans on a GTX 560 ti Axel Kohlmeyer (Fri Jul 22 2011 - 08:56:17 CDT)
  - Re: Controlling fans on a GTX 560 ti Ajasja LjubetiÄ (Fri Jul 22 2011 - 09:12:29 CDT)
Re: Yan: analysis question Bjoern Olausson (Fri Jul 22 2011 - 03:01:05 CDT)
how to calculate partial charge for ligand based on CHARMM principle? AB (Thu Jul 21 2011 - 11:49:39 CDT)
- Re: how to calculate partial charge for ligand based on CHARMM principle? Jeffrey Potoff (Thu Jul 21 2011 - 12:02:49 CDT)
Molecule2.C Andy Somogyi (Thu Jul 21 2011 - 11:45:11 CDT)
- Re: Molecule2.C Jim Phillips (Tue Jul 26 2011 - 11:36:33 CDT)
Suspend NAMD (to RAM) Ajasja LjubetiÄ (Wed Jul 20 2011 - 17:10:06 CDT)
- Re: Suspend NAMD (to RAM) Giacomo Fiorin (Wed Jul 20 2011 - 20:41:27 CDT)
- Re: Suspend NAMD (to RAM) Nicholas M Glykos (Thu Jul 21 2011 - 01:20:14 CDT)
  - Re: Suspend NAMD (to RAM) Ajasja LjubetiÄ (Sat Jul 30 2011 - 09:44:23 CDT)
namd files Hasan haska (Wed Jul 20 2011 - 08:17:34 CDT)
- Re: namd files Axel Kohlmeyer (Wed Jul 20 2011 - 08:48:08 CDT)
TIP4P water model Molecular Dynamics (Wed Jul 20 2011 - 07:34:47 CDT)
- Re: TIP4P water model Chris Harrison (Thu Jul 21 2011 - 16:54:33 CDT)
Equilibration Andres Morales N (Tue Jul 19 2011 - 13:39:37 CDT)
- Re: Equilibration bharat gupta (Wed Jun 29 2011 - 01:06:10 CDT)
- Re: Equilibration Chris Harrison (Tue Jul 19 2011 - 14:42:06 CDT)
  - Re: Equilibration Erik Nordgren (Thu Jul 21 2011 - 20:44:38 CDT)
- Membranes Andres Morales N (Tue Jul 19 2011 - 15:46:54 CDT)
  - Re: Membranes Erik Nordgren (Thu Jul 21 2011 - 20:54:46 CDT)
expect NAMD survey emails this week Jim Phillips (Tue Jul 19 2011 - 11:51:22 CDT)
Query about switch function using AMBER ff99SB forcefield and NAMD simulation code Madhurima Jana (Tue Jul 19 2011 - 06:41:25 CDT)
analysis question Namd Namd (Tue Jul 19 2011 - 04:32:06 CDT)
- Re: analysis question Bjoern Olausson (Tue Jul 19 2011 - 05:43:34 CDT)
vmd-l: No APBS output: 'cannot access output file' error Christian Jorgensen (Mon Jul 18 2011 - 18:44:07 CDT)
zinc-finger protein simulation hamze rahimi (Mon Jul 18 2011 - 06:55:08 CDT)
PME or not PME? What happens if PME is turned off? Bjoern Olausson (Mon Jul 18 2011 - 04:10:08 CDT)
- Re: PME or not PME? What happens if PME is turned off? Jérôme Hénin (Mon Jul 18 2011 - 15:27:09 CDT)
  - Re: PME or not PME? What happens if PME is turned off? Bjoern Olausson (Tue Jul 19 2011 - 01:48:50 CDT)
  - Re: PME or not PME? What happens if PME is turned off? Chris Harrison (Tue Jul 19 2011 - 14:45:48 CDT)
Pico scale to nanoscale simulation....alteration if .conf files required amit banerjee (Sun Jul 17 2011 - 21:28:43 CDT)
- Re: Pico scale to nanoscale simulation....alteration if .conf files required Erik Nordgren (Thu Jul 21 2011 - 20:22:25 CDT)
  - Re: Pico scale to nanoscale simulation....alteration if .conf files required amit banerjee (Mon Jul 25 2011 - 07:42:35 CDT)
    - Re: Pico scale to nanoscale simulation....alteration if .conf files required Erik Nordgren (Tue Jul 26 2011 - 20:54:30 CDT)
control distance between solvent and solute Kang Hee Cho (Fri Jul 15 2011 - 20:07:56 CDT)
- Re: control distance between solvent and solute Jim Phillips (Wed Jul 20 2011 - 11:57:16 CDT)
FATAL ERROR: Setting parameter fixedAtomsFile from script failed! Jorgen Simonsen (Fri Jul 15 2011 - 15:55:26 CDT)
- Re: FATAL ERROR: Setting parameter fixedAtomsFile from script failed! Rajan Vatassery (Fri Jul 15 2011 - 16:43:04 CDT)
how to define the numsteps in ABF or metadynamics simulation? ÕÅÓÂ (Thu Jul 14 2011 - 19:48:32 CDT)
- Re: how to define the numsteps in ABF or metadynamics simulation? Jérôme Hénin (Sat Jul 16 2011 - 10:57:21 CDT)
TIP5P-model Maria Kamm (Thu Jul 14 2011 - 19:07:48 CDT)
- Re: TIP5P-model Rajan Vatassery (Thu Jul 14 2011 - 20:30:00 CDT)
hi kanchi subbarao rao (Thu Jul 14 2011 - 12:31:06 CDT)
- Re: hi Sándor Kovács (Thu Jul 14 2011 - 14:19:52 CDT)
FATAL ERROR: Unable to open binary file sibel.cakan (Thu Jul 14 2011 - 05:34:57 CDT)
Colvars "tilt" component force constant units for WHAM Robert Elder (Tue Jul 12 2011 - 16:36:55 CDT)
- Colvars "tilt" component force constant units for WHAM Robert Elder (Tue Jul 12 2011 - 16:48:48 CDT)
  - Re: Colvars "tilt" component force constant units for WHAM Giacomo Fiorin (Tue Jul 12 2011 - 23:19:31 CDT)
    - Re: Colvars "tilt" component force constant units for WHAM Robert Elder (Fri Jul 22 2011 - 11:06:16 CDT)
hi kanchi subbarao rao (Wed Jul 13 2011 - 13:47:30 CDT)
Low global exclusion count errors Austin B. Yongye (Wed Jul 13 2011 - 13:10:10 CDT)
- Re: Low global exclusion count errors Jim Phillips (Mon Jul 18 2011 - 17:00:02 CDT)
protein moving out during npt equilibration bharat gupta (Wed Jul 13 2011 - 10:48:48 CDT)
- Re: protein moving out during npt equilibration Giacomo Fiorin (Wed Jul 13 2011 - 10:54:10 CDT)
Help required for nanoscale simulation amit banerjee (Wed Jul 13 2011 - 03:03:45 CDT)
unsubscribe Tibbitt, Jeffrey A. (Tue Jul 12 2011 - 19:32:21 CDT)
Low global exclusion count Austin B. Yongye (Tue Jul 12 2011 - 15:08:51 CDT)
Problem while using MARTINI force field with NAMD 2.8 rohan uttarwar (Tue Jul 12 2011 - 11:42:14 CDT)
how to define the numsteps in ABF or metadynamics simulation? Clark Zhang (Wed Jul 06 2011 - 23:08:50 CDT)
- Re: how to define the numsteps in ABF or metadynamics simulation? Giacomo Fiorin (Tue Jul 12 2011 - 15:06:17 CDT)
tesla 2050 benchmark Burgess, Don E (Tue Jul 12 2011 - 13:56:45 CDT)
- Re: tesla 2050 benchmark Axel Kohlmeyer (Tue Jul 12 2011 - 14:04:00 CDT)
where can I find parameters for t-BuO(C=O)NH-? AlbertAlbert (Tue Jul 12 2011 - 12:33:39 CDT)
Filtered mail? Austin B. Yongye (Tue Jul 12 2011 - 09:04:32 CDT)
- Re: Filtered mail? Jérôme Hénin (Tue Jul 12 2011 - 10:19:41 CDT)
Using VMD paratool æŽä½³é”® (Mon Jul 11 2011 - 16:24:12 CDT)
Fixed COM Ali Khanlarkhani (Mon Jul 11 2011 - 13:30:32 CDT)
- RE: Fixed COM Parisa Akhski (Mon Jul 11 2011 - 13:52:21 CDT)
  - Re: Fixed COM Ajasja LjubetiÄ (Mon Jul 11 2011 - 14:37:43 CDT)
    - Re: Fixed COM Ajasja LjubetiÄ (Tue Jul 12 2011 - 08:11:04 CDT)
NAMD chares Andy Somogyi (Mon Jul 11 2011 - 10:35:17 CDT)
- Re: NAMD chares Jim Phillips (Mon Jul 18 2011 - 16:47:44 CDT)
Possibility of modifying the non-bonded terms of the potential Ali Emileh (Fri Jul 08 2011 - 16:58:44 CDT)
- Re: Possibility of modifying the non-bonded terms of the potential Jérôme Hénin (Sat Jul 09 2011 - 03:34:36 CDT)
Patch link flavio seixas (Fri Jul 08 2011 - 14:11:38 CDT)
- Re: Patch link Erik Nordgren (Sun Jul 10 2011 - 03:27:51 CDT)
  - Re: Patch link flavio seixas (Mon Jul 11 2011 - 10:16:54 CDT)
temperature-TS with NAMDplot Molecular Dynamics (Fri Jul 08 2011 - 05:44:50 CDT)
- AW: temperature-TS with NAMDplot Norman Geist (Fri Jul 08 2011 - 06:02:14 CDT)
- Re: temperature-TS with NAMDplot Bjoern Olausson (Fri Jul 08 2011 - 06:30:09 CDT)
  - Re: temperature-TS with NAMDplot Axel Kohlmeyer (Fri Jul 08 2011 - 08:09:57 CDT)
    - Re: temperature-TS with NAMDplot Bjoern Olausson (Fri Jul 08 2011 - 09:07:43 CDT)
  - Re: temperature-TS with NAMDplot johan strumpfer (Fri Jul 08 2011 - 07:23:44 CDT)
Implicit solvent simulation jaya c.jose (Fri Jul 08 2011 - 05:35:40 CDT)
- Re: Implicit solvent simulation Bjoern Olausson (Fri Jul 08 2011 - 05:57:03 CDT)
does any body have the parameter file for aldehyde group? AlbertAlbert (Fri Jul 08 2011 - 01:34:22 CDT)
- Re: does any body have the parameter file for aldehyde group? felmerino_at_uchile.cl (Fri Jul 08 2011 - 01:44:15 CDT)
free energy of binding Francesco Pietra (Thu Jul 07 2011 - 04:52:38 CDT)
- AW: free energy of binding Norman Geist (Thu Jul 07 2011 - 05:35:07 CDT)
- Re: free energy of binding Dong Luo (Thu Jul 07 2011 - 10:50:07 CDT)
  - Re: free energy of binding Francesco Pietra (Thu Jul 07 2011 - 16:50:12 CDT)
Failure to run namd-cuda with gtx-470 Francesco Pietra (Wed Jul 06 2011 - 10:44:38 CDT)
- Re: Failure to run namd-cuda with gtx-470 Francesco Pietra (Wed Jul 06 2011 - 16:18:53 CDT)
  - Re: Failure to run namd-cuda with gtx-470 Francesco Pietra (Thu Jul 07 2011 - 01:57:25 CDT)
Transferring environment variables when using charmrun Ajasja LjubetiÄ (Wed Jul 06 2011 - 05:08:54 CDT)
- Re: Transferring environment variables when using charmrun Axel Kohlmeyer (Wed Jul 06 2011 - 07:47:46 CDT)
Difference between cwd and cd Ajasja LjubetiÄ (Wed Jul 06 2011 - 04:43:43 CDT)
- Re: Difference between cwd and cd Axel Kohlmeyer (Wed Jul 06 2011 - 07:49:18 CDT)
  - Re: Difference between cwd and cd Ajasja LjubetiÄ (Wed Jul 06 2011 - 08:59:30 CDT)
membrane simulation ERROR rattle algorithm Jorgen Simonsen (Tue Jul 05 2011 - 10:13:57 CDT)
- Re: membrane simulation ERROR rattle algorithm sajad falsafi (Tue Jul 05 2011 - 11:44:10 CDT)
  - Re: membrane simulation ERROR rattle algorithm Ajasja LjubetiÄ (Tue Jul 05 2011 - 12:01:53 CDT)
clustering of trajectory Bala subramanian (Tue Jul 05 2011 - 09:46:24 CDT)
- Re: clustering of trajectory Nicholas M Glykos (Tue Jul 05 2011 - 09:57:50 CDT)
- Re: clustering of trajectory Jun Zhang (Tue Jul 05 2011 - 20:18:16 CDT)
Re: Re: Protein moving out of box during npt simulation bharat gupta (Tue Jul 05 2011 - 03:40:59 CDT)
- Re: Re: Protein moving out of box during npt simulation Bjoern Olausson (Tue Jul 05 2011 - 04:22:50 CDT)
  - Re: Re: Protein moving out of box during npt simulation snoze pa (Tue Jul 05 2011 - 10:00:23 CDT)
- Re: Re: Protein moving out of box during npt simulation bharat gupta (Tue Jul 05 2011 - 21:25:04 CDT)
  - Re: Re: Protein moving out of box during npt simulation snoze pa (Thu Jul 07 2011 - 10:02:09 CDT)
- Re: Re: Protein moving out of box during npt simulation Bjoern Olausson (Fri Jul 08 2011 - 02:50:29 CDT)
DNA terminal Patch / How could I retain the primes in DNA raghav singh (Tue Jul 05 2011 - 03:23:21 CDT)
Win64-MPI Patriche Simona (Tue Jul 05 2011 - 02:04:17 CDT)
- Re: Win64-MPI Ajasja LjubetiÄ (Tue Jul 05 2011 - 02:11:25 CDT)
  - Re: Win64-MPI Patriche Simona (Tue Jul 12 2011 - 08:08:14 CDT)
    - AW: Win64-MPI Norman Geist (Tue Jul 12 2011 - 08:20:11 CDT)
    - Re: Win64-MPI Ajasja LjubetiÄ (Tue Jul 12 2011 - 08:24:28 CDT)
Re: Protein moving out of box during npt simulation bharat gupta (Tue Jul 05 2011 - 00:33:30 CDT)
- AW: Re: Protein moving out of box during npt simulation Norman Geist (Tue Jul 05 2011 - 01:15:20 CDT)
Re: distortion of some bonds during structure preparation bharat gupta (Mon Jul 04 2011 - 03:36:39 CDT)
bigdcd file help snoze pa (Mon Jul 04 2011 - 01:29:23 CDT)
- RE: bigdcd file help Cosseddu, Salvatore (Mon Jul 04 2011 - 04:11:55 CDT)
  - Re: bigdcd file help sajad falsafi (Mon Jul 04 2011 - 08:52:36 CDT)
Hi: some doubt about nvt and npt equilibration bharat gupta (Sun Jul 03 2011 - 20:36:19 CDT)
- Re: Hi: some doubt about nvt and npt equilibration johan strumpfer (Sun Jul 03 2011 - 20:53:47 CDT)
a bundle of coor files Massimiliano Porrini (Sat Jul 02 2011 - 13:21:56 CDT)
- Re: a bundle of coor files Rajan Vatassery (Sat Jul 02 2011 - 16:26:32 CDT)
  - Re: a bundle of coor files Massimiliano Porrini (Sat Jul 02 2011 - 20:16:05 CDT)
  - Re: a bundle of coor files Massimiliano Porrini (Tue Jul 05 2011 - 10:34:16 CDT)
restart simulation writing in the same .dcd file. Ranyere Deyler (Sat Jul 02 2011 - 02:25:51 CDT)
- SV: restart simulation writing in the same .dcd file. Maria Musgaard (Sat Jul 02 2011 - 03:03:26 CDT)
- Re: restart simulation writing in the same .dcd file. saman amiri (Sat Jul 02 2011 - 10:00:29 CDT)
Re: NPT equilibration bharat gupta (Fri Jul 01 2011 - 04:04:56 CDT)
- AW: Re: NPT equilibration Norman Geist (Fri Jul 01 2011 - 05:49:38 CDT)
- AW: Re: NPT equilibration Norman Geist (Fri Jul 01 2011 - 05:50:23 CDT)
Re: Fatal Error Periodic cell has become too small for original patch grid bharat gupta (Fri Jul 01 2011 - 00:59:56 CDT)
Re: Final production run in MD bharat gupta (Thu Jun 30 2011 - 18:42:23 CDT)
- Re: Re: Final production run in MD Jérôme Hénin (Fri Jul 01 2011 - 02:31:04 CDT)
Fwd: nvidia 275.09.07 driver. SOLVED, NO DRIVER PROBLEM Francesco Pietra (Thu Jun 30 2011 - 14:49:56 CDT)
can RHDO crystal shape works in NAMD pxq_at_dicp.ac.cn (Fri Jul 01 2011 - 01:33:14 CDT)
Accessing Colvars Within NAMD TCL David Rogers (Thu Jun 30 2011 - 10:28:33 CDT)
- Re: Accessing Colvars Within NAMD TCL Jérôme Hénin (Thu Jun 30 2011 - 12:05:01 CDT)
nvidia 275.09.07 driver Francesco Pietra (Thu Jun 30 2011 - 03:24:48 CDT)
Re: Equilibration - NVT & NPT bharat gupta (Thu Jun 30 2011 - 01:36:56 CDT)
Namd-I: Implicit solvent problem Ye Yang (Wed Jun 29 2011 - 16:07:55 CDT)
- Re: Namd-I: Implicit solvent problem Francesco Oteri (Wed Jun 29 2011 - 16:17:21 CDT)
  - Re: Namd-I: Implicit solvent problem Gianluca Interlandi (Wed Jun 29 2011 - 16:31:49 CDT)
How to simulate a charged surface Yingzhe Liu (Wed Jun 22 2011 - 02:53:56 CDT)
Charmm parameter for H2 gas Zhao Lina (Wed Jun 29 2011 - 04:41:15 CDT)
- Re: Charmm parameter for H2 gas Mikhail Suyetin (Wed Jun 29 2011 - 05:00:05 CDT)
AW: Re: Equilibration Norman Geist (Wed Jun 29 2011 - 04:08:26 CDT)
AW: Re: Equilibration Norman Geist (Wed Jun 29 2011 - 04:04:42 CDT)
Re: Energy minimization bharat gupta (Tue Jun 28 2011 - 18:49:01 CDT)
Cannot find bond parameters Gayatri Rathod (Tue Jun 28 2011 - 11:03:45 CDT)
- Re: Cannot find bond parameters Axel Kohlmeyer (Tue Jun 28 2011 - 11:09:12 CDT)
SWM4 water model simulation saman amiri (Mon Jun 27 2011 - 12:27:34 CDT)
Restarting an alchemic FEP calculation Giovanni Bellesia (Mon Jun 27 2011 - 09:32:25 CDT)
- Re: Restarting an alchemic FEP calculation Jérôme Hénin (Mon Jun 27 2011 - 11:03:55 CDT)
Implicit solvent Massimiliano Porrini (Mon Jun 27 2011 - 06:35:00 CDT)
- Re: Implicit solvent David Tanner (Mon Jun 27 2011 - 09:04:24 CDT)
Re: vmd-l: protein-water RDF Ajasja LjubetiÄ (Mon Jun 27 2011 - 03:29:44 CDT)
- Re: vmd-l: protein-water RDF Ajasja LjubetiÄ (Mon Jun 27 2011 - 03:33:13 CDT)
Methanol - Autocorrelation of total dipole moment Chathurika Abeyrathne (Sat Jun 25 2011 - 03:36:06 CDT)
Memory leak and crash before first step Pedro Gonnet (Fri Jun 24 2011 - 14:28:08 CDT)
- Re: Memory leak and crash before first step Pedro Gonnet (Tue Jul 05 2011 - 08:25:34 CDT)
- Re: Memory leak and crash before first step Erik Nordgren (Sun Jul 10 2011 - 04:02:05 CDT)
  - Re: Memory leak and crash before first step Pedro Gonnet (Tue Jul 12 2011 - 15:00:45 CDT)
- Re: Memory leak and crash before first step Jim Phillips (Mon Jul 18 2011 - 16:26:38 CDT)
interpretation of timing data in output Hannes Loeffler (Fri Jun 24 2011 - 04:29:42 CDT)
- Re: interpretation of timing data in output Jim Phillips (Wed Jul 20 2011 - 11:47:04 CDT)
CG-MD high electrostatic energy values sibel.cakan (Fri Jun 24 2011 - 03:40:32 CDT)
Re: formyl and ethanolamide parameters and topology flavio seixas (Thu Jun 23 2011 - 12:08:58 CDT)
- Re: formyl and ethanolamide parameters and topology flavio seixas (Thu Jun 23 2011 - 21:58:27 CDT)
- Re: formyl and ethanolamide parameters and topology Branko (Fri Jun 24 2011 - 03:52:32 CDT)
formyl and ethanolamide parameters and topology Jorgen Simonsen (Thu Jun 23 2011 - 09:52:18 CDT)
- Re: formyl and ethanolamide parameters and topology poker_at_physics.usyd.edu.au (Thu Jun 23 2011 - 19:11:57 CDT)
FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR C H (ATOMS 2 1) Jorgen Simonsen (Thu Jun 23 2011 - 08:51:52 CDT)
- Re: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR C H (ATOMS 2 1) JC Gumbart (Thu Jun 23 2011 - 16:17:59 CDT)
  - Re: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR C H (ATOMS 2 1) Ajasja LjubetiÄ (Fri Jun 24 2011 - 03:46:18 CDT)
slow heating md Hasan haska (Thu Jun 23 2011 - 06:11:51 CDT)
- Re: slow heating md Ajasja LjubetiÄ (Thu Jun 23 2011 - 06:32:24 CDT)
  - Re: slow heating md Richard Wood (Thu Jun 23 2011 - 08:13:25 CDT)
    - Re: slow heating md Grazia Cottone (Thu Jun 23 2011 - 08:33:37 CDT)
    - Re: slow heating md Axel Kohlmeyer (Thu Jun 23 2011 - 09:06:01 CDT)
  - Re: slow heating md poker_at_physics.usyd.edu.au (Thu Jun 23 2011 - 20:00:54 CDT)
How to simulate a charged surface Yingzhe Liu (Thu Jun 23 2011 - 05:43:49 CDT)
finding water around protein divya nayar (Thu Jun 23 2011 - 00:59:56 CDT)
how to get the energy in vacuum of a molecule in NAMD jnsong (Wed Jun 22 2011 - 08:36:40 CDT)
- Re: how to get the energy in vacuum of a molecule in NAMD Jim Phillips (Wed Jul 20 2011 - 11:25:59 CDT)
Re: patch for phosphotyrosine residue bharat gupta (Tue Jun 21 2011 - 20:53:38 CDT)
- Re: Re: patch for phosphotyrosine residue Jim Phillips (Wed Jun 22 2011 - 10:46:17 CDT)
NAMD with TIP5P water David Huggins (Tue Jun 21 2011 - 13:24:49 CDT)
hello murffyp_at_gmail.com (Tue Jun 21 2011 - 07:54:59 CDT)
simulated annealing protocol Massimiliano Porrini (Tue Jun 21 2011 - 07:41:00 CDT)
- Re: simulated annealing protocol Jim Phillips (Wed Jul 20 2011 - 11:31:19 CDT)
  - Re: simulated annealing protocol Massimiliano Porrini (Wed Jul 20 2011 - 12:25:18 CDT)
Re: aligning two molecules by principal axes of inertia using measure.c Ajasja LjubetiÄ (Mon Jun 20 2011 - 09:40:20 CDT)
aligning two molecules by principal axes of inertia using measure.c Ada Sedova (Mon Jun 20 2011 - 08:18:41 CDT)
- AW: aligning two molecules by principal axes of inertia using measure.c Norman Geist (Mon Jun 20 2011 - 09:30:02 CDT)
restraining groups of atoms Massimiliano Porrini (Mon Jun 20 2011 - 07:03:09 CDT)
- Re: restraining groups of atoms Jérôme Hénin (Mon Jun 20 2011 - 07:56:06 CDT)
- Re: restraining groups of atoms Wang Yi (Mon Jun 20 2011 - 08:54:13 CDT)
Periodic Boundary conditions ishiikai08_at_yahoo.co.jp (Mon Jun 20 2011 - 06:11:49 CDT)
vdw value in parameter file ÅÓ´ºÀö (Mon Jun 20 2011 - 02:26:06 CDT)
Re: phosphotyrosine bharat gupta (Sun Jun 19 2011 - 19:26:37 CDT)
- Fwd: phosphotyrosine bharat gupta (Mon Jun 20 2011 - 00:29:04 CDT)
  - Re: Fwd: phosphotyrosine poker_at_physics.usyd.edu.au (Mon Jun 20 2011 - 01:42:49 CDT)
- Re: Re: phosphotyrosine johan strumpfer (Mon Jun 20 2011 - 06:30:03 CDT)
patch needed for tuple is missing JC Gumbart (Sat Jun 18 2011 - 23:49:47 CDT)
- Re: patch needed for tuple is missing Jim Phillips (Mon Jul 18 2011 - 15:35:28 CDT)
How to calculate Binding Free energy in NAMD jnsong (Sat Jun 18 2011 - 01:00:49 CDT)
- Re: How to calculate Binding Free energy in NAMD Chris Chipot (Sat Jun 18 2011 - 07:51:20 CDT)
SWM4 water model simulation saman amiri (Fri Jun 17 2011 - 16:07:14 CDT)
REMD exchange ratios Massimiliano Porrini (Fri Jun 17 2011 - 08:47:48 CDT)
- Re: REMD exchange ratios Jim Phillips (Fri Jun 17 2011 - 12:43:19 CDT)
Re: Fwd: "cuda error cudastreamcreate", Francesco Pietra (Fri Jun 17 2011 - 00:50:05 CDT)
- Re: vmd-l: Re: Fwd: "cuda error cudastreamcreate", John Stone (Fri Jun 17 2011 - 01:22:50 CDT)
  - Re: vmd-l: Re: Fwd: "cuda error cudastreamcreate", Francesco Pietra (Fri Jun 17 2011 - 02:36:49 CDT)
Tcl issue with config script opronkri_at_msu.edu (Fri Jun 17 2011 - 00:06:53 CDT)
- Re: Tcl issue with config script Cristhian Boetsch (Fri Jun 17 2011 - 10:13:25 CDT)
  - RE: Tcl issue with config script Kristopher Opron (Fri Jun 17 2011 - 15:40:31 CDT)
rescaling velocity esmael (Wed Jun 15 2011 - 18:17:58 CDT)
- Re: rescaling velocity Jim Phillips (Fri Jun 17 2011 - 12:45:44 CDT)
  - Re: rescaling velocity esmael (Fri Jun 17 2011 - 13:04:10 CDT)
    - Re: rescaling velocity Ajasja LjubetiÄ (Fri Jun 17 2011 - 13:14:32 CDT)
    - Re: rescaling velocity Jim Phillips (Fri Jun 17 2011 - 13:16:44 CDT)
namd-I: Problems with Namd coarsegrain and Gromacs top file Ye Yang (Wed Jun 15 2011 - 14:50:23 CDT)
Channel flow equilibration Mao Mao (Wed Jun 15 2011 - 11:46:26 CDT)
- Re: Channel flow equilibration Jim Phillips (Wed Jun 15 2011 - 17:02:10 CDT)
NAMD-l: Get the PDB file from Steered Molecular Dynamics output files albus hawking (Tue Jun 14 2011 - 22:56:55 CDT)
- Re: NAMD-l: Get the PDB file from Steered Molecular Dynamics output files Jim Phillips (Fri Jun 17 2011 - 13:14:11 CDT)
Question about equilibration snoze pa (Wed Jun 15 2011 - 11:02:53 CDT)
- Re: Question about equilibration snoze pa (Wed Jun 15 2011 - 11:07:51 CDT)
Re: AW: NAMD crashes with OpenMPI/OpenMX Thomas Albers (Wed Jun 15 2011 - 09:10:28 CDT)
- AW: AW: NAMD crashes with OpenMPI/OpenMX Norman Geist (Wed Jun 15 2011 - 09:37:40 CDT)
  - Re: AW: AW: NAMD crashes with OpenMPI/OpenMX Thomas Albers (Wed Jun 15 2011 - 10:01:00 CDT)
    - AW: AW: AW: NAMD crashes with OpenMPI/OpenMX Norman Geist (Wed Jun 15 2011 - 10:37:47 CDT)
    - Re: AW: AW: AW: NAMD crashes with OpenMPI/OpenMX Jim Phillips (Wed Jun 15 2011 - 11:17:47 CDT)
hi all kanchi subbarao rao (Wed Jun 15 2011 - 04:14:04 CDT)
- Fwd: hi all kanchi subbarao rao (Wed Jun 15 2011 - 11:46:09 CDT)
- Fwd: hi all kanchi subbarao rao (Thu Jun 16 2011 - 07:16:22 CDT)
  - Re: hi all Ajasja LjubetiÄ (Thu Jun 16 2011 - 07:29:53 CDT)
Fwd: cuda error cudastreamcreate. SOLVED (probably) Francesco Pietra (Wed Jun 15 2011 - 02:45:26 CDT)
- Fwd: cuda error cudastreamcreate. SOLVED (probably) Francesco Pietra (Wed Jun 15 2011 - 09:43:28 CDT)
  - Re: cuda error cudastreamcreate. SOLVED (probably) Axel Kohlmeyer (Wed Jun 15 2011 - 09:51:33 CDT)
    - Re: cuda error cudastreamcreate. SOLVED (probably) Francesco Pietra (Thu Jun 16 2011 - 00:57:15 CDT)
    - Re: cuda error cudastreamcreate. SOLVED (probably) Axel Kohlmeyer (Thu Jun 16 2011 - 04:40:03 CDT)
AW: AW: NAMD crashes with OpenMPI/OpenMX Norman Geist (Wed Jun 15 2011 - 01:01:25 CDT)
- Re: AW: AW: NAMD crashes with OpenMPI/OpenMX Jim Phillips (Wed Jun 15 2011 - 11:25:34 CDT)
water is forming bonds between oxigens PAUL NEWMAN (Tue Jun 14 2011 - 16:36:33 CDT)
- AW: water is forming bonds between oxigens Norman Geist (Wed Jun 15 2011 - 01:05:35 CDT)
Impropers in Charmm and OPLS Henriette Elisabeth Autzen (Tue Jun 14 2011 - 08:33:58 CDT)
- Re: Impropers in Charmm and OPLS johan strumpfer (Tue Jun 14 2011 - 10:01:13 CDT)
umbrella sampling by NAMD jafar azamat (Tue Jun 14 2011 - 06:27:45 CDT)
- Re: umbrella sampling by NAMD Jérôme Hénin (Tue Jun 14 2011 - 07:31:53 CDT)
cuda error cudastreamcreate Francesco Pietra (Tue Jun 14 2011 - 00:45:37 CDT)
- Re: cuda error cudastreamcreate Ajasja LjubetiÄ (Tue Jun 14 2011 - 08:23:23 CDT)
- Re: cuda error cudastreamcreate Jim Phillips (Tue Jun 14 2011 - 11:02:33 CDT)
A question on Jarkynski equation Jun Zhang (Mon Jun 13 2011 - 22:01:59 CDT)
- Re: A question on Jarkynski equation Jérôme Hénin (Tue Jun 14 2011 - 03:43:55 CDT)
  - Re: A question on Jarkynski equation Wang Yi (Tue Jun 14 2011 - 08:11:46 CDT)
  - Re: A question on Jarkynski equation Jun Zhang (Tue Jun 14 2011 - 23:03:53 CDT)
namd ( please help me!!! ) Namd Namd (Mon Jun 13 2011 - 14:29:40 CDT)
- Re: namd ( please help me!!! ) Axel Kohlmeyer (Mon Jun 13 2011 - 14:36:24 CDT)
- Re: namd ( please help me!!! ) snoze pa (Mon Jun 13 2011 - 15:12:19 CDT)
NAMD crashes with OpenMPI/OpenMX Thomas Albers (Mon Jun 13 2011 - 11:50:35 CDT)
- Re: NAMD crashes with OpenMPI/OpenMX Jim Phillips (Tue Jun 14 2011 - 11:33:35 CDT)
Protein distort during equilibration snoze pa (Mon Jun 13 2011 - 10:22:10 CDT)
changing solventDielectric in GBIS Andres Colubri (Mon Jun 13 2011 - 07:36:41 CDT)
- Re: changing solventDielectric in GBIS Ajasja LjubetiÄ (Mon Jun 13 2011 - 07:50:42 CDT)
  - Re: changing solventDielectric in GBIS Andres Colubri (Mon Jun 13 2011 - 08:17:36 CDT)
force field Namd Namd (Mon Jun 13 2011 - 03:36:04 CDT)
Iron Oxide and Arsenic Salvador H-V (Sat Jun 11 2011 - 17:09:20 CDT)
- Re: Iron Oxide and Arsenic Axel Kohlmeyer (Sat Jun 11 2011 - 17:16:06 CDT)
  - Re: Iron Oxide and Arsenic Salvador H-V (Sat Jun 11 2011 - 17:25:25 CDT)
Compiling NAMD for CUDA Thomas Albers (Sat Jun 11 2011 - 16:23:01 CDT)
- Re: Compiling NAMD for CUDA Axel Kohlmeyer (Sat Jun 11 2011 - 16:43:28 CDT)
  - Re: Compiling NAMD for CUDA Thomas Albers (Sat Jun 11 2011 - 21:53:56 CDT)
about charmm force field oguz gurbulak (Fri Jun 10 2011 - 09:55:26 CDT)
Re: max number of CPU PEs per GPU? Ajasja LjubetiÄ (Fri Jun 10 2011 - 06:50:44 CDT)
- Re: max number of CPU PEs per GPU? Danny Xu (Fri Jun 10 2011 - 11:20:13 CDT)
  - Re: max number of CPU PEs per GPU? Ajasja LjubetiÄ (Fri Jun 10 2011 - 15:17:43 CDT)
    - Re: max number of CPU PEs per GPU? Danny Xu (Fri Jun 10 2011 - 22:34:34 CDT)
AW: max number of CPU PEs per GPU? Norman Geist (Fri Jun 10 2011 - 06:25:45 CDT)
max number of CPU PEs per GPU? Danny Xu (Fri Jun 10 2011 - 01:17:53 CDT)
- AW: max number of CPU PEs per GPU? Norman Geist (Fri Jun 10 2011 - 02:56:30 CDT)
- Re: max number of CPU PEs per GPU? Jim Phillips (Fri Jun 10 2011 - 15:15:19 CDT)
  - Re: max number of CPU PEs per GPU? Danny Xu (Sat Jun 11 2011 - 00:49:10 CDT)
    - Re: max number of CPU PEs per GPU? Jim Phillips (Sat Jun 11 2011 - 14:12:35 CDT)
Re: Problem with NAMD 2.8 (but not in 2.7) : Endless loop repeating "The last position output ..." Jim Phillips (Thu Jun 09 2011 - 10:53:46 CDT)
about log file Molecular Dynamics (Thu Jun 09 2011 - 04:30:30 CDT)
- Re: about log file Bjoern Olausson (Thu Jun 09 2011 - 05:02:36 CDT)
Problem with NAMD 2.8 (but not in 2.7) : Endless loop repeating "The last position output ..." David McGiven (Wed Jun 08 2011 - 09:00:34 CDT)
- AW: Problem with NAMD 2.8 (but not in 2.7) : Endless loop repeating "The last position output ..." Norman Geist (Thu Jun 09 2011 - 00:26:13 CDT)
- AW: Problem with NAMD 2.8 (but not in 2.7) : Endless loop repeating "The last position output ..." Norman Geist (Thu Jun 09 2011 - 00:36:44 CDT)
- AW: Problem with NAMD 2.8 (but not in 2.7) : Endless loop repeating "The last position output ..." Norman Geist (Thu Jun 09 2011 - 00:44:01 CDT)
Multiple Runs in a Single Conf File Rajan Vatassery (Wed Jun 08 2011 - 03:00:55 CDT)
- AW: Multiple Runs in a Single Conf File Norman Geist (Wed Jun 08 2011 - 03:27:54 CDT)
  - Re: Multiple Runs in a Single Conf File Rajan Vatassery (Wed Jun 08 2011 - 09:53:55 CDT)
    - AW: Multiple Runs in a Single Conf File Norman Geist (Thu Jun 09 2011 - 00:40:18 CDT)
Membrane simulation, Box X,Y enlarge, Z shrink and membrane thickness shrink juan du (Tue Jun 07 2011 - 18:27:25 CDT)
Re: atom select within hbond analysis sajad falsafi (Tue Jun 07 2011 - 09:21:09 CDT)
question about v2.8 sibel.cakan (Tue Jun 07 2011 - 09:01:58 CDT)
atom select within hbond analysis Branko (Tue Jun 07 2011 - 07:40:09 CDT)
Re: Gibbs potential sajad falsafi (Tue Jun 07 2011 - 02:14:40 CDT)
Gibbs potential Patriche Simona (Mon Jun 06 2011 - 10:10:01 CDT)
water equilibration Narasimhan LOGANATHAN (Mon Jun 06 2011 - 08:07:38 CDT)
- Re: water equilibration Wang Yi (Mon Jun 06 2011 - 08:42:26 CDT)
  - Re: water equilibration Narasimhan LOGANATHAN (Mon Jun 06 2011 - 08:55:39 CDT)
Re: AMD-PhenomII-1075_GTX470 NAMD-CUDA performance Axel Kohlmeyer (Mon Jun 06 2011 - 05:50:24 CDT)
- AW: AMD-PhenomII-1075_GTX470 NAMD-CUDA performance Norman Geist (Mon Jun 06 2011 - 06:11:18 CDT)
- Re: AMD-PhenomII-1075_GTX470 NAMD-CUDA performance Axel Kohlmeyer (Mon Jun 06 2011 - 06:29:38 CDT)
  - AW: AMD-PhenomII-1075_GTX470 NAMD-CUDA performance Norman Geist (Mon Jun 06 2011 - 06:49:06 CDT)
- Re: AMD-PhenomII-1075_GTX470 NAMD-CUDA performance Axel Kohlmeyer (Mon Jun 06 2011 - 06:57:35 CDT)
  - AW: AMD-PhenomII-1075_GTX470 NAMD-CUDA performance Norman Geist (Mon Jun 06 2011 - 07:22:45 CDT)
AMD-PhenomII-1075_GTX470 NAMD-CUDA performance Francesco Pietra (Mon Jun 06 2011 - 02:54:52 CDT)
- Fwd: AMD-PhenomII-1075_GTX470 NAMD-CUDA performance Francesco Pietra (Mon Jun 06 2011 - 04:15:44 CDT)
  - Fwd: AMD-PhenomII-1075_GTX470 NAMD-CUDA performance Francesco Pietra (Mon Jun 06 2011 - 04:30:46 CDT)
  - AW: AMD-PhenomII-1075_GTX470 NAMD-CUDA performance Norman Geist (Mon Jun 06 2011 - 04:51:31 CDT)
MARTINI parameters and Bead definitions Edroaldo Lummertz da Rocha (Fri Jun 03 2011 - 18:56:49 CDT)
I M wants to share "legis_2011" with you Dropbox (Fri Jun 03 2011 - 15:20:24 CDT)
metadynamics combined with PCV Anurag Sethi (Fri Jun 03 2011 - 12:14:18 CDT)
- Re: metadynamics combined with PCV Giacomo Fiorin (Fri Jun 03 2011 - 12:28:53 CDT)
  - Re: metadynamics combined with PCV Anurag Sethi (Fri Jun 03 2011 - 14:11:54 CDT)
Ä°lt: Re: heat annealing conf file Molecular Dynamics (Fri Jun 03 2011 - 09:57:07 CDT)
prm and top files for charmm19 force field oguz gurbulak (Fri Jun 03 2011 - 09:22:47 CDT)
CthCreate failed to create fiber Patriche Simona (Fri Jun 03 2011 - 08:52:28 CDT)
- Re: CthCreate failed to create fiber Jim Phillips (Fri Jun 03 2011 - 11:42:44 CDT)
  - Re: CthCreate failed to create fiber Ajasja LjubetiÄ (Tue Jun 07 2011 - 13:57:00 CDT)
    - Re: CthCreate failed to create fiber Jim Phillips (Tue Jun 07 2011 - 18:02:21 CDT)
    - Re: CthCreate failed to create fiber Ajasja LjubetiÄ (Thu Jun 09 2011 - 15:29:25 CDT)
conf file script ( help needed ) Molecular Dynamics (Fri Jun 03 2011 - 08:37:57 CDT)
- Re: conf file script ( help needed ) Axel Kohlmeyer (Fri Jun 03 2011 - 08:45:27 CDT)
  - Re: conf file script ( help needed ) flavio seixas (Mon Jun 06 2011 - 07:02:41 CDT)
- Re: conf file script ( help needed ) flavio seixas (Sat Jun 04 2011 - 07:53:08 CDT)
Alpha P.M.F. with NAMD 2.8 Prathit Chatterjee (Fri Jun 03 2011 - 06:21:46 CDT)
- Re: Alpha P.M.F. with NAMD 2.8 Ajasja LjubetiÄ (Fri Jun 03 2011 - 07:05:47 CDT)
- Re: Alpha P.M.F. with NAMD 2.8 Giacomo Fiorin (Fri Jun 03 2011 - 07:16:05 CDT)
  - Re: Re: Alpha P.M.F. with NAMD 2.8 Prathit Chatterjee (Fri Jun 03 2011 - 07:55:52 CDT)
Periodic Boundary Condition in NAMD Van Ngo (Thu Jun 02 2011 - 23:55:08 CDT)
- Re: Periodic Boundary Condition in NAMD Jim Phillips (Fri Jun 03 2011 - 09:57:38 CDT)
lengthening time-step with constraints causes RMSD "jump" P.-L. Chau (Thu Jun 02 2011 - 06:53:05 CDT)
- Re: lengthening time-step with constraints causes RMSD "jump" Jim Phillips (Thu Jun 02 2011 - 11:11:28 CDT)
  - Re: lengthening time-step with constraints causes RMSD "jump" P.-L. Chau (Thu Jun 02 2011 - 11:23:34 CDT)
    - Re: lengthening time-step with constraints causes RMSD "jump" Jim Phillips (Thu Jun 02 2011 - 15:36:33 CDT)
    - Re: lengthening time-step with constraints causes RMSD "jump" P.-L. Chau (Thu Jun 02 2011 - 16:03:53 CDT)
heat annealing conf file Molecular Dynamics (Thu Jun 02 2011 - 05:26:17 CDT)
- RE: heat annealing conf file Ada Zhan (Thu Jun 02 2011 - 14:02:06 CDT)
Re: Advice on buying GPUs Ajasja LjubetiÄ (Thu Jun 02 2011 - 03:13:10 CDT)
- Re: Advice on buying GPUs Axel Kohlmeyer (Thu Jun 02 2011 - 06:17:14 CDT)
  - Re: Advice on buying GPUs Ajasja Ljubetiè (Thu Jun 02 2011 - 08:27:47 CDT)
regarding vmd kamal Kishor Thakur (Thu Jun 02 2011 - 01:28:36 CDT)
- Re: regarding vmd scott stensland (Thu Jun 02 2011 - 08:59:15 CDT)
question on residue rmsd.tcl amit banerjee (Wed Jun 01 2011 - 22:49:17 CDT)
- RE: question on residue rmsd.tcl Ada Zhan (Thu Jun 02 2011 - 14:06:00 CDT)
  - Re: question on residue rmsd.tcl amit banerjee (Mon Jun 06 2011 - 00:18:48 CDT)
    - RE: question on residue rmsd.tcl Ada Zhan (Mon Jun 06 2011 - 14:25:36 CDT)
problem in distance.tcl amit banerjee (Wed Jun 01 2011 - 22:37:42 CDT)
Fwd: Fwd: hi kanchi subbarao rao (Wed Jun 01 2011 - 13:32:41 CDT)
- Fwd: Fwd: hi kanchi subbarao rao (Thu Jun 02 2011 - 12:44:27 CDT)
  - Re: Fwd: Fwd: hi Axel Kohlmeyer (Thu Jun 02 2011 - 12:52:25 CDT)
Advice on buying GPUs Ajasja LjubetiÄ (Wed Jun 01 2011 - 09:43:24 CDT)
PBC Werner Crous (Wed Jun 01 2011 - 05:09:27 CDT)
- Re: PBC johan strumpfer (Wed Jun 01 2011 - 11:03:04 CDT)
  - Re: PBC johan strumpfer (Wed Jun 01 2011 - 12:19:04 CDT)
Periodic Boundary conditions ishiikai08_at_yahoo.co.jp (Tue May 31 2011 - 21:57:03 CDT)
- Re: Periodic Boundary conditions Jim Phillips (Wed Jun 01 2011 - 13:08:55 CDT)
  - Re:Re: Periodic Boundary conditions ishiikai08_at_yahoo.co.jp (Thu Jun 02 2011 - 03:14:12 CDT)
    - Re: Re: Periodic Boundary conditions Axel Kohlmeyer (Thu Jun 02 2011 - 06:19:54 CDT)
NAMD 2.8 released Jim Phillips (Tue May 31 2011 - 14:55:34 CDT)
restart a simulation Mao Mao (Tue May 31 2011 - 14:50:22 CDT)
- Re: restart a simulation Jim Phillips (Tue May 31 2011 - 15:00:23 CDT)
  - Re: restart a simulation upayan baul (Fri Mar 16 2012 - 06:51:28 CDT)
Fail to Run VMD Àî¼Ñ¼ü (Tue May 31 2011 - 13:53:07 CDT)
- Re: Fail to Run VMD Axel Kohlmeyer (Tue May 31 2011 - 13:57:24 CDT)
Fwd: hi kanchi subbarao rao (Tue May 31 2011 - 05:10:32 CDT)
vdw parameter of metal ion ÅÓ´ºÀö (Tue May 31 2011 - 04:49:55 CDT)
- Re: vdw parameter of metal ion yandong Huang (Thu Jun 02 2011 - 07:32:41 CDT)
  - Re:Re: vdw parameter of metal ion yandong Huang (Thu Jun 02 2011 - 07:34:20 CDT)
Script Help flavio seixas (Sun May 29 2011 - 18:16:51 CDT)
- Re: Script Help Axel Kohlmeyer (Sun May 29 2011 - 18:58:44 CDT)
Question about end of log file Rajan Vatassery (Sun May 29 2011 - 14:14:34 CDT)
- Re: Question about end of log file Jim Phillips (Sun May 29 2011 - 22:37:30 CDT)
  - Re: Question about end of log file Azat Mukhametov (Mon May 30 2011 - 21:53:50 CDT)
Re PMF Branko (Sat May 28 2011 - 12:18:22 CDT)
RBCG water simulation Cristhian Boetsch (Fri May 27 2011 - 12:17:38 CDT)
- Re: RBCG water simulation Chris Harrison (Fri May 27 2011 - 12:49:08 CDT)
  - Re: RBCG water simulation Cristhian Boetsch (Fri Jun 03 2011 - 07:22:38 CDT)
NADPH topology flavio seixas (Fri May 27 2011 - 08:58:17 CDT)
NAMD with GPU error : "Number of VDW types exceeds CUDA LJ_TABLE_SIZE" David McGiven (Fri May 27 2011 - 06:12:42 CDT)
TIP5P water simulation David Huggins (Thu May 26 2011 - 15:57:25 CDT)
Re: vmd-l: measure fit - wrong alignment Jérôme Hénin (Thu May 26 2011 - 13:09:29 CDT)
about conf file oguz gurbulak (Thu May 26 2011 - 09:11:29 CDT)
- Re: about conf file Jim Phillips (Thu May 26 2011 - 09:55:14 CDT)
PSF and PDB file for SWM4 water models saman amiri (Thu May 26 2011 - 07:37:04 CDT)
- Re: PSF and PDB file for SWM4 water models Jim Phillips (Thu May 26 2011 - 09:39:22 CDT)
Truncated octahedron box issues (?) Massimiliano Porrini (Wed May 25 2011 - 10:38:03 CDT)
- Re: Truncated octahedron box issues Q=3F=29?= Nikolaos Glykos (Wed May 25 2011 - 12:15:44 CDT)
- Re: Truncated octahedron box issues Q=3F=29?= Nikolaos Glykos (Wed May 25 2011 - 12:19:03 CDT)
- Re: Truncated octahedron box issues (?) Jim Phillips (Wed May 25 2011 - 13:57:05 CDT)
  - Re: Truncated octahedron box issues (?) Massimiliano Porrini (Thu May 26 2011 - 14:00:49 CDT)
    - Re: Truncated octahedron box issues (?) Jim Phillips (Thu May 26 2011 - 22:59:06 CDT)
restart with constraints causes RMSD "jump" P.-L. Chau (Wed May 25 2011 - 07:24:11 CDT)
- Re: restart with constraints causes RMSD "jump" Jim Phillips (Wed May 25 2011 - 11:31:29 CDT)
  - Re: restart with constraints causes RMSD "jump" P.-L. Chau (Wed May 25 2011 - 12:56:41 CDT)
    - Re: restart with constraints causes RMSD "jump" Jim Phillips (Wed May 25 2011 - 13:40:21 CDT)
The Nudged Elastic Band Approach to Find the Lowest Energy Pathway Between two States Buddhadev Maiti (Tue May 24 2011 - 22:14:14 CDT)
Joining PSF Files PAUL NEWMAN (Tue May 24 2011 - 08:58:24 CDT)
- Re: Joining PSF Files Axel Kohlmeyer (Tue May 24 2011 - 09:00:57 CDT)
  - Re: Joining PSF Files PAUL NEWMAN (Tue May 24 2011 - 09:04:24 CDT)
    - Re: Joining PSF Files Axel Kohlmeyer (Tue May 24 2011 - 09:08:32 CDT)
- Re: Joining PSF Files Jeffrey Potoff (Tue May 24 2011 - 09:04:53 CDT)
the meaning of " 5-ZEROS" " 9-ZEROS" in the DCD file jnsong (Tue May 24 2011 - 03:12:57 CDT)
- Re: the meaning of " 5-ZEROS" " 9-ZEROS" in the DCD file Bjoern Olausson (Tue May 24 2011 - 03:44:23 CDT)
Coulombic component of configurational energy divya nayar (Tue May 24 2011 - 03:12:24 CDT)
Development plan of NAMD? Norman Geist (Tue May 24 2011 - 02:03:37 CDT)
- Re: Development plan of NAMD? Jim Phillips (Tue May 24 2011 - 13:54:09 CDT)
PMF jafar azamat (Tue May 24 2011 - 00:47:30 CDT)
AW: AW: AW: question about wrap atoms to its original coordinates Norman Geist (Mon May 23 2011 - 01:03:53 CDT)
PMF calculation jafar azamat (Mon May 23 2011 - 07:31:13 CDT)
Problem building NAMD (multiple definitions) Miroslav Hodak (Mon May 23 2011 - 05:47:08 CDT)
- Re: Problem building NAMD (multiple definitions) Jim Phillips (Mon May 23 2011 - 17:08:21 CDT)
  - Re: Problem building NAMD (multiple definitions) Axel Kohlmeyer (Mon May 23 2011 - 17:12:21 CDT)
hi murffyp_at_gmail.com (Sun May 22 2011 - 23:14:11 CDT)
Dear friend Niraj kumar (Sun May 22 2011 - 20:29:53 CDT)
questions about the heat diffusion calculation in the tutorial charlie (Sun May 22 2011 - 11:57:56 CDT)
dcd files Molecular Dynamics (Sun May 22 2011 - 08:02:48 CDT)
- Re: dcd files PAUL NEWMAN (Sun May 22 2011 - 08:24:15 CDT)
  - Re: dcd files Axel Kohlmeyer (Sun May 22 2011 - 09:15:48 CDT)
  - Re: dcd files Jim Phillips (Sun May 22 2011 - 14:38:55 CDT)
- Re: dcd files Axel Kohlmeyer (Sun May 22 2011 - 09:10:29 CDT)
error in the orientationAngle Prathit Chatterjee (Sat May 21 2011 - 03:51:10 CDT)
- Re: error in the orientationAngle Giacomo Fiorin (Sat May 21 2011 - 09:47:49 CDT)
  - Re: error in the orientationAngle Prathit Chatterjee (Sun May 22 2011 - 05:01:55 CDT)
    - Re: error in the orientationAngle Ajasja LjubetiÄ (Sun May 22 2011 - 05:48:29 CDT)
SMD of three atom at a time snoze pa (Fri May 20 2011 - 11:32:03 CDT)
- Re: SMD of three atom at a time Chris Harrison (Fri May 20 2011 - 12:22:09 CDT)
  - Re: SMD of three atom at a time snoze pa (Wed Jun 01 2011 - 08:14:39 CDT)
Re: simulation box PAUL NEWMAN (Fri May 20 2011 - 11:11:52 CDT)
- Re: simulation box Axel Kohlmeyer (Fri May 20 2011 - 11:25:36 CDT)
  - Re: simulation box PAUL NEWMAN (Fri May 20 2011 - 11:30:43 CDT)
    - Re: simulation box Axel Kohlmeyer (Fri May 20 2011 - 11:33:20 CDT)
    - Re: simulation box Jeffrey Potoff (Fri May 20 2011 - 11:36:57 CDT)
simulation box PAUL NEWMAN (Fri May 20 2011 - 10:39:48 CDT)
NAMD crashes when writing restart file and dcdfreq is 1 Ajasja LjubetiÄ (Fri May 20 2011 - 05:16:30 CDT)
- Re: NAMD crashes when writing restart file and dcdfreq is 1 Ajasja LjubetiÄ (Fri May 20 2011 - 05:25:31 CDT)
- Re: NAMD crashes when writing restart file and dcdfreq is 1 Jim Phillips (Fri May 20 2011 - 17:06:32 CDT)
My benchmark results with TeslaC2050 Norman Geist (Fri May 20 2011 - 01:02:36 CDT)
Minimisation algorithm Christian Jorgensen (Thu May 19 2011 - 18:31:03 CDT)
- Re: Minimisation algorithm Jim Phillips (Sun May 22 2011 - 14:49:16 CDT)
NAMD 2.8b3 released Jim Phillips (Thu May 19 2011 - 16:28:04 CDT)
Build .pdb and .psf after coarse graining results in errors Edroaldo Lummertz da Rocha (Thu May 19 2011 - 13:37:15 CDT)
last frame and restart are different Francesco Oteri (Thu May 19 2011 - 11:12:22 CDT)
- Re: last frame and restart are different Jim Phillips (Thu May 19 2011 - 14:02:25 CDT)
  - Re: last frame and restart are different Francesco Oteri (Thu May 19 2011 - 15:50:06 CDT)
unsubscribe Cole Gleason (Thu May 19 2011 - 09:37:36 CDT)
Typo in NAMD 2.8b2 output for Accelerated MD Bjoern Olausson (Thu May 19 2011 - 07:25:51 CDT)
- Re: Typo in NAMD 2.8b2 output for Accelerated MD Chris Harrison (Thu May 19 2011 - 09:32:11 CDT)
AW: AW: Automatic GPU selection in NAMD ? Norman Geist (Thu May 19 2011 - 01:41:37 CDT)
Is there any difference between SMD and tclForces? Jun Zhang (Wed May 18 2011 - 20:29:07 CDT)
- Re: Is there any difference between SMD and tclForces? Axel Kohlmeyer (Wed May 18 2011 - 20:34:13 CDT)
RE: CUDA simulation memory usage Jesper SÃ¸rensen (Wed May 18 2011 - 05:55:59 CDT)
- RE: CUDA simulation memory usage Jesper SÃ¸rensen (Wed May 18 2011 - 06:14:51 CDT)
  - AW: CUDA simulation memory usage Norman Geist (Wed May 18 2011 - 07:10:58 CDT)
CUDA simulation memory usage Jesper SÃ¸rensen (Wed May 18 2011 - 05:03:17 CDT)
- Re: CUDA simulation memory usage Jim Phillips (Wed May 18 2011 - 17:37:45 CDT)
  - RE: CUDA simulation memory usage Jesper SÃ¸rensen (Thu May 19 2011 - 03:11:41 CDT)
hi kanchi subbarao rao (Wed May 18 2011 - 03:43:25 CDT)
- Re: hi Giacomo Fiorin (Wed May 18 2011 - 10:28:48 CDT)
  - Re: hi Jim Phillips (Wed May 18 2011 - 17:52:49 CDT)
- Re: hi Bjoern Olausson (Thu May 19 2011 - 04:29:14 CDT)
question about wrap atoms to its original coordinates jnsong (Wed May 18 2011 - 00:06:20 CDT)
- AW: question about wrap atoms to its original coordinates Norman Geist (Wed May 18 2011 - 00:34:33 CDT)
  - Re: AW: question about wrap atoms to its original coordinates jnsong (Thu May 19 2011 - 21:31:54 CDT)
    - AW: AW: question about wrap atoms to its original coordinates Norman Geist (Fri May 20 2011 - 00:04:48 CDT)
Umbrella Sampling Buddhadev Maiti (Tue May 17 2011 - 21:52:38 CDT)
- Re: Umbrella Sampling Jérôme Hénin (Wed May 18 2011 - 09:40:25 CDT)
trajectory_path.tcl Jacopo Sgrignani (Tue May 17 2011 - 09:16:47 CDT)
- Re: trajectory_path.tcl Axel Kohlmeyer (Tue May 17 2011 - 09:38:19 CDT)
Automatic GPU selection in NAMD ? Jesper Sørensen (Tue May 17 2011 - 06:17:43 CDT)
Automatic GPU selection in NAMD ? David McGiven (Tue May 17 2011 - 04:58:56 CDT)
- RE: Automatic GPU selection in NAMD ? Jesper Sørensen (Tue May 17 2011 - 05:05:27 CDT)
  - Re: Automatic GPU selection in NAMD ? David McGiven (Tue May 17 2011 - 05:34:21 CDT)
GPU-CPU small-scale machine for NAMD Francesco Pietra (Mon May 16 2011 - 03:45:37 CDT)
- Re: GPU-CPU small-scale machine for NAMD Darko Stefanovski (Tue May 17 2011 - 12:10:31 CDT)
  - Re: GPU-CPU small-scale machine for NAMD Jim Phillips (Wed May 18 2011 - 12:48:52 CDT)
deca-Ala simulations with different cutoff produce different results Jun Zhang (Mon May 16 2011 - 00:48:36 CDT)
- RE: deca-Ala simulations with different cutoff produce different results Norman Geist (Mon May 16 2011 - 02:12:40 CDT)
  - RE: deca-Ala simulations with different cutoff produce different results Jun Zhang (Mon May 16 2011 - 03:47:44 CDT)
    - AW: deca-Ala simulations with different cutoff produce different results Norman Geist (Mon May 16 2011 - 04:20:58 CDT)
(no subject) Chandra Ramananjara (Sun May 15 2011 - 12:32:07 CDT)
NAMD question snoze pa (Fri May 13 2011 - 16:34:16 CDT)
Re: NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 Bjoern Olausson (Fri May 13 2011 - 13:10:46 CDT)
- Re: NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 Jim Phillips (Fri May 13 2011 - 14:52:53 CDT)
  - Re: NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 Bjoern Olausson (Sat May 14 2011 - 01:12:57 CDT)
- Re: NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 Bjoern Olausson (Mon May 16 2011 - 04:02:51 CDT)
- Re: NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 Bjoern Olausson (Mon May 16 2011 - 13:45:14 CDT)
  - Re: NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 Jim Phillips (Tue May 17 2011 - 13:21:49 CDT)
REMD segmentation fault Massimiliano Porrini (Fri May 13 2011 - 07:58:45 CDT)
- Re: REMD segmentation fault Jim Phillips (Fri May 13 2011 - 08:30:08 CDT)
  - Re: REMD segmentation fault Massimiliano Porrini (Fri May 13 2011 - 08:41:09 CDT)
    - Re: REMD segmentation fault Jim Phillips (Fri May 13 2011 - 08:52:47 CDT)
PhD position in Computational Structural Biology at MPI Muenster Vlad Cojocaru (Fri May 13 2011 - 04:47:24 CDT)
parameter for TFA (trifluoroacetic acid) liupeng012_at_mail.nankai.edu.cn (Fri May 13 2011 - 03:36:55 CDT)
(no subject) Chandra Ramananjara (Thu May 12 2011 - 19:58:21 CDT)
NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 Bjoern Olausson (Thu May 12 2011 - 17:20:09 CDT)
Error when run Replica Exchange Method on Ranger Guoxiong Su (Thu May 12 2011 - 14:13:59 CDT)
FATAL error when run Replica Exchange Method on Franklin Guoxiong Su (Thu May 12 2011 - 14:03:58 CDT)
CUDA limitations Ajasja LjubetiÄ (Thu May 12 2011 - 03:07:02 CDT)
- Re: CUDA limitations Jim Phillips (Thu May 12 2011 - 12:45:44 CDT)
  - Re: CUDA limitations Ajasja LjubetiÄ (Fri May 13 2011 - 07:00:49 CDT)
    - Re: CUDA limitations Jim Phillips (Fri May 13 2011 - 09:02:36 CDT)
    - Re: CUDA limitations Ajasja LjubetiÄ (Thu Jun 09 2011 - 15:32:09 CDT)
  - Re: CUDA limitations Ajasja LjubetiÄ (Fri Jun 24 2011 - 07:37:13 CDT)
NAMD 2.8b2 released Jim Phillips (Wed May 11 2011 - 17:15:43 CDT)
Re: NAMDEnergy Plugin - setting PMEGridSize / mesh density Michael S. Sellers (Cont, ARL/WMRD) (Wed May 11 2011 - 15:29:25 CDT)
NAMDEnergy Plugin - setting PMEGridSize / mesh density Lela Vukovic (Wed May 11 2011 - 14:48:51 CDT)
Corrupt dcd files Marc Baaden (Wed May 11 2011 - 11:15:55 CDT)
- AW: Corrupt dcd files Norman Geist (Thu May 12 2011 - 01:46:51 CDT)
  - Re: AW: Corrupt dcd files Marc Baaden (Sat May 14 2011 - 16:23:30 CDT)
- AW: Corrupt dcd files Norman Geist (Thu May 12 2011 - 01:51:56 CDT)
- AW: Corrupt dcd files Norman Geist (Thu May 12 2011 - 01:53:23 CDT)
  - Re: AW: Corrupt dcd files Jim Phillips (Thu May 12 2011 - 17:20:36 CDT)
    - Re: AW: Corrupt dcd files Marc Baaden (Sun May 15 2011 - 06:28:38 CDT)
what will be the best way to simulate substrate interaction only within a binding pocket of a large protein. Arun Kumar Subramanian (Sat May 07 2011 - 21:20:29 CDT)
- Re: what will be the best way to simulate substrate interaction only within a binding pocket of a large protein. Giacomo Fiorin (Tue May 10 2011 - 15:20:18 CDT)
  - Re: what will be the best way to simulate substrate interaction only within a binding pocket of a large protein. Ajasja LjubetiÄ (Tue May 10 2011 - 15:57:58 CDT)
Namdstats.tcl flavio seixas (Tue May 10 2011 - 14:51:13 CDT)
print center of mass Jacopo Sgrignani (Tue May 10 2011 - 10:54:09 CDT)
- Re: print center of mass Axel Kohlmeyer (Tue May 10 2011 - 11:01:35 CDT)
  - Re: print center of mass Ajasja LjubetiÄ (Tue May 10 2011 - 11:10:48 CDT)
force field for 2-methyl-2,4-pentanediol (MPD) Yang Gao (Tue May 10 2011 - 10:40:40 CDT)
A newer version of win32 libraries Ajasja LjubetiÄ (Mon May 09 2011 - 07:35:47 CDT)
- Re: A newer version of win32 libraries Jim Phillips (Tue May 10 2011 - 14:39:25 CDT)
  - Re: A newer version of win32 libraries Ajasja LjubetiÄ (Tue May 10 2011 - 15:55:06 CDT)
large load rate using implicit solvent charlie (Sun May 08 2011 - 20:45:10 CDT)
(no subject) Chandra Ramananjara (Sun May 08 2011 - 09:37:04 CDT)
ABF atom selection Parisa Akhski (Sat May 07 2011 - 18:14:24 CDT)
- Re: ABF atom selection Jérôme Hénin (Sun May 08 2011 - 11:41:09 CDT)
  - RE: ABF atom selection Parisa Akhski (Tue May 10 2011 - 09:16:29 CDT)
    - Re: ABF atom selection Jérôme Hénin (Tue May 10 2011 - 09:59:08 CDT)
(no subject) Chandra Ramananjara (Sat May 07 2011 - 14:00:37 CDT)
Re: compilation of namd johan strumpfer (Fri May 06 2011 - 09:09:35 CDT)
- Q=AD=94=E5=A4=8D:__compilation_of_namd?= TAO WANG (Sun May 08 2011 - 19:34:03 CDT)
- Q=AD=94=E5=A4=8D:__compilation_of_namd?= TAO WANG (Mon May 09 2011 - 01:27:12 CDT)
  - unsubscribe Gary M. Skinner (Mon May 09 2011 - 03:31:45 CDT)
  - Re: Q=AD=94=E5=A4=8D:__compilation_of_namd?= Jim Phillips (Tue May 10 2011 - 20:32:27 CDT)
REMD across gpus Massimiliano Porrini (Fri May 06 2011 - 07:39:56 CDT)
- REMD across gpus Massimiliano Porrini (Sun May 08 2011 - 06:02:19 CDT)
  - REMD across gpus Massimiliano Porrini (Mon May 09 2011 - 09:28:51 CDT)
AW: AW: Running NAMD parallel on two machines with 3 CUDAs Norman Geist (Fri May 06 2011 - 01:36:20 CDT)
ABF atom selection question Parisa Akhski (Thu May 05 2011 - 21:50:00 CDT)
compilation of namd TAO WANG (Thu May 05 2011 - 21:08:37 CDT)
- AW: compilation of namd Norman Geist (Fri May 06 2011 - 00:46:01 CDT)
  - ??: compilation of namd TAO WANG (Fri May 06 2011 - 00:56:41 CDT)
    - AW: compilation of namd Norman Geist (Fri May 06 2011 - 01:16:56 CDT)
msd calculation for lipid bilayers cnu gromacs (Thu May 05 2011 - 14:22:24 CDT)
Running NAMD parallel on two machines with 3 CUDAs Darko Stefanovski (Thu May 05 2011 - 11:53:40 CDT)
- AW: Running NAMD parallel on two machines with 3 CUDAs Norman Geist (Fri May 06 2011 - 00:36:27 CDT)
- AW: Running NAMD parallel on two machines with 3 CUDAs Norman Geist (Fri May 06 2011 - 00:41:11 CDT)
AMD Multicore + CUDA Benchmarks, are them ok ? David McGiven (Thu May 05 2011 - 04:08:30 CDT)
- Re: AMD Multicore + CUDA Benchmarks, are them ok ? Nicholas M Glykos (Thu May 05 2011 - 04:31:52 CDT)
  - Re: AMD Multicore + CUDA Benchmarks, are them ok ? Axel Kohlmeyer (Thu May 05 2011 - 08:47:56 CDT)
  - Re: AMD Multicore + CUDA Benchmarks, are them ok ? Axel Kohlmeyer (Thu May 05 2011 - 08:57:18 CDT)
alpha pmf Prathit Chatterjee (Wed May 04 2011 - 00:55:40 CDT)
- Re: alpha pmf felmerino_at_uchile.cl (Wed May 04 2011 - 02:37:06 CDT)
  - Re: alpha pmf Ajasja LjubetiÄ (Wed May 04 2011 - 03:04:14 CDT)
  - Re: alpha pmf Jérôme Hénin (Tue May 10 2011 - 03:37:24 CDT)
(no subject) Nicolas Sapay (Tue May 03 2011 - 11:51:42 CDT)
run tests with CUDA Massimiliano Porrini (Mon May 02 2011 - 16:25:17 CDT)
- Re: run tests with CUDA Axel Kohlmeyer (Mon May 02 2011 - 16:55:18 CDT)
- Re: run tests with CUDA Nicholas M Glykos (Tue May 03 2011 - 03:09:12 CDT)
  - Re: run tests with CUDA Massimiliano Porrini (Wed May 04 2011 - 11:45:09 CDT)
implicit solvent and cuda Francesco Oteri (Mon May 02 2011 - 16:03:15 CDT)
- Re: implicit solvent and cuda Jim Phillips (Tue May 10 2011 - 20:24:17 CDT)
Forcefield for simulating peptide with heparin!!!! Aditya Ranganathan (Mon May 02 2011 - 07:24:56 CDT)
WG: Abnormal EOF Error in Extra Bonds File Norman Geist (Mon May 02 2011 - 06:48:41 CDT)
NAMD_2.7_AIX-POWER-MPI Buddhadev Maiti (Sun May 01 2011 - 21:28:41 CDT)
Add bonds and topology file problem Edroaldo Lummertz da Rocha (Sun May 01 2011 - 16:57:16 CDT)
Add bonds and topology file problem Edroaldo Lummertz da Rocha (Sun May 01 2011 - 15:20:01 CDT)
- Re: Add bonds and topology file problem Axel Kohlmeyer (Sun May 01 2011 - 15:52:30 CDT)
non-bonded potential in NAMD Molecular Dynamics (Sat Apr 30 2011 - 15:06:58 CDT)
- Re: non-bonded potential in NAMD Jérôme Hénin (Sat Apr 30 2011 - 17:28:14 CDT)
colvars orientation problem appears in 2.8 only? JC Gumbart (Thu Apr 28 2011 - 18:41:17 CDT)
- Re: colvars orientation problem appears in 2.8 only? Jérôme Hénin (Fri Apr 29 2011 - 06:16:55 CDT)
ERROR: CUDA-enabled NAMD requires at least one patch per process Arash Azari (Wed Apr 27 2011 - 23:49:56 CDT)
question about rotation force in SMD jnsong (Wed Apr 27 2011 - 09:34:09 CDT)
- Re: question about rotation force in SMD Giacomo Fiorin (Wed Apr 27 2011 - 10:00:33 CDT)
freeEnergy parsing error Lada Biedermannová (Wed Apr 27 2011 - 09:08:46 CDT)
how to apply different temperature simultaneously to different atoms in the same system charlie (Wed Apr 27 2011 - 02:41:08 CDT)
A namd2.8b1 bug ? charlie (Wed Apr 27 2011 - 02:23:56 CDT)
- Re: A namd2.8b1 bug ? Jim Phillips (Tue May 10 2011 - 21:02:49 CDT)
modify NAMD code for Lee-Edwards boundary conditions and compute stress tensor Van Ngo (Tue Apr 26 2011 - 19:17:47 CDT)
Abnormal EOF Error in Extra Bonds File Eli Fine (Tue Apr 26 2011 - 14:22:11 CDT)
- Re: Abnormal EOF Error in Extra Bonds File Jim Phillips (Tue May 10 2011 - 20:15:18 CDT)
Coarse Graining problem resolved Stefan Franzen (Tue Apr 26 2011 - 05:32:21 CDT)
Coarse Graining setup question Stefan Franzen (Tue Apr 26 2011 - 05:13:23 CDT)
CG parameterization problem Stefan Franzen (Tue Apr 26 2011 - 05:07:32 CDT)
velocity error during steered MD Markus K. Dahlgren (Tue Apr 26 2011 - 09:08:32 CDT)
ABF calculation using RMSD Buddhadev Maiti (Mon Apr 25 2011 - 22:14:39 CDT)
- Re: ABF calculation using RMSD Giacomo Fiorin (Mon Apr 25 2011 - 22:26:54 CDT)
Gold nanoparticle and 1-octanethiol Edroaldo Lummertz da Rocha (Mon Apr 25 2011 - 13:14:22 CDT)
- Re: Gold nanoparticle and 1-octanethiol Edroaldo Lummertz da Rocha (Wed Apr 27 2011 - 07:01:52 CDT)
  - Re: Gold nanoparticle and 1-octanethiol Edroaldo Lummertz da Rocha (Thu Apr 28 2011 - 19:07:44 CDT)
'cutting' colvars.traj file Branko (Sat Apr 23 2011 - 12:28:58 CDT)
- Re: 'cutting' colvars.traj file Wang Yi (Sat Apr 23 2011 - 12:54:15 CDT)
  - Re: 'cutting' colvars.traj file Branko (Sat Apr 23 2011 - 13:07:20 CDT)
    - Re: 'cutting' colvars.traj file Bjoern Olausson (Wed Apr 27 2011 - 05:53:41 CDT)
  - Re: 'cutting' colvars.traj file Bjoern Olausson (Tue May 03 2011 - 05:45:23 CDT)
FATAL ERROR: Bad global angle count! PAUL NEWMAN (Fri Apr 22 2011 - 19:42:02 CDT)
- Re: FATAL ERROR: Bad global angle count! PAUL NEWMAN (Sat Apr 23 2011 - 22:04:37 CDT)
  - Re: FATAL ERROR: Bad global angle count! johan strumpfer (Sun Apr 24 2011 - 16:16:52 CDT)
pbc wrap option for x,y,z lengths Zumot, Elia Nabil (Fri Apr 22 2011 - 14:03:29 CDT)
- Re: pbc wrap option for x,y,z lengths Axel Kohlmeyer (Fri Apr 22 2011 - 22:21:56 CDT)
  - RE: pbc wrap option for x,y,z lengths Zumot, Elia Nabil (Fri Apr 22 2011 - 22:52:11 CDT)
question on modifyAppliedForces() Bennion, Brian (Fri Apr 22 2011 - 12:11:27 CDT)
- Re: question on modifyAppliedForces() Jim Phillips (Tue May 10 2011 - 21:31:42 CDT)
Can I set a range to limit the ABF Shen, Han (Wed Apr 20 2011 - 10:24:46 CDT)
- Re: Can I set a range to limit the ABF Giacomo Fiorin (Wed Apr 20 2011 - 11:25:44 CDT)
infrequent rattle failure with charmm36 Edward Lyman (Wed Apr 20 2011 - 08:47:59 CDT)
- Re: infrequent rattle failure with charmm36 Markus K. Dahlgren (Wed Apr 20 2011 - 09:30:11 CDT)
  - Re: infrequent rattle failure with charmm36 Edward Lyman (Wed Apr 20 2011 - 09:50:37 CDT)
new error in NAMD2.8b1 with fixedAtoms dklose_at_uni-osnabrueck.de (Tue Apr 19 2011 - 11:45:25 CDT)
- Re: new error in NAMD2.8b1 with fixedAtoms Jim Phillips (Tue May 10 2011 - 20:01:25 CDT)
  - Re: new error in NAMD2.8b1 with fixedAtoms alex digenova bravo (Fri May 13 2011 - 23:19:54 CDT)
ABF simulation with extendedLagrangian on keeps crashing Ajasja LjubetiÄ (Tue Apr 19 2011 - 10:55:57 CDT)
- Re: ABF simulation with extendedLagrangian on keeps crashing Ajasja LjubetiÄ (Tue Apr 19 2011 - 11:05:09 CDT)
  - Re: ABF simulation with extendedLagrangian on keeps crashing Giacomo Fiorin (Tue Apr 19 2011 - 11:41:55 CDT)
Reduce the frequency of load balancer output Ajasja LjubetiÄ (Tue Apr 19 2011 - 09:23:04 CDT)
- Re: Reduce the frequency of load balancer output Jim Phillips (Tue May 10 2011 - 19:12:30 CDT)
Does GB Implicit Solvent handle explicit ions? David Tanner (Sun Apr 17 2011 - 06:39:19 CDT)
- Re: Does GB Implicit Solvent handle explicit ions? Gianluca Interlandi (Sun Apr 17 2011 - 22:43:37 CDT)
SMD for two steered directions å¸¸å§—ç‡• (Sun Apr 17 2011 - 09:51:12 CDT)
- Re: SMD for two steered directions felmerino_at_uchile.cl (Sun Apr 17 2011 - 13:53:35 CDT)
  - Re: SMD for two steered directions Jérôme Hénin (Sun Apr 17 2011 - 14:31:36 CDT)
question on the center of mass calculation in colvar Hyonseok Hwang (Sat Apr 16 2011 - 09:57:16 CDT)
- Re: question on the center of mass calculation in colvar Giacomo Fiorin (Sat Apr 16 2011 - 10:33:23 CDT)
- Re: question on the center of mass calculation in colvar Jérôme Hénin (Sat Apr 16 2011 - 10:55:11 CDT)
topology and parameter files Molecular Dynamics (Sat Apr 16 2011 - 07:13:28 CDT)
NAMDenergy calculations for nucleic acid systems mon_sharma_at_research.iiit.ac.in (Sat Apr 16 2011 - 03:22:37 CDT)
- Re: NAMDenergy calculations for nucleic acid systems Peter Freddolino (Sat Apr 16 2011 - 05:48:31 CDT)
  - Re: NAMDenergy calculations for nucleic acid systems mon_sharma_at_research.iiit.ac.in (Sat Apr 16 2011 - 08:18:17 CDT)
NAMD cell dimension increasing in Z direction, problem with periodic cell snoze pa (Fri Apr 15 2011 - 13:23:53 CDT)
Oh dear, 'namd2 invoked oom-killer' ... Nicholas M Glykos (Fri Apr 15 2011 - 09:55:35 CDT)
- Re: Oh dear, 'namd2 invoked oom-killer' ... Jim Phillips (Fri Apr 15 2011 - 11:34:14 CDT)
  - Re: Oh dear, 'namd2 invoked oom-killer' ... Nicholas M Glykos (Fri Apr 15 2011 - 12:16:06 CDT)
Error: keyword "group1" is not supported, or not recognized in this context. Shen, Han (Fri Apr 15 2011 - 09:14:11 CDT)
- Re: Error: keyword "group1" is not supported, or not recognized in this context. Giacomo Fiorin (Fri Apr 15 2011 - 11:02:03 CDT)
Replica Exchange alamng_at_uci.edu (Fri Apr 15 2011 - 04:35:47 CDT)
- Re: Replica Exchange Jim Phillips (Tue May 10 2011 - 18:59:03 CDT)
GeForce vs Tesla GPUs for high performance computing Salvador H-V (Thu Apr 14 2011 - 13:58:30 CDT)
- Re: GeForce vs Tesla GPUs for high performance computing Axel Kohlmeyer (Thu Apr 14 2011 - 14:23:50 CDT)
  - Re: GeForce vs Tesla GPUs for high performance computing Gianluca Interlandi (Thu Apr 14 2011 - 14:48:58 CDT)
    - Re: GeForce vs Tesla GPUs for high performance computing Axel Kohlmeyer (Thu Apr 14 2011 - 14:57:16 CDT)
problem in restarting ipsita basu (Thu Apr 14 2011 - 02:11:24 CDT)
- Re: problem in restarting Axel Kohlmeyer (Thu Apr 14 2011 - 08:29:24 CDT)
  - Re: problem in restarting Jérôme Hénin (Thu Apr 14 2011 - 09:52:59 CDT)
    - Re: problem in restarting Ajasja LjubetiÄ (Thu Apr 14 2011 - 10:28:19 CDT)
    - Re: problem in restarting Axel Kohlmeyer (Thu Apr 14 2011 - 11:42:59 CDT)
- Re: problem in restarting Jim Phillips (Fri Apr 15 2011 - 08:06:56 CDT)
fixing group of atoms, Proper for manipualation M Mahjour (Wed Apr 13 2011 - 17:06:43 CDT)
NAMD feture request Ajasja LjubetiÄ (Wed Apr 13 2011 - 09:46:07 CDT)
- Re: NAMD feture request Giacomo Fiorin (Wed Apr 13 2011 - 10:17:27 CDT)
  - Re: NAMD feture request Thomas Evangelidis (Wed Apr 13 2011 - 12:06:57 CDT)
Recent Geforce Cuda GPU cards(GT 440, GTX 560ti) Burgess, Don E (Wed Apr 13 2011 - 08:21:15 CDT)
- Re: Recent Geforce Cuda GPU cards(GT 440, GTX 560ti) Axel Kohlmeyer (Wed Apr 13 2011 - 09:25:58 CDT)
about rigid bonds oguz gurbulak (Wed Apr 13 2011 - 03:39:34 CDT)
- Re: about rigid bonds Jim Phillips (Wed Apr 13 2011 - 10:32:07 CDT)
- Re: about rigid bonds Axel Kohlmeyer (Wed Apr 13 2011 - 10:38:19 CDT)
problem for simulation of membrane protein system Buddhadev Maiti (Tue Apr 12 2011 - 11:06:30 CDT)
- Re: problem for simulation of membrane protein system Jeffrey Potoff (Tue Apr 12 2011 - 11:29:25 CDT)
- Re: problem for simulation of membrane protein system Giacomo Fiorin (Tue Apr 12 2011 - 11:30:39 CDT)
Re: Replica Exchange Simulations on Blue Gene/P Dong Luo (Tue Apr 12 2011 - 09:54:31 CDT)
- Re: Replica Exchange Simulations on Blue Gene/P Axel Kohlmeyer (Tue Apr 12 2011 - 10:03:16 CDT)
Replica Exchange Simulations on Blue Gene/P Jan H. Meinke (Tue Apr 12 2011 - 07:09:32 CDT)
QM/MM QFrank_X=2E_V=E1zquez=22?= (Mon Apr 11 2011 - 18:23:26 CDT)
(no subject) Buddhadev Maiti (Mon Apr 11 2011 - 14:27:13 CDT)
- (no subject) Erik Nordgren (Mon Apr 11 2011 - 21:38:33 CDT)
  - Re: Re: Jim Phillips (Wed Apr 13 2011 - 10:19:45 CDT)
- (no subject) David Rogers (Mon Apr 11 2011 - 22:26:09 CDT)
vmd-l: ParseFEP output errors Christian Jorgensen (Mon Apr 11 2011 - 11:27:08 CDT)
- Re: vmd-l: ParseFEP output errors Chris Chipot (Mon Apr 11 2011 - 11:40:10 CDT)
dihedral rotation with ABF kakali sen (Sun Apr 10 2011 - 12:48:17 CDT)
Help building a desktop for namd Salvador H-V (Sun Apr 10 2011 - 12:40:05 CDT)
- Re: Help building a desktop for namd Axel Kohlmeyer (Sun Apr 10 2011 - 12:52:59 CDT)
  - Re: Help building a desktop for namd Salvador H-V (Mon Apr 11 2011 - 12:22:01 CDT)
(no subject) Buddhadev Maiti (Fri Apr 08 2011 - 10:45:19 CDT)
protein on solid surface Giovanni Bellesia (Fri Apr 08 2011 - 09:48:50 CDT)
- Re: protein on solid surface Giacomo Fiorin (Fri Apr 08 2011 - 11:21:33 CDT)
  - Re: protein on solid surface Giovanni Bellesia (Fri Apr 08 2011 - 13:45:31 CDT)
SMD simulation: stop applying force during simulation? THANH NGUYEN (Thu Apr 07 2011 - 22:05:35 CDT)
- Re: SMD simulation: stop applying force during simulation? Axel Kohlmeyer (Fri Apr 08 2011 - 07:46:54 CDT)
Abe versus Lincoln Gianluca Interlandi (Thu Apr 07 2011 - 13:22:37 CDT)
- Re: Abe versus Lincoln johan strumpfer (Thu Apr 07 2011 - 13:40:13 CDT)
  - Re: Abe versus Lincoln Axel Kohlmeyer (Thu Apr 07 2011 - 13:46:34 CDT)
  - Re: Abe versus Lincoln Gianluca Interlandi (Thu Apr 07 2011 - 13:50:45 CDT)
Fwd: ramd seed Francesco Pietra (Thu Apr 07 2011 - 08:41:08 CDT)
NVT setup for monolayer Bjoern Olausson (Thu Apr 07 2011 - 08:24:32 CDT)
- Re: NVT setup for monolayer Jim Phillips (Wed Apr 13 2011 - 10:09:49 CDT)
  - Re: NVT setup for monolayer Bjoern Olausson (Thu Apr 14 2011 - 02:17:35 CDT)
FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT Gary M. Skinner (Thu Apr 07 2011 - 07:17:14 CDT)
- Re: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT johan strumpfer (Thu Apr 07 2011 - 09:23:02 CDT)
multilevel summation in NAMD Francesco Oteri (Wed Apr 06 2011 - 17:32:49 CDT)
- Re: multilevel summation in NAMD Chris Harrison (Wed Apr 06 2011 - 21:56:19 CDT)
FEP with flattened free energy surface? Ivan Vyalov (Wed Apr 06 2011 - 04:49:50 CDT)
- Re: FEP with flattened free energy surface? Jérôme Hénin (Wed Apr 06 2011 - 11:45:29 CDT)
  - Re: FEP with flattened free energy surface? Ivan Vyalov (Fri Apr 08 2011 - 14:12:38 CDT)
topology for monophosphate Irene Newhouse (Tue Apr 05 2011 - 15:25:52 CDT)
- RE: topology for monophosphate Irene Newhouse (Wed Apr 06 2011 - 14:02:30 CDT)
NAMD speed on MPICH2 Ubuntu 64 bit Cluster Robert McCarrick (Tue Apr 05 2011 - 13:51:55 CDT)
- Re: NAMD speed on MPICH2 Ubuntu 64 bit Cluster Robert McCarrick (Wed Apr 06 2011 - 11:19:16 CDT)
  - Re: NAMD speed on MPICH2 Ubuntu 64 bit Cluster Axel Kohlmeyer (Wed Apr 06 2011 - 12:06:41 CDT)
- Re: NAMD speed on MPICH2 Ubuntu 64 bit Cluster Norman Geist (Fri Apr 15 2011 - 07:46:00 CDT)
NPT simulations in NAMD Hasan haska (Tue Apr 05 2011 - 07:31:52 CDT)
- Re: NPT simulations in NAMD Axel Kohlmeyer (Tue Apr 05 2011 - 08:09:26 CDT)
NAMD for windows cannot run correctly according to namd tutorials sciencekey (Tue Apr 05 2011 - 04:00:11 CDT)
Wrong exit from RAMD runs Francesco Pietra (Tue Apr 05 2011 - 03:11:29 CDT)
- Fwd: Wrong exit from RAMD runs Francesco Pietra (Tue Apr 05 2011 - 15:34:19 CDT)
  - Re: Fwd: Wrong exit from RAMD runs Jim Phillips (Wed Apr 13 2011 - 09:59:25 CDT)
    - Re: Fwd: Wrong exit from RAMD runs Jim Phillips (Wed Apr 13 2011 - 10:02:18 CDT)
    - Re: Fwd: Wrong exit from RAMD runs Vlad Cojocaru (Thu Apr 14 2011 - 03:08:54 CDT)
implicit solvent job error in NAMD2.8b1 harish vashisth (Mon Apr 04 2011 - 15:47:33 CDT)
- Re: implicit solvent job error in NAMD2.8b1 David Tanner (Mon Apr 04 2011 - 16:34:11 CDT)
  - Re: implicit solvent job error in NAMD2.8b1 harish vashisth (Mon Apr 04 2011 - 17:14:20 CDT)
    - Re: implicit solvent job error in NAMD2.8b1 David Tanner (Tue Apr 05 2011 - 11:35:49 CDT)
gromacs analysis tools Molecular Dynamics (Sun Apr 03 2011 - 04:33:14 CDT)
gromacs analysis tools Molecular Dynamics (Sun Apr 03 2011 - 04:54:35 CDT)
- Re: gromacs analysis tools Joshua Adelman (Sun Apr 03 2011 - 10:45:16 CDT)
  - Re: gromacs analysis tools Francesco Oteri (Sun Apr 03 2011 - 13:47:19 CDT)
    - Re: gromacs analysis tools Axel Kohlmeyer (Sun Apr 03 2011 - 14:28:04 CDT)
Why NAMD writes colvars step by step Leonardo Herrera (Fri Apr 01 2011 - 19:04:21 CDT)
- Re: Why NAMD writes colvars step by step Giacomo Fiorin (Fri Apr 01 2011 - 21:10:15 CDT)
  - Re: Why NAMD writes colvars step by step Leonardo Herrera (Sat Apr 02 2011 - 19:22:23 CDT)
    - Re: Why NAMD writes colvars step by step Giacomo Fiorin (Sat Apr 02 2011 - 19:38:26 CDT)
Why NAMD writes colvars step by step Leonardo Herrera (Fri Apr 01 2011 - 17:06:03 CDT)
- Re: Why NAMD writes colvars step by step Jérôme Hénin (Sat Apr 02 2011 - 02:34:02 CDT)
Multi node run causes "CUDA error cudaStreamCreate" Michael S. Sellers (Cont, ARL/WMRD) (Fri Apr 01 2011 - 12:32:35 CDT)
- Re: Multi node run causes "CUDA error cudaStreamCreate" Axel Kohlmeyer (Fri Apr 01 2011 - 15:02:18 CDT)
  - Re: Multi node run causes "CUDA error cudaStreamCreate" Michael S. Sellers (Cont, ARL/WMRD) (Fri Apr 01 2011 - 15:46:21 CDT)
set dummyAtom position changing christos.lamprakis_at_dcb.unibe.ch (Fri Apr 01 2011 - 09:44:39 CDT)
Setting up aMD simulation of a membrane protein Raul Araya (Fri Apr 01 2011 - 09:05:32 CDT)
- Re: Setting up aMD simulation of a membrane protein Jeff Wereszczynski (Fri Apr 01 2011 - 11:00:23 CDT)
- Re: Setting up aMD simulation of a membrane protein Yi Wang (Fri Apr 01 2011 - 13:59:01 CDT)
New collective variable: biolRel Jérôme Hénin (Fri Apr 01 2011 - 09:01:53 CDT)
Re: vmd-l: No probability distribution plot in ParseFEP liupeng012_at_mail.nankai.edu.cn (Thu Mar 31 2011 - 21:08:46 CDT)
angles flavio seixas (Thu Mar 31 2011 - 15:57:33 CDT)
- Re: angles Giacomo Fiorin (Thu Mar 31 2011 - 18:05:28 CDT)
Accelerated MD: question about dual boost mode patrick wintrode (Thu Mar 31 2011 - 15:01:49 CDT)
- Re: Accelerated MD: question about dual boost mode Jeff Wereszczynski (Thu Mar 31 2011 - 17:07:07 CDT)
  - Re: Accelerated MD: question about dual boost mode Bjoern Olausson (Tue May 10 2011 - 07:32:13 CDT)
  - Re: Accelerated MD: question about dual boost mode Bjoern Olausson (Tue May 10 2011 - 10:17:59 CDT)
vmd-l: No probability distribution plot in ParseFEP Christian Jorgensen (Thu Mar 31 2011 - 13:24:27 CDT)
- RE: vmd-l: No probability distribution plot in ParseFEP Christian Jorgensen (Fri Apr 01 2011 - 04:09:12 CDT)
unsubscribe Chen, Zhihong (chenz2) (Thu Mar 31 2011 - 13:02:05 CDT)
reassignFreq expression and relation with SMD Kang Hee Cho (Thu Mar 31 2011 - 10:56:47 CDT)
- external forces Matteo Rotter (Mon Apr 04 2011 - 08:13:24 CDT)
  - Re: external forces johan strumpfer (Mon Apr 04 2011 - 11:07:02 CDT)
  - Re: external forces Jim Phillips (Wed Apr 13 2011 - 09:47:03 CDT)
Reverse Mapping of RBCG Model Sibel Cakan (Thu Mar 31 2011 - 06:20:08 CDT)
Reverse Mapping of RBCG Model Sibel Cakan (Thu Mar 31 2011 - 03:51:57 CDT)
NAMD_CVS_Source Leonardo Herrera (Wed Mar 30 2011 - 16:43:52 CDT)
- Re: NAMD_CVS_Source Axel Kohlmeyer (Wed Mar 30 2011 - 17:27:04 CDT)
The biggest system simulated on one TESLA C2050 ? Marek Maly (Wed Mar 30 2011 - 13:30:11 CDT)
- Re: The biggest system simulated on one TESLA C2050 ? Axel Kohlmeyer (Wed Mar 30 2011 - 14:42:56 CDT)
- Re: The biggest system simulated on one TESLA C2050 ? Jim Phillips (Wed Apr 13 2011 - 09:37:46 CDT)
Generalized Born implicit solvent model in 2.8b1 Enrico Guarnera (Wed Mar 30 2011 - 09:40:45 CDT)
- Re: Generalized Born implicit solvent model in 2.8b1 David Tanner (Wed Mar 30 2011 - 12:04:20 CDT)
Switching function for cut-off method yandongÂ Huang (Wed Mar 30 2011 - 08:54:09 CDT)
Network version gives inconsistent wall clock timings yashodhan karandikar (Wed Mar 30 2011 - 08:39:15 CDT)
- Re: Network version gives inconsistent wall clock timings Jim Phillips (Wed Apr 13 2011 - 09:04:46 CDT)
Incompatibility between colvars and tclforces? Francesco Pietra (Wed Mar 30 2011 - 05:04:02 CDT)
- Re: Incompatibility between colvars and tclforces? Ajasja LjubetiÄ (Wed Mar 30 2011 - 06:21:23 CDT)
  - Re: Incompatibility between colvars and tclforces? Wang Yi (Wed Mar 30 2011 - 09:16:25 CDT)
- Re: Incompatibility between colvars and tclforces? Jérôme Hénin (Wed Mar 30 2011 - 06:23:42 CDT)
  - Re: Incompatibility between colvars and tclforces? Francesco Pietra (Wed Mar 30 2011 - 09:06:13 CDT)
Setting PME Grid Size da xue (Tue Mar 29 2011 - 20:28:26 CDT)
- Re: Setting PME Grid Size Jim Phillips (Wed Apr 13 2011 - 08:55:23 CDT)
NAMD 2.7/2.8b1 and BlueGeneL Dong Luo (Tue Mar 29 2011 - 11:00:22 CDT)
- Re: NAMD 2.7/2.8b1 and BlueGeneL Jim Phillips (Wed Apr 13 2011 - 08:46:26 CDT)
  - Re: NAMD 2.7/2.8b1 and BlueGeneL Dong Luo (Wed Apr 13 2011 - 16:46:00 CDT)
Velocity distribution Philip Peartree (Tue Mar 29 2011 - 05:45:30 CDT)
- Re: Velocity distribution Jim Phillips (Wed Apr 13 2011 - 08:38:58 CDT)
vmd: ParseFEP plot mistake Christian Jorgensen (Tue Mar 29 2011 - 04:45:07 CDT)
- Re: vmd: ParseFEP plot mistake Chris Chipot (Tue Mar 29 2011 - 07:06:46 CDT)
  - RE: vmd: ParseFEP plot mistake Christian Jorgensen (Tue Mar 29 2011 - 10:08:35 CDT)
Get restart file (restart.coor) from DCD Ismail, Mohd F. (Mon Mar 28 2011 - 17:41:56 CDT)
- Re: Get restart file (restart.coor) from DCD Joshua D. Moore (Mon Mar 28 2011 - 20:18:11 CDT)
Fwd: RAMD Setting parameter TclForces from script failed Francesco Pietra (Mon Mar 28 2011 - 15:19:57 CDT)
- Fwd: RAMD Setting parameter TclForces from script failed Francesco Pietra (Mon Mar 28 2011 - 15:37:24 CDT)
  - Re: RAMD Setting parameter TclForces from script failed Francesco Pietra (Mon Mar 28 2011 - 16:09:55 CDT)
    - RE: RAMD Setting parameter TclForces from script failed Cojocaru, Vlad (Mon Mar 28 2011 - 16:55:14 CDT)
  - Re: Fwd: RAMD Setting parameter TclForces from script failed Jim Phillips (Mon Mar 28 2011 - 16:49:25 CDT)
    - RE: Fwd: RAMD Setting parameter TclForces from script failed Cojocaru, Vlad (Mon Mar 28 2011 - 16:55:44 CDT)
Accelerated MD with membrane embedded proteins. Raul Araya (Mon Mar 28 2011 - 13:45:36 CDT)
RAMD Setting parameter TclForces from script failed Francesco Pietra (Mon Mar 28 2011 - 05:26:21 CDT)
- Re: RAMD Setting parameter TclForces from script failed Vlad Cojocaru (Mon Mar 28 2011 - 08:45:49 CDT)
  - Re: RAMD Setting parameter TclForces from script failed Francesco Pietra (Mon Mar 28 2011 - 09:50:31 CDT)
    - RE: RAMD Setting parameter TclForces from script failed Cojocaru, Vlad (Mon Mar 28 2011 - 14:20:56 CDT)
    - Re: RAMD Setting parameter TclForces from script failed Francesco Pietra (Mon Mar 28 2011 - 14:43:34 CDT)
  - Re: RAMD Setting parameter TclForces from script failed Francesco Pietra (Tue Mar 29 2011 - 02:51:19 CDT)
- Re: RAMD Setting parameter TclForces from script failed Jim Phillips (Mon Mar 28 2011 - 14:33:32 CDT)
Net forces on each atom can be written to PDB in NAMD 2.8b1 oguz gurbulak (Mon Mar 28 2011 - 04:53:55 CDT)
output forces with tclBC Eduardo Cruz-Chu (Mon Mar 28 2011 - 04:33:15 CDT)
Net forces on each atom can be written to PDB in NAMD 2.8b1 oguz gurbulak (Mon Mar 28 2011 - 04:06:05 CDT)
- Re: Net forces on each atom can be written to PDB in NAMD 2.8b1 Jim Phillips (Mon Mar 28 2011 - 12:00:59 CDT)
ramd firstRamdAtom Francesco Pietra (Mon Mar 28 2011 - 02:22:20 CDT)
- Fwd: ramd firstRamdAtom Francesco Pietra (Mon Mar 28 2011 - 03:15:56 CDT)
NAMD 2.8b1 released Jim Phillips (Sun Mar 27 2011 - 12:25:13 CDT)
partial charges for organic ligands Francesco Pietra (Sat Mar 26 2011 - 11:45:26 CDT)
- Re: partial charges for organic ligands johan strumpfer (Sat Mar 26 2011 - 12:40:48 CDT)
- Re: partial charges for organic ligands Branko (Sat Mar 26 2011 - 12:42:32 CDT)
  - Re: partial charges for organic ligands Francesco Pietra (Sat Mar 26 2011 - 15:23:05 CDT)
    - Re: partial charges for organic ligands Branko (Sat Mar 26 2011 - 16:09:35 CDT)
    - Re: partial charges for organic ligands Richard Wood (Sat Mar 26 2011 - 22:18:50 CDT)
how to convert X_PLOR to CHARMM? Lisa Brown (Fri Mar 25 2011 - 11:01:26 CDT)
CHARMM parameters for Mn 2+ ion Lisa Brown (Fri Mar 25 2011 - 10:43:45 CDT)
- Re: vmd-l: CHARMM parameters for Mn 2+ ion Jernej Zidar (Fri Mar 25 2011 - 12:57:00 CDT)
  - Re: Re: vmd-l: CHARMM parameters for Mn 2+ ion Daniel Aguayo (Fri Mar 25 2011 - 14:45:15 CDT)
ewald method Hasan haska (Fri Mar 25 2011 - 09:49:57 CDT)
- Re: ewald method David Hardy (Fri Mar 25 2011 - 10:27:11 CDT)
charmm 19 parameters Hasan haska (Fri Mar 25 2011 - 09:49:24 CDT)
ewald method Hasan haska (Fri Mar 25 2011 - 09:45:45 CDT)
charmm 19 parameters Hasan haska (Fri Mar 25 2011 - 09:38:41 CDT)
Domain error ParseFEP Christian Jorgensen (Fri Mar 25 2011 - 09:14:02 CDT)
- Re: Domain error ParseFEP Chris Chipot (Fri Mar 25 2011 - 09:41:25 CDT)
  - RE: Domain error ParseFEP Christian Jorgensen (Fri Mar 25 2011 - 09:42:29 CDT)
    - Re: Domain error ParseFEP Chris Chipot (Fri Mar 25 2011 - 09:57:19 CDT)
Re: vmd-l: How to maximize the VMD display window Ajasja LjubetiÄ (Fri Mar 25 2011 - 07:48:24 CDT)
Advisable limit on the number of quadrants a 2D ABF simulation can be split. Ajasja LjubetiÄ (Fri Mar 25 2011 - 04:52:09 CDT)
- Re: Advisable limit on the number of quadrants a 2D ABF simulation can be split. Jérôme Hénin (Fri Mar 25 2011 - 06:25:30 CDT)
  - Re: Advisable limit on the number of quadrants a 2D ABF simulation can be split. Ajasja LjubetiÄ (Mon Mar 28 2011 - 09:06:40 CDT)
    - Re: Advisable limit on the number of quadrants a 2D ABF simulation can be split. Jérôme Hénin (Mon Mar 28 2011 - 09:42:33 CDT)
how to write the bond across the cell boundary Íõ—² (Fri Mar 25 2011 - 01:52:15 CDT)
- Re: how to write the bond across the cell boundary Ajasja LjubetiÄ (Fri Mar 25 2011 - 03:44:41 CDT)
  - Re: how to write the bond across the cell boundary Axel Kohlmeyer (Fri Mar 25 2011 - 08:17:05 CDT)
Why are the pressures in my box of water systematically off? Tom Sisan (Thu Mar 24 2011 - 18:33:39 CDT)
- Re: Why are the pressures in my box of water systematically off? Jim Phillips (Sun Mar 27 2011 - 10:04:35 CDT)
  - Re: Why are the pressures in my box of water systematically off? Tom Sisan (Wed Mar 30 2011 - 12:40:58 CDT)
  - Re: Why are the pressures in my box of water systematically off? Tom Sisan (Thu Mar 31 2011 - 17:04:03 CDT)
Re: Using RAMD for studiying conformational changes in proteins Vlad Cojocaru (Thu Mar 24 2011 - 17:59:22 CDT)
Using RAMD for studiying conformational changes in proteins Raul Araya (Thu Mar 24 2011 - 15:23:39 CDT)
Re: question about force information Osman Yogurtcu (Thu Mar 24 2011 - 09:56:25 CDT)
- Re: question about force information Ajasja LjubetiÄ (Thu Mar 24 2011 - 14:22:10 CDT)
question about force information oguz gurbulak (Thu Mar 24 2011 - 06:02:14 CDT)
question about force information oguz gurbulak (Thu Mar 24 2011 - 04:43:20 CDT)
switching function yandongÂ Huang (Wed Mar 23 2011 - 22:52:32 CDT)
subscribe namd-l Michael Zimmermann (Wed Mar 23 2011 - 13:24:38 CDT)
Re: how obtain .xst form .dcd file? wood irene (Wed Mar 23 2011 - 12:59:01 CDT)
- Re: how obtain .xst form .dcd file? Ajasja LjubetiÄ (Wed Mar 23 2011 - 14:11:27 CDT)
- Re: how obtain .xst form .dcd file? Erik Santiso (Wed Mar 23 2011 - 17:24:16 CDT)
GBIS question and possible Bug for colvar "outputSystemForce" declaration in NAMD CVS-2011-03-03 Bjoern Olausson (Tue Mar 22 2011 - 17:56:09 CDT)
- Re: GBIS question and possible Bug for colvar "outputSystemForce" declaration in NAMD CVS-2011-03-03 Giacomo Fiorin (Tue Mar 22 2011 - 21:07:53 CDT)
  - Re: GBIS question and possible Bug for colvar "outputSystemForce" declaration in NAMD CVS-2011-03-03 Bjoern Olausson (Wed Mar 23 2011 - 03:18:22 CDT)
    - Re: GBIS question and possible Bug for colvar "outputSystemForce" declaration in NAMD CVS-2011-03-03 Jérôme Hénin (Wed Mar 23 2011 - 05:39:51 CDT)
    - Re: GBIS question and possible Bug for colvar "outputSystemForce" declaration in NAMD CVS-2011-03-03 Bjoern Olausson (Wed Mar 23 2011 - 07:06:21 CDT)
Am I using the right version for accelerated MD? patrick wintrode (Tue Mar 22 2011 - 15:34:29 CDT)
- Re: Am I using the right version for accelerated MD? Chris Harrison (Tue Mar 22 2011 - 16:11:35 CDT)
implementing RBCG Michael Zimmermann (Tue Mar 22 2011 - 15:11:30 CDT)
- Re: implementing RBCG Peter Freddolino (Tue Mar 22 2011 - 21:17:32 CDT)
  - Re: implementing RBCG Chris Harrison (Tue Mar 22 2011 - 21:25:54 CDT)
    - Re: implementing RBCG Peter Freddolino (Wed Mar 23 2011 - 20:19:09 CDT)
GBIS not compatible with CUDA at this time Michael S. Sellers (Cont, ARL/WMRD) (Tue Mar 22 2011 - 13:27:48 CDT)
- Re: GBIS not compatible with CUDA at this time David Tanner (Tue Mar 22 2011 - 14:21:09 CDT)
"FATAL ERROR: Bad global improper count" revisited Markus K. Dahlgren (Tue Mar 22 2011 - 10:42:49 CDT)
- Re: "FATAL ERROR: Bad global improper count" revisited johan strumpfer (Tue Mar 22 2011 - 12:41:42 CDT)
Fw: topology file for nucleic acids including ammonium ion Alex Liu (Mon Mar 21 2011 - 16:40:55 CDT)
A "strange" observation during ColVar calculations Wang Yi (Mon Mar 21 2011 - 13:49:45 CDT)
- Re: A "strange" observation during ColVar calculations Giacomo Fiorin (Mon Mar 21 2011 - 15:46:27 CDT)
  - Re: A "strange" observation during ColVar calculations Wang Yi (Mon Mar 21 2011 - 15:58:17 CDT)
rule of thumb for dcd sampling frequency? Irene Newhouse (Mon Mar 21 2011 - 13:26:25 CDT)
- Re: rule of thumb for dcd sampling frequency? Branko (Mon Mar 21 2011 - 14:13:51 CDT)
  - Re: rule of thumb for dcd sampling frequency? Richard Wood (Mon Mar 21 2011 - 18:43:30 CDT)
- Re: rule of thumb for dcd sampling frequency? Axel Kohlmeyer (Mon Mar 21 2011 - 14:12:00 CDT)
- Re: rule of thumb for dcd sampling frequency? Nikolaos Glykos (Mon Mar 21 2011 - 14:51:09 CDT)
  - namd and Fedora14 flavio seixas (Tue Mar 22 2011 - 07:28:27 CDT)
Re: [ppl] Help Regarding NAMD Application Testing Phil Miller (Mon Mar 21 2011 - 09:00:13 CDT)
how obtain .xst form .dcd file? wood irene (Mon Mar 21 2011 - 09:25:47 CDT)
dcd to trr using catdcd Neelanjana Sengupta (Mon Mar 21 2011 - 05:44:39 CDT)
- Re: dcd to trr using catdcd Neelanjana Sengupta (Tue Mar 22 2011 - 00:11:33 CDT)
  - Re: dcd to trr using catdcd Anurag Sethi (Tue Mar 22 2011 - 02:03:56 CDT)
NAMD on GPU Ismail, Mohd F. (Sun Mar 20 2011 - 21:24:09 CDT)
- Re: NAMD on GPU Jun Zhang (Mon Mar 21 2011 - 19:45:10 CDT)
html manual 2.8, ref 46 and some GBIS questions Branko (Sun Mar 20 2011 - 09:05:27 CDT)
ABF colvar error-capped nanotube interaction sakthi kumaran (Sat Mar 19 2011 - 11:12:57 CDT)
- Re: ABF colvar error-capped nanotube interaction Axel Kohlmeyer (Sat Mar 19 2011 - 12:02:53 CDT)
- Re: ABF colvar error-capped nanotube interaction Giacomo Fiorin (Sat Mar 19 2011 - 13:54:37 CDT)
  - Re: ABF colvar error-capped nanotube interaction sakthi kumaran (Sun Mar 20 2011 - 01:55:30 CDT)
    - Re: ABF colvar error-capped nanotube interaction sakthi kumaran (Sun Mar 20 2011 - 11:26:04 CDT)
    - Re: ABF colvar error-capped nanotube interaction Axel Kohlmeyer (Sun Mar 20 2011 - 12:13:43 CDT)
Unpredictable crash at runtime pellegrini (Fri Mar 18 2011 - 03:14:22 CDT)
ABF Restart Buddhadev Maiti (Thu Mar 17 2011 - 21:46:37 CDT)
- Re: ABF Restart Jérôme Hénin (Fri Mar 18 2011 - 04:08:34 CDT)
Re: NAMD 2.7 released Gianluca Interlandi (Thu Mar 17 2011 - 17:58:46 CDT)
GBIS and ABF Branko (Thu Mar 17 2011 - 15:50:40 CDT)
- Re: GBIS and ABF Giacomo Fiorin (Thu Mar 17 2011 - 20:02:37 CDT)
VMD inorganic builder plugin dota alexiou (Thu Mar 17 2011 - 05:36:31 CDT)
- Re: VMD inorganic builder plugin Robert Brunner (Thu Mar 17 2011 - 14:17:48 CDT)
specify acceptance ratio in REMD Neelanjana Sengupta (Thu Mar 17 2011 - 01:47:32 CDT)
targeted molecular dynamics sakthi kumaran (Thu Mar 17 2011 - 01:28:59 CDT)
- Re: targeted molecular dynamics sakthi kumaran (Thu Mar 17 2011 - 09:08:25 CDT)
Fwd: Re: Bactenecine Branko (Wed Mar 16 2011 - 16:35:57 CDT)
RE: Bactenecine Andres Morales N (Wed Mar 16 2011 - 14:22:09 CDT)
- Re: Bactenecine johan strumpfer (Wed Mar 16 2011 - 15:54:46 CDT)
Multiple runs of NAMD highly take fluctuating times yashodhan karandikar (Tue Mar 15 2011 - 23:06:59 CDT)
- Re: Multiple runs of NAMD highly take fluctuating times Axel Kohlmeyer (Wed Mar 16 2011 - 00:36:28 CDT)
  - Re: Multiple runs of NAMD highly take fluctuating times yashodhan karandikar (Wed Mar 16 2011 - 00:48:27 CDT)
Rotate two linked proteins against each other and calculate energy profile Bjoern Olausson (Tue Mar 15 2011 - 14:20:00 CDT)
- Re: Rotate two linked proteins against each other and calculate energy profile Ajasja LjubetiÄ (Tue Mar 15 2011 - 16:56:39 CDT)
  - Re: Rotate two linked proteins against each other and calculate energy profile Bjoern Olausson (Sun Mar 20 2011 - 11:03:32 CDT)
New NAMD version 2011-03-03 uses Christian Jorgensen (Tue Mar 15 2011 - 09:52:27 CDT)
- Re: New NAMD version 2011-03-03 uses Chris Chipot (Tue Mar 15 2011 - 10:00:17 CDT)
  - Re: New NAMD version 2011-03-03 uses Chris Harrison (Tue Mar 15 2011 - 10:48:04 CDT)
  - Re: New NAMD version 2011-03-03 uses Jeff Wereszczynski (Tue Mar 15 2011 - 11:49:28 CDT)
Accelerated MD documentation? patrick wintrode (Tue Mar 15 2011 - 08:05:19 CDT)
- Re: Accelerated MD documentation? Bjoern Olausson (Tue Mar 15 2011 - 08:59:48 CDT)
  - Re: Accelerated MD documentation? Chris Harrison (Tue Mar 15 2011 - 09:28:35 CDT)
    - Re: Accelerated MD documentation? Francesco Pietra (Tue Mar 15 2011 - 10:20:18 CDT)
    - Re: Accelerated MD documentation? Chris Harrison (Sat Mar 19 2011 - 00:15:15 CDT)
- Re: Accelerated MD documentation? Chris Harrison (Tue Mar 15 2011 - 09:22:55 CDT)
  - Re: Accelerated MD documentation? Bjoern Olausson (Tue Mar 15 2011 - 10:47:21 CDT)
moving inner wall of nanotube with outer wall fixed sakthi kumaran (Tue Mar 15 2011 - 04:29:02 CDT)
- Re: moving inner wall of nanotube with outer wall fixed johan strumpfer (Tue Mar 15 2011 - 12:01:36 CDT)
Bactenecine Andres Morales N (Mon Mar 14 2011 - 23:11:05 CDT)
Setting up values in distance colvar Francesco Pietra (Sun Mar 13 2011 - 12:49:51 CDT)
- Re: Setting up values in distance colvar Jérôme Hénin (Sun Mar 13 2011 - 14:45:43 CDT)
Fwd: Keyword "lower" not supported...colvars Francesco Pietra (Sun Mar 13 2011 - 05:37:41 CDT)
Keyword "lower" not supported...colvars Francesco Pietra (Sat Mar 12 2011 - 11:16:19 CST)
- Re: Keyword "lower" not supported...colvars Axel Kohlmeyer (Sat Mar 12 2011 - 16:02:38 CST)
  - Re: Keyword "lower" not supported...colvars Chris Harrison (Sat Mar 12 2011 - 20:52:30 CST)
psf problem ipsita basu (Sat Mar 12 2011 - 04:33:39 CST)
Re: BOUNCE namd-l@ks.uiuc.edu: Message too long (>40000 chars) Francesco Pietra (Fri Mar 11 2011 - 11:46:30 CST)
Automatic PSF Builder Problem Marc Charendoff (Fri Mar 11 2011 - 10:43:15 CST)
- Re: Automatic PSF Builder Problem ehenriques_at_qui.uc.pt (Sat Mar 12 2011 - 10:49:05 CST)
psf problem ipsita basu (Fri Mar 11 2011 - 08:24:10 CST)
creating .psf file for a nanotube sakthi kumaran (Fri Mar 11 2011 - 02:36:02 CST)
- Re: creating .psf file for a nanotube sakthi kumaran (Fri Mar 11 2011 - 05:13:34 CST)
- Re: creating .psf file for a nanotube Axel Kohlmeyer (Fri Mar 11 2011 - 05:18:57 CST)
  - Re: creating .psf file for a nanotube sakthi kumaran (Fri Mar 11 2011 - 06:34:36 CST)
    - Re: creating .psf file for a nanotube Axel Kohlmeyer (Fri Mar 11 2011 - 08:26:58 CST)
psfgen - ACE cap on PRO Marc Charendoff (Thu Mar 10 2011 - 19:07:33 CST)
- Re: psfgen - ACE cap on PRO Peter Freddolino (Thu Mar 10 2011 - 19:59:14 CST)
topology file for nanotube sakthi kumaran (Thu Mar 10 2011 - 00:57:44 CST)
- Re: topology file for nanotube Ranyere Deyler (Thu Mar 10 2011 - 02:10:13 CST)
  - Re: topology file for nanotube Axel Kohlmeyer (Thu Mar 10 2011 - 04:43:37 CST)
  - Re: topology file for nanotube Axel Kohlmeyer (Thu Mar 10 2011 - 08:11:13 CST)
- Re: topology file for nanotube Axel Kohlmeyer (Thu Mar 10 2011 - 04:38:27 CST)
Re: pentacoordinate heme grazia cottone (Tue Mar 08 2011 - 16:58:27 CST)
IBverbs charmrun problem Seren Soner (Tue Mar 08 2011 - 05:41:33 CST)
Fwd: vmd-l: Re: hBond colvars and patching Francesco Pietra (Tue Mar 08 2011 - 00:34:36 CST)
- Re: Fwd: vmd-l: Re: hBond colvars and patching Peter Freddolino (Tue Mar 08 2011 - 13:48:53 CST)
- Re: Fwd: vmd-l: Re: hBond colvars and patching Francesco Pietra (Fri Mar 11 2011 - 09:07:20 CST)
  - Re: Fwd: vmd-l: Re: hBond colvars and patching Giacomo Fiorin (Fri Mar 11 2011 - 11:40:06 CST)
CT1 terminal patch for THR GONZALEZ NOYA, EVA (Mon Mar 07 2011 - 14:47:57 CST)
colvars PMF history problem Ajasja LjubetiÄ (Mon Mar 07 2011 - 08:43:08 CST)
- Re: colvars PMF history problem Axel Kohlmeyer (Mon Mar 07 2011 - 09:27:19 CST)
  - Re: colvars PMF history problem Ajasja Ljubetiè (Mon Mar 07 2011 - 09:43:02 CST)
Job scheduling (managing) software recommendation Ajasja LjubetiÄ (Mon Mar 07 2011 - 05:36:42 CST)
- Re: Job scheduling (managing) software recommendation Francesco Oteri (Mon Mar 07 2011 - 06:30:53 CST)
  - Re: Job scheduling (managing) software recommendation Nicholas M Glykos (Mon Mar 07 2011 - 07:50:07 CST)
- Re: Job scheduling (managing) software recommendation Axel Kohlmeyer (Mon Mar 07 2011 - 09:16:38 CST)
  - Re: Job scheduling (managing) software recommendation Ajasja LjubetiÄ (Mon Mar 07 2011 - 15:13:48 CST)
- Re: Job scheduling (managing) software recommendation Ajasja LjubetiÄ (Wed Mar 09 2011 - 03:15:41 CST)
(NAMD2.7b1) loadtotalforces gives output even when there are no forces in system Aoife Fogarty (Mon Mar 07 2011 - 03:43:14 CST)
- Re: (NAMD2.7b1) loadtotalforces gives output even when there are no forces in system Hugh Heldenbrand (Mon Mar 07 2011 - 07:10:09 CST)
  - Re: (NAMD2.7b1) loadtotalforces gives output even when there are no forces in system Aoife Fogarty (Tue Mar 15 2011 - 13:15:04 CDT)
hBond colvars and patching Francesco Pietra (Sun Mar 06 2011 - 14:05:47 CST)
- Re: hBond colvars and patching Giacomo Fiorin (Sun Mar 06 2011 - 22:57:04 CST)
  - Re: hBond colvars and patching Francesco Pietra (Mon Mar 07 2011 - 00:12:54 CST)
pentacoordinate heme grazia cottone (Sun Mar 06 2011 - 09:43:02 CST)
hBond component in colvars and patching Francesco Pietra (Sat Mar 05 2011 - 14:38:45 CST)
- Fwd: hBond component in colvars and patching Francesco Pietra (Sun Mar 06 2011 - 02:36:10 CST)
Error while using larger timesteps in Coarse grained Simulation of Polymer rohan uttarwar (Fri Mar 04 2011 - 15:53:56 CST)
Problem with SPC/E water simulation Davide Vanzo/FS/VCU (Fri Mar 04 2011 - 15:07:42 CST)
- Re: Problem with SPC/E water simulation Axel Kohlmeyer (Fri Mar 04 2011 - 15:50:13 CST)
- Re: Problem with SPC/E water simulation Joshua D. Moore (Fri Mar 04 2011 - 17:54:20 CST)
Model system spherical sieve Francesco Pietra (Fri Mar 04 2011 - 14:28:32 CST)
membrane equilibration jeremy adler (Thu Mar 03 2011 - 13:02:57 CST)
- Re: membrane equilibration Axel Kohlmeyer (Thu Mar 03 2011 - 13:43:48 CST)
  - Re: membrane equilibration jeremy adler (Thu Mar 03 2011 - 17:03:18 CST)
Uma wants to chat Uma (Thu Mar 03 2011 - 07:33:27 CST)
NAMD2.7 on BluegeneL hang at "LDB: Central LB being created..." Dong Luo (Wed Mar 02 2011 - 21:42:57 CST)
- Re: NAMD2.7 on BluegeneL hang at "LDB: Central LB being created..." Axel Kohlmeyer (Wed Mar 02 2011 - 22:32:28 CST)
  - Re: NAMD2.7 on BluegeneL hang at "LDB: Central LB being created..." Dong Luo (Tue Apr 12 2011 - 09:44:09 CDT)
- Re: NAMD2.7 on BluegeneL hang at "LDB: Central LB being created..." Chris Harrison (Thu Mar 03 2011 - 00:41:50 CST)
  - Re: NAMD2.7 on BluegeneL hang at "LDB: Central LB being created..." Dong Luo (Thu Mar 03 2011 - 19:59:10 CST)
example psf and pdb files for simulations with tip4p Ana Celia Vila Verde (Wed Mar 02 2011 - 12:21:44 CST)
- Re: example psf and pdb files for simulations with tip4p Peter Freddolino (Wed Mar 02 2011 - 13:28:48 CST)
Positional restraints - Dielectric constant Francesco Pietra (Wed Mar 02 2011 - 10:56:18 CST)
- Re: Positional restraints - Dielectric constant Axel Kohlmeyer (Wed Mar 02 2011 - 11:39:39 CST)
- Re: Positional restraints - Dielectric constant Giacomo Fiorin (Wed Mar 02 2011 - 13:42:33 CST)
GBIS synamics Francesco Oteri (Wed Mar 02 2011 - 05:02:29 CST)
- Re: GBIS synamics David Tanner (Wed Mar 02 2011 - 07:56:59 CST)
Re: Psfgen Errors for C-type Heme Thomas Freeman (Tue Mar 01 2011 - 14:15:56 CST)
Technique issue with free energy calculation on GPU Jun Zhang (Tue Mar 01 2011 - 08:24:59 CST)
binaryrestart/binaryoutput problem Francesco Pietra (Tue Mar 01 2011 - 02:54:26 CST)
- Fwd: binaryrestart/binaryoutput problem Francesco Pietra (Tue Mar 01 2011 - 02:56:29 CST)
  - help needed Richard Wood (Tue Mar 01 2011 - 09:25:51 CST)
    - Re: help needed harish vashisth (Tue Mar 01 2011 - 10:00:46 CST)
Psfgen Errors for C-type Heme Thomas Freeman (Mon Feb 28 2011 - 13:46:04 CST)
Compiling NAMD on Cray XE6 Jeff Wereszczynski (Mon Feb 28 2011 - 11:38:48 CST)
Can paratools really parametrize a structure? Is it really finished? Ranyere Deyler (Mon Feb 28 2011 - 10:56:35 CST)
- RE: Can paratools really parametrize a structure? Is it really finished? JC Gumbart (Mon Feb 28 2011 - 11:23:54 CST)
  - Re: Can paratools really parametrize a structure? Is it really finished? Ranyere Deyler (Mon Feb 28 2011 - 13:28:30 CST)
    - Re: Can paratools really parametrize a structure? Is it really finished? JC Gumbart (Mon Feb 28 2011 - 13:31:16 CST)
NAMDenergy electrostatic energies Sebastian Maximilian Wilhelm (Mon Feb 28 2011 - 10:41:03 CST)
Namd-1: problems using increment of temperature during simulation Ye Yang (Sun Feb 27 2011 - 14:27:16 CST)
CG parameters from dcd file for protein CG modelling Nicolás Pérez (Sun Feb 27 2011 - 13:32:18 CST)
maximum number of atoms per patch Branko (Sun Feb 27 2011 - 12:21:56 CST)
- RE: maximum number of atoms per patch JC Gumbart (Sun Feb 27 2011 - 12:34:36 CST)
Paratool`s error reading single point calculation. Ranyere Deyler (Sat Feb 26 2011 - 00:50:59 CST)
Replica exchange MD with NAMD with SGE.... Raul Araya (Fri Feb 25 2011 - 15:14:19 CST)
- Re: Replica exchange MD with NAMD with SGE.... Guoxiong Su (Wed Jul 13 2011 - 17:50:57 CDT)
Hi, I am a new user of Namd, and I met some problems using increment of temperature during simulation Ye Yang (Fri Feb 25 2011 - 13:40:43 CST)
NAMD + Plumed on Abe Gianluca Interlandi (Fri Feb 25 2011 - 00:03:17 CST)
Turning off Electrostatics Completely gaborekt_at_duq.edu (Thu Feb 24 2011 - 16:05:41 CST)
- Re: Turning off Electrostatics Completely David Tanner (Thu Feb 24 2011 - 18:50:56 CST)
- Re: Turning off Electrostatics Completely Daniel Aguayo (Mon Mar 07 2011 - 11:53:55 CST)
namd at ranger(tacc) Lei Shi (Thu Feb 24 2011 - 12:56:29 CST)
- Re: namd at ranger(tacc) Axel Kohlmeyer (Thu Feb 24 2011 - 15:20:02 CST)
- Re: namd at ranger(tacc) Jim Phillips (Thu Feb 24 2011 - 15:36:18 CST)
- Re: namd at ranger(tacc) Sándor Kovács (Thu Feb 24 2011 - 16:46:41 CST)
  - Re: namd at ranger(tacc) Peter Freddolino (Thu Feb 24 2011 - 17:02:27 CST)
using TIP4P 2005 in namd Ana Celia Vila Verde (Wed Feb 23 2011 - 11:57:03 CST)
- Re: using TIP4P 2005 in namd V.Ovchinnikov (Wed Feb 23 2011 - 15:54:26 CST)
Computing interaction energies in namd Samy Hamdouche (Tue Feb 22 2011 - 14:40:31 CST)
- Re: Computing interaction energies in namd JC Gumbart (Tue Feb 22 2011 - 14:48:51 CST)
  - Re: Computing interaction energies in namd Samy Hamdouche (Tue Feb 22 2011 - 18:21:46 CST)
    - Re: Computing interaction energies in namd Axel Kohlmeyer (Tue Feb 22 2011 - 19:07:11 CST)
    - Re: Computing interaction energies in namd Jérôme Hénin (Wed Feb 23 2011 - 03:42:14 CST)
accuracy of measurement Pletezhov Alexandr (Mon Feb 21 2011 - 17:14:16 CST)
- Re: accuracy of measurement Gianluca Interlandi (Mon Feb 21 2011 - 22:11:43 CST)
Simulating more than 20 Million atom system Harshad Joshi (Mon Feb 21 2011 - 16:01:47 CST)
how to write out the dcd file by vmd python command? mjyang (Mon Feb 21 2011 - 08:53:58 CST)
Calculation of IR spectra using VMD IRspec Plug-in Mikhail Suyetin (Thu Feb 17 2011 - 01:22:00 CST)
- Re: Calculation of IR spectra using VMD IRspec Plug-in Branko (Sat Feb 19 2011 - 11:54:48 CST)
- Re: Calculation of IR spectra using VMD IRspec Plug-in Axel Kohlmeyer (Sun Feb 20 2011 - 12:40:41 CST)
ABF calculation using RMSD Buddhadev Maiti (Wed Feb 16 2011 - 21:04:11 CST)
- RE: ABF calculation using RMSD JC Gumbart (Wed Feb 16 2011 - 21:24:01 CST)
CHARMM General Force Field (CGENFF) Gianluca Interlandi (Wed Feb 16 2011 - 18:56:33 CST)
forces on fixed atoms Bennion, Brian (Wed Feb 16 2011 - 16:01:44 CST)
- Re: forces on fixed atoms Jérôme Hénin (Wed Feb 16 2011 - 17:58:28 CST)
  - RE: forces on fixed atoms Bennion, Brian (Wed Feb 16 2011 - 18:04:30 CST)
Re: membrane simulation Constraint failure in RATTLE algorithm snoze pa (Wed Feb 16 2011 - 14:43:06 CST)
membrane simulation Constraint failure in RATTLE algorithm snoze pa (Wed Feb 16 2011 - 12:15:11 CST)
- Re: membrane simulation Constraint failure in RATTLE algorithm Jeffrey Potoff (Wed Feb 16 2011 - 14:58:38 CST)
  - Re: membrane simulation Constraint failure in RATTLE algorithm snoze pa (Wed Feb 16 2011 - 17:51:32 CST)
    - Re: membrane simulation Constraint failure in RATTLE algorithm Jeffrey Potoff (Wed Feb 16 2011 - 22:18:57 CST)
    - Re: membrane simulation Constraint failure in RATTLE algorithm snoze pa (Thu Feb 17 2011 - 10:00:44 CST)
Langevin Buffer Region David Huggins (Wed Feb 16 2011 - 04:19:51 CST)
initial structures for md simulations oguz gurbulak (Wed Feb 16 2011 - 07:52:26 CST)
- Re: initial structures for md simulations Jeffrey J. Potoff (Wed Feb 16 2011 - 09:02:13 CST)
initial structures for md simulations oguz gurbulak (Wed Feb 16 2011 - 06:22:11 CST)
Current status of polarizable force fields in NAMD lucie delemotte (Wed Feb 16 2011 - 04:37:03 CST)
Setting Up A Langevin Buffer Region David Huggins (Wed Feb 16 2011 - 04:30:44 CST)
- Re: Setting Up A Langevin Buffer Region Jérôme Hénin (Wed Feb 16 2011 - 06:34:58 CST)
Can I do protein-ligand docking using NAMD? Àî¼Ñ¼ü (Tue Feb 15 2011 - 23:32:03 CST)
- Re: Can I do protein-ligand docking using NAMD? Bo Liu (Wed Feb 16 2011 - 00:30:54 CST)
  - RE: Can I do protein-ligand docking using NAMD? JC Gumbart (Wed Feb 16 2011 - 01:08:36 CST)
Computing several pair interactions Samy Hamdouche (Tue Feb 15 2011 - 18:11:25 CST)
energy jump between minimization and simulation Eva Gonzalez Noya (Tue Feb 15 2011 - 18:06:25 CST)
- Re: energy jump between minimization and simulation Ajasja LjubetiÄ (Wed Feb 16 2011 - 03:27:53 CST)
  - Re: energy jump between minimization and simulation Eva Gonzalez Noya (Wed Feb 16 2011 - 10:14:45 CST)
energy jump running a simulation after minimization Eva Gonzalez Noya (Tue Feb 15 2011 - 17:23:07 CST)
energy jump running a simulation after minimization Eva Gonzalez Noya (Tue Feb 15 2011 - 16:37:59 CST)
Parameter in configuration NVE or NPT snoze pa (Tue Feb 15 2011 - 11:17:03 CST)
- Re: Parameter in configuration NVE or NPT David Tanner (Wed Feb 16 2011 - 08:37:31 CST)
problem with MD hamze rahimi (Tue Feb 15 2011 - 00:25:25 CST)
Force constant for Umbrella Sampling Buddhadev Maiti (Mon Feb 14 2011 - 19:19:02 CST)
ABF calculation using RMSD Buddhadev Maiti (Mon Feb 14 2011 - 19:08:32 CST)
- Re: ABF calculation using RMSD Jérôme Hénin (Tue Feb 15 2011 - 04:46:25 CST)
How to write gradual heating config files Cristina Rodríguez (Mon Feb 14 2011 - 19:08:07 CST)
Re: Tetramer protein complex snoze pa (Mon Feb 14 2011 - 15:01:31 CST)
NCS flavio seixas (Mon Feb 14 2011 - 14:09:35 CST)
- Re: NCS snoze pa (Mon Feb 14 2011 - 15:09:33 CST)
  - Re: NCS flavio seixas (Tue Feb 15 2011 - 05:04:33 CST)
  - Re: NCS flavio seixas (Tue Feb 15 2011 - 17:20:49 CST)
New colvar feature request -- angleXY Ajasja LjubetiÄ (Mon Feb 14 2011 - 07:19:46 CST)
- Re: New colvar feature request -- angleXY Giacomo Fiorin (Mon Feb 14 2011 - 09:43:33 CST)
- Re: New colvar feature request -- angleXY Jérôme Hénin (Mon Feb 14 2011 - 10:06:45 CST)
  - Re: New colvar feature request -- angleXY Ajasja Ljubetiè (Mon Feb 14 2011 - 10:13:28 CST)
    - Re: New colvar feature request -- angleXY Ajasja Ljubetiè (Mon Feb 14 2011 - 16:04:27 CST)
    - Re: New colvar feature request -- angleXY Giacomo Fiorin (Mon Feb 14 2011 - 17:07:05 CST)
ABF reproducibility Parisa Akhski (Sun Feb 13 2011 - 15:08:26 CST)
- Re: ABF reproducibility Jérôme Hénin (Mon Feb 14 2011 - 06:29:40 CST)
Tetramer protein complex snoze pa (Sun Feb 13 2011 - 00:54:34 CST)
psfgen - any version capable of reading extended PSF files? Bjoern Olausson (Fri Feb 11 2011 - 05:47:05 CST)
coarse-grained MD Demet Akten (Fri Feb 11 2011 - 03:34:56 CST)
job termination ipsita basu (Fri Feb 11 2011 - 00:46:17 CST)
- Re: job termination Chris Harrison (Fri Feb 11 2011 - 11:50:20 CST)
PME for electrostatics and cutoff for vdW? Christian Jorgensen (Thu Feb 10 2011 - 11:07:53 CST)
FEP - Protein binding to Membrane surface Bjoern Olausson (Thu Feb 10 2011 - 03:50:37 CST)
Mirror Image Energy Discrepency Keith Battle (Wed Feb 09 2011 - 13:23:28 CST)
- Re: Mirror Image Energy Discrepency Jérôme Hénin (Wed Feb 09 2011 - 14:40:06 CST)
  - Re: Mirror Image Energy Discrepency Jérôme Hénin (Thu Feb 10 2011 - 13:01:33 CST)
- Re: Mirror Image Energy Discrepency Richard Wood (Wed Feb 09 2011 - 16:42:18 CST)
I need help with this Richard Wood (Wed Feb 09 2011 - 13:01:25 CST)
- Re: I need help with this Cruz-Chu Eduardo Roberto (Thu Feb 10 2011 - 02:51:43 CST)
  - Re: I need help with this Richard Wood (Fri Feb 11 2011 - 06:07:23 CST)
    - Re: I need help with this felmerino_at_uchile.cl (Fri Feb 11 2011 - 10:35:52 CST)
    - Re: I need help with this Richard Wood (Fri Feb 11 2011 - 11:07:42 CST)
- Re: I need help with this Chris Harrison (Fri Feb 11 2011 - 11:42:41 CST)
  - Re: I need help with this Richard Wood (Fri Feb 11 2011 - 12:00:11 CST)
water box deformation ais_at_fh.huji.ac.il (Wed Feb 09 2011 - 09:47:27 CST)
- Re: water box deformation Jeffrey Potoff (Wed Feb 09 2011 - 10:51:41 CST)
- Re: water box deformation felmerino_at_uchile.cl (Wed Feb 09 2011 - 12:57:23 CST)
Abf force output stefhoor (Tue Feb 08 2011 - 20:58:39 CST)
- Re: Abf force output Jérôme Hénin (Wed Feb 09 2011 - 03:25:59 CST)
  - Re: Abf force output stefhoor (Wed Feb 09 2011 - 04:12:50 CST)
    - Re: Abf force output Jérôme Hénin (Wed Feb 09 2011 - 07:30:16 CST)
calculating energy term from extrabonds Segun Jung (Mon Feb 07 2011 - 23:50:43 CST)
rescaling and reassignment parameter Kang Hee Cho (Mon Feb 07 2011 - 22:35:44 CST)
calculating energy term from extrabonds Segun Jung (Mon Feb 07 2011 - 20:08:33 CST)
Get number of timesteps from DCD via script Bjoern Olausson (Mon Feb 07 2011 - 06:52:39 CST)
- Re: Get number of timesteps from DCD via script Chris Harrison (Mon Feb 07 2011 - 12:34:25 CST)
  - Re: Get number of timesteps from DCD via script Bjoern Olausson (Tue Feb 08 2011 - 05:24:29 CST)
Re: [ppl] NAMD at linux on sparc Phil Miller (Sun Feb 06 2011 - 21:18:32 CST)
determining force constant in exterbonds (harmonic potential) Segun Jung (Sat Feb 05 2011 - 10:09:50 CST)
SMD negative forces S Richmond (Fri Feb 04 2011 - 10:39:44 CST)
- Re: SMD negative forces S Richmond (Mon Feb 07 2011 - 17:37:09 CST)
  - Re: SMD negative forces S Richmond (Thu Feb 10 2011 - 15:32:35 CST)
    - Re: SMD negative forces Jérôme Hénin (Fri Feb 11 2011 - 03:24:54 CST)
charmm force field Swarna M Patra (Thu Feb 03 2011 - 21:55:22 CST)
Strange (very large) atom motions Craig Jolley (Thu Feb 03 2011 - 17:14:42 CST)
- Re: Strange (very large) atom motions Chris Harrison (Thu Feb 03 2011 - 18:18:24 CST)
(no subject) Alexandra Nemkevich (Thu Feb 03 2011 - 04:30:50 CST)
- Re: Giacomo Fiorin (Thu Feb 03 2011 - 10:49:22 CST)
- Re: Jérôme Hénin (Thu Feb 03 2011 - 11:13:22 CST)
Proposed Feature in Targeted MD Ryan McGreevy (Wed Feb 02 2011 - 12:48:58 CST)
ABF question (sampling and colvars output file) Parisa Akhski (Tue Feb 01 2011 - 10:27:43 CST)
- ABF question (sampling and colvars output file) Parisa Akhski (Sun Feb 06 2011 - 15:20:47 CST)
  - Re: ABF question (sampling and colvars output file) Jérôme Hénin (Mon Feb 07 2011 - 04:20:28 CST)
    - Re: ABF question (sampling and colvars output file) Jérôme Hénin (Mon Feb 07 2011 - 11:16:28 CST)
    - RE: ABF question (sampling and colvars output file) Parisa Akhski (Mon Feb 07 2011 - 14:27:03 CST)
volume calculation Swarna M Patra (Tue Feb 01 2011 - 04:02:48 CST)
unsubscribe Purushottam Dixit (Mon Jan 31 2011 - 20:59:01 CST)
Proposed Feature in Targeted MD Minh, David D. (Mon Jan 31 2011 - 13:12:38 CST)
- Re: Proposed Feature in Targeted MD V.Ovchinnikov (Mon Jan 31 2011 - 15:14:15 CST)
  - Re: Proposed Feature in Targeted MD Minh, David D. (Mon Jan 31 2011 - 15:33:42 CST)
  - Re: Proposed Feature in Targeted MD Minh, David D. (Mon Jan 31 2011 - 15:34:48 CST)
Problems compiling NAMD on 8-core Mac Minh, David D. (Mon Jan 31 2011 - 12:25:40 CST)
- Re: Problems compiling NAMD on 8-core Mac Jim Phillips (Mon Jan 31 2011 - 16:39:49 CST)
  - Re: Problems compiling NAMD on 8-core Mac Chris Harrison (Mon Jan 31 2011 - 22:49:39 CST)
- Re: Problems compiling NAMD on 8-core Mac Chris Harrison (Mon Jan 31 2011 - 16:44:23 CST)
  - Re: Problems compiling NAMD on 8-core Mac Minh, David D. (Mon Jan 31 2011 - 17:44:01 CST)
Question regarding NAMD membrane tutorial snoze pa (Mon Jan 31 2011 - 10:49:07 CST)
- Re: Question regarding NAMD membrane tutorial Chris Harrison (Mon Jan 31 2011 - 11:11:43 CST)
  - Re: Question regarding NAMD membrane tutorial snoze pa (Wed Feb 02 2011 - 13:03:38 CST)
    - Re: Question regarding NAMD membrane tutorial Chris Harrison (Thu Feb 03 2011 - 18:32:04 CST)
Help With colvars/abf Please Angelo Rossi (Sun Jan 30 2011 - 07:09:41 CST)
- Re: Help With colvars/abf Please Jérôme Hénin (Sun Jan 30 2011 - 09:10:50 CST)
  - Re: Help With colvars/abf Please Angelo Rossi (Sun Jan 30 2011 - 11:00:38 CST)
Coarse_Graining tempetrature Sibel Cakan (Fri Jan 28 2011 - 09:12:43 CST)
Coarse_Graining tempetrature Sibel Cakan (Fri Jan 28 2011 - 08:31:02 CST)
CG_MD temperature Sibel Cakan (Fri Jan 28 2011 - 07:52:15 CST)
topology for DNA Neelanjana Sengupta (Fri Jan 28 2011 - 06:28:03 CST)
- Re: topology for DNA Chris Harrison (Fri Jan 28 2011 - 07:59:06 CST)
  - Re: topology for DNA Eduardo Cruz-Chu (Fri Jan 28 2011 - 08:23:33 CST)
water content Kang Hee Cho (Thu Jan 27 2011 - 23:18:24 CST)
bond lengths angles in namd oguz gurbulak (Thu Jan 27 2011 - 06:35:34 CST)
Equilibration when splitting an ABF calculation Ajasja LjubetiÄ (Thu Jan 27 2011 - 06:25:04 CST)
- Re: Equilibration when splitting an ABF calculation Jérôme Hénin (Thu Jan 27 2011 - 08:08:12 CST)
  - Re: Equilibration when splitting an ABF calculation Ajasja LjubetiÄ (Thu Jan 27 2011 - 08:48:48 CST)
    - Re: Equilibration when splitting an ABF calculation Ajasja LjubetiÄ (Fri Jan 28 2011 - 06:26:58 CST)
    - Re: Equilibration when splitting an ABF calculation Jérôme Hénin (Fri Jan 28 2011 - 06:44:32 CST)
bond lengths angles in namd oguz gurbulak (Thu Jan 27 2011 - 05:43:09 CST)
- Re: bond lengths angles in namd Jérôme Hénin (Thu Jan 27 2011 - 06:55:28 CST)
- Re: bond lengths angles in namd Ajasja LjubetiÄ (Thu Jan 27 2011 - 07:14:26 CST)
Cu+2 parameters jose correa (Wed Jan 26 2011 - 07:36:59 CST)
the meaning and effect of reassignFreq and reassignTemp Kang Hee Cho (Tue Jan 25 2011 - 08:46:39 CST)
- How to set the right PME parameters for amber's prmtop and inpcrd files? a a (Wed Jan 26 2011 - 04:17:32 CST)
  - How to set the right PME parameters for amber's prmtop and inpcrd files? a a (Wed Jan 26 2011 - 04:34:33 CST)
mainboard-power source for GPU Francesco Pietra (Tue Jan 25 2011 - 01:47:42 CST)
- Re: mainboard-power source for GPU Axel Kohlmeyer (Tue Jan 25 2011 - 06:36:57 CST)
NBFIX support in CUDA NAMD Burgess, Don E (Mon Jan 24 2011 - 20:41:26 CST)
REMD with IBM SP6 LoadLeveler Luca Bellucci (Sat Jan 22 2011 - 11:45:31 CST)
- Re: REMD with IBM SP6 LoadLeveler Andrew Emerson (Mon Jan 24 2011 - 02:24:58 CST)
distance calculation between atoms of two segments mjyang (Sat Jan 22 2011 - 10:51:00 CST)
- Re: distance calculation between atoms of two segments Ajasja LjubetiÄ (Sat Jan 22 2011 - 13:48:54 CST)
the meaning of reassignFreq and reassignTemp Kang Hee Cho (Sat Jan 22 2011 - 04:28:22 CST)
- Re: the meaning of reassignFreq and reassignTemp Chris Harrison (Sun Jan 23 2011 - 09:51:01 CST)
Missing angle parameters NH1 CT1 NH1 Christian Jorgensen (Fri Jan 21 2011 - 04:39:07 CST)
- Re: Missing angle parameters NH1 CT1 NH1 Jérôme Hénin (Fri Jan 21 2011 - 06:44:14 CST)
  - RE: Missing angle parameters NH1 CT1 NH1 Christian Jorgensen (Fri Jan 21 2011 - 12:01:09 CST)
  - Re: Missing angle parameters NH1 CT1 NH1 Jérôme Hénin (Fri Jan 21 2011 - 11:01:56 CST)
discrete energy value after restart Kang Hee Cho (Thu Jan 20 2011 - 21:25:46 CST)
- Re: discrete energy value after restart Chris Harrison (Sun Jan 23 2011 - 10:00:07 CST)
question from a tutorial Lisa Brown (Thu Jan 20 2011 - 14:17:29 CST)
- Re: question from a tutorial JC Gumbart (Thu Jan 20 2011 - 14:29:23 CST)
4 x Opteron 12-core or 4 x Xeon 8-core ? David McGiven (Thu Jan 20 2011 - 05:59:13 CST)
increasing MAX_EXCLUSIONS Francesco Oteri (Wed Jan 19 2011 - 16:07:05 CST)
- Re: increasing MAX_EXCLUSIONS Axel Kohlmeyer (Wed Jan 19 2011 - 16:42:29 CST)
- Re: increasing MAX_EXCLUSIONS Francesco Oteri (Thu Jan 20 2011 - 09:56:35 CST)
non-zero charge Kwee Hong (Wed Jan 19 2011 - 10:17:45 CST)
- Re: non-zero charge Bo Liu (Wed Jan 19 2011 - 16:31:22 CST)
- Re: non-zero charge Chris Harrison (Wed Jan 19 2011 - 21:08:22 CST)
peptide structure ipsita basu (Tue Jan 18 2011 - 23:05:34 CST)
- Re: peptide structure Chris Harrison (Sun Jan 23 2011 - 10:10:08 CST)
  - Re: peptide structure ipsita basu (Thu Jan 27 2011 - 02:29:21 CST)
Various practical colvar module related questions Ajasja LjubetiÄ (Tue Jan 18 2011 - 11:31:46 CST)
- Re: Various practical colvar module related questions Jérôme Hénin (Wed Jan 19 2011 - 09:46:23 CST)
  - Re: Various practical colvar module related questions Ajasja LjubetiÄ (Thu Jan 20 2011 - 09:12:30 CST)
Protein-DNA simulations S.Archana (Mon Jan 17 2011 - 04:41:27 CST)
- Re: Protein-DNA simulations Chris Harrison (Wed Jan 19 2011 - 21:24:43 CST)
NBFIX for carbonyl atoms and potassium ions -- User Defined Force -- CUDA Burgess, Don E (Mon Jan 17 2011 - 15:35:28 CST)
Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein Ajasja LjubetiÄ (Mon Jan 17 2011 - 09:56:28 CST)
- Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein Jérôme Hénin (Mon Jan 17 2011 - 11:44:24 CST)
  - Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein Ajasja LjubetiÄ (Tue Jan 18 2011 - 08:40:56 CST)
Feature request for the colvars module -- TCL syntax Ajasja LjubetiÄ (Mon Jan 17 2011 - 09:26:47 CST)
- Re: Feature request for the colvars module -- TCL syntax Jérôme Hénin (Mon Jan 17 2011 - 11:52:23 CST)
  - Re: Feature request for the colvars module -- TCL syntax Ajasja LjubetiÄ (Tue Jan 18 2011 - 07:17:54 CST)
- Re: Feature request for the colvars module -- TCL syntax Chris Harrison (Mon Jan 17 2011 - 11:00:22 CST)
temperature range for residue-based CG Demet Akten (Mon Jan 17 2011 - 08:02:59 CST)
Membrane protein simulaton snoze pa (Fri Jan 14 2011 - 18:19:24 CST)
- Re: Membrane protein simulaton Eduard Schreiner (Fri Jan 14 2011 - 19:08:43 CST)
NAMD CUDA error message snoze pa (Fri Jan 14 2011 - 11:37:54 CST)
- RE: NAMD CUDA error message JC Gumbart (Fri Jan 14 2011 - 11:46:39 CST)
Can DCD trajectory files contain only protein but water surround yandongÂ Huang (Thu Jan 13 2011 - 08:44:10 CST)
- Re£º Can DCD trajectory files contain only protein but water surround Jun Zhang (Thu Jan 13 2011 - 19:22:10 CST)
- Re: Can DCD trajectory files contain only protein but water surround Axel Kohlmeyer (Thu Jan 13 2011 - 19:57:05 CST)
Error on closing binary file Seren Soner (Thu Jan 13 2011 - 06:42:50 CST)
Constraint failure; simulation has become unstable Wendy González (Fri Jan 07 2011 - 14:42:46 CST)
- Re: Constraint failure; simulation has become unstable Athanassios Stavrakoudis (Fri Jan 07 2011 - 15:04:08 CST)
  - Re: Constraint failure; simulation has become unstable Wendy González (Fri Jan 07 2011 - 15:18:20 CST)
NAMD initial coordinate file Ismail, Mohd F. (Fri Jan 07 2011 - 00:10:47 CST)
- Re: NAMD initial coordinate file Chris Harrison (Mon Jan 10 2011 - 06:27:07 CST)
  - Re: NAMD initial coordinate file Mohd Farid Ismail (Thu Jan 13 2011 - 12:40:03 CST)
Compiling NAMD 2.7 with the PLUMED patch Gianluca Interlandi (Thu Jan 06 2011 - 16:55:03 CST)
- Re: Compiling NAMD 2.7 with the PLUMED patch Gianluca Interlandi (Thu Jan 06 2011 - 17:41:23 CST)
- Re: Compiling NAMD 2.7 with the PLUMED patch Davide Branduardi (Thu Jan 06 2011 - 17:42:56 CST)
Fix atoms-Colvars Alex Liu (Thu Jan 06 2011 - 15:46:14 CST)
- Re: Fix atoms-Colvars Jérôme Hénin (Fri Jan 07 2011 - 13:04:10 CST)
NAMD Tutorial Problem Jane Ren (Thu Jan 06 2011 - 13:19:50 CST)
water sphere sara (Thu Jan 06 2011 - 03:14:01 CST)
- Re: water sphere Axel Kohlmeyer (Thu Jan 06 2011 - 08:18:57 CST)
(no subject) Chen, Zhihong (chenz2) (Wed Jan 05 2011 - 18:43:15 CST)
Benchmark for NAMD2.7 (curent version) Branko (Wed Jan 05 2011 - 14:19:19 CST)
unsubcribe Charlie Forde (Wed Jan 05 2011 - 10:49:54 CST)
Distance XY-colvars Alex Liu (Tue Jan 04 2011 - 15:56:56 CST)
- Re: Distance XY-colvars Giacomo Fiorin (Wed Jan 05 2011 - 16:12:32 CST)
NAG simulation problem with CPS Adrian Jasiñski (Wed Jan 05 2011 - 05:36:00 CST)
- RE: NAG simulation problem with CPS JC Gumbart (Wed Jan 05 2011 - 08:04:24 CST)
free energy perturbation BIN ZHANG (Wed Jan 05 2011 - 02:07:57 CST)
- Re: free energy perturbation Jérôme Hénin (Wed Jan 05 2011 - 07:39:37 CST)
  - Re: free energy perturbation Jérôme Hénin (Wed Jan 05 2011 - 12:07:39 CST)
restart problem charlie (Wed Jan 05 2011 - 02:07:48 CST)
- Re: restart problem JC Gumbart (Wed Jan 05 2011 - 14:23:32 CST)
parameter file for DMPC lipid and protein system but with CHARMM36 lipids Erica Smith (Mon Jan 03 2011 - 21:53:59 CST)
- RE: parameter file for DMPC lipid and protein system but with CHARMM36 lipids JC Gumbart (Mon Jan 03 2011 - 23:34:18 CST)
- Re: parameter file for DMPC lipid and protein system but with CHARMM36 lipids Prathit Chatterjee (Tue Jan 04 2011 - 01:14:10 CST)
.colvars.state file in ABF Alex Liu (Mon Jan 03 2011 - 15:53:45 CST)
- .colvars.state file in ABF Parisa Akhski (Tue Jan 04 2011 - 15:51:09 CST)
- Re: .colvars.state file in ABF Jérôme Hénin (Wed Jan 05 2011 - 07:15:45 CST)
Re: Running bias exchange metadynamics simulations with NAMD Jérôme Hénin (Sat Jan 01 2011 - 15:48:06 CST)
- Re: Running bias exchange metadynamics simulations with NAMD Ajasja LjubetiÄ (Sun Jan 02 2011 - 15:03:48 CST)
  - Re: Running bias exchange metadynamics simulations with NAMD Giacomo Fiorin (Mon Jan 03 2011 - 18:13:21 CST)
concatenate pmf files in colvars Parisa Akhski (Sat Jan 01 2011 - 12:23:06 CST)

Last message date: Fri May 25 2012 - 14:53:54 CDT
Archived on: Fri May 25 2012 - 23:20:48 CDT

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