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NAMD-L: By Thread

By Thread

1662 messages sorted by: [ author ] [ date ] [ subject ] [ attachment ]
About this archive

Starting: Mon Sep 08 2003 - 09:54:14 CDT
Ending: Fri Dec 31 2004 - 13:16:29 CST

• mpi opteron myrinet Damon Smith (Thu Dec 30 2004 - 22:23:09 CST)
  • Re: mpi opteron myrinet Gengbin Zheng (Thu Dec 30 2004 - 22:50:45 CST)
    • Re: mpi opteron myrinet Damon Smith (Thu Dec 30 2004 - 23:51:01 CST)
      • Re: mpi opteron myrinet Gengbin Zheng (Fri Dec 31 2004 - 00:08:20 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)
• problems on Fedora Core 3 Ruxandra Dima (Tue Dec 28 2004 - 22:48:43 CST)
  • Re: problems on Fedora Core 3 John Saeger (Thu Dec 30 2004 - 13:20:16 CST)
    • Re: problems on Fedora Core 3 Gengbin Zheng (Thu Dec 30 2004 - 15:23:30 CST)
      • Re: problems on Fedora Core 3 lc_at_chem.au.dk (Fri Dec 31 2004 - 13:10:04 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)
  • Re: FATAL ERROR: Asymmetric water molecule ? bora erdemli (Wed Dec 22 2004 - 02:26:19 CST)
• Failed to set coordinate for atom errors! Shirley Hui (Mon Dec 20 2004 - 16:32:10 CST)
  • RE: Failed to set coordinate for atom errors! Blake Charlebois (Mon Dec 20 2004 - 19:27:51 CST)
    • Re: Failed to set coordinate for atom errors! Shirley Hui (Mon Dec 20 2004 - 21:39:30 CST)
• How to use restrin command in NAMD configuration file debashis.sikdar_at_ndsu.edu (Mon Dec 20 2004 - 09:35:28 CST)
  • Re: How to use restrin command in NAMD configuration file Charles Danko (Mon Dec 20 2004 - 10:40:30 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)
  • RE: What the result difference between AMD and Intel CPUS? Blake Charlebois (Mon Dec 20 2004 - 09:43:57 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)
  • Re: resolved: BUG ALERT: Mother atom with hydrogenGroupSize of 0! Vani Krishna (Fri Dec 17 2004 - 18:47:21 CST)
• charmm and dihedral multiplicity mdcooper (Thu Dec 16 2004 - 13:19:02 CST)
  • Re: charmm and dihedral multiplicity Brian Bennion (Fri Dec 17 2004 - 10:55:34 CST)
    • Re: charmm and dihedral multiplicity Vani Krishna (Fri Dec 17 2004 - 18:46:04 CST)
• NamdCompile Problem HUSSER Jacky 113956 (Thu Dec 16 2004 - 05:17:41 CST)
  • Re: NamdCompile Problem Gengbin Zheng (Thu Dec 16 2004 - 13:19:57 CST)
  • Re: NamdCompile Problem Brian Bennion (Thu Dec 16 2004 - 14:39:33 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)
  • xsc information in the dcd file? Gianluca Interlandi (Wed Dec 15 2004 - 10:57:26 CST)
    • Re: xsc information in the dcd file? Jérôme Hénin (Wed Dec 15 2004 - 12:22:39 CST)
      • Re: xsc information in the dcd file? Gianluca Interlandi (Thu Dec 16 2004 - 11:25:50 CST)
  • Re: turning off fixed atoms in the middle of simulation Jim Phillips (Wed Dec 15 2004 - 11:15:47 CST)
    • How to move COM during minimization? Shahid Qamar (Wed Dec 15 2004 - 12:03:12 CST)
• Autoionize plugin problem Gaurav Sharma (Tue Dec 14 2004 - 12:52:03 CST)
  • Re: vmd-l: Autoionize plugin problem John Stone (Thu Dec 16 2004 - 11:30:21 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)
  • Infiniband and PME gridsize Gianluca Interlandi (Tue Dec 14 2004 - 06:06:03 CST)
    • Re: Infiniband and PME gridsize Brian Bennion (Tue Dec 14 2004 - 12:06:36 CST)
      • Re: Infiniband and PME gridsize Gengbin Zheng (Tue Dec 14 2004 - 12:16:55 CST)
      • Re: Infiniband and PME gridsize Gianluca Interlandi (Tue Dec 14 2004 - 12:54:55 CST)
      • Re: Infiniband and PME gridsize Gengbin Zheng (Tue Dec 14 2004 - 13:05:45 CST)
  • Re: fatal error Brian Bennion (Tue Dec 14 2004 - 12:01:25 CST)
    • Re: fatal error Gengbin Zheng (Tue Dec 14 2004 - 12:14:28 CST)
    • Re: fatal error vivek sharma (Wed Dec 15 2004 - 04:11:45 CST)
• more than 99999 atoms in PDB files Gilbert G.Feng (Mon Dec 13 2004 - 15:30:55 CST)
  • Re: more than 99999 atoms in PDB files LEWYN LI (Mon Dec 13 2004 - 16:53:26 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 carlos n. a. (Mon Dec 13 2004 - 13:36:10 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)
  • Re: Building NAMD with Portland's C++ Comipler Gengbin Zheng (Thu Dec 09 2004 - 12:47:54 CST)
    • Re: Building NAMD with Portland's C++ Comipler Suxing Hu (Thu Dec 09 2004 - 21:08:54 CST)
• namdplot vivek sharma (Thu Dec 09 2004 - 02:13:26 CST)
  • Re: namdplot nordgren_at_sas.upenn.edu (Thu Dec 09 2004 - 05:59:11 CST)
    • Re: namdplot vivek sharma (Thu Dec 09 2004 - 10:38:14 CST)
      • Re: namdplot LEWYN LI (Thu Dec 09 2004 - 11:17:33 CST)
  • RE: namdplot Blake Charlebois (Thu Dec 09 2004 - 07:15:41 CST)
• Vaccum simulation Narender Singh (Wed Dec 08 2004 - 10:57:48 CST)
  • Re: Vaccum simulation nordgren_at_sas.upenn.edu (Wed Dec 08 2004 - 15:57:10 CST)
• Periodic cell size Suxing Hu (Wed Dec 08 2004 - 10:06:24 CST)
  • Re: Periodic cell size Edward Patrick Obrien (Wed Dec 08 2004 - 10:54:37 CST)
  • Re: Periodic cell size Brian Bennion (Wed Dec 08 2004 - 11:43:02 CST)
    • RE: Periodic cell size Blake Charlebois (Wed Dec 08 2004 - 23:54:04 CST)
• Variation of results in iterations Pijush Ghosh (Mon Dec 06 2004 - 17:25:43 CST)
  • Re: Variation of results in iterations Edward Patrick Obrien (Mon Dec 06 2004 - 17:44:43 CST)
    • Re: Variation of results in iterations Jérôme Hénin (Mon Dec 06 2004 - 19:01:32 CST)
      • Re: Variation of results in iterations Edward Patrick Obrien (Mon Dec 06 2004 - 19:37:43 CST)
      • Re: Variation of results in iterations Robert Brunner (Mon Dec 06 2004 - 21:15:00 CST)
    • Re: Variation of results in iterations Pijush Ghosh (Mon Dec 06 2004 - 22:00:21 CST)
      • Re: Variation of results in iterations Edward Patrick Obrien (Mon Dec 06 2004 - 22:13:26 CST)
      • RE: Variation of results in iterations Blake Charlebois (Tue Dec 07 2004 - 20:12:18 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)
  • Re: PME ERROR Brian Bennion (Wed Dec 01 2004 - 12:02:55 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)
  • Re: NAMD on Xeon EM64T Chris Samuel (Thu Dec 02 2004 - 22:18:39 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)
  • GROMACS to CHARMM chandran karunakaran (Mon Nov 29 2004 - 11:14:48 CST)
    • Re: GROMACS to CHARMM Alessandro Pedretti (Tue Nov 30 2004 - 01:47:01 CST)
  • Re: psfgen Brian Bennion (Mon Nov 29 2004 - 17:01:33 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: Question:about harmonic restraint decrease! Jérôme Hénin (Fri Nov 26 2004 - 03:22:51 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)
  • Re: spherical boundary condition griadi_at_utalca.cl (Mon Nov 29 2004 - 02:29:51 CST)
• rmsd calculation Francesco Iori (Tue Nov 23 2004 - 06:56:32 CST)
  • Re: rmsd calculation Charles Danko (Tue Nov 23 2004 - 09:50:49 CST)
    • Compiling charm on a opteron cluster Gianluca Interlandi (Fri Dec 03 2004 - 15:03:11 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)
  • Job is terminated in the middle Shahid Qamar (Fri Nov 19 2004 - 11:23:15 CST)
  • Re: Working on cluster to do umbrella sampling Michael Grabe (Mon Nov 22 2004 - 13:47:14 CST)
• NAMD Source Hassan K. Al-Ali Merheby (Fri Nov 19 2004 - 02:06:44 CST)
  • Re: NAMD Source Robert Brunner (Fri Nov 19 2004 - 10:54:16 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: Writing pdb file.. easier way? LEWYN LI (Thu Nov 18 2004 - 16:29:36 CST)
    • Re: Writing pdb file.. easier way? Uday Chippada (Thu Nov 18 2004 - 17:19:14 CST)
  • Re: Writing pdb file.. easier way? Neema Salimi (Thu Nov 18 2004 - 16:54:58 CST)
  • Re: Writing pdb file.. easier way? Jérôme Hénin (Thu Nov 18 2004 - 17:28:36 CST)
    • Re: Writing pdb file.. easier way? griadi_at_utalca.cl (Tue Nov 23 2004 - 12:44:03 CST)
• Re: Rif: Re: Rif: Re: Rif: Re: linux cluster trouble Brian Bennion (Thu Nov 18 2004 - 10:56:17 CST)
  • Re: Rif: Re: Rif: Re: Rif: Re: linux cluster trouble Gengbin Zheng (Thu Nov 18 2004 - 13:01:25 CST)
    • Re: Rif: Re: Rif: Re: Rif: Re: linux cluster trouble Gengbin Zheng (Thu Nov 18 2004 - 13:20:46 CST)
    • Rif: Re: Rif: Re: Rif: Re: Rif: Re: linux cluster trouble max (Fri Nov 19 2004 - 03:47:01 CST)
      • Re: Rif: Re: Rif: Re: Rif: Re: Rif: Re: linux cluster trouble Gengbin Zheng (Fri Nov 19 2004 - 09:18:28 CST)
      • Pair interaction, PBC included? Edward Patrick Obrien (Sat Nov 20 2004 - 14:22:39 CST)
      • Chloroform Solvent Box Harindar Keer (Tue Nov 23 2004 - 11:17:45 CST)
• Move molecule Uday Chippada (Thu Nov 18 2004 - 10:18:36 CST)
  • Re: Move molecule Edward Patrick Obrien (Thu Nov 18 2004 - 12:39:00 CST)
    • Re: Move molecule Uday Chippada (Thu Nov 18 2004 - 14:07:50 CST)
      • NAMD at Data Star SDSC Shahid Qamar (Mon Nov 22 2004 - 15:19:11 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)
  • Re: linux cluster trouble Brian Bennion (Tue Nov 16 2004 - 10:40:57 CST)
• Layers Laura De Luca (Tue Nov 16 2004 - 10:00:07 CST)
  • Re: Layers LEWYN LI (Tue Nov 16 2004 - 13:38:13 CST)
• fatal error running namd Enrico Piccinini (Mon Nov 15 2004 - 04:30:06 CST)
  • Re: fatal error running namd Brian Bennion (Mon Nov 15 2004 - 10:52:34 CST)
• gcc and G5 Xserves Michael Grabe (Mon Nov 15 2004 - 02:06:03 CST)
  • Re: gcc and G5 Xserves Charles McCallum (Mon Nov 15 2004 - 23:07:17 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)
  • Re: Generating topology file li (Sun Nov 14 2004 - 02:45:43 CST)
  • Re: Generating topology file li (Tue Nov 16 2004 - 01:11:51 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)
  • RE: Implicit water dielectric constant. Blake Charlebois (Tue Nov 16 2004 - 15:06:50 CST)
• linux cluster trouble mpappala_at_unict.it (Tue Nov 09 2004 - 05:47:48 CST)
  • Re: linux cluster trouble Mounir Tarek (Tue Nov 09 2004 - 06:27:55 CST)
    • Re: linux cluster trouble Gengbin Zheng (Tue Nov 09 2004 - 08:19:10 CST)
      • Re: linux cluster trouble Mounir Tarek (Tue Nov 09 2004 - 08:43:03 CST)
      • Re: linux cluster trouble Brian Bennion (Wed Nov 10 2004 - 11:26:36 CST)
      • Berendsen or Langevin Temp control? Edward Patrick Obrien (Wed Nov 10 2004 - 15:54:07 CST)
    • Rif: Re: linux cluster trouble max (Wed Nov 10 2004 - 03:00:42 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)
  • Re: How to make a negatively charged surface Charles Danko (Mon Nov 08 2004 - 15:26:53 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)
  • Re: rmsd and simulation Charles McCallum (Fri Nov 05 2004 - 11:23:58 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)
  • Re: Solvent mixture Brian Bennion (Fri Nov 05 2004 - 15:40:47 CST)
    • Re: Solvent mixture Edward Patrick Obrien (Fri Nov 05 2004 - 16:43:21 CST)
      • Re: Solvent mixture Brian Bennion (Fri Nov 05 2004 - 16:53:11 CST)
      • Re: Solvent mixture Ahmet Bakan (Fri Nov 05 2004 - 17:02:06 CST)
• Sample Configuratiion files Leandro Martinez (Wed Nov 03 2004 - 15:40:38 CST)
• Sample Configuratiion files Raymond C. Fort Jr. (Wed Nov 03 2004 - 14:59:44 CST)
  • Re: Sample Configuratiion files Charles Danko (Wed Nov 03 2004 - 15:50:49 CST)
    • Re: Sample Configuratiion files Cheri M Turman (Wed Nov 03 2004 - 19:47:25 CST)
• How to decide the protonation of some residues?? mashaojie163 (Wed Nov 03 2004 - 07:05:19 CST)
  • Re: How to decide the protonation of some residues?? Brian Bennion (Wed Nov 03 2004 - 10:35:07 CST)
• Edge Water in PBC Cetin Baloglu (Wed Nov 03 2004 - 05:01:40 CST)
  • Re: Edge Water in PBC Brian Bennion (Wed Nov 03 2004 - 10:32:58 CST)
• Tcl dihedral restraints in CG minimisation Ben Roberts (Tue Nov 02 2004 - 17:01:28 CST)
  • Re: Tcl dihedral restraints in CG minimisation Jérôme Hénin (Tue Nov 02 2004 - 18:24:07 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)
  • Re: [Periodic Boundary]: from charmm to namd Charles Danko (Tue Nov 02 2004 - 11:35:23 CST)
    • Re: [Periodic Boundary]: from charmm to namd Sascha Tayefeh (Tue Nov 02 2004 - 12:46:02 CST)
• HEM residue in NAMD Peter Bazeley (Tue Nov 02 2004 - 02:23:50 CST)
  • RE: HEM residue in NAMD Blake Charlebois (Tue Nov 02 2004 - 04:03:00 CST)
• Hessian mdcooper (Mon Nov 01 2004 - 18:08:24 CST)
• Fwd: missing atom prob surendra negi (Mon Nov 01 2004 - 17:58:33 CST)
• Fwd: PSFgen error surendra negi (Mon Nov 01 2004 - 17:58:12 CST)
  • Re: Fwd: PSFgen error Brian Bennion (Tue Nov 02 2004 - 10:14:50 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 02 2004 - 13:09:32 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: 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)
  • Re: firsttimestep: simple question Brian Bennion (Fri Oct 29 2004 - 17:34:53 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)
  • Re: BOND CP2 - CT2 IN PARAMETER FILES Brian Bennion (Fri Oct 29 2004 - 11:32:18 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)
    • Methane residue file Edward Patrick Obrien (Wed Oct 27 2004 - 19:19:28 CDT)
    • Re: Compiling NAMD on IA64 cluter Brian Bennion (Wed Nov 03 2004 - 10:39:23 CST)
      • Re: Re: Compiling NAMD on IA64 cluter Gengbin Zheng (Wed Nov 03 2004 - 11:24:27 CST)
    • Re: Compiling NAMD on IA64 cluter li (Thu Nov 04 2004 - 05:48:16 CST)
• communication with NAMD? Hui-Hsu Tsai (Tue Oct 26 2004 - 15:37:37 CDT)
  • Re: communication with NAMD? Brian Bennion (Tue Oct 26 2004 - 18:10:07 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)
  • Re: Bug in Pair force interaction calculation was fixed? Brian Bennion (Tue Oct 26 2004 - 12:20:36 CDT)
    • Re: Bug in Pair force interaction calculation was fixed? Zhong Wenyu (Wed Oct 27 2004 - 09:26:26 CDT)
      • Re: Bug in Pair force interaction calculation was fixed? Brian Bennion (Wed Oct 27 2004 - 10:19:49 CDT)
• Hydrogen cut off distance Uday Chippada (Mon Oct 25 2004 - 16:16:46 CDT)
  • Re: Hydrogen cut off distance Brian Bennion (Tue Oct 26 2004 - 12:38:20 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)
  • Re: D-amino acids Aaron Oakley (Tue Oct 26 2004 - 03:05:28 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)
  • Re: output to multiple files Brian Bennion (Fri Oct 22 2004 - 14:37:37 CDT)
    • Re: output to multiple files Leandro Martinez (Tue Oct 26 2004 - 13:09:26 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 Chris Samuel (Wed Oct 20 2004 - 18:05:49 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)
  • Re: bug report and stray pme Brian Bennion (Tue Oct 19 2004 - 15:31:43 CDT)
• pair-interaction energy Vani Krishna (Sun Oct 17 2004 - 17:37:18 CDT)
• a different bug alert Meric Ayse Ovacik (Sun Oct 17 2004 - 09:27:23 CDT)
  • Fw: a different bug alert Meric Ayse Ovacik (Sun Oct 17 2004 - 09:21:47 CDT)
• question on force autocorrelation function Hyonseok Hwang (Wed Oct 13 2004 - 11:20:47 CDT)
  • Question on harmonic constraints Edward Patrick Obrien (Thu Oct 14 2004 - 19:39:00 CDT)
• Gradient Tolerance mdcooper (Tue Oct 12 2004 - 18:52:43 CDT)
  • Re: Gradient Tolerance Brian Bennion (Wed Oct 13 2004 - 14:43:04 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: [Fwd: counterion software] bora erdemli (Mon Oct 11 2004 - 02:03:05 CDT)
• Re: vmd-l: how can I get hole program mashaojie163 (Sun Oct 10 2004 - 09:23:13 CDT)
  • counterion software Cetin Baloglu (Sun Oct 10 2004 - 23:51:56 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 Alberto Santana (Mon Oct 11 2004 - 14:19:31 CDT)
      • Re: NAMD on Linux cluster with Myrinet Brian Bennion (Mon Oct 11 2004 - 15:53:14 CDT)
      • Re: NAMD on Linux cluster with Myrinet Gengbin Zheng (Tue Oct 12 2004 - 00:17:53 CDT)
    • Re: NAMD on Linux cluster with Myrinet Alberto Santana (Mon Oct 18 2004 - 11:59:31 CDT)
      • Re: NAMD on Linux cluster with Myrinet Gengbin Zheng (Mon Oct 18 2004 - 13:28:36 CDT)
      • Re: NAMD on Linux cluster with Myrinet Chris Samuel (Mon Oct 18 2004 - 23:02:27 CDT)
  • Re: NAMD on Linux cluster with Myrinet Florian Barth (Mon Oct 11 2004 - 19:49:48 CDT)
    • Re: NAMD on Linux cluster with Myrinet Alberto Santana (Thu Oct 14 2004 - 11:26:08 CDT)
      • Re: NAMD on Linux cluster with Myrinet Brian Bennion (Thu Oct 14 2004 - 13:20:59 CDT)
      • Re: NAMD on Linux cluster with Myrinet Alberto Santana (Thu Oct 14 2004 - 13:59:27 CDT)
      • Re: NAMD on Linux cluster with Myrinet Gengbin Zheng (Thu Oct 14 2004 - 14:03:12 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)
  • Re: How can I move an atom by 10nm with a step of 0.1nm Brian Bennion (Tue Oct 05 2004 - 10:44:01 CDT)
    • Spherical Boundary Conditions Edward Patrick Obrien (Tue Oct 05 2004 - 16:14:12 CDT)
• Not all atoms have unique coordinates - revisited Alberto Santana (Fri Oct 01 2004 - 18:52:27 CDT)
  • Re: Not all atoms have unique coordinates - revisited Brian Bennion (Sat Oct 02 2004 - 00:37:12 CDT)
    • Re: Not all atoms have unique coordinates - revisited Alberto Santana (Sat Oct 02 2004 - 08:32:59 CDT)
      • Re: Not all atoms have unique coordinates - revisited Brian Bennion (Mon Oct 04 2004 - 10:22:04 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)
  • RE: temperature rescaling and canonical ensemble Blake Charlebois (Fri Oct 01 2004 - 01:15:05 CDT)
• Can we fix the position of two atoms while minimization? Shahid Qamar (Wed Sep 29 2004 - 15:18:31 CDT)
  • Re: Can we fix the position of two atoms while minimization? Brian Bennion (Wed Sep 29 2004 - 18:00:43 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)
  • Re: To PME , Do the simulation need a neutral charged system? Jérôme Hénin (Tue Sep 21 2004 - 05:16:26 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)
  • Re: binding constant Jérôme Hénin (Mon Sep 20 2004 - 17:16:43 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)
  • RE: generating psf files (and more!) Luis Rosales (Tue Sep 14 2004 - 17:40:20 CDT)
• Tcl loops in configuration files Streiff, John H. (Tue Sep 14 2004 - 10:26:12 CDT)
  • Output only protein .dcd Nur Aida Abdul Rahim (Tue Sep 14 2004 - 13:41:38 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)
  • Re: Cell Basis Vector. Edward Patrick Obrien (Tue Sep 07 2004 - 18:45:13 CDT)
  • RE: Cell Basis Vector. Pijush Ghosh (Wed Sep 08 2004 - 23:20:22 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)
  • Re: 64 nodes behaviour Gengbin Zheng (Thu Sep 02 2004 - 13:19:03 CDT)
    • Re: 64 nodes behaviour Alexandre Chauvin (Fri Sep 03 2004 - 02:52:30 CDT)
      • Re: 64 nodes behaviour Gengbin Zheng (Fri Sep 03 2004 - 14:37:05 CDT)
• calculate the binding energy or binding free energy? ying xiong (Thu Sep 02 2004 - 03:49:40 CDT)
  • Re: calculate the binding energy or binding free energy? LEWYN LI (Thu Sep 02 2004 - 14:27:03 CDT)
    • RE: calculate the binding energy or binding free energy? Blake Charlebois (Thu Sep 02 2004 - 15:31:42 CDT)
    • Re: calculate the binding energy or binding free energy? Vani Krishna (Thu Sep 02 2004 - 21:13:58 CDT)
• Questions on periodic boundary condition LEWYN LI (Thu Sep 02 2004 - 00:38:24 CDT)
  • Re: Questions on periodic boundary condition Edward Patrick Obrien (Thu Sep 02 2004 - 10:51:56 CDT)
    • Re: Questions on periodic boundary condition LEWYN LI (Thu Sep 02 2004 - 11:00:47 CDT)
• SMD on a group of atoms: Confusion Vani Krishna (Wed Sep 01 2004 - 10:47:41 CDT)
  • RE: SMD on a group of atoms: Confusion Blake Charlebois (Fri Sep 03 2004 - 05:41:24 CDT)
• Calculation of velocities Eric Cyr (Tue Aug 31 2004 - 15:44:47 CDT)
  • RE: Calculation of velocities Blake Charlebois (Thu Sep 02 2004 - 08:21:34 CDT)
    • Re: Calculation of velocities Eric Cyr (Fri Sep 03 2004 - 14:27:38 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)
  • Re: Temperature Edward Patrick Obrien (Mon Aug 30 2004 - 13:12:17 CDT)
• DPPC Eunice Ramirez Melendez (Mon Aug 30 2004 - 02:28:55 CDT)
  • Re: DPPC Jérôme Hénin (Mon Aug 30 2004 - 11:48:39 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)
  • Re: vmd-l: Protonated GLU/ASP in PSF generation Justin Gullingsrud (Sun Aug 29 2004 - 21:01:52 CDT)
• convert DCD files to GROMACS .XTC format Vani Krishna (Sat Aug 28 2004 - 17:43:11 CDT)
  • Re: vmd-l: convert DCD files to GROMACS .XTC format John Stone (Tue Aug 31 2004 - 15:11:09 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)
  • Re: vmd-l: rmsd problem John Stone (Tue Aug 31 2004 - 15:11:47 CDT)
    • rmsd problem,script and version bora erdemli (Fri Sep 03 2004 - 00:23:42 CDT)
• Compilation on Opteron Alexandre Chauvin (Wed Aug 25 2004 - 12:22:43 CDT)
  • Re: Compilation on Opteron Leandro Martinez (Wed Aug 25 2004 - 13:35:13 CDT)
    • Re: Compilation on Opteron Alexandre Chauvin (Fri Aug 27 2004 - 03:05:43 CDT)
  • Re: Compilation on Opteron Chris Samuel (Thu Aug 26 2004 - 00:04:07 CDT)
  • Re: Compilation on Opteron Gengbin Zheng (Thu Aug 26 2004 - 00:25:44 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: numerical inaccuracy upon restart nordgren_at_sas.upenn.edu (Wed Aug 25 2004 - 22:40:31 CDT)
    • Re: Re: numerical inaccuracy upon restart Harald Tepper (Tue Aug 31 2004 - 05:21:21 CDT)
      • Re: Re: numerical inaccuracy upon restart Jim Phillips (Fri Sep 03 2004 - 17:21:25 CDT)
      • Re: Re: numerical inaccuracy upon restart tepper_at_amolf.nl (Mon Sep 06 2004 - 06:30:22 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)
  • Re: Direction of the force in Pair interactions Jim Phillips (Tue Aug 24 2004 - 11:06:52 CDT)
• Symmetry operations \ (Mon Aug 23 2004 - 16:42:22 CDT)
  • Re: Symmetry operations Brian Bennion (Mon Aug 23 2004 - 17:55:24 CDT)
  • Re: Symmetry operations Juan Carlos Mobarec (Mon Aug 23 2004 - 19:21:22 CDT)
    • Re: Symmetry operations \ (Tue Aug 24 2004 - 13:58:19 CDT)
      • Re: Symmetry operations Aaron Oakley (Tue Aug 24 2004 - 18:34:47 CDT)
      • Re: Symmetry operations \ (Thu Sep 02 2004 - 21:44:39 CDT)
• cff91 force field in namd Rowan Hargreaves (Mon Aug 23 2004 - 06:35:38 CDT)
  • RE: cff91 force field in namd + A Question Ahmet Bakan (Wed Aug 25 2004 - 10:53:59 CDT)
• surface pressure/tension nordgren_at_sas.upenn.edu (Sun Aug 22 2004 - 02:37:11 CDT)
  • RE: surface pressure/tension Erik Nordgren (Thu Sep 09 2004 - 13:56:27 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)
  • Re: question on the parallel job on NCSA Xeon cluster Gengbin Zheng (Tue Aug 17 2004 - 23:01:02 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: > 10000 ato Brian Bennion (Fri Aug 13 2004 - 15:14:05 CDT)
• RE: radial distribution function Liu, Zhanwu (Fri Aug 13 2004 - 08:40:51 CDT)
  • Clustermatic with SCSI Leandro Martinez (Wed Aug 18 2004 - 18:15:11 CDT)
    • Re: Clustermatic with SCSI Chris Samuel (Wed Aug 18 2004 - 20:17:05 CDT)
      • Re: Clustermatic with SCSI Leandro Martinez (Thu Aug 19 2004 - 07:12:57 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: Has NAMD been ported to Itanium2 + Linux? Shantenu Jha (Tue Aug 10 2004 - 16:25:28 CDT)
    • Re: Has NAMD been ported to Itanium2 + Linux? Gengbin Zheng (Tue Aug 10 2004 - 16:54:08 CDT)
• RE: Need to add Hydrogens to over 300 distinct PDB's Kamp, Marc vander (Tue Aug 10 2004 - 09:46:15 CDT)
  • RE: Need to add Hydrogens to over 300 distinct PDB's Edward Patrick Obrien (Tue Aug 10 2004 - 10:20:47 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)
  • Need to add Hydrogens to over 300 distinct PDB's Edward Patrick Obrien (Mon Aug 09 2004 - 13:03:40 CDT)
    • Re: Need to add Hydrogens to over 300 distinct PDB's Edward Patrick Obrien (Wed Aug 11 2004 - 13:05:33 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)
  • Re: render format John Stone (Mon Aug 02 2004 - 13:14:50 CDT)
  • Re: render format Brian Bennion (Mon Aug 02 2004 - 14:44:08 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)
  • Re: compiled namd on clustermatic fails ! Gengbin Zheng (Tue Aug 03 2004 - 10:23:19 CDT)
    • Re: compiled namd on clustermatic fails ! Amit Paliwal (Tue Aug 03 2004 - 06:38:31 CDT)
      • Re: compiled namd on clustermatic fails ! Gengbin Zheng (Tue Aug 03 2004 - 11:31:31 CDT)
• HYP parameters Valodymyr Nechyporuk-Zloy (Thu Jul 29 2004 - 03:59:44 CDT)
  • Re: HYP parameters Ivan Vinogradov (Thu Jul 29 2004 - 07:44:27 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)
  • Fw: Constraint failure in RATTLE algorithm Zhong Wenyu (Sun Sep 19 2004 - 02:14:27 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)
  • Re: type of the water molecule Brian Bennion (Fri Jul 23 2004 - 11:55:57 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)
  • Re: Myrinet and MPI question Brian Bennion (Thu Jul 22 2004 - 11:21:34 CDT)
    • Re: Myrinet and MPI question Gengbin Zheng (Thu Jul 22 2004 - 11:49:07 CDT)
• phase equilibria using NAMD nasrat kamal (Wed Jul 21 2004 - 07:33:45 CDT)
  • Re: phase equilibria using NAMD Brian Bennion (Thu Jul 22 2004 - 10:53:00 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)
  • Re: mimization warnings - bad global exclusion count Brian Bennion (Wed Jul 21 2004 - 17:29:51 CDT)
• psfgen Ken Sale (Wed Jul 21 2004 - 15:14:43 CDT)
  • Re: psfgen Brian Bennion (Wed Jul 21 2004 - 18:23:41 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)
  • Re: Segmentation violation Brian Bennion (Tue Jul 20 2004 - 12:30:06 CDT)
  • Re: Segmentation violation Gengbin Zheng (Tue Jul 20 2004 - 14:18:06 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)
  • Re: Questions Edward Patrick Obrien (Mon Jul 19 2004 - 17:02:29 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)
  • How to do pH simulation on NAMD? Xin Chen (Thu Jul 15 2004 - 15:28:50 CDT)
    • Re: How to do pH simulation on NAMD? Jérôme Hénin (Fri Jul 16 2004 - 05:00:03 CDT)
• NAMD on the TeraGrid p.w.fowler_at_qmul.ac.uk (Thu Jul 15 2004 - 05:12:47 CDT)
  • Re: NAMD on the TeraGrid Gengbin Zheng (Thu Jul 15 2004 - 10:53:20 CDT)
• Re: compiler flags. Brian Bennion (Wed Jul 14 2004 - 23:41:22 CDT)
  • Re: compiler flags. gengbin (Wed Jul 14 2004 - 23:58:54 CDT)
• Dynamically resizing waterbox Nur Aida Abdul Rahim (Wed Jul 14 2004 - 14:22:26 CDT)
  • Re: Dynamically resizing waterbox Edward Patrick Obrien (Wed Jul 14 2004 - 15:01:00 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)
  • Re: Common Problem!: Periodic cell has become too small for original patch grid! Meric Ayse Ovacik (Mon Jul 12 2004 - 03:25:04 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)
  • Re: ***** SPAM POSSIBLE ***** Warning: Not all atoms have unique coordinates. Jérôme Hénin (Thu Jul 08 2004 - 11:01:54 CDT)
  • Re: Warning: Not all atoms have unique coordinates. Brian Bennion (Thu Jul 08 2004 - 11:06:08 CDT)
    • Re: Warning: Not all atoms have unique coordinates. Shirley Hui (Thu Jul 08 2004 - 17:45:47 CDT)
      • Re: Warning: Not all atoms have unique coordinates. Shirley Hui (Thu Jul 08 2004 - 18:15:29 CDT)
• cellBasisVector x,y,z values Shirley Hui (Thu Jul 08 2004 - 08:46:16 CDT)
  • Re: cellBasisVector x,y,z values Edward Patrick Obrien (Thu Jul 08 2004 - 09:36:43 CDT)
  • Re: cellBasisVector x,y,z values p.w.fowler_at_qmul.ac.uk (Thu Jul 08 2004 - 10:30:31 CDT)
  • Re: cellBasisVector x,y,z values Brian Bennion (Thu Jul 08 2004 - 10:35:11 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)
  • Re: octahedral period BCs Mark Abraham (Wed Jul 07 2004 - 22:35:44 CDT)
    • Re: octahedral period BCs Mark Abraham (Wed Jul 07 2004 - 22:43:57 CDT)
• namd and Tcl 8.3.5 Sean Michael Whipkey (Wed Jul 07 2004 - 09:42:26 CDT)
  • Re: namd and Tcl 8.3.5 Brian Bennion (Wed Jul 07 2004 - 11:33:23 CDT)
    • Re: namd and Tcl 8.3.5 Sean Michael Whipkey (Wed Jul 07 2004 - 16:06:35 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)
  • RE: COM position Mauricio Carrillo Tripp (Tue Jul 06 2004 - 10:45:53 CDT)
    • RE: COM position Brian Bennion (Tue Jul 06 2004 - 12:11:28 CDT)
      • RE: COM position Mauricio Carrillo Tripp (Tue Jul 06 2004 - 12:43:40 CDT)
      • RE: COM position Brian Bennion (Tue Jul 06 2004 - 12:50:52 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)
  • Re: Suse 9.0 or Fedora Core 1.0 Alex V. (Fri Jul 02 2004 - 07:27:08 CDT)
• icc compilation problem Sean Michael Whipkey (Thu Jul 01 2004 - 16:19:55 CDT)
  • Re: icc compilation problem Chris Samuel (Thu Jul 01 2004 - 18:11:57 CDT)
    • Re: icc compilation problem Sean Michael Whipkey (Fri Jul 02 2004 - 09:27:55 CDT)
      • Re: icc compilation problem Brian Bennion (Fri Jul 02 2004 - 11:05:29 CDT)
      • Re: icc compilation problem Chris Samuel (Sun Jul 04 2004 - 20:41:14 CDT)
• hexagonal unit cell Anna Modzelewska (Thu Jul 01 2004 - 03:49:56 CDT)
• best choice of linux cluster to run NAMD Nikolai Skrynnikov (Thu Jul 01 2004 - 03:02:10 CDT)
• (no subject) ying xiong (Thu Jul 01 2004 - 01:57:18 CDT)
  • Re: Jérôme Hénin (Thu Jul 01 2004 - 04:47:55 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)
  • Re: DIHEDral drift [2] ? Brian Bennion (Wed Jun 30 2004 - 12:30:15 CDT)
    • Re: DIHEDral drift [2] ? Nicholas M Glykos (Wed Jun 30 2004 - 13:08:14 CDT)
      • Re: DIHEDral drift [2] ? Brian Bennion (Wed Jun 30 2004 - 17:16:39 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)
  • Parameters for iodine atoms Leandro Martinez (Thu Aug 05 2004 - 12:55:28 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)
  • Re: vmd-l: incompatibility between VMD & NAMD for reading Amber crd files John Stone (Mon Jun 21 2004 - 14:53:13 CDT)
  • RE: vmd-l: incompatibility between VMD & NAMD for reading Amber crd files Kamp, Marc vander (Tue Jun 22 2004 - 04:20:16 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)
  • Re: vmd-l: incompatibility between VMD & NAMD for reading Amber crd files John Stone (Mon Jun 21 2004 - 09:58:31 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)
  • Re: recentering protein in the waterbox Gianluca Interlandi (Fri Jun 18 2004 - 18:16:35 CDT)
• What binaries should I take? Valodymyr Nechyporuk-Zloy (Fri Jun 18 2004 - 03:49:14 CDT)
  • Re: What binaries should I take? Edward Patrick Obrien (Fri Jun 18 2004 - 08:18:38 CDT)
    • Re: What binaries should I take? Gianluca Interlandi (Fri Jun 18 2004 - 08:38:39 CDT)
• errors building charm on ia64 Allison Heath (Thu Jun 17 2004 - 11:18:29 CDT)
  • Re: errors building charm on ia64 Gianluca Interlandi (Thu Jun 17 2004 - 11:31:42 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)
  • Re: Simulated Annealing Config Jérôme Hénin (Tue Jun 15 2004 - 12:20:45 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)
  • Re: Namd RedHat9 compilation problem Gengbin Zheng (Tue Jun 15 2004 - 11:39:49 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)
  • Re: build charm on ia-64 linux Sichun Yang (Fri Jun 11 2004 - 19:41:26 CDT)
    • Re: build charm on ia-64 linux Gengbin Zheng (Fri Jun 11 2004 - 20:57:01 CDT)
      • Re: build charm on ia-64 linux Sichun Yang (Fri Jun 11 2004 - 21:44:12 CDT)
      • Re: build charm on ia-64 linux Gengbin Zheng (Fri Jun 11 2004 - 21:54:20 CDT)
    • Re: build charm on ia-64 linux Chris Samuel (Tue Jun 15 2004 - 18:23:17 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)
  • RE: psfgen problem Brian Bennion (Wed Jun 09 2004 - 15:59:33 CDT)
• question about running equilibration in NAMD jz7_at_duke.edu (Tue Jun 08 2004 - 14:25:41 CDT)
  • Re: question about running equilibration in NAMD Brian Bennion (Tue Jun 08 2004 - 15:50:28 CDT)
  • question about autogen in topology file jz7_at_duke.edu (Thu Jun 10 2004 - 13:41:00 CDT)
• psfgen problem Kamp, Marc vander (Tue Jun 08 2004 - 04:53:39 CDT)
  • Re: psfgen problem Brian Bennion (Tue Jun 08 2004 - 12:01:58 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)
  • Re: psfgen issue Edward Patrick Obrien (Mon Jun 07 2004 - 09:23:23 CDT)
    • Re: psfgen issue Rad Balu (Sun Jun 06 2004 - 22:03:07 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)
• How do we know the velocity? Uday Chippada (Thu Jun 03 2004 - 10:17:10 CDT)
  • Re: How do we know the velocity? Leandro Martinez (Thu Jun 03 2004 - 11:47:05 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)
  • Re: submitting a job in a queue Gengbin Zheng (Thu Jun 03 2004 - 11:33:25 CDT)
  • Re: submitting a job in a queue Alex V. (Fri Jun 04 2004 - 13:46:18 CDT)
• question about using Amber force field in namd jz7_at_duke.edu (Wed Jun 02 2004 - 09:35:54 CDT)
  • Re: question about using Amber force field in namd Brian Bennion (Wed Jun 02 2004 - 16:07:28 CDT)
    • Re: question about using Amber force field in namd jz7_at_duke.edu (Wed Jun 02 2004 - 16:13:14 CDT)
      • Re: question about using Amber force field in namd Brian Bennion (Wed Jun 02 2004 - 16:21:21 CDT)
    • Re: question about using Amber force field in namd Brian Bennion (Wed Jun 02 2004 - 16:31:48 CDT)
• "GRADIENT TOLERANCE: nan", Why? Zhong Wenyu (Wed Jun 02 2004 - 07:42:50 CDT)
  • Re: "GRADIENT TOLERANCE: nan", Why? Brian Bennion (Wed Jun 02 2004 - 16:04:15 CDT)
    • Re: "GRADIENT TOLERANCE: nan", Why? Zhong Wenyu (Thu Jun 03 2004 - 09:02:01 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)
  • Re: NPT calculations in NAMD Peter Jones (Mon May 31 2004 - 22:04:51 CDT)
    • Re: NPT calculations in NAMD Leandro Martinez (Tue Jun 01 2004 - 07:17:58 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)
  • Re: Single point energy calculation Rad Balu (Mon May 31 2004 - 04:13:16 CDT)
• NAMD on HP-IA64 Linux Ioana Cozmuta (Sun May 30 2004 - 20:58:00 CDT)
  • Re: NAMD on HP-IA64 Linux Gengbin Zheng (Sun May 30 2004 - 22:20:51 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)
  • Re: NAMD on HP with Itanium2 Processors Brian Bennion (Sat May 29 2004 - 17:48:32 CDT)
    • Re: NAMD on HP with Itanium2 Processors Brian Bennion (Sun May 30 2004 - 01:27:19 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)
  • Re: three-site carbon monoxide model Brian Bennion (Thu May 27 2004 - 17:12:22 CDT)
• Info about forces on atoms Vani Krishna (Thu May 27 2004 - 11:58:32 CDT)
  • Re: Info about forces on atoms g srinivasa murthy (Fri May 28 2004 - 03:27:23 CDT)
    • Compiling NAMD on Linux cluster Xin Chen (Fri May 28 2004 - 15:14:12 CDT)
      • Re: Compiling NAMD on Linux cluster Gengbin Zheng (Fri May 28 2004 - 15:48:41 CDT)
    • How to calculate specific heat capacity in NAMD? Xin Chen (Wed Jul 07 2004 - 10:02:02 CDT)
      • Re: How to calculate specific heat capacity in NAMD? Edward Patrick Obrien (Wed Jul 07 2004 - 10:39:38 CDT)
      • Re: How to calculate specific heat capacity in NAMD? Brian Bennion (Wed Jul 07 2004 - 11:28:40 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)
  • Re: Periodic cell too small Brian Bennion (Tue May 25 2004 - 17:39:45 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: psfgen non-bonded atom pairs Shirley Hui (Sat May 22 2004 - 12:35:52 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)
  • Re: Why Vmd didn't show the Pt-Cl bond Edward Patrick Obrien (Wed May 19 2004 - 20:10:40 CDT)
• hanging at startup phase allison (Wed May 19 2004 - 14:00:25 CDT)
  • NAN GRADIENT TOLERANCE - & - RESTARTING CONJUGATE GRADIENT ALGORITHM Peter Spijker (Wed May 19 2004 - 18:30:57 CDT)
  • Re: hanging at startup phase Gengbin Zheng (Fri May 21 2004 - 00:59:55 CDT)
    • Re: hanging at startup phase Allison Heath (Fri May 21 2004 - 10:29:49 CDT)
      • Re: hanging at startup phase Gengbin Zheng (Fri May 21 2004 - 10:53:23 CDT)
      • Force Calculation in NAMD Xin Chen (Fri May 21 2004 - 13:02:09 CDT)
      • Re: Force Calculation in NAMD Gadi Oron (Sun May 23 2004 - 02:37:27 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)
  • Re: charm++ mpi-linux compilation errors g srinivasa murthy (Thu May 20 2004 - 09:57:55 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)
  • Re: Where to download the inorganic pdb file Brian Bennion (Wed May 19 2004 - 10:20:11 CDT)
    • RE: Where to download the inorganic pdb file myang (Wed May 19 2004 - 14:02:49 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)
  • Re: autoionize script Olya Kravchenko (Mon May 17 2004 - 14:00:12 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)
  • RE: Calculating parameters. Ahmet Bakan (Fri May 14 2004 - 16:59:15 CDT)
  • Re: Calculating parameters. Jan Saam (Sat May 15 2004 - 10:32:36 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)
  • 32 vs. 64 bits Leandro Martinez (Fri May 14 2004 - 08:07:14 CDT)
• how to generate your own pdb file myang (Thu May 13 2004 - 00:12:45 CDT)
  • Re: how to generate your own pdb file Tim Isgro (Fri May 14 2004 - 17:26:00 CDT)
    • RE: how to generate your own pdb file Ahmet Bakan (Fri May 14 2004 - 21:55:28 CDT)
  • Re: how to generate your own pdb file Josef Scheiber (Sat May 15 2004 - 04:28:47 CDT)
• Systems of > 100,000 atoms, *.psf files & *.crd files Crozier, Paul S (Tue May 11 2004 - 18:02:51 CDT)
  • Re: Systems of > 100,000 atoms, *.psf files & *.crd files Brian Bennion (Wed May 12 2004 - 10:19:29 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)
  • NAMD "freezes" up (further clarification) Eric R Johnson (Tue May 11 2004 - 08:49:33 CDT)
    • Re: NAMD "freezes" up (further clarification) Brian Bennion (Tue May 11 2004 - 10:10:46 CDT)
      • Re: NAMD "freezes" up (further clarification) Eric R Johnson (Tue May 11 2004 - 11:10:44 CDT)
      • Re: NAMD "freezes" up (further clarification) Eric R Johnson (Tue May 11 2004 - 12:34:32 CDT)
• how many steps do we need do for energy minimization ? ying xiong (Tue May 11 2004 - 01:19:39 CDT)
  • Re: how many steps do we need do for energy minimization ? Edward Patrick Obrien (Tue May 11 2004 - 08:39:17 CDT)
• Parameter File Problem beckloni_at_umdnj.edu (Mon May 10 2004 - 19:47:24 CDT)
  • Re: Parameter File Problem Brian Bennion (Mon May 10 2004 - 23:59:53 CDT)
• restart simulation Marcela P.Aliste (Mon May 10 2004 - 16:01:28 CDT)
  • Re: restart simulation J. Rui Rodrigues (Mon May 10 2004 - 17:10:25 CDT)
    • Re: restart simulation Tim Isgro (Tue May 11 2004 - 00:31:18 CDT)
• implementing angle dependent non-bonded interaction? Julius Su (Mon May 10 2004 - 13:09:14 CDT)
  • Re: implementing angle dependent non-bonded interaction? Brian Bennion (Mon May 10 2004 - 14:51:26 CDT)
• Problems witn parameter files! Galina Petrova (Mon May 10 2004 - 08:54:25 CDT)
• installing on beowulf cluster Cheri M Turman (Sun May 09 2004 - 19:58:25 CDT)
• PSF file generation beckloni_at_umdnj.edu (Sun May 09 2004 - 10:00:59 CDT)
  • Re: PSF file generation Brian Bennion (Mon May 10 2004 - 10:39:42 CDT)
    • Re: PSF file generation beckloni_at_umdnj.edu (Mon May 10 2004 - 10:48:22 CDT)
• New cluster configuration? nalianarmen (Fri May 07 2004 - 17:19:11 CDT)
• "Constrain failure" in NAMD Michael Chen (Fri May 07 2004 - 14:43:41 CDT)
  • Re: "Constrain failure" in NAMD Edward Patrick Obrien (Fri May 07 2004 - 17:59:05 CDT)
    • Re: "Constrain failure" in NAMD Brian Bennion (Mon May 10 2004 - 10:47:29 CDT)
• coarse grained model Giovanni (Fri May 07 2004 - 05:02:57 CDT)
• error: Number of atoms in fixed atoms PDB doesn't match coordinate PDB Olya Kravchenko (Thu May 06 2004 - 19:03:49 CDT)
  • Re: error: Number of atoms in fixed atoms PDB doesn't match coordinate PDB Tim Isgro (Tue May 11 2004 - 00:01:55 CDT)
    • Re: error: Number of atoms in fixed atoms PDB doesn't match coordinate PDB Olya Kravchenko (Tue May 11 2004 - 17:43:22 CDT)
• 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)
  • Re: installing on beowulf cluster Jerry Ebalunode (Thu May 06 2004 - 14:17:01 CDT)
  • Re: installing on beowulf cluster Brian Bennion (Thu May 06 2004 - 14:41:08 CDT)
• AMBER FF and pmf ladam (Thu May 06 2004 - 03:33:34 CDT)
  • Re: AMBER FF and pmf Fangqiang Zhu (Thu May 06 2004 - 18:18:58 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)
  • Re: ,log and .out files with namd running on mac os x (panther) Brian Bennion (Fri May 07 2004 - 10:51:14 CDT)
• question on self-diffusion constant of TIP3P water Hyonseok Hwang (Wed May 05 2004 - 16:54:45 CDT)
  • Re: question on self-diffusion constant of TIP3P water Brian Bennion (Wed May 05 2004 - 17:37:46 CDT)
    • Re: question on self-diffusion constant of TIP3P water Brian Bennion (Wed May 05 2004 - 18:18:19 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: Binding free energy of a protein complex Ahmet Bakan (Mon May 03 2004 - 06:02:29 CDT)
    • RE: Binding free energy of a protein complex Gadi Oron (Wed May 05 2004 - 09:31:52 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)
  • Re: vmd-l: Re: dcd files generated with catdcd J. Rui Rodrigues (Fri Apr 30 2004 - 14:02:49 CDT)
• dcd files generated with catdcd Giovanni (Fri Apr 30 2004 - 04:11:00 CDT)
  • Re: dcd files generated with catdcd J. Rui Rodrigues (Fri Apr 30 2004 - 10:51:27 CDT)
• Atom number limitations? Hrant Gharabekyan (Thu Apr 29 2004 - 22:50:26 CDT)
  • Re: Atom number limitations? Leandro Martinez (Fri Apr 30 2004 - 08:16:19 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)
  • Re: NAMD parser Mike McCallum (Thu Apr 29 2004 - 17:03:02 CDT)
  • Re: NAMD parser Xiaobing Tian (Fri Apr 30 2004 - 14:56:18 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)
  • Re: Help! There is no angle or dihedral definitions for patches in .psf! Edward Patrick Obrien (Thu Apr 29 2004 - 13:09:05 CDT)
  • Re: Help! There is no angle or dihedral definitions for patches in .psf! Brian Bennion (Thu Apr 29 2004 - 13:23:55 CDT)
• questions about set cellBasisVector and a ligand ... Xiaobing Tian (Thu Apr 29 2004 - 10:06:53 CDT)
  • Re: questions about set cellBasisVector and a ligand ... Edward Patrick Obrien (Thu Apr 29 2004 - 12:59:15 CDT)
• RE: Lithium Scott, Greg (Wed Apr 28 2004 - 23:30:08 CDT)
  • RE: Lithium Ahmet Bakan (Thu Apr 29 2004 - 11:14:56 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)
  • Re: Lithium Brian Bennion (Wed Apr 28 2004 - 22:59:38 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)
  • Re: Issues with SMD Brian Bennion (Mon May 10 2004 - 11:04:13 CDT)
    • Re: Issues with SMD Tim Isgro (Mon May 10 2004 - 23:53:13 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: Hi himanshu chandola (Sat Apr 24 2004 - 02:09:57 CDT)
    • Re: Hi Shirley Hui (Fri Apr 23 2004 - 16:02:54 CDT)
• Re: Fw: Calculating Free Energy Change Brian Bennion (Fri Apr 23 2004 - 11:08:12 CDT)
  • Re: Fw: Calculating Free Energy Change Shirley Hui (Fri Apr 23 2004 - 13:44:17 CDT)
    • Re: Fw: Calculating Free Energy Change Jérôme Hénin (Fri Apr 23 2004 - 15:00:25 CDT)
      • Re: Fw: Calculating Free Energy Change Shirley Hui (Fri Apr 23 2004 - 15:30:01 CDT)
      • Re: Fw: Calculating Free Energy Change Jérôme Hénin (Fri Apr 23 2004 - 16:07:52 CDT)
• NAMD: Force Fields Galina Petrova (Fri Apr 23 2004 - 09:00:57 CDT)
  • Re: NAMD: Force Fields Olya Kravchenko (Fri Apr 23 2004 - 11:32:52 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)
    • Re: What, if no temperatue control specified? Juan Alfredo Freites (Thu Apr 22 2004 - 11:54:16 CDT)
      • Re: What, if no temperatue control specified? Brian Bennion (Thu Apr 22 2004 - 12:02:41 CDT)
      • Re: What, if no temperatue control specified? Jérôme Hénin (Fri Apr 23 2004 - 14:19:48 CDT)
    • Re: What, if no temperatue control specified? Gianluca Interlandi (Fri Apr 23 2004 - 03:59:45 CDT)
      • Re: What, if no temperatue control specified? Brian Bennion (Fri Apr 23 2004 - 10:57:09 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)
  • Re: temperature question in logfile Brian Bennion (Tue Apr 20 2004 - 18:21:12 CDT)
• can i restrain the center of molecule in aqueous solution? li (Tue Apr 20 2004 - 03:43:12 CDT)
• Finished install beckloni_at_umdnj.edu (Tue Apr 20 2004 - 00:53:09 CDT)
• how to remove all hydrogen atoms from PDB file? Olya Kravchenko (Mon Apr 19 2004 - 17:41:22 CDT)
  • Re: how to remove all hydrogen atoms from PDB file? J. Rui Rodrigues (Tue Apr 20 2004 - 09:01:20 CDT)
    • Re: how to remove all hydrogen atoms from PDB file? J. Rui Rodrigues (Tue Apr 20 2004 - 09:04:46 CDT)
    • Re: how to remove all hydrogen atoms from PDB file? Olya Kravchenko (Wed Apr 21 2004 - 16:34:41 CDT)
• Parallelization of a code from TCB Summer School 2003 Yang Yang (Fri Apr 16 2004 - 21:54:46 CDT)
  • Re: Parallelization of a code from TCB Summer School 2003 Alex V. (Mon Apr 19 2004 - 02:49:05 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)
  • Re: simulations ceased without any hint Brian Bennion (Fri Apr 16 2004 - 00:09:26 CDT)
• FW: Cable, Sam B ERDC-ITL-MS Contractor (Thu Apr 15 2004 - 15:44:57 CDT)
• still problems with namdplot Cheri M Turman (Thu Apr 15 2004 - 14:13:57 CDT)
  • Re: still problems with namdplot Gadi Oron (Sun Apr 18 2004 - 01:51:42 CDT)
• (no subject) Cable, Sam B ERDC-ITL-MS Contractor (Thu Apr 15 2004 - 11:17:53 CDT)
  • Re: Gengbin Zheng (Thu Apr 15 2004 - 12:14:36 CDT)
    • Source file in the tutorial Xin Chen (Thu Apr 22 2004 - 16:58:46 CDT)
    • Energy minimization at NAMD Xin Chen (Tue Jun 15 2004 - 15:25:38 CDT)
      • Re: Energy minimization at NAMD Edward Patrick Obrien (Tue Jun 15 2004 - 16:07:06 CDT)
      • Re: Energy minimization at NAMD Michael Grabe (Tue Jun 15 2004 - 16:55:01 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)
  • Re: peptid bond omega, problems with settings? Brian Bennion (Thu Apr 15 2004 - 11:25:56 CDT)
• Compiling NAMD on amd64 Wenyu Zhong (Thu Apr 15 2004 - 01:42:17 CDT)
  • Re: Compiling NAMD on amd64 Wenyu Zhong (Thu Apr 15 2004 - 06:35:08 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)
  • Discrepency in cell volume? Cell origin can move in NPT? Edward Patrick Obrien (Sun Apr 25 2004 - 12:56:36 CDT)
    • NPT ensemble restart, put in new basis vectors? Edward Patrick Obrien (Sun Apr 25 2004 - 13:19:21 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)
  • Re: Using checkpoints in simulation himanshu chandola (Fri Apr 09 2004 - 19:41:18 CDT)
    • Converting PSF TYPES: from XPLOr to CHARMM Eric Hajjar (Tue Apr 13 2004 - 07:15:58 CDT)
      • Re: Converting PSF TYPES: from XPLOr to CHARMM Mike McCallum (Tue Apr 13 2004 - 09:08:04 CDT)
• using restart files Ioana Cozmuta (Thu Apr 08 2004 - 14:59:26 CDT)
  • Re: using restart files himanshu chandola (Fri Apr 09 2004 - 02:36:55 CDT)
• Generating psf files for non-proteins Scott, Greg (Thu Apr 08 2004 - 13:08:21 CDT)
  • Re: Generating psf files for non-proteins Mike McCallum (Thu Apr 08 2004 - 16:22:43 CDT)
  • Re: Generating psf files for non-proteins Alessandro Pedretti (Fri Apr 09 2004 - 07:09:52 CDT)
• Fatal Socket error Juan Carlos Mobarec (Thu Apr 08 2004 - 11:05:30 CDT)
  • Re: Fatal Socket error Gengbin Zheng (Thu Apr 08 2004 - 16:16:35 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)
  • Re: using restart files Brian Bennion (Thu Apr 08 2004 - 10:00:01 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)
  • Re: compiling NAMD Gengbin Zheng (Wed Apr 07 2004 - 20:10:12 CDT)
  • Re: compiling NAMD Brian Bennion (Fri Jul 09 2004 - 12:27:28 CDT)
    • Re: compiling NAMD gzheng (Fri Jul 09 2004 - 20:52:04 CDT)
• Installing NAMD beckloni_at_umdnj.edu (Wed Apr 07 2004 - 15:56:21 CDT)
  • Re: Installing NAMD Brian Bennion (Wed Apr 07 2004 - 16:56:14 CDT)
• how to disable NTER and CTER patches? Olya Kravchenko (Wed Apr 07 2004 - 15:18:54 CDT)
  • Re: how to disable NTER and CTER patches? Brian Bennion (Wed Apr 07 2004 - 15:56:44 CDT)
    • Re: how to disable NTER and CTER patches? Olya Kravchenko (Wed Apr 07 2004 - 16:12:19 CDT)
• Re: Restarting problem with Langevin dynamics Xin Chen (Wed Apr 07 2004 - 01:01:55 CDT)
  • Re: Restarting problem with Langevin dynamics Brian Bennion (Wed Apr 07 2004 - 09:59:45 CDT)
    • Re: Restarting problem with Langevin dynamics Xin Chen (Wed Apr 07 2004 - 13:45:39 CDT)
      • Re: Restarting problem with Langevin dynamics Brian Bennion (Wed Apr 07 2004 - 13:50:00 CDT)
      • pair interaction calculations Xin Chen (Thu Jul 29 2004 - 17:18:36 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)
• capping by psfgen tsaih_at_ncifcrf.gov (Sun Apr 04 2004 - 13:36:58 CDT)
  • Re: capping by psfgen Brian Bennion (Mon Apr 05 2004 - 11:59:38 CDT)
    • Running namd on Rice Teracluster Amarda Shehu (Sun Apr 11 2004 - 19:15:41 CDT)
      • Re: Running namd on Rice Teracluster Gengbin Zheng (Mon Apr 12 2004 - 13:28:10 CDT)
      • Re: Running namd on Rice Teracluster Chris Samuel (Tue Apr 13 2004 - 20:47:46 CDT)
      • Re: Running namd on Rice Teracluster Chris Samuel (Tue Apr 13 2004 - 20:43:18 CDT)
• 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)
  • Re: namd2.5 on myrinet cluster Gengbin Zheng (Sat Apr 03 2004 - 20:40:12 CST)
    • Re: namd2.5 on myrinet cluster Florian Barth (Sun Apr 04 2004 - 18:34:40 CDT)
• _alloca undefined symbol (OS X/XL compiler) Mike McCallum (Fri Apr 02 2004 - 18:29:26 CST)
  • Re: _alloca undefined symbol (OS X/XL compiler) Gengbin Zheng (Mon Apr 05 2004 - 00:20:45 CDT)
• 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)
  • Re: More NAMD/gm2 problems Chris Samuel (Wed Mar 31 2004 - 00:40:36 CST)
    • Re: More NAMD/gm2 problems Gengbin Zheng (Wed Mar 31 2004 - 02:17:57 CST)
      • Re: More NAMD/gm2 problems Chris Samuel (Thu Apr 08 2004 - 00:55:40 CDT)
• water box Amit Paliwal (Tue Mar 30 2004 - 06:03:30 CST)
  • timeout on running namd Amarda Shehu (Tue Mar 30 2004 - 12:09:02 CST)
    • Re: timeout on running namd Gengbin Zheng (Tue Mar 30 2004 - 13:23:15 CST)
  • Re: water box Brian Bennion (Tue Mar 30 2004 - 12:36:30 CST)
    • Re: water box Amit Paliwal (Tue Mar 30 2004 - 08:45:01 CST)
• Problems compiling Charm++ for Myrinet David Chalmers (Mon Mar 29 2004 - 18:53:46 CST)
  • Re: Problems compiling Charm++ for Myrinet Gengbin Zheng (Tue Mar 30 2004 - 12:40:05 CST)
• Spring Constant Uday Chippada (Mon Mar 29 2004 - 17:48:56 CST)
• counterions himanshu chandola (Tue Mar 30 2004 - 02:53:19 CST)
  • Re: counterions Brian Bennion (Tue Mar 30 2004 - 12:41:03 CST)
    • Re: counterions himanshu chandola (Wed Mar 31 2004 - 03:13:51 CST)
    • Re: counterions David Chalmers (Tue Mar 30 2004 - 23:12:17 CST)
• # of processors Neema Salimi (Mon Mar 29 2004 - 13:02:30 CST)
  • Re: # of processors Gengbin Zheng (Mon Apr 05 2004 - 00:41:44 CDT)
• A tool to set up alchemical FEP transformations Jérôme Hénin (Mon Mar 29 2004 - 10:27:12 CST)
  • Restarting problem with Langevin dynamics Xin Chen (Wed Mar 31 2004 - 15:11:58 CST)
    • Restarting problem with Langevin dynamics Xin Chen (Tue Apr 06 2004 - 00:05:19 CDT)
• 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)
  • Re: FEP calculations: defining hybrid residues Jérôme Hénin (Wed Mar 24 2004 - 11:55:54 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)
  • Re: FEP and restraints Jérôme Hénin (Tue Mar 23 2004 - 14:42:12 CST)
• Getting forces: segmentation violation or illegal instruction Justyna Jaroniec (Mon Mar 22 2004 - 11:09:25 CST)
  • Re: Getting forces: segmentation violation or illegal instruction Fangqiang Zhu (Mon Mar 22 2004 - 11:54:41 CST)
    • adding ions Amarda Shehu (Mon Mar 22 2004 - 13:30:09 CST)
      • Re: adding ions Brian Bennion (Mon Mar 22 2004 - 14:11:46 CST)
      • Re: adding ions Michael Grabe (Mon Mar 22 2004 - 14:36:35 CST)
• Unwrap molecules Ekta Khurana (Sun Mar 21 2004 - 21:55:06 CST)
• large increase in pressure after minimization Satyavani Vemparala (Sun Mar 21 2004 - 20:23:33 CST)
• initial temp of simulation Streiff, John H. (Fri Mar 19 2004 - 11:35:10 CST)
  • Re: initial temp of simulation mashaojie (Thu Mar 25 2004 - 07:39:17 CST)
    • Re: initial temp of simulation Tim Isgro (Thu Mar 25 2004 - 11:11:07 CST)
      • Re: initial temp of simulation yxiong_at_mail.ccnu.edu.cn (Thu Mar 25 2004 - 19:47:01 CST)
      • Re: initial temp of simulation Tim Isgro (Fri Mar 26 2004 - 10:46:49 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)
  • Re: hydrogen bonds in NAMD Tim Isgro (Fri Mar 19 2004 - 11:25:47 CST)
• NAMD support for Myranet GM2 drivers David Chalmers (Thu Mar 18 2004 - 22:29:52 CST)
  • Re: NAMD support for Myranet GM2 drivers Gengbin Zheng (Fri Mar 19 2004 - 01:30:49 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)
  • Re: minimization problem Brian Bennion (Thu Mar 18 2004 - 18:00:23 CST)
  • Re: minimization problem himanshu chandola (Fri Mar 19 2004 - 05:42:41 CST)
  • RE: minimization problem Ahmet Bakan (Thu Mar 18 2004 - 18:43:00 CST)
• GdHCl parameters Ruxandra Dima (Thu Mar 18 2004 - 16:18:16 CST)
  • Re: GdHCl parameters Brian Bennion (Thu Mar 18 2004 - 17:19:38 CST)
• undefined loops Stern, Julie (Thu Mar 18 2004 - 11:47:39 CST)
  • Re: undefined loops Brian Bennion (Thu Mar 18 2004 - 12:16:58 CST)
• charmrun vs. miprun and nature of parallelism Stern, Julie (Thu Mar 18 2004 - 11:39:39 CST)
  • Re: charmrun vs. miprun and nature of parallelism Gengbin Zheng (Fri Mar 19 2004 - 02:10:26 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)
  • Re: dimer minimisation and psfgen problem Brian Bennion (Wed Mar 17 2004 - 10:18:12 CST)
    • Re: dimer minimisation and psfgen problem Uday Chippada (Thu Mar 18 2004 - 14:44:35 CST)
      • Re: dimer minimisation and psfgen problem Brian Bennion (Thu Mar 18 2004 - 17:24:45 CST)
• Namd with intel compilers. Hansang Bae (Tue Mar 16 2004 - 14:51:47 CST)
  • Re: Namd with intel compilers. Gengbin Zheng (Wed Mar 17 2004 - 10:52:27 CST)
• Load balance strategy Alex V. (Tue Mar 16 2004 - 09:23:28 CST)
  • Re: Load balance strategy Brian Bennion (Tue Mar 16 2004 - 11:31:15 CST)
  • Re: Load balance strategy Gadi Oron (Tue Mar 16 2004 - 15:44:03 CST)
    • Re: Load balance strategy Gengbin Zheng (Wed Mar 17 2004 - 11:31:03 CST)
      • Re: Load balance strategy Alex V. (Thu Mar 18 2004 - 00:03:19 CST)
      • Re: Load balance strategy Gengbin Zheng (Fri Mar 19 2004 - 01:41:44 CST)
• psf question Hua Wong (Tue Mar 16 2004 - 03:12:38 CST)
  • Re: psf question Brian Bennion (Tue Mar 16 2004 - 11:02:21 CST)
• Urea and GdHCl parameters Ruxandra Dima (Mon Mar 15 2004 - 12:01:51 CST)
  • RE: Urea and GdHCl parameters Ahmet Bakan (Mon Mar 15 2004 - 13:15:18 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)
    • Re: Is it necessary to neutralize the system with NAMD program? Aaron Oakley (Tue Mar 16 2004 - 16:18:00 CST)
      • Re: Is it necessary to neutralize the system with NAMD program? Brian Bennion (Tue Mar 16 2004 - 16:58:52 CST)
    • Re: Is it necessary to neutralize the system with NAMD program? Jérôme Hénin (Fri Mar 19 2004 - 04:39:06 CST)
• Running on Alpha cluster Alex V. (Fri Mar 12 2004 - 22:27:26 CST)
  • Re: Running on Alpha cluster Gengbin Zheng (Mon Mar 15 2004 - 10:07:24 CST)
    • Re: Running on Alpha cluster Alex V. (Fri Mar 26 2004 - 03:31:22 CST)
      • Re: Running on Alpha cluster Gengbin Zheng (Fri Mar 26 2004 - 11:43:38 CST)
• Question on finding suitable force field for MD simulations Fung Wai Keung (Fri Mar 12 2004 - 21:00:06 CST)
• Paper on Classical treatment for calculating pKas Brian Bennion (Fri Mar 12 2004 - 13:40:33 CST)
  • Re: Paper on Classical treatment for calculating pKas Volodymyr Nechiporuk-Zloy (Mon Mar 15 2004 - 03:31:21 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)
  • Re: Segmentation fault. Alex V. (Wed Mar 10 2004 - 09:04:33 CST)
• Solvate Package Satyavani Vemparala (Wed Mar 10 2004 - 18:22:54 CST)
  • clustering Leandro Martinez (Fri Mar 12 2004 - 07:15:35 CST)
    • Re: clustering yu275197_at_yorku.ca (Fri Mar 12 2004 - 10:57:04 CST)
      • Re: clustering - fault tolerant NAMD Gengbin Zheng (Fri Mar 12 2004 - 13:18:01 CST)
• FIRSTTIMESTEP in config file Satyavani Vemparala (Wed Mar 10 2004 - 05:49:55 CST)
  • Re: FIRSTTIMESTEP in config file Gadi Oron (Mon Mar 15 2004 - 04:02:07 CST)
• Clustermatic 4.0 Jerry Ebalunode (Mon Mar 08 2004 - 14:16:20 CST)
  • Re: Clustermatic 4.0 Gengbin Zheng (Fri Mar 12 2004 - 21:36:16 CST)
• Binding Energy Ahmet Bakan (Mon Mar 08 2004 - 12:57:18 CST)
  • Re: Binding Energy Brian Bennion (Mon Mar 08 2004 - 13:23:38 CST)
    • Re: Binding Energy Gadi Oron (Tue Mar 09 2004 - 07:37:22 CST)
      • Re: Binding Energy Brian Bennion (Tue Mar 09 2004 - 10:42:19 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)
  • Re: Generate PSF structure Brian Bennion (Mon Mar 08 2004 - 12:17:52 CST)
    • Re: Generate PSF structure Peter Spijker (Mon Mar 08 2004 - 12:23:12 CST)
      • Re: Generate PSF structure Tim Isgro (Tue Mar 09 2004 - 10:24:01 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)
  • Re: SMD with different pH Brian Bennion (Fri Mar 05 2004 - 10:16:09 CST)
    • Re: SMD with different pH Volodymyr Nechiporuk-Zloy (Wed Mar 10 2004 - 06:37:39 CST)
      • Re: SMD with different pH Brian Bennion (Wed Mar 10 2004 - 10:47:37 CST)
• TCL: getting forces Bartosz Dobrzelecki (Fri Mar 05 2004 - 04:58:31 CST)
  • Re: TCL: getting forces Fangqiang Zhu (Fri Mar 05 2004 - 14:04:31 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)
  • Re: Amber on with H-bond Fangqiang Zhu (Wed Mar 03 2004 - 21:45:15 CST)
    • Re: Amber on with H-bond Sichun Yang (Thu Mar 04 2004 - 00:15:56 CST)
      • Re: Amber on with H-bond Fangqiang Zhu (Thu Mar 04 2004 - 01:00:31 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)
  • Re: Locally Enhanced Sampling Fangqiang Zhu (Tue Mar 02 2004 - 11:51:09 CST)
    • Sampling trajectories Harindar Keer (Fri Jun 04 2004 - 17:03:02 CDT)
• temp coupling coefficients Peter Jones (Tue Mar 02 2004 - 01:03:53 CST)
  • Re: temp coupling coefficients Jérôme Hénin (Tue Mar 02 2004 - 03:58:28 CST)
    • Re: temp coupling coefficients Hyonseok Hwang (Tue Mar 02 2004 - 13:18:22 CST)
      • Re: temp coupling coefficients Jérôme Hénin (Tue Mar 02 2004 - 15:39:24 CST)
• CP3-NH3 error Han Choe (Mon Mar 01 2004 - 21:36:44 CST)
  • Re: CP3-NH3 error Tim Isgro (Tue Mar 02 2004 - 17:31:08 CST)
    • Re: CP3-NH3 error Tim Isgro (Thu Mar 04 2004 - 13:56:44 CST)
      • RE: CP3-NH3 error Han Choe (Thu Mar 04 2004 - 16:48:46 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)
• Restart using amber force field Sichun Yang (Fri Feb 27 2004 - 11:30:47 CST)
  • Re: Restart using amber force field Fangqiang Zhu (Fri Feb 27 2004 - 15:00:29 CST)
    • Re: Restart using amber force field Sichun Yang (Fri Feb 27 2004 - 16:13:25 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)
  • Re: TIP5P Brian Bennion (Fri Feb 27 2004 - 13:39:04 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)
  • Re: <no subject> Brian Bennion (Thu Feb 26 2004 - 14:44:07 CST)
• Timestep in restart output Sichun Yang (Thu Feb 26 2004 - 12:38:08 CST)
  • Re: Timestep in restart output Brian Bennion (Thu Feb 26 2004 - 15:29:38 CST)
    • Re: Timestep in restart output Tim Isgro (Thu Feb 26 2004 - 21:01:21 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)
  • Re: Charm++ Problem Brian Bennion (Thu Feb 26 2004 - 12:09:18 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)
  • Re: psf file for zeolite-water system Fangqiang Zhu (Mon Feb 23 2004 - 14:16:26 CST)
• psf file for zeolite-water system Ozgur YAZAYDIN (Sun Feb 22 2004 - 21:21:03 CST)
• Re: warnings during NAMD simulations. li (Sat Feb 23 2008 - 08:43:42 CST)
• electron density calculations of lipid bilayers Satyavani Vemparala (Sun Feb 22 2004 - 17:45:58 CST)
  • Re: electron density calculations of lipid bilayers Jérôme Hénin (Mon Feb 23 2004 - 01:47:11 CST)
• (no subject) yu275197_at_yorku.ca (Sun Feb 22 2004 - 00:37:27 CST)
  • Re: your mail Brian Bennion (Sun Feb 22 2004 - 00:44:16 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)
  • Re: Langevin dynamics Jérôme Hénin (Thu Feb 19 2004 - 15:33:20 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)
  • Re: langevin with waterbox ? Jérôme Hénin (Thu Feb 19 2004 - 11:48:13 CST)
    • Re: langevin with waterbox ? Lei Guo (Thu Feb 19 2004 - 13:12:01 CST)
      • Re: langevin with waterbox ? Jérôme Hénin (Thu Feb 19 2004 - 13:43:04 CST)
      • Re: langevin with waterbox ? Lei Guo (Thu Feb 19 2004 - 13:48:36 CST)
• CoM motion not removed Neema Salimi (Wed Feb 18 2004 - 13:00:22 CST)
  • Re: CoM motion not removed Jim Phillips (Mon Feb 23 2004 - 11:01:02 CST)
• atom numbers limitation Wei Fu (Wed Feb 18 2004 - 14:43:27 CST)
  • Re: atom numbers limitation Jim Phillips (Tue Feb 24 2004 - 15:31:06 CST)
• firsttimestep Ekta Khurana (Tue Feb 17 2004 - 18:50:30 CST)
  • Re: firsttimestep Jim Phillips (Tue Feb 24 2004 - 15:22:27 CST)
• Problem with Tcl & psfgen scott.brown_at_abbott.com (Tue Feb 17 2004 - 13:36:56 CST)
  • Re: Problem with Tcl & psfgen Jim Phillips (Tue Feb 17 2004 - 17:33:20 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)
  • Re: Argon solvent Jérôme Hénin (Tue Feb 17 2004 - 12:03:16 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)
  • Re: retinal parameters Brian Bennion (Thu Feb 12 2004 - 10:11:48 CST)
    • Re: too much rattle Amarda Shehu (Thu Feb 12 2004 - 16:16:40 CST)
      • Re: Re: too much rattle Brian Bennion (Thu Feb 12 2004 - 16:50:30 CST)
      • Re: Re: too much rattle Amarda Shehu (Fri Feb 13 2004 - 12:24:12 CST)
      • Re: Re: too much rattle Brian Bennion (Fri Feb 13 2004 - 12:51:50 CST)
• Compiling NAMD on Tungsten.ncsa Satyavani Vemparala (Wed Feb 11 2004 - 20:18:12 CST)
  • Re: Compiling NAMD on Tungsten.ncsa Jim Phillips (Fri Feb 13 2004 - 17:35:20 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)
  • Temperature control methods in NAMD Satyavani Vemparala (Wed Feb 11 2004 - 18:07:13 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)
  • Re: concatenating two DCD files J. Rui Rodrigues (Tue Feb 10 2004 - 18:01:10 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)
  • Re: problem:psfgen- not unique coordinates Tim Isgro (Mon Feb 09 2004 - 20:05:30 CST)
• minimization scripts Gerald Quon (Mon Feb 09 2004 - 12:09:29 CST)
  • Re: minimization scripts Tim Isgro (Mon Feb 09 2004 - 16:53:33 CST)
• improving parallel on mac cluster yu275197_at_yorku.ca (Mon Feb 09 2004 - 11:44:31 CST)
  • Re: improving parallel on mac cluster Brian Bennion (Mon Feb 09 2004 - 12:05:09 CST)
    • Re: improving parallel on mac cluster yu275197_at_yorku.ca (Tue Feb 10 2004 - 16:47:34 CST)
      • Re: improving parallel on mac cluster David E. Konerding (Tue Feb 10 2004 - 18:21:32 CST)
    • Re: improving parallel on mac cluster yu275197_at_yorku.ca (Tue Feb 10 2004 - 18:23:39 CST)
• Changing SMD parameters Gadi Oron (Mon Feb 09 2004 - 07:32:11 CST)
  • SMD: many atom pulling Harindar Keer (Thu Mar 04 2004 - 21:29:12 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)
  • Re: Minimization with CHARMM Tim Isgro (Mon Feb 09 2004 - 17:04:13 CST)
    • Source code for NAMD Satyavani Vemparala (Tue Feb 10 2004 - 10:30:13 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)
  • Re: mac clustering Gengbin Zheng (Sat Feb 07 2004 - 00:10:28 CST)
• user-supplied conformational restraints Simon Sharpe (Thu Feb 05 2004 - 14:13:31 CST)
  • Re: user-supplied conformational restraints Hyonseok Hwang (Thu Feb 05 2004 - 15:41:49 CST)
  • some cluster questions Leandro Martinez (Wed Feb 18 2004 - 07:51:13 CST)
• distance constraint Hyonseok Hwang (Wed Feb 04 2004 - 17:56:20 CST)
  • Re: distance constraint Jim Phillips (Fri Feb 06 2004 - 14:34:50 CST)
• Running AIX version of NAMD on IBM cluster aida_at_mit.edu (Wed Feb 04 2004 - 14:54:21 CST)
  • Re: Running AIX version of NAMD on IBM cluster Hansang Bae (Tue Feb 17 2004 - 17:13:47 CST)
    • Re: Running AIX version of NAMD on IBM cluster Gengbin Zheng (Wed Feb 18 2004 - 21:37:55 CST)
      • Re: Running AIX version of NAMD on IBM cluster Brian Bennion (Thu Feb 19 2004 - 14:06:20 CST)
      • Re: Running AIX version of NAMD on IBM cluster Jim Phillips (Mon Feb 23 2004 - 10:50:50 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)
  • Re: NAMD and Vega? Alessandro Pedretti (Wed Feb 04 2004 - 06:33:52 CST)
• Momenta output format Neema Salimi (Mon Feb 02 2004 - 13:59:45 CST)
  • Re: Momenta output format Jim Phillips (Tue Feb 03 2004 - 16:54:28 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)
  • Re: How do we combine chains in the end Jim Phillips (Mon Feb 02 2004 - 11:54:51 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)
  • Re: Pair interaction energy Ioana Cozmuta (Fri Jan 30 2004 - 11:57:16 CST)
    • Re: Pair interaction energy Brian Bennion (Fri Jan 30 2004 - 12:08:38 CST)
      • Re: Pair interaction energy Ioana Cozmuta (Fri Jan 30 2004 - 12:28:05 CST)
      • Re: Pair interaction energy Brian Bennion (Fri Jan 30 2004 - 12:38:35 CST)
• psfgen question MinSoo Kim (Fri Jan 30 2004 - 04:00:35 CST)
  • Re: psfgen question Brian Bennion (Fri Jan 30 2004 - 10:13:35 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)
  • Re: dcd format Brian Bennion (Thu Jan 29 2004 - 17:11:37 CST)
    • Re: dcd format himanshu chandola (Fri Jan 30 2004 - 14:10:21 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)
• rotating constraints himanshu chandola (Fri Jan 30 2004 - 01:28:51 CST)
• previous question about multiplicity Brian Bennion (Tue Jan 27 2004 - 19:06:02 CST)
  • Re: previous question about multiplicity Jim Phillips (Wed Jan 28 2004 - 14:12:45 CST)
    • Re: previous question about multiplicity Brian Bennion (Wed Jan 28 2004 - 14:18:20 CST)
      • Re: previous question about multiplicity Jim Phillips (Wed Jan 28 2004 - 14:27:50 CST)
      • Re: previous question about multiplicity Brian Bennion (Wed Jan 28 2004 - 15:32:35 CST)
• Weird dihedral error Brian Bennion (Tue Jan 27 2004 - 13:16:51 CST)
  • Re: Weird dihedral error Brian Bennion (Mon Apr 19 2004 - 12:22:35 CDT)
• 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)
  • Re: question on potential energy for individual atoms Jim Phillips (Mon Jan 26 2004 - 17:52:55 CST)
• (no subject) Michael Grabe (Fri Jan 23 2004 - 17:22:54 CST)
  • Re: Jim Phillips (Mon Jan 26 2004 - 17:51:12 CST)
• Hydroxyprolin force field. ivan.vinogradov_at_utoronto.ca (Fri Jan 23 2004 - 11:01:36 CST)
  • Re: Hydroxyprolin force field. Brian Bennion (Fri Jan 23 2004 - 11:15:30 CST)
    • Re: Hydroxyprolin force field. Jim Phillips (Mon Jan 26 2004 - 17:44:10 CST)
• Parameters and topologies for aa at different protonation states Bartosz Dobrzelecki (Fri Jan 23 2004 - 06:45:26 CST)
  • Re: Parameters and topologies for aa at different protonation states Brian Bennion (Fri Jan 23 2004 - 11:14:18 CST)
• seed value in SMD Ioana Cozmuta (Thu Jan 22 2004 - 20:54:15 CST)
  • Re: seed value in SMD Jim Phillips (Mon Jan 26 2004 - 17:46:59 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)
  • Re: question on Berendsen's temperature coupling method Jim Phillips (Thu Jan 22 2004 - 17:19:22 CST)
    • Re: question on Berendsen's temperature coupling method Vlad Cojocaru (Fri Jan 23 2004 - 02:54:03 CST)
• missing atoms warnings for psfgen Frances Leung (Mon Jan 19 2004 - 21:47:33 CST)
  • Re: missing atoms warnings for psfgen Jim Phillips (Thu Jan 22 2004 - 17:08:27 CST)
• problem with running namd on Linux cluster zhilei chen (Mon Jan 19 2004 - 11:51:11 CST)
  • Re: problem with running namd on Linux cluster Gengbin Zheng (Tue Jan 20 2004 - 11:18:20 CST)
• implicit solvent model Frances Leung (Mon Jan 19 2004 - 20:10:59 CST)
• TCl question Ioana Cozmuta (Mon Jan 19 2004 - 16:41:52 CST)
  • Re: TCl question Jim Phillips (Thu Jan 22 2004 - 16:52:35 CST)
• test and a short question! Vlad Cojocaru (Mon Jan 19 2004 - 08:18:50 CST)
  • Re: test and a short question! Fangqiang Zhu (Mon Jan 19 2004 - 15:15:15 CST)
• Hybond calulator and display Jerry Ebalunode (Fri Jan 16 2004 - 12:24:30 CST)
  • Re: Hybond calulator and display John Stone (Fri Jan 16 2004 - 13:07:09 CST)
    • Bad global exclusion count Harindar Keer (Fri Jan 16 2004 - 14:06:28 CST)
• 1QSU Uday Chippada (Thu Jan 15 2004 - 13:45:03 CST)
  • Re: 1QSU Tim Isgro (Thu Jan 15 2004 - 15:32:22 CST)
• NAMD linking problem Valery Miftakhov (Tue Jan 13 2004 - 22:15:59 CST)
  • Re: NAMD linking problem Gengbin Zheng (Fri Jan 16 2004 - 15:46:09 CST)
• charmm27 Wei Fu (Tue Jan 13 2004 - 17:15:49 CST)
  • Re: charmm27 Brian Bennion (Tue Jan 13 2004 - 17:24:49 CST)
  • Re: charmm27 Amit Paliwal (Tue Jan 13 2004 - 12:31:50 CST)
  • Re:charmm27 Wei Fu (Tue Jan 13 2004 - 19:27:02 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)
  • Re: limit on the number of residues in each segment Brian Bennion (Fri Jan 09 2004 - 16:53:20 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)
  • Re: total energy stuck between two levels Jérôme Hénin (Wed Jan 07 2004 - 02:42:33 CST)
  • Re: total energy stuck between two levels Jim Phillips (Wed Jan 07 2004 - 09:22:27 CST)
    • Interaction energy between fixed atoms Amit Paliwal (Wed Jan 07 2004 - 08:03:12 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)
  • Re: Potential Terms Jim Phillips (Wed Jan 07 2004 - 09:45:11 CST)
• SMD force (fwd) Ioana Cozmuta (Mon Jan 05 2004 - 13:36:16 CST)
  • Re: SMD force (fwd) Fangqiang Zhu (Tue Jan 06 2004 - 17:14:56 CST)
    • Re: SMD force (fwd) Ioana Cozmuta (Tue Jan 06 2004 - 18:25:20 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)
  • Re: NAMD for Opteron? Gengbin Zheng (Sun Jan 04 2004 - 18:32:21 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)
• Energy units Sundaramoorthy, Munirathinam (Tue Dec 30 2003 - 12:21:59 CST)
  • Re: Energy units Brian Bennion (Tue Dec 30 2003 - 13:53:17 CST)
• big systems using namd on 700 cpus Brian Bennion (Mon Dec 29 2003 - 13:47:04 CST)
• Truncation errors. hansang bae (Mon Dec 29 2003 - 09:19:53 CST)
• (no subject) li (Mon Dec 29 2008 - 16:46:32 CST)
  • Hi Wang Yu (Mon Dec 29 2003 - 07:44:57 CST)
• Periodic cell has become too small for original patch grid? yxiong_at_mail.ccnu.edu.cn (Wed Dec 24 2003 - 03:44:58 CST)
• flexible cell Juan Alfredo Freites (Mon Dec 22 2003 - 12:10:32 CST)
• Bun in charmd? Gadi Oron (Sun Dec 21 2003 - 08:53:49 CST)
  • Re: Bun in charmd? Gengbin Zheng (Sun Dec 21 2003 - 14:11:56 CST)
• Molecular stress tensor Lei Guo (Sat Dec 20 2003 - 16:50:17 CST)
• about HIS residue yxiong_at_mail.ccnu.edu.cn (Fri Dec 19 2003 - 20:40:35 CST)
  • Re: about HIS residue J. Rui Rodrigues (Sun Dec 21 2003 - 13:47:28 CST)
• Simulating RNA+PROTEIN complexes Bartosz Dobrzelecki (Fri Dec 19 2003 - 14:30:23 CST)
  • Re: Simulating RNA+PROTEIN complexes Jim Phillips (Fri Dec 19 2003 - 16:26:31 CST)
• weird energies during minimization Brian Bennion (Fri Dec 19 2003 - 13:04:56 CST)
  • Re: weird energies during minimization Jim Phillips (Fri Dec 19 2003 - 16:23:36 CST)
    • Re: weird energies during minimization Brian Bennion (Fri Dec 19 2003 - 16:25:19 CST)
• Charm++ nodelist commands Gadi Oron (Thu Dec 18 2003 - 05:48:02 CST)
  • Re: Charm++ nodelist commands Gengbin Zheng (Thu Dec 18 2003 - 13:04:28 CST)
    • Re: Charm++ nodelist commands Gadi Oron (Sun Dec 21 2003 - 02:38:11 CST)
      • Re: Charm++ nodelist commands Alexandre Vakhrouchev (Thu Dec 18 2003 - 06:33:16 CST)
      • Re: Charm++ nodelist commands Gadi Oron (Mon Dec 22 2003 - 05:10:39 CST)
      • Re: Charm++ nodelist commands Alexandre Vakhrouchev (Thu Dec 18 2003 - 11:36:11 CST)
      • Re: Charm++ nodelist commands Gadi Oron (Mon Dec 22 2003 - 11:30:55 CST)
      • Re: Charm++ nodelist commands Gengbin Zheng (Tue Dec 23 2003 - 17:22:29 CST)
      • Re: Charm++ nodelist commands Gadi Oron (Tue Dec 30 2003 - 08:10:29 CST)
      • Re: Charm++ nodelist commands Gengbin Zheng (Tue Dec 30 2003 - 13:14:52 CST)
      • Re: Charm++ nodelist commands Gengbin Zheng (Tue Dec 30 2003 - 18:05:36 CST)
      • Re: Charm++ nodelist commands Gadi Oron (Wed Dec 31 2003 - 03:31:17 CST)
      • Re: Charm++ nodelist commands Gengbin Zheng (Wed Dec 31 2003 - 11:59:00 CST)
      • Intel C/C++ compiler Version 8 for compiling NAMD on IA64 Jerry Ebalunode (Wed Dec 31 2003 - 12:57:53 CST)
      • Re: Intel C/C++ compiler Version 8 for compiling NAMD on IA64 Gengbin Zheng (Wed Dec 31 2003 - 13:25:53 CST)
      • Re: Re: Intel C/C++ compiler Version 8 for compiling NAMD on IA64 Jerry Ebalunode (Fri Jan 02 2004 - 12:04:41 CST)
      • Re: Re: Intel C/C++ compiler Version 8 for compiling NAMD on IA64 Gengbin Zheng (Fri Jan 02 2004 - 12:16:32 CST)
      • Re: Charm++ nodelist commands Gadi Oron (Thu Jan 08 2004 - 02:40:06 CST)
      • Re: Charm++ nodelist commands Gengbin Zheng (Fri Jan 02 2004 - 12:09:51 CST)
    • Re: Charm++ nodelist commands Gengbin Zheng (Sun Jan 04 2004 - 16:23:27 CST)
      • Re: Charm++ nodelist commands Gengbin Zheng (Sun Jan 04 2004 - 23:18:42 CST)
• how should I run NAMD on parallel platform? yxiong_at_mail.ccnu.edu.cn (Thu Dec 18 2003 - 01:33:14 CST)
  • Re: how should I run NAMD on parallel platform? Gengbin Zheng (Thu Dec 18 2003 - 02:40:16 CST)
    • Re: how should I run NAMD on parallel platform? yxiong_at_mail.ccnu.edu.cn (Thu Dec 18 2003 - 04:40:58 CST)
      • Re: how should I run NAMD on parallel platform? Jim Phillips (Thu Dec 18 2003 - 13:27:24 CST)
      • geometric mean Leandro Martinez (Thu Jan 29 2004 - 07:53:58 CST)
• TIP3P model Amit Paliwal (Wed Dec 17 2003 - 13:10:45 CST)
• periodic boundary conditions with lipids Jee Eun Rim (Wed Dec 17 2003 - 12:29:45 CST)
• dielectric Michael Grabe (Wed Dec 17 2003 - 11:30:59 CST)
• different dielectric constant during simulation Liu, Zhanwu (Wed Dec 17 2003 - 10:24:30 CST)
• HIS modification yxiong_at_mail.ccnu.edu.cn (Wed Dec 17 2003 - 04:37:24 CST)
• Re: problems compiling charm++ for clustermatic 4 Zheng Gengbin (Tue Dec 16 2003 - 02:21:36 CST)
  • Re: problems compiling charm++ for clustermatic 4 Mike Grommet (Tue Dec 16 2003 - 08:47:52 CST)
• Density AHMET BAKAN (Tue Dec 16 2003 - 12:45:26 CST)
• clustermatic 4 binaries? Mike Grommet (Tue Dec 16 2003 - 01:05:59 CST)
  • Re: clustermatic 4 binaries? Jim Phillips (Tue Dec 16 2003 - 22:22:08 CST)
• restraints Michael Grabe (Mon Dec 15 2003 - 20:04:29 CST)
  • Re: restraints Jim Phillips (Tue Dec 16 2003 - 22:19:08 CST)
• Polymer Simulations AHMET BAKAN (Mon Dec 15 2003 - 16:49:22 CST)
• LDB questions/problems Brian Bennion (Mon Dec 15 2003 - 12:58:15 CST)
  • Re: LDB questions/problems himanshu chandola (Tue Dec 16 2003 - 00:29:26 CST)
    • Re: LDB questions/problems Brian Bennion (Mon Dec 15 2003 - 15:41:32 CST)
      • Re: LDB questions/problems Gengbin Zheng (Tue Dec 16 2003 - 02:33:09 CST)
      • Re: LDB questions/problems Brian Bennion (Tue Dec 16 2003 - 15:32:51 CST)
      • Re: LDB questions/problems Jim Phillips (Tue Dec 16 2003 - 22:44:32 CST)
      • Re: LDB questions/problems Brian Bennion (Thu Dec 18 2003 - 10:23:25 CST)
      • Stray PME grid charges Harindar Keer (Tue Sep 07 2004 - 13:42:39 CDT)
      • Re: Stray PME grid charges Vani Krishna (Tue Sep 07 2004 - 21:16:35 CDT)
      • NAMD programming guide Harindar Keer (Thu Sep 16 2004 - 19:55:52 CDT)
• Help with NAMD + Clustermatic 4 please Mike Grommet (Sun Dec 14 2003 - 01:01:55 CST)
• Which version MPICH-VMI does namd-ia64-vmi run on? intel compiled version or gcc complied version? Jerry Ebalunode (Thu Dec 11 2003 - 03:11:03 CST)
  • Re: Which version MPICH-VMI does namd-ia64-vmi run on? intel compiled version or gcc complied version? Gengbin Zheng (Thu Dec 11 2003 - 16:08:08 CST)
• Harmonic constraint parameter k zhilei chen (Thu Dec 11 2003 - 08:39:48 CST)
  • Re: Harmonic constraint parameter k Tim Isgro (Thu Dec 11 2003 - 18:21:48 CST)
• Help! unstable simulation. Gadi Oron (Thu Dec 11 2003 - 01:51:14 CST)
  • Re: Help! unstable simulation. Alexandre Vakhrouchev (Fri Dec 12 2003 - 03:16:55 CST)
    • Re: Help! unstable simulation - ARG go nuts... Gadi Oron (Tue Dec 16 2003 - 09:33:25 CST)
      • Re: Help! unstable simulation - ARG go nuts... Jim Phillips (Tue Dec 16 2003 - 22:10:31 CST)
      • Re: Help! unstable simulation - ARG go nuts... Gadi Oron (Wed Dec 17 2003 - 04:36:47 CST)
      • Re: Help! unstable simulation - ARG go nuts... Jim Phillips (Wed Dec 17 2003 - 09:23:02 CST)
• processors information Ioana Cozmuta (Wed Dec 10 2003 - 21:28:23 CST)
• .psf and .params files for IMD Harit Jani (Wed Dec 10 2003 - 19:08:54 CST)
• coorfile Shunzhou Wan (Wed Dec 10 2003 - 11:23:46 CST)
• how should I set those PMEGridSizeX,Y,Z? yxiong_at_mail.ccnu.edu.cn (Wed Dec 10 2003 - 00:13:55 CST)
  • Re: how should I set those PMEGridSizeX,Y,Z? Tim Isgro (Wed Dec 10 2003 - 14:18:37 CST)
    • Re: how should I set those PMEGridSizeX,Y,Z? yxiong_at_mail.ccnu.edu.cn (Wed Dec 10 2003 - 18:51:51 CST)
      • Re: how should I set those PMEGridSizeX,Y,Z? Tim Isgro (Thu Dec 11 2003 - 18:00:13 CST)
• where to find the force field parameters for F and P atom? yxiong_at_mail.ccnu.edu.cn (Tue Dec 09 2003 - 20:04:01 CST)
  • Re: CCL:where to find the force field parameters for F and P atom? Joey Harriman (Fri Dec 12 2003 - 09:22:15 CST)
• Some parameters AHMET BAKAN (Tue Dec 09 2003 - 06:06:50 CST)
• forces during SMD zhilei chen (Sun Dec 07 2003 - 10:16:43 CST)
• DOWSER Peter Jones (Mon Dec 08 2003 - 02:26:35 CST)
• Re: 2 domains rigid body rotation with IMD Matteo Cattaneo (Sun Dec 07 2003 - 14:33:47 CST)
• reading in large water boxes (PDB format)? David E. Konerding (Sun Dec 07 2003 - 12:26:32 CST)
  • Re: reading in large water boxes (PDB format)? Juan Alfredo Freites (Sun Dec 07 2003 - 19:32:09 CST)
• PSF generation AHMET BAKAN (Sun Dec 07 2003 - 10:08:47 CST)
  • Re: PSF generation yxiong_at_mail.ccnu.edu.cn (Sun Dec 07 2003 - 19:12:58 CST)
    • Re: PSF generation Josef Scheiber (Mon Dec 08 2003 - 02:50:37 CST)
• (no subject) Alexandre Vakhrouchev (Sun Dec 07 2003 - 01:47:07 CST)
  • Re: james tomomi macdonald (Mon Dec 08 2003 - 08:46:54 CST)
• about temperature reassign? yxiong_at_mail.ccnu.edu.cn (Sat Dec 06 2003 - 03:42:30 CST)
• I have known how to do a constrained MD before a normal MD yxiong_at_mail.ccnu.edu.cn (Sat Dec 06 2003 - 02:58:36 CST)
• problem with flipbinpdb yxiong_at_mail.ccnu.edu.cn (Sat Dec 06 2003 - 02:33:01 CST)
• About the SMD output file zhilei chen (Fri Dec 05 2003 - 16:17:41 CST)
  • Re: About the SMD output file Ioana Cozmuta (Fri Dec 05 2003 - 16:47:31 CST)
• binary troubles Michael Grabe (Fri Dec 05 2003 - 13:14:54 CST)
  • Re: binary troubles Brian Bennion (Fri Dec 05 2003 - 13:40:35 CST)
• 2 domains rigid body rotation with IMD Matteo Cattaneo (Fri Dec 05 2003 - 08:28:22 CST)
• I have known how to find and click the atoms accurately and easily. yxiong_at_mail.ccnu.edu.cn (Fri Dec 05 2003 - 01:30:48 CST)
  • Re: I have known how to find and click the atoms accurately and easily. nathalie reuter (Fri Dec 05 2003 - 02:16:29 CST)
• how to get the plot of selected bond over time? yxiong_at_mail.ccnu.edu.cn (Thu Dec 04 2003 - 21:38:16 CST)
  • Re: how to get the plot of selected bond over time? Alessandro Pedretti (Fri Dec 05 2003 - 07:19:45 CST)
• SHAKE algorithm and MD at constant T and P? yxiong_at_mail.ccnu.edu.cn (Thu Dec 04 2003 - 19:54:15 CST)
• Solute KE Shantenu Jha (Thu Dec 04 2003 - 16:36:31 CST)
  • Re: Solute KE Shantenu Jha (Thu Dec 04 2003 - 17:08:23 CST)
• psfgen: pdb and nucleic acid David E. Konerding (Wed Dec 03 2003 - 13:52:52 CST)
  • Re: psfgen: pdb and nucleic acid Brian Bennion (Wed Dec 03 2003 - 14:30:29 CST)
• (no subject) Alexandre Vakhrouchev (Wed Dec 03 2003 - 02:57:04 CST)
  • RE: Cesar Delgado (Wed Dec 03 2003 - 08:46:12 CST)
  • Re: Jim Phillips (Wed Dec 03 2003 - 15:03:46 CST)
• Basic question. hansang bae (Tue Dec 02 2003 - 13:03:16 CST)
  • Re: Basic question. Brian Bennion (Tue Dec 02 2003 - 13:30:30 CST)
  • Re: Basic question. Jérôme Hénin (Tue Dec 02 2003 - 13:50:38 CST)
• Binary conversions Hua Wong (Tue Dec 02 2003 - 02:11:10 CST)
  • Re: Binary conversions Jim Phillips (Wed Dec 03 2003 - 15:08:17 CST)
• Free energy constraints and logfile David Chalmers (Mon Dec 01 2003 - 22:54:01 CST)
• RE: IMD on MPI versions of NAMD Cesar Delgado (Mon Dec 01 2003 - 16:44:05 CST)
  • RE: IMD on MPI versions of NAMD Brian Bennion (Mon Dec 01 2003 - 16:58:16 CST)
• RE: VMD problems Cesar Delgado (Mon Dec 01 2003 - 13:05:39 CST)
• VMD problems Hua Wong (Mon Dec 01 2003 - 07:46:44 CST)
• how the charges of those residues of protein(for example LYS) are determined in CHARMM topology file yxiong_at_mail.ccnu.edu.cn (Mon Dec 01 2003 - 04:27:52 CST)
• rotational energy, Tcl and environment variable(s) in Linux 2.5 Shantenu Jha (Sun Nov 30 2003 - 18:47:07 CST)
  • Re: rotational energy, Tcl and environment variable(s) in Linux 2.5 Fangqiang Zhu (Tue Dec 02 2003 - 00:38:01 CST)
    • Re: rotational energy, Tcl and environment variable(s) in Linux 2.5 Shantenu Jha (Thu Dec 04 2003 - 15:59:10 CST)
      • Re: rotational energy, Tcl and environment variable(s) inLinux 2.5 Fangqiang Zhu (Thu Dec 04 2003 - 18:05:24 CST)
• how to add counterions ? yxiong_at_mail.ccnu.edu.cn (Sun Nov 30 2003 - 04:59:36 CST)
  • Re: how to add counterions ? Fangqiang Zhu (Tue Dec 02 2003 - 00:24:16 CST)
    • Re: how to add counterions ? yxiong_at_mail.ccnu.edu.cn (Tue Dec 02 2003 - 01:54:09 CST)
      • Re: how to add counterions ? Fangqiang Zhu (Tue Dec 02 2003 - 18:19:19 CST)
  • Re: how to add counterions ? Alessandro Pedretti (Tue Dec 02 2003 - 06:18:58 CST)
• Why "fixedAtomsForces on" for constant pressure? Jan Saam (Tue Nov 25 2003 - 18:30:09 CST)
  • Re: Why "fixedAtomsForces on" for constant pressure? Fangqiang Zhu (Tue Dec 02 2003 - 00:04:16 CST)
    • Re: Why "fixedAtomsForces on" for constant pressure? Jim Phillips (Wed Dec 03 2003 - 16:24:45 CST)
• how to get Charge of new residue? yxiong_at_mail.ccnu.edu.cn (Fri Nov 28 2003 - 23:29:34 CST)
  • Re: how to get Charge of new residue? Fangqiang Zhu (Sat Nov 29 2003 - 01:03:31 CST)
    • Re: how to get Charge of new residue? yxiong_at_mail.ccnu.edu.cn (Sun Nov 30 2003 - 03:51:26 CST)
• (no subject) yxiong_at_mail.ccnu.edu.cn (Fri Nov 28 2003 - 20:35:59 CST)
  • Re: Fangqiang Zhu (Sat Nov 29 2003 - 00:41:44 CST)
• Re: Temp in SMD taeho.kim_at_utoronto.ca (Fri Nov 28 2003 - 17:53:27 CST)
  • Re: Temp in SMD Fangqiang Zhu (Sat Nov 29 2003 - 00:34:30 CST)
• how can I know which type HIS belong to?(HSD,HSE,HSP) yxiong_at_mail.ccnu.edu.cn (Fri Nov 28 2003 - 04:02:05 CST)
  • Re: how can I know which type HIS belong to?(HSD,HSE,HSP) Fangqiang Zhu (Sat Nov 29 2003 - 00:22:03 CST)
    • Re: how can I know which type HIS belong to?(HSD,HSE,HSP) Jérôme Hénin (Sat Nov 29 2003 - 04:37:30 CST)
• Topology and parameters files for FAD cofator PQCHEN (Fri Nov 28 2003 - 04:04:55 CST)
• the Atom velocity is beyond the limit? yxiong_at_mail.ccnu.edu.cn (Fri Nov 28 2003 - 03:33:03 CST)
  • Re: the Atom velocity is beyond the limit? Fangqiang Zhu (Fri Nov 28 2003 - 23:44:19 CST)
• the problem on segment a ligand in NAMD ? yxiong_at_mail.ccnu.edu.cn (Thu Nov 27 2003 - 21:53:42 CST)
  • Re: the problem on segment a ligand in NAMD ? Brian Bennion (Fri Nov 28 2003 - 00:30:13 CST)
    • Re: the problem on segment a ligand in NAMD ? yxiong_at_mail.ccnu.edu.cn (Fri Nov 28 2003 - 02:02:24 CST)
  • Re: the problem on segment a ligand in NAMD ? Fangqiang Zhu (Fri Nov 28 2003 - 00:41:19 CST)
• Minimisation error Hua Wong (Thu Nov 27 2003 - 08:47:29 CST)
  • Re: Minimisation error Brian Bennion (Thu Nov 27 2003 - 21:49:25 CST)
    • Re: Minimisation error Hua Wong (Fri Nov 28 2003 - 02:32:49 CST)
      • Re: Minimisation error J. Rui Rodrigues (Fri Nov 28 2003 - 09:40:46 CST)
    • Addendum to Re: Minimisation error Hua Wong (Fri Nov 28 2003 - 02:36:02 CST)
• FATAL ERROR Hua Wong (Thu Nov 27 2003 - 08:32:15 CST)
  • Re: FATAL ERROR Fangqiang Zhu (Thu Nov 27 2003 - 23:47:41 CST)
• NAMD minimisation Hua Wong (Thu Nov 27 2003 - 07:29:27 CST)
  • Re: NAMD minimisation Jan Saam (Thu Nov 27 2003 - 08:15:26 CST)
• problems with psfgen Hua Wong (Thu Nov 27 2003 - 04:39:25 CST)
  • Re: problems with psfgen yxiong_at_mail.ccnu.edu.cn (Thu Nov 27 2003 - 06:57:35 CST)
• xst format Zoe Cournia (Thu Nov 27 2003 - 04:17:44 CST)
  • Re: xst format Fangqiang Zhu (Thu Nov 27 2003 - 23:27:34 CST)
• something about the TIP3P water model PQCHEN (Wed Nov 26 2003 - 20:05:59 CST)
  • Re: something about the TIP3P water model Fangqiang Zhu (Thu Nov 27 2003 - 23:11:33 CST)
• hydrogengroupsize of 0! Brian Bennion (Wed Nov 26 2003 - 17:57:28 CST)
  • Re: hydrogengroupsize of 0! Jan Saam (Thu Nov 27 2003 - 02:43:26 CST)
    • Re: hydrogengroupsize of 0! Brian Bennion (Thu Dec 18 2003 - 13:03:01 CST)
• updating coordinates using IMD David E. Konerding (Wed Nov 26 2003 - 14:09:10 CST)
  • Re: updating coordinates using IMD Fangqiang Zhu (Mon Dec 01 2003 - 11:47:08 CST)
    • IMD on MPI versions of NAMD Brian Bennion (Mon Dec 01 2003 - 12:19:28 CST)
      • Re: IMD on MPI versions of NAMD Jim Phillips (Wed Dec 03 2003 - 15:38:04 CST)
• parameter for phosphonate yxiong_at_mail.ccnu.edu.cn (Wed Nov 26 2003 - 07:23:45 CST)
• parameter for phosphonate yxiong_at_mail.ccnu.edu.cn (Wed Nov 26 2003 - 00:14:37 CST)
• about internal coordinate IC statement of CHARMM force field yxiong_at_mail.ccnu.edu.cn (Tue Nov 25 2003 - 01:24:23 CST)
  • Re: about internal coordinate IC statement of CHARMM force field Brian Bennion (Tue Nov 25 2003 - 13:09:41 CST)
• Energy problem after restart Alessandro Pedretti (Thu Nov 20 2003 - 07:13:56 CST)
  • Re: Energy problem after restart Fangqiang Zhu (Thu Nov 20 2003 - 17:15:11 CST)
    • Re: Energy problem after restart Alessandro Pedretti (Mon Nov 24 2003 - 03:00:11 CST)
      • Re: Energy problem after restart Fangqiang Zhu (Mon Nov 24 2003 - 15:15:56 CST)
      • Re: Energy problem after restart Fangqiang Zhu (Tue Nov 25 2003 - 09:47:30 CST)
• configuration files Michael Grabe (Wed Nov 19 2003 - 16:38:24 CST)
• Parameter-Topology-Repository Jan Saam (Wed Nov 19 2003 - 11:56:41 CST)
  • Re: LYC Parameter-Topology ? Harindar Keer (Wed Nov 19 2003 - 13:01:55 CST)
• ATP fix (fwd) himanshu chandola (Wed Nov 19 2003 - 11:32:17 CST)
  • Re: ATP fix (fwd) Brian Bennion (Wed Nov 19 2003 - 11:06:19 CST)
    • Re: ATP fix (fwd) himanshu chandola (Wed Nov 19 2003 - 23:36:48 CST)
• rot constraints himanshu chandola (Tue Nov 18 2003 - 20:42:17 CST)
• rotating constraints himanshu chandola (Tue Nov 18 2003 - 20:17:14 CST)
• charmm restart file to NAMD Giovanni Settanni (Mon Nov 17 2003 - 05:27:03 CST)
• zinc parameter? yxiong_at_mail.ccnu.edu.cn (Sun Nov 16 2003 - 02:09:54 CST)
  • Re: zinc parameter? Fangqiang Zhu (Mon Nov 17 2003 - 18:24:08 CST)
• ADP again himanshu chandola (Sun Nov 16 2003 - 04:27:48 CST)
  • Re: ADP again Brian Bennion (Sun Nov 16 2003 - 00:26:00 CST)
    • Re: ADP again himanshu chandola (Mon Nov 17 2003 - 02:13:25 CST)
      • Re: ADP again Brian Bennion (Mon Nov 17 2003 - 11:18:09 CST)
      • Re: ADP again Brian Bennion (Mon Nov 17 2003 - 12:58:56 CST)
      • Re: ADP again Fangqiang Zhu (Mon Nov 17 2003 - 18:47:59 CST)
      • Re: ADP again Brian Bennion (Tue Nov 18 2003 - 10:24:33 CST)
      • Re: ADP again Fangqiang Zhu (Tue Nov 18 2003 - 18:44:24 CST)
      • Re: ADP again Brian Bennion (Wed Nov 19 2003 - 11:00:40 CST)
• Re: How to do FEP simulations to calculate the absolute free energy of solvation? PQCHEN (Sat Nov 15 2003 - 05:43:48 CST)
• How to do FEP simulations to calculate the absolute free energy of solvation? PQCHEN (Fri Nov 14 2003 - 22:24:01 CST)
  • Re: How to do FEP simulations to calculate the absolute free energy of solvation? Jérôme Hénin (Sat Nov 15 2003 - 04:27:35 CST)
    • Re: How to do FEP simulations to calculate the absolute free energy of solvation? Jérôme Hénin (Sat Nov 15 2003 - 08:30:50 CST)
• SC2003 and NAMD support Jim Phillips (Fri Nov 14 2003 - 16:41:25 CST)
• psfgen questions welcome on NAMD-L Jim Phillips (Fri Nov 14 2003 - 14:52:22 CST)
• Simulating DNA in vacuum C. Ecker (Fri Nov 14 2003 - 08:47:54 CST)
• sorted out problem himanshu chandola (Fri Nov 14 2003 - 14:24:45 CST)
• MOE program and difference between MD and SA? yxiong_at_mail.ccnu.edu.cn (Fri Nov 14 2003 - 02:57:25 CST)
  • Re: MOE program and difference between MD and SA? Brian Bennion (Fri Nov 14 2003 - 10:35:15 CST)
  • Re: MOE program and difference between MD and SA? Jim Phillips (Fri Nov 14 2003 - 15:20:00 CST)
• lipids Michael Grabe (Fri Nov 14 2003 - 02:07:21 CST)
• high temperature, 498K, unfolding simulations james tomomi macdonald (Thu Nov 13 2003 - 11:47:29 CST)
  • Re: high temperature, 498K, unfolding simulations Brian Bennion (Thu Nov 13 2003 - 12:23:13 CST)
  • Re: high temperature, 498K, unfolding simulations Michael Grabe (Thu Nov 13 2003 - 12:31:28 CST)
• tcl interface C. Ecker (Thu Nov 13 2003 - 05:07:04 CST)
  • Re: tcl interface Jérôme Hénin (Thu Nov 13 2003 - 05:16:20 CST)
• error in starting the minimization Ruxandra Dima (Wed Nov 12 2003 - 17:06:44 CST)
  • Re: error in starting the minimization Brian Bennion (Wed Nov 12 2003 - 18:11:42 CST)
    • Re: error in starting the minimization Ruxandra Dima (Wed Nov 12 2003 - 18:20:53 CST)
      • Re: error in starting the minimization Jim Phillips (Fri Nov 14 2003 - 14:41:35 CST)
• Re: vmd-l: POV-Ray Oscar Moran (Wed Nov 12 2003 - 03:49:31 CST)
• rotation constraints himanshu chandola (Tue Nov 11 2003 - 17:59:45 CST)
  • Re: rotation constraints Jim Phillips (Thu Nov 13 2003 - 15:18:49 CST)
• G5 or P4 cluster Grischa R. Meyer (Tue Nov 11 2003 - 00:58:07 CST)
• dcd files himanshu chandola (Tue Nov 11 2003 - 09:44:21 CST)
  • Re: dcd files Brian Bennion (Tue Nov 11 2003 - 10:27:42 CST)
    • Re: dcd files himanshu chandola (Tue Nov 11 2003 - 23:52:13 CST)
      • Re: dcd files Juan Alfredo Freites (Tue Nov 11 2003 - 15:50:11 CST)
  • Re: dcd files Jim Phillips (Fri Nov 14 2003 - 14:36:29 CST)
• A problem with intermediate files Zhilei Chen (Mon Nov 10 2003 - 21:52:57 CST)
  • Re: A problem with intermediate files Ioana Cozmuta (Mon Nov 10 2003 - 22:09:20 CST)
  • Re: A problem with intermediate files Ioana Cozmuta (Mon Nov 10 2003 - 22:12:05 CST)
  • Re: A problem with intermediate files J. Rui Rodrigues (Tue Nov 11 2003 - 07:46:33 CST)
• restarting suspended namd jobs J. Rui Rodrigues (Mon Nov 10 2003 - 13:56:54 CST)
  • Re: restarting suspended namd jobs Jim Phillips (Thu Nov 13 2003 - 15:55:45 CST)
• Distance-dependent dielectrics in NAMD Sarah Harris (Mon Nov 10 2003 - 05:05:36 CST)
  • Re: Distance-dependent dielectrics in NAMD Jim Phillips (Thu Nov 13 2003 - 15:52:31 CST)
• IBM SP build David Skinner (Sun Nov 09 2003 - 00:21:31 CST)
  • Re: IBM SP build Jim Phillips (Thu Nov 13 2003 - 14:57:20 CST)
• uninitialized coordinates himanshu chandola (Sun Nov 09 2003 - 02:22:35 CST)
  • Re: uninitialized coordinates Brian Bennion (Mon Nov 10 2003 - 10:40:31 CST)
• fixed atoms parameters himanshu chandola (Fri Nov 07 2003 - 23:54:04 CST)
  • Re: fixed atoms parameters Jérôme Hénin (Fri Nov 07 2003 - 16:17:48 CST)
• rotation constraints himanshu chandola (Fri Nov 07 2003 - 23:49:26 CST)
  • Re: rotation constraints Jim Phillips (Thu Nov 13 2003 - 15:20:49 CST)
• Parameter/topology repository Jan Saam (Fri Nov 07 2003 - 06:05:13 CST)
  • Re: Parameter/topology repository Brian Bennion (Fri Nov 07 2003 - 10:12:22 CST)
  • Re: Parameter/topology repository Jim Phillips (Fri Nov 07 2003 - 11:05:11 CST)
• Re: vmd-l: running vmd in batch mode Ioana Cozmuta (Thu Nov 06 2003 - 19:19:30 CST)
  • Re: vmd-l: running vmd in batch mode John Stone (Thu Nov 06 2003 - 19:26:27 CST)
• running vmd in batch mode Ioana Cozmuta (Thu Nov 06 2003 - 15:46:19 CST)
• how to set harmonic constraints to alpha carbon Zhilei Chen (Thu Nov 06 2003 - 15:07:05 CST)
  • Re: how to set harmonic constraints to alpha carbon Brian Bennion (Thu Nov 06 2003 - 16:34:53 CST)
    • Re: how to set harmonic constraints to alpha carbon Jim Phillips (Fri Nov 07 2003 - 10:37:51 CST)
• contraint failure in RATTLE algorithm ELENA JEAN LEVIN (Thu Nov 06 2003 - 13:45:19 CST)
  • Re: contraint failure in RATTLE algorithm Brian Bennion (Thu Nov 06 2003 - 14:10:49 CST)
    • Re: contraint failure in RATTLE algorithm ELENA JEAN LEVIN (Thu Nov 06 2003 - 16:01:07 CST)
      • Re: contraint failure in RATTLE algorithm Jim Phillips (Fri Nov 07 2003 - 10:33:01 CST)
• (no subject) Alexandre Vakhrouchev (Thu Nov 06 2003 - 02:18:39 CST)
• bigdcd Ioana Cozmuta (Wed Nov 05 2003 - 17:00:40 CST)
  • Re: vmd-l: bigdcd Brian Bennion (Wed Nov 05 2003 - 17:52:38 CST)
    • Re: Re: vmd-l: bigdcd Ioana Cozmuta (Wed Nov 05 2003 - 18:29:25 CST)
• repulsive/hard sphere simulation AMIT PALIWAL (Wed Nov 05 2003 - 15:07:21 CST)
  • Re: repulsive/hard sphere simulation Brian Bennion (Wed Nov 05 2003 - 15:22:16 CST)
    • Re: repulsive/hard sphere simulation AMIT PALIWAL (Wed Nov 05 2003 - 15:50:53 CST)
    • Re: repulsive/hard sphere simulation AMIT PALIWAL (Wed Nov 05 2003 - 15:53:17 CST)
  • Re: repulsive/hard sphere simulation Jim Phillips (Fri Nov 07 2003 - 10:42:57 CST)
• about charmm topology file Zhilei Chen (Wed Nov 05 2003 - 10:00:56 CST)
  • Re: about charmm topology file Brian Bennion (Wed Nov 05 2003 - 10:27:51 CST)
    • Re: about charmm topology file Jim Phillips (Wed Nov 05 2003 - 13:15:48 CST)
• Re: SMD -apply the force via Tcl script Taeho Kim (Tue Nov 04 2003 - 11:27:52 CST)
• RE: Question about AUTOGENERATE Zhilei Chen (Tue Nov 04 2003 - 09:48:01 CST)
  • RE: Question about AUTOGENERATE Brian Bennion (Tue Nov 04 2003 - 10:24:58 CST)
  • RE: Question about AUTOGENERATE Jim Phillips (Wed Nov 05 2003 - 12:38:32 CST)
• periodic boxes Michael Grabe (Mon Nov 03 2003 - 23:13:50 CST)
  • Re: periodic boxes Jim Phillips (Fri Nov 07 2003 - 10:47:13 CST)
• Question about AUTOGENERATE Zhilei Chen (Mon Nov 03 2003 - 20:50:09 CST)
  • Re: Question about AUTOGENERATE Jim Phillips (Mon Nov 03 2003 - 21:43:56 CST)
• excluding water in dcd files himanshu chandola (Mon Nov 03 2003 - 02:31:41 CST)
  • Re: excluding water in dcd files Brian Bennion (Mon Nov 03 2003 - 11:23:38 CST)
    • Re: excluding water in dcd files himanshu chandola (Tue Nov 04 2003 - 02:00:18 CST)
      • Re: excluding water in dcd files Jim Phillips (Mon Nov 03 2003 - 17:21:00 CST)
      • Re: excluding water in dcd files himanshu chandola (Tue Nov 04 2003 - 11:45:28 CST)
      • Re: excluding water in dcd files Brian Bennion (Tue Nov 04 2003 - 10:35:55 CST)
      • Re: excluding water in dcd files Jim Phillips (Wed Nov 05 2003 - 13:36:37 CST)
      • atoms moving too fast himanshu chandola (Thu Nov 06 2003 - 03:21:12 CST)
      • Re: atoms moving too fast Brian Bennion (Wed Nov 05 2003 - 16:50:53 CST)
      • Re: atoms moving too fast himanshu chandola (Thu Nov 06 2003 - 03:59:10 CST)
      • Re: atoms moving too fast Brian Bennion (Wed Nov 05 2003 - 17:36:51 CST)
      • Re: atoms moving too fast himanshu chandola (Thu Nov 06 2003 - 19:11:58 CST)
      • Re: atoms moving too fast Brian Bennion (Thu Nov 06 2003 - 11:16:03 CST)
      • Re: atoms moving too fast himanshu chandola (Fri Nov 07 2003 - 20:21:27 CST)
      • Re: atoms moving too fast Jim Phillips (Fri Nov 07 2003 - 11:10:34 CST)
      • Re: atoms moving too fast Jim Phillips (Fri Nov 07 2003 - 10:11:43 CST)
    • Urey-Bradley term Cosmin ROMAN (Tue Nov 18 2003 - 08:34:18 CST)
      • Re: Urey-Bradley term Fangqiang Zhu (Tue Nov 18 2003 - 18:24:46 CST)
      • Re: Urey-Bradley term Cosmin ROMAN (Wed Nov 19 2003 - 04:05:27 CST)
      • Re: Urey-Bradley term Fangqiang Zhu (Wed Nov 19 2003 - 17:39:23 CST)
  • Re: excluding water in dcd files Jerry Ebalunode (Mon Nov 03 2003 - 06:42:28 CST)
• solvate himanshu chandola (Sun Nov 02 2003 - 17:41:24 CST)
  • Re: solvate Brian Bennion (Mon Nov 03 2003 - 11:27:56 CST)
• SMD: constant velocity or force pulling? Ioana Cozmuta (Thu Oct 30 2003 - 21:02:54 CST)
• running namd on solaris 5.6 himanshu chandola (Thu Oct 30 2003 - 22:50:16 CST)
  • Re: running namd on solaris 5.6 Jim Phillips (Thu Oct 30 2003 - 13:41:19 CST)
• charmm param. for ADP himanshu chandola (Mon Oct 27 2003 - 18:45:58 CST)
  • Re: charmm param. for ADP Brian Bennion (Mon Oct 27 2003 - 10:20:34 CST)
  • Re: charmm param. for ADP Cosmin ROMAN (Mon Oct 27 2003 - 11:14:08 CST)
    • Re: charmm param. for ADP himanshu chandola (Tue Oct 28 2003 - 01:27:28 CST)
      • Re: charmm param. for ADP Brian Bennion (Mon Oct 27 2003 - 15:14:57 CST)
• tert-butylthiol CHARMM params Cosmin ROMAN (Mon Oct 27 2003 - 05:46:47 CST)
• IMD forces and corresponding energies .. Marc Baaden (Wed Oct 22 2003 - 16:36:35 CDT)
  • Re: IMD forces and corresponding energies .. Jim Phillips (Wed Oct 22 2003 - 18:16:05 CDT)
• Scyld cluster Amit Paliwal (Wed Oct 22 2003 - 07:52:06 CDT)
  • Re: Scyld cluster Jim Phillips (Wed Oct 22 2003 - 16:09:42 CDT)
    • Re: Scyld cluster Amit Paliwal (Wed Oct 22 2003 - 12:26:55 CDT)
      • Re: Scyld cluster Jim Phillips (Wed Oct 22 2003 - 16:59:38 CDT)
• (no subject) Peter Jones (Sun Oct 19 2003 - 23:56:25 CDT)
  • RE: Cesar Delgado (Mon Oct 20 2003 - 01:13:08 CDT)
  • Re: Ioana Cozmuta (Mon Oct 20 2003 - 12:32:02 CDT)
    • switch for equilibrisation himanshu chandola (Wed Oct 22 2003 - 17:24:29 CDT)
      • Re: switch for equilibrisation Jim Phillips (Tue Oct 28 2003 - 18:11:33 CST)
• pair Interaction and electric field Ioana Cozmuta (Sun Oct 19 2003 - 14:09:22 CDT)
  • Re: pair Interaction and electric field Jim Phillips (Mon Oct 27 2003 - 13:22:52 CST)
• RE: cluseter node freezes while running namd 2.5/2.5b1 EPF (Esben Peter Friis) (Sun Oct 19 2003 - 14:00:00 CDT)
• cluseter node freezes while running namd 2.5/2.5b1 Richard Brown (Sat Oct 18 2003 - 22:48:30 CDT)
• Small Organic Compounds with NAMD AHMET BAKAN (Sat Oct 18 2003 - 18:40:37 CDT)
• Charm++ workshop webcast Oct 20-22 Jim Phillips (Fri Oct 17 2003 - 17:41:56 CDT)
  • namd/charmm steroid parameterization Brian Bennion (Fri Oct 24 2003 - 11:08:07 CDT)
• pair Interaction Calculation Ioana Cozmuta (Thu Oct 16 2003 - 17:36:18 CDT)
  • Re: pair Interaction Calculation Ioana Cozmuta (Thu Oct 16 2003 - 17:50:47 CDT)
• Error Running ubq-get-energy.conf Raymond C. Fort Jr. (Thu Oct 16 2003 - 12:13:35 CDT)
  • Re: Error Running ubq-get-energy.conf Jim Phillips (Wed Oct 22 2003 - 18:50:49 CDT)
• cylindrical boundary conditions Ioana Cozmuta (Wed Oct 15 2003 - 16:48:08 CDT)
  • Re: cylindrical boundary conditions Jim Phillips (Mon Oct 27 2003 - 13:40:51 CST)
• Autogene angles dihed / patch / psfgen problem Andersen, Kim Vilbour (KVA) (Wed Oct 15 2003 - 06:27:17 CDT)
  • Re: Autogene angles dihed / patch / psfgen problem Jim Phillips (Wed Oct 15 2003 - 13:53:38 CDT)
  • constraining movement of atoms himanshu chandola (Thu Oct 16 2003 - 02:49:01 CDT)
• Topology file for model compounds AHMET BAKAN (Tue Oct 14 2003 - 10:24:40 CDT)
• NAMD: force field for hybrid systems (fwd) Ioana Cozmuta (Sun Oct 12 2003 - 12:59:01 CDT)
• PMEGridSize Peter Jones (Fri Oct 10 2003 - 02:08:19 CDT)
  • Re: PMEGridSize Jim Phillips (Mon Oct 13 2003 - 13:34:44 CDT)
• 64 bit G5 plans for NAMD Ken Sale (Wed Oct 08 2003 - 14:01:39 CDT)
  • Re: 64 bit G5 plans for NAMD Jim Phillips (Wed Oct 08 2003 - 17:14:27 CDT)
• top files for ligands Oliver Hucke (Wed Oct 08 2003 - 13:02:42 CDT)
• Error Running NAMD Raymond C. Fort Jr. (Wed Oct 08 2003 - 08:18:00 CDT)
  • Re: Error Running NAMD Jim Phillips (Wed Oct 08 2003 - 11:04:41 CDT)
• Error when running NAMD_2.5 on mytinet Cesar Delgado (Sat Oct 04 2003 - 18:20:13 CDT)
• Help with: Constraint failure in RATTLE algorithm Cartailler, Jean-Philippe (Thu Oct 02 2003 - 11:17:58 CDT)
  • Re: Help with: Constraint failure in RATTLE algorithm Jim Phillips (Fri Oct 03 2003 - 13:09:35 CDT)
• nodelist ignored? Nathalie Reuter (Mon Sep 29 2003 - 12:26:51 CDT)
  • Re: nodelist ignored? Gengbin Zheng (Mon Sep 29 2003 - 14:23:42 CDT)
    • Re: nodelist ignored? Jim Phillips (Mon Sep 29 2003 - 14:27:45 CDT)
• NAMD 2.5 Released Jim Phillips (Mon Sep 29 2003 - 14:02:48 CDT)
• NAMD2.5b2 and amber force field james tomomi macdonald (Mon Sep 29 2003 - 12:02:09 CDT)
  • Re: NAMD2.5b2 and amber force field Jim Phillips (Mon Sep 29 2003 - 12:34:55 CDT)
• simulated annealing script Cheri M Turman (Thu Sep 25 2003 - 13:15:10 CDT)
  • Re: simulated annealing script Jim Phillips (Thu Sep 25 2003 - 18:47:22 CDT)
• Launching namd with PBS Scott Stagg (Wed Sep 24 2003 - 19:12:14 CDT)
  • Re: Launching namd with PBS Brian Bennion (Wed Sep 24 2003 - 19:15:49 CDT)
    • Re: Launching namd with PBS Jim Phillips (Wed Sep 24 2003 - 19:58:59 CDT)
  • Re: Launching namd with PBS Juan Alfredo Freites (Wed Sep 24 2003 - 20:03:09 CDT)
• coorfile command fail Liu, Zhanwu (Mon Sep 22 2003 - 20:53:13 CDT)
  • Re: coorfile command fail Jim Phillips (Tue Sep 23 2003 - 11:20:13 CDT)
• Re: seg fault and namdplot problem Cheri M Turman (Mon Sep 22 2003 - 16:22:46 CDT)
  • Re: Re: seg fault and namdplot problem Jim Phillips (Mon Sep 22 2003 - 18:20:20 CDT)
    • Re: Re: seg fault and namdplot problem Cheri M Turman (Mon Sep 22 2003 - 18:58:30 CDT)
      • Re: Re: seg fault and namdplot problem Jim Phillips (Tue Sep 23 2003 - 21:44:24 CDT)
• hard sphere simulation Amit Paliwal (Sat Sep 20 2003 - 11:01:18 CDT)
  • Re: hard sphere simulation Jim Phillips (Mon Sep 22 2003 - 14:38:11 CDT)
    • Re: hard sphere simulation AMIT PALIWAL (Mon Sep 22 2003 - 20:08:31 CDT)
      • Re: hard sphere simulation Jim Phillips (Tue Sep 23 2003 - 10:52:14 CDT)
• NAMD 2.5b3 Released Jim Phillips (Fri Sep 19 2003 - 18:02:58 CDT)
  • implicit solvent models james tomomi macdonald (Wed Sep 24 2003 - 12:53:28 CDT)
    • Re: implicit solvent models Jim Phillips (Wed Sep 24 2003 - 14:09:14 CDT)
• Minimization Question Saladino, Alex (Thu Sep 18 2003 - 15:25:08 CDT)
  • Re: Minimization Question Jim Phillips (Thu Sep 18 2003 - 16:30:49 CDT)
• Re: output warning in using namd2 "Warning: Not all atoms have unique coordinates." more errors Jerry Ebalunode (Wed Sep 17 2003 - 07:54:46 CDT)
  • Re: output warning in using namd2 "Warning: Not all atoms have unique coordinates." more errors Jim Phillips (Wed Sep 17 2003 - 13:07:47 CDT)
• help needed on node list srinivasa murthy (Tue Sep 16 2003 - 23:36:51 CDT)
• output warning in using namd2 "Warning: Not all atoms have unique coordinates." Jerry Ebalunode (Tue Sep 16 2003 - 13:44:49 CDT)
  • Re: output warning in using namd2 "Warning: Not all atoms have unique coordinates." Jim Phillips (Tue Sep 16 2003 - 21:19:03 CDT)
    • Re: output warning in using namd2 "Warning: Not all atoms have unique coordinates." Jerry Ebalunode (Wed Sep 17 2003 - 06:21:53 CDT)
• error in notes on compiling namd2.5b2 with plugins Jerry Ebalunode (Tue Sep 16 2003 - 13:06:20 CDT)
• Re: seg fault Brian Bennion (Tue Sep 16 2003 - 16:22:44 CDT)
• segmentation fault Cheri M Turman (Tue Sep 16 2003 - 14:12:43 CDT)
  • Re: segmentation fault Jim Phillips (Tue Sep 16 2003 - 15:27:10 CDT)
• Thank you Brian Bennion (Mon Sep 15 2003 - 23:43:52 CDT)
• NAMD 2.5b2 Released Jim Phillips (Mon Sep 15 2003 - 19:51:49 CDT)
• libc6 on debian x86 Grischa R. Meyer (Thu Sep 11 2003 - 22:42:17 CDT)
• build NAMD bioinfo Gu (Mon Sep 08 2003 - 09:54:12 CDT)