NAMD-L: By Date

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NAMD-L: By Date

By Date

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Starting: Tue Jan 02 2007 - 09:52:55 CST
Ending: Wed Dec 31 2008 - 05:25:21 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)
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)
base stacking analysis of the trajectory of a nucleic acids simulation Tianjiao Wang (Tue Dec 30 2008 - 15:54:31 CST)
Re: compiling NAMD failed on windows with Cygwin Axel Kohlmeyer (Mon Dec 29 2008 - 09:36:45 CST)
Re: gpu pressure control JC Gumbart (Sun Dec 28 2008 - 23:27:07 CST)
gpu pressure control Daniel Miscevski (Sun Dec 28 2008 - 23:10:46 CST)
compiling NAMD failed on windows with Cygwin accomp lin (Sun Dec 28 2008 - 22:32:51 CST)
Re: Changing the Secondary Structure of a Protein Giacomo Fiorin (Sun Dec 28 2008 - 16:33:28 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)
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: solvating protein Peter Freddolino (Fri Dec 26 2008 - 19:53:29 CST)
Re: NAMD-L: autoionize error Axel Kohlmeyer (Fri Dec 26 2008 - 14:45:55 CST)
Re: Stupid question about compiling NAMD with cygwin on windows Axel Kohlmeyer (Fri Dec 26 2008 - 14:35:54 CST)
Re: Problems on SMD simulation Axel Kohlmeyer (Fri Dec 26 2008 - 14:31:18 CST)
NAMD-L: autoionize error jfgaff_at_ncsu.edu (Fri Dec 26 2008 - 13:21:17 CST)
solvating protein Jorgen Simonsen (Fri Dec 26 2008 - 10:27:31 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)
Problems on SMD simulation ÕÅÓÂ (Thu Dec 25 2008 - 01:08:27 CST)
Re: CGMD parameters Peter Freddolino (Wed Dec 24 2008 - 07:27:25 CST)
CGMD parameters BIN ZHANG (Tue Dec 23 2008 - 20:06:32 CST)
Re: Unsure about current setting of Periodic Boundary Conditions Axel Kohlmeyer (Tue Dec 23 2008 - 19:39:12 CST)
Re: Unsure about current setting of Periodic Boundary Conditions Diego Alejandro Vargas (Tue Dec 23 2008 - 18:58:03 CST)
compiling namd on SGI Altix Blake Mertz (Tue Dec 23 2008 - 11:09:10 CST)
Re: Axel Kohlmeyer (Tue Dec 23 2008 - 10:22:51 CST)
tclforces: switch from md with external forces to standard md Vlad Cojocaru (Tue Dec 23 2008 - 09:01:36 CST)
addforce on the com of a group of atoms and loadforces command Vlad Cojocaru (Tue Dec 23 2008 - 07:57:29 CST)
Re: Namd job terminates after ~10000+ itrations Rudra Banerjee (Tue Dec 23 2008 - 05:57:16 CST)
Re: Fwd: regarding protein-dna complex simulation please reply....... JC Gumbart (Tue Dec 23 2008 - 01:21:11 CST)
Namd job terminates after ~10000+ itrations Sangamesh B (Tue Dec 23 2008 - 00:29:25 CST)
(no subject) karthik s (Tue Dec 23 2008 - 00:07:39 CST)
Re: Unsure about current setting of Periodic Boundary Conditions Peter Freddolino (Mon Dec 22 2008 - 13:58:18 CST)
Re: Fwd: regarding protein-dna complex simulation please reply....... JC Gumbart (Mon Dec 22 2008 - 13:30:58 CST)
Fwd: regarding protein-dna complex simulation please reply....... prasun kumar (Mon Dec 22 2008 - 09:44:08 CST)
Re: Unsure about current setting of Periodic Boundary Conditions Diego Alejandro Vargas (Mon Dec 22 2008 - 08:50:16 CST)
Re: xsc file format Luca Muccioli (Mon Dec 22 2008 - 06:57:52 CST)
Re: xsc file format Kyriakos Kachrimanis (Mon Dec 22 2008 - 06:40:44 CST)
NAMD for Intel Xeon Cluster with MPICH DimitryASuplatov (Mon Dec 22 2008 - 06:33:48 CST)
Re: xsc file format Luca Muccioli (Mon Dec 22 2008 - 05:22:16 CST)
xsc file format Kyriakos Kachrimanis (Mon Dec 22 2008 - 03:24:46 CST)
Problems with CUDA Build Christopher Share (Sun Dec 21 2008 - 23:58:47 CST)
Re: alchemical FEP question seleg25_at_rsvs.ulaval.ca (Sun Dec 21 2008 - 12:14:41 CST)
regarding protein-dna complex simulation please reply....... prasun kumar (Sun Dec 21 2008 - 19:30:07 CST)
Re: alchemical FEP question Chris Chipot (Sun Dec 21 2008 - 13:27:57 CST)
Re: alchemical FEP question Christophe.Chipot_at_edam.uhp-nancy.fr (Sat Dec 20 2008 - 05:23:16 CST)
Re: topology/parameter entries for methane? Christophe.Chipot_at_edam.uhp-nancy.fr (Sat Dec 20 2008 - 05:15:12 CST)
Re: entropy calculation Nicholas M Glykos (Sat Dec 20 2008 - 04:26:26 CST)
alchemical FEP question Nandhini Sokkalingam (Fri Dec 19 2008 - 21:44:52 CST)
Re: regarding protein-dna complex simulation Leonardo Trabuco (Fri Dec 19 2008 - 21:08:15 CST)
Re: regarding protein-dna complex simulation Leonardo Trabuco (Fri Dec 19 2008 - 20:44:16 CST)
Re: regarding protein-dna complex simulation Leonardo Trabuco (Fri Dec 19 2008 - 20:16:04 CST)
Re: regarding protein-dna complex simulation Leonardo Trabuco (Fri Dec 19 2008 - 19:53:28 CST)
regarding protein-dna complex simulation prasun kumar (Fri Dec 19 2008 - 19:47:21 CST)
Re: angle deformation Leonardo Trabuco (Fri Dec 19 2008 - 19:45:44 CST)
Re: angle deformation Peter Freddolino (Fri Dec 19 2008 - 19:11:38 CST)
RE: angle deformation CHINDEA Vlad (Fri Dec 19 2008 - 18:02:06 CST)
Re: topology/parameter entries for methane? Jerome Henin (Wed Dec 17 2008 - 20:25:32 CST)
entropy calculation hodak_at_chips.ncsu.edu (Fri Dec 19 2008 - 15:18:28 CST)
RE: How to fix the Center of mass of protein when performing SMD? JC Gumbart (Thu Dec 18 2008 - 23:22:39 CST)
RE: angle deformation JC Gumbart (Thu Dec 18 2008 - 23:04:17 CST)
Re: filling hydrophobic cavity with... methane? Axel Kohlmeyer (Thu Dec 18 2008 - 17:44:23 CST)
filling hydrophobic cavity with... methane? Sebastian Stolzenberg (Thu Dec 18 2008 - 16:10:00 CST)
Re: failure in RATTLE Sangamesh B (Thu Dec 18 2008 - 03:51:54 CST)
Re: How to fix the Center of mass of protein when performing SMD? ÕÅÓÂ (Wed Dec 17 2008 - 22:06:14 CST)
topology/parameter file for ligands bo baker (Wed Dec 17 2008 - 20:56:50 CST)
topology/parameter entries for methane? Sebastian Stolzenberg (Wed Dec 17 2008 - 18:08:25 CST)
angle deformation CHINDEA Vlad (Wed Dec 17 2008 - 17:00:49 CST)
Re: patch DISU to 2 residues jose correa (Wed Dec 17 2008 - 12:34:19 CST)
Re: patch DISU to 2 residues Eric H. Lee (Wed Dec 17 2008 - 12:13:20 CST)
patch DISU to 2 residues jose correa (Wed Dec 17 2008 - 11:58:14 CST)
Re: failure in RATTLE Axel Kohlmeyer (Wed Dec 17 2008 - 09:52:13 CST)
Re: parameter for compiling Ting Zhou (Wed Dec 17 2008 - 07:57:23 CST)
Re: parameter for compiling Peter Freddolino (Wed Dec 17 2008 - 07:53:37 CST)
parameter for compiling Ting Zhou (Wed Dec 17 2008 - 07:42:06 CST)
Re: failure in RATTLE Sangamesh B (Wed Dec 17 2008 - 03:02:38 CST)
Re: Access to CVS Roman Petrenko (Tue Dec 16 2008 - 20:14:00 CST)
Access to CVS Christopher Share (Tue Dec 16 2008 - 19:08:53 CST)
Re: NAMD compile error itvasile_at_nipne.ro (Tue Dec 16 2008 - 14:20:48 CST)
Re: failure in RATTLE Axel Kohlmeyer (Tue Dec 16 2008 - 13:26:09 CST)
Re: NAMD compile error Axel Kohlmeyer (Tue Dec 16 2008 - 13:18:45 CST)
failure in RATTLE Sangamesh B (Tue Dec 16 2008 - 08:20:24 CST)
NAMD compile error itvasile_at_nipne.ro (Tue Dec 16 2008 - 10:43:20 CST)
Unsure about current setting of Periodic Boundary Conditions Diego Alejandro Vargas (Tue Dec 16 2008 - 00:09:12 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)
Re: Single topology FEP Sébastien Légaré (Fri Dec 12 2008 - 19:34:26 CST)
Re: how to get 2 identical trajectories using NAMD in parallel David Hardy (Fri Dec 12 2008 - 11:25:25 CST)
Re: combine PMF/dual FEP -> correct free energies? Jerome Henin (Fri Dec 12 2008 - 11:10:14 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 gaillard_at_chimie.u-strasbg.fr (Fri Dec 12 2008 - 10:49:47 CST)
how to get 2 identical trajectories using NAMD in parallel Vlad Cojocaru (Fri Dec 12 2008 - 09:33:44 CST)
combine PMF/dual FEP -> correct free energies? Sebastian Stolzenberg (Thu Dec 11 2008 - 19:09:28 CST)
Re: Single topology FEP Jerome Henin (Thu Dec 11 2008 - 15:29:46 CST)
Single topology FEP Sébastien Légaré (Thu Dec 11 2008 - 15:05:07 CST)
Re: Loops in tclForcesScript BIN ZHANG (Thu Dec 11 2008 - 14:45:38 CST)
Re: how to apply restraints for phi and psi for alpha helix regions Leonardo Trabuco (Thu Dec 11 2008 - 14:37:08 CST)
Re: how to apply restraints for phi and psi for alpha helix regions Leonardo Trabuco (Thu Dec 11 2008 - 13:12:14 CST)
Loops in tclForcesScript Yang, Lee Wei (Thu Dec 11 2008 - 12:01:08 CST)
Re: FW: Multiplicity of parameters for improper bonds .............. of 1 exceeded. Peter Freddolino (Thu Dec 11 2008 - 11:51:15 CST)
Re: water box getting deformed Peter Freddolino (Thu Dec 11 2008 - 11:43:15 CST)
Re: water box getting deformed Joshua Adelman (Thu Dec 11 2008 - 11:01:34 CST)
Re: lithium parameters Jawahar Neelankatan (Thu Dec 11 2008 - 10:24:39 CST)
Re: srand in a tclforces script Vlad Cojocaru (Thu Dec 11 2008 - 08:31:37 CST)
Re: water box getting deformed Eric H. Lee (Thu Dec 11 2008 - 07:45:58 CST)
how to apply restraints for phi and psi for alpha helix regions Achani K. Yatawara (Thu Dec 11 2008 - 07:42:37 CST)
water box getting deformed sunita gupta (Thu Dec 11 2008 - 07:06:30 CST)
srand in a tclforces script Vlad Cojocaru (Thu Dec 11 2008 - 06:55:53 CST)
FW: Multiplicity of parameters for improper bonds .............. of 1 exceeded. CHINDEA Vlad (Thu Dec 11 2008 - 06:17:20 CST)
(no subject) CHINDEA Vlad (Thu Dec 11 2008 - 06:12:05 CST)
Re: Reading multiple .log files Anirban Ghosh (Wed Dec 10 2008 - 23:21:48 CST)
Re: minimization with amberff ramya narasimhan (Wed Dec 10 2008 - 22:02:35 CST)
Re: Reading multiple .log files Alexander A. Vakhrushev (Wed Dec 10 2008 - 21:48:17 CST)
lithium parameters Sebastian Stolzenberg (Wed Dec 10 2008 - 19:11:47 CST)
DMF solvent parameters Austin B. Yongye (Wed Dec 10 2008 - 16:08:17 CST)
Re: Reading multiple .log files JC Gumbart (Wed Dec 10 2008 - 16:03:11 CST)
POLL: free energy of conformational change Jerome Henin (Wed Dec 10 2008 - 10:25:14 CST)
RE: problem in solvating the protein JC Gumbart (Wed Dec 10 2008 - 08:13:06 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: minimization with amberff Leonardo Trabuco (Wed Dec 10 2008 - 06:09:44 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 - 02:15:38 CST)
minimization with amberff ramya narasimhan (Wed Dec 10 2008 - 01:47:34 CST)
Reading multiple .log files Anirban Ghosh (Tue Dec 09 2008 - 22:42:15 CST)
RE: Increase the decimal points of energy output Yang, Lee Wei (Tue Dec 09 2008 - 20:26:16 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)
Re: Increase the decimal points of energy output Robert Brunner (Tue Dec 09 2008 - 12:14:48 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)
Coulombic virials Benjamin Roberts (Mon Dec 08 2008 - 22:14:00 CST)
Re: CGMD timestep Jerome Henin (Mon Dec 08 2008 - 16:00:03 CST)
Re: CGMD timestep Axel Kohlmeyer (Mon Dec 08 2008 - 12:11:54 CST)
Re: CGMD timestep BIN ZHANG (Mon Dec 08 2008 - 11:51:46 CST)
Re: CGMD timestep Axel Kohlmeyer (Mon Dec 08 2008 - 11:37:37 CST)
Re: CGMD timestep BIN ZHANG (Mon Dec 08 2008 - 11:29:05 CST)
Re: parameters and topology file needed for coarse-grain simulation BIN ZHANG (Mon Dec 08 2008 - 11:12:22 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: TCL8.5? or Axel Kohlmeyer (Mon Dec 08 2008 - 03:36:50 CST)
Re: CGMD timestep Axel Kohlmeyer (Mon Dec 08 2008 - 03:26:43 CST)
Re: Reading multiple .log files into one Anirban Ghosh (Mon Dec 08 2008 - 03:21:07 CST)
TCL8.5? or Christopher Hartshorn (Sun Dec 07 2008 - 23:16:42 CST)
CGMD timestep BIN ZHANG (Sun Dec 07 2008 - 14:44:23 CST)
Re: Equilibration simulation too slow. Christopher Gillespie (Sun Dec 07 2008 - 10:43:17 CST)
Equilibration simulation too slow. Diego Alejandro Vargas (Sun Dec 07 2008 - 09:59:35 CST)
Re: CGMD problem Anton Arkhipov (Sat Dec 06 2008 - 16:31:18 CST)
Re: CGMD problem BIN ZHANG (Sat Dec 06 2008 - 16:19:32 CST)
Re: CGMD problem Anton Arkhipov (Sat Dec 06 2008 - 15:45:15 CST)
Re: CGMD problem BIN ZHANG (Sat Dec 06 2008 - 14:30:39 CST)
error in explicit membrane protein simulations gurvisha_at_leadinvent.com (Sat Dec 06 2008 - 04:11:50 CST)
Re: namd2 erratic performance over 104 procs Axel Kohlmeyer (Sat Dec 06 2008 - 03:18:29 CST)
Re: Energy conversation Alexander A. Vakhrushev (Sat Dec 06 2008 - 01:23:26 CST)
Re: Energy conversation Peter Freddolino (Sat Dec 06 2008 - 00:39:56 CST)
Re: Energy conversation Alexander A. Vakhrushev (Fri Dec 05 2008 - 23:06:30 CST)
Re: Energy conversation Roman Petrenko (Fri Dec 05 2008 - 20:48:24 CST)
namd2 erratic performance over 104 procs Zailo Leite (Fri Dec 05 2008 - 12:52:36 CST)
Re: MacOSX 64bit binaries Christopher Hartshorn (Fri Dec 05 2008 - 11:55:02 CST)
Re: HP Cluster Platform 4000 Giacomo Fiorin (Fri Dec 05 2008 - 09:13:07 CST)
HP Cluster Platform 4000 Hannes Loeffler (Fri Dec 05 2008 - 07:52:02 CST)
Energy conversation Alexander A. Vakhrushev (Fri Dec 05 2008 - 07:51:06 CST)
Re: regarding writemol2 Axel Kohlmeyer (Fri Dec 05 2008 - 03:13:48 CST)
Re: mpirun compilation for NAMD Axel Kohlmeyer (Fri Dec 05 2008 - 03:10:24 CST)
Re: mpirun compilation for NAMD Axel Kohlmeyer (Fri Dec 05 2008 - 02:56:30 CST)
output while tclforces active Vlad Cojocaru (Fri Dec 05 2008 - 02:46:10 CST)
Re: Electron density profile? Leonardo Trabuco (Fri Dec 05 2008 - 01:59:05 CST)
Electron density profile? BIN ZHANG (Fri Dec 05 2008 - 01:40:53 CST)
regarding writemol2 jani sahil (Thu Dec 04 2008 - 23:16:49 CST)
Re: mpirun compilation for NAMD Neelanjana Sengupta (Thu Dec 04 2008 - 20:34:35 CST)
Re: mpirun compilation for NAMD Warner Yuen (Thu Dec 04 2008 - 12:54:37 CST)
Re: mpirun compilation for NAMD Giacomo Fiorin (Thu Dec 04 2008 - 12:13:14 CST)
Re: create inositol molecule dimka (Thu Dec 04 2008 - 12:11:20 CST)
Re: mpirun compilation for NAMD Warner Yuen (Thu Dec 04 2008 - 12:08:37 CST)
install namd on dell power edge 1900 Ramon Rocha (Thu Dec 04 2008 - 11:43:08 CST)
Re: Reading multiple .log files into one Robert Brunner (Thu Dec 04 2008 - 09:14:29 CST)
Re: Reading multiple .log files into one Eric H. Lee (Thu Dec 04 2008 - 08:59:19 CST)
Reading multiple .log files into one Anirban Ghosh (Thu Dec 04 2008 - 08:25:05 CST)
Re: MacOSX 64bit binaries Axel Kohlmeyer (Wed Dec 03 2008 - 15:14:23 CST)
Re: CGMD problem Anton Arkhipov (Wed Dec 03 2008 - 11:39:32 CST)
Re: MacOSX 64bit binaries Giacomo Fiorin (Wed Dec 03 2008 - 10:49:10 CST)
create inositol molecule politr_at_huji.ac.il (Wed Dec 03 2008 - 10:48:38 CST)
Re: mpirun compilation for NAMD Giacomo Fiorin (Wed Dec 03 2008 - 10:42:44 CST)
mpirun compilation for NAMD Neelanjana Sengupta (Wed Dec 03 2008 - 07:46:54 CST)
MacOSX 64bit binaries Christopher Hartshorn (Wed Dec 03 2008 - 01:34:26 CST)
submit namd job in cluster Rudra Banerjee (Tue Dec 02 2008 - 23:04:29 CST)
Re: CGMD problem Peter Freddolino (Tue Dec 02 2008 - 22:39:52 CST)
CGMD problem BIN ZHANG (Tue Dec 02 2008 - 11:10:34 CST)
Help: do you have the top parameter of Gla Wang,Ying (Tue Dec 02 2008 - 10:27:56 CST)
Re: bash: namd2: command not found Joshua Adelman (Tue Dec 02 2008 - 00:40:37 CST)
bash: namd2: command not found Sukesh Chandra Gain (Tue Dec 02 2008 - 00:31:42 CST)
Modification of the NAMD forcefield functions ??? Maxim Paliy (Mon Dec 01 2008 - 13:39:31 CST)
Re: namd cvs compilation Peter Freddolino (Mon Dec 01 2008 - 13:14:10 CST)
Re: MD-problems-GPCR in POPC bilayer JC Gumbart (Mon Dec 01 2008 - 12:53:00 CST)
Re: namd cvs compilation BIN ZHANG (Mon Dec 01 2008 - 11:59:39 CST)
Errors on Missing Atoms for Some Bonds Taekyung Kwon (Sun Nov 30 2008 - 22:19:29 CST)
Re: namdEnergy gives significantly different values from those in log file? Peter Freddolino (Sat Nov 29 2008 - 23:12:01 CST)
Re: namdEnergy gives significantly different values from those in log file? Steven Samuel Plotkin (Sat Nov 29 2008 - 21:39:07 CST)
Biotin-X charmm topology Taekyung Kwon (Sat Nov 29 2008 - 17:13:47 CST)
Re: namd cvs compilation Peter Freddolino (Sat Nov 29 2008 - 06:52:25 CST)
Re: namd cvs compilation Peter Freddolino (Fri Nov 28 2008 - 21:10:36 CST)
SMD-Applied Forces and Analysis ÖÜÎÄ²ý (Fri Nov 28 2008 - 02:27:24 CST)
Re: namd cvs compilation BIN ZHANG (Fri Nov 28 2008 - 00:11:14 CST)
Re: namd cvs compilation Anirban Ghosh (Thu Nov 27 2008 - 22:46:34 CST)
Re: namd cvs compilation BIN ZHANG (Thu Nov 27 2008 - 20:20:46 CST)
running namd on cluster Rudra Banerjee (Thu Nov 27 2008 - 04:25:18 CST)
Re: namd cvs compilation Anirban Ghosh (Thu Nov 27 2008 - 02:27:57 CST)
Re: namd cvs compilation BIN ZHANG (Thu Nov 27 2008 - 01:00:14 CST)
constraint failure problem. ydhuang2727 (Wed Nov 26 2008 - 20:54:30 CST)
Re: TIP4 water model NAMD Peter Freddolino (Wed Nov 26 2008 - 20:39:05 CST)
Re: namd cvs compilation BIN ZHANG (Wed Nov 26 2008 - 19:24:19 CST)
namd cvs compilation BIN ZHANG (Wed Nov 26 2008 - 18:55:07 CST)
Re: Compiling 8Core macs Robert Brunner (Wed Nov 26 2008 - 15:21:58 CST)
force potentials for residue-based CG Dolan, Michael (NIH/NIAID) [C] (Wed Nov 26 2008 - 13:36:51 CST)
Re: TIP4 water model NAMD Mehdi Bagheri-Hamaneh (Wed Nov 26 2008 - 12:15:01 CST)
Re: namdEnergy gives significantly different values from those in log file? Peter Freddolino (Wed Nov 26 2008 - 12:10:37 CST)
Re: TIP4 water model NAMD Axel Kohlmeyer (Wed Nov 26 2008 - 11:19:20 CST)
Re: NAMD CVS Installation Axel Kohlmeyer (Wed Nov 26 2008 - 10:53:10 CST)
Re: namdEnergy gives significantly different values from those in log file? Jerome Henin (Wed Nov 26 2008 - 10:16:12 CST)
TIP4 water model NAMD Mehdi Bagheri-Hamaneh (Wed Nov 26 2008 - 10:28:25 CST)
NAMD CVS Installation Anirban Ghosh (Wed Nov 26 2008 - 05:53:38 CST)
RAM/node Alessio Alexiadis (Wed Nov 26 2008 - 05:37:17 CST)
Re: namdplot Unmatched " error maria goranovic (Wed Nov 26 2008 - 04:58:43 CST)
Re: How do you keep atoms a fixed distance apart? Leonardo Trabuco (Wed Nov 26 2008 - 01:23:18 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: namdEnergy gives significantly different values from those in log file? Steven Samuel Plotkin (Wed Nov 26 2008 - 00:18:13 CST)
Re: Re: tclforce script in FEP: global variable Sebastian Stolzenberg (Tue Nov 25 2008 - 23:53:44 CST)
Re: Re: tclforce script in FEP: global variable Jerome Henin (Tue Nov 25 2008 - 20:34:45 CST)
Re: FEP on charged residue mutation Jerome Henin (Tue Nov 25 2008 - 20:26:41 CST)
Re: FEP on charged residue mutation Sebastian Stolzenberg (Tue Nov 25 2008 - 19:48:21 CST)
Re: FEP on charged residue mutation Sebastian Stolzenberg (Tue Nov 25 2008 - 19:30:08 CST)
Re: Re: tclforce script in FEP: global variable Sebastian Stolzenberg (Tue Nov 25 2008 - 18:21:12 CST)
Re: vmd-l: CG bead definition Anton Arkhipov (Tue Nov 25 2008 - 15:31:45 CST)
Re: Compiling 8Core macs Christopher Hartshorn (Tue Nov 25 2008 - 15:28:51 CST)
Re: vmd-l: CG bead definition BIN ZHANG (Tue Nov 25 2008 - 15:01:37 CST)
MD-problems-GPCR in POPC bilayer jose correa (Tue Nov 25 2008 - 09:30:50 CST)
Re: tclforce script in FEP: global variable Jerome Henin (Tue Nov 25 2008 - 08:57:24 CST)
Re: namd energy self interaction reality check Peter Freddolino (Tue Nov 25 2008 - 08:00:25 CST)
Re: Free energy calculation fixing the dihedrals Luca Bellucci (Tue Nov 25 2008 - 02:48:06 CST)
tclforce script in FEP: global variable Sebastian Stolzenberg (Tue Nov 25 2008 - 01:27:09 CST)
Free energy calculation fixing the dihedrals Jagan Mohan (Tue Nov 25 2008 - 01:12:10 CST)
Free energy calculation fixing the dihedrals Jagan Mohan (Tue Nov 25 2008 - 01:09:46 CST)
namd energy self interaction reality check Thomas C. Bishop (Mon Nov 24 2008 - 23:38:51 CST)
Re: namdEnergy gives significantly different values from those in log file? Peter Freddolino (Mon Nov 24 2008 - 21:29:34 CST)
Re: regarding cgmd Peter Freddolino (Mon Nov 24 2008 - 21:17:10 CST)
Compiling 8Core macs Christopher Hartshorn (Mon Nov 24 2008 - 17:03:40 CST)
NAMD with CUDA Status ? David McGiven (Mon Nov 24 2008 - 11:06:05 CST)
Re: NAMD with mpirun Axel Kohlmeyer (Mon Nov 24 2008 - 06:08:11 CST)
NAMD with mpirun Neelanjana Sengupta (Mon Nov 24 2008 - 05:27:15 CST)
Re: namdEnergy gives significantly different values from those in log file? Steven Samuel Plotkin (Mon Nov 24 2008 - 01:50:02 CST)
Re: namdEnergy gives significantly different values from those in log file? Steven Samuel Plotkin (Mon Nov 24 2008 - 01:01:21 CST)
Re: build missing residues in pdb Schreiner Eduard (Mon Nov 24 2008 - 00:09:18 CST)
build missing residues in pdb Anuradha Mittal (Sun Nov 23 2008 - 18:48:47 CST)
regarding cgmd jani sahil (Sun Nov 23 2008 - 23:14:34 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)
Re: namdEnergy gives significantly different values from those in log file? Peter Freddolino (Sun Nov 23 2008 - 12:33:56 CST)
Re: Re: pairlist i_upper mismatch! Schreiner Eduard (Sun Nov 23 2008 - 02:08:40 CST)
Re: namdEnergy gives significantly different values from those in log file? Peter Freddolino (Sun Nov 23 2008 - 01:55:51 CST)
namdEnergy gives significantly different values from those in log file? Steven Samuel Plotkin (Sat Nov 22 2008 - 23:39:40 CST)
Re: pairlist i_upper mismatch! Diego Alejandro Vargas (Sat Nov 22 2008 - 22:20:31 CST)
Re: CG modeling using NAMD Peter Freddolino (Sat Nov 22 2008 - 20:49:22 CST)
Re: bond length in terminal patches Peter Freddolino (Sat Nov 22 2008 - 20:33:38 CST)
CG modeling using NAMD BIN ZHANG (Sat Nov 22 2008 - 18:54:05 CST)
Re: FEP on charged residue mutation Jerome Henin (Sat Nov 22 2008 - 16:30:52 CST)
bond length in terminal patches CHINDEA Vlad (Sat Nov 22 2008 - 16:29:55 CST)
Re: FEP on charged residue mutation Sebastian Stolzenberg (Sat Nov 22 2008 - 13:48:14 CST)
Re: FEP on charged residue mutation Jerome Henin (Sat Nov 22 2008 - 12:27:19 CST)
Re: FEP on charged residue mutation Sebastian Stolzenberg (Sat Nov 22 2008 - 12:14:57 CST)
Re: FEP on charged residue mutation Jerome Henin (Sat Nov 22 2008 - 11:57:11 CST)
Re: FEP on charged residue mutation Sebastian Stolzenberg (Sat Nov 22 2008 - 11:34:10 CST)
Direction of steered molecular dynamics ÖÜÎÄ²ý (Sat Nov 22 2008 - 08:39:51 CST)
Re: pairlist i_upper mismatch! Floris Buelens (Sat Nov 22 2008 - 04:22:10 CST)
Re: pairlist i_upper mismatch! Schreiner Eduard (Sat Nov 22 2008 - 01:47:01 CST)
Re: pairlist i_upper mismatch! Diego Alejandro Vargas (Sat Nov 22 2008 - 01:09:13 CST)
Re: pairlist i_upper mismatch! Schreiner Eduard (Sat Nov 22 2008 - 00:41:08 CST)
Re: pairlist i_upper mismatch! Diego Alejandro Vargas (Sat Nov 22 2008 - 00:20:25 CST)
Re: par-extraterms.inp file needed JC Gumbart (Fri Nov 21 2008 - 22:22:18 CST)
Re: namdplot Unmatched " error JC Gumbart (Fri Nov 21 2008 - 22:18:48 CST)
Re: FEP on charged residue mutation Jerome Henin (Fri Nov 21 2008 - 16:54:40 CST)
FEP on charged residue mutation Sebastian Stolzenberg (Fri Nov 21 2008 - 16:22:45 CST)
Re: Fwd: How can I load two forcefied at the same time Leonardo Trabuco (Fri Nov 21 2008 - 11:16:34 CST)
Re: Re: vmd-l: Loading .vel file in VMD Thomas C. Bishop (Fri Nov 21 2008 - 09:11:42 CST)
Re: A way to check for non-unique coordinates? Axel Kohlmeyer (Fri Nov 21 2008 - 04:36:21 CST)
Re: vmd-l: Loading .vel file in VMD Axel Kohlmeyer (Fri Nov 21 2008 - 03:45:39 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: Regarding Installation Alexander A. Vakhrushev (Thu Nov 20 2008 - 22:45:22 CST)
Re: Regarding Installation Gary Lyons (Thu Nov 20 2008 - 22:12:34 CST)
A way to check for non-unique coordinates? Diego Alejandro Vargas (Thu Nov 20 2008 - 21:22:21 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: pairlist i_upper mismatch! Peter Freddolino (Thu Nov 20 2008 - 10:56:30 CST)
Re: pairlist i_upper mismatch! Diego Alejandro Vargas (Thu Nov 20 2008 - 10:52:34 CST)
H-bond occupancy in nucleic acids Tianjiao Wang (Thu Nov 20 2008 - 10:08:27 CST)
Re: pairlist i_upper mismatch! Peter Freddolino (Thu Nov 20 2008 - 09:03:56 CST)
namdplot Unmatched " error maria goranovic (Thu Nov 20 2008 - 08:50:52 CST)
Regarding Installation Jagan Mohan (Thu Nov 20 2008 - 04:22:49 CST)
pairlist i_upper mismatch! Diego Alejandro Vargas (Wed Nov 19 2008 - 22:28:41 CST)
Re£ºHow to fix atoms during minimization? ´÷Î°Ãñ (Wed Nov 19 2008 - 19:52:49 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: FEP simulations? Jerome Henin (Tue Nov 18 2008 - 15:43:42 CST)
FEP simulations? Christopher Hartshorn (Tue Nov 18 2008 - 13:19:13 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)
periodic cell has become too small for original patch grid! ydhuang2727 (Tue Nov 18 2008 - 02:54:42 CST)
Re: restart Christopher Hartshorn (Tue Nov 18 2008 - 01:49:32 CST)
restart sripad chandan (Mon Nov 17 2008 - 23:14:12 CST)
Re: Problems with minimization Diego Alejandro Vargas (Mon Nov 17 2008 - 20:54:14 CST)
How do you evaluate forces on a fixed atom? Bill K (Mon Nov 17 2008 - 15:33:38 CST)
FEP calculation of dimerization Christopher Hartshorn (Sun Nov 16 2008 - 23:45:05 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)
Re: Problems with minimization Diego Alejandro Vargas (Sun Nov 16 2008 - 00:28:53 CST)
Re: Problems with minimization Peter Freddolino (Sat Nov 15 2008 - 12:43:56 CST)
Re: Problems with minimization Christopher Gillespie (Sat Nov 15 2008 - 12:10:46 CST)
Re: Problems with minimization Diego Alejandro Vargas (Sat Nov 15 2008 - 11:53:06 CST)
Re: Problems with minimization Christopher Gillespie (Sat Nov 15 2008 - 11:38:26 CST)
Problems with minimization Diego Alejandro Vargas (Sat Nov 15 2008 - 10:57:23 CST)
How can I monitor the force during constant velocity SMD? wayj86 wayj86 (Sat Nov 15 2008 - 07:26:02 CST)
Re: scalability problem on linux cluster Ruchi Sachdeva (Sat Nov 15 2008 - 00:31:24 CST)
langevinDamping Roman Petrenko (Fri Nov 14 2008 - 20:45:10 CST)
Re: constraint failure in RATTLE algorithm for atom 3205 Schreiner Eduard (Fri Nov 14 2008 - 20:13:30 CST)
constraint failure in RATTLE algorithm for atom 3205 ydhuang2727 (Fri Nov 14 2008 - 19:42:20 CST)
Re: NAMD Simulation error Anton Arkhipov (Fri Nov 14 2008 - 15:10:27 CST)
Approach energy with SMD (2) Austin B. Yongye (Fri Nov 14 2008 - 13:31:36 CST)
NAMD Simulation error Anirban Ghosh (Fri Nov 14 2008 - 02:36:16 CST)
NAMD Simulation error Anirban Ghosh (Wed Nov 12 2008 - 22:41:07 CST)
Re: Atoms moving too fast OR constraint failure in RATTLE algorithm Diego Alejandro Vargas (Wed Nov 12 2008 - 19:00:37 CST)
Load balancing off Jonathan Bourne (Wed Nov 12 2008 - 12:20:25 CST)
Re: Force field parameters Ramya Gamini (Wed Nov 12 2008 - 12:05:41 CST)
Re: scalability problem on linux cluster Axel Kohlmeyer (Wed Nov 12 2008 - 11:10:52 CST)
Re: scalability problem on linux cluster Giacomo Fiorin (Wed Nov 12 2008 - 10:30:25 CST)
Re: scalability problem on linux cluster Peter Freddolino (Wed Nov 12 2008 - 10:29:57 CST)
Force field parameters Rabab Toubar (Wed Nov 12 2008 - 10:27:58 CST)
Re: scalability problem on linux cluster Ruchi Sachdeva (Wed Nov 12 2008 - 10:14:49 CST)
Re: scalability problem on linux cluster Giacomo Fiorin (Wed Nov 12 2008 - 09:40:07 CST)
Re: failure in RATTLE algorithm using the adaptive biasing force method Jerome Henin (Wed Nov 12 2008 - 08:43:56 CST)
scalability problem on linux cluster Ruchi Sachdeva (Wed Nov 12 2008 - 08:28:09 CST)
par-extraterms.inp file needed mahesh kulharia (Wed Nov 12 2008 - 04:07:32 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: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE HT1 ramya narasimhan (Tue Nov 11 2008 - 22:18:25 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 Jerome Henin (Tue Nov 11 2008 - 14:19:01 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: solvate using Helmut Grubmuller's SOLVATE and then VMD, then how to minimize properly! Peter Freddolino (Tue Nov 11 2008 - 10:29:34 CST)
Re: protein instability Peter Freddolino (Tue Nov 11 2008 - 10:26:36 CST)
Re: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE HT1 Giacomo Fiorin (Tue Nov 11 2008 - 08:58:10 CST)
Re: converting AMBER trajectory file to CHARMM trajectory file Giacomo Fiorin (Tue Nov 11 2008 - 08:43:54 CST)
converting AMBER trajectory file to CHARMM trajectory file sunita gupta (Tue Nov 11 2008 - 04:37:27 CST)
FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE HT1 ramya narasimhan (Tue Nov 11 2008 - 03:23:43 CST)
solvate using Helmut Grubmuller's SOLVATE and then VMD, then how to minimize properly! ydhuang2727 (Tue Nov 11 2008 - 02:30:40 CST)
protein instability sripad chandan (Mon Nov 10 2008 - 21:27:18 CST)
Re: Simulation issues: water box deformation after minimization and shifting protein coordinates during production run Peter Freddolino (Mon Nov 10 2008 - 20:02:10 CST)
Non-standard amino acid Austin B. Yongye (Mon Nov 10 2008 - 17:05:01 CST)
Re: Simulation issues: water box deformation after minimization and shifting protein coordinates during production run Mamta Mohan (Mon Nov 10 2008 - 14:20:49 CST)
Re: Simulation issues: water box deformation after minimization and shifting protein coordinates during production run Peter Freddolino (Mon Nov 10 2008 - 13:52:11 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)
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 Peter Freddolino (Mon Nov 10 2008 - 11:26:05 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: Error while using NAMD Axel Kohlmeyer (Sun Nov 09 2008 - 16:16:32 CST)
Re: Error while using NAMD Eric H. Lee (Sun Nov 09 2008 - 16:00:57 CST)
Error while using NAMD Marcus Batista (Sun Nov 09 2008 - 15:54:38 CST)
Re: impropers for aromatic residues Jerome Henin (Sun Nov 09 2008 - 15:37:43 CST)
impropers for aromatic residues CHINDEA Vlad (Sat Nov 08 2008 - 15:17:44 CST)
Re: Atoms moving too fast OR constraint failure in RATTLE algorithm Diego Alejandro Vargas (Sat Nov 08 2008 - 17:31:30 CST)
Re: Charm++ Fatal error ! Periodic cell has become too small for original patch grid! Peter Freddolino (Fri Nov 07 2008 - 14:38:47 CST)
Re: Charm++ Fatal error ! Periodic cell has become too small for original patch grid! Roman Petrenko (Fri Nov 07 2008 - 13:57:33 CST)
Re: Charm++ Fatal error ! Periodic cell has become too small for original patch grid! Peter Freddolino (Fri Nov 07 2008 - 12:45:34 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)
Re: Charm++ Fatal error ! Periodic cell has become too small for original patch grid! Joshua Adelman (Fri Nov 07 2008 - 11:31:59 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: PME non-zero charge Axel Kohlmeyer (Fri Nov 07 2008 - 01:51:03 CST)
RE: PME non-zero charge Himanshu Khandelia (Fri Nov 07 2008 - 01:10:42 CST)
RE: generating psf & energy calculation for unusual amino acid - Aib JC Gumbart (Fri Nov 07 2008 - 00:43:29 CST)
generating psf & energy calculation for unusual amino acid - Aib balaji nagarajan (Thu Nov 06 2008 - 21:57:17 CST)
Re: PME non-zero charge Roman Petrenko (Thu Nov 06 2008 - 19:42:25 CST)
Re: PME non-zero charge Peter Freddolino (Thu Nov 06 2008 - 18:09:27 CST)
Re: PME non-zero charge Axel Kohlmeyer (Thu Nov 06 2008 - 16:49:09 CST)
PME non-zero charge Roman Petrenko (Thu Nov 06 2008 - 15:07:56 CST)
NAMD2.6 appears to be freezing at or during load balancing Jonathan Bourne (Thu Nov 06 2008 - 12:33:23 CST)
Re: segmentation fault? Joachim Hein (Thu Nov 06 2008 - 12:18:50 CST)
Re: segmentation fault? Giacomo Fiorin (Wed Nov 05 2008 - 18:42:04 CST)
Re: segmentation fault? Giacomo Fiorin (Wed Nov 05 2008 - 17:46:19 CST)
Re: Atoms moving too fast OR constraint failure in RATTLE algorithm Diego Alejandro Vargas (Wed Nov 05 2008 - 23:17:56 CST)
Re: segmentation fault? Axel Kohlmeyer (Wed Nov 05 2008 - 19:14:32 CST)
Re: segmentation fault? BIN ZHANG (Wed Nov 05 2008 - 18:33:29 CST)
Fw: NAMD mail bounce problem. Mamta Mohan (Wed Nov 05 2008 - 16:59:15 CST)
segmentation fault? BIN ZHANG (Wed Nov 05 2008 - 15:58:58 CST)
Re: Add ions Christopher Gillespie (Wed Nov 05 2008 - 07:06:51 CST)
Re: How can I specify an exact initial velocity? Jerome Henin (Wed Nov 05 2008 - 03:56:46 CST)
Add ions ydhuang2727 (Wed Nov 05 2008 - 02:16:33 CST)
Re: building namd on CRAY-XT3 Axel Kohlmeyer (Wed Nov 05 2008 - 02:10:32 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 - 00:49:51 CST)
Re: building namd on CRAY-XT3 BIN ZHANG (Wed Nov 05 2008 - 00:16:34 CST)
Re: How can I specify an exact initial velocity? wayj86 wayj86 (Tue Nov 04 2008 - 20:01:09 CST)
building namd on CRAY-XT3 BIN ZHANG (Tue Nov 04 2008 - 13:38:35 CST)
Re: Atoms moving too fast OR constraint failure in RATTLE algorithm Joshua Adelman (Tue Nov 04 2008 - 12:58:44 CST)
Atoms moving too fast OR constraint failure in RATTLE algorithm Diego Alejandro Vargas (Tue Nov 04 2008 - 12:34:00 CST)
Re: How can I specify an exact initial velocity? Jerome Henin (Tue Nov 04 2008 - 09:07:14 CST)
How can I specify an exact initial velocity? wayj86 wayj86 (Tue Nov 04 2008 - 02:29:07 CST)
Re: log file problem BIN ZHANG (Mon Nov 03 2008 - 20:49:30 CST)
Re: log file problem Peter Freddolino (Mon Nov 03 2008 - 20:17:05 CST)
Re: cyclic peptides Peter Freddolino (Mon Nov 03 2008 - 20:13:14 CST)
log file problem ydhuang2727 (Mon Nov 03 2008 - 19:57:08 CST)
cyclic peptides Austin B. Yongye (Mon Nov 03 2008 - 16:38:40 CST)
Fw: NAMD mail bounce problem. Mamta Mohan (Mon Nov 03 2008 - 12:35:46 CST)
Approach energy with SMD Austin B. Yongye (Mon Nov 03 2008 - 11:01:26 CST)
Re: multiple simulations Sebastian Stolzenberg (Sun Nov 02 2008 - 23:15:00 CST)
multiple simulations sripad chandan (Sun Nov 02 2008 - 22:32:11 CST)
Re: AMBER ff99SB on NAMD Luis Cunha (Sun Nov 02 2008 - 09:21:17 CST)
Re: AMBER ff99SB on NAMD Luca (Sun Nov 02 2008 - 02:26:52 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: restart PMF: grow phase required? "lambdaRef"? more documentation on NAMD PMF? Peter Freddolino (Sat Nov 01 2008 - 17:33:10 CDT)
NAMD2.6 repeatedly freezing on new desktop Jonathan Bourne (Sat Nov 01 2008 - 16:03:53 CDT)
Re: restart PMF: grow phase required? "lambdaRef"? more documentation on NAMD PMF? Sebastian Stolzenberg (Sat Nov 01 2008 - 12:58:37 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)
Re: combining 2 dcd files into one Anirban Ghosh (Fri Oct 31 2008 - 13:43:14 CDT)
Re: ions behavior in protein-water box: Emanuelle Bachelet (Fri Oct 31 2008 - 12:08:53 CDT)
Re: Could I do the equilibration again with the same dcd file obtained? Schreiner Eduard (Thu Oct 30 2008 - 21:42:54 CDT)
Could I do the equilibration again with the same dcd file obtained? wayj86 wayj86 (Thu Oct 30 2008 - 20:40:09 CDT)
Re: ions behavior in protein-water box: Leandro Martínez (Thu Oct 30 2008 - 17:02:16 CDT)
Re: combining 2 dcd files into one Christopher Gillespie (Thu Oct 30 2008 - 16:26:34 CDT)
combining 2 dcd files into one Rabab Toubar (Thu Oct 30 2008 - 15:20:34 CDT)
Re: ions behavior in protein-water box: Emanuelle Bachelet (Thu Oct 30 2008 - 14:38:13 CDT)
Re: ions behavior in protein-water box: Christopher Gillespie (Thu Oct 30 2008 - 13:50:38 CDT)
Re: ions behavior in protein-water box: Joshua Adelman (Thu Oct 30 2008 - 13:40:45 CDT)
Re: ions behavior in protein-water box: Emanuelle Bachelet (Thu Oct 30 2008 - 12:24:27 CDT)
Problem with temperature increase in equilibration. Diego Alejandro Vargas (Thu Oct 30 2008 - 11:14:54 CDT)
Re: ABF - using gyration Jerome Henin (Thu Oct 30 2008 - 10:29:12 CDT)
Re: ABF - using gyration Subramanian Vaitheeswaran (Thu Oct 30 2008 - 09:59:29 CDT)
RE: carbohydrates: CHARMM versus AMBER Matthew Tessier (Thu Oct 30 2008 - 09:43:27 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)
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: carbohydrates: CHARMM versus AMBER Dong Xu (Wed Oct 29 2008 - 18:47:49 CDT)
Re: ions behavior in protein-water box: Axel Kohlmeyer (Wed Oct 29 2008 - 17:39:03 CDT)
Re: ions behavior in protein-water box: Christopher Gillespie (Wed Oct 29 2008 - 17:12:23 CDT)
Re: ions behavior in protein-water box: Emanuelle Bachelet (Wed Oct 29 2008 - 16:56:10 CDT)
Re: ions behavior in protein-water box: Christopher Gillespie (Wed Oct 29 2008 - 15:05:19 CDT)
ions behavior in protein-water box: Emanuelle Bachelet (Wed Oct 29 2008 - 13:44:59 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? Purushottam Dixit (Wed Oct 29 2008 - 10:36:42 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: ABF - using gyration Subramanian Vaitheeswaran (Tue Oct 28 2008 - 15:19:55 CDT)
Re: ABF - using gyration Jerome Henin (Tue Oct 28 2008 - 15:11:43 CDT)
Re: Membrane Simulations Jerome Henin (Tue Oct 28 2008 - 14:19:12 CDT)
Re: Membrane Simulations Anshu Bhatia (Tue Oct 28 2008 - 12:31:55 CDT)
Re: Membrane Simulations Anshu Bhatia (Tue Oct 28 2008 - 12:27:57 CDT)
Re: ABF - using gyration Jerome Henin (Tue Oct 28 2008 - 11:52:49 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: dcd to pdb conversion Claw Isthelaw (Mon Oct 27 2008 - 04:35:26 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 AyÅŸe Ã–zlem Aykut (Mon Oct 27 2008 - 03:58:58 CDT)
Re: dcd to pdb conversion Eric H. Lee (Mon Oct 27 2008 - 03:39:09 CDT)
dcd to pdb conversion AyÅŸe Ã–zlem Aykut (Mon Oct 27 2008 - 03:28:16 CDT)
Re: Full Electrostatic Calculations on Protein in Vacuo MIke S (Fri Oct 24 2008 - 16:26:02 CDT)
Re: applying stress to study elasticity Axel Kohlmeyer (Fri Oct 24 2008 - 13:35:20 CDT)
Re: applying stress to study elasticity Lam Nguyen (Fri Oct 24 2008 - 12:56:49 CDT)
Re: applying stress to study elasticity Jen Hsin (Fri Oct 24 2008 - 11:20:05 CDT)
applying stress to study elasticity Lam Nguyen (Fri Oct 24 2008 - 11:06:35 CDT)
Re: CG Name Prefix Problem Anton Arkhipov (Fri Oct 24 2008 - 10:30:05 CDT)
CG Name Prefix Problem Anirban Ghosh (Fri Oct 24 2008 - 00:24:58 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)
Re: How to keep Total Energy constant when an external force is added? Axel Kohlmeyer (Thu Oct 23 2008 - 09:58:15 CDT)
Re: Membrane Simulations Vlad Cojocaru (Thu Oct 23 2008 - 02:06:33 CDT)
How to keep Total Energy constant when an external force is added? Fred (Rui FENG) (Wed Oct 22 2008 - 22:48:43 CDT)
Membrane Simulations Anshu Bhatia (Wed Oct 22 2008 - 20:04:38 CDT)
RE: megatest test failure/MPI problem Meij, Henk (Wed Oct 22 2008 - 10:00:05 CDT)
RE: Calcium ion binding protein JC Gumbart (Wed Oct 22 2008 - 09:40:47 CDT)
Re: Non Bonded Paramters Jerome Henin (Tue Oct 21 2008 - 18:05:22 CDT)
Non Bonded Paramters abhijit ramachandran (Tue Oct 21 2008 - 17:25:04 CDT)
Calcium ion binding protein vsweta_at_iastate.edu (Tue Oct 21 2008 - 16:27:31 CDT)
fixedAtoms may not be enabled in a script Christopher Hartshorn (Tue Oct 21 2008 - 10:54:17 CDT)
Re: restart_minimization Peter Freddolino (Tue Oct 21 2008 - 07:30:39 CDT)
restart_minimization sripad chandan (Tue Oct 21 2008 - 05:30:12 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)
Re: Inquire on gradual temperature increase. jose correa (Mon Oct 20 2008 - 09:39:40 CDT)
Re: How to set values for cellBasisVector and PMEGridSize properly Anirban Ghosh (Mon Oct 20 2008 - 08:30:23 CDT)
Inquire on gradual temperature increase. Diego Alejandro Vargas (Mon Oct 20 2008 - 08:59:46 CDT)
Re: rms gradient Peter Freddolino (Mon Oct 20 2008 - 07:51:40 CDT)
Re: How to set values for cellBasisVector and PMEGridSize properly Peter Freddolino (Mon Oct 20 2008 - 07:06:16 CDT)
rms gradient sripad chandan (Mon Oct 20 2008 - 04:59:07 CDT)
How to set values for cellBasisVector and PMEGridSize properly ydhuang2727 (Mon Oct 20 2008 - 03:00:15 CDT)
restart PMF: grow phase required? "lambdaRef"? more documentation on NAMD PMF? Sebastian Stolzenberg (Sun Oct 19 2008 - 13:43:56 CDT)
Re: Atom velocities too high. Joshua Adelman (Sun Oct 19 2008 - 11:48:34 CDT)
Atom velocities too high. Diego Alejandro Vargas (Sun Oct 19 2008 - 09:59:10 CDT)
Re: How can I calculate the distance between two atoms frame by frame? Jerome Henin (Sun Oct 19 2008 - 09:51:51 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? Axel Kohlmeyer (Sat Oct 18 2008 - 22:07:13 CDT)
How can I calculate the distance between two atoms frame by frame? wayj86 wayj86 (Sat Oct 18 2008 - 21:15:25 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 Peter Freddolino (Fri Oct 17 2008 - 10:07:28 CDT)
RE: Using NAMD to calculate pair energy with many subset permutations brmorgan_at_clarku.edu (Fri Oct 17 2008 - 09:39:05 CDT)
right_protocal sripad chandan (Fri Oct 17 2008 - 06:02:54 CDT)
RE: Using NAMD to calculate pair energy with many subset permutations JC Gumbart (Fri Oct 17 2008 - 00:15:23 CDT)
restraint on a group of atoms at their center of mass? Dan W. (Thu Oct 16 2008 - 14:16:19 CDT)
Re: Error while running NPT Simulation Peter Freddolino (Thu Oct 16 2008 - 14:07:26 CDT)
Re: Error while running NPT Simulation Audrey Salazar (Thu Oct 16 2008 - 13:55:55 CDT)
Re: Error while running NPT Simulation Audrey Salazar (Thu Oct 16 2008 - 13:51:30 CDT)
Re: Error while running NPT Simulation Axel Kohlmeyer (Thu Oct 16 2008 - 13:27:24 CDT)
Error while running NPT Simulation Nd S (Thu Oct 16 2008 - 12:44:50 CDT)
Re: Getting total energy of system + pressure and temperature bath. Jerome Henin (Thu Oct 16 2008 - 11:21:55 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 Axel Kohlmeyer (Thu Oct 16 2008 - 10:08:23 CDT)
Re: Pressure related issue Axel Kohlmeyer (Thu Oct 16 2008 - 09:16:02 CDT)
Pressure related issue Anirban Ghosh (Wed Oct 15 2008 - 08:23:29 CDT)
Re: ERROR: DIDN'T FIND "NATOM" IN PSF FILE jose correa (Thu Oct 16 2008 - 07:19:50 CDT)
Full Electrostatic Calculations on Protein in Vacuo MIke S (Thu Oct 16 2008 - 02:07:29 CDT)
ERROR: DIDN'T FIND "NATOM" IN PSF FILE Diego Alejandro Vargas (Wed Oct 15 2008 - 23:12:01 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: Quantitative Test for Equilibration of Data Time Series Peter Freddolino (Wed Oct 15 2008 - 15:01:18 CDT)
RE: megatest test failure/MPI problem Axel Kohlmeyer (Wed Oct 15 2008 - 14:45:16 CDT)
Re: Quantitative Test for Equilibration of Data Time Series Dave Rogers (Wed Oct 15 2008 - 13:27:23 CDT)
RE: megatest test failure/MPI problem Meij, Henk (Wed Oct 15 2008 - 13:26:52 CDT)
Using NAMD to calculate pair energy with many subset permutations brmorgan_at_clarku.edu (Wed Oct 15 2008 - 13:08:42 CDT)
RE: Error with External Electric Filed module Devendra (Wed Oct 15 2008 - 12:29:56 CDT)
Quantitative Test for Equilibration of Data Time Series Joshua Adelman (Wed Oct 15 2008 - 12:06:00 CDT)
Re: How to choose force field? Jerome Henin (Wed Oct 15 2008 - 11:11:16 CDT)
Re: How to choose force field? Axel Kohlmeyer (Wed Oct 15 2008 - 10:57:01 CDT)
Re: megatest test failure/MPI problem Axel Kohlmeyer (Wed Oct 15 2008 - 10:50:14 CDT)
megatest test failure/MPI problem Meij, Henk (Wed Oct 15 2008 - 10:14:48 CDT)
How to choose force field? Diego Alejandro Vargas (Tue Oct 14 2008 - 23:34:20 CDT)
Re: Membrane Simulations bo liu (Tue Oct 14 2008 - 22:09:09 CDT)
Re: Error with External Electric Filed module Ramya Gamini (Tue Oct 14 2008 - 17:08:39 CDT)
Re: FEP: How check equilibration sufficiency? calculate dG? Jerome Henin (Tue Oct 14 2008 - 16:00:24 CDT)
Re: FEP: How check equilibration sufficiency? calculate dG? L. Michel Espinoza-Fonseca (Tue Oct 14 2008 - 15:11:50 CDT)
Membrane Simulations Anshu Bhatia (Tue Oct 14 2008 - 14:05:55 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? Sebastian Stolzenberg (Tue Oct 14 2008 - 11:44:51 CDT)
Error with External Electric Filed module Devendra (Tue Oct 14 2008 - 10:39:05 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? Floris Buelens (Tue Oct 14 2008 - 02:45:50 CDT)
FEP: How check equilibration sufficiency? calculate dG? Sebastian Stolzenberg (Mon Oct 13 2008 - 23:50:43 CDT)
Re: Constraints protocol Peter Freddolino (Mon Oct 13 2008 - 13:34:58 CDT)
Re: Constant z axis Nd S (Mon Oct 13 2008 - 12:27:23 CDT)
Constraints protocol Kamilla Kopec (Mon Oct 13 2008 - 09:41:30 CDT)
pressure calculation Matthew Ambrosia (Mon Oct 13 2008 - 05:11:06 CDT)
Re: Query Regarding FEP tutorial: NPT or NVT? mon_sharma_at_research.iiit.ac.in (Mon Oct 13 2008 - 01:54:21 CDT)
Re: Constant z axis Chris Harrison (Sat Oct 11 2008 - 22:59:31 CDT)
Re: Constant z axis Chris Harrison (Sat Oct 11 2008 - 17:13:54 CDT)
Re: charmrun socket error Chris Harrison (Sat Oct 11 2008 - 17:02:49 CDT)
RE: PMEGridSize JC Gumbart (Sat Oct 11 2008 - 01:01:58 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 (Sun Oct 12 2008 - 06:26:27 CDT)
RE: Constant z axis Navdeep (Sat Oct 11 2008 - 22:25:56 CDT)
Re: Query Regarding FEP tutorial: NPT or NVT? Chris Harrison (Sat Oct 11 2008 - 18:05:52 CDT)
Re: PMEGridSize Chris Harrison (Sat Oct 11 2008 - 16:52:03 CDT)
Query Regarding FEP tutorial: NPT or NVT? mon_sharma_at_research.iiit.ac.in (Sat Oct 11 2008 - 16:33:04 CDT)
RE: PMEGridSize JC Gumbart (Sat Oct 11 2008 - 14:44:16 CDT)
Re: PSF of Tryptophane methyl ester Peter Freddolino (Sat Oct 11 2008 - 12:48:34 CDT)
Re: velocities Peter Freddolino (Sat Oct 11 2008 - 12:46:05 CDT)
PSF of Tryptophane methyl ester CHINDEA Vlad (Sat Oct 11 2008 - 11:43:43 CDT)
velocities Magnus Heltstrom (Sat Oct 11 2008 - 11:00:54 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)
Re: PMEGridSize V.Ovchinnikov (Fri Oct 10 2008 - 09:49:12 CDT)
Re: PMEGridSize Rabab Toubar (Fri Oct 10 2008 - 08:32:18 CDT)
embedding protein in membrane jose correa (Fri Oct 10 2008 - 07:24:36 CDT)
Re: embedding protein in membrane Chris Harrison (Fri Oct 10 2008 - 00:49:44 CDT)
Re: PMEGridSize Chris Harrison (Fri Oct 10 2008 - 00:37:59 CDT)
Re: FEP: delta_G, memory of Hamiltonians corresponding to last G value? Jerome Henin (Thu Oct 09 2008 - 19:29:03 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 - 17:49:05 CDT)
charmrun socket error David A. Horita (Thu Oct 09 2008 - 13:49:21 CDT)
RE: Problems compiling NAMD Jesper Soerensen (Wed Oct 08 2008 - 06:23:16 CDT)
Re: problems with combine.tcl jose correa (Thu Oct 09 2008 - 14:37:24 CDT)
Re: swig wrapping c++ code on nersc Axel Kohlmeyer (Thu Oct 09 2008 - 14:28:03 CDT)
Re: problems with combine.tcl Axel Kohlmeyer (Thu Oct 09 2008 - 14:19:19 CDT)
FEP: delta_G, memory of Hamiltonians corresponding to last G value? Sebastian Stolzenberg (Thu Oct 09 2008 - 14:10:20 CDT)
swig wrapping c++ code on nersc BIN ZHANG (Thu Oct 09 2008 - 11:30:12 CDT)
problems with combine.tcl jose correa (Wed Oct 08 2008 - 20:21:12 CDT)
Constant z axis Nd S (Wed Oct 08 2008 - 19:59:43 CDT)
Re: Use tclforces to find systematic forces on fixed atoms? Bill Kowallis (Wed Oct 08 2008 - 11:45:12 CDT)
embedding protein in membrane jose correa (Wed Oct 08 2008 - 09:08:12 CDT)
RE: Problems compiling NAMD Philip Peartree (Wed Oct 08 2008 - 06:03:06 CDT)
RE: Problems compiling NAMD Axel Kohlmeyer (Tue Oct 07 2008 - 18:44:06 CDT)
RE: Problems compiling NAMD Jesper Sørensen (Tue Oct 07 2008 - 17:19:44 CDT)
Re: Use tclforces to find systematic forces on fixed atoms? Jerome Henin (Tue Oct 07 2008 - 17:08:20 CDT)
Use tclforces to find systematic forces on fixed atoms? Bill K (Tue Oct 07 2008 - 16:20:44 CDT)
Re: Problems compiling NAMD Axel Kohlmeyer (Tue Oct 07 2008 - 11:54:21 CDT)
Re: Problems compiling NAMD Jesper Soerensen (Tue Oct 07 2008 - 03:50:50 CDT)
Re: Problems compiling NAMD Alexander A. Vakhrushev (Tue Oct 07 2008 - 05:04:47 CDT)
Re: equilibration of solvent box and pressure Peter Freddolino (Mon Oct 06 2008 - 15:24:08 CDT)
Re: Problems compiling NAMD Jesper Soerensen (Mon Oct 06 2008 - 09:54:25 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)
Re: Cyclopeptide: connectivity between the first and last residues List (Mon Oct 06 2008 - 11:58:17 CDT)
RE: Problems compiling NAMD Jesper Soerensen (Fri Oct 03 2008 - 15:50:37 CDT)
Re: Problems compiling NAMD Alexander A. Vakhrushev (Mon Oct 06 2008 - 11:00:38 CDT)
Re: PMEGridSize Rabab Toubar (Mon Oct 06 2008 - 10:51:27 CDT)
Re: MD performance on 10 GBit/s or 20Gbit/s infiniband Axel Kohlmeyer (Mon Oct 06 2008 - 10:02:45 CDT)
MD performance on 10 GBit/s or 20Gbit/s infiniband Himanshu Khandelia (Mon Oct 06 2008 - 09:08:35 CDT)
firsttimestep question Dong Xu (Mon Oct 06 2008 - 00:00:46 CDT)
equilibration of solvent box and pressure Hiroaki Maekawa (Sun Oct 05 2008 - 22:10:49 CDT)
(no subject) CHINDEA Vlad (Sun Oct 05 2008 - 15:27:31 CDT)
Re: PMEGridSize JC Gumbart (Fri Oct 03 2008 - 21:53:25 CDT)
Re: PMEGridSize Rabab Toubar (Fri Oct 03 2008 - 15:22:19 CDT)
Re: Problems compiling NAMD Alexander A. Vakhrushev (Fri Oct 03 2008 - 12:44:57 CDT)
Problems compiling NAMD Jesper Soerensen (Fri Oct 03 2008 - 06:54:20 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)
Re: PMEGridSize Roman Petrenko (Thu Oct 02 2008 - 15:22:49 CDT)
PMEGridSize Rabab Toubar (Thu Oct 02 2008 - 13:55:04 CDT)
Re: psf generation for a small non-peptide molecule - again Peter Freddolino (Thu Oct 02 2008 - 10:12:44 CDT)
Re: psf generation for a small non-peptide molecule - again Floris Buelens (Thu Oct 02 2008 - 09:57:49 CDT)
Re: DCD file format Andrew Emerson (Thu Oct 02 2008 - 02:32:08 CDT)
Re: DCD file format Alexander A. Vakhrushev (Wed Oct 01 2008 - 23:43:12 CDT)
Re: psf generation for a small non-peptide molecule - again Peter Freddolino (Wed Oct 01 2008 - 23:06:49 CDT)
psf generation for a small non-peptide molecule - again CHINDEA Vlad (Wed Oct 01 2008 - 16:38:27 CDT)
Re: DCD file format Audrey Salazar (Wed Oct 01 2008 - 15:04:28 CDT)
Re: DCD file format Jerome Henin (Wed Oct 01 2008 - 14:38:35 CDT)
Re: DCD file format Dave Rogers (Wed Oct 01 2008 - 14:17:10 CDT)
DCD file format Santanu Chatterjee (Wed Oct 01 2008 - 13:35:25 CDT)
intramolecular LJ parameters Hamsa Priya Mohana sundaram (Wed Oct 01 2008 - 12:19:56 CDT)
Re: autopsf and hydrogen-sites Peter Freddolino (Wed Oct 01 2008 - 07:59:00 CDT)
autopsf and hydrogen-sites Christine Horejs DI (Wed Oct 01 2008 - 04:09:44 CDT)
Re: How to compute interaction energies between individual amino acid residues Vivek Sharma (Tue Sep 30 2008 - 22:20:18 CDT)
Re: Cyclopeptide: connectivity between the first and last residues List (Tue Sep 30 2008 - 19:08:44 CDT)
Re: How to compute interaction energies between individual amino acid residues harish vashisth (Tue Sep 30 2008 - 12:34:53 CDT)
How to compute interaction energies between individual amino acid residues Jemmy Hu (Tue Sep 30 2008 - 11:24:33 CDT)
Simple query dipti lele (Tue Sep 30 2008 - 04:33:24 CDT)
Re: FW: psf generation for a small non-peptide molecule - again Peter Freddolino (Mon Sep 29 2008 - 19:43:21 CDT)
Re: asphaltene parameters jose correa (Mon Sep 29 2008 - 18:55:27 CDT)
Re: Cyclopeptide: connectivity between the first and last residues Jerome Henin (Mon Sep 29 2008 - 17:31:30 CDT)
FW: psf generation for a small non-peptide molecule - again CHINDEA Vlad (Mon Sep 29 2008 - 17:21:16 CDT)
Re: Cyclopeptide: connectivity between the first and last residues David Tanner (Mon Sep 29 2008 - 15:36:31 CDT)
Re: namd 2.5 compilation error Axel Kohlmeyer (Mon Sep 29 2008 - 14:45:44 CDT)
Re: namd 2.5 compilation error Dong Xu (Mon Sep 29 2008 - 14:38:12 CDT)
Re: namd 2.5 compilation error Axel Kohlmeyer (Mon Sep 29 2008 - 13:12:10 CDT)
Cyclopeptide: connectivity between the first and last residues List (Mon Sep 29 2008 - 12:52:14 CDT)
Re: namd 2.5 compilation error Dong Xu (Mon Sep 29 2008 - 12:15:07 CDT)
Re: Running Multiple TMD simultaneously Jerome Henin (Mon Sep 29 2008 - 11:34:14 CDT)
Re: Running Multiple TMD simultaneously Richard Law (Sat Sep 27 2008 - 20:34:53 CDT)
Re: asphaltene parameters L. Michel Espinoza-Fonseca (Mon Sep 29 2008 - 09:36:02 CDT)
asphaltene parameters jose correa (Mon Sep 29 2008 - 08:55:30 CDT)
How to apply velocity to the entire system with COMmotion enabled Yinglong Miao (Mon Sep 29 2008 - 08:43:38 CDT)
Re: namd 2.5 compilation error Axel Kohlmeyer (Sun Sep 28 2008 - 13:27:38 CDT)
Re: Running Multiple TMD simultaneously Axel Kohlmeyer (Sun Sep 28 2008 - 13:24:16 CDT)
namd 2.5 compilation error Dong Xu (Sun Sep 28 2008 - 01:53:14 CDT)
Running Multiple TMD simultaneously Joshua Adelman (Sat Sep 27 2008 - 14:57:09 CDT)
Re: Managing Log files bo liu (Sat Sep 27 2008 - 03:22:21 CDT)
Re: Managing Log files Nd S (Fri Sep 26 2008 - 22:55:24 CDT)
Re: Managing Log files bo liu (Fri Sep 26 2008 - 22:01:40 CDT)
Re: minimization Audrey Salazar (Fri Sep 26 2008 - 11:41:13 CDT)
Re: minimization Nd S (Fri Sep 26 2008 - 10:12:00 CDT)
Re: minimization Chris Harrison (Fri Sep 26 2008 - 07:19:21 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)
Re: minimization Jerome Henin (Thu Sep 25 2008 - 21:10:46 CDT)
minimization jose correa (Thu Sep 25 2008 - 20:11:36 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)
RE: membrane JC Gumbart (Thu Sep 25 2008 - 11:15:14 CDT)
membrane jose correa (Thu Sep 25 2008 - 09:08:11 CDT)
Re: TCL force Peter Freddolino (Thu Sep 25 2008 - 08:15:30 CDT)
Re: Monte Carlo with NAMD L. Michel Espinoza-Fonseca (Thu Sep 25 2008 - 07:28:15 CDT)
Re: Monte Carlo with NAMD Neelanjana Sengupta (Thu Sep 25 2008 - 06:28:27 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)
Re: How to use bigdcd on a trajectory while skipping first 1000 frames Eric H. Lee (Thu Sep 25 2008 - 04:54:29 CDT)
How to use bigdcd on a trajectory while skipping first 1000 frames maria goranovic (Thu Sep 25 2008 - 04:42:29 CDT)
RE: membrane JC Gumbart (Thu Sep 25 2008 - 00:28:04 CDT)
membrane jose correa (Wed Sep 24 2008 - 18:43:55 CDT)
Re: Periodic BCs L. Michel Espinoza-Fonseca (Wed Sep 24 2008 - 14:51:18 CDT)
Re: TCL force BIN ZHANG (Wed Sep 24 2008 - 14:23:38 CDT)
Re: Managing Log files Nd S (Wed Sep 24 2008 - 13:46:51 CDT)
Re: Managing Log files Alexander A. Vakhrushev (Wed Sep 24 2008 - 13:01:54 CDT)
Re: Periodic BCs Alexander A. Vakhrushev (Wed Sep 24 2008 - 12:58:40 CDT)
Re: Managing Log files Joshua Adelman (Wed Sep 24 2008 - 12:08:46 CDT)
Re: Periodic BCs Nd S (Wed Sep 24 2008 - 12:01:48 CDT)
Managing Log files Nd S (Wed Sep 24 2008 - 11:52:58 CDT)
Re: TCL force Chi-Cheng Chiu (Wed Sep 24 2008 - 10:42:10 CDT)
Re: TCL force Chi-Cheng Chiu (Wed Sep 24 2008 - 10:36:34 CDT)
Re: TCL force Peter Freddolino (Tue Sep 23 2008 - 23:27:31 CDT)
Re: Namd water density Peter Freddolino (Tue Sep 23 2008 - 23:11:11 CDT)
Re: Periodic BCs Jerome Henin (Tue Sep 23 2008 - 18:11:53 CDT)
Periodic BCs Navdeep (Tue Sep 23 2008 - 17:38:52 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)
Re: restarting heating protocol problem: Parminder Mankoo (Tue Sep 23 2008 - 14:37:32 CDT)
Re: restarting heating protocol problem: JC Gumbart (Tue Sep 23 2008 - 14:29:49 CDT)
restarting heating protocol problem: Parminder Mankoo (Tue Sep 23 2008 - 12:55:42 CDT)
Re: Monte Carlo with NAMD harish vashisth (Tue Sep 23 2008 - 11:38:29 CDT)
Re: TCL force BIN ZHANG (Tue Sep 23 2008 - 11:20:40 CDT)
Monte Carlo with NAMD Neelanjana Sengupta (Tue Sep 23 2008 - 10:50:29 CDT)
Re: TCL force Peter Freddolino (Tue Sep 23 2008 - 09:05:16 CDT)
Re: TCL force BIN ZHANG (Tue Sep 23 2008 - 00:43:52 CDT)
Re: Re: Replica Exhange error: POSIX EINTR {interrupted system call} Peter Freddolino (Tue Sep 23 2008 - 00:40:11 CDT)
Re: TCL force Peter Freddolino (Tue Sep 23 2008 - 00:37:01 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)
TCL force BIN ZHANG (Mon Sep 22 2008 - 20:40:59 CDT)
Re: Compile NAMD on Bluegene Christopher Gillespie (Mon Sep 22 2008 - 16:54:48 CDT)
Re: Replica Exhange error: POSIX EINTR {interrupted system call} Dirar Homouz (Mon Sep 22 2008 - 15:07:16 CDT)
Re: need help on CG modelling Peter Freddolino (Mon Sep 22 2008 - 14:24:09 CDT)
Re: need help on CG modelling Nicolas Sapay (Mon Sep 22 2008 - 13:59:16 CDT)
Re: Calcium ion-Protein Binding JC Gumbart (Mon Sep 22 2008 - 13:42:28 CDT)
Re: Calcium ion-Protein Binding MIke S (Mon Sep 22 2008 - 13:33:39 CDT)
Re: need help on CG modelling Peter Freddolino (Mon Sep 22 2008 - 12:48:28 CDT)
Re: Calcium ion-Protein Binding MIke S (Mon Sep 22 2008 - 12:54:20 CDT)
Re: need help on CG modelling Nicolas Sapay (Mon Sep 22 2008 - 12:34:47 CDT)
Compile NAMD on Bluegene Yang Gao (Mon Sep 22 2008 - 10:37:58 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)
Re: psfgen Peter Freddolino (Sat Sep 20 2008 - 21:26:17 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: Re: vmd-l: counting gas molecules inside the nanotube bo liu (Fri Sep 19 2008 - 11:38:19 CDT)
Re: Restarting a Simulation & Langevin Peter Freddolino (Fri Sep 19 2008 - 08:26:59 CDT)
Restarting a Simulation & Langevin Anirban Ghosh (Fri Sep 19 2008 - 08:12:34 CDT)
psfgen Magnus Heltstrom (Fri Sep 19 2008 - 06:42:32 CDT)
Re: vmd-l: counting gas molecules inside the nanotube John Stone (Thu Sep 18 2008 - 12:29:34 CDT)
Re: vmd-l: counting gas molecules inside the nanotube John Stone (Thu Sep 18 2008 - 11:18:43 CDT)
counting gas molecules inside the nanotube mishacat_at_udm.ru (Thu Sep 18 2008 - 06:52:51 CDT)
Re: Calcium ion-Protein Binding JC Gumbart (Thu Sep 18 2008 - 14:22:41 CDT)
Calcium ion-Protein Binding MIke S (Thu Sep 18 2008 - 14:13:34 CDT)
Re: vmd-l: counting gas molecules inside the nanotube Alexander A. Vakhrushev (Thu Sep 18 2008 - 12:11:04 CDT)
Re: Can I use "vecnorm" in the tclforce scripts? Alexander A. Vakhrushev (Thu Sep 18 2008 - 09:29:43 CDT)
Can I use "vecnorm" in the tclforce scripts? Ming (Thu Sep 18 2008 - 08:58:19 CDT)
Re: convergence of abf Eric H. Lee (Thu Sep 18 2008 - 05:19:49 CDT)
Re: velocity DCD data retrieval Peter Freddolino (Wed Sep 17 2008 - 23:35:21 CDT)
velocity DCD data retrieval Matthew Ambrosia (Wed Sep 17 2008 - 23:02:35 CDT)
Oligomer Nejo (Wed Sep 17 2008 - 19:28:18 CDT)
Re: Calcium ions and psfgen MIke S (Wed Sep 17 2008 - 18:18:47 CDT)
Re: Calcium ions and psfgen V.Ovchinnikov (Wed Sep 17 2008 - 18:12:18 CDT)
Calcium ions and psfgen MIke S (Wed Sep 17 2008 - 16:53:16 CDT)
Re: COOH patch? MIke S (Wed Sep 17 2008 - 11:39:25 CDT)
Re: config files no longer working after software 'upgrades' Peter Freddolino (Tue Sep 16 2008 - 19:39:07 CDT)
config files no longer working after software 'upgrades' Irene Newhouse (Tue Sep 16 2008 - 18:18:43 CDT)
Restraint Potential blicebauma_at_duq.edu (Tue Sep 16 2008 - 08:53:59 CDT)
Re: Re: TCL Forces : OUT OF MEMORY V.Ovchinnikov (Fri Sep 12 2008 - 18:58:59 CDT)
Re: TCL Forces : OUT OF MEMORY BIN ZHANG (Fri Sep 12 2008 - 17:43:06 CDT)
TCL Forces : OUT OF MEMORY BIN ZHANG (Fri Sep 12 2008 - 13:38:17 CDT)
convergence of abf Jorgen Simonsen (Fri Sep 12 2008 - 10:03:17 CDT)
Re: namd1 - abf analysis Jerome Henin (Thu Sep 11 2008 - 11:11:10 CDT)
namd1 - abf analysis blicebauma_at_duq.edu (Thu Sep 11 2008 - 08:19:46 CDT)
Re: parameter file to make cholesterol psf file Alexander A. Vakhrushev (Wed Sep 10 2008 - 21:28:59 CDT)
parameter file to make cholesterol psf file peach gil (Wed Sep 10 2008 - 17:39:59 CDT)
Re: Regarding REMD Peter Freddolino (Wed Sep 10 2008 - 09:56:22 CDT)
Re: trifluoroethanol (TFE) solvent L. Michel Espinoza-Fonseca (Wed Sep 10 2008 - 09:41:44 CDT)
Re: trifluoroethanol (TFE) solvent Himanshu Khandelia (Wed Sep 10 2008 - 07:41:39 CDT)
Regarding REMD jani sahil (Wed Sep 10 2008 - 00:04:19 CDT)
Re: trifluoroethanol (TFE) solvent Roman Petrenko (Tue Sep 09 2008 - 22:17:22 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 - 20:26:24 CDT)
trifluoroethanol (TFE) solvent Roman Petrenko (Tue Sep 09 2008 - 19:30:06 CDT)
Re: NAMD vs. CHARMM. Is complete correspondence possible? Axel Kohlmeyer (Tue Sep 09 2008 - 15:56:52 CDT)
Re: Questions concerning NAMD Peter Freddolino (Tue Sep 09 2008 - 15:07:22 CDT)
NAMD vs. CHARMM. Is complete correspondence possible? Niels Johan Christensen (Tue Sep 09 2008 - 14:18:21 CDT)
Re: vmd-l: How to generate more segments? John Stone (Tue Sep 09 2008 - 01:46:41 CDT)
Questions concerning NAMD mxenos_at_notes.cc.sunysb.edu (Tue Sep 09 2008 - 10:26:55 CDT)
Re: restarting a simulation Peter Freddolino (Tue Sep 09 2008 - 09:04:26 CDT)
Re: How to retrieve IC50 of a specific compound from NCBI? L. Michel Espinoza-Fonseca (Tue Sep 09 2008 - 04:25:15 CDT)
How to retrieve IC50 of a specific compound from NCBI? Ming (Tue Sep 09 2008 - 03:54:38 CDT)
vmd-l: How to generate more segments? mishacat_at_udm.ru (Tue Sep 09 2008 - 01:30:05 CDT)
restarting a simulation Raul Araya (Mon Sep 08 2008 - 17:47:35 CDT)
Fwd: convergence of abf Eric H. Lee (Mon Sep 08 2008 - 14:45:53 CDT)
Re: psfgen: more problem Axel Kohlmeyer (Mon Sep 08 2008 - 14:17:28 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)
convergence of abf Jorgen Simonsen (Mon Sep 08 2008 - 09:16:20 CDT)
Re: psf gen Peter Freddolino (Sun Sep 07 2008 - 08:03:40 CDT)
psf gen Rudra Banerjee (Sun Sep 07 2008 - 07:21:22 CDT)
Compile NAMD on MIPS cpu(Loongson 2F) Guo Zhi (Fri Sep 05 2008 - 23:23:38 CDT)
Re: Coarse grained model force fields Anton Arkhipov (Thu Sep 04 2008 - 14:17:52 CDT)
Coarse grained model force fields Myunggi Yi (Thu Sep 04 2008 - 14:01:49 CDT)
Re: Constraint failure & velocity problem bo liu (Thu Sep 04 2008 - 00:26:14 CDT)
RE: Constraint failure & velocity problem Shultz, Jack (Wed Sep 03 2008 - 20:13:24 CDT)
Re: minimization warning and errors Lam T Nguyen (Wed Sep 03 2008 - 11:01:34 CDT)
Re: Struggling with the compilation of NAMD 2.6 on a PBS Cluster with LAM/MPI Frank Thommen (Wed Sep 03 2008 - 10:57:28 CDT)
Re: Constraint failure & velocity problem bo liu (Wed Sep 03 2008 - 00:08:15 CDT)
vdW parameter Diego Alejandro Vargas (Wed Sep 03 2008 - 00:02:22 CDT)
Re: minimization warning and errors Peter Freddolino (Tue Sep 02 2008 - 22:39:34 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 - 14:01:53 CDT)
Re: Constraint failure & velocity problem Peter Freddolino (Tue Sep 02 2008 - 14:00:41 CDT)
Constraint failure & velocity problem Shultz, Jack (Tue Sep 02 2008 - 13:40:09 CDT)
minimization warning and errors Lam T Nguyen (Tue Sep 02 2008 - 13:22:14 CDT)
Re: COOH patch? MIke S (Mon Sep 01 2008 - 18:46:36 CDT)
Re: Platinum paramaters Axel Kohlmeyer (Mon Sep 01 2008 - 15:05:39 CDT)
Platinum paramaters Neelanjana Sengupta (Mon Sep 01 2008 - 08:13:41 CDT)
RE: monitor a distance between two molecules JC Gumbart (Sun Aug 31 2008 - 23:31:17 CDT)
Re: topology file for 2 sugar rings connected 1-1 between them Peter Freddolino (Sun Aug 31 2008 - 08:46:38 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: Struggling with the compilation of NAMD 2.6 on a PBS Cluster with LAM/MPI Frank Thommen (Sun Aug 31 2008 - 06:56:39 CDT)
Re: COOH patch? Thomas Gaillard (Sat Aug 30 2008 - 19:08:41 CDT)
monitor a distance between two molecules me00109_at_cc.uoi.gr (Sat Aug 30 2008 - 18:06:11 CDT)
COOH patch? MIke S (Sat Aug 30 2008 - 17:24:20 CDT)
Re: conskfile Axel Kohlmeyer (Sat Aug 30 2008 - 13:33:07 CDT)
conskfile Shultz, Jack (Sat Aug 30 2008 - 12:46:29 CDT)
Re: Trouble with params file when trying to perform basic dynamics with alanine. Axel Kohlmeyer (Sat Aug 30 2008 - 11:31:18 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: nvidia and namd Chris Harrison (Fri Aug 29 2008 - 12:07:53 CDT)
Re: Struggling with the compilation of NAMD 2.6 on a PBS Cluster with LAM/MPI Axel Kohlmeyer (Fri Aug 29 2008 - 13:55:27 CDT)
Re: Struggling with the compilation of NAMD 2.6 on a PBS Cluster with LAM/MPI Frank Thommen (Fri Aug 29 2008 - 11:59:54 CDT)
nvidia and namd Jorgen Simonsen (Fri Aug 29 2008 - 10:21:17 CDT)
Re: Why turning on 'pressureProfile' make NAMD get into sleep? Huang (Fri Aug 29 2008 - 08:33:57 CDT)
NPT enzemble and ABF Jorgen Simonsen (Fri Aug 29 2008 - 07:07:39 CDT)
Re: vmd-l: TXT program editor Sabuj Pattanayek (Thu Aug 28 2008 - 17:03:11 CDT)
Re: Explicit Membrane Protein Simulations in NAMD/VMD Richard Law (Thu Aug 28 2008 - 15:40:10 CDT)
Re: TXT program editor Giovanni Bellesia (Thu Aug 28 2008 - 16:21:03 CDT)
Re: vmd-l: TXT program editor Axel Kohlmeyer (Thu Aug 28 2008 - 15:50:21 CDT)
RE: Explicit Membrane Protein Simulations in NAMD/VMD Shultz, Jack (Thu Aug 28 2008 - 15:07:24 CDT)
Re: vmd-l: TXT program editor Peter Freddolino (Thu Aug 28 2008 - 15:06:53 CDT)
Re: Explicit Membrane Protein Simulations in NAMD/VMD Jerome Henin (Thu Aug 28 2008 - 14:57:07 CDT)
TXT program editor Alejandro Ortega (Thu Aug 28 2008 - 14:43:14 CDT)
Re: Struggling with the compilation of NAMD 2.6 on a PBS Cluster with LAM/MPI Axel Kohlmeyer (Thu Aug 28 2008 - 14:16:18 CDT)
Re: NAMD compilation / TACC Ranger Axel Kohlmeyer (Thu Aug 28 2008 - 14:12:36 CDT)
Re: change in box geometry for simulation of pure water Axel Kohlmeyer (Thu Aug 28 2008 - 14:06:47 CDT)
Re: PME questions Gianluca Interlandi (Thu Aug 28 2008 - 12:39:31 CDT)
Explicit Membrane Protein Simulations in NAMD/VMD Shultz, Jack (Thu Aug 28 2008 - 12:25:23 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)
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: basic question about drawing methods Ramya Gamini (Thu Aug 28 2008 - 11:55:16 CDT)
NAMD compilation / TACC Ranger Arturas Ziemys (Thu Aug 28 2008 - 11:25:14 CDT)
PME questions Lam T Nguyen (Thu Aug 28 2008 - 10:58:54 CDT)
basic question about drawing methods Subhashis Biswas (Thu Aug 28 2008 - 10:25:16 CDT)
Re: change in box geometry for simulation of pure water Chris Harrison (Wed Aug 27 2008 - 21:23:22 CDT)
Re: Why turning on 'pressureProfile' make NAMD get into sleep? Huang (Thu Aug 28 2008 - 08:20:15 CDT)
Re: change in box geometry for simulation of pure water maria goranovic (Thu Aug 28 2008 - 02:11:31 CDT)
Re: parallel execution speedup bo liu (Thu Aug 28 2008 - 01:51:29 CDT)
Re: diffusion coefficient from rmsd bo liu (Thu Aug 28 2008 - 01:38:38 CDT)
Re: change in box geometry for simulation of pure water Peter Freddolino (Wed Aug 27 2008 - 22:58:07 CDT)
Re: diffusion coefficient from rmsd Axel Kohlmeyer (Wed Aug 27 2008 - 22:39:52 CDT)
diffusion coefficient from rmsd Rudra Banerjee (Wed Aug 27 2008 - 21:55:28 CDT)
Re: corrupt DCD file Axel Kohlmeyer (Wed Aug 27 2008 - 18:56:20 CDT)
corrupt DCD file Forbes, Jeff (NIH/NIAMS) [E] (Wed Aug 27 2008 - 16:54:07 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 Axel Kohlmeyer (Wed Aug 27 2008 - 12:12:00 CDT)
Re: Fe-S cluster topology parameters Chang, Christopher (Wed Aug 27 2008 - 11:51:45 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)
Fe-S cluster topology parameters jose correa (Wed Aug 27 2008 - 09:20:58 CDT)
change in box geometry for simulation of pure water maria goranovic (Wed Aug 27 2008 - 07:48:12 CDT)
Re: error with calling exec: child process exited abnormally Yinglong Miao (Tue Aug 26 2008 - 16:22:21 CDT)
Re: error with calling exec: child process exited abnormally Peter Freddolino (Tue Aug 26 2008 - 14:38:52 CDT)
error with calling exec: child process exited abnormally Yinglong Miao (Tue Aug 26 2008 - 10:37:25 CDT)
Re: van der walls-understanding problem Peter Freddolino (Tue Aug 26 2008 - 10:08:24 CDT)
Re: van der walls-understanding problem Schreiner Eduard (Tue Aug 26 2008 - 10:05:28 CDT)
van der walls-understanding problem Rudra Banerjee (Tue Aug 26 2008 - 09:50:31 CDT)
Re: running precompiled NAMD with multiple processors Axel Kohlmeyer (Tue Aug 26 2008 - 09:41:49 CDT)
running precompiled NAMD with multiple processors Neelanjana Sengupta (Tue Aug 26 2008 - 01:04:57 CDT)
Re: How to write gradual heating config file Hyundeok Song (Mon Aug 25 2008 - 19:30:26 CDT)
Re: How to write gradual heating config file Audrey Salazar (Mon Aug 25 2008 - 18:23:41 CDT)
How to write gradual heating config file Audrey Salazar (Mon Aug 25 2008 - 17:41:59 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: parallel execution speedup Eric H. Lee (Thu Aug 21 2008 - 16:31:32 CDT)
Re: parallel execution speedup Joshua Adelman (Thu Aug 21 2008 - 16:26:06 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: storing velocity data of a NVE simulation David Hardy (Thu Aug 21 2008 - 11:47:26 CDT)
storing velocity data of a NVE simulation sudipta sinha (Thu Aug 21 2008 - 11:32:37 CDT)
Re: SMD more than once Gungor Ozer (Wed Aug 20 2008 - 23:40:58 CDT)
Re: SMD more than once Eric H. Lee (Wed Aug 20 2008 - 14:39:37 CDT)
SMD more than once JARROD EDWARD CHARLES NICKEL (Wed Aug 20 2008 - 14:24:17 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)
Re: Problems with TMD could not be solved with the CVS version Robert Schulz (Mon Aug 18 2008 - 02:47:47 CDT)
Re: TMD and TclForces Gianluca Interlandi (Fri Aug 15 2008 - 12:14:06 CDT)
Re: TMD and TclForces Peter Freddolino (Fri Aug 15 2008 - 07:53:23 CDT)
Re: Problems with TMD could not be solved with the CVS version Peter Freddolino (Fri Aug 15 2008 - 07:51:45 CDT)
Re: Please unsubscribe me Gianluca Interlandi (Thu Aug 14 2008 - 15:42:00 CDT)
Re: Please unsubscribe me Axel Kohlmeyer (Thu Aug 14 2008 - 14:26:26 CDT)
Please unsubscribe me Eva Nong (Thu Aug 14 2008 - 13:52:01 CDT)
Benchmark calculation rebeca_at_mmb.pcb.ub.es (Thu Aug 14 2008 - 12:36:55 CDT)
Re: Problems with TMD could not be solved with the CVS version Semorale (Thu Aug 14 2008 - 12:26:58 CDT)
Re: Problems with TMD could not be solved with the CVS version Peter Freddolino (Thu Aug 14 2008 - 11:41:26 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 - 11:34:43 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)
TMD and TclForces Gianluca Interlandi (Thu Aug 14 2008 - 01:35:21 CDT)
FATAL ERROR: Patch needed for tuple is missing rebeca_at_mmb.pcb.ub.es (Wed Aug 13 2008 - 17:31:27 CDT)
Re: NAMD crashed with TclForce turned on Chi-Cheng Chiu (Wed Aug 13 2008 - 10:33:36 CDT)
Re: Dihedral angle calculation over the trajectories Peter Freddolino (Wed Aug 13 2008 - 10:24:59 CDT)
Dihedral angle calculation over the trajectories sunita gupta (Wed Aug 13 2008 - 10:17:14 CDT)
Re: NAMD crashed with TclForce turned on Vlad Cojocaru (Wed Aug 13 2008 - 07:31:03 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)
Re: SMD force units Eric H. Lee (Mon Aug 11 2008 - 17:50:30 CDT)
Re: SMD force units Eric H. Lee (Mon Aug 11 2008 - 17:46:15 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: namd mpi version with smp Philip Peartree (Mon Aug 11 2008 - 08:35:41 CDT)
namd mpi version with smp Vlad Cojocaru (Mon Aug 11 2008 - 05:22:18 CDT)
Re: NAMD crashed with TclForce turned on Vlad Cojocaru (Mon Aug 11 2008 - 01:50:09 CDT)
RE: NAMD crashed with TclForce turned on Axel Kohlmeyer (Sun Aug 10 2008 - 15:35:28 CDT)
RE: NAMD crashed with TclForce turned on Cojocaru,Vlad (Sun Aug 10 2008 - 11:32:57 CDT)
Re: Abnormal EOF found - buffer Rene Prieto (Sun Aug 10 2008 - 09:37:47 CDT)
Re: NAMD crashed with TclForce turned on Axel Kohlmeyer (Sat Aug 09 2008 - 17:14:26 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)
Re: restartfreq question.... JC Gumbart (Fri Aug 08 2008 - 13:25:56 CDT)
Turn off H-bonding on select residues dora guzman (Fri Aug 08 2008 - 13:21:35 CDT)
Re: Abnormal EOF found - buffer David Tanner (Fri Aug 08 2008 - 10:14:21 CDT)
RE: Problems with the charge (membrane simulation) JC Gumbart (Fri Aug 08 2008 - 10:04:54 CDT)
Re: build smp version of namd with intel 10.1 Vlad Cojocaru (Fri Aug 08 2008 - 05:18:42 CDT)
Re: Value 99999999.9999 during minimization Schreiner Eduard (Fri Aug 08 2008 - 03:44:12 CDT)
Value 99999999.9999 during minimization rebeca_at_mmb.pcb.ub.es (Fri Aug 08 2008 - 03:16:57 CDT)
restartfreq question.... Dr. Luis Rosales León (Thu Aug 07 2008 - 16:31:54 CDT)
Average Velocity and How to choose Right Alias abhijit ramachandran (Thu Aug 07 2008 - 16:13:06 CDT)
RE: NAMD crashed with TclForce turned on Cojocaru,Vlad (Thu Aug 07 2008 - 14:48:11 CDT)
RE: NAMD crashed with TclForce turned on Cojocaru,Vlad (Thu Aug 07 2008 - 14:43:02 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 Axel Kohlmeyer (Thu Aug 07 2008 - 12:08:34 CDT)
Re: NAMD crashed with TclForce turned on Chi-Cheng Chiu (Thu Aug 07 2008 - 11:17:16 CDT)
build smp version of namd with intel 10.1 Vlad Cojocaru (Thu Aug 07 2008 - 10:44:02 CDT)
Re: Re: unwanted bonds in .pdb file while using molefacture José (Wed Aug 06 2008 - 15:40:45 CDT)
Re: NAMD crashed with TclForce turned on Vlad Cojocaru (Thu Aug 07 2008 - 03:05:30 CDT)
Abnormal EOF found - buffer Rene Prieto (Thu Aug 07 2008 - 00:46:37 CDT)
Re: NAMD crashed with TclForce turned on Axel Kohlmeyer (Wed Aug 06 2008 - 17:20:55 CDT)
Re: Impropers in histidine residues Jerome Henin (Wed Aug 06 2008 - 16:54:15 CDT)
NAMD crashed with TclForce turned on Chi-Cheng Chiu (Wed Aug 06 2008 - 16:10:01 CDT)
Re: unwanted bonds in .pdb file while using molefacture Subhashis Biswas (Wed Aug 06 2008 - 14:23:23 CDT)
Problems with the charge (membrane simulation) rebeca_at_mmb.pcb.ub.es (Wed Aug 06 2008 - 13:18:34 CDT)
Re: Error with Shape Based CG Model Anton Arkhipov (Wed Aug 06 2008 - 11:39:38 CDT)
Re: Re: segmentation fault when running ABF Axel Kohlmeyer (Wed Aug 06 2008 - 11:31:42 CDT)
Re: Re: segmentation fault when running ABF Vlad Cojocaru (Wed Aug 06 2008 - 11:23:45 CDT)
Re: Warning in log file Axel Kohlmeyer (Wed Aug 06 2008 - 11:17:34 CDT)
Re: [Fwd: Notice:Re: Re: segmentation fault when running ABF] Axel Kohlmeyer (Wed Aug 06 2008 - 11:15:06 CDT)
Re: Re: segmentation fault when running ABF Axel Kohlmeyer (Wed Aug 06 2008 - 11:10:48 CDT)
Re: WCA Particle Joshua D. Moore (Wed Aug 06 2008 - 09:48:45 CDT)
Warning in log file tinni sona (Wed Aug 06 2008 - 06:23:50 CDT)
[Fwd: Notice:Re: Re: segmentation fault when running ABF] Vlad Cojocaru (Wed Aug 06 2008 - 05:15:19 CDT)
Error with Shape Based CG Model Anirban Ghosh (Wed Aug 06 2008 - 05:04:27 CDT)
Re: Re: segmentation fault when running ABF Vlad Cojocaru (Wed Aug 06 2008 - 04:13:05 CDT)
membrane using OPLS force field rebeca_at_mmb.pcb.ub.es (Tue Aug 05 2008 - 07:48:45 CDT)
Re: Re: segmentation fault when running ABF Axel Kohlmeyer (Tue Aug 05 2008 - 12:13:56 CDT)
Some question about Target MD Yang Gao (Tue Aug 05 2008 - 10:40:10 CDT)
Re: segmentation fault when running ABF Vlad Cojocaru (Tue Aug 05 2008 - 10:34:48 CDT)
segmentation fault when running ABF Vlad Cojocaru (Tue Aug 05 2008 - 10:20:32 CDT)
Re: Zinc-NAMD parameters L. Michel Espinoza-Fonseca (Mon Aug 04 2008 - 15:05:45 CDT)
Zinc-NAMD parameters jose correa (Mon Aug 04 2008 - 14:14:13 CDT)
how do you debug tcl scripts in vmd ? Andriy Volynets (Mon Aug 04 2008 - 12:12:18 CDT)
Re: compilation of the CVS code Vlad Cojocaru (Mon Aug 04 2008 - 10:02:03 CDT)
Re: compilation of the CVS code Peter Freddolino (Mon Aug 04 2008 - 09:22:00 CDT)
Re: compilation of the CVS code Peter Freddolino (Mon Aug 04 2008 - 07:36:20 CDT)
Re: compilation of the CVS code Vlad Cojocaru (Mon Aug 04 2008 - 01:53:41 CDT)
compilation of the CVS code Vlad Cojocaru (Mon Aug 04 2008 - 01:46:11 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: PME fails no matter what Roman Petrenko (Fri Aug 01 2008 - 18:02:03 CDT)
Can this be modelled in NAMD S.K. Ghosh (Fri Aug 01 2008 - 11:38:38 CDT)
Re: psf-generation. Peter Freddolino (Fri Aug 01 2008 - 00:06:19 CDT)
psf-generation. yambem soniya (Thu Jul 31 2008 - 16:57:08 CDT)
Re: SMD in water Marcos Sotomayor (Thu Jul 31 2008 - 13:01:12 CDT)
Re: SMD in water Roman Petrenko (Thu Jul 31 2008 - 12:34:26 CDT)
Re: coord file output minus solvation box Joshua Adelman (Thu Jul 31 2008 - 12:05:08 CDT)
coord file output minus solvation box brosbam_at_berkeley.edu (Wed Jul 30 2008 - 18:21:18 CDT)
Re: SMD in water Axel Kohlmeyer (Thu Jul 31 2008 - 09:16:01 CDT)
Re: Re: build charm++ and namd Peter Freddolino (Thu Jul 31 2008 - 08:39:07 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 - 07:38:31 CDT)
Re: build charm++ and namd Vlad Cojocaru (Thu Jul 31 2008 - 06:46:31 CDT)
SMD in water Roman Petrenko (Thu Jul 31 2008 - 06:22:43 CDT)
build charm++ and namd Vlad Cojocaru (Thu Jul 31 2008 - 05:06:44 CDT)
Re: g(r) Philip Fowler (Thu Jul 31 2008 - 02:29:47 CDT)
Re: g(r) Rudra Banerjee (Thu Jul 31 2008 - 01:51:17 CDT)
Re: g(r) Alexandre A. Vakhrouchev (Thu Jul 31 2008 - 01:10:05 CDT)
g(r) Rudra Banerjee (Thu Jul 31 2008 - 00:39:47 CDT)
Re: output .coor minus solvation box Peter Freddolino (Wed Jul 30 2008 - 23:45:25 CDT)
Re: phosphate (PO4) topology Victor Ovchinnikov (Wed Jul 30 2008 - 21:34:31 CDT)
output .coor minus solvation box brosbam_at_berkeley.edu (Wed Jul 30 2008 - 18:27:01 CDT)
phosphate (PO4) topology Dr. Luis Rosales León (Wed Jul 30 2008 - 17:37:19 CDT)
Re: namd linked to tcl8.5 Axel Kohlmeyer (Wed Jul 30 2008 - 10:20:55 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)
Does anyone have a sample tcl file for counting H-bonds Yang Gao (Wed Jul 30 2008 - 09:33:18 CDT)
Re: namdenergy and amber trajectory Peter Freddolino (Wed Jul 30 2008 - 00:46:57 CDT)
Re: namdenergy and amber trajectory V.Ovchinnikov (Tue Jul 29 2008 - 17:30:53 CDT)
namdenergy and amber trajectory Alessandro Nascimento (Tue Jul 29 2008 - 14:58:56 CDT)
Re: recenter atom and remove rotation (translation) Roman Petrenko (Tue Jul 29 2008 - 15:58:03 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: PME fails no matter what David Hardy (Tue Jul 29 2008 - 12:39:04 CDT)
Re: PME fails no matter what Gianluca Interlandi (Tue Jul 29 2008 - 14:41:50 CDT)
Re: ABF simulations Chris Chipot (Tue Jul 29 2008 - 09:55:41 CDT)
Re: PME fails no matter what Joshua Adelman (Tue Jul 29 2008 - 12:00:11 CDT)
Re: Running CGMD using NAMD Peter Freddolino (Tue Jul 29 2008 - 11:39:54 CDT)
Re: PME fails no matter what Peter Freddolino (Tue Jul 29 2008 - 11:38:20 CDT)
Re: PME fails no matter what Axel Kohlmeyer (Tue Jul 29 2008 - 03:18:21 CDT)
Re: fixed residue Gianluca Interlandi (Tue Jul 29 2008 - 01:03:40 CDT)
Re: PME fails no matter what Roman Petrenko (Tue Jul 29 2008 - 00:17:41 CDT)
Running CGMD using NAMD Anirban Ghosh (Mon Jul 28 2008 - 23:46:54 CDT)
Re: PME fails no matter what Joshua Adelman (Mon Jul 28 2008 - 23:50:19 CDT)
Re: fixed residue Roman Petrenko (Mon Jul 28 2008 - 23:38:10 CDT)
Re: fixed residue Roman Petrenko (Mon Jul 28 2008 - 23:36:45 CDT)
PME fails no matter what Roman Petrenko (Mon Jul 28 2008 - 23:29:54 CDT)
Re: fixed residue Joshua Adelman (Mon Jul 28 2008 - 23:16:41 CDT)
fixed residue Rudra Banerjee (Mon Jul 28 2008 - 22:49:36 CDT)
ABF simulations Raul Araya (Mon Jul 28 2008 - 14:45:46 CDT)
Re: ubuntu reads my psf as an audio file Axel Kohlmeyer (Mon Jul 28 2008 - 13:58:34 CDT)
ubuntu reads my psf as an audio file patrick wintrode (Mon Jul 28 2008 - 13:29:17 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)
Re: NAMD + TMD on Abe Gianluca Interlandi (Fri Jul 25 2008 - 12:58:08 CDT)
Different dcd files for minimize and MD Lam T Nguyen (Fri Jul 25 2008 - 07:50:38 CDT)
Re: NAMD + TMD on Abe Peter Freddolino (Fri Jul 25 2008 - 14:55:13 CDT)
Different dcd files for minimize and MD Lam T Nguyen (Thu Jul 24 2008 - 15:20:17 CDT)
Re: PME and infinite polymer Arturas Ziemys (Fri Jul 25 2008 - 09:26:53 CDT)
Re: PME and infinite polymer Axel Kohlmeyer (Fri Jul 25 2008 - 08:24:30 CDT)
Re: PME and infinite polymer Peter Freddolino (Fri Jul 25 2008 - 09:23:28 CDT)
Re: NAMD + TMD on Abe Peter Freddolino (Fri Jul 25 2008 - 09:21:05 CDT)
PME and infinite polymer Arturas Ziemys (Thu Jul 24 2008 - 20:59:33 CDT)
NAMD + TMD on Abe Gianluca Interlandi (Thu Jul 24 2008 - 23:05:38 CDT)
Re: Appending dcd when restarting a simulation Eric H. Lee (Thu Jul 24 2008 - 08:58:21 CDT)
Re: Appending dcd when restarting a simulation Axel Kohlmeyer (Thu Jul 24 2008 - 08:52:56 CDT)
Appending dcd when restarting a simulation pellegrini (Thu Jul 24 2008 - 03:17:02 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)
Re: MD problems Schreiner Eduard (Sun Jul 20 2008 - 22:13:47 CDT)
MD problems jose correa (Sun Jul 20 2008 - 21:37:13 CDT)
Re: memory overflow problem of Tcl scripting when dealing with trajectories Chris Harrison (Sun Jul 20 2008 - 15:21:16 CDT)
Re: CHARMM parameters for H2S Jeffrey J. Potoff (Sat Jul 19 2008 - 22:34:21 CDT)
CHARMM parameters for H2S Raul Araya (Fri Jul 18 2008 - 17:51:50 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)
Re: ERROR(S) IN THE CONFIGURATION FILE when running on a cluster. Axel Kohlmeyer (Fri Jul 18 2008 - 14:18:02 CDT)
Re: ERROR(S) IN THE CONFIGURATION FILE when running on a cluster. Joaquim Rui Rodrigues (Fri Jul 18 2008 - 14:17:43 CDT)
ERROR(S) IN THE CONFIGURATION FILE when running on a cluster. Lam T Nguyen (Fri Jul 18 2008 - 13:32:14 CDT)
how to generate psf file using the AMBER topology file tinni sona (Fri Jul 18 2008 - 05:38:45 CDT)
Problem while installing NAMD Karan Maroo (Thu Jul 17 2008 - 04:06:17 CDT)
Constraining center of mass of monomers S.K. Ghosh (Wed Jul 16 2008 - 17:45:57 CDT)
Re: Avoiding alpha-helix distortions Chris Harrison (Sun Jul 06 2008 - 07:52:41 CDT)
Re: LangevinTemp and KE calculation E. Prabhu Raman (Wed Jul 16 2008 - 12:56:22 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)
Re: LangevinTemp and KE calculation Peter Freddolino (Wed Jul 16 2008 - 06:53:01 CDT)
memory overflow problem of Tcl scripting when dealing with trajectories bo liu (Wed Jul 16 2008 - 03:16:31 CDT)
LangevinTemp and KE calculation E. Prabhu Raman (Tue Jul 15 2008 - 18:25:49 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)
Re: trajectories Anton Arkhipov (Mon Jul 14 2008 - 14:58:14 CDT)
Re: trajectories Jerome Henin (Mon Jul 14 2008 - 14:45:23 CDT)
Re: trajectories Schreiner Eduard (Mon Jul 14 2008 - 14:53:52 CDT)
trajectories jfgaff_at_ncsu.edu (Mon Jul 14 2008 - 13:38:39 CDT)
Re: use of charmm27 & NPT ensemble for lipid bilayer simulation Ruchi Sachdeva (Sun Jul 13 2008 - 23:09:57 CDT)
Re: NAMD OUTPUT Ramya Gamini (Sun Jul 13 2008 - 17:14:48 CDT)
Re: NAMD OUTPUT Jerome Henin (Sun Jul 13 2008 - 16:37:39 CDT)
Re: cannot find -lsrfftw... collect2: ld returned 1 exit status Axel Kohlmeyer (Sun Jul 13 2008 - 15:54:54 CDT)
NAMD OUTPUT Semorale (Sun Jul 13 2008 - 15:37:14 CDT)
cannot find -lsrfftw... collect2: ld returned 1 exit status Anupam Nath Jha (Sun Jul 13 2008 - 12:59:09 CDT)
DNA simulation by NAMD sudipta sinha (Sun Jul 13 2008 - 06:07:20 CDT)
Re: use of charmm27 & NPT ensemble for lipid bilayer simulation JC Gumbart (Sat Jul 12 2008 - 22:07:00 CDT)
Re: minimization and MD in one configuration file? NGUYEN LAM (Sat Jul 12 2008 - 14:23:13 CDT)
Re: minimization and MD in one configuration file? arajan_at_ks.uiuc.edu (Sat Jul 12 2008 - 14:14:45 CDT)
RE: minimization and MD in one configuration file? JC Gumbart (Sat Jul 12 2008 - 13:13:52 CDT)
minimization and MD in one configuration file? NGUYEN LAM (Sat Jul 12 2008 - 10:46:38 CDT)
Re: installation of charm-6.0 in ia-64 cluster machine Peter Freddolino (Fri Jul 11 2008 - 12:23:30 CDT)
Re: NAMD on blue gene BG/P George Madalin Giambasu (Fri Jul 11 2008 - 10:17:27 CDT)
installation of charm-6.0 in ia-64 cluster machine Anupam Nath Jha (Fri Jul 11 2008 - 06:49:34 CDT)
Re: NAMD on blue gene BG/P Andrew Emerson (Fri Jul 11 2008 - 05:44:16 CDT)
Re: WCA Particle Giovanni Bellesia (Thu Jul 10 2008 - 16:07:25 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: NAMD on blue gene BG/P George Madalin Giambasu (Thu Jul 10 2008 - 17:00:50 CDT)
Re: alkane-silicon_dioxide simulation Eduardo Cruz-Chu (Thu Jul 10 2008 - 15:46:25 CDT)
NAMD on blue gene BG/P Andrew Emerson (Thu Jul 10 2008 - 05:46:36 CDT)
alkane-silicon_dioxide simulation Raul Araya Secchi (Thu Jul 10 2008 - 15:18:06 CDT)
Re: WCA Particle Peter Freddolino (Thu Jul 10 2008 - 11:25:51 CDT)
Re: Rise in Total Energy in NVE Leandro Martínez (Thu Jul 10 2008 - 07:28:18 CDT)
WCA Particle Dave Rogers (Wed Jul 09 2008 - 21:45:48 CDT)
Re: Rise in Total Energy in NVE S.K. Ghosh (Thu Jul 10 2008 - 06:30:40 CDT)
Re: Rise in Total Energy in NVE Chris Harrison (Wed Jul 09 2008 - 20:46:53 CDT)
Re: Rise in Total Energy in NVE S.K. Ghosh (Wed Jul 09 2008 - 12:33:37 CDT)
Re: Rise in Total Energy in NVE Peter Freddolino (Wed Jul 09 2008 - 10:37:19 CDT)
Re: TMD SIMULATION - RMSD DOUBT Semorale (Wed Jul 09 2008 - 10:30:34 CDT)
Re: Rise in Total Energy in NVE S.K. Ghosh (Wed Jul 09 2008 - 10:25:35 CDT)
Re: TMD SIMULATION - RMSD DOUBT Joshua Adelman (Tue Jul 08 2008 - 22:04:51 CDT)
Re: Interaction energy Peter Freddolino (Tue Jul 08 2008 - 21:07:10 CDT)
TMD SIMULATION - RMSD DOUBT Semorale (Tue Jul 08 2008 - 20:05:37 CDT)
Interaction energy abhijit ramachandran (Tue Jul 08 2008 - 15:57:47 CDT)
Re: Maximum Velocities Chris Harrison (Tue Jul 08 2008 - 15:33:19 CDT)
Re: Maximum Velocities Eric H. Lee (Tue Jul 08 2008 - 13:50:51 CDT)
Maximum Velocities Alejandro Ortega (Tue Jul 08 2008 - 13:20:33 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)
Re: relating to NAMD Energy Plugin scripting Peter Freddolino (Mon Jul 07 2008 - 12:47:25 CDT)
Re: Implementation of TCL script in NAMD .conf file Benjamin Bouvier (Mon Jul 07 2008 - 04:34:54 CDT)
relating to NAMD Energy Plugin scripting bo liu (Sun Jul 06 2008 - 23:19:44 CDT)
Re: Problem with TclBC when run in more than one processor Alexandre A. Vakhrouchev (Wed Jun 04 2008 - 22:52:43 CDT)
Re: Avoiding alpha-helix distortions Eric H. Lee (Sat Jul 05 2008 - 12:22:24 CDT)
Re: Avoiding alpha-helix distortions Praveen Agrawal (Sat Jul 05 2008 - 00:38:45 CDT)
Implementation of TCL script in NAMD .conf file sudipta sinha (Sat Jul 05 2008 - 00:18:25 CDT)
Re: won't launch on linux ubuntu cluster for a parallel run Peter Freddolino (Fri Jul 04 2008 - 22:34:03 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: ABF Method digenova (Thu Jul 03 2008 - 08:52:29 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: Avoiding alpha-helix distortions Eric H. Lee (Wed Jul 02 2008 - 10:41:01 CDT)
drop in Temp from NVT to NVE S.K. Ghosh (Wed Jul 02 2008 - 10:18:41 CDT)
ABF Method Bonnie A Merchant (Wed Jul 02 2008 - 09:19:39 CDT)
RE: carbohydrates: CHARMM versus AMBER Matthew Tessier (Wed Jul 02 2008 - 08:02:24 CDT)
Re: Avoiding alpha-helix distortions Peter Freddolino (Wed Jul 02 2008 - 07:59:15 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: NAMD 2.7? Branduardi Davide (Wed Jul 02 2008 - 02:14:27 CDT)
Re: NAMD 2.7? Davide Branduardi (Tue Jul 01 2008 - 02:04:26 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)
Re: Large MD simulations and atom number limits with NAMD Peter Freddolino (Mon Jun 30 2008 - 14:43:08 CDT)
Re: NAMD 2.7? Chris Harrison (Mon Jun 30 2008 - 12:54:29 CDT)
Re: NAMD 2.7? Jerome Henin (Mon Jun 30 2008 - 15:52:29 CDT)
Re: NAMD 2.7? Peter Freddolino (Mon Jun 30 2008 - 14:40:39 CDT)
Re: NAMD 2.7? L. Michel Espinoza-Fonseca (Mon Jun 30 2008 - 14:15:38 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)
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Re: carbohydrates: CHARMM versus AMBER L. Michel Espinoza-Fonseca (Fri Jun 27 2008 - 17:44:41 CDT)
carbohydrates: CHARMM versus AMBER Gianluca Interlandi (Fri Jun 27 2008 - 17:16:26 CDT)
carbohydrates: CHARMM versus AMBER Gianluca Interlandi (Fri Jun 27 2008 - 14:16:08 CDT)
Re: Problem in making cyclic peptide Peter Freddolino (Fri Jun 27 2008 - 16:11:21 CDT)
Re: Problem in making cyclic peptide JC Gumbart (Fri Jun 27 2008 - 16:01:27 CDT)
Problem in making cyclic peptide Narang, Pooja, Ph.D. (Fri Jun 27 2008 - 15:24:38 CDT)
Re: Output of forces. Hidekazu WATANABE (Fri Jun 27 2008 - 04:11:56 CDT)
Re: Running minimization, heating and FEP simulation within the same configuration file. Jawahar Neelankatan (Thu Jun 26 2008 - 21:44:25 CDT)
Re: Running minimization, heating and FEP simulation within the same configuration file. Floris Buelens (Thu Jun 26 2008 - 02:46:41 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)
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)
Re: charmrun not found Alexandre A. Vakhrouchev (Tue Jun 24 2008 - 22:50:45 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: Problem regarding psfgen Peter Freddolino (Tue Jun 24 2008 - 21:18:33 CDT)
Problem regarding psfgen haosheng_at_hec.utah.edu (Tue Jun 24 2008 - 18:03:08 CDT)
Re: Incorrect PSF file for min.pme Peter Freddolino (Tue Jun 24 2008 - 10:37:34 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)
Re: Dihedral scan in NAMD? Chris Chipot (Mon Jun 23 2008 - 15:21:57 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: Dihedral scan in NAMD? L. Michel Espinoza-Fonseca (Mon Jun 23 2008 - 10:47:07 CDT)
Dihedral scan in NAMD? Kamilla Kopec (Mon Jun 23 2008 - 10:06:30 CDT)
Re: psf file Peter Freddolino (Mon Jun 23 2008 - 06:54:08 CDT)
psf file Christine Horejs DI (Mon Jun 23 2008 - 06:22:48 CDT)
Impressive Glashutte timepieces Becky Peoples (Sat Jun 21 2008 - 22:17:24 CDT)
Re: Typical maximization steps JC Gumbart (Fri Jun 20 2008 - 21:23:44 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)
error messages with "reinitvels" Yinglong Miao (Fri Jun 20 2008 - 13:56:25 CDT)
Re: PME and r-RESPA issue in NAMD Thomas C. Bishop (Fri Jun 20 2008 - 09:56:25 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: problem compiling NAMD2.6 in a MacOSX-PPC Peter Freddolino (Fri Jun 20 2008 - 08:16:56 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)
Re: Simulation with non-periodic boundary condition Victor Ovchinnikov (Thu Jun 19 2008 - 15:15:47 CDT)
problem compiling NAMD2.6 in a MacOSX-PPC Andrea Diaz (Thu Jun 19 2008 - 16:30:57 CDT)
Simulation with non-periodic boundary condition S.K. Ghosh (Thu Jun 19 2008 - 13:36:50 CDT)
NVT simulation by NAMD sudipta sinha (Thu Jun 19 2008 - 08:06:50 CDT)
Re: amber parameters for congo red Shaheen Ahmed (Thu Jun 19 2008 - 02:19:08 CDT)
Time step is incompatible in the NAMD DCD file analyzed with CHARMM twshen (Wed Jun 18 2008 - 14:07:02 CDT)
Re: amber parameters for congo red L. Michel Espinoza-Fonseca (Thu Jun 19 2008 - 04:07:31 CDT)
Re: amber parameters for congo red L. Michel Espinoza-Fonseca (Wed Jun 18 2008 - 16:07:30 CDT)
Re: Time step is incompatible in the NAMD DCD file analyzed with CHARMM Victor Ovchinnikov (Wed Jun 18 2008 - 16:35:42 CDT)
amber parameters for congo red Shaheen Ahmed (Wed Jun 18 2008 - 15:29:22 CDT)
Time step is incompatible in the NAMD DCD file analyzed with CHARMM tw shen (Wed Jun 18 2008 - 14:42:32 CDT)
Time Step is Incompatible in the NAMD DCD Analyzed with CHARMM twshen (Wed Jun 18 2008 - 12:28:22 CDT)
Re: Trouble in energy minimization with warning to increase cutoff Peter Freddolino (Wed Jun 18 2008 - 00:01:29 CDT)
Trouble in energy minimization with warning to increase cutoff Eva Nong (Tue Jun 17 2008 - 18:57:49 CDT)
2D periodic boundary condn & PME Harindar Keer (Tue Jun 17 2008 - 14:12:28 CDT)
Re: NAMD & CUDA, still in development ? Peter Freddolino (Tue Jun 17 2008 - 14:43:55 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: Charmm is not free so how to learn it jfgaff_at_ncsu.edu (Sun Jun 15 2008 - 18:51:19 CDT)
Re: NAMD log file analysis script problem (namdstats.tcl) Axel Kohlmeyer (Sun Jun 15 2008 - 13:09:50 CDT)
Re: Charmm is not free so how to learn it Philip Peartree (Sun Jun 15 2008 - 09:38:02 CDT)
Re: NAMD log file analysis script problem (namdstats.tcl) Demet Akten (Sun Jun 15 2008 - 03:35:49 CDT)
NAMD log file analysis script problem (namdstats.tcl) sudipta sinha (Sat Jun 14 2008 - 13:39:32 CDT)
Charmm is not free so how to learn it abhijit ramachandran (Fri Jun 13 2008 - 15:01:50 CDT)
Re: nonbonded interactions Victor Ovchinnikov (Fri Jun 13 2008 - 13:16:24 CDT)
Re: paramter snoze pa (Fri Jun 13 2008 - 10:37:55 CDT)
Re: use of 'measure hbonds' Axel Kohlmeyer (Fri Jun 13 2008 - 07:43:12 CDT)
use of 'measure hbonds' DEEPESH AGARWAL (Thu Jun 12 2008 - 23:54:34 CDT)
Re: paramter snoze pa (Thu Jun 12 2008 - 16:16:21 CDT)
Seeking suggestions to decide on realistic configuration values S.K. Ghosh (Thu Jun 12 2008 - 14:40:27 CDT)
Re: Language Used and Elementary doubts Peter Freddolino (Thu Jun 12 2008 - 12:26:50 CDT)
Re: Language Used and Elementary doubts Alexandre A. Vakhrouchev (Thu Jun 12 2008 - 12:15:43 CDT)
Re: use of 'measure hbonds' mon_sharma_at_research.iiit.ac.in (Thu Jun 12 2008 - 11:08:12 CDT)
Language Used and Elementary doubts abhijit ramachandran (Thu Jun 12 2008 - 00:08:27 CDT)
use of 'measure hbonds' DEEPESH AGARWAL (Thu Jun 12 2008 - 06:03:06 CDT)
ApoB structure Alexandre A. Vakhrouchev (Thu Jun 12 2008 - 01:12:02 CDT)
Re: paramter JC Gumbart (Wed Jun 11 2008 - 21:08:26 CDT)
paramter snoze pa (Wed Jun 11 2008 - 17:44:10 CDT)
Re: Velocity scaling and thermostatting both at a time Jerome Henin (Wed Jun 11 2008 - 17:37:24 CDT)
Velocity scaling and thermostatting both at a time sudipta sinha (Wed Jun 11 2008 - 13:36:46 CDT)
Re: Different Hbonds values on different machines using same script for same trajectories John Stone (Wed Jun 11 2008 - 03:11:11 CDT)
April promo on watches Priscilla Dahl (Tue Jun 10 2008 - 16:41:36 CDT)
Re: Correctness of Simulation Results Peter Freddolino (Tue Jun 10 2008 - 11:45:03 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: Correctness of Simulation Results Rahul (Tue Jun 10 2008 - 10:15:56 CDT)
Replica or Original? Terrence Hare (Tue Jun 10 2008 - 07:43:09 CDT)
Re: Temperature rescaling and reassignment parameters sudipta sinha (Tue Jun 10 2008 - 05:35:03 CDT)
Re: Classic timepieces replicas Axel Kohlmeyer (Tue Jun 10 2008 - 04:37:57 CDT)
Re: Temperature rescaling and reassignment parameters Alexandre A. Vakhrouchev (Tue Jun 10 2008 - 04:53:44 CDT)
Re: Classic timepieces replicas Alexandre A. Vakhrouchev (Tue Jun 10 2008 - 04:41:40 CDT)
Classic timepieces replicas Cole Cox (Mon Jun 09 2008 - 19:10:25 CDT)
Re: Temperature rescaling and reassignment parameters sudipta sinha (Mon Jun 09 2008 - 23:46:29 CDT)
capping of end residues sudipta sinha (Mon Jun 09 2008 - 23:55:56 CDT)
Re: Temperature rescaling and reassignment parameters Alexandre A. Vakhrouchev (Mon Jun 09 2008 - 23:20:38 CDT)
Re: psgfen patch Peter Freddolino (Mon Jun 09 2008 - 23:09:06 CDT)
psgfen patch Hatley, Jade M (Mon Jun 09 2008 - 12:05:15 CDT)
Re: S-OXY CYSTEINE parameter snoze pa (Mon Jun 09 2008 - 16:19:38 CDT)
Re: Which conformation is more proper for the SMD Eric H. Lee (Mon Jun 09 2008 - 13:47:27 CDT)
Re: Which conformation is more proper for the SMD Shulin Zhuang (Mon Jun 09 2008 - 13:21:57 CDT)
Re: Correctness of Simulation Results Axel Kohlmeyer (Mon Jun 09 2008 - 12:03:06 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)
Correctness of Simulation Results Rahul (Mon Jun 09 2008 - 09:16:13 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: NAMD compilation on linux cluster Axel Kohlmeyer (Sun Jun 08 2008 - 11:32:26 CDT)
NAMD compilation on linux cluster sudipta sinha (Sun Jun 08 2008 - 10:55:36 CDT)
Re: PME and r-RESPA issue in NAMD Axel Kohlmeyer (Sat Jun 07 2008 - 09:50:59 CDT)
PME and r-RESPA issue in NAMD sudipta sinha (Sat Jun 07 2008 - 07:05:37 CDT)
Re: Multiple successive addforce calls Benjamin Bouvier (Thu Jun 05 2008 - 15:05:40 CDT)
Re: output area JC Gumbart (Thu Jun 05 2008 - 17:35:17 CDT)
output area JARROD EDWARD CHARLES NICKEL (Thu Jun 05 2008 - 15:26:49 CDT)
Re: Multiple successive addforce calls Peter Freddolino (Thu Jun 05 2008 - 15:25:31 CDT)
Re: Multiple successive addforce calls Peter Freddolino (Thu Jun 05 2008 - 14:02:46 CDT)
Re: Multiple successive addforce calls Gungor Ozer (Thu Jun 05 2008 - 13:53:12 CDT)
Re: Multiple successive addforce calls Benjamin Bouvier (Thu Jun 05 2008 - 12:35:31 CDT)
free enrgy calculations - an additional information politr_at_huji.ac.il (Wed Jun 04 2008 - 07:07:01 CDT)
Re: Problem with TclBC when run in more than one processor Peter Freddolino (Thu Jun 05 2008 - 08:36:51 CDT)
Multiple successive addforce calls Benjamin Bouvier (Thu Jun 05 2008 - 08:18:16 CDT)
NAMD in water vs in vacuum Yang Gao (Thu Jun 05 2008 - 09:54:48 CDT)
Re: steepest descent technique Peter Freddolino (Thu Jun 05 2008 - 08:32:43 CDT)
Re: Bond energy become Zero!!! Peter Freddolino (Thu Jun 05 2008 - 08:25:55 CDT)
Bond energy become Zero!!! Ming (Thu Jun 05 2008 - 04:17:01 CDT)
steepest descent technique DEEPESH AGARWAL (Thu Jun 05 2008 - 00:53:30 CDT)
Re: molefacture in vmd Peter Freddolino (Wed Jun 04 2008 - 17:27:06 CDT)
Re: molefacture in vmd Subhashis Biswas (Wed Jun 04 2008 - 17:03:29 CDT)
Re: The correct topology/parameter file and pgn S.K. Ghosh (Wed Jun 04 2008 - 13:48:41 CDT)
Problem with TclBC when run in more than one processor fett_at_vtr.net (Wed Jun 04 2008 - 12:08:57 CDT)
Re: free energy calculations Peter Freddolino (Wed Jun 04 2008 - 11:52:02 CDT)
Re: free energy calculations Eric H. Lee (Wed Jun 04 2008 - 11:28:13 CDT)
free energy calculations politr_at_huji.ac.il (Wed Jun 04 2008 - 05:34:01 CDT)
Re: The correct topology/parameter file and pgn S.K. Ghosh (Wed Jun 04 2008 - 03:51:24 CDT)
Re: The correct topology/parameter file and pgn Peter Freddolino (Tue Jun 03 2008 - 21:56:24 CDT)
Re: The correct topology/parameter file and pgn S.K. Ghosh (Tue Jun 03 2008 - 18:15:44 CDT)
Re: The correct topology/parameter file and pgn Peter Freddolino (Tue Jun 03 2008 - 15:11:55 CDT)
Thank you for your advices feng jack (Tue Jun 03 2008 - 11:15:41 CDT)
Re: Mindboggling Problem Related To NAMD2 Code Rahul (Mon Jun 02 2008 - 23:02:42 CDT)
Re: Mindboggling Problem Related To NAMD2 Code Peter Freddolino (Mon Jun 02 2008 - 22:16:39 CDT)
Re: Mindboggling Problem Related To NAMD2 Code Axel Kohlmeyer (Mon Jun 02 2008 - 18:42:04 CDT)
Postdoctoral Position in Scientific Computing David Brandon (Mon Jun 02 2008 - 15:08:45 CDT)
Re: Mindboggling Problem Related To NAMD2 Code Graham Jenkins (Mon Jun 02 2008 - 17:43:27 CDT)
The correct topology/parameter file and pgn S.K. Ghosh (Mon Jun 02 2008 - 15:55:06 CDT)
Re: Average energy in NAMD Axel Kohlmeyer (Sun Jun 01 2008 - 16:51:15 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 - 19:22:51 CDT)
Re: Average energy in NAMD JC Gumbart (Sun Jun 01 2008 - 18:06:29 CDT)
Average energy in NAMD feng jack (Sun Jun 01 2008 - 16:31:16 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 Axel Kohlmeyer (Sun Jun 01 2008 - 08:01:34 CDT)
Mindboggling Problem Related To NAMD2 Code Rahul (Sun Jun 01 2008 - 04:19:13 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. Khaled Barakat (Fri May 30 2008 - 19:30:23 CDT)
(no subject) feng jack (Fri May 30 2008 - 16:04:44 CDT)
Re: NAMD trajectory format Konrad Hinsen (Fri May 30 2008 - 15:33:40 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 - 14:32:09 CDT)
Re: Building Namd on a linux cluster. Axel Kohlmeyer (Fri May 30 2008 - 07:38:12 CDT)
Re: NAMD trajectory format Peter Freddolino (Fri May 30 2008 - 09:24:17 CDT)
Re: NAMD trajectory format Peter Freddolino (Fri May 30 2008 - 09:15:48 CDT)
Re: NAMD trajectory format Axel Kohlmeyer (Fri May 30 2008 - 08:29:26 CDT)
Re: NAMD trajectory format Peter Freddolino (Fri May 30 2008 - 08:28:08 CDT)
Re: constraintScaling - FOR LOOP Peter Freddolino (Fri May 30 2008 - 08:30:07 CDT)
Re: NAMD trajectory format Axel Kohlmeyer (Fri May 30 2008 - 07:34:52 CDT)
Re: aromatic-aromatic interaction L. Michel Espinoza-Fonseca (Fri May 30 2008 - 06:57:51 CDT)
Re: Building Namd on a linux cluster. Alexandre A. Vakhrouchev (Fri May 30 2008 - 00:38:25 CDT)
Re: NAMD trajectory format Konrad Hinsen (Thu May 29 2008 - 11:43:13 CDT)
Building Namd on a linux cluster. Khaled Barakat (Thu May 29 2008 - 21:39:53 CDT)
changing dcd output file DURING run? Sebastian Stolzenberg (Thu May 29 2008 - 12:49:36 CDT)
Re: benchmarking of NAMD: sustained performance (TF) Axel Kohlmeyer (Thu May 29 2008 - 09:05:40 CDT)
Re: benchmarking of NAMD: sustained performance (TF) Philip Peartree (Thu May 29 2008 - 04:35:50 CDT)
aromatic-aromatic interaction ramya narasimhan (Thu May 29 2008 - 00:20:43 CDT)
benchmarking of NAMD: sustained performance (TF) satya work (Wed May 28 2008 - 22:47:30 CDT)
constraintScaling - FOR LOOP Semorale (Wed May 28 2008 - 20:29:23 CDT)
Re: NAMD trajectory format John Stone (Wed May 28 2008 - 11:18:26 CDT)
Re: NAMD trajectory format Axel Kohlmeyer (Wed May 28 2008 - 09:05:46 CDT)
Re: NAMD trajectory format Konrad Hinsen (Wed May 28 2008 - 07:35:17 CDT)
Re: dihedral force constant Jerome Henin (Tue May 27 2008 - 20:38:40 CDT)
dihedral force constant jfgaff_at_ncsu.edu (Tue May 27 2008 - 18:38:06 CDT)
Re: Error Parsing Config File MIke S (Tue May 27 2008 - 14:27:47 CDT)
Re: Acceptable pressure values Peter Freddolino (Tue May 27 2008 - 14:33:00 CDT)
Re: Error Parsing Config File MIke S (Tue May 27 2008 - 09:07:03 CDT)
Re: charmm parameter and topology files Jerome Henin (Tue May 27 2008 - 11:20:30 CDT)
charmm parameter and topology files me00109_at_cc.uoi.gr (Tue May 27 2008 - 10:17:52 CDT)
Re: NAMD trajectory format Axel Kohlmeyer (Tue May 27 2008 - 05:27:04 CDT)
NAMD trajectory format Konrad Hinsen (Tue May 27 2008 - 02:41:29 CDT)
Charm++ compilation sudipta sinha (Tue May 27 2008 - 01:51:12 CDT)
Re: dihedral restraints "on-the-fly"? JC Gumbart (Mon May 26 2008 - 22:06:46 CDT)
Re: Acceptable pressure values Fabio Zegarra (Mon May 26 2008 - 19:32:21 CDT)
dihedral restraints "on-the-fly"? Sebastian Stolzenberg (Mon May 26 2008 - 19:40:32 CDT)
Re: Error Parsing Config File Peter Freddolino (Mon May 26 2008 - 19:03:55 CDT)
Re: Error Parsing Config File MIke S (Mon May 26 2008 - 15:46:19 CDT)
Re: harmonic restraint between two atoms Leonardo Trabuco (Mon May 26 2008 - 12:01:15 CDT)
Re: harmonic restraint between two atoms Leonardo Trabuco (Mon May 26 2008 - 11:34:27 CDT)
harmonic restraint between two atoms Esben A. Gad (Mon May 26 2008 - 03:55:16 CDT)
Re: REMD Khaled Barakat (Sun May 25 2008 - 18:43:11 CDT)
Re: PROTEIN VACUUM MINIMIZATION ERROR Peter Freddolino (Sat May 24 2008 - 20:46:34 CDT)
Re: REMD Peter Freddolino (Sat May 24 2008 - 20:45:00 CDT)
Re: REMD Khaled Barakat (Sat May 24 2008 - 15:02:00 CDT)
PROTEIN VACUUM MINIMIZATION ERROR Semorale (Sat May 24 2008 - 10:24:47 CDT)
Re: Acceptable pressure values Peter Freddolino (Sat May 24 2008 - 09:27:24 CDT)
Re: REMD Peter Freddolino (Sat May 24 2008 - 09:01:10 CDT)
Re: Error Parsing Config File Alexandre A. Vakhrouchev (Sat May 24 2008 - 03:06:29 CDT)
REMD Khaled Barakat (Sat May 24 2008 - 02:58:54 CDT)
Error Parsing Config File MIke S (Sat May 24 2008 - 00:01:43 CDT)
Acceptable pressure values Fabio Zegarra (Fri May 23 2008 - 17:24:22 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 Subramanian Vaitheeswaran (Fri May 23 2008 - 16:55:53 CDT)
Re: ABF:reversibility and number of samples Eric Cyr (Fri May 23 2008 - 15:11:29 CDT)
Re: ABF:reversibility and number of samples Luca (Fri May 23 2008 - 14:26:03 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 Chris Chipot (Fri May 23 2008 - 10:43:59 CDT)
ABF:reversibility and number of samples Luca Bellucci (Fri May 23 2008 - 07:33:27 CDT)
Re: Unable to edit files in NAMD folder. Diego Alejandro Vargas (Thu May 22 2008 - 13:31:59 CDT)
Re: Applying weak harmonic force between two proteins Floris Buelens (Thu May 22 2008 - 09:06:57 CDT)
Re: a question about equilibrium Joshua Adelman (Wed May 21 2008 - 21:07:35 CDT)
a question about equilibrium taojinwuhan_at_sohu.com (Wed May 21 2008 - 20:32:14 CDT)
Re: Applying weak harmonic force between two proteins Joshua Adelman (Wed May 21 2008 - 11:42:15 CDT)
Re: Simulation of Thiolated Biotin-Streptavidin on Gold Jerome Henin (Wed May 21 2008 - 11:29:42 CDT)
Applying weak harmonic force between two proteins greddy1_at_umd.edu (Wed May 21 2008 - 11:12:18 CDT)
Re: Simulation of Thiolated Biotin-Streptavidin on Gold S.K. Ghosh (Wed May 21 2008 - 08:16:24 CDT)
scaling the interaction energy Krishnan, Marimuthu (Wed May 21 2008 - 07:21:20 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. Alexandre A. Vakhrouchev (Wed May 21 2008 - 03:37:52 CDT)
Unable to edit files in NAMD folder. Diego Alejandro Vargas (Tue May 20 2008 - 23:39:51 CDT)
Re: Simulation of Thiolated Biotin-Streptavidin on Gold Axel Kohlmeyer (Tue May 20 2008 - 08:27:50 CDT)
Re: minimization of the squared gradient Peter Freddolino (Tue May 20 2008 - 08:19:58 CDT)
Simulation of Thiolated Biotin-Streptavidin on Gold S.K. Ghosh (Tue May 20 2008 - 07:11:36 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)
RE: minimization of the squared gradient Krishnan, Marimuthu (Mon May 19 2008 - 13:36:01 CDT)
Re: minimization of the squared gradient Victor Ovchinnikov (Mon May 19 2008 - 10:24:28 CDT)
Re: minimization of the squared gradient Peter Freddolino (Mon May 19 2008 - 09:20:17 CDT)
RE: minimization of the squared gradient Krishnan, Marimuthu (Mon May 19 2008 - 08:56:31 CDT)
Re: minimization of the squared gradient Peter Freddolino (Mon May 19 2008 - 06:40:33 CDT)
minimization of the squared gradient Krishnan, Marimuthu (Mon May 19 2008 - 01:53:05 CDT)
scaling the interaction energy Krishnan, Marimuthu (Mon May 19 2008 - 01:41:53 CDT)
Re: Error: transport retry exceeded error Axel Kohlmeyer (Sat May 17 2008 - 15:37:12 CDT)
Re: pair interaction Osman Yogurtcu (Sat May 17 2008 - 05:54:14 CDT)
Re: Error: transport retry exceeded error Alexandre A. Vakhrouchev (Sat May 17 2008 - 00:03:03 CDT)
pair interaction Osman Yogurtcu (Fri May 16 2008 - 13:34:21 CDT)
Re: Error: transport retry exceeded error Axel Kohlmeyer (Fri May 16 2008 - 10:49:46 CDT)
Re: vmd-l: Re: Truncated Octahedron for VMD and NAMD simulation Vlad Cojocaru (Fri May 16 2008 - 09:51:44 CDT)
Re: NVE ENSEMBLE Vlad Cojocaru (Fri May 16 2008 - 03:36:38 CDT)
Re: Truncated Octahedron for VMD and NAMD simulation George Madalin Giambasu (Thu May 15 2008 - 15:23:51 CDT)
Truncated Octahedron for VMD and NAMD simulation Yinglong Miao (Thu May 15 2008 - 14:31:48 CDT)
Error: transport retry exceeded error Alexandre A. Vakhrouchev (Thu May 15 2008 - 13:41:21 CDT)
Re: Energy plot script bo liu (Thu May 15 2008 - 13:00:23 CDT)
NVE ENSEMBLE Semorale (Thu May 15 2008 - 10:24:21 CDT)
Re: Energy plot script Subramanian Vaitheeswaran (Thu May 15 2008 - 07:28:20 CDT)
Energy plot script Alexandre A. Vakhrouchev (Wed May 14 2008 - 22:11:19 CDT)
RE: Trajectory file formats & structural alignment JC Gumbart (Wed May 14 2008 - 00:15:17 CDT)
Re: Trajectory file formats & structural alignment Wei Huang (Tue May 13 2008 - 21:57:01 CDT)
Re: NAMD electrostatics no cutoff or switching Peter Freddolino (Tue May 13 2008 - 21:25:30 CDT)
how to prepare *.paramas file Kalyan chaitanya (Tue May 13 2008 - 17:48:54 CDT)
Re: ZINC parameter Jerome Henin (Tue May 13 2008 - 14:57:48 CDT)
S-OXY CYSTEINE parameter snoze pa (Tue May 13 2008 - 13:53:57 CDT)
NAMD electrostatics no cutoff or switching Alvaro Foletti (Tue May 13 2008 - 12:44:01 CDT)
ZINC parameter surendra negi (Tue May 13 2008 - 12:22:47 CDT)
Re: DCD file size Joshua D. Moore (Tue May 13 2008 - 01:39:57 CDT)
Re: DCD file size Peter Freddolino (Mon May 12 2008 - 21:56:26 CDT)
Re: DCD file size Alexandre A. Vakhrouchev (Mon May 12 2008 - 21:50:25 CDT)
Re: DCD file size JC Gumbart (Mon May 12 2008 - 15:08:48 CDT)
DCD file size Alexandre A. Vakhrouchev (Mon May 12 2008 - 14:19:57 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)
Re: 2 pdb files Peter Freddolino (Fri May 09 2008 - 07:15:00 CDT)
2 pdb files Christine Horejs DI (Fri May 09 2008 - 06:58:01 CDT)
spermine force field bqluan (Thu May 08 2008 - 18:47:54 CDT)
Re: Trajectory file formats & structural alignment Giovanni Bellesia (Thu May 08 2008 - 18:00:18 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: recalculating energy using dcd file JC Gumbart (Wed May 07 2008 - 17:08:16 CDT)
Re: running NAMD with ranger@tacc Peter Freddolino (Wed May 07 2008 - 13:23:36 CDT)
running NAMD with ranger@tacc Lei Shi (Wed May 07 2008 - 13:08:50 CDT)
Re: Negative Pressure Vlad Cojocaru (Wed May 07 2008 - 09:39:02 CDT)
recalculating energy using dcd file gurvisha_at_leadinvent.com (Wed May 07 2008 - 09:19:14 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)
Question about a shift in rmsd using fixedatom off snoze pa (Tue May 06 2008 - 11:47:45 CDT)
Re: Re: BOUNCE namd-l@ks.uiuc.edu: Message too long (>40000 chars) snoze pa (Tue May 06 2008 - 10:20:47 CDT)
Re: NAMDENERGY: function of 'cutoff' parameter when -pme option is enabled Peter Freddolino (Tue May 06 2008 - 00:37:54 CDT)
NAMDENERGY: function of 'cutoff' parameter when -pme option is enabled Ghalib Bello (Mon May 05 2008 - 23:02:45 CDT)
Re: question related to rmsd JC Gumbart (Mon May 05 2008 - 17:58:43 CDT)
Re: BOUNCE namd-l@ks.uiuc.edu: Message too long (>40000 chars) snoze pa (Mon May 05 2008 - 16:49:43 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 - 16:19:47 CDT)
question related to rmsd snoze pa (Mon May 05 2008 - 15:03:07 CDT)
Re: question on ABF L. Michel Espinoza-Fonseca (Mon May 05 2008 - 09:16:44 CDT)
help with calcforces Prabhakar Bhimalapuram (Fri May 02 2008 - 13:32:22 CDT)
Re: compilaton error Leonardo Trabuco (Fri May 02 2008 - 01:25:35 CDT)
Re: compilaton error Swarna Patra (Fri May 02 2008 - 01:06:48 CDT)
Re: compilaton error Leonardo Trabuco (Thu May 01 2008 - 23:47:06 CDT)
Re: compilaton error Swarna Patra (Thu May 01 2008 - 20:04:47 CDT)
Re: error on installing ImageMagick Richard Law (Thu May 01 2008 - 14:53:37 CDT)
Re: error on installing ImageMagick Peter Freddolino (Thu May 01 2008 - 14:02:39 CDT)
error on installing ImageMagick Hero (Thu May 01 2008 - 13:54:57 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)
Re: compilaton error Leonardo Trabuco (Thu May 01 2008 - 11:32:22 CDT)
Re: How to save the animation movie into files? Jianhui Tian (Thu May 01 2008 - 09:16:50 CDT)
How to save the animation movie into files? Hero (Thu May 01 2008 - 01:48:35 CDT)
RE: Neutral arginine patch in topology file. JC Gumbart (Thu May 01 2008 - 00:15:28 CDT)
compilaton error Swarna Patra (Wed Apr 30 2008 - 23:32:45 CDT)
Re: Running NAMD on cluster Philip Peartree (Wed Apr 30 2008 - 07:21:28 CDT)
Running NAMD on cluster sudipta sinha (Wed Apr 30 2008 - 04:41:53 CDT)
Neutral arginine patch in topology file. Alexandre F. G. (Tue Apr 29 2008 - 16:45:29 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 - 13:40:29 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)
Re: velocity units in .vel file Joshua D. Moore (Mon Apr 28 2008 - 17:47:48 CDT)
velocity units in .vel file Neelanjana Sengupta (Mon Apr 28 2008 - 15:21:06 CDT)
Re: How to save the animation movie into files? Low Soo Mei (Mon Apr 28 2008 - 00:51:37 CDT)
How to save the animation movie into files? Hero (Mon Apr 28 2008 - 00:23:49 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)
Re: How to run namd2 on ubuntu linux? Leandro Martínez (Sat Apr 26 2008 - 16:10:35 CDT)
Re: FEP triangular bracket average Mert Gür (Sat Apr 26 2008 - 15:26:21 CDT)
How to run namd2 on ubuntu linux? Hero (Sat Apr 26 2008 - 14:45:01 CDT)
Re: install VMD on Ubuntu Hero (Sat Apr 26 2008 - 14:38:19 CDT)
Re: install VMD on Ubuntu Low Soo Mei (Sat Apr 26 2008 - 14:25:32 CDT)
install VMD on Ubuntu Hero (Sat Apr 26 2008 - 14:09:39 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 - 13:14:29 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)
Re: FEP triangular bracket average Jerome Henin (Sat Apr 26 2008 - 11:30:37 CDT)
FEP triangular bracket average Mert Gür (Sat Apr 26 2008 - 05:56:26 CDT)
Re: install NAMD on Ubuntu Alexandre A. Vakhrouchev (Sat Apr 26 2008 - 01:12:30 CDT)
install NAMD on Ubuntu Hero (Fri Apr 25 2008 - 23:46:07 CDT)
Re: A question about restaints force. Victor Ovchinnikov (Fri Apr 25 2008 - 17:48:40 CDT)
Re: A question about restaints force. Gungor Ozer (Fri Apr 25 2008 - 16:17:13 CDT)
A question about restaints force. Yang Gao (Fri Apr 25 2008 - 15:23:01 CDT)
Time factor Alexandre A. Vakhrouchev (Thu Apr 24 2008 - 23:16:04 CDT)
Re: reversing constant velocity SMD Peter Freddolino (Thu Apr 24 2008 - 08:24:55 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: What does "cellOrigin" really mean? Alexandre A. Vakhrouchev (Wed Apr 23 2008 - 08:36:51 CDT)
What does "cellOrigin" really mean? bo liu (Wed Apr 23 2008 - 05:48:45 CDT)
RE: question on ABF Xu, Jiancong (Mon Apr 21 2008 - 10:35:16 CDT)
Re: question on ABF Chris Chipot (Mon Apr 21 2008 - 07:01:39 CDT)
Re: VMD-NAMD-commands Vivek Sharma (Sun Apr 20 2008 - 21:06:36 CDT)
Re: VMD-NAMD-commands Peter Freddolino (Sun Apr 20 2008 - 20:20:27 CDT)
Re: RE: Reading and writing Binary Restart or Output files with Fortran V.Ovchinnikov (Sat Apr 19 2008 - 16:10:32 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 - 10:40:46 CDT)
Re: VMD-NAMD-commands Alexandre A. Vakhrouchev (Sat Apr 19 2008 - 00:16:08 CDT)
VMD-NAMD-commands Vivek Sharma (Fri Apr 18 2008 - 23:06:12 CDT)
Re: question on ABF Jerome Henin (Fri Apr 18 2008 - 22:14:45 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)
question on ABF L. Michel Espinoza-Fonseca (Fri Apr 18 2008 - 18:40:08 CDT)
What does "cellOrigin" really mean? bo liu (Fri Apr 18 2008 - 09:38:56 CDT)
Re: temperature stepping during heating Low Soo Mei (Fri Apr 18 2008 - 04:00:41 CDT)
Re: temperature stepping during heating Low Soo Mei (Thu Apr 17 2008 - 21:14:34 CDT)
Multiple Different Harmonic Restraint Defitions Joshua Adelman (Thu Apr 17 2008 - 20:13:23 CDT)
Re: temperature stepping during heating JC Gumbart (Thu Apr 17 2008 - 16:35:13 CDT)
Re: 2 molecule pair interactions Ben Chern (Wed Apr 16 2008 - 23:49:33 CDT)
Re: 2 molecule pair interactions Peter Freddolino (Wed Apr 16 2008 - 17:11:52 CDT)
2 molecule pair interactions Arturas Ziemys (Wed Apr 16 2008 - 16:26:27 CDT)
Re: add calcium chloride Thomas C. Bishop (Wed Apr 16 2008 - 10:12:24 CDT)
Re: add calcium chloride Christine Horejs DI (Wed Apr 16 2008 - 08:22:28 CDT)
Re: add calcium chloride Christine Horejs DI (Wed Apr 16 2008 - 07:30:41 CDT)
Re: Which namd on amd64? V.Ovchinnikov (Tue Apr 15 2008 - 17:19:43 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)
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? Peter Freddolino (Tue Apr 15 2008 - 15:34:11 CDT)
Which namd on amd64? Corenflos, Steven Charles (Tue Apr 15 2008 - 15:26:25 CDT)
binary install question winsvern_at_isu.edu (Tue Apr 15 2008 - 15:23:29 CDT)
Re: Electrostatics cutoff with PME Christopher Gillespie (Tue Apr 15 2008 - 15:21:06 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: Electrostatics cutoff with PME Peter Freddolino (Tue Apr 15 2008 - 14:31:35 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: Electrostatics cutoff with PME L. Michel Espinoza-Fonseca (Tue Apr 15 2008 - 14:00:03 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: restarting ABF simulation Jerome Henin (Tue Apr 15 2008 - 13:16:28 CDT)
Electrostatics cutoff with PME Gianluca Interlandi (Tue Apr 15 2008 - 13:01:48 CDT)
Re: help regarding NAMD equilibration Dr. Luis Rosales León (Tue Apr 15 2008 - 12:39:24 CDT)
Re: restarting ABF simulation Subramanian Vaitheeswaran (Tue Apr 15 2008 - 11:16:36 CDT)
Re: help regarding NAMD equilibration snoze pa (Tue Apr 15 2008 - 10:39:54 CDT)
temperature stepping during heating Low Soo Mei (Tue Apr 15 2008 - 05:21:43 CDT)
Re: help regarding NAMD equilibration Low Soo Mei (Tue Apr 15 2008 - 01:05:25 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: Re: TMD bug correction??? Peter Freddolino (Mon Apr 14 2008 - 16:15:44 CDT)
NAMD CVS RUN ERROR Samuel Morales (Mon Apr 14 2008 - 16:13:31 CDT)
Re: TMD bug correction??? Samuel Morales (Mon Apr 14 2008 - 15:55:04 CDT)
Building NAMD on SGI Altix Rogan Carr (Mon Apr 14 2008 - 15:04:27 CDT)
Re: restarting ABF simulation Jerome Henin (Mon Apr 14 2008 - 13:58:57 CDT)
Re: restarting ABF simulation Subramanian Vaitheeswaran (Mon Apr 14 2008 - 12:21:43 CDT)
Re: TclForces JC Gumbart (Mon Apr 14 2008 - 10:21:22 CDT)
Re: Restarting simulation goes the different temperature JC Gumbart (Mon Apr 14 2008 - 10:18:08 CDT)
Re: restarting ABF simulation Luca Bellucci (Mon Apr 14 2008 - 10:00:21 CDT)
Re: restarting ABF simulation Jerome Henin (Mon Apr 14 2008 - 08:54:07 CDT)
Re: restarting ABF simulation Luca Bellucci (Mon Apr 14 2008 - 08:04:01 CDT)
Re: restarting ABF simulation Jerome Henin (Mon Apr 14 2008 - 06:43:40 CDT)
rmsd_RNA_DNA sripad chandan (Mon Apr 14 2008 - 05:27:45 CDT)
Re: Restarting simulation goes the different temperature Magnus Heltstrom (Mon Apr 14 2008 - 04:55:57 CDT)
restarting ABF simulation Luca Bellucci (Mon Apr 14 2008 - 04:14:19 CDT)
Re: problem with VMD installation- libstdc++.so.5 => not found Jerome Henin (Sun Apr 13 2008 - 14:59:21 CDT)
problem with VMD installation- libstdc++.so.5 => not found steve_at_phas.ubc.ca (Sat Apr 12 2008 - 22:03:05 CDT)
Re: langevin dynamics Giovanni Bellesia (Sat Apr 12 2008 - 18:03:35 CDT)
spawn_namd_command How to properly execute this command bptilaka_at_mail.uh.edu (Sat Apr 12 2008 - 17:32:17 CDT)
Re: langevin dynamics Giovanni Bellesia (Sat Apr 12 2008 - 15:20:20 CDT)
langevin dynamics Dibyadeep Paul (Sat Apr 12 2008 - 14:21:52 CDT)
TclForces Vivek Sharma (Fri Apr 11 2008 - 05:42:50 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)
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)
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: vmd-l: How to read specific DCD frames directly in Fortran? John Stone (Sat Apr 05 2008 - 13:43:21 CDT)
Re: add calcium chloride Peter Freddolino (Mon Apr 07 2008 - 08:09:58 CDT)
Re: Kinetic Momentum of Translation and/or Rotation Peter Freddolino (Mon Apr 07 2008 - 08:09:44 CDT)
add calcium chloride Christine Horejs DI (Mon Apr 07 2008 - 03:21:59 CDT)
Kinetic Momentum of Translation and/or Rotation Joshua D. Moore (Mon Apr 07 2008 - 01:54:38 CDT)
Re: vmd-l: How to read specific DCD frames directly in Fortran? Yinglong Miao (Sun Apr 06 2008 - 10:51:40 CDT)
Calculating PMF from a constant velocity SMD simulation! Gungor Ozer (Sat Apr 05 2008 - 19:10:06 CDT)
Re: vmd-l: How to read specific DCD frames directly in Fortran? Peter Freddolino (Sat Apr 05 2008 - 13:38:39 CDT)
How to read specific DCD frames directly in Fortran? Yinglong Miao (Sat Apr 05 2008 - 13:21:53 CDT)
Rigid body effect, translational kinetic momentum Joshua D. Moore (Fri Apr 04 2008 - 19:40:35 CDT)
RE: Running NAMD at TACC (Ranger) Richard Swenson (Fri Apr 04 2008 - 12:42:49 CDT)
Re: problems sourcing namdstats in vmd Jim Phillips (Fri Apr 04 2008 - 12:09:43 CDT)
problems sourcing namdstats in vmd Shaheen Ahmed (Fri Apr 04 2008 - 09:37:15 CDT)
RE: Running NAMD at TACC (Ranger) Richard Swenson (Thu Apr 03 2008 - 18:09:22 CDT)
Re: TMD bug correction??? Peter Freddolino (Wed Apr 02 2008 - 14:39:37 CDT)
TMD bug correction??? Samuel Morales (Wed Apr 02 2008 - 13:28:35 CDT)
MacOSX net version segmentation fault Joshua Adelman (Mon Mar 31 2008 - 18:25:29 CDT)
Re: Running NAMD at TACC (Ranger) JC Gumbart (Sun Mar 30 2008 - 13:20:45 CDT)
Re: Running NAMD at TACC (Ranger) Peter Freddolino (Sun Mar 30 2008 - 09:28:06 CDT)
Running NAMD at TACC (Ranger) Jim Pfaendtner (Sun Mar 30 2008 - 07:16:57 CDT)
coarse grained simulation Demet Akten (Fri Mar 28 2008 - 09:11:19 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)
Re: Pressure oscillation in NPT Peter Freddolino (Thu Mar 27 2008 - 11:07:02 CDT)
Pressure oscillation in NPT Xinguang Cheng (Thu Mar 27 2008 - 10:14:38 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)
NAMDenergy + PME for constant pressure trajectories (variable box and .xst files) Maxim Paliy (Wed Mar 26 2008 - 16:28:52 CDT)
Re: NAMDenergy + PME for constant pressure trajectories (variable box and .xst files) Peter Freddolino (Wed Mar 26 2008 - 16:38:23 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)
FATAL ERROR: Periodic cell has become too small for original patch grid! Seth Lilavivat (Wed Mar 26 2008 - 15:36:48 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)
Re: ABF tutorial; updated FEP tutorial Jerome Henin (Fri Mar 21 2008 - 18:53:58 CDT)
Re: FEP output dEavg and dG Jerome Henin (Fri Mar 21 2008 - 17:16:18 CDT)
FEP output dEavg and dG Payel Das (Fri Mar 21 2008 - 16:26:02 CDT)
NAMD+MPI on AMD64 Artem Zhmurov (Fri Mar 21 2008 - 12:30:29 CDT)
Re: ABF tutorial; updated FEP tutorial Lei Shi (Thu Mar 20 2008 - 17:38:40 CDT)
ABF tutorial; updated FEP tutorial Jerome Henin (Thu Mar 20 2008 - 15:55:10 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)
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)
Re: namd: ABF query Peter Freddolino (Thu Mar 20 2008 - 11:16:50 CDT)
namd: ABF query gurvisha_at_leadinvent.com (Thu Mar 20 2008 - 05:12:55 CDT)
namd: ABF query gurvisha_at_leadinvent.com (Thu Mar 20 2008 - 05:12:30 CDT)
Re: Rigid bonds and hydrogen bonds "on" inaccurate/invalid? Peter Freddolino (Wed Mar 19 2008 - 15:41:14 CDT)
Re: Generating PSF from modified AMBER ff Seth Lilavivat (Wed Mar 19 2008 - 12:53:27 CDT)
Re: Generating PSF from modified AMBER ff Peter Freddolino (Wed Mar 19 2008 - 12:39:50 CDT)
Re: Rigid bonds and hydrogen bonds "on" inaccurate/invalid? Kamilla Kopec (Wed Mar 19 2008 - 12:38:24 CDT)
Generating PSF from modified AMBER ff Seth Lilavivat (Wed Mar 19 2008 - 12:30:03 CDT)
Re: Rigid bonds and hydrogen bonds "on" inaccurate/invalid? Peter Freddolino (Wed Mar 19 2008 - 10:38:21 CDT)
using Amber paramter snoze pa (Tue Mar 18 2008 - 13:23:31 CDT)
Re: Rigid bonds and hydrogen bonds "on" inaccurate/invalid? Kamilla Kopec (Tue Mar 18 2008 - 07:49:24 CDT)
Rigid bonds and hydrogen bonds "on" inaccurate/invalid? Kamilla Kopec (Mon Mar 17 2008 - 13:50:45 CDT)
Re: fixed atoms / pressure Peter Freddolino (Sun Mar 16 2008 - 09:19:53 CDT)
Re: quartz slab / pairInteractionSelf / Bad global exclusion count! Peter Freddolino (Sun Mar 16 2008 - 09:06:25 CDT)
Re: langevinHydrogen off with rigidBonds all? Peter Freddolino (Sun Mar 16 2008 - 08:55:42 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 (Fri Mar 14 2008 - 15:21:51 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)
FEP + MCTI in one MD simulation List (Thu Mar 13 2008 - 16:25:36 CDT)
Re: FEP: FATAL ERROR: Periodic cell has become too small for original patch grid! List (Thu Mar 13 2008 - 16:16:04 CDT)
langevinHydrogen off with rigidBonds all? Low Soo Mei (Fri Mar 14 2008 - 04:57:27 CDT)
Free Energy of Conformational Change PMF - documentation on method? David Sivak (Thu Mar 13 2008 - 18:07:56 CDT)
Re: fixed atoms / pressure Arturas Ziemys (Thu Mar 13 2008 - 10:52:41 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: TARGETED MD ERROR mon_sharma_at_research.iiit.ac.in (Thu Mar 13 2008 - 01:52:57 CDT)
Re: TARGETED MD ERROR Jerome Henin (Thu Mar 13 2008 - 00:54:49 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)
FEP: FATAL ERROR: Periodic cell has become too small for original patch grid! List (Wed Mar 12 2008 - 13:29:38 CDT)
Re: fixed atoms / pressure Peter Freddolino (Wed Mar 12 2008 - 18:55:07 CDT)
Re: variation between results on different OSes Peter Freddolino (Wed Mar 12 2008 - 18:48:00 CDT)
Re: Question about 'NAMD TUTORIAL' Peter Freddolino (Wed Mar 12 2008 - 18:46:55 CDT)
Question about 'NAMD TUTORIAL' Ben Chern (Wed Mar 12 2008 - 07:21:50 CDT)
variation between results on different OSes Dibyadeep Paul (Wed Mar 12 2008 - 02:31:40 CDT)
fixed atoms / pressure Arturas Ziemys (Mon Mar 10 2008 - 12:31:27 CDT)
Re: merge dcd files ,catdcd sripad chandan (Mon Mar 10 2008 - 06:47:10 CDT)
merge dcd files ,catdcd sripad chandan (Mon Mar 10 2008 - 06:45:58 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)
Re: change segID using segment command in psfgen Low Soo Mei (Thu Mar 06 2008 - 19:33:33 CST)
RE: change segID using segment command in psfgen JC Gumbart (Thu Mar 06 2008 - 08:28:12 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)
Replica Server Tutorial Joshua Adelman (Thu Mar 06 2008 - 00:23:02 CST)
Re: Restarting simulation goes the different temperature JC Gumbart (Wed Mar 05 2008 - 18:08:30 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)
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)
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)
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)
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)
protein_RNA simulation sripad chandan (Sat Mar 01 2008 - 08:43:22 CST)
Re: ABF error calculation Chris Chipot (Fri Feb 29 2008 - 16:26:00 CST)
Re: ABF error calculation Jerome Henin (Fri Feb 29 2008 - 16:16:29 CST)
ABF error calculation Xu, Jiancong (Fri Feb 29 2008 - 14:47:48 CST)
Re: Protein moving out of water-box after 10 ns simulation snoze pa (Fri Feb 29 2008 - 10:55:32 CST)
Re: PME Grid Size - how far to deviate from cell basis vectors. JC Gumbart (Thu Feb 28 2008 - 18:48:48 CST)
Re: Protein moving out of water-box after 10 ns simulation JC Gumbart (Thu Feb 28 2008 - 18:45:54 CST)
Re: NAMD 2.6 - PME Error on Large Protein-DNA System! Peter Freddolino (Thu Feb 28 2008 - 14:27:20 CST)
RE: NAMD 2.6 - PME Error on Large Protein-DNA System! Sean Law (Thu Feb 28 2008 - 11:35:42 CST)
Re: Periodic Box Size vs. Water Box Size Seth Lilavivat (Thu Feb 28 2008 - 11:13:45 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: Waterbox unexpectedly deformed after minimization. Peter Freddolino (Thu Feb 28 2008 - 11:08:09 CST)
Periodic Box Size vs. Water Box Size Seth Lilavivat (Thu Feb 28 2008 - 10:33:04 CST)
Waterbox unexpectedly deformed after minimization. Kamilla Kopec (Thu Feb 28 2008 - 10:22:38 CST)
Re: NAMD 2.6 - PME Error on Large Protein-DNA System! Peter Freddolino (Wed Feb 27 2008 - 23:59:41 CST)
NAMD 2.6 - PME Error on Large Protein-DNA System! Sean Law (Wed Feb 27 2008 - 18:03:44 CST)
Inorganic Builder Plugin Subhashis Biswas (Wed Feb 27 2008 - 17:57:12 CST)
Coordinates go to zero! Alex Huang (Wed Feb 27 2008 - 14:52:28 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: Protein moving out of water-box after 10 ns simulation Jie-rong Huang (Wed Feb 27 2008 - 10:34:15 CST)
PME Grid Size - how far to deviate from cell basis vectors. Kamilla Kopec (Wed Feb 27 2008 - 10:05:47 CST)
Re: Protein moving out of water-box after 10 ns simulation Per Jr. Greisen (Wed Feb 27 2008 - 09:40:49 CST)
Protein moving out of water-box after 10 ns simulation Jie-rong Huang (Wed Feb 27 2008 - 08:13:24 CST)
Re: Soft core potential - tested or not? Chris Chipot (Tue Feb 26 2008 - 15:24:57 CST)
Re: implicit solvent energy calculation Neema Salimi (Tue Feb 26 2008 - 15:10:25 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)
RE: implicit solvent energy calculation Chang, Christopher (Tue Feb 26 2008 - 13:51:26 CST)
Re: RNA_minimization jrui_at_ci.uc.pt (Tue Feb 26 2008 - 13:45:04 CST)
RNA_minimization sripad chandan (Tue Feb 26 2008 - 12:04:50 CST)
implicit solvent energy calculation regafan_at_usc.es (Tue Feb 26 2008 - 04:03:49 CST)
Re: umbrella sampling of decalanine using the ABF module Ilja Khavrutskii (Mon Feb 25 2008 - 16:34:41 CST)
Re: Re: umbrella sampling of decalanine using the ABF module George Madalin Giambasu (Mon Feb 25 2008 - 13:48:55 CST)
RE: Re: umbrella sampling of decalanine using the ABF module Xu, Jiancong (Mon Feb 25 2008 - 12:37:02 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)
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)
langevinHydrogen off with rigidbonds off? Justine Taylor (Fri Feb 22 2008 - 08:36:25 CST)
Re: Re: Creating topology for carbon nanotube / any new structure Peter Freddolino (Fri Feb 22 2008 - 07:03:16 CST)
problem in NAMD minimized structure when viewed in VMD ramaplot ramya narasimhan (Fri Feb 22 2008 - 04:41:23 CST)
Re: Re: Creating topology for carbon nanotube / any new structure prateeksha s (Fri Feb 22 2008 - 00:17:12 CST)
Re: phosphohistidine parameters ??? L. Michel Espinoza-Fonseca (Thu Feb 21 2008 - 13:45:27 CST)
phosphohistidine parameters ??? paco ty (Thu Feb 21 2008 - 12:33:10 CST)
Re: How to run NVT simulations without applying periodic boundary conditions? Yinglong Miao (Thu Feb 21 2008 - 09:44:45 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 - 08:24:55 CST)
Re: A difficult problem to explain the SMD force difference Lewyn Li (Thu Feb 21 2008 - 06:59:26 CST)
Re: Alchemical FEP NAMD tutorial - problems with reproducing the results Chris Chipot (Thu Feb 21 2008 - 03:19:42 CST)
A difficult problem to explain the SMD force difference Shulin Zhuang (Wed Feb 20 2008 - 22:36:15 CST)
Re: How to run NVT simulations without applying periodic boundary conditions? Yinglong Miao (Wed Feb 20 2008 - 15:55:23 CST)
Re: Alchemical FEP NAMD tutorial - problems with reproducing the results Jawahar Neelankatan (Wed Feb 20 2008 - 14:48:54 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)
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)
Re: Pair Interaction Calculations to get Charmm Charges? Jan Saam (Tue Feb 19 2008 - 17:55:30 CST)
Pair Interaction Calculations to get Charmm Charges? Kamilla Kopec (Tue Feb 19 2008 - 10:23:24 CST)
Re: Alchemical FEP NAMD tutorial - problems with reproducing the results Chris Chipot (Tue Feb 19 2008 - 07:14:13 CST)
Alchemical FEP NAMD tutorial - problems with reproducing the results Jawahar Neelankatan (Mon Feb 18 2008 - 21:25:54 CST)
RE: PSFGEN Warnings about H positions on standard amino acids Chang, Christopher (Mon Feb 18 2008 - 18:17:48 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: Tcl "loadtotalforces" question (forces never seem to be saved) Jerome Henin (Sun Feb 17 2008 - 15:13:42 CST)
Re: Tcl "loadtotalforces" question (forces never seem to be saved) Christopher Calderon (Sun Feb 17 2008 - 14:52:23 CST)
Re: Tcl "loadtotalforces" question (forces never seem to be saved) Jerome Henin (Sun Feb 17 2008 - 13:52:28 CST)
Re: Tcl "loadtotalforces" question (forces never seem to be saved) Christopher Calderon (Sun Feb 17 2008 - 13:06:31 CST)
Re: Tcl "loadtotalforces" question (forces never seem to be saved) Jerome Henin (Sun Feb 17 2008 - 12:39:01 CST)
Tcl "loadtotalforces" question (forces never seem to be saved) Christopher Calderon (Sun Feb 17 2008 - 11:51:23 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)
RE: PCA calculation Chang, Christopher (Thu Feb 14 2008 - 13:31:03 CST)
RE: PCA calculation Chang, Christopher (Thu Feb 14 2008 - 12:58:55 CST)
Re: NAMD 2.6 dcd and breaking XPLOR Peter Freddolino (Thu Feb 14 2008 - 07:14:02 CST)
Re: NAMD 2.6 dcd and breaking XPLOR Neema Salimi (Wed Feb 13 2008 - 19:50:38 CST)
Re: restarting files converge to new temperature Peter Freddolino (Wed Feb 13 2008 - 10:13:55 CST)
Re: restarting files converge to new temperature Jorgen Simonsen (Wed Feb 13 2008 - 10:08:24 CST)
Re: PCA calculation Richard Wood (Wed Feb 13 2008 - 10:00:19 CST)
ABF question Matthew Davies (Wed Feb 13 2008 - 11:00:44 CST)
Re: PCA calculation Himanshu Khandelia (Wed Feb 13 2008 - 09:00:45 CST)
Re: restarting files converge to new temperature Peter Freddolino (Wed Feb 13 2008 - 07:55:48 CST)
Re: PCA calculation Peter Freddolino (Wed Feb 13 2008 - 07:11:27 CST)
Re: restarting files converge to new temperature Jorgen Simonsen (Wed Feb 13 2008 - 02:13:09 CST)
Re: PCA calculation ramya narasimhan (Tue Feb 12 2008 - 22:59:49 CST)
Re: restarting files converge to new temperature Peter Freddolino (Tue Feb 12 2008 - 13:34:55 CST)
Re: PCA calculation Peter Freddolino (Tue Feb 12 2008 - 10:24:33 CST)
Re: PCA calculation Richard Wood (Tue Feb 12 2008 - 09:57:42 CST)
restarting files converge to new temperature Jorgen Simonsen (Tue Feb 12 2008 - 05:21:09 CST)
To incorporate an energy term ramya narasimhan (Tue Feb 12 2008 - 04:32:54 CST)
RE: PCA calculation Nicholas M Glykos (Tue Feb 12 2008 - 02:03:04 CST)
an aptamer and a lot of stupid problems Xxxxxxxx Xxxxxxx (Mon Feb 11 2008 - 23:09:38 CST)
Re: PCA calculation NAVEEN P MICHAUD AGRAWAL (Mon Feb 11 2008 - 12:37:07 CST)
Re: PCA calculation Peter Freddolino (Mon Feb 11 2008 - 12:09:16 CST)
Re: PCA calculation NAVEEN P MICHAUD AGRAWAL (Mon Feb 11 2008 - 11:58:34 CST)
Re: PCA calculation L. Michel Espinoza-Fonseca (Mon Feb 11 2008 - 11:34:07 CST)
Re: PCA calculation Peter Freddolino (Mon Feb 11 2008 - 10:38:15 CST)
RE: PCA calculation Xu, Jiancong (Mon Feb 11 2008 - 10:21:08 CST)
PCA calculation ramya narasimhan (Mon Feb 11 2008 - 01:49:06 CST)
Re: rigid body model Hidekazu WATANABE (Mon Feb 11 2008 - 01:19:23 CST)
Re: HSE and gromacs Peter Freddolino (Sun Feb 10 2008 - 10:49:46 CST)
Re: HSE and gromacs Peter Freddolino (Sun Feb 10 2008 - 10:47:19 CST)
HSE and gromacs patrick wintrode (Sun Feb 10 2008 - 10:41:01 CST)
Re: HP-MPI on Xeon Infiniband Alexandre A. Vakhrouchev (Sun Feb 10 2008 - 10:10:22 CST)
Re: HP-MPI on Xeon Infiniband Alexandre A. Vakhrouchev (Sun Feb 10 2008 - 08:26:25 CST)
HP-MPI on Xeon Infiniband Alexandre A. Vakhrouchev (Sun Feb 10 2008 - 06:43:58 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)
Re: Constrain centers of mass for selected atoms poker_at_physics.usyd.edu.au (Thu Feb 07 2008 - 18:36:00 CST)
NAMD 2.6 dcd and breaking XPLOR Neema Salimi (Thu Feb 07 2008 - 17:15:10 CST)
Re: catDCD 32 bit Vs. 64 bit Version Philip Peartree (Thu Feb 07 2008 - 09:28:15 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)
Constrain centers of mass for selected atoms michael_at_perfect-kreim.de (Thu Feb 07 2008 - 04:12:39 CST)
Re: water models supported in NAMD L. Michel Espinoza-Fonseca (Wed Feb 06 2008 - 18:18:34 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 Philip Peartree (Wed Feb 06 2008 - 12:33:19 CST)
water models supported in NAMD L. Michel Espinoza-Fonseca (Wed Feb 06 2008 - 10:26:09 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)
Re: NAMD: constraints while heating Peter Freddolino (Tue Feb 05 2008 - 06:53:23 CST)
Re: namd energy Peter Freddolino (Tue Feb 05 2008 - 06:40:09 CST)
namd energy Leandro Martínez (Tue Feb 05 2008 - 03:39:30 CST)
NAMD: constraints while heating Seth Lilavivat (Mon Feb 04 2008 - 15:35:46 CST)
Re: OPLS-AA toppar files John R. Dowdle (Mon Feb 04 2008 - 11:48:07 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)
Re: catDCD 32 bit Vs. 64 bit Version Philip Peartree (Sat Feb 02 2008 - 10:21:44 CST)
OPLS-AA toppar files John R. Dowdle (Sat Feb 02 2008 - 08:20:46 CST)
Re: Applying SMD to a domain of protein harish vashisth (Fri Feb 01 2008 - 11:13:58 CST)
ABF with different bin size Xu, Jiancong (Fri Feb 01 2008 - 11:11:58 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 Peter Freddolino (Fri Feb 01 2008 - 09:56:19 CST)
Re: FATAL ERROR: Periodic cell Jianhui Tian (Fri Feb 01 2008 - 08:44:54 CST)
FATAL ERROR: Periodic cell Jorgen Simonsen (Fri Feb 01 2008 - 04:50:34 CST)
Re: catDCD 32 bit Vs. 64 bit Version juneja_at_speakeasy.net (Fri Feb 01 2008 - 04:00:51 CST)
Applying SMD to a domain of protein Monika (Fri Feb 01 2008 - 00:49:37 CST)
FEP configuration file List (Mon Jan 28 2008 - 10:55:21 CST)
Re: catDCD 32 bit Vs. 64 bit Version Peter Freddolino (Thu Jan 31 2008 - 13:26:09 CST)
Re: NAMDENERGY in parellel Peter Freddolino (Thu Jan 31 2008 - 13:13:19 CST)
Re: catDCD 32 bit Vs. 64 bit Version juneja_at_speakeasy.net (Thu Jan 31 2008 - 11:51:28 CST)
NAMDENERGY in parellel Ghalib Bello (Thu Jan 31 2008 - 11:30:18 CST)
Re: catDCD 32 bit Vs. 64 bit Version Monika Sharma (Thu Jan 31 2008 - 08:09:46 CST)
Re: Cholesterol structure Alexandre A. Vakhrouchev (Thu Jan 31 2008 - 08:06:03 CST)
catDCD 32 bit Vs. 64 bit Version Alok Juneja (Thu Jan 31 2008 - 03:51:40 CST)
Re: Cholesterol structure Alexandre A. Vakhrouchev (Thu Jan 31 2008 - 02:02:46 CST)
Re: Cholesterol structure Alexandre A. Vakhrouchev (Thu Jan 31 2008 - 01:38:03 CST)
Re: Cholesterol structure Per Jr. Greisen (Thu Jan 31 2008 - 01:29:52 CST)
Re: Cholesterol structure Alexandre A. Vakhrouchev (Thu Jan 31 2008 - 00:50:13 CST)
Re: FATAL ERROR: Periodic cell has become too small for original patch grid! Peter Freddolino (Wed Jan 30 2008 - 15:57:53 CST)
Re: FATAL ERROR: Periodic cell has become too small for original patch grid! Joshua Adelman (Wed Jan 30 2008 - 15:50:10 CST)
Re: FATAL ERROR: Periodic cell has become too small for original patch grid! Peter Freddolino (Wed Jan 30 2008 - 11:55:21 CST)
Re: FATAL ERROR: Periodic cell has become too small for original patch grid! Joshua Adelman (Wed Jan 30 2008 - 11:47:16 CST)
Re: FATAL ERROR: Periodic cell has become too small for original patch grid! Peter Freddolino (Wed Jan 30 2008 - 10:52:48 CST)
FATAL ERROR: Periodic cell has become too small for original patch grid! Joshua Adelman (Wed Jan 30 2008 - 10:42:06 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)
Re: Dihedral coordinate ABF scheme Jerome Henin (Tue Jan 29 2008 - 16:25:57 CST)
Dihedral coordinate ABF scheme Luca (Tue Jan 29 2008 - 15:32:01 CST)
Re: Sudden expansion of box when continuing NPT simulation Peter Freddolino (Tue Jan 29 2008 - 12:24:46 CST)
Re: Cholesterol structure Richard Wood (Tue Jan 29 2008 - 09:19:07 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: Grand canonical ensemble Peter Freddolino (Mon Jan 28 2008 - 08:51:09 CST)
Grand canonical ensemble michael_at_perfect-kreim.de (Mon Jan 28 2008 - 07:20:11 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)
Re: SMD vs RAMD Vlad Cojocaru (Thu Jan 24 2008 - 12:28:37 CST)
Re: SMD vs RAMD harish vashisth (Thu Jan 24 2008 - 12:25:20 CST)
SMD vs RAMD Francesco Pietra (Thu Jan 24 2008 - 11:22:18 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)
Re: Inconsistencies in NAMD simulations Ana Vila Verde (Tue Jan 22 2008 - 06:14:52 CST)
Re: Is it better to align all the trajectory before calculating rmsd? Ana Vila Verde (Tue Jan 22 2008 - 05:31:12 CST)
Is it better to align all the trajectory before calculating rmsd? dongsheng lei (Tue Jan 22 2008 - 03:05:47 CST)
Inconsistencies in NAMD simulations Chandra Ramananjara (Tue Jan 22 2008 - 02:49:53 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: 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 (Sat Jan 19 2008 - 23:02:22 CST)
Re: About Amber force fields Jan Saam (Sat Jan 19 2008 - 23:00:45 CST)
Re: Defining a group of atoms in a simulation Ilja Khavrutskii (Sat Jan 19 2008 - 14:02:58 CST)
Re: Shear flow: Lees-Edwards Boundary Conditions Richard Wood (Sat Jan 19 2008 - 12:57:12 CST)
Defining a group of atoms in a simulation Arneh Babakhani (Sat Jan 19 2008 - 11:15:03 CST)
About Amber force fields Francesco Pietra (Sat Jan 19 2008 - 08:54:30 CST)
RE: vmd-l: C NH1 C minimization error Sourmaidou, Damiani (Sat Jan 19 2008 - 03:28:51 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)
Re: vmd-l: C NH1 C minimization error L. Michel Espinoza-Fonseca (Thu Jan 17 2008 - 07:13:33 CST)
C NH1 C minimization error Sourmaidou, Damiani (Thu Jan 17 2008 - 06:43:18 CST)
Re: Problems restarting an amber simulation Guanglei Cui (Wed Jan 16 2008 - 14:35:30 CST)
RE: Problems restarting an amber simulation Irene Newhouse (Wed Jan 16 2008 - 12:34:41 CST)
Problems restarting an amber simulation Seth Lilavivat (Wed Jan 16 2008 - 11:04:14 CST)
Re: Converting DCD file to XTC format Alessandro Pedretti (Wed Jan 16 2008 - 02:11:20 CST)
Converting DCD file to XTC format Jianping Lin (Tue Jan 15 2008 - 17:09:39 CST)
resonable dcdfreq Lixia Jin Day (Tue Jan 15 2008 - 16:21:58 CST)
Re: Characteristic time of atomic vibrations and collisions? Yinglong Miao (Tue Jan 15 2008 - 10:06:29 CST)
Re: Characteristic time of atomic vibrations and collisions? Victor Ovchinnikov (Mon Jan 14 2008 - 17:33:42 CST)
Characteristic time of atomic vibrations and collisions? Yinglong Miao (Mon Jan 14 2008 - 16:16:11 CST)
Re: ABF question Jerome Henin (Mon Jan 14 2008 - 11:40:49 CST)
RE: ABF question Xu, Jiancong (Mon Jan 14 2008 - 11:19:27 CST)
RE: ABF question jia (Sun Jan 13 2008 - 12:55:37 CST)
Re: ABF question Jerome Henin (Mon Jan 14 2008 - 11:02:35 CST)
RE: ABF question Xu, Jiancong (Mon Jan 14 2008 - 10:14:07 CST)
changing position of atoms during NAMD simulation michael_at_perfect-kreim.de (Mon Jan 14 2008 - 07:11:52 CST)
Re: ABF using distance-com but with negative xiMin Jerome Henin (Fri Jan 11 2008 - 17:19:32 CST)
ABF using distance-com but with negative xiMin Philip Fowler (Fri Jan 11 2008 - 09:21:48 CST)
Question about Error Message Alex Huang (Thu Jan 10 2008 - 09:33:49 CST)
Re: ABF question Jerome Henin (Wed Jan 09 2008 - 11:26:57 CST)
ABF question Xu, Jiancong (Wed Jan 09 2008 - 10:04:19 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)
RE: problems-periodic cell Irene Newhouse (Tue Jan 01 2008 - 14:41:36 CST)
Re: problems-periodic cell Christopher Gillespie (Tue Jan 01 2008 - 12:23:25 CST)
problems-periodic cell jose correa (Tue Jan 01 2008 - 09:30:10 CST)
charmm charge style carlos alberto gueto tettay (Thu Dec 27 2007 - 12:55:00 CST)
Re: Dihedral energy not getting generated ( is zero ) prateeksha s (Wed Dec 26 2007 - 02:01:50 CST)
Dihedral energy not getting generated ( is zero ) prateeksha s (Wed Dec 26 2007 - 01:58:15 CST)
Problems of mpi with namd 2.6 cong chen (Mon Dec 24 2007 - 00:53:25 CST)
Compiling NAMD on PPC G4 w/Apple's Leopard Joshua Adelman (Sun Dec 23 2007 - 10:31:57 CST)
(no subject) jfgaff_at_ncsu.edu (Sat Dec 22 2007 - 08:30:16 CST)
Re: enery evaluation inside Tcl-Forces? harish vashisth (Fri Dec 21 2007 - 16:16:23 CST)
ligand parameters... I know the next step carlos alberto gueto tettay (Fri Dec 21 2007 - 11:36:53 CST)
ligands parameters carlos alberto gueto tettay (Fri Dec 21 2007 - 08:42:15 CST)
Re: Segmentation violation when running without an internet connection Robert Brunner (Thu Dec 20 2007 - 14:45:41 CST)
Re: Segmentation violation when running without an internet connection Christopher Gillespie (Thu Dec 20 2007 - 13:53:30 CST)
Segmentation violation when running without an internet connection jadelman_at_berkeley.edu (Thu Dec 20 2007 - 12:20:51 CST)
enery evaluation inside Tcl-Forces? harish vashisth (Thu Dec 20 2007 - 10:14:48 CST)
Re: Creating topology for carbon nanotube / any new structure prateeksha s (Wed Dec 19 2007 - 22:24:49 CST)
Re: Creating topology for carbon nanotube / any new structure prateeksha s (Wed Dec 19 2007 - 22:21:44 CST)
fluorescent probes jayant james (Wed Dec 19 2007 - 20:08:33 CST)
psfgen for pre-equilibrated membrane bilayer Myunggi Yi (Wed Dec 19 2007 - 18:47:10 CST)
Tcl-forces query Harish Lnu (Wed Dec 19 2007 - 10:23:01 CST)
Creating topology for carbon nanotube / any new structure prateeksha s (Tue Dec 18 2007 - 22:41:04 CST)
Re: ABF: split reaction coordinate in widows Subramanian Vaitheeswaran (Tue Dec 18 2007 - 10:40:39 CST)
ABF: split reaction coordinate in widows Vlad Cojocaru (Tue Dec 18 2007 - 08:01:55 CST)
Re: Compilation of Charm++ then NAMD 2.6 on Opteron with Portland compilers Philip Peartree (Sat Dec 15 2007 - 22:04:08 CST)
Re: Compilation of Charm++ then NAMD 2.6 on Opteron with Portland compilers Dow_Hurst (Sat Dec 15 2007 - 21:49:11 CST)
namd-l : Topology info - RESidue information for carbon nanotube prateeksha s (Sat Dec 15 2007 - 07:25:19 CST)
Topology info - RESidue information for carbon nanotube prateeksha s (Sat Dec 15 2007 - 07:23:08 CST)
Re: Compilation of Charm++ then NAMD 2.6 on Opteron with Portland compilers Philip Peartree (Fri Dec 14 2007 - 16:01:56 CST)
Re: Compilation of Charm++ then NAMD 2.6 on Opteron with Portland compilers Philip Peartree (Fri Dec 14 2007 - 12:52:44 CST)
Re: ABF - PMF Calculation Jerome Henin (Fri Dec 14 2007 - 11:15:15 CST)
ABF - PMF Calculation Jason O'Young (Fri Dec 14 2007 - 10:00:48 CST)
Re: Compilation of Charm++ then NAMD 2.6 on Opteron with Portland compilers Philip Peartree (Fri Dec 14 2007 - 07:29:01 CST)
re: Scripting: Handle for energy terms in the PSF file? Chang, Christopher (Thu Dec 13 2007 - 13:39:18 CST)
add Mg2+ Lixia Jin Day (Thu Dec 13 2007 - 11:30:26 CST)
Re: Compilation of Charm++ then NAMD 2.6 on Opteron with Portland compilers Philip Peartree (Wed Dec 12 2007 - 17:47:59 CST)
Re: Compilation of Charm++ then NAMD 2.6 on Opteron with Portland compilers Philip Peartree (Wed Dec 12 2007 - 16:54:09 CST)
Re: Compilation of Charm++ then NAMD 2.6 on Opteron with Portlandcompilers Philip Peartree (Wed Dec 12 2007 - 15:35:10 CST)
RE: Scripting: Handle for energy terms in the PSF file? Chang, Christopher (Wed Dec 12 2007 - 15:32:56 CST)
Re: Compilation of Charm++ then NAMD 2.6 on Opteron with Portland compilers Philip Peartree (Wed Dec 12 2007 - 15:22:14 CST)
Compilation of Charm++ then NAMD 2.6 on Opteron with Portland compilers Philip Peartree (Wed Dec 12 2007 - 09:20:23 CST)
Re: Scripting: Handle for energy terms in the PSF file? Peter Freddolino (Tue Dec 11 2007 - 20:30:22 CST)
re: Scripting: Handle for energy terms in the PSF file? Chang, Christopher (Tue Dec 11 2007 - 19:19:02 CST)
Scripting: Handle for energy terms in the PSF file? Chang, Christopher (Mon Dec 10 2007 - 21:18:24 CST)
force field parameters for fullerenes Adam Fraser (Mon Dec 10 2007 - 13:18:16 CST)
Re: force dcd files?? Joshua D. Moore (Mon Dec 10 2007 - 10:32:36 CST)
SMD question Qiang Zhong (Sat Dec 08 2007 - 19:26:03 CST)
Re: nonbonded interactions Joseph Heil (Fri Dec 07 2007 - 20:42:24 CST)
Re: ABF - restricting reaction coordinate Jerome Henin (Fri Dec 07 2007 - 15:04:21 CST)
Re: MD runs at different clusters JC Gumbart (Fri Dec 07 2007 - 14:53:56 CST)
Re: ABF - restricting reaction coordinate Subramanian Vaitheeswaran (Fri Dec 07 2007 - 14:49:55 CST)
nonbonded interactions Xu, Jiancong (Fri Dec 07 2007 - 13:34:46 CST)
Re: Re: ABF - restricting reaction coordinate Jerome Henin (Fri Dec 07 2007 - 10:43:49 CST)
Re: ABF - restricting reaction coordinate Jerome Henin (Fri Dec 07 2007 - 10:01:47 CST)
Re: ABF - restricting reaction coordinate Subramanian Vaitheeswaran (Fri Dec 07 2007 - 09:38:36 CST)
ABF - restricting reaction coordinate Subramanian Vaitheeswaran (Fri Dec 07 2007 - 08:55:48 CST)
MD runs at different clusters Monika Sharma (Fri Dec 07 2007 - 04:04:35 CST)
force dcd files?? Thomas C. Bishop (Thu Dec 06 2007 - 15:22:49 CST)
Re: force constant matrix Ahlam Al-Rawi (Thu Dec 06 2007 - 14:20:07 CST)
SYSTEM ENERGY MINIMIZATION Samuel Morales (Thu Dec 06 2007 - 12:40:54 CST)
Re: Generating a gromacs topology file for analyzing NAMD trajectories Giovanni Bellesia (Thu Dec 06 2007 - 12:25:37 CST)
Re: Simple TCL (Forces) question - defining bond vector Victor Ovchinnikov (Thu Dec 06 2007 - 12:53:37 CST)
Re: Generating a gromacs topology file for analyzing NAMD trajectories Richard Wood (Thu Dec 06 2007 - 11:51:03 CST)
RE: Generating a gromacs topology file for analyzing NAMD trajectories Xu, Jiancong (Thu Dec 06 2007 - 09:41:22 CST)
Re: Simple TCL (Forces) question - defining bond vector Jeff Wereszczynski (Thu Dec 06 2007 - 11:43:45 CST)
Simple TCL (Forces) question - defining bond vector Jim Pfaendtner (Thu Dec 06 2007 - 09:33:59 CST)
Re: Generating a gromacs topology file for analyzing NAMD trajectories L. Michel Espinoza-Fonseca (Thu Dec 06 2007 - 09:11:44 CST)
Re: Generating a gromacs topology file for analyzing NAMD trajectories patrick wintrode (Thu Dec 06 2007 - 08:54:25 CST)
Re: Generating a gromacs topology file for analyzing NAMD trajectories Ilya Chorny (Wed Dec 05 2007 - 16:13:31 CST)
Re: Generating a gromacs topology file for analyzing NAMD trajectories Giovanni Bellesia (Wed Dec 05 2007 - 15:25:42 CST)
SYSTEM ENERGY MINIMIZATION El Escuchado por DIOS (Wed Dec 05 2007 - 15:06:48 CST)
Re: Generating a gromacs topology file for analyzing NAMD trajectories L. Michel Espinoza-Fonseca (Wed Dec 05 2007 - 14:52:52 CST)
Generating a gromacs topology file for analyzing NAMD trajectories patrick wintrode (Wed Dec 05 2007 - 14:15:11 CST)
Re: simulation of fullerenes Adam Fraser (Wed Dec 05 2007 - 12:31:45 CST)
simulation of fullerenes Adam Fraser (Wed Dec 05 2007 - 12:16:39 CST)
Re: Convergence of ABF calculation: n_samples Jerome Henin (Wed Dec 05 2007 - 10:14:37 CST)
Re: Convergence of ABF calculation: n_samples Chris Chipot (Wed Dec 05 2007 - 09:53:39 CST)
Re: how to perform MD with two proteins Mert Gür (Wed Dec 05 2007 - 09:04:57 CST)
Convergence of ABF calculation: n_samples Subramanian Vaitheeswaran (Wed Dec 05 2007 - 08:39:47 CST)
DEN residue name in Amber prateeksha s (Wed Dec 05 2007 - 00:10:42 CST)
Re: Pressure fluctuations Peter Freddolino (Mon Dec 03 2007 - 22:01:04 CST)
Re: ABF fullsamples Jerome Henin (Mon Dec 03 2007 - 18:13:40 CST)
Protein hydrogens causing "Atoms too fast" error Christopher Gillespie (Mon Dec 03 2007 - 18:03:59 CST)
Re: Is there solution to numerical inaccuracy Peter Freddolino (Mon Dec 03 2007 - 17:02:51 CST)
Re: ABF fullsamples Chris Chipot (Mon Dec 03 2007 - 15:47:06 CST)
ABF fullsamples Jason O'Young (Mon Dec 03 2007 - 13:18:40 CST)
Re: Is there solution to numerical inaccuracy Alok Juneja (Mon Dec 03 2007 - 12:49:50 CST)
different 1-4scaling values for different atom types? cong chen (Sun Dec 02 2007 - 23:51:11 CST)
Re: ABF Output File Chris Chipot (Sun Dec 02 2007 - 13:22:03 CST)
ABF Output File Jason Wyonn O'Young (Sun Dec 02 2007 - 12:47:26 CST)
Re: how to perform MD with two proteins Peter Freddolino (Sun Dec 02 2007 - 10:31:54 CST)
Re: how to perform MD with two proteins Richard Wood (Sun Dec 02 2007 - 10:00:43 CST)
how to perform MD with two proteins Mert Gür (Sun Dec 02 2007 - 09:12:28 CST)
how to perform MD with two proteins Mert Gür (Sun Dec 02 2007 - 08:37:18 CST)
how to perform MD with two proteins Mert Gür (Sun Dec 02 2007 - 07:35:14 CST)
Re: SMD behavior Adam Fraser (Sat Dec 01 2007 - 12:03:40 CST)
Re: tip4p - namd follwup luca (Sat Dec 01 2007 - 03:45:35 CST)
About para file format cong chen (Sat Dec 01 2007 - 00:14:36 CST)
Unsubscribe Raja Natesan (Fri Nov 30 2007 - 23:44:12 CST)
Periodic boundary conditions Gianluca Interlandi (Fri Nov 30 2007 - 19:20:07 CST)
Re: paratool for MG Philip Peartree (Fri Nov 30 2007 - 15:51:53 CST)
paratool for MG Tianjiao Wang (Fri Nov 30 2007 - 12:48:05 CST)
tip4p - namd follwup Bishop, Thomas C (Fri Nov 30 2007 - 10:37:24 CST)
Parameter or patch for thioester Jianping Lin (Fri Nov 30 2007 - 12:23:52 CST)
Re: abf: multiple distance Jerome Henin (Fri Nov 30 2007 - 11:44:39 CST)
Re: abf: multiple distance Jerome Henin (Fri Nov 30 2007 - 11:34:09 CST)
Re: PME on a negatively charged system Hai Long (Fri Nov 30 2007 - 11:09:35 CST)
SMD ensemble? gian peralta (Thu Nov 29 2007 - 17:49:09 CST)
Pressure fluctuations Ayþe Özlem Sezerman (Fri Nov 30 2007 - 10:50:32 CST)
TMD and RMSD constrained dynamcs M. Madhu (Fri Nov 30 2007 - 10:22:48 CST)
How is the maximum velocity limit set? Yinglong Miao (Fri Nov 30 2007 - 10:22:40 CST)
Re: abf: multiple distance Vlad Cojocaru (Fri Nov 30 2007 - 10:05:43 CST)
Re: abf: multiple distance luca (Fri Nov 30 2007 - 09:50:58 CST)
Re: abf: multiple distance Jerome Henin (Fri Nov 30 2007 - 09:01:39 CST)
Re: tcl script for applying constraints luca (Fri Nov 30 2007 - 02:20:50 CST)
Re: problems replicating a DOPC membrane Richard Swenson (Thu Nov 29 2007 - 14:57:35 CST)
PME on a negatively charged system. Richard Swenson (Thu Nov 29 2007 - 14:53:18 CST)
tcl script for applying constraints Pijush Ghosh (Thu Nov 29 2007 - 14:35:13 CST)
Re: Is there solution to numerical inaccuracy Ilya Chorny (Thu Nov 29 2007 - 13:53:47 CST)
Re: Is there solution to numerical inaccuracy Peter Freddolino (Thu Nov 29 2007 - 13:25:35 CST)
Re: Is there solution to numerical inaccuracy Ilya Chorny (Thu Nov 29 2007 - 13:24:50 CST)
problems replicating a DOPC membrane regafan_at_usc.es (Thu Nov 29 2007 - 12:26:29 CST)
Re: Is there solution to numerical inaccuracy Alok Juneja (Thu Nov 29 2007 - 12:04:50 CST)
abf: multiple distance Luca Bellucci (Thu Nov 29 2007 - 04:18:19 CST)
Re: Re: Parameters for NH3, NH4+, and CO2 Himanshu Khandelia (Thu Nov 29 2007 - 01:51:56 CST)
Re: Re: Parameters for NH3, NH4+, and CO2 Jeffrey J. Potoff (Wed Nov 28 2007 - 23:08:34 CST)
Re: Re: Parameters for NH3, NH4+, and CO2 Richard Wood (Wed Nov 28 2007 - 22:58:30 CST)
Re: Re: Parameters for NH3, NH4+, and CO2 Ilya Chorny (Wed Nov 28 2007 - 21:51:19 CST)
Re: Re: Parameters for NH3, NH4+, and CO2 Jeffrey J. Potoff (Wed Nov 28 2007 - 21:34:29 CST)
Re: Parameters for NH3, NH4+, and CO2 Ilya Chorny (Wed Nov 28 2007 - 20:31:09 CST)
Re: uncharged ends L. Michel Espinoza-Fonseca (Wed Nov 28 2007 - 10:30:15 CST)
uncharged ends Xavier GALLET (Wed Nov 28 2007 - 09:46:22 CST)
RE: problem with *.pdb and *.psf Richard Swenson (Wed Nov 28 2007 - 09:18:30 CST)
problem with *.pdb and *.psf jose correa (Wed Nov 28 2007 - 08:16:38 CST)
Flying ions jia (Tue Nov 27 2007 - 21:00:32 CST)
REMD Dirar Homouz (Tue Nov 27 2007 - 14:33:46 CST)
Is there solution to numerical inaccuracy Alok Juneja (Tue Nov 20 2007 - 06:07:57 CST)
Re: Is there solution to numerical inaccuracy Alok Juneja (Fri Nov 23 2007 - 12:14:01 CST)
Re: Is there solution to numerical inaccuracy Peter Freddolino (Mon Nov 26 2007 - 14:16:40 CST)
Re: Is there solution to numerical inaccuracy Peter Freddolino (Mon Nov 26 2007 - 14:08:16 CST)
Re: SMD Constant Velocity: Force Peter Freddolino (Mon Nov 26 2007 - 14:03:38 CST)
Re: SMD Constant Velocity: Force Vamshi Gangupomu (Mon Nov 26 2007 - 09:33:51 CST)
Re: Is there solution to numerical inaccuracy Alok Juneja (Mon Nov 26 2007 - 04:54:22 CST)
Avoiding self-interaction with PME. Niels Christensen (Sun Nov 25 2007 - 09:59:57 CST)
SMD Constant Velocity: Force Vamshi Gangupomu (Sun Nov 25 2007 - 00:33:24 CST)
Re: energy per residue Peter Freddolino (Sat Nov 24 2007 - 08:38:48 CST)
replicating a DOPC membrane regafan_at_usc.es (Fri Nov 23 2007 - 12:30:30 CST)
replica exchange trajectories Raul Alcantara (Fri Nov 23 2007 - 13:12:48 CST)
energy per residue Xavier GALLET (Fri Nov 23 2007 - 09:15:49 CST)
Re: minimization-problem Karol Kaszuba (Thu Nov 22 2007 - 10:20:41 CST)
Re: minimization-problem Karol Kaszuba (Thu Nov 22 2007 - 10:18:12 CST)
Re: Is there solution to numerical inaccuracy Peter Freddolino (Thu Nov 22 2007 - 09:15:29 CST)
minimization-problem jose correa (Thu Nov 22 2007 - 08:13:51 CST)
Re: Is there solution to numerical inaccuracy David Hardy (Thu Nov 22 2007 - 07:35:01 CST)
Re: Is there solution to numerical inaccuracy Himanshu Khandelia (Thu Nov 22 2007 - 02:19:55 CST)
Re: ABF calculations Chris Chipot (Wed Nov 21 2007 - 18:37:32 CST)
Re: SMD behavior poker_at_physics.usyd.edu.au (Wed Nov 21 2007 - 18:18:13 CST)
PO3 psf Ahlam Al-Rawi (Wed Nov 21 2007 - 16:06:22 CST)
Re: psfGen error JC Gumbart (Wed Nov 21 2007 - 15:28:22 CST)
Re: ABF : dihedral-com.tcl Subramanian Vaitheeswaran (Wed Nov 21 2007 - 11:16:37 CST)
Re: ABF : dihedral-com.tcl Chris Chipot (Wed Nov 21 2007 - 10:36:37 CST)
Re: ABF : dihedral-com.tcl Vlad Cojocaru (Wed Nov 21 2007 - 10:36:31 CST)
Re: Is there solution to numerical inaccuracy David Hardy (Wed Nov 21 2007 - 09:54:41 CST)
ABF : dihedral-com.tcl Subramanian Vaitheeswaran (Wed Nov 21 2007 - 09:59:37 CST)
SMD behavior Adam Fraser (Wed Nov 21 2007 - 09:47:54 CST)
Re: psfGen error Joseph Heil (Tue Nov 20 2007 - 23:37:32 CST)
Dixitpd wants to Share Favorites with you dixitpd_at_gmail.com (Tue Nov 20 2007 - 22:05:54 CST)
How to freeze some atoms cong chen (Tue Nov 20 2007 - 20:11:24 CST)
Re: New ABF order parameters Subramanian Vaitheeswaran (Tue Nov 20 2007 - 16:43:45 CST)
Re: New ABF order parameters Subramanian Vaitheeswaran (Tue Nov 20 2007 - 16:29:25 CST)
Re: New ABF order parameters Jerome Henin (Tue Nov 20 2007 - 16:07:01 CST)
New ABF order parameters Subramanian Vaitheeswaran (Tue Nov 20 2007 - 15:56:20 CST)
Re: Installing NAMD brmorgan_at_clarku.edu (Tue Nov 20 2007 - 13:02:42 CST)
Re: Any flag values returned when executing "minimize" and "run"? Yinglong Miao (Tue Nov 20 2007 - 12:46:10 CST)
Re: Is there solution to numerical inaccuracy Peter Freddolino (Tue Nov 20 2007 - 11:48:58 CST)
Re: Any flag values returned when executing "minimize" and "run"? Victor Ovchinnikov (Tue Nov 20 2007 - 11:35:51 CST)
Re: Any flag values returned when executing "minimize" and "run"? Peter Freddolino (Tue Nov 20 2007 - 11:20:39 CST)
Re: Is there solution to numerical inaccuracy Alok Juneja (Tue Nov 20 2007 - 10:53:04 CST)
MD of DNA lily jin (Tue Nov 20 2007 - 10:31:39 CST)
Re: Any flag values returned when executing "minimize" and "run"? Yinglong Miao (Tue Nov 20 2007 - 10:10:52 CST)
Re: Any flag values returned when executing "minimize" and "run"? Peter Freddolino (Tue Nov 20 2007 - 09:19:33 CST)
Re: psfGen error Jeffrey J. Potoff (Tue Nov 20 2007 - 09:17:00 CST)
Re: Is there solution to numerical inaccuracy Peter Freddolino (Tue Nov 20 2007 - 09:14:47 CST)
RE: ABF calculations jia (Tue Nov 20 2007 - 09:14:42 CST)
Is there solution to numerical inaccuracy Alok Juneja (Tue Nov 20 2007 - 07:54:29 CST)
Re: Installing NAMD Jason Russler (Tue Nov 20 2007 - 07:39:58 CST)
Re: psfGen error Karol Kaszuba (Tue Nov 20 2007 - 03:44:41 CST)
About RMSD cong chen (Tue Nov 20 2007 - 03:29:32 CST)
Re: Replica Exchange NAMD John Dowdle (Mon Nov 19 2007 - 22:55:09 CST)
psfGen error Joseph Heil (Mon Nov 19 2007 - 22:00:57 CST)
Re: Replica Exchange NAMD John R. Dowdle (Mon Nov 19 2007 - 20:16:43 CST)
Re: ABF calculations Chris Chipot (Mon Nov 19 2007 - 16:30:42 CST)
Re: ABF calculations Jerome Henin (Mon Nov 19 2007 - 15:56:17 CST)
ABF calculations jia (Mon Nov 19 2007 - 14:33:51 CST)
Any flag values returned when executing "minimize" and "run"? Yinglong Miao (Mon Nov 19 2007 - 10:52:44 CST)
Does rmsd is the judge of system equilibrium in all conditions? cong chen (Mon Nov 19 2007 - 06:08:12 CST)
Re: howcan I use amber forcefield in NAMD? mashaojie163 (Sat Nov 17 2007 - 01:28:51 CST)
RE: What is an IC table in the .inp files Richard Swenson (Fri Nov 16 2007 - 14:45:02 CST)
Re: What is an IC table in the .inp files Alessandro Cembran (Fri Nov 16 2007 - 14:23:08 CST)
Re: What is an IC table in the .inp files Richard Wood (Fri Nov 16 2007 - 13:46:26 CST)
Re: What is an IC table in the .inp files Ilya Chorny (Fri Nov 16 2007 - 13:31:44 CST)
Installing NAMD brmorgan_at_clarku.edu (Fri Nov 16 2007 - 11:28:47 CST)
ABF or SMD jia (Fri Nov 16 2007 - 11:26:20 CST)
Re: howcan I use amber forcefield in NAMD? Floris Buelens (Fri Nov 16 2007 - 05:19:37 CST)
Re: Using NAMD DCD in CHARMM Himanshu Khandelia (Fri Nov 16 2007 - 01:19:21 CST)
Re: Using NAMD DCD in CHARMM Peter Freddolino (Thu Nov 15 2007 - 23:23:36 CST)
Re: howcan I use amber forcefield in NAMD? Richard Wood (Thu Nov 15 2007 - 22:32:56 CST)
RE: howcan I use amber forcefield in NAMD? JC Gumbart (Thu Nov 15 2007 - 22:01:54 CST)
Re: howcan I use amber forcefield in NAMD? Richard Wood (Thu Nov 15 2007 - 21:33:00 CST)
Re: What is an IC table in the .inp files Richard Wood (Thu Nov 15 2007 - 21:29:12 CST)
Fw: What is an IC table in the .inp files char_at_ks.uiuc.edu (Thu Nov 15 2007 - 21:10:29 CST)
[Fwd: Re: What is an IC table in the .inp files] Victor Ovchinnikov (Thu Nov 15 2007 - 21:00:51 CST)
Re: howcan I use amber forcefield in NAMD? mashaojie163 (Thu Nov 15 2007 - 20:55:53 CST)
Re: What is an IC table in the .inp files Chris Harrison (Thu Nov 15 2007 - 20:53:43 CST)
What is an IC table in the .inp files Ilya Chorny (Thu Nov 15 2007 - 19:02:07 CST)
RE: howcan I use amber forcefield in NAMD? Huy N. Ha (Thu Nov 15 2007 - 17:24:36 CST)
Using NAMD DCD in CHARMM Ahlam Al-Rawi (Thu Nov 15 2007 - 13:38:58 CST)
question switching function Peter Kiss (Thu Nov 15 2007 - 12:12:08 CST)
Re: user defined restraint in ABF Jerome Henin (Thu Nov 15 2007 - 12:09:29 CST)
user defined restraint in ABF Vlad Cojocaru (Thu Nov 15 2007 - 10:15:17 CST)
Re: DCD trajectories produced by SMD simulation Peter Freddolino (Thu Nov 15 2007 - 09:46:47 CST)
Re: DCD trajectories produced by SMD simulation Vlad Cojocaru (Thu Nov 15 2007 - 07:49:58 CST)
Re: howcan I use amber forcefield in NAMD? mashaojie163 (Thu Nov 15 2007 - 06:23:49 CST)
Re: OPLS Lipid topology/potenital for NAMD Himanshu Khandelia (Thu Nov 15 2007 - 02:12:50 CST)
RE: howcan I use amber forcefield in NAMD? Irene Newhouse (Thu Nov 15 2007 - 00:51:41 CST)
Re: DCD trajectories produced by SMD simulation Marcos Sotomayor (Thu Nov 15 2007 - 00:23:02 CST)
Re: DCD trajectories produced by SMD simulation Peter Freddolino (Thu Nov 15 2007 - 00:17:01 CST)
howcan I use amber forcefield in NAMD? mashaojie163 (Wed Nov 14 2007 - 21:58:39 CST)
Ligand Bound. kparra_at_mail.usf.edu (Wed Nov 14 2007 - 12:30:27 CST)
Re: OPLS Lipid topology/potenital for NAMD Ilya Chorny (Wed Nov 14 2007 - 11:18:04 CST)
Re: OPLS Lipid topology/potenital for NAMD Himanshu Khandelia (Wed Nov 14 2007 - 11:12:37 CST)
Re: OPLS Lipid topology/potenital for NAMD Ilya Chorny (Wed Nov 14 2007 - 08:37:49 CST)
Re: OPLS Lipid topology/potenital for NAMD Himanshu Khandelia (Wed Nov 14 2007 - 02:36:07 CST)
OPLS Lipid topology/potenital for NAMD Ilya Chorny (Tue Nov 13 2007 - 16:44:02 CST)
Re: ANN: MDAnalysis python library nmichaud_at_jhu.edu (Tue Nov 13 2007 - 16:42:06 CST)
Replica Exchange NAMD Dirar Homouz (Tue Nov 13 2007 - 12:09:52 CST)
Re: ABF application Vlad Cojocaru (Tue Nov 13 2007 - 11:52:53 CST)
Re: ABF application Jerome Henin (Tue Nov 13 2007 - 11:37:27 CST)
Re: ABF application Vlad Cojocaru (Tue Nov 13 2007 - 09:39:43 CST)
Re: DCD trajectories produced by SMD simulation Vlad Cojocaru (Tue Nov 13 2007 - 04:05:14 CST)
Problem in Running namd2 Sanjay H A (Tue Nov 13 2007 - 01:23:09 CST)
loadtotalforces error Pijush Ghosh (Mon Nov 12 2007 - 19:14:25 CST)
ANN: MDAnalysis 0.3 python library nmichaud_at_jhu.edu (Mon Nov 12 2007 - 16:01:11 CST)
change center of spherical BC during sim paco ty (Mon Nov 12 2007 - 14:33:34 CST)
Vega ZZ Script for calculating area/lipid. Ilya Chorny (Mon Nov 12 2007 - 13:15:07 CST)
Re: DCD trajectories produced by SMD simulation Peter Freddolino (Mon Nov 12 2007 - 11:32:09 CST)
DCD trajectories produced by SMD simulation Vlad Cojocaru (Mon Nov 12 2007 - 07:43:55 CST)
Re: NPT_NPgammaT_or_NPAT_for_membrane_with_CHARMM_forcefield Karol Kaszuba (Mon Nov 12 2007 - 04:57:58 CST)
Re: NPT_NPgammaT_or_NPAT_for_membrane_with_CHARMM_forcefield Jerome Henin (Sun Nov 11 2007 - 14:40:16 CST)
Re: NPT_NPgammaT_or_NPAT_for_membrane_with_CHARMM_forcefield Himanshu Khandelia (Sun Nov 11 2007 - 05:04:33 CST)
Re: NPT_NPgammaT_or_NPAT_for_membrane_with_CHARMM_forcefield L. Michel Espinoza-Fonseca (Sat Nov 10 2007 - 19:29:31 CST)
Re: serine phosphorylation modeling L. Michel Espinoza-Fonseca (Sat Nov 10 2007 - 19:15:40 CST)
Re: NAMD Installation Problem Tom Joseph (Sat Nov 10 2007 - 08:42:12 CST)
serine phosphorylation modeling Wei Liu (Sat Nov 10 2007 - 11:22:36 CST)
Re: NPT_NPgammaT_or_NPAT_for_membrane_with_CHARMM_forcefield Richard Wood (Sat Nov 10 2007 - 07:43:09 CST)
Re: NPT_NPgammaT_or_NPAT_for_membrane_with_CHARMM_forcefield Himanshu Khandelia (Sat Nov 10 2007 - 02:20:47 CST)
NAMD Installation Problem Sanjay H A (Fri Nov 09 2007 - 20:11:17 CST)
Re: NPT_NPgammaT_or_NPAT_for_membrane_with_CHARMM_forcefield Richard Law (Fri Nov 09 2007 - 17:43:07 CST)
Re: NPT_NPgammaT_or_NPAT_for_membrane_with_CHARMM_forcefield Richard Wood (Fri Nov 09 2007 - 16:31:13 CST)
Re: NPT_NPgammaT_or_NPAT_for_membrane_with_CHARMM_forcefield Himanshu Khandelia (Fri Nov 09 2007 - 13:57:10 CST)
Re: saving the coordinates for huge trajectory file JC Gumbart (Fri Nov 09 2007 - 12:08:39 CST)
Re: NPT_NPgammaT_or_NPAT_for_membrane_with_CHARMM_forcefield JC Gumbart (Fri Nov 09 2007 - 12:05:54 CST)
NAMD Carbohydrate Simulations Niels Johan Christensen (Fri Nov 09 2007 - 06:39:10 CST)
about signal 11 received,exiting mashaojie163 (Fri Nov 09 2007 - 10:11:15 CST)
Re: ABF application Vlad Cojocaru (Fri Nov 09 2007 - 03:23:57 CST)
Question on SMD simulation in spheric water . cgji (Fri Nov 09 2007 - 02:46:03 CST)
(no subject) cgji (Fri Nov 09 2007 - 02:43:27 CST)
Re: Getting density of water.. Arun Krishnan (Fri Nov 09 2007 - 02:08:39 CST)
Getting density of water.. Arun Krishnan (Fri Nov 09 2007 - 01:24:36 CST)
[Fwd: Re: VMD/psfgen scripting: undefined variable] Victor Ovchinnikov (Fri Nov 09 2007 - 00:33:00 CST)
Re: VMD/psfgen scripting: undefined variable Jerome Henin (Thu Nov 08 2007 - 23:34:55 CST)
VMD/psfgen scripting: undefined variable Richard Baxter (Thu Nov 08 2007 - 22:30:12 CST)
Re: ABF application Jerome Henin (Thu Nov 08 2007 - 14:42:58 CST)
Re: vmd-l: merging two pdb files Neelanjana Sengupta (Thu Nov 08 2007 - 09:29:54 CST)
ABF application Vlad Cojocaru (Thu Nov 08 2007 - 08:28:23 CST)
NPT_NPgammaT_or_NPAT_for_membrane_with_CHARMM_forcefield Karol Kaszuba (Thu Nov 08 2007 - 06:00:33 CST)
saving the coordinates for huge trajectory file ramya narasimhan (Tue Nov 06 2007 - 23:19:50 CST)
Re: NAMD on Abe Gianluca Interlandi (Tue Nov 06 2007 - 21:54:46 CST)
Re: problem with NAMD RNA run Samuel Coulbourn Flores (Tue Nov 06 2007 - 21:36:49 CST)
Re: problem with NAMD RNA run Samuel Coulbourn Flores (Tue Nov 06 2007 - 20:53:51 CST)
NAMD on Abe Richard Swenson (Tue Nov 06 2007 - 19:17:38 CST)
Re: problem with NAMD RNA run Peter Freddolino (Tue Nov 06 2007 - 18:38:09 CST)
Re: problem with NAMD RNA run Samuel Coulbourn Flores (Tue Nov 06 2007 - 18:31:04 CST)
NAMD on Abe Richard Swenson (Tue Nov 06 2007 - 15:54:05 CST)
Re: Free energy perturbation of a double mutant Chris Chipot (Tue Nov 06 2007 - 17:03:51 CST)
Free energy perturbation of a double mutant jia (Tue Nov 06 2007 - 16:37:35 CST)
problem with NAMD RNA run Samuel Coulbourn Flores (Tue Nov 06 2007 - 15:11:04 CST)
Periodic boundary conditionds-Surface Energy Rahul Bhowmik (Tue Nov 06 2007 - 12:46:06 CST)
Strange termination-possible load ballancing issues Richard Swenson (Tue Nov 06 2007 - 10:13:02 CST)
(no subject) Demet Akten (Tue Nov 06 2007 - 03:26:52 CST)
to heat up the system lily jin (Mon Nov 05 2007 - 13:51:39 CST)
Re: compiling namd2 Tom Joseph (Mon Nov 05 2007 - 13:18:25 CST)
Re: compiling namd2 Sabuj Pattanayek (Mon Nov 05 2007 - 13:09:01 CST)
compiling namd2 hazards_at_musc.edu (Mon Nov 05 2007 - 10:18:22 CST)
Re: Re: Simulation in water sphere meet with a FATAL ERROR about Bad global exclusion count Yinglong Miao (Mon Nov 05 2007 - 08:09:45 CST)
The experimental data of POPE? Ming (Mon Nov 05 2007 - 02:55:43 CST)
Area per lipid. Ming (Mon Nov 05 2007 - 01:02:53 CST)
Re: Re: Simulation in water sphere meet with a FATAL ERROR about Bad global exclusion count Shulin Zhuang (Sun Nov 04 2007 - 22:05:29 CST)
Re: Simulation in water sphere meet with a FATAL ERROR about Bad global exclusion count Shulin Zhuang (Sun Nov 04 2007 - 21:25:45 CST)
Simulation in water sphere meet with a FATAL ERROR about Bad global exclusion count Shulin Zhuang (Sun Nov 04 2007 - 21:01:45 CST)
Re: forces on atom Victor Ovchinnikov (Sun Nov 04 2007 - 11:08:57 CST)
forces on atom Pijush Ghosh (Sun Nov 04 2007 - 09:22:00 CST)
Re: charmrun: execve failed to start; intel dual core Redhat Richard Baxter (Sat Nov 03 2007 - 23:24:50 CDT)
Re: length of an ABF simulation Chris Chipot (Sat Nov 03 2007 - 10:44:25 CDT)
Re: Potential function (force field) in NAMD Rahul Bhowmik (Sat Nov 03 2007 - 10:43:57 CDT)
Re: length of an ABF simulation Jerome Henin (Sat Nov 03 2007 - 10:37:48 CDT)
length of an ABF simulation Vlad Cojocaru (Sat Nov 03 2007 - 09:41:43 CDT)
Potential function (force field) in NAMD rahul.bhowmik_at_ndsu.edu (Fri Nov 02 2007 - 18:49:27 CDT)
charmrun: execve failed to start; intel dual core Redhat Richard Baxter (Thu Nov 01 2007 - 16:42:55 CDT)
Re: residue_rmsd.tcl question Ilya Chorny (Fri Nov 02 2007 - 10:57:19 CDT)
TMD in NAMD: cannot reach target lily jin (Fri Nov 02 2007 - 10:43:55 CDT)
charmrun: execve failed to start; intel dual core Redhat Richard Baxter (Fri Nov 02 2007 - 10:42:30 CDT)
residue_rmsd.tcl question Christian Blouin (Fri Nov 02 2007 - 08:12:51 CDT)
How to evaluate the area per lipid and thickness of a lipid bilayer? Ming (Thu Nov 01 2007 - 22:24:03 CDT)
POPE/protein simuliation. Ming (Thu Nov 01 2007 - 20:06:37 CDT)
Will reducing the cell basis vector in X and Y force my lipids to pack Ilya Chorny (Thu Nov 01 2007 - 18:59:42 CDT)
Re: force constant matrix JC Gumbart (Thu Nov 01 2007 - 16:03:21 CDT)
force constant matrix Ahlam Al-Rawi (Thu Nov 01 2007 - 08:29:23 CDT)
Membrnae (POPE)/protein simuliation. ÁõÃ÷ (Thu Nov 01 2007 - 07:44:10 CDT)
Re: TMD in NAMD: cannot reach target Thomas Gaillard (Thu Nov 01 2007 - 14:00:17 CDT)
TMD in NAMD: cannot reach target lily jin (Thu Nov 01 2007 - 13:13:23 CDT)
FW: Controlling the area per lipid Richard Swenson (Thu Nov 01 2007 - 11:53:28 CDT)
Re: Controlling the area per lipid Ilya Chorny (Thu Nov 01 2007 - 10:32:50 CDT)
heat flux when using langevin dynamics Philipp Schön (Thu Nov 01 2007 - 09:12:56 CDT)
Re: Controlling the area per lipid Himanshu Khandelia (Thu Nov 01 2007 - 06:20:10 CDT)
Re: Controlling the area per lipid Ilya Chorny (Thu Nov 01 2007 - 01:45:31 CDT)
Re: Controlling the area per lipid JC Gumbart (Thu Nov 01 2007 - 00:56:27 CDT)
Light dummy atoms (source code question) Tom Joseph (Wed Oct 31 2007 - 20:58:30 CDT)
Controlling the area per lipid Ilya Chorny (Wed Oct 31 2007 - 20:23:44 CDT)
timestep in TMD lily jin (Wed Oct 31 2007 - 14:02:58 CDT)
scripting in namd Adam Fraser (Wed Oct 31 2007 - 07:39:36 CDT)
How can I get parameters of unknown residues dongsheng lei (Wed Oct 31 2007 - 04:26:16 CDT)
Accepted temperature and pressure oscillation cong chen (Wed Oct 31 2007 - 03:14:55 CDT)
Re: NAMD to CHARMM unit cell information in DCD Victor Ovchinnikov (Tue Oct 30 2007 - 18:10:38 CDT)
Re: NAMD to CHARMM unit cell information in DCD Gianluca Interlandi (Tue Oct 30 2007 - 16:14:02 CDT)
NAMD to CHARMM unit cell information in DCD François Marchand (Tue Oct 30 2007 - 14:29:41 CDT)
Re: NAMDEnergy lily jin (Tue Oct 30 2007 - 12:34:43 CDT)
Re: NAMDEnergy Peter Freddolino (Tue Oct 30 2007 - 12:20:16 CDT)
NAMDEnergy lily jin (Tue Oct 30 2007 - 12:00:57 CDT)
Replica exchange error message Dirar Homouz (Mon Oct 29 2007 - 19:05:24 CDT)
Re: apply force along an internally defined direction Chris Chipot (Mon Oct 29 2007 - 13:22:52 CDT)
Re: apply force along an internally defined direction Vlad Cojocaru (Mon Oct 29 2007 - 12:59:00 CDT)
Re: apply force along an internally defined direction Jerome Henin (Mon Oct 29 2007 - 11:20:29 CDT)
Re: NAMD cg configuration file Peter Freddolino (Mon Oct 29 2007 - 07:36:23 CDT)
apply force along an internally defined direction Vlad Cojocaru (Mon Oct 29 2007 - 07:24:02 CDT)
looking for paramter snoze pa (Sun Oct 28 2007 - 20:04:31 CDT)
NAMD cg configuration file Alexe Bojovschi (Sun Oct 28 2007 - 19:02:44 CDT)
Building Charm .. mpi-linux-amd64-ifort/tmp/traceCore.h .. and .. mpi-linux-amd64-ifort/tmp/MsgPacker.h Graham Jenkins (Sat Oct 27 2007 - 15:56:34 CDT)
Re: simulation_of_big_membrane Karol Kaszuba (Sat Oct 27 2007 - 07:03:08 CDT)
RE: how to restart FEP jia (Fri Oct 26 2007 - 15:29:12 CDT)
Re: how to restart FEP Jerome Henin (Fri Oct 26 2007 - 14:32:38 CDT)
how to restart FEP jia (Fri Oct 26 2007 - 13:50:44 CDT)
Re: simulation_of_big_membrane Ilya Chorny (Fri Oct 26 2007 - 10:38:34 CDT)
Re: restart a NAMD simulation after coordinate transformation in VMD (solution) Vlad Cojocaru (Fri Oct 26 2007 - 09:10:10 CDT)
Re: restart a NAMD simulation after coordinate transformation in VMD Vlad Cojocaru (Fri Oct 26 2007 - 07:03:24 CDT)
simulation_of_big_membrane Karol Kaszuba (Fri Oct 26 2007 - 04:57:35 CDT)
restart a NAMD simulation after coordinate transformation in VMD Vlad Cojocaru (Fri Oct 26 2007 - 04:47:11 CDT)
Re: Help with TCl script Ilya Chorny (Fri Oct 26 2007 - 00:38:05 CDT)
Help with TCl script Ilya Chorny (Thu Oct 25 2007 - 23:44:49 CDT)
NCSA Abe versus TACC Lonestar Gianluca Interlandi (Thu Oct 25 2007 - 19:47:48 CDT)
Re: printing and global variables within TclBC script Leandro Martínez (Thu Oct 25 2007 - 02:11:09 CDT)
Re: printing and global variables within TclBC script Peter Freddolino (Wed Oct 24 2007 - 21:44:39 CDT)
Re: printing and global variables within TclBC script Leandro Martínez (Wed Oct 24 2007 - 02:55:55 CDT)
Re: Re: Peter Freddolino (Tue Oct 23 2007 - 18:20:52 CDT)
Re: Re: Peter Freddolino (Tue Oct 23 2007 - 18:18:22 CDT)
Re: Re: David Hardy (Tue Oct 23 2007 - 18:09:50 CDT)
Re: Peter Freddolino (Tue Oct 23 2007 - 14:54:38 CDT)
Re: printing and global variables within TclBC script Peter Freddolino (Tue Oct 23 2007 - 14:50:03 CDT)
Re: abf - zeros as output Jerome Henin (Tue Oct 23 2007 - 13:32:14 CDT)
abf - zeros as output Per Jr. Greisen (Tue Oct 23 2007 - 12:49:45 CDT)
Re: Applying conformational constraints during simulation poker_at_physics.usyd.edu.au (Tue Oct 23 2007 - 08:51:25 CDT)
RE: Itanium_and_CMAP Karol Kaszuba (Tue Oct 23 2007 - 06:15:24 CDT)
printing and global variables within TclBC script Leandro Martínez (Tue Oct 23 2007 - 01:55:23 CDT)
Errors during equilibration: segmentation fault and bad global exclusion count Ambrish (Tue Oct 23 2007 - 01:45:05 CDT)
(no subject) ramya narasimhan (Tue Oct 23 2007 - 00:45:16 CDT)
Re: Applying conformational constraints during simulation Victor Ovchinnikov (Mon Oct 22 2007 - 23:21:09 CDT)
Applying conformational constraints during simulation poker_at_physics.usyd.edu.au (Mon Oct 22 2007 - 22:08:46 CDT)
Re: ABF - stretching deca-alanine Jerome Henin (Mon Oct 22 2007 - 09:22:40 CDT)
RE: Itanium_and_CMAP JC Gumbart (Mon Oct 22 2007 - 09:13:08 CDT)
Re: ABF - stretching deca-alanine Jerome Henin (Mon Oct 22 2007 - 08:21:23 CDT)
ABF - stretching deca-alanine Per Jr. Greisen (Mon Oct 22 2007 - 06:34:25 CDT)
RE: Itanium_and_CMAP Karol Kaszuba (Mon Oct 22 2007 - 06:16:07 CDT)
Re: How to get around with "atoms moving too fast" yi wang (Fri Oct 19 2007 - 22:34:32 CDT)
How to get around with "atoms moving too fast" Yinglong Miao (Fri Oct 19 2007 - 11:45:50 CDT)
RE: Itanium_and_CMAP JC Gumbart (Fri Oct 19 2007 - 10:31:30 CDT)
Itanium_and_CMAP Karol Kaszuba (Fri Oct 19 2007 - 05:09:47 CDT)
Re: how to apply different damping coefficients simultaneously to different atoms in the same system. L. Michel Espinoza-Fonseca (Fri Oct 19 2007 - 00:09:06 CDT)
Re: how to apply different damping coefficients simultaneously to different atoms in the same system. Wang, Boyang (Thu Oct 18 2007 - 22:44:09 CDT)
Re: how to apply different damping coefficients simultaneously to different atoms in the same system. Jerome Henin (Thu Oct 18 2007 - 22:03:45 CDT)
how to apply different damping coefficients simultaneously to different atoms in the same system. Wang, Boyang (Thu Oct 18 2007 - 20:25:36 CDT)
Interrupted system call claudia (Thu Oct 18 2007 - 08:25:22 CDT)
pmf segname for amber ff. MAIN? George Madalin Giambasu (Thu Oct 18 2007 - 00:51:36 CDT)
For slowly heating, temperature reassignment or Temperature coupling Shulin Zhuang (Tue Oct 16 2007 - 14:41:41 CDT)
Re: parameterizing a beta aminocyclohexanecarboxylic acid Richard Wood (Tue Oct 16 2007 - 12:47:51 CDT)
Re: parameterizing a beta aminocyclohexanecarboxylic acid Karol Kaszuba (Tue Oct 16 2007 - 09:46:31 CDT)
parameterizing a beta aminocyclohexanecarboxylic acid regafan_at_usc.es (Tue Oct 16 2007 - 05:30:36 CDT)
Re: Drift in performance Peter Freddolino (Mon Oct 15 2007 - 14:07:49 CDT)
Drift in performance Jerome Henin (Mon Oct 15 2007 - 12:02:32 CDT)
Re: Membrane Protein Simulation Problems Peter Freddolino (Sat Oct 13 2007 - 15:29:19 CDT)
Re: Converting a PSF file from one forcefield top another Ilya Chorny (Sat Oct 13 2007 - 15:01:42 CDT)
Re: Converting a PSF file from one forcefield top another Christopher Harrison (Sat Oct 13 2007 - 14:55:34 CDT)
Re: Converting a PSF file from one forcefield top another Christopher Harrison (Sat Oct 13 2007 - 14:43:35 CDT)
Re: Membrane Protein Simulation Problems Marcos Sotomayor (Sat Oct 13 2007 - 13:51:01 CDT)
Converting a PSF file from one forcefield top another Ilya Chorny (Sat Oct 13 2007 - 13:14:30 CDT)
Re: Membrane Protein Simulation Problems Ilya Chorny (Sat Oct 13 2007 - 11:57:56 CDT)
Re: Membrane Protein Simulation Problems Marcos Sotomayor (Sat Oct 13 2007 - 11:53:03 CDT)
Re: Membrane Protein Simulation Problems Ilya Chorny (Sat Oct 13 2007 - 11:46:26 CDT)
Re: Membrane Protein Simulation Problems L. Michel Espinoza-Fonseca (Sat Oct 13 2007 - 11:42:45 CDT)
Re: Membrane Protein Simulation Problems L. Michel Espinoza-Fonseca (Sat Oct 13 2007 - 11:41:19 CDT)
Re: Membrane Protein Simulation Problems Ilya Chorny (Sat Oct 13 2007 - 11:40:35 CDT)
Re: Membrane Protein Simulation Problems Ilya Chorny (Sat Oct 13 2007 - 11:37:09 CDT)
Re: Membrane Protein Simulation Problems Ilya Chorny (Sat Oct 13 2007 - 11:26:57 CDT)
Scaling the Tiny benchmark Dow_Hurst (Sat Oct 13 2007 - 11:20:16 CDT)
Re: Membrane Protein Simulation Problems Marcos Sotomayor (Sat Oct 13 2007 - 11:17:49 CDT)
Re: Membrane Protein Simulation Problems L. Michel Espinoza-Fonseca (Sat Oct 13 2007 - 11:01:02 CDT)
Re: Membrane Protein Simulation Problems Marcos Sotomayor (Sat Oct 13 2007 - 10:36:06 CDT)
Re: Membrane Protein Simulation Problems Ilya Chorny (Sat Oct 13 2007 - 10:13:56 CDT)
Re: Membrane Protein Simulation Problems Marcos Sotomayor (Sat Oct 13 2007 - 10:07:59 CDT)
Re: Membrane Protein Simulation Problems Richard Law (Sat Oct 13 2007 - 03:05:02 CDT)
Re: vmd-l: Small molecules Christopher Harrison (Fri Oct 12 2007 - 23:41:23 CDT)
Membrane Protein Simulation Problems Ilya Chorny (Fri Oct 12 2007 - 22:31:28 CDT)
Re: Large Benchmarks Richard Henchman (Fri Oct 12 2007 - 14:36:34 CDT)
2-D periodic boundary condition Rahul Bhownik (Fri Oct 12 2007 - 13:00:09 CDT)
Re: Large Benchmarks Richard Wood (Fri Oct 12 2007 - 08:52:44 CDT)
Re: Large Benchmarks Richard Wood (Thu Oct 11 2007 - 20:03:22 CDT)
Re: Large Benchmarks Philip Peartree (Thu Oct 11 2007 - 18:09:13 CDT)
Re: Large Benchmarks Philip Peartree (Thu Oct 11 2007 - 16:03:34 CDT)
Re: Large Benchmarks Richard Law (Thu Oct 11 2007 - 15:00:15 CDT)
Large Benchmarks Philip Peartree (Thu Oct 11 2007 - 13:50:39 CDT)
Multiple constraint file Pijush Ghosh (Wed Oct 10 2007 - 17:13:47 CDT)
lock / unlock threads paul.dalhaimer_at_yale.edu (Wed Oct 10 2007 - 13:27:47 CDT)
Re: Howto lengthen a collagen strand (which tool to use) Peter Freddolino (Wed Oct 10 2007 - 10:09:52 CDT)
Re: Howto lengthen a collagen strand (which tool to use) QMarcus_R=F6lz=22?= (Wed Oct 10 2007 - 08:08:17 CDT)
Re: Molecule drifts and high average RMSD per residue Luis Gracia (Tue Oct 09 2007 - 15:15:08 CDT)
Re: Molecule drifts and high average RMSD per residue Ambrish (Tue Oct 09 2007 - 15:53:31 CDT)
.xsc file and .restart.xsc file lily jin (Tue Oct 09 2007 - 12:06:22 CDT)
Re: Molecule drifts and high average RMSD per residue Peter Freddolino (Tue Oct 09 2007 - 09:58:06 CDT)
Re: Molecule drifts and high average RMSD per residue Ilya Chorny (Tue Oct 09 2007 - 09:53:50 CDT)
Re: vmd-l: Re: Molecule drifts and high average RMSD per residue Peter Freddolino (Tue Oct 09 2007 - 09:51:07 CDT)
Re: Howto lengthen a collagen strand (which tool to use) Peter Freddolino (Tue Oct 09 2007 - 09:47:28 CDT)
Re: Molecule drifts and high average RMSD per residue Peter Freddolino (Tue Oct 09 2007 - 09:45:23 CDT)
Howto lengthen a collagen strand (which tool to use) QMarcus_R=F6lz=22?= (Tue Oct 09 2007 - 07:23:03 CDT)
ptraj Ambrish (Mon Oct 08 2007 - 18:30:59 CDT)
Re: Molecule drifts and high average RMSD per residue Richard Wood (Mon Oct 08 2007 - 18:01:18 CDT)
Re: Molecule drifts and high average RMSD per residue Ilya Chorny (Mon Oct 08 2007 - 16:17:33 CDT)
Re: Molecule drifts and high average RMSD per residue E. Prabhu Raman (Mon Oct 08 2007 - 14:57:00 CDT)
Molecule drifts and high average RMSD per residue Ambrish (Mon Oct 08 2007 - 11:02:49 CDT)
Re: Charmm 22 vs Charmm 27 Joshua D. Moore (Sat Oct 06 2007 - 11:55:47 CDT)
Re: Charmm 22 vs Charmm 27 Richard Wood (Sat Oct 06 2007 - 11:24:47 CDT)
Re: Charmm 22 vs Charmm 27 Ilya Chorny (Sat Oct 06 2007 - 10:30:25 CDT)
Re: Charmm 22 vs Charmm 27 Richard Wood (Fri Oct 05 2007 - 17:10:54 CDT)
Re: Charmm 22 vs Charmm 27 Thomas Gaillard (Fri Oct 05 2007 - 16:07:47 CDT)
Re: Charmm 22 vs Charmm 27 Ilya Chorny (Fri Oct 05 2007 - 15:02:51 CDT)
Charmm 22 vs Charmm 27 Ilya Chorny (Fri Oct 05 2007 - 14:13:33 CDT)
Re: all atom simulations with explicit water molecules and langevin thermostat Margaret S. Cheung (Fri Oct 05 2007 - 09:54:20 CDT)
C1 splitting documentation Floris Buelens (Fri Oct 05 2007 - 08:10:21 CDT)
Re: all atom simulations with explicit water molecules and langevin thermostat Jojart Balazs (Fri Oct 05 2007 - 05:41:14 CDT)
Re: all atom simulations with explicit water molecules and langevinthermostat wzhuang (Thu Oct 04 2007 - 20:16:04 CDT)
all atom simulations with explicit water molecules and langevin thermostat Margaret S. Cheung (Thu Oct 04 2007 - 16:28:14 CDT)
Re: Initial and final state fix MD Gungor Ozer (Thu Oct 04 2007 - 16:57:01 CDT)
Re: Initial and final state fix MD JC Gumbart (Thu Oct 04 2007 - 16:56:58 CDT)
Initial and final state fix MD Ugur Akgun (Thu Oct 04 2007 - 16:21:25 CDT)
Re: solvating long protein Leonardo Trabuco (Wed Oct 03 2007 - 14:04:25 CDT)
solvating long protein Dhiraj Srivastava (Wed Oct 03 2007 - 13:54:47 CDT)
Re: Problems with Mutator1.1, mutations and FEP Jerome Henin (Tue Oct 02 2007 - 20:16:46 CDT)
Re: Problems with Mutator1.1, mutations and FEP Chris Chipot (Tue Oct 02 2007 - 14:42:38 CDT)
Re: Problems with Mutator1.1, mutations and FEP SvenBlumenschein_at_gmx.de (Tue Oct 02 2007 - 08:51:30 CDT)
Free energy Calculations alex digenova bravo (Mon Oct 01 2007 - 17:59:34 CDT)
Question regarding SETTLE (RigidWater) Siddharth (Mon Oct 01 2007 - 17:02:11 CDT)
Re: extracting interaction energies Peter Freddolino (Mon Oct 01 2007 - 15:38:57 CDT)
extracting interaction energies Narender Singh Maan (Mon Oct 01 2007 - 15:20:36 CDT)
Re: Problems with Mutator1.1, mutations and FEP Jerome Henin (Mon Oct 01 2007 - 14:47:53 CDT)
Re: Problems with Mutator1.1, mutations and FEP Chris Chipot (Mon Oct 01 2007 - 13:57:58 CDT)
Problems with Mutator1.1, mutations and FEP SvenBlumenschein_at_gmx.de (Mon Oct 01 2007 - 08:58:06 CDT)
Re: ABF parameters Jerome Henin (Mon Oct 01 2007 - 10:53:41 CDT)
ABF parameters Subramanian Vaitheeswaran (Mon Oct 01 2007 - 08:45:12 CDT)
Binding free energy by LIE Narender Singh Maan (Fri Sep 28 2007 - 14:21:21 CDT)
Globus-WS Submission of a NAMD Job .. Graham Jenkins (Fri Sep 28 2007 - 02:19:28 CDT)
restraining backbone atoms san_namd roy (Fri Sep 28 2007 - 00:59:09 CDT)
Re: for the isntall and run NAMD soft on 8 core (dual quad-core Xeons) system Sabuj Pattanayek (Thu Sep 27 2007 - 23:47:21 CDT)
Re: for the isntall and run NAMD soft on 8 core (dual quad-core Xeons) system Victor Ovchinnikov (Thu Sep 27 2007 - 21:28:46 CDT)
Re: for the isntall and run NAMD soft on 8 core (dual quad-core Xeons) system Ilya Chorny (Thu Sep 27 2007 - 20:48:10 CDT)
Re: for the isntall and run NAMD soft on 8 core (dual quad-core Xeons) system Victor Ovchinnikov (Thu Sep 27 2007 - 19:11:27 CDT)
Re: Determining Transition State from an Unfolding Simulation Eduardo Tejera (Thu Sep 27 2007 - 17:27:28 CDT)
Re: Determining Transition State from an Unfolding Simulation Richard Wood (Thu Sep 27 2007 - 16:34:20 CDT)
Re: Determining Transition State from an Unfolding Simulation Arun Krishnan (Thu Sep 27 2007 - 16:17:15 CDT)
Re: Determining Transition State from an Unfolding Simulation Christopher Harrison (Thu Sep 27 2007 - 15:43:54 CDT)
Re: Determining Transition State from an Unfolding Simulation Eduardo Tejera (Thu Sep 27 2007 - 15:09:41 CDT)
Re: Determining Transition State from an Unfolding Simulation Richard Wood (Thu Sep 27 2007 - 14:28:49 CDT)
Re: Determining Transition State from an Unfolding Simulation Richard Wood (Thu Sep 27 2007 - 13:24:13 CDT)
Re: Determining Transition State from an Unfolding Simulation Neema Salimi (Thu Sep 27 2007 - 13:22:08 CDT)
Re: Determining Transition State from an Unfolding Simulation Thomas Gaillard (Thu Sep 27 2007 - 12:29:08 CDT)
Re: Determining Transition State from an Unfolding Simulation Christopher Harrison (Thu Sep 27 2007 - 11:45:16 CDT)
Re: Determining Transition State from an Unfolding Simulation Richard Wood (Thu Sep 27 2007 - 11:22:57 CDT)
Re: restarting an AMBER simulation (truncated octahedron PBC) in NAMD fails Vlad Cojocaru (Thu Sep 27 2007 - 10:08:51 CDT)
restarting an AMBER simulation (truncated octahedron PBC) in NAMD fails Vlad Cojocaru (Thu Sep 27 2007 - 08:45:34 CDT)
Re: Determining Transition State from an Unfolding Simulation Richard Wood (Thu Sep 27 2007 - 07:34:06 CDT)
Re: Determining Transition State from an Unfolding Simulation Richard Wood (Thu Sep 27 2007 - 07:24:20 CDT)
Determining Transition State from an Unfolding Simulation paco ty (Thu Sep 27 2007 - 04:35:14 CDT)
Re: Determining Transition State from an Unfolding Simulation Peter Freddolino (Wed Sep 26 2007 - 23:12:43 CDT)
Re: for the isntall and run NAMD soft on 8 core (dual quad-core Xeons) system Ilya Chorny (Wed Sep 26 2007 - 18:20:36 CDT)
Re: Determining Transition State from an Unfolding Simulation Richard Wood (Wed Sep 26 2007 - 17:30:51 CDT)
for the isntall and run NAMD soft on 8 core (dual quad-core Xeons) system Shulin Zhuang (Wed Sep 26 2007 - 17:08:20 CDT)
Re: Determining Transition State from an Unfolding Simulation Richard Wood (Wed Sep 26 2007 - 15:30:58 CDT)
Re: Determining Transition State from an Unfolding Simulation E. Prabhu Raman (Wed Sep 26 2007 - 12:24:03 CDT)
Re: Determining Transition State from an Unfolding Simulation Richard Wood (Wed Sep 26 2007 - 11:13:40 CDT)
Re: Meaning of lines in "run" part of log file. David Hardy (Wed Sep 26 2007 - 10:16:42 CDT)
Re: Determining Transition State from an Unfolding Simulation Neelanjana Sengupta (Wed Sep 26 2007 - 10:44:58 CDT)
Re: Meaning of lines in "run" part of log file. Subramanian Vaitheeswaran (Wed Sep 26 2007 - 07:04:26 CDT)
Re: Meaning of lines in "run" part of log file. Audrey Salazar (Wed Sep 26 2007 - 09:55:42 CDT)
Fwd: Determining Transition State from an Unfolding Simulation Arun Krishnan (Wed Sep 26 2007 - 08:19:13 CDT)
Re: Determining Transition State from an Unfolding Simulation E. Prabhu Raman (Wed Sep 26 2007 - 08:09:07 CDT)
Re: Meaning of lines in "run" part of log file. Arun Krishnan (Wed Sep 26 2007 - 00:38:00 CDT)
Re: Meaning of lines in "run" part of log file. Brian Bennion (Wed Sep 26 2007 - 00:01:53 CDT)
Re: Determining Transition State from an Unfolding Simulation Arun Krishnan (Tue Sep 25 2007 - 23:56:52 CDT)
Re: Meaning of lines in "run" part of log file. Richard Wood (Tue Sep 25 2007 - 22:58:19 CDT)
Re: Meaning of lines in "run" part of log file. Audrey Salazar (Tue Sep 25 2007 - 22:24:48 CDT)
Meaning of lines in "run" part of log file. Audrey Salazar (Tue Sep 25 2007 - 20:08:31 CDT)
Re: Determining Transition State from an Unfolding Simulation E. Prabhu Raman (Sun Sep 23 2007 - 21:43:36 CDT)
Re: Determining Transition State from an Unfolding Simulation Neelanjana Sengupta (Sun Sep 23 2007 - 18:33:44 CDT)
Re: Determining Transition State from an Unfolding Simulation Neelanjana Sengupta (Sun Sep 23 2007 - 18:32:34 CDT)
Determining Transition State from an Unfolding Simulation Arun Krishnan (Sun Sep 23 2007 - 15:57:17 CDT)
Re: Performance Problems on Linux Cluster / Bad Scaling Dow_Hurst (Sun Sep 23 2007 - 08:39:40 CDT)
Re: NAMD on dual quad-core Xeon's with Infiniband backbone Philip Peartree (Sun Sep 23 2007 - 06:24:32 CDT)
Re: NAMD on dual quad-core Xeon's with Infiniband backbone Dow_Hurst (Sat Sep 22 2007 - 18:28:17 CDT)
NAMD on dual quad-core Xeon's with Infiniband backbone Carsten Olbrich (Sat Sep 22 2007 - 06:44:29 CDT)
NAMD on dual quad-core Xeon's with Infiniband backbone Stephen M. Dutz (Fri Sep 21 2007 - 14:02:21 CDT)
Re: Temperature dependent unfolding.. Eduardo Tejera (Fri Sep 21 2007 - 06:15:42 CDT)
Re: Temperature dependent unfolding.. Arun Krishnan (Thu Sep 20 2007 - 20:24:52 CDT)
Re: Switching Function Jason O'Young (Thu Sep 20 2007 - 14:41:00 CDT)
Re: Switching Function David Hardy (Thu Sep 20 2007 - 13:39:45 CDT)
Switching Function Jason O'Young (Thu Sep 20 2007 - 13:00:10 CDT)
effects of box size Narender Singh Maan (Thu Sep 20 2007 - 10:31:02 CDT)
Re: How to restart a simulation Audrey Salazar (Thu Sep 20 2007 - 10:28:06 CDT)
How to restart a simulation Audrey Salazar (Thu Sep 20 2007 - 10:25:10 CDT)
FATAL ERROR: called "save_callback" with too many arguments when running replica exchange Ana Vila Verde (Wed Sep 19 2007 - 11:23:50 CDT)
Re: Charmm to Namd!! Himanshu Khandelia (Wed Sep 19 2007 - 10:39:23 CDT)
psfgen: merging of 2 dna chains Carsten Olbrich (Wed Sep 19 2007 - 08:19:09 CDT)
Re: ABF question Chris Chipot (Wed Sep 19 2007 - 08:17:12 CDT)
Re: Charmm to Namd!! Philip Peartree (Wed Sep 19 2007 - 07:51:59 CDT)
ABF question Matthew Davies (Wed Sep 19 2007 - 06:45:05 CDT)
Charmm to Namd!! priyanka srivastava (Wed Sep 19 2007 - 05:49:22 CDT)
namdenergy strange behaviour !!! paco ty (Wed Sep 19 2007 - 03:20:44 CDT)
running_NAMD_on_ALPHA_workstation Karol Kaszuba (Tue Sep 18 2007 - 05:43:58 CDT)
Re: Performance Problems on Linux Cluster / Bad Scaling Philip Peartree (Tue Sep 18 2007 - 10:34:22 CDT)
Performance Problems on Linux Cluster / Bad Scaling QMarcus_R=F6lz=22?= (Tue Sep 18 2007 - 08:17:15 CDT)
Charmrun and ssh problem Andrea Cristiani (Tue Sep 18 2007 - 04:50:23 CDT)
Re: Question for 2D periodic boundary condition JC Gumbart (Mon Sep 17 2007 - 17:41:03 CDT)
Re: Charmm format topology and parameter files for FAD Richard Wood (Mon Sep 17 2007 - 17:30:59 CDT)
Re: NAD topology and parameter file Dhiraj Srivastava (Mon Sep 17 2007 - 16:50:29 CDT)
NAD topology and parameter file Dhiraj Srivastava (Mon Sep 17 2007 - 16:30:20 CDT)
TOTAL energy increase Dirar Homouz (Mon Sep 17 2007 - 15:26:10 CDT)
Charmm format topology and parameter files for FAD mon_sharma_at_research.iiit.ac.in (Mon Sep 17 2007 - 14:17:26 CDT)
Re: namdenergy strange behaviour !!! Peter Freddolino (Mon Sep 17 2007 - 11:23:38 CDT)
Re: namdenergy strange behaviour !!! Peter Freddolino (Mon Sep 17 2007 - 11:23:04 CDT)
Re: namdenergy strange behaviour !!! Brian Bennion (Mon Sep 17 2007 - 11:15:18 CDT)
namdenergy strange behaviour !!! paco ty (Mon Sep 17 2007 - 09:49:33 CDT)
Question for 2D periodic boundary condition Chin_Wei (Mon Sep 17 2007 - 09:18:13 CDT)
Re: OPLS force field in namd Joshua D. Moore (Sat Sep 15 2007 - 02:48:56 CDT)
OPLS force field in namd Adam Fraser (Fri Sep 14 2007 - 17:11:15 CDT)
Re: protonation of some histidine residues Richard Law (Fri Sep 14 2007 - 17:08:00 CDT)
Re: protonation of some histidine residues L. Michel Espinoza-Fonseca (Fri Sep 14 2007 - 16:56:03 CDT)
Re: protonation of some histidine residues L. Michel Espinoza-Fonseca (Fri Sep 14 2007 - 16:53:10 CDT)
protonation of some histidine residues mdametto_at_mail.usf.edu (Fri Sep 14 2007 - 16:05:53 CDT)
Re: the size of membrane? Richard Law (Fri Sep 14 2007 - 16:00:08 CDT)
the size of membrane? youbin tu (Fri Sep 14 2007 - 14:02:43 CDT)
Running Error: The periodicity of dihedral #2 is zero Jianhui Tian (Fri Sep 14 2007 - 11:14:36 CDT)
Re: Simulation of large bilayer crashes with "ERROR: Stray PME grid charges detected" Peter Freddolino (Fri Sep 14 2007 - 07:19:38 CDT)
Re: Simulation of large bilayer crashes with "ERROR: Stray PME grid charges detected" Philip Peartree (Fri Sep 14 2007 - 04:13:04 CDT)
Re: Simulation of large bilayer crashes with "ERROR: Stray PME grid charges detected" Peter Freddolino (Thu Sep 13 2007 - 20:40:46 CDT)
Re: Simulation of large bilayer crashes with "ERROR: Stray PME grid charges detected" maria goranovic (Thu Sep 13 2007 - 08:39:46 CDT)
Re: Simulation of large bilayer crashes with "ERROR: Stray PME grid charges detected" Philip Peartree (Thu Sep 13 2007 - 11:13:44 CDT)
Re: Simulation of large bilayer crashes with "ERROR: Stray PME grid charges detected" Richard Wood (Thu Sep 13 2007 - 08:00:09 CDT)
Re: Simulation of large bilayer crashes with "ERROR: Stray PME grid charges detected" Philip Peartree (Thu Sep 13 2007 - 07:24:42 CDT)
Simulation of large bilayer crashes with "ERROR: Stray PME grid charges detected" maria goranovic (Thu Sep 13 2007 - 05:01:18 CDT)
------------- Processor 0 Exiting: Called CmiAbort ------------ jestin mandumpal (Thu Sep 13 2007 - 02:57:50 CDT)
Re: NAMD run Arun Krishnan (Wed Sep 12 2007 - 19:48:27 CDT)
NAMD run Ahlam Al-Rawi (Mon Sep 10 2007 - 10:32:56 CDT)
Re: Switching PSF files during a run. Joshua D. Moore (Tue Sep 11 2007 - 03:18:35 CDT)
PMF of SMD using CHARMM generated trajectories Rathinavelan, Thenmalarchelvi (Mon Sep 10 2007 - 12:31:56 CDT)
Re: Code question: Partitioning the patch contents into water and non-water Floris Buelens (Mon Sep 10 2007 - 11:00:13 CDT)
Re: The charged states of histidines in green fluorescent protein. Floris Buelens (Mon Sep 10 2007 - 09:50:46 CDT)
STRIDE Algorithm Yu Liu (Mon Sep 10 2007 - 09:22:09 CDT)
Re: Potentials of mean force using ABF Subramanian Vaitheeswaran (Mon Sep 10 2007 - 08:47:27 CDT)
Re: The charged states of histidines in green fluorescent protein. Peter Freddolino (Sun Sep 09 2007 - 21:29:51 CDT)
The charged states of histidines in green fluorescent protein. Wang, Boyang (Sun Sep 09 2007 - 19:47:33 CDT)
Re: RATTLE failure Philip Peartree (Sun Sep 09 2007 - 13:41:47 CDT)
Re: RATTLE failure Himanshu Khandelia (Sun Sep 09 2007 - 08:35:01 CDT)
Patch needed for tuple is missing Error with POPC bilayer maria goranovic (Sun Sep 09 2007 - 07:37:50 CDT)
How to load velocities during simulations. Wang, Boyang (Sat Sep 08 2007 - 19:56:55 CDT)
Re: Potentials of mean force using ABF Jerome Henin (Sat Sep 08 2007 - 18:09:28 CDT)
Potentials of mean force using ABF Subramanian Vaitheeswaran (Sat Sep 08 2007 - 17:06:57 CDT)
Re: RATTLE failure Philip Peartree (Sat Sep 08 2007 - 15:41:20 CDT)
Re: atoms moving fast Victor Ovchinnikov (Sat Sep 08 2007 - 10:22:53 CDT)
atoms moving fast Xiang Mao (Sat Sep 08 2007 - 08:31:30 CDT)
Re: RATTLE failure Philip Peartree (Fri Sep 07 2007 - 16:43:57 CDT)
NAMD on dual quad-core Xeon's with Infiniband backbone Stephen M. Dutz (Fri Sep 07 2007 - 14:32:55 CDT)
Re: Temperature dependent unfolding.. Neema Salimi (Fri Sep 07 2007 - 13:02:49 CDT)
Re: FEP question luca (Fri Sep 07 2007 - 12:43:24 CDT)
Switching PSF files during a run. Wang, Boyang (Fri Sep 07 2007 - 11:35:35 CDT)
Re: FEP question Jerome Henin (Fri Sep 07 2007 - 10:33:47 CDT)
One question about running NAMD Wang, Boyang (Fri Sep 07 2007 - 09:48:39 CDT)
Freezing point Dr. Tamal Banerjee (Fri Sep 07 2007 - 08:22:05 CDT)
Re: Temperature dependent unfolding.. Richard Wood (Fri Sep 07 2007 - 07:20:40 CDT)
Re: FEP question luca (Fri Sep 07 2007 - 03:26:24 CDT)
Two NICs on each node? paco ty (Fri Sep 07 2007 - 02:55:35 CDT)
Re: Reason: FATAL ERROR: Simulation config file is not accessible. Guillaume LETELLIER (Fri Sep 07 2007 - 02:42:33 CDT)
Re: Reason: FATAL ERROR: Simulation config file is not accessible. luca (Fri Sep 07 2007 - 02:02:47 CDT)
Re: Temperature dependent unfolding.. gs_at_mrc-lmb.cam.ac.uk (Fri Sep 07 2007 - 00:42:34 CDT)
Re: Temperature dependent unfolding.. Richard Wood (Thu Sep 06 2007 - 21:55:44 CDT)
Re: Temperature dependent unfolding.. Arun Krishnan (Thu Sep 06 2007 - 20:25:54 CDT)
Re: Temperature dependent unfolding.. Arun Krishnan (Thu Sep 06 2007 - 20:09:46 CDT)
Reason: FATAL ERROR: Simulation config file is not accessible. Dirar Homouz (Thu Sep 06 2007 - 15:51:52 CDT)
Re: Temperature dependent unfolding.. Richard Wood (Thu Sep 06 2007 - 15:41:21 CDT)
Re: Temperature dependent unfolding.. gs_at_mrc-lmb.cam.ac.uk (Thu Sep 06 2007 - 14:21:34 CDT)
Re: FEP question Jerome Henin (Thu Sep 06 2007 - 14:00:05 CDT)
Re: Temperature dependent unfolding.. Neema Salimi (Thu Sep 06 2007 - 12:45:22 CDT)
Re: FEP question Victor Ovchinnikov (Thu Sep 06 2007 - 11:29:23 CDT)
Re: Temperature dependent unfolding.. Giovanni Settanni (Thu Sep 06 2007 - 04:04:46 CDT)
Re: FEP question Jerome Henin (Thu Sep 06 2007 - 09:28:20 CDT)
Re: A basic question? Jerome Henin (Thu Sep 06 2007 - 09:04:16 CDT)
FEP question Matthew WIlce (Thu Sep 06 2007 - 08:32:09 CDT)
Re: Temperature dependent unfolding.. Giovanni Settanni (Thu Sep 06 2007 - 06:34:51 CDT)
A basic question? Dr. Tamal Banerjee (Thu Sep 06 2007 - 05:33:09 CDT)
Re: Temperature dependent unfolding.. Neema Salimi (Wed Sep 05 2007 - 12:30:29 CDT)
Re: Temperature dependent unfolding.. Arun Krishnan (Wed Sep 05 2007 - 12:21:55 CDT)
Re: Temperature dependent unfolding.. Neema Salimi (Wed Sep 05 2007 - 12:19:13 CDT)
Re: Temperature dependent unfolding.. Arun Krishnan (Wed Sep 05 2007 - 11:40:56 CDT)
Re: Temperature dependent unfolding.. Peter Freddolino (Wed Sep 05 2007 - 11:32:58 CDT)
How to access energies after MD step with Tcl ? Arturas Ziemys (Wed Sep 05 2007 - 11:30:31 CDT)
Re: Temperature dependent unfolding.. Arun Krishnan (Wed Sep 05 2007 - 11:02:21 CDT)
Re: Temperature dependent unfolding.. Arun Krishnan (Wed Sep 05 2007 - 10:56:56 CDT)
Re: Temperature dependent unfolding.. Peter Freddolino (Wed Sep 05 2007 - 10:37:32 CDT)
Re: Temperature dependent unfolding.. Arun Krishnan (Wed Sep 05 2007 - 09:26:26 CDT)
Re: Temperature dependent unfolding.. Peter Freddolino (Wed Sep 05 2007 - 09:06:31 CDT)
Re: Temperature dependent unfolding.. Arun Krishnan (Wed Sep 05 2007 - 08:37:45 CDT)
Re: Temperature dependent unfolding.. Fabio Passetti (Wed Sep 05 2007 - 07:41:39 CDT)
Re: Temperature dependent unfolding.. Monika Sharma (Wed Sep 05 2007 - 04:00:51 CDT)
Temperature dependent unfolding.. Arun Krishnan (Tue Sep 04 2007 - 20:13:35 CDT)
Re: Total external work calculation in SMD-PMF calculation JC Gumbart (Tue Sep 04 2007 - 13:30:41 CDT)
scaling issues in distributed environment Viral D. Tejani (Tue Sep 04 2007 - 15:34:20 CDT)
Re: question about ACE and NME patch Victor Ovchinnikov (Tue Sep 04 2007 - 12:01:56 CDT)
transmembrane electrical potential gradient in NAMD maria goranovic (Tue Sep 04 2007 - 11:03:31 CDT)
Re: system density Peter Freddolino (Tue Sep 04 2007 - 10:51:20 CDT)
Re: question about ACE and NME patch JC Gumbart (Tue Sep 04 2007 - 10:38:17 CDT)
question about ACE and NME patch Xiang Mao (Tue Sep 04 2007 - 10:10:30 CDT)
system density Adam Fraser (Tue Sep 04 2007 - 10:04:40 CDT)
Best NAMD version for Rocks 4.3 IBM xseries 3665 andrea carotti (Tue Sep 04 2007 - 06:06:32 CDT)
RATTLE failure Philip Peartree (Tue Sep 04 2007 - 06:54:56 CDT)
Re: Recommended solvation box size Philip Peartree (Mon Sep 03 2007 - 16:18:22 CDT)
Re: Copper and Zinc: top_all27_prot_lipid.inp Cesar Luis Avila (Mon Sep 03 2007 - 10:47:35 CDT)
Re: Recommended solvation box size Cesar Luis Avila (Mon Sep 03 2007 - 07:44:26 CDT)
Implicit solvent simulation Cesar Avila (Mon Sep 03 2007 - 08:45:16 CDT)
question regarding nearest-image resolution in NAMD Vincent Kraeutler (Mon Sep 03 2007 - 03:23:24 CDT)
Re: calculate interaction energies for a system with amber forcefield Peter Freddolino (Sun Sep 02 2007 - 17:18:22 CDT)
calculate interaction energies for a system with amber forcefield Rima Chaudhuri (Sat Sep 01 2007 - 19:15:36 CDT)
Total external work calculation in SMD-PMF calculation Rathinavelan, Thenmalarchelvi (Sat Sep 01 2007 - 17:53:55 CDT)
Re: About QM-MM Christopher Harrison (Thu Aug 30 2007 - 08:30:05 CDT)
Re: About QM-MM Francesco Pietra (Thu Aug 30 2007 - 00:50:35 CDT)
Re: About QM-MM Dow_Hurst (Thu Aug 30 2007 - 00:02:52 CDT)
Re: About QM-MM Ilya Chorny (Wed Aug 29 2007 - 12:26:19 CDT)
Re: About QM-MM Dhiraj Srivastava (Wed Aug 29 2007 - 12:05:26 CDT)
Re: About QM-MM Francesco Pietra (Wed Aug 29 2007 - 11:59:28 CDT)
Re: About QM-MM Francesco Pietra (Wed Aug 29 2007 - 11:54:12 CDT)
Re: About QM-MM Dhiraj Srivastava (Wed Aug 29 2007 - 11:45:39 CDT)
Re: About QM-MM Francesco Pietra (Wed Aug 29 2007 - 11:34:45 CDT)
Re: About QM-MM Dhiraj Srivastava (Wed Aug 29 2007 - 11:31:00 CDT)
Re: Recommended solvation box size Vincent Kraeutler (Wed Aug 29 2007 - 07:46:48 CDT)
Re: Recommended solvation box size Guillaume LETELLIER (Wed Aug 29 2007 - 06:25:55 CDT)
Recommended solvation box size Philip Peartree (Wed Aug 29 2007 - 05:33:36 CDT)
Re: About QM-MM Francesco Pietra (Wed Aug 29 2007 - 01:38:17 CDT)
Re: About QM-MM Eduardo Tejera (Tue Aug 28 2007 - 18:26:48 CDT)
Re: About QM-MM Francesco Pietra (Tue Aug 28 2007 - 15:19:05 CDT)
Re: About QM-MM Francesco Pietra (Tue Aug 28 2007 - 14:46:49 CDT)
Re: Compiling NAMD 2.6 from Source: no charm-5.9.tar Audrey Salazar (Tue Aug 28 2007 - 14:27:50 CDT)
Re: Compiling NAMD 2.6 from Source: no charm-5.9.tar Thomas Gaillard (Tue Aug 28 2007 - 14:23:40 CDT)
Compiling NAMD 2.6 from Source: no charm-5.9.tar Audrey Salazar (Tue Aug 28 2007 - 13:42:14 CDT)
Re: About QM-MM Christopher Harrison (Tue Aug 28 2007 - 12:42:51 CDT)
Re: About QM-MM Ilya Chorny (Tue Aug 28 2007 - 10:21:24 CDT)
Re: biotin charmm topology/parameters Barry Isralewitz (Tue Aug 28 2007 - 10:00:21 CDT)
About QM-MM Francesco Pietra (Tue Aug 28 2007 - 08:18:18 CDT)
Re: Re: pressure vs density tip3p Roy Kimura (Tue Aug 28 2007 - 07:38:48 CDT)
biotin charmm topology/parameters Matthew Wilce (Mon Aug 27 2007 - 18:41:46 CDT)
Problem en equilibration Protein into a bilayer membrane POPC Gabriel J (Mon Aug 27 2007 - 17:50:49 CDT)
Re: Re: pressure vs density tip3p Vincent Kraeutler (Mon Aug 27 2007 - 16:55:47 CDT)
Re: Re: pressure vs density tip3p Peter Freddolino (Mon Aug 27 2007 - 16:42:43 CDT)
Re: pressure vs density tip3p Roy Kimura (Mon Aug 27 2007 - 16:04:24 CDT)
pressure vs density tip3p Roy Kimura (Mon Aug 27 2007 - 15:54:40 CDT)
Building 64-bit NAMD Warner Yuen (Mon Aug 27 2007 - 10:23:58 CDT)
Re: Dihedral Parameterization Jan Saam (Mon Aug 27 2007 - 03:47:04 CDT)
biotin charmm topology/parameters Matthew Wilce (Mon Aug 27 2007 - 01:48:13 CDT)
Re: setting solvent density during solvation jestin mandumpal (Mon Aug 27 2007 - 01:05:32 CDT)
size of water box Mehmet Sen (Fri Aug 24 2007 - 23:47:41 CDT)
Re: question about equilibration step Peter Freddolino (Fri Aug 24 2007 - 20:40:03 CDT)
Re: question about equilibration step Peter Freddolino (Fri Aug 24 2007 - 20:36:54 CDT)
Re: Replica Exhange error: POSIX EINTR {interrupted system call} Peter Freddolino (Fri Aug 24 2007 - 20:08:14 CDT)
Replica Exhange error: POSIX EINTR {interrupted system call} Arturas Ziemys (Fri Aug 24 2007 - 16:45:51 CDT)
Re: Copper and Zinc: top_all27_prot_lipid.inp Deepangi Pandit (Fri Aug 24 2007 - 15:27:47 CDT)
Re: question about equilibration step Neema Salimi (Fri Aug 24 2007 - 14:59:19 CDT)
Re: question about equilibration step Richard Wood (Fri Aug 24 2007 - 14:45:31 CDT)
Re: question about equilibration step Neema Salimi (Fri Aug 24 2007 - 14:32:17 CDT)
Re: Running thermal unfolding with nose hoover langevin piston Neema Salimi (Fri Aug 24 2007 - 14:26:55 CDT)
Re: question about equilibration step Brian Bennion (Fri Aug 24 2007 - 13:01:07 CDT)
Re: question about equilibration step Peter Freddolino (Fri Aug 24 2007 - 12:25:03 CDT)
Re: question about equilibration step Audrey Salazar (Fri Aug 24 2007 - 12:22:29 CDT)
Re: Copper and Zinc: top_all27_prot_lipid.inp Harish Lnu (Fri Aug 24 2007 - 12:22:11 CDT)
Re: question about equilibration step Richard Wood (Fri Aug 24 2007 - 11:59:22 CDT)
Running thermal unfolding with nose hoover langevin piston Zhang, Wei (Fri Aug 24 2007 - 11:53:25 CDT)
Copper and Zinc: top_all27_prot_lipid.inp Deepangi Pandit (Fri Aug 24 2007 - 11:51:39 CDT)
Re: question about equilibration step Peter Freddolino (Fri Aug 24 2007 - 11:45:06 CDT)
Re: question about equilibration step Richard Wood (Fri Aug 24 2007 - 11:22:01 CDT)
Re: question about equilibration step Peter Freddolino (Fri Aug 24 2007 - 10:09:39 CDT)
Re: question about equilibration step Audrey Salazar (Fri Aug 24 2007 - 09:04:28 CDT)
Re: Error bad vdW format in Charmm parameter file Subramanian Vaitheeswaran (Fri Aug 24 2007 - 07:54:41 CDT)
Re: The algorithm of nose hoover langevin pressure control Giovanni Bellesia (Fri Aug 24 2007 - 00:21:50 CDT)
The algorithm of nose hoover langevin pressure control Zhang, Wei (Thu Aug 23 2007 - 21:47:54 CDT)
question about equilibration step Audrey Salazar (Thu Aug 23 2007 - 17:33:03 CDT)
Just can't seem to compile charm++ Dale Marinenko (Thu Aug 23 2007 - 17:01:53 CDT)
Error bad vdW format in Charmm parameter file shyamala iyer (Thu Aug 23 2007 - 14:09:30 CDT)
error message Ahlam Al-Rawi (Wed Aug 22 2007 - 19:49:12 CDT)
Re: How to implement an additional interaction potential? Vincent Kraeutler (Thu Aug 23 2007 - 07:53:05 CDT)
How to implement an additional interaction potential? Philipp Schön (Thu Aug 23 2007 - 07:00:12 CDT)
Re: REMD using PBS qeue Peter Freddolino (Wed Aug 22 2007 - 12:28:50 CDT)
Re: COM restraint in NAMD JC Gumbart (Wed Aug 22 2007 - 11:49:13 CDT)
COM restraint in NAMD Victor Ovchinnikov (Wed Aug 22 2007 - 10:55:56 CDT)
Re: Charm++ Compilation Philip Peartree (Wed Aug 22 2007 - 10:32:50 CDT)
REMD using PBS qeue Arturas Ziemys (Wed Aug 22 2007 - 10:31:04 CDT)
Re: Charm++ Compilation Dow_Hurst (Wed Aug 22 2007 - 09:58:56 CDT)
Charm++ Compilation Philip Peartree (Wed Aug 22 2007 - 08:35:00 CDT)
Re: How to include parameters from stream files in calculations Qiang Zhong (Tue Aug 21 2007 - 19:43:57 CDT)
How to include parameters from stream files in calculations Spiro Pavlopoulos (Tue Aug 21 2007 - 15:02:39 CDT)
Re: energy drift in NVE David Hardy (Mon Aug 20 2007 - 22:12:54 CDT)
Re: setting solvent density during solvation Cesar Luis Avila (Mon Aug 20 2007 - 16:47:37 CDT)
Dihedral Parameterization Venky (Mon Aug 20 2007 - 19:17:28 CDT)
Re: setting solvent density during solvation Cesar Luis Avila (Mon Aug 20 2007 - 15:29:17 CDT)
Re: setting solvent density during solvation Cesar Luis Avila (Mon Aug 20 2007 - 14:46:01 CDT)
setting solvent density during solvation Adam Fraser (Mon Aug 20 2007 - 11:23:58 CDT)
Re: energy drift in NVE Peter Freddolino (Mon Aug 20 2007 - 08:35:02 CDT)
Re: energy drift in NVE Victor Ovchinnikov (Mon Aug 20 2007 - 08:24:51 CDT)
Complete Beginner Philip Peartree (Mon Aug 20 2007 - 07:38:30 CDT)
drift in protein membrane simulation. membrane and protein one way, water the other way maria goranovic (Mon Aug 20 2007 - 05:20:06 CDT)
Re: energy drift in NVE Vincent Kraeutler (Mon Aug 20 2007 - 02:22:49 CDT)
Re: energy drift in NVE Peter Freddolino (Mon Aug 20 2007 - 02:15:11 CDT)
Re: energy drift in NVE David Hardy (Mon Aug 20 2007 - 01:27:14 CDT)
Re: energy drift in NVE Peter Freddolino (Sun Aug 19 2007 - 15:53:58 CDT)
energy drift in NVE Victor Ovchinnikov (Sun Aug 19 2007 - 15:21:22 CDT)
Re: binaryoutput option doesn't work for dcd file Jerome Henin (Sat Aug 18 2007 - 10:40:35 CDT)
binaryoutput option doesn't work for dcd file Devendra (Sat Aug 18 2007 - 09:26:28 CDT)
Re: Code question: Partitioning the patch contents into water and non-water Floris Buelens (Sat Aug 18 2007 - 05:20:32 CDT)
Latency vs Bandwidth over Infiniband Dow_Hurst (Fri Aug 17 2007 - 17:37:07 CDT)
Re: Code question: Partitioning the patch contents into water and non-water Jim Phillips (Fri Aug 17 2007 - 11:10:55 CDT)
Re: Code question: Partitioning the patch contents into water and non-water David Hardy (Fri Aug 17 2007 - 10:24:18 CDT)
Re: seperate files-par, top and pdb files for solvents, needed? Jeffrey J. Potoff (Fri Aug 17 2007 - 08:20:28 CDT)
seperate files-par, top and pdb files for solvents, needed? jestin mandumpal (Fri Aug 17 2007 - 04:53:00 CDT)
Code question: Partitioning the patch contents into water and non-water Vincent Kraeutler (Fri Aug 17 2007 - 04:01:24 CDT)
Number of atoms to high for mdenergy Marek Dynowski (Thu Aug 16 2007 - 07:41:51 CDT)
Re: Storing atom coordinates at each time step Peter Freddolino (Wed Aug 15 2007 - 20:40:14 CDT)
Re: Storing atom coordinates at each time step Peter Freddolino (Wed Aug 15 2007 - 20:30:01 CDT)
Re: Re: NAMD: Exiting Prematurely Arun Krishnan (Wed Aug 15 2007 - 20:23:39 CDT)
Re: Re: NAMD: Exiting Prematurely Arun Krishnan (Wed Aug 15 2007 - 20:22:50 CDT)
Re: Re: NAMD: Exiting Prematurely Arun Krishnan (Wed Aug 15 2007 - 20:20:42 CDT)
Re: Re: NAMD: Exiting Prematurely Arun Krishnan (Wed Aug 15 2007 - 20:19:17 CDT)
Re: Storing atom coordinates at each time step Richard Wood (Wed Aug 15 2007 - 19:49:07 CDT)
Re: What happened when PBC is on but PME is off? JC Gumbart (Wed Aug 15 2007 - 17:50:58 CDT)
Re: Storing atom coordinates at each time step Jason O'Young (Wed Aug 15 2007 - 17:21:28 CDT)
Building NAMD with Myrinet MX Warner Yuen (Wed Aug 15 2007 - 15:59:24 CDT)
Re: Storing atom coordinates at each time step Jeffrey J. Potoff (Wed Aug 15 2007 - 15:48:18 CDT)
What happened when PBC is on but PME is off? Dong Luo (Wed Aug 15 2007 - 15:18:22 CDT)
SAMs using NAMD Yu Liu (Wed Aug 15 2007 - 15:17:25 CDT)
Storing atom coordinates at each time step Audrey Salazar (Wed Aug 15 2007 - 15:03:37 CDT)
Re: Re: NAMD: Exiting Prematurely Vincent Kraeutler (Wed Aug 15 2007 - 14:06:44 CDT)
Re: Re: NAMD: Exiting Prematurely Jason O'Young (Wed Aug 15 2007 - 11:37:22 CDT)
Re: Re: NAMD: Exiting Prematurely Subramanian Vaitheeswaran (Wed Aug 15 2007 - 09:19:21 CDT)
Re: Re: NAMD: Exiting Prematurely Jeffrey J. Potoff (Wed Aug 15 2007 - 07:10:42 CDT)
Re: Hoe to create psf file of C-terminous of protein? Qiang Zhong (Wed Aug 15 2007 - 02:48:53 CDT)
Re: NAMD: Exiting Prematurely Arun Krishnan (Wed Aug 15 2007 - 00:58:25 CDT)
NAMD: Exiting Prematurely Arun Krishnan (Tue Aug 14 2007 - 19:59:54 CDT)
Re: Hoe to create psf file of C-terminous of protein? JC Gumbart (Tue Aug 14 2007 - 19:49:33 CDT)
Re: Hoe to create psf file of C-terminous of protein? Qiang Zhong (Tue Aug 14 2007 - 19:07:24 CDT)
new spam filtering Jim Phillips (Tue Aug 14 2007 - 18:07:32 CDT)
Re: How to use NPT ensemble to fix water density Jeffrey J. Potoff (Tue Aug 14 2007 - 15:01:35 CDT)
RE: How to use NPT ensemble to fix water density Irene Newhouse (Tue Aug 14 2007 - 14:59:59 CDT)
water molecules and silicon wall Yu Liu (Tue Aug 14 2007 - 14:53:47 CDT)
How to use NPT ensemble to fix water density Adam Fraser (Tue Aug 14 2007 - 14:28:18 CDT)
Re: Temperature Control: Rescaling and Reassignment luca (Thu Aug 09 2007 - 13:05:07 CDT)
Re: Very peculiar problem while using bigdcd. Help ! Peter Freddolino (Tue Aug 14 2007 - 09:02:49 CDT)
Re: Hoe to create psf file of C-terminous of protein? Peter Freddolino (Tue Aug 14 2007 - 09:00:20 CDT)
Re: Very peculiar problem while using bigdcd. Help ! maria goranovic (Tue Aug 14 2007 - 07:01:28 CDT)
Don't get mad, get Val1um! Jarred Whitlock (Mon Aug 13 2007 - 22:47:48 CDT)
Re: Your Pharm4cy 0rder #3728660 Lelia Frost (Mon Aug 13 2007 - 21:57:15 CDT)
One Year written repl1ca w4tches warranty Simone Darling (Mon Aug 13 2007 - 18:42:22 CDT)
Re: bilayer thickness in simulation of POPC membranes Ilya Chorny (Mon Aug 13 2007 - 10:00:10 CDT)
Re: vmd-l: Re: bilayer thickness in simulation of POPC membranes maria goranovic (Mon Aug 13 2007 - 09:16:09 CDT)
Very peculiar problem while using bigdcd. Help ! maria goranovic (Mon Aug 13 2007 - 08:47:00 CDT)
Re: bilayer thickness in simulation of POPC membranes maria goranovic (Mon Aug 13 2007 - 07:55:48 CDT)
How to avoid => ERROR: Step 100920 cell rescaling factor limited. Philipp Schön (Mon Aug 13 2007 - 07:28:39 CDT)
Hoe to create psf file of C-terminous of protein? Qiang Zhong (Mon Aug 13 2007 - 06:53:13 CDT)
Re: FIXED atoms not included as described in the documentation Joshua D. Moore (Mon Aug 13 2007 - 04:55:35 CDT)
FIXED atoms not included as described in the documentation Joshua D. Moore (Mon Aug 13 2007 - 04:49:03 CDT)
Re: Infinite Armchair Single Wall Carbon Nanotubes and Periodic Boundary Conditions (PBC) Joshua D. Moore (Sat Aug 11 2007 - 15:21:44 CDT)
Re: Margin Error Peter Freddolino (Sat Aug 11 2007 - 15:10:52 CDT)
Re: Infinite Armchair Single Wall Carbon Nanotubes and Periodic Boundary Conditions (PBC) Peter Freddolino (Sat Aug 11 2007 - 15:05:20 CDT)
cis/trans prolyl sfrickenhaus (Sat Aug 11 2007 - 03:40:55 CDT)
Infinite Armchair Single Wall Carbon Nanotubes and Periodic Boundary Conditions (PBC) Joshua D. Moore (Sat Aug 11 2007 - 01:33:01 CDT)
Prescr1ption med1cations... without a prescr1ption! Mercedes Dougherty (Sat Aug 11 2007 - 01:19:45 CDT)
Famous repl1ca w4tches r0lex Cartier Bvlgari Goldie Huffman (Sat Aug 11 2007 - 01:24:31 CDT)
Re: bunch of water molecules sathish kumar gurupatham (Fri Aug 10 2007 - 13:30:45 CDT)
CHARMRUN vs MPI Jason O'Young (Fri Aug 10 2007 - 13:14:22 CDT)
Margin Error Hsing Pao (Fri Aug 10 2007 - 12:43:20 CDT)
bilayer thickness in simulation of POPC membranes Vlad Cojocaru (Fri Aug 10 2007 - 10:56:41 CDT)
Re: Minimization using Fixed Atoms Peter Freddolino (Fri Aug 10 2007 - 10:25:01 CDT)
Re: Multiplicity of Parameters Philip Peartree (Fri Aug 10 2007 - 07:25:33 CDT)
Minimization using Fixed Atoms Rita Cassia (Fri Aug 10 2007 - 05:16:48 CDT)
Re: Multiplicity of Parameters Peter Freddolino (Thu Aug 09 2007 - 20:09:29 CDT)
Re: Multiplicity of Parameters Philip Peartree (Thu Aug 09 2007 - 18:50:06 CDT)
Re: Multiplicity of Parameters Peter Freddolino (Thu Aug 09 2007 - 18:22:18 CDT)
Re: Multiplicity of Parameters Philip Peartree (Thu Aug 09 2007 - 17:59:26 CDT)
Re: Multiplicity of Parameters Peter Freddolino (Thu Aug 09 2007 - 15:26:21 CDT)
Re: bunch of water molecules Jerome Henin (Thu Aug 09 2007 - 15:03:12 CDT)
bunch of water molecules sathish kumar gurupatham (Thu Aug 09 2007 - 13:39:51 CDT)
Multiplicity of Parameters Philip Peartree (Thu Aug 09 2007 - 10:56:33 CDT)
Re: Storage of large files Vincent Kraeutler (Thu Aug 09 2007 - 04:03:32 CDT)
Storage of large files Monika Sharma (Thu Aug 09 2007 - 01:47:57 CDT)
Temperature Control: Rescaling and Reassignment Adilah Hussein (Wed Aug 08 2007 - 12:43:00 CDT)
Temperature Control: Rescaling and Reassignment Adilah Hussien (Wed Aug 08 2007 - 04:52:16 CDT)
Re: How to construct .prm file of phospho-THR? Qiang Zhong (Tue Aug 07 2007 - 18:34:25 CDT)
Re: How to construct .prm file of phospho-THR? L. Michel Espinoza-Fonseca (Tue Aug 07 2007 - 09:09:19 CDT)
How to construct .prm file of phospho-THR? Qiang Zhong (Tue Aug 07 2007 - 08:55:52 CDT)
Re: NAMD hangs at "OPENING EXTENDED SYSTEM TRAJECTORY FILE" / PME error Jim Pfaendtner (Mon Aug 06 2007 - 14:13:54 CDT)
Re: NAMD hangs at "OPENING EXTENDED SYSTEM TRAJECTORY FILE" / PME error Cesar Luis Avila (Mon Aug 06 2007 - 10:16:47 CDT)
NAMD hangs at "OPENING EXTENDED SYSTEM TRAJECTORY FILE" / PME error Jim Pfaendtner (Mon Aug 06 2007 - 11:51:41 CDT)
Finding size of water box Audrey Salazar (Mon Aug 06 2007 - 11:15:41 CDT)
Building NAMD/CHARM++ Mac OS X Intel Warner Yuen (Mon Aug 06 2007 - 10:52:19 CDT)
attractive harmonic potential between 2 molecules Adam Fraser (Mon Aug 06 2007 - 10:25:29 CDT)
CHARMM partial charges and paratool Jose R. Sabino (Fri Aug 03 2007 - 16:48:55 CDT)
Re: Constructing a small molecule Peter Freddolino (Mon Aug 06 2007 - 08:14:32 CDT)
Constructing a small molecule Yu Liu (Sun Aug 05 2007 - 20:41:58 CDT)
Building NAMD 64-bit Mac OSX with GCC Warner Yuen (Sun Aug 05 2007 - 15:17:02 CDT)
Re: Is very slow heating "bad"? Vincent Kraeutler (Sat Aug 04 2007 - 11:06:11 CDT)
Is very slow heating "bad"? Arun Krishnan (Sat Aug 04 2007 - 01:49:14 CDT)
Re: vmd-l: How to calculate the C alpha RMSD from NAMD trajectory John Stone (Fri Aug 03 2007 - 10:58:13 CDT)
Re: How to calculate the C alpha RMSD from NAMD trajectory priti arora (Fri Aug 03 2007 - 06:10:53 CDT)
no effect on velocity scaling Philipp Schön (Fri Aug 03 2007 - 02:36:19 CDT)
How to calculate the C alpha RMSD from NAMD trajectory Shulin Zhuang (Fri Aug 03 2007 - 02:31:22 CDT)
Re: Unfolding protocol.. Arun Krishnan (Fri Aug 03 2007 - 01:35:01 CDT)
Unfolding protocol.. Arun Krishnan (Fri Aug 03 2007 - 00:58:58 CDT)
Re: Pairinteractions Peter Freddolino (Thu Aug 02 2007 - 21:37:16 CDT)
Re: Pairinteractions Peter Freddolino (Thu Aug 02 2007 - 21:36:28 CDT)
TEMPERATURE and TEMPAVG : nan Andrea Diaz (Thu Aug 02 2007 - 16:58:39 CDT)
bad global exclusion count error Jim Pfaendtner (Thu Aug 02 2007 - 15:56:18 CDT)
Re: Pairinteractions Ilya Chorny (Thu Aug 02 2007 - 15:47:23 CDT)
Re: Steered MD with NAMD? L. Michel Espinoza-Fonseca (Thu Aug 02 2007 - 15:21:38 CDT)
Re: Steered MD with NAMD? Vincent Kraeutler (Thu Aug 02 2007 - 14:47:06 CDT)
Steered MD with NAMD? List (Wed Aug 01 2007 - 15:05:48 CDT)
multiple tcouples? Jonathan Lee (Thu Aug 02 2007 - 13:17:12 CDT)
Re: Pairinteractions Ilya Chorny (Thu Aug 02 2007 - 12:24:14 CDT)
job stall w/ incresed cpu usage jfgaff_at_ncsu.edu (Thu Aug 02 2007 - 12:23:36 CDT)
Re: how to restart/continue NAMD run maruthi_at_imsc.res.in (Thu Aug 02 2007 - 04:05:52 CDT)
BigDCD Per Jr. Greisen (Thu Aug 02 2007 - 03:40:13 CDT)
Re: Pairinteractions Peter Freddolino (Thu Aug 02 2007 - 00:41:56 CDT)
Re: Pairinteractions Ilya Chorny (Wed Aug 01 2007 - 17:09:41 CDT)
Pairinteractions Ilya Chorny (Wed Aug 01 2007 - 16:43:12 CDT)
NAMD/Infinipath installations Jason Russler (Wed Aug 01 2007 - 08:54:08 CDT)
about 'loadforces' command...help! hl332_at_drexel.edu (Tue Jul 31 2007 - 15:00:17 CDT)
Re: vdW parameter for atom type CN7 in ATP L. Michel Espinoza-Fonseca (Tue Jul 31 2007 - 06:18:24 CDT)
vdW parameter for atom type CN7 in ATP Veronika Brazdova (Tue Jul 31 2007 - 05:55:10 CDT)
RE: extracting coordinates from dcd file M. Madhu (Mon Jul 30 2007 - 23:31:27 CDT)
Re: Question regarding NAMD nonbonded routines Peter Freddolino (Mon Jul 30 2007 - 21:21:01 CDT)
Re: extracting coordinates from dcd file JC Gumbart (Mon Jul 30 2007 - 17:09:17 CDT)
Re: Re: 128+ proccessor jobs on 64bit Widows hang upon completion of the simulation. Ilya Chorny (Mon Jul 30 2007 - 16:36:02 CDT)
extracting coordinates from dcd file M. Madhu (Mon Jul 30 2007 - 13:50:00 CDT)
Re: 128+ proccessor jobs on 64bit Widows hang upon completion of the simulation. Eric Bohm (Mon Jul 30 2007 - 11:13:09 CDT)
Re: 128+ proccessor jobs on 64bit Widows hang upon completion of the simulation. Eric Bohm (Mon Jul 30 2007 - 10:26:01 CDT)
Re: 128+ proccessor jobs on 64bit Widows hang upon completion of the simulation. Eric Bohm (Mon Jul 30 2007 - 08:09:28 CDT)
Re: 128+ proccessor jobs on 64bit Widows hang upon completion of the simulation. Ilya Chorny (Mon Jul 30 2007 - 10:46:48 CDT)
NAMD on dual core, dual processor machine? Brian Genge (Mon Jul 30 2007 - 10:23:31 CDT)
Re: 128+ proccessor jobs on 64bit Widows hang upon completion of the simulation. Ilya Chorny (Mon Jul 30 2007 - 10:22:59 CDT)
Re: 128+ proccessor jobs on 64bit Widows hang upon completion of the simulation. Ilya Chorny (Mon Jul 30 2007 - 10:19:15 CDT)
Re: FATAL ERROR: Unable to open extended system file. Jianhui Tian (Mon Jul 30 2007 - 08:58:58 CDT)
Q=D4=D7=C5=D4:__128+_proccessor_jobs_on_64bit_?= Widows hang upon completion of the simulation. Alexandre A. Vakhrouchev (Mon Jul 30 2007 - 04:20:41 CDT)
FATAL ERROR: Unable to open extended system file. Arun Krishnan (Mon Jul 30 2007 - 02:27:49 CDT)
128+ proccessor jobs on 64bit Widows hang upon completion of the simulation. Ilya Chorny (Sun Jul 29 2007 - 22:54:57 CDT)
Re: *.dcd and *.dcd.BAK dora guzman (Sun Jul 29 2007 - 15:46:28 CDT)
Re: *.dcd and *.dcd.BAK L. Michel Espinoza-Fonseca (Sun Jul 29 2007 - 13:39:50 CDT)
*.dcd and *.dcd.BAK Per Jr. Greisen (Sun Jul 29 2007 - 10:08:04 CDT)
Residue name for Dimethyl sulfoxide jestin mandumpal (Sun Jul 29 2007 - 05:00:46 CDT)
Re: RE: NAMD crashes on winx64 during parallel run. Ilya Chorny (Sun Jul 29 2007 - 02:48:53 CDT)
Q=D4=D7=C5=D4:__RE:_NAMD_crashes?= on winx64 during parallel run. Alexandre A. Vakhrouchev (Sun Jul 29 2007 - 00:42:38 CDT)
Re: SIDECHAIN _RMSD_Thank_you Karol Kaszuba (Sat Jul 28 2007 - 15:50:04 CDT)
RE: guesscoord fails, hydrogen adding problem, output pdb is all zeros JC Gumbart (Sat Jul 28 2007 - 10:06:45 CDT)
RE: NAMD crashes on winx64 during parallel run. Ilya Chorny (Sat Jul 28 2007 - 09:52:15 CDT)
Re: SIDECHAIN _RMSD Peter Freddolino (Sat Jul 28 2007 - 07:54:35 CDT)
Re: Can NAMD be used as for general Newtonian mechanics simulations? Vincent Kraeutler (Sat Jul 28 2007 - 07:11:27 CDT)
guesscoord fails, hydrogen adding problem, output pdb is all zeros Venky (Sat Jul 28 2007 - 03:45:05 CDT)
Can NAMD be used as for general Newtonian mechanics simulations? Arneh Babakhani (Fri Jul 27 2007 - 15:21:20 CDT)
SIDECHAIN _RMSD Karol Kaszuba (Fri Jul 27 2007 - 13:56:22 CDT)
Re: Question regarding NAMD nonbonded routines Vincent Kraeutler (Fri Jul 27 2007 - 12:57:28 CDT)
Re: Downloading CHARMM Parameter and Topology Files JC Gumbart (Fri Jul 27 2007 - 12:01:34 CDT)
Re: Question regarding NAMD nonbonded routines Peter Freddolino (Fri Jul 27 2007 - 11:41:08 CDT)
Downloading CHARMM Parameter and Topology Files Audrey Salazar (Fri Jul 27 2007 - 11:31:54 CDT)
Re: Help Needed>Compiling source namd mpi enabled for a linux cluster Vincent Kraeutler (Fri Jul 27 2007 - 03:47:40 CDT)
Re: Question regarding NAMD nonbonded routines Vincent Kraeutler (Thu Jul 26 2007 - 12:27:29 CDT)
wrapping Arturas Ziemys (Thu Jul 26 2007 - 10:59:38 CDT)
Re: Question regarding NAMD nonbonded routines Floris Buelens (Thu Jul 26 2007 - 05:04:55 CDT)
Re: Question regarding NAMD nonbonded routines Peter Freddolino (Wed Jul 25 2007 - 20:48:19 CDT)
Re: pairinteractions Peter Freddolino (Wed Jul 25 2007 - 20:33:27 CDT)
pairinteractions dimka (Wed Jul 25 2007 - 17:03:37 CDT)
Help Needed>Compiling source namd mpi enabled for a linux cluster Daniel.G.Roberts_at_sanofi-aventis.com (Wed Jul 25 2007 - 16:31:35 CDT)
PDB residue renumbering snoze pa (Wed Jul 25 2007 - 16:29:54 CDT)
Re: Can I do ¡°accelerated molecular dynamics¡±in NAMD? L. Michel Espinoza-Fonseca (Wed Jul 25 2007 - 15:43:27 CDT)
Question regarding NAMD nonbonded routines Vincent Kraeutler (Wed Jul 25 2007 - 11:55:40 CDT)
Can I do ¡°accelerated molecular dynamics¡±in NAMD? Qiang Zhong (Wed Jul 25 2007 - 08:22:49 CDT)
Re: A serious problem of NAMD output. Wang, Boyang (Tue Jul 24 2007 - 20:43:50 CDT)
Re: A serious problem of NAMD output. Peter Freddolino (Tue Jul 24 2007 - 18:57:42 CDT)
Re: A serious problem of NAMD output. Brian Bennion (Tue Jul 24 2007 - 18:43:05 CDT)
Re: A serious problem of NAMD output. Peter Freddolino (Tue Jul 24 2007 - 17:44:32 CDT)
A serious problem of NAMD output. Wang, Boyang (Tue Jul 24 2007 - 17:35:08 CDT)
Re: Net charge of the system is not zero JC Gumbart (Tue Jul 24 2007 - 17:00:56 CDT)
Is it possible to compile NAMD win64 with MPI (windows MPI) Ilya Chorny (Tue Jul 24 2007 - 16:52:09 CDT)
temperature control for small molecule simulations in vacuum Floris Buelens (Tue Jul 24 2007 - 06:50:01 CDT)
Net charge of the system is not zero utiramerur_at_ecr6.ohio-state.edu (Mon Jul 23 2007 - 08:28:25 CDT)
FATAL ERROR: Bad global improper count! andrea carotti (Mon Jul 23 2007 - 03:47:16 CDT)
Unit cell angles information Andrea Diaz (Sat Jul 21 2007 - 16:46:41 CDT)
Simulated annealing out of mainstream Francesco Pietra (Sat Jul 21 2007 - 08:18:25 CDT)
Re: Parameter snoze pa (Fri Jul 20 2007 - 14:49:18 CDT)
Re: Treatment of a Neutral N-terminus Thomas Gaillard (Fri Jul 20 2007 - 13:29:39 CDT)
Re: Parameter Leonardo Trabuco (Fri Jul 20 2007 - 13:21:40 CDT)
spherical boundary conditions jfgaff_at_ncsu.edu (Fri Jul 20 2007 - 13:03:45 CDT)
Parameter snoze pa (Fri Jul 20 2007 - 12:03:12 CDT)
Treatment of a Neutral N-terminus Maria Bagonis (Fri Jul 20 2007 - 11:51:32 CDT)
Re: NAMD message snoze pa (Fri Jul 20 2007 - 10:20:58 CDT)
Can I use FEP in NAMD for reaction of ATP with Kinase? Qiang Zhong (Fri Jul 20 2007 - 06:46:38 CDT)
free energy,energy,entropy calculation for pushing ATP to active site of kinase! Qiang Zhong (Fri Jul 20 2007 - 06:40:44 CDT)
Re: NAMD message Leonardo Trabuco (Thu Jul 19 2007 - 17:50:38 CDT)
NAMD message snoze pa (Thu Jul 19 2007 - 17:44:48 CDT)
RE: molecule leaves water box during md Irene Newhouse (Thu Jul 19 2007 - 16:40:36 CDT)
Re: molecule leaves water box during md Peter Freddolino (Thu Jul 19 2007 - 16:00:31 CDT)
Re: charmm str file Peter Freddolino (Thu Jul 19 2007 - 15:58:10 CDT)
charmm str file snoze pa (Thu Jul 19 2007 - 15:04:22 CDT)
molecule leaves water box during md Irene Newhouse (Thu Jul 19 2007 - 13:38:02 CDT)
Re: ATP molecule Per Jr. Greisen (Thu Jul 19 2007 - 13:23:24 CDT)
Re: ATP molecule snoze pa (Thu Jul 19 2007 - 12:40:35 CDT)
Re: ATP molecule L. Michel Espinoza-Fonseca (Thu Jul 19 2007 - 10:42:06 CDT)
ATP molecule snoze pa (Thu Jul 19 2007 - 10:22:43 CDT)
Re: free energy,energy,entropy calculation for pushing ATP to active site of kinase! Dong Luo (Thu Jul 19 2007 - 09:15:13 CDT)
Re: NAMD Installation - SUSE Linux 9.1 on IBM X Series 335 Jimmy Tang (Thu Jul 19 2007 - 08:23:55 CDT)
free energy,energy,entropy calculation for pushing ATP to active site of kinase! Qiang Zhong (Thu Jul 19 2007 - 06:11:39 CDT)
CHARMM forcefield is free? wavedalla\_at_libero\.it (Thu Jul 19 2007 - 01:12:35 CDT)
Restarting calculation missmatches Alexandre A. Vakhrouchev (Thu Jul 19 2007 - 00:59:36 CDT)
Re: Extended System Conservation David Hardy (Wed Jul 18 2007 - 15:36:37 CDT)
Re: Extended System Conservation Peter Freddolino (Wed Jul 18 2007 - 14:23:07 CDT)
Re: Vanishing bonds in small molecule during psf generation. Peter Freddolino (Wed Jul 18 2007 - 14:19:26 CDT)
RE: Vanishing bonds in small molecule during psf generation. Christian Blouin (Wed Jul 18 2007 - 14:13:33 CDT)
NAMD Installation - SUSE Linux 9.1 on IBM X Series 335 Deepangi Pandit (Wed Jul 18 2007 - 13:39:18 CDT)
NAMD Installation - SUSE Linux 9.1 on IBM X Series 335 Deepangi Pandit (Wed Jul 18 2007 - 13:20:19 CDT)
Extended System Conservation jadelman_at_berkeley.edu (Wed Jul 18 2007 - 13:02:31 CDT)
Re: Vanishing bonds in small molecule during psf generation. JC Gumbart (Wed Jul 18 2007 - 11:29:36 CDT)
Vanishing bonds in small molecule during psf generation. Christian Blouin (Wed Jul 18 2007 - 08:58:13 CDT)
NAMD in Solaris X86 Allen Chen (Tue Jul 17 2007 - 17:01:50 CDT)
namddat syntax error Sayan Bagchi (Tue Jul 17 2007 - 12:35:47 CDT)
Re: removing waters from big dcd files regafan_at_usc.es (Tue Jul 17 2007 - 10:02:50 CDT)
Re: removing waters from big dcd files Dong Luo (Mon Jul 16 2007 - 23:00:25 CDT)
Re: removing waters from big dcd files Peter Freddolino (Mon Jul 16 2007 - 15:13:20 CDT)
Re: removing waters from big dcd files regafan_at_usc.es (Mon Jul 16 2007 - 15:09:01 CDT)
Re: removing waters from big dcd files regafan_at_usc.es (Mon Jul 16 2007 - 15:01:12 CDT)
FW: <no subject> Grabe, Michael David (Mon Jul 16 2007 - 14:49:23 CDT)
Re: removing waters from big dcd files Dong Luo (Mon Jul 16 2007 - 14:40:55 CDT)
Re: how to kill namd job in TCL FORCES Script? Jerome Henin (Mon Jul 16 2007 - 12:41:59 CDT)
how to kill namd job in TCL FORCES Script? hl332_at_drexel.edu (Mon Jul 16 2007 - 12:22:50 CDT)
Re: removing waters from big dcd files Jerome Henin (Mon Jul 16 2007 - 12:17:20 CDT)
removing waters from big dcd files regafan_at_usc.es (Mon Jul 16 2007 - 11:08:57 CDT)
´ð¸´: How to build the psf file and the parameter file of a ligand Yu Liu (Mon Jul 16 2007 - 08:32:16 CDT)
How to build the psf file and the parameter file of a ligand taojinwuhan_at_sohu.com (Mon Jul 16 2007 - 03:08:33 CDT)
Re: balck box: what is the coupling constant when using langenvinFile? JC Gumbart (Fri Jul 13 2007 - 19:35:07 CDT)
SGE and NAMD Kevin Jander (Fri Jul 13 2007 - 14:14:05 CDT)
water HOH angle of 102 defrees Alessio Alexiadis (Fri Jul 13 2007 - 13:13:23 CDT)
balck box: what is the coupling constant when using langenvinFile? Philipp Schön (Fri Jul 13 2007 - 06:53:38 CDT)
eq. info. shivam ghosh (Fri Jul 13 2007 - 00:53:05 CDT)
Push ATP to active site of kinase! Qiang Zhong (Thu Jul 12 2007 - 22:20:43 CDT)
Re: tclforces: force not a vector Peter Freddolino (Thu Jul 12 2007 - 09:34:02 CDT)
Re: tclforces: force not a vector maria goranovic (Thu Jul 12 2007 - 08:11:55 CDT)
Re: Force field for coarse grained simulations (and other questions) Peter Freddolino (Thu Jul 12 2007 - 07:58:12 CDT)
Re: tclforces: force not a vector Peter Freddolino (Thu Jul 12 2007 - 07:24:37 CDT)
tclforces: force not a vector maria goranovic (Thu Jul 12 2007 - 01:53:57 CDT)
Force field for coarse grained simulations (and other questions) patrick wintrode (Wed Jul 11 2007 - 16:20:20 CDT)
tracing not available with CMK_OPTIMIZE jfgaff_at_ncsu.edu (Wed Jul 11 2007 - 13:10:08 CDT)
FATAL ERROR: Tried to find atom type on node other than node 0 Jeffrey J. Potoff (Wed Jul 11 2007 - 11:28:31 CDT)
Re: Problems with using multiple Tclforces scripts sequentially Victor Ovchinnikov (Wed Jul 11 2007 - 11:09:27 CDT)
Re: Problems with using multiple Tclforces scripts sequentially Peter Freddolino (Wed Jul 11 2007 - 10:30:04 CDT)
Re: TCL: force not a vector Peter Freddolino (Wed Jul 11 2007 - 10:23:54 CDT)
Re: Problems with using multiple Tclforces scripts sequentially maria goranovic (Wed Jul 11 2007 - 09:14:58 CDT)
Re: Re: Charmrun issues and namd on Win 64 Gengbin Zheng (Wed Jul 11 2007 - 01:34:26 CDT)
Re: Fwd: namd2 installation.. Gengbin Zheng (Wed Jul 11 2007 - 01:31:30 CDT)
Fwd: namd2 installation.. Arun Krishnan (Wed Jul 11 2007 - 01:26:58 CDT)
Re: Velocity Units David Hardy (Tue Jul 10 2007 - 23:48:28 CDT)
TCL: force not a vector Peter Jones (Tue Jul 10 2007 - 21:39:04 CDT)
UNC Paths in the configuration parameters Ilya Chorny (Tue Jul 10 2007 - 15:46:47 CDT)
Velocity Units Jason O'Young (Mon Jul 09 2007 - 20:57:18 CDT)
Problems with using multiple Tclforces scripts sequentially maria goranovic (Tue Jul 10 2007 - 12:46:48 CDT)
can i somehow use reassigntemp for selected atoms only? Philipp Schön (Tue Jul 10 2007 - 11:06:51 CDT)
NAMD-lite - Heun's method implementation Nick Schafer (Tue Jul 10 2007 - 11:01:36 CDT)
rmsd_fullthrotle script problem priti arora (Tue Jul 10 2007 - 07:28:34 CDT)
Re: Velocity Units Victor Ovchinnikov (Mon Jul 09 2007 - 22:30:13 CDT)
Writing to DCD file error - pelase help Istomin, Andrei (Mon Jul 09 2007 - 22:16:54 CDT)
Hydrogen Atoms and Water Molecules Yu Liu (Mon Jul 09 2007 - 21:21:38 CDT)
Velocity Units Jason Wyonn O'Young (Mon Jul 09 2007 - 20:58:11 CDT)
Error compiling NAMD with MPI Kevin Jander (Mon Jul 09 2007 - 16:07:16 CDT)
Re: Unfolding simulations Neema Salimi (Mon Jul 09 2007 - 12:17:08 CDT)
Did anybody really use TIP4P? Alessio Alexiadis (Mon Jul 09 2007 - 09:52:47 CDT)
namd2 installation.. Arun Krishnan (Mon Jul 09 2007 - 01:20:19 CDT)
Unfolding simulations Arun Krishnan (Mon Jul 09 2007 - 01:18:26 CDT)
Re: Do we need to renumber atoms after solvate? Peter Freddolino (Mon Jul 09 2007 - 00:33:59 CDT)
Do we need to renumber atoms after solvate? Arun Krishnan (Sun Jul 08 2007 - 20:31:20 CDT)
centre of mass fixed Moumita Maiti (Sun Jul 08 2007 - 11:29:50 CDT)
Re: Re: Charmrun issues and namd on Win 64 Ilya Chorny (Sat Jul 07 2007 - 16:21:33 CDT)
Re: Re: Charmrun issues and namd on Win 64 Ilya Chorny (Fri Jul 06 2007 - 18:53:23 CDT)
Re: Re: Charmrun issues and namd on Win 64 Gengbin Zheng (Fri Jul 06 2007 - 16:17:28 CDT)
Re: Charmrun issues and namd on Win 64 Ilya Chorny (Fri Jul 06 2007 - 14:51:50 CDT)
Re: ABF - changing the reaction coordinate Jerome Henin (Fri Jul 06 2007 - 10:54:02 CDT)
ABF - changing the reaction coordinate Per Jr. Greisen (Fri Jul 06 2007 - 10:18:00 CDT)
Re: Re: Installing NAMD 2.6 on SMP machine... charm++ install errors Claudio Redaelli (Fri Jul 06 2007 - 04:14:39 CDT)
Re: Installing NAMD 2.6 on SMP machine... charm++ install errors Arun Krishnan (Fri Jul 06 2007 - 01:45:46 CDT)
TIP4P examples Alessio Alexiadis (Fri Jul 06 2007 - 01:31:37 CDT)
Installing NAMD 2.6 on SMP machine... charm++ install errors Arun Krishnan (Fri Jul 06 2007 - 01:29:25 CDT)
Re: ABF restrain Chris Chipot (Thu Jul 05 2007 - 13:05:30 CDT)
Re: ABF restrain alex digenova bravo (Thu Jul 05 2007 - 11:48:12 CDT)
RATTLE error and GROMACS parameters Jason O'Young (Thu Jul 05 2007 - 11:39:50 CDT)
TMPyP4 force field parameters Francesco Iori (Thu Jul 05 2007 - 10:21:42 CDT)
Re: Count protein solvent HBs? Dong Luo (Thu Jul 05 2007 - 09:21:36 CDT)
Re: ABF restrain Chris Chipot (Wed Jul 04 2007 - 17:17:41 CDT)
Re: problems with mutation in psfgen L. Michel Espinoza-Fonseca (Wed Jul 04 2007 - 15:58:41 CDT)
ABF restrain alex digenova bravo (Wed Jul 04 2007 - 15:31:19 CDT)
Re: problems with mutation in psfgen JC Gumbart (Wed Jul 04 2007 - 15:29:49 CDT)
problems with mutation in psfgen L. Michel Espinoza-Fonseca (Wed Jul 04 2007 - 15:18:45 CDT)
error: DID NOT FIND NIMPHI AFTER ATOM LIST IN PSF Karol Kaszuba (Wed Jul 04 2007 - 14:10:12 CDT)
SMD of proteins in water box without PBC dora guzman (Wed Jul 04 2007 - 11:56:46 CDT)
vdw parameter priti arora (Wed Jul 04 2007 - 09:31:25 CDT)
Re: Count protein solvent HBs? JC Gumbart (Tue Jul 03 2007 - 17:44:15 CDT)
Re: problem with periodic boundaries Peter Freddolino (Tue Jul 03 2007 - 17:09:40 CDT)
Re: Building a pdb file Peter Freddolino (Tue Jul 03 2007 - 16:43:14 CDT)
Building a pdb file Audrey Salazar (Tue Jul 03 2007 - 16:14:41 CDT)
Count protein solvent HBs? paco ty (Tue Jul 03 2007 - 13:10:51 CDT)
Re: Compilation on IBM-Power (Linux) Monika Sharma (Tue Jul 03 2007 - 13:00:18 CDT)
Re: mismatch of topology with parameter file JC Gumbart (Tue Jul 03 2007 - 12:23:19 CDT)
problem with periodic boundaries Philipp Schön (Tue Jul 03 2007 - 10:13:04 CDT)
mismatch of topology with parameter file Moumita Maiti (Tue Jul 03 2007 - 05:28:30 CDT)
problem in running equilibration shivam ghosh (Tue Jul 03 2007 - 00:02:53 CDT)
Re: High background load warning message Cesar Luis Avila (Mon Jul 02 2007 - 14:48:33 CDT)
Re: compile NAMD on Intel-64 Peter Freddolino (Mon Jul 02 2007 - 10:57:55 CDT)
Re: compile NAMD on Intel-64 Ilya Chorny (Mon Jul 02 2007 - 10:41:17 CDT)
Re: Charm compile: "xlC: command not found" Peter Freddolino (Mon Jul 02 2007 - 10:32:56 CDT)
Charm compile: "xlC: command not found" Jianhui Tian (Mon Jul 02 2007 - 09:55:36 CDT)
compile NAMD on Intel-64 Wei Liu (Mon Jul 02 2007 - 09:38:31 CDT)
Compilation on IBM-Power (Linux) Monika Sharma (Mon Jul 02 2007 - 06:10:20 CDT)
Re: Re: Can NAMD perform random expulsion moleculardynamics(REMD)? Sting (Sat Jun 30 2007 - 21:12:50 CDT)
Can NAMD perform random expulsion molecular dynamics(REMD)? Sting (Sat Jun 30 2007 - 09:03:02 CDT)
Re: about normal mode analisys Jojart Balazs (Fri Jun 29 2007 - 16:13:27 CDT)
about normal mode analisys S³awek Or³owski (Fri Jun 29 2007 - 04:00:35 CDT)
Re: constructing a topology entry for hexadecane Victor Ovchinnikov (Fri Jun 29 2007 - 10:37:19 CDT)
(no subject) mashaojienuaa (Fri Jun 29 2007 - 08:52:35 CDT)
Re: constructing a topology entry for hexadecane Adam Fraser (Fri Jun 29 2007 - 08:31:57 CDT)
TIP4P in NAMD? Alessio Alexiadis (Fri Jun 29 2007 - 07:52:57 CDT)
constructing a topology entry for hexadecane Adam Fraser (Thu Jun 28 2007 - 18:25:27 CDT)
Re: SPC/E water model Himanshu Khandelia (Thu Jun 28 2007 - 12:06:29 CDT)
Re: SPC/E water model Ilya Chorny (Thu Jun 28 2007 - 10:38:57 CDT)
SPC/E water model Anuradha Mittal (Thu Jun 28 2007 - 09:15:13 CDT)
tcl forces help hl332_at_drexel.edu (Wed Jun 27 2007 - 14:53:47 CDT)
Re: finding free energy at a time step using abf Jerome Henin (Wed Jun 27 2007 - 13:56:14 CDT)
finding free energy at a time step using abf rmsmith_at_iastate.edu (Wed Jun 27 2007 - 13:24:47 CDT)
Re: Re: Diffusion of Protein through the membrane Peter Freddolino (Wed Jun 27 2007 - 10:35:31 CDT)
Re: Re: Diffusion of Protein through the membrane Peter Freddolino (Wed Jun 27 2007 - 10:32:49 CDT)
Re: Re: Diffusion of Protein through the membrane Ilya Chorny (Wed Jun 27 2007 - 09:57:49 CDT)
Re: Re: Diffusion of Protein through the membrane Alessandro Cembran (Wed Jun 27 2007 - 09:08:32 CDT)
Re: Re: Diffusion of Protein through the membrane Peter Freddolino (Wed Jun 27 2007 - 08:51:04 CDT)
Re: Re: Diffusion of Protein through the membrane Cesar Luis Avila (Wed Jun 27 2007 - 08:12:00 CDT)
Re: abf "force not a vector" error maria goranovic (Wed Jun 27 2007 - 01:42:51 CDT)
Re: force on SMD atom Moumita Maiti (Wed Jun 27 2007 - 01:10:06 CDT)
Re: Diffusion of Protein through the membrane Ilya Chorny (Tue Jun 26 2007 - 22:12:22 CDT)
Determining Equillibration of a membrane protein Ilya Chorny (Tue Jun 26 2007 - 18:57:32 CDT)
Re: turn off intermolecular interaction Victor Ovchinnikov (Tue Jun 26 2007 - 17:21:45 CDT)
Re: About pmf Sterling Paramore (Tue Jun 26 2007 - 16:58:01 CDT)
Re: turn off intermolecular interaction JC Gumbart (Tue Jun 26 2007 - 15:37:01 CDT)
Re: About pmf JC Gumbart (Tue Jun 26 2007 - 15:24:01 CDT)
Re: has anyone patched NAG to ASN? JC Gumbart (Tue Jun 26 2007 - 14:16:00 CDT)
Re: abf "force not a vector" error Jerome Henin (Tue Jun 26 2007 - 13:49:49 CDT)
Re: NNB in PSF and alchemify Jerome Henin (Tue Jun 26 2007 - 13:46:50 CDT)
NNB in PSF and alchemify Luca Bellucci (Tue Jun 26 2007 - 10:27:25 CDT)
abf "force not a vector" error maria goranovic (Tue Jun 26 2007 - 10:31:58 CDT)
Re: working with non-protein files Peter Freddolino (Tue Jun 26 2007 - 09:44:13 CDT)
Re: barostats in NAMD Peter Freddolino (Tue Jun 26 2007 - 09:38:17 CDT)
working with non-protein files Adam Fraser (Mon Jun 25 2007 - 21:57:31 CDT)
Re: About pmf Sting (Mon Jun 25 2007 - 21:38:26 CDT)
has anyone patched NAG to ASN? Irene Newhouse (Mon Jun 25 2007 - 20:57:03 CDT)
CellBasisVector jfgaff_at_ncsu.edu (Mon Jun 25 2007 - 19:53:47 CDT)
barostats in NAMD Audrey Salazar (Mon Jun 25 2007 - 18:41:55 CDT)
Re: About pmf JC Gumbart (Mon Jun 25 2007 - 14:30:51 CDT)
Re: Re£º Re: heat diffusion Jonathan Lee (Mon Jun 25 2007 - 12:38:12 CDT)
turn off intermolecular interaction milton sonoda (Mon Jun 25 2007 - 11:52:28 CDT)
Re: Changing loop to helix: restraining about 20 dihedral angles maria goranovic (Mon Jun 25 2007 - 07:06:28 CDT)
Re: problem with ABF "can't read forces(80)" maria goranovic (Mon Jun 25 2007 - 07:05:35 CDT)
Re: High background load warning message Cesar Avila (Sun Jun 24 2007 - 13:56:24 CDT)
Re: problem with ABF "can't read forces(80)" Jerome Henin (Sun Jun 24 2007 - 11:41:04 CDT)
Re: Changing loop to helix: restraining about 20 dihedral angles Jerome Henin (Sun Jun 24 2007 - 11:37:53 CDT)
PMF, defining end point Per Jr. Greisen (Sun Jun 24 2007 - 10:34:28 CDT)
problem with ABF "can't read forces(80)" maria goranovic (Sun Jun 24 2007 - 07:30:05 CDT)
Re: Changing loop to helix: restraining about 20 dihedral angles maria goranovic (Sun Jun 24 2007 - 07:06:32 CDT)
Re: About pmf Sting (Sat Jun 23 2007 - 21:23:24 CDT)
Re: High background load warning message Jerome Henin (Sat Jun 23 2007 - 20:57:37 CDT)
High background load warning message Cesar Luis Avila (Sat Jun 23 2007 - 19:12:32 CDT)
force on SMD atom Moumita Maiti (Fri Jun 22 2007 - 14:43:27 CDT)
Re: heat diffusion Jonathan Lee (Fri Jun 22 2007 - 11:36:55 CDT)
Re: SMD atoms are not moving in accordance with steering parameters! Peter Freddolino (Fri Jun 22 2007 - 07:59:14 CDT)
RE: namddat Irene Newhouse (Fri Jun 22 2007 - 01:29:08 CDT)
negative force shivam ghosh (Fri Jun 22 2007 - 00:42:24 CDT)
Re: SMD atoms are not moving in accordance with steering parameters! Gungor Ozer (Thu Jun 21 2007 - 21:43:03 CDT)
Re: SMD atoms are not moving in accordance with steering parameters! Gungor Ozer (Thu Jun 21 2007 - 21:37:35 CDT)
Re: ABF inFiles Subramanian Vaitheeswaran (Thu Jun 21 2007 - 12:29:02 CDT)
Re: ABF inFiles Jerome Henin (Thu Jun 21 2007 - 11:57:35 CDT)
Re: Changing loop to helix: restraining about 20 dihedral angles Subramanian Vaitheeswaran (Thu Jun 21 2007 - 11:29:40 CDT)
replies Richard Wood (Thu Jun 21 2007 - 11:11:21 CDT)
ABF inFiles Subramanian Vaitheeswaran (Thu Jun 21 2007 - 11:03:47 CDT)
Re: Changing loop to helix: restraining about 20 dihedral angles Peter Freddolino (Thu Jun 21 2007 - 09:06:00 CDT)
Re: namddat Peter Freddolino (Thu Jun 21 2007 - 08:54:53 CDT)
Re: SMD atoms are not moving in accordance with steering parameters! Peter Freddolino (Thu Jun 21 2007 - 08:51:14 CDT)
TMD David Wright (Thu Jun 21 2007 - 06:03:07 CDT)
Re: SMD atoms are not moving in accordance with steering parameters! Matt Jones (Thu Jun 21 2007 - 02:28:03 CDT)
namddat Irene Newhouse (Thu Jun 21 2007 - 02:01:54 CDT)
Re: Changing loop to helix: restraining about 20 dihedral angles maria goranovic (Thu Jun 21 2007 - 01:33:30 CDT)
SMD atoms are not moving in accordance with steering parameters! Gungor Ozer (Wed Jun 20 2007 - 22:35:59 CDT)
Re: charmrun simulations over macpros pedro.borkowski_at_utoronto.ca (Wed Jun 20 2007 - 20:44:42 CDT)
heat diffusion Jonathan Lee (Wed Jun 20 2007 - 17:39:22 CDT)
Re: Fw: namd-l-outgoing2@halifax.ks.uiuc.edu Jim Phillips (Wed Jun 20 2007 - 17:29:45 CDT)
Fw: namd-l-outgoing2@halifax.ks.uiuc.edu lily jin (Wed Jun 20 2007 - 15:25:56 CDT)
Re: extracting forces from dcd files Peter Freddolino (Wed Jun 20 2007 - 13:44:46 CDT)
Re: charmrun simulations over macpros Cesar Luis Avila (Wed Jun 20 2007 - 13:30:10 CDT)
[Fwd: Re: Using CHARMM27] Victor Ovchinnikov (Wed Jun 20 2007 - 11:49:36 CDT)
extracting forces from dcd files Todd Trimble (Wed Jun 20 2007 - 12:31:49 CDT)
namd-l-outgoing2@halifax.ks.uiuc.edu sanghyuk_at_ewha.ac.kr (Wed Jun 20 2007 - 12:03:59 CDT)
Using CHARMM27 alsalazar_at_northwestern.edu (Wed Jun 20 2007 - 10:27:53 CDT)
Using CHARMM27 Audrey Salazar (Wed Jun 20 2007 - 09:48:45 CDT)
Re: About pmf Sting (Tue Jun 19 2007 - 22:38:39 CDT)
Re: Re: heat diffusion calculation Jonathan Lee (Tue Jun 19 2007 - 15:13:12 CDT)
Changing loop to helix: restraining about 20 dihedral angles maria goranovic (Tue Jun 19 2007 - 10:59:16 CDT)
Re: About pmf bqluan (Tue Jun 19 2007 - 10:35:02 CDT)
How could I find which part of the protein became more flexible Yuxiao Wang (Tue Jun 19 2007 - 07:56:23 CDT)
Error in equlibration Wei Liu (Tue Jun 19 2007 - 06:50:12 CDT)
Re: About pmf JC Gumbart (Tue Jun 19 2007 - 00:02:42 CDT)
About pmf Sting (Mon Jun 18 2007 - 23:00:38 CDT)
Re: Differences between 32bit and 64bit version of NAMD? Carsten Olbrich (Mon Jun 18 2007 - 17:12:37 CDT)
Re: Re: heat diffusion calculation Jonathan Lee (Mon Jun 18 2007 - 16:13:00 CDT)
Re: Re: heat diffusion calculation Victor Ovchinnikov (Mon Jun 18 2007 - 14:58:13 CDT)
Re: Re: heat diffusion calculation QJos=E9_R=2E_Sabino=22?= (Mon Jun 18 2007 - 14:11:17 CDT)
Re: Normal mode analysis L. Michel Espinoza-Fonseca (Mon Jun 18 2007 - 14:02:46 CDT)
Re: Differences between 32bit and 64bit version of NAMD? Carsten Olbrich (Mon Jun 18 2007 - 13:34:45 CDT)
Normal mode analysis Raul Araya Secchi (Mon Jun 18 2007 - 13:18:43 CDT)
Re: heat diffusion calculation Jonathan Lee (Mon Jun 18 2007 - 12:16:20 CDT)
Differences between 32bit and 64bit version of NAMD? Carsten Olbrich (Mon Jun 18 2007 - 11:04:30 CDT)
Temperature Control accomp lin (Mon Jun 18 2007 - 09:31:53 CDT)
Re: NAMD Parameter File Creation J T (Sun Jun 17 2007 - 17:31:27 CDT)
NAMD Parameter File Creation Peter Murphy (Sun Jun 17 2007 - 12:04:51 CDT)
Re: Re: About smd Sting (Sat Jun 16 2007 - 04:14:57 CDT)
Error: Compile charm-5.9 on Fedora core 6? Qiang Zhong (Fri Jun 15 2007 - 22:13:19 CDT)
heat diffusion calculation Jonathan Lee (Fri Jun 15 2007 - 17:40:52 CDT)
Gas phase minimization Purushottam Dixit (Fri Jun 15 2007 - 16:58:44 CDT)
charmrun simulations over macpros pedro.borkowski_at_utoronto.ca (Fri Jun 15 2007 - 13:07:02 CDT)
About smd Sting (Fri Jun 15 2007 - 04:46:54 CDT)
Re: affecting the atom velocities Luca Muccioli (Fri Jun 15 2007 - 04:02:01 CDT)
affecting the atom velocities Philipp Schoen1 (Fri Jun 15 2007 - 02:20:55 CDT)
About pmf Sting (Thu Jun 14 2007 - 21:49:03 CDT)
Re: CNT modeling Jonathan Lee (Thu Jun 14 2007 - 14:44:32 CDT)
Re: help!! JC Gumbart (Thu Jun 14 2007 - 14:07:59 CDT)
checkpoint / revert Arturas Ziemys (Thu Jun 14 2007 - 13:09:24 CDT)
Re: margin value Peter Freddolino (Thu Jun 14 2007 - 09:58:01 CDT)
help!! shivam ghosh (Thu Jun 14 2007 - 06:43:31 CDT)
Reassign temperature for selected atoms? Philipp Schoen1 (Thu Jun 14 2007 - 04:03:46 CDT)
Re: CNT modeling Jonathan Lee (Wed Jun 13 2007 - 13:02:58 CDT)
Re: Turning off tcl forces Victor Ovchinnikov (Wed Jun 13 2007 - 11:19:25 CDT)
RE: Turning off tcl forces JC Gumbart (Wed Jun 13 2007 - 10:30:29 CDT)
Stationary temperature gradient - defining 2 langevinFiles? Philipp Schoen1 (Wed Jun 13 2007 - 09:50:21 CDT)
Turning off tcl forces Cesar Luis Avila (Wed Jun 13 2007 - 09:42:28 CDT)
Re: FATAL ERROR: Bad global exclusion count Peter Freddolino (Tue Jun 12 2007 - 20:48:31 CDT)
RE: FATAL ERROR: Bad global exclusion count Huy N. Ha (Tue Jun 12 2007 - 19:24:27 CDT)
RE: margin value M. Madhu (Tue Jun 12 2007 - 17:19:26 CDT)
minLineGoal comannd Raul Araya Secchi (Tue Jun 12 2007 - 16:13:53 CDT)
(no subject) Raul Araya Secchi (Tue Jun 12 2007 - 16:10:48 CDT)
FATAL ERROR: Bad global exclusion count Idit Buch (Tue Jun 12 2007 - 09:04:17 CDT)
Re: CNT modeling Cesar Luis Avila (Tue Jun 12 2007 - 16:05:21 CDT)
CNT modeling Jonathan Lee (Tue Jun 12 2007 - 15:29:49 CDT)
Re: margin value Peter Freddolino (Tue Jun 12 2007 - 15:28:48 CDT)
Nobody will know about your problems. Adam Sosa (Tue Jun 12 2007 - 13:05:30 CDT)
Re: How to "twist" a molecule? (resubmit) Margaret.Cheung_at_mail.uh.edu (Tue Jun 12 2007 - 11:19:36 CDT)
margin value M. Madhu (Tue Jun 12 2007 - 08:58:11 CDT)
Switch ON your penis! Brittany Calderon (Tue Jun 12 2007 - 07:46:25 CDT)
Nobody will know about your problems. Mary Paul (Tue Jun 12 2007 - 06:49:48 CDT)
To buy or not to buy? Yesenia Clark (Tue Jun 12 2007 - 05:40:37 CDT)
Happy Viagra Brittany Collier (Tue Jun 12 2007 - 03:36:22 CDT)
Tired of your poor health? Aaron Mccall (Mon Jun 11 2007 - 21:51:11 CDT)
Re: How to "twist" a molecule? (resubmit) Victor Ovchinnikov (Mon Jun 11 2007 - 20:21:35 CDT)
Re: How to "twist" a molecule? (resubmit) Margaret S. Cheung (Mon Jun 11 2007 - 17:49:57 CDT)
Can you satisfy your girlfriend? Deborah Stanton (Mon Jun 11 2007 - 17:18:55 CDT)
Power penis Friedrich Salas (Mon Jun 11 2007 - 07:27:35 CDT)
Can you satisfy your girlfriend? Todd Prince (Mon Jun 11 2007 - 05:04:59 CDT)
Want to be on the top all night long? Michael Rich (Sun Jun 10 2007 - 18:26:46 CDT)
Orgasm power Kristen Kemp (Sun Jun 10 2007 - 16:20:44 CDT)
steered md with a constant velocity pulling Moumita Maiti (Sun Jun 10 2007 - 14:45:49 CDT)
Crazy defoliator Allison Chan (Sun Jun 10 2007 - 14:18:35 CDT)
Penis Launcher Stephanie Dodson (Sun Jun 10 2007 - 09:49:07 CDT)
Products that can improve you life! Peter Crosby (Sun Jun 10 2007 - 04:00:27 CDT)
Can't stand sex all night long? Tara England (Sat Jun 09 2007 - 19:28:38 CDT)
Can you satisfy your girlfriend? Zoe Baker (Sat Jun 09 2007 - 17:16:07 CDT)
Can you imagine? Steven Juarez (Sat Jun 09 2007 - 15:44:10 CDT)
Can't find a good drug store? Derek Finley (Sat Jun 09 2007 - 13:20:14 CDT)
Want to be a hero in bed? Natalie Roman (Sat Jun 09 2007 - 09:07:11 CDT)
Your dick is not only for pissing Nicolas Melton (Sat Jun 09 2007 - 07:10:50 CDT)
Hymen penetrator Natasha Davidson (Sat Jun 09 2007 - 01:15:47 CDT)
Re: Partial charges on amino acids Aaron Oakley (Fri Jun 08 2007 - 23:43:54 CDT)
Re: Solvating protein with ions Stephen Hicks (Wed Jun 06 2007 - 17:14:50 CDT)
Re: Water molecules inside protein? Stephen Hicks (Tue Jun 05 2007 - 11:09:19 CDT)
Orgasmotron Natalie Frank (Fri Jun 08 2007 - 23:07:06 CDT)
The best medications for the best price Nicolas Gibbs (Fri Jun 08 2007 - 17:22:46 CDT)
Partial charges on amino acids Purushottam Dixit (Fri Jun 08 2007 - 16:02:18 CDT)
FYEO Zachary Tyson (Fri Jun 08 2007 - 13:28:09 CDT)
rmsd calculation for RNA Moumita Maiti (Fri Jun 08 2007 - 11:48:58 CDT)
RE: Parameter file for Gold ? Ana Celia Araujo Vila Verde (Fri Jun 08 2007 - 09:58:58 CDT)
Parameter file for Gold ? utiramerur_at_ecr6.ohio-state.edu (Fri Jun 08 2007 - 08:51:36 CDT)
Happy Viagra Natasha Kerr (Fri Jun 08 2007 - 07:54:55 CDT)
Report Richard Justice (Thu Jun 07 2007 - 23:37:01 CDT)
Straining yourself when you are with a woman? Friedrick Mcdowell (Thu Jun 07 2007 - 17:49:13 CDT)
problem building Namd frm source... hl332_at_drexel.edu (Thu Jun 07 2007 - 12:32:18 CDT)
Want to be a hero in bed? Amanda Chase (Thu Jun 07 2007 - 11:46:40 CDT)
Say "NO" to erectile dysfunction! Amanda Pearson (Thu Jun 07 2007 - 06:48:07 CDT)
Re: nonbonded interpolation Roy Kimura (Thu Jun 07 2007 - 06:39:09 CDT)
nonbonded interpolation Roy Kimura (Thu Jun 07 2007 - 06:14:57 CDT)
Tired of your poor health? Steven Bowen (Thu Jun 07 2007 - 00:59:57 CDT)
Hymen destroyer Barbara Riddle (Wed Jun 06 2007 - 19:31:28 CDT)
Re: Solvating protein with ions Richard Law (Wed Jun 06 2007 - 19:09:57 CDT)
Re: Solvating protein with ions Leandro Martínez (Wed Jun 06 2007 - 18:21:47 CDT)
Solvating protein with ions B.R.Silver_at_warwick.ac.uk (Wed Jun 06 2007 - 15:20:43 CDT)
Re: Acetaldehyde Dihedral Parameters Peter Freddolino (Wed Jun 06 2007 - 14:28:20 CDT)
Re: Water molecules inside protein? Gianluca Interlandi (Wed Jun 06 2007 - 12:53:03 CDT)
Happy Viagra Dustin Waller (Wed Jun 06 2007 - 12:48:07 CDT)
Re: Acetaldehyde Dihedral Parameters L. Michel Espinoza-Fonseca (Wed Jun 06 2007 - 12:21:38 CDT)
Re: Acetaldehyde Dihedral Parameters Peter Freddolino (Wed Jun 06 2007 - 11:51:57 CDT)
Re: Water molecules inside protein? hl332_at_drexel.edu (Wed Jun 06 2007 - 11:25:40 CDT)
Re: Acetaldehyde Dihedral Parameters Peter Freddolino (Wed Jun 06 2007 - 11:19:42 CDT)
Re: Acetaldehyde Dihedral Parameters L. Michel Espinoza-Fonseca (Wed Jun 06 2007 - 11:05:20 CDT)
Re: Water molecules inside protein? Stephen Hicks (Wed Jun 06 2007 - 11:04:28 CDT)
Acetaldehyde Dihedral Parameters Kevser Göçmen Topal (Wed Jun 06 2007 - 10:33:14 CDT)
Re: Water molecules inside protein? hl332_at_drexel.edu (Wed Jun 06 2007 - 10:25:16 CDT)
Maestro Penis Bridget Walsh (Wed Jun 06 2007 - 06:55:35 CDT)
Worry about your erection? Mary Holcomb (Wed Jun 06 2007 - 00:48:13 CDT)
Re: Water molecules inside protein? Stephen Hicks (Tue Jun 05 2007 - 21:07:47 CDT)
Re: TMD: different behaviour between serial and mpi versions Thomas Gaillard (Tue Jun 05 2007 - 19:25:48 CDT)
To buy or not to buy? Renee Gilmore (Tue Jun 05 2007 - 18:27:11 CDT)
Error on the constraints Jianping Lin (Tue Jun 05 2007 - 16:27:10 CDT)
convergence monitoring... Raul Araya Secchi (Tue Jun 05 2007 - 14:52:57 CDT)
Improve your sexual life and save up to 80% Matthew Hughes (Tue Jun 05 2007 - 12:16:03 CDT)
Re: TMD: different behaviour between serial and mpi versions Jerome Henin (Tue Jun 05 2007 - 11:27:40 CDT)
Rattle Error Ilya Chorny (Tue Jun 05 2007 - 10:45:33 CDT)
Re: Running NAMD on Cluster machine with Myrinet network with MPI and PBS Alexandre A. Vakhrouchev (Tue Jun 05 2007 - 10:34:39 CDT)
Water molecules inside protein? hl332_at_drexel.edu (Tue Jun 05 2007 - 10:23:13 CDT)
TMD: different behaviour between serial and mpi versions Thomas Gaillard (Tue Jun 05 2007 - 09:57:20 CDT)
Sexual power Teresa Jackson (Tue Jun 05 2007 - 07:33:37 CDT)
Running NAMD on Cluster machine with Myrinet network with MPI and PBS Alessio Alexiadis (Tue Jun 05 2007 - 05:23:38 CDT)
Wet miracle Amy Mccormick (Tue Jun 05 2007 - 01:45:44 CDT)
Want to be a hero in bed? Violet Calderon (Mon Jun 04 2007 - 14:18:55 CDT)
load balancing question Stern, Julie (Mon Jun 04 2007 - 09:39:21 CDT)
Report Peter Forbes (Mon Jun 04 2007 - 09:22:19 CDT)
Hymen destroyer George Benton (Mon Jun 04 2007 - 06:25:11 CDT)
RE: POPC bilayer- System size JC Gumbart (Sun Jun 03 2007 - 18:35:19 CDT)
POPC bilayer- System size Purushottam Dixit (Sun Jun 03 2007 - 17:46:09 CDT)
RE: combine pdb files JC Gumbart (Sun Jun 03 2007 - 10:33:02 CDT)
Re: combine pdb files Jeffrey J. Potoff (Sun Jun 03 2007 - 10:11:49 CDT)
NAMD plot plugin Richard Casey (Sun Jun 03 2007 - 10:08:48 CDT)
Re: combine pdb files Alexandre A. Vakhrouchev (Sun Jun 03 2007 - 08:39:30 CDT)
combine pdb files Richard Casey (Sun Jun 03 2007 - 07:24:35 CDT)
Re: Pressure calculation method Alexandre A. Vakhrouchev (Sun Jun 03 2007 - 03:23:04 CDT)
Umbrella Sampling for NAMD Victor Ovchinnikov (Sat Jun 02 2007 - 16:13:41 CDT)
Problems with (Restrained) TMD in NAMD Victor Ovchinnikov (Sat Jun 02 2007 - 16:08:55 CDT)
Re: multiple topology files Peter Freddolino (Sat Jun 02 2007 - 13:45:49 CDT)
multiple topology files Richard Casey (Sat Jun 02 2007 - 13:31:09 CDT)
Re: sugar topology files Peter Freddolino (Sat Jun 02 2007 - 11:24:24 CDT)
sugar topology files Richard Casey (Sat Jun 02 2007 - 11:02:14 CDT)
Re: faulty kernel? Leandro Martínez (Fri Jun 01 2007 - 12:21:24 CDT)
Re: Pressure calculation method JC Gumbart (Fri Jun 01 2007 - 11:59:23 CDT)
faulty kernel? Brian Bennion (Fri Jun 01 2007 - 10:59:39 CDT)
Pressure calculation method Alexandre A. Vakhrouchev (Fri Jun 01 2007 - 09:05:46 CDT)
apply periodic boundary condition in one direction ali alizadeh (Thu May 31 2007 - 07:53:37 CDT)
Re: surface tension Marcos Sotomayor (Thu May 31 2007 - 01:10:51 CDT)
clustermatic 4 Peter Jones (Wed May 30 2007 - 21:18:26 CDT)
surface tension Giovanni Bellesia (Wed May 30 2007 - 19:06:42 CDT)
Re: Replica exchange MD Richard Law (Wed May 30 2007 - 15:15:54 CDT)
Re: Replica exchange MD L. Michel Espinoza-Fonseca (Wed May 30 2007 - 14:03:35 CDT)
Tcl callback, run, revert, measure Xiuping Tao (Wed May 30 2007 - 10:08:55 CDT)
Re: Energy shift during simulation Cesar Luis Avila (Tue May 29 2007 - 16:45:17 CDT)
Re: Energy shift during simulation JC Gumbart (Tue May 29 2007 - 16:10:33 CDT)
Re: Energy shift during simulation Cesar Luis Avila (Tue May 29 2007 - 15:51:55 CDT)
RE: Replica exchange MD Ana Celia Araujo Vila Verde (Tue May 29 2007 - 14:51:45 CDT)
Replica exchange MD L. Michel Espinoza-Fonseca (Tue May 29 2007 - 12:47:34 CDT)
Re: Energy shift during simulation Cesar Luis Avila (Tue May 29 2007 - 09:53:31 CDT)
temperature and pressure control Alessio Alexiadis (Tue May 29 2007 - 00:40:02 CDT)
Re: Energy shift during simulation Cesar Luis Avila (Mon May 28 2007 - 18:26:29 CDT)
Re: Energy shift during simulation hl332_at_drexel.edu (Mon May 28 2007 - 17:47:44 CDT)
Energy shift during simulation Cesar Luis Avila (Mon May 28 2007 - 16:21:29 CDT)
NAMD on Power5 Joachim Hein (Mon May 28 2007 - 11:29:17 CDT)
Re: Protein in/out of box Monika Sharma (Mon May 28 2007 - 11:23:38 CDT)
Re: constraints on zinc ions Richard Wood (Mon May 28 2007 - 11:04:17 CDT)
Re: Protein in/out of box Gianluca Interlandi (Mon May 28 2007 - 10:45:29 CDT)
Re: Protein in/out of box Gianluca Interlandi (Mon May 28 2007 - 10:33:29 CDT)
Re: constraints on zinc ions Peter Freddolino (Mon May 28 2007 - 08:58:19 CDT)
Re: Protein in/out of box Peter Freddolino (Mon May 28 2007 - 08:50:17 CDT)
constraints on zinc ions Wei Liu (Mon May 28 2007 - 07:42:17 CDT)
Protein in/out of box Monika Sharma (Mon May 28 2007 - 06:10:43 CDT)
Re: heating system Luca Bellucci (Mon May 28 2007 - 03:01:38 CDT)
Re: how to simulate sugars George Madalin Giambasu (Sun May 27 2007 - 19:51:35 CDT)
Re: how to simulate sugars Aaron Oakley (Sun May 27 2007 - 19:19:55 CDT)
charm installation problem Govardhan Reddy (Sun May 27 2007 - 16:43:43 CDT)
Re: heating system baxy (Sun May 27 2007 - 13:45:44 CDT)
Re: Why is SHAKE not being used in typical NAMD simulations ? L. Michel Espinoza-Fonseca (Sun May 27 2007 - 12:49:54 CDT)
how to simulate sugars Richard Casey (Sun May 27 2007 - 12:21:26 CDT)
Re: Why is SHAKE not being used in typical NAMD simulations ? Peter Freddolino (Sun May 27 2007 - 12:01:30 CDT)
About cutoff parameter for real space calculation in PME xiaojing gong (Sun May 27 2007 - 06:47:26 CDT)
Re: Why is SHAKE not being used in typical NAMD simulations ? L. Michel Espinoza-Fonseca (Sun May 27 2007 - 05:53:31 CDT)
Re: heating system Luca (Sun May 27 2007 - 04:16:36 CDT)
Pressure calculation method Alexandre A. Vakhrouchev (Sat May 26 2007 - 22:42:36 CDT)
Re: Why is SHAKE not being used in typical NAMD simulations ? Peter Freddolino (Sat May 26 2007 - 11:10:34 CDT)
Re: Why is SHAKE not being used in typical NAMD simulations ? Himanshu Khandelia (Sat May 26 2007 - 05:44:38 CDT)
Re: heating system baxy (Sat May 26 2007 - 05:09:20 CDT)
Re: Why is SHAKE not being used in typical NAMD simulations ? Gianluca Interlandi (Sat May 26 2007 - 01:03:25 CDT)
Re: Why is SHAKE not being used in typical NAMD simulations ? Gianluca Interlandi (Sat May 26 2007 - 00:16:30 CDT)
Re: Running NVT simulations Richard Law (Fri May 25 2007 - 22:27:39 CDT)
Re: Running NVT simulations JC Gumbart (Fri May 25 2007 - 21:06:36 CDT)
Fwd: Laptop for Molecular Dynamics - Summary Deepangi Pandit (Fri May 25 2007 - 20:41:09 CDT)
Re: Laptop for Molecular Dynamics - Summary Deepangi Pandit (Fri May 25 2007 - 20:39:45 CDT)
Running NVT simulations Eric Perim (Fri May 25 2007 - 18:03:48 CDT)
Re: Laptop for Molecular Dynamics Peter Freddolino (Fri May 25 2007 - 17:56:58 CDT)
Re: Laptop for Molecular Dynamics Sabuj Pattanayek (Fri May 25 2007 - 17:52:27 CDT)
Re: Laptop for Molecular Dynamics Marcos Sotomayor (Fri May 25 2007 - 17:16:42 CDT)
Re: Laptop for Molecular Dynamics Deepangi Pandit (Fri May 25 2007 - 16:01:24 CDT)
Re: force-field parameters for glycoproteins Kramer Campen (Fri May 25 2007 - 15:54:11 CDT)
Re: heating system Richard Law (Fri May 25 2007 - 14:52:31 CDT)
GPU acceleration press Jim Phillips (Fri May 25 2007 - 14:00:42 CDT)
Re: Laptop for Molecular Dynamics SÅ‚awek OrÅ‚owski (Fri May 25 2007 - 07:23:48 CDT)
heating system baxy (Fri May 25 2007 - 13:06:50 CDT)
force-field parameters for glycoproteins Gaurav Sharma (Fri May 25 2007 - 13:14:33 CDT)
Re: Fortran and tclForces Peter Freddolino (Fri May 25 2007 - 13:02:50 CDT)
Re: vmd-l: hl332_at_drexel.edu (Fri May 25 2007 - 11:48:20 CDT)
Re: Why is SHAKE not being used in typical NAMD simulations ? Himanshu Khandelia (Fri May 25 2007 - 10:07:55 CDT)
Re: Why is SHAKE not being used in typical NAMD simulations ? Peter Freddolino (Fri May 25 2007 - 09:52:47 CDT)
RE: Why is SHAKE not being used in typical NAMD simulations ? Himanshu Khandelia (Fri May 25 2007 - 04:05:26 CDT)
Fortran and tclForces Luca Bellucci (Fri May 25 2007 - 03:22:11 CDT)
Re: UAB BlueGene Thomas Caulfield (Thu May 24 2007 - 15:39:31 CDT)
Re: Laptop for Molecular Dynamics Sabuj Pattanayek (Thu May 24 2007 - 15:14:20 CDT)
Laptop for Molecular Dynamics Deepangi Pandit (Thu May 24 2007 - 13:09:55 CDT)
help Sathish Kumar Gurupatham (Thu May 24 2007 - 11:31:39 CDT)
RE: Why is SHAKE not being used in typical NAMD simulations ? Ana Celia Araujo Vila Verde (Thu May 24 2007 - 10:42:30 CDT)
Re: Why is SHAKE not being used in typical NAMD simulations ? Himanshu Khandelia (Thu May 24 2007 - 08:46:59 CDT)
Re: namd crash: Signal: segmentation violation Leandro Martínez (Thu May 24 2007 - 08:37:06 CDT)
Temperature Coupling Alessio Alexiadis (Thu May 24 2007 - 02:59:31 CDT)
Re: basic pdb file run with namd and vmd J T (Wed May 23 2007 - 21:49:02 CDT)
Re: Why is SHAKE not being used in typical NAMD simulations ? Gianluca Interlandi (Wed May 23 2007 - 18:05:18 CDT)
basic pdb file run with namd and vmd Kayode Karunwi (Wed May 23 2007 - 16:05:01 CDT)
Re: namd crash: Signal: segmentation violation Gengbin Zheng (Wed May 23 2007 - 14:53:23 CDT)
namd crash: Signal: segmentation violation Leandro Martínez (Wed May 23 2007 - 14:30:05 CDT)
Re: Why is SHAKE not being used in typical NAMD simulations ? L. Michel Espinoza-Fonseca (Wed May 23 2007 - 13:35:46 CDT)
Re: Why is SHAKE not being used in typical NAMD simulations ? L. Michel Espinoza-Fonseca (Wed May 23 2007 - 13:32:25 CDT)
Re: Why is SHAKE not being used in typical NAMD simulations ? Himanshu Khandelia (Wed May 23 2007 - 13:30:11 CDT)
Re: Why is SHAKE not being used in typical NAMD simulations ? Eric Cyr (Wed May 23 2007 - 13:20:34 CDT)
Re: namd crash: Signal: segmentation violation Leandro Martínez (Wed May 23 2007 - 13:00:28 CDT)
Re: Why is SHAKE not being used in typical NAMD simulations ? L. Michel Espinoza-Fonseca (Wed May 23 2007 - 11:15:42 CDT)
Re: How could I fixed the system just in Z-coordinate? Himanshu Khandelia (Wed May 23 2007 - 10:51:49 CDT)
NAMD on RedHat Linux godawr_at_rpi.edu (Wed May 23 2007 - 10:04:22 CDT)
How could I fixed the system just in Z-coordinate? ali alizadeh (Wed May 23 2007 - 09:34:32 CDT)
Re: No effect of periodic boundary conditions? Peter Freddolino (Wed May 23 2007 - 09:24:21 CDT)
No effect of periodic boundary conditions? Philipp Schoen1 (Wed May 23 2007 - 09:12:13 CDT)
Why is SHAKE not being used in typical NAMD simulations ? Himanshu Khandelia (Wed May 23 2007 - 08:06:04 CDT)
Re: Minimization Luca (Wed May 23 2007 - 02:42:31 CDT)
Re: FullSamples variable in ABF Christophe.Chipot_at_edam.uhp-nancy.fr (Wed May 23 2007 - 02:04:37 CDT)
FullSamples variable in ABF alex digenova bravo (Tue May 22 2007 - 23:50:36 CDT)
Compiling namd on ibm-power + red hat linux Caio Julio Martins Veloso (Tue May 22 2007 - 20:23:36 CDT)
Re: namd crash: Signal: segmentation violation Brian Bennion (Tue May 22 2007 - 14:39:43 CDT)
Re: namd crash: Signal: segmentation violation Leandro Martínez (Tue May 22 2007 - 12:55:22 CDT)
Re: namd crash: Signal: segmentation violation Brian Bennion (Tue May 22 2007 - 10:53:59 CDT)
Re: namd crash: Signal: segmentation violation Gengbin Zheng (Tue May 22 2007 - 10:49:08 CDT)
Re: namd crash: Signal: segmentation violation Leandro Martínez (Tue May 22 2007 - 08:17:33 CDT)
load balance strategy query hl332_at_drexel.edu (Mon May 21 2007 - 11:49:22 CDT)
Re: Can´t use charmm to perform dcd analysis Himanshu Khandelia (Mon May 21 2007 - 01:17:58 CDT)
Can´t use charmm to perform dcd analysis Victor Capistrán (Sun May 20 2007 - 22:56:18 CDT)
problems compiling NAMD on SCALI architecture satya work (Sun May 20 2007 - 05:56:54 CDT)
Overlaoded processors when running NAMD on NCSA Altix Gianluca Interlandi (Sat May 19 2007 - 20:06:08 CDT)
RE: OPLS dihedrals JC Gumbart (Sat May 19 2007 - 11:35:08 CDT)
OPLS dihedrals Arturas Ziemys (Sat May 19 2007 - 10:47:16 CDT)
Re: NAMD question Peter Freddolino (Sat May 19 2007 - 09:40:43 CDT)
Re: namd.conf with OPLS options Peter Freddolino (Sat May 19 2007 - 09:39:03 CDT)
NAMD question Cheri McFerrin (Sat May 19 2007 - 08:11:57 CDT)
q=D8=B8=B4=A3=BA=20Re:=20=BB=D8=B8=B4=A3=BA=20Re:=20?= qHow=20to=20compile=20NAMD2.6=20on=20core2=20operons,=20x86=5F?= 64-redhat-linux,which is the proper choice in Arch .?= xiaojing gong (Fri May 18 2007 - 19:28:14 CDT)
namd.conf with OPLS options Alexis Salas (Fri May 18 2007 - 17:43:52 CDT)
Re: namd crash: Signal: segmentation violation Gengbin Zheng (Fri May 18 2007 - 16:28:54 CDT)
Re: namd crash: Signal: segmentation violation Leandro Martínez (Fri May 18 2007 - 16:19:33 CDT)
Re: namd crash: Signal: segmentation violation Brian Bennion (Fri May 18 2007 - 15:43:20 CDT)
Re: namd crash: Signal: segmentation violation Gengbin Zheng (Fri May 18 2007 - 15:30:34 CDT)
Re: namd crash: Signal: segmentation violation Leandro Martínez (Fri May 18 2007 - 15:13:00 CDT)
Re: namd crash: Signal: segmentation violation Leandro Martínez (Fri May 18 2007 - 14:49:06 CDT)
Re: namd crash: Signal: segmentation violation Leandro Martínez (Fri May 18 2007 - 13:53:15 CDT)
Re: namd crash: Signal: segmentation violation Leandro Martínez (Fri May 18 2007 - 12:41:24 CDT)
Re: namd crash: Signal: segmentation violation Brian Bennion (Fri May 18 2007 - 10:25:46 CDT)
Re: namd crash: Signal: segmentation violation Leandro Martínez (Fri May 18 2007 - 07:25:02 CDT)
improper torsion Hidekazu WATANABE (Fri May 18 2007 - 04:56:37 CDT)
Re: pdb file Jeffrey A Tibbitt (Thu May 17 2007 - 17:49:35 CDT)
Re: namd crash: Signal: segmentation violation Brian Bennion (Thu May 17 2007 - 17:06:15 CDT)
Re: pdb file Peter Freddolino (Thu May 17 2007 - 16:47:33 CDT)
Re: pdb file Leandro Martínez (Thu May 17 2007 - 15:56:37 CDT)
Re: namd crash: Signal: segmentation violation Leandro Martínez (Thu May 17 2007 - 15:39:56 CDT)
pdb file Sathish Kumar Gurupatham (Thu May 17 2007 - 15:32:58 CDT)
Re: namd crash: Signal: segmentation violation Brian Bennion (Thu May 17 2007 - 15:25:48 CDT)
namd crash: Signal: segmentation violation Leandro Martínez (Thu May 17 2007 - 13:34:43 CDT)
Re: Sulphate Ion Parameters (fwd) Parminder Mankoo (Thu May 17 2007 - 10:00:18 CDT)
RE: System charge JC Gumbart (Thu May 17 2007 - 09:14:42 CDT)
double precision numerical accuracy issue Himanshu Khandelia (Thu May 17 2007 - 08:51:36 CDT)
Re: Sulphate Ion Parameters Arturas Ziemys (Thu May 17 2007 - 08:42:09 CDT)
Sulphate Ion Parameters Maria Bagonis (Thu May 17 2007 - 07:47:38 CDT)
problems compiling NAMD on SCALI architecture satya work (Thu May 17 2007 - 05:49:58 CDT)
System charge Ayþe Özlem Sezerman (Thu May 17 2007 - 04:02:50 CDT)
Re: How to unsubscribe ? Gianluca Interlandi (Wed May 16 2007 - 14:43:41 CDT)
Re: Minimization Peter Freddolino (Wed May 16 2007 - 13:48:58 CDT)
Re: How to unsubscribe ? Richard Law (Wed May 16 2007 - 13:41:30 CDT)
Tcl in NAMD (math::interpolate) Chi-Cheng Chiu (Wed May 16 2007 - 13:03:03 CDT)
How to unsubscribe ? Viswanadham Sridhara (Wed May 16 2007 - 12:30:38 CDT)
Minimization Rita Cassia (Wed May 16 2007 - 12:19:51 CDT)
Re: how to use measure hbonds to calculate occupancy of all hbonds in simulation? lnubiofox (Wed May 16 2007 - 09:57:51 CDT)
Re: Conversion of .dcd into .xtc format Alessandro Pedretti (Wed May 16 2007 - 09:33:13 CDT)
Re: How to link two proteins Peter Freddolino (Wed May 16 2007 - 07:25:26 CDT)
Re: Conversion of .dcd into .xtc format L. Michel Espinoza-Fonseca (Wed May 16 2007 - 07:22:26 CDT)
Conversion of .dcd into .xtc format priti arora (Wed May 16 2007 - 07:03:11 CDT)
Specified Electric Field accomp lin (Wed May 16 2007 - 06:41:22 CDT)
compiling namd intel 9.1 Alberto Santana (Wed May 16 2007 - 06:06:35 CDT)
How to link two proteins olivier walker (Wed May 16 2007 - 02:50:00 CDT)
q=D8=B8=B4=A3=BA=20Re:=20=20How=20to=20compile=20NAMD?= 2.6 on core2 operons, x86_64-redhat-linux,which isqthe=20proper=20choice=20in=20Arch.?= xiaojing gong (Wed May 16 2007 - 01:42:59 CDT)
Re: how to use measure hbonds to calculate occupancy of all hbonds in simulation? Dong Luo (Tue May 15 2007 - 18:27:01 CDT)
User defined potentials of Lennard-Jones type possible? Philipp Schoen1 (Tue May 15 2007 - 09:23:51 CDT)
how to use measure hbonds to calculate occupancy of all hbonds in simulation? lnubiofox (Tue May 15 2007 - 09:21:33 CDT)
How to compile NAMD2.6 on core2 operons, x86_64-redhat-linux,which is the proper choice in Arch. xiaojing gong (Mon May 14 2007 - 21:41:43 CDT)
Re: simulation problems Giovanni Bellesia (Mon May 14 2007 - 17:24:48 CDT)
simulation problems baxy (Mon May 14 2007 - 16:42:44 CDT)
Deformations under constant strain rates Andrea Diaz (Mon May 14 2007 - 12:28:18 CDT)
DPMTA instead of PME without PBC possible? Philipp Schoen1 (Mon May 14 2007 - 07:15:52 CDT)
TCL script for umbrella sampling arijit_r_at_chem.iitkgp.ernet.in (Mon May 14 2007 - 05:07:01 CDT)
Re: how to caculate the hydrogen bonds occupancy? Gianluca Interlandi (Sun May 13 2007 - 13:43:57 CDT)
how to caculate the hydrogen bonds occupancy? lnubiofox (Sun May 13 2007 - 09:36:35 CDT)
Re: first aid Francesco Pietra (Fri May 11 2007 - 16:14:06 CDT)
Re: vmd-l: Fast routines for distance evaluations using PBC. John Stone (Fri May 11 2007 - 13:15:27 CDT)
Re: recalculating energies Peter Freddolino (Fri May 11 2007 - 12:28:04 CDT)
recalculating energies dimka (Fri May 11 2007 - 12:19:27 CDT)
Fast routines for distance evaluations using PBC. Arturas Ziemys (Fri May 11 2007 - 11:52:49 CDT)
Re: NAMD on CELL BE David Kunzman (Thu May 10 2007 - 17:03:37 CDT)
about PMF and MCTI Luca Bellucci (Fri May 11 2007 - 09:02:33 CDT)
Zn parameters Fabio Passetti (Fri May 11 2007 - 08:17:31 CDT)
Re: files for air Jeffrey J. Potoff (Fri May 11 2007 - 07:21:20 CDT)
files for air SMAHANE CHALABI (Fri May 11 2007 - 04:01:27 CDT)
Re: NAMD on CELL BE Gengbin Zheng (Thu May 10 2007 - 15:56:36 CDT)
Re: NAMD on CELL BE Gengbin Zheng (Thu May 10 2007 - 15:43:23 CDT)
Re: Simulating air with NAMD surendra negi (Thu May 10 2007 - 12:48:15 CDT)
Re: Question about ABF Jerome Henin (Thu May 10 2007 - 10:26:30 CDT)
Re: water models: a basic question Jeffrey J. Potoff (Thu May 10 2007 - 09:10:47 CDT)
Re: water models: a basic question Luca Muccioli (Thu May 10 2007 - 08:18:44 CDT)
water models: a basic question Alessio Alexiadis (Thu May 10 2007 - 06:31:26 CDT)
cd /people/himanshu/hkhandel/SOPIP2/OPEN/PE/PERMEATIONRe: fixed system just in Z direction Himanshu Khandelia (Thu May 10 2007 - 06:15:49 CDT)
fixed system just in Z direction ali alizadeh (Thu May 10 2007 - 03:36:04 CDT)
Question about ABF German Saavedra (Wed May 09 2007 - 19:09:45 CDT)
Re: query about wrapped coordinates: Problem SOLVED Jerome Henin (Wed May 09 2007 - 13:46:02 CDT)
Re: query about wrapped coordinates: Problem SOLVED Gianluca Interlandi (Wed May 09 2007 - 12:28:27 CDT)
Re: query about wrapped coordinates: Problem SOLVED hl332_at_drexel.edu (Wed May 09 2007 - 09:22:29 CDT)
"Timeout waiting for node-program to connect" error, only sometimes Himanshu Khandelia (Wed May 09 2007 - 02:58:29 CDT)
Re: first aid Peter Freddolino (Tue May 08 2007 - 17:06:43 CDT)
Re: first aid JC Gumbart (Tue May 08 2007 - 17:01:40 CDT)
first aid Francesco Pietra (Tue May 08 2007 - 16:46:29 CDT)
my simulation dont be minimized when I fixed the channel ali alizadeh (Tue May 08 2007 - 09:48:35 CDT)
Re: Simulating air with NAMD dimka (Tue May 08 2007 - 13:53:28 CDT)
Re: query about wrapped coordinates Gianluca Interlandi (Tue May 08 2007 - 13:37:53 CDT)
Re: query about wrapped coordinates hl332_at_drexel.edu (Tue May 08 2007 - 13:15:34 CDT)
Re: query about wrapped coordinates Cesar Luis Avila (Tue May 08 2007 - 08:46:13 CDT)
Re: Simulating air with NAMD Mark Abraham (Mon May 07 2007 - 19:42:12 CDT)
Re: query about wrapped coordinates Gianluca Interlandi (Mon May 07 2007 - 19:29:54 CDT)
RE: Harmonic dihedral restraints Jeff Wereszczynski (Mon May 07 2007 - 19:15:30 CDT)
Re: query about wrapped coordinates hl332_at_drexel.edu (Mon May 07 2007 - 19:05:40 CDT)
Harmonic dihedral restraints Christopher Rowley (Mon May 07 2007 - 16:57:08 CDT)
Re: query about wrapped coordinates hl332_at_drexel.edu (Mon May 07 2007 - 16:09:07 CDT)
Re: Simulating air with NAMD Richard Wood (Mon May 07 2007 - 07:26:09 CDT)
Re: Simulating air with NAMD Mark Abraham (Mon May 07 2007 - 00:26:59 CDT)
Re: Simulating air with NAMD Jim Phillips (Sun May 06 2007 - 22:31:27 CDT)
Re: Simulating air with NAMD Jeffrey J. Potoff (Sun May 06 2007 - 21:38:35 CDT)
Re: Simulating air with NAMD Mark Abraham (Sun May 06 2007 - 21:20:14 CDT)
Re: Simulating air with NAMD JC Gumbart (Sun May 06 2007 - 21:14:56 CDT)
Re: Simulating air with NAMD Mark Abraham (Sun May 06 2007 - 20:18:57 CDT)
Re: Simulating air with NAMD Mark Abraham (Sun May 06 2007 - 20:15:48 CDT)
Re: Simulating air with NAMD JC Gumbart (Sun May 06 2007 - 19:09:03 CDT)
RE: Simulating air with NAMD JC Gumbart (Sun May 06 2007 - 14:37:03 CDT)
Re: Simulating air with NAMD Richard Wood (Sun May 06 2007 - 13:43:28 CDT)
Re: Simulating air with NAMD Mark Abraham (Sun May 06 2007 - 12:11:51 CDT)
Simulating air with NAMD Lechuga, Javier (Sun May 06 2007 - 10:05:04 CDT)
Re: query about wrapped coordinates Gianluca Interlandi (Fri May 04 2007 - 17:53:42 CDT)
Re: query about wrapped coordinates Gianluca Interlandi (Fri May 04 2007 - 14:54:20 CDT)
query about wrapped coordinates hl332_at_drexel.edu (Fri May 04 2007 - 13:00:07 CDT)
Timestep Mustapha Hamdi (Fri May 04 2007 - 12:48:18 CDT)
Re: abrupt deviation in rmsd values Monika Sharma (Fri May 04 2007 - 12:41:24 CDT)
Help RICARDO VAZQUEZ (Thu May 03 2007 - 18:26:06 CDT)
error messages in log file Stern, Julie (Fri May 04 2007 - 10:41:14 CDT)
Re: Regarding Trajectory analysis Peter Freddolino (Fri May 04 2007 - 10:12:22 CDT)
Regarding Trajectory analysis priti arora (Fri May 04 2007 - 09:45:14 CDT)
Problems with version 2.6 for amd64 Carsten Olbrich (Fri May 04 2007 - 03:37:08 CDT)
Re: System Charge Luca Muccioli (Fri May 04 2007 - 01:26:13 CDT)
Re: abrupt deviation in rmsd values Peter Freddolino (Thu May 03 2007 - 19:25:27 CDT)
System Charge alex digenova bravo (Thu May 03 2007 - 18:26:39 CDT)
Re: abrupt deviation in rmsd values Giovanni Bellesia (Thu May 03 2007 - 11:34:22 CDT)
Re: abrupt deviation in rmsd values Monika Sharma (Thu May 03 2007 - 10:43:29 CDT)
Re: water and air box by VMD Mark Abraham (Thu May 03 2007 - 02:49:55 CDT)
water and air box by VMD SMAHANE CHALABI (Thu May 03 2007 - 02:36:36 CDT)
Re: Re: Calculating macroscopic properties Mark Abraham (Thu May 03 2007 - 00:42:26 CDT)
Re: Calculating macroscopic properties poker_at_physics.usyd.edu.au (Wed May 02 2007 - 22:00:28 CDT)
Re: abrupt deviation in rmsd values Peter Freddolino (Wed May 02 2007 - 20:28:57 CDT)
Re: "RESTARTING CONJUGATE GRADIENT ALGORITHM" Peter Freddolino (Wed May 02 2007 - 20:15:32 CDT)
"RESTARTING CONJUGATE GRADIENT ALGORITHM" Ugur Akgun (Wed May 02 2007 - 11:14:10 CDT)
abrupt deviation in rmsd values Monika Sharma (Wed May 02 2007 - 10:35:38 CDT)
Re: dcd binary file format Peter Freddolino (Tue May 01 2007 - 17:34:27 CDT)
Re: dcd binary file format Jeffrey A Tibbitt (Tue May 01 2007 - 16:57:47 CDT)
dcd binary file format Jianhui Tian (Tue May 01 2007 - 14:41:53 CDT)
Re: Calculating macroscopic properties Marcos Sotomayor (Tue May 01 2007 - 11:49:44 CDT)
Re: infinite layer Peter Freddolino (Tue May 01 2007 - 11:17:28 CDT)
Re: infinite layer Nicolas Belloy (Tue May 01 2007 - 08:18:40 CDT)
RE: Calculating macroscopic properties JC Gumbart (Tue May 01 2007 - 01:13:35 CDT)
Re: Parameterizing ligands with protein Mark Abraham (Tue May 01 2007 - 00:26:08 CDT)
Parameterizing ligands with protein Lakshmi Dharmarajan (Tue May 01 2007 - 00:17:37 CDT)
Re: Calculating macroscopic properties Mark Abraham (Mon Apr 30 2007 - 21:51:49 CDT)
Calculating macroscopic properties poker_at_physics.usyd.edu.au (Mon Apr 30 2007 - 21:38:37 CDT)
dcd trajectory format Jianhui Tian (Mon Apr 30 2007 - 11:26:31 CDT)
Re: Amber PARM Input File Example? Vlad Cojocaru (Fri Apr 27 2007 - 10:19:56 CDT)
NAMD on CELL BE Alexandre A. Vakhrouchev (Fri Apr 27 2007 - 09:52:50 CDT)
Re: Polarizable force fields Leonardo Trabuco (Fri Apr 27 2007 - 08:34:25 CDT)
RE: Amber PARM Input File Example? Huy N. Ha (Fri Apr 27 2007 - 07:39:57 CDT)
Re: Amber PARM Input File Example? wang (Fri Apr 27 2007 - 02:43:38 CDT)
Re: Amber PARM Input File Example? Mark Abraham (Fri Apr 27 2007 - 00:58:33 CDT)
Amber PARM Input File Example? Huy N. Ha (Fri Apr 27 2007 - 00:51:37 CDT)
Polarizable force fields dtmirij (Fri Apr 27 2007 - 00:44:13 CDT)
Troubles with Free Energy of Conformation Change Masya Mix (Thu Apr 26 2007 - 14:23:13 CDT)
Re: Fep questions about FepEquilSteps Chris Chipot (Wed Apr 25 2007 - 16:25:11 CDT)
Fep questions about FepEquilSteps alex digenova bravo (Wed Apr 25 2007 - 14:50:43 CDT)
Re: PBC related query Gianluca Interlandi (Wed Apr 25 2007 - 13:13:25 CDT)
Re: Problem for to use/compile NAMD with mpiexec Nicolas Sapay (Wed Apr 25 2007 - 11:50:59 CDT)
Re: a topology file in VMD Cesar Luis Avila (Wed Apr 25 2007 - 10:07:49 CDT)
PBC related query hl332_at_drexel.edu (Wed Apr 25 2007 - 09:49:09 CDT)
Re: a topology file in VMD Cesar Luis Avila (Wed Apr 25 2007 - 08:58:01 CDT)
a topology file in VMD SMAHANE CHALABI (Wed Apr 25 2007 - 02:57:42 CDT)
Problem for to use/compile NAMD with mpiexec Nicolas Sapay (Tue Apr 24 2007 - 17:20:52 CDT)
a topology file in VMD SMAHANE CHALABI (Tue Apr 24 2007 - 10:28:07 CDT)
Re: errors in energy minimization Peter Freddolino (Tue Apr 24 2007 - 09:49:59 CDT)
COntraints for lipid bilayer simulation priti arora (Tue Apr 24 2007 - 05:56:12 CDT)
errors in energy minimization Wei Liu (Tue Apr 24 2007 - 05:27:52 CDT)
units of OutputMomenta Stern, Julie (Mon Apr 23 2007 - 12:28:09 CDT)
topology file SMAHANE CHALABI (Mon Apr 23 2007 - 08:40:54 CDT)
Run NAMD in loops Neelanjana Sengupta (Sun Apr 22 2007 - 05:36:33 CDT)
Re: abf output Chris Chipot (Fri Apr 20 2007 - 17:08:47 CDT)
Re: Pressure Discrepancy Richard Wood (Fri Apr 20 2007 - 15:23:18 CDT)
Re: Pressure Discrepancy Morad Alawneh (Fri Apr 20 2007 - 12:30:37 CDT)
segmentation fault: Please Help hl332_at_drexel.edu (Fri Apr 20 2007 - 11:22:09 CDT)
Re: Pressure Discrepancy Sterling Paramore (Fri Apr 20 2007 - 11:18:39 CDT)
Re: Pressure Discrepancy Morad Alawneh (Fri Apr 20 2007 - 10:56:07 CDT)
Re: Charges in NAMD topology file Richard Wood (Fri Apr 20 2007 - 09:53:08 CDT)
Periodic Run Crash hl332_at_drexel.edu (Fri Apr 20 2007 - 09:37:39 CDT)
Re: namd: DSPC and DAPC for a phospholipid bilayer SMAHANE CHALABI (Fri Apr 20 2007 - 09:10:28 CDT)
abf output Christine Horejs (Fri Apr 20 2007 - 07:19:12 CDT)
Re: Charges in NAMD topology file Jawahar Neelankatan (Fri Apr 20 2007 - 07:10:59 CDT)
Re: Pressure Discrepancy Richard Wood (Fri Apr 20 2007 - 06:01:44 CDT)
namd: DSPC and DAPC for a phospholipid bilayer SMAHANE CHALABI (Fri Apr 20 2007 - 04:55:21 CDT)
PMF Christine Horejs (Fri Apr 20 2007 - 03:59:11 CDT)
Re: Pressure Discrepancy Sterling Paramore (Thu Apr 19 2007 - 22:16:04 CDT)
Re: Charges in NAMD topology file JC Gumbart (Thu Apr 19 2007 - 18:21:34 CDT)
Charges in NAMD topology file Jawahar Neelankatan (Thu Apr 19 2007 - 16:51:08 CDT)
Re: Pressure Discrepancy Morad Alawneh (Thu Apr 19 2007 - 16:05:05 CDT)
Re: top_all27_prot_na.inp and par_all27_prot_na.inp JC Gumbart (Thu Apr 19 2007 - 15:36:45 CDT)
top_all27_prot_na.inp and par_all27_prot_na.inp Wei Liu (Thu Apr 19 2007 - 15:19:22 CDT)
Membrame Volume Increasing after restart Vamshi Gangupomu (Thu Apr 19 2007 - 13:24:24 CDT)
Announcement: QM/MM Workshop Jerome Henin (Thu Apr 19 2007 - 13:13:36 CDT)
Re: general question on protein-membrane simulations -complete message! Luca (Thu Apr 19 2007 - 02:48:21 CDT)
general question on protein-membrane simulations -complete message! L. Michel Espinoza-Fonseca (Wed Apr 18 2007 - 11:38:10 CDT)
general question on protein-membrane simulations L. Michel Espinoza-Fonseca (Wed Apr 18 2007 - 11:26:46 CDT)
pure TIP5P water system with AMBER7 parameters satya work (Wed Apr 18 2007 - 11:23:26 CDT)
Re: infinite layer Nicolas Belloy (Wed Apr 18 2007 - 06:06:52 CDT)
Re: question on heating L. Michel Espinoza-Fonseca (Wed Apr 18 2007 - 05:29:49 CDT)
Double bond-pheyl group bonding parameters Kevser Göçmen Topal (Wed Apr 18 2007 - 01:19:03 CDT)
Re: question on heating Leandro Martínez (Tue Apr 17 2007 - 16:33:05 CDT)
question on heating L. Michel Espinoza-Fonseca (Tue Apr 17 2007 - 15:59:12 CDT)
hexagonal box dimka (Tue Apr 17 2007 - 12:11:09 CDT)
pmf calculation Christine Horejs (Tue Apr 17 2007 - 08:20:41 CDT)
Re: 2 proteins L. Michel Espinoza-Fonseca (Tue Apr 17 2007 - 05:30:02 CDT)
2 proteins Christine Horejs (Tue Apr 17 2007 - 04:59:11 CDT)
different results for parallel vs serial runs for NAMD Yousung Jung (Mon Apr 16 2007 - 23:04:56 CDT)
Re: How to make alkaline ph pgn file Gaurav Sharma (Mon Apr 16 2007 - 21:59:26 CDT)
Re: cubic periodic boundary box: what happen if I use a rectangular box? Margaret S. Cheung (Mon Apr 16 2007 - 15:22:25 CDT)
Re: cubic periodic boundary box: what happen if I use a rectangular box? JC Gumbart (Mon Apr 16 2007 - 15:48:09 CDT)
cubic periodic boundary box: what happen if I use a rectangular box? Margaret S. Cheung (Mon Apr 16 2007 - 14:43:13 CDT)
How to make alkaline ph pgn file ravi sharma (Mon Apr 16 2007 - 14:11:47 CDT)
total force on atom Todd Trimble (Mon Apr 16 2007 - 14:59:13 CDT)
TMD constrained energy M. Madhu (Mon Apr 16 2007 - 11:31:11 CDT)
Re: infinite layer Peter Freddolino (Fri Apr 13 2007 - 21:57:58 CDT)
Re: compiling NAMD on an elan-linux-ia64 arch Peter Freddolino (Fri Apr 13 2007 - 21:33:32 CDT)
Re: compiling NAMD on an elan-linux-ia64 arch Vlad Cojocaru (Fri Apr 13 2007 - 03:50:20 CDT)
how to kill namd2 child process after power cut Philipp Schoen1 (Fri Apr 13 2007 - 03:16:59 CDT)
Re: compiling NAMD on an elan-linux-ia64 arch Peter Freddolino (Thu Apr 12 2007 - 16:01:44 CDT)
infinite layer Nicolas Belloy (Thu Apr 12 2007 - 11:59:26 CDT)
which charm paco ty (Thu Apr 12 2007 - 10:41:48 CDT)
namd seg fault on Intel cluster Smith, Ian (Thu Apr 12 2007 - 10:20:40 CDT)
returning the host list where NAMD runs from an LSF batch system Vlad Cojocaru (Thu Apr 12 2007 - 09:16:41 CDT)
q=D8=B8=B4=A3=BA=20Re:=20How=20to=20build=20charm++=20on=20c?= ore2 processor xiaojing gong (Thu Apr 12 2007 - 09:09:58 CDT)
compiling NAMD on an elan-linux-ia64 arch Vlad Cojocaru (Thu Apr 12 2007 - 04:51:41 CDT)
How to define a spatial grid for a temperature landscape/contour Philipp Schoen1 (Thu Apr 12 2007 - 04:36:31 CDT)
Re: RATTLE algorithm error Peter Freddolino (Wed Apr 11 2007 - 19:09:03 CDT)
Re: Minimizer Peter Freddolino (Wed Apr 11 2007 - 19:01:17 CDT)
Re: How to build charm++ on core2 processor Gengbin Zheng (Wed Apr 11 2007 - 14:26:06 CDT)
RATTLE algorithm error Marcelo Puiatti (Wed Apr 11 2007 - 09:46:38 CDT)
"binaryoutput no" doesn't work Philipp Schoen1 (Wed Apr 11 2007 - 05:55:02 CDT)
Minimizer Ayþe Özlem Sezerman (Wed Apr 11 2007 - 05:38:48 CDT)
Re: problem about pairlistdistance... hl332_at_drexel.edu (Tue Apr 10 2007 - 16:23:22 CDT)
Re: zCoord-1atom and ** General remark: Subject lines ** Jerome Henin (Tue Apr 10 2007 - 15:28:27 CDT)
Re: problem about pairlistdistance... Peter Freddolino (Tue Apr 10 2007 - 13:39:39 CDT)
problem about pairlistdistance... hl332_at_drexel.edu (Tue Apr 10 2007 - 11:24:15 CDT)
zCoord-1atom German Saavedra (Tue Apr 10 2007 - 11:24:05 CDT)
How to build charm++ on core2 processor xiaojing gong (Tue Apr 10 2007 - 07:12:40 CDT)
help! How to build charm++ on core 2 computer processor xiaojing gong (Tue Apr 10 2007 - 06:29:09 CDT)
warning about pairlistdist: hl332_at_drexel.edu (Mon Apr 09 2007 - 23:35:22 CDT)
unsubscribe Xiongce Zhao (Mon Apr 09 2007 - 09:29:55 CDT)
Re: equilibration of "big" membrane L. Michel Espinoza-Fonseca (Mon Apr 09 2007 - 07:42:09 CDT)
I'm sorry ... please ignore the junk !! Vlad Cojocaru (Mon Apr 09 2007 - 05:50:54 CDT)
Vlad has Tagged you! :) Vlad Cojocaru (Mon Apr 09 2007 - 05:06:40 CDT)
Re: equilibration of "big" membrane Richard Law (Sun Apr 08 2007 - 19:21:34 CDT)
namd 2.6 installation on i686 problems Stern, Julie (Sun Apr 08 2007 - 15:30:00 CDT)
RE: wrong velocity in steered molecular dynamics Ana Celia Araujo Vila Verde (Sun Apr 08 2007 - 14:57:29 CDT)
RE: wrong velocity in steered molecular dynamics JC Gumbart (Sun Apr 08 2007 - 14:38:15 CDT)
Re: equilibration of "big" membrane L. Michel Espinoza-Fonseca (Sun Apr 08 2007 - 14:02:44 CDT)
RE: wrong velocity in steered molecular dynamics Ana Celia Araujo Vila Verde (Sun Apr 08 2007 - 13:56:29 CDT)
Re: wrong velocity in steered molecular dynamics JC Gumbart (Sat Apr 07 2007 - 18:38:16 CDT)
Re: can someone comment? hl332_at_drexel.edu (Sat Apr 07 2007 - 17:36:12 CDT)
Re: equilibration of "big" membrane Richard Law (Sat Apr 07 2007 - 17:34:44 CDT)
wrong velocity in steered molecular dynamics Ana Celia Araujo Vila Verde (Sat Apr 07 2007 - 14:29:18 CDT)
equilibration of "big" membrane L. Michel Espinoza-Fonseca (Sat Apr 07 2007 - 13:49:05 CDT)
Re: can someone comment? Cesar Avila (Sat Apr 07 2007 - 11:57:49 CDT)
can someone comment? hl332_at_drexel.edu (Fri Apr 06 2007 - 22:17:32 CDT)
Re: Pressure fluctuations Mark Abraham (Thu Apr 05 2007 - 22:09:25 CDT)
Pressure fluctuations Cyril Falvo (Thu Apr 05 2007 - 14:30:13 CDT)
Re: NAMD on Infiniband - problems and successes Jimmy Tang (Thu Apr 05 2007 - 12:19:24 CDT)
error on running NAMD on a large cluster with prun Vlad Cojocaru (Thu Apr 05 2007 - 04:14:33 CDT)
Re: NAMD 2.6 installation problem QJos=E9_R=2E_Sabino=22?= (Wed Apr 04 2007 - 17:03:52 CDT)
NAMD 2.6 installation problem Stern, Julie (Wed Apr 04 2007 - 15:06:50 CDT)
Translation to NAMD psf file. Hidekazu WATANABE (Wed Apr 04 2007 - 08:17:05 CDT)
Re: RE:Re: Help !!! ERROR: Atoms mooving too fast Luis Cunha (Tue Apr 03 2007 - 20:53:10 CDT)
Re: Pressure Discrepancy Sterling Paramore (Tue Apr 03 2007 - 20:44:36 CDT)
Re: Atoms mooving too fast ... still the problem Peter Freddolino (Tue Apr 03 2007 - 20:12:05 CDT)
Atoms mooving too fast ... still the problem Andrea Diaz (Tue Apr 03 2007 - 19:51:39 CDT)
RE: Re: Help !!! ERROR: Atoms mooving too fast Jeff Wereszczynski (Tue Apr 03 2007 - 18:02:33 CDT)
RE:Re: Help !!! ERROR: Atoms mooving too fast Andrea Diaz (Tue Apr 03 2007 - 14:46:36 CDT)
Re: Pressure Discrepancy Morad Alawneh (Tue Apr 03 2007 - 11:39:08 CDT)
Re: membrane simulation: pressure control parameters JC Gumbart (Mon Apr 02 2007 - 17:23:05 CDT)
read dcd binary trajectory milton sonoda (Mon Apr 02 2007 - 14:25:03 CDT)
membrane simulation: pressure control parameters Vlad Cojocaru (Mon Apr 02 2007 - 06:55:10 CDT)
Re: Creating PDB from PSF and COOR files Peter Freddolino (Fri Mar 30 2007 - 17:20:19 CDT)
Creating PDB from PSF and COOR files Vamshi Gangupomu (Fri Mar 30 2007 - 16:08:16 CDT)
MM works MD does not in Fixed system Pedro Borkowski (Fri Mar 30 2007 - 15:45:42 CDT)
Problem about momentum correction hl332_at_drexel.edu (Fri Mar 30 2007 - 12:11:59 CDT)
Re: It doesn't work with using amber files. Hidekazu WATANABE (Fri Mar 30 2007 - 07:32:15 CDT)
How can I use TIP4-P water model with NAMD? Nils Zimmermann (Fri Mar 30 2007 - 04:29:01 CDT)
Re: Pressure Discrepancy Richard Wood (Thu Mar 29 2007 - 17:44:41 CDT)
Re: Pressure Discrepancy Richard Wood (Thu Mar 29 2007 - 17:38:49 CDT)
Re: Pressure Discrepancy Morad Alawneh (Thu Mar 29 2007 - 17:00:14 CDT)
Re: Pressure Discrepancy Peter Freddolino (Thu Mar 29 2007 - 16:52:02 CDT)
Re: Pressure Discrepancy Morad Alawneh (Thu Mar 29 2007 - 16:29:04 CDT)
Re: Pressure Discrepancy Peter Freddolino (Thu Mar 29 2007 - 13:41:29 CDT)
Re: Pressure Discrepancy Sterling Paramore (Thu Mar 29 2007 - 13:39:15 CDT)
Re: Coarse-grained Modeling/User defined FF Peter Freddolino (Thu Mar 29 2007 - 13:23:17 CDT)
Re: Pressure Discrepancy Morad Alawneh (Thu Mar 29 2007 - 13:18:06 CDT)
Coarse-grained Modeling/User defined FF Joshua Adelman (Thu Mar 29 2007 - 13:13:17 CDT)
Re: It doesn't work with using amber files. campen_at_geosc.psu.edu (Thu Mar 29 2007 - 11:28:36 CDT)
Re: Pressure Discrepancy Sterling Paramore (Thu Mar 29 2007 - 08:53:48 CDT)
Re: It doesn't work with using amber files. Vlad Cojocaru (Thu Mar 29 2007 - 07:46:19 CDT)
It doesn't work with using amber files. Hidekazu WATANABE (Thu Mar 29 2007 - 07:09:25 CDT)
Re: Pressure Discrepancy Peter Freddolino (Wed Mar 28 2007 - 23:07:44 CDT)
Re: Pressure Discrepancy Richard Wood (Wed Mar 28 2007 - 22:33:48 CDT)
Re: Pressure Discrepancy Sterling Paramore (Wed Mar 28 2007 - 22:19:36 CDT)
Re: Pressure Discrepancy Morad Alawneh (Wed Mar 28 2007 - 20:47:16 CDT)
Re: Pressure Discrepancy Richard Wood (Wed Mar 28 2007 - 18:23:22 CDT)
libstdc++.so.5 Stern, Julie (Wed Mar 28 2007 - 18:15:13 CDT)
Re: Pressure Discrepancy Sterling Paramore (Wed Mar 28 2007 - 16:12:06 CDT)
Re: Pressure Discrepancy Morad Alawneh (Wed Mar 28 2007 - 15:50:13 CDT)
Re: Pressure Discrepancy Sterling Paramore (Wed Mar 28 2007 - 15:43:55 CDT)
unsubscribe Xiongce Zhao (Wed Mar 28 2007 - 16:07:17 CDT)
Re: Pressure Discrepancy Morad Alawneh (Wed Mar 28 2007 - 15:00:51 CDT)
Re: Pressure Discrepancy Peter Freddolino (Wed Mar 28 2007 - 14:00:56 CDT)
Re: Pressure Discrepancy Morad Alawneh (Wed Mar 28 2007 - 13:55:43 CDT)
Re: Pressure Discrepancy Peter Freddolino (Wed Mar 28 2007 - 13:40:36 CDT)
Re: Pressure Discrepancy Marcos Sotomayor (Wed Mar 28 2007 - 13:36:41 CDT)
Re: Pressure Discrepancy Morad Alawneh (Wed Mar 28 2007 - 13:23:04 CDT)
Re: Pressure Discrepancy Marcos Sotomayor (Wed Mar 28 2007 - 13:16:47 CDT)
Re: Pressure Discrepancy Morad Alawneh (Wed Mar 28 2007 - 12:40:23 CDT)
NAMD2.6 requirments on p690 Dong Luo (Wed Mar 28 2007 - 10:47:11 CDT)
Re: How to "twist" a molecule? (resubmit) Grzegorz Jezierski (Wed Mar 28 2007 - 04:56:42 CDT)
dcd file produced with NAMD can be used with AMBER? Rita Cassia (Wed Mar 28 2007 - 04:11:56 CDT)
RE: Difficulties is minimizing capped peptides - solution kate.nairn_at_csiro.au (Tue Mar 27 2007 - 19:59:03 CDT)
Help !!! ERROR: Atoms mooving too fast Juan Diaz (Tue Mar 27 2007 - 18:21:05 CDT)
Help !!! ERROR: Atoms mooving too fast Juan Diaz (Tue Mar 27 2007 - 18:17:29 CDT)
multiple time stepping in namd: Query hl332_at_drexel.edu (Tue Mar 27 2007 - 14:54:33 CDT)
Re: the relationship between system size and cpu numbers Cesar Luis Avila (Tue Mar 27 2007 - 14:33:35 CDT)
Re: How to use the transformation matrix in VMD to obtain the tetramer JC Gumbart (Tue Mar 27 2007 - 14:17:46 CDT)
Pressure Discrepancy Morad Alawneh (Tue Mar 27 2007 - 13:23:42 CDT)
unsubscribe vmd-l Narender Singh Maan (Tue Mar 27 2007 - 11:39:36 CDT)
Re: the relationship between system size and cpu numbers Marcos Sotomayor (Tue Mar 27 2007 - 11:34:20 CDT)
Re: the relationship between system size and cpu numbers Cesar Luis Avila (Tue Mar 27 2007 - 11:19:18 CDT)
the relationship between system size and cpu numbers Dong Luo (Tue Mar 27 2007 - 10:28:54 CDT)
NAMD fails with LAM (can't run example) Smith, Ian (Tue Mar 27 2007 - 10:13:54 CDT)
How to use the transformation matrix in VMD to obtain the tetramer xiaojing gong (Tue Mar 27 2007 - 07:22:47 CDT)
charmrun + NAMD on dual quad-core intel procs Ravinder Abrol (Mon Mar 26 2007 - 15:39:09 CDT)
Re: How to "twist" a molecule? (resubmit) Margaret S. Cheung (Mon Mar 26 2007 - 14:09:33 CDT)
Re: ERROR: Number of pdb and psf atoms are not the same! Peter Freddolino (Mon Mar 26 2007 - 14:16:37 CDT)
ERROR: Number of pdb and psf atoms are not the same! Arturas Ziemys (Mon Mar 26 2007 - 14:08:36 CDT)
Re: How to "twist" a molecule? (resubmit) Grzegorz Jezierski (Mon Mar 26 2007 - 04:46:53 CDT)
Re: How to "twist" a molecule? (resubmit) Margaret S. Cheung (Mon Mar 26 2007 - 08:51:16 CDT)
Re: How to "twist" a molecule? (resubmit) Margaret S. Cheung (Mon Mar 26 2007 - 08:49:42 CDT)
RE: Periodic Boundary Conditions JC Gumbart (Mon Mar 26 2007 - 09:42:15 CDT)
Periodic Boundary Conditions Per Jr. Greisen (Mon Mar 26 2007 - 02:26:19 CDT)
protein/lipid simulation Stephen M. Dutz (Sun Mar 25 2007 - 20:41:23 CDT)
NAMD on Infiniband - problems and successes Martin Cuma (Sun Mar 25 2007 - 12:30:57 CDT)
Re: How to "twist" a molecule? (resubmit) JC Gumbart (Sun Mar 25 2007 - 00:33:00 CDT)
Re: Extraction of force data JC Gumbart (Fri Mar 23 2007 - 23:36:03 CDT)
viarecv.c rhandle->len' failed. on infiniband Rene Salmon (Fri Mar 23 2007 - 17:44:59 CDT)
Re: Extraction of force data Viral D. Tejani (Fri Mar 23 2007 - 13:00:51 CDT)
How to "twist" a molecule? (resubmit) Margaret S. Cheung (Fri Mar 23 2007 - 11:05:16 CDT)
equilibration amit dong (Fri Mar 23 2007 - 11:30:06 CDT)
Re: restart NAMD job Cesar Luis Avila (Fri Mar 23 2007 - 10:10:54 CDT)
restart NAMD job Jianhui Tian (Fri Mar 23 2007 - 09:03:38 CDT)
Re: Extraction of force data Marcos Sotomayor (Thu Mar 22 2007 - 22:30:35 CDT)
Re: Extraction of force data JC Gumbart (Thu Mar 22 2007 - 22:29:20 CDT)
Extraction of force data Viral D. Tejani (Thu Mar 22 2007 - 22:12:02 CDT)
Re: Simulation explodes as soon as minimization starts "GRADIENT TOLERANCE: nan" Peter Freddolino (Thu Mar 22 2007 - 19:24:26 CDT)
How to "twist" a molecule? Margaret S. Cheung (Thu Mar 22 2007 - 18:02:57 CDT)
Re: Simulation explodes as soon as minimization starts "GRADIENT TOLERANCE: nan" namd vmd (Thu Mar 22 2007 - 07:55:00 CDT)
Re: distance constraints with an upper bound Luca (Thu Mar 22 2007 - 04:20:27 CDT)
unsubscribe Jonathan D. Proulx (Wed Mar 21 2007 - 14:44:47 CDT)
Re: Simulation explodes as soon as minimization starts "GRADIENT TOLERANCE: nan" Cesar Luis Avila (Wed Mar 21 2007 - 13:54:47 CDT)
distance constraints with an upper bound Neema Salimi (Wed Mar 21 2007 - 13:19:19 CDT)
Simulation explodes as soon as minimization starts "GRADIENT TOLERANCE: nan" namd vmd (Wed Mar 21 2007 - 12:38:42 CDT)
hexagonal crystal Allison Langham (Wed Mar 21 2007 - 11:22:26 CDT)
Re: user defined L-J parameters Peter Freddolino (Wed Mar 21 2007 - 09:54:38 CDT)
Re: user defined L-J parameters Arturas Ziemys (Wed Mar 21 2007 - 08:59:21 CDT)
Re: user defined L-J parameters Neelanjana Sengupta (Wed Mar 21 2007 - 07:05:52 CDT)
user defined L-J parameters Alessio Alexiadis (Wed Mar 21 2007 - 05:18:17 CDT)
Dihedral restraints do not work Neelanjana Sengupta (Tue Mar 20 2007 - 10:44:10 CDT)
query about thermostat.. hl332_at_drexel.edu (Mon Mar 19 2007 - 14:01:43 CDT)
Re: non-parallel NAMD compilation Gengbin Zheng (Mon Mar 19 2007 - 13:59:49 CDT)
parameters for GABA (gamma-amino butyric acid) namd vmd (Sun Mar 18 2007 - 07:33:57 CDT)
Re: problem with namddat_unix: Plz help... hl332_at_drexel.edu (Fri Mar 16 2007 - 13:58:38 CDT)
Re: problem with namddat_unix: Plz help... JC Gumbart (Fri Mar 16 2007 - 13:49:48 CDT)
problem with namddat_unix: Plz help... hl332_at_drexel.edu (Fri Mar 16 2007 - 12:10:13 CDT)
Re: applying experimental constraints to a MD simulation Jerome Henin (Fri Mar 16 2007 - 11:57:25 CDT)
applying experimental constraints to a MD simulation L. Michel Espinoza-Fonseca (Fri Mar 16 2007 - 11:31:41 CDT)
Re: Stray PME grid charges detected yi wang (Thu Mar 15 2007 - 18:42:59 CDT)
Re: psfgen and bond topology specification L. Michel Espinoza-Fonseca (Thu Mar 15 2007 - 16:53:03 CDT)
Re: how to convert dcd files from namd to charmm L. Michel Espinoza-Fonseca (Thu Mar 15 2007 - 16:20:40 CDT)
psfgen and bond topology specification Neelanjana Sengupta (Thu Mar 15 2007 - 16:20:24 CDT)
Re: how to convert dcd files from namd to charmm Peter Freddolino (Thu Mar 15 2007 - 15:49:06 CDT)
Re: how to convert dcd files from namd to charmm Alessandro Cembran (Thu Mar 15 2007 - 15:38:37 CDT)
Re: how to convert dcd files from namd to charmm regafan_at_usc.es (Thu Mar 15 2007 - 15:34:31 CDT)
Re: how to convert dcd files from namd to charmm regafan_at_usc.es (Thu Mar 15 2007 - 15:33:41 CDT)
Re: how to convert dcd files from namd to charmm Peter Freddolino (Thu Mar 15 2007 - 15:16:25 CDT)
Re: how to convert dcd files from namd to charmm regafan_at_usc.es (Thu Mar 15 2007 - 15:06:16 CDT)
Why is water density not 1.0g/cm3? lw257_at_email.med.yale.edu (Wed Mar 14 2007 - 18:57:06 CDT)
Problem with NVE run: Help hl332_at_drexel.edu (Thu Mar 15 2007 - 14:19:55 CDT)
Third node stops the simulation paco ty (Thu Mar 15 2007 - 12:45:46 CDT)
Re: Water density is not 1.0g/cm3 Peter Freddolino (Thu Mar 15 2007 - 12:25:44 CDT)
Why is water density not 1.0g/cm3? Liguo Wang (Thu Mar 15 2007 - 14:01:12 CDT)
Warning: overloaded due to high background load Jianhui Tian (Thu Mar 15 2007 - 10:15:57 CDT)
Re: how to convert dcd files from namd to charmm regafan_at_usc.es (Thu Mar 15 2007 - 09:56:03 CDT)
Re: how to convert dcd files from namd to charmm Alessandro Cembran (Thu Mar 15 2007 - 08:08:25 CDT)
Re: how to convert dcd files from namd to charmm Alessandro Cembran (Thu Mar 15 2007 - 07:59:01 CDT)
how to convert dcd files from namd to charmm regafan_at_usc.es (Thu Mar 15 2007 - 06:50:45 CDT)
Re: Why minimization before Molecular Dynamics? Luca Muccioli (Thu Mar 15 2007 - 06:50:43 CDT)
Why minimization before Molecular Dynamics? Pedro Borkowski (Thu Mar 15 2007 - 04:25:05 CDT)
non-parallel NAMD compilation Xiuping Tao (Tue Mar 13 2007 - 15:07:47 CDT)
Re: Incorrect Atom Count vivek behera (Tue Mar 13 2007 - 23:22:16 CDT)
protein spinning and total enegy not constant in NVE hl332_at_drexel.edu (Tue Mar 13 2007 - 14:06:07 CDT)
Re: Free Energy/ ERROR Kramer Campen (Tue Mar 13 2007 - 09:11:25 CDT)
Re: Kinetic Energy frm MDEnergy (energy evaluation tool) Jan Saam (Mon Mar 12 2007 - 19:13:31 CDT)
Kinetic Energy frm MDEnergy (energy evaluation tool) Rahul Bhowmik (Mon Mar 12 2007 - 18:11:36 CDT)
Free Energy/ ERROR Arturas Ziemys (Mon Mar 12 2007 - 15:37:31 CDT)
Free Energy of Conformation Change Arturas Ziemys (Mon Mar 12 2007 - 13:16:57 CDT)
Re: applying experimental constraints to a MD simulation Luca Muccioli (Mon Mar 12 2007 - 02:45:29 CDT)
Re: applying experimental constraints to a MD simulation L. Michel Espinoza-Fonseca (Sun Mar 11 2007 - 18:55:26 CDT)
Re: applying experimental constraints to a MD simulation Mark Abraham (Sun Mar 11 2007 - 18:36:01 CDT)
applying experimental constraints to a MD simulation L. Michel Espinoza-Fonseca (Sun Mar 11 2007 - 18:14:16 CDT)
DMPC Atoms moving too fast ! mustapha.hamdi_at_ensi-bourges.fr (Sat Mar 10 2007 - 10:08:08 CST)
question about the influence of water box size in FEP jieru.zheng_at_duke.edu (Fri Mar 09 2007 - 09:30:40 CST)
topology problem! ramya wwjd (Fri Mar 09 2007 - 03:04:58 CST)
Re: Premature stop Cesar Luis Avila (Thu Mar 08 2007 - 07:32:56 CST)
multiple timestep and dcdfreq Luca Muccioli (Thu Mar 08 2007 - 07:27:32 CST)
Re: Problems with energy conservation in NVE dynamics with 2fs timestep Marcos Sotomayor (Thu Mar 08 2007 - 07:17:57 CST)
Re: Problems with energy conservation in NVE dynamics with 2fs timestep Peter Freddolino (Thu Mar 08 2007 - 07:03:46 CST)
Premature stop paco ty (Thu Mar 08 2007 - 03:57:15 CST)
Re: restraining parts of a molecule AyÅŸe Ã–zlem Sezerman (Thu Mar 08 2007 - 00:11:00 CST)
Re: protein diffuses to boundary.. hl332_at_drexel.edu (Wed Mar 07 2007 - 18:59:01 CST)
Re: protein diffuses to boundary.. George Madalin Giambasu (Wed Mar 07 2007 - 18:15:08 CST)
protein diffuses to boundary.. hl332_at_drexel.edu (Wed Mar 07 2007 - 16:21:24 CST)
firstLdbStep and ldbPeriod Gianluca Interlandi (Wed Mar 07 2007 - 13:11:37 CST)
Re: Re: vmd-l: DCD for windows xing jing (Tue Mar 06 2007 - 22:43:15 CST)
Re: vmd-l: DCD for windows John Stone (Tue Mar 06 2007 - 16:20:27 CST)
Re: DCD for windows Richard Wood (Tue Mar 06 2007 - 19:50:22 CST)
Re: Changing the protonation states of residues hl332_at_drexel.edu (Tue Mar 06 2007 - 18:31:08 CST)
Re: Changing the protonation states of residues Gaurav Sharma (Tue Mar 06 2007 - 18:08:04 CST)
Re: DCD for windows Gianluca Interlandi (Tue Mar 06 2007 - 17:32:09 CST)
*** topology file for AMP? *** Daniel Keedy (Tue Mar 06 2007 - 15:50:56 CST)
DCD for windows lily jin (Tue Mar 06 2007 - 15:25:40 CST)
Re: Configuration file Jeffrey J. Potoff (Tue Mar 06 2007 - 08:22:18 CST)
Configuration file Rita Cassia (Tue Mar 06 2007 - 07:54:51 CST)
Problems with energy conservation in NVE dynamics with 2fs timestep ahenneck_at_ix.urz.uni-heidelberg.de (Tue Mar 06 2007 - 04:27:03 CST)
Re: Difficulties is minimizing capped peptides Gianluca Interlandi (Tue Mar 06 2007 - 00:19:08 CST)
Changing the protonation states of residues Nabajyoti Goswami (Mon Mar 05 2007 - 03:27:07 CST)
Problem with water box ramya wwjd (Fri Mar 02 2007 - 06:50:26 CST)
Difficulties is minimizing capped peptides kate.nairn_at_csiro.au (Mon Mar 05 2007 - 21:18:01 CST)
distance restraint w/upper bound example Neema Salimi (Mon Mar 05 2007 - 15:27:05 CST)
RE: restraining parts of a molecule Stern, Julie (Mon Mar 05 2007 - 13:33:08 CST)
how to get the velocities from the dcd file Alessio Alexiadis (Mon Mar 05 2007 - 09:25:49 CST)
Re: restraining parts of a molecule AyÅŸe Ã–zlem Sezerman (Mon Mar 05 2007 - 09:00:14 CST)
Re: restraining parts of a molecule JC Gumbart (Sun Mar 04 2007 - 22:31:47 CST)
restraining parts of a molecule Stern, Julie (Sun Mar 04 2007 - 21:20:28 CST)
Re: reproduciblity between software Mark Abraham (Fri Mar 02 2007 - 17:59:17 CST)
Re: reproduciblity between software Cesar Luis Avila (Fri Mar 02 2007 - 15:07:02 CST)
reproduciblity between software Stern, Julie (Fri Mar 02 2007 - 10:43:23 CST)
Re: different output in processors Marcos Sotomayor (Wed Feb 28 2007 - 04:08:32 CST)
dimer minimization ayk_at_mail.ecc.u-tokyo.ac.jp (Wed Feb 28 2007 - 03:54:40 CST)
Re: Crystal Structure Analysis George Madalin Giambasu (Tue Feb 27 2007 - 18:51:21 CST)
Crystal Structure Analysis pedro.borkowski_at_utoronto.ca (Tue Feb 27 2007 - 12:02:23 CST)
different output in processors dora guzman (Tue Feb 27 2007 - 14:18:24 CST)
Incorrect Atom Count vivek behera (Tue Feb 27 2007 - 09:02:17 CST)
Periodic Cell error on CO2 MD Ugur Akgun (Mon Feb 26 2007 - 16:32:24 CST)
Tcl: callback, run, revert, measure Tao, Xiuping (Sun Feb 25 2007 - 22:25:41 CST)
Re: Varying Force Simulations Gianluca Interlandi (Mon Feb 26 2007 - 14:52:35 CST)
Restraints and System COM Drift Philip Blood (Mon Feb 26 2007 - 13:48:01 CST)
Tcl: callback, run, revert, measure Xiuping Tao (Mon Feb 26 2007 - 12:50:28 CST)
Re: uses of patches for changing the protonation states of residues Peter Freddolino (Mon Feb 26 2007 - 08:40:24 CST)
namd2 run error Moumita Maiti (Mon Feb 26 2007 - 07:14:20 CST)
Re: Varying Force Simulations Marcos Sotomayor (Mon Feb 26 2007 - 03:23:43 CST)
Re: Varying Force Simulations Mark Abraham (Mon Feb 26 2007 - 02:19:01 CST)
Re: Varying Force Simulations Viral D. Tejani (Mon Feb 26 2007 - 02:10:47 CST)
Re: Varying Force Simulations Gianluca Interlandi (Sun Feb 25 2007 - 23:35:56 CST)
Re: force field for H2PO4- and HPO4(-2) ions Mark Abraham (Sun Feb 25 2007 - 00:35:35 CST)
Re: force field for H2PO4- and HPO4(-2) ions Richard Wood (Sat Feb 24 2007 - 20:35:13 CST)
Varying Force Simulations Viral D. Tejani (Sat Feb 24 2007 - 19:47:23 CST)
Re: force field for H2PO4- and HPO4(-2) ions Mark Abraham (Sat Feb 24 2007 - 17:44:13 CST)
Re: force field for H2PO4- and HPO4(-2) ions Richard Wood (Sat Feb 24 2007 - 15:42:55 CST)
Re: force field for H2PO4- and HPO4(-2) ions George Madalin Giambasu (Sat Feb 24 2007 - 14:33:16 CST)
Re: force field for H2PO4- and HPO4(-2) ions Mark Abraham (Sat Feb 24 2007 - 10:20:05 CST)
force field for H2PO4- and HPO4(-2) ions Pawel Weronski (Sat Feb 24 2007 - 10:01:43 CST)
aligning ligands Narender Singh Maan (Fri Feb 23 2007 - 12:39:45 CST)
TMD and TclForces Jeff Wereszczynski (Fri Feb 23 2007 - 10:56:55 CST)
Re: NAMD + nice Gengbin Zheng (Wed Feb 21 2007 - 14:39:31 CST)
Re: RDF.tcl question L. Michel Espinoza-Fonseca (Wed Feb 21 2007 - 13:36:05 CST)
RDF.tcl question Jianhui Tian (Wed Feb 21 2007 - 12:43:24 CST)
Re: Does pair interaction calculations uses PBC ? Peter Freddolino (Wed Feb 21 2007 - 11:26:38 CST)
Does pair interaction calculations uses PBC ? Arturas Ziemys (Wed Feb 21 2007 - 11:18:22 CST)
Re: vmd-l: Re: Nanopore simulation subhasish chatterjee (Wed Feb 21 2007 - 00:00:07 CST)
Re: vmd-l: Re: Nanopore simulation subhasish chatterjee (Tue Feb 20 2007 - 23:54:32 CST)
Re: Nanopore simulation Mark Abraham (Tue Feb 20 2007 - 22:14:46 CST)
Nanopore simulation subhasish chatterjee (Tue Feb 20 2007 - 21:58:54 CST)
NAMD + nice Gianluca Interlandi (Tue Feb 20 2007 - 18:16:44 CST)
Re: a philosophical question... dstrahs_at_pace.edu (Mon Feb 19 2007 - 20:57:31 CST)
Re: a philosophical question... Richard Wood (Mon Feb 19 2007 - 18:19:46 CST)
Re: a philosophical question... Jerome Henin (Mon Feb 19 2007 - 18:09:49 CST)
Re: a philosophical question... Richard Wood (Mon Feb 19 2007 - 17:16:52 CST)
TOTAL, TOTAL2 and TOTAL3 Alessandro Cembran (Mon Feb 19 2007 - 11:36:16 CST)
NVE ensemble configuration file Lechuga, Javier (Mon Feb 19 2007 - 06:11:29 CST)
Parallel performance on Intel Woodcrest Himanshu Khandelia (Sun Feb 18 2007 - 15:19:20 CST)
Invalid cpus 2 in nodelist ignored Gianluca Interlandi (Fri Feb 16 2007 - 19:16:59 CST)
const vel SMD Narender Singh Maan (Fri Feb 16 2007 - 14:03:40 CST)
Re: Problem about cellBasisVector Cesar Luis Avila (Fri Feb 16 2007 - 12:56:57 CST)
Problem about cellBasisVector Jianhui Tian (Fri Feb 16 2007 - 09:14:00 CST)
Error compile charm++ Jianhui Tian (Thu Feb 15 2007 - 12:40:22 CST)
NAMD Integration algorithm Nava Whiteford (Thu Feb 15 2007 - 07:44:03 CST)
Re: tabulated potentials? Peter Freddolino (Tue Feb 13 2007 - 19:23:31 CST)
tabulated potentials? Nicolas Bock (Tue Feb 13 2007 - 15:35:03 CST)
Re: Temperature problem Cesar Luis Avila (Tue Feb 13 2007 - 15:19:20 CST)
Re: Temperature problem Jerome Henin (Tue Feb 13 2007 - 14:42:55 CST)
Temperature problem Al-Rawi, Ahlam (Tue Feb 13 2007 - 14:05:35 CST)
Re: Velocities of different Atoms Leandro Martínez (Tue Feb 13 2007 - 10:49:51 CST)
Velocities of different Atoms Rahul Bhowmik (Tue Feb 13 2007 - 09:18:28 CST)
Re: ionize (big, big, big system!) Jacob Poehlsgaard (Tue Feb 13 2007 - 02:22:23 CST)
Re: Re: vmd-l: ionize (big, big, big system!) Alessandro Cembran (Mon Feb 12 2007 - 18:57:05 CST)
Re: Protein partially denatures during pulling Marcos Sotomayor (Mon Feb 12 2007 - 18:29:00 CST)
Re: Re: vmd-l: ionize (big, big, big system!) L. Michel Espinoza-Fonseca (Mon Feb 12 2007 - 17:49:25 CST)
Re: ionize (big, big, big system!) Peter Freddolino (Mon Feb 12 2007 - 13:07:08 CST)
Re: ionize (big, big, big system!) Cesar Luis Avila (Mon Feb 12 2007 - 12:58:11 CST)
Re: Re: vmd-l: ionize (big, big, big system!) Alessandro Cembran (Mon Feb 12 2007 - 11:37:20 CST)
Re: vmd-l: ionize (big, big, big system!) L. Michel Espinoza-Fonseca (Mon Feb 12 2007 - 11:19:57 CST)
Re: vmd-l: ionize (big, big, big system!) Peter Freddolino (Mon Feb 12 2007 - 11:07:50 CST)
ionize (big, big, big system!) L. Michel Espinoza-Fonseca (Mon Feb 12 2007 - 10:58:32 CST)
Protein partially denatures during pulling Gianluca Interlandi (Sun Feb 11 2007 - 01:01:40 CST)
Re: SMD and CPT? Gianluca Interlandi (Fri Feb 09 2007 - 22:50:45 CST)
RE: DMPC psf. mustapha.hamdi_at_ensi-bourges.fr (Fri Feb 09 2007 - 18:41:51 CST)
Re: SMD and CPT? (fwd) Marcos Sotomayor (Fri Feb 09 2007 - 17:22:11 CST)
Re: SMD and CPT? (fwd) Sterling Paramore (Fri Feb 09 2007 - 17:08:12 CST)
Re: SMD and CPT? (fwd) Marcos Sotomayor (Fri Feb 09 2007 - 16:49:13 CST)
Re: SMD and CPT? (fwd) Sterling Paramore (Fri Feb 09 2007 - 16:35:56 CST)
RE: DMPC psf. Lea Thøgersen (Fri Feb 09 2007 - 16:33:01 CST)
Re: SMD and CPT? (fwd) Sterling Paramore (Fri Feb 09 2007 - 16:08:38 CST)
Re: SMD and CPT? (fwd) Sterling Paramore (Fri Feb 09 2007 - 16:03:02 CST)
Re: SMD and CPT? (fwd) Marcos Sotomayor (Fri Feb 09 2007 - 15:23:38 CST)
Re: SMD and CPT? (fwd) Sterling Paramore (Fri Feb 09 2007 - 14:50:52 CST)
Re: SMD and CPT? (fwd) Gianluca Interlandi (Fri Feb 09 2007 - 13:52:23 CST)
Re: SMD and CPT? Sterling Paramore (Fri Feb 09 2007 - 12:53:35 CST)
Re: DMPC psf. Cesar Luis Avila (Fri Feb 09 2007 - 12:36:40 CST)
Re: SMD and CPT? Cesar Luis Avila (Fri Feb 09 2007 - 12:21:07 CST)
Re: SMD and CPT? Marcos Sotomayor (Fri Feb 09 2007 - 12:13:05 CST)
Re: SMD and CPT? Gianluca Interlandi (Fri Feb 09 2007 - 12:03:40 CST)
DMPC psf. mustapha.hamdi_at_ensi-bourges.fr (Fri Feb 09 2007 - 10:10:24 CST)
Re: pH in NAMD Mark Abraham (Fri Feb 09 2007 - 09:54:34 CST)
Re: SMD and CPT? Sterling Paramore (Fri Feb 09 2007 - 08:34:21 CST)
Re: pH in NAMD MW Van der Kamp, School of Chemistry (Fri Feb 09 2007 - 02:48:48 CST)
SMD and CPT? Gianluca Interlandi (Fri Feb 09 2007 - 00:49:45 CST)
Re: pH in NAMD Mark Abraham (Thu Feb 08 2007 - 19:12:40 CST)
Re: "atoms moving too fast" error in bilayer simulation Himanshu Khandelia (Thu Feb 08 2007 - 15:04:12 CST)
Re: pH in NAMD Richard Wood (Thu Feb 08 2007 - 13:13:52 CST)
tclForces: relation between force and velocity Westley A Sherman (Thu Feb 08 2007 - 12:55:19 CST)
Re: Compiling Questions Ulf Markwardt (Thu Feb 08 2007 - 07:01:40 CST)
Re: pH in NAMD Richard Law (Thu Feb 08 2007 - 11:03:07 CST)
Re: pH in NAMD Jan Saam (Thu Feb 08 2007 - 11:21:02 CST)
Re: pH in NAMD Peter Freddolino (Thu Feb 08 2007 - 10:29:44 CST)
Re: pH in NAMD Richard Wood (Thu Feb 08 2007 - 10:24:29 CST)
Re: pH in NAMD Jerome Henin (Thu Feb 08 2007 - 09:58:50 CST)
Re: pH in NAMD Richard Wood (Thu Feb 08 2007 - 09:36:19 CST)
force constant for zer-velocity SMD namd vmd (Thu Feb 08 2007 - 06:35:53 CST)
Re: pH in NAMD Mark Abraham (Thu Feb 08 2007 - 06:20:06 CST)
pH in NAMD Per Jr. Greisen (Thu Feb 08 2007 - 05:37:39 CST)
tclbc example scripts namd vmd (Thu Feb 08 2007 - 04:46:54 CST)
Compiling Questions Joshua D. Moore (Wed Feb 07 2007 - 23:55:39 CST)
Problem compiling NAMD on BlueGene Jianhui Tian (Tue Feb 06 2007 - 13:08:06 CST)
Pressure problem when using restart file Jacob Poehlsgaard (Tue Feb 06 2007 - 10:11:53 CST)
Re: vmd-l: Re: too large an area/lipid in POPE bilayers using membrane plugin Richard Law (Mon Feb 05 2007 - 15:08:05 CST)
Re: vmd-l: Re: too large an area/lipid in POPE bilayers using membrane plugin John Stone (Mon Feb 05 2007 - 14:52:48 CST)
Re: too large an area/lipid in POPE bilayers using membrane plugin Richard Law (Mon Feb 05 2007 - 12:49:07 CST)
Re: fixing internal coordinates Jerome Henin (Mon Feb 05 2007 - 14:32:57 CST)
Re: vmd-l: too large an area/lipid in POPE bilayers using membrane plugin Jerome Henin (Mon Feb 05 2007 - 14:26:10 CST)
fixing internal coordinates Martin McCullagh (Mon Feb 05 2007 - 14:01:55 CST)
too large an area/lipid in POPE bilayers using membrane plugin Himanshu Khandelia (Mon Feb 05 2007 - 11:50:04 CST)
RE: Calculation of CHARMM Parameters from GAMESS Output. JC Gumbart (Mon Feb 05 2007 - 10:15:40 CST)
Calculation of CHARMM Parameters from GAMESS Output. Klon, Anthony (Mon Feb 05 2007 - 09:27:09 CST)
problems running more than 9 Replicas in replica exchange simulations Ana Celia Araujo Vila Verde (Sun Feb 04 2007 - 14:33:41 CST)
Re: "atoms moving too fast" error in bilayer simulation Peter Freddolino (Sun Feb 04 2007 - 08:15:38 CST)
Re: "atoms moving too fast" error in bilayer simulation Himanshu Khandelia (Sun Feb 04 2007 - 06:11:03 CST)
Error: parameter multiplicity.plz reply. hl332_at_drexel.edu (Sat Feb 03 2007 - 12:36:45 CST)
Re: "atoms moving too fast" error in bilayer simulation Peter Freddolino (Sat Feb 03 2007 - 08:38:58 CST)
Re: Energy Minimization Leandro Martínez (Sat Feb 03 2007 - 06:35:32 CST)
Re: "atoms moving too fast" error in bilayer simulation Himanshu Khandelia (Sat Feb 03 2007 - 01:21:35 CST)
RE: NAMD - Pronunciation? JC Gumbart (Fri Feb 02 2007 - 23:24:27 CST)
Re: Energy Minimization Peter Freddolino (Fri Feb 02 2007 - 22:06:50 CST)
RE: "Unknown pragma ivdep and pragma vector" errors when compiling on BlueGene Joshua D. Moore (Fri Feb 02 2007 - 21:09:23 CST)
Re: NAMD - Pronunciation? Neelanjana Sengupta (Fri Feb 02 2007 - 20:42:27 CST)
Re: NAMD - Pronunciation? JC Gumbart (Fri Feb 02 2007 - 20:06:56 CST)
NAMD - Pronunciation? Shirley Hui (Fri Feb 02 2007 - 19:57:47 CST)
Energy Minimization Shirley Hui (Fri Feb 02 2007 - 14:23:01 CST)
Re: "atoms moving too fast" error in bilayer simulation Peter Freddolino (Fri Feb 02 2007 - 09:29:44 CST)
Re: flexiblecell and constant ratio Peter Freddolino (Fri Feb 02 2007 - 09:26:48 CST)
Re: DNA hydrogen bonds Peter Freddolino (Fri Feb 02 2007 - 09:08:06 CST)
"atoms moving too fast" error in bilayer simulation Himanshu Khandelia (Fri Feb 02 2007 - 07:31:53 CST)
flexiblecell and constant ratio regafan_at_usc.es (Fri Feb 02 2007 - 06:09:00 CST)
DNA hydrogen bonds Maxim Karachevtsev (Fri Feb 02 2007 - 02:00:46 CST)
(no subject) Maxim Karachevtsev (Fri Feb 02 2007 - 02:00:12 CST)
"Unknown pragma ivdep and pragma vector" errors when compiling on BlueGene Joshua D. Moore (Thu Feb 01 2007 - 23:29:59 CST)
Binding Free Energy Shirley Hui (Thu Feb 01 2007 - 15:40:27 CST)
Question about compiling NAMD Jianhui Tian (Thu Feb 01 2007 - 14:44:15 CST)
DNA H-bonds Maxim Karachevtsev (Thu Feb 01 2007 - 03:51:26 CST)
problems running Replica Exchange simulations using SSH to spawn the processes Ana Celia Araujo Vila Verde (Thu Feb 01 2007 - 13:28:06 CST)
Re: vmd-l: DNA and low pH Peter Freddolino (Wed Jan 31 2007 - 19:51:26 CST)
Re: a philosophical question... Richard Wood (Wed Jan 31 2007 - 18:01:46 CST)
DNA and low pH Gaurav Sharma (Wed Jan 31 2007 - 15:06:46 CST)
MPI compile of NAMD runs on dual core machines but not quad core machines Joshua D. Moore (Wed Jan 31 2007 - 14:47:14 CST)
Re: a philosophical question... Alexander Vaughn (Tue Jan 30 2007 - 17:07:46 CST)
peptide conformation search examples Andrew D. Fant (Tue Jan 30 2007 - 14:21:49 CST)
Re: a philosophical question... Richard Wood (Tue Jan 30 2007 - 13:35:25 CST)
DNA helix model lily jin (Tue Jan 30 2007 - 13:26:26 CST)
Re: a philosophical question... L. Michel Espinoza-Fonseca (Tue Jan 30 2007 - 12:54:06 CST)
a philosophical question... Richard Wood (Tue Jan 30 2007 - 12:21:06 CST)
Re: FAO developers: vdW energies, forces and derivatives Jim Phillips (Mon Jan 29 2007 - 16:55:40 CST)
Questions re: protein-DNA complex Shirley Hui (Mon Jan 29 2007 - 16:20:02 CST)
FAO developers: vdW energies, forces and derivatives Floris Buelens (Mon Jan 29 2007 - 05:23:43 CST)
Re: constant velocity SMD Narender Singh Maan (Fri Jan 26 2007 - 12:49:07 CST)
Re: Re:constant velocity SMD JC Gumbart (Fri Jan 26 2007 - 12:48:52 CST)
Re: constant velocity SMD Cesar Luis Avila (Fri Jan 26 2007 - 12:34:36 CST)
Re:constant velocity SMD Narender Singh Maan (Fri Jan 26 2007 - 12:33:18 CST)
Re: constant velocity SMD JC Gumbart (Fri Jan 26 2007 - 11:59:46 CST)
constant velocity SMD Narender Singh Maan (Fri Jan 26 2007 - 11:44:41 CST)
constant velocity SMD Narender Singh Maan (Fri Jan 26 2007 - 11:11:39 CST)
Re: membrane constraints on thickness Philip Blood (Fri Jan 26 2007 - 11:09:55 CST)
minimization error - high IMPRP energy Richard Lonsdale (Fri Jan 26 2007 - 10:31:44 CST)
Re: membrane constraints on thickness Philip Blood (Fri Jan 26 2007 - 09:52:27 CST)
Re: membrane constraints on thickness Morad Alawneh (Fri Jan 26 2007 - 09:25:12 CST)
Re: membrane constraints on thickness Peter Freddolino (Fri Jan 26 2007 - 08:18:24 CST)
Re: membrane constraints on thickness Himanshu Khandelia (Fri Jan 26 2007 - 07:27:21 CST)
Re: membrane constraints on thickness Peter Freddolino (Fri Jan 26 2007 - 07:02:49 CST)
Re: membrane constraints on thickness Peter Freddolino (Fri Jan 26 2007 - 07:01:35 CST)
compilation of charm++ L. Michel Espinoza-Fonseca (Fri Jan 26 2007 - 06:53:47 CST)
Re: membrane constraints on thickness Himanshu Khandelia (Fri Jan 26 2007 - 03:45:40 CST)
Re: 0 coordinates for LES atoms in pdb file after solvation arijit_r_at_chem.iitkgp.ernet.in (Thu Jan 25 2007 - 22:11:04 CST)
Simulations with large number of constraints crash at startup phase 1 on Indiana's Bigred Philip Blood (Thu Jan 25 2007 - 13:42:20 CST)
Re: membrane constraints on thickness Peter Freddolino (Thu Jan 25 2007 - 13:24:21 CST)
membrane constraints on thickness Himanshu Khandelia (Thu Jan 25 2007 - 11:58:39 CST)
Re: 0 coordinates for LES atoms in pdb file after solvation Dhiraj Srivastava (Thu Jan 25 2007 - 11:24:16 CST)
Replica Exchange (Parallel) M. Madhu (Thu Jan 25 2007 - 11:18:33 CST)
How to write a new dcd.file by using Tcl xiaojing gong (Thu Jan 25 2007 - 08:28:21 CST)
Re: 0 coordinates for LES atoms in pdb file after solvation arijit_r_at_chem.iitkgp.ernet.in (Thu Jan 25 2007 - 03:11:44 CST)
0 coordinates for LES atoms in pdb file after solvation Dhiraj Srivastava (Thu Jan 25 2007 - 01:45:32 CST)
Re: modified patch to PROline Peter Freddolino (Wed Jan 24 2007 - 18:03:39 CST)
Re: modified patch to PROline Neelanjana Sengupta (Wed Jan 24 2007 - 15:50:09 CST)
Re: Tcl Scripting Lorant Janosi (Wed Jan 24 2007 - 14:17:37 CST)
Re: modified patch to PROline Peter Freddolino (Wed Jan 24 2007 - 13:09:04 CST)
NAMD install problem. Wang, Boyang (Wed Jan 24 2007 - 12:59:54 CST)
modified patch to PROline Neelanjana Sengupta (Wed Jan 24 2007 - 12:25:21 CST)
RE: Tcl Scripting Ana Celia Araujo Vila Verde (Wed Jan 24 2007 - 11:34:54 CST)
Tcl Scripting M. Madhu (Wed Jan 24 2007 - 11:01:37 CST)
Re: Simulation of Eukaryotic membrane protein Jerome Henin (Wed Jan 24 2007 - 09:58:43 CST)
Re: minimizing bad system: bad global excl. count Peter Freddolino (Wed Jan 24 2007 - 08:07:40 CST)
Re: minimizing bad system: bad global excl. count Himanshu Khandelia (Wed Jan 24 2007 - 05:53:51 CST)
Re: minimizing bad system: bad global excl. count Brian Bennion (Tue Jan 23 2007 - 14:35:19 CST)
minimizing bad system: bad global excl. count Himanshu Khandelia (Tue Jan 23 2007 - 11:32:41 CST)
Simulation of Eukaryotic membrane protein Aaron Oakley (Sun Jan 21 2007 - 23:23:12 CST)
heating with restraints AYTUG TUNCEL (Fri Jan 19 2007 - 12:12:05 CST)
AcetylProlineAmide topology Neelanjana Sengupta (Wed Jan 17 2007 - 12:35:45 CST)
lj parameters for gold for NAMD sukesh shenoy (Tue Jan 16 2007 - 19:16:41 CST)
harmonic distance restraint X Zheng (Tue Jan 16 2007 - 16:02:59 CST)
fixed atoms appearing on the other side of simulation box Ana Celia Araujo Vila Verde (Tue Jan 16 2007 - 13:38:33 CST)
SHAKE: Constrain EVERY bond length and bond angle Neelanjana Sengupta (Tue Jan 16 2007 - 13:21:52 CST)
Constrain EVERY bond length and bond angle Neelanjana Sengupta (Tue Jan 16 2007 - 13:18:59 CST)
Re: Restart Simulation Brian Bennion (Tue Jan 16 2007 - 10:42:45 CST)
Restart Simulation Karol Kaszuba (Tue Jan 16 2007 - 05:49:34 CST)
Re: Scalability problem with NAMD2.6 on Intel Xeon EM64T processors Morad Alawneh (Mon Jan 15 2007 - 14:54:38 CST)
g(r) plugin Ayþe Özlem Sezerman (Mon Jan 15 2007 - 04:09:56 CST)
C:CA bond getting stretched Dhiraj Srivastava (Mon Jan 15 2007 - 01:45:37 CST)
Re: Scalability problem with NAMD2.6 on Intel Xeon EM64T processors Morad Alawneh (Sat Jan 13 2007 - 10:18:46 CST)
Scalability problem with NAMD2.6 on Intel Xeon EM64T processors Morad Alawneh (Fri Jan 12 2007 - 10:56:07 CST)
Re: FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE JC Gumbart (Thu Jan 11 2007 - 20:13:41 CST)
FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE Alexander Vaughn (Thu Jan 11 2007 - 19:37:34 CST)
Re: Replica Exchange MD using Amber parameters Kramer Campen (Thu Jan 11 2007 - 17:14:46 CST)
Re: Replica Exchange MD using Amber parameters Mark Abraham (Thu Jan 11 2007 - 16:15:54 CST)
"CWeb performance data sent to wrong processor..." Jon Halverson (Thu Jan 11 2007 - 15:47:57 CST)
Replica Exchange MD using Amber parameters Kramer Campen (Thu Jan 11 2007 - 08:39:32 CST)
H-bond energy amit dong (Thu Jan 11 2007 - 04:24:04 CST)
experimental phi-values as restraints regafan_at_usc.es (Wed Jan 10 2007 - 10:08:42 CST)
Stray PME grid charges detected Simon Watson (Tue Jan 09 2007 - 12:06:53 CST)
Why does lipid move out of water box Nitin Bhardwaj (Tue Jan 09 2007 - 11:29:24 CST)
generalized born routine Rie Nygaard (Tue Jan 09 2007 - 07:10:18 CST)
Anyone have catdcd-4.0 for BlueGene? Joshua D. Moore (Mon Jan 08 2007 - 15:34:09 CST)
Re: Protein, ligand, ion out of the water box. Peter Freddolino (Mon Jan 08 2007 - 14:33:13 CST)
Protein, ligand, ion out of the water box. Rima Chaudhuri (Mon Jan 08 2007 - 12:35:07 CST)
Thermodynamic Integration (free energy of conformation change) Kramer Campen (Mon Jan 08 2007 - 12:11:02 CST)
Re: topology of carbon dioxide compatible with Charmm arijit_r_at_chem.iitkgp.ernet.in (Mon Jan 08 2007 - 11:56:26 CST)
Re: topology of carbon dioxide compatible with Charmm JC Gumbart (Mon Jan 08 2007 - 11:27:20 CST)
ligand parameterization Idit Buch (Mon Jan 08 2007 - 05:26:54 CST)
topology of carbon dioxide compatible with Charmm arijit_r_at_chem.iitkgp.ernet.in (Mon Jan 08 2007 - 05:06:07 CST)
Re: "Not all atoms have unique coordinates" Marcos Sotomayor (Fri Jan 05 2007 - 13:39:17 CST)
Re: "Not all atoms have unique coordinates" Neelanjana Sengupta (Fri Jan 05 2007 - 13:16:40 CST)
RE: "Not all atoms have unique coordinates" Ana Celia Araujo Vila Verde (Fri Jan 05 2007 - 12:58:23 CST)
The NAMD job do not go forward Fabio Passetti (Fri Jan 05 2007 - 12:43:13 CST)
"Not all atoms have unique coordinates" Nitin Bhardwaj (Fri Jan 05 2007 - 12:31:18 CST)
SPC/E water model laura (Fri Jan 05 2007 - 07:05:40 CST)
Free Energy of Conformation Change Units Kramer Campen (Tue Jan 02 2007 - 15:45:23 CST)
Tcl_BC: [nexatom] twice in script Arturas Ziemys (Tue Jan 02 2007 - 09:52:53 CST)

Last message date: Wed Dec 31 2008 - 05:25:21 CST
Archived on: Wed Feb 29 2012 - 15:48:53 CST

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