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NAMD-L: By Author

By Author

11227 messages sorted by: [ date ] [ thread ] [ subject ] [ attachment ]
About this archive

Starting: Mon Sep 08 2003 - 09:54:14 CDT
Ending: Fri Nov 20 2009 - 20:07:14 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)
• _at_huji.ac.il
  • namd question (Tue Dec 26 2006 - 04:44:42 CST)
• A D
  • Unimportant bug in output xst file writing process (Wed Nov 18 2009 - 18:18:37 CST)
  • zeroMomentum command (Fri Oct 16 2009 - 18:29:08 CDT)
  • How to put a COM restraint on a membrane protein? (Tue Oct 06 2009 - 18:03:25 CDT)
• 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
  • Re: Gromacs simulation not running in NAMD (Tue Mar 24 2009 - 10:44:47 CDT)
  • Gromacs simulation not running in NAMD (Mon Mar 23 2009 - 21:19:32 CDT)
  • Re: polymer topology file (Mon Mar 23 2009 - 10:01:50 CDT)
  • Re: polymer topology file (Mon Mar 23 2009 - 10:00:35 CDT)
  • Non Bonded Paramters (Tue Oct 21 2008 - 17:25:04 CDT)
  • Average Velocity and How to choose Right Alias (Thu Aug 07 2008 - 16:13:06 CDT)
  • Interaction energy (Tue Jul 08 2008 - 15:57:47 CDT)
  • 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
  • lammps input data file (Sun Apr 05 2009 - 21:44:56 CDT)
  • polymer topology file (Mon Mar 23 2009 - 07:41:38 CDT)
  • Re: compiling NAMD failed on windows with Cygwin (Tue Jan 13 2009 - 22:31:12 CST)
  • Re: compiling NAMD failed on windows with Cygwin (Sun Jan 11 2009 - 02:02:54 CST)
  • Re: compiling NAMD failed on windows with Cygwin (Fri Jan 09 2009 - 22:06:37 CST)
  • Re: Gradient tolerance nan for A three-atom simulation (Fri Jan 09 2009 - 02:51:43 CST)
  • RE: Gradient tolerance nan for A three-atom simulation (Tue Jan 06 2009 - 22:20:18 CST)
  • Gradient tolerance nan for A three-atom simulation (Mon Jan 05 2009 - 23:09:41 CST)
  • compiling NAMD failed on windows with Cygwin (Sun Dec 28 2008 - 22:32:51 CST)
  • compiling charm++ failed on window with Cygwin (Sun Dec 28 2008 - 01:23:13 CST)
  • Stupid question about compiling NAMD with cygwin on windows (Thu Dec 25 2008 - 21:19:50 CST)
  • 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)
• Achani K. Yatawara
  • Re: Re: namdcvs (Mon Jan 05 2009 - 14:37:02 CST)
  • how to apply restraints for phi and psi for alpha helix regions (Thu Dec 11 2008 - 07:42:37 CST)
  • phi and psi restraints for 2 helix regions (Wed Dec 10 2008 - 07:13:57 CST)
• Achani.K.Yatawara_at_Dartmouth.edu
  • Re: Re: namdcvs (Mon Jan 05 2009 - 15:00:54 CST)
  • Re: Re: namdcvs (Mon Jan 05 2009 - 14:32:43 CST)
  • Re: namdcvs (Mon Jan 05 2009 - 13:32:34 CST)
• 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)
• Agostino
  • How the seed influences the molecular dynamics simulations? (Wed Sep 23 2009 - 04:15:26 CDT)
• 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
  • structure problem (Wed Apr 22 2009 - 12:22:29 CDT)
  • 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)
• Ahmad Firoz
  • How to minimize our model by SD using namd (Tue May 19 2009 - 00:33:01 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)
• Ale Gomez
  • Re: Error in Minimization (Wed Nov 11 2009 - 22:58:18 CST)
  • Re: Error in Minimization (Mon Nov 09 2009 - 21:19:06 CST)
  • Re: Error in Minimization (Sun Nov 08 2009 - 11:19:28 CST)
  • Fwd: Error in Minimization (Sun Nov 08 2009 - 09:15:02 CST)
  • Error in Minimization (Sat Nov 07 2009 - 10:45:24 CST)
• Alejandro Ortega
  • TXT program editor (Thu Aug 28 2008 - 14:43:14 CDT)
  • Maximum Velocities (Tue Jul 08 2008 - 13:20:33 CDT)
• Aleksei Aksimentiev
  • Postdoc position in computational biophysics and nanotechnology (Tue May 05 2009 - 14:34:04 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 Nascimento
  • Re: Software to Mutate DNA (Mon May 25 2009 - 10:19:25 CDT)
  • namdenergy and amber trajectory (Wed Jul 30 2008 - 10:06:27 CDT)
  • namdenergy and amber trajectory (Tue Jul 29 2008 - 14:58:56 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)
• alessandro.venturelli_at_univr.it
  • cell on namd 2.7b1 (Wed Apr 29 2009 - 08:10:01 CDT)
• Alessio Alexiadis
  • RAM/node (Wed Nov 26 2008 - 05:37:17 CST)
  • 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 A. Vakhrushev
  • Re: Reading multiple .log files (Wed Dec 10 2008 - 21:48:17 CST)
  • Re: Energy conversation (Sat Dec 06 2008 - 01:23:26 CST)
  • Re: Energy conversation (Fri Dec 05 2008 - 23:06:30 CST)
  • Energy conversation (Fri Dec 05 2008 - 07:51:06 CST)
  • Re: Regarding Installation (Thu Nov 20 2008 - 22:45:22 CST)
  • Re: Problems compiling NAMD (Tue Oct 07 2008 - 05:04:47 CDT)
  • Re: Problems compiling NAMD (Mon Oct 06 2008 - 11:00:38 CDT)
  • Re: Problems compiling NAMD (Fri Oct 03 2008 - 12:44:57 CDT)
  • Re: DCD file format (Wed Oct 01 2008 - 23:43:12 CDT)
  • Re: How to use bigdcd on a trajectory while skipping first 1000 frames (Thu Sep 25 2008 - 06:14:35 CDT)
  • Re: Managing Log files (Wed Sep 24 2008 - 13:01:54 CDT)
  • Re: Periodic BCs (Wed Sep 24 2008 - 12:58:40 CDT)
  • Re: vmd-l: counting gas molecules inside the nanotube (Thu Sep 18 2008 - 12:11:04 CDT)
  • Re: Can I use "vecnorm" in the tclforce scripts? (Thu Sep 18 2008 - 09:29:43 CDT)
  • Re: parameter file to make cholesterol psf file (Wed Sep 10 2008 - 21:28:59 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: g(r) (Thu Jul 31 2008 - 01:10:05 CDT)
  • Re: Problem with TclBC when run in more than one processor (Wed Jun 04 2008 - 22:52:43 CDT)
  • 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)
• Ali Emileh
  • Re: 2.7b metadynamics ::alpha module :: folding of a single helix in water (Wed Jul 22 2009 - 21:18:11 CDT)
  • Re: 2.7b metadynamics ::hBond component :: folding of a single helix in water (Mon Jun 22 2009 - 14:23:57 CDT)
  • Re: 2.7b metadynamics ::alpha module :: folding of a single helix in water (Tue Jun 09 2009 - 18:02:12 CDT)
  • Re: 2.7b metadynamics ::alpha module :: folding of a single helix in water (Tue Jun 09 2009 - 11:52:19 CDT)
  • 2.7b metadynamics ::alpha module :: folding of a single helix in water (Tue Jun 02 2009 - 18:39:25 CDT)
  • Parallel TMD (2.7b) dies : "MPICH internal error" (Mon Apr 20 2009 - 11:00:11 CDT)
  • Re: TMD RMSD problem (Fri Apr 10 2009 - 13:27:40 CDT)
  • NAMD 2.7b1 on Teragrid (Mon Mar 30 2009 - 09:55:33 CDT)
  • Fwd: Job submission to Lonestar on TACC (Thu Mar 05 2009 - 13:13:38 CST)
  • Job submission to Lonestar on TACC (Wed Mar 04 2009 - 17:19:03 CST)
• 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)
• Amr Zeinalabideen Majul
  • Regarding NAMD CPU usage (Fri Sep 11 2009 - 08:22:08 CDT)
  • Re: Defining Temperature for Langevin for Namd restart. (Wed Aug 05 2009 - 16:20:41 CDT)
  • Defining Temperature for Langevin for Namd restart. (Wed Aug 05 2009 - 14:20:15 CDT)
  • Does NAMD have any capability to assign coordiantes to novel sequences? (Thu Jun 25 2009 - 10:34:43 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: hole on the surface of the waterbox (Fri Aug 28 2009 - 07:48:35 CDT)
  • Re: hole on the surface of the waterbox (Fri Aug 28 2009 - 07:26:14 CDT)
  • Re: hole on the surface of the waterbox (Fri Aug 28 2009 - 06:19:41 CDT)
  • Re: hole on the surface of the waterbox (Fri Aug 28 2009 - 05:54:06 CDT)
  • 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)
• Andres Morales N
  • FW: Loop (Thu Oct 01 2009 - 09:05:35 CDT)
  • Loop (Thu Oct 01 2009 - 07:59:27 CDT)
• 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 Emerson
  • Re: namd cvs compilation with a maximum number of cores to run on (Fri Feb 13 2009 - 03:36:30 CST)
  • Re: DCD file format (Thu Oct 02 2008 - 02:32:08 CDT)
  • Re: NAMD on blue gene BG/P (Fri Jul 11 2008 - 05:44:16 CDT)
  • NAMD on blue gene BG/P (Thu Jul 10 2008 - 05:46:36 CDT)
• Andrew Fant
  • PSF/top/inp for joint charmm/amber benchmark (Tue Mar 31 2009 - 17:03:48 CDT)
• Andrew Thomas
  • Large MD simulations and atom number limits with NAMD (Fri Jun 20 2008 - 09:53:50 CDT)
• Andriy Volynets
  • how do you debug tcl scripts in vmd ? (Mon Aug 04 2008 - 12:12:18 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)
• andy.mastellone_at_alice.it
  • R: I: Running Charm++ over MPI does not work (Fri Jan 23 2009 - 02:37:21 CST)
  • I: Running Charm++ over MPI does not work (Thu Jan 22 2009 - 08:23:58 CST)
  • Running Charm++ over MPI does not work (Thu Jan 22 2009 - 07:20:28 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)
• Angelo Rossi
  • Re: NAMD 2.7b1 on Teragrid (Tue Mar 31 2009 - 17:40:36 CDT)
• Anirban
  • Re: PCA Analysis of CGMD (Wed Apr 15 2009 - 15:42:44 CDT)
  • Re: PCA Analysis of CGMD (Wed Apr 15 2009 - 14:44:29 CDT)
  • Re: Background load problem (Fri Feb 27 2009 - 03:38:16 CST)
  • Re: Background load problem (Thu Feb 26 2009 - 08:15:04 CST)
• Anirban Ghosh
  • PCA Calculation (Tue Oct 06 2009 - 00:13:08 CDT)
  • RE: PCA Analysis of CGMD (Fri Apr 10 2009 - 04:08:25 CDT)
  • PCA Analysis of CGMD (Thu Apr 09 2009 - 07:23:04 CDT)
  • Background load problem (Thu Feb 26 2009 - 03:34:53 CST)
  • Problem with number of steps > 1000000 (Mon Jan 05 2009 - 07:52:55 CST)
  • Re: Reading multiple .log files (Wed Dec 10 2008 - 23:21:48 CST)
  • Reading multiple .log files (Tue Dec 09 2008 - 22:42:15 CST)
  • Re: Reading multiple .log files into one (Mon Dec 08 2008 - 03:21:07 CST)
  • Reading multiple .log files into one (Thu Dec 04 2008 - 08:25:05 CST)
  • Re: namd cvs compilation (Thu Nov 27 2008 - 22:46:34 CST)
  • Re: namd cvs compilation (Thu Nov 27 2008 - 02:27:57 CST)
  • NAMD CVS Installation (Wed Nov 26 2008 - 05:53:38 CST)
  • How to fix atoms during minimization? (Wed Nov 19 2008 - 08:06:29 CST)
  • NAMD Simulation error (Fri Nov 14 2008 - 02:36:16 CST)
  • NAMD Simulation error (Wed Nov 12 2008 - 22:41:07 CST)
  • Re: combining 2 dcd files into one (Fri Oct 31 2008 - 13:43:14 CDT)
  • CG Name Prefix Problem (Fri Oct 24 2008 - 00:24:58 CDT)
  • Re: How to set values for cellBasisVector and PMEGridSize properly (Mon Oct 20 2008 - 08:30:23 CDT)
  • Pressure related issue (Wed Oct 15 2008 - 08:23:29 CDT)
  • Restarting a Simulation & Langevin (Fri Sep 19 2008 - 08:12:34 CDT)
  • Error with Shape Based CG Model (Wed Aug 06 2008 - 05:04:27 CDT)
  • Running CGMD using NAMD (Mon Jul 28 2008 - 23:46:54 CDT)
• Anna Blice-Baum
  • unsubscribe (Sun Jun 28 2009 - 14:40:10 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)
• Anneta Tzampazi
  • Problem with creating psf file from structure made by inorganic builder (Fri Oct 03 2008 - 04:43:19 CDT)
• Anshu Bhatia
  • Re: Membrane Simulations (Tue Oct 28 2008 - 12:27:57 CDT)
  • Re: Membrane Simulations (Tue Oct 28 2008 - 12:31:55 CDT)
  • Membrane Simulations (Wed Oct 22 2008 - 20:04:38 CDT)
  • Membrane Simulations (Tue Oct 14 2008 - 14:05:55 CDT)
• Anton Arkhipov
  • Re: protein folding (Fri Jul 10 2009 - 10:37:29 CDT)
  • Re: Langevin damping coefficient (Wed May 06 2009 - 11:13:13 CDT)
  • Re: Langevin damping coefficient (Wed May 06 2009 - 10:25:49 CDT)
  • Re: dielectric parameter? (Thu Jan 15 2009 - 10:00:04 CST)
  • Re: CGMD problem (Sat Dec 06 2008 - 16:31:18 CST)
  • Re: CGMD problem (Sat Dec 06 2008 - 15:45:15 CST)
  • Re: CGMD problem (Wed Dec 03 2008 - 11:39:32 CST)
  • Re: vmd-l: CG bead definition (Tue Nov 25 2008 - 15:31:45 CST)
  • Re: NAMD Simulation error (Fri Nov 14 2008 - 15:10:27 CST)
  • Re: CG Name Prefix Problem (Fri Oct 24 2008 - 10:30:05 CDT)
  • Re: Coarse grained model force fields (Thu Sep 04 2008 - 14:17:52 CDT)
  • Re: Error with Shape Based CG Model (Wed Aug 06 2008 - 11:39:38 CDT)
  • Re: trajectories (Mon Jul 14 2008 - 14:58:14 CDT)
• Anupam Nath Jha
  • how to run namd in cluster (Sun Jul 27 2008 - 13:23:22 CDT)
  • cannot find -lsrfftw... collect2: ld returned 1 exit status (Sun Jul 13 2008 - 12:59:09 CDT)
  • installation of charm-6.0 in ia-64 cluster machine (Fri Jul 11 2008 - 06:49:34 CDT)
• Anuradha Mittal
  • build missing residues in pdb (Sun Nov 23 2008 - 18:48:47 CST)
  • 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)
• arajan_at_ks.uiuc.edu
  • Re: minimization and MD in one configuration file? (Sat Jul 12 2008 - 14:14:45 CDT)
• 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
  • unsubscribe (Sat Jun 27 2009 - 09:25:57 CDT)
  • Confira meu perfil no Facebook (Sat Jan 03 2009 - 12:31:41 CST)
  • (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
  • Re: CUDA version status (Fri Jan 23 2009 - 19:09:47 CST)
  • NAMD+MPI on AMD64 (Fri Mar 21 2008 - 12:30:29 CDT)
  • Parallelism issue (Thu Mar 20 2008 - 15:45:15 CDT)
• Arturas Ziemys
  • combining abf reaction path (Sat Jan 31 2009 - 12:20:55 CST)
  • advice on van Hove (Thu Jan 15 2009 - 12:08:40 CST)
  • NVT/NPT pressures w fixed particles (Mon Oct 20 2008 - 10:03:43 CDT)
  • NAMD compilation / TACC Ranger (Thu Aug 28 2008 - 11:25:14 CDT)
  • bad exclusion error - searching remedies (Mon Aug 18 2008 - 18:12:48 CDT)
  • Re: PME and infinite polymer (Fri Jul 25 2008 - 09:26:53 CDT)
  • PME and infinite polymer (Thu Jul 24 2008 - 20:59:33 CDT)
  • 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)
• Athanassios Stavrakoudis
  • eucb - beta testers wanted for trajectory analysis program (Thu Feb 05 2009 - 18:18:08 CST)
• Audrey Salazar
  • Re: Error while running NPT Simulation (Thu Oct 16 2008 - 13:51:30 CDT)
  • Re: Error while running NPT Simulation (Thu Oct 16 2008 - 13:55:55 CDT)
  • Getting total energy of system + pressure and temperature bath. (Wed Oct 15 2008 - 16:23:12 CDT)
  • Re: DCD file format (Wed Oct 01 2008 - 15:04:28 CDT)
  • Re: minimization (Fri Sep 26 2008 - 11:41:13 CDT)
  • Re: minimization (Thu Sep 25 2008 - 21:51:03 CDT)
  • Re: How to write gradual heating config file (Mon Aug 25 2008 - 18:23:41 CDT)
  • How to write gradual heating config file (Mon Aug 25 2008 - 17:41:59 CDT)
  • 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)
• Aurum Bai
  • About the namd tutorial err (Tue Aug 18 2009 - 23:55:01 CDT)
  • About "Parameterizing a Novel Residue" tutorial problem (Wed Aug 12 2009 - 00:18:09 CDT)
  • What is the different between "periodic boundary ,spherical harmonic boundary and cylindrical harmonic boundary conditions"? (Fri Aug 07 2009 - 11:04:50 CDT)
  • How to set magnitude of cellBasisVector? (Fri Jul 24 2009 - 00:52:19 CDT)
• Austin B. Yongye
  • Re: Fullerene topology (Wed Oct 28 2009 - 11:41:49 CDT)
  • Fullerene topology (Mon Oct 26 2009 - 13:40:17 CDT)
  • Saving a subset of atoms (Fri Sep 11 2009 - 12:32:44 CDT)
  • Implicit membrane models (Wed Sep 09 2009 - 09:03:53 CDT)
  • Membrane simulations (Tue Sep 01 2009 - 10:24:36 CDT)
  • Topology and parameter file for DMF (Sun Mar 01 2009 - 07:00:34 CST)
  • DMF solvent parameters (Wed Dec 10 2008 - 16:08:17 CST)
  • Approach energy with SMD (2) (Fri Nov 14 2008 - 13:31:36 CST)
  • Non-standard amino acid (Mon Nov 10 2008 - 17:05:01 CST)
  • cyclic peptides (Mon Nov 03 2008 - 16:38:40 CST)
  • Approach energy with SMD (Mon Nov 03 2008 - 11:01:26 CST)
• Axel Kohlmeyer
  • Re: FW: simulation configuration file not accesible - other reasons (Fri Nov 20 2009 - 18:37:51 CST)
  • Re: help with running namd-cuda for the tutorials (Fri Nov 20 2009 - 11:25:14 CST)
  • Re: NAMD file limitation in Win32 - windows XP (Tue Nov 17 2009 - 12:33:09 CST)
  • Re: error in scripting (Mon Nov 16 2009 - 07:36:50 CST)
  • Re: Memory keep increasing. (Sun Nov 15 2009 - 08:59:42 CST)
  • Re: The MD of aquaporin in NAMD (Sat Nov 14 2009 - 09:52:05 CST)
  • Re: Formating of logfile (Sat Nov 14 2009 - 10:11:01 CST)
  • Re: Formating of logfile (Fri Nov 13 2009 - 15:17:49 CST)
  • Re: NAMD 2.7b1 Performance loss with CUDA 2.3 (Thu Nov 12 2009 - 21:07:57 CST)
  • Re: 32 bit + 64 bit mixed architecture problem (Thu Nov 12 2009 - 10:12:36 CST)
  • Re: Memory keep increasing. (Thu Nov 12 2009 - 07:36:00 CST)
  • Re: 32 bit + 64 bit mixed architecture problem (Wed Nov 11 2009 - 12:08:02 CST)
  • Re: Error in Minimization (Tue Nov 10 2009 - 13:30:10 CST)
  • Re: missing libraries for NAMD 2.7 on Linux cluster? (Mon Nov 09 2009 - 07:32:15 CST)
  • Re: dielectric constant assignment (Mon Nov 09 2009 - 07:22:35 CST)
  • Re: temperature calculations from velocities in NAMD? (Sun Nov 08 2009 - 19:33:18 CST)
  • Re: temperature calculations from velocities in NAMD? (Sun Nov 08 2009 - 11:17:20 CST)
  • Re: Error in Minimization (Sun Nov 08 2009 - 11:05:47 CST)
  • Re: temperature calculations from velocities in NAMD? (Sat Nov 07 2009 - 16:55:13 CST)
  • Re: Is it a bug? TCL Script may Lead to Overflow (Sat Nov 07 2009 - 14:47:08 CST)
  • Re: temperature calculations from velocities in NAMD? (Sat Nov 07 2009 - 14:21:40 CST)
  • Re: How to apply an unsteady magnetic field? (Fri Oct 30 2009 - 15:40:32 CDT)
  • Re: Hydrogen molecule model (Fri Oct 30 2009 - 15:00:12 CDT)
  • Re: abnormal water surface after nvt and npt for POPC membrane (Wed Oct 28 2009 - 10:55:16 CDT)
  • Re: Namd benchmark problem (Mon Oct 26 2009 - 09:45:46 CDT)
  • Re: Namd benchmark problem (Mon Oct 26 2009 - 08:26:03 CDT)
  • Re: Namd benchmark problem (Mon Oct 26 2009 - 08:16:55 CDT)
  • Re: Namd benchmark problem (Sun Oct 25 2009 - 15:48:23 CDT)
  • Re: Namd benchmark problem (Sat Oct 24 2009 - 11:30:45 CDT)
  • Re: namd cvs memory leak? (Thu Oct 22 2009 - 19:24:52 CDT)
  • Re: Modification of equlibrated simulation box (Wed Oct 21 2009 - 09:00:55 CDT)
  • Re: Tcl forces (Fri Oct 16 2009 - 16:21:04 CDT)
  • Re: spontaneous system explosion after 2 ns of normal run (Thu Oct 15 2009 - 11:15:23 CDT)
  • Re: Slow heating in namd (Thu Oct 15 2009 - 09:57:17 CDT)
  • Re: spontaneous system explosion after 2 ns of normal run (Thu Oct 15 2009 - 10:01:00 CDT)
  • Re: Ionization with VMD (Thu Oct 15 2009 - 09:48:29 CDT)
  • Re: Slow heating in namd (Thu Oct 15 2009 - 10:05:07 CDT)
  • Re: Re: spontaneous system explosion after 2 ns of normal run (Thu Oct 15 2009 - 09:30:34 CDT)
  • Re: size of integration step (Tue Oct 13 2009 - 11:24:57 CDT)
  • Re: Generation of average trajectory (Mon Oct 12 2009 - 10:40:08 CDT)
  • Re: Changing the atomtype of a particle on the fly (Mon Oct 05 2009 - 02:14:41 CDT)
  • Re: questions regarding new single node box for NAMD: re components, CUDA, Fermi (Mon Oct 05 2009 - 02:01:47 CDT)
  • Re: running namd in parallel (Sun Oct 04 2009 - 05:23:58 CDT)
  • Re: Changing the atomtype of a particle on the fly (Fri Oct 02 2009 - 14:57:43 CDT)
  • Re: Changing the atomtype of a particle on the fly (Fri Oct 02 2009 - 13:30:57 CDT)
  • Re: Changing the atomtype of a particle on the fly (Fri Oct 02 2009 - 13:09:12 CDT)
  • Re: questions regarding new single node box for NAMD: re components, CUDA, Fermi (Fri Oct 02 2009 - 12:51:26 CDT)
  • RE: questions regarding new single node box for NAMD: re components, CUDA, Fermi (Fri Oct 02 2009 - 12:57:39 CDT)
  • Re: Minimisation Protocol (Fri Oct 02 2009 - 12:24:56 CDT)
  • Re: Loop (Thu Oct 01 2009 - 16:56:45 CDT)
  • Re: g(r) GUI Plugin problem (Tue Sep 29 2009 - 14:02:16 CDT)
  • Re: NAMD2.7b1 performance (Fri Sep 25 2009 - 18:07:14 CDT)
  • Re: NAMD2.7b1 performance (Fri Sep 25 2009 - 09:45:53 CDT)
  • Re: topology files (Thu Sep 24 2009 - 14:16:17 CDT)
  • Re: extracting info from output files (Tue Sep 22 2009 - 14:03:12 CDT)
  • Re: Precision of Coordinate data (Tue Sep 22 2009 - 13:22:47 CDT)
  • Re: GPU Selection in NAMD CUDA (Tue Sep 22 2009 - 04:39:59 CDT)
  • Re: Temperature rescaling vs. reassignment (Tue Sep 15 2009 - 10:15:23 CDT)
  • Re: CUDA-accelerated NAMD does not support NBFIX parameters [RESOLVED] (Mon Sep 14 2009 - 15:57:12 CDT)
  • Re: CUDA-accelerated NAMD does not support NBFIX parameters (Sun Sep 13 2009 - 14:49:47 CDT)
  • Re: Constraint failure in RATTLE algorithm - shouldn't a rerun fail at the same step? (Wed Sep 09 2009 - 09:51:42 CDT)
  • Re: Periodic boundary conditions in membrane simulation (Mon Aug 31 2009 - 13:01:26 CDT)
  • Re: Cuda benchmarks namd2.7b1 - effects of configuration parameters and hardware. (Sun Aug 30 2009 - 15:33:08 CDT)
  • Re: Tesla Utilization -- NAMD 2.7b1 (Fri Aug 28 2009 - 10:20:21 CDT)
  • Re: how to set up force parameters of a novel residue? (Thu Aug 27 2009 - 16:14:17 CDT)
  • Re: question on forces / theory (Wed Aug 26 2009 - 06:04:17 CDT)
  • Re: multi-cluster configuration (Mon Aug 24 2009 - 17:12:42 CDT)
  • Re: Alignment of velocity dcd file (Sat Aug 22 2009 - 15:49:19 CDT)
  • Re: NAMD performance with 10GbE interconnect (Tue Aug 11 2009 - 11:25:25 CDT)
  • Re: NAMD CUDA performance degradation (Thu Jul 23 2009 - 15:19:16 CDT)
  • RE: RE: NAMD CUDA on dual Nvidia 295 GPUs (Thu Jul 23 2009 - 12:28:24 CDT)
  • Re: RescaleFreq of temperature =1? (Thu Jul 23 2009 - 11:00:13 CDT)
  • Re: RescaleFreq of temperature =1? (Thu Jul 23 2009 - 10:19:42 CDT)
  • Re: RE: NAMD CUDA on dual Nvidia 295 GPUs (Thu Jul 23 2009 - 10:02:45 CDT)
  • RE: NAMD CUDA on dual Nvidia 295 GPUs (Thu Jul 23 2009 - 09:59:10 CDT)
  • Re: NAMD CUDA on dual Nvidia 295 GPUs (Thu Jul 23 2009 - 08:04:42 CDT)
  • Re: about compile namd2.7 (Sun Jul 19 2009 - 11:18:33 CDT)
  • Re: on NAMD simulation of DNA translocation through nanopores (Sun Jul 19 2009 - 11:24:06 CDT)
  • Re: CPU USAGE (Sun Jul 19 2009 - 11:15:14 CDT)
  • Re: CPU USAGE (Sat Jul 18 2009 - 11:50:25 CDT)
  • Re: VMD-Installation problems (Wed Jul 15 2009 - 19:56:00 CDT)
  • Re: Wtrlt: Smeart out 9/3 LJ wall (Wed Jul 15 2009 - 12:10:53 CDT)
  • Re: protein folding (Fri Jul 10 2009 - 07:48:02 CDT)
  • Re: FATAL ERROR: Sorry, combined TI and FEP is not implemented (Thu Jul 09 2009 - 06:38:57 CDT)
  • Re: Another strange error: MStream checksums do not agree (Thu Jul 09 2009 - 06:40:19 CDT)
  • Re: Re: vmd-l: Hardware for NAMD / VMD machine (Mon Jul 06 2009 - 16:46:40 CDT)
  • Re: Re: namd2.7b1 slower with openmpi 1.3.2 than namd2.6 withopenmpi 1.2.6 (Sun Jul 05 2009 - 11:38:37 CDT)
  • Re: namd2.7b1 slower with openmpi 1.3.2 than namd2.6 with openmpi 1.2.6 (Fri Jul 03 2009 - 13:42:08 CDT)
  • Re: Hardware for NAMD / VMD machine (Fri Jul 03 2009 - 11:56:08 CDT)
  • Re: NAMD Installation (Wed Jul 01 2009 - 08:07:03 CDT)
  • Re: location of the SMD source code (Tue Jun 30 2009 - 13:59:10 CDT)
  • GPGPU Programming summer school at University of Tennessee, Aug 10-14. (Mon Jun 29 2009 - 14:43:11 CDT)
  • Re: Can I use another solvent rather than TI3P model in namd for MD simulations ? (Mon Jun 29 2009 - 08:32:30 CDT)
  • Re: unsubscribe (Mon Jun 29 2009 - 08:35:36 CDT)
  • Re: Protein collpasing problem! (Mon Jun 29 2009 - 08:25:06 CDT)
  • the recent flood of unsubscribe requests (Sat Jun 27 2009 - 10:07:28 CDT)
  • Re: skip frames with bigdcd (Fri Jun 26 2009 - 15:41:03 CDT)
  • Re: launch NAMD from tcl script - bug? (Wed Jun 24 2009 - 12:21:13 CDT)
  • Re: launch NAMD from tcl script - bug? (Wed Jun 24 2009 - 11:36:33 CDT)
  • Re: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR NH3 HC NH3 (Sun Jun 21 2009 - 12:54:51 CDT)
  • Re: need advices for running NAMD efficiently. (Mon Jun 15 2009 - 13:19:05 CDT)
  • Re: question about repeating output text (Tue Jun 09 2009 - 08:09:31 CDT)
  • Re: Problem namd2 and mpich2 (Mon Jun 08 2009 - 09:01:42 CDT)
  • Re: Read DCD file in Java (Sat Jun 06 2009 - 11:23:50 CDT)
  • Re: NAMD on GPU (Thu Jun 04 2009 - 09:16:13 CDT)
  • Re: Exclusions and CUDA (Thu Jun 04 2009 - 09:03:24 CDT)
  • Re: Measuring protein diffusion: results too small? (Wed Jun 03 2009 - 17:53:53 CDT)
  • Re: lamboot -v nodelist (Wed Jun 03 2009 - 10:27:06 CDT)
  • Re: compile namd2.7b1 on infiniband (Tue Jun 02 2009 - 22:17:01 CDT)
  • Re: NAMD infiniband performance (Mon Jun 01 2009 - 21:58:49 CDT)
  • Re: NAMD infiniband performance (Mon Jun 01 2009 - 15:54:17 CDT)
  • Re: flipdcd (Mon Jun 01 2009 - 12:05:35 CDT)
  • Re: FATAL ERROR: Bad global exclusion count! (Mon Jun 01 2009 - 13:05:24 CDT)
  • Re: Regd: Error (Mon Jun 01 2009 - 09:46:39 CDT)
  • Re: Regd: Error (Mon Jun 01 2009 - 09:00:36 CDT)
  • Re: Regd :parameter file (Fri May 29 2009 - 16:28:41 CDT)
  • Re: FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE (Fri May 29 2009 - 10:59:30 CDT)
  • Re: NAMD 2.7b1 running & performance issues (Mon May 25 2009 - 10:13:13 CDT)
  • Re: calculating energy for large log files (Thu May 21 2009 - 09:30:51 CDT)
  • Re: NAMD infiniband performance (Tue May 19 2009 - 17:13:50 CDT)
  • Re: namd-openmosix (Tue May 19 2009 - 09:55:57 CDT)
  • Re: NAMD infiniband performance (Tue May 19 2009 - 10:00:11 CDT)
  • Re: Error running NAMD on CUDA (Mon May 18 2009 - 08:44:05 CDT)
  • Re: namd-cuda-intel vs. namd-intel (Fri May 15 2009 - 10:41:39 CDT)
  • Re: collective variable space PMF, including biasing potential terms? (Wed May 13 2009 - 17:52:30 CDT)
  • RE: peptides on surface (Wed May 13 2009 - 16:29:23 CDT)
  • Re: Make NAMD2.7b1 with cuda bug? (Wed May 13 2009 - 10:03:44 CDT)
  • Re: namd-cuda-intel vs. namd-intel (Tue May 12 2009 - 11:11:19 CDT)
  • Re: namd-cuda-intel vs. namd-intel (Tue May 12 2009 - 06:24:04 CDT)
  • Re: HW - HW IN PARAMETER FILES (Thu May 07 2009 - 07:47:07 CDT)
  • Re: two independent groups of constraints (Thu Apr 30 2009 - 08:14:01 CDT)
  • Re: running problem (Thu Apr 30 2009 - 06:08:00 CDT)
  • Re: protein shifts out of the water box (Wed Apr 29 2009 - 19:14:18 CDT)
  • Re: cell on namd 2.7b1 (Wed Apr 29 2009 - 08:34:08 CDT)
  • Re: Yet another NAMD speed concerns (Sat Apr 25 2009 - 09:10:14 CDT)
  • Re: compile NAMD 2.7b1 on Intel Xeon(R) infiniband cluster (Sat Apr 25 2009 - 09:01:24 CDT)
  • Re: Copper parameters for CHARMM (Fri Apr 24 2009 - 11:37:09 CDT)
  • Re: I can't keep my pulling directions the same with the SMD vector (Tue Apr 21 2009 - 07:27:50 CDT)
  • Re: I can't keep my pulling directions the same with the SMD vector (Mon Apr 20 2009 - 08:41:22 CDT)
  • Re: Speeding up: Dummy constructions for aromatics or hydrogens (Fri Apr 17 2009 - 16:05:34 CDT)
  • Re: Speeding up: Dummy constructions for aromatics or hydrogens (Fri Apr 17 2009 - 15:22:04 CDT)
  • Re: Writing 3 subsequent timesteps to the DCD file (Fri Apr 10 2009 - 12:02:06 CDT)
  • Re: Re: NAMD job dies on 2-quad core server (Thu Apr 09 2009 - 09:03:24 CDT)
  • Re: Writing 3 subsequent timesteps to the DCD file (Wed Apr 08 2009 - 10:26:17 CDT)
  • Re: Writing 3 subsequent timesteps to the DCD file (Wed Apr 08 2009 - 08:23:26 CDT)
  • Re: Compiling NAMD on Ranger (Wed Apr 08 2009 - 08:15:51 CDT)
  • Re: Writing 3 subsequent timesteps to the DCD file (Tue Apr 07 2009 - 19:45:45 CDT)
  • Re: Writing 3 subsequent timesteps to the DCD file (Tue Apr 07 2009 - 07:45:54 CDT)
  • Re: lammps input data file (Mon Apr 06 2009 - 08:36:26 CDT)
  • Re: NAMD job dies on 2-quad core server (Mon Apr 06 2009 - 08:44:54 CDT)
  • Re: NAMD and CFF forcefields (Sat Mar 28 2009 - 15:20:58 CDT)
  • Re: NAMD is too slow?! (Sun Mar 29 2009 - 10:23:44 CDT)
  • Re: NAMD and multi-rail IB for improved latency (Fri Mar 27 2009 - 09:28:40 CDT)
  • Re: NAMD 2.7b1 on SGI Altix 330 (Thu Mar 26 2009 - 10:56:40 CDT)
  • Re: Using Amber FF in NAMD (Wed Mar 18 2009 - 18:38:31 CDT)
  • Re: cg protein folding (Wed Mar 18 2009 - 13:57:31 CDT)
  • Re: how to get rid of TCL messages in namd.log from tclForcesScript (Fri Mar 13 2009 - 19:24:25 CDT)
  • Re: How to get the acceptance ratio in REMD (Thu Mar 12 2009 - 08:22:38 CDT)
  • Re: problem about NAMD compile (Tue Mar 10 2009 - 09:03:20 CDT)
  • Re: removing water from big dcd files (Wed Mar 04 2009 - 13:49:48 CST)
  • Re: about calculation of PMF from SMD trajectories (with pasted smd_config_file) (Wed Mar 04 2009 - 12:52:47 CST)
  • Re: Background load problem (Thu Feb 26 2009 - 10:13:06 CST)
  • Re: Thiol on gold simulation in NAMD (Thu Feb 26 2009 - 10:00:05 CST)
  • Re: Thiol on gold simulation in NAMD (Wed Feb 25 2009 - 10:53:44 CST)
  • Re: solution for generating IC (Sat Feb 21 2009 - 18:26:13 CST)
  • Re: Thiol on gold simulation in NAMD (Tue Feb 17 2009 - 14:54:51 CST)
  • Re: Problem running NAMD on ranger@TACC (Tue Feb 17 2009 - 08:43:49 CST)
  • Re: log file from 3 different protein simulations (Mon Feb 16 2009 - 09:13:31 CST)
  • Re: namd cvs compilation with a maximum number of cores to run on (Fri Feb 13 2009 - 07:21:33 CST)
  • Re: namd cvs compilation with a maximum number of cores to run on (Thu Feb 12 2009 - 10:35:05 CST)
  • Re: vmd-l: How to specify processors for running VMD on a cluster? (Tue Feb 10 2009 - 15:35:46 CST)
  • Re: vmd-l: How to specify processors for running VMD on a cluster? (Tue Feb 10 2009 - 12:24:58 CST)
  • Re: Periodic boundary condition in a membrane simulation (Mon Feb 09 2009 - 19:29:40 CST)
  • Re: Accessing atoms and velocities during NVE run (Fri Feb 06 2009 - 15:42:20 CST)
  • Re: TCL: divide by zero (Thu Feb 05 2009 - 08:52:41 CST)
  • Re: tcl script (Mon Feb 02 2009 - 23:01:26 CST)
  • Re: loading large dcd files (Thu Jan 29 2009 - 09:03:44 CST)
  • Re: NAMD on a virtual grid (Mon Jan 26 2009 - 16:02:30 CST)
  • Re: RMSD and merging trajectories (Sat Jan 24 2009 - 19:18:51 CST)
  • Re: CUDA version status (Fri Jan 23 2009 - 20:28:27 CST)
  • Re: some recommendations for parametrizing new molecules required (Fri Jan 23 2009 - 09:25:01 CST)
  • Re: some recommendations for parametrizing new molecules required (Fri Jan 23 2009 - 09:20:50 CST)
  • Re: (Tue Jan 20 2009 - 09:03:51 CST)
  • Re: Single vs. Double precision (Mon Jan 19 2009 - 10:25:36 CST)
  • Re: Creating bonds during a run (Mon Jan 12 2009 - 10:09:24 CST)
  • Re: compiling NAMD failed on windows with Cygwin (Sun Jan 11 2009 - 14:11:04 CST)
  • Re: compiling NAMD failed on windows with Cygwin (Sat Jan 10 2009 - 09:20:44 CST)
  • Re: FATAL ERROR: Setting parameter constraints from script failed! (Fri Jan 09 2009 - 08:54:26 CST)
  • Re: binary trajectories (Fri Jan 09 2009 - 08:29:27 CST)
  • Re: NAMD disk writes and quota overflow (Thu Jan 08 2009 - 16:19:19 CST)
  • Re: FATAL ERROR: Setting parameter constraints from script failed! (Thu Jan 08 2009 - 10:58:05 CST)
  • Re: compiling NAMD failed on windows with Cygwin (Mon Dec 29 2008 - 09:36:45 CST)
  • Re: NAMD-L: autoionize error (Fri Dec 26 2008 - 14:45:55 CST)
  • Re: Problems on SMD simulation (Fri Dec 26 2008 - 14:31:18 CST)
  • Re: Stupid question about compiling NAMD with cygwin on windows (Fri Dec 26 2008 - 14:35:54 CST)
  • Re: Unsure about current setting of Periodic Boundary Conditions (Tue Dec 23 2008 - 19:39:12 CST)
  • Re: (Tue Dec 23 2008 - 10:22:51 CST)
  • Re: filling hydrophobic cavity with... methane? (Thu Dec 18 2008 - 17:44:23 CST)
  • Re: failure in RATTLE (Wed Dec 17 2008 - 09:52:13 CST)
  • Re: failure in RATTLE (Tue Dec 16 2008 - 13:26:09 CST)
  • Re: NAMD compile error (Tue Dec 16 2008 - 13:18:45 CST)
  • Re: CGMD timestep (Mon Dec 08 2008 - 12:11:54 CST)
  • Re: CGMD timestep (Mon Dec 08 2008 - 11:37:37 CST)
  • Re: CGMD timestep (Mon Dec 08 2008 - 03:26:43 CST)
  • Re: TCL8.5? or (Mon Dec 08 2008 - 03:36:50 CST)
  • Re: namd2 erratic performance over 104 procs (Sat Dec 06 2008 - 03:18:29 CST)
  • Re: regarding writemol2 (Fri Dec 05 2008 - 03:13:48 CST)
  • Re: mpirun compilation for NAMD (Fri Dec 05 2008 - 03:10:24 CST)
  • Re: mpirun compilation for NAMD (Fri Dec 05 2008 - 02:56:30 CST)
  • Re: MacOSX 64bit binaries (Wed Dec 03 2008 - 15:14:23 CST)
  • Re: TIP4 water model NAMD (Wed Nov 26 2008 - 11:19:20 CST)
  • Re: NAMD CVS Installation (Wed Nov 26 2008 - 10:53:10 CST)
  • Re: NAMD with mpirun (Mon Nov 24 2008 - 06:08:11 CST)
  • Re: A way to check for non-unique coordinates? (Fri Nov 21 2008 - 04:36:21 CST)
  • Re: vmd-l: Loading .vel file in VMD (Fri Nov 21 2008 - 03:45:39 CST)
  • Re: periodic cell has become too small for original patch grid! (Tue Nov 18 2008 - 03:33:59 CST)
  • Re: scalability problem on linux cluster (Wed Nov 12 2008 - 11:10:52 CST)
  • Re: Error while using NAMD (Sun Nov 09 2008 - 16:16:32 CST)
  • RE: PME non-zero charge (Fri Nov 07 2008 - 01:51:03 CST)
  • Re: PME non-zero charge (Thu Nov 06 2008 - 16:49:09 CST)
  • Re: segmentation fault? (Wed Nov 05 2008 - 19:14:32 CST)
  • Re: building namd on CRAY-XT3 (Wed Nov 05 2008 - 02:10:32 CST)
  • Re: building namd on CRAY-XT3 (Wed Nov 05 2008 - 00:49:51 CST)
  • Re: ions behavior in protein-water box: (Wed Oct 29 2008 - 17:39:03 CDT)
  • Re: applying stress to study elasticity (Fri Oct 24 2008 - 13:35:20 CDT)
  • Re: How to keep Total Energy constant when an external force is added? (Thu Oct 23 2008 - 09:58:15 CDT)
  • Re: How can I calculate the distance between two atoms frame by frame? (Sat Oct 18 2008 - 22:07:13 CDT)
  • Re: Error while running NPT Simulation (Thu Oct 16 2008 - 13:27:24 CDT)
  • Re: Full Electrostatic Calculations on Protein in Vacuo (Thu Oct 16 2008 - 10:08:23 CDT)
  • Re: Pressure related issue (Thu Oct 16 2008 - 09:16:02 CDT)
  • RE: megatest test failure/MPI problem (Wed Oct 15 2008 - 14:45:16 CDT)
  • Re: How to choose force field? (Wed Oct 15 2008 - 10:57:01 CDT)
  • Re: megatest test failure/MPI problem (Wed Oct 15 2008 - 10:50:14 CDT)
  • Re: Query Regarding FEP tutorial: NPT or NVT? (Sun Oct 12 2008 - 19:48:28 CDT)
  • Re: problems with combine.tcl (Thu Oct 09 2008 - 14:19:19 CDT)
  • Re: swig wrapping c++ code on nersc (Thu Oct 09 2008 - 14:28:03 CDT)
  • RE: Problems compiling NAMD (Tue Oct 07 2008 - 18:44:06 CDT)
  • Re: Problems compiling NAMD (Tue Oct 07 2008 - 11:54:21 CDT)
  • Re: MD performance on 10 GBit/s or 20Gbit/s infiniband (Mon Oct 06 2008 - 10:02:45 CDT)
  • Re: namd 2.5 compilation error (Mon Sep 29 2008 - 14:45:44 CDT)
  • Re: namd 2.5 compilation error (Mon Sep 29 2008 - 13:12:10 CDT)
  • Re: namd 2.5 compilation error (Sun Sep 28 2008 - 13:27:38 CDT)
  • Re: Running Multiple TMD simultaneously (Sun Sep 28 2008 - 13:24:16 CDT)
  • Re: NAMD vs. CHARMM. Is complete correspondence possible? (Tue Sep 09 2008 - 15:56:52 CDT)
  • Re: psfgen: more problem (Mon Sep 08 2008 - 14:17:28 CDT)
  • Re: Platinum paramaters (Mon Sep 01 2008 - 15:05:39 CDT)
  • Re: conskfile (Sat Aug 30 2008 - 13:33:07 CDT)
  • Re: Trouble with params file when trying to perform basic dynamics with alanine. (Sat Aug 30 2008 - 11:31:18 CDT)
  • Re: Struggling with the compilation of NAMD 2.6 on a PBS Cluster with LAM/MPI (Fri Aug 29 2008 - 13:55:27 CDT)
  • Re: vmd-l: TXT program editor (Thu Aug 28 2008 - 15:50:21 CDT)
  • Re: NAMD compilation / TACC Ranger (Thu Aug 28 2008 - 14:12:36 CDT)
  • Re: Struggling with the compilation of NAMD 2.6 on a PBS Cluster with LAM/MPI (Thu Aug 28 2008 - 14:16:18 CDT)
  • Re: change in box geometry for simulation of pure water (Thu Aug 28 2008 - 14:06:47 CDT)
  • Re: diffusion coefficient from rmsd (Wed Aug 27 2008 - 22:39:52 CDT)
  • Re: corrupt DCD file (Wed Aug 27 2008 - 18:56:20 CDT)
  • Re: Struggling with the compilation of NAMD 2.6 on a PBS Cluster with LAM/MPI (Wed Aug 27 2008 - 12:12:00 CDT)
  • Re: running precompiled NAMD with multiple processors (Tue Aug 26 2008 - 09:41:49 CDT)
  • Re: Please unsubscribe me (Thu Aug 14 2008 - 14:26:26 CDT)
  • RE: NAMD crashed with TclForce turned on (Sun Aug 10 2008 - 15:35:28 CDT)
  • Re: NAMD crashed with TclForce turned on (Sat Aug 09 2008 - 17:14:26 CDT)
  • Re: build smp version of namd with intel 10.1 (Thu Aug 07 2008 - 12:08:34 CDT)
  • Re: NAMD crashed with TclForce turned on (Wed Aug 06 2008 - 17:20:55 CDT)
  • Re: Warning in log file (Wed Aug 06 2008 - 11:17:34 CDT)
  • Re: Re: segmentation fault when running ABF (Wed Aug 06 2008 - 11:31:42 CDT)
  • Re: Re: segmentation fault when running ABF (Wed Aug 06 2008 - 11:10:48 CDT)
  • Re: [Fwd: Notice:Re: Re: segmentation fault when running ABF] (Wed Aug 06 2008 - 11:15:06 CDT)
  • Re: Re: segmentation fault when running ABF (Tue Aug 05 2008 - 12:13:56 CDT)
  • Re: SMD in water (Thu Jul 31 2008 - 09:16:01 CDT)
  • Re: namd linked to tcl8.5 (Wed Jul 30 2008 - 10:20:55 CDT)
  • Re: PME fails no matter what (Tue Jul 29 2008 - 03:18:21 CDT)
  • Re: ubuntu reads my psf as an audio file (Mon Jul 28 2008 - 13:58:34 CDT)
  • Re: PME and infinite polymer (Fri Jul 25 2008 - 08:24:30 CDT)
  • Re: Appending dcd when restarting a simulation (Thu Jul 24 2008 - 08:52:56 CDT)
  • Re: how to generate psf file using the AMBER topology file (Fri Jul 18 2008 - 12:09:48 CDT)
  • Re: ERROR(S) IN THE CONFIGURATION FILE when running on a cluster. (Fri Jul 18 2008 - 14:18:02 CDT)
  • Re: cannot find -lsrfftw... collect2: ld returned 1 exit status (Sun Jul 13 2008 - 15:54:54 CDT)
  • 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 Aykut
  • Re: dcd to pdb conversion (Mon Oct 27 2008 - 03:58:58 CDT)
  • dcd to pdb conversion (Mon Oct 27 2008 - 03:28:16 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
  • Molecular dynamics of multiple organic molecules with NAMD (Thu Oct 22 2009 - 09:39:06 CDT)
• B.R.Silver_at_warwick.ac.uk
  • Solvating protein with ions (Wed Jun 06 2007 - 15:20:43 CDT)
• balaji nagarajan
  • lipidmonolayer (Wed Apr 22 2009 - 14:58:25 CDT)
  • how to install namd in windows xp (Sat Apr 04 2009 - 01:11:00 CDT)
  • reg parameter of ions (Fri Dec 12 2008 - 22:43:41 CST)
  • generating psf & energy calculation for unusual amino acid - Aib (Thu Nov 06 2008 - 21:57:17 CST)
• 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)
• bay__gulf618_at_sina.com
  • Re: Reassign temp (Wed Jun 17 2009 - 20:44:15 CDT)
  • Fw: NAMD 2.7b1 running problem (Wed May 20 2009 - 20:10:15 CDT)
  • how to install NAMD on suse10_ppc64 without xlc (Fri Apr 24 2009 - 05:18:04 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)
• benc_at_bsc.es
  • maximum residues using AMBER parm with NAMD (Wed Jul 22 2009 - 05:09:17 CDT)
• Benjamin Bouvier
  • Group forces in tclForces (Mon Jul 27 2009 - 06:02:12 CDT)
  • Re: Measuring the molarity (Wed Jul 22 2009 - 16:25:40 CDT)
  • Re: CPU USAGE (Sun Jul 19 2009 - 04:51:32 CDT)
  • Re: regarding psfgen algorithm (Thu Jun 18 2009 - 03:50:14 CDT)
  • Re: regarding protein-protein interaction (Fri Jun 05 2009 - 03:50:21 CDT)
  • Exclusions and CUDA (Thu Jun 04 2009 - 03:40:22 CDT)
  • Re: Amber ff99sb force-field in namd (Wed Mar 18 2009 - 18:19:23 CDT)
  • Re: NAMD on a virtual grid (Mon Jan 26 2009 - 14:38:56 CST)
  • NAMD on a virtual grid (Mon Jan 26 2009 - 09:38:30 CST)
  • Re: Implementation of TCL script in NAMD .conf file (Mon Jul 07 2008 - 04:34:54 CDT)
  • 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)
• Benjamin Roberts
  • Coulombic virials (Mon Dec 08 2008 - 22:14:00 CST)
• Benjamin Stauch
  • diffusion / fex peptide problem (Wed May 06 2009 - 10:24:16 CDT)
• Bernardo Sosa Padilla Araujo
  • Harmonic restraint parameters (Mon Nov 09 2009 - 13:49:37 CST)
  • Re: Namd benchmark problem (Mon Oct 26 2009 - 00:10:25 CDT)
  • heating a system (Thu Oct 01 2009 - 11:51:10 CDT)
  • Kemp elimination substrate charmm parameters (Mon Sep 21 2009 - 15:41:01 CDT)
  • FATAL ERROR: Couldn't open DCD file ubq_wb_eq.dcd: No such file or directory (Tue Sep 15 2009 - 18:26:25 CDT)
  • error running namd (Mon Jul 27 2009 - 16:37:17 CDT)
  • NAMD installation (Wed Jul 22 2009 - 17:33:15 CDT)
• Bertrand P. S. Russell
  • (no subject) (Sat Nov 01 2008 - 20:50:16 CDT)
  • unsubscribe (Fri Oct 31 2008 - 23:10:48 CDT)
  • 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)
• Biff Forbush
  • Re: NAMD file limitation in Win32 - windows XP (Tue Nov 17 2009 - 15:29:21 CST)
  • Re: questions regarding new single node box for NAMD: re components, CUDA, Fermi (Sun Oct 04 2009 - 20:37:43 CDT)
  • questions regarding new single node box for NAMD: re components, CUDA, Fermi (Thu Oct 01 2009 - 17:27:06 CDT)
• Bill K
  • How do you evaluate forces on a fixed atom? (Mon Nov 17 2008 - 15:33:38 CST)
  • Use tclforces to find systematic forces on fixed atoms? (Tue Oct 07 2008 - 16:20:44 CDT)
• Bill Kowallis
  • Re: Use tclforces to find systematic forces on fixed atoms? (Wed Oct 08 2008 - 11:45:12 CDT)
• BIN ZHANG
  • NAMD bonded energy function (Thu Nov 12 2009 - 01:23:16 CST)
  • Re: namd cvs memory leak? (Thu Oct 22 2009 - 19:57:08 CDT)
  • Re: CG bead definition (Thu Oct 22 2009 - 18:05:32 CDT)
  • namd cvs memory leak? (Thu Oct 22 2009 - 18:12:08 CDT)
  • fresh file not ready to read? (Thu Oct 22 2009 - 01:46:10 CDT)
  • Re: CG bead definition (Tue Oct 20 2009 - 15:12:04 CDT)
  • Fwd: vmd-l: CG bead definition (Tue Oct 20 2009 - 11:19:30 CDT)
  • Re: center of mass of dummyAtom in colvar (Wed Oct 14 2009 - 19:06:01 CDT)
  • center of mass of dummyAtom in colvar (Wed Oct 14 2009 - 16:57:13 CDT)
  • Re: restraining the COM of a group of atoms (Sun Oct 11 2009 - 12:53:10 CDT)
  • restraining the COM of a group of atoms (Fri Oct 09 2009 - 19:19:56 CDT)
  • Re: nonbonded potential (Thu Oct 08 2009 - 16:07:05 CDT)
  • nonbonded potential (Thu Oct 08 2009 - 00:19:30 CDT)
  • Re: Changing the atomtype of a particle on the fly (Fri Oct 02 2009 - 13:50:21 CDT)
  • Changing the atomtype of a particle on the fly (Fri Oct 02 2009 - 01:15:07 CDT)
  • Re: bug or custom? (Thu Jul 09 2009 - 13:53:52 CDT)
  • bug or custom? (Thu Jul 09 2009 - 13:00:44 CDT)
  • force output of pairInteraction (Mon Jun 01 2009 - 17:20:07 CDT)
  • Re: calculating forces from dcd trajectory (Thu May 21 2009 - 12:40:15 CDT)
  • Re: calculating forces from dcd trajectory (Wed May 20 2009 - 12:18:20 CDT)
  • calculating forces from dcd trajectory (Wed May 20 2009 - 02:18:26 CDT)
  • Re: Calculating displacement in a system with periodic boundary (Tue May 12 2009 - 02:25:48 CDT)
  • CGMD ? Hydrophobic scale (Fri May 01 2009 - 17:00:12 CDT)
  • Re: compiling error of NAMD2.7b1 (Mon Apr 20 2009 - 13:41:01 CDT)
  • Re: compiling error of NAMD2.7b1 (Mon Apr 20 2009 - 12:30:17 CDT)
  • cvs logs (Fri Apr 17 2009 - 13:53:54 CDT)
  • elastic network (Tue Apr 14 2009 - 18:10:37 CDT)
  • Re: Exiting prematurely (Fri Apr 03 2009 - 11:10:04 CDT)
  • Exiting prematurely (Fri Apr 03 2009 - 02:22:28 CDT)
  • Re: cgmd stability (Thu Feb 19 2009 - 11:25:41 CST)
  • Re: cgmd stability (Thu Feb 19 2009 - 00:31:35 CST)
  • Re: cgmd stability (Wed Feb 18 2009 - 20:20:52 CST)
  • cgmd stability (Wed Feb 18 2009 - 17:13:14 CST)
  • Re: Fatal error in configuration file (Thu Feb 05 2009 - 22:28:26 CST)
  • Re: Fatal error in configuration file (Wed Feb 04 2009 - 22:12:55 CST)
  • dielectric parameter? (Thu Jan 15 2009 - 01:10:36 CST)
  • question about cellBasisVector*? (Tue Jan 13 2009 - 00:13:25 CST)
  • Re: Gradient tolerance nan for A three-atom simulation (Mon Jan 12 2009 - 12:03:52 CST)
  • Re: Re: namdcvs (Mon Jan 05 2009 - 14:12:59 CST)
  • CGMD parameters (Tue Dec 23 2008 - 20:06:32 CST)
  • Re: Loops in tclForcesScript (Thu Dec 11 2008 - 14:45:38 CST)
  • Re: CGMD timestep (Mon Dec 08 2008 - 11:51:46 CST)
  • Re: CGMD timestep (Mon Dec 08 2008 - 11:29:05 CST)
  • Re: parameters and topology file needed for coarse-grain simulation (Mon Dec 08 2008 - 11:12:22 CST)
  • CGMD timestep (Sun Dec 07 2008 - 14:44:23 CST)
  • Re: CGMD problem (Sat Dec 06 2008 - 16:19:32 CST)
  • Re: CGMD problem (Sat Dec 06 2008 - 14:30:39 CST)
  • Electron density profile? (Fri Dec 05 2008 - 01:40:53 CST)
  • CGMD problem (Tue Dec 02 2008 - 11:10:34 CST)
  • Re: namd cvs compilation (Mon Dec 01 2008 - 11:59:39 CST)
  • Re: namd cvs compilation (Fri Nov 28 2008 - 00:11:14 CST)
  • Re: namd cvs compilation (Thu Nov 27 2008 - 20:20:46 CST)
  • Re: namd cvs compilation (Thu Nov 27 2008 - 01:00:14 CST)
  • Re: namd cvs compilation (Wed Nov 26 2008 - 19:24:19 CST)
  • namd cvs compilation (Wed Nov 26 2008 - 18:55:07 CST)
  • Re: vmd-l: CG bead definition (Tue Nov 25 2008 - 15:01:37 CST)
  • CG modeling using NAMD (Sat Nov 22 2008 - 18:54:05 CST)
  • Re: segmentation fault? (Wed Nov 05 2008 - 18:33:29 CST)
  • segmentation fault? (Wed Nov 05 2008 - 15:58:58 CST)
  • Re: building namd on CRAY-XT3 (Wed Nov 05 2008 - 01:19:37 CST)
  • Re: building namd on CRAY-XT3 (Wed Nov 05 2008 - 00:16:34 CST)
  • building namd on CRAY-XT3 (Tue Nov 04 2008 - 13:38:35 CST)
  • Re: log file problem (Mon Nov 03 2008 - 20:49:30 CST)
  • restarting issue (Fri Oct 10 2008 - 14:42:43 CDT)
  • Re: restarting issue (Fri Oct 10 2008 - 15:00:36 CDT)
  • swig wrapping c++ code on nersc (Thu Oct 09 2008 - 11:30:12 CDT)
  • Re: vmd-l: TAB key in vmd terminal (Fri Oct 03 2008 - 11:04:02 CDT)
  • Re: TCL force (Wed Sep 24 2008 - 14:23:38 CDT)
  • Re: TCL force (Tue Sep 23 2008 - 11:20:40 CDT)
  • Re: TCL force (Tue Sep 23 2008 - 00:43:52 CDT)
  • TCL force (Mon Sep 22 2008 - 20:40:59 CDT)
  • Re: TCL Forces : OUT OF MEMORY (Fri Sep 12 2008 - 17:43:06 CDT)
  • TCL Forces : OUT OF MEMORY (Fri Sep 12 2008 - 13:38:17 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
  • RE: Modification of equlibrated simulation box: OPTION 4 (Wed Oct 21 2009 - 18:57:48 CDT)
  • processor counts FFT and NAMD (Wed Mar 25 2009 - 10:42:43 CDT)
  • tip4p - namd follwup (Fri Nov 30 2007 - 10:37:24 CST)
• Bjoern Olausson
  • Re: Formating of logfile (Sat Nov 14 2009 - 20:42:37 CST)
  • Re: Formating of logfile (Fri Nov 13 2009 - 21:47:31 CST)
  • Re: Formating of logfile (Fri Nov 13 2009 - 14:31:22 CST)
  • Re: Formating of logfile (Fri Nov 13 2009 - 02:55:02 CST)
  • Re: Will MPICH2 work for NAMD? and the best way to build/compile NAMD to exploit my hardware resource? (Fri Nov 13 2009 - 03:39:32 CST)
  • Re: Will MPICH2 work for NAMD? (Wed Nov 11 2009 - 07:07:47 CST)
  • Formating of logfile (Wed Nov 11 2009 - 07:07:34 CST)
  • Formating of logfile (Wed Nov 11 2009 - 06:58:44 CST)
  • Re: Will MPICH2 work for NAMD? (Tue Nov 10 2009 - 02:52:03 CST)
  • Re: ibverbs crash (Wed Nov 04 2009 - 08:38:25 CST)
  • Re: ibverbs crash (Wed Nov 04 2009 - 04:06:48 CST)
  • Re: ibverbs crash (Wed Nov 04 2009 - 08:38:45 CST)
  • Re: Constraint failure in RATTLE algorithm - shouldn't a rerun fail at the same step? (Thu Sep 10 2009 - 05:38:18 CDT)
  • Re: Constraint failure in RATTLE algorithm - shouldn't a rerun fail at the same step? (Thu Sep 10 2009 - 05:26:00 CDT)
  • Constraint failure in RATTLE algorithm - shouldn't a rerun fail at the same step? (Tue Sep 08 2009 - 03:12:04 CDT)
  • Constraint failure in RATTLE algorithm - shouldn't a rerun fail at the same step? (Tue Sep 08 2009 - 03:13:02 CDT)
  • Re: charm++ how to handle SMP/Multicore (Thu Aug 20 2009 - 11:41:16 CDT)
  • charm++ how to handle SMP/Multicore (Sun Aug 09 2009 - 17:01:48 CDT)
  • NAMD 2.7b1 with APBS/iAPBS (Wed Jul 22 2009 - 02:56:07 CDT)
  • Re: Value for "firsttimestep" when restarting MD (Thu Jul 02 2009 - 04:05:23 CDT)
  • Which compiler-suite was used... (Tue May 12 2009 - 07:26:00 CDT)
  • Re: Value for "firsttimestep" when restarting MD (Tue May 05 2009 - 12:45:56 CDT)
  • Value for "firsttimestep" when restarting MD (Tue May 05 2009 - 09:50:42 CDT)
  • Re: NPAT - NPgT ensemble (Sun May 03 2009 - 15:54:27 CDT)
  • NPAT - NPgT ensemble (Sat May 02 2009 - 07:43:34 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)
• Blake Mertz
  • compiling namd on SGI Altix (Tue Dec 23 2008 - 11:09:10 CST)
• blicebauma_at_duq.edu
  • Restraint Potential (Tue Sep 16 2008 - 08:53:59 CDT)
  • namd1 - abf analysis (Thu Sep 11 2008 - 08:19:46 CDT)
• bo baker
  • topology/parameter file for ligands (Wed Dec 17 2008 - 20:56:50 CST)
  • top_all22_model.inp (Mon Dec 15 2008 - 22:50:07 CST)
  • 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: Optimizing configuration option for fast calculations (Thu Apr 30 2009 - 12:12:59 CDT)
  • Re: Peptide in Membrane Environment: loosing water from one leaflet (Mon Apr 20 2009 - 08:35:33 CDT)
  • Need Charmm FF for Gangliosides (Wed Feb 11 2009 - 11:36:19 CST)
  • Re: Membrane Simulations (Tue Oct 14 2008 - 22:09:09 CDT)
  • Re: Managing Log files (Sat Sep 27 2008 - 03:22:21 CDT)
  • Re: Managing Log files (Fri Sep 26 2008 - 22:01:40 CDT)
  • Re: Re: vmd-l: counting gas molecules inside the nanotube (Fri Sep 19 2008 - 11:38:19 CDT)
  • Re: Constraint failure & velocity problem (Thu Sep 04 2008 - 00:26:14 CDT)
  • Re: Constraint failure & velocity problem (Wed Sep 03 2008 - 00:08:15 CDT)
  • Re: diffusion coefficient from rmsd (Thu Aug 28 2008 - 01:38:38 CDT)
  • Re: parallel execution speedup (Thu Aug 28 2008 - 01:51:29 CDT)
  • memory overflow problem of Tcl scripting when dealing with trajectories (Wed Jul 16 2008 - 03:16:31 CDT)
  • relating to NAMD Energy Plugin scripting (Sun Jul 06 2008 - 23:19:44 CDT)
  • 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)
• Bonnie Merchant
  • Re: colvars: Error: undefined output or restart file. (Mon Jun 29 2009 - 11:00:07 CDT)
  • colvars: Error: undefined output or restart file. (Fri Jun 26 2009 - 13:41:42 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)
• Branko
  • g(r) GUI Plugin problem (Tue Sep 29 2009 - 05:32:03 CDT)
  • Replay to Parametrizing a novel residue] (Fri Sep 18 2009 - 13:58:11 CDT)
  • Re: Regarding ABF Simulation (Mon Sep 14 2009 - 15:34:17 CDT)
  • Re: what is the charge of sulfur on thiol? (Mon Aug 17 2009 - 03:41:18 CDT)
  • Re: Restarting ABF (Thu Aug 13 2009 - 13:56:59 CDT)
  • Restarting ABF (Thu Aug 13 2009 - 11:05:18 CDT)
  • Re: how to use ethanol as solvent in namd for MD simulations? (Fri Jul 31 2009 - 07:59:03 CDT)
  • Re: how to use ethanol as solvent in namd for MD simulations ? (Fri Jul 31 2009 - 04:50:17 CDT)
  • Equilibration "substraction" from obtained PMF from MD (Tue Jul 28 2009 - 16:32:00 CDT)
  • RE: ABF simulations (Tue Jun 23 2009 - 14:52:42 CDT)
  • Re: abf with colvars example (Thu Jun 04 2009 - 15:17:42 CDT)
  • Re: Free energy of conformational change (Fri May 29 2009 - 06:44:32 CDT)
  • Free energy of conformational change (Wed May 20 2009 - 06:15:57 CDT)
• brian
  • strange memory behavior (Thu Nov 16 2006 - 11:20:06 CST)
• Brian Bennion
  • recent papers on MD gotchas with PRNG seeds (Fri May 08 2009 - 14:20:39 CDT)
  • Re: Accessing atoms and velocities during NVE run (Fri Feb 06 2009 - 13:08:24 CST)
  • Re: Full Electrostatic Calculations on Protein in Vacuo (Thu Oct 16 2008 - 10:19:32 CDT)
  • 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 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)
  • Re: Energy units (Tue Dec 30 2003 - 13:53:17 CST)
  • big systems using namd on 700 cpus (Mon Dec 29 2003 - 13:47:04 CST)
  • Re: weird energies during minimization (Fri Dec 19 2003 - 16:25:19 CST)
  • weird energies during minimization (Fri Dec 19 2003 - 13:04:56 CST)
  • Re: hydrogengroupsize of 0! (Thu Dec 18 2003 - 13:03:01 CST)
  • Re: LDB questions/problems (Thu Dec 18 2003 - 10:23:25 CST)
  • Re: LDB questions/problems (Tue Dec 16 2003 - 15:32:51 CST)
  • Re: LDB questions/problems (Mon Dec 15 2003 - 15:41:32 CST)
  • LDB questions/problems (Mon Dec 15 2003 - 12:58:15 CST)
  • Re: binary troubles (Fri Dec 05 2003 - 13:40:35 CST)
  • Re: psfgen: pdb and nucleic acid (Wed Dec 03 2003 - 14:30:29 CST)
  • Re: Basic question. (Tue Dec 02 2003 - 13:30:30 CST)
  • RE: IMD on MPI versions of NAMD (Mon Dec 01 2003 - 16:58:16 CST)
  • IMD on MPI versions of NAMD (Mon Dec 01 2003 - 12:19:28 CST)
  • Re: the problem on segment a ligand in NAMD ? (Fri Nov 28 2003 - 00:30:13 CST)
  • Re: Minimisation error (Thu Nov 27 2003 - 21:49:25 CST)
  • hydrogengroupsize of 0! (Wed Nov 26 2003 - 17:57:28 CST)
  • Re: about internal coordinate IC statement of CHARMM force field (Tue Nov 25 2003 - 13:09:41 CST)
  • Re: ATP fix (fwd) (Wed Nov 19 2003 - 11:06:19 CST)
  • Re: ADP again (Wed Nov 19 2003 - 11:00:40 CST)
  • Re: ADP again (Tue Nov 18 2003 - 10:24:33 CST)
  • Re: ADP again (Mon Nov 17 2003 - 12:58:56 CST)
  • Re: ADP again (Mon Nov 17 2003 - 11:18:09 CST)
  • Re: ADP again (Sun Nov 16 2003 - 00:26:00 CST)
  • Re: MOE program and difference between MD and SA? (Fri Nov 14 2003 - 10:35:15 CST)
  • Re: high temperature, 498K, unfolding simulations (Thu Nov 13 2003 - 12:23:13 CST)
  • Re: error in starting the minimization (Wed Nov 12 2003 - 18:11:42 CST)
  • Re: dcd files (Tue Nov 11 2003 - 10:27:42 CST)
  • Re: uninitialized coordinates (Mon Nov 10 2003 - 10:40:31 CST)
  • Re: Parameter/topology repository (Fri Nov 07 2003 - 10:12:22 CST)
  • Re: how to set harmonic constraints to alpha carbon (Thu Nov 06 2003 - 16:34:53 CST)
  • Re: contraint failure in RATTLE algorithm (Thu Nov 06 2003 - 14:10:49 CST)
  • Re: atoms moving too fast (Thu Nov 06 2003 - 11:16:03 CST)
  • Re: vmd-l: bigdcd (Wed Nov 05 2003 - 17:52:38 CST)
  • Re: atoms moving too fast (Wed Nov 05 2003 - 17:36:51 CST)
  • Re: atoms moving too fast (Wed Nov 05 2003 - 16:50:53 CST)
  • Re: repulsive/hard sphere simulation (Wed Nov 05 2003 - 15:22:16 CST)
  • Re: about charmm topology file (Wed Nov 05 2003 - 10:27:51 CST)
  • Re: excluding water in dcd files (Tue Nov 04 2003 - 10:35:55 CST)
  • RE: Question about AUTOGENERATE (Tue Nov 04 2003 - 10:24:58 CST)
  • Re: solvate (Mon Nov 03 2003 - 11:27:56 CST)
  • Re: excluding water in dcd files (Mon Nov 03 2003 - 11:23:38 CST)
  • Re: charmm param. for ADP (Mon Oct 27 2003 - 15:14:57 CST)
  • Re: charmm param. for ADP (Mon Oct 27 2003 - 10:20:34 CST)
  • namd/charmm steroid parameterization (Fri Oct 24 2003 - 11:08:07 CDT)
  • Re: Launching namd with PBS (Wed Sep 24 2003 - 19:15:49 CDT)
  • Re: seg fault (Tue Sep 16 2003 - 16:22:44 CDT)
  • Thank you (Mon Sep 15 2003 - 23:43:52 CDT)
• Brian Genge
  • NAMD on dual core, dual processor machine? (Mon Jul 30 2007 - 10:23:31 CDT)
• Brian J. Bennion
  • RE: namd27: tclforces activate TI calculation by default (Mon Aug 10 2009 - 10:36:01 CDT)
• Brian R Novak
  • bicarbonate parameters (Wed Jul 08 2009 - 13:31:28 CDT)
  • RE: Total energy of a residue (Tue Jun 23 2009 - 11:03:45 CDT)
  • RE: selectively write atom coordinates on-the-fly (Thu May 21 2009 - 12:44:33 CDT)
  • RE: peptides on surface (Wed May 13 2009 - 15:25:19 CDT)
  • RE: biotin parameters and topology (Tue Apr 28 2009 - 15:43:15 CDT)
  • biotin parameters and topology (Tue Apr 28 2009 - 12:37:53 CDT)
• Bridget Walsh
  • Maestro Penis (Wed Jun 06 2007 - 06:55:35 CDT)
• Brittany Calderon
  • Switch ON your penis! (Tue Jun 12 2007 - 07:46:25 CDT)
• Brittany Collier
  • Happy Viagra (Tue Jun 12 2007 - 03:36:22 CDT)
• Brittany Morgan
  • RE: Random Expulsion MD (REMD) (Mon Oct 26 2009 - 11:37:27 CDT)
  • RE: Minimization convergence issue (Thu Mar 05 2009 - 12:46:28 CST)
  • RE: Minimization convergence issue (Thu Mar 05 2009 - 07:56:47 CST)
  • RE: Minimization convergence issue (Wed Mar 04 2009 - 13:36:38 CST)
  • RE: Minimization convergence issue (Mon Mar 02 2009 - 10:53:55 CST)
  • Minimization convergence issue (Mon Mar 02 2009 - 09:59:21 CST)
• brmorgan_at_clarku.edu
  • Re: use of tiElecLambdaStart (NAMD 2.7b1) (Mon Mar 30 2009 - 13:21:34 CDT)
  • use of tiElecLambdaStart (NAMD 2.7b1) (Fri Mar 27 2009 - 11:00:51 CDT)
  • RE: Using NAMD to calculate pair energy with many subset permutations (Fri Oct 17 2008 - 09:39:05 CDT)
  • Using NAMD to calculate pair energy with many subset permutations (Wed Oct 15 2008 - 13:08:42 CDT)
  • Tests not running for Charm++ Myrinet with MPICH-MX (Wed Jan 23 2008 - 14:35:05 CST)
  • Re: Installing NAMD (Tue Nov 20 2007 - 13:02:42 CST)
  • Installing NAMD (Fri Nov 16 2007 - 11:28:47 CST)
• brosbam_at_berkeley.edu
  • coord file output minus solvation box (Wed Jul 30 2008 - 18:21:18 CDT)
  • output .coor minus solvation box (Wed Jul 30 2008 - 18:27:01 CDT)
• by way of Jérôme Hénin
  • Re: alchemical free energy perturbation (Mon Jan 05 2004 - 09:10:52 CST)
• C. Denise Enekwa
  • unsubscribe (Sat Jun 27 2009 - 06:41:19 CDT)
  • NAMD and CFF forcefields (Sat Mar 28 2009 - 13:22:36 CDT)
• C. Ecker
  • Simulating DNA in vacuum (Fri Nov 14 2003 - 08:47:54 CST)
  • tcl interface (Thu Nov 13 2003 - 05:07:04 CST)
• Cable, Sam B ERDC-ITL-MS Contractor
  • FW: (Thu Apr 15 2004 - 15:44:57 CDT)
  • (no subject) (Thu Apr 15 2004 - 11:17:53 CDT)
• Caio Julio Martins Veloso
  • Compiling namd on ibm-power + red hat linux (Tue May 22 2007 - 20:23:36 CDT)
  • Benzamidine parameters (Sat Mar 25 2006 - 12:54:52 CST)
• Cameron Abrams
  • How to use lset inside tclforces/calc_forces (Mon Mar 09 2009 - 09:00:51 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)
• campen_at_geosc.psu.edu
  • Re: It doesn't work with using amber files. (Thu Mar 29 2007 - 11:28:36 CDT)
• carles ferrer
  • problems NAMD_2.6 (fwd) (Thu Sep 29 2005 - 04:06:09 CDT)
• carlos alberto gueto tettay
  • charmm charge style (Thu Dec 27 2007 - 12:55:00 CST)
  • ligand parameters... I know the next step (Fri Dec 21 2007 - 11:36:53 CST)
  • ligands parameters (Fri Dec 21 2007 - 08:42:15 CST)
• 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)
• Carlos Simoes
  • Re: Saving coordinates of each frame into one separate .pdb file from a 100-frame .dcd file. (Sat Jan 21 2006 - 11:04:54 CST)
  • wrong simulation times or misleading time counting? (Wed Jan 18 2006 - 17:48:59 CST)
• Carsten Olbrich
  • NAMD on dual quad-core Xeon's with Infiniband backbone (Sat Sep 22 2007 - 06:44:29 CDT)
  • psfgen: merging of 2 dna chains (Wed Sep 19 2007 - 08:19:09 CDT)
  • Re: Differences between 32bit and 64bit version of NAMD? (Mon Jun 18 2007 - 17:12:37 CDT)
  • Re: Differences between 32bit and 64bit version of NAMD? (Mon Jun 18 2007 - 13:34:45 CDT)
  • Differences between 32bit and 64bit version of NAMD? (Mon Jun 18 2007 - 11:04:30 CDT)
  • Problems with version 2.6 for amd64 (Fri May 04 2007 - 03:37:08 CDT)
• Cartailler, Jean-Philippe
  • Help with: Constraint failure in RATTLE algorithm (Thu Oct 02 2003 - 11:17:58 CDT)
• Casey,Richard
  • Inorganic compounds (Thu Jan 08 2009 - 12:20:34 CST)
• casoni\_at_libero\.it
  • calculate potential energy from DCD file (Tue Sep 05 2006 - 07:21:57 CDT)
• Cesar Avila
  • Implicit solvent simulation (Mon Sep 03 2007 - 08:45:16 CDT)
  • Re: High background load warning message (Sun Jun 24 2007 - 13:56:24 CDT)
  • Re: can someone comment? (Sat Apr 07 2007 - 11:57:49 CDT)
  • Re: Possible bug on NAMD 2.6B1? (Tue Jul 18 2006 - 09:46:02 CDT)
  • Possible bug on NAMD 2.6B1? (Sat Jul 15 2006 - 11:06:23 CDT)
• Cesar Delgado
  • RE: (Wed Dec 03 2003 - 08:46:12 CST)
  • RE: IMD on MPI versions of NAMD (Mon Dec 01 2003 - 16:44:05 CST)
  • RE: VMD problems (Mon Dec 01 2003 - 13:05:39 CST)
  • RE: (Mon Oct 20 2003 - 01:13:08 CDT)
  • Error when running NAMD_2.5 on mytinet (Sat Oct 04 2003 - 18:20:13 CDT)
• Cesar Luis Avila
  • Re: Copper and Zinc: top_all27_prot_lipid.inp (Mon Sep 03 2007 - 10:47:35 CDT)
  • Re: Recommended solvation box size (Mon Sep 03 2007 - 07:44:26 CDT)
  • Re: setting solvent density during solvation (Mon Aug 20 2007 - 16:47:37 CDT)
  • Re: setting solvent density during solvation (Mon Aug 20 2007 - 15:29:17 CDT)
  • Re: setting solvent density during solvation (Mon Aug 20 2007 - 14:46:01 CDT)
  • Re: NAMD hangs at "OPENING EXTENDED SYSTEM TRAJECTORY FILE" / PME error (Mon Aug 06 2007 - 10:16:47 CDT)
  • Re: High background load warning message (Mon Jul 02 2007 - 14:48:33 CDT)
  • Re: Re: Diffusion of Protein through the membrane (Wed Jun 27 2007 - 08:12:00 CDT)
  • High background load warning message (Sat Jun 23 2007 - 19:12:32 CDT)
  • Re: charmrun simulations over macpros (Wed Jun 20 2007 - 13:30:10 CDT)
  • Turning off tcl forces (Wed Jun 13 2007 - 09:42:28 CDT)
  • Re: CNT modeling (Tue Jun 12 2007 - 16:05:21 CDT)
  • Re: Energy shift during simulation (Tue May 29 2007 - 16:45:17 CDT)
  • Re: Energy shift during simulation (Tue May 29 2007 - 15:51:55 CDT)
  • Re: Energy shift during simulation (Tue May 29 2007 - 09:53:31 CDT)
  • Re: Energy shift during simulation (Mon May 28 2007 - 18:26:29 CDT)
  • Energy shift during simulation (Mon May 28 2007 - 16:21:29 CDT)
  • Re: query about wrapped coordinates (Tue May 08 2007 - 08:46:13 CDT)
  • Re: a topology file in VMD (Wed Apr 25 2007 - 10:07:49 CDT)
  • Re: a topology file in VMD (Wed Apr 25 2007 - 08:58:01 CDT)
  • Re: the relationship between system size and cpu numbers (Tue Mar 27 2007 - 14:33:35 CDT)
  • Re: the relationship between system size and cpu numbers (Tue Mar 27 2007 - 11:19:18 CDT)
  • Re: restart NAMD job (Fri Mar 23 2007 - 10:10:54 CDT)
  • Re: Simulation explodes as soon as minimization starts "GRADIENT TOLERANCE: nan" (Wed Mar 21 2007 - 13:54:47 CDT)
  • Re: Premature stop (Thu Mar 08 2007 - 07:32:56 CST)
  • Re: reproduciblity between software (Fri Mar 02 2007 - 15:07:02 CST)
  • Re: Problem about cellBasisVector (Fri Feb 16 2007 - 12:56:57 CST)
  • Re: Temperature problem (Tue Feb 13 2007 - 15:19:20 CST)
  • Re: ionize (big, big, big system!) (Mon Feb 12 2007 - 12:58:11 CST)
  • Re: DMPC psf. (Fri Feb 09 2007 - 12:36:40 CST)
  • Re: SMD and CPT? (Fri Feb 09 2007 - 12:21:07 CST)
  • Re: constant velocity SMD (Fri Jan 26 2007 - 12:34:36 CST)
  • Re: simulation of membrane-protein systems (Wed Dec 13 2006 - 09:14:07 CST)
  • Help. Parameters for PSGL needed (Thu Dec 07 2006 - 09:49:48 CST)
  • Re: dissociation of water (Mon Oct 09 2006 - 11:33:52 CDT)
  • Re: vmd-l: trace to newcartoon inconsistent display problem (Thu Oct 05 2006 - 15:58:11 CDT)
  • Namd list administration (Tue Sep 26 2006 - 10:13:58 CDT)
  • Re: load balancer, athlon 64 dual core (Wed Sep 13 2006 - 07:54:48 CDT)
  • Accelerating groups of atoms (Tue Sep 05 2006 - 15:18:59 CDT)
  • Re: Re: vmd-l: Angles and dihedral generation (Tue Sep 05 2006 - 08:15:18 CDT)
  • Re: Re: vmd-l: Angles and dihedral generation (Mon Sep 04 2006 - 10:00:35 CDT)
  • Angles and dihedral generation (Fri Sep 01 2006 - 20:02:36 CDT)
  • Re: Segmentation violation from APOA1 simulation on AMD64 (Thu Aug 31 2006 - 10:42:41 CDT)
  • Re: Using PsfGen (Mon Aug 28 2006 - 15:23:05 CDT)
  • Segmentation violation from APOA1 simulation on AMD64 (Mon Aug 28 2006 - 13:49:25 CDT)
  • Re: Re: Info: Adjusted background load on 11 nodes. (Sat Aug 26 2006 - 17:00:08 CDT)
  • Re: Re: Info: Adjusted background load on 11 nodes. (Sat Aug 26 2006 - 16:40:15 CDT)
  • Linking with -memory paranoid (Thu Aug 10 2006 - 10:49:43 CDT)
  • Running NAMD on debug mode (Wed Aug 09 2006 - 09:46:06 CDT)
  • Re: Possible bug on NAMD 2.6B1? (Tue Jul 25 2006 - 09:39:02 CDT)
  • Re: Compiling NAMD on AMD64 dual core (Mon Jul 10 2006 - 10:57:59 CDT)
  • Compiling NAMD on AMD64 dual core (Tue Jul 04 2006 - 10:46:58 CDT)
  • Simulation Hangs during minimization (Mon Jul 03 2006 - 15:20:38 CDT)
  • Heating Up a system. (Thu Jun 29 2006 - 16:06:21 CDT)
  • Re: Generating lipid bilayer model (Mon Mar 27 2006 - 13:23:06 CST)
  • Gigabit ethernet switch for cluster (Tue Mar 21 2006 - 14:43:45 CST)
  • Building cluster (Sat Mar 18 2006 - 12:54:38 CST)
• Cesar Millan
  • Re: vmd-l: rmsd matrix (Thu Sep 03 2009 - 11:23:20 CDT)
  • Re: collective variables (Wed Jun 17 2009 - 15:29:02 CDT)
• 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)
• cgji
  • Question on SMD simulation in spheric water . (Fri Nov 09 2007 - 02:46:03 CST)
  • (no subject) (Fri Nov 09 2007 - 02:43:27 CST)
• Chaloin Laurent
  • Tcl force (Wed Oct 07 2009 - 05:22:01 CDT)
• Chandra Ramananjara
  • Inconsistencies in NAMD simulations (Tue Jan 22 2008 - 02:49:53 CST)
  • namdenergy plugin (Sun Jul 09 2006 - 23:47:10 CDT)
  • Question about Van der Waals radii (Mon Jun 26 2006 - 09:14:10 CDT)
  • Re: vmd-l: error using Namdenergy (Wed Jun 21 2006 - 21:17:13 CDT)
  • error using Namdenergy (Wed Jun 21 2006 - 15:04:19 CDT)
  • NAMD support for MNDO semi-empirical model (Mon May 15 2006 - 10:34:07 CDT)
  • Tcl scripting within NAMD configuration file (Fri Mar 24 2006 - 09:26:18 CST)
  • TCL scripting within NAMD Configuration File (Thu Mar 23 2006 - 09:12:56 CST)
  • Re: vmd-l: Problem with VMD 'animate' command (Mon Feb 13 2006 - 01:37:31 CST)
  • Problem with VMD 'animate' command (Sun Feb 12 2006 - 10:12:36 CST)
• chandran karunakaran
  • GROMACS to CHARMM (Mon Nov 29 2004 - 11:14:48 CST)
• Chang, Christopher
  • Re: Fe-S cluster topology parameters (Wed Aug 27 2008 - 11:51:45 CDT)
  • RE: implicit solvent energy calculation (Tue Feb 26 2008 - 13:51:26 CST)
  • RE: PSFGEN Warnings about H positions on standard amino acids (Mon Feb 18 2008 - 18:17:48 CST)
  • RE: PCA calculation (Thu Feb 14 2008 - 13:31:03 CST)
  • RE: PCA calculation (Thu Feb 14 2008 - 12:58:55 CST)
  • re: Scripting: Handle for energy terms in the PSF file? (Thu Dec 13 2007 - 13:39:18 CST)
  • RE: Scripting: Handle for energy terms in the PSF file? (Wed Dec 12 2007 - 15:32:56 CST)
  • re: Scripting: Handle for energy terms in the PSF file? (Tue Dec 11 2007 - 19:19:02 CST)
  • Scripting: Handle for energy terms in the PSF file? (Mon Dec 10 2007 - 21:18:24 CST)
  • RE: Bizarre atom behavior (Thu Apr 06 2006 - 16:40:04 CDT)
  • Bizarre atom behavior (Wed Apr 05 2006 - 11:35:54 CDT)
  • Dihedral parameters for multiple minima (Wed Mar 15 2006 - 19:34:22 CST)
  • 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)
• Chao Mei
  • Re: .inter.bin files? (Thu Apr 02 2009 - 13:05:11 CDT)
• char_at_ks.uiuc.edu
  • Fw: What is an IC table in the .inp files (Thu Nov 15 2007 - 21:10:29 CST)
• Charles Danko
  • Re: How to make a disulphide bond (Tue May 16 2006 - 13:47:37 CDT)
  • 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)
• Charles Taylor
  • Re: Make NAMD2.7b1 with cuda bug? (Wed May 13 2009 - 09:29:27 CDT)
  • 2.7b1 + CUDA + STMV (Tue Apr 21 2009 - 09:25:44 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)
  • simulated annealing script (Thu Sep 25 2003 - 13:15:10 CDT)
  • Re: Re: seg fault and namdplot problem (Mon Sep 22 2003 - 18:58:30 CDT)
  • Re: seg fault and namdplot problem (Mon Sep 22 2003 - 16:22:46 CDT)
  • segmentation fault (Tue Sep 16 2003 - 14:12:43 CDT)
• Cheri McFerrin
  • NAMD question (Sat May 19 2007 - 08:11:57 CDT)
• Chi-Cheng Chiu
  • TclBC - multiple iteration (Wed Nov 19 2008 - 12:15:48 CST)
  • Re: TCL force (Wed Sep 24 2008 - 10:42:10 CDT)
  • Re: TCL force (Wed Sep 24 2008 - 10:36:34 CDT)
  • Re: NAMD crashed with TclForce turned on (Wed Aug 13 2008 - 10:33:36 CDT)
  • Re: NAMD crashed with TclForce turned on (Thu Aug 07 2008 - 11:17:16 CDT)
  • NAMD crashed with TclForce turned on (Wed Aug 06 2008 - 16:10:01 CDT)
  • Tcl in NAMD (math::interpolate) (Wed May 16 2007 - 13:03:03 CDT)
• Chin_Wei
  • Question for 2D periodic boundary condition (Mon Sep 17 2007 - 09:18:13 CDT)
• CHINDEA Vlad
  • FW: simulation configuration file not accesible - other reasons (Fri Nov 20 2009 - 17:57:29 CST)
  • simulation configuration file not accesible - other reasons (Thu Nov 19 2009 - 16:46:23 CST)
  • FW: issues with AutoPSF for a cyclodextrin - addendum (Fri Oct 30 2009 - 18:30:51 CDT)
  • RE: issues with AutoPSF for a cyclodextrin (Fri Oct 30 2009 - 17:02:48 CDT)
  • issues with AutoPSF for a cyclodextrin (Thu Oct 29 2009 - 18:32:50 CDT)
  • solution for generating IC (Sat Feb 21 2009 - 17:20:11 CST)
  • RE: Autopsf error with a modified top file (Sat Feb 21 2009 - 06:04:19 CST)
  • RE: Autopsf error with a modified top file (Fri Feb 20 2009 - 19:28:28 CST)
  • RE: Autopsf error with a modified top file (Thu Feb 19 2009 - 18:15:45 CST)
  • Autopsf error with a modified top file (Wed Feb 18 2009 - 15:17:52 CST)
  • Re: some recommendations for parametrizing new molecules requiredþ (Fri Jan 23 2009 - 16:30:16 CST)
  • some recommendations for parametrizing new molecules required (Fri Jan 23 2009 - 03:31:04 CST)
  • RE: syntax error in expression "(": premature end of expression - namdstats (Sat Jan 17 2009 - 16:18:33 CST)
  • syntax error in expression "(": premature end of expression - namdstats (Fri Jan 16 2009 - 17:08:54 CST)
  • RE: problem in fitting Maxwell-Boltzmann distribution (Fri Jan 16 2009 - 13:30:26 CST)
  • RE: problem in fitting Maxwell-Boltzmann distribution (Thu Jan 15 2009 - 06:39:47 CST)
  • problem in fitting Maxwell-Boltzmann distribution (Wed Jan 14 2009 - 17:08:48 CST)
  • RE: angle deformation (Fri Dec 19 2008 - 18:02:06 CST)
  • angle deformation (Wed Dec 17 2008 - 17:00:49 CST)
  • (no subject) (Thu Dec 11 2008 - 06:12:05 CST)
  • FW: Multiplicity of parameters for improper bonds .............. of 1 exceeded. (Thu Dec 11 2008 - 06:17:20 CST)
  • bond length in terminal patches (Sat Nov 22 2008 - 16:29:55 CST)
  • impropers for aromatic residues (Sat Nov 08 2008 - 15:17:44 CST)
  • Charm++ Fatal error ! Periodic cell has become too small for original patch grid! (Thu Nov 06 2008 - 17:40:35 CST)
  • PSF of Tryptophane methyl ester (Sat Oct 11 2008 - 11:43:43 CDT)
  • (no subject) (Sun Oct 05 2008 - 15:27:31 CDT)
  • psf generation for a small non-peptide molecule - again (Wed Oct 01 2008 - 16:38:27 CDT)
  • FW: psf generation for a small non-peptide molecule - again (Mon Sep 29 2008 - 17:21:16 CDT)
  • psf generation for a small non-peptide molecule (Thu Sep 25 2008 - 16:18:40 CDT)
• Ching Wong
  • running 2 jobs simutaneously? (Mon Oct 23 2006 - 21:14:41 CDT)
  • bulid psf for structure already with hydrogens (Wed Jul 19 2006 - 14:02:32 CDT)
  • any SD minimization in NAMD? (Thu Jul 13 2006 - 14:59:57 CDT)
  • many short runs or one long run? (Mon Jul 10 2006 - 15:04:42 CDT)
  • Protonation state (Mon Jul 10 2006 - 14:49:57 CDT)
  • Protonation states (Fri Jun 30 2006 - 19:04:32 CDT)
  • support TIP5? doubt on high temperature MD (Mon Jun 19 2006 - 20:31:52 CDT)
  • extended system or Basis Vector (Mon Jun 19 2006 - 20:29:01 CDT)
  • Tpr (Tue Apr 04 2006 - 10:55:33 CDT)
  • Use extendedSystem or cellBasisVector? (Wed Mar 22 2006 - 16:45:45 CST)
  • 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)
• Chongbo Sun
  • can the harmonic constraint parameters be changed between run or minimize? (Sun Nov 23 2008 - 14:03:39 CST)
• Chris Chipot
  • Re: Restarting ABF (Thu Aug 13 2009 - 11:32:13 CDT)
  • Re: ABF question (free energy partition) (Sun Aug 09 2009 - 12:32:54 CDT)
  • Re: ABF tutorial (Mon Jul 20 2009 - 09:09:57 CDT)
  • Re: namd 2.7b: measure free energy difference "growing" a force constant (Sat Jun 20 2009 - 10:07:16 CDT)
  • Re: collective variable space PMF, including biasing potential terms? (Wed May 13 2009 - 18:16:54 CDT)
  • Re: collective variable space PMF, including biasing potential terms? (Wed May 13 2009 - 17:37:04 CDT)
  • Re: alchemify with CMAP? (Thu Apr 16 2009 - 19:21:19 CDT)
  • Re: FEP/binding free energy difference WT vs Mut (Sun Feb 15 2009 - 20:03:27 CST)
  • Re: combining abf reaction path (Sat Jan 31 2009 - 13:03:29 CST)
  • Stratification schemes (Sat Jan 24 2009 - 16:28:37 CST)
  • Re: double-wide sampling with soft-core (Thu Jan 22 2009 - 12:23:55 CST)
  • Re: abf convergence problems (Thu Jan 22 2009 - 11:54:08 CST)
  • Re: double-wide sampling with soft-core (Wed Jan 21 2009 - 17:32:52 CST)
  • Re: FEP simulations? (Mon Jan 05 2009 - 05:24:00 CST)
  • Re: alchemical FEP question (Sun Dec 21 2008 - 13:27:57 CST)
  • Re: FEP: How check equilibration sufficiency? calculate dG? (Tue Oct 14 2008 - 04:12:43 CDT)
  • Re: ABF simulations (Tue Jul 29 2008 - 09:55:41 CDT)
  • Re: Dihedral scan in NAMD? (Mon Jun 23 2008 - 15:21:57 CDT)
  • Re: ABF:reversibility and number of samples (Fri May 23 2008 - 10:43:59 CDT)
  • Re: question on ABF (Mon Apr 21 2008 - 07:01:39 CDT)
  • Re: ABF error calculation (Fri Feb 29 2008 - 16:26:00 CST)
  • Re: Soft core potential - tested or not? (Tue Feb 26 2008 - 15:24:57 CST)
  • Re: Alchemical FEP NAMD tutorial - problems with reproducing the results (Thu Feb 21 2008 - 03:19:42 CST)
  • Re: Alchemical FEP NAMD tutorial - problems with reproducing the results (Tue Feb 19 2008 - 07:14:13 CST)
  • Re: Convergence of ABF calculation: n_samples (Wed Dec 05 2007 - 09:53:39 CST)
  • Re: ABF fullsamples (Mon Dec 03 2007 - 15:47:06 CST)
  • Re: ABF Output File (Sun Dec 02 2007 - 13:22:03 CST)
  • Re: ABF calculations (Wed Nov 21 2007 - 18:37:32 CST)
  • Re: ABF : dihedral-com.tcl (Wed Nov 21 2007 - 10:36:37 CST)
  • Re: ABF calculations (Mon Nov 19 2007 - 16:30:42 CST)
  • Re: Free energy perturbation of a double mutant (Tue Nov 06 2007 - 17:03:51 CST)
  • Re: length of an ABF simulation (Sat Nov 03 2007 - 10:44:25 CDT)
  • Re: apply force along an internally defined direction (Mon Oct 29 2007 - 13:22:52 CDT)
  • Re: Problems with Mutator1.1, mutations and FEP (Tue Oct 02 2007 - 14:42:38 CDT)
  • Re: Problems with Mutator1.1, mutations and FEP (Mon Oct 01 2007 - 13:57:58 CDT)
  • Re: ABF question (Wed Sep 19 2007 - 08:17:12 CDT)
  • Re: ABF restrain (Thu Jul 05 2007 - 13:05:30 CDT)
  • Re: ABF restrain (Wed Jul 04 2007 - 17:17:41 CDT)
  • Re: Fep questions about FepEquilSteps (Wed Apr 25 2007 - 16:25:11 CDT)
  • Re: abf output (Fri Apr 20 2007 - 17:08:47 CDT)
  • Re: question on free energy pert. (Wed Nov 22 2006 - 14:05:58 CST)
  • Re: ABF - zCoord for more than one monomer (Mon Nov 13 2006 - 07:47:30 CST)
  • Re: ABF on a single molecule (Mon Nov 06 2006 - 15:19:17 CST)
  • Re: ABF on a single molecule (Sun Nov 05 2006 - 03:26:53 CST)
  • Re: error estimate in FEP calculation (Sun Oct 29 2006 - 09:51:43 CST)
  • Re: question about total charge change in FEP calculation (Fri Jun 09 2006 - 02:05:46 CDT)
  • Re: question about total charge change in FEP calculation (Thu Jun 08 2006 - 14:47:27 CDT)
  • Re: FEP error "atoms moving too fast" (Sun Jun 04 2006 - 16:01:23 CDT)
  • Re: questions regrading ABF (Tue May 30 2006 - 01:04:28 CDT)
  • Re: questions regrading ABF (Mon May 29 2006 - 16:50:46 CDT)
  • Re: How to deal with a long path in ABF simulation? (Wed Apr 26 2006 - 15:01:10 CDT)
  • Re: FEP, IONS, DUMMY atoms, LARGE numbers (Tue Apr 18 2006 - 08:57:03 CDT)
  • Re: question about total charge change in FEP calculation (Sun Mar 05 2006 - 05:04:43 CST)
  • Re: how to make dual-hybrid topology? (Mon Feb 13 2006 - 08:31:45 CST)
  • 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 Harrison
  • Re: Minimization issue. (Tue Aug 18 2009 - 10:51:20 CDT)
  • Re: restating simuation and periodic cell conditions (Tue Aug 18 2009 - 07:08:07 CDT)
  • Re: FATAL ERROR: Tried to find atom type on node other than node 0 (Mon Aug 17 2009 - 09:44:35 CDT)
  • Re: Minimization issue. (Mon Aug 17 2009 - 10:43:24 CDT)
  • Re: Kanamycin topology (Mon Aug 17 2009 - 09:53:25 CDT)
  • Re: increase the temperature step by step after minimization (Mon Aug 10 2009 - 05:01:08 CDT)
  • Re: SMD output : which col represents force, second or last (Wed Aug 05 2009 - 12:27:08 CDT)
  • Re: Simulating molecules in bulk water & VMD installation problems (Wed Aug 05 2009 - 08:53:01 CDT)
  • Re: Steered Molecular Dynamics (Wed Aug 05 2009 - 08:46:52 CDT)
  • Re: frozen water Oxygens (Wed Aug 05 2009 - 09:01:24 CDT)
  • Re: how to generate DNA psf files? (Wed Aug 05 2009 - 09:10:25 CDT)
  • Re: Re: THERMODYNAMIC INTEGRATION ON in namd 2.7b1 compiled 24.07 when TCL forces active (Wed Jul 29 2009 - 05:45:08 CDT)
  • Re: FEP implementation in NAMD 2.6 vs. 2.7b1 (Wed Jul 29 2009 - 06:11:33 CDT)
  • Re: NAMD documentation regarding compiling (Thu Jul 23 2009 - 16:56:28 CDT)
  • Re: how to run namd2.7b1 on multiple nodes (Thu Jul 23 2009 - 18:16:08 CDT)
  • Re: PMEGridSize (Thu Jul 23 2009 - 16:52:06 CDT)
  • Re: Reassign Temp during the Production Run (Thu Jul 16 2009 - 13:04:03 CDT)
  • Re: Grid Forces documentation (Thu Jul 16 2009 - 12:24:00 CDT)
  • Re: Reassign Temp during the Production Run (Thu Jul 16 2009 - 12:17:02 CDT)
  • Re: Bad global exclusion count (Mon Jul 13 2009 - 09:54:50 CDT)
  • Fwd: one atom off in the minimization result (Sun Jul 12 2009 - 18:23:10 CDT)
  • Fwd: Minimization problem of a protein-DNA complex with namd (Sun Jul 12 2009 - 18:23:40 CDT)
  • Fwd: 99999999.9999 as vander waals energy (Sat Jul 11 2009 - 19:38:30 CDT)
  • Re: pdbalias for PO4 residue (Sat Jul 11 2009 - 19:37:53 CDT)
  • Re: Generation of .psf file of DNA (Thu Jul 09 2009 - 09:42:10 CDT)
  • Fwd: Tried to find atom type on node other than node 0 (Thu Jul 09 2009 - 09:45:23 CDT)
  • Re: Fatal Error Help (Thu Jul 09 2009 - 09:49:25 CDT)
  • Re: FATAL ERROR: Sorry, combined TI and FEP is not implemented (Wed Jul 08 2009 - 09:58:51 CDT)
  • Re: Grid Forces (Sat Jun 27 2009 - 09:53:55 CDT)
  • Re: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR NH3 HC NH3 (Sun Jun 21 2009 - 19:11:54 CDT)
  • Re: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR NH3 HC NH3 (Sat Jun 20 2009 - 13:35:08 CDT)
  • Re: namd 2.7b: measure free energy difference "growing" a force constant (Sat Jun 20 2009 - 14:01:30 CDT)
  • Re: soft-core FEP in namd 2.7b (Fri May 08 2009 - 16:14:44 CDT)
  • Re: running namd2.7 problem (Thu May 07 2009 - 07:16:44 CDT)
  • Re: dummy atom mass changed (Wed May 06 2009 - 13:09:26 CDT)
  • Re: dummy atom mass changed (Tue May 05 2009 - 12:53:00 CDT)
  • Re: dummy atom mass changed (Mon May 04 2009 - 22:24:32 CDT)
  • Re: dummy atom mass changed (Mon May 04 2009 - 15:33:57 CDT)
  • Re: crash with more than 96 processors (v2.7b1) (Thu Apr 30 2009 - 19:41:55 CDT)
  • Re: FEP tutorial graph question (Thu Apr 30 2009 - 10:23:25 CDT)
  • Re: Benzene PSF (Wed Apr 29 2009 - 19:29:25 CDT)
  • Re: FEP tutorial graph question (Wed Apr 29 2009 - 16:17:07 CDT)
  • Re: crash with more than 96 processors (v2.7b1) (Tue Apr 28 2009 - 18:30:16 CDT)
  • Re: crash with more than 96 processors (v2.7b1) (Tue Apr 28 2009 - 16:50:57 CDT)
  • Re: System expands: CCL4 simulation; NPT(Langevin Piston) (Tue Apr 28 2009 - 16:56:35 CDT)
  • Re: Namd and MM-PBSA (Thu Apr 23 2009 - 12:22:34 CDT)
  • Re: I can't keep my pulling directions the same with the SMD vector (Sun Apr 19 2009 - 18:27:24 CDT)
  • Re: I can't keep my pulling directions the same with the SMD vector (Sun Apr 19 2009 - 10:25:14 CDT)
  • Re: Error : DIDN'T FIND vdW PARAMETER FOR ATOM TYPE C11 (Sat Apr 11 2009 - 10:20:44 CDT)
  • Re: Keyword to start FEP calculation in NAMD 2.7b1 (Fri Apr 10 2009 - 15:41:05 CDT)
  • Re: Jarzynski equality and the pull direction in SMD (Sun Apr 05 2009 - 03:09:54 CDT)
  • Re: regarding implicit solvent models (Sun Apr 05 2009 - 02:57:40 CDT)
  • Re: Pulling atoms in different directions (Sun Mar 29 2009 - 19:05:33 CDT)
  • Re: use of tiElecLambdaStart (NAMD 2.7b1) (Fri Mar 27 2009 - 17:28:22 CDT)
  • Re: use of tiElecLambdaStart (NAMD 2.7b1) (Fri Mar 27 2009 - 15:45:41 CDT)
  • Re: use of tiElecLambdaStart (NAMD 2.7b1) (Fri Mar 27 2009 - 14:33:04 CDT)
  • Re: Free energy of conformational change (Wed Mar 25 2009 - 17:51:17 CDT)
  • Re: alchemical fep amber topology (Sat Mar 14 2009 - 08:47:49 CDT)
  • Re: alchemical fep amber topology (Sat Mar 14 2009 - 08:33:48 CDT)
  • Re: Reference file for the constraining force in Umbrella Sampling (Sat Mar 14 2009 - 08:19:54 CDT)
  • Re: FEP with fixed explicit environment? (Thu Mar 12 2009 - 22:05:24 CDT)
  • Re: FEP restart? (Thu Mar 12 2009 - 07:14:23 CDT)
  • Re: FEP restart? (Wed Mar 11 2009 - 19:53:09 CDT)
  • Re: Selectively turning off electrostatic interactions (Wed Mar 11 2009 - 18:00:21 CDT)
  • Re: FATAL ERROR: Duplicate bond (Wed Mar 11 2009 - 17:48:13 CDT)
  • Re: Selectively turning off electrostatic interactions (Wed Mar 11 2009 - 15:28:46 CDT)
  • Re: Minimization convergence issue (Thu Mar 05 2009 - 17:05:51 CST)
  • Re: Minimization convergence issue (Wed Mar 04 2009 - 19:41:06 CST)
  • Re: regarding topology file generation (Wed Mar 04 2009 - 11:25:53 CST)
  • Re: help running NAMD energy at multiple stable temperatures (newbie) (Wed Mar 04 2009 - 11:12:52 CST)
  • Re: ligand flies away from binding pocket (Fri Feb 13 2009 - 18:07:44 CST)
  • Re: FEP/binding free energy difference WT vs Mut (Fri Feb 13 2009 - 17:57:21 CST)
  • Re: Accessing atoms and velocities during NVE run (Fri Feb 06 2009 - 15:00:36 CST)
  • Re: Accessing atoms and velocities during NVE run (Fri Feb 06 2009 - 12:06:58 CST)
  • Re: Fatal error in configuration file (Thu Feb 05 2009 - 23:51:39 CST)
  • Re: Fatal error in configuration file (Thu Feb 05 2009 - 20:27:23 CST)
  • Re: Aligning the distance between two centroids with an axis (Fri Jan 30 2009 - 21:31:43 CST)
  • Re: pdb and rmsd (Fri Jan 30 2009 - 21:21:54 CST)
  • Re: CUDA version status (Sat Jan 24 2009 - 16:36:34 CST)
  • Re: SMD output (Thu Jan 22 2009 - 11:36:35 CST)
  • Re: double-wide sampling with soft-core (Thu Jan 22 2009 - 11:48:23 CST)
  • Re: I: Running Charm++ over MPI does not work (Thu Jan 22 2009 - 10:53:50 CST)
  • Re: double-wide sampling with soft-core (Thu Jan 22 2009 - 11:21:15 CST)
  • Re: Question on mutator in VMD (Wed Jan 14 2009 - 23:15:20 CST)
  • Re: Inorganic compounds (Wed Jan 14 2009 - 23:25:19 CST)
  • Re: error during heating of the minimized system: (please reply!) (Wed Jan 14 2009 - 23:11:31 CST)
  • Re: Re: namdcvs (Tue Jan 06 2009 - 08:41:21 CST)
  • Re: gpu pressure control (Sun Jan 04 2009 - 12:23:48 CST)
  • Re: namdcvs Re: how to apply restraints for phi and psi for alpha helix regions (Sun Jan 04 2009 - 12:28:23 CST)
  • Re: How to get over with the error "Atoms moving too fast; simulation has become unstable and Exiting prematurely (Sun Jan 04 2009 - 12:03:37 CST)
  • Re: base stacking analysis of the trajectory of a nucleic acids simulation (Sun Jan 04 2009 - 12:12:07 CST)
  • Re: Constant z axis (Sat Oct 11 2008 - 17:13:54 CDT)
  • Re: charmrun socket error (Sat Oct 11 2008 - 17:02:49 CDT)
  • Re: Constant z axis (Sat Oct 11 2008 - 22:59:31 CDT)
  • Re: Query Regarding FEP tutorial: NPT or NVT? (Sat Oct 11 2008 - 18:05:52 CDT)
  • Re: PMEGridSize (Sat Oct 11 2008 - 16:52:03 CDT)
  • Re: PMEGridSize (Fri Oct 10 2008 - 00:37:59 CDT)
  • Re: embedding protein in membrane (Fri Oct 10 2008 - 00:49:44 CDT)
  • Re: firsttimestep question (Mon Oct 06 2008 - 07:32:25 CDT)
  • Re: minimization (Fri Sep 26 2008 - 07:19:21 CDT)
  • Re: nvidia and namd (Fri Aug 29 2008 - 12:07:53 CDT)
  • Re: change in box geometry for simulation of pure water (Wed Aug 27 2008 - 21:23:22 CDT)
  • Re: memory overflow problem of Tcl scripting when dealing with trajectories (Sun Jul 20 2008 - 15:21:16 CDT)
  • Re: Avoiding alpha-helix distortions (Sun Jul 06 2008 - 07:52:41 CDT)
  • Re: Rise in Total Energy in NVE (Wed Jul 09 2008 - 20:46:53 CDT)
  • Re: Maximum Velocities (Tue Jul 08 2008 - 15:33:19 CDT)
  • Re: NAMD 2.7? (Mon Jun 30 2008 - 12:54:29 CDT)
  • Re: What is an IC table in the .inp files (Thu Nov 15 2007 - 20:53:43 CST)
• 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)
• Chris Share
  • Re: Building NAMD for Opteron Cluster with ICC (Sat Mar 07 2009 - 21:02:39 CST)
  • Building NAMD for Opteron Cluster with ICC (Fri Mar 06 2009 - 21:53:02 CST)
• Christian Blouin
  • residue_rmsd.tcl question (Fri Nov 02 2007 - 08:12:51 CDT)
  • RE: Vanishing bonds in small molecule during psf generation. (Wed Jul 18 2007 - 14:13:33 CDT)
  • Vanishing bonds in small molecule during psf generation. (Wed Jul 18 2007 - 08:58:13 CDT)
• Christine Horejs
  • abf output (Fri Apr 20 2007 - 07:19:12 CDT)
  • PMF (Fri Apr 20 2007 - 03:59:11 CDT)
  • pmf calculation (Tue Apr 17 2007 - 08:20:41 CDT)
  • 2 proteins (Tue Apr 17 2007 - 04:59:11 CDT)
• Christine Horejs DI
  • autopsf and hydrogen-sites (Wed Oct 01 2008 - 04:09:44 CDT)
  • psf file (Mon Jun 23 2008 - 06:22:48 CDT)
  • 2 pdb files (Fri May 09 2008 - 06:58:01 CDT)
  • Re: add calcium chloride (Wed Apr 16 2008 - 08:22:28 CDT)
  • Re: add calcium chloride (Wed Apr 16 2008 - 07:30:41 CDT)
  • add calcium chloride (Mon Apr 07 2008 - 03:21:59 CDT)
• Christophe Chipot
  • Re: dummy atoms and FEP (Thu Apr 06 2006 - 12:19:06 CDT)
• Christophe Combet [PBIL/IBCP/CNRS]
  • Re: linux cluster problems (Mon Jul 17 2006 - 05:38:04 CDT)
  • Re: NAMD Linux LAM/MPI 7.1 execution error (Thu Mar 09 2006 - 05:26:24 CST)
  • NAMD Linux LAM/MPI 7.1 execution error (Tue Mar 07 2006 - 07:45:35 CST)
• Christophe.Chipot_at_edam.uhp-nancy.fr
  • Re: alchemical FEP question (Sat Dec 20 2008 - 05:23:16 CST)
  • Re: topology/parameter entries for methane? (Sat Dec 20 2008 - 05:15:12 CST)
  • Re: FullSamples variable in ABF (Wed May 23 2007 - 02:04:37 CDT)
• Christopher Calderon
  • Re: Tcl "loadtotalforces" question (forces never seem to be saved) (Sun Feb 17 2008 - 14:52:23 CST)
  • Re: Tcl "loadtotalforces" question (forces never seem to be saved) (Sun Feb 17 2008 - 13:06:31 CST)
  • Tcl "loadtotalforces" question (forces never seem to be saved) (Sun Feb 17 2008 - 11:51:23 CST)
  • SMD temperature scaling (Wed Mar 22 2006 - 17:09:44 CST)
• Christopher Gillespie
  • Re: Minimization convergence issue (Thu Mar 05 2009 - 12:04:02 CST)
  • Re: some recommendations for parametrizing new molecules required (Fri Jan 23 2009 - 09:37:17 CST)
  • Re: some recommendations for parametrizing new molecules required (Fri Jan 23 2009 - 07:36:30 CST)
  • Re: Equilibration simulation too slow. (Sun Dec 07 2008 - 10:43:17 CST)
  • Re: Problems with minimization (Sat Nov 15 2008 - 12:10:46 CST)
  • Re: Problems with minimization (Sat Nov 15 2008 - 11:38:26 CST)
  • Re: Add ions (Wed Nov 05 2008 - 07:06:51 CST)
  • Re: combining 2 dcd files into one (Thu Oct 30 2008 - 16:26:34 CDT)
  • Re: ions behavior in protein-water box: (Thu Oct 30 2008 - 13:50:38 CDT)
  • Re: ions behavior in protein-water box: (Wed Oct 29 2008 - 17:12:23 CDT)
  • Re: ions behavior in protein-water box: (Wed Oct 29 2008 - 15:05:19 CDT)
  • Re: minimization (Thu Sep 25 2008 - 21:42:22 CDT)
  • Re: Compile NAMD on Bluegene (Mon Sep 22 2008 - 16:54:48 CDT)
  • Re: trifluoroethanol (TFE) solvent (Tue Sep 09 2008 - 20:39:27 CDT)
  • Re: Struggling with the compilation of NAMD 2.6 on a PBS Cluster with LAM/MPI (Wed Aug 27 2008 - 12:49:31 CDT)
  • Re: Electrostatics cutoff with PME (Tue Apr 15 2008 - 15:21:06 CDT)
  • Re: problems-periodic cell (Tue Jan 01 2008 - 12:23:25 CST)
  • Re: Segmentation violation when running without an internet connection (Thu Dec 20 2007 - 13:53:30 CST)
  • Protein hydrogens causing "Atoms too fast" error (Mon Dec 03 2007 - 18:03:59 CST)
• Christopher Harrison
  • Re: Converting a PSF file from one forcefield top another (Sat Oct 13 2007 - 14:55:34 CDT)
  • Re: Converting a PSF file from one forcefield top another (Sat Oct 13 2007 - 14:43:35 CDT)
  • Re: vmd-l: Small molecules (Fri Oct 12 2007 - 23:41:23 CDT)
  • Re: Determining Transition State from an Unfolding Simulation (Thu Sep 27 2007 - 15:43:54 CDT)
  • Re: Determining Transition State from an Unfolding Simulation (Thu Sep 27 2007 - 11:45:16 CDT)
  • Re: About QM-MM (Thu Aug 30 2007 - 08:30:05 CDT)
  • Re: About QM-MM (Tue Aug 28 2007 - 12:42:51 CDT)
• Christopher Hartshorn
  • FEP on 2.7b1 (Mon May 11 2009 - 15:38:37 CDT)
  • SiCortex with Pathscale (Sat May 09 2009 - 19:52:29 CDT)
  • Re: FEP tutorial graph question (Fri May 01 2009 - 12:05:21 CDT)
  • Re: FEP tutorial graph question (Wed Apr 29 2009 - 19:52:28 CDT)
  • FEP tutorial graph question (Wed Apr 29 2009 - 15:35:27 CDT)
  • Re: FEP restart? (Thu Mar 12 2009 - 00:35:02 CDT)
  • FEP restart? (Wed Mar 11 2009 - 19:34:59 CDT)
  • PME and fixed atoms questions (Mon Mar 09 2009 - 13:31:52 CDT)
  • Re: vmd-l: Membrane builder ?'s (Tue Feb 24 2009 - 00:47:57 CST)
  • FEP anomaly? (Mon Feb 23 2009 - 12:53:15 CST)
  • FEP on NAMD2.6 versus latest CVS NAMD build (Fri Jan 30 2009 - 00:54:54 CST)
  • Problems deciphering fepout (Fri Jan 16 2009 - 16:28:21 CST)
  • Re: FEP simulations? (Mon Jan 05 2009 - 03:20:53 CST)
  • TCL8.5? or (Sun Dec 07 2008 - 23:16:42 CST)
  • Re: MacOSX 64bit binaries (Fri Dec 05 2008 - 11:55:02 CST)
  • MacOSX 64bit binaries (Wed Dec 03 2008 - 01:34:26 CST)
  • Re: Compiling 8Core macs (Tue Nov 25 2008 - 15:28:51 CST)
  • Compiling 8Core macs (Mon Nov 24 2008 - 17:03:40 CST)
  • FEP simulations? (Tue Nov 18 2008 - 13:19:13 CST)
  • Re: restart (Tue Nov 18 2008 - 01:49:32 CST)
  • FEP calculation of dimerization (Sun Nov 16 2008 - 23:45:05 CST)
  • fixedAtoms may not be enabled in a script (Tue Oct 21 2008 - 10:54:17 CDT)
• Christopher Rowley
  • Harmonic dihedral restraints (Mon May 07 2007 - 16:57:08 CDT)
• Christopher Share
  • Problems with CUDA Build (Sun Dec 21 2008 - 23:58:47 CST)
  • Access to CVS (Tue Dec 16 2008 - 19:08:53 CST)
• claudia
  • Interrupted system call (Thu Oct 18 2007 - 08:25:22 CDT)
• Claudio Redaelli
  • Re: Re: Installing NAMD 2.6 on SMP machine... charm++ install errors (Fri Jul 06 2007 - 04:14:39 CDT)
• Claw Isthelaw
  • RE: dcd to pdb conversion (Mon Oct 27 2008 - 04:35:26 CDT)
  • Re: NAMD 2.7 (Tue Jul 08 2008 - 00:30:52 CDT)
  • Cannot spot error in namd config file (Thu Jun 26 2008 - 10:41:53 CDT)
• CMM QM/MM Workshop
  • CFP: 3rd Annual CMM Workshop on QM/MM Simulations (Mon May 19 2008 - 13:43:55 CDT)
• Cojocaru,Vlad
  • RE: glibc detected : corrupted double-linked list: 0xa4657ad8 (Tue Aug 18 2009 - 15:52:59 CDT)
  • RE: namd27: tclforces activate TI calculation by default (Sat Aug 08 2009 - 17:53:16 CDT)
  • RE: NAMD crashed with TclForce turned on (Sun Aug 10 2008 - 11:32:57 CDT)
  • RE: NAMD crashed with TclForce turned on (Thu Aug 07 2008 - 14:48:11 CDT)
  • RE: NAMD crashed with TclForce turned on (Thu Aug 07 2008 - 14:43:02 CDT)
• Cole Cox
  • Classic timepieces replicas (Mon Jun 09 2008 - 19:10:25 CDT)
• cong chen
  • About NAN error (Fri Sep 18 2009 - 01:35:51 CDT)
  • about limitdist (Mon May 18 2009 - 06:11:48 CDT)
  • q=D8=B8=B4=A3=BA=20Re:=20=20nodelist=20being=20ignore?= d during paralleling (Sun Apr 27 2008 - 21:50:34 CDT)
  • nodelist being ignored during paralleling (Sat Apr 26 2008 - 22:24:17 CDT)
  • Problems of mpi with namd 2.6 (Mon Dec 24 2007 - 00:53:25 CST)
  • different 1-4scaling values for different atom types? (Sun Dec 02 2007 - 23:51:11 CST)
  • About para file format (Sat Dec 01 2007 - 00:14:36 CST)
  • How to freeze some atoms (Tue Nov 20 2007 - 20:11:24 CST)
  • About RMSD (Tue Nov 20 2007 - 03:29:32 CST)
  • Does rmsd is the judge of system equilibrium in all conditions? (Mon Nov 19 2007 - 06:08:12 CST)
  • Accepted temperature and pressure oscillation (Wed Oct 31 2007 - 03:14:55 CDT)
• Corenflos, Steven Charles
  • How does NAMD count atoms in PDB files? (Thu Aug 21 2008 - 16:15:18 CDT)
  • compiling namd: cannot find -lmodulecommlib (Wed Apr 23 2008 - 14:42:18 CDT)
  • Which namd on amd64? (Tue Apr 15 2008 - 15:26:25 CDT)
  • TCL/NAMD: FATAL ERROR: error reading output from command: interrupted system call (Wed Mar 05 2008 - 15:03:47 CST)
• Corey Fugate
  • Topology files (Thu Feb 26 2009 - 16:08:38 CST)
  • Fatal error in configuration file (Wed Feb 04 2009 - 21:05:36 CST)
• Cosmin ROMAN
  • Re: Urey-Bradley term (Wed Nov 19 2003 - 04:05:27 CST)
  • Urey-Bradley term (Tue Nov 18 2003 - 08:34:18 CST)
  • Re: charmm param. for ADP (Mon Oct 27 2003 - 11:14:08 CST)
  • tert-butylthiol CHARMM params (Mon Oct 27 2003 - 05:46:47 CST)
• creston .
  • creation and equilibration of a monolayer (Fri Jun 20 2008 - 16:01:06 CDT)
• 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
  • Re: electric field and MISC energy (Tue Nov 14 2006 - 02:55:04 CST)
  • forward and backward pulling (Thu Oct 05 2006 - 10:59:10 CDT)
  • Re: Energy due to electric field (Tue Apr 04 2006 - 10:37:28 CDT)
  • LES with PME and neutralizing charges (Thu Mar 09 2006 - 11:48:41 CST)
  • temperature "coupling coefficient" in NAMD (Fri Nov 18 2005 - 11:09:13 CST)
• Cyril Falvo
  • Pressure fluctuations (Thu Apr 05 2007 - 14:30:13 CDT)
• d b
  • bonding in periodic boundary conditions (Tue Aug 11 2009 - 15:05:08 CDT)
  • combining segments (Mon Aug 10 2009 - 09:06:51 CDT)
• Dale Marinenko
  • Just can't seem to compile charm++ (Thu Aug 23 2007 - 17:01:53 CDT)
• dalton banks
  • solvate plugin with solvent other than water (Tue Aug 11 2009 - 15:02:13 CDT)
• 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 Bolintineanu
  • FEP implementation in NAMD 2.6 vs. 2.7b1 (Tue Jul 28 2009 - 16:50:37 CDT)
  • Re: Issue with rhombic dodecahedron / CHARMM compatibility (Mon Dec 04 2006 - 17:12:58 CST)
  • Issue with rhombic dodecahedron / CHARMM compatibility (Mon Dec 04 2006 - 17:03:21 CST)
• Dan Strahs
  • checkpoint software for NAMD? (Thu Sep 21 2006 - 15:37:47 CDT)
  • Win64 version (Wed Sep 06 2006 - 14:50:25 CDT)
  • Re: Rattle Error During Equilibration of Lipid Bilayer Membrane (Mon Feb 13 2006 - 11:30:35 CST)
  • Re: extra lines in PSF !!! (Fri Feb 10 2006 - 13:32:07 CST)
  • Re: unusual, periodic crash in Linux FC3/GM/MPI/CHARM/NAMD (Thu Feb 09 2006 - 20:09:02 CST)
  • Re: unusual, periodic crash in Linux FC3/GM/MPI/CHARM/NAMD (Thu Feb 09 2006 - 18:41:29 CST)
  • unusual, periodic crash in Linux FC3/GM/MPI/CHARM/NAMD (Thu Feb 09 2006 - 17:01:30 CST)
  • Re: updating TCL version for NAMD? (Mon Jan 09 2006 - 11:18:16 CST)
  • updating TCL version for NAMD? (Fri Jan 06 2006 - 17:42:35 CST)
  • Re: NAMD distribute (Thu Oct 13 2005 - 15:46:42 CDT)
  • NAMD distribute (Wed Oct 12 2005 - 20:28:49 CDT)
• Dan W.
  • restraint on a group of atoms at their center of mass? (Thu Oct 16 2008 - 14:16:19 CDT)
• Dan Willenbring
  • Re: Problems deciphering fepout (Sat Jan 17 2009 - 08:58:14 CST)
• daniel aguayo
  • Re: spontaneous system explosion after 2 ns of normal run (Thu Oct 15 2009 - 19:46:12 CDT)
  • Re: Changing the atomtype of a particle on the fly (Sun Oct 04 2009 - 18:59:00 CDT)
  • Re: truncated octahedral (Tue May 05 2009 - 10:16:12 CDT)
  • Re: dummy atom mass changed (Tue May 05 2009 - 10:18:39 CDT)
  • truncated octahedral (Mon May 04 2009 - 20:21:37 CDT)
  • Re: dummy atom mass changed (Mon May 04 2009 - 19:53:14 CDT)
• Daniel Keedy
  • *** topology file for AMP? *** (Tue Mar 06 2007 - 15:50:56 CST)
• Daniel Miscevski
  • gpu pressure control (Sun Dec 28 2008 - 23:10:46 CST)
• Daniel.G.Roberts_at_sanofi-aventis.com
  • Help Needed>Compiling source namd mpi enabled for a linux cluster (Wed Jul 25 2007 - 16:31:35 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)
• Dave Rogers
  • Re: Charm++ Fatal error ! Periodic cell has become too small for original patch grid! (Fri Nov 07 2008 - 12:23:52 CST)
  • Re: Quantitative Test for Equilibration of Data Time Series (Wed Oct 15 2008 - 13:27:23 CDT)
  • Re: DCD file format (Wed Oct 01 2008 - 14:17:10 CDT)
  • WCA Particle (Wed Jul 09 2008 - 21:45:48 CDT)
• Dave Venky
  • clustering conformations (Mon Nov 20 2006 - 12:42:58 CST)
• David A. Horita
  • ibverbs crash (Tue Nov 03 2009 - 14:17:17 CST)
  • smd output (v2.6) (Mon Oct 19 2009 - 12:04:05 CDT)
  • RE: Intel 11 compilers (Fri Jul 10 2009 - 13:37:54 CDT)
  • nose-hoover (Wed Jul 01 2009 - 10:36:30 CDT)
  • abf with colvars example (Thu Jun 04 2009 - 12:53:20 CDT)
  • generating xsc and vel files (Mon Feb 02 2009 - 10:29:29 CST)
  • tcl forces/membranes (Tue Dec 09 2008 - 15:28:07 CST)
  • charmrun socket error (Thu Oct 09 2008 - 13:49:21 CDT)
• David Brandon
  • Postdoctoral Position in Scientific Computing (Mon Jun 02 2008 - 15:08:45 CDT)
  • "Hands-On" Workshop on Computational Biophysics (Fri Mar 11 2005 - 15:23:27 CST)
• David Chalmers
  • NAMD CUDA on dual Nvidia 295 GPUs (Thu Jul 23 2009 - 07:20:34 CDT)
  • More NAMD/gm2 problems (Tue Mar 30 2004 - 23:58:20 CST)
  • Re: counterions (Tue Mar 30 2004 - 23:12:17 CST)
  • Problems compiling Charm++ for Myrinet (Mon Mar 29 2004 - 18:53:46 CST)
  • NAMD support for Myranet GM2 drivers (Thu Mar 18 2004 - 22:29:52 CST)
  • General and specific atom types in NAMD? (Thu Mar 04 2004 - 18:21:42 CST)
  • Converting Gromacs OPLS parameters to Charmm format (Mon Mar 01 2004 - 17:41:57 CST)
  • NAMD and Gromac OPLS parameters (Thu Feb 26 2004 - 21:46:12 CST)
  • NAMD for Opteron? (Sun Jan 04 2004 - 17:55:15 CST)
  • Free energy constraints and logfile (Mon Dec 01 2003 - 22:54:01 CST)
• David E. Konerding
  • Re: improving parallel on mac cluster (Tue Feb 10 2004 - 18:21:32 CST)
  • reading in large water boxes (PDB format)? (Sun Dec 07 2003 - 12:26:32 CST)
  • psfgen: pdb and nucleic acid (Wed Dec 03 2003 - 13:52:52 CST)
  • updating coordinates using IMD (Wed Nov 26 2003 - 14:09:10 CST)
• David Hardy
  • Re: TIP4P topology (Tue Nov 03 2009 - 15:32:33 CST)
  • Re: NAMD FFTW question? (Fri Aug 07 2009 - 12:47:30 CDT)
  • Re: Minimization problem of a protein-DNA complex with namd (Sun Jul 12 2009 - 19:38:21 CDT)
  • Re: NAMD2.6 - 1D Periodic Boundary and PME - FATAL ERROR: PME requires periodic boundary conditions. (Thu May 21 2009 - 15:55:42 CDT)
  • Re: water models and some questions (Thu May 07 2009 - 13:54:09 CDT)
  • Re: protein shifts out of the water box (Wed Apr 29 2009 - 23:51:25 CDT)
  • Re: Yet another NAMD speed concerns (Sat Apr 25 2009 - 12:28:46 CDT)
  • Re: Writing 3 subsequent timesteps to the DCD file (Wed Apr 08 2009 - 09:33:40 CDT)
  • Re: how to get 2 identical trajectories using NAMD in parallel (Fri Dec 12 2008 - 11:25:25 CST)
  • Re: storing velocity data of a NVE simulation (Thu Aug 21 2008 - 11:47:26 CDT)
  • Re: PME fails no matter what (Tue Jul 29 2008 - 12:39:04 CDT)
  • Re: Is there solution to numerical inaccuracy (Thu Nov 22 2007 - 07:35:01 CST)
  • Re: Is there solution to numerical inaccuracy (Wed Nov 21 2007 - 09:54:41 CST)
  • Re: Re: (Tue Oct 23 2007 - 18:09:50 CDT)
  • Re: Meaning of lines in "run" part of log file. (Wed Sep 26 2007 - 10:16:42 CDT)
  • Re: Switching Function (Thu Sep 20 2007 - 13:39:45 CDT)
  • Re: energy drift in NVE (Mon Aug 20 2007 - 22:12:54 CDT)
  • Re: energy drift in NVE (Mon Aug 20 2007 - 01:27:14 CDT)
  • Re: Code question: Partitioning the patch contents into water and non-water (Fri Aug 17 2007 - 10:24:18 CDT)
  • Re: Extended System Conservation (Wed Jul 18 2007 - 15:36:37 CDT)
  • Re: Velocity Units (Tue Jul 10 2007 - 23:48:28 CDT)
• David Jiang
  • Re: VMD/NAMD two identical molecules solvate in a water sphere (Tue Jun 23 2009 - 14:02:48 CDT)
  • Re: VMD/NAMD two identical molecules solvate in a water sphere (Tue Jun 23 2009 - 11:34:04 CDT)
  • Re: VMD/NAMD two identical molecules solvate in a water sphere (Tue Jun 23 2009 - 10:27:07 CDT)
  • VMD/NAMD two identical molecules solvate in a water sphere (Sat Jun 20 2009 - 11:02:49 CDT)
• David Kunzman
  • Re: NAMD on CELL BE (Thu May 10 2007 - 17:03:37 CDT)
  • 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 McGiven
  • NAMD 2.7b1 on SGI Altix 330 (Thu Mar 26 2009 - 08:50:31 CDT)
  • NAMD with CUDA Status ? (Mon Nov 24 2008 - 11:06:05 CST)
• David P. Brandon
  • TCBG "Hands-On" Workshop on Computational Biophysics in Boston, Dec. 5-9 (Tue Nov 02 2004 - 10:16:21 CST)
• David Sept
  • InfiniPath and NAMD (Mon Jul 24 2006 - 14:57:03 CDT)
• David Sivak
  • Free Energy of Conformational Change PMF - documentation on method? (Thu Mar 13 2008 - 18:07:56 CDT)
• David Skinner
  • IBM SP build (Sun Nov 09 2003 - 00:21:31 CST)
• David Tanner
  • Re: Steered Molecular Dynamics for more than one atom (Mon Aug 10 2009 - 15:31:09 CDT)
  • Re: SMD output : which col represents force, second or last (Wed Aug 05 2009 - 12:03:30 CDT)
  • Re: SMD working only at high velocity (Fri Jul 10 2009 - 15:20:23 CDT)
  • Re: SMD working only at high velocity (Fri Jul 10 2009 - 15:12:06 CDT)
  • Re: implicit solvent model in NAMD? (Sat Jul 04 2009 - 06:50:14 CDT)
  • Re: No log file (Mon Jul 06 2009 - 09:45:47 CDT)
  • Re: What decides the pulling direction in SMD? (Fri Jun 12 2009 - 07:04:27 CDT)
  • Re: MINIMIZER SLOWLY MOVING ATOMS WITH BAD CONTACTS DOWNHILL (Wed Mar 25 2009 - 14:24:31 CDT)
  • MINIMIZER SLOWLY MOVING ATOMS WITH BAD CONTACTS DOWNHILL (Wed Mar 25 2009 - 12:47:44 CDT)
  • Re: Cyclopeptide: connectivity between the first and last residues (Mon Sep 29 2008 - 15:36:31 CDT)
  • Re: Abnormal EOF found - buffer (Fri Aug 08 2008 - 10:14:21 CDT)
• David Wright
  • TMD (Thu Jun 21 2007 - 06:03:07 CDT)
• Davide Branduardi
  • Re: NAMD 2.7? (Tue Jul 01 2008 - 02:04:26 CDT)
• 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)
• Deborah Stanton
  • Can you satisfy your girlfriend? (Mon Jun 11 2007 - 17:18:55 CDT)
• Deepangi Pandit
  • Re: Copper and Zinc: top_all27_prot_lipid.inp (Fri Aug 24 2007 - 15:27:47 CDT)
  • Copper and Zinc: top_all27_prot_lipid.inp (Fri Aug 24 2007 - 11:51:39 CDT)
  • NAMD Installation - SUSE Linux 9.1 on IBM X Series 335 (Wed Jul 18 2007 - 13:39:18 CDT)
  • NAMD Installation - SUSE Linux 9.1 on IBM X Series 335 (Wed Jul 18 2007 - 13:20:19 CDT)
  • Fwd: Laptop for Molecular Dynamics - Summary (Fri May 25 2007 - 20:41:09 CDT)
  • Re: Laptop for Molecular Dynamics - Summary (Fri May 25 2007 - 20:39:45 CDT)
  • Re: Laptop for Molecular Dynamics (Fri May 25 2007 - 16:01:24 CDT)
  • Laptop for Molecular Dynamics (Thu May 24 2007 - 13:09:55 CDT)
• Deepesh
  • , Build your vocab (word power)-Get emails daily Fr.ee (Thu Jun 26 2008 - 00:02:52 CDT)
• DEEPESH AGARWAL
  • Topology cartoon of proteins (Wed Jul 02 2008 - 06:13:59 CDT)
  • use of 'measure hbonds' (Thu Jun 12 2008 - 23:54:34 CDT)
  • use of 'measure hbonds' (Thu Jun 12 2008 - 06:03:06 CDT)
  • steepest descent technique (Thu Jun 05 2008 - 00:53:30 CDT)
• Demet Akten
  • Re: topology and parameter file for FAD (Mon Mar 02 2009 - 02:47:01 CST)
  • topology and parameter file for FAD (Sat Feb 28 2009 - 08:40:31 CST)
  • Re: NAMD log file analysis script problem (namdstats.tcl) (Sun Jun 15 2008 - 03:35:49 CDT)
  • coarse grained simulation (Fri Mar 28 2008 - 09:11:19 CDT)
  • (no subject) (Tue Nov 06 2007 - 03:26:52 CST)
• Dennis Glass
  • PRESSURE, GPRESSURE, PRESSAVG, and GPRESSAVG (Wed Mar 18 2009 - 11:13:12 CDT)
• Derek Finley
  • Can't find a good drug store? (Sat Jun 09 2007 - 13:20:14 CDT)
• Deva Priyakumar
  • Re: High VDW energies during minimization and dynamics (Thu Apr 13 2006 - 14:41:22 CDT)
  • High VDW energies during minimization and dynamics (Thu Apr 13 2006 - 10:23:38 CDT)
• Devendra
  • RE: Error with External Electric Filed module (Wed Oct 15 2008 - 12:29:56 CDT)
  • Error with External Electric Filed module (Tue Oct 14 2008 - 10:39:05 CDT)
  • binaryoutput option doesn't work for dcd file (Sat Aug 18 2007 - 09:26:28 CDT)
• Dhiraj Srivastava
  • solvating long protein (Wed Oct 03 2007 - 13:54:47 CDT)
  • Re: NAD topology and parameter file (Mon Sep 17 2007 - 16:50:29 CDT)
  • NAD topology and parameter file (Mon Sep 17 2007 - 16:30:20 CDT)
  • Re: About QM-MM (Wed Aug 29 2007 - 12:05:26 CDT)
  • Re: About QM-MM (Wed Aug 29 2007 - 11:45:39 CDT)
  • Re: About QM-MM (Wed Aug 29 2007 - 11:31:00 CDT)
  • Re: 0 coordinates for LES atoms in pdb file after solvation (Thu Jan 25 2007 - 11:24:16 CST)
  • 0 coordinates for LES atoms in pdb file after solvation (Thu Jan 25 2007 - 01:45:32 CST)
  • C:CA bond getting stretched (Mon Jan 15 2007 - 01:45:37 CST)
  • Re: RE: about topology generation (Tue Dec 05 2006 - 01:34:08 CST)
  • atomlist command in matdcd (Sun Nov 12 2006 - 02:20:25 CST)
  • how to remove translational and rotational motion from dcd file (Thu Nov 09 2006 - 14:59:28 CST)
  • protein is moving from center to one corner of water box. (Mon Nov 06 2006 - 01:06:53 CST)
  • Warning: 1 processors are overloaded due to high background load (Fri Nov 03 2006 - 11:30:34 CST)
  • production in NVE ensemble after equilibration in NPT ensemble (Thu Nov 02 2006 - 23:54:30 CST)
  • equilibration of protein (Wed Nov 01 2006 - 12:31:17 CST)
  • rmsd is not stabilizing even after 0.6 ns (Tue Oct 31 2006 - 13:41:54 CST)
  • Re: Atoms moving too fast error (Fri Oct 27 2006 - 18:01:00 CDT)
  • constrained simulation (Fri Oct 27 2006 - 03:32:15 CDT)
  • Re: NPT ensemble with Periodic boundary condition (Wed Oct 25 2006 - 01:40:11 CDT)
  • NPT ensemble with Periodic boundary condition (Tue Oct 24 2006 - 17:07:38 CDT)
  • Re: deformed water box after heating (Tue Oct 24 2006 - 07:42:57 CDT)
  • Re: deformed water box after heating (Mon Oct 23 2006 - 22:12:29 CDT)
  • deformed water box after heating (Mon Oct 23 2006 - 21:40:37 CDT)
  • temperature reassignment (Mon Oct 23 2006 - 03:07:28 CDT)
  • Re: deformed water box during equilibration. (Sat Oct 21 2006 - 05:19:33 CDT)
  • deformed water box during equilibration. (Sat Oct 21 2006 - 05:13:35 CDT)
  • Re: charge on protein (Thu Oct 19 2006 - 13:50:59 CDT)
  • adding extra ions to neutralize charge on protein (Thu Oct 19 2006 - 11:42:48 CDT)
  • charge on protein (Wed Oct 18 2006 - 21:57:28 CDT)
  • NAMD on Dual processor computer (Sun Oct 15 2006 - 14:28:31 CDT)
  • Re: problem with reassigning temperature (Sun Oct 15 2006 - 14:08:31 CDT)
  • problem with reassigning temperature (Sat Oct 14 2006 - 21:55:15 CDT)
  • simulation in nve ensemble (Fri Oct 13 2006 - 21:45:37 CDT)
  • Re: "reinitvel" parameter in config file (Thu Oct 12 2006 - 13:03:38 CDT)
  • "reinitvel" parameter in config file (Wed Oct 11 2006 - 18:34:21 CDT)
  • Re: line too long in pdb file restart.coor (Wed Oct 11 2006 - 18:12:54 CDT)
  • line too long in pdb file restart.coor (Wed Oct 11 2006 - 14:28:41 CDT)
  • equilibration at three different temperature (Tue Oct 10 2006 - 18:00:52 CDT)
  • Re: restraining the protein not to move during equilibration (Sun Oct 08 2006 - 23:36:41 CDT)
  • restraining the protein not to move during equilibration (Sun Oct 08 2006 - 23:30:39 CDT)
  • restarting the simulation (Sun Oct 08 2006 - 16:17:38 CDT)
  • Re: value of B column is zero (Sun Oct 08 2006 - 12:26:57 CDT)
  • Re: zero kinetic energy during minimization (Sun Oct 08 2006 - 12:23:31 CDT)
  • value of B column is zero (Sun Oct 08 2006 - 00:34:16 CDT)
  • zero kinetic energy during minimization (Sun Oct 08 2006 - 00:12:39 CDT)
  • Re: How can I do protein complex's simulation? (Mon Oct 02 2006 - 19:58:29 CDT)
  • Re: "measure" command (Wed Sep 27 2006 - 17:56:50 CDT)
  • equilibrating the system with constrained Protein (Thu Sep 14 2006 - 13:12:31 CDT)
  • combined QM/MM calculation with NAMD (Thu Sep 14 2006 - 10:35:28 CDT)
  • assigning atom type for parameterization (Fri Sep 08 2006 - 15:23:02 CDT)
  • no parameter for CN8-ON6 (Wed Sep 06 2006 - 19:45:59 CDT)
  • parameterizing novel molecule (Wed Sep 06 2006 - 01:52:47 CDT)
  • error in loading "import hessian/charge from single point calculation" in paratool (Mon Aug 28 2006 - 17:53:11 CDT)
  • bad global exclusion count in LES (Fri Aug 18 2006 - 02:11:11 CDT)
  • topology and parameter file for non aromatic nitrogen in ring system. (Thu Aug 17 2006 - 22:15:57 CDT)
  • deprotonated form of Proline molecule (Tue Aug 15 2006 - 14:55:35 CDT)
  • Re: n terminal patch on proline (Tue Aug 15 2006 - 14:09:24 CDT)
  • Re: n terminal patch on proline (Tue Aug 15 2006 - 12:53:37 CDT)
  • n terminal patch on proline (Tue Aug 15 2006 - 11:53:47 CDT)
  • negatively charged proline as substrate (Mon Aug 14 2006 - 11:08:40 CDT)
  • atom type HZ4 not found (Sat Aug 05 2006 - 13:27:12 CDT)
  • fad topology and parameter file (Thu Aug 03 2006 - 02:11:45 CDT)
  • two chain in pdb file (Tue Aug 01 2006 - 01:46:01 CDT)
  • missing atoms in pdb file. (Tue Aug 01 2006 - 01:36:04 CDT)
  • collision correction of Locally Enhanced Sampling (Sun Jul 30 2006 - 15:14:52 CDT)
• Dibyadeep Paul
  • langevin dynamics (Sat Apr 12 2008 - 14:21:52 CDT)
  • variation between results on different OSes (Wed Mar 12 2008 - 02:31:40 CDT)
  • python vs tcl (Mon Feb 04 2008 - 11:14:56 CST)
  • namd vs gromacs vs charmm vs amber (Sun Jan 20 2008 - 04:43:41 CST)
• Diego Alejandro Vargas
  • Re: Unsure about current setting of Periodic Boundary Conditions (Tue Dec 23 2008 - 18:58:03 CST)
  • Re: Unsure about current setting of Periodic Boundary Conditions (Mon Dec 22 2008 - 08:50:16 CST)
  • Unsure about current setting of Periodic Boundary Conditions (Tue Dec 16 2008 - 00:09:12 CST)
  • Equilibration simulation too slow. (Sun Dec 07 2008 - 09:59:35 CST)
  • Re: pairlist i_upper mismatch! (Sat Nov 22 2008 - 22:20:31 CST)
  • Re: pairlist i_upper mismatch! (Sat Nov 22 2008 - 01:09:13 CST)
  • Re: pairlist i_upper mismatch! (Sat Nov 22 2008 - 00:20:25 CST)
  • A way to check for non-unique coordinates? (Thu Nov 20 2008 - 23:15:58 CST)
  • A way to check for non-unique coordinates? (Thu Nov 20 2008 - 21:22:21 CST)
  • Re: pairlist i_upper mismatch! (Thu Nov 20 2008 - 10:52:34 CST)
  • pairlist i_upper mismatch! (Wed Nov 19 2008 - 22:28:41 CST)
  • Re: Problems with minimization (Mon Nov 17 2008 - 20:54:14 CST)
  • Re: Problems with minimization (Sun Nov 16 2008 - 00:28:53 CST)
  • Re: Problems with minimization (Sat Nov 15 2008 - 11:53:06 CST)
  • Problems with minimization (Sat Nov 15 2008 - 10:57:23 CST)
  • Re: Atoms moving too fast OR constraint failure in RATTLE algorithm (Wed Nov 12 2008 - 19:00:37 CST)
  • Re: Atoms moving too fast OR constraint failure in RATTLE algorithm (Sat Nov 08 2008 - 17:31:30 CST)
  • Re: Atoms moving too fast OR constraint failure in RATTLE algorithm (Wed Nov 05 2008 - 23:17:56 CST)
  • Atoms moving too fast OR constraint failure in RATTLE algorithm (Tue Nov 04 2008 - 12:34:00 CST)
  • Problem with temperature increase in equilibration. (Thu Oct 30 2008 - 11:14:54 CDT)
  • Inquire on gradual temperature increase. (Mon Oct 20 2008 - 08:59:46 CDT)
  • Atom velocities too high. (Sun Oct 19 2008 - 09:59:10 CDT)
  • ERROR: DIDN'T FIND "NATOM" IN PSF FILE (Wed Oct 15 2008 - 23:12:01 CDT)
  • How to choose force field? (Tue Oct 14 2008 - 23:34:20 CDT)
  • vdW parameter (Wed Sep 03 2008 - 00:02:22 CDT)
  • Trouble with params file when trying to perform basic dynamics with alanine. (Fri Aug 29 2008 - 23:11:03 CDT)
  • charmrun not found (Tue Jun 24 2008 - 21:59:24 CDT)
  • Re: Unable to edit files in NAMD folder. (Thu May 22 2008 - 13:31:59 CDT)
  • Unable to edit files in NAMD folder. (Tue May 20 2008 - 23:39:51 CDT)
• digenova
  • Re: ABF Method (Thu Jul 03 2008 - 08:52:29 CDT)
• Dimitar V Pachov
  • Re: angle in colvars (Sun Nov 08 2009 - 22:17:20 CST)
  • Re: ATP and Stream files (Thu Oct 15 2009 - 08:55:02 CDT)
  • Re: CHARMM to NAMD (Thu Sep 03 2009 - 10:54:17 CDT)
  • Re: Cell Data in DCD files - CHARMM compatibility (Fri Aug 07 2009 - 19:50:30 CDT)
• DimitryASuplatov
  • Re: scripiting problem (Wed Nov 11 2009 - 03:06:05 CST)
  • Re: scripiting problem (Tue Nov 10 2009 - 11:21:55 CST)
  • Automatic namd 2.7b1 installation (Mon Nov 09 2009 - 11:36:22 CST)
  • PMEGridSpacing (Sat Oct 31 2009 - 05:46:04 CDT)
  • Using restraints (Wed Oct 28 2009 - 10:55:44 CDT)
  • Re: NAMD2.7 scaling problems (Wed Oct 28 2009 - 08:30:44 CDT)
  • NAMD2.7 scaling problems (Wed Oct 28 2009 - 04:06:13 CDT)
  • Re: Replay to Parametrizing a novel residue] (Fri Sep 18 2009 - 15:19:33 CDT)
  • Kanamycin topology (Wed Aug 12 2009 - 12:16:33 CDT)
  • Using preprotonated structure with NAMD (Tue Jul 28 2009 - 09:48:18 CDT)
  • Offset for frame ids in dcd trajectory (Sat May 23 2009 - 11:11:09 CDT)
  • Re: Optimizing configuration option for fast calculations (Thu Apr 30 2009 - 14:17:03 CDT)
  • Setting PME Grid (Thu Apr 30 2009 - 11:13:46 CDT)
  • Energy minimization failure (Thu Apr 30 2009 - 05:23:31 CDT)
  • +1 offset to VMD index file? (Tue Apr 28 2009 - 08:40:33 CDT)
  • Optimizing configuration option for fast calculations (Tue Apr 28 2009 - 07:16:00 CDT)
  • Re: Adding a new bond to CHARMM (Sat Apr 25 2009 - 08:56:05 CDT)
  • Adding a new bond to CHARMM (Sat Apr 25 2009 - 08:23:19 CDT)
  • Yet another NAMD speed concerns (Sat Apr 25 2009 - 04:44:44 CDT)
  • Re: compile NAMD 2.7b1 on Intel Xeon(R) infiniband cluster (Sat Apr 25 2009 - 03:51:27 CDT)
  • Copper parameters for CHARMM (Fri Apr 24 2009 - 11:02:50 CDT)
  • Constraints in NAMD (Wed Apr 22 2009 - 09:50:37 CDT)
  • FATAL ERROR: Periodic cell has become too small for original patch grid! (Wed Apr 22 2009 - 01:44:45 CDT)
  • Pressure coupling and system heating (Mon Apr 20 2009 - 03:38:36 CDT)
  • Re: Speeding up: Dummy constructions for aromatics or hydrogens (Fri Apr 17 2009 - 15:50:03 CDT)
  • Speeding up: Dummy constructions for aromatics or hydrogens (Fri Apr 17 2009 - 12:11:27 CDT)
  • Selectively write atoms to dcd files (Mon Apr 13 2009 - 12:20:01 CDT)
  • Water is boiling with namd and charmm (Mon Apr 13 2009 - 09:27:54 CDT)
  • Re: NAMD is too slow?! (Sun Mar 29 2009 - 12:23:05 CDT)
  • NAMD is too slow?! (Sun Mar 29 2009 - 04:37:39 CDT)
  • Interactive protonation (Sat Mar 28 2009 - 16:46:51 CDT)
  • NAMD for Intel Xeon Cluster with MPICH (Mon Dec 22 2008 - 06:33:48 CST)
• dimka
  • cutoffs in direct and indirect space used in PME? (Thu Aug 06 2009 - 23:13:05 CDT)
  • SMD output (Fri Jan 16 2009 - 12:59:43 CST)
  • Re: create inositol molecule (Thu Dec 04 2008 - 12:11:20 CST)
  • pairinteractions (Wed Jul 25 2007 - 17:03:37 CDT)
  • recalculating energies (Fri May 11 2007 - 12:19:27 CDT)
  • Re: Simulating air with NAMD (Tue May 08 2007 - 13:53:28 CDT)
  • hexagonal box (Tue Apr 17 2007 - 12:11:09 CDT)
  • PME for a hexagonal system (Fri Dec 22 2006 - 15:17:16 CST)
  • Re: Is the GBSA model in NAMD ? (Tue Jun 13 2006 - 15:17:55 CDT)
  • Re: Unit of harmonic restraint force constant (Fri Feb 24 2006 - 18:31:27 CST)
  • 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)
• dipti lele
  • Re- Loading .vel file in VMD (Sun Nov 23 2008 - 19:18:06 CST)
  • Loading .vel file in VMD (Thu Nov 20 2008 - 23:03:42 CST)
  • Simple query (Tue Sep 30 2008 - 04:33:24 CDT)
• Dirar Homouz
  • Re: Replica Exhange error: POSIX EINTR {interrupted system call} (Mon Sep 22 2008 - 15:07:16 CDT)
  • Replica Exhange error: POSIX EINTR {interrupted system call} (Sat Sep 20 2008 - 04:11:55 CDT)
  • REMD (Tue Nov 27 2007 - 14:33:46 CST)
  • Replica Exchange NAMD (Tue Nov 13 2007 - 12:09:52 CST)
  • Replica exchange error message (Mon Oct 29 2007 - 19:05:24 CDT)
  • TOTAL energy increase (Mon Sep 17 2007 - 15:26:10 CDT)
  • Reason: FATAL ERROR: Simulation config file is not accessible. (Thu Sep 06 2007 - 15:51:52 CDT)
• dixitpd_at_gmail.com
  • Dixitpd wants to Share Favorites with you (Tue Nov 20 2007 - 22:05:54 CST)
• Dmitry Lupyan
  • SMD output (Thu Jan 15 2009 - 16:50:08 CST)
• Do Nhu Trang
  • Re: FATAL ERROR: Setting parameter constraints from script failed! (Fri Jan 09 2009 - 10:17:02 CST)
  • Re: FATAL ERROR: Setting parameter constraints from script failed! (Fri Jan 09 2009 - 08:31:02 CST)
  • FATAL ERROR: Setting parameter constraints from script failed! (Thu Jan 08 2009 - 09:57:28 CST)
• Dolan, Michael (NIH/NIAID) [C]
  • FATAL ERROR: FixedAtoms may not be enabled in a script (Fri Mar 06 2009 - 11:32:52 CST)
  • force potentials for residue-based CG (Wed Nov 26 2008 - 13:36:51 CST)
• Dong Luo
  • Re: protein folding (Fri Jul 10 2009 - 08:13:56 CDT)
  • Hexafluoro-2-propanol (HFIP) force parameters (Wed Jan 21 2009 - 15:04:43 CST)
  • What happened when PBC is on but PME is off? (Wed Aug 15 2007 - 15:18:22 CDT)
  • Re: free energy,energy,entropy calculation for pushing ATP to active site of kinase! (Thu Jul 19 2007 - 09:15:13 CDT)
  • Re: removing waters from big dcd files (Mon Jul 16 2007 - 23:00:25 CDT)
  • Re: removing waters from big dcd files (Mon Jul 16 2007 - 14:40:55 CDT)
  • Re: Count protein solvent HBs? (Thu Jul 05 2007 - 09:21:36 CDT)
  • Re: how to use measure hbonds to calculate occupancy of all hbonds in simulation? (Tue May 15 2007 - 18:27:01 CDT)
  • NAMD2.6 requirments on p690 (Wed Mar 28 2007 - 10:47:11 CDT)
  • the relationship between system size and cpu numbers (Tue Mar 27 2007 - 10:28:54 CDT)
  • Re: Compile NAMD on Bluegene (Fri Jun 16 2006 - 13:56:46 CDT)
  • Re: Compile NAMD on Bluegene (Thu Jun 15 2006 - 14:16:30 CDT)
  • Re: Compile NAMD on Bluegene (Thu Jun 15 2006 - 11:35:18 CDT)
  • Re: Compile NAMD on Bluegene (Thu Jun 15 2006 - 09:48:32 CDT)
  • Compile NAMD on Bluegene (Wed Jun 14 2006 - 16:17:13 CDT)
  • Re: NAMD configuration files for NVT ensemble (Mon Apr 24 2006 - 15:10:11 CDT)
  • Re: simulated annealing with explicit water (Mon Apr 24 2006 - 13:05:31 CDT)
  • Re: Aligning structures (Fri Mar 10 2006 - 11:11:03 CST)
  • What's the highest temperature I can go? (Thu Jan 05 2006 - 13:11:19 CST)
  • 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)
• Dong Xu
  • Re: carbohydrates: CHARMM versus AMBER (Wed Oct 29 2008 - 18:47:49 CDT)
  • Re: firsttimestep question (Mon Oct 06 2008 - 13:00:08 CDT)
  • firsttimestep question (Mon Oct 06 2008 - 00:00:46 CDT)
  • Re: namd 2.5 compilation error (Mon Sep 29 2008 - 14:38:12 CDT)
  • Re: namd 2.5 compilation error (Mon Sep 29 2008 - 12:15:07 CDT)
  • namd 2.5 compilation error (Sun Sep 28 2008 - 01:53:14 CDT)
• dongsheng lei
  • Is it better to align all the trajectory before calculating rmsd? (Tue Jan 22 2008 - 03:05:47 CST)
  • How can I get parameters of unknown residues (Wed Oct 31 2007 - 04:26:16 CDT)
• dora guzman
  • Turn off H-bonding on select residues (Fri Aug 08 2008 - 13:21:35 CDT)
  • Re: *.dcd and *.dcd.BAK (Sun Jul 29 2007 - 15:46:28 CDT)
  • SMD of proteins in water box without PBC (Wed Jul 04 2007 - 11:56:46 CDT)
  • different output in processors (Tue Feb 27 2007 - 14:18:24 CST)
  • forming disulfide after equilibrating system (Fri Dec 22 2006 - 17:24:10 CST)
  • Re: Autoionize error: spontaneously quits (Fri Jun 23 2006 - 12:18:02 CDT)
  • Autoionize error: spontaneously quits (Wed Jun 21 2006 - 18:38:51 CDT)
  • [Fwd: Re: SMD of small molecule dimer] (Tue May 02 2006 - 11:59:32 CDT)
  • SMD of small molecule dimer (Fri Apr 28 2006 - 12:05:39 CDT)
  • SMD of small molecule dimer (Thu Apr 27 2006 - 19:28:20 CDT)
  • [Fwd: SMD of titin domain] (Wed Feb 08 2006 - 17:05:34 CST)
  • [Fwd: increasing RMSD after 2 ns minimization-equilibration] (Wed Feb 08 2006 - 17:05:51 CST)
  • error parsing config file (Thu Sep 29 2005 - 14:00:00 CDT)
• dota
  • constraints (Wed Apr 08 2009 - 04:23:40 CDT)
• doty alexiou
  • protein folding (Fri Jul 10 2009 - 03:00:37 CDT)
  • protein folding cg (Fri Jun 05 2009 - 01:21:16 CDT)
  • exclude 1-2 (Fri May 15 2009 - 01:55:09 CDT)
  • exclude 1-2 or 1-4? (Tue May 12 2009 - 09:56:31 CDT)
  • cg protein folding (Wed Mar 18 2009 - 09:51:17 CDT)
• Doug Moby
  • Constraining a molecule and measuring the corresponding constraint force (Sat Sep 30 2006 - 08:36:31 CDT)
• Dow Hurst
  • Re: About CUDA version of NAMD 2.7 B1 (Sat Mar 28 2009 - 14:20:30 CDT)
  • Re: NAMD and multi-rail IB for improved latency (Fri Mar 27 2009 - 00:05:58 CDT)
  • NAMD and multi-rail IB for improved latency (Thu Mar 26 2009 - 21:55:13 CDT)
  • CUDA version status (Tue Jan 20 2009 - 12:39:20 CST)
  • 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
  • NAMD Tuning page on the wiki vs. NAMD/CUDA (Wed May 20 2009 - 18:09:21 CDT)
  • Re: namd-cuda-intel vs. namd-intel (Fri May 15 2009 - 10:25:05 CDT)
  • Re: namd-cuda-intel vs. namd-intel (Wed May 13 2009 - 11:19:48 CDT)
  • Re: CUDA version status (Fri Jan 23 2009 - 13:44:07 CST)
  • Re: CUDA version status (Wed Jan 21 2009 - 13:12:32 CST)
  • Re: Compilation of Charm++ then NAMD 2.6 on Opteron with Portland compilers (Sat Dec 15 2007 - 21:49:11 CST)
  • Scaling the Tiny benchmark (Sat Oct 13 2007 - 11:20:16 CDT)
  • Re: Performance Problems on Linux Cluster / Bad Scaling (Sun Sep 23 2007 - 08:39:40 CDT)
  • Re: NAMD on dual quad-core Xeon's with Infiniband backbone (Sat Sep 22 2007 - 18:28:17 CDT)
  • Re: About QM-MM (Thu Aug 30 2007 - 00:02:52 CDT)
  • Re: Charm++ Compilation (Wed Aug 22 2007 - 09:58:56 CDT)
  • Latency vs Bandwidth over Infiniband (Fri Aug 17 2007 - 17:37:07 CDT)
  • Re: Gigabit ethernet switch for cluster (Wed Mar 22 2006 - 21:33:57 CST)
  • 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)
• Dr. Luis Rosales León
  • restartfreq question.... (Thu Aug 07 2008 - 16:31:54 CDT)
  • phosphate (PO4) topology (Wed Jul 30 2008 - 17:37:19 CDT)
  • Re: help regarding NAMD equilibration (Tue Apr 15 2008 - 12:39:24 CDT)
• Dr. Tamal Banerjee
  • Freezing point (Fri Sep 07 2007 - 08:22:05 CDT)
  • A basic question? (Thu Sep 06 2007 - 05:33:09 CDT)
• drmartin_at_fizyka.umk.pl
  • Re: Modeling familial amyloidotic polyneuropathy (Mon Oct 26 2009 - 10:17:07 CDT)
  • Modeling familial amyloidotic polyneuropathy (Mon Oct 26 2009 - 07:04:03 CDT)
• dstrahs_at_pace.edu
  • Re: a philosophical question... (Mon Feb 19 2007 - 20:57:31 CST)
• dtmirij
  • Polarizable force fields (Fri Apr 27 2007 - 00:44:13 CDT)
• Dustin Waller
  • Happy Viagra (Wed Jun 06 2007 - 12:48:07 CDT)
• E. Davis Oldham
  • NANMD errors: PME, qsub (Sat Apr 16 2005 - 12:37:37 CDT)
• E. Prabhu Raman
  • Re: LangevinTemp and KE calculation (Wed Jul 16 2008 - 12:56:22 CDT)
  • LangevinTemp and KE calculation (Tue Jul 15 2008 - 18:25:49 CDT)
  • Re: Molecule drifts and high average RMSD per residue (Mon Oct 08 2007 - 14:57:00 CDT)
  • Re: Determining Transition State from an Unfolding Simulation (Wed Sep 26 2007 - 12:24:03 CDT)
  • Re: Determining Transition State from an Unfolding Simulation (Wed Sep 26 2007 - 08:09:07 CDT)
  • Re: Determining Transition State from an Unfolding Simulation (Sun Sep 23 2007 - 21:43:36 CDT)
  • Replica-Exchange MD (Mon Oct 23 2006 - 13:53:41 CDT)
  • trajectory extension (Fri Sep 29 2006 - 13:39:55 CDT)
  • parameter file name (Fri Sep 08 2006 - 18:46:41 CDT)
  • atom name based paremeters (Tue Sep 05 2006 - 14:31:30 CDT)
  • mass of atoms changable? (Wed Aug 30 2006 - 16:19:46 CDT)
• Edelmiro Moman
  • Re: two chain in pdb file (Tue Aug 01 2006 - 03:40:12 CDT)
  • Re: third time..can someone help!! (Wed Jul 12 2006 - 03:13:58 CDT)
  • Re: third time..can someone help!! (Wed Jul 12 2006 - 02:40:03 CDT)
  • Tcl, minimization and MD (Warning: I am a lazy ignorant) (Tue Jun 20 2006 - 10:20:09 CDT)
  • Interrupted system call (Fri Jun 09 2006 - 02:21:25 CDT)
  • DCD to PDB conversion (Thu Jun 08 2006 - 02:57:31 CDT)
  • Factorization in PMEGridSize (Wed Jun 07 2006 - 04:36:54 CDT)
  • Where to put the "nodelist" file (Wed Jun 07 2006 - 02:45:37 CDT)
  • 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)
• edu
  • Re: Time of MD (Mon Jul 03 2006 - 12:05:44 CDT)
  • Time of MD (Fri Jun 30 2006 - 11:18:16 CDT)
  • Re: Time of MD (Thu Jun 29 2006 - 10:02:26 CDT)
  • Time of MD (Fri Jun 23 2006 - 13:59:54 CDT)
  • calculation (continue) (Wed Jun 21 2006 - 16:03:40 CDT)
  • Re: Re. Namd window network problem (Fri Jun 16 2006 - 14:08:09 CDT)
  • chage free energy (Fri Jun 16 2006 - 13:58:08 CDT)
  • Re. Namd window network problem (Fri Jun 16 2006 - 10:33:25 CDT)
  • Namd window network problem (Thu Jun 15 2006 - 13:55:51 CDT)
• Eduardo
  • Re: lipid bi-layer and SiO2 (Fri May 08 2009 - 14:49:32 CDT)
  • Re: lipidmonolayer (Wed Apr 22 2009 - 22:23:46 CDT)
• Eduardo Cruz-Chu
  • Re: atomic structure of some surfaces (Sat Sep 12 2009 - 15:31:12 CDT)
  • Re: on NAMD simulation of DNA translocation through nanopores (Sun Jul 19 2009 - 15:21:19 CDT)
  • Re: Grid Forces documentation (Thu Jul 16 2009 - 14:20:11 CDT)
  • Re: peptides on surface (Wed May 13 2009 - 17:02:19 CDT)
  • Re: two independent groups of constraints (Thu Apr 30 2009 - 13:54:18 CDT)
  • Re: alkane-silicon_dioxide simulation (Thu Jul 10 2008 - 15:46:25 CDT)
• Eduardo Tejera
  • Re: problems-protein minimization (Mon Jan 26 2009 - 04:04:43 CST)
  • Rv: Value 99999999.9999 during minimization (Fri Aug 08 2008 - 14:50:45 CDT)
  • Re: Determining Transition State from an Unfolding Simulation (Thu Sep 27 2007 - 17:27:28 CDT)
  • Re: Determining Transition State from an Unfolding Simulation (Thu Sep 27 2007 - 15:09:41 CDT)
  • Re: Temperature dependent unfolding.. (Fri Sep 21 2007 - 06:15:42 CDT)
  • Re: About QM-MM (Tue Aug 28 2007 - 18:26:48 CDT)
• Edward Lyman
  • Re: TIP4P topology (Tue Nov 03 2009 - 15:43:43 CST)
  • namd2.7b1, tip4p, and dummies (Wed Sep 30 2009 - 13:56:47 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
  • electric field (Sat Sep 02 2006 - 20:17:21 CDT)
  • 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)
• El Escuchado por DIOS
  • SYSTEM ENERGY MINIMIZATION (Wed Dec 05 2007 - 15:06:48 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)
  • Re: contraint failure in RATTLE algorithm (Thu Nov 06 2003 - 16:01:07 CST)
  • contraint failure in RATTLE algorithm (Thu Nov 06 2003 - 13:45:19 CST)
• Elham Hamed
  • FW: Hydroxylysine parameters (Mon Jun 09 2008 - 10:53:08 CDT)
• Elia Zomot
  • changing protonation states for a pdb with more than a single polypeptide (Tue May 12 2009 - 18:47:41 CDT)
• Elia Zumot
  • Re: Constraint failure in RATTLE algorithm - shouldn't a rerun fail at the same step? (Wed Sep 09 2009 - 10:40:29 CDT)
  • Re: Membrane simulations (Tue Sep 01 2009 - 12:54:36 CDT)
  • Re: SMD with force applied to two seperate molecules (Thu Aug 13 2009 - 11:07:06 CDT)
  • SMD with force applied to two seperate molecules (Tue Aug 11 2009 - 10:09:17 CDT)
  • Re: Error with GUI NAMD Energy (Sat Aug 08 2009 - 12:10:31 CDT)
  • Error with GUI NAMD Energy (Fri Aug 07 2009 - 16:45:23 CDT)
  • Re: SMD working only at high velocity (Mon Jul 13 2009 - 10:54:42 CDT)
  • Re: SMD working only at high velocity (Fri Jul 10 2009 - 14:48:34 CDT)
  • SMD working only at high velocity (Fri Jul 10 2009 - 13:20:33 CDT)
• Elif Ozkirimli
  • Re: TMD RMSD problem (Fri Apr 10 2009 - 15:50:50 CDT)
  • Re: TMD RMSD problem (Thu Apr 09 2009 - 11:24:21 CDT)
  • TMD RMSD problem (Wed Apr 08 2009 - 15:21:16 CDT)
  • tmd algorithm (Tue Feb 10 2009 - 09:22:58 CST)
• Elijah Roberts
  • Re: Simulation in vaccum (Sun Jan 08 2006 - 10:53:43 CST)
• Elsa F. Sousa Henriques
  • Re: psfgen and charmm19: is there any inconsistency? (Thu Jun 29 2006 - 03:33:59 CDT)
  • Re: Vibrational mode analysis (Fri Jun 16 2006 - 02:11:55 CDT)
  • Re: Where to put the "nodelist" file (Wed Jun 07 2006 - 04:24:33 CDT)
  • Re: namd: adding water molecules (Thu May 11 2006 - 02:11:32 CDT)
  • Re: Heme - Cysteine link (Tue May 09 2006 - 09:09:33 CDT)
  • Asymmetric water molecule found??? (Wed May 03 2006 - 02:59:26 CDT)
• Elsa Fernanda de Sousa Henriques
  • Re: [***** SPAM *****] About APBS calculation (Fri Oct 30 2009 - 04:40:20 CDT)
  • Re: Cylindrical harmonic BC and constraintScaling (Mon Apr 20 2009 - 08:25:20 CDT)
  • Cylindrical harmonic BC and constraintScaling (Mon Apr 20 2009 - 05:22:25 CDT)
• Elsa S. Henriques
  • Re: DPPC.Pdb file needed (Tue Sep 05 2006 - 08:42:29 CDT)
• Emanuelle Bachelet
  • Re: ions behavior in protein-water box: (Fri Oct 31 2008 - 12:08:53 CDT)
  • Re: ions behavior in protein-water box: (Thu Oct 30 2008 - 14:38:13 CDT)
  • Re: ions behavior in protein-water box: (Thu Oct 30 2008 - 12:24:27 CDT)
  • Re: ions behavior in protein-water box: (Wed Oct 29 2008 - 16:56:10 CDT)
  • ions behavior in protein-water box: (Wed Oct 29 2008 - 13:44:59 CDT)
• emilia wu
  • ERROR! Explicit exclusions or fluctuating charges not supported, atom ignored. (Thu Jul 02 2009 - 18:35:32 CDT)
• emilia.l.wu
  • Re: Re: about psfgen (Sat Jul 04 2009 - 10:53:18 CDT)
  • about psfgen (Sat Jul 04 2009 - 08:59:44 CDT)
• emir mahmut bahsi
  • running namd with condor (Mon May 19 2008 - 15:42:38 CDT)
• End'tasa
  • Aslos (Fri Aug 28 2009 - 11:55:17 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)
• enz1+_at_pitt.edu
  • water molecules "collapse" during equilibration (Fri May 29 2009 - 11:38:06 CDT)
• EPF (Esben Peter Friis)
  • RE: creating Charmm psf from Xplor format (Wed Feb 04 2004 - 07:40:50 CST)
  • RE: cluseter node freezes while running namd 2.5/2.5b1 (Sun Oct 19 2003 - 14:00:00 CDT)
• EPF \(Esben Peter Friis\)
  • RE: Aligning structures (Fri Mar 10 2006 - 01:34:40 CST)
  • RE: starting simulation in charmm, continuing in NAMD ? (Mon Mar 06 2006 - 03:48:06 CST)
  • RE: starting simulation in charmm, continuing in NAMD ? (Sun Mar 05 2006 - 14:35:18 CST)
  • RE: xplor to charmm (Mon Nov 01 2004 - 15:21:08 CST)
• eprates_at_iqm.unicamp.br
  • Re: Periodic boundary condition in a membrane simulation (Mon Feb 09 2009 - 18:14:44 CST)
  • Energy drif in NVE ensemble (Thu Jan 15 2009 - 11:51:54 CST)
• Eric Bohm
  • Re: 128+ proccessor jobs on 64bit Widows hang upon completion of the simulation. (Mon Jul 30 2007 - 10:26:01 CDT)
  • Re: 128+ proccessor jobs on 64bit Widows hang upon completion of the simulation. (Mon Jul 30 2007 - 11:13:09 CDT)
  • Re: 128+ proccessor jobs on 64bit Widows hang upon completion of the simulation. (Mon Jul 30 2007 - 08:09:28 CDT)
  • Re: charm++ 5.9 megatest failure too (Tue Aug 02 2005 - 17:49:31 CDT)
• Eric Cyr
  • Re: ABF:reversibility and number of samples (Fri May 23 2008 - 15:11:29 CDT)
  • Re: Why is SHAKE not being used in typical NAMD simulations ? (Wed May 23 2007 - 13:20:34 CDT)
  • 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 H. Lee
  • Re: ABF 'Xi' log output producing strange results (Thu Aug 27 2009 - 10:48:50 CDT)
  • Re: molecule jumps from one site to the other? (Mon Jul 13 2009 - 21:33:42 CDT)
  • Re: SMD working only at high velocity (Fri Jul 10 2009 - 15:06:20 CDT)
  • Re: Translocation problem while attempting to use ABF (Mon Jul 06 2009 - 11:34:11 CDT)
  • Re: Does NAMD have any capability to assign coordiantes to novel sequences? (Thu Jun 25 2009 - 11:16:16 CDT)
  • Re: regarding positioning of protein molecule (Wed Jun 24 2009 - 17:46:53 CDT)
  • Re: Pair interaction : Energy values are zero (Sun Jun 21 2009 - 16:23:43 CDT)
  • Re: VMD/NAMD two identical molecules solvate in a water sphere (Sat Jun 20 2009 - 12:46:25 CDT)
  • Re: Need help to generate ubq-get-energy.conf (Thu May 14 2009 - 02:52:20 CDT)
  • Re: Calculating displacement in a system with periodic boundary (Tue May 12 2009 - 01:15:56 CDT)
  • Re: Calculating displacement in a system with periodic boundary (Mon May 11 2009 - 23:49:25 CDT)
  • Re: protein shifts out of the water box (Fri May 08 2009 - 18:31:02 CDT)
  • Re: PARAM22 and CMAP correction (Wed Apr 22 2009 - 22:34:19 CDT)
  • Re: how to install namd in windows xp (Sat Apr 04 2009 - 01:29:58 CDT)
  • Re: smd direction (Mon Mar 30 2009 - 11:39:17 CDT)
  • Re: smd direction (Mon Mar 30 2009 - 10:52:05 CDT)
  • Re: Reference file for the constraining force in Umbrella Sampling (Thu Mar 12 2009 - 18:30:07 CDT)
  • Re: help running NAMD energy at multiple stable temperatures (newbie) (Tue Mar 03 2009 - 00:05:58 CST)
  • Re: patch DISU to 2 residues (Wed Dec 17 2008 - 12:13:20 CST)
  • Re: water box getting deformed (Thu Dec 11 2008 - 07:45:58 CST)
  • Re: Reading multiple .log files into one (Thu Dec 04 2008 - 08:59:19 CST)
  • Re: periodic cell has become too small for original patch grid! (Tue Nov 18 2008 - 03:22:03 CST)
  • Re: Error while using NAMD (Sun Nov 09 2008 - 16:00:57 CST)
  • Re: dcd to pdb conversion (Mon Oct 27 2008 - 04:11:51 CDT)
  • Re: dcd to pdb conversion (Mon Oct 27 2008 - 03:39:09 CDT)
  • Re: How to use bigdcd on a trajectory while skipping first 1000 frames (Thu Sep 25 2008 - 04:54:29 CDT)
  • Re: convergence of abf (Thu Sep 18 2008 - 05:19:49 CDT)
  • Fwd: convergence of abf (Mon Sep 08 2008 - 14:45:53 CDT)
  • Re: parallel execution speedup (Thu Aug 21 2008 - 16:31:32 CDT)
  • Re: SMD more than once (Wed Aug 20 2008 - 14:39:37 CDT)
  • Re: SMD force units (Mon Aug 11 2008 - 17:50:30 CDT)
  • Re: SMD force units (Mon Aug 11 2008 - 17:46:15 CDT)
  • Re: Appending dcd when restarting a simulation (Thu Jul 24 2008 - 08:58:21 CDT)
  • Re: Maximum Velocities (Tue Jul 08 2008 - 13:50:51 CDT)
  • Re: Avoiding alpha-helix distortions (Sat Jul 05 2008 - 12:22:24 CDT)
  • Re: ABF Method (Wed Jul 02 2008 - 10:45:15 CDT)
  • Re: Avoiding alpha-helix distortions (Wed Jul 02 2008 - 10:41:01 CDT)
  • Re: Which conformation is more proper for the SMD (Mon Jun 09 2008 - 13:47:27 CDT)
  • Re: free energy calculations (Wed Jun 04 2008 - 11:28:13 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 Hu
  • Re: Periodic boundary condition in a membrane simulation (Mon Feb 09 2009 - 19:20:18 CST)
  • Periodic boundary condition in a membrane simulation (Mon Feb 09 2009 - 17:28:38 CST)
• Eric Perim
  • Different ensembles in the same system (Wed Jul 29 2009 - 14:48:39 CDT)
  • Running NVT simulations (Fri May 25 2007 - 18:03:48 CDT)
  • Constant Energy Simulations (Fri Jun 30 2006 - 08:42:48 CDT)
  • 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)
• Eric Userlist
  • Re: protein shifts out of the water box (Fri May 08 2009 - 18:22:52 CDT)
  • protein shifts out of the water box (Wed Apr 29 2009 - 18:52:16 CDT)
• Erik Nordgren
  • missing libraries for NAMD 2.7 on Linux cluster? (Sat Nov 07 2009 - 01:09:17 CST)
  • RE: surface pressure/tension (Thu Sep 09 2004 - 13:56:27 CDT)
• ershela.durresi_at_yale.edu
  • question about repeating output text (Tue Jun 09 2009 - 05:58:20 CDT)
• Esben A. Gad
  • harmonic restraint between two atoms (Mon May 26 2008 - 03:55:16 CDT)
• Esteban Gabriel Vega Hissi
  • Re: Unable to generate PSF file due to an unparametrized component (Tue Jul 28 2009 - 18:18:49 CDT)
  • Namd and MM-PBSA (Thu Apr 23 2009 - 10:42:49 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)
• Eva Nong
  • Please unsubscribe me (Thu Aug 14 2008 - 13:52:01 CDT)
  • Incorrect PSF file for min.pme (Mon Jun 23 2008 - 15:32:58 CDT)
  • Trouble in energy minimization with warning to increase cutoff (Tue Jun 17 2008 - 18:57:49 CDT)
• Fabien Cailliez
  • namd and amber force field (Thu Feb 23 2006 - 11:38:01 CST)
• Fabio Passetti
  • Re: Temperature dependent unfolding.. (Wed Sep 05 2007 - 07:41:39 CDT)
  • Zn parameters (Fri May 11 2007 - 08:17:31 CDT)
  • The NAMD job do not go forward (Fri Jan 05 2007 - 12:43:13 CST)
• Fabio Zegarra
  • Re: Acceptable pressure values (Mon May 26 2008 - 19:32:21 CDT)
  • Acceptable pressure values (Fri May 23 2008 - 17:24:22 CDT)
  • Negative Pressure (Tue May 06 2008 - 15:44:53 CDT)
• Falgun Shah
  • about calculation of PMF from SMD trajectories (with pasted smd_config_file) (Wed Mar 04 2009 - 12:04:52 CST)
  • about calculation of PMF from SMD trajectories (Wed Mar 04 2009 - 11:58:52 CST)
  • tutorial for calculation of PMF using namd (Mon Mar 02 2009 - 22:44:15 CST)
  • charm27 forcefield_topology (Wed Feb 25 2009 - 11:02:02 CST)
  • smd force vs time (Sun Feb 22 2009 - 13:31:07 CST)
  • center of mass for SMD (Tue Feb 10 2009 - 17:52:06 CST)
  • pdb and rmsd (Fri Jan 30 2009 - 13:46:42 CST)
  • RMSD and merging trajectories (Sat Jan 24 2009 - 17:20:27 CST)
  • use of berendsenPressure during heating (Thu Jan 22 2009 - 22:22:29 CST)
  • error during heating of the minimized system: (please reply!) (Wed Jan 14 2009 - 01:08:28 CST)
• Fam Eklund
  • Re: Re: slow NAMD simulations on a AMD athlon64 in SUSE linux (Thu Jun 15 2006 - 02:19:34 CDT)
  • slow NAMD simulations on a AMD athlon64 in SUSE linux (Wed Jun 14 2006 - 16:28:38 CDT)
• Fangqiang Zhu
  • Re: AMBER FF and pmf (Thu May 06 2004 - 18:18:58 CDT)
  • Re: Getting forces: segmentation violation or illegal instruction (Mon Mar 22 2004 - 11:54:41 CST)
  • Re: TCL: getting forces (Fri Mar 05 2004 - 14:04:31 CST)
  • Re: Amber on with H-bond (Thu Mar 04 2004 - 01:00:31 CST)
  • Re: Amber on with H-bond (Wed Mar 03 2004 - 21:45:15 CST)
  • Generating novel structure (Tue Mar 02 2004 - 13:38:12 CST)
  • Re: Locally Enhanced Sampling (Tue Mar 02 2004 - 11:51:09 CST)
  • Re: Restart using amber force field (Fri Feb 27 2004 - 15:00:29 CST)
  • Re: psf file for zeolite-water system (Mon Feb 23 2004 - 14:16:26 CST)
  • Re: test and a short question! (Mon Jan 19 2004 - 15:15:15 CST)
  • Re: SMD force (fwd) (Tue Jan 06 2004 - 17:14:56 CST)
  • Re: rotational energy, Tcl and environment variable(s) inLinux 2.5 (Thu Dec 04 2003 - 18:05:24 CST)
  • Re: how to add counterions ? (Tue Dec 02 2003 - 18:19:19 CST)
  • Re: rotational energy, Tcl and environment variable(s) in Linux 2.5 (Tue Dec 02 2003 - 00:38:01 CST)
  • Re: how to add counterions ? (Tue Dec 02 2003 - 00:24:16 CST)
  • Re: Why "fixedAtomsForces on" for constant pressure? (Tue Dec 02 2003 - 00:04:16 CST)
  • Re: updating coordinates using IMD (Mon Dec 01 2003 - 11:47:08 CST)
  • Re: how to get Charge of new residue? (Sat Nov 29 2003 - 01:03:31 CST)
  • Re: (Sat Nov 29 2003 - 00:41:44 CST)
  • Re: Temp in SMD (Sat Nov 29 2003 - 00:34:30 CST)
  • Re: how can I know which type HIS belong to?(HSD,HSE,HSP) (Sat Nov 29 2003 - 00:22:03 CST)
  • Re: the Atom velocity is beyond the limit? (Fri Nov 28 2003 - 23:44:19 CST)
  • Re: the problem on segment a ligand in NAMD ? (Fri Nov 28 2003 - 00:41:19 CST)
  • Re: FATAL ERROR (Thu Nov 27 2003 - 23:47:41 CST)
  • Re: xst format (Thu Nov 27 2003 - 23:27:34 CST)
  • Re: something about the TIP3P water model (Thu Nov 27 2003 - 23:11:33 CST)
  • Re: Energy problem after restart (Tue Nov 25 2003 - 09:47:30 CST)
  • Re: Energy problem after restart (Mon Nov 24 2003 - 15:15:56 CST)
  • Re: Energy problem after restart (Thu Nov 20 2003 - 17:15:11 CST)
  • Re: Urey-Bradley term (Wed Nov 19 2003 - 17:39:23 CST)
  • Re: ADP again (Tue Nov 18 2003 - 18:44:24 CST)
  • Re: Urey-Bradley term (Tue Nov 18 2003 - 18:24:46 CST)
  • Re: ADP again (Mon Nov 17 2003 - 18:47:59 CST)
  • Re: zinc parameter? (Mon Nov 17 2003 - 18:24:08 CST)
• Felipe Merino
  • Re: angle in colvars (Mon Nov 09 2009 - 06:19:03 CST)
  • angle in colvars (Sun Nov 08 2009 - 21:52:10 CST)
  • Re: zeroMomentum command (Fri Oct 16 2009 - 20:53:10 CDT)
  • Re: zeroMomentum command (Fri Oct 16 2009 - 20:49:24 CDT)
  • Re: TMD biasing (Thu May 14 2009 - 07:55:55 CDT)
  • TMD biasing (Thu May 14 2009 - 06:23:23 CDT)
• felmerino_at_uchile.cl
  • soft-core potential for FEP (Wed Apr 08 2009 - 17:46:33 CDT)
• feng jack
  • Thank you for your advices (Tue Jun 03 2008 - 11:15:41 CDT)
  • Average energy in NAMD (Sun Jun 01 2008 - 16:31:16 CDT)
  • (no subject) (Fri May 30 2008 - 16:04:44 CDT)
• FengXian Zheng
  • Why is the temperature set different in the membrane proteins tutorial? (Sat Sep 26 2009 - 19:58:28 CDT)
  • FATAL ERROR: ABNORMAL EOF FOUND - buffer=*0 0 0* (Fri Aug 21 2009 - 10:14:38 CDT)
• fereshteh moradi
  • How to apply an unsteady magnetic field? (Sun Oct 25 2009 - 01:52:29 CDT)
• fett_at_vtr.net
  • Re: water models and some questions (Fri May 08 2009 - 09:45:02 CDT)
  • water models and some questions (Thu May 07 2009 - 06:02:39 CDT)
  • tip4p on namd 2.7b (Tue Apr 21 2009 - 07:45:40 CDT)
  • tcl script (Mon Feb 02 2009 - 21:31:04 CST)
  • Problem with TclBC when run in more than one processor (Wed Jun 04 2008 - 12:08:57 CDT)
• 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)
• Florian Janetzko
  • REMD on AIX5.3 (Tue May 19 2009 - 06:44:34 CDT)
• Floris Buelens
  • Re: question about FEP soft-core (Tue Sep 15 2009 - 08:56:43 CDT)
  • Re: Fep performance (Wed Aug 26 2009 - 01:26:49 CDT)
  • Re: FEP implementation in NAMD 2.6 vs. 2.7b1 (Wed Jul 29 2009 - 01:50:40 CDT)
  • Re: inconsistence in NAMD and AMBER energy (Tue Jul 21 2009 - 10:57:41 CDT)
  • Re: inconsistence in NAMD and AMBER energy (Tue Jul 21 2009 - 02:11:51 CDT)
  • Re: NAMD_ti.pl (Thu Jul 02 2009 - 02:26:35 CDT)
  • Re: launch NAMD from tcl script - bug? (Wed Jun 24 2009 - 12:58:27 CDT)
  • Re: launch NAMD from tcl script - bug? (Wed Jun 24 2009 - 11:52:57 CDT)
  • Re: launch NAMD from tcl script - bug? (Wed Jun 24 2009 - 10:54:24 CDT)
  • launch NAMD from tcl script (Wed Jun 24 2009 - 06:55:06 CDT)
  • Re: How is dG caluclated from dE during FEP? (Fri Jun 19 2009 - 02:39:05 CDT)
  • Re: Re: Thermodynamic integration script - where is it? (Tue Jun 16 2009 - 02:37:44 CDT)
  • Re: water tail correction (Thu May 28 2009 - 17:52:51 CDT)
  • Re: water tail correction (Wed May 27 2009 - 03:16:33 CDT)
  • Re: water tail correction (Mon May 25 2009 - 15:51:16 CDT)
  • Re: water tail correction (Fri May 22 2009 - 05:40:00 CDT)
  • Re: dummy atom mass changed (Thu May 07 2009 - 05:09:36 CDT)
  • water tail correction (Wed Apr 29 2009 - 05:51:55 CDT)
  • Re: use of tiElecLambdaStart (NAMD 2.7b1) (Tue Mar 31 2009 - 04:29:56 CDT)
  • Re: alchemical fep amber topology (Sat Mar 14 2009 - 05:53:37 CDT)
  • Re: alchemical fep amber topology (Sat Mar 14 2009 - 06:16:37 CDT)
  • Re: FEP anomaly? (Wed Feb 25 2009 - 09:13:22 CST)
  • Re: FEP on NAMD2.6 versus latest CVS NAMD build (Fri Jan 30 2009 - 03:36:00 CST)
  • Re: double-wide sampling with soft-core (Thu Jan 22 2009 - 13:25:19 CST)
  • Re: double-wide sampling with soft-core (Thu Jan 22 2009 - 12:02:36 CST)
  • Re: double-wide sampling with soft-core (Thu Jan 22 2009 - 04:58:40 CST)
  • Re: Single vs. Double precision (Mon Jan 19 2009 - 09:58:06 CST)
  • Re: Problems deciphering fepout (Sun Jan 18 2009 - 06:13:34 CST)
  • Re: pairlist i_upper mismatch! (Sat Nov 22 2008 - 04:22:10 CST)
  • Re: FEP: How check equilibration sufficiency? calculate dG? (Tue Oct 14 2008 - 02:45:50 CDT)
  • Re: psf generation for a small non-peptide molecule - again (Thu Oct 02 2008 - 09:57:49 CDT)
  • Re: Running minimization, heating and FEP simulation within the same configuration file. (Thu Jun 26 2008 - 02:46:41 CDT)
  • Re: Applying weak harmonic force between two proteins (Thu May 22 2008 - 09:06:57 CDT)
  • puase MD integration to communicate between jobs (Sun May 11 2008 - 12:31:50 CDT)
  • Re: howcan I use amber forcefield in NAMD? (Fri Nov 16 2007 - 05:19:37 CST)
  • C1 splitting documentation (Fri Oct 05 2007 - 08:10:21 CDT)
  • Re: Code question: Partitioning the patch contents into water and non-water (Mon Sep 10 2007 - 11:00:13 CDT)
  • Re: The charged states of histidines in green fluorescent protein. (Mon Sep 10 2007 - 09:50:46 CDT)
  • Re: Code question: Partitioning the patch contents into water and non-water (Sat Aug 18 2007 - 05:20:32 CDT)
  • Re: Question regarding NAMD nonbonded routines (Thu Jul 26 2007 - 05:04:55 CDT)
  • temperature control for small molecule simulations in vacuum (Tue Jul 24 2007 - 06:50:01 CDT)
  • FAO developers: vdW energies, forces and derivatives (Mon Jan 29 2007 - 05:23:43 CST)
  • NAMD constraint force and energy (Wed Dec 20 2006 - 04:53:12 CST)
  • 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)
• Forbes, Jeff (NIH/NIAMS) [E]
  • corrupt DCD file (Wed Aug 27 2008 - 16:54:07 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
  • TMPyP4 force field parameters (Thu Jul 05 2007 - 10:21:42 CDT)
  • bad exclusion count (Fri Nov 17 2006 - 15:19:37 CST)
  • rmsd calculation (Tue Nov 23 2004 - 06:56:32 CST)
• Francesco Pietra
  • Error: failed on end of segment with RBCG (Sun Nov 15 2009 - 03:18:57 CST)
  • Fwd: RBCG tutorial (Wed Nov 11 2009 - 03:56:35 CST)
  • RBCG tutorial (Wed Nov 11 2009 - 03:08:03 CST)
  • About ref frame for rmsd vs time (Wed Jan 30 2008 - 00:52:48 CST)
  • SMD vs RAMD (Thu Jan 24 2008 - 11:22:18 CST)
  • About Amber force fields (Sat Jan 19 2008 - 08:54:30 CST)
  • Re: About QM-MM (Thu Aug 30 2007 - 00:50:35 CDT)
  • Re: About QM-MM (Wed Aug 29 2007 - 11:54:12 CDT)
  • Re: About QM-MM (Wed Aug 29 2007 - 11:34:45 CDT)
  • Re: About QM-MM (Wed Aug 29 2007 - 11:59:28 CDT)
  • Re: About QM-MM (Wed Aug 29 2007 - 01:38:17 CDT)
  • Re: About QM-MM (Tue Aug 28 2007 - 15:19:05 CDT)
  • Re: About QM-MM (Tue Aug 28 2007 - 14:46:49 CDT)
  • About QM-MM (Tue Aug 28 2007 - 08:18:18 CDT)
  • Simulated annealing out of mainstream (Sat Jul 21 2007 - 08:18:25 CDT)
  • Re: first aid (Fri May 11 2007 - 16:14:06 CDT)
  • first aid (Tue May 08 2007 - 16:46:29 CDT)
• Francisco Castro
  • Atom Positions during simulation (Wed Dec 14 2005 - 16:27:12 CST)
• Frank Thommen
  • Re: Struggling with the compilation of NAMD 2.6 on a PBS Cluster with LAM/MPI (Wed Sep 03 2008 - 10:57:28 CDT)
  • Re: Struggling with the compilation of NAMD 2.6 on a PBS Cluster with LAM/MPI (Sun Aug 31 2008 - 06:56:39 CDT)
  • Re: Struggling with the compilation of NAMD 2.6 on a PBS Cluster with LAM/MPI (Fri Aug 29 2008 - 11:59:54 CDT)
  • Re: Struggling with the compilation of NAMD 2.6 on a PBS Cluster with LAM/MPI (Thu Aug 28 2008 - 12:21:56 CDT)
  • Re: Struggling with the compilation of NAMD 2.6 on a PBS Cluster with LAM/MPI (Thu Aug 28 2008 - 12:22:57 CDT)
  • Struggling with the compilation of NAMD 2.6 on a PBS Cluster with LAM/MPI (Wed Aug 27 2008 - 11:41:08 CDT)
• 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)
• François Marchand
  • NAMD to CHARMM unit cell information in DCD (Tue Oct 30 2007 - 14:29:41 CDT)
• Fred (Rui FENG)
  • Re: Is it a bug? TCL Script may Lead to Overflow (Mon Nov 09 2009 - 14:04:25 CST)
  • Re: Is it a bug? TCL Script may Lead to Overflow (Sat Nov 07 2009 - 15:31:29 CST)
  • Re: Is it a bug? TCL Script may Lead to Overflow (Sat Nov 07 2009 - 14:01:53 CST)
  • Is it a bug? TCL Script may Lead to Overflow (Sat Nov 07 2009 - 03:09:28 CST)
  • Rescale Temperature when velocity of COM is not zero (Mon Jun 01 2009 - 15:12:05 CDT)
  • Re: Calculating displacement in a system with periodic boundary (Tue May 12 2009 - 02:52:49 CDT)
  • Re: Calculating displacement in a system with periodic boundary (Tue May 12 2009 - 01:37:58 CDT)
  • Re: Calculating displacement in a system with periodic boundary (Tue May 12 2009 - 01:07:22 CDT)
  • Calculating displacement in a system with periodic boundary (Mon May 11 2009 - 23:26:21 CDT)
  • Re: Can I get the pressure value in a cube? (Mon Feb 23 2009 - 00:57:29 CST)
  • Re: Can I get the pressure value in a cube? (Thu Feb 19 2009 - 23:49:26 CST)
  • Can I get the pressure value in a cube? (Thu Feb 19 2009 - 22:12:35 CST)
  • Re: Constant pressure simulation: can I get the changed volume? (Thu Feb 19 2009 - 04:25:26 CST)
  • Re: Constant pressure simulation: can I get the changed volume? (Thu Feb 19 2009 - 04:26:50 CST)
  • Constant pressure simulation: can I get the changed volume? (Thu Feb 19 2009 - 01:52:55 CST)
  • Re: The limit of atom number on Blue Gene/L (Mon Jan 19 2009 - 20:41:51 CST)
  • Re: The limit of atom number on Blue Gene/L (Mon Jan 19 2009 - 17:42:03 CST)
  • The limit of atom number on Blue Gene/L (Mon Jan 19 2009 - 02:09:15 CST)
  • Re: How to keep Total Energy constant when an external force is added? (Thu Oct 23 2008 - 11:58:29 CDT)
  • How to keep Total Energy constant when an external force is added? (Wed Oct 22 2008 - 22:48:43 CDT)
• freddie salsbury
  • NAMD on itanium? (Thu Mar 11 2004 - 18:04:10 CST)
• Friedrich Salas
  • Power penis (Mon Jun 11 2007 - 07:27:35 CDT)
• Friedrick Mcdowell
  • Straining yourself when you are with a woman? (Thu Jun 07 2007 - 17:49:13 CDT)
• 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)
• FyD
  • R.E.D.-III.3 tools release - q4md-forcefieldtools.org (Sun Oct 04 2009 - 09:37:06 CDT)
• 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)
• Gabriel J
  • Problem en equilibration Protein into a bilayer membrane POPC (Mon Aug 27 2007 - 17:50:49 CDT)
• Gadi Oron
  • Re: Force Calculation in NAMD (Sun May 23 2004 - 02:37:27 CDT)
  • RE: Binding free energy of a protein complex (Wed May 05 2004 - 09:31:52 CDT)
  • Binding free energy of a protein complex (Mon May 03 2004 - 02:06:05 CDT)
  • Issues with SMD (Mon Apr 26 2004 - 07:05:26 CDT)
  • Re: still problems with namdplot (Sun Apr 18 2004 - 01:51:42 CDT)
  • Re: Load balance strategy (Tue Mar 16 2004 - 15:44:03 CST)
  • Re: FIRSTTIMESTEP in config file (Mon Mar 15 2004 - 04:02:07 CST)
  • TCL question (Sun Mar 14 2004 - 08:13:55 CST)
  • Re: Binding Energy (Tue Mar 09 2004 - 07:37:22 CST)
  • Dealing with hyperthreading (Sun Mar 07 2004 - 04:43:09 CST)
  • Pair interaction output. (Thu Feb 12 2004 - 06:21:23 CST)
  • Changing SMD parameters (Mon Feb 09 2004 - 07:32:11 CST)
  • Re: Charm++ nodelist commands (Thu Jan 08 2004 - 02:40:06 CST)
  • Re: Charm++ nodelist commands (Wed Dec 31 2003 - 03:31:17 CST)
  • Re: Charm++ nodelist commands (Tue Dec 30 2003 - 08:10:29 CST)
  • Re: Charm++ nodelist commands (Mon Dec 22 2003 - 11:30:55 CST)
  • Re: Charm++ nodelist commands (Mon Dec 22 2003 - 05:10:39 CST)
  • Bun in charmd? (Sun Dec 21 2003 - 08:53:49 CST)
  • Re: Charm++ nodelist commands (Sun Dec 21 2003 - 02:38:11 CST)
  • Charm++ nodelist commands (Thu Dec 18 2003 - 05:48:02 CST)
  • Re: Help! unstable simulation - ARG go nuts... (Wed Dec 17 2003 - 04:36:47 CST)
  • Re: Help! unstable simulation - ARG go nuts... (Tue Dec 16 2003 - 09:33:25 CST)
  • Help! unstable simulation. (Thu Dec 11 2003 - 01:51:14 CST)
• gaillard_at_chimie.u-strasbg.fr
  • Re: Software to Mutate DNA (Tue May 26 2009 - 09:35:18 CDT)
  • Re: force-field for ATP (Tue Apr 28 2009 - 19:41:13 CDT)
  • Re: display all frames simultaneously (Thu Apr 16 2009 - 22:20:37 CDT)
  • Re: how to get 2 identical trajectories using NAMD in parallel (Fri Dec 12 2008 - 11:03:26 CST)
  • Re: how to get 2 identical trajectories using NAMD in parallel (Fri Dec 12 2008 - 10:49:47 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)
• gamini_at_ncbs.res.in
  • Re: Queries on patches, GDP-topology (Tue Jul 25 2006 - 03:16:20 CDT)
  • Re: Queries on patches, GDP-topology (Mon Jul 24 2006 - 14:13:41 CDT)
  • Queries on patches, GDP-topology (Sat Jul 22 2006 - 07:36:15 CDT)
  • Re: Computing Potential of Mean Force --SMD-cv (Thu Jul 13 2006 - 07:58:37 CDT)
  • Computing Potential of Mean Force --SMD-cv (Tue Jul 11 2006 - 15:36:45 CDT)
• Gan, Yong
  • VDW energy in CHARMM force field (Tue Jul 25 2006 - 15:49:37 CDT)
  • Generating lipid bilayer model (Sat Mar 25 2006 - 23:31:18 CST)
• 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)
• Gary Lyons
  • Re: Regarding Installation (Thu Nov 20 2008 - 22:12:34 CST)
• gaurav bhatti
  • Steered Molecular Dynamics for more than one atom (Mon Aug 10 2009 - 13:55:10 CDT)
  • Steered Molecular Dynamics (Fri Jul 31 2009 - 00:33:50 CDT)
  • RE: How to calculate free energy for conformational change (Thu Jul 30 2009 - 23:51:05 CDT)
• Gaurav Sharma
  • force-field parameters for glycoproteins (Fri May 25 2007 - 13:14:33 CDT)
  • Re: How to make alkaline ph pgn file (Mon Apr 16 2007 - 21:59:26 CDT)
  • Re: Changing the protonation states of residues (Tue Mar 06 2007 - 18:08:04 CST)
  • DNA and low pH (Wed Jan 31 2007 - 15:06:46 CST)
  • Re: small query... (Fri Nov 17 2006 - 21:15:50 CST)
  • Re: small query... (Wed Nov 15 2006 - 19:56:07 CST)
  • Question about ABF (Wed Oct 25 2006 - 18:03:13 CDT)
  • mechanical force calculation (Thu Aug 31 2006 - 22:23:55 CDT)
  • Re: coordination chemistry with NAMD (Thu Aug 03 2006 - 21:06:33 CDT)
  • coordination chemistry with NAMD (Wed Aug 02 2006 - 14:04:04 CDT)
  • force calculation during to conformational change (Tue Jul 11 2006 - 11:38:15 CDT)
  • force-field parameters for TOAC (Mon Mar 27 2006 - 17:02:31 CST)
  • 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)
• gbellesia_at_chem.ucsb.edu
  • Grid Forces (Thu Jun 25 2009 - 15:31:19 CDT)
  • about TCL boundary forces (Sat Apr 29 2006 - 17:16:54 CDT)
  • still on tcl boundary forces (Tue Apr 25 2006 - 12:34:52 CDT)
  • error related to tcl boundary forces (Tue Apr 25 2006 - 00:52:38 CDT)
• gengbin
  • Re: compiler flags. (Wed Jul 14 2004 - 23:58:54 CDT)
• Gengbin Zheng
  • Re: Make NAMD2.7b1 with cuda bug? (Wed May 13 2009 - 15:47:44 CDT)
  • Re: Make NAMD2.7b1 with cuda bug? (Wed May 13 2009 - 12:09:03 CDT)
  • Re: NAMD job dies on 2-quad core server (Thu Apr 09 2009 - 23:14:31 CDT)
  • Re: NAMD job dies on 2-quad core server (Thu Apr 09 2009 - 10:22:04 CDT)
  • Re: build smp version of namd with intel 10.1 (Thu Aug 07 2008 - 10:49:00 CDT)
  • Re: Fwd: namd2 installation.. (Wed Jul 11 2007 - 01:31:30 CDT)
  • Re: Re: Charmrun issues and namd on Win 64 (Wed Jul 11 2007 - 01:34:26 CDT)
  • Re: Re: Charmrun issues and namd on Win 64 (Fri Jul 06 2007 - 16:17:28 CDT)
  • Re: namd crash: Signal: segmentation violation (Wed May 23 2007 - 14:53:23 CDT)
  • Re: namd crash: Signal: segmentation violation (Tue May 22 2007 - 10:49:08 CDT)
  • Re: namd crash: Signal: segmentation violation (Fri May 18 2007 - 16:28:54 CDT)
  • Re: namd crash: Signal: segmentation violation (Fri May 18 2007 - 15:30:34 CDT)
  • Re: NAMD on CELL BE (Thu May 10 2007 - 15:56:36 CDT)
  • Re: NAMD on CELL BE (Thu May 10 2007 - 15:43:23 CDT)
  • Re: How to build charm++ on core2 processor (Wed Apr 11 2007 - 14:26:06 CDT)
  • Re: non-parallel NAMD compilation (Mon Mar 19 2007 - 13:59:49 CDT)
  • Re: NAMD + nice (Wed Feb 21 2007 - 14:39:31 CST)
  • Re: problems with paralellism (Tue Nov 28 2006 - 13:44:45 CST)
  • Re: problems for runing NAMD on parallel computers (Wed Jun 28 2006 - 22:08:02 CDT)
  • Re: Re: Is clock skew a problem for charm++ (Wed Jun 21 2006 - 23:17:07 CDT)
  • Re: Re: Is clock skew a problem for charm++ (Wed Jun 21 2006 - 02:08:08 CDT)
  • Re: Re. Namd window network problem (Fri Jun 16 2006 - 10:52:23 CDT)
  • Re: NAMD: compile problem (Thu Jun 15 2006 - 19:21:19 CDT)
  • Re: Namd window network problem (Thu Jun 15 2006 - 14:58:08 CDT)
  • Re: Compile NAMD on Bluegene (Thu Jun 15 2006 - 12:16:40 CDT)
  • Re: Compile NAMD on Bluegene (Thu Jun 15 2006 - 12:04:49 CDT)
  • Re: Compile NAMD on Bluegene (Thu Jun 15 2006 - 01:11:34 CDT)
  • Re: running NAMD on beowulf cluster (Thu Apr 06 2006 - 00:09:18 CDT)
  • Re: running NAMD on beowulf cluster (Wed Apr 05 2006 - 16:30:27 CDT)
  • Re: help on error message during compiling (Wed Apr 05 2006 - 11:32:45 CDT)
  • Re: compile error on amd64 in src/ComputeTclBC.C (Wed Mar 15 2006 - 14:38:19 CST)
  • Re: build script in charm++-5.9 does not find mpicc or mpicxx for mpi-linux version (Tue Mar 14 2006 - 00:02:33 CST)
  • Re: charm++ over MPI (Fri Feb 17 2006 - 10:30:18 CST)
  • Re: charm++ over MPI (Thu Feb 16 2006 - 15:40:18 CST)
  • Re: charm++ over MPI (Wed Feb 15 2006 - 11:00:53 CST)
  • Re: NAMD with Myrinet MX on MacOS X (Fri Feb 03 2006 - 17:38:53 CST)
  • Re: NAMD fails on Altix (Fri Jan 13 2006 - 02:15:56 CST)
  • 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)
  • Re: Intel C/C++ compiler Version 8 for compiling NAMD on IA64 (Wed Dec 31 2003 - 13:25:53 CST)
  • Re: Charm++ nodelist commands (Wed Dec 31 2003 - 11:59:00 CST)
  • Re: Charm++ nodelist commands (Tue Dec 30 2003 - 18:05:36 CST)
  • Re: Charm++ nodelist commands (Tue Dec 30 2003 - 13:14:52 CST)
  • Re: Charm++ nodelist commands (Tue Dec 23 2003 - 17:22:29 CST)
  • Re: Bun in charmd? (Sun Dec 21 2003 - 14:11:56 CST)
  • Re: Charm++ nodelist commands (Thu Dec 18 2003 - 13:04:28 CST)
  • Re: how should I run NAMD on parallel platform? (Thu Dec 18 2003 - 02:40:16 CST)
  • Re: LDB questions/problems (Tue Dec 16 2003 - 02:33:09 CST)
  • Re: Which version MPICH-VMI does namd-ia64-vmi run on? intel compiled version or gcc complied version? (Thu Dec 11 2003 - 16:08:08 CST)
  • Re: nodelist ignored? (Mon Sep 29 2003 - 14:23:42 CDT)
• genie lfs
  • periodic cell too small (Wed May 10 2006 - 04:48:44 CDT)
  • simulated annealing (Mon May 01 2006 - 11:04:35 CDT)
  • how long should the simulation be run (Sat Apr 29 2006 - 04:33:50 CDT)
• George Benton
  • Hymen destroyer (Mon Jun 04 2007 - 06:25:11 CDT)
• George M. Giambasu
  • non-cubic boxes for Periodic Boundary Conditions (Mon Jun 19 2006 - 17:38:31 CDT)
• George Madalin Giambasu
  • Re: glibc detected : corrupted double-linked list: 0xa4657ad8 (Tue Aug 18 2009 - 12:05:22 CDT)
  • namd27: tclforces activate TI calculation by default (Sat Aug 08 2009 - 16:12:34 CDT)
  • Re: inconsistence in NAMD and AMBER energy (Tue Jul 21 2009 - 11:27:03 CDT)
  • Re: DCOLVARS_DEBUG (Tue May 05 2009 - 16:46:59 CDT)
  • Re: DCOLVARS_DEBUG (Tue May 05 2009 - 15:29:43 CDT)
  • Re: DCOLVARS_DEBUG (Tue May 05 2009 - 10:17:43 CDT)
  • DCOLVARS_DEBUG (Mon May 04 2009 - 22:49:17 CDT)
  • Re: crash with more than 96 processors (v2.7b1) (Fri May 01 2009 - 10:28:50 CDT)
  • Re: alchemical fep amber topology (Fri Mar 13 2009 - 15:38:29 CDT)
  • alchemical fep amber topology (Fri Mar 13 2009 - 13:55:22 CDT)
  • namd latest CVS version on BluegeneP (Thu Nov 20 2008 - 16:05:13 CST)
  • Re: NAMD on blue gene BG/P (Fri Jul 11 2008 - 10:17:27 CDT)
  • Re: NAMD on blue gene BG/P (Thu Jul 10 2008 - 17:00:50 CDT)
  • Re: Truncated Octahedron for VMD and NAMD simulation (Thu May 15 2008 - 15:23:51 CDT)
  • Re: PME Grid Size - how far to deviate from cell basis vectors. (Wed Feb 27 2008 - 11:04:08 CST)
  • Re: Re: umbrella sampling of decalanine using the ABF module (Mon Feb 25 2008 - 13:48:55 CST)
  • pmf segname for amber ff. MAIN? (Thu Oct 18 2007 - 00:51:36 CDT)
  • Re: how to simulate sugars (Sun May 27 2007 - 19:51:35 CDT)
  • Re: protein diffuses to boundary.. (Wed Mar 07 2007 - 18:15:08 CST)
  • Re: Crystal Structure Analysis (Tue Feb 27 2007 - 18:51:21 CST)
  • Re: force field for H2PO4- and HPO4(-2) ions (Sat Feb 24 2007 - 14:33:16 CST)
  • corrupt dcd file >2GB on PowerPc (Wed Oct 18 2006 - 10:09:48 CDT)
• Georgios Papadopoulos
  • top par for NAG, BMA ? (Mon Sep 11 2006 - 11:47:38 CDT)
  • user defined restraints? (Fri Aug 11 2006 - 04:41:17 CDT)
  • HD speed ?? (Sun Apr 30 2006 - 03:13:36 CDT)