NAMD-L: By Date

NAMD

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NAMD-L: By Date

By Date

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About this archive

Starting: Fri Jan 02 2004 - 12:06:46 CST
Ending: Wed Dec 28 2005 - 17:21:37 CST

Re: FEP setup Chris Chipot (Wed Dec 28 2005 - 17:21:28 CST)
FEP setup Richard Wood (Tue Dec 27 2005 - 11:43:53 CST)
About the Source code. Boyang Wang (Mon Dec 26 2005 - 21:40:56 CST)
How does NAMD calculate Electrostatic potential energy (no periodic boundary condition)? Boyang Wang (Mon Dec 26 2005 - 17:46:55 CST)
NAMD Energy Plugin bo baker (Tue Dec 27 2005 - 18:15:40 CST)
Re: preparing a dimeric protein for NAMD (Thank you) Shirley Li (Tue Dec 27 2005 - 12:38:15 CST)
Thanks a lot Shirley Li (Tue Dec 27 2005 - 12:28:52 CST)
Re: Re: FATAL ERROR: unknown floating-point error, errno = 4 Chris Chipot (Mon Dec 26 2005 - 10:52:40 CST)
Re: vmd-l: convert DCD files to CRD format Angel Gonzalez Wong (Mon Dec 26 2005 - 09:19:53 CST)
Re: Can extending MIN solve the problem of "Constraint failure in RATTLE algorithm" dimka (Sat Dec 24 2005 - 19:51:31 CST)
FATAL ERROR: Tried to find atom type on node other than node 0 Ivan Ufimtsev (Sat Dec 24 2005 - 17:26:26 CST)
Can extending MIN solve the problem of "Constraint failure in RATTLE algorithm" Shirley Li (Sat Dec 24 2005 - 12:58:55 CST)
Dose restart frequently affect the results? liu xin (Fri Dec 23 2005 - 21:33:40 CST)
Re: preparing a dimeric protein for NAMD Peter Freddolino (Fri Dec 23 2005 - 22:00:55 CST)
Re: Re: Besides PSFGEN, (Thank you) Shirley Li (Fri Dec 23 2005 - 17:42:54 CST)
Re: preparing a dimeric protein for NAMD Shirley Li (Fri Dec 23 2005 - 17:35:59 CST)
Re: preparing a dimeric protein for NAMD Peter Freddolino (Fri Dec 23 2005 - 14:41:19 CST)
Re: Question about Generating DCD files with only specified atoms pijush.ghosh_at_ndsu.edu (Thu Dec 22 2005 - 19:36:07 CST)
Re: FATAL ERROR: unknown floating-point error, errno = 4 Manori Indira Jayasinghe (Fri Dec 23 2005 - 11:47:10 CST)
ABSOLUTE IMPRECISION and RELATIVE IMPRECISION IN TABLE FORCE Joshua D. Moore (Fri Dec 23 2005 - 03:01:17 CST)
Re: UNABLE TO OPEN .psf FILE Joshua D. Moore (Fri Dec 23 2005 - 02:56:34 CST)
UNABLE TO OPEN .psf FILE Joshua D. Moore (Fri Dec 23 2005 - 02:53:00 CST)
Re: FATAL ERROR: unknown floating-point error, errno = 4 Chris Chipot (Fri Dec 23 2005 - 01:22:32 CST)
FATAL ERROR: unknown floating-point error, errno = 4 Manori Indira Jayasinghe (Thu Dec 22 2005 - 23:16:41 CST)
Re: Question about Generating DCD files with only specified atoms Joshua D. Moore (Thu Dec 22 2005 - 22:23:02 CST)
preparing a dimeric protein for NAMD Irene Newhouse (Thu Dec 22 2005 - 21:28:21 CST)
Re: Question about Generating DCD files with only specified atoms Sterling Paramore (Thu Dec 22 2005 - 21:17:41 CST)
Re: Besides PSFGEN, are there any other good ways of generating .psf file Joshua D. Moore (Thu Dec 22 2005 - 21:01:31 CST)
Besides PSFGEN, are there any other good ways of generating .psf file Shirley Li (Thu Dec 22 2005 - 19:01:36 CST)
Question about Generating DCD files with only specified atoms Joshua D. Moore (Thu Dec 22 2005 - 18:06:09 CST)
Re: The HT-HT-OT angle parameter for TIP3? Joshua D. Moore (Thu Dec 22 2005 - 18:03:57 CST)
Re: ANGLE PARAMETERS (It works now) Shirley Li (Thu Dec 22 2005 - 16:54:06 CST)
The HT-HT-OT angle parameter for TIP3? Shirley Li (Thu Dec 22 2005 - 14:57:19 CST)
Re: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT Peter Freddolino (Thu Dec 22 2005 - 14:35:37 CST)
UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT Shirley Li (Thu Dec 22 2005 - 13:16:00 CST)
The angle parameters for CN7 are missing in NAMD? Shirley Li (Wed Dec 21 2005 - 18:02:07 CST)
Locally Enhanced Sampling milton sonoda (Wed Dec 21 2005 - 17:34:23 CST)
Re: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CN7 CN7 CN7 Joshua D. Moore (Wed Dec 21 2005 - 16:57:37 CST)
FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CN7 CN7 CN7 Shirley Li (Wed Dec 21 2005 - 14:56:36 CST)
Kinetic Energy difference using restart binaries Mikolai Fajer (Wed Dec 21 2005 - 12:54:13 CST)
Re: define abf1 and abf2 for CM of water and CM of molecule Chris Chipot (Wed Dec 21 2005 - 12:18:36 CST)
Re: define abf1 and abf2 for CM of water and CM of molecule Manori Indira Jayasinghe (Wed Dec 21 2005 - 11:26:37 CST)
PSF file format Jindal Shah (Tue Dec 20 2005 - 15:55:23 CST)
Re: define abf1 and abf2 for CM of water and CM of molecule Chris Chipot (Tue Dec 20 2005 - 01:28:32 CST)
define abf1 and abf2 for CM of water and CM of molecule Manori Indira Jayasinghe (Mon Dec 19 2005 - 22:53:42 CST)
Re: charmm27 fatal error arijit_r_at_chem.iitkgp.ernet.in (Mon Dec 19 2005 - 22:24:36 CST)
flipDCD and Unit Cell information? Joshua D. Moore (Mon Dec 19 2005 - 17:54:06 CST)
checking for correct construction of dihedrals, etc. Ralph Jimenez (Mon Dec 19 2005 - 16:51:52 CST)
RE: charmm27 fatal error Michel Espinoza-Fonseca (Mon Dec 19 2005 - 15:30:41 CST)
charmm27 fatal error Arturas Ziemys (Mon Dec 19 2005 - 14:06:00 CST)
NAMD/CHARM source installation option Jyh-Shyong Ho (Sat Dec 17 2005 - 23:36:55 CST)
extra points in NAMD Mgr. Lubos Vrbka (Sat Dec 17 2005 - 06:51:46 CST)
Some warnings from log file after minimization Grace Shen (Fri Dec 16 2005 - 13:05:53 CST)
pause simulation Leandro Martínez (Fri Dec 16 2005 - 12:53:23 CST)
Re: Some problem on compiling NAMD Gengbin Zheng (Thu Dec 15 2005 - 22:04:28 CST)
Some problem on compiling NAMD ËïÍ¥¹ã (Thu Dec 15 2005 - 21:24:18 CST)
Atom Positions during simulation Francisco Castro (Wed Dec 14 2005 - 16:27:12 CST)
return molecule to its principal axes mpavlova_at_purdue.edu (Wed Dec 14 2005 - 13:54:32 CST)
Re: Counterions: how to decide how many to put it? jonathan_at_ibt.unam.mx (Tue Dec 13 2005 - 21:05:34 CST)
Counterions: how to decide how many to put it? Ching Wong (Tue Dec 13 2005 - 17:44:33 CST)
Re: NAMD on Win64 Gengbin Zheng (Mon Dec 12 2005 - 21:04:07 CST)
RE: NAMD on Win64 Michel Espinoza-Fonseca (Mon Dec 12 2005 - 10:53:19 CST)
NAMD on Win64 Lea Thøgersen (Mon Dec 12 2005 - 10:26:11 CST)
Re: center of mass motion: problems Leandro Martínez (Thu Dec 08 2005 - 17:49:23 CST)
center of mass motion: problems Vani Krishna (Thu Dec 08 2005 - 16:27:06 CST)
Re: Reading from DCD file and running MD Jérôme Hénin (Wed Dec 07 2005 - 16:19:08 CST)
Reading from DCD file and running MD Shahid Qamar (Wed Dec 07 2005 - 14:35:05 CST)
Re: Packaging 100 cations and anions in a box Joshua D. Moore (Wed Dec 07 2005 - 02:25:23 CST)
Packaging 100 cations and anions in a box ir7_at_njit.edu (Tue Dec 06 2005 - 22:47:56 CST)
Re: how is NAMD output written in parallel mode? Ravinder Abrol (Tue Dec 06 2005 - 17:30:01 CST)
Re: Atoms moving too fast Brian Bennion (Tue Dec 06 2005 - 15:28:50 CST)
Re: successive minimization with different sets of fixed atoms Marc Q. Ma (Tue Dec 06 2005 - 12:31:36 CST)
Re: Atoms moving too fast LEWYN LI (Tue Dec 06 2005 - 13:55:24 CST)
Re: Atoms moving too fast Marcos Sotomayor (Tue Dec 06 2005 - 13:43:54 CST)
Atoms moving too fast Eric Perim (Tue Dec 06 2005 - 13:05:10 CST)
Re: A question regarding generate pdb and psf file JC Gumbart (Tue Dec 06 2005 - 11:37:55 CST)
successive minimization with different sets of fixed atoms JIMENEZ Ralph (Tue Dec 06 2005 - 11:14:25 CST)
A question regarding generate pdb and psf file Grace Shen (Tue Dec 06 2005 - 11:06:27 CST)
Building NAMD 2.6b1 on IBM Power5 Joachim Hein (Tue Dec 06 2005 - 03:49:53 CST)
Re: how is NAMD output written in parallel mode? Nicolas Sapay (Mon Dec 05 2005 - 08:17:58 CST)
Chamrun/NAMD processes and PBS cluster Nicolas Sapay (Mon Dec 05 2005 - 07:55:15 CST)
how is NAMD output written in parallel mode? Ravinder Abrol (Mon Dec 05 2005 - 02:09:38 CST)
how to constrains the smd atom on a line when do my smd simulation?? ÎâºéÃ÷ (Mon Dec 05 2005 - 01:59:09 CST)
Adding amino acids to an existing pdb structure LEWYN LI (Sun Dec 04 2005 - 21:30:49 CST)
Re: restart problem Marcos Sotomayor (Fri Dec 02 2005 - 00:10:18 CST)
restart problem liu xin (Fri Dec 02 2005 - 00:01:26 CST)
Re: Problems opening the Extended Trajectory File LEWYN LI (Thu Dec 01 2005 - 14:57:42 CST)
Problems opening the Extended Trajectory File Eric Perim (Thu Dec 01 2005 - 13:36:36 CST)
Re: merge trajectory from NAMD Joshua D. Moore (Wed Nov 30 2005 - 21:43:13 CST)
Re: merge trajectory from NAMD nmichaud_at_jhu.edu (Wed Nov 30 2005 - 21:05:19 CST)
Warning in namd output file Uma Mahankali (Wed Nov 30 2005 - 18:27:48 CST)
merge trajectory from NAMD michael jerry (Wed Nov 30 2005 - 16:19:57 CST)
Re: pair.pdb and cutoff for pairInteraction JC Gumbart (Wed Nov 30 2005 - 00:10:44 CST)
Re: pair.pdb and cutoff for pairInteraction JC Gumbart (Tue Nov 29 2005 - 23:52:51 CST)
Re: pair.pdb and cutoff for pairInteraction Shirley Li (Tue Nov 29 2005 - 22:33:36 CST)
Re: pair.pdb and cutoff for pairInteraction Peter Freddolino (Tue Nov 29 2005 - 11:26:19 CST)
pair.pdb and cutoff for pairInteraction Shirley Li (Tue Nov 29 2005 - 11:00:02 CST)
Re: segmentation fault on Linux dimka (Mon Nov 28 2005 - 12:41:25 CST)
problem with the NAMD CPU time consumption on a batch queueing system Nicolas Sapay (Mon Nov 28 2005 - 11:46:08 CST)
Water Box Shrinks Ching Wong (Fri Nov 25 2005 - 19:10:46 CST)
Update on Implicit Solvent Models in NAMD? Joshua D. Moore (Fri Nov 25 2005 - 14:01:31 CST)
Interaction between metal and metal-water. Taeho Kim (Fri Nov 25 2005 - 10:39:22 CST)
CHARMM compatible Methotrexate params Aaron Oakley (Thu Nov 24 2005 - 22:17:18 CST)
RE: Na ions got into the catalytic site during Production Run Michel Espinoza-Fonseca (Mon Nov 21 2005 - 10:16:38 CST)
Re: Na ions got into the catalytic site during Production Run Marc Q. Ma (Mon Nov 21 2005 - 09:29:51 CST)
Re: Namd2.6b1 FATAL ERROR: Memory allocation failed on AIX53 IBM-SP4 Mauricio Arenas Salinas (Mon Nov 21 2005 - 09:10:16 CST)
Re: Namd2.6b1 FATAL ERROR: Memory allocation failed on AIX53 IBM-SP4 Sascha Tayefeh (Mon Nov 21 2005 - 06:16:14 CST)
Re: Namd2.6b1 FATAL ERROR: Memory allocation failed on AIX53 IBM-SP4 Joachim Hein (Mon Nov 21 2005 - 04:12:05 CST)
Namd2.6b1 FATAL ERROR: Memory allocation failed on AIX53 IBM-SP4 Sascha Tayefeh (Mon Nov 21 2005 - 02:56:34 CST)
Na ions got into the catalytic site during Production Run Ching Wong (Sun Nov 20 2005 - 17:34:01 CST)
Re: temperature "coupling coefficient" in NAMD JC Gumbart (Fri Nov 18 2005 - 12:02:37 CST)
temperature "coupling coefficient" in NAMD curcio (Fri Nov 18 2005 - 11:09:13 CST)
Re: Replica-Exchange MD Paul R Brenner (Fri Nov 18 2005 - 09:49:38 CST)
Re: Replica-Exchange MD Mark Abraham (Fri Nov 18 2005 - 08:00:36 CST)
Replica-Exchange MD Marc Baaden (Fri Nov 18 2005 - 03:18:19 CST)
Re: freeEnergy of conformational change of a test molecule Chris Chipot (Thu Nov 17 2005 - 11:37:07 CST)
Re: freeEnergy of conformational change of a test molecule Uma Mahankali (Thu Nov 17 2005 - 08:45:12 CST)
Re: freeEnergy of conformational change of a test molecule Chris Chipot (Thu Nov 17 2005 - 03:44:55 CST)
The psf format conversion Grace Shen (Wed Nov 16 2005 - 16:54:42 CST)
freeEnergy of conformational change of a test molecule Uma Mahankali (Wed Nov 16 2005 - 13:33:18 CST)
NAMD on Intel XEON EM64T Sterling Paramore (Mon Nov 14 2005 - 16:55:50 CST)
munch: The input file main.o is not valid in the current object mode Raj NK (Mon Nov 14 2005 - 16:14:36 CST)
Re: Problem with NAMD on Opteron cluster Marc Q. Ma (Mon Nov 14 2005 - 08:37:55 CST)
Re: ABF for conformational analysis Jérôme Hénin (Mon Nov 14 2005 - 03:34:21 CST)
parameter and topology for 4-MI arijit_r_at_chem.iitkgp.ernet.in (Mon Nov 14 2005 - 00:19:27 CST)
Problem with NAMD on Opteron cluster tepper_at_amolf.nl (Fri Nov 11 2005 - 10:36:39 CST)
Errors: Periodic cell became too small for original patch grid & Setting parameter binaryoutput from script failed! Nitin Bhardwaj (Sun Nov 13 2005 - 12:26:35 CST)
Re: Different solvents Marc Baaden (Sun Nov 13 2005 - 07:49:19 CST)
Problem with NAMD on Opteron cluster Harald Tepper (Sat Nov 12 2005 - 05:29:33 CST)
ABF for conformational analysis Uma Mahankali (Fri Nov 11 2005 - 16:54:11 CST)
Re: FEP.... Wei Chen (Fri Nov 11 2005 - 11:28:20 CST)
Re: FEP.... Chris Chipot (Fri Nov 11 2005 - 10:35:19 CST)
FEP.... Raul Araya Secchi (Fri Nov 11 2005 - 09:39:41 CST)
Re: Pair Interaction options Peter Freddolino (Thu Nov 10 2005 - 10:27:14 CST)
Pair Interaction options Uma Mahankali (Thu Nov 10 2005 - 10:20:24 CST)
Energy for part of system Ralph Jimenez (Wed Nov 09 2005 - 16:55:14 CST)
Different solvents Gaurav Sharma (Tue Nov 08 2005 - 13:09:27 CST)
General question about NAMD michael jerry (Tue Nov 08 2005 - 10:52:04 CST)
Problem with compiling NAMD on Suse 9.3 fu guoxing (Tue Nov 08 2005 - 06:23:10 CST)
Re: PMF calculation using fixed restraints Chris Chipot (Sun Nov 06 2005 - 14:54:16 CST)
PMF calculation using fixed restraints Vani Krishna (Sun Nov 06 2005 - 12:26:22 CST)
RE: NAMD 2.6 in IBM SP Xinghua Shi (Sun Nov 06 2005 - 05:41:18 CST)
Re: NAMD 2.6 in IBM SP Gengbin Zheng (Sat Nov 05 2005 - 09:55:13 CST)
NAMD 2.6 in IBM SP Xinghua Shi (Sat Nov 05 2005 - 09:41:35 CST)
NAMD 2.6 in IBM SP Xinghua Shi (Sat Nov 05 2005 - 09:12:12 CST)
Re: A question on minimization Marcos Sotomayor (Fri Nov 04 2005 - 16:18:46 CST)
restart a simulation Shirley Li (Fri Nov 04 2005 - 16:15:35 CST)
A question on minimization santanu chatterjee (Fri Nov 04 2005 - 15:44:32 CST)
Re: The vector direction in SMD Marcos Sotomayor (Fri Nov 04 2005 - 15:29:52 CST)
Re: The vector direction in SMD JC Gumbart (Fri Nov 04 2005 - 15:16:30 CST)
The vector direction in SMD Grace Shen (Fri Nov 04 2005 - 15:01:51 CST)
Re: Size of water box Marcos Sotomayor (Fri Nov 04 2005 - 14:59:17 CST)
Re: namd: advice Mark Abraham (Fri Nov 04 2005 - 14:30:55 CST)
Re: Size of water box Mark Abraham (Fri Nov 04 2005 - 14:29:36 CST)
Size of water box santanu chatterjee (Fri Nov 04 2005 - 13:06:07 CST)
Re: RE: namd: advice Sergio Anis (Fri Nov 04 2005 - 09:43:25 CST)
RE: namd: advice Grace Shen (Fri Nov 04 2005 - 09:20:13 CST)
namd: advice Sergio Anis (Fri Nov 04 2005 - 07:56:34 CST)
questions about applying patches Ralph Jimenez (Thu Nov 03 2005 - 14:23:27 CST)
RE: more Heme troubles Ralph Jimenez (Thu Nov 03 2005 - 13:19:54 CST)
Re: Increasing temp during MD Peter Freddolino (Thu Nov 03 2005 - 12:43:33 CST)
Increasing temp during MD Grace Shen (Thu Nov 03 2005 - 12:11:27 CST)
Re: How to atomselect several residues Nara Dashdorj (Wed Nov 02 2005 - 19:12:10 CST)
Re: How to atomselect several residues JC Gumbart (Wed Nov 02 2005 - 18:38:27 CST)
Re: POPC or POPE? Philip Blood (Wed Nov 02 2005 - 18:16:19 CST)
How to atomselect several residues Grace Shen (Wed Nov 02 2005 - 17:28:50 CST)
Re: CA CL CA angle? Richard Wood (Wed Nov 02 2005 - 10:31:05 CST)
Re: How to patch segments of aminoacids Brian Bennion (Wed Nov 02 2005 - 10:35:19 CST)
Re: ABF Simulation Lionel Perrin (Wed Nov 02 2005 - 08:28:25 CST)
ERROR: Constraint failure in RATTLE algorithm for atom 598! Raul Araya Secchi (Wed Nov 02 2005 - 08:17:29 CST)
How to patch segments of aminoacids Alexe Bojovschi (Wed Nov 02 2005 - 03:09:08 CST)
IC Removal and Problem Nara Dashdorj (Tue Nov 01 2005 - 22:31:53 CST)
POPC or POPE? Charles Danko (Tue Nov 01 2005 - 22:20:04 CST)
ABF.TCl file ??? Shahid Qamar (Tue Nov 01 2005 - 13:56:25 CST)
RE: About ADP Michel Espinoza-Fonseca (Tue Nov 01 2005 - 13:21:22 CST)
Re: CA CL CA angle? Brian Bennion (Tue Nov 01 2005 - 12:57:43 CST)
CA CL CA angle? Richard Wood (Tue Nov 01 2005 - 11:11:44 CST)
RE: About ADP Grace Shen (Tue Nov 01 2005 - 10:15:47 CST)
RE: About ADP Michel Espinoza-Fonseca (Tue Nov 01 2005 - 10:16:43 CST)
About ADP Grace Shen (Tue Nov 01 2005 - 09:48:43 CST)
Replica-Exchange MD Mark Abraham (Mon Oct 31 2005 - 22:57:17 CST)
Re: Question regarding SMD Leandro Martínez (Mon Oct 31 2005 - 17:26:23 CST)
Question regarding SMD Grace Shen (Mon Oct 31 2005 - 15:11:01 CST)
RE: Myrinet NAMD Jason Lee (Mon Oct 31 2005 - 15:00:25 CST)
beta-peptides ... Nicholas M Glykos (Mon Oct 31 2005 - 06:34:20 CST)
How can I increase the computing rate on the computer cluster xiaojing gong (Sun Oct 30 2005 - 05:44:24 CST)
Fwd: All or Nothing at All?? griadi_at_utalca.cl (Sat Oct 29 2005 - 14:02:12 CDT)
Re: questions about running namd on NCSA cluster tungsten Gengbin Zheng (Sat Oct 29 2005 - 12:11:50 CDT)
All or Nothing at All?? Angelo R. Rossi (Sat Oct 29 2005 - 11:41:32 CDT)
Re: About RMSD calculation. Boyang Wang (Fri Oct 28 2005 - 16:56:09 CDT)
questions about running namd on NCSA cluster tungsten Wei Zhuang (Fri Oct 28 2005 - 17:09:22 CDT)
Re: About RMSD calculation. Peter Freddolino (Fri Oct 28 2005 - 16:20:48 CDT)
Re: About RMSD calculation. Boyang Wang (Fri Oct 28 2005 - 15:55:41 CDT)
Re: About RMSD calculation. LEWYN LI (Fri Oct 28 2005 - 15:30:20 CDT)
About RMSD calculation. Boyang Wang (Fri Oct 28 2005 - 10:49:14 CDT)
Myrinet NAMD Wei Zhuang (Fri Oct 28 2005 - 14:01:21 CDT)
new problem Richard Wood (Thu Oct 27 2005 - 21:52:17 CDT)
Re: ABF Simulation Jérôme Hénin (Fri Oct 28 2005 - 04:05:52 CDT)
(no subject) Michael Grabe (Thu Oct 27 2005 - 22:39:35 CDT)
Re: urestraint doesn't work Michael Grabe (Thu Oct 27 2005 - 20:55:49 CDT)
Re: Re: urestraint doesn't work Wei Zhuang (Thu Oct 27 2005 - 21:45:37 CDT)
Re: Re: urestraint doesn't work Wei Zhuang (Thu Oct 27 2005 - 20:35:22 CDT)
Re: urestraint doesn't work Michael Grabe (Thu Oct 27 2005 - 19:06:01 CDT)
urestraint doesn't work Wei Zhuang (Thu Oct 27 2005 - 16:56:55 CDT)
RE: How to append charmm stream file Michel Espinoza-Fonseca (Wed Oct 26 2005 - 12:36:01 CDT)
Re: trying to generate a peptide Richard Wood (Wed Oct 26 2005 - 11:39:44 CDT)
How to append charmm stream file Grace Shen (Wed Oct 26 2005 - 12:01:23 CDT)
Re: trying to generate a peptide Giovanni Bellesia (Wed Oct 26 2005 - 11:27:43 CDT)
Re: fixed atoms wzhuang_at_uci.edu (Wed Oct 26 2005 - 11:12:25 CDT)
Re: Only part of the protein is moving in MD simulation Leandro Martínez (Wed Oct 26 2005 - 10:58:19 CDT)
Re: ABF Simulation Lionel Perrin (Wed Oct 26 2005 - 10:52:53 CDT)
Only part of the protein is moving in MD simulation Uma Mahankali (Wed Oct 26 2005 - 10:12:13 CDT)
RE: trying to generate a peptide Jim Phillips (Wed Oct 26 2005 - 09:39:56 CDT)
RE: trying to generate a peptide Richard Wood (Wed Oct 26 2005 - 09:26:48 CDT)
RE: trying to generate a peptide Michel Espinoza-Fonseca (Wed Oct 26 2005 - 09:19:08 CDT)
RE: trying to generate a peptide Richard Wood (Wed Oct 26 2005 - 07:34:59 CDT)
RE: trying to generate a peptide Michel Espinoza-Fonseca (Wed Oct 26 2005 - 03:35:23 CDT)
fixed atoms Gan, Yong $UMC-Student$ (Tue Oct 25 2005 - 23:18:59 CDT)
trying to generate a peptide Richard Wood (Tue Oct 25 2005 - 20:07:01 CDT)
Re: saving coordinates as a PDB file after minimization in NAMD Richard Wood (Tue Oct 25 2005 - 16:11:44 CDT)
Can I miminimize some atoms in system Shahid Qamar (Tue Oct 25 2005 - 16:40:06 CDT)
Re: saving coordinates as a PDB file after minimization in NAMD LEWYN LI (Tue Oct 25 2005 - 16:32:19 CDT)
Re: saving coordinates as a PDB file after minimization in NAMD Richard Law (Tue Oct 25 2005 - 16:14:18 CDT)
Re: saving coordinates as a PDB file after minimization in NAMD Richard Law (Tue Oct 25 2005 - 15:44:17 CDT)
saving coordinates as a PDB file after minimization in NAMD Richard Wood (Tue Oct 25 2005 - 13:12:02 CDT)
Box size Gan, Yong $UMC-Student$ (Tue Oct 25 2005 - 11:50:06 CDT)
Assign the ligand force field parameters Grace Shen (Mon Oct 24 2005 - 16:32:13 CDT)
Water Sphere Raul Araya Secchi (Mon Oct 24 2005 - 15:21:27 CDT)
Re: Serious Steric Atom Clashes Brian Bennion (Mon Oct 24 2005 - 15:01:41 CDT)
Re: Serious Steric Atom Clashes Nara Dashdorj (Mon Oct 24 2005 - 14:51:18 CDT)
Re: Serious Steric Atom Clashes Marcos Sotomayor (Mon Oct 24 2005 - 13:51:13 CDT)
Re: Serious Steric Atom Clashes Brian Bennion (Mon Oct 24 2005 - 13:48:23 CDT)
Re: Serious Steric Atom Clashes Nara Dashdorj (Mon Oct 24 2005 - 13:09:32 CDT)
Re: Serious Steric Atom Clashes Brian Bennion (Mon Oct 24 2005 - 10:41:05 CDT)
Serious Steric Atom Clashes Nara Dashdorj (Sun Oct 23 2005 - 13:45:43 CDT)
scaling issue Robert Bjornson (Fri Oct 21 2005 - 15:56:13 CDT)
Question about load balancing Robert Bjornson (Fri Oct 21 2005 - 15:44:46 CDT)
Re: Michael Grabe (Fri Oct 21 2005 - 12:15:15 CDT)
(no subject) Shahid Qamar (Fri Oct 21 2005 - 11:20:08 CDT)
Re: ABF Simulation Lionel Perrin (Fri Oct 21 2005 - 04:03:02 CDT)
Can NAMD control pressure gradually increase? weikai (Fri Oct 21 2005 - 02:30:41 CDT)
Gromacs parameters in NAMD Kasson (Thu Oct 20 2005 - 13:21:06 CDT)
(no subject) Michael Grabe (Wed Oct 19 2005 - 19:09:19 CDT)
Re: SGE (Grid Engine) on Rocks Cluster Jim Phillips (Wed Oct 19 2005 - 17:42:20 CDT)
SGE (Grid Engine) on Rocks Cluster Mauricio Carrillo Tripp (Wed Oct 19 2005 - 17:27:57 CDT)
Re: How to run namd on NCSA Tungsten Hyonseok Hwang (Wed Oct 19 2005 - 16:56:30 CDT)
(no subject) Michael Grabe (Wed Oct 19 2005 - 14:53:14 CDT)
How to run namd on NCSA Tungsten snoze pa (Wed Oct 19 2005 - 14:38:58 CDT)
Warning: add bond failed in patch of ACE Per Jr. Greisen (Wed Oct 19 2005 - 14:14:24 CDT)
Autoionize: net charge NOT equal to zero Shirley Li (Wed Oct 19 2005 - 11:44:34 CDT)
Re: ABF Simulation Jérôme Hénin (Wed Oct 19 2005 - 04:11:17 CDT)
NAMD on myrinet Hyonseok Hwang (Tue Oct 18 2005 - 16:12:36 CDT)
Re: Compilation of NAMD on 64-bit NUMA with icc Brian Bennion (Tue Oct 18 2005 - 10:47:16 CDT)
Compilation of NAMD on 64-bit NUMA with icc ashwin joshi (Tue Oct 18 2005 - 02:46:18 CDT)
RE: A question on psfgen JC Gumbart (Tue Oct 18 2005 - 02:09:05 CDT)
A question on psfgen santanu chatterjee (Tue Oct 18 2005 - 01:55:39 CDT)
running NAMD on tungsten Wei Zhuang (Tue Oct 18 2005 - 01:59:57 CDT)
Re: namdplot: command not found bo baker (Mon Oct 17 2005 - 19:50:01 CDT)
NAMD time step: AKMA? Parminder Mankoo (Mon Oct 17 2005 - 18:52:26 CDT)
PSF file ATP Per Jr. Greisen (Sat Oct 15 2005 - 15:01:36 CDT)
How to have neutral terminal ends eladp_at_hplus.tau.ac.il (Sat Oct 15 2005 - 04:15:01 CDT)
Re: namdplot: command not found Brian Bennion (Fri Oct 14 2005 - 14:44:14 CDT)
Re: gcc4 Gengbin Zheng (Fri Oct 14 2005 - 14:21:57 CDT)
Re: namdplot: command not found bo baker (Fri Oct 14 2005 - 14:04:53 CDT)
PSC WORKSHOP: COMPUTATIONAL BIOPHYSICS WORKSHOP Troy Wymore (Fri Oct 14 2005 - 13:18:27 CDT)
ATP PDB file Per Jr. Greisen (Fri Oct 14 2005 - 07:25:40 CDT)
ATP nucleotides using NAMD greisen_at_binf.ku.dk (Fri Oct 14 2005 - 04:56:45 CDT)
Re: NAMD distribute Shantenu Jha (Thu Oct 13 2005 - 18:08:56 CDT)
Re: NAMD distribute Robert Brunner (Thu Oct 13 2005 - 17:40:26 CDT)
Re: CMAP in VMD error JC Gumbart (Thu Oct 13 2005 - 16:16:04 CDT)
Re: namdplot: command not found Brian Bennion (Thu Oct 13 2005 - 16:09:03 CDT)
Re: NAMD distribute Brian Bennion (Thu Oct 13 2005 - 16:05:59 CDT)
CMAP in VMD error greisen_at_binf.ku.dk (Thu Oct 13 2005 - 15:58:33 CDT)
Re: NAMD distribute Dan Strahs (Thu Oct 13 2005 - 15:46:42 CDT)
Re: namdplot: command not found Robert Brunner (Thu Oct 13 2005 - 15:11:37 CDT)
Re: namdplot: command not found Sterling Paramore (Thu Oct 13 2005 - 14:59:36 CDT)
Re: namdplot: command not found bo baker (Thu Oct 13 2005 - 14:26:47 CDT)
Re: Metal Ion and Protein binding LEWYN LI (Thu Oct 13 2005 - 13:38:07 CDT)
Metal Ion and Protein binding Gaurav Sharma (Thu Oct 13 2005 - 12:23:23 CDT)
Re: NAMD distribute Brian Bennion (Thu Oct 13 2005 - 10:18:41 CDT)
Re: NAMD distribute Michael Grabe (Wed Oct 12 2005 - 21:31:10 CDT)
NAMD distribute Dan Strahs (Wed Oct 12 2005 - 20:28:49 CDT)
Question about cutoff distance Leonardo Sepulveda Durán (Tue Oct 11 2005 - 17:06:10 CDT)
Re: namdplot: command not found JC Gumbart (Wed Oct 12 2005 - 15:41:43 CDT)
Re: namdplot: command not found bo baker (Wed Oct 12 2005 - 15:27:23 CDT)
Re: NAMD restarts binary files LEWYN LI (Wed Oct 12 2005 - 11:27:01 CDT)
make namd2 problem prodakt_at_o2.pl (Wed Oct 12 2005 - 06:21:53 CDT)
NAMD restarts binary files snoze pa (Wed Oct 12 2005 - 10:21:46 CDT)
Re: namdplot: command not found Pawel Weronski (Wed Oct 12 2005 - 08:57:32 CDT)
Re: namdplot: command not found bo baker (Tue Oct 11 2005 - 18:56:10 CDT)
gcc4 Gianluca Interlandi (Tue Oct 11 2005 - 16:34:32 CDT)
problem with PSFGEN: the O3A atom cannot be recognized Shirley Li (Tue Oct 11 2005 - 12:52:49 CDT)
Re: problem with PSFGEN JC Gumbart (Tue Oct 11 2005 - 11:54:42 CDT)
running NAMD2 in parallel Gan, Yong $UMC-Student$ (Tue Oct 11 2005 - 10:42:42 CDT)
Re: namdplot: command not found Robert Brunner (Tue Oct 11 2005 - 10:32:00 CDT)
Re: namdplot: command not found Pawel Weronski (Tue Oct 11 2005 - 08:22:18 CDT)
Re: running NAMD2 in parallel dimka (Mon Oct 10 2005 - 23:33:59 CDT)
Re: running NAMD2 in parallel Leonardo Sepulveda Durán (Mon Oct 10 2005 - 23:24:46 CDT)
RE: running NAMD2 in parallel Gan, Yong $UMC-Student$ (Mon Oct 10 2005 - 22:34:32 CDT)
Re: running NAMD2 in parallel Leonardo Sepulveda Durán (Mon Oct 10 2005 - 22:03:27 CDT)
running NAMD2 in parallel Gan, Yong $UMC-Student$ (Mon Oct 10 2005 - 21:23:46 CDT)
problem with PSFGEN Shirley Li (Mon Oct 10 2005 - 18:15:58 CDT)
RE: water box and the procedure Shirley Li (Mon Oct 10 2005 - 18:05:34 CDT)
namdplot: command not found bo baker (Mon Oct 10 2005 - 17:36:32 CDT)
Re: topology and parameter for acetylcholine Leyla Celik (Mon Oct 10 2005 - 01:27:41 CDT)
Re: fix backbone atom JC Gumbart (Sun Oct 09 2005 - 02:29:57 CDT)
fix backbone atom bo baker (Sun Oct 09 2005 - 01:52:35 CDT)
developing parameters for charmm snoze pa (Sat Oct 08 2005 - 19:40:54 CDT)
reconstruct PMF akash.khandelwal_at_ndsu.edu (Sat Oct 08 2005 - 15:54:26 CDT)
Recalculating energies from DCD file Chang, Christopher (Fri Oct 07 2005 - 18:05:37 CDT)
RE: water box and the procedure JC Gumbart (Fri Oct 07 2005 - 20:38:26 CDT)
Re: Running NAMD 2.6b1 on Linux Networks Peter Freddolino (Fri Oct 07 2005 - 17:09:31 CDT)
Running NAMD 2.6b1 on Linux Networks Gan, Yong $UMC-Student$ (Fri Oct 07 2005 - 16:44:53 CDT)
NAMD 2.6b1 error writing DCD file on Cray XT3 Philip Blood (Fri Oct 07 2005 - 13:24:47 CDT)
Re: Penetration of water Mauricio Carrillo Tripp (Fri Oct 07 2005 - 10:40:13 CDT)
Re: About the potantial of IONS Mauricio Carrillo Tripp (Fri Oct 07 2005 - 10:29:17 CDT)
Re: About the potential of NAMD Brian Bennion (Fri Oct 07 2005 - 10:35:42 CDT)
Re: help generating psf files Peter Freddolino (Fri Oct 07 2005 - 10:18:02 CDT)
water box and the procedure Shirley Li (Fri Oct 07 2005 - 09:50:15 CDT)
Re: help generating psf files Anna Modzelewska (Fri Oct 07 2005 - 09:16:57 CDT)
topology and parameter for acetylcholine Michel Espinoza-Fonseca (Fri Oct 07 2005 - 06:28:38 CDT)
Re: help generating psf files Anna Modzelewska (Fri Oct 07 2005 - 02:58:19 CDT)
Penetration of water bo baker (Fri Oct 07 2005 - 00:20:46 CDT)
About the potential of NAMD yangbing00_at_mails.tsinghua.edu.cn (Thu Oct 06 2005 - 22:53:46 CDT)
About the potantial of IONS yangbing00_at_mails.tsinghua.edu.cn (Thu Oct 06 2005 - 22:16:17 CDT)
Re: ion concentration JC Gumbart (Thu Oct 06 2005 - 20:21:20 CDT)
ion concentration Shirley Li (Thu Oct 06 2005 - 18:36:26 CDT)
command to run MPI and ABF Shahid Qamar (Thu Oct 06 2005 - 18:10:39 CDT)
more heme troubles JIMENEZ Ralph (Thu Oct 06 2005 - 16:14:45 CDT)
Re: autoionize and psfgen, which one first? JC Gumbart (Thu Oct 06 2005 - 16:11:43 CDT)
autoionize and psfgen, which one first? Shirley Li (Thu Oct 06 2005 - 16:01:42 CDT)
Re: VMD scripting (Thanks a lot) Shirley Li (Thu Oct 06 2005 - 15:54:24 CDT)
Re: help generating psf files Peter Freddolino (Thu Oct 06 2005 - 15:22:01 CDT)
Re: VMD scripting JC Gumbart (Thu Oct 06 2005 - 14:39:51 CDT)
VMD scripting Shirley Li (Thu Oct 06 2005 - 14:33:21 CDT)
rigid bonds for other atoms Kyle Gustafson (Thu Oct 06 2005 - 13:40:23 CDT)
Re: ABF Simulation Lionel Perrin (Thu Oct 06 2005 - 09:13:45 CDT)
Re: help generating psf files Anna Modzelewska (Thu Oct 06 2005 - 08:55:18 CDT)
Re: help generating psf files Anna Modzelewska (Thu Oct 06 2005 - 02:37:14 CDT)
Re: About calculating RMSD with rmsd.tcl Peter Freddolino (Wed Oct 05 2005 - 22:22:23 CDT)
Re: pairInteraction energies? Peter Freddolino (Wed Oct 05 2005 - 22:19:30 CDT)
Re: 1-4 interactions scaling Peter Freddolino (Wed Oct 05 2005 - 22:15:36 CDT)
Re: help generating psf files Peter Freddolino (Wed Oct 05 2005 - 22:09:07 CDT)
namd 2.6b1 Gan, Yong $UMC-Student$ (Wed Oct 05 2005 - 20:50:57 CDT)
Does NAMD calculate the potential energy of FIXED ATOMS? Boyang Wang (Wed Oct 05 2005 - 12:14:36 CDT)
difficulties using SMD on atoms in large systems Philip Blood (Tue Oct 04 2005 - 12:42:01 CDT)
help generating psf files Richard Wood (Tue Oct 04 2005 - 11:37:08 CDT)
1-4 interactions scaling Mauricio Carrillo Tripp (Mon Oct 03 2005 - 14:30:00 CDT)
Re: Re water box and system charge Boyang Wang (Fri Sep 30 2005 - 21:18:04 CDT)
About calculating RMSD with rmsd.tcl Boyang Wang (Fri Sep 30 2005 - 19:55:26 CDT)
Re water box and system charge Boyang Wang (Fri Sep 30 2005 - 19:47:16 CDT)
Re water box and system charge Boyang Wang (Fri Sep 30 2005 - 14:22:12 CDT)
Re: error parsing config file Brian Bennion (Fri Sep 30 2005 - 10:30:30 CDT)
RE: error parsing config file Pijush Ghosh (Thu Sep 29 2005 - 21:52:09 CDT)
namd cluster run, connection refused snoze pa (Thu Sep 29 2005 - 20:06:57 CDT)
ensemble Wei Chen (Wed Oct 05 2005 - 16:34:12 CDT)
psfgen trouble with heme JIMENEZ Ralph (Wed Oct 05 2005 - 14:54:26 CDT)
Question about cutoff distance Leonardo Sepulveda Durán (Wed Oct 05 2005 - 12:56:24 CDT)
Re: ABF Simulation Jérôme Hénin (Wed Oct 05 2005 - 11:35:25 CDT)
Re: ABF Simulation Chris Chipot (Wed Oct 05 2005 - 07:58:57 CDT)
ABF Simulation Lionel Perrin (Wed Oct 05 2005 - 06:41:44 CDT)
NAMD: error messages Sergio Anis (Tue Oct 04 2005 - 06:21:31 CDT)
Is there a method to choose what is saved in DCD files xiaojing gong (Sun Oct 02 2005 - 09:34:02 CDT)
Fedora Core 4 problems [2] ... Nicholas M Glykos (Sat Oct 01 2005 - 08:42:21 CDT)
Fedora Core 4 problems (?) ... Nicholas M Glykos (Sat Oct 01 2005 - 08:08:55 CDT)
namd 2.6b1 job crash error dimka (Fri Sep 30 2005 - 16:18:43 CDT)
water box and system charge snoze pa (Fri Sep 30 2005 - 11:44:21 CDT)
NAMD cluster run snoze pa (Fri Sep 30 2005 - 10:35:22 CDT)
Ca++ topology&param files mustapha.hamdi_at_ensi-bourges.fr (Fri Sep 30 2005 - 04:11:31 CDT)
pairInteraction energies? Georgios Papadopoulos (Fri Sep 30 2005 - 01:32:46 CDT)
error parsing config file dora guzman (Thu Sep 29 2005 - 14:00:00 CDT)
Re: unexpected end with NAMD on quad-dual core opteron machine Gengbin Zheng (Thu Sep 29 2005 - 13:39:22 CDT)
unexpected end with NAMD on quad-dual core opteron machine JIMENEZ Ralph (Thu Sep 29 2005 - 12:59:42 CDT)
problems NAMD_2.6 (fwd) carles ferrer (Thu Sep 29 2005 - 04:06:09 CDT)
NAMD on SUN floquet_at_icsn.cnrs-gif.fr (Thu Sep 29 2005 - 01:31:03 CDT)
NAMD for Xeon clusters Xiongce Zhao (Wed Sep 28 2005 - 17:13:06 CDT)
Re: About ions Representation in NAMD Gianluca Interlandi (Wed Sep 28 2005 - 07:33:39 CDT)
About Potential Addition in NAMD yangbing00_at_mails.tsinghua.edu.cn (Wed Sep 28 2005 - 06:45:18 CDT)
About ions Representation in NAMD yangbing00_at_mails.tsinghua.edu.cn (Wed Sep 28 2005 - 06:40:45 CDT)
Using an arbitrary tabulated potential in NAMD Joshua D. Moore (Tue Sep 27 2005 - 21:44:26 CDT)
RE: random seed JC Gumbart (Tue Sep 27 2005 - 20:30:05 CDT)
random seed ioana_at_pegasus.arc.nasa.gov (Tue Sep 27 2005 - 20:14:25 CDT)
Re: calculate enthalpy of binding Peter Freddolino (Tue Sep 27 2005 - 17:27:44 CDT)
NAMD running problem Jason Lee (Tue Sep 27 2005 - 15:02:27 CDT)
SHAKE or not? Gianluca Interlandi (Tue Sep 27 2005 - 14:42:43 CDT)
Re: Another question about MD simulation of a domain. \ (Tue Sep 27 2005 - 14:15:59 CDT)
Another question about MD simulation of a domain. Boyang Wang (Tue Sep 27 2005 - 12:30:43 CDT)
A question about MD simulation of peptide. Boyang Wang (Tue Sep 27 2005 - 12:24:59 CDT)
calculate enthalpy of binding Georgios Papadopoulos (Tue Sep 27 2005 - 11:33:33 CDT)
Re: vmd-l: ptraj John Stone (Tue Sep 27 2005 - 09:57:34 CDT)
Re: ptraj Nicolas Sapay (Tue Sep 27 2005 - 10:03:18 CDT)
ptraj Michel Espinoza-Fonseca (Tue Sep 27 2005 - 06:24:50 CDT)
Re: hi all, I want to know how to turn the debug mode on of the namd q=E2=BA=E9=C3=F7?= (Mon Sep 26 2005 - 23:43:25 CDT)
Re: It is posible to allow Bond and angle degrees of freedom in tip3 water?? JC Gumbart (Mon Sep 26 2005 - 22:27:04 CDT)
It is posible to allow Bond and angle degrees of freedom in tip3 water?? Leonardo Sepulveda Durán (Mon Sep 26 2005 - 16:52:55 CDT)
RE: Constraint failure Michel Espinoza-Fonseca (Mon Sep 26 2005 - 13:54:52 CDT)
Constraint failure Po Hu (Sat Sep 24 2005 - 13:42:42 CDT)
hi all, I want to know how to turn the debug mode on of the namd q=E2=BA=E9=C3=F7?= (Mon Sep 26 2005 - 09:56:17 CDT)
temperature coupling and pressure coupling xiaojing gong (Mon Sep 26 2005 - 01:44:16 CDT)
energy minimization xiaojing gong (Sun Sep 25 2005 - 22:05:32 CDT)
energy minimization xiaojing gong (Sun Sep 25 2005 - 21:57:00 CDT)
RE: autoionize & namd2 Michel Espinoza-Fonseca (Thu Sep 22 2005 - 02:51:08 CDT)
Re: log file bo baker (Wed Sep 21 2005 - 18:49:38 CDT)
RE: autoionize & namd2 Michel Espinoza-Fonseca (Wed Sep 21 2005 - 09:57:17 CDT)
RE: autoionize & namd2 paul.dalhaimer_at_yale.edu (Wed Sep 21 2005 - 09:47:37 CDT)
RE: autoionize & namd2 Michel Espinoza-Fonseca (Wed Sep 21 2005 - 09:32:45 CDT)
Re: rotating constraints Anna Modzelewska (Wed Sep 21 2005 - 04:22:30 CDT)
RE: autoionize & namd2 Michel Espinoza-Fonseca (Wed Sep 21 2005 - 02:24:09 CDT)
Fix distance Ekta Khurana (Tue Sep 20 2005 - 18:11:06 CDT)
autoionize & namd2 bo baker (Tue Sep 20 2005 - 18:07:34 CDT)
reconstructing backbone with psfgen Michel Espinoza-Fonseca (Tue Sep 20 2005 - 09:07:04 CDT)
reconstructing backbone with psfgen Michel Espinoza-Fonseca (Tue Sep 20 2005 - 05:45:10 CDT)
How to use AMBER force field in NAMD? Po Hu (Mon Sep 19 2005 - 20:31:13 CDT)
Re: log file bo baker (Mon Sep 19 2005 - 18:38:35 CDT)
Re: log file Gengbin Zheng (Mon Sep 19 2005 - 16:58:43 CDT)
Re: log file bo baker (Mon Sep 19 2005 - 16:55:33 CDT)
segmentation fault on Linux dimka (Mon Sep 19 2005 - 16:48:02 CDT)
log file bo baker (Mon Sep 19 2005 - 14:09:42 CDT)
Re: "Segmentation violation" on running namd2.6b1 Dong Luo (Mon Sep 19 2005 - 13:09:38 CDT)
"Segmentation violation" on running namd2.6b1 Dong Luo (Mon Sep 19 2005 - 10:36:30 CDT)
Binding Energies for a Peptide-RNA System rossi_at_york.cuny.edu (Sat Sep 17 2005 - 14:37:11 CDT)
NAMD2.6b1 (&2.5) binaries on Scyld (missing libbproc.so.2 lib?) Nicolae-Viorel Buchete (Thu Sep 15 2005 - 16:44:28 CDT)
Partial charges for fluorescein/topology file Shahid Qamar (Thu Sep 15 2005 - 13:19:41 CDT)
PSC WORKSHOP: COMPUTATIONAL BIOPHYSICS WORKSHOP Troy Wymore (Thu Sep 15 2005 - 11:22:29 CDT)
problem while running NAMD Imran Khan (Wed Sep 14 2005 - 11:25:56 CDT)
Re: energy values LEWYN LI (Tue Sep 13 2005 - 15:16:48 CDT)
Re: energy values \ (Tue Sep 13 2005 - 13:30:50 CDT)
Re: energy values Leonardo Sepulveda Durán (Tue Sep 13 2005 - 11:38:21 CDT)
Re: energy values Peter Freddolino (Tue Sep 13 2005 - 11:31:22 CDT)
Re: energy values paul.dalhaimer_at_yale.edu (Tue Sep 13 2005 - 11:13:44 CDT)
energy values Anna Modzelewska (Tue Sep 13 2005 - 06:29:27 CDT)
Re: Free Energy of Conformational Change Calculations Error: "Problem parsing input parameters Error: Invalid AtomID" Joshua D. Moore (Sat Sep 10 2005 - 17:49:26 CDT)
Re: NAMD2.6b1 on an OSX cluster Michael Grabe (Fri Sep 09 2005 - 15:39:15 CDT)
namd performance on altix machines Michel Espinoza-Fonseca (Fri Sep 09 2005 - 07:10:48 CDT)
Free Energy of Conformational Change Calculations Error: "Problem parsing input parameters Error: Invalid AtomID" Joshua D. Moore (Thu Sep 08 2005 - 22:13:17 CDT)
surface density of lipid bilayer Gan, Yong $UMC-Student$ (Thu Sep 08 2005 - 12:42:21 CDT)
namd2.6b1 hang on IBM p-690 Dong Luo (Thu Sep 08 2005 - 10:50:21 CDT)
Modified DNA bases PDB files Shahid Qamar (Wed Sep 07 2005 - 14:00:54 CDT)
Re: vmd-l: script Luis Gracia (Tue Sep 06 2005 - 13:21:40 CDT)
Re: vmd-l: script LEWYN LI (Tue Sep 06 2005 - 11:12:35 CDT)
RE: Sybyl trajectory Edelmiro Moman (Tue Sep 06 2005 - 10:33:37 CDT)
Re: vmd-l: Sybyl trajectory John Stone (Tue Sep 06 2005 - 09:43:23 CDT)
Re: abf Jérôme Hénin (Tue Sep 06 2005 - 08:48:25 CDT)
Re: Sybyl trajectory Grzegorz Jezierski (Tue Sep 06 2005 - 08:32:17 CDT)
vmd-l: script Sergio Anis (Tue Sep 06 2005 - 07:11:50 CDT)
Re: vmd-l: Sybyl trajectory Josef Scheiber (Tue Sep 06 2005 - 05:38:38 CDT)
Ammasso interconnect performance, LDB question Dow Hurst (Mon Sep 05 2005 - 23:21:12 CDT)
Sybyl trajectory Josef Scheiber (Mon Sep 05 2005 - 01:56:04 CDT)
abf michael atkinson (Sun Sep 04 2005 - 22:21:29 CDT)
Re: pair interactions in NPT Joshua D. Moore (Sun Sep 04 2005 - 18:12:59 CDT)
Re: Re: Charmm++5.9 build on Mac OS X by IB xlc compiler Gengbin Zheng (Sun Sep 04 2005 - 11:08:03 CDT)
vmdtext and .cshrc. bo baker (Fri Sep 02 2005 - 18:26:29 CDT)
CAN'T FIND BOND PARAMETERS FOR BOND FE - S surendra negi (Fri Sep 02 2005 - 15:36:43 CDT)
Problem in restarting simulation Pijush Ghosh (Fri Sep 02 2005 - 10:54:54 CDT)
NAMD running only at 40-50% CPU capacity LEWYN LI (Fri Sep 02 2005 - 11:00:35 CDT)
Re: Re: Charmm++5.9 build on Mac OS X by IB xlc compiler Jason Lee (Fri Sep 02 2005 - 10:55:13 CDT)
Re: pair interactions in NPT Anna Modzelewska (Fri Sep 02 2005 - 03:58:05 CDT)
Re: pair interactions in NPT Philip Fowler (Fri Sep 02 2005 - 02:22:21 CDT)
Re: Re: Charmm++5.9 build on Mac OS X by IB xlc compiler Gengbin Zheng (Fri Sep 02 2005 - 00:34:03 CDT)
NAMD & Gromacs FF Mauricio Carrillo Tripp (Thu Sep 01 2005 - 16:21:50 CDT)
Re: Re: Charmm++5.9 build on Mac OS X by IB xlc compiler Jason Lee (Thu Sep 01 2005 - 16:46:24 CDT)
wallclock and cputime Marc Q. Ma (Thu Sep 01 2005 - 16:31:01 CDT)
Calculating forces Gaurav Sharma (Thu Sep 01 2005 - 12:32:59 CDT)
vectorized NAMD version? Grzegorz Jezierski (Thu Sep 01 2005 - 09:42:35 CDT)
pair interactions in NPT Anna Modzelewska (Thu Sep 01 2005 - 03:21:46 CDT)
Can NAMD deal with solid-state system? weikai (Wed Aug 31 2005 - 21:57:21 CDT)
Re: Re: Charmm++5.9 build on Mac OS X by IB xlc compiler Gengbin Zheng (Wed Aug 31 2005 - 14:18:07 CDT)
Re: Re: Charmm++5.9 build on Mac OS X by IB xlc compiler Gengbin Zheng (Wed Aug 31 2005 - 12:32:56 CDT)
Re: problem when heating the system Phoenix (Tue Aug 30 2005 - 21:39:29 CDT)
Re: moments of inertia, principal axes \ (Tue Aug 30 2005 - 20:29:08 CDT)
RE: Re: Charmm++5.9 build on Mac OS X by IB xlc compiler Jason Lee (Tue Aug 30 2005 - 18:04:43 CDT)
RE: problem when heating the system Pijush Ghosh (Tue Aug 30 2005 - 00:09:08 CDT)
Re: problem when heating the system Leonardo Sepulveda Durán (Tue Aug 30 2005 - 07:53:49 CDT)
Re: problem when heating the system Sascha Tayefeh (Tue Aug 30 2005 - 01:26:25 CDT)
NAMD 2.6b1 Skipped Writing Velocity Restart File Joshua D. Moore (Tue Aug 30 2005 - 01:09:20 CDT)
problem when heating the system Phoenix (Mon Aug 29 2005 - 23:07:42 CDT)
dramatical standard deviation in the pressure profile Nicolas Sapay (Mon Aug 29 2005 - 07:12:27 CDT)
NPT and FIXED atoms Sascha Tayefeh (Mon Aug 29 2005 - 02:14:28 CDT)
NAMD on PSC Gan, Yong $UMC-Student$ (Sun Aug 28 2005 - 12:26:30 CDT)
creating a pdb file based on sequence and psi phi omega values only Matan Dishon (Sun Aug 28 2005 - 04:58:07 CDT)
Re: About the command "loadtotalforces" Marc Q. Ma (Fri Aug 26 2005 - 09:25:58 CDT)
Re: NAMD2.6b1 on an OSX cluster Jim Phillips (Thu Aug 25 2005 - 18:36:34 CDT)
Re: About the command "loadtotalforces" Jim Phillips (Thu Aug 25 2005 - 18:14:34 CDT)
Re: peptide out of the water-box Jim Phillips (Thu Aug 25 2005 - 18:08:52 CDT)
Re: Pressure Profile Simulation Jim Phillips (Thu Aug 25 2005 - 18:00:25 CDT)
Re: Pressure Profile Simulation Nicolas Sapay (Thu Aug 25 2005 - 04:32:40 CDT)
Pressure Profile Simulation Gan, Yong $UMC-Student$ (Wed Aug 24 2005 - 21:36:51 CDT)
Re: NAMD_2.6b1 shared lib problem on amd64 clustermatic using intel compilers Rene Salmon (Wed Aug 24 2005 - 15:01:26 CDT)
Crash during free energy calculation (MCTI) Grzegorz Jezierski (Wed Aug 24 2005 - 02:47:07 CDT)
NAMD2.6b1 on an OSX cluster Michael Grabe (Tue Aug 23 2005 - 17:16:56 CDT)
Extra terms in the expression for potential energy Grzegorz Jezierski (Tue Aug 23 2005 - 12:04:35 CDT)
About the command "loadtotalforces" LEWYN LI (Mon Aug 22 2005 - 21:25:44 CDT)
Re: namd 6-1- abf Jim Phillips (Mon Aug 22 2005 - 18:35:49 CDT)
Re: NBFix command to apply Lorentz-Berthelot mixing rules Jim Phillips (Mon Aug 22 2005 - 18:33:41 CDT)
Re: NAMD_2.6b1 shared lib problem on amd64 clustermatic using intel compilers Jim Phillips (Mon Aug 22 2005 - 18:23:48 CDT)
Re: Compilation of NAMD on 64-bit NUMA Jim Phillips (Mon Aug 22 2005 - 17:47:52 CDT)
Re: vdwGeometricSigma for OPLS in NAMD 2.6b1 Release Jim Phillips (Mon Aug 22 2005 - 17:40:53 CDT)
peptide out of the water-box Navratna Vajpai (Mon Aug 22 2005 - 02:52:11 CDT)
NBFix command to apply Lorentz-Berthelot mixing rules Joshua D. Moore (Sun Aug 21 2005 - 14:45:59 CDT)
Re: problem when do equilibration JC Gumbart (Sun Aug 21 2005 - 14:14:12 CDT)
Re: problem when do equilibration Pedro Borkowski (Sun Aug 21 2005 - 11:09:17 CDT)
problem when do equilibration ÎâºéÃ÷ (Sun Aug 21 2005 - 03:40:44 CDT)
Compiling charm++-5.9: Problems with g++ Gianluca Interlandi (Sat Aug 20 2005 - 05:36:26 CDT)
Fatal error on PE 0> FATAL ERROR: DIHEDRALS INDEX 150255520 Brian Bennion (Fri Aug 19 2005 - 16:47:19 CDT)
Re: Large Box Sizes and Total Energies Observed in NAMD 2.6b1 Binaries of AIX-POWER-MPI and Origin2000-MPI Joshua D. Moore (Fri Aug 19 2005 - 14:42:02 CDT)
Re: NAMD_2.6b1 shared lib problem on amd64 clustermatic using intel compilers Jerry Ebalunode (Fri Aug 19 2005 - 13:33:42 CDT)
RE: par_all27_prot_lipid.inp Michel Espinoza-Fonseca (Fri Aug 19 2005 - 11:28:07 CDT)
RE: par_all27_prot_lipid.inp Jerry Ebalunode (Fri Aug 19 2005 - 10:59:10 CDT)
NAMD_2.6b1 shared lib problem on amd64 clustermatic using intel compilers Rene Salmon (Fri Aug 19 2005 - 10:38:20 CDT)
Re: Large Box Sizes and Total Energies Observed in NAMD 2.6b1 Binaries of AIX-POWER-MPI and Origin2000-MPI Joshua D. Moore (Fri Aug 19 2005 - 06:38:04 CDT)
Re: par_all27_prot_lipid.inp bo baker (Thu Aug 18 2005 - 19:44:03 CDT)
Large Box Sizes and Total Energies Observed in NAMD 2.6b1 Binaries of AIX-POWER-MPI and Origin2000-MPI Joshua D. Moore (Thu Aug 18 2005 - 17:35:21 CDT)
Re: par_all27_prot_lipid.inp JC Gumbart (Thu Aug 18 2005 - 17:26:08 CDT)
Re: par_all27_prot_lipid.inp Richard Law (Thu Aug 18 2005 - 17:13:19 CDT)
par_all27_prot_lipid.inp bo baker (Thu Aug 18 2005 - 16:29:15 CDT)
RE: errno = 2 Jerry Ebalunode (Thu Aug 18 2005 - 14:02:21 CDT)
Re: errno = 2 bo baker (Thu Aug 18 2005 - 13:12:41 CDT)
Linux-MPI binary of NAMD 2.6b1 Joshua D. Moore (Thu Aug 18 2005 - 06:09:41 CDT)
RE: moments of inertia, principal axes Blake Charlebois (Thu Aug 18 2005 - 05:30:37 CDT)
Re: moments of inertia, principal axes Giovanni Bellesia (Thu Aug 18 2005 - 04:42:20 CDT)
Re: errno = 2 bo baker (Wed Aug 17 2005 - 20:09:43 CDT)
Re: vmd-l: Script for calculating energy of a water molecule John Stone (Wed Aug 17 2005 - 14:32:41 CDT)
moments of inertia, principal axes Stern, Julie (Wed Aug 17 2005 - 19:00:53 CDT)
Re: vmd-l: Script for calculating energy of a water molecule Jindal Shah (Wed Aug 17 2005 - 17:07:12 CDT)
RE: errno = 2 Jerry Ebalunode (Wed Aug 17 2005 - 16:08:51 CDT)
Re: undefined symbol errors:__builtin_bzero and _alloca building mpi-ppc-darwin version of namd2.6b1 Gengbin Zheng (Wed Aug 17 2005 - 14:14:43 CDT)
RE: errno = 2 Jerry Ebalunode (Wed Aug 17 2005 - 14:05:48 CDT)
undefined symbol errors:__builtin_bzero and _alloca building mpi-ppc-darwin version of namd2.6b1 Jerry Ebalunode (Wed Aug 17 2005 - 13:58:40 CDT)
Re: errno = 2 bo baker (Wed Aug 17 2005 - 12:30:27 CDT)
New BioCoRE server released Robert Brunner (Wed Aug 17 2005 - 12:00:16 CDT)
Script for calculating energy of a water molecule Jindal Shah (Wed Aug 17 2005 - 11:41:23 CDT)
scripts for binding free energy calculation using SMD and Jarzynski's equality Marc Q. Ma (Wed Aug 17 2005 - 09:45:12 CDT)
Compilation of NAMD on 64-bit NUMA Imran Khan (Wed Aug 17 2005 - 04:58:23 CDT)
Re: errno = 2 bo baker (Tue Aug 16 2005 - 19:04:49 CDT)
RE: PSF file generation JC Gumbart (Tue Aug 16 2005 - 01:00:32 CDT)
PSF file generation Tamal Banerjee (Tue Aug 16 2005 - 00:16:46 CDT)
errno = 2 bo baker (Mon Aug 15 2005 - 19:05:21 CDT)
RE: shape change of water box and peptide move out Dong Luo (Mon Aug 15 2005 - 10:46:48 CDT)
Manipulating structure Mikolai Fajer (Mon Aug 15 2005 - 09:57:03 CDT)
problem about equilibration xiaojing gong (Mon Aug 15 2005 - 08:30:44 CDT)
namd 6-1- abf michael atkinson (Mon Aug 15 2005 - 01:38:36 CDT)
Re: vdwGeometricSigma for OPLS in NAMD 2.6b1 Release Joshua D. Moore (Sat Aug 13 2005 - 03:21:44 CDT)
Psfgen within NAMD Mikolai Fajer (Fri Aug 12 2005 - 12:01:37 CDT)
(no subject) Giovanni Bellesia (Thu Aug 11 2005 - 15:50:38 CDT)
rescaling of coordinates in PBC simulations Giovanni Bellesia (Thu Aug 11 2005 - 12:41:52 CDT)
vdwGeometricSigma for OPLS in NAMD 2.6b1 Release Joshua D. Moore (Wed Aug 10 2005 - 18:59:45 CDT)
RE: Protonation state of HIS Blake Charlebois (Wed Aug 10 2005 - 17:44:11 CDT)
Protonation state of HIS surendra negi (Wed Aug 10 2005 - 16:57:06 CDT)
Re: Charmm++5.9 build on Mac OS X by IB xlc compiler Gengbin Zheng (Tue Aug 09 2005 - 11:59:15 CDT)
Re: How to "extract" coordinates from a DCD trajectory file? Darren Anderson (Tue Aug 09 2005 - 07:54:51 CDT)
How to "extract" coordinates from a DCD trajectory file? Edelmiro Moman (Tue Aug 09 2005 - 07:10:00 CDT)
namd hangs Uma Mahankali (Mon Aug 08 2005 - 23:10:13 CDT)
Charmm++5.9 build on Mac OS X by IB xlc compiler Jason Lee (Mon Aug 08 2005 - 14:58:21 CDT)
Re: Incorrect periodic box imaging with AMBER parameters Grzegorz Jezierski (Mon Aug 08 2005 - 12:43:20 CDT)
RE: For help with .log file. Boyang Wang (Sun Aug 07 2005 - 21:42:49 CDT)
Re: For help with .log file. nmichaud_at_jhu.edu (Mon Aug 08 2005 - 09:38:02 CDT)
RE: add ions Blake Charlebois (Mon Aug 08 2005 - 09:34:41 CDT)
add ions Mahalakshmi Sahasranaman (Mon Aug 08 2005 - 07:41:33 CDT)
Periodic boundary conditions Navratna Vajpai (Mon Aug 08 2005 - 03:34:34 CDT)
Re: For help with .log file. Joshua D. Moore (Sun Aug 07 2005 - 23:43:30 CDT)
RE: For help with .log file. JC Gumbart (Sun Aug 07 2005 - 14:57:58 CDT)
For help with .log file. Boyang Wang (Sun Aug 07 2005 - 14:13:33 CDT)
Re: LDB question Jason Lee (Sun Aug 07 2005 - 11:32:08 CDT)
Re: volume from VMD and NAMD different? Jim Phillips (Fri Aug 05 2005 - 17:46:25 CDT)
4th Annual Workshop on Charm++ and its Applications 2005 Jim Phillips (Fri Aug 05 2005 - 17:40:30 CDT)
Re: volume from VMD and NAMD different? Brian Bennion (Fri Aug 05 2005 - 17:38:27 CDT)
Re: volume from VMD and NAMD different? Jim Phillips (Fri Aug 05 2005 - 17:34:45 CDT)
volume from VMD and NAMD different? Brian Bennion (Fri Aug 05 2005 - 16:12:34 CDT)
Re: error running namd Jim Phillips (Fri Aug 05 2005 - 12:48:40 CDT)
Re: Running NAMD on a multiprocessor computer Jim Phillips (Fri Aug 05 2005 - 12:44:31 CDT)
Re: error in config file Jim Phillips (Fri Aug 05 2005 - 12:36:07 CDT)
Re: LDB question Jim Phillips (Fri Aug 05 2005 - 12:28:10 CDT)
error in config file Brian Bennion (Fri Aug 05 2005 - 11:28:14 CDT)
Re: Fatal error: Jim Phillips (Fri Aug 05 2005 - 11:17:30 CDT)
Re: H-H bond in TIP3 water Jim Phillips (Fri Aug 05 2005 - 11:11:15 CDT)
Re: shake and minimzation, equilibration Jim Phillips (Fri Aug 05 2005 - 10:58:09 CDT)
Re: rigidBond water Jim Phillips (Fri Aug 05 2005 - 10:54:44 CDT)
Re: velocity quenching Jim Phillips (Fri Aug 05 2005 - 10:52:37 CDT)
Re: 2.6b1 source missing file Jim Phillips (Fri Aug 05 2005 - 10:42:38 CDT)
Re: Incorrect periodic box imaging with AMBER parameters Grzegorz Jezierski (Fri Aug 05 2005 - 06:23:57 CDT)
Re: vmd-l: Nanotube Simulations Jordi Cohen (Tue Aug 02 2005 - 14:41:03 CDT)
Re: ERROR: Margin is too small (BUG?) nordgren_at_sas.upenn.edu (Thu Aug 04 2005 - 17:52:49 CDT)
Re: Incorrect periodic box imaging with AMBER parameters nordgren_at_sas.upenn.edu (Thu Aug 04 2005 - 17:40:58 CDT)
Re: Incorrect periodic box imaging with AMBER parameters surendra negi (Thu Aug 04 2005 - 16:11:15 CDT)
Re: Incorrect periodic box imaging with AMBER parameters Grzegorz Jezierski (Thu Aug 04 2005 - 13:04:05 CDT)
RE: Fatal error: vivek sharma (Thu Aug 04 2005 - 09:04:30 CDT)
RE: Fatal error: JC Gumbart (Thu Aug 04 2005 - 08:50:01 CDT)
Fatal error: vivek sharma (Thu Aug 04 2005 - 07:58:30 CDT)
Re: mpi problems on opteron Kyle Gustafson (Thu Aug 04 2005 - 07:54:20 CDT)
wrap ions Stern, Julie (Wed Aug 03 2005 - 23:13:05 CDT)
Re: mpi problems on opteron Dow Hurst (Wed Aug 03 2005 - 22:39:35 CDT)
Re: Re: charm++ 5.9 megatest failure too Dow Hurst (Wed Aug 03 2005 - 22:11:54 CDT)
Help with psf and par for small molecules santanu chatterjee (Wed Aug 03 2005 - 15:12:40 CDT)
Re: rigidBond water Marc Q. Ma (Wed Aug 03 2005 - 14:57:26 CDT)
shake and minimzation, equilibration Stern, Julie (Wed Aug 03 2005 - 14:56:13 CDT)
rigidBond water Stern, Julie (Wed Aug 03 2005 - 13:45:07 CDT)
ERROR: Margin is too small (BUG?) Mauricio Carrillo Tripp (Wed Aug 03 2005 - 10:02:42 CDT)
Re: charm++ 5.9 megatest failure too Eric Bohm (Tue Aug 02 2005 - 17:49:31 CDT)
Re: Re: charm++ 5.9 megatest failure too Dow Hurst (Wed Aug 03 2005 - 07:37:49 CDT)
velocity quenching Stern, Julie (Tue Aug 02 2005 - 23:15:45 CDT)
steepest descent minimization Stern, Julie (Tue Aug 02 2005 - 22:35:00 CDT)
Running NAMD on a multiprocessor computer Gan, Yong $UMC-Student$ (Tue Aug 02 2005 - 19:00:05 CDT)
Re: charm++ 5.9 megatest failure too Gengbin Zheng (Tue Aug 02 2005 - 18:21:51 CDT)
charm++ 5.9 megatest failure too Dow_Hurst (Tue Aug 02 2005 - 17:25:38 CDT)
charm++ 5.9 build fails, NAMD 2.6b1 make fails Dow_Hurst (Tue Aug 02 2005 - 17:16:55 CDT)
2.6b1 source missing file Dow_Hurst (Tue Aug 02 2005 - 16:58:30 CDT)
learning how to do a Cys palmitoyl patch seigneuret_at_cochin.inserm.fr (Tue Aug 02 2005 - 16:24:19 CDT)
Link Ammasso MPI with NAMD Dow_Hurst (Tue Aug 02 2005 - 14:46:59 CDT)
Link Ammasso MPI with NAMD Dow_Hurst (Tue Aug 02 2005 - 14:43:17 CDT)
RE: Nanotube Simulations Jason Lee (Tue Aug 02 2005 - 14:23:32 CDT)
Re: vmd-l: Nanotube Simulations Gaurav Sharma (Tue Aug 02 2005 - 13:56:15 CDT)
Re: vmd-l: Nanotube Simulations John Stone (Tue Aug 02 2005 - 12:34:58 CDT)
RE: Nanotube Simulations Michel Espinoza-Fonseca (Tue Aug 02 2005 - 09:50:18 CDT)
Nanotube Simulations Gaurav Sharma (Tue Aug 02 2005 - 08:51:14 CDT)
RE: LDB question Lee Jason (Tue Aug 02 2005 - 08:01:52 CDT)
LDB question Jason Lee (Mon Aug 01 2005 - 21:06:19 CDT)
H-H bond in TIP3 water Jorge Pikunic (Mon Aug 01 2005 - 17:21:26 CDT)
running on two different machines.... Navratna Vajpai (Sun Jul 31 2005 - 02:24:39 CDT)
error running namd 13200178 Hendra Tampang Allo (Mon Aug 01 2005 - 04:39:38 CDT)
RE: running on two different machines.... Blake Charlebois (Sun Jul 31 2005 - 11:17:20 CDT)
running on two different machines.... Navratna Vajpai (Sun Jul 31 2005 - 02:27:57 CDT)
Re: how to use the dual-processor machines Gengbin Zheng (Sat Jul 30 2005 - 17:52:42 CDT)
problem using visual_mdenergy: program has trouble reading the dat file patrick wintrode (Sat Jul 30 2005 - 17:08:45 CDT)
Re: Report on a trajectory incompatibility between NAMD and CHARMM: Unfolding and RDFs NAVEEN P MICHAUD AGRAWAL (Fri Jul 29 2005 - 23:30:23 CDT)
Re: Report on a trajectory incompatibility between NAMD and CHARMM: Unfolding and RDFs NAVEEN P MICHAUD AGRAWAL (Sat Jul 30 2005 - 10:42:29 CDT)
Re: H-H bond in solvate Jorge Pikunic (Sat Jul 30 2005 - 09:35:13 CDT)
H-H bond in solvate Jorge Pikunic (Sat Jul 30 2005 - 08:57:59 CDT)
how to use the dual-processor machines Xiaoqing Wang (Sat Jul 30 2005 - 08:37:39 CDT)
constraint constant in equilibration xiaojing gong (Sat Jul 30 2005 - 00:19:26 CDT)
NAMD 2.6b1 Released Jim Phillips (Fri Jul 29 2005 - 18:55:59 CDT)
Re: shape change of water box and peptide move out Kyle Gustafson (Fri Jul 29 2005 - 16:46:11 CDT)
Report on a trajectory incompatibility between NAMD and CHARMM: Unfolding and RDFs Mauricio Carrillo Tripp (Fri Jul 29 2005 - 16:36:07 CDT)
RE: shape change of water box and peptide move out Michel Espinoza-Fonseca (Fri Jul 29 2005 - 12:35:09 CDT)
shape change of water box and peptide move out Dong Luo (Fri Jul 29 2005 - 12:09:58 CDT)
ATP in the Topology file Pedro Borkowski (Fri Jul 29 2005 - 11:31:27 CDT)
opteron 64bit installation Kyle Gustafson (Fri Jul 29 2005 - 10:29:11 CDT)
Parameter files for Nanotube Simulation Gaurav Sharma (Thu Jul 28 2005 - 16:26:49 CDT)
Re: system becomes very large when set LangevinPiston on Xiaoqing Wang (Wed Jul 27 2005 - 21:32:01 CDT)
Re: Re: fep Floris Buelens (Wed Jul 27 2005 - 04:41:06 CDT)
Re: mpi problems on opteron Gengbin Zheng (Wed Jul 27 2005 - 00:08:32 CDT)
Re: system becomes very large when set LangevinPiston on Xiaoqing Wang (Tue Jul 26 2005 - 22:02:34 CDT)
RE: restarting SMD jobs JC Gumbart (Tue Jul 26 2005 - 21:07:17 CDT)
Re: VMD solvate in CCl4 Joshua D. Moore (Tue Jul 26 2005 - 20:55:03 CDT)
restarting SMD jobs Vani Krishna (Tue Jul 26 2005 - 20:25:38 CDT)
Re: fep Wei Chen (Tue Jul 26 2005 - 17:05:39 CDT)
Re: system becomes very large when set LangevinPiston on nordgren_at_sas.upenn.edu (Tue Jul 26 2005 - 12:20:50 CDT)
VMD solvate in CCl4 Jack (Tue Jul 26 2005 - 08:37:08 CDT)
Re: mpi problems on opteron Leandro Martínez (Mon Jul 25 2005 - 19:11:13 CDT)
Re: mpi problems on opteron Leandro Martínez (Mon Jul 25 2005 - 19:00:04 CDT)
Re: system becomes very large when set LangevinPiston on Xiaoqing Wang (Tue Jul 26 2005 - 04:48:13 CDT)
Class I vs Class II force fields Aaron Oakley (Tue Jul 26 2005 - 00:42:01 CDT)
compiling NAMD: plugins Kyle Gustafson (Mon Jul 25 2005 - 19:53:01 CDT)
Re: mpi problems on opteron Kyle Gustafson (Mon Jul 25 2005 - 19:04:56 CDT)
mpi problems on opteron Kyle Gustafson (Mon Jul 25 2005 - 16:05:02 CDT)
Re: vmd-l: Re: catdcd and dcdunitcell John Stone (Mon Jul 25 2005 - 13:50:03 CDT)
Re: vmd-l: Re: catdcd and dcdunitcell Joshua D. Moore (Mon Jul 25 2005 - 14:16:16 CDT)
NAMD on dual opterons Kyle Gustafson (Mon Jul 25 2005 - 13:30:44 CDT)
fep file Deborah Jameson (Mon Jul 25 2005 - 11:10:54 CDT)
CCS ERROR during simulation Jason Lee (Mon Jul 25 2005 - 08:52:16 CDT)
Re: Incorrect periodic box imaging with AMBER parameters Charles Danko (Mon Jul 25 2005 - 08:32:20 CDT)
Incorrect periodic box imaging with AMBER parameters Grzegorz Jezierski (Mon Jul 25 2005 - 04:11:20 CDT)
system becomes very large when set LangevinPiston on Xiaoqing Wang (Sun Jul 24 2005 - 22:06:43 CDT)
Re: Fixed atoms and dcd file with DCDunitCell on nordgren_at_sas.upenn.edu (Sat Jul 23 2005 - 12:11:46 CDT)
Re: the difference between the min_nacl.vel and min_nacl.restart.vel Blake Charlebois (Sat Jul 23 2005 - 09:25:48 CDT)
the difference between the min_nacl.vel and min_nacl.restart.vel xiaojing gong (Sat Jul 23 2005 - 07:59:48 CDT)
Fixed atoms and dcd file with DCDunitCell on Joshua D. Moore (Fri Jul 22 2005 - 16:46:15 CDT)
Re: catdcd and dcdunitcell Joshua D. Moore (Fri Jul 22 2005 - 16:04:00 CDT)
output in tcl samantha cox (Fri Jul 22 2005 - 15:06:06 CDT)
Re: TM protein in octane slab questions Richard Law (Fri Jul 22 2005 - 12:30:54 CDT)
TM protein in octane slab questions Michel Seigneuret (Fri Jul 22 2005 - 03:52:50 CDT)
added more bases to DNA using psfgen Stern, Julie (Thu Jul 21 2005 - 21:50:55 CDT)
Re: FATAL ERROR: Asymmetric water molecule?? Richard Law (Thu Jul 21 2005 - 20:21:40 CDT)
namdplot error Stern, Julie (Thu Jul 21 2005 - 20:06:53 CDT)
Re: catdcd-generated files and CHARMM Mauricio Carrillo Tripp (Thu Jul 21 2005 - 16:10:11 CDT)
Re: catdcd-generated files and CHARMM Mauricio Carrillo Tripp (Thu Jul 21 2005 - 14:05:10 CDT)
catdcd-generated files and CHARMM Chang, Christopher (Thu Jul 21 2005 - 11:55:25 CDT)
RE: removing water from DCD Jerry Parks (Thu Jul 21 2005 - 11:27:43 CDT)
RE: removing water from DCD Pijush Ghosh (Wed Jul 20 2005 - 22:03:20 CDT)
RE: constrain or fix the system only in Z direction JC Gumbart (Thu Jul 21 2005 - 09:34:22 CDT)
constrain or fix the system only in Z direction xiaojing gong (Thu Jul 21 2005 - 07:01:33 CDT)
Re: removing water from DCD Alessandro Pedretti (Thu Jul 21 2005 - 01:55:34 CDT)
Re: removing water from DCD s.bora erdemli (Wed Jul 20 2005 - 21:06:53 CDT)
Energy Problem (Order of Magnitude) s.bora erdemli (Wed Jul 20 2005 - 15:05:03 CDT)
Re: removing water from DCD JC Gumbart (Wed Jul 20 2005 - 20:50:49 CDT)
Re: removing water from DCD Shirley Hui (Wed Jul 20 2005 - 20:25:51 CDT)
removing water from DCD Stern, Julie (Wed Jul 20 2005 - 19:49:12 CDT)
Re: RE: Help with SMD Eunice Ramirez Melendez (Wed Jul 20 2005 - 03:37:44 CDT)
How to run for periodic boundary Conditions? Snigdha Chakraborty (Wed Jul 20 2005 - 12:19:32 CDT)
RE: Help with SMD Michel Espinoza-Fonseca (Wed Jul 20 2005 - 11:18:31 CDT)
RE: Help with SMD Blake Charlebois (Wed Jul 20 2005 - 11:10:47 CDT)
Re: Help with SMD Richard Law (Wed Jul 20 2005 - 10:54:50 CDT)
RE: cellBasisVectors and xsc files Wei Chen (Wed Jul 20 2005 - 10:47:21 CDT)
Re: changing file Wei Chen (Wed Jul 20 2005 - 10:43:24 CDT)
Help with SMD Eunice Ramirez Melendez (Tue Jul 19 2005 - 12:08:34 CDT)
hbonds output!!! Eunice Ramirez Melendez (Tue Jul 19 2005 - 11:59:30 CDT)
Re: Ca trace only Sergio Anis (Wed Jul 20 2005 - 06:52:05 CDT)
Re: changing file Jérôme Hénin (Wed Jul 20 2005 - 05:07:19 CDT)
Re: changing file Giovanni Bellesia (Wed Jul 20 2005 - 04:57:29 CDT)
changing file Deborah Jameson (Wed Jul 20 2005 - 03:18:12 CDT)
Bromine Matthew Wilce (Wed Jul 20 2005 - 01:43:43 CDT)
RE: cellBasisVectors and xsc files JC Gumbart (Tue Jul 19 2005 - 21:03:07 CDT)
cellBasisVectors and xsc files Stern, Julie (Tue Jul 19 2005 - 20:53:01 CDT)
force shifted cutoff Stern, Julie (Tue Jul 19 2005 - 18:37:10 CDT)
Ca trace only Shirley Hui (Tue Jul 19 2005 - 18:37:11 CDT)
Re: Velocity after heating JC Gumbart (Mon Jul 18 2005 - 13:35:44 CDT)
RE: Velocity after heating wmsmith (Mon Jul 18 2005 - 13:04:14 CDT)
Re: Velocity after heating JC Gumbart (Mon Jul 18 2005 - 12:18:52 CDT)
Re: setting configuration file for free energy perturbation Jérôme Hénin (Mon Jul 18 2005 - 12:18:39 CDT)
setting configuration file for free energy perturbation Deborah Jameson (Mon Jul 18 2005 - 10:25:02 CDT)
Velocity after heating mustapha.hamdi_at_ensi-bourges.fr (Mon Jul 18 2005 - 06:56:03 CDT)
pressure control in config file xiaojing gong (Sun Jul 17 2005 - 20:06:16 CDT)
Re: Random forces in Langevin temperature control -- three questions \ (Sun Jul 17 2005 - 12:09:41 CDT)
Re: Runnig same config file many times Mauricio Carrillo Tripp (Fri Jul 15 2005 - 17:33:48 CDT)
It appears that the Claim that NAMD works with gromacs is false Jim Kress (Sat Jul 16 2005 - 19:43:42 CDT)
Re: fep Chris Chipot (Sat Jul 16 2005 - 04:48:02 CDT)
FEP alchemical Amir Shamloo (Fri Jul 15 2005 - 19:51:23 CDT)
psfgen and poorly guessed coordinates Stern, Julie (Fri Jul 15 2005 - 18:17:56 CDT)
Re: Runnig same config file many times Mauricio Carrillo Tripp (Fri Jul 15 2005 - 16:45:05 CDT)
Runnig same config file many times Shahid Qamar (Fri Jul 15 2005 - 14:38:38 CDT)
patch failed Hidekazu WATANABE (Fri Jul 15 2005 - 05:19:19 CDT)
Random forces in Langevin temperature control -- three questions Blake Charlebois (Fri Jul 15 2005 - 00:05:03 CDT)
patch PYRT and extending DNA Stern, Julie (Thu Jul 14 2005 - 20:17:04 CDT)
Re: psfgen patches Brian Bennion (Thu Jul 14 2005 - 18:37:37 CDT)
Re: psfgen and extending 5' end of DNA Richard Law (Thu Jul 14 2005 - 17:45:48 CDT)
Re: psfgen patches Richard Law (Thu Jul 14 2005 - 17:28:41 CDT)
Re: psfgen patches JC Gumbart (Thu Jul 14 2005 - 17:10:06 CDT)
psfgen and extending 5' end of DNA Stern, Julie (Thu Jul 14 2005 - 17:07:23 CDT)
psfgen patches Stern, Julie (Thu Jul 14 2005 - 17:04:51 CDT)
Re: PDB files for carbon nanotubes Sascha Tayefeh (Thu Jul 14 2005 - 16:13:25 CDT)
PDB files for carbon nanotubes Gaurav Sharma (Thu Jul 14 2005 - 14:33:05 CDT)
Re: sync buffer overflow Gengbin Zheng (Wed Jul 13 2005 - 22:32:31 CDT)
sync buffer overflow Brian Bennion (Wed Jul 13 2005 - 16:44:36 CDT)
MDenergy error floquet_at_icsn.cnrs-gif.fr (Wed Jul 13 2005 - 14:43:15 CDT)
FATAL ERROR: child atom 39 bonded only to child H atoms Boyang Wang (Wed Jul 13 2005 - 11:06:19 CDT)
Mother atom with hydrogenGroupSize of 0 Boyang Wang (Mon Jul 11 2005 - 17:57:51 CDT)
Re: Energy Order of Magnitude Jérôme Hénin (Mon Jul 11 2005 - 14:49:49 CDT)
Energy Order of Magnitude s.bora erdemli (Mon Jul 11 2005 - 11:20:15 CDT)
Re: pka calculations and their use in simulations Darren Anderson (Mon Jul 11 2005 - 08:49:20 CDT)
RE: pka calculations and their use in simulations Michel Espinoza-Fonseca (Mon Jul 11 2005 - 07:41:49 CDT)
pka calculations and their use in simulations Richard Law (Sun Jul 10 2005 - 18:12:00 CDT)
NAMD/iAPBS Jerry Parks (Fri Jul 08 2005 - 16:19:15 CDT)
SPC/E Water Model and RigidBonds Joshua D. Moore (Fri Jul 08 2005 - 15:46:41 CDT)
xplor parameter to charmm ËïæÃæÃ (Fri Jul 08 2005 - 03:54:19 CDT)
force shifted cutoff Stern, Julie (Thu Jul 07 2005 - 18:06:15 CDT)
Re: XPLOR psf format Sterling Paramore (Thu Jul 07 2005 - 14:40:01 CDT)
XPLOR psf format Stern, Julie (Thu Jul 07 2005 - 14:16:48 CDT)
Re. van der waals energy Boyang Wang (Thu Jul 07 2005 - 13:23:52 CDT)
Van Der Waals energy sabri bora erdemli (Thu Jul 07 2005 - 09:07:44 CDT)
van der waals energy SABRI BORA ERDEMLI (Thu Jul 07 2005 - 09:25:45 CDT)
infinite DNA Stern, Julie (Wed Jul 06 2005 - 11:52:17 CDT)
RE: Some questions about TCL wmsmith (Tue Jul 05 2005 - 17:20:54 CDT)
Some questions about TCL Shahid Qamar (Tue Jul 05 2005 - 16:38:28 CDT)
problems with autoionize total charge and minimization Leonardo Sepulveda Durán (Tue Jul 05 2005 - 14:18:25 CDT)
dmpc membrane Swarna Patra (Mon Jul 04 2005 - 20:17:43 CDT)
Re: Unable to Generate PSF file ! JC Gumbart (Mon Jul 04 2005 - 14:01:14 CDT)
RE: Unable to Generate PSF file ! JC Gumbart (Mon Jul 04 2005 - 11:42:44 CDT)
RE: Unable to Generate PSF file ! JC Gumbart (Mon Jul 04 2005 - 10:06:46 CDT)
Unable to Generate PSF file ! Tamal Banerjee (Mon Jul 04 2005 - 08:09:43 CDT)
Re: FEP - one long simulation vs many short ones Floris Buelens (Mon Jul 04 2005 - 07:22:55 CDT)
Re: FEP - one long simulation vs many short ones Jérôme Hénin (Sat Jul 02 2005 - 18:45:11 CDT)
Re: FEP - one long simulation vs many short ones Mauricio Carrillo Tripp (Fri Jul 01 2005 - 18:27:24 CDT)
RE: RE: [Scalex86 - linux] FW: segfaults in mm_malloc Tim Sirianni (Fri Jul 01 2005 - 17:46:03 CDT)
Re: FEP - one long simulation vs many short ones Wei Chen (Sat Jul 02 2005 - 12:13:51 CDT)
Re: RE: [Scalex86 - linux] FW: segfaults in mm_malloc \ (Fri Jul 01 2005 - 11:40:25 CDT)
FEP - one long simulation vs many short ones Floris Buelens (Fri Jul 01 2005 - 07:07:14 CDT)
MD stops when COM or atom reaches a distance Shahid Qamar (Fri Jul 01 2005 - 11:34:39 CDT)
Segmentation fault with two processors floquet_at_icsn.cnrs-gif.fr (Fri Jul 01 2005 - 04:12:57 CDT)
RE: [Scalex86 - linux] FW: segfaults in mm_malloc Tim Sirianni (Thu Jun 30 2005 - 18:20:44 CDT)
How MD stopes at a specific distance? Shahid Qamar (Thu Jun 30 2005 - 12:41:54 CDT)
psfgen/auto none vivek sharma (Thu Jun 30 2005 - 02:50:30 CDT)
Re: Re: segfaults in mm_malloc Niraj kumar (Thu Jun 30 2005 - 00:25:18 CDT)
RE: Adding Misc. Potentials (e.g. spherical/repulsive restraints/constraints ) wmsmith (Wed Jun 29 2005 - 13:43:44 CDT)
removing a covalent bond during a simulation patrick wintrode (Wed Jun 29 2005 - 12:10:56 CDT)
Segment atom number limitation Jason Lee (Wed Jun 29 2005 - 11:18:50 CDT)
RE: Adding Misc. Potentials (e.g. spherical/repulsive restraints/constraints ) JC Gumbart (Wed Jun 29 2005 - 11:18:23 CDT)
Re: Adding Misc. Potentials (e.g. spherical/repulsive restraints/constraints ) Sascha Tayefeh (Wed Jun 29 2005 - 09:56:54 CDT)
RE: Adding Misc. Potentials (e.g. spherical/repulsive restraints/constraints ) JC Gumbart (Wed Jun 29 2005 - 09:40:41 CDT)
Adding Misc. Potentials (e.g. spherical/repulsive restraints/constraints ) Sascha Tayefeh (Wed Jun 29 2005 - 09:31:23 CDT)
Re: free energy pertubation,binding energy and constant Chris Chipot (Wed Jun 29 2005 - 08:14:27 CDT)
Re: Re: segfaults in mm_malloc Niraj kumar (Wed Jun 29 2005 - 05:48:20 CDT)
Re: interactions in flexible cel Anna Modzelewska (Wed Jun 29 2005 - 02:07:04 CDT)
interactions in flexible cel Anna Modzelewska (Wed Jun 29 2005 - 00:34:51 CDT)
convert_from_namd_to_amber Wei Chen (Tue Jun 28 2005 - 22:02:18 CDT)
Re: catdcd and dcdunitcell Ben Roberts (Tue Jun 28 2005 - 18:27:07 CDT)
free energy pertubation,binding energy and constant s.bora erdemli (Tue Jun 28 2005 - 14:30:07 CDT)
Re: segfaults in mm_malloc David Kunzman (Tue Jun 28 2005 - 12:29:01 CDT)
Re: catdcd and dcdunitcell Philip Fowler (Tue Jun 28 2005 - 11:07:38 CDT)
Re: catdcd and dcdunitcell Jérôme Hénin (Tue Jun 28 2005 - 10:54:09 CDT)
segfaults in mm_malloc Brian Bennion (Tue Jun 28 2005 - 10:27:31 CDT)
Re: catdcd and dcdunitcell Philip Fowler (Tue Jun 28 2005 - 09:27:06 CDT)
Re: catdcd and dcdunitcell Jérôme Hénin (Tue Jun 28 2005 - 09:14:32 CDT)
Re: catdcd and dcdunitcell Philip Fowler (Tue Jun 28 2005 - 07:18:15 CDT)
Re: catdcd and dcdunitcell Philip Fowler (Tue Jun 28 2005 - 07:15:36 CDT)
Periodic Boundary Conditions and Wrap Joshua D. Moore (Tue Jun 28 2005 - 03:31:38 CDT)
PMF force restraint question Leonardo Sepulveda Durán (Mon Jun 27 2005 - 19:11:11 CDT)
cross products wmsmith (Mon Jun 27 2005 - 14:35:18 CDT)
Re: Accessing beta / occupancy values from NAMD tcl Jérôme Hénin (Mon Jun 27 2005 - 11:52:05 CDT)
namdplot, grpah is empty Raeanne Napoleon (Mon Jun 27 2005 - 11:01:58 CDT)
Re: Using FEP as non-disruptive mutation procedure Michael Grabe (Mon Jun 27 2005 - 11:19:13 CDT)
membrane protein md protocol rob yang (Mon Jun 27 2005 - 10:36:15 CDT)
Accessing beta / occupancy values from NAMD tcl wmsmith (Mon Jun 27 2005 - 10:24:47 CDT)
Re: catdcd and dcdunitcell Ben Roberts (Mon Jun 27 2005 - 07:47:39 CDT)
catdcd and dcdunitcell Philip Fowler (Mon Jun 27 2005 - 05:07:01 CDT)
Re: Using FEP as non-disruptive mutation procedure Jérôme Hénin (Mon Jun 27 2005 - 05:19:37 CDT)
Re: new approach to counter FEP end-point VDW clashes Jérôme Hénin (Mon Jun 27 2005 - 03:31:34 CDT)
peptide simulation Matan Dishon (Mon Jun 27 2005 - 03:28:18 CDT)
Using FEP as non-disruptive mutation procedure Leonardo Sepulveda Durán (Sun Jun 26 2005 - 17:10:17 CDT)
Re: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? Leonardo Sepulveda Durán (Sun Jun 26 2005 - 15:53:29 CDT)
Re: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? Marcos Sotomayor (Sun Jun 26 2005 - 14:04:28 CDT)
new approach to counter FEP end-point VDW clashes Floris Buelens (Sun Jun 26 2005 - 07:41:14 CDT)
Re: Error on Solaris Tirath Ramdas (Sat Jun 25 2005 - 20:10:21 CDT)
Re: Error on Solaris Marcos Sotomayor (Sat Jun 25 2005 - 17:53:52 CDT)
Error on Solaris Tirath Ramdas (Sat Jun 25 2005 - 12:57:53 CDT)
changuing dihedral angle slowly (complete message) Leonardo Sepulveda Durán (Fri Jun 24 2005 - 17:47:02 CDT)
changuing dihedral angle slowly Leonardo Sepulveda Durán (Fri Jun 24 2005 - 17:35:20 CDT)
Re: basic: combining two pdb files? Luis Rosales (Fri Jun 24 2005 - 03:25:46 CDT)
Re: Hi,how can I generate a psf file with a pdb file contain some special amino acid like TYS Leonardo Sepulveda Durán (Fri Jun 24 2005 - 10:33:40 CDT)
Re: Hi,how can I generate a psf file with a pdb file contain some special amino acid like TYS Phoenix (Fri Jun 24 2005 - 09:59:13 CDT)
Re: Hi,how can I generate a psf file with a pdb file contain some special amino acid like TYS Leonardo Sepulveda Durán (Fri Jun 24 2005 - 09:30:26 CDT)
interactions in flexible cell Anna Modzelewska (Fri Jun 24 2005 - 04:31:27 CDT)
Hi,how can I generate a psf file with a pdb file contain some special amino acid like TYS Phoenix (Fri Jun 24 2005 - 00:08:37 CDT)
how to build AQP1 tetramer xiaojing gong (Thu Jun 23 2005 - 21:31:13 CDT)
Re: basic: combining two pdb files? Wei Chen (Thu Jun 23 2005 - 21:03:30 CDT)
basic: combining two pdb files? Meunier, Vincent (Thu Jun 23 2005 - 20:16:45 CDT)
Zeros at the beginning of each line in the output Joshua D. Moore (Thu Jun 23 2005 - 19:17:43 CDT)
hard wall Mauricio Carrillo Tripp (Thu Jun 23 2005 - 11:24:00 CDT)
electron density profiles (EDP) akash.khandelwal_at_ndsu.edu (Wed Jun 22 2005 - 14:25:23 CDT)
Re: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? Leonardo Sepulveda Durán (Wed Jun 22 2005 - 12:12:48 CDT)
Re: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? apw397_at_soton.ac.uk (Wed Jun 22 2005 - 10:42:04 CDT)
Re: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? apw397_at_soton.ac.uk (Wed Jun 22 2005 - 10:41:58 CDT)
Z-origin set to zero by Linux/Mac 2.5 binaries, Minimisation shaila_at_biof.ufrj.br (Wed Jun 22 2005 - 07:01:14 CDT)
Re: vmd-l: autoimd on windows Anna Modzelewska (Wed Jun 22 2005 - 05:29:52 CDT)
Understanding NAMD performance data Niraj kumar (Wed Jun 22 2005 - 05:27:10 CDT)
RE: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? Joshua D. Moore (Wed Jun 22 2005 - 00:58:48 CDT)
Fluorophors ? Georgios Papadopoulos (Wed Jun 22 2005 - 00:27:25 CDT)
Re: Fixed restraint Leonardo Sepulveda Durán (Tue Jun 21 2005 - 18:56:45 CDT)
Fixed restraint Shahid Qamar (Tue Jun 21 2005 - 17:56:09 CDT)
RE: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? Brian Bennion (Tue Jun 21 2005 - 17:40:15 CDT)
Re: set center Luis Rosales (Tue Jun 21 2005 - 17:33:53 CDT)
Re: vmd-l: autoimd on windows John Stone (Tue Jun 21 2005 - 15:43:11 CDT)
Re: restart syntax Wei Chen (Tue Jun 21 2005 - 16:26:19 CDT)
Re: namdplot, graph is empty Cetin Baloglu (Tue Jun 21 2005 - 15:44:29 CDT)
RE: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? Blake Charlebois (Tue Jun 21 2005 - 15:41:19 CDT)
langevin vs coupling to a heat bath patrick wintrode (Tue Jun 21 2005 - 15:25:29 CDT)
Re: namdplot, graph is empty Leonardo Sepulveda Durán (Tue Jun 21 2005 - 15:10:22 CDT)
Re: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? Marc Q. Ma (Tue Jun 21 2005 - 14:11:43 CDT)
namdplot, graph is empty Raeanne Napoleon (Tue Jun 21 2005 - 13:48:34 CDT)
restart syntax Mark A. Hallman (Tue Jun 21 2005 - 13:23:16 CDT)
Re: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? Leonardo Sepulveda Durán (Tue Jun 21 2005 - 12:42:07 CDT)
Re: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? Brian Bennion (Tue Jun 21 2005 - 10:08:32 CDT)
Re: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? Aaron Oakley (Tue Jun 21 2005 - 01:48:52 CDT)
Gramicidin Swarna Patra (Mon Jun 20 2005 - 20:54:09 CDT)
Re: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? Leonardo Sepulveda Durán (Mon Jun 20 2005 - 12:53:09 CDT)
Re: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? Brian Bennion (Mon Jun 20 2005 - 10:26:49 CDT)
Re: velocity file of atoms at each time step nordgren_at_sas.upenn.edu (Mon Jun 20 2005 - 10:23:07 CDT)
shmget error Gianluca Interlandi (Mon Jun 20 2005 - 07:46:28 CDT)
autoimd on windows Anna Modzelewska (Mon Jun 20 2005 - 06:40:29 CDT)
velocity file of atoms at each time step debashis.sikdar_at_ndsu.edu (Sun Jun 19 2005 - 22:28:14 CDT)
Error when running NAMD at SDSC Joshua D. Moore (Sun Jun 19 2005 - 22:13:20 CDT)
Solvent model other than TIP3 for use with CHARMM FF in NAMD?? Leonardo Sepulveda Durán (Sun Jun 19 2005 - 12:58:18 CDT)
optimisation for dual CPU sytem Floris Buelens (Sat Jun 18 2005 - 08:25:39 CDT)
Pressure_control Wei Chen (Fri Jun 17 2005 - 21:41:19 CDT)
Re: binding free energy , binding constant Wei Chen (Fri Jun 17 2005 - 15:46:35 CDT)
Re: Radial Distribution Function Jianping Wang (Fri Jun 17 2005 - 13:55:40 CDT)
Re: binding free energy , binding constant Chris Chipot (Fri Jun 17 2005 - 11:07:11 CDT)
Re: Charmm 1,4 Interactions - Scaling Question Paul R Brenner (Fri Jun 17 2005 - 09:08:54 CDT)
binding free energy , binding constant sabri bora erdemli (Fri Jun 17 2005 - 08:11:33 CDT)
Problem with mdenergy floquet_at_icsn.cnrs-gif.fr (Fri Jun 17 2005 - 08:05:41 CDT)
RE: set center Blake Charlebois (Fri Jun 17 2005 - 00:03:24 CDT)
set center Swarna Patra (Thu Jun 16 2005 - 22:53:28 CDT)
RE: tcl question Blake Charlebois (Thu Jun 16 2005 - 22:32:39 CDT)
RE: tcl question Samuel Flores (Thu Jun 16 2005 - 22:01:23 CDT)
RE: tcl question Blake Charlebois (Thu Jun 16 2005 - 21:15:59 CDT)
tcl question Samuel Flores (Thu Jun 16 2005 - 20:03:29 CDT)
Re: Charmm 1,4 Interactions - Scaling Question Jan Saam (Thu Jun 16 2005 - 18:20:22 CDT)
aquaporin question Samuel Flores (Thu Jun 16 2005 - 15:39:11 CDT)
RE: vmdtext? Samuel Flores (Thu Jun 16 2005 - 15:38:47 CDT)
RE: changing default directory in VMD? Samuel Flores (Thu Jun 16 2005 - 14:20:31 CDT)
Re: vmdtext? Luis Rosales (Thu Jun 16 2005 - 15:09:01 CDT)
Charmm 1,4 Interactions - Scaling Question Paul R Brenner (Thu Jun 16 2005 - 12:00:05 CDT)
force calculation Manuela Cavallari (Thu Jun 16 2005 - 11:53:13 CDT)
Radial Distribution Function Pijush Ghosh (Thu Jun 16 2005 - 10:43:18 CDT)
Re: How to conservate energy during NVE simulations??? Marcos Sotomayor (Thu Jun 16 2005 - 10:30:28 CDT)
How to conservate energy during NVE simulations??? Leonardo Sepulveda Durán (Wed Jun 15 2005 - 20:55:29 CDT)
Re: FEP and solvent Surjit Dixit (Thu Jun 16 2005 - 09:06:17 CDT)
Re: Tcl forces Jérôme Hénin (Thu Jun 16 2005 - 07:19:13 CDT)
Tcl forces Manuela Cavallari (Thu Jun 16 2005 - 05:51:05 CDT)
Fw: changing default directory in VMD? Shirley Hui (Wed Jun 15 2005 - 15:34:51 CDT)
RE: changing default directory in VMD? Blake Charlebois (Wed Jun 15 2005 - 15:21:43 CDT)
changing default directory in VMD? Samuel Flores (Wed Jun 15 2005 - 14:09:25 CDT)
Re: c-shell into NAMD configuration file nordgren_at_sas.upenn.edu (Wed Jun 15 2005 - 09:23:20 CDT)
Re: Script for MD in a loop? nordgren_at_sas.upenn.edu (Wed Jun 15 2005 - 09:13:44 CDT)
Re: Multiple Harmonic Constraints nordgren_at_sas.upenn.edu (Wed Jun 15 2005 - 08:37:34 CDT)
RE: addforce Pijush Ghosh (Tue Jun 14 2005 - 14:23:05 CDT)
Poorly guessed coordinates Maria Lin (Tue Jun 14 2005 - 14:03:59 CDT)
Re: addforce LEWYN LI (Tue Jun 14 2005 - 14:07:10 CDT)
addforce Leandro Martínez (Tue Jun 14 2005 - 10:02:28 CDT)
Re: MM/PBSA Jerry Ebalunode (Mon Jun 13 2005 - 18:22:51 CDT)
MM/PBSA Wei Chen (Mon Jun 13 2005 - 15:41:45 CDT)
urestraint ? Shahid Qamar (Mon Jun 13 2005 - 13:12:22 CDT)
vmdtext? Samuel Flores (Mon Jun 13 2005 - 11:41:12 CDT)
RE: Adjusting Density of waterbox used by solvate Wolbach, Jeffrey P $WOLBACH$ (Mon Jun 13 2005 - 11:36:11 CDT)
c-shell into NAMD configuration file Ioana Cozmuta (Mon Jun 13 2005 - 02:02:48 CDT)
Re: Simulation terminating due to RATTLE constraint failure nordgren_at_sas.upenn.edu (Mon Jun 13 2005 - 01:51:35 CDT)
FEP and TI Matthew Wilce (Sun Jun 12 2005 - 22:42:05 CDT)
FEP and solvent Matthew Wilce (Sun Jun 12 2005 - 22:35:32 CDT)
Simulation terminating due to RATTLE constraint failure Shirley Hui (Sun Jun 12 2005 - 22:21:09 CDT)
Adjusting Density of waterbox used by solvate Leonardo Sepulveda Durán (Sun Jun 12 2005 - 21:51:51 CDT)
velocity unit Gan, Yong $UMC-Student$ (Sun Jun 12 2005 - 21:49:52 CDT)
plugins.tar.gz & charm_src.tar.gz !!! Georgios Papadopoulos (Sat Jun 11 2005 - 05:38:27 CDT)
Re: water density calculation LEWYN LI (Fri Jun 10 2005 - 22:22:42 CDT)
water density calculation Leonardo Sepulveda Durán (Fri Jun 10 2005 - 21:19:50 CDT)
it is posible to do NVE simulations in NAMD??? Leonardo Sepulveda Durán (Fri Jun 10 2005 - 18:04:16 CDT)
interface with external program Leandro Martínez (Fri Jun 10 2005 - 13:15:30 CDT)
Re: interface with external program Leandro Martínez (Fri Jun 10 2005 - 13:55:53 CDT)
Re: Avoiding Rotation and translation of protein Marc Q. Ma (Fri Jun 10 2005 - 11:35:04 CDT)
Re: implicit solvent Michael Grabe (Fri Jun 10 2005 - 11:18:34 CDT)
RESTARTING CONJUGATE GRADIENT ALGORITHM Jason Lee (Fri Jun 10 2005 - 10:18:33 CDT)
Re: Re: vmd-l: multiple automated calls to NAMD Axel Kohlmeyer (Fri Jun 10 2005 - 02:17:32 CDT)
Script for MD in a loop? Shahid Qamar (Fri Jun 10 2005 - 10:05:34 CDT)
Re: implicit solvent Marc Q. Ma (Fri Jun 10 2005 - 08:28:21 CDT)
Re: Re: vmd-l: multiple automated calls to NAMD nordgren_at_sas.upenn.edu (Thu Jun 09 2005 - 21:56:31 CDT)
Re: implicit solvent Leonardo Sepulveda Durán (Thu Jun 09 2005 - 21:26:40 CDT)
implicit solvent Wei Zhuang (Thu Jun 09 2005 - 17:47:48 CDT)
Re: large vanderwalls energy during minimization Leonardo Sepulveda Durán (Thu Jun 09 2005 - 16:42:15 CDT)
FEP error: Rattle atom constriant Shahid Qamar (Thu Jun 09 2005 - 15:59:11 CDT)
Re: large vanderwalls energy during minimization Leonardo Sepulveda Durán (Thu Jun 09 2005 - 14:50:31 CDT)
large vanderwalls energy during minimization shgnwgn_at_eden.rutgers.edu (Thu Jun 09 2005 - 13:31:53 CDT)
RE: Number of Steps Blake Charlebois (Thu Jun 09 2005 - 11:53:35 CDT)
Re: vmd-l: multiple automated calls to NAMD Axel Kohlmeyer (Thu Jun 09 2005 - 02:38:35 CDT)
Namd on Mac os X Maria Lin (Wed Jun 08 2005 - 18:57:10 CDT)
Number of Steps Pijush Ghosh (Wed Jun 08 2005 - 13:39:34 CDT)
Re: Multiple Harmonic Constraints Sascha Tayefeh (Thu Jun 09 2005 - 08:28:52 CDT)
Multiple Harmonic Constraints Sascha Tayefeh (Thu Jun 09 2005 - 02:31:38 CDT)
multiple automated calls to NAMD nordgren_at_sas.upenn.edu (Wed Jun 08 2005 - 20:57:56 CDT)
Re: Reverse Free Energy perturbation (FEP)? Chris Chipot (Wed Jun 08 2005 - 17:59:42 CDT)
Re: Avoiding Rotation and translation of protein Marc Q. Ma (Wed Jun 08 2005 - 16:58:02 CDT)
Reverse Free Energy perturbation (FEP)? Shahid Qamar (Wed Jun 08 2005 - 15:35:30 CDT)
RE: Avoiding Rotation and translation of protein Shirley Hui (Wed Jun 08 2005 - 12:45:04 CDT)
RE: Avoiding Rotation and translation of protein Blake Charlebois (Wed Jun 08 2005 - 12:39:06 CDT)
Namd hangs on Bproc cluster Rene Salmon (Wed Jun 08 2005 - 11:55:00 CDT)
Avoiding Rotation and translation of protein Leonardo Sepulveda Durán (Wed Jun 08 2005 - 10:58:33 CDT)
Re: config files Gengbin Zheng (Tue Jun 07 2005 - 14:23:31 CDT)
Re: NAMD on IBM pSeries (690, 655) Gengbin Zheng (Tue Jun 07 2005 - 14:05:07 CDT)
Re: NAMD on IBM pSeries (690, 655) Dong Luo (Tue Jun 07 2005 - 14:01:54 CDT)
Re: NAMD on IBM pSeries (690, 655) Gengbin Zheng (Tue Jun 07 2005 - 14:00:04 CDT)
Re: Installing NAMD on beowulf cluster, 64 bit, opteron, 4 processors. Gengbin Zheng (Tue Jun 07 2005 - 13:58:15 CDT)
config files Mark A. Hallman (Tue Jun 07 2005 - 12:17:35 CDT)
Re: NAMD on fedora 3 core? Gengbin Zheng (Tue Jun 07 2005 - 12:00:22 CDT)
NAMD on IBM pSeries (690, 655) Dong Luo (Tue Jun 07 2005 - 11:45:53 CDT)
NAMD on fedora 3 core? Georgios Papadopoulos (Tue Jun 07 2005 - 01:33:49 CDT)
Re: how to apply a random force on a atom Phoenix (Tue Jun 07 2005 - 01:08:36 CDT)
Installing NAMD on beowulf cluster, 64 bit, opteron, 4 processors. Wang, Boyang (Mon Jun 06 2005 - 22:23:59 CDT)
relating FEP-derived ddG values to experimental IC50 Floris Buelens (Mon Jun 06 2005 - 17:49:54 CDT)
Re: FEP charge perturbation Floris Buelens (Mon Jun 06 2005 - 17:40:44 CDT)
RE: how to apply a random force on a atom Blake Charlebois (Mon Jun 06 2005 - 16:06:44 CDT)
how to apply a random force on a atom q=E2=BA=E9=C3=F7?= (Mon Jun 06 2005 - 12:31:46 CDT)
hi ,everyone.I have a problem about random force q=E2=BA=E9=C3=F7?= (Mon Jun 06 2005 - 11:48:08 CDT)
inorganic surface peptide simulation Matan Dishon (Mon Jun 06 2005 - 07:13:07 CDT)
rigidBonds water Joshua D. Moore (Sun Jun 05 2005 - 21:39:09 CDT)
Fe2+ parameters? Georgios Papadopoulos (Sun Jun 05 2005 - 04:52:09 CDT)
charmm parameters for PEG li jianguo (Sat Jun 04 2005 - 23:42:26 CDT)
NADP hydrogen zero Hemant Kushwaha (Fri Jun 03 2005 - 22:30:08 CDT)
Re: NADP problem Hemant Kushwaha (Fri Jun 03 2005 - 22:07:08 CDT)
Re: FEP charge perturbation Chris Chipot (Fri Jun 03 2005 - 12:08:13 CDT)
Re: NADP problem Hemant Kushwaha (Fri Jun 03 2005 - 08:28:56 CDT)
ligands in VMD Leonardo Sepulveda Durán (Wed Jun 01 2005 - 20:20:02 CDT)
Periodic Boundary Condition Gan, Yong $UMC-Student$ (Wed Jun 01 2005 - 16:56:41 CDT)
Generating a lot of segments in proper order and selection around a center of mass Leonardo Sepulveda Durán (Wed Jun 01 2005 - 16:13:35 CDT)
question about nonnbonded parameters Leonardo Sepulveda Durán (Tue May 31 2005 - 11:04:23 CDT)
Re: PSFGEN pijush.ghosh_at_ndsu.edu (Sun May 29 2005 - 15:50:15 CDT)
Problem with solvate and PSF files in CHARMM format Leonardo Sepulveda Durán (Mon May 30 2005 - 18:37:05 CDT)
Nanotube simulation in water problem Jason Lee (Mon May 30 2005 - 09:30:12 CDT)
FEP charge perturbation Floris Buelens (Sun May 29 2005 - 17:50:28 CDT)
NAMD hangs Michael Grabe (Sun May 29 2005 - 15:53:09 CDT)
Re: PSFGEN Charles McCallum (Sun May 29 2005 - 12:48:59 CDT)
the lastest version of NAMD source junwang (Sun May 29 2005 - 12:29:35 CDT)
RE: PSFGEN Wei Chen (Sat May 28 2005 - 20:42:40 CDT)
questions about anisotropic pressure coupling Frank Yong Jiang (Sat May 28 2005 - 10:34:45 CDT)
RE: PSFGEN Pijush Ghosh (Fri May 27 2005 - 17:10:47 CDT)
libimf.so problems Brian Bennion (Fri May 27 2005 - 15:22:07 CDT)
PSFGEN Wei Chen (Fri May 27 2005 - 15:10:30 CDT)
Multiple dihedral multiplicity floquet_at_icsn.cnrs-gif.fr (Fri May 27 2005 - 08:09:14 CDT)
Re: about *.psf Alessandro Pedretti (Fri May 27 2005 - 05:30:10 CDT)
about *.psf ËïæÃæÃ (Thu May 26 2005 - 23:59:07 CDT)
Segmentation violation in NAMD ! Parag Adhangale (Thu May 26 2005 - 11:04:41 CDT)
Re: Compilation of Charm++ on Linux opteron cluster with MPICH-GM installed Gengbin Zheng (Wed May 25 2005 - 23:05:47 CDT)
Re: Megatest fails on Linux cluster Gengbin Zheng (Wed May 25 2005 - 22:54:23 CDT)
Re: namddat not working Leonardo Sepulveda Durán (Wed May 25 2005 - 15:43:28 CDT)
Re: CHARM/NAMD network problems on amd64 Clustermatic Rene Salmon (Wed May 25 2005 - 12:12:05 CDT)
Re: namddat not working Cetin Baloglu (Tue May 24 2005 - 20:31:02 CDT)
Re: namddat not working Cameron Mura (Tue May 24 2005 - 17:30:33 CDT)
namddat not working Leonardo Sepulveda Durán (Tue May 24 2005 - 16:34:24 CDT)
how to use gromacs force field in NAMD? Frank Yong Jiang (Tue May 24 2005 - 15:50:05 CDT)
Re: Re: Simulated Annealing Config Leonardo Sepulveda Durán (Tue May 24 2005 - 14:55:49 CDT)
pressure Wei Chen (Mon May 23 2005 - 19:50:28 CDT)
Compilation of NAMD on opteron cluster with myrinet junwang (Mon May 23 2005 - 19:44:41 CDT)
RE: Error in running tutorial files Ragothaman Yennamalli (Mon May 23 2005 - 02:00:38 CDT)
psfgen problem Hemant Kushwaha (Fri May 20 2005 - 23:41:13 CDT)
Milestoning in NAMD Shahid Qamar (Wed May 18 2005 - 15:46:19 CDT)
RE: Error in running tutorial files Pijush Ghosh (Wed May 18 2005 - 13:55:31 CDT)
Error in running tutorial files Ragothaman Yennamalli (Wed May 18 2005 - 12:20:50 CDT)
RE: regenerating PSF file Pijush Ghosh (Wed May 18 2005 - 10:01:51 CDT)
inconsistencies with amber force fields due to scnb and 1-4scalin g Stern, Julie (Wed May 18 2005 - 10:38:51 CDT)
steered molecular dynamics docking WONG Hua (Wed May 18 2005 - 04:55:37 CDT)
Re: regenerating PSF file Cetin Baloglu (Wed May 18 2005 - 02:50:38 CDT)
Re: regenerating PSF file Michael Grabe (Wed May 18 2005 - 02:11:41 CDT)
regenerating PSF file Cetin Baloglu (Wed May 18 2005 - 01:07:05 CDT)
How to set a molecule to be rigid in NAMD? Boyang Wang (Mon May 16 2005 - 14:37:44 CDT)
Tyrocine dynamics came out wrong. Boyang Wang (Sun May 15 2005 - 20:08:08 CDT)
Re: Converting Gromacs OPLS parameters to Charmm format Joshua D. Moore (Tue May 17 2005 - 17:35:18 CDT)
NADP problem Hemant Kushwaha (Tue May 17 2005 - 07:12:29 CDT)
Condition for stopping MD sim. with NAMD Nicolas Floquet (Tue May 17 2005 - 02:56:45 CDT)
Re: "make" Linux-amd64-g++ error Xiaoqing Wang (Mon May 16 2005 - 09:08:03 CDT)
Re: "make" Linux-amd64-g++ error Xiaoqing Wang (Mon May 16 2005 - 07:45:38 CDT)
Re: Re: NAMD 2.5 crashes unpredictably on a 8 way SMP (Linux x86) Niraj kumar (Mon May 16 2005 - 05:14:31 CDT)
"make" Linux-amd64-g++ error Xiaoqing Wang (Sun May 15 2005 - 22:31:47 CDT)
What's wrong with my namd2 Xiaoqing Wang (Sun May 15 2005 - 07:01:13 CDT)
Generating psf for a drug, trimethoprim Charles Moad (Sat May 14 2005 - 18:00:08 CDT)
benzene in NAMD Boyang Wang (Sat May 14 2005 - 15:33:13 CDT)
Re: Trajectory file. s.bora erdemli (Fri May 13 2005 - 17:30:58 CDT)
Re: Trajectory file. Gianluca Interlandi (Fri May 13 2005 - 16:39:37 CDT)
Trajectory file. Boyang Wang (Fri May 13 2005 - 16:20:17 CDT)
Megatest fails on Linux cluster Sterling Paramore (Fri May 13 2005 - 14:40:11 CDT)
Re: namddat: Command not found Mikolai Fajer (Thu May 12 2005 - 14:50:20 CDT)
Re: namddat: Command not found Giovanni Bellesia (Thu May 12 2005 - 13:49:45 CDT)
Re: namddat: Command not found Giovanni Bellesia (Thu May 12 2005 - 13:48:10 CDT)
Re: dielectric constant Leandro Martínez (Thu May 12 2005 - 13:24:10 CDT)
RE: dielectric constant Pijush Ghosh (Thu May 12 2005 - 12:53:32 CDT)
namddat: Command not found Mikolai Fajer (Thu May 12 2005 - 12:41:46 CDT)
dielectric constant Dong Luo (Thu May 12 2005 - 11:52:42 CDT)
scnb scaling factor and compatibility with AMBER force fields Stern, Julie (Thu May 12 2005 - 11:47:01 CDT)
Re: FEP Wei Chen (Thu May 12 2005 - 11:19:48 CDT)
Force constant of harmonic restraint picot.delphine_at_neuf.fr (Thu May 12 2005 - 03:50:11 CDT)
Re: FEP Philip Fowler (Thu May 12 2005 - 04:37:31 CDT)
libimf.so error when compiling charm++ Ben Roberts (Thu May 12 2005 - 01:09:36 CDT)
Re: CHARM/NAMD network problems on amd64 Clustermatic Gengbin Zheng (Wed May 11 2005 - 22:21:36 CDT)
Re: Compliling NAMD in RedHat9 Gengbin Zheng (Wed May 11 2005 - 22:09:15 CDT)
Re: Re: NAMD 2.5 crashes unpredictably on a 8 way SMP (Linux x86) Gengbin Zheng (Wed May 11 2005 - 22:07:13 CDT)
Compliling NAMD in RedHat9 Karina Martinez (Wed May 11 2005 - 21:59:28 CDT)
FEP Chris Chipot (Wed May 11 2005 - 17:34:47 CDT)
FEP Wei Chen (Wed May 11 2005 - 13:49:53 CDT)
CHARM/NAMD network problems on amd64 Clustermatic Rene Salmon (Wed May 11 2005 - 13:07:25 CDT)
Re: Space environment simulations carlos n. a. (Wed May 11 2005 - 11:11:29 CDT)
Re: Energy minimization Nicolas Sapay (Wed May 11 2005 - 11:06:15 CDT)
Energy minimization mustapha.hamdi_at_ensi-bourges.fr (Wed May 11 2005 - 12:33:01 CDT)
Re: different result from different cpu Xiaoqing Wang (Tue May 10 2005 - 19:59:45 CDT)
Energy minimization mustapha.hamdi_at_ensi-bourges.fr (Wed May 11 2005 - 09:46:40 CDT)
Re: non-repeatability NAMD simulations Jérôme Hénin (Wed May 11 2005 - 03:00:55 CDT)
Re: Re: NAMD 2.5 crashes unpredictably on a 8 way SMP (Linux x86) Niraj kumar (Wed May 11 2005 - 01:40:56 CDT)
non-repeatability NAMD simulations roberte_at_organ.su.se (Tue May 10 2005 - 17:08:30 CDT)
Re: Space environment simulations carlos n. a. (Tue May 10 2005 - 16:02:28 CDT)
RE: Bad global exclusion count. Pijush Ghosh (Tue May 10 2005 - 14:12:06 CDT)
Bad global exclusion count. Boyang Wang (Tue May 10 2005 - 11:56:32 CDT)
Re: Space environment simulations Robert Brunner (Tue May 10 2005 - 11:41:37 CDT)
Re: different result from different cpu Jérôme Hénin (Tue May 10 2005 - 11:40:25 CDT)
saving picture from namdplot debashis.sikdar_at_ndsu.edu (Tue May 10 2005 - 11:31:04 CDT)
Re: NAMD 2.5 crashes unpredictably on a 8 way SMP (Linux x86) Gengbin Zheng (Tue May 10 2005 - 09:57:04 CDT)
different result from different cpu Xiaoqing Wang (Tue May 10 2005 - 07:31:31 CDT)
NOE constraints with NAMD Gianluca Interlandi (Tue May 10 2005 - 09:25:35 CDT)
Re: NAMD 2.5 crashes unpredictably on a 8 way SMP (Linux x86) Niraj kumar (Tue May 10 2005 - 04:48:59 CDT)
Re: NAMD 2.5 crashes unpredictably on a 8 way SMP (Linux x86) Gengbin Zheng (Tue May 10 2005 - 01:45:25 CDT)
Re: compile "mpi" charm++ on amd64 Gengbin Zheng (Tue May 10 2005 - 01:31:51 CDT)
compile "mpi" charm++ on amd64 Xiaoqing Wang (Mon May 09 2005 - 22:09:32 CDT)
Minimization with NAMD valesrdp (Mon May 09 2005 - 09:17:57 CDT)
NAMD 2.5 crashes unpredictably on a 8 way SMP (Linux x86) Niraj kumar (Mon May 09 2005 - 06:03:19 CDT)
NAMD automation nordgren_at_sas.upenn.edu (Sat May 07 2005 - 23:39:16 CDT)
Re: Fixing atoms during simulation nordgren_at_sas.upenn.edu (Sat May 07 2005 - 23:17:30 CDT)
Fixing atoms during simulation Uma Mahankali (Sat May 07 2005 - 19:33:49 CDT)
Problems compiling NAMD on linux/clustermatic 5 roberte_at_organ.su.se (Sat May 07 2005 - 05:54:18 CDT)
Re: how to restart/continue NAMD run Wei Chen (Fri May 06 2005 - 15:47:25 CDT)
Space environment simulations Gaurav Sharma (Fri May 06 2005 - 13:36:40 CDT)
Space environment simulations Gaurav Sharma (Fri May 06 2005 - 13:20:53 CDT)
how to restart/continue NAMD run Jerry Xu (Fri May 06 2005 - 11:28:33 CDT)
Re: error message surendra negi (Fri May 06 2005 - 10:22:55 CDT)
Re: charmm paramter Boyang Wang (Thu May 05 2005 - 22:23:56 CDT)
protein/DNA complexes Matthew Wilce (Fri May 06 2005 - 00:27:34 CDT)
RE: Restartname Boyang Wang (Thu May 05 2005 - 21:52:36 CDT)
RE: About Restart Michel Espinoza-Fonseca (Thu May 05 2005 - 21:50:29 CDT)
RE: Restartname Michel Espinoza-Fonseca (Thu May 05 2005 - 21:48:00 CDT)
charmm paramter akash.khandelwal_at_ndsu.edu (Thu May 05 2005 - 20:57:34 CDT)
Re: socket closed error Brady Chang (Thu May 05 2005 - 20:40:05 CDT)
Restartname Boyang Wang (Thu May 05 2005 - 19:19:26 CDT)
About Restart Boyang Wang (Thu May 05 2005 - 18:50:52 CDT)
Problem using the GROMACS force field ! Parag Adhangale (Thu May 05 2005 - 16:23:52 CDT)
RE: About PDB file with fixed atom flags. Michel Espinoza-Fonseca (Thu May 05 2005 - 14:29:01 CDT)
Re: hanging at startup phase 0 Dong Luo (Thu May 05 2005 - 13:59:37 CDT)
Re: HEME patch surendra negi (Thu May 05 2005 - 13:38:37 CDT)
RE: About PDB file with fixed atom flags. Hidekazu WATANABE (Thu May 05 2005 - 12:36:21 CDT)
Re: hanging at startup phase 0 surendra negi (Thu May 05 2005 - 12:25:06 CDT)
Re: hanging at startup phase 0 Gengbin Zheng (Thu May 05 2005 - 11:00:22 CDT)
hanging at startup phase 0 Dong Luo (Thu May 05 2005 - 10:47:31 CDT)
RE: NAMD: HEM residue Michel Espinoza-Fonseca (Wed May 04 2005 - 17:17:01 CDT)
RE: NAMD: HEM residue Turman, Cheri M (Wed May 04 2005 - 17:07:50 CDT)
RE: About PDB file with fixed atom flags. Michel Espinoza-Fonseca (Wed May 04 2005 - 17:07:13 CDT)
About PDB file with fixed atom flags. Hidekazu WATANABE (Wed May 04 2005 - 16:40:23 CDT)
RE: NAMD: HEM residue Michel Espinoza-Fonseca (Wed May 04 2005 - 15:17:34 CDT)
NAMD simulation: HEME surendra negi (Wed May 04 2005 - 15:16:58 CDT)
NAMD: HEM residue surendra negi (Wed May 04 2005 - 14:56:58 CDT)
How to change psf file in the half way of VMD simulation? Boyang Wang (Tue May 03 2005 - 21:48:23 CDT)
namd2 compile linux-i686-mpi Bing Xiong (Tue May 03 2005 - 15:38:27 CDT)
compiling NAMD on a redhat-pentium-dell workstation paul.dalhaimer_at_yale.edu (Tue May 03 2005 - 11:54:56 CDT)
Minimization after a MD simulation valesrdp (Tue May 03 2005 - 04:48:14 CDT)
Re: SMD-drifting of center of mass Boyang Wang (Sun May 01 2005 - 22:21:46 CDT)
RE: Parameter file. Boyang Wang (Sun May 01 2005 - 17:28:48 CDT)
RE: Fwd: Parameter file. Pijush Ghosh (Sun May 01 2005 - 16:39:10 CDT)
NADP topology Hemant Kushwaha (Mon May 02 2005 - 04:40:58 CDT)
Dihedral and Improper, Nonbonded. Wang, Boyang (Sun May 01 2005 - 22:46:22 CDT)
RE: SMD-drifting of center of mass Blake Charlebois (Sun May 01 2005 - 21:23:48 CDT)
SMD-drifting of center of mass Ekta Khurana (Sun May 01 2005 - 16:47:19 CDT)
Parameter file again. Boyang Wang (Sat Apr 30 2005 - 12:20:19 CDT)
Fwd: Parameter file. Boyang Wang (Sat Apr 30 2005 - 12:15:45 CDT)
Parameter file. Boyang Wang (Fri Apr 29 2005 - 23:20:52 CDT)
Re: Combine pdb and psf files Luis Rosales (Fri Apr 29 2005 - 18:26:06 CDT)
Combine pdb and psf files Gan, Yong $UMC-Student$ (Fri Apr 29 2005 - 16:04:23 CDT)
Re: Re: vmd-l: Interactive Simulations, ligand size limits.... Marc Baaden (Fri Apr 29 2005 - 04:01:27 CDT)
Tcl interface--dynamically changing simulation parameters Philip Blood (Thu Apr 28 2005 - 17:19:42 CDT)
Regulating density of water Pijush Ghosh (Thu Apr 28 2005 - 13:44:35 CDT)
Re: Re: vmd-l: Interactive Simulations, ligand size limits.... John Stone (Thu Apr 28 2005 - 13:05:40 CDT)
Re: Re: vmd-l: Interactive Simulations, ligand size limits.... Brian Bennion (Thu Apr 28 2005 - 12:01:32 CDT)
RE: Generate psf file of DMPC membrane Gan, Yong $UMC-Student$ (Thu Apr 28 2005 - 11:58:02 CDT)
Re: solvate and write pdb, psf file. \ (Thu Apr 28 2005 - 11:33:40 CDT)
Re: Re: vmd-l: Interactive Simulations, ligand size limits.... John Stone (Thu Apr 28 2005 - 10:08:17 CDT)
Re: Re: vmd-l: Interactive Simulations, ligand size limits.... Luis Rosales (Wed Apr 27 2005 - 21:29:51 CDT)
solvate and write pdb, psf file. Boyang Wang (Wed Apr 27 2005 - 19:16:28 CDT)
Generate psf file of DMPC membrane Gan, Yong $UMC-Student$ (Wed Apr 27 2005 - 22:10:34 CDT)
Re: Molecular Dynamics or Langevin Dynamics Giovanni Bellesia (Wed Apr 27 2005 - 19:18:58 CDT)
Re: Molecular Dynamics or Langevin Dynamics Marc Q. Ma (Wed Apr 27 2005 - 12:39:29 CDT)
(no subject) Wei Chen (Wed Apr 27 2005 - 11:04:07 CDT)
Re: Molecular Dynamics or Langevin Dynamics Giovanni Bellesia (Wed Apr 27 2005 - 10:59:27 CDT)
Re: Molecular Dynamics or Langevin Dynamics Marc Q. Ma (Wed Apr 27 2005 - 09:38:13 CDT)
Molecular Dynamics or Langevin Dynamics sabri bora erdemli (Tue Apr 26 2005 - 11:21:00 CDT)
Gradient tolerance--total or per atom? Chang, Christopher (Tue Apr 26 2005 - 11:46:07 CDT)
NAMD and dual core Opterons, thoughts? Dow Hurst (Tue Apr 26 2005 - 11:36:02 CDT)
NAMD job abnormally killed with PBS Nicolas Sapay (Tue Apr 26 2005 - 02:14:33 CDT)
Re: a target molecule in a water box. Wei Chen (Mon Apr 25 2005 - 22:33:54 CDT)
a target molecule in a water box. Wang, Boyang (Mon Apr 25 2005 - 21:12:02 CDT)
unwrapping dcd trajectory Mauricio Carrillo Tripp (Mon Apr 25 2005 - 16:47:42 CDT)
Ferric heme Eunice Ramirez (Mon Apr 25 2005 - 11:54:41 CDT)
Heat Capacity & Relaxation Functions Cetin Baloglu (Mon Apr 25 2005 - 03:22:11 CDT)
Re: Setting target minimization gradient? Luis Rosales (Fri Apr 22 2005 - 19:49:18 CDT)
Setting target minimization gradient? Chang, Christopher (Fri Apr 22 2005 - 13:15:01 CDT)
Re: Re: vmd-l: Interactive Simulations, ligand size limits.... John Stone (Thu Apr 21 2005 - 16:28:08 CDT)
Re: Re: vmd-l: Interactive Simulations, ligand size limits.... Luis Rosales (Wed Apr 20 2005 - 22:22:10 CDT)
(no subject) valesrdp (Thu Apr 21 2005 - 03:54:58 CDT)
Re: vmd-l: Interactive Simulations, ligand size limits.... Luis Rosales (Wed Apr 20 2005 - 18:19:58 CDT)
Re: vmd-l: Interactive Simulations, ligand size limits.... John Stone (Wed Apr 20 2005 - 16:12:20 CDT)
Interactive Simulations, ligand size limits.... Luis Rosales (Tue Apr 19 2005 - 22:51:52 CDT)
RE: duplicated key CA in psfgen mustapha.hamdi_at_ensi-bourges.fr (Wed Apr 20 2005 - 07:13:24 CDT)
RE: duplicated key CA in psfgen mustapha.hamdi_at_ensi-bourges.fr (Wed Apr 20 2005 - 07:12:36 CDT)
RE: duplicated key CA in psfgen Pijush Ghosh (Tue Apr 19 2005 - 13:04:48 CDT)
Re: addforce Leandro Martínez (Tue Apr 19 2005 - 11:37:55 CDT)
RE: protein interact with its image Blake Charlebois (Tue Apr 19 2005 - 12:10:20 CDT)
duplicated key CA in psfgen mustapha.hamdi_at_ensi-bourges.fr (Tue Apr 19 2005 - 12:49:33 CDT)
Re: addforce Jérôme Hénin (Tue Apr 19 2005 - 11:21:21 CDT)
Re: addforce Marc Q. Ma (Tue Apr 19 2005 - 11:17:20 CDT)
protein interact with its image Shunzhou Wan (Tue Apr 19 2005 - 10:23:58 CDT)
addforce Leandro Martínez (Tue Apr 19 2005 - 09:38:50 CDT)
Topology for nano tubes Alex Vakhrouchev (Tue Apr 19 2005 - 06:59:04 CDT)
Re: NANMD errors: PME, qsub Brian Bennion (Mon Apr 18 2005 - 17:23:35 CDT)
Re: concatenating two or more dcd files Marc Q. Ma (Mon Apr 18 2005 - 12:13:51 CDT)
concatenating two or more dcd files Jorge Pikunic (Mon Apr 18 2005 - 10:44:07 CDT)
NANMD errors: PME, qsub E. Davis Oldham (Sat Apr 16 2005 - 12:37:37 CDT)
RE: minimization problem Brian Bennion (Thu Apr 14 2005 - 18:28:42 CDT)
RE: minimization problem Stern, Julie (Thu Apr 14 2005 - 16:53:15 CDT)
RE: minimization problem Michel Espinoza-Fonseca (Thu Apr 14 2005 - 15:52:05 CDT)
Re: minimization problem Pijush Ghosh (Thu Apr 14 2005 - 14:52:05 CDT)
RE: minimization problem Stern, Julie (Thu Apr 14 2005 - 15:26:04 CDT)
minimization problem Stern, Julie (Thu Apr 14 2005 - 13:41:19 CDT)
Re: Periodic cell has become too small for original patch grid Charles Danko (Thu Apr 14 2005 - 10:48:52 CDT)
Re: Re[2]: ERROR: Constraint failure in RATTLE algorithm for atom 127! Charles Danko (Thu Apr 14 2005 - 10:40:10 CDT)
RE: Periodic cell has become too small for original patch grid Xiaoqing Wang (Thu Apr 14 2005 - 09:29:02 CDT)
Re[2]: ERROR: Constraint failure in RATTLE algorithm for atom 127! Hrant Gharabekyan (Thu Apr 14 2005 - 05:48:08 CDT)
Re: Periodic cell has become too small for original patch grid Hrant Gharabekyan (Thu Apr 14 2005 - 05:25:01 CDT)
RE: about protonation of HIS in membrane protein Michel Espinoza-Fonseca (Wed Apr 13 2005 - 19:47:52 CDT)
Re: about protonation of HIS in membrane protein Aaron Oakley (Wed Apr 13 2005 - 19:10:18 CDT)
RE: ERROR: Constraint failure in RATTLE algorithm for atom 127! Michel Espinoza-Fonseca (Wed Apr 13 2005 - 16:20:53 CDT)
ERROR: Constraint failure in RATTLE algorithm for atom 127! Shahid Qamar (Wed Apr 13 2005 - 14:20:16 CDT)
RE: Periodic cell has become too small for original patch grid Michel Espinoza-Fonseca (Wed Apr 13 2005 - 11:32:17 CDT)
unstable simulation with AMBER ff in AMBER! Lina Nilsson (Wed Apr 13 2005 - 04:05:36 CDT)
Re: Periodic cell has become too small for original patch grid Charles Danko (Wed Apr 13 2005 - 09:32:03 CDT)
about protonation of HIS in membrane protein Baoqiang Cao (Wed Apr 13 2005 - 09:21:08 CDT)
Re: AMBER ff system has too high velocities in NAMD Marc Q. Ma (Wed Apr 13 2005 - 08:59:31 CDT)
Periodic cell has become too small for original patch grid Xiaoqing Wang (Wed Apr 13 2005 - 03:38:33 CDT)
AMBER ff system has too high velocities in NAMD Lina Nilsson (Wed Apr 13 2005 - 03:16:45 CDT)
RE: ELECT energy Michel Espinoza-Fonseca (Mon Apr 11 2005 - 16:18:10 CDT)
Re: bonding to image Glenn Johnson (Mon Apr 11 2005 - 16:02:28 CDT)
ELECT energy Stern, Julie (Mon Apr 11 2005 - 14:37:57 CDT)
bonding to image Glenn Johnson (Mon Apr 11 2005 - 13:56:33 CDT)
distance restraints during a dynamic Nicolas Sapay (Mon Apr 11 2005 - 11:13:40 CDT)
density calculation Swarna Patra (Sun Apr 10 2005 - 20:24:51 CDT)
Re: RE: RE: error: UNABLE TO FIND ANGLE PARAMETERS FOR C NH1 C Baoqiang Cao (Sat Apr 09 2005 - 22:46:44 CDT)
Re: any script to build membrane+protein+solvent? Leandro Martínez (Sat Apr 09 2005 - 07:20:07 CDT)
RE: RE: error: UNABLE TO FIND ANGLE PARAMETERS FOR C NH1 C Michel Espinoza-Fonseca (Sat Apr 09 2005 - 20:31:18 CDT)
Re: RE: error: UNABLE TO FIND ANGLE PARAMETERS FOR C NH1 C Baoqiang Cao (Sat Apr 09 2005 - 21:26:03 CDT)
RE: error: UNABLE TO FIND ANGLE PARAMETERS FOR C NH1 C Michel Espinoza-Fonseca (Sat Apr 09 2005 - 15:41:45 CDT)
error: UNABLE TO FIND ANGLE PARAMETERS FOR C NH1 C Baoqiang Cao (Sat Apr 09 2005 - 14:40:37 CDT)
Re: any script to build membrane+protein+solvent? Xiaoqing Wang (Fri Apr 08 2005 - 21:23:48 CDT)
Re: box size changes under anisotropic pressure coupling Philip Blood (Fri Apr 08 2005 - 14:28:11 CDT)
Re: Leandro Martínez (Fri Apr 08 2005 - 13:50:34 CDT)
Re: box size changes under anisotropic pressure coupling Jerome Henin (Fri Apr 08 2005 - 13:44:19 CDT)
Re: FEP output in NAMD Jerome Henin (Fri Apr 08 2005 - 13:37:41 CDT)
Re: Michael Grabe (Fri Apr 08 2005 - 12:31:36 CDT)
RE: Michel Espinoza-Fonseca (Fri Apr 08 2005 - 12:27:54 CDT)
phosphoserine Michel Espinoza-Fonseca (Fri Apr 08 2005 - 12:18:35 CDT)
(no subject) Michael Grabe (Fri Apr 08 2005 - 12:04:37 CDT)
box size changes under anisotropic pressure coupling Philip Blood (Fri Apr 08 2005 - 11:14:40 CDT)
RE: Membrane configuration file Michel Espinoza-Fonseca (Fri Apr 08 2005 - 11:21:28 CDT)
Membrane configuration file Lechuga, Javier (Fri Apr 08 2005 - 10:24:01 CDT)
any script to build membrane+protein+solvent? Baoqiang Cao (Fri Apr 08 2005 - 10:02:36 CDT)
Re: modifying cut off Brian Bennion (Fri Apr 08 2005 - 09:59:37 CDT)
Different electrostatic and Van der Waals cutoff Peter Spijker (Fri Apr 08 2005 - 04:56:42 CDT)
RE: modifying cut off Michel Espinoza-Fonseca (Thu Apr 07 2005 - 19:45:30 CDT)
Re: modifying cut off Michael Grabe (Thu Apr 07 2005 - 19:38:03 CDT)
performance differences on 2.4 vs. 2.6 Linux kernels Matt Harrington (Thu Apr 07 2005 - 19:10:54 CDT)
RE: modifying cut off Michel Espinoza-Fonseca (Thu Apr 07 2005 - 19:01:03 CDT)
Re: modifying cut off Michael Grabe (Thu Apr 07 2005 - 19:00:31 CDT)
modifying cut off Michel Espinoza-Fonseca (Thu Apr 07 2005 - 18:30:23 CDT)
temperature autocorrelation Glenn Johnson (Thu Apr 07 2005 - 17:39:28 CDT)
NAMD Myrinet issue - Strange behavior Edward Patrick Obrien (Thu Apr 07 2005 - 12:04:31 CDT)
Re: Duplicate lines in the output file ! Rene Salmon (Thu Apr 07 2005 - 10:13:59 CDT)
Checkpoint on IRIX of namd 2.5 job not MPI enabled Dow_Hurst (Thu Apr 07 2005 - 09:40:55 CDT)
Re: NMAD job abnormally killed with PBS Chris Samuel (Wed Apr 06 2005 - 22:32:01 CDT)
Re: FATAL ERROR: Stale NFS file handle Chris Samuel (Wed Apr 06 2005 - 22:29:59 CDT)
Re: Nanotube psf file. Brian Bennion (Wed Apr 06 2005 - 13:28:34 CDT)
Myrinet vs. Infiniband wzhuang_at_uci.edu (Wed Apr 06 2005 - 12:36:10 CDT)
RE: Nanotube psf file. Michel Espinoza-Fonseca (Wed Apr 06 2005 - 12:34:44 CDT)
Nanotube psf file. mustapha.hamdi_at_ensi-bourges.fr (Wed Apr 06 2005 - 13:06:59 CDT)
Duplicate lines in the output file ! Parag Adhangale (Wed Apr 06 2005 - 11:52:56 CDT)
add water on the top of the protein border Xiaoqing Wang (Wed Apr 06 2005 - 09:11:47 CDT)
FEP output in NAMD Vani Krishna (Tue Apr 05 2005 - 11:26:39 CDT)
namd and node freeze Brady Chang (Tue Apr 05 2005 - 03:39:26 CDT)
Re: RATTLE and DNA Nicholas M Glykos (Tue Apr 05 2005 - 10:02:24 CDT)
Re: RATTLE and DNA Marc Q. Ma (Tue Apr 05 2005 - 09:01:35 CDT)
RATTLE and DNA Nicholas M Glykos (Tue Apr 05 2005 - 05:33:48 CDT)
Re: problem running namd Chris Samuel (Mon Apr 04 2005 - 18:10:58 CDT)
RE: problem running namd Michel Espinoza-Fonseca (Mon Apr 04 2005 - 16:48:48 CDT)
Re: problem running namd Jerry Ebalunode (Mon Apr 04 2005 - 16:44:44 CDT)
Re: problem running namd Brian Bennion (Mon Apr 04 2005 - 15:26:06 CDT)
Re: problem running namd Jerry Ebalunode (Mon Apr 04 2005 - 15:21:38 CDT)
Re: problem running namd Jerry Ebalunode (Mon Apr 04 2005 - 14:15:19 CDT)
RE: problem running namd Michel Espinoza-Fonseca (Mon Apr 04 2005 - 13:48:02 CDT)
Re: problem running namd Brian Bennion (Mon Apr 04 2005 - 13:12:08 CDT)
problem running namd Michel Espinoza-Fonseca (Mon Apr 04 2005 - 11:54:45 CDT)
problem running namd Michel Espinoza-Fonseca (Mon Apr 04 2005 - 11:18:01 CDT)
Re: Errors compiling NAMD 2.5 Gengbin Zheng (Mon Apr 04 2005 - 03:13:33 CDT)
Errors compiling NAMD 2.5 Koo Kee Kiat (Mon Apr 04 2005 - 01:46:34 CDT)
Re: Charm++ problem on EM64T/Myrinet cluster Gengbin Zheng (Fri Apr 01 2005 - 01:23:51 CST)
binary restraint reference coordinates? Cameron Mura (Thu Mar 31 2005 - 20:31:42 CST)
Re: NAMD recognizes only one MPI process Gengbin Zheng (Thu Mar 31 2005 - 17:41:20 CST)
Charm++ problem on EM64T/Myrinet cluster Chona S. Guiang (Thu Mar 31 2005 - 16:08:38 CST)
NAMD recognizes only one MPI process Randy Crawford (Thu Mar 31 2005 - 11:46:45 CST)
Re: glucose CHARMM force field Hyonseok Hwang (Thu Mar 31 2005 - 12:29:13 CST)
Re: vmd-l: conformational alignment Wen Li (Thu Mar 31 2005 - 12:26:20 CST)
Re: vmd-l: conformational alignment Wen Li (Thu Mar 31 2005 - 10:32:51 CST)
Re: vmd-l: conformational alignment Wen Li (Thu Mar 31 2005 - 10:24:18 CST)
Re: conformational alignment Giovanni Bellesia (Wed Mar 30 2005 - 16:40:36 CST)
Re: vmd-l: conformational alignment John Stone (Wed Mar 30 2005 - 15:30:26 CST)
conformational alignment Wen Li (Wed Mar 30 2005 - 15:21:26 CST)
Re: multiple MD simulations Marc Q. Ma (Wed Mar 30 2005 - 11:57:11 CST)
Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC Chris Samuel (Wed Mar 30 2005 - 00:05:44 CST)
Re: glucose CHARMM force field Aaron Oakley (Tue Mar 29 2005 - 23:34:00 CST)
RE: glucose CHARMM force field Wei Chen (Tue Mar 29 2005 - 23:05:06 CST)
RE: glucose CHARMM force field Michel Espinoza-Fonseca (Tue Mar 29 2005 - 22:13:35 CST)
glucose CHARMM force field Hyonseok Hwang (Tue Mar 29 2005 - 21:37:34 CST)
Re: multiple MD simulations Marc Q. Ma (Tue Mar 29 2005 - 07:42:46 CST)
Re: socket closed error Josef Scheiber (Tue Mar 29 2005 - 01:01:34 CST)
multiple MD simulations Aaron Oakley (Mon Mar 28 2005 - 18:29:39 CST)
Re: socket closed error Brian Bennion (Fri Mar 25 2005 - 16:25:48 CST)
socket closed error brady chang (Fri Mar 25 2005 - 14:54:01 CST)
Modeling a polymer Glenn Johnson (Thu Mar 24 2005 - 13:44:29 CST)
question about patch jz7_at_duke.edu (Thu Mar 24 2005 - 09:33:04 CST)
pairlist distance debashis.sikdar_at_ndsu.edu (Wed Mar 23 2005 - 09:32:48 CST)
RE: molecules distorted Michel Espinoza-Fonseca (Tue Mar 22 2005 - 15:37:19 CST)
molecules distorted Samuel Flores (Tue Mar 22 2005 - 15:35:03 CST)
How to read charmm binary trajectory file using home-made C/C++ code Wei Zhuang (Tue Mar 22 2005 - 14:39:15 CST)
pairlist distance debashis.sikdar_at_ndsu.edu (Tue Mar 22 2005 - 14:28:20 CST)
RE: visualizing dynamics output Michel Espinoza-Fonseca (Tue Mar 22 2005 - 14:17:12 CST)
RE: visualizing dynamics output Samuel Flores (Tue Mar 22 2005 - 13:51:07 CST)
Re: visualizing dynamics output Brian Bennion (Tue Mar 22 2005 - 12:55:00 CST)
visualizing dynamics output Samuel Flores (Tue Mar 22 2005 - 11:31:31 CST)
Re: path problems Gengbin Zheng (Tue Mar 22 2005 - 01:37:52 CST)
path problems Michael Grabe (Tue Mar 22 2005 - 01:29:25 CST)
RE: running VMD from a script? -- oops, never mind! Samuel Flores (Mon Mar 21 2005 - 19:49:50 CST)
RE: running VMD from a script? Samuel Flores (Mon Mar 21 2005 - 19:28:41 CST)
Re: psfgen for DNA Brian Bennion (Mon Mar 21 2005 - 11:51:21 CST)
psfgen for DNA Nicholas M Glykos (Mon Mar 21 2005 - 10:20:49 CST)
Re: running VMD from a script? Nicolas Sapay (Mon Mar 21 2005 - 02:29:34 CST)
Re: question about par_all27_prot_lipid.inp Leandro Martínez (Sun Mar 20 2005 - 06:13:17 CST)
Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC Chris Samuel (Sun Mar 20 2005 - 20:04:50 CST)
running VMD from a script? Samuel Flores (Sun Mar 20 2005 - 18:22:23 CST)
RE: question about par_all27_prot_lipid.inp Michel Espinoza-Fonseca (Sun Mar 20 2005 - 15:22:19 CST)
Re: Not getting good speed up Dow Hurst (Sun Mar 20 2005 - 02:22:00 CST)
question about par_all27_prot_lipid.inp Samuel Flores (Sun Mar 20 2005 - 01:34:58 CST)
Re: Not getting good speed up Mauricio Carrillo Tripp (Fri Mar 18 2005 - 16:12:30 CST)
convert namd structure/coordinate files to gromacs topology file Glenn Johnson (Fri Mar 18 2005 - 14:00:54 CST)
NAMD on new P4 Gan, Yong $UMC-Student$ (Fri Mar 18 2005 - 13:04:54 CST)
Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC Chris Samuel (Thu Mar 17 2005 - 23:23:24 CST)
Re: strange behaviour when running apoa1 on 1 processor Gengbin Zheng (Thu Mar 17 2005 - 13:56:03 CST)
strange behaviour when running apoa1 on 1 processor Mauricio Carrillo Tripp (Thu Mar 17 2005 - 13:36:47 CST)
isotropic pressure tensor Gan, Yong $UMC-Student$ (Wed Mar 16 2005 - 21:56:49 CST)
Re: Re: Trouble with NAMD on Myrinet Gengbin Zheng (Wed Mar 16 2005 - 11:27:19 CST)
Re: Trouble with NAMD on Myrinet Edward Patrick Obrien (Wed Mar 16 2005 - 10:04:20 CST)
Bio-Image summer school in Paris this year Marc Baaden (Wed Mar 16 2005 - 05:42:59 CST)
Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC Chris Samuel (Wed Mar 16 2005 - 04:37:07 CST)
Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC Gengbin Zheng (Wed Mar 16 2005 - 00:24:54 CST)
Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC Chris Samuel (Wed Mar 16 2005 - 00:06:21 CST)
membrane files Gan, Yong $UMC-Student$ (Tue Mar 15 2005 - 20:54:41 CST)
Re: Trouble with NAMD on Myrinet Gengbin Zheng (Tue Mar 15 2005 - 14:14:14 CST)
Trouble with NAMD on Myrinet Edward Patrick Obrien (Tue Mar 15 2005 - 14:02:40 CST)
Re: Not getting good speed up Dow_Hurst (Tue Mar 15 2005 - 12:31:11 CST)
Re: Not getting good speed up Mauricio Carrillo Tripp (Tue Mar 15 2005 - 10:55:16 CST)
Re: namd and fftw Joachim Hein (Tue Mar 15 2005 - 03:56:13 CST)
computing resource Wei Chen (Mon Mar 14 2005 - 23:08:48 CST)
namd and fftw Michel Espinoza-Fonseca (Mon Mar 14 2005 - 18:11:43 CST)
Re: Not getting good speed up Mauricio Carrillo Tripp (Sat Mar 12 2005 - 15:38:06 CST)
Re: Submitting jobs on myrinet...problem Jerry Ebalunode (Fri Mar 11 2005 - 22:21:55 CST)
Submitting jobs on myrinet...problem Edward Patrick Obrien (Fri Mar 11 2005 - 18:29:19 CST)
Re: Not getting good speed up Gengbin Zheng (Fri Mar 11 2005 - 16:04:53 CST)
Re: Not getting good speed up Mauricio Carrillo Tripp (Fri Mar 11 2005 - 15:32:38 CST)
Re: peridic boundary condition Jérôme Hénin (Fri Mar 11 2005 - 15:31:47 CST)
"Hands-On" Workshop on Computational Biophysics David Brandon (Fri Mar 11 2005 - 15:23:27 CST)
Re: peridic boundary condition John Kerrigan (Fri Mar 11 2005 - 15:18:48 CST)
Re: peridic boundary condition Marc Q. Ma (Fri Mar 11 2005 - 14:00:37 CST)
Re: peridic boundary condition Himanshu Khandelia (Fri Mar 11 2005 - 13:57:23 CST)
Re: peridic boundary condition Marc Q. Ma (Fri Mar 11 2005 - 13:15:31 CST)
Re: peridic boundary condition Edward Patrick Obrien (Fri Mar 11 2005 - 13:09:43 CST)
Re: namd2 mpi error Brian Bennion (Fri Mar 11 2005 - 11:05:18 CST)
Re: peridic boundary condition Marc Q. Ma (Fri Mar 11 2005 - 10:38:15 CST)
peridic boundary condition debashis.sikdar_at_ndsu.edu (Fri Mar 11 2005 - 09:08:37 CST)
Re: compiling Namd on amd64 olivier Walker (Fri Mar 11 2005 - 02:42:30 CST)
RE: Compiling on Linux-PPC970-Myrinet-MPI-xlC Brian Bennion (Thu Mar 10 2005 - 18:22:43 CST)
RE: Compiling on Linux-PPC970-Myrinet-MPI-xlC Jordi Camps (Thu Mar 10 2005 - 18:08:02 CST)
namd2 mpi error Mauricio Carrillo Tripp (Thu Mar 10 2005 - 14:58:37 CST)
flexible cell for MD simulations Michel Espinoza-Fonseca (Thu Mar 10 2005 - 16:25:17 CST)
Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC Brian Bennion (Thu Mar 10 2005 - 15:59:33 CST)
Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC Gengbin Zheng (Thu Mar 10 2005 - 15:54:56 CST)
Re: Compiling NAMD with mpicc myrinet Jerry Ebalunode (Thu Mar 10 2005 - 15:45:54 CST)
Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC Brian Bennion (Thu Mar 10 2005 - 14:11:29 CST)
Re: Compiling NAMD with mpicc myrinet Brian Bennion (Thu Mar 10 2005 - 14:08:44 CST)
Compiling on Linux-PPC970-Myrinet-MPI-xlC Jordi Camps (Thu Mar 10 2005 - 12:57:47 CST)
Compiling NAMD with mpicc myrinet Edward Patrick Obrien (Thu Mar 10 2005 - 12:19:50 CST)
Re: compiling Namd on amd64 olivier Walker (Thu Mar 10 2005 - 11:55:03 CST)
Re: compiling Namd on amd64 Brian Bennion (Thu Mar 10 2005 - 10:20:46 CST)
example scripts Himanshu Khandelia (Thu Mar 10 2005 - 10:03:53 CST)
Re: CAN'T FIND BOND PARAMETERS FOR BOND (error) Jérôme Hénin (Thu Mar 10 2005 - 07:59:14 CST)
Re: CAN'T FIND BOND PARAMETERS FOR BOND (error) sabri bora erdemli (Thu Mar 10 2005 - 05:36:33 CST)
Re: CAN'T FIND BOND PARAMETERS FOR BOND (error) Jérôme Hénin (Thu Mar 10 2005 - 05:16:35 CST)
compiling Namd on amd64 olivier Walker (Thu Mar 10 2005 - 04:08:08 CST)
CAN'T FIND BOND PARAMETERS FOR BOND (error) sabri bora erdemli (Thu Mar 10 2005 - 03:23:02 CST)
modeling sucrose Glenn Johnson (Wed Mar 09 2005 - 17:19:12 CST)
Re: installing NAMD on opteron cluster with MPI John Saeger (Wed Mar 09 2005 - 15:12:08 CST)
Re: namd on Altix Gengbin Zheng (Wed Mar 09 2005 - 13:36:21 CST)
RE: namd on Altix Michel Espinoza-Fonseca (Wed Mar 09 2005 - 13:33:35 CST)
loodking or topology file for zinc finger Wang Tianhua (Tue Mar 08 2005 - 19:43:02 CST)
Re: namd on Altix Gengbin Zheng (Tue Mar 08 2005 - 16:54:16 CST)
Re: namd on Altix Gengbin Zheng (Tue Mar 08 2005 - 18:43:47 CST)
RE: namd on Altix Michel Espinoza-Fonseca (Tue Mar 08 2005 - 17:31:15 CST)
Re: namd on Altix Gengbin Zheng (Tue Mar 08 2005 - 17:21:13 CST)
RE: namd on Altix Michel Espinoza-Fonseca (Tue Mar 08 2005 - 17:17:46 CST)
Re: namd on Altix Gengbin Zheng (Tue Mar 08 2005 - 17:09:47 CST)
RE: namd on Altix Michel Espinoza-Fonseca (Tue Mar 08 2005 - 17:05:52 CST)
Re: namd on Altix Gengbin Zheng (Tue Mar 08 2005 - 17:00:05 CST)
RE: namd on Altix Michel Espinoza-Fonseca (Tue Mar 08 2005 - 16:57:08 CST)
Re: G5 cluster Gengbin Zheng (Tue Mar 08 2005 - 16:41:06 CST)
RE: namd on Altix Michel Espinoza-Fonseca (Tue Mar 08 2005 - 15:03:49 CST)
Re: G5 clusters Gengbin Zheng (Tue Mar 08 2005 - 12:44:25 CST)
G5 clusters Michael Grabe (Tue Mar 08 2005 - 11:17:42 CST)
Re: NAMD restarts binary files Shirley Hui (Tue Mar 08 2005 - 10:26:59 CST)
NAMD restarts binary files Shirley Hui (Tue Mar 08 2005 - 10:13:08 CST)
Re: installing NAMD on opteron cluster with MPI Lina Nilsson (Tue Mar 08 2005 - 02:27:25 CST)
Re: namd on Altix Gengbin Zheng (Mon Mar 07 2005 - 19:11:33 CST)
RE: namd on Altix Michel Espinoza-Fonseca (Mon Mar 07 2005 - 19:06:35 CST)
Re: namd on Altix Gengbin Zheng (Mon Mar 07 2005 - 18:59:02 CST)
RE: namd on Altix Michel Espinoza-Fonseca (Mon Mar 07 2005 - 18:43:25 CST)
Re: namd on Altix Gengbin Zheng (Mon Mar 07 2005 - 18:28:20 CST)
Installing NAMD Michel Espinoza-Fonseca (Mon Mar 07 2005 - 18:18:43 CST)
Re: question (fwd) Gengbin Zheng (Mon Mar 07 2005 - 15:51:50 CST)
Potential energies in TCL interface Eric Cyr (Mon Mar 07 2005 - 15:36:09 CST)
Re: question (fwd) Michael Grabe (Mon Mar 07 2005 - 15:30:48 CST)
Re: namd on Altix Gengbin Zheng (Mon Mar 07 2005 - 15:03:07 CST)
RE: namd on Altix Michel Espinoza-Fonseca (Mon Mar 07 2005 - 15:00:02 CST)
atom specification in smd/tclforces for amber topology/parameter based systems Jerry Ebalunode (Mon Mar 07 2005 - 14:50:20 CST)
Re: namd on Altix Gengbin Zheng (Mon Mar 07 2005 - 14:22:53 CST)
RE: namd on Altix Michel Espinoza-Fonseca (Mon Mar 07 2005 - 14:16:16 CST)
Re: namd on Altix Gengbin Zheng (Mon Mar 07 2005 - 13:39:49 CST)
RE: namd on Altix Michel Espinoza-Fonseca (Mon Mar 07 2005 - 13:37:11 CST)
Re: namd on Altix Gengbin Zheng (Mon Mar 07 2005 - 13:33:40 CST)
namd on Altix Michel Espinoza-Fonseca (Mon Mar 07 2005 - 13:14:07 CST)
Influence of PME grid size and cell basis vectors over simulation result debashis.sikdar_at_ndsu.edu (Mon Mar 07 2005 - 13:01:19 CST)
Re: clustermatic nodelist file Rene Salmon (Fri Mar 04 2005 - 14:53:47 CST)
Re: installing NAMD on opteron cluster with MPI Gengbin Zheng (Fri Mar 04 2005 - 01:00:59 CST)
Patch Gan, Yong $UMC-Student$ (Thu Mar 03 2005 - 17:28:35 CST)
installing NAMD on opteron cluster with MPI Lina M Nilsson (Thu Mar 03 2005 - 16:06:13 CST)
Re: Not getting good speed up Mauricio Carrillo Tripp (Thu Mar 03 2005 - 13:44:55 CST)
Re: Not getting good speed up Gengbin Zheng (Thu Mar 03 2005 - 13:34:56 CST)
Re: Not getting good speed up Mauricio Carrillo Tripp (Thu Mar 03 2005 - 13:16:24 CST)
Pair interaction calculation for large number different pairs Harindar Keer (Wed Mar 02 2005 - 22:26:06 CST)
Re: Not getting good speed up Gengbin Zheng (Wed Mar 02 2005 - 21:42:39 CST)
Re: clustermatic nodelist file Gengbin Zheng (Wed Mar 02 2005 - 21:29:40 CST)
Re: Problems with the nodelist file ! Gengbin Zheng (Wed Mar 02 2005 - 21:15:41 CST)
Re: Problems with the nodelist file ! Edward Patrick Obrien (Wed Mar 02 2005 - 17:22:02 CST)
Problems with the nodelist file ! Parag Adhangale (Wed Mar 02 2005 - 16:38:13 CST)
Not getting good speed up Mauricio Carrillo Tripp (Wed Mar 02 2005 - 16:37:18 CST)
Re: NAMD attempting to read FFTW Shirley Hui (Wed Mar 02 2005 - 13:27:57 CST)
Re: NAMD attempting to read FFTW Brian Bennion (Wed Mar 02 2005 - 13:22:00 CST)
difference between two kinds of dimers olivier Walker (Wed Mar 02 2005 - 06:19:56 CST)
NAMD attempting to read FFTW Shirley Hui (Tue Mar 01 2005 - 13:59:21 CST)
Re: Hexagonal cell and PME grid. Jan Saam (Tue Mar 01 2005 - 05:34:17 CST)
NAMD_utilities Wei Chen (Tue Mar 01 2005 - 12:43:56 CST)
capping using Amber FF Hui-Hsu Tsai (Tue Mar 01 2005 - 12:32:24 CST)
Hexagonal cell and PME grid. Nicholas M Glykos (Tue Mar 01 2005 - 05:17:44 CST)
Re: Kinetic energy Marc Q. Ma (Fri Feb 25 2005 - 15:24:33 CST)
Kinetic energy Gan, Yong $UMC-Student$ (Fri Feb 25 2005 - 12:55:09 CST)
PMEGridSize Naveen Michaud-Agrawal (Thu Feb 24 2005 - 16:02:10 CST)
Re: PMEGridSize Marc Q. Ma (Thu Feb 24 2005 - 16:52:19 CST)
Amber and SHAKE algorimth Marcela P.Aliste (Thu Feb 24 2005 - 16:14:26 CST)
PMEGridSize Glenn Johnson (Thu Feb 24 2005 - 15:25:03 CST)
NMAD job abnormally killed with PBS Nicolas Sapay (Thu Feb 24 2005 - 12:09:19 CST)
warning on unique coordinates Stern, Julie (Wed Feb 23 2005 - 15:07:19 CST)
cellOrigin Marc Q. Ma (Tue Feb 22 2005 - 14:06:04 CST)
Pressure tensor and periodic boundary condition Gan, Yong $UMC-Student$ (Mon Feb 21 2005 - 21:40:58 CST)
Re: writeback periodic cell info in dcd output Jérôme Hénin (Mon Feb 21 2005 - 17:49:55 CST)
writeback periodic cell info in dcd output Marc Q. Ma (Mon Feb 21 2005 - 16:16:01 CST)
Lipid membrane simulation by NAMD Gan, Yong $UMC-Student$ (Fri Feb 18 2005 - 17:40:25 CST)
FATAL ERROR: Stale NFS file handle Edward Patrick Obrien (Fri Feb 18 2005 - 15:51:53 CST)
Re: alchemify FEP Wei Chen (Fri Feb 18 2005 - 12:54:44 CST)
Re: alchemify FEP Michael Grabe (Fri Feb 18 2005 - 01:26:17 CST)
mmtools Swarna Patra (Thu Feb 17 2005 - 23:32:55 CST)
energy Swarna Patra (Thu Feb 17 2005 - 16:58:36 CST)
Re: using namd to compute energies Jan Saam (Thu Feb 17 2005 - 15:44:57 CST)
Re: alchemify FEP Jérôme Hénin (Thu Feb 17 2005 - 15:04:18 CST)
alchemify FEP Wei Chen (Thu Feb 17 2005 - 13:14:20 CST)
constraining center of mass-constrained MD Vani Krishna (Thu Feb 17 2005 - 02:51:12 CST)
rotation constraint angular velocity Xiongce Zhao (Wed Feb 16 2005 - 10:32:14 CST)
RE: using namd to compute energies Wolbach, Jeffrey P $WOLBACH$ (Wed Feb 16 2005 - 07:30:41 CST)
1 D Periodic Boundary Xiongce Zhao (Tue Feb 15 2005 - 14:43:42 CST)
Re: using namd to compute energies Shirley Hui (Tue Feb 15 2005 - 14:24:46 CST)
using namd to compute energies Leandro Martinez (Tue Feb 15 2005 - 13:24:20 CST)
how to image molecules back into a PBC box Xiongce Zhao (Tue Feb 15 2005 - 09:08:21 CST)
RE: conditional statements in conf files Glenn Johnson (Mon Feb 14 2005 - 15:49:46 CST)
conditional statements in conf files Glenn Johnson (Mon Feb 14 2005 - 14:59:02 CST)
question on tcl script for rmsd calculation Olya Kravchenko (Mon Feb 14 2005 - 13:44:41 CST)
Complementary programs for NAMD Glenn Johnson (Mon Feb 14 2005 - 13:32:24 CST)
Re: Analysis of NAMD output with CHARMM \ (Mon Feb 14 2005 - 12:15:58 CST)
Re: Analysis of NAMD output with CHARMM Nathalie Reuter (Mon Feb 14 2005 - 09:51:07 CST)
Re: Analysis of NAMD output with CHARMM Nathalie Reuter (Mon Feb 14 2005 - 07:21:56 CST)
Re: Analysis of NAMD output with CHARMM Leyla Celik (Mon Feb 14 2005 - 09:44:53 CST)
Re: Analysis of NAMD output with CHARMM Gianluca Interlandi (Mon Feb 14 2005 - 08:07:49 CST)
Re: Analysis of NAMD output with CHARMM Leyla Celik (Mon Feb 14 2005 - 07:48:28 CST)
Analysis of NAMD output with CHARMM Leyla Celik (Mon Feb 14 2005 - 02:47:42 CST)
Unprotonating GLU, ASP Gaurav Sharma (Sun Feb 13 2005 - 18:14:31 CST)
psfgen error "Missing atom for conformation definition" bora erdemli (Sat Feb 12 2005 - 06:16:30 CST)
RE: namdplot not working Glenn Johnson (Fri Feb 11 2005 - 17:30:33 CST)
Re: namdplot not working vivek sharma (Fri Feb 11 2005 - 16:04:06 CST)
namdplot not working Glenn Johnson (Fri Feb 11 2005 - 14:39:45 CST)
Re: Re: Complie NAMD on Suse Linux Gengbin Zheng (Wed Feb 09 2005 - 17:53:10 CST)
Re: Complie NAMD on Suse Linux Jason Lee (Wed Feb 09 2005 - 16:51:28 CST)
namd2.5 on linux-cluster Alexe Bojovschi (Wed Feb 09 2005 - 04:41:43 CST)
XPLOR topology to CHARMM bora erdemli (Wed Feb 09 2005 - 03:01:15 CST)
Re: Protein moving out of PBC water box Jérôme Hénin (Tue Feb 08 2005 - 17:08:05 CST)
Protein moving out of PBC water box Leyla Celik (Tue Feb 08 2005 - 15:23:31 CST)
Question about Constraint failure in RATTLE algorithm for atom Hrant Gharabekyan (Tue Feb 08 2005 - 05:06:46 CST)
PMF Calculation matteo (Tue Feb 08 2005 - 04:38:20 CST)
run NPT equilibration Wen Li (Tue Feb 08 2005 - 11:30:07 CST)
NAMD crashes with LES option ON Karunesh Arora (Mon Feb 07 2005 - 14:07:18 CST)
Re: Complie NAMD on Suse Linux Gengbin Zheng (Mon Feb 07 2005 - 13:02:32 CST)
Re: question on running NAMD2 using Amber files Wen Li (Mon Feb 07 2005 - 12:15:41 CST)
Re: Complie NAMD on Suse Linux Brian Bennion (Mon Feb 07 2005 - 11:56:01 CST)
Re: gradient nan Brian Bennion (Mon Feb 07 2005 - 11:33:00 CST)
question on running NAMD2 using Amber files (fwd) Wen Li (Mon Feb 07 2005 - 10:25:32 CST)
Complie NAMD on Suse Linux Jason Lee (Mon Feb 07 2005 - 09:32:02 CST)
question on running NAMD2 using Amber files Wen Li (Mon Feb 07 2005 - 08:40:56 CST)
gradient nan Hemant Kushwaha (Mon Feb 07 2005 - 00:17:04 CST)
SMD by pulling two groups apart Ekta Khurana (Fri Feb 04 2005 - 16:27:06 CST)
Re: parameters for NAD,NAG,NAP Aaron Oakley (Thu Feb 03 2005 - 21:14:14 CST)
Re: area of a hydrophobic patch Aaron Oakley (Thu Feb 03 2005 - 16:35:56 CST)
area of a hydrophobic patch Narender Singh Maan (Wed Feb 02 2005 - 23:23:24 CST)
Complie NAMD on Suse Linux cunning cunning (Thu Feb 03 2005 - 08:18:46 CST)
parameters for NAD,NAG,NAP bora erdemli (Thu Feb 03 2005 - 03:39:00 CST)
Re: FEP Jérôme Hénin (Tue Feb 01 2005 - 13:14:05 CST)
FEP Wei Chen (Tue Feb 01 2005 - 11:15:24 CST)
force constraints Swarna Patra (Mon Jan 31 2005 - 19:49:07 CST)
autocorrelation analysis in timeseries Aaron Oakley (Mon Jan 31 2005 - 16:21:56 CST)
Hi, call NAMD from C Jerry Xu (Mon Jan 31 2005 - 09:28:44 CST)
simulated annealing step size Peter Bazeley (Fri Jan 28 2005 - 20:23:19 CST)
electrostatics under spherical harmonic conditions Giovanni Bellesia (Fri Jan 28 2005 - 13:59:57 CST)
tRNA simulation psf file generation explicit solvent and ions Tom Caulfield (Thu Jan 27 2005 - 02:29:47 CST)
SMD Swarna Patra (Wed Jan 26 2005 - 20:52:27 CST)
Qestions about NPT simulations. Lv Shouqin (Wed Jan 26 2005 - 07:29:47 CST)
Catdcd Naveen Michaud-Agrawal (Wed Jan 26 2005 - 08:44:45 CST)
Re: qsub Brian Bennion (Tue Jan 25 2005 - 10:11:54 CST)
qsub Swarna Patra (Mon Jan 24 2005 - 23:02:37 CST)
Re: NAMD on IBM cluster AIX-RS6000 Gengbin Zheng (Mon Jan 24 2005 - 15:17:14 CST)
Re: NAMD on IBM cluster AIX-RS6000 Harindar Keer (Mon Jan 24 2005 - 14:38:47 CST)
BUG ALERT: Mother atom with hydrogenGroupSize of 0! Xiaoqing Wang (Mon Jan 24 2005 - 01:26:21 CST)
Re: NAMD on IBM cluster AIX-RS6000 Gengbin Zheng (Fri Jan 21 2005 - 22:06:32 CST)
NAMD on IBM cluster AIX-RS6000 Harindar Keer (Fri Jan 21 2005 - 18:46:29 CST)
Question about pair interaction feature Eric Peterson (Thu Jan 20 2005 - 17:43:49 CST)
resetting restartfreq parameter Peter Bazeley (Thu Jan 20 2005 - 17:17:16 CST)
Rotating a structure about an atom Pijush Ghosh (Wed Jan 19 2005 - 12:47:56 CST)
Re: DOWSER Charles Danko (Wed Jan 19 2005 - 09:01:18 CST)
DOWSER Charles Danko (Tue Jan 18 2005 - 16:20:06 CST)
Re: hydrogens collapsing lc_at_chem.au.dk (Tue Jan 18 2005 - 12:12:04 CST)
Re: segmentation violation!! Robert Brunner (Tue Jan 18 2005 - 11:05:00 CST)
Re: segmentation violation!! Brian Bennion (Tue Jan 18 2005 - 10:34:47 CST)
Re: about rigid bonds Brian Bennion (Tue Jan 18 2005 - 10:29:19 CST)
Re: hydrogens collapsing Brian Bennion (Tue Jan 18 2005 - 10:23:40 CST)
hydrogens collapsing lc_at_chem.au.dk (Tue Jan 18 2005 - 08:46:23 CST)
Obtain message from MD Xiaoqing Wang (Tue Jan 18 2005 - 01:30:23 CST)
smd and loadforces Leandro Martinez (Mon Jan 17 2005 - 11:06:50 CST)
about rigid bonds mashaojie163 (Mon Jan 17 2005 - 07:24:39 CST)
Re: pmf Swarna Patra (Sun Jan 16 2005 - 20:17:55 CST)
Re: segmentation violation!! bora erdemli (Sun Jan 16 2005 - 03:59:08 CST)
Re: Compiling the NAMD on HPUX-ia64 system Error! Gengbin Zheng (Sat Jan 15 2005 - 11:03:51 CST)
Compiling the NAMD on HPUX-ia64 system Error! Îº¿ (Sat Jan 15 2005 - 08:35:00 CST)
Re: charm++ compile problem on x86_64 Steven A. DuChene (Fri Jan 14 2005 - 17:09:42 CST)
Re: charm++ compile problem on x86_64 Gengbin Zheng (Fri Jan 14 2005 - 15:32:10 CST)
charm++ compile problem on x86_64 Steven A. DuChene (Fri Jan 14 2005 - 15:24:02 CST)
Re: scyld no longer a supported option for building charm++ ? Gengbin Zheng (Fri Jan 14 2005 - 14:43:56 CST)
scyld no longer a supported option for building charm++ ? Steven A. DuChene (Fri Jan 14 2005 - 14:30:10 CST)
Re: extracting time from DCDs Brian Bennion (Fri Jan 14 2005 - 14:10:02 CST)
Re: How to Compile NAMD on HPUX-ia64 system~ Gengbin Zheng (Fri Jan 14 2005 - 12:36:56 CST)
Re: segmentation violation!! Brian Bennion (Fri Jan 14 2005 - 10:20:49 CST)
last call for early registrations for "Horizons2005" Vlad Cojocaru (Fri Jan 14 2005 - 07:19:00 CST)
How to Compile NAMD on HPUX-ia64 system~ Îº¿ (Fri Jan 14 2005 - 04:56:14 CST)
Re: segmentation violation!! bora erdemli (Fri Jan 14 2005 - 03:06:55 CST)
extracting time from DCDs nordgren_at_sas.upenn.edu (Thu Jan 13 2005 - 19:54:30 CST)
Re: success with opteron myrinet mpi etc Damon Smith (Thu Jan 13 2005 - 18:24:24 CST)
rattle errors. Brian Bennion (Thu Jan 13 2005 - 10:56:25 CST)
Re: segmentation violation!! Brian Bennion (Thu Jan 13 2005 - 10:48:11 CST)
Re: success with opteron myrinet mpi etc Brian Bennion (Thu Jan 13 2005 - 10:16:54 CST)
segmentation violation!! bora erdemli (Thu Jan 13 2005 - 02:15:19 CST)
success with opteron myrinet mpi etc Damon Smith (Thu Jan 13 2005 - 01:28:30 CST)
Re: multiple jobs on a cluster Brian Bennion (Wed Jan 12 2005 - 17:15:05 CST)
Electric Field Swarna Patra (Wed Jan 12 2005 - 16:57:02 CST)
multiple jobs on a cluster Cheri M Turman (Wed Jan 12 2005 - 15:55:42 CST)
constraint failure Xiaoqing Wang (Tue Jan 11 2005 - 21:07:08 CST)
Re: pmf Edward Patrick Obrien (Tue Jan 11 2005 - 19:24:04 CST)
pmf Swarna Patra (Tue Jan 11 2005 - 18:55:44 CST)
RE: equilibrated the system Luis Rosales (Tue Jan 11 2005 - 17:49:16 CST)
Re: equilibrated the system apw397_at_soton.ac.uk (Tue Jan 11 2005 - 09:58:27 CST)
equilibrated the system Xiaoqing Wang (Tue Jan 11 2005 - 08:43:17 CST)
AMD64 or PIV Prescott ... Slawomir Orlowski (Tue Jan 11 2005 - 05:52:48 CST)
namdstats lc_at_chem.au.dk (Tue Jan 11 2005 - 01:54:54 CST)
Re: thermodynamic integration and NAMD: soft-core or "separation-shifted" vdw potentials Jérôme Hénin (Mon Jan 10 2005 - 15:57:01 CST)
thermodynamic integration and NAMD: soft-core or "separation-shifted" vdw potentials Philip Fowler (Mon Jan 10 2005 - 11:12:41 CST)
Re: Compiling Gengbin Zheng (Sun Jan 09 2005 - 11:00:43 CST)
Re: Error in when using charmrun Gengbin Zheng (Sat Jan 08 2005 - 22:50:24 CST)
Re: Error in when using charmrun Eric Peterson (Sat Jan 08 2005 - 22:24:11 CST)
Re: Error in when using charmrun Gengbin Zheng (Sat Jan 08 2005 - 21:20:08 CST)
Re: Error in when using charmrun Eric Peterson (Sat Jan 08 2005 - 21:16:47 CST)
Re: Error in when using charmrun Gengbin Zheng (Sat Jan 08 2005 - 21:00:03 CST)
Error in when using charmrun Eric Peterson (Sat Jan 08 2005 - 20:39:45 CST)
Re: restarting a simulation accurately Charles Danko (Sat Jan 08 2005 - 15:06:24 CST)
Harmonic restraints for moving residue positions?? Charles Danko (Sat Jan 08 2005 - 15:03:50 CST)
restarting a simulation accurately Stern, Julie (Sat Jan 08 2005 - 14:32:41 CST)
tclForces - addforce to group of atoms Jan Saam (Fri Jan 07 2005 - 17:27:40 CST)
tclForces - addforce to group of atoms Jan Saam (Fri Jan 07 2005 - 17:01:13 CST)
namd on lemieux Stern, Julie (Fri Jan 07 2005 - 11:51:53 CST)
Re: parameters for NVT ensemble Jérôme Hénin (Fri Jan 07 2005 - 07:58:12 CST)
parameters for NVT ensemble lc_at_chem.au.dk (Fri Jan 07 2005 - 04:51:07 CST)
Re: Compiling Ruxandra Dima (Thu Jan 06 2005 - 20:13:50 CST)
Compiling Damon Smith (Thu Jan 06 2005 - 19:02:04 CST)
tcoupling coefficient Peter Bazeley (Wed Jan 05 2005 - 06:31:07 CST)
Re: increase in energy over time Edward Patrick Obrien (Tue Jan 04 2005 - 11:01:53 CST)
Re: Bug alert!!! Brian Bennion (Tue Jan 04 2005 - 10:46:40 CST)
Re: increase in energy over time Peter Bazeley (Mon Jan 03 2005 - 21:19:33 CST)
Re: Bug alert!!! bora erdemli (Tue Jan 04 2005 - 01:13:37 CST)
Re: increase in energy over time Edward Patrick Obrien (Mon Jan 03 2005 - 18:29:46 CST)
increase in energy over time Peter Bazeley (Mon Jan 03 2005 - 17:27:45 CST)
Re: About charm++/namd on AMD64 cluster Gengbin Zheng (Mon Jan 03 2005 - 14:46:58 CST)
Re: About charm++/namd on AMD64 cluster q=F5=D0=A1=C7=E5?= (Mon Jan 03 2005 - 04:15:19 CST)
prmtop reading error Stern, Julie (Sun Jan 02 2005 - 15:35:42 CST)
Re: clustermatic 4 and 5 Namd/charm John Saeger (Sun Jan 02 2005 - 14:18:31 CST)
Re: About charm++/namd on AMD64 cluster Gengbin Zheng (Sun Jan 02 2005 - 02:50:56 CST)
About charm++/namd on AMD64 cluster q=F5=D0=A1=C7=E5?= (Sun Jan 02 2005 - 02:01:32 CST)
Re: clustermatic 4 and 5 Namd/charm Gengbin Zheng (Sat Jan 01 2005 - 15:15:45 CST)
Re: clustermatic 4 and 5 Namd/charm Rene Salmon (Sat Jan 01 2005 - 14:56:56 CST)
Re: problems on Fedora Core 3 lc_at_chem.au.dk (Fri Dec 31 2004 - 13:10:04 CST)
Re: clustermatic 4 and 5 Namd/charm Gengbin Zheng (Fri Dec 31 2004 - 12:10:17 CST)
Re: clustermatic 4 and 5 Namd/charm Rene Salmon (Fri Dec 31 2004 - 10:08:21 CST)
Re: mpi opteron myrinet Gengbin Zheng (Fri Dec 31 2004 - 00:08:20 CST)
Re: mpi opteron myrinet Damon Smith (Thu Dec 30 2004 - 23:51:01 CST)
Re: mpi opteron myrinet Gengbin Zheng (Thu Dec 30 2004 - 22:50:45 CST)
mpi opteron myrinet Damon Smith (Thu Dec 30 2004 - 22:23:09 CST)
Re: clustermatic 4 and 5 Namd/charm Gengbin Zheng (Thu Dec 30 2004 - 18:52:47 CST)
clustermatic 4 and 5 Namd/charm Rene Salmon (Thu Dec 30 2004 - 17:49:47 CST)
Re: problems on Fedora Core 3 Gengbin Zheng (Thu Dec 30 2004 - 15:23:30 CST)
Re: problems on Fedora Core 3 John Saeger (Thu Dec 30 2004 - 13:20:16 CST)
problems on Fedora Core 3 Ruxandra Dima (Tue Dec 28 2004 - 22:48:43 CST)
Residence time Uday Chippada (Tue Dec 28 2004 - 10:58:41 CST)
about MCTI output mashaojie163 (Mon Dec 27 2004 - 01:29:36 CST)
Bug alert!!! bora erdemli (Fri Dec 24 2004 - 01:06:32 CST)
restart files after minimization? Peter Bazeley (Thu Dec 23 2004 - 18:52:53 CST)
interaction energy vivek sharma (Thu Dec 23 2004 - 05:36:35 CST)
Re: FATAL ERROR: Asymmetric water molecule ? bora erdemli (Wed Dec 22 2004 - 02:26:19 CST)
FATAL ERROR: Asymmetric water molecule ? Gaurav Sharma (Tue Dec 21 2004 - 14:58:11 CST)
Re: Failed to set coordinate for atom errors! Shirley Hui (Mon Dec 20 2004 - 21:39:30 CST)
RE: Failed to set coordinate for atom errors! Blake Charlebois (Mon Dec 20 2004 - 19:27:51 CST)
Failed to set coordinate for atom errors! Shirley Hui (Mon Dec 20 2004 - 16:32:10 CST)
Re: How to use restrin command in NAMD configuration file Charles Danko (Mon Dec 20 2004 - 10:40:30 CST)
RE: What the result difference between AMD and Intel CPUS? Blake Charlebois (Mon Dec 20 2004 - 09:43:57 CST)
How to use restrin command in NAMD configuration file debashis.sikdar_at_ndsu.edu (Mon Dec 20 2004 - 09:35:28 CST)
binding free energy bora erdemli (Mon Dec 20 2004 - 08:39:06 CST)
What the result difference between AMD and Intel CPUS? Îº¿ (Mon Dec 20 2004 - 08:30:14 CST)
how to use restrain command in configuration file in NAMD. debashis.sikdar_at_ndsu.edu (Fri Dec 17 2004 - 23:10:34 CST)
Re: resolved: BUG ALERT: Mother atom with hydrogenGroupSize of 0! Vani Krishna (Fri Dec 17 2004 - 18:47:21 CST)
Re: charmm and dihedral multiplicity Vani Krishna (Fri Dec 17 2004 - 18:46:04 CST)
BUG ALERT: Mother atom with hydrogenGroupSize of 0! Vani Krishna (Fri Dec 17 2004 - 11:39:30 CST)
Re: charmm and dihedral multiplicity Brian Bennion (Fri Dec 17 2004 - 10:55:34 CST)
Re: NamdCompile Problem Brian Bennion (Thu Dec 16 2004 - 14:39:33 CST)
Re: NamdCompile Problem Gengbin Zheng (Thu Dec 16 2004 - 13:19:57 CST)
charmm and dihedral multiplicity mdcooper (Thu Dec 16 2004 - 13:19:02 CST)
Re: vmd-l: Autoionize plugin problem John Stone (Thu Dec 16 2004 - 11:30:21 CST)
NamdCompile Problem HUSSER Jacky 113956 (Thu Dec 16 2004 - 05:17:41 CST)
Re: xsc information in the dcd file? Gianluca Interlandi (Thu Dec 16 2004 - 11:25:50 CST)
How to chech the harmonic constraint work normally~ Îº¿ (Thu Dec 16 2004 - 03:21:17 CST)
statistical test Aaron Oakley (Wed Dec 15 2004 - 23:17:57 CST)
Re: xsc information in the dcd file? Jérôme Hénin (Wed Dec 15 2004 - 12:22:39 CST)
How to move COM during minimization? Shahid Qamar (Wed Dec 15 2004 - 12:03:12 CST)
Re: turning off fixed atoms in the middle of simulation Jim Phillips (Wed Dec 15 2004 - 11:15:47 CST)
xsc information in the dcd file? Gianluca Interlandi (Wed Dec 15 2004 - 10:57:26 CST)
turning off fixed atoms in the middle of simulation Vani Krishna (Wed Dec 15 2004 - 10:42:17 CST)
Re: fatal error vivek sharma (Wed Dec 15 2004 - 04:11:45 CST)
Re: How I can run two simulations one after an other Michael Grabe (Tue Dec 14 2004 - 15:15:36 CST)
How I can run two simulations one after an other Shahid Qamar (Tue Dec 14 2004 - 14:30:08 CST)
Re: high (or low) pressure readings Charles Danko (Tue Dec 14 2004 - 13:31:21 CST)
Re: Infiniband and PME gridsize Gengbin Zheng (Tue Dec 14 2004 - 13:05:45 CST)
Re: Infiniband and PME gridsize Gianluca Interlandi (Tue Dec 14 2004 - 12:54:55 CST)
Autoionize plugin problem Gaurav Sharma (Tue Dec 14 2004 - 12:52:03 CST)
Re: Infiniband and PME gridsize Gengbin Zheng (Tue Dec 14 2004 - 12:16:55 CST)
Re: fatal error Gengbin Zheng (Tue Dec 14 2004 - 12:14:28 CST)
Re: Infiniband and PME gridsize Brian Bennion (Tue Dec 14 2004 - 12:06:36 CST)
Re: fatal error Brian Bennion (Tue Dec 14 2004 - 12:01:25 CST)
Re: high (or low) pressure readings Brian Bennion (Tue Dec 14 2004 - 11:45:13 CST)
binding energy bora erdemli (Tue Dec 14 2004 - 07:38:05 CST)
Infiniband and PME gridsize Gianluca Interlandi (Tue Dec 14 2004 - 06:06:03 CST)
fatal error vivek sharma (Tue Dec 14 2004 - 00:49:59 CST)
Re: high (or low) pressure readings nordgren_at_sas.upenn.edu (Mon Dec 13 2004 - 18:30:51 CST)
Re: more than 99999 atoms in PDB files LEWYN LI (Mon Dec 13 2004 - 16:53:26 CST)
more than 99999 atoms in PDB files Gilbert G.Feng (Mon Dec 13 2004 - 15:30:55 CST)
RE: high (or low) pressure readings carlos n. a. (Mon Dec 13 2004 - 13:36:10 CST)
Re: high (or low) pressure readings Brian Bennion (Mon Dec 13 2004 - 11:13:42 CST)
high (or low) pressure readings Charles Danko (Mon Dec 13 2004 - 09:42:52 CST)
saving forces using loadforces Ragan Robertson (Sat Dec 11 2004 - 15:39:42 CST)
Re: System minimization: fail after 199 steps Charles Danko (Fri Dec 10 2004 - 13:32:28 CST)
Re: Building NAMD with Portland's C++ Comipler Suxing Hu (Thu Dec 09 2004 - 21:08:54 CST)
Re: System minimization: fail after 199 steps Charles Danko (Thu Dec 09 2004 - 16:01:26 CST)
Re: Building NAMD with Portland's C++ Comipler Gengbin Zheng (Thu Dec 09 2004 - 12:47:54 CST)
Building NAMD with Portland's C++ Comipler Suxing Hu (Thu Dec 09 2004 - 12:29:57 CST)
Re: System minimization: fail after 199 steps Brian Bennion (Thu Dec 09 2004 - 12:19:20 CST)
Re: System minimization: fail after 199 steps Charles Danko (Thu Dec 09 2004 - 11:20:26 CST)
Re: namdplot LEWYN LI (Thu Dec 09 2004 - 11:17:33 CST)
Re: namdplot vivek sharma (Thu Dec 09 2004 - 10:38:14 CST)
RE: namdplot Blake Charlebois (Thu Dec 09 2004 - 07:15:41 CST)
Re: namdplot nordgren_at_sas.upenn.edu (Thu Dec 09 2004 - 05:59:11 CST)
namdplot vivek sharma (Thu Dec 09 2004 - 02:13:26 CST)
RE: Periodic cell size Blake Charlebois (Wed Dec 08 2004 - 23:54:04 CST)
Re: Vaccum simulation nordgren_at_sas.upenn.edu (Wed Dec 08 2004 - 15:57:10 CST)
Vaccum simulation Narender Singh (Wed Dec 08 2004 - 10:57:48 CST)
Re: Periodic cell size Brian Bennion (Wed Dec 08 2004 - 11:43:02 CST)
Re: Periodic cell size Edward Patrick Obrien (Wed Dec 08 2004 - 10:54:37 CST)
Periodic cell size Suxing Hu (Wed Dec 08 2004 - 10:06:24 CST)
RE: Variation of results in iterations Blake Charlebois (Tue Dec 07 2004 - 20:12:18 CST)
Re: Variation of results in iterations Edward Patrick Obrien (Mon Dec 06 2004 - 22:13:26 CST)
Re: Variation of results in iterations Pijush Ghosh (Mon Dec 06 2004 - 22:00:21 CST)
Re: Variation of results in iterations Robert Brunner (Mon Dec 06 2004 - 21:15:00 CST)
Re: Variation of results in iterations Edward Patrick Obrien (Mon Dec 06 2004 - 19:37:43 CST)
Re: Variation of results in iterations Jérôme Hénin (Mon Dec 06 2004 - 19:01:32 CST)
Re: Variation of results in iterations Edward Patrick Obrien (Mon Dec 06 2004 - 17:44:43 CST)
Variation of results in iterations Pijush Ghosh (Mon Dec 06 2004 - 17:25:43 CST)
Compiling charm on a opteron cluster Gianluca Interlandi (Fri Dec 03 2004 - 15:11:18 CST)
Compiling charm on a opteron cluster Gianluca Interlandi (Fri Dec 03 2004 - 15:03:11 CST)
constant velocity smd with distance restraints Gilbert G.Feng (Fri Dec 03 2004 - 14:22:50 CST)
Re: NAMD on Xeon EM64T Chris Samuel (Thu Dec 02 2004 - 22:18:39 CST)
Re: PME ERROR Brian Bennion (Wed Dec 01 2004 - 12:02:55 CST)
PME ERROR Eunice Ramirez Melendez (Wed Dec 01 2004 - 01:52:13 CST)
charmm->gromacs->charmm force field conversion Enrico Piccinini (Wed Dec 01 2004 - 09:36:06 CST)
NAMD on Xeon EM64T Alberto Santana (Wed Dec 01 2004 - 06:42:05 CST)
Charmm27 Xplor format Peter Jones (Tue Nov 30 2004 - 03:56:22 CST)
Re: GROMACS to CHARMM Alessandro Pedretti (Tue Nov 30 2004 - 01:47:01 CST)
How to treat the terminal residue psfgen in NAMD~ Îº¿ (Mon Nov 29 2004 - 20:11:37 CST)
Re: psfgen Brian Bennion (Mon Nov 29 2004 - 17:01:33 CST)
GROMACS to CHARMM chandran karunakaran (Mon Nov 29 2004 - 11:14:48 CST)
Re: spherical boundary condition griadi_at_utalca.cl (Mon Nov 29 2004 - 02:29:51 CST)
psfgen Hemant Kushwaha (Mon Nov 29 2004 - 01:16:44 CST)
covalent bonds across periodic boundaries Philip Blood (Sat Nov 27 2004 - 11:39:33 CST)
A confused question on amber param and in charmm form~ Îº¿ (Fri Nov 26 2004 - 07:41:55 CST)
Re: Question:about harmonic restraint decrease! Jérôme Hénin (Fri Nov 26 2004 - 03:22:51 CST)
Question:about equilibration~ Îº¿ (Thu Nov 25 2004 - 22:05:59 CST)
Question:about harmonic restraint decrease! Îº¿ (Wed Nov 24 2004 - 22:13:49 CST)
Re: Chloroform Solvent Box alessandro.pedretti_at_unimi.it (Tue Nov 23 2004 - 14:19:11 CST)
Re: Writing pdb file.. easier way? griadi_at_utalca.cl (Tue Nov 23 2004 - 12:44:03 CST)
Re: System minimization: fail after 199 steps Brian Bennion (Tue Nov 23 2004 - 12:46:15 CST)
Chloroform Solvent Box Harindar Keer (Tue Nov 23 2004 - 11:17:45 CST)
Re: rmsd calculation Charles Danko (Tue Nov 23 2004 - 09:50:49 CST)
spherical boundary condition Giovanni Bellesia (Tue Nov 23 2004 - 07:35:17 CST)
rmsd calculation Francesco Iori (Tue Nov 23 2004 - 06:56:32 CST)
essential dynamics analysis Armen Nalian (Mon Nov 22 2004 - 15:58:10 CST)
NAMD at Data Star SDSC Shahid Qamar (Mon Nov 22 2004 - 15:19:11 CST)
Re: Working on cluster to do umbrella sampling Michael Grabe (Mon Nov 22 2004 - 13:47:14 CST)
Pair interaction, PBC included? Edward Patrick Obrien (Sat Nov 20 2004 - 14:22:39 CST)
Job is terminated in the middle Shahid Qamar (Fri Nov 19 2004 - 11:23:15 CST)
Re: NAMD Source Robert Brunner (Fri Nov 19 2004 - 10:54:16 CST)
Rif: Re: Rif: Re: Rif: Re: Rif: Re: linux cluster trouble max (Fri Nov 19 2004 - 03:47:01 CST)
Re: Rif: Re: Rif: Re: Rif: Re: Rif: Re: linux cluster trouble Gengbin Zheng (Fri Nov 19 2004 - 09:18:28 CST)
Working on cluster to do umbrella sampling Enrico Piccinini (Fri Nov 19 2004 - 04:39:13 CST)
NAMD Source Hassan K. Al-Ali Merheby (Fri Nov 19 2004 - 02:06:44 CST)
Minimizing and Equilibrating Shirley Hui (Thu Nov 18 2004 - 19:05:25 CST)
Re: Writing pdb file.. easier way? Jérôme Hénin (Thu Nov 18 2004 - 17:28:36 CST)
Re: Writing pdb file.. easier way? Uday Chippada (Thu Nov 18 2004 - 17:19:14 CST)
Re: Writing pdb file.. easier way? Neema Salimi (Thu Nov 18 2004 - 16:54:58 CST)
Re: Writing pdb file.. easier way? LEWYN LI (Thu Nov 18 2004 - 16:29:36 CST)
Writing pdb file.. easier way? Uday Chippada (Thu Nov 18 2004 - 15:58:20 CST)
Re: Move molecule Uday Chippada (Thu Nov 18 2004 - 14:07:50 CST)
Re: Rif: Re: Rif: Re: Rif: Re: linux cluster trouble Gengbin Zheng (Thu Nov 18 2004 - 13:20:46 CST)
Re: Rif: Re: Rif: Re: Rif: Re: linux cluster trouble Gengbin Zheng (Thu Nov 18 2004 - 13:01:25 CST)
Re: Move molecule Edward Patrick Obrien (Thu Nov 18 2004 - 12:39:00 CST)
Re: Rif: Re: Rif: Re: Rif: Re: linux cluster trouble Brian Bennion (Thu Nov 18 2004 - 10:56:17 CST)
Move molecule Uday Chippada (Thu Nov 18 2004 - 10:18:36 CST)
How to make a surface Shahid Qamar (Wed Nov 17 2004 - 14:08:06 CST)
RE: Implicit water dielectric constant. Blake Charlebois (Tue Nov 16 2004 - 15:06:50 CST)
Re: Layers LEWYN LI (Tue Nov 16 2004 - 13:38:13 CST)
linux cluster trouble max (Tue Nov 16 2004 - 04:44:36 CST)
Re: linux cluster trouble Brian Bennion (Tue Nov 16 2004 - 10:40:57 CST)
Layers Laura De Luca (Tue Nov 16 2004 - 10:00:07 CST)
Re: Generating topology file li (Tue Nov 16 2004 - 01:11:51 CST)
Re: gcc and G5 Xserves Charles McCallum (Mon Nov 15 2004 - 23:07:17 CST)
Re: System minimization: fail after 199 steps Charles Danko (Mon Nov 15 2004 - 11:10:40 CST)
Re: fatal error running namd Brian Bennion (Mon Nov 15 2004 - 10:52:34 CST)
fatal error running namd Enrico Piccinini (Mon Nov 15 2004 - 04:30:06 CST)
gcc and G5 Xserves Michael Grabe (Mon Nov 15 2004 - 02:06:03 CST)
Some question about Constraint~ Îº¿ (Sun Nov 14 2004 - 21:02:34 CST)
Re: Generating topology file li (Sun Nov 14 2004 - 02:45:43 CST)
A strange thing about psfgen~ Îº¿ (Sat Nov 13 2004 - 06:21:35 CST)
Clustermatic PCI IDs Peter Jones (Thu Nov 11 2004 - 22:54:37 CST)
Re: System minimization: fail after 199 steps Brian Bennion (Thu Nov 11 2004 - 10:18:49 CST)
Re: System minimization: fail after 199 steps Charles Danko (Thu Nov 11 2004 - 10:07:00 CST)
Re: Generating topology file li (Thu Nov 11 2004 - 04:03:37 CST)
Generating topology file ANDY NG (Thu Nov 11 2004 - 00:59:51 CST)
Berendsen or Langevin Temp control? Edward Patrick Obrien (Wed Nov 10 2004 - 15:54:07 CST)
Re: linux cluster trouble Brian Bennion (Wed Nov 10 2004 - 11:26:36 CST)
Implicit water dielectric constant. Ivan Vinogradov (Wed Nov 10 2004 - 10:16:57 CST)
Rif: Re: linux cluster trouble max (Wed Nov 10 2004 - 03:00:42 CST)
Re: System minimization: fail after 199 steps Brian Bennion (Tue Nov 09 2004 - 15:40:39 CST)
Re: System minimization: fail after 199 steps Charles Danko (Tue Nov 09 2004 - 12:24:00 CST)
Re: linux cluster trouble Mounir Tarek (Tue Nov 09 2004 - 08:43:03 CST)
Re: linux cluster trouble Gengbin Zheng (Tue Nov 09 2004 - 08:19:10 CST)
Re: linux cluster trouble Mounir Tarek (Tue Nov 09 2004 - 06:27:55 CST)
linux cluster trouble mpappala_at_unict.it (Tue Nov 09 2004 - 05:47:48 CST)
eigenvector projections Peter Jones (Mon Nov 08 2004 - 23:41:36 CST)
Re: How to make a negatively charged surface Charles Danko (Mon Nov 08 2004 - 15:26:53 CST)
How to make a negatively charged surface Shahid Qamar (Mon Nov 08 2004 - 14:25:30 CST)
xsc file reading and segmentation fault li (Sat Nov 06 2004 - 20:16:28 CST)
Constraint failure in RATTLE again li (Sat Nov 06 2004 - 20:13:26 CST)
Re: Solvent mixture Ahmet Bakan (Fri Nov 05 2004 - 17:02:06 CST)
Re: Solvent mixture Brian Bennion (Fri Nov 05 2004 - 16:53:11 CST)
Re: Solvent mixture Edward Patrick Obrien (Fri Nov 05 2004 - 16:43:21 CST)
Re: Solvent mixture Brian Bennion (Fri Nov 05 2004 - 15:40:47 CST)
Re: rmsd and simulation Charles McCallum (Fri Nov 05 2004 - 11:23:58 CST)
rmsd and simulation bora erdemli (Fri Nov 05 2004 - 03:24:59 CST)
loadtotalforces: 1000+ pN per atom! LEWYN LI (Thu Nov 04 2004 - 20:10:07 CST)
constant angle NPT simulation Joseph E. Curtis, Ph. D. (Thu Nov 04 2004 - 12:16:21 CST)
Re: Compiling NAMD on IA64 cluter li (Thu Nov 04 2004 - 05:48:16 CST)
Solvent mixture Josef Scheiber (Thu Nov 04 2004 - 02:29:17 CST)
Re: Sample Configuratiion files Cheri M Turman (Wed Nov 03 2004 - 19:47:25 CST)
Re: Sample Configuratiion files Charles Danko (Wed Nov 03 2004 - 15:50:49 CST)
Sample Configuratiion files Leandro Martinez (Wed Nov 03 2004 - 15:40:38 CST)
Sample Configuratiion files Raymond C. Fort Jr. (Wed Nov 03 2004 - 14:59:44 CST)
Re: System minimization: fail after 199 steps Brian Bennion (Wed Nov 03 2004 - 13:05:56 CST)
Re: System minimization: fail after 199 steps Charles Danko (Wed Nov 03 2004 - 11:53:06 CST)
Re: Re: Compiling NAMD on IA64 cluter Gengbin Zheng (Wed Nov 03 2004 - 11:24:27 CST)
Re: Compiling NAMD on IA64 cluter Brian Bennion (Wed Nov 03 2004 - 10:39:23 CST)
Re: How to decide the protonation of some residues?? Brian Bennion (Wed Nov 03 2004 - 10:35:07 CST)
Re: Edge Water in PBC Brian Bennion (Wed Nov 03 2004 - 10:32:58 CST)
How to decide the protonation of some residues?? mashaojie163 (Wed Nov 03 2004 - 07:05:19 CST)
Edge Water in PBC Cetin Baloglu (Wed Nov 03 2004 - 05:01:40 CST)
Re: Tcl dihedral restraints in CG minimisation Jérôme Hénin (Tue Nov 02 2004 - 18:24:07 CST)
Tcl dihedral restraints in CG minimisation Ben Roberts (Tue Nov 02 2004 - 17:01:28 CST)
Re: System minimization: fail after 199 steps \ (Tue Nov 02 2004 - 13:22:50 CST)
Re: System minimization: fail after 199 steps Brian Bennion (Tue Nov 02 2004 - 13:09:32 CST)
Re: [Periodic Boundary]: from charmm to namd Sascha Tayefeh (Tue Nov 02 2004 - 12:46:02 CST)
Re: [Periodic Boundary]: from charmm to namd Charles Danko (Tue Nov 02 2004 - 11:35:23 CST)
Re: System minimization: fail after 199 steps Charles Danko (Tue Nov 02 2004 - 11:20:21 CST)
TCBG "Hands-On" Workshop on Computational Biophysics in Boston, Dec. 5-9 David P. Brandon (Tue Nov 02 2004 - 10:16:21 CST)
Re: Fwd: PSFgen error Brian Bennion (Tue Nov 02 2004 - 10:14:50 CST)
[Periodic Boundary]: from charmm to namd Sascha Tayefeh (Tue Nov 02 2004 - 09:08:42 CST)
RE: HEM residue in NAMD Blake Charlebois (Tue Nov 02 2004 - 04:03:00 CST)
HEM residue in NAMD Peter Bazeley (Tue Nov 02 2004 - 02:23:50 CST)
Hessian mdcooper (Mon Nov 01 2004 - 18:08:24 CST)
Fwd: missing atom prob surendra negi (Mon Nov 01 2004 - 17:58:33 CST)
Fwd: PSFgen error surendra negi (Mon Nov 01 2004 - 17:58:12 CST)
Re: System minimization: fail after 199 steps Brian Bennion (Mon Nov 01 2004 - 17:56:32 CST)
System minimization: fail after 199 steps Charles Danko (Mon Nov 01 2004 - 16:30:12 CST)
RE: xplor to charmm EPF $Esben Peter Friis$ (Mon Nov 01 2004 - 15:21:08 CST)
BUG ALERT: Hydrogen group error caught in rattle1 li (Sun Oct 31 2004 - 05:44:31 CST)
Re: firsttimestep: simple question Brian Bennion (Fri Oct 29 2004 - 17:34:53 CDT)
firsttimestep: simple question Sascha Tayefeh (Fri Oct 29 2004 - 16:16:56 CDT)
Re: BOND CP2 - CT2 IN PARAMETER FILES Brian Bennion (Fri Oct 29 2004 - 11:32:18 CDT)
RE: How do you specify which coordinates are to be fixed? Luis Rosales (Thu Oct 28 2004 - 18:32:28 CDT)
Re: How do you specify which coordinates are to be fixed? Brian Bennion (Thu Oct 28 2004 - 18:08:26 CDT)
RE: How do you specify which coordinates are to be fixed? Blake Charlebois (Thu Oct 28 2004 - 17:36:56 CDT)
How do you specify which coordinates are to be fixed? Charles Danko (Thu Oct 28 2004 - 16:44:21 CDT)
BOND CP2 - CT2 IN PARAMETER FILES bora erdemli (Thu Oct 28 2004 - 16:42:09 CDT)
FK506 ligand topology file(1FKF) MERIC AYSE OVACIK (Thu Oct 28 2004 - 05:29:21 CDT)
Methane residue file Edward Patrick Obrien (Wed Oct 27 2004 - 19:19:28 CDT)
Re: Bug in Pair force interaction calculation was fixed? Brian Bennion (Wed Oct 27 2004 - 10:19:49 CDT)
Re: Compiling NAMD on IA64 cluter Brian Bennion (Wed Oct 27 2004 - 10:19:16 CDT)
Re: Bug in Pair force interaction calculation was fixed? Zhong Wenyu (Wed Oct 27 2004 - 09:26:26 CDT)
Fw: about ExcludeFromPressure mashaojie163 (Tue Oct 26 2004 - 21:59:50 CDT)
Compiling NAMD on IA64 cluter li (Tue Oct 26 2004 - 19:28:34 CDT)
Re: communication with NAMD? Brian Bennion (Tue Oct 26 2004 - 18:10:07 CDT)
communication with NAMD? Hui-Hsu Tsai (Tue Oct 26 2004 - 15:37:37 CDT)
RE: SMD and minimizations mdcooper (Tue Oct 26 2004 - 14:31:38 CDT)
Re: output to multiple files Leandro Martinez (Tue Oct 26 2004 - 13:09:26 CDT)
Re: Hydrogen cut off distance Brian Bennion (Tue Oct 26 2004 - 12:38:20 CDT)
Re: Bug in Pair force interaction calculation was fixed? Brian Bennion (Tue Oct 26 2004 - 12:20:36 CDT)
Re: vmd-l: psfgen and xplor topology Charles McCallum (Tue Oct 26 2004 - 11:36:37 CDT)
Re: D-amino acids Aaron Oakley (Tue Oct 26 2004 - 03:05:28 CDT)
Bug in Pair force interaction calculation was fixed? Zhong Wenyu (Mon Oct 25 2004 - 22:11:12 CDT)
Hydrogen cut off distance Uday Chippada (Mon Oct 25 2004 - 16:16:46 CDT)
charamrun / Rocks distribution problem Mounir Tarek (Mon Oct 25 2004 - 10:20:28 CDT)
D-amino acids Giovanni Bellesia (Mon Oct 25 2004 - 07:00:46 CDT)
PMEgrindsize for hexagon ego_wayne-namd_at_yahoo.com.cn (Sat Oct 23 2004 - 07:47:38 CDT)
Re: output to multiple files Brian Bennion (Fri Oct 22 2004 - 14:37:37 CDT)
about ExcludeFromPressure mashaojie163 (Fri Oct 22 2004 - 03:52:15 CDT)
output to multiple files Leandro Martinez (Thu Oct 21 2004 - 12:06:52 CDT)
Re: Compilation on an Opteron Server SuSE Linux Enterprise System Version 8 Marek Dynowski (Thu Oct 21 2004 - 03:03:54 CDT)
Re: Compilation on an Opteron Server SuSE Linux Enterprise System Version 8 Chris Samuel (Wed Oct 20 2004 - 18:05:49 CDT)
International PhD Symppozium "DECODING NATURE: HIERARCHY OF INTERACTIONS" Vlad Cojocaru (Wed Oct 20 2004 - 11:10:43 CDT)
Re: Compilation on an Opteron Server SuSE Linux Enterprise System Version 8 Gengbin Zheng (Wed Oct 20 2004 - 10:24:09 CDT)
Re: Compilation on an Opteron Server SuSE Linux Enterprise System Version 8 Marek Dynowski (Wed Oct 20 2004 - 10:20:16 CDT)
Re: Compilation on an Opteron Server SuSE Linux Enterprise System Version 8 Leandro Martinez (Wed Oct 20 2004 - 09:30:57 CDT)
Re: Compilation on an Opteron Server SuSE Linux Enterprise System Version 8 Leandro Martinez (Wed Oct 20 2004 - 08:27:50 CDT)
Compilation on an Opteron Server SuSE Linux Enterprise System Version 8 Marek Dynowski (Wed Oct 20 2004 - 07:26:14 CDT)
Re: bug report and stray pme Brian Bennion (Tue Oct 19 2004 - 15:31:43 CDT)
NAMD interaction with VMD Adam Kubach (Tue Oct 19 2004 - 13:54:18 CDT)
Re: NAMD on Linux cluster with Myrinet Chris Samuel (Mon Oct 18 2004 - 23:02:27 CDT)
bug report and stray pme Cheri M Turman (Mon Oct 18 2004 - 16:23:42 CDT)
Re: NAMD on Linux cluster with Myrinet Gengbin Zheng (Mon Oct 18 2004 - 13:28:36 CDT)
Re: NAMD on Linux cluster with Myrinet Alberto Santana (Mon Oct 18 2004 - 11:59:31 CDT)
pair-interaction energy Vani Krishna (Sun Oct 17 2004 - 17:37:18 CDT)
a different bug alert Meric Ayse Ovacik (Sun Oct 17 2004 - 09:27:23 CDT)
Fw: a different bug alert Meric Ayse Ovacik (Sun Oct 17 2004 - 09:21:47 CDT)
Question on harmonic constraints Edward Patrick Obrien (Thu Oct 14 2004 - 19:39:00 CDT)
Re: NAMD on Linux cluster with Myrinet Gengbin Zheng (Thu Oct 14 2004 - 14:03:12 CDT)
Re: NAMD on Linux cluster with Myrinet Alberto Santana (Thu Oct 14 2004 - 13:59:27 CDT)
Re: NAMD on Linux cluster with Myrinet Brian Bennion (Thu Oct 14 2004 - 13:20:59 CDT)
Re: NAMD on Linux cluster with Myrinet Alberto Santana (Thu Oct 14 2004 - 11:26:08 CDT)
Re: Gradient Tolerance Brian Bennion (Wed Oct 13 2004 - 14:43:04 CDT)
question on force autocorrelation function Hyonseok Hwang (Wed Oct 13 2004 - 11:20:47 CDT)
Gradient Tolerance mdcooper (Tue Oct 12 2004 - 18:52:43 CDT)
Re: NAMD on Linux cluster with Myrinet Gengbin Zheng (Tue Oct 12 2004 - 00:17:53 CDT)
Re: NAMD on Linux cluster with Myrinet Florian Barth (Mon Oct 11 2004 - 19:49:48 CDT)
Re: NAMD on Linux cluster with Myrinet Brian Bennion (Mon Oct 11 2004 - 15:53:14 CDT)
Re: NAMD on Linux cluster with Myrinet Alberto Santana (Mon Oct 11 2004 - 14:19:31 CDT)
RE: vmd-l: PSFGEN problem Brian Bennion (Mon Oct 11 2004 - 11:19:56 CDT)
Anyone having problems under Solaris 7? Charles Danko (Mon Oct 11 2004 - 11:05:33 CDT)
Re: [Fwd: counterion software] bora erdemli (Mon Oct 11 2004 - 02:03:05 CDT)
Re: counterion software mashaojie163 (Mon Oct 11 2004 - 01:46:24 CDT)
[Fwd: counterion software] Cetin Baloglu (Sun Oct 10 2004 - 23:55:20 CDT)
counterion software Cetin Baloglu (Sun Oct 10 2004 - 23:51:56 CDT)
Re: vmd-l: how can I get hole program mashaojie163 (Sun Oct 10 2004 - 09:23:13 CDT)
Re: NAMD on Linux cluster with Myrinet Brian Bennion (Sat Oct 09 2004 - 21:59:57 CDT)
NAMD on Linux cluster with Myrinet Alberto Santana (Sat Oct 09 2004 - 20:42:55 CDT)
NAMD on OSX built with XLC? Matt Harrington (Fri Oct 08 2004 - 13:48:21 CDT)
CMAP in CHARMM force field Jorge Pikunic (Fri Oct 08 2004 - 12:27:47 CDT)
Spherical Boundary Conditions Edward Patrick Obrien (Tue Oct 05 2004 - 16:14:12 CDT)
Re: How can I move an atom by 10nm with a step of 0.1nm Brian Bennion (Tue Oct 05 2004 - 10:44:01 CDT)
How can I move an atom by 10nm with a step of 0.1nm Shahid Qamar (Mon Oct 04 2004 - 17:22:36 CDT)
Re: Not all atoms have unique coordinates - revisited Brian Bennion (Mon Oct 04 2004 - 10:22:04 CDT)
Re: Not all atoms have unique coordinates - revisited Alberto Santana (Sat Oct 02 2004 - 08:32:59 CDT)
Re: Not all atoms have unique coordinates - revisited Brian Bennion (Sat Oct 02 2004 - 00:37:12 CDT)
Not all atoms have unique coordinates - revisited Alberto Santana (Fri Oct 01 2004 - 18:52:27 CDT)
PSFGEN problems in nanotube tutorial David L. Azevedo (Fri Oct 01 2004 - 01:36:36 CDT)
RE: temperature rescaling and canonical ensemble Blake Charlebois (Fri Oct 01 2004 - 01:15:05 CDT)
temperature rescaling and canonical ensemble Jan Lipfert (Thu Sep 30 2004 - 23:27:28 CDT)
Re: Can we fix the position of two atoms while minimization? Brian Bennion (Wed Sep 29 2004 - 18:00:43 CDT)
Can we fix the position of two atoms while minimization? Shahid Qamar (Wed Sep 29 2004 - 15:18:31 CDT)
Re: TCL: can't use floating-point value as operand of "-" li (Mon Sep 27 2004 - 21:57:12 CDT)
TCL: can't use floating-point value as operand of "-" li (Mon Sep 27 2004 - 03:16:52 CDT)
Converting Gromacs parameters to Charmm format Ben Roberts (Mon Sep 27 2004 - 01:35:23 CDT)
Pair interaction energies: TCL error Vani Krishna (Fri Sep 24 2004 - 21:06:30 CDT)
Generating simulation with large conformational changes Shirley Hui (Sat Feb 21 2004 - 18:36:12 CST)
(no subject) mdcooper (Fri Sep 24 2004 - 14:32:46 CDT)
Error in temperature calculation Raymond C. Fort Jr. (Fri Sep 24 2004 - 13:57:08 CDT)
question on pair interaction energy and force Hyonseok Hwang (Tue Sep 21 2004 - 23:39:41 CDT)
switching SMD in execution script? barner_at_physik.hu-berlin.de (Tue Sep 21 2004 - 09:43:17 CDT)
Re: To PME , Do the simulation need a neutral charged system? Jérôme Hénin (Tue Sep 21 2004 - 05:16:26 CDT)
To PME , Do the simulation need a neutral charged system? mashaojie163 (Tue Sep 21 2004 - 04:54:57 CDT)
output files always go to same node Alberto Santana (Mon Sep 20 2004 - 18:31:03 CDT)
Re: binding constant Jérôme Hénin (Mon Sep 20 2004 - 17:16:43 CDT)
Re: binding constant Oliver Hucke (Mon Sep 20 2004 - 15:23:20 CDT)
binding constant bora erdemli (Mon Sep 20 2004 - 13:33:45 CDT)
Fw: Constraint failure in RATTLE algorithm Zhong Wenyu (Sun Sep 19 2004 - 02:14:27 CDT)
NAMD prog. guide Giovanni Bellesia (Sat Sep 18 2004 - 19:53:46 CDT)
How I can get the hole program? mashaojie163 (Sat Sep 18 2004 - 11:08:05 CDT)
NAMD programming guide Harindar Keer (Thu Sep 16 2004 - 19:55:52 CDT)
pulling plus restraint li (Thu Sep 16 2004 - 03:56:47 CDT)
Energy Determination mdcooper (Wed Sep 15 2004 - 17:48:11 CDT)
RE: Output only protein .dcd Meric Ayse Ovacik (Wed Sep 15 2004 - 02:23:03 CDT)
RE: generating psf files (and more!) Luis Rosales (Tue Sep 14 2004 - 17:40:20 CDT)
generating psf files (and more!) mdcooper (Tue Sep 14 2004 - 16:52:38 CDT)
Output only protein .dcd Nur Aida Abdul Rahim (Tue Sep 14 2004 - 13:41:38 CDT)
Tcl loops in configuration files Streiff, John H. (Tue Sep 14 2004 - 10:26:12 CDT)
Minimization questions... Luis Rosales (Mon Sep 13 2004 - 19:53:16 CDT)
How I can get the hole program? mashaojie163 (Mon Sep 13 2004 - 19:04:36 CDT)
Compiling NAMD from SRC: Tungsten@NCSA Vani Krishna (Fri Sep 10 2004 - 19:54:55 CDT)
Clustermatic 4: Charmrun> error 1 attaching to node: Roy Campbell (Fri Sep 10 2004 - 12:24:05 CDT)
Fw: Problem with PSFGEN? Shirley Hui (Thu Sep 09 2004 - 21:51:53 CDT)
RE: surface pressure/tension Erik Nordgren (Thu Sep 09 2004 - 13:56:27 CDT)
RE: Cell Basis Vector. Pijush Ghosh (Wed Sep 08 2004 - 23:20:22 CDT)
Question about Gradient Tolerance during minimization Wolbach, Jeffrey P $WOLBACH$ (Wed Sep 08 2004 - 13:00:15 CDT)
Re: Stray PME grid charges Vani Krishna (Tue Sep 07 2004 - 21:16:35 CDT)
Re: Cell Basis Vector. Edward Patrick Obrien (Tue Sep 07 2004 - 18:45:13 CDT)
Cell Basis Vector. Pijush Ghosh (Tue Sep 07 2004 - 18:28:46 CDT)
Stray PME grid charges Harindar Keer (Tue Sep 07 2004 - 13:42:39 CDT)
CHARMM Eunice Ramirez Melendez (Mon Sep 06 2004 - 21:30:50 CDT)
Re: Re: numerical inaccuracy upon restart tepper_at_amolf.nl (Mon Sep 06 2004 - 06:30:22 CDT)
torsion angle bora erdemli (Mon Sep 06 2004 - 06:18:22 CDT)
Euro QSAR 2004 Ahmet Bakan (Sun Sep 05 2004 - 15:42:27 CDT)
NAMD-MPI compilation on P4 cluster Amit Paliwal (Sat Sep 04 2004 - 18:37:55 CDT)
Re: Re: numerical inaccuracy upon restart Jim Phillips (Fri Sep 03 2004 - 17:21:25 CDT)
compiling NAMD on OSC P4 cluster Amit Paliwal (Fri Sep 03 2004 - 12:11:51 CDT)
Re: 64 nodes behaviour Gengbin Zheng (Fri Sep 03 2004 - 14:37:05 CDT)
Re: Calculation of velocities Eric Cyr (Fri Sep 03 2004 - 14:27:38 CDT)
RE: SMD on a group of atoms: Confusion Blake Charlebois (Fri Sep 03 2004 - 05:41:24 CDT)
Re: 64 nodes behaviour Alexandre Chauvin (Fri Sep 03 2004 - 02:52:30 CDT)
rmsd problem,script and version bora erdemli (Fri Sep 03 2004 - 00:23:42 CDT)
Re: Symmetry operations \ (Thu Sep 02 2004 - 21:44:39 CDT)
Re: calculate the binding energy or binding free energy? Vani Krishna (Thu Sep 02 2004 - 21:13:58 CDT)
SMD: Group of atoms COM fixed? Vani Krishna (Thu Sep 02 2004 - 20:58:44 CDT)
RE: calculate the binding energy or binding free energy? Blake Charlebois (Thu Sep 02 2004 - 15:31:42 CDT)
Re: calculate the binding energy or binding free energy? LEWYN LI (Thu Sep 02 2004 - 14:27:03 CDT)
Re: 64 nodes behaviour Gengbin Zheng (Thu Sep 02 2004 - 13:19:03 CDT)
64 nodes behaviour Alexandre Chauvin (Thu Sep 02 2004 - 12:53:23 CDT)
Re: Questions on periodic boundary condition LEWYN LI (Thu Sep 02 2004 - 11:00:47 CDT)
Re: Questions on periodic boundary condition Edward Patrick Obrien (Thu Sep 02 2004 - 10:51:56 CDT)
RE: Calculation of velocities Blake Charlebois (Thu Sep 02 2004 - 08:21:34 CDT)
calculate the binding energy or binding free energy? ying xiong (Thu Sep 02 2004 - 03:49:40 CDT)
Questions on periodic boundary condition LEWYN LI (Thu Sep 02 2004 - 00:38:24 CDT)
SMD on a group of atoms: Confusion Vani Krishna (Wed Sep 01 2004 - 10:47:41 CDT)
Re: vmd-l: rmsd problem John Stone (Tue Aug 31 2004 - 15:11:47 CDT)
Re: vmd-l: convert DCD files to GROMACS .XTC format John Stone (Tue Aug 31 2004 - 15:11:09 CDT)
Calculation of velocities Eric Cyr (Tue Aug 31 2004 - 15:44:47 CDT)
estradiol lc_at_chem.au.dk (Tue Aug 31 2004 - 06:56:44 CDT)
Re: Re: numerical inaccuracy upon restart Harald Tepper (Tue Aug 31 2004 - 05:21:21 CDT)
replica exchange Justin Gullingsrud (Mon Aug 30 2004 - 16:09:42 CDT)
Re: Temperature Edward Patrick Obrien (Mon Aug 30 2004 - 13:12:17 CDT)
Temperature Raymond C. Fort Jr. (Mon Aug 30 2004 - 12:47:07 CDT)
Re: DPPC Jérôme Hénin (Mon Aug 30 2004 - 11:48:39 CDT)
DPPC Eunice Ramirez Melendez (Mon Aug 30 2004 - 02:28:55 CDT)
charm++ with gm Alexandre Chauvin (Mon Aug 30 2004 - 09:41:49 CDT)
Re: vmd-l: Protonated GLU/ASP in PSF generation Justin Gullingsrud (Sun Aug 29 2004 - 21:01:52 CDT)
Protonated GLU/ASP in PSF generation Vani Krishna (Sun Aug 29 2004 - 16:23:00 CDT)
convert DCD files to GROMACS .XTC format Vani Krishna (Sat Aug 28 2004 - 17:43:11 CDT)
Xserve G5 Streiff, John H. (Fri Aug 27 2004 - 15:37:48 CDT)
Re: Compilation on Opteron Alexandre Chauvin (Fri Aug 27 2004 - 03:05:43 CDT)
Error opening XSC output file...Invalid argument Randy Crawford (Thu Aug 26 2004 - 13:48:38 CDT)
rmsd problem bora erdemli (Thu Aug 26 2004 - 14:10:05 CDT)
Re: Compilation on Opteron Gengbin Zheng (Thu Aug 26 2004 - 00:25:44 CDT)
Re: Compilation on Opteron Chris Samuel (Thu Aug 26 2004 - 00:04:07 CDT)
Re: numerical inaccuracy upon restart nordgren_at_sas.upenn.edu (Wed Aug 25 2004 - 22:40:31 CDT)
Re: Compilation on Opteron Leandro Martinez (Wed Aug 25 2004 - 13:35:13 CDT)
Compilation on Opteron Alexandre Chauvin (Wed Aug 25 2004 - 12:22:43 CDT)
Re: cff91 force field in namd + A Question Rowan Hargreaves (Wed Aug 25 2004 - 12:06:18 CDT)
RE: cff91 force field in namd + A Question Ahmet Bakan (Wed Aug 25 2004 - 10:53:59 CDT)
numerical inaccuracy upon restart Blake Charlebois (Wed Aug 25 2004 - 09:24:08 CDT)
RE: Direction of the force in Pair interactions Kamp, Marc vander (Wed Aug 25 2004 - 01:29:18 CDT)
Re: Symmetry operations Aaron Oakley (Tue Aug 24 2004 - 18:34:47 CDT)
recommendation for 32 CPU cluster: Opteron or ? Matt Harrington (Tue Aug 24 2004 - 17:52:03 CDT)
Re: Symmetry operations \ (Tue Aug 24 2004 - 13:58:19 CDT)
Re: Direction of the force in Pair interactions Jim Phillips (Tue Aug 24 2004 - 11:06:52 CDT)
Direction of the force in Pair interactions Jérôme Hénin (Tue Aug 24 2004 - 03:46:33 CDT)
Re: Symmetry operations Juan Carlos Mobarec (Mon Aug 23 2004 - 19:21:22 CDT)
Re: Symmetry operations Brian Bennion (Mon Aug 23 2004 - 17:55:24 CDT)
Symmetry operations \ (Mon Aug 23 2004 - 16:42:22 CDT)
cff91 force field in namd Rowan Hargreaves (Mon Aug 23 2004 - 06:35:38 CDT)
surface pressure/tension nordgren_at_sas.upenn.edu (Sun Aug 22 2004 - 02:37:11 CDT)
Re: Clustermatic with SCSI Leandro Martinez (Thu Aug 19 2004 - 07:12:57 CDT)
Re: Clustermatic with SCSI Chris Samuel (Wed Aug 18 2004 - 20:17:05 CDT)
Node list Shahid Qamar (Wed Aug 18 2004 - 19:25:41 CDT)
Clustermatic with SCSI Leandro Martinez (Wed Aug 18 2004 - 18:15:11 CDT)
how to get hydrogen-bond energy? Lv Shouqin (Tue Aug 17 2004 - 21:34:17 CDT)
Re: question on the parallel job on NCSA Xeon cluster Gengbin Zheng (Tue Aug 17 2004 - 23:01:02 CDT)
question on the parallel job on NCSA Xeon cluster Hyonseok Hwang (Tue Aug 17 2004 - 22:51:13 CDT)
Bringing Up To Temp Tim Cm (Sun Aug 15 2004 - 16:48:42 CDT)
Re: > 10000 ato Brian Bennion (Fri Aug 13 2004 - 15:14:05 CDT)
> 10000 atoms Jhih-Wei Chu (Fri Aug 13 2004 - 13:32:25 CDT)
RE: radial distribution function Liu, Zhanwu (Fri Aug 13 2004 - 08:40:51 CDT)
radial distribution function bora erdemli (Fri Aug 13 2004 - 08:16:51 CDT)
mean square displacemente and diffusion of water at T=298 K Maira Aguilar (Thu Aug 12 2004 - 18:44:16 CDT)
Re: Need to add Hydrogens to over 300 distinct PDB's Edward Patrick Obrien (Wed Aug 11 2004 - 13:05:33 CDT)
Re: Has NAMD been ported to Itanium2 + Linux? Gengbin Zheng (Tue Aug 10 2004 - 16:54:08 CDT)
Re: Has NAMD been ported to Itanium2 + Linux? Shantenu Jha (Tue Aug 10 2004 - 16:25:28 CDT)
Has NAMD been ported to Itanium2 + Linux? Randy Crawford (Tue Aug 10 2004 - 10:06:44 CDT)
RE: Need to add Hydrogens to over 300 distinct PDB's Edward Patrick Obrien (Tue Aug 10 2004 - 10:20:47 CDT)
RE: Need to add Hydrogens to over 300 distinct PDB's Kamp, Marc vander (Tue Aug 10 2004 - 09:46:15 CDT)
SMD atoms not read properly! Vani Krishna (Tue Aug 10 2004 - 07:49:42 CDT)
Need to add Hydrogens to over 300 distinct PDB's Edward Patrick Obrien (Mon Aug 09 2004 - 13:03:40 CDT)
IA64 and MPICH and mpiexec runtime shmem errors Randy Crawford (Thu Aug 05 2004 - 14:38:06 CDT)
Parameters for iodine atoms Leandro Martinez (Thu Aug 05 2004 - 12:55:28 CDT)
PC-DL Deluxe, Dual Xeon Armen Nalian (Wed Aug 04 2004 - 17:32:54 CDT)
Fatal Socket error: code 93523-Error in accept Armen Nalian (Wed Aug 04 2004 - 15:05:17 CDT)
HYP residue and unknown residue type NH2 Valodymyr Nechyporuk-Zloy (Wed Aug 04 2004 - 07:06:47 CDT)
HYP files Ivan Vinogradov (Tue Aug 03 2004 - 12:55:52 CDT)
Re: compiled namd on clustermatic fails ! Gengbin Zheng (Tue Aug 03 2004 - 11:31:31 CDT)
Re: compiled namd on clustermatic fails ! Amit Paliwal (Tue Aug 03 2004 - 06:38:31 CDT)
Re: compiled namd on clustermatic fails ! Gengbin Zheng (Tue Aug 03 2004 - 10:23:19 CDT)
Re: render format Brian Bennion (Mon Aug 02 2004 - 14:44:08 CDT)
Re: render format John Stone (Mon Aug 02 2004 - 13:14:50 CDT)
render format Marcela Madrid (Mon Aug 02 2004 - 13:15:17 CDT)
Torsional barrier(adding parameters) Vani Krishna (Mon Aug 02 2004 - 10:11:48 CDT)
how to fix the atoms of backbone ? ying xiong (Fri Jul 30 2004 - 19:48:23 CDT)
Need of an ASCII-PHI converter, any help is appreciated to use wat2ions from Delphi output Eric Hajjar (Fri Jul 30 2004 - 02:45:05 CDT)
Re: compiled namd on clustermatic fails ! AMIT PALIWAL (Thu Jul 29 2004 - 19:24:52 CDT)
compiled namd on clustermatic fails ! Amit Paliwal (Thu Jul 29 2004 - 13:33:10 CDT)
pair interaction calculations Xin Chen (Thu Jul 29 2004 - 17:18:36 CDT)
Re: HYP parameters Ivan Vinogradov (Thu Jul 29 2004 - 07:44:27 CDT)
HYP parameters Valodymyr Nechyporuk-Zloy (Thu Jul 29 2004 - 03:59:44 CDT)
Position of the Virtual atom Shahid Qamar (Wed Jul 28 2004 - 16:46:29 CDT)
Constraint failure in RATTLE algorithm bora erdemli (Wed Jul 28 2004 - 15:05:47 CDT)
Torsion potential barrier (low?) in NAMD Vani Krishna (Wed Jul 28 2004 - 10:57:56 CDT)
charm++ MPICH and Myrinet Mauricio Carrillo Tripp (Mon Jul 26 2004 - 17:34:53 CDT)
topology file for compound Yanlong Xu (Mon Jul 26 2004 - 12:15:28 CDT)
AMBER parameters and SMD Valodymyr Nechyporuk-Zloy (Mon Jul 26 2004 - 04:42:55 CDT)
pair interaction forces Kamp, Marc vander (Mon Jul 26 2004 - 03:24:20 CDT)
Re: type of the water molecule Brian Bennion (Fri Jul 23 2004 - 11:55:57 CDT)
type of the water molecule bora erdemli (Fri Jul 23 2004 - 10:31:49 CDT)
Scale on Force vs Time plot? Shahid Qamar (Thu Jul 22 2004 - 15:06:53 CDT)
Re: Myrinet and MPI question Gengbin Zheng (Thu Jul 22 2004 - 11:49:07 CDT)
Re: Myrinet and MPI question Brian Bennion (Thu Jul 22 2004 - 11:21:34 CDT)
Re: phase equilibria using NAMD Brian Bennion (Thu Jul 22 2004 - 10:53:00 CDT)
Myrinet and MPI question Hrant Gharabekyan (Thu Jul 22 2004 - 09:20:01 CDT)
Re: psfgen Brian Bennion (Wed Jul 21 2004 - 18:23:41 CDT)
phase equilibria using NAMD nasrat kamal (Wed Jul 21 2004 - 07:33:45 CDT)
Psfgen klsale (Wed Jul 21 2004 - 14:57:56 CDT)
Re: mimization warnings - bad global exclusion count Brian Bennion (Wed Jul 21 2004 - 17:29:51 CDT)
Making PSF file Shahid Qamar (Wed Jul 21 2004 - 16:36:35 CDT)
truncated octahedron boundary conditions Mike Bradley (Wed Jul 21 2004 - 16:26:09 CDT)
mimization warnings - bad global exclusion count Stern, Julie (Wed Jul 21 2004 - 16:20:34 CDT)
psfgen Ken Sale (Wed Jul 21 2004 - 15:14:43 CDT)
Pt LJ Parameters Ahmet Bakan (Wed Jul 21 2004 - 11:56:52 CDT)
Re: Segmentation violation Gengbin Zheng (Tue Jul 20 2004 - 14:18:06 CDT)
Re: Segmentation violation Brian Bennion (Tue Jul 20 2004 - 12:30:06 CDT)
Segmentation violation Eunice Ramirez Melendez (Mon Jul 19 2004 - 22:26:22 CDT)
Thermostat problems Sarah Williams (Tue Jul 20 2004 - 04:13:19 CDT)
Unit cell coordinates and radial distribution functions Ben Roberts (Mon Jul 19 2004 - 21:12:38 CDT)
how to read amino acid such as 27, 27A,27B,27C in pdb file? yxiong_at_mail.ccnu.edu.cn (Mon Jul 19 2004 - 20:45:45 CDT)
Re: Questions Edward Patrick Obrien (Mon Jul 19 2004 - 17:02:29 CDT)
Questions Manali Mehendale (Mon Jul 19 2004 - 14:08:10 CDT)
Output files creation problem in MPI. Hrant Gharabekyan (Mon Jul 19 2004 - 07:59:38 CDT)
Output files creation problem in MPI. Hrant Gharabekyan (Mon Jul 19 2004 - 02:35:11 CDT)
RE: fixed particles Kamp, Marc vander (Sat Jul 17 2004 - 03:20:33 CDT)
fixed particles AMIT PALIWAL (Fri Jul 16 2004 - 18:22:23 CDT)
Re: How to do pH simulation on NAMD? Jérôme Hénin (Fri Jul 16 2004 - 05:00:03 CDT)
How to do pH simulation on NAMD? Xin Chen (Thu Jul 15 2004 - 15:28:50 CDT)
Tcl load Saladino, Alex (Thu Jul 15 2004 - 14:52:25 CDT)
Re: NAMD on the TeraGrid Gengbin Zheng (Thu Jul 15 2004 - 10:53:20 CDT)
NAMD on the TeraGrid p.w.fowler_at_qmul.ac.uk (Thu Jul 15 2004 - 05:12:47 CDT)
Re: compiler flags. gengbin (Wed Jul 14 2004 - 23:58:54 CDT)
Re: compiler flags. Brian Bennion (Wed Jul 14 2004 - 23:41:22 CDT)
Re: Dynamically resizing waterbox Edward Patrick Obrien (Wed Jul 14 2004 - 15:01:00 CDT)
Dynamically resizing waterbox Nur Aida Abdul Rahim (Wed Jul 14 2004 - 14:22:26 CDT)
Reset reference position Saladino, Alex (Wed Jul 14 2004 - 13:46:38 CDT)
INTEL 8.0 optimization flags Brian Bennion (Tue Jul 13 2004 - 14:22:05 CDT)
Reset Saladino, Alex (Tue Jul 13 2004 - 10:28:49 CDT)
Re: Common Problem!: Periodic cell has become too small for original patch grid! Meric Ayse Ovacik (Mon Jul 12 2004 - 03:25:04 CDT)
Re: compiling NAMD gzheng (Fri Jul 09 2004 - 20:52:04 CDT)
Common Problem!: Periodic cell has become too small for original patch grid! Shirley Hui (Fri Jul 09 2004 - 15:24:43 CDT)
Re: compiling NAMD Brian Bennion (Fri Jul 09 2004 - 12:27:28 CDT)
compiling NAMD Brian Bennion (Fri Jul 09 2004 - 11:56:03 CDT)
Re: Warning: Not all atoms have unique coordinates. Shirley Hui (Thu Jul 08 2004 - 18:15:29 CDT)
Re: Warning: Not all atoms have unique coordinates. Shirley Hui (Thu Jul 08 2004 - 17:45:47 CDT)
Re: Warning: Not all atoms have unique coordinates. Brian Bennion (Thu Jul 08 2004 - 11:06:08 CDT)
Re: ***** SPAM POSSIBLE ***** Warning: Not all atoms have unique coordinates. Jérôme Hénin (Thu Jul 08 2004 - 11:01:54 CDT)
Re: cellBasisVector x,y,z values Brian Bennion (Thu Jul 08 2004 - 10:35:11 CDT)
Re: cellBasisVector x,y,z values p.w.fowler_at_qmul.ac.uk (Thu Jul 08 2004 - 10:30:31 CDT)
RE: cellBasisVector x,y,z values Kamp, Marc vander (Thu Jul 08 2004 - 10:18:42 CDT)
Re: cellBasisVector x,y,z values Edward Patrick Obrien (Thu Jul 08 2004 - 09:36:43 CDT)
Warning: Not all atoms have unique coordinates. Shirley Hui (Thu Jul 08 2004 - 09:25:13 CDT)
cellBasisVector x,y,z values Shirley Hui (Thu Jul 08 2004 - 08:46:16 CDT)
about symmetry operations mashaojie163 (Wed Jul 07 2004 - 10:23:45 CDT)
Re: octahedral period BCs Mark Abraham (Wed Jul 07 2004 - 22:43:57 CDT)
Re: octahedral period BCs Mark Abraham (Wed Jul 07 2004 - 22:35:44 CDT)
Re: octahedral period BCs Peter Jones (Wed Jul 07 2004 - 21:34:52 CDT)
Re: namd and Tcl 8.3.5 Sean Michael Whipkey (Wed Jul 07 2004 - 16:06:35 CDT)
Re: namd and Tcl 8.3.5 Brian Bennion (Wed Jul 07 2004 - 11:33:23 CDT)
Re: How to calculate specific heat capacity in NAMD? Brian Bennion (Wed Jul 07 2004 - 11:28:40 CDT)
Re: How to calculate specific heat capacity in NAMD? Edward Patrick Obrien (Wed Jul 07 2004 - 10:39:38 CDT)
How to calculate specific heat capacity in NAMD? Xin Chen (Wed Jul 07 2004 - 10:02:02 CDT)
namd and Tcl 8.3.5 Sean Michael Whipkey (Wed Jul 07 2004 - 09:42:26 CDT)
NAMD2.5 and the TeraGrid p.w.fowler_at_qmul.ac.uk (Wed Jul 07 2004 - 06:02:40 CDT)
namd linux source or binary Cetin Baloglu (Wed Jul 07 2004 - 03:10:56 CDT)
RE: COM position Brian Bennion (Tue Jul 06 2004 - 12:50:52 CDT)
RE: COM position Mauricio Carrillo Tripp (Tue Jul 06 2004 - 12:43:40 CDT)
RE: COM position Brian Bennion (Tue Jul 06 2004 - 12:11:28 CDT)
Re: COM position Mauricio Carrillo Tripp (Tue Jul 06 2004 - 12:12:49 CDT)
RE: COM position Mauricio Carrillo Tripp (Tue Jul 06 2004 - 10:45:53 CDT)
RE: PME off Kamp, Marc vander (Tue Jul 06 2004 - 01:50:24 CDT)
RE: COM position Kamp, Marc vander (Tue Jul 06 2004 - 01:40:01 CDT)
Order of improper dihedrals Ben Roberts (Tue Jul 06 2004 - 00:21:01 CDT)
PME off Michael Grabe (Mon Jul 05 2004 - 17:21:47 CDT)
COM position Mauricio Carrillo Tripp (Mon Jul 05 2004 - 14:47:51 CDT)
RE: Cell Basis Vectors Kamp, Marc vander (Mon Jul 05 2004 - 09:46:24 CDT)
Cell Basis Vectors Raymond C. Fort Jr. (Mon Jul 05 2004 - 07:57:53 CDT)
Re: icc compilation problem Chris Samuel (Sun Jul 04 2004 - 20:41:14 CDT)
Re: Node 0 could not initialize network! Alberto Santana (Sun Jul 04 2004 - 13:25:32 CDT)
Node 0 could not initialize network! Alberto Santana (Sat Jul 03 2004 - 18:16:01 CDT)
Re: Suse 9.0 or Fedora Core 1.0 Alex V. (Fri Jul 02 2004 - 07:27:08 CDT)
COM position Mauricio Carrillo Tripp (Fri Jul 02 2004 - 16:54:01 CDT)
Re: icc compilation problem Brian Bennion (Fri Jul 02 2004 - 11:05:29 CDT)
Re: icc compilation problem Sean Michael Whipkey (Fri Jul 02 2004 - 09:27:55 CDT)
Suse 9.0 or Fedora Core 1.0 nalianarmen (Thu Jul 01 2004 - 23:37:18 CDT)
Re: icc compilation problem Chris Samuel (Thu Jul 01 2004 - 18:11:57 CDT)
icc compilation problem Sean Michael Whipkey (Thu Jul 01 2004 - 16:19:55 CDT)
hexagonal unit cell Anna Modzelewska (Thu Jul 01 2004 - 03:49:56 CDT)
best choice of linux cluster to run NAMD Nikolai Skrynnikov (Thu Jul 01 2004 - 03:02:10 CDT)
(no subject) ying xiong (Thu Jul 01 2004 - 01:57:18 CDT)
Re: DIHEDral drift [2] ? Brian Bennion (Wed Jun 30 2004 - 17:16:39 CDT)
Re: DIHEDral drift [2] ? Nicholas M Glykos (Wed Jun 30 2004 - 13:08:14 CDT)
Re: DIHEDral drift [2] ? Brian Bennion (Wed Jun 30 2004 - 12:30:15 CDT)
Fixing position of COM Mauricio Carrillo Tripp (Wed Jun 30 2004 - 10:42:10 CDT)
DIHEDral drift [2] ? Nicholas M Glykos (Wed Jun 30 2004 - 09:26:43 CDT)
NAMD with HPUX/IA64. Hansang Bae (Tue Jun 29 2004 - 13:31:20 CDT)
compiling linux scyld mpi 64bit Eric Franz (Tue Jun 29 2004 - 10:40:31 CDT)
equilibration of protein in water box Valodymyr Nechyporuk-Zloy (Tue Jun 29 2004 - 09:08:01 CDT)
Box Dimension Valodymyr Nechyporuk-Zloy (Tue Jun 29 2004 - 09:00:53 CDT)
PBCwrap: wrapping DCD files Vani Krishna (Mon Jun 28 2004 - 22:03:45 CDT)
tcl scripting interface in namd 2.5 for IBM-SP Jorge Pikunic (Mon Jun 28 2004 - 16:23:14 CDT)
wrapping DCD files Vani Krishna (Mon Jun 28 2004 - 14:25:24 CDT)
minimum imgae convention Vani Krishna (Mon Jun 28 2004 - 09:59:24 CDT)
RE: Amber94 files in CHARMM format Kamp, Marc vander (Wed Jun 23 2004 - 10:08:47 CDT)
Amber94 files in CHARMM format Aaron Oakley (Wed Jun 23 2004 - 08:08:13 CDT)
RE: Temperature reassignment problem Kamp, Marc vander (Wed Jun 23 2004 - 05:13:34 CDT)
namd on PPC, linux Nathalie Reuter (Wed Jun 23 2004 - 04:40:05 CDT)
Gromacs force field paramets: Syntax error in ATOMS Sichun Yang (Wed Jun 23 2004 - 03:09:39 CDT)
RE: vmd-l: incompatibility between VMD & NAMD for reading Amber crd files Kamp, Marc vander (Tue Jun 22 2004 - 04:20:16 CDT)
Re: vmd-l: incompatibility between VMD & NAMD for reading Amber crd files John Stone (Mon Jun 21 2004 - 14:53:13 CDT)
RE: vmd-l: incompatibility between VMD & NAMD for reading Amber crd files Kamp, Marc vander (Mon Jun 21 2004 - 14:39:05 CDT)
pmf error mashaojie163 (Mon Jun 21 2004 - 10:17:20 CDT)
Re: vmd-l: incompatibility between VMD & NAMD for reading Amber crd files John Stone (Mon Jun 21 2004 - 09:58:31 CDT)
incompatibility between VMD & NAMD for reading Amber crd files Kamp, Marc vander (Mon Jun 21 2004 - 07:33:11 CDT)
setting constraints to off in execution script Kamp, Marc vander (Mon Jun 21 2004 - 04:20:26 CDT)
Temperature reassignment problem Kamp, Marc vander (Mon Jun 21 2004 - 04:19:03 CDT)
about pmf mashaojie163 (Sun Jun 20 2004 - 21:10:00 CDT)
Re: recentering protein in the waterbox Gianluca Interlandi (Fri Jun 18 2004 - 18:16:35 CDT)
margin errors Stern, Julie (Fri Jun 18 2004 - 14:48:36 CDT)
recentering protein in the waterbox Jerry Ebalunode (Fri Jun 18 2004 - 07:04:58 CDT)
Re: What binaries should I take? Gianluca Interlandi (Fri Jun 18 2004 - 08:38:39 CDT)
Re: What binaries should I take? Edward Patrick Obrien (Fri Jun 18 2004 - 08:18:38 CDT)
What binaries should I take? Valodymyr Nechyporuk-Zloy (Fri Jun 18 2004 - 03:49:14 CDT)
Re: errors building charm on ia64 Gianluca Interlandi (Thu Jun 17 2004 - 11:31:42 CDT)
errors building charm on ia64 Allison Heath (Thu Jun 17 2004 - 11:18:29 CDT)
question on Lithium force field Hyonseok Hwang (Wed Jun 16 2004 - 16:20:12 CDT)
RE: about psf file Kamp, Marc vander (Wed Jun 16 2004 - 11:34:51 CDT)
about psf file mashaojie163 (Wed Jun 16 2004 - 09:33:07 CDT)
Re: psfgen : wrong guess for leucine hydrogen li (Wed Jun 16 2004 - 01:58:18 CDT)
Re: build charm on ia-64 linux Chris Samuel (Tue Jun 15 2004 - 18:23:17 CDT)
Re: Energy minimization at NAMD Michael Grabe (Tue Jun 15 2004 - 16:55:01 CDT)
harmonic restraint Amit Paliwal (Tue Jun 15 2004 - 12:23:10 CDT)
Re: Energy minimization at NAMD Edward Patrick Obrien (Tue Jun 15 2004 - 16:07:06 CDT)
Energy minimization at NAMD Xin Chen (Tue Jun 15 2004 - 15:25:38 CDT)
Re: Simulated Annealing Config Jérôme Hénin (Tue Jun 15 2004 - 12:20:45 CDT)
Re: Namd RedHat9 compilation problem Gengbin Zheng (Tue Jun 15 2004 - 11:39:49 CDT)
Simulated Annealing Config Ahmet Bakan (Tue Jun 15 2004 - 08:24:59 CDT)
psfgen : wrong guess for leucine hydrogen Jérôme Hénin (Tue Jun 15 2004 - 10:33:47 CDT)
Namd RedHat9 compilation problem ghg_at_xalt.am (Tue Jun 15 2004 - 05:56:36 CDT)
question on veldcd Hyonseok Hwang (Mon Jun 14 2004 - 10:19:59 CDT)
questions about "psfgen". Lv Shouqin (Sat Jun 12 2004 - 00:12:14 CDT)
about membrane protein mashaojie163 (Mon Jun 14 2004 - 09:39:41 CDT)
Re: build charm on ia-64 linux Gengbin Zheng (Fri Jun 11 2004 - 21:54:20 CDT)
Re: build charm on ia-64 linux Sichun Yang (Fri Jun 11 2004 - 21:44:12 CDT)
start fep calculation mashaojie163 (Fri Jun 11 2004 - 21:13:45 CDT)
Re: build charm on ia-64 linux Gengbin Zheng (Fri Jun 11 2004 - 20:57:01 CDT)
Re: build charm on ia-64 linux Sichun Yang (Fri Jun 11 2004 - 19:41:26 CDT)
build charm on ia-64 linux Sichun Yang (Fri Jun 11 2004 - 18:40:29 CDT)
question on veldcd Hyonseok Hwang (Fri Jun 11 2004 - 12:35:42 CDT)
question about autogen in topology file jz7_at_duke.edu (Thu Jun 10 2004 - 13:41:00 CDT)
DIHEDral drift ? Nicholas M Glykos (Thu Jun 10 2004 - 13:15:09 CDT)
RE: psfgen problem Brian Bennion (Wed Jun 09 2004 - 15:59:33 CDT)
charmm restart file Mauricio Carrillo Tripp (Wed Jun 09 2004 - 12:57:47 CDT)
gromacs/gromos96 force field Jorge Pikunic (Wed Jun 09 2004 - 11:11:30 CDT)
RE: psfgen problem Kamp, Marc vander (Wed Jun 09 2004 - 04:22:00 CDT)
Re: question about running equilibration in NAMD Brian Bennion (Tue Jun 08 2004 - 15:50:28 CDT)
question about running equilibration in NAMD jz7_at_duke.edu (Tue Jun 08 2004 - 14:25:41 CDT)
Urey-Bradley term? Gianluca Interlandi (Tue Jun 08 2004 - 12:29:34 CDT)
Re: psfgen problem Brian Bennion (Tue Jun 08 2004 - 12:01:58 CDT)
psfgen problem Kamp, Marc vander (Tue Jun 08 2004 - 04:53:39 CDT)
Re: psfgen issue Rad Balu (Sun Jun 06 2004 - 22:03:07 CDT)
pressure profile Mauricio Carrillo Tripp (Mon Jun 07 2004 - 17:00:51 CDT)
(no subject) Mauricio Carrillo Tripp (Mon Jun 07 2004 - 11:46:18 CDT)
Re: psfgen issue Edward Patrick Obrien (Mon Jun 07 2004 - 09:23:23 CDT)
Re: IO error when running NAMD on new cluster Edward Patrick Obrien (Mon Jun 07 2004 - 09:21:44 CDT)
question on a chared system MD simulation Hyonseok Hwang (Sun Jun 06 2004 - 18:05:35 CDT)
psfgen issue Rad Balu (Sat Jun 05 2004 - 12:49:34 CDT)
Re: IO error when running NAMD on new cluster Alex V. (Sat Jun 05 2004 - 23:07:22 CDT)
IO error when running NAMD on new cluster Edward Patrick Obrien (Sat Jun 05 2004 - 14:44:10 CDT)
Re: Re: Simulation with ammonia AHMET BAKAN (Fri Jun 04 2004 - 17:23:39 CDT)
Sampling trajectories Harindar Keer (Fri Jun 04 2004 - 17:03:02 CDT)
Re: Simulation with ammonia AHMET BAKAN (Fri Jun 04 2004 - 15:01:04 CDT)
Re: submitting a job in a queue Alex V. (Fri Jun 04 2004 - 13:46:18 CDT)
Re: Simulation with ammonia Leandro Martinez (Fri Jun 04 2004 - 13:13:45 CDT)
Simulation with ammonia Marek Dynowski (Fri Jun 04 2004 - 10:53:27 CDT)
Re: How do we know the velocity? Leandro Martinez (Thu Jun 03 2004 - 11:47:05 CDT)
Re: submitting a job in a queue Gengbin Zheng (Thu Jun 03 2004 - 11:33:25 CDT)
How do we know the velocity? Uday Chippada (Thu Jun 03 2004 - 10:17:10 CDT)
about this bug alert jz7_at_duke.edu (Thu Jun 03 2004 - 09:46:54 CDT)
Re: "GRADIENT TOLERANCE: nan", Why? Zhong Wenyu (Thu Jun 03 2004 - 09:02:01 CDT)
RE: question about using Amber force field in namd Kamp, Marc vander (Thu Jun 03 2004 - 01:19:12 CDT)
Re: question about using Amber force field in namd Brian Bennion (Wed Jun 02 2004 - 16:31:48 CDT)
Re: question about using Amber force field in namd Brian Bennion (Wed Jun 02 2004 - 16:21:21 CDT)
Re: question about using Amber force field in namd jz7_at_duke.edu (Wed Jun 02 2004 - 16:13:14 CDT)
Re: question about using Amber force field in namd Brian Bennion (Wed Jun 02 2004 - 16:07:28 CDT)
Re: "GRADIENT TOLERANCE: nan", Why? Brian Bennion (Wed Jun 02 2004 - 16:04:15 CDT)
submitting a job in a queue Giovanni (Wed Jun 02 2004 - 10:55:37 CDT)
question about using Amber force field in namd jz7_at_duke.edu (Wed Jun 02 2004 - 09:35:54 CDT)
"GRADIENT TOLERANCE: nan", Why? Zhong Wenyu (Wed Jun 02 2004 - 07:42:50 CDT)
Does anybody have gromacs topology example, which works OK using NAMD?? Armen Poghosyan (Tue Jun 01 2004 - 14:24:00 CDT)
Margin violation Leandro Martinez (Tue Jun 01 2004 - 08:10:20 CDT)
Re: NPT calculations in NAMD Leandro Martinez (Tue Jun 01 2004 - 07:17:58 CDT)
Re: NPT calculations in NAMD Peter Jones (Mon May 31 2004 - 22:04:51 CDT)
Effect of FullDirect electrostatics Ben Roberts (Mon May 31 2004 - 18:22:45 CDT)
NPT calculations in NAMD Hui-Hsu (Gavin) Tsai [contr] (Mon May 31 2004 - 11:06:04 CDT)
Re: Single point energy calculation Rad Balu (Mon May 31 2004 - 04:13:16 CDT)
How to use GROMACS force field in NAMD? Armen Poghosyan (Mon May 31 2004 - 02:34:06 CDT)
Re: NAMD on HP-IA64 Linux Gengbin Zheng (Sun May 30 2004 - 22:20:51 CDT)
Single point energy calculation Ben Roberts (Sun May 30 2004 - 21:05:00 CDT)
NAMD on HP-IA64 Linux Ioana Cozmuta (Sun May 30 2004 - 20:58:00 CDT)
benchmarking mistake? Ioana Cozmuta (Sun May 30 2004 - 20:12:52 CDT)
Re: NAMD on HP with Itanium2 Processors Brian Bennion (Sun May 30 2004 - 01:27:19 CDT)
NAMD C++ API Rad Balu (Sat May 29 2004 - 17:58:42 CDT)
Re: NAMD on HP with Itanium2 Processors Brian Bennion (Sat May 29 2004 - 17:48:32 CDT)
NAMD on HP with Itanium2 Processors Ioana Cozmuta (Fri May 28 2004 - 18:08:37 CDT)
Re: Compiling NAMD on Linux cluster Gengbin Zheng (Fri May 28 2004 - 15:48:41 CDT)
Compiling NAMD on Linux cluster Xin Chen (Fri May 28 2004 - 15:14:12 CDT)
Re: Info about forces on atoms g srinivasa murthy (Fri May 28 2004 - 03:27:23 CDT)
question on the wrapping algorithm in NAMD Hyonseok Hwang (Thu May 27 2004 - 18:18:26 CDT)
Re: three-site carbon monoxide model Brian Bennion (Thu May 27 2004 - 17:12:22 CDT)
three-site carbon monoxide model ELENA JEAN LEVIN (Thu May 27 2004 - 16:40:11 CDT)
Info about forces on atoms Vani Krishna (Thu May 27 2004 - 11:58:32 CDT)
Electrostatics energy calculation Ben Roberts (Wed May 26 2004 - 20:09:43 CDT)
Atom type explaination for NAMD myang (Wed May 26 2004 - 18:04:05 CDT)
Re: Periodic cell too small Brian Bennion (Tue May 25 2004 - 17:39:45 CDT)
Periodic cell too small Ekta Khurana (Tue May 25 2004 - 16:22:00 CDT)
error Amit Paliwal (Mon May 24 2004 - 04:29:43 CDT)
Re: Force Calculation in NAMD Gadi Oron (Sun May 23 2004 - 02:37:27 CDT)
Re: psfgen non-bonded atom pairs Shirley Hui (Sat May 22 2004 - 12:35:52 CDT)
psfgen non-bonded atom pairs Shirley Hui (Sat May 22 2004 - 01:08:57 CDT)
Force Calculation in NAMD Xin Chen (Fri May 21 2004 - 13:02:09 CDT)
Re: hanging at startup phase Gengbin Zheng (Fri May 21 2004 - 10:53:23 CDT)
Re: hanging at startup phase Allison Heath (Fri May 21 2004 - 10:29:49 CDT)
Re: hanging at startup phase Gengbin Zheng (Fri May 21 2004 - 00:59:55 CDT)
Re: NAN GRADIENT TOLERANCE - & - RESTARTING CONJUGATE GRADIENT ALGORITHM Peter Spijker (Thu May 20 2004 - 12:47:57 CDT)
Re: charm++ mpi-linux compilation errors g srinivasa murthy (Thu May 20 2004 - 09:57:55 CDT)
ATOMS moving too fast Michael Chen (Thu May 20 2004 - 09:50:23 CDT)
Re: Why Vmd didn't show the Pt-Cl bond Edward Patrick Obrien (Wed May 19 2004 - 20:10:40 CDT)
Why Vmd didn't show the Pt-Cl bond myang (Wed May 19 2004 - 18:46:31 CDT)
NAN GRADIENT TOLERANCE - & - RESTARTING CONJUGATE GRADIENT ALGORITHM Peter Spijker (Wed May 19 2004 - 18:30:57 CDT)
hanging at startup phase allison (Wed May 19 2004 - 14:00:25 CDT)
RE: Where to download the inorganic pdb file myang (Wed May 19 2004 - 14:02:49 CDT)
replica-ex NAMD? Sichun Yang (Wed May 19 2004 - 12:28:20 CDT)
charm++ mpi-linux compilation errors ghg_at_xalt.am (Wed May 19 2004 - 11:38:28 CDT)
solvent bands and periodic boundary conditions Stern, Julie (Wed May 19 2004 - 10:45:09 CDT)
Re: Where to download the inorganic pdb file Brian Bennion (Wed May 19 2004 - 10:20:11 CDT)
Myrinet and MPI ghg_at_xalt.am (Wed May 19 2004 - 09:20:20 CDT)
numerical inaccuracy upon restart Harald Tepper (Wed May 19 2004 - 08:45:07 CDT)
Where to download the inorganic pdb file myang (Wed May 19 2004 - 00:49:05 CDT)
flexible cell AMIT PALIWAL (Tue May 18 2004 - 17:08:41 CDT)
Re: autoionize script Olya Kravchenko (Mon May 17 2004 - 14:00:12 CDT)
autoionize script amodzelewska_at_dns.iimcb.gov.pl (Sun May 16 2004 - 13:21:58 CDT)
calculate energy with water excluded li (Mon May 17 2004 - 01:04:39 CDT)
Calculate Potential Energy Shirley Hui (Sat May 15 2004 - 17:20:03 CDT)
Re: Calculating parameters. Jan Saam (Sat May 15 2004 - 10:32:36 CDT)
Re: how to generate your own pdb file Josef Scheiber (Sat May 15 2004 - 04:28:47 CDT)
RE: how to generate your own pdb file Ahmet Bakan (Fri May 14 2004 - 21:55:28 CDT)
psfgen: failed on segment Olya Kravchenko (Fri May 14 2004 - 19:46:26 CDT)
Re: how to generate your own pdb file Tim Isgro (Fri May 14 2004 - 17:26:00 CDT)
RE: Calculating parameters. Ahmet Bakan (Fri May 14 2004 - 16:59:15 CDT)
NAMD with Amber Amit Paliwal (Fri May 14 2004 - 12:42:10 CDT)
Calculating parameters. ivan.vinogradov_at_utoronto.ca (Fri May 14 2004 - 13:29:50 CDT)
32 vs. 64 bits Leandro Martinez (Fri May 14 2004 - 08:07:14 CDT)
Problem using Gromacs topology file Josef Scheiber (Fri May 14 2004 - 03:59:24 CDT)
Unit of force using Haptic in IMD Harit Jani (Fri May 14 2004 - 01:33:10 CDT)
urestraint Michael Grabe (Thu May 13 2004 - 16:24:35 CDT)
how to generate your own pdb file myang (Thu May 13 2004 - 00:12:45 CDT)
Re: Systems of > 100,000 atoms, *.psf files & *.crd files Brian Bennion (Wed May 12 2004 - 10:19:29 CDT)
Systems of > 100,000 atoms, *.psf files & *.crd files Crozier, Paul S (Tue May 11 2004 - 18:02:51 CDT)
Re: error: Number of atoms in fixed atoms PDB doesn't match coordinate PDB Olya Kravchenko (Tue May 11 2004 - 17:43:22 CDT)
Re: NAMD "freezes" up (further clarification) Eric R Johnson (Tue May 11 2004 - 12:34:32 CDT)
Re: NAMD "freezes" up (further clarification) Eric R Johnson (Tue May 11 2004 - 11:10:44 CDT)
Re: NAMD "freezes" up (further clarification) Brian Bennion (Tue May 11 2004 - 10:10:46 CDT)
Re: NAMD node freeze Eric R Johnson (Tue May 11 2004 - 08:43:42 CDT)
Re: NAMD "freezes" up Eric R Johnson (Tue May 11 2004 - 08:35:51 CDT)
NAMD "freezes" up (further clarification) Eric R Johnson (Tue May 11 2004 - 08:49:33 CDT)
Re: how many steps do we need do for energy minimization ? Edward Patrick Obrien (Tue May 11 2004 - 08:39:17 CDT)
NAMD "freezes" up Eric R Johnson (Tue May 11 2004 - 04:20:58 CDT)
how many steps do we need do for energy minimization ? ying xiong (Tue May 11 2004 - 01:19:39 CDT)
Re: restart simulation Tim Isgro (Tue May 11 2004 - 00:31:18 CDT)
Re: error: Number of atoms in fixed atoms PDB doesn't match coordinate PDB Tim Isgro (Tue May 11 2004 - 00:01:55 CDT)
Re: Parameter File Problem Brian Bennion (Mon May 10 2004 - 23:59:53 CDT)
Re: Issues with SMD Tim Isgro (Mon May 10 2004 - 23:53:13 CDT)
Parameter File Problem beckloni_at_umdnj.edu (Mon May 10 2004 - 19:47:24 CDT)
Re: restart simulation J. Rui Rodrigues (Mon May 10 2004 - 17:10:25 CDT)
restart simulation Marcela P.Aliste (Mon May 10 2004 - 16:01:28 CDT)
Re: implementing angle dependent non-bonded interaction? Brian Bennion (Mon May 10 2004 - 14:51:26 CDT)
implementing angle dependent non-bonded interaction? Julius Su (Mon May 10 2004 - 13:09:14 CDT)
Re: Issues with SMD Brian Bennion (Mon May 10 2004 - 11:04:13 CDT)
Re: PSF file generation beckloni_at_umdnj.edu (Mon May 10 2004 - 10:48:22 CDT)
Re: "Constrain failure" in NAMD Brian Bennion (Mon May 10 2004 - 10:47:29 CDT)
Re: PSF file generation Brian Bennion (Mon May 10 2004 - 10:39:42 CDT)
Problems witn parameter files! Galina Petrova (Mon May 10 2004 - 08:54:25 CDT)
installing on beowulf cluster Cheri M Turman (Sun May 09 2004 - 19:58:25 CDT)
PSF file generation beckloni_at_umdnj.edu (Sun May 09 2004 - 10:00:59 CDT)
Re: "Constrain failure" in NAMD Edward Patrick Obrien (Fri May 07 2004 - 17:59:05 CDT)
New cluster configuration? nalianarmen (Fri May 07 2004 - 17:19:11 CDT)
"Constrain failure" in NAMD Michael Chen (Fri May 07 2004 - 14:43:41 CDT)
Re: ,log and .out files with namd running on mac os x (panther) Brian Bennion (Fri May 07 2004 - 10:51:14 CDT)
coarse grained model Giovanni (Fri May 07 2004 - 05:02:57 CDT)
error: Number of atoms in fixed atoms PDB doesn't match coordinate PDB Olya Kravchenko (Thu May 06 2004 - 19:03:49 CDT)
Re: AMBER FF and pmf Fangqiang Zhu (Thu May 06 2004 - 18:18:58 CDT)
How to create a substrate parameter file ? Davit Hakobyan (Thu May 06 2004 - 15:09:00 CDT)
Re: installing on beowulf cluster Brian Bennion (Thu May 06 2004 - 14:41:08 CDT)
Re: installing on beowulf cluster Jerry Ebalunode (Thu May 06 2004 - 14:17:01 CDT)
installing on beowulf cluster Cheri M Turman (Thu May 06 2004 - 13:38:16 CDT)
AMBER FF and pmf ladam (Thu May 06 2004 - 03:33:34 CDT)
FATAL ERROR: Patch needed for tuple is missing. Armen Poghosyan (Thu May 06 2004 - 07:21:57 CDT)
Re: question on self-diffusion constant of TIP3P water Brian Bennion (Wed May 05 2004 - 18:18:19 CDT)
Re: question on self-diffusion constant of TIP3P water Brian Bennion (Wed May 05 2004 - 17:37:46 CDT)
Re: ,log and .out files with namd running on mac os x (panther) Arieana Moore (Wed May 05 2004 - 17:30:28 CDT)
question on self-diffusion constant of TIP3P water Hyonseok Hwang (Wed May 05 2004 - 16:54:45 CDT)
,log and .out files with namd running on mac os x (panther) Arieana Moore (Wed May 05 2004 - 14:37:19 CDT)
RE: Binding free energy of a protein complex Gadi Oron (Wed May 05 2004 - 09:31:52 CDT)
rsh on nodes nalianarmen (Mon May 03 2004 - 23:30:38 CDT)
RE: Binding free energy of a protein complex Ahmet Bakan (Mon May 03 2004 - 06:02:29 CDT)
Binding free energy of a protein complex Gadi Oron (Mon May 03 2004 - 02:06:05 CDT)
Re: Help, MD run errors Xiaobing Tian (Sun May 02 2004 - 21:06:58 CDT)
tcl script for calculate RMS of MD calculation ? ying xiong (Sat May 01 2004 - 21:06:04 CDT)
question on autocorrelation function and temperature controlling Hyonseok Hwang (Fri Apr 30 2004 - 17:09:44 CDT)
Re: NAMD parser Xiaobing Tian (Fri Apr 30 2004 - 14:56:18 CDT)
Re: vmd-l: Re: dcd files generated with catdcd J. Rui Rodrigues (Fri Apr 30 2004 - 14:02:49 CDT)
Re: vmd-l: Re: dcd files generated with catdcd Giovanni (Fri Apr 30 2004 - 13:08:33 CDT)
Re: dcd files generated with catdcd J. Rui Rodrigues (Fri Apr 30 2004 - 10:51:27 CDT)
Re: Atom number limitations? Leandro Martinez (Fri Apr 30 2004 - 08:16:19 CDT)
dcd files generated with catdcd Giovanni (Fri Apr 30 2004 - 04:11:00 CDT)
Atom number limitations? Hrant Gharabekyan (Thu Apr 29 2004 - 22:50:26 CDT)
Lithium Scott, Greg (Thu Apr 29 2004 - 22:01:52 CDT)
Re: NAMD parser Mike McCallum (Thu Apr 29 2004 - 17:03:02 CDT)
Re: NAMD parser Xiaobing Tian (Thu Apr 29 2004 - 16:25:14 CDT)
Re: Help! There is no angle or dihedral definitions for patches in .psf! Brian Bennion (Thu Apr 29 2004 - 13:23:55 CDT)
Re: Help! There is no angle or dihedral definitions for patches in .psf! Edward Patrick Obrien (Thu Apr 29 2004 - 13:09:05 CDT)
Re: questions about set cellBasisVector and a ligand ... Edward Patrick Obrien (Thu Apr 29 2004 - 12:59:15 CDT)
RE: Lithium Ahmet Bakan (Thu Apr 29 2004 - 11:14:56 CDT)
NAMD parser Xiaobing Tian (Thu Apr 29 2004 - 11:16:35 CDT)
Help! There is no angle or dihedral definitions for patches in .psf! Edward Patrick Obrien (Thu Apr 29 2004 - 10:43:09 CDT)
questions about set cellBasisVector and a ligand ... Xiaobing Tian (Thu Apr 29 2004 - 10:06:53 CDT)
RE: Lithium Scott, Greg (Wed Apr 28 2004 - 23:30:08 CDT)
Fwd: vmd-l: MOE discussion Mike McCallum (Wed Apr 28 2004 - 23:11:43 CDT)
Re: Lithium Brian Bennion (Wed Apr 28 2004 - 22:59:38 CDT)
Lithium Scott, Greg (Wed Apr 28 2004 - 22:04:14 CDT)
problems with namdplot fixed by using new plotting program Cheri M Turman (Tue Apr 27 2004 - 16:34:42 CDT)
Heteroatom entries Mithun Mitra (Tue Apr 27 2004 - 10:17:00 CDT)
Question about external forces Yang Yang (Tue Apr 27 2004 - 01:55:13 CDT)
compiling namd on amd opteron arch : TCL problems (fwd) Jerry Ebalunode (Fri Apr 23 2004 - 17:07:40 CDT)
Re: Discrepency in cell volume? Cell origin can move in NPT? Edward Patrick Obrien (Mon Apr 26 2004 - 09:11:34 CDT)
Issues with SMD Gadi Oron (Mon Apr 26 2004 - 07:05:26 CDT)
NPT ensemble restart, put in new basis vectors? Edward Patrick Obrien (Sun Apr 25 2004 - 13:19:21 CDT)
Discrepency in cell volume? Cell origin can move in NPT? Edward Patrick Obrien (Sun Apr 25 2004 - 12:56:36 CDT)
Binding energy analysis AHMET BAKAN (Sat Apr 24 2004 - 21:09:45 CDT)
Re: Fw: Calculating Free Energy Change Jérôme Hénin (Fri Apr 23 2004 - 16:07:52 CDT)
Re: Hi Shirley Hui (Fri Apr 23 2004 - 16:02:54 CDT)
Re: Fw: Calculating Free Energy Change Shirley Hui (Fri Apr 23 2004 - 15:30:01 CDT)
RE: Hi Uday Chippada (Fri Apr 23 2004 - 15:20:56 CDT)
Re: Fw: Calculating Free Energy Change Jérôme Hénin (Fri Apr 23 2004 - 15:00:25 CDT)
Re: Hi himanshu chandola (Sat Apr 24 2004 - 02:09:57 CDT)
Re: What, if no temperatue control specified? Jérôme Hénin (Fri Apr 23 2004 - 14:19:48 CDT)
Re: Fw: Calculating Free Energy Change Shirley Hui (Fri Apr 23 2004 - 13:44:17 CDT)
Hi Uday Chippada (Fri Apr 23 2004 - 12:57:23 CDT)
Re: NAMD: Force Fields Olya Kravchenko (Fri Apr 23 2004 - 11:32:52 CDT)
Re: Fw: Calculating Free Energy Change Brian Bennion (Fri Apr 23 2004 - 11:08:12 CDT)
Re: What, if no temperatue control specified? Brian Bennion (Fri Apr 23 2004 - 10:57:09 CDT)
NAMD: Force Fields Galina Petrova (Fri Apr 23 2004 - 09:00:57 CDT)
Re: What, if no temperatue control specified? Gianluca Interlandi (Fri Apr 23 2004 - 03:59:45 CDT)
Source file in the tutorial Xin Chen (Thu Apr 22 2004 - 16:58:46 CDT)
Fw: Calculating Free Energy Change Shirley Hui (Thu Apr 22 2004 - 13:02:07 CDT)
Re: What, if no temperatue control specified? Brian Bennion (Thu Apr 22 2004 - 12:02:41 CDT)
Re: What, if no temperatue control specified? Juan Alfredo Freites (Thu Apr 22 2004 - 11:54:16 CDT)
Re: What, if no temperatue control specified? Brian Bennion (Thu Apr 22 2004 - 10:20:05 CDT)
Re: What, if no temperatue control specified? Mike McCallum (Thu Apr 22 2004 - 09:43:13 CDT)
What, if no temperatue control specified? Gianluca Interlandi (Thu Apr 22 2004 - 05:56:39 CDT)
Re: how to remove all hydrogen atoms from PDB file? Olya Kravchenko (Wed Apr 21 2004 - 16:34:41 CDT)
opinions on queueing system choices? Matt Harrington (Wed Apr 21 2004 - 16:04:31 CDT)
Temperature control? Gianluca Interlandi (Wed Apr 21 2004 - 10:32:14 CDT)
Re: temperature question in logfile Brian Bennion (Tue Apr 20 2004 - 18:21:12 CDT)
temperature question in logfile Cheri M Turman (Tue Apr 20 2004 - 17:13:28 CDT)
Re: how to remove all hydrogen atoms from PDB file? J. Rui Rodrigues (Tue Apr 20 2004 - 09:04:46 CDT)
Re: how to remove all hydrogen atoms from PDB file? J. Rui Rodrigues (Tue Apr 20 2004 - 09:01:20 CDT)
can i restrain the center of molecule in aqueous solution? li (Tue Apr 20 2004 - 03:43:12 CDT)
Finished install beckloni_at_umdnj.edu (Tue Apr 20 2004 - 00:53:09 CDT)
how to remove all hydrogen atoms from PDB file? Olya Kravchenko (Mon Apr 19 2004 - 17:41:22 CDT)
Re: Weird dihedral error Brian Bennion (Mon Apr 19 2004 - 12:22:35 CDT)
Re: Parallelization of a code from TCB Summer School 2003 Alex V. (Mon Apr 19 2004 - 02:49:05 CDT)
Re: still problems with namdplot Gadi Oron (Sun Apr 18 2004 - 01:51:42 CDT)
Parallelization of a code from TCB Summer School 2003 Yang Yang (Fri Apr 16 2004 - 21:54:46 CDT)
peptid bond omega, problems with settings? Hua Wong (Fri Apr 16 2004 - 09:25:22 CDT)
Re: simulations ceased without any hint Brian Bennion (Fri Apr 16 2004 - 00:09:26 CDT)
simulations ceased without any hint li (Thu Apr 15 2004 - 22:23:13 CDT)
FW: Cable, Sam B ERDC-ITL-MS Contractor (Thu Apr 15 2004 - 15:44:57 CDT)
still problems with namdplot Cheri M Turman (Thu Apr 15 2004 - 14:13:57 CDT)
Re: Gengbin Zheng (Thu Apr 15 2004 - 12:14:36 CDT)
Re: peptid bond omega, problems with settings? Brian Bennion (Thu Apr 15 2004 - 11:25:56 CDT)
(no subject) Cable, Sam B ERDC-ITL-MS Contractor (Thu Apr 15 2004 - 11:17:53 CDT)
COM velocity Amit Paliwal (Thu Apr 15 2004 - 04:50:29 CDT)
Re: Compiling NAMD on amd64 Wenyu Zhong (Thu Apr 15 2004 - 06:35:08 CDT)
namd-L: tcl script for calculate RMS of MD calculation yxiong_at_mail.ccnu.edu.cn (Thu Apr 15 2004 - 03:01:28 CDT)
peptid bond omega, problems with settings? Hua Wong (Thu Apr 15 2004 - 02:27:38 CDT)
Compiling NAMD on amd64 Wenyu Zhong (Thu Apr 15 2004 - 01:42:17 CDT)
fix or Harmonic constraint ? li (Wed Apr 14 2004 - 02:05:19 CDT)
Re: Illegal instruction signal at startup. (with net-rs6k smp) Hansang Bae (Tue Apr 13 2004 - 22:00:48 CDT)
Re: Running namd on Rice Teracluster Chris Samuel (Tue Apr 13 2004 - 20:47:46 CDT)
Re: Running namd on Rice Teracluster Chris Samuel (Tue Apr 13 2004 - 20:43:18 CDT)
Creating Parmtop files for NAMD Edward Patrick Obrien (Tue Apr 13 2004 - 19:42:25 CDT)
Re: Converting PSF TYPES: from XPLOr to CHARMM Mike McCallum (Tue Apr 13 2004 - 09:08:04 CDT)
Converting PSF TYPES: from XPLOr to CHARMM Eric Hajjar (Tue Apr 13 2004 - 07:15:58 CDT)
Re: Running namd on Rice Teracluster Gengbin Zheng (Mon Apr 12 2004 - 13:28:10 CDT)
Running namd on Rice Teracluster Amarda Shehu (Sun Apr 11 2004 - 19:15:41 CDT)
BUG ALERT: Stray PME grid charges detected. li (Fri Apr 09 2004 - 22:04:45 CDT)
Re: Illegal instruction signal at startup. (with net-rs6k smp) Gengbin Zheng (Fri Apr 09 2004 - 18:36:19 CDT)
Re: Illegal instruction signal at startup. (with net-rs6k smp) Hansang Bae (Fri Apr 09 2004 - 16:20:20 CDT)
Re: Illegal instruction signal at startup. (with net-rs6k smp) Brian Bennion (Fri Apr 09 2004 - 15:14:55 CDT)
Re: Illegal instruction signal at startup. (with net-rs6k smp) Hansang Bae (Fri Apr 09 2004 - 14:21:52 CDT)
initial translation of the system Satyavani Vemparala (Fri Apr 09 2004 - 14:17:09 CDT)
Re: Using checkpoints in simulation himanshu chandola (Fri Apr 09 2004 - 19:41:18 CDT)
Re: Generating psf files for non-proteins Alessandro Pedretti (Fri Apr 09 2004 - 07:09:52 CDT)
Using checkpoints in simulation Alex V. (Fri Apr 09 2004 - 05:08:35 CDT)
Re: Illegal instruction signal at startup. (with net-rs6k smp) Gengbin Zheng (Thu Apr 08 2004 - 17:36:49 CDT)
Re: Illegal instruction signal at startup. (with net-rs6k smp) Gengbin Zheng (Thu Apr 08 2004 - 16:31:27 CDT)
Re: Illegal instruction signal at startup. (with net-rs6k smp) Hansang Bae (Thu Apr 08 2004 - 16:26:37 CDT)
Re: Generating psf files for non-proteins Mike McCallum (Thu Apr 08 2004 - 16:22:43 CDT)
Re: Illegal instruction signal at startup. (with net-rs6k smp) Gengbin Zheng (Thu Apr 08 2004 - 16:21:29 CDT)
Re: Fatal Socket error Gengbin Zheng (Thu Apr 08 2004 - 16:16:35 CDT)
Re: using restart files himanshu chandola (Fri Apr 09 2004 - 02:36:55 CDT)
using restart files Ioana Cozmuta (Thu Apr 08 2004 - 14:59:26 CDT)
Generating psf files for non-proteins Scott, Greg (Thu Apr 08 2004 - 13:08:21 CDT)
Fatal Socket error Juan Carlos Mobarec (Thu Apr 08 2004 - 11:05:30 CDT)
Feedback on "alchemify" tool Jérôme Hénin (Thu Apr 08 2004 - 10:52:31 CDT)
Re: using restart files Brian Bennion (Thu Apr 08 2004 - 10:00:01 CDT)
using restart files himanshu chandola (Thu Apr 08 2004 - 18:00:14 CDT)
periodic cell has become too small li (Thu Apr 08 2004 - 02:32:31 CDT)
Re: More NAMD/gm2 problems Chris Samuel (Thu Apr 08 2004 - 00:55:40 CDT)
Re: compiling NAMD Gengbin Zheng (Wed Apr 07 2004 - 20:10:12 CDT)
Re: compiling NAMD Ken Sale (Wed Apr 07 2004 - 19:23:07 CDT)
Re: Installing NAMD Brian Bennion (Wed Apr 07 2004 - 16:56:14 CDT)
Re: how to disable NTER and CTER patches? Olya Kravchenko (Wed Apr 07 2004 - 16:12:19 CDT)
Installing NAMD beckloni_at_umdnj.edu (Wed Apr 07 2004 - 15:56:21 CDT)
Re: how to disable NTER and CTER patches? Brian Bennion (Wed Apr 07 2004 - 15:56:44 CDT)
how to disable NTER and CTER patches? Olya Kravchenko (Wed Apr 07 2004 - 15:18:54 CDT)
Re: Restarting problem with Langevin dynamics Brian Bennion (Wed Apr 07 2004 - 13:50:00 CDT)
Re: Restarting problem with Langevin dynamics Xin Chen (Wed Apr 07 2004 - 13:45:39 CDT)
Re: Restarting problem with Langevin dynamics Brian Bennion (Wed Apr 07 2004 - 09:59:45 CDT)
Re: Restarting problem with Langevin dynamics Xin Chen (Wed Apr 07 2004 - 01:01:55 CDT)
Illegal instruction signal at startup. (with net-rs6k smp) Hansang Bae (Tue Apr 06 2004 - 22:08:02 CDT)
Restarting problem with Langevin dynamics Xin Chen (Tue Apr 06 2004 - 00:05:19 CDT)
Re: capping by psfgen Brian Bennion (Mon Apr 05 2004 - 11:59:38 CDT)
Re: # of processors Gengbin Zheng (Mon Apr 05 2004 - 00:41:44 CDT)
Re: _alloca undefined symbol (OS X/XL compiler) Gengbin Zheng (Mon Apr 05 2004 - 00:20:45 CDT)
Re: namd2.5 on myrinet cluster Florian Barth (Sun Apr 04 2004 - 18:34:40 CDT)
capping by psfgen tsaih_at_ncifcrf.gov (Sun Apr 04 2004 - 13:36:58 CDT)
restart files himanshu chandola (Sun Apr 04 2004 - 19:51:34 CDT)
Re: namd2.5 on myrinet cluster Gengbin Zheng (Sat Apr 03 2004 - 20:40:12 CST)
namd2.5 on myrinet cluster Florian Barth (Sat Apr 03 2004 - 17:59:39 CST)
_alloca undefined symbol (OS X/XL compiler) Mike McCallum (Fri Apr 02 2004 - 18:29:26 CST)
coarse grained force field Giovanni (Fri Apr 02 2004 - 15:29:06 CST)
Haptic Device Uday Chippada (Fri Apr 02 2004 - 13:55:42 CST)
about delta-G in PMF calculation Hyonseok Hwang (Thu Apr 01 2004 - 22:36:27 CST)
Restarting problem with Langevin dynamics Xin Chen (Wed Mar 31 2004 - 15:11:58 CST)
Re: More NAMD/gm2 problems Gengbin Zheng (Wed Mar 31 2004 - 02:17:57 CST)
Re: More NAMD/gm2 problems Chris Samuel (Wed Mar 31 2004 - 00:40:36 CST)
More NAMD/gm2 problems David Chalmers (Tue Mar 30 2004 - 23:58:20 CST)
Re: counterions David Chalmers (Tue Mar 30 2004 - 23:12:17 CST)
Re: counterions himanshu chandola (Wed Mar 31 2004 - 03:13:51 CST)
Re: water box Amit Paliwal (Tue Mar 30 2004 - 08:45:01 CST)
Re: timeout on running namd Gengbin Zheng (Tue Mar 30 2004 - 13:23:15 CST)
Re: counterions Brian Bennion (Tue Mar 30 2004 - 12:41:03 CST)
Re: Problems compiling Charm++ for Myrinet Gengbin Zheng (Tue Mar 30 2004 - 12:40:05 CST)
Re: water box Brian Bennion (Tue Mar 30 2004 - 12:36:30 CST)
timeout on running namd Amarda Shehu (Tue Mar 30 2004 - 12:09:02 CST)
water box Amit Paliwal (Tue Mar 30 2004 - 06:03:30 CST)
Problems compiling Charm++ for Myrinet David Chalmers (Mon Mar 29 2004 - 18:53:46 CST)
Spring Constant Uday Chippada (Mon Mar 29 2004 - 17:48:56 CST)
counterions himanshu chandola (Tue Mar 30 2004 - 02:53:19 CST)
# of processors Neema Salimi (Mon Mar 29 2004 - 13:02:30 CST)
A tool to set up alchemical FEP transformations Jérôme Hénin (Mon Mar 29 2004 - 10:27:12 CST)
Re: Tcl: loadtotalforces Jérôme Hénin (Mon Mar 29 2004 - 07:33:29 CST)
Tcl: loadtotalforces g srinivasa murthy (Mon Mar 29 2004 - 05:11:49 CST)
Processor load Alex V. (Sun Mar 28 2004 - 09:11:01 CST)
Re: Running on Alpha cluster Gengbin Zheng (Fri Mar 26 2004 - 11:43:38 CST)
Re: initial temp of simulation Tim Isgro (Fri Mar 26 2004 - 10:46:49 CST)
How do I Heat, then Switch to NPT in the same *.config? Jerry W. Jenkins (Fri Mar 26 2004 - 10:42:22 CST)
Re: Running on Alpha cluster Alex V. (Fri Mar 26 2004 - 03:31:22 CST)
psfgen question li (Fri Mar 26 2004 - 01:06:21 CST)
Re: initial temp of simulation yxiong_at_mail.ccnu.edu.cn (Thu Mar 25 2004 - 19:47:01 CST)
Re: initial temp of simulation Tim Isgro (Thu Mar 25 2004 - 11:11:07 CST)
Re: initial temp of simulation mashaojie (Thu Mar 25 2004 - 07:39:17 CST)
warning messages in psfgen tsaih_at_ncifcrf.gov (Wed Mar 24 2004 - 14:35:43 CST)
Re: FEP calculations: defining hybrid residues Jérôme Hénin (Wed Mar 24 2004 - 11:55:54 CST)
FEP calculations: defining hybrid residues Satyavani Vemparala (Wed Mar 24 2004 - 10:04:53 CST)
Protonated aspartic acid apw397_at_soton.ac.uk (Wed Mar 24 2004 - 06:10:11 CST)
residence time Ioana Cozmuta (Tue Mar 23 2004 - 21:51:10 CST)
Re: FEP and restraints Jérôme Hénin (Tue Mar 23 2004 - 14:42:12 CST)
FEP and restraints Michael Grabe (Tue Mar 23 2004 - 13:45:32 CST)
Re: adding ions Michael Grabe (Mon Mar 22 2004 - 14:36:35 CST)
Re: adding ions Brian Bennion (Mon Mar 22 2004 - 14:11:46 CST)
adding ions Amarda Shehu (Mon Mar 22 2004 - 13:30:09 CST)
Re: Getting forces: segmentation violation or illegal instruction Fangqiang Zhu (Mon Mar 22 2004 - 11:54:41 CST)
Getting forces: segmentation violation or illegal instruction Justyna Jaroniec (Mon Mar 22 2004 - 11:09:25 CST)
Unwrap molecules Ekta Khurana (Sun Mar 21 2004 - 21:55:06 CST)
large increase in pressure after minimization Satyavani Vemparala (Sun Mar 21 2004 - 20:23:33 CST)
initial temp of simulation Streiff, John H. (Fri Mar 19 2004 - 11:35:10 CST)
Re: hydrogen bonds in NAMD Tim Isgro (Fri Mar 19 2004 - 11:25:47 CST)
running multiple minimizations Stern, Julie (Fri Mar 19 2004 - 09:20:34 CST)
Re: construct a protein surrounded by membrane mashaojie (Fri Mar 19 2004 - 08:41:20 CST)
distance constraints in NAMD tsaih_at_ncifcrf.gov (Fri Mar 19 2004 - 07:06:34 CST)
Re: Is it necessary to neutralize the system with NAMD program? Jérôme Hénin (Fri Mar 19 2004 - 04:39:06 CST)
Re: charmrun vs. miprun and nature of parallelism Gengbin Zheng (Fri Mar 19 2004 - 02:10:26 CST)
construct a protein surrounded by membrane mashaojie (Fri Mar 19 2004 - 01:52:37 CST)
Re: Load balance strategy Gengbin Zheng (Fri Mar 19 2004 - 01:41:44 CST)
Re: NAMD support for Myranet GM2 drivers Gengbin Zheng (Fri Mar 19 2004 - 01:30:49 CST)
hydrogen bonds in NAMD Ioana Cozmuta (Fri Mar 19 2004 - 01:02:25 CST)
NAMD support for Myranet GM2 drivers David Chalmers (Thu Mar 18 2004 - 22:29:52 CST)
RE: minimization problem Ahmet Bakan (Thu Mar 18 2004 - 18:43:00 CST)
RE: minimization problem Ahmet Bakan (Thu Mar 18 2004 - 18:31:09 CST)
Re: minimization problem himanshu chandola (Fri Mar 19 2004 - 05:42:41 CST)
Re: minimization problem Brian Bennion (Thu Mar 18 2004 - 18:00:23 CST)
minimization problem Olya Kravchenko (Thu Mar 18 2004 - 17:32:17 CST)
Re: dimer minimisation and psfgen problem Brian Bennion (Thu Mar 18 2004 - 17:24:45 CST)
Re: GdHCl parameters Brian Bennion (Thu Mar 18 2004 - 17:19:38 CST)
GdHCl parameters Ruxandra Dima (Thu Mar 18 2004 - 16:18:16 CST)
Re: dimer minimisation and psfgen problem Uday Chippada (Thu Mar 18 2004 - 14:44:35 CST)
Re: undefined loops Brian Bennion (Thu Mar 18 2004 - 12:16:58 CST)
undefined loops Stern, Julie (Thu Mar 18 2004 - 11:47:39 CST)
charmrun vs. miprun and nature of parallelism Stern, Julie (Thu Mar 18 2004 - 11:39:39 CST)
Re: Load balance strategy Alex V. (Thu Mar 18 2004 - 00:03:19 CST)
Re: Load balance strategy Gengbin Zheng (Wed Mar 17 2004 - 11:31:03 CST)
Surface tension Adrian Wiley (Wed Mar 17 2004 - 10:43:37 CST)
Re: Namd with intel compilers. Gengbin Zheng (Wed Mar 17 2004 - 10:52:27 CST)
Re: dimer minimisation and psfgen problem Brian Bennion (Wed Mar 17 2004 - 10:18:12 CST)
dimer minimisation and psfgen problem Hua Wong (Wed Mar 17 2004 - 03:17:57 CST)
Re: Is it necessary to neutralize the system with NAMD program? Brian Bennion (Tue Mar 16 2004 - 16:58:52 CST)
Re: Is it necessary to neutralize the system with NAMD program? Aaron Oakley (Tue Mar 16 2004 - 16:18:00 CST)
Re: Load balance strategy Gadi Oron (Tue Mar 16 2004 - 15:44:03 CST)
Namd with intel compilers. Hansang Bae (Tue Mar 16 2004 - 14:51:47 CST)
Re: Is it necessary to neutralize the system with NAMD program? Brian Bennion (Tue Mar 16 2004 - 13:07:07 CST)
Re: Load balance strategy Brian Bennion (Tue Mar 16 2004 - 11:31:15 CST)
Re: psf question Brian Bennion (Tue Mar 16 2004 - 11:02:21 CST)
Load balance strategy Alex V. (Tue Mar 16 2004 - 09:23:28 CST)
psf question Hua Wong (Tue Mar 16 2004 - 03:12:38 CST)
RE: Urea and GdHCl parameters Ahmet Bakan (Mon Mar 15 2004 - 13:15:18 CST)
Urea and GdHCl parameters Ruxandra Dima (Mon Mar 15 2004 - 12:01:51 CST)
Re: Running on Alpha cluster Gengbin Zheng (Mon Mar 15 2004 - 10:07:24 CST)
Re: FIRSTTIMESTEP in config file Gadi Oron (Mon Mar 15 2004 - 04:02:07 CST)
Re: Paper on Classical treatment for calculating pKas Volodymyr Nechiporuk-Zloy (Mon Mar 15 2004 - 03:31:21 CST)
constraintScaling parameter Peter Jones (Sun Mar 14 2004 - 10:33:40 CST)
TCL question Gadi Oron (Sun Mar 14 2004 - 08:13:55 CST)
Is it necessary to neutralize the system with NAMD program? yxiong_at_mail.ccnu.edu.cn (Sun Mar 14 2004 - 02:56:41 CST)
Running on Alpha cluster Alex V. (Fri Mar 12 2004 - 22:27:26 CST)
Re: Clustermatic 4.0 Gengbin Zheng (Fri Mar 12 2004 - 21:36:16 CST)
Question on finding suitable force field for MD simulations Fung Wai Keung (Fri Mar 12 2004 - 21:00:06 CST)
Paper on Classical treatment for calculating pKas Brian Bennion (Fri Mar 12 2004 - 13:40:33 CST)
Re: clustering - fault tolerant NAMD Gengbin Zheng (Fri Mar 12 2004 - 13:18:01 CST)
Re: clustering yu275197_at_yorku.ca (Fri Mar 12 2004 - 10:57:04 CST)
Segmantation fault writing dcd files. Ivan Vinogradov (Fri Mar 12 2004 - 09:07:26 CST)
Re: Segmentation fault. Alex V. (Wed Mar 10 2004 - 09:04:33 CST)
octahedral period BCs Peter Jones (Fri Mar 12 2004 - 08:01:13 CST)
clustering Leandro Martinez (Fri Mar 12 2004 - 07:15:35 CST)
Running on Alpha cluster Alex V. (Wed Mar 10 2004 - 03:40:12 CST)
NAMD on itanium? freddie salsbury (Thu Mar 11 2004 - 18:04:10 CST)
Segmentation fault. ivan.vinogradov_at_utoronto.ca (Thu Mar 11 2004 - 16:21:24 CST)
Solvate Package Satyavani Vemparala (Wed Mar 10 2004 - 18:22:54 CST)
Re: SMD with different pH Brian Bennion (Wed Mar 10 2004 - 10:47:37 CST)
Re: SMD with different pH Volodymyr Nechiporuk-Zloy (Wed Mar 10 2004 - 06:37:39 CST)
FIRSTTIMESTEP in config file Satyavani Vemparala (Wed Mar 10 2004 - 05:49:55 CST)
Re: Binding Energy Brian Bennion (Tue Mar 09 2004 - 10:42:19 CST)
Re: Generate PSF structure Tim Isgro (Tue Mar 09 2004 - 10:24:01 CST)
Re: Binding Energy Gadi Oron (Tue Mar 09 2004 - 07:37:22 CST)
Clustermatic 4.0 Jerry Ebalunode (Mon Mar 08 2004 - 14:16:20 CST)
Re: Binding Energy Brian Bennion (Mon Mar 08 2004 - 13:23:38 CST)
Binding Energy Ahmet Bakan (Mon Mar 08 2004 - 12:57:18 CST)
Re: Generate PSF structure Peter Spijker (Mon Mar 08 2004 - 12:23:12 CST)
Re: Generate PSF structure Brian Bennion (Mon Mar 08 2004 - 12:17:52 CST)
question on PMF output Hyonseok Hwang (Mon Mar 08 2004 - 12:08:13 CST)
Generate PSF structure Peter Spijker (Mon Mar 08 2004 - 12:01:28 CST)
selectConstrZ Ekta Khurana (Mon Mar 08 2004 - 12:01:09 CST)
how to fix some atoms? yingxiong (Mon Mar 08 2004 - 03:55:35 CST)
Dealing with hyperthreading Gadi Oron (Sun Mar 07 2004 - 04:43:09 CST)
hydrogen bonds during MD yu275197_at_yorku.ca (Sat Mar 06 2004 - 11:03:49 CST)
Re: TCL: getting forces Fangqiang Zhu (Fri Mar 05 2004 - 14:04:31 CST)
Re: SMD with different pH Brian Bennion (Fri Mar 05 2004 - 10:16:09 CST)
SMD with different pH Volodymyr Nechiporuk-Zloy (Fri Mar 05 2004 - 07:52:55 CST)
TCL: getting forces Bartosz Dobrzelecki (Fri Mar 05 2004 - 04:58:31 CST)
A question about RMSD calculation Chen Yongzhi (Thu Mar 04 2004 - 22:54:08 CST)
SMD: many atom pulling Harindar Keer (Thu Mar 04 2004 - 21:29:12 CST)
A question about RMSD calculation Chen Yongzhi (Thu Mar 04 2004 - 21:07:52 CST)
General and specific atom types in NAMD? David Chalmers (Thu Mar 04 2004 - 18:21:42 CST)
RE: CP3-NH3 error Han Choe (Thu Mar 04 2004 - 16:48:46 CST)
Re: CP3-NH3 error Tim Isgro (Thu Mar 04 2004 - 13:56:44 CST)
generating PSF files using CHARMM for FEP calculations Satyavani Vemparala (Thu Mar 04 2004 - 11:56:07 CST)
Re: Amber on with H-bond Fangqiang Zhu (Thu Mar 04 2004 - 01:00:31 CST)
Re: Amber on with H-bond Sichun Yang (Thu Mar 04 2004 - 00:15:56 CST)
Re: Amber on with H-bond Fangqiang Zhu (Wed Mar 03 2004 - 21:45:15 CST)
about guesscoord mashaojie (Wed Mar 03 2004 - 21:31:05 CST)
Amber on with H-bond Sichun Yang (Wed Mar 03 2004 - 17:59:55 CST)
BUG ALERT: Bad global exclusion count! li (Mon Mar 03 2008 - 17:56:01 CST)
Re: rotating constraints constant himanshu chandola (Wed Mar 03 2004 - 05:57:11 CST)
Re: CP3-NH3 error Tim Isgro (Tue Mar 02 2004 - 17:31:08 CST)
Re: temp coupling coefficients Jérôme Hénin (Tue Mar 02 2004 - 15:39:24 CST)
rotating constraints constant himanshu chandola (Wed Mar 03 2004 - 02:12:34 CST)
Generating novel structure Fangqiang Zhu (Tue Mar 02 2004 - 13:38:12 CST)
Re: temp coupling coefficients Hyonseok Hwang (Tue Mar 02 2004 - 13:18:22 CST)
Re: Locally Enhanced Sampling Fangqiang Zhu (Tue Mar 02 2004 - 11:51:09 CST)
Locally Enhanced Sampling Vlad Cojocaru (Tue Mar 02 2004 - 07:46:01 CST)
Re: temp coupling coefficients Jérôme Hénin (Tue Mar 02 2004 - 03:58:28 CST)
temp coupling coefficients Peter Jones (Tue Mar 02 2004 - 01:03:53 CST)
CP3-NH3 error Han Choe (Mon Mar 01 2004 - 21:36:44 CST)
Converting Gromacs OPLS parameters to Charmm format David Chalmers (Mon Mar 01 2004 - 17:41:57 CST)
Re: Constant pressure contril Sichun Yang (Sun Feb 29 2004 - 22:48:15 CST)
Re: Constant pressure contril Jérôme Hénin (Sun Feb 29 2004 - 02:41:07 CST)
Re: Constant pressure contril Sichun Yang (Sat Feb 28 2004 - 20:39:58 CST)
Re: Constant pressure contril Juan Alfredo Freites (Sat Feb 28 2004 - 20:18:51 CST)
Re: Constant pressure contril Sichun Yang (Sat Feb 28 2004 - 18:32:31 CST)
Re: Constant pressure contril Jérôme Hénin (Sat Feb 28 2004 - 17:50:46 CST)
Constant pressure contril Sichun Yang (Sat Feb 28 2004 - 17:05:03 CST)
Re: Restart using amber force field Sichun Yang (Fri Feb 27 2004 - 16:13:25 CST)
Re: Restart using amber force field Fangqiang Zhu (Fri Feb 27 2004 - 15:00:29 CST)
Re: TIP5P Brian Bennion (Fri Feb 27 2004 - 13:39:04 CST)
Restart using amber force field Sichun Yang (Fri Feb 27 2004 - 11:30:47 CST)
distance dependant dielectric constant Wagener, M. (Markus) (Fri Feb 27 2004 - 06:58:43 CST)
NAMD and Gromac OPLS parameters David Chalmers (Thu Feb 26 2004 - 21:46:12 CST)
Re: Timestep in restart output Tim Isgro (Thu Feb 26 2004 - 21:01:21 CST)
TIP5P Aaron Oakley (Thu Feb 26 2004 - 18:40:22 CST)
PME grid sizes Satyavani Vemparala (Thu Feb 26 2004 - 17:05:01 CST)
Re: Compiling on G5 using xlC klsale (Thu Feb 26 2004 - 15:38:47 CST)
Re: Compiling on G5 using xlC Gengbin Zheng (Thu Feb 26 2004 - 15:40:59 CST)
Re: Timestep in restart output Brian Bennion (Thu Feb 26 2004 - 15:29:38 CST)
Re: <no subject> Brian Bennion (Thu Feb 26 2004 - 14:44:07 CST)
<no subject> klsale (Thu Feb 26 2004 - 13:02:36 CST)
Timestep in restart output Sichun Yang (Thu Feb 26 2004 - 12:38:08 CST)
Re: Charm++ Problem Brian Bennion (Thu Feb 26 2004 - 12:09:18 CST)
palindromic error reading in a restart file. Brian Bennion (Thu Feb 26 2004 - 12:04:49 CST)
Charm++ Problem Ben Brooks (Thu Feb 26 2004 - 11:32:28 CST)
restraints Michael Grabe (Wed Feb 25 2004 - 15:47:31 CST)
error codes in charmrun/namd? J. Rui Rodrigues (Wed Feb 25 2004 - 14:02:43 CST)
Re: atom numbers limitation Jim Phillips (Tue Feb 24 2004 - 15:31:06 CST)
Re: firsttimestep Jim Phillips (Tue Feb 24 2004 - 15:22:27 CST)
temperature coupling in NAMD Satyavani Vemparala (Tue Feb 24 2004 - 15:09:57 CST)
namd on linux cluster Giovanni (Tue Feb 24 2004 - 13:45:44 CST)
entropy calculations Ioana Cozmuta (Mon Feb 23 2004 - 17:41:54 CST)
langevin coupling coefficient Hyonseok Hwang (Mon Feb 23 2004 - 14:39:47 CST)
Re: psf file for zeolite-water system Fangqiang Zhu (Mon Feb 23 2004 - 14:16:26 CST)
Re: CoM motion not removed Jim Phillips (Mon Feb 23 2004 - 11:01:02 CST)
Re: Running AIX version of NAMD on IBM cluster Jim Phillips (Mon Feb 23 2004 - 10:50:50 CST)
Re: psf file for zeolite-water system $B:,>k(J $B6Q(J (Mon Feb 23 2004 - 02:22:31 CST)
Re: electron density calculations of lipid bilayers Jérôme Hénin (Mon Feb 23 2004 - 01:47:11 CST)
psf file for zeolite-water system Ozgur YAZAYDIN (Sun Feb 22 2004 - 21:21:03 CST)
Re: warnings during NAMD simulations. li (Sat Feb 23 2008 - 08:43:42 CST)
electron density calculations of lipid bilayers Satyavani Vemparala (Sun Feb 22 2004 - 17:45:58 CST)
Re: your mail Brian Bennion (Sun Feb 22 2004 - 00:44:16 CST)
(no subject) yu275197_at_yorku.ca (Sun Feb 22 2004 - 00:37:27 CST)
query on memory usuage g srinivasa murthy (Sat Feb 21 2004 - 22:58:26 CST)
Alchemical FEP calculations in NAMD Satyavani Vemparala (Fri Feb 20 2004 - 22:09:43 CST)
warnings during NAMD simulations. Lv Shouqin (Fri Feb 20 2004 - 06:25:12 CST)
crash in FFT optimizing... Brian Bennion (Thu Feb 19 2004 - 15:44:28 CST)
Re: Langevin dynamics Jérôme Hénin (Thu Feb 19 2004 - 15:33:20 CST)
Langevin Dynamics again Wei Fu (Thu Feb 19 2004 - 15:23:22 CST)
Langevin dynamics Wei Fu (Thu Feb 19 2004 - 14:26:13 CST)
(no subject) Michael Grabe (Thu Feb 19 2004 - 14:29:21 CST)
Re: Running AIX version of NAMD on IBM cluster Brian Bennion (Thu Feb 19 2004 - 14:06:20 CST)
Re: langevin with waterbox ? Lei Guo (Thu Feb 19 2004 - 13:48:36 CST)
Re: langevin with waterbox ? Jérôme Hénin (Thu Feb 19 2004 - 13:43:04 CST)
Re: langevin with waterbox ? Lei Guo (Thu Feb 19 2004 - 13:12:01 CST)
Re: langevin with waterbox ? Jérôme Hénin (Thu Feb 19 2004 - 11:48:13 CST)
langevin with waterbox ? Manali Mehendale (Thu Feb 19 2004 - 10:41:16 CST)
Re: Running AIX version of NAMD on IBM cluster Gengbin Zheng (Wed Feb 18 2004 - 21:37:55 CST)
CoM motion not removed Neema Salimi (Wed Feb 18 2004 - 13:00:22 CST)
atom numbers limitation Wei Fu (Wed Feb 18 2004 - 14:43:27 CST)
some cluster questions Leandro Martinez (Wed Feb 18 2004 - 07:51:13 CST)
firsttimestep Ekta Khurana (Tue Feb 17 2004 - 18:50:30 CST)
Re: Problem with Tcl & psfgen Jim Phillips (Tue Feb 17 2004 - 17:33:20 CST)
Re: Running AIX version of NAMD on IBM cluster Hansang Bae (Tue Feb 17 2004 - 17:13:47 CST)
Problem with Tcl & psfgen scott.brown_at_abbott.com (Tue Feb 17 2004 - 13:36:56 CST)
Regarding SMD atom and forces Uday Chippada (Tue Feb 17 2004 - 12:37:37 CST)
Re: Argon solvent Jérôme Hénin (Tue Feb 17 2004 - 12:03:16 CST)
Argon solvent Gianni De Fabritiis (Tue Feb 17 2004 - 09:55:02 CST)
Direction of SMD force aida_at_mit.edu (Tue Feb 17 2004 - 09:06:16 CST)
for help from all! Lv Shouqin (Sat Feb 14 2004 - 23:14:38 CST)
NAMD on OpenMosix. Nicholas M Glykos (Sat Feb 14 2004 - 10:40:44 CST)
Temperature control methods in NAMD Satyavani Vemparala (Sat Feb 14 2004 - 07:32:22 CST)
Re: Compiling NAMD on Tungsten.ncsa Jim Phillips (Fri Feb 13 2004 - 17:35:20 CST)
Re: Re: too much rattle Amarda Shehu (Fri Feb 13 2004 - 12:24:12 CST)
Re: Re: too much rattle Brian Bennion (Fri Feb 13 2004 - 12:51:50 CST)
Re: Re: too much rattle Brian Bennion (Thu Feb 12 2004 - 16:50:30 CST)
Re: too much rattle Amarda Shehu (Thu Feb 12 2004 - 16:16:40 CST)
Re: retinal parameters Brian Bennion (Thu Feb 12 2004 - 10:11:48 CST)
Pair interaction output. Gadi Oron (Thu Feb 12 2004 - 06:21:23 CST)
retinal parameters Anna Modzelewska (Thu Feb 12 2004 - 05:28:40 CST)
Compiling NAMD on Tungsten.ncsa Satyavani Vemparala (Wed Feb 11 2004 - 20:18:12 CST)
segmantation violation li (Tue Feb 12 2008 - 09:13:36 CST)
Temperature control methods in NAMD Satyavani Vemparala (Wed Feb 11 2004 - 18:07:13 CST)
Regarding SMD atom and forces Uday Chippada (Wed Feb 11 2004 - 16:00:11 CST)
water box is too small li (Mon Feb 11 2008 - 08:37:46 CST)
Re: improving parallel on mac cluster yu275197_at_yorku.ca (Tue Feb 10 2004 - 18:23:39 CST)
Re: improving parallel on mac cluster David E. Konerding (Tue Feb 10 2004 - 18:21:32 CST)
Re: concatenating two DCD files J. Rui Rodrigues (Tue Feb 10 2004 - 18:01:10 CST)
concatenating two DCD files Satyavani Vemparala (Tue Feb 10 2004 - 17:28:27 CST)
Re: improving parallel on mac cluster yu275197_at_yorku.ca (Tue Feb 10 2004 - 16:47:34 CST)
clustering macs yu275197_at_yorku.ca (Tue Feb 10 2004 - 16:04:58 CST)
Source code for NAMD Satyavani Vemparala (Tue Feb 10 2004 - 10:30:13 CST)
Warning: 1 margin violations li (Sun Feb 10 2008 - 15:12:43 CST)
Re: problem:psfgen- not unique coordinates Tim Isgro (Mon Feb 09 2004 - 20:05:30 CST)
Re: Minimization with CHARMM Tim Isgro (Mon Feb 09 2004 - 17:04:13 CST)
Re: minimization scripts Tim Isgro (Mon Feb 09 2004 - 16:53:33 CST)
problem:psfgen- not unique coordinates Satyavani Vemparala (Mon Feb 09 2004 - 15:14:02 CST)
minimization scripts Gerald Quon (Mon Feb 09 2004 - 12:09:29 CST)
Re: improving parallel on mac cluster Brian Bennion (Mon Feb 09 2004 - 12:05:09 CST)
improving parallel on mac cluster yu275197_at_yorku.ca (Mon Feb 09 2004 - 11:44:31 CST)
Changing SMD parameters Gadi Oron (Mon Feb 09 2004 - 07:32:11 CST)
temperature control question Hyonseok Hwang (Sun Feb 08 2004 - 22:31:39 CST)
building charm++ on macosX yu275197_at_yorku.ca (Sat Feb 07 2004 - 16:51:15 CST)
Minimization with CHARMM ted q (Sat Feb 07 2004 - 15:56:11 CST)
Missing coordinates and psfgen Eric R Johnson (Sat Feb 07 2004 - 14:56:55 CST)
Re: mac clustering Gengbin Zheng (Sat Feb 07 2004 - 00:10:28 CST)
mac clustering yu275197_at_yorku.ca (Fri Feb 06 2004 - 23:34:41 CST)
Re: distance constraint Jim Phillips (Fri Feb 06 2004 - 14:34:50 CST)
Re: user-supplied conformational restraints Hyonseok Hwang (Thu Feb 05 2004 - 15:41:49 CST)
user-supplied conformational restraints Simon Sharpe (Thu Feb 05 2004 - 14:13:31 CST)
distance constraint Hyonseok Hwang (Wed Feb 04 2004 - 17:56:20 CST)
Running AIX version of NAMD on IBM cluster aida_at_mit.edu (Wed Feb 04 2004 - 14:54:21 CST)
RE: creating Charmm psf from Xplor format EPF (Esben Peter Friis) (Wed Feb 04 2004 - 07:40:50 CST)
creating Charmm psf from Xplor format Shunzhou Wan (Wed Feb 04 2004 - 06:32:42 CST)
Re: NAMD and Vega? Alessandro Pedretti (Wed Feb 04 2004 - 06:33:52 CST)
NAMD and Vega? Josef Scheiber (Wed Feb 04 2004 - 05:04:01 CST)
Re: Momenta output format Jim Phillips (Tue Feb 03 2004 - 16:54:28 CST)
Momenta output format Neema Salimi (Mon Feb 02 2004 - 13:59:45 CST)
Re: rotating constraints Jim Phillips (Mon Feb 02 2004 - 13:27:10 CST)
Re: How do we combine chains in the end Jim Phillips (Mon Feb 02 2004 - 11:54:51 CST)
Pair interaction calculations in precompiled NAMD Liu, Zhanwu (Mon Feb 02 2004 - 05:34:03 CST)
How do we combine chains in the end Uday Chippada (Sat Jan 31 2004 - 11:37:42 CST)
thankyou MinSoo Kim (Fri Jan 30 2004 - 12:54:32 CST)
Re: Pair interaction energy Brian Bennion (Fri Jan 30 2004 - 12:38:35 CST)
Re: Pair interaction energy Ioana Cozmuta (Fri Jan 30 2004 - 12:28:05 CST)
Re: Pair interaction energy Brian Bennion (Fri Jan 30 2004 - 12:08:38 CST)
Re: Pair interaction energy Ioana Cozmuta (Fri Jan 30 2004 - 11:57:16 CST)
Pair interaction energy Sundaramoorthy, Munirathinam (Fri Jan 30 2004 - 10:46:22 CST)
RE: minimization problem - "Bad global exclusion count,possible error!" Brian Bennion (Fri Jan 30 2004 - 10:43:36 CST)
RE: minimization problem - "Bad global exclusion count,possible error!" Frances Leung (Fri Jan 30 2004 - 02:52:09 CST)
Re: psfgen question Brian Bennion (Fri Jan 30 2004 - 10:13:35 CST)
RE: minimization problem - "Bad global exclusion count, possible error!" Brian Bennion (Fri Jan 30 2004 - 10:09:19 CST)
psfgen question MinSoo Kim (Fri Jan 30 2004 - 04:00:35 CST)
Re: dcd format himanshu chandola (Fri Jan 30 2004 - 14:10:21 CST)
generating psf for RNA using psfgen MinSoo Kim (Fri Jan 30 2004 - 01:53:40 CST)
RE: minimization problem - "Bad global exclusion count, possible error!" Harindar Keer (Thu Jan 29 2004 - 18:21:19 CST)
RE: minimization problem - "Bad global exclusion count, possible error!" Frances Leung (Thu Jan 29 2004 - 21:20:54 CST)
Re: minimization problem - "Bad global exclusion count, possible error!" Brian Bennion (Thu Jan 29 2004 - 17:46:34 CST)
Re: minimization problem - "Bad global exclusion count, possible error!" Uday Chippada (Thu Jan 29 2004 - 17:05:54 CST)
Re: minimization problem - "Bad global exclusion count, possible error!" Brian Bennion (Thu Jan 29 2004 - 17:19:39 CST)
Re: dcd format Brian Bennion (Thu Jan 29 2004 - 17:11:37 CST)
dcd format himanshu chandola (Fri Jan 30 2004 - 04:25:28 CST)
minimization problem - "Bad global exclusion count, possible error!" Frances Leung (Thu Jan 29 2004 - 19:25:27 CST)
rotating constraints himanshu chandola (Fri Jan 30 2004 - 01:28:51 CST)
geometric mean Leandro Martinez (Thu Jan 29 2004 - 07:53:58 CST)
Re: previous question about multiplicity Brian Bennion (Wed Jan 28 2004 - 15:32:35 CST)
Re: previous question about multiplicity Jim Phillips (Wed Jan 28 2004 - 14:27:50 CST)
Re: previous question about multiplicity Brian Bennion (Wed Jan 28 2004 - 14:18:20 CST)
Re: previous question about multiplicity Jim Phillips (Wed Jan 28 2004 - 14:12:45 CST)
previous question about multiplicity Brian Bennion (Tue Jan 27 2004 - 19:06:02 CST)
Weird dihedral error Brian Bennion (Tue Jan 27 2004 - 13:16:51 CST)
Re: question on Berendsen's temperature coupling method Vlad Cojocaru (Fri Jan 23 2004 - 02:54:03 CST)
NAMD on p690 IBM cluster Vlad Cojocaru (Tue Jan 27 2004 - 03:56:35 CST)
Re: question on potential energy for individual atoms Jim Phillips (Mon Jan 26 2004 - 17:52:55 CST)
Re: Jim Phillips (Mon Jan 26 2004 - 17:51:12 CST)
Re: seed value in SMD Jim Phillips (Mon Jan 26 2004 - 17:46:59 CST)
Re: Hydroxyprolin force field. Jim Phillips (Mon Jan 26 2004 - 17:44:10 CST)
question on potential energy for individual atoms Hyonseok Hwang (Fri Jan 23 2004 - 19:59:53 CST)
(no subject) Michael Grabe (Fri Jan 23 2004 - 17:22:54 CST)
Re: Hydroxyprolin force field. Brian Bennion (Fri Jan 23 2004 - 11:15:30 CST)
Re: Parameters and topologies for aa at different protonation states Brian Bennion (Fri Jan 23 2004 - 11:14:18 CST)
Hydroxyprolin force field. ivan.vinogradov_at_utoronto.ca (Fri Jan 23 2004 - 11:01:36 CST)
Parameters and topologies for aa at different protonation states Bartosz Dobrzelecki (Fri Jan 23 2004 - 06:45:26 CST)
seed value in SMD Ioana Cozmuta (Thu Jan 22 2004 - 20:54:15 CST)
Re: question on Berendsen's temperature coupling method Jim Phillips (Thu Jan 22 2004 - 17:19:22 CST)
Re: missing atoms warnings for psfgen Jim Phillips (Thu Jan 22 2004 - 17:08:27 CST)
Heme A topology? Olya Kravchenko (Thu Jan 22 2004 - 17:05:49 CST)
Re: TCl question Jim Phillips (Thu Jan 22 2004 - 16:52:35 CST)
question on Berendsen's temperature coupling method Hyonseok Hwang (Tue Jan 20 2004 - 13:13:59 CST)
Re: problem with running namd on Linux cluster Gengbin Zheng (Tue Jan 20 2004 - 11:18:20 CST)
missing atoms warnings for psfgen Frances Leung (Mon Jan 19 2004 - 21:47:33 CST)
problem with running namd on Linux cluster zhilei chen (Mon Jan 19 2004 - 11:51:11 CST)
implicit solvent model Frances Leung (Mon Jan 19 2004 - 20:10:59 CST)
TCl question Ioana Cozmuta (Mon Jan 19 2004 - 16:41:52 CST)
Re: test and a short question! Fangqiang Zhu (Mon Jan 19 2004 - 15:15:15 CST)
test and a short question! Vlad Cojocaru (Mon Jan 19 2004 - 08:18:50 CST)
Re: NAMD linking problem Gengbin Zheng (Fri Jan 16 2004 - 15:46:09 CST)
Bad global exclusion count Harindar Keer (Fri Jan 16 2004 - 14:06:28 CST)
Re: Hybond calulator and display John Stone (Fri Jan 16 2004 - 13:07:09 CST)
Hybond calulator and display Jerry Ebalunode (Fri Jan 16 2004 - 12:24:30 CST)
Re: 1QSU Tim Isgro (Thu Jan 15 2004 - 15:32:22 CST)
1QSU Uday Chippada (Thu Jan 15 2004 - 13:45:03 CST)
NAMD linking problem Valery Miftakhov (Tue Jan 13 2004 - 22:15:59 CST)
Re:charmm27 Wei Fu (Tue Jan 13 2004 - 19:27:02 CST)
Re: charmm27 Amit Paliwal (Tue Jan 13 2004 - 12:31:50 CST)
Re: charmm27 Brian Bennion (Tue Jan 13 2004 - 17:24:49 CST)
charmm27 Wei Fu (Tue Jan 13 2004 - 17:15:49 CST)
Periodic cell too small Alemayehu Gorfe Abebe (Tue Jan 13 2004 - 16:42:59 CST)
Periodic cel too small Alemayehu Gorfe Abebe (Tue Jan 13 2004 - 08:33:39 CST)
Dihedral restraint : question closed Jérôme Hénin (Mon Jan 12 2004 - 05:04:49 CST)
langevin dynamics Wei Fu (Sun Jan 11 2004 - 15:04:41 CST)
Dihedral restraint Jérôme Hénin (Sun Jan 11 2004 - 13:08:05 CST)
SMD-velocity unit Ioana Cozmuta (Sat Jan 10 2004 - 18:24:18 CST)
Interaction energy for fixed atoms AMIT PALIWAL (Fri Jan 09 2004 - 17:35:13 CST)
Re: limit on the number of residues in each segment Brian Bennion (Fri Jan 09 2004 - 16:53:20 CST)
limit on the number of residues in each segment junxie_at_uwm.edu (Fri Jan 09 2004 - 16:45:31 CST)
RATTLE Alg junxie_at_uwm.edu (Fri Jan 09 2004 - 16:41:51 CST)
Re: Charm++ nodelist commands Gadi Oron (Thu Jan 08 2004 - 02:40:06 CST)
Interaction energy between fixed atoms Amit Paliwal (Wed Jan 07 2004 - 08:03:12 CST)
[Fwd: total energy stuck between two levels] Amit Paliwal (Wed Jan 07 2004 - 05:10:03 CST)
Re: Potential Terms Jim Phillips (Wed Jan 07 2004 - 09:45:11 CST)
Re: total energy stuck between two levels Jim Phillips (Wed Jan 07 2004 - 09:22:27 CST)
Re: total energy stuck between two levels Jérôme Hénin (Wed Jan 07 2004 - 02:42:33 CST)
total energy stuck between two levels AMIT PALIWAL (Tue Jan 06 2004 - 22:20:10 CST)
Re: SMD force (fwd) Ioana Cozmuta (Tue Jan 06 2004 - 18:25:20 CST)
Re: SMD force (fwd) Fangqiang Zhu (Tue Jan 06 2004 - 17:14:56 CST)
interaction energy zhilei chen (Tue Jan 06 2004 - 13:26:47 CST)
how to get "the rms force and maximum force" of energy minimization ? yxiong_at_mail.ccnu.edu.cn (Mon Jan 05 2004 - 23:45:18 CST)
Potential Terms AHMET BAKAN (Mon Jan 05 2004 - 12:20:02 CST)
SMD force (fwd) Ioana Cozmuta (Mon Jan 05 2004 - 13:36:16 CST)
Re: alchemical free energy perturbation by way of Jérôme Hénin (Mon Jan 05 2004 - 09:10:52 CST)
alchemical free energy perturbation AMIT PALIWAL (Mon Jan 05 2004 - 00:37:05 CST)
Re: Charm++ nodelist commands Gengbin Zheng (Sun Jan 04 2004 - 23:18:42 CST)
Warning: 8 margin violations li (Sat Jan 05 2008 - 10:05:25 CST)
Re: NAMD for Opteron? Gengbin Zheng (Sun Jan 04 2004 - 18:32:21 CST)
NAMD for Opteron? David Chalmers (Sun Jan 04 2004 - 17:55:15 CST)
Re: Charm++ nodelist commands Gengbin Zheng (Sun Jan 04 2004 - 16:23:27 CST)
SMD force Ioana Cozmuta (Sat Jan 03 2004 - 22:01:45 CST)
flexible cell Juan Alfredo Freites (Sat Jan 03 2004 - 21:44:05 CST)
different result when I run the same *.conf file many times. yxiong_at_mail.ccnu.edu.cn (Sat Jan 03 2004 - 05:18:48 CST)
question on the coordinates of hydrogen atoms Hyonseok Hwang (Fri Jan 02 2004 - 17:45:50 CST)
Re: Re: Intel C/C++ compiler Version 8 for compiling NAMD on IA64 Gengbin Zheng (Fri Jan 02 2004 - 12:16:32 CST)
Re: Charm++ nodelist commands Gengbin Zheng (Fri Jan 02 2004 - 12:09:51 CST)
Re: Re: Intel C/C++ compiler Version 8 for compiling NAMD on IA64 Jerry Ebalunode (Fri Jan 02 2004 - 12:04:41 CST)

Last message date: Wed Dec 28 2005 - 17:21:37 CST
Archived on: Wed Feb 29 2012 - 15:40:15 CST

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