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NAMD-L: By Author

By Author

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

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

• $B:,>k(J $B6Q(J
  • Re: psf file for zeolite-water system (Mon Feb 23 2004 - 02:22:31 CST)
• \
  • Re: System minimization: fail after 199 steps (Tue Nov 02 2004 - 13:22:50 CST)
  • Re: Symmetry operations (Thu Sep 02 2004 - 21:44:39 CDT)
  • Re: Symmetry operations (Tue Aug 24 2004 - 13:58:19 CDT)
  • Symmetry operations (Mon Aug 23 2004 - 16:42:22 CDT)
• Aaron Oakley
  • statistical test (Wed Dec 15 2004 - 23:17:57 CST)
  • Re: D-amino acids (Tue Oct 26 2004 - 03:05:28 CDT)
  • Re: Symmetry operations (Tue Aug 24 2004 - 18:34:47 CDT)
  • Amber94 files in CHARMM format (Wed Jun 23 2004 - 08:08:13 CDT)
  • Re: Is it necessary to neutralize the system with NAMD program? (Tue Mar 16 2004 - 16:18:00 CST)
  • TIP5P (Thu Feb 26 2004 - 18:40:22 CST)
• Adam Kubach
  • NAMD interaction with VMD (Tue Oct 19 2004 - 13:54:18 CDT)
• Adrian Wiley
  • Surface tension (Wed Mar 17 2004 - 10:43:37 CST)
• Ahmet Bakan
  • Re: Solvent mixture (Fri Nov 05 2004 - 17:02:06 CST)
  • Euro QSAR 2004 (Sun Sep 05 2004 - 15:42:27 CDT)
  • RE: cff91 force field in namd + A Question (Wed Aug 25 2004 - 10:53:59 CDT)
  • Pt LJ Parameters (Wed Jul 21 2004 - 11:56:52 CDT)
  • Simulated Annealing Config (Tue Jun 15 2004 - 08:24:59 CDT)
  • Re: Re: Simulation with ammonia (Fri Jun 04 2004 - 17:23:39 CDT)
  • Re: Simulation with ammonia (Fri Jun 04 2004 - 15:01:04 CDT)
  • RE: how to generate your own pdb file (Fri May 14 2004 - 21:55:28 CDT)
  • RE: Calculating parameters. (Fri May 14 2004 - 16:59:15 CDT)
  • RE: Binding free energy of a protein complex (Mon May 03 2004 - 06:02:29 CDT)
  • RE: Lithium (Thu Apr 29 2004 - 11:14:56 CDT)
  • Binding energy analysis (Sat Apr 24 2004 - 21:09:45 CDT)
  • RE: minimization problem (Thu Mar 18 2004 - 18:43:00 CST)
  • RE: minimization problem (Thu Mar 18 2004 - 18:31:09 CST)
  • RE: Urea and GdHCl parameters (Mon Mar 15 2004 - 13:15:18 CST)
  • Binding Energy (Mon Mar 08 2004 - 12:57:18 CST)
  • Potential Terms (Mon Jan 05 2004 - 12:20:02 CST)
  • Density (Tue Dec 16 2003 - 12:45:26 CST)
  • Polymer Simulations (Mon Dec 15 2003 - 16:49:22 CST)
  • Some parameters (Tue Dec 09 2003 - 06:06:50 CST)
  • PSF generation (Sun Dec 07 2003 - 10:08:47 CST)
  • Small Organic Compounds with NAMD (Sat Oct 18 2003 - 18:40:37 CDT)
  • Topology file for model compounds (Tue Oct 14 2003 - 10:24:40 CDT)
• aida_at_mit.edu
  • Direction of SMD force (Tue Feb 17 2004 - 09:06:16 CST)
  • Running AIX version of NAMD on IBM cluster (Wed Feb 04 2004 - 14:54:21 CST)
• Alberto Santana
  • NAMD on Xeon EM64T (Wed Dec 01 2004 - 06:42:05 CST)
  • Re: NAMD on Linux cluster with Myrinet (Mon Oct 18 2004 - 11:59:31 CDT)
  • Re: NAMD on Linux cluster with Myrinet (Thu Oct 14 2004 - 13:59:27 CDT)
  • Re: NAMD on Linux cluster with Myrinet (Thu Oct 14 2004 - 11:26:08 CDT)
  • Re: NAMD on Linux cluster with Myrinet (Mon Oct 11 2004 - 14:19:31 CDT)
  • NAMD on Linux cluster with Myrinet (Sat Oct 09 2004 - 20:42:55 CDT)
  • Re: Not all atoms have unique coordinates - revisited (Sat Oct 02 2004 - 08:32:59 CDT)
  • Not all atoms have unique coordinates - revisited (Fri Oct 01 2004 - 18:52:27 CDT)
  • output files always go to same node (Mon Sep 20 2004 - 18:31:03 CDT)
  • Re: Node 0 could not initialize network! (Sun Jul 04 2004 - 13:25:32 CDT)
  • Node 0 could not initialize network! (Sat Jul 03 2004 - 18:16:01 CDT)
• Alemayehu Gorfe Abebe
  • Periodic cell too small (Tue Jan 13 2004 - 16:42:59 CST)
  • Periodic cel too small (Tue Jan 13 2004 - 08:33:39 CST)
• Alessandro Pedretti
  • Re: GROMACS to CHARMM (Tue Nov 30 2004 - 01:47:01 CST)
  • Re: Generating psf files for non-proteins (Fri Apr 09 2004 - 07:09:52 CDT)
  • Re: NAMD and Vega? (Wed Feb 04 2004 - 06:33:52 CST)
  • Re: how to get the plot of selected bond over time? (Fri Dec 05 2003 - 07:19:45 CST)
  • Re: how to add counterions ? (Tue Dec 02 2003 - 06:18:58 CST)
  • Re: Energy problem after restart (Mon Nov 24 2003 - 03:00:11 CST)
  • Energy problem after restart (Thu Nov 20 2003 - 07:13:56 CST)
• alessandro.pedretti_at_unimi.it
  • Re: Chloroform Solvent Box (Tue Nov 23 2004 - 14:19:11 CST)
• Alex V.
  • Re: Suse 9.0 or Fedora Core 1.0 (Fri Jul 02 2004 - 07:27:08 CDT)
  • Re: IO error when running NAMD on new cluster (Sat Jun 05 2004 - 23:07:22 CDT)
  • Re: submitting a job in a queue (Fri Jun 04 2004 - 13:46:18 CDT)
  • Re: Parallelization of a code from TCB Summer School 2003 (Mon Apr 19 2004 - 02:49:05 CDT)
  • Using checkpoints in simulation (Fri Apr 09 2004 - 05:08:35 CDT)
  • Processor load (Sun Mar 28 2004 - 09:11:01 CST)
  • Re: Running on Alpha cluster (Fri Mar 26 2004 - 03:31:22 CST)
  • Re: Load balance strategy (Thu Mar 18 2004 - 00:03:19 CST)
  • Load balance strategy (Tue Mar 16 2004 - 09:23:28 CST)
  • Running on Alpha cluster (Fri Mar 12 2004 - 22:27:26 CST)
  • Re: Segmentation fault. (Wed Mar 10 2004 - 09:04:33 CST)
  • Running on Alpha cluster (Wed Mar 10 2004 - 03:40:12 CST)
• Alexandre Chauvin
  • Re: 64 nodes behaviour (Fri Sep 03 2004 - 02:52:30 CDT)
  • 64 nodes behaviour (Thu Sep 02 2004 - 12:53:23 CDT)
  • charm++ with gm (Mon Aug 30 2004 - 09:41:49 CDT)
  • Re: Compilation on Opteron (Fri Aug 27 2004 - 03:05:43 CDT)
  • Compilation on Opteron (Wed Aug 25 2004 - 12:22:43 CDT)
• Alexandre Vakhrouchev
  • Re: Charm++ nodelist commands (Thu Dec 18 2003 - 11:36:11 CST)
  • Re: Charm++ nodelist commands (Thu Dec 18 2003 - 06:33:16 CST)
  • Re: Help! unstable simulation. (Fri Dec 12 2003 - 03:16:55 CST)
  • (no subject) (Sun Dec 07 2003 - 01:47:07 CST)
  • (no subject) (Wed Dec 03 2003 - 02:57:04 CST)
  • (no subject) (Thu Nov 06 2003 - 02:18:39 CST)
• allison
  • hanging at startup phase (Wed May 19 2004 - 14:00:25 CDT)
• Allison Heath
  • errors building charm on ia64 (Thu Jun 17 2004 - 11:18:29 CDT)
  • Re: hanging at startup phase (Fri May 21 2004 - 10:29:49 CDT)
• Amarda Shehu
  • Running namd on Rice Teracluster (Sun Apr 11 2004 - 19:15:41 CDT)
  • timeout on running namd (Tue Mar 30 2004 - 12:09:02 CST)
  • adding ions (Mon Mar 22 2004 - 13:30:09 CST)
  • Re: Re: too much rattle (Fri Feb 13 2004 - 12:24:12 CST)
  • Re: too much rattle (Thu Feb 12 2004 - 16:16:40 CST)
• Amit Paliwal
  • NAMD-MPI compilation on P4 cluster (Sat Sep 04 2004 - 18:37:55 CDT)
  • compiling NAMD on OSC P4 cluster (Fri Sep 03 2004 - 12:11:51 CDT)
  • Re: compiled namd on clustermatic fails ! (Tue Aug 03 2004 - 06:38:31 CDT)
  • Re: compiled namd on clustermatic fails ! (Thu Jul 29 2004 - 19:24:52 CDT)
  • compiled namd on clustermatic fails ! (Thu Jul 29 2004 - 13:33:10 CDT)
  • fixed particles (Fri Jul 16 2004 - 18:22:23 CDT)
  • harmonic restraint (Tue Jun 15 2004 - 12:23:10 CDT)
  • error (Mon May 24 2004 - 04:29:43 CDT)
  • flexible cell (Tue May 18 2004 - 17:08:41 CDT)
  • NAMD with Amber (Fri May 14 2004 - 12:42:10 CDT)
  • COM velocity (Thu Apr 15 2004 - 04:50:29 CDT)
  • Re: water box (Tue Mar 30 2004 - 08:45:01 CST)
  • water box (Tue Mar 30 2004 - 06:03:30 CST)
  • Re: charmm27 (Tue Jan 13 2004 - 12:31:50 CST)
  • Interaction energy for fixed atoms (Fri Jan 09 2004 - 17:35:13 CST)
  • Interaction energy between fixed atoms (Wed Jan 07 2004 - 08:03:12 CST)
  • [Fwd: total energy stuck between two levels] (Wed Jan 07 2004 - 05:10:03 CST)
  • total energy stuck between two levels (Tue Jan 06 2004 - 22:20:10 CST)
  • alchemical free energy perturbation (Mon Jan 05 2004 - 00:37:05 CST)
  • TIP3P model (Wed Dec 17 2003 - 13:10:45 CST)
  • Re: repulsive/hard sphere simulation (Wed Nov 05 2003 - 15:53:17 CST)
  • Re: repulsive/hard sphere simulation (Wed Nov 05 2003 - 15:50:53 CST)
  • repulsive/hard sphere simulation (Wed Nov 05 2003 - 15:07:21 CST)
  • Re: Scyld cluster (Wed Oct 22 2003 - 12:26:55 CDT)
  • Scyld cluster (Wed Oct 22 2003 - 07:52:06 CDT)
  • Re: hard sphere simulation (Mon Sep 22 2003 - 20:08:31 CDT)
  • hard sphere simulation (Sat Sep 20 2003 - 11:01:18 CDT)
• amodzelewska_at_dns.iimcb.gov.pl
  • autoionize script (Sun May 16 2004 - 13:21:58 CDT)
• Andersen, Kim Vilbour (KVA)
  • Autogene angles dihed / patch / psfgen problem (Wed Oct 15 2003 - 06:27:17 CDT)
• ANDY NG
  • Generating topology file (Thu Nov 11 2004 - 00:59:51 CST)
• Anna Modzelewska
  • hexagonal unit cell (Thu Jul 01 2004 - 03:49:56 CDT)
  • retinal parameters (Thu Feb 12 2004 - 05:28:40 CST)
• apw397_at_soton.ac.uk
  • Protonated aspartic acid (Wed Mar 24 2004 - 06:10:11 CST)
• Arieana Moore
  • Re: ,log and .out files with namd running on mac os x (panther) (Wed May 05 2004 - 17:30:28 CDT)
  • ,log and .out files with namd running on mac os x (panther) (Wed May 05 2004 - 14:37:19 CDT)
• Armen Nalian
  • essential dynamics analysis (Mon Nov 22 2004 - 15:58:10 CST)
  • PC-DL Deluxe, Dual Xeon (Wed Aug 04 2004 - 17:32:54 CDT)
  • Fatal Socket error: code 93523-Error in accept (Wed Aug 04 2004 - 15:05:17 CDT)
• Armen Poghosyan
  • Does anybody have gromacs topology example, which works OK using NAMD?? (Tue Jun 01 2004 - 14:24:00 CDT)
  • How to use GROMACS force field in NAMD? (Mon May 31 2004 - 02:34:06 CDT)
  • FATAL ERROR: Patch needed for tuple is missing. (Thu May 06 2004 - 07:21:57 CDT)
• barner_at_physik.hu-berlin.de
  • switching SMD in execution script? (Tue Sep 21 2004 - 09:43:17 CDT)
• Bartosz Dobrzelecki
  • TCL: getting forces (Fri Mar 05 2004 - 04:58:31 CST)
  • Parameters and topologies for aa at different protonation states (Fri Jan 23 2004 - 06:45:26 CST)
  • Simulating RNA+PROTEIN complexes (Fri Dec 19 2003 - 14:30:23 CST)
• beckloni_at_umdnj.edu
  • Parameter File Problem (Mon May 10 2004 - 19:47:24 CDT)
  • Re: PSF file generation (Mon May 10 2004 - 10:48:22 CDT)
  • PSF file generation (Sun May 09 2004 - 10:00:59 CDT)
  • Finished install (Tue Apr 20 2004 - 00:53:09 CDT)
  • Installing NAMD (Wed Apr 07 2004 - 15:56:21 CDT)
• Ben Brooks
  • Charm++ Problem (Thu Feb 26 2004 - 11:32:28 CST)
• Ben Roberts
  • Tcl dihedral restraints in CG minimisation (Tue Nov 02 2004 - 17:01:28 CST)
  • Converting Gromacs parameters to Charmm format (Mon Sep 27 2004 - 01:35:23 CDT)
  • Unit cell coordinates and radial distribution functions (Mon Jul 19 2004 - 21:12:38 CDT)
  • Order of improper dihedrals (Tue Jul 06 2004 - 00:21:01 CDT)
  • Effect of FullDirect electrostatics (Mon May 31 2004 - 18:22:45 CDT)
  • Single point energy calculation (Sun May 30 2004 - 21:05:00 CDT)
  • Electrostatics energy calculation (Wed May 26 2004 - 20:09:43 CDT)
• bioinfo Gu
  • build NAMD (Mon Sep 08 2003 - 09:54:12 CDT)
• Blake Charlebois
  • RE: Failed to set coordinate for atom errors! (Mon Dec 20 2004 - 19:27:51 CST)
  • RE: What the result difference between AMD and Intel CPUS? (Mon Dec 20 2004 - 09:43:57 CST)
  • RE: namdplot (Thu Dec 09 2004 - 07:15:41 CST)
  • RE: Periodic cell size (Wed Dec 08 2004 - 23:54:04 CST)
  • RE: Variation of results in iterations (Tue Dec 07 2004 - 20:12:18 CST)
  • RE: Implicit water dielectric constant. (Tue Nov 16 2004 - 15:06:50 CST)
  • RE: HEM residue in NAMD (Tue Nov 02 2004 - 04:03:00 CST)
  • RE: How do you specify which coordinates are to be fixed? (Thu Oct 28 2004 - 17:36:56 CDT)
  • RE: temperature rescaling and canonical ensemble (Fri Oct 01 2004 - 01:15:05 CDT)
  • RE: SMD on a group of atoms: Confusion (Fri Sep 03 2004 - 05:41:24 CDT)
  • RE: calculate the binding energy or binding free energy? (Thu Sep 02 2004 - 15:31:42 CDT)
  • RE: Calculation of velocities (Thu Sep 02 2004 - 08:21:34 CDT)
  • numerical inaccuracy upon restart (Wed Aug 25 2004 - 09:24:08 CDT)
• bora erdemli
  • Bug alert!!! (Fri Dec 24 2004 - 01:06:32 CST)
  • Re: FATAL ERROR: Asymmetric water molecule ? (Wed Dec 22 2004 - 02:26:19 CST)
  • binding free energy (Mon Dec 20 2004 - 08:39:06 CST)
  • binding energy (Tue Dec 14 2004 - 07:38:05 CST)
  • rmsd and simulation (Fri Nov 05 2004 - 03:24:59 CST)
  • BOND CP2 - CT2 IN PARAMETER FILES (Thu Oct 28 2004 - 16:42:09 CDT)
  • Re: [Fwd: counterion software] (Mon Oct 11 2004 - 02:03:05 CDT)
  • binding constant (Mon Sep 20 2004 - 13:33:45 CDT)
  • torsion angle (Mon Sep 06 2004 - 06:18:22 CDT)
  • rmsd problem,script and version (Fri Sep 03 2004 - 00:23:42 CDT)
  • rmsd problem (Thu Aug 26 2004 - 14:10:05 CDT)
  • radial distribution function (Fri Aug 13 2004 - 08:16:51 CDT)
  • Constraint failure in RATTLE algorithm (Wed Jul 28 2004 - 15:05:47 CDT)
  • type of the water molecule (Fri Jul 23 2004 - 10:31:49 CDT)
• Brian Bennion
  • Re: charmm and dihedral multiplicity (Fri Dec 17 2004 - 10:55:34 CST)
  • Re: NamdCompile Problem (Thu Dec 16 2004 - 14:39:33 CST)
  • Re: Infiniband and PME gridsize (Tue Dec 14 2004 - 12:06:36 CST)
  • Re: fatal error (Tue Dec 14 2004 - 12:01:25 CST)
  • Re: high (or low) pressure readings (Tue Dec 14 2004 - 11:45:13 CST)
  • Re: high (or low) pressure readings (Mon Dec 13 2004 - 11:13:42 CST)
  • Re: System minimization: fail after 199 steps (Thu Dec 09 2004 - 12:19:20 CST)
  • Re: Periodic cell size (Wed Dec 08 2004 - 11:43:02 CST)
  • Re: PME ERROR (Wed Dec 01 2004 - 12:02:55 CST)
  • Re: psfgen (Mon Nov 29 2004 - 17:01:33 CST)
  • Re: System minimization: fail after 199 steps (Tue Nov 23 2004 - 12:46:15 CST)
  • Re: Rif: Re: Rif: Re: Rif: Re: linux cluster trouble (Thu Nov 18 2004 - 10:56:17 CST)
  • Re: linux cluster trouble (Tue Nov 16 2004 - 10:40:57 CST)
  • Re: fatal error running namd (Mon Nov 15 2004 - 10:52:34 CST)
  • Re: System minimization: fail after 199 steps (Thu Nov 11 2004 - 10:18:49 CST)
  • Re: linux cluster trouble (Wed Nov 10 2004 - 11:26:36 CST)
  • Re: System minimization: fail after 199 steps (Tue Nov 09 2004 - 15:40:39 CST)
  • Re: Solvent mixture (Fri Nov 05 2004 - 16:53:11 CST)
  • Re: Solvent mixture (Fri Nov 05 2004 - 15:40:47 CST)
  • Re: System minimization: fail after 199 steps (Wed Nov 03 2004 - 13:05:56 CST)
  • Re: Compiling NAMD on IA64 cluter (Wed Nov 03 2004 - 10:39:23 CST)
  • Re: How to decide the protonation of some residues?? (Wed Nov 03 2004 - 10:35:07 CST)
  • Re: Edge Water in PBC (Wed Nov 03 2004 - 10:32:58 CST)
  • Re: System minimization: fail after 199 steps (Tue Nov 02 2004 - 13:09:32 CST)
  • Re: Fwd: PSFgen error (Tue Nov 02 2004 - 10:14:50 CST)
  • Re: System minimization: fail after 199 steps (Mon Nov 01 2004 - 17:56:32 CST)
  • Re: firsttimestep: simple question (Fri Oct 29 2004 - 17:34:53 CDT)
  • Re: BOND CP2 - CT2 IN PARAMETER FILES (Fri Oct 29 2004 - 11:32:18 CDT)
  • Re: How do you specify which coordinates are to be fixed? (Thu Oct 28 2004 - 18:08:26 CDT)
  • Re: Bug in Pair force interaction calculation was fixed? (Wed Oct 27 2004 - 10:19:49 CDT)
  • Re: Compiling NAMD on IA64 cluter (Wed Oct 27 2004 - 10:19:16 CDT)
  • Re: communication with NAMD? (Tue Oct 26 2004 - 18:10:07 CDT)
  • Re: Hydrogen cut off distance (Tue Oct 26 2004 - 12:38:20 CDT)
  • Re: Bug in Pair force interaction calculation was fixed? (Tue Oct 26 2004 - 12:20:36 CDT)
  • Re: output to multiple files (Fri Oct 22 2004 - 14:37:37 CDT)
  • Re: bug report and stray pme (Tue Oct 19 2004 - 15:31:43 CDT)
  • Re: NAMD on Linux cluster with Myrinet (Thu Oct 14 2004 - 13:20:59 CDT)
  • Re: Gradient Tolerance (Wed Oct 13 2004 - 14:43:04 CDT)
  • Re: NAMD on Linux cluster with Myrinet (Mon Oct 11 2004 - 15:53:14 CDT)
  • RE: vmd-l: PSFGEN problem (Mon Oct 11 2004 - 11:19:56 CDT)
  • Re: NAMD on Linux cluster with Myrinet (Sat Oct 09 2004 - 21:59:57 CDT)
  • Re: How can I move an atom by 10nm with a step of 0.1nm (Tue Oct 05 2004 - 10:44:01 CDT)
  • Re: Not all atoms have unique coordinates - revisited (Mon Oct 04 2004 - 10:22:04 CDT)
  • Re: Not all atoms have unique coordinates - revisited (Sat Oct 02 2004 - 00:37:12 CDT)
  • Re: Can we fix the position of two atoms while minimization? (Wed Sep 29 2004 - 18:00:43 CDT)
  • Re: Symmetry operations (Mon Aug 23 2004 - 17:55:24 CDT)
  • Re: > 10000 ato (Fri Aug 13 2004 - 15:14:05 CDT)
  • Re: render format (Mon Aug 02 2004 - 14:44:08 CDT)
  • Re: type of the water molecule (Fri Jul 23 2004 - 11:55:57 CDT)
  • Re: Myrinet and MPI question (Thu Jul 22 2004 - 11:21:34 CDT)
  • Re: phase equilibria using NAMD (Thu Jul 22 2004 - 10:53:00 CDT)
  • Re: psfgen (Wed Jul 21 2004 - 18:23:41 CDT)
  • Re: mimization warnings - bad global exclusion count (Wed Jul 21 2004 - 17:29:51 CDT)
  • Re: Segmentation violation (Tue Jul 20 2004 - 12:30:06 CDT)
  • Re: compiler flags. (Wed Jul 14 2004 - 23:41:22 CDT)
  • INTEL 8.0 optimization flags (Tue Jul 13 2004 - 14:22:05 CDT)
  • Re: compiling NAMD (Fri Jul 09 2004 - 12:27:28 CDT)
  • compiling NAMD (Fri Jul 09 2004 - 11:56:03 CDT)
  • Re: Warning: Not all atoms have unique coordinates. (Thu Jul 08 2004 - 11:06:08 CDT)
  • Re: cellBasisVector x,y,z values (Thu Jul 08 2004 - 10:35:11 CDT)
  • Re: namd and Tcl 8.3.5 (Wed Jul 07 2004 - 11:33:23 CDT)
  • Re: How to calculate specific heat capacity in NAMD? (Wed Jul 07 2004 - 11:28:40 CDT)
  • RE: COM position (Tue Jul 06 2004 - 12:50:52 CDT)
  • RE: COM position (Tue Jul 06 2004 - 12:11:28 CDT)
  • Re: icc compilation problem (Fri Jul 02 2004 - 11:05:29 CDT)
  • Re: DIHEDral drift [2] ? (Wed Jun 30 2004 - 17:16:39 CDT)
  • Re: DIHEDral drift [2] ? (Wed Jun 30 2004 - 12:30:15 CDT)
  • RE: psfgen problem (Wed Jun 09 2004 - 15:59:33 CDT)
  • Re: question about running equilibration in NAMD (Tue Jun 08 2004 - 15:50:28 CDT)
  • Re: psfgen problem (Tue Jun 08 2004 - 12:01:58 CDT)
  • Re: question about using Amber force field in namd (Wed Jun 02 2004 - 16:31:48 CDT)
  • Re: question about using Amber force field in namd (Wed Jun 02 2004 - 16:21:21 CDT)
  • Re: question about using Amber force field in namd (Wed Jun 02 2004 - 16:07:28 CDT)
  • Re: "GRADIENT TOLERANCE: nan", Why? (Wed Jun 02 2004 - 16:04:15 CDT)
  • Re: NAMD on HP with Itanium2 Processors (Sun May 30 2004 - 01:27:19 CDT)
  • Re: NAMD on HP with Itanium2 Processors (Sat May 29 2004 - 17:48:32 CDT)
  • Re: three-site carbon monoxide model (Thu May 27 2004 - 17:12:22 CDT)
  • Re: Periodic cell too small (Tue May 25 2004 - 17:39:45 CDT)
  • Re: Where to download the inorganic pdb file (Wed May 19 2004 - 10:20:11 CDT)
  • Re: Systems of > 100,000 atoms, *.psf files & *.crd files (Wed May 12 2004 - 10:19:29 CDT)
  • Re: NAMD "freezes" up (further clarification) (Tue May 11 2004 - 10:10:46 CDT)
  • Re: Parameter File Problem (Mon May 10 2004 - 23:59:53 CDT)
  • Re: implementing angle dependent non-bonded interaction? (Mon May 10 2004 - 14:51:26 CDT)
  • Re: Issues with SMD (Mon May 10 2004 - 11:04:13 CDT)
  • Re: "Constrain failure" in NAMD (Mon May 10 2004 - 10:47:29 CDT)
  • Re: PSF file generation (Mon May 10 2004 - 10:39:42 CDT)
  • Re: ,log and .out files with namd running on mac os x (panther) (Fri May 07 2004 - 10:51:14 CDT)
  • Re: installing on beowulf cluster (Thu May 06 2004 - 14:41:08 CDT)
  • Re: question on self-diffusion constant of TIP3P water (Wed May 05 2004 - 18:18:19 CDT)
  • Re: question on self-diffusion constant of TIP3P water (Wed May 05 2004 - 17:37:46 CDT)
  • Re: Help! There is no angle or dihedral definitions for patches in .psf! (Thu Apr 29 2004 - 13:23:55 CDT)
  • Re: Lithium (Wed Apr 28 2004 - 22:59:38 CDT)
  • Re: What, if no temperatue control specified? (Fri Apr 23 2004 - 10:57:09 CDT)
  • Re: Fw: Calculating Free Energy Change (Fri Apr 23 2004 - 11:08:12 CDT)
  • Re: What, if no temperatue control specified? (Thu Apr 22 2004 - 12:02:41 CDT)
  • Re: What, if no temperatue control specified? (Thu Apr 22 2004 - 10:20:05 CDT)
  • Re: temperature question in logfile (Tue Apr 20 2004 - 18:21:12 CDT)
  • Re: Weird dihedral error (Mon Apr 19 2004 - 12:22:35 CDT)
  • Re: simulations ceased without any hint (Fri Apr 16 2004 - 00:09:26 CDT)
  • Re: peptid bond omega, problems with settings? (Thu Apr 15 2004 - 11:25:56 CDT)
  • Re: Illegal instruction signal at startup. (with net-rs6k smp) (Fri Apr 09 2004 - 15:14:55 CDT)
  • Re: using restart files (Thu Apr 08 2004 - 10:00:01 CDT)
  • Re: Installing NAMD (Wed Apr 07 2004 - 16:56:14 CDT)
  • Re: how to disable NTER and CTER patches? (Wed Apr 07 2004 - 15:56:44 CDT)
  • Re: Restarting problem with Langevin dynamics (Wed Apr 07 2004 - 13:50:00 CDT)
  • Re: Restarting problem with Langevin dynamics (Wed Apr 07 2004 - 09:59:45 CDT)
  • Re: capping by psfgen (Mon Apr 05 2004 - 11:59:38 CDT)
  • Re: counterions (Tue Mar 30 2004 - 12:41:03 CST)
  • Re: water box (Tue Mar 30 2004 - 12:36:30 CST)
  • Re: adding ions (Mon Mar 22 2004 - 14:11:46 CST)
  • Re: minimization problem (Thu Mar 18 2004 - 18:00:23 CST)
  • Re: GdHCl parameters (Thu Mar 18 2004 - 17:19:38 CST)
  • Re: dimer minimisation and psfgen problem (Thu Mar 18 2004 - 17:24:45 CST)
  • Re: undefined loops (Thu Mar 18 2004 - 12:16:58 CST)
  • Re: dimer minimisation and psfgen problem (Wed Mar 17 2004 - 10:18:12 CST)
  • Re: Is it necessary to neutralize the system with NAMD program? (Tue Mar 16 2004 - 16:58:52 CST)
  • Re: Is it necessary to neutralize the system with NAMD program? (Tue Mar 16 2004 - 13:07:07 CST)
  • Re: Load balance strategy (Tue Mar 16 2004 - 11:31:15 CST)
  • Re: psf question (Tue Mar 16 2004 - 11:02:21 CST)
  • Paper on Classical treatment for calculating pKas (Fri Mar 12 2004 - 13:40:33 CST)
  • Re: SMD with different pH (Wed Mar 10 2004 - 10:47:37 CST)
  • Re: Binding Energy (Tue Mar 09 2004 - 10:42:19 CST)
  • Re: Binding Energy (Mon Mar 08 2004 - 13:23:38 CST)
  • Re: Generate PSF structure (Mon Mar 08 2004 - 12:17:52 CST)
  • Re: SMD with different pH (Fri Mar 05 2004 - 10:16:09 CST)
  • Re: TIP5P (Fri Feb 27 2004 - 13:39:04 CST)
  • Re: Timestep in restart output (Thu Feb 26 2004 - 15:29:38 CST)
  • Re: <no subject> (Thu Feb 26 2004 - 14:44:07 CST)
  • Re: Charm++ Problem (Thu Feb 26 2004 - 12:09:18 CST)
  • palindromic error reading in a restart file. (Thu Feb 26 2004 - 12:04:49 CST)
  • Re: your mail (Sun Feb 22 2004 - 00:44:16 CST)
  • crash in FFT optimizing... (Thu Feb 19 2004 - 15:44:28 CST)
  • Re: Running AIX version of NAMD on IBM cluster (Thu Feb 19 2004 - 14:06:20 CST)
  • Re: Re: too much rattle (Fri Feb 13 2004 - 12:51:50 CST)
  • Re: Re: too much rattle (Thu Feb 12 2004 - 16:50:30 CST)
  • Re: retinal parameters (Thu Feb 12 2004 - 10:11:48 CST)
  • Re: improving parallel on mac cluster (Mon Feb 09 2004 - 12:05:09 CST)
  • Re: Pair interaction energy (Fri Jan 30 2004 - 12:38:35 CST)
  • Re: Pair interaction energy (Fri Jan 30 2004 - 12:08:38 CST)
  • RE: minimization problem - "Bad global exclusion count,possible error!" (Fri Jan 30 2004 - 10:43:36 CST)
  • Re: psfgen question (Fri Jan 30 2004 - 10:13:35 CST)
  • RE: minimization problem - "Bad global exclusion count, possible error!" (Fri Jan 30 2004 - 10:09:19 CST)
  • Re: minimization problem - "Bad global exclusion count, possible error!" (Thu Jan 29 2004 - 17:46:34 CST)
  • Re: dcd format (Thu Jan 29 2004 - 17:11:37 CST)
  • Re: minimization problem - "Bad global exclusion count, possible error!" (Thu Jan 29 2004 - 17:19:39 CST)
  • Re: previous question about multiplicity (Wed Jan 28 2004 - 15:32:35 CST)
  • Re: previous question about multiplicity (Wed Jan 28 2004 - 14:18:20 CST)
  • previous question about multiplicity (Tue Jan 27 2004 - 19:06:02 CST)
  • Weird dihedral error (Tue Jan 27 2004 - 13:16:51 CST)
  • Re: Hydroxyprolin force field. (Fri Jan 23 2004 - 11:15:30 CST)
  • Re: Parameters and topologies for aa at different protonation states (Fri Jan 23 2004 - 11:14:18 CST)
  • Re: charmm27 (Tue Jan 13 2004 - 17:24:49 CST)
  • Re: limit on the number of residues in each segment (Fri Jan 09 2004 - 16:53:20 CST)
  • Re: Energy units (Tue Dec 30 2003 - 13:53:17 CST)
  • big systems using namd on 700 cpus (Mon Dec 29 2003 - 13:47:04 CST)
  • Re: weird energies during minimization (Fri Dec 19 2003 - 16:25:19 CST)
  • weird energies during minimization (Fri Dec 19 2003 - 13:04:56 CST)
  • Re: hydrogengroupsize of 0! (Thu Dec 18 2003 - 13:03:01 CST)
  • Re: LDB questions/problems (Thu Dec 18 2003 - 10:23:25 CST)
  • Re: LDB questions/problems (Tue Dec 16 2003 - 15:32:51 CST)
  • Re: LDB questions/problems (Mon Dec 15 2003 - 15:41:32 CST)
  • LDB questions/problems (Mon Dec 15 2003 - 12:58:15 CST)
  • Re: binary troubles (Fri Dec 05 2003 - 13:40:35 CST)
  • Re: psfgen: pdb and nucleic acid (Wed Dec 03 2003 - 14:30:29 CST)
  • Re: Basic question. (Tue Dec 02 2003 - 13:30:30 CST)
  • RE: IMD on MPI versions of NAMD (Mon Dec 01 2003 - 16:58:16 CST)
  • IMD on MPI versions of NAMD (Mon Dec 01 2003 - 12:19:28 CST)
  • Re: the problem on segment a ligand in NAMD ? (Fri Nov 28 2003 - 00:30:13 CST)
  • Re: Minimisation error (Thu Nov 27 2003 - 21:49:25 CST)
  • hydrogengroupsize of 0! (Wed Nov 26 2003 - 17:57:28 CST)
  • Re: about internal coordinate IC statement of CHARMM force field (Tue Nov 25 2003 - 13:09:41 CST)
  • Re: ATP fix (fwd) (Wed Nov 19 2003 - 11:06:19 CST)
  • Re: ADP again (Wed Nov 19 2003 - 11:00:40 CST)
  • Re: ADP again (Tue Nov 18 2003 - 10:24:33 CST)
  • Re: ADP again (Mon Nov 17 2003 - 12:58:56 CST)
  • Re: ADP again (Mon Nov 17 2003 - 11:18:09 CST)
  • Re: ADP again (Sun Nov 16 2003 - 00:26:00 CST)
  • Re: MOE program and difference between MD and SA? (Fri Nov 14 2003 - 10:35:15 CST)
  • Re: high temperature, 498K, unfolding simulations (Thu Nov 13 2003 - 12:23:13 CST)
  • Re: error in starting the minimization (Wed Nov 12 2003 - 18:11:42 CST)
  • Re: dcd files (Tue Nov 11 2003 - 10:27:42 CST)
  • Re: uninitialized coordinates (Mon Nov 10 2003 - 10:40:31 CST)
  • Re: Parameter/topology repository (Fri Nov 07 2003 - 10:12:22 CST)
  • Re: how to set harmonic constraints to alpha carbon (Thu Nov 06 2003 - 16:34:53 CST)
  • Re: contraint failure in RATTLE algorithm (Thu Nov 06 2003 - 14:10:49 CST)
  • Re: atoms moving too fast (Thu Nov 06 2003 - 11:16:03 CST)
  • Re: vmd-l: bigdcd (Wed Nov 05 2003 - 17:52:38 CST)
  • Re: atoms moving too fast (Wed Nov 05 2003 - 17:36:51 CST)
  • Re: atoms moving too fast (Wed Nov 05 2003 - 16:50:53 CST)
  • Re: repulsive/hard sphere simulation (Wed Nov 05 2003 - 15:22:16 CST)
  • Re: about charmm topology file (Wed Nov 05 2003 - 10:27:51 CST)
  • Re: excluding water in dcd files (Tue Nov 04 2003 - 10:35:55 CST)
  • RE: Question about AUTOGENERATE (Tue Nov 04 2003 - 10:24:58 CST)
  • Re: solvate (Mon Nov 03 2003 - 11:27:56 CST)
  • Re: excluding water in dcd files (Mon Nov 03 2003 - 11:23:38 CST)
  • Re: charmm param. for ADP (Mon Oct 27 2003 - 15:14:57 CST)
  • Re: charmm param. for ADP (Mon Oct 27 2003 - 10:20:34 CST)
  • namd/charmm steroid parameterization (Fri Oct 24 2003 - 11:08:07 CDT)
  • Re: Launching namd with PBS (Wed Sep 24 2003 - 19:15:49 CDT)
  • Re: seg fault (Tue Sep 16 2003 - 16:22:44 CDT)
  • Thank you (Mon Sep 15 2003 - 23:43:52 CDT)
• by way of Jérôme Hénin
  • Re: alchemical free energy perturbation (Mon Jan 05 2004 - 09:10:52 CST)
• C. Ecker
  • Simulating DNA in vacuum (Fri Nov 14 2003 - 08:47:54 CST)
  • tcl interface (Thu Nov 13 2003 - 05:07:04 CST)
• Cable, Sam B ERDC-ITL-MS Contractor
  • FW: (Thu Apr 15 2004 - 15:44:57 CDT)
  • (no subject) (Thu Apr 15 2004 - 11:17:53 CDT)
• carlos n. a.
  • RE: high (or low) pressure readings (Mon Dec 13 2004 - 13:36:10 CST)
• Cartailler, Jean-Philippe
  • Help with: Constraint failure in RATTLE algorithm (Thu Oct 02 2003 - 11:17:58 CDT)
• Cesar Delgado
  • RE: (Wed Dec 03 2003 - 08:46:12 CST)
  • RE: IMD on MPI versions of NAMD (Mon Dec 01 2003 - 16:44:05 CST)
  • RE: VMD problems (Mon Dec 01 2003 - 13:05:39 CST)
  • RE: (Mon Oct 20 2003 - 01:13:08 CDT)
  • Error when running NAMD_2.5 on mytinet (Sat Oct 04 2003 - 18:20:13 CDT)
• Cetin Baloglu
  • Edge Water in PBC (Wed Nov 03 2004 - 05:01:40 CST)
  • [Fwd: counterion software] (Sun Oct 10 2004 - 23:55:20 CDT)
  • counterion software (Sun Oct 10 2004 - 23:51:56 CDT)
  • namd linux source or binary (Wed Jul 07 2004 - 03:10:56 CDT)
• chandran karunakaran
  • GROMACS to CHARMM (Mon Nov 29 2004 - 11:14:48 CST)
• Charles Danko
  • Re: How to use restrin command in NAMD configuration file (Mon Dec 20 2004 - 10:40:30 CST)
  • Re: high (or low) pressure readings (Tue Dec 14 2004 - 13:31:21 CST)
  • high (or low) pressure readings (Mon Dec 13 2004 - 09:42:52 CST)
  • Re: System minimization: fail after 199 steps (Fri Dec 10 2004 - 13:32:28 CST)
  • Re: System minimization: fail after 199 steps (Thu Dec 09 2004 - 16:01:26 CST)
  • Re: System minimization: fail after 199 steps (Thu Dec 09 2004 - 11:20:26 CST)
  • Re: rmsd calculation (Tue Nov 23 2004 - 09:50:49 CST)
  • Re: System minimization: fail after 199 steps (Mon Nov 15 2004 - 11:10:40 CST)
  • Re: System minimization: fail after 199 steps (Thu Nov 11 2004 - 10:07:00 CST)
  • Re: System minimization: fail after 199 steps (Tue Nov 09 2004 - 12:24:00 CST)
  • Re: How to make a negatively charged surface (Mon Nov 08 2004 - 15:26:53 CST)
  • Re: Sample Configuratiion files (Wed Nov 03 2004 - 15:50:49 CST)
  • Re: System minimization: fail after 199 steps (Wed Nov 03 2004 - 11:53:06 CST)
  • Re: [Periodic Boundary]: from charmm to namd (Tue Nov 02 2004 - 11:35:23 CST)
  • Re: System minimization: fail after 199 steps (Tue Nov 02 2004 - 11:20:21 CST)
  • System minimization: fail after 199 steps (Mon Nov 01 2004 - 16:30:12 CST)
  • How do you specify which coordinates are to be fixed? (Thu Oct 28 2004 - 16:44:21 CDT)
  • Anyone having problems under Solaris 7? (Mon Oct 11 2004 - 11:05:33 CDT)
• Charles McCallum
  • Re: gcc and G5 Xserves (Mon Nov 15 2004 - 23:07:17 CST)
  • Re: rmsd and simulation (Fri Nov 05 2004 - 11:23:58 CST)
  • Re: vmd-l: psfgen and xplor topology (Tue Oct 26 2004 - 11:36:37 CDT)
• Chen Yongzhi
  • A question about RMSD calculation (Thu Mar 04 2004 - 22:54:08 CST)
  • A question about RMSD calculation (Thu Mar 04 2004 - 21:07:52 CST)
• Cheri M Turman
  • Re: Sample Configuratiion files (Wed Nov 03 2004 - 19:47:25 CST)
  • bug report and stray pme (Mon Oct 18 2004 - 16:23:42 CDT)
  • installing on beowulf cluster (Sun May 09 2004 - 19:58:25 CDT)
  • installing on beowulf cluster (Thu May 06 2004 - 13:38:16 CDT)
  • problems with namdplot fixed by using new plotting program (Tue Apr 27 2004 - 16:34:42 CDT)
  • temperature question in logfile (Tue Apr 20 2004 - 17:13:28 CDT)
  • still problems with namdplot (Thu Apr 15 2004 - 14:13:57 CDT)
  • simulated annealing script (Thu Sep 25 2003 - 13:15:10 CDT)
  • Re: Re: seg fault and namdplot problem (Mon Sep 22 2003 - 18:58:30 CDT)
  • Re: seg fault and namdplot problem (Mon Sep 22 2003 - 16:22:46 CDT)
  • segmentation fault (Tue Sep 16 2003 - 14:12:43 CDT)
• Chris Samuel
  • Re: NAMD on Xeon EM64T (Thu Dec 02 2004 - 22:18:39 CST)
  • Re: Compilation on an Opteron Server SuSE Linux Enterprise System Version 8 (Wed Oct 20 2004 - 18:05:49 CDT)
  • Re: NAMD on Linux cluster with Myrinet (Mon Oct 18 2004 - 23:02:27 CDT)
  • Re: Compilation on Opteron (Thu Aug 26 2004 - 00:04:07 CDT)
  • Re: Clustermatic with SCSI (Wed Aug 18 2004 - 20:17:05 CDT)
  • Re: icc compilation problem (Sun Jul 04 2004 - 20:41:14 CDT)
  • Re: icc compilation problem (Thu Jul 01 2004 - 18:11:57 CDT)
  • Re: build charm on ia-64 linux (Tue Jun 15 2004 - 18:23:17 CDT)
  • Re: Running namd on Rice Teracluster (Tue Apr 13 2004 - 20:47:46 CDT)
  • Re: Running namd on Rice Teracluster (Tue Apr 13 2004 - 20:43:18 CDT)
  • Re: More NAMD/gm2 problems (Thu Apr 08 2004 - 00:55:40 CDT)
  • Re: More NAMD/gm2 problems (Wed Mar 31 2004 - 00:40:36 CST)
• Cosmin ROMAN
  • Re: Urey-Bradley term (Wed Nov 19 2003 - 04:05:27 CST)
  • Urey-Bradley term (Tue Nov 18 2003 - 08:34:18 CST)
  • Re: charmm param. for ADP (Mon Oct 27 2003 - 11:14:08 CST)
  • tert-butylthiol CHARMM params (Mon Oct 27 2003 - 05:46:47 CST)
• Crozier, Paul S
  • Systems of > 100,000 atoms, *.psf files & *.crd files (Tue May 11 2004 - 18:02:51 CDT)
• Damon Smith
  • Re: mpi opteron myrinet (Thu Dec 30 2004 - 23:51:01 CST)
  • mpi opteron myrinet (Thu Dec 30 2004 - 22:23:09 CST)
• David Chalmers
  • More NAMD/gm2 problems (Tue Mar 30 2004 - 23:58:20 CST)
  • Re: counterions (Tue Mar 30 2004 - 23:12:17 CST)
  • Problems compiling Charm++ for Myrinet (Mon Mar 29 2004 - 18:53:46 CST)
  • NAMD support for Myranet GM2 drivers (Thu Mar 18 2004 - 22:29:52 CST)
  • General and specific atom types in NAMD? (Thu Mar 04 2004 - 18:21:42 CST)
  • Converting Gromacs OPLS parameters to Charmm format (Mon Mar 01 2004 - 17:41:57 CST)
  • NAMD and Gromac OPLS parameters (Thu Feb 26 2004 - 21:46:12 CST)
  • NAMD for Opteron? (Sun Jan 04 2004 - 17:55:15 CST)
  • Free energy constraints and logfile (Mon Dec 01 2003 - 22:54:01 CST)
• David E. Konerding
  • Re: improving parallel on mac cluster (Tue Feb 10 2004 - 18:21:32 CST)
  • reading in large water boxes (PDB format)? (Sun Dec 07 2003 - 12:26:32 CST)
  • psfgen: pdb and nucleic acid (Wed Dec 03 2003 - 13:52:52 CST)
  • updating coordinates using IMD (Wed Nov 26 2003 - 14:09:10 CST)
• David L. Azevedo
  • PSFGEN problems in nanotube tutorial (Fri Oct 01 2004 - 01:36:36 CDT)
• David P. Brandon
  • TCBG "Hands-On" Workshop on Computational Biophysics in Boston, Dec. 5-9 (Tue Nov 02 2004 - 10:16:21 CST)
• David Skinner
  • IBM SP build (Sun Nov 09 2003 - 00:21:31 CST)
• Davit Hakobyan
  • How to create a substrate parameter file ? (Thu May 06 2004 - 15:09:00 CDT)
• debashis.sikdar_at_ndsu.edu
  • How to use restrin command in NAMD configuration file (Mon Dec 20 2004 - 09:35:28 CST)
  • how to use restrain command in configuration file in NAMD. (Fri Dec 17 2004 - 23:10:34 CST)
• Edward Patrick Obrien
  • Re: Periodic cell size (Wed Dec 08 2004 - 10:54:37 CST)
  • Re: Variation of results in iterations (Mon Dec 06 2004 - 22:13:26 CST)
  • Re: Variation of results in iterations (Mon Dec 06 2004 - 19:37:43 CST)
  • Re: Variation of results in iterations (Mon Dec 06 2004 - 17:44:43 CST)
  • Pair interaction, PBC included? (Sat Nov 20 2004 - 14:22:39 CST)
  • Re: Move molecule (Thu Nov 18 2004 - 12:39:00 CST)
  • Berendsen or Langevin Temp control? (Wed Nov 10 2004 - 15:54:07 CST)
  • Re: Solvent mixture (Fri Nov 05 2004 - 16:43:21 CST)
  • Methane residue file (Wed Oct 27 2004 - 19:19:28 CDT)
  • Question on harmonic constraints (Thu Oct 14 2004 - 19:39:00 CDT)
  • Spherical Boundary Conditions (Tue Oct 05 2004 - 16:14:12 CDT)
  • Re: Cell Basis Vector. (Tue Sep 07 2004 - 18:45:13 CDT)
  • Re: Questions on periodic boundary condition (Thu Sep 02 2004 - 10:51:56 CDT)
  • Re: Temperature (Mon Aug 30 2004 - 13:12:17 CDT)
  • Re: Need to add Hydrogens to over 300 distinct PDB's (Wed Aug 11 2004 - 13:05:33 CDT)
  • RE: Need to add Hydrogens to over 300 distinct PDB's (Tue Aug 10 2004 - 10:20:47 CDT)
  • Need to add Hydrogens to over 300 distinct PDB's (Mon Aug 09 2004 - 13:03:40 CDT)
  • Re: Questions (Mon Jul 19 2004 - 17:02:29 CDT)
  • Re: Dynamically resizing waterbox (Wed Jul 14 2004 - 15:01:00 CDT)
  • Re: cellBasisVector x,y,z values (Thu Jul 08 2004 - 09:36:43 CDT)
  • Re: How to calculate specific heat capacity in NAMD? (Wed Jul 07 2004 - 10:39:38 CDT)
  • Re: What binaries should I take? (Fri Jun 18 2004 - 08:18:38 CDT)
  • Re: Energy minimization at NAMD (Tue Jun 15 2004 - 16:07:06 CDT)
  • Re: psfgen issue (Mon Jun 07 2004 - 09:23:23 CDT)
  • Re: IO error when running NAMD on new cluster (Mon Jun 07 2004 - 09:21:44 CDT)
  • IO error when running NAMD on new cluster (Sat Jun 05 2004 - 14:44:10 CDT)
  • Re: Why Vmd didn't show the Pt-Cl bond (Wed May 19 2004 - 20:10:40 CDT)
  • Re: how many steps do we need do for energy minimization ? (Tue May 11 2004 - 08:39:17 CDT)
  • Re: "Constrain failure" in NAMD (Fri May 07 2004 - 17:59:05 CDT)
  • Re: Help! There is no angle or dihedral definitions for patches in .psf! (Thu Apr 29 2004 - 13:09:05 CDT)
  • Re: questions about set cellBasisVector and a ligand ... (Thu Apr 29 2004 - 12:59:15 CDT)
  • Help! There is no angle or dihedral definitions for patches in .psf! (Thu Apr 29 2004 - 10:43:09 CDT)
  • Re: Discrepency in cell volume? Cell origin can move in NPT? (Mon Apr 26 2004 - 09:11:34 CDT)
  • NPT ensemble restart, put in new basis vectors? (Sun Apr 25 2004 - 13:19:21 CDT)
  • Discrepency in cell volume? Cell origin can move in NPT? (Sun Apr 25 2004 - 12:56:36 CDT)
  • Creating Parmtop files for NAMD (Tue Apr 13 2004 - 19:42:25 CDT)
• ego_wayne-namd_at_yahoo.com.cn
  • PMEgrindsize for hexagon (Sat Oct 23 2004 - 07:47:38 CDT)
• Ekta Khurana
  • Periodic cell too small (Tue May 25 2004 - 16:22:00 CDT)
  • Unwrap molecules (Sun Mar 21 2004 - 21:55:06 CST)
  • selectConstrZ (Mon Mar 08 2004 - 12:01:09 CST)
  • firsttimestep (Tue Feb 17 2004 - 18:50:30 CST)
• ELENA JEAN LEVIN
  • three-site carbon monoxide model (Thu May 27 2004 - 16:40:11 CDT)
  • Re: contraint failure in RATTLE algorithm (Thu Nov 06 2003 - 16:01:07 CST)
  • contraint failure in RATTLE algorithm (Thu Nov 06 2003 - 13:45:19 CST)
• Enrico Piccinini
  • charmm->gromacs->charmm force field conversion (Wed Dec 01 2004 - 09:36:06 CST)
  • Working on cluster to do umbrella sampling (Fri Nov 19 2004 - 04:39:13 CST)
  • fatal error running namd (Mon Nov 15 2004 - 04:30:06 CST)
• EPF (Esben Peter Friis)
  • RE: creating Charmm psf from Xplor format (Wed Feb 04 2004 - 07:40:50 CST)
  • RE: cluseter node freezes while running namd 2.5/2.5b1 (Sun Oct 19 2003 - 14:00:00 CDT)
• EPF \(Esben Peter Friis\)
  • RE: xplor to charmm (Mon Nov 01 2004 - 15:21:08 CST)
• Eric Cyr
  • Re: Calculation of velocities (Fri Sep 03 2004 - 14:27:38 CDT)
  • Calculation of velocities (Tue Aug 31 2004 - 15:44:47 CDT)
• Eric Franz
  • compiling linux scyld mpi 64bit (Tue Jun 29 2004 - 10:40:31 CDT)
• Eric Hajjar
  • Need of an ASCII-PHI converter, any help is appreciated to use wat2ions from Delphi output (Fri Jul 30 2004 - 02:45:05 CDT)
  • Converting PSF TYPES: from XPLOr to CHARMM (Tue Apr 13 2004 - 07:15:58 CDT)
• Eric R Johnson
  • Re: NAMD "freezes" up (further clarification) (Tue May 11 2004 - 12:34:32 CDT)
  • Re: NAMD "freezes" up (further clarification) (Tue May 11 2004 - 11:10:44 CDT)
  • Re: NAMD "freezes" up (Tue May 11 2004 - 08:35:51 CDT)
  • Re: NAMD node freeze (Tue May 11 2004 - 08:43:42 CDT)
  • NAMD "freezes" up (further clarification) (Tue May 11 2004 - 08:49:33 CDT)
  • NAMD "freezes" up (Tue May 11 2004 - 04:20:58 CDT)
  • Missing coordinates and psfgen (Sat Feb 07 2004 - 14:56:55 CST)
• Erik Nordgren
  • RE: surface pressure/tension (Thu Sep 09 2004 - 13:56:27 CDT)
• Eunice Ramirez Melendez
  • PME ERROR (Wed Dec 01 2004 - 01:52:13 CST)
  • CHARMM (Mon Sep 06 2004 - 21:30:50 CDT)
  • DPPC (Mon Aug 30 2004 - 02:28:55 CDT)
  • Segmentation violation (Mon Jul 19 2004 - 22:26:22 CDT)
• Fangqiang Zhu
  • Re: AMBER FF and pmf (Thu May 06 2004 - 18:18:58 CDT)
  • Re: Getting forces: segmentation violation or illegal instruction (Mon Mar 22 2004 - 11:54:41 CST)
  • Re: TCL: getting forces (Fri Mar 05 2004 - 14:04:31 CST)
  • Re: Amber on with H-bond (Thu Mar 04 2004 - 01:00:31 CST)
  • Re: Amber on with H-bond (Wed Mar 03 2004 - 21:45:15 CST)
  • Generating novel structure (Tue Mar 02 2004 - 13:38:12 CST)
  • Re: Locally Enhanced Sampling (Tue Mar 02 2004 - 11:51:09 CST)
  • Re: Restart using amber force field (Fri Feb 27 2004 - 15:00:29 CST)
  • Re: psf file for zeolite-water system (Mon Feb 23 2004 - 14:16:26 CST)
  • Re: test and a short question! (Mon Jan 19 2004 - 15:15:15 CST)
  • Re: SMD force (fwd) (Tue Jan 06 2004 - 17:14:56 CST)
  • Re: rotational energy, Tcl and environment variable(s) inLinux 2.5 (Thu Dec 04 2003 - 18:05:24 CST)
  • Re: how to add counterions ? (Tue Dec 02 2003 - 18:19:19 CST)
  • Re: rotational energy, Tcl and environment variable(s) in Linux 2.5 (Tue Dec 02 2003 - 00:38:01 CST)
  • Re: how to add counterions ? (Tue Dec 02 2003 - 00:24:16 CST)
  • Re: Why "fixedAtomsForces on" for constant pressure? (Tue Dec 02 2003 - 00:04:16 CST)
  • Re: updating coordinates using IMD (Mon Dec 01 2003 - 11:47:08 CST)
  • Re: how to get Charge of new residue? (Sat Nov 29 2003 - 01:03:31 CST)
  • Re: (Sat Nov 29 2003 - 00:41:44 CST)
  • Re: Temp in SMD (Sat Nov 29 2003 - 00:34:30 CST)
  • Re: how can I know which type HIS belong to?(HSD,HSE,HSP) (Sat Nov 29 2003 - 00:22:03 CST)
  • Re: the Atom velocity is beyond the limit? (Fri Nov 28 2003 - 23:44:19 CST)
  • Re: the problem on segment a ligand in NAMD ? (Fri Nov 28 2003 - 00:41:19 CST)
  • Re: FATAL ERROR (Thu Nov 27 2003 - 23:47:41 CST)
  • Re: xst format (Thu Nov 27 2003 - 23:27:34 CST)
  • Re: something about the TIP3P water model (Thu Nov 27 2003 - 23:11:33 CST)
  • Re: Energy problem after restart (Tue Nov 25 2003 - 09:47:30 CST)
  • Re: Energy problem after restart (Mon Nov 24 2003 - 15:15:56 CST)
  • Re: Energy problem after restart (Thu Nov 20 2003 - 17:15:11 CST)
  • Re: Urey-Bradley term (Wed Nov 19 2003 - 17:39:23 CST)
  • Re: ADP again (Tue Nov 18 2003 - 18:44:24 CST)
  • Re: Urey-Bradley term (Tue Nov 18 2003 - 18:24:46 CST)
  • Re: ADP again (Mon Nov 17 2003 - 18:47:59 CST)
  • Re: zinc parameter? (Mon Nov 17 2003 - 18:24:08 CST)
• Florian Barth
  • Re: NAMD on Linux cluster with Myrinet (Mon Oct 11 2004 - 19:49:48 CDT)
  • Re: namd2.5 on myrinet cluster (Sun Apr 04 2004 - 18:34:40 CDT)
  • namd2.5 on myrinet cluster (Sat Apr 03 2004 - 17:59:39 CST)
• Frances Leung
  • RE: minimization problem - "Bad global exclusion count,possible error!" (Fri Jan 30 2004 - 02:52:09 CST)
  • RE: minimization problem - "Bad global exclusion count, possible error!" (Thu Jan 29 2004 - 21:20:54 CST)
  • minimization problem - "Bad global exclusion count, possible error!" (Thu Jan 29 2004 - 19:25:27 CST)
  • missing atoms warnings for psfgen (Mon Jan 19 2004 - 21:47:33 CST)
  • implicit solvent model (Mon Jan 19 2004 - 20:10:59 CST)
• Francesco Iori
  • rmsd calculation (Tue Nov 23 2004 - 06:56:32 CST)
• freddie salsbury
  • NAMD on itanium? (Thu Mar 11 2004 - 18:04:10 CST)
• Fung Wai Keung
  • Question on finding suitable force field for MD simulations (Fri Mar 12 2004 - 21:00:06 CST)
• g srinivasa murthy
  • Re: Info about forces on atoms (Fri May 28 2004 - 03:27:23 CDT)
  • Re: charm++ mpi-linux compilation errors (Thu May 20 2004 - 09:57:55 CDT)
  • Tcl: loadtotalforces (Mon Mar 29 2004 - 05:11:49 CST)
  • query on memory usuage (Sat Feb 21 2004 - 22:58:26 CST)
• Gadi Oron
  • Re: Force Calculation in NAMD (Sun May 23 2004 - 02:37:27 CDT)
  • RE: Binding free energy of a protein complex (Wed May 05 2004 - 09:31:52 CDT)
  • Binding free energy of a protein complex (Mon May 03 2004 - 02:06:05 CDT)
  • Issues with SMD (Mon Apr 26 2004 - 07:05:26 CDT)
  • Re: still problems with namdplot (Sun Apr 18 2004 - 01:51:42 CDT)
  • Re: Load balance strategy (Tue Mar 16 2004 - 15:44:03 CST)
  • Re: FIRSTTIMESTEP in config file (Mon Mar 15 2004 - 04:02:07 CST)
  • TCL question (Sun Mar 14 2004 - 08:13:55 CST)
  • Re: Binding Energy (Tue Mar 09 2004 - 07:37:22 CST)
  • Dealing with hyperthreading (Sun Mar 07 2004 - 04:43:09 CST)
  • Pair interaction output. (Thu Feb 12 2004 - 06:21:23 CST)
  • Changing SMD parameters (Mon Feb 09 2004 - 07:32:11 CST)
  • Re: Charm++ nodelist commands (Thu Jan 08 2004 - 02:40:06 CST)
  • Re: Charm++ nodelist commands (Wed Dec 31 2003 - 03:31:17 CST)
  • Re: Charm++ nodelist commands (Tue Dec 30 2003 - 08:10:29 CST)
  • Re: Charm++ nodelist commands (Mon Dec 22 2003 - 11:30:55 CST)
  • Re: Charm++ nodelist commands (Mon Dec 22 2003 - 05:10:39 CST)
  • Bun in charmd? (Sun Dec 21 2003 - 08:53:49 CST)
  • Re: Charm++ nodelist commands (Sun Dec 21 2003 - 02:38:11 CST)
  • Charm++ nodelist commands (Thu Dec 18 2003 - 05:48:02 CST)
  • Re: Help! unstable simulation - ARG go nuts... (Wed Dec 17 2003 - 04:36:47 CST)
  • Re: Help! unstable simulation - ARG go nuts... (Tue Dec 16 2003 - 09:33:25 CST)
  • Help! unstable simulation. (Thu Dec 11 2003 - 01:51:14 CST)
• Galina Petrova
  • Problems witn parameter files! (Mon May 10 2004 - 08:54:25 CDT)
  • NAMD: Force Fields (Fri Apr 23 2004 - 09:00:57 CDT)
• Gaurav Sharma
  • FATAL ERROR: Asymmetric water molecule ? (Tue Dec 21 2004 - 14:58:11 CST)
  • Autoionize plugin problem (Tue Dec 14 2004 - 12:52:03 CST)
• gengbin
  • Re: compiler flags. (Wed Jul 14 2004 - 23:58:54 CDT)
• Gengbin Zheng
  • Re: clustermatic 4 and 5 Namd/charm (Fri Dec 31 2004 - 12:10:17 CST)
  • Re: mpi opteron myrinet (Fri Dec 31 2004 - 00:08:20 CST)
  • Re: mpi opteron myrinet (Thu Dec 30 2004 - 22:50:45 CST)
  • Re: clustermatic 4 and 5 Namd/charm (Thu Dec 30 2004 - 18:52:47 CST)
  • Re: problems on Fedora Core 3 (Thu Dec 30 2004 - 15:23:30 CST)
  • Re: NamdCompile Problem (Thu Dec 16 2004 - 13:19:57 CST)
  • Re: Infiniband and PME gridsize (Tue Dec 14 2004 - 13:05:45 CST)
  • Re: Infiniband and PME gridsize (Tue Dec 14 2004 - 12:16:55 CST)
  • Re: fatal error (Tue Dec 14 2004 - 12:14:28 CST)
  • Re: Building NAMD with Portland's C++ Comipler (Thu Dec 09 2004 - 12:47:54 CST)
  • Re: Rif: Re: Rif: Re: Rif: Re: Rif: Re: linux cluster trouble (Fri Nov 19 2004 - 09:18:28 CST)
  • Re: Rif: Re: Rif: Re: Rif: Re: linux cluster trouble (Thu Nov 18 2004 - 13:20:46 CST)
  • Re: Rif: Re: Rif: Re: Rif: Re: linux cluster trouble (Thu Nov 18 2004 - 13:01:25 CST)
  • Re: linux cluster trouble (Tue Nov 09 2004 - 08:19:10 CST)
  • Re: Re: Compiling NAMD on IA64 cluter (Wed Nov 03 2004 - 11:24:27 CST)
  • Re: Compilation on an Opteron Server SuSE Linux Enterprise System Version 8 (Wed Oct 20 2004 - 10:24:09 CDT)
  • Re: NAMD on Linux cluster with Myrinet (Mon Oct 18 2004 - 13:28:36 CDT)
  • Re: NAMD on Linux cluster with Myrinet (Thu Oct 14 2004 - 14:03:12 CDT)
  • Re: NAMD on Linux cluster with Myrinet (Tue Oct 12 2004 - 00:17:53 CDT)
  • Re: 64 nodes behaviour (Fri Sep 03 2004 - 14:37:05 CDT)
  • Re: 64 nodes behaviour (Thu Sep 02 2004 - 13:19:03 CDT)
  • Re: Compilation on Opteron (Thu Aug 26 2004 - 00:25:44 CDT)
  • Re: question on the parallel job on NCSA Xeon cluster (Tue Aug 17 2004 - 23:01:02 CDT)
  • Re: Has NAMD been ported to Itanium2 + Linux? (Tue Aug 10 2004 - 16:54:08 CDT)
  • Re: compiled namd on clustermatic fails ! (Tue Aug 03 2004 - 11:31:31 CDT)
  • Re: compiled namd on clustermatic fails ! (Tue Aug 03 2004 - 10:23:19 CDT)
  • Re: Myrinet and MPI question (Thu Jul 22 2004 - 11:49:07 CDT)
  • Re: Segmentation violation (Tue Jul 20 2004 - 14:18:06 CDT)
  • Re: NAMD on the TeraGrid (Thu Jul 15 2004 - 10:53:20 CDT)
  • Re: Namd RedHat9 compilation problem (Tue Jun 15 2004 - 11:39:49 CDT)
  • Re: build charm on ia-64 linux (Fri Jun 11 2004 - 21:54:20 CDT)
  • Re: build charm on ia-64 linux (Fri Jun 11 2004 - 20:57:01 CDT)
  • Re: submitting a job in a queue (Thu Jun 03 2004 - 11:33:25 CDT)
  • Re: NAMD on HP-IA64 Linux (Sun May 30 2004 - 22:20:51 CDT)
  • Re: Compiling NAMD on Linux cluster (Fri May 28 2004 - 15:48:41 CDT)
  • Re: hanging at startup phase (Fri May 21 2004 - 10:53:23 CDT)
  • Re: hanging at startup phase (Fri May 21 2004 - 00:59:55 CDT)
  • Re: (Thu Apr 15 2004 - 12:14:36 CDT)
  • Re: Running namd on Rice Teracluster (Mon Apr 12 2004 - 13:28:10 CDT)
  • Re: Illegal instruction signal at startup. (with net-rs6k smp) (Fri Apr 09 2004 - 18:36:19 CDT)
  • Re: Illegal instruction signal at startup. (with net-rs6k smp) (Thu Apr 08 2004 - 17:36:49 CDT)
  • Re: Illegal instruction signal at startup. (with net-rs6k smp) (Thu Apr 08 2004 - 16:31:27 CDT)
  • Re: Illegal instruction signal at startup. (with net-rs6k smp) (Thu Apr 08 2004 - 16:21:29 CDT)
  • Re: Fatal Socket error (Thu Apr 08 2004 - 16:16:35 CDT)
  • Re: compiling NAMD (Wed Apr 07 2004 - 20:10:12 CDT)
  • Re: # of processors (Mon Apr 05 2004 - 00:41:44 CDT)
  • Re: _alloca undefined symbol (OS X/XL compiler) (Mon Apr 05 2004 - 00:20:45 CDT)
  • Re: namd2.5 on myrinet cluster (Sat Apr 03 2004 - 20:40:12 CST)
  • Re: More NAMD/gm2 problems (Wed Mar 31 2004 - 02:17:57 CST)
  • Re: timeout on running namd (Tue Mar 30 2004 - 13:23:15 CST)
  • Re: Problems compiling Charm++ for Myrinet (Tue Mar 30 2004 - 12:40:05 CST)
  • Re: Running on Alpha cluster (Fri Mar 26 2004 - 11:43:38 CST)
  • Re: charmrun vs. miprun and nature of parallelism (Fri Mar 19 2004 - 02:10:26 CST)
  • Re: Load balance strategy (Fri Mar 19 2004 - 01:41:44 CST)
  • Re: NAMD support for Myranet GM2 drivers (Fri Mar 19 2004 - 01:30:49 CST)
  • Re: Load balance strategy (Wed Mar 17 2004 - 11:31:03 CST)
  • Re: Namd with intel compilers. (Wed Mar 17 2004 - 10:52:27 CST)
  • Re: Running on Alpha cluster (Mon Mar 15 2004 - 10:07:24 CST)
  • Re: Clustermatic 4.0 (Fri Mar 12 2004 - 21:36:16 CST)
  • Re: clustering - fault tolerant NAMD (Fri Mar 12 2004 - 13:18:01 CST)
  • Re: Compiling on G5 using xlC (Thu Feb 26 2004 - 15:40:59 CST)
  • Re: Running AIX version of NAMD on IBM cluster (Wed Feb 18 2004 - 21:37:55 CST)
  • Re: mac clustering (Sat Feb 07 2004 - 00:10:28 CST)
  • Re: problem with running namd on Linux cluster (Tue Jan 20 2004 - 11:18:20 CST)
  • Re: NAMD linking problem (Fri Jan 16 2004 - 15:46:09 CST)
  • Re: Charm++ nodelist commands (Sun Jan 04 2004 - 23:18:42 CST)
  • Re: NAMD for Opteron? (Sun Jan 04 2004 - 18:32:21 CST)
  • Re: Charm++ nodelist commands (Sun Jan 04 2004 - 16:23:27 CST)
  • Re: Re: Intel C/C++ compiler Version 8 for compiling NAMD on IA64 (Fri Jan 02 2004 - 12:16:32 CST)
  • Re: Charm++ nodelist commands (Fri Jan 02 2004 - 12:09:51 CST)
  • Re: Intel C/C++ compiler Version 8 for compiling NAMD on IA64 (Wed Dec 31 2003 - 13:25:53 CST)
  • Re: Charm++ nodelist commands (Wed Dec 31 2003 - 11:59:00 CST)
  • Re: Charm++ nodelist commands (Tue Dec 30 2003 - 18:05:36 CST)
  • Re: Charm++ nodelist commands (Tue Dec 30 2003 - 13:14:52 CST)
  • Re: Charm++ nodelist commands (Tue Dec 23 2003 - 17:22:29 CST)
  • Re: Bun in charmd? (Sun Dec 21 2003 - 14:11:56 CST)
  • Re: Charm++ nodelist commands (Thu Dec 18 2003 - 13:04:28 CST)
  • Re: how should I run NAMD on parallel platform? (Thu Dec 18 2003 - 02:40:16 CST)
  • Re: LDB questions/problems (Tue Dec 16 2003 - 02:33:09 CST)
  • Re: Which version MPICH-VMI does namd-ia64-vmi run on? intel compiled version or gcc complied version? (Thu Dec 11 2003 - 16:08:08 CST)
  • Re: nodelist ignored? (Mon Sep 29 2003 - 14:23:42 CDT)
• Gerald Quon
  • minimization scripts (Mon Feb 09 2004 - 12:09:29 CST)
• ghg_at_xalt.am
  • Namd RedHat9 compilation problem (Tue Jun 15 2004 - 05:56:36 CDT)
  • charm++ mpi-linux compilation errors (Wed May 19 2004 - 11:38:28 CDT)
  • Myrinet and MPI (Wed May 19 2004 - 09:20:20 CDT)
• Gianluca Interlandi
  • Re: xsc information in the dcd file? (Thu Dec 16 2004 - 11:25:50 CST)
  • xsc information in the dcd file? (Wed Dec 15 2004 - 10:57:26 CST)
  • Re: Infiniband and PME gridsize (Tue Dec 14 2004 - 12:54:55 CST)
  • Infiniband and PME gridsize (Tue Dec 14 2004 - 06:06:03 CST)
  • Compiling charm on a opteron cluster (Fri Dec 03 2004 - 15:11:18 CST)
  • Compiling charm on a opteron cluster (Fri Dec 03 2004 - 15:03:11 CST)
  • Re: recentering protein in the waterbox (Fri Jun 18 2004 - 18:16:35 CDT)
  • Re: What binaries should I take? (Fri Jun 18 2004 - 08:38:39 CDT)
  • Re: errors building charm on ia64 (Thu Jun 17 2004 - 11:31:42 CDT)
  • Urey-Bradley term? (Tue Jun 08 2004 - 12:29:34 CDT)
  • Re: What, if no temperatue control specified? (Fri Apr 23 2004 - 03:59:45 CDT)
  • What, if no temperatue control specified? (Thu Apr 22 2004 - 05:56:39 CDT)
  • Temperature control? (Wed Apr 21 2004 - 10:32:14 CDT)
• Gianni De Fabritiis
  • Argon solvent (Tue Feb 17 2004 - 09:55:02 CST)
• Gilbert G.Feng
  • more than 99999 atoms in PDB files (Mon Dec 13 2004 - 15:30:55 CST)
  • constant velocity smd with distance restraints (Fri Dec 03 2004 - 14:22:50 CST)
• Giovanni
  • submitting a job in a queue (Wed Jun 02 2004 - 10:55:37 CDT)
  • coarse grained model (Fri May 07 2004 - 05:02:57 CDT)
  • Re: vmd-l: Re: dcd files generated with catdcd (Fri Apr 30 2004 - 13:08:33 CDT)
  • dcd files generated with catdcd (Fri Apr 30 2004 - 04:11:00 CDT)
  • coarse grained force field (Fri Apr 02 2004 - 15:29:06 CST)
  • namd on linux cluster (Tue Feb 24 2004 - 13:45:44 CST)
• Giovanni Bellesia
  • spherical boundary condition (Tue Nov 23 2004 - 07:35:17 CST)
  • D-amino acids (Mon Oct 25 2004 - 07:00:46 CDT)
  • NAMD prog. guide (Sat Sep 18 2004 - 19:53:46 CDT)
• Giovanni Settanni
  • charmm restart file to NAMD (Mon Nov 17 2003 - 05:27:03 CST)
• griadi_at_utalca.cl
  • Re: spherical boundary condition (Mon Nov 29 2004 - 02:29:51 CST)
  • Re: Writing pdb file.. easier way? (Tue Nov 23 2004 - 12:44:03 CST)
• Grischa R. Meyer
  • G5 or P4 cluster (Tue Nov 11 2003 - 00:58:07 CST)
  • libc6 on debian x86 (Thu Sep 11 2003 - 22:42:17 CDT)
• gzheng
  • Re: compiling NAMD (Fri Jul 09 2004 - 20:52:04 CDT)
• Han Choe
  • RE: CP3-NH3 error (Thu Mar 04 2004 - 16:48:46 CST)
  • CP3-NH3 error (Mon Mar 01 2004 - 21:36:44 CST)
• Hansang Bae
  • NAMD with HPUX/IA64. (Tue Jun 29 2004 - 13:31:20 CDT)
  • Re: Illegal instruction signal at startup. (with net-rs6k smp) (Tue Apr 13 2004 - 22:00:48 CDT)
  • Re: Illegal instruction signal at startup. (with net-rs6k smp) (Fri Apr 09 2004 - 16:20:20 CDT)
  • Re: Illegal instruction signal at startup. (with net-rs6k smp) (Fri Apr 09 2004 - 14:21:52 CDT)
  • Re: Illegal instruction signal at startup. (with net-rs6k smp) (Thu Apr 08 2004 - 16:26:37 CDT)
  • Illegal instruction signal at startup. (with net-rs6k smp) (Tue Apr 06 2004 - 22:08:02 CDT)
  • Namd with intel compilers. (Tue Mar 16 2004 - 14:51:47 CST)
  • Re: Running AIX version of NAMD on IBM cluster (Tue Feb 17 2004 - 17:13:47 CST)
  • Truncation errors. (Mon Dec 29 2003 - 09:19:53 CST)
  • Basic question. (Tue Dec 02 2003 - 13:03:16 CST)
• Harald Tepper
  • Re: Re: numerical inaccuracy upon restart (Tue Aug 31 2004 - 05:21:21 CDT)
  • numerical inaccuracy upon restart (Wed May 19 2004 - 08:45:07 CDT)
• Harindar Keer
  • Chloroform Solvent Box (Tue Nov 23 2004 - 11:17:45 CST)
  • NAMD programming guide (Thu Sep 16 2004 - 19:55:52 CDT)
  • Stray PME grid charges (Tue Sep 07 2004 - 13:42:39 CDT)
  • Sampling trajectories (Fri Jun 04 2004 - 17:03:02 CDT)
  • SMD: many atom pulling (Thu Mar 04 2004 - 21:29:12 CST)
  • RE: minimization problem - "Bad global exclusion count, possible error!" (Thu Jan 29 2004 - 18:21:19 CST)
  • Bad global exclusion count (Fri Jan 16 2004 - 14:06:28 CST)
  • Re: LYC Parameter-Topology ? (Wed Nov 19 2003 - 13:01:55 CST)
• Harit Jani
  • Unit of force using Haptic in IMD (Fri May 14 2004 - 01:33:10 CDT)
  • .psf and .params files for IMD (Wed Dec 10 2003 - 19:08:54 CST)
• Hassan K. Al-Ali Merheby
  • NAMD Source (Fri Nov 19 2004 - 02:06:44 CST)
• Hemant Kushwaha
  • psfgen (Mon Nov 29 2004 - 01:16:44 CST)
• himanshu chandola
  • Re: Hi (Sat Apr 24 2004 - 02:09:57 CDT)
  • Re: Using checkpoints in simulation (Fri Apr 09 2004 - 19:41:18 CDT)
  • Re: using restart files (Fri Apr 09 2004 - 02:36:55 CDT)
  • using restart files (Thu Apr 08 2004 - 18:00:14 CDT)
  • restart files (Sun Apr 04 2004 - 19:51:34 CDT)
  • Re: counterions (Wed Mar 31 2004 - 03:13:51 CST)
  • counterions (Tue Mar 30 2004 - 02:53:19 CST)
  • Re: minimization problem (Fri Mar 19 2004 - 05:42:41 CST)
  • Re: rotating constraints constant (Wed Mar 03 2004 - 05:57:11 CST)
  • rotating constraints constant (Wed Mar 03 2004 - 02:12:34 CST)
  • Re: dcd format (Fri Jan 30 2004 - 14:10:21 CST)
  • dcd format (Fri Jan 30 2004 - 04:25:28 CST)
  • rotating constraints (Fri Jan 30 2004 - 01:28:51 CST)
  • Re: LDB questions/problems (Tue Dec 16 2003 - 00:29:26 CST)
  • Re: ATP fix (fwd) (Wed Nov 19 2003 - 23:36:48 CST)
  • ATP fix (fwd) (Wed Nov 19 2003 - 11:32:17 CST)
  • rot constraints (Tue Nov 18 2003 - 20:42:17 CST)
  • rotating constraints (Tue Nov 18 2003 - 20:17:14 CST)
  • Re: ADP again (Mon Nov 17 2003 - 02:13:25 CST)
  • ADP again (Sun Nov 16 2003 - 04:27:48 CST)
  • sorted out problem (Fri Nov 14 2003 - 14:24:45 CST)
  • Re: dcd files (Tue Nov 11 2003 - 23:52:13 CST)
  • rotation constraints (Tue Nov 11 2003 - 17:59:45 CST)
  • dcd files (Tue Nov 11 2003 - 09:44:21 CST)
  • uninitialized coordinates (Sun Nov 09 2003 - 02:22:35 CST)
  • fixed atoms parameters (Fri Nov 07 2003 - 23:54:04 CST)
  • rotation constraints (Fri Nov 07 2003 - 23:49:26 CST)
  • Re: atoms moving too fast (Fri Nov 07 2003 - 20:21:27 CST)
  • Re: atoms moving too fast (Thu Nov 06 2003 - 19:11:58 CST)
  • Re: atoms moving too fast (Thu Nov 06 2003 - 03:59:10 CST)
  • atoms moving too fast (Thu Nov 06 2003 - 03:21:12 CST)
  • Re: excluding water in dcd files (Tue Nov 04 2003 - 11:45:28 CST)
  • Re: excluding water in dcd files (Tue Nov 04 2003 - 02:00:18 CST)
  • excluding water in dcd files (Mon Nov 03 2003 - 02:31:41 CST)
  • solvate (Sun Nov 02 2003 - 17:41:24 CST)
  • running namd on solaris 5.6 (Thu Oct 30 2003 - 22:50:16 CST)
  • Re: charmm param. for ADP (Tue Oct 28 2003 - 01:27:28 CST)
  • charmm param. for ADP (Mon Oct 27 2003 - 18:45:58 CST)
  • switch for equilibrisation (Wed Oct 22 2003 - 17:24:29 CDT)
  • constraining movement of atoms (Thu Oct 16 2003 - 02:49:01 CDT)
• Hrant Gharabekyan
  • Myrinet and MPI question (Thu Jul 22 2004 - 09:20:01 CDT)
  • Output files creation problem in MPI. (Mon Jul 19 2004 - 07:59:38 CDT)
  • Output files creation problem in MPI. (Mon Jul 19 2004 - 02:35:11 CDT)
  • Atom number limitations? (Thu Apr 29 2004 - 22:50:26 CDT)
• Hua Wong
  • peptid bond omega, problems with settings? (Fri Apr 16 2004 - 09:25:22 CDT)
  • peptid bond omega, problems with settings? (Thu Apr 15 2004 - 02:27:38 CDT)
  • dimer minimisation and psfgen problem (Wed Mar 17 2004 - 03:17:57 CST)
  • psf question (Tue Mar 16 2004 - 03:12:38 CST)
  • Binary conversions (Tue Dec 02 2003 - 02:11:10 CST)
  • VMD problems (Mon Dec 01 2003 - 07:46:44 CST)
  • Addendum to Re: Minimisation error (Fri Nov 28 2003 - 02:36:02 CST)
  • Re: Minimisation error (Fri Nov 28 2003 - 02:32:49 CST)
  • Minimisation error (Thu Nov 27 2003 - 08:47:29 CST)
  • FATAL ERROR (Thu Nov 27 2003 - 08:32:15 CST)
  • NAMD minimisation (Thu Nov 27 2003 - 07:29:27 CST)
  • problems with psfgen (Thu Nov 27 2003 - 04:39:25 CST)
• Hui-Hsu (Gavin) Tsai [contr]
  • NPT calculations in NAMD (Mon May 31 2004 - 11:06:04 CDT)
• Hui-Hsu Tsai
  • communication with NAMD? (Tue Oct 26 2004 - 15:37:37 CDT)
• HUSSER Jacky 113956
  • NamdCompile Problem (Thu Dec 16 2004 - 05:17:41 CST)
• Hyonseok Hwang
  • question on force autocorrelation function (Wed Oct 13 2004 - 11:20:47 CDT)
  • question on pair interaction energy and force (Tue Sep 21 2004 - 23:39:41 CDT)
  • question on the parallel job on NCSA Xeon cluster (Tue Aug 17 2004 - 22:51:13 CDT)
  • question on Lithium force field (Wed Jun 16 2004 - 16:20:12 CDT)
  • question on veldcd (Mon Jun 14 2004 - 10:19:59 CDT)
  • question on veldcd (Fri Jun 11 2004 - 12:35:42 CDT)
  • question on a chared system MD simulation (Sun Jun 06 2004 - 18:05:35 CDT)
  • question on the wrapping algorithm in NAMD (Thu May 27 2004 - 18:18:26 CDT)
  • question on self-diffusion constant of TIP3P water (Wed May 05 2004 - 16:54:45 CDT)
  • question on autocorrelation function and temperature controlling (Fri Apr 30 2004 - 17:09:44 CDT)
  • about delta-G in PMF calculation (Thu Apr 01 2004 - 22:36:27 CST)
  • question on PMF output (Mon Mar 08 2004 - 12:08:13 CST)
  • Re: temp coupling coefficients (Tue Mar 02 2004 - 13:18:22 CST)
  • langevin coupling coefficient (Mon Feb 23 2004 - 14:39:47 CST)
  • temperature control question (Sun Feb 08 2004 - 22:31:39 CST)
  • Re: user-supplied conformational restraints (Thu Feb 05 2004 - 15:41:49 CST)
  • distance constraint (Wed Feb 04 2004 - 17:56:20 CST)
  • question on potential energy for individual atoms (Fri Jan 23 2004 - 19:59:53 CST)
  • question on Berendsen's temperature coupling method (Tue Jan 20 2004 - 13:13:59 CST)
  • question on the coordinates of hydrogen atoms (Fri Jan 02 2004 - 17:45:50 CST)
• Ioana Cozmuta
  • NAMD on HP-IA64 Linux (Sun May 30 2004 - 20:58:00 CDT)
  • benchmarking mistake? (Sun May 30 2004 - 20:12:52 CDT)
  • NAMD on HP with Itanium2 Processors (Fri May 28 2004 - 18:08:37 CDT)
  • using restart files (Thu Apr 08 2004 - 14:59:26 CDT)
  • residence time (Tue Mar 23 2004 - 21:51:10 CST)
  • hydrogen bonds in NAMD (Fri Mar 19 2004 - 01:02:25 CST)
  • entropy calculations (Mon Feb 23 2004 - 17:41:54 CST)
  • Re: Pair interaction energy (Fri Jan 30 2004 - 12:28:05 CST)
  • Re: Pair interaction energy (Fri Jan 30 2004 - 11:57:16 CST)
  • seed value in SMD (Thu Jan 22 2004 - 20:54:15 CST)
  • TCl question (Mon Jan 19 2004 - 16:41:52 CST)
  • SMD-velocity unit (Sat Jan 10 2004 - 18:24:18 CST)
  • Re: SMD force (fwd) (Tue Jan 06 2004 - 18:25:20 CST)
  • SMD force (fwd) (Mon Jan 05 2004 - 13:36:16 CST)
  • SMD force (Sat Jan 03 2004 - 22:01:45 CST)
  • processors information (Wed Dec 10 2003 - 21:28:23 CST)
  • Re: About the SMD output file (Fri Dec 05 2003 - 16:47:31 CST)
  • Re: A problem with intermediate files (Mon Nov 10 2003 - 22:12:05 CST)
  • Re: A problem with intermediate files (Mon Nov 10 2003 - 22:09:20 CST)
  • Re: vmd-l: running vmd in batch mode (Thu Nov 06 2003 - 19:19:30 CST)
  • running vmd in batch mode (Thu Nov 06 2003 - 15:46:19 CST)
  • Re: Re: vmd-l: bigdcd (Wed Nov 05 2003 - 18:29:25 CST)
  • bigdcd (Wed Nov 05 2003 - 17:00:40 CST)
  • SMD: constant velocity or force pulling? (Thu Oct 30 2003 - 21:02:54 CST)
  • Re: (Mon Oct 20 2003 - 12:32:02 CDT)
  • pair Interaction and electric field (Sun Oct 19 2003 - 14:09:22 CDT)
  • Re: pair Interaction Calculation (Thu Oct 16 2003 - 17:50:47 CDT)
  • pair Interaction Calculation (Thu Oct 16 2003 - 17:36:18 CDT)
  • cylindrical boundary conditions (Wed Oct 15 2003 - 16:48:08 CDT)
  • NAMD: force field for hybrid systems (fwd) (Sun Oct 12 2003 - 12:59:01 CDT)
• Ivan Vinogradov
  • Implicit water dielectric constant. (Wed Nov 10 2004 - 10:16:57 CST)
  • HYP files (Tue Aug 03 2004 - 12:55:52 CDT)
  • Re: HYP parameters (Thu Jul 29 2004 - 07:44:27 CDT)
  • Segmantation fault writing dcd files. (Fri Mar 12 2004 - 09:07:26 CST)
• ivan.vinogradov_at_utoronto.ca
  • Calculating parameters. (Fri May 14 2004 - 13:29:50 CDT)
  • Segmentation fault. (Thu Mar 11 2004 - 16:21:24 CST)
  • Hydroxyprolin force field. (Fri Jan 23 2004 - 11:01:36 CST)
• J. Rui Rodrigues
  • Re: restart simulation (Mon May 10 2004 - 17:10:25 CDT)
  • Re: vmd-l: Re: dcd files generated with catdcd (Fri Apr 30 2004 - 14:02:49 CDT)
  • Re: dcd files generated with catdcd (Fri Apr 30 2004 - 10:51:27 CDT)
  • Re: how to remove all hydrogen atoms from PDB file? (Tue Apr 20 2004 - 09:04:46 CDT)
  • Re: how to remove all hydrogen atoms from PDB file? (Tue Apr 20 2004 - 09:01:20 CDT)
  • error codes in charmrun/namd? (Wed Feb 25 2004 - 14:02:43 CST)
  • Re: concatenating two DCD files (Tue Feb 10 2004 - 18:01:10 CST)
  • Re: about HIS residue (Sun Dec 21 2003 - 13:47:28 CST)
  • Re: Minimisation error (Fri Nov 28 2003 - 09:40:46 CST)
  • Re: A problem with intermediate files (Tue Nov 11 2003 - 07:46:33 CST)
  • restarting suspended namd jobs (Mon Nov 10 2003 - 13:56:54 CST)
• james tomomi macdonald
  • Re: (Mon Dec 08 2003 - 08:46:54 CST)
  • high temperature, 498K, unfolding simulations (Thu Nov 13 2003 - 11:47:29 CST)
  • NAMD2.5b2 and amber force field (Mon Sep 29 2003 - 12:02:09 CDT)
  • implicit solvent models (Wed Sep 24 2003 - 12:53:28 CDT)
• Jan Lipfert
  • temperature rescaling and canonical ensemble (Thu Sep 30 2004 - 23:27:28 CDT)
• Jan Saam
  • Re: Calculating parameters. (Sat May 15 2004 - 10:32:36 CDT)
  • Why "fixedAtomsForces on" for constant pressure? (Tue Nov 25 2003 - 18:30:09 CST)
  • Re: NAMD minimisation (Thu Nov 27 2003 - 08:15:26 CST)
  • Re: hydrogengroupsize of 0! (Thu Nov 27 2003 - 02:43:26 CST)
  • Parameter-Topology-Repository (Wed Nov 19 2003 - 11:56:41 CST)
  • Parameter/topology repository (Fri Nov 07 2003 - 06:05:13 CST)
• Jee Eun Rim
  • periodic boundary conditions with lipids (Wed Dec 17 2003 - 12:29:45 CST)
• Jerry Ebalunode
  • recentering protein in the waterbox (Fri Jun 18 2004 - 07:04:58 CDT)
  • Re: installing on beowulf cluster (Thu May 06 2004 - 14:17:01 CDT)
  • compiling namd on amd opteron arch : TCL problems (fwd) (Fri Apr 23 2004 - 17:07:40 CDT)
  • Clustermatic 4.0 (Mon Mar 08 2004 - 14:16:20 CST)
  • Hybond calulator and display (Fri Jan 16 2004 - 12:24:30 CST)
  • Re: Re: Intel C/C++ compiler Version 8 for compiling NAMD on IA64 (Fri Jan 02 2004 - 12:04:41 CST)
  • Intel C/C++ compiler Version 8 for compiling NAMD on IA64 (Wed Dec 31 2003 - 12:57:53 CST)
  • Which version MPICH-VMI does namd-ia64-vmi run on? intel compiled version or gcc complied version? (Thu Dec 11 2003 - 03:11:03 CST)
  • Re: excluding water in dcd files (Mon Nov 03 2003 - 06:42:28 CST)
  • Re: output warning in using namd2 "Warning: Not all atoms have unique coordinates." more errors (Wed Sep 17 2003 - 07:54:46 CDT)
  • Re: output warning in using namd2 "Warning: Not all atoms have unique coordinates." (Wed Sep 17 2003 - 06:21:53 CDT)
  • output warning in using namd2 "Warning: Not all atoms have unique coordinates." (Tue Sep 16 2003 - 13:44:49 CDT)
  • error in notes on compiling namd2.5b2 with plugins (Tue Sep 16 2003 - 13:06:20 CDT)
• Jerry W. Jenkins
  • How do I Heat, then Switch to NPT in the same *.config? (Fri Mar 26 2004 - 10:42:22 CST)
• Jhih-Wei Chu
  • > 10000 atoms (Fri Aug 13 2004 - 13:32:25 CDT)
• Jim Phillips
  • Re: turning off fixed atoms in the middle of simulation (Wed Dec 15 2004 - 11:15:47 CST)
  • Re: Re: numerical inaccuracy upon restart (Fri Sep 03 2004 - 17:21:25 CDT)
  • Re: Direction of the force in Pair interactions (Tue Aug 24 2004 - 11:06:52 CDT)
  • Re: atom numbers limitation (Tue Feb 24 2004 - 15:31:06 CST)
  • Re: firsttimestep (Tue Feb 24 2004 - 15:22:27 CST)
  • Re: CoM motion not removed (Mon Feb 23 2004 - 11:01:02 CST)
  • Re: Running AIX version of NAMD on IBM cluster (Mon Feb 23 2004 - 10:50:50 CST)
  • Re: Problem with Tcl & psfgen (Tue Feb 17 2004 - 17:33:20 CST)
  • Re: Compiling NAMD on Tungsten.ncsa (Fri Feb 13 2004 - 17:35:20 CST)
  • Re: distance constraint (Fri Feb 06 2004 - 14:34:50 CST)
  • Re: Momenta output format (Tue Feb 03 2004 - 16:54:28 CST)
  • Re: rotating constraints (Mon Feb 02 2004 - 13:27:10 CST)
  • Re: How do we combine chains in the end (Mon Feb 02 2004 - 11:54:51 CST)
  • Re: previous question about multiplicity (Wed Jan 28 2004 - 14:27:50 CST)
  • Re: previous question about multiplicity (Wed Jan 28 2004 - 14:12:45 CST)
  • Re: seed value in SMD (Mon Jan 26 2004 - 17:46:59 CST)
  • Re: question on potential energy for individual atoms (Mon Jan 26 2004 - 17:52:55 CST)
  • Re: Hydroxyprolin force field. (Mon Jan 26 2004 - 17:44:10 CST)
  • Re: (Mon Jan 26 2004 - 17:51:12 CST)
  • Re: question on Berendsen's temperature coupling method (Thu Jan 22 2004 - 17:19:22 CST)
  • Re: missing atoms warnings for psfgen (Thu Jan 22 2004 - 17:08:27 CST)
  • Re: TCl question (Thu Jan 22 2004 - 16:52:35 CST)
  • Re: Potential Terms (Wed Jan 07 2004 - 09:45:11 CST)
  • Re: total energy stuck between two levels (Wed Jan 07 2004 - 09:22:27 CST)
  • Re: Simulating RNA+PROTEIN complexes (Fri Dec 19 2003 - 16:26:31 CST)
  • Re: weird energies during minimization (Fri Dec 19 2003 - 16:23:36 CST)
  • Re: how should I run NAMD on parallel platform? (Thu Dec 18 2003 - 13:27:24 CST)
  • Re: Help! unstable simulation - ARG go nuts... (Wed Dec 17 2003 - 09:23:02 CST)
  • Re: LDB questions/problems (Tue Dec 16 2003 - 22:44:32 CST)
  • Re: clustermatic 4 binaries? (Tue Dec 16 2003 - 22:22:08 CST)
  • Re: restraints (Tue Dec 16 2003 - 22:19:08 CST)
  • Re: Help! unstable simulation - ARG go nuts... (Tue Dec 16 2003 - 22:10:31 CST)
  • Re: Why "fixedAtomsForces on" for constant pressure? (Wed Dec 03 2003 - 16:24:45 CST)
  • Re: IMD on MPI versions of NAMD (Wed Dec 03 2003 - 15:38:04 CST)
  • Re: Binary conversions (Wed Dec 03 2003 - 15:08:17 CST)
  • Re: (Wed Dec 03 2003 - 15:03:46 CST)
  • SC2003 and NAMD support (Fri Nov 14 2003 - 16:41:25 CST)
  • psfgen questions welcome on NAMD-L (Fri Nov 14 2003 - 14:52:22 CST)
  • Re: MOE program and difference between MD and SA? (Fri Nov 14 2003 - 15:20:00 CST)
  • Re: error in starting the minimization (Fri Nov 14 2003 - 14:41:35 CST)
  • Re: dcd files (Fri Nov 14 2003 - 14:36:29 CST)
  • Re: restarting suspended namd jobs (Thu Nov 13 2003 - 15:55:45 CST)
  • Re: Distance-dependent dielectrics in NAMD (Thu Nov 13 2003 - 15:52:31 CST)
  • Re: rotation constraints (Thu Nov 13 2003 - 15:18:49 CST)
  • Re: rotation constraints (Thu Nov 13 2003 - 15:20:49 CST)
  • Re: IBM SP build (Thu Nov 13 2003 - 14:57:20 CST)
  • Re: atoms moving too fast (Fri Nov 07 2003 - 11:10:34 CST)
  • Re: Parameter/topology repository (Fri Nov 07 2003 - 11:05:11 CST)
  • Re: periodic boxes (Fri Nov 07 2003 - 10:47:13 CST)
  • Re: repulsive/hard sphere simulation (Fri Nov 07 2003 - 10:42:57 CST)
  • Re: how to set harmonic constraints to alpha carbon (Fri Nov 07 2003 - 10:37:51 CST)
  • Re: contraint failure in RATTLE algorithm (Fri Nov 07 2003 - 10:33:01 CST)
  • Re: atoms moving too fast (Fri Nov 07 2003 - 10:11:43 CST)
  • Re: excluding water in dcd files (Wed Nov 05 2003 - 13:36:37 CST)
  • Re: about charmm topology file (Wed Nov 05 2003 - 13:15:48 CST)
  • RE: Question about AUTOGENERATE (Wed Nov 05 2003 - 12:38:32 CST)
  • Re: Question about AUTOGENERATE (Mon Nov 03 2003 - 21:43:56 CST)
  • Re: excluding water in dcd files (Mon Nov 03 2003 - 17:21:00 CST)
  • Re: running namd on solaris 5.6 (Thu Oct 30 2003 - 13:41:19 CST)
  • Re: switch for equilibrisation (Tue Oct 28 2003 - 18:11:33 CST)
  • Re: cylindrical boundary conditions (Mon Oct 27 2003 - 13:40:51 CST)
  • Re: pair Interaction and electric field (Mon Oct 27 2003 - 13:22:52 CST)
  • Re: Error Running ubq-get-energy.conf (Wed Oct 22 2003 - 18:50:49 CDT)
  • Re: IMD forces and corresponding energies .. (Wed Oct 22 2003 - 18:16:05 CDT)
  • Re: Scyld cluster (Wed Oct 22 2003 - 16:59:38 CDT)
  • Re: Scyld cluster (Wed Oct 22 2003 - 16:09:42 CDT)
  • Charm++ workshop webcast Oct 20-22 (Fri Oct 17 2003 - 17:41:56 CDT)
  • Re: Autogene angles dihed / patch / psfgen problem (Wed Oct 15 2003 - 13:53:38 CDT)
  • Re: PMEGridSize (Mon Oct 13 2003 - 13:34:44 CDT)
  • Re: 64 bit G5 plans for NAMD (Wed Oct 08 2003 - 17:14:27 CDT)
  • Re: Error Running NAMD (Wed Oct 08 2003 - 11:04:41 CDT)
  • Re: Help with: Constraint failure in RATTLE algorithm (Fri Oct 03 2003 - 13:09:35 CDT)
  • Re: nodelist ignored? (Mon Sep 29 2003 - 14:27:45 CDT)
  • NAMD 2.5 Released (Mon Sep 29 2003 - 14:02:48 CDT)
  • Re: NAMD2.5b2 and amber force field (Mon Sep 29 2003 - 12:34:55 CDT)
  • Re: simulated annealing script (Thu Sep 25 2003 - 18:47:22 CDT)
  • Re: Launching namd with PBS (Wed Sep 24 2003 - 19:58:59 CDT)
  • Re: implicit solvent models (Wed Sep 24 2003 - 14:09:14 CDT)
  • Re: Re: seg fault and namdplot problem (Tue Sep 23 2003 - 21:44:24 CDT)
  • Re: coorfile command fail (Tue Sep 23 2003 - 11:20:13 CDT)
  • Re: hard sphere simulation (Tue Sep 23 2003 - 10:52:14 CDT)
  • Re: Re: seg fault and namdplot problem (Mon Sep 22 2003 - 18:20:20 CDT)
  • Re: hard sphere simulation (Mon Sep 22 2003 - 14:38:11 CDT)
  • NAMD 2.5b3 Released (Fri Sep 19 2003 - 18:02:58 CDT)
  • Re: Minimization Question (Thu Sep 18 2003 - 16:30:49 CDT)
  • Re: output warning in using namd2 "Warning: Not all atoms have unique coordinates." more errors (Wed Sep 17 2003 - 13:07:47 CDT)
  • Re: output warning in using namd2 "Warning: Not all atoms have unique coordinates." (Tue Sep 16 2003 - 21:19:03 CDT)
  • Re: segmentation fault (Tue Sep 16 2003 - 15:27:10 CDT)
  • NAMD 2.5b2 Released (Mon Sep 15 2003 - 19:51:49 CDT)
• Joey Harriman
  • Re: CCL:where to find the force field parameters for F and P atom? (Fri Dec 12 2003 - 09:22:15 CST)
• John Saeger
  • Re: problems on Fedora Core 3 (Thu Dec 30 2004 - 13:20:16 CST)
• John Stone
  • Re: vmd-l: Autoionize plugin problem (Thu Dec 16 2004 - 11:30:21 CST)
  • Re: vmd-l: convert DCD files to GROMACS .XTC format (Tue Aug 31 2004 - 15:11:09 CDT)
  • Re: vmd-l: rmsd problem (Tue Aug 31 2004 - 15:11:47 CDT)
  • Re: render format (Mon Aug 02 2004 - 13:14:50 CDT)
  • Re: vmd-l: incompatibility between VMD & NAMD for reading Amber crd files (Mon Jun 21 2004 - 14:53:13 CDT)
  • Re: vmd-l: incompatibility between VMD & NAMD for reading Amber crd files (Mon Jun 21 2004 - 09:58:31 CDT)
  • Re: Hybond calulator and display (Fri Jan 16 2004 - 13:07:09 CST)
  • Re: vmd-l: running vmd in batch mode (Thu Nov 06 2003 - 19:26:27 CST)
• Jorge Pikunic
  • CMAP in CHARMM force field (Fri Oct 08 2004 - 12:27:47 CDT)
  • tcl scripting interface in namd 2.5 for IBM-SP (Mon Jun 28 2004 - 16:23:14 CDT)
  • gromacs/gromos96 force field (Wed Jun 09 2004 - 11:11:30 CDT)
• Josef Scheiber
  • Solvent mixture (Thu Nov 04 2004 - 02:29:17 CST)
  • Re: how to generate your own pdb file (Sat May 15 2004 - 04:28:47 CDT)
  • Problem using Gromacs topology file (Fri May 14 2004 - 03:59:24 CDT)
  • NAMD and Vega? (Wed Feb 04 2004 - 05:04:01 CST)
  • Re: PSF generation (Mon Dec 08 2003 - 02:50:37 CST)
• Joseph E. Curtis, Ph. D.
  • constant angle NPT simulation (Thu Nov 04 2004 - 12:16:21 CST)
• Juan Alfredo Freites
  • Re: What, if no temperatue control specified? (Thu Apr 22 2004 - 11:54:16 CDT)
  • Re: Constant pressure contril (Sat Feb 28 2004 - 20:18:51 CST)
  • flexible cell (Sat Jan 03 2004 - 21:44:05 CST)
  • flexible cell (Mon Dec 22 2003 - 12:10:32 CST)
  • Re: reading in large water boxes (PDB format)? (Sun Dec 07 2003 - 19:32:09 CST)
  • Re: dcd files (Tue Nov 11 2003 - 15:50:11 CST)
  • Re: Launching namd with PBS (Wed Sep 24 2003 - 20:03:09 CDT)
• Juan Carlos Mobarec
  • Re: Symmetry operations (Mon Aug 23 2004 - 19:21:22 CDT)
  • Fatal Socket error (Thu Apr 08 2004 - 11:05:30 CDT)
• Julius Su
  • implementing angle dependent non-bonded interaction? (Mon May 10 2004 - 13:09:14 CDT)
• junxie_at_uwm.edu
  • RATTLE Alg (Fri Jan 09 2004 - 16:41:51 CST)
  • limit on the number of residues in each segment (Fri Jan 09 2004 - 16:45:31 CST)
• Justin Gullingsrud
  • replica exchange (Mon Aug 30 2004 - 16:09:42 CDT)
  • Re: vmd-l: Protonated GLU/ASP in PSF generation (Sun Aug 29 2004 - 21:01:52 CDT)
• Justyna Jaroniec
  • Getting forces: segmentation violation or illegal instruction (Mon Mar 22 2004 - 11:09:25 CST)
• jz7_at_duke.edu
  • question about autogen in topology file (Thu Jun 10 2004 - 13:41:00 CDT)
  • question about running equilibration in NAMD (Tue Jun 08 2004 - 14:25:41 CDT)
  • about this bug alert (Thu Jun 03 2004 - 09:46:54 CDT)
  • Re: question about using Amber force field in namd (Wed Jun 02 2004 - 16:13:14 CDT)
  • question about using Amber force field in namd (Wed Jun 02 2004 - 09:35:54 CDT)
• Jérôme Hénin
  • Re: (Thu Jul 01 2004 - 04:47:55 CDT)
• Jérôme Hénin
  • Re: xsc information in the dcd file? (Wed Dec 15 2004 - 12:22:39 CST)
  • Re: Variation of results in iterations (Mon Dec 06 2004 - 19:01:32 CST)
  • Re: Question:about harmonic restraint decrease! (Fri Nov 26 2004 - 03:22:51 CST)
  • Re: Writing pdb file.. easier way? (Thu Nov 18 2004 - 17:28:36 CST)
  • Re: Tcl dihedral restraints in CG minimisation (Tue Nov 02 2004 - 18:24:07 CST)
  • Re: To PME , Do the simulation need a neutral charged system? (Tue Sep 21 2004 - 05:16:26 CDT)
  • Re: binding constant (Mon Sep 20 2004 - 17:16:43 CDT)
  • Re: DPPC (Mon Aug 30 2004 - 11:48:39 CDT)
  • Direction of the force in Pair interactions (Tue Aug 24 2004 - 03:46:33 CDT)
  • Re: How to do pH simulation on NAMD? (Fri Jul 16 2004 - 05:00:03 CDT)
  • Re: ***** SPAM POSSIBLE ***** Warning: Not all atoms have unique coordinates. (Thu Jul 08 2004 - 11:01:54 CDT)
  • Re: Simulated Annealing Config (Tue Jun 15 2004 - 12:20:45 CDT)
  • psfgen : wrong guess for leucine hydrogen (Tue Jun 15 2004 - 10:33:47 CDT)
  • Re: Fw: Calculating Free Energy Change (Fri Apr 23 2004 - 16:07:52 CDT)
  • Re: Fw: Calculating Free Energy Change (Fri Apr 23 2004 - 15:00:25 CDT)
  • Re: What, if no temperatue control specified? (Fri Apr 23 2004 - 14:19:48 CDT)
  • Feedback on "alchemify" tool (Thu Apr 08 2004 - 10:52:31 CDT)
  • A tool to set up alchemical FEP transformations (Mon Mar 29 2004 - 10:27:12 CST)
  • Re: Tcl: loadtotalforces (Mon Mar 29 2004 - 07:33:29 CST)
  • Re: FEP calculations: defining hybrid residues (Wed Mar 24 2004 - 11:55:54 CST)
  • Re: FEP and restraints (Tue Mar 23 2004 - 14:42:12 CST)
  • Re: Is it necessary to neutralize the system with NAMD program? (Fri Mar 19 2004 - 04:39:06 CST)
  • Re: temp coupling coefficients (Tue Mar 02 2004 - 15:39:24 CST)
  • Re: temp coupling coefficients (Tue Mar 02 2004 - 03:58:28 CST)
  • Re: Constant pressure contril (Sun Feb 29 2004 - 02:41:07 CST)
  • Re: Constant pressure contril (Sat Feb 28 2004 - 17:50:46 CST)
  • Re: electron density calculations of lipid bilayers (Mon Feb 23 2004 - 01:47:11 CST)
  • Re: Langevin dynamics (Thu Feb 19 2004 - 15:33:20 CST)
  • Re: langevin with waterbox ? (Thu Feb 19 2004 - 13:43:04 CST)
  • Re: langevin with waterbox ? (Thu Feb 19 2004 - 11:48:13 CST)
  • Re: Argon solvent (Tue Feb 17 2004 - 12:03:16 CST)
  • Dihedral restraint : question closed (Mon Jan 12 2004 - 05:04:49 CST)
  • Dihedral restraint (Sun Jan 11 2004 - 13:08:05 CST)
  • Re: total energy stuck between two levels (Wed Jan 07 2004 - 02:42:33 CST)
  • Re: Basic question. (Tue Dec 02 2003 - 13:50:38 CST)
  • Re: how can I know which type HIS belong to?(HSD,HSE,HSP) (Sat Nov 29 2003 - 04:37:30 CST)
  • Re: How to do FEP simulations to calculate the absolute free energy of solvation? (Sat Nov 15 2003 - 08:30:50 CST)
  • Re: How to do FEP simulations to calculate the absolute free energy of solvation? (Sat Nov 15 2003 - 04:27:35 CST)
  • Re: tcl interface (Thu Nov 13 2003 - 05:16:20 CST)
  • Re: fixed atoms parameters (Fri Nov 07 2003 - 16:17:48 CST)
• Kamp, Marc vander
  • RE: Direction of the force in Pair interactions (Wed Aug 25 2004 - 01:29:18 CDT)
  • RE: Need to add Hydrogens to over 300 distinct PDB's (Tue Aug 10 2004 - 09:46:15 CDT)
  • pair interaction forces (Mon Jul 26 2004 - 03:24:20 CDT)
  • RE: fixed particles (Sat Jul 17 2004 - 03:20:33 CDT)
  • RE: cellBasisVector x,y,z values (Thu Jul 08 2004 - 10:18:42 CDT)
  • RE: PME off (Tue Jul 06 2004 - 01:50:24 CDT)
  • RE: COM position (Tue Jul 06 2004 - 01:40:01 CDT)
  • RE: Cell Basis Vectors (Mon Jul 05 2004 - 09:46:24 CDT)
  • RE: Amber94 files in CHARMM format (Wed Jun 23 2004 - 10:08:47 CDT)
  • RE: Temperature reassignment problem (Wed Jun 23 2004 - 05:13:34 CDT)
  • RE: vmd-l: incompatibility between VMD & NAMD for reading Amber crd files (Tue Jun 22 2004 - 04:20:16 CDT)
  • RE: vmd-l: incompatibility between VMD & NAMD for reading Amber crd files (Mon Jun 21 2004 - 14:39:05 CDT)
  • incompatibility between VMD & NAMD for reading Amber crd files (Mon Jun 21 2004 - 07:33:11 CDT)
  • setting constraints to off in execution script (Mon Jun 21 2004 - 04:20:26 CDT)
  • Temperature reassignment problem (Mon Jun 21 2004 - 04:19:03 CDT)
  • RE: about psf file (Wed Jun 16 2004 - 11:34:51 CDT)
  • RE: psfgen problem (Wed Jun 09 2004 - 04:22:00 CDT)
  • psfgen problem (Tue Jun 08 2004 - 04:53:39 CDT)
  • RE: question about using Amber force field in namd (Thu Jun 03 2004 - 01:19:12 CDT)
• Ken Sale
  • psfgen (Wed Jul 21 2004 - 15:14:43 CDT)
  • Re: compiling NAMD (Wed Apr 07 2004 - 19:23:07 CDT)
  • 64 bit G5 plans for NAMD (Wed Oct 08 2003 - 14:01:39 CDT)
• klsale
  • Psfgen (Wed Jul 21 2004 - 14:57:56 CDT)
  • Re: Compiling on G5 using xlC (Thu Feb 26 2004 - 15:38:47 CST)
  • <no subject> (Thu Feb 26 2004 - 13:02:36 CST)
• ladam
  • AMBER FF and pmf (Thu May 06 2004 - 03:33:34 CDT)
• Laura De Luca
  • Layers (Tue Nov 16 2004 - 10:00:07 CST)
• lc_at_chem.au.dk
  • Re: problems on Fedora Core 3 (Fri Dec 31 2004 - 13:10:04 CST)
  • estradiol (Tue Aug 31 2004 - 06:56:44 CDT)
• Leandro Martinez
  • Sample Configuratiion files (Wed Nov 03 2004 - 15:40:38 CST)
  • Re: output to multiple files (Tue Oct 26 2004 - 13:09:26 CDT)
  • output to multiple files (Thu Oct 21 2004 - 12:06:52 CDT)
  • Re: Compilation on an Opteron Server SuSE Linux Enterprise System Version 8 (Wed Oct 20 2004 - 09:30:57 CDT)
  • Re: Compilation on an Opteron Server SuSE Linux Enterprise System Version 8 (Wed Oct 20 2004 - 08:27:50 CDT)
  • Re: Compilation on Opteron (Wed Aug 25 2004 - 13:35:13 CDT)
  • Re: Clustermatic with SCSI (Thu Aug 19 2004 - 07:12:57 CDT)
  • Clustermatic with SCSI (Wed Aug 18 2004 - 18:15:11 CDT)
  • Parameters for iodine atoms (Thu Aug 05 2004 - 12:55:28 CDT)
  • Re: Simulation with ammonia (Fri Jun 04 2004 - 13:13:45 CDT)
  • Re: How do we know the velocity? (Thu Jun 03 2004 - 11:47:05 CDT)
  • Margin violation (Tue Jun 01 2004 - 08:10:20 CDT)
  • Re: NPT calculations in NAMD (Tue Jun 01 2004 - 07:17:58 CDT)
  • 32 vs. 64 bits (Fri May 14 2004 - 08:07:14 CDT)
  • Re: Atom number limitations? (Fri Apr 30 2004 - 08:16:19 CDT)
  • clustering (Fri Mar 12 2004 - 07:15:35 CST)
  • some cluster questions (Wed Feb 18 2004 - 07:51:13 CST)
  • geometric mean (Thu Jan 29 2004 - 07:53:58 CST)
• Lei Guo
  • Re: langevin with waterbox ? (Thu Feb 19 2004 - 13:48:36 CST)
  • Re: langevin with waterbox ? (Thu Feb 19 2004 - 13:12:01 CST)
  • Molecular stress tensor (Sat Dec 20 2003 - 16:50:17 CST)
• LEWYN LI
  • Re: more than 99999 atoms in PDB files (Mon Dec 13 2004 - 16:53:26 CST)
  • Re: namdplot (Thu Dec 09 2004 - 11:17:33 CST)
  • Re: Writing pdb file.. easier way? (Thu Nov 18 2004 - 16:29:36 CST)
  • Re: Layers (Tue Nov 16 2004 - 13:38:13 CST)
  • loadtotalforces: 1000+ pN per atom! (Thu Nov 04 2004 - 20:10:07 CST)
  • Re: calculate the binding energy or binding free energy? (Thu Sep 02 2004 - 14:27:03 CDT)
  • Re: Questions on periodic boundary condition (Thu Sep 02 2004 - 11:00:47 CDT)
  • Questions on periodic boundary condition (Thu Sep 02 2004 - 00:38:24 CDT)
• li
  • Re: Generating topology file (Tue Nov 16 2004 - 01:11:51 CST)
  • Re: Generating topology file (Sun Nov 14 2004 - 02:45:43 CST)
  • Re: Generating topology file (Thu Nov 11 2004 - 04:03:37 CST)
  • xsc file reading and segmentation fault (Sat Nov 06 2004 - 20:16:28 CST)
  • Constraint failure in RATTLE again (Sat Nov 06 2004 - 20:13:26 CST)
  • Re: Compiling NAMD on IA64 cluter (Thu Nov 04 2004 - 05:48:16 CST)
  • BUG ALERT: Hydrogen group error caught in rattle1 (Sun Oct 31 2004 - 05:44:31 CST)
  • Compiling NAMD on IA64 cluter (Tue Oct 26 2004 - 19:28:34 CDT)
  • Re: TCL: can't use floating-point value as operand of "-" (Mon Sep 27 2004 - 21:57:12 CDT)
  • TCL: can't use floating-point value as operand of "-" (Mon Sep 27 2004 - 03:16:52 CDT)
  • pulling plus restraint (Thu Sep 16 2004 - 03:56:47 CDT)
  • Re: psfgen : wrong guess for leucine hydrogen (Wed Jun 16 2004 - 01:58:18 CDT)
  • calculate energy with water excluded (Mon May 17 2004 - 01:04:39 CDT)
  • can i restrain the center of molecule in aqueous solution? (Tue Apr 20 2004 - 03:43:12 CDT)
  • simulations ceased without any hint (Thu Apr 15 2004 - 22:23:13 CDT)
  • fix or Harmonic constraint ? (Wed Apr 14 2004 - 02:05:19 CDT)
  • BUG ALERT: Stray PME grid charges detected. (Fri Apr 09 2004 - 22:04:45 CDT)
  • periodic cell has become too small (Thu Apr 08 2004 - 02:32:31 CDT)
  • psfgen question (Fri Mar 26 2004 - 01:06:21 CST)
  • BUG ALERT: Bad global exclusion count! (Mon Mar 03 2008 - 17:56:01 CST)
  • Re: warnings during NAMD simulations. (Sat Feb 23 2008 - 08:43:42 CST)
  • segmantation violation (Tue Feb 12 2008 - 09:13:36 CST)
  • water box is too small (Mon Feb 11 2008 - 08:37:46 CST)
  • Warning: 1 margin violations (Sun Feb 10 2008 - 15:12:43 CST)
  • Warning: 8 margin violations (Sat Jan 05 2008 - 10:05:25 CST)
  • (no subject) (Mon Dec 29 2008 - 16:46:32 CST)
• Liu, Zhanwu
  • RE: radial distribution function (Fri Aug 13 2004 - 08:40:51 CDT)
  • Pair interaction calculations in precompiled NAMD (Mon Feb 02 2004 - 05:34:03 CST)
  • different dielectric constant during simulation (Wed Dec 17 2003 - 10:24:30 CST)
  • coorfile command fail (Mon Sep 22 2003 - 20:53:13 CDT)
• Luis Rosales
  • RE: How do you specify which coordinates are to be fixed? (Thu Oct 28 2004 - 18:32:28 CDT)
  • RE: generating psf files (and more!) (Tue Sep 14 2004 - 17:40:20 CDT)
  • Minimization questions... (Mon Sep 13 2004 - 19:53:16 CDT)
• Lv Shouqin
  • how to get hydrogen-bond energy? (Tue Aug 17 2004 - 21:34:17 CDT)
  • questions about "psfgen". (Sat Jun 12 2004 - 00:12:14 CDT)
  • warnings during NAMD simulations. (Fri Feb 20 2004 - 06:25:12 CST)
  • for help from all! (Sat Feb 14 2004 - 23:14:38 CST)
• Maira Aguilar
  • mean square displacemente and diffusion of water at T=298 K (Thu Aug 12 2004 - 18:44:16 CDT)
• Manali Mehendale
  • Questions (Mon Jul 19 2004 - 14:08:10 CDT)
  • langevin with waterbox ? (Thu Feb 19 2004 - 10:41:16 CST)
• Marc Baaden
  • IMD forces and corresponding energies .. (Wed Oct 22 2003 - 16:36:35 CDT)
• Marcela Madrid
  • render format (Mon Aug 02 2004 - 13:15:17 CDT)
• Marcela P.Aliste
  • restart simulation (Mon May 10 2004 - 16:01:28 CDT)
• Marek Dynowski
  • Re: Compilation on an Opteron Server SuSE Linux Enterprise System Version 8 (Thu Oct 21 2004 - 03:03:54 CDT)
  • Re: Compilation on an Opteron Server SuSE Linux Enterprise System Version 8 (Wed Oct 20 2004 - 10:20:16 CDT)
  • Compilation on an Opteron Server SuSE Linux Enterprise System Version 8 (Wed Oct 20 2004 - 07:26:14 CDT)
  • Simulation with ammonia (Fri Jun 04 2004 - 10:53:27 CDT)
• Mark Abraham
  • Re: octahedral period BCs (Wed Jul 07 2004 - 22:43:57 CDT)
  • Re: octahedral period BCs (Wed Jul 07 2004 - 22:35:44 CDT)
• mashaojie
  • Re: initial temp of simulation (Thu Mar 25 2004 - 07:39:17 CST)
  • Re: construct a protein surrounded by membrane (Fri Mar 19 2004 - 08:41:20 CST)
  • construct a protein surrounded by membrane (Fri Mar 19 2004 - 01:52:37 CST)
  • about guesscoord (Wed Mar 03 2004 - 21:31:05 CST)
• mashaojie163
  • about MCTI output (Mon Dec 27 2004 - 01:29:36 CST)
  • How to decide the protonation of some residues?? (Wed Nov 03 2004 - 07:05:19 CST)
  • Fw: about ExcludeFromPressure (Tue Oct 26 2004 - 21:59:50 CDT)
  • about ExcludeFromPressure (Fri Oct 22 2004 - 03:52:15 CDT)
  • Re: counterion software (Mon Oct 11 2004 - 01:46:24 CDT)
  • Re: vmd-l: how can I get hole program (Sun Oct 10 2004 - 09:23:13 CDT)
  • To PME , Do the simulation need a neutral charged system? (Tue Sep 21 2004 - 04:54:57 CDT)
  • How I can get the hole program? (Sat Sep 18 2004 - 11:08:05 CDT)
  • How I can get the hole program? (Mon Sep 13 2004 - 19:04:36 CDT)
  • about symmetry operations (Wed Jul 07 2004 - 10:23:45 CDT)
  • pmf error (Mon Jun 21 2004 - 10:17:20 CDT)
  • about pmf (Sun Jun 20 2004 - 21:10:00 CDT)
  • about psf file (Wed Jun 16 2004 - 09:33:07 CDT)
  • about membrane protein (Mon Jun 14 2004 - 09:39:41 CDT)
  • start fep calculation (Fri Jun 11 2004 - 21:13:45 CDT)
• Matt Harrington
  • NAMD on OSX built with XLC? (Fri Oct 08 2004 - 13:48:21 CDT)
  • recommendation for 32 CPU cluster: Opteron or ? (Tue Aug 24 2004 - 17:52:03 CDT)
  • opinions on queueing system choices? (Wed Apr 21 2004 - 16:04:31 CDT)
• Matteo Cattaneo
  • Re: 2 domains rigid body rotation with IMD (Sun Dec 07 2003 - 14:33:47 CST)
  • 2 domains rigid body rotation with IMD (Fri Dec 05 2003 - 08:28:22 CST)
• Mauricio Carrillo Tripp
  • charm++ MPICH and Myrinet (Mon Jul 26 2004 - 17:34:53 CDT)
  • RE: COM position (Tue Jul 06 2004 - 12:43:40 CDT)
  • Re: COM position (Tue Jul 06 2004 - 12:12:49 CDT)
  • RE: COM position (Tue Jul 06 2004 - 10:45:53 CDT)
  • COM position (Mon Jul 05 2004 - 14:47:51 CDT)
  • COM position (Fri Jul 02 2004 - 16:54:01 CDT)
  • Fixing position of COM (Wed Jun 30 2004 - 10:42:10 CDT)
  • charmm restart file (Wed Jun 09 2004 - 12:57:47 CDT)
  • pressure profile (Mon Jun 07 2004 - 17:00:51 CDT)
  • (no subject) (Mon Jun 07 2004 - 11:46:18 CDT)
• max
  • Rif: Re: Rif: Re: Rif: Re: Rif: Re: linux cluster trouble (Fri Nov 19 2004 - 03:47:01 CST)
  • linux cluster trouble (Tue Nov 16 2004 - 04:44:36 CST)
  • Rif: Re: linux cluster trouble (Wed Nov 10 2004 - 03:00:42 CST)
• mdcooper
  • charmm and dihedral multiplicity (Thu Dec 16 2004 - 13:19:02 CST)
  • Hessian (Mon Nov 01 2004 - 18:08:24 CST)
  • RE: SMD and minimizations (Tue Oct 26 2004 - 14:31:38 CDT)
  • Gradient Tolerance (Tue Oct 12 2004 - 18:52:43 CDT)
  • (no subject) (Fri Sep 24 2004 - 14:32:46 CDT)
  • Energy Determination (Wed Sep 15 2004 - 17:48:11 CDT)
  • generating psf files (and more!) (Tue Sep 14 2004 - 16:52:38 CDT)
• MERIC AYSE OVACIK
  • FK506 ligand topology file(1FKF) (Thu Oct 28 2004 - 05:29:21 CDT)
  • a different bug alert (Sun Oct 17 2004 - 09:27:23 CDT)
  • Fw: a different bug alert (Sun Oct 17 2004 - 09:21:47 CDT)
  • RE: Output only protein .dcd (Wed Sep 15 2004 - 02:23:03 CDT)
  • Re: Common Problem!: Periodic cell has become too small for original patch grid! (Mon Jul 12 2004 - 03:25:04 CDT)
• Michael Chen
  • ATOMS moving too fast (Thu May 20 2004 - 09:50:23 CDT)
  • "Constrain failure" in NAMD (Fri May 07 2004 - 14:43:41 CDT)
• Michael Grabe
  • Re: How I can run two simulations one after an other (Tue Dec 14 2004 - 15:15:36 CST)
  • Re: Working on cluster to do umbrella sampling (Mon Nov 22 2004 - 13:47:14 CST)
  • gcc and G5 Xserves (Mon Nov 15 2004 - 02:06:03 CST)
  • PME off (Mon Jul 05 2004 - 17:21:47 CDT)
  • Re: Energy minimization at NAMD (Tue Jun 15 2004 - 16:55:01 CDT)
  • urestraint (Thu May 13 2004 - 16:24:35 CDT)
  • FEP and restraints (Tue Mar 23 2004 - 13:45:32 CST)
  • Re: adding ions (Mon Mar 22 2004 - 14:36:35 CST)
  • restraints (Wed Feb 25 2004 - 15:47:31 CST)
  • (no subject) (Thu Feb 19 2004 - 14:29:21 CST)
  • (no subject) (Fri Jan 23 2004 - 17:22:54 CST)
  • dielectric (Wed Dec 17 2003 - 11:30:59 CST)
  • restraints (Mon Dec 15 2003 - 20:04:29 CST)
  • binary troubles (Fri Dec 05 2003 - 13:14:54 CST)
  • configuration files (Wed Nov 19 2003 - 16:38:24 CST)
  • lipids (Fri Nov 14 2003 - 02:07:21 CST)
  • Re: high temperature, 498K, unfolding simulations (Thu Nov 13 2003 - 12:31:28 CST)
  • periodic boxes (Mon Nov 03 2003 - 23:13:50 CST)
• Mike Bradley
  • truncated octahedron boundary conditions (Wed Jul 21 2004 - 16:26:09 CDT)
• Mike Grommet
  • Re: problems compiling charm++ for clustermatic 4 (Tue Dec 16 2003 - 08:47:52 CST)
  • clustermatic 4 binaries? (Tue Dec 16 2003 - 01:05:59 CST)
  • Help with NAMD + Clustermatic 4 please (Sun Dec 14 2003 - 01:01:55 CST)
• Mike McCallum
  • Re: NAMD parser (Thu Apr 29 2004 - 17:03:02 CDT)
  • Fwd: vmd-l: MOE discussion (Wed Apr 28 2004 - 23:11:43 CDT)
  • Re: What, if no temperatue control specified? (Thu Apr 22 2004 - 09:43:13 CDT)
  • Re: Converting PSF TYPES: from XPLOr to CHARMM (Tue Apr 13 2004 - 09:08:04 CDT)
  • Re: Generating psf files for non-proteins (Thu Apr 08 2004 - 16:22:43 CDT)
  • _alloca undefined symbol (OS X/XL compiler) (Fri Apr 02 2004 - 18:29:26 CST)
• MinSoo Kim
  • thankyou (Fri Jan 30 2004 - 12:54:32 CST)
  • psfgen question (Fri Jan 30 2004 - 04:00:35 CST)
  • generating psf for RNA using psfgen (Fri Jan 30 2004 - 01:53:40 CST)
• Mithun Mitra
  • Heteroatom entries (Tue Apr 27 2004 - 10:17:00 CDT)
• Mounir Tarek
  • Re: linux cluster trouble (Tue Nov 09 2004 - 08:43:03 CST)
  • Re: linux cluster trouble (Tue Nov 09 2004 - 06:27:55 CST)
  • charamrun / Rocks distribution problem (Mon Oct 25 2004 - 10:20:28 CDT)
• mpappala_at_unict.it
  • linux cluster trouble (Tue Nov 09 2004 - 05:47:48 CST)
• myang
  • Atom type explaination for NAMD (Wed May 26 2004 - 18:04:05 CDT)
  • Why Vmd didn't show the Pt-Cl bond (Wed May 19 2004 - 18:46:31 CDT)
  • RE: Where to download the inorganic pdb file (Wed May 19 2004 - 14:02:49 CDT)
  • Where to download the inorganic pdb file (Wed May 19 2004 - 00:49:05 CDT)
  • how to generate your own pdb file (Thu May 13 2004 - 00:12:45 CDT)
• nalianarmen
  • Suse 9.0 or Fedora Core 1.0 (Thu Jul 01 2004 - 23:37:18 CDT)
  • New cluster configuration? (Fri May 07 2004 - 17:19:11 CDT)
  • rsh on nodes (Mon May 03 2004 - 23:30:38 CDT)
• Narender Singh
  • Vaccum simulation (Wed Dec 08 2004 - 10:57:48 CST)
• nasrat kamal
  • phase equilibria using NAMD (Wed Jul 21 2004 - 07:33:45 CDT)
• Nathalie Reuter
  • namd on PPC, linux (Wed Jun 23 2004 - 04:40:05 CDT)
  • Re: I have known how to find and click the atoms accurately and easily. (Fri Dec 05 2003 - 02:16:29 CST)
  • nodelist ignored? (Mon Sep 29 2003 - 12:26:51 CDT)
• Neema Salimi
  • Re: Writing pdb file.. easier way? (Thu Nov 18 2004 - 16:54:58 CST)
  • # of processors (Mon Mar 29 2004 - 13:02:30 CST)
  • CoM motion not removed (Wed Feb 18 2004 - 13:00:22 CST)
  • Momenta output format (Mon Feb 02 2004 - 13:59:45 CST)
• Nicholas M Glykos
  • Re: DIHEDral drift [2] ? (Wed Jun 30 2004 - 13:08:14 CDT)
  • DIHEDral drift [2] ? (Wed Jun 30 2004 - 09:26:43 CDT)
  • DIHEDral drift ? (Thu Jun 10 2004 - 13:15:09 CDT)
  • NAMD on OpenMosix. (Sat Feb 14 2004 - 10:40:44 CST)
• Nikolai Skrynnikov
  • best choice of linux cluster to run NAMD (Thu Jul 01 2004 - 03:02:10 CDT)
• nordgren_at_sas.upenn.edu
  • Re: high (or low) pressure readings (Mon Dec 13 2004 - 18:30:51 CST)
  • Re: namdplot (Thu Dec 09 2004 - 05:59:11 CST)
  • Re: Vaccum simulation (Wed Dec 08 2004 - 15:57:10 CST)
  • Re: numerical inaccuracy upon restart (Wed Aug 25 2004 - 22:40:31 CDT)
  • surface pressure/tension (Sun Aug 22 2004 - 02:37:11 CDT)
• Nur Aida Abdul Rahim
  • Output only protein .dcd (Tue Sep 14 2004 - 13:41:38 CDT)
  • Dynamically resizing waterbox (Wed Jul 14 2004 - 14:22:26 CDT)
• Oliver Hucke
  • Re: binding constant (Mon Sep 20 2004 - 15:23:20 CDT)
  • top files for ligands (Wed Oct 08 2003 - 13:02:42 CDT)
• Olya Kravchenko
  • Re: autoionize script (Mon May 17 2004 - 14:00:12 CDT)
  • psfgen: failed on segment (Fri May 14 2004 - 19:46:26 CDT)
  • Re: error: Number of atoms in fixed atoms PDB doesn't match coordinate PDB (Tue May 11 2004 - 17:43:22 CDT)
  • error: Number of atoms in fixed atoms PDB doesn't match coordinate PDB (Thu May 06 2004 - 19:03:49 CDT)
  • Re: NAMD: Force Fields (Fri Apr 23 2004 - 11:32:52 CDT)
  • Re: how to remove all hydrogen atoms from PDB file? (Wed Apr 21 2004 - 16:34:41 CDT)
  • how to remove all hydrogen atoms from PDB file? (Mon Apr 19 2004 - 17:41:22 CDT)
  • Re: how to disable NTER and CTER patches? (Wed Apr 07 2004 - 16:12:19 CDT)
  • how to disable NTER and CTER patches? (Wed Apr 07 2004 - 15:18:54 CDT)
  • minimization problem (Thu Mar 18 2004 - 17:32:17 CST)
  • Heme A topology? (Thu Jan 22 2004 - 17:05:49 CST)
• Oscar Moran
  • Re: vmd-l: POV-Ray (Wed Nov 12 2003 - 03:49:31 CST)
• Ozgur YAZAYDIN
  • psf file for zeolite-water system (Sun Feb 22 2004 - 21:21:03 CST)
• p.w.fowler_at_qmul.ac.uk
  • NAMD on the TeraGrid (Thu Jul 15 2004 - 05:12:47 CDT)
  • Re: cellBasisVector x,y,z values (Thu Jul 08 2004 - 10:30:31 CDT)
  • NAMD2.5 and the TeraGrid (Wed Jul 07 2004 - 06:02:40 CDT)
• Peter Bazeley
  • restart files after minimization? (Thu Dec 23 2004 - 18:52:53 CST)
  • HEM residue in NAMD (Tue Nov 02 2004 - 02:23:50 CST)
• Peter Jones
  • Charmm27 Xplor format (Tue Nov 30 2004 - 03:56:22 CST)
  • Clustermatic PCI IDs (Thu Nov 11 2004 - 22:54:37 CST)
  • eigenvector projections (Mon Nov 08 2004 - 23:41:36 CST)
  • Re: octahedral period BCs (Wed Jul 07 2004 - 21:34:52 CDT)
  • Re: NPT calculations in NAMD (Mon May 31 2004 - 22:04:51 CDT)
  • constraintScaling parameter (Sun Mar 14 2004 - 10:33:40 CST)
  • octahedral period BCs (Fri Mar 12 2004 - 08:01:13 CST)
  • temp coupling coefficients (Tue Mar 02 2004 - 01:03:53 CST)
  • DOWSER (Mon Dec 08 2003 - 02:26:35 CST)
  • (no subject) (Sun Oct 19 2003 - 23:56:25 CDT)
  • PMEGridSize (Fri Oct 10 2003 - 02:08:19 CDT)
• Peter Spijker
  • Re: NAN GRADIENT TOLERANCE - & - RESTARTING CONJUGATE GRADIENT ALGORITHM (Thu May 20 2004 - 12:47:57 CDT)
  • NAN GRADIENT TOLERANCE - & - RESTARTING CONJUGATE GRADIENT ALGORITHM (Wed May 19 2004 - 18:30:57 CDT)
  • Re: Generate PSF structure (Mon Mar 08 2004 - 12:23:12 CST)
  • Generate PSF structure (Mon Mar 08 2004 - 12:01:28 CST)
• Philip Blood
  • covalent bonds across periodic boundaries (Sat Nov 27 2004 - 11:39:33 CST)
• Pijush Ghosh
  • Re: Variation of results in iterations (Mon Dec 06 2004 - 22:00:21 CST)
  • Variation of results in iterations (Mon Dec 06 2004 - 17:25:43 CST)
  • RE: Cell Basis Vector. (Wed Sep 08 2004 - 23:20:22 CDT)
  • Cell Basis Vector. (Tue Sep 07 2004 - 18:28:46 CDT)
• PQCHEN
  • Topology and parameters files for FAD cofator (Fri Nov 28 2003 - 04:04:55 CST)
  • something about the TIP3P water model (Wed Nov 26 2003 - 20:05:59 CST)
  • Re: How to do FEP simulations to calculate the absolute free energy of solvation? (Sat Nov 15 2003 - 05:43:48 CST)
  • How to do FEP simulations to calculate the absolute free energy of solvation? (Fri Nov 14 2003 - 22:24:01 CST)
• Rad Balu
  • Re: psfgen issue (Sun Jun 06 2004 - 22:03:07 CDT)
  • psfgen issue (Sat Jun 05 2004 - 12:49:34 CDT)
  • Re: Single point energy calculation (Mon May 31 2004 - 04:13:16 CDT)
  • NAMD C++ API (Sat May 29 2004 - 17:58:42 CDT)
• Ragan Robertson
  • saving forces using loadforces (Sat Dec 11 2004 - 15:39:42 CST)
• Randy Crawford
  • Error opening XSC output file...Invalid argument (Thu Aug 26 2004 - 13:48:38 CDT)
  • Has NAMD been ported to Itanium2 + Linux? (Tue Aug 10 2004 - 10:06:44 CDT)
  • IA64 and MPICH and mpiexec runtime shmem errors (Thu Aug 05 2004 - 14:38:06 CDT)
• Raymond C. Fort Jr.
  • Sample Configuratiion files (Wed Nov 03 2004 - 14:59:44 CST)
  • Error in temperature calculation (Fri Sep 24 2004 - 13:57:08 CDT)
  • Temperature (Mon Aug 30 2004 - 12:47:07 CDT)
  • Cell Basis Vectors (Mon Jul 05 2004 - 07:57:53 CDT)
  • Error Running ubq-get-energy.conf (Thu Oct 16 2003 - 12:13:35 CDT)
  • Error Running NAMD (Wed Oct 08 2003 - 08:18:00 CDT)
• Rene Salmon
  • Re: clustermatic 4 and 5 Namd/charm (Fri Dec 31 2004 - 10:08:21 CST)
  • clustermatic 4 and 5 Namd/charm (Thu Dec 30 2004 - 17:49:47 CST)
• Richard Brown
  • cluseter node freezes while running namd 2.5/2.5b1 (Sat Oct 18 2003 - 22:48:30 CDT)
• Robert Brunner
  • Re: Variation of results in iterations (Mon Dec 06 2004 - 21:15:00 CST)
  • Re: NAMD Source (Fri Nov 19 2004 - 10:54:16 CST)
• Rowan Hargreaves
  • Re: cff91 force field in namd + A Question (Wed Aug 25 2004 - 12:06:18 CDT)
  • cff91 force field in namd (Mon Aug 23 2004 - 06:35:38 CDT)
• Roy Campbell
  • Clustermatic 4: Charmrun> error 1 attaching to node: (Fri Sep 10 2004 - 12:24:05 CDT)
• Ruxandra Dima
  • problems on Fedora Core 3 (Tue Dec 28 2004 - 22:48:43 CST)
  • GdHCl parameters (Thu Mar 18 2004 - 16:18:16 CST)
  • Urea and GdHCl parameters (Mon Mar 15 2004 - 12:01:51 CST)
  • Re: error in starting the minimization (Wed Nov 12 2003 - 18:20:53 CST)
  • error in starting the minimization (Wed Nov 12 2003 - 17:06:44 CST)
• Saladino, Alex
  • Tcl load (Thu Jul 15 2004 - 14:52:25 CDT)
  • Reset reference position (Wed Jul 14 2004 - 13:46:38 CDT)
  • Reset (Tue Jul 13 2004 - 10:28:49 CDT)
  • Minimization Question (Thu Sep 18 2003 - 15:25:08 CDT)
• Sarah Harris
  • Distance-dependent dielectrics in NAMD (Mon Nov 10 2003 - 05:05:36 CST)
• Sarah Williams
  • Thermostat problems (Tue Jul 20 2004 - 04:13:19 CDT)
• Sascha Tayefeh
  • Re: [Periodic Boundary]: from charmm to namd (Tue Nov 02 2004 - 12:46:02 CST)
  • [Periodic Boundary]: from charmm to namd (Tue Nov 02 2004 - 09:08:42 CST)
  • firsttimestep: simple question (Fri Oct 29 2004 - 16:16:56 CDT)
• Satyavani Vemparala
  • initial translation of the system (Fri Apr 09 2004 - 14:17:09 CDT)
  • FEP calculations: defining hybrid residues (Wed Mar 24 2004 - 10:04:53 CST)
  • large increase in pressure after minimization (Sun Mar 21 2004 - 20:23:33 CST)
  • Solvate Package (Wed Mar 10 2004 - 18:22:54 CST)
  • FIRSTTIMESTEP in config file (Wed Mar 10 2004 - 05:49:55 CST)
  • generating PSF files using CHARMM for FEP calculations (Thu Mar 04 2004 - 11:56:07 CST)
  • PME grid sizes (Thu Feb 26 2004 - 17:05:01 CST)
  • temperature coupling in NAMD (Tue Feb 24 2004 - 15:09:57 CST)
  • electron density calculations of lipid bilayers (Sun Feb 22 2004 - 17:45:58 CST)
  • Alchemical FEP calculations in NAMD (Fri Feb 20 2004 - 22:09:43 CST)
  • Temperature control methods in NAMD (Sat Feb 14 2004 - 07:32:22 CST)
  • Compiling NAMD on Tungsten.ncsa (Wed Feb 11 2004 - 20:18:12 CST)
  • Temperature control methods in NAMD (Wed Feb 11 2004 - 18:07:13 CST)
  • concatenating two DCD files (Tue Feb 10 2004 - 17:28:27 CST)
  • Source code for NAMD (Tue Feb 10 2004 - 10:30:13 CST)
  • problem:psfgen- not unique coordinates (Mon Feb 09 2004 - 15:14:02 CST)
• Scott Stagg
  • Launching namd with PBS (Wed Sep 24 2003 - 19:12:14 CDT)
• Scott, Greg
  • Lithium (Thu Apr 29 2004 - 22:01:52 CDT)
  • RE: Lithium (Wed Apr 28 2004 - 23:30:08 CDT)
  • Lithium (Wed Apr 28 2004 - 22:04:14 CDT)
  • Generating psf files for non-proteins (Thu Apr 08 2004 - 13:08:21 CDT)
• scott.brown_at_abbott.com
  • Problem with Tcl & psfgen (Tue Feb 17 2004 - 13:36:56 CST)
• Sean Michael Whipkey
  • Re: namd and Tcl 8.3.5 (Wed Jul 07 2004 - 16:06:35 CDT)
  • namd and Tcl 8.3.5 (Wed Jul 07 2004 - 09:42:26 CDT)
  • Re: icc compilation problem (Fri Jul 02 2004 - 09:27:55 CDT)
  • icc compilation problem (Thu Jul 01 2004 - 16:19:55 CDT)
• Shahid Qamar
  • How to move COM during minimization? (Wed Dec 15 2004 - 12:03:12 CST)
  • How I can run two simulations one after an other (Tue Dec 14 2004 - 14:30:08 CST)
  • NAMD at Data Star SDSC (Mon Nov 22 2004 - 15:19:11 CST)
  • Job is terminated in the middle (Fri Nov 19 2004 - 11:23:15 CST)
  • How to make a surface (Wed Nov 17 2004 - 14:08:06 CST)
  • How to make a negatively charged surface (Mon Nov 08 2004 - 14:25:30 CST)
  • How can I move an atom by 10nm with a step of 0.1nm (Mon Oct 04 2004 - 17:22:36 CDT)
  • Can we fix the position of two atoms while minimization? (Wed Sep 29 2004 - 15:18:31 CDT)
  • Node list (Wed Aug 18 2004 - 19:25:41 CDT)
  • Position of the Virtual atom (Wed Jul 28 2004 - 16:46:29 CDT)
  • Scale on Force vs Time plot? (Thu Jul 22 2004 - 15:06:53 CDT)
  • Making PSF file (Wed Jul 21 2004 - 16:36:35 CDT)
• Shantenu Jha
  • Re: Has NAMD been ported to Itanium2 + Linux? (Tue Aug 10 2004 - 16:25:28 CDT)
  • Re: Solute KE (Thu Dec 04 2003 - 17:08:23 CST)
  • Solute KE (Thu Dec 04 2003 - 16:36:31 CST)
  • Re: rotational energy, Tcl and environment variable(s) in Linux 2.5 (Thu Dec 04 2003 - 15:59:10 CST)
  • rotational energy, Tcl and environment variable(s) in Linux 2.5 (Sun Nov 30 2003 - 18:47:07 CST)
• Shirley Hui
  • Re: Failed to set coordinate for atom errors! (Mon Dec 20 2004 - 21:39:30 CST)
  • Failed to set coordinate for atom errors! (Mon Dec 20 2004 - 16:32:10 CST)
  • Minimizing and Equilibrating (Thu Nov 18 2004 - 19:05:25 CST)
  • Generating simulation with large conformational changes (Sat Feb 21 2004 - 18:36:12 CST)
  • Fw: Problem with PSFGEN? (Thu Sep 09 2004 - 21:51:53 CDT)
  • Common Problem!: Periodic cell has become too small for original patch grid! (Fri Jul 09 2004 - 15:24:43 CDT)
  • Re: Warning: Not all atoms have unique coordinates. (Thu Jul 08 2004 - 18:15:29 CDT)
  • Re: Warning: Not all atoms have unique coordinates. (Thu Jul 08 2004 - 17:45:47 CDT)
  • Warning: Not all atoms have unique coordinates. (Thu Jul 08 2004 - 09:25:13 CDT)
  • cellBasisVector x,y,z values (Thu Jul 08 2004 - 08:46:16 CDT)
  • Re: psfgen non-bonded atom pairs (Sat May 22 2004 - 12:35:52 CDT)
  • psfgen non-bonded atom pairs (Sat May 22 2004 - 01:08:57 CDT)
  • Calculate Potential Energy (Sat May 15 2004 - 17:20:03 CDT)
  • Re: Hi (Fri Apr 23 2004 - 16:02:54 CDT)
  • Re: Fw: Calculating Free Energy Change (Fri Apr 23 2004 - 15:30:01 CDT)
  • Re: Fw: Calculating Free Energy Change (Fri Apr 23 2004 - 13:44:17 CDT)
  • Fw: Calculating Free Energy Change (Thu Apr 22 2004 - 13:02:07 CDT)
• Shunzhou Wan
  • creating Charmm psf from Xplor format (Wed Feb 04 2004 - 06:32:42 CST)
  • coorfile (Wed Dec 10 2003 - 11:23:46 CST)
• Sichun Yang
  • Gromacs force field paramets: Syntax error in ATOMS (Wed Jun 23 2004 - 03:09:39 CDT)
  • Re: build charm on ia-64 linux (Fri Jun 11 2004 - 21:44:12 CDT)
  • Re: build charm on ia-64 linux (Fri Jun 11 2004 - 19:41:26 CDT)
  • build charm on ia-64 linux (Fri Jun 11 2004 - 18:40:29 CDT)
  • replica-ex NAMD? (Wed May 19 2004 - 12:28:20 CDT)
  • Re: Amber on with H-bond (Thu Mar 04 2004 - 00:15:56 CST)
  • Amber on with H-bond (Wed Mar 03 2004 - 17:59:55 CST)
  • Re: Constant pressure contril (Sun Feb 29 2004 - 22:48:15 CST)
  • Re: Constant pressure contril (Sat Feb 28 2004 - 20:39:58 CST)
  • Re: Constant pressure contril (Sat Feb 28 2004 - 18:32:31 CST)
  • Constant pressure contril (Sat Feb 28 2004 - 17:05:03 CST)
  • Re: Restart using amber force field (Fri Feb 27 2004 - 16:13:25 CST)
  • Restart using amber force field (Fri Feb 27 2004 - 11:30:47 CST)
  • Timestep in restart output (Thu Feb 26 2004 - 12:38:08 CST)
• Simon Sharpe
  • user-supplied conformational restraints (Thu Feb 05 2004 - 14:13:31 CST)
• srinivasa murthy
  • help needed on node list (Tue Sep 16 2003 - 23:36:51 CDT)
• Stern, Julie
  • mimization warnings - bad global exclusion count (Wed Jul 21 2004 - 16:20:34 CDT)
  • margin errors (Fri Jun 18 2004 - 14:48:36 CDT)
  • solvent bands and periodic boundary conditions (Wed May 19 2004 - 10:45:09 CDT)
  • running multiple minimizations (Fri Mar 19 2004 - 09:20:34 CST)
  • undefined loops (Thu Mar 18 2004 - 11:47:39 CST)
  • charmrun vs. miprun and nature of parallelism (Thu Mar 18 2004 - 11:39:39 CST)
• Streiff, John H.
  • Tcl loops in configuration files (Tue Sep 14 2004 - 10:26:12 CDT)
  • Xserve G5 (Fri Aug 27 2004 - 15:37:48 CDT)
  • initial temp of simulation (Fri Mar 19 2004 - 11:35:10 CST)
• Sundaramoorthy, Munirathinam
  • Pair interaction energy (Fri Jan 30 2004 - 10:46:22 CST)
  • Energy units (Tue Dec 30 2003 - 12:21:59 CST)
• surendra negi
  • Fwd: missing atom prob (Mon Nov 01 2004 - 17:58:33 CST)
  • Fwd: PSFgen error (Mon Nov 01 2004 - 17:58:12 CST)
• Suxing Hu
  • Re: Building NAMD with Portland's C++ Comipler (Thu Dec 09 2004 - 21:08:54 CST)
  • Building NAMD with Portland's C++ Comipler (Thu Dec 09 2004 - 12:29:57 CST)
  • Periodic cell size (Wed Dec 08 2004 - 10:06:24 CST)
• Taeho Kim
  • Re: SMD -apply the force via Tcl script (Tue Nov 04 2003 - 11:27:52 CST)
• taeho.kim_at_utoronto.ca
  • Re: Temp in SMD (Fri Nov 28 2003 - 17:53:27 CST)
• ted q
  • Minimization with CHARMM (Sat Feb 07 2004 - 15:56:11 CST)
• tepper_at_amolf.nl
  • Re: Re: numerical inaccuracy upon restart (Mon Sep 06 2004 - 06:30:22 CDT)
• Tim Cm
  • Bringing Up To Temp (Sun Aug 15 2004 - 16:48:42 CDT)
• Tim Isgro
  • Re: how to generate your own pdb file (Fri May 14 2004 - 17:26:00 CDT)
  • Re: restart simulation (Tue May 11 2004 - 00:31:18 CDT)
  • Re: error: Number of atoms in fixed atoms PDB doesn't match coordinate PDB (Tue May 11 2004 - 00:01:55 CDT)
  • Re: Issues with SMD (Mon May 10 2004 - 23:53:13 CDT)
  • Re: initial temp of simulation (Fri Mar 26 2004 - 10:46:49 CST)
  • Re: initial temp of simulation (Thu Mar 25 2004 - 11:11:07 CST)
  • Re: hydrogen bonds in NAMD (Fri Mar 19 2004 - 11:25:47 CST)
  • Re: Generate PSF structure (Tue Mar 09 2004 - 10:24:01 CST)
  • Re: CP3-NH3 error (Thu Mar 04 2004 - 13:56:44 CST)
  • Re: CP3-NH3 error (Tue Mar 02 2004 - 17:31:08 CST)
  • Re: Timestep in restart output (Thu Feb 26 2004 - 21:01:21 CST)
  • Re: problem:psfgen- not unique coordinates (Mon Feb 09 2004 - 20:05:30 CST)
  • Re: Minimization with CHARMM (Mon Feb 09 2004 - 17:04:13 CST)
  • Re: minimization scripts (Mon Feb 09 2004 - 16:53:33 CST)
  • Re: 1QSU (Thu Jan 15 2004 - 15:32:22 CST)
  • Re: Harmonic constraint parameter k (Thu Dec 11 2003 - 18:21:48 CST)
  • Re: how should I set those PMEGridSizeX,Y,Z? (Thu Dec 11 2003 - 18:00:13 CST)
  • Re: how should I set those PMEGridSizeX,Y,Z? (Wed Dec 10 2003 - 14:18:37 CST)
• tsaih_at_ncifcrf.gov
  • capping by psfgen (Sun Apr 04 2004 - 13:36:58 CDT)
  • warning messages in psfgen (Wed Mar 24 2004 - 14:35:43 CST)
  • distance constraints in NAMD (Fri Mar 19 2004 - 07:06:34 CST)
• Uday Chippada
  • Residence time (Tue Dec 28 2004 - 10:58:41 CST)
  • Re: Writing pdb file.. easier way? (Thu Nov 18 2004 - 17:19:14 CST)
  • Writing pdb file.. easier way? (Thu Nov 18 2004 - 15:58:20 CST)
  • Re: Move molecule (Thu Nov 18 2004 - 14:07:50 CST)
  • Move molecule (Thu Nov 18 2004 - 10:18:36 CST)
  • Hydrogen cut off distance (Mon Oct 25 2004 - 16:16:46 CDT)
  • How do we know the velocity? (Thu Jun 03 2004 - 10:17:10 CDT)
  • RE: Hi (Fri Apr 23 2004 - 15:20:56 CDT)
  • Hi (Fri Apr 23 2004 - 12:57:23 CDT)
  • Haptic Device (Fri Apr 02 2004 - 13:55:42 CST)
  • Spring Constant (Mon Mar 29 2004 - 17:48:56 CST)
  • Re: dimer minimisation and psfgen problem (Thu Mar 18 2004 - 14:44:35 CST)
  • Regarding SMD atom and forces (Tue Feb 17 2004 - 12:37:37 CST)
  • Regarding SMD atom and forces (Wed Feb 11 2004 - 16:00:11 CST)
  • How do we combine chains in the end (Sat Jan 31 2004 - 11:37:42 CST)
  • Re: minimization problem - "Bad global exclusion count, possible error!" (Thu Jan 29 2004 - 17:05:54 CST)
  • 1QSU (Thu Jan 15 2004 - 13:45:03 CST)
• Valery Miftakhov
  • NAMD linking problem (Tue Jan 13 2004 - 22:15:59 CST)
• Valodymyr Nechyporuk-Zloy
  • HYP residue and unknown residue type NH2 (Wed Aug 04 2004 - 07:06:47 CDT)
  • HYP parameters (Thu Jul 29 2004 - 03:59:44 CDT)
  • AMBER parameters and SMD (Mon Jul 26 2004 - 04:42:55 CDT)
  • equilibration of protein in water box (Tue Jun 29 2004 - 09:08:01 CDT)
  • Box Dimension (Tue Jun 29 2004 - 09:00:53 CDT)
  • What binaries should I take? (Fri Jun 18 2004 - 03:49:14 CDT)
• Vani Krishna
  • Re: resolved: BUG ALERT: Mother atom with hydrogenGroupSize of 0! (Fri Dec 17 2004 - 18:47:21 CST)
  • Re: charmm and dihedral multiplicity (Fri Dec 17 2004 - 18:46:04 CST)
  • BUG ALERT: Mother atom with hydrogenGroupSize of 0! (Fri Dec 17 2004 - 11:39:30 CST)
  • turning off fixed atoms in the middle of simulation (Wed Dec 15 2004 - 10:42:17 CST)
  • pair-interaction energy (Sun Oct 17 2004 - 17:37:18 CDT)
  • Pair interaction energies: TCL error (Fri Sep 24 2004 - 21:06:30 CDT)
  • Compiling NAMD from SRC: Tungsten@NCSA (Fri Sep 10 2004 - 19:54:55 CDT)
  • Re: Stray PME grid charges (Tue Sep 07 2004 - 21:16:35 CDT)
  • Re: calculate the binding energy or binding free energy? (Thu Sep 02 2004 - 21:13:58 CDT)
  • SMD: Group of atoms COM fixed? (Thu Sep 02 2004 - 20:58:44 CDT)
  • SMD on a group of atoms: Confusion (Wed Sep 01 2004 - 10:47:41 CDT)
  • Protonated GLU/ASP in PSF generation (Sun Aug 29 2004 - 16:23:00 CDT)
  • convert DCD files to GROMACS .XTC format (Sat Aug 28 2004 - 17:43:11 CDT)
  • SMD atoms not read properly! (Tue Aug 10 2004 - 07:49:42 CDT)
  • Torsional barrier(adding parameters) (Mon Aug 02 2004 - 10:11:48 CDT)
  • Torsion potential barrier (low?) in NAMD (Wed Jul 28 2004 - 10:57:56 CDT)
  • PBCwrap: wrapping DCD files (Mon Jun 28 2004 - 22:03:45 CDT)
  • wrapping DCD files (Mon Jun 28 2004 - 14:25:24 CDT)
  • minimum imgae convention (Mon Jun 28 2004 - 09:59:24 CDT)
  • Info about forces on atoms (Thu May 27 2004 - 11:58:32 CDT)
• vivek sharma
  • interaction energy (Thu Dec 23 2004 - 05:36:35 CST)
  • Re: fatal error (Wed Dec 15 2004 - 04:11:45 CST)
  • fatal error (Tue Dec 14 2004 - 00:49:59 CST)
  • Re: namdplot (Thu Dec 09 2004 - 10:38:14 CST)
  • namdplot (Thu Dec 09 2004 - 02:13:26 CST)
• Vlad Cojocaru
  • International PhD Symppozium "DECODING NATURE: HIERARCHY OF INTERACTIONS" (Wed Oct 20 2004 - 11:10:43 CDT)
  • Locally Enhanced Sampling (Tue Mar 02 2004 - 07:46:01 CST)
  • Re: question on Berendsen's temperature coupling method (Fri Jan 23 2004 - 02:54:03 CST)
  • NAMD on p690 IBM cluster (Tue Jan 27 2004 - 03:56:35 CST)
  • test and a short question! (Mon Jan 19 2004 - 08:18:50 CST)
• Volodymyr Nechiporuk-Zloy
  • Re: Paper on Classical treatment for calculating pKas (Mon Mar 15 2004 - 03:31:21 CST)
  • Re: SMD with different pH (Wed Mar 10 2004 - 06:37:39 CST)
  • SMD with different pH (Fri Mar 05 2004 - 07:52:55 CST)
• Wagener, M. (Markus)
  • distance dependant dielectric constant (Fri Feb 27 2004 - 06:58:43 CST)
• Wang Yu
  • Hi (Mon Dec 29 2003 - 07:44:57 CST)
• Wei Fu
  • Langevin Dynamics again (Thu Feb 19 2004 - 15:23:22 CST)
  • Langevin dynamics (Thu Feb 19 2004 - 14:26:13 CST)
  • atom numbers limitation (Wed Feb 18 2004 - 14:43:27 CST)
  • Re:charmm27 (Tue Jan 13 2004 - 19:27:02 CST)
  • charmm27 (Tue Jan 13 2004 - 17:15:49 CST)
  • langevin dynamics (Sun Jan 11 2004 - 15:04:41 CST)
• Wenyu Zhong
  • Re: Compiling NAMD on amd64 (Thu Apr 15 2004 - 06:35:08 CDT)
  • Compiling NAMD on amd64 (Thu Apr 15 2004 - 01:42:17 CDT)
• Wolbach, Jeffrey P \(WOLBACH\)
  • Question about Gradient Tolerance during minimization (Wed Sep 08 2004 - 13:00:15 CDT)
• Xiaobing Tian
  • Re: Help, MD run errors (Sun May 02 2004 - 21:06:58 CDT)
  • Re: NAMD parser (Fri Apr 30 2004 - 14:56:18 CDT)
  • Re: NAMD parser (Thu Apr 29 2004 - 16:25:14 CDT)
  • NAMD parser (Thu Apr 29 2004 - 11:16:35 CDT)
  • questions about set cellBasisVector and a ligand ... (Thu Apr 29 2004 - 10:06:53 CDT)
• Xin Chen
  • pair interaction calculations (Thu Jul 29 2004 - 17:18:36 CDT)
  • How to do pH simulation on NAMD? (Thu Jul 15 2004 - 15:28:50 CDT)
  • How to calculate specific heat capacity in NAMD? (Wed Jul 07 2004 - 10:02:02 CDT)
  • Energy minimization at NAMD (Tue Jun 15 2004 - 15:25:38 CDT)
  • Compiling NAMD on Linux cluster (Fri May 28 2004 - 15:14:12 CDT)
  • Force Calculation in NAMD (Fri May 21 2004 - 13:02:09 CDT)
  • Source file in the tutorial (Thu Apr 22 2004 - 16:58:46 CDT)
  • Re: Restarting problem with Langevin dynamics (Wed Apr 07 2004 - 13:45:39 CDT)
  • Re: Restarting problem with Langevin dynamics (Wed Apr 07 2004 - 01:01:55 CDT)
  • Restarting problem with Langevin dynamics (Tue Apr 06 2004 - 00:05:19 CDT)
  • Restarting problem with Langevin dynamics (Wed Mar 31 2004 - 15:11:58 CST)
• Yang Yang
  • Question about external forces (Tue Apr 27 2004 - 01:55:13 CDT)
  • Parallelization of a code from TCB Summer School 2003 (Fri Apr 16 2004 - 21:54:46 CDT)
• Yanlong Xu
  • topology file for compound (Mon Jul 26 2004 - 12:15:28 CDT)
• ying xiong
  • calculate the binding energy or binding free energy? (Thu Sep 02 2004 - 03:49:40 CDT)
  • how to fix the atoms of backbone ? (Fri Jul 30 2004 - 19:48:23 CDT)
  • (no subject) (Thu Jul 01 2004 - 01:57:18 CDT)
  • how many steps do we need do for energy minimization ? (Tue May 11 2004 - 01:19:39 CDT)
  • tcl script for calculate RMS of MD calculation ? (Sat May 01 2004 - 21:06:04 CDT)
• yingxiong
  • how to fix some atoms? (Mon Mar 08 2004 - 03:55:35 CST)
• yu275197_at_yorku.ca
  • Re: clustering (Fri Mar 12 2004 - 10:57:04 CST)
  • hydrogen bonds during MD (Sat Mar 06 2004 - 11:03:49 CST)
  • (no subject) (Sun Feb 22 2004 - 00:37:27 CST)
  • Re: improving parallel on mac cluster (Tue Feb 10 2004 - 18:23:39 CST)
  • Re: improving parallel on mac cluster (Tue Feb 10 2004 - 16:47:34 CST)
  • clustering macs (Tue Feb 10 2004 - 16:04:58 CST)
  • improving parallel on mac cluster (Mon Feb 09 2004 - 11:44:31 CST)
  • building charm++ on macosX (Sat Feb 07 2004 - 16:51:15 CST)
  • mac clustering (Fri Feb 06 2004 - 23:34:41 CST)
• yxiong_at_mail.ccnu.edu.cn
  • how to read amino acid such as 27, 27A,27B,27C in pdb file? (Mon Jul 19 2004 - 20:45:45 CDT)
  • namd-L: tcl script for calculate RMS of MD calculation (Thu Apr 15 2004 - 03:01:28 CDT)
  • Re: initial temp of simulation (Thu Mar 25 2004 - 19:47:01 CST)
  • Is it necessary to neutralize the system with NAMD program? (Sun Mar 14 2004 - 02:56:41 CST)
  • how to get "the rms force and maximum force" of energy minimization ? (Mon Jan 05 2004 - 23:45:18 CST)
  • different result when I run the same *.conf file many times. (Sat Jan 03 2004 - 05:18:48 CST)
  • Periodic cell has become too small for original patch grid? (Wed Dec 24 2003 - 03:44:58 CST)
  • about HIS residue (Fri Dec 19 2003 - 20:40:35 CST)
  • Re: how should I run NAMD on parallel platform? (Thu Dec 18 2003 - 04:40:58 CST)
  • how should I run NAMD on parallel platform? (Thu Dec 18 2003 - 01:33:14 CST)
  • HIS modification (Wed Dec 17 2003 - 04:37:24 CST)
  • Re: how should I set those PMEGridSizeX,Y,Z? (Wed Dec 10 2003 - 18:51:51 CST)
  • how should I set those PMEGridSizeX,Y,Z? (Wed Dec 10 2003 - 00:13:55 CST)
  • where to find the force field parameters for F and P atom? (Tue Dec 09 2003 - 20:04:01 CST)
  • Re: PSF generation (Sun Dec 07 2003 - 19:12:58 CST)
  • about temperature reassign? (Sat Dec 06 2003 - 03:42:30 CST)
  • I have known how to do a constrained MD before a normal MD (Sat Dec 06 2003 - 02:58:36 CST)
  • problem with flipbinpdb (Sat Dec 06 2003 - 02:33:01 CST)
  • I have known how to find and click the atoms accurately and easily. (Fri Dec 05 2003 - 01:30:48 CST)
  • how to get the plot of selected bond over time? (Thu Dec 04 2003 - 21:38:16 CST)
  • SHAKE algorithm and MD at constant T and P? (Thu Dec 04 2003 - 19:54:15 CST)
  • Re: how to add counterions ? (Tue Dec 02 2003 - 01:54:09 CST)
  • how the charges of those residues of protein(for example LYS) are determined in CHARMM topology file (Mon Dec 01 2003 - 04:27:52 CST)
  • how to add counterions ? (Sun Nov 30 2003 - 04:59:36 CST)
  • Re: how to get Charge of new residue? (Sun Nov 30 2003 - 03:51:26 CST)
  • how to get Charge of new residue? (Fri Nov 28 2003 - 23:29:34 CST)
  • (no subject) (Fri Nov 28 2003 - 20:35:59 CST)
  • how can I know which type HIS belong to?(HSD,HSE,HSP) (Fri Nov 28 2003 - 04:02:05 CST)
  • the Atom velocity is beyond the limit? (Fri Nov 28 2003 - 03:33:03 CST)
  • Re: the problem on segment a ligand in NAMD ? (Fri Nov 28 2003 - 02:02:24 CST)
  • the problem on segment a ligand in NAMD ? (Thu Nov 27 2003 - 21:53:42 CST)
  • Re: problems with psfgen (Thu Nov 27 2003 - 06:57:35 CST)
  • parameter for phosphonate (Wed Nov 26 2003 - 07:23:45 CST)
  • parameter for phosphonate (Wed Nov 26 2003 - 00:14:37 CST)
  • about internal coordinate IC statement of CHARMM force field (Tue Nov 25 2003 - 01:24:23 CST)
  • zinc parameter? (Sun Nov 16 2003 - 02:09:54 CST)
  • MOE program and difference between MD and SA? (Fri Nov 14 2003 - 02:57:25 CST)
• Zheng Gengbin
  • Re: problems compiling charm++ for clustermatic 4 (Tue Dec 16 2003 - 02:21:36 CST)
• zhilei chen
  • problem with running namd on Linux cluster (Mon Jan 19 2004 - 11:51:11 CST)
  • interaction energy (Tue Jan 06 2004 - 13:26:47 CST)
  • Harmonic constraint parameter k (Thu Dec 11 2003 - 08:39:48 CST)
  • forces during SMD (Sun Dec 07 2003 - 10:16:43 CST)
  • About the SMD output file (Fri Dec 05 2003 - 16:17:41 CST)
  • A problem with intermediate files (Mon Nov 10 2003 - 21:52:57 CST)
  • how to set harmonic constraints to alpha carbon (Thu Nov 06 2003 - 15:07:05 CST)
  • about charmm topology file (Wed Nov 05 2003 - 10:00:56 CST)
  • RE: Question about AUTOGENERATE (Tue Nov 04 2003 - 09:48:01 CST)
  • Question about AUTOGENERATE (Mon Nov 03 2003 - 20:50:09 CST)
• Zhong Wenyu
  • Re: Bug in Pair force interaction calculation was fixed? (Wed Oct 27 2004 - 09:26:26 CDT)
  • Bug in Pair force interaction calculation was fixed? (Mon Oct 25 2004 - 22:11:12 CDT)
  • Fw: Constraint failure in RATTLE algorithm (Sun Sep 19 2004 - 02:14:27 CDT)
  • Re: "GRADIENT TOLERANCE: nan", Why? (Thu Jun 03 2004 - 09:02:01 CDT)
  • "GRADIENT TOLERANCE: nan", Why? (Wed Jun 02 2004 - 07:42:50 CDT)
• Zoe Cournia
  • xst format (Thu Nov 27 2003 - 04:17:44 CST)
• κ¿­
  • What the result difference between AMD and Intel CPUS? (Mon Dec 20 2004 - 08:30:14 CST)
  • How to chech the harmonic constraint work normally~ (Thu Dec 16 2004 - 03:21:17 CST)
  • How to treat the terminal residue psfgen in NAMD~ (Mon Nov 29 2004 - 20:11:37 CST)
  • A confused question on amber param and in charmm form~ (Fri Nov 26 2004 - 07:41:55 CST)
  • Question:about equilibration~ (Thu Nov 25 2004 - 22:05:59 CST)
  • Question:about harmonic restraint decrease! (Wed Nov 24 2004 - 22:13:49 CST)
  • Some question about Constraint~ (Sun Nov 14 2004 - 21:02:34 CST)
  • A strange thing about psfgen~ (Sat Nov 13 2004 - 06:21:35 CST)