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NAMD-L: By Author

By Author

2851 messages sorted by: [ date ] [ thread ] [ subject ] [ attachment ]
About this archive

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

• $B:,>k(J $B6Q(J
  • Re: psf file for zeolite-water system (Mon Feb 23 2004 - 02:22:31 CST)
• 13200178 Hendra Tampang Allo
  • error running namd (Mon Aug 01 2005 - 04:39:38 CDT)
• \
  • Re: Another question about MD simulation of a domain. (Tue Sep 27 2005 - 14:15:59 CDT)
  • Re: energy values (Tue Sep 13 2005 - 13:30:50 CDT)
  • Re: moments of inertia, principal axes (Tue Aug 30 2005 - 20:29:08 CDT)
  • Re: Random forces in Langevin temperature control -- three questions (Sun Jul 17 2005 - 12:09:41 CDT)
  • Re: RE: [Scalex86 - linux] FW: segfaults in mm_malloc (Fri Jul 01 2005 - 11:40:25 CDT)
  • Re: solvate and write pdb, psf file. (Thu Apr 28 2005 - 11:33:40 CDT)
  • Re: Analysis of NAMD output with CHARMM (Mon Feb 14 2005 - 12:15:58 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
  • CHARMM compatible Methotrexate params (Thu Nov 24 2005 - 22:17:18 CST)
  • Class I vs Class II force fields (Tue Jul 26 2005 - 00:42:01 CDT)
  • Re: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? (Tue Jun 21 2005 - 01:48:52 CDT)
  • Re: about protonation of HIS in membrane protein (Wed Apr 13 2005 - 19:10:18 CDT)
  • Re: glucose CHARMM force field (Tue Mar 29 2005 - 23:34:00 CST)
  • multiple MD simulations (Mon Mar 28 2005 - 18:29:39 CST)
  • Re: parameters for NAD,NAG,NAP (Thu Feb 03 2005 - 21:14:14 CST)
  • Re: area of a hydrophobic patch (Thu Feb 03 2005 - 16:35:56 CST)
  • autocorrelation analysis in timeseries (Mon Jan 31 2005 - 16:21:56 CST)
  • 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)
• 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)
• akash.khandelwal_at_ndsu.edu
  • reconstruct PMF (Sat Oct 08 2005 - 15:54:26 CDT)
  • electron density profiles (EDP) (Wed Jun 22 2005 - 14:25:23 CDT)
  • charmm paramter (Thu May 05 2005 - 20:57:34 CDT)
• 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: removing water from DCD (Thu Jul 21 2005 - 01:55:34 CDT)
  • Re: about *.psf (Fri May 27 2005 - 05:30:10 CDT)
  • 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)
• 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)
• Alex Vakhrouchev
  • Topology for nano tubes (Tue Apr 19 2005 - 06:59:04 CDT)
• 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)
• Alexe Bojovschi
  • How to patch segments of aminoacids (Wed Nov 02 2005 - 03:09:08 CST)
  • namd2.5 on linux-cluster (Wed Feb 09 2005 - 04:41:43 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)
• Amir Shamloo
  • FEP alchemical (Fri Jul 15 2005 - 19:51:23 CDT)
• 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)
• amodzelewska_at_dns.iimcb.gov.pl
  • autoionize script (Sun May 16 2004 - 13:21:58 CDT)
• ANDY NG
  • Generating topology file (Thu Nov 11 2004 - 00:59:51 CST)
• Angel Gonzalez Wong
  • Re: vmd-l: convert DCD files to CRD format (Mon Dec 26 2005 - 09:19:53 CST)
• Angelo R. Rossi
  • All or Nothing at All?? (Sat Oct 29 2005 - 11:41:32 CDT)
• Anna Modzelewska
  • Re: help generating psf files (Fri Oct 07 2005 - 09:16:57 CDT)
  • Re: help generating psf files (Fri Oct 07 2005 - 02:58:19 CDT)
  • Re: help generating psf files (Thu Oct 06 2005 - 08:55:18 CDT)
  • Re: help generating psf files (Thu Oct 06 2005 - 02:37:14 CDT)
  • Re: rotating constraints (Wed Sep 21 2005 - 04:22:30 CDT)
  • energy values (Tue Sep 13 2005 - 06:29:27 CDT)
  • Re: pair interactions in NPT (Fri Sep 02 2005 - 03:58:05 CDT)
  • pair interactions in NPT (Thu Sep 01 2005 - 03:21:46 CDT)
  • Re: interactions in flexible cel (Wed Jun 29 2005 - 02:07:04 CDT)
  • interactions in flexible cel (Wed Jun 29 2005 - 00:34:51 CDT)
  • interactions in flexible cell (Fri Jun 24 2005 - 04:31:27 CDT)
  • Re: vmd-l: autoimd on windows (Wed Jun 22 2005 - 05:29:52 CDT)
  • autoimd on windows (Mon Jun 20 2005 - 06:40:29 CDT)
  • 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
  • Re: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? (Wed Jun 22 2005 - 10:42:04 CDT)
  • Re: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? (Wed Jun 22 2005 - 10:41:58 CDT)
  • Re: equilibrated the system (Tue Jan 11 2005 - 09:58:27 CST)
  • 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)
• arijit_r_at_chem.iitkgp.ernet.in
  • Re: charmm27 fatal error (Mon Dec 19 2005 - 22:24:36 CST)
  • parameter and topology for 4-MI (Mon Nov 14 2005 - 00:19:27 CST)
• 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)
• Arturas Ziemys
  • charmm27 fatal error (Mon Dec 19 2005 - 14:06:00 CST)
• ashwin joshi
  • Compilation of NAMD on 64-bit NUMA with icc (Tue Oct 18 2005 - 02:46:18 CDT)
• Axel Kohlmeyer
  • Re: Re: vmd-l: multiple automated calls to NAMD (Fri Jun 10 2005 - 02:17:32 CDT)
  • Re: vmd-l: multiple automated calls to NAMD (Thu Jun 09 2005 - 02:38:35 CDT)
• Baoqiang Cao
  • about protonation of HIS in membrane protein (Wed Apr 13 2005 - 09:21:08 CDT)
  • Re: RE: RE: error: UNABLE TO FIND ANGLE PARAMETERS FOR C NH1 C (Sat Apr 09 2005 - 22:46:44 CDT)
  • Re: RE: error: UNABLE TO FIND ANGLE PARAMETERS FOR C NH1 C (Sat Apr 09 2005 - 21:26:03 CDT)
  • error: UNABLE TO FIND ANGLE PARAMETERS FOR C NH1 C (Sat Apr 09 2005 - 14:40:37 CDT)
  • any script to build membrane+protein+solvent? (Fri Apr 08 2005 - 10:02:36 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)
• 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
  • Re: catdcd and dcdunitcell (Tue Jun 28 2005 - 18:27:07 CDT)
  • Re: catdcd and dcdunitcell (Mon Jun 27 2005 - 07:47:39 CDT)
  • libimf.so error when compiling charm++ (Thu May 12 2005 - 01:09:36 CDT)
  • 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)
• Bing Xiong
  • namd2 compile linux-i686-mpi (Tue May 03 2005 - 15:38:27 CDT)
• Blake Charlebois
  • RE: moments of inertia, principal axes (Thu Aug 18 2005 - 05:30:37 CDT)
  • RE: Protonation state of HIS (Wed Aug 10 2005 - 17:44:11 CDT)
  • RE: add ions (Mon Aug 08 2005 - 09:34:41 CDT)
  • RE: running on two different machines.... (Sun Jul 31 2005 - 11:17:20 CDT)
  • Re: the difference between the min_nacl.vel and min_nacl.restart.vel (Sat Jul 23 2005 - 09:25:48 CDT)
  • RE: Help with SMD (Wed Jul 20 2005 - 11:10:47 CDT)
  • Random forces in Langevin temperature control -- three questions (Fri Jul 15 2005 - 00:05:03 CDT)
  • RE: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? (Tue Jun 21 2005 - 15:41:19 CDT)
  • RE: set center (Fri Jun 17 2005 - 00:03:24 CDT)
  • RE: tcl question (Thu Jun 16 2005 - 22:32:39 CDT)
  • RE: tcl question (Thu Jun 16 2005 - 21:15:59 CDT)
  • RE: changing default directory in VMD? (Wed Jun 15 2005 - 15:21:43 CDT)
  • RE: Number of Steps (Thu Jun 09 2005 - 11:53:35 CDT)
  • RE: Avoiding Rotation and translation of protein (Wed Jun 08 2005 - 12:39:06 CDT)
  • RE: how to apply a random force on a atom (Mon Jun 06 2005 - 16:06:44 CDT)
  • RE: SMD-drifting of center of mass (Sun May 01 2005 - 21:23:48 CDT)
  • RE: protein interact with its image (Tue Apr 19 2005 - 12:10:20 CDT)
  • 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)
• bo baker
  • NAMD Energy Plugin (Tue Dec 27 2005 - 18:15:40 CST)
  • Re: namdplot: command not found (Mon Oct 17 2005 - 19:50:01 CDT)
  • Re: namdplot: command not found (Fri Oct 14 2005 - 14:04:53 CDT)
  • Re: namdplot: command not found (Thu Oct 13 2005 - 14:26:47 CDT)
  • Re: namdplot: command not found (Wed Oct 12 2005 - 15:27:23 CDT)
  • Re: namdplot: command not found (Tue Oct 11 2005 - 18:56:10 CDT)
  • namdplot: command not found (Mon Oct 10 2005 - 17:36:32 CDT)
  • fix backbone atom (Sun Oct 09 2005 - 01:52:35 CDT)
  • Penetration of water (Fri Oct 07 2005 - 00:20:46 CDT)
  • Re: log file (Wed Sep 21 2005 - 18:49:38 CDT)
  • autoionize & namd2 (Tue Sep 20 2005 - 18:07:34 CDT)
  • Re: log file (Mon Sep 19 2005 - 18:38:35 CDT)
  • Re: log file (Mon Sep 19 2005 - 16:55:33 CDT)
  • log file (Mon Sep 19 2005 - 14:09:42 CDT)
  • vmdtext and .cshrc. (Fri Sep 02 2005 - 18:26:29 CDT)
  • Re: par_all27_prot_lipid.inp (Thu Aug 18 2005 - 19:44:03 CDT)
  • par_all27_prot_lipid.inp (Thu Aug 18 2005 - 16:29:15 CDT)
  • Re: errno = 2 (Thu Aug 18 2005 - 13:12:41 CDT)
  • Re: errno = 2 (Wed Aug 17 2005 - 20:09:43 CDT)
  • Re: errno = 2 (Wed Aug 17 2005 - 12:30:27 CDT)
  • Re: errno = 2 (Tue Aug 16 2005 - 19:04:49 CDT)
  • errno = 2 (Mon Aug 15 2005 - 19:05:21 CDT)
• bora erdemli
  • psfgen error "Missing atom for conformation definition" (Sat Feb 12 2005 - 06:16:30 CST)
  • XPLOR topology to CHARMM (Wed Feb 09 2005 - 03:01:15 CST)
  • parameters for NAD,NAG,NAP (Thu Feb 03 2005 - 03:39:00 CST)
  • Re: segmentation violation!! (Sun Jan 16 2005 - 03:59:08 CST)
  • Re: segmentation violation!! (Fri Jan 14 2005 - 03:06:55 CST)
  • segmentation violation!! (Thu Jan 13 2005 - 02:15:19 CST)
  • Re: Bug alert!!! (Tue Jan 04 2005 - 01:13:37 CST)
  • 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)
• Boyang Wang
  • How does NAMD calculate Electrostatic potential energy (no periodic boundary condition)? (Mon Dec 26 2005 - 17:46:55 CST)
  • About the Source code. (Mon Dec 26 2005 - 21:40:56 CST)
  • Re: About RMSD calculation. (Fri Oct 28 2005 - 16:56:09 CDT)
  • Re: About RMSD calculation. (Fri Oct 28 2005 - 15:55:41 CDT)
  • About RMSD calculation. (Fri Oct 28 2005 - 10:49:14 CDT)
  • Does NAMD calculate the potential energy of FIXED ATOMS? (Wed Oct 05 2005 - 12:14:36 CDT)
  • Re: Re water box and system charge (Fri Sep 30 2005 - 21:18:04 CDT)
  • About calculating RMSD with rmsd.tcl (Fri Sep 30 2005 - 19:55:26 CDT)
  • Re water box and system charge (Fri Sep 30 2005 - 19:47:16 CDT)
  • Re water box and system charge (Fri Sep 30 2005 - 14:22:12 CDT)
  • A question about MD simulation of peptide. (Tue Sep 27 2005 - 12:24:59 CDT)
  • Another question about MD simulation of a domain. (Tue Sep 27 2005 - 12:30:43 CDT)
  • RE: For help with .log file. (Sun Aug 07 2005 - 21:42:49 CDT)
  • For help with .log file. (Sun Aug 07 2005 - 14:13:33 CDT)
  • FATAL ERROR: child atom 39 bonded only to child H atoms (Wed Jul 13 2005 - 11:06:19 CDT)
  • Mother atom with hydrogenGroupSize of 0 (Mon Jul 11 2005 - 17:57:51 CDT)
  • Re. van der waals energy (Thu Jul 07 2005 - 13:23:52 CDT)
  • How to set a molecule to be rigid in NAMD? (Mon May 16 2005 - 14:37:44 CDT)
  • Tyrocine dynamics came out wrong. (Sun May 15 2005 - 20:08:08 CDT)
  • benzene in NAMD (Sat May 14 2005 - 15:33:13 CDT)
  • Trajectory file. (Fri May 13 2005 - 16:20:17 CDT)
  • Bad global exclusion count. (Tue May 10 2005 - 11:56:32 CDT)
  • Re: charmm paramter (Thu May 05 2005 - 22:23:56 CDT)
  • RE: Restartname (Thu May 05 2005 - 21:52:36 CDT)
  • Restartname (Thu May 05 2005 - 19:19:26 CDT)
  • About Restart (Thu May 05 2005 - 18:50:52 CDT)
  • How to change psf file in the half way of VMD simulation? (Tue May 03 2005 - 21:48:23 CDT)
  • Re: SMD-drifting of center of mass (Sun May 01 2005 - 22:21:46 CDT)
  • RE: Parameter file. (Sun May 01 2005 - 17:28:48 CDT)
  • Parameter file. (Fri Apr 29 2005 - 23:20:52 CDT)
  • Fwd: Parameter file. (Sat Apr 30 2005 - 12:15:45 CDT)
  • Parameter file again. (Sat Apr 30 2005 - 12:20:19 CDT)
  • solvate and write pdb, psf file. (Wed Apr 27 2005 - 19:16:28 CDT)
• Brady Chang
  • Re: socket closed error (Thu May 05 2005 - 20:40:05 CDT)
  • namd and node freeze (Tue Apr 05 2005 - 03:39:26 CDT)
  • socket closed error (Fri Mar 25 2005 - 14:54:01 CST)
• Brian Bennion
  • Re: Atoms moving too fast (Tue Dec 06 2005 - 15:28:50 CST)
  • Re: How to patch segments of aminoacids (Wed Nov 02 2005 - 10:35:19 CST)
  • Re: CA CL CA angle? (Tue Nov 01 2005 - 12:57:43 CST)
  • Re: Serious Steric Atom Clashes (Mon Oct 24 2005 - 15:01:41 CDT)
  • Re: Serious Steric Atom Clashes (Mon Oct 24 2005 - 13:48:23 CDT)
  • Re: Serious Steric Atom Clashes (Mon Oct 24 2005 - 10:41:05 CDT)
  • Re: Compilation of NAMD on 64-bit NUMA with icc (Tue Oct 18 2005 - 10:47:16 CDT)
  • Re: namdplot: command not found (Fri Oct 14 2005 - 14:44:14 CDT)
  • Re: namdplot: command not found (Thu Oct 13 2005 - 16:09:03 CDT)
  • Re: NAMD distribute (Thu Oct 13 2005 - 16:05:59 CDT)
  • Re: NAMD distribute (Thu Oct 13 2005 - 10:18:41 CDT)
  • Re: About the potential of NAMD (Fri Oct 07 2005 - 10:35:42 CDT)
  • Re: error parsing config file (Fri Sep 30 2005 - 10:30:30 CDT)
  • Fatal error on PE 0> FATAL ERROR: DIHEDRALS INDEX 150255520 (Fri Aug 19 2005 - 16:47:19 CDT)
  • Re: volume from VMD and NAMD different? (Fri Aug 05 2005 - 17:38:27 CDT)
  • volume from VMD and NAMD different? (Fri Aug 05 2005 - 16:12:34 CDT)
  • error in config file (Fri Aug 05 2005 - 11:28:14 CDT)
  • Re: psfgen patches (Thu Jul 14 2005 - 18:37:37 CDT)
  • sync buffer overflow (Wed Jul 13 2005 - 16:44:36 CDT)
  • segfaults in mm_malloc (Tue Jun 28 2005 - 10:27:31 CDT)
  • RE: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? (Tue Jun 21 2005 - 17:40:15 CDT)
  • Re: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? (Tue Jun 21 2005 - 10:08:32 CDT)
  • Re: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? (Mon Jun 20 2005 - 10:26:49 CDT)
  • libimf.so problems (Fri May 27 2005 - 15:22:07 CDT)
  • Re: Re: vmd-l: Interactive Simulations, ligand size limits.... (Thu Apr 28 2005 - 12:01:32 CDT)
  • Re: NANMD errors: PME, qsub (Mon Apr 18 2005 - 17:23:35 CDT)
  • RE: minimization problem (Thu Apr 14 2005 - 18:28:42 CDT)
  • Re: modifying cut off (Fri Apr 08 2005 - 09:59:37 CDT)
  • Re: Nanotube psf file. (Wed Apr 06 2005 - 13:28:34 CDT)
  • Re: problem running namd (Mon Apr 04 2005 - 15:26:06 CDT)
  • Re: problem running namd (Mon Apr 04 2005 - 13:12:08 CDT)
  • Re: socket closed error (Fri Mar 25 2005 - 16:25:48 CST)
  • Re: visualizing dynamics output (Tue Mar 22 2005 - 12:55:00 CST)
  • Re: psfgen for DNA (Mon Mar 21 2005 - 11:51:21 CST)
  • Re: namd2 mpi error (Fri Mar 11 2005 - 11:05:18 CST)
  • RE: Compiling on Linux-PPC970-Myrinet-MPI-xlC (Thu Mar 10 2005 - 18:22:43 CST)
  • Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC (Thu Mar 10 2005 - 15:59:33 CST)
  • Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC (Thu Mar 10 2005 - 14:11:29 CST)
  • Re: Compiling NAMD with mpicc myrinet (Thu Mar 10 2005 - 14:08:44 CST)
  • Re: compiling Namd on amd64 (Thu Mar 10 2005 - 10:20:46 CST)
  • Re: NAMD attempting to read FFTW (Wed Mar 02 2005 - 13:22:00 CST)
  • Re: Complie NAMD on Suse Linux (Mon Feb 07 2005 - 11:56:01 CST)
  • Re: gradient nan (Mon Feb 07 2005 - 11:33:00 CST)
  • Re: qsub (Tue Jan 25 2005 - 10:11:54 CST)
  • Re: segmentation violation!! (Tue Jan 18 2005 - 10:34:47 CST)
  • Re: about rigid bonds (Tue Jan 18 2005 - 10:29:19 CST)
  • Re: hydrogens collapsing (Tue Jan 18 2005 - 10:23:40 CST)
  • Re: extracting time from DCDs (Fri Jan 14 2005 - 14:10:02 CST)
  • Re: segmentation violation!! (Fri Jan 14 2005 - 10:20:49 CST)
  • rattle errors. (Thu Jan 13 2005 - 10:56:25 CST)
  • Re: segmentation violation!! (Thu Jan 13 2005 - 10:48:11 CST)
  • Re: success with opteron myrinet mpi etc (Thu Jan 13 2005 - 10:16:54 CST)
  • Re: multiple jobs on a cluster (Wed Jan 12 2005 - 17:15:05 CST)
  • Re: Bug alert!!! (Tue Jan 04 2005 - 10:46:40 CST)
  • 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)
• by way of Jérôme Hénin
  • Re: alchemical free energy perturbation (Mon Jan 05 2004 - 09:10:52 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)
• Cameron Mura
  • Re: namddat not working (Tue May 24 2005 - 17:30:33 CDT)
  • binary restraint reference coordinates? (Thu Mar 31 2005 - 20:31:42 CST)
• carles ferrer
  • problems NAMD_2.6 (fwd) (Thu Sep 29 2005 - 04:06:09 CDT)
• carlos n. a.
  • Re: Space environment simulations (Wed May 11 2005 - 11:11:29 CDT)
  • Re: Space environment simulations (Tue May 10 2005 - 16:02:28 CDT)
  • RE: high (or low) pressure readings (Mon Dec 13 2004 - 13:36:10 CST)
• Cetin Baloglu
  • Re: namdplot, graph is empty (Tue Jun 21 2005 - 15:44:29 CDT)
  • Re: namddat not working (Tue May 24 2005 - 20:31:02 CDT)
  • Re: regenerating PSF file (Wed May 18 2005 - 02:50:38 CDT)
  • regenerating PSF file (Wed May 18 2005 - 01:07:05 CDT)
  • Heat Capacity & Relaxation Functions (Mon Apr 25 2005 - 03:22:11 CDT)
  • 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)
• Chang, Christopher
  • Recalculating energies from DCD file (Fri Oct 07 2005 - 18:05:37 CDT)
  • catdcd-generated files and CHARMM (Thu Jul 21 2005 - 11:55:25 CDT)
  • Gradient tolerance--total or per atom? (Tue Apr 26 2005 - 11:46:07 CDT)
  • Setting target minimization gradient? (Fri Apr 22 2005 - 13:15:01 CDT)
• Charles Danko
  • POPC or POPE? (Tue Nov 01 2005 - 22:20:04 CST)
  • Re: Incorrect periodic box imaging with AMBER parameters (Mon Jul 25 2005 - 08:32:20 CDT)
  • Re: Periodic cell has become too small for original patch grid (Thu Apr 14 2005 - 10:48:52 CDT)
  • Re: Re[2]: ERROR: Constraint failure in RATTLE algorithm for atom 127! (Thu Apr 14 2005 - 10:40:10 CDT)
  • Re: Periodic cell has become too small for original patch grid (Wed Apr 13 2005 - 09:32:03 CDT)
  • Re: DOWSER (Wed Jan 19 2005 - 09:01:18 CST)
  • DOWSER (Tue Jan 18 2005 - 16:20:06 CST)
  • Re: restarting a simulation accurately (Sat Jan 08 2005 - 15:06:24 CST)
  • Harmonic restraints for moving residue positions?? (Sat Jan 08 2005 - 15:03:50 CST)
  • 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: PSFGEN (Sun May 29 2005 - 12:48:59 CDT)
  • 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)
• Charles Moad
  • Generating psf for a drug, trimethoprim (Sat May 14 2005 - 18:00:08 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
  • multiple jobs on a cluster (Wed Jan 12 2005 - 15:55:42 CST)
  • 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)
• Ching Wong
  • Counterions: how to decide how many to put it? (Tue Dec 13 2005 - 17:44:33 CST)
  • Water Box Shrinks (Fri Nov 25 2005 - 19:10:46 CST)
  • Na ions got into the catalytic site during Production Run (Sun Nov 20 2005 - 17:34:01 CST)
• Chona S. Guiang
  • Charm++ problem on EM64T/Myrinet cluster (Thu Mar 31 2005 - 16:08:38 CST)
• Chris Chipot
  • Re: FEP setup (Wed Dec 28 2005 - 17:21:28 CST)
  • Re: Re: FATAL ERROR: unknown floating-point error, errno = 4 (Mon Dec 26 2005 - 10:52:40 CST)
  • Re: FATAL ERROR: unknown floating-point error, errno = 4 (Fri Dec 23 2005 - 01:22:32 CST)
  • Re: define abf1 and abf2 for CM of water and CM of molecule (Wed Dec 21 2005 - 12:18:36 CST)
  • Re: define abf1 and abf2 for CM of water and CM of molecule (Tue Dec 20 2005 - 01:28:32 CST)
  • Re: freeEnergy of conformational change of a test molecule (Thu Nov 17 2005 - 11:37:07 CST)
  • Re: freeEnergy of conformational change of a test molecule (Thu Nov 17 2005 - 03:44:55 CST)
  • Re: FEP.... (Fri Nov 11 2005 - 10:35:19 CST)
  • Re: PMF calculation using fixed restraints (Sun Nov 06 2005 - 14:54:16 CST)
  • Re: ABF Simulation (Wed Oct 05 2005 - 07:58:57 CDT)
  • Re: fep (Sat Jul 16 2005 - 04:48:02 CDT)
  • Re: free energy pertubation,binding energy and constant (Wed Jun 29 2005 - 08:14:27 CDT)
  • Re: binding free energy , binding constant (Fri Jun 17 2005 - 11:07:11 CDT)
  • Re: Reverse Free Energy perturbation (FEP)? (Wed Jun 08 2005 - 17:59:42 CDT)
  • Re: FEP charge perturbation (Fri Jun 03 2005 - 12:08:13 CDT)
  • FEP (Wed May 11 2005 - 17:34:47 CDT)
• Chris Samuel
  • Re: FATAL ERROR: Stale NFS file handle (Wed Apr 06 2005 - 22:29:59 CDT)
  • Re: NMAD job abnormally killed with PBS (Wed Apr 06 2005 - 22:32:01 CDT)
  • Re: problem running namd (Mon Apr 04 2005 - 18:10:58 CDT)
  • Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC (Wed Mar 30 2005 - 00:05:44 CST)
  • Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC (Sun Mar 20 2005 - 20:04:50 CST)
  • Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC (Thu Mar 17 2005 - 23:23:24 CST)
  • Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC (Wed Mar 16 2005 - 04:37:07 CST)
  • Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC (Wed Mar 16 2005 - 00:06:21 CST)
  • 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)
• Crozier, Paul S
  • Systems of > 100,000 atoms, *.psf files & *.crd files (Tue May 11 2004 - 18:02:51 CDT)
• cunning cunning
  • Complie NAMD on Suse Linux (Thu Feb 03 2005 - 08:18:46 CST)
• curcio
  • temperature "coupling coefficient" in NAMD (Fri Nov 18 2005 - 11:09:13 CST)
• Damon Smith
  • Re: success with opteron myrinet mpi etc (Thu Jan 13 2005 - 18:24:24 CST)
  • success with opteron myrinet mpi etc (Thu Jan 13 2005 - 01:28:30 CST)
  • Compiling (Thu Jan 06 2005 - 19:02:04 CST)
  • Re: mpi opteron myrinet (Thu Dec 30 2004 - 23:51:01 CST)
  • mpi opteron myrinet (Thu Dec 30 2004 - 22:23:09 CST)
• Dan Strahs
  • Re: NAMD distribute (Thu Oct 13 2005 - 15:46:42 CDT)
  • NAMD distribute (Wed Oct 12 2005 - 20:28:49 CDT)
• Darren Anderson
  • Re: How to "extract" coordinates from a DCD trajectory file? (Tue Aug 09 2005 - 07:54:51 CDT)
  • Re: pka calculations and their use in simulations (Mon Jul 11 2005 - 08:49:20 CDT)
• David Brandon
  • "Hands-On" Workshop on Computational Biophysics (Fri Mar 11 2005 - 15:23:27 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)
• David E. Konerding
  • Re: improving parallel on mac cluster (Tue Feb 10 2004 - 18:21:32 CST)
• David Kunzman
  • Re: segfaults in mm_malloc (Tue Jun 28 2005 - 12:29:01 CDT)
• 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)
• Davit Hakobyan
  • How to create a substrate parameter file ? (Thu May 06 2004 - 15:09:00 CDT)
• debashis.sikdar_at_ndsu.edu
  • velocity file of atoms at each time step (Sun Jun 19 2005 - 22:28:14 CDT)
  • saving picture from namdplot (Tue May 10 2005 - 11:31:04 CDT)
  • pairlist distance (Wed Mar 23 2005 - 09:32:48 CST)
  • pairlist distance (Tue Mar 22 2005 - 14:28:20 CST)
  • peridic boundary condition (Fri Mar 11 2005 - 09:08:37 CST)
  • Influence of PME grid size and cell basis vectors over simulation result (Mon Mar 07 2005 - 13:01:19 CST)
  • 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)
• Deborah Jameson
  • fep file (Mon Jul 25 2005 - 11:10:54 CDT)
  • changing file (Wed Jul 20 2005 - 03:18:12 CDT)
  • setting configuration file for free energy perturbation (Mon Jul 18 2005 - 10:25:02 CDT)
• dimka
  • Re: Can extending MIN solve the problem of "Constraint failure in RATTLE algorithm" (Sat Dec 24 2005 - 19:51:31 CST)
  • Re: segmentation fault on Linux (Mon Nov 28 2005 - 12:41:25 CST)
  • Re: running NAMD2 in parallel (Mon Oct 10 2005 - 23:33:59 CDT)
  • namd 2.6b1 job crash error (Fri Sep 30 2005 - 16:18:43 CDT)
  • segmentation fault on Linux (Mon Sep 19 2005 - 16:48:02 CDT)
• Dong Luo
  • Re: "Segmentation violation" on running namd2.6b1 (Mon Sep 19 2005 - 13:09:38 CDT)
  • "Segmentation violation" on running namd2.6b1 (Mon Sep 19 2005 - 10:36:30 CDT)
  • namd2.6b1 hang on IBM p-690 (Thu Sep 08 2005 - 10:50:21 CDT)
  • RE: shape change of water box and peptide move out (Mon Aug 15 2005 - 10:46:48 CDT)
  • shape change of water box and peptide move out (Fri Jul 29 2005 - 12:09:58 CDT)
  • Re: NAMD on IBM pSeries (690, 655) (Tue Jun 07 2005 - 14:01:54 CDT)
  • NAMD on IBM pSeries (690, 655) (Tue Jun 07 2005 - 11:45:53 CDT)
  • dielectric constant (Thu May 12 2005 - 11:52:42 CDT)
  • Re: hanging at startup phase 0 (Thu May 05 2005 - 13:59:37 CDT)
  • hanging at startup phase 0 (Thu May 05 2005 - 10:47:31 CDT)
• dora guzman
  • error parsing config file (Thu Sep 29 2005 - 14:00:00 CDT)
• Dow Hurst
  • Ammasso interconnect performance, LDB question (Mon Sep 05 2005 - 23:21:12 CDT)
  • Re: mpi problems on opteron (Wed Aug 03 2005 - 22:39:35 CDT)
  • Re: Re: charm++ 5.9 megatest failure too (Wed Aug 03 2005 - 22:11:54 CDT)
  • Re: Re: charm++ 5.9 megatest failure too (Wed Aug 03 2005 - 07:37:49 CDT)
  • NAMD and dual core Opterons, thoughts? (Tue Apr 26 2005 - 11:36:02 CDT)
  • Re: Not getting good speed up (Sun Mar 20 2005 - 02:22:00 CST)
• Dow_Hurst
  • charm++ 5.9 megatest failure too (Tue Aug 02 2005 - 17:25:38 CDT)
  • charm++ 5.9 build fails, NAMD 2.6b1 make fails (Tue Aug 02 2005 - 17:16:55 CDT)
  • 2.6b1 source missing file (Tue Aug 02 2005 - 16:58:30 CDT)
  • Link Ammasso MPI with NAMD (Tue Aug 02 2005 - 14:46:59 CDT)
  • Link Ammasso MPI with NAMD (Tue Aug 02 2005 - 14:43:17 CDT)
  • Checkpoint on IRIX of namd 2.5 job not MPI enabled (Thu Apr 07 2005 - 09:40:55 CDT)
  • Re: Not getting good speed up (Tue Mar 15 2005 - 12:31:11 CST)
• E. Davis Oldham
  • NANMD errors: PME, qsub (Sat Apr 16 2005 - 12:37:37 CDT)
• Edelmiro Moman
  • RE: Sybyl trajectory (Tue Sep 06 2005 - 10:33:37 CDT)
  • How to "extract" coordinates from a DCD trajectory file? (Tue Aug 09 2005 - 07:10:00 CDT)
• Edward Patrick Obrien
  • NAMD Myrinet issue - Strange behavior (Thu Apr 07 2005 - 12:04:31 CDT)
  • Re: Trouble with NAMD on Myrinet (Wed Mar 16 2005 - 10:04:20 CST)
  • Trouble with NAMD on Myrinet (Tue Mar 15 2005 - 14:02:40 CST)
  • Submitting jobs on myrinet...problem (Fri Mar 11 2005 - 18:29:19 CST)
  • Re: peridic boundary condition (Fri Mar 11 2005 - 13:09:43 CST)
  • Compiling NAMD with mpicc myrinet (Thu Mar 10 2005 - 12:19:50 CST)
  • Re: Problems with the nodelist file ! (Wed Mar 02 2005 - 17:22:02 CST)
  • FATAL ERROR: Stale NFS file handle (Fri Feb 18 2005 - 15:51:53 CST)
  • Re: pmf (Tue Jan 11 2005 - 19:24:04 CST)
  • Re: increase in energy over time (Tue Jan 04 2005 - 11:01:53 CST)
  • Re: increase in energy over time (Mon Jan 03 2005 - 18:29:46 CST)
  • 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
  • Fix distance (Tue Sep 20 2005 - 18:11:06 CDT)
  • SMD-drifting of center of mass (Sun May 01 2005 - 16:47:19 CDT)
  • SMD by pulling two groups apart (Fri Feb 04 2005 - 16:27:06 CST)
  • 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)
• eladp_at_hplus.tau.ac.il
  • How to have neutral terminal ends (Sat Oct 15 2005 - 04:15:01 CDT)
• ELENA JEAN LEVIN
  • three-site carbon monoxide model (Thu May 27 2004 - 16:40:11 CDT)
• 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)
• EPF \(Esben Peter Friis\)
  • RE: xplor to charmm (Mon Nov 01 2004 - 15:21:08 CST)
• Eric Bohm
  • Re: charm++ 5.9 megatest failure too (Tue Aug 02 2005 - 17:49:31 CDT)
• Eric Cyr
  • Potential energies in TCL interface (Mon Mar 07 2005 - 15:36:09 CST)
  • 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 Perim
  • Atoms moving too fast (Tue Dec 06 2005 - 13:05:10 CST)
  • Problems opening the Extended Trajectory File (Thu Dec 01 2005 - 13:36:36 CST)
• Eric Peterson
  • Question about pair interaction feature (Thu Jan 20 2005 - 17:43:49 CST)
  • Re: Error in when using charmrun (Sat Jan 08 2005 - 22:24:11 CST)
  • Re: Error in when using charmrun (Sat Jan 08 2005 - 21:16:47 CST)
  • Error in when using charmrun (Sat Jan 08 2005 - 20:39:45 CST)
• 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
  • Ferric heme (Mon Apr 25 2005 - 11:54:41 CDT)
• Eunice Ramirez Melendez
  • Re: RE: Help with SMD (Wed Jul 20 2005 - 03:37:44 CDT)
  • Help with SMD (Tue Jul 19 2005 - 12:08:34 CDT)
  • hbonds output!!! (Tue Jul 19 2005 - 11:59:30 CDT)
  • 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)
• floquet_at_icsn.cnrs-gif.fr
  • NAMD on SUN (Thu Sep 29 2005 - 01:31:03 CDT)
  • MDenergy error (Wed Jul 13 2005 - 14:43:15 CDT)
  • Segmentation fault with two processors (Fri Jul 01 2005 - 04:12:57 CDT)
  • Problem with mdenergy (Fri Jun 17 2005 - 08:05:41 CDT)
  • Multiple dihedral multiplicity (Fri May 27 2005 - 08:09:14 CDT)
• 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)
• Floris Buelens
  • Re: Re: fep (Wed Jul 27 2005 - 04:41:06 CDT)
  • Re: FEP - one long simulation vs many short ones (Mon Jul 04 2005 - 07:22:55 CDT)
  • FEP - one long simulation vs many short ones (Fri Jul 01 2005 - 07:07:14 CDT)
  • new approach to counter FEP end-point VDW clashes (Sun Jun 26 2005 - 07:41:14 CDT)
  • optimisation for dual CPU sytem (Sat Jun 18 2005 - 08:25:39 CDT)
  • relating FEP-derived ddG values to experimental IC50 (Mon Jun 06 2005 - 17:49:54 CDT)
  • Re: FEP charge perturbation (Mon Jun 06 2005 - 17:40:44 CDT)
  • FEP charge perturbation (Sun May 29 2005 - 17:50:28 CDT)
• 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)
• Francisco Castro
  • Atom Positions during simulation (Wed Dec 14 2005 - 16:27:12 CST)
• Frank Yong Jiang
  • questions about anisotropic pressure coupling (Sat May 28 2005 - 10:34:45 CDT)
  • how to use gromacs force field in NAMD? (Tue May 24 2005 - 15:50:05 CDT)
• freddie salsbury
  • NAMD on itanium? (Thu Mar 11 2004 - 18:04:10 CST)
• fu guoxing
  • Problem with compiling NAMD on Suse 9.3 (Tue Nov 08 2005 - 06:23:10 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)
• 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)
• Gan, Yong \(UMC-Student\)
  • fixed atoms (Tue Oct 25 2005 - 23:18:59 CDT)
  • Box size (Tue Oct 25 2005 - 11:50:06 CDT)
  • running NAMD2 in parallel (Tue Oct 11 2005 - 10:42:42 CDT)
  • RE: running NAMD2 in parallel (Mon Oct 10 2005 - 22:34:32 CDT)
  • running NAMD2 in parallel (Mon Oct 10 2005 - 21:23:46 CDT)
  • Running NAMD 2.6b1 on Linux Networks (Fri Oct 07 2005 - 16:44:53 CDT)
  • namd 2.6b1 (Wed Oct 05 2005 - 20:50:57 CDT)
  • surface density of lipid bilayer (Thu Sep 08 2005 - 12:42:21 CDT)
  • NAMD on PSC (Sun Aug 28 2005 - 12:26:30 CDT)
  • Pressure Profile Simulation (Wed Aug 24 2005 - 21:36:51 CDT)
  • Running NAMD on a multiprocessor computer (Tue Aug 02 2005 - 19:00:05 CDT)
  • velocity unit (Sun Jun 12 2005 - 21:49:52 CDT)
  • Periodic Boundary Condition (Wed Jun 01 2005 - 16:56:41 CDT)
  • Combine pdb and psf files (Fri Apr 29 2005 - 16:04:23 CDT)
  • RE: Generate psf file of DMPC membrane (Thu Apr 28 2005 - 11:58:02 CDT)
  • Generate psf file of DMPC membrane (Wed Apr 27 2005 - 22:10:34 CDT)
  • NAMD on new P4 (Fri Mar 18 2005 - 13:04:54 CST)
  • isotropic pressure tensor (Wed Mar 16 2005 - 21:56:49 CST)
  • membrane files (Tue Mar 15 2005 - 20:54:41 CST)
  • Patch (Thu Mar 03 2005 - 17:28:35 CST)
  • Kinetic energy (Fri Feb 25 2005 - 12:55:09 CST)
  • Pressure tensor and periodic boundary condition (Mon Feb 21 2005 - 21:40:58 CST)
  • Lipid membrane simulation by NAMD (Fri Feb 18 2005 - 17:40:25 CST)
• Gaurav Sharma
  • Different solvents (Tue Nov 08 2005 - 13:09:27 CST)
  • Metal Ion and Protein binding (Thu Oct 13 2005 - 12:23:23 CDT)
  • Calculating forces (Thu Sep 01 2005 - 12:32:59 CDT)
  • Re: vmd-l: Nanotube Simulations (Tue Aug 02 2005 - 13:56:15 CDT)
  • Nanotube Simulations (Tue Aug 02 2005 - 08:51:14 CDT)
  • Parameter files for Nanotube Simulation (Thu Jul 28 2005 - 16:26:49 CDT)
  • PDB files for carbon nanotubes (Thu Jul 14 2005 - 14:33:05 CDT)
  • Space environment simulations (Fri May 06 2005 - 13:36:40 CDT)
  • Space environment simulations (Fri May 06 2005 - 13:20:53 CDT)
  • Unprotonating GLU, ASP (Sun Feb 13 2005 - 18:14:31 CST)
  • 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: Some problem on compiling NAMD (Thu Dec 15 2005 - 22:04:28 CST)
  • Re: NAMD on Win64 (Mon Dec 12 2005 - 21:04:07 CST)
  • Re: NAMD 2.6 in IBM SP (Sat Nov 05 2005 - 09:55:13 CST)
  • Re: questions about running namd on NCSA cluster tungsten (Sat Oct 29 2005 - 12:11:50 CDT)
  • Re: gcc4 (Fri Oct 14 2005 - 14:21:57 CDT)
  • Re: unexpected end with NAMD on quad-dual core opteron machine (Thu Sep 29 2005 - 13:39:22 CDT)
  • Re: log file (Mon Sep 19 2005 - 16:58:43 CDT)
  • Re: Re: Charmm++5.9 build on Mac OS X by IB xlc compiler (Sun Sep 04 2005 - 11:08:03 CDT)
  • Re: Re: Charmm++5.9 build on Mac OS X by IB xlc compiler (Fri Sep 02 2005 - 00:34:03 CDT)
  • Re: Re: Charmm++5.9 build on Mac OS X by IB xlc compiler (Wed Aug 31 2005 - 14:18:07 CDT)
  • Re: Re: Charmm++5.9 build on Mac OS X by IB xlc compiler (Wed Aug 31 2005 - 12:32:56 CDT)
  • Re: undefined symbol errors:__builtin_bzero and _alloca building mpi-ppc-darwin version of namd2.6b1 (Wed Aug 17 2005 - 14:14:43 CDT)
  • Re: Charmm++5.9 build on Mac OS X by IB xlc compiler (Tue Aug 09 2005 - 11:59:15 CDT)
  • Re: charm++ 5.9 megatest failure too (Tue Aug 02 2005 - 18:21:51 CDT)
  • Re: how to use the dual-processor machines (Sat Jul 30 2005 - 17:52:42 CDT)
  • Re: mpi problems on opteron (Wed Jul 27 2005 - 00:08:32 CDT)
  • Re: sync buffer overflow (Wed Jul 13 2005 - 22:32:31 CDT)
  • Re: config files (Tue Jun 07 2005 - 14:23:31 CDT)
  • Re: NAMD on IBM pSeries (690, 655) (Tue Jun 07 2005 - 14:05:07 CDT)
  • Re: NAMD on IBM pSeries (690, 655) (Tue Jun 07 2005 - 14:00:04 CDT)
  • Re: Installing NAMD on beowulf cluster, 64 bit, opteron, 4 processors. (Tue Jun 07 2005 - 13:58:15 CDT)
  • Re: NAMD on fedora 3 core? (Tue Jun 07 2005 - 12:00:22 CDT)
  • Re: Compilation of Charm++ on Linux opteron cluster with MPICH-GM installed (Wed May 25 2005 - 23:05:47 CDT)
  • Re: Megatest fails on Linux cluster (Wed May 25 2005 - 22:54:23 CDT)
  • Re: CHARM/NAMD network problems on amd64 Clustermatic (Wed May 11 2005 - 22:21:36 CDT)
  • Re: Compliling NAMD in RedHat9 (Wed May 11 2005 - 22:09:15 CDT)
  • Re: Re: NAMD 2.5 crashes unpredictably on a 8 way SMP (Linux x86) (Wed May 11 2005 - 22:07:13 CDT)
  • Re: NAMD 2.5 crashes unpredictably on a 8 way SMP (Linux x86) (Tue May 10 2005 - 09:57:04 CDT)
  • Re: NAMD 2.5 crashes unpredictably on a 8 way SMP (Linux x86) (Tue May 10 2005 - 01:45:25 CDT)
  • Re: compile "mpi" charm++ on amd64 (Tue May 10 2005 - 01:31:51 CDT)
  • Re: hanging at startup phase 0 (Thu May 05 2005 - 11:00:22 CDT)
  • Re: Errors compiling NAMD 2.5 (Mon Apr 04 2005 - 03:13:33 CDT)
  • Re: Charm++ problem on EM64T/Myrinet cluster (Fri Apr 01 2005 - 01:23:51 CST)
  • Re: NAMD recognizes only one MPI process (Thu Mar 31 2005 - 17:41:20 CST)
  • Re: path problems (Tue Mar 22 2005 - 01:37:52 CST)
  • Re: strange behaviour when running apoa1 on 1 processor (Thu Mar 17 2005 - 13:56:03 CST)
  • Re: Re: Trouble with NAMD on Myrinet (Wed Mar 16 2005 - 11:27:19 CST)
  • Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC (Wed Mar 16 2005 - 00:24:54 CST)
  • Re: Trouble with NAMD on Myrinet (Tue Mar 15 2005 - 14:14:14 CST)
  • Re: Not getting good speed up (Fri Mar 11 2005 - 16:04:53 CST)
  • Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC (Thu Mar 10 2005 - 15:54:56 CST)
  • Re: namd on Altix (Wed Mar 09 2005 - 13:36:21 CST)
  • Re: namd on Altix (Tue Mar 08 2005 - 16:54:16 CST)
  • Re: namd on Altix (Tue Mar 08 2005 - 18:43:47 CST)
  • Re: namd on Altix (Tue Mar 08 2005 - 17:21:13 CST)
  • Re: namd on Altix (Tue Mar 08 2005 - 17:09:47 CST)
  • Re: namd on Altix (Tue Mar 08 2005 - 17:00:05 CST)
  • Re: G5 cluster (Tue Mar 08 2005 - 16:41:06 CST)
  • Re: G5 clusters (Tue Mar 08 2005 - 12:44:25 CST)
  • Re: namd on Altix (Mon Mar 07 2005 - 19:11:33 CST)
  • Re: namd on Altix (Mon Mar 07 2005 - 18:59:02 CST)
  • Re: namd on Altix (Mon Mar 07 2005 - 18:28:20 CST)
  • Re: question (fwd) (Mon Mar 07 2005 - 15:51:50 CST)
  • Re: namd on Altix (Mon Mar 07 2005 - 15:03:07 CST)
  • Re: namd on Altix (Mon Mar 07 2005 - 14:22:53 CST)
  • Re: namd on Altix (Mon Mar 07 2005 - 13:39:49 CST)
  • Re: namd on Altix (Mon Mar 07 2005 - 13:33:40 CST)
  • Re: installing NAMD on opteron cluster with MPI (Fri Mar 04 2005 - 01:00:59 CST)
  • Re: Not getting good speed up (Thu Mar 03 2005 - 13:34:56 CST)
  • Re: Not getting good speed up (Wed Mar 02 2005 - 21:42:39 CST)
  • Re: clustermatic nodelist file (Wed Mar 02 2005 - 21:29:40 CST)
  • Re: Problems with the nodelist file ! (Wed Mar 02 2005 - 21:15:41 CST)
  • Re: Re: Complie NAMD on Suse Linux (Wed Feb 09 2005 - 17:53:10 CST)
  • Re: Complie NAMD on Suse Linux (Mon Feb 07 2005 - 13:02:32 CST)
  • Re: NAMD on IBM cluster AIX-RS6000 (Mon Jan 24 2005 - 15:17:14 CST)
  • Re: NAMD on IBM cluster AIX-RS6000 (Fri Jan 21 2005 - 22:06:32 CST)
  • Re: Compiling the NAMD on HPUX-ia64 system Error! (Sat Jan 15 2005 - 11:03:51 CST)
  • Re: charm++ compile problem on x86_64 (Fri Jan 14 2005 - 15:32:10 CST)
  • Re: scyld no longer a supported option for building charm++ ? (Fri Jan 14 2005 - 14:43:56 CST)
  • Re: How to Compile NAMD on HPUX-ia64 system~ (Fri Jan 14 2005 - 12:36:56 CST)
  • Re: Compiling (Sun Jan 09 2005 - 11:00:43 CST)
  • Re: Error in when using charmrun (Sat Jan 08 2005 - 22:50:24 CST)
  • Re: Error in when using charmrun (Sat Jan 08 2005 - 21:20:08 CST)
  • Re: Error in when using charmrun (Sat Jan 08 2005 - 21:00:03 CST)
  • Re: About charm++/namd on AMD64 cluster (Mon Jan 03 2005 - 14:46:58 CST)
  • Re: About charm++/namd on AMD64 cluster (Sun Jan 02 2005 - 02:50:56 CST)
  • Re: clustermatic 4 and 5 Namd/charm (Sat Jan 01 2005 - 15:15:45 CST)
  • 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)
• Georgios Papadopoulos
  • pairInteraction energies? (Fri Sep 30 2005 - 01:32:46 CDT)
  • calculate enthalpy of binding (Tue Sep 27 2005 - 11:33:33 CDT)
  • Fluorophors ? (Wed Jun 22 2005 - 00:27:25 CDT)
  • plugins.tar.gz & charm_src.tar.gz !!! (Sat Jun 11 2005 - 05:38:27 CDT)
  • NAMD on fedora 3 core? (Tue Jun 07 2005 - 01:33:49 CDT)
  • Fe2+ parameters? (Sun Jun 05 2005 - 04:52:09 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
  • gcc4 (Tue Oct 11 2005 - 16:34:32 CDT)
  • Re: About ions Representation in NAMD (Wed Sep 28 2005 - 07:33:39 CDT)
  • SHAKE or not? (Tue Sep 27 2005 - 14:42:43 CDT)
  • Compiling charm++-5.9: Problems with g++ (Sat Aug 20 2005 - 05:36:26 CDT)
  • shmget error (Mon Jun 20 2005 - 07:46:28 CDT)
  • Re: Trajectory file. (Fri May 13 2005 - 16:39:37 CDT)
  • NOE constraints with NAMD (Tue May 10 2005 - 09:25:35 CDT)
  • Re: Analysis of NAMD output with CHARMM (Mon Feb 14 2005 - 08:07:49 CST)
  • 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
  • Re: trying to generate a peptide (Wed Oct 26 2005 - 11:27:43 CDT)
  • Re: moments of inertia, principal axes (Thu Aug 18 2005 - 04:42:20 CDT)
  • (no subject) (Thu Aug 11 2005 - 15:50:38 CDT)
  • rescaling of coordinates in PBC simulations (Thu Aug 11 2005 - 12:41:52 CDT)
  • Re: changing file (Wed Jul 20 2005 - 04:57:29 CDT)
  • Re: namddat: Command not found (Thu May 12 2005 - 13:49:45 CDT)
  • Re: namddat: Command not found (Thu May 12 2005 - 13:48:10 CDT)
  • Re: Molecular Dynamics or Langevin Dynamics (Wed Apr 27 2005 - 19:18:58 CDT)
  • Re: Molecular Dynamics or Langevin Dynamics (Wed Apr 27 2005 - 10:59:27 CDT)
  • Re: conformational alignment (Wed Mar 30 2005 - 16:40:36 CST)
  • electrostatics under spherical harmonic conditions (Fri Jan 28 2005 - 13:59:57 CST)
  • 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)
• Glenn Johnson
  • Re: bonding to image (Mon Apr 11 2005 - 16:02:28 CDT)
  • bonding to image (Mon Apr 11 2005 - 13:56:33 CDT)
  • temperature autocorrelation (Thu Apr 07 2005 - 17:39:28 CDT)
  • Modeling a polymer (Thu Mar 24 2005 - 13:44:29 CST)
  • convert namd structure/coordinate files to gromacs topology file (Fri Mar 18 2005 - 14:00:54 CST)
  • modeling sucrose (Wed Mar 09 2005 - 17:19:12 CST)
  • PMEGridSize (Thu Feb 24 2005 - 15:25:03 CST)
  • RE: conditional statements in conf files (Mon Feb 14 2005 - 15:49:46 CST)
  • conditional statements in conf files (Mon Feb 14 2005 - 14:59:02 CST)
  • Complementary programs for NAMD (Mon Feb 14 2005 - 13:32:24 CST)
  • RE: namdplot not working (Fri Feb 11 2005 - 17:30:33 CST)
  • namdplot not working (Fri Feb 11 2005 - 14:39:45 CST)
• Grace Shen
  • Some warnings from log file after minimization (Fri Dec 16 2005 - 13:05:53 CST)
  • A question regarding generate pdb and psf file (Tue Dec 06 2005 - 11:06:27 CST)
  • The psf format conversion (Wed Nov 16 2005 - 16:54:42 CST)
  • The vector direction in SMD (Fri Nov 04 2005 - 15:01:51 CST)
  • RE: namd: advice (Fri Nov 04 2005 - 09:20:13 CST)
  • Increasing temp during MD (Thu Nov 03 2005 - 12:11:27 CST)
  • How to atomselect several residues (Wed Nov 02 2005 - 17:28:50 CST)
  • RE: About ADP (Tue Nov 01 2005 - 10:15:47 CST)
  • About ADP (Tue Nov 01 2005 - 09:48:43 CST)
  • Question regarding SMD (Mon Oct 31 2005 - 15:11:01 CST)
  • How to append charmm stream file (Wed Oct 26 2005 - 12:01:23 CDT)
  • Assign the ligand force field parameters (Mon Oct 24 2005 - 16:32:13 CDT)
• greisen_at_binf.ku.dk
  • ATP nucleotides using NAMD (Fri Oct 14 2005 - 04:56:45 CDT)
  • CMAP in VMD error (Thu Oct 13 2005 - 15:58:33 CDT)
• griadi_at_utalca.cl
  • Fwd: All or Nothing at All?? (Sat Oct 29 2005 - 14:02:12 CDT)
  • 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)
• Grzegorz Jezierski
  • Re: Sybyl trajectory (Tue Sep 06 2005 - 08:32:17 CDT)
  • vectorized NAMD version? (Thu Sep 01 2005 - 09:42:35 CDT)
  • Crash during free energy calculation (MCTI) (Wed Aug 24 2005 - 02:47:07 CDT)
  • Extra terms in the expression for potential energy (Tue Aug 23 2005 - 12:04:35 CDT)
  • Re: Incorrect periodic box imaging with AMBER parameters (Mon Aug 08 2005 - 12:43:20 CDT)
  • Re: Incorrect periodic box imaging with AMBER parameters (Fri Aug 05 2005 - 06:23:57 CDT)
  • Re: Incorrect periodic box imaging with AMBER parameters (Thu Aug 04 2005 - 13:04:05 CDT)
  • Incorrect periodic box imaging with AMBER parameters (Mon Jul 25 2005 - 04:11:20 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)
• Harald Tepper
  • Problem with NAMD on Opteron cluster (Sat Nov 12 2005 - 05:29:33 CST)
  • 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
  • Pair interaction calculation for large number different pairs (Wed Mar 02 2005 - 22:26:06 CST)
  • Re: NAMD on IBM cluster AIX-RS6000 (Mon Jan 24 2005 - 14:38:47 CST)
  • NAMD on IBM cluster AIX-RS6000 (Fri Jan 21 2005 - 18:46:29 CST)
  • 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)
• Harit Jani
  • Unit of force using Haptic in IMD (Fri May 14 2004 - 01:33:10 CDT)
• Hassan K. Al-Ali Merheby
  • NAMD Source (Fri Nov 19 2004 - 02:06:44 CST)
• Hemant Kushwaha
  • NADP hydrogen zero (Fri Jun 03 2005 - 22:30:08 CDT)
  • Re: NADP problem (Fri Jun 03 2005 - 22:07:08 CDT)
  • Re: NADP problem (Fri Jun 03 2005 - 08:28:56 CDT)
  • psfgen problem (Fri May 20 2005 - 23:41:13 CDT)
  • NADP problem (Tue May 17 2005 - 07:12:29 CDT)
  • NADP topology (Mon May 02 2005 - 04:40:58 CDT)
  • gradient nan (Mon Feb 07 2005 - 00:17:04 CST)
  • psfgen (Mon Nov 29 2004 - 01:16:44 CST)
• Hidekazu WATANABE
  • patch failed (Fri Jul 15 2005 - 05:19:19 CDT)
  • RE: About PDB file with fixed atom flags. (Thu May 05 2005 - 12:36:21 CDT)
  • About PDB file with fixed atom flags. (Wed May 04 2005 - 16:40:23 CDT)
• 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)
• Himanshu Khandelia
  • Re: peridic boundary condition (Fri Mar 11 2005 - 13:57:23 CST)
  • example scripts (Thu Mar 10 2005 - 10:03:53 CST)
• Hrant Gharabekyan
  • Re[2]: ERROR: Constraint failure in RATTLE algorithm for atom 127! (Thu Apr 14 2005 - 05:48:08 CDT)
  • Re: Periodic cell has become too small for original patch grid (Thu Apr 14 2005 - 05:25:01 CDT)
  • Question about Constraint failure in RATTLE algorithm for atom (Tue Feb 08 2005 - 05:06:46 CST)
  • 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)
• Hui-Hsu (Gavin) Tsai [contr]
  • NPT calculations in NAMD (Mon May 31 2004 - 11:06:04 CDT)
• Hui-Hsu Tsai
  • capping using Amber FF (Tue Mar 01 2005 - 12:32:24 CST)
  • 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
  • Re: How to run namd on NCSA Tungsten (Wed Oct 19 2005 - 16:56:30 CDT)
  • NAMD on myrinet (Tue Oct 18 2005 - 16:12:36 CDT)
  • Re: glucose CHARMM force field (Thu Mar 31 2005 - 12:29:13 CST)
  • glucose CHARMM force field (Tue Mar 29 2005 - 21:37:34 CST)
  • 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)
• Imran Khan
  • problem while running NAMD (Wed Sep 14 2005 - 11:25:56 CDT)
  • Compilation of NAMD on 64-bit NUMA (Wed Aug 17 2005 - 04:58:23 CDT)
• Ioana Cozmuta
  • c-shell into NAMD configuration file (Mon Jun 13 2005 - 02:02:48 CDT)
  • 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)
• ioana_at_pegasus.arc.nasa.gov
  • random seed (Tue Sep 27 2005 - 20:14:25 CDT)
• ir7_at_njit.edu
  • Packaging 100 cations and anions in a box (Tue Dec 06 2005 - 22:47:56 CST)
• Irene Newhouse
  • preparing a dimeric protein for NAMD (Thu Dec 22 2005 - 21:28:21 CST)
• Ivan Ufimtsev
  • FATAL ERROR: Tried to find atom type on node other than node 0 (Sat Dec 24 2005 - 17:26:26 CST)
• 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)
• Jack
  • VMD solvate in CCl4 (Tue Jul 26 2005 - 08:37:08 CDT)
• Jan Lipfert
  • temperature rescaling and canonical ensemble (Thu Sep 30 2004 - 23:27:28 CDT)
• Jan Saam
  • Re: Charmm 1,4 Interactions - Scaling Question (Thu Jun 16 2005 - 18:20:22 CDT)
  • Re: Hexagonal cell and PME grid. (Tue Mar 01 2005 - 05:34:17 CST)
  • Re: using namd to compute energies (Thu Feb 17 2005 - 15:44:57 CST)
  • tclForces - addforce to group of atoms (Fri Jan 07 2005 - 17:27:40 CST)
  • tclForces - addforce to group of atoms (Fri Jan 07 2005 - 17:01:13 CST)
  • Re: Calculating parameters. (Sat May 15 2004 - 10:32:36 CDT)
• Jason Lee
  • RE: Myrinet NAMD (Mon Oct 31 2005 - 15:00:25 CST)
  • NAMD running problem (Tue Sep 27 2005 - 15:02:27 CDT)
  • Re: Re: Charmm++5.9 build on Mac OS X by IB xlc compiler (Fri Sep 02 2005 - 10:55:13 CDT)
  • Re: Re: Charmm++5.9 build on Mac OS X by IB xlc compiler (Thu Sep 01 2005 - 16:46:24 CDT)
  • RE: Re: Charmm++5.9 build on Mac OS X by IB xlc compiler (Tue Aug 30 2005 - 18:04:43 CDT)
  • Charmm++5.9 build on Mac OS X by IB xlc compiler (Mon Aug 08 2005 - 14:58:21 CDT)
  • Re: LDB question (Sun Aug 07 2005 - 11:32:08 CDT)
  • RE: Nanotube Simulations (Tue Aug 02 2005 - 14:23:32 CDT)
  • LDB question (Mon Aug 01 2005 - 21:06:19 CDT)
  • CCS ERROR during simulation (Mon Jul 25 2005 - 08:52:16 CDT)
  • Segment atom number limitation (Wed Jun 29 2005 - 11:18:50 CDT)
  • RESTARTING CONJUGATE GRADIENT ALGORITHM (Fri Jun 10 2005 - 10:18:33 CDT)
  • Nanotube simulation in water problem (Mon May 30 2005 - 09:30:12 CDT)
  • Re: Complie NAMD on Suse Linux (Wed Feb 09 2005 - 16:51:28 CST)
  • Complie NAMD on Suse Linux (Mon Feb 07 2005 - 09:32:02 CST)
• JC Gumbart
  • Re: A question regarding generate pdb and psf file (Tue Dec 06 2005 - 11:37:55 CST)
  • Re: pair.pdb and cutoff for pairInteraction (Wed Nov 30 2005 - 00:10:44 CST)
  • Re: pair.pdb and cutoff for pairInteraction (Tue Nov 29 2005 - 23:52:51 CST)
  • Re: temperature "coupling coefficient" in NAMD (Fri Nov 18 2005 - 12:02:37 CST)
  • Re: The vector direction in SMD (Fri Nov 04 2005 - 15:16:30 CST)
  • Re: How to atomselect several residues (Wed Nov 02 2005 - 18:38:27 CST)
  • RE: A question on psfgen (Tue Oct 18 2005 - 02:09:05 CDT)
  • Re: CMAP in VMD error (Thu Oct 13 2005 - 16:16:04 CDT)
  • Re: namdplot: command not found (Wed Oct 12 2005 - 15:41:43 CDT)
  • Re: problem with PSFGEN (Tue Oct 11 2005 - 11:54:42 CDT)
  • Re: fix backbone atom (Sun Oct 09 2005 - 02:29:57 CDT)
  • RE: water box and the procedure (Fri Oct 07 2005 - 20:38:26 CDT)
  • Re: ion concentration (Thu Oct 06 2005 - 20:21:20 CDT)
  • Re: autoionize and psfgen, which one first? (Thu Oct 06 2005 - 16:11:43 CDT)
  • Re: VMD scripting (Thu Oct 06 2005 - 14:39:51 CDT)
  • RE: random seed (Tue Sep 27 2005 - 20:30:05 CDT)
  • Re: It is posible to allow Bond and angle degrees of freedom in tip3 water?? (Mon Sep 26 2005 - 22:27:04 CDT)
  • Re: problem when do equilibration (Sun Aug 21 2005 - 14:14:12 CDT)
  • Re: par_all27_prot_lipid.inp (Thu Aug 18 2005 - 17:26:08 CDT)
  • RE: PSF file generation (Tue Aug 16 2005 - 01:00:32 CDT)
  • RE: For help with .log file. (Sun Aug 07 2005 - 14:57:58 CDT)
  • RE: Fatal error: (Thu Aug 04 2005 - 08:50:01 CDT)
  • RE: restarting SMD jobs (Tue Jul 26 2005 - 21:07:17 CDT)
  • RE: constrain or fix the system only in Z direction (Thu Jul 21 2005 - 09:34:22 CDT)
  • Re: removing water from DCD (Wed Jul 20 2005 - 20:50:49 CDT)
  • RE: cellBasisVectors and xsc files (Tue Jul 19 2005 - 21:03:07 CDT)
  • Re: Velocity after heating (Mon Jul 18 2005 - 13:35:44 CDT)
  • Re: Velocity after heating (Mon Jul 18 2005 - 12:18:52 CDT)
  • Re: psfgen patches (Thu Jul 14 2005 - 17:10:06 CDT)
  • Re: Unable to Generate PSF file ! (Mon Jul 04 2005 - 14:01:14 CDT)
  • RE: Unable to Generate PSF file ! (Mon Jul 04 2005 - 11:42:44 CDT)
  • RE: Unable to Generate PSF file ! (Mon Jul 04 2005 - 10:06:46 CDT)
  • RE: Adding Misc. Potentials (e.g. spherical/repulsive restraints/constraints ) (Wed Jun 29 2005 - 11:18:23 CDT)
  • RE: Adding Misc. Potentials (e.g. spherical/repulsive restraints/constraints ) (Wed Jun 29 2005 - 09:40:41 CDT)
• Jerome Henin
  • Re: box size changes under anisotropic pressure coupling (Fri Apr 08 2005 - 13:44:19 CDT)
  • Re: FEP output in NAMD (Fri Apr 08 2005 - 13:37:41 CDT)
• Jerry Ebalunode
  • Re: NAMD_2.6b1 shared lib problem on amd64 clustermatic using intel compilers (Fri Aug 19 2005 - 13:33:42 CDT)
  • RE: par_all27_prot_lipid.inp (Fri Aug 19 2005 - 10:59:10 CDT)
  • RE: errno = 2 (Thu Aug 18 2005 - 14:02:21 CDT)
  • RE: errno = 2 (Wed Aug 17 2005 - 16:08:51 CDT)
  • RE: errno = 2 (Wed Aug 17 2005 - 14:05:48 CDT)
  • undefined symbol errors:__builtin_bzero and _alloca building mpi-ppc-darwin version of namd2.6b1 (Wed Aug 17 2005 - 13:58:40 CDT)
  • Re: MM/PBSA (Mon Jun 13 2005 - 18:22:51 CDT)
  • Re: problem running namd (Mon Apr 04 2005 - 16:44:44 CDT)
  • Re: problem running namd (Mon Apr 04 2005 - 15:21:38 CDT)
  • Re: problem running namd (Mon Apr 04 2005 - 14:15:19 CDT)
  • Re: Submitting jobs on myrinet...problem (Fri Mar 11 2005 - 22:21:55 CST)
  • Re: Compiling NAMD with mpicc myrinet (Thu Mar 10 2005 - 15:45:54 CST)
  • atom specification in smd/tclforces for amber topology/parameter based systems (Mon Mar 07 2005 - 14:50:20 CST)
  • 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)
• Jerry Parks
  • RE: removing water from DCD (Thu Jul 21 2005 - 11:27:43 CDT)
  • NAMD/iAPBS (Fri Jul 08 2005 - 16:19:15 CDT)
• Jerry W. Jenkins
  • How do I Heat, then Switch to NPT in the same *.config? (Fri Mar 26 2004 - 10:42:22 CST)
• Jerry Xu
  • how to restart/continue NAMD run (Fri May 06 2005 - 11:28:33 CDT)
  • Hi, call NAMD from C (Mon Jan 31 2005 - 09:28:44 CST)
• Jhih-Wei Chu
  • > 10000 atoms (Fri Aug 13 2004 - 13:32:25 CDT)
• Jianping Wang
  • Re: Radial Distribution Function (Fri Jun 17 2005 - 13:55:40 CDT)
• Jim Kress
  • It appears that the Claim that NAMD works with gromacs is false (Sat Jul 16 2005 - 19:43:42 CDT)
• Jim Phillips
  • RE: trying to generate a peptide (Wed Oct 26 2005 - 09:39:56 CDT)
  • Re: SGE (Grid Engine) on Rocks Cluster (Wed Oct 19 2005 - 17:42:20 CDT)
  • Re: NAMD2.6b1 on an OSX cluster (Thu Aug 25 2005 - 18:36:34 CDT)
  • Re: About the command "loadtotalforces" (Thu Aug 25 2005 - 18:14:34 CDT)
  • Re: peptide out of the water-box (Thu Aug 25 2005 - 18:08:52 CDT)
  • Re: Pressure Profile Simulation (Thu Aug 25 2005 - 18:00:25 CDT)
  • Re: namd 6-1- abf (Mon Aug 22 2005 - 18:35:49 CDT)
  • Re: NBFix command to apply Lorentz-Berthelot mixing rules (Mon Aug 22 2005 - 18:33:41 CDT)
  • Re: NAMD_2.6b1 shared lib problem on amd64 clustermatic using intel compilers (Mon Aug 22 2005 - 18:23:48 CDT)
  • Re: Compilation of NAMD on 64-bit NUMA (Mon Aug 22 2005 - 17:47:52 CDT)
  • Re: vdwGeometricSigma for OPLS in NAMD 2.6b1 Release (Mon Aug 22 2005 - 17:40:53 CDT)
  • Re: volume from VMD and NAMD different? (Fri Aug 05 2005 - 17:46:25 CDT)
  • 4th Annual Workshop on Charm++ and its Applications 2005 (Fri Aug 05 2005 - 17:40:30 CDT)
  • Re: volume from VMD and NAMD different? (Fri Aug 05 2005 - 17:34:45 CDT)
  • Re: error running namd (Fri Aug 05 2005 - 12:48:40 CDT)
  • Re: Running NAMD on a multiprocessor computer (Fri Aug 05 2005 - 12:44:31 CDT)
  • Re: error in config file (Fri Aug 05 2005 - 12:36:07 CDT)
  • Re: LDB question (Fri Aug 05 2005 - 12:28:10 CDT)
  • Re: Fatal error: (Fri Aug 05 2005 - 11:17:30 CDT)
  • Re: H-H bond in TIP3 water (Fri Aug 05 2005 - 11:11:15 CDT)
  • Re: shake and minimzation, equilibration (Fri Aug 05 2005 - 10:58:09 CDT)
  • Re: rigidBond water (Fri Aug 05 2005 - 10:54:44 CDT)
  • Re: velocity quenching (Fri Aug 05 2005 - 10:52:37 CDT)
  • Re: 2.6b1 source missing file (Fri Aug 05 2005 - 10:42:38 CDT)
  • NAMD 2.6b1 Released (Fri Jul 29 2005 - 18:55:59 CDT)
  • 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)
• JIMENEZ Ralph
  • successive minimization with different sets of fixed atoms (Tue Dec 06 2005 - 11:14:25 CST)
  • more heme troubles (Thu Oct 06 2005 - 16:14:45 CDT)
  • psfgen trouble with heme (Wed Oct 05 2005 - 14:54:26 CDT)
  • unexpected end with NAMD on quad-dual core opteron machine (Thu Sep 29 2005 - 12:59:42 CDT)
• Jindal Shah
  • PSF file format (Tue Dec 20 2005 - 15:55:23 CST)
  • Re: vmd-l: Script for calculating energy of a water molecule (Wed Aug 17 2005 - 17:07:12 CDT)
  • Script for calculating energy of a water molecule (Wed Aug 17 2005 - 11:41:23 CDT)
• Joachim Hein
  • Building NAMD 2.6b1 on IBM Power5 (Tue Dec 06 2005 - 03:49:53 CST)
  • Re: Namd2.6b1 FATAL ERROR: Memory allocation failed on AIX53 IBM-SP4 (Mon Nov 21 2005 - 04:12:05 CST)
  • Re: namd and fftw (Tue Mar 15 2005 - 03:56:13 CST)
• John Kerrigan
  • Re: peridic boundary condition (Fri Mar 11 2005 - 15:18:48 CST)
• John Saeger
  • Re: installing NAMD on opteron cluster with MPI (Wed Mar 09 2005 - 15:12:08 CST)
  • Re: clustermatic 4 and 5 Namd/charm (Sun Jan 02 2005 - 14:18:31 CST)
  • Re: problems on Fedora Core 3 (Thu Dec 30 2004 - 13:20:16 CST)
• John Stone
  • Re: vmd-l: ptraj (Tue Sep 27 2005 - 09:57:34 CDT)
  • Re: vmd-l: Sybyl trajectory (Tue Sep 06 2005 - 09:43:23 CDT)
  • Re: vmd-l: Script for calculating energy of a water molecule (Wed Aug 17 2005 - 14:32:41 CDT)
  • Re: vmd-l: Nanotube Simulations (Tue Aug 02 2005 - 12:34:58 CDT)
  • Re: vmd-l: Re: catdcd and dcdunitcell (Mon Jul 25 2005 - 13:50:03 CDT)
  • Re: vmd-l: autoimd on windows (Tue Jun 21 2005 - 15:43:11 CDT)
  • Re: Re: vmd-l: Interactive Simulations, ligand size limits.... (Thu Apr 28 2005 - 13:05:40 CDT)
  • Re: Re: vmd-l: Interactive Simulations, ligand size limits.... (Thu Apr 28 2005 - 10:08:17 CDT)
  • Re: Re: vmd-l: Interactive Simulations, ligand size limits.... (Thu Apr 21 2005 - 16:28:08 CDT)
  • Re: vmd-l: Interactive Simulations, ligand size limits.... (Wed Apr 20 2005 - 16:12:20 CDT)
  • Re: vmd-l: conformational alignment (Wed Mar 30 2005 - 15:30:26 CST)
  • 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)
• jonathan_at_ibt.unam.mx
  • Re: Counterions: how to decide how many to put it? (Tue Dec 13 2005 - 21:05:34 CST)
• Jordi Camps
  • RE: Compiling on Linux-PPC970-Myrinet-MPI-xlC (Thu Mar 10 2005 - 18:08:02 CST)
  • Compiling on Linux-PPC970-Myrinet-MPI-xlC (Thu Mar 10 2005 - 12:57:47 CST)
• Jordi Cohen
  • Re: vmd-l: Nanotube Simulations (Tue Aug 02 2005 - 14:41:03 CDT)
• Jorge Pikunic
  • H-H bond in TIP3 water (Mon Aug 01 2005 - 17:21:26 CDT)
  • Re: H-H bond in solvate (Sat Jul 30 2005 - 09:35:13 CDT)
  • H-H bond in solvate (Sat Jul 30 2005 - 08:57:59 CDT)
  • concatenating two or more dcd files (Mon Apr 18 2005 - 10:44:07 CDT)
  • 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
  • Re: vmd-l: Sybyl trajectory (Tue Sep 06 2005 - 05:38:38 CDT)
  • Sybyl trajectory (Mon Sep 05 2005 - 01:56:04 CDT)
  • Re: socket closed error (Tue Mar 29 2005 - 01:01:34 CST)
  • 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)
• Joseph E. Curtis, Ph. D.
  • constant angle NPT simulation (Thu Nov 04 2004 - 12:16:21 CST)
• Joshua D. Moore
  • ABSOLUTE IMPRECISION and RELATIVE IMPRECISION IN TABLE FORCE (Fri Dec 23 2005 - 03:01:17 CST)
  • Re: UNABLE TO OPEN .psf FILE (Fri Dec 23 2005 - 02:56:34 CST)
  • UNABLE TO OPEN .psf FILE (Fri Dec 23 2005 - 02:53:00 CST)
  • Re: Question about Generating DCD files with only specified atoms (Thu Dec 22 2005 - 22:23:02 CST)
  • Re: Besides PSFGEN, are there any other good ways of generating .psf file (Thu Dec 22 2005 - 21:01:31 CST)
  • Question about Generating DCD files with only specified atoms (Thu Dec 22 2005 - 18:06:09 CST)
  • Re: The HT-HT-OT angle parameter for TIP3? (Thu Dec 22 2005 - 18:03:57 CST)
  • Re: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CN7 CN7 CN7 (Wed Dec 21 2005 - 16:57:37 CST)
  • flipDCD and Unit Cell information? (Mon Dec 19 2005 - 17:54:06 CST)
  • Re: Packaging 100 cations and anions in a box (Wed Dec 07 2005 - 02:25:23 CST)
  • Re: merge trajectory from NAMD (Wed Nov 30 2005 - 21:43:13 CST)
  • Update on Implicit Solvent Models in NAMD? (Fri Nov 25 2005 - 14:01:31 CST)
  • Using an arbitrary tabulated potential in NAMD (Tue Sep 27 2005 - 21:44:26 CDT)
  • Re: Free Energy of Conformational Change Calculations Error: "Problem parsing input parameters Error: Invalid AtomID" (Sat Sep 10 2005 - 17:49:26 CDT)
  • Free Energy of Conformational Change Calculations Error: "Problem parsing input parameters Error: Invalid AtomID" (Thu Sep 08 2005 - 22:13:17 CDT)
  • Re: pair interactions in NPT (Sun Sep 04 2005 - 18:12:59 CDT)
  • NAMD 2.6b1 Skipped Writing Velocity Restart File (Tue Aug 30 2005 - 01:09:20 CDT)
  • NBFix command to apply Lorentz-Berthelot mixing rules (Sun Aug 21 2005 - 14:45:59 CDT)
  • Re: Large Box Sizes and Total Energies Observed in NAMD 2.6b1 Binaries of AIX-POWER-MPI and Origin2000-MPI (Fri Aug 19 2005 - 14:42:02 CDT)
  • Re: Large Box Sizes and Total Energies Observed in NAMD 2.6b1 Binaries of AIX-POWER-MPI and Origin2000-MPI (Fri Aug 19 2005 - 06:38:04 CDT)
  • Large Box Sizes and Total Energies Observed in NAMD 2.6b1 Binaries of AIX-POWER-MPI and Origin2000-MPI (Thu Aug 18 2005 - 17:35:21 CDT)
  • Linux-MPI binary of NAMD 2.6b1 (Thu Aug 18 2005 - 06:09:41 CDT)
  • Re: vdwGeometricSigma for OPLS in NAMD 2.6b1 Release (Sat Aug 13 2005 - 03:21:44 CDT)
  • vdwGeometricSigma for OPLS in NAMD 2.6b1 Release (Wed Aug 10 2005 - 18:59:45 CDT)
  • Re: For help with .log file. (Sun Aug 07 2005 - 23:43:30 CDT)
  • Re: VMD solvate in CCl4 (Tue Jul 26 2005 - 20:55:03 CDT)
  • Re: vmd-l: Re: catdcd and dcdunitcell (Mon Jul 25 2005 - 14:16:16 CDT)
  • Fixed atoms and dcd file with DCDunitCell on (Fri Jul 22 2005 - 16:46:15 CDT)
  • Re: catdcd and dcdunitcell (Fri Jul 22 2005 - 16:04:00 CDT)
  • SPC/E Water Model and RigidBonds (Fri Jul 08 2005 - 15:46:41 CDT)
  • Periodic Boundary Conditions and Wrap (Tue Jun 28 2005 - 03:31:38 CDT)
  • Zeros at the beginning of each line in the output (Thu Jun 23 2005 - 19:17:43 CDT)
  • RE: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? (Wed Jun 22 2005 - 00:58:48 CDT)
  • Error when running NAMD at SDSC (Sun Jun 19 2005 - 22:13:20 CDT)
  • rigidBonds water (Sun Jun 05 2005 - 21:39:09 CDT)
  • Re: Converting Gromacs OPLS parameters to Charmm format (Tue May 17 2005 - 17:35:18 CDT)
• 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)
• 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)
• junwang
  • the lastest version of NAMD source (Sun May 29 2005 - 12:29:35 CDT)
  • Compilation of NAMD on opteron cluster with myrinet (Mon May 23 2005 - 19:44:41 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)
• Jyh-Shyong Ho
  • NAMD/CHARM source installation option (Sat Dec 17 2005 - 23:36:55 CST)
• jz7_at_duke.edu
  • question about patch (Thu Mar 24 2005 - 09:33:04 CST)
  • 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: Reading from DCD file and running MD (Wed Dec 07 2005 - 16:19:08 CST)
  • Re: ABF for conformational analysis (Mon Nov 14 2005 - 03:34:21 CST)
  • Re: ABF Simulation (Fri Oct 28 2005 - 04:05:52 CDT)
  • Re: ABF Simulation (Wed Oct 19 2005 - 04:11:17 CDT)
  • Re: ABF Simulation (Wed Oct 05 2005 - 11:35:25 CDT)
  • Re: abf (Tue Sep 06 2005 - 08:48:25 CDT)
  • Re: changing file (Wed Jul 20 2005 - 05:07:19 CDT)
  • Re: setting configuration file for free energy perturbation (Mon Jul 18 2005 - 12:18:39 CDT)
  • Re: Energy Order of Magnitude (Mon Jul 11 2005 - 14:49:49 CDT)
  • Re: FEP - one long simulation vs many short ones (Sat Jul 02 2005 - 18:45:11 CDT)
  • Re: catdcd and dcdunitcell (Tue Jun 28 2005 - 10:54:09 CDT)
  • Re: catdcd and dcdunitcell (Tue Jun 28 2005 - 09:14:32 CDT)
  • Re: Accessing beta / occupancy values from NAMD tcl (Mon Jun 27 2005 - 11:52:05 CDT)
  • Re: Using FEP as non-disruptive mutation procedure (Mon Jun 27 2005 - 05:19:37 CDT)
  • Re: new approach to counter FEP end-point VDW clashes (Mon Jun 27 2005 - 03:31:34 CDT)
  • Re: Tcl forces (Thu Jun 16 2005 - 07:19:13 CDT)
  • Re: non-repeatability NAMD simulations (Wed May 11 2005 - 03:00:55 CDT)
  • Re: different result from different cpu (Tue May 10 2005 - 11:40:25 CDT)
  • Re: addforce (Tue Apr 19 2005 - 11:21:21 CDT)
  • Re: peridic boundary condition (Fri Mar 11 2005 - 15:31:47 CST)
  • Re: CAN'T FIND BOND PARAMETERS FOR BOND (error) (Thu Mar 10 2005 - 07:59:14 CST)
  • Re: CAN'T FIND BOND PARAMETERS FOR BOND (error) (Thu Mar 10 2005 - 05:16:35 CST)
  • Re: writeback periodic cell info in dcd output (Mon Feb 21 2005 - 17:49:55 CST)
  • Re: alchemify FEP (Thu Feb 17 2005 - 15:04:18 CST)
  • Re: Protein moving out of PBC water box (Tue Feb 08 2005 - 17:08:05 CST)
  • Re: FEP (Tue Feb 01 2005 - 13:14:05 CST)
  • Re: thermodynamic integration and NAMD: soft-core or "separation-shifted" vdw potentials (Mon Jan 10 2005 - 15:57:01 CST)
  • Re: parameters for NVT ensemble (Fri Jan 07 2005 - 07:58:12 CST)
  • 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)
• 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)
• Karina Martinez
  • Compliling NAMD in RedHat9 (Wed May 11 2005 - 21:59:28 CDT)
• Karunesh Arora
  • NAMD crashes with LES option ON (Mon Feb 07 2005 - 14:07:18 CST)
• Kasson
  • Gromacs parameters in NAMD (Thu Oct 20 2005 - 13:21:06 CDT)
• Ken Sale
  • psfgen (Wed Jul 21 2004 - 15:14:43 CDT)
  • Re: compiling NAMD (Wed Apr 07 2004 - 19:23:07 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)
• Koo Kee Kiat
  • Errors compiling NAMD 2.5 (Mon Apr 04 2005 - 01:46:34 CDT)
• Kyle Gustafson
  • rigid bonds for other atoms (Thu Oct 06 2005 - 13:40:23 CDT)
  • Re: mpi problems on opteron (Thu Aug 04 2005 - 07:54:20 CDT)
  • Re: shape change of water box and peptide move out (Fri Jul 29 2005 - 16:46:11 CDT)
  • opteron 64bit installation (Fri Jul 29 2005 - 10:29:11 CDT)
  • compiling NAMD: plugins (Mon Jul 25 2005 - 19:53:01 CDT)
  • Re: mpi problems on opteron (Mon Jul 25 2005 - 19:04:56 CDT)
  • mpi problems on opteron (Mon Jul 25 2005 - 16:05:02 CDT)
  • NAMD on dual opterons (Mon Jul 25 2005 - 13:30:44 CDT)
• 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: hydrogens collapsing (Tue Jan 18 2005 - 12:12:04 CST)
  • hydrogens collapsing (Tue Jan 18 2005 - 08:46:23 CST)
  • namdstats (Tue Jan 11 2005 - 01:54:54 CST)
  • parameters for NVT ensemble (Fri Jan 07 2005 - 04:51:07 CST)
  • Re: problems on Fedora Core 3 (Fri Dec 31 2004 - 13:10:04 CST)
  • estradiol (Tue Aug 31 2004 - 06:56:44 CDT)
• Lea Thøgersen
  • NAMD on Win64 (Mon Dec 12 2005 - 10:26:11 CST)
• Leandro Martinez
  • using namd to compute energies (Tue Feb 15 2005 - 13:24:20 CST)
  • smd and loadforces (Mon Jan 17 2005 - 11:06:50 CST)
  • 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)
• Leandro Martínez
  • pause simulation (Fri Dec 16 2005 - 12:53:23 CST)
  • Re: center of mass motion: problems (Thu Dec 08 2005 - 17:49:23 CST)
  • Re: Question regarding SMD (Mon Oct 31 2005 - 17:26:23 CST)
  • Re: Only part of the protein is moving in MD simulation (Wed Oct 26 2005 - 10:58:19 CDT)
  • Re: mpi problems on opteron (Mon Jul 25 2005 - 19:11:13 CDT)
  • Re: mpi problems on opteron (Mon Jul 25 2005 - 19:00:04 CDT)
  • addforce (Tue Jun 14 2005 - 10:02:28 CDT)
  • interface with external program (Fri Jun 10 2005 - 13:15:30 CDT)
  • Re: interface with external program (Fri Jun 10 2005 - 13:55:53 CDT)
  • Re: dielectric constant (Thu May 12 2005 - 13:24:10 CDT)
  • Re: addforce (Tue Apr 19 2005 - 11:37:55 CDT)
  • addforce (Tue Apr 19 2005 - 09:38:50 CDT)
  • Re: any script to build membrane+protein+solvent? (Sat Apr 09 2005 - 07:20:07 CDT)
  • Re: (Fri Apr 08 2005 - 13:50:34 CDT)
  • Re: question about par_all27_prot_lipid.inp (Sun Mar 20 2005 - 06:13:17 CST)
• Lechuga, Javier
  • Membrane configuration file (Fri Apr 08 2005 - 10:24:01 CDT)
• Lee Jason
  • RE: LDB question (Tue Aug 02 2005 - 08:01:52 CDT)
• 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)
• Leonardo Sepulveda Durán
  • Question about cutoff distance (Tue Oct 11 2005 - 17:06:10 CDT)
  • Re: running NAMD2 in parallel (Mon Oct 10 2005 - 23:24:46 CDT)
  • Re: running NAMD2 in parallel (Mon Oct 10 2005 - 22:03:27 CDT)
  • Question about cutoff distance (Wed Oct 05 2005 - 12:56:24 CDT)
  • It is posible to allow Bond and angle degrees of freedom in tip3 water?? (Mon Sep 26 2005 - 16:52:55 CDT)
  • Re: energy values (Tue Sep 13 2005 - 11:38:21 CDT)
  • Re: problem when heating the system (Tue Aug 30 2005 - 07:53:49 CDT)
  • problems with autoionize total charge and minimization (Tue Jul 05 2005 - 14:18:25 CDT)
  • PMF force restraint question (Mon Jun 27 2005 - 19:11:11 CDT)
  • Using FEP as non-disruptive mutation procedure (Sun Jun 26 2005 - 17:10:17 CDT)
  • Re: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? (Sun Jun 26 2005 - 15:53:29 CDT)
  • changuing dihedral angle slowly (complete message) (Fri Jun 24 2005 - 17:47:02 CDT)
  • changuing dihedral angle slowly (Fri Jun 24 2005 - 17:35:20 CDT)
  • Re: Hi,how can I generate a psf file with a pdb file contain some special amino acid like TYS (Fri Jun 24 2005 - 10:33:40 CDT)
  • Re: Hi,how can I generate a psf file with a pdb file contain some special amino acid like TYS (Fri Jun 24 2005 - 09:30:26 CDT)
  • Re: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? (Wed Jun 22 2005 - 12:12:48 CDT)
  • Re: Fixed restraint (Tue Jun 21 2005 - 18:56:45 CDT)
  • Re: namdplot, graph is empty (Tue Jun 21 2005 - 15:10:22 CDT)
  • Re: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? (Tue Jun 21 2005 - 12:42:07 CDT)
  • Re: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? (Mon Jun 20 2005 - 12:53:09 CDT)
  • Solvent model other than TIP3 for use with CHARMM FF in NAMD?? (Sun Jun 19 2005 - 12:58:18 CDT)
  • How to conservate energy during NVE simulations??? (Wed Jun 15 2005 - 20:55:29 CDT)
  • Adjusting Density of waterbox used by solvate (Sun Jun 12 2005 - 21:51:51 CDT)
  • water density calculation (Fri Jun 10 2005 - 21:19:50 CDT)
  • it is posible to do NVE simulations in NAMD??? (Fri Jun 10 2005 - 18:04:16 CDT)
  • Re: implicit solvent (Thu Jun 09 2005 - 21:26:40 CDT)
  • Re: large vanderwalls energy during minimization (Thu Jun 09 2005 - 16:42:15 CDT)
  • Re: large vanderwalls energy during minimization (Thu Jun 09 2005 - 14:50:31 CDT)
  • Avoiding Rotation and translation of protein (Wed Jun 08 2005 - 10:58:33 CDT)
  • ligands in VMD (Wed Jun 01 2005 - 20:20:02 CDT)
  • Generating a lot of segments in proper order and selection around a center of mass (Wed Jun 01 2005 - 16:13:35 CDT)
  • question about nonnbonded parameters (Tue May 31 2005 - 11:04:23 CDT)
  • Problem with solvate and PSF files in CHARMM format (Mon May 30 2005 - 18:37:05 CDT)
  • Re: namddat not working (Wed May 25 2005 - 15:43:28 CDT)
  • namddat not working (Tue May 24 2005 - 16:34:24 CDT)
  • Re: Re: Simulated Annealing Config (Tue May 24 2005 - 14:55:49 CDT)
• LEWYN LI
  • Re: Atoms moving too fast (Tue Dec 06 2005 - 13:55:24 CST)
  • Adding amino acids to an existing pdb structure (Sun Dec 04 2005 - 21:30:49 CST)
  • Re: Problems opening the Extended Trajectory File (Thu Dec 01 2005 - 14:57:42 CST)
  • Re: About RMSD calculation. (Fri Oct 28 2005 - 15:30:20 CDT)
  • Re: saving coordinates as a PDB file after minimization in NAMD (Tue Oct 25 2005 - 16:32:19 CDT)
  • Re: Metal Ion and Protein binding (Thu Oct 13 2005 - 13:38:07 CDT)
  • Re: NAMD restarts binary files (Wed Oct 12 2005 - 11:27:01 CDT)
  • Re: energy values (Tue Sep 13 2005 - 15:16:48 CDT)
  • Re: vmd-l: script (Tue Sep 06 2005 - 11:12:35 CDT)
  • NAMD running only at 40-50% CPU capacity (Fri Sep 02 2005 - 11:00:35 CDT)
  • About the command "loadtotalforces" (Mon Aug 22 2005 - 21:25:44 CDT)
  • Re: addforce (Tue Jun 14 2005 - 14:07:10 CDT)
  • Re: water density calculation (Fri Jun 10 2005 - 22:22:42 CDT)
  • 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)
• Leyla Celik
  • Re: topology and parameter for acetylcholine (Mon Oct 10 2005 - 01:27:41 CDT)
  • Re: Analysis of NAMD output with CHARMM (Mon Feb 14 2005 - 09:44:53 CST)
  • Re: Analysis of NAMD output with CHARMM (Mon Feb 14 2005 - 07:48:28 CST)
  • Analysis of NAMD output with CHARMM (Mon Feb 14 2005 - 02:47:42 CST)
  • Protein moving out of PBC water box (Tue Feb 08 2005 - 15:23:31 CST)
• 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)
• li jianguo
  • charmm parameters for PEG (Sat Jun 04 2005 - 23:42:26 CDT)
• Lina M Nilsson
  • installing NAMD on opteron cluster with MPI (Thu Mar 03 2005 - 16:06:13 CST)
• Lina Nilsson
  • unstable simulation with AMBER ff in AMBER! (Wed Apr 13 2005 - 04:05:36 CDT)
  • AMBER ff system has too high velocities in NAMD (Wed Apr 13 2005 - 03:16:45 CDT)
  • Re: installing NAMD on opteron cluster with MPI (Tue Mar 08 2005 - 02:27:25 CST)
• Lionel Perrin
  • Re: ABF Simulation (Wed Nov 02 2005 - 08:28:25 CST)
  • Re: ABF Simulation (Wed Oct 26 2005 - 10:52:53 CDT)
  • Re: ABF Simulation (Fri Oct 21 2005 - 04:03:02 CDT)
  • Re: ABF Simulation (Thu Oct 06 2005 - 09:13:45 CDT)
  • ABF Simulation (Wed Oct 05 2005 - 06:41:44 CDT)
• liu xin
  • Dose restart frequently affect the results? (Fri Dec 23 2005 - 21:33:40 CST)
  • restart problem (Fri Dec 02 2005 - 00:01:26 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)
• Luis Gracia
  • Re: vmd-l: script (Tue Sep 06 2005 - 13:21:40 CDT)
• Luis Rosales
  • Re: basic: combining two pdb files? (Fri Jun 24 2005 - 03:25:46 CDT)
  • Re: set center (Tue Jun 21 2005 - 17:33:53 CDT)
  • Re: vmdtext? (Thu Jun 16 2005 - 15:09:01 CDT)
  • Re: Combine pdb and psf files (Fri Apr 29 2005 - 18:26:06 CDT)
  • Re: Re: vmd-l: Interactive Simulations, ligand size limits.... (Wed Apr 27 2005 - 21:29:51 CDT)
  • Re: Setting target minimization gradient? (Fri Apr 22 2005 - 19:49:18 CDT)
  • Re: Re: vmd-l: Interactive Simulations, ligand size limits.... (Wed Apr 20 2005 - 22:22:10 CDT)
  • Re: vmd-l: Interactive Simulations, ligand size limits.... (Wed Apr 20 2005 - 18:19:58 CDT)
  • Interactive Simulations, ligand size limits.... (Tue Apr 19 2005 - 22:51:52 CDT)
  • RE: equilibrated the system (Tue Jan 11 2005 - 17:49:16 CST)
  • 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
  • Qestions about NPT simulations. (Wed Jan 26 2005 - 07:29:47 CST)
  • 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)
• Mahalakshmi Sahasranaman
  • add ions (Mon Aug 08 2005 - 07:41:33 CDT)
• 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)
• Manori Indira Jayasinghe
  • Re: FATAL ERROR: unknown floating-point error, errno = 4 (Fri Dec 23 2005 - 11:47:10 CST)
  • FATAL ERROR: unknown floating-point error, errno = 4 (Thu Dec 22 2005 - 23:16:41 CST)
  • Re: define abf1 and abf2 for CM of water and CM of molecule (Wed Dec 21 2005 - 11:26:37 CST)
  • define abf1 and abf2 for CM of water and CM of molecule (Mon Dec 19 2005 - 22:53:42 CST)
• Manuela Cavallari
  • force calculation (Thu Jun 16 2005 - 11:53:13 CDT)
  • Tcl forces (Thu Jun 16 2005 - 05:51:05 CDT)
• Marc Baaden
  • Replica-Exchange MD (Fri Nov 18 2005 - 03:18:19 CST)
  • Re: Different solvents (Sun Nov 13 2005 - 07:49:19 CST)
  • Re: Re: vmd-l: Interactive Simulations, ligand size limits.... (Fri Apr 29 2005 - 04:01:27 CDT)
  • Bio-Image summer school in Paris this year (Wed Mar 16 2005 - 05:42:59 CST)
• Marc Q. Ma
  • Re: successive minimization with different sets of fixed atoms (Tue Dec 06 2005 - 12:31:36 CST)
  • Re: Na ions got into the catalytic site during Production Run (Mon Nov 21 2005 - 09:29:51 CST)
  • Re: Problem with NAMD on Opteron cluster (Mon Nov 14 2005 - 08:37:55 CST)
  • wallclock and cputime (Thu Sep 01 2005 - 16:31:01 CDT)
  • Re: About the command "loadtotalforces" (Fri Aug 26 2005 - 09:25:58 CDT)
  • scripts for binding free energy calculation using SMD and Jarzynski's equality (Wed Aug 17 2005 - 09:45:12 CDT)
  • Re: rigidBond water (Wed Aug 03 2005 - 14:57:26 CDT)
  • Re: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? (Tue Jun 21 2005 - 14:11:43 CDT)
  • Re: Avoiding Rotation and translation of protein (Fri Jun 10 2005 - 11:35:04 CDT)
  • Re: implicit solvent (Fri Jun 10 2005 - 08:28:21 CDT)
  • Re: Avoiding Rotation and translation of protein (Wed Jun 08 2005 - 16:58:02 CDT)
  • Re: Molecular Dynamics or Langevin Dynamics (Wed Apr 27 2005 - 12:39:29 CDT)
  • Re: Molecular Dynamics or Langevin Dynamics (Wed Apr 27 2005 - 09:38:13 CDT)
  • Re: addforce (Tue Apr 19 2005 - 11:17:20 CDT)
  • Re: concatenating two or more dcd files (Mon Apr 18 2005 - 12:13:51 CDT)
  • Re: AMBER ff system has too high velocities in NAMD (Wed Apr 13 2005 - 08:59:31 CDT)
  • Re: RATTLE and DNA (Tue Apr 05 2005 - 09:01:35 CDT)
  • Re: multiple MD simulations (Wed Mar 30 2005 - 11:57:11 CST)
  • Re: multiple MD simulations (Tue Mar 29 2005 - 07:42:46 CST)
  • Re: peridic boundary condition (Fri Mar 11 2005 - 14:00:37 CST)
  • Re: peridic boundary condition (Fri Mar 11 2005 - 13:15:31 CST)
  • Re: peridic boundary condition (Fri Mar 11 2005 - 10:38:15 CST)
  • Re: Kinetic energy (Fri Feb 25 2005 - 15:24:33 CST)
  • Re: PMEGridSize (Thu Feb 24 2005 - 16:52:19 CST)
  • cellOrigin (Tue Feb 22 2005 - 14:06:04 CST)
  • writeback periodic cell info in dcd output (Mon Feb 21 2005 - 16:16:01 CST)
• Marcela Madrid
  • render format (Mon Aug 02 2004 - 13:15:17 CDT)
• Marcela P.Aliste
  • Amber and SHAKE algorimth (Thu Feb 24 2005 - 16:14:26 CST)
  • restart simulation (Mon May 10 2004 - 16:01:28 CDT)
• Marcos Sotomayor
  • Re: Atoms moving too fast (Tue Dec 06 2005 - 13:43:54 CST)
  • Re: restart problem (Fri Dec 02 2005 - 00:10:18 CST)
  • Re: A question on minimization (Fri Nov 04 2005 - 16:18:46 CST)
  • Re: The vector direction in SMD (Fri Nov 04 2005 - 15:29:52 CST)
  • Re: Size of water box (Fri Nov 04 2005 - 14:59:17 CST)
  • Re: Serious Steric Atom Clashes (Mon Oct 24 2005 - 13:51:13 CDT)
  • Re: Solvent model other than TIP3 for use with CHARMM FF in NAMD?? (Sun Jun 26 2005 - 14:04:28 CDT)
  • Re: Error on Solaris (Sat Jun 25 2005 - 17:53:52 CDT)
  • Re: How to conservate energy during NVE simulations??? (Thu Jun 16 2005 - 10:30:28 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)
• Maria Lin
  • Poorly guessed coordinates (Tue Jun 14 2005 - 14:03:59 CDT)
  • Namd on Mac os X (Wed Jun 08 2005 - 18:57:10 CDT)
• Mark A. Hallman
  • restart syntax (Tue Jun 21 2005 - 13:23:16 CDT)
  • config files (Tue Jun 07 2005 - 12:17:35 CDT)
• Mark Abraham
  • Re: Replica-Exchange MD (Fri Nov 18 2005 - 08:00:36 CST)
  • Re: namd: advice (Fri Nov 04 2005 - 14:30:55 CST)
  • Re: Size of water box (Fri Nov 04 2005 - 14:29:36 CST)
  • Replica-Exchange MD (Mon Oct 31 2005 - 22:57:17 CST)
  • 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 rigid bonds (Mon Jan 17 2005 - 07:24:39 CST)
  • 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)
• Matan Dishon
  • creating a pdb file based on sequence and psi phi omega values only (Sun Aug 28 2005 - 04:58:07 CDT)
  • peptide simulation (Mon Jun 27 2005 - 03:28:18 CDT)
  • inorganic surface peptide simulation (Mon Jun 06 2005 - 07:13:07 CDT)
• Matt Harrington
  • performance differences on 2.4 vs. 2.6 Linux kernels (Thu Apr 07 2005 - 19:10:54 CDT)
  • 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
  • PMF Calculation (Tue Feb 08 2005 - 04:38:20 CST)
• Matthew Wilce
  • Bromine (Wed Jul 20 2005 - 01:43:43 CDT)
  • FEP and TI (Sun Jun 12 2005 - 22:42:05 CDT)
  • FEP and solvent (Sun Jun 12 2005 - 22:35:32 CDT)
  • protein/DNA complexes (Fri May 06 2005 - 00:27:34 CDT)
• Mauricio Arenas Salinas
  • Re: Namd2.6b1 FATAL ERROR: Memory allocation failed on AIX53 IBM-SP4 (Mon Nov 21 2005 - 09:10:16 CST)
• Mauricio Carrillo Tripp
  • SGE (Grid Engine) on Rocks Cluster (Wed Oct 19 2005 - 17:27:57 CDT)
  • Re: Penetration of water (Fri Oct 07 2005 - 10:40:13 CDT)
  • Re: About the potantial of IONS (Fri Oct 07 2005 - 10:29:17 CDT)
  • 1-4 interactions scaling (Mon Oct 03 2005 - 14:30:00 CDT)
  • NAMD & Gromacs FF (Thu Sep 01 2005 - 16:21:50 CDT)
  • ERROR: Margin is too small (BUG?) (Wed Aug 03 2005 - 10:02:42 CDT)
  • Report on a trajectory incompatibility between NAMD and CHARMM: Unfolding and RDFs (Fri Jul 29 2005 - 16:36:07 CDT)
  • Re: catdcd-generated files and CHARMM (Thu Jul 21 2005 - 16:10:11 CDT)
  • Re: catdcd-generated files and CHARMM (Thu Jul 21 2005 - 14:05:10 CDT)
  • Re: Runnig same config file many times (Fri Jul 15 2005 - 17:33:48 CDT)
  • Re: Runnig same config file many times (Fri Jul 15 2005 - 16:45:05 CDT)
  • Re: FEP - one long simulation vs many short ones (Fri Jul 01 2005 - 18:27:24 CDT)
  • hard wall (Thu Jun 23 2005 - 11:24:00 CDT)
  • unwrapping dcd trajectory (Mon Apr 25 2005 - 16:47:42 CDT)
  • Re: Not getting good speed up (Fri Mar 18 2005 - 16:12:30 CST)
  • strange behaviour when running apoa1 on 1 processor (Thu Mar 17 2005 - 13:36:47 CST)
  • Re: Not getting good speed up (Tue Mar 15 2005 - 10:55:16 CST)
  • Re: Not getting good speed up (Sat Mar 12 2005 - 15:38:06 CST)
  • Re: Not getting good speed up (Fri Mar 11 2005 - 15:32:38 CST)
  • namd2 mpi error (Thu Mar 10 2005 - 14:58:37 CST)
  • Re: Not getting good speed up (Thu Mar 03 2005 - 13:44:55 CST)
  • Re: Not getting good speed up (Thu Mar 03 2005 - 13:16:24 CST)
  • Not getting good speed up (Wed Mar 02 2005 - 16:37:18 CST)
  • 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)
• Meunier, Vincent
  • basic: combining two pdb files? (Thu Jun 23 2005 - 20:16:45 CDT)
• Mgr. Lubos Vrbka
  • extra points in NAMD (Sat Dec 17 2005 - 06:51:46 CST)
• michael atkinson
  • abf (Sun Sep 04 2005 - 22:21:29 CDT)
  • namd 6-1- abf (Mon Aug 15 2005 - 01:38:36 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
  • (no subject) (Thu Oct 27 2005 - 22:39:35 CDT)
  • Re: urestraint doesn't work (Thu Oct 27 2005 - 20:55:49 CDT)
  • Re: urestraint doesn't work (Thu Oct 27 2005 - 19:06:01 CDT)
  • Re: (Fri Oct 21 2005 - 12:15:15 CDT)
  • (no subject) (Wed Oct 19 2005 - 19:09:19 CDT)
  • (no subject) (Wed Oct 19 2005 - 14:53:14 CDT)
  • Re: NAMD distribute (Wed Oct 12 2005 - 21:31:10 CDT)
  • Re: NAMD2.6b1 on an OSX cluster (Fri Sep 09 2005 - 15:39:15 CDT)
  • NAMD2.6b1 on an OSX cluster (Tue Aug 23 2005 - 17:16:56 CDT)
  • Re: Using FEP as non-disruptive mutation procedure (Mon Jun 27 2005 - 11:19:13 CDT)
  • Re: implicit solvent (Fri Jun 10 2005 - 11:18:34 CDT)
  • NAMD hangs (Sun May 29 2005 - 15:53:09 CDT)
  • Re: regenerating PSF file (Wed May 18 2005 - 02:11:41 CDT)
  • Re: (Fri Apr 08 2005 - 12:31:36 CDT)
  • (no subject) (Fri Apr 08 2005 - 12:04:37 CDT)
  • Re: modifying cut off (Thu Apr 07 2005 - 19:38:03 CDT)
  • Re: modifying cut off (Thu Apr 07 2005 - 19:00:31 CDT)
  • path problems (Tue Mar 22 2005 - 01:29:25 CST)
  • G5 clusters (Tue Mar 08 2005 - 11:17:42 CST)
  • Re: question (fwd) (Mon Mar 07 2005 - 15:30:48 CST)
  • Re: alchemify FEP (Fri Feb 18 2005 - 01:26:17 CST)
  • 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)
• michael jerry
  • merge trajectory from NAMD (Wed Nov 30 2005 - 16:19:57 CST)
  • General question about NAMD (Tue Nov 08 2005 - 10:52:04 CST)
• Michel Espinoza-Fonseca
  • RE: charmm27 fatal error (Mon Dec 19 2005 - 15:30:41 CST)
  • RE: NAMD on Win64 (Mon Dec 12 2005 - 10:53:19 CST)
  • RE: Na ions got into the catalytic site during Production Run (Mon Nov 21 2005 - 10:16:38 CST)
  • RE: About ADP (Tue Nov 01 2005 - 13:21:22 CST)
  • RE: About ADP (Tue Nov 01 2005 - 10:16:43 CST)
  • RE: How to append charmm stream file (Wed Oct 26 2005 - 12:36:01 CDT)
  • RE: trying to generate a peptide (Wed Oct 26 2005 - 09:19:08 CDT)
  • RE: trying to generate a peptide (Wed Oct 26 2005 - 03:35:23 CDT)
  • topology and parameter for acetylcholine (Fri Oct 07 2005 - 06:28:38 CDT)
  • ptraj (Tue Sep 27 2005 - 06:24:50 CDT)
  • RE: Constraint failure (Mon Sep 26 2005 - 13:54:52 CDT)
  • RE: autoionize & namd2 (Thu Sep 22 2005 - 02:51:08 CDT)
  • RE: autoionize & namd2 (Wed Sep 21 2005 - 09:57:17 CDT)
  • RE: autoionize & namd2 (Wed Sep 21 2005 - 09:32:45 CDT)
  • RE: autoionize & namd2 (Wed Sep 21 2005 - 02:24:09 CDT)
  • reconstructing backbone with psfgen (Tue Sep 20 2005 - 09:07:04 CDT)
  • reconstructing backbone with psfgen (Tue Sep 20 2005 - 05:45:10 CDT)
  • namd performance on altix machines (Fri Sep 09 2005 - 07:10:48 CDT)
  • RE: par_all27_prot_lipid.inp (Fri Aug 19 2005 - 11:28:07 CDT)
  • RE: Nanotube Simulations (Tue Aug 02 2005 - 09:50:18 CDT)
  • RE: shape change of water box and peptide move out (Fri Jul 29 2005 - 12:35:09 CDT)
  • RE: Help with SMD (Wed Jul 20 2005 - 11:18:31 CDT)
  • RE: pka calculations and their use in simulations (Mon Jul 11 2005 - 07:41:49 CDT)
  • RE: About Restart (Thu May 05 2005 - 21:50:29 CDT)
  • RE: Restartname (Thu May 05 2005 - 21:48:00 CDT)
  • RE: About PDB file with fixed atom flags. (Thu May 05 2005 - 14:29:01 CDT)
  • RE: NAMD: HEM residue (Wed May 04 2005 - 17:17:01 CDT)
  • RE: About PDB file with fixed atom flags. (Wed May 04 2005 - 17:07:13 CDT)
  • RE: NAMD: HEM residue (Wed May 04 2005 - 15:17:34 CDT)
  • RE: minimization problem (Thu Apr 14 2005 - 15:52:05 CDT)
  • RE: about protonation of HIS in membrane protein (Wed Apr 13 2005 - 19:47:52 CDT)
  • RE: ERROR: Constraint failure in RATTLE algorithm for atom 127! (Wed Apr 13 2005 - 16:20:53 CDT)
  • RE: Periodic cell has become too small for original patch grid (Wed Apr 13 2005 - 11:32:17 CDT)
  • RE: ELECT energy (Mon Apr 11 2005 - 16:18:10 CDT)
  • RE: RE: error: UNABLE TO FIND ANGLE PARAMETERS FOR C NH1 C (Sat Apr 09 2005 - 20:31:18 CDT)
  • RE: error: UNABLE TO FIND ANGLE PARAMETERS FOR C NH1 C (Sat Apr 09 2005 - 15:41:45 CDT)
  • RE: (Fri Apr 08 2005 - 12:27:54 CDT)
  • phosphoserine (Fri Apr 08 2005 - 12:18:35 CDT)
  • RE: Membrane configuration file (Fri Apr 08 2005 - 11:21:28 CDT)
  • RE: modifying cut off (Thu Apr 07 2005 - 19:45:30 CDT)
  • RE: modifying cut off (Thu Apr 07 2005 - 19:01:03 CDT)
  • modifying cut off (Thu Apr 07 2005 - 18:30:23 CDT)
  • RE: Nanotube psf file. (Wed Apr 06 2005 - 12:34:44 CDT)
  • RE: problem running namd (Mon Apr 04 2005 - 16:48:48 CDT)
  • RE: problem running namd (Mon Apr 04 2005 - 13:48:02 CDT)
  • problem running namd (Mon Apr 04 2005 - 11:54:45 CDT)
  • problem running namd (Mon Apr 04 2005 - 11:18:01 CDT)
  • RE: glucose CHARMM force field (Tue Mar 29 2005 - 22:13:35 CST)
  • RE: molecules distorted (Tue Mar 22 2005 - 15:37:19 CST)
  • RE: visualizing dynamics output (Tue Mar 22 2005 - 14:17:12 CST)
  • RE: question about par_all27_prot_lipid.inp (Sun Mar 20 2005 - 15:22:19 CST)
  • namd and fftw (Mon Mar 14 2005 - 18:11:43 CST)
  • flexible cell for MD simulations (Thu Mar 10 2005 - 16:25:17 CST)
  • RE: namd on Altix (Wed Mar 09 2005 - 13:33:35 CST)
  • RE: namd on Altix (Tue Mar 08 2005 - 17:31:15 CST)
  • RE: namd on Altix (Tue Mar 08 2005 - 17:17:46 CST)
  • RE: namd on Altix (Tue Mar 08 2005 - 17:05:52 CST)
  • RE: namd on Altix (Tue Mar 08 2005 - 16:57:08 CST)
  • RE: namd on Altix (Tue Mar 08 2005 - 15:03:49 CST)
  • RE: namd on Altix (Mon Mar 07 2005 - 19:06:35 CST)
  • RE: namd on Altix (Mon Mar 07 2005 - 18:43:25 CST)
  • Installing NAMD (Mon Mar 07 2005 - 18:18:43 CST)
  • RE: namd on Altix (Mon Mar 07 2005 - 15:00:02 CST)
  • RE: namd on Altix (Mon Mar 07 2005 - 14:16:16 CST)
  • RE: namd on Altix (Mon Mar 07 2005 - 13:37:11 CST)
  • namd on Altix (Mon Mar 07 2005 - 13:14:07 CST)
• Michel Seigneuret
  • TM protein in octane slab questions (Fri Jul 22 2005 - 03:52:50 CDT)
• Mike Bradley
  • truncated octahedron boundary conditions (Wed Jul 21 2004 - 16:26:09 CDT)
• 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)
• Mikolai Fajer
  • Kinetic Energy difference using restart binaries (Wed Dec 21 2005 - 12:54:13 CST)
  • Manipulating structure (Mon Aug 15 2005 - 09:57:03 CDT)
  • Psfgen within NAMD (Fri Aug 12 2005 - 12:01:37 CDT)
  • Re: namddat: Command not found (Thu May 12 2005 - 14:50:20 CDT)
  • namddat: Command not found (Thu May 12 2005 - 12:41:46 CDT)
• milton sonoda
  • Locally Enhanced Sampling (Wed Dec 21 2005 - 17:34:23 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)
• mpavlova_at_purdue.edu
  • return molecule to its principal axes (Wed Dec 14 2005 - 13:54:32 CST)
• mustapha.hamdi_at_ensi-bourges.fr
  • Ca++ topology&param files (Fri Sep 30 2005 - 04:11:31 CDT)
  • Velocity after heating (Mon Jul 18 2005 - 06:56:03 CDT)
  • Energy minimization (Wed May 11 2005 - 12:33:01 CDT)
  • Energy minimization (Wed May 11 2005 - 09:46:40 CDT)
  • RE: duplicated key CA in psfgen (Wed Apr 20 2005 - 07:12:36 CDT)
  • RE: duplicated key CA in psfgen (Wed Apr 20 2005 - 07:13:24 CDT)
  • duplicated key CA in psfgen (Tue Apr 19 2005 - 12:49:33 CDT)
  • Nanotube psf file. (Wed Apr 06 2005 - 13:06:59 CDT)
• 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)
• Nara Dashdorj
  • Re: How to atomselect several residues (Wed Nov 02 2005 - 19:12:10 CST)
  • IC Removal and Problem (Tue Nov 01 2005 - 22:31:53 CST)
  • Re: Serious Steric Atom Clashes (Mon Oct 24 2005 - 14:51:18 CDT)
  • Re: Serious Steric Atom Clashes (Mon Oct 24 2005 - 13:09:32 CDT)
  • Serious Steric Atom Clashes (Sun Oct 23 2005 - 13:45:43 CDT)
• Narender Singh
  • Vaccum simulation (Wed Dec 08 2004 - 10:57:48 CST)
• Narender Singh Maan
  • area of a hydrophobic patch (Wed Feb 02 2005 - 23:23:24 CST)
• nasrat kamal
  • phase equilibria using NAMD (Wed Jul 21 2004 - 07:33:45 CDT)
• Nathalie Reuter
  • Re: Analysis of NAMD output with CHARMM (Mon Feb 14 2005 - 09:51:07 CST)
  • Re: Analysis of NAMD output with CHARMM (Mon Feb 14 2005 - 07:21:56 CST)
  • namd on PPC, linux (Wed Jun 23 2004 - 04:40:05 CDT)
• Naveen Michaud-Agrawal
  • PMEGridSize (Thu Feb 24 2005 - 16:02:10 CST)
  • Catdcd (Wed Jan 26 2005 - 08:44:45 CST)
• NAVEEN P MICHAUD AGRAWAL
  • Re: Report on a trajectory incompatibility between NAMD and CHARMM: Unfolding and RDFs (Fri Jul 29 2005 - 23:30:23 CDT)
  • Re: Report on a trajectory incompatibility between NAMD and CHARMM: Unfolding and RDFs (Sat Jul 30 2005 - 10:42:29 CDT)
• Navratna Vajpai
  • peptide out of the water-box (Mon Aug 22 2005 - 02:52:11 CDT)
  • Periodic boundary conditions (Mon Aug 08 2005 - 03:34:34 CDT)
  • running on two different machines.... (Sun Jul 31 2005 - 02:24:39 CDT)
  • running on two different machines.... (Sun Jul 31 2005 - 02:27:57 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
  • beta-peptides ... (Mon Oct 31 2005 - 06:34:20 CST)
  • Fedora Core 4 problems [2] ... (Sat Oct 01 2005 - 08:42:21 CDT)
  • Fedora Core 4 problems (?) ... (Sat Oct 01 2005 - 08:08:55 CDT)
  • Re: RATTLE and DNA (Tue Apr 05 2005 - 10:02:24 CDT)
  • RATTLE and DNA (Tue Apr 05 2005 - 05:33:48 CDT)
  • psfgen for DNA (Mon Mar 21 2005 - 10:20:49 CST)
  • Hexagonal cell and PME grid. (Tue Mar 01 2005 - 05:17:44 CST)
  • 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)
• Nicolae-Viorel Buchete
  • NAMD2.6b1 (&2.5) binaries on Scyld (missing libbproc.so.2 lib?) (Thu Sep 15 2005 - 16:44:28 CDT)
• Nicolas Floquet
  • Condition for stopping MD sim. with NAMD (Tue May 17 2005 - 02:56:45 CDT)
• Nicolas Sapay
  • Re: how is NAMD output written in parallel mode? (Mon Dec 05 2005 - 08:17:58 CST)
  • Chamrun/NAMD processes and PBS cluster (Mon Dec 05 2005 - 07:55:15 CST)
  • problem with the NAMD CPU time consumption on a batch queueing system (Mon Nov 28 2005 - 11:46:08 CST)
  • Re: ptraj (Tue Sep 27 2005 - 10:03:18 CDT)
  • dramatical standard deviation in the pressure profile (Mon Aug 29 2005 - 07:12:27 CDT)
  • Re: Pressure Profile Simulation (Thu Aug 25 2005 - 04:32:40 CDT)
  • Re: Energy minimization (Wed May 11 2005 - 11:06:15 CDT)
  • NAMD job abnormally killed with PBS (Tue Apr 26 2005 - 02:14:33 CDT)
  • distance restraints during a dynamic (Mon Apr 11 2005 - 11:13:40 CDT)
  • Re: running VMD from a script? (Mon Mar 21 2005 - 02:29:34 CST)
  • NMAD job abnormally killed with PBS (Thu Feb 24 2005 - 12:09:19 CST)
• Nikolai Skrynnikov
  • best choice of linux cluster to run NAMD (Thu Jul 01 2004 - 03:02:10 CDT)
• Niraj kumar
  • Re: Re: segfaults in mm_malloc (Thu Jun 30 2005 - 00:25:18 CDT)
  • Re: Re: segfaults in mm_malloc (Wed Jun 29 2005 - 05:48:20 CDT)
  • Understanding NAMD performance data (Wed Jun 22 2005 - 05:27:10 CDT)
  • Re: Re: NAMD 2.5 crashes unpredictably on a 8 way SMP (Linux x86) (Mon May 16 2005 - 05:14:31 CDT)
  • Re: Re: NAMD 2.5 crashes unpredictably on a 8 way SMP (Linux x86) (Wed May 11 2005 - 01:40:56 CDT)
  • Re: NAMD 2.5 crashes unpredictably on a 8 way SMP (Linux x86) (Tue May 10 2005 - 04:48:59 CDT)
  • NAMD 2.5 crashes unpredictably on a 8 way SMP (Linux x86) (Mon May 09 2005 - 06:03:19 CDT)
• Nitin Bhardwaj
  • Errors: Periodic cell became too small for original patch grid & Setting parameter binaryoutput from script failed! (Sun Nov 13 2005 - 12:26:35 CST)
• nmichaud_at_jhu.edu
  • Re: merge trajectory from NAMD (Wed Nov 30 2005 - 21:05:19 CST)
  • Re: For help with .log file. (Mon Aug 08 2005 - 09:38:02 CDT)
• nordgren_at_sas.upenn.edu
  • Re: ERROR: Margin is too small (BUG?) (Thu Aug 04 2005 - 17:52:49 CDT)
  • Re: Incorrect periodic box imaging with AMBER parameters (Thu Aug 04 2005 - 17:40:58 CDT)
  • Re: system becomes very large when set LangevinPiston on (Tue Jul 26 2005 - 12:20:50 CDT)
  • Re: Fixed atoms and dcd file with DCDunitCell on (Sat Jul 23 2005 - 12:11:46 CDT)
  • Re: velocity file of atoms at each time step (Mon Jun 20 2005 - 10:23:07 CDT)
  • Re: c-shell into NAMD configuration file (Wed Jun 15 2005 - 09:23:20 CDT)
  • Re: Script for MD in a loop? (Wed Jun 15 2005 - 09:13:44 CDT)
  • Re: Multiple Harmonic Constraints (Wed Jun 15 2005 - 08:37:34 CDT)
  • Re: Simulation terminating due to RATTLE constraint failure (Mon Jun 13 2005 - 01:51:35 CDT)
  • Re: Re: vmd-l: multiple automated calls to NAMD (Thu Jun 09 2005 - 21:56:31 CDT)
  • multiple automated calls to NAMD (Wed Jun 08 2005 - 20:57:56 CDT)
  • NAMD automation (Sat May 07 2005 - 23:39:16 CDT)
  • Re: Fixing atoms during simulation (Sat May 07 2005 - 23:17:30 CDT)
  • extracting time from DCDs (Thu Jan 13 2005 - 19:54:30 CST)
  • 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)
• olivier Walker
  • Re: compiling Namd on amd64 (Fri Mar 11 2005 - 02:42:30 CST)
  • Re: compiling Namd on amd64 (Thu Mar 10 2005 - 11:55:03 CST)
  • compiling Namd on amd64 (Thu Mar 10 2005 - 04:08:08 CST)
  • difference between two kinds of dimers (Wed Mar 02 2005 - 06:19:56 CST)
• Olya Kravchenko
  • question on tcl script for rmsd calculation (Mon Feb 14 2005 - 13:44:41 CST)
  • 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)
• 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)
• Parag Adhangale
  • Segmentation violation in NAMD ! (Thu May 26 2005 - 11:04:41 CDT)
  • Problem using the GROMACS force field ! (Thu May 05 2005 - 16:23:52 CDT)
  • Duplicate lines in the output file ! (Wed Apr 06 2005 - 11:52:56 CDT)
  • Problems with the nodelist file ! (Wed Mar 02 2005 - 16:38:13 CST)
• Parminder Mankoo
  • NAMD time step: AKMA? (Mon Oct 17 2005 - 18:52:26 CDT)
• patrick wintrode
  • problem using visual_mdenergy: program has trouble reading the dat file (Sat Jul 30 2005 - 17:08:45 CDT)
  • removing a covalent bond during a simulation (Wed Jun 29 2005 - 12:10:56 CDT)
  • langevin vs coupling to a heat bath (Tue Jun 21 2005 - 15:25:29 CDT)
• Paul R Brenner
  • Re: Replica-Exchange MD (Fri Nov 18 2005 - 09:49:38 CST)
  • Re: Charmm 1,4 Interactions - Scaling Question (Fri Jun 17 2005 - 09:08:54 CDT)
  • Charmm 1,4 Interactions - Scaling Question (Thu Jun 16 2005 - 12:00:05 CDT)
• paul.dalhaimer_at_yale.edu
  • RE: autoionize & namd2 (Wed Sep 21 2005 - 09:47:37 CDT)
  • Re: energy values (Tue Sep 13 2005 - 11:13:44 CDT)
  • compiling NAMD on a redhat-pentium-dell workstation (Tue May 03 2005 - 11:54:56 CDT)
• Pawel Weronski
  • Re: namdplot: command not found (Wed Oct 12 2005 - 08:57:32 CDT)
  • Re: namdplot: command not found (Tue Oct 11 2005 - 08:22:18 CDT)
• Pedro Borkowski
  • Re: problem when do equilibration (Sun Aug 21 2005 - 11:09:17 CDT)
  • ATP in the Topology file (Fri Jul 29 2005 - 11:31:27 CDT)
• Per Jr. Greisen
  • Warning: add bond failed in patch of ACE (Wed Oct 19 2005 - 14:14:24 CDT)
  • PSF file ATP (Sat Oct 15 2005 - 15:01:36 CDT)
  • ATP PDB file (Fri Oct 14 2005 - 07:25:40 CDT)
• Peter Bazeley
  • simulated annealing step size (Fri Jan 28 2005 - 20:23:19 CST)
  • resetting restartfreq parameter (Thu Jan 20 2005 - 17:17:16 CST)
  • tcoupling coefficient (Wed Jan 05 2005 - 06:31:07 CST)
  • Re: increase in energy over time (Mon Jan 03 2005 - 21:19:33 CST)
  • increase in energy over time (Mon Jan 03 2005 - 17:27:45 CST)
  • 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 Freddolino
  • Re: preparing a dimeric protein for NAMD (Fri Dec 23 2005 - 22:00:55 CST)
  • Re: preparing a dimeric protein for NAMD (Fri Dec 23 2005 - 14:41:19 CST)
  • Re: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT (Thu Dec 22 2005 - 14:35:37 CST)
  • Re: pair.pdb and cutoff for pairInteraction (Tue Nov 29 2005 - 11:26:19 CST)
  • Re: Pair Interaction options (Thu Nov 10 2005 - 10:27:14 CST)
  • Re: Increasing temp during MD (Thu Nov 03 2005 - 12:43:33 CST)
  • Re: About RMSD calculation. (Fri Oct 28 2005 - 16:20:48 CDT)
  • Re: Running NAMD 2.6b1 on Linux Networks (Fri Oct 07 2005 - 17:09:31 CDT)
  • Re: help generating psf files (Fri Oct 07 2005 - 10:18:02 CDT)
  • Re: help generating psf files (Thu Oct 06 2005 - 15:22:01 CDT)
  • Re: About calculating RMSD with rmsd.tcl (Wed Oct 05 2005 - 22:22:23 CDT)
  • Re: pairInteraction energies? (Wed Oct 05 2005 - 22:19:30 CDT)
  • Re: 1-4 interactions scaling (Wed Oct 05 2005 - 22:15:36 CDT)
  • Re: help generating psf files (Wed Oct 05 2005 - 22:09:07 CDT)
  • Re: calculate enthalpy of binding (Tue Sep 27 2005 - 17:27:44 CDT)
  • Re: energy values (Tue Sep 13 2005 - 11:31:22 CDT)
• 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)
• Peter Spijker
  • Different electrostatic and Van der Waals cutoff (Fri Apr 08 2005 - 04:56:42 CDT)
  • 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
  • Re: POPC or POPE? (Wed Nov 02 2005 - 18:16:19 CST)
  • NAMD 2.6b1 error writing DCD file on Cray XT3 (Fri Oct 07 2005 - 13:24:47 CDT)
  • difficulties using SMD on atoms in large systems (Tue Oct 04 2005 - 12:42:01 CDT)
  • Tcl interface--dynamically changing simulation parameters (Thu Apr 28 2005 - 17:19:42 CDT)
  • Re: box size changes under anisotropic pressure coupling (Fri Apr 08 2005 - 14:28:11 CDT)
  • box size changes under anisotropic pressure coupling (Fri Apr 08 2005 - 11:14:40 CDT)
  • covalent bonds across periodic boundaries (Sat Nov 27 2004 - 11:39:33 CST)
• Philip Fowler
  • Re: pair interactions in NPT (Fri Sep 02 2005 - 02:22:21 CDT)
  • Re: catdcd and dcdunitcell (Tue Jun 28 2005 - 11:07:38 CDT)
  • Re: catdcd and dcdunitcell (Tue Jun 28 2005 - 09:27:06 CDT)
  • Re: catdcd and dcdunitcell (Tue Jun 28 2005 - 07:18:15 CDT)
  • Re: catdcd and dcdunitcell (Tue Jun 28 2005 - 07:15:36 CDT)
  • catdcd and dcdunitcell (Mon Jun 27 2005 - 05:07:01 CDT)
  • Re: FEP (Thu May 12 2005 - 04:37:31 CDT)
  • thermodynamic integration and NAMD: soft-core or "separation-shifted" vdw potentials (Mon Jan 10 2005 - 11:12:41 CST)
• Phoenix
  • Re: problem when heating the system (Tue Aug 30 2005 - 21:39:29 CDT)
  • problem when heating the system (Mon Aug 29 2005 - 23:07:42 CDT)
  • Re: Hi,how can I generate a psf file with a pdb file contain some special amino acid like TYS (Fri Jun 24 2005 - 09:59:13 CDT)
  • Hi,how can I generate a psf file with a pdb file contain some special amino acid like TYS (Fri Jun 24 2005 - 00:08:37 CDT)
  • Re: how to apply a random force on a atom (Tue Jun 07 2005 - 01:08:36 CDT)
• picot.delphine_at_neuf.fr
  • Force constant of harmonic restraint (Thu May 12 2005 - 03:50:11 CDT)
• Pijush Ghosh
  • RE: error parsing config file (Thu Sep 29 2005 - 21:52:09 CDT)
  • Problem in restarting simulation (Fri Sep 02 2005 - 10:54:54 CDT)
  • RE: problem when heating the system (Tue Aug 30 2005 - 00:09:08 CDT)
  • RE: removing water from DCD (Wed Jul 20 2005 - 22:03:20 CDT)
  • Radial Distribution Function (Thu Jun 16 2005 - 10:43:18 CDT)
  • RE: addforce (Tue Jun 14 2005 - 14:23:05 CDT)
  • Number of Steps (Wed Jun 08 2005 - 13:39:34 CDT)
  • RE: PSFGEN (Fri May 27 2005 - 17:10:47 CDT)
  • RE: Error in running tutorial files (Wed May 18 2005 - 13:55:31 CDT)
  • RE: regenerating PSF file (Wed May 18 2005 - 10:01:51 CDT)
  • RE: dielectric constant (Thu May 12 2005 - 12:53:32 CDT)
  • RE: Bad global exclusion count. (Tue May 10 2005 - 14:12:06 CDT)
  • RE: Fwd: Parameter file. (Sun May 01 2005 - 16:39:10 CDT)
  • Regulating density of water (Thu Apr 28 2005 - 13:44:35 CDT)
  • RE: duplicated key CA in psfgen (Tue Apr 19 2005 - 13:04:48 CDT)
  • Re: minimization problem (Thu Apr 14 2005 - 14:52:05 CDT)
  • Rotating a structure about an atom (Wed Jan 19 2005 - 12:47:56 CST)
  • 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)
• pijush.ghosh_at_ndsu.edu
  • Re: Question about Generating DCD files with only specified atoms (Thu Dec 22 2005 - 19:36:07 CST)
  • Re: PSFGEN (Sun May 29 2005 - 15:50:15 CDT)
• Po Hu
  • Constraint failure (Sat Sep 24 2005 - 13:42:42 CDT)
  • How to use AMBER force field in NAMD? (Mon Sep 19 2005 - 20:31:13 CDT)
• prodakt_at_o2.pl
  • make namd2 problem (Wed Oct 12 2005 - 06:21:53 CDT)
• q=E2=BA=E9=C3=F7?=
  • Re: hi all, I want to know how to turn the debug mode on of the namd (Mon Sep 26 2005 - 23:43:25 CDT)
  • hi all, I want to know how to turn the debug mode on of the namd (Mon Sep 26 2005 - 09:56:17 CDT)
  • how to apply a random force on a atom (Mon Jun 06 2005 - 12:31:46 CDT)
  • hi ,everyone.I have a problem about random force (Mon Jun 06 2005 - 11:48:08 CDT)
• q=F5=D0=A1=C7=E5?=
  • Re: About charm++/namd on AMD64 cluster (Mon Jan 03 2005 - 04:15:19 CST)
  • About charm++/namd on AMD64 cluster (Sun Jan 02 2005 - 02:01:32 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)
• Raeanne Napoleon
  • namdplot, grpah is empty (Mon Jun 27 2005 - 11:01:58 CDT)
  • namdplot, graph is empty (Tue Jun 21 2005 - 13:48:34 CDT)
• Ragan Robertson
  • saving forces using loadforces (Sat Dec 11 2004 - 15:39:42 CST)
• Ragothaman Yennamalli
  • RE: Error in running tutorial files (Mon May 23 2005 - 02:00:38 CDT)
  • Error in running tutorial files (Wed May 18 2005 - 12:20:50 CDT)
• Raj NK
  • munch: The input file main.o is not valid in the current object mode (Mon Nov 14 2005 - 16:14:36 CST)
• Ralph Jimenez
  • checking for correct construction of dihedrals, etc. (Mon Dec 19 2005 - 16:51:52 CST)
  • Energy for part of system (Wed Nov 09 2005 - 16:55:14 CST)
  • questions about applying patches (Thu Nov 03 2005 - 14:23:27 CST)
  • RE: more Heme troubles (Thu Nov 03 2005 - 13:19:54 CST)
• Randy Crawford
  • NAMD recognizes only one MPI process (Thu Mar 31 2005 - 11:46:45 CST)
  • 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)
• Raul Araya Secchi
  • FEP.... (Fri Nov 11 2005 - 09:39:41 CST)
  • ERROR: Constraint failure in RATTLE algorithm for atom 598! (Wed Nov 02 2005 - 08:17:29 CST)
  • Water Sphere (Mon Oct 24 2005 - 15:21:27 CDT)
• Ravinder Abrol
  • Re: how is NAMD output written in parallel mode? (Tue Dec 06 2005 - 17:30:01 CST)
  • how is NAMD output written in parallel mode? (Mon Dec 05 2005 - 02:09:38 CST)
• 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)
• Rene Salmon
  • Re: NAMD_2.6b1 shared lib problem on amd64 clustermatic using intel compilers (Wed Aug 24 2005 - 15:01:26 CDT)
  • NAMD_2.6b1 shared lib problem on amd64 clustermatic using intel compilers (Fri Aug 19 2005 - 10:38:20 CDT)
  • Namd hangs on Bproc cluster (Wed Jun 08 2005 - 11:55:00 CDT)
  • Re: CHARM/NAMD network problems on amd64 Clustermatic (Wed May 25 2005 - 12:12:05 CDT)
  • CHARM/NAMD network problems on amd64 Clustermatic (Wed May 11 2005 - 13:07:25 CDT)
  • Re: Duplicate lines in the output file ! (Thu Apr 07 2005 - 10:13:59 CDT)
  • Re: clustermatic nodelist file (Fri Mar 04 2005 - 14:53:47 CST)
  • Re: clustermatic 4 and 5 Namd/charm (Sat Jan 01 2005 - 14:56:56 CST)
  • 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 Law
  • Re: saving coordinates as a PDB file after minimization in NAMD (Tue Oct 25 2005 - 16:14:18 CDT)
  • Re: saving coordinates as a PDB file after minimization in NAMD (Tue Oct 25 2005 - 15:44:17 CDT)
  • Re: par_all27_prot_lipid.inp (Thu Aug 18 2005 - 17:13:19 CDT)
  • Re: TM protein in octane slab questions (Fri Jul 22 2005 - 12:30:54 CDT)
  • Re: FATAL ERROR: Asymmetric water molecule?? (Thu Jul 21 2005 - 20:21:40 CDT)
  • Re: Help with SMD (Wed Jul 20 2005 - 10:54:50 CDT)
  • Re: psfgen and extending 5' end of DNA (Thu Jul 14 2005 - 17:45:48 CDT)
  • Re: psfgen patches (Thu Jul 14 2005 - 17:28:41 CDT)
  • pka calculations and their use in simulations (Sun Jul 10 2005 - 18:12:00 CDT)
• Richard Wood
  • FEP setup (Tue Dec 27 2005 - 11:43:53 CST)
  • Re: CA CL CA angle? (Wed Nov 02 2005 - 10:31:05 CST)
  • CA CL CA angle? (Tue Nov 01 2005 - 11:11:44 CST)
  • new problem (Thu Oct 27 2005 - 21:52:17 CDT)
  • Re: trying to generate a peptide (Wed Oct 26 2005 - 11:39:44 CDT)
  • RE: trying to generate a peptide (Wed Oct 26 2005 - 09:26:48 CDT)
  • RE: trying to generate a peptide (Wed Oct 26 2005 - 07:34:59 CDT)
  • Re: saving coordinates as a PDB file after minimization in NAMD (Tue Oct 25 2005 - 16:11:44 CDT)
  • trying to generate a peptide (Tue Oct 25 2005 - 20:07:01 CDT)
  • saving coordinates as a PDB file after minimization in NAMD (Tue Oct 25 2005 - 13:12:02 CDT)
  • help generating psf files (Tue Oct 04 2005 - 11:37:08 CDT)
• rob yang
  • membrane protein md protocol (Mon Jun 27 2005 - 10:36:15 CDT)
• Robert Bjornson
  • scaling issue (Fri Oct 21 2005 - 15:56:13 CDT)
  • Question about load balancing (Fri Oct 21 2005 - 15:44:46 CDT)
• Robert Brunner
  • Re: NAMD distribute (Thu Oct 13 2005 - 17:40:26 CDT)
  • Re: namdplot: command not found (Thu Oct 13 2005 - 15:11:37 CDT)
  • Re: namdplot: command not found (Tue Oct 11 2005 - 10:32:00 CDT)
  • New BioCoRE server released (Wed Aug 17 2005 - 12:00:16 CDT)
  • Re: Space environment simulations (Tue May 10 2005 - 11:41:37 CDT)
  • Re: segmentation violation!! (Tue Jan 18 2005 - 11:05:00 CST)
  • 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)
• roberte_at_organ.su.se
  • non-repeatability NAMD simulations (Tue May 10 2005 - 17:08:30 CDT)
  • Problems compiling NAMD on linux/clustermatic 5 (Sat May 07 2005 - 05:54:18 CDT)
• rossi_at_york.cuny.edu
  • Binding Energies for a Peptide-RNA System (Sat Sep 17 2005 - 14:37:11 CDT)
• 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
  • Re: Compiling (Thu Jan 06 2005 - 20:13:50 CST)
  • 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)
• s.bora erdemli
  • Re: removing water from DCD (Wed Jul 20 2005 - 21:06:53 CDT)
  • Energy Problem (Order of Magnitude) (Wed Jul 20 2005 - 15:05:03 CDT)
  • Energy Order of Magnitude (Mon Jul 11 2005 - 11:20:15 CDT)
  • free energy pertubation,binding energy and constant (Tue Jun 28 2005 - 14:30:07 CDT)
  • Re: Trajectory file. (Fri May 13 2005 - 17:30:58 CDT)
• sabri bora erdemli
  • Van Der Waals energy (Thu Jul 07 2005 - 09:07:44 CDT)
  • van der waals energy (Thu Jul 07 2005 - 09:25:45 CDT)
  • binding free energy , binding constant (Fri Jun 17 2005 - 08:11:33 CDT)
  • Molecular Dynamics or Langevin Dynamics (Tue Apr 26 2005 - 11:21:00 CDT)
  • Re: CAN'T FIND BOND PARAMETERS FOR BOND (error) (Thu Mar 10 2005 - 05:36:33 CST)
  • CAN'T FIND BOND PARAMETERS FOR BOND (error) (Thu Mar 10 2005 - 03:23:02 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)
• samantha cox
  • output in tcl (Fri Jul 22 2005 - 15:06:06 CDT)
• Samuel Flores
  • RE: tcl question (Thu Jun 16 2005 - 22:01:23 CDT)
  • tcl question (Thu Jun 16 2005 - 20:03:29 CDT)
  • RE: vmdtext? (Thu Jun 16 2005 - 15:38:47 CDT)
  • aquaporin question (Thu Jun 16 2005 - 15:39:11 CDT)
  • RE: changing default directory in VMD? (Thu Jun 16 2005 - 14:20:31 CDT)
  • changing default directory in VMD? (Wed Jun 15 2005 - 14:09:25 CDT)
  • vmdtext? (Mon Jun 13 2005 - 11:41:12 CDT)
  • molecules distorted (Tue Mar 22 2005 - 15:35:03 CST)
  • RE: visualizing dynamics output (Tue Mar 22 2005 - 13:51:07 CST)
  • visualizing dynamics output (Tue Mar 22 2005 - 11:31:31 CST)
  • RE: running VMD from a script? -- oops, never mind! (Mon Mar 21 2005 - 19:49:50 CST)
  • RE: running VMD from a script? (Mon Mar 21 2005 - 19:28:41 CST)
  • running VMD from a script? (Sun Mar 20 2005 - 18:22:23 CST)
  • question about par_all27_prot_lipid.inp (Sun Mar 20 2005 - 01:34:58 CST)
• santanu chatterjee
  • A question on minimization (Fri Nov 04 2005 - 15:44:32 CST)
  • Size of water box (Fri Nov 04 2005 - 13:06:07 CST)
  • A question on psfgen (Tue Oct 18 2005 - 01:55:39 CDT)
  • Help with psf and par for small molecules (Wed Aug 03 2005 - 15:12:40 CDT)
• Sarah Williams
  • Thermostat problems (Tue Jul 20 2004 - 04:13:19 CDT)
• Sascha Tayefeh
  • Re: Namd2.6b1 FATAL ERROR: Memory allocation failed on AIX53 IBM-SP4 (Mon Nov 21 2005 - 06:16:14 CST)
  • Namd2.6b1 FATAL ERROR: Memory allocation failed on AIX53 IBM-SP4 (Mon Nov 21 2005 - 02:56:34 CST)
  • Re: problem when heating the system (Tue Aug 30 2005 - 01:26:25 CDT)
  • NPT and FIXED atoms (Mon Aug 29 2005 - 02:14:28 CDT)
  • Re: PDB files for carbon nanotubes (Thu Jul 14 2005 - 16:13:25 CDT)
  • Re: Adding Misc. Potentials (e.g. spherical/repulsive restraints/constraints ) (Wed Jun 29 2005 - 09:56:54 CDT)
  • Adding Misc. Potentials (e.g. spherical/repulsive restraints/constraints ) (Wed Jun 29 2005 - 09:31:23 CDT)
  • Re: Multiple Harmonic Constraints (Thu Jun 09 2005 - 08:28:52 CDT)
  • Multiple Harmonic Constraints (Thu Jun 09 2005 - 02:31:38 CDT)
  • 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, 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)
• seigneuret_at_cochin.inserm.fr
  • learning how to do a Cys palmitoyl patch (Tue Aug 02 2005 - 16:24:19 CDT)
• Sergio Anis
  • Re: RE: namd: advice (Fri Nov 04 2005 - 09:43:25 CST)
  • namd: advice (Fri Nov 04 2005 - 07:56:34 CST)
  • NAMD: error messages (Tue Oct 04 2005 - 06:21:31 CDT)
  • vmd-l: script (Tue Sep 06 2005 - 07:11:50 CDT)
  • Re: Ca trace only (Wed Jul 20 2005 - 06:52:05 CDT)
• Shahid Qamar
  • Reading from DCD file and running MD (Wed Dec 07 2005 - 14:35:05 CST)
  • ABF.TCl file ??? (Tue Nov 01 2005 - 13:56:25 CST)
  • Can I miminimize some atoms in system (Tue Oct 25 2005 - 16:40:06 CDT)
  • (no subject) (Fri Oct 21 2005 - 11:20:08 CDT)
  • command to run MPI and ABF (Thu Oct 06 2005 - 18:10:39 CDT)
  • Partial charges for fluorescein/topology file (Thu Sep 15 2005 - 13:19:41 CDT)
  • Modified DNA bases PDB files (Wed Sep 07 2005 - 14:00:54 CDT)
  • Runnig same config file many times (Fri Jul 15 2005 - 14:38:38 CDT)
  • Some questions about TCL (Tue Jul 05 2005 - 16:38:28 CDT)
  • MD stops when COM or atom reaches a distance (Fri Jul 01 2005 - 11:34:39 CDT)
  • How MD stopes at a specific distance? (Thu Jun 30 2005 - 12:41:54 CDT)
  • Fixed restraint (Tue Jun 21 2005 - 17:56:09 CDT)
  • urestraint ? (Mon Jun 13 2005 - 13:12:22 CDT)
  • Script for MD in a loop? (Fri Jun 10 2005 - 10:05:34 CDT)
  • FEP error: Rattle atom constriant (Thu Jun 09 2005 - 15:59:11 CDT)
  • Reverse Free Energy perturbation (FEP)? (Wed Jun 08 2005 - 15:35:30 CDT)
  • Milestoning in NAMD (Wed May 18 2005 - 15:46:19 CDT)
  • ERROR: Constraint failure in RATTLE algorithm for atom 127! (Wed Apr 13 2005 - 14:20:16 CDT)
  • 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)
• shaila_at_biof.ufrj.br
  • Z-origin set to zero by Linux/Mac 2.5 binaries, Minimisation (Wed Jun 22 2005 - 07:01:14 CDT)
• Shantenu Jha
  • Re: NAMD distribute (Thu Oct 13 2005 - 18:08:56 CDT)
  • Re: Has NAMD been ported to Itanium2 + Linux? (Tue Aug 10 2004 - 16:25:28 CDT)
• shgnwgn_at_eden.rutgers.edu
  • large vanderwalls energy during minimization (Thu Jun 09 2005 - 13:31:53 CDT)
• Shirley Hui
  • Re: removing water from DCD (Wed Jul 20 2005 - 20:25:51 CDT)
  • Ca trace only (Tue Jul 19 2005 - 18:37:11 CDT)
  • Fw: changing default directory in VMD? (Wed Jun 15 2005 - 15:34:51 CDT)
  • Simulation terminating due to RATTLE constraint failure (Sun Jun 12 2005 - 22:21:09 CDT)
  • RE: Avoiding Rotation and translation of protein (Wed Jun 08 2005 - 12:45:04 CDT)
  • Re: NAMD restarts binary files (Tue Mar 08 2005 - 10:26:59 CST)
  • NAMD restarts binary files (Tue Mar 08 2005 - 10:13:08 CST)
  • Re: NAMD attempting to read FFTW (Wed Mar 02 2005 - 13:27:57 CST)
  • NAMD attempting to read FFTW (Tue Mar 01 2005 - 13:59:21 CST)
  • Re: using namd to compute energies (Tue Feb 15 2005 - 14:24:46 CST)
  • 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)
• Shirley Li
  • Re: preparing a dimeric protein for NAMD (Thank you) (Tue Dec 27 2005 - 12:38:15 CST)
  • Thanks a lot (Tue Dec 27 2005 - 12:28:52 CST)
  • Can extending MIN solve the problem of "Constraint failure in RATTLE algorithm" (Sat Dec 24 2005 - 12:58:55 CST)
  • Re: Re: Besides PSFGEN, (Thank you) (Fri Dec 23 2005 - 17:42:54 CST)
  • Re: preparing a dimeric protein for NAMD (Fri Dec 23 2005 - 17:35:59 CST)
  • Besides PSFGEN, are there any other good ways of generating .psf file (Thu Dec 22 2005 - 19:01:36 CST)
  • Re: ANGLE PARAMETERS (It works now) (Thu Dec 22 2005 - 16:54:06 CST)
  • The HT-HT-OT angle parameter for TIP3? (Thu Dec 22 2005 - 14:57:19 CST)
  • UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT (Thu Dec 22 2005 - 13:16:00 CST)
  • The angle parameters for CN7 are missing in NAMD? (Wed Dec 21 2005 - 18:02:07 CST)
  • FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CN7 CN7 CN7 (Wed Dec 21 2005 - 14:56:36 CST)
  • Re: pair.pdb and cutoff for pairInteraction (Tue Nov 29 2005 - 22:33:36 CST)
  • pair.pdb and cutoff for pairInteraction (Tue Nov 29 2005 - 11:00:02 CST)
  • restart a simulation (Fri Nov 04 2005 - 16:15:35 CST)
  • Autoionize: net charge NOT equal to zero (Wed Oct 19 2005 - 11:44:34 CDT)
  • problem with PSFGEN: the O3A atom cannot be recognized (Tue Oct 11 2005 - 12:52:49 CDT)
  • problem with PSFGEN (Mon Oct 10 2005 - 18:15:58 CDT)
  • RE: water box and the procedure (Mon Oct 10 2005 - 18:05:34 CDT)
  • water box and the procedure (Fri Oct 07 2005 - 09:50:15 CDT)
  • ion concentration (Thu Oct 06 2005 - 18:36:26 CDT)
  • autoionize and psfgen, which one first? (Thu Oct 06 2005 - 16:01:42 CDT)
  • Re: VMD scripting (Thanks a lot) (Thu Oct 06 2005 - 15:54:24 CDT)
  • VMD scripting (Thu Oct 06 2005 - 14:33:21 CDT)
• Shunzhou Wan
  • protein interact with its image (Tue Apr 19 2005 - 10:23:58 CDT)
  • creating Charmm psf from Xplor format (Wed Feb 04 2004 - 06:32:42 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)
• Slawomir Orlowski
  • AMD64 or PIV Prescott ... (Tue Jan 11 2005 - 05:52:48 CST)
• Snigdha Chakraborty
  • How to run for periodic boundary Conditions? (Wed Jul 20 2005 - 12:19:32 CDT)
• snoze pa
  • How to run namd on NCSA Tungsten (Wed Oct 19 2005 - 14:38:58 CDT)
  • NAMD restarts binary files (Wed Oct 12 2005 - 10:21:46 CDT)
  • developing parameters for charmm (Sat Oct 08 2005 - 19:40:54 CDT)
  • namd cluster run, connection refused (Thu Sep 29 2005 - 20:06:57 CDT)
  • water box and system charge (Fri Sep 30 2005 - 11:44:21 CDT)
  • NAMD cluster run (Fri Sep 30 2005 - 10:35:22 CDT)
• Sterling Paramore
  • Re: Question about Generating DCD files with only specified atoms (Thu Dec 22 2005 - 21:17:41 CST)
  • NAMD on Intel XEON EM64T (Mon Nov 14 2005 - 16:55:50 CST)
  • Re: namdplot: command not found (Thu Oct 13 2005 - 14:59:36 CDT)
  • Re: XPLOR psf format (Thu Jul 07 2005 - 14:40:01 CDT)
  • Megatest fails on Linux cluster (Fri May 13 2005 - 14:40:11 CDT)
• Stern, Julie
  • moments of inertia, principal axes (Wed Aug 17 2005 - 19:00:53 CDT)
  • wrap ions (Wed Aug 03 2005 - 23:13:05 CDT)
  • shake and minimzation, equilibration (Wed Aug 03 2005 - 14:56:13 CDT)
  • rigidBond water (Wed Aug 03 2005 - 13:45:07 CDT)
  • velocity quenching (Tue Aug 02 2005 - 23:15:45 CDT)
  • steepest descent minimization (Tue Aug 02 2005 - 22:35:00 CDT)
  • added more bases to DNA using psfgen (Thu Jul 21 2005 - 21:50:55 CDT)
  • namdplot error (Thu Jul 21 2005 - 20:06:53 CDT)
  • removing water from DCD (Wed Jul 20 2005 - 19:49:12 CDT)
  • cellBasisVectors and xsc files (Tue Jul 19 2005 - 20:53:01 CDT)
  • force shifted cutoff (Tue Jul 19 2005 - 18:37:10 CDT)
  • psfgen and poorly guessed coordinates (Fri Jul 15 2005 - 18:17:56 CDT)
  • patch PYRT and extending DNA (Thu Jul 14 2005 - 20:17:04 CDT)
  • psfgen and extending 5' end of DNA (Thu Jul 14 2005 - 17:07:23 CDT)
  • psfgen patches (Thu Jul 14 2005 - 17:04:51 CDT)
  • force shifted cutoff (Thu Jul 07 2005 - 18:06:15 CDT)
  • XPLOR psf format (Thu Jul 07 2005 - 14:16:48 CDT)
  • infinite DNA (Wed Jul 06 2005 - 11:52:17 CDT)
  • inconsistencies with amber force fields due to scnb and 1-4scalin g (Wed May 18 2005 - 10:38:51 CDT)
  • scnb scaling factor and compatibility with AMBER force fields (Thu May 12 2005 - 11:47:01 CDT)
  • RE: minimization problem (Thu Apr 14 2005 - 16:53:15 CDT)
  • RE: minimization problem (Thu Apr 14 2005 - 15:26:04 CDT)
  • minimization problem (Thu Apr 14 2005 - 13:41:19 CDT)
  • ELECT energy (Mon Apr 11 2005 - 14:37:57 CDT)
  • warning on unique coordinates (Wed Feb 23 2005 - 15:07:19 CST)
  • restarting a simulation accurately (Sat Jan 08 2005 - 14:32:41 CST)
  • namd on lemieux (Fri Jan 07 2005 - 11:51:53 CST)
  • prmtop reading error (Sun Jan 02 2005 - 15:35:42 CST)
  • 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)
• Steven A. DuChene
  • Re: charm++ compile problem on x86_64 (Fri Jan 14 2005 - 17:09:42 CST)
  • charm++ compile problem on x86_64 (Fri Jan 14 2005 - 15:24:02 CST)
  • scyld no longer a supported option for building charm++ ? (Fri Jan 14 2005 - 14:30:10 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)
• surendra negi
  • CAN'T FIND BOND PARAMETERS FOR BOND FE - S (Fri Sep 02 2005 - 15:36:43 CDT)
  • Protonation state of HIS (Wed Aug 10 2005 - 16:57:06 CDT)
  • Re: Incorrect periodic box imaging with AMBER parameters (Thu Aug 04 2005 - 16:11:15 CDT)
  • Re: error message (Fri May 06 2005 - 10:22:55 CDT)
  • Re: HEME patch (Thu May 05 2005 - 13:38:37 CDT)
  • Re: hanging at startup phase 0 (Thu May 05 2005 - 12:25:06 CDT)
  • NAMD simulation: HEME (Wed May 04 2005 - 15:16:58 CDT)
  • NAMD: HEM residue (Wed May 04 2005 - 14:56:58 CDT)
  • Fwd: missing atom prob (Mon Nov 01 2004 - 17:58:33 CST)
  • Fwd: PSFgen error (Mon Nov 01 2004 - 17:58:12 CST)
• Surjit Dixit
  • Re: FEP and solvent (Thu Jun 16 2005 - 09:06:17 CDT)
• 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)
• Swarna Patra
  • dmpc membrane (Mon Jul 04 2005 - 20:17:43 CDT)
  • Gramicidin (Mon Jun 20 2005 - 20:54:09 CDT)
  • set center (Thu Jun 16 2005 - 22:53:28 CDT)
  • density calculation (Sun Apr 10 2005 - 20:24:51 CDT)
  • mmtools (Thu Feb 17 2005 - 23:32:55 CST)
  • energy (Thu Feb 17 2005 - 16:58:36 CST)
  • force constraints (Mon Jan 31 2005 - 19:49:07 CST)
  • SMD (Wed Jan 26 2005 - 20:52:27 CST)
  • qsub (Mon Jan 24 2005 - 23:02:37 CST)
  • Re: pmf (Sun Jan 16 2005 - 20:17:55 CST)
  • Electric Field (Wed Jan 12 2005 - 16:57:02 CST)
  • pmf (Tue Jan 11 2005 - 18:55:44 CST)
• Taeho Kim
  • Interaction between metal and metal-water. (Fri Nov 25 2005 - 10:39:22 CST)
• Tamal Banerjee
  • PSF file generation (Tue Aug 16 2005 - 00:16:46 CDT)
  • Unable to Generate PSF file ! (Mon Jul 04 2005 - 08:09:43 CDT)
• ted q
  • Minimization with CHARMM (Sat Feb 07 2004 - 15:56:11 CST)
• tepper_at_amolf.nl
  • Problem with NAMD on Opteron cluster (Fri Nov 11 2005 - 10:36:39 CST)
  • 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)
• Tim Sirianni
  • RE: RE: [Scalex86 - linux] FW: segfaults in mm_malloc (Fri Jul 01 2005 - 17:46:03 CDT)
  • RE: [Scalex86 - linux] FW: segfaults in mm_malloc (Thu Jun 30 2005 - 18:20:44 CDT)
• Tirath Ramdas
  • Re: Error on Solaris (Sat Jun 25 2005 - 20:10:21 CDT)
  • Error on Solaris (Sat Jun 25 2005 - 12:57:53 CDT)
• Tom Caulfield
  • tRNA simulation psf file generation explicit solvent and ions (Thu Jan 27 2005 - 02:29:47 CST)
• Troy Wymore
  • PSC WORKSHOP: COMPUTATIONAL BIOPHYSICS WORKSHOP (Fri Oct 14 2005 - 13:18:27 CDT)
  • PSC WORKSHOP: COMPUTATIONAL BIOPHYSICS WORKSHOP (Thu Sep 15 2005 - 11:22:29 CDT)
• 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)
• Turman, Cheri M
  • RE: NAMD: HEM residue (Wed May 04 2005 - 17:07:50 CDT)
• 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)
• Uma Mahankali
  • Warning in namd output file (Wed Nov 30 2005 - 18:27:48 CST)
  • Re: freeEnergy of conformational change of a test molecule (Thu Nov 17 2005 - 08:45:12 CST)
  • freeEnergy of conformational change of a test molecule (Wed Nov 16 2005 - 13:33:18 CST)
  • ABF for conformational analysis (Fri Nov 11 2005 - 16:54:11 CST)
  • Pair Interaction options (Thu Nov 10 2005 - 10:20:24 CST)
  • Only part of the protein is moving in MD simulation (Wed Oct 26 2005 - 10:12:13 CDT)
  • namd hangs (Mon Aug 08 2005 - 23:10:13 CDT)
  • Fixing atoms during simulation (Sat May 07 2005 - 19:33:49 CDT)
• Valery Miftakhov
  • NAMD linking problem (Tue Jan 13 2004 - 22:15:59 CST)
• valesrdp
  • Minimization with NAMD (Mon May 09 2005 - 09:17:57 CDT)
  • Minimization after a MD simulation (Tue May 03 2005 - 04:48:14 CDT)
  • (no subject) (Thu Apr 21 2005 - 03:54:58 CDT)
• 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
  • center of mass motion: problems (Thu Dec 08 2005 - 16:27:06 CST)
  • PMF calculation using fixed restraints (Sun Nov 06 2005 - 12:26:22 CST)
  • restarting SMD jobs (Tue Jul 26 2005 - 20:25:38 CDT)
  • FEP output in NAMD (Tue Apr 05 2005 - 11:26:39 CDT)
  • constraining center of mass-constrained MD (Thu Feb 17 2005 - 02:51:12 CST)
  • 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
  • RE: Fatal error: (Thu Aug 04 2005 - 09:04:30 CDT)
  • Fatal error: (Thu Aug 04 2005 - 07:58:30 CDT)
  • psfgen/auto none (Thu Jun 30 2005 - 02:50:30 CDT)
  • Re: namdplot not working (Fri Feb 11 2005 - 16:04:06 CST)
  • 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
  • last call for early registrations for "Horizons2005" (Fri Jan 14 2005 - 07:19:00 CST)
  • 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 Tianhua
  • loodking or topology file for zinc finger (Tue Mar 08 2005 - 19:43:02 CST)
• Wang, Boyang
  • Installing NAMD on beowulf cluster, 64 bit, opteron, 4 processors. (Mon Jun 06 2005 - 22:23:59 CDT)
  • Dihedral and Improper, Nonbonded. (Sun May 01 2005 - 22:46:22 CDT)
  • a target molecule in a water box. (Mon Apr 25 2005 - 21:12:02 CDT)
• Wei Chen
  • Re: FEP.... (Fri Nov 11 2005 - 11:28:20 CST)
  • ensemble (Wed Oct 05 2005 - 16:34:12 CDT)
  • Re: fep (Tue Jul 26 2005 - 17:05:39 CDT)
  • RE: cellBasisVectors and xsc files (Wed Jul 20 2005 - 10:47:21 CDT)
  • Re: changing file (Wed Jul 20 2005 - 10:43:24 CDT)
  • Re: FEP - one long simulation vs many short ones (Sat Jul 02 2005 - 12:13:51 CDT)
  • convert_from_namd_to_amber (Tue Jun 28 2005 - 22:02:18 CDT)
  • Re: basic: combining two pdb files? (Thu Jun 23 2005 - 21:03:30 CDT)
  • Re: restart syntax (Tue Jun 21 2005 - 16:26:19 CDT)
  • Pressure_control (Fri Jun 17 2005 - 21:41:19 CDT)
  • Re: binding free energy , binding constant (Fri Jun 17 2005 - 15:46:35 CDT)
  • MM/PBSA (Mon Jun 13 2005 - 15:41:45 CDT)
  • RE: PSFGEN (Sat May 28 2005 - 20:42:40 CDT)
  • PSFGEN (Fri May 27 2005 - 15:10:30 CDT)
  • pressure (Mon May 23 2005 - 19:50:28 CDT)
  • Re: FEP (Thu May 12 2005 - 11:19:48 CDT)
  • FEP (Wed May 11 2005 - 13:49:53 CDT)
  • Re: how to restart/continue NAMD run (Fri May 06 2005 - 15:47:25 CDT)
  • (no subject) (Wed Apr 27 2005 - 11:04:07 CDT)
  • Re: a target molecule in a water box. (Mon Apr 25 2005 - 22:33:54 CDT)
  • RE: glucose CHARMM force field (Tue Mar 29 2005 - 23:05:06 CST)
  • computing resource (Mon Mar 14 2005 - 23:08:48 CST)
  • NAMD_utilities (Tue Mar 01 2005 - 12:43:56 CST)
  • Re: alchemify FEP (Fri Feb 18 2005 - 12:54:44 CST)
  • alchemify FEP (Thu Feb 17 2005 - 13:14:20 CST)
  • FEP (Tue Feb 01 2005 - 11:15:24 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)
• Wei Zhuang
  • questions about running namd on NCSA cluster tungsten (Fri Oct 28 2005 - 17:09:22 CDT)
  • Myrinet NAMD (Fri Oct 28 2005 - 14:01:21 CDT)
  • Re: Re: urestraint doesn't work (Thu Oct 27 2005 - 21:45:37 CDT)
  • Re: Re: urestraint doesn't work (Thu Oct 27 2005 - 20:35:22 CDT)
  • urestraint doesn't work (Thu Oct 27 2005 - 16:56:55 CDT)
  • running NAMD on tungsten (Tue Oct 18 2005 - 01:59:57 CDT)
  • implicit solvent (Thu Jun 09 2005 - 17:47:48 CDT)
  • How to read charmm binary trajectory file using home-made C/C++ code (Tue Mar 22 2005 - 14:39:15 CST)
• weikai
  • Can NAMD control pressure gradually increase? (Fri Oct 21 2005 - 02:30:41 CDT)
  • Can NAMD deal with solid-state system? (Wed Aug 31 2005 - 21:57:21 CDT)
• Wen Li
  • Re: vmd-l: conformational alignment (Thu Mar 31 2005 - 12:26:20 CST)
  • Re: vmd-l: conformational alignment (Thu Mar 31 2005 - 10:32:51 CST)
  • Re: vmd-l: conformational alignment (Thu Mar 31 2005 - 10:24:18 CST)
  • conformational alignment (Wed Mar 30 2005 - 15:21:26 CST)
  • run NPT equilibration (Tue Feb 08 2005 - 11:30:07 CST)
  • Re: question on running NAMD2 using Amber files (Mon Feb 07 2005 - 12:15:41 CST)
  • question on running NAMD2 using Amber files (fwd) (Mon Feb 07 2005 - 10:25:32 CST)
  • question on running NAMD2 using Amber files (Mon Feb 07 2005 - 08:40:56 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)
• wmsmith
  • RE: Velocity after heating (Mon Jul 18 2005 - 13:04:14 CDT)
  • RE: Some questions about TCL (Tue Jul 05 2005 - 17:20:54 CDT)
  • RE: Adding Misc. Potentials (e.g. spherical/repulsive restraints/constraints ) (Wed Jun 29 2005 - 13:43:44 CDT)
  • cross products (Mon Jun 27 2005 - 14:35:18 CDT)
  • Accessing beta / occupancy values from NAMD tcl (Mon Jun 27 2005 - 10:24:47 CDT)
• Wolbach, Jeffrey P \(WOLBACH\)
  • RE: Adjusting Density of waterbox used by solvate (Mon Jun 13 2005 - 11:36:11 CDT)
  • RE: using namd to compute energies (Wed Feb 16 2005 - 07:30:41 CST)
  • Question about Gradient Tolerance during minimization (Wed Sep 08 2004 - 13:00:15 CDT)
• WONG Hua
  • steered molecular dynamics docking (Wed May 18 2005 - 04:55:37 CDT)
• wzhuang_at_uci.edu
  • Re: fixed atoms (Wed Oct 26 2005 - 11:12:25 CDT)
  • Myrinet vs. Infiniband (Wed Apr 06 2005 - 12:36:10 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)
• xiaojing gong
  • How can I increase the computing rate on the computer cluster (Sun Oct 30 2005 - 05:44:24 CST)
  • Is there a method to choose what is saved in DCD files (Sun Oct 02 2005 - 09:34:02 CDT)
  • temperature coupling and pressure coupling (Mon Sep 26 2005 - 01:44:16 CDT)
  • energy minimization (Sun Sep 25 2005 - 22:05:32 CDT)
  • energy minimization (Sun Sep 25 2005 - 21:57:00 CDT)
  • problem about equilibration (Mon Aug 15 2005 - 08:30:44 CDT)
  • constraint constant in equilibration (Sat Jul 30 2005 - 00:19:26 CDT)
  • the difference between the min_nacl.vel and min_nacl.restart.vel (Sat Jul 23 2005 - 07:59:48 CDT)
  • constrain or fix the system only in Z direction (Thu Jul 21 2005 - 07:01:33 CDT)
  • pressure control in config file (Sun Jul 17 2005 - 20:06:16 CDT)
  • how to build AQP1 tetramer (Thu Jun 23 2005 - 21:31:13 CDT)
• Xiaoqing Wang
  • how to use the dual-processor machines (Sat Jul 30 2005 - 08:37:39 CDT)
  • Re: system becomes very large when set LangevinPiston on (Wed Jul 27 2005 - 21:32:01 CDT)
  • Re: system becomes very large when set LangevinPiston on (Tue Jul 26 2005 - 22:02:34 CDT)
  • Re: system becomes very large when set LangevinPiston on (Tue Jul 26 2005 - 04:48:13 CDT)
  • system becomes very large when set LangevinPiston on (Sun Jul 24 2005 - 22:06:43 CDT)
  • Re: "make" Linux-amd64-g++ error (Mon May 16 2005 - 09:08:03 CDT)
  • Re: "make" Linux-amd64-g++ error (Mon May 16 2005 - 07:45:38 CDT)
  • "make" Linux-amd64-g++ error (Sun May 15 2005 - 22:31:47 CDT)
  • What's wrong with my namd2 (Sun May 15 2005 - 07:01:13 CDT)
  • Re: different result from different cpu (Tue May 10 2005 - 19:59:45 CDT)
  • different result from different cpu (Tue May 10 2005 - 07:31:31 CDT)
  • compile "mpi" charm++ on amd64 (Mon May 09 2005 - 22:09:32 CDT)
  • RE: Periodic cell has become too small for original patch grid (Thu Apr 14 2005 - 09:29:02 CDT)
  • Periodic cell has become too small for original patch grid (Wed Apr 13 2005 - 03:38:33 CDT)
  • Re: any script to build membrane+protein+solvent? (Fri Apr 08 2005 - 21:23:48 CDT)
  • add water on the top of the protein border (Wed Apr 06 2005 - 09:11:47 CDT)
  • BUG ALERT: Mother atom with hydrogenGroupSize of 0! (Mon Jan 24 2005 - 01:26:21 CST)
  • Obtain message from MD (Tue Jan 18 2005 - 01:30:23 CST)
  • constraint failure (Tue Jan 11 2005 - 21:07:08 CST)
  • equilibrated the system (Tue Jan 11 2005 - 08:43:17 CST)
• 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)
• Xinghua Shi
  • RE: NAMD 2.6 in IBM SP (Sun Nov 06 2005 - 05:41:18 CST)
  • NAMD 2.6 in IBM SP (Sat Nov 05 2005 - 09:41:35 CST)
  • NAMD 2.6 in IBM SP (Sat Nov 05 2005 - 09:12:12 CST)
• Xiongce Zhao
  • NAMD for Xeon clusters (Wed Sep 28 2005 - 17:13:06 CDT)
  • rotation constraint angular velocity (Wed Feb 16 2005 - 10:32:14 CST)
  • 1 D Periodic Boundary (Tue Feb 15 2005 - 14:43:42 CST)
  • how to image molecules back into a PBC box (Tue Feb 15 2005 - 09:08:21 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)
• yangbing00_at_mails.tsinghua.edu.cn
  • About the potential of NAMD (Thu Oct 06 2005 - 22:53:46 CDT)
  • About the potantial of IONS (Thu Oct 06 2005 - 22:16:17 CDT)
  • About Potential Addition in NAMD (Wed Sep 28 2005 - 06:45:18 CDT)
  • About ions Representation in NAMD (Wed Sep 28 2005 - 06:40:45 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)
• 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)
• 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)
• ËïæÃæÃ
  • xplor parameter to charmm (Fri Jul 08 2005 - 03:54:19 CDT)
  • about *.psf (Thu May 26 2005 - 23:59:07 CDT)
• ËïÍ¥¹ã
  • Some problem on compiling NAMD (Thu Dec 15 2005 - 21:24:18 CST)
• κ¿­
  • Compiling the NAMD on HPUX-ia64 system Error! (Sat Jan 15 2005 - 08:35:00 CST)
  • How to Compile NAMD on HPUX-ia64 system~ (Fri Jan 14 2005 - 04:56:14 CST)
  • 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)
• ÎâºéÃ÷
  • how to constrains the smd atom on a line when do my smd simulation?? (Mon Dec 05 2005 - 01:59:09 CST)
  • problem when do equilibration (Sun Aug 21 2005 - 03:40:44 CDT)