NAMD-L: By Thread
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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
- 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: vmd-l: convert DCD files to CRD format Angel Gonzalez Wong (Mon Dec 26 2005 - 09:19:53 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)
- FATAL ERROR: unknown floating-point error, errno = 4 Manori Indira Jayasinghe (Thu Dec 22 2005 - 23:16:41 CST)
- Re: FATAL ERROR: unknown floating-point error, errno = 4 Chris Chipot (Fri Dec 23 2005 - 01:22:32 CST)
- UNABLE TO OPEN .psf FILE Joshua D. Moore (Fri Dec 23 2005 - 02:53:00 CST)
- preparing a dimeric protein for NAMD Irene Newhouse (Thu Dec 22 2005 - 21:28:21 CST)
- Question about Generating DCD files with only specified atoms Joshua D. Moore (Thu Dec 22 2005 - 18:06:09 CST)
- The HT-HT-OT angle parameter for TIP3? Shirley Li (Thu Dec 22 2005 - 14:57:19 CST)
- Locally Enhanced Sampling milton sonoda (Wed Dec 21 2005 - 17:34:23 CST)
- Kinetic Energy difference using restart binaries Mikolai Fajer (Wed Dec 21 2005 - 12:54:13 CST)
- FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CN7 CN7 CN7 Shirley Li (Wed Dec 21 2005 - 14:56:36 CST)
- Re: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CN7 CN7 CN7 Joshua D. Moore (Wed Dec 21 2005 - 16:57:37 CST)
- The angle parameters for CN7 are missing in NAMD? Shirley Li (Wed Dec 21 2005 - 18:02:07 CST)
- UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT Shirley Li (Thu Dec 22 2005 - 13:16:00 CST)
- Re: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT Peter Freddolino (Thu Dec 22 2005 - 14:35:37 CST)
- Re: ANGLE PARAMETERS (It works now) Shirley Li (Thu Dec 22 2005 - 16:54:06 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)
- PSF file format Jindal Shah (Tue Dec 20 2005 - 15:55:23 CST)
- define abf1 and abf2 for CM of water and CM of molecule Manori Indira Jayasinghe (Mon Dec 19 2005 - 22:53:42 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)
- 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)
- Counterions: how to decide how many to put it? Ching Wong (Tue Dec 13 2005 - 17:44:33 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)
- center of mass motion: problems Vani Krishna (Thu Dec 08 2005 - 16:27:06 CST)
- Reading from DCD file and running MD Shahid Qamar (Wed Dec 07 2005 - 14:35:05 CST)
- Packaging 100 cations and anions in a box ir7_at_njit.edu (Tue Dec 06 2005 - 22:47:56 CST)
- Atoms moving too fast Eric Perim (Tue Dec 06 2005 - 13:05:10 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)
- 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)
- Adding amino acids to an existing pdb structure LEWYN LI (Sun Dec 04 2005 - 21:30:49 CST)
- restart problem liu xin (Fri Dec 02 2005 - 00:01:26 CST)
- Problems opening the Extended Trajectory File Eric Perim (Thu Dec 01 2005 - 13:36:36 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)
- 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)
- 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)
- temperature "coupling coefficient" in NAMD curcio (Fri Nov 18 2005 - 11:09:13 CST)
- Replica-Exchange MD Marc Baaden (Fri Nov 18 2005 - 03:18:19 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)
- 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)
- 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)
- FEP.... Raul Araya Secchi (Fri Nov 11 2005 - 09:39:41 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)
- PMF calculation using fixed restraints Vani Krishna (Sun Nov 06 2005 - 12:26:22 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)
- 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)
- The vector direction in SMD Grace Shen (Fri Nov 04 2005 - 15:01:51 CST)
- Size of water box santanu chatterjee (Fri Nov 04 2005 - 13:06:07 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)
- Increasing temp during MD Grace Shen (Thu Nov 03 2005 - 12:11:27 CST)
- How to atomselect several residues Grace Shen (Wed Nov 02 2005 - 17:28:50 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)
- CA CL CA angle? Richard Wood (Tue Nov 01 2005 - 11:11:44 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)
- Question regarding SMD Grace Shen (Mon Oct 31 2005 - 15:11:01 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)
- All or Nothing at All?? Angelo R. Rossi (Sat Oct 29 2005 - 11:41:32 CDT)
- questions about running namd on NCSA cluster tungsten Wei Zhuang (Fri Oct 28 2005 - 17:09:22 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)
- (no subject) Michael Grabe (Thu Oct 27 2005 - 22:39:35 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)
- How to append charmm stream file Grace Shen (Wed Oct 26 2005 - 12:01:23 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 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)
- Can I miminimize some atoms in system Shahid Qamar (Tue Oct 25 2005 - 16:40:06 CDT)
- saving coordinates as a PDB file after minimization in NAMD Richard Wood (Tue Oct 25 2005 - 13:12:02 CDT)
- Re: saving coordinates as a PDB file after minimization in NAMD Richard Law (Tue Oct 25 2005 - 15:44:17 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)
- 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)
- (no subject) Shahid Qamar (Fri Oct 21 2005 - 11:20:08 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)
- SGE (Grid Engine) on Rocks Cluster Mauricio Carrillo Tripp (Wed Oct 19 2005 - 17:27:57 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)
- NAMD on myrinet Hyonseok Hwang (Tue Oct 18 2005 - 16:12:36 CDT)
- Compilation of NAMD on 64-bit NUMA with icc ashwin joshi (Tue Oct 18 2005 - 02:46:18 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)
- 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)
- 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)
- CMAP in VMD error greisen_at_binf.ku.dk (Thu Oct 13 2005 - 15:58:33 CDT)
- Metal Ion and Protein binding Gaurav Sharma (Thu Oct 13 2005 - 12:23:23 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)
- 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)
- gcc4 Gianluca Interlandi (Tue Oct 11 2005 - 16:34:32 CDT)
- running NAMD2 in parallel Gan, Yong \(UMC-Student\) (Tue Oct 11 2005 - 10:42:42 CDT)
- RE: running NAMD2 in parallel Gan, Yong \(UMC-Student\) (Mon Oct 10 2005 - 22:34:32 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)
- namdplot: command not found bo baker (Mon Oct 10 2005 - 17:36:32 CDT)
- Re: namdplot: command not found Pawel Weronski (Tue Oct 11 2005 - 08:22:18 CDT)
- Re: namdplot: command not found Robert Brunner (Tue Oct 11 2005 - 10:32:00 CDT)
- Re: namdplot: command not found bo baker (Tue Oct 11 2005 - 18:56:10 CDT)
- Re: namdplot: command not found bo baker (Wed Oct 12 2005 - 15:27:23 CDT)
- Re: namdplot: command not found bo baker (Thu Oct 13 2005 - 14:26:47 CDT)
- Re: namdplot: command not found Sterling Paramore (Thu Oct 13 2005 - 14:59:36 CDT)
- Re: namdplot: command not found Robert Brunner (Thu Oct 13 2005 - 15:11:37 CDT)
- Re: namdplot: command not found bo baker (Fri Oct 14 2005 - 14:04:53 CDT)
- Re: namdplot: command not found Brian Bennion (Fri Oct 14 2005 - 14:44:14 CDT)
- Re: namdplot: command not found Brian Bennion (Thu Oct 13 2005 - 16:09:03 CDT)
- Re: namdplot: command not found bo baker (Mon Oct 17 2005 - 19:50:01 CDT)
- Re: namdplot: command not found Pawel Weronski (Tue Oct 11 2005 - 08:22:18 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)
- 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)
- topology and parameter for acetylcholine Michel Espinoza-Fonseca (Fri Oct 07 2005 - 06:28:38 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)
- 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)
- autoionize and psfgen, which one first? Shirley Li (Thu Oct 06 2005 - 16:01:42 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)
- 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)
- Re: help generating psf files Peter Freddolino (Wed Oct 05 2005 - 22:09:07 CDT)
- Re: help generating psf files Anna Modzelewska (Thu Oct 06 2005 - 02:37:14 CDT)
- 1-4 interactions scaling Mauricio Carrillo Tripp (Mon Oct 03 2005 - 14:30:00 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)
- 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)
- ABF Simulation Lionel Perrin (Wed Oct 05 2005 - 06:41:44 CDT)
- Re: ABF Simulation Chris Chipot (Wed Oct 05 2005 - 07:58:57 CDT)
- Re: ABF Simulation Lionel Perrin (Thu Oct 06 2005 - 09:13:45 CDT)
- Re: ABF Simulation Jérôme Hénin (Wed Oct 19 2005 - 04:11:17 CDT)
- Re: ABF Simulation Lionel Perrin (Fri Oct 21 2005 - 04:03:02 CDT)
- Re: ABF Simulation Lionel Perrin (Wed Oct 26 2005 - 10:52:53 CDT)
- Re: ABF Simulation Jérôme Hénin (Fri Oct 28 2005 - 04:05:52 CDT)
- Re: ABF Simulation Lionel Perrin (Wed Nov 02 2005 - 08:28:25 CST)
- Re: ABF Simulation Lionel Perrin (Thu Oct 06 2005 - 09:13:45 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)
- 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¶m 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)
- 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)
- 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)
- random seed ioana_at_pegasus.arc.nasa.gov (Tue Sep 27 2005 - 20:14:25 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)
- 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)
- 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)
- 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 (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 - 16:55:33 CDT)
- segmentation fault on Linux dimka (Mon Sep 19 2005 - 16:48:02 CDT)
- Re: segmentation fault on Linux dimka (Mon Nov 28 2005 - 12:41:25 CST)
- pair.pdb and cutoff for pairInteraction Shirley Li (Tue Nov 29 2005 - 11:00:02 CST)
- Re: pair.pdb and cutoff for pairInteraction Peter Freddolino (Tue Nov 29 2005 - 11:26:19 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 JC Gumbart (Tue Nov 29 2005 - 23:52:51 CST)
- Re: pair.pdb and cutoff for pairInteraction JC Gumbart (Wed Nov 30 2005 - 00:10:44 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)
- log file bo baker (Mon Sep 19 2005 - 14:09:42 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)
- energy values Anna Modzelewska (Tue Sep 13 2005 - 06:29:27 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)
- RE: Sybyl trajectory Edelmiro Moman (Tue Sep 06 2005 - 10:33:37 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)
- vmdtext and .cshrc. bo baker (Fri Sep 02 2005 - 18:26:29 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)
- NAMD & Gromacs FF Mauricio Carrillo Tripp (Thu Sep 01 2005 - 16:21:50 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)
- 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)
- Pressure Profile Simulation Gan, Yong \(UMC-Student\) (Wed Aug 24 2005 - 21:36:51 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)
- 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)
- 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)
- 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)
- 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)
- par_all27_prot_lipid.inp bo baker (Thu Aug 18 2005 - 16:29:15 CDT)
- Linux-MPI binary of NAMD 2.6b1 Joshua D. Moore (Thu Aug 18 2005 - 06:09:41 CDT)
- moments of inertia, principal axes Stern, Julie (Wed Aug 17 2005 - 19:00:53 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)
- New BioCoRE server released Robert Brunner (Wed Aug 17 2005 - 12:00:16 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)
- 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)
- 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)
- 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)
- 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: Charmm++5.9 build on Mac OS X by IB xlc compiler Gengbin Zheng (Tue Aug 09 2005 - 11:59:15 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: Re: Charmm++5.9 build on Mac OS X by IB xlc compiler Gengbin Zheng (Wed Aug 31 2005 - 12:32:56 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 Jason Lee (Thu Sep 01 2005 - 16:46:24 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)
- 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: Re: Charmm++5.9 build on Mac OS X by IB xlc compiler Gengbin Zheng (Sun Sep 04 2005 - 11:08:03 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: Charmm++5.9 build on Mac OS X by IB xlc compiler Gengbin Zheng (Tue Aug 09 2005 - 11:59:15 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)
- For help with .log file. Boyang Wang (Sun Aug 07 2005 - 14:13:33 CDT)
- 4th Annual Workshop on Charm++ and its Applications 2005 Jim Phillips (Fri Aug 05 2005 - 17:40:30 CDT)
- volume from VMD and NAMD different? Brian Bennion (Fri Aug 05 2005 - 16:12:34 CDT)
- error in config file Brian Bennion (Fri Aug 05 2005 - 11:28:14 CDT)
- Fatal error: vivek sharma (Thu Aug 04 2005 - 07:58:30 CDT)
- wrap ions Stern, Julie (Wed Aug 03 2005 - 23:13:05 CDT)
- Help with psf and par for small molecules santanu chatterjee (Wed Aug 03 2005 - 15:12:40 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)
- 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)
- 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 Michel Espinoza-Fonseca (Tue Aug 02 2005 - 09:50:18 CDT)
- Nanotube Simulations Gaurav Sharma (Tue Aug 02 2005 - 08:51:14 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)
- running on two different machines.... Navratna Vajpai (Sun Jul 31 2005 - 02:27:57 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 (Sat Jul 30 2005 - 10:42:29 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)
- 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)
- restarting SMD jobs Vani Krishna (Tue Jul 26 2005 - 20:25:38 CDT)
- VMD solvate in CCl4 Jack (Tue Jul 26 2005 - 08:37:08 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)
- 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)
- Incorrect periodic box imaging with AMBER parameters Grzegorz Jezierski (Mon Jul 25 2005 - 04:11:20 CDT)
- Re: Incorrect periodic box imaging with AMBER parameters Charles Danko (Mon Jul 25 2005 - 08:32:20 CDT)
- Re: Incorrect periodic box imaging with AMBER parameters Grzegorz Jezierski (Thu Aug 04 2005 - 13:04:05 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 nordgren_at_sas.upenn.edu (Thu Aug 04 2005 - 17:40:58 CDT)
- Re: Incorrect periodic box imaging with AMBER parameters Grzegorz Jezierski (Fri Aug 05 2005 - 06:23:57 CDT)
- Re: Incorrect periodic box imaging with AMBER parameters Grzegorz Jezierski (Thu Aug 04 2005 - 13:04:05 CDT)
- Re: Incorrect periodic box imaging with AMBER parameters Grzegorz Jezierski (Mon Aug 08 2005 - 12:43:20 CDT)
- Re: Incorrect periodic box imaging with AMBER parameters Charles Danko (Mon Jul 25 2005 - 08:32:20 CDT)
- system becomes very large when set LangevinPiston on Xiaoqing Wang (Sun Jul 24 2005 - 22:06:43 CDT)
- Re: system becomes very large when set LangevinPiston on Xiaoqing Wang (Tue Jul 26 2005 - 04:48:13 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)
- output in tcl samantha cox (Fri Jul 22 2005 - 15:06:06 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)
- namdplot error Stern, Julie (Thu Jul 21 2005 - 20:06:53 CDT)
- catdcd-generated files and CHARMM Chang, Christopher (Thu Jul 21 2005 - 11:55:25 CDT)
- constrain or fix the system only in Z direction xiaojing gong (Thu Jul 21 2005 - 07:01:33 CDT)
- Energy Problem (Order of Magnitude) s.bora erdemli (Wed Jul 20 2005 - 15:05:03 CDT)
- removing water from DCD Stern, Julie (Wed Jul 20 2005 - 19:49:12 CDT)
- Re: removing water from DCD Shirley Hui (Wed Jul 20 2005 - 20:25:51 CDT)
- Re: removing water from DCD JC Gumbart (Wed Jul 20 2005 - 20:50:49 CDT)
- Re: removing water from DCD s.bora erdemli (Wed Jul 20 2005 - 21:06:53 CDT)
- Re: removing water from DCD Alessandro Pedretti (Thu Jul 21 2005 - 01:55:34 CDT)
- RE: removing water from DCD Pijush Ghosh (Wed Jul 20 2005 - 22:03:20 CDT)
- How to run for periodic boundary Conditions? Snigdha Chakraborty (Wed Jul 20 2005 - 12:19:32 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)
- changing file Deborah Jameson (Wed Jul 20 2005 - 03:18:12 CDT)
- Bromine Matthew Wilce (Wed Jul 20 2005 - 01:43:43 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 wmsmith (Mon Jul 18 2005 - 13:04:14 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)
- 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)
- 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)
- 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)
- PDB files for carbon nanotubes Gaurav Sharma (Thu Jul 14 2005 - 14:33:05 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)
- Energy Order of Magnitude s.bora erdemli (Mon Jul 11 2005 - 11:20:15 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 ËïæÃæà (Fri Jul 08 2005 - 03:54:19 CDT)
- force shifted cutoff Stern, Julie (Thu Jul 07 2005 - 18:06:15 CDT)
- XPLOR psf format Stern, Julie (Thu Jul 07 2005 - 14:16:48 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)
- Unable to Generate PSF file ! Tamal Banerjee (Mon Jul 04 2005 - 08:09:43 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)
- 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 ) Sascha Tayefeh (Wed Jun 29 2005 - 09:56:54 CDT)
- Adding Misc. Potentials (e.g. spherical/repulsive restraints/constraints ) Sascha Tayefeh (Wed Jun 29 2005 - 09:31:23 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)
- free energy pertubation,binding energy and constant s.bora erdemli (Tue Jun 28 2005 - 14:30:07 CDT)
- segfaults in mm_malloc Brian Bennion (Tue Jun 28 2005 - 10:27:31 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)
- namdplot, grpah is empty Raeanne Napoleon (Mon Jun 27 2005 - 11:01:58 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)
- catdcd and dcdunitcell Philip Fowler (Mon Jun 27 2005 - 05:07:01 CDT)
- Re: catdcd and dcdunitcell Ben Roberts (Mon Jun 27 2005 - 07:47:39 CDT)
- Re: catdcd and dcdunitcell Philip Fowler (Tue Jun 28 2005 - 07:15:36 CDT)
- Re: catdcd and dcdunitcell Philip Fowler (Tue Jun 28 2005 - 07:18:15 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 - 09:27:06 CDT)
- Re: catdcd and dcdunitcell Jérôme Hénin (Tue Jun 28 2005 - 10:54:09 CDT)
- Re: catdcd and dcdunitcell Philip Fowler (Tue Jun 28 2005 - 11:07:38 CDT)
- Re: catdcd and dcdunitcell Ben Roberts (Tue Jun 28 2005 - 18:27:07 CDT)
- Re: catdcd and dcdunitcell Joshua D. Moore (Fri Jul 22 2005 - 16:04:00 CDT)
- Re: catdcd and dcdunitcell Ben Roberts (Mon Jun 27 2005 - 07:47:39 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)
- new approach to counter FEP end-point VDW clashes Floris Buelens (Sun Jun 26 2005 - 07:41:14 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)
- 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)
- 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)
- 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)
- 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)
- Fixed restraint Shahid Qamar (Tue Jun 21 2005 - 17:56:09 CDT)
- langevin vs coupling to a heat bath patrick wintrode (Tue Jun 21 2005 - 15:25:29 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)
- Gramicidin Swarna Patra (Mon Jun 20 2005 - 20:54:09 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)
- 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)
- velocity file of atoms at each time step debashis.sikdar_at_ndsu.edu (Sun Jun 19 2005 - 22:28:14 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: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? Aaron Oakley (Tue Jun 21 2005 - 01:48:52 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?? Leonardo Sepulveda Durán (Tue Jun 21 2005 - 12:42:07 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)
- RE: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? Blake Charlebois (Tue Jun 21 2005 - 15:41:19 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: 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?? apw397_at_soton.ac.uk (Wed Jun 22 2005 - 10:41:58 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?? Marcos Sotomayor (Sun Jun 26 2005 - 14:04:28 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)
- 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)
- set center Swarna Patra (Thu Jun 16 2005 - 22:53:28 CDT)
- aquaporin question Samuel Flores (Thu Jun 16 2005 - 15:39:11 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)
- How to conservate energy during NVE simulations??? Leonardo Sepulveda Durán (Wed Jun 15 2005 - 20:55:29 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)
- Poorly guessed coordinates Maria Lin (Tue Jun 14 2005 - 14:03:59 CDT)
- addforce Leandro Martínez (Tue Jun 14 2005 - 10:02:28 CDT)
- MM/PBSA Wei Chen (Mon Jun 13 2005 - 15:41:45 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)
- 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)
- 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)
- RESTARTING CONJUGATE GRADIENT ALGORITHM Jason Lee (Fri Jun 10 2005 - 10:18:33 CDT)
- Script for MD in a loop? Shahid Qamar (Fri Jun 10 2005 - 10:05:34 CDT)
- implicit solvent Wei Zhuang (Thu Jun 09 2005 - 17:47:48 CDT)
- FEP error: Rattle atom constriant Shahid Qamar (Thu Jun 09 2005 - 15:59:11 CDT)
- large vanderwalls energy during minimization shgnwgn_at_eden.rutgers.edu (Thu Jun 09 2005 - 13:31:53 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)
- 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)
- Reverse Free Energy perturbation (FEP)? Shahid Qamar (Wed Jun 08 2005 - 15:35:30 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: 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)
- 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)
- 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)
- 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)
- 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)
- 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)
- the lastest version of NAMD source junwang (Sun May 29 2005 - 12:29:35 CDT)
- questions about anisotropic pressure coupling Frank Yong Jiang (Sat May 28 2005 - 10:34:45 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)
- about *.psf ËïæÃæà (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)
- 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)
- 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)
- Milestoning in NAMD Shahid Qamar (Wed May 18 2005 - 15:46:19 CDT)
- Error in running tutorial files Ragothaman Yennamalli (Wed May 18 2005 - 12:20:50 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)
- 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)
- Condition for stopping MD sim. with NAMD Nicolas Floquet (Tue May 17 2005 - 02:56:45 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)
- 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)
- 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)
- Force constant of harmonic restraint picot.delphine_at_neuf.fr (Thu May 12 2005 - 03:50:11 CDT)
- libimf.so error when compiling charm++ Ben Roberts (Thu May 12 2005 - 01:09:36 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)
- Energy minimization mustapha.hamdi_at_ensi-bourges.fr (Wed May 11 2005 - 12:33:01 CDT)
- Energy minimization mustapha.hamdi_at_ensi-bourges.fr (Wed May 11 2005 - 09:46:40 CDT)
- non-repeatability NAMD simulations roberte_at_organ.su.se (Tue May 10 2005 - 17:08:30 CDT)
- Bad global exclusion count. Boyang Wang (Tue May 10 2005 - 11:56:32 CDT)
- different result from different cpu Xiaoqing Wang (Tue May 10 2005 - 07:31:31 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)
- Re: NAMD 2.5 crashes unpredictably on a 8 way SMP (Linux x86) Gengbin Zheng (Tue May 10 2005 - 01:45:25 CDT)
- Re: NAMD 2.5 crashes unpredictably on a 8 way SMP (Linux x86) Niraj kumar (Tue May 10 2005 - 04:48:59 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) Gengbin Zheng (Tue May 10 2005 - 09:57:04 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)
- Re: Re: NAMD 2.5 crashes unpredictably on a 8 way SMP (Linux x86) Gengbin Zheng (Wed May 11 2005 - 22:07:13 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)
- 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)
- NAMD automation nordgren_at_sas.upenn.edu (Sat May 07 2005 - 23:39:16 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)
- 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)
- 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: 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)
- 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: HEME patch surendra negi (Thu May 05 2005 - 13:38:37 CDT)
- hanging at startup phase 0 Dong Luo (Thu May 05 2005 - 10:47:31 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)
- 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)
- 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)
- Combine pdb and psf files Gan, Yong \(UMC-Student\) (Fri Apr 29 2005 - 16:04:23 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: Generate psf file of DMPC membrane Gan, Yong \(UMC-Student\) (Thu Apr 28 2005 - 11:58:02 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)
- (no subject) Wei Chen (Wed Apr 27 2005 - 11:04:07 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)
- 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)
- Setting target minimization gradient? Chang, Christopher (Fri Apr 22 2005 - 13:15:01 CDT)
- (no subject) valesrdp (Thu Apr 21 2005 - 03:54:58 CDT)
- Interactive Simulations, ligand size limits.... Luis Rosales (Tue Apr 19 2005 - 22:51:52 CDT)
- Re: vmd-l: Interactive Simulations, ligand size limits.... John Stone (Wed Apr 20 2005 - 16:12:20 CDT)
- Re: vmd-l: Interactive Simulations, ligand size limits.... Luis Rosales (Wed Apr 20 2005 - 18:19:58 CDT)
- Re: Re: vmd-l: Interactive Simulations, ligand size limits.... Luis Rosales (Wed Apr 20 2005 - 22:22:10 CDT)
- Re: Re: vmd-l: Interactive Simulations, ligand size limits.... Luis Rosales (Wed Apr 27 2005 - 21:29:51 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.... Brian Bennion (Thu Apr 28 2005 - 12:01:32 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.... Marc Baaden (Fri Apr 29 2005 - 04:01:27 CDT)
- Re: vmd-l: Interactive Simulations, ligand size limits.... John Stone (Wed Apr 20 2005 - 16:12:20 CDT)
- duplicated key CA in psfgen mustapha.hamdi_at_ensi-bourges.fr (Tue Apr 19 2005 - 12:49:33 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)
- 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)
- minimization problem Stern, Julie (Thu Apr 14 2005 - 13:41:19 CDT)
- RE: about protonation of HIS in membrane protein Michel Espinoza-Fonseca (Wed Apr 13 2005 - 19:47:52 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)
- about protonation of HIS in membrane protein Baoqiang Cao (Wed Apr 13 2005 - 09:21:08 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)
- 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: 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: 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)
- Different electrostatic and Van der Waals cutoff Peter Spijker (Fri Apr 08 2005 - 04:56:42 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)
- 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)
- Checkpoint on IRIX of namd 2.5 job not MPI enabled Dow_Hurst (Thu Apr 07 2005 - 09:40:55 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)
- RATTLE and DNA Nicholas M Glykos (Tue Apr 05 2005 - 05:33:48 CDT)
- RE: problem running namd Michel Espinoza-Fonseca (Mon Apr 04 2005 - 13:48:02 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)
- Errors compiling NAMD 2.5 Koo Kee Kiat (Mon Apr 04 2005 - 01:46:34 CDT)
- binary restraint reference coordinates? Cameron Mura (Thu Mar 31 2005 - 20:31:42 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)
- conformational alignment Wen Li (Wed Mar 30 2005 - 15:21:26 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)
- multiple MD simulations Aaron Oakley (Mon Mar 28 2005 - 18:29:39 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)
- pairlist distance debashis.sikdar_at_ndsu.edu (Tue Mar 22 2005 - 14:28:20 CST)
- path problems Michael Grabe (Tue Mar 22 2005 - 01:29:25 CST)
- Re: path problems Gengbin Zheng (Tue Mar 22 2005 - 01:37:52 CST)
- visualizing dynamics output Samuel Flores (Tue Mar 22 2005 - 11:31:31 CST)
- Re: visualizing dynamics output Brian Bennion (Tue Mar 22 2005 - 12:55:00 CST)
- RE: visualizing dynamics output Samuel Flores (Tue Mar 22 2005 - 13:51:07 CST)
- RE: visualizing dynamics output Michel Espinoza-Fonseca (Tue Mar 22 2005 - 14:17:12 CST)
- molecules distorted Samuel Flores (Tue Mar 22 2005 - 15:35:03 CST)
- RE: molecules distorted Michel Espinoza-Fonseca (Tue Mar 22 2005 - 15:37:19 CST)
- How to read charmm binary trajectory file using home-made C/C++ code Wei Zhuang (Tue Mar 22 2005 - 14:39:15 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)
- RE: running VMD from a script? -- oops, never mind! Samuel Flores (Mon Mar 21 2005 - 19:49:50 CST)
- psfgen for DNA Nicholas M Glykos (Mon Mar 21 2005 - 10:20:49 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)
- question about par_all27_prot_lipid.inp Samuel Flores (Sun Mar 20 2005 - 01:34:58 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)
- 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)
- Bio-Image summer school in Paris this year Marc Baaden (Wed Mar 16 2005 - 05:42:59 CST)
- membrane files Gan, Yong \(UMC-Student\) (Tue Mar 15 2005 - 20:54:41 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)
- "Hands-On" Workshop on Computational Biophysics David Brandon (Fri Mar 11 2005 - 15:23:27 CST)
- peridic boundary condition debashis.sikdar_at_ndsu.edu (Fri Mar 11 2005 - 09:08:37 CST)
- Re: peridic boundary condition Marc Q. Ma (Fri Mar 11 2005 - 10:38:15 CST)
- Re: peridic boundary condition Edward Patrick Obrien (Fri Mar 11 2005 - 13:09:43 CST)
- Re: peridic boundary condition Marc Q. Ma (Fri Mar 11 2005 - 13:15:31 CST)
- Re: peridic boundary condition Himanshu Khandelia (Fri Mar 11 2005 - 13:57:23 CST)
- Re: peridic boundary condition John Kerrigan (Fri Mar 11 2005 - 15:18:48 CST)
- Submitting jobs on myrinet...problem Edward Patrick Obrien (Fri Mar 11 2005 - 18:29:19 CST)
- Re: Submitting jobs on myrinet...problem Jerry Ebalunode (Fri Mar 11 2005 - 22:21:55 CST)
- Re: peridic boundary condition Jérôme Hénin (Fri Mar 11 2005 - 15:31:47 CST)
- Re: peridic boundary condition Marc Q. Ma (Fri Mar 11 2005 - 14:00:37 CST)
- Re: peridic boundary condition Marc Q. Ma (Fri Mar 11 2005 - 10:38:15 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)
- Compiling on Linux-PPC970-Myrinet-MPI-xlC Jordi Camps (Thu Mar 10 2005 - 12:57:47 CST)
- Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC Brian Bennion (Thu Mar 10 2005 - 14:11:29 CST)
- Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC Gengbin Zheng (Thu Mar 10 2005 - 15:54:56 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 Jordi Camps (Thu Mar 10 2005 - 18:08:02 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 Chris Samuel (Wed Mar 16 2005 - 00:06:21 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 - 04:37:07 CST)
- Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC Gengbin Zheng (Thu Mar 10 2005 - 15:54:56 CST)
- Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC Brian Bennion (Thu Mar 10 2005 - 14:11:29 CST)
- example scripts Himanshu Khandelia (Thu Mar 10 2005 - 10:03:53 CST)
- compiling Namd on amd64 olivier Walker (Thu Mar 10 2005 - 04:08:08 CST)
- Re: compiling Namd on amd64 Brian Bennion (Thu Mar 10 2005 - 10:20:46 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)
- loodking or topology file for zinc finger Wang Tianhua (Tue Mar 08 2005 - 19:43:02 CST)
- Re: G5 cluster Gengbin Zheng (Tue Mar 08 2005 - 16:41:06 CST)
- G5 clusters Michael Grabe (Tue Mar 08 2005 - 11:17:42 CST)
- NAMD restarts binary files Shirley Hui (Tue Mar 08 2005 - 10:13:08 CST)
- Installing NAMD Michel Espinoza-Fonseca (Mon Mar 07 2005 - 18:18:43 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)
- 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 Michel Espinoza-Fonseca (Mon Mar 07 2005 - 13:37:11 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 - 14:16:16 CST)
- RE: namd on Altix Michel Espinoza-Fonseca (Mon Mar 07 2005 - 15:00:02 CST)
- RE: namd on Altix Michel Espinoza-Fonseca (Mon Mar 07 2005 - 18:43:25 CST)
- RE: namd on Altix Michel Espinoza-Fonseca (Mon Mar 07 2005 - 19:06:35 CST)
- RE: namd on Altix Michel Espinoza-Fonseca (Tue Mar 08 2005 - 15:03:49 CST)
- RE: namd on Altix Michel Espinoza-Fonseca (Tue Mar 08 2005 - 16:57:08 CST)
- RE: namd on Altix Michel Espinoza-Fonseca (Tue Mar 08 2005 - 17:05:52 CST)
- RE: namd on Altix Michel Espinoza-Fonseca (Tue Mar 08 2005 - 17:17:46 CST)
- RE: namd on Altix Michel Espinoza-Fonseca (Tue Mar 08 2005 - 17:31:15 CST)
- RE: namd on Altix Michel Espinoza-Fonseca (Wed Mar 09 2005 - 13:33:35 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)
- 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: clustermatic nodelist file Gengbin Zheng (Wed Mar 02 2005 - 21:29:40 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: Not getting good speed up Gengbin Zheng (Wed Mar 02 2005 - 21:42:39 CST)
- Re: Not getting good speed up Mauricio Carrillo Tripp (Thu Mar 03 2005 - 13:16:24 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 - 13:44:55 CST)
- Re: Not getting good speed up Mauricio Carrillo Tripp (Fri Mar 11 2005 - 15:32:38 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 (Sat Mar 12 2005 - 15:38:06 CST)
- Re: Not getting good speed up Mauricio Carrillo Tripp (Tue Mar 15 2005 - 10:55:16 CST)
- Trouble with NAMD on Myrinet Edward Patrick Obrien (Tue Mar 15 2005 - 14:02:40 CST)
- Re: Trouble with NAMD on Myrinet Gengbin Zheng (Tue Mar 15 2005 - 14:14:14 CST)
- Re: Trouble with NAMD on Myrinet Edward Patrick Obrien (Wed Mar 16 2005 - 10:04:20 CST)
- Re: Re: Trouble with NAMD on Myrinet Gengbin Zheng (Wed Mar 16 2005 - 11:27:19 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 (Thu Mar 03 2005 - 13:16:24 CST)
- Re: Not getting good speed up Gengbin Zheng (Wed Mar 02 2005 - 21:42:39 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)
- 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)
- Kinetic energy Gan, Yong \(UMC-Student\) (Fri Feb 25 2005 - 12:55:09 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)
- 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)
- energy Swarna Patra (Thu Feb 17 2005 - 16:58:36 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)
- 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)
- 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)
- 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)
- 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)
- NAMD crashes with LES option ON Karunesh Arora (Mon Feb 07 2005 - 14:07:18 CST)
- Re: question on running NAMD2 using Amber files Wen Li (Mon Feb 07 2005 - 12:15:41 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)
- 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)
- FEP Wei Chen (Tue Feb 01 2005 - 11:15:24 CST)
- force constraints Swarna Patra (Mon Jan 31 2005 - 19:49:07 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)
- 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)
- BUG ALERT: Mother atom with hydrogenGroupSize of 0! Xiaoqing Wang (Mon Jan 24 2005 - 01:26:21 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)
- DOWSER Charles Danko (Tue Jan 18 2005 - 16:20:06 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)
- Compiling the NAMD on HPUX-ia64 system Error! κ¿ (Sat Jan 15 2005 - 08:35:00 CST)
- charm++ compile problem on x86_64 Steven A. DuChene (Fri Jan 14 2005 - 15:24:02 CST)
- scyld no longer a supported option for building charm++ ? Steven A. DuChene (Fri Jan 14 2005 - 14:30:10 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~ κ¿ (Fri Jan 14 2005 - 04:56:14 CST)
- extracting time from DCDs nordgren_at_sas.upenn.edu (Thu Jan 13 2005 - 19:54:30 CST)
- rattle errors. Brian Bennion (Thu Jan 13 2005 - 10:56:25 CST)
- segmentation violation!! bora erdemli (Thu Jan 13 2005 - 02:15:19 CST)
- Re: segmentation violation!! Brian Bennion (Thu Jan 13 2005 - 10:48:11 CST)
- Re: segmentation violation!! bora erdemli (Fri Jan 14 2005 - 03:06:55 CST)
- Re: segmentation violation!! Brian Bennion (Fri Jan 14 2005 - 10:20:49 CST)
- Re: segmentation violation!! bora erdemli (Sun Jan 16 2005 - 03:59:08 CST)
- Re: segmentation violation!! Brian Bennion (Tue Jan 18 2005 - 10:34:47 CST)
- Re: segmentation violation!! Robert Brunner (Tue Jan 18 2005 - 11:05:00 CST)
- Re: segmentation violation!! bora erdemli (Fri Jan 14 2005 - 03:06:55 CST)
- Re: segmentation violation!! Brian Bennion (Thu Jan 13 2005 - 10:48:11 CST)
- success with opteron myrinet mpi etc Damon Smith (Thu Jan 13 2005 - 01:28:30 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)
- 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)
- thermodynamic integration and NAMD: soft-core or "separation-shifted" vdw potentials Philip Fowler (Mon Jan 10 2005 - 11:12:41 CST)
- Error in when using charmrun Eric Peterson (Sat Jan 08 2005 - 20:39:45 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)
- parameters for NVT ensemble lc_at_chem.au.dk (Fri Jan 07 2005 - 04:51:07 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: Bug alert!!! bora erdemli (Tue Jan 04 2005 - 01:13:37 CST)
- increase in energy over time Peter Bazeley (Mon Jan 03 2005 - 17:27:45 CST)
- prmtop reading error Stern, Julie (Sun Jan 02 2005 - 15:35:42 CST)
- About charm++/namd on AMD64 cluster q=F5=D0=A1=C7=E5?= (Sun Jan 02 2005 - 02:01:32 CST)
- mpi opteron myrinet Damon Smith (Thu Dec 30 2004 - 22:23:09 CST)
- clustermatic 4 and 5 Namd/charm Rene Salmon (Thu Dec 30 2004 - 17:49:47 CST)
- Re: clustermatic 4 and 5 Namd/charm Gengbin Zheng (Thu Dec 30 2004 - 18:52:47 CST)
- Re: clustermatic 4 and 5 Namd/charm Rene Salmon (Fri Dec 31 2004 - 10:08:21 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 (Sat Jan 01 2005 - 14:56:56 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 John Saeger (Sun Jan 02 2005 - 14:18:31 CST)
- Re: clustermatic 4 and 5 Namd/charm Rene Salmon (Fri Dec 31 2004 - 10:08:21 CST)
- Re: clustermatic 4 and 5 Namd/charm Gengbin Zheng (Thu Dec 30 2004 - 18:52:47 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)
- FATAL ERROR: Asymmetric water molecule ? Gaurav Sharma (Tue Dec 21 2004 - 14:58:11 CST)
- Failed to set coordinate for atom errors! Shirley Hui (Mon Dec 20 2004 - 16:32:10 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? κ¿ (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)
- BUG ALERT: Mother atom with hydrogenGroupSize of 0! Vani Krishna (Fri Dec 17 2004 - 11:39:30 CST)
- charmm and dihedral multiplicity mdcooper (Thu Dec 16 2004 - 13:19:02 CST)
- NamdCompile Problem HUSSER Jacky 113956 (Thu Dec 16 2004 - 05:17:41 CST)
- How to chech the harmonic constraint work normally~ κ¿ (Thu Dec 16 2004 - 03:21:17 CST)
- statistical test Aaron Oakley (Wed Dec 15 2004 - 23:17:57 CST)
- turning off fixed atoms in the middle of simulation Vani Krishna (Wed Dec 15 2004 - 10:42:17 CST)
- Autoionize plugin problem Gaurav Sharma (Tue Dec 14 2004 - 12:52:03 CST)
- binding energy bora erdemli (Tue Dec 14 2004 - 07:38:05 CST)
- fatal error vivek sharma (Tue Dec 14 2004 - 00:49:59 CST)
- more than 99999 atoms in PDB files Gilbert G.Feng (Mon Dec 13 2004 - 15:30:55 CST)
- high (or low) pressure readings Charles Danko (Mon Dec 13 2004 - 09:42:52 CST)
- Re: high (or low) pressure readings Brian Bennion (Mon Dec 13 2004 - 11:13:42 CST)
- Re: high (or low) pressure readings nordgren_at_sas.upenn.edu (Mon Dec 13 2004 - 18:30:51 CST)
- Re: high (or low) pressure readings Brian Bennion (Tue Dec 14 2004 - 11:45:13 CST)
- Re: high (or low) pressure readings Charles Danko (Tue Dec 14 2004 - 13:31:21 CST)
- How I can run two simulations one after an other Shahid Qamar (Tue Dec 14 2004 - 14:30:08 CST)
- Re: How I can run two simulations one after an other Michael Grabe (Tue Dec 14 2004 - 15:15:36 CST)
- Re: high (or low) pressure readings nordgren_at_sas.upenn.edu (Mon Dec 13 2004 - 18:30:51 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)
- saving forces using loadforces Ragan Robertson (Sat Dec 11 2004 - 15:39:42 CST)
- Building NAMD with Portland's C++ Comipler Suxing Hu (Thu Dec 09 2004 - 12:29:57 CST)
- namdplot vivek sharma (Thu Dec 09 2004 - 02:13:26 CST)
- Vaccum simulation Narender Singh (Wed Dec 08 2004 - 10:57:48 CST)
- Periodic cell size Suxing Hu (Wed Dec 08 2004 - 10:06:24 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)
- constant velocity smd with distance restraints Gilbert G.Feng (Fri Dec 03 2004 - 14:22:50 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)
- How to treat the terminal residue psfgen in NAMD~ κ¿ (Mon Nov 29 2004 - 20:11:37 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~ κ¿ (Fri Nov 26 2004 - 07:41:55 CST)
- Question:about equilibration~ κ¿ (Thu Nov 25 2004 - 22:05:59 CST)
- Question:about harmonic restraint decrease! κ¿ (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)
- 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)
- 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)
- Writing pdb file.. easier way? Uday Chippada (Thu Nov 18 2004 - 15:58:20 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)
- linux cluster trouble max (Tue Nov 16 2004 - 04:44:36 CST)
- Layers Laura De Luca (Tue Nov 16 2004 - 10:00:07 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~ κ¿ (Sun Nov 14 2004 - 21:02:34 CST)
- A strange thing about psfgen~ κ¿ (Sat Nov 13 2004 - 06:21:35 CST)
- Clustermatic PCI IDs Peter Jones (Thu Nov 11 2004 - 22:54:37 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)
- Implicit water dielectric constant. Ivan Vinogradov (Wed Nov 10 2004 - 10:16:57 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)
- 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)
- 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)
- Solvent mixture Josef Scheiber (Thu Nov 04 2004 - 02:29:17 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)
- 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)
- Tcl dihedral restraints in CG minimisation Ben Roberts (Tue Nov 02 2004 - 17:01:28 CST)
- TCBG "Hands-On" Workshop on Computational Biophysics in Boston, Dec. 5-9 David P. Brandon (Tue Nov 02 2004 - 10:16:21 CST)
- [Periodic Boundary]: from charmm to namd Sascha Tayefeh (Tue Nov 02 2004 - 09:08:42 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)
- System minimization: fail after 199 steps Charles Danko (Mon Nov 01 2004 - 16:30:12 CST)
- Re: System minimization: fail after 199 steps Brian Bennion (Mon Nov 01 2004 - 17:56:32 CST)
- Re: System minimization: fail after 199 steps Charles Danko (Tue Nov 02 2004 - 11:20:21 CST)
- Re: System minimization: fail after 199 steps Brian Bennion (Tue Nov 23 2004 - 12:46:15 CST)
- Re: System minimization: fail after 199 steps Charles Danko (Thu Dec 09 2004 - 11:20:26 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 - 16:01:26 CST)
- Re: System minimization: fail after 199 steps Charles Danko (Fri Dec 10 2004 - 13:32:28 CST)
- Re: System minimization: fail after 199 steps \ (Tue Nov 02 2004 - 13:22:50 CST)
- Re: System minimization: fail after 199 steps Charles Danko (Wed Nov 03 2004 - 11:53:06 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 (Tue Nov 09 2004 - 12:24:00 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 (Thu Nov 11 2004 - 10:07:00 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 (Mon Nov 15 2004 - 11:10:40 CST)
- Re: System minimization: fail after 199 steps Charles Danko (Wed Nov 03 2004 - 11:53:06 CST)
- Re: System minimization: fail after 199 steps Brian Bennion (Mon Nov 01 2004 - 17:56:32 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)
- firsttimestep: simple question Sascha Tayefeh (Fri Oct 29 2004 - 16:16:56 CDT)
- How do you specify which coordinates are to be fixed? Charles Danko (Thu Oct 28 2004 - 16:44:21 CDT)
- RE: How do you specify which coordinates are to be fixed? Blake Charlebois (Thu Oct 28 2004 - 17:36:56 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? Luis Rosales (Thu Oct 28 2004 - 18:32:28 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)
- 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: Compiling NAMD on IA64 cluter Brian Bennion (Wed Oct 27 2004 - 10:19:16 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: vmd-l: psfgen and xplor topology Charles McCallum (Tue Oct 26 2004 - 11:36:37 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)
- 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)
- International PhD Symppozium "DECODING NATURE: HIERARCHY OF INTERACTIONS" Vlad Cojocaru (Wed Oct 20 2004 - 11:10:43 CDT)
- Compilation on an Opteron Server SuSE Linux Enterprise System Version 8 Marek Dynowski (Wed Oct 20 2004 - 07:26:14 CDT)
- Re: Compilation on an Opteron Server SuSE Linux Enterprise System Version 8 Leandro Martinez (Wed Oct 20 2004 - 08:27:50 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 Gengbin Zheng (Wed Oct 20 2004 - 10:24:09 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 Marek Dynowski (Wed Oct 20 2004 - 10:20:16 CDT)
- Re: Compilation on an Opteron Server SuSE Linux Enterprise System Version 8 Chris Samuel (Wed Oct 20 2004 - 18:05:49 CDT)
- Re: Compilation on an Opteron Server SuSE Linux Enterprise System Version 8 Leandro Martinez (Wed Oct 20 2004 - 08:27:50 CDT)
- NAMD interaction with VMD Adam Kubach (Tue Oct 19 2004 - 13:54:18 CDT)
- bug report and stray pme Cheri M Turman (Mon Oct 18 2004 - 16:23:42 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)
- 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: 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: counterion software mashaojie163 (Mon Oct 11 2004 - 01:46:24 CDT)
- [Fwd: counterion software] Cetin Baloglu (Sun Oct 10 2004 - 23:55:20 CDT)
- Re: vmd-l: how can I get hole program mashaojie163 (Sun Oct 10 2004 - 09:23:13 CDT)
- NAMD on Linux cluster with Myrinet Alberto Santana (Sat Oct 09 2004 - 20:42:55 CDT)
- Re: NAMD on Linux cluster with Myrinet Brian Bennion (Sat Oct 09 2004 - 21:59:57 CDT)
- Re: NAMD on Linux cluster with Myrinet Florian Barth (Mon Oct 11 2004 - 19:49:48 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)
- How can I move an atom by 10nm with a step of 0.1nm Shahid Qamar (Mon Oct 04 2004 - 17:22:36 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)
- temperature rescaling and canonical ensemble Jan Lipfert (Thu Sep 30 2004 - 23:27:28 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)
- 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 Oliver Hucke (Mon Sep 20 2004 - 15:23:20 CDT)
- binding constant bora erdemli (Mon Sep 20 2004 - 13:33:45 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)
- 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)
- generating psf files (and more!) mdcooper (Tue Sep 14 2004 - 16:52:38 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)
- Question about Gradient Tolerance during minimization Wolbach, Jeffrey P \(WOLBACH\) (Wed Sep 08 2004 - 13:00:15 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)
- 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)
- compiling NAMD on OSC P4 cluster Amit Paliwal (Fri Sep 03 2004 - 12:11:51 CDT)
- SMD: Group of atoms COM fixed? Vani Krishna (Thu Sep 02 2004 - 20:58:44 CDT)
- 64 nodes behaviour Alexandre Chauvin (Thu Sep 02 2004 - 12:53:23 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)
- 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)
- replica exchange Justin Gullingsrud (Mon Aug 30 2004 - 16:09:42 CDT)
- Temperature Raymond C. Fort Jr. (Mon Aug 30 2004 - 12:47:07 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)
- 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)
- 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)
- 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)
- 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)
- recommendation for 32 CPU cluster: Opteron or ? Matt Harrington (Tue Aug 24 2004 - 17:52:03 CDT)
- Direction of the force in Pair interactions Jérôme Hénin (Tue Aug 24 2004 - 03:46:33 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)
- Node list Shahid Qamar (Wed Aug 18 2004 - 19:25:41 CDT)
- how to get hydrogen-bond energy? Lv Shouqin (Tue Aug 17 2004 - 21:34:17 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)
- > 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)
- 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 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)
- IA64 and MPICH and mpiexec runtime shmem errors Randy Crawford (Thu Aug 05 2004 - 14:38:06 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)
- 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)
- 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)
- 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)
- Myrinet and MPI question Hrant Gharabekyan (Thu Jul 22 2004 - 09:20:01 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)
- 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)
- 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)
- 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)
- Tcl load Saladino, Alex (Thu Jul 15 2004 - 14:52:25 CDT)
- NAMD on the TeraGrid p.w.fowler_at_qmul.ac.uk (Thu Jul 15 2004 - 05:12:47 CDT)
- Re: compiler flags. Brian Bennion (Wed Jul 14 2004 - 23:41:22 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)
- Common Problem!: Periodic cell has become too small for original patch grid! Shirley Hui (Fri Jul 09 2004 - 15:24:43 CDT)
- compiling NAMD Brian Bennion (Fri Jul 09 2004 - 11:56:03 CDT)
- RE: cellBasisVector x,y,z values Kamp, Marc vander (Thu Jul 08 2004 - 10:18:42 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 Peter Jones (Wed Jul 07 2004 - 21:34:52 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 Mauricio Carrillo Tripp (Tue Jul 06 2004 - 12:12:49 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: 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)
- COM position Mauricio Carrillo Tripp (Fri Jul 02 2004 - 16:54:01 CDT)
- Suse 9.0 or Fedora Core 1.0 nalianarmen (Thu Jul 01 2004 - 23:37:18 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)
- 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 (Mon Jun 21 2004 - 14:39:05 CDT)
- pmf error mashaojie163 (Mon Jun 21 2004 - 10:17:20 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)
- 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)
- What binaries should I take? Valodymyr Nechyporuk-Zloy (Fri Jun 18 2004 - 03:49:14 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)
- harmonic restraint Amit Paliwal (Tue Jun 15 2004 - 12:23:10 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)
- start fep calculation mashaojie163 (Fri Jun 11 2004 - 21:13:45 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)
- DIHEDral drift ? Nicholas M Glykos (Thu Jun 10 2004 - 13:15:09 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)
- question about running equilibration in NAMD jz7_at_duke.edu (Tue Jun 08 2004 - 14:25:41 CDT)
- psfgen problem Kamp, Marc vander (Tue Jun 08 2004 - 04:53:39 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)
- 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)
- Simulation with ammonia Marek Dynowski (Fri Jun 04 2004 - 10:53:27 CDT)
- Re: Simulation with ammonia Leandro Martinez (Fri Jun 04 2004 - 13:13:45 CDT)
- Re: Simulation with ammonia AHMET BAKAN (Fri Jun 04 2004 - 15:01:04 CDT)
- Re: Re: Simulation with ammonia AHMET BAKAN (Fri Jun 04 2004 - 17:23:39 CDT)
- IO error when running NAMD on new cluster Edward Patrick Obrien (Sat Jun 05 2004 - 14:44:10 CDT)
- Re: IO error when running NAMD on new cluster Alex V. (Sat Jun 05 2004 - 23:07:22 CDT)
- Re: IO error when running NAMD on new cluster Edward Patrick Obrien (Mon Jun 07 2004 - 09:21:44 CDT)
- Re: Simulation with ammonia AHMET BAKAN (Fri Jun 04 2004 - 15:01:04 CDT)
- Re: Simulation with ammonia Leandro Martinez (Fri Jun 04 2004 - 13:13:45 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: question about using Amber force field in namd Kamp, Marc vander (Thu Jun 03 2004 - 01:19:12 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)
- 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)
- How to use GROMACS force field in NAMD? Armen Poghosyan (Mon May 31 2004 - 02:34:06 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)
- NAMD C++ API Rad Balu (Sat May 29 2004 - 17:58:42 CDT)
- NAMD on HP with Itanium2 Processors Ioana Cozmuta (Fri May 28 2004 - 18:08:37 CDT)
- question on the wrapping algorithm in NAMD Hyonseok Hwang (Thu May 27 2004 - 18:18:26 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)
- 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)
- psfgen non-bonded atom pairs Shirley Hui (Sat May 22 2004 - 01:08:57 CDT)
- Re: NAN GRADIENT TOLERANCE - & - RESTARTING CONJUGATE GRADIENT ALGORITHM Peter Spijker (Thu May 20 2004 - 12:47:57 CDT)
- ATOMS moving too fast Michael Chen (Thu May 20 2004 - 09:50:23 CDT)
- Why Vmd didn't show the Pt-Cl bond myang (Wed May 19 2004 - 18:46:31 CDT)
- hanging at startup phase allison (Wed May 19 2004 - 14:00:25 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)
- 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)
- 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)
- psfgen: failed on segment Olya Kravchenko (Fri May 14 2004 - 19:46:26 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)
- 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)
- Systems of > 100,000 atoms, *.psf files & *.crd files Crozier, Paul S (Tue May 11 2004 - 18:02:51 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 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)
- Parameter File Problem beckloni_at_umdnj.edu (Mon May 10 2004 - 19:47:24 CDT)
- restart simulation Marcela P.Aliste (Mon May 10 2004 - 16:01:28 CDT)
- implementing angle dependent non-bonded interaction? Julius Su (Mon May 10 2004 - 13:09:14 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)
- 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)
- 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)
- How to create a substrate parameter file ? Davit Hakobyan (Thu May 06 2004 - 15:09:00 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: ,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)
- rsh on nodes nalianarmen (Mon May 03 2004 - 23:30:38 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: vmd-l: Re: dcd files generated with catdcd Giovanni (Fri Apr 30 2004 - 13:08:33 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 Xiaobing Tian (Thu Apr 29 2004 - 16:25:14 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)
- 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)
- Binding energy analysis AHMET BAKAN (Sat Apr 24 2004 - 21:09:45 CDT)
- RE: Hi Uday Chippada (Fri Apr 23 2004 - 15:20:56 CDT)
- Hi Uday Chippada (Fri Apr 23 2004 - 12:57:23 CDT)
- Re: Fw: Calculating Free Energy Change Brian Bennion (Fri Apr 23 2004 - 11:08:12 CDT)
- NAMD: Force Fields Galina Petrova (Fri Apr 23 2004 - 09:00:57 CDT)
- Fw: Calculating Free Energy Change Shirley Hui (Thu Apr 22 2004 - 13:02:07 CDT)
- What, if no temperatue control specified? Gianluca Interlandi (Thu Apr 22 2004 - 05:56:39 CDT)
- Re: What, if no temperatue control specified? Mike McCallum (Thu Apr 22 2004 - 09:43:13 CDT)
- Re: What, if no temperatue control specified? Brian Bennion (Thu Apr 22 2004 - 10:20:05 CDT)
- Urey-Bradley term? Gianluca Interlandi (Tue Jun 08 2004 - 12:29:34 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)
- temperature question in logfile Cheri M Turman (Tue Apr 20 2004 - 17:13:28 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)
- 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)
- 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)
- (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)
- 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)
- Creating Parmtop files for NAMD Edward Patrick Obrien (Tue Apr 13 2004 - 19:42:25 CDT)
- BUG ALERT: Stray PME grid charges detected. li (Fri Apr 09 2004 - 22:04:45 CDT)
- initial translation of the system Satyavani Vemparala (Fri Apr 09 2004 - 14:17:09 CDT)
- Using checkpoints in simulation Alex V. (Fri Apr 09 2004 - 05:08:35 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)
- 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: compiling NAMD Ken Sale (Wed Apr 07 2004 - 19:23:07 CDT)
- Installing NAMD beckloni_at_umdnj.edu (Wed Apr 07 2004 - 15:56:21 CDT)
- how to disable NTER and CTER patches? Olya Kravchenko (Wed Apr 07 2004 - 15:18:54 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)
- Re: Illegal instruction signal at startup. (with net-rs6k smp) Gengbin Zheng (Thu Apr 08 2004 - 16:21:29 CDT)
- Re: Illegal instruction signal at startup. (with net-rs6k smp) Hansang Bae (Thu Apr 08 2004 - 16:26:37 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) Gengbin Zheng (Thu Apr 08 2004 - 17:36:49 CDT)
- Re: Illegal instruction signal at startup. (with net-rs6k smp) Hansang Bae (Fri Apr 09 2004 - 14:21:52 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 - 16:20:20 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 (Tue Apr 13 2004 - 22:00:48 CDT)
- Re: Illegal instruction signal at startup. (with net-rs6k smp) Hansang Bae (Thu Apr 08 2004 - 16:26:37 CDT)
- Re: Illegal instruction signal at startup. (with net-rs6k smp) Gengbin Zheng (Thu Apr 08 2004 - 16:21:29 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)
- 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)
- More NAMD/gm2 problems David Chalmers (Tue Mar 30 2004 - 23:58:20 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)
- How do I Heat, then Switch to NPT in the same *.config? Jerry W. Jenkins (Fri Mar 26 2004 - 10:42:22 CST)
- psfgen question li (Fri Mar 26 2004 - 01:06:21 CST)
- warning messages in psfgen tsaih_at_ncifcrf.gov (Wed Mar 24 2004 - 14:35:43 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)
- FEP and restraints Michael Grabe (Tue Mar 23 2004 - 13:45:32 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)
- 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)
- construct a protein surrounded by membrane mashaojie (Fri Mar 19 2004 - 01:52:37 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 - 18:31:09 CST)
- minimization problem Olya Kravchenko (Thu Mar 18 2004 - 17:32:17 CST)
- GdHCl parameters Ruxandra Dima (Thu Mar 18 2004 - 16:18:16 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)
- Surface tension Adrian Wiley (Wed Mar 17 2004 - 10:43:37 CST)
- dimer minimisation and psfgen problem Hua Wong (Wed Mar 17 2004 - 03:17:57 CST)
- Namd with intel compilers. Hansang Bae (Tue Mar 16 2004 - 14:51:47 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)
- Urea and GdHCl parameters Ruxandra Dima (Mon Mar 15 2004 - 12:01:51 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)
- Re: Is it necessary to neutralize the system with NAMD program? Brian Bennion (Tue Mar 16 2004 - 13:07:07 CST)
- Running on Alpha cluster Alex V. (Fri Mar 12 2004 - 22:27:26 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)
- Segmantation fault writing dcd files. Ivan Vinogradov (Fri Mar 12 2004 - 09:07:26 CST)
- octahedral period BCs Peter Jones (Fri Mar 12 2004 - 08:01:13 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)
- FIRSTTIMESTEP in config file Satyavani Vemparala (Wed Mar 10 2004 - 05:49:55 CST)
- Clustermatic 4.0 Jerry Ebalunode (Mon Mar 08 2004 - 14:16:20 CST)
- Binding Energy Ahmet Bakan (Mon Mar 08 2004 - 12:57:18 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)
- 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)
- 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)
- generating PSF files using CHARMM for FEP calculations Satyavani Vemparala (Thu Mar 04 2004 - 11:56:07 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)
- 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)
- Locally Enhanced Sampling Vlad Cojocaru (Tue Mar 02 2004 - 07:46:01 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)
- Constant pressure contril Sichun Yang (Sat Feb 28 2004 - 17:05:03 CST)
- Re: Constant pressure contril Jérôme Hénin (Sat Feb 28 2004 - 17:50:46 CST)
- Re: Constant pressure contril Sichun Yang (Sat Feb 28 2004 - 18:32:31 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 - 20:39:58 CST)
- Re: Constant pressure contril Jérôme Hénin (Sun Feb 29 2004 - 02:41:07 CST)
- Re: Constant pressure contril Sichun Yang (Sun Feb 29 2004 - 22:48:15 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)
- 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)
- TIP5P Aaron Oakley (Thu Feb 26 2004 - 18:40:22 CST)
- PME grid sizes Satyavani Vemparala (Thu Feb 26 2004 - 17:05:01 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)
- 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)
- 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 $B:,>k(J $B6Q(J (Mon Feb 23 2004 - 02:22:31 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)
- (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)
- 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)
- langevin with waterbox ? Manali Mehendale (Thu Feb 19 2004 - 10:41:16 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)
- firsttimestep Ekta Khurana (Tue Feb 17 2004 - 18:50:30 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)
- 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)
- 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)
- 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)
- concatenating two DCD files Satyavani Vemparala (Tue Feb 10 2004 - 17:28:27 CST)
- clustering macs yu275197_at_yorku.ca (Tue Feb 10 2004 - 16:04:58 CST)
- Warning: 1 margin violations li (Sun Feb 10 2008 - 15:12:43 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)
- 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)
- mac clustering yu275197_at_yorku.ca (Fri Feb 06 2004 - 23:34:41 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)
- NAMD and Vega? Josef Scheiber (Wed Feb 04 2004 - 05:04:01 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)
- 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)
- Pair interaction energy Sundaramoorthy, Munirathinam (Fri Jan 30 2004 - 10:46:22 CST)
- psfgen question MinSoo Kim (Fri Jan 30 2004 - 04:00:35 CST)
- generating psf for RNA using psfgen MinSoo Kim (Fri Jan 30 2004 - 01:53:40 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)
- Re: minimization problem - "Bad global exclusion count, possible error!" Brian Bennion (Thu Jan 29 2004 - 17:19:39 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 - 17:46:34 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!" Harindar Keer (Thu Jan 29 2004 - 18:21:19 CST)
- RE: minimization problem - "Bad global exclusion count, possible error!" Brian Bennion (Fri Jan 30 2004 - 10:09:19 CST)
- RE: minimization problem - "Bad global exclusion count,possible error!" Frances Leung (Fri Jan 30 2004 - 02:52:09 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!" 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)
- rotating constraints himanshu chandola (Fri Jan 30 2004 - 01:28:51 CST)
- geometric mean Leandro Martinez (Thu Jan 29 2004 - 07:53:58 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)
- NAMD on p690 IBM cluster Vlad Cojocaru (Tue Jan 27 2004 - 03:56:35 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)
- 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)
- Heme A topology? Olya Kravchenko (Thu Jan 22 2004 - 17:05:49 CST)
- question on Berendsen's temperature coupling method Hyonseok Hwang (Tue Jan 20 2004 - 13:13:59 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)
- test and a short question! Vlad Cojocaru (Mon Jan 19 2004 - 08:18:50 CST)
- Hybond calulator and display Jerry Ebalunode (Fri Jan 16 2004 - 12:24:30 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)
- 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)
- 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)
- [Fwd: total energy stuck between two levels] Amit Paliwal (Wed Jan 07 2004 - 05:10:03 CST)
- total energy stuck between two levels AMIT PALIWAL (Tue Jan 06 2004 - 22:20:10 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)
- Warning: 8 margin violations li (Sat Jan 05 2008 - 10:05:25 CST)
- NAMD for Opteron? David Chalmers (Sun Jan 04 2004 - 17:55:15 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: 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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