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NAMD-L: By Author

By Author

7959 messages sorted by: [ date ] [ thread ] [ subject ] [ attachment ]
About this archive

Starting: Mon Sep 08 2003 - 09:54:14 CDT
Ending: Fri Jul 04 2008 - 12:24:54 CDT

• $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)
• _at_huji.ac.il
  • namd question (Tue Dec 26 2006 - 04:44:42 CST)
• a-yermakova_at_northwestern.edu
  • TeraGrid Efficiency (Mon Jul 31 2006 - 12:22:41 CDT)
  • topology files (Wed Jul 26 2006 - 12:54:21 CDT)
  • Autopsf (Fri Jul 21 2006 - 16:00:41 CDT)
  • (No subject) (Fri Jul 21 2006 - 15:04:47 CDT)
  • PME grid error during minimization (Fri Jul 21 2006 - 15:05:10 CDT)
  • #QNAN: Please help! (Wed Jul 19 2006 - 14:09:40 CDT)
  • Re: About the unit of "efield" (Wed Jul 19 2006 - 13:24:39 CDT)
  • Minimizing and Equilibrating (Mon Jul 17 2006 - 13:12:52 CDT)
  • log File - pressure not read (Thu Jul 13 2006 - 15:32:37 CDT)
  • NAMD on TeraGrid: OpenMP? (Thu Jul 13 2006 - 12:43:53 CDT)
  • solvating a protein (Thu Jul 13 2006 - 11:16:04 CDT)
  • NAMD on TeraGrid (Thu Jul 13 2006 - 11:04:17 CDT)
  • Re: (No subject) (Wed Jul 12 2006 - 11:46:35 CDT)
  • (No subject) (Mon Jul 10 2006 - 12:50:19 CDT)
• A. Ozlem T. Bishop
  • imprecision in table energy (Sun Sep 24 2006 - 09:57:50 CDT)
• Aaron Mccall
  • Tired of your poor health? (Mon Jun 11 2007 - 21:51:11 CDT)
• Aaron Oakley
  • Re: Partial charges on amino acids (Fri Jun 08 2007 - 23:43:54 CDT)
  • Re: how to simulate sugars (Sun May 27 2007 - 19:19:55 CDT)
  • Simulation of Eukaryotic membrane protein (Sun Jan 21 2007 - 23:23:12 CST)
  • Re: many short runs or one long run? (Mon Jul 10 2006 - 21:17:19 CDT)
  • 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)
• abhijit ramachandran
  • Force Calibration Interaction (Thu Jun 19 2008 - 17:31:57 CDT)
  • Charmm is not free so how to learn it (Fri Jun 13 2008 - 15:01:50 CDT)
  • Language Used and Elementary doubts (Thu Jun 12 2008 - 00:08:27 CDT)
• accomp lin
  • won't launch on linux ubuntu cluster for a parallel run (Fri Jul 04 2008 - 12:21:18 CDT)
  • Temperature Control (Mon Jun 18 2007 - 09:31:53 CDT)
  • Specified Electric Field (Wed May 16 2007 - 06:41:22 CDT)
• Adam Fraser
  • force field parameters for fullerenes (Mon Dec 10 2007 - 13:18:16 CST)
  • Re: simulation of fullerenes (Wed Dec 05 2007 - 12:31:45 CST)
  • simulation of fullerenes (Wed Dec 05 2007 - 12:16:39 CST)
  • Re: SMD behavior (Sat Dec 01 2007 - 12:03:40 CST)
  • SMD behavior (Wed Nov 21 2007 - 09:47:54 CST)
  • scripting in namd (Wed Oct 31 2007 - 07:39:36 CDT)
  • OPLS force field in namd (Fri Sep 14 2007 - 17:11:15 CDT)
  • system density (Tue Sep 04 2007 - 10:04:40 CDT)
  • setting solvent density during solvation (Mon Aug 20 2007 - 11:23:58 CDT)
  • How to use NPT ensemble to fix water density (Tue Aug 14 2007 - 14:28:18 CDT)
  • attractive harmonic potential between 2 molecules (Mon Aug 06 2007 - 10:25:29 CDT)
  • Re: constructing a topology entry for hexadecane (Fri Jun 29 2007 - 08:31:57 CDT)
  • constructing a topology entry for hexadecane (Thu Jun 28 2007 - 18:25:27 CDT)
  • working with non-protein files (Mon Jun 25 2007 - 21:57:31 CDT)
• Adam Kubach
  • NAMD interaction with VMD (Tue Oct 19 2004 - 13:54:18 CDT)
• Adam Sosa
  • Nobody will know about your problems. (Tue Jun 12 2007 - 13:05:30 CDT)
• Adilah Hussein
  • Temperature Control: Rescaling and Reassignment (Wed Aug 08 2007 - 12:43:00 CDT)
• Adilah Hussien
  • Temperature Control: Rescaling and Reassignment (Wed Aug 08 2007 - 04:52:16 CDT)
• Adrian Wiley
  • Surface tension (Wed Mar 17 2004 - 10:43:37 CST)
• ahenneck_at_ix.urz.uni-heidelberg.de
  • Problems with energy conservation in NVE dynamics with 2fs timestep (Tue Mar 06 2007 - 04:27:03 CST)
• Ahlam Al-Rawi
  • pbc (Tue May 06 2008 - 18:41:33 CDT)
  • Re: force constant matrix (Thu Dec 06 2007 - 14:20:07 CST)
  • PO3 psf (Wed Nov 21 2007 - 16:06:22 CST)
  • Using NAMD DCD in CHARMM (Thu Nov 15 2007 - 13:38:58 CST)
  • force constant matrix (Thu Nov 01 2007 - 08:29:23 CDT)
  • NAMD run (Mon Sep 10 2007 - 10:32:56 CDT)
  • error message (Wed Aug 22 2007 - 19:49:12 CDT)
• Ahmet Bakan
  • Re: Solvent mixture (Fri Nov 05 2004 - 17:02:06 CST)
  • Euro QSAR 2004 (Sun Sep 05 2004 - 15:42:27 CDT)
  • RE: cff91 force field in namd + A Question (Wed Aug 25 2004 - 10:53:59 CDT)
  • Pt LJ Parameters (Wed Jul 21 2004 - 11:56:52 CDT)
  • Simulated Annealing Config (Tue Jun 15 2004 - 08:24:59 CDT)
  • Re: Re: Simulation with ammonia (Fri Jun 04 2004 - 17:23:39 CDT)
  • Re: Simulation with ammonia (Fri Jun 04 2004 - 15:01:04 CDT)
  • RE: how to generate your own pdb file (Fri May 14 2004 - 21:55:28 CDT)
  • RE: Calculating parameters. (Fri May 14 2004 - 16:59:15 CDT)
  • RE: Binding free energy of a protein complex (Mon May 03 2004 - 06:02:29 CDT)
  • RE: Lithium (Thu Apr 29 2004 - 11:14:56 CDT)
  • Binding energy analysis (Sat Apr 24 2004 - 21:09:45 CDT)
  • RE: minimization problem (Thu Mar 18 2004 - 18:43:00 CST)
  • RE: minimization problem (Thu Mar 18 2004 - 18:31:09 CST)
  • RE: Urea and GdHCl parameters (Mon Mar 15 2004 - 13:15:18 CST)
  • Binding Energy (Mon Mar 08 2004 - 12:57:18 CST)
  • Potential Terms (Mon Jan 05 2004 - 12:20:02 CST)
  • Density (Tue Dec 16 2003 - 12:45:26 CST)
  • Polymer Simulations (Mon Dec 15 2003 - 16:49:22 CST)
  • Some parameters (Tue Dec 09 2003 - 06:06:50 CST)
  • PSF generation (Sun Dec 07 2003 - 10:08:47 CST)
  • Small Organic Compounds with NAMD (Sat Oct 18 2003 - 18:40:37 CDT)
  • Topology file for model compounds (Tue Oct 14 2003 - 10:24:40 CDT)
• aida_at_mit.edu
  • Direction of SMD force (Tue Feb 17 2004 - 09:06:16 CST)
  • Running AIX version of NAMD on IBM cluster (Wed Feb 04 2004 - 14:54:21 CST)
• 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)
• Al-Rawi, Ahlam
  • Temperature problem (Tue Feb 13 2007 - 14:05:35 CST)
  • external force (Thu Nov 02 2006 - 12:16:23 CST)
  • external force (Tue Oct 24 2006 - 17:30:43 CDT)
  • external force (Tue Oct 24 2006 - 14:39:42 CDT)
• Alberto Santana
  • compiling namd intel 9.1 (Wed May 16 2007 - 06:06:35 CDT)
  • 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 Cembran
  • unsubscribe namd-l (Tue Feb 26 2008 - 14:11:36 CST)
  • Re: What is an IC table in the .inp files (Fri Nov 16 2007 - 14:23:08 CST)
  • Re: Re: Diffusion of Protein through the membrane (Wed Jun 27 2007 - 09:08:32 CDT)
  • Re: how to convert dcd files from namd to charmm (Thu Mar 15 2007 - 15:38:37 CDT)
  • Re: how to convert dcd files from namd to charmm (Thu Mar 15 2007 - 08:08:25 CDT)
  • Re: how to convert dcd files from namd to charmm (Thu Mar 15 2007 - 07:59:01 CDT)
  • TOTAL, TOTAL2 and TOTAL3 (Mon Feb 19 2007 - 11:36:16 CST)
  • Re: Re: vmd-l: ionize (big, big, big system!) (Mon Feb 12 2007 - 18:57:05 CST)
  • Re: Re: vmd-l: ionize (big, big, big system!) (Mon Feb 12 2007 - 11:37:20 CST)
  • Re: unequal PMEGridSizes (Fri Dec 29 2006 - 17:07:58 CST)
  • Re: Linux HP Itanium Quadrics (Tue Nov 14 2006 - 13:39:27 CST)
  • Linux HP Itanium Quadrics (Fri Nov 10 2006 - 17:04:45 CST)
  • Re: deformations in a water box during equilibration in NAMD (Fri Nov 03 2006 - 09:42:52 CST)
  • Re: Hexagonal boundary conditions (Thu Sep 21 2006 - 10:34:51 CDT)
  • Re: PBS & local (scratch) space (Wed Sep 20 2006 - 16:19:19 CDT)
  • Re: Altix Performance Tuning (Wed Sep 20 2006 - 11:03:53 CDT)
  • Altix Performance Tuning (Mon Sep 18 2006 - 13:18:52 CDT)
  • Re: Lipids into NAMD (Mon Aug 21 2006 - 13:54:30 CDT)
  • Re: Lipids into NAMD (Mon Aug 21 2006 - 10:21:02 CDT)
  • Ion Channel Jarzynski (Thu Aug 10 2006 - 17:56:29 CDT)
  • UseConstantRatio between "run" (Mon Jul 10 2006 - 18:37:38 CDT)
  • Altix performances (Tue Jun 13 2006 - 17:40:59 CDT)
  • Pairlist warnings (Sat Jun 10 2006 - 16:58:07 CDT)
• Alessandro Pedretti
  • Re: Converting DCD file to XTC format (Wed Jan 16 2008 - 02:11:20 CST)
  • Re: Conversion of .dcd into .xtc format (Wed May 16 2007 - 09:33:13 CDT)
  • Re: problems reading large dcd file (Sat Jan 07 2006 - 04:14:55 CST)
  • 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)
  • Re: how to get the plot of selected bond over time? (Fri Dec 05 2003 - 07:19:45 CST)
  • Re: how to add counterions ? (Tue Dec 02 2003 - 06:18:58 CST)
  • Re: Energy problem after restart (Mon Nov 24 2003 - 03:00:11 CST)
  • Energy problem after restart (Thu Nov 20 2003 - 07:13:56 CST)
• alessandro.pedretti_at_unimi.it
  • Re: Chloroform Solvent Box (Tue Nov 23 2004 - 14:19:11 CST)
• Alessio Alexiadis
  • water HOH angle of 102 defrees (Fri Jul 13 2007 - 13:13:23 CDT)
  • Did anybody really use TIP4P? (Mon Jul 09 2007 - 09:52:47 CDT)
  • TIP4P examples (Fri Jul 06 2007 - 01:31:37 CDT)
  • TIP4P in NAMD? (Fri Jun 29 2007 - 07:52:57 CDT)
  • Running NAMD on Cluster machine with Myrinet network with MPI and PBS (Tue Jun 05 2007 - 05:23:38 CDT)
  • temperature and pressure control (Tue May 29 2007 - 00:40:02 CDT)
  • Temperature Coupling (Thu May 24 2007 - 02:59:31 CDT)
  • water models: a basic question (Thu May 10 2007 - 06:31:26 CDT)
  • user defined L-J parameters (Wed Mar 21 2007 - 05:18:17 CDT)
  • how to get the velocities from the dcd file (Mon Mar 05 2007 - 09:25:49 CST)
• alex digenova bravo
  • Free energy Calculations (Mon Oct 01 2007 - 17:59:34 CDT)
  • Re: ABF restrain (Thu Jul 05 2007 - 11:48:12 CDT)
  • ABF restrain (Wed Jul 04 2007 - 15:31:19 CDT)
  • FullSamples variable in ABF (Tue May 22 2007 - 23:50:36 CDT)
  • System Charge (Thu May 03 2007 - 18:26:39 CDT)
  • Fep questions about FepEquilSteps (Wed Apr 25 2007 - 14:50:43 CDT)
• Alex Huang
  • Coordinates go to zero! (Wed Feb 27 2008 - 14:52:28 CST)
  • Question about Error Message (Thu Jan 10 2008 - 09:33:49 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)
• Alexander Vaughn
  • Re: a philosophical question... (Tue Jan 30 2007 - 17:07:46 CST)
  • FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE (Thu Jan 11 2007 - 19:37:34 CST)
• Alexandre A. Vakhrouchev
  • Re: charmrun not found (Tue Jun 24 2008 - 22:50:45 CDT)
  • Re: Language Used and Elementary doubts (Thu Jun 12 2008 - 12:15:43 CDT)
  • ApoB structure (Thu Jun 12 2008 - 01:12:02 CDT)
  • Re: Temperature rescaling and reassignment parameters (Tue Jun 10 2008 - 04:53:44 CDT)
  • Re: Classic timepieces replicas (Tue Jun 10 2008 - 04:41:40 CDT)
  • Re: Temperature rescaling and reassignment parameters (Mon Jun 09 2008 - 23:20:38 CDT)
  • Re: Building Namd on a linux cluster. (Fri May 30 2008 - 00:38:25 CDT)
  • Re: Error Parsing Config File (Sat May 24 2008 - 03:06:29 CDT)
  • Unable to edit files in NAMD folder. (Wed May 21 2008 - 03:37:52 CDT)
  • Re: Error: transport retry exceeded error (Sat May 17 2008 - 00:03:03 CDT)
  • Error: transport retry exceeded error (Thu May 15 2008 - 13:41:21 CDT)
  • Energy plot script (Wed May 14 2008 - 22:11:19 CDT)
  • Re: DCD file size (Mon May 12 2008 - 21:50:25 CDT)
  • DCD file size (Mon May 12 2008 - 14:19:57 CDT)
  • Re: install NAMD on Ubuntu (Sat Apr 26 2008 - 01:12:30 CDT)
  • Time factor (Thu Apr 24 2008 - 23:16:04 CDT)
  • Re: What does "cellOrigin" really mean? (Wed Apr 23 2008 - 08:36:51 CDT)
  • Re: VMD-NAMD-commands (Sat Apr 19 2008 - 00:16:08 CDT)
  • Re: HP-MPI on Xeon Infiniband (Sun Feb 10 2008 - 10:10:22 CST)
  • Re: HP-MPI on Xeon Infiniband (Sun Feb 10 2008 - 08:26:25 CST)
  • HP-MPI on Xeon Infiniband (Sun Feb 10 2008 - 06:43:58 CST)
  • Re: Cholesterol structure (Thu Jan 31 2008 - 08:06:03 CST)
  • Re: Cholesterol structure (Thu Jan 31 2008 - 02:02:46 CST)
  • Re: Cholesterol structure (Thu Jan 31 2008 - 01:38:03 CST)
  • Re: Cholesterol structure (Thu Jan 31 2008 - 00:50:13 CST)
  • Cholesterol structure (Tue Jan 29 2008 - 04:48:07 CST)
  • Q=D4=D7=C5=D4:__128+_proccessor_jobs_on_64bit_?= Widows hang upon completion of the simulation. (Mon Jul 30 2007 - 04:20:41 CDT)
  • Q=D4=D7=C5=D4:__RE:_NAMD_crashes?= on winx64 during parallel run. (Sun Jul 29 2007 - 00:42:38 CDT)
  • Restarting calculation missmatches (Thu Jul 19 2007 - 00:59:36 CDT)
  • Re: Running NAMD on Cluster machine with Myrinet network with MPI and PBS (Tue Jun 05 2007 - 10:34:39 CDT)
  • Re: combine pdb files (Sun Jun 03 2007 - 08:39:30 CDT)
  • Re: Pressure calculation method (Sun Jun 03 2007 - 03:23:04 CDT)
  • Pressure calculation method (Fri Jun 01 2007 - 09:05:46 CDT)
  • Pressure calculation method (Sat May 26 2007 - 22:42:36 CDT)
  • NAMD on CELL BE (Fri Apr 27 2007 - 09:52:50 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)
• Alexandre F. G.
  • Neutral arginine patch in topology file. (Tue Apr 29 2008 - 16:45:29 CDT)
• Alexandre Vakhrouchev
  • Re: Charm++ nodelist commands (Thu Dec 18 2003 - 11:36:11 CST)
  • Re: Charm++ nodelist commands (Thu Dec 18 2003 - 06:33:16 CST)
  • Re: Help! unstable simulation. (Fri Dec 12 2003 - 03:16:55 CST)
  • (no subject) (Sun Dec 07 2003 - 01:47:07 CST)
  • (no subject) (Wed Dec 03 2003 - 02:57:04 CST)
  • (no subject) (Thu Nov 06 2003 - 02:18:39 CST)
• Alexe Bojovschi
  • NAMD cg configuration file (Sun Oct 28 2007 - 19:02:44 CDT)
  • CHARMM top and par files for PO4 (Mon Aug 14 2006 - 03:53:20 CDT)
  • Configurational temperature - coordinates (Wed Jan 18 2006 - 21:11:32 CST)
  • 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)
• Alexis Salas
  • namd.conf with OPLS options (Fri May 18 2007 - 17:43:52 CDT)
• ali alizadeh
  • apply periodic boundary condition in one direction (Thu May 31 2007 - 07:53:37 CDT)
  • How could I fixed the system just in Z-coordinate? (Wed May 23 2007 - 09:34:32 CDT)
  • fixed system just in Z direction (Thu May 10 2007 - 03:36:04 CDT)
  • my simulation dont be minimized when I fixed the channel (Tue May 08 2007 - 09:48:35 CDT)
• Allan Haldane
  • Re: popc pressure profile (Wed Nov 15 2006 - 21:18:13 CST)
  • popc pressure profile (Tue Oct 10 2006 - 11:40:43 CDT)
• Allen Chen
  • NAMD in Solaris X86 (Tue Jul 17 2007 - 17:01:50 CDT)
• allison
  • hanging at startup phase (Wed May 19 2004 - 14:00:25 CDT)
• Allison Chan
  • Crazy defoliator (Sun Jun 10 2007 - 14:18:35 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)
• Allison Langham
  • hexagonal crystal (Wed Mar 21 2007 - 11:22:26 CDT)
• Alok Juneja
  • catDCD 32 bit Vs. 64 bit Version (Thu Jan 31 2008 - 03:51:40 CST)
  • Re: Is there solution to numerical inaccuracy (Mon Dec 03 2007 - 12:49:50 CST)
  • Re: Is there solution to numerical inaccuracy (Thu Nov 29 2007 - 12:04:50 CST)
  • Is there solution to numerical inaccuracy (Tue Nov 20 2007 - 06:07:57 CST)
  • Re: Is there solution to numerical inaccuracy (Fri Nov 23 2007 - 12:14:01 CST)
  • Re: Is there solution to numerical inaccuracy (Mon Nov 26 2007 - 04:54:22 CST)
  • Re: Is there solution to numerical inaccuracy (Tue Nov 20 2007 - 10:53:04 CST)
  • Is there solution to numerical inaccuracy (Tue Nov 20 2007 - 07:54:29 CST)
• alsalazar_at_northwestern.edu
  • Using CHARMM27 (Wed Jun 20 2007 - 10:27:53 CDT)
• Alvaro Foletti
  • NAMD electrostatics no cutoff or switching (Tue May 13 2008 - 12:44:01 CDT)
• Amanda Chase
  • Want to be a hero in bed? (Thu Jun 07 2007 - 11:46:40 CDT)
• Amanda Pearson
  • Say "NO" to erectile dysfunction! (Thu Jun 07 2007 - 06:48:07 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)
• Ambrish
  • Errors during equilibration: segmentation fault and bad global exclusion count (Tue Oct 23 2007 - 01:45:05 CDT)
  • Re: Molecule drifts and high average RMSD per residue (Tue Oct 09 2007 - 15:53:31 CDT)
  • ptraj (Mon Oct 08 2007 - 18:30:59 CDT)
  • Molecule drifts and high average RMSD per residue (Mon Oct 08 2007 - 11:02:49 CDT)
• Amin R. Mazloom
  • Velocity unit ofvelocity in NAMD the binary files (Tue Jun 13 2006 - 15:43:09 CDT)
  • Unit of Velocity in the Velocity files (Tue Jun 13 2006 - 11:36:56 CDT)
  • getting #.IND #QNAN after phase 8 (Mon Jun 05 2006 - 14:25:25 CDT)
• Amir Shamloo
  • FEP alchemical (Fri Jul 15 2005 - 19:51:23 CDT)
• amit dong
  • equilibration (Fri Mar 23 2007 - 11:30:06 CDT)
  • H-bond energy (Thu Jan 11 2007 - 04:24:04 CST)
• Amit Paliwal
  • NAMD-MPI compilation on P4 cluster (Sat Sep 04 2004 - 18:37:55 CDT)
  • compiling NAMD on OSC P4 cluster (Fri Sep 03 2004 - 12:11:51 CDT)
  • Re: compiled namd on clustermatic fails ! (Tue Aug 03 2004 - 06:38:31 CDT)
  • Re: compiled namd on clustermatic fails ! (Thu Jul 29 2004 - 19:24:52 CDT)
  • compiled namd on clustermatic fails ! (Thu Jul 29 2004 - 13:33:10 CDT)
  • fixed particles (Fri Jul 16 2004 - 18:22:23 CDT)
  • harmonic restraint (Tue Jun 15 2004 - 12:23:10 CDT)
  • error (Mon May 24 2004 - 04:29:43 CDT)
  • flexible cell (Tue May 18 2004 - 17:08:41 CDT)
  • NAMD with Amber (Fri May 14 2004 - 12:42:10 CDT)
  • COM velocity (Thu Apr 15 2004 - 04:50:29 CDT)
  • Re: water box (Tue Mar 30 2004 - 08:45:01 CST)
  • water box (Tue Mar 30 2004 - 06:03:30 CST)
  • Re: charmm27 (Tue Jan 13 2004 - 12:31:50 CST)
  • Interaction energy for fixed atoms (Fri Jan 09 2004 - 17:35:13 CST)
  • Interaction energy between fixed atoms (Wed Jan 07 2004 - 08:03:12 CST)
  • [Fwd: total energy stuck between two levels] (Wed Jan 07 2004 - 05:10:03 CST)
  • total energy stuck between two levels (Tue Jan 06 2004 - 22:20:10 CST)
  • alchemical free energy perturbation (Mon Jan 05 2004 - 00:37:05 CST)
  • TIP3P model (Wed Dec 17 2003 - 13:10:45 CST)
  • Re: repulsive/hard sphere simulation (Wed Nov 05 2003 - 15:53:17 CST)
  • Re: repulsive/hard sphere simulation (Wed Nov 05 2003 - 15:50:53 CST)
  • repulsive/hard sphere simulation (Wed Nov 05 2003 - 15:07:21 CST)
  • Re: Scyld cluster (Wed Oct 22 2003 - 12:26:55 CDT)
  • Scyld cluster (Wed Oct 22 2003 - 07:52:06 CDT)
  • Re: hard sphere simulation (Mon Sep 22 2003 - 20:08:31 CDT)
  • hard sphere simulation (Sat Sep 20 2003 - 11:01:18 CDT)
• amodzelewska_at_dns.iimcb.gov.pl
  • autoionize script (Sun May 16 2004 - 13:21:58 CDT)
• Amy Mccormick
  • Wet miracle (Tue Jun 05 2007 - 01:45:44 CDT)
• Ana Celia Araujo Vila Verde
  • RE: Parameter file for Gold ? (Fri Jun 08 2007 - 09:58:58 CDT)
  • RE: Replica exchange MD (Tue May 29 2007 - 14:51:45 CDT)
  • RE: Why is SHAKE not being used in typical NAMD simulations ? (Thu May 24 2007 - 10:42:30 CDT)
  • RE: wrong velocity in steered molecular dynamics (Sun Apr 08 2007 - 14:57:29 CDT)
  • RE: wrong velocity in steered molecular dynamics (Sun Apr 08 2007 - 13:56:29 CDT)
  • wrong velocity in steered molecular dynamics (Sat Apr 07 2007 - 14:29:18 CDT)
  • problems running more than 9 Replicas in replica exchange simulations (Sun Feb 04 2007 - 14:33:41 CST)
  • problems running Replica Exchange simulations using SSH to spawn the processes (Thu Feb 01 2007 - 13:28:06 CST)
  • RE: Tcl Scripting (Wed Jan 24 2007 - 11:34:54 CST)
  • fixed atoms appearing on the other side of simulation box (Tue Jan 16 2007 - 13:38:33 CST)
  • RE: "Not all atoms have unique coordinates" (Fri Jan 05 2007 - 12:58:23 CST)
  • RE: water box deformation (Thu Nov 30 2006 - 17:15:35 CST)
  • RE: is there any maximum limt of atom numbers in VMD or NAMD? (Wed Nov 29 2006 - 10:07:10 CST)
  • RE: NAMD for inorganics?? (Thu Nov 23 2006 - 10:39:05 CST)
  • RE: rmsd is not stabilizing even after 0.6 ns (Tue Oct 31 2006 - 14:27:23 CST)
  • RE: "reinitvel" parameter in config file (Thu Oct 12 2006 - 07:50:30 CDT)
  • RE: vmd-l: imposing period boundary conditions in a simulation with a crystal (Wed Sep 06 2006 - 08:31:59 CDT)
  • Do I need to use an xsc file to restart a simulation in NVT? (Wed Jun 28 2006 - 10:41:07 CDT)
  • Do I need to use an xsc file to restart a simulation in NVT? (Wed Jun 28 2006 - 14:05:27 CDT)
• Ana Vila Verde
  • Re: Inconsistencies in NAMD simulations (Tue Jan 22 2008 - 06:14:52 CST)
  • Re: Is it better to align all the trajectory before calculating rmsd? (Tue Jan 22 2008 - 05:31:12 CST)
  • FATAL ERROR: called "save_callback" with too many arguments when running replica exchange (Wed Sep 19 2007 - 11:23:50 CDT)
• Anahita Tafvizi
  • Re: adding extra ions to neutralize charge on protein (Thu Oct 19 2006 - 12:30:02 CDT)
  • Re: rigid protein (Thu Oct 19 2006 - 10:50:01 CDT)
  • Re: rigid protein (Thu Oct 19 2006 - 10:23:16 CDT)
  • Re: rigid protein (Thu Oct 19 2006 - 08:21:45 CDT)
  • constraining distance (Wed Oct 04 2006 - 13:16:29 CDT)
  • question regarding the use of reaction coordinate "distance-com" in ABF method (Sun Sep 10 2006 - 12:51:46 CDT)
  • History file of an ABF smiulation (Sat Sep 09 2006 - 13:55:58 CDT)
  • Re: questions regarding output data of an ABF simulation (Mon Aug 07 2006 - 17:52:11 CDT)
  • questions regarding output data of an ABF simulation (Mon Aug 07 2006 - 15:27:34 CDT)
• Andersen, Kim Vilbour (KVA)
  • Autogene angles dihed / patch / psfgen problem (Wed Oct 15 2003 - 06:27:17 CDT)
• andrea carotti
  • Best NAMD version for Rocks 4.3 IBM xseries 3665 (Tue Sep 04 2007 - 06:06:32 CDT)
  • FATAL ERROR: Bad global improper count! (Mon Jul 23 2007 - 03:47:16 CDT)
• Andrea Cristiani
  • Charmrun and ssh problem (Tue Sep 18 2007 - 04:50:23 CDT)
• Andrea Diaz
  • problem compiling NAMD2.6 in a MacOSX-PPC (Thu Jun 19 2008 - 10:15:27 CDT)
  • problem compiling NAMD2.6 in a MacOSX-PPC (Thu Jun 19 2008 - 16:30:57 CDT)
  • FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE HN (Sun Feb 03 2008 - 16:29:59 CST)
  • TEMPERATURE and TEMPAVG : nan (Thu Aug 02 2007 - 16:58:39 CDT)
  • Unit cell angles information (Sat Jul 21 2007 - 16:46:41 CDT)
  • Deformations under constant strain rates (Mon May 14 2007 - 12:28:18 CDT)
  • Atoms mooving too fast ... still the problem (Tue Apr 03 2007 - 19:51:39 CDT)
  • RE:Re: Help !!! ERROR: Atoms mooving too fast (Tue Apr 03 2007 - 14:46:36 CDT)
• Andrei Istomin
  • Appending to the existing dcd file after restart (Wed Jan 30 2008 - 02:06:55 CST)
• Andrew D. Fant
  • peptide conformation search examples (Tue Jan 30 2007 - 14:21:49 CST)
  • Re: simulation of membrane-protein systems (Mon Dec 18 2006 - 13:42:31 CST)
  • Re: Building PDB files for DNA. (Fri Dec 15 2006 - 12:08:23 CST)
• Andrew Thomas
  • Large MD simulations and atom number limits with NAMD (Fri Jun 20 2008 - 09:53:50 CDT)
• ANDY NG
  • Generating topology file (Thu Nov 11 2004 - 00:59:51 CST)
• Andy Shelley
  • Heat flux along CNT (Tue Jul 01 2008 - 14:13:36 CDT)
• 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
  • nve ensemble (Thu Jan 19 2006 - 05:08:29 CST)
  • 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)
• Annalisa Marsico
  • problem reading topolgy files (Sun Dec 10 2006 - 06:14:51 CST)
  • combine.tcl (Tue Nov 21 2006 - 12:40:00 CST)
• Anuradha Mittal
  • SPC/E water model (Thu Jun 28 2007 - 09:15:13 CDT)
  • PMEGridSize (Sun Apr 02 2006 - 21:18:38 CDT)
• 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
  • TCL script for umbrella sampling (Mon May 14 2007 - 05:07:01 CDT)
  • Re: 0 coordinates for LES atoms in pdb file after solvation (Thu Jan 25 2007 - 22:11:04 CST)
  • Re: 0 coordinates for LES atoms in pdb file after solvation (Thu Jan 25 2007 - 03:11:44 CST)
  • Re: topology of carbon dioxide compatible with Charmm (Mon Jan 08 2007 - 11:56:26 CST)
  • topology of carbon dioxide compatible with Charmm (Mon Jan 08 2007 - 05:06:07 CST)
  • 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)
• Ariovaldo de Souza Junior
  • (no subject) (Fri Jun 20 2008 - 05:27:36 CDT)
• Armen Nalian
  • essential dynamics analysis (Mon Nov 22 2004 - 15:58:10 CST)
  • PC-DL Deluxe, Dual Xeon (Wed Aug 04 2004 - 17:32:54 CDT)
  • Fatal Socket error: code 93523-Error in accept (Wed Aug 04 2004 - 15:05:17 CDT)
• Armen Poghosyan
  • Does anybody have gromacs topology example, which works OK using NAMD?? (Tue Jun 01 2004 - 14:24:00 CDT)
  • How to use GROMACS force field in NAMD? (Mon May 31 2004 - 02:34:06 CDT)
  • FATAL ERROR: Patch needed for tuple is missing. (Thu May 06 2004 - 07:21:57 CDT)
• Arneh Babakhani
  • Defining a group of atoms in a simulation (Sat Jan 19 2008 - 11:15:03 CST)
  • Can NAMD be used as for general Newtonian mechanics simulations? (Fri Jul 27 2007 - 15:21:20 CDT)
  • Re: Simulation failed during the stage of heat (Fri Mar 24 2006 - 12:29:34 CST)
  • Re: Re:Re:error caused by lipid membrane (Tue Mar 21 2006 - 00:35:02 CST)
  • Re: error caused by atoms of lipid membrane (Mon Mar 20 2006 - 10:35:14 CST)
  • Re: question on membrane crushing (Tue Mar 14 2006 - 15:59:53 CST)
  • Re: question on membrane crushing (Mon Mar 13 2006 - 16:52:04 CST)
  • Re: question on membrane crushing (Fri Mar 03 2006 - 14:49:42 CST)
  • Re: gradually pressure change (increase/decrease) (Tue Feb 28 2006 - 12:44:58 CST)
  • Re: Rattle Error During Equilibration of Lipid Bilayer Membrane (Wed Feb 22 2006 - 14:09:23 CST)
  • Re: Rattle Error During Equilibration of Lipid Bilayer Membrane (Sun Feb 12 2006 - 21:11:29 CST)
  • Re: Rattle Error During Equilibration of Lipid Bilayer Membrane (Sun Feb 12 2006 - 15:40:20 CST)
  • Rattle Error During Equilibration of Lipid Bilayer Membrane (Fri Feb 10 2006 - 22:32:51 CST)
• Artem Zhmurov
  • NAMD+MPI on AMD64 (Fri Mar 21 2008 - 12:30:29 CDT)
  • Parallelism issue (Thu Mar 20 2008 - 15:45:15 CDT)
• Arturas Ziemys
  • electrostatics NAMD vs CHARMM (Thu May 01 2008 - 11:29:49 CDT)
  • 2 molecule pair interactions (Wed Apr 16 2008 - 16:26:27 CDT)
  • quartz slab / pairInteractionSelf / Bad global exclusion count! (Fri Mar 14 2008 - 12:55:11 CDT)
  • Re: fixed atoms / pressure (Thu Mar 13 2008 - 10:52:41 CDT)
  • fixed atoms / pressure (Mon Mar 10 2008 - 12:31:27 CDT)
  • quartz / FF(Lopez&MacKerrel) (Fri Feb 08 2008 - 15:00:36 CST)
  • How to access energies after MD step with Tcl ? (Wed Sep 05 2007 - 11:30:31 CDT)
  • Replica Exhange error: POSIX EINTR {interrupted system call} (Fri Aug 24 2007 - 16:45:51 CDT)
  • REMD using PBS qeue (Wed Aug 22 2007 - 10:31:04 CDT)
  • wrapping (Thu Jul 26 2007 - 10:59:38 CDT)
  • checkpoint / revert (Thu Jun 14 2007 - 13:09:24 CDT)
  • OPLS dihedrals (Sat May 19 2007 - 10:47:16 CDT)
  • Re: Sulphate Ion Parameters (Thu May 17 2007 - 08:42:09 CDT)
  • Fast routines for distance evaluations using PBC. (Fri May 11 2007 - 11:52:49 CDT)
  • ERROR: Number of pdb and psf atoms are not the same! (Mon Mar 26 2007 - 14:08:36 CDT)
  • Re: user defined L-J parameters (Wed Mar 21 2007 - 08:59:21 CDT)
  • Free Energy/ ERROR (Mon Mar 12 2007 - 15:37:31 CDT)
  • Free Energy of Conformation Change (Mon Mar 12 2007 - 13:16:57 CDT)
  • Does pair interaction calculations uses PBC ? (Wed Feb 21 2007 - 11:18:22 CST)
  • Tcl_BC: [nexatom] twice in script (Tue Jan 02 2007 - 09:52:53 CST)
  • loadforces problem (Thu Dec 21 2006 - 13:58:44 CST)
  • addforce (Wed Dec 13 2006 - 14:16:43 CST)
  • particle access in tclBC (Thu Dec 07 2006 - 13:24:05 CST)
  • Tcl_Forces / 'loadcoords' loads NOT wrapped coordinates ? (Thu Dec 07 2006 - 12:19:31 CST)
  • Re: Tcl_Forces = pressure shifts while Langevin Piston is ON (Tue Dec 05 2006 - 13:47:08 CST)
  • polyethylene topology (Tue Dec 05 2006 - 12:05:57 CST)
  • Tcl_Forces = pressure shifts while Langevin Piston is ON (Fri Dec 01 2006 - 16:53:01 CST)
  • getbond (Tcl forces) / PBC (Thu Nov 30 2006 - 10:12:32 CST)
  • Dummy particles (Wed Nov 22 2006 - 14:55:36 CST)
  • Re: How to create repulsive particle ? (Tue Nov 21 2006 - 15:45:01 CST)
  • How to create repulsive particle ? (Tue Nov 21 2006 - 13:47:51 CST)
  • LES / cLES (Mon Nov 13 2006 - 09:40:09 CST)
  • LES : size (Fri Nov 10 2006 - 12:09:50 CST)
  • Replica Exchange (Thu Oct 26 2006 - 10:53:16 CDT)
  • heat capacity: NPT vs. NVT (Wed Oct 25 2006 - 09:53:37 CDT)
  • Re: (Thu Sep 28 2006 - 08:10:19 CDT)
  • Qmeasure=22?= command (Wed Sep 27 2006 - 16:30:24 CDT)
  • PBS & local (scratch) space (Wed Sep 20 2006 - 15:42:18 CDT)
  • Re: Recentering the box on target molecule and wraping (Mon Sep 11 2006 - 11:56:59 CDT)
  • Recentering the box on target molecule and wraping (Mon Sep 11 2006 - 10:39:55 CDT)
  • charmm toppology : internal coordinates (Tue Aug 22 2006 - 16:39:00 CDT)
  • parallel NAMD output problem (Tue May 30 2006 - 11:27:36 CDT)
  • bulk density in RDF.tcl (Wed Mar 29 2006 - 10:28:44 CST)
  • System after pressure change - confirmation needed (Wed Mar 01 2006 - 09:30:20 CST)
  • gradually pressure change (increase/decrease) (Tue Feb 28 2006 - 11:44:08 CST)
  • how gradually change (increase/decrease) pressure ? (Mon Feb 27 2006 - 11:59:15 CST)
  • dublicated residue numbers in PDB/PSF (Wed Feb 01 2006 - 09:14:53 CST)
  • Tools to "open" domains (Tue Jan 31 2006 - 10:12:03 CST)
  • charmm27 fatal error (Mon Dec 19 2005 - 14:06:00 CST)
• Arun Krishnan
  • Re: Getting density of water.. (Fri Nov 09 2007 - 02:08:39 CST)
  • Getting density of water.. (Fri Nov 09 2007 - 01:24:36 CST)
  • Re: Determining Transition State from an Unfolding Simulation (Thu Sep 27 2007 - 16:17:15 CDT)
  • Fwd: Determining Transition State from an Unfolding Simulation (Wed Sep 26 2007 - 08:19:13 CDT)
  • Re: Meaning of lines in "run" part of log file. (Wed Sep 26 2007 - 00:38:00 CDT)
  • Re: Determining Transition State from an Unfolding Simulation (Tue Sep 25 2007 - 23:56:52 CDT)
  • Determining Transition State from an Unfolding Simulation (Sun Sep 23 2007 - 15:57:17 CDT)
  • Re: Temperature dependent unfolding.. (Thu Sep 20 2007 - 20:24:52 CDT)
  • Re: NAMD run (Wed Sep 12 2007 - 19:48:27 CDT)
  • Re: Temperature dependent unfolding.. (Thu Sep 06 2007 - 20:25:54 CDT)
  • Re: Temperature dependent unfolding.. (Thu Sep 06 2007 - 20:09:46 CDT)
  • Re: Temperature dependent unfolding.. (Wed Sep 05 2007 - 12:21:55 CDT)
  • Re: Temperature dependent unfolding.. (Wed Sep 05 2007 - 11:40:56 CDT)
  • Re: Temperature dependent unfolding.. (Wed Sep 05 2007 - 10:56:56 CDT)
  • Re: Temperature dependent unfolding.. (Wed Sep 05 2007 - 11:02:21 CDT)
  • Re: Temperature dependent unfolding.. (Wed Sep 05 2007 - 09:26:26 CDT)
  • Re: Temperature dependent unfolding.. (Wed Sep 05 2007 - 08:37:45 CDT)
  • Temperature dependent unfolding.. (Tue Sep 04 2007 - 20:13:35 CDT)
  • Re: Re: NAMD: Exiting Prematurely (Wed Aug 15 2007 - 20:22:50 CDT)
  • Re: Re: NAMD: Exiting Prematurely (Wed Aug 15 2007 - 20:23:39 CDT)
  • Re: Re: NAMD: Exiting Prematurely (Wed Aug 15 2007 - 20:19:17 CDT)
  • Re: Re: NAMD: Exiting Prematurely (Wed Aug 15 2007 - 20:20:42 CDT)
  • Re: NAMD: Exiting Prematurely (Wed Aug 15 2007 - 00:58:25 CDT)
  • NAMD: Exiting Prematurely (Tue Aug 14 2007 - 19:59:54 CDT)
  • Is very slow heating "bad"? (Sat Aug 04 2007 - 01:49:14 CDT)
  • Re: Unfolding protocol.. (Fri Aug 03 2007 - 01:35:01 CDT)
  • Unfolding protocol.. (Fri Aug 03 2007 - 00:58:58 CDT)
  • FATAL ERROR: Unable to open extended system file. (Mon Jul 30 2007 - 02:27:49 CDT)
  • Fwd: namd2 installation.. (Wed Jul 11 2007 - 01:26:58 CDT)
  • Unfolding simulations (Mon Jul 09 2007 - 01:18:26 CDT)
  • namd2 installation.. (Mon Jul 09 2007 - 01:20:19 CDT)
  • Do we need to renumber atoms after solvate? (Sun Jul 08 2007 - 20:31:20 CDT)
  • Re: Installing NAMD 2.6 on SMP machine... charm++ install errors (Fri Jul 06 2007 - 01:45:46 CDT)
  • Installing NAMD 2.6 on SMP machine... charm++ install errors (Fri Jul 06 2007 - 01:29:25 CDT)
• ashwin joshi
  • Compilation of NAMD on 64-bit NUMA with icc (Tue Oct 18 2005 - 02:46:18 CDT)
• Audrey Salazar
  • Re: Meaning of lines in "run" part of log file. (Wed Sep 26 2007 - 09:55:42 CDT)
  • Re: Meaning of lines in "run" part of log file. (Tue Sep 25 2007 - 22:24:48 CDT)
  • Meaning of lines in "run" part of log file. (Tue Sep 25 2007 - 20:08:31 CDT)
  • Re: How to restart a simulation (Thu Sep 20 2007 - 10:28:06 CDT)
  • How to restart a simulation (Thu Sep 20 2007 - 10:25:10 CDT)
  • Re: Compiling NAMD 2.6 from Source: no charm-5.9.tar (Tue Aug 28 2007 - 14:27:50 CDT)
  • Compiling NAMD 2.6 from Source: no charm-5.9.tar (Tue Aug 28 2007 - 13:42:14 CDT)
  • Re: question about equilibration step (Fri Aug 24 2007 - 12:22:29 CDT)
  • Re: question about equilibration step (Fri Aug 24 2007 - 09:04:28 CDT)
  • question about equilibration step (Thu Aug 23 2007 - 17:33:03 CDT)
  • Storing atom coordinates at each time step (Wed Aug 15 2007 - 15:03:37 CDT)
  • Finding size of water box (Mon Aug 06 2007 - 11:15:41 CDT)
  • Downloading CHARMM Parameter and Topology Files (Fri Jul 27 2007 - 11:31:54 CDT)
  • Building a pdb file (Tue Jul 03 2007 - 16:14:41 CDT)
  • barostats in NAMD (Mon Jun 25 2007 - 18:41:55 CDT)
  • Using CHARMM27 (Wed Jun 20 2007 - 09:48:45 CDT)
• Axel Kohlmeyer
  • Re: NAMD log file analysis script problem (namdstats.tcl) (Sun Jun 15 2008 - 13:09:50 CDT)
  • Re: use of 'measure hbonds' (Fri Jun 13 2008 - 07:43:12 CDT)
  • Re: Classic timepieces replicas (Tue Jun 10 2008 - 04:37:57 CDT)
  • Re: Correctness of Simulation Results (Mon Jun 09 2008 - 12:03:06 CDT)
  • Re: NAMD compilation on linux cluster (Sun Jun 08 2008 - 11:32:26 CDT)
  • Re: PME and r-RESPA issue in NAMD (Sat Jun 07 2008 - 09:50:59 CDT)
  • Re: Mindboggling Problem Related To NAMD2 Code (Mon Jun 02 2008 - 18:42:04 CDT)
  • Re: Average energy in NAMD (Sun Jun 01 2008 - 16:51:15 CDT)
  • Re: Average energy in NAMD (Sun Jun 01 2008 - 19:22:51 CDT)
  • Re: Mindboggling Problem Related To NAMD2 Code (Sun Jun 01 2008 - 08:01:34 CDT)
  • Re: Building Namd on a linux cluster. (Fri May 30 2008 - 19:25:00 CDT)
  • Re: Building Namd on a linux cluster. (Fri May 30 2008 - 14:41:27 CDT)
  • Re: Building Namd on a linux cluster. (Fri May 30 2008 - 07:38:12 CDT)
  • Re: NAMD trajectory format (Fri May 30 2008 - 08:29:26 CDT)
  • Re: NAMD trajectory format (Fri May 30 2008 - 07:34:52 CDT)
  • Re: benchmarking of NAMD: sustained performance (TF) (Thu May 29 2008 - 09:05:40 CDT)
  • Re: NAMD trajectory format (Wed May 28 2008 - 09:05:46 CDT)
  • Re: NAMD trajectory format (Tue May 27 2008 - 05:27:04 CDT)
  • Re: Simulation of Thiolated Biotin-Streptavidin on Gold (Tue May 20 2008 - 08:27:50 CDT)
  • Re: Error: transport retry exceeded error (Sat May 17 2008 - 15:37:12 CDT)
  • Re: Error: transport retry exceeded error (Fri May 16 2008 - 10:49:46 CDT)
  • Re: vmd-l: imposing period boundary conditions in a simulation with a crystal (Tue Sep 05 2006 - 12:00:19 CDT)
  • Re: vmd-l: Problem with VMD 'animate' command (Sun Feb 12 2006 - 20:00:46 CST)
  • 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)
• ayhan duzgun
  • how to add charged particles manually. (Wed Apr 26 2006 - 21:24:13 CDT)
• ayk_at_mail.ecc.u-tokyo.ac.jp
  • dimer minimization (Wed Feb 28 2007 - 03:54:40 CST)
• Ayse Ozlem Sezerman
  • re: DCD file (Thu May 18 2006 - 10:02:41 CDT)
  • re: DCD file (Thu May 18 2006 - 10:02:43 CDT)
  • re:DCD file (Thu May 18 2006 - 07:06:44 CDT)
  • DCD file (Thu May 18 2006 - 02:09:40 CDT)
• AYTUG TUNCEL
  • heating with restraints (Fri Jan 19 2007 - 12:12:05 CST)
  • Reassigning Velocities (Thu Dec 07 2006 - 06:47:58 CST)
  • minimization temperature and constraints (Tue Dec 05 2006 - 17:20:22 CST)
  • Re: RE: water box deformation (Fri Dec 01 2006 - 10:10:15 CST)
  • Re: Re: high vdw energy (Fri Dec 01 2006 - 09:38:34 CST)
  • water box deformation (Thu Nov 30 2006 - 16:59:15 CST)
  • high vdw energy (Thu Nov 30 2006 - 16:44:39 CST)
  • caps (Mon Jul 10 2006 - 12:53:23 CDT)
  • NAMD to Amber (Tue Jul 04 2006 - 18:56:23 CDT)
  • part of a protein (Tue Apr 25 2006 - 02:58:42 CDT)
• AyÅŸe Özlem Sezerman
  • Re: restraining parts of a molecule (Thu Mar 08 2007 - 00:11:00 CST)
  • Re: restraining parts of a molecule (Mon Mar 05 2007 - 09:00:14 CST)
  • Re: DCD to PDB conversion (Thu Jun 08 2006 - 04:13:22 CDT)
• Ayþe Özlem Sezerman
  • Pressure fluctuations (Fri Nov 30 2007 - 10:50:32 CST)
  • System charge (Thu May 17 2007 - 04:02:50 CDT)
  • Minimizer (Wed Apr 11 2007 - 05:38:48 CDT)
  • g(r) plugin (Mon Jan 15 2007 - 04:09:56 CST)
  • g(r) (Wed Dec 20 2006 - 04:20:51 CST)
  • [Fwd: Re: Specific Heat Calculation with VMD] (Mon May 29 2006 - 08:31:31 CDT)
  • Re: Specific Heat Calculation with VMD (Mon May 29 2006 - 00:38:52 CDT)
  • [Fwd: Specific Heat Calculation with VMD] (Fri May 26 2006 - 09:29:31 CDT)
  • Specific Heat Calculation with VMD (Fri May 26 2006 - 08:46:02 CDT)
  • Saving the coordinates of DCD file in pdb format (Mon May 22 2006 - 04:50:45 CDT)
• B.R.Silver_at_warwick.ac.uk
  • Solvating protein with ions (Wed Jun 06 2007 - 15:20:43 CDT)
• Balazs JOJART
  • palmytoilated (Mon Jun 30 2008 - 07:09:03 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)
• Barbara Riddle
  • Hymen destroyer (Wed Jun 06 2007 - 19:31:28 CDT)
• barner_at_physik.hu-berlin.de
  • switching SMD in execution script? (Tue Sep 21 2004 - 09:43:17 CDT)
• Barry Isralewitz
  • Re: biotin charmm topology/parameters (Tue Aug 28 2007 - 10:00:21 CDT)
• Bartosz Dobrzelecki
  • TCL: getting forces (Fri Mar 05 2004 - 04:58:31 CST)
  • Parameters and topologies for aa at different protonation states (Fri Jan 23 2004 - 06:45:26 CST)
  • Simulating RNA+PROTEIN complexes (Fri Dec 19 2003 - 14:30:23 CST)
• Baudilio Tejerina
  • Problem with C++ libraries (Tue Jun 27 2006 - 10:29:32 CDT)
• baxy
  • Re: heating system (Sun May 27 2007 - 13:45:44 CDT)
  • Re: heating system (Sat May 26 2007 - 05:09:20 CDT)
  • heating system (Fri May 25 2007 - 13:06:50 CDT)
  • simulation problems (Mon May 14 2007 - 16:42:44 CDT)
• 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)
• Becky Peoples
  • Impressive Glashutte timepieces (Sat Jun 21 2008 - 22:17:24 CDT)
• Ben Brooks
  • Charm++ Problem (Thu Feb 26 2004 - 11:32:28 CST)
• Ben Chern
  • Re: 2 molecule pair interactions (Wed Apr 16 2008 - 23:49:33 CDT)
  • Re: Question about 'NAMD TUTORIAL' (Thu Mar 13 2008 - 00:18:21 CDT)
  • Question about 'NAMD TUTORIAL' (Wed Mar 12 2008 - 07:21:50 CDT)
• Ben Roberts
  • Re: Unit cell information in binary output files (Tue Sep 05 2006 - 23:54:15 CDT)
  • Unit cell information in binary output files (Tue Sep 05 2006 - 22:23:13 CDT)
  • 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)
• Benjamin Bouvier
  • Re: Multiple successive addforce calls (Thu Jun 05 2008 - 15:05:40 CDT)
  • Re: Multiple successive addforce calls (Thu Jun 05 2008 - 12:35:31 CDT)
  • Multiple successive addforce calls (Thu Jun 05 2008 - 08:18:16 CDT)
• Bertrand P. S. Russell
  • unsubscribe-namd (Fri Mar 07 2008 - 06:19:02 CST)
• bertrand russell
  • NAMD-2.6 Insatallation help (Tue Dec 05 2006 - 04:29:43 CST)
  • Installation Problem (Fri Oct 06 2006 - 06:52:00 CDT)
• Bing Xiong
  • namd2 compile linux-i686-mpi (Tue May 03 2005 - 15:38:27 CDT)
• Binquan luan
  • help on compiling error (Thu Jun 01 2006 - 11:32:44 CDT)
  • Re: Water simulation with namd (Fri May 26 2006 - 15:09:17 CDT)
  • Re: sound velocity of water (Fri May 05 2006 - 14:41:08 CDT)
  • Re: sound velocity of water (Fri May 05 2006 - 13:08:39 CDT)
  • Re: sound velocity of water (Fri May 05 2006 - 10:39:27 CDT)
  • sound velocity of water (Thu May 04 2006 - 18:10:53 CDT)
  • Re: why pressure is fluctuating so much (Wed May 03 2006 - 18:56:25 CDT)
  • help on NAMD code (Tue Apr 11 2006 - 13:12:12 CDT)
  • help on error message during compiling (Mon Apr 03 2006 - 19:43:14 CDT)
• bioinfo Gu
  • build NAMD (Mon Sep 08 2003 - 09:54:12 CDT)
• Bishop, Thomas C
  • tip4p - namd follwup (Fri Nov 30 2007 - 10:37:24 CST)
• 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
  • unable to open charmm parameter file in Window (Tue Nov 14 2006 - 01:16:37 CST)
  • NAMD: run problem (Wed Jun 21 2006 - 14:53:41 CDT)
  • Re: NAMD: compile problem (Fri Jun 16 2006 - 11:49:12 CDT)
  • NAMD: compile problem (Thu Jun 15 2006 - 19:04:58 CDT)
  • NAMD compile in Mac OSX and IBM XL C/C++ (Thu Jun 15 2006 - 15:18:56 CDT)
  • namd: problem (Wed Jun 14 2006 - 12:04:47 CDT)
  • namd: problem (Tue Jun 13 2006 - 14:16:56 CDT)
  • setenv: command not found (Mon Jun 12 2006 - 18:55:39 CDT)
  • MD problem (Sun Mar 26 2006 - 16:54:38 CST)
  • MD Run frozen (Fri Mar 24 2006 - 15:42:47 CST)
  • run frozen (Thu Mar 23 2006 - 20:08:58 CST)
  • Re: velocity error, still (Wed Jan 11 2006 - 16:20:37 CST)
  • simulation and equilibration (Tue Jan 10 2006 - 16:00:19 CST)
  • simulation and equilibration (Tue Jan 10 2006 - 18:01:46 CST)
  • velocity error, still (Tue Jan 10 2006 - 15:20:58 CST)
  • Re: Simulation in vaccum (Sat Jan 07 2006 - 19:12:56 CST)
  • Re: Simulation in vaccum (Fri Jan 06 2006 - 22:12:40 CST)
  • Simulation in vaccum (Fri Jan 06 2006 - 19:17:03 CST)
  • Re: velocity error (Thu Jan 05 2006 - 18:02:35 CST)
  • Atom distance & ptraj (Thu Jan 05 2006 - 11:47:46 CST)
  • Re: atom distances (Wed Jan 04 2006 - 18:09:31 CST)
  • Re: Re velocity error (Wed Jan 04 2006 - 17:20:51 CST)
  • Re: Energy Plugin (Wed Jan 04 2006 - 16:26:24 CST)
  • Re: atom distances (Wed Jan 04 2006 - 15:22:59 CST)
  • atom distances (Wed Jan 04 2006 - 14:17:29 CST)
  • velocity error (Wed Jan 04 2006 - 13:12:45 CST)
  • Energy Plugin (Mon Jan 02 2006 - 18:54:12 CST)
  • 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)
• bo liu
  • Re: Energy plot script (Thu May 15 2008 - 13:00:23 CDT)
  • What does "cellOrigin" really mean? (Wed Apr 23 2008 - 05:48:45 CDT)
  • What does "cellOrigin" really mean? (Fri Apr 18 2008 - 09:38:56 CDT)
• Bo Zhang
  • PSFGEN Warnings about H positions on standard amino acids (Mon Feb 18 2008 - 07:07:39 CST)
• Bogdan Costescu
  • Re: NAMD Linux LAM/MPI 7.1 execution error (Tue Mar 07 2006 - 10:30:13 CST)
  • Re: charm++ over MPI (Fri Feb 17 2006 - 06:27:52 CST)
  • Re: charm++ over MPI (Thu Feb 16 2006 - 08:48:43 CST)
  • charm++ over MPI (Tue Feb 14 2006 - 11:07:19 CST)
• Bonnie A Merchant
  • ABF Method (Wed Jul 02 2008 - 09:19:39 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
  • question about RMSD defined in NAMD (Sat Dec 02 2006 - 19:46:40 CST)
  • Type of force values in the tclForces script. (Fri Aug 25 2006 - 11:34:44 CDT)
  • About pressureProfile command for non-equilibrium system. (Wed Jul 26 2006 - 19:50:20 CDT)
  • Re: Boiling temperature of water. (Thu Jun 22 2006 - 21:38:54 CDT)
  • Boiling temperature of water. (Thu Jun 22 2006 - 19:20:09 CDT)
  • A puzzling problem about adsorption energy in solution. (Thu Jun 01 2006 - 17:39:26 CDT)
  • About loadcoors -- is there a loadvelocity? (Fri May 19 2006 - 13:01:11 CDT)
  • Re: About timestep again. (Mon May 08 2006 - 17:38:07 CDT)
  • Timestep -- Can I use 2 fs timestep for 50 nanoseconds simulation? (Mon May 08 2006 - 10:22:05 CDT)
  • About timestep again. -- Fastest motion O-H streching period 10 fs. (Mon May 08 2006 - 11:14:37 CDT)
  • Timestep. (Mon May 08 2006 - 10:05:17 CDT)
  • Re: About the command "set z [lindex $coorList($i) 2]". (Sun Apr 16 2006 - 19:45:30 CDT)
  • About the command "set z [lindex $coorList($i) 2]". (Sat Apr 15 2006 - 19:47:04 CDT)
  • About restart.vel.old file. (Fri Apr 07 2006 - 22:15:58 CDT)
  • Re£º difference in total energy values (Wed Mar 15 2006 - 15:44:33 CST)
  • Re: About Langevin Dynamics. (Thu Mar 02 2006 - 11:30:46 CST)
  • About Langevin Dynamics. (Wed Mar 01 2006 - 12:18:30 CST)
  • About Langevin Damping Coefficient. (Fri Feb 24 2006 - 17:57:24 CST)
  • Modeling HCN. (Wed Feb 08 2006 - 18:47:14 CST)
  • How to model HCN gas molecule by NAMD? (Wed Feb 08 2006 - 18:44:42 CST)
  • Re: About "mutate" command in psfgen package. (Thu Feb 02 2006 - 22:56:17 CST)
  • About "mutate" command in psfgen package. (Thu Feb 02 2006 - 17:24:42 CST)
  • Re£º question on 1-4scaling factor (Mon Jan 23 2006 - 09:48:29 CST)
  • Re: Saving coordinates of each frame into one separate .pdb file from a 100-frame .dcd file. (Sat Jan 21 2006 - 12:54:04 CST)
  • Saving coordinates of each frame into one separate .pdb file from a 100-frame .dcd file. (Fri Jan 20 2006 - 10:44:36 CST)
  • About "get z" command in MD script language. (Sat Jan 07 2006 - 20:57:08 CST)
  • Re: Re velocity error (Wed Jan 04 2006 - 17:46:46 CST)
  • Re velocity error (Wed Jan 04 2006 - 15:57:44 CST)
  • 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)
• bptilaka_at_mail.uh.edu
  • spawn_namd_command How to properly execute this command (Sat Apr 12 2008 - 17:32:17 CDT)
  • Replica Exchange Method (Wed Apr 09 2008 - 23:08:43 CDT)
  • Question regarding ABF simulations (Tue Feb 26 2008 - 14:50:14 CST)
• bqluan
  • spermine force field (Thu May 08 2008 - 18:47:54 CDT)
  • spermine force field (Thu May 08 2008 - 17:24:01 CDT)
  • Re: About pmf (Tue Jun 19 2007 - 10:35:02 CDT)
  • about diahedra entry in top_all22_sugar.inp (Fri Oct 13 2006 - 13:31:35 CDT)
  • sialic acid (Tue Oct 03 2006 - 15:36:00 CDT)
  • Urea parameter (Wed Sep 13 2006 - 21:20:05 CDT)
  • data structure of neighbor list (Tue Aug 08 2006 - 10:37:52 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)
• Branduardi Davide
  • RE: NAMD 2.7? (Wed Jul 02 2008 - 02:14:27 CDT)
• brian
  • strange memory behavior (Thu Nov 16 2006 - 11:20:06 CST)
• Brian Bennion
  • Re: Meaning of lines in "run" part of log file. (Wed Sep 26 2007 - 00:01:53 CDT)
  • Re: namdenergy strange behaviour !!! (Mon Sep 17 2007 - 11:15:18 CDT)
  • Re: question about equilibration step (Fri Aug 24 2007 - 13:01:07 CDT)
  • Re: A serious problem of NAMD output. (Tue Jul 24 2007 - 18:43:05 CDT)
  • faulty kernel? (Fri Jun 01 2007 - 10:59:39 CDT)
  • Re: namd crash: Signal: segmentation violation (Tue May 22 2007 - 14:39:43 CDT)
  • Re: namd crash: Signal: segmentation violation (Tue May 22 2007 - 10:53:59 CDT)
  • Re: namd crash: Signal: segmentation violation (Fri May 18 2007 - 15:43:20 CDT)
  • Re: namd crash: Signal: segmentation violation (Fri May 18 2007 - 10:25:46 CDT)
  • Re: namd crash: Signal: segmentation violation (Thu May 17 2007 - 17:06:15 CDT)
  • Re: namd crash: Signal: segmentation violation (Thu May 17 2007 - 15:25:48 CDT)
  • Re: minimizing bad system: bad global excl. count (Tue Jan 23 2007 - 14:35:19 CST)
  • Re: Restart Simulation (Tue Jan 16 2007 - 10:42:45 CST)
  • Re: pressure calculation in applied field (Tue Nov 28 2006 - 16:06:10 CST)
  • Re: Fwd: GRADIENT TOLERANCE: nan (Thu Oct 26 2006 - 11:29:00 CDT)
  • Re: NAMD installation on Xeon64 cluster (Mon Sep 18 2006 - 18:34:38 CDT)
  • Re: FW: Compilation problems on intel woodcrest (Thu Sep 07 2006 - 12:59:52 CDT)
  • wall clock vs secs/step metrics (Tue Sep 05 2006 - 12:02:29 CDT)
  • Re: Simulation of a 1000 water molecules (Thu Aug 03 2006 - 15:05:16 CDT)
  • Re: help!!! (Wed Jul 19 2006 - 01:14:52 CDT)
  • Re: qsub on a linux cluster (Fri Jul 14 2006 - 10:38:06 CDT)
  • Re: NAMD results depend on # of processors!!?? (was Re: Is clock skew a problem for charm++) (Wed Jun 21 2006 - 17:24:11 CDT)
  • Re: Angle CO2 Problem (Fri Jun 16 2006 - 10:28:49 CDT)
  • Re: Angle CO2 Problem (Fri Jun 16 2006 - 10:08:04 CDT)
  • Re: why pressure is fluctuating so much (Wed May 03 2006 - 21:19:45 CDT)
  • Re: High VDW energies during minimization and dynamics (Thu Apr 13 2006 - 12:47:30 CDT)
  • Re: Can someone PLEASE explain the "firsttimestep" parameter ? (Wed Mar 22 2006 - 16:43:18 CST)
  • Re: problems with .conf script (Fri Mar 17 2006 - 15:16:24 CST)
  • Re: during namd build / compile -ltcl8.4 linking error (Mon Mar 13 2006 - 17:56:41 CST)
  • Re: build script in charm++-5.9 does not find mpicc or mpicxx for mpi-linux version (Mon Mar 13 2006 - 14:18:15 CST)
  • Re: namd2.6b1 has bad scaling (Wed Jan 25 2006 - 14:03:28 CST)
  • Re: Problem with NAMD and constraint failures (Fri Jan 20 2006 - 01:00:55 CST)
  • 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 V