NAMD-L: By Thread

Home
Overview
Publications
Research
Software
NAMD
VMD
GPU Computing
Lattice Microbes
Atomic Resolution Brownian Dynamics
MDFF
QwikMD
Other
Outreach

NAMD

NamdWiki

NAMD-L: By Thread

By Thread

4228 messages sorted by: [ author ] [ date ] [ subject ] [ attachment ]
About this archive

Starting: Tue Jan 01 2008 - 09:30:16 CST
Ending: Thu Dec 31 2009 - 04:18:43 CST

Definition of two colvars for ABF Branko (Wed Dec 30 2009 - 14:41:20 CST)
How to get the coordinate of a certain atom with tcl in the config file? Íõ—² (Mon Dec 28 2009 - 04:14:23 CST)
useconstantarea Francesco Pietra (Mon Dec 28 2009 - 03:35:48 CST)
subscribe Íõ—² (Mon Dec 28 2009 - 02:56:07 CST)
dmpc bilayer Syed Kashif Zafar (Sun Dec 27 2009 - 15:10:26 CST)
- Re: dmpc bilayer Axel Kohlmeyer (Mon Dec 28 2009 - 02:59:07 CST)
  - RE: dmpc bilayer Song, Hyundeok (songhk) (Mon Dec 28 2009 - 10:03:38 CST)
  - Re: dmpc bilayer Syed Kashif Zafar (Mon Dec 28 2009 - 13:10:46 CST)
CG equilibration recurring crashes Francesco Pietra (Sun Dec 27 2009 - 08:47:12 CST)
- Re: CG equilibration recurring crashes Axel Kohlmeyer (Sun Dec 27 2009 - 09:47:46 CST)
  - Re: CG equilibration recurring crashes Axel Kohlmeyer (Sun Dec 27 2009 - 12:44:08 CST)
How to read trajectory within CHARMM generated by NAMD Yang MIngjun (Sun Dec 27 2009 - 01:36:53 CST)
- Re: How to read trajectory within CHARMM generated by NAMD Axel Kohlmeyer (Sun Dec 27 2009 - 02:36:30 CST)
  - Fw: Re: Re: How to read trajectory within CHARMM generated by NAMD Yang MIngjun (Sun Dec 27 2009 - 20:06:44 CST)
  - Re: How to read trajectory within CHARMM generated by NAMD Dimitar V Pachov (Mon Dec 28 2009 - 11:52:59 CST)
- Re: How to read trajectory within CHARMM generated by NAMD gaillard_at_chimie.u-strasbg.fr (Mon Dec 28 2009 - 08:44:16 CST)
Periodic cell has become too small Francesco Pietra (Thu Dec 24 2009 - 03:35:52 CST)
- Fwd: Periodic cell has become too small Francesco Pietra (Thu Dec 24 2009 - 03:49:16 CST)
- Re: Periodic cell has become too small Axel Kohlmeyer (Thu Dec 24 2009 - 04:31:11 CST)
problems compiling charm and NAMD on intel cluster using MPI over ethernet Corenflos, Steven (Wed Dec 23 2009 - 23:48:28 CST)
- Re: problems compiling charm and NAMD on intel cluster using MPI over ethernet Axel Kohlmeyer (Thu Dec 24 2009 - 02:30:34 CST)
hi Segun Jung (Wed Dec 23 2009 - 00:59:44 CST)
How to acetylate at the N terminus and amidate at the C terminus ydhuang2727 (Tue Dec 22 2009 - 21:10:45 CST)
NAMD 2.7b2 new features Myunggi Yi (Tue Dec 22 2009 - 14:16:49 CST)
- Re: NAMD 2.7b2 new features Leonardo Trabuco (Wed Dec 23 2009 - 06:37:39 CST)
SelectConstraints problem priyodorshi satpati (Tue Dec 22 2009 - 08:43:15 CST)
namd: Running namd on a node on cluster Rabab Toubar (Tue Dec 22 2009 - 06:44:21 CST)
reassignFreq script Francesco Pietra (Mon Dec 21 2009 - 11:33:33 CST)
NAMD 2.7b2 with CUDA and infinband Jyh-Shyong (Sun Dec 20 2009 - 23:03:37 CST)
- Re: NAMD 2.7b2 with CUDA and infinband Axel Kohlmeyer (Mon Dec 21 2009 - 02:12:08 CST)
how to output the velocity for one selected atom in the system chengh_at_ringo.chem.pitt.edu (Sat Dec 19 2009 - 10:49:54 CST)
Does amber force field in NAMD 2.7b2 work stable? yudaqi (Fri Dec 18 2009 - 21:02:50 CST)
How to prevent cg water entering a membrane Francesco Pietra (Fri Dec 18 2009 - 16:49:55 CST)
error in install NAMD_2.7b2_Linux-x86_64-CUDA hamze rahimi (Fri Dec 18 2009 - 06:59:43 CST)
ABF - sequence of MD runs Krishnan, Marimuthu (Thu Dec 17 2009 - 21:55:59 CST)
defined path for NAMD2 hamze rahimi (Thu Dec 17 2009 - 06:45:56 CST)
- Re: defined path for NAMD2 Leonardo Trabuco (Fri Dec 18 2009 - 02:41:12 CST)
- Re: defined path for NAMD2 Andreas Forster (Fri Dec 18 2009 - 06:35:29 CST)
NAMD on current CPUs Jérôme Hénin (Thu Dec 17 2009 - 08:34:22 CST)
- Re: NAMD on current CPUs Axel Kohlmeyer (Thu Dec 17 2009 - 09:26:53 CST)
  - Re: NAMD on current CPUs Jérôme Hénin (Thu Dec 17 2009 - 12:56:25 CST)
Problem generating psf file in psfgen Ranyere Deyler (Wed Dec 16 2009 - 23:20:57 CST)
- Re: Problem generating psf file in psfgen Axel Kohlmeyer (Thu Dec 17 2009 - 01:38:00 CST)
How to obtain the system force on a fixed atom chengh_at_ringo.chem.pitt.edu (Wed Dec 16 2009 - 08:40:37 CST)
- Re: How to obtain the system force on a fixed atom Roman Petrenko (Wed Dec 16 2009 - 09:34:36 CST)
  - Re: How to obtain the system force on a fixed atom Roman Petrenko (Wed Dec 16 2009 - 09:41:57 CST)
  - Re: How to obtain the system force on a fixed atom Jérôme Hénin (Wed Dec 16 2009 - 12:01:33 CST)
- Re: How to obtain the system force on a fixed atom Jérôme Hénin (Wed Dec 16 2009 - 10:38:55 CST)
  - Re: How to obtain the system force on a fixed atom chengh_at_ringo.chem.pitt.edu (Mon Dec 21 2009 - 15:18:47 CST)
    - Re: How to obtain the system force on a fixed atom Axel Kohlmeyer (Tue Dec 22 2009 - 03:34:27 CST)
    - Re: Re: How to obtain the system force on a fixed atom Jian Liu (Mon Dec 21 2009 - 07:34:30 CST)
documentation on parallel implementation Paul Rigor (uci) (Wed Dec 16 2009 - 08:33:03 CST)
force constant in abf configuration file Madhurima Jana (Tue Dec 15 2009 - 23:01:02 CST)
- Fwd: force constant in abf configuration file Madhurima Jana (Thu Dec 17 2009 - 11:29:50 CST)
conf file for coarse grained simulation Francesco Pietra (Sun Dec 13 2009 - 15:08:59 CST)
- Fwd: conf file for coarse grained simulation Francesco Pietra (Mon Dec 14 2009 - 02:19:52 CST)
  - Re: Fwd: conf file for coarse grained simulation Axel Kohlmeyer (Tue Dec 15 2009 - 02:17:45 CST)
- Re: conf file for coarse grained simulation Peter Freddolino (Mon Dec 14 2009 - 19:15:57 CST)
reference of ewald method Hidekazu WATANABE (Sun Dec 13 2009 - 06:02:27 CST)
ABF error calculation Valeria M. (Fri Dec 11 2009 - 09:57:25 CST)
- FW: ABF error calculation Valeria M. (Fri Dec 11 2009 - 11:04:33 CST)
  - Re: FW: ABF error calculation BIN ZHANG (Fri Dec 11 2009 - 12:03:34 CST)
  - Re: FW: ABF error calculation Jérôme Hénin (Sat Dec 12 2009 - 03:53:07 CST)
Re: vmd-l: namd CG minimization error: unable to find angle parameters for nxg nxx nxg Francesco Pietra (Fri Dec 11 2009 - 09:52:43 CST)
namd CG minimization error: unable to find angle parameters for nxg nxx nxg Francesco Pietra (Thu Dec 10 2009 - 10:27:13 CST)
- Re: vmd-l: namd CG minimization error: unable to find angle parameters for nxg nxx nxg Peter Freddolino (Thu Dec 10 2009 - 15:06:05 CST)
Re: Request for information regarding ABF in NAMD. Jérôme Hénin (Fri Dec 11 2009 - 08:51:35 CST)
MD papers Corey Fugate (Thu Dec 10 2009 - 15:25:31 CST)
unsubscribe Rajiv Abhyankar (Thu Dec 10 2009 - 00:35:13 CST)
About "Visualization and Analysis of CPMD data with VMD" tutorial Aurum Bai (Wed Dec 09 2009 - 21:43:44 CST)
- Re: About "Visualization and Analysis of CPMD data with VMD" tutorial Axel Kohlmeyer (Thu Dec 10 2009 - 00:11:45 CST)
"-Wno-long-double" linking error David Tanner (Wed Dec 09 2009 - 14:24:14 CST)
- Re: "-Wno-long-double" linking error Axel Kohlmeyer (Wed Dec 09 2009 - 18:06:03 CST)
- Re: "-Wno-long-double" linking error Jim Phillips (Wed Dec 09 2009 - 18:05:25 CST)
Fwd: vmd-l: Restraints on coarse grained model Francesco Pietra (Wed Dec 09 2009 - 03:07:36 CST)
- Re: vmd-l: Restraints on coarse grained model Anton Arkhipov (Wed Dec 09 2009 - 10:58:56 CST)
Free Energy Calculation of a protein Mert Gür (Wed Dec 09 2009 - 14:19:42 CST)
- Re: Free Energy Calculation of a protein Pu Tian (Wed Dec 09 2009 - 15:53:35 CST)
  - Re: Free Energy Calculation of a protein Mert Gür (Thu Dec 10 2009 - 03:14:28 CST)
gradual increase in the temperature after minimization gurunath katagi (Wed Dec 09 2009 - 12:21:34 CST)
'dSmooth' no longer in the ABF procedure? Hugh Martin (Wed Dec 09 2009 - 09:08:30 CST)
- Re: 'dSmooth' no longer in the ABF procedure? Jérôme Hénin (Wed Dec 09 2009 - 10:25:14 CST)
  - Re: 'dSmooth' no longer in the ABF procedure? Hugh Martin (Wed Dec 09 2009 - 10:44:45 CST)
Re: What is LINK Patch? Jian Liu (Mon Dec 07 2009 - 23:42:48 CST)
PSFGEN Hyun Chul Lee (Mon Dec 07 2009 - 15:36:44 CST)
- CUDA on Win32 NAMD Priyan Amaras (Tue Dec 08 2009 - 14:19:07 CST)
- Re: PSFGEN Hyun Chul Lee (Thu Dec 10 2009 - 22:27:04 CST)
What is LINK Patch? Myunggi Yi (Mon Dec 07 2009 - 13:47:20 CST)
Running a simulation with coarse-grained protein in membrane Francesco Pietra (Mon Dec 07 2009 - 12:36:16 CST)
- Fwd: Running a simulation with coarse-grained protein in membrane Francesco Pietra (Tue Dec 08 2009 - 09:54:46 CST)
About the Nucleic Acid parameter and protein parameters Aurum Bai (Sun Dec 06 2009 - 05:59:36 CST)
Could namd realizes the QM-MM method? Aurum Bai (Fri Dec 04 2009 - 01:31:32 CST)
(no subject) Jim Parker (Thu Dec 03 2009 - 21:48:51 CST)
pressure profile Ziemys, Arturas (Thu Dec 03 2009 - 16:22:41 CST)
- Re: pressure profile Grace Brannigan (Fri Dec 04 2009 - 10:04:46 CST)
constraints doty alexiou (Thu Dec 03 2009 - 15:06:49 CST)
- Re: constraints Roman Petrenko (Thu Dec 03 2009 - 16:02:52 CST)
(no subject) Jim Parker (Thu Dec 03 2009 - 07:13:58 CST)
[Solved] Re: TclForces and getstep Jim Parker (Thu Dec 03 2009 - 07:10:12 CST)
- NAMD on 64 bit windows 2007 Priyan Amaras (Fri Dec 04 2009 - 13:23:04 CST)
  - RE: NAMD on 64 bit windows 2007 Richard Owczarzy (Fri Dec 04 2009 - 14:53:42 CST)
    - Re: NAMD on 64 bit windows 2007 Charles Zhao (Fri Dec 04 2009 - 18:55:20 CST)
  - Re: NAMD on 64 bit windows 2007 Charles Zhao (Fri Dec 04 2009 - 15:51:34 CST)
    - Re: NAMD on 64 bit windows 2007 Priyan Amaras (Mon Dec 07 2009 - 10:36:18 CST)
which portions of NAMD are CUDA accelerated? Paul Rigor (uci) (Wed Dec 02 2009 - 20:00:27 CST)
- Re: which portions of NAMD are CUDA accelerated? Axel Kohlmeyer (Wed Dec 02 2009 - 22:09:38 CST)
  - Re: which portions of NAMD are CUDA accelerated? Biff Forbush (Thu Dec 03 2009 - 20:29:16 CST)
  - Re: which portions of NAMD are CUDA accelerated? Paul Rigor (uci) (Wed Dec 16 2009 - 03:57:36 CST)
Incorrect Atom Count Charles Zhao (Wed Dec 02 2009 - 15:53:51 CST)
- Re: Incorrect Atom Count BIN ZHANG (Wed Dec 02 2009 - 16:31:20 CST)
  - Re: Incorrect Atom Count Charles Zhao (Wed Dec 02 2009 - 17:58:03 CST)
    - Re: Incorrect Atom Count Charles Zhao (Thu Dec 03 2009 - 01:26:32 CST)
TclForces and getstep Jim Parker (Wed Dec 02 2009 - 00:33:37 CST)
How are the SMD atoms connected to the center of mass Mert Gür (Tue Dec 01 2009 - 07:31:47 CST)
- Re: How are the SMD atoms connected to the center of mass Mert Gür (Wed Dec 02 2009 - 07:45:26 CST)
Small discrepancy in Kinetic Energy after restarting the simulation Mert Gür (Tue Dec 01 2009 - 03:10:30 CST)
- Re: Small discrepancy in Kinetic Energy after restarting the simulation Roman Petrenko (Tue Dec 01 2009 - 10:55:40 CST)
  - Re: Small discrepancy in Kinetic Energy after restarting the simulation Peter Freddolino (Tue Dec 01 2009 - 11:25:40 CST)
    - Re: Small discrepancy in Kinetic Energy after restarting the simulation Mert Gür (Tue Dec 01 2009 - 11:35:08 CST)
RMSD for individual residue gurunath katagi (Mon Nov 30 2009 - 11:55:34 CST)
- Re: RMSD for individual residue Joshua Adelman (Mon Nov 30 2009 - 12:10:14 CST)
rigidTolerance question snoze pa (Sun Nov 29 2009 - 19:06:15 CST)
- Re: rigidTolerance question Axel Kohlmeyer (Sun Nov 29 2009 - 19:51:28 CST)
psfgen fails to set coords for all atoms Blake Mertz (Fri Nov 27 2009 - 15:06:47 CST)
- Re: psfgen fails to set coords for all atoms Axel Kohlmeyer (Fri Nov 27 2009 - 15:56:05 CST)
- Re: psfgen fails to set coords for all atoms Jérôme Hénin (Sat Nov 28 2009 - 18:02:52 CST)
adding constraints doty alexiou (Thu Nov 26 2009 - 15:40:09 CST)
Re: FreeEnergy: Not enough steps to complete pfm & mcti blocks priyodorshi satpati (Thu Nov 26 2009 - 03:19:48 CST)
- Re: FreeEnergy: Not enough steps to complete pfm & mcti blocks priyodorshi satpati (Fri Nov 27 2009 - 03:26:01 CST)
  - Re: FreeEnergy: Not enough steps to complete pfm & mcti blocks Jérôme Hénin (Fri Nov 27 2009 - 06:42:59 CST)
    - Re: FreeEnergy: Not enough steps to complete pfm & mcti blocks priyodorshi satpati (Wed Dec 02 2009 - 10:28:44 CST)
stopping protein rotation with colvars David A. Horita (Wed Nov 25 2009 - 13:55:56 CST)
FreeEnergy: Not enough steps to complete pfm & mcti blocks priyodorshi satpati (Wed Nov 25 2009 - 09:31:15 CST)
Re: Multiplicity of Parameters for dihedral bond exceeded Ajasja LjubetiÄ (Wed Nov 25 2009 - 03:42:35 CST)
Re: Re: vmd-l: problems with CG protein-lipidbilayer-water system Francesco Pietra (Sun Nov 22 2009 - 15:32:18 CST)
problems with CG protein-lipidbilayer-water system Francesco Pietra (Sat Nov 21 2009 - 12:00:54 CST)
- Re: vmd-l: problems with CG protein-lipidbilayer-water system Axel Kohlmeyer (Sat Nov 21 2009 - 16:54:04 CST)
- Re: vmd-l: problems with CG protein-lipidbilayer-water system Anton Arkhipov (Mon Nov 23 2009 - 00:51:43 CST)
maximum number of devices supported per namd process Paul Rigor (uci) (Mon Nov 23 2009 - 21:45:08 CST)
Difference between Linux-x86_64-TCP and Linux-x86_64 Lee Wei Yang (Mon Nov 23 2009 - 16:33:12 CST)
- Re: Difference between Linux-x86_64-TCP and Linux-x86_64 Axel Kohlmeyer (Tue Nov 24 2009 - 07:53:57 CST)
GeForce vs. Tesla Tian, Pu (NIH/NIDDK) [C] (Mon Nov 23 2009 - 10:01:13 CST)
- The Future of NAMD was Re: GeForce vs. Tesla Biff Forbush (Wed Nov 25 2009 - 15:22:22 CST)
  - Re: The Future of NAMD was Re: GeForce vs. Tesla Axel Kohlmeyer (Wed Nov 25 2009 - 17:07:27 CST)
    - RE: The Future of NAMD was Re: GeForce vs. Tesla Tian, Pu (NIH/NIDDK) [C] (Thu Nov 26 2009 - 07:23:20 CST)
Stray PME grid charges detected: colvars Vamshi Gangupomu (Mon Nov 23 2009 - 09:44:39 CST)
Signal: segmentation violation gurunath katagi (Fri Nov 20 2009 - 15:20:16 CST)
help with running namd-cuda for the tutorials Paul Rigor (uci) (Fri Nov 20 2009 - 10:24:20 CST)
- Re: help with running namd-cuda for the tutorials Axel Kohlmeyer (Fri Nov 20 2009 - 11:25:14 CST)
  - Re: help with running namd-cuda for the tutorials Paul Rigor (uci) (Fri Nov 20 2009 - 20:06:38 CST)
    - Re: help with running namd-cuda for the tutorials Axel Kohlmeyer (Fri Nov 20 2009 - 20:56:52 CST)
    - Re: help with running namd-cuda for the tutorials Paul Rigor (uci) (Fri Nov 20 2009 - 21:05:48 CST)
Finer details of an ABF/colvar simulation Hugh Martin (Fri Nov 20 2009 - 09:10:08 CST)
- Re: Finer details of an ABF/colvar simulation Jerome Henin (Sun Nov 22 2009 - 13:37:32 CST)
  - Re: Finer details of an ABF/colvar simulation Hugh Martin (Tue Nov 24 2009 - 10:07:46 CST)
Fwd: error in scripting ipsita basu (Thu Nov 19 2009 - 23:33:25 CST)
- Re: error in scripting ipsita basu (Wed Nov 25 2009 - 00:08:04 CST)
  - Re: error in scripting Axel Kohlmeyer (Wed Nov 25 2009 - 01:08:21 CST)
simulation configuration file not accesible - other reasons CHINDEA Vlad (Thu Nov 19 2009 - 16:46:23 CST)
- RE: simulation configuration file not accesible - other reasons Richard Owczarzy (Thu Nov 19 2009 - 17:38:15 CST)
  - FW: simulation configuration file not accesible - other reasons CHINDEA Vlad (Fri Nov 20 2009 - 17:57:29 CST)
    - Re: FW: simulation configuration file not accesible - other reasons Axel Kohlmeyer (Fri Nov 20 2009 - 18:37:51 CST)
    - FW: simulation configuration file not accesible - other reasons CHINDEA Vlad (Sun Nov 22 2009 - 15:04:27 CST)
Generating psf for NPC1 Joshua Lioi (Thu Nov 19 2009 - 10:45:07 CST)
Fwd: error in scripting ipsita basu (Thu Nov 19 2009 - 03:28:03 CST)
iAPBS 1.0.0 released Robert Konecny (Wed Nov 18 2009 - 22:55:24 CST)
Unimportant bug in output xst file writing process A D (Wed Nov 18 2009 - 18:18:37 CST)
Simultaneous water and protein minimization jkmann_at_buffalo.edu (Wed Nov 18 2009 - 15:58:22 CST)
- RE: Simultaneous water and protein minimization Richard Owczarzy (Wed Nov 18 2009 - 16:52:09 CST)
  - RE: Simultaneous water and protein minimization jkmann_at_buffalo.edu (Thu Nov 19 2009 - 11:04:17 CST)
  - RE: Simultaneous water and protein minimization Richard Owczarzy (Thu Nov 19 2009 - 11:55:08 CST)
    - Re: Simultaneous water and protein minimization Grace Brannigan (Thu Nov 19 2009 - 14:06:53 CST)
    - Re: Simultaneous water and protein minimization jkmann_at_buffalo.edu (Thu Nov 19 2009 - 15:07:54 CST)
calculation of periodic box Michael Thomas (Tue Nov 17 2009 - 22:16:05 CST)
- Re: calculation of periodic box Joshua Adelman (Tue Nov 17 2009 - 22:29:13 CST)
- Re: calculation of periodic box Roman Petrenko (Tue Nov 17 2009 - 22:51:27 CST)
  - Re: calculation of periodic box Michael Thomas (Tue Nov 17 2009 - 22:56:55 CST)
NAMD file limitation in Win32 - windows XP Richard Owczarzy (Tue Nov 17 2009 - 11:51:52 CST)
- Re: NAMD file limitation in Win32 - windows XP Axel Kohlmeyer (Tue Nov 17 2009 - 12:33:09 CST)
  - Re: NAMD file limitation in Win32 - windows XP Biff Forbush (Tue Nov 17 2009 - 15:29:21 CST)
Error: failed on end of segment with RBCG Francesco Pietra (Sun Nov 15 2009 - 03:18:57 CST)
- Re: vmd-l: Error: failed on end of segment with RBCG Peter Freddolino (Sun Nov 15 2009 - 08:46:47 CST)
error in scripting ipsita basu (Mon Nov 16 2009 - 00:47:57 CST)
- Re: error in scripting Axel Kohlmeyer (Mon Nov 16 2009 - 07:36:50 CST)
Segmentation Violation: colvars Vamshi Gangupomu (Sun Nov 15 2009 - 05:32:42 CST)
The MD of aquaporin in NAMD Ning Zhang (Sat Nov 14 2009 - 01:31:31 CST)
- Re: The MD of aquaporin in NAMD Axel Kohlmeyer (Sat Nov 14 2009 - 09:52:05 CST)
NAMD 2.7b2 Released Jim Phillips (Fri Nov 13 2009 - 17:03:52 CST)
CUDA-accelarated NAMD does not use the video card? Lee Wei Yang (Fri Nov 13 2009 - 16:55:15 CST)
- Re: CUDA-accelarated NAMD does not use the video card? Jim Phillips (Fri Nov 13 2009 - 17:06:48 CST)
- RE: CUDA-accelarated NAMD does not use the video card? Lee Wei Yang (Fri Nov 13 2009 - 18:15:27 CST)
Re: Will MPICH2 work for NAMD? and the best way to build/compile NAMD to exploit my hardware resource? Bjoern Olausson (Fri Nov 13 2009 - 03:39:32 CST)
- RE: Will MPICH2 work for NAMD? and the best way to build/compile NAMD to exploit my hardware resource? Lee Wei Yang (Fri Nov 13 2009 - 16:12:50 CST)
Re: Formating of logfile Bjoern Olausson (Fri Nov 13 2009 - 02:55:02 CST)
- Re: Formating of logfile Bjoern Olausson (Fri Nov 13 2009 - 14:31:22 CST)
  - Re: Formating of logfile Axel Kohlmeyer (Fri Nov 13 2009 - 15:17:49 CST)
NAMD 2.7b1 Performance loss with CUDA 2.3 Joakim Swedberg (Thu Nov 12 2009 - 20:07:23 CST)
- Re: NAMD 2.7b1 Performance loss with CUDA 2.3 Axel Kohlmeyer (Thu Nov 12 2009 - 21:07:57 CST)
Memory keep increasing. Ming (Thu Nov 12 2009 - 06:14:05 CST)
- Re: Memory keep increasing. Axel Kohlmeyer (Thu Nov 12 2009 - 07:36:00 CST)
NAMD bonded energy function BIN ZHANG (Thu Nov 12 2009 - 01:23:16 CST)
32 bit + 64 bit mixed architecture problem Yogesh Aher (Wed Nov 11 2009 - 10:17:27 CST)
- Re: 32 bit + 64 bit mixed architecture problem Axel Kohlmeyer (Wed Nov 11 2009 - 12:08:02 CST)
  - Re: 32 bit + 64 bit mixed architecture problem Axel Kohlmeyer (Thu Nov 12 2009 - 10:12:36 CST)
Formating of logfile Bjoern Olausson (Wed Nov 11 2009 - 07:07:34 CST)
Formating of logfile Bjoern Olausson (Wed Nov 11 2009 - 06:58:44 CST)
RBCG tutorial Francesco Pietra (Wed Nov 11 2009 - 03:08:03 CST)
- Fwd: RBCG tutorial Francesco Pietra (Wed Nov 11 2009 - 03:56:35 CST)
FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT gurunath katagi (Tue Nov 10 2009 - 12:08:13 CST)
Retrieving standard deviation values while using collective variables (ABF) Hugh Martin (Tue Nov 10 2009 - 05:55:53 CST)
- Re: Retrieving standard deviation values while using collective variables (ABF) Jerome Henin (Tue Nov 10 2009 - 10:52:34 CST)
  - Re: Retrieving standard deviation values while using collective variables (ABF) Hugh Martin (Thu Nov 26 2009 - 07:38:13 CST)
    - Re: Retrieving standard deviation values while using collective variables (ABF) Jerome Henin (Thu Nov 26 2009 - 09:04:19 CST)
    - Re: Retrieving standard deviation values while using collective variables (ABF) Hugh Martin (Thu Nov 26 2009 - 09:30:21 CST)
scripiting problem ipsita basu (Tue Nov 10 2009 - 01:30:51 CST)
- Re: scripiting problem DimitryASuplatov (Tue Nov 10 2009 - 11:21:55 CST)
  - Re: scripiting problem DimitryASuplatov (Wed Nov 11 2009 - 03:06:05 CST)
Harmonic restraint parameters Bernardo Sosa Padilla Araujo (Mon Nov 09 2009 - 13:49:37 CST)
Will MPICH2 work for NAMD? Lee Wei Yang (Mon Nov 09 2009 - 12:37:58 CST)
- Re: Will MPICH2 work for NAMD? Bjoern Olausson (Tue Nov 10 2009 - 02:52:03 CST)
  - Re: Will MPICH2 work for NAMD? Bjoern Olausson (Wed Nov 11 2009 - 07:07:47 CST)
Automatic namd 2.7b1 installation DimitryASuplatov (Mon Nov 09 2009 - 11:36:22 CST)
fixing the protein during minimization Mert Gür (Mon Nov 09 2009 - 08:22:24 CST)
- Help pls: Got error on FEP calculation: ERROR: The following variables are NOT VALID lambda2... Li, Hongzhi (Mon Nov 09 2009 - 12:18:59 CST)
dielectric constant assignment Rajiv Abhyankar (Mon Nov 09 2009 - 06:22:04 CST)
- Re: dielectric constant assignment Axel Kohlmeyer (Mon Nov 09 2009 - 07:22:35 CST)
missing libraries for NAMD 2.7 on Linux cluster? Erik Nordgren (Sat Nov 07 2009 - 01:09:17 CST)
- Re: missing libraries for NAMD 2.7 on Linux cluster? Axel Kohlmeyer (Mon Nov 09 2009 - 07:32:15 CST)
Re: angle in colvars Dimitar V Pachov (Sun Nov 08 2009 - 22:17:20 CST)
- Re: angle in colvars Felipe Merino (Mon Nov 09 2009 - 06:19:03 CST)
  - Re: angle in colvars Jerome Henin (Mon Nov 09 2009 - 09:09:17 CST)
angle in colvars Felipe Merino (Sun Nov 08 2009 - 21:52:10 CST)
Fwd: Error in Minimization Ale Gomez (Sun Nov 08 2009 - 09:15:02 CST)
- Re: Error in Minimization Roman Petrenko (Sun Nov 08 2009 - 10:29:47 CST)
  - Re: Error in Minimization Ale Gomez (Sun Nov 08 2009 - 11:19:28 CST)
- Re: Error in Minimization Axel Kohlmeyer (Sun Nov 08 2009 - 11:05:47 CST)
  - Re: Error in Minimization Ale Gomez (Mon Nov 09 2009 - 21:19:06 CST)
water box size gurunath katagi (Sun Nov 08 2009 - 07:23:41 CST)
- Re: water box size Joshua Adelman (Sun Nov 08 2009 - 07:57:36 CST)
  - Re: water box size Roman Petrenko (Sun Nov 08 2009 - 10:52:03 CST)
Error in Minimization Ale Gomez (Sat Nov 07 2009 - 10:45:24 CST)
- Re: Error in Minimization Joshua Adelman (Sun Nov 08 2009 - 08:05:11 CST)
Is it a bug? TCL Script may Lead to Overflow Fred (Rui FENG) (Sat Nov 07 2009 - 03:09:28 CST)
- Re: Is it a bug? TCL Script may Lead to Overflow Fred (Rui FENG) (Sat Nov 07 2009 - 14:01:53 CST)
  - Re: Is it a bug? TCL Script may Lead to Overflow Axel Kohlmeyer (Sat Nov 07 2009 - 14:47:08 CST)
Tuning NAMD CUDA? Ronald Salesky (Fri Nov 06 2009 - 18:07:14 CST)
strange error from NAMD with CUDA t s (Thu Nov 05 2009 - 13:55:14 CST)
NAMD-problem jose correa (Thu Nov 05 2009 - 17:29:30 CST)
Atom constraint in certain direction Priyan Amaras (Thu Nov 05 2009 - 11:15:31 CST)
molecular dynamics simulation ipsita basu (Thu Nov 05 2009 - 04:35:33 CST)
- Re: molecular dynamics simulation Roman Petrenko (Thu Nov 05 2009 - 10:27:14 CST)
  - Re: molecular dynamics simulation ipsita basu (Thu Nov 05 2009 - 22:54:45 CST)
Running NAMD w/ CUDA under Linux Ronald Salesky (Wed Nov 04 2009 - 21:23:30 CST)
- Re: Running NAMD w/ CUDA under Linux Praveen Agrawal (Thu Nov 05 2009 - 11:58:24 CST)
- RE: Running NAMD w/ CUDA under Linux Lee Wei Yang (Thu Nov 05 2009 - 18:32:40 CST)
Read dcd file and calculate (distance/constraint energy Vs snapshots) using NAMD priyodorshi satpati (Wed Nov 04 2009 - 11:05:33 CST)
Re: ibverbs crash Bjoern Olausson (Wed Nov 04 2009 - 08:38:45 CST)
TIP4P Luca Mammucari (Tue Nov 03 2009 - 17:07:10 CST)
TIP4P topology Luca Bellucci (Tue Nov 03 2009 - 14:24:04 CST)
- Re: TIP4P topology Robert Brunner (Tue Nov 03 2009 - 15:11:18 CST)
  - Re: TIP4P topology David Hardy (Tue Nov 03 2009 - 15:32:33 CST)
  - Re: TIP4P topology Edward Lyman (Tue Nov 03 2009 - 15:43:43 CST)
- Re: TIP4P topology Robert Brunner (Tue Nov 03 2009 - 15:31:20 CST)
ibverbs crash David A. Horita (Tue Nov 03 2009 - 14:17:17 CST)
- Re: ibverbs crash Bjoern Olausson (Wed Nov 04 2009 - 04:06:48 CST)
- Re: ibverbs crash Bjoern Olausson (Wed Nov 04 2009 - 08:38:25 CST)
(no subject) l.mammucari_at_tin.it (Mon Nov 02 2009 - 15:47:14 CST)
(no subject) Luca M. (Mon Nov 02 2009 - 14:33:36 CST)
Abnormal EOF found -buffer=*END* Patrick Yee (Mon Nov 02 2009 - 12:35:52 CST)
PMEGridSpacing DimitryASuplatov (Sat Oct 31 2009 - 05:46:04 CDT)
- Re: PMEGridSpacing Roman Petrenko (Sat Oct 31 2009 - 15:17:58 CDT)
  - Re: PMEGridSpacing Roman Petrenko (Sat Oct 31 2009 - 15:19:36 CDT)
How to apply an unsteady magnetic field? fereshteh moradi (Sun Oct 25 2009 - 01:52:29 CDT)
- Re: How to apply an unsteady magnetic field? Axel Kohlmeyer (Fri Oct 30 2009 - 15:40:32 CDT)
Namd benchmark problem Sangamesh B (Thu Oct 22 2009 - 10:29:17 CDT)
- Namd benchmark problem Sangamesh B (Sat Oct 24 2009 - 02:12:05 CDT)
  - Re: Namd benchmark problem Axel Kohlmeyer (Sat Oct 24 2009 - 11:30:45 CDT)
Molecular dynamics of multiple organic molecules with NAMD B (Thu Oct 22 2009 - 09:39:06 CDT)
Error on renaming file: Permission denied Stephen Hicks (Mon Jun 04 2007 - 00:38:28 CDT)
Hydrogen molecule model Mikhail Suyetin (Fri Oct 30 2009 - 10:42:19 CDT)
- Re: Hydrogen molecule model Axel Kohlmeyer (Fri Oct 30 2009 - 15:00:12 CDT)
issues with AutoPSF for a cyclodextrin CHINDEA Vlad (Thu Oct 29 2009 - 18:32:50 CDT)
- Re: issues with AutoPSF for a cyclodextrin Peter Freddolino (Thu Oct 29 2009 - 19:31:00 CDT)
  - RE: issues with AutoPSF for a cyclodextrin CHINDEA Vlad (Fri Oct 30 2009 - 17:02:48 CDT)
    - FW: issues with AutoPSF for a cyclodextrin - addendum CHINDEA Vlad (Fri Oct 30 2009 - 18:30:51 CDT)
    - Re: FW: issues with AutoPSF for a cyclodextrin - addendum Peter Freddolino (Fri Oct 30 2009 - 19:20:03 CDT)
RAMD in NAMD; bugs and new version 4.0 Vlad Cojocaru (Thu Oct 29 2009 - 11:13:39 CDT)
About APBS calculation «J ¦¼¯Â (Thu Oct 29 2009 - 09:22:48 CDT)
- Re: [***** SPAM *****] About APBS calculation Elsa Fernanda de Sousa Henriques (Fri Oct 30 2009 - 04:40:20 CDT)
Using restraints DimitryASuplatov (Wed Oct 28 2009 - 10:55:44 CDT)
Re: NAMD2.7 scaling problems DimitryASuplatov (Wed Oct 28 2009 - 08:30:44 CDT)
NAMD2.7 scaling problems DimitryASuplatov (Wed Oct 28 2009 - 04:06:13 CDT)
abnormal water surface after nvt and npt for POPC membrane pxq ÅÓÑ©ÇÛ (Tue Oct 27 2009 - 19:57:58 CDT)
- Re: abnormal water surface after nvt and npt for POPC membrane Axel Kohlmeyer (Wed Oct 28 2009 - 10:55:16 CDT)
order parameter, lipid segments as vectors Raul Araya (Tue Oct 27 2009 - 08:48:32 CDT)
Tcl forces Myunggi Yi (Mon Oct 26 2009 - 13:12:50 CDT)
Modeling familial amyloidotic polyneuropathy drmartin_at_fizyka.umk.pl (Mon Oct 26 2009 - 07:04:03 CDT)
- Re: Modeling familial amyloidotic polyneuropathy Jerome Henin (Mon Oct 26 2009 - 07:48:12 CDT)
  - Re: Modeling familial amyloidotic polyneuropathy drmartin_at_fizyka.umk.pl (Mon Oct 26 2009 - 10:17:07 CDT)
Random Expulsion MD (REMD) kristian krantz (Mon Oct 26 2009 - 06:07:11 CDT)
- Re: Random Expulsion MD (REMD) Vlad Cojocaru (Mon Oct 26 2009 - 06:45:30 CDT)
  - RE: Random Expulsion MD (REMD) Brittany Morgan (Mon Oct 26 2009 - 11:37:27 CDT)
namd cvs memory leak? BIN ZHANG (Thu Oct 22 2009 - 18:12:08 CDT)
- Re: namd cvs memory leak? Axel Kohlmeyer (Thu Oct 22 2009 - 19:24:52 CDT)
  - Re: namd cvs memory leak? BIN ZHANG (Thu Oct 22 2009 - 19:57:08 CDT)
Pair interaction runtime analysis skipping dcd frames lucie delemotte (Thu Oct 22 2009 - 09:30:08 CDT)
- Re: Pair interaction runtime analysis skipping dcd frames Jerome Henin (Thu Oct 22 2009 - 12:14:46 CDT)
fresh file not ready to read? BIN ZHANG (Thu Oct 22 2009 - 01:46:10 CDT)
Modification of equlibrated simulation box namd_chcwaaa_at_yahoo.com.cn (Wed Oct 21 2009 - 00:36:37 CDT)
- Re: Modification of equlibrated simulation box Axel Kohlmeyer (Wed Oct 21 2009 - 09:00:55 CDT)
  - RE: Modification of equlibrated simulation box: OPTION 4 Bishop, Thomas C (Wed Oct 21 2009 - 18:57:48 CDT)
Re: CG bead definition BIN ZHANG (Tue Oct 20 2009 - 15:12:04 CDT)
- Re: CG bead definition BIN ZHANG (Thu Oct 22 2009 - 18:05:32 CDT)
unsubscribe Vinit Rege (Tue Oct 20 2009 - 13:26:56 CDT)
Fwd: vmd-l: CG bead definition BIN ZHANG (Tue Oct 20 2009 - 11:19:30 CDT)
COARSE GRAINED WATER MODEL Valeria Marquez (Tue Oct 20 2009 - 08:52:10 CDT)
- Re: COARSE GRAINED WATER MODEL L. Michel Espinoza-Fonseca (Tue Oct 20 2009 - 09:36:00 CDT)
- Re: COARSE GRAINED WATER MODEL Valeria Marquez (Tue Oct 20 2009 - 10:16:04 CDT)
smd output (v2.6) David A. Horita (Mon Oct 19 2009 - 12:04:05 CDT)
Water Sphere Solvation Peter Murphy (Sun Oct 18 2009 - 08:41:38 CDT)
Tolerance for SHAKE Nicholas M Glykos (Sun Oct 18 2009 - 07:58:20 CDT)
zeroMomentum command A D (Fri Oct 16 2009 - 18:29:08 CDT)
- Re: zeroMomentum command Felipe Merino (Fri Oct 16 2009 - 20:49:24 CDT)
- Re: zeroMomentum command Felipe Merino (Fri Oct 16 2009 - 20:53:10 CDT)
tcl force Seungho Choe (Fri Oct 16 2009 - 16:34:58 CDT)
- Re: tcl force Seungho Choe (Fri Oct 16 2009 - 23:17:19 CDT)
- Re: tcl force Seungho Choe (Sat Oct 17 2009 - 00:21:08 CDT)
  - RE: tcl force JC Gumbart (Sat Oct 17 2009 - 00:56:45 CDT)
Tcl forces Myunggi Yi (Fri Oct 16 2009 - 15:06:45 CDT)
- Re: Tcl forces Myunggi Yi (Fri Oct 16 2009 - 16:22:40 CDT)
  - Re: Tcl forces Myunggi Yi (Fri Oct 16 2009 - 16:23:32 CDT)
- Re: Tcl forces Axel Kohlmeyer (Fri Oct 16 2009 - 16:21:04 CDT)
ATP and Stream files Luis Agullo (LAB) (Fri Oct 16 2009 - 03:39:30 CDT)
Slow heating in namd Pavan G (Thu Oct 15 2009 - 09:10:02 CDT)
- Re: Slow heating in namd Axel Kohlmeyer (Thu Oct 15 2009 - 10:05:07 CDT)
- Re: Slow heating in namd Axel Kohlmeyer (Thu Oct 15 2009 - 09:57:17 CDT)
- Re: Slow heating in namd Roman Petrenko (Thu Oct 15 2009 - 10:32:43 CDT)
  - Re: Slow heating in namd Pavan G (Thu Oct 15 2009 - 10:37:47 CDT)
Ionization with VMD Luis Agullo (LAB) (Thu Oct 15 2009 - 09:07:13 CDT)
- Re: Ionization with VMD Axel Kohlmeyer (Thu Oct 15 2009 - 09:48:29 CDT)
ATP and Stream files Luis Agullo (LAB) (Thu Oct 15 2009 - 07:49:58 CDT)
- Re: ATP and Stream files Dimitar V Pachov (Thu Oct 15 2009 - 08:55:02 CDT)
- Re: ATP and Stream files L. Michel Espinoza-Fonseca (Fri Oct 16 2009 - 00:42:52 CDT)
spontaneous system explosion after 2 ns of normal run Roman Petrenko (Wed Oct 14 2009 - 22:57:34 CDT)
- Re: spontaneous system explosion after 2 ns of normal run Roman Petrenko (Wed Oct 14 2009 - 23:09:36 CDT)
- Re: spontaneous system explosion after 2 ns of normal run Luis Agullo (LAB) (Thu Oct 15 2009 - 08:40:06 CDT)
  - Re: Re: spontaneous system explosion after 2 ns of normal run Axel Kohlmeyer (Thu Oct 15 2009 - 09:30:34 CDT)
- Re: spontaneous system explosion after 2 ns of normal run Axel Kohlmeyer (Thu Oct 15 2009 - 10:01:00 CDT)
  - Re: spontaneous system explosion after 2 ns of normal run Roman Petrenko (Thu Oct 15 2009 - 10:22:44 CDT)
  - Re: spontaneous system explosion after 2 ns of normal run Jian Liu (Mon Oct 19 2009 - 01:45:24 CDT)
center of mass of dummyAtom in colvar BIN ZHANG (Wed Oct 14 2009 - 16:57:13 CDT)
- Re: center of mass of dummyAtom in colvar Giacomo Fiorin (Wed Oct 14 2009 - 18:57:43 CDT)
  - Re: center of mass of dummyAtom in colvar BIN ZHANG (Wed Oct 14 2009 - 19:06:01 CDT)
    - Re: center of mass of dummyAtom in colvar Giacomo Fiorin (Wed Oct 14 2009 - 19:19:31 CDT)
    - Re: center of mass of dummyAtom in colvar Giacomo Fiorin (Wed Oct 28 2009 - 13:04:41 CDT)
Unusual bond between residues: 0 (none) and 1 (protein) Song, Hyundeok (songhk) (Wed Oct 14 2009 - 11:33:15 CDT)
- RE: Unusual bond between residues: 0 (none) and 1 (protein) Song, Hyundeok (songhk) (Fri Oct 16 2009 - 22:23:29 CDT)
How to fix relative position of a group Yang (Tue Oct 13 2009 - 15:40:53 CDT)
- Re: How to fix relative position of a group JC Gumbart (Tue Oct 13 2009 - 19:27:40 CDT)
  - Re: PRESSURE, GPRESSURE, PRESSAVG, and GPRESSAVG Sebastian Stolzenberg (Wed Nov 04 2009 - 18:10:32 CST)
size of integration step Jorgen Simonsen (Tue Oct 13 2009 - 10:44:47 CDT)
- Re: size of integration step Axel Kohlmeyer (Tue Oct 13 2009 - 11:24:57 CDT)
Incorrect Atom Count in binary file Yogesh Aher (Tue Oct 13 2009 - 03:42:44 CDT)
- Re: Incorrect Atom Count in binary file namd_chcwaaa_at_yahoo.com.cn (Tue Oct 13 2009 - 06:30:06 CDT)
Generation of average trajectory mon_sharma_at_research.iiit.ac.in (Mon Oct 12 2009 - 02:26:02 CDT)
- Re: Generation of average trajectory Nicholas M Glykos (Mon Oct 12 2009 - 05:06:26 CDT)
  - Re: Generation of average trajectory Monika Sharma (Mon Oct 12 2009 - 09:24:16 CDT)
  - Re: Generation of average trajectory Roman Petrenko (Mon Oct 12 2009 - 21:02:03 CDT)
restraining the COM of a group of atoms BIN ZHANG (Fri Oct 09 2009 - 19:19:56 CDT)
- Re: restraining the COM of a group of atoms Joshua Adelman (Fri Oct 09 2009 - 19:43:04 CDT)
  - Re: restraining the COM of a group of atoms Giacomo Fiorin (Sat Oct 10 2009 - 01:21:25 CDT)
    - Re: restraining the COM of a group of atoms BIN ZHANG (Sun Oct 11 2009 - 12:53:10 CDT)
- Re: restraining the COM of a group of atoms Jerome Henin (Sat Oct 10 2009 - 15:03:52 CDT)
Lennard-Jones potential in CHARMM Lixia Jin Day (Thu Oct 08 2009 - 16:19:16 CDT)
- Re: Lennard-Jones potential in CHARMM Roman Petrenko (Fri Oct 09 2009 - 17:13:55 CDT)
nonbonded potential BIN ZHANG (Thu Oct 08 2009 - 00:19:30 CDT)
- Re: nonbonded potential Gianluca Interlandi (Thu Oct 08 2009 - 16:24:44 CDT)
  - Re: nonbonded potential BIN ZHANG (Thu Oct 08 2009 - 16:07:05 CDT)
  - mgridforce Karim Elsawy (Fri Oct 09 2009 - 09:07:32 CDT)
about restart namd_chcwaaa_at_yahoo.com.cn (Thu Oct 08 2009 - 06:46:07 CDT)
NAMD CUDA release steve.kaminski_at_mail.tu-berlin.de (Wed Oct 07 2009 - 16:01:12 CDT)
followup question on error calculation in ABF Giovanni Bellesia (Wed Oct 07 2009 - 13:50:55 CDT)
- Re: followup question on error calculation in ABF Ramya Gamini (Wed Oct 07 2009 - 15:26:15 CDT)
  - Re: followup question on error calculation in ABF Giovanni Bellesia (Wed Oct 07 2009 - 15:35:39 CDT)
    - Re: followup question on error calculation in ABF Ramya Gamini (Wed Oct 07 2009 - 16:41:57 CDT)
    - Re: followup question on error calculation in ABF Jerome Henin (Thu Oct 08 2009 - 04:04:51 CDT)
Tcl force Chaloin Laurent (Wed Oct 07 2009 - 05:22:01 CDT)
How to put a COM restraint on a membrane protein? A D (Tue Oct 06 2009 - 18:03:25 CDT)
constraint energy contributions Michael Thomas (Tue Oct 06 2009 - 06:33:25 CDT)
PCA Calculation Anirban Ghosh (Tue Oct 06 2009 - 00:13:08 CDT)
- Re: PCA Calculation Nicholas M Glykos (Tue Oct 06 2009 - 03:47:05 CDT)
  - Re: PCA Calculation Joshua Adelman (Tue Oct 06 2009 - 06:47:09 CDT)
R.E.D.-III.3 tools release - q4md-forcefieldtools.org FyD (Sun Oct 04 2009 - 09:37:06 CDT)
running namd in parallel Jorgen Simonsen (Sat Oct 03 2009 - 16:18:57 CDT)
- Re: running namd in parallel itvasile_at_nipne.ro (Sun Oct 04 2009 - 03:34:35 CDT)
- Re: running namd in parallel Axel Kohlmeyer (Sun Oct 04 2009 - 05:23:58 CDT)
CMAP w/ D-amino acid Ziemys, Arturas (Fri Oct 02 2009 - 10:51:24 CDT)
Changing the atomtype of a particle on the fly BIN ZHANG (Fri Oct 02 2009 - 01:15:07 CDT)
- error termination Sridhar Vaddadi (Fri Oct 02 2009 - 11:08:02 CDT)
- Minimisation Protocol Philip Peartree (Fri Oct 02 2009 - 11:36:49 CDT)
  - Re: Minimisation Protocol Axel Kohlmeyer (Fri Oct 02 2009 - 12:24:56 CDT)
- Re: Changing the atomtype of a particle on the fly Axel Kohlmeyer (Fri Oct 02 2009 - 13:09:12 CDT)
  - Re: Changing the atomtype of a particle on the fly Axel Kohlmeyer (Fri Oct 02 2009 - 13:30:57 CDT)
questions regarding new single node box for NAMD: re components, CUDA, Fermi Biff Forbush (Thu Oct 01 2009 - 17:27:06 CDT)
- RE: questions regarding new single node box for NAMD: re components, CUDA, Fermi Richard Owczarzy (Fri Oct 02 2009 - 10:42:12 CDT)
  - RE: questions regarding new single node box for NAMD: re components, CUDA, Fermi Axel Kohlmeyer (Fri Oct 02 2009 - 12:57:39 CDT)
- Re: questions regarding new single node box for NAMD: re components, CUDA, Fermi Axel Kohlmeyer (Fri Oct 02 2009 - 12:51:26 CDT)
  - Re: questions regarding new single node box for NAMD: re components, CUDA, Fermi Biff Forbush (Sun Oct 04 2009 - 20:37:43 CDT)
Loop Andres Morales N (Thu Oct 01 2009 - 07:59:27 CDT)
- FW: Loop Andres Morales N (Thu Oct 01 2009 - 09:05:35 CDT)
- Re: Loop Axel Kohlmeyer (Thu Oct 01 2009 - 16:56:45 CDT)
heating a system Bernardo Sosa Padilla Araujo (Thu Oct 01 2009 - 11:51:10 CDT)
ABF + LES Ziemys, Arturas (Thu Oct 01 2009 - 11:45:38 CDT)
- Re: ABF + LES Jerome Henin (Thu Oct 01 2009 - 12:19:48 CDT)
namd2.7b1, tip4p, and dummies Edward Lyman (Wed Sep 30 2009 - 13:56:47 CDT)
- Re: namd2.7b1, tip4p, and dummies Peter Freddolino (Wed Sep 30 2009 - 21:43:54 CDT)
Re: vmd-l: namd2.7b1, tip4p, and dummies Joshua D. Moore (Wed Sep 30 2009 - 05:24:34 CDT)
NAMD 2.7b1 ABF + free energy windows Reichert, David (Tue Sep 29 2009 - 15:33:48 CDT)
- Re: NAMD 2.7b1 ABF + free energy windows Giovanni Bellesia (Tue Sep 29 2009 - 16:57:15 CDT)
- Re: NAMD 2.7b1 ABF + free energy windows Giovanni Bellesia (Tue Sep 29 2009 - 17:24:11 CDT)
  - Re: NAMD 2.7b1 ABF + free energy windows Jerome Henin (Wed Sep 30 2009 - 04:44:58 CDT)
- NAMD on Ranger performance Gianluca Interlandi (Tue Sep 29 2009 - 17:51:12 CDT)
g(r) GUI Plugin problem Branko (Tue Sep 29 2009 - 05:32:03 CDT)
- Re: g(r) GUI Plugin problem Axel Kohlmeyer (Tue Sep 29 2009 - 14:02:16 CDT)
a timing question; 206,000atoms > 512cores not good Thomas C. Bishop (Mon Sep 28 2009 - 12:17:07 CDT)
Why is the temperature set different in the membrane proteins tutorial? FengXian Zheng (Sat Sep 26 2009 - 19:58:28 CDT)
NAMD2.7b1 performance Myunggi Yi (Fri Sep 25 2009 - 08:54:33 CDT)
- Re: NAMD2.7b1 performance Axel Kohlmeyer (Fri Sep 25 2009 - 09:45:53 CDT)
- Re: NAMD2.7b1 performance Nicholas M Glykos (Fri Sep 25 2009 - 11:09:40 CDT)
- Re: NAMD2.7b1 performance Gianluca Interlandi (Fri Sep 25 2009 - 11:53:05 CDT)
  - Re: NAMD2.7b1 performance Nicholas M Glykos (Fri Sep 25 2009 - 16:53:07 CDT)
    - Re: NAMD2.7b1 performance Axel Kohlmeyer (Fri Sep 25 2009 - 18:07:14 CDT)
Namd not detecting my CUDA enabled GPU nicolabrisotto (Thu Sep 24 2009 - 11:07:35 CDT)
where can I find the file: cornell.rtf (in bionano tutorial) Jian Liu (Thu Sep 24 2009 - 02:03:38 CDT)
How the seed influences the molecular dynamics simulations? Agostino (Wed Sep 23 2009 - 04:15:26 CDT)
extracting info from output files Rajiv Abhyankar (Tue Sep 22 2009 - 13:26:08 CDT)
- Re: extracting info from output files Axel Kohlmeyer (Tue Sep 22 2009 - 14:03:12 CDT)
- Re: extracting info from output files Giacomo Fiorin (Tue Sep 22 2009 - 15:12:05 CDT)
- Re: extracting info from output files Rajiv Abhyankar (Tue Sep 22 2009 - 17:56:19 CDT)
- RE: extracting info from output files Zumot, Elia Nabil (Tue Sep 22 2009 - 16:22:40 CDT)
Precision of Coordinate data Rick Calloway (Tue Sep 22 2009 - 12:08:34 CDT)
- Re: Precision of Coordinate data Axel Kohlmeyer (Tue Sep 22 2009 - 13:22:47 CDT)
- help requested Sridhar Vaddadi (Wed Sep 23 2009 - 11:23:36 CDT)
  - topology files Sridhar Vaddadi (Wed Sep 23 2009 - 13:59:02 CDT)
Do top_all27_prot_na.inp and cornell.prm share the same naming rules of atom types? ºÎØ¹»Ô (Tue Sep 22 2009 - 02:51:56 CDT)
GPU Selection in NAMD CUDA Ron Stubbs (Mon Sep 21 2009 - 14:56:42 CDT)
- Re: GPU Selection in NAMD CUDA Axel Kohlmeyer (Tue Sep 22 2009 - 04:39:59 CDT)
adding specific forces between atoms Michael Zimmermann (Mon Sep 21 2009 - 15:44:48 CDT)
Kemp elimination substrate charmm parameters Bernardo Sosa Padilla Araujo (Mon Sep 21 2009 - 15:41:01 CDT)
Regarding Lipid Order Parameter Calculation Jagan Mohan (Mon Sep 21 2009 - 00:54:18 CDT)
ABF calculation - normalization of the PMF Giovanni Bellesia (Sat Sep 19 2009 - 16:59:46 CDT)
- Re: ABF calculation - normalization of the PMF Jerome Henin (Sun Sep 27 2009 - 16:36:23 CDT)
  - Re: ABF calculation - normalization of the PMF Giovanni Bellesia (Tue Sep 29 2009 - 10:40:01 CDT)
    - Re: ABF calculation - normalization of the PMF Jerome Henin (Wed Sep 30 2009 - 04:42:32 CDT)
    - periodic boundary conditions Sridhar Vaddadi (Wed Sep 30 2009 - 14:08:31 CDT)
Replay to Parametrizing a novel residue] Branko (Fri Sep 18 2009 - 13:58:11 CDT)
- Re: Replay to Parametrizing a novel residue] DimitryASuplatov (Fri Sep 18 2009 - 15:19:33 CDT)
Parametrizing a novel residue Q=C1=D2=D8=D1_=FB=C1=CC=C1=C5=D7=C1?= (Fri Sep 18 2009 - 10:25:18 CDT)
- FEP to replace a PMF calculation? Sebastian Stolzenberg (Fri Sep 18 2009 - 18:26:42 CDT)
  - Paratool: where is "tip3.xbgf"? Sebastian Stolzenberg (Fri Sep 25 2009 - 10:54:38 CDT)
    - Re: Paratool: where is "tip3.xbgf"? saam (Fri Sep 25 2009 - 11:53:26 CDT)
  - Re: FEP to replace a PMF calculation? Jerome Henin (Sun Sep 27 2009 - 16:27:52 CDT)
About NAN error cong chen (Fri Sep 18 2009 - 01:35:51 CDT)
How to access velocity coordinates from within TclForces script Patrick Hogan (Thu Sep 17 2009 - 14:43:21 CDT)
- Re: How to access velocity coordinates from within TclForces script Giacomo Fiorin (Thu Sep 17 2009 - 16:37:03 CDT)
how to get psf files of DNA but not RNA with psfgen? ºÎØ¹»Ô (Thu Sep 17 2009 - 06:25:02 CDT)
- Re: how to get psf files of DNA but not RNA with psfgen? Xueqing Zou (Thu Sep 17 2009 - 09:52:19 CDT)
can't load forces in tclforces James Servantie (Thu Sep 17 2009 - 05:54:21 CDT)
AlF4 Laurent Chaloin (Thu Sep 17 2009 - 04:54:14 CDT)
scripts for starting namd with condor John Wise (Wed Sep 16 2009 - 17:06:26 CDT)
FAD topology and parameters of FAD jose correa (Wed Sep 16 2009 - 11:21:58 CDT)
how to use volmap analysing a series of dcd. liupeng012_at_mail.nankai.edu.cn (Wed Sep 16 2009 - 08:39:50 CDT)
Re: NVT with truncated octahedron or with sphere? Werner Crous (Wed Sep 16 2009 - 06:04:31 CDT)
FATAL ERROR: Couldn't open DCD file ubq_wb_eq.dcd: No such file or directory Bernardo Sosa Padilla Araujo (Tue Sep 15 2009 - 18:26:25 CDT)
NVT with truncated octahedron or with sphere? Werner Crous (Tue Sep 15 2009 - 03:03:06 CDT)
Temperature rescaling vs. reassignment Luis Agullo (LAB) (Tue Sep 15 2009 - 09:26:48 CDT)
- Re: Temperature rescaling vs. reassignment Axel Kohlmeyer (Tue Sep 15 2009 - 10:15:23 CDT)
Visit my Netlog profile Moumita Maiti (Tue Sep 15 2009 - 00:07:31 CDT)
question about FEP soft-core yun luo (Mon Sep 14 2009 - 15:03:16 CDT)
- Re: question about FEP soft-core Floris Buelens (Tue Sep 15 2009 - 08:56:43 CDT)
Re: CUDA-accelerated NAMD does not support NBFIX parameters [RESOLVED] Héctor Urbina (Mon Sep 14 2009 - 07:24:35 CDT)
- Re: CUDA-accelerated NAMD does not support NBFIX parameters [RESOLVED] Axel Kohlmeyer (Mon Sep 14 2009 - 15:57:12 CDT)
Regarding ABF Simulation Jagan Mohan (Mon Sep 14 2009 - 04:48:19 CDT)
- Re: Regarding ABF Simulation Branko (Mon Sep 14 2009 - 15:34:17 CDT)
  - Re: Regarding ABF Simulation Jagan Mohan (Mon Sep 14 2009 - 23:58:03 CDT)
- Re: Regarding ABF Simulation Jerome Henin (Mon Sep 14 2009 - 17:57:28 CDT)
  - Re: Regarding ABF Simulation Jagan Mohan (Tue Sep 15 2009 - 00:10:48 CDT)
CUDA-accelerated NAMD does not support NBFIX parameters Héctor Urbina (Sun Sep 13 2009 - 13:47:33 CDT)
- Re: CUDA-accelerated NAMD does not support NBFIX parameters Axel Kohlmeyer (Sun Sep 13 2009 - 14:49:47 CDT)
Saving a subset of atoms Austin B. Yongye (Fri Sep 11 2009 - 12:32:44 CDT)
Regarding NAMD CPU usage Amr Zeinalabideen Majul (Fri Sep 11 2009 - 08:22:08 CDT)
- Re: Regarding NAMD CPU usage Giacomo Fiorin (Fri Sep 11 2009 - 11:11:12 CDT)
- Re: Regarding NAMD CPU usage Robert Brunner (Fri Sep 11 2009 - 11:34:12 CDT)
atomic structure of some surfaces Roman Petrenko (Thu Sep 10 2009 - 19:57:14 CDT)
- Re: atomic structure of some surfaces Eduardo Cruz-Chu (Sat Sep 12 2009 - 15:31:12 CDT)
  - Re: atomic structure of some surfaces Roman Petrenko (Fri Sep 18 2009 - 15:31:18 CDT)
FAD-parameters jose correa (Thu Sep 10 2009 - 13:50:33 CDT)
[off topic] The mailing list's mailer ... Nicholas M Glykos (Wed Sep 09 2009 - 12:50:58 CDT)
Implicit membrane models Austin B. Yongye (Wed Sep 09 2009 - 09:03:53 CDT)
- fixing parts of an equilibrated protein's environment Sebastian Stolzenberg (Wed Sep 09 2009 - 10:26:17 CDT)
Constraint failure in RATTLE algorithm - shouldn't a rerun fail at the same step? Bjoern Olausson (Tue Sep 08 2009 - 03:12:04 CDT)
- Re: Constraint failure in RATTLE algorithm - shouldn't a rerun fail at the same step? Axel Kohlmeyer (Wed Sep 09 2009 - 09:51:42 CDT)
  - Re: Constraint failure in RATTLE algorithm - shouldn't a rerun fail at the same step? Bjoern Olausson (Thu Sep 10 2009 - 05:38:18 CDT)
Constraint failure in RATTLE algorithm - shouldn't a rerun fail at the same step? Bjoern Olausson (Tue Sep 08 2009 - 03:13:02 CDT)
- Re: Constraint failure in RATTLE algorithm - shouldn't a rerun fail at the same step? Elia Zumot (Wed Sep 09 2009 - 10:40:29 CDT)
  - Re: Constraint failure in RATTLE algorithm - shouldn't a rerun fail at the same step? Bjoern Olausson (Thu Sep 10 2009 - 05:26:00 CDT)
- Re: Constraint failure in RATTLE algorithm - shouldn't a rerun fail at the same step? Nicholas M Glykos (Wed Sep 09 2009 - 10:46:51 CDT)
(no subject) Jim Phillips (Tue Sep 08 2009 - 17:21:54 CDT)
PMF: free energy calcs in "grow" phase? Sebastian Stolzenberg (Fri Sep 04 2009 - 15:57:00 CDT)
CAN'T FIND DIHEDRAL PARAMETERS FOR CN8B CN7 ON5 HN5 Sujata Sovani (Fri Sep 04 2009 - 15:35:56 CDT)
Re: vmd-l: rmsd matrix Cesar Millan (Thu Sep 03 2009 - 11:23:20 CDT)
- Re: Re: vmd-l: rmsd matrix Mert Gür (Fri Sep 04 2009 - 09:09:07 CDT)
- Re: Re: vmd-l: rmsd matrix Luis Gracia (Thu Sep 03 2009 - 16:47:36 CDT)
Membrane simulations Austin B. Yongye (Tue Sep 01 2009 - 10:24:36 CDT)
- Re: Membrane simulations Elia Zumot (Tue Sep 01 2009 - 12:54:36 CDT)
CHARMM to NAMD Yang MIngjun (Tue Sep 01 2009 - 09:03:13 CDT)
- Re: CHARMM to NAMD Yang MIngjun (Thu Sep 03 2009 - 01:37:21 CDT)
  - Re: CHARMM to NAMD Dimitar V Pachov (Thu Sep 03 2009 - 10:54:17 CDT)
Re-posting - Methylated Histidine topology file Sujata Sovani (Mon Aug 31 2009 - 12:47:16 CDT)
Methylated Histidine topology file Sujata Sovani (Mon Aug 31 2009 - 12:38:03 CDT)
Periodic boundary conditions in membrane simulation jouko_at_uchicago.edu (Mon Aug 31 2009 - 11:56:22 CDT)
- Re: Periodic boundary conditions in membrane simulation Joshua Adelman (Mon Aug 31 2009 - 12:24:14 CDT)
- Re: Periodic boundary conditions in membrane simulation Axel Kohlmeyer (Mon Aug 31 2009 - 13:01:26 CDT)
  - Re: Periodic boundary conditions in membrane simulation jouko_at_uchicago.edu (Mon Aug 31 2009 - 16:02:43 CDT)
Doubts and problem in ABF simulations Paulo Cesar Telles de Souza (Mon Aug 31 2009 - 11:00:57 CDT)
- Re: Doubts and problem in ABF simulations Jerome Henin (Mon Aug 31 2009 - 17:18:52 CDT)
  - Re: Doubts and problem in ABF simulations Paulo Cesar Telles de Souza (Wed Sep 02 2009 - 10:55:19 CDT)
    - Re: Doubts and problem in ABF simulations Giacomo Fiorin (Wed Sep 02 2009 - 13:21:09 CDT)
    - Re: Doubts and problem in ABF simulations Jerome Henin (Wed Sep 02 2009 - 15:34:54 CDT)
  - Re: Doubts and problem in ABF simulations Paulo Cesar Telles de Souza (Wed Sep 02 2009 - 13:11:07 CDT)
PMF via constrained dynamics in NAMD satya work (Mon Aug 31 2009 - 09:01:43 CDT)
for your suggestions on Pressure Control of transmembrane protein (GPCR) pxq ÅÓÑ©ÇÛ (Sun Aug 30 2009 - 22:18:47 CDT)
Cuda benchmarks namd2.7b1 - effects of configuration parameters and hardware. Mike Kuiper (Sun Aug 30 2009 - 03:54:57 CDT)
- Re: Cuda benchmarks namd2.7b1 - effects of configuration parameters and hardware. Gianluca Interlandi (Sun Aug 30 2009 - 14:11:25 CDT)
  - Re: Cuda benchmarks namd2.7b1 - effects of configuration parameters and hardware. Axel Kohlmeyer (Sun Aug 30 2009 - 15:33:08 CDT)
    - Re: Cuda benchmarks namd2.7b1 - effects of configuration parameters and hardware. Gianluca Interlandi (Sun Aug 30 2009 - 18:41:41 CDT)
    - Re: Cuda benchmarks namd2.7b1 - effects of configuration parameters and hardware. Gianluca Interlandi (Sun Aug 30 2009 - 23:55:57 CDT)
- Re: Cuda benchmarks namd2.7b1 - effects of configuration parameters and hardware. Roman Petrenko (Sun Aug 30 2009 - 16:06:26 CDT)
Aslos End'tasa (Fri Aug 28 2009 - 11:55:17 CDT)
hole on the surface of the waterbox Mert Gür (Fri Aug 28 2009 - 05:08:09 CDT)
- Re: hole on the surface of the waterbox Ana Vila Verde (Fri Aug 28 2009 - 05:54:06 CDT)
  - Re: hole on the surface of the waterbox Mert Gür (Fri Aug 28 2009 - 06:12:25 CDT)
- Re: hole on the surface of the waterbox Nicholas M Glykos (Fri Aug 28 2009 - 07:38:00 CDT)
  - Re: hole on the surface of the waterbox Mert Gür (Fri Aug 28 2009 - 17:14:00 CDT)
ERROR: Constraint failure in RATTLE algorithm for atom 9080! gurunath katagi (Fri Aug 28 2009 - 00:16:01 CDT)
Tesla Utilization -- NAMD 2.7b1 Ron Stubbs (Thu Aug 27 2009 - 13:06:19 CDT)
- Re: Tesla Utilization -- NAMD 2.7b1 Gianluca Interlandi (Thu Aug 27 2009 - 19:03:54 CDT)
  - Re: Tesla Utilization -- NAMD 2.7b1 Axel Kohlmeyer (Fri Aug 28 2009 - 10:20:21 CDT)
    - Re: Tesla Utilization -- NAMD 2.7b1 Gianluca Interlandi (Fri Aug 28 2009 - 11:13:13 CDT)
    - Re: Tesla Utilization -- NAMD 2.7b1 Roman Petrenko (Fri Aug 28 2009 - 11:49:18 CDT)
ABF 'Xi' log output producing strange results Hugh Martin (Thu Aug 27 2009 - 10:30:22 CDT)
- Re: ABF 'Xi' log output producing strange results Eric H. Lee (Thu Aug 27 2009 - 10:48:50 CDT)
- Re: ABF 'Xi' log output producing strange results Jerome Henin (Thu Aug 27 2009 - 16:39:35 CDT)
  - Re: ABF 'Xi' log output producing strange results Hugh Martin (Thu Aug 27 2009 - 23:41:18 CDT)
Running a simulation with a protein and a sugar pellegrini (Thu Aug 27 2009 - 04:06:48 CDT)
how to set up force parameters of a novel residue? He Yuhui (Thu Aug 27 2009 - 02:37:12 CDT)
- Re: how to set up force parameters of a novel residue? Axel Kohlmeyer (Thu Aug 27 2009 - 16:14:17 CDT)
Postdoc position in biomolecular simulation Ivaylo Ivanov (Wed Aug 26 2009 - 16:40:02 CDT)
question on forces / theory Ziemys, Arturas (Tue Aug 25 2009 - 22:07:07 CDT)
- Re: question on forces / theory Axel Kohlmeyer (Wed Aug 26 2009 - 06:04:17 CDT)
  - Re: question on forces / theory Mert Gür (Wed Aug 26 2009 - 13:21:18 CDT)
    - Re: question on forces / theory Mert Gür (Wed Aug 26 2009 - 13:23:23 CDT)
fixed atoms pdb Mark M Huntress (Mon Aug 24 2009 - 17:13:20 CDT)
multi-cluster configuration Piotr Kopta (Mon Aug 24 2009 - 16:18:42 CDT)
- Re: multi-cluster configuration Axel Kohlmeyer (Mon Aug 24 2009 - 17:12:42 CDT)
Parameters for esters Jorgen Simonsen (Mon Aug 24 2009 - 11:55:08 CDT)
- Re: Parameters for esters Jerome Henin (Tue Aug 25 2009 - 14:36:58 CDT)
About DPD «J ¦¼¯Â (Sun Aug 23 2009 - 09:52:59 CDT)
SMD on membrane protein. Yoav Beck (Sun Aug 23 2009 - 09:04:55 CDT)
- Fep performance matteo.rotter (Mon Aug 24 2009 - 10:51:27 CDT)
  - Re: Fep performance Floris Buelens (Wed Aug 26 2009 - 01:26:49 CDT)
    - Re: Fep performance matteo.rotter (Thu Sep 17 2009 - 08:43:00 CDT)
Alignment of velocity dcd file Mert Gür (Sat Aug 22 2009 - 15:03:10 CDT)
- Re: Alignment of velocity dcd file Axel Kohlmeyer (Sat Aug 22 2009 - 15:49:19 CDT)
FATAL ERROR: ABNORMAL EOF FOUND - buffer=*0 0 0* FengXian Zheng (Fri Aug 21 2009 - 10:14:38 CDT)
Questions from new user «J ¦¼¯Â (Thu Aug 20 2009 - 21:57:05 CDT)
Force extension from SMD log file snoze pa (Thu Aug 20 2009 - 17:25:20 CDT)
Re: ABF Colvars Configuration File Neelanjana Sengupta (Thu Aug 20 2009 - 09:21:41 CDT)
- Re: ABF Colvars Configuration File Giacomo Fiorin (Thu Aug 20 2009 - 10:59:35 CDT)
unbinding SMD skill question Sangbae Lee (Wed Aug 19 2009 - 15:24:59 CDT)
protocol to start MD jose correa (Wed Aug 19 2009 - 09:27:29 CDT)
- Re: protocol to start MD Vlad Cojocaru (Wed Aug 19 2009 - 10:22:37 CDT)
- Re: protocol to start MD Rabab Toubar (Wed Aug 19 2009 - 11:04:12 CDT)
glibc runtime errors on BlueGeneP occur only if running the cvs code (18.08) and not namd 2.6 Vlad Cojocaru (Wed Aug 19 2009 - 05:38:47 CDT)
- Re: glibc runtime errors on BlueGeneP occur only if running the cvs code (18.08) and not namd 2.6 Vlad Cojocaru (Wed Aug 19 2009 - 06:02:26 CDT)
About the namd tutorial err Aurum Bai (Tue Aug 18 2009 - 23:55:01 CDT)
how to save pdb file after "moveby" command in VMD? He Yuhui (Tue Aug 18 2009 - 21:33:42 CDT)
- Re: how to save pdb file after "moveby" command in VMD? Joshua Adelman (Tue Aug 18 2009 - 22:14:18 CDT)
glibc detected : corrupted double-linked list: 0xa4657ad8 Vlad Cojocaru (Tue Aug 18 2009 - 05:15:55 CDT)
- Re: glibc detected : corrupted double-linked list: 0xa4657ad8 Vlad Cojocaru (Tue Aug 18 2009 - 05:44:58 CDT)
  - Re: glibc detected : corrupted double-linked list: 0xa4657ad8 George Madalin Giambasu (Tue Aug 18 2009 - 12:05:22 CDT)
Berendsen, explicit water Sandra Rennebaum, Biochemisches Inst. (Tue Aug 18 2009 - 04:54:07 CDT)
restating simuation and periodic cell conditions gurunath katagi (Tue Aug 18 2009 - 03:23:20 CDT)
- Re: restating simuation and periodic cell conditions Chris Harrison (Tue Aug 18 2009 - 07:08:07 CDT)
what is the charge of sulfur on thiol? He Yuhui (Mon Aug 17 2009 - 01:38:01 CDT)
- Re: what is the charge of sulfur on thiol? Branko (Mon Aug 17 2009 - 03:41:18 CDT)
Colvars Configuration File Neelanjana Sengupta (Sat Aug 15 2009 - 02:16:19 CDT)
- Re: Colvars Configuration File Giacomo Fiorin (Sat Aug 15 2009 - 08:56:38 CDT)
  - Re: Colvars Configuration File Neelanjana Sengupta (Sat Aug 15 2009 - 10:12:55 CDT)
  - Re: Colvars Configuration File Neelanjana Sengupta (Sun Aug 16 2009 - 23:52:30 CDT)
(is there) a dependence of dynamics on WRAPPING satya work (Sat Aug 15 2009 - 01:33:26 CDT)
- Re: (is there) a dependence of dynamics on WRAPPING Giacomo Fiorin (Sat Aug 15 2009 - 08:59:46 CDT)
Restarting ABF Branko (Thu Aug 13 2009 - 11:05:18 CDT)
- Re: Restarting ABF Chris Chipot (Thu Aug 13 2009 - 11:32:13 CDT)
- Re: Restarting ABF Jerome Henin (Thu Aug 13 2009 - 11:39:00 CDT)
  - Re: Restarting ABF Branko (Thu Aug 13 2009 - 13:56:59 CDT)
    - Re: Restarting ABF Giacomo Fiorin (Thu Aug 13 2009 - 16:00:20 CDT)
Re: About SMD Roman Petrenko (Thu Aug 13 2009 - 10:33:34 CDT)
FATAL ERROR: Tried to find atom type on node other than node 0 Yoav Beck (Thu Aug 13 2009 - 09:21:38 CDT)
- Re: FATAL ERROR: Tried to find atom type on node other than node 0 yzliu (Sat Aug 15 2009 - 11:06:10 CDT)
  - Re: FATAL ERROR: Tried to find atom type on node other than node 0 Yoav Beck (Mon Aug 17 2009 - 05:04:48 CDT)
Bug advisory: ABF integration tool Jerome Henin (Wed Aug 12 2009 - 17:49:24 CDT)
Kanamycin topology DimitryASuplatov (Wed Aug 12 2009 - 12:16:33 CDT)
- Re: Kanamycin topology Chris Harrison (Mon Aug 17 2009 - 09:53:25 CDT)
symmetric behavior Narender Singh Maan (Wed Aug 12 2009 - 09:16:39 CDT)
- Re: symmetric behavior Joshua Adelman (Wed Aug 12 2009 - 09:49:10 CDT)
  - Re: symmetric behavior Narender Singh Maan (Thu Aug 13 2009 - 14:17:43 CDT)
About "Parameterizing a Novel Residue" tutorial problem Aurum Bai (Wed Aug 12 2009 - 00:18:09 CDT)
About SMD Yang MIngjun (Tue Aug 11 2009 - 22:11:51 CDT)
solvate plugin with solvent other than water dalton banks (Tue Aug 11 2009 - 15:02:13 CDT)
- Re: solvate plugin with solvent other than water Peter Freddolino (Tue Aug 11 2009 - 21:24:41 CDT)
bonding in periodic boundary conditions d b (Tue Aug 11 2009 - 15:05:08 CDT)
Berendsen- two baths Sandra Rennebaum, Biochemisches Inst. (Tue Aug 11 2009 - 01:55:10 CDT)
SMD with force applied to two seperate molecules Elia Zumot (Tue Aug 11 2009 - 10:09:17 CDT)
- Re: SMD with force applied to two seperate molecules Roman Petrenko (Thu Aug 13 2009 - 10:24:02 CDT)
  - Re: SMD with force applied to two seperate molecules Roman Petrenko (Thu Aug 13 2009 - 10:48:44 CDT)
  - Re: SMD with force applied to two seperate molecules Elia Zumot (Thu Aug 13 2009 - 11:07:06 CDT)
how to simulate a protein-ligand complex ? ydhuang2727 (Tue Aug 11 2009 - 08:29:25 CDT)
namd-SMD constant Force missing smdatom location snoze pa (Mon Aug 10 2009 - 14:40:51 CDT)
- Re: namd-SMD constant Force missing smdatom location snoze pa (Mon Aug 10 2009 - 17:48:38 CDT)
  - Re: namd-SMD constant Force missing smdatom location Ramya Gamini (Mon Aug 10 2009 - 18:52:06 CDT)
  - Re: namd-SMD constant Force missing smdatom location snoze pa (Tue Aug 11 2009 - 08:53:46 CDT)
    - Re: namd-SMD constant Force missing smdatom location snoze pa (Tue Aug 11 2009 - 12:06:57 CDT)
    - Re: namd-SMD constant Force missing smdatom location snoze pa (Wed Aug 12 2009 - 12:37:30 CDT)
Steered Molecular Dynamics for more than one atom gaurav bhatti (Mon Aug 10 2009 - 13:55:10 CDT)
- Re: Steered Molecular Dynamics for more than one atom David Tanner (Mon Aug 10 2009 - 15:31:09 CDT)
- Re: Steered Molecular Dynamics for more than one atom Marcos Sotomayor (Mon Aug 10 2009 - 21:11:11 CDT)
Clarification regarding some finer details in ABF simulations Hugh Martin (Mon Aug 10 2009 - 12:33:47 CDT)
- Re: Clarification regarding some finer details in ABF simulations Jerome Henin (Sat Aug 15 2009 - 15:55:35 CDT)
  - Re: Clarification regarding some finer details in ABF simulations Hugh Martin (Tue Aug 18 2009 - 10:01:08 CDT)
    - Re: Clarification regarding some finer details in ABF simulations Jerome Henin (Tue Aug 18 2009 - 16:01:56 CDT)
combining segments d b (Mon Aug 10 2009 - 09:06:51 CDT)
- Re: combining segments Robert Brunner (Mon Aug 10 2009 - 11:32:26 CDT)
increase the temperature step by step after minimization gurunath katagi (Mon Aug 10 2009 - 00:27:03 CDT)
- Re: increase the temperature step by step after minimization Chris Harrison (Mon Aug 10 2009 - 05:01:08 CDT)
how to write a command to close vmd in shell script? He Yuhui (Sun Aug 09 2009 - 22:21:34 CDT)
- Re: how to write a command to close vmd in shell script? Schreiner Eduard (Sun Aug 09 2009 - 22:39:36 CDT)
On naming rules in force-field parameter files? He Yuhui (Sun Aug 09 2009 - 20:12:21 CDT)
- Re: On naming rules in force-field parameter files? Schreiner Eduard (Sun Aug 09 2009 - 20:27:17 CDT)
- Re: On naming rules in force-field parameter files? Ramya Gamini (Mon Aug 10 2009 - 09:07:12 CDT)
charm++ how to handle SMP/Multicore Bjoern Olausson (Sun Aug 09 2009 - 17:01:48 CDT)
- Re: charm++ how to handle SMP/Multicore Bjoern Olausson (Thu Aug 20 2009 - 11:41:16 CDT)
ABF question (free energy partition) Lei Shi (Sun Aug 09 2009 - 11:36:10 CDT)
- Re: ABF question (free energy partition) Chris Chipot (Sun Aug 09 2009 - 12:32:54 CDT)
namd27: tclforces activate TI calculation by default George Madalin Giambasu (Sat Aug 08 2009 - 16:12:34 CDT)
- RE: namd27: tclforces activate TI calculation by default Cojocaru,Vlad (Sat Aug 08 2009 - 17:53:16 CDT)
  - RE: namd27: tclforces activate TI calculation by default Brian J. Bennion (Mon Aug 10 2009 - 10:36:01 CDT)
    - RE: namd27: tclforces activate TI calculation by default Jim Phillips (Wed Aug 12 2009 - 16:16:04 CDT)
    - Re: namd27: tclforces activate TI calculation by default Vlad Cojocaru (Thu Aug 13 2009 - 10:16:12 CDT)
Re: Cell Data in DCD files - CHARMM compatibility Dimitar V Pachov (Fri Aug 07 2009 - 19:50:30 CDT)
- Re: Re: Cell Data in DCD files - CHARMM compatibility Joshua D. Moore (Fri Aug 07 2009 - 22:26:07 CDT)
Error with GUI NAMD Energy Elia Zumot (Fri Aug 07 2009 - 16:45:23 CDT)
- Re: Error with GUI NAMD Energy Peter Freddolino (Fri Aug 07 2009 - 19:16:53 CDT)
  - Re: Error with GUI NAMD Energy Elia Zumot (Sat Aug 08 2009 - 12:10:31 CDT)
- Re: Error with GUI NAMD Energy snoze pa (Mon Aug 10 2009 - 11:32:53 CDT)
SMD and Temperature control snoze pa (Fri Aug 07 2009 - 15:25:51 CDT)
- Re: SMD and Temperature control Marcos Sotomayor (Mon Aug 10 2009 - 20:35:24 CDT)
  - Re: SMD and Temperature control snoze pa (Tue Aug 11 2009 - 08:58:27 CDT)
NAMD performance with 10GbE interconnect Prakash Velayutham (Fri Aug 07 2009 - 15:02:55 CDT)
- Re: NAMD performance with 10GbE interconnect Axel Kohlmeyer (Tue Aug 11 2009 - 11:25:25 CDT)
  - Re: NAMD performance with 10GbE interconnect Prakash Velayutham (Tue Aug 11 2009 - 11:40:07 CDT)
NAMD FFTW question? snoze pa (Fri Aug 07 2009 - 11:17:58 CDT)
- Re: NAMD FFTW question? David Hardy (Fri Aug 07 2009 - 12:47:30 CDT)
- Re: NAMD FFTW question? Gianluca Interlandi (Fri Aug 07 2009 - 12:54:26 CDT)
- Re: NAMD FFTW question? Giacomo Fiorin (Fri Aug 07 2009 - 14:06:05 CDT)
  - Re: NAMD FFTW question? snoze pa (Fri Aug 07 2009 - 14:47:18 CDT)
What is the different between "periodic boundary ,spherical harmonic boundary and cylindrical harmonic boundary conditions"? Aurum Bai (Fri Aug 07 2009 - 11:04:50 CDT)
- Re: What is the different between "periodic boundary ,spherical harmonic boundary and cylindrical harmonic boundary conditions"? Robert Brunner (Fri Aug 07 2009 - 12:03:50 CDT)
Would my simulation setting aï¬€ect the result? About the parameter "fixedAtomsForces" wayj86 wayj86 (Fri Aug 07 2009 - 05:51:42 CDT)
NAMDenergy: does rewrite temp files at different timesteps Neelanjana Sengupta (Fri Aug 07 2009 - 00:18:14 CDT)
cutoffs in direct and indirect space used in PME? dimka (Thu Aug 06 2009 - 23:13:05 CDT)
Continuing simulation after constraint failure error? Sujata Sovani (Thu Aug 06 2009 - 11:59:28 CDT)
- Re: Continuing simulation after constraint failure error? Giacomo Fiorin (Thu Aug 06 2009 - 13:17:48 CDT)
- RE: Continuing simulation after constraint failure error? Sadhu, Shubho (NIH/NCI) [F] (Thu Aug 06 2009 - 14:23:06 CDT)
Re: Proteine-membrane simulation. Yoav Beck (Thu Aug 06 2009 - 07:46:05 CDT)
Defining Temperature for Langevin for Namd restart. Amr Zeinalabideen Majul (Wed Aug 05 2009 - 14:20:15 CDT)
- Re: Defining Temperature for Langevin for Namd restart. Roman Petrenko (Wed Aug 05 2009 - 15:13:57 CDT)
  - Re: Defining Temperature for Langevin for Namd restart. Amr Zeinalabideen Majul (Wed Aug 05 2009 - 16:20:41 CDT)
    - Re: Defining Temperature for Langevin for Namd restart. Joshua Adelman (Wed Aug 05 2009 - 16:36:23 CDT)
  - Re: Defining Temperature for Langevin for Namd restart. Gianluca Interlandi (Wed Aug 05 2009 - 17:16:33 CDT)
- Re: Defining Temperature for Langevin for Namd restart. Gianluca Interlandi (Wed Aug 05 2009 - 16:35:14 CDT)
  - Re: Defining Temperature for Langevin for Namd restart. Roman Petrenko (Thu Aug 06 2009 - 05:41:17 CDT)
Re: frozen water Oxygens Chris Harrison (Wed Aug 05 2009 - 09:01:24 CDT)
SMD output : which col represents force, second or last snoze pa (Wed Aug 05 2009 - 11:42:42 CDT)
SMD output : which col represents force, second or last snoze pa (Wed Aug 05 2009 - 11:25:35 CDT)
- Re: SMD output : which col represents force, second or last Roman Petrenko (Wed Aug 05 2009 - 12:05:16 CDT)
- RE: SMD output : which col represents force, second or last Sadhu, Shubho (NIH/NCI) [F] (Wed Aug 05 2009 - 12:19:27 CDT)
- Re: SMD output : which col represents force, second or last David Tanner (Wed Aug 05 2009 - 12:03:30 CDT)
- Re: SMD output : which col represents force, second or last Gianluca Interlandi (Wed Aug 05 2009 - 13:10:34 CDT)
  - Re: SMD output : which col represents force, second or last snoze pa (Wed Aug 05 2009 - 13:34:15 CDT)
- Re: SMD output : which col represents force, second or last Chris Harrison (Wed Aug 05 2009 - 12:27:08 CDT)
water molecules in channel protein Narender Singh Maan (Wed Aug 05 2009 - 10:57:50 CDT)
- Re: water molecules in channel protein Roman Petrenko (Wed Aug 05 2009 - 11:59:21 CDT)
How to do a complex dynamics simulation ydhuang2727 (Wed Aug 05 2009 - 03:25:10 CDT)
Simulating molecules in bulk water & VMD installation problems Vincent Su (Tue Aug 04 2009 - 14:27:38 CDT)
- Re: Simulating molecules in bulk water & VMD installation problems Chris Harrison (Wed Aug 05 2009 - 08:53:01 CDT)
SMD restrain point in NAMD snoze pa (Tue Aug 04 2009 - 11:40:05 CDT)
- Re: SMD restrain point in NAMD Gianluca Interlandi (Tue Aug 04 2009 - 13:09:26 CDT)
  - Re: SMD restrain point in NAMD snoze pa (Tue Aug 04 2009 - 14:45:39 CDT)
    - Re: SMD restrain point in NAMD Gianluca Interlandi (Tue Aug 04 2009 - 16:55:52 CDT)
frozen water Oxygens Mark M Huntress (Tue Aug 04 2009 - 11:13:12 CDT)
Proteine-membrane simulation. Yoav Beck (Tue Aug 04 2009 - 10:08:55 CDT)
Does Berendsen increase viscosity of water? Gianluca Interlandi (Tue Aug 04 2009 - 00:36:38 CDT)
- Re: Does Berendsen increase viscosity of water? Gianluca Interlandi (Wed Aug 05 2009 - 13:19:25 CDT)
A script for performing calculations divided by quanta Mikhail Suyetin (Mon Aug 03 2009 - 08:26:28 CDT)
- Re: A script for performing calculations divided by quanta Joshua Adelman (Mon Aug 03 2009 - 10:05:50 CDT)
  - Re: A script for performing calculations divided by quanta Mikhail Suyetin (Mon Aug 03 2009 - 10:30:28 CDT)
    - Re: A script for performing calculations divided by quanta Joshua Adelman (Mon Aug 03 2009 - 10:38:35 CDT)
    - Re: A script for performing calculations divided by quanta Nicholas M Glykos (Tue Aug 04 2009 - 08:15:17 CDT)
The steps in protein and membrane simulation Narender Singh Maan (Sat Aug 01 2009 - 23:23:49 CDT)
NAMD water sphere problem snoze pa (Fri Jul 31 2009 - 17:19:12 CDT)
- Re: NAMD water sphere problem Roman Petrenko (Fri Jul 31 2009 - 19:37:50 CDT)
how to use ethanol as solvent in namd for MD simulations ? Wang Yf (Fri Jul 31 2009 - 04:06:55 CDT)
- Re: how to use ethanol as solvent in namd for MD simulations ? Branko (Fri Jul 31 2009 - 04:50:17 CDT)
compilation error "could not set locale" with intel 11.0 Vlad Cojocaru (Fri Jul 31 2009 - 03:03:53 CDT)
- Re: compilation error "could not set locale" with intel 11.0 Vlad Cojocaru (Fri Jul 31 2009 - 03:35:12 CDT)
Steered Molecular Dynamics gaurav bhatti (Fri Jul 31 2009 - 00:33:50 CDT)
- Re: Steered Molecular Dynamics Mert Gür (Wed Aug 05 2009 - 06:57:17 CDT)
- Re: Steered Molecular Dynamics Chris Harrison (Wed Aug 05 2009 - 08:46:52 CDT)
How to calculate free energy for conformational change Lixia Jin Day (Thu Jul 30 2009 - 16:46:07 CDT)
- RE: How to calculate free energy for conformational change gaurav bhatti (Thu Jul 30 2009 - 23:51:05 CDT)
CUDA Linux-x86 doesn't compile Sadhu, Shubho (NIH/NCI) [F] (Thu Jul 30 2009 - 09:06:04 CDT)
how to generate DNA psf files? He Yuhui (Wed Jul 29 2009 - 21:04:27 CDT)
- Re: how to generate DNA psf files? Roman Petrenko (Fri Jul 31 2009 - 00:22:31 CDT)
  - Re: how to generate DNA psf files? Chris Harrison (Wed Aug 05 2009 - 09:10:25 CDT)
Different ensembles in the same system Eric Perim (Wed Jul 29 2009 - 14:48:39 CDT)
THERMODYNAMIC INTEGRATION ON in namd 2.7b1 compiled 24.07 when TCL forces active Vlad Cojocaru (Wed Jul 29 2009 - 05:03:27 CDT)
- Re: THERMODYNAMIC INTEGRATION ON in namd 2.7b1 compiled 24.07 when TCL forces active Vlad Cojocaru (Wed Jul 29 2009 - 05:27:00 CDT)
  - Re: Re: THERMODYNAMIC INTEGRATION ON in namd 2.7b1 compiled 24.07 when TCL forces active Chris Harrison (Wed Jul 29 2009 - 05:45:08 CDT)
Unable to generate PSF file due to an unparametrized component Sujata Sovani (Tue Jul 28 2009 - 16:33:09 CDT)
- Re: Unable to generate PSF file due to an unparametrized component Esteban Gabriel Vega Hissi (Tue Jul 28 2009 - 18:18:49 CDT)
(no subject) Sujata Sovani (Tue Jul 28 2009 - 17:02:30 CDT)
FEP implementation in NAMD 2.6 vs. 2.7b1 Dan Bolintineanu (Tue Jul 28 2009 - 16:50:37 CDT)
- Re: FEP implementation in NAMD 2.6 vs. 2.7b1 Floris Buelens (Wed Jul 29 2009 - 01:50:40 CDT)
- Re: FEP implementation in NAMD 2.6 vs. 2.7b1 Chris Harrison (Wed Jul 29 2009 - 06:11:33 CDT)
Equilibration "substraction" from obtained PMF from MD Branko (Tue Jul 28 2009 - 16:32:00 CDT)
- Re: Equilibration "substraction" from obtained PMF from MD Jerome Henin (Sat Aug 15 2009 - 16:01:01 CDT)
Using preprotonated structure with NAMD DimitryASuplatov (Tue Jul 28 2009 - 09:48:18 CDT)
- Re: Using preprotonated structure with NAMD Giacomo Fiorin (Tue Jul 28 2009 - 11:03:23 CDT)
PLUMED release 1.1.0 available Massimiliano Bonomi (Tue Jul 28 2009 - 03:12:27 CDT)
use tclForce and tclBC together? yun luo (Mon Jul 27 2009 - 20:14:45 CDT)
- Re: use tclForce and tclBC together? yun luo (Tue Jul 28 2009 - 14:00:58 CDT)
error running namd Bernardo Sosa Padilla Araujo (Mon Jul 27 2009 - 16:37:17 CDT)
- Re: error running namd Giacomo Fiorin (Mon Jul 27 2009 - 18:07:12 CDT)
- Re: error running namd Robert Brunner (Mon Jul 27 2009 - 20:44:15 CDT)
hydroxyls in phosphate group collapsing Yvonne.Westermaier_at_unige.ch (Mon Jul 27 2009 - 09:41:20 CDT)
Group forces in tclForces Benjamin Bouvier (Mon Jul 27 2009 - 06:02:12 CDT)
Re: An outlier appear on the curve of RMSD wayj86 wayj86 (Sun Jul 26 2009 - 20:42:13 CDT)
- Re: An outlier appear on the curve of RMSD JC Gumbart (Sun Jul 26 2009 - 21:14:22 CDT)
How to set magnitude of cellBasisVector? Aurum Bai (Fri Jul 24 2009 - 00:52:19 CDT)
- Re: How to set magnitude of cellBasisVector? Joshua Adelman (Fri Jul 24 2009 - 01:13:24 CDT)
An outlier appear on the curve of RMSD wayj86 wayj86 (Thu Jul 23 2009 - 22:37:04 CDT)
how to run namd2.7b1 on multiple nodes Roman Petrenko (Thu Jul 23 2009 - 17:48:19 CDT)
- Re: how to run namd2.7b1 on multiple nodes Chris Harrison (Thu Jul 23 2009 - 18:16:08 CDT)
- Re: how to run namd2.7b1 on multiple nodes Roman Petrenko (Fri Jul 24 2009 - 11:13:22 CDT)
NAMD documentation regarding compiling Thomas C. Bishop (Thu Jul 23 2009 - 15:25:19 CDT)
- Re: NAMD documentation regarding compiling Chris Harrison (Thu Jul 23 2009 - 16:56:28 CDT)
RescaleFreq of temperature =1? Mikhail Suyetin (Thu Jul 23 2009 - 09:48:54 CDT)
- Re: RescaleFreq of temperature =1? Axel Kohlmeyer (Thu Jul 23 2009 - 10:19:42 CDT)
  - Re: RescaleFreq of temperature =1? Axel Kohlmeyer (Thu Jul 23 2009 - 11:00:13 CDT)
NAMD CUDA on dual Nvidia 295 GPUs David Chalmers (Thu Jul 23 2009 - 07:20:34 CDT)
- Re: NAMD CUDA on dual Nvidia 295 GPUs Axel Kohlmeyer (Thu Jul 23 2009 - 08:04:42 CDT)
  - RE: NAMD CUDA on dual Nvidia 295 GPUs Sadhu, Shubho (NIH/NCI) [F] (Thu Jul 23 2009 - 09:43:34 CDT)
    - RE: NAMD CUDA on dual Nvidia 295 GPUs Axel Kohlmeyer (Thu Jul 23 2009 - 09:59:10 CDT)
- RE: NAMD CUDA on dual Nvidia 295 GPUs Sadhu, Shubho (NIH/NCI) [F] (Thu Jul 23 2009 - 09:11:48 CDT)
  - Re: RE: NAMD CUDA on dual Nvidia 295 GPUs Axel Kohlmeyer (Thu Jul 23 2009 - 10:02:45 CDT)
maximum residues using AMBER parm with NAMD benc_at_bsc.es (Wed Jul 22 2009 - 05:09:17 CDT)
NAMD installation Bernardo Sosa Padilla Araujo (Wed Jul 22 2009 - 17:33:15 CDT)
- Re: NAMD installation Joshua Adelman (Wed Jul 22 2009 - 17:51:42 CDT)
NAMD 2.7b1 with APBS/iAPBS Bjoern Olausson (Wed Jul 22 2009 - 02:56:07 CDT)
Measuring the molarity Rabab Toubar (Wed Jul 22 2009 - 15:16:58 CDT)
- Re: Measuring the molarity Leonardo Trabuco (Wed Jul 22 2009 - 16:09:28 CDT)
- Re: Measuring the molarity Benjamin Bouvier (Wed Jul 22 2009 - 16:25:40 CDT)
inconsistence in NAMD and AMBER energy Yi Shang (Mon Jul 20 2009 - 18:31:47 CDT)
- Re: inconsistence in NAMD and AMBER energy Goutham (Tue Jul 21 2009 - 01:13:48 CDT)
- Re: inconsistence in NAMD and AMBER energy Floris Buelens (Tue Jul 21 2009 - 02:11:51 CDT)
  - Re: inconsistence in NAMD and AMBER energy Thomas C. Bishop (Tue Jul 21 2009 - 09:33:35 CDT)
ABF tutorial sudipta (Mon Jul 20 2009 - 08:57:54 CDT)
- Re: ABF tutorial Chris Chipot (Mon Jul 20 2009 - 09:09:57 CDT)
  - Re: ABF tutorial sudipta (Tue Jul 21 2009 - 05:39:03 CDT)
  - Re: ABF tutorial sudipta (Tue Jul 21 2009 - 05:40:58 CDT)
on NAMD simulation of DNA translocation through nanopores yuhuihe_at_ime.pku.edu.cn (Sun Jul 19 2009 - 07:27:55 CDT)
- Re: on NAMD simulation of DNA translocation through nanopores Axel Kohlmeyer (Sun Jul 19 2009 - 11:24:06 CDT)
- Re: on NAMD simulation of DNA translocation through nanopores Eduardo Cruz-Chu (Sun Jul 19 2009 - 15:21:19 CDT)
about compile namd2.7 liupeng012 (Sun Jul 19 2009 - 05:58:05 CDT)
- Re: about compile namd2.7 Axel Kohlmeyer (Sun Jul 19 2009 - 11:18:33 CDT)
CPU USAGE mahmoud mirzaei (Sat Jul 18 2009 - 11:14:10 CDT)
- Re: CPU USAGE Axel Kohlmeyer (Sat Jul 18 2009 - 11:50:25 CDT)
  - Re: CPU USAGE mahmoud mirzaei (Sat Jul 18 2009 - 23:07:26 CDT)
NAMD 2.7b1 Jianhui Tian (Fri Jul 17 2009 - 10:52:28 CDT)
NAMD hanging on GPU Sadhu, Shubho (NIH/NCI) [F] (Fri Jul 17 2009 - 08:00:21 CDT)
- RE: NAMD hanging on GPU Sadhu, Shubho (NIH/NCI) [F] (Tue Jul 28 2009 - 09:17:48 CDT)
Reassign Temp during the Production Run twshen (Thu Jul 16 2009 - 12:04:03 CDT)
- Re: Reassign Temp during the Production Run Chris Harrison (Thu Jul 16 2009 - 12:17:02 CDT)
  - Re: Reassign Temp during the Production Run twshen (Thu Jul 16 2009 - 12:32:40 CDT)
    - Re: Reassign Temp during the Production Run Chris Harrison (Thu Jul 16 2009 - 13:04:03 CDT)
Grid Forces documentation Hugh Martin (Thu Jul 16 2009 - 08:02:04 CDT)
- Re: Grid Forces documentation Chris Harrison (Thu Jul 16 2009 - 12:24:00 CDT)
- Re: Grid Forces documentation Eduardo Cruz-Chu (Thu Jul 16 2009 - 14:20:11 CDT)
VMD-Installation problems jose correa (Wed Jul 15 2009 - 19:16:35 CDT)
- Re: VMD-Installation problems Axel Kohlmeyer (Wed Jul 15 2009 - 19:56:00 CDT)
molecule jumps from one site to the other? uu zhu (Mon Jul 13 2009 - 21:11:52 CDT)
- Re: molecule jumps from one site to the other? Eric H. Lee (Mon Jul 13 2009 - 21:33:42 CDT)
Implementation of graphite walls Sabine Leroch (Mon Jul 13 2009 - 07:36:05 CDT)
- Wtrlt: Smeart out 9/3 LJ wall Sabine Leroch (Wed Jul 15 2009 - 07:48:07 CDT)
  - Re: Wtrlt: Smeart out 9/3 LJ wall Axel Kohlmeyer (Wed Jul 15 2009 - 12:10:53 CDT)
    - Re: Wtrlt: Smeart out 9/3 LJ wall Joshua Adelman (Wed Jul 15 2009 - 12:21:09 CDT)
Fwd: one atom off in the minimization result Chris Harrison (Sun Jul 12 2009 - 18:23:10 CDT)
Re: Tried to find atom type on node other than node 0 Narender Singh Maan (Mon Jul 13 2009 - 10:46:47 CDT)
Bad global exclusion count Yogesh Aher (Mon Jul 13 2009 - 05:57:18 CDT)
- Re: Bad global exclusion count Chris Harrison (Mon Jul 13 2009 - 09:54:50 CDT)
  - Re: Bad global exclusion count Yogesh Aher (Wed Jul 15 2009 - 09:49:33 CDT)
Fwd: PROBLEM OF INSTALLATION OF NAMD ipsita basu (Sun Jul 12 2009 - 23:28:30 CDT)
- Re: Fwd: PROBLEM OF INSTALLATION OF NAMD Sadhu, Shubho (NIH/NCI) [F] (Fri Jul 17 2009 - 08:07:36 CDT)
Fwd: Minimization problem of a protein-DNA complex with namd Chris Harrison (Sun Jul 12 2009 - 18:23:40 CDT)
- Re: Minimization problem of a protein-DNA complex with namd David Hardy (Sun Jul 12 2009 - 19:38:21 CDT)
one atom off in the minimization result mgssal (Sun Jul 12 2009 - 03:22:46 CDT)
Minimization problem of a protein-DNA complex with namd sudipta (Sun Jul 12 2009 - 02:21:36 CDT)
Fwd: 99999999.9999 as vander waals energy Chris Harrison (Sat Jul 11 2009 - 19:38:30 CDT)
Simulating Protonated base pairs of RNA Monika Sharma (Sat Jul 11 2009 - 07:07:29 CDT)
pdbalias for PO4 residue gurunath katagi (Sat Jul 11 2009 - 01:09:29 CDT)
- Re: pdbalias for PO4 residue Chris Harrison (Sat Jul 11 2009 - 19:37:53 CDT)
99999999.9999 as vander waals energy Uma Mageshwari (Sat Jul 11 2009 - 00:18:19 CDT)
SMD working only at high velocity Elia Zumot (Fri Jul 10 2009 - 13:20:33 CDT)
- Re: SMD working only at high velocity JC Gumbart (Fri Jul 10 2009 - 13:26:06 CDT)
  - Re: SMD working only at high velocity Elia Zumot (Fri Jul 10 2009 - 14:48:34 CDT)
    - Re: SMD working only at high velocity Eric H. Lee (Fri Jul 10 2009 - 15:06:20 CDT)
    - Re: SMD working only at high velocity David Tanner (Fri Jul 10 2009 - 15:20:23 CDT)
- Re: SMD working only at high velocity David Tanner (Fri Jul 10 2009 - 15:12:06 CDT)
  - Re: SMD working only at high velocity Elia Zumot (Mon Jul 13 2009 - 10:54:42 CDT)
Intel 11 compilers Xavier Deupi (Fri Jul 10 2009 - 08:52:58 CDT)
- Re: Intel 11 compilers Nicholas M Glykos (Fri Jul 10 2009 - 10:01:59 CDT)
- Re: Intel 11 compilers Guanglei Cui (Fri Jul 10 2009 - 10:45:17 CDT)
  - RE: Intel 11 compilers David A. Horita (Fri Jul 10 2009 - 13:37:54 CDT)
protein folding doty alexiou (Fri Jul 10 2009 - 03:00:37 CDT)
- Re: protein folding Axel Kohlmeyer (Fri Jul 10 2009 - 07:48:02 CDT)
  - Re: protein folding Anton Arkhipov (Fri Jul 10 2009 - 10:37:29 CDT)
- Re: protein folding Dong Luo (Fri Jul 10 2009 - 08:13:56 CDT)
  - Re: protein folding Vlad Cojocaru (Fri Jul 10 2009 - 08:51:56 CDT)
    - Re: protein folding Hannes Loeffler (Fri Jul 10 2009 - 10:44:24 CDT)
bug or custom? BIN ZHANG (Thu Jul 09 2009 - 13:00:44 CDT)
- Re: bug or custom? BIN ZHANG (Thu Jul 09 2009 - 13:53:52 CDT)
Fwd: Tried to find atom type on node other than node 0 Chris Harrison (Thu Jul 09 2009 - 09:45:23 CDT)
Tried to find atom type on node other than node 0 Narender Singh Maan (Thu Jul 09 2009 - 09:00:44 CDT)
Re: Generation of .psf file of DNA Jian Liu (Thu Jul 09 2009 - 07:43:21 CDT)
- Re: Generation of .psf file of DNA Chris Harrison (Thu Jul 09 2009 - 09:42:10 CDT)
Re: namd hangs or exits with segmentation faults on opteron cluster with infiniband Vlad Cojocaru (Thu Jul 09 2009 - 06:59:31 CDT)
Another strange error: MStream checksums do not agree Vlad Cojocaru (Thu Jul 09 2009 - 03:05:13 CDT)
- Re: Another strange error: MStream checksums do not agree Axel Kohlmeyer (Thu Jul 09 2009 - 06:40:19 CDT)
Generation of .psf file of DNA sudipta (Thu Jul 09 2009 - 01:53:25 CDT)
bicarbonate parameters Brian R Novak (Wed Jul 08 2009 - 13:31:28 CDT)
FATAL ERROR: Sorry, combined TI and FEP is not implemented Vlad Cojocaru (Wed Jul 08 2009 - 05:41:00 CDT)
- Re: FATAL ERROR: Sorry, combined TI and FEP is not implemented Chris Harrison (Wed Jul 08 2009 - 09:58:51 CDT)
  - Re: FATAL ERROR: Sorry, combined TI and FEP is not implemented Vlad Cojocaru (Thu Jul 09 2009 - 03:22:44 CDT)
    - Re: FATAL ERROR: Sorry, combined TI and FEP is not implemented Axel Kohlmeyer (Thu Jul 09 2009 - 06:38:57 CDT)
LES problem Irene Newhouse (Tue Jul 07 2009 - 00:30:50 CDT)
Fatal Error Help Goutham (Mon Jul 06 2009 - 16:10:18 CDT)
- Re: Fatal Error Help Chris Harrison (Thu Jul 09 2009 - 09:49:25 CDT)
  - Re: Fatal Error Help Narender Singh Maan (Thu Jul 09 2009 - 10:47:11 CDT)
Translocation problem while attempting to use ABF Hugh Martin (Mon Jul 06 2009 - 10:39:38 CDT)
- Re: Translocation problem while attempting to use ABF Jerome Henin (Mon Jul 06 2009 - 11:37:20 CDT)
  - Re: Translocation problem while attempting to use ABF Hugh Martin (Wed Aug 05 2009 - 12:26:30 CDT)
    - Re: Translocation problem while attempting to use ABF Hugh Martin (Mon Aug 31 2009 - 07:52:40 CDT)
- Re: Translocation problem while attempting to use ABF Eric H. Lee (Mon Jul 06 2009 - 11:34:11 CDT)
END: No log file Luis Agullo (LAB) (Mon Jul 06 2009 - 09:56:15 CDT)
No log file Luis Agullo (LAB) (Mon Jul 06 2009 - 08:41:14 CDT)
- Re: No log file Nicholas M Glykos (Mon Jul 06 2009 - 09:35:27 CDT)
- Re: No log file David Tanner (Mon Jul 06 2009 - 09:45:47 CDT)
protein collapsing problem ydhuang2727 (Sun Jul 05 2009 - 20:12:38 CDT)
Re: Re: namd2.7b1 slower with openmpi 1.3.2 than namd2.6 withopenmpi 1.2.6 liupeng012 (Sat Jul 04 2009 - 21:17:15 CDT)
- Re: Re: namd2.7b1 slower with openmpi 1.3.2 than namd2.6 withopenmpi 1.2.6 Axel Kohlmeyer (Sun Jul 05 2009 - 11:38:37 CDT)
about psfgen emilia.l.wu (Sat Jul 04 2009 - 08:59:44 CDT)
- Re: about psfgen Ramya Gamini (Sat Jul 04 2009 - 09:40:46 CDT)
  - Re: Re: about psfgen emilia.l.wu (Sat Jul 04 2009 - 10:53:18 CDT)
    - Re: Re: about psfgen Ramya Gamini (Sat Jul 04 2009 - 14:33:32 CDT)
    - Re: Re: about psfgen Ramya Gamini (Sat Jul 04 2009 - 14:43:53 CDT)
implicit solvent model in NAMD? Yinglong Miao (Fri Jul 03 2009 - 15:18:17 CDT)
- Re: implicit solvent model in NAMD? David Tanner (Sat Jul 04 2009 - 06:50:14 CDT)
namd hangs or exits with segmentation faults on opteron cluster with infiniband Vlad Cojocaru (Fri Jul 03 2009 - 08:16:28 CDT)
Hardware for NAMD / VMD machine Olve Peersen (Fri Jul 03 2009 - 01:26:11 CDT)
- Re: Hardware for NAMD / VMD machine Axel Kohlmeyer (Fri Jul 03 2009 - 11:56:08 CDT)
- Re: vmd-l: Hardware for NAMD / VMD machine John Stone (Mon Jul 06 2009 - 11:04:30 CDT)
  - Re: vmd-l: Hardware for NAMD / VMD machine Olve Peersen (Mon Jul 06 2009 - 13:39:53 CDT)
    - Re: Re: vmd-l: Hardware for NAMD / VMD machine Axel Kohlmeyer (Mon Jul 06 2009 - 16:46:40 CDT)
ERROR! Explicit exclusions or fluctuating charges not supported, atom ignored. emilia wu (Thu Jul 02 2009 - 18:35:32 CDT)
- Re: ERROR! Explicit exclusions or fluctuating charges not supported, atom ignored. Leonardo Trabuco (Thu Jul 02 2009 - 18:55:23 CDT)
  - Re: ERROR! Explicit exclusions or fluctuating charges not supported, atom ignored. Leonardo Trabuco (Thu Jul 02 2009 - 19:09:23 CDT)
NAMD_ti.pl Philip Fowler (Wed Jul 01 2009 - 06:45:31 CDT)
Par and Top files for BCL Kovács, Sándor Ádám (Thu Jul 02 2009 - 12:08:08 CDT)
- RE: Par and Top files for BCL Kovács, Sándor Ádám (Thu Jul 09 2009 - 13:35:54 CDT)
namd2.7b1 slower with openmpi 1.3.2 than namd2.6 with openmpi 1.2.6 Vlad Cojocaru (Thu Jul 02 2009 - 10:41:23 CDT)
- Re: namd2.7b1 slower with openmpi 1.3.2 than namd2.6 with openmpi 1.2.6 Axel Kohlmeyer (Fri Jul 03 2009 - 13:42:08 CDT)
nose-hoover David A. Horita (Wed Jul 01 2009 - 10:36:30 CDT)
- Re: nose-hoover Jerome Henin (Wed Jul 01 2009 - 11:56:22 CDT)
NAMD_ti.pl Philip Fowler (Wed Jul 01 2009 - 07:50:26 CDT)
- Re: NAMD_ti.pl Floris Buelens (Thu Jul 02 2009 - 02:26:35 CDT)
NAMD Installation mahmoud (Wed Jul 01 2009 - 02:53:51 CDT)
- Re: NAMD Installation Nicholas M Glykos (Wed Jul 01 2009 - 03:57:44 CDT)
- Re: NAMD Installation Axel Kohlmeyer (Wed Jul 01 2009 - 08:07:03 CDT)
location of the SMD source code Liang (Tue Jun 30 2009 - 13:17:48 CDT)
- Re: location of the SMD source code Axel Kohlmeyer (Tue Jun 30 2009 - 13:59:10 CDT)
Hi,all, the parameters for Strain uu zhu (Tue Jun 30 2009 - 01:32:26 CDT)
GPGPU Programming summer school at University of Tennessee, Aug 10-14. Axel Kohlmeyer (Mon Jun 29 2009 - 14:43:11 CDT)
namd cvs 26.06.09, tcl 8.5, loadcoords Vlad Cojocaru (Mon Jun 29 2009 - 09:10:46 CDT)
- Re: namd cvs 26.06.09, tcl 8.5, loadcoords Vlad Cojocaru (Tue Jun 30 2009 - 02:45:21 CDT)
Modeling of Gramicidin A Jian Liu (Mon Jun 29 2009 - 08:08:41 CDT)
Protein collpasing problem! ydhuang2727 (Mon Jun 29 2009 - 01:12:47 CDT)
- Re: Protein collpasing problem! Axel Kohlmeyer (Mon Jun 29 2009 - 08:25:06 CDT)
  - Re: Protein collpasing problem! Joshua Adelman (Fri Jul 03 2009 - 10:55:53 CDT)
- Re: Protein collpasing problem! Joshua Adelman (Mon Jun 29 2009 - 11:23:33 CDT)
defenestrate Peter Freddolino (Sun Jun 28 2009 - 15:20:11 CDT)
unsubscribe Anna Blice-Baum (Sun Jun 28 2009 - 14:40:10 CDT)
unsubscribe wavedalla\_at_libero\.it (Sun Jun 28 2009 - 09:49:09 CDT)
- Re: unsubscribe Jerome Henin (Sun Jun 28 2009 - 10:40:46 CDT)
  - Re: unsubscribe Axel Kohlmeyer (Mon Jun 29 2009 - 08:35:36 CDT)
- unsubscribe Shen, Lingling (Sun Jun 28 2009 - 10:59:53 CDT)
Can I use another solvent rather than TI3P model in namd for MD simulations ? Wang Yf (Sat Jun 27 2009 - 22:30:04 CDT)
- Re: Can I use another solvent rather than TI3P model in namd for MD simulations ? Joshua Adelman (Sun Jun 28 2009 - 20:14:02 CDT)
- Re: Can I use another solvent rather than TI3P model in namd for MD simulations ? Axel Kohlmeyer (Mon Jun 29 2009 - 08:32:30 CDT)
the recent flood of unsubscribe requests Axel Kohlmeyer (Sat Jun 27 2009 - 10:07:28 CDT)
unsubscribe Ariovaldo de Souza Junior (Sat Jun 27 2009 - 09:25:57 CDT)
unsubscribe C. Denise Enekwa (Sat Jun 27 2009 - 06:41:19 CDT)
unsubscribe Nd S (Sat Jun 27 2009 - 00:41:38 CDT)
unsubscribe Vinit Rege (Fri Jun 26 2009 - 22:27:45 CDT)
unsubscribe Hatley, Jade M (Fri Jun 26 2009 - 19:02:48 CDT)
colvars: Error: undefined output or restart file. Bonnie Merchant (Fri Jun 26 2009 - 13:41:42 CDT)
- Re: colvars: Error: undefined output or restart file. Jerome Henin (Fri Jun 26 2009 - 14:26:47 CDT)
  - Re: colvars: Error: undefined output or restart file. Bonnie Merchant (Mon Jun 29 2009 - 11:00:07 CDT)
- skip frames with bigdcd Payel Das (Fri Jun 26 2009 - 15:15:21 CDT)
  - Re: skip frames with bigdcd Axel Kohlmeyer (Fri Jun 26 2009 - 15:41:03 CDT)
- Re: colvars: Error: undefined output or restart file. Giacomo Fiorin (Fri Jun 26 2009 - 15:03:27 CDT)
My protein went out of the water box in SMD. Would it have a bad effect on the result? wayj86 wayj86 (Fri Jun 26 2009 - 03:02:46 CDT)
- Re: My protein went out of the water box in SMD. Would it have a bad effect on the result? Roman Petrenko (Mon Jun 29 2009 - 12:57:38 CDT)
  - Re: My protein went out of the water box in SMD. Would it have a bad effect on the result? wayj86 wayj86 (Tue Jun 30 2009 - 03:36:49 CDT)
- how work: harmonic position "constraints" module + "WrapAll on"? Sebastian Stolzenberg (Mon Jul 20 2009 - 07:12:04 CDT)
  - Re: how work: harmonic position "constraints" module + "WrapAll on"? Joshua Adelman (Mon Jul 20 2009 - 09:23:13 CDT)
    - Re: how work: harmonic position "constraints" module + "WrapAll on"? Sebastian Stolzenberg (Mon Jul 20 2009 - 12:52:06 CDT)
Grid Forces gbellesia_at_chem.ucsb.edu (Thu Jun 25 2009 - 15:31:19 CDT)
- Re: Grid Forces Chris Harrison (Sat Jun 27 2009 - 09:53:55 CDT)
Does NAMD have any capability to assign coordiantes to novel sequences? Amr Zeinalabideen Majul (Thu Jun 25 2009 - 10:34:43 CDT)
- Re: Does NAMD have any capability to assign coordiantes to novel sequences? Nicholas M Glykos (Thu Jun 25 2009 - 11:36:02 CDT)
- Re: Does NAMD have any capability to assign coordiantes to novel sequences? Eric H. Lee (Thu Jun 25 2009 - 11:16:16 CDT)
protein collapsing problem! ydhuang2727 (Thu Jun 25 2009 - 00:08:29 CDT)
- Re: protein collapsing problem! Joshua Adelman (Thu Jun 25 2009 - 01:10:52 CDT)
  - Re: protein collapsing problem! Joshua Adelman (Sun Jun 28 2009 - 03:10:43 CDT)
regarding positioning of protein molecule prasun kumar (Wed Jun 24 2009 - 17:39:15 CDT)
- Re: regarding positioning of protein molecule Eric H. Lee (Wed Jun 24 2009 - 17:46:53 CDT)
- Re: regarding positioning of protein molecule Ramya Gamini (Wed Jun 24 2009 - 22:52:06 CDT)
bugfixes in the colvars module (ABF, metadynamics etc.) Giacomo Fiorin (Wed Jun 24 2009 - 16:00:27 CDT)
Re: launch NAMD from tcl script J Liu (Wed Jun 24 2009 - 08:58:47 CDT)
- Re: launch NAMD from tcl script - bug? Floris Buelens (Wed Jun 24 2009 - 10:54:24 CDT)
  - Re: launch NAMD from tcl script - bug? Axel Kohlmeyer (Wed Jun 24 2009 - 11:36:33 CDT)
launch NAMD from tcl script Floris Buelens (Wed Jun 24 2009 - 06:55:06 CDT)
Total energy of a residue Mert Gür (Tue Jun 23 2009 - 10:08:12 CDT)
- RE: Total energy of a residue Brian R Novak (Tue Jun 23 2009 - 11:03:45 CDT)
  - Re: Total energy of a residue Mert Gür (Tue Jun 23 2009 - 14:59:19 CDT)
Re: 2.7b metadynamics ::hBond component :: folding of a single helix in water Ali Emileh (Mon Jun 22 2009 - 14:23:57 CDT)
- Re: 2.7b metadynamics ::hBond component :: folding of a single helix in water Giacomo Fiorin (Mon Jun 22 2009 - 15:18:52 CDT)
Pair interaction : Energy values are zero Navendu bhatnagar (Sun Jun 21 2009 - 16:01:45 CDT)
- Re: Pair interaction : Energy values are zero Eric H. Lee (Sun Jun 21 2009 - 16:23:43 CDT)
FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR NH3 HC NH3 gurunath katagi (Sat Jun 20 2009 - 12:59:51 CDT)
- Re: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR NH3 HC NH3 Axel Kohlmeyer (Sun Jun 21 2009 - 12:54:51 CDT)
  - Re: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR NH3 HC NH3 gurunath katagi (Sun Jun 21 2009 - 16:35:42 CDT)
    - Re: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR NH3 HC NH3 Chris Harrison (Sun Jun 21 2009 - 19:11:54 CDT)
- Re: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR NH3 HC NH3 Chris Harrison (Sat Jun 20 2009 - 13:35:08 CDT)
VMD/NAMD two identical molecules solvate in a water sphere David Jiang (Sat Jun 20 2009 - 11:02:49 CDT)
- Re: VMD/NAMD two identical molecules solvate in a water sphere Eric H. Lee (Sat Jun 20 2009 - 12:46:25 CDT)
- Re: VMD/NAMD two identical molecules solvate in a water sphere Joshua Adelman (Sat Jun 20 2009 - 12:21:49 CDT)
  - Re: VMD/NAMD two identical molecules solvate in a water sphere David Jiang (Tue Jun 23 2009 - 10:27:07 CDT)
Developing a neutral arginine patch in a topology file urmit shah (Fri Jun 19 2009 - 17:54:19 CDT)
- namd 2.7b: measure free energy difference "growing" a force constant Sebastian Stolzenberg (Sat Jun 20 2009 - 09:33:13 CDT)
  - Re: namd 2.7b: measure free energy difference "growing" a force constant Chris Chipot (Sat Jun 20 2009 - 10:07:16 CDT)
  - Re: namd 2.7b: measure free energy difference "growing" a force constant Chris Harrison (Sat Jun 20 2009 - 14:01:30 CDT)
Re: Reassign temp bay__gulf618_at_sina.com (Wed Jun 17 2009 - 20:44:15 CDT)
Reassign temp Marcelo Puiatti (Wed Jun 17 2009 - 15:27:18 CDT)
- Re: Reassign temp Peter Freddolino (Wed Jun 17 2009 - 20:51:03 CDT)
collective variables Jarrod Nickel (Wed Jun 17 2009 - 11:07:26 CDT)
- Re: collective variables Giacomo Fiorin (Wed Jun 17 2009 - 13:26:44 CDT)
  - Re: collective variables Cesar Millan (Wed Jun 17 2009 - 15:29:02 CDT)
    - Re: collective variables Giacomo Fiorin (Wed Jun 17 2009 - 15:43:21 CDT)
How is dG caluclated from dE during FEP? Michael Thomas (Wed Jun 17 2009 - 06:51:31 CDT)
- Re: How is dG caluclated from dE during FEP? Floris Buelens (Fri Jun 19 2009 - 02:39:05 CDT)
Re: Re: Thermodynamic integration script - where is it? Floris Buelens (Tue Jun 16 2009 - 02:37:44 CDT)
to run NAMD on a PC Lixia Jin Day (Mon Jun 15 2009 - 12:59:08 CDT)
need advices for running NAMD efficiently. Lixia Jin Day (Mon Jun 15 2009 - 12:44:55 CDT)
- Re: need advices for running NAMD efficiently. Axel Kohlmeyer (Mon Jun 15 2009 - 13:19:05 CDT)
Postdoc position in biomolecular simulation Ivaylo, Ivanov (Sat Jun 13 2009 - 02:08:07 CDT)
Postdoc position in biomolecular simulation Ivaylo, Ivanov (Sat Jun 13 2009 - 01:37:55 CDT)
Histamine topology file r charbel maroun (Fri Jun 12 2009 - 11:32:35 CDT)
- Re: Histamine topology file Peter Freddolino (Fri Jun 12 2009 - 13:52:12 CDT)
regarding psfgen algorithm prasun kumar (Fri Jun 12 2009 - 03:22:04 CDT)
- regarding psfgen algorithm prasun kumar (Wed Jun 17 2009 - 23:59:58 CDT)
  - Re: regarding psfgen algorithm Benjamin Bouvier (Thu Jun 18 2009 - 03:50:14 CDT)
    - Re: regarding psfgen algorithm Jerome Henin (Thu Jun 18 2009 - 10:07:36 CDT)
What decides the pulling direction in SMD? Àîè (Fri Jun 12 2009 - 02:35:15 CDT)
- Re: What decides the pulling direction in SMD? David Tanner (Fri Jun 12 2009 - 07:04:27 CDT)
Force Constant Units Kamilla Kopec (Wed Jun 10 2009 - 12:08:24 CDT)
- Re: Force Constant Units Ramya Gamini (Wed Jun 10 2009 - 14:01:28 CDT)
compile NAMD with TCP and SMP sudipta (Wed Jun 10 2009 - 00:19:18 CDT)
ABF simulations Sumanth Jamadagni (Tue Jun 09 2009 - 21:08:10 CDT)
- Re: ABF simulations Sébastien Légaré (Tue Jun 23 2009 - 11:01:22 CDT)
  - Re: ABF simulations Sumanth Jamadagni (Tue Jun 23 2009 - 11:32:43 CDT)
    - RE: ABF simulations Ziemys, Arturas (Tue Jun 23 2009 - 13:04:24 CDT)
    - RE: ABF simulations Branko (Tue Jun 23 2009 - 14:52:42 CDT)
question about repeating output text ershela.durresi_at_yale.edu (Tue Jun 09 2009 - 05:58:20 CDT)
- Re: question about repeating output text Axel Kohlmeyer (Tue Jun 09 2009 - 08:09:31 CDT)
How to set the parameters for two different baths in one molecule? uu zhu (Mon Jun 08 2009 - 20:14:36 CDT)
Bug advisory: RMSD and ABF Jerome Henin (Mon Jun 08 2009 - 17:55:10 CDT)
Problem namd2 and mpich2 sudipta (Mon Jun 08 2009 - 01:40:58 CDT)
- Re: Problem namd2 and mpich2 Axel Kohlmeyer (Mon Jun 08 2009 - 09:01:42 CDT)
Read DCD file in Java Kejun (Kevin) Dong (Sat Jun 06 2009 - 00:39:27 CDT)
- Re: Read DCD file in Java Axel Kohlmeyer (Sat Jun 06 2009 - 11:23:50 CDT)
  - Re: Read DCD file in Java Kejun (Kevin) Dong (Mon Jun 08 2009 - 12:33:58 CDT)
regarding protein-protein interaction prasun kumar (Fri Jun 05 2009 - 02:51:37 CDT)
- Re: regarding protein-protein interaction Marcin Krol (Fri Jun 05 2009 - 03:23:13 CDT)
- Re: regarding protein-protein interaction L. Michel Espinoza-Fonseca (Fri Jun 05 2009 - 03:19:43 CDT)
- Re: regarding protein-protein interaction Benjamin Bouvier (Fri Jun 05 2009 - 03:50:21 CDT)
- Re: regarding protein-protein interaction Joshua Adelman (Fri Jun 05 2009 - 10:41:44 CDT)
protein folding cg doty alexiou (Fri Jun 05 2009 - 01:21:16 CDT)
- Re: protein folding cg Joshua Adelman (Fri Jun 05 2009 - 02:01:51 CDT)
Please disregard the spam "Lei sent you private photos on Tagged :)" Lei Shi (Thu Jun 04 2009 - 17:04:05 CDT)
tclforces and minimization Roman Petrenko (Thu Jun 04 2009 - 16:42:27 CDT)
abf with colvars example David A. Horita (Thu Jun 04 2009 - 12:53:20 CDT)
- Re: abf with colvars example Jerome Henin (Thu Jun 04 2009 - 13:44:06 CDT)
  - Re: abf with colvars example Roman Petrenko (Thu Jun 04 2009 - 14:35:53 CDT)
  - Re: abf with colvars example Branko (Thu Jun 04 2009 - 15:17:42 CDT)
Charmrun/INTEL MAC/2.7 Grabe, Michael David (Thu Jun 04 2009 - 09:21:21 CDT)
- Re: Charmrun/INTEL MAC/2.7 Marius Micluta (Fri Jun 05 2009 - 04:36:57 CDT)
Exclusions and CUDA Benjamin Bouvier (Thu Jun 04 2009 - 03:40:22 CDT)
- Re: Exclusions and CUDA Axel Kohlmeyer (Thu Jun 04 2009 - 09:03:24 CDT)
NAMD on GPU xiaojing gong (Thu Jun 04 2009 - 02:53:18 CDT)
- Re: NAMD on GPU Axel Kohlmeyer (Thu Jun 04 2009 - 09:16:13 CDT)
- Re: NAMD on GPU Prakash Velayutham (Thu Jun 04 2009 - 08:49:52 CDT)
namd 2.7b1 on infiniband about the error : stack Traceback liupeng012 (Thu Jun 04 2009 - 00:10:32 CDT)
Measuring protein diffusion: results too small? Stephen Hicks (Wed Jun 03 2009 - 16:49:03 CDT)
- Re: Measuring protein diffusion: results too small? Axel Kohlmeyer (Wed Jun 03 2009 - 17:53:53 CDT)
  - Re: Measuring protein diffusion: results too small? Stephen Hicks (Thu Jun 04 2009 - 02:56:28 CDT)
    - Re: Measuring protein diffusion: results too small? Joshua D. Moore (Fri Jun 05 2009 - 21:49:22 CDT)
- Re: Measuring protein diffusion: results too small? Peter Freddolino (Fri Jun 05 2009 - 10:16:29 CDT)
  - Re: Measuring protein diffusion: results too small? Stephen Hicks (Tue Jun 09 2009 - 12:01:23 CDT)
lamboot -v nodelist Yogesh Aher (Wed Jun 03 2009 - 09:49:15 CDT)
- Re: lamboot -v nodelist Axel Kohlmeyer (Wed Jun 03 2009 - 10:27:06 CDT)
compile namd2.7b1 on infiniband liupeng012 (Tue Jun 02 2009 - 21:43:16 CDT)
- Re: compile namd2.7b1 on infiniband Axel Kohlmeyer (Tue Jun 02 2009 - 22:17:01 CDT)
Namd lite Goutham (Tue Jun 02 2009 - 19:54:21 CDT)
2.7b metadynamics ::alpha module :: folding of a single helix in water Ali Emileh (Tue Jun 02 2009 - 18:39:25 CDT)
- Re: 2.7b metadynamics ::alpha module :: folding of a single helix in water Giacomo Fiorin (Fri Jun 05 2009 - 10:53:48 CDT)
  - Re: 2.7b metadynamics ::alpha module :: folding of a single helix in water Ali Emileh (Tue Jun 09 2009 - 11:52:19 CDT)
Fwd: RESP and CHARMM r charbel maroun (Tue Jun 02 2009 - 08:35:17 CDT)
IMD, Hostname and Port Nano Group (Tue Jun 02 2009 - 07:40:01 CDT)
force output of pairInteraction BIN ZHANG (Mon Jun 01 2009 - 17:20:07 CDT)
Rescale Temperature when velocity of COM is not zero Fred (Rui FENG) (Mon Jun 01 2009 - 15:12:05 CDT)
- Re: Rescale Temperature when velocity of COM is not zero Peter Freddolino (Mon Jun 01 2009 - 21:03:37 CDT)
Re: Thermodynamic integration script - where is it? Lela Vukovic (Mon Jun 01 2009 - 12:52:38 CDT)
FATAL ERROR: Bad global exclusion count! KIRTANA S (Mon Jun 01 2009 - 12:37:38 CDT)
- Re: FATAL ERROR: Bad global exclusion count! Axel Kohlmeyer (Mon Jun 01 2009 - 13:05:24 CDT)
flipdcd Michael Kreim (Sat May 30 2009 - 07:12:34 CDT)
- Re: flipdcd Axel Kohlmeyer (Mon Jun 01 2009 - 12:05:35 CDT)
Regd: Error KIRTANA S (Sun May 31 2009 - 22:52:15 CDT)
- Re: Regd: Error Axel Kohlmeyer (Mon Jun 01 2009 - 09:00:36 CDT)
  - Re: Regd: Error Axel Kohlmeyer (Mon Jun 01 2009 - 09:46:39 CDT)
regd: my parameter file KIRTANA S (Fri May 29 2009 - 16:05:26 CDT)
- Re: regd: my parameter file Joshua Adelman (Fri May 29 2009 - 16:16:29 CDT)
Regd :parameter file KIRTANA S (Fri May 29 2009 - 15:56:04 CDT)
- Re: Regd :parameter file Axel Kohlmeyer (Fri May 29 2009 - 16:28:41 CDT)
visualize energy on a structure Michael Zimmermann (Fri May 29 2009 - 12:20:24 CDT)
using amber topology and parameter files in NAMD KIRTANA S (Fri May 29 2009 - 12:16:54 CDT)
- Re: using amber topology and parameter files in NAMD Nicholas M Glykos (Fri May 29 2009 - 13:05:06 CDT)
- Re: using amber topology and parameter files in NAMD Joshua Adelman (Fri May 29 2009 - 12:23:57 CDT)
water molecules "collapse" during equilibration enz1+_at_pitt.edu (Fri May 29 2009 - 11:38:06 CDT)
- Re: water molecules "collapse" during equilibration Nicholas M Glykos (Fri May 29 2009 - 12:49:56 CDT)
  - Re: water molecules "collapse" during equilibration JC Gumbart (Fri May 29 2009 - 15:00:51 CDT)
  - Re: water molecules "collapse" during equilibration JC Gumbart (Fri May 29 2009 - 17:01:01 CDT)
    - Re: water molecules "collapse" during equilibration Peter Freddolino (Fri May 29 2009 - 17:05:05 CDT)
- Re: water molecules "collapse" during equilibration JC Gumbart (Fri May 29 2009 - 14:14:19 CDT)
FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE Yogesh Aher (Fri May 29 2009 - 09:34:13 CDT)
- Re: FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE Axel Kohlmeyer (Fri May 29 2009 - 10:59:30 CDT)
- Re: FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE Joachim Hein (Fri May 29 2009 - 11:07:56 CDT)
  - Re: FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE Joachim Hein (Fri May 29 2009 - 11:40:41 CDT)
electric field along z-direction Roman Petrenko (Wed May 27 2009 - 16:21:27 CDT)
unknown path type LSN ÖÜÎÄ²ý (Tue May 26 2009 - 07:48:49 CDT)
- Re: unknown path type LSN Peter Freddolino (Tue May 26 2009 - 09:32:55 CDT)
TMD for moving ion across membrane yun luo (Mon May 25 2009 - 12:10:59 CDT)
- Re: TMD for moving ion across membrane yun luo (Tue May 26 2009 - 13:50:55 CDT)
Software to Mutate DNA sunita gupta (Mon May 25 2009 - 08:39:51 CDT)
- Re: Software to Mutate DNA Alessandro Nascimento (Mon May 25 2009 - 10:19:25 CDT)
- Re: Software to Mutate DNA gaillard_at_chimie.u-strasbg.fr (Tue May 26 2009 - 09:35:18 CDT)
NAMD 2.7b1 running & performance issues Marius Micluta (Mon May 25 2009 - 06:13:07 CDT)
- Re: NAMD 2.7b1 running & performance issues Axel Kohlmeyer (Mon May 25 2009 - 10:13:13 CDT)
- Re: NAMD 2.7b1 running & performance issues Nicholas M Glykos (Mon May 25 2009 - 12:43:07 CDT)
  - Re: NAMD 2.7b1 running & performance issues Marius Micluta (Mon Jun 01 2009 - 07:15:56 CDT)
Force on multiple atoms in ABF Mert Gür (Sun May 24 2009 - 11:26:16 CDT)
Postdoctoral Position in Scientific Computing VMD NAMD Postdoc Position (Sat May 23 2009 - 13:41:27 CDT)
Offset for frame ids in dcd trajectory DimitryASuplatov (Sat May 23 2009 - 11:11:09 CDT)
- Re: Offset for frame ids in dcd trajectory Joshua Adelman (Sat May 23 2009 - 12:15:01 CDT)
- Re: vmd-l: Offset for frame ids in dcd trajectory John Stone (Tue May 26 2009 - 15:32:40 CDT)
Warning: Not all atoms have unique coordinates Jarrod Nickel (Fri May 22 2009 - 14:08:34 CDT)
GridForces methodology in NAMD 2.7b1 Giovanni Bellesia (Fri May 22 2009 - 13:26:16 CDT)
- Re: GridForces methodology in NAMD 2.7b1 Robert Brunner (Thu May 28 2009 - 16:46:16 CDT)
triazol parameters Ziemys, Arturas (Thu May 21 2009 - 16:01:53 CDT)
NAMD2.6 - 1D Periodic Boundary and PME - FATAL ERROR: PME requires periodic boundary conditions. Greg Guthe (Thu May 21 2009 - 15:32:47 CDT)
- Re: NAMD2.6 - 1D Periodic Boundary and PME - FATAL ERROR: PME requires periodic boundary conditions. David Hardy (Thu May 21 2009 - 15:55:42 CDT)
selectively write atom coordinates on-the-fly Vasudevan V (Thu May 21 2009 - 11:29:35 CDT)
- RE: selectively write atom coordinates on-the-fly Brian R Novak (Thu May 21 2009 - 12:44:33 CDT)
- Re: selectively write atom coordinates on-the-fly Joshua Adelman (Thu May 21 2009 - 11:41:11 CDT)
Harmonically constrained simulations Sumanth Jamadagni (Thu May 21 2009 - 10:00:13 CDT)
- Re: Harmonically constrained simulations JT (Thu May 21 2009 - 11:25:55 CDT)
  - Re: Harmonically constrained simulations Sumanth Jamadagni (Thu May 21 2009 - 11:47:26 CDT)
calculating energy for large log files gurunath katagi (Thu May 21 2009 - 02:30:40 CDT)
- Re: calculating energy for large log files Axel Kohlmeyer (Thu May 21 2009 - 09:30:51 CDT)
Fw: NAMD 2.7b1 running problem bay__gulf618_at_sina.com (Wed May 20 2009 - 20:10:15 CDT)
- Re: Fw: NAMD 2.7b1 running problem Matteo Rotter (Thu May 21 2009 - 03:30:06 CDT)
NAMD Tuning page on the wiki vs. NAMD/CUDA Dow_Hurst (Wed May 20 2009 - 18:09:21 CDT)
tmao molecule Vasudevan V (Wed May 20 2009 - 09:43:40 CDT)
- Re: tmao molecule Peter Freddolino (Wed May 20 2009 - 09:51:43 CDT)
  - Re: tmao molecule Peter Freddolino (Wed May 20 2009 - 10:13:29 CDT)
    - Re: tmao molecule Vasudevan V (Wed May 20 2009 - 10:19:45 CDT)
Free energy of conformational change Branko (Wed May 20 2009 - 06:15:57 CDT)
- Re: Free energy of conformational change Giacomo Fiorin (Wed May 20 2009 - 11:22:38 CDT)
NAMD 2.7b1 running problem ÖÜÎÄ²ý (Wed May 20 2009 - 05:19:19 CDT)
- Re: NAMD 2.7b1 running problem Peter Freddolino (Wed May 20 2009 - 06:52:58 CDT)
calculating forces from dcd trajectory BIN ZHANG (Wed May 20 2009 - 02:18:26 CDT)
- Re: calculating forces from dcd trajectory Peter Freddolino (Wed May 20 2009 - 06:51:11 CDT)
  - Re: calculating forces from dcd trajectory BIN ZHANG (Wed May 20 2009 - 12:18:20 CDT)
namd-openmosix jose correa (Tue May 19 2009 - 07:29:49 CDT)
- Re: namd-openmosix Axel Kohlmeyer (Tue May 19 2009 - 09:55:57 CDT)
  - Re: namd-openmosix Nicholas M Glykos (Tue May 19 2009 - 11:19:51 CDT)
REMD on AIX5.3 Florian Janetzko (Tue May 19 2009 - 06:44:34 CDT)
How to minimize our model by SD using namd Ahmad Firoz (Tue May 19 2009 - 00:33:01 CDT)
Periodic Forcing Functions Rick Calloway (Mon May 18 2009 - 16:50:42 CDT)
NAMD infiniband performance Guanglei Cui (Mon May 18 2009 - 16:10:55 CDT)
- Re: NAMD infiniband performance Lev Lafayette (Tue May 19 2009 - 01:31:47 CDT)
  - Re: NAMD infiniband performance Guanglei Cui (Tue May 19 2009 - 08:56:00 CDT)
about limitdist cong chen (Mon May 18 2009 - 06:11:48 CDT)
- ERROR: Constraint failure in RATTLE algorithm for atom 1880! jinhyo_at_comcast.net (Mon May 18 2009 - 11:19:04 CDT)
Error running NAMD on CUDA jani sahil (Mon May 18 2009 - 03:34:11 CDT)
- Re: Error running NAMD on CUDA Axel Kohlmeyer (Mon May 18 2009 - 08:44:05 CDT)
the external electric field vector uu zhu (Mon May 18 2009 - 01:56:29 CDT)
exclude 1-2 doty alexiou (Fri May 15 2009 - 01:55:09 CDT)
- Re: exclude 1-2 Peter Freddolino (Fri May 15 2009 - 06:55:37 CDT)
charm++ build problem Yogesh (Thu May 14 2009 - 08:24:42 CDT)
TMD biasing Felipe Merino (Thu May 14 2009 - 06:23:23 CDT)
- Re: TMD biasing Felipe Merino (Thu May 14 2009 - 07:55:55 CDT)
peptides on surface Jorgen Simonsen (Wed May 13 2009 - 13:16:51 CDT)
- RE: peptides on surface Brian R Novak (Wed May 13 2009 - 15:25:19 CDT)
  - RE: peptides on surface Axel Kohlmeyer (Wed May 13 2009 - 16:29:23 CDT)
- Re: peptides on surface Eduardo Cruz-Chu (Wed May 13 2009 - 17:02:19 CDT)
  - Re: peptides on surface Roman Petrenko (Wed May 13 2009 - 17:30:00 CDT)
Need help to generate ubq-get-energy.conf Mert Gür (Wed May 13 2009 - 10:06:55 CDT)
- Re: Need help to generate ubq-get-energy.conf Peter Freddolino (Wed May 13 2009 - 12:03:55 CDT)
  - Re: Need help to generate ubq-get-energy.conf Mert Gür (Wed May 13 2009 - 15:49:24 CDT)
Make NAMD2.7b1 with cuda bug? Lev Lafayette (Tue May 12 2009 - 22:48:04 CDT)
- Re: Make NAMD2.7b1 with cuda bug? Roman Petrenko (Wed May 13 2009 - 08:56:02 CDT)
changing protonation states for a pdb with more than a single polypeptide Elia Zomot (Tue May 12 2009 - 18:47:41 CDT)
PSF file KIRTANA S (Tue May 12 2009 - 14:29:05 CDT)
exclude 1-2 or 1-4? doty alexiou (Tue May 12 2009 - 09:56:31 CDT)
- Re: exclude 1-2 or 1-4? Peter Freddolino (Tue May 12 2009 - 10:07:42 CDT)
Which compiler-suite was used... Bjoern Olausson (Tue May 12 2009 - 07:26:00 CDT)
Asymmetric water molecule found Jorgen Simonsen (Tue May 12 2009 - 05:00:45 CDT)
- Re: Asymmetric water molecule found Peter Freddolino (Tue May 12 2009 - 06:45:32 CDT)
namd-cuda-intel vs. namd-intel Roman Petrenko (Tue May 12 2009 - 00:32:58 CDT)
- Re: namd-cuda-intel vs. namd-intel Axel Kohlmeyer (Tue May 12 2009 - 06:24:04 CDT)
Calculating displacement in a system with periodic boundary Fred (Rui FENG) (Mon May 11 2009 - 23:26:21 CDT)
- Re: Calculating displacement in a system with periodic boundary Joshua Adelman (Mon May 11 2009 - 23:44:23 CDT)
- Re: Calculating displacement in a system with periodic boundary Eric H. Lee (Mon May 11 2009 - 23:49:25 CDT)
  - Re: Calculating displacement in a system with periodic boundary Fred (Rui FENG) (Tue May 12 2009 - 01:07:22 CDT)
FEP on 2.7b1 Christopher Hartshorn (Mon May 11 2009 - 15:38:37 CDT)
- collective variable space PMF, including biasing potential terms? Sebastian Stolzenberg (Wed May 13 2009 - 14:48:05 CDT)
  - Re: collective variable space PMF, including biasing potential terms? Jerome Henin (Wed May 13 2009 - 16:23:49 CDT)
  - Re: collective variable space PMF, including biasing potential terms? Giacomo Fiorin (Wed May 13 2009 - 16:38:56 CDT)
SiCortex with Pathscale Christopher Hartshorn (Sat May 09 2009 - 19:52:29 CDT)
- Re: SiCortex with Pathscale Peter Freddolino (Mon May 11 2009 - 12:02:14 CDT)
ERROR: Multiple definitions of 'LangevinPiston' roberta.rostagno (Mon May 11 2009 - 07:15:42 CDT)
ERROR: Multiple definitions of 'LangevinPiston' roberta.rostagno (Mon May 11 2009 - 07:38:38 CDT)
- Re: ERROR: Multiple definitions of 'LangevinPiston' Peter Freddolino (Mon May 11 2009 - 08:09:40 CDT)
  - Re: ERROR: Multiple definitions of 'LangevinPiston' roberta.rostagno (Mon May 11 2009 - 08:20:29 CDT)
lipid bi-layer and SiO2 Raul Araya (Fri May 08 2009 - 14:36:41 CDT)
- Re: lipid bi-layer and SiO2 Eduardo (Fri May 08 2009 - 14:49:32 CDT)
NAMD with CUDA Prakash Velayutham (Thu May 07 2009 - 13:06:04 CDT)
- Re: NAMD with CUDA Prakash Velayutham (Mon May 11 2009 - 11:46:13 CDT)
HW - HW IN PARAMETER FILES Jorgen Simonsen (Thu May 07 2009 - 06:17:19 CDT)
- Re: HW - HW IN PARAMETER FILES Axel Kohlmeyer (Thu May 07 2009 - 07:47:07 CDT)
water models and some questions fett_at_vtr.net (Thu May 07 2009 - 06:02:39 CDT)
- Re: water models and some questions Peter Freddolino (Thu May 07 2009 - 11:57:51 CDT)
  - Re: water models and some questions David Hardy (Thu May 07 2009 - 13:54:09 CDT)
    - Re: water models and some questions fett_at_vtr.net (Fri May 08 2009 - 09:45:02 CDT)
running namd2.7 problem ydhuang2727 (Thu May 07 2009 - 01:23:46 CDT)
- Re: running namd2.7 problem Chris Harrison (Thu May 07 2009 - 07:16:44 CDT)
force-field for cy3, cy5 dyes Roman Petrenko (Wed May 06 2009 - 19:26:54 CDT)
(no subject) Wang,Ying (Wed May 06 2009 - 13:50:12 CDT)
diffusion / fex peptide problem Benjamin Stauch (Wed May 06 2009 - 10:24:16 CDT)
- Re: diffusion / fex peptide problem Roman Petrenko (Wed May 06 2009 - 12:33:49 CDT)
fatal error: tried to assign bond index before all parameter files were read Jorgen Simonsen (Wed May 06 2009 - 05:36:16 CDT)
umbrella sampling script Hyundeok Song (Tue May 05 2009 - 17:30:28 CDT)
Langevin damping coefficient Gianluca Interlandi (Tue May 05 2009 - 16:49:30 CDT)
- Re: Langevin damping coefficient Anton Arkhipov (Wed May 06 2009 - 10:25:49 CDT)
  - Re: Langevin damping coefficient Gianluca Interlandi (Wed May 06 2009 - 11:04:21 CDT)
    - Re: Langevin damping coefficient Anton Arkhipov (Wed May 06 2009 - 11:13:13 CDT)
Postdoc position in computational biophysics and nanotechnology Aleksei Aksimentiev (Tue May 05 2009 - 14:34:04 CDT)
Re: Value for "firsttimestep" when restarting MD Bjoern Olausson (Tue May 05 2009 - 12:45:56 CDT)
- Re: Value for "firsttimestep" when restarting MD Bjoern Olausson (Thu Jul 02 2009 - 04:05:23 CDT)
Value for "firsttimestep" when restarting MD Bjoern Olausson (Tue May 05 2009 - 09:50:42 CDT)
regarding simulation prasun kumar (Tue May 05 2009 - 08:48:00 CDT)
- Re: regarding simulation Peter Freddolino (Tue May 05 2009 - 10:16:04 CDT)
  - Re: regarding simulation Peter Freddolino (Tue May 05 2009 - 10:22:25 CDT)
DCOLVARS_DEBUG George Madalin Giambasu (Mon May 04 2009 - 22:49:17 CDT)
- Re: DCOLVARS_DEBUG Jerome Henin (Tue May 05 2009 - 10:00:09 CDT)
  - Re: DCOLVARS_DEBUG George Madalin Giambasu (Tue May 05 2009 - 10:17:43 CDT)
    - Re: DCOLVARS_DEBUG Giacomo Fiorin (Tue May 05 2009 - 13:53:18 CDT)
- Re: DCOLVARS_DEBUG Giacomo Fiorin (Tue May 05 2009 - 10:23:33 CDT)
  - Re: DCOLVARS_DEBUG George Madalin Giambasu (Tue May 05 2009 - 15:29:43 CDT)
truncated octahedral daniel aguayo (Mon May 04 2009 - 20:21:37 CDT)
- Re: truncated octahedral Nicholas M Glykos (Tue May 05 2009 - 05:18:15 CDT)
  - Re: truncated octahedral daniel aguayo (Tue May 05 2009 - 10:16:12 CDT)
geomtery optimization with namd Roman Petrenko (Mon May 04 2009 - 16:18:03 CDT)
dummy atom mass changed yun luo (Mon May 04 2009 - 14:54:27 CDT)
- Re: dummy atom mass changed Chris Harrison (Mon May 04 2009 - 15:33:57 CDT)
  - Re: dummy atom mass changed yun luo (Mon May 04 2009 - 16:24:59 CDT)
Regarding amber parameters using NAMD Jorgen Simonsen (Mon May 04 2009 - 03:22:27 CDT)
- Re: Regarding amber parameters using NAMD Joshua Adelman (Mon May 04 2009 - 10:41:52 CDT)
  - Re: Regarding amber parameters using NAMD Joshua Adelman (Tue May 05 2009 - 10:44:55 CDT)
NAMD 2.7b1 and clustermatic Gianluca Interlandi (Sun May 03 2009 - 19:26:08 CDT)
NPAT - NPgT ensemble Bjoern Olausson (Sat May 02 2009 - 07:43:34 CDT)
- Re: NPAT - NPgT ensemble Peter Freddolino (Sat May 02 2009 - 20:18:46 CDT)
  - Re: NPAT - NPgT ensemble Bjoern Olausson (Sun May 03 2009 - 15:54:27 CDT)
CGMD ? Hydrophobic scale BIN ZHANG (Fri May 01 2009 - 17:00:12 CDT)
- Re: CGMD ? Hydrophobic scale Peter Freddolino (Fri May 01 2009 - 22:18:00 CDT)
Force Fields Goutham (Fri May 01 2009 - 00:36:09 CDT)
FreeEnergy and minimization Roman Petrenko (Thu Apr 30 2009 - 23:31:55 CDT)
crash with more than 96 processors (v2.7b1) Grace Brannigan (Thu Apr 30 2009 - 14:49:58 CDT)
- Re: crash with more than 96 processors (v2.7b1) Chris Harrison (Thu Apr 30 2009 - 19:41:55 CDT)
  - Re: crash with more than 96 processors (v2.7b1) Grace Brannigan (Fri May 01 2009 - 09:48:09 CDT)
    - Re: crash with more than 96 processors (v2.7b1) George Madalin Giambasu (Fri May 01 2009 - 10:28:50 CDT)
    - Re: crash with more than 96 processors (v2.7b1) Grace Brannigan (Fri May 01 2009 - 16:36:11 CDT)
  - Re: crash with more than 96 processors (v2.7b1) Grace Brannigan (Fri May 01 2009 - 09:58:56 CDT)
Setting PME Grid DimitryASuplatov (Thu Apr 30 2009 - 11:13:46 CDT)
- Re: Setting PME Grid Gianluca Interlandi (Thu Apr 30 2009 - 12:52:09 CDT)
- Re: Setting PME Grid Giacomo Fiorin (Thu Apr 30 2009 - 14:00:10 CDT)
two independent groups of constraints Marcin Krol (Thu Apr 30 2009 - 07:44:41 CDT)
- Re: two independent groups of constraints Axel Kohlmeyer (Thu Apr 30 2009 - 08:14:01 CDT)
- Re: two independent groups of constraints Eduardo Cruz-Chu (Thu Apr 30 2009 - 13:54:18 CDT)
Energy minimization failure DimitryASuplatov (Thu Apr 30 2009 - 05:23:31 CDT)
running problem ydhuang2727 (Thu Apr 30 2009 - 05:08:22 CDT)
- Re: running problem Axel Kohlmeyer (Thu Apr 30 2009 - 06:08:00 CDT)
NAMD 2.7b1 on NCSA Abe Gianluca Interlandi (Wed Apr 29 2009 - 22:16:32 CDT)
- Re: NAMD 2.7b1 on NCSA Abe Peter Freddolino (Thu Apr 30 2009 - 06:41:50 CDT)
  - Re: NAMD 2.7b1 on NCSA Abe Gianluca Interlandi (Thu Apr 30 2009 - 12:15:37 CDT)
Benzene PSF Matt Krems (Wed Apr 29 2009 - 19:04:27 CDT)
- Re: Benzene PSF Chris Harrison (Wed Apr 29 2009 - 19:29:25 CDT)
  - Re: Benzene PSF Jerome Henin (Thu Apr 30 2009 - 11:22:01 CDT)
protein shifts out of the water box Eric Userlist (Wed Apr 29 2009 - 18:52:16 CDT)
- Re: protein shifts out of the water box Axel Kohlmeyer (Wed Apr 29 2009 - 19:14:18 CDT)
  - Re: protein shifts out of the water box Rabab Toubar (Wed Apr 29 2009 - 20:59:41 CDT)
- Re: protein shifts out of the water box Joshua Adelman (Wed Apr 29 2009 - 19:07:05 CDT)
FEP tutorial graph question Christopher Hartshorn (Wed Apr 29 2009 - 15:35:27 CDT)
- Re: FEP tutorial graph question Chris Harrison (Wed Apr 29 2009 - 16:17:07 CDT)
  - Re: FEP tutorial graph question Christopher Hartshorn (Wed Apr 29 2009 - 19:52:28 CDT)
    - Re: FEP tutorial graph question Chris Harrison (Thu Apr 30 2009 - 10:23:25 CDT)
  - Re: FEP tutorial graph question Christopher Hartshorn (Fri May 01 2009 - 12:05:21 CDT)
    - Re: FEP tutorial graph question Jerome Henin (Fri May 01 2009 - 14:28:24 CDT)
- Re: FEP tutorial graph question Jerome Henin (Wed Apr 29 2009 - 18:36:35 CDT)
cell on namd 2.7b1 alessandro.venturelli_at_univr.it (Wed Apr 29 2009 - 08:10:01 CDT)
- Re: cell on namd 2.7b1 Axel Kohlmeyer (Wed Apr 29 2009 - 08:34:08 CDT)
water tail correction Floris Buelens (Wed Apr 29 2009 - 05:51:55 CDT)
- Re: water tail correction Peter Freddolino (Wed Apr 29 2009 - 07:09:45 CDT)
  - Re: water tail correction Floris Buelens (Thu May 28 2009 - 17:52:51 CDT)
- Re: water tail correction Peter Freddolino (Wed Apr 29 2009 - 10:26:24 CDT)
  - Re: water tail correction Floris Buelens (Fri May 22 2009 - 05:40:00 CDT)
how to set initial velocity? uu zhu (Tue Apr 28 2009 - 21:27:37 CDT)
- Re: how to set initial velocity? Joshua Adelman (Tue Apr 28 2009 - 21:59:21 CDT)
  - Re: how to set initial velocity? uu zhu (Wed Apr 29 2009 - 01:58:13 CDT)
    - Re: how to set initial velocity? Joshua Adelman (Wed Apr 29 2009 - 15:09:34 CDT)
force-field for ATP Roman Petrenko (Tue Apr 28 2009 - 18:55:05 CDT)
- Re: force-field for ATP Roman Petrenko (Tue Apr 28 2009 - 19:20:57 CDT)
- Re: force-field for ATP gaillard_at_chimie.u-strasbg.fr (Tue Apr 28 2009 - 19:41:13 CDT)
- Re: force-field for ATP Leandro Martínez (Tue Apr 28 2009 - 20:05:54 CDT)
System expands: CCL4 simulation; NPT(Langevin Piston) satya work (Tue Apr 28 2009 - 16:10:32 CDT)
- Re: System expands: CCL4 simulation; NPT(Langevin Piston) Chris Harrison (Tue Apr 28 2009 - 16:56:35 CDT)
  - Re: System expands: CCL4 simulation; NPT(Langevin Piston) satya work (Tue Apr 28 2009 - 23:44:02 CDT)
crash with more than 96 processors (v2.7b1) Grace Brannigan (Tue Apr 28 2009 - 14:16:07 CDT)
- Re: crash with more than 96 processors (v2.7b1) Chris Harrison (Tue Apr 28 2009 - 16:50:57 CDT)
  - Re: crash with more than 96 processors (v2.7b1) Grace Brannigan (Tue Apr 28 2009 - 17:36:23 CDT)
    - Re: crash with more than 96 processors (v2.7b1) Chris Harrison (Tue Apr 28 2009 - 18:30:16 CDT)
biotin parameters and topology Brian R Novak (Tue Apr 28 2009 - 12:37:53 CDT)
- Re: biotin parameters and topology Peter Freddolino (Tue Apr 28 2009 - 15:13:08 CDT)
  - RE: biotin parameters and topology Brian R Novak (Tue Apr 28 2009 - 15:43:15 CDT)
+1 offset to VMD index file? DimitryASuplatov (Tue Apr 28 2009 - 08:40:33 CDT)
- Re: +1 offset to VMD index file? Jerome Henin (Tue Apr 28 2009 - 11:13:38 CDT)
- Re: +1 offset to VMD index file? Giacomo Fiorin (Tue Apr 28 2009 - 11:19:58 CDT)
Optimizing configuration option for fast calculations DimitryASuplatov (Tue Apr 28 2009 - 07:16:00 CDT)
- Re: Optimizing configuration option for fast calculations bo liu (Thu Apr 30 2009 - 12:12:59 CDT)
  - Re: Optimizing configuration option for fast calculations DimitryASuplatov (Thu Apr 30 2009 - 14:17:03 CDT)
Adding a new bond to CHARMM DimitryASuplatov (Sat Apr 25 2009 - 08:23:19 CDT)
- Re: Adding a new bond to CHARMM DimitryASuplatov (Sat Apr 25 2009 - 08:56:05 CDT)
Yet another NAMD speed concerns DimitryASuplatov (Sat Apr 25 2009 - 04:44:44 CDT)
- Re: Yet another NAMD speed concerns Axel Kohlmeyer (Sat Apr 25 2009 - 09:10:14 CDT)
- Re: Yet another NAMD speed concerns Gianluca Interlandi (Sat Apr 25 2009 - 11:43:40 CDT)
  - Re: Yet another NAMD speed concerns Gianluca Interlandi (Sat Apr 25 2009 - 12:05:17 CDT)
  - Re: Yet another NAMD speed concerns David Hardy (Sat Apr 25 2009 - 12:28:46 CDT)
compile NAMD 2.7b1 on Intel Xeon(R) infiniband cluster æµ·æ¸… æ¢ (Sat Apr 25 2009 - 01:44:24 CDT)
- Re: compile NAMD 2.7b1 on Intel Xeon(R) infiniband cluster DimitryASuplatov (Sat Apr 25 2009 - 03:51:27 CDT)
  - Re: compile NAMD 2.7b1 on Intel Xeon(R) infiniband cluster Axel Kohlmeyer (Sat Apr 25 2009 - 09:01:24 CDT)
Copper parameters for CHARMM DimitryASuplatov (Fri Apr 24 2009 - 11:02:50 CDT)
- Re: Copper parameters for CHARMM Axel Kohlmeyer (Fri Apr 24 2009 - 11:37:09 CDT)
how to install NAMD on suse10_ppc64 without xlc bay__gulf618_at_sina.com (Fri Apr 24 2009 - 05:18:04 CDT)
Namd and MM-PBSA Esteban Gabriel Vega Hissi (Thu Apr 23 2009 - 10:42:49 CDT)
- Re: Namd and MM-PBSA Chris Harrison (Thu Apr 23 2009 - 12:22:34 CDT)
- Re: Namd and MM-PBSA JT (Thu Apr 23 2009 - 12:43:17 CDT)
- Re: Namd and MM-PBSA Giacomo Fiorin (Thu Apr 23 2009 - 13:28:20 CDT)
unsubscribe Matthew Ambrosia (Thu Apr 23 2009 - 09:08:56 CDT)
Compile Problem xiaojing gong (Thu Apr 23 2009 - 07:42:51 CDT)
lipidmonolayer balaji nagarajan (Wed Apr 22 2009 - 14:58:25 CDT)
- Re: lipidmonolayer Eduardo (Wed Apr 22 2009 - 22:23:46 CDT)
mapping of force vectors during SMD Jeff Forbes (Wed Apr 22 2009 - 13:42:23 CDT)
structure problem Ahlam Al-Rawi (Wed Apr 22 2009 - 12:22:29 CDT)
Constraints in NAMD DimitryASuplatov (Wed Apr 22 2009 - 09:50:37 CDT)
- Re: Constraints in NAMD Jerome Henin (Wed Apr 22 2009 - 10:30:44 CDT)
- Re: Constraints in NAMD Joshua Adelman (Wed Apr 22 2009 - 10:37:39 CDT)
FATAL ERROR: Periodic cell has become too small for original patch grid! DimitryASuplatov (Wed Apr 22 2009 - 01:44:45 CDT)
- Re: FATAL ERROR: Periodic cell has become too small for original patch grid! Peter Freddolino (Wed Apr 22 2009 - 09:27:37 CDT)
- Re: FATAL ERROR: Periodic cell has become too small for original patch grid! Jerome Henin (Wed Apr 22 2009 - 10:11:15 CDT)
VDW distance in energy minimized conformation Lixia Jin Day (Tue Apr 21 2009 - 17:11:42 CDT)
can I change coordinate before restart? Mark M Huntress (Tue Apr 21 2009 - 16:03:55 CDT)
- Re: can I change coordinate before restart? Joshua Adelman (Tue Apr 21 2009 - 20:50:47 CDT)
  - Re: can I change coordinate before restart? Joshua Adelman (Wed Apr 22 2009 - 15:11:55 CDT)
2.7b1 + CUDA + STMV Charles Taylor (Tue Apr 21 2009 - 09:25:44 CDT)
- Re: 2.7b1 + CUDA + STMV Peter Freddolino (Tue Apr 21 2009 - 09:41:56 CDT)
tip4p on namd 2.7b fett_at_vtr.net (Tue Apr 21 2009 - 07:45:40 CDT)
- Re: tip4p on namd 2.7b Peter Freddolino (Tue Apr 21 2009 - 09:36:39 CDT)
  - Re: tip4p on namd 2.7b Guanglei Cui (Wed Apr 22 2009 - 10:52:19 CDT)
Parallel TMD (2.7b) dies : "MPICH internal error" Ali Emileh (Mon Apr 20 2009 - 11:00:11 CDT)
Re: compiling error of NAMD2.7b1 Joachim Hein (Mon Apr 20 2009 - 06:05:38 CDT)
- Re: compiling error of NAMD2.7b1 BIN ZHANG (Mon Apr 20 2009 - 12:30:17 CDT)
  - Re: compiling error of NAMD2.7b1 Peter Freddolino (Mon Apr 20 2009 - 13:12:01 CDT)
  - Re: compiling error of NAMD2.7b1 Joachim Hein (Mon Apr 20 2009 - 12:53:59 CDT)
Peptide in Membrane Environment: loosing water from one leaflet Praveen Agrawal (Mon Apr 20 2009 - 05:53:23 CDT)
- Re: Peptide in Membrane Environment: loosing water from one leaflet bo liu (Mon Apr 20 2009 - 08:35:33 CDT)
Metadynamics in NAMD ÖÜÎÄ²ý (Mon Apr 20 2009 - 05:50:42 CDT)
- Re: Metadynamics in NAMD Giacomo Fiorin (Mon Apr 20 2009 - 12:21:46 CDT)
Cylindrical harmonic BC and constraintScaling Elsa Fernanda de Sousa Henriques (Mon Apr 20 2009 - 05:22:25 CDT)
- Re: Cylindrical harmonic BC and constraintScaling Elsa Fernanda de Sousa Henriques (Mon Apr 20 2009 - 08:25:20 CDT)
Pressure coupling and system heating DimitryASuplatov (Mon Apr 20 2009 - 03:38:36 CDT)
NAMD and new sugar parameter set Gianluca Interlandi (Mon Apr 20 2009 - 00:42:14 CDT)
- Re: NAMD and new sugar parameter set Rogan Carr (Mon Apr 20 2009 - 14:17:06 CDT)
  - Re: NAMD and new sugar parameter set Gianluca Interlandi (Mon Apr 20 2009 - 15:39:31 CDT)
    - Re: NAMD and new sugar parameter set Rogan Carr (Mon Apr 20 2009 - 18:43:58 CDT)
I can't keep my pulling directions the same with the SMD vector Mert Gür (Sun Apr 19 2009 - 07:56:00 CDT)
- Re: I can't keep my pulling directions the same with the SMD vector Chris Harrison (Sun Apr 19 2009 - 10:25:14 CDT)
  - Re: I can't keep my pulling directions the same with the SMD vector Mert Gür (Sun Apr 19 2009 - 11:10:11 CDT)
compiling error of NAMD2.7b1 zhngbn_at_gmail.com (Sun Apr 19 2009 - 03:02:44 CDT)
restart REMD simulation Segun Jung (Sat Apr 18 2009 - 21:32:55 CDT)
cvs logs BIN ZHANG (Fri Apr 17 2009 - 13:53:54 CDT)
RE: display all frames simultaneously Luis Gracia (Fri Apr 17 2009 - 00:35:29 CDT)
Speeding up: Dummy constructions for aromatics or hydrogens DimitryASuplatov (Fri Apr 17 2009 - 12:11:27 CDT)
- Re: Speeding up: Dummy constructions for aromatics or hydrogens Axel Kohlmeyer (Fri Apr 17 2009 - 15:22:04 CDT)
  - Re: Speeding up: Dummy constructions for aromatics or hydrogens DimitryASuplatov (Fri Apr 17 2009 - 15:50:03 CDT)
    - Re: Speeding up: Dummy constructions for aromatics or hydrogens Axel Kohlmeyer (Fri Apr 17 2009 - 16:05:34 CDT)
NAMD 2.7b1 on Ranger/MPI Problems? Jeff Wereszczynski (Fri Apr 17 2009 - 00:56:30 CDT)
- Re: NAMD 2.7b1 on Ranger/MPI Problems? Haosheng Cui (Fri Apr 17 2009 - 02:12:54 CDT)
  - Re: NAMD 2.7b1 on Ranger/MPI Problems? Jeff Wereszczynski (Fri Apr 17 2009 - 16:59:42 CDT)
    - Re: NAMD 2.7b1 on Ranger/MPI Problems? Lei Shi (Mon Apr 20 2009 - 15:04:00 CDT)
    - Re: NAMD 2.7b1 on Ranger/MPI Problems? Jeff Wereszczynski (Mon Apr 20 2009 - 15:56:18 CDT)
display all frames simultaneously Samuel Coulbourn Flores èŠ±å±± (Thu Apr 16 2009 - 21:35:59 CDT)
- Re: display all frames simultaneously gaillard_at_chimie.u-strasbg.fr (Thu Apr 16 2009 - 22:20:37 CDT)
- Re: display all frames simultaneously uu zhu (Thu Apr 16 2009 - 22:16:52 CDT)
- Re: vmd-l: display all frames simultaneously Peter Freddolino (Thu Apr 16 2009 - 22:32:26 CDT)
How to set the parameters for C60? uu zhu (Thu Apr 16 2009 - 05:06:37 CDT)
Dihedral Restraints during MD simulation Matthieu Wilhelm (Wed Apr 15 2009 - 12:33:04 CDT)
- Re: Dihedral Restraints during MD simulation Sebastian Stolzenberg (Wed Apr 15 2009 - 13:18:47 CDT)
  - Re: Dihedral Restraints during MD simulation Jerome Henin (Wed Apr 15 2009 - 13:49:29 CDT)
  - Re: Dihedral Restraints during MD simulation Matthieu Wilhelm (Thu Apr 16 2009 - 03:56:59 CDT)
- Re: Dihedral Restraints during MD simulation Leonardo Trabuco (Wed Apr 15 2009 - 13:43:18 CDT)
  - Re: Dihedral Restraints during MD simulation Leonardo Trabuco (Wed Apr 15 2009 - 14:03:22 CDT)
NAMD 1.7b1 quits writing files/hangs Jason Russler (Wed Apr 15 2009 - 08:00:49 CDT)
elastic network BIN ZHANG (Tue Apr 14 2009 - 18:10:37 CDT)
How can I fix lipid lateral area in membrane simulation? Leonardo Herrera (Tue Apr 14 2009 - 12:39:38 CDT)
4 sequential jobs work on laptops, but only first one works on supercomputer JT (Mon Apr 13 2009 - 18:00:49 CDT)
- Re: 4 sequential jobs work on laptops, but only first one works on supercomputer JT (Mon Apr 13 2009 - 21:59:23 CDT)
  - Re: 4 sequential jobs work on laptops, but only first one works on supercomputer JT (Mon Apr 13 2009 - 22:02:54 CDT)
    - Re: 4 sequential jobs work on laptops, but only first one works on supercomputer JT (Mon Apr 13 2009 - 23:12:06 CDT)
    - Re: 4 sequential jobs work on laptops, but only first one works on supercomputer JT (Tue Apr 14 2009 - 01:24:25 CDT)
Selectively write atoms to dcd files DimitryASuplatov (Mon Apr 13 2009 - 12:20:01 CDT)
- Re: Selectively write atoms to dcd files Joshua Adelman (Mon Apr 13 2009 - 12:32:52 CDT)
- Re: Selectively write atoms to dcd files jose correa (Mon Apr 13 2009 - 13:10:55 CDT)
Water is boiling with namd and charmm DimitryASuplatov (Mon Apr 13 2009 - 09:27:54 CDT)
- Re: Water is boiling with namd and charmm Roman Petrenko (Mon Apr 13 2009 - 10:25:43 CDT)
  - Re: Water is boiling with namd and charmm Joshua Adelman (Mon Apr 13 2009 - 10:50:31 CDT)
- Re: Water is boiling with namd and charmm Giovanni Bellesia (Mon Apr 13 2009 - 11:42:38 CDT)
Fwd: psf file creation gurunath katagi (Sun Apr 12 2009 - 19:43:48 CDT)
Error : DIDN'T FIND vdW PARAMETER FOR ATOM TYPE C11 Goutham (Sat Apr 11 2009 - 00:54:22 CDT)
- Re: Error : DIDN'T FIND vdW PARAMETER FOR ATOM TYPE C11 Chris Harrison (Sat Apr 11 2009 - 10:20:44 CDT)
Keyword to start FEP calculation in NAMD 2.7b1 govardhan reddy (Fri Apr 10 2009 - 15:22:30 CDT)
- Re: Keyword to start FEP calculation in NAMD 2.7b1 Chris Harrison (Fri Apr 10 2009 - 15:41:05 CDT)
PCA Analysis of CGMD Anirban Ghosh (Thu Apr 09 2009 - 07:23:04 CDT)
- Re: PCA Analysis of CGMD Joshua Adelman (Thu Apr 09 2009 - 10:28:06 CDT)
  - RE: PCA Analysis of CGMD Anirban Ghosh (Fri Apr 10 2009 - 04:08:25 CDT)
soft-core potential for FEP felmerino_at_uchile.cl (Wed Apr 08 2009 - 17:46:33 CDT)
TMD RMSD problem Elif Ozkirimli (Wed Apr 08 2009 - 15:21:16 CDT)
- Re: TMD RMSD problem Joshua Adelman (Wed Apr 08 2009 - 15:35:12 CDT)
  - Re: TMD RMSD problem Elif Ozkirimli (Thu Apr 09 2009 - 11:24:21 CDT)
    - Re: TMD RMSD problem Ali Emileh (Fri Apr 10 2009 - 13:27:40 CDT)
    - Re: TMD RMSD problem Elif Ozkirimli (Fri Apr 10 2009 - 15:50:50 CDT)
Evaluating kinetic energy from a modified DCD file Mert Gür (Wed Apr 08 2009 - 14:33:05 CDT)
- Re: Evaluating kinetic energy from a modified DCD file Peter Freddolino (Wed Apr 08 2009 - 15:15:00 CDT)
  - Re: Evaluating kinetic energy from a modified DCD file Mert Gür (Wed Apr 08 2009 - 16:57:01 CDT)
  - Re: Evaluating kinetic energy from a modified DCD file JT (Fri Apr 10 2009 - 11:36:52 CDT)
problem namd2-MPICH jose correa (Wed Apr 08 2009 - 14:05:09 CDT)
- Re: problem namd2-MPICH jose correa (Mon Jun 08 2009 - 07:34:53 CDT)
  - Re: Re: problem namd2-MPICH sudipta (Mon Jun 08 2009 - 08:14:06 CDT)
Compiling NAMD on Ranger shayan_at_msu.edu (Wed Apr 08 2009 - 07:33:26 CDT)
- Re: Compiling NAMD on Ranger Axel Kohlmeyer (Wed Apr 08 2009 - 08:15:51 CDT)
  - Re: Compiling NAMD on Ranger shayan_at_msu.edu (Wed Apr 08 2009 - 10:09:11 CDT)
    - Re: Compiling NAMD on Ranger Peter Freddolino (Wed Apr 08 2009 - 10:16:36 CDT)
    - Re: Compiling NAMD on Ranger shayan_at_msu.edu (Wed Apr 08 2009 - 12:51:26 CDT)
erergy gradient tolerance in Configuration Files uu zhu (Wed Apr 08 2009 - 05:55:49 CDT)
- Re: erergy gradient tolerance in Configuration Files Jim Phillips (Wed Apr 08 2009 - 13:51:15 CDT)
constraints dota (Wed Apr 08 2009 - 04:23:40 CDT)
Writing 3 subsequent timesteps to the DCD file Mert Gür (Tue Apr 07 2009 - 06:24:18 CDT)
- Re: Writing 3 subsequent timesteps to the DCD file Axel Kohlmeyer (Tue Apr 07 2009 - 07:45:54 CDT)
  - Re: Writing 3 subsequent timesteps to the DCD file Goutham (Tue Apr 07 2009 - 14:29:16 CDT)
    - Re: Writing 3 subsequent timesteps to the DCD file JT (Tue Apr 07 2009 - 18:53:38 CDT)
    - Re: Writing 3 subsequent timesteps to the DCD file Axel Kohlmeyer (Tue Apr 07 2009 - 19:45:45 CDT)
- Re: Writing 3 subsequent timesteps to the DCD file Mert Gür (Wed Apr 08 2009 - 04:44:09 CDT)
  - Re: Writing 3 subsequent timesteps to the DCD file Axel Kohlmeyer (Wed Apr 08 2009 - 08:23:26 CDT)
outputname and restartname Neelanjana Sengupta (Tue Apr 07 2009 - 01:45:19 CDT)
- Re: outputname and restartname Peter Freddolino (Tue Apr 07 2009 - 06:12:59 CDT)
  - Re: outputname and restartname Neelanjana Sengupta (Tue Apr 07 2009 - 07:45:07 CDT)
NAMD job dies on 2-quad core server vivek.viv.sharma_at_gmail.com (Sun Apr 05 2009 - 23:45:28 CDT)
- Re: NAMD job dies on 2-quad core server Axel Kohlmeyer (Mon Apr 06 2009 - 08:44:54 CDT)
  - Re: Re: NAMD job dies on 2-quad core server vivek.viv.sharma_at_gmail.com (Thu Apr 09 2009 - 01:44:01 CDT)
lammps input data file accomp lin (Sun Apr 05 2009 - 21:44:56 CDT)
- Re: lammps input data file Axel Kohlmeyer (Mon Apr 06 2009 - 08:36:26 CDT)
how to install namd in windows xp balaji nagarajan (Sat Apr 04 2009 - 01:11:00 CDT)
- Re: how to install namd in windows xp Eric H. Lee (Sat Apr 04 2009 - 01:29:58 CDT)
Exiting prematurely BIN ZHANG (Fri Apr 03 2009 - 02:22:28 CDT)
- Re: Exiting prematurely Giacomo Fiorin (Fri Apr 03 2009 - 10:21:40 CDT)
  - Re: Exiting prematurely BIN ZHANG (Fri Apr 03 2009 - 11:10:04 CDT)
regarding implicit solvent models ramya narasimhan (Fri Apr 03 2009 - 01:59:57 CDT)
- Re: regarding implicit solvent models JT (Fri Apr 03 2009 - 03:29:16 CDT)
- Re: regarding implicit solvent models Chris Harrison (Sun Apr 05 2009 - 02:57:40 CDT)
psf file creation gurunath katagi (Fri Apr 03 2009 - 00:41:24 CDT)
- Re: psf file creation Peter Freddolino (Fri Apr 03 2009 - 15:55:14 CDT)
Jarzynski equality and the pull direction in SMD Paulo Cesar Telles de Souza (Thu Apr 02 2009 - 19:00:40 CDT)
- Re: Jarzynski equality and the pull direction in SMD Chris Harrison (Sun Apr 05 2009 - 03:09:54 CDT)
NAMD 2.7b1 on Athlon64 Gigabit MPI - Compile Error "src/Settle.C:153: error: ‘_mm_cvtsd_f64’ was not declared in this scope" Greg Guthe (Thu Apr 02 2009 - 18:50:44 CDT)
- Re: NAMD 2.7b1 on Athlon64 Gigabit MPI - Compile Error "src/Settle.C:153: error: ‘_mm_cvtsd_f64’ was not declared in this scope" Peter Freddolino (Thu Apr 02 2009 - 20:39:37 CDT)
  - Re: NAMD 2.7b1 on Athlon64 Gigabit MPI - Compile Error "src/Settle.C:153: error: ‘_mm_cvtsd_f64’ was not declared in this scope" Greg Guthe (Thu Apr 02 2009 - 21:02:44 CDT)
.inter.bin files? Joachim Hein (Thu Apr 02 2009 - 10:24:20 CDT)
- Re: .inter.bin files? Chao Mei (Thu Apr 02 2009 - 13:05:11 CDT)
PSF/top/inp for joint charmm/amber benchmark Andrew Fant (Tue Mar 31 2009 - 17:03:48 CDT)
RAMD in NAMD Vlad Cojocaru (Wed Apr 01 2009 - 03:24:52 CDT)
- Re: RAMD in NAMD harish vashisth (Thu Apr 02 2009 - 17:13:12 CDT)
  - Re: RAMD in NAMD Vlad Cojocaru (Fri Apr 03 2009 - 07:02:15 CDT)
    - Re: RAMD in NAMD harish vashisth (Fri Apr 03 2009 - 07:22:51 CDT)
how to config two different files for fixed atoms karthik s (Tue Mar 31 2009 - 06:54:10 CDT)
smd direction Wang,Ying (Mon Mar 30 2009 - 10:04:28 CDT)
- Re: smd direction Eric H. Lee (Mon Mar 30 2009 - 10:52:05 CDT)
  - Re: smd direction Wang,Ying (Mon Mar 30 2009 - 11:15:06 CDT)
    - Re: smd direction Eric H. Lee (Mon Mar 30 2009 - 11:39:17 CDT)
    - Re: smd direction Leandro Martínez (Mon Mar 30 2009 - 12:59:29 CDT)
NAMD 2.7b1 on Teragrid Ali Emileh (Mon Mar 30 2009 - 09:55:33 CDT)
- Re: NAMD 2.7b1 on Teragrid Jim Phillips (Tue Mar 31 2009 - 15:53:11 CDT)
  - Re: NAMD 2.7b1 on Teragrid Angelo Rossi (Tue Mar 31 2009 - 17:40:36 CDT)
    - Re: NAMD 2.7b1 on Teragrid Jim Phillips (Wed Apr 01 2009 - 14:18:55 CDT)
Pulling atoms in different directions Rahul Bhowmik (Sun Mar 29 2009 - 15:59:01 CDT)
- Re: Pulling atoms in different directions Chris Harrison (Sun Mar 29 2009 - 19:05:33 CDT)
Error generating file.psf for cholesterol, missing coordinates in file.pdb. Leonardo Herrera (Sun Mar 29 2009 - 14:56:20 CDT)
NAMD is too slow?! DimitryASuplatov (Sun Mar 29 2009 - 04:37:39 CDT)
- Re: NAMD is too slow?! Peter Freddolino (Sun Mar 29 2009 - 09:42:38 CDT)
  - Re: NAMD is too slow?! DimitryASuplatov (Sun Mar 29 2009 - 12:23:05 CDT)
    - Re: NAMD is too slow?! Peter Freddolino (Sun Mar 29 2009 - 22:37:16 CDT)
- Re: NAMD is too slow?! Axel Kohlmeyer (Sun Mar 29 2009 - 10:23:44 CDT)
Interactive protonation DimitryASuplatov (Sat Mar 28 2009 - 16:46:51 CDT)
- Re: Interactive protonation Giacomo Fiorin (Sat Mar 28 2009 - 18:48:43 CDT)
  - Re: Interactive protonation Peter Freddolino (Sat Mar 28 2009 - 19:26:51 CDT)
NAMD and CFF forcefields C. Denise Enekwa (Sat Mar 28 2009 - 13:22:36 CDT)
- Re: NAMD and CFF forcefields Axel Kohlmeyer (Sat Mar 28 2009 - 15:20:58 CDT)
modifying a nucleobase jfgaff_at_ncsu.edu (Sat Mar 28 2009 - 09:05:01 CDT)
- Re: modifying a nucleobase Peter Freddolino (Sat Mar 28 2009 - 10:59:48 CDT)
use of tiElecLambdaStart (NAMD 2.7b1) brmorgan_at_clarku.edu (Fri Mar 27 2009 - 11:00:51 CDT)
- Re: use of tiElecLambdaStart (NAMD 2.7b1) Chris Harrison (Fri Mar 27 2009 - 14:33:04 CDT)
NAMD and multi-rail IB for improved latency Dow Hurst (Thu Mar 26 2009 - 21:55:13 CDT)
- Re: NAMD and multi-rail IB for improved latency Dow Hurst (Fri Mar 27 2009 - 00:05:58 CDT)
  - Re: NAMD and multi-rail IB for improved latency Axel Kohlmeyer (Fri Mar 27 2009 - 09:28:40 CDT)
BUILDING BPTI jose correa (Thu Mar 26 2009 - 14:53:43 CDT)
- Re: BUILDING BPTI Jim Phillips (Thu Mar 26 2009 - 16:22:58 CDT)
NAMD 2.7b1 on SGI Altix 330 David McGiven (Thu Mar 26 2009 - 08:50:31 CDT)
- Re: NAMD 2.7b1 on SGI Altix 330 Axel Kohlmeyer (Thu Mar 26 2009 - 10:56:40 CDT)
Free energy of conformational change Lixia Jin Day (Wed Mar 25 2009 - 15:21:19 CDT)
- Re: Free energy of conformational change Chris Harrison (Wed Mar 25 2009 - 17:51:17 CDT)
  - Re: Free energy of conformational change Lixia Jin Day (Wed Mar 25 2009 - 18:04:37 CDT)
  - Re: Free energy of conformational change Branko (Fri May 29 2009 - 06:44:32 CDT)
    - Re: Free energy of conformational change Jerome Henin (Fri May 29 2009 - 11:31:00 CDT)
Scale for Potential Bond Parameter Mohamed Seyam (Wed Mar 25 2009 - 14:32:28 CDT)
- Re: Scale for Potential Bond Parameter Jim Phillips (Wed Mar 25 2009 - 16:39:15 CDT)
MINIMIZER SLOWLY MOVING ATOMS WITH BAD CONTACTS DOWNHILL David Tanner (Wed Mar 25 2009 - 12:47:44 CDT)
- Re: MINIMIZER SLOWLY MOVING ATOMS WITH BAD CONTACTS DOWNHILL Giacomo Fiorin (Wed Mar 25 2009 - 14:18:43 CDT)
  - Re: MINIMIZER SLOWLY MOVING ATOMS WITH BAD CONTACTS DOWNHILL David Tanner (Wed Mar 25 2009 - 14:24:31 CDT)
    - Re: MINIMIZER SLOWLY MOVING ATOMS WITH BAD CONTACTS DOWNHILL Jim Phillips (Thu Mar 26 2009 - 16:51:03 CDT)
TMD on tRNA does not converge Segun Jung (Wed Mar 25 2009 - 11:13:21 CDT)
- Re: TMD on tRNA does not converge Jim Phillips (Wed Mar 25 2009 - 11:16:51 CDT)
Rosetta Academic Training Webinar Nir London (Wed Mar 25 2009 - 11:09:54 CDT)
processor counts FFT and NAMD Bishop, Thomas C (Wed Mar 25 2009 - 10:42:43 CDT)
- Re: processor counts FFT and NAMD Jim Phillips (Wed Mar 25 2009 - 11:13:56 CDT)
NAMD 2.7b1 release Jim Phillips (Wed Mar 25 2009 - 10:16:18 CDT)
phosphoserine simulation using toppar files and NAMD hgrabner (Wed Mar 25 2009 - 06:55:56 CDT)
- Re: phosphoserine simulation using toppar files and NAMD L. Michel Espinoza-Fonseca (Wed Mar 25 2009 - 07:55:45 CDT)
About CUDA version of NAMD 2.7 B1 wang (Wed Mar 25 2009 - 00:57:33 CDT)
- Re: About CUDA version of NAMD 2.7 B1 Jim Phillips (Wed Mar 25 2009 - 08:34:29 CDT)
  - Re: About CUDA version of NAMD 2.7 B1 Dow Hurst (Sat Mar 28 2009 - 14:20:30 CDT)
Gromacs simulation not running in NAMD abhijit ramachandran (Mon Mar 23 2009 - 21:19:32 CDT)
- alanine dipeptide: no dihdral energy terms? Sebastian Stolzenberg (Mon Mar 23 2009 - 22:33:03 CDT)
  - Re: alanine dipeptide: no dihdral energy terms? Peter Freddolino (Mon Mar 23 2009 - 22:45:01 CDT)
- Re: Gromacs simulation not running in NAMD Peter Freddolino (Mon Mar 23 2009 - 22:43:27 CDT)
  - Re: Gromacs simulation not running in NAMD abhijit ramachandran (Tue Mar 24 2009 - 10:44:47 CDT)
polymer topology file accomp lin (Mon Mar 23 2009 - 07:41:38 CDT)
- Re: polymer topology file abhijit ramachandran (Mon Mar 23 2009 - 10:00:35 CDT)
- Re: polymer topology file abhijit ramachandran (Mon Mar 23 2009 - 10:01:50 CDT)
Re: vmd-l: GTP topology file Peter Freddolino (Fri Mar 20 2009 - 12:03:01 CDT)
GTP topology file tiziano gallo cassarino (Fri Mar 20 2009 - 08:47:23 CDT)
acridine orange Rudra Banerjee (Thu Mar 19 2009 - 23:54:50 CDT)
Re: FW: NAMD 2.6, AMD64, MVAPICH2 compile error Thomas C. Bishop (Thu Mar 19 2009 - 16:31:27 CDT)
- Re: Re: FW: NAMD 2.6, AMD64, MVAPICH2 compile error Jim Phillips (Tue Mar 24 2009 - 22:56:40 CDT)
how to use constraints properly Roman Petrenko (Thu Mar 19 2009 - 13:38:24 CDT)
- Re: how to use constraints properly Joshua Adelman (Thu Mar 19 2009 - 13:53:09 CDT)
Using Amber FF in NAMD Joshua Adelman (Wed Mar 18 2009 - 18:13:33 CDT)
- Re: Using Amber FF in NAMD Axel Kohlmeyer (Wed Mar 18 2009 - 18:38:31 CDT)
Amber ff99sb force-field in namd Joshua Adelman (Wed Mar 18 2009 - 17:25:13 CDT)
- Re: Amber ff99sb force-field in namd Benjamin Bouvier (Wed Mar 18 2009 - 18:19:23 CDT)
PRESSURE, GPRESSURE, PRESSAVG, and GPRESSAVG Dennis Glass (Wed Mar 18 2009 - 11:13:12 CDT)
- Re: PRESSURE, GPRESSURE, PRESSAVG, and GPRESSAVG Peter Freddolino (Wed Mar 18 2009 - 13:59:50 CDT)
cg protein folding doty alexiou (Wed Mar 18 2009 - 09:51:17 CDT)
- Re: cg protein folding Hannes Loeffler (Wed Mar 18 2009 - 11:42:46 CDT)
  - Re: cg protein folding Axel Kohlmeyer (Wed Mar 18 2009 - 13:57:31 CDT)
bracket in the log file Lei Zhang (Tue Mar 17 2009 - 16:29:07 CDT)
how to get rid of TCL messages in namd.log from tclForcesScript Roman Petrenko (Fri Mar 13 2009 - 18:45:21 CDT)
- Re: how to get rid of TCL messages in namd.log from tclForcesScript Axel Kohlmeyer (Fri Mar 13 2009 - 19:24:25 CDT)
  - Re: how to get rid of TCL messages in namd.log from tclForcesScript Roman Petrenko (Fri Mar 13 2009 - 20:47:30 CDT)
alchemical fep amber topology George Madalin Giambasu (Fri Mar 13 2009 - 13:55:22 CDT)
- Re: alchemical fep amber topology Jerome Henin (Fri Mar 13 2009 - 15:24:43 CDT)
  - Re: alchemical fep amber topology George Madalin Giambasu (Fri Mar 13 2009 - 15:38:29 CDT)
    - Re: alchemical fep amber topology Jerome Henin (Fri Mar 13 2009 - 15:43:47 CDT)
  - Re: alchemical fep amber topology Floris Buelens (Sat Mar 14 2009 - 06:16:37 CDT)
- Re: alchemical fep amber topology Jerome Henin (Fri Mar 13 2009 - 15:26:34 CDT)
- Re: alchemical fep amber topology Floris Buelens (Sat Mar 14 2009 - 05:53:37 CDT)
  - Re: alchemical fep amber topology Chris Harrison (Sat Mar 14 2009 - 08:33:48 CDT)
    - Re: alchemical fep amber topology Chris Harrison (Sat Mar 14 2009 - 08:47:49 CDT)
Reference file for the constraining force in Umbrella Sampling Mert Gür (Thu Mar 12 2009 - 18:02:24 CDT)
- Re: Reference file for the constraining force in Umbrella Sampling Eric H. Lee (Thu Mar 12 2009 - 18:30:07 CDT)
  - Re: Reference file for the constraining force in Umbrella Sampling Mert Gür (Sat Mar 14 2009 - 07:10:35 CDT)
    - Re: Reference file for the constraining force in Umbrella Sampling Chris Harrison (Sat Mar 14 2009 - 08:19:54 CDT)
    - Re: Reference file for the constraining force in Umbrella Sampling Mert Gür (Sat Mar 14 2009 - 10:44:31 CDT)
FEP restart? Christopher Hartshorn (Wed Mar 11 2009 - 19:34:59 CDT)
- Re: FEP restart? Chris Harrison (Wed Mar 11 2009 - 19:53:09 CDT)
  - Re: FEP restart? Christopher Hartshorn (Thu Mar 12 2009 - 00:35:02 CDT)
    - Re: FEP restart? Chris Harrison (Thu Mar 12 2009 - 07:14:23 CDT)
FATAL ERROR: Duplicate bond ç’€ æŽ (Wed Mar 11 2009 - 02:45:17 CDT)
- Re: FATAL ERROR: Duplicate bond JC Gumbart (Wed Mar 11 2009 - 17:17:36 CDT)
  - Re: FATAL ERROR: Duplicate bond Chris Harrison (Wed Mar 11 2009 - 17:48:13 CDT)
Selectively turning off electrostatic interactions govardhan reddy (Wed Mar 11 2009 - 11:36:57 CDT)
- Re: Selectively turning off electrostatic interactions JC Gumbart (Wed Mar 11 2009 - 12:07:03 CDT)
  - Re: Selectively turning off electrostatic interactions govardhan reddy (Wed Mar 11 2009 - 12:47:18 CDT)
    - Re: Selectively turning off electrostatic interactions Jerome Henin (Wed Mar 11 2009 - 13:38:28 CDT)
- Re: Selectively turning off electrostatic interactions Chris Harrison (Wed Mar 11 2009 - 15:28:46 CDT)
  - Re: Selectively turning off electrostatic interactions govardhan reddy (Wed Mar 11 2009 - 15:57:33 CDT)
    - Re: Selectively turning off electrostatic interactions Chris Harrison (Wed Mar 11 2009 - 18:00:21 CDT)
    - Re: Selectively turning off electrostatic interactions govardhan reddy (Wed Mar 11 2009 - 20:05:59 CDT)
Re: some problem about ABF Jerome Henin (Wed Mar 11 2009 - 09:18:14 CDT)
FW: Water density of water Box Shahid Qamar (Wed Mar 11 2009 - 07:07:15 CDT)
- Re: FW: Water density of water Box Peter Freddolino (Wed Mar 11 2009 - 10:24:00 CDT)
- Re: FW: Water density of water Box Giacomo Fiorin (Wed Mar 11 2009 - 10:30:05 CDT)
- Re: FW: Water density of water Box Grace Brannigan (Wed Mar 11 2009 - 09:26:08 CDT)
Problems with OPLS in NAMD Kalavera_at_gmx.net (Wed Mar 11 2009 - 04:32:56 CDT)
- Re: Problems with OPLS in NAMD Peter Freddolino (Wed Mar 11 2009 - 10:26:25 CDT)
some problem about ABF liupeng012 (Wed Mar 11 2009 - 03:59:53 CDT)
Error running simulation on KRAKEN XT5 harish vashisth (Tue Mar 10 2009 - 18:49:03 CDT)
- Re: Error running simulation on KRAKEN XT5 Peter Freddolino (Tue Mar 10 2009 - 23:32:45 CDT)
How to get the acceptance ratio in REMD Yunlang Li (Mon Mar 09 2009 - 16:59:50 CDT)
- Re: How to get the acceptance ratio in REMD Axel Kohlmeyer (Thu Mar 12 2009 - 08:22:38 CDT)
Problem to generate water segments and lipid reading in membrane Leonardo Herrera (Tue Mar 10 2009 - 05:18:15 CDT)
Problem to generate water segments and lipid reading in membrane Leonardo Herrera (Tue Mar 10 2009 - 05:17:36 CDT)
problem about NAMD compile liupeng012 (Tue Mar 10 2009 - 03:15:27 CDT)
- Re: problem about NAMD compile Axel Kohlmeyer (Tue Mar 10 2009 - 09:03:20 CDT)
  - Re: problem about NAMD compile itvasile_at_nipne.ro (Fri Mar 13 2009 - 14:49:31 CDT)
How to use lset inside tclforces/calc_forces Cameron Abrams (Mon Mar 09 2009 - 09:00:51 CDT)
REX simulations on lonestar or ranger Giovanni Bellesia (Mon Mar 09 2009 - 13:59:57 CDT)
PME and fixed atoms questions Christopher Hartshorn (Mon Mar 09 2009 - 13:31:52 CDT)
- Re: PME and fixed atoms questions Peter Freddolino (Mon Mar 09 2009 - 13:51:17 CDT)
Re: about the memery lock in openMPI on infiniband ÁõÅô (Mon Mar 09 2009 - 04:27:11 CDT)
- Re: about the memery lock in openMPI on infiniband Jim Phillips (Tue Mar 24 2009 - 22:44:29 CDT)
about the memery lock in openMPI on infiniband ÁõÅô (Sun Mar 08 2009 - 03:55:40 CDT)
job submission script on KRAKEN @ NICS harish vashisth (Fri Mar 06 2009 - 22:22:50 CST)
- Re: job submission script on KRAKEN @ NICS Peter Freddolino (Fri Mar 06 2009 - 23:12:24 CST)
  - Re: job submission script on KRAKEN @ NICS harish vashisth (Fri Mar 06 2009 - 23:28:30 CST)
    - Re: job submission script on KRAKEN @ NICS Peter Freddolino (Tue Mar 10 2009 - 11:22:21 CDT)
    - Re: job submission script on KRAKEN @ NICS harish vashisth (Tue Mar 10 2009 - 12:10:03 CDT)
Building NAMD for Opteron Cluster with ICC Chris Share (Fri Mar 06 2009 - 21:53:02 CST)
- Re: Building NAMD for Opteron Cluster with ICC Peter Freddolino (Fri Mar 06 2009 - 23:18:12 CST)
  - Re: Building NAMD for Opteron Cluster with ICC Chris Share (Sat Mar 07 2009 - 21:02:39 CST)
    - Re: Building NAMD for Opteron Cluster with ICC Peter Freddolino (Sat Mar 07 2009 - 21:56:29 CST)
FATAL ERROR: FixedAtoms may not be enabled in a script Dolan, Michael (NIH/NIAID) [C] (Fri Mar 06 2009 - 11:32:52 CST)
how to use hydrogen bond parameter during minimization and simulation prasun kumar (Thu Mar 05 2009 - 23:27:47 CST)
Job submission to Lonestar on TACC Ali Emileh (Wed Mar 04 2009 - 17:19:03 CST)
- Re: Job submission to Lonestar on TACC Peter Freddolino (Thu Mar 05 2009 - 02:15:57 CST)
  - Fwd: Job submission to Lonestar on TACC Ali Emileh (Thu Mar 05 2009 - 13:13:38 CST)
    - Re: Fwd: Job submission to Lonestar on TACC Peter Freddolino (Thu Mar 05 2009 - 20:04:29 CST)
about calculation of PMF from SMD trajectories (with pasted smd_config_file) Falgun Shah (Wed Mar 04 2009 - 12:04:52 CST)
- Re: about calculation of PMF from SMD trajectories (with pasted smd_config_file) Axel Kohlmeyer (Wed Mar 04 2009 - 12:52:47 CST)
about calculation of PMF from SMD trajectories Falgun Shah (Wed Mar 04 2009 - 11:58:52 CST)
removing water from big dcd files jose correa (Tue Mar 03 2009 - 20:36:24 CST)
- Re: removing water from big dcd files Joshua Adelman (Tue Mar 03 2009 - 21:07:54 CST)
- Re: removing water from big dcd files Nicholas M Glykos (Wed Mar 04 2009 - 03:41:34 CST)
  - Re: removing water from big dcd files jose correa (Wed Mar 04 2009 - 11:51:35 CST)
    - Re: removing water from big dcd files Roman Petrenko (Wed Mar 04 2009 - 13:05:22 CST)
    - Re: removing water from big dcd files Axel Kohlmeyer (Wed Mar 04 2009 - 13:49:48 CST)
regarding topology file generation prasun kumar (Tue Mar 03 2009 - 04:55:16 CST)
- Re: regarding topology file generation Chris Harrison (Wed Mar 04 2009 - 11:25:53 CST)
Re: tutorial for calculation of PMF using namd Hyundeok Song (Mon Mar 02 2009 - 23:46:21 CST)
help running NAMD energy at multiple stable temperatures (newbie) Marie N (Mon Mar 02 2009 - 23:32:04 CST)
- Re: help running NAMD energy at multiple stable temperatures (newbie) Peter Freddolino (Mon Mar 02 2009 - 23:37:11 CST)
  - Re: help running NAMD energy at multiple stable temperatures (newbie) Eric H. Lee (Tue Mar 03 2009 - 00:05:58 CST)
- Re: help running NAMD energy at multiple stable temperatures (newbie) Chris Harrison (Wed Mar 04 2009 - 11:12:52 CST)
tutorial for calculation of PMF using namd Falgun Shah (Mon Mar 02 2009 - 22:44:15 CST)
- Re: tutorial for calculation of PMF using namd Ramya Gamini (Tue Mar 03 2009 - 00:44:38 CST)
Coordinate Output in both binary and ASCII. Or converting binary to ASCII in the command line Hugh Martin (Mon Mar 02 2009 - 10:09:56 CST)
- Re: Coordinate Output in both binary and ASCII. Or converting binary to ASCII in the command line Peter Freddolino (Mon Mar 02 2009 - 10:33:22 CST)
  - Re: Coordinate Output in both binary and ASCII. Or converting binary to ASCII in the command line Hugh Martin (Mon Mar 02 2009 - 10:42:53 CST)
    - Re: Coordinate Output in both binary and ASCII. Or converting binary to ASCII in the command line Peter Freddolino (Mon Mar 02 2009 - 10:51:44 CST)
- Re: Coordinate Output in both binary and ASCII. Or converting binary to ASCII in the command line Leandro Martínez (Mon Mar 02 2009 - 11:02:08 CST)
  - Re: Coordinate Output in both binary and ASCII. Or converting binary to ASCII in the command line Hugh Martin (Fri Mar 06 2009 - 23:26:30 CST)
Minimization convergence issue Brittany Morgan (Mon Mar 02 2009 - 09:59:21 CST)
- Re: Minimization convergence issue Peter Freddolino (Mon Mar 02 2009 - 10:29:32 CST)
  - RE: Minimization convergence issue Brittany Morgan (Mon Mar 02 2009 - 10:53:55 CST)
topology and parameter file for FAD Demet Akten (Sat Feb 28 2009 - 08:40:31 CST)
- Re: topology and parameter file for FAD Schreiner Eduard (Sun Mar 01 2009 - 01:52:09 CST)
  - Topology and parameter file for DMF Austin B. Yongye (Sun Mar 01 2009 - 07:00:34 CST)
  - Re: topology and parameter file for FAD Demet Akten (Mon Mar 02 2009 - 02:47:01 CST)
How can I find topology and parameter files for heterocyclic, heteroaromatic, halogens and sugar compounds Lisa Brown (Fri Feb 27 2009 - 11:02:51 CST)
error in writing restart files Ruchi Sachdeva (Fri Feb 27 2009 - 03:55:30 CST)
paramater about Amphotericin B ÁõÅô (Fri Feb 27 2009 - 03:25:46 CST)
Topology files Corey Fugate (Thu Feb 26 2009 - 16:08:38 CST)
PLUMED release 1.0.0 available Massimiliano Bonomi (Thu Feb 26 2009 - 07:12:04 CST)
Background load problem Anirban Ghosh (Thu Feb 26 2009 - 03:34:53 CST)
- Re: Background load problem Peter Freddolino (Thu Feb 26 2009 - 07:50:36 CST)
  - Re: Background load problem Anirban (Thu Feb 26 2009 - 08:15:04 CST)
loading of large dcd files sripad chandan (Wed Feb 25 2009 - 23:54:58 CST)
- Re: loading of large dcd files Joshua Adelman (Thu Feb 26 2009 - 00:10:44 CST)
- Re: loading of large dcd files sripad chandan (Thu Feb 26 2009 - 00:08:17 CST)
charm27 forcefield_topology Falgun Shah (Wed Feb 25 2009 - 11:02:02 CST)
- Re: charm27 forcefield_topology Peter Freddolino (Wed Feb 25 2009 - 15:09:23 CST)
Re: vmd-l: Membrane builder ?'s Christopher Hartshorn (Tue Feb 24 2009 - 00:47:57 CST)
FEP anomaly? Christopher Hartshorn (Mon Feb 23 2009 - 12:53:15 CST)
- Re: FEP anomaly? Floris Buelens (Wed Feb 25 2009 - 09:13:22 CST)
- Re: FEP anomaly? Jerome Henin (Tue Feb 24 2009 - 09:37:14 CST)
how to do a MD of small part of a protein, using namd? Lisa Brown (Mon Feb 23 2009 - 10:23:43 CST)
- Re: how to do a MD of small part of a protein, using namd? Giacomo Fiorin (Mon Feb 23 2009 - 11:53:43 CST)
smd force vs time Falgun Shah (Sun Feb 22 2009 - 13:31:07 CST)
- RE: smd force vs time JC Gumbart (Mon Feb 23 2009 - 00:47:26 CST)
solution for generating IC CHINDEA Vlad (Sat Feb 21 2009 - 17:20:11 CST)
- Re: solution for generating IC Axel Kohlmeyer (Sat Feb 21 2009 - 18:26:13 CST)
- Re: solution for generating IC Roman Petrenko (Sat Feb 21 2009 - 22:48:54 CST)
Re: A beginner's question for using NAMD to do cell membrane simulation and molecular transportation Ramya Gamini (Sat Feb 21 2009 - 15:34:24 CST)
A beginner's question for using NAMD to do cell membrane simulation and molecular transportation Xu Dong (Sat Feb 21 2009 - 14:23:49 CST)
memory optimised version and exclusion check Joachim Hein (Fri Feb 20 2009 - 13:48:24 CST)
- Re: memory optimised version and exclusion check Peter Freddolino (Sat Feb 21 2009 - 22:24:08 CST)
(no subject) gurunath katagi (Fri Feb 20 2009 - 06:08:37 CST)
Can I get the pressure value in a cube? Fred (Rui FENG) (Thu Feb 19 2009 - 22:12:35 CST)
- Re: Can I get the pressure value in a cube? Peter Freddolino (Thu Feb 19 2009 - 22:26:27 CST)
  - Re: Can I get the pressure value in a cube? Fred (Rui FENG) (Thu Feb 19 2009 - 23:49:26 CST)
NAMD CVS Luis Cunha (Thu Feb 19 2009 - 18:01:39 CST)
Re: Constant pressure simulation: can I get the changed volume? Fred (Rui FENG) (Thu Feb 19 2009 - 04:26:50 CST)
- Re: Constant pressure simulation: can I get the changed volume? Fred (Rui FENG) (Thu Feb 19 2009 - 04:25:26 CST)
Constant pressure simulation: can I get the changed volume? Fred (Rui FENG) (Thu Feb 19 2009 - 01:52:55 CST)
LD with explicit water molecules ramya narasimhan (Wed Feb 18 2009 - 22:14:40 CST)
cgmd stability BIN ZHANG (Wed Feb 18 2009 - 17:13:14 CST)
- Re: cgmd stability Peter Freddolino (Wed Feb 18 2009 - 20:05:57 CST)
Autopsf error with a modified top file CHINDEA Vlad (Wed Feb 18 2009 - 15:17:52 CST)
- Re: Autopsf error with a modified top file Peter Freddolino (Wed Feb 18 2009 - 15:24:59 CST)
  - RE: Autopsf error with a modified top file CHINDEA Vlad (Thu Feb 19 2009 - 18:15:45 CST)
fail to run replica exchange on more than one node Linchen Gong (Wed Feb 18 2009 - 01:31:24 CST)
Thiol on gold simulation in NAMD S.K. Ghosh (Tue Feb 17 2009 - 14:14:36 CST)
- Re: Thiol on gold simulation in NAMD Axel Kohlmeyer (Tue Feb 17 2009 - 14:54:51 CST)
how can i get the energy of a molecule of a whole system? Wang,Ying (Tue Feb 17 2009 - 10:30:11 CST)
- Re: how can i get the energy of a molecule of a whole system? JC Gumbart (Tue Feb 17 2009 - 14:28:36 CST)
Problem running NAMD on ranger@TACC shayan_at_msu.edu (Tue Feb 17 2009 - 07:01:27 CST)
- Re: Problem running NAMD on ranger@TACC Axel Kohlmeyer (Tue Feb 17 2009 - 08:43:49 CST)
  - Re: Problem running NAMD on ranger@TACC shayan_at_msu.edu (Tue Feb 17 2009 - 09:41:06 CST)
Forces on Atoms and Potential Energy Mohamed Seyam (Mon Feb 16 2009 - 13:57:01 CST)
- Re: Forces on Atoms and Potential Energy JC Gumbart (Tue Feb 17 2009 - 14:29:52 CST)
unsubscribe Vinit Rege (Mon Feb 16 2009 - 12:07:11 CST)
log file from 3 different protein simulations sripad chandan (Mon Feb 16 2009 - 05:50:36 CST)
- Re: log file from 3 different protein simulations Axel Kohlmeyer (Mon Feb 16 2009 - 09:13:31 CST)
Re: FEP/binding free energy difference WT vs Mut Chris Harrison (Fri Feb 13 2009 - 17:57:21 CST)
- Re: FEP/binding free energy difference WT vs Mut Jerome Henin (Fri Feb 13 2009 - 18:08:24 CST)
  - Re: FEP/binding free energy difference WT vs Mut Chris Chipot (Sun Feb 15 2009 - 20:03:27 CST)
- Re: FEP/binding free energy difference WT vs Mut Jerome Henin (Mon Feb 16 2009 - 11:18:50 CST)
  - Re: FEP/binding free energy difference WT vs Mut Luis Cunha (Tue Feb 17 2009 - 11:50:20 CST)
FEP/binding free energy difference WT vs Mut Luis Cunha (Fri Feb 13 2009 - 16:43:27 CST)
Membrane Proteins Tutorial Marcos Sotomayor (Fri Feb 13 2009 - 16:25:15 CST)
unsubscribe Lee, Se I (Thu Feb 12 2009 - 13:26:01 CST)
ligand flies away from binding pocket Osman Yogurtcu (Thu Feb 12 2009 - 11:39:04 CST)
- Re: ligand flies away from binding pocket Mert Gür (Fri Feb 13 2009 - 13:34:58 CST)
- Re: ligand flies away from binding pocket Chris Harrison (Fri Feb 13 2009 - 18:07:44 CST)
namd ubuntu-instalation jose correa (Thu Feb 12 2009 - 09:23:15 CST)
(no subject) gurunath katagi (Thu Feb 12 2009 - 03:13:47 CST)
namd cvs compilation with a maximum number of cores to run on Vlad Cojocaru (Thu Feb 12 2009 - 03:11:50 CST)
- Re: namd cvs compilation with a maximum number of cores to run on Peter Freddolino (Thu Feb 12 2009 - 08:32:59 CST)
  - Re: namd cvs compilation with a maximum number of cores to run on Vlad Cojocaru (Thu Feb 12 2009 - 09:04:14 CST)
reg dynamics hari prasad (Thu Feb 12 2009 - 01:58:55 CST)
(Á¦¸ñ ¾øÀ½) Taeho Kim (Wed Feb 11 2009 - 22:29:19 CST)
pressure profile calculations Grace Brannigan (Wed Feb 11 2009 - 16:58:06 CST)
cuda 1.0 binaries on cuda 1.1 Roman Petrenko (Wed Feb 11 2009 - 13:47:32 CST)
Need Charmm FF for Gangliosides bo liu (Wed Feb 11 2009 - 11:36:19 CST)
- Re: Need Charmm FF for Gangliosides Jerome Henin (Wed Feb 11 2009 - 13:52:22 CST)
(no subject) gurunath katagi (Wed Feb 11 2009 - 10:49:16 CST)
center of mass for SMD Falgun Shah (Tue Feb 10 2009 - 17:52:06 CST)
- RE: center of mass for SMD JC Gumbart (Wed Feb 11 2009 - 22:44:01 CST)
How to specify processors for running VMD on a cluster? Yinglong Miao (Tue Feb 10 2009 - 10:45:27 CST)
- Re: vmd-l: How to specify processors for running VMD on a cluster? Axel Kohlmeyer (Tue Feb 10 2009 - 12:24:58 CST)
  - Re: vmd-l: How to specify processors for running VMD on a cluster? Yinglong Miao (Tue Feb 10 2009 - 15:21:34 CST)
    - Re: vmd-l: How to specify processors for running VMD on a cluster? Axel Kohlmeyer (Tue Feb 10 2009 - 15:35:46 CST)
tmd algorithm Elif Ozkirimli (Tue Feb 10 2009 - 09:22:58 CST)
Periodic boundary condition in a membrane simulation Eric Hu (Mon Feb 09 2009 - 17:28:38 CST)
- Re: Periodic boundary condition in a membrane simulation Nd S (Mon Feb 09 2009 - 18:05:20 CST)
  - Re: Periodic boundary condition in a membrane simulation Axel Kohlmeyer (Mon Feb 09 2009 - 19:29:40 CST)
- Re: Periodic boundary condition in a membrane simulation eprates_at_iqm.unicamp.br (Mon Feb 09 2009 - 18:14:44 CST)
  - Re: Periodic boundary condition in a membrane simulation Eric Hu (Mon Feb 09 2009 - 19:20:18 CST)
any experiences with executing parallel NAMD in a NAMD simulation Yinglong Miao (Mon Feb 09 2009 - 15:59:07 CST)
- Re: any experiences with executing parallel NAMD in a NAMD simulation Peter Freddolino (Mon Feb 09 2009 - 16:26:39 CST)
  - Re: any experiences with executing parallel NAMD in a NAMD simulation Yinglong Miao (Mon Feb 09 2009 - 19:56:44 CST)
Take a look at jaxtr! Sudipta Sinha (Sun Feb 08 2009 - 22:20:40 CST)
Accessing atoms and velocities during NVE run Nd S (Fri Feb 06 2009 - 10:57:02 CST)
- Re: Accessing atoms and velocities during NVE run Chris Harrison (Fri Feb 06 2009 - 12:06:58 CST)
  - Re: Accessing atoms and velocities during NVE run Brian Bennion (Fri Feb 06 2009 - 13:08:24 CST)
  - Re: Accessing atoms and velocities during NVE run Nd S (Fri Feb 06 2009 - 13:33:53 CST)
eucb - beta testers wanted for trajectory analysis program Athanassios Stavrakoudis (Thu Feb 05 2009 - 18:18:08 CST)
"Hands-On" Workshop on Computational Biophysics, July 6-10 and August 10-14, 2009 TCBG Workshop (Thu Feb 05 2009 - 15:52:30 CST)
Fwd:Re: TCL: divide by zero supram_at_nankai.edu.cn (Thu Feb 05 2009 - 10:28:45 CST)
TCL: divide by zero supram_at_nankai.edu.cn (Thu Feb 05 2009 - 10:08:11 CST)
TCL: divide by zero supram_at_nankai.edu.cn (Thu Feb 05 2009 - 06:26:11 CST)
- Re: TCL: divide by zero Axel Kohlmeyer (Thu Feb 05 2009 - 08:52:41 CST)
- Re: TCL: divide by zero Grace Brannigan (Thu Feb 05 2009 - 10:12:01 CST)
Fwd:Re: ABF-Zcoord: ÁõÓý (Wed Feb 04 2009 - 22:04:40 CST)
Fatal error in configuration file Corey Fugate (Wed Feb 04 2009 - 21:05:36 CST)
- Re: Fatal error in configuration file BIN ZHANG (Wed Feb 04 2009 - 22:12:55 CST)
  - Re: Fatal error in configuration file Chris Harrison (Thu Feb 05 2009 - 20:27:23 CST)
    - Re: Fatal error in configuration file BIN ZHANG (Thu Feb 05 2009 - 22:28:26 CST)
    - Re: Fatal error in configuration file Chris Harrison (Thu Feb 05 2009 - 23:51:39 CST)
ABF:restraint in free energy calculation in Zcoord-method ÁõÓý (Tue Feb 03 2009 - 22:15:42 CST)
Variable results for the same simulation Nd S (Tue Feb 03 2009 - 12:18:24 CST)
ABF-Zcoord: ÁõÓý (Tue Feb 03 2009 - 07:29:23 CST)
- Re: ABF-Zcoord: Giacomo Fiorin (Wed Feb 04 2009 - 18:13:50 CST)
tcl script fett_at_vtr.net (Mon Feb 02 2009 - 21:31:04 CST)
- Re: tcl script Axel Kohlmeyer (Mon Feb 02 2009 - 23:01:26 CST)
- Re: tcl script Grace Brannigan (Mon Feb 02 2009 - 23:26:34 CST)
generating xsc and vel files David A. Horita (Mon Feb 02 2009 - 10:29:29 CST)
- Re: generating xsc and vel files Peter Freddolino (Mon Feb 02 2009 - 10:46:40 CST)
Correlation matrix of the Ca atoms sripad chandan (Sun Feb 01 2009 - 22:46:14 CST)
- Re: Correlation matrix of the Ca atoms Joshua Adelman (Sun Feb 01 2009 - 23:22:07 CST)
  - Re: Correlation matrix of the Ca atoms Joshua Adelman (Sun Feb 01 2009 - 23:56:04 CST)
- Re: Correlation matrix of the Ca atoms Nicholas M Glykos (Mon Feb 02 2009 - 02:17:39 CST)
  - FEP with fixed explicit environment? Sebastian Stolzenberg (Thu Mar 12 2009 - 18:50:32 CDT)
  - FEP with fixed explicit environment? Sebastian Stolzenberg (Thu Mar 12 2009 - 18:51:05 CDT)
combining abf reaction path Arturas Ziemys (Sat Jan 31 2009 - 12:20:55 CST)
- Re: combining abf reaction path Chris Chipot (Sat Jan 31 2009 - 13:03:29 CST)
pdb and rmsd Falgun Shah (Fri Jan 30 2009 - 13:46:42 CST)
- Re: pdb and rmsd Chris Harrison (Fri Jan 30 2009 - 21:21:54 CST)
Aligning the distance between two centroids with an axis Mert Gür (Fri Jan 30 2009 - 04:02:55 CST)
- Re: Aligning the distance between two centroids with an axis Nicholas M Glykos (Fri Jan 30 2009 - 05:08:19 CST)
- Re: Aligning the distance between two centroids with an axis Grace Brannigan (Fri Jan 30 2009 - 10:01:55 CST)
- Re: Aligning the distance between two centroids with an axis Chris Harrison (Fri Jan 30 2009 - 21:31:43 CST)
  - Re: Aligning the distance between two centroids with an axis Mert Gür (Sat Jan 31 2009 - 02:13:38 CST)
FEP on NAMD2.6 versus latest CVS NAMD build Christopher Hartshorn (Fri Jan 30 2009 - 00:54:54 CST)
- Re: FEP on NAMD2.6 versus latest CVS NAMD build Floris Buelens (Fri Jan 30 2009 - 03:36:00 CST)
running NAMD on Kraken Cray-XT4 Xu, Jiancong (Thu Jan 29 2009 - 15:44:58 CST)
New open() for DCDs in v.2.6 ? Nicholas M Glykos (Thu Jan 29 2009 - 11:34:37 CST)
- Re: New open() for DCDs in v.2.6 ? Nicholas M Glykos (Thu Jan 29 2009 - 12:33:55 CST)
loading large dcd files sripad chandan (Thu Jan 29 2009 - 04:30:29 CST)
- Re: loading large dcd files Per Jr. Greisen (Thu Jan 29 2009 - 05:15:34 CST)
- Re: loading large dcd files Axel Kohlmeyer (Thu Jan 29 2009 - 09:03:44 CST)
asymmetric water found! OZGE ENGIN (Wed Jan 28 2009 - 07:26:07 CST)
- Re: asymmetric water found! Peter Freddolino (Wed Jan 28 2009 - 10:00:03 CST)
value 9999999.99999 during simulation uma mageshwari (Wed Jan 28 2009 - 04:11:57 CST)
- Re: value 9999999.99999 during simulation Peter Freddolino (Wed Jan 28 2009 - 07:22:34 CST)
alpha character error in the psf file OZGE ENGIN (Wed Jan 28 2009 - 03:30:26 CST)
- Re: alpha character error in the psf file Peter Freddolino (Wed Jan 28 2009 - 07:18:52 CST)
  - Re: Re: alpha character error in the psf file OZGE ENGIN (Wed Jan 28 2009 - 07:22:51 CST)
(no subject) OZGE ENGIN (Wed Jan 28 2009 - 03:29:03 CST)
- Re: Joshua D. Moore (Thu Jan 29 2009 - 10:01:28 CST)
how to add ions to a system uma mageshwari (Wed Jan 28 2009 - 03:18:19 CST)
- Re: how to add ions to a system/DASHOFSALT Thomas C. Bishop (Wed Jan 28 2009 - 09:10:23 CST)
how to add ions to a system uma mageshwari (Wed Jan 28 2009 - 01:57:09 CST)
how to add ions to a system uma mageshwari (Wed Jan 28 2009 - 01:08:12 CST)
- Re: how to add ions to a system jose correa (Wed Jan 28 2009 - 06:48:03 CST)
Rosetta Academic Training Workshop Nir London (Tue Jan 27 2009 - 07:04:42 CST)
NAMD on a virtual grid Benjamin Bouvier (Mon Jan 26 2009 - 09:38:30 CST)
- Re: NAMD on a virtual grid Robert Brunner (Mon Jan 26 2009 - 13:50:13 CST)
  - Re: NAMD on a virtual grid Benjamin Bouvier (Mon Jan 26 2009 - 14:38:56 CST)
    - Re: NAMD on a virtual grid Robert Brunner (Mon Jan 26 2009 - 15:31:09 CST)
    - Re: NAMD on a virtual grid Axel Kohlmeyer (Mon Jan 26 2009 - 16:02:30 CST)
RMSD and merging trajectories Falgun Shah (Sat Jan 24 2009 - 17:20:27 CST)
- Re: RMSD and merging trajectories Axel Kohlmeyer (Sat Jan 24 2009 - 19:18:51 CST)
Stratification schemes Chris Chipot (Sat Jan 24 2009 - 16:28:37 CST)
NADP jose correa (Fri Jan 23 2009 - 18:43:07 CST)
Re: some recommendations for parametrizing new molecules requiredþ CHINDEA Vlad (Fri Jan 23 2009 - 16:30:16 CST)
- Re: Re: some recommendations for parametrizing new molecules requiredþ Giacomo Fiorin (Fri Jan 23 2009 - 18:41:14 CST)
Re: problems-protein minimization jose correa (Fri Jan 23 2009 - 14:27:59 CST)
- Re: problems-protein minimization Eduardo Tejera (Mon Jan 26 2009 - 04:04:43 CST)
problems-protein minimization jose correa (Fri Jan 23 2009 - 12:40:22 CST)
some recommendations for parametrizing new molecules required CHINDEA Vlad (Fri Jan 23 2009 - 03:31:04 CST)
- Re: some recommendations for parametrizing new molecules required Christopher Gillespie (Fri Jan 23 2009 - 07:36:30 CST)
  - Re: some recommendations for parametrizing new molecules required Axel Kohlmeyer (Fri Jan 23 2009 - 09:25:01 CST)
    - Re: some recommendations for parametrizing new molecules required Christopher Gillespie (Fri Jan 23 2009 - 09:37:17 CST)
- Re: some recommendations for parametrizing new molecules required Axel Kohlmeyer (Fri Jan 23 2009 - 09:20:50 CST)
- Re: some recommendations for parametrizing new molecules required JC Gumbart (Fri Jan 23 2009 - 11:17:09 CST)
use of berendsenPressure during heating Falgun Shah (Thu Jan 22 2009 - 22:22:29 CST)
- Re: use of berendsenPressure during heating Peter Freddolino (Fri Jan 23 2009 - 12:22:10 CST)
abf convergence problems Jorgen Simonsen (Thu Jan 22 2009 - 11:16:36 CST)
- Re: abf convergence problems Chris Chipot (Thu Jan 22 2009 - 11:54:08 CST)
- Re: abf convergence problems Jerome Henin (Thu Jan 22 2009 - 11:52:29 CST)
  - Re: abf convergence problems Jorgen Simonsen (Thu Jan 22 2009 - 12:56:40 CST)
    - Re: abf convergence problems Jerome Henin (Thu Jan 22 2009 - 14:17:26 CST)
    - Re: abf convergence problems Jorgen Simonsen (Thu Jan 22 2009 - 14:37:05 CST)
I: Running Charm++ over MPI does not work andy.mastellone_at_alice.it (Thu Jan 22 2009 - 08:23:58 CST)
- Re: I: Running Charm++ over MPI does not work Chris Harrison (Thu Jan 22 2009 - 10:53:50 CST)
  - R: I: Running Charm++ over MPI does not work andy.mastellone_at_alice.it (Fri Jan 23 2009 - 02:37:21 CST)
Running Charm++ over MPI does not work andy.mastellone_at_alice.it (Thu Jan 22 2009 - 07:20:28 CST)
Hexafluoro-2-propanol (HFIP) force parameters Dong Luo (Wed Jan 21 2009 - 15:04:43 CST)
Re: CUDA version status Dow_Hurst (Wed Jan 21 2009 - 13:12:32 CST)
- Re: CUDA version status Peter Freddolino (Thu Jan 22 2009 - 15:40:54 CST)
- Re: CUDA version status Dow_Hurst (Fri Jan 23 2009 - 13:44:07 CST)
  - Re: CUDA version status Artem Zhmurov (Fri Jan 23 2009 - 19:09:47 CST)
    - Re: CUDA version status Axel Kohlmeyer (Fri Jan 23 2009 - 20:28:27 CST)
    - Re: CUDA version status Chris Harrison (Sat Jan 24 2009 - 16:36:34 CST)
IBVerbs NAMD build segfaults Jason Russler (Wed Jan 21 2009 - 08:47:28 CST)
double-wide sampling with soft-core Sébastien Légaré (Tue Jan 20 2009 - 14:27:32 CST)
- Re: double-wide sampling with soft-core Jerome Henin (Wed Jan 21 2009 - 16:02:24 CST)
  - Re: double-wide sampling with soft-core Chris Chipot (Wed Jan 21 2009 - 17:32:52 CST)
  - Re: double-wide sampling with soft-core Floris Buelens (Thu Jan 22 2009 - 04:58:40 CST)
CUDA version status Dow Hurst (Tue Jan 20 2009 - 12:39:20 CST)
(no subject) gurunath katagi (Tue Jan 20 2009 - 08:25:06 CST)
- Re: Axel Kohlmeyer (Tue Jan 20 2009 - 09:03:51 CST)
Single vs. Double precision Neelanjana Sengupta (Mon Jan 19 2009 - 05:27:27 CST)
- Re: Single vs. Double precision Floris Buelens (Mon Jan 19 2009 - 09:58:06 CST)
- Re: Single vs. Double precision Axel Kohlmeyer (Mon Jan 19 2009 - 10:25:36 CST)
The limit of atom number on Blue Gene/L Fred (Rui FENG) (Mon Jan 19 2009 - 02:09:15 CST)
- Re: The limit of atom number on Blue Gene/L Peter Freddolino (Mon Jan 19 2009 - 07:41:43 CST)
  - Re: The limit of atom number on Blue Gene/L Fred (Rui FENG) (Mon Jan 19 2009 - 17:42:03 CST)
    - Re: The limit of atom number on Blue Gene/L Peter Freddolino (Mon Jan 19 2009 - 18:40:24 CST)
    - Re: The limit of atom number on Blue Gene/L Fred (Rui FENG) (Mon Jan 19 2009 - 20:41:51 CST)
TMD comments Michael Feig (Fri Jan 16 2009 - 23:06:07 CST)
- Re: TMD comments Peter Freddolino (Sat Jan 17 2009 - 11:01:06 CST)
  - RE: TMD comments Michael Feig (Tue Jan 20 2009 - 07:02:23 CST)
    - RE: TMD comments V.Ovchinnikov (Tue Jan 20 2009 - 09:38:45 CST)
    - RE: TMD comments Michael Feig (Tue Jan 20 2009 - 21:27:31 CST)
- Re: TMD comments Jerome Henin (Sat Jan 17 2009 - 19:52:40 CST)
syntax error in expression "(": premature end of expression - namdstats CHINDEA Vlad (Fri Jan 16 2009 - 17:08:54 CST)
- RE: syntax error in expression "(": premature end of expression - namdstats JC Gumbart (Sat Jan 17 2009 - 01:34:41 CST)
  - RE: syntax error in expression "(": premature end of expression - namdstats CHINDEA Vlad (Sat Jan 17 2009 - 16:18:33 CST)
Problems deciphering fepout Christopher Hartshorn (Fri Jan 16 2009 - 16:28:21 CST)
- Re: Problems deciphering fepout Dan Willenbring (Sat Jan 17 2009 - 08:58:14 CST)
- Re: Problems deciphering fepout Floris Buelens (Sun Jan 18 2009 - 06:13:34 CST)
SMD output dimka (Fri Jan 16 2009 - 12:59:43 CST)
SMD output Dmitry Lupyan (Thu Jan 15 2009 - 16:50:08 CST)
- Re: SMD output Chris Harrison (Thu Jan 22 2009 - 11:36:35 CST)
ABF calculation with TclForces script in the configuration file govardhan reddy (Fri Jan 16 2009 - 09:18:40 CST)
- Re: ABF calculation with TclForces script in the configuration file govardhan reddy (Fri Jan 16 2009 - 11:10:47 CST)
- Re: ABF calculation with TclForces script in the configuration file Jerome Henin (Fri Jan 16 2009 - 11:20:27 CST)
advice on van Hove Arturas Ziemys (Thu Jan 15 2009 - 12:08:40 CST)
Energy drif in NVE ensemble eprates_at_iqm.unicamp.br (Thu Jan 15 2009 - 11:51:54 CST)
- Re: Energy drif in NVE ensemble Peter Freddolino (Thu Jan 15 2009 - 11:56:33 CST)
dielectric parameter? BIN ZHANG (Thu Jan 15 2009 - 01:10:36 CST)
- Re: dielectric parameter? Peter Freddolino (Thu Jan 15 2009 - 09:24:11 CST)
- Re: dielectric parameter? Anton Arkhipov (Thu Jan 15 2009 - 10:00:04 CST)
problem in fitting Maxwell-Boltzmann distribution CHINDEA Vlad (Wed Jan 14 2009 - 17:08:48 CST)
- Re: problem in fitting Maxwell-Boltzmann distribution JC Gumbart (Wed Jan 14 2009 - 19:00:12 CST)
  - RE: problem in fitting Maxwell-Boltzmann distribution CHINDEA Vlad (Thu Jan 15 2009 - 06:39:47 CST)
error during heating of the minimized system: (please reply!) Falgun Shah (Wed Jan 14 2009 - 01:08:28 CST)
- Re: error during heating of the minimized system: (please reply!) Chris Harrison (Wed Jan 14 2009 - 23:11:31 CST)
question about cellBasisVector*? BIN ZHANG (Tue Jan 13 2009 - 00:13:25 CST)
- Re: question about cellBasisVector*? Peter Freddolino (Tue Jan 13 2009 - 09:33:20 CST)
Creating bonds during a run Marcin S. (Mon Jan 12 2009 - 09:41:23 CST)
- Re: Creating bonds during a run Axel Kohlmeyer (Mon Jan 12 2009 - 10:09:24 CST)
  - Re: Creating bonds during a run Jerome Henin (Mon Jan 12 2009 - 11:25:43 CST)
    - Re: Creating bonds during a run Praveen Agrawal (Wed Jan 21 2009 - 04:18:43 CST)
Question on mutator in VMD Jianping Lin (Sun Jan 11 2009 - 17:00:54 CST)
- Re: Question on mutator in VMD Chris Harrison (Wed Jan 14 2009 - 23:15:20 CST)
binary trajectories karthik s (Fri Jan 09 2009 - 04:53:54 CST)
- Re: binary trajectories Axel Kohlmeyer (Fri Jan 09 2009 - 08:29:27 CST)
NAMD disk writes and quota overflow Jeff Forbes (Thu Jan 08 2009 - 15:45:05 CST)
- Re: NAMD disk writes and quota overflow Axel Kohlmeyer (Thu Jan 08 2009 - 16:19:19 CST)
how to save output file in plain text? Segun Jung (Thu Jan 08 2009 - 15:09:02 CST)
- Re: how to save output file in plain text? JC Gumbart (Thu Jan 08 2009 - 16:05:30 CST)
  - Re: how to save output file in plain text? JC Gumbart (Thu Jan 08 2009 - 16:30:58 CST)
Single or double precision? mm148881 (Thu Jan 08 2009 - 13:09:21 CST)
- Re: Single or double precision? Robert Brunner (Fri Jan 09 2009 - 15:14:33 CST)
Inorganic compounds Casey,Richard (Thu Jan 08 2009 - 12:20:34 CST)
- Re: Inorganic compounds Chris Harrison (Wed Jan 14 2009 - 23:25:19 CST)
FATAL ERROR: Setting parameter constraints from script failed! Do Nhu Trang (Thu Jan 08 2009 - 09:57:28 CST)
- Re: FATAL ERROR: Setting parameter constraints from script failed! Axel Kohlmeyer (Thu Jan 08 2009 - 10:58:05 CST)
  - Re: FATAL ERROR: Setting parameter constraints from script failed! Joshua Adelman (Thu Jan 08 2009 - 11:14:24 CST)
tcl forces interface Vlad Cojocaru (Wed Jan 07 2009 - 04:36:13 CST)
Gradient tolerance nan for A three-atom simulation accomp lin (Mon Jan 05 2009 - 23:09:41 CST)
- RE: Gradient tolerance nan for A three-atom simulation JC Gumbart (Mon Jan 05 2009 - 23:24:35 CST)
  - RE: Gradient tolerance nan for A three-atom simulation accomp lin (Tue Jan 06 2009 - 22:20:18 CST)
Re: namdcvs Achani.K.Yatawara_at_Dartmouth.edu (Mon Jan 05 2009 - 13:32:34 CST)
- Re: Re: namdcvs Peter Freddolino (Mon Jan 05 2009 - 13:51:02 CST)
  - Re: Re: namdcvs Peter Freddolino (Mon Jan 05 2009 - 14:21:51 CST)
    - Re: Re: namdcvs Achani.K.Yatawara_at_Dartmouth.edu (Mon Jan 05 2009 - 14:32:43 CST)
  - Re: Re: namdcvs Achani K. Yatawara (Mon Jan 05 2009 - 14:37:02 CST)
    - Re: Re: namdcvs Achani.K.Yatawara_at_Dartmouth.edu (Mon Jan 05 2009 - 15:00:54 CST)
    - Re: Re: namdcvs Chris Harrison (Tue Jan 06 2009 - 08:41:21 CST)
- Re: Re: namdcvs Peter Freddolino (Mon Jan 05 2009 - 14:02:58 CST)
- Re: Re: namdcvs BIN ZHANG (Mon Jan 05 2009 - 14:12:59 CST)
Problem with number of steps > 1000000 Anirban Ghosh (Mon Jan 05 2009 - 07:52:55 CST)
- Re: Problem with number of steps > 1000000 Peter Freddolino (Mon Jan 05 2009 - 08:11:57 CST)
Confira meu perfil no Facebook Ariovaldo De Souza Junior (Sat Jan 03 2009 - 12:31:41 CST)
How to get over with the error "Atoms moving too fast; simulation has become unstable and Exiting prematurely sunita gupta (Fri Jan 02 2009 - 03:58:37 CST)
- Re: How to get over with the error "Atoms moving too fast; simulation has become unstable and Exiting prematurely Chris Harrison (Sun Jan 04 2009 - 12:03:37 CST)
Re: namdcvs Re: how to apply restraints for phi and psi for alpha helix regions Leonardo Trabuco (Fri Jan 02 2009 - 02:55:40 CST)
- Re: namdcvs Re: how to apply restraints for phi and psi for alpha helix regions Chris Harrison (Sun Jan 04 2009 - 12:28:23 CST)
How to get over with the error "Atoms moving too fast; simulation has become unstable and Exiting prematurely. sunita gupta (Wed Dec 31 2008 - 00:27:08 CST)
- Re: How to get over with the error "Atoms moving too fast; simulation has become unstable and Exiting prematurely. jani sahil (Wed Dec 31 2008 - 05:25:10 CST)
base stacking analysis of the trajectory of a nucleic acids simulation Tianjiao Wang (Tue Dec 30 2008 - 15:54:31 CST)
- Re: base stacking analysis of the trajectory of a nucleic acids simulation Chris Harrison (Sun Jan 04 2009 - 12:12:07 CST)
gpu pressure control Daniel Miscevski (Sun Dec 28 2008 - 23:10:46 CST)
- Re: gpu pressure control JC Gumbart (Sun Dec 28 2008 - 23:27:07 CST)
- Re: gpu pressure control Chris Harrison (Sun Jan 04 2009 - 12:23:48 CST)
compiling NAMD failed on windows with Cygwin accomp lin (Sun Dec 28 2008 - 22:32:51 CST)
- Re: compiling NAMD failed on windows with Cygwin Axel Kohlmeyer (Mon Dec 29 2008 - 09:36:45 CST)
  - Re: compiling NAMD failed on windows with Cygwin accomp lin (Fri Jan 09 2009 - 22:06:37 CST)
compiling charm++ failed on window with Cygwin accomp lin (Sun Dec 28 2008 - 01:23:13 CST)
Changing the Secondary Structure of a Protein MIke S (Sun Dec 28 2008 - 01:18:23 CST)
- Re: Changing the Secondary Structure of a Protein JC Gumbart (Sun Dec 28 2008 - 08:55:03 CST)
- Re: Changing the Secondary Structure of a Protein Peter Freddolino (Sun Dec 28 2008 - 08:48:38 CST)
- Re: Changing the Secondary Structure of a Protein Giacomo Fiorin (Sun Dec 28 2008 - 16:33:28 CST)
NAMD-L: autoionize error jfgaff_at_ncsu.edu (Fri Dec 26 2008 - 13:21:17 CST)
- Re: NAMD-L: autoionize error Axel Kohlmeyer (Fri Dec 26 2008 - 14:45:55 CST)
solvating protein Jorgen Simonsen (Fri Dec 26 2008 - 10:27:31 CST)
- Re: solvating protein Peter Freddolino (Fri Dec 26 2008 - 19:53:29 CST)
topology/parameter entries for asphaltenes? jose correa (Fri Dec 26 2008 - 09:21:52 CST)
Stupid question about compiling NAMD with cygwin on windows accomp lin (Thu Dec 25 2008 - 21:19:50 CST)
- Re: Stupid question about compiling NAMD with cygwin on windows Axel Kohlmeyer (Fri Dec 26 2008 - 14:35:54 CST)
Problems on SMD simulation ÕÅÓÂ (Thu Dec 25 2008 - 01:08:27 CST)
- Re: Problems on SMD simulation Axel Kohlmeyer (Fri Dec 26 2008 - 14:31:18 CST)
CGMD parameters BIN ZHANG (Tue Dec 23 2008 - 20:06:32 CST)
- Re: CGMD parameters Peter Freddolino (Wed Dec 24 2008 - 07:27:25 CST)
compiling namd on SGI Altix Blake Mertz (Tue Dec 23 2008 - 11:09:10 CST)
tclforces: switch from md with external forces to standard md Vlad Cojocaru (Tue Dec 23 2008 - 09:01:36 CST)
- Re: tclforces: switch from md with external forces to standard md Peter Freddolino (Thu Jan 08 2009 - 13:38:05 CST)
  - Re: tclforces: switch from md with external forces to standard md Jerome Henin (Fri Jan 09 2009 - 10:24:24 CST)
addforce on the com of a group of atoms and loadforces command Vlad Cojocaru (Tue Dec 23 2008 - 07:57:29 CST)
Namd job terminates after ~10000+ itrations Sangamesh B (Tue Dec 23 2008 - 00:29:25 CST)
- Re: Namd job terminates after ~10000+ itrations Rudra Banerjee (Tue Dec 23 2008 - 05:57:16 CST)
(no subject) karthik s (Tue Dec 23 2008 - 00:07:39 CST)
- Re: Axel Kohlmeyer (Tue Dec 23 2008 - 10:22:51 CST)
NAMD for Intel Xeon Cluster with MPICH DimitryASuplatov (Mon Dec 22 2008 - 06:33:48 CST)
xsc file format Kyriakos Kachrimanis (Mon Dec 22 2008 - 03:24:46 CST)
- Re: xsc file format Luca Muccioli (Mon Dec 22 2008 - 05:22:16 CST)
  - Re: xsc file format Kyriakos Kachrimanis (Mon Dec 22 2008 - 06:40:44 CST)
    - Re: xsc file format Luca Muccioli (Mon Dec 22 2008 - 06:57:52 CST)
Problems with CUDA Build Christopher Share (Sun Dec 21 2008 - 23:58:47 CST)
regarding protein-dna complex simulation please reply....... prasun kumar (Sun Dec 21 2008 - 19:30:07 CST)
- Fwd: regarding protein-dna complex simulation please reply....... prasun kumar (Mon Dec 22 2008 - 09:44:08 CST)
  - Re: Fwd: regarding protein-dna complex simulation please reply....... JC Gumbart (Mon Dec 22 2008 - 13:30:58 CST)
    - Re: Fwd: regarding protein-dna complex simulation please reply....... JC Gumbart (Tue Dec 23 2008 - 01:21:11 CST)
alchemical FEP question Nandhini Sokkalingam (Fri Dec 19 2008 - 21:44:52 CST)
- Re: alchemical FEP question Christophe.Chipot_at_edam.uhp-nancy.fr (Sat Dec 20 2008 - 05:23:16 CST)
  - Re: alchemical FEP question seleg25_at_rsvs.ulaval.ca (Sun Dec 21 2008 - 12:14:41 CST)
    - Re: alchemical FEP question Chris Chipot (Sun Dec 21 2008 - 13:27:57 CST)
    - Re: alchemical FEP question SÃ©bastien LÃ©garÃ© (Sun Dec 21 2008 - 20:03:07 CST)
regarding protein-dna complex simulation prasun kumar (Fri Dec 19 2008 - 19:47:21 CST)
- Re: regarding protein-dna complex simulation Leonardo Trabuco (Fri Dec 19 2008 - 19:53:28 CST)
entropy calculation hodak_at_chips.ncsu.edu (Fri Dec 19 2008 - 15:18:28 CST)
- Re: entropy calculation Nicholas M Glykos (Sat Dec 20 2008 - 04:26:26 CST)
filling hydrophobic cavity with... methane? Sebastian Stolzenberg (Thu Dec 18 2008 - 16:10:00 CST)
- Re: filling hydrophobic cavity with... methane? Axel Kohlmeyer (Thu Dec 18 2008 - 17:44:23 CST)
Re: How to fix the Center of mass of protein when performing SMD? ÕÅÓÂ (Wed Dec 17 2008 - 22:06:14 CST)
- RE: How to fix the Center of mass of protein when performing SMD? JC Gumbart (Thu Dec 18 2008 - 23:22:39 CST)
topology/parameter file for ligands bo baker (Wed Dec 17 2008 - 20:56:50 CST)
angle deformation CHINDEA Vlad (Wed Dec 17 2008 - 17:00:49 CST)
- RE: angle deformation JC Gumbart (Thu Dec 18 2008 - 23:04:17 CST)
  - RE: angle deformation CHINDEA Vlad (Fri Dec 19 2008 - 18:02:06 CST)
    - Re: angle deformation Peter Freddolino (Fri Dec 19 2008 - 19:11:38 CST)
    - Re: angle deformation Leonardo Trabuco (Fri Dec 19 2008 - 19:45:44 CST)
patch DISU to 2 residues jose correa (Wed Dec 17 2008 - 11:58:14 CST)
- Re: patch DISU to 2 residues Eric H. Lee (Wed Dec 17 2008 - 12:13:20 CST)
  - Re: patch DISU to 2 residues jose correa (Wed Dec 17 2008 - 12:34:19 CST)
parameter for compiling Ting Zhou (Wed Dec 17 2008 - 07:42:06 CST)
- Re: parameter for compiling Peter Freddolino (Wed Dec 17 2008 - 07:53:37 CST)
  - Re: parameter for compiling Ting Zhou (Wed Dec 17 2008 - 07:57:23 CST)
Access to CVS Christopher Share (Tue Dec 16 2008 - 19:08:53 CST)
- Re: Access to CVS Roman Petrenko (Tue Dec 16 2008 - 20:14:00 CST)
failure in RATTLE Sangamesh B (Tue Dec 16 2008 - 08:20:24 CST)
- Re: failure in RATTLE Axel Kohlmeyer (Tue Dec 16 2008 - 13:26:09 CST)
  - Re: failure in RATTLE Sangamesh B (Wed Dec 17 2008 - 03:02:38 CST)
    - Re: failure in RATTLE Axel Kohlmeyer (Wed Dec 17 2008 - 09:52:13 CST)
    - Re: failure in RATTLE Sangamesh B (Thu Dec 18 2008 - 03:51:54 CST)
NAMD compile error itvasile_at_nipne.ro (Tue Dec 16 2008 - 10:43:20 CST)
- Re: NAMD compile error Axel Kohlmeyer (Tue Dec 16 2008 - 13:18:45 CST)
  - Re: NAMD compile error itvasile_at_nipne.ro (Tue Dec 16 2008 - 14:20:48 CST)
Unsure about current setting of Periodic Boundary Conditions Diego Alejandro Vargas (Tue Dec 16 2008 - 00:09:12 CST)
- Re: Unsure about current setting of Periodic Boundary Conditions Diego Alejandro Vargas (Mon Dec 22 2008 - 08:50:16 CST)
  - Re: Unsure about current setting of Periodic Boundary Conditions Peter Freddolino (Mon Dec 22 2008 - 13:58:18 CST)
    - Re: Unsure about current setting of Periodic Boundary Conditions Diego Alejandro Vargas (Tue Dec 23 2008 - 18:58:03 CST)
    - Re: Unsure about current setting of Periodic Boundary Conditions Axel Kohlmeyer (Tue Dec 23 2008 - 19:39:12 CST)
top_all22_model.inp bo baker (Mon Dec 15 2008 - 22:50:07 CST)
How to fix the Center of mass of protein when performing SMD? ÕÅÓÂ (Mon Dec 15 2008 - 21:54:20 CST)
compiling latest CVS on altix L. Michel Espinoza-Fonseca (Sat Dec 13 2008 - 10:10:24 CST)
To channel bond or not ? Nicholas M Glykos (Sat Dec 13 2008 - 04:33:02 CST)
reg parameter of ions balaji nagarajan (Fri Dec 12 2008 - 22:43:41 CST)
how to get 2 identical trajectories using NAMD in parallel Vlad Cojocaru (Fri Dec 12 2008 - 09:33:44 CST)
- Re: how to get 2 identical trajectories using NAMD in parallel gaillard_at_chimie.u-strasbg.fr (Fri Dec 12 2008 - 10:49:47 CST)
  - Re: how to get 2 identical trajectories using NAMD in parallel gaillard_at_chimie.u-strasbg.fr (Fri Dec 12 2008 - 11:03:26 CST)
- Re: how to get 2 identical trajectories using NAMD in parallel David Hardy (Fri Dec 12 2008 - 11:25:25 CST)
Single topology FEP Sébastien Légaré (Thu Dec 11 2008 - 15:05:07 CST)
- Re: Single topology FEP Jerome Henin (Thu Dec 11 2008 - 15:29:46 CST)
  - Re: Single topology FEP Sébastien Légaré (Fri Dec 12 2008 - 19:34:26 CST)
Re: Loops in tclForcesScript BIN ZHANG (Thu Dec 11 2008 - 14:45:38 CST)
Loops in tclForcesScript Yang, Lee Wei (Thu Dec 11 2008 - 12:01:08 CST)
how to apply restraints for phi and psi for alpha helix regions Achani K. Yatawara (Thu Dec 11 2008 - 07:42:37 CST)
- Re: how to apply restraints for phi and psi for alpha helix regions Leonardo Trabuco (Thu Dec 11 2008 - 13:12:14 CST)
  - Re: how to apply restraints for phi and psi for alpha helix regions Leonardo Trabuco (Thu Dec 11 2008 - 14:37:08 CST)
water box getting deformed sunita gupta (Thu Dec 11 2008 - 07:06:30 CST)
- Re: water box getting deformed Eric H. Lee (Thu Dec 11 2008 - 07:45:58 CST)
  - Re: water box getting deformed Joshua Adelman (Thu Dec 11 2008 - 11:01:34 CST)
- Re: water box getting deformed Peter Freddolino (Thu Dec 11 2008 - 11:43:15 CST)
srand in a tclforces script Vlad Cojocaru (Thu Dec 11 2008 - 06:55:53 CST)
- Re: srand in a tclforces script Vlad Cojocaru (Thu Dec 11 2008 - 08:31:37 CST)
FW: Multiplicity of parameters for improper bonds .............. of 1 exceeded. CHINDEA Vlad (Thu Dec 11 2008 - 06:17:20 CST)
- Re: FW: Multiplicity of parameters for improper bonds .............. of 1 exceeded. Peter Freddolino (Thu Dec 11 2008 - 11:51:15 CST)
(no subject) CHINDEA Vlad (Thu Dec 11 2008 - 06:12:05 CST)
DMF solvent parameters Austin B. Yongye (Wed Dec 10 2008 - 16:08:17 CST)
POLL: free energy of conformational change Jerome Henin (Wed Dec 10 2008 - 10:25:14 CST)
phi and psi restraints for 2 helix regions Achani K. Yatawara (Wed Dec 10 2008 - 07:13:57 CST)
problem in solvating the protein sunita gupta (Wed Dec 10 2008 - 06:14:50 CST)
- RE: problem in solvating the protein JC Gumbart (Wed Dec 10 2008 - 08:13:06 CST)
minimization with amberff ramya narasimhan (Wed Dec 10 2008 - 01:47:34 CST)
- Re: minimization with amberff Leonardo Trabuco (Wed Dec 10 2008 - 02:15:38 CST)
  - Re: minimization with amberff ramya narasimhan (Wed Dec 10 2008 - 06:02:16 CST)
    - Re: minimization with amberff Leonardo Trabuco (Wed Dec 10 2008 - 06:09:44 CST)
    - Re: minimization with amberff ramya narasimhan (Wed Dec 10 2008 - 22:02:35 CST)
Reading multiple .log files Anirban Ghosh (Tue Dec 09 2008 - 22:42:15 CST)
- Re: Reading multiple .log files JC Gumbart (Wed Dec 10 2008 - 16:03:11 CST)
  - Re: Reading multiple .log files Anirban Ghosh (Wed Dec 10 2008 - 23:21:48 CST)
- Re: Reading multiple .log files Alexander A. Vakhrushev (Wed Dec 10 2008 - 21:48:17 CST)
How to reverse the smd pcv pulling simulation Wang,Ying (Tue Dec 09 2008 - 16:49:29 CST)
tcl forces/membranes David A. Horita (Tue Dec 09 2008 - 15:28:07 CST)
Wrap ions? Rabab Toubar (Tue Dec 09 2008 - 10:56:07 CST)
Increase the decimal points of energy output Yang, Lee Wei (Tue Dec 09 2008 - 05:14:10 CST)
- Re: Increase the decimal points of energy output Robert Brunner (Tue Dec 09 2008 - 12:14:48 CST)
  - RE: Increase the decimal points of energy output Yang, Lee Wei (Tue Dec 09 2008 - 20:26:16 CST)
Coulombic virials Benjamin Roberts (Mon Dec 08 2008 - 22:14:00 CST)
Output force acting on each atom in the system Yang, Lee Wei (Mon Dec 08 2008 - 09:10:26 CST)
parameters and topology file needed for coarse-grain simulation sunita gupta (Mon Dec 08 2008 - 04:35:38 CST)
- Re: parameters and topology file needed for coarse-grain simulation BIN ZHANG (Mon Dec 08 2008 - 11:12:22 CST)
TCL8.5? or Christopher Hartshorn (Sun Dec 07 2008 - 23:16:42 CST)
- Re: TCL8.5? or Axel Kohlmeyer (Mon Dec 08 2008 - 03:36:50 CST)
CGMD timestep BIN ZHANG (Sun Dec 07 2008 - 14:44:23 CST)
- Re: CGMD timestep Axel Kohlmeyer (Mon Dec 08 2008 - 03:26:43 CST)
  - Re: CGMD timestep BIN ZHANG (Mon Dec 08 2008 - 11:29:05 CST)
Equilibration simulation too slow. Diego Alejandro Vargas (Sun Dec 07 2008 - 09:59:35 CST)
- Re: Equilibration simulation too slow. Christopher Gillespie (Sun Dec 07 2008 - 10:43:17 CST)
error in explicit membrane protein simulations gurvisha_at_leadinvent.com (Sat Dec 06 2008 - 04:11:50 CST)
HP Cluster Platform 4000 Hannes Loeffler (Fri Dec 05 2008 - 07:52:02 CST)
- Re: HP Cluster Platform 4000 Giacomo Fiorin (Fri Dec 05 2008 - 09:13:07 CST)
  - namd2 erratic performance over 104 procs Zailo Leite (Fri Dec 05 2008 - 12:52:36 CST)
    - Re: namd2 erratic performance over 104 procs Axel Kohlmeyer (Sat Dec 06 2008 - 03:18:29 CST)
Energy conversation Alexander A. Vakhrushev (Fri Dec 05 2008 - 07:51:06 CST)
- Re: Energy conversation Roman Petrenko (Fri Dec 05 2008 - 20:48:24 CST)
  - Re: Energy conversation Alexander A. Vakhrushev (Fri Dec 05 2008 - 23:06:30 CST)
    - Re: Energy conversation Peter Freddolino (Sat Dec 06 2008 - 00:39:56 CST)
    - Re: Energy conversation Alexander A. Vakhrushev (Sat Dec 06 2008 - 01:23:26 CST)
output while tclforces active Vlad Cojocaru (Fri Dec 05 2008 - 02:46:10 CST)
Electron density profile? BIN ZHANG (Fri Dec 05 2008 - 01:40:53 CST)
- Re: Electron density profile? Leonardo Trabuco (Fri Dec 05 2008 - 01:59:05 CST)
regarding writemol2 jani sahil (Thu Dec 04 2008 - 23:16:49 CST)
- Re: regarding writemol2 Axel Kohlmeyer (Fri Dec 05 2008 - 03:13:48 CST)
install namd on dell power edge 1900 Ramon Rocha (Thu Dec 04 2008 - 11:43:08 CST)
Reading multiple .log files into one Anirban Ghosh (Thu Dec 04 2008 - 08:25:05 CST)
- Re: Reading multiple .log files into one Eric H. Lee (Thu Dec 04 2008 - 08:59:19 CST)
  - Re: Reading multiple .log files into one Anirban Ghosh (Mon Dec 08 2008 - 03:21:07 CST)
- Re: Reading multiple .log files into one Robert Brunner (Thu Dec 04 2008 - 09:14:29 CST)
create inositol molecule politr_at_huji.ac.il (Wed Dec 03 2008 - 10:48:38 CST)
- Re: create inositol molecule dimka (Thu Dec 04 2008 - 12:11:20 CST)
mpirun compilation for NAMD Neelanjana Sengupta (Wed Dec 03 2008 - 07:46:54 CST)
- Re: mpirun compilation for NAMD Giacomo Fiorin (Wed Dec 03 2008 - 10:42:44 CST)
  - Re: mpirun compilation for NAMD Warner Yuen (Thu Dec 04 2008 - 12:08:37 CST)
MacOSX 64bit binaries Christopher Hartshorn (Wed Dec 03 2008 - 01:34:26 CST)
- Re: MacOSX 64bit binaries Giacomo Fiorin (Wed Dec 03 2008 - 10:49:10 CST)
  - Re: MacOSX 64bit binaries Axel Kohlmeyer (Wed Dec 03 2008 - 15:14:23 CST)
  - Re: MacOSX 64bit binaries Christopher Hartshorn (Fri Dec 05 2008 - 11:55:02 CST)
submit namd job in cluster Rudra Banerjee (Tue Dec 02 2008 - 23:04:29 CST)
CGMD problem BIN ZHANG (Tue Dec 02 2008 - 11:10:34 CST)
- Re: CGMD problem Peter Freddolino (Tue Dec 02 2008 - 22:39:52 CST)
  - Re: CGMD problem Anton Arkhipov (Wed Dec 03 2008 - 11:39:32 CST)
Help: do you have the top parameter of Gla Wang,Ying (Tue Dec 02 2008 - 10:27:56 CST)
bash: namd2: command not found Sukesh Chandra Gain (Tue Dec 02 2008 - 00:31:42 CST)
- Re: bash: namd2: command not found Joshua Adelman (Tue Dec 02 2008 - 00:40:37 CST)
Modification of the NAMD forcefield functions ??? Maxim Paliy (Mon Dec 01 2008 - 13:39:31 CST)
Errors on Missing Atoms for Some Bonds Taekyung Kwon (Sun Nov 30 2008 - 22:19:29 CST)
Biotin-X charmm topology Taekyung Kwon (Sat Nov 29 2008 - 17:13:47 CST)
SMD-Applied Forces and Analysis ÖÜÎÄ²ý (Fri Nov 28 2008 - 02:27:24 CST)
constraint failure problem. ydhuang2727 (Wed Nov 26 2008 - 20:54:30 CST)
namd cvs compilation BIN ZHANG (Wed Nov 26 2008 - 18:55:07 CST)
- Re: namd cvs compilation BIN ZHANG (Wed Nov 26 2008 - 19:24:19 CST)
  - Re: namd cvs compilation BIN ZHANG (Thu Nov 27 2008 - 01:00:14 CST)
force potentials for residue-based CG Dolan, Michael (NIH/NIAID) [C] (Wed Nov 26 2008 - 13:36:51 CST)
TIP4 water model NAMD Mehdi Bagheri-Hamaneh (Wed Nov 26 2008 - 10:28:25 CST)
- Re: TIP4 water model NAMD Axel Kohlmeyer (Wed Nov 26 2008 - 11:19:20 CST)
  - Re: TIP4 water model NAMD Mehdi Bagheri-Hamaneh (Wed Nov 26 2008 - 12:15:01 CST)
    - Re: TIP4 water model NAMD Peter Freddolino (Wed Nov 26 2008 - 20:39:05 CST)
NAMD CVS Installation Anirban Ghosh (Wed Nov 26 2008 - 05:53:38 CST)
- Re: NAMD CVS Installation Axel Kohlmeyer (Wed Nov 26 2008 - 10:53:10 CST)
RAM/node Alessio Alexiadis (Wed Nov 26 2008 - 05:37:17 CST)
How do you keep atoms a fixed distance apart? timko_at_physics.usyd.edu.au (Wed Nov 26 2008 - 00:59:47 CST)
- Re: How do you keep atoms a fixed distance apart? Leonardo Trabuco (Wed Nov 26 2008 - 01:23:18 CST)
Re: Compiling 8Core macs Christopher Hartshorn (Tue Nov 25 2008 - 15:28:51 CST)
- Re: Compiling 8Core macs Robert Brunner (Wed Nov 26 2008 - 15:21:58 CST)
Re: vmd-l: CG bead definition BIN ZHANG (Tue Nov 25 2008 - 15:01:37 CST)
- Re: vmd-l: CG bead definition Anton Arkhipov (Tue Nov 25 2008 - 15:31:45 CST)
MD-problems-GPCR in POPC bilayer jose correa (Tue Nov 25 2008 - 09:30:50 CST)
- Re: MD-problems-GPCR in POPC bilayer JC Gumbart (Mon Dec 01 2008 - 12:53:00 CST)
Free energy calculation fixing the dihedrals Jagan Mohan (Tue Nov 25 2008 - 01:09:46 CST)
- Free energy calculation fixing the dihedrals Jagan Mohan (Tue Nov 25 2008 - 01:12:10 CST)
  - Re: Free energy calculation fixing the dihedrals Luca Bellucci (Tue Nov 25 2008 - 02:48:06 CST)
Compiling 8Core macs Christopher Hartshorn (Mon Nov 24 2008 - 17:03:40 CST)
- namd energy self interaction reality check Thomas C. Bishop (Mon Nov 24 2008 - 23:38:51 CST)
  - Re: namd energy self interaction reality check Peter Freddolino (Tue Nov 25 2008 - 08:00:25 CST)
NAMD with CUDA Status ? David McGiven (Mon Nov 24 2008 - 11:06:05 CST)
NAMD with mpirun Neelanjana Sengupta (Mon Nov 24 2008 - 05:27:15 CST)
- Re: NAMD with mpirun Axel Kohlmeyer (Mon Nov 24 2008 - 06:08:11 CST)
build missing residues in pdb Anuradha Mittal (Sun Nov 23 2008 - 18:48:47 CST)
- Re: build missing residues in pdb Schreiner Eduard (Mon Nov 24 2008 - 00:09:18 CST)
regarding cgmd jani sahil (Sun Nov 23 2008 - 23:14:34 CST)
- Re: regarding cgmd Peter Freddolino (Mon Nov 24 2008 - 21:17:10 CST)
Re- Loading .vel file in VMD dipti lele (Sun Nov 23 2008 - 19:18:06 CST)
can the harmonic constraint parameters be changed between run or minimize? Chongbo Sun (Sun Nov 23 2008 - 14:03:39 CST)
namdEnergy gives significantly different values from those in log file? Steven Samuel Plotkin (Sat Nov 22 2008 - 23:39:40 CST)
- Re: namdEnergy gives significantly different values from those in log file? Peter Freddolino (Sun Nov 23 2008 - 01:55:51 CST)
  - Re: namdEnergy gives significantly different values from those in log file? Steven Samuel Plotkin (Mon Nov 24 2008 - 01:01:21 CST)
- Re: namdEnergy gives significantly different values from those in log file? Peter Freddolino (Sun Nov 23 2008 - 12:33:56 CST)
  - Re: namdEnergy gives significantly different values from those in log file? Steven Samuel Plotkin (Mon Nov 24 2008 - 01:50:02 CST)
bond length in terminal patches CHINDEA Vlad (Sat Nov 22 2008 - 16:29:55 CST)
- Re: bond length in terminal patches Peter Freddolino (Sat Nov 22 2008 - 20:33:38 CST)
Direction of steered molecular dynamics ÖÜÎÄ²ý (Sat Nov 22 2008 - 08:39:51 CST)
A way to check for non-unique coordinates? Diego Alejandro Vargas (Thu Nov 20 2008 - 23:15:58 CST)
Loading .vel file in VMD dipti lele (Thu Nov 20 2008 - 23:03:42 CST)
- Re: vmd-l: Loading .vel file in VMD Axel Kohlmeyer (Fri Nov 21 2008 - 03:45:39 CST)
  - Re: Re: vmd-l: Loading .vel file in VMD Thomas C. Bishop (Fri Nov 21 2008 - 09:11:42 CST)
A way to check for non-unique coordinates? Diego Alejandro Vargas (Thu Nov 20 2008 - 21:22:21 CST)
- Re: A way to check for non-unique coordinates? Axel Kohlmeyer (Fri Nov 21 2008 - 04:36:21 CST)
ERROR: Constraint failure in RATTLE algorithm for atom 872 ydhuang2727 (Thu Nov 20 2008 - 19:49:08 CST)
namd latest CVS version on BluegeneP George Madalin Giambasu (Thu Nov 20 2008 - 16:05:13 CST)
Fwd: How can I load two forcefied at the same time Wang,Ying (Thu Nov 20 2008 - 13:24:10 CST)
- Re: Fwd: How can I load two forcefied at the same time Leonardo Trabuco (Fri Nov 21 2008 - 11:16:34 CST)
H-bond occupancy in nucleic acids Tianjiao Wang (Thu Nov 20 2008 - 10:08:27 CST)
namdplot Unmatched " error maria goranovic (Thu Nov 20 2008 - 08:50:52 CST)
- Re: namdplot Unmatched " error JC Gumbart (Fri Nov 21 2008 - 22:18:48 CST)
  - Re: namdplot Unmatched " error maria goranovic (Wed Nov 26 2008 - 04:58:43 CST)
Regarding Installation Jagan Mohan (Thu Nov 20 2008 - 04:22:49 CST)
- Re: Regarding Installation Gary Lyons (Thu Nov 20 2008 - 22:12:34 CST)
- Re: Regarding Installation Alexander A. Vakhrushev (Thu Nov 20 2008 - 22:45:22 CST)
pairlist i_upper mismatch! Diego Alejandro Vargas (Wed Nov 19 2008 - 22:28:41 CST)
- Re: pairlist i_upper mismatch! Peter Freddolino (Thu Nov 20 2008 - 09:03:56 CST)
  - Re: pairlist i_upper mismatch! Diego Alejandro Vargas (Thu Nov 20 2008 - 10:52:34 CST)
- Re: pairlist i_upper mismatch! Diego Alejandro Vargas (Sat Nov 22 2008 - 22:20:31 CST)
  - Re: Re: pairlist i_upper mismatch! Schreiner Eduard (Sun Nov 23 2008 - 02:08:40 CST)
TclBC - multiple iteration Chi-Cheng Chiu (Wed Nov 19 2008 - 12:15:48 CST)
How to fix atoms during minimization? Anirban Ghosh (Wed Nov 19 2008 - 08:06:29 CST)
- Re£ºHow to fix atoms during minimization? ´÷Î°Ãñ (Wed Nov 19 2008 - 19:52:49 CST)
FEP simulations? Christopher Hartshorn (Tue Nov 18 2008 - 13:19:13 CST)
- Re: FEP simulations? Jerome Henin (Tue Nov 18 2008 - 15:43:42 CST)
  - FEP on charged residue mutation Sebastian Stolzenberg (Fri Nov 21 2008 - 16:22:45 CST)
  - Re: FEP simulations? Christopher Hartshorn (Mon Jan 05 2009 - 03:20:53 CST)
    - Re: FEP simulations? Chris Chipot (Mon Jan 05 2009 - 05:24:00 CST)
    - "within" command in NAMD? Sebastian Stolzenberg (Mon Jan 05 2009 - 14:20:51 CST)
periodic cell has become too small for original patch grid! ydhuang2727 (Tue Nov 18 2008 - 02:54:42 CST)
- Re: periodic cell has become too small for original patch grid! Axel Kohlmeyer (Tue Nov 18 2008 - 03:33:59 CST)
- Re: periodic cell has become too small for original patch grid! Eric H. Lee (Tue Nov 18 2008 - 03:22:03 CST)
restart sripad chandan (Mon Nov 17 2008 - 23:14:12 CST)
- Re: restart Christopher Hartshorn (Tue Nov 18 2008 - 01:49:32 CST)
FEP calculation of dimerization Christopher Hartshorn (Sun Nov 16 2008 - 23:45:05 CST)
- How do you evaluate forces on a fixed atom? Bill K (Mon Nov 17 2008 - 15:33:38 CST)
ABF:problems with calculating Free Energy Profile supram_at_nankai.edu.cn (Sun Nov 16 2008 - 20:55:39 CST)
Re: langevinDamping Hyundeok Song (Sun Nov 16 2008 - 18:03:58 CST)
Problems with minimization Diego Alejandro Vargas (Sat Nov 15 2008 - 10:57:23 CST)
- Re: Problems with minimization Christopher Gillespie (Sat Nov 15 2008 - 11:38:26 CST)
  - Re: Problems with minimization Diego Alejandro Vargas (Sat Nov 15 2008 - 11:53:06 CST)
How can I monitor the force during constant velocity SMD? wayj86 wayj86 (Sat Nov 15 2008 - 07:26:02 CST)
langevinDamping Roman Petrenko (Fri Nov 14 2008 - 20:45:10 CST)
constraint failure in RATTLE algorithm for atom 3205 ydhuang2727 (Fri Nov 14 2008 - 19:42:20 CST)
- Re: constraint failure in RATTLE algorithm for atom 3205 Schreiner Eduard (Fri Nov 14 2008 - 20:13:30 CST)
NAMD Simulation error Anirban Ghosh (Fri Nov 14 2008 - 02:36:16 CST)
- Re: NAMD Simulation error Anton Arkhipov (Fri Nov 14 2008 - 15:10:27 CST)
NAMD Simulation error Anirban Ghosh (Wed Nov 12 2008 - 22:41:07 CST)
Load balancing off Jonathan Bourne (Wed Nov 12 2008 - 12:20:25 CST)
Force field parameters Rabab Toubar (Wed Nov 12 2008 - 10:27:58 CST)
- Re: Force field parameters Ramya Gamini (Wed Nov 12 2008 - 12:05:41 CST)
scalability problem on linux cluster Ruchi Sachdeva (Wed Nov 12 2008 - 08:28:09 CST)
- Re: scalability problem on linux cluster Giacomo Fiorin (Wed Nov 12 2008 - 09:40:07 CST)
  - Re: scalability problem on linux cluster Ruchi Sachdeva (Wed Nov 12 2008 - 10:14:49 CST)
- Re: scalability problem on linux cluster Axel Kohlmeyer (Wed Nov 12 2008 - 11:10:52 CST)
par-extraterms.inp file needed mahesh kulharia (Wed Nov 12 2008 - 04:07:32 CST)
- Re: par-extraterms.inp file needed JC Gumbart (Fri Nov 21 2008 - 22:22:18 CST)
failure in RATTLE algorithm using the adaptive biasing force method steve.kaminski_at_mail.tu-berlin.de (Tue Nov 11 2008 - 13:43:51 CST)
- Re: failure in RATTLE algorithm using the adaptive biasing force method Jerome Henin (Tue Nov 11 2008 - 14:19:01 CST)
- Re: failure in RATTLE algorithm using the adaptive biasing force method Giacomo Fiorin (Tue Nov 11 2008 - 14:52:19 CST)
  - Re: failure in RATTLE algorithm using the adaptive biasing force method steve.kaminski_at_mail.tu-berlin.de (Wed Nov 12 2008 - 03:37:11 CST)
    - Re: failure in RATTLE algorithm using the adaptive biasing force method Jerome Henin (Wed Nov 12 2008 - 08:43:56 CST)
converting AMBER trajectory file to CHARMM trajectory file sunita gupta (Tue Nov 11 2008 - 04:37:27 CST)
- Re: converting AMBER trajectory file to CHARMM trajectory file Giacomo Fiorin (Tue Nov 11 2008 - 08:43:54 CST)
FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE HT1 ramya narasimhan (Tue Nov 11 2008 - 03:23:43 CST)
- Re: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE HT1 Giacomo Fiorin (Tue Nov 11 2008 - 08:58:10 CST)
  - Re: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE HT1 ramya narasimhan (Tue Nov 11 2008 - 22:18:25 CST)
solvate using Helmut Grubmuller's SOLVATE and then VMD, then how to minimize properly! ydhuang2727 (Tue Nov 11 2008 - 02:30:40 CST)
- Re: solvate using Helmut Grubmuller's SOLVATE and then VMD, then how to minimize properly! Peter Freddolino (Tue Nov 11 2008 - 10:29:34 CST)
protein instability sripad chandan (Mon Nov 10 2008 - 21:27:18 CST)
- Re: protein instability Peter Freddolino (Tue Nov 11 2008 - 10:26:36 CST)
Simulation issues: water box deformation after minimization and shifting protein coordinates during production run Mamta Mohan (Mon Nov 10 2008 - 10:50:57 CST)
- Re: Simulation issues: water box deformation after minimization and shifting protein coordinates during production run Peter Freddolino (Mon Nov 10 2008 - 11:26:05 CST)
  - Re: Simulation issues: water box deformation after minimization and shifting protein coordinates during production run Mamta Mohan (Mon Nov 10 2008 - 13:39:18 CST)
  - Re: Simulation issues: water box deformation after minimization and shifting protein coordinates during production run Mamta Mohan (Mon Nov 10 2008 - 13:48:49 CST)
- Non-standard amino acid Austin B. Yongye (Mon Nov 10 2008 - 17:05:01 CST)
Error while using NAMD Marcus Batista (Sun Nov 09 2008 - 15:54:38 CST)
- Re: Error while using NAMD Eric H. Lee (Sun Nov 09 2008 - 16:00:57 CST)
- Re: Error while using NAMD Axel Kohlmeyer (Sun Nov 09 2008 - 16:16:32 CST)
impropers for aromatic residues CHINDEA Vlad (Sat Nov 08 2008 - 15:17:44 CST)
- Re: impropers for aromatic residues Jerome Henin (Sun Nov 09 2008 - 15:37:43 CST)
Charm++ Fatal error ! Periodic cell has become too small for original patch grid! CHINDEA Vlad (Thu Nov 06 2008 - 17:40:35 CST)
- Re: Charm++ Fatal error ! Periodic cell has become too small for original patch grid! Joshua Adelman (Fri Nov 07 2008 - 11:31:59 CST)
  - Re: Charm++ Fatal error ! Periodic cell has become too small for original patch grid! Dave Rogers (Fri Nov 07 2008 - 12:23:52 CST)
generating psf & energy calculation for unusual amino acid - Aib balaji nagarajan (Thu Nov 06 2008 - 21:57:17 CST)
- RE: generating psf & energy calculation for unusual amino acid - Aib JC Gumbart (Fri Nov 07 2008 - 00:43:29 CST)
PME non-zero charge Roman Petrenko (Thu Nov 06 2008 - 15:07:56 CST)
- Re: PME non-zero charge Axel Kohlmeyer (Thu Nov 06 2008 - 16:49:09 CST)
- Re: PME non-zero charge Peter Freddolino (Thu Nov 06 2008 - 18:09:27 CST)
  - Re: PME non-zero charge Roman Petrenko (Thu Nov 06 2008 - 19:42:25 CST)
  - RE: PME non-zero charge Himanshu Khandelia (Fri Nov 07 2008 - 01:10:42 CST)
    - RE: PME non-zero charge Axel Kohlmeyer (Fri Nov 07 2008 - 01:51:03 CST)
NAMD2.6 appears to be freezing at or during load balancing Jonathan Bourne (Thu Nov 06 2008 - 12:33:23 CST)
segmentation fault? BIN ZHANG (Wed Nov 05 2008 - 15:58:58 CST)
- Re: segmentation fault? Giacomo Fiorin (Wed Nov 05 2008 - 17:46:19 CST)
  - Re: segmentation fault? BIN ZHANG (Wed Nov 05 2008 - 18:33:29 CST)
Add ions ydhuang2727 (Wed Nov 05 2008 - 02:16:33 CST)
- Re: Add ions Christopher Gillespie (Wed Nov 05 2008 - 07:06:51 CST)
Re: building namd on CRAY-XT3 BIN ZHANG (Wed Nov 05 2008 - 00:16:34 CST)
- Re: building namd on CRAY-XT3 Axel Kohlmeyer (Wed Nov 05 2008 - 00:49:51 CST)
  - Re: building namd on CRAY-XT3 BIN ZHANG (Wed Nov 05 2008 - 01:19:37 CST)
    - Re: building namd on CRAY-XT3 Axel Kohlmeyer (Wed Nov 05 2008 - 02:10:32 CST)
building namd on CRAY-XT3 BIN ZHANG (Tue Nov 04 2008 - 13:38:35 CST)
Atoms moving too fast OR constraint failure in RATTLE algorithm Diego Alejandro Vargas (Tue Nov 04 2008 - 12:34:00 CST)
- Re: Atoms moving too fast OR constraint failure in RATTLE algorithm Joshua Adelman (Tue Nov 04 2008 - 12:58:44 CST)
  - Re: Atoms moving too fast OR constraint failure in RATTLE algorithm Diego Alejandro Vargas (Wed Nov 05 2008 - 23:17:56 CST)
  - Re: Atoms moving too fast OR constraint failure in RATTLE algorithm Diego Alejandro Vargas (Sat Nov 08 2008 - 17:31:30 CST)
    - Re: Atoms moving too fast OR constraint failure in RATTLE algorithm Diego Alejandro Vargas (Wed Nov 12 2008 - 19:00:37 CST)
How can I specify an exact initial velocity? wayj86 wayj86 (Tue Nov 04 2008 - 02:29:07 CST)
- Re: How can I specify an exact initial velocity? Jerome Henin (Tue Nov 04 2008 - 09:07:14 CST)
  - Re: How can I specify an exact initial velocity? wayj86 wayj86 (Tue Nov 04 2008 - 20:01:09 CST)
    - Re: How can I specify an exact initial velocity? Jerome Henin (Wed Nov 05 2008 - 03:56:46 CST)
log file problem ydhuang2727 (Mon Nov 03 2008 - 19:57:08 CST)
- Re: log file problem Peter Freddolino (Mon Nov 03 2008 - 20:17:05 CST)
  - Re: log file problem BIN ZHANG (Mon Nov 03 2008 - 20:49:30 CST)
Fw: NAMD mail bounce problem. Mamta Mohan (Mon Nov 03 2008 - 12:35:46 CST)
- Fw: NAMD mail bounce problem. Mamta Mohan (Wed Nov 05 2008 - 16:59:15 CST)
Approach energy with SMD Austin B. Yongye (Mon Nov 03 2008 - 11:01:26 CST)
- cyclic peptides Austin B. Yongye (Mon Nov 03 2008 - 16:38:40 CST)
  - Re: cyclic peptides Peter Freddolino (Mon Nov 03 2008 - 20:13:14 CST)
- Approach energy with SMD (2) Austin B. Yongye (Fri Nov 14 2008 - 13:31:36 CST)
multiple simulations sripad chandan (Sun Nov 02 2008 - 22:32:11 CST)
- Re: multiple simulations Sebastian Stolzenberg (Sun Nov 02 2008 - 23:15:00 CST)
(no subject) Bertrand P. S. Russell (Sat Nov 01 2008 - 20:50:16 CDT)
AMBER ff99SB on NAMD Luis Cunha (Sat Nov 01 2008 - 19:43:30 CDT)
- Re: AMBER ff99SB on NAMD Luca (Sun Nov 02 2008 - 02:26:52 CST)
  - Re: AMBER ff99SB on NAMD Luis Cunha (Sun Nov 02 2008 - 09:21:17 CST)
NAMD2.6 repeatedly freezing on new desktop Jonathan Bourne (Sat Nov 01 2008 - 16:03:53 CDT)
unsubscribe Bertrand P. S. Russell (Fri Oct 31 2008 - 23:10:48 CDT)
Two questions about free dynamics simulation wayj86 wayj86 (Fri Oct 31 2008 - 21:46:25 CDT)
Could I do the equilibration again with the same dcd file obtained? wayj86 wayj86 (Thu Oct 30 2008 - 20:40:09 CDT)
- Re: Could I do the equilibration again with the same dcd file obtained? Schreiner Eduard (Thu Oct 30 2008 - 21:42:54 CDT)
combining 2 dcd files into one Rabab Toubar (Thu Oct 30 2008 - 15:20:34 CDT)
- Re: combining 2 dcd files into one Christopher Gillespie (Thu Oct 30 2008 - 16:26:34 CDT)
- Re: combining 2 dcd files into one Anirban Ghosh (Fri Oct 31 2008 - 13:43:14 CDT)
Problem with temperature increase in equilibration. Diego Alejandro Vargas (Thu Oct 30 2008 - 11:14:54 CDT)
ions behavior in protein-water box: Emanuelle Bachelet (Wed Oct 29 2008 - 13:44:59 CDT)
- Re: ions behavior in protein-water box: Christopher Gillespie (Wed Oct 29 2008 - 15:05:19 CDT)
  - Re: ions behavior in protein-water box: Emanuelle Bachelet (Wed Oct 29 2008 - 16:56:10 CDT)
Why there is a bond between the two Hydrogens of the TIP3P water in Amber force field? Ming (Wed Oct 29 2008 - 10:20:31 CDT)
- Re: Why there is a bond between the two Hydrogens of the TIP3P water in Amber force field? Purushottam Dixit (Wed Oct 29 2008 - 10:36:42 CDT)
  - Re: Why there is a bond between the two Hydrogens of the TIP3P water in Amber force field? Peter Freddolino (Wed Oct 29 2008 - 11:07:13 CDT)
    - Re: Why there is a bond between the two Hydrogens of the TIP3P water in Amber force field? Neelanjana Sengupta (Thu Oct 30 2008 - 00:39:47 CDT)
    - Re: Why there is a bond between the two Hydrogens of the TIP3P water in Amber force field? Peter Freddolino (Thu Oct 30 2008 - 08:02:52 CDT)
  - Re: Why there is a bond between the two Hydrogens of the TIP3P water in Amber force field? Ming (Thu Oct 30 2008 - 01:51:16 CDT)
ABF backbone dihedral Sébastien Légaré (Tue Oct 28 2008 - 11:44:21 CDT)
Backbone dihedral ABF Sébastien Légaré (Tue Oct 28 2008 - 11:50:02 CDT)
ABF - using gyration Subramanian Vaitheeswaran (Tue Oct 28 2008 - 10:18:08 CDT)
- Re: ABF - using gyration Jerome Henin (Tue Oct 28 2008 - 11:52:49 CDT)
dcd to pdb conversion AyÅŸe Ã–zlem Aykut (Mon Oct 27 2008 - 03:28:16 CDT)
- Re: dcd to pdb conversion Eric H. Lee (Mon Oct 27 2008 - 03:39:09 CDT)
  - Re: dcd to pdb conversion AyÅŸe Ã–zlem Aykut (Mon Oct 27 2008 - 03:58:58 CDT)
    - Re: dcd to pdb conversion Eric H. Lee (Mon Oct 27 2008 - 04:11:51 CDT)
  - Re: dcd to pdb conversion L. Michel Espinoza-Fonseca (Mon Oct 27 2008 - 04:05:12 CDT)
- RE: dcd to pdb conversion Claw Isthelaw (Mon Oct 27 2008 - 04:35:26 CDT)
applying stress to study elasticity Lam Nguyen (Fri Oct 24 2008 - 11:06:35 CDT)
- Re: applying stress to study elasticity Jen Hsin (Fri Oct 24 2008 - 11:20:05 CDT)
  - Re: applying stress to study elasticity Lam Nguyen (Fri Oct 24 2008 - 12:56:49 CDT)
- Re: applying stress to study elasticity Axel Kohlmeyer (Fri Oct 24 2008 - 13:35:20 CDT)
CG Name Prefix Problem Anirban Ghosh (Fri Oct 24 2008 - 00:24:58 CDT)
- Re: CG Name Prefix Problem Anton Arkhipov (Fri Oct 24 2008 - 10:30:05 CDT)
How to keep Total Energy constant when an external force is added? Fred (Rui FENG) (Wed Oct 22 2008 - 22:48:43 CDT)
- Re: How to keep Total Energy constant when an external force is added? Axel Kohlmeyer (Thu Oct 23 2008 - 09:58:15 CDT)
  - Re: How to keep Total Energy constant when an external force is added? Fred (Rui FENG) (Thu Oct 23 2008 - 11:58:29 CDT)
- Re: How to keep Total Energy constant when an external force is added? Jerome Henin (Thu Oct 23 2008 - 10:11:33 CDT)
Membrane Simulations Anshu Bhatia (Wed Oct 22 2008 - 20:04:38 CDT)
- Re: Membrane Simulations Vlad Cojocaru (Thu Oct 23 2008 - 02:06:33 CDT)
  - Re: Membrane Simulations Anshu Bhatia (Tue Oct 28 2008 - 12:31:55 CDT)
Non Bonded Paramters abhijit ramachandran (Tue Oct 21 2008 - 17:25:04 CDT)
- Re: Non Bonded Paramters Jerome Henin (Tue Oct 21 2008 - 18:05:22 CDT)
Calcium ion binding protein vsweta_at_iastate.edu (Tue Oct 21 2008 - 16:27:31 CDT)
- RE: Calcium ion binding protein JC Gumbart (Wed Oct 22 2008 - 09:40:47 CDT)
fixedAtoms may not be enabled in a script Christopher Hartshorn (Tue Oct 21 2008 - 10:54:17 CDT)
restart_minimization sripad chandan (Tue Oct 21 2008 - 05:30:12 CDT)
- Re: restart_minimization Peter Freddolino (Tue Oct 21 2008 - 07:30:39 CDT)
Re: from NPT to NVT Hiroaki Maekawa (Mon Oct 20 2008 - 12:00:46 CDT)
NVT/NPT pressures w fixed particles Arturas Ziemys (Mon Oct 20 2008 - 10:03:43 CDT)
Inquire on gradual temperature increase. Diego Alejandro Vargas (Mon Oct 20 2008 - 08:59:46 CDT)
- Re: Inquire on gradual temperature increase. jose correa (Mon Oct 20 2008 - 09:39:40 CDT)
rms gradient sripad chandan (Mon Oct 20 2008 - 04:59:07 CDT)
- Re: rms gradient Peter Freddolino (Mon Oct 20 2008 - 07:51:40 CDT)
How to set values for cellBasisVector and PMEGridSize properly ydhuang2727 (Mon Oct 20 2008 - 03:00:15 CDT)
- Re: How to set values for cellBasisVector and PMEGridSize properly Peter Freddolino (Mon Oct 20 2008 - 07:06:16 CDT)
- Re: How to set values for cellBasisVector and PMEGridSize properly Anirban Ghosh (Mon Oct 20 2008 - 08:30:23 CDT)
restart PMF: grow phase required? "lambdaRef"? more documentation on NAMD PMF? Sebastian Stolzenberg (Sun Oct 19 2008 - 13:43:56 CDT)
- Re: restart PMF: grow phase required? "lambdaRef"? more documentation on NAMD PMF? Sebastian Stolzenberg (Sat Nov 01 2008 - 12:58:37 CDT)
  - Re: restart PMF: grow phase required? "lambdaRef"? more documentation on NAMD PMF? Peter Freddolino (Sat Nov 01 2008 - 17:33:10 CDT)
Atom velocities too high. Diego Alejandro Vargas (Sun Oct 19 2008 - 09:59:10 CDT)
- Re: Atom velocities too high. Joshua Adelman (Sun Oct 19 2008 - 11:48:34 CDT)
How can I calculate the distance between two atoms frame by frame? wayj86 wayj86 (Sat Oct 18 2008 - 21:15:25 CDT)
- Re: How can I calculate the distance between two atoms frame by frame? Axel Kohlmeyer (Sat Oct 18 2008 - 22:07:13 CDT)
  - Re: How can I calculate the distance between two atoms frame by frame? Grace Brannigan (Sun Oct 19 2008 - 01:39:03 CDT)
- Re: How can I calculate the distance between two atoms frame by frame? Grace Brannigan (Sat Oct 18 2008 - 23:05:45 CDT)
- Re: How can I calculate the distance between two atoms frame by frame? Jerome Henin (Sun Oct 19 2008 - 09:51:51 CDT)
from NPT to NVT Hiroaki Maekawa (Fri Oct 17 2008 - 16:37:16 CDT)
RE: Using NAMD to calculate pair energy with many subset permutations brmorgan_at_clarku.edu (Fri Oct 17 2008 - 09:39:05 CDT)
- Re: Using NAMD to calculate pair energy with many subset permutations Peter Freddolino (Fri Oct 17 2008 - 10:07:28 CDT)
right_protocal sripad chandan (Fri Oct 17 2008 - 06:02:54 CDT)
restraint on a group of atoms at their center of mass? Dan W. (Thu Oct 16 2008 - 14:16:19 CDT)
Error while running NPT Simulation Nd S (Thu Oct 16 2008 - 12:44:50 CDT)
- Re: Error while running NPT Simulation Axel Kohlmeyer (Thu Oct 16 2008 - 13:27:24 CDT)
- Re: Error while running NPT Simulation Audrey Salazar (Thu Oct 16 2008 - 13:51:30 CDT)
  - Re: Error while running NPT Simulation Audrey Salazar (Thu Oct 16 2008 - 13:55:55 CDT)
- Re: Error while running NPT Simulation Peter Freddolino (Thu Oct 16 2008 - 14:07:26 CDT)
Pressure related issue Anirban Ghosh (Wed Oct 15 2008 - 08:23:29 CDT)
- Re: Pressure related issue Axel Kohlmeyer (Thu Oct 16 2008 - 09:16:02 CDT)
Full Electrostatic Calculations on Protein in Vacuo MIke S (Thu Oct 16 2008 - 02:07:29 CDT)
- Re: Full Electrostatic Calculations on Protein in Vacuo Axel Kohlmeyer (Thu Oct 16 2008 - 10:08:23 CDT)
  - Re: Full Electrostatic Calculations on Protein in Vacuo Brian Bennion (Thu Oct 16 2008 - 10:19:32 CDT)
  - Re: Full Electrostatic Calculations on Protein in Vacuo MIke S (Fri Oct 24 2008 - 16:26:02 CDT)
ERROR: DIDN'T FIND "NATOM" IN PSF FILE Diego Alejandro Vargas (Wed Oct 15 2008 - 23:12:01 CDT)
- Re: ERROR: DIDN'T FIND "NATOM" IN PSF FILE jose correa (Thu Oct 16 2008 - 07:19:50 CDT)
Density Calculation Nd S (Wed Oct 15 2008 - 22:25:57 CDT)
Getting total energy of system + pressure and temperature bath. Audrey Salazar (Wed Oct 15 2008 - 16:23:12 CDT)
- Re: Getting total energy of system + pressure and temperature bath. Jerome Henin (Thu Oct 16 2008 - 11:21:55 CDT)
Using NAMD to calculate pair energy with many subset permutations brmorgan_at_clarku.edu (Wed Oct 15 2008 - 13:08:42 CDT)
- RE: Using NAMD to calculate pair energy with many subset permutations JC Gumbart (Fri Oct 17 2008 - 00:15:23 CDT)
Quantitative Test for Equilibration of Data Time Series Joshua Adelman (Wed Oct 15 2008 - 12:06:00 CDT)
- Re: Quantitative Test for Equilibration of Data Time Series Dave Rogers (Wed Oct 15 2008 - 13:27:23 CDT)
- Re: Quantitative Test for Equilibration of Data Time Series Peter Freddolino (Wed Oct 15 2008 - 15:01:18 CDT)
megatest test failure/MPI problem Meij, Henk (Wed Oct 15 2008 - 10:14:48 CDT)
- Re: megatest test failure/MPI problem Axel Kohlmeyer (Wed Oct 15 2008 - 10:50:14 CDT)
  - RE: megatest test failure/MPI problem Meij, Henk (Wed Oct 15 2008 - 13:26:52 CDT)
    - RE: megatest test failure/MPI problem Axel Kohlmeyer (Wed Oct 15 2008 - 14:45:16 CDT)
- RE: megatest test failure/MPI problem Meij, Henk (Wed Oct 22 2008 - 10:00:05 CDT)
How to choose force field? Diego Alejandro Vargas (Tue Oct 14 2008 - 23:34:20 CDT)
- Re: How to choose force field? Axel Kohlmeyer (Wed Oct 15 2008 - 10:57:01 CDT)
- Re: How to choose force field? Jerome Henin (Wed Oct 15 2008 - 11:11:16 CDT)
Re: Error with External Electric Filed module Ramya Gamini (Tue Oct 14 2008 - 17:08:39 CDT)
- RE: Error with External Electric Filed module Devendra (Wed Oct 15 2008 - 12:29:56 CDT)
Membrane Simulations Anshu Bhatia (Tue Oct 14 2008 - 14:05:55 CDT)
- Re: Membrane Simulations bo liu (Tue Oct 14 2008 - 22:09:09 CDT)
  - Re: Membrane Simulations Anshu Bhatia (Tue Oct 28 2008 - 12:27:57 CDT)
    - Re: Membrane Simulations Jerome Henin (Tue Oct 28 2008 - 14:19:12 CDT)
Error with External Electric Filed module Devendra (Tue Oct 14 2008 - 10:39:05 CDT)
- restart PMF calculation: what is "lambdaRef" output? Sebastian Stolzenberg (Tue Oct 14 2008 - 12:37:22 CDT)
Re: FEP: How check equilibration sufficiency? calculate dG? Floris Buelens (Tue Oct 14 2008 - 02:45:50 CDT)
- Re: FEP: How check equilibration sufficiency? calculate dG? Chris Chipot (Tue Oct 14 2008 - 04:12:43 CDT)
  - Re: FEP: How check equilibration sufficiency? calculate dG? Sebastian Stolzenberg (Tue Oct 14 2008 - 11:44:51 CDT)
    - Re: FEP: How check equilibration sufficiency? calculate dG? L. Michel Espinoza-Fonseca (Tue Oct 14 2008 - 15:11:50 CDT)
    - Re: FEP: How check equilibration sufficiency? calculate dG? Jerome Henin (Tue Oct 14 2008 - 16:00:24 CDT)
Constraints protocol Kamilla Kopec (Mon Oct 13 2008 - 09:41:30 CDT)
- Re: Constraints protocol Peter Freddolino (Mon Oct 13 2008 - 13:34:58 CDT)
pressure calculation Matthew Ambrosia (Mon Oct 13 2008 - 05:11:06 CDT)
Query Regarding FEP tutorial: NPT or NVT? mon_sharma_at_research.iiit.ac.in (Sat Oct 11 2008 - 16:33:04 CDT)
- Re: Query Regarding FEP tutorial: NPT or NVT? Chris Harrison (Sat Oct 11 2008 - 18:05:52 CDT)
  - Re: Query Regarding FEP tutorial: NPT or NVT? mon_sharma_at_research.iiit.ac.in (Sun Oct 12 2008 - 06:26:27 CDT)
    - Re: Query Regarding FEP tutorial: NPT or NVT? Axel Kohlmeyer (Sun Oct 12 2008 - 19:48:28 CDT)
    - Re: Query Regarding FEP tutorial: NPT or NVT? mon_sharma_at_research.iiit.ac.in (Mon Oct 13 2008 - 01:54:21 CDT)
PSF of Tryptophane methyl ester CHINDEA Vlad (Sat Oct 11 2008 - 11:43:43 CDT)
- Re: PSF of Tryptophane methyl ester Peter Freddolino (Sat Oct 11 2008 - 12:48:34 CDT)
velocities Magnus Heltstrom (Sat Oct 11 2008 - 11:00:54 CDT)
- Re: velocities Peter Freddolino (Sat Oct 11 2008 - 12:46:05 CDT)
Re: restarting issue BIN ZHANG (Fri Oct 10 2008 - 15:00:36 CDT)
restarting issue BIN ZHANG (Fri Oct 10 2008 - 14:42:43 CDT)
embedding protein in membrane jose correa (Fri Oct 10 2008 - 07:24:36 CDT)
charmrun socket error David A. Horita (Thu Oct 09 2008 - 13:49:21 CDT)
- Re: charmrun socket error Chris Harrison (Sat Oct 11 2008 - 17:02:49 CDT)
FEP: delta_G, memory of Hamiltonians corresponding to last G value? Sebastian Stolzenberg (Thu Oct 09 2008 - 14:10:20 CDT)
- Re: FEP: delta_G, memory of Hamiltonians corresponding to last G value? Jerome Henin (Thu Oct 09 2008 - 17:49:05 CDT)
  - Re: FEP: delta_G, memory of Hamiltonians corresponding to last G value? Sebastian Stolzenberg (Thu Oct 09 2008 - 18:01:13 CDT)
    - Re: FEP: delta_G, memory of Hamiltonians corresponding to last G value? Jerome Henin (Thu Oct 09 2008 - 19:29:03 CDT)
    - FEP: How check equilibration sufficiency? calculate dG? Sebastian Stolzenberg (Mon Oct 13 2008 - 23:50:43 CDT)
swig wrapping c++ code on nersc BIN ZHANG (Thu Oct 09 2008 - 11:30:12 CDT)
- Re: swig wrapping c++ code on nersc Axel Kohlmeyer (Thu Oct 09 2008 - 14:28:03 CDT)
problems with combine.tcl jose correa (Wed Oct 08 2008 - 20:21:12 CDT)
- Re: problems with combine.tcl Axel Kohlmeyer (Thu Oct 09 2008 - 14:19:19 CDT)
  - Re: problems with combine.tcl jose correa (Thu Oct 09 2008 - 14:37:24 CDT)
Constant z axis Nd S (Wed Oct 08 2008 - 19:59:43 CDT)
- Re: Constant z axis Chris Harrison (Sat Oct 11 2008 - 17:13:54 CDT)
  - RE: Constant z axis Navdeep (Sat Oct 11 2008 - 22:25:56 CDT)
    - Re: Constant z axis Chris Harrison (Sat Oct 11 2008 - 22:59:31 CDT)
    - Re: Constant z axis Nd S (Mon Oct 13 2008 - 12:27:23 CDT)
embedding protein in membrane jose correa (Wed Oct 08 2008 - 09:08:12 CDT)
- Re: embedding protein in membrane Chris Harrison (Fri Oct 10 2008 - 00:49:44 CDT)
Use tclforces to find systematic forces on fixed atoms? Bill K (Tue Oct 07 2008 - 16:20:44 CDT)
- Re: Use tclforces to find systematic forces on fixed atoms? Jerome Henin (Tue Oct 07 2008 - 17:08:20 CDT)
  - Re: Use tclforces to find systematic forces on fixed atoms? Bill Kowallis (Wed Oct 08 2008 - 11:45:12 CDT)
RE: Problems compiling NAMD Jesper Soerensen (Fri Oct 03 2008 - 15:50:37 CDT)
MD performance on 10 GBit/s or 20Gbit/s infiniband Himanshu Khandelia (Mon Oct 06 2008 - 09:08:35 CDT)
- Re: MD performance on 10 GBit/s or 20Gbit/s infiniband Axel Kohlmeyer (Mon Oct 06 2008 - 10:02:45 CDT)
firsttimestep question Dong Xu (Mon Oct 06 2008 - 00:00:46 CDT)
- Re: firsttimestep question Chris Harrison (Mon Oct 06 2008 - 07:32:25 CDT)
  - Re: firsttimestep question Dong Xu (Mon Oct 06 2008 - 13:00:08 CDT)
equilibration of solvent box and pressure Hiroaki Maekawa (Sun Oct 05 2008 - 22:10:49 CDT)
- Re: equilibration of solvent box and pressure Peter Freddolino (Mon Oct 06 2008 - 15:24:08 CDT)
(no subject) CHINDEA Vlad (Sun Oct 05 2008 - 15:27:31 CDT)
Problems compiling NAMD Jesper Soerensen (Fri Oct 03 2008 - 06:54:20 CDT)
- Re: Problems compiling NAMD Alexander A. Vakhrushev (Fri Oct 03 2008 - 12:44:57 CDT)
  - Re: Problems compiling NAMD Jesper Soerensen (Mon Oct 06 2008 - 09:54:25 CDT)
unknown residue LIP jose correa (Fri Oct 03 2008 - 12:07:24 CDT)
Re: vmd-l: TAB key in vmd terminal BIN ZHANG (Fri Oct 03 2008 - 11:04:02 CDT)
Problem with creating psf file from structure made by inorganic builder Anneta Tzampazi (Fri Oct 03 2008 - 04:43:19 CDT)
error in atom type Rudra Banerjee (Thu Oct 02 2008 - 23:03:30 CDT)
(no subject) Rudra Banerjee (Thu Oct 02 2008 - 23:01:25 CDT)
PMEGridSize Rabab Toubar (Thu Oct 02 2008 - 13:55:04 CDT)
- Re: PMEGridSize Roman Petrenko (Thu Oct 02 2008 - 15:22:49 CDT)
  - Re: PMEGridSize Rabab Toubar (Fri Oct 03 2008 - 15:22:19 CDT)
psf generation for a small non-peptide molecule - again CHINDEA Vlad (Wed Oct 01 2008 - 16:38:27 CDT)
- FW: psf generation for a small non-peptide molecule - again CHINDEA Vlad (Mon Sep 29 2008 - 17:21:16 CDT)
  - Re: FW: psf generation for a small non-peptide molecule - again Peter Freddolino (Mon Sep 29 2008 - 19:43:21 CDT)
- Re: psf generation for a small non-peptide molecule - again Peter Freddolino (Wed Oct 01 2008 - 23:06:49 CDT)
  - Re: psf generation for a small non-peptide molecule - again Floris Buelens (Thu Oct 02 2008 - 09:57:49 CDT)
    - Re: psf generation for a small non-peptide molecule - again Peter Freddolino (Thu Oct 02 2008 - 10:12:44 CDT)
DCD file format Santanu Chatterjee (Wed Oct 01 2008 - 13:35:25 CDT)
- Re: DCD file format Dave Rogers (Wed Oct 01 2008 - 14:17:10 CDT)
- Re: DCD file format Jerome Henin (Wed Oct 01 2008 - 14:38:35 CDT)
- Re: DCD file format Audrey Salazar (Wed Oct 01 2008 - 15:04:28 CDT)
- Re: DCD file format Alexander A. Vakhrushev (Wed Oct 01 2008 - 23:43:12 CDT)
- Re: DCD file format Andrew Emerson (Thu Oct 02 2008 - 02:32:08 CDT)
intramolecular LJ parameters Hamsa Priya Mohana sundaram (Wed Oct 01 2008 - 12:19:56 CDT)
autopsf and hydrogen-sites Christine Horejs DI (Wed Oct 01 2008 - 04:09:44 CDT)
- Re: autopsf and hydrogen-sites Peter Freddolino (Wed Oct 01 2008 - 07:59:00 CDT)
How to compute interaction energies between individual amino acid residues Jemmy Hu (Tue Sep 30 2008 - 11:24:33 CDT)
- Re: How to compute interaction energies between individual amino acid residues harish vashisth (Tue Sep 30 2008 - 12:34:53 CDT)
- Re: How to compute interaction energies between individual amino acid residues Vivek Sharma (Tue Sep 30 2008 - 22:20:18 CDT)
Simple query dipti lele (Tue Sep 30 2008 - 04:33:24 CDT)
Cyclopeptide: connectivity between the first and last residues List (Mon Sep 29 2008 - 12:52:14 CDT)
- Re: Cyclopeptide: connectivity between the first and last residues David Tanner (Mon Sep 29 2008 - 15:36:31 CDT)
  - Re: Cyclopeptide: connectivity between the first and last residues Jerome Henin (Mon Sep 29 2008 - 17:31:30 CDT)
    - Re: Cyclopeptide: connectivity between the first and last residues List (Tue Sep 30 2008 - 19:08:44 CDT)
    - Re: Cyclopeptide: connectivity between the first and last residues List (Mon Oct 06 2008 - 11:58:17 CDT)
asphaltene parameters jose correa (Mon Sep 29 2008 - 08:55:30 CDT)
- Re: asphaltene parameters L. Michel Espinoza-Fonseca (Mon Sep 29 2008 - 09:36:02 CDT)
  - Re: asphaltene parameters jose correa (Mon Sep 29 2008 - 18:55:27 CDT)
How to apply velocity to the entire system with COMmotion enabled Yinglong Miao (Mon Sep 29 2008 - 08:43:38 CDT)
namd 2.5 compilation error Dong Xu (Sun Sep 28 2008 - 01:53:14 CDT)
- Re: namd 2.5 compilation error Axel Kohlmeyer (Sun Sep 28 2008 - 13:27:38 CDT)
  - Re: namd 2.5 compilation error Dong Xu (Mon Sep 29 2008 - 12:15:07 CDT)
Running Multiple TMD simultaneously Joshua Adelman (Sat Sep 27 2008 - 14:57:09 CDT)
- Re: Running Multiple TMD simultaneously Axel Kohlmeyer (Sun Sep 28 2008 - 13:24:16 CDT)
- Re: Running Multiple TMD simultaneously Richard Law (Sat Sep 27 2008 - 20:34:53 CDT)
  - Re: Running Multiple TMD simultaneously Jerome Henin (Mon Sep 29 2008 - 11:34:14 CDT)
minimization jose correa (Thu Sep 25 2008 - 20:11:36 CDT)
- Re: minimization Jerome Henin (Thu Sep 25 2008 - 21:10:46 CDT)
  - Re: minimization jose correa (Fri Sep 26 2008 - 07:03:00 CDT)
- Re: minimization Audrey Salazar (Thu Sep 25 2008 - 21:51:03 CDT)
- Re: minimization Christopher Gillespie (Thu Sep 25 2008 - 21:42:22 CDT)
psf generation for a small non-peptide molecule CHINDEA Vlad (Thu Sep 25 2008 - 16:18:40 CDT)
OXT in pdb file Rabab Toubar (Thu Sep 25 2008 - 13:38:06 CDT)
patch LINK - cyclizing a protein Rabab Toubar (Thu Sep 25 2008 - 13:34:19 CDT)
membrane jose correa (Thu Sep 25 2008 - 09:08:11 CDT)
- RE: membrane JC Gumbart (Thu Sep 25 2008 - 11:15:14 CDT)
How to use bigdcd on a trajectory while skipping first 1000 frames maria goranovic (Thu Sep 25 2008 - 04:42:29 CDT)
- Re: How to use bigdcd on a trajectory while skipping first 1000 frames Eric H. Lee (Thu Sep 25 2008 - 04:54:29 CDT)
- Re: How to use bigdcd on a trajectory while skipping first 1000 frames Alexander A. Vakhrushev (Thu Sep 25 2008 - 06:14:35 CDT)
membrane jose correa (Wed Sep 24 2008 - 18:43:55 CDT)
- RE: membrane JC Gumbart (Thu Sep 25 2008 - 00:28:04 CDT)
Managing Log files Nd S (Wed Sep 24 2008 - 11:52:58 CDT)
- Re: Managing Log files Joshua Adelman (Wed Sep 24 2008 - 12:08:46 CDT)
  - Re: Managing Log files Alexander A. Vakhrushev (Wed Sep 24 2008 - 13:01:54 CDT)
Periodic BCs Navdeep (Tue Sep 23 2008 - 17:38:52 CDT)
- Re: Periodic BCs Jerome Henin (Tue Sep 23 2008 - 18:11:53 CDT)
  - Re: Periodic BCs Nd S (Wed Sep 24 2008 - 12:01:48 CDT)
    - Re: Periodic BCs L. Michel Espinoza-Fonseca (Wed Sep 24 2008 - 14:51:18 CDT)
  - Re: Periodic BCs Alexander A. Vakhrushev (Wed Sep 24 2008 - 12:58:40 CDT)
restarting heating protocol problem: Parminder Mankoo (Tue Sep 23 2008 - 12:47:42 CDT)
Membrane potential Lea Vinther Thøgersen (Tue Sep 23 2008 - 05:00:54 CDT)
restarting heating protocol problem: Parminder Mankoo (Tue Sep 23 2008 - 12:55:42 CDT)
- Re: restarting heating protocol problem: JC Gumbart (Tue Sep 23 2008 - 14:29:49 CDT)
  - Re: restarting heating protocol problem: Parminder Mankoo (Tue Sep 23 2008 - 14:37:32 CDT)
Monte Carlo with NAMD Neelanjana Sengupta (Tue Sep 23 2008 - 10:50:29 CDT)
- Re: Monte Carlo with NAMD harish vashisth (Tue Sep 23 2008 - 11:38:29 CDT)
  - Re: Monte Carlo with NAMD Neelanjana Sengupta (Thu Sep 25 2008 - 06:28:27 CDT)
    - Re: Monte Carlo with NAMD L. Michel Espinoza-Fonseca (Thu Sep 25 2008 - 07:28:15 CDT)
solvate a molecule Rudra Banerjee (Tue Sep 23 2008 - 00:01:16 CDT)
Namd water density jouko_at_uchicago.edu (Mon Sep 22 2008 - 21:36:11 CDT)
- Re: Namd water density Peter Freddolino (Tue Sep 23 2008 - 23:11:11 CDT)
TCL force BIN ZHANG (Mon Sep 22 2008 - 20:40:59 CDT)
- Re: TCL force Peter Freddolino (Tue Sep 23 2008 - 00:37:01 CDT)
Re: need help on CG modelling Nicolas Sapay (Mon Sep 22 2008 - 12:34:47 CDT)
- Re: need help on CG modelling Peter Freddolino (Mon Sep 22 2008 - 12:48:28 CDT)
  - Re: need help on CG modelling Nicolas Sapay (Mon Sep 22 2008 - 13:59:16 CDT)
Compile NAMD on Bluegene Yang Gao (Mon Sep 22 2008 - 10:37:58 CDT)
- Re: Compile NAMD on Bluegene Christopher Gillespie (Mon Sep 22 2008 - 16:54:48 CDT)
carma v.0.9 Nicholas M Glykos (Mon Sep 22 2008 - 05:52:23 CDT)
need help on CG modelling Liao Chuan (Mon Sep 22 2008 - 03:23:02 CDT)
adjusted background load Roman Petrenko (Sat Sep 20 2008 - 10:13:08 CDT)
Replica Exhange error: POSIX EINTR {interrupted system call} Dirar Homouz (Sat Sep 20 2008 - 04:11:55 CDT)
- Re: Replica Exhange error: POSIX EINTR {interrupted system call} Dirar Homouz (Mon Sep 22 2008 - 15:07:16 CDT)
  - Re: Re: Replica Exhange error: POSIX EINTR {interrupted system call} Peter Freddolino (Tue Sep 23 2008 - 00:40:11 CDT)
Restarting a Simulation & Langevin Anirban Ghosh (Fri Sep 19 2008 - 08:12:34 CDT)
- Re: Restarting a Simulation & Langevin Peter Freddolino (Fri Sep 19 2008 - 08:26:59 CDT)
psfgen Magnus Heltstrom (Fri Sep 19 2008 - 06:42:32 CDT)
- Re: psfgen Peter Freddolino (Sat Sep 20 2008 - 21:26:17 CDT)
counting gas molecules inside the nanotube mishacat_at_udm.ru (Thu Sep 18 2008 - 06:52:51 CDT)
- Re: vmd-l: counting gas molecules inside the nanotube John Stone (Thu Sep 18 2008 - 11:18:43 CDT)
  - Re: vmd-l: counting gas molecules inside the nanotube Alexander A. Vakhrushev (Thu Sep 18 2008 - 12:11:04 CDT)
    - Re: vmd-l: counting gas molecules inside the nanotube John Stone (Thu Sep 18 2008 - 12:29:34 CDT)
    - Re: Re: vmd-l: counting gas molecules inside the nanotube bo liu (Fri Sep 19 2008 - 11:38:19 CDT)
Calcium ion-Protein Binding MIke S (Thu Sep 18 2008 - 14:13:34 CDT)
- Re: Calcium ion-Protein Binding JC Gumbart (Thu Sep 18 2008 - 14:22:41 CDT)
  - Re: Calcium ion-Protein Binding MIke S (Mon Sep 22 2008 - 12:54:20 CDT)
    - Re: Calcium ion-Protein Binding MIke S (Mon Sep 22 2008 - 13:33:39 CDT)
    - Re: Calcium ion-Protein Binding JC Gumbart (Mon Sep 22 2008 - 13:42:28 CDT)
Can I use "vecnorm" in the tclforce scripts? Ming (Thu Sep 18 2008 - 08:58:19 CDT)
- Re: Can I use "vecnorm" in the tclforce scripts? Alexander A. Vakhrushev (Thu Sep 18 2008 - 09:29:43 CDT)
Re: convergence of abf Eric H. Lee (Thu Sep 18 2008 - 05:19:49 CDT)
velocity DCD data retrieval Matthew Ambrosia (Wed Sep 17 2008 - 23:02:35 CDT)
- Re: velocity DCD data retrieval Peter Freddolino (Wed Sep 17 2008 - 23:35:21 CDT)
Oligomer Nejo (Wed Sep 17 2008 - 19:28:18 CDT)
Calcium ions and psfgen MIke S (Wed Sep 17 2008 - 16:53:16 CDT)
- Re: Calcium ions and psfgen V.Ovchinnikov (Wed Sep 17 2008 - 18:12:18 CDT)
  - Re: Calcium ions and psfgen MIke S (Wed Sep 17 2008 - 18:18:47 CDT)
config files no longer working after software 'upgrades' Irene Newhouse (Tue Sep 16 2008 - 18:18:43 CDT)
- Re: config files no longer working after software 'upgrades' Peter Freddolino (Tue Sep 16 2008 - 19:39:07 CDT)
TCL Forces : OUT OF MEMORY BIN ZHANG (Fri Sep 12 2008 - 13:38:17 CDT)
- Re: TCL Forces : OUT OF MEMORY BIN ZHANG (Fri Sep 12 2008 - 17:43:06 CDT)
  - Re: Re: TCL Forces : OUT OF MEMORY V.Ovchinnikov (Fri Sep 12 2008 - 18:58:59 CDT)
convergence of abf Jorgen Simonsen (Fri Sep 12 2008 - 10:03:17 CDT)
parameter file to make cholesterol psf file peach gil (Wed Sep 10 2008 - 17:39:59 CDT)
- Re: parameter file to make cholesterol psf file Alexander A. Vakhrushev (Wed Sep 10 2008 - 21:28:59 CDT)
Regarding REMD jani sahil (Wed Sep 10 2008 - 00:04:19 CDT)
- Re: Regarding REMD Peter Freddolino (Wed Sep 10 2008 - 09:56:22 CDT)
trifluoroethanol (TFE) solvent Roman Petrenko (Tue Sep 09 2008 - 19:30:06 CDT)
- Re: trifluoroethanol (TFE) solvent Roman Petrenko (Tue Sep 09 2008 - 20:26:24 CDT)
- Re: trifluoroethanol (TFE) solvent Christopher Gillespie (Tue Sep 09 2008 - 20:39:27 CDT)
  - Re: trifluoroethanol (TFE) solvent Roman Petrenko (Tue Sep 09 2008 - 22:17:22 CDT)
    - Re: trifluoroethanol (TFE) solvent Himanshu Khandelia (Wed Sep 10 2008 - 07:41:39 CDT)
- Re: trifluoroethanol (TFE) solvent L. Michel Espinoza-Fonseca (Wed Sep 10 2008 - 09:41:44 CDT)
NAMD vs. CHARMM. Is complete correspondence possible? Niels Johan Christensen (Tue Sep 09 2008 - 14:18:21 CDT)
- Re: NAMD vs. CHARMM. Is complete correspondence possible? Axel Kohlmeyer (Tue Sep 09 2008 - 15:56:52 CDT)
Questions concerning NAMD mxenos_at_notes.cc.sunysb.edu (Tue Sep 09 2008 - 10:26:55 CDT)
- Re: Questions concerning NAMD Peter Freddolino (Tue Sep 09 2008 - 15:07:22 CDT)
How to retrieve IC50 of a specific compound from NCBI? Ming (Tue Sep 09 2008 - 03:54:38 CDT)
- Re: How to retrieve IC50 of a specific compound from NCBI? L. Michel Espinoza-Fonseca (Tue Sep 09 2008 - 04:25:15 CDT)
vmd-l: How to generate more segments? mishacat_at_udm.ru (Tue Sep 09 2008 - 01:30:05 CDT)
- Re: vmd-l: How to generate more segments? John Stone (Tue Sep 09 2008 - 01:46:41 CDT)
restarting a simulation Raul Araya (Mon Sep 08 2008 - 17:47:35 CDT)
- Re: restarting a simulation Peter Freddolino (Tue Sep 09 2008 - 09:04:26 CDT)
Fwd: convergence of abf Eric H. Lee (Mon Sep 08 2008 - 14:45:53 CDT)
FATAL ERROR: chdir() failed! LAM NGUYEN (Sat Sep 06 2008 - 14:56:57 CDT)
psfgen: more problem Rudra Banerjee (Mon Sep 08 2008 - 13:30:31 CDT)
- Re: psfgen: more problem Axel Kohlmeyer (Mon Sep 08 2008 - 14:17:28 CDT)
convergence of abf Jorgen Simonsen (Mon Sep 08 2008 - 09:16:20 CDT)
- namd1 - abf analysis blicebauma_at_duq.edu (Thu Sep 11 2008 - 08:19:46 CDT)
  - Re: namd1 - abf analysis Jerome Henin (Thu Sep 11 2008 - 11:11:10 CDT)
    - Restraint Potential blicebauma_at_duq.edu (Tue Sep 16 2008 - 08:53:59 CDT)
psf gen Rudra Banerjee (Sun Sep 07 2008 - 07:21:22 CDT)
- Re: psf gen Peter Freddolino (Sun Sep 07 2008 - 08:03:40 CDT)
Compile NAMD on MIPS cpu(Loongson 2F) Guo Zhi (Fri Sep 05 2008 - 23:23:38 CDT)
Coarse grained model force fields Myunggi Yi (Thu Sep 04 2008 - 14:01:49 CDT)
- Re: Coarse grained model force fields Anton Arkhipov (Thu Sep 04 2008 - 14:17:52 CDT)
vdW parameter Diego Alejandro Vargas (Wed Sep 03 2008 - 00:02:22 CDT)
minimization warning and errors Lam T Nguyen (Tue Sep 02 2008 - 13:22:14 CDT)
- Re: minimization warning and errors Peter Freddolino (Tue Sep 02 2008 - 14:01:53 CDT)
  - Re: minimization warning and errors Lam T Nguyen (Tue Sep 02 2008 - 14:11:44 CDT)
    - Re: minimization warning and errors Peter Freddolino (Tue Sep 02 2008 - 22:39:34 CDT)
    - Re: minimization warning and errors Lam T Nguyen (Wed Sep 03 2008 - 11:01:34 CDT)
Platinum paramaters Neelanjana Sengupta (Mon Sep 01 2008 - 08:13:41 CDT)
- Re: Platinum paramaters Axel Kohlmeyer (Mon Sep 01 2008 - 15:05:39 CDT)
topology file for 2 sugar rings connected 1-1 between them politr_at_huji.ac.il (Sun Aug 31 2008 - 07:09:20 CDT)
- Re: topology file for 2 sugar rings connected 1-1 between them Peter Freddolino (Sun Aug 31 2008 - 08:46:38 CDT)
monitor a distance between two molecules me00109_at_cc.uoi.gr (Sat Aug 30 2008 - 18:06:11 CDT)
- RE: monitor a distance between two molecules JC Gumbart (Sun Aug 31 2008 - 23:31:17 CDT)
COOH patch? MIke S (Sat Aug 30 2008 - 17:24:20 CDT)
- Re: COOH patch? Thomas Gaillard (Sat Aug 30 2008 - 19:08:41 CDT)
  - Re: COOH patch? MIke S (Mon Sep 01 2008 - 18:46:36 CDT)
  - Re: COOH patch? MIke S (Wed Sep 17 2008 - 11:39:25 CDT)
conskfile Shultz, Jack (Sat Aug 30 2008 - 12:46:29 CDT)
- Re: conskfile Axel Kohlmeyer (Sat Aug 30 2008 - 13:33:07 CDT)
  - Constraint failure & velocity problem Shultz, Jack (Tue Sep 02 2008 - 13:40:09 CDT)
Trouble with params file when trying to perform basic dynamics with alanine. Diego Alejandro Vargas (Fri Aug 29 2008 - 23:11:03 CDT)
- Re: Trouble with params file when trying to perform basic dynamics with alanine. Axel Kohlmeyer (Sat Aug 30 2008 - 11:31:18 CDT)
nvidia and namd Jorgen Simonsen (Fri Aug 29 2008 - 10:21:17 CDT)
- Re: nvidia and namd Chris Harrison (Fri Aug 29 2008 - 12:07:53 CDT)
NPT enzemble and ABF Jorgen Simonsen (Fri Aug 29 2008 - 07:07:39 CDT)
TXT program editor Alejandro Ortega (Thu Aug 28 2008 - 14:43:14 CDT)
- Re: vmd-l: TXT program editor Peter Freddolino (Thu Aug 28 2008 - 15:06:53 CDT)
- Re: vmd-l: TXT program editor Axel Kohlmeyer (Thu Aug 28 2008 - 15:50:21 CDT)
- Re: TXT program editor Giovanni Bellesia (Thu Aug 28 2008 - 16:21:03 CDT)
- Re: vmd-l: TXT program editor Sabuj Pattanayek (Thu Aug 28 2008 - 17:03:11 CDT)
NAMD compilation / TACC Ranger Arturas Ziemys (Thu Aug 28 2008 - 11:25:14 CDT)
- Re: NAMD compilation / TACC Ranger Axel Kohlmeyer (Thu Aug 28 2008 - 14:12:36 CDT)
PME questions Lam T Nguyen (Thu Aug 28 2008 - 10:58:54 CDT)
- Explicit Membrane Protein Simulations in NAMD/VMD Shultz, Jack (Thu Aug 28 2008 - 12:25:23 CDT)
  - Re: Explicit Membrane Protein Simulations in NAMD/VMD Jerome Henin (Thu Aug 28 2008 - 14:57:07 CDT)
    - RE: Explicit Membrane Protein Simulations in NAMD/VMD Shultz, Jack (Thu Aug 28 2008 - 15:07:24 CDT)
    - Re: Explicit Membrane Protein Simulations in NAMD/VMD Richard Law (Thu Aug 28 2008 - 15:40:10 CDT)
- Re: PME questions Gianluca Interlandi (Thu Aug 28 2008 - 12:39:31 CDT)
diffusion coefficient from rmsd Rudra Banerjee (Wed Aug 27 2008 - 21:55:28 CDT)
- Re: diffusion coefficient from rmsd Axel Kohlmeyer (Wed Aug 27 2008 - 22:39:52 CDT)
  - Re: diffusion coefficient from rmsd bo liu (Thu Aug 28 2008 - 01:38:38 CDT)
corrupt DCD file Forbes, Jeff (NIH/NIAMS) [E] (Wed Aug 27 2008 - 16:54:07 CDT)
- Re: corrupt DCD file Axel Kohlmeyer (Wed Aug 27 2008 - 18:56:20 CDT)
Struggling with the compilation of NAMD 2.6 on a PBS Cluster with LAM/MPI Frank Thommen (Wed Aug 27 2008 - 11:41:08 CDT)
- Re: Struggling with the compilation of NAMD 2.6 on a PBS Cluster with LAM/MPI Axel Kohlmeyer (Wed Aug 27 2008 - 12:12:00 CDT)
  - Re: Struggling with the compilation of NAMD 2.6 on a PBS Cluster with LAM/MPI Frank Thommen (Thu Aug 28 2008 - 12:21:56 CDT)
- Re: Struggling with the compilation of NAMD 2.6 on a PBS Cluster with LAM/MPI Christopher Gillespie (Wed Aug 27 2008 - 12:49:31 CDT)
  - Re: Struggling with the compilation of NAMD 2.6 on a PBS Cluster with LAM/MPI Frank Thommen (Thu Aug 28 2008 - 12:22:57 CDT)
Fe-S cluster topology parameters jose correa (Wed Aug 27 2008 - 09:20:58 CDT)
- Re: Fe-S cluster topology parameters Chang, Christopher (Wed Aug 27 2008 - 11:51:45 CDT)
change in box geometry for simulation of pure water maria goranovic (Wed Aug 27 2008 - 07:48:12 CDT)
- Re: change in box geometry for simulation of pure water Peter Freddolino (Wed Aug 27 2008 - 22:58:07 CDT)
  - Re: change in box geometry for simulation of pure water maria goranovic (Thu Aug 28 2008 - 02:11:31 CDT)
- Re: change in box geometry for simulation of pure water Chris Harrison (Wed Aug 27 2008 - 21:23:22 CDT)
  - Re: change in box geometry for simulation of pure water Axel Kohlmeyer (Thu Aug 28 2008 - 14:06:47 CDT)
error with calling exec: child process exited abnormally Yinglong Miao (Tue Aug 26 2008 - 10:37:25 CDT)
- Re: error with calling exec: child process exited abnormally Peter Freddolino (Tue Aug 26 2008 - 14:38:52 CDT)
  - Re: error with calling exec: child process exited abnormally Yinglong Miao (Tue Aug 26 2008 - 16:22:21 CDT)
van der walls-understanding problem Rudra Banerjee (Tue Aug 26 2008 - 09:50:31 CDT)
- Re: van der walls-understanding problem Schreiner Eduard (Tue Aug 26 2008 - 10:05:28 CDT)
- Re: van der walls-understanding problem Peter Freddolino (Tue Aug 26 2008 - 10:08:24 CDT)
running precompiled NAMD with multiple processors Neelanjana Sengupta (Tue Aug 26 2008 - 01:04:57 CDT)
- Re: running precompiled NAMD with multiple processors Axel Kohlmeyer (Tue Aug 26 2008 - 09:41:49 CDT)
Re: How to write gradual heating config file Hyundeok Song (Mon Aug 25 2008 - 19:30:26 CDT)
How to write gradual heating config file Audrey Salazar (Mon Aug 25 2008 - 17:41:59 CDT)
- Re: How to write gradual heating config file Audrey Salazar (Mon Aug 25 2008 - 18:23:41 CDT)
NAMD COMPILATION ERROR Semorale (Mon Aug 25 2008 - 08:43:13 CDT)
Why turning on 'pressureProfile' make NAMD get into sleep? loligo huang (Sun Aug 24 2008 - 21:49:55 CDT)
- Re: Why turning on 'pressureProfile' make NAMD get into sleep? Huang (Thu Aug 28 2008 - 08:20:15 CDT)
  - basic question about drawing methods Subhashis Biswas (Thu Aug 28 2008 - 10:25:16 CDT)
    - Re: basic question about drawing methods Ramya Gamini (Thu Aug 28 2008 - 11:55:16 CDT)
  - Re: Why turning on 'pressureProfile' make NAMD get into sleep? Huang (Fri Aug 29 2008 - 08:33:57 CDT)
How does NAMD count atoms in PDB files? Corenflos, Steven Charles (Thu Aug 21 2008 - 16:15:18 CDT)
parallel execution speedup Roman Petrenko (Thu Aug 21 2008 - 15:51:57 CDT)
- Re: parallel execution speedup Joshua Adelman (Thu Aug 21 2008 - 16:26:06 CDT)
  - Re: parallel execution speedup Eric H. Lee (Thu Aug 21 2008 - 16:31:32 CDT)
    - Re: parallel execution speedup bo liu (Thu Aug 28 2008 - 01:51:29 CDT)
storing velocity data of a NVE simulation sudipta sinha (Thu Aug 21 2008 - 11:32:37 CDT)
- Re: storing velocity data of a NVE simulation David Hardy (Thu Aug 21 2008 - 11:47:26 CDT)
SMD more than once JARROD EDWARD CHARLES NICKEL (Wed Aug 20 2008 - 14:24:17 CDT)
- Re: SMD more than once Eric H. Lee (Wed Aug 20 2008 - 14:39:37 CDT)
- Re: SMD more than once Gungor Ozer (Wed Aug 20 2008 - 23:40:58 CDT)
about force fields oguz gurbulak (Tue Aug 19 2008 - 09:54:14 CDT)
bad exclusion error - searching remedies Arturas Ziemys (Mon Aug 18 2008 - 18:12:48 CDT)
Benchmark calculation rebeca_at_mmb.pcb.ub.es (Thu Aug 14 2008 - 12:36:55 CDT)
Problem in energy conservation in NVE ensemble with 1fs timestep tinni sona (Thu Aug 14 2008 - 11:34:43 CDT)
- Re: Problem in energy conservation in NVE ensemble with 1fs timestep Peter Freddolino (Thu Aug 14 2008 - 11:40:32 CDT)
Problem in energy conservation in NVE ensemble with 1fs timestep tinni sona (Thu Aug 14 2008 - 11:27:18 CDT)
Problems with TMD could not be solved with the CVS version Robert Schulz (Thu Aug 14 2008 - 10:06:44 CDT)
- Re: Problems with TMD could not be solved with the CVS version Peter Freddolino (Thu Aug 14 2008 - 11:41:26 CDT)
TMD and TclForces Gianluca Interlandi (Thu Aug 14 2008 - 01:35:21 CDT)
- Re: TMD and TclForces Peter Freddolino (Fri Aug 15 2008 - 07:53:23 CDT)
  - Re: TMD and TclForces Gianluca Interlandi (Fri Aug 15 2008 - 12:14:06 CDT)
FATAL ERROR: Patch needed for tuple is missing rebeca_at_mmb.pcb.ub.es (Wed Aug 13 2008 - 17:31:27 CDT)
Dihedral angle calculation over the trajectories sunita gupta (Wed Aug 13 2008 - 10:17:14 CDT)
- Re: Dihedral angle calculation over the trajectories Peter Freddolino (Wed Aug 13 2008 - 10:24:59 CDT)
TclForces and wrapping Gianluca Interlandi (Wed Aug 13 2008 - 03:05:43 CDT)
namd: 64 p job runs; 128 p job fails why? Sangamesh B (Tue Aug 12 2008 - 12:27:18 CDT)
128 core namd job fails to run Sangamesh B (Tue Aug 12 2008 - 10:14:03 CDT)
SMD forces Roman Petrenko (Mon Aug 11 2008 - 17:38:18 CDT)
SMD force units Roman Petrenko (Mon Aug 11 2008 - 17:33:25 CDT)
- Re: SMD force units Eric H. Lee (Mon Aug 11 2008 - 17:46:15 CDT)
  - Re: SMD force units Eric H. Lee (Mon Aug 11 2008 - 17:50:30 CDT)
namd mpi version with smp Vlad Cojocaru (Mon Aug 11 2008 - 05:22:18 CDT)
- Re: namd mpi version with smp Philip Peartree (Mon Aug 11 2008 - 08:35:41 CDT)
torsion potentials for phi/psi angles in CHARMM force field? Roman Petrenko (Sat Aug 09 2008 - 14:52:55 CDT)
Rv: Value 99999999.9999 during minimization Eduardo Tejera (Fri Aug 08 2008 - 14:50:45 CDT)
Turn off H-bonding on select residues dora guzman (Fri Aug 08 2008 - 13:21:35 CDT)
Value 99999999.9999 during minimization rebeca_at_mmb.pcb.ub.es (Fri Aug 08 2008 - 03:16:57 CDT)
- Re: Value 99999999.9999 during minimization Schreiner Eduard (Fri Aug 08 2008 - 03:44:12 CDT)
restartfreq question.... Dr. Luis Rosales León (Thu Aug 07 2008 - 16:31:54 CDT)
- Re: restartfreq question.... JC Gumbart (Fri Aug 08 2008 - 13:25:56 CDT)
Average Velocity and How to choose Right Alias abhijit ramachandran (Thu Aug 07 2008 - 16:13:06 CDT)
build smp version of namd with intel 10.1 Vlad Cojocaru (Thu Aug 07 2008 - 10:44:02 CDT)
- Re: build smp version of namd with intel 10.1 Axel Kohlmeyer (Thu Aug 07 2008 - 12:08:34 CDT)
- Re: build smp version of namd with intel 10.1 Gengbin Zheng (Thu Aug 07 2008 - 10:49:00 CDT)
  - Re: build smp version of namd with intel 10.1 Vlad Cojocaru (Fri Aug 08 2008 - 05:18:42 CDT)
Abnormal EOF found - buffer Rene Prieto (Thu Aug 07 2008 - 00:46:37 CDT)
- Re: Abnormal EOF found - buffer David Tanner (Fri Aug 08 2008 - 10:14:21 CDT)
  - Re: Abnormal EOF found - buffer Rene Prieto (Sun Aug 10 2008 - 09:37:47 CDT)
NAMD crashed with TclForce turned on Chi-Cheng Chiu (Wed Aug 06 2008 - 16:10:01 CDT)
- Re: NAMD crashed with TclForce turned on Axel Kohlmeyer (Wed Aug 06 2008 - 17:20:55 CDT)
  - Re: NAMD crashed with TclForce turned on Chi-Cheng Chiu (Thu Aug 07 2008 - 11:17:16 CDT)
  - Re: NAMD crashed with TclForce turned on Chi-Cheng Chiu (Wed Aug 13 2008 - 10:33:36 CDT)
- Re: NAMD crashed with TclForce turned on Vlad Cojocaru (Thu Aug 07 2008 - 03:05:30 CDT)
Problems with the charge (membrane simulation) rebeca_at_mmb.pcb.ub.es (Wed Aug 06 2008 - 13:18:34 CDT)
- RE: Problems with the charge (membrane simulation) JC Gumbart (Fri Aug 08 2008 - 10:04:54 CDT)
Warning in log file tinni sona (Wed Aug 06 2008 - 06:23:50 CDT)
- Re: Warning in log file Axel Kohlmeyer (Wed Aug 06 2008 - 11:17:34 CDT)
[Fwd: Notice:Re: Re: segmentation fault when running ABF] Vlad Cojocaru (Wed Aug 06 2008 - 05:15:19 CDT)
- Re: [Fwd: Notice:Re: Re: segmentation fault when running ABF] Axel Kohlmeyer (Wed Aug 06 2008 - 11:15:06 CDT)
Error with Shape Based CG Model Anirban Ghosh (Wed Aug 06 2008 - 05:04:27 CDT)
- Re: Error with Shape Based CG Model Anton Arkhipov (Wed Aug 06 2008 - 11:39:38 CDT)
membrane using OPLS force field rebeca_at_mmb.pcb.ub.es (Tue Aug 05 2008 - 07:48:45 CDT)
- Re: unwanted bonds in .pdb file while using molefacture Subhashis Biswas (Wed Aug 06 2008 - 14:23:23 CDT)
  - Re: Re: unwanted bonds in .pdb file while using molefacture José (Wed Aug 06 2008 - 15:40:45 CDT)
Some question about Target MD Yang Gao (Tue Aug 05 2008 - 10:40:10 CDT)
segmentation fault when running ABF Vlad Cojocaru (Tue Aug 05 2008 - 10:20:32 CDT)
- Re: segmentation fault when running ABF Vlad Cojocaru (Tue Aug 05 2008 - 10:34:48 CDT)
  - Re: Re: segmentation fault when running ABF Axel Kohlmeyer (Tue Aug 05 2008 - 12:13:56 CDT)
Zinc-NAMD parameters jose correa (Mon Aug 04 2008 - 14:14:13 CDT)
- Re: Zinc-NAMD parameters L. Michel Espinoza-Fonseca (Mon Aug 04 2008 - 15:05:45 CDT)
how do you debug tcl scripts in vmd ? Andriy Volynets (Mon Aug 04 2008 - 12:12:18 CDT)
compilation of the CVS code Vlad Cojocaru (Mon Aug 04 2008 - 01:46:11 CDT)
- Re: compilation of the CVS code Vlad Cojocaru (Mon Aug 04 2008 - 01:53:41 CDT)
- Re: compilation of the CVS code Peter Freddolino (Mon Aug 04 2008 - 07:36:20 CDT)
  - Re: compilation of the CVS code Peter Freddolino (Mon Aug 04 2008 - 09:22:00 CDT)
    - Re: compilation of the CVS code Vlad Cojocaru (Mon Aug 04 2008 - 10:02:03 CDT)
TMD + temperature/pressure coupling Gianluca Interlandi (Sat Aug 02 2008 - 17:04:31 CDT)
Impropers in histidine residues Marc Baaden (Sat Aug 02 2008 - 03:56:17 CDT)
- Re: Impropers in histidine residues Jerome Henin (Wed Aug 06 2008 - 16:54:15 CDT)
psf-generation. yambem soniya (Thu Jul 31 2008 - 16:57:08 CDT)
- Re: psf-generation. Peter Freddolino (Fri Aug 01 2008 - 00:06:19 CDT)
  - Can this be modelled in NAMD S.K. Ghosh (Fri Aug 01 2008 - 11:38:38 CDT)
coord file output minus solvation box brosbam_at_berkeley.edu (Wed Jul 30 2008 - 18:21:18 CDT)
- Re: coord file output minus solvation box Joshua Adelman (Thu Jul 31 2008 - 12:05:08 CDT)
SMD in water Roman Petrenko (Thu Jul 31 2008 - 06:22:43 CDT)
- Re: SMD in water Axel Kohlmeyer (Thu Jul 31 2008 - 09:16:01 CDT)
  - Re: SMD in water Roman Petrenko (Thu Jul 31 2008 - 12:34:26 CDT)
    - Re: SMD in water Marcos Sotomayor (Thu Jul 31 2008 - 13:01:12 CDT)
build charm++ and namd Vlad Cojocaru (Thu Jul 31 2008 - 05:06:44 CDT)
- Re: build charm++ and namd Vlad Cojocaru (Thu Jul 31 2008 - 06:46:31 CDT)
  - Re: Re: build charm++ and namd Peter Freddolino (Thu Jul 31 2008 - 07:38:31 CDT)
    - Re: Re: build charm++ and namd Vlad Cojocaru (Thu Jul 31 2008 - 07:57:36 CDT)
    - Re: Re: build charm++ and namd Peter Freddolino (Thu Jul 31 2008 - 08:39:07 CDT)
g(r) Rudra Banerjee (Thu Jul 31 2008 - 00:39:47 CDT)
- Re: g(r) Alexandre A. Vakhrouchev (Thu Jul 31 2008 - 01:10:05 CDT)
  - Re: g(r) Rudra Banerjee (Thu Jul 31 2008 - 01:51:17 CDT)
- Re: g(r) Philip Fowler (Thu Jul 31 2008 - 02:29:47 CDT)
output .coor minus solvation box brosbam_at_berkeley.edu (Wed Jul 30 2008 - 18:27:01 CDT)
- Re: output .coor minus solvation box Peter Freddolino (Wed Jul 30 2008 - 23:45:25 CDT)
phosphate (PO4) topology Dr. Luis Rosales León (Wed Jul 30 2008 - 17:37:19 CDT)
- Re: phosphate (PO4) topology Victor Ovchinnikov (Wed Jul 30 2008 - 21:34:31 CDT)
namdenergy and amber trajectory Alessandro Nascimento (Wed Jul 30 2008 - 10:06:27 CDT)
namd linked to tcl8.5 Vlad Cojocaru (Wed Jul 30 2008 - 09:58:23 CDT)
- Re: namd linked to tcl8.5 Axel Kohlmeyer (Wed Jul 30 2008 - 10:20:55 CDT)
Does anyone have a sample tcl file for counting H-bonds Yang Gao (Wed Jul 30 2008 - 09:33:18 CDT)
namdenergy and amber trajectory Alessandro Nascimento (Tue Jul 29 2008 - 14:58:56 CDT)
- Re: namdenergy and amber trajectory V.Ovchinnikov (Tue Jul 29 2008 - 17:30:53 CDT)
- Re: namdenergy and amber trajectory Peter Freddolino (Wed Jul 30 2008 - 00:46:57 CDT)
DNA pdb file xing jing (Tue Jul 29 2008 - 15:16:16 CDT)
recenter atom and remove rotation (translation) Lam T Nguyen (Tue Jul 29 2008 - 12:28:11 CDT)
- Re: recenter atom and remove rotation (translation) Roman Petrenko (Tue Jul 29 2008 - 15:58:03 CDT)
Running CGMD using NAMD Anirban Ghosh (Mon Jul 28 2008 - 23:46:54 CDT)
- Re: Running CGMD using NAMD Peter Freddolino (Tue Jul 29 2008 - 11:39:54 CDT)
PME fails no matter what Roman Petrenko (Mon Jul 28 2008 - 23:29:54 CDT)
- Re: PME fails no matter what Joshua Adelman (Mon Jul 28 2008 - 23:50:19 CDT)
  - Re: PME fails no matter what Roman Petrenko (Tue Jul 29 2008 - 00:17:41 CDT)
    - Re: PME fails no matter what Axel Kohlmeyer (Tue Jul 29 2008 - 03:18:21 CDT)
- Re: PME fails no matter what Peter Freddolino (Tue Jul 29 2008 - 11:38:20 CDT)
  - Re: PME fails no matter what Joshua Adelman (Tue Jul 29 2008 - 12:00:11 CDT)
    - Re: PME fails no matter what David Hardy (Tue Jul 29 2008 - 12:39:04 CDT)
    - Re: PME fails no matter what Roman Petrenko (Fri Aug 01 2008 - 18:02:03 CDT)
  - Re: PME fails no matter what Gianluca Interlandi (Tue Jul 29 2008 - 14:41:50 CDT)
fixed residue Rudra Banerjee (Mon Jul 28 2008 - 22:49:36 CDT)
- Re: fixed residue Roman Petrenko (Mon Jul 28 2008 - 23:36:45 CDT)
  - Re: fixed residue Roman Petrenko (Mon Jul 28 2008 - 23:38:10 CDT)
- Re: fixed residue Joshua Adelman (Mon Jul 28 2008 - 23:16:41 CDT)
- Re: fixed residue Gianluca Interlandi (Tue Jul 29 2008 - 01:03:40 CDT)
ABF simulations Raul Araya (Mon Jul 28 2008 - 14:45:46 CDT)
- Re: ABF simulations Chris Chipot (Tue Jul 29 2008 - 09:55:41 CDT)
ubuntu reads my psf as an audio file patrick wintrode (Mon Jul 28 2008 - 13:29:17 CDT)
- Re: ubuntu reads my psf as an audio file Axel Kohlmeyer (Mon Jul 28 2008 - 13:58:34 CDT)
how to run namd in cluster Anupam Nath Jha (Sun Jul 27 2008 - 13:23:22 CDT)
TMD + harmonic restraints Gianluca Interlandi (Sat Jul 26 2008 - 16:17:42 CDT)
Different dcd files for minimize and MD Lam T Nguyen (Fri Jul 25 2008 - 07:50:38 CDT)
Different dcd files for minimize and MD Lam T Nguyen (Thu Jul 24 2008 - 15:20:17 CDT)
NAMD + TMD on Abe Gianluca Interlandi (Thu Jul 24 2008 - 23:05:38 CDT)
- Re: NAMD + TMD on Abe Peter Freddolino (Fri Jul 25 2008 - 09:21:05 CDT)
  - Re: NAMD + TMD on Abe Gianluca Interlandi (Fri Jul 25 2008 - 12:58:08 CDT)
    - Re: NAMD + TMD on Abe Peter Freddolino (Fri Jul 25 2008 - 14:55:13 CDT)
Appending dcd when restarting a simulation pellegrini (Thu Jul 24 2008 - 03:17:02 CDT)
- Re: Appending dcd when restarting a simulation Axel Kohlmeyer (Thu Jul 24 2008 - 08:52:56 CDT)
- Re: Appending dcd when restarting a simulation Eric H. Lee (Thu Jul 24 2008 - 08:58:21 CDT)
- PME and infinite polymer Arturas Ziemys (Thu Jul 24 2008 - 20:59:33 CDT)
  - Re: PME and infinite polymer Peter Freddolino (Fri Jul 25 2008 - 09:23:28 CDT)
  - Re: PME and infinite polymer Axel Kohlmeyer (Fri Jul 25 2008 - 08:24:30 CDT)
    - Re: PME and infinite polymer Arturas Ziemys (Fri Jul 25 2008 - 09:26:53 CDT)
virtual and heavy hydrogens in NAMD rebeca_at_mmb.pcb.ub.es (Wed Jul 23 2008 - 09:22:12 CDT)
Protonation of nucleic acid phosphates in CHARMM for use in NAMD Hughtendo Martin (Tue Jul 22 2008 - 08:43:09 CDT)
MD problems jose correa (Sun Jul 20 2008 - 21:37:13 CDT)
- Re: MD problems Schreiner Eduard (Sun Jul 20 2008 - 22:13:47 CDT)
CHARMM parameters for H2S Raul Araya (Fri Jul 18 2008 - 17:51:50 CDT)
- Re: CHARMM parameters for H2S Jeffrey J. Potoff (Sat Jul 19 2008 - 22:34:21 CDT)
ERROR(S) IN THE CONFIGURATION FILE when running on a cluster. Lam T Nguyen (Fri Jul 18 2008 - 13:32:14 CDT)
- Re: ERROR(S) IN THE CONFIGURATION FILE when running on a cluster. Joaquim Rui Rodrigues (Fri Jul 18 2008 - 14:17:43 CDT)
- Re: ERROR(S) IN THE CONFIGURATION FILE when running on a cluster. Axel Kohlmeyer (Fri Jul 18 2008 - 14:18:02 CDT)
how to generate psf file using the AMBER topology file tinni sona (Fri Jul 18 2008 - 05:38:45 CDT)
- Re: how to generate psf file using the AMBER topology file Axel Kohlmeyer (Fri Jul 18 2008 - 12:09:48 CDT)
- Re: how to generate psf file using the AMBER topology file Peter Freddolino (Fri Jul 18 2008 - 15:30:45 CDT)
Problem while installing NAMD Karan Maroo (Thu Jul 17 2008 - 04:06:17 CDT)
Re: vmd-l: Fwd: memory overflow problem of Tcl scripting when dealing with trajectories(sorry for cross mailing...) Peter Freddolino (Wed Jul 16 2008 - 07:20:26 CDT)
memory overflow problem of Tcl scripting when dealing with trajectories bo liu (Wed Jul 16 2008 - 03:16:31 CDT)
- Re: memory overflow problem of Tcl scripting when dealing with trajectories Chris Harrison (Sun Jul 20 2008 - 15:21:16 CDT)
LangevinTemp and KE calculation E. Prabhu Raman (Tue Jul 15 2008 - 18:25:49 CDT)
- Re: LangevinTemp and KE calculation Peter Freddolino (Wed Jul 16 2008 - 06:53:01 CDT)
  - Re: LangevinTemp and KE calculation E. Prabhu Raman (Wed Jul 16 2008 - 12:56:22 CDT)
  - Constraining center of mass of monomers S.K. Ghosh (Wed Jul 16 2008 - 17:45:57 CDT)
Error in NAMD Time Steps Hsing Pao (Tue Jul 15 2008 - 14:29:36 CDT)
NAMD Timestep Hsing Pao (Mon Jul 14 2008 - 19:11:59 CDT)
trajectories jfgaff_at_ncsu.edu (Mon Jul 14 2008 - 13:38:39 CDT)
- Re: trajectories Schreiner Eduard (Mon Jul 14 2008 - 14:53:52 CDT)
- Re: trajectories Jerome Henin (Mon Jul 14 2008 - 14:45:23 CDT)
- Re: trajectories Anton Arkhipov (Mon Jul 14 2008 - 14:58:14 CDT)
NAMD OUTPUT Semorale (Sun Jul 13 2008 - 15:37:14 CDT)
- Re: NAMD OUTPUT Jerome Henin (Sun Jul 13 2008 - 16:37:39 CDT)
  - Re: NAMD OUTPUT Ramya Gamini (Sun Jul 13 2008 - 17:14:48 CDT)
cannot find -lsrfftw... collect2: ld returned 1 exit status Anupam Nath Jha (Sun Jul 13 2008 - 12:59:09 CDT)
- Re: cannot find -lsrfftw... collect2: ld returned 1 exit status Axel Kohlmeyer (Sun Jul 13 2008 - 15:54:54 CDT)
DNA simulation by NAMD sudipta sinha (Sun Jul 13 2008 - 06:07:20 CDT)
minimization and MD in one configuration file? NGUYEN LAM (Sat Jul 12 2008 - 10:46:38 CDT)
- RE: minimization and MD in one configuration file? JC Gumbart (Sat Jul 12 2008 - 13:13:52 CDT)
installation of charm-6.0 in ia-64 cluster machine Anupam Nath Jha (Fri Jul 11 2008 - 06:49:34 CDT)
- Re: installation of charm-6.0 in ia-64 cluster machine Peter Freddolino (Fri Jul 11 2008 - 12:23:30 CDT)
Hi,Thank you! Peter Murphy (Fri Jul 11 2008 - 03:46:57 CDT)
Hi,Thank you! Peter Murphy (Fri Jul 11 2008 - 03:35:29 CDT)
use of charmm27 & NPT ensemble for lipid bilayer simulation Ruchi Sachdeva (Fri Jul 11 2008 - 00:26:17 CDT)
- Re: use of charmm27 & NPT ensemble for lipid bilayer simulation JC Gumbart (Sat Jul 12 2008 - 22:07:00 CDT)
  - Re: use of charmm27 & NPT ensemble for lipid bilayer simulation Ruchi Sachdeva (Sun Jul 13 2008 - 23:09:57 CDT)
NAMD on blue gene BG/P Andrew Emerson (Thu Jul 10 2008 - 05:46:36 CDT)
- Re: NAMD on blue gene BG/P George Madalin Giambasu (Thu Jul 10 2008 - 17:00:50 CDT)
  - Re: NAMD on blue gene BG/P Andrew Emerson (Fri Jul 11 2008 - 05:44:16 CDT)
    - Re: NAMD on blue gene BG/P George Madalin Giambasu (Fri Jul 11 2008 - 10:17:27 CDT)
alkane-silicon_dioxide simulation Raul Araya Secchi (Thu Jul 10 2008 - 15:18:06 CDT)
- Re: alkane-silicon_dioxide simulation Eduardo Cruz-Chu (Thu Jul 10 2008 - 15:46:25 CDT)
WCA Particle Dave Rogers (Wed Jul 09 2008 - 21:45:48 CDT)
- Re: WCA Particle Peter Freddolino (Thu Jul 10 2008 - 11:25:51 CDT)
  - Re: WCA Particle Giovanni Bellesia (Thu Jul 10 2008 - 16:07:25 CDT)
    - Re: WCA Particle Joshua D. Moore (Wed Aug 06 2008 - 09:48:45 CDT)
TMD SIMULATION - RMSD DOUBT Semorale (Tue Jul 08 2008 - 20:05:37 CDT)
- Re: TMD SIMULATION - RMSD DOUBT Joshua Adelman (Tue Jul 08 2008 - 22:04:51 CDT)
  - Re: TMD SIMULATION - RMSD DOUBT Semorale (Wed Jul 09 2008 - 10:30:34 CDT)
Interaction energy abhijit ramachandran (Tue Jul 08 2008 - 15:57:47 CDT)
- Re: Interaction energy Peter Freddolino (Tue Jul 08 2008 - 21:07:10 CDT)
Maximum Velocities Alejandro Ortega (Tue Jul 08 2008 - 13:20:33 CDT)
- Re: Maximum Velocities Eric H. Lee (Tue Jul 08 2008 - 13:50:51 CDT)
- Re: Maximum Velocities Chris Harrison (Tue Jul 08 2008 - 15:33:19 CDT)
Re: NAMD 2.7 Claw Isthelaw (Tue Jul 08 2008 - 00:30:52 CDT)
unsubscribe namd-l Richard Swenson (Mon Jul 07 2008 - 14:36:39 CDT)
relating to NAMD Energy Plugin scripting bo liu (Sun Jul 06 2008 - 23:19:44 CDT)
- Re: relating to NAMD Energy Plugin scripting Peter Freddolino (Mon Jul 07 2008 - 12:47:25 CDT)
Implementation of TCL script in NAMD .conf file sudipta sinha (Sat Jul 05 2008 - 00:18:25 CDT)
- Re: Implementation of TCL script in NAMD .conf file Benjamin Bouvier (Mon Jul 07 2008 - 04:34:54 CDT)
won't launch on linux ubuntu cluster for a parallel run LinJia Qi (Fri Jul 04 2008 - 21:23:45 CDT)
won't launch on linux ubuntu cluster for a parallel run accomp lin (Fri Jul 04 2008 - 12:21:18 CDT)
- Re: won't launch on linux ubuntu cluster for a parallel run Peter Freddolino (Fri Jul 04 2008 - 22:34:03 CDT)
ABF Method Bonnie A Merchant (Wed Jul 02 2008 - 09:19:39 CDT)
- drop in Temp from NVT to NVE S.K. Ghosh (Wed Jul 02 2008 - 10:18:41 CDT)
  - Re: drop in Temp from NVT to NVE Peter Freddolino (Wed Jul 02 2008 - 10:49:15 CDT)
- Re: ABF Method Eric H. Lee (Wed Jul 02 2008 - 10:45:15 CDT)
- Re: ABF Method digenova (Thu Jul 03 2008 - 08:52:29 CDT)
Topology cartoon of proteins DEEPESH AGARWAL (Wed Jul 02 2008 - 06:13:59 CDT)
Avoiding alpha-helix distortions Valeria Losasso (Wed Jul 02 2008 - 03:38:20 CDT)
- Re: Avoiding alpha-helix distortions Peter Freddolino (Wed Jul 02 2008 - 07:59:15 CDT)
  - Re: Avoiding alpha-helix distortions Eric H. Lee (Wed Jul 02 2008 - 10:41:01 CDT)
Heat flux along CNT Andy Shelley (Tue Jul 01 2008 - 14:13:36 CDT)
2 dimension PBC politr_at_huji.ac.il (Tue Jul 01 2008 - 07:15:29 CDT)
palmytoilated Balazs JOJART (Mon Jun 30 2008 - 07:09:03 CDT)
NAMD 2.7? L. Michel Espinoza-Fonseca (Mon Jun 30 2008 - 06:42:59 CDT)
- Re: NAMD 2.7? Peter Freddolino (Mon Jun 30 2008 - 14:40:39 CDT)
  - Re: NAMD 2.7? Jerome Henin (Mon Jun 30 2008 - 15:52:29 CDT)
- Re: NAMD 2.7? Chris Harrison (Mon Jun 30 2008 - 12:54:29 CDT)
  - Re: NAMD 2.7? L. Michel Espinoza-Fonseca (Mon Jun 30 2008 - 14:15:38 CDT)
    - Re: NAMD 2.7? Davide Branduardi (Tue Jul 01 2008 - 02:04:26 CDT)
    - RE: NAMD 2.7? Branduardi Davide (Wed Jul 02 2008 - 02:14:27 CDT)
underage russian lolita preteen lolita lolita preteen nude preteen models young preteens underage lolita preteen girls nude kids nymphets homerbruce571 homerbruce571 (Sat Jun 28 2008 - 09:32:04 CDT)
naked preteens pre teen model websites underage sex nude lolita loli bbs preteens preteen panties young child models underage lolitas preteen bbs homerbruce571 homerbruce571 (Sat Jun 28 2008 - 09:18:10 CDT)
nude lolitas lolita nude preteen naked young lolitas hussyfan lolita bbs pre teens have sex preteen model child pornography lolitas homerbruce571 homerbruce571 (Sat Jun 28 2008 - 09:17:48 CDT)
child models little lolita lolita sex nude preteen girls preteen pics preteen incest sun bbs underage nudist sexy preteens bbs homerbruce571 homerbruce571 (Sat Jun 28 2008 - 09:32:28 CDT)
preteen art underage models kid porn preteen pussy kids nude nude preteen illegal immigration ls magazine young lolita nude preteens homerbruce571 homerbruce571 (Sat Jun 28 2008 - 09:32:48 CDT)
carbohydrates: CHARMM versus AMBER Gianluca Interlandi (Fri Jun 27 2008 - 17:16:26 CDT)
- RE: carbohydrates: CHARMM versus AMBER Matthew Tessier (Wed Jul 02 2008 - 08:02:24 CDT)
  - Re: carbohydrates: CHARMM versus AMBER Dong Xu (Wed Oct 29 2008 - 18:47:49 CDT)
    - RE: carbohydrates: CHARMM versus AMBER Matthew Tessier (Thu Oct 30 2008 - 09:43:27 CDT)
carbohydrates: CHARMM versus AMBER Gianluca Interlandi (Fri Jun 27 2008 - 14:16:08 CDT)
- Re: carbohydrates: CHARMM versus AMBER L. Michel Espinoza-Fonseca (Fri Jun 27 2008 - 17:44:41 CDT)
Problem in making cyclic peptide Narang, Pooja, Ph.D. (Fri Jun 27 2008 - 15:24:38 CDT)
- Re: Problem in making cyclic peptide JC Gumbart (Fri Jun 27 2008 - 16:01:27 CDT)
- Re: Problem in making cyclic peptide Peter Freddolino (Fri Jun 27 2008 - 16:11:21 CDT)
Re: Running minimization, heating and FEP simulation within the same configuration file. Floris Buelens (Thu Jun 26 2008 - 02:46:41 CDT)
- Re: Running minimization, heating and FEP simulation within the same configuration file. Jawahar Neelankatan (Thu Jun 26 2008 - 21:44:25 CDT)
Cannot spot error in namd config file Claw Isthelaw (Thu Jun 26 2008 - 10:41:53 CDT)
Re: Output of forces. Osman Yogurtcu (Thu Jun 26 2008 - 02:30:25 CDT)
- Re: Output of forces. Hidekazu WATANABE (Fri Jun 27 2008 - 04:11:56 CDT)
Output of forces. Hidekazu WATANABE (Thu Jun 26 2008 - 00:26:51 CDT)
, Build your vocab (word power)-Get emails daily Fr.ee Deepesh (Thu Jun 26 2008 - 00:02:52 CDT)
MD for phospho-aspartate using NAMD sunita gupta (Wed Jun 25 2008 - 03:37:51 CDT)
Running minimization, heating and FEP simulation within the same configuration file. Jawahar Neelankatan (Tue Jun 24 2008 - 20:28:21 CDT)
charmrun not found Diego Alejandro Vargas (Tue Jun 24 2008 - 21:59:24 CDT)
- Re: charmrun not found Alexandre A. Vakhrouchev (Tue Jun 24 2008 - 22:50:45 CDT)
Problem regarding psfgen haosheng_at_hec.utah.edu (Tue Jun 24 2008 - 18:03:08 CDT)
- Re: Problem regarding psfgen Peter Freddolino (Tue Jun 24 2008 - 21:18:33 CDT)
problem with executing MPI program in NAMD simulation Yinglong Miao (Mon Jun 23 2008 - 17:12:56 CDT)
Incorrect PSF file for min.pme Eva Nong (Mon Jun 23 2008 - 15:32:58 CDT)
- Re: Incorrect PSF file for min.pme Peter Freddolino (Tue Jun 24 2008 - 10:37:34 CDT)
Dihedral scan in NAMD? Kamilla Kopec (Mon Jun 23 2008 - 10:06:30 CDT)
- Re: Dihedral scan in NAMD? L. Michel Espinoza-Fonseca (Mon Jun 23 2008 - 10:47:07 CDT)
  - Re: Dihedral scan in NAMD? Chris Chipot (Mon Jun 23 2008 - 15:21:57 CDT)
    - Re: Dihedral scan in NAMD? L. Michel Espinoza-Fonseca (Tue Jun 24 2008 - 02:23:53 CDT)
- Re: Dihedral scan in NAMD? Peter Freddolino (Mon Jun 23 2008 - 15:02:14 CDT)
psf file Christine Horejs DI (Mon Jun 23 2008 - 06:22:48 CDT)
- Re: psf file Peter Freddolino (Mon Jun 23 2008 - 06:54:08 CDT)
Impressive Glashutte timepieces Becky Peoples (Sat Jun 21 2008 - 22:17:24 CDT)
creation and equilibration of a monolayer creston . (Fri Jun 20 2008 - 16:01:06 CDT)
Typical maximization steps S.K. Ghosh (Fri Jun 20 2008 - 14:05:36 CDT)
- Re: Typical maximization steps JC Gumbart (Fri Jun 20 2008 - 21:23:44 CDT)
error messages with "reinitvels" Yinglong Miao (Fri Jun 20 2008 - 13:56:25 CDT)
mutate G->U? paco ty (Fri Jun 20 2008 - 11:16:13 CDT)
Large MD simulations and atom number limits with NAMD Andrew Thomas (Fri Jun 20 2008 - 09:53:50 CDT)
- Re: Large MD simulations and atom number limits with NAMD Peter Freddolino (Mon Jun 30 2008 - 14:43:08 CDT)
(no subject) Ariovaldo de Souza Junior (Fri Jun 20 2008 - 05:27:36 CDT)
problem compiling NAMD2.6 in a MacOSX-PPC Andrea Diaz (Thu Jun 19 2008 - 10:15:27 CDT)
Force Calibration Interaction abhijit ramachandran (Thu Jun 19 2008 - 17:31:57 CDT)
problem compiling NAMD2.6 in a MacOSX-PPC Andrea Diaz (Thu Jun 19 2008 - 16:30:57 CDT)
- Re: problem compiling NAMD2.6 in a MacOSX-PPC Peter Freddolino (Fri Jun 20 2008 - 08:16:56 CDT)
Simulation with non-periodic boundary condition S.K. Ghosh (Thu Jun 19 2008 - 13:36:50 CDT)
- Re: Simulation with non-periodic boundary condition Victor Ovchinnikov (Thu Jun 19 2008 - 15:15:47 CDT)
NVT simulation by NAMD sudipta sinha (Thu Jun 19 2008 - 08:06:50 CDT)
Time step is incompatible in the NAMD DCD file analyzed with CHARMM twshen (Wed Jun 18 2008 - 14:07:02 CDT)
amber parameters for congo red Shaheen Ahmed (Wed Jun 18 2008 - 15:29:22 CDT)
- Re: amber parameters for congo red L. Michel Espinoza-Fonseca (Wed Jun 18 2008 - 16:07:30 CDT)
  - Re: amber parameters for congo red Shaheen Ahmed (Thu Jun 19 2008 - 02:19:08 CDT)
    - Re: amber parameters for congo red L. Michel Espinoza-Fonseca (Thu Jun 19 2008 - 04:07:31 CDT)
Time step is incompatible in the NAMD DCD file analyzed with CHARMM tw shen (Wed Jun 18 2008 - 14:42:32 CDT)
- Re: Time step is incompatible in the NAMD DCD file analyzed with CHARMM Victor Ovchinnikov (Wed Jun 18 2008 - 16:35:42 CDT)
Time Step is Incompatible in the NAMD DCD Analyzed with CHARMM twshen (Wed Jun 18 2008 - 12:28:22 CDT)
Trouble in energy minimization with warning to increase cutoff Eva Nong (Tue Jun 17 2008 - 18:57:49 CDT)
- Re: Trouble in energy minimization with warning to increase cutoff Peter Freddolino (Wed Jun 18 2008 - 00:01:29 CDT)
2D periodic boundary condn & PME Harindar Keer (Tue Jun 17 2008 - 14:12:28 CDT)
Simulation stalled at startup Sean Law (Mon Jun 16 2008 - 11:01:06 CDT)
Problem with .conf file of NAMD sudipta sinha (Mon Jun 16 2008 - 06:30:57 CDT)
NAMD & CUDA, still in development ? Michael Heymann (Mon Jun 16 2008 - 06:40:24 CDT)
- Re: NAMD & CUDA, still in development ? Peter Freddolino (Tue Jun 17 2008 - 14:43:55 CDT)
NAMD log file analysis script problem (namdstats.tcl) sudipta sinha (Sat Jun 14 2008 - 13:39:32 CDT)
- Re: NAMD log file analysis script problem (namdstats.tcl) Demet Akten (Sun Jun 15 2008 - 03:35:49 CDT)
  - Re: NAMD log file analysis script problem (namdstats.tcl) Axel Kohlmeyer (Sun Jun 15 2008 - 13:09:50 CDT)
Charmm is not free so how to learn it abhijit ramachandran (Fri Jun 13 2008 - 15:01:50 CDT)
- Re: Charmm is not free so how to learn it Philip Peartree (Sun Jun 15 2008 - 09:38:02 CDT)
  - Re: Charmm is not free so how to learn it jfgaff_at_ncsu.edu (Sun Jun 15 2008 - 18:51:19 CDT)
Re: nonbonded interactions Victor Ovchinnikov (Fri Jun 13 2008 - 13:16:24 CDT)
use of 'measure hbonds' DEEPESH AGARWAL (Thu Jun 12 2008 - 23:54:34 CDT)
- Re: use of 'measure hbonds' Axel Kohlmeyer (Fri Jun 13 2008 - 07:43:12 CDT)
Seeking suggestions to decide on realistic configuration values S.K. Ghosh (Thu Jun 12 2008 - 14:40:27 CDT)
Language Used and Elementary doubts abhijit ramachandran (Thu Jun 12 2008 - 00:08:27 CDT)
- Re: Language Used and Elementary doubts Alexandre A. Vakhrouchev (Thu Jun 12 2008 - 12:15:43 CDT)
- Re: Language Used and Elementary doubts Peter Freddolino (Thu Jun 12 2008 - 12:26:50 CDT)
use of 'measure hbonds' DEEPESH AGARWAL (Thu Jun 12 2008 - 06:03:06 CDT)
- Re: use of 'measure hbonds' mon_sharma_at_research.iiit.ac.in (Thu Jun 12 2008 - 11:08:12 CDT)
ApoB structure Alexandre A. Vakhrouchev (Thu Jun 12 2008 - 01:12:02 CDT)
paramter snoze pa (Wed Jun 11 2008 - 17:44:10 CDT)
- Re: paramter JC Gumbart (Wed Jun 11 2008 - 21:08:26 CDT)
  - Re: paramter snoze pa (Thu Jun 12 2008 - 16:16:21 CDT)
  - Re: paramter snoze pa (Fri Jun 13 2008 - 10:37:55 CDT)
Velocity scaling and thermostatting both at a time sudipta sinha (Wed Jun 11 2008 - 13:36:46 CDT)
- Re: Velocity scaling and thermostatting both at a time Jerome Henin (Wed Jun 11 2008 - 17:37:24 CDT)
April promo on watches Priscilla Dahl (Tue Jun 10 2008 - 16:41:36 CDT)
Replica or Original? Terrence Hare (Tue Jun 10 2008 - 07:43:09 CDT)
Classic timepieces replicas Cole Cox (Mon Jun 09 2008 - 19:10:25 CDT)
- Re: Classic timepieces replicas Alexandre A. Vakhrouchev (Tue Jun 10 2008 - 04:41:40 CDT)
  - Re: Classic timepieces replicas Axel Kohlmeyer (Tue Jun 10 2008 - 04:37:57 CDT)
capping of end residues sudipta sinha (Mon Jun 09 2008 - 23:55:56 CDT)
psgfen patch Hatley, Jade M (Mon Jun 09 2008 - 12:05:15 CDT)
- Re: psgfen patch Peter Freddolino (Mon Jun 09 2008 - 23:09:06 CDT)
Re: Which conformation is more proper for the SMD Shulin Zhuang (Mon Jun 09 2008 - 13:21:57 CDT)
- Re: Which conformation is more proper for the SMD Eric H. Lee (Mon Jun 09 2008 - 13:47:27 CDT)
Inexpensive IWC watches Janie Sweeney (Mon Jun 09 2008 - 12:47:28 CDT)
Which conformation is more proper for the SMD Shulin Zhuang (Mon Jun 09 2008 - 11:43:56 CDT)
FW: Hydroxylysine parameters Elham Hamed (Mon Jun 09 2008 - 10:53:08 CDT)
Temperature rescaling and reassignment parameters sudipta sinha (Mon Jun 09 2008 - 10:04:24 CDT)
- Re: Temperature rescaling and reassignment parameters Alexandre A. Vakhrouchev (Mon Jun 09 2008 - 23:20:38 CDT)
  - Re: Temperature rescaling and reassignment parameters sudipta sinha (Mon Jun 09 2008 - 23:46:29 CDT)
    - Re: Temperature rescaling and reassignment parameters Alexandre A. Vakhrouchev (Tue Jun 10 2008 - 04:53:44 CDT)
    - Re: Temperature rescaling and reassignment parameters sudipta sinha (Tue Jun 10 2008 - 05:35:03 CDT)
Correctness of Simulation Results Rahul (Mon Jun 09 2008 - 09:16:13 CDT)
- Re: Correctness of Simulation Results Axel Kohlmeyer (Mon Jun 09 2008 - 12:03:06 CDT)
  - Re: Correctness of Simulation Results Rahul (Tue Jun 10 2008 - 10:15:56 CDT)
    - Re: Correctness of Simulation Results Peter Freddolino (Tue Jun 10 2008 - 11:45:03 CDT)
Temperature rescaling and reassignment parameters sudipta sinha (Mon Jun 09 2008 - 05:14:59 CDT)
Different Hbonds values on different machines using same script for same trajectories sunita gupta (Mon Jun 09 2008 - 02:29:57 CDT)
- Re: Different Hbonds values on different machines using same script for same trajectories John Stone (Tue Jun 10 2008 - 00:18:07 CDT)
- Re: Different Hbonds values on different machines using same script for same trajectories John Stone (Wed Jun 11 2008 - 03:11:11 CDT)
NAMD compilation on linux cluster sudipta sinha (Sun Jun 08 2008 - 10:55:36 CDT)
- Re: NAMD compilation on linux cluster Axel Kohlmeyer (Sun Jun 08 2008 - 11:32:26 CDT)
PME and r-RESPA issue in NAMD sudipta sinha (Sat Jun 07 2008 - 07:05:37 CDT)
- Re: PME and r-RESPA issue in NAMD Axel Kohlmeyer (Sat Jun 07 2008 - 09:50:59 CDT)
  - Re: PME and r-RESPA issue in NAMD Thomas C. Bishop (Fri Jun 20 2008 - 09:56:25 CDT)
output area JARROD EDWARD CHARLES NICKEL (Thu Jun 05 2008 - 15:26:49 CDT)
- Re: output area JC Gumbart (Thu Jun 05 2008 - 17:35:17 CDT)
free enrgy calculations - an additional information politr_at_huji.ac.il (Wed Jun 04 2008 - 07:07:01 CDT)
Multiple successive addforce calls Benjamin Bouvier (Thu Jun 05 2008 - 08:18:16 CDT)
- Re: Multiple successive addforce calls Benjamin Bouvier (Thu Jun 05 2008 - 12:35:31 CDT)
  - Re: Multiple successive addforce calls Gungor Ozer (Thu Jun 05 2008 - 13:53:12 CDT)
  - Re: Multiple successive addforce calls Peter Freddolino (Thu Jun 05 2008 - 14:02:46 CDT)
    - Re: Multiple successive addforce calls Benjamin Bouvier (Thu Jun 05 2008 - 15:05:40 CDT)
    - Re: Multiple successive addforce calls Peter Freddolino (Thu Jun 05 2008 - 15:25:31 CDT)
NAMD in water vs in vacuum Yang Gao (Thu Jun 05 2008 - 09:54:48 CDT)
Bond energy become Zero!!! Ming (Thu Jun 05 2008 - 04:17:01 CDT)
- Re: Bond energy become Zero!!! Peter Freddolino (Thu Jun 05 2008 - 08:25:55 CDT)
steepest descent technique DEEPESH AGARWAL (Thu Jun 05 2008 - 00:53:30 CDT)
- Re: steepest descent technique Peter Freddolino (Thu Jun 05 2008 - 08:32:43 CDT)
free energy calculations politr_at_huji.ac.il (Wed Jun 04 2008 - 05:34:01 CDT)
- Re: free energy calculations Eric H. Lee (Wed Jun 04 2008 - 11:28:13 CDT)
- Problem with TclBC when run in more than one processor fett_at_vtr.net (Wed Jun 04 2008 - 12:08:57 CDT)
  - Re: Problem with TclBC when run in more than one processor Peter Freddolino (Thu Jun 05 2008 - 08:36:51 CDT)
  - Re: Problem with TclBC when run in more than one processor Alexandre A. Vakhrouchev (Wed Jun 04 2008 - 22:52:43 CDT)
- Re: free energy calculations Peter Freddolino (Wed Jun 04 2008 - 11:52:02 CDT)
Thank you for your advices feng jack (Tue Jun 03 2008 - 11:15:41 CDT)
Postdoctoral Position in Scientific Computing David Brandon (Mon Jun 02 2008 - 15:08:45 CDT)
Average energy in NAMD feng jack (Sun Jun 01 2008 - 16:31:16 CDT)
- Re: Average energy in NAMD JC Gumbart (Sun Jun 01 2008 - 18:06:29 CDT)
  - Re: Average energy in NAMD Axel Kohlmeyer (Sun Jun 01 2008 - 19:22:51 CDT)
    - Re: Average energy in NAMD JC Gumbart (Sun Jun 01 2008 - 21:02:40 CDT)
- Re: Average energy in NAMD Axel Kohlmeyer (Sun Jun 01 2008 - 16:51:15 CDT)
Mindboggling Problem Related To NAMD2 Code Rahul (Sun Jun 01 2008 - 04:19:13 CDT)
- Re: Mindboggling Problem Related To NAMD2 Code Axel Kohlmeyer (Sun Jun 01 2008 - 08:01:34 CDT)
- Re: Mindboggling Problem Related To NAMD2 Code Peter Freddolino (Sun Jun 01 2008 - 09:56:21 CDT)
  - Re: Mindboggling Problem Related To NAMD2 Code Graham Jenkins (Mon Jun 02 2008 - 17:43:27 CDT)
(no subject) feng jack (Fri May 30 2008 - 16:04:44 CDT)
Building Namd on a linux cluster. Khaled Barakat (Thu May 29 2008 - 21:39:53 CDT)
- Re: Building Namd on a linux cluster. Alexandre A. Vakhrouchev (Fri May 30 2008 - 00:38:25 CDT)
  - Re: Building Namd on a linux cluster. Khaled Barakat (Fri May 30 2008 - 14:32:09 CDT)
    - Re: Building Namd on a linux cluster. Axel Kohlmeyer (Fri May 30 2008 - 14:41:27 CDT)
  - Re: Building Namd on a linux cluster. Khaled Barakat (Fri May 30 2008 - 19:30:23 CDT)
    - Re: Building Namd on a linux cluster. Axel Kohlmeyer (Fri May 30 2008 - 19:25:00 CDT)
- Re: Building Namd on a linux cluster. Axel Kohlmeyer (Fri May 30 2008 - 07:38:12 CDT)
aromatic-aromatic interaction ramya narasimhan (Thu May 29 2008 - 00:20:43 CDT)
- Re: aromatic-aromatic interaction L. Michel Espinoza-Fonseca (Fri May 30 2008 - 06:57:51 CDT)
benchmarking of NAMD: sustained performance (TF) satya work (Wed May 28 2008 - 22:47:30 CDT)
- Re: benchmarking of NAMD: sustained performance (TF) Philip Peartree (Thu May 29 2008 - 04:35:50 CDT)
- Re: benchmarking of NAMD: sustained performance (TF) Axel Kohlmeyer (Thu May 29 2008 - 09:05:40 CDT)
constraintScaling - FOR LOOP Semorale (Wed May 28 2008 - 20:29:23 CDT)
- Re: constraintScaling - FOR LOOP Peter Freddolino (Fri May 30 2008 - 08:30:07 CDT)
dihedral force constant jfgaff_at_ncsu.edu (Tue May 27 2008 - 18:38:06 CDT)
- Re: dihedral force constant Jerome Henin (Tue May 27 2008 - 20:38:40 CDT)
charmm parameter and topology files me00109_at_cc.uoi.gr (Tue May 27 2008 - 10:17:52 CDT)
- Re: charmm parameter and topology files Jerome Henin (Tue May 27 2008 - 11:20:30 CDT)
NAMD trajectory format Konrad Hinsen (Tue May 27 2008 - 02:41:29 CDT)
- Re: NAMD trajectory format Axel Kohlmeyer (Tue May 27 2008 - 05:27:04 CDT)
  - Re: NAMD trajectory format Konrad Hinsen (Wed May 28 2008 - 07:35:17 CDT)
Charm++ compilation sudipta sinha (Tue May 27 2008 - 01:51:12 CDT)
dihedral restraints "on-the-fly"? Sebastian Stolzenberg (Mon May 26 2008 - 19:40:32 CDT)
- Re: dihedral restraints "on-the-fly"? JC Gumbart (Mon May 26 2008 - 22:06:46 CDT)
- changing dcd output file DURING run? Sebastian Stolzenberg (Thu May 29 2008 - 12:49:36 CDT)
harmonic restraint between two atoms Esben A. Gad (Mon May 26 2008 - 03:55:16 CDT)
- Re: harmonic restraint between two atoms Leonardo Trabuco (Mon May 26 2008 - 11:34:27 CDT)
  - Re: harmonic restraint between two atoms Leonardo Trabuco (Mon May 26 2008 - 12:01:15 CDT)
PROTEIN VACUUM MINIMIZATION ERROR Semorale (Sat May 24 2008 - 10:24:47 CDT)
- Re: PROTEIN VACUUM MINIMIZATION ERROR Peter Freddolino (Sat May 24 2008 - 20:46:34 CDT)
REMD Khaled Barakat (Sat May 24 2008 - 02:58:54 CDT)
- Re: REMD Peter Freddolino (Sat May 24 2008 - 09:01:10 CDT)
  - Re: REMD Khaled Barakat (Sat May 24 2008 - 15:02:00 CDT)
    - Re: REMD Peter Freddolino (Sat May 24 2008 - 20:45:00 CDT)
  - Re: REMD Khaled Barakat (Sun May 25 2008 - 18:43:11 CDT)
Error Parsing Config File MIke S (Sat May 24 2008 - 00:01:43 CDT)
- Re: Error Parsing Config File Alexandre A. Vakhrouchev (Sat May 24 2008 - 03:06:29 CDT)
  - Re: Error Parsing Config File MIke S (Mon May 26 2008 - 15:46:19 CDT)
Acceptable pressure values Fabio Zegarra (Fri May 23 2008 - 17:24:22 CDT)
- Re: Acceptable pressure values Peter Freddolino (Sat May 24 2008 - 09:27:24 CDT)
  - Re: Acceptable pressure values Fabio Zegarra (Mon May 26 2008 - 19:32:21 CDT)
    - Re: Acceptable pressure values Peter Freddolino (Tue May 27 2008 - 14:33:00 CDT)
ABF:reversibility and number of samples Luca Bellucci (Fri May 23 2008 - 07:33:27 CDT)
- Re: ABF:reversibility and number of samples Chris Chipot (Fri May 23 2008 - 10:43:59 CDT)
  - Re: ABF:reversibility and number of samples Luca (Fri May 23 2008 - 14:26:03 CDT)
  - Re: ABF:reversibility and number of samples Subramanian Vaitheeswaran (Fri May 23 2008 - 16:55:53 CDT)
    - Re: ABF:reversibility and number of samples Jerome Henin (Fri May 23 2008 - 17:21:35 CDT)
- Re: ABF:reversibility and number of samples Jerome Henin (Fri May 23 2008 - 12:15:11 CDT)
  - Re: ABF:reversibility and number of samples Eric Cyr (Fri May 23 2008 - 15:11:29 CDT)
a question about equilibrium taojinwuhan_at_sohu.com (Wed May 21 2008 - 20:32:14 CDT)
- Re: a question about equilibrium Joshua Adelman (Wed May 21 2008 - 21:07:35 CDT)
Applying weak harmonic force between two proteins greddy1_at_umd.edu (Wed May 21 2008 - 11:12:18 CDT)
- Re: Applying weak harmonic force between two proteins Joshua Adelman (Wed May 21 2008 - 11:42:15 CDT)
  - Re: Applying weak harmonic force between two proteins Floris Buelens (Thu May 22 2008 - 09:06:57 CDT)
scaling the interaction energy Krishnan, Marimuthu (Wed May 21 2008 - 07:21:20 CDT)
Unable to edit files in NAMD folder. Alexandre A. Vakhrouchev (Wed May 21 2008 - 03:37:52 CDT)
- Re: Unable to edit files in NAMD folder. Low Soo Mei (Wed May 21 2008 - 05:40:21 CDT)
Unable to edit files in NAMD folder. Diego Alejandro Vargas (Tue May 20 2008 - 23:39:51 CDT)
- Re: Unable to edit files in NAMD folder. Diego Alejandro Vargas (Thu May 22 2008 - 13:31:59 CDT)
running namd with condor emir mahmut bahsi (Mon May 19 2008 - 15:42:38 CDT)
CFP: 3rd Annual CMM Workshop on QM/MM Simulations CMM QM/MM Workshop (Mon May 19 2008 - 13:43:55 CDT)
minimization of the squared gradient Krishnan, Marimuthu (Mon May 19 2008 - 01:53:05 CDT)
- Re: minimization of the squared gradient Peter Freddolino (Mon May 19 2008 - 06:40:33 CDT)
  - RE: minimization of the squared gradient Krishnan, Marimuthu (Mon May 19 2008 - 08:56:31 CDT)
  - Re: minimization of the squared gradient Victor Ovchinnikov (Mon May 19 2008 - 10:24:28 CDT)
scaling the interaction energy Krishnan, Marimuthu (Mon May 19 2008 - 01:41:53 CDT)
pair interaction Osman Yogurtcu (Fri May 16 2008 - 13:34:21 CDT)
- Re: pair interaction Osman Yogurtcu (Sat May 17 2008 - 05:54:14 CDT)
Re: vmd-l: Re: Truncated Octahedron for VMD and NAMD simulation Vlad Cojocaru (Fri May 16 2008 - 09:51:44 CDT)
Truncated Octahedron for VMD and NAMD simulation Yinglong Miao (Thu May 15 2008 - 14:31:48 CDT)
- Re: Truncated Octahedron for VMD and NAMD simulation George Madalin Giambasu (Thu May 15 2008 - 15:23:51 CDT)
Error: transport retry exceeded error Alexandre A. Vakhrouchev (Thu May 15 2008 - 13:41:21 CDT)
- Re: Error: transport retry exceeded error Axel Kohlmeyer (Fri May 16 2008 - 10:49:46 CDT)
  - Re: Error: transport retry exceeded error Alexandre A. Vakhrouchev (Sat May 17 2008 - 00:03:03 CDT)
    - Re: Error: transport retry exceeded error Axel Kohlmeyer (Sat May 17 2008 - 15:37:12 CDT)
NVE ENSEMBLE Semorale (Thu May 15 2008 - 10:24:21 CDT)
- Re: NVE ENSEMBLE Vlad Cojocaru (Fri May 16 2008 - 03:36:38 CDT)
  - Simulation of Thiolated Biotin-Streptavidin on Gold S.K. Ghosh (Tue May 20 2008 - 07:11:36 CDT)
Re: Energy plot script Subramanian Vaitheeswaran (Thu May 15 2008 - 07:28:20 CDT)
- Re: Energy plot script bo liu (Thu May 15 2008 - 13:00:23 CDT)
Energy plot script Alexandre A. Vakhrouchev (Wed May 14 2008 - 22:11:19 CDT)
how to prepare *.paramas file Kalyan chaitanya (Tue May 13 2008 - 17:48:54 CDT)
S-OXY CYSTEINE parameter snoze pa (Tue May 13 2008 - 13:53:57 CDT)
- Re: S-OXY CYSTEINE parameter snoze pa (Mon Jun 09 2008 - 16:19:38 CDT)
NAMD electrostatics no cutoff or switching Alvaro Foletti (Tue May 13 2008 - 12:44:01 CDT)
- Re: NAMD electrostatics no cutoff or switching Peter Freddolino (Tue May 13 2008 - 21:25:30 CDT)
ZINC parameter surendra negi (Tue May 13 2008 - 12:22:47 CDT)
- Re: ZINC parameter Jerome Henin (Tue May 13 2008 - 14:57:48 CDT)
DCD file size Alexandre A. Vakhrouchev (Mon May 12 2008 - 14:19:57 CDT)
- Re: DCD file size JC Gumbart (Mon May 12 2008 - 15:08:48 CDT)
  - Re: DCD file size Alexandre A. Vakhrouchev (Mon May 12 2008 - 21:50:25 CDT)
    - Re: DCD file size Peter Freddolino (Mon May 12 2008 - 21:56:26 CDT)
    - Re: DCD file size Joshua D. Moore (Tue May 13 2008 - 01:39:57 CDT)
puase MD integration to communicate between jobs Floris Buelens (Sun May 11 2008 - 12:31:50 CDT)
Run NPT ensemble simulation with sphericalBC? Yinglong Miao (Fri May 09 2008 - 13:37:04 CDT)
2 pdb files Christine Horejs DI (Fri May 09 2008 - 06:58:01 CDT)
- Re: 2 pdb files Peter Freddolino (Fri May 09 2008 - 07:15:00 CDT)
spermine force field bqluan (Thu May 08 2008 - 18:47:54 CDT)
spermine force field bqluan (Thu May 08 2008 - 17:24:01 CDT)
Trajectory file formats & structural alignment Wei Huang (Thu May 08 2008 - 15:46:13 CDT)
- Re: Trajectory file formats & structural alignment Giovanni Bellesia (Thu May 08 2008 - 18:00:18 CDT)
  - Re: Trajectory file formats & structural alignment Wei Huang (Tue May 13 2008 - 21:57:01 CDT)
    - RE: Trajectory file formats & structural alignment JC Gumbart (Wed May 14 2008 - 00:15:17 CDT)
running NAMD with ranger@tacc Lei Shi (Wed May 07 2008 - 13:08:50 CDT)
- Re: running NAMD with ranger@tacc Peter Freddolino (Wed May 07 2008 - 13:23:36 CDT)
recalculating energy using dcd file gurvisha_at_leadinvent.com (Wed May 07 2008 - 09:19:14 CDT)
- Re: recalculating energy using dcd file JC Gumbart (Wed May 07 2008 - 17:08:16 CDT)
- Re: recalculating energy using dcd file Rabab Toubar (Wed Aug 05 2009 - 09:43:44 CDT)
  - Re: Re: recalculating energy using dcd file Joshua Adelman (Wed Aug 05 2009 - 09:58:22 CDT)
    - Re: Re: recalculating energy using dcd file Rabab Toubar (Thu Aug 06 2009 - 09:06:21 CDT)
  - Re: Re: recalculating energy using dcd file Mert Gür (Thu Aug 06 2009 - 15:09:58 CDT)
pbc Ahlam Al-Rawi (Tue May 06 2008 - 18:41:33 CDT)
Negative Pressure Fabio Zegarra (Tue May 06 2008 - 15:44:53 CDT)
- Re: Negative Pressure Vlad Cojocaru (Wed May 07 2008 - 09:39:02 CDT)
Question about a shift in rmsd using fixedatom off snoze pa (Tue May 06 2008 - 11:47:45 CDT)
NAMDENERGY: function of 'cutoff' parameter when -pme option is enabled Ghalib Bello (Mon May 05 2008 - 23:02:45 CDT)
- Re: NAMDENERGY: function of 'cutoff' parameter when -pme option is enabled Peter Freddolino (Tue May 06 2008 - 00:37:54 CDT)
Re: BOUNCE namd-l@ks.uiuc.edu: Message too long (>40000 chars) snoze pa (Mon May 05 2008 - 16:49:43 CDT)
- Re: Re: BOUNCE namd-l@ks.uiuc.edu: Message too long (>40000 chars) snoze pa (Tue May 06 2008 - 10:20:47 CDT)
question related to rmsd snoze pa (Mon May 05 2008 - 15:03:07 CDT)
- Re: question related to rmsd JC Gumbart (Mon May 05 2008 - 16:19:47 CDT)
  - Re: question related to rmsd snoze pa (Mon May 05 2008 - 16:35:21 CDT)
    - Re: question related to rmsd JC Gumbart (Mon May 05 2008 - 17:58:43 CDT)
help with calcforces Prabhakar Bhimalapuram (Fri May 02 2008 - 13:32:22 CDT)
error on installing ImageMagick Hero (Thu May 01 2008 - 13:54:57 CDT)
- Re: error on installing ImageMagick Peter Freddolino (Thu May 01 2008 - 14:02:39 CDT)
- Re: error on installing ImageMagick Richard Law (Thu May 01 2008 - 14:53:37 CDT)
electrostatics NAMD vs CHARMM Arturas Ziemys (Thu May 01 2008 - 11:29:49 CDT)
langevin dynamics and random seeds Peter Freddolino (Thu May 01 2008 - 11:44:40 CDT)
How to save the animation movie into files? Hero (Thu May 01 2008 - 01:48:35 CDT)
- Re: How to save the animation movie into files? Jianhui Tian (Thu May 01 2008 - 09:16:50 CDT)
compilaton error Swarna Patra (Wed Apr 30 2008 - 23:32:45 CDT)
- Re: compilaton error Leonardo Trabuco (Thu May 01 2008 - 11:32:22 CDT)
  - Re: compilaton error Swarna Patra (Thu May 01 2008 - 20:04:47 CDT)
Running NAMD on cluster sudipta sinha (Wed Apr 30 2008 - 04:41:53 CDT)
- Re: Running NAMD on cluster Philip Peartree (Wed Apr 30 2008 - 07:21:28 CDT)
Neutral arginine patch in topology file. Alexandre F. G. (Tue Apr 29 2008 - 16:45:29 CDT)
- RE: Neutral arginine patch in topology file. JC Gumbart (Thu May 01 2008 - 00:15:28 CDT)
NAMD on a remote UNIX and VMD on local Windows - does this work? S.K. Ghosh (Tue Apr 29 2008 - 13:40:29 CDT)
- Re: NAMD on a remote UNIX and VMD on local Windows - does this work? Tao Wu (Tue Apr 29 2008 - 15:49:57 CDT)
NAMD on a remote UNIX and VMD on local Windows - does this work? S.K. Ghosh (Tue Apr 29 2008 - 13:31:34 CDT)
velocity units in .vel file Neelanjana Sengupta (Mon Apr 28 2008 - 15:21:06 CDT)
- Re: velocity units in .vel file Joshua D. Moore (Mon Apr 28 2008 - 17:47:48 CDT)
How to save the animation movie into files? Hero (Mon Apr 28 2008 - 00:23:49 CDT)
- Re: How to save the animation movie into files? Low Soo Mei (Mon Apr 28 2008 - 00:51:37 CDT)
A question about restaints force. Yang Gao (Fri Apr 25 2008 - 11:28:20 CDT)
q=D8=B8=B4=A3=BA=20Re:=20=20nodelist=20being=20ignore?= d during paralleling cong chen (Sun Apr 27 2008 - 21:50:34 CDT)
How to save vmd figures to jpg or tiff? Hero (Sun Apr 27 2008 - 16:18:35 CDT)
help with TCL forces script Jim Pfaendtner (Sun Apr 27 2008 - 05:47:30 CDT)
nodelist being ignored during paralleling cong chen (Sat Apr 26 2008 - 22:24:17 CDT)
How to play molecule trajectory with VMD? Hero (Sat Apr 26 2008 - 20:00:52 CDT)
tracing not available with CMK_OPTIMIZE! Semorale (Sat Apr 26 2008 - 16:26:13 CDT)
How to run namd2 on ubuntu linux? Hero (Sat Apr 26 2008 - 14:45:01 CDT)
- Re: How to run namd2 on ubuntu linux? Leandro Martínez (Sat Apr 26 2008 - 16:10:35 CDT)
Re: install VMD on Ubuntu Hero (Sat Apr 26 2008 - 14:38:19 CDT)
install VMD on Ubuntu Hero (Sat Apr 26 2008 - 14:09:39 CDT)
- Re: install VMD on Ubuntu Low Soo Mei (Sat Apr 26 2008 - 14:25:32 CDT)
Configurations-Statistical Mechanics Mert Gür (Sat Apr 26 2008 - 13:00:08 CDT)
How to install VMD and NAMD on Ubuntu? Hero (Sat Apr 26 2008 - 12:55:17 CDT)
FEP triangular bracket average Mert Gür (Sat Apr 26 2008 - 05:56:26 CDT)
- Re: FEP triangular bracket average Jerome Henin (Sat Apr 26 2008 - 11:30:37 CDT)
  - Re: FEP triangular bracket average Mert Gür (Sat Apr 26 2008 - 13:14:29 CDT)
    - Re: FEP triangular bracket average Jerome Henin (Sat Apr 26 2008 - 13:54:31 CDT)
    - Re: FEP triangular bracket average Mert Gür (Sat Apr 26 2008 - 15:26:21 CDT)
install NAMD on Ubuntu Hero (Fri Apr 25 2008 - 23:46:07 CDT)
- Re: install NAMD on Ubuntu Alexandre A. Vakhrouchev (Sat Apr 26 2008 - 01:12:30 CDT)
A question about restaints force. Yang Gao (Fri Apr 25 2008 - 15:23:01 CDT)
- Re: A question about restaints force. Gungor Ozer (Fri Apr 25 2008 - 16:17:13 CDT)
  - Re: A question about restaints force. Victor Ovchinnikov (Fri Apr 25 2008 - 17:48:40 CDT)
Time factor Alexandre A. Vakhrouchev (Thu Apr 24 2008 - 23:16:04 CDT)
TMD AND RIGIDBONDS Samuel Morales (Wed Apr 23 2008 - 20:50:43 CDT)
compiling namd: cannot find -lmodulecommlib Corenflos, Steven Charles (Wed Apr 23 2008 - 14:42:18 CDT)
reversing constant velocity SMD Jeff Forbes (Wed Apr 23 2008 - 14:36:16 CDT)
- Re: reversing constant velocity SMD Peter Freddolino (Thu Apr 24 2008 - 08:24:55 CDT)
VMD-NAMD-commands Vivek Sharma (Fri Apr 18 2008 - 23:06:12 CDT)
- Re: VMD-NAMD-commands Alexandre A. Vakhrouchev (Sat Apr 19 2008 - 00:16:08 CDT)
- Re: VMD-NAMD-commands Peter Freddolino (Sun Apr 20 2008 - 20:20:27 CDT)
  - Re: VMD-NAMD-commands Vivek Sharma (Sun Apr 20 2008 - 21:06:36 CDT)
Format of Binary Restart and Output Coordinate and Velocity Files Joshua D. Moore (Fri Apr 18 2008 - 19:34:20 CDT)
RE: Reading and writing Binary Restart or Output files with Fortran Joshua D. Moore (Fri Apr 18 2008 - 19:25:55 CDT)
- Re: RE: Reading and writing Binary Restart or Output files with Fortran V.Ovchinnikov (Sat Apr 19 2008 - 10:40:46 CDT)
  - Re: RE: Reading and writing Binary Restart or Output files with Fortran Leandro Martínez (Sat Apr 19 2008 - 12:51:58 CDT)
    - Re: RE: Reading and writing Binary Restart or Output files with Fortran V.Ovchinnikov (Sat Apr 19 2008 - 16:10:32 CDT)
question on ABF L. Michel Espinoza-Fonseca (Fri Apr 18 2008 - 18:40:08 CDT)
- Re: question on ABF Jerome Henin (Fri Apr 18 2008 - 22:14:45 CDT)
  - Re: question on ABF Chris Chipot (Mon Apr 21 2008 - 07:01:39 CDT)
    - Re: question on ABF L. Michel Espinoza-Fonseca (Mon May 05 2008 - 09:16:44 CDT)
  - RE: question on ABF Xu, Jiancong (Mon Apr 21 2008 - 10:35:16 CDT)
What does "cellOrigin" really mean? bo liu (Fri Apr 18 2008 - 09:38:56 CDT)
- What does "cellOrigin" really mean? bo liu (Wed Apr 23 2008 - 05:48:45 CDT)
  - Re: What does "cellOrigin" really mean? Alexandre A. Vakhrouchev (Wed Apr 23 2008 - 08:36:51 CDT)
Multiple Different Harmonic Restraint Defitions Joshua Adelman (Thu Apr 17 2008 - 20:13:23 CDT)
2 molecule pair interactions Arturas Ziemys (Wed Apr 16 2008 - 16:26:27 CDT)
- Re: 2 molecule pair interactions Peter Freddolino (Wed Apr 16 2008 - 17:11:52 CDT)
  - Re: 2 molecule pair interactions Ben Chern (Wed Apr 16 2008 - 23:49:33 CDT)
Which namd on amd64? Corenflos, Steven Charles (Tue Apr 15 2008 - 15:26:25 CDT)
- Re: Which namd on amd64? V.Ovchinnikov (Tue Apr 15 2008 - 17:19:43 CDT)
binary install question winsvern_at_isu.edu (Tue Apr 15 2008 - 15:23:29 CDT)
How to write different DCD files for separate MD runs in one simulation? Yinglong Miao (Tue Apr 15 2008 - 13:55:14 CDT)
- Re: How to write different DCD files for separate MD runs in one simulation? Peter Freddolino (Tue Apr 15 2008 - 14:07:03 CDT)
- Re: How to write different DCD files for separate MD runs in one simulation? V.Ovchinnikov (Tue Apr 15 2008 - 15:14:20 CDT)
  - Re: How to write different DCD files for separate MD runs in one simulation? Peter Freddolino (Tue Apr 15 2008 - 15:34:11 CDT)
    - Re: How to write different DCD files for separate MD runs in one simulation? V.Ovchinnikov (Tue Apr 15 2008 - 15:52:07 CDT)
    - Re: How to write different DCD files for separate MD runs in one simulation? Yinglong Miao (Tue Apr 15 2008 - 16:22:18 CDT)
Electrostatics cutoff with PME Gianluca Interlandi (Tue Apr 15 2008 - 13:01:48 CDT)
- Re: Electrostatics cutoff with PME L. Michel Espinoza-Fonseca (Tue Apr 15 2008 - 14:00:03 CDT)
  - Re: Electrostatics cutoff with PME Christopher Gillespie (Tue Apr 15 2008 - 15:21:06 CDT)
- Re: Electrostatics cutoff with PME Peter Freddolino (Tue Apr 15 2008 - 14:31:35 CDT)
temperature stepping during heating Low Soo Mei (Tue Apr 15 2008 - 05:21:43 CDT)
- Re: temperature stepping during heating JC Gumbart (Thu Apr 17 2008 - 16:35:13 CDT)
  - Re: temperature stepping during heating Low Soo Mei (Thu Apr 17 2008 - 21:14:34 CDT)
    - Re: temperature stepping during heating Low Soo Mei (Fri Apr 18 2008 - 04:00:41 CDT)
Problem with NAMD crashing without warning or error messages Jacob Durrant (Mon Apr 14 2008 - 20:36:25 CDT)
help regarding NAMD equilibration snoze pa (Mon Apr 14 2008 - 18:11:46 CDT)
- Re: help regarding NAMD equilibration Low Soo Mei (Tue Apr 15 2008 - 01:05:25 CDT)
  - Re: help regarding NAMD equilibration snoze pa (Tue Apr 15 2008 - 10:39:54 CDT)
  - Re: help regarding NAMD equilibration Dr. Luis Rosales León (Tue Apr 15 2008 - 12:39:24 CDT)
NAMD CVS RUN ERROR Samuel Morales (Mon Apr 14 2008 - 16:13:31 CDT)
rmsd_RNA_DNA sripad chandan (Mon Apr 14 2008 - 05:27:45 CDT)
restarting ABF simulation Luca Bellucci (Mon Apr 14 2008 - 04:14:19 CDT)
- Re: restarting ABF simulation Jerome Henin (Mon Apr 14 2008 - 06:43:40 CDT)
problem with VMD installation- libstdc++.so.5 => not found steve_at_phas.ubc.ca (Sat Apr 12 2008 - 22:03:05 CDT)
- Re: problem with VMD installation- libstdc++.so.5 => not found Jerome Henin (Sun Apr 13 2008 - 14:59:21 CDT)
spawn_namd_command How to properly execute this command bptilaka_at_mail.uh.edu (Sat Apr 12 2008 - 17:32:17 CDT)
langevin dynamics Dibyadeep Paul (Sat Apr 12 2008 - 14:21:52 CDT)
- Re: langevin dynamics Giovanni Bellesia (Sat Apr 12 2008 - 15:20:20 CDT)
  - Re: langevin dynamics Giovanni Bellesia (Sat Apr 12 2008 - 18:03:35 CDT)
TclForces Vivek Sharma (Fri Apr 11 2008 - 05:42:50 CDT)
- Re: TclForces JC Gumbart (Mon Apr 14 2008 - 10:21:22 CDT)
Questions about equilibration pellegrini (Thu Apr 10 2008 - 10:19:57 CDT)
PMF calculation floating-point error will (Thu Apr 10 2008 - 08:12:41 CDT)
periodic cell conditions for membrane simulation Low Soo Mei (Thu Apr 10 2008 - 03:54:07 CDT)
Replica Exchange Method bptilaka_at_mail.uh.edu (Wed Apr 09 2008 - 23:08:43 CDT)
bug in NAMD CVS starting March 7, now fixed Jim Phillips (Tue Apr 08 2008 - 14:22:55 CDT)
Dynamics with a glycerol molecule Lucio Montero (Mon Apr 07 2008 - 17:34:39 CDT)
How to circumvent: FATAL ERROR: Periodic cell has become too small for original patch grid! Maxim Paliy (Mon Apr 07 2008 - 14:36:09 CDT)
- Re: How to circumvent: FATAL ERROR: Periodic cell has become too small for original patch grid! L. Michel Espinoza-Fonseca (Mon Apr 07 2008 - 15:10:43 CDT)
add calcium chloride Christine Horejs DI (Mon Apr 07 2008 - 03:21:59 CDT)
- Re: add calcium chloride Peter Freddolino (Mon Apr 07 2008 - 08:09:58 CDT)
  - Re: add calcium chloride Christine Horejs DI (Wed Apr 16 2008 - 07:30:41 CDT)
    - Re: add calcium chloride Christine Horejs DI (Wed Apr 16 2008 - 08:22:28 CDT)
    - Re: add calcium chloride Thomas C. Bishop (Wed Apr 16 2008 - 10:12:24 CDT)
Kinetic Momentum of Translation and/or Rotation Joshua D. Moore (Mon Apr 07 2008 - 01:54:38 CDT)
- Re: Kinetic Momentum of Translation and/or Rotation Peter Freddolino (Mon Apr 07 2008 - 08:09:44 CDT)
Calculating PMF from a constant velocity SMD simulation! Gungor Ozer (Sat Apr 05 2008 - 19:10:06 CDT)
How to read specific DCD frames directly in Fortran? Yinglong Miao (Sat Apr 05 2008 - 13:21:53 CDT)
- Re: vmd-l: How to read specific DCD frames directly in Fortran? Peter Freddolino (Sat Apr 05 2008 - 13:38:39 CDT)
  - Re: vmd-l: How to read specific DCD frames directly in Fortran? Yinglong Miao (Sun Apr 06 2008 - 10:51:40 CDT)
- Re: vmd-l: How to read specific DCD frames directly in Fortran? John Stone (Sat Apr 05 2008 - 13:43:21 CDT)
Rigid body effect, translational kinetic momentum Joshua D. Moore (Fri Apr 04 2008 - 19:40:35 CDT)
problems sourcing namdstats in vmd Shaheen Ahmed (Fri Apr 04 2008 - 09:37:15 CDT)
- Re: problems sourcing namdstats in vmd Jim Phillips (Fri Apr 04 2008 - 12:09:43 CDT)
TMD bug correction??? Samuel Morales (Wed Apr 02 2008 - 13:28:35 CDT)
- Re: TMD bug correction??? Peter Freddolino (Wed Apr 02 2008 - 14:39:37 CDT)
- Re: TMD bug correction??? Samuel Morales (Mon Apr 14 2008 - 15:55:04 CDT)
  - Re: Re: TMD bug correction??? Peter Freddolino (Mon Apr 14 2008 - 16:15:44 CDT)
MacOSX net version segmentation fault Joshua Adelman (Mon Mar 31 2008 - 18:25:29 CDT)
Running NAMD at TACC (Ranger) Jim Pfaendtner (Sun Mar 30 2008 - 07:16:57 CDT)
- Re: Running NAMD at TACC (Ranger) Peter Freddolino (Sun Mar 30 2008 - 09:28:06 CDT)
  - Re: Running NAMD at TACC (Ranger) JC Gumbart (Sun Mar 30 2008 - 13:20:45 CDT)
    - RE: Running NAMD at TACC (Ranger) Richard Swenson (Fri Apr 04 2008 - 12:42:49 CDT)
- RE: Running NAMD at TACC (Ranger) Richard Swenson (Thu Apr 03 2008 - 18:09:22 CDT)
coarse grained simulation Demet Akten (Fri Mar 28 2008 - 09:11:19 CDT)
Pressure oscillation in NPT Xinguang Cheng (Thu Mar 27 2008 - 10:14:38 CDT)
- Re: Pressure oscillation in NPT Peter Freddolino (Thu Mar 27 2008 - 11:07:02 CDT)
  - Re: Re: Pressure oscillation in NPT lcr312 (Thu Mar 27 2008 - 21:53:07 CDT)
- Re: Pressure oscillation in NPT Per Jr. Greisen (Thu Mar 27 2008 - 11:30:04 CDT)
NAMDenergy + PME for constant pressure trajectories (variable box and .xst files) Maxim Paliy (Wed Mar 26 2008 - 16:28:52 CDT)
NAMDenergy + PME for constant pressure trajectories (variable box and .xst files) Maxim Paliy (Wed Mar 26 2008 - 16:37:01 CDT)
NAMDenergy + PME for constant pressure trajectories (variable box and .xst files) Maxim Paliy (Wed Mar 26 2008 - 16:30:41 CDT)
- Re: NAMDenergy + PME for constant pressure trajectories (variable box and .xst files) Peter Freddolino (Wed Mar 26 2008 - 16:38:23 CDT)
FATAL ERROR: Periodic cell has become too small for original patch grid! Seth Lilavivat (Wed Mar 26 2008 - 15:36:48 CDT)
- Re: FATAL ERROR: Periodic cell has become too small for original patch grid! Jeffrey J. Potoff (Wed Mar 26 2008 - 18:27:05 CDT)
abf and tcl scripting in NAMD Vlad Cojocaru (Wed Mar 26 2008 - 11:18:15 CDT)
TMD SCRIPT Samuel Morales (Sat Mar 22 2008 - 17:30:59 CDT)
FEP output dEavg and dG Payel Das (Fri Mar 21 2008 - 16:26:02 CDT)
- Re: FEP output dEavg and dG Jerome Henin (Fri Mar 21 2008 - 17:16:18 CDT)
NAMD+MPI on AMD64 Artem Zhmurov (Fri Mar 21 2008 - 12:30:29 CDT)
ABF tutorial; updated FEP tutorial Jerome Henin (Thu Mar 20 2008 - 15:55:10 CDT)
- Re: ABF tutorial; updated FEP tutorial Lei Shi (Thu Mar 20 2008 - 17:38:40 CDT)
  - Re: ABF tutorial; updated FEP tutorial Jerome Henin (Fri Mar 21 2008 - 18:53:58 CDT)
Parallelism issue Artem Zhmurov (Thu Mar 20 2008 - 15:45:15 CDT)
EM and MD of GPCRs Kalyan chaitanya (Thu Mar 20 2008 - 12:34:23 CDT)
namd: ABF query gurvisha_at_leadinvent.com (Thu Mar 20 2008 - 05:12:55 CDT)
- Re: namd: ABF query Peter Freddolino (Thu Mar 20 2008 - 11:16:50 CDT)
  - Re: namd: ABF query Peter Freddolino (Thu Mar 20 2008 - 11:49:33 CDT)
- Re: namd: ABF query Jerome Henin (Thu Mar 20 2008 - 11:29:30 CDT)
namd: ABF query gurvisha_at_leadinvent.com (Thu Mar 20 2008 - 05:12:30 CDT)
Generating PSF from modified AMBER ff Seth Lilavivat (Wed Mar 19 2008 - 12:30:03 CDT)
- Re: Generating PSF from modified AMBER ff Peter Freddolino (Wed Mar 19 2008 - 12:39:50 CDT)
  - Re: Generating PSF from modified AMBER ff Seth Lilavivat (Wed Mar 19 2008 - 12:53:27 CDT)
using Amber paramter snoze pa (Tue Mar 18 2008 - 13:23:31 CDT)
Rigid bonds and hydrogen bonds "on" inaccurate/invalid? Kamilla Kopec (Mon Mar 17 2008 - 13:50:45 CDT)
- Re: Rigid bonds and hydrogen bonds "on" inaccurate/invalid? Kamilla Kopec (Tue Mar 18 2008 - 07:49:24 CDT)
  - Re: Rigid bonds and hydrogen bonds "on" inaccurate/invalid? Peter Freddolino (Wed Mar 19 2008 - 10:38:21 CDT)
    - Re: Rigid bonds and hydrogen bonds "on" inaccurate/invalid? Kamilla Kopec (Wed Mar 19 2008 - 12:38:24 CDT)
    - Re: Rigid bonds and hydrogen bonds "on" inaccurate/invalid? Peter Freddolino (Wed Mar 19 2008 - 15:41:14 CDT)
TARGETED MD - GRADUAL INCREASE OF FORCE Samuel Morales (Fri Mar 14 2008 - 15:21:51 CDT)
- Re: TARGETED MD - GRADUAL INCREASE OF FORCE lcr312 (Sat Mar 15 2008 - 11:45:24 CDT)
TARGETED MD - GRADUAL INCREASE OF FORCE Samuel Morales Navarro (Fri Mar 14 2008 - 14:20:06 CDT)
quartz slab / pairInteractionSelf / Bad global exclusion count! Arturas Ziemys (Fri Mar 14 2008 - 12:55:11 CDT)
- Re: quartz slab / pairInteractionSelf / Bad global exclusion count! Peter Freddolino (Sun Mar 16 2008 - 09:06:25 CDT)
langevinHydrogen off with rigidBonds all? Low Soo Mei (Fri Mar 14 2008 - 04:57:27 CDT)
- Re: langevinHydrogen off with rigidBonds all? Peter Freddolino (Sun Mar 16 2008 - 08:55:42 CDT)
Free Energy of Conformational Change PMF - documentation on method? David Sivak (Thu Mar 13 2008 - 18:07:56 CDT)
Re: TARGETED MD ERROR Jerome Henin (Thu Mar 13 2008 - 00:54:49 CDT)
- Re: TARGETED MD ERROR mon_sharma_at_research.iiit.ac.in (Thu Mar 13 2008 - 01:52:57 CDT)
FEP: FATAL ERROR: Periodic cell has become too small for original patch grid! List (Wed Mar 12 2008 - 13:29:38 CDT)
- Re: FEP: FATAL ERROR: Periodic cell has become too small for original patch grid! Jeffrey J. Potoff (Thu Mar 13 2008 - 10:22:18 CDT)
  - Re: FEP: FATAL ERROR: Periodic cell has become too small for original patch grid! List (Thu Mar 13 2008 - 16:16:04 CDT)
  - FEP + MCTI in one MD simulation List (Thu Mar 13 2008 - 16:25:36 CDT)
Question about 'NAMD TUTORIAL' Ben Chern (Wed Mar 12 2008 - 07:21:50 CDT)
- Re: Question about 'NAMD TUTORIAL' Peter Freddolino (Wed Mar 12 2008 - 18:46:55 CDT)
  - Re: Question about 'NAMD TUTORIAL' Ben Chern (Thu Mar 13 2008 - 00:18:21 CDT)
- TARGETED MD ERROR Samuel Morales Navarro (Wed Mar 12 2008 - 13:33:56 CDT)
variation between results on different OSes Dibyadeep Paul (Wed Mar 12 2008 - 02:31:40 CDT)
- Re: variation between results on different OSes Peter Freddolino (Wed Mar 12 2008 - 18:48:00 CDT)
fixed atoms / pressure Arturas Ziemys (Mon Mar 10 2008 - 12:31:27 CDT)
- Re: fixed atoms / pressure Peter Freddolino (Wed Mar 12 2008 - 18:55:07 CDT)
  - Re: fixed atoms / pressure Arturas Ziemys (Thu Mar 13 2008 - 10:52:41 CDT)
    - Re: fixed atoms / pressure Peter Freddolino (Sun Mar 16 2008 - 09:19:53 CDT)
merge dcd files ,catdcd sripad chandan (Mon Mar 10 2008 - 06:45:58 CDT)
- Re: merge dcd files ,catdcd sripad chandan (Mon Mar 10 2008 - 06:47:10 CDT)
(no subject) me01136_at_cc.uoi.gr (Fri Mar 07 2008 - 12:29:57 CST)
unsubscribe-namd Bertrand P. S. Russell (Fri Mar 07 2008 - 06:19:02 CST)
clarification needed for wrapAll and wrapWater Yinglong Miao (Thu Mar 06 2008 - 08:13:40 CST)
change segID using segment command in psfgen Low Soo Mei (Thu Mar 06 2008 - 03:01:18 CST)
- RE: change segID using segment command in psfgen JC Gumbart (Thu Mar 06 2008 - 08:28:12 CST)
  - Re: change segID using segment command in psfgen Low Soo Mei (Thu Mar 06 2008 - 19:33:33 CST)
Replica Server Tutorial Joshua Adelman (Thu Mar 06 2008 - 00:23:02 CST)
TCL/NAMD: FATAL ERROR: error reading output from command: interrupted system call Corenflos, Steven Charles (Wed Mar 05 2008 - 15:03:47 CST)
Restarting simulation goes the different temperature Magnus Heltstrom (Wed Mar 05 2008 - 10:19:53 CST)
- Re: Restarting simulation goes the different temperature JC Gumbart (Wed Mar 05 2008 - 18:08:30 CST)
  - Re: Restarting simulation goes the different temperature Magnus Heltstrom (Mon Apr 14 2008 - 04:55:57 CDT)
    - Re: Restarting simulation goes the different temperature JC Gumbart (Mon Apr 14 2008 - 10:18:08 CDT)
How to analyze? Namdstats, namdplots, etc. Seth Lilavivat (Tue Mar 04 2008 - 11:55:19 CST)
NAMD stops running without error messages or termination Yinglong Miao (Mon Mar 03 2008 - 17:18:12 CST)
solvate replicates water box (2 by 2 by 2) and segments (8X) for no apparent reason Steven Samuel Plotkin (Sun Mar 02 2008 - 22:56:20 CST)
- Re: solvate replicates water box (2 by 2 by 2) and segments (8X) for no apparent reason L. Michel Espinoza-Fonseca (Sun Mar 02 2008 - 23:53:14 CST)
  - Re: solvate replicates water box (2 by 2 by 2) and segments (8X) for no apparent reason Steven Samuel Plotkin (Mon Mar 03 2008 - 00:26:11 CST)
protein_RNA simulation sripad chandan (Sat Mar 01 2008 - 08:43:22 CST)
ABF error calculation Xu, Jiancong (Fri Feb 29 2008 - 14:47:48 CST)
- Re: ABF error calculation Jerome Henin (Fri Feb 29 2008 - 16:16:29 CST)
- Re: ABF error calculation Chris Chipot (Fri Feb 29 2008 - 16:26:00 CST)
Periodic Box Size vs. Water Box Size Seth Lilavivat (Thu Feb 28 2008 - 10:33:04 CST)
- Re: Periodic Box Size vs. Water Box Size Peter Freddolino (Thu Feb 28 2008 - 11:10:44 CST)
- Re: Periodic Box Size vs. Water Box Size Jeffrey J. Potoff (Thu Feb 28 2008 - 11:07:50 CST)
  - Re: Periodic Box Size vs. Water Box Size Seth Lilavivat (Thu Feb 28 2008 - 11:13:45 CST)
Waterbox unexpectedly deformed after minimization. Kamilla Kopec (Thu Feb 28 2008 - 10:22:38 CST)
- Re: Waterbox unexpectedly deformed after minimization. Peter Freddolino (Thu Feb 28 2008 - 11:08:09 CST)
NAMD 2.6 - PME Error on Large Protein-DNA System! Sean Law (Wed Feb 27 2008 - 18:03:44 CST)
- Re: NAMD 2.6 - PME Error on Large Protein-DNA System! Peter Freddolino (Wed Feb 27 2008 - 23:59:41 CST)
  - RE: NAMD 2.6 - PME Error on Large Protein-DNA System! Sean Law (Thu Feb 28 2008 - 11:35:42 CST)
    - Re: NAMD 2.6 - PME Error on Large Protein-DNA System! Peter Freddolino (Thu Feb 28 2008 - 14:27:20 CST)
Coordinates go to zero! Alex Huang (Wed Feb 27 2008 - 14:52:28 CST)
- Inorganic Builder Plugin Subhashis Biswas (Wed Feb 27 2008 - 17:57:12 CST)
PME Grid Size - how far to deviate from cell basis vectors. Kamilla Kopec (Wed Feb 27 2008 - 10:05:47 CST)
- Re: PME Grid Size - how far to deviate from cell basis vectors. George Madalin Giambasu (Wed Feb 27 2008 - 11:04:08 CST)
- Re: PME Grid Size - how far to deviate from cell basis vectors. JC Gumbart (Thu Feb 28 2008 - 18:48:48 CST)
Protein moving out of water-box after 10 ns simulation Jie-rong Huang (Wed Feb 27 2008 - 08:13:24 CST)
- Re: Protein moving out of water-box after 10 ns simulation Per Jr. Greisen (Wed Feb 27 2008 - 09:40:49 CST)
  - Re: Protein moving out of water-box after 10 ns simulation Jie-rong Huang (Wed Feb 27 2008 - 10:34:15 CST)
    - Re: Protein moving out of water-box after 10 ns simulation JC Gumbart (Thu Feb 28 2008 - 18:45:54 CST)
    - Re: Protein moving out of water-box after 10 ns simulation snoze pa (Fri Feb 29 2008 - 10:55:32 CST)
Question regarding ABF simulations bptilaka_at_mail.uh.edu (Tue Feb 26 2008 - 14:50:14 CST)
unsubscribe namd-l Alessandro Cembran (Tue Feb 26 2008 - 14:11:36 CST)
RNA_minimization sripad chandan (Tue Feb 26 2008 - 12:04:50 CST)
- Re: RNA_minimization jrui_at_ci.uc.pt (Tue Feb 26 2008 - 13:45:04 CST)
implicit solvent energy calculation regafan_at_usc.es (Tue Feb 26 2008 - 04:03:49 CST)
- RE: implicit solvent energy calculation Chang, Christopher (Tue Feb 26 2008 - 13:51:26 CST)
- Re: implicit solvent energy calculation Neema Salimi (Tue Feb 26 2008 - 15:10:25 CST)
umbrella sampling of decalanine using the ABF module Philip Fowler (Mon Feb 25 2008 - 06:21:56 CST)
- Re: umbrella sampling of decalanine using the ABF module Jerome Henin (Mon Feb 25 2008 - 10:44:24 CST)
  - RE: Re: umbrella sampling of decalanine using the ABF module Xu, Jiancong (Mon Feb 25 2008 - 12:37:02 CST)
    - Re: Re: umbrella sampling of decalanine using the ABF module George Madalin Giambasu (Mon Feb 25 2008 - 13:48:55 CST)
    - Re: umbrella sampling of decalanine using the ABF module Ilja Khavrutskii (Mon Feb 25 2008 - 16:34:41 CST)
  - Building NAMD on SGI Altix Rogan Carr (Mon Apr 14 2008 - 15:04:27 CDT)
useGroupPressure with no RigidBonds ? Niels Christensen (Sun Feb 24 2008 - 16:50:55 CST)
center-of-mass tcl and coordinate wrapping Ilja Khavrutskii (Sun Feb 24 2008 - 15:45:15 CST)
namd_minimize sripad chandan (Sun Feb 24 2008 - 10:51:47 CST)
subscribe namd-l Magnus Heltstrom (Fri Feb 22 2008 - 14:47:26 CST)
restarting calc giving new temperatures Magnus Heltstrom (Fri Feb 22 2008 - 14:39:58 CST)
Soft core potential - tested or not? Pawel Weronski (Fri Feb 22 2008 - 13:45:22 CST)
- Re: Soft core potential - tested or not? Chris Chipot (Tue Feb 26 2008 - 15:24:57 CST)
langevinHydrogen off with rigidbonds off? Justine Taylor (Fri Feb 22 2008 - 08:36:25 CST)
problem in NAMD minimized structure when viewed in VMD ramaplot ramya narasimhan (Fri Feb 22 2008 - 04:41:23 CST)
phosphohistidine parameters ??? paco ty (Thu Feb 21 2008 - 12:33:10 CST)
- Re: phosphohistidine parameters ??? L. Michel Espinoza-Fonseca (Thu Feb 21 2008 - 13:45:27 CST)
A difficult problem to explain the SMD force difference Shulin Zhuang (Wed Feb 20 2008 - 22:36:15 CST)
- Re: A difficult problem to explain the SMD force difference Lewyn Li (Thu Feb 21 2008 - 06:59:26 CST)
The correlation of SMD force vs. AFM data Shulin Zhuang (Wed Feb 20 2008 - 14:51:15 CST)
Re: How to run NVT simulations without applying periodic boundary conditions? Yinglong Miao (Wed Feb 20 2008 - 13:59:44 CST)
- Re: How to run NVT simulations without applying periodic boundary conditions? Yinglong Miao (Wed Feb 20 2008 - 15:55:23 CST)
- Re: How to run NVT simulations without applying periodic boundary conditions? Yinglong Miao (Thu Feb 21 2008 - 08:24:55 CST)
  - Re: How to run NVT simulations without applying periodic boundary conditions? Leandro Martínez (Thu Feb 21 2008 - 08:34:49 CST)
    - Re: How to run NVT simulations without applying periodic boundary conditions? Yinglong Miao (Thu Feb 21 2008 - 09:44:45 CST)
MD analysis Seth Lilavivat (Wed Feb 20 2008 - 13:46:42 CST)
How to run NVT simulations without applying periodic boundary conditions? Yinglong Miao (Wed Feb 20 2008 - 12:16:13 CST)
Pair Interaction Calculations to get Charmm Charges? Kamilla Kopec (Tue Feb 19 2008 - 10:23:24 CST)
- Re: Pair Interaction Calculations to get Charmm Charges? Jan Saam (Tue Feb 19 2008 - 17:55:30 CST)
Alchemical FEP NAMD tutorial - problems with reproducing the results Jawahar Neelankatan (Mon Feb 18 2008 - 21:25:54 CST)
- Re: Alchemical FEP NAMD tutorial - problems with reproducing the results Chris Chipot (Tue Feb 19 2008 - 07:14:13 CST)
  - Re: Alchemical FEP NAMD tutorial - problems with reproducing the results Jawahar Neelankatan (Wed Feb 20 2008 - 14:48:54 CST)
    - Re: Alchemical FEP NAMD tutorial - problems with reproducing the results Chris Chipot (Thu Feb 21 2008 - 03:19:42 CST)
ptraj --- 2drms Philip Peartree (Mon Feb 18 2008 - 09:52:46 CST)
PSFGEN Warnings about H positions on standard amino acids Bo Zhang (Mon Feb 18 2008 - 07:07:39 CST)
- RE: PSFGEN Warnings about H positions on standard amino acids Chang, Christopher (Mon Feb 18 2008 - 18:17:48 CST)
Tcl "loadtotalforces" question (forces never seem to be saved) Christopher Calderon (Sun Feb 17 2008 - 11:51:23 CST)
- Re: Tcl "loadtotalforces" question (forces never seem to be saved) Jerome Henin (Sun Feb 17 2008 - 12:39:01 CST)
  - Re: Tcl "loadtotalforces" question (forces never seem to be saved) Christopher Calderon (Sun Feb 17 2008 - 13:06:31 CST)
energy minimization sripad chandan (Sat Feb 16 2008 - 10:11:22 CST)
Question about catdcd and DCDunitcell Joshua D. Moore (Fri Feb 15 2008 - 05:16:21 CST)
Converting PSF *BACK* to CHARMM Philip Peartree (Fri Feb 15 2008 - 03:17:12 CST)
ABF question Matthew Davies (Wed Feb 13 2008 - 11:00:44 CST)
restarting files converge to new temperature Jorgen Simonsen (Tue Feb 12 2008 - 05:21:09 CST)
- Re: restarting files converge to new temperature Peter Freddolino (Tue Feb 12 2008 - 13:34:55 CST)
  - Re: restarting files converge to new temperature Jorgen Simonsen (Wed Feb 13 2008 - 02:13:09 CST)
To incorporate an energy term ramya narasimhan (Tue Feb 12 2008 - 04:32:54 CST)
an aptamer and a lot of stupid problems Xxxxxxxx Xxxxxxx (Mon Feb 11 2008 - 23:09:38 CST)
PCA calculation ramya narasimhan (Mon Feb 11 2008 - 01:49:06 CST)
- RE: PCA calculation Xu, Jiancong (Mon Feb 11 2008 - 10:21:08 CST)
Re: rigid body model Hidekazu WATANABE (Mon Feb 11 2008 - 01:19:23 CST)
HSE and gromacs patrick wintrode (Sun Feb 10 2008 - 10:41:01 CST)
- Re: HSE and gromacs Peter Freddolino (Sun Feb 10 2008 - 10:47:19 CST)
  - Re: HSE and gromacs Peter Freddolino (Sun Feb 10 2008 - 10:49:46 CST)
HP-MPI on Xeon Infiniband Alexandre A. Vakhrouchev (Sun Feb 10 2008 - 06:43:58 CST)
- Re: HP-MPI on Xeon Infiniband Alexandre A. Vakhrouchev (Sun Feb 10 2008 - 08:26:25 CST)
  - Re: HP-MPI on Xeon Infiniband Alexandre A. Vakhrouchev (Sun Feb 10 2008 - 10:10:22 CST)
energy minimization help sripad chandan (Sat Feb 09 2008 - 09:03:50 CST)
quartz / FF(Lopez&MacKerrel) Arturas Ziemys (Fri Feb 08 2008 - 15:00:36 CST)
rigid body model Hidekazu WATANABE (Fri Feb 08 2008 - 02:24:30 CST)
NAMD 2.6 dcd and breaking XPLOR Neema Salimi (Thu Feb 07 2008 - 17:15:10 CST)
- Re: NAMD 2.6 dcd and breaking XPLOR Neema Salimi (Wed Feb 13 2008 - 19:50:38 CST)
  - Re: NAMD 2.6 dcd and breaking XPLOR Peter Freddolino (Thu Feb 14 2008 - 07:14:02 CST)
how to minimize the energy of a protein using CHARMM FF in NAMD Kalyan chaitanya (Thu Feb 07 2008 - 09:29:08 CST)
Re: Constrain=?ISO-8859-1?Q? centers of mass for ?= selected atoms michael_at_perfect-kreim.de (Thu Feb 07 2008 - 07:03:17 CST)
- Re: Constrain centers of mass for selected atoms poker_at_physics.usyd.edu.au (Thu Feb 07 2008 - 18:36:00 CST)
Constrain centers of mass for selected atoms michael_at_perfect-kreim.de (Thu Feb 07 2008 - 04:12:39 CST)
water models supported in NAMD L. Michel Espinoza-Fonseca (Wed Feb 06 2008 - 10:26:09 CST)
- Re: water models supported in NAMD Philip Peartree (Wed Feb 06 2008 - 12:33:19 CST)
  - Re: water models supported in NAMD Jeffrey J. Potoff (Wed Feb 06 2008 - 14:14:27 CST)
- Re: water models supported in NAMD Peter Freddolino (Wed Feb 06 2008 - 12:48:38 CST)
  - Re: water models supported in NAMD L. Michel Espinoza-Fonseca (Wed Feb 06 2008 - 18:18:34 CST)
TCL forces mon_sharma_at_research.iiit.ac.in (Wed Feb 06 2008 - 10:11:45 CST)
TCL forces Monika Sharma (Wed Feb 06 2008 - 07:15:13 CST)
namd energy Leandro Martínez (Tue Feb 05 2008 - 03:39:30 CST)
- Re: namd energy Peter Freddolino (Tue Feb 05 2008 - 06:40:09 CST)
NAMD: constraints while heating Seth Lilavivat (Mon Feb 04 2008 - 15:35:46 CST)
- Re: NAMD: constraints while heating Peter Freddolino (Tue Feb 05 2008 - 06:53:23 CST)
python vs tcl Dibyadeep Paul (Mon Feb 04 2008 - 11:14:56 CST)
FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE HN Andrea Diaz (Sun Feb 03 2008 - 16:29:59 CST)
OPLS-AA toppar files John R. Dowdle (Sat Feb 02 2008 - 08:20:46 CST)
- Re: OPLS-AA toppar files John R. Dowdle (Mon Feb 04 2008 - 11:48:07 CST)
ABF with different bin size Xu, Jiancong (Fri Feb 01 2008 - 11:11:58 CST)
FATAL ERROR: Periodic cell Jorgen Simonsen (Fri Feb 01 2008 - 04:50:34 CST)
- Re: FATAL ERROR: Periodic cell Jianhui Tian (Fri Feb 01 2008 - 08:44:54 CST)
Applying SMD to a domain of protein Monika (Fri Feb 01 2008 - 00:49:37 CST)
- Re: Applying SMD to a domain of protein harish vashisth (Fri Feb 01 2008 - 11:13:58 CST)
FEP configuration file List (Mon Jan 28 2008 - 10:55:21 CST)
NAMDENERGY in parellel Ghalib Bello (Thu Jan 31 2008 - 11:30:18 CST)
- Re: NAMDENERGY in parellel Peter Freddolino (Thu Jan 31 2008 - 13:13:19 CST)
Re: catDCD 32 bit Vs. 64 bit Version Monika Sharma (Thu Jan 31 2008 - 08:09:46 CST)
- Re: catDCD 32 bit Vs. 64 bit Version juneja_at_speakeasy.net (Thu Jan 31 2008 - 11:51:28 CST)
- Re: catDCD 32 bit Vs. 64 bit Version juneja_at_speakeasy.net (Fri Feb 01 2008 - 04:00:51 CST)
  - Re: catDCD 32 bit Vs. 64 bit Version Peter Freddolino (Fri Feb 01 2008 - 09:56:19 CST)
- Re: catDCD 32 bit Vs. 64 bit Version juneja_at_speakeasy.net (Fri Feb 01 2008 - 10:59:52 CST)
  - Re: catDCD 32 bit Vs. 64 bit Version Philip Peartree (Sat Feb 02 2008 - 10:21:44 CST)
- Re: catDCD 32 bit Vs. 64 bit Version Philip Peartree (Thu Feb 07 2008 - 09:28:15 CST)
catDCD 32 bit Vs. 64 bit Version Alok Juneja (Thu Jan 31 2008 - 03:51:40 CST)
- Re: catDCD 32 bit Vs. 64 bit Version Peter Freddolino (Thu Jan 31 2008 - 13:26:09 CST)
FATAL ERROR: Periodic cell has become too small for original patch grid! Joshua Adelman (Wed Jan 30 2008 - 10:42:06 CST)
- Re: FATAL ERROR: Periodic cell has become too small for original patch grid! Peter Freddolino (Wed Jan 30 2008 - 10:52:48 CST)
  - Re: FATAL ERROR: Periodic cell has become too small for original patch grid! Joshua Adelman (Wed Jan 30 2008 - 11:47:16 CST)
About ref frame for rmsd vs time Francesco Pietra (Wed Jan 30 2008 - 00:52:48 CST)
Appending to the existing dcd file after restart Andrei Istomin (Wed Jan 30 2008 - 02:06:55 CST)
Dihedral coordinate ABF scheme Luca (Tue Jan 29 2008 - 15:32:01 CST)
- Re: Dihedral coordinate ABF scheme Jerome Henin (Tue Jan 29 2008 - 16:25:57 CST)
Re: Cholesterol structure Richard Wood (Tue Jan 29 2008 - 09:19:07 CST)
- Re: Cholesterol structure Alexandre A. Vakhrouchev (Thu Jan 31 2008 - 00:50:13 CST)
  - Re: Cholesterol structure Per Jr. Greisen (Thu Jan 31 2008 - 01:29:52 CST)
Cholesterol structure Alexandre A. Vakhrouchev (Tue Jan 29 2008 - 04:48:07 CST)
Sudden expansion of box when continuing NPT simulation Jawahar Neelankatan (Mon Jan 28 2008 - 12:11:52 CST)
- Re: Sudden expansion of box when continuing NPT simulation Peter Freddolino (Tue Jan 29 2008 - 12:24:46 CST)
Grand canonical ensemble michael_at_perfect-kreim.de (Mon Jan 28 2008 - 07:20:11 CST)
- Re: Grand canonical ensemble Peter Freddolino (Mon Jan 28 2008 - 08:51:09 CST)
How can I set Tcouple ? mashaojie163 (Fri Jan 25 2008 - 20:13:26 CST)
Re: SMD vs RAMD / TMD Vlad Cojocaru (Fri Jan 25 2008 - 04:00:10 CST)
Re: Fwd: Re: SMD vs RAMD Vlad Cojocaru (Fri Jan 25 2008 - 03:37:46 CST)
SMD vs RAMD Francesco Pietra (Thu Jan 24 2008 - 11:22:18 CST)
- Re: SMD vs RAMD harish vashisth (Thu Jan 24 2008 - 12:25:20 CST)
- Re: SMD vs RAMD Vlad Cojocaru (Thu Jan 24 2008 - 12:28:37 CST)
Tests not running for Charm++ Myrinet with MPICH-MX brmorgan_at_clarku.edu (Wed Jan 23 2008 - 14:35:05 CST)
minimization command Sourmaidou, Damiani (Wed Jan 23 2008 - 12:35:49 CST)
can we run EM of 2 or more proteins simultaneously Kalyan chaitanya (Tue Jan 22 2008 - 08:47:16 CST)
is there any informatn on callback??= michael_at_perfect-kreim.de (Tue Jan 22 2008 - 08:31:59 CST)
Is it better to align all the trajectory before calculating rmsd? dongsheng lei (Tue Jan 22 2008 - 03:05:47 CST)
- Re: Is it better to align all the trajectory before calculating rmsd? Ana Vila Verde (Tue Jan 22 2008 - 05:31:12 CST)
Inconsistencies in NAMD simulations Chandra Ramananjara (Tue Jan 22 2008 - 02:49:53 CST)
- Re: Inconsistencies in NAMD simulations Ana Vila Verde (Tue Jan 22 2008 - 06:14:52 CST)
What is the unit of coupling coefficient when using tCouple to control temperatue? mashaojie163 (Mon Jan 21 2008 - 06:42:42 CST)
namd vs gromacs vs charmm vs amber Dibyadeep Paul (Sun Jan 20 2008 - 04:43:41 CST)
Re: Re: Creating topology for carbon nanotube / any new structure prateeksha s (Sat Jan 19 2008 - 23:02:22 CST)
- Re: Creating topology for carbon nanotube / any new structure prateeksha s (Sat Jan 19 2008 - 23:05:28 CST)
  - Re: Re: Creating topology for carbon nanotube / any new structure prateeksha s (Fri Feb 22 2008 - 00:17:12 CST)
    - Re: Re: Creating topology for carbon nanotube / any new structure Peter Freddolino (Fri Feb 22 2008 - 07:03:16 CST)
Re: Shear flow: Lees-Edwards Boundary Conditions Richard Wood (Sat Jan 19 2008 - 12:57:12 CST)
About Amber force fields Francesco Pietra (Sat Jan 19 2008 - 08:54:30 CST)
- Defining a group of atoms in a simulation Arneh Babakhani (Sat Jan 19 2008 - 11:15:03 CST)
  - Re: Defining a group of atoms in a simulation Ilja Khavrutskii (Sat Jan 19 2008 - 14:02:58 CST)
- Re: About Amber force fields Jan Saam (Sat Jan 19 2008 - 23:00:45 CST)
Problems found --- [Fwd: Bad global dihedral count.] Wang, Boyang (Fri Jan 18 2008 - 19:56:22 CST)
Shear flow: Lees-Edwards Boundary Conditions Prabhakar Bhimalapuram (Fri Jan 18 2008 - 17:44:10 CST)
Bad global dihedral count. Wang, Boyang (Fri Jan 18 2008 - 14:44:11 CST)
C NH1 C minimization error Sourmaidou, Damiani (Thu Jan 17 2008 - 06:43:18 CST)
- Re: vmd-l: C NH1 C minimization error L. Michel Espinoza-Fonseca (Thu Jan 17 2008 - 07:13:33 CST)
  - RE: vmd-l: C NH1 C minimization error Sourmaidou, Damiani (Sat Jan 19 2008 - 03:28:51 CST)
Problems restarting an amber simulation Seth Lilavivat (Wed Jan 16 2008 - 11:04:14 CST)
- RE: Problems restarting an amber simulation Irene Newhouse (Wed Jan 16 2008 - 12:34:41 CST)
- Re: Problems restarting an amber simulation Guanglei Cui (Wed Jan 16 2008 - 14:35:30 CST)
Converting DCD file to XTC format Jianping Lin (Tue Jan 15 2008 - 17:09:39 CST)
- Re: Converting DCD file to XTC format Alessandro Pedretti (Wed Jan 16 2008 - 02:11:20 CST)
resonable dcdfreq Lixia Jin Day (Tue Jan 15 2008 - 16:21:58 CST)
Characteristic time of atomic vibrations and collisions? Yinglong Miao (Mon Jan 14 2008 - 16:16:11 CST)
- Re: Characteristic time of atomic vibrations and collisions? Victor Ovchinnikov (Mon Jan 14 2008 - 17:33:42 CST)
  - Re: Characteristic time of atomic vibrations and collisions? Yinglong Miao (Tue Jan 15 2008 - 10:06:29 CST)
RE: ABF question jia (Sun Jan 13 2008 - 12:55:37 CST)
changing position of atoms during NAMD simulation michael_at_perfect-kreim.de (Mon Jan 14 2008 - 07:11:52 CST)
ABF using distance-com but with negative xiMin Philip Fowler (Fri Jan 11 2008 - 09:21:48 CST)
- Re: ABF using distance-com but with negative xiMin Jerome Henin (Fri Jan 11 2008 - 17:19:32 CST)
Question about Error Message Alex Huang (Thu Jan 10 2008 - 09:33:49 CST)
ABF question Xu, Jiancong (Wed Jan 09 2008 - 10:04:19 CST)
- Re: ABF question Jerome Henin (Wed Jan 09 2008 - 11:26:57 CST)
  - RE: ABF question Xu, Jiancong (Mon Jan 14 2008 - 10:14:07 CST)
Help snoze pa (Mon Jan 07 2008 - 13:41:47 CST)
NAMD binaries Sangamesh B (Fri Jan 04 2008 - 22:50:58 CST)
Coarse grained psf file and parameter luca (Fri Jan 04 2008 - 08:37:21 CST)
Strange Input Error Jason Wyonn O'Young (Thu Jan 03 2008 - 02:05:37 CST)
Re: charmm charge style Jan Saam (Wed Jan 02 2008 - 15:48:27 CST)
Help reg. input file snoze pa (Wed Jan 02 2008 - 12:35:19 CST)
problems-periodic cell jose correa (Tue Jan 01 2008 - 09:30:10 CST)
- Re: problems-periodic cell Christopher Gillespie (Tue Jan 01 2008 - 12:23:25 CST)
  - RE: problems-periodic cell Irene Newhouse (Tue Jan 01 2008 - 14:41:36 CST)

Last message date: Thu Dec 31 2009 - 04:18:43 CST
Archived on: Wed Feb 29 2012 - 15:51:50 CST

4228 messages sorted by: [ author ] [ date ] [ subject ] [ attachment ]
About this archive