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NAMD-L: By Author

By Author

4323 messages sorted by: [ date ] [ thread ] [ subject ] [ attachment ]
About this archive

Starting: Fri Jan 02 2009 - 02:55:43 CST
Ending: Fri Dec 31 2010 - 20:32:36 CST

• 
  • about NAMD nonbonded routines (Tue Feb 23 2010 - 02:55:29 CST)
• #SHEPHERDSON IGNATIUS MARK#
  • (no subject) (Fri Apr 09 2010 - 20:24:37 CDT)
  • FW: Parallel Simulations (Sat Feb 06 2010 - 09:56:55 CST)
• a a
  • How to generate the tcouple file for NAMD runs? (Fri Oct 29 2010 - 22:45:42 CDT)
• A D
  • Allowed CMAP dimensions in NAMD (Thu Mar 18 2010 - 20:11:24 CDT)
  • CMAP dimensions in NAMD (Thu Mar 18 2010 - 19:07:43 CDT)
  • 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)
• Aakash C R
  • (no subject) (Sat Aug 28 2010 - 04:35:48 CDT)
  • REGARDING Topology file (Fri Apr 09 2010 - 16:57:31 CDT)
• 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)
• 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)
• Achani K. Yatawara
  • Re: Re: namdcvs (Mon Jan 05 2009 - 14:37:02 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)
• Ada Zhan
  • RE: protein fixed in simulation (Wed Oct 27 2010 - 18:04:55 CDT)
  • Re:Re: Incorrect Atom Count in binary file (Wed Oct 20 2010 - 14:20:08 CDT)
• Aditya Ranganathan
  • Re: Modifying a peptide and introducing residues (Sat Aug 14 2010 - 12:02:19 CDT)
  • Modifying a peptide and introducing residues (Sat Aug 14 2010 - 05:57:28 CDT)
  • Size of Timestep (Mon Apr 05 2010 - 06:33:48 CDT)
  • Fwd: STRIDE Question from article "Interpeptide interactions induce helix to strand structural transition in Abeta peptides" (Tue Mar 23 2010 - 01:34:47 CDT)
  • STRIDE Structure Assignment and Ramachandran Plot Beta Strand allowed regions (Tue Mar 23 2010 - 01:36:42 CDT)
  • Re: Water Box Shape Changing during NVT Simulation! (Tue Mar 09 2010 - 04:12:29 CST)
  • Water Box Shape Changing during NVT Simulation! (Fri Mar 05 2010 - 21:59:26 CST)
  • Volume of the Solution used for MD simulation (Thu Mar 04 2010 - 06:32:57 CST)
  • Fwd: Coarse Graining Problem (Wed Feb 24 2010 - 05:59:51 CST)
• Agostino
  • How the seed influences the molecular dynamics simulations? (Wed Sep 23 2009 - 04:15:26 CDT)
• Agostino Bruno
  • Problem with Targeted molecular dynamics (Sun Feb 28 2010 - 10:07:25 CST)
• Ahlam Al-Rawi
  • structure problem (Wed Apr 22 2009 - 12:22:29 CDT)
• Ahmad Firoz
  • How to minimize our model by SD using namd (Tue May 19 2009 - 00:33:01 CDT)
• Ajasja LjubetiÄ�
  • Running bias exchange metadynamics simulations with NAMD (Thu Dec 30 2010 - 16:13:13 CST)
  • Which compiler is used for the official (windows) NAMD binaries (Thu Dec 16 2010 - 07:09:52 CST)
  • Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein (Thu Dec 16 2010 - 07:04:19 CST)
  • Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein (Wed Dec 15 2010 - 10:34:43 CST)
  • Using ABF to explore the conformational space of a spin label attached to a membrane protein (Wed Dec 15 2010 - 07:21:54 CST)
  • Using ABF to explore the conformational space of a spin label attached to a membrane protein (Wed Dec 08 2010 - 10:31:16 CST)
  • Re: Allowed CMAP dimensions (Fri Nov 26 2010 - 10:23:23 CST)
  • Allowed CMAP dimensions (Tue Nov 23 2010 - 11:07:33 CST)
  • Re: MD simulations increasing electrostatic potential of a certain residue (Wed Nov 17 2010 - 02:32:28 CST)
  • Re: Using NAMD for Metropolis Monte Carlo conformational searches (Wed Nov 10 2010 - 04:22:53 CST)
  • Re: Using NAMD for Metropolis Monte Carlo conformational searches (Wed Nov 10 2010 - 04:04:31 CST)
  • Using NAMD for Metropolis Monte Carlo conformational searches (Tue Nov 09 2010 - 09:12:29 CST)
  • Re: extending namd / shared library build (UNCLASSIFIED) (Tue Nov 09 2010 - 08:39:47 CST)
  • Re: Radius of gyration (Sat Oct 30 2010 - 15:57:33 CDT)
  • Constraint failure in RATTLE algorithm for atom 268 (Fri Oct 29 2010 - 05:46:16 CDT)
  • Re: global and internal motion of protein (Wed Oct 27 2010 - 03:12:08 CDT)
  • Re: protein fixed in simulation (Wed Oct 27 2010 - 02:31:11 CDT)
  • Re: Relaxed dihedral scans (or how to constrain a dihedral angle to a changing value). (Mon Oct 25 2010 - 02:18:07 CDT)
  • Relaxed dihedral scans (or how to constrain a dihedral angle to a changing value). (Thu Oct 21 2010 - 08:45:43 CDT)
  • Re: Angle in parameter file (Thu Oct 21 2010 - 07:13:17 CDT)
  • Re: how to cenvert NAMD binary coordinate file to text file (Thu Oct 21 2010 - 03:24:19 CDT)
  • Re: tmd log file (Fri Oct 15 2010 - 07:24:59 CDT)
  • Re: Namd using Charmm restart files (Thu Oct 14 2010 - 02:31:41 CDT)
  • Re: cholestrerol (Mon Aug 30 2010 - 06:15:38 CDT)
  • Re: water escape (Tue Aug 24 2010 - 12:02:25 CDT)
  • Constraints on the plane and on the atom positions (in the same simulation) (Fri Aug 06 2010 - 03:15:16 CDT)
  • Re: Using CHARMM-GUI membrane builder with NAMD (Mon Aug 02 2010 - 07:59:54 CDT)
  • Re: Using CHARMM-GUI membrane builder with NAMD (Mon Aug 02 2010 - 03:43:53 CDT)
  • Using CHARMM-GUI membrane builder with NAMD (Fri Jul 30 2010 - 09:17:36 CDT)
  • Re: Pressure is not constant in NPT ensemble (Fri Jul 30 2010 - 02:11:59 CDT)
  • Re: Running namd on multiple win32 nodes (Wed Jul 28 2010 - 07:18:16 CDT)
  • Running namd on multiple win32 nodes (Wed Jul 28 2010 - 04:42:20 CDT)
  • Re: about DCD file format document (Mon Jul 12 2010 - 08:52:05 CDT)
  • Re: Dihedral angle potential energy function (Fri Jul 02 2010 - 08:09:44 CDT)
  • Dihedral angle potential energy function (Thu Jul 01 2010 - 05:07:27 CDT)
  • NAMD terminates prematurely without error. (Wed Jun 23 2010 - 02:41:24 CDT)
  • Re: Simulation configuration file not accesible (Wed Jun 23 2010 - 02:24:38 CDT)
  • Re: multiplicity of dihedrals (Thu May 27 2010 - 03:45:45 CDT)
  • Re: software/algorithm to cluster protein conformations (Fri Apr 30 2010 - 12:08:48 CDT)
  • calculate side-chain dihedral/torsion angles (Mon Apr 12 2010 - 02:40:47 CDT)
  • Re: Re: Generate missing atoms of a coarse grained structure (Tue Apr 06 2010 - 10:22:02 CDT)
  • Re: how to set pH (Wed Mar 31 2010 - 06:59:06 CDT)
  • Re: Regenerating a .dcd file (Tue Mar 09 2010 - 07:52:18 CST)
  • Re: Multiplicity of Parameters for dihedral bond exceeded (Tue Feb 09 2010 - 06:07:22 CST)
  • Re: dcd (Mon Feb 01 2010 - 05:40:14 CST)
  • Re: dcd (Mon Feb 01 2010 - 04:25:25 CST)
  • Re: Info: Attempting to read FFTW data from FFTW_NAMD_2.7b1_Linux-Itanium-MPI-Altix.txt (Mon Feb 01 2010 - 04:09:24 CST)
  • Re: scripting error (Mon Jan 25 2010 - 07:19:48 CST)
  • Re: scripting error (Fri Jan 22 2010 - 01:48:34 CST)
  • Re: Multiplicity of Parameters for dihedral bond exceeded (Wed Nov 25 2009 - 03:42:35 CST)
• ajay singh
  • regarding parameter and topology files for a new molecule (Mon Jun 28 2010 - 02:31:26 CDT)
• Al-Ali, Hassan
  • Issue with Load Balancing (Fri Nov 05 2010 - 10:15:52 CDT)
• Ale Gomez
  • Dowser with RESIDUE LYR (Mon Aug 16 2010 - 12:02:18 CDT)
  • Re: RetinalTop (Wed Aug 04 2010 - 11:47:09 CDT)
  • Re: RetinalTop (Tue Aug 03 2010 - 11:22:19 CDT)
  • Re: RetinalTop (Mon Aug 02 2010 - 22:53:13 CDT)
  • Re: RetinalTop (Mon Aug 02 2010 - 20:00:49 CDT)
  • Re: RetinalTop (Mon Aug 02 2010 - 11:07:52 CDT)
  • Re: RetinalTop (Mon Aug 02 2010 - 10:15:41 CDT)
  • RetinalTop (Mon Aug 02 2010 - 00:47:44 CDT)
  • RetinalTop (Mon Aug 02 2010 - 08:52:10 CDT)
  • Re: Protein in a Lipid Membrane (Fri Jun 11 2010 - 08:40:33 CDT)
  • Protein in a Lipid Membrane (Thu Jun 10 2010 - 05:22:33 CDT)
  • Unstable atoms (Sat Mar 06 2010 - 23:00:30 CST)
  • 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)
• Aleksei Aksimentiev
  • Postdoc position in computational biophysics and nanotechnology (Tue May 05 2009 - 14:34:04 CDT)
• Alessandro Cembran
  • NAMD on Shared Memory (Altix UV 1000) (Thu Dec 02 2010 - 18:11:45 CST)
• Alessandro Nascimento
  • Re: Software to Mutate DNA (Mon May 25 2009 - 10:19:25 CDT)
• alessandro.venturelli_at_univr.it
  • cell on namd 2.7b1 (Wed Apr 29 2009 - 08:10:01 CDT)
• Alex Curutiu
  • specific heat - instability (Sun Aug 15 2010 - 05:49:52 CDT)
• Alex Liu
  • Colvars-history file (Sat Dec 25 2010 - 18:39:21 CST)
  • ABF on NAMD 2.7b3 (Mon Dec 20 2010 - 15:03:22 CST)
  • problem in generating psf file (Tue Nov 30 2010 - 09:12:36 CST)
• Alexander Predeus
  • Warning about PSF file (Wed Nov 24 2010 - 15:27:22 CST)
  • Re: force field for replica exchange with NAMD (Thu Oct 28 2010 - 16:15:05 CDT)
  • Cube vs. Truncated Octahedron Performance (Thu Oct 21 2010 - 17:04:42 CDT)
  • PME Kappa and Non-bonded Cutoff (Tue Oct 19 2010 - 18:20:12 CDT)
  • Modification of Colvar Module Components (Tue Oct 12 2010 - 15:44:20 CDT)
  • Re: Colvars: Using "Alpha" Component (Fri Sep 24 2010 - 16:56:21 CDT)
  • Re: Colvars: Using "Alpha" Component (Fri Sep 24 2010 - 16:10:46 CDT)
  • Re: Colvars: Using "Alpha" Component (Fri Sep 24 2010 - 13:25:31 CDT)
  • Colvars: Using "Alpha" Component (Thu Sep 23 2010 - 19:26:31 CDT)
• Alexandre Suman de Araujo
  • Re: Strange behavior of NAMD 2.7b1 (Thu Jan 14 2010 - 06:25:33 CST)
  • Strange behavior of NAMD 2.7b1 (Wed Jan 13 2010 - 12:25:49 CST)
• 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)
• alpertunga daðcan
  • CMAP dimension limited to 24 dimensions (Thu Mar 18 2010 - 21:42:03 CDT)
• Amodeo, Pietro
  • CUDA error in NAMD 2.7: Increase MAX_EXCLUSIONS (Fri Nov 26 2010 - 11:21:22 CST)
• Amr Zeinalabideen Majul
  • Slab Boundary Conditions. (Mon May 24 2010 - 14:48:47 CDT)
  • 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)
• 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)
• anas .
  • Building PSF file for protein with ions (Wed Sep 01 2010 - 05:22:50 CDT)
• Andreas Forster
  • Re: defined path for NAMD2 (Fri Dec 18 2009 - 06:35:29 CST)
• Andreas Förster
  • Re: Restart MD from a certain point? (Thu Oct 14 2010 - 10:50:14 CDT)
  • Re: coordinates and cells (Thu Feb 18 2010 - 04:47:29 CST)
  • Re: trouble in dynamics (Thu Feb 18 2010 - 04:54:31 CST)
  • coordinates and cells (Wed Feb 17 2010 - 11:00:54 CST)
  • Re: installation of namd in parallel mode (Mon Feb 15 2010 - 03:46:03 CST)
• Andreini Matteo
  • RE: anomalous behaviour of ASPP and GLUP during MD run (Thu Feb 25 2010 - 10:57:23 CST)
  • anomalous behaviour of ASPP and GLUP during MD run (Thu Feb 25 2010 - 08:24:45 CST)
  • anomalous behaviour of ASPP and GLUP during MD run (Thu Feb 25 2010 - 02:31:45 CST)
• Andres Morales
  • Andres Morales sent you a little gift (Sun Apr 11 2010 - 20:33:49 CDT)
• Andres Morales N
  • Protonation (Sat Aug 28 2010 - 21:11:49 CDT)
  • RE: TMD simulations (Mon May 03 2010 - 21:25:29 CDT)
  • FW: TMD simulations (Fri Apr 30 2010 - 19:42:08 CDT)
  • TMD simulations (Fri Apr 30 2010 - 02:52:52 CDT)
  • FW: Loop (Thu Oct 01 2009 - 09:05:35 CDT)
  • Loop (Thu Oct 01 2009 - 07:59:27 CDT)
• Andrew Emerson
  • Re: 1us simulation of 80k atom system -- how much gross structure movement is expected? (Tue Jul 20 2010 - 05:09:05 CDT)
  • Re: protein unfolding (Thu Jan 21 2010 - 09:45:55 CST)
  • Re: namd cvs compilation with a maximum number of cores to run on (Fri Feb 13 2009 - 03:36:30 CST)
• Andrew Fant
  • PSF/top/inp for joint charmm/amber benchmark (Tue Mar 31 2009 - 17:03:48 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)
• Angela Weiss
  • NAMD/VMD Research Programmer Position available (Tue Apr 06 2010 - 08:41:21 CDT)
  • Postdoc Position available (Tue Apr 06 2010 - 10:35:04 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
  • Bioinformatics Symposium at C-DAC, Pune (Fri Sep 03 2010 - 00:41:23 CDT)
  • 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)
• Anna Blice-Baum
  • unsubscribe (Sun Jun 28 2009 - 14:40:10 CDT)
• Anna Dejardin
  • psfgen error (Wed Feb 03 2010 - 07:35:54 CST)
• Anton Arkhipov
  • Re: coarse graining (Sat Aug 07 2010 - 20:41:23 CDT)
  • Re: coarse-grained model building (Tue Apr 06 2010 - 10:31:57 CDT)
  • Re: Fwd: Coarse Graining Problem (Wed Feb 24 2010 - 11:20:08 CST)
  • Re: vmd-l: Restraints on coarse grained model (Wed Dec 09 2009 - 10:58:56 CST)
  • Re: vmd-l: problems with CG protein-lipidbilayer-water system (Mon Nov 23 2009 - 00:51:43 CST)
  • 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)
• 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)
• Armen H. Poghosyan
  • About viscosity calculation (Sun Feb 21 2010 - 18:22:12 CST)
• Artem Zhmurov
  • Re: NAMD starts AMBER calculation only from 3rd run (Mon Mar 01 2010 - 14:47:14 CST)
  • Re: CUDA version status (Fri Jan 23 2009 - 19:09:47 CST)
• 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)
• asknamd asknamd
  • How to analysis RAMD data? (Tue Sep 28 2010 - 13:43:33 CDT)
• Asmita Gupta
  • unsubscribe (Fri Oct 08 2010 - 10:56:18 CDT)
  • unsubscribe (Wed Sep 22 2010 - 03:17:24 CDT)
  • error while running config file (Thu Apr 22 2010 - 13:41:29 CDT)
  • NAMD CONFIG FILE:: (Wed Apr 21 2010 - 12:50:51 CDT)
  • simulating dna (Tue Apr 20 2010 - 12:02:36 CDT)
  • simulating DNA using namd:: (Tue Apr 20 2010 - 07:07:34 CDT)
• Athanassios Stavrakoudis
  • Re: Conjugate gradient reference (Fri Oct 15 2010 - 11:24:58 CDT)
  • Re: how to save a DCD file without water in NAMD ? (Fri Aug 13 2010 - 10:23:01 CDT)
  • eucb - beta testers wanted for trajectory analysis program (Thu Feb 05 2009 - 18:18:08 CST)
• Aurum Bai
  • How do I connect the non-overlwindows of ABF's results? (Sun Jun 27 2010 - 23:14:38 CDT)
  • Could namd use the method ONIOM of Gaussian? (Thu Jun 10 2010 - 04:51:29 CDT)
  • How to solve the out of cell box for long time in Periodic Boundary Conditions? (Wed May 19 2010 - 21:06:38 CDT)
  • Could namd support the ATI-GPU (Wed Mar 17 2010 - 07:35:34 CDT)
  • About the err of "distanceZ"! (Mon Feb 22 2010 - 03:28:31 CST)
  • The problem of annihilating the solute in the aqueous (Mon Feb 22 2010 - 00:47:45 CST)
  • About the err of "Constraint failure" (Sun Feb 21 2010 - 03:13:25 CST)
  • About "equilibrate.conf' of FEP tutorial (Sat Feb 20 2010 - 07:15:58 CST)
  • About "Visualization and Analysis of CPMD data with VMD" tutorial (Wed Dec 09 2009 - 21:43:44 CST)
  • About the Nucleic Acid parameter and protein parameters (Sun Dec 06 2009 - 05:59:36 CST)
  • Could namd realizes the QM-MM method? (Fri Dec 04 2009 - 01:31:32 CST)
  • 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
  • Solute moves outside of solvent box (Thu Jan 28 2010 - 12:28:37 CST)
  • ABF question (Tue Jan 26 2010 - 17:07:05 CST)
  • Re: ABF questions (Wed Jan 13 2010 - 11:45:51 CST)
  • Re: ABF questions (Wed Jan 06 2010 - 09:56:28 CST)
  • Re: ABF questions (Tue Jan 05 2010 - 16:19:57 CST)
  • Re: ABF questions (Tue Jan 05 2010 - 12:10:04 CST)
  • ABF questions (Tue Jan 05 2010 - 10:27:47 CST)
  • 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)
• avl211_at_lehigh.edu
  • Issue with NAMD Not understand (Fri Nov 12 2010 - 12:29:32 CST)
• Axel Kohlmeyer
  • Re: Errata to: Update to CUDA error in NAMD 2.7: Increase MAX_EXCLUSIONS: problem persists and CPU-only MD scales poorly (Tue Dec 28 2010 - 03:46:37 CST)
  • Re: About plumed installation problem in NAMD_2.6_AIX-POWER-MPI (Tue Dec 28 2010 - 03:35:00 CST)
  • Re: Adding special VdW parameters (Sat Dec 25 2010 - 11:22:38 CST)
  • Re: Re: question about repeating output text (Thu Dec 23 2010 - 04:07:46 CST)
  • Re: NBFIX and cuda (Wed Dec 22 2010 - 10:51:19 CST)
  • Re: Why do different versions of NAMD deserve different simulation results? (Mon Dec 20 2010 - 06:54:53 CST)
  • Re: Why do different versions of NAMD deserve different simulation results? (Mon Dec 20 2010 - 06:48:27 CST)
  • Re: counting h-bond in system with vmd (Sat Dec 18 2010 - 04:51:30 CST)
  • Re: Langevin Damping = 0? (Fri Dec 17 2010 - 14:40:03 CST)
  • Re: Adding extra bond (Fri Dec 17 2010 - 04:20:11 CST)
  • Re: Interaction potentials W-S (Thu Dec 16 2010 - 05:31:58 CST)
  • Re: problem with cuda version (Thu Dec 16 2010 - 05:24:44 CST)
  • Re: Asking for some sample PDB and PSF files of carbon nanotube (Wed Dec 15 2010 - 10:52:08 CST)
  • Re: memory allocation failed on processor 0 (Wed Dec 15 2010 - 10:40:47 CST)
  • Re: questions about user defined potential in NAMD (Tue Dec 14 2010 - 04:10:05 CST)
  • Re: Fwd: Installing NAMD on windows (Sat Dec 04 2010 - 13:51:41 CST)
  • Re: NAMD on Shared Memory (Altix UV 1000) (Thu Dec 02 2010 - 21:24:44 CST)
  • Re: pair interaction energy for 2 water molecules (Thu Dec 02 2010 - 21:35:23 CST)
  • Re: pair interaction energy for 2 water molecules (Mon Nov 29 2010 - 04:56:45 CST)
  • Re: writing back coordinates of waters that cross the unit cell (Fri Nov 26 2010 - 11:26:13 CST)
  • Re: writing back coordinates of waters that cross the unit cell (Thu Nov 25 2010 - 09:07:55 CST)
  • Re: morse potentials in NAMD revisited (Wed Nov 24 2010 - 13:05:31 CST)
  • Re: Different Dielectric constant value for different segment (Mon Nov 22 2010 - 09:07:06 CST)
  • Re: how best to build a GPU-accelerated desktop machine for NAMD? (Fri Nov 19 2010 - 22:00:38 CST)
  • Re: Bad Global Exclusion Count Errors in (Relatively) Simple System (Tue Nov 16 2010 - 21:27:25 CST)
  • Re: berendsen thermostat (Mon Nov 15 2010 - 08:56:01 CST)
  • Re: pair interaction calculations (Sun Nov 14 2010 - 11:58:19 CST)
  • Interactive MD driver/controller software no longer in beta (Fri Nov 12 2010 - 09:41:59 CST)
  • Re: Using NAMD for Metropolis Monte Carlo conformational searches (Wed Nov 10 2010 - 09:10:02 CST)
  • Re: Using NAMD for Metropolis Monte Carlo conformational searches (Tue Nov 09 2010 - 10:06:58 CST)
  • Re: finding appropriate topology file for polymers (Sun Nov 07 2010 - 12:29:28 CST)
  • Re: about Hydrogen Bond correlation function (Thu Nov 04 2010 - 08:59:45 CDT)
  • Re: a question about modifying the NAMD input file (Mon Oct 25 2010 - 12:56:36 CDT)
  • Re: getting desired angle (Mon Oct 25 2010 - 08:08:30 CDT)
  • Re: NAMD with missing residues (Sun Oct 24 2010 - 18:10:13 CDT)
  • Re: getting desired angle (Sun Oct 24 2010 - 18:06:00 CDT)
  • Re: Cube vs. Truncated Octahedron Performance (Thu Oct 21 2010 - 18:02:20 CDT)
  • Re: Amber topology in CUDA NAMD - can it be done? (Tue Oct 19 2010 - 08:32:45 CDT)
  • Re: Amber topology in CUDA NAMD - can it be done? (Tue Oct 19 2010 - 08:42:15 CDT)
  • Re: Changing functions without recompiling (Mon Oct 18 2010 - 22:12:10 CDT)
  • Re: Changing functions without recompiling (Mon Oct 18 2010 - 17:39:28 CDT)
  • Re: Denied permission on dcd file preventing simulation (Mon Oct 18 2010 - 10:06:45 CDT)
  • Re: top file for CNT (Sun Oct 17 2010 - 13:49:44 CDT)
  • Re: change force field in NAMD (Fri Oct 15 2010 - 10:58:33 CDT)
  • Re: Restart MD from a certain point? (Thu Oct 14 2010 - 09:04:49 CDT)
  • Re: how to improve the occupation of GPU with NAMD-2.7b3-CUDA (Mon Oct 11 2010 - 22:09:15 CDT)
  • Re: Regarding answering questions in a forum. Re: Langevin process in NAMD tutorial (Mon Oct 11 2010 - 18:54:28 CDT)
  • Re: Regarding answering questions in a forum. Re: Langevin process in NAMD tutorial (Mon Oct 11 2010 - 15:16:21 CDT)
  • Re: Langevin process in NAMD tutorial (Mon Oct 11 2010 - 12:21:04 CDT)
  • Re: how to improve the occupation of GPU with NAMD-2.7b3-CUDA (Mon Oct 11 2010 - 08:55:41 CDT)
  • Re: Flushing memory into output file (Thu Oct 07 2010 - 16:30:44 CDT)
  • Re: Flushing memory into output file (Thu Oct 07 2010 - 12:42:50 CDT)
  • Re: Is the DCD file size consistent for consecutive runs? (Thu Oct 07 2010 - 10:07:53 CDT)
  • Re: NAMD installation (Mon Oct 04 2010 - 10:04:58 CDT)
  • Re: unable to open binary file (Mon Oct 04 2010 - 10:03:32 CDT)
  • Re: FFTW and NAMD problems during compiling on BluegeneL (Wed Sep 29 2010 - 05:52:15 CDT)
  • Re: question on hydrogen bond (Mon Sep 06 2010 - 04:08:32 CDT)
  • Re: NAMD Cuda NBFIX Terms (Thu Sep 02 2010 - 16:42:56 CDT)
  • Re: claen water (Mon Aug 30 2010 - 07:53:17 CDT)
  • Re: parameter file for carbon nanotube (Tue Aug 17 2010 - 04:12:56 CDT)
  • Re: how to save a DCD file without water in NAMD ? (Fri Aug 13 2010 - 08:54:51 CDT)
  • Re: positive total energy (Wed Aug 11 2010 - 08:44:03 CDT)
  • Re: Mysterious Formation of Solvent Spheres (Wed Aug 11 2010 - 05:23:36 CDT)
  • Re: positive total energy (Wed Aug 11 2010 - 04:35:43 CDT)
  • Re: question regarding warning. (Mon Aug 09 2010 - 05:07:39 CDT)
  • Re: Reason of FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT (Sat Aug 07 2010 - 15:28:29 CDT)
  • Re: Reason of FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT (Sat Aug 07 2010 - 13:10:15 CDT)
  • Re: Using CHARMM-GUI membrane builder with NAMD (Mon Aug 02 2010 - 07:45:53 CDT)
  • Re: Interaction energy difference (Thu Jul 29 2010 - 00:08:52 CDT)
  • Re: tclforces: measure distances in NAMD 2.6b2 ? (Sun Jul 25 2010 - 18:43:59 CDT)
  • Re: Running namd on Apple's XGrid (Sun Jul 25 2010 - 07:19:56 CDT)
  • Re: Running NAMD on SGI Altix system (Thu Jul 22 2010 - 16:08:22 CDT)
  • Re: running namd faster (Tue Jul 20 2010 - 05:52:40 CDT)
  • Re: 1us simulation of 80k atom system -- how much gross structure movement is expected? (Mon Jul 19 2010 - 21:03:22 CDT)
  • Re: CPU GPU comparison (Fri Jul 16 2010 - 08:39:18 CDT)
  • Re: about DCD file format document (Mon Jul 12 2010 - 07:29:02 CDT)
  • Re: couldn´t find rsh program (Thu Jun 17 2010 - 15:36:10 CDT)
  • Re: Could namd use the method ONIOM of Gaussian? (Thu Jun 10 2010 - 05:36:00 CDT)
  • Re: help whit distance restraint (Wed Jun 02 2010 - 18:11:00 CDT)
  • Re: Dowser (Sat May 29 2010 - 20:09:24 CDT)
  • Re: Two questions about essential dynamics (Mon May 24 2010 - 07:41:35 CDT)
  • Re: Input/output error (Tue May 18 2010 - 04:18:20 CDT)
  • Re: Atom movement within a range of Z value (Tue May 11 2010 - 15:27:44 CDT)
  • Re: installation of namd without tcl and fftw (Tue May 11 2010 - 08:11:24 CDT)
  • Re: installation of namd without tcl and fftw (Tue May 11 2010 - 06:55:33 CDT)
  • Re: installation of namd without tcl and fftw (Mon May 10 2010 - 06:58:59 CDT)
  • Re: Re: Re:Re: Re: Re: Re: Dielectric Constant (Tue May 04 2010 - 08:03:08 CDT)
  • Re: Re:Re: Re: Re: Re: Dielectric Constant (Sat May 01 2010 - 13:22:10 CDT)
  • Re: Re: Re: Re: Dielectric Constant (Thu Apr 29 2010 - 21:34:42 CDT)
  • Re: Re: Re: Dielectric Constant (Thu Apr 29 2010 - 08:34:36 CDT)
  • Re: Re: Dielectric Constant (Thu Apr 29 2010 - 00:06:18 CDT)
  • Re: Re: Dielectric Constant (Wed Apr 28 2010 - 23:44:20 CDT)
  • Re: Dielectric Constant (Wed Apr 28 2010 - 11:17:58 CDT)
  • VRPN driver for Novint Falcon haptic device available - Looking for testers (Fri Apr 23 2010 - 16:03:08 CDT)
  • Re: setting transfer rate in IMD protocol (Wed Apr 21 2010 - 10:57:30 CDT)
  • Re: colvars error running ABF (Tue Apr 13 2010 - 22:03:23 CDT)
  • Re: Performance peoblem about NAMD-CUDA benchmarks (Tue Apr 13 2010 - 13:44:21 CDT)
  • Re: Ionize script (Thu Apr 08 2010 - 11:52:45 CDT)
  • Re: Ionize script (Wed Apr 07 2010 - 19:15:28 CDT)
  • Re: NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance. (Tue Apr 06 2010 - 12:04:40 CDT)
  • Re: Size of Timestep (Mon Apr 05 2010 - 07:54:27 CDT)
  • Re: NAMD on GPU (Sun Apr 04 2010 - 10:37:24 CDT)
  • Re: how to set pH (Wed Mar 31 2010 - 05:54:15 CDT)
  • Re: Parameter file problem (Tue Mar 30 2010 - 15:29:19 CDT)
  • Re: psf file error (Mon Mar 29 2010 - 09:23:17 CDT)
  • Re: NAMD with two GPUs (Wed Mar 24 2010 - 22:41:50 CDT)
  • Re: NAMD CUDA (Wed Mar 17 2010 - 08:51:52 CDT)
  • Re: benchmarking on Cray XT4 (Tue Mar 16 2010 - 10:35:56 CDT)
  • Re: benchmarking on Cray XT4 (Tue Mar 16 2010 - 06:49:58 CDT)
  • Re: What is the Potential Energy of a Protein in Namdenergy (Tue Mar 16 2010 - 06:55:55 CDT)
  • Re: (Tue Mar 16 2010 - 06:59:05 CDT)
  • Re: question about NAMD (Fri Mar 12 2010 - 04:56:19 CST)
  • Re: question about NAMD (Thu Mar 11 2010 - 19:55:11 CST)
  • Re: vmd-l: water molecules around proteins (Thu Mar 11 2010 - 11:49:50 CST)
  • Re: NAMD CUDA (Thu Mar 11 2010 - 03:50:25 CST)
  • Re: Regenerating a .dcd file (Tue Mar 09 2010 - 08:17:47 CST)
  • Re: Water Box Shape Changing during NVT Simulation! (Tue Mar 09 2010 - 03:38:09 CST)
  • Re: Water Box Shape Changing during NVT Simulation! (Mon Mar 08 2010 - 12:39:16 CST)
  • Re: creating an output file from a dcd file (Thu Mar 04 2010 - 11:20:31 CST)
  • Re: creating an output file from a dcd file (Tue Mar 02 2010 - 11:27:20 CST)
  • Re: Problem on periodic boundary condition (Wed Feb 24 2010 - 08:13:10 CST)
  • Re: psfgen error (Wed Feb 24 2010 - 00:19:44 CST)
  • Re: Lipid and protein interactions (Sat Feb 20 2010 - 09:49:08 CST)
  • Re: installation of namd (Tue Feb 16 2010 - 06:40:06 CST)
  • Re: error in scripting (Tue Feb 16 2010 - 06:28:55 CST)
  • Re: Generating binvelocities, bincoordinates, and extendedSystem files (AMBER) (Sun Feb 14 2010 - 04:54:11 CST)
  • Re: Bringing UMA-type mainboards to TESLA (Tue Feb 09 2010 - 18:03:38 CST)
  • Re: Re: Colvar on 2.7b2 win vs Linux MPI instalation (Tue Feb 09 2010 - 16:01:44 CST)
  • Re: FW: Parallel Simulations (Sat Feb 06 2010 - 21:16:14 CST)
  • Re: FW: Parallel Simulations (Sat Feb 06 2010 - 10:40:15 CST)
  • Re: Simulations with NAMD (Fri Feb 05 2010 - 11:14:19 CST)
  • Re: Changing the Potential Energy Function (Thu Feb 04 2010 - 22:50:30 CST)
  • Re: water structure (Tue Feb 02 2010 - 04:56:41 CST)
  • Re: unsubscribe (Mon Feb 01 2010 - 12:53:12 CST)
  • Re: water structure (Mon Feb 01 2010 - 06:15:22 CST)
  • Re: Tcl Forces error (Sun Jan 31 2010 - 16:19:53 CST)
  • Re: langevinTemp and system temperature (Fri Jan 29 2010 - 10:01:21 CST)
  • Re: Magnesium Ions Placement (Wed Jan 27 2010 - 19:52:40 CST)
  • Re: how to get .coor .vel and .xsc for a .dcd file (Wed Jan 27 2010 - 09:13:17 CST)
  • Re: velocities from a DCD file (Wed Jan 27 2010 - 08:46:28 CST)
  • Re: the maximum numbers of atoms in NAMD? (Wed Jan 27 2010 - 07:57:10 CST)
  • Re: problem whit comand "COM" (Tue Jan 26 2010 - 21:54:40 CST)
  • Re: reading dcd file (Mon Jan 25 2010 - 05:44:37 CST)
  • Re: NAMD on linux (Thu Jan 21 2010 - 11:25:00 CST)
  • Re: protein unfolding (Thu Jan 21 2010 - 08:15:10 CST)
  • Re: Reply:Re: How to convert the GROMOS parameter unit into charmm22 style (Wed Jan 20 2010 - 07:50:29 CST)
  • Re: Center of Mass Harmonic Potentials (Mon Jan 18 2010 - 19:33:18 CST)
  • Re: Strange behavior of NAMD 2.7b1 (Thu Jan 14 2010 - 08:53:43 CST)
  • Re: Strange behavior of NAMD 2.7b1 (Wed Jan 13 2010 - 13:22:13 CST)
  • Re: CPU usage when exec function is used (Fri Jan 08 2010 - 15:31:16 CST)
  • Re: dmpc bilayer (Mon Dec 28 2009 - 02:59:07 CST)
  • Re: Fw: Re: Re: How to read trajectory within CHARMM generated by NAMD (Mon Dec 28 2009 - 02:46:34 CST)
  • Re: CG equilibration recurring crashes (Sun Dec 27 2009 - 12:44:08 CST)
  • Re: CG equilibration recurring crashes (Sun Dec 27 2009 - 09:47:46 CST)
  • Re: How to read trajectory within CHARMM generated by NAMD (Sun Dec 27 2009 - 02:36:30 CST)
  • Re: Periodic cell has become too small (Thu Dec 24 2009 - 04:31:11 CST)
  • Re: problems compiling charm and NAMD on intel cluster using MPI over ethernet (Thu Dec 24 2009 - 02:30:34 CST)
  • Re: How to obtain the system force on a fixed atom (Tue Dec 22 2009 - 03:34:27 CST)
  • Re: NAMD 2.7b2 with CUDA and infinband (Mon Dec 21 2009 - 02:12:08 CST)
  • Re: NAMD on current CPUs (Thu Dec 17 2009 - 09:26:53 CST)
  • Re: Problem generating psf file in psfgen (Thu Dec 17 2009 - 01:38:00 CST)
  • Re: vmd-l: Re: Fwd: conf file for coarse grained simulation (Tue Dec 15 2009 - 11:16:14 CST)
  • Re: Free Energy Calculation of a protein (Tue Dec 15 2009 - 03:40:07 CST)
  • Re: Fwd: conf file for coarse grained simulation (Tue Dec 15 2009 - 02:17:45 CST)
  • Re: NAMD benchmark results for dual-Nehalem, was Re: questions regarding new single node box for NAMD: re components, CUDA, Fermi (Thu Dec 10 2009 - 00:52:52 CST)
  • Re: About "Visualization and Analysis of CPMD data with VMD" tutorial (Thu Dec 10 2009 - 00:11:45 CST)
  • Re: "-Wno-long-double" linking error (Wed Dec 09 2009 - 18:06:03 CST)
  • Re: which portions of NAMD are CUDA accelerated? (Wed Dec 02 2009 - 22:09:38 CST)
  • Re: rigidTolerance question (Sun Nov 29 2009 - 19:51:28 CST)
  • Re: psfgen fails to set coords for all atoms (Fri Nov 27 2009 - 15:56:05 CST)
  • Re: The Future of NAMD was Re: GeForce vs. Tesla (Wed Nov 25 2009 - 17:07:27 CST)
  • Re: error in scripting (Wed Nov 25 2009 - 01:08:21 CST)
  • Re: Difference between Linux-x86_64-TCP and Linux-x86_64 (Tue Nov 24 2009 - 07:53:57 CST)
  • Re: vmd-l: problems with CG protein-lipidbilayer-water system (Sat Nov 21 2009 - 16:54:04 CST)
  • Re: help with running namd-cuda for the tutorials (Fri Nov 20 2009 - 20:56:52 CST)
  • 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)
• B
  • Molecular dynamics of multiple organic molecules with NAMD (Thu Oct 22 2009 - 09:39:06 CDT)
• B. Nandy
  • SMD constant velocity pulling (Thu Dec 02 2010 - 00:21:32 CST)
  • Re: SMD constant velocity pulling (Wed Dec 01 2010 - 23:17:37 CST)
  • SMD constant velocity pulling (Wed Dec 01 2010 - 03:51:45 CST)
  • SMD constant velocity pulling (Wed Dec 01 2010 - 02:51:41 CST)
• bahare bamdad
  • NAMD on GPU (Sun Apr 04 2010 - 09:38:00 CDT)
  • NAMD CUDA (Tue Mar 16 2010 - 03:23:04 CDT)
  • NAMD CUDA (Thu Mar 11 2010 - 03:11:21 CST)
  • NAMD running error (Mon Feb 22 2010 - 09:38:37 CST)
• Bala subramanian
  • wrapping ions (Tue Mar 02 2010 - 03:05:45 CST)
  • multiple trajectories (Fri Feb 26 2010 - 10:50:38 CST)
  • namd job crashed (Mon Feb 01 2010 - 10:55:23 CST)
  • Info: Attempting to read FFTW data from FFTW_NAMD_2.7b1_Linux-Itanium-MPI-Altix.txt (Mon Feb 01 2010 - 03:12:04 CST)
• balaji nagarajan
  • interaction-energy (Wed Aug 18 2010 - 05:15:03 CDT)
  • lipidmonolayer (Wed Apr 22 2009 - 14:58:25 CDT)
  • how to install namd in windows xp (Sat Apr 04 2009 - 01:11:00 CDT)
• Balazs Jojart
  • Re: AW: update: segmentation faults with AMBER topology and RAMD tcl scripts (Wed Feb 24 2010 - 01:52:26 CST)
  • Re: AW: update: segmentation faults with AMBER topology and RAMD tcl scripts (Wed Feb 24 2010 - 05:41:28 CST)
  • Re: RAMD scripts and tcl version (Tue Feb 23 2010 - 04:27:03 CST)
  • Re: RAMD scripts and tcl version (Tue Feb 23 2010 - 03:33:24 CST)
• Basak Isin
  • Re: Regarding answering questions in a forum. Re: Langevin process in NAMD tutorial (Mon Oct 11 2010 - 18:11:14 CDT)
  • Re: Regarding answering questions in a forum. Re: Langevin process in NAMD tutorial (Mon Oct 11 2010 - 15:44:42 CDT)
  • Regarding answering questions in a forum. Re: Langevin process in NAMD tutorial (Mon Oct 11 2010 - 14:56:17 CDT)
  • dihedral terms for a parameter file (Sun Jul 25 2010 - 17:09:09 CDT)
  • Re: Protein in a Lipid Membrane (Thu Jun 10 2010 - 18:18:03 CDT)
  • Re: Dowser (Sat May 29 2010 - 21:48:12 CDT)
  • Re: Dowser (Sat May 29 2010 - 20:21:38 CDT)
  • Dowser (Sat May 29 2010 - 19:25:37 CDT)
  • software/algorithm to cluster protein conformations (Thu Apr 29 2010 - 17:51:59 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)
• benc_at_bsc.es
  • maximum residues using AMBER parm with NAMD (Wed Jul 22 2009 - 05:09:17 CDT)
• Benjamin Bouvier
  • Re: Distance Restraint (Tue Nov 23 2010 - 11:00:45 CST)
  • Amber topology in CUDA NAMD - can it be done? (Tue Oct 19 2010 - 07:27:48 CDT)
  • Re: saving psf (Tue Feb 02 2010 - 02:18:51 CST)
  • 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)
• Benjamin Stauch
  • diffusion / fex peptide problem (Wed May 06 2009 - 10:24:16 CDT)
• Bennion, Brian
  • RE: modifying velocities within global master (Tue Apr 20 2010 - 15:09:06 CDT)
  • apologize for the typo (Fri Feb 12 2010 - 13:13:30 CST)
  • RE: Questions about lattice information in NAMD2.7b2 (Fri Feb 12 2010 - 12:42:45 CST)
  • Definitions of certain routine names in source (Wed Feb 03 2010 - 17:01:52 CST)
• 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)
• bharat gupta
  • Fwd: Installing NAMD on windows (Sat Dec 04 2010 - 02:07:05 CST)
• Biff Forbush
  • Re: Performance peoblem about NAMD-CUDA benchmarks (Mon Apr 12 2010 - 14:42:37 CDT)
  • Re: NAMD on GPU (Sun Apr 04 2010 - 16:58:34 CDT)
  • Re: Bringing UMA-type mainboards to TESLA (Wed Feb 10 2010 - 12:34:57 CST)
  • Re: Fwd: suitable motherboards for both graphical visualization and NAMD-CUDA computation? (Wed Jan 20 2010 - 20:32:06 CST)
  • Re: suitable motherboards for both graphical visualization and NAMD-CUDA computation? (Wed Jan 20 2010 - 17:29:49 CST)
  • NAMD-CUDA benchmarks, dual GTX295, dual Xeon Nehalem system (Sat Jan 09 2010 - 22:16:41 CST)
  • Re: CUDA-NAMD hangs -- check the Northbridge temp! (Wed Jan 06 2010 - 18:12:08 CST)
  • CUDA-NAMD hangs -- check the Northbridge temp! (Tue Jan 05 2010 - 21:51:51 CST)
  • Re: NAMD benchmark results for dual-Nehalem, was Re: questions regarding new single node box for NAMD: re components, CUDA, Fermi (Thu Dec 10 2009 - 19:47:58 CST)
  • Re: NAMD benchmark results for dual-Nehalem, was Re: questions regarding new single node box for NAMD: re components, CUDA, Fermi (Thu Dec 10 2009 - 19:57:02 CST)
  • NAMD benchmark results for dual-Nehalem, was Re: questions regarding new single node box for NAMD: re components, CUDA, Fermi (Wed Dec 09 2009 - 20:53:00 CST)
  • Re: which portions of NAMD are CUDA accelerated? (Thu Dec 03 2009 - 20:29:16 CST)
  • The Future of NAMD was Re: GeForce vs. Tesla (Wed Nov 25 2009 - 15:22:22 CST)
  • 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)
• BIN ZHANG
  • Re: NAMD and Gromacs (Thu Sep 30 2010 - 17:02:04 CDT)
  • phosphate parameters (Fri Jun 18 2010 - 12:42:18 CDT)
  • Re: Calculating interaction energy in NAMD (Sun Mar 28 2010 - 13:50:38 CDT)
  • patch missing residues (Mon Mar 15 2010 - 15:42:49 CDT)
  • implicit solvent with iapbs (Thu Jan 28 2010 - 01:33:38 CST)
  • Re: colvar module question (Tue Jan 26 2010 - 23:54:19 CST)
  • Re: colvar module question (Tue Jan 26 2010 - 01:32:50 CST)
  • colvar module question (Mon Jan 25 2010 - 15:09:24 CST)
  • colvarsInput filename problem (Wed Jan 06 2010 - 19:51:43 CST)
  • Re: FW: ABF error calculation (Fri Dec 11 2009 - 12:03:34 CST)
  • Re: Incorrect Atom Count (Wed Dec 02 2009 - 16:31:20 CST)
  • 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)
• 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)
• Bjoern Olausson
  • Re: Is the DCD file size consistent for consecutive runs? (Fri Oct 08 2010 - 11:30:36 CDT)
  • Re: Is the DCD file size consistent for consecutive runs? (Fri Oct 08 2010 - 04:27:54 CDT)
  • Re: Is the DCD file size consistent for consecutive runs? (Thu Oct 07 2010 - 06:40:17 CDT)
  • Is the DCD file size consistent for consecutive runs? (Wed Oct 06 2010 - 03:36:04 CDT)
  • Reading NAMD coor files in CHARMM -> Fail for 64Bit (Wed Aug 11 2010 - 06:57:27 CDT)
  • Re: question regarding warning. (Mon Aug 09 2010 - 03:13:58 CDT)
  • Re: RetinalTop (Tue Aug 03 2010 - 02:57:26 CDT)
  • Re: RetinalTop (Mon Aug 02 2010 - 09:49:32 CDT)
  • Re: Using CHARMM-GUI membrane builder with NAMD (Mon Aug 02 2010 - 08:21:07 CDT)
  • Re: Using CHARMM-GUI membrane builder with NAMD (Mon Aug 02 2010 - 06:56:14 CDT)
  • Re: Using CHARMM-GUI membrane builder with NAMD (Mon Aug 02 2010 - 02:37:09 CDT)
  • Re: how to submit job on a HPC equipped with infiniband (Mon Jul 26 2010 - 04:31:55 CDT)
  • Re: Helix tilt (Tue Jul 06 2010 - 10:59:54 CDT)
  • Re: namd2 still works but without any new messages in log file (Thu Jul 01 2010 - 09:27:47 CDT)
  • Re: Sudden crash - any clue about the cause? --> wc[0] status 12 wc[i].opcode 0 (Wed Jun 02 2010 - 10:13:32 CDT)
  • Sudden crash - any clue about the cause? --> wc[0] status 12 wc[i].opcode 0 (Wed Jun 02 2010 - 08:32:24 CDT)
  • Re: Run simulation in NAMD using files generated by CHARMM-GUI (Tue Jun 01 2010 - 03:22:25 CDT)
  • Re: error : atom moving too fast (Thu May 06 2010 - 06:34:45 CDT)
  • 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)
• bkziervogel_at_uchicago.edu
  • CatDCD installation (Mon Aug 30 2010 - 11:24:04 CDT)
  • Applying a positional restraint with colvars module (Mon Aug 16 2010 - 12:06:24 CDT)
• Blake Mertz
  • psfgen fails to set coords for all atoms (Fri Nov 27 2009 - 15:06:47 CST)
• Bo Liu
  • Re: Distance Restraint (Tue Nov 23 2010 - 11:16:42 CST)
  • Re: Timestep 594 (Tue May 11 2010 - 18:50:09 CDT)
  • Re: Timestep 594 (Sun May 09 2010 - 11:28:05 CDT)
  • 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)
• 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)
• Boyang Wang
  • How to set improper dihedral for trans-double bond. (Mon Nov 29 2010 - 06:15:16 CST)
• Branko
  • par_all36_cgenff.prm with NAMD2.7 - problem of file reading (Fri Dec 17 2010 - 09:19:44 CST)
  • Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein (Wed Dec 08 2010 - 11:09:53 CST)
  • Re: script for calculation of an rmsd (Sat Oct 30 2010 - 07:09:44 CDT)
  • Re: Stray PME grid charges detected possible bug 2.7b2 (Sun Oct 10 2010 - 11:23:41 CDT)
  • 2 Stray PME grid charges detected possible bug 2.7b2 (Sun Oct 10 2010 - 11:12:09 CDT)
  • Stray PME grid charges detected possible bug 2.7b2 (Sun Oct 10 2010 - 10:54:11 CDT)
  • Re: Protonation (Sun Aug 29 2010 - 06:20:03 CDT)
  • Re: change solvent (Wed Aug 18 2010 - 10:54:18 CDT)
  • ABF problem with gyration radius/Cl and Br (Wed Aug 11 2010 - 07:25:41 CDT)
  • Re: 1us simulation of 80k atom system -- how much gross structure movement is expected? (Tue Jul 20 2010 - 07:58:01 CDT)
  • Re: headgroup area calculation (Mon Jul 12 2010 - 08:14:19 CDT)
  • Re: distance colvar (Mon Jun 07 2010 - 06:17:34 CDT)
  • Re: ABF non-uniform sampling (Sun May 02 2010 - 13:36:40 CDT)
  • Re: ABF non-uniform sampling (Fri Apr 16 2010 - 05:04:37 CDT)
  • Atom type for protonated pyridine N (Fri Mar 26 2010 - 02:24:16 CDT)
  • Atom type for protonated pyridine N (Fri Mar 26 2010 - 02:31:59 CDT)
  • Re: Is two colvars file output possible during single simulation (ABF/2.7b) (Sat Feb 20 2010 - 08:58:04 CST)
  • Is two colvars file output possible during single simulation (ABF/2.7b) (Fri Feb 19 2010 - 10:51:10 CST)
  • Re: Re: Colvar on 2.7b2 win vs Linux MPI instalation (Tue Feb 09 2010 - 15:15:46 CST)
  • Re: apoa1 bencmark for 2.7 MPI compiled (Fri Feb 05 2010 - 16:02:29 CST)
  • apoa1 bencmark for 2.7 MPI compiled (Fri Feb 05 2010 - 13:00:21 CST)
  • Re: dcd] (Mon Feb 01 2010 - 10:59:57 CST)
  • Re: Colvar on 2.7b2 win vs Linux MPI instalation (Sat Jan 23 2010 - 05:32:48 CST)
  • Colvar on 2.7b2 win vs Linux MPI instalation (Fri Jan 22 2010 - 14:28:30 CST)
  • Re: Number of MC steps in ABF integrate gives entirely diferent surfaces (Thu Jan 14 2010 - 05:30:42 CST)
  • Number of MC steps in ABF integrate gives entirely diferent surfaces (Thu Jan 14 2010 - 04:42:14 CST)
  • Re: ABF questions (Wed Jan 06 2010 - 07:17:02 CST)
  • Re: Definition of two colvars for ABF (Tue Jan 05 2010 - 08:19:14 CST)
  • Re: Definition of two colvars for ABF (Fri Jan 01 2010 - 09:58:30 CST)
  • Definition of two colvars for ABF (Wed Dec 30 2009 - 14:41:20 CST)
  • 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)
• Branko2
  • Re: Fwd: Installing NAMD on windows (Sat Dec 04 2010 - 11:25:29 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)
• Brian J. Bennion
  • RE: namd27: tclforces activate TI calculation by default (Mon Aug 10 2009 - 10:36:01 CDT)
• Brian Novak
  • Re: Removing some water from a .dcd file or .coor file (Sat Mar 27 2010 - 10:27:27 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)
• Brittany Morgan
  • Tcl Forces error (Thu Jan 28 2010 - 19:39:16 CST)
  • Tcl Forces error (Thu Jan 28 2010 - 20:00:10 CST)
  • 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)
• Bruno Rodrigues
  • Problems installing NAMD (Sat Jul 31 2010 - 01:12:12 CDT)
• Bryan Holland
  • Re: Nightly build version: Parallel IO can not be used with langevin On (Wed May 19 2010 - 10:21:59 CDT)
  • Re: Nightly build version: Parallel IO can not be used with langevin On (Wed May 19 2010 - 09:21:25 CDT)
  • Issue attaching to nodes (Thu Feb 25 2010 - 10:24:13 CST)
• Buddhadev Maiti
  • About plumed installation problem in NAMD_2.6_AIX-POWER-MPI (Mon Dec 27 2010 - 21:30:38 CST)
  • wrapping problem (Mon Nov 29 2010 - 13:41:38 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. Navarro
  • positive total energy (Tue Aug 10 2010 - 08:48:59 CDT)
• c00jsw00
  • About the solvate package (Thu Aug 19 2010 - 22:25:31 CDT)
• Cameron Abrams
  • How to use lset inside tclforces/calc_forces (Mon Mar 09 2009 - 09:00:51 CDT)
• Carles Corbi Verge
  • Re: NANMA free energy surface vacuum map problems (Thu Nov 04 2010 - 09:37:34 CDT)
  • Re: NANMA free energy surface vacuum map problems (Mon Nov 01 2010 - 06:16:36 CDT)
  • NANMA free energy surface vacuum map problems (Fri Oct 29 2010 - 08:03:54 CDT)
• Casey,Richard
  • Inorganic compounds (Thu Jan 08 2009 - 12:20:34 CST)
• Cem Meydan
  • Waterbox used in minimization? (Thu May 13 2010 - 07:25:30 CDT)
• 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)
• Chaloin Laurent
  • Tcl force (Wed Oct 07 2009 - 05:22:01 CDT)
• Chao Mei
  • Re: .inter.bin files? (Thu Apr 02 2009 - 13:05:11 CDT)
• Chao Zhang
  • Different types of constraints at the same time (Thu Jul 15 2010 - 14:05:30 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)
• Charles Zhao
  • Re: Mysterious Formation of Solvent Spheres (Wed Aug 11 2010 - 18:19:07 CDT)
  • Re: Mysterious Formation of Solvent Spheres (Wed Aug 11 2010 - 15:23:53 CDT)
  • Re: Mysterious Formation of Solvent Spheres (Wed Aug 11 2010 - 11:42:16 CDT)
  • Mysterious Formation of Solvent Spheres (Wed Aug 11 2010 - 01:32:52 CDT)
  • Re: Excluding interactions? (Wed Jan 20 2010 - 13:44:47 CST)
  • Re: Excluding interactions? (Fri Jan 15 2010 - 21:12:23 CST)
  • Excluding interactions? (Thu Jan 14 2010 - 19:46:57 CST)
  • Re: NAMD on 64 bit windows 2007 (Fri Dec 04 2009 - 18:55:20 CST)
  • Re: NAMD on 64 bit windows 2007 (Fri Dec 04 2009 - 15:51:34 CST)
  • Re: Incorrect Atom Count (Thu Dec 03 2009 - 01:26:32 CST)
  • Re: Incorrect Atom Count (Wed Dec 02 2009 - 17:58:03 CST)
  • Incorrect Atom Count (Wed Dec 02 2009 - 15:53:51 CST)
• charlie
  • a cv-smd puzzle (Thu Dec 16 2010 - 10:09:55 CST)
  • a cv-smd puzzle (Thu Dec 16 2010 - 09:21:43 CST)
  • questions about smd (Wed Dec 15 2010 - 22:37:33 CST)
  • questions about smd (Wed Dec 15 2010 - 21:42:56 CST)
  • some questions about smd (Wed Dec 15 2010 - 21:03:17 CST)
  • some questions about smd (Wed Dec 15 2010 - 20:08:45 CST)
• Charlie Forde
  • Re: Umbrella Sampling Methodology (Wed Aug 18 2010 - 11:39:17 CDT)
  • Umbrella Sampling Methodology (Mon Aug 16 2010 - 06:23:15 CDT)
• Chen, Zhihong (chenz2)
  • questions about user defined potential in NAMD (Mon Dec 13 2010 - 15:48:47 CST)
  • change force field in NAMD (Fri Oct 15 2010 - 09:50:14 CDT)
  • change force field in NAMD (Fri Oct 15 2010 - 09:51:04 CDT)
  • change force field in NAMD (Thu Oct 07 2010 - 09:49:45 CDT)
  • change force field in NAMD (Mon Oct 04 2010 - 14:11:11 CDT)
  • change force field in NAMD (Fri Sep 24 2010 - 14:36:09 CDT)
  • total charge correction (Fri Sep 17 2010 - 11:33:38 CDT)
  • ewald self energy (Thu Sep 16 2010 - 15:12:07 CDT)
  • problem on pair interaction (Tue Sep 07 2010 - 15:49:04 CDT)
• chengh_at_ringo.chem.pitt.edu
  • ABF calculations: Jacobian term describing geometry entropy (Mon Aug 23 2010 - 08:13:37 CDT)
  • restraint potential used in the ABF calculations (Tue Mar 23 2010 - 13:36:22 CDT)
  • Re: The accuracy of FEP calculation (Thu Feb 11 2010 - 11:51:54 CST)
  • The accuracy of FEP calculation (Thu Feb 11 2010 - 09:58:20 CST)
  • Re: How to obtain the system force on a fixed atom (Mon Dec 21 2009 - 15:18:47 CST)
  • how to output the velocity for one selected atom in the system (Sat Dec 19 2009 - 10:49:54 CST)
  • How to obtain the system force on a fixed atom (Wed Dec 16 2009 - 08:40:37 CST)
• CHINDEA Vlad
  • FW: simulation configuration file not accesible - other reasons (Sun Nov 22 2009 - 15:04:27 CST)
  • 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)
• Chris Chipot
  • Re: FEP calculation is doing nothing (Tue Aug 10 2010 - 11:06:11 CDT)
  • Re: Query regarding ABF Tutorial on Methane Hydration (Thu Jun 24 2010 - 18:23:43 CDT)
  • Re: Query regarding ABF Tutorial on Methane Hydration (Tue Jun 22 2010 - 15:18:10 CDT)
  • Re: new NAMD user ABF setup question (Mon May 31 2010 - 10:29:53 CDT)
  • Re: (Sat Apr 17 2010 - 19:34:24 CDT)
  • Re: The accuracy of FEP calculation (Thu Feb 11 2010 - 10:45:18 CST)
  • 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)
• Chris Harrison
  • Re: ABF on NAMD 2.7b3 (Tue Dec 21 2010 - 08:20:43 CST)
  • Re: atom type (Fri Nov 19 2010 - 09:39:56 CST)
  • Re: atom type (Fri Nov 19 2010 - 06:41:57 CST)
  • Re: about Hydrogen Bond correlation function (Thu Nov 04 2010 - 06:49:40 CDT)
  • Re: Re: vmd-l: Asymmetric water molecule (Wed Nov 03 2010 - 06:02:40 CDT)
  • Re: namd install (Mon Nov 01 2010 - 13:20:56 CDT)
  • Re: MINIMIZER SLOWLY MOVING 810 ATOMS WITH BAD CONTACTS DOWNHILL (Mon Nov 01 2010 - 13:26:21 CDT)
  • Re: rmsd (Mon Nov 01 2010 - 13:23:36 CDT)
  • Re: minimization problem (Sun Oct 31 2010 - 08:43:45 CDT)
  • Re: Force field for replica (Sun Oct 31 2010 - 08:47:09 CDT)
  • Re: script for calculation of an rmsd (Sun Oct 31 2010 - 08:28:58 CDT)
  • Re: How to generate the tcouple file for NAMD runs? (Sun Oct 31 2010 - 08:23:46 CDT)
  • Re: targeted molecular dynamics (Thu Oct 14 2010 - 17:28:22 CDT)
  • Re: Alchemical FEP tutorial files (Thu Oct 07 2010 - 07:23:24 CDT)
  • Re: Accelerated MD? (Thu Sep 23 2010 - 11:17:07 CDT)
  • Re: solute movement in periodic box (Fri Sep 03 2010 - 10:57:44 CDT)
  • Re: Charmm carbohydrate force field (Tue Aug 31 2010 - 13:30:03 CDT)
  • Re: FEP substrate transformation with common moiety (Fri Aug 27 2010 - 21:47:26 CDT)
  • Re: Bin Coordinate file to pdb (Thu Jul 08 2010 - 18:26:51 CDT)
  • Re: save trajectory only for two residues (Tue Jul 06 2010 - 09:42:40 CDT)
  • Re: hydration in membrane-protein simulations (Tue Jul 06 2010 - 09:36:22 CDT)
  • Re: OPENING EXTENDED SYSTEM TRAJECTORY FILE (Mon Jun 28 2010 - 20:23:43 CDT)
  • Re: different values of "1-4scaling" in a system (Fri Jun 18 2010 - 11:49:49 CDT)
  • Re: Alchemical calculations in CUDA version of NAMD? (Wed Mar 17 2010 - 02:37:21 CDT)
  • Re: patch missing residues (Wed Mar 17 2010 - 01:10:27 CDT)
  • Re: job script for Kraken (Wed Mar 17 2010 - 00:54:50 CDT)
  • Re: restarting a simulation ? (Wed Mar 17 2010 - 00:39:27 CDT)
  • Re: Fixatoms minimization problem!! (Wed Mar 17 2010 - 00:27:37 CDT)
  • Re: FATAL ERROR:BAD GLOBAL EXCLUSION COUNT:Please help (Wed Mar 17 2010 - 00:13:12 CDT)
  • Re: (Tue Mar 16 2010 - 23:58:40 CDT)
  • Re: How to get information of computing time for LJ calculation and pair list generation (Wed Mar 17 2010 - 00:06:07 CDT)
  • Re: RAMD scripts version 4.1 (Fri Mar 05 2010 - 06:57:34 CST)
  • 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)
• 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 Jorgensen
  • Problem with topology file (Sat Dec 18 2010 - 07:35:25 CST)
  • FEP VdW and electrostatic decoupling parameters (Fri Dec 17 2010 - 10:21:39 CST)
  • Simultaneous FEP simulation of two distinct residues (Tue Dec 14 2010 - 13:44:10 CST)
  • Problem when using psfgen (Sat Dec 11 2010 - 14:56:06 CST)
  • Free energy perturbation (FEP) hybrid pdb file (Tue Dec 07 2010 - 21:36:31 CST)
  • Minimization does not converge (Thu Nov 11 2010 - 17:42:42 CST)
  • RE: Free-energy perturbation in NAMD: Evaluation of electrostatic and van der Waals terms (Tue Nov 09 2010 - 09:42:22 CST)
  • Free-energy perturbation in NAMD: Evaluation of electrostatic and van der Waals terms (Mon Nov 08 2010 - 16:23:51 CST)
  • Error in configuration file (Tue Nov 02 2010 - 11:33:12 CDT)
  • Missing angle parameters CT3 CT3 CT3 (Mon Nov 01 2010 - 18:12:06 CDT)
  • Angle in parameter file (Thu Oct 21 2010 - 06:08:03 CDT)
  • psfgen gives wrong psf file (Wed Oct 20 2010 - 04:32:56 CDT)
  • Denied permission on dcd file preventing simulation (Mon Oct 18 2010 - 09:32:07 CDT)
  • Assigning partial charges in topology file (Thu Oct 14 2010 - 13:57:30 CDT)
  • RE: Alchemical FEP tutorial files (Thu Oct 07 2010 - 09:35:31 CDT)
  • Alchemical FEP tutorial files (Thu Oct 07 2010 - 06:55:09 CDT)
• 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)
• 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)
• christos.lamprakis_at_dcb.unibe.ch
  • dissociated quartz SiO2 groups in surface (Tue Dec 14 2010 - 05:39:59 CST)
• Cojocaru,Vlad
  • unsubscribe (Thu May 06 2010 - 03:12:48 CDT)
  • RE: RAMD scripts version 4.1 (Fri Mar 05 2010 - 13:56:20 CST)
  • RE: Re: RAMD scripts version 4.1 (Fri Mar 05 2010 - 13:54:14 CST)
  • segmentation fault with AMBER topology (cvs code 03.03.2010) (Thu Mar 04 2010 - 05:28:38 CST)
  • 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)
• Cole Gleason
  • Re: Changing functions without recompiling (Tue Oct 19 2010 - 13:53:17 CDT)
  • Re: Changing functions without recompiling (Mon Oct 18 2010 - 21:24:01 CDT)
  • Re: Changing functions without recompiling (Mon Oct 18 2010 - 21:27:27 CDT)
  • Changing functions without recompiling (Mon Oct 18 2010 - 16:53:32 CDT)
• cong chen
  • About NAN error (Fri Sep 18 2009 - 01:35:51 CDT)
  • about limitdist (Mon May 18 2009 - 06:11:48 CDT)
• Corenflos, Steven
  • problems compiling charm and NAMD on intel cluster using MPI over ethernet (Wed Dec 23 2009 - 23:48:28 CST)
• Corey Fugate
  • MD papers (Thu Dec 10 2009 - 15:25:31 CST)
  • Topology files (Thu Feb 26 2009 - 16:08:38 CST)
  • Fatal error in configuration file (Wed Feb 04 2009 - 21:05:36 CST)
• Courtney Taylor
  • Re: Constraint failures and TI electrostatic calcs (Mon Dec 06 2010 - 14:18:40 CST)
  • Constraint failures and TI electrostatic calcs (Mon Dec 06 2010 - 13:26:52 CST)
  • Re: Namd using Charmm restart files (Fri Oct 15 2010 - 11:55:53 CDT)
  • Re: Namd using Charmm restart files (Thu Oct 14 2010 - 10:09:34 CDT)
  • Namd using Charmm restart files (Wed Oct 13 2010 - 16:55:00 CDT)
  • Re: Selection of alchElecLambdaStart (Tue Sep 28 2010 - 15:02:34 CDT)
  • Selection of alchElecLambdaStart (Tue Sep 28 2010 - 10:50:24 CDT)
  • RE: Questions about thermodynamic integration in NAMD 2.7b2 (Tue Sep 21 2010 - 15:14:22 CDT)
• crazylyf
  • Q=B4=D7=D4crazylyf@163.com=B5=C4=D3=CA=BC=FE?= (Tue Sep 07 2010 - 22:17:50 CDT)
  • Z-direction shrinking (Thu Jul 29 2010 - 03:33:11 CDT)
  • rough edges of energy landscape when running ABF (Thu Jun 10 2010 - 09:34:56 CDT)
  • Fatal error when running ABF simulation (Tue Jun 08 2010 - 01:00:01 CDT)
  • lipids moving (Thu Apr 22 2010 - 21:05:33 CDT)
  • how to ensure molecules adopt their favor orientations in SMD simulation (Tue Apr 06 2010 - 22:39:11 CDT)
  • how to set pH (Wed Mar 31 2010 - 05:23:58 CDT)
• Cristina Rodríguez
  • Local elevation method in NAMD? (Thu Nov 25 2010 - 16:54:12 CST)
  • Local elevation method in NAMD? (Fri Nov 26 2010 - 12:07:20 CST)
• 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)
• D70039
  • different values of "1-4scaling" in a system (Wed Jun 16 2010 - 06:00:06 CDT)
• Dai, Jian1
  • Run simulation in NAMD using files generated by CHARMM-GUI (Tue Jun 01 2010 - 00:09:27 CDT)
  • Drift of the center of mass of lipid bilayer (Mon May 24 2010 - 13:26:39 CDT)
  • Generate psf files from Scott Feller's lipid coordinates (Sat May 15 2010 - 13:46:36 CDT)
• Dale l. Schruben
  • FW: ammonia to methane/ c/o Jerome Henin (Mon Apr 26 2010 - 21:18:01 CDT)
  • FW: ammonia to methane/ c/o Jerome Henin (Fri Apr 23 2010 - 10:19:19 CDT)
  • FW: ammonia to methane/DISREGARD this post-changes to files below make methane work now (Wed Apr 07 2010 - 22:36:49 CDT)
  • ammonia to methane (Wed Apr 07 2010 - 11:37:10 CDT)
• dalton banks
  • solvate plugin with solvent other than water (Tue Aug 11 2009 - 15:02:13 CDT)
• Dan Bolintineanu
  • FEP implementation in NAMD 2.6 vs. 2.7b1 (Tue Jul 28 2009 - 16:50:37 CDT)
• Dan J Martingano
  • Loadleveler Script on Bluegene for NAMD (Fri Jul 02 2010 - 22:48:42 CDT)
• Dan Willenbring
  • Re: Problems deciphering fepout (Sat Jan 17 2009 - 08:58:14 CST)
• daniel aguayo
  • Re: Enhance electrostatic interactions? (Fri Oct 22 2010 - 16:34:19 CDT)
  • Re: CPU usage when exec function is used (Fri Jan 08 2010 - 17:46:30 CST)
  • CPU usage when exec function is used (Fri Jan 08 2010 - 14:48:42 CST)
  • 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 Hornburg
  • (no subject) (Tue Mar 16 2010 - 07:17:02 CDT)
  • (no subject) (Tue Mar 16 2010 - 06:19:40 CDT)
• David A. Horita
  • RE: namd 2.7 iverbs error 93620 attaching to node (Fri Dec 03 2010 - 11:42:46 CST)
  • RE: Fw: Re: Re: How to read trajectory within CHARMM generated by NAMD (Mon Dec 28 2009 - 08:33:31 CST)
  • stopping protein rotation with colvars (Wed Nov 25 2009 - 13:55:56 CST)
  • 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)
• David Brandon
  • "Hands-On" Workshop on Computational Biophysics, March 21-25, 2011, Atlanta, GA, USA (Tue Dec 21 2010 - 14:34:17 CST)
• David Chalmers
  • NAMD CUDA on dual Nvidia 295 GPUs (Thu Jul 23 2009 - 07:20:34 CDT)
• David Hardy
  • Re: 1-4 pair generation (Thu Sep 02 2010 - 13:30:57 CDT)
  • Re: Drude polarizability parameters (Thu May 06 2010 - 18:12:58 CDT)
  • Re: Dielectric Constant (Wed May 05 2010 - 21:16:06 CDT)
  • Re: Drude polarizability parameters (Sat Feb 20 2010 - 10:17:55 CST)
  • Re: StepsPerCycle (Wed Feb 03 2010 - 10:28:38 CST)
  • Re: StepsPerCycle (Wed Feb 03 2010 - 10:07:36 CST)
  • 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)
• 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 Kelly
  • Help: NAMD on cluster; nodes reject multiple connections (Thu Jul 01 2010 - 00:33:11 CDT)
• David Lee Braun
  • NAMD 2.7 performance issues and Questions about Compiling (Wed Nov 03 2010 - 15:27:58 CDT)
• David McGiven
  • NAMD 2.7b1 on SGI Altix 330 (Thu Mar 26 2009 - 08:50:31 CDT)
• David Tanner
  • Re: How to confirm water box is big enough? (Tue Mar 30 2010 - 15:13:10 CDT)
  • Re: rigid molecule (Sun Mar 28 2010 - 19:25:37 CDT)
  • Re: electrostatic vs van der waals (Mon Mar 01 2010 - 11:49:07 CST)
  • "-Wno-long-double" linking error (Wed Dec 09 2009 - 14:24:14 CST)
  • 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)
• DDR
  • Installation of NAMD & charm - fatal errors (Sat Mar 27 2010 - 18:23:25 CDT)
• Demet Akten
  • residue based coarse-grained simulation (Tue Nov 09 2010 - 07:03:05 CST)
  • ion concentration in residue-based coarse-grained model (Wed Sep 22 2010 - 02:49:01 CDT)
  • configuration file (Wed Sep 22 2010 - 02:51:48 CDT)
  • CmiAbort+0x5f (Fri Apr 02 2010 - 05:25:54 CDT)
  • script for lipid density (Mon Mar 08 2010 - 05:34:39 CST)
  • bonded FAD topology file (Tue Feb 16 2010 - 07:23:13 CST)
  • 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)
• Dennis Glass
  • PRESSURE, GPRESSURE, PRESSAVG, and GPRESSAVG (Wed Mar 18 2009 - 11:13:12 CDT)
• dhacademic
  • Re: pair interaction calculations (Sun Nov 14 2010 - 17:42:59 CST)
  • pair interaction calculations (Sun Nov 14 2010 - 09:51:40 CST)
  • Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. (Fri Sep 10 2010 - 14:11:23 CDT)
  • Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. (Wed Sep 08 2010 - 17:07:09 CDT)
  • Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. (Wed Sep 08 2010 - 16:46:37 CDT)
  • Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. (Tue Sep 07 2010 - 15:31:07 CDT)
  • Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. (Mon Sep 06 2010 - 17:26:29 CDT)
  • Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. (Mon Sep 06 2010 - 10:29:38 CDT)
  • Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. (Mon Sep 06 2010 - 03:29:31 CDT)
  • Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. (Fri Sep 03 2010 - 23:26:49 CDT)
  • Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. (Fri Sep 03 2010 - 12:30:57 CDT)
  • FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. (Tue Aug 31 2010 - 08:25:35 CDT)
  • hydration in membrane-protein simulations (Sat Jul 03 2010 - 10:20:23 CDT)
  • impose restraint on the internal coordinate of protein (Mon Jun 21 2010 - 13:43:58 CDT)
• Dhanashree Khanale
  • Radius of gyration (Sat Oct 30 2010 - 08:43:22 CDT)
• Dhiraj Srivastava
  • reinitvels vs restart.vel (Fri Aug 06 2010 - 15:06:05 CDT)
  • heating and binvelocities (Tue Aug 03 2010 - 11:26:36 CDT)
  • Deprotonated Lys (Thu Jul 22 2010 - 21:13:50 CDT)
• Dimitar V Pachov
  • Re: How to confirm water box is big enough? (Tue Mar 30 2010 - 15:53:46 CDT)
  • Re: high pressure (Thu Mar 11 2010 - 09:09:56 CST)
  • Re: How to read trajectory within CHARMM generated by NAMD (Mon Dec 28 2009 - 11:52:59 CST)
  • 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: Installation of NAMD & charm - fatal errors (Sun Mar 28 2010 - 04:24:43 CDT)
  • Calculating interaction energy in NAMD (Sun Mar 28 2010 - 04:28:52 CDT)
  • Re: Simulations with NAMD (Sun Feb 07 2010 - 04:39:40 CST)
  • 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)
• 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)
• divya nayar
  • switching function for electrostaic interaction (Tue Nov 30 2010 - 10:13:58 CST)
  • pair interaction energy for 2 water molecules (Mon Nov 29 2010 - 04:00:14 CST)
  • Re: pair interaction of water molecules (Sun Nov 28 2010 - 08:54:43 CST)
  • pair interaction of water molecules (Wed Nov 24 2010 - 03:41:13 CST)
  • berendsen thermostat (Mon Nov 15 2010 - 08:15:37 CST)
  • rmsd (Mon Nov 01 2010 - 03:30:11 CDT)
  • Enthalpy calculation (Thu Oct 28 2010 - 10:12:00 CDT)
  • Least squares fitting of frames of trajectory (Wed Oct 27 2010 - 23:01:29 CDT)
  • global and internal motion of protein (Wed Oct 27 2010 - 02:39:04 CDT)
  • protein fixed in simulation (Wed Oct 27 2010 - 00:53:56 CDT)
  • Tcl script in NAMD (Tue Oct 19 2010 - 08:21:48 CDT)
  • CHARMM Lorentz-berthelot mixing rules (Mon Oct 18 2010 - 05:21:52 CDT)
• 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)
• Dong Luo
  • LES dcd file split (Fri Apr 09 2010 - 15:09:08 CDT)
  • Is it possible to run replica exchange simulation on BlueGeneL? (Fri Feb 12 2010 - 11:47:21 CST)
  • 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)
• dota
  • constraints (Wed Apr 08 2009 - 04:23:40 CDT)
• dota alexiou
  • RBCG (Tue Nov 30 2010 - 02:44:51 CST)
  • RBCG-dcd files (Tue Sep 21 2010 - 16:40:00 CDT)
• doty alexiou
  • RE: RBCG (Wed Jul 14 2010 - 04:33:12 CDT)
  • RBCG (Tue Jul 13 2010 - 02:42:53 CDT)
  • residue based CG method (Tue Jul 06 2010 - 06:22:30 CDT)
  • constraints (Thu Dec 03 2009 - 15:06:49 CST)
  • adding constraints (Thu Nov 26 2009 - 15:40:09 CST)
  • 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)
• Dow Hurst
  • Re: NAMD benchmark results for dual-Nehalem, was Re: questions regarding new single node box for NAMD: re components, CUDA, Fermi (Thu Dec 10 2009 - 05:14:54 CST)
  • 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)
• 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)
• Drew buschhorn
  • Re: tutorial-l: Nanotubes tutorial - coorList(577) no such element (Thu Feb 18 2010 - 20:30:10 CST)
  • tutorial-l: Nanotubes tutorial - coorList(577) no such element (Thu Feb 18 2010 - 00:45:24 CST)
• 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)
• Eduard Schreiner
  • Re: H-bond and salt bridge between protein dimer (Sat Oct 30 2010 - 08:31:02 CDT)
  • Re: ADENOSINE-5-DIPHOSPHORIBOSE topology (Tue Oct 05 2010 - 22:11:50 CDT)
  • Re: write out the snapshot from MD trajectory (Fri Aug 27 2010 - 05:55:00 CDT)
  • Re: (Tue Jul 06 2010 - 16:21:53 CDT)
  • Re: Helix tilt (Tue Jul 06 2010 - 12:27:50 CDT)
  • Re: impose restraint on the internal coordinate of protein (Mon Jun 21 2010 - 14:41:53 CDT)
  • Re: scripting problem (Mon Jan 25 2010 - 01:04:06 CST)
• Eduardo
  • Re: dissociated quartz SiO2 groups in surface (Tue Dec 14 2010 - 11:01:13 CST)
  • Re: build a layer (Wed Aug 25 2010 - 12:29:27 CDT)
  • Re: save trajectory only for two residues (Tue Jul 06 2010 - 11:47:22 CDT)
  • Re: Dihedral angle energy in silica block (Mon Mar 01 2010 - 15:46:54 CST)
  • Re: Dihedral angle energy in silica block (Sun Feb 28 2010 - 22:41:09 CST)
  • 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: Atom movement within a range of Z value (Tue May 11 2010 - 15:45:59 CDT)
  • 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)
• Eduardo Tejera
  • Re: problems-protein minimization (Mon Jan 26 2009 - 04:04:43 CST)
• Edward Lyman
  • building a MARTINI bilayer (Wed Apr 21 2010 - 12:41:35 CDT)
  • coarse-grained model building (Mon Apr 05 2010 - 13:12:50 CDT)
  • Re: TIP4P topology (Tue Nov 03 2009 - 15:43:43 CST)
  • namd2.7b1, tip4p, and dummies (Wed Sep 30 2009 - 13:56:47 CDT)
• ehenriques_at_qui.uc.pt
  • Re: psf of insulin (Thu Nov 18 2010 - 05:08:19 CST)
  • Re: psfgen gives wrong psf file (Wed Oct 20 2010 - 08:51:16 CDT)
  • Re: beta column (Fri Sep 10 2010 - 04:25:10 CDT)
  • Re: question on hydrogen bond (Mon Sep 06 2010 - 05:06:57 CDT)
  • Re: Building PSF file for protein with ions (Wed Sep 01 2010 - 09:02:17 CDT)
  • Re: problem at maintaining geometry coordinate (Tue Aug 24 2010 - 05:51:07 CDT)
  • Re: problem at maintaining geometry coordinate (Mon Aug 23 2010 - 05:11:45 CDT)
  • Re: About the solvate package (Fri Aug 20 2010 - 03:47:28 CDT)
  • Re: change solvent (Thu Aug 19 2010 - 05:32:51 CDT)
  • Re: structure breaking (Tue Jul 27 2010 - 04:40:21 CDT)
  • Re: Help with cys unprotonated (Tue Jun 15 2010 - 05:08:55 CDT)
  • Re: parameter file for CHARMM (Wed May 26 2010 - 03:53:39 CDT)
  • Re: duplicate residue key ALA will be ignored (Tue May 18 2010 - 04:28:24 CDT)
  • Re: Acetyl group patch for lysine residue (Mon May 17 2010 - 03:56:01 CDT)
  • Re: FW: ammonia to methane/ c/o Jerome Henin (Mon Apr 26 2010 - 08:38:41 CDT)
  • Re: Regarding ligand forcefield (Fri Apr 09 2010 - 04:52:07 CDT)
  • Re: Ionize script (Thu Apr 08 2010 - 10:55:44 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)
• Elio Cino
  • standard state correction of delta G from a PMF (Tue Jun 22 2010 - 10:06:30 CDT)
  • Re: new NAMD user ABF setup question (Mon May 31 2010 - 09:57:21 CDT)
  • Re: new NAMD user ABF setup question (Fri May 28 2010 - 07:48:03 CDT)
  • new NAMD user ABF setup question (Thu May 27 2010 - 14:10:04 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)
• 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)
• Emily Chen
  • "didn't find VdW parameter for atom type NH3" error (Tue Jun 29 2010 - 07:06:33 CDT)
• End'tasa
  • Aslos (Fri Aug 28 2009 - 11:55:17 CDT)
• enz1+_at_pitt.edu
  • water molecules "collapse" during equilibration (Fri May 29 2009 - 11:38:06 CDT)
• 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 H. Lee
  • Re: Running namd on Mac OS (Tue Jul 20 2010 - 13:06:51 CDT)
  • 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)
• 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
  • Hello! (Wed Mar 17 2010 - 07:45:19 CDT)
  • Different ensembles in the same system (Wed Jul 29 2009 - 14:48:39 CDT)
• 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
  • Re: Adding extra bond (Thu Dec 16 2010 - 13:00:34 CST)
  • Re: problem in generating psf file (Tue Nov 30 2010 - 18:44:33 CST)
  • subtlety with PSFGEN - angle/dihedral regeneration (Wed Nov 24 2010 - 20:55:06 CST)
  • how best to build a GPU-accelerated desktop machine for NAMD? (Fri Nov 19 2010 - 20:08:48 CST)
  • VdW parameters for Zn and Fe in metalloproteins (Fri Nov 12 2010 - 22:05:33 CST)
  • missing libraries for NAMD 2.7 on Linux cluster? (Sat Nov 07 2009 - 01:09:17 CST)
• Erik Santiso
  • Re: change force field in NAMD (Fri Oct 22 2010 - 11:05:50 CDT)
  • Re: change force field in NAMD (Fri Oct 15 2010 - 15:30:04 CDT)
• ershela.durresi_at_yale.edu
  • question about repeating output text (Tue Jun 09 2009 - 05:58:20 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)
• Evgeniya Volkova
  • Interaction potentials W-S (Wed Dec 15 2010 - 08:13:40 CST)
• Falgun Shah
  • unsubscribe (Sun Apr 18 2010 - 22:53:44 CDT)
  • 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)
• Fatemeh Khalili
  • Re: Jarzinsky's equation (Tue Dec 07 2010 - 12:39:45 CST)
  • Re: Jarzinsky's equation (Fri Dec 03 2010 - 13:25:31 CST)
  • Re: Jarzinsky's equation (Thu Dec 02 2010 - 13:54:33 CST)
• Felipe Merino
  • Re: new NAMD user ABF setup question (Tue Jun 01 2010 - 20:15:53 CDT)
  • Re: Dowser (Sat May 29 2010 - 21:51:28 CDT)
  • About RMSD based PMF's (Thu May 13 2010 - 23:03:44 CDT)
  • Re: FEP yields the same results for forward and backward computation! (Thu May 13 2010 - 01:24:37 CDT)
  • Re: rigid molecule (Sun Mar 28 2010 - 17:45:56 CDT)
  • 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
  • Re: questions about user defined potential in NAMD (Mon Dec 13 2010 - 18:23:42 CST)
  • Re: system density (Sat Nov 27 2010 - 09:08:28 CST)
  • Re: Distance Restraint (Tue Nov 23 2010 - 13:12:23 CST)
  • Re: VdW parameters for Zn and Fe in metalloproteins (Sat Nov 13 2010 - 21:55:27 CST)
  • Re: VdW parameters for Zn and Fe in metalloproteins (Sat Nov 13 2010 - 18:10:23 CST)
  • RE: Free-energy perturbation in NAMD: Evaluation of electrostatic and van der Waals terms (Tue Nov 09 2010 - 10:26:55 CST)
  • Re: Free-energy perturbation in NAMD: Evaluation of electrostatic and van der Waals terms (Tue Nov 09 2010 - 00:38:58 CST)
  • Re: Missing angle parameters CT3 CT3 CT3 (Mon Nov 01 2010 - 20:50:45 CDT)
  • Re: parameters for Glutathione and BSO (Thu Sep 09 2010 - 22:32:29 CDT)
  • Re: g(r) calculation for CNT (Thu Sep 02 2010 - 10:30:55 CDT)
  • Re: NAMD Cuda NBFIX Terms (Wed Sep 01 2010 - 22:54:45 CDT)
  • Re: Modifying a peptide and introducing residues (Sat Aug 14 2010 - 19:09:37 CDT)
  • Re: Reason of FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT (Sat Aug 07 2010 - 19:13:59 CDT)
  • Re: Deprotonated Lys (Thu Jul 22 2010 - 23:33:39 CDT)
  • Re: RBCG (Tue Jul 13 2010 - 23:08:57 CDT)
  • Re: Constraint Failure in SMD simulation (Tue Jul 13 2010 - 23:18:47 CDT)
  • Re: "didn't find VdW parameter for atom type NH3" error (Tue Jun 29 2010 - 21:20:47 CDT)
  • Re: "didn't find VdW parameter for atom type NH3" error (Tue Jun 29 2010 - 20:34:07 CDT)
  • Re: Minimization at higher temperature (Thu Jun 03 2010 - 17:41:15 CDT)
  • Re: Constraint Failure in SMD simulation (Wed May 19 2010 - 14:48:31 CDT)
  • Re: NAMD2.7/MEtadynamics simulation analysis disparity (Thu Apr 29 2010 - 20:49:34 CDT)
  • Re: how to set pH (Wed Mar 31 2010 - 15:01:01 CDT)
  • Re: free energy changes of one subunit (Tue Mar 16 2010 - 15:29:17 CDT)
  • soft-core potential for FEP (Wed Apr 08 2009 - 17:46:33 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)
• Ferenc Ötvös, PhD
  • colvar error (Fri Mar 26 2010 - 04:45:27 CDT)
• fereshteh moradi
  • (no subject) (Wed Sep 22 2010 - 04:59:49 CDT)
  • (no subject) (Sun Aug 01 2010 - 23:25:34 CDT)
  • Dreiding parameters (Wed Jun 09 2010 - 07:17:21 CDT)
  • a gap in flowing water (Tue May 11 2010 - 06:45:31 CDT)
  • blank between nanotube and the bulk water (Fri May 07 2010 - 23:29:22 CDT)
  • How to apply an unsteady magnetic field? (Sun Oct 25 2009 - 01:52:29 CDT)
• fett_at_vtr.net
  • charges in psf and in namd (or vmd) (Wed Jun 02 2010 - 11:12:07 CDT)
  • Re: parameter file for CHARMM (Wed Jun 02 2010 - 09:57:09 CDT)
  • OPLS mixing rules (Tue Apr 06 2010 - 09:40:05 CDT)
  • 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)
• flavio seixas
  • Re: VdW parameters for Zn and Fe in metalloproteins (Sat Nov 13 2010 - 14:06:59 CST)
  • Problems with AutoPSF (Wed Aug 04 2010 - 21:20:26 CDT)
  • Re: duplicate residue key ALA will be ignored (Tue May 18 2010 - 11:21:07 CDT)
  • Re: Timestep 594 (Tue May 11 2010 - 15:38:14 CDT)
  • mininization do not go on (Sun May 09 2010 - 08:58:19 CDT)
  • Timestep 594 (Sun May 09 2010 - 09:39:36 CDT)
• Florian Janetzko
  • REMD on AIX5.3 (Tue May 19 2009 - 06:44:34 CDT)
• Floris Buelens
  • Re: Strange vdw_dU/dl values in thermodynamic integration (Tue Oct 26 2010 - 01:23:47 CDT)
  • Re: Strange vdw_dU/dl values in thermodynamic integration (Fri Oct 22 2010 - 01:36:45 CDT)
  • 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)
• Francesco Oteri
  • Re: problem regarding rattle algorithm (Fri Dec 31 2010 - 03:57:29 CST)
  • Re: Adding extra bond (Fri Dec 17 2010 - 05:52:46 CST)
  • Adding extra bond (Sun Dec 12 2010 - 04:22:05 CST)
  • Re: NAMD with missing residues (Fri Oct 22 2010 - 16:33:12 CDT)
  • I can patch namd for amber ff on GPU (Sun Oct 17 2010 - 21:50:58 CDT)
  • Re: simulation time instead of frames (Thu Oct 14 2010 - 07:12:33 CDT)
  • Re: NAMD and Gromacs (Thu Sep 30 2010 - 07:55:48 CDT)
  • Re: membrane tutorial. (Wed Sep 22 2010 - 15:49:38 CDT)
  • Re: ion concentration in residue-based coarse-grained model (Wed Sep 22 2010 - 03:50:41 CDT)
  • Re: membrane tutorial. (Wed Sep 22 2010 - 03:24:58 CDT)
  • namd2.7b3 vs namd2.7b2 (Thu Aug 12 2010 - 17:11:42 CDT)
  • Re: 1us simulation of 80k atom system -- how much gross structure movement is expected? (Mon Jul 19 2010 - 13:39:54 CDT)
  • Re: CPU GPU comparison (Fri Jul 16 2010 - 03:13:17 CDT)
  • CPU GPU comparison (Tue Jul 13 2010 - 11:47:05 CDT)
  • Re: couldn´t find rsh program (Wed Jun 23 2010 - 14:22:43 CDT)
  • Re: usage of NAMD with AMBER commands (Tue Jun 15 2010 - 16:29:15 CDT)
  • Re: error : atom moving too fast (Mon Jun 14 2010 - 02:32:07 CDT)
  • Re: error : atom moving too fast (Fri Jun 11 2010 - 01:26:57 CDT)
  • Re: Wrong energies in CUDA version (Thu Jun 03 2010 - 15:10:00 CDT)
  • Re: high atom velocity (Wed May 05 2010 - 14:12:49 CDT)
  • Re: high atom velocity (Tue May 04 2010 - 16:33:43 CDT)
  • Re: something is wrong with my equilibration (Mon Apr 26 2010 - 05:12:04 CDT)
  • Re: file writing stopped (Mon Apr 19 2010 - 10:47:30 CDT)
  • file writing stopped (Wed Apr 14 2010 - 03:34:59 CDT)
  • Re: velocities from a DCD file (Wed Jan 27 2010 - 08:37:28 CST)
• Francesco Pietra
  • Re: AW: update: segmentation faults with AMBER topology and RAMD tcl scripts (Wed Feb 24 2010 - 15:57:17 CST)
  • Re: version of tcl in binary builds (Mon Feb 22 2010 - 11:38:22 CST)
  • version of tcl in binary builds (Mon Feb 22 2010 - 10:53:08 CST)
  • Re: Can't find C-PDB bond parameters (Mon Feb 15 2010 - 11:44:52 CST)
  • Can't find C-PDB bond parameters (Mon Feb 15 2010 - 03:46:29 CST)
  • CAN'T FIND BOND PARAMETERS FOR BOND C - CPB IN PARAMETER FILES (Sun Feb 14 2010 - 10:26:01 CST)
  • Bringing UMA-type mainboards to TESLA (Tue Feb 09 2010 - 15:59:16 CST)
  • useconstantarea (Mon Dec 28 2009 - 03:35:48 CST)
  • CG equilibration recurring crashes (Sun Dec 27 2009 - 08:47:12 CST)
  • Fwd: Periodic cell has become too small (Thu Dec 24 2009 - 03:49:16 CST)
  • Periodic cell has become too small (Thu Dec 24 2009 - 03:35:52 CST)
  • reassignFreq script (Mon Dec 21 2009 - 11:33:33 CST)
  • How to prevent cg water entering a membrane (Fri Dec 18 2009 - 16:49:55 CST)
  • Fwd: vmd-l: Re: Fwd: conf file for coarse grained simulation (Wed Dec 16 2009 - 03:01:27 CST)
  • Re: vmd-l: Re: Fwd: conf file for coarse grained simulation (Wed Dec 16 2009 - 02:13:59 CST)
  • Re: Fwd: conf file for coarse grained simulation (Tue Dec 15 2009 - 10:01:30 CST)
  • Re: Fwd: conf file for coarse grained simulation (Tue Dec 15 2009 - 02:40:55 CST)
  • Fwd: conf file for coarse grained simulation (Mon Dec 14 2009 - 02:19:52 CST)
  • conf file for coarse grained simulation (Sun Dec 13 2009 - 15:08:59 CST)
  • Re: vmd-l: namd CG minimization error: unable to find angle parameters for nxg nxx nxg (Fri Dec 11 2009 - 09:52:43 CST)
  • namd CG minimization error: unable to find angle parameters for nxg nxx nxg (Thu Dec 10 2009 - 10:27:13 CST)
  • Fwd: vmd-l: Restraints on coarse grained model (Wed Dec 09 2009 - 03:07:36 CST)
  • Fwd: Running a simulation with coarse-grained protein in membrane (Tue Dec 08 2009 - 09:54:46 CST)
  • Running a simulation with coarse-grained protein in membrane (Mon Dec 07 2009 - 12:36:16 CST)
  • problems with CG protein-lipidbilayer-water system (Sat Nov 21 2009 - 12:00:54 CST)
  • Re: Re: vmd-l: problems with CG protein-lipidbilayer-water system (Sun Nov 22 2009 - 15:32:18 CST)
  • 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)
• 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)
• FyD
  • Release of R.E.D. Server 2.0 (Thu Nov 04 2010 - 04:50:36 CDT)
  • Release of the R.E.D.-III.4 tools (Wed Jul 07 2010 - 02:04:36 CDT)
  • R.E.D.-III.3 tools release - q4md-forcefieldtools.org (Sun Oct 04 2009 - 09:37:06 CDT)
• Gabriel Jara
  • Re: Nightly build version: Parallel IO can not be used with langevin On (Wed May 19 2010 - 07:46:18 CDT)
  • Compiling NAMD under SGE and OpenMPI (Thu May 13 2010 - 11:34:49 CDT)
• gaillard_at_chimie.u-strasbg.fr
  • Re: How to read trajectory within CHARMM generated by NAMD (Mon Dec 28 2009 - 08:44:16 CST)
  • 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)
• 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)
• gbellesia_at_chem.ucsb.edu
  • Re: namd job crashed (Mon Feb 01 2010 - 11:29:33 CST)
  • Grid Forces (Thu Jun 25 2009 - 15:31:19 CDT)
• Gengbin Zheng
  • Re: NAMD benchmark results for dual-Nehalem, was Re: questions regarding new single node box for NAMD: re components, CUDA, Fermi (Thu Dec 10 2009 - 11:54:33 CST)
  • 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)
• George Khelashvili
  • How to restraint angle in NAMD (Fri Oct 01 2010 - 21:32:29 CDT)
• George Madalin Giambasu
  • Re: Re: namd 2.7b2 or later - amberff/prmtop causes segfault during startup phase (Tue Apr 06 2010 - 12:12:44 CDT)
  • Re: RAMD scripts and tcl version (Tue Feb 23 2010 - 09:52:30 CST)
  • Re: namd 2.7b2 or later - amberff/prmtop causes segfault during startup phase (Mon Feb 22 2010 - 10:50:13 CST)
  • Re: namd 2.7b2 or later - amberff/prmtop causes segfault during startup phase (Mon Feb 22 2010 - 10:26:46 CST)
  • namd 2.7b2 or later - amberff/prmtop causes segfault during startup phase (Sun Feb 21 2010 - 18:01:43 CST)
  • 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)
• Germain Salvato Vallverdu
  • Re: vmd-l: RMSD Question (Mon Nov 29 2010 - 02:56:05 CST)
• Giacomo Fiorin
  • Re: questions about ABF simulations (Thu Oct 28 2010 - 15:33:19 CDT)
  • Re: Restraint on XY Plane (Fri Oct 15 2010 - 10:39:24 CDT)
  • Re: Re: metadynamics simulations slow down and down (Mon Oct 11 2010 - 11:47:44 CDT)
  • Re: metadynamics simulations slow down and down (Sun Sep 26 2010 - 08:38:51 CDT)
  • Re: Colvars: Using "Alpha" Component (Fri Sep 24 2010 - 16:35:44 CDT)
  • Re: Colvars: Using "Alpha" Component (Fri Sep 24 2010 - 17:01:27 CDT)
  • Re: Colvars: Using "Alpha" Component (Fri Sep 24 2010 - 15:48:59 CDT)
  • Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. (Wed Sep 08 2010 - 16:28:50 CDT)
  • Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. (Tue Sep 07 2010 - 11:23:35 CDT)
  • Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. (Mon Sep 06 2010 - 14:10:06 CDT)
  • Re: ABF calculations: Jacobian term describing geometry entropy (Mon Aug 23 2010 - 11:00:43 CDT)
  • Re: Umbrella Sampling Methodology (Tue Aug 17 2010 - 10:58:46 CDT)
  • Re: Applying a positional restraint with colvars module (Mon Aug 16 2010 - 16:26:23 CDT)
  • Re: Z-direction shrinking (Thu Jul 29 2010 - 09:43:23 CDT)
  • Re: impose restraint on the internal coordinate of protein (Mon Jun 21 2010 - 16:09:20 CDT)
  • Re: Hepl whit colvar subrutiene (Fri Jun 18 2010 - 20:11:10 CDT)
  • Re: Re: colvar atom syntax (Wed Jun 16 2010 - 11:20:33 CDT)
  • Re: colvars don't run with minimization ... (Mon Jun 14 2010 - 23:06:03 CDT)
  • Re: colvars: Error: in parsing "centers" (Thu Jun 10 2010 - 21:10:55 CDT)
  • Re: Re: colvar atom syntax (Thu Jun 10 2010 - 17:20:18 CDT)
  • Re: rough edges of energy landscape when running ABF (Thu Jun 10 2010 - 12:04:14 CDT)
  • Re: colvar atom syntax (Tue Jun 08 2010 - 15:01:41 CDT)
  • Re: Fatal error when running ABF simulation (Tue Jun 08 2010 - 08:45:10 CDT)
  • Re: new NAMD user ABF setup question (Thu May 27 2010 - 16:27:02 CDT)
  • Re: new NAMD user ABF setup question (Fri May 28 2010 - 09:03:59 CDT)
  • Re: ABF question (Tue May 25 2010 - 20:07:51 CDT)
  • Re: Question about Tcl/customising the colvar module (Tue May 25 2010 - 08:54:17 CDT)
  • Re: ABF in various simulations (Mon May 17 2010 - 21:17:32 CDT)
  • Re: Waterbox used in minimization? (Thu May 13 2010 - 16:08:13 CDT)
  • Re: NAMD 2.7b1 distanceDir (Fri May 07 2010 - 17:16:31 CDT)
  • Re: NAMD 2.7b1 distanceDir (Thu May 06 2010 - 17:22:40 CDT)
  • Re: Using RMSD in colvar (Tue May 04 2010 - 16:41:37 CDT)
  • Re: ABF non-uniform sampling (Sat May 01 2010 - 14:37:22 CDT)
  • Re: colvar: coordnum output (Fri Apr 30 2010 - 09:25:14 CDT)
  • Re: NAMD2.7/MEtadynamics simulation analysis disparity (Fri Apr 30 2010 - 09:16:17 CDT)
  • Re: ABF: moving system in Z direction (Tue Apr 20 2010 - 09:06:52 CDT)
  • Re: ABF: moving system in Z direction (Mon Apr 19 2010 - 12:16:08 CDT)
  • Re: which one is better to use - fixed atoms or constraints? (Wed Apr 14 2010 - 14:21:35 CDT)
  • Re: Installation problem on Win64 (Fri Apr 02 2010 - 09:11:02 CDT)
  • Re: How to confirm water box is big enough? (Tue Mar 30 2010 - 17:36:12 CDT)
  • Re: How to confirm water box is big enough? (Tue Mar 30 2010 - 16:38:00 CDT)
  • Re: NAMD/metadynamics (Fri Mar 26 2010 - 09:14:17 CDT)
  • Re: restraint potential used in the ABF calculations (Tue Mar 23 2010 - 17:41:11 CDT)
  • Re: Restarting A NAMD job with velocity file (Mon Mar 22 2010 - 17:30:00 CDT)
  • Re: free energy changes of one subunit (Tue Mar 16 2010 - 15:43:52 CDT)
  • Re: high pressure (Thu Mar 11 2010 - 13:00:56 CST)
  • Re: run multiple walkers (Fri Mar 12 2010 - 16:03:18 CST)
  • colvars fixes (Tue Mar 09 2010 - 19:36:08 CST)
  • Re: job script for Kraken (Wed Mar 03 2010 - 13:15:11 CST)
  • Re: version of tcl in binary builds (Tue Feb 23 2010 - 01:52:23 CST)
  • Re: Is two colvars file output possible during single simulation (ABF/2.7b) (Fri Feb 19 2010 - 18:44:21 CST)
  • Re: Is two colvars file output possible during single simulation (ABF/2.7b) (Sun Feb 21 2010 - 00:15:53 CST)
  • Re: Is two colvars file output possible during single simulation (ABF/2.7b) (Fri Feb 19 2010 - 18:45:48 CST)
  • Re: colvar module question (Tue Jan 26 2010 - 08:18:15 CST)
  • Re: center of mass of dummyAtom in colvar (Wed Oct 28 2009 - 13:04:41 CDT)
  • Re: center of mass of dummyAtom in colvar (Wed Oct 14 2009 - 19:19:31 CDT)
  • Re: center of mass of dummyAtom in colvar (Wed Oct 14 2009 - 18:57:43 CDT)
  • Re: restraining the COM of a group of atoms (Sat Oct 10 2009 - 01:21:25 CDT)
  • Re: extracting info from output files (Tue Sep 22 2009 - 15:12:05 CDT)
  • Re: How to access velocity coordinates from within TclForces script (Thu Sep 17 2009 - 16:37:03 CDT)
  • Re: Regarding NAMD CPU usage (Fri Sep 11 2009 - 11:11:12 CDT)
  • Re: Doubts and problem in ABF simulations (Wed Sep 02 2009 - 13:21:09 CDT)
  • Re: ABF Colvars Configuration File (Thu Aug 20 2009 - 10:59:35 CDT)
  • Re: Colvars Configuration File (Wed Aug 19 2009 - 17:16:24 CDT)
  • Re: Colvars Configuration File (Mon Aug 17 2009 - 08:46:45 CDT)
  • Re: (is there) a dependence of dynamics on WRAPPING (Sat Aug 15 2009 - 08:59:46 CDT)
  • Re: Colvars Configuration File (Sat Aug 15 2009 - 08:56:38 CDT)
  • Re: Restarting ABF (Thu Aug 13 2009 - 16:00:20 CDT)
  • Re: NAMD FFTW question? (Fri Aug 07 2009 - 14:06:05 CDT)
  • Re: Continuing simulation after constraint failure error? (Thu Aug 06 2009 - 13:17:48 CDT)
  • Re: Using preprotonated structure with NAMD (Tue Jul 28 2009 - 11:03:23 CDT)
  • Re: error running namd (Mon Jul 27 2009 - 18:07:12 CDT)
  • Re: 2.7b metadynamics ::alpha module :: folding of a single helix in water (Mon Jul 27 2009 - 11:52:44 CDT)
  • Re: colvars: Error: undefined output or restart file. (Fri Jun 26 2009 - 15:03:27 CDT)
  • bugfixes in the colvars module (ABF, metadynamics etc.) (Wed Jun 24 2009 - 16:00:27 CDT)
  • Re: 2.7b metadynamics ::hBond component :: folding of a single helix in water (Mon Jun 22 2009 - 15:18:52 CDT)
  • Re: collective variables (Wed Jun 17 2009 - 15:43:21 CDT)
  • Re: collective variables (Wed Jun 17 2009 - 13:26:44 CDT)
  • Re: 2.7b metadynamics ::alpha module :: folding of a single helix in water (Wed Jun 10 2009 - 08:57:38 CDT)
  • Re: 2.7b metadynamics ::alpha module :: folding of a single helix in water (Tue Jun 09 2009 - 12:24:39 CDT)
  • Re: 2.7b metadynamics ::alpha module :: folding of a single helix in water (Fri Jun 05 2009 - 10:53:48 CDT)
  • Re: Free energy of conformational change (Wed May 20 2009 - 11:22:38 CDT)
  • Re: NAMD 2.7b1: metadynamics+tclForces => "... design error, GlobalMasterServer..." (Thu May 14 2009 - 19:23:19 CDT)
  • Re: collective variable space PMF, including biasing potential terms? (Wed May 13 2009 - 16:38:56 CDT)
  • Re: DCOLVARS_DEBUG (Tue May 05 2009 - 17:14:49 CDT)
  • Re: DCOLVARS_DEBUG (Tue May 05 2009 - 16:19:57 CDT)
  • Re: DCOLVARS_DEBUG (Tue May 05 2009 - 13:53:18 CDT)
  • Re: DCOLVARS_DEBUG (Tue May 05 2009 - 10:23:33 CDT)
  • Re: Setting PME Grid (Thu Apr 30 2009 - 14:00:10 CDT)
  • Re: +1 offset to VMD index file? (Tue Apr 28 2009 - 11:19:58 CDT)
  • Re: Namd and MM-PBSA (Thu Apr 23 2009 - 13:28:20 CDT)
  • Re: Metadynamics in NAMD (Mon Apr 20 2009 - 12:21:46 CDT)
  • Re: PCA Analysis of CGMD (Wed Apr 15 2009 - 11:20:39 CDT)
  • Re: Writing 3 subsequent timesteps to the DCD file (Wed Apr 08 2009 - 10:22:46 CDT)
  • Re: Exiting prematurely (Fri Apr 03 2009 - 10:21:40 CDT)
  • Re: Interactive protonation (Sat Mar 28 2009 - 18:48:43 CDT)
  • Re: MINIMIZER SLOWLY MOVING ATOMS WITH BAD CONTACTS DOWNHILL (Wed Mar 25 2009 - 14:18:43 CDT)
  • Re: FW: Water density of water Box (Wed Mar 11 2009 - 10:30:05 CDT)
  • Re: how to do a MD of small part of a protein, using namd? (Mon Feb 23 2009 - 11:53:43 CST)
  • Re: ABF-Zcoord: (Wed Feb 04 2009 - 18:13:50 CST)
  • Re: Re: some recommendations for parametrizing new molecules requiredþ (Fri Jan 23 2009 - 18:41:14 CST)
• Gianluca Interlandi
  • Re: Langevin Damping = 0? (Fri Dec 17 2010 - 15:47:00 CST)
  • Re: Fwd: Installing NAMD on windows (Sat Dec 04 2010 - 10:43:34 CST)
  • Re: Jarzinsky's equation (Fri Dec 03 2010 - 14:08:00 CST)
  • Re: Jarzinsky's equation (Thu Dec 02 2010 - 14:35:54 CST)
  • Re: SMD constant velocity pulling (Thu Dec 02 2010 - 11:30:02 CST)
  • Re: SMD constant velocity pulling (Thu Dec 02 2010 - 01:38:59 CST)
  • Re: SMD constant velocity pulling (Wed Dec 01 2010 - 17:22:40 CST)
  • Re: SMD constant velocity pulling (Wed Dec 01 2010 - 12:49:50 CST)
  • Re: SMD constant velocity pulling (Wed Dec 01 2010 - 10:36:07 CST)
  • Re: SMD constant velocity pulling (Wed Dec 01 2010 - 10:33:19 CST)
  • Jarzinsky's equation (Wed Dec 01 2010 - 01:54:57 CST)
  • Re: NAMD 2.7 released (Wed Oct 20 2010 - 15:33:33 CDT)
  • Re: NAMD 2.7 released (Tue Oct 19 2010 - 20:26:03 CDT)
  • Re: Regarding answering questions in a forum. Re: Langevin process in NAMD tutorial (Mon Oct 11 2010 - 16:56:03 CDT)
  • Re: unsubscribe namd-l (Sat Aug 28 2010 - 19:13:24 CDT)
  • K25 NIH award (Wed May 26 2010 - 19:45:33 CDT)
  • Re: analysis of dcd (Mon Feb 01 2010 - 01:13:45 CST)
  • Re: Simulation question (Tue Jan 19 2010 - 13:18:58 CST)
  • Re: nonbonded potential (Thu Oct 08 2009 - 16:24:44 CDT)
  • NAMD on Ranger performance (Tue Sep 29 2009 - 17:51:12 CDT)
  • Re: NAMD2.7b1 performance (Fri Sep 25 2009 - 11:53:05 CDT)
  • Re: Cuda benchmarks namd2.7b1 - effects of configuration parameters and hardware. (Sun Aug 30 2009 - 23:55:57 CDT)
  • Re: Cuda benchmarks namd2.7b1 - effects of configuration parameters and hardware. (Sun Aug 30 2009 - 18:41:41 CDT)
  • Re: Cuda benchmarks namd2.7b1 - effects of configuration parameters and hardware. (Sun Aug 30 2009 - 14:11:25 CDT)
  • Re: Tesla Utilization -- NAMD 2.7b1 (Fri Aug 28 2009 - 11:13:13 CDT)
  • Re: Tesla Utilization -- NAMD 2.7b1 (Thu Aug 27 2009 - 19:03:54 CDT)
  • Re: NAMD FFTW question? (Fri Aug 07 2009 - 12:54:26 CDT)
  • Re: Defining Temperature for Langevin for Namd restart. (Wed Aug 05 2009 - 17:16:33 CDT)
  • Re: Defining Temperature for Langevin for Namd restart. (Wed Aug 05 2009 - 16:35:14 CDT)
  • Re: SMD output : which col represents force, second or last (Wed Aug 05 2009 - 13:10:34 CDT)
  • Re: Does Berendsen increase viscosity of water? (Wed Aug 05 2009 - 13:19:25 CDT)
  • Re: SMD restrain point in NAMD (Tue Aug 04 2009 - 16:55:52 CDT)
  • Re: SMD restrain point in NAMD (Tue Aug 04 2009 - 13:09:26 CDT)
  • Does Berendsen increase viscosity of water? (Tue Aug 04 2009 - 00:36:38 CDT)
  • Re: Langevin damping coefficient (Wed May 06 2009 - 11:04:21 CDT)
  • Re: NAMD 2.7b1 on NCSA Abe (Tue May 05 2009 - 16:53:27 CDT)
  • Langevin damping coefficient (Tue May 05 2009 - 16:49:30 CDT)
  • NAMD 2.7b1 and clustermatic (Sun May 03 2009 - 19:26:08 CDT)
  • Re: NAMD 2.7b1 on NCSA Abe (Fri May 01 2009 - 12:18:05 CDT)
  • Re: NAMD 2.7b1 on NCSA Abe (Thu Apr 30 2009 - 22:58:09 CDT)
  • Re: Setting PME Grid (Thu Apr 30 2009 - 12:52:09 CDT)
  • Re: NAMD 2.7b1 on NCSA Abe (Thu Apr 30 2009 - 12:15:37 CDT)
  • NAMD 2.7b1 on NCSA Abe (Wed Apr 29 2009 - 22:16:32 CDT)
  • NAMD 2.7b1 on Abe (Sat Apr 25 2009 - 12:17:06 CDT)
  • Re: Yet another NAMD speed concerns (Sat Apr 25 2009 - 12:05:17 CDT)
  • Re: Yet another NAMD speed concerns (Sat Apr 25 2009 - 11:43:40 CDT)
  • PARAM22 and CMAP correction (Wed Apr 22 2009 - 13:30:48 CDT)
  • Re: NAMD and new sugar parameter set (Mon Apr 20 2009 - 15:39:31 CDT)
  • NAMD and new sugar parameter set (Mon Apr 20 2009 - 00:42:14 CDT)
• Giovanni Bellesia
  • Re: followup question on error calculation in ABF (Wed Oct 07 2009 - 15:35:39 CDT)
  • followup question on error calculation in ABF (Wed Oct 07 2009 - 13:50:55 CDT)
  • Re: NAMD 2.7b1 ABF + free energy windows (Tue Sep 29 2009 - 17:24:11 CDT)
  • Re: NAMD 2.7b1 ABF + free energy windows (Tue Sep 29 2009 - 16:57:15 CDT)
  • Re: ABF calculation - normalization of the PMF (Tue Sep 29 2009 - 10:40:01 CDT)
  • ABF calculation - normalization of the PMF (Sat Sep 19 2009 - 16:59:46 CDT)
  • GridForces methodology in NAMD 2.7b1 (Fri May 22 2009 - 13:26:16 CDT)
  • Re: Water is boiling with namd and charmm (Mon Apr 13 2009 - 11:42:38 CDT)
  • REX simulations on lonestar or ranger (Mon Mar 09 2009 - 13:59:57 CDT)
• Giovanni Nico
  • usage of NAMD with AMBER commands (Tue Jun 15 2010 - 11:51:08 CDT)
• Gong Xiaojing
  • About matdcd (Sat Apr 03 2010 - 21:23:39 CDT)
• Goutham
  • minimization gradient question (Thu Feb 04 2010 - 19:20:32 CST)
  • Re: inconsistence in NAMD and AMBER energy (Tue Jul 21 2009 - 01:13:48 CDT)
  • Fatal Error Help (Mon Jul 06 2009 - 16:10:18 CDT)
  • Namd lite (Tue Jun 02 2009 - 19:54:21 CDT)
  • Force Fields (Fri May 01 2009 - 00:36:09 CDT)
  • Error : DIDN'T FIND vdW PARAMETER FOR ATOM TYPE C11 (Sat Apr 11 2009 - 00:54:22 CDT)
  • Re: Writing 3 subsequent timesteps to the DCD file (Tue Apr 07 2009 - 14:29:16 CDT)
• govardhan reddy
  • Keyword to start FEP calculation in NAMD 2.7b1 (Fri Apr 10 2009 - 15:22:30 CDT)
  • Re: Selectively turning off electrostatic interactions (Wed Mar 11 2009 - 20:05:59 CDT)
  • Re: Selectively turning off electrostatic interactions (Wed Mar 11 2009 - 15:57:33 CDT)
  • Re: Selectively turning off electrostatic interactions (Wed Mar 11 2009 - 12:47:18 CDT)
  • Selectively turning off electrostatic interactions (Wed Mar 11 2009 - 11:36:57 CDT)
  • Re: ABF calculation with TclForces script in the configuration file (Fri Jan 16 2009 - 11:10:47 CST)
  • ABF calculation with TclForces script in the configuration file (Fri Jan 16 2009 - 09:18:40 CST)
• Grabe, Michael David
  • Charmrun/INTEL MAC/2.7 (Thu Jun 04 2009 - 09:21:21 CDT)
• Grace Brannigan
  • Re: altering residues in .pdb files (Mon Mar 29 2010 - 15:20:39 CDT)
  • Re: rigid molecule (Mon Mar 29 2010 - 14:10:40 CDT)
  • Re: CMAP dimension limited to 24 dimensions (Fri Mar 19 2010 - 14:29:13 CDT)
  • Re: pressure profile (Fri Dec 04 2009 - 10:04:46 CST)
  • Re: Simultaneous water and protein minimization (Thu Nov 19 2009 - 14:06:53 CST)
  • Re: crash with more than 96 processors (v2.7b1) (Fri May 01 2009 - 16:36:11 CDT)
  • Re: crash with more than 96 processors (v2.7b1) (Fri May 01 2009 - 09:58:56 CDT)
  • Re: crash with more than 96 processors (v2.7b1) (Fri May 01 2009 - 09:48:09 CDT)
  • crash with more than 96 processors (v2.7b1) (Thu Apr 30 2009 - 14:49:58 CDT)
  • Re: crash with more than 96 processors (v2.7b1) (Tue Apr 28 2009 - 17:36:23 CDT)
  • crash with more than 96 processors (v2.7b1) (Tue Apr 28 2009 - 14:16:07 CDT)
  • Re: Writing 3 subsequent timesteps to the DCD file (Wed Apr 08 2009 - 17:36:19 CDT)
  • Re: FW: Water density of water Box (Wed Mar 11 2009 - 09:26:08 CDT)
  • pressure profile calculations (Wed Feb 11 2009 - 16:58:06 CST)
  • Re: TCL: divide by zero (Thu Feb 05 2009 - 10:12:01 CST)
  • Re: tcl script (Mon Feb 02 2009 - 23:26:34 CST)
  • Re: Aligning the distance between two centroids with an axis (Fri Jan 30 2009 - 10:01:55 CST)
• grazia cottone
  • ligand parameters (Wed Oct 20 2010 - 06:43:23 CDT)
• Greg Guthe
  • NAMD2.6 - 1D Periodic Boundary and PME - FATAL ERROR: PME requires periodic boundary conditions. (Thu May 21 2009 - 15:32:47 CDT)
  • Re: NAMD 2.7b1 on Athlon64 Gigabit MPI - Compile Error "src/Settle.C:153: error: ‘_mm_cvtsd_f64’ was not declared in this scope" (Thu Apr 02 2009 - 21:02:44 CDT)
  • NAMD 2.7b1 on Athlon64 Gigabit MPI - Compile Error "src/Settle.C:153: error: ‘_mm_cvtsd_f64’ was not declared in this scope" (Thu Apr 02 2009 - 18:50:44 CDT)
• Guanglei Cui
  • requirements for running the precompiled Linux-x86_64-ibverbs (Thu May 20 2010 - 08:49:26 CDT)
  • Re: NAMD 2.7b1 distanceDir (Mon May 10 2010 - 11:04:25 CDT)
  • Re: NAMD 2.7b1 distanceDir (Fri May 07 2010 - 12:02:15 CDT)
  • NAMD 2.7b1 distanceDir (Thu May 06 2010 - 13:03:34 CDT)
  • Re: Intel 11 compilers (Fri Jul 10 2009 - 10:45:17 CDT)
  • Re: NAMD infiniband performance (Mon Jun 01 2009 - 21:27:07 CDT)
  • Re: NAMD infiniband performance (Mon Jun 01 2009 - 15:15:23 CDT)
  • Re: NAMD infiniband performance (Tue May 19 2009 - 11:04:39 CDT)
  • Re: NAMD infiniband performance (Tue May 19 2009 - 11:06:09 CDT)
  • Re: NAMD infiniband performance (Tue May 19 2009 - 08:56:00 CDT)
  • NAMD infiniband performance (Mon May 18 2009 - 16:10:55 CDT)
  • Re: tip4p on namd 2.7b (Wed Apr 22 2009 - 16:17:57 CDT)
  • Re: tip4p on namd 2.7b (Wed Apr 22 2009 - 10:52:19 CDT)
• guardiani_at_fi.infn.it
  • Force constant scaling (Tue Aug 31 2010 - 09:45:14 CDT)
• Guillaume Stirnemann
  • simulating TIP4P with NAMD 2.7b2 (Tue Mar 16 2010 - 08:33:48 CDT)
• Guoxiong Su
  • How were the output files of the Replica Exchange Method sorted? (Sun Dec 12 2010 - 14:11:37 CST)
  • trajectory in temperature from Replica Exchange MD (Thu Dec 02 2010 - 13:45:04 CST)
• Gurunath Katagi
  • FATAL ERROR: CAN'T FIND CROSSTERM PARAMETERS FOR CC NH1 CT1 C NH1 CT1 C NH1 (Sat Nov 06 2010 - 02:41:31 CDT)
  • gradual increase in the temperature after minimization (Wed Dec 09 2009 - 12:21:34 CST)
  • RMSD for individual residue (Mon Nov 30 2009 - 11:55:34 CST)
  • Signal: segmentation violation (Fri Nov 20 2009 - 15:20:16 CST)
  • FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT (Tue Nov 10 2009 - 12:08:13 CST)
  • water box size (Sun Nov 08 2009 - 07:23:41 CST)
  • ERROR: Constraint failure in RATTLE algorithm for atom 9080! (Fri Aug 28 2009 - 00:16:01 CDT)
  • restating simuation and periodic cell conditions (Tue Aug 18 2009 - 03:23:20 CDT)
  • increase the temperature step by step after minimization (Mon Aug 10 2009 - 00:27:03 CDT)
  • pdbalias for PO4 residue (Sat Jul 11 2009 - 01:09:29 CDT)
  • Re: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR NH3 HC NH3 (Sun Jun 21 2009 - 16:35:42 CDT)
  • FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR NH3 HC NH3 (Sat Jun 20 2009 - 12:59:51 CDT)
  • calculating energy for large log files (Thu May 21 2009 - 02:30:40 CDT)
  • Fwd: psf file creation (Sun Apr 12 2009 - 19:43:48 CDT)
  • psf file creation (Fri Apr 03 2009 - 00:41:24 CDT)
  • (no subject) (Fri Feb 20 2009 - 06:08:37 CST)
  • (no subject) (Thu Feb 12 2009 - 03:13:47 CST)
  • (no subject) (Wed Feb 11 2009 - 10:49:16 CST)
  • (no subject) (Tue Jan 20 2009 - 08:25:06 CST)
• hamid mosaddeghi
  • build a layer (Wed Aug 25 2010 - 07:58:46 CDT)
• hamze rahimi
  • problem with cuda version (Wed Dec 08 2010 - 12:30:23 CST)
  • run NAMD_2.7B2 (Sat Jan 02 2010 - 00:58:42 CST)
  • error in install NAMD_2.7b2_Linux-x86_64-CUDA (Fri Dec 18 2009 - 06:59:43 CST)
  • defined path for NAMD2 (Thu Dec 17 2009 - 06:45:56 CST)
• Hannes Loeffler
  • Re: Namd with Amber ff for RNA minimization (Tue Nov 23 2010 - 07:28:26 CST)
  • Re: residue based coarse-grained simulation (Tue Nov 09 2010 - 09:37:18 CST)
  • Re: about Hydrogen Bond correlation function (Thu Nov 04 2010 - 08:42:59 CDT)
  • Re: about Hydrogen Bond correlation function (Thu Nov 04 2010 - 08:11:16 CDT)
  • Re: [ppl] error compiling charm-6.2.2 for bluegenep-xlc (Thu Oct 28 2010 - 04:18:33 CDT)
  • Re: how to cenvert NAMD binary coordinate file to text file (Thu Oct 21 2010 - 04:48:59 CDT)
  • Re: High RMSD of Coarse grain Protein (Mon Oct 18 2010 - 09:01:20 CDT)
  • Re: NAMD and Gromacs (Thu Sep 30 2010 - 10:26:56 CDT)
  • Re: benchmarking on Cray XT4 (Tue Mar 16 2010 - 09:32:38 CDT)
  • benchmarking on Cray XT4 (Tue Mar 16 2010 - 05:50:17 CDT)
  • Re: protein folding (Fri Jul 10 2009 - 10:44:24 CDT)
  • Re: cg protein folding (Wed Mar 18 2009 - 11:42:46 CDT)
• hannes.loeffler_at_stfc.ac.uk
  • error compiling charm-6.2.2 for bluegenep-xlc (Tue Oct 26 2010 - 14:22:50 CDT)
  • RE: Loadleveler Script on Bluegene for NAMD (Sat Jul 03 2010 - 06:56:49 CDT)
• Haosheng Cui
  • Re: NAMD 2.7b1 on Ranger/MPI Problems? (Fri Apr 17 2009 - 02:12:54 CDT)
• hari prasad
  • reg dynamics (Thu Feb 12 2009 - 01:58:55 CST)
• harish vashisth
  • jobs get stuck using NAMDv2.7 and stop producing output in the log-file (Fri Dec 17 2010 - 10:20:10 CST)
  • Re: Issue with NAMD Not understand (Fri Nov 12 2010 - 13:57:14 CST)
  • NAMDv2.7 stops producing output in the log-file--any help? (Tue Nov 09 2010 - 08:24:22 CST)
  • Question for Developers: NAMD 2.7 performance issues and Questions about Compiling (Thu Nov 04 2010 - 05:43:49 CDT)
  • Re: looking for topology and parameters of methamphetamine (Sun May 09 2010 - 12:42:37 CDT)
  • Re: RAMD in NAMD (Fri Apr 03 2009 - 07:22:51 CDT)
  • Re: RAMD in NAMD (Thu Apr 02 2009 - 17:13:12 CDT)
  • Error running simulation on KRAKEN XT5 (Tue Mar 10 2009 - 18:49:03 CDT)
  • Re: job submission script on KRAKEN @ NICS (Tue Mar 10 2009 - 12:10:03 CDT)
  • Re: job submission script on KRAKEN @ NICS (Fri Mar 06 2009 - 23:28:30 CST)
  • job submission script on KRAKEN @ NICS (Fri Mar 06 2009 - 22:22:50 CST)
• Hasan haska
  • NAMD installation (Mon Oct 04 2010 - 05:25:06 CDT)
• Hatley, Jade M
  • unsubscribe (Fri Jun 26 2009 - 19:02:48 CDT)
• He Yuhui
  • how to set up force parameters of a novel residue? (Thu Aug 27 2009 - 02:37:12 CDT)
  • how to save pdb file after "moveby" command in VMD? (Tue Aug 18 2009 - 21:33:42 CDT)
  • what is the charge of sulfur on thiol? (Mon Aug 17 2009 - 01:38:01 CDT)
  • how to write a command to close vmd in shell script? (Sun Aug 09 2009 - 22:21:34 CDT)
  • On naming rules in force-field parameter files? (Sun Aug 09 2009 - 20:12:21 CDT)
  • how to generate DNA psf files? (Wed Jul 29 2009 - 21:04:27 CDT)
• henri mone
  • Format of namd restartfile *.coor, *.vel) (2nd try ;) ) (Thu Nov 18 2010 - 10:05:15 CST)
  • Restart simulation (Thu Nov 11 2010 - 19:54:39 CST)
  • FATAL ERROR: Couldn't open DCD file equil0.dcd: No such file or directory (Sun Sep 05 2010 - 10:16:27 CDT)
• hgrabner
  • error codes: 255 (Wed Oct 20 2010 - 03:57:07 CDT)
  • phosphoserine simulation using toppar files and NAMD (Wed Mar 25 2009 - 06:55:56 CDT)
• Hidekazu WATANABE
  • reference of ewald method (Sun Dec 13 2009 - 06:02:27 CST)
• Hideya Nakamura
  • Re: How to get information of computing time for LJ calculation and pair list generation (Wed Mar 17 2010 - 03:32:31 CDT)
  • How to get information of computing time for LJ calculation and pair list generation (Mon Mar 15 2010 - 12:08:20 CDT)
  • How to get information of computing time for LJ calculation and pair list generation (Mon Mar 15 2010 - 12:15:18 CDT)
• Hok-Hei Tam
  • NAMD Pair Interactions Finite Box Size Correction (Tue Aug 03 2010 - 09:58:53 CDT)
  • Cationic Dummy Atom models (Sun Mar 21 2010 - 16:31:39 CDT)
  • Changing the Potential Energy Function (Thu Feb 04 2010 - 22:08:41 CST)
• Hugh Heldenbrand
  • Re: pair interaction energy for 2 water molecules (Thu Dec 02 2010 - 20:21:01 CST)
  • Re: Strange vdw_dU/dl values in thermodynamic integration (Fri Oct 22 2010 - 07:28:05 CDT)
  • Strange vdw_dU/dl values in thermodynamic integration (Thu Oct 21 2010 - 19:37:25 CDT)
  • Re: TIP4P water in AMBER parm7 format fails with 2010-06-07 nightly build (Fri Jun 11 2010 - 15:55:24 CDT)
  • TIP4P water in AMBER parm7 format fails with 2010-06-07 nightly build (Tue Jun 08 2010 - 10:30:41 CDT)
• Hugh Martin
  • Re: 'dSmooth' no longer in the ABF procedure? (Wed Dec 09 2009 - 10:44:45 CST)
  • 'dSmooth' no longer in the ABF procedure? (Wed Dec 09 2009 - 09:08:30 CST)
  • Re: Retrieving standard deviation values while using collective variables (ABF) (Thu Nov 26 2009 - 09:30:21 CST)
  • Re: Retrieving standard deviation values while using collective variables (ABF) (Thu Nov 26 2009 - 07:38:13 CST)
  • Re: Finer details of an ABF/colvar simulation (Tue Nov 24 2009 - 10:07:46 CST)
  • Finer details of an ABF/colvar simulation (Fri Nov 20 2009 - 09:10:08 CST)
  • Retrieving standard deviation values while using collective variables (ABF) (Tue Nov 10 2009 - 05:55:53 CST)
  • Re: Translocation problem while attempting to use ABF (Mon Aug 31 2009 - 07:52:40 CDT)
  • Re: ABF 'Xi' log output producing strange results (Thu Aug 27 2009 - 23:41:18 CDT)
  • ABF 'Xi' log output producing strange results (Thu Aug 27 2009 - 10:30:22 CDT)
  • Re: Clarification regarding some finer details in ABF simulations (Tue Aug 18 2009 - 10:01:08 CDT)
  • Clarification regarding some finer details in ABF simulations (Mon Aug 10 2009 - 12:33:47 CDT)
  • Re: Translocation problem while attempting to use ABF (Wed Aug 05 2009 - 12:26:30 CDT)
  • Grid Forces documentation (Thu Jul 16 2009 - 08:02:04 CDT)
  • Translocation problem while attempting to use ABF (Mon Jul 06 2009 - 10:39:38 CDT)
  • Re: Coordinate Output in both binary and ASCII. Or converting binary to ASCII in the command line (Fri Mar 06 2009 - 23:26:30 CST)
  • Re: Coordinate Output in both binary and ASCII. Or converting binary to ASCII in the command line (Mon Mar 02 2009 - 10:42:53 CST)
  • Coordinate Output in both binary and ASCII. Or converting binary to ASCII in the command line (Mon Mar 02 2009 - 10:09:56 CST)
• Hyonseok Hwang
  • parallel scaling issues (Wed Jul 21 2010 - 09:11:18 CDT)
• Hyun Chul Lee
  • Re: PSFGEN (Thu Dec 10 2009 - 22:27:04 CST)
  • PSFGEN (Mon Dec 07 2009 - 15:36:44 CST)
• Hyundeok Song
  • umbrella sampling script (Tue May 05 2009 - 17:30:28 CDT)
  • Re: tutorial for calculation of PMF using namd (Mon Mar 02 2009 - 23:46:21 CST)
• Héctor Urbina
  • Re: CUDA-accelerated NAMD does not support NBFIX parameters [RESOLVED] (Mon Sep 14 2009 - 07:24:35 CDT)
  • CUDA-accelerated NAMD does not support NBFIX parameters (Sun Sep 13 2009 - 13:47:33 CDT)
• I. Vyalov
  • FFTW and NAMD problems during compiling on BluegeneL (Wed Sep 29 2010 - 05:00:55 CDT)
  • (âÅÚ ÔÅÍÙ) (Wed Sep 29 2010 - 04:46:48 CDT)
• Ian Stokes-Rees
  • Re: Running namd on Mac OS (Tue Jul 20 2010 - 13:38:05 CDT)
  • Re: 1us simulation of 80k atom system -- how much gross structure movement is expected? (Mon Jul 19 2010 - 20:06:05 CDT)
  • 1us simulation of 80k atom system -- how much gross structure movement is expected? (Mon Jul 19 2010 - 12:18:55 CDT)
• Ibrahim Abou Hamad
  • unsubscribe (Tue Oct 12 2010 - 18:21:20 CDT)
  • segmentation faults with AMBER topology (Fri Mar 12 2010 - 13:39:59 CST)
• Ido Gan
  • Running namd on Apple's XGrid (Sun Jul 25 2010 - 02:16:44 CDT)
• Igor Petrik
  • Re: Drude polarizability parameters (Thu May 06 2010 - 17:35:20 CDT)
  • Re: Dihedral parameters for side-chains? (Mon Apr 26 2010 - 07:54:41 CDT)
  • Re: Dihedral parameters for side-chains? (Sat Apr 24 2010 - 22:41:06 CDT)
  • Dihedral parameters for side-chains? (Fri Apr 23 2010 - 11:50:30 CDT)
  • Drude polarizability parameters (Fri Feb 19 2010 - 06:09:57 CST)
• Ihsan Omur Akdag
  • zeroMomentum for SMD (Fri Aug 20 2010 - 05:58:18 CDT)
• Indrajit Deb
  • Problem on periodic boundary condition (Wed Feb 24 2010 - 07:25:28 CST)
• ipsita basu
  • namd install (Mon Nov 01 2010 - 05:53:21 CDT)
  • Fwd: minimization problem (Fri Oct 29 2010 - 00:25:58 CDT)
  • minimization problem (Wed Oct 27 2010 - 01:00:23 CDT)
  • (no subject) (Fri Oct 08 2010 - 06:00:41 CDT)
  • coarse graining (Tue Aug 03 2010 - 04:43:20 CDT)
  • structure breaking (Tue Jul 27 2010 - 00:36:35 CDT)
  • running namd faster (Tue Jul 20 2010 - 00:55:34 CDT)
  • Re: headgroup area calculation (Wed Jul 14 2010 - 02:05:22 CDT)
  • headgroup area calculation (Mon Jul 12 2010 - 07:33:47 CDT)
  • Re: error : atom moving too fast (Mon Jun 14 2010 - 01:52:37 CDT)
  • Re: error : atom moving too fast (Fri Jun 11 2010 - 00:19:15 CDT)
  • Fwd: error : atom moving too fast (Tue Jun 08 2010 - 00:20:24 CDT)
  • Re: error : atom moving too fast (Fri May 14 2010 - 00:14:30 CDT)
  • Re: installation of namd without tcl and fftw (Tue May 11 2010 - 08:02:11 CDT)
  • Re: installation of namd without tcl and fftw (Tue May 11 2010 - 00:40:59 CDT)
  • installation of namd without tcl and fftw (Mon May 10 2010 - 06:11:39 CDT)
  • Re: error : atom moving too fast (Thu May 06 2010 - 05:32:13 CDT)
  • error : atom moving too fast (Wed May 05 2010 - 01:10:33 CDT)
  • running tcl scripting (Tue Feb 23 2010 - 04:26:05 CST)
  • Fwd: reading prameter file (Mon Feb 22 2010 - 00:27:10 CST)
  • reading prameter file (Fri Feb 19 2010 - 03:58:16 CST)
  • Re: error in scripting (Wed Feb 17 2010 - 23:09:16 CST)
  • error in scripting (Tue Feb 16 2010 - 05:26:07 CST)
  • installation of namd (Tue Feb 16 2010 - 04:00:23 CST)
  • installation of namd in parallel mode (Sat Feb 13 2010 - 01:40:28 CST)
  • saving psf (Tue Feb 02 2010 - 00:53:38 CST)
  • Re: water structure (Mon Feb 01 2010 - 23:52:03 CST)
  • water structure (Mon Feb 01 2010 - 05:40:54 CST)
  • dcd (Mon Feb 01 2010 - 03:27:17 CST)
  • analysis of dcd (Sun Jan 31 2010 - 22:58:41 CST)
  • reading dcd file (Mon Jan 25 2010 - 03:20:39 CST)
  • scripting problem (Mon Jan 25 2010 - 00:15:51 CST)
  • scripting error (Thu Jan 21 2010 - 23:36:02 CST)
  • Re: starting namd (Thu Jan 21 2010 - 00:14:49 CST)
  • simulation error (Thu Jan 21 2010 - 00:13:46 CST)
  • starting namd (Tue Jan 19 2010 - 04:50:41 CST)
  • starting a job (Wed Jan 13 2010 - 04:39:34 CST)
  • Re: error in scripting (Wed Nov 25 2009 - 00:08:04 CST)
  • Fwd: error in scripting (Thu Nov 19 2009 - 23:33:25 CST)
  • Fwd: error in scripting (Thu Nov 19 2009 - 03:28:03 CST)
  • error in scripting (Mon Nov 16 2009 - 00:47:57 CST)
  • scripiting problem (Tue Nov 10 2009 - 01:30:51 CST)
  • Re: molecular dynamics simulation (Thu Nov 05 2009 - 22:54:45 CST)
  • molecular dynamics simulation (Thu Nov 05 2009 - 04:35:33 CST)
  • Fwd: PROBLEM OF INSTALLATION OF NAMD (Sun Jul 12 2009 - 23:28:30 CDT)
• Irene Newhouse
  • compiling NAMD w. infiniband (Fri Jun 04 2010 - 16:21:37 CDT)
  • LES problem (Tue Jul 07 2009 - 00:30:50 CDT)
• Irina Tuszynska
  • Re: Namd with Amber ff for RNA minimization (Tue Nov 23 2010 - 09:37:59 CST)
  • Re: Namd with Amber ff for RNA minimization (Tue Nov 23 2010 - 05:29:33 CST)
  • Namd with Amber ff for RNA minimization (Tue Nov 23 2010 - 00:43:56 CST)
• itvasile_at_nipne.ro
  • Re: running namd in parallel (Sun Oct 04 2009 - 03:34:35 CDT)
  • Re: problem about NAMD compile (Fri Mar 13 2009 - 14:49:31 CDT)
• Ivaylo Ivanov
  • Postdoc position in biomolecular simulation (Wed Aug 26 2009 - 16:40:02 CDT)
• Ivaylo, Ivanov
  • Postdoc position in biomolecular simulation (Sat Jun 13 2009 - 02:08:07 CDT)
  • Postdoc position in biomolecular simulation (Sat Jun 13 2009 - 01:37:55 CDT)
• J Liu
  • Re: launch NAMD from tcl script (Wed Jun 24 2009 - 08:58:47 CDT)
• Jacopo Sgrignani
  • NBFIX and cuda (Wed Dec 22 2010 - 03:13:48 CST)
  • compiling namd gpu (Tue Dec 21 2010 - 03:13:57 CST)
  • Distance Restraint (Tue Nov 23 2010 - 10:23:27 CST)
• Jagan Mohan
  • Re: Error: atom group "group1" is set, but has no definition (Mon Mar 08 2010 - 00:34:43 CST)
  • Error: atom group "group1" is set, but has no definition (Mon Mar 08 2010 - 00:05:08 CST)
  • Regarding Periodic Boundary (Tue Jan 19 2010 - 23:45:44 CST)
  • Regarding Lipid Order Parameter Calculation (Mon Sep 21 2009 - 00:54:18 CDT)
  • Re: Regarding ABF Simulation (Tue Sep 15 2009 - 00:10:48 CDT)
  • Re: Regarding ABF Simulation (Mon Sep 14 2009 - 23:58:03 CDT)
  • Regarding ABF Simulation (Mon Sep 14 2009 - 04:48:19 CDT)
• Jaime Gonzalez
  • Debug NAMD with CharmDebug (Tue Jul 20 2010 - 03:41:45 CDT)
• James Servantie
  • can't load forces in tclforces (Thu Sep 17 2009 - 05:54:21 CDT)
• jampani srinivas
  • problem with NVT using TIP4P (Tue Apr 06 2010 - 09:26:09 CDT)
  • Fwd: help to improve the script to predict mean square displacement (Fri Mar 12 2010 - 14:51:55 CST)
• Jane Ren
  • RE: NAMD Cuda NBFIX Terms (Thu Sep 02 2010 - 15:45:18 CDT)
  • NAMD Cuda NBFIX Terms (Wed Sep 01 2010 - 20:21:20 CDT)
• jani sahil
  • Error running NAMD on CUDA (Mon May 18 2009 - 03:34:11 CDT)
  • Re: Make NAMD2.7b1 with cuda bug? (Fri May 15 2009 - 04:23:17 CDT)
  • Re: Make NAMD2.7b1 with cuda bug? (Fri May 15 2009 - 03:00:35 CDT)
• jani vinod
  • Regarding NAMD algorithm (Tue Jun 15 2010 - 07:38:29 CDT)
  • Re: Analysis of Results of only Lipid Bilayer Simulations (Wed May 19 2010 - 06:36:09 CDT)
• Jarrod Nickel
  • collective variables (Wed Jun 17 2009 - 11:07:26 CDT)
  • Warning: Not all atoms have unique coordinates (Fri May 22 2009 - 14:08:34 CDT)
• Jason Richard Mick
  • Bad Global Exclusion Count Errors in (Relatively) Simple System (Tue Nov 16 2010 - 18:32:49 CST)
  • Re: Modifying a peptide and introducing residues (Sat Aug 14 2010 - 08:37:31 CDT)
  • Best tool to use to generate a custom (patched) polypeptide PDB? (Thu May 06 2010 - 17:23:54 CDT)
• Jason Russler
  • Parallel replicas? (Thu Mar 11 2010 - 14:40:41 CST)
  • NAMD 1.7b1 quits writing files/hangs (Wed Apr 15 2009 - 08:00:49 CDT)
  • IBVerbs NAMD build segfaults (Wed Jan 21 2009 - 08:47:28 CST)
• jaya c.jose
  • Acceptance ratio of REMD simulation (Tue Sep 07 2010 - 05:47:04 CDT)
  • Running REMD with CHARMM f.f. (Thu Apr 22 2010 - 06:37:05 CDT)
  • Running REMD with CHARMM f.f. (Tue Apr 20 2010 - 06:52:58 CDT)
• jbp087_at_gmail.com
  • error (Tue Mar 02 2010 - 23:48:53 CST)
• JC Gumbart
  • Re: ABF on NAMD 2.7b3 (Mon Dec 20 2010 - 18:11:08 CST)
  • Re: ABF on NAMD 2.7b3 (Mon Dec 20 2010 - 15:37:54 CST)
  • RE: Asking for some sample PDB and PSF files of carbon nanotube (Wed Dec 15 2010 - 10:52:32 CST)
  • Re: Problem when using psfgen (Mon Dec 13 2010 - 13:14:40 CST)
  • RE: Free energy perturbation (FEP) hybrid pdb file (Tue Dec 07 2010 - 23:04:18 CST)
  • Re: NAMD FEP and GPU (Tue Nov 09 2010 - 19:01:26 CST)
  • Re: Error in configuration file (Tue Nov 02 2010 - 11:46:34 CDT)
  • RE: NANMA free energy surface vacuum map problems (Tue Nov 02 2010 - 07:23:30 CDT)
  • Re: NANMA free energy surface vacuum map problems (Mon Nov 01 2010 - 20:33:14 CDT)
  • Re: Missing angle parameters CT3 CT3 CT3 (Mon Nov 01 2010 - 18:52:17 CDT)
  • Re: Symmetry in NAMD, how to achieve during a MD simulation? (Wed Oct 27 2010 - 18:37:35 CDT)
  • RE: Alchemical FEP tutorial files (Thu Oct 07 2010 - 07:36:13 CDT)
  • Re: flexible-cell constant pressure not supported in CUDA (Mon Sep 27 2010 - 18:45:26 CDT)
  • RE: psfgen problem, not generating angles/dihedrals (Sat Sep 11 2010 - 07:10:02 CDT)
  • RE: psfgen problem, not generating angles/dihedrals (Fri Sep 10 2010 - 23:43:20 CDT)
  • Re: simulation cell enlarging too much after restart (Thu Sep 02 2010 - 18:16:08 CDT)
  • Re: Charmm carbohydrate force field (Tue Aug 31 2010 - 13:55:44 CDT)
  • RE: problem at applying patch (Sat Aug 28 2010 - 13:21:14 CDT)
  • Re: Proline hybrid topology file for FEP (Tue Aug 24 2010 - 14:49:16 CDT)
  • RE: psf creating for carbon nanotube (Sun Aug 15 2010 - 07:52:34 CDT)
  • RE: phosphate parameters (Sun Jun 20 2010 - 08:55:26 CDT)
  • RE: Regenerating a .dcd file (Tue Mar 09 2010 - 07:31:51 CST)
  • Re: Regenerating a .dcd file (Mon Mar 08 2010 - 19:14:39 CST)
  • Re: Can't find C-PDB bond parameters (Mon Feb 15 2010 - 12:06:41 CST)
  • RE: Can't find C-PDB bond parameters (Mon Feb 15 2010 - 08:15:53 CST)
  • Re: water-molecules/coordenates (Fri Feb 12 2010 - 12:20:25 CST)
  • Re: water-molecules/coordenates (Thu Feb 11 2010 - 15:16:28 CST)
  • Re: Parameter File (Sun Jan 31 2010 - 21:34:21 CST)
  • RE: tcl force (Sun Oct 18 2009 - 22:45:56 CDT)
  • RE: tcl force (Sun Oct 18 2009 - 08:57:10 CDT)
  • RE: tcl force (Sat Oct 17 2009 - 00:56:45 CDT)
  • Re: How to fix relative position of a group (Tue Oct 13 2009 - 19:27:40 CDT)
  • Re: An outlier appear on the curve of RMSD (Sun Jul 26 2009 - 21:14:22 CDT)
  • Re: PMEGridSize (Thu Jul 23 2009 - 19:08:52 CDT)
  • RE: CPU USAGE (Sun Jul 19 2009 - 00:16:30 CDT)
  • Re: SMD working only at high velocity (Fri Jul 10 2009 - 13:26:06 CDT)
  • Re: water molecules "collapse" during equilibration (Fri May 29 2009 - 17:01:01 CDT)
  • Re: water molecules "collapse" during equilibration (Fri May 29 2009 - 15:00:51 CDT)
  • Re: water molecules "collapse" during equilibration (Fri May 29 2009 - 14:14:19 CDT)
  • Re: FATAL ERROR: Duplicate bond (Wed Mar 11 2009 - 17:17:36 CDT)
  • Re: Selectively turning off electrostatic interactions (Wed Mar 11 2009 - 12:07:03 CDT)
  • RE: smd force vs time (Mon Feb 23 2009 - 00:47:26 CST)
  • Re: how can i get the energy of a molecule of a whole system? (Tue Feb 17 2009 - 14:28:36 CST)
  • Re: Forces on Atoms and Potential Energy (Tue Feb 17 2009 - 14:29:52 CST)
  • RE: center of mass for SMD (Wed Feb 11 2009 - 22:44:01 CST)
  • Re: some recommendations for parametrizing new molecules required (Fri Jan 23 2009 - 11:17:09 CST)
  • RE: syntax error in expression "(": premature end of expression - namdstats (Sat Jan 17 2009 - 01:34:41 CST)
  • Re: problem in fitting Maxwell-Boltzmann distribution (Wed Jan 14 2009 - 19:00:12 CST)
  • Re: how to save output file in plain text? (Thu Jan 08 2009 - 16:30:58 CST)
  • Re: how to save output file in plain text? (Thu Jan 08 2009 - 16:05:30 CST)
  • RE: Gradient tolerance nan for A three-atom simulation (Mon Jan 05 2009 - 23:24:35 CST)
• JC S
  • Run-time system modification (Mon Nov 22 2010 - 23:38:54 CST)
• Jeff Forbes
  • mapping of force vectors during SMD (Wed Apr 22 2009 - 13:42:23 CDT)
  • NAMD disk writes and quota overflow (Thu Jan 08 2009 - 15:45:05 CST)
• Jeff Wereszczynski
  • Re: Wrong energies in CUDA version (Thu Jun 03 2010 - 21:25:45 CDT)
  • Wrong energies in CUDA version (Thu Jun 03 2010 - 11:45:13 CDT)
  • Re: Periodic cell has become too small for original patch grid! (Fri Apr 02 2010 - 17:05:50 CDT)
  • Re: NAMD 2.7b1 on Ranger/MPI Problems? (Mon Apr 20 2009 - 15:56:18 CDT)
  • Re: NAMD 2.7b1 on Ranger/MPI Problems? (Fri Apr 17 2009 - 16:59:42 CDT)
  • NAMD 2.7b1 on Ranger/MPI Problems? (Fri Apr 17 2009 - 00:56:30 CDT)
• Jeffery Klauda
  • TIP4P with NPT (Thu Nov 18 2010 - 12:44:56 CST)
• Jeffrey J. Potoff
  • Re: problem with water (Tue Aug 24 2010 - 11:55:44 CDT)
  • Re: Periodic cell has become too small for original patch grid! (Tue Apr 06 2010 - 11:18:24 CDT)
  • Re: Water Box Shape Changing during NVT Simulation! (Mon Mar 08 2010 - 15:05:10 CST)
  • Re: cell basis vector restart (Tue Mar 02 2010 - 13:09:37 CST)
  • Re: Explicit Water System Condensing (Thu Feb 25 2010 - 10:13:43 CST)
  • Re: error in scripting (Tue Feb 16 2010 - 11:51:03 CST)
  • Re: Solute moves outside of solvent box (Tue Feb 02 2010 - 10:26:09 CST)
  • Questions about thermodynamic integration in NAMD 2.7b2 (Mon Feb 01 2010 - 14:27:22 CST)
  • Re: Solute moves outside of solvent box (Thu Jan 28 2010 - 12:55:08 CST)
• Jeffrey Potoff
  • Re: system density (Sun Nov 28 2010 - 20:55:33 CST)
  • Re: ERROR: Atoms moving too fast with RBCG model (Wed Nov 24 2010 - 15:21:48 CST)
  • Re: Minimization does not converge (Sat Nov 13 2010 - 19:37:37 CST)
  • Re: expansion of solvation box at high temperature (Sun Oct 17 2010 - 11:44:53 CDT)
  • Re: Generate psf files from Scott Feller's lipid coordinates (Sun May 16 2010 - 01:35:23 CDT)
• Jerome Henin
  • Re: Is two colvars file output possible during single simulation (ABF/2.7b) (Sat Feb 20 2010 - 10:05:26 CST)
  • Re: Colvar on 2.7b2 win vs Linux MPI instalation (Fri Jan 22 2010 - 15:19:33 CST)
  • Re: Number of MC steps in ABF integrate gives entirely diferent surfaces (Thu Jan 14 2010 - 05:00:18 CST)
  • Re: Retrieving standard deviation values while using collective variables (ABF) (Thu Nov 26 2009 - 09:04:19 CST)
  • Re: Finer details of an ABF/colvar simulation (Sun Nov 22 2009 - 13:37:32 CST)
  • Re: Retrieving standard deviation values while using collective variables (ABF) (Tue Nov 10 2009 - 10:52:34 CST)
  • Re: angle in colvars (Mon Nov 09 2009 - 09:09:17 CST)
  • Re: Modeling familial amyloidotic polyneuropathy (Mon Oct 26 2009 - 07:48:12 CDT)
  • Re: Pair interaction runtime analysis skipping dcd frames (Thu Oct 22 2009 - 12:14:46 CDT)
  • Re: restraining the COM of a group of atoms (Sat Oct 10 2009 - 15:03:52 CDT)
  • Re: followup question on error calculation in ABF (Thu Oct 08 2009 - 04:04:51 CDT)
  • Re: ABF + LES (Thu Oct 01 2009 - 12:19:48 CDT)
  • Re: ABF calculation - normalization of the PMF (Wed Sep 30 2009 - 04:42:32 CDT)
  • Re: NAMD 2.7b1 ABF + free energy windows (Wed Sep 30 2009 - 04:44:58 CDT)
  • Re: ABF calculation - normalization of the PMF (Sun Sep 27 2009 - 16:36:23 CDT)
  • Re: FEP to replace a PMF calculation? (Sun Sep 27 2009 - 16:27:52 CDT)
  • Re: Regarding ABF Simulation (Mon Sep 14 2009 - 17:57:28 CDT)
  • Re: Doubts and problem in ABF simulations (Wed Sep 02 2009 - 15:34:54 CDT)
  • Re: Doubts and problem in ABF simulations (Mon Aug 31 2009 - 17:18:52 CDT)
  • Re: ABF 'Xi' log output producing strange results (Thu Aug 27 2009 - 16:39:35 CDT)
  • Re: Parameters for esters (Tue Aug 25 2009 - 14:36:58 CDT)
  • Re: Clarification regarding some finer details in ABF simulations (Tue Aug 18 2009 - 16:01:56 CDT)
  • Re: Equilibration "substraction" from obtained PMF from MD (Sat Aug 15 2009 - 16:01:01 CDT)
  • Re: Clarification regarding some finer details in ABF simulations (Sat Aug 15 2009 - 15:55:35 CDT)
  • Re: Restarting ABF (Thu Aug 13 2009 - 11:39:00 CDT)
  • Bug advisory: ABF integration tool (Wed Aug 12 2009 - 17:49:24 CDT)
  • Re: Translocation problem while attempting to use ABF (Mon Jul 06 2009 - 11:37:20 CDT)
  • Re: nose-hoover (Wed Jul 01 2009 - 11:56:22 CDT)
  • Re: unsubscribe (Sun Jun 28 2009 - 10:40:46 CDT)
  • Re: colvars: Error: undefined output or restart file. (Fri Jun 26 2009 - 14:26:47 CDT)
  • Re: regarding psfgen algorithm (Thu Jun 18 2009 - 10:07:36 CDT)
  • Bug advisory: RMSD and ABF (Mon Jun 08 2009 - 17:55:10 CDT)
  • Re: abf with colvars example (Thu Jun 04 2009 - 13:44:06 CDT)
  • Re: Free energy of conformational change (Fri May 29 2009 - 11:31:00 CDT)
  • Re: collective variable space PMF, including biasing potential terms? (Wed May 13 2009 - 16:23:49 CDT)
  • Re: dummy atom mass changed (Tue May 12 2009 - 11:51:55 CDT)
  • Re: soft-core FEP in namd 2.7b (Mon May 11 2009 - 16:39:37 CDT)
  • Re: soft-core FEP in namd 2.7b (Sun May 10 2009 - 22:19:52 CDT)
  • Re: soft-core FEP in namd 2.7b (Sun May 10 2009 - 11:50:25 CDT)
  • Re: dummy atom mass changed (Tue May 05 2009 - 10:43:48 CDT)
  • Re: DCOLVARS_DEBUG (Tue May 05 2009 - 10:00:09 CDT)
  • Re: dummy atom mass changed (Mon May 04 2009 - 17:39:22 CDT)
  • Re: FEP tutorial graph question (Fri May 01 2009 - 14:28:24 CDT)
  • Re: Benzene PSF (Thu Apr 30 2009 - 11:22:01 CDT)
  • Re: FEP tutorial graph question (Wed Apr 29 2009 - 18:36:35 CDT)
  • Re: +1 offset to VMD index file? (Tue Apr 28 2009 - 11:13:38 CDT)
  • Re: FATAL ERROR: Periodic cell has become too small for original patch grid! (Wed Apr 22 2009 - 10:11:15 CDT)
  • Re: Constraints in NAMD (Wed Apr 22 2009 - 10:30:44 CDT)
  • Re: Re: alchemify with CMAP? (Mon Apr 20 2009 - 11:42:05 CDT)
  • Re: Re: alchemify with CMAP? (Fri Apr 17 2009 - 14:44:11 CDT)
  • Re: alchemify with CMAP? (Thu Apr 16 2009 - 19:21:51 CDT)
  • Re: Dihedral Restraints during MD simulation (Wed Apr 15 2009 - 13:49:29 CDT)
  • Re: use of tiElecLambdaStart (NAMD 2.7b1) (Fri Mar 27 2009 - 16:32:31 CDT)
  • Re: tclforces included in the NAMD-FEP \delta_G values? (Thu Mar 19 2009 - 15:47:32 CDT)
  • Re: alchemical fep amber topology (Fri Mar 13 2009 - 15:43:47 CDT)
  • Re: alchemical fep amber topology (Fri Mar 13 2009 - 15:26:34 CDT)
  • Re: alchemical fep amber topology (Fri Mar 13 2009 - 15:24:43 CDT)
  • Re: Selectively turning off electrostatic interactions (Wed Mar 11 2009 - 13:38:28 CDT)
  • Re: some problem about ABF (Wed Mar 11 2009 - 09:18:14 CDT)
  • Re: FEP anomaly? (Tue Feb 24 2009 - 09:37:14 CST)
  • Re: FEP/binding free energy difference WT vs Mut (Mon Feb 16 2009 - 11:18:50 CST)
  • Re: FEP/binding free energy difference WT vs Mut (Fri Feb 13 2009 - 18:08:24 CST)
  • Re: Need Charmm FF for Gangliosides (Wed Feb 11 2009 - 13:52:22 CST)
  • Re: abf convergence problems (Thu Jan 22 2009 - 14:17:26 CST)
  • Re: double-wide sampling with soft-core (Thu Jan 22 2009 - 11:35:39 CST)
  • Re: abf convergence problems (Thu Jan 22 2009 - 11:52:29 CST)
  • Re: double-wide sampling with soft-core (Wed Jan 21 2009 - 16:02:24 CST)
  • Re: TMD comments (Sat Jan 17 2009 - 19:52:40 CST)
  • Re: ABF calculation with TclForces script in the configuration file (Fri Jan 16 2009 - 11:20:27 CST)
  • Re: Creating bonds during a run (Mon Jan 12 2009 - 11:25:43 CST)
  • Re: tclforces: switch from md with external forces to standard md (Fri Jan 09 2009 - 10:24:24 CST)
• Jesper Soerensen
  • NAMD ibverbs not working on new cluster (Wed Jan 20 2010 - 03:11:35 CST)
• jfgaff_at_ncsu.edu
  • modifying a nucleobase (Sat Mar 28 2009 - 09:05:01 CDT)
• Jian Liu
  • Re: Re: hexane (Sun Oct 17 2010 - 23:10:34 CDT)
  • Re: hexane (Sat Oct 16 2010 - 20:32:09 CDT)
  • Re: parameter file for carbon nanotube (Mon Aug 16 2010 - 23:53:56 CDT)
  • Re: Re: psf creating for carbon nanotube (Mon Aug 16 2010 - 00:23:54 CDT)
  • Re: psf creating for carbon nanotube (Sun Aug 15 2010 - 07:40:32 CDT)
  • How to get PMF from SMD with colvars (Sat Apr 10 2010 - 03:45:05 CDT)
  • Re: About the err of "distanceZ"! (Mon Feb 22 2010 - 07:57:37 CST)
  • Re: tutorial-l: Nanotubes tutorial - coorList(577) no such element (Thu Feb 18 2010 - 04:09:25 CST)
  • Re: starting a job (Wed Jan 13 2010 - 07:35:03 CST)
  • Re: Re: How to obtain the system force on a fixed atom (Mon Dec 21 2009 - 07:34:30 CST)
  • Re: What is LINK Patch? (Mon Dec 07 2009 - 23:42:48 CST)
  • Re: spontaneous system explosion after 2 ns of normal run (Mon Oct 19 2009 - 01:45:24 CDT)
  • where can I find the file: cornell.rtf (in bionano tutorial) (Thu Sep 24 2009 - 02:03:38 CDT)
  • Re: Re: how to use ethanol as solvent in namd for MD simulations? (Fri Jul 31 2009 - 07:33:35 CDT)
  • Re: Generation of .psf file of DNA (Thu Jul 09 2009 - 07:43:21 CDT)
  • Modeling of Gramicidin A (Mon Jun 29 2009 - 08:08:41 CDT)
• Jianhui Tian
  • 1-4 pair generation (Thu Sep 02 2010 - 13:12:42 CDT)
  • Charmm carbohydrate force field (Tue Aug 31 2010 - 13:09:58 CDT)
  • NAMD 2.7b1 (Fri Jul 17 2009 - 10:52:28 CDT)
• Jianing Song
  • RE: how to improve the occupation of GPU with NAMD-2.7b3-CUDA (Wed Oct 13 2010 - 20:45:59 CDT)
  • Comparision of GPU and multi-CPUs version of NAMD (Sun Oct 10 2010 - 09:51:54 CDT)
  • how to improve the occupation of GPU with NAMD-2.7b3-CUDA (Sun Oct 10 2010 - 09:43:58 CDT)
  • flexible-cell constant pressure not supported in CUDA (Fri Sep 24 2010 - 19:50:26 CDT)
• Jianping Lin
  • Question on mutator in VMD (Sun Jan 11 2009 - 17:00:54 CST)
• Jignesh Patel
  • FATAL ERROR: ABNORMAL EOF FOUND-buffer (Thu Apr 15 2010 - 15:11:55 CDT)
  • which one is better to use - fixed atoms or constraints? (Wed Apr 14 2010 - 12:09:07 CDT)
  • Regarding ligand forcefield (Thu Apr 08 2010 - 14:13:15 CDT)
  • Warning: DUPLICATE ANGLE ENTRY FOR CPH1-NR1-CPH2 PREVIOUS VALUES (Thu Mar 04 2010 - 11:29:03 CST)
• Jim Parker
  • (no subject) (Thu Dec 03 2009 - 21:48:51 CST)
  • (no subject) (Thu Dec 03 2009 - 07:13:58 CST)
  • [Solved] Re: TclForces and getstep (Thu Dec 03 2009 - 07:10:12 CST)
  • TclForces and getstep (Wed Dec 02 2009 - 00:33:37 CST)
• Jim Phillips
  • Re: vmd-l: why atom positions are reset after readpsf, coordpdb commands? (Fri Dec 17 2010 - 10:58:39 CST)
  • Re: extending namd / shared library build (UNCLASSIFIED) (Mon Nov 01 2010 - 15:05:07 CDT)
  • Re: Charmrun: error on request socket-- (Thu Oct 28 2010 - 14:14:28 CDT)
  • Re: force field for replica exchange with NAMD (Thu Oct 28 2010 - 14:18:46 CDT)
  • Re: Warning: Bad global exclusion count, possible error! (Mon Oct 25 2010 - 13:21:03 CDT)
  • Re: potential functions in NAMD (Mon Oct 25 2010 - 13:24:38 CDT)
  • Re: Relaxed dihedral scans (or how to constrain a dihedral angle to a changing value). (Fri Oct 22 2010 - 10:30:59 CDT)
  • Re: NAMD 2.7 released (Wed Oct 20 2010 - 14:47:28 CDT)
  • Re: error codes: 255 (Wed Oct 20 2010 - 14:35:05 CDT)
  • NAMD 2.7 released (Tue Oct 19 2010 - 14:57:57 CDT)
  • Re: Amber topology in CUDA NAMD - can it be done? (Tue Oct 19 2010 - 11:43:10 CDT)
  • Re: Changing functions without recompiling (Tue Oct 19 2010 - 11:56:40 CDT)
  • Re: Tcl script in NAMD (Tue Oct 19 2010 - 11:49:16 CDT)
  • Re: Denied permission on dcd file preventing simulation (Mon Oct 18 2010 - 11:40:28 CDT)
  • Re: CHARMM Lorentz-berthelot mixing rules (Mon Oct 18 2010 - 11:38:12 CDT)
  • RE: expansion of solvation box at high temperature (Mon Oct 18 2010 - 11:32:18 CDT)
  • Re: Namd using Charmm restart files (Thu Oct 14 2010 - 14:28:09 CDT)
  • Re: Regarding answering questions in a forum. Re: Langevin process in NAMD tutorial (Wed Oct 13 2010 - 09:46:57 CDT)
  • Re: 2 Stray PME grid charges detected possible bug 2.7b2 (Wed Oct 13 2010 - 09:33:24 CDT)
  • Re: Is the DCD file size consistent for consecutive runs? (Fri Oct 08 2010 - 09:21:52 CDT)
  • Re: problem caused by cluster? (Fri Oct 08 2010 - 08:34:23 CDT)
  • Re: Flushing memory into output file (Thu Oct 07 2010 - 17:06:26 CDT)
  • Re: Fermi NVidia (Thu Oct 07 2010 - 15:36:47 CDT)
  • NAMD 2.7b4 released (Tue Sep 21 2010 - 21:38:22 CDT)
  • Re: NAMD Energy types (Fri Sep 17 2010 - 14:39:29 CDT)
  • Re: Bad atom ID in extra bond file (Fri Sep 17 2010 - 14:22:59 CDT)
  • Re: Does "rigidbond off" work instead of "rigidbonds none" (Fri Sep 17 2010 - 14:19:26 CDT)
  • Re: LJ correction in NAMD2.7b3 (Thu Aug 12 2010 - 15:14:41 CDT)
  • last call for 2.7b3 bug reports! (Fri Aug 06 2010 - 09:59:00 CDT)
  • Re: Specifying Values for Rotating Constraints (Fri Aug 06 2010 - 09:27:38 CDT)
  • Re: Constraints on the plane and on the atom positions (in the same simulation) (Fri Aug 06 2010 - 09:40:30 CDT)
  • Re: Problems with AutoPSF (Fri Aug 06 2010 - 09:36:28 CDT)
  • Re: heating and binvelocities (Fri Aug 06 2010 - 09:30:38 CDT)
  • Re: "gradient tolerance" for minimization (Thu Jul 22 2010 - 14:52:07 CDT)
  • Re: parallel scaling issues (Thu Jul 22 2010 - 13:15:04 CDT)
  • Re: Timeout waiting for node-program to connect (Thu Jul 22 2010 - 13:20:56 CDT)
  • Re: namd2 still works but without any new messages in log file (Tue Jul 06 2010 - 14:22:38 CDT)
  • NAMD 2.7b3 released (Tue Jul 06 2010 - 13:45:58 CDT)
  • Job Offer (Fri Feb 12 2010 - 20:21:33 CST)
  • Re: "-Wno-long-double" linking error (Wed Dec 09 2009 - 18:05:25 CST)
  • NAMD 2.7b2 Released (Fri Nov 13 2009 - 17:03:52 CST)
  • Re: CUDA-accelarated NAMD does not use the video card? (Fri Nov 13 2009 - 17:06:48 CST)
  • Re: Is it a bug? TCL Script may Lead to Overflow (Mon Nov 09 2009 - 11:55:33 CST)
  • (no subject) (Tue Sep 08 2009 - 17:21:54 CDT)
  • RE: namd27: tclforces activate TI calculation by default (Wed Aug 12 2009 - 16:16:04 CDT)
  • Re: Make NAMD2.7b1 with cuda bug? (Wed May 13 2009 - 13:41:29 CDT)
  • Re: Make NAMD2.7b1 with cuda bug? (Wed May 13 2009 - 11:58:30 CDT)
  • Re: erergy gradient tolerance in Configuration Files (Wed Apr 08 2009 - 13:51:15 CDT)
  • Re: NAMD 2.7b1 on Teragrid (Wed Apr 01 2009 - 14:18:55 CDT)
  • Re: NAMD 2.7b1 on Teragrid (Tue Mar 31 2009 - 15:53:11 CDT)
  • Re: MINIMIZER SLOWLY MOVING ATOMS WITH BAD CONTACTS DOWNHILL (Thu Mar 26 2009 - 16:51:03 CDT)
  • Re: BUILDING BPTI (Thu Mar 26 2009 - 16:22:58 CDT)
  • Re: Scale for Potential Bond Parameter (Wed Mar 25 2009 - 16:39:15 CDT)
  • Re: processor counts FFT and NAMD (Wed Mar 25 2009 - 11:13:56 CDT)
  • Re: TMD on tRNA does not converge (Wed Mar 25 2009 - 11:16:51 CDT)
  • NAMD 2.7b1 release (Wed Mar 25 2009 - 10:16:18 CDT)
  • Re: About CUDA version of NAMD 2.7 B1 (Wed Mar 25 2009 - 08:34:29 CDT)
  • Re: Re: FW: NAMD 2.6, AMD64, MVAPICH2 compile error (Tue Mar 24 2009 - 22:56:40 CDT)
  • Re: about the memery lock in openMPI on infiniband (Tue Mar 24 2009 - 22:44:29 CDT)
• Jin Liu
  • Re: How to confirm water box is big enough? (Tue Mar 30 2010 - 17:48:37 CDT)
  • Re: How to confirm water box is big enough? (Tue Mar 30 2010 - 17:09:06 CDT)
  • Re: How to confirm water box is big enough? (Tue Mar 30 2010 - 15:44:26 CDT)
  • How to confirm water box is big enough? (Tue Mar 30 2010 - 14:29:15 CDT)
• Jindal Shah
  • Re: Dihedral angle energy in silica block (Mon Mar 01 2010 - 09:11:47 CST)
  • Dihedral angle energy in silica block (Sun Feb 28 2010 - 21:51:15 CST)
• jinhyo_at_comcast.net
  • ERROR: Constraint failure in RATTLE algorithm for atom 1880! (Mon May 18 2009 - 11:19:04 CDT)
• jkmann_at_buffalo.edu
  • Re: Simultaneous water and protein minimization (Thu Nov 19 2009 - 15:07:54 CST)
  • RE: Simultaneous water and protein minimization (Thu Nov 19 2009 - 11:04:17 CST)
  • Simultaneous water and protein minimization (Wed Nov 18 2009 - 15:58:22 CST)
• jnsong
  • how to get topology and parameter file for ligand (Thu Dec 16 2010 - 08:58:07 CST)
  • how to generate the topology and parameter file for ligand (Thu Dec 16 2010 - 07:45:52 CST)
  • how to generate topology and parameter file for ligand (Thu Dec 16 2010 - 07:40:38 CST)
  • the usage of ++nodelist and ++local (Sun Nov 14 2010 - 06:25:21 CST)
  • the storage format of the coordinate binary file in NAMD (Thu Oct 21 2010 - 03:55:27 CDT)
  • Re: how to cenvert NAMD binary coordinate file to text file (Thu Oct 21 2010 - 03:40:42 CDT)
  • Re: how to cenvert NAMD binary coordinate file to text file (Thu Oct 21 2010 - 03:34:11 CDT)
  • how to cenvert NAMD binary coordinate file to text file (Thu Oct 21 2010 - 02:27:06 CDT)
• Joachim Hein
  • Re: FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE (Fri May 29 2009 - 11:07:56 CDT)
  • Re: FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE (Fri May 29 2009 - 11:40:41 CDT)
  • Re: compiling error of NAMD2.7b1 (Tue Apr 21 2009 - 04:18:14 CDT)
  • Re: compiling error of NAMD2.7b1 (Mon Apr 20 2009 - 12:53:59 CDT)
  • Re: compiling error of NAMD2.7b1 (Mon Apr 20 2009 - 13:22:11 CDT)
  • Re: compiling error of NAMD2.7b1 (Mon Apr 20 2009 - 06:05:38 CDT)
  • .inter.bin files? (Thu Apr 02 2009 - 10:24:20 CDT)
  • memory optimised version and exclusion check (Fri Feb 20 2009 - 13:48:24 CST)
• Joakim Swedberg
  • Charmm parameters for (Wed Apr 28 2010 - 21:47:03 CDT)
  • NAMD 2.7b1 Performance loss with CUDA 2.3 (Thu Nov 12 2009 - 20:07:23 CST)
• Johann Morr
  • Generating binvelocities, bincoordinates, and extendedSystem files (AMBER) (Sat Feb 13 2010 - 23:01:32 CST)
• John Stone
  • Re: vmd-l: Hardware for NAMD / VMD machine (Mon Jul 06 2009 - 11:04:30 CDT)
  • Re: vmd-l: Offset for frame ids in dcd trajectory (Tue May 26 2009 - 15:32:40 CDT)
• John Wise
  • scripts for starting namd with condor (Wed Sep 16 2009 - 17:06:26 CDT)
• Jorgen Simonsen
  • replica exchange trans cis isomerisme (Sat Sep 11 2010 - 03:02:30 CDT)
  • degrees of freedom (Sat Sep 11 2010 - 00:26:10 CDT)
  • restart from different snap shots (Tue Aug 10 2010 - 06:05:25 CDT)
  • version of namd to install (Mon Aug 09 2010 - 04:47:43 CDT)
  • FATAL ERROR: Asymmetric water molecule found??? This can't be right. (Wed Jul 07 2010 - 17:34:44 CDT)
  • convergence of ABF (Sun Jan 17 2010 - 20:42:30 CST)
  • size of integration step (Tue Oct 13 2009 - 10:44:47 CDT)
  • running namd in parallel (Sat Oct 03 2009 - 16:18:57 CDT)
  • Parameters for esters (Mon Aug 24 2009 - 11:55:08 CDT)
  • peptides on surface (Wed May 13 2009 - 13:16:51 CDT)
  • Asymmetric water molecule found (Tue May 12 2009 - 05:00:45 CDT)
  • HW - HW IN PARAMETER FILES (Thu May 07 2009 - 06:17:19 CDT)
  • fatal error: tried to assign bond index before all parameter files were read (Wed May 06 2009 - 05:36:16 CDT)
  • Regarding amber parameters using NAMD (Mon May 04 2009 - 03:22:27 CDT)
  • Re: Thiol on gold simulation in NAMD (Thu Feb 26 2009 - 03:05:51 CST)
  • Re: Thiol on gold simulation in NAMD (Wed Feb 25 2009 - 04:36:47 CST)
  • Re: abf convergence problems (Thu Jan 22 2009 - 14:37:05 CST)
  • Re: abf convergence problems (Thu Jan 22 2009 - 12:56:40 CST)
  • abf convergence problems (Thu Jan 22 2009 - 11:16:36 CST)
• Jose Borreguero
  • evaluating energy in a trajectory of variable box size? (Tue Apr 27 2010 - 14:04:11 CDT)
  • isopropanol parameters? (Thu Mar 04 2010 - 09:24:58 CST)
• jose correa
  • Fermi NVidia (Thu Sep 30 2010 - 09:13:47 CDT)
  • Re: Reply: couldn´t find rsh program (Fri Jun 18 2010 - 10:00:21 CDT)
  • couldn´t find rsh program (Thu Jun 17 2010 - 14:39:56 CDT)
  • Re: Parameter file problem (Tue Mar 30 2010 - 15:29:45 CDT)
  • Re: Namd. Small molecules (Fri Mar 19 2010 - 21:37:57 CDT)
  • Re: water-molecules/coordenates (Fri Feb 12 2010 - 12:45:49 CST)
  • Re: water-molecules/coordenates (Thu Feb 11 2010 - 16:10:09 CST)
  • water-molecules/coordenates (Thu Feb 11 2010 - 13:19:01 CST)
  • Re: protein unfolding (Thu Jan 21 2010 - 11:03:27 CST)
  • Re: protein unfolding (Thu Jan 21 2010 - 09:55:14 CST)
  • Re: protein unfolding (Thu Jan 21 2010 - 09:29:42 CST)
  • protein unfolding (Thu Jan 21 2010 - 08:57:06 CST)
  • protein unfolding (Thu Jan 21 2010 - 07:29:13 CST)
  • NAMD-problem (Thu Nov 05 2009 - 17:29:30 CST)
  • FAD topology and parameters of FAD (Wed Sep 16 2009 - 11:21:58 CDT)
  • FAD-parameters (Thu Sep 10 2009 - 13:50:33 CDT)
  • protocol to start MD (Wed Aug 19 2009 - 09:27:29 CDT)
  • VMD-Installation problems (Wed Jul 15 2009 - 19:16:35 CDT)
  • Re: problem namd2-MPICH (Mon Jun 08 2009 - 07:34:53 CDT)
  • namd-openmosix (Tue May 19 2009 - 07:29:49 CDT)
  • Re: Selectively write atoms to dcd files (Mon Apr 13 2009 - 13:10:55 CDT)
  • problem namd2-MPICH (Wed Apr 08 2009 - 14:05:09 CDT)
  • BUILDING BPTI (Thu Mar 26 2009 - 14:53:43 CDT)
  • Re: removing water from big dcd files (Wed Mar 04 2009 - 11:51:35 CST)
  • removing water from big dcd files (Tue Mar 03 2009 - 20:36:24 CST)
  • namd ubuntu-instalation (Thu Feb 12 2009 - 09:23:15 CST)
  • Re: how to add ions to a system (Wed Jan 28 2009 - 06:48:03 CST)
  • NADP (Fri Jan 23 2009 - 18:43:07 CST)
  • Re: problems-protein minimization (Fri Jan 23 2009 - 14:27:59 CST)
  • problems-protein minimization (Fri Jan 23 2009 - 12:40:22 CST)
• Joshua Adelman
  • Re: residue based coarse-grained simulation (Tue Nov 09 2010 - 09:51:03 CST)
  • Re: Changing functions without recompiling (Mon Oct 18 2010 - 20:42:42 CDT)
  • Re: expansion of solvation box at high temperature (Sun Oct 17 2010 - 12:25:19 CDT)
  • Re: FW: TMD simulations (Fri Apr 30 2010 - 21:21:15 CDT)
  • Re: software/algorithm to cluster protein conformations (Thu Apr 29 2010 - 18:06:38 CDT)
  • Re: namd trouble (Thu Feb 18 2010 - 07:08:46 CST)
  • Re: langevinTemp and system temperature (Fri Jan 29 2010 - 09:42:19 CST)
  • Re: RMSD for individual residue (Mon Nov 30 2009 - 12:10:14 CST)
  • Re: calculation of periodic box (Tue Nov 17 2009 - 22:29:13 CST)
  • Re: Error in Minimization (Sun Nov 08 2009 - 08:05:11 CST)
  • Re: water box size (Sun Nov 08 2009 - 07:57:36 CST)
  • Re: Namd benchmark problem (Sun Oct 25 2009 - 08:18:23 CDT)
  • Re: Generation of average trajectory (Mon Oct 12 2009 - 09:43:56 CDT)
  • Re: restraining the COM of a group of atoms (Fri Oct 09 2009 - 19:43:04 CDT)
  • Re: PCA Calculation (Tue Oct 06 2009 - 06:47:09 CDT)
  • Re: Periodic boundary conditions in membrane simulation (Mon Aug 31 2009 - 12:24:14 CDT)
  • Re: how to save pdb file after "moveby" command in VMD? (Tue Aug 18 2009 - 22:14:18 CDT)
  • Re: symmetric behavior (Wed Aug 12 2009 - 09:49:10 CDT)
  • Re: Defining Temperature for Langevin for Namd restart. (Wed Aug 05 2009 - 16:36:23 CDT)
  • Re: Re: recalculating energy using dcd file (Wed Aug 05 2009 - 09:58:22 CDT)
  • Re: A script for performing calculations divided by quanta (Mon Aug 03 2009 - 10:38:35 CDT)
  • Re: A script for performing calculations divided by quanta (Mon Aug 03 2009 - 10:05:50 CDT)
  • Re: How to set magnitude of cellBasisVector? (Fri Jul 24 2009 - 01:13:24 CDT)
  • Re: NAMD installation (Wed Jul 22 2009 - 17:51:42 CDT)
  • Re: how work: harmonic position "constraints" module + "WrapAll on"? (Mon Jul 20 2009 - 09:23:13 CDT)
  • Re: Wtrlt: Smeart out 9/3 LJ wall (Wed Jul 15 2009 - 12:21:09 CDT)
  • Re: Protein collpasing problem! (Fri Jul 03 2009 - 10:55:53 CDT)
  • Re: Protein collpasing problem! (Mon Jun 29 2009 - 11:23:33 CDT)
  • Re: Can I use another solvent rather than TI3P model in namd for MD simulations ? (Sun Jun 28 2009 - 20:14:02 CDT)
  • Re: protein collapsing problem! (Sun Jun 28 2009 - 03:10:43 CDT)
  • Re: protein collapsing problem! (Thu Jun 25 2009 - 01:10:52 CDT)
  • Re: VMD/NAMD two identical molecules solvate in a water sphere (Sat Jun 20 2009 - 12:21:49 CDT)
  • Re: regarding protein-protein interaction (Fri Jun 05 2009 - 10:41:44 CDT)
  • Re: protein folding cg (Fri Jun 05 2009 - 02:01:51 CDT)
  • Re: regd: my parameter file (Fri May 29 2009 - 16:16:29 CDT)
  • Re: using amber topology and parameter files in NAMD (Fri May 29 2009 - 12:23:57 CDT)
  • Re: Offset for frame ids in dcd trajectory (Sat May 23 2009 - 12:15:01 CDT)
  • Re: selectively write atom coordinates on-the-fly (Thu May 21 2009 - 11:41:11 CDT)
  • Re: Calculating displacement in a system with periodic boundary (Mon May 11 2009 - 23:44:23 CDT)
  • Re: Regarding amber parameters using NAMD (Tue May 05 2009 - 10:44:55 CDT)
  • Re: Regarding amber parameters using NAMD (Mon May 04 2009 - 10:41:52 CDT)
  • Re: protein shifts out of the water box (Wed Apr 29 2009 - 19:07:05 CDT)
  • Re: how to set initial velocity? (Wed Apr 29 2009 - 15:09:34 CDT)
  • Re: how to set initial velocity? (Tue Apr 28 2009 - 21:59:21 CDT)
  • Re: can I change coordinate before restart? (Wed Apr 22 2009 - 15:11:55 CDT)
  • Re: Constraints in NAMD (Wed Apr 22 2009 - 10:37:39 CDT)
  • Re: can I change coordinate before restart? (Tue Apr 21 2009 - 20:50:47 CDT)
  • Re: PCA Analysis of CGMD (Wed Apr 15 2009 - 10:35:00 CDT)
  • Re: PCA Analysis of CGMD (Wed Apr 15 2009 - 09:45:53 CDT)
  • Re: Selectively write atoms to dcd files (Mon Apr 13 2009 - 12:32:52 CDT)
  • Re: Water is boiling with namd and charmm (Mon Apr 13 2009 - 10:50:31 CDT)
  • Re: PCA Analysis of CGMD (Fri Apr 10 2009 - 10:20:04 CDT)
  • Re: PCA Analysis of CGMD (Thu Apr 09 2009 - 10:28:06 CDT)
  • Re: TMD RMSD problem (Wed Apr 08 2009 - 15:35:12 CDT)
  • Re: how to use constraints properly (Thu Mar 19 2009 - 13:53:09 CDT)
  • Using Amber FF in NAMD (Wed Mar 18 2009 - 18:13:33 CDT)
  • Amber ff99sb force-field in namd (Wed Mar 18 2009 - 17:25:13 CDT)
  • Re: removing water from big dcd files (Tue Mar 03 2009 - 21:07:54 CST)
  • Re: loading of large dcd files (Thu Feb 26 2009 - 00:10:44 CST)
  • Re: Correlation matrix of the Ca atoms (Sun Feb 01 2009 - 23:56:04 CST)
  • Re: Correlation matrix of the Ca atoms (Sun Feb 01 2009 - 23:22:07 CST)
  • Re: FATAL ERROR: Setting parameter constraints from script failed! (Thu Jan 08 2009 - 11:14:24 CST)
• Joshua D. Moore
  • Re: Format of namd restartfile *.coor, *.vel) (2nd try ;) ) (Thu Nov 18 2010 - 18:27:22 CST)
  • Re: vmd-l: namd2.7b1, tip4p, and dummies (Wed Sep 30 2009 - 05:24:34 CDT)
  • Re: Re: Cell Data in DCD files - CHARMM compatibility (Fri Aug 07 2009 - 22:26:07 CDT)
  • Re: Measuring protein diffusion: results too small? (Fri Jun 05 2009 - 21:49:22 CDT)
  • Re: (Thu Jan 29 2009 - 10:01:28 CST)
• Joshua Lioi
  • Generating psf for NPC1 (Thu Nov 19 2009 - 10:45:07 CST)
• jouko_at_uchicago.edu
  • Re: Periodic boundary conditions in membrane simulation (Mon Aug 31 2009 - 16:02:43 CDT)
  • Periodic boundary conditions in membrane simulation (Mon Aug 31 2009 - 11:56:22 CDT)
• jp d
  • rotation question (Mon Oct 18 2010 - 16:35:55 CDT)
• jp2854_at_columbia.edu
  • crash (Mon Nov 29 2010 - 11:18:24 CST)
• JT
  • Re: Harmonically constrained simulations (Thu May 21 2009 - 11:25:55 CDT)
  • Re: Namd and MM-PBSA (Thu Apr 23 2009 - 12:43:17 CDT)
  • Re: 4 sequential jobs work on laptops, but only first one works on supercomputer (Tue Apr 14 2009 - 01:24:25 CDT)
  • Re: 4 sequential jobs work on laptops, but only first one works on supercomputer (Mon Apr 13 2009 - 23:12:06 CDT)
  • Re: 4 sequential jobs work on laptops, but only first one works on supercomputer (Mon Apr 13 2009 - 21:59:23 CDT)
  • Re: 4 sequential jobs work on laptops, but only first one works on supercomputer (Mon Apr 13 2009 - 22:02:54 CDT)
  • 4 sequential jobs work on laptops, but only first one works on supercomputer (Mon Apr 13 2009 - 18:00:49 CDT)
  • RE: Evaluating kinetic energy from a modified DCD file (Sat Apr 11 2009 - 03:47:57 CDT)
  • Re: Evaluating kinetic energy from a modified DCD file (Fri Apr 10 2009 - 11:36:52 CDT)
  • Re: Evaluating kinetic energy from a modified DCD file (Wed Apr 08 2009 - 22:04:20 CDT)
  • Re: Evaluating kinetic energy from a modified DCD file (Wed Apr 08 2009 - 19:59:48 CDT)
  • Re: Writing 3 subsequent timesteps to the DCD file (Tue Apr 07 2009 - 18:53:38 CDT)
  • Re: regarding implicit solvent models (Fri Apr 03 2009 - 03:29:16 CDT)
• juan du
  • Restart, discontinuity of energy (Wed Dec 01 2010 - 09:56:51 CST)
  • Restart, RMSD increase (Wed Nov 24 2010 - 08:58:05 CST)
  • Restart RMSD increase (Wed Nov 24 2010 - 07:54:45 CST)
  • Restart RMSD increase (Wed Nov 24 2010 - 08:00:49 CST)
• Jufang Shan
  • NAMD 2.7b1 on Lonestar (Mon Oct 05 2009 - 10:44:23 CDT)
• Jun Zhang
  • Re: compiling namd gpu (Wed Dec 22 2010 - 18:17:01 CST)
  • SHAKE convergence property for CUDA and nonCUDA NAMD (Wed Dec 08 2010 - 06:54:10 CST)
  • SHAKE convergence property for CUDA and nonCUDA NAMD (Wed Dec 08 2010 - 05:59:53 CST)
  • Re: about Hydrogen Bond correlation function (Sat Nov 06 2010 - 23:24:02 CDT)
  • about Hydrogen Bond correlation function (Thu Nov 04 2010 - 00:55:28 CDT)
  • about DCD file format document (Mon Jul 12 2010 - 06:43:02 CDT)
  • Multi-step MD in a single .conf file (Mon Jun 21 2010 - 19:02:22 CDT)
  • (no subject) (Mon Jun 21 2010 - 08:13:01 CDT)
  • Reply: couldn´t find rsh program (Thu Jun 17 2010 - 19:03:41 CDT)
  • Two questions about essential dynamics (Mon May 24 2010 - 06:48:34 CDT)
  • Re: FEP yields the same results for forward and backward computation! (Thu May 13 2010 - 08:48:42 CDT)
  • FEP yields the same results for forward and backward computation! (Wed May 12 2010 - 22:38:44 CDT)
  • Re: Free energy calculation yields strange results (Tue May 11 2010 - 21:25:57 CDT)
  • Free energy calculation yields strange results (Sun May 09 2010 - 07:53:36 CDT)
  • Re: Dihedral parameters for side-chains? (Sat Apr 24 2010 - 22:29:12 CDT)
  • re a problem with "Charging a spherical ion" (Sun Apr 18 2010 - 03:21:38 CDT)
• Jyh-Shyong
  • NAMD 2.7b2 with CUDA and infinband (Sun Dec 20 2009 - 23:03:37 CST)
• Jérôme Hénin
  • colvars-history file (Wed Dec 29 2010 - 02:24:17 CST)
  • Re: Zcoord for ABF (Wed Dec 22 2010 - 15:11:29 CST)
  • Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein (Thu Dec 16 2010 - 07:47:42 CST)
  • Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein (Wed Dec 15 2010 - 11:07:20 CST)
  • Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein (Wed Dec 15 2010 - 09:31:20 CST)
  • Re: Simultaneous FEP simulation of two distinct residues (Wed Dec 15 2010 - 04:04:47 CST)
  • Re: ABF questions (Concatenate output files/force constant) (Thu Dec 09 2010 - 04:51:14 CST)
  • Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein (Wed Dec 08 2010 - 16:16:58 CST)
  • Re: ABF question (Fri Dec 03 2010 - 10:45:24 CST)
  • Lowe-Andersen thermostat (Thu Dec 02 2010 - 09:12:12 CST)
  • Re: SMD constant velocity pulling (Wed Dec 01 2010 - 16:55:20 CST)
  • Re: SMD constant velocity pulling (Wed Dec 01 2010 - 11:40:25 CST)
  • Re: SMD constant velocity pulling (Wed Dec 01 2010 - 05:35:29 CST)
  • Re: restart ABF (Mon Nov 29 2010 - 11:38:29 CST)
  • Re: "GroupPressure no" resulting in negative pressure outputs (Mon Nov 29 2010 - 10:26:16 CST)
  • Re: Run-time system modification (Mon Nov 29 2010 - 06:26:47 CST)
  • Re: "GroupPressure no" resulting in negative pressure outputs (Thu Nov 25 2010 - 14:56:08 CST)
  • Re: Zcoord-1atom for ABF (Thu Nov 25 2010 - 02:42:47 CST)
  • Re: Distance Restraint (Tue Nov 23 2010 - 11:27:03 CST)
  • Re: MOnte carlo simulation (Tue Nov 23 2010 - 03:14:31 CST)
  • Re: Run-time system modification (Tue Nov 23 2010 - 02:05:39 CST)
  • Re: Namd with Amber ff for RNA minimization (Tue Nov 23 2010 - 02:14:20 CST)
  • Re: berendsen thermostat (Mon Nov 15 2010 - 09:24:13 CST)
  • Re: questions about ABF simulations (Wed Nov 03 2010 - 05:51:48 CDT)
  • Re: vmd-l: Asymmetric water molecule (Wed Nov 03 2010 - 05:03:40 CDT)
  • Re: NANMA free energy surface vacuum map problems (Tue Nov 02 2010 - 08:18:30 CDT)
  • Re: NANMA free energy surface vacuum map problems (Tue Nov 02 2010 - 05:40:08 CDT)
  • Re: Radius of gyration (Sun Oct 31 2010 - 04:22:25 CDT)
  • Re: NANMA free energy surface vacuum map problems (Fri Oct 29 2010 - 09:33:37 CDT)
  • Re: questions about ABF simulations (Thu Oct 28 2010 - 14:37:29 CDT)
  • Re: Enthalpy calculation (Thu Oct 28 2010 - 11:58:00 CDT)
  • Re: the storage format of the coordinate binary file in NAMD (Thu Oct 21 2010 - 05:06:36 CDT)
  • Re: Modification of Colvar Module Components (Wed Oct 13 2010 - 02:24:55 CDT)
  • Re: change force field in NAMD (Tue Oct 05 2010 - 03:38:27 CDT)
  • Re: Selection of alchElecLambdaStart (Tue Sep 28 2010 - 15:53:26 CDT)
  • Re: Selection of alchElecLambdaStart (Tue Sep 28 2010 - 14:51:36 CDT)
  • Re: metadynamics simulations slow down and down (Sun Sep 26 2010 - 05:47:28 CDT)
  • Re: Colvars and COM restraints for protein+membrane; plus a minor bug (Fri Sep 24 2010 - 04:59:59 CDT)
  • Re: Colvars: Using "Alpha" Component (Fri Sep 24 2010 - 03:27:40 CDT)
  • Re: Colvars and COM restraints for protein+membrane; plus a minor bug (Thu Sep 23 2010 - 14:37:52 CDT)
  • Colvars in NAMD 2.7b4 (Tue Sep 21 2010 - 07:06:29 CDT)
  • Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. (Sat Sep 11 2010 - 04:02:52 CDT)
  • Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. (Thu Sep 09 2010 - 11:06:33 CDT)
  • Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. (Mon Sep 06 2010 - 10:14:25 CDT)
  • Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. (Sat Sep 04 2010 - 02:50:54 CDT)
  • Re: Force constant scaling (Wed Sep 01 2010 - 06:11:58 CDT)
  • Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. (Tue Aug 31 2010 - 10:22:06 CDT)
  • Re: FEP substrate transformation with common moiety (Sat Aug 28 2010 - 08:52:46 CDT)
  • Re: ABF calculations: Jacobian term describing geometry entropy (Mon Aug 23 2010 - 10:51:53 CDT)
  • Re: ABF problem with gyration radius/Cl and Br (Wed Aug 11 2010 - 08:31:44 CDT)
  • Re: abf_integrate (Fri Aug 06 2010 - 05:20:59 CDT)
  • Re: FEP for GLY and PRO Mutations (Tue Jul 27 2010 - 05:01:36 CDT)
  • Re: Dihedral angle potential energy function (Fri Jul 02 2010 - 07:13:10 CDT)
  • Re: ABF question (Wed Jun 23 2010 - 05:17:56 CDT)
  • Re: Distance constraint (Thu Jun 17 2010 - 06:31:23 CDT)
  • Re: Re: colvar atom syntax (Wed Jun 16 2010 - 11:42:09 CDT)
  • Re: Re: colvar atom syntax (Wed Jun 16 2010 - 07:24:51 CDT)
  • Re: Possible way of performing a temperature gradient?? (Tue Jun 15 2010 - 04:57:21 CDT)
  • Re: where do I find info about freeEnergy ? (Tue Jun 08 2010 - 15:36:49 CDT)
  • Re: distance colvar (Mon Jun 07 2010 - 06:27:00 CDT)
  • Re: rotational restrains (Fri Jun 04 2010 - 16:03:13 CDT)
  • Re: new NAMD user ABF setup question (Wed Jun 02 2010 - 09:53:05 CDT)
  • Re: new NAMD user ABF setup question (Sat May 29 2010 - 05:06:50 CDT)
  • Re: Temperature gradient! (Thu May 27 2010 - 07:39:32 CDT)
  • Re: backbone restraints (Wed May 26 2010 - 14:47:13 CDT)
  • Re: ABF (NAMD 2.7x) speed ? (Wed May 26 2010 - 04:52:22 CDT)
  • Re: ABF (NAMD 2.7x) speed ? (Tue May 25 2010 - 10:47:32 CDT)
  • Re: ABF question (Tue May 25 2010 - 10:35:52 CDT)
  • Re: selective rigidbonds (Fri May 21 2010 - 05:47:29 CDT)
  • Re: How to solve the out of cell box for long time in Periodic Boundary Conditions? (Thu May 20 2010 - 10:00:08 CDT)
  • Re: ABF in various simulations (Mon May 17 2010 - 11:08:28 CDT)
  • Re: About RMSD based PMF's (Fri May 14 2010 - 06:05:28 CDT)
  • Re: Atom movement within a range of Z value (Wed May 12 2010 - 02:31:51 CDT)
  • Re: installation of namd without tcl and fftw (Tue May 11 2010 - 05:16:01 CDT)
  • Re: installation of namd without tcl and fftw (Tue May 11 2010 - 03:41:00 CDT)
  • Re: Free energy calculation yields strange results (Mon May 10 2010 - 08:04:43 CDT)
  • Re: installation of namd without tcl and fftw (Mon May 10 2010 - 07:51:53 CDT)
  • Re: Using RMSD in colvar (Tue May 04 2010 - 15:07:38 CDT)
  • Re: colvars: free energy change with rmsd (Tue May 04 2010 - 10:41:19 CDT)
  • Re: colvars: free energy change with rmsd (Tue May 04 2010 - 10:37:47 CDT)
  • Re: colvar: coordnum output (Sat May 01 2010 - 03:28:02 CDT)
  • Re: colvar: coordnum output (Fri Apr 30 2010 - 07:44:20 CDT)
  • Re: colvar: coordnum output (Fri Apr 30 2010 - 07:16:44 CDT)
  • Re: Re: Re: Dielectric Constant (Thu Apr 29 2010 - 10:06:57 CDT)
  • Re: Re: Dielectric Constant (Thu Apr 29 2010 - 02:59:42 CDT)
  • Re: Dihedral parameters for side-chains? (Mon Apr 26 2010 - 07:29:40 CDT)
  • Re: FW: ammonia to methane/ c/o Jerome Henin (Fri Apr 23 2010 - 10:57:05 CDT)
  • Re: help (Thu Apr 22 2010 - 16:44:58 CDT)
  • Re: the total energy of single H2O molecule (Wed Apr 21 2010 - 11:50:13 CDT)
  • Re: colvar for PMF calculation (Wed Apr 21 2010 - 05:13:48 CDT)
  • Re: ABF: moving system in Z direction (Mon Apr 19 2010 - 11:20:35 CDT)
  • Re: unsubscribe (Mon Apr 19 2010 - 11:10:47 CDT)
  • Re: colvar: atom group defn. fails (Fri Apr 16 2010 - 07:17:38 CDT)
  • Re: ABF non-uniform sampling (Fri Apr 16 2010 - 04:48:17 CDT)
  • Re: which one is better to use - fixed atoms or constraints? (Wed Apr 14 2010 - 16:41:09 CDT)
  • Re: colvars: free energy change with rmsd (Wed Apr 14 2010 - 04:39:57 CDT)
  • Re: how to set pH (Wed Mar 31 2010 - 06:29:20 CDT)
  • Re: ABF Simulation Crash from TCL script (Wed Mar 31 2010 - 04:55:00 CDT)
  • Re: ABF Displacement (Mon Mar 29 2010 - 12:10:04 CDT)
  • Re: colvar error (Fri Mar 26 2010 - 06:34:11 CDT)
  • Re: What is the Potential Energy of a Protein in Namdenergy (Tue Mar 16 2010 - 07:10:00 CDT)
  • Re: question about NAMD (Fri Mar 12 2010 - 02:49:24 CST)
  • Re: Is two colvars file output possible during single simulation (ABF/2.7b) (Wed Feb 24 2010 - 11:55:26 CST)
  • Re: Parameters/topology entries for non-standard nucleotides (Sat Feb 20 2010 - 10:40:04 CST)
  • Re: About "equilibrate.conf' of FEP tutorial (Sat Feb 20 2010 - 10:36:43 CST)
  • Re: Pressure Questions (Wed Feb 10 2010 - 11:52:30 CST)
  • Re: velocities from a DCD file (Wed Jan 27 2010 - 09:08:52 CST)
  • Re: ABF question (Wed Jan 27 2010 - 04:18:13 CST)
  • Re: scripting error (Mon Jan 25 2010 - 09:10:19 CST)
  • Re: Erratic behavior of TclBC in parallel (Fri Jan 22 2010 - 11:08:02 CST)
  • Re: Excluding interactions? (Thu Jan 21 2010 - 08:17:26 CST)
  • Erratic behavior of TclBC in parallel (Thu Jan 21 2010 - 08:38:35 CST)
  • Re: Reply:Re: How to convert the GROMOS parameter unit into charmm22 style (Wed Jan 20 2010 - 07:05:37 CST)
  • Re: How to convert the GROMOS parameter unit into charmm22 style (Wed Jan 20 2010 - 03:27:42 CST)
  • Re: Center of Mass Harmonic Potentials (Tue Jan 19 2010 - 01:56:34 CST)
  • Re: Excluding interactions? (Sat Jan 16 2010 - 12:37:26 CST)
  • Re: Excluding interactions? (Fri Jan 15 2010 - 06:53:51 CST)
  • Re: ABF questions (Wed Jan 13 2010 - 10:40:49 CST)
  • Re: starting a job (Wed Jan 13 2010 - 07:00:58 CST)
  • Re: colvarsInput filename problem (Thu Jan 07 2010 - 04:28:09 CST)
  • Re: ABF - sequence of MD runs (Tue Jan 05 2010 - 11:26:22 CST)
  • Re: ABF questions (Tue Jan 05 2010 - 11:44:58 CST)
  • Re: NAMD-FEP tutorial-alchemify problem (Tue Jan 05 2010 - 10:54:38 CST)
  • Re: Definition of two colvars for ABF (Tue Jan 05 2010 - 08:12:47 CST)
  • Re: CMAP in NAMD output (Mon Jan 04 2010 - 17:07:38 CST)
  • Re: Definition of two colvars for ABF (Mon Jan 04 2010 - 16:59:22 CST)
  • Re: NAMD on current CPUs (Thu Dec 17 2009 - 12:56:25 CST)
  • NAMD on current CPUs (Thu Dec 17 2009 - 08:34:22 CST)
  • Re: How to obtain the system force on a fixed atom (Wed Dec 16 2009 - 12:01:33 CST)
  • Re: How to obtain the system force on a fixed atom (Wed Dec 16 2009 - 10:38:55 CST)
  • Re: FW: ABF error calculation (Sat Dec 12 2009 - 03:53:07 CST)
  • Re: Request for information regarding ABF in NAMD. (Fri Dec 11 2009 - 08:51:35 CST)
  • Re: 'dSmooth' no longer in the ABF procedure? (Wed Dec 09 2009 - 10:25:14 CST)
  • Re: psfgen fails to set coords for all atoms (Sat Nov 28 2009 - 18:02:52 CST)
  • Re: FreeEnergy: Not enough steps to complete pfm & mcti blocks (Fri Nov 27 2009 - 06:42:59 CST)
• kakali sen
  • writing back coordinates of waters that cross the unit cell (Thu Nov 25 2010 - 08:29:09 CST)
• Kalavera_at_gmx.net
  • Problems with OPLS in NAMD (Wed Mar 11 2009 - 04:32:56 CDT)
• Kalyan Pulipaka
  • Check out my photos on Facebook (Sat Oct 02 2010 - 21:57:26 CDT)
• Kamilla Kopec
  • Force Constant Units (Wed Jun 10 2009 - 12:08:24 CDT)
• Karim Elsawy
  • mgridforce (Fri Oct 09 2009 - 09:07:32 CDT)
• karthik s
  • how to config two different files for fixed atoms (Tue Mar 31 2009 - 06:54:10 CDT)
  • binary trajectories (Fri Jan 09 2009 - 04:53:54 CST)
• Katherine Parra
  • unsubscribe (Tue Oct 12 2010 - 16:58:06 CDT)
  • unsubscribe (Wed Sep 15 2010 - 09:42:24 CDT)
• Keith Battle
  • dual all-atom/coarse grain simulation (Tue Jul 20 2010 - 15:52:30 CDT)
  • Consecutive Simulations (Thu Feb 25 2010 - 09:25:33 CST)
  • Explicit Water System Condensing (Thu Feb 25 2010 - 09:17:53 CST)
  • Center of Mass Harmonic Potentials (Mon Jan 18 2010 - 18:59:25 CST)
• Kejun (Kevin) Dong
  • Re: Read DCD file in Java (Mon Jun 08 2009 - 12:33:58 CDT)
  • Read DCD file in Java (Sat Jun 06 2009 - 00:39:27 CDT)
• Kimura, Roy
  • pair interaction self in 2.7b3 (Tue Jul 20 2010 - 09:28:48 CDT)
  • pairinteractionself in 2.7b3 (Thu Jul 15 2010 - 14:33:04 CDT)
• KIRTANA S
  • FATAL ERROR: Bad global exclusion count! (Mon Jun 01 2009 - 12:37:38 CDT)
  • Regd: Error (Sun May 31 2009 - 22:52:15 CDT)
  • Regd :parameter file (Fri May 29 2009 - 15:56:04 CDT)
  • regd: my parameter file (Fri May 29 2009 - 16:05:26 CDT)
  • using amber topology and parameter files in NAMD (Fri May 29 2009 - 12:16:54 CDT)
  • PSF file (Tue May 12 2009 - 14:29:05 CDT)
• Kovács, Sándor Ádám
  • RE: Par and Top files for BCL (Thu Jul 09 2009 - 13:35:54 CDT)
  • Par and Top files for BCL (Thu Jul 02 2009 - 12:08:08 CDT)
• Krishnan, Marimuthu
  • ABF - sequence of MD runs (Thu Dec 17 2009 - 21:55:59 CST)
• kristian krantz
  • Random Expulsion MD (REMD) (Mon Oct 26 2009 - 06:07:11 CDT)
• Kwee Hong
  • plotting potential energy (Thu Dec 09 2010 - 03:37:04 CST)
  • Re: system density (Sun Nov 28 2010 - 00:31:17 CST)
  • system density (Sat Nov 27 2010 - 05:18:19 CST)
  • Re: Constant pressure (Thu Nov 25 2010 - 13:16:52 CST)
  • Constant pressure (Thu Nov 25 2010 - 10:29:29 CST)
  • Re: Charmrun: error on request socket-- (Thu Oct 28 2010 - 22:05:27 CDT)
  • Re: Charmrun: error on request socket-- (Wed Oct 27 2010 - 21:01:33 CDT)
  • Charmrun: error on request socket-- (Wed Oct 27 2010 - 12:08:11 CDT)
  • Re: coordinate not the same between the input and frame 0 (Tue Oct 26 2010 - 05:06:22 CDT)
  • coordinate not the same between the input and frame 0 (Tue Oct 26 2010 - 03:27:25 CDT)
  • Re: unable to open binary file (Tue Oct 26 2010 - 01:26:10 CDT)
  • Warning: Bad global exclusion count, possible error! (Sun Oct 24 2010 - 22:07:39 CDT)
  • Re: getting desired angle (Sun Oct 24 2010 - 22:06:33 CDT)
  • getting desired angle (Sat Oct 23 2010 - 03:49:23 CDT)
  • simulation time instead of frames (Thu Oct 14 2010 - 06:05:47 CDT)
  • problem caused by cluster? (Tue Oct 05 2010 - 20:17:50 CDT)
  • Re: unable to open binary file (Mon Oct 04 2010 - 22:55:00 CDT)
  • unable to open binary file (Mon Oct 04 2010 - 09:00:10 CDT)
  • question on hydrogen bond (Sun Sep 05 2010 - 22:40:40 CDT)
  • Re: Bad atom ID in extra bond file (Sat Sep 04 2010 - 05:08:03 CDT)
  • Bad atom ID in extra bond file (Sat Sep 04 2010 - 03:10:25 CDT)
  • protein shifts out of water box (Tue Aug 31 2010 - 05:20:53 CDT)
  • problem at applying patch (Sat Aug 28 2010 - 12:58:21 CDT)
  • charge calculation (Sat Aug 28 2010 - 09:09:12 CDT)
  • Re: problem at maintaining geometry coordinate (Mon Aug 23 2010 - 23:02:54 CDT)
  • problem at maintaining geometry coordinate (Mon Aug 23 2010 - 02:22:53 CDT)
  • Re: problem at maintaining geometry coordinate (Tue Aug 17 2010 - 23:43:25 CDT)
  • problem at maintaining geometry coordinate (Tue Aug 17 2010 - 22:48:35 CDT)
  • Re: question regarding warning. (Mon Aug 09 2010 - 21:48:14 CDT)
  • Re: question regarding warning. (Mon Aug 09 2010 - 04:29:16 CDT)
  • question regarding warning. (Mon Aug 09 2010 - 02:28:16 CDT)
  • Installation problem on Win64 (Fri Apr 02 2010 - 04:46:28 CDT)
• Kyle Hong
  • Re: colvars: free energy change with rmsd (Wed Apr 14 2010 - 04:05:03 CDT)
• L. Michel Espinoza-Fonseca
  • Re: COARSE GRAINED WATER MODEL (Tue Oct 20 2009 - 09:36:00 CDT)
  • Re: ATP and Stream files (Fri Oct 16 2009 - 00:42:52 CDT)
  • Re: regarding protein-protein interaction (Fri Jun 05 2009 - 03:19:43 CDT)
  • Re: phosphoserine simulation using toppar files and NAMD (Wed Mar 25 2009 - 07:55:45 CDT)
• l.mammucari_at_tin.it
  • (no subject) (Mon Nov 02 2009 - 15:47:14 CST)
• La Fosca
  • Re: anomalous behaviour of ASPP and GLUP during MD run (Thu Feb 25 2010 - 09:04:29 CST)
• Lada Biedermannová
  • Re: NAMD Energy types (Thu Sep 09 2010 - 08:16:44 CDT)
  • Re: NAMD Energy types (Thu Sep 09 2010 - 03:51:12 CDT)
  • NAMD Energy types (Wed Sep 08 2010 - 04:16:30 CDT)
• Lan Hua
  • Re: periodic boundary conditions in namd energy calculation (Tue Nov 30 2010 - 16:04:52 CST)
  • periodic boundary conditions in namd energy calculation (Mon Nov 29 2010 - 15:52:43 CST)
• lara lara
  • Re: hexane (Sun Oct 17 2010 - 23:29:53 CDT)
  • hexane (Sat Oct 16 2010 - 04:00:09 CDT)
  • reg_membrane_peptide_interaction (Sat Sep 25 2010 - 04:24:09 CDT)
• Laurent Chaloin
  • Re: NAMD 2.7b2 versy slow on multiple nodes (Wed May 26 2010 - 07:43:56 CDT)
  • NAMD 2.7b2 versy slow on multiple nodes (Tue May 25 2010 - 16:30:51 CDT)
  • AlF4 (Thu Sep 17 2009 - 04:54:14 CDT)
• Leandro Martínez
  • Re: Asking for some sample PDB and PSF files of carbon nanotube (Wed Dec 15 2010 - 04:55:59 CST)
  • change solvent (Wed Aug 18 2010 - 11:36:59 CDT)
  • Re: force-field for ATP (Tue Apr 28 2009 - 20:05:54 CDT)
  • Re: smd direction (Mon Mar 30 2009 - 12:59:29 CDT)
  • Re: Coordinate Output in both binary and ASCII. Or converting binary to ASCII in the command line (Mon Mar 02 2009 - 11:02:08 CST)
• Lee Wei Yang
  • Difference between Linux-x86_64-TCP and Linux-x86_64 (Mon Nov 23 2009 - 16:33:12 CST)
  • RE: CUDA-accelarated NAMD does not use the video card? (Fri Nov 13 2009 - 18:15:27 CST)
  • CUDA-accelarated NAMD does not use the video card? (Fri Nov 13 2009 - 16:55:15 CST)
  • RE: Will MPICH2 work for NAMD? and the best way to build/compile NAMD to exploit my hardware resource? (Fri Nov 13 2009 - 16:12:50 CST)
  • Will MPICH2 work for NAMD? (Mon Nov 09 2009 - 12:37:58 CST)
  • RE: Running NAMD w/ CUDA under Linux (Thu Nov 05 2009 - 18:32:40 CST)
• Lee, Se I
  • unsubscribe (Thu Feb 12 2009 - 13:26:01 CST)
• Lei Shi
  • ABF question (free energy partition) (Sun Aug 09 2009 - 11:36:10 CDT)
  • Please disregard the spam "Lei sent you private photos on Tagged :)" (Thu Jun 04 2009 - 17:04:05 CDT)
  • Re: NAMD 2.7b1 on Ranger/MPI Problems? (Mon Apr 20 2009 - 15:04:00 CDT)
• Lei Zhang
  • bracket in the log file (Tue Mar 17 2009 - 16:29:07 CDT)
• Lela Vukovic
  • Re: FEP yields the same results for forward and backward computation! (Tue May 18 2010 - 13:08:02 CDT)
  • Can AMBER topology be used in NAMD-CUDA? (Fri Apr 09 2010 - 14:54:08 CDT)
  • Re: Alchemical calculations in CUDA version of NAMD? (Wed Mar 17 2010 - 01:28:50 CDT)
  • Re: Alchemical calculations in CUDA version of NAMD? (Wed Mar 03 2010 - 12:01:03 CST)
  • Alchemical calculations in CUDA version of NAMD? (Wed Mar 03 2010 - 11:33:36 CST)
  • suitable motherboards for both graphical visualization and NAMD-CUDA computation? (Wed Jan 20 2010 - 14:56:45 CST)
  • Re: Thermodynamic integration script - where is it? (Mon Jun 01 2009 - 12:52:38 CDT)
• Leonardo Herrera
  • Interface analisis (Tue Aug 03 2010 - 12:20:00 CDT)
  • Hepl whit colvar subrutiene (Fri Jun 18 2010 - 16:11:19 CDT)
  • Re: colvars don't run with minimization ... (Tue Jun 15 2010 - 11:45:02 CDT)
  • Re: Help with cys unprotonated (Tue Jun 15 2010 - 11:43:47 CDT)
  • Help with cys unprotonated (Mon Jun 14 2010 - 20:24:39 CDT)
  • colvars don't run with minimization ... (Mon Jun 14 2010 - 19:44:21 CDT)
  • colvars: Error: in parsing "centers" (Thu Jun 10 2010 - 19:25:16 CDT)
  • where do I find info about freeEnergy ? (Tue Jun 08 2010 - 13:28:15 CDT)
  • Problem with extraBonds (Thu Jun 03 2010 - 20:23:32 CDT)
  • help whit distance restraint (Wed Jun 02 2010 - 17:37:57 CDT)
  • How I can insert de harmonic restraint? (Fri May 07 2010 - 15:33:18 CDT)
  • problem whit comand "COM" (Tue Jan 26 2010 - 20:21:19 CST)
  • How can I fix lipid lateral area in membrane simulation? (Tue Apr 14 2009 - 12:39:38 CDT)
  • Error generating file.psf for cholesterol, missing coordinates in file.pdb. (Sun Mar 29 2009 - 14:56:20 CDT)
  • Problem to generate water segments and lipid reading in membrane (Tue Mar 10 2009 - 05:18:15 CDT)
  • Problem to generate water segments and lipid reading in membrane (Tue Mar 10 2009 - 05:17:36 CDT)
• Leonardo Trabuco
  • Re: Bad atom ID in extra bond file (Sat Sep 04 2010 - 04:41:00 CDT)
  • Re: Does "rigidbond off" work instead of "rigidbonds none" (Fri Sep 03 2010 - 01:21:01 CDT)
  • Re: Difference between the two Dowsers (Fri Jun 04 2010 - 02:47:21 CDT)
  • Re: run NAMD_2.7B2 (Mon Jan 04 2010 - 13:57:27 CST)
  • Re: NAMD 2.7b2 new features (Wed Dec 23 2009 - 06:37:39 CST)
  • Re: defined path for NAMD2 (Fri Dec 18 2009 - 02:41:12 CST)
  • Re: Measuring the molarity (Wed Jul 22 2009 - 16:09:28 CDT)
  • Re: ERROR! Explicit exclusions or fluctuating charges not supported, atom ignored. (Thu Jul 02 2009 - 19:09:23 CDT)
  • Re: ERROR! Explicit exclusions or fluctuating charges not supported, atom ignored. (Thu Jul 02 2009 - 18:55:23 CDT)
  • Re: Dihedral Restraints during MD simulation (Wed Apr 15 2009 - 14:03:22 CDT)
  • Re: Dihedral Restraints during MD simulation (Wed Apr 15 2009 - 13:43:18 CDT)
  • Re: namdcvs Re: how to apply restraints for phi and psi for alpha helix regions (Fri Jan 02 2009 - 02:55:40 CST)
• Lev Lafayette
  • Re: NAMD infiniband performance (Tue May 19 2009 - 01:31:47 CDT)
  • Re: Make NAMD2.7b1 with cuda bug? (Thu May 14 2009 - 01:12:41 CDT)
  • Make NAMD2.7b1 with cuda bug? (Tue May 12 2009 - 22:48:04 CDT)
• Lewyn Li
  • Re: Consecutive Simulations (Thu Feb 25 2010 - 10:08:47 CST)
• Li, Hongzhi
  • Help pls: Got error on FEP calculation: ERROR: The following variables are NOT VALID lambda2... (Mon Nov 09 2009 - 12:18:59 CST)
• Liang
  • location of the SMD source code (Tue Jun 30 2009 - 13:17:48 CDT)
• Liao Chen
  • looking for topology and parameters of methamphetamine (Sun May 09 2010 - 08:47:46 CDT)
  • get total force on a group of atoms within GlobalMasterSMD (Sun Apr 11 2010 - 19:02:16 CDT)
• Liao Chuan
  • Implementation of Martini CG FF in NAMD (Wed Apr 14 2010 - 11:25:50 CDT)
• Linchen Gong
  • fail to run replica exchange on more than one node (Wed Feb 18 2009 - 01:31:24 CST)
• Lisa Brown
  • Re: how to save a DCD file without water in NAMD ? (Fri Aug 13 2010 - 11:02:36 CDT)
  • Re: how to save a DCD file without water in NAMD ? (Fri Aug 13 2010 - 08:06:36 CDT)
  • how to save a DCD file without water in NAMD ? (Thu Aug 12 2010 - 15:00:40 CDT)
  • Re: NAMD-FEP tutorial-alchemify problem (Tue Jan 05 2010 - 12:38:43 CST)
  • NAMD-FEP tutorial-alchemify problem (Tue Jan 05 2010 - 09:21:41 CST)
  • How can I find topology and parameter files for heterocyclic, heteroaromatic, halogens and sugar compounds (Fri Feb 27 2009 - 11:02:51 CST)
  • how to do a MD of small part of a protein, using namd? (Mon Feb 23 2009 - 10:23:43 CST)
• listowel agyarko
  • Simulation configuration file not accesible (Tue Jun 22 2010 - 15:30:59 CDT)
• liupeng012
  • how to submit job on a HPC equipped with infiniband (Mon Jul 26 2010 - 02:59:34 CDT)
  • about compile namd2.7 (Sun Jul 19 2009 - 05:58:05 CDT)
  • Re: Re: namd2.7b1 slower with openmpi 1.3.2 than namd2.6 withopenmpi 1.2.6 (Sat Jul 04 2009 - 21:17:15 CDT)
  • namd 2.7b1 on infiniband about the error : stack Traceback (Thu Jun 04 2009 - 00:10:32 CDT)
  • compile namd2.7b1 on infiniband (Tue Jun 02 2009 - 21:43:16 CDT)
  • some problem about ABF (Wed Mar 11 2009 - 03:59:53 CDT)
  • problem about NAMD compile (Tue Mar 10 2009 - 03:15:27 CDT)
• liupeng012_at_mail.nankai.edu.cn
  • how to use volmap analysing a series of dcd. (Wed Sep 16 2009 - 08:39:50 CDT)
• lixb07_at_lzu.cn
  • Running problem with NAMD2.7b (Mon Jul 12 2010 - 21:01:40 CDT)
  • the problem with NAMD2.7b (Mon Jul 12 2010 - 05:13:41 CDT)
  • namd2 still works but without any new messages in log file (Thu Jul 01 2010 - 07:21:18 CDT)
  • modification of CHARMM force field (Fri Jun 25 2010 - 20:05:56 CDT)
• Lixia Jin Day
  • free energy changes of one subunit (Tue Mar 16 2010 - 13:39:55 CDT)
  • NAMD on linux (Thu Jan 21 2010 - 10:55:57 CST)
  • Lennard-Jones potential in CHARMM (Thu Oct 08 2009 - 16:19:16 CDT)
  • How to calculate free energy for conformational change (Thu Jul 30 2009 - 16:46:07 CDT)
  • need advices for running NAMD efficiently. (Mon Jun 15 2009 - 12:44:55 CDT)
  • to run NAMD on a PC (Mon Jun 15 2009 - 12:59:08 CDT)
  • VDW distance in energy minimized conformation (Tue Apr 21 2009 - 17:11:42 CDT)
  • Re: Free energy of conformational change (Wed Mar 25 2009 - 18:04:37 CDT)
  • Free energy of conformational change (Wed Mar 25 2009 - 15:21:19 CDT)
• Luca Bellucci
  • Adding special VdW parameters (Sat Dec 25 2010 - 10:04:55 CST)
  • TIP4P topology (Tue Nov 03 2009 - 14:24:04 CST)
• Luca M.
  • (no subject) (Mon Nov 02 2009 - 14:33:36 CST)
• Luca Mammucari
  • TIP4P (Tue Nov 03 2009 - 17:07:10 CST)
• Luca Muccioli
  • Re: Fwd: help to improve the script to predict mean square displacement (Fri Mar 12 2010 - 17:08:31 CST)
  • Re: Fullerene topology (Wed Oct 28 2009 - 15:31:38 CDT)
  • Re: Fullerene topology (Wed Oct 28 2009 - 10:55:11 CDT)
  • Re: Thiol on gold simulation in NAMD (Thu Feb 26 2009 - 04:41:28 CST)
• lucie delemotte
  • NAMD stalled at startup phase 0 when working on a large numbr of processors (Wed Mar 24 2010 - 13:07:44 CDT)
  • Pair interaction runtime analysis skipping dcd frames (Thu Oct 22 2009 - 09:30:08 CDT)
• Luis Agullo (LAB)
  • ATP and Stream files (Fri Oct 16 2009 - 03:39:30 CDT)
  • Ionization with VMD (Thu Oct 15 2009 - 09:07:13 CDT)
  • Re: spontaneous system explosion after 2 ns of normal run (Thu Oct 15 2009 - 08:40:06 CDT)
  • ATP and Stream files (Thu Oct 15 2009 - 07:49:58 CDT)
  • Temperature rescaling vs. reassignment (Tue Sep 15 2009 - 09:26:48 CDT)
  • END: No log file (Mon Jul 06 2009 - 09:56:15 CDT)
  • No log file (Mon Jul 06 2009 - 08:41:14 CDT)
• Luis Cunha
  • NAMD CVS (Thu Feb 19 2009 - 18:01:39 CST)
  • Re: FEP/binding free energy difference WT vs Mut (Tue Feb 17 2009 - 11:50:20 CST)
  • FEP/binding free energy difference WT vs Mut (Fri Feb 13 2009 - 16:43:27 CST)
• Luis Gracia
  • Re: Re: vmd-l: rmsd matrix (Thu Sep 03 2009 - 16:47:36 CDT)
  • RE: display all frames simultaneously (Fri Apr 17 2009 - 00:35:29 CDT)
• m.raviprasad_at_ndsu.edu
  • CHARMM FF parameters for O2 Gas (Fri Aug 06 2010 - 14:39:11 CDT)
  • Interaction energy difference (Wed Jul 28 2010 - 22:42:07 CDT)
  • Re: Problems about FEP simulation (Fri May 21 2010 - 14:52:53 CDT)
  • Re: Error in running minimization (Fri May 21 2010 - 09:27:08 CDT)
• Madhurima Jana
  • Re: Different Dielectric constant value for different segment (Wed Nov 24 2010 - 05:25:06 CST)
  • Different Dielectric constant value for different segment (Mon Nov 22 2010 - 07:48:39 CST)
  • tcl script for saving .coor of each frame from dcd file (Wed Sep 15 2010 - 23:51:41 CDT)
  • alchemy FEP query (Fri Jul 16 2010 - 01:05:44 CDT)
  • Fwd: force constant in abf configuration file (Thu Dec 17 2009 - 11:29:50 CST)
  • force constant in abf configuration file (Tue Dec 15 2009 - 23:01:02 CST)
• Magdalena Gruziel
  • setting transfer rate in IMD protocol (Wed Apr 21 2010 - 09:22:22 CDT)
• Maggie Pruitt
  • Need help preventing hydration of the lipid-protein interface in my system (Fri Nov 19 2010 - 09:46:45 CST)
• mahmoud
  • RE: CPU USAGE (Sun Jul 19 2009 - 04:15:08 CDT)
  • NAMD Installation (Wed Jul 01 2009 - 02:53:51 CDT)
• mahmoud mirzaei
  • Re: CPU USAGE (Sat Jul 18 2009 - 23:07:26 CDT)
  • CPU USAGE (Sat Jul 18 2009 - 11:14:10 CDT)
• Marc Baaden
  • Re: Using NAMD for Metropolis Monte Carlo conformational searches (Thu Nov 25 2010 - 06:26:43 CST)
  • Re: Colvars and COM restraints for protein+membrane; plus a minor bug (Fri Sep 24 2010 - 03:44:41 CDT)
  • Colvars and COM restraints for protein+membrane; plus a minor bug (Thu Sep 23 2010 - 09:24:59 CDT)
• Marcello Sega
  • Re: Re: namd 2.7b2 or later - amberff/prmtop causes segfault during startup phase (Sat Apr 03 2010 - 19:35:01 CDT)
• Marcelo Puiatti
  • Reassign temp (Wed Jun 17 2009 - 15:27:18 CDT)
• Marcin Krol
  • Re: regarding protein-protein interaction (Fri Jun 05 2009 - 03:23:13 CDT)
  • two independent groups of constraints (Thu Apr 30 2009 - 07:44:41 CDT)
• Marcin S.
  • Creating bonds during a run (Mon Jan 12 2009 - 09:41:23 CST)
• Marcos Sotomayor
  • Re: Steered Molecular Dynamics for more than one atom (Mon Aug 10 2009 - 21:11:11 CDT)
  • Re: SMD and Temperature control (Mon Aug 10 2009 - 20:35:24 CDT)
  • Membrane Proteins Tutorial (Fri Feb 13 2009 - 16:25:15 CST)
• Marie N
  • Lipid and protein interactions (Fri Feb 19 2010 - 17:25:29 CST)
  • help running NAMD energy at multiple stable temperatures (newbie) (Mon Mar 02 2009 - 23:32:04 CST)
• Marius Micluta
  • Re: Charmrun/INTEL MAC/2.7 (Fri Jun 05 2009 - 04:36:57 CDT)
  • Re: NAMD 2.7b1 running & performance issues (Mon Jun 01 2009 - 07:15:56 CDT)
  • NAMD 2.7b1 running & performance issues (Mon May 25 2009 - 06:13:07 CDT)
• Mark M Huntress
  • solute movement in periodic box (Fri Sep 03 2010 - 09:53:38 CDT)
  • high atom velocity (Tue May 04 2010 - 14:36:56 CDT)
  • langevinhydrogen on with rigidbonds water (Fri Apr 30 2010 - 11:29:55 CDT)
  • rigid molecule (Sun Mar 28 2010 - 15:34:30 CDT)
  • RE: cell basis vector restart (Tue Mar 02 2010 - 12:09:07 CST)
  • RE: cell basis vector restart (Tue Mar 02 2010 - 09:51:21 CST)
  • cell basis vector restart (Mon Mar 01 2010 - 16:47:47 CST)
  • electrostatic vs van der waals (Mon Mar 01 2010 - 09:57:35 CST)
  • fixed atoms pdb (Mon Aug 24 2009 - 17:13:20 CDT)
  • frozen water Oxygens (Tue Aug 04 2009 - 11:13:12 CDT)
  • can I change coordinate before restart? (Tue Apr 21 2009 - 16:03:55 CDT)
• Markus K. Dahlgren
  • Re: Missing angle parameters CT3 CT3 CT3 (Tue Nov 02 2010 - 07:38:08 CDT)
• Mary Newcomb
  • Error: This application has requested the Runtime to terminate it in an unusual way: Please contact the application's support team for more information" after specifying the namd2.exe path (Fri Mar 19 2010 - 16:17:27 CDT)
• masoumeh ozmaeian
  • finding appropriate topology file for polymers (Sun Nov 07 2010 - 08:45:23 CST)
• Massimiliano Bonomi
  • PLUMED release 1.2.0 available (Tue May 18 2010 - 06:47:05 CDT)
  • PLUMED tutorial announcement (Tue Jan 26 2010 - 02:38:12 CST)
  • PLUMED release 1.1.0 available (Tue Jul 28 2009 - 03:12:27 CDT)
  • PLUMED release 1.0.0 available (Thu Feb 26 2009 - 07:12:04 CST)
• Matt Krems
  • Benzene PSF (Wed Apr 29 2009 - 19:04:27 CDT)
• Matteo Rotter
  • Re: Fw: NAMD 2.7b1 running problem (Thu May 21 2009 - 03:30:06 CDT)
• matteo.rotter
  • Re: Fep performance (Thu Sep 17 2009 - 08:43:00 CDT)
  • Fep performance (Mon Aug 24 2009 - 10:51:27 CDT)
• Matthew Ambrosia
  • unsubscribe (Thu Apr 23 2009 - 09:08:56 CDT)
• Matthieu Wilhelm
  • Re: Dihedral Restraints during MD simulation (Thu Apr 16 2009 - 03:56:59 CDT)
  • Dihedral Restraints during MD simulation (Wed Apr 15 2009 - 12:33:04 CDT)
• matziast_at_med.uth.gr
  • help with the equilibration script (Tue Dec 28 2010 - 16:31:44 CST)
  • structure of an equilibration script (Sun Dec 26 2010 - 07:23:53 CST)
  • equilibration script from restart files (Sun Dec 26 2010 - 06:24:16 CST)
  • memory allocation failed on processor 0 (Wed Dec 15 2010 - 04:07:02 CST)
  • atom type (Fri Nov 19 2010 - 06:21:47 CST)
  • atom type (Fri Nov 19 2010 - 05:03:28 CST)
  • script for calculation of an rmsd (Sat Oct 30 2010 - 03:41:41 CDT)
  • tmd log file (Fri Oct 15 2010 - 06:35:37 CDT)
  • script for targeted molecular dynamics (Fri Oct 15 2010 - 03:15:20 CDT)
  • targeted molecular dynamics (Thu Oct 14 2010 - 17:22:30 CDT)
  • multiplicity of dihedrals (Thu May 27 2010 - 03:02:16 CDT)
  • parameter file for CHARMM (Tue May 25 2010 - 16:05:09 CDT)
• MD. ZILLUR RAHMAN
  • CHARM parameter file needed for simple organic molecules like Methanol, Formamide, Chloroform, TCE, Toluene (Sun Mar 21 2010 - 22:07:46 CDT)
• Megan Scoppa
  • Specifying Values for Rotating Constraints (Tue Aug 03 2010 - 11:09:54 CDT)
• Melanie Santos Marrero
  • (no subject) (Tue Jul 06 2010 - 15:35:18 CDT)
• Mengchen Pu
  • multistep minimization with different constraint (Fri May 28 2010 - 06:29:34 CDT)
• Mert Gür
  • Re: Does "rigidbond off" work instead of "rigidbonds none" (Fri Sep 17 2010 - 14:44:14 CDT)
  • Re: Low temperature Molecular Dynamics (Thu Sep 16 2010 - 14:49:01 CDT)
  • Low temperature Molecular Dynamics (Tue Sep 14 2010 - 15:42:53 CDT)
  • Re: Does "rigidbond off" work instead of "rigidbonds none" (Fri Sep 03 2010 - 04:25:40 CDT)
  • Does "rigidbond off" work instead of "rigidbonds none" (Thu Sep 02 2010 - 15:03:21 CDT)
  • Re: how to save a DCD file without water in NAMD ? (Fri Aug 13 2010 - 08:56:44 CDT)
  • Re: positive total energy (Wed Aug 11 2010 - 07:48:29 CDT)
  • Re: positive total energy (Wed Aug 11 2010 - 03:15:26 CDT)
  • Re: restart from different snap shots (Tue Aug 10 2010 - 07:48:32 CDT)
  • Re: Reason of FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT (Mon Aug 09 2010 - 08:14:39 CDT)
  • Re: Reason of FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT (Sun Aug 08 2010 - 17:07:56 CDT)
  • Re: Reason of FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT (Sat Aug 07 2010 - 15:12:15 CDT)
  • Re: Reason of FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT (Sat Aug 07 2010 - 11:39:13 CDT)
  • Reason of FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT (Sat Aug 07 2010 - 10:20:19 CDT)
  • Re: waterbox changes shape during steered molecular dynamics (Sat Jul 03 2010 - 05:58:39 CDT)
  • waterbox changes shape during steered molecular dynamics (Mon Jun 21 2010 - 14:50:58 CDT)
  • waterbox changes shape during steered molecular dynamics (Mon Jun 21 2010 - 14:13:21 CDT)
  • Re: duplicate residue key ALA will be ignored (Tue May 18 2010 - 11:37:57 CDT)
  • duplicate residue key ALA will be ignored (Mon May 17 2010 - 16:42:59 CDT)
  • (no subject) (Mon May 17 2010 - 16:11:22 CDT)
  • Re: Re: Generate missing atoms of a coarse grained structure (Wed Apr 14 2010 - 03:34:41 CDT)
  • Re: Generate missing atoms of a coarse grained structure (Wed Apr 14 2010 - 03:35:13 CDT)
  • Generate missing atoms of a coarse grained structure (Sun Apr 04 2010 - 04:40:13 CDT)
  • Re: About matdcd (Sun Apr 04 2010 - 04:20:50 CDT)
  • Re: What is the Potential Energy of a Protein in Namdenergy (Tue Mar 16 2010 - 07:59:31 CDT)
  • What is the Potential Energy of a Protein in Namdenergy (Tue Mar 16 2010 - 05:51:39 CDT)
  • Re: trouble in dynamics (Thu Feb 18 2010 - 04:32:18 CST)
  • Re: installation of namd in parallel mode (Sun Feb 14 2010 - 05:51:55 CST)
  • Re: reading dcd file (Tue Jan 26 2010 - 15:46:00 CST)
  • Re: Free Energy Calculation of a protein (Wed Dec 16 2009 - 08:41:50 CST)
  • Re: Free Energy Calculation of a protein (Tue Dec 15 2009 - 02:48:31 CST)
  • Re: Free Energy Calculation of a protein (Thu Dec 10 2009 - 03:48:22 CST)
  • Re: Free Energy Calculation of a protein (Thu Dec 10 2009 - 03:14:28 CST)
  • Free Energy Calculation of a protein (Wed Dec 09 2009 - 14:19:42 CST)
  • Re: How are the SMD atoms connected to the center of mass (Wed Dec 02 2009 - 07:45:26 CST)
  • Re: Small discrepancy in Kinetic Energy after restarting the simulation (Tue Dec 01 2009 - 11:35:08 CST)
  • How are the SMD atoms connected to the center of mass (Tue Dec 01 2009 - 07:31:47 CST)
  • Small discrepancy in Kinetic Energy after restarting the simulation (Tue Dec 01 2009 - 03:10:30 CST)
  • fixing the protein during minimization (Mon Nov 09 2009 - 08:22:24 CST)
  • Re: Re: vmd-l: rmsd matrix (Fri Sep 04 2009 - 09:09:07 CDT)
  • Re: hole on the surface of the waterbox (Fri Aug 28 2009 - 17:14:00 CDT)
  • Re: hole on the surface of the waterbox (Fri Aug 28 2009 - 13:45:03 CDT)
  • Re: hole on the surface of the waterbox (Fri Aug 28 2009 - 07:36:16 CDT)
  • Re: hole on the surface of the waterbox (Fri Aug 28 2009 - 07:20:09 CDT)
  • Re: hole on the surface of the waterbox (Fri Aug 28 2009 - 06:12:25 CDT)
  • hole on the surface of the waterbox (Fri Aug 28 2009 - 05:08:09 CDT)
  • Re: question on forces / theory (Wed Aug 26 2009 - 13:21:18 CDT)
  • Re: question on forces / theory (Wed Aug 26 2009 - 13:23:23 CDT)
  • Alignment of velocity dcd file (Sat Aug 22 2009 - 15:03:10 CDT)
  • Re: Re: recalculating energy using dcd file (Thu Aug 06 2009 - 15:09:58 CDT)
  • Re: Steered Molecular Dynamics (Wed Aug 05 2009 - 06:57:17 CDT)
  • Re: Total energy of a residue (Tue Jun 23 2009 - 14:59:19 CDT)
  • Total energy of a residue (Tue Jun 23 2009 - 10:08:12 CDT)
  • Force on multiple atoms in ABF (Sun May 24 2009 - 11:26:16 CDT)
  • Re: Need help to generate ubq-get-energy.conf (Thu May 14 2009 - 13:00:57 CDT)
  • Re: Need help to generate ubq-get-energy.conf (Thu May 14 2009 - 05:43:46 CDT)
  • Re: Need help to generate ubq-get-energy.conf (Thu May 14 2009 - 02:01:27 CDT)
  • Re: Need help to generate ubq-get-energy.conf (Wed May 13 2009 - 15:49:24 CDT)
  • Need help to generate ubq-get-energy.conf (Wed May 13 2009 - 10:06:55 CDT)
  • Re: I can't keep my pulling directions the same with the SMD vector (Tue Apr 21 2009 - 02:49:19 CDT)
  • Re: I can't keep my pulling directions the same with the SMD vector (Mon Apr 20 2009 - 03:16:39 CDT)
  • Re: I can't keep my pulling directions the same with the SMD vector (Sun Apr 19 2009 - 11:10:11 CDT)
  • I can't keep my pulling directions the same with the SMD vector (Sun Apr 19 2009 - 07:56:00 CDT)
  • Re: Evaluating kinetic energy from a modified DCD file (Sun Apr 12 2009 - 08:11:21 CDT)
  • Re: Evaluating kinetic energy from a modified DCD file (Fri Apr 10 2009 - 12:52:08 CDT)
  • Re: Writing 3 subsequent timesteps to the DCD file (Fri Apr 10 2009 - 10:24:23 CDT)
  • Re: Evaluating kinetic energy from a modified DCD file (Wed Apr 08 2009 - 16:57:01 CDT)
  • Re: Writing 3 subsequent timesteps to the DCD file (Wed Apr 08 2009 - 14:36:45 CDT)
  • Re: Writing 3 subsequent timesteps to the DCD file (Wed Apr 08 2009 - 13:40:43 CDT)
  • Evaluating kinetic energy from a modified DCD file (Wed Apr 08 2009 - 14:33:05 CDT)
  • Re: Writing 3 subsequent timesteps to the DCD file (Wed Apr 08 2009 - 04:44:09 CDT)
  • Writing 3 subsequent timesteps to the DCD file (Tue Apr 07 2009 - 06:24:18 CDT)
  • Re: Reference file for the constraining force in Umbrella Sampling (Sat Mar 14 2009 - 10:44:31 CDT)
  • Re: Reference file for the constraining force in Umbrella Sampling (Sat Mar 14 2009 - 07:10:35 CDT)
  • Reference file for the constraining force in Umbrella Sampling (Thu Mar 12 2009 - 18:02:24 CDT)
  • Re: ligand flies away from binding pocket (Fri Feb 13 2009 - 13:34:58 CST)
  • Re: Aligning the distance between two centroids with an axis (Sat Jan 31 2009 - 02:13:38 CST)
  • Aligning the distance between two centroids with an axis (Fri Jan 30 2009 - 04:02:55 CST)
• mgssal
  • one atom off in the minimization result (Sun Jul 12 2009 - 03:22:46 CDT)
• Michael Di Domenico
  • GPU heavy models? (Tue Dec 14 2010 - 08:03:52 CST)
• Michael Feig
  • RE: TMD comments (Tue Jan 20 2009 - 21:27:31 CST)
  • RE: TMD comments (Tue Jan 20 2009 - 07:02:23 CST)
  • TMD comments (Fri Jan 16 2009 - 23:06:07 CST)
• Michael Harney
  • NAMD checkpoint mechanism. (Fri Jul 09 2010 - 15:38:46 CDT)
• Michael Homa
  • Problem Compiling NAMD (version 2.7b2) (Fri Mar 12 2010 - 12:06:34 CST)
• Michael Kreim
  • flipdcd (Sat May 30 2009 - 07:12:34 CDT)
• Michael LeVine
  • FEP for GLY and PRO Mutations (Mon Jul 26 2010 - 10:10:28 CDT)
• Michael S. Sellers (Cont, ARL/WMRD)
  • Re: periodic boundary conditions in namd energy calculation (Tue Nov 30 2010 - 14:06:09 CST)
  • Creating a NAMD Shared Library -> Undefined Symbols in Charm libs (Mon Nov 29 2010 - 15:22:40 CST)
  • Creating a NAMD Shared Library -> Undefined Symbols in Charm libs (Mon Nov 29 2010 - 15:07:21 CST)
• Michael Thomas
  • Re: calculation of periodic box (Tue Nov 17 2009 - 22:56:55 CST)
  • calculation of periodic box (Tue Nov 17 2009 - 22:16:05 CST)
  • constraint energy contributions (Tue Oct 06 2009 - 06:33:25 CDT)
  • How is dG caluclated from dE during FEP? (Wed Jun 17 2009 - 06:51:31 CDT)
• Michael Zimmermann
  • Re: Re: colvar atom syntax (Wed Jun 16 2010 - 10:24:50 CDT)
  • Re: Re: colvar atom syntax (Tue Jun 15 2010 - 15:59:09 CDT)
  • Re: colvar atom syntax (Thu Jun 10 2010 - 15:40:53 CDT)
  • Re: colvar atom syntax (Thu Jun 10 2010 - 15:15:41 CDT)
  • colvar atom syntax (Tue Jun 08 2010 - 13:11:29 CDT)
  • are tclForces included in minimization? (Fri May 28 2010 - 00:41:26 CDT)
  • backbone restraints (Wed May 26 2010 - 10:46:09 CDT)
  • adding specific forces between atoms (Mon Sep 21 2009 - 15:44:48 CDT)
  • visualize energy on a structure (Fri May 29 2009 - 12:20:24 CDT)
• Michel Espinoza-Fonseca
  • Re: anomalous behaviour of ASPP and GLUP during MD run (Thu Feb 25 2010 - 10:51:36 CST)
• Mike Kuiper
  • Cuda benchmarks namd2.7b1 - effects of configuration parameters and hardware. (Sun Aug 30 2009 - 03:54:57 CDT)
• Mikhail Suyetin
  • problem wuth solvate plugin (Mon Jul 12 2010 - 05:53:28 CDT)
  • error during charm-6.1.3 building (Mon Jun 21 2010 - 13:40:04 CDT)
  • calculation van der Waals force field parameters (Wed Feb 17 2010 - 13:27:50 CST)
  • Fwd: electric field unit conversion (Wed Feb 17 2010 - 11:25:21 CST)
  • Re: electric field unit conversion (Wed Feb 17 2010 - 11:27:25 CST)
  • Hydrogen molecule model (Fri Oct 30 2009 - 10:42:19 CDT)
  • Re: A script for performing calculations divided by quanta (Mon Aug 03 2009 - 10:30:28 CDT)
  • A script for performing calculations divided by quanta (Mon Aug 03 2009 - 08:26:28 CDT)
  • RescaleFreq of temperature =1? (Thu Jul 23 2009 - 09:48:54 CDT)
• Milton Sonoda
  • Re: topology file for dissacharides with psfgen (Thu Apr 22 2010 - 00:11:03 CDT)
  • topology file for dissacharides with psfgen (Wed Apr 21 2010 - 23:38:56 CDT)
• Ming
  • Re: Memory keep increasing. (Tue Nov 17 2009 - 22:24:48 CST)
  • Re: Memory keep increasing. (Sun Nov 15 2009 - 04:14:10 CST)
  • Re: Memory keep increasing. (Sat Nov 14 2009 - 20:28:49 CST)
  • Re: Memory keep increasing. (Thu Nov 12 2009 - 23:51:38 CST)
  • Memory keep increasing. (Thu Nov 12 2009 - 06:14:05 CST)
• mjyang
  • RE: questions about ABF simulations (Mon Nov 01 2010 - 09:49:17 CDT)
  • questions about ABF simulations (Thu Oct 28 2010 - 13:26:59 CDT)
  • RE: expansion of solvation box at high temperature (Mon Oct 18 2010 - 22:31:13 CDT)
  • RE: expansion of solvation box at high temperature (Sun Oct 17 2010 - 10:56:15 CDT)
  • RE: expansion of solvation box at high temperature (Sun Oct 17 2010 - 10:18:26 CDT)
  • expansion of solvation box at high temperature (Sun Oct 17 2010 - 04:41:25 CDT)
  • expansion of solvation box at high temperature (Sun Oct 17 2010 - 02:03:31 CDT)
  • RE: write out the snapshot from MD trajectory (Fri Aug 27 2010 - 10:28:25 CDT)
  • write out the snapshot from MD trajectory (Fri Aug 27 2010 - 04:59:32 CDT)
• mm148881
  • Single or double precision? (Thu Jan 08 2009 - 13:09:21 CST)
• Mohamed Seyam
  • Scale for Potential Bond Parameter (Wed Mar 25 2009 - 14:32:28 CDT)
  • Forces on Atoms and Potential Energy (Mon Feb 16 2009 - 13:57:01 CST)
• Mohd Farid Ismail
  • Langevin Damping = 0? (Fri Dec 17 2010 - 13:19:03 CST)
  • Windows binaries of NAMD 2.72b supports CUDA? (Wed Feb 17 2010 - 09:52:16 CST)
• mon_sharma_at_research.iiit.ac.in
  • Generation of average trajectory (Mon Oct 12 2009 - 02:26:02 CDT)
• Monika Sharma
  • Re: Generation of average trajectory (Mon Oct 12 2009 - 09:24:16 CDT)
  • Simulating Protonated base pairs of RNA (Sat Jul 11 2009 - 07:07:29 CDT)
• Moumita Maiti
  • Visit my Netlog profile (Tue Sep 15 2009 - 00:07:31 CDT)
• muniyamuthu.raviprasad_at_ndsu.edu
  • Re: error : atom moving too fast (Wed May 19 2010 - 09:40:00 CDT)
  • Re: error : atom moving too fast (Fri May 14 2010 - 14:20:42 CDT)
  • Atom movement within a range of Z value (Tue May 11 2010 - 14:47:15 CDT)
  • Re: mininization do not go on (Mon May 10 2010 - 22:18:19 CDT)
  • Re: error : atom moving too fast (Thu May 06 2010 - 09:35:02 CDT)
  • Re: error : atom moving too fast (Wed May 05 2010 - 09:58:50 CDT)
  • Re: error while running config file (Thu Apr 22 2010 - 16:01:30 CDT)
  • Re: problem with NVT using TIP4P (Tue Apr 06 2010 - 11:50:49 CDT)
  • Re: Installation problem on Win64 (Fri Apr 02 2010 - 10:27:02 CDT)
  • Re: altering residues in .pdb files (Mon Mar 29 2010 - 11:20:08 CDT)
• Myunggi Yi
  • unsubscribe namd-l (Fri Aug 27 2010 - 21:01:19 CDT)
  • StepsPerCycle (Wed Feb 03 2010 - 09:33:08 CST)
  • NAMD 2.7b2 new features (Tue Dec 22 2009 - 14:16:49 CST)
  • What is LINK Patch? (Mon Dec 07 2009 - 13:47:20 CST)
  • Tcl forces (Mon Oct 26 2009 - 13:12:50 CDT)
  • Re: Tcl forces (Fri Oct 16 2009 - 16:23:32 CDT)
  • Re: Tcl forces (Fri Oct 16 2009 - 16:22:40 CDT)
  • Tcl forces (Fri Oct 16 2009 - 15:06:45 CDT)
  • NAMD2.7b1 performance (Fri Sep 25 2009 - 08:54:33 CDT)
• Naiyin Yu
  • run multiple walkers (Thu Mar 11 2010 - 16:15:33 CST)
  • harmonic constraint when equilibrate the system (Sun Jan 17 2010 - 00:32:57 CST)
• namd_chcwaaa_at_yahoo.com.cn
  • Modification of equlibrated simulation box (Wed Oct 21 2009 - 00:36:37 CDT)
  • Re: Incorrect Atom Count in binary file (Tue Oct 13 2009 - 06:30:06 CDT)
  • about restart (Thu Oct 08 2009 - 06:46:07 CDT)
• Nano Group
  • IMD, Hostname and Port (Tue Jun 02 2009 - 07:40:01 CDT)
• Narender Singh Maan
  • Re: FATAL ERROR: Tried to find atom type on node other than node 0 (Mon Aug 17 2009 - 08:43:41 CDT)
  • Re: symmetric behavior (Thu Aug 13 2009 - 14:17:43 CDT)
  • symmetric behavior (Wed Aug 12 2009 - 09:16:39 CDT)
  • water molecules in channel protein (Wed Aug 05 2009 - 10:57:50 CDT)
  • The steps in protein and membrane simulation (Sat Aug 01 2009 - 23:23:49 CDT)
  • Re: Tried to find atom type on node other than node 0 (Mon Jul 13 2009 - 10:46:47 CDT)
  • Re: Fatal Error Help (Thu Jul 09 2009 - 10:47:11 CDT)
  • Tried to find atom type on node other than node 0 (Thu Jul 09 2009 - 09:00:44 CDT)
• Navendu bhatnagar
  • Query regarding ABF Tutorial on Methane Hydration (Thu Jun 24 2010 - 12:38:42 CDT)
  • Query regarding ABF Tutorial on Methane Hydration (Tue Jun 22 2010 - 14:52:41 CDT)
  • colvar for PMF calculation (Tue Apr 20 2010 - 18:02:28 CDT)
  • Pair interaction : Energy values are zero (Sun Jun 21 2009 - 16:01:45 CDT)
• Nd S
  • unsubscribe (Sat Jun 27 2009 - 00:41:38 CDT)
  • Re: Periodic boundary condition in a membrane simulation (Mon Feb 09 2009 - 18:05:20 CST)
  • Re: Accessing atoms and velocities during NVE run (Fri Feb 06 2009 - 15:14:59 CST)
  • Re: Accessing atoms and velocities during NVE run (Fri Feb 06 2009 - 13:33:53 CST)
  • Accessing atoms and velocities during NVE run (Fri Feb 06 2009 - 10:57:02 CST)
  • Variable results for the same simulation (Tue Feb 03 2009 - 12:18:24 CST)
• Neelanjana Sengupta
  • Re: parameter format for REMD simulations (Thu Jun 10 2010 - 04:00:41 CDT)
  • distance colvar (Mon Jun 07 2010 - 03:07:51 CDT)
  • Re: colvar: coordnum output (Thu May 06 2010 - 05:17:19 CDT)
  • Re: colvar: coordnum output (Fri Apr 30 2010 - 07:32:55 CDT)
  • colvar: coordnum output (Fri Apr 30 2010 - 05:34:29 CDT)
  • colvar: atom group defn. fails (Fri Apr 16 2010 - 05:29:29 CDT)
  • colvars: free energy change with rmsd (Wed Apr 14 2010 - 00:54:08 CDT)
  • Re: ABF Colvars Configuration File (Thu Aug 20 2009 - 09:21:41 CDT)
  • Re: Colvars Configuration File (Wed Aug 19 2009 - 05:03:34 CDT)
  • Re: Colvars Configuration File (Sun Aug 16 2009 - 23:52:30 CDT)
  • Re: Colvars Configuration File (Sat Aug 15 2009 - 10:12:55 CDT)
  • Colvars Configuration File (Sat Aug 15 2009 - 02:16:19 CDT)
  • NAMDenergy: does rewrite temp files at different timesteps (Fri Aug 07 2009 - 00:18:14 CDT)
  • Re: outputname and restartname (Tue Apr 07 2009 - 23:23:48 CDT)
  • Re: outputname and restartname (Tue Apr 07 2009 - 07:45:07 CDT)
  • outputname and restartname (Tue Apr 07 2009 - 01:45:19 CDT)
  • Single vs. Double precision (Mon Jan 19 2009 - 05:27:27 CST)
• neville forlemu
  • Re: NAMD2.7/MEtadynamics simulation analysis disparity (Fri Apr 30 2010 - 09:20:41 CDT)
  • NAMD2.7/MEtadynamics simulation analysis disparity (Thu Apr 29 2010 - 13:30:42 CDT)
  • Job restart (Fri Apr 09 2010 - 16:39:57 CDT)
  • Re: Restarting A NAMD job with velocity file (Thu Mar 25 2010 - 21:59:01 CDT)
  • NAMD/metadynamics (Thu Mar 25 2010 - 21:16:08 CDT)
  • Restarting A NAMD job with velocity file (Mon Mar 22 2010 - 15:50:07 CDT)
  • NAMD on Ranger (Wed Feb 03 2010 - 17:57:14 CST)
  • Plumed and NAMD (Wed Feb 03 2010 - 12:45:37 CST)
• Ng Yao Zong
  • Re: question about repeating output text (Wed Dec 22 2010 - 21:37:13 CST)
• Nicholas J Musolino
  • Re: Interaction energy difference (Thu Jul 29 2010 - 10:42:35 CDT)
• Nicholas M Glykos
  • Re: writing back coordinates of waters that cross the unit cell (Thu Nov 25 2010 - 09:53:19 CST)
  • Re: Recover high precision coordinates from binary .coor file (Sat Nov 06 2010 - 06:30:01 CDT)
  • Re: global and internal motion of protein (Wed Oct 27 2010 - 04:43:08 CDT)
  • Re: coordinate not the same between the input and frame 0 (Tue Oct 26 2010 - 05:10:29 CDT)
  • Re: Flushing memory into output file (Thu Oct 07 2010 - 14:39:25 CDT)
  • Carma v.1.0 released. (Wed Oct 06 2010 - 06:14:15 CDT)
  • Re: claen water (Mon Aug 30 2010 - 08:26:44 CDT)
  • Re: claen water (Mon Aug 30 2010 - 04:22:31 CDT)
  • Re: Cartesian vs dihedral angle space PCA (Tue Jul 13 2010 - 04:35:22 CDT)
  • Re: about DCD file format document (Mon Jul 12 2010 - 08:15:50 CDT)
  • Re: Helix tilt (Tue Jul 06 2010 - 11:48:22 CDT)
  • Balancer and singularities ... (Thu Jun 10 2010 - 10:52:05 CDT)
  • Re: NAMD 2.7b2 versy slow on multiple nodes (Wed May 26 2010 - 08:59:07 CDT)
  • Re: software/algorithm to cluster protein conformations (Fri Apr 30 2010 - 04:40:02 CDT)
  • Re: file writing stopped (Wed Apr 14 2010 - 05:01:06 CDT)
  • Re: creating an output file from a dcd file (Tue Mar 02 2010 - 15:11:54 CST)
  • Re: creating an output file from a dcd file (Tue Mar 02 2010 - 12:30:49 CST)
  • Re: Problem on periodic boundary condition (Wed Feb 24 2010 - 08:41:12 CST)
  • Re: Namd benchmark problem (Mon Oct 26 2009 - 10:08:01 CDT)
  • Re: Namd benchmark problem (Mon Oct 26 2009 - 09:14:36 CDT)
  • Re: Namd benchmark problem (Mon Oct 26 2009 - 04:57:22 CDT)
  • Tolerance for SHAKE (Sun Oct 18 2009 - 07:58:20 CDT)
  • Re: Generation of average trajectory (Mon Oct 12 2009 - 12:55:11 CDT)
  • Re: Generation of average trajectory (Mon Oct 12 2009 - 05:06:26 CDT)
  • Re: PCA Calculation (Tue Oct 06 2009 - 03:47:05 CDT)
  • Re: NAMD2.7b1 performance (Fri Sep 25 2009 - 16:53:07 CDT)
  • Re: NAMD2.7b1 performance (Fri Sep 25 2009 - 11:09:40 CDT)
  • [off topic] The mailing list's mailer ... (Wed Sep 09 2009 - 12:50:58 CDT)
  • Re: Constraint failure in RATTLE algorithm - shouldn't a rerun fail at the same step? (Wed Sep 09 2009 - 10:46:51 CDT)
  • Re: hole on the surface of the waterbox (Fri Aug 28 2009 - 07:38:00 CDT)
  • Re: A script for performing calculations divided by quanta (Tue Aug 04 2009 - 08:15:17 CDT)
  • Re: CPU USAGE (Sun Jul 19 2009 - 06:57:56 CDT)
  • Re: Intel 11 compilers (Fri Jul 10 2009 - 10:01:59 CDT)
  • Re: No log file (Mon Jul 06 2009 - 09:35:27 CDT)
  • Re: NAMD Installation (Wed Jul 01 2009 - 03:57:44 CDT)
  • Re: Does NAMD have any capability to assign coordiantes to novel sequences? (Thu Jun 25 2009 - 11:36:02 CDT)
  • Re: water molecules "collapse" during equilibration (Fri May 29 2009 - 12:49:56 CDT)
  • Re: using amber topology and parameter files in NAMD (Fri May 29 2009 - 13:05:06 CDT)
  • Re: NAMD 2.7b1 running & performance issues (Mon May 25 2009 - 12:43:07 CDT)
  • Re: namd-openmosix (Tue May 19 2009 - 11:19:51 CDT)
  • Re: namd-cuda-intel vs. namd-intel (Wed May 13 2009 - 13:21:23 CDT)
  • Re: truncated octahedral (Tue May 05 2009 - 05:18:15 CDT)
  • Re: removing water from big dcd files (Wed Mar 04 2009 - 03:41:34 CST)
  • Re: Background load problem (Thu Feb 26 2009 - 09:29:58 CST)
  • Re: Correlation matrix of the Ca atoms (Mon Feb 02 2009 - 02:17:39 CST)
  • Re: Aligning the distance between two centroids with an axis (Fri Jan 30 2009 - 05:08:19 CST)
  • Re: New open() for DCDs in v.2.6 ? (Thu Jan 29 2009 - 12:33:55 CST)
  • New open() for DCDs in v.2.6 ? (Thu Jan 29 2009 - 11:34:37 CST)
• Nicholas Musolino
  • Re: Least squares fitting of frames of trajectory (Thu Oct 28 2010 - 08:14:39 CDT)
  • Re: build nanoparticle (Wed Oct 27 2010 - 13:25:57 CDT)
  • Re: Changing functions without recompiling (Mon Oct 18 2010 - 20:20:58 CDT)
  • Re: expansion of solvation box at high temperature (Sun Oct 17 2010 - 10:27:40 CDT)
  • Re: expansion of solvation box at high temperature (Sun Oct 17 2010 - 08:29:06 CDT)
  • Re: beta column (Fri Sep 10 2010 - 07:48:46 CDT)
  • Re: change solvent (Wed Aug 18 2010 - 12:00:57 CDT)
  • Re: Namd 2.6 on ubuntu 9.10 (Wed Jul 28 2010 - 16:16:30 CDT)
  • namd development mailing list? (Tue Jul 20 2010 - 12:09:38 CDT)
  • modifying velocities within global master (Sun Apr 18 2010 - 16:42:51 CDT)
• nicolabrisotto
  • Namd not detecting my CUDA enabled GPU (Thu Sep 24 2009 - 11:07:35 CDT)
• Nicolas Floquet
  • NAMD time connect out on multi-computers (Fri Jul 23 2010 - 07:00:12 CDT)
  • Timeout waiting for node-program to connect (Wed Jul 21 2010 - 10:43:02 CDT)
  • Distance constraint (Thu Jun 17 2010 - 03:30:45 CDT)
• Nicolas Sapay
  • Re: namd 2.7b2 or later - amberff/prmtop causes segfault during startup phase (Wed Feb 24 2010 - 06:49:47 CST)
• Nikolaos Glykos
  • Re: Does CHARMM stabilize alpha helices? (Sun Aug 22 2010 - 03:57:22 CDT)
  • RE: Pressure is not constant in NPT ensemble (Sun Aug 01 2010 - 15:37:17 CDT)
  • Re: running namd faster (Tue Jul 20 2010 - 06:01:41 CDT)
• Ning Zhang
  • Difference between the two Dowsers (Fri May 21 2010 - 05:26:37 CDT)
  • something is wrong with my equilibration (Sun Apr 25 2010 - 21:52:10 CDT)
  • The MD of aquaporin in NAMD (Sat Nov 14 2009 - 01:31:31 CST)
• Nir London
  • Rosetta Academic Training Webinar (Wed Mar 25 2009 - 11:09:54 CDT)
  • Rosetta Academic Training Workshop (Tue Jan 27 2009 - 07:04:42 CST)
• nishtha mishra
  • MINIMIZER SLOWLY MOVING 810 ATOMS WITH BAD CONTACTS DOWNHILL (Sat Oct 30 2010 - 08:40:36 CDT)
• nishtha.mishra
  • MINIMIZER SLOWLY MOVING 810 ATOMS WITH BAD CONTACTS DOWNHILL (Mon Nov 01 2010 - 02:18:06 CDT)
  • MINIMIZER SLOWLY MOVING 810 ATOMS WITH BAD CONTACTS DOWNHILL (Mon Nov 01 2010 - 02:27:18 CDT)
• Odysseas Axillews
  • protein unfolding no increase in conf energy (Wed May 12 2010 - 05:25:24 CDT)
  • request help- namd error abortion stack error (Sun Mar 21 2010 - 20:24:30 CDT)
  • request help- namd error abortion stack error (Thu Mar 18 2010 - 21:21:44 CDT)
• oguz gurbulak
  • potential functions in NAMD (Fri Oct 22 2010 - 04:22:45 CDT)
  • Re: NAMD and Gromacs (Thu Sep 30 2010 - 16:06:46 CDT)
  • NAMD and Gromacs (Thu Sep 30 2010 - 06:36:51 CDT)
  • Namd 2.6 on ubuntu 9.10 (Wed Jul 28 2010 - 14:22:09 CDT)
• OiniL
  • Re: how to cenvert NAMD binary coordinate file to text file (Thu Oct 21 2010 - 03:15:16 CDT)
  • Re: metadynamics simulations slow down and down (Mon Oct 11 2010 - 09:36:29 CDT)
  • metadynamics simulations slow down and down (Sat Sep 25 2010 - 23:06:17 CDT)
• Olve Peersen
  • Re: vmd-l: Hardware for NAMD / VMD machine (Mon Jul 06 2009 - 13:39:53 CDT)
  • Hardware for NAMD / VMD machine (Fri Jul 03 2009 - 01:26:11 CDT)
• Osman Yogurtcu
  • ligand flies away from binding pocket (Thu Feb 12 2009 - 11:39:04 CST)
• OZGE ENGIN
  • asymmetric water found! (Wed Jan 28 2009 - 07:26:07 CST)
  • Re: Re: alpha character error in the psf file (Wed Jan 28 2009 - 07:22:51 CST)
  • (no subject) (Wed Jan 28 2009 - 03:29:03 CST)
  • alpha character error in the psf file (Wed Jan 28 2009 - 03:30:26 CST)
• Pablo Campomanes
  • Re: Water Box Shape Changing during NVT Simulation! (Sat Mar 06 2010 - 11:50:45 CST)
  • Re: Water Box Shape Changing during NVT Simulation! (Fri Mar 05 2010 - 22:50:53 CST)
• Parisa Akhski
  • Zcoord for ABF (Fri Dec 17 2010 - 13:22:49 CST)
  • ABF questions (Concatenate output files/force constant) (Wed Dec 08 2010 - 17:57:40 CST)
  • ABF question (Fri Dec 03 2010 - 09:16:07 CST)
  • restart ABF (Mon Nov 29 2010 - 10:43:26 CST)
  • Zcoord-1atom for ABF (Wed Nov 24 2010 - 16:11:16 CST)
  • RE: Flushing memory into output file (Fri Oct 08 2010 - 09:04:37 CDT)
  • Flushing memory into output file (Thu Oct 07 2010 - 11:58:46 CDT)
  • simulation cell enlarging too much after restart (Thu Sep 02 2010 - 17:26:40 CDT)
  • RE: Pressure is not constant in NPT ensemble (Sun Aug 01 2010 - 13:31:11 CDT)
  • Pressure is not constant in NPT ensemble (Thu Jul 29 2010 - 14:01:05 CDT)
  • Pressure parameter in minimization (Tue Jul 27 2010 - 16:31:03 CDT)
  • "gradient tolerance" for minimization (Thu Jul 22 2010 - 11:29:19 CDT)
  • OPENING EXTENDED SYSTEM TRAJECTORY FILE (Mon Jun 28 2010 - 13:47:39 CDT)
  • ABF question (Thu Jun 24 2010 - 16:03:15 CDT)
  • ABF question (Tue Jun 22 2010 - 13:06:55 CDT)
  • ABF question (Tue Jun 22 2010 - 11:43:06 CDT)
• parsons_at_umbi.umd.edu
  • problems with NAMD plot and .DCD file (Mon Jan 25 2010 - 11:35:13 CST)
• Patargias, George
  • AMBER force field in NAMD (Fri Sep 10 2010 - 09:48:01 CDT)
  • Running namd on Mac OS (Tue Jul 20 2010 - 12:25:04 CDT)
• Patriche Simona
  • How can I connect different structures between them using VMD and NAMD? (Sun Jul 04 2010 - 19:45:15 CDT)
  • Distance Analysis for Constant Force Pulling for kinesin neck linker (Fri Mar 05 2010 - 05:44:37 CST)
• Patrick Hogan
  • How to access velocity coordinates from within TclForces script (Thu Sep 17 2009 - 14:43:21 CDT)
• patrick wintrode
  • Accelerated MD? (Thu Sep 23 2010 - 09:44:41 CDT)
  • Cartesian vs dihedral angle space PCA (Mon Jul 12 2010 - 10:12:29 CDT)
• Patrick Yee
  • Re: Possible way of performing a temperature gradient?? (Tue Jun 15 2010 - 07:26:45 CDT)
  • Re: Question about Tcl/customising the colvar module (Tue May 25 2010 - 18:47:35 CDT)
  • RE: ABF question (Tue May 25 2010 - 13:38:33 CDT)
  • Re: ABF in various simulations (Mon May 17 2010 - 10:47:58 CDT)
  • Re: ABF non-uniform sampling (Sat May 01 2010 - 11:14:52 CDT)
  • Re: NAMD CONFIG FILE:: (Wed Apr 21 2010 - 14:34:49 CDT)
  • ABF non-uniform sampling (Thu Apr 15 2010 - 22:19:45 CDT)
  • colvars error running ABF (Tue Apr 13 2010 - 20:47:21 CDT)
  • Re: ABF Simulation Crash from TCL script (Sun Apr 11 2010 - 14:07:52 CDT)
  • ABF Simulation Crash from TCL script (Tue Mar 30 2010 - 17:10:49 CDT)
  • ABF Displacement (Sat Mar 27 2010 - 14:42:18 CDT)
  • Abnormal EOF found -buffer=*END* (Mon Nov 02 2009 - 12:35:52 CST)
• Paul Rigor (uci)
  • documentation on parallel implementation (Wed Dec 16 2009 - 08:33:03 CST)
  • Re: which portions of NAMD are CUDA accelerated? (Wed Dec 16 2009 - 03:57:36 CST)
  • which portions of NAMD are CUDA accelerated? (Wed Dec 02 2009 - 20:00:27 CST)
  • maximum number of devices supported per namd process (Mon Nov 23 2009 - 21:45:08 CST)
  • Re: help with running namd-cuda for the tutorials (Fri Nov 20 2009 - 21:05:48 CST)
  • Re: help with running namd-cuda for the tutorials (Fri Nov 20 2009 - 20:06:38 CST)
  • help with running namd-cuda for the tutorials (Fri Nov 20 2009 - 10:24:20 CST)
• Paul Rigor (uci-ics)
  • Re: Simulation question (Tue Jan 19 2010 - 18:29:03 CST)
  • Re: CUDA-NAMD hangs -- check the Northbridge temp! (Wed Jan 06 2010 - 17:12:54 CST)
  • Re: run NAMD_2.7B2 (Mon Jan 04 2010 - 15:29:08 CST)
  • Re: which portions of NAMD are CUDA accelerated? (Fri Dec 04 2009 - 21:59:12 CST)
• Paulo Cesar Telles de Souza
  • Re: Doubts and problem in ABF simulations (Wed Sep 02 2009 - 13:11:07 CDT)
  • Re: Doubts and problem in ABF simulations (Wed Sep 02 2009 - 10:55:19 CDT)
  • Doubts and problem in ABF simulations (Mon Aug 31 2009 - 11:00:57 CDT)
  • Jarzynski equality and the pull direction in SMD (Thu Apr 02 2009 - 19:00:40 CDT)
• Pavan G
  • Re: Minimization messes up C terminal (Fri Jun 25 2010 - 09:19:42 CDT)
  • Minimization messes up C terminal (Wed Jun 16 2010 - 10:32:42 CDT)
  • Re: Slow heating in namd (Thu Oct 15 2009 - 10:37:47 CDT)
  • Slow heating in namd (Thu Oct 15 2009 - 09:10:02 CDT)
• Payel Das
  • Proline hybrid topology file for FEP (Fri Aug 20 2010 - 19:54:28 CDT)
  • skip frames with bigdcd (Fri Jun 26 2009 - 15:15:21 CDT)
  • topology and parameter files for guanidinium ion (Thu Apr 30 2009 - 15:04:48 CDT)
• Pegah Khalili
  • problems with temperature control (Wed Nov 03 2010 - 04:35:50 CDT)
  • problems with temperature control (Wed Nov 03 2010 - 04:28:59 CDT)
• Peixi Zhu
  • Re: Restraint on XY Plane (Fri Oct 15 2010 - 11:24:26 CDT)
  • Re: Restraint on XY Plane (Fri Oct 15 2010 - 00:33:38 CDT)
  • Restraint on XY Plane (Thu Oct 14 2010 - 16:12:30 CDT)
• pellegrini
  • NVE crash (Wed Apr 28 2010 - 10:30:09 CDT)
  • Running a simulation with a protein and a sugar (Thu Aug 27 2009 - 04:06:48 CDT)
• Pengcheng Yin
  • Re: question about NAMD (Fri Mar 12 2010 - 09:03:09 CST)
  • question about NAMD (Thu Mar 11 2010 - 19:20:21 CST)
• Per Jr. Greisen
  • Re: loading large dcd files (Thu Jan 29 2009 - 05:15:34 CST)
• Peter Freddolino
  • Re: TIP4P with NPT (Fri Nov 19 2010 - 21:50:10 CST)
  • Re: TIP4P with NPT (Thu Nov 18 2010 - 19:17:03 CST)
  • Re: pair interaction calculations (Sun Nov 14 2010 - 11:56:25 CST)
  • Re: problems with temperature control (Wed Nov 03 2010 - 19:58:06 CDT)
  • Re: RBCG-dcd files (Tue Sep 21 2010 - 23:42:18 CDT)
  • Re: NAMD Energy types (Fri Sep 17 2010 - 18:20:55 CDT)
  • Re: Problem facing during Solvation of Coarse Grain Model (Tue Sep 14 2010 - 18:59:54 CDT)
  • Re: NAMD Energy types (Thu Sep 09 2010 - 20:40:15 CDT)
  • Re: NAMD Energy types (Thu Sep 09 2010 - 07:04:49 CDT)
  • Re: NAMD Energy types (Wed Sep 08 2010 - 19:19:02 CDT)
  • Re: possible bug with NAMD Energy plugin (Tue Aug 31 2010 - 19:42:59 CDT)
  • Re: TIP4P/Ice usage in NAMD (Tue Aug 24 2010 - 09:14:39 CDT)
  • Re: possible bug with NAMD Energy plugin (Mon Aug 23 2010 - 18:58:26 CDT)
  • Re: 1us simulation of 80k atom system -- how much gross structure movement is expected? (Mon Jul 19 2010 - 20:52:48 CDT)
  • Re: 1us simulation of 80k atom system -- how much gross structure movement is expected? (Mon Jul 19 2010 - 18:52:20 CDT)
  • Re: "didn't find VdW parameter for atom type NH3" error (Tue Jun 29 2010 - 22:02:21 CDT)
  • Re: "didn't find VdW parameter for atom type NH3" error (Tue Jun 29 2010 - 13:17:44 CDT)
  • Re: Minimization messes up C terminal (Fri Jun 25 2010 - 20:02:41 CDT)
  • Re: Minimization messes up C terminal (Wed Jun 16 2010 - 11:48:05 CDT)
  • Re: TIP4P water in AMBER parm7 format fails with 2010-06-07 nightly build (Sat Jun 12 2010 - 08:41:24 CDT)
  • Re: TIP4P water in AMBER parm7 format fails with 2010-06-07 nightly build (Tue Jun 08 2010 - 19:12:11 CDT)
  • Re: building a MARTINI bilayer (Wed Apr 21 2010 - 13:16:00 CDT)
  • Re: problem with NVT using TIP4P (Tue Apr 06 2010 - 13:59:27 CDT)
  • Re: Generate missing atoms of a coarse grained structure (Sun Apr 04 2010 - 07:55:56 CDT)
  • Re: simulating TIP4P with NAMD 2.7b2 (Tue Mar 16 2010 - 14:42:36 CDT)
  • Re: Fwd: vmd-l: Re: Fwd: conf file for coarse grained simulation (Wed Dec 16 2009 - 18:49:13 CST)
  • Re: Fwd: vmd-l: Re: Fwd: conf file for coarse grained simulation (Wed Dec 16 2009 - 15:46:39 CST)
  • Re: vmd-l: Re: Fwd: conf file for coarse grained simulation (Tue Dec 15 2009 - 10:45:27 CST)
  • Re: conf file for coarse grained simulation (Mon Dec 14 2009 - 19:15:57 CST)
  • Re: vmd-l: namd CG minimization error: unable to find angle parameters for nxg nxx nxg (Thu Dec 10 2009 - 15:06:05 CST)
  • Re: Small discrepancy in Kinetic Energy after restarting the simulation (Tue Dec 01 2009 - 11:25:40 CST)
  • Re: vmd-l: Error: failed on end of segment with RBCG (Sun Nov 15 2009 - 08:46:47 CST)
  • Re: FW: issues with AutoPSF for a cyclodextrin - addendum (Fri Oct 30 2009 - 19:20:03 CDT)
  • Re: issues with AutoPSF for a cyclodextrin (Thu Oct 29 2009 - 19:31:00 CDT)
  • Re: namd2.7b1, tip4p, and dummies (Wed Sep 30 2009 - 21:43:54 CDT)
  • Re: solvate plugin with solvent other than water (Tue Aug 11 2009 - 21:24:41 CDT)
  • Re: Error with GUI NAMD Energy (Fri Aug 07 2009 - 19:16:53 CDT)
  • defenestrate (Sun Jun 28 2009 - 15:20:11 CDT)
  • Re: VMD/NAMD two identical molecules solvate in a water sphere (Tue Jun 23 2009 - 14:11:15 CDT)
  • Re: VMD/NAMD two identical molecules solvate in a water sphere (Tue Jun 23 2009 - 12:06:21 CDT)
  • Re: VMD/NAMD two identical molecules solvate in a water sphere (Tue Jun 23 2009 - 11:17:54 CDT)
  • Re: Reassign temp (Wed Jun 17 2009 - 20:51:03 CDT)
  • Re: Histamine topology file (Fri Jun 12 2009 - 13:52:12 CDT)
  • Re: Measuring protein diffusion: results too small? (Fri Jun 05 2009 - 10:16:29 CDT)
  • Re: Rescale Temperature when velocity of COM is not zero (Mon Jun 01 2009 - 21:03:37 CDT)
  • Re: water molecules "collapse" during equilibration (Fri May 29 2009 - 17:05:05 CDT)
  • Re: water tail correction (Thu May 28 2009 - 13:12:04 CDT)
  • Re: water tail correction (Tue May 26 2009 - 14:17:03 CDT)
  • Re: unknown path type LSN (Tue May 26 2009 - 09:32:55 CDT)
  • Re: water tail correction (Fri May 22 2009 - 16:16:59 CDT)
  • Re: water tail correction (Fri May 22 2009 - 13:34:16 CDT)
  • Re: calculating forces from dcd trajectory (Thu May 21 2009 - 06:55:47 CDT)
  • Re: calculating forces from dcd trajectory (Thu May 21 2009 - 06:54:08 CDT)
  • Re: tmao molecule (Wed May 20 2009 - 10:13:29 CDT)
  • Re: ERROR: Multiple definitions of 'LangevinPiston' (Wed May 20 2009 - 09:59:45 CDT)
  • Re: tmao molecule (Wed May 20 2009 - 09:51:43 CDT)
  • Re: calculating forces from dcd trajectory (Wed May 20 2009 - 06:51:11 CDT)
  • Re: NAMD 2.7b1 running problem (Wed May 20 2009 - 06:52:58 CDT)
  • Re: exclude 1-2 (Fri May 15 2009 - 06:55:37 CDT)
  • Re: ERROR: Multiple definitions of 'LangevinPiston' (Fri May 15 2009 - 05:54:11 CDT)
  • Re: Need help to generate ubq-get-energy.conf (Thu May 14 2009 - 11:33:57 CDT)
  • Re: ERROR: Multiple definitions of 'LangevinPiston' (Thu May 14 2009 - 10:19:28 CDT)
  • Re: Need help to generate ubq-get-energy.conf (Thu May 14 2009 - 10:33:10 CDT)
  • Re: Need help to generate ubq-get-energy.conf (Wed May 13 2009 - 15:55:29 CDT)
  • Re: Need help to generate ubq-get-energy.conf (Wed May 13 2009 - 12:03:55 CDT)
  • Re: exclude 1-2 or 1-4? (Tue May 12 2009 - 10:07:42 CDT)
  • Re: Asymmetric water molecule found (Tue May 12 2009 - 06:45:32 CDT)
  • Re: ERROR: Multiple definitions of 'LangevinPiston' (Tue May 12 2009 - 06:41:29 CDT)
  • Re: ERROR: Multiple definitions of 'LangevinPiston' (Mon May 11 2009 - 12:11:57 CDT)
  • Re: SiCortex with Pathscale (Mon May 11 2009 - 12:02:14 CDT)
  • Re: ERROR: Multiple definitions of 'LangevinPiston' (Mon May 11 2009 - 08:09:40 CDT)
  • Re: recent papers on MD gotchas with PRNG seeds (Sat May 09 2009 - 17:22:43 CDT)
  • Re: water models and some questions (Thu May 07 2009 - 11:57:51 CDT)
  • Re: regarding simulation (Tue May 05 2009 - 10:22:25 CDT)
  • Re: regarding simulation (Tue May 05 2009 - 10:16:04 CDT)
  • Re: NPAT - NPgT ensemble (Sat May 02 2009 - 20:18:46 CDT)
  • Re: CGMD ? Hydrophobic scale (Fri May 01 2009 - 22:18:00 CDT)
  • Re: NAMD 2.7b1 on NCSA Abe (Fri May 01 2009 - 06:41:23 CDT)
  • Re: NAMD 2.7b1 on NCSA Abe (Thu Apr 30 2009 - 20:11:27 CDT)
  • Re: topology and parameter files for guanidinium ion (Thu Apr 30 2009 - 16:32:21 CDT)
  • Re: NAMD 2.7b1 on NCSA Abe (Thu Apr 30 2009 - 06:41:50 CDT)
  • Re: water tail correction (Wed Apr 29 2009 - 10:26:24 CDT)
  • Re: water tail correction (Wed Apr 29 2009 - 07:09:45 CDT)
  • Re: biotin parameters and topology (Tue Apr 28 2009 - 15:13:08 CDT)
  • Re: tip4p on namd 2.7b (Wed Apr 22 2009 - 12:19:33 CDT)
  • Re: FATAL ERROR: Periodic cell has become too small for original patch grid! (Wed Apr 22 2009 - 09:27:37 CDT)
  • Re: 2.7b1 + CUDA + STMV (Tue Apr 21 2009 - 09:41:56 CDT)
  • Re: tip4p on namd 2.7b (Tue Apr 21 2009 - 09:36:39 CDT)
  • Re: compiling error of NAMD2.7b1 (Mon Apr 20 2009 - 14:49:07 CDT)
  • Re: compiling error of NAMD2.7b1 (Mon Apr 20 2009 - 14:47:09 CDT)
  • Re: compiling error of NAMD2.7b1 (Mon Apr 20 2009 - 13:12:01 CDT)
  • Re: vmd-l: display all frames simultaneously (Thu Apr 16 2009 - 22:32:26 CDT)
  • Re: Evaluating kinetic energy from a modified DCD file (Wed Apr 08 2009 - 19:17:16 CDT)
  • Re: Evaluating kinetic energy from a modified DCD file (Wed Apr 08 2009 - 15:15:00 CDT)
  • Re: Compiling NAMD on Ranger (Wed Apr 08 2009 - 10:16:36 CDT)
  • Re: outputname and restartname (Wed Apr 08 2009 - 07:21:33 CDT)
  • Re: outputname and restartname (Tue Apr 07 2009 - 09:34:34 CDT)
  • Re: outputname and restartname (Tue Apr 07 2009 - 06:12:59 CDT)
  • Re: psf file creation (Fri Apr 03 2009 - 15:55:14 CDT)
  • Re: NAMD 2.7b1 on Athlon64 Gigabit MPI - Compile Error "src/Settle.C:153: error: ‘_mm_cvtsd_f64’ was not declared in this scope" (Thu Apr 02 2009 - 20:39:37 CDT)
  • Re: NAMD is too slow?! (Sun Mar 29 2009 - 22:37:16 CDT)
  • Re: NAMD is too slow?! (Sun Mar 29 2009 - 09:42:38 CDT)
  • Re: Interactive protonation (Sat Mar 28 2009 - 19:26:51 CDT)
  • Re: modifying a nucleobase (Sat Mar 28 2009 - 10:59:48 CDT)
  • Re: alanine dipeptide: no dihdral energy terms? (Fri Mar 27 2009 - 14:42:54 CDT)
  • Re: Gromacs simulation not running in NAMD (Mon Mar 23 2009 - 22:43:27 CDT)
  • Re: alanine dipeptide: no dihdral energy terms? (Mon Mar 23 2009 - 22:45:01 CDT)
  • Re: vmd-l: GTP topology file (Fri Mar 20 2009 - 12:03:01 CDT)
  • Re: multiple FEP experiments in one NAMD-FEP run? (Wed Mar 18 2009 - 15:42:27 CDT)
  • Re: PRESSURE, GPRESSURE, PRESSAVG, and GPRESSAVG (Wed Mar 18 2009 - 13:59:50 CDT)
  • Re: FEP with fixed explicit environment? (Tue Mar 17 2009 - 14:10:07 CDT)
  • Re: Problems with OPLS in NAMD (Wed Mar 11 2009 - 10:26:25 CDT)
  • Re: FW: Water density of water Box (Wed Mar 11 2009 - 10:24:00 CDT)
  • Re: Error running simulation on KRAKEN XT5 (Tue Mar 10 2009 - 23:32:45 CDT)
  • Re: job submission script on KRAKEN @ NICS (Tue Mar 10 2009 - 11:22:21 CDT)
  • Re: PME and fixed atoms questions (Mon Mar 09 2009 - 13:51:17 CDT)
  • Re: Building NAMD for Opteron Cluster with ICC (Sat Mar 07 2009 - 21:56:29 CST)
  • Re: job submission script on KRAKEN @ NICS (Fri Mar 06 2009 - 23:12:24 CST)
  • Re: Building NAMD for Opteron Cluster with ICC (Fri Mar 06 2009 - 23:18:12 CST)
  • Re: Fwd: Job submission to Lonestar on TACC (Thu Mar 05 2009 - 20:04:29 CST)
  • Re: Job submission to Lonestar on TACC (Thu Mar 05 2009 - 02:15:57 CST)
  • Re: help running NAMD energy at multiple stable temperatures (newbie) (Mon Mar 02 2009 - 23:37:11 CST)
  • Re: Coordinate Output in both binary and ASCII. Or converting binary to ASCII in the command line (Mon Mar 02 2009 - 10:51:44 CST)
  • Re: Minimization convergence issue (Mon Mar 02 2009 - 10:29:32 CST)
  • Re: Coordinate Output in both binary and ASCII. Or converting binary to ASCII in the command line (Mon Mar 02 2009 - 10:33:22 CST)
  • Re: Background load problem (Fri Feb 27 2009 - 15:10:29 CST)
  • Re: Background load problem (Thu Feb 26 2009 - 11:45:00 CST)
  • Re: Background load problem (Thu Feb 26 2009 - 07:50:36 CST)
  • Re: cgmd stability (Thu Feb 26 2009 - 02:13:16 CST)
  • Re: charm27 forcefield_topology (Wed Feb 25 2009 - 15:09:23 CST)
  • Re: cgmd stability (Tue Feb 24 2009 - 04:22:31 CST)
  • Re: cgmd stability (Mon Feb 23 2009 - 22:05:03 CST)
  • Re: Can I get the pressure value in a cube? (Mon Feb 23 2009 - 03:29:58 CST)
  • Re: memory optimised version and exclusion check (Sat Feb 21 2009 - 22:24:08 CST)
  • Re: Autopsf error with a modified top file (Fri Feb 20 2009 - 23:19:22 CST)
  • Re: Can I get the pressure value in a cube? (Fri Feb 20 2009 - 10:09:52 CST)
  • Re: Can I get the pressure value in a cube? (Thu Feb 19 2009 - 22:26:27 CST)
  • Re: Autopsf error with a modified top file (Thu Feb 19 2009 - 19:52:52 CST)
  • Re: cgmd stability (Thu Feb 19 2009 - 06:46:40 CST)
  • Re: cgmd stability (Thu Feb 19 2009 - 07:16:46 CST)
  • Re: cgmd stability (Wed Feb 18 2009 - 23:41:27 CST)
  • Re: cgmd stability (Wed Feb 18 2009 - 20:05:57 CST)
  • Re: Autopsf error with a modified top file (Wed Feb 18 2009 - 15:24:59 CST)
  • Re: namd cvs compilation with a maximum number of cores to run on (Thu Feb 12 2009 - 09:41:27 CST)
  • Re: namd cvs compilation with a maximum number of cores to run on (Thu Feb 12 2009 - 08:32:59 CST)
  • Re: any experiences with executing parallel NAMD in a NAMD simulation (Tue Feb 10 2009 - 12:45:34 CST)
  • Re: any experiences with executing parallel NAMD in a NAMD simulation (Tue Feb 10 2009 - 09:26:02 CST)
  • Re: any experiences with executing parallel NAMD in a NAMD simulation (Mon Feb 09 2009 - 22:13:43 CST)
  • Re: any experiences with executing parallel NAMD in a NAMD simulation (Mon Feb 09 2009 - 16:26:39 CST)
  • Re: generating xsc and vel files (Mon Feb 02 2009 - 10:46:40 CST)
  • Re: asymmetric water found! (Wed Jan 28 2009 - 10:00:03 CST)
  • Re: value 9999999.99999 during simulation (Wed Jan 28 2009 - 07:22:34 CST)
  • Re: alpha character error in the psf file (Wed Jan 28 2009 - 07:18:52 CST)
  • Re: use of berendsenPressure during heating (Fri Jan 23 2009 - 12:22:10 CST)
  • Re: CUDA version status (Thu Jan 22 2009 - 15:40:54 CST)
  • Re: double-wide sampling with soft-core (Thu Jan 22 2009 - 11:34:07 CST)
  • Re: The limit of atom number on Blue Gene/L (Mon Jan 19 2009 - 18:40:24 CST)
  • Re: The limit of atom number on Blue Gene/L (Mon Jan 19 2009 - 07:41:43 CST)
  • Re: TMD comments (Sat Jan 17 2009 - 11:01:06 CST)
  • Re: problem in fitting Maxwell-Boltzmann distribution (Fri Jan 16 2009 - 13:48:27 CST)
  • Re: Energy drif in NVE ensemble (Thu Jan 15 2009 - 11:56:33 CST)
  • Re: dielectric parameter? (Thu Jan 15 2009 - 09:24:11 CST)
  • Re: problem in fitting Maxwell-Boltzmann distribution (Thu Jan 15 2009 - 08:22:19 CST)
  • Re: question about cellBasisVector*? (Tue Jan 13 2009 - 09:33:20 CST)
  • Re: Gradient tolerance nan for A three-atom simulation (Mon Jan 12 2009 - 12:17:49 CST)
  • Re: Gradient tolerance nan for A three-atom simulation (Fri Jan 09 2009 - 16:14:48 CST)
  • Re: tclforces: switch from md with external forces to standard md (Fri Jan 09 2009 - 15:49:35 CST)
  • Re: Gradient tolerance nan for A three-atom simulation (Fri Jan 09 2009 - 16:14:33 CST)
  • Re: tclforces: switch from md with external forces to standard md (Fri Jan 09 2009 - 16:03:56 CST)
  • Re: tclforces: switch from md with external forces to standard md (Fri Jan 09 2009 - 10:46:05 CST)
  • Re: tclforces: switch from md with external forces to standard md (Thu Jan 08 2009 - 13:38:05 CST)
  • Re: Gradient tolerance nan for A three-atom simulation (Thu Jan 08 2009 - 13:19:39 CST)
  • Re: Re: namdcvs (Mon Jan 05 2009 - 14:21:51 CST)
  • Re: Re: namdcvs (Mon Jan 05 2009 - 14:02:58 CST)
  • Re: Re: namdcvs (Mon Jan 05 2009 - 13:51:02 CST)
  • Re: Problem with number of steps > 1000000 (Mon Jan 05 2009 - 08:11:57 CST)
• Peter Jones
  • RE: altering residues in .pdb files (Fri Mar 26 2010 - 20:29:00 CDT)
  • RE: atom charges for protonated carboxyl termini (Mon Feb 22 2010 - 18:46:25 CST)
• Peter Murphy
  • Water Sphere Solvation (Sun Oct 18 2009 - 08:41:38 CDT)
• Phil Greer
  • namd cuda with geforce 470 (fermi) gpu fatal error at runtime (Tue May 25 2010 - 13:52:41 CDT)
• Phil Miller
  • Re: [ppl] error compiling charm-6.2.2 for bluegenep-xlc (Wed Oct 27 2010 - 23:14:34 CDT)
• Philip Fowler
  • NAMD_ti.pl (Wed Jul 01 2009 - 06:45:31 CDT)
  • NAMD_ti.pl (Wed Jul 01 2009 - 07:50:26 CDT)
• Philip Peartree
  • Conjugate gradient reference (Fri Oct 15 2010 - 10:33:16 CDT)
  • Bin Coordinate file to pdb (Thu Jul 08 2010 - 15:50:34 CDT)
  • Re: modification of CHARMM force field (Sat Jun 26 2010 - 02:45:09 CDT)
  • Appropriate dcdfreq (Thu Jun 03 2010 - 15:33:53 CDT)
  • Re: Periodic cell has become too small for original patch grid! (Tue Apr 06 2010 - 17:56:17 CDT)
  • Re: Periodic cell has become too small for original patch grid! (Tue Apr 06 2010 - 16:19:15 CDT)
  • Re: Periodic cell has become too small for original patch grid! (Tue Apr 06 2010 - 09:52:59 CDT)
  • NPT simulation schemes (Fri Apr 02 2010 - 18:04:55 CDT)
  • Re: Periodic cell has become too small for original patch grid! (Fri Apr 02 2010 - 18:06:43 CDT)
  • Re: Periodic cell has become too small for original patch grid! (Fri Apr 02 2010 - 15:36:54 CDT)
  • Periodic cell has become too small for original patch grid! (Thu Apr 01 2010 - 09:27:16 CDT)
  • Re: benchmarking on Cray XT4 (Tue Mar 16 2010 - 07:59:49 CDT)
  • Minimisation Protocol (Fri Oct 02 2009 - 11:36:49 CDT)
• Philipp M.
  • Re: namd 2.7b2 or later - amberff/prmtop causes segfault during startup phase (Mon Feb 22 2010 - 05:23:20 CST)
  • Re: Crashing ibverbs binary of NAMD_2.7b2 (Thu Feb 11 2010 - 05:16:47 CST)
  • Re: Crashing ibverbs binary of NAMD_2.7b2 (Thu Feb 11 2010 - 05:30:32 CST)
  • Crashing ibverbs binary of NAMD_2.7b2 (Wed Feb 10 2010 - 10:58:03 CST)
  • Problem compiling namd (Mon Jan 11 2010 - 07:19:43 CST)
• philipp.coloc_at_gmx.de
  • Fatal Error by charmc - Compiling NAMD_2.7b2_Source (Wed Feb 10 2010 - 04:59:30 CST)
  • Re: Problem compiling namd (Wed Feb 10 2010 - 03:53:21 CST)
• Pietro Amodeo
  • Re: Errata to: Update to CUDA error in NAMD 2.7: Increase MAX_EXCLUSIONS: problem persists and CPU-only MD scales poorly (Tue Dec 28 2010 - 05:45:16 CST)
  • Errata to: Update to CUDA error in NAMD 2.7: Increase MAX_EXCLUSIONS: problem persists and CPU-only MD scales poorly (Mon Dec 27 2010 - 14:20:03 CST)
  • Update to CUDA error in NAMD 2.7: Increase MAX_EXCLUSIONS: problem persists and CPU-only MD scales poorly (Mon Dec 27 2010 - 14:01:04 CST)
  • CUDA error in NAMD 2.7: Increase MAX_EXCLUSIONS (Fri Nov 26 2010 - 18:07:46 CST)
  • (Infiniband-related?) NAMD 2.7b2 (ibverbs x86_64) runtime error during a MD run (Tue Jan 19 2010 - 05:03:21 CST)
• Piotr Kopta
  • multi-cluster configuration (Mon Aug 24 2009 - 16:18:42 CDT)
• Pletezhov Alexandr
  • Output of forces (Thu Dec 02 2010 - 06:04:46 CST)
• poker_at_physics.usyd.edu.au
  • Re: Appropriate dcdfreq (Fri Jun 04 2010 - 01:22:07 CDT)
  • Re: Question about Tcl/customising the colvar module (Tue May 25 2010 - 22:39:48 CDT)
  • Question about Tcl/customising the colvar module (Tue May 25 2010 - 04:25:34 CDT)
• Prakash Velayutham
  • Re: NAMD performance with 10GbE interconnect (Tue Aug 11 2009 - 11:40:07 CDT)
  • NAMD performance with 10GbE interconnect (Fri Aug 07 2009 - 15:02:55 CDT)
  • Re: NAMD on GPU (Thu Jun 04 2009 - 08:49:52 CDT)
  • Re: NAMD with CUDA (Mon May 11 2009 - 11:46:13 CDT)
  • NAMD with CUDA (Thu May 07 2009 - 13:06:04 CDT)
• prasun kumar
  • unsubscribe (Mon Feb 01 2010 - 12:00:49 CST)
  • regarding positioning of protein molecule (Wed Jun 24 2009 - 17:39:15 CDT)
  • regarding psfgen algorithm (Wed Jun 17 2009 - 23:59:58 CDT)
  • regarding psfgen algorithm (Fri Jun 12 2009 - 03:22:04 CDT)
  • regarding protein-protein interaction (Fri Jun 05 2009 - 02:51:37 CDT)
  • regarding simulation (Tue May 05 2009 - 08:48:00 CDT)
  • how to use hydrogen bond parameter during minimization and simulation (Thu Mar 05 2009 - 23:27:47 CST)
  • regarding topology file generation (Tue Mar 03 2009 - 04:55:16 CST)
• Prathit Chatterjee
  • problem regarding rattle algorithm (Fri Dec 31 2010 - 02:29:43 CST)
• Praveen Agrawal
  • Re: Running NAMD w/ CUDA under Linux (Thu Nov 05 2009 - 11:58:24 CST)
  • Peptide in Membrane Environment: loosing water from one leaflet (Mon Apr 20 2009 - 05:53:23 CDT)
  • Re: Creating bonds during a run (Wed Jan 21 2009 - 04:18:43 CST)
• Pri...
  • Unsubscribe (Mon Dec 27 2010 - 23:03:02 CST)
• Prija Ponnan
  • Error in running minimization (Fri May 21 2010 - 05:24:58 CDT)
  • Acetyl group patch for lysine residue (Sat May 15 2010 - 08:19:51 CDT)
• Priyan Amaras
  • Pair interaction calculation - Direction of the force (Thu May 06 2010 - 10:25:44 CDT)
  • NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance. (Tue Apr 06 2010 - 11:36:25 CDT)
  • NAMD with two GPUs (Wed Mar 24 2010 - 21:35:46 CDT)
  • Re: No. of processors in the namd command. (Tue Mar 23 2010 - 10:04:52 CDT)
  • No. of processors in the namd command. (Mon Mar 22 2010 - 21:13:55 CDT)
  • CUDA error memcpy to exclusions: invalid argument (Tue Mar 16 2010 - 09:37:28 CDT)
  • CUDA on Win32 NAMD (Tue Dec 08 2009 - 14:19:07 CST)
  • Re: NAMD on 64 bit windows 2007 (Mon Dec 07 2009 - 10:36:18 CST)
  • NAMD on 64 bit windows 2007 (Fri Dec 04 2009 - 13:23:04 CST)
  • Atom constraint in certain direction (Thu Nov 05 2009 - 11:15:31 CST)
• priyodorshi satpati
  • SelectConstraints problem (Tue Dec 22 2009 - 08:43:15 CST)
  • Re: FreeEnergy: Not enough steps to complete pfm & mcti blocks (Wed Dec 02 2009 - 10:28:44 CST)
  • Re: FreeEnergy: Not enough steps to complete pfm & mcti blocks (Fri Nov 27 2009 - 03:26:01 CST)
  • Re: FreeEnergy: Not enough steps to complete pfm & mcti blocks (Thu Nov 26 2009 - 03:19:48 CST)
  • FreeEnergy: Not enough steps to complete pfm & mcti blocks (Wed Nov 25 2009 - 09:31:15 CST)
  • Read dcd file and calculate (distance/constraint energy Vs snapshots) using NAMD (Wed Nov 04 2009 - 11:05:33 CST)
• Pu Tian
  • Re: protein unfolding (Thu Jan 21 2010 - 09:19:16 CST)
  • Re: CUDA-NAMD hangs -- check the Northbridge temp! (Wed Jan 06 2010 - 09:36:55 CST)
  • Re: Free Energy Calculation of a protein (Wed Dec 09 2009 - 15:53:35 CST)
• pxq ÅÓÑ©ÇÛ
  • abnormal water surface after nvt and npt for POPC membrane (Tue Oct 27 2009 - 19:57:58 CDT)
  • problems of "Stray PME grid charges" (Tue Sep 08 2009 - 09:40:44 CDT)
  • for your suggestions on Pressure Control of transmembrane protein (GPCR) (Sun Aug 30 2009 - 22:18:47 CDT)
  • can we control the number and distribution of solvate molecular (Wed Aug 12 2009 - 02:21:23 CDT)
• q md
  • O-PHOSPHOTYROSINE link to DNA base pair. (Sun Jul 04 2010 - 02:37:44 CDT)
• Q=C1=D2=D8=D1_=FB=C1=CC=C1=C5=D7=C1?=
  • NAMD starts AMBER calculation only from 3rd run (Mon Mar 01 2010 - 09:38:43 CST)
  • Parametrizing a novel residue (Fri Sep 18 2009 - 10:25:18 CDT)
• r charbel maroun
  • Histamine topology file (Fri Jun 12 2009 - 11:32:35 CDT)
  • Fwd: RESP and CHARMM (Tue Jun 02 2009 - 08:35:17 CDT)
• Rabab Toubar
  • Does CHARMM stabilize alpha helices? (Sat Aug 21 2010 - 15:58:24 CDT)
  • RDF.tcl selections (Mon Jun 07 2010 - 13:40:56 CDT)
  • Minimization at higher temperature (Thu Jun 03 2010 - 14:08:37 CDT)
  • Phi MD (Thu May 20 2010 - 08:07:45 CDT)
  • Removing some water from a .dcd file or .coor file (Wed Mar 17 2010 - 15:36:14 CDT)
  • Re: Regenerating a .dcd file (Tue Mar 09 2010 - 07:27:35 CST)
  • Regenerating a .dcd file (Mon Mar 08 2010 - 14:02:15 CST)
  • Re: creating an output file from a dcd file (Thu Mar 04 2010 - 10:40:12 CST)
  • Re: creating an output file from a dcd file (Tue Mar 02 2010 - 14:51:20 CST)
  • creating an output file from a dcd file (Tue Mar 02 2010 - 10:34:15 CST)
  • Re: electrostatic vs van der waals (Tue Mar 02 2010 - 08:16:20 CST)
  • namd: Running namd on a node on cluster (Tue Dec 22 2009 - 06:44:21 CST)
  • Re: protocol to start MD (Wed Aug 19 2009 - 11:04:12 CDT)
  • Re: Re: recalculating energy using dcd file (Thu Aug 06 2009 - 09:06:21 CDT)
  • Re: recalculating energy using dcd file (Wed Aug 05 2009 - 09:43:44 CDT)
  • RE: PMEGridSize (Thu Jul 23 2009 - 15:13:03 CDT)
  • Measuring the molarity (Wed Jul 22 2009 - 15:16:58 CDT)
  • Re: protein shifts out of the water box (Wed Apr 29 2009 - 20:59:41 CDT)
• Rachel Ruskin
  • Re: Large protein translation during minimization (Mon Feb 15 2010 - 23:48:00 CST)
  • Large protein translation during minimization (Mon Feb 15 2010 - 16:24:20 CST)
• Rahul Bhowmik
  • Pulling atoms in different directions (Sun Mar 29 2009 - 15:59:01 CDT)
• Rajan Vatassery
  • Re: Recover high precision coordinates from binary .coor file (Wed Dec 08 2010 - 15:15:56 CST)
  • Recover high precision coordinates from binary .coor file (Fri Nov 05 2010 - 19:37:48 CDT)
  • Electrostatic Potential Problems, WRT Minimizations (Thu Oct 21 2010 - 21:34:23 CDT)
  • Distribute Points Evenly on Surface of a Sphere (Mon Oct 18 2010 - 13:57:53 CDT)
  • Importance of the Topology File, .rtf, and Other Files (Sat Oct 16 2010 - 13:57:10 CDT)
  • RE: psfgen problem, not generating angles/dihedrals (Sat Sep 11 2010 - 01:24:48 CDT)
  • psfgen problem, not generating angles/dihedrals (Fri Sep 10 2010 - 23:33:42 CDT)
• Rajiv Abhyankar
  • unsubscribe (Thu Dec 10 2009 - 00:35:13 CST)
  • dielectric constant assignment (Mon Nov 09 2009 - 06:22:04 CST)
  • Re: extracting info from output files (Tue Sep 22 2009 - 17:56:19 CDT)
  • extracting info from output files (Tue Sep 22 2009 - 13:26:08 CDT)
• Ramin Omidvar
  • Why NAMD run Slow down (Fri Sep 17 2010 - 11:32:07 CDT)
  • Re: Constraint Failure in SMD simulation (Tue Jul 13 2010 - 08:04:20 CDT)
  • NAMD parralel processor windows (Thu Jun 17 2010 - 13:25:54 CDT)
  • Constraint Failure in SMD simulation (Wed May 19 2010 - 11:51:20 CDT)
• Ramon Rocha
  • flashmob namd (Tue Aug 03 2010 - 10:52:15 CDT)
• Ramya Gamini
  • Re: followup question on error calculation in ABF (Wed Oct 07 2009 - 16:41:57 CDT)
  • Re: followup question on error calculation in ABF (Wed Oct 07 2009 - 15:26:15 CDT)
  • Re: topology files (Wed Sep 23 2009 - 17:17:28 CDT)
  • Re: namd-SMD constant Force missing smdatom location (Mon Aug 10 2009 - 18:52:06 CDT)
  • Re: On naming rules in force-field parameter files? (Mon Aug 10 2009 - 09:07:12 CDT)
  • Re: Re: about psfgen (Sat Jul 04 2009 - 14:43:53 CDT)
  • Re: Re: about psfgen (Sat Jul 04 2009 - 14:33:32 CDT)
  • Re: about psfgen (Sat Jul 04 2009 - 09:40:46 CDT)
  • Re: regarding positioning of protein molecule (Wed Jun 24 2009 - 22:52:06 CDT)
  • Re: Force Constant Units (Wed Jun 10 2009 - 14:01:28 CDT)
  • Re: tutorial for calculation of PMF using namd (Tue Mar 03 2009 - 00:44:38 CST)
  • Re: A beginner's question for using NAMD to do cell membrane simulation and molecular transportation (Sat Feb 21 2009 - 15:34:24 CST)
• Ramya Narasimhan
  • MOnte carlo simulation (Tue Nov 23 2010 - 01:04:10 CST)
  • user-defined energy function (Mon Sep 06 2010 - 04:53:47 CDT)
  • gradient tolerance (Tue Jun 08 2010 - 05:48:11 CDT)
  • Regarding temperature accelerated MD (Tue Jun 08 2010 - 05:32:34 CDT)
  • regarding implicit solvent models (Fri Apr 03 2009 - 01:59:57 CDT)
  • LD with explicit water molecules (Wed Feb 18 2009 - 22:14:40 CST)
• Ranyere Deyler
  • VdW and fixatoms (Sat Aug 28 2010 - 00:07:06 CDT)
  • Possible way of performing a temperature gradient?? (Sun Jun 13 2010 - 23:19:10 CDT)
  • Temperature gradient! (Wed May 26 2010 - 22:35:35 CDT)
  • Re: Generate psf files from Scott Feller's lipid coordinates (Mon May 17 2010 - 16:57:10 CDT)
  • ReassignFreq script fail!! (Sat May 08 2010 - 03:10:14 CDT)
  • Problem in energy minimization using Fixatoms or Constraints (Tue Mar 30 2010 - 12:52:09 CDT)
  • Re: Fixatoms minimization problem!! (Mon Mar 29 2010 - 18:41:29 CDT)
  • Re: Fixatoms minimization problem!! (Mon Mar 29 2010 - 09:14:13 CDT)
  • Fixatoms minimization problem!! (Tue Mar 16 2010 - 12:45:57 CDT)
  • Problem in minimization, Energy "-1.#IND" and bad dcd file. (Sun Mar 14 2010 - 17:36:19 CDT)
  • Problem in minimization, Energy "-1.#IND" and bad dcd file. (Sun Mar 14 2010 - 17:28:58 CDT)
  • Problem generating psf file in psfgen (Wed Dec 16 2009 - 23:20:57 CST)
• Raul Araya
  • ADENOSINE-5-DIPHOSPHORIBOSE topology (Tue Oct 05 2010 - 20:56:42 CDT)
  • parameters for Glutathione and BSO (Thu Sep 09 2010 - 11:44:38 CDT)
  • velocities from a DCD file (Wed Jan 27 2010 - 08:01:00 CST)
  • order parameter, lipid segments as vectors (Tue Oct 27 2009 - 08:48:32 CDT)
  • lipid bi-layer and SiO2 (Fri May 08 2009 - 14:36:41 CDT)
• Ravinder Abrol
  • TIP4P/Ice usage in NAMD (Tue Aug 24 2010 - 03:22:17 CDT)
• Reichert, David
  • restarting a simulation ? (Fri Mar 05 2010 - 13:17:14 CST)
  • NAMD 2.7b1 ABF + free energy windows (Tue Sep 29 2009 - 15:33:48 CDT)
• Richard Owczarzy
  • New NVIDIA GPU C2050 (Tue May 25 2010 - 00:29:24 CDT)
  • RE: Installation problem on Win64 (Fri Apr 02 2010 - 09:39:19 CDT)
  • RE: Error: This application has requested the Runtime to terminate it in an unusual way: Please contact the application's support team for more information" after specifying the namd2.exe path (Fri Mar 19 2010 - 17:13:53 CDT)
  • RE: Info: Attempting to read FFTW data from FFTW_NAMD_2.7b1_Linux-Itanium-MPI-Altix.txt (Mon Feb 01 2010 - 10:27:44 CST)
  • RE: NAMD on 64 bit windows 2007 (Fri Dec 04 2009 - 14:53:42 CST)
  • RE: simulation configuration file not accesible - other reasons (Thu Nov 19 2009 - 17:38:15 CST)
  • RE: Simultaneous water and protein minimization (Thu Nov 19 2009 - 11:55:08 CST)
  • RE: Simultaneous water and protein minimization (Wed Nov 18 2009 - 16:52:09 CST)
  • NAMD file limitation in Win32 - windows XP (Tue Nov 17 2009 - 11:51:52 CST)
  • RE: questions regarding new single node box for NAMD: re components, CUDA, Fermi (Fri Oct 02 2009 - 10:42:12 CDT)
• Rick Calloway
  • Pressure Questions (Wed Feb 10 2010 - 08:16:50 CST)
  • Precision of Coordinate data (Tue Sep 22 2009 - 12:08:34 CDT)
  • Periodic Forcing Functions (Mon May 18 2009 - 16:50:42 CDT)
• riya david
  • monolayere (Fri Jul 30 2010 - 14:29:48 CDT)
• Robert Brunner
  • Re: TIP4P topology (Tue Nov 03 2009 - 15:31:20 CST)
  • Re: TIP4P topology (Tue Nov 03 2009 - 15:11:18 CST)
  • Re: Regarding NAMD CPU usage (Fri Sep 11 2009 - 11:34:12 CDT)
  • Re: combining segments (Mon Aug 10 2009 - 11:32:26 CDT)
  • Re: What is the different between "periodic boundary ,spherical harmonic boundary and cylindrical harmonic boundary conditions"? (Fri Aug 07 2009 - 12:03:50 CDT)
  • Re: error running namd (Mon Jul 27 2009 - 20:44:15 CDT)
  • Re: GridForces methodology in NAMD 2.7b1 (Thu May 28 2009 - 16:46:16 CDT)
  • Re: NAMD on a virtual grid (Mon Jan 26 2009 - 15:31:09 CST)
  • Re: NAMD on a virtual grid (Mon Jan 26 2009 - 13:50:13 CST)
  • Re: Single or double precision? (Fri Jan 09 2009 - 15:14:33 CST)
• Robert Elder
  • Re: ABF in various simulations (Mon May 17 2010 - 18:43:41 CDT)
  • Re: ABF in various simulations (Mon May 17 2010 - 14:42:30 CDT)
• Robert Konecny
  • Re: implicit solvent with iapbs (Mon Feb 01 2010 - 17:30:09 CST)
  • iAPBS 1.0.0 released (Wed Nov 18 2009 - 22:55:24 CST)
• Roberta Rostagno
  • Re: ERROR: Multiple definitions of 'LangevinPiston' (Fri May 15 2009 - 02:19:09 CDT)
• roberta.rostagno
  • ERROR: Stray PME grid charges detected (Mon May 25 2009 - 04:34:11 CDT)
  • Re: ERROR: Multiple definitions of 'LangevinPiston' (Wed May 20 2009 - 09:44:02 CDT)
  • Re: ERROR: Multiple definitions of 'LangevinPiston' (Thu May 14 2009 - 04:02:29 CDT)
  • Re: ERROR: Multiple definitions of 'LangevinPiston' (Tue May 12 2009 - 03:02:45 CDT)
  • ERROR: Multiple definitions of 'LangevinPiston' (Mon May 11 2009 - 07:15:42 CDT)
  • Re: ERROR: Multiple definitions of 'LangevinPiston' (Mon May 11 2009 - 08:20:29 CDT)
  • ERROR: Multiple definitions of 'LangevinPiston' (Mon May 11 2009 - 07:38:38 CDT)
• Roberto Rivera
  • Namd. Small molecules (Fri Mar 19 2010 - 18:53:45 CDT)
• Rocchia Walter
  • monitoring instantaneous kinetic energy of a subsystem (Thu May 27 2010 - 06:52:16 CDT)
• Rogan Carr
  • Re: coordinates and cells (Wed Feb 17 2010 - 11:25:06 CST)
  • Re: NAMD and new sugar parameter set (Mon Apr 20 2009 - 18:43:58 CDT)
  • Re: NAMD and new sugar parameter set (Mon Apr 20 2009 - 14:17:06 CDT)
  • RE: PCA Analysis of CGMD (Fri Apr 10 2009 - 09:47:35 CDT)
• Roman Petrenko
  • Re: Size of Timestep (Mon Apr 05 2010 - 11:20:26 CDT)
  • Re: No. of processors in the namd command. (Tue Mar 23 2010 - 10:45:50 CDT)
  • Re: electric field unit conversion (Wed Feb 17 2010 - 11:53:02 CST)
  • Re: analysis of dcd (Sun Jan 31 2010 - 23:25:36 CST)
  • Re: How to obtain the system force on a fixed atom (Wed Dec 16 2009 - 09:34:36 CST)
  • Re: How to obtain the system force on a fixed atom (Wed Dec 16 2009 - 09:41:57 CST)
  • Re: constraints (Thu Dec 03 2009 - 16:02:52 CST)
  • Re: Small discrepancy in Kinetic Energy after restarting the simulation (Tue Dec 01 2009 - 10:55:40 CST)
  • Re: calculation of periodic box (Tue Nov 17 2009 - 22:51:27 CST)
  • Re: Error in Minimization (Tue Nov 10 2009 - 14:00:53 CST)
  • Re: water box size (Sun Nov 08 2009 - 10:52:03 CST)
  • Re: Error in Minimization (Sun Nov 08 2009 - 10:29:47 CST)
  • Re: molecular dynamics simulation (Thu Nov 05 2009 - 10:27:14 CST)
  • Re: PMEGridSpacing (Sat Oct 31 2009 - 15:17:58 CDT)
  • Re: PMEGridSpacing (Sat Oct 31 2009 - 15:19:36 CDT)
  • Re: spontaneous system explosion after 2 ns of normal run (Sun Oct 18 2009 - 22:59:08 CDT)
  • Re: Slow heating in namd (Thu Oct 15 2009 - 10:32:43 CDT)
  • Re: spontaneous system explosion after 2 ns of normal run (Thu Oct 15 2009 - 10:22:44 CDT)
  • Re: spontaneous system explosion after 2 ns of normal run (Wed Oct 14 2009 - 23:09:36 CDT)
  • spontaneous system explosion after 2 ns of normal run (Wed Oct 14 2009 - 22:57:34 CDT)
  • Re: Generation of average trajectory (Mon Oct 12 2009 - 21:02:03 CDT)
  • Re: Lennard-Jones potential in CHARMM (Fri Oct 09 2009 - 17:13:55 CDT)
  • Re: atomic structure of some surfaces (Fri Sep 18 2009 - 15:31:18 CDT)
  • atomic structure of some surfaces (Thu Sep 10 2009 - 19:57:14 CDT)
  • Re: Cuda benchmarks namd2.7b1 - effects of configuration parameters and hardware. (Sun Aug 30 2009 - 16:06:26 CDT)
  • Re: Tesla Utilization -- NAMD 2.7b1 (Fri Aug 28 2009 - 11:49:18 CDT)
  • Re: SMD with force applied to two seperate molecules (Thu Aug 13 2009 - 10:48:44 CDT)
  • Re: About SMD (Thu Aug 13 2009 - 10:33:34 CDT)
  • Re: SMD with force applied to two seperate molecules (Thu Aug 13 2009 - 10:24:02 CDT)
  • Re: Defining Temperature for Langevin for Namd restart. (Thu Aug 06 2009 - 05:41:17 CDT)
  • Re: Defining Temperature for Langevin for Namd restart. (Wed Aug 05 2009 - 15:13:57 CDT)
  • Re: SMD output : which col represents force, second or last (Wed Aug 05 2009 - 12:05:16 CDT)
  • Re: water molecules in channel protein (Wed Aug 05 2009 - 11:59:21 CDT)
  • Re: NAMD water sphere problem (Fri Jul 31 2009 - 19:37:50 CDT)
  • Re: how to generate DNA psf files? (Fri Jul 31 2009 - 00:22:31 CDT)
  • Re: how to run namd2.7b1 on multiple nodes (Fri Jul 24 2009 - 11:13:22 CDT)
  • how to run namd2.7b1 on multiple nodes (Thu Jul 23 2009 - 17:48:19 CDT)
  • Re: My protein went out of the water box in SMD. Would it have a bad effect on the result? (Mon Jun 29 2009 - 12:57:38 CDT)
  • tclforces and minimization (Thu Jun 04 2009 - 16:42:27 CDT)
  • Re: abf with colvars example (Thu Jun 04 2009 - 14:35:53 CDT)
  • electric field along z-direction (Wed May 27 2009 - 16:21:27 CDT)
  • Re: collective variable space PMF, including biasing potential terms? (Wed May 13 2009 - 17:45:29 CDT)
  • Re: peptides on surface (Wed May 13 2009 - 17:30:00 CDT)
  • Re: collective variable space PMF, including biasing potential terms? (Wed May 13 2009 - 17:00:49 CDT)
  • Re: namd-cuda-intel vs. namd-intel (Wed May 13 2009 - 11:58:24 CDT)
  • Re: Make NAMD2.7b1 with cuda bug? (Wed May 13 2009 - 08:56:02 CDT)
  • Re: namd-cuda-intel vs. namd-intel (Tue May 12 2009 - 10:19:55 CDT)
  • namd-cuda-intel vs. namd-intel (Tue May 12 2009 - 00:32:58 CDT)
  • force-field for cy3, cy5 dyes (Wed May 06 2009 - 19:26:54 CDT)
  • Re: diffusion / fex peptide problem (Wed May 06 2009 - 12:33:49 CDT)
  • geomtery optimization with namd (Mon May 04 2009 - 16:18:03 CDT)
  • FreeEnergy and minimization (Thu Apr 30 2009 - 23:31:55 CDT)
  • Re: force-field for ATP (Tue Apr 28 2009 - 19:20:57 CDT)
  • force-field for ATP (Tue Apr 28 2009 - 18:55:05 CDT)
  • Re: Water is boiling with namd and charmm (Mon Apr 13 2009 - 10:25:43 CDT)
  • how to use constraints properly (Thu Mar 19 2009 - 13:38:24 CDT)
  • Re: how to get rid of TCL messages in namd.log from tclForcesScript (Fri Mar 13 2009 - 20:47:30 CDT)
  • how to get rid of TCL messages in namd.log from tclForcesScript (Fri Mar 13 2009 - 18:45:21 CDT)
  • Re: removing water from big dcd files (Wed Mar 04 2009 - 13:05:22 CST)
  • Re: solution for generating IC (Sat Feb 21 2009 - 22:48:54 CST)
  • cuda 1.0 binaries on cuda 1.1 (Wed Feb 11 2009 - 13:47:32 CST)
• Ron Stubbs
  • GPU Selection in NAMD CUDA (Mon Sep 21 2009 - 14:56:42 CDT)
  • Tesla Utilization -- NAMD 2.7b1 (Thu Aug 27 2009 - 13:06:19 CDT)
• Ronald Salesky
  • Running NAMD on SGI Altix system (Thu Jul 22 2010 - 15:13:31 CDT)
  • Re: simulating dna (Tue Apr 20 2010 - 14:18:51 CDT)
  • NAMD regression test suite? (Fri Mar 26 2010 - 11:46:59 CDT)
  • Re: Water Box Shape Changing during NVT Simulation! (Mon Mar 08 2010 - 11:46:24 CST)
  • Tuning NAMD CUDA? (Fri Nov 06 2009 - 18:07:14 CST)
  • Running NAMD w/ CUDA under Linux (Wed Nov 04 2009 - 21:23:30 CST)
• Roy Kim
  • Resources for trying out NVIDIA GPUs for free with NAMD (Wed Aug 18 2010 - 12:22:09 CDT)
• Ruchi Sachdeva
  • error in writing restart files (Fri Feb 27 2009 - 03:55:30 CST)
• Rudra Banerjee
  • acridine orange (Thu Mar 19 2009 - 23:54:50 CDT)
• Rukman Hertadi
  • Simulation crash due to charmrun error (Tue Oct 27 2009 - 03:38:20 CDT)
• S.K. Ghosh
  • Re: Thiol on gold simulation in NAMD (Wed Feb 18 2009 - 15:45:00 CST)
  • Thiol on gold simulation in NAMD (Tue Feb 17 2009 - 14:14:36 CST)
• saam
  • Re: Paratool: where is "tip3.xbgf"? (Fri Sep 25 2009 - 11:53:26 CDT)
• Sabine Leroch
  • Wtrlt: Smeart out 9/3 LJ wall (Wed Jul 15 2009 - 07:48:07 CDT)
  • Implementation of graphite walls (Mon Jul 13 2009 - 07:36:05 CDT)
• Sabyashachi Mishra
  • abf_integrate (Wed Aug 04 2010 - 04:50:08 CDT)
  • selective rigidbonds (Fri May 21 2010 - 04:29:57 CDT)
• Sadhu, Shubho (NIH/NCI) [F]
  • RE: Continuing simulation after constraint failure error? (Thu Aug 06 2009 - 14:23:06 CDT)
  • RE: SMD output : which col represents force, second or last (Wed Aug 05 2009 - 12:19:27 CDT)
  • CUDA Linux-x86 doesn't compile (Thu Jul 30 2009 - 09:06:04 CDT)
  • RE: NAMD hanging on GPU (Tue Jul 28 2009 - 09:17:48 CDT)
  • RE: RE: NAMD CUDA on dual Nvidia 295 GPUs (Thu Jul 23 2009 - 12:14:42 CDT)
  • RE: NAMD CUDA on dual Nvidia 295 GPUs (Thu Jul 23 2009 - 09:43:34 CDT)
  • RE: NAMD CUDA on dual Nvidia 295 GPUs (Thu Jul 23 2009 - 09:11:48 CDT)
  • Re: Fwd: PROBLEM OF INSTALLATION OF NAMD (Fri Jul 17 2009 - 08:07:36 CDT)
  • NAMD hanging on GPU (Fri Jul 17 2009 - 08:00:21 CDT)
• Samuel Coulbourn Flores 花山
  • display all frames simultaneously (Thu Apr 16 2009 - 21:35:59 CDT)
• Sandra Rennebaum, Biochemisches Inst.
  • Berendsen, explicit water (Tue Aug 18 2009 - 04:54:07 CDT)
  • Berendsen- two baths (Tue Aug 11 2009 - 01:55:10 CDT)
• Sangamesh B
  • Namd benchmark problem (Thu Oct 22 2009 - 10:29:17 CDT)
  • Re: Namd benchmark problem (Sun Oct 25 2009 - 01:46:29 CDT)
  • Namd benchmark problem (Sat Oct 24 2009 - 02:12:05 CDT)
• Sangbae Lee
  • unbinding SMD skill question (Wed Aug 19 2009 - 15:24:59 CDT)
• Santanu Chatterjee
  • Simulations with NAMD (Fri Feb 05 2010 - 10:37:44 CST)
  • Re: starting namd (Tue Jan 19 2010 - 10:35:30 CST)
• sara
  • counting h-bond in system with vmd (Fri Dec 17 2010 - 15:10:21 CST)
  • psf of insulin (Wed Nov 17 2010 - 10:27:20 CST)
  • build nanoparticle (Wed Oct 27 2010 - 11:10:58 CDT)
  • top file for CNT (Sun Oct 17 2010 - 03:10:13 CDT)
  • g(r) calculation for CNT (Thu Sep 02 2010 - 04:34:48 CDT)
  • restarting simulation (Sun Aug 29 2010 - 03:18:07 CDT)
  • build a wall (Wed Aug 25 2010 - 11:01:39 CDT)
  • change solvent (Wed Aug 18 2010 - 10:26:20 CDT)
  • parameter file for carbon nanotube (Mon Aug 16 2010 - 10:34:53 CDT)
  • psf creating for carbon nanotube (Sun Aug 15 2010 - 02:48:36 CDT)
• sathish kumar gurupatham
  • unsubscribe namd-l (Sat Aug 28 2010 - 14:07:25 CDT)
  • unsubscribe (Mon Apr 19 2010 - 09:25:06 CDT)
• satya work
  • PMF via constrained dynamics in NAMD (Mon Aug 31 2009 - 09:01:43 CDT)
  • (is there) a dependence of dynamics on WRAPPING (Sat Aug 15 2009 - 01:33:26 CDT)
  • Re: System expands: CCL4 simulation; NPT(Langevin Piston) (Tue Apr 28 2009 - 23:44:02 CDT)
  • System expands: CCL4 simulation; NPT(Langevin Piston) (Tue Apr 28 2009 - 16:10:32 CDT)
• Saumya
  • Analysis of Results of only Lipid Bilayer Simulations (Wed May 19 2010 - 05:22:06 CDT)
• Schreiner Eduard
  • Re: Minimization issue. (Mon Aug 17 2009 - 10:33:57 CDT)
  • Re: how to write a command to close vmd in shell script? (Sun Aug 09 2009 - 22:39:36 CDT)
  • Re: On naming rules in force-field parameter files? (Sun Aug 09 2009 - 20:27:17 CDT)
  • Re: topology and parameter file for FAD (Sun Mar 01 2009 - 01:52:09 CST)
• Scooter Willis
  • IMD VMD NAMD adding frames (Mon Feb 01 2010 - 13:35:37 CST)
  • Parameter File (Sun Jan 31 2010 - 21:19:32 CST)
• Scott Boyken
  • constraintScaling to gradually release harmonic restraints during minimization (Tue Jul 20 2010 - 15:22:08 CDT)
• Sebastian Stolzenberg
  • Re: "GroupPressure no" resulting in negative pressure outputs (Thu Dec 02 2010 - 10:46:45 CST)
  • Re: "GroupPressure no" resulting in negative pressure outputs (Fri Nov 26 2010 - 13:03:56 CST)
  • "GroupPressure no" resulting in negative pressure outputs (Thu Nov 25 2010 - 13:51:13 CST)
  • Re: Constant pressure (Thu Nov 25 2010 - 13:04:51 CST)
  • FEP substrate transformation with common moiety (Fri Aug 27 2010 - 20:35:01 CDT)
  • tclforces: measure distances in NAMD 2.6b2 ? (Sat Jul 24 2010 - 21:46:51 CDT)
  • TMD SCRIPT (Thu Apr 29 2010 - 11:11:42 CDT)
  • in NAMD tutorials: why "HSE" instead of "HSD"? (Mon Apr 26 2010 - 18:57:04 CDT)
  • Re: temperature from binary velocities file (Tue Dec 15 2009 - 09:41:23 CST)
  • temperature from binary velocities file (Mon Dec 14 2009 - 14:59:42 CST)
  • Re: temperature calculations from velocities in NAMD? (Tue Nov 10 2009 - 23:00:44 CST)
  • Re: temperature calculations from velocities in NAMD? (Sun Nov 08 2009 - 19:24:12 CST)
  • Re: temperature calculations from velocities in NAMD? (Sat Nov 07 2009 - 20:13:55 CST)
  • Re: temperature calculations from velocities in NAMD? (Sat Nov 07 2009 - 19:49:18 CST)
  • Re: temperature calculations from velocities in NAMD? (Sat Nov 07 2009 - 16:31:48 CST)
  • temperature calculations from velocities in NAMD? (Sat Nov 07 2009 - 13:32:41 CST)
  • Re: Re: PRESSURE, GPRESSURE, PRESSAVG, and GPRESSAVG (Sat Nov 07 2009 - 12:33:32 CST)
  • Re: PRESSURE, GPRESSURE, PRESSAVG, and GPRESSAVG (Wed Nov 04 2009 - 18:10:32 CST)
  • Paratool: where is "tip3.xbgf"? (Fri Sep 25 2009 - 10:54:38 CDT)
  • FEP to replace a PMF calculation? (Fri Sep 18 2009 - 18:26:42 CDT)
  • fixing parts of an equilibrated protein's environment (Wed Sep 09 2009 - 10:26:17 CDT)
  • PMF: free energy calcs in "grow" phase? (Fri Sep 04 2009 - 15:57:00 CDT)
  • Re: how work: harmonic position "constraints" module + "WrapAll on"? (Mon Jul 20 2009 - 12:52:06 CDT)
  • how work: harmonic position "constraints" module + "WrapAll on"? (Mon Jul 20 2009 - 07:12:04 CDT)
  • namd 2.7b: measure free energy difference "growing" a force constant (Sat Jun 20 2009 - 09:33:13 CDT)
  • mercury ion parameters? (Sat May 23 2009 - 11:12:04 CDT)
  • NAMD 2.7b1: metadynamics+tclForces => "... design error, GlobalMasterServer..." (Thu May 14 2009 - 16:41:16 CDT)
  • collective variable space PMF, including biasing potential terms? (Wed May 13 2009 - 14:48:05 CDT)
  • Re: soft-core FEP in namd 2.7b (Sun May 10 2009 - 21:29:32 CDT)
  • Re: soft-core FEP in namd 2.7b (Sun May 10 2009 - 10:36:47 CDT)
  • soft-core FEP in namd 2.7b (Fri May 08 2009 - 11:57:10 CDT)
  • alchemify with CMAP? (Thu Apr 16 2009 - 19:11:53 CDT)
  • Re: Unfavorable anti conformation after GLUP patching? (Thu Apr 16 2009 - 11:00:17 CDT)
  • Re: Dihedral Restraints during MD simulation (Wed Apr 15 2009 - 13:18:47 CDT)
  • Unfavorable anti conformation after GLUP patching? (Tue Apr 14 2009 - 19:13:21 CDT)
  • how to do: FEP e2?, a protonating mutation? (Tue Apr 07 2009 - 19:15:19 CDT)
  • Re: alanine dipeptide: no dihdral energy terms? (Thu Mar 26 2009 - 19:21:04 CDT)
  • alanine dipeptide: no dihdral energy terms? (Mon Mar 23 2009 - 22:33:03 CDT)
  • tclforces included in the NAMD-FEP \delta_G values? (Thu Mar 19 2009 - 13:11:10 CDT)
  • multiple FEP experiments in one NAMD-FEP run? (Tue Mar 17 2009 - 15:51:14 CDT)
  • Re: FEP with fixed explicit environment? (Tue Mar 17 2009 - 13:21:12 CDT)
  • FEP with fixed explicit environment? (Sun Mar 15 2009 - 12:03:28 CDT)
  • Re: FEP with fixed explicit environment? (Fri Mar 13 2009 - 16:42:35 CDT)
  • Re: FEP with fixed explicit environment? (Fri Mar 13 2009 - 10:58:32 CDT)
  • FEP with fixed explicit environment? (Thu Mar 12 2009 - 18:51:05 CDT)
  • FEP with fixed explicit environment? (Thu Mar 12 2009 - 18:50:32 CDT)
  • "within" command in NAMD? (Mon Jan 05 2009 - 14:20:51 CST)
• sefer baday
  • Re: ABF: moving system in Z direction (Tue Apr 20 2010 - 04:58:51 CDT)
  • Re: ABF: moving system in Z direction (Mon Apr 19 2010 - 11:59:03 CDT)
  • ABF: moving system in Z direction (Mon Apr 19 2010 - 08:49:09 CDT)
• Segun Jung
  • Re: Parallel replicas? (Fri Mar 12 2010 - 10:51:05 CST)
  • hi (Wed Dec 23 2009 - 00:59:44 CST)
  • restart REMD simulation (Sat Apr 18 2009 - 21:32:55 CDT)
  • TMD on tRNA does not converge (Wed Mar 25 2009 - 11:13:21 CDT)
  • how to save output file in plain text? (Thu Jan 08 2009 - 15:09:02 CST)
• Sellers, Michael S. (Cont, ARL/WMRD)
  • extending namd / shared library build (UNCLASSIFIED) (Fri Oct 29 2010 - 08:23:41 CDT)
• Seungho Choe
  • Re: tcl force (Sun Oct 18 2009 - 20:59:43 CDT)
  • Re: tcl force (Sat Oct 17 2009 - 13:08:11 CDT)
  • Re: tcl force (Sat Oct 17 2009 - 02:02:47 CDT)
  • Re: tcl force (Sat Oct 17 2009 - 00:21:08 CDT)
  • Re: tcl force (Fri Oct 16 2009 - 23:17:19 CDT)
  • tcl force (Fri Oct 16 2009 - 16:34:58 CDT)
• Shahid Qamar
  • FW: Water density of water Box (Wed Mar 11 2009 - 07:07:15 CDT)
• shayan_at_msu.edu
  • Re: Compiling NAMD on Ranger (Wed Apr 08 2009 - 12:51:26 CDT)
  • Re: Compiling NAMD on Ranger (Wed Apr 08 2009 - 10:09:11 CDT)
  • Compiling NAMD on Ranger (Wed Apr 08 2009 - 07:33:26 CDT)
  • Re: Problem running NAMD on ranger@TACC (Tue Feb 17 2009 - 09:41:06 CST)
  • Problem running NAMD on ranger@TACC (Tue Feb 17 2009 - 07:01:27 CST)
• Shen, Lingling
  • unsubscribe (Sun Jun 28 2009 - 10:59:53 CDT)
• Shi, Chuanyin
  • Extract trajectory from replica exchange simulation (Mon Jul 19 2010 - 09:19:21 CDT)
  • NAMD with Replica Exchange Simulations on Teragrid (Thu Jul 01 2010 - 00:17:45 CDT)
• shivam ghosh
  • unsubscribe (Sat Apr 17 2010 - 21:10:14 CDT)
• Shulin Zhuang
  • Re: Re: RAMD scripts version 4.1 (Fri Mar 05 2010 - 11:43:01 CST)
  • Problem of compiling Version Nightly Build (2010-02-16) (Tue Feb 16 2010 - 18:28:30 CST)
• Sibo Lin
  • trouble running metalloprotein simulation from literature (Sat May 15 2010 - 14:44:40 CDT)
  • psfgen creates too many bonds in a distorted Fe4S4 cluster (Mon May 10 2010 - 22:50:00 CDT)
• Siddharth Srinivasan
  • Unsubscribe (Thu Jun 03 2010 - 16:58:21 CDT)
• snoze pa
  • RMSD Question (Sun Nov 28 2010 - 11:08:25 CST)
  • Re: NAMD with missing residues (Wed Oct 27 2010 - 09:27:06 CDT)
  • NAMD with missing residues (Fri Oct 22 2010 - 15:46:34 CDT)
  • NAMD error message (Fri Sep 24 2010 - 17:04:45 CDT)
  • Re: Periodic cell has become too small for original patch grid! (Tue Apr 06 2010 - 10:26:09 CDT)
  • Re: Periodic cell has become too small for original patch grid! (Fri Apr 02 2010 - 13:33:35 CDT)
  • Re: How to confirm water box is big enough? (Tue Mar 30 2010 - 15:11:44 CDT)
  • NAMD in TACC lonestar (Mon Mar 29 2010 - 10:51:57 CDT)
  • Re: Lipid and protein interactions (Mon Feb 22 2010 - 10:24:55 CST)
  • Re: Re: namd trouble (Thu Feb 18 2010 - 14:08:42 CST)
  • SMD normal vector (Wed Feb 10 2010 - 17:48:00 CST)
  • Re: Crashing ibverbs binary of NAMD_2.7b2 (Wed Feb 10 2010 - 17:44:24 CST)
  • Re: Simulations with NAMD (Sat Feb 06 2010 - 19:13:11 CST)
  • Re: FW: Parallel Simulations (Sat Feb 06 2010 - 19:08:28 CST)
  • SMD and langevin dynamics (Sat Feb 06 2010 - 19:00:15 CST)
  • Re: psfgen error (Wed Feb 03 2010 - 10:25:43 CST)
  • Re: namd job crashed (Mon Feb 01 2010 - 11:26:42 CST)
  • Re: dcd] (Mon Feb 01 2010 - 11:33:56 CST)
  • firsttimestep in NAMD (Mon Feb 01 2010 - 11:31:42 CST)
  • ERROR: Constraint failure in RATTLE algorithm for atom (Sun Jan 31 2010 - 12:41:16 CST)
  • Re: langevinTemp and system temperature (Fri Jan 29 2010 - 11:19:28 CST)
  • langevinTemp and system temperature (Fri Jan 29 2010 - 09:30:07 CST)
  • Simulation question (Tue Jan 19 2010 - 11:26:06 CST)
  • rigidTolerance question (Sun Nov 29 2009 - 19:06:15 CST)
  • Force extension from SMD log file (Thu Aug 20 2009 - 17:25:20 CDT)
  • Re: namd-SMD constant Force missing smdatom location (Wed Aug 12 2009 - 12:37:30 CDT)
  • Re: namd-SMD constant Force missing smdatom location (Tue Aug 11 2009 - 12:06:57 CDT)
  • Re: namd-SMD constant Force missing smdatom location (Tue Aug 11 2009 - 08:53:46 CDT)
  • Re: SMD and Temperature control (Tue Aug 11 2009 - 08:58:27 CDT)
  • Re: namd-SMD constant Force missing smdatom location (Mon Aug 10 2009 - 17:48:38 CDT)
  • namd-SMD constant Force missing smdatom location (Mon Aug 10 2009 - 14:40:51 CDT)
  • Re: Error with GUI NAMD Energy (Mon Aug 10 2009 - 11:32:53 CDT)
  • SMD and Temperature control (Fri Aug 07 2009 - 15:25:51 CDT)
  • Re: NAMD FFTW question? (Fri Aug 07 2009 - 14:47:18 CDT)
  • NAMD FFTW question? (Fri Aug 07 2009 - 11:17:58 CDT)
  • Re: SMD output : which col represents force, second or last (Wed Aug 05 2009 - 13:34:15 CDT)
  • SMD output : which col represents force, second or last (Wed Aug 05 2009 - 11:42:42 CDT)
  • SMD output : which col represents force, second or last (Wed Aug 05 2009 - 11:25:35 CDT)
  • Re: SMD restrain point in NAMD (Tue Aug 04 2009 - 14:45:39 CDT)
  • SMD restrain point in NAMD (Tue Aug 04 2009 - 11:40:05 CDT)
  • NAMD water sphere problem (Fri Jul 31 2009 - 17:19:12 CDT)
• Song, Hyundeok (songhk)
  • RE: Dowser (Sat May 29 2010 - 22:22:15 CDT)
  • RE: Dowser (Sat May 29 2010 - 20:42:49 CDT)
  • RE: NAMD in TACC lonestar (Mon Mar 29 2010 - 11:42:32 CDT)
  • RE: dmpc bilayer (Mon Dec 28 2009 - 10:03:38 CST)
  • RE: Unusual bond between residues: 0 (none) and 1 (protein) (Fri Oct 16 2009 - 22:23:29 CDT)
  • Unusual bond between residues: 0 (none) and 1 (protein) (Wed Oct 14 2009 - 11:33:15 CDT)
• Soran
  • NAMD OPLS Parameters (Thu Nov 04 2010 - 16:57:56 CDT)
• Sridhar Vaddadi
  • error termination (Fri Oct 02 2009 - 11:08:02 CDT)
  • periodic boundary conditions (Wed Sep 30 2009 - 14:08:31 CDT)
  • RE: topology files (Thu Sep 24 2009 - 13:17:26 CDT)
  • RE: pdb file (Thu Sep 24 2009 - 11:34:38 CDT)
  • RE: topology files (Wed Sep 23 2009 - 17:37:20 CDT)
  • psfgen (Wed Sep 23 2009 - 17:11:37 CDT)
  • topology files (Wed Sep 23 2009 - 13:59:02 CDT)
  • help requested (Wed Sep 23 2009 - 11:23:36 CDT)
• sripad chandan
  • unsubscribe namd-l (Thu Dec 16 2010 - 09:04:49 CST)
  • unsubscribe namd-l (Sat Aug 28 2010 - 09:08:12 CDT)
  • Re: loading of large dcd files (Thu Feb 26 2009 - 00:08:17 CST)
  • loading of large dcd files (Wed Feb 25 2009 - 23:54:58 CST)
  • log file from 3 different protein simulations (Mon Feb 16 2009 - 05:50:36 CST)
  • Correlation matrix of the Ca atoms (Sun Feb 01 2009 - 22:46:14 CST)
  • loading large dcd files (Thu Jan 29 2009 - 04:30:29 CST)
• Stefan Franzen
  • Using RMSD in colvar (Mon May 03 2010 - 17:42:18 CDT)
  • Particle Mesh Ewald question (from the tutorial) (Mon May 03 2010 - 17:39:38 CDT)
• Stefano Pieraccini
  • input file for memory optimised version (Tue Dec 14 2010 - 03:43:12 CST)
• stefhoor
  • Helix tilt (Tue Jul 06 2010 - 09:29:42 CDT)
  • Re: ABF in various simulations (Mon May 17 2010 - 15:18:57 CDT)
  • Re: ABF in various simulations (Mon May 17 2010 - 11:31:03 CDT)
  • ABF in various simulations (Mon May 17 2010 - 08:30:36 CDT)
• Stephen Hicks
  • Error on renaming file: Permission denied (Mon Jun 04 2007 - 00:38:28 CDT)
  • Re: Measuring protein diffusion: results too small? (Tue Jun 09 2009 - 12:01:23 CDT)
  • Re: Measuring protein diffusion: results too small? (Thu Jun 04 2009 - 02:56:28 CDT)
  • Measuring protein diffusion: results too small? (Wed Jun 03 2009 - 16:49:03 CDT)
• steve.kaminski_at_mail.tu-berlin.de
  • NAMD CUDA release (Wed Oct 07 2009 - 16:01:12 CDT)
• SUBHA KALYAANAMOORTHY
  • simulating Acetylated lysine substrate complex (Sun Nov 14 2010 - 23:12:11 CST)
• sudipta
  • script for energy minimization of a .dcd file (Fri Sep 03 2010 - 02:39:22 CDT)
  • Enthalpy calculation from NPT simulation (Wed Aug 11 2010 - 13:54:16 CDT)
  • FEP calculation is doing nothing (Tue Aug 10 2010 - 10:09:29 CDT)
  • mutation of DNA (Thu Jul 15 2010 - 05:57:46 CDT)
  • How to calculate binding free energy of a protein-DNA complex by using NAMD? (Fri Jun 25 2010 - 11:14:38 CDT)
  • units of position coordinate velocity coordinate and timestep in .dcd and .veldcd file (Tue Jan 19 2010 - 04:57:58 CST)
  • Re: ABF tutorial (Tue Jul 21 2009 - 05:40:58 CDT)
  • Re: ABF tutorial (Tue Jul 21 2009 - 05:39:03 CDT)
  • ABF tutorial (Mon Jul 20 2009 - 08:57:54 CDT)
  • Minimization problem of a protein-DNA complex with namd (Sun Jul 12 2009 - 02:21:36 CDT)
  • Generation of .psf file of DNA (Thu Jul 09 2009 - 01:53:25 CDT)
  • compile NAMD with TCP and SMP (Wed Jun 10 2009 - 00:19:18 CDT)
  • Re: Re: problem namd2-MPICH (Mon Jun 08 2009 - 08:14:06 CDT)
  • Problem namd2 and mpich2 (Mon Jun 08 2009 - 01:40:58 CDT)
• Sudipta Sinha
  • Take a look at jaxtr! (Sun Feb 08 2009 - 22:20:40 CST)
• Sujata Sovani
  • CAN'T FIND DIHEDRAL PARAMETERS FOR CN8B CN7 ON5 HN5 (Fri Sep 04 2009 - 15:35:56 CDT)
  • Re-posting - Methylated Histidine topology file (Mon Aug 31 2009 - 12:47:16 CDT)
  • Methylated Histidine topology file (Mon Aug 31 2009 - 12:38:03 CDT)
  • Continuing simulation after constraint failure error? (Thu Aug 06 2009 - 11:59:28 CDT)
  • Unable to generate PSF file due to an unparametrized component (Tue Jul 28 2009 - 16:33:09 CDT)
  • (no subject) (Tue Jul 28 2009 - 17:02:30 CDT)
• Sumanth Jamadagni
  • Re: ABF simulations (Tue Jun 23 2009 - 11:32:43 CDT)
  • ABF simulations (Tue Jun 09 2009 - 21:08:10 CDT)
  • Re: Harmonically constrained simulations (Thu May 21 2009 - 11:47:26 CDT)
  • Harmonically constrained simulations (Thu May 21 2009 - 10:00:13 CDT)
• sunita gupta
  • High RMSD of Coarse grain Protein (Mon Oct 18 2010 - 06:52:18 CDT)
  • High RMSD in Coarse Grain Simulation of Protein (Wed Oct 13 2010 - 03:06:22 CDT)
  • problem in cgsolvate.tcl while adding CG water to the system (Sat Sep 04 2010 - 02:52:12 CDT)
  • Software to Mutate DNA (Mon May 25 2009 - 08:39:51 CDT)
  • How to get over with the error "Atoms moving too fast; simulation has become unstable and Exiting prematurely (Fri Jan 02 2009 - 03:58:37 CST)
• superdirac
  • the unit of dipole moment in the calculation of dielectric constant. (Sun Apr 25 2010 - 21:58:11 CDT)
• supram_at_nankai.edu.cn
  • TCL: divide by zero (Thu Feb 05 2009 - 10:08:11 CST)
  • Fwd:Re: TCL: divide by zero (Thu Feb 05 2009 - 10:28:45 CST)
  • TCL: divide by zero (Thu Feb 05 2009 - 06:26:11 CST)
• surendra jain
  • H-bond and salt bridge between protein dimer (Sat Oct 30 2010 - 07:17:55 CDT)
  • Constraint failure in RATTLE algorithm for atom 268 (Fri Oct 29 2010 - 04:54:38 CDT)
• Swarna M Patra
  • salt bridge (Mon Nov 08 2010 - 02:09:21 CST)
  • Minimization problem on cluster (Mon Oct 04 2010 - 23:09:07 CDT)
  • Minimization problem on cluster (Mon Oct 04 2010 - 23:11:41 CDT)
  • membrane tutorial. (Wed Sep 22 2010 - 01:44:23 CDT)
  • beta column (Fri Sep 10 2010 - 00:57:04 CDT)
  • cholestrerol (Mon Aug 30 2010 - 04:29:38 CDT)
  • claen water (Sun Aug 29 2010 - 22:28:22 CDT)
  • problem with water (Tue Aug 24 2010 - 11:26:45 CDT)
  • WorkDistrib: Recursive bisection fails,invoking least-load algorithm (Tue Aug 24 2010 - 11:42:45 CDT)
  • water escape (Tue Aug 24 2010 - 10:38:31 CDT)
• Sweta Ramachandran
  • trouble in dynamics (Wed Feb 17 2010 - 23:18:48 CST)
• Syed Kashif Zafar
  • psfgen error (Tue Feb 23 2010 - 22:44:21 CST)
  • Re: dmpc bilayer (Mon Dec 28 2009 - 13:10:46 CST)
  • dmpc bilayer (Sun Dec 27 2009 - 15:10:26 CST)
• S¨¢ndor Kov¨¢cs
  • Re: force field for replica exchange with NAMD (Thu Oct 28 2010 - 17:47:21 CDT)
• Sébastien Légaré
  • Re: Re: Unfavorable anti conformation after GLUP patching? (Sat Apr 18 2009 - 21:43:22 CDT)
  • Re: how to do: FEP e2?, a protonating mutation? (Wed Apr 15 2009 - 22:32:27 CDT)
• Sébastien Légaré
  • Re: Free Energy Calculation of a protein (Thu Dec 10 2009 - 14:19:01 CST)
  • Re: ABF simulations (Tue Jun 23 2009 - 11:01:22 CDT)
  • Re: Re: alchemify with CMAP? (Fri Apr 17 2009 - 11:01:08 CDT)
  • Re: Unfavorable anti conformation after GLUP patching? (Wed Apr 15 2009 - 22:06:14 CDT)
  • Re: how to do: FEP e2?, a protonating mutation? (Thu Apr 09 2009 - 10:48:06 CDT)
  • double-wide sampling with soft-core (Tue Jan 20 2009 - 14:27:32 CST)
• t s
  • strange error from NAMD with CUDA (Thu Nov 05 2009 - 13:55:14 CST)
• Taeho Kim
  • (Á¦¸ñ ¾øÀ½) (Wed Feb 11 2009 - 22:29:19 CST)
• TAEJIN KIM
  • Control DCD file (Mon Jun 07 2010 - 17:09:20 CDT)
• TCBG Workshop
  • "Hands-On" Workshop on Computational Biophysics, July 6-10 and August 10-14, 2009 (Thu Feb 05 2009 - 15:52:30 CST)
• TCBG Workshops
  • "Hands-On" Workshop on Computational Biophysics, November 1-5, 2010 & November 29-December 3, 2010 in Urbana, IL (Thu Aug 12 2010 - 17:04:39 CDT)
  • Workshop on GPU Programming for Molecular Modeling, August 6-8, 2010, at the Beckman Institute in Urbana, Illinois (Fri Jun 11 2010 - 17:28:26 CDT)
  • TCBG "Hands-on" Workshop on Computational Biophysics, July 12-16, 2010, at San Diego (Thu May 13 2010 - 16:33:11 CDT)
  • Announcement: TCBG workshop at Pittsburgh Supercomputing Center May 10-14, 2010 (Tue Jan 26 2010 - 13:41:36 CST)
• Thomas C Bishop
  • Re: how to save a DCD file without water in NAMD: COMMAND LINE (Fri Aug 13 2010 - 08:44:09 CDT)
  • Re: Helix tilt (Tue Jul 13 2010 - 01:08:45 CDT)
• Thomas C. Bishop
  • namd 2.7 iverbs error 93620 attaching to node (Tue Nov 23 2010 - 12:11:38 CST)
  • morse potentials in NAMD revisited (Wed Nov 24 2010 - 11:29:05 CST)
  • LJ correction in NAMD2.7b3 (Thu Aug 12 2010 - 14:05:04 CDT)
  • Re: Mysterious Formation of Solvent Spheres (Wed Aug 11 2010 - 13:48:10 CDT)
  • Re: mutation of DNA (Thu Jul 15 2010 - 10:56:27 CDT)
  • pairinteractions (Tue Jun 15 2010 - 17:34:27 CDT)
  • Re: usage of NAMD with AMBER commands (Tue Jun 15 2010 - 14:25:13 CDT)
  • highthroughput NAMD (Thu Mar 11 2010 - 11:25:35 CST)
  • a timing question; 206,000atoms > 512cores not good (Mon Sep 28 2009 - 12:17:07 CDT)
  • NAMD documentation regarding compiling (Thu Jul 23 2009 - 15:25:19 CDT)
  • NAMD CUDA performance degradation (Thu Jul 23 2009 - 14:31:10 CDT)
  • Re: inconsistence in NAMD and AMBER energy: AMBER truncted octahedron (Tue Jul 21 2009 - 11:30:35 CDT)
  • Re: inconsistence in NAMD and AMBER energy (Tue Jul 21 2009 - 11:11:39 CDT)
  • Re: inconsistence in NAMD and AMBER energy (Tue Jul 21 2009 - 10:14:28 CDT)
  • Re: inconsistence in NAMD and AMBER energy (Tue Jul 21 2009 - 09:33:35 CDT)
  • Re: FW: NAMD 2.6, AMD64, MVAPICH2 compile error (Thu Mar 19 2009 - 16:31:27 CDT)
  • Re: how to add ions to a system/DASHOFSALT (Wed Jan 28 2009 - 09:10:23 CST)
• Thomas Evangelidis
  • nodelist file for concurrent execution of 2 nodes (Fri Dec 03 2010 - 05:08:28 CST)
  • Re: writing back coordinates of waters that cross the unit cell (Fri Nov 26 2010 - 08:19:19 CST)
  • selecting potential binding cavities with MD (Fri Apr 09 2010 - 14:11:21 CDT)
• Thomas Kahn
  • altering residues in .pdb files (Fri Mar 26 2010 - 18:34:53 CDT)
  • Parameters/topology entries for non-standard nucleotides (Fri Feb 19 2010 - 16:14:33 CST)
  • Topology files (Fri Feb 12 2010 - 17:13:48 CST)
  • Magnesium Ions Placement (Wed Jan 27 2010 - 19:18:02 CST)
• Tian, Pu (NIH/NIDDK) [C]
  • RE: which portions of NAMD are CUDA accelerated? (Wed Dec 09 2009 - 08:08:28 CST)
  • RE: The Future of NAMD was Re: GeForce vs. Tesla (Thu Nov 26 2009 - 07:23:20 CST)
  • GeForce vs. Tesla (Mon Nov 23 2009 - 10:01:13 CST)
• Tibbitt, Jeffrey A.
  • RE: Evaluating kinetic energy from a modified DCD file (Fri Apr 10 2009 - 15:03:24 CDT)
• Tillmann Utesch
  • Re: high pressure (Thu Mar 11 2010 - 15:05:59 CST)
  • Re: high pressure (Thu Mar 11 2010 - 10:29:22 CST)
• tillmann.utesch_at_mail.tu-berlin.de
  • Re: RetinalTop (Tue Aug 03 2010 - 03:23:22 CDT)
  • Re: high pressure (Tue Apr 20 2010 - 06:52:01 CDT)
  • Re: Removing some water from a .dcd file or .coor file (Thu Mar 18 2010 - 07:29:55 CDT)
  • high pressure (Thu Mar 11 2010 - 06:01:06 CST)
• tiziano gallo cassarino
  • GTP topology file (Fri Mar 20 2009 - 08:47:23 CDT)
• TJ Mustard
  • NAMD FEP and GPU (Tue Nov 09 2010 - 13:26:26 CST)
  • FEP and GPU (Mon Nov 08 2010 - 15:06:51 CST)
• Tommy Kahn
  • Ionize script (Wed Apr 07 2010 - 18:35:55 CDT)
• tpreeprem3_at_gatech.edu
  • psfgen errors (Thu Feb 25 2010 - 00:37:46 CST)
• twshen
  • Re: Reassign Temp during the Production Run (Thu Jul 16 2009 - 12:32:40 CDT)
  • Reassign Temp during the Production Run (Thu Jul 16 2009 - 12:04:03 CDT)
• udbhav ojha
  • Unsubscribe namd-l (Sat Aug 28 2010 - 16:20:45 CDT)
  • unsubscribe namd-l (Sat Aug 28 2010 - 02:23:20 CDT)
  • Parameter file problem (Tue Mar 30 2010 - 14:54:23 CDT)
  • psf file error (Mon Mar 29 2010 - 08:47:36 CDT)
• Uma Mageshwari
  • 99999999.9999 as vander waals energy (Sat Jul 11 2009 - 00:18:19 CDT)
  • value 9999999.99999 during simulation (Wed Jan 28 2009 - 04:11:57 CST)
  • how to add ions to a system (Wed Jan 28 2009 - 03:18:19 CST)
  • how to add ions to a system (Wed Jan 28 2009 - 01:57:09 CST)
  • how to add ions to a system (Wed Jan 28 2009 - 01:08:12 CST)
• urmit shah
  • Developing a neutral arginine patch in a topology file (Fri Jun 19 2009 - 17:54:19 CDT)
• uu zhu
  • Re: the total energy of single H2O molecule (Wed Apr 21 2010 - 21:04:24 CDT)
  • the total energy of single H2O molecule (Wed Apr 21 2010 - 09:11:45 CDT)
  • Re: No. of processors in the namd command. (Tue Mar 23 2010 - 00:39:29 CDT)
  • the maximum numbers of atoms in NAMD? (Wed Jan 27 2010 - 06:19:58 CST)
  • molecule jumps from one site to the other? (Mon Jul 13 2009 - 21:11:52 CDT)
  • Hi,all, the parameters for Strain (Tue Jun 30 2009 - 01:32:26 CDT)
  • How to set the parameters for two different baths in one molecule? (Mon Jun 08 2009 - 20:14:36 CDT)
  • the external electric field vector (Mon May 18 2009 - 01:56:29 CDT)
  • Re: how to set initial velocity? (Wed Apr 29 2009 - 01:58:13 CDT)
  • how to set initial velocity? (Tue Apr 28 2009 - 21:27:37 CDT)
  • Re: display all frames simultaneously (Thu Apr 16 2009 - 22:16:52 CDT)
  • How to set the parameters for C60? (Thu Apr 16 2009 - 05:06:37 CDT)
  • erergy gradient tolerance in Configuration Files (Wed Apr 08 2009 - 05:55:49 CDT)
• V.Ovchinnikov
  • RE: TMD comments (Tue Jan 20 2009 - 09:38:45 CST)
• Valeria M.
  • ABF error calculation (Fri Dec 11 2009 - 09:57:25 CST)
  • FW: ABF error calculation (Fri Dec 11 2009 - 11:04:33 CST)
• Valeria Marquez
  • Re: COARSE GRAINED WATER MODEL (Tue Oct 20 2009 - 10:16:04 CDT)
  • COARSE GRAINED WATER MODEL (Tue Oct 20 2009 - 08:52:10 CDT)
• Vamshi Gangupomu
  • Stray PME grid charges detected: colvars (Mon Nov 23 2009 - 09:44:39 CST)
  • Segmentation Violation: colvars (Sun Nov 15 2009 - 05:32:42 CST)
• Vasudevan V
  • selectively write atom coordinates on-the-fly (Thu May 21 2009 - 11:29:35 CDT)
  • Re: tmao molecule (Wed May 20 2009 - 10:19:45 CDT)
  • tmao molecule (Wed May 20 2009 - 09:43:40 CDT)
• Victor Ovchinnikov
  • Re: namd development mailing list? (Tue Jul 20 2010 - 15:00:52 CDT)
  • Re: Minimization messes up C terminal (Sat Jun 26 2010 - 09:07:45 CDT)
• Vincent Su
  • Simulating molecules in bulk water & VMD installation problems (Tue Aug 04 2009 - 14:27:38 CDT)
• Vinit Rege
  • unsubscribe (Tue Oct 20 2009 - 13:26:56 CDT)
  • unsubscribe (Fri Jun 26 2009 - 22:27:45 CDT)
  • unsubscribe (Mon Feb 16 2009 - 12:07:11 CST)
• vivek.viv.sharma_at_gmail.com
  • Re: Re: NAMD job dies on 2-quad core server (Thu Apr 09 2009 - 22:32:12 CDT)
  • Re: Re: NAMD job dies on 2-quad core server (Thu Apr 09 2009 - 01:44:01 CDT)
  • NAMD job dies on 2-quad core server (Sun Apr 05 2009 - 23:45:28 CDT)
• Vlad Cojocaru
  • Re: How to analysis RAMD data? (Wed Sep 29 2010 - 02:26:28 CDT)
  • RAMD patch in NAMD CVS (Fri Jul 23 2010 - 04:18:15 CDT)
  • Re: namd 2.7b2 or later - amberff/prmtop causes segfault during startup phase (Wed Mar 31 2010 - 07:02:07 CDT)
  • tcl forces and tcl 8.5 (Fri Mar 05 2010 - 03:19:16 CST)
  • RAMD scripts version 4.1 (Fri Mar 05 2010 - 03:08:51 CST)
  • update: segmentation faults with AMBER topology (cvscode 03 Mar 2010) (Thu Mar 04 2010 - 07:43:09 CST)
  • Re: AW: update: segmentation faults with AMBER topology and RAMD tcl scripts (Thu Feb 25 2010 - 03:02:25 CST)
  • Re: Re: namd 2.7b2 or later - amberff/prmtop causes segfault during startup phase (Wed Feb 24 2010 - 07:11:42 CST)
  • Re: AW: update: segmentation faults with AMBER topology and RAMD tcl scripts (Wed Feb 24 2010 - 05:52:49 CST)
  • Re: AW: update: segmentation faults with AMBER topology and RAMD tcl scripts (Wed Feb 24 2010 - 02:43:15 CST)
  • update: segmentation faults with AMBER topology and RAMD tcl scripts (Tue Feb 23 2010 - 08:31:27 CST)
  • Re: RAMD scripts and tcl version (Tue Feb 23 2010 - 03:45:44 CST)
  • RAMD scripts and tcl version (Tue Feb 23 2010 - 02:37:25 CST)
  • Re: namd 2.7b2 or later - amberff/prmtop causes segfault during startup phase (Mon Feb 22 2010 - 10:30:25 CST)
  • Re: namd 2.7b2 or later - amberff/prmtop causes segfault during startup phase (Mon Feb 22 2010 - 01:31:07 CST)
  • NAMD on AMD Istanbul versus intel Nehalem with infiniband (Fri Jan 22 2010 - 07:56:11 CST)
  • NAMD on AMD Istanbul versus intel Nehalem with infiniband (Fri Jan 22 2010 - 08:47:58 CST)
  • release of RAMD scripts for NAMD 2.6 and 2.7 (Fri Jan 08 2010 - 05:52:52 CST)
  • RAMD in NAMD; bugs and new version 4.0 (Thu Oct 29 2009 - 11:13:39 CDT)
  • Re: Random Expulsion MD (REMD) (Mon Oct 26 2009 - 06:45:30 CDT)
  • Re: protocol to start MD (Wed Aug 19 2009 - 10:22:37 CDT)
  • Re: glibc runtime errors on BlueGeneP occur only if running the cvs code (18.08) and not namd 2.6 (Wed Aug 19 2009 - 06:02:26 CDT)
  • glibc runtime errors on BlueGeneP occur only if running the cvs code (18.08) and not namd 2.6 (Wed Aug 19 2009 - 05:38:47 CDT)
  • Re: glibc detected : corrupted double-linked list: 0xa4657ad8 (Wed Aug 19 2009 - 04:43:40 CDT)
  • Re: glibc detected : corrupted double-linked list: 0xa4657ad8 (Wed Aug 19 2009 - 02:17:55 CDT)
  • Re: glibc detected : corrupted double-linked list: 0xa4657ad8 (Wed Aug 19 2009 - 02:46:08 CDT)
  • Re: glibc detected : corrupted double-linked list: 0xa4657ad8 (Tue Aug 18 2009 - 05:44:58 CDT)
  • glibc detected : corrupted double-linked list: 0xa4657ad8 (Tue Aug 18 2009 - 05:15:55 CDT)
  • Re: namd27: tclforces activate TI calculation by default (Thu Aug 13 2009 - 10:16:12 CDT)
  • Re: compilation error "could not set locale" with intel 11.0 (Fri Jul 31 2009 - 03:35:12 CDT)
  • compilation error "could not set locale" with intel 11.0 (Fri Jul 31 2009 - 03:03:53 CDT)
  • Re: THERMODYNAMIC INTEGRATION ON in namd 2.7b1 compiled 24.07 when TCL forces active (Wed Jul 29 2009 - 05:27:00 CDT)
  • THERMODYNAMIC INTEGRATION ON in namd 2.7b1 compiled 24.07 when TCL forces active (Wed Jul 29 2009 - 05:03:27 CDT)
  • Re: inconsistence in NAMD and AMBER energy: AMBER truncted octahedron (Wed Jul 22 2009 - 04:44:45 CDT)
  • Re: inconsistence in NAMD and AMBER energy: AMBER truncted octahedron (Tue Jul 21 2009 - 11:08:40 CDT)
  • Re: protein folding (Fri Jul 10 2009 - 08:51:56 CDT)
  • Re: namd hangs or exits with segmentation faults on opteron cluster with infiniband (Thu Jul 09 2009 - 06:59:31 CDT)
  • Re: FATAL ERROR: Sorry, combined TI and FEP is not implemented (Thu Jul 09 2009 - 03:22:44 CDT)
  • Another strange error: MStream checksums do not agree (Thu Jul 09 2009 - 03:05:13 CDT)
  • FATAL ERROR: Sorry, combined TI and FEP is not implemented (Wed Jul 08 2009 - 05:41:00 CDT)
  • namd hangs or exits with segmentation faults on opteron cluster with infiniband (Fri Jul 03 2009 - 08:16:28 CDT)
  • namd2.7b1 slower with openmpi 1.3.2 than namd2.6 with openmpi 1.2.6 (Thu Jul 02 2009 - 10:41:23 CDT)
  • Re: namd cvs 26.06.09, tcl 8.5, loadcoords (Tue Jun 30 2009 - 02:45:21 CDT)
  • namd cvs 26.06.09, tcl 8.5, loadcoords (Mon Jun 29 2009 - 09:10:46 CDT)
  • Re: RAMD in NAMD (Fri Apr 03 2009 - 07:02:15 CDT)
  • RAMD in NAMD (Wed Apr 01 2009 - 03:24:52 CDT)
  • Re: namd cvs compilation with a maximum number of cores to run on (Thu Feb 12 2009 - 09:04:14 CST)
  • namd cvs compilation with a maximum number of cores to run on (Thu Feb 12 2009 - 03:11:50 CST)
  • Re: tclforces: switch from md with external forces to standard md (Mon Jan 12 2009 - 01:57:20 CST)
  • tcl forces interface (Wed Jan 07 2009 - 04:36:13 CST)
• VMD NAMD Postdoc Position
  • Postdoctoral Position in Scientific Computing (Sat May 23 2009 - 13:41:27 CDT)
• wang
  • About CUDA version of NAMD 2.7 B1 (Wed Mar 25 2009 - 00:57:33 CDT)
  • Re: cgmd stability (Wed Feb 25 2009 - 21:43:41 CST)
  • Re: cgmd stability (Mon Feb 23 2009 - 23:49:47 CST)
  • Re: cgmd stability (Thu Feb 19 2009 - 03:15:56 CST)
• Wang Yf
  • how to use ethanol as solvent in namd for MD simulations ? (Fri Jul 31 2009 - 04:06:55 CDT)
  • Can I use another solvent rather than TI3P model in namd for MD simulations ? (Sat Jun 27 2009 - 22:30:04 CDT)
• Wang,Ying
  • (no subject) (Wed May 06 2009 - 13:50:12 CDT)
  • Re: smd direction (Mon Mar 30 2009 - 11:15:06 CDT)
  • smd direction (Mon Mar 30 2009 - 10:04:28 CDT)
  • how can i get the energy of a molecule of a whole system? (Tue Feb 17 2009 - 10:30:11 CST)
• wavedalla\_at_libero\.it
  • unsubscribe (Sun Jun 28 2009 - 09:49:09 CDT)
• wayj86 wayj86
  • Would my simulation setting affect the result? About the parameter "fixedAtomsForces" (Fri Aug 07 2009 - 05:51:42 CDT)
  • Re: An outlier appear on the curve of RMSD (Sun Jul 26 2009 - 20:42:13 CDT)
  • An outlier appear on the curve of RMSD (Thu Jul 23 2009 - 22:37:04 CDT)
  • Re: My protein went out of the water box in SMD. Would it have a bad effect on the result? (Tue Jun 30 2009 - 03:36:49 CDT)
  • My protein went out of the water box in SMD. Would it have a bad effect on the result? (Fri Jun 26 2009 - 03:02:46 CDT)
• Wei Chen
  • Re: AMBER force field in NAMD (Fri Sep 10 2010 - 12:48:15 CDT)
  • Re: Restarting A NAMD job with velocity file (Mon Mar 22 2010 - 16:25:50 CDT)
• Wei Huang
  • Problems with tcl scripts for REMD simulation (Fri Apr 16 2010 - 15:41:25 CDT)
• wenchangyu2006_at_gmail.com
  • ERROR: Atoms moving too fast with RBCG model (Wed Nov 24 2010 - 10:00:57 CST)
  • save trajectory only for two residues (Tue Jul 06 2010 - 08:13:42 CDT)
  • Pressure profile calculation problem (Tue Mar 23 2010 - 15:38:56 CDT)
• Wendy González
  • reloadCharges command (Wed Nov 24 2010 - 13:35:07 CST)
  • MD simulations increasing electrostatic potential of a certain residue (Tue Nov 16 2010 - 16:35:06 CST)
  • Symmetry in NAMD, how to achieve during a MD simulation? (Wed Oct 27 2010 - 10:46:03 CDT)
  • Enhance electrostatic interactions? (Thu Oct 21 2010 - 07:32:46 CDT)
  • Re: Restart MD from a certain point? (Thu Oct 21 2010 - 07:22:24 CDT)
  • Restart MD from a certain point? (Thu Oct 14 2010 - 07:45:48 CDT)
  • Minimization convergence (Thu Sep 02 2010 - 15:55:19 CDT)
  • Version 2.7 problems! (Thu Aug 26 2010 - 11:55:47 CDT)
• Wenyu Zhong
  • Re: which portions of NAMD are CUDA accelerated? (Wed Dec 09 2009 - 23:45:54 CST)
  • Re: which portions of NAMD are CUDA accelerated? (Wed Dec 09 2009 - 00:29:25 CST)
• Werner Crous
  • Re: Namd using Charmm restart files (Fri Oct 15 2010 - 08:55:56 CDT)
  • Re: FATAL ERROR:BAD GLOBAL EXCLUSION COUNT:Please help (Thu Mar 18 2010 - 04:29:55 CDT)
  • Re: FATAL ERROR:BAD GLOBAL EXCLUSION COUNT:Please help (Thu Mar 18 2010 - 04:23:55 CDT)
  • FATAL ERROR:BAD GLOBAL EXCLUSION COUNT:Please help (Sat Mar 13 2010 - 10:22:47 CST)
  • Re: NVT with truncated octahedron or with sphere? (Wed Sep 16 2009 - 06:04:31 CDT)
  • NVT with truncated octahedron or with sphere? (Tue Sep 15 2009 - 03:03:06 CDT)
• Xavier Deupi
  • Intel 11 compilers (Fri Jul 10 2009 - 08:52:58 CDT)
• Xiang Yu
  • force field for replica exchange with NAMD (Wed Oct 27 2010 - 23:06:32 CDT)
  • Force field for replica (Thu Oct 28 2010 - 09:12:25 CDT)
• Xiao Ju Zhang
  • NAMD cal with AMBER forces: Polarizable parameters in AMBER (Thu Dec 16 2010 - 13:21:01 CST)
• xiaoguang liu
  • Performance peoblem about NAMD-CUDA benchmarks (Sun Apr 11 2010 - 06:53:16 CDT)
• xiaojing gong
  • NAMD on GPU (Thu Jun 04 2009 - 02:53:18 CDT)
  • Compile Problem (Thu Apr 23 2009 - 07:42:51 CDT)
• Xu Dong
  • A beginner's question for using NAMD to do cell membrane simulation and molecular transportation (Sat Feb 21 2009 - 14:23:49 CST)
• Xu, Jiancong
  • running NAMD on Kraken Cray-XT4 (Thu Jan 29 2009 - 15:44:58 CST)
• Xueqing Zou
  • Re: simulating DNA using namd:: (Tue Apr 20 2010 - 09:48:46 CDT)
  • Re: how to get psf files of DNA but not RNA with psfgen? (Thu Sep 17 2009 - 09:52:19 CDT)
• xyhu1127
  • error of the energy output when equilibration (Thu Jan 14 2010 - 19:17:18 CST)
• y_ja
  • Q=B4=D7=D4y=5Fja@163.com=B5=C4=D3=CA=BC=FE?= (Mon Apr 19 2010 - 02:09:29 CDT)
• y_ja_at_163.com
  • Re: colvar: atom group defn. fails (Fri Apr 16 2010 - 05:35:46 CDT)
  • Re:Re: Generate missing atoms of a coarse grained structure (Sun Apr 04 2010 - 08:25:06 CDT)
• yandong Huang
  • Re: Re: Allowed CMAP dimensions (Tue Dec 28 2010 - 03:39:33 CST)
  • grid-based correction map (Thu Aug 12 2010 - 08:52:33 CDT)
• Yang
  • How to fix relative position of a group (Tue Oct 13 2009 - 15:40:53 CDT)
• Yang Gao
  • Problems about FEP simulation (Fri May 21 2010 - 11:03:08 CDT)
• Yang MIngjun
  • CMAP in NAMD output (Mon Jan 04 2010 - 01:50:47 CST)
  • Re: RE: Fw: Re: Re: How to read trajectory within CHARMM generated by NAMD (Thu Dec 31 2009 - 04:18:13 CST)
  • Fw: Re: Re: How to read trajectory within CHARMM generated by NAMD (Sun Dec 27 2009 - 20:06:44 CST)
  • How to read trajectory within CHARMM generated by NAMD (Sun Dec 27 2009 - 01:36:53 CST)
  • Re: CHARMM to NAMD (Thu Sep 03 2009 - 01:37:21 CDT)
  • CHARMM to NAMD (Tue Sep 01 2009 - 09:03:13 CDT)
  • About SMD (Tue Aug 11 2009 - 22:11:51 CDT)
• ydhuang2727
  • Re:Re: Re: Re:Re: Re: Re: Re: Dielectric Constant (Wed May 05 2010 - 09:45:20 CDT)
  • Re:Re: Re: Re: Re: Dielectric Constant (Sat May 01 2010 - 08:03:01 CDT)
  • Re:Re: Re: Re: Dielectric Constant (Thu Apr 29 2010 - 20:59:23 CDT)
  • Re:Re: Re: Dielectric Constant (Thu Apr 29 2010 - 07:39:49 CDT)
  • Re:Re: Re: Dielectric Constant (Thu Apr 29 2010 - 01:19:46 CDT)
  • Re:Re: Dielectric Constant (Wed Apr 28 2010 - 22:54:30 CDT)
  • Dielectric Constant (Tue Apr 27 2010 - 20:23:11 CDT)
  • How to acetylate at the N terminus and amidate at the C terminus (Tue Dec 22 2009 - 21:10:45 CST)
  • how to simulate a protein-ligand complex ? (Tue Aug 11 2009 - 08:29:25 CDT)
  • How to do a complex dynamics simulation (Wed Aug 05 2009 - 03:25:10 CDT)
  • protein collapsing problem (Sun Jul 05 2009 - 20:12:38 CDT)
  • Protein collpasing problem! (Mon Jun 29 2009 - 01:12:47 CDT)
  • protein collapsing problem! (Thu Jun 25 2009 - 00:08:29 CDT)
  • running namd2.7 problem (Thu May 07 2009 - 01:23:46 CDT)
  • running problem (Thu Apr 30 2009 - 05:08:22 CDT)
• yi jiang
  • Re: Regarding answering questions in a forum. Re: Langevin process in NAMD tutorial (Mon Oct 11 2010 - 20:42:05 CDT)
  • Langevin process in NAMD tutorial (Mon Oct 11 2010 - 11:14:22 CDT)
• Yi Shang
  • Re: inconsistence in NAMD and AMBER energy (Tue Jul 21 2009 - 11:04:18 CDT)
  • Re: inconsistence in NAMD and AMBER energy (Tue Jul 21 2009 - 10:22:45 CDT)
  • Re: inconsistence in NAMD and AMBER energy (Tue Jul 21 2009 - 09:56:04 CDT)
  • inconsistence in NAMD and AMBER energy (Mon Jul 20 2009 - 18:31:47 CDT)
• ying yu
  • a question about modifying the NAMD input file (Mon Oct 25 2010 - 12:06:50 CDT)
• Yinglong Miao
  • implicit solvent model in NAMD? (Fri Jul 03 2009 - 15:18:17 CDT)
  • Re: vmd-l: How to specify processors for running VMD on a cluster? (Tue Feb 10 2009 - 15:21:34 CST)
  • Re: any experiences with executing parallel NAMD in a NAMD simulation (Tue Feb 10 2009 - 10:13:56 CST)
  • How to specify processors for running VMD on a cluster? (Tue Feb 10 2009 - 10:45:27 CST)
  • Re: any experiences with executing parallel NAMD in a NAMD simulation (Mon Feb 09 2009 - 22:26:37 CST)
  • Re: any experiences with executing parallel NAMD in a NAMD simulation (Mon Feb 09 2009 - 19:56:44 CST)
  • any experiences with executing parallel NAMD in a NAMD simulation (Mon Feb 09 2009 - 15:59:07 CST)
• Yingzhe Liu
  • Force field for PDMS (Fri Dec 31 2010 - 20:32:20 CST)
  • The outputs of REMD were suspended (Sun Dec 19 2010 - 08:21:11 CST)
  • Problem of running NAMD (Wed Dec 08 2010 - 04:37:45 CST)
  • Problem of running NAMD (Tue Dec 07 2010 - 05:16:35 CST)
• Yoav Beck
  • SMD on membrane protein. (Sun Aug 23 2009 - 09:04:55 CDT)
  • Re: Minimization issue. (Wed Aug 19 2009 - 07:11:21 CDT)
  • Minimization issue. (Mon Aug 17 2009 - 10:20:41 CDT)
  • Re: FATAL ERROR: Tried to find atom type on node other than node 0 (Mon Aug 17 2009 - 05:04:48 CDT)
  • FATAL ERROR: Tried to find atom type on node other than node 0 (Thu Aug 13 2009 - 09:21:38 CDT)
  • Re: Proteine-membrane simulation. (Thu Aug 06 2009 - 07:46:05 CDT)
  • Proteine-membrane simulation. (Tue Aug 04 2009 - 10:08:55 CDT)
• Yogesh
  • charm++ build problem (Thu May 14 2009 - 08:24:42 CDT)
• Yogesh Aher
  • 32 bit + 64 bit mixed architecture problem (Wed Nov 11 2009 - 10:17:27 CST)
  • Incorrect Atom Count in binary file (Tue Oct 13 2009 - 03:42:44 CDT)
  • Re: Bad global exclusion count (Wed Jul 15 2009 - 09:49:33 CDT)
  • Bad global exclusion count (Mon Jul 13 2009 - 05:57:18 CDT)
  • lamboot -v nodelist (Wed Jun 03 2009 - 09:49:15 CDT)
  • FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE (Fri May 29 2009 - 09:34:13 CDT)
• yudaqi
  • Re: AW: update: segmentation faults with AMBER topology and RAMD tcl scripts (Wed Feb 24 2010 - 06:37:25 CST)
  • Does amber force field in NAMD 2.7b2 work stable? (Fri Dec 18 2009 - 21:02:50 CST)
• Yudong Sun
  • Re: Nightly build version: Parallel IO can not be used with langevin On (Wed May 19 2010 - 07:01:51 CDT)
  • Nightly build version: Parallel IO can not be used with langevin On (Fri May 07 2010 - 06:21:57 CDT)
• yuhuihe_at_ime.pku.edu.cn
  • on NAMD simulation of DNA translocation through nanopores (Sun Jul 19 2009 - 07:27:55 CDT)
• yun luo
  • question about FEP soft-core (Mon Sep 14 2009 - 15:03:16 CDT)
  • Re: use tclForce and tclBC together? (Tue Jul 28 2009 - 14:00:58 CDT)
  • use tclForce and tclBC together? (Mon Jul 27 2009 - 20:14:45 CDT)
  • Re: TMD for moving ion across membrane (Tue May 26 2009 - 13:50:55 CDT)
  • TMD for moving ion across membrane (Mon May 25 2009 - 12:10:59 CDT)
  • Re: dummy atom mass changed (Tue May 12 2009 - 11:10:11 CDT)
  • Re: soft-core FEP in namd 2.7b (Mon May 11 2009 - 12:31:49 CDT)
  • Re: dummy atom mass changed (Thu May 07 2009 - 11:18:43 CDT)
  • Re: dummy atom mass changed (Wed May 06 2009 - 11:50:06 CDT)
  • Re: dummy atom mass changed (Tue May 05 2009 - 15:26:46 CDT)
  • Re: dummy atom mass changed (Tue May 05 2009 - 12:19:05 CDT)
  • Re: dummy atom mass changed (Tue May 05 2009 - 11:49:06 CDT)
  • Re: dummy atom mass changed (Mon May 04 2009 - 16:24:59 CDT)
  • dummy atom mass changed (Mon May 04 2009 - 14:54:27 CDT)
• Yunlang Li
  • How to get the acceptance ratio in REMD (Mon Mar 09 2009 - 16:59:50 CDT)
• Yvonne.Westermaier_at_unige.ch
  • hydroxyls in phosphate group collapsing (Mon Jul 27 2009 - 09:41:20 CDT)
• yzliu
  • Re: FATAL ERROR: Tried to find atom type on node other than node 0 (Sat Aug 15 2009 - 11:06:10 CDT)
• Zhang, Jiong (MU-Student)
  • about protein phosphorylation (Wed Sep 22 2010 - 11:59:36 CDT)
  • (no subject) (Tue Sep 21 2010 - 20:01:38 CDT)
• zhangliqun
  • my problem was solved (Wed Aug 18 2010 - 15:39:36 CDT)
  • about recentering of namd trajectory (Tue Aug 17 2010 - 10:50:54 CDT)
• zhngbn_at_gmail.com
  • compiling error of NAMD2.7b1 (Sun Apr 19 2009 - 03:02:44 CDT)
• Ziemys, Arturas
  • rotational restrains (Fri Jun 04 2010 - 13:34:18 CDT)
  • RE: ABF (NAMD 2.7x) speed ? (Wed May 26 2010 - 07:24:54 CDT)
  • ABF (NAMD 2.7x) speed ? (Tue May 25 2010 - 09:51:33 CDT)
  • ABF question (Tue May 25 2010 - 08:51:39 CDT)
  • sucrose top/par (Mon Feb 22 2010 - 13:41:14 CST)
  • electric field unit conversion (Wed Feb 17 2010 - 09:45:46 CST)
  • pressure profile (Thu Dec 03 2009 - 16:22:41 CST)
  • CMAP w/ D-amino acid (Fri Oct 02 2009 - 10:51:24 CDT)
  • ABF + LES (Thu Oct 01 2009 - 11:45:38 CDT)
  • question on forces / theory (Tue Aug 25 2009 - 22:07:07 CDT)
  • RE: ABF simulations (Tue Jun 23 2009 - 13:04:24 CDT)
  • triazol parameters (Thu May 21 2009 - 16:01:53 CDT)
• Zumot, Elia Nabil
  • RE: possible bug with NAMD Energy plugin (Tue Aug 31 2010 - 18:00:17 CDT)
  • RE: possible bug with NAMD Energy plugin (Tue Aug 24 2010 - 12:15:35 CDT)
  • possible bug with NAMD Energy plugin (Mon Aug 23 2010 - 15:19:07 CDT)
  • RE: how to save a DCD file without water in NAMD ? (Thu Aug 12 2010 - 16:52:51 CDT)
  • NAMD on Ranger at Teragrid (Thu Jun 10 2010 - 15:08:16 CDT)
  • RE: job script for Kraken (Thu Mar 11 2010 - 16:04:56 CST)
  • RE: error (Wed Mar 03 2010 - 08:23:41 CST)
  • job script for Kraken (Wed Mar 03 2010 - 09:14:15 CST)
  • RE: creating an output file from a dcd file (Tue Mar 02 2010 - 12:52:17 CST)
  • atom charges for protonated carboxyl termini (Mon Feb 22 2010 - 14:48:59 CST)
  • RE: extracting info from output files (Tue Sep 22 2009 - 16:22:40 CDT)
• «J ¦¼¯Â
  • About APBS calculation (Thu Oct 29 2009 - 09:22:48 CDT)
  • About DPD (Sun Aug 23 2009 - 09:52:59 CDT)
  • Questions from new user (Thu Aug 20 2009 - 21:57:05 CDT)
• ºÎع»Ô
  • Why do different versions of NAMD deserve different simulation results? (Mon Dec 20 2010 - 06:03:03 CST)
  • Asking for some sample PDB and PSF files of carbon nanotube (Wed Dec 15 2010 - 04:19:22 CST)
  • parameters for graphene nanoribbons annealed by hydrogen (Tue Jun 29 2010 - 03:09:15 CDT)
  • Do top_all27_prot_na.inp and cornell.prm share the same naming rules of atom types? (Tue Sep 22 2009 - 02:51:56 CDT)
  • how to get psf files of DNA but not RNA with psfgen? (Thu Sep 17 2009 - 06:25:02 CDT)
• Àîè­
  • What decides the pulling direction in SMD? (Fri Jun 12 2009 - 02:35:15 CDT)
• ÁõÅô
  • Re: about the memery lock in openMPI on infiniband (Mon Mar 09 2009 - 04:27:11 CDT)
  • about the memery lock in openMPI on infiniband (Sun Mar 08 2009 - 03:55:40 CDT)
  • paramater about Amphotericin B (Fri Feb 27 2009 - 03:25:46 CST)
• ÁõÏþ¹â
  • FW: namd cuda with geforce 470 (fermi) gpu fatal error at runtime (Sun Jun 06 2010 - 06:50:56 CDT)
• ÁõÓý
  • Fwd:Re: ABF-Zcoord: (Wed Feb 04 2009 - 22:04:40 CST)
  • ABF:restraint in free energy calculation in Zcoord-method (Tue Feb 03 2009 - 22:15:42 CST)
  • ABF-Zcoord: (Tue Feb 03 2009 - 07:29:23 CST)
• ä¿žç¿”
  • Re: force field for replica exchange with NAMD (Thu Oct 28 2010 - 17:56:58 CDT)
• 张鋆
  • (no subject) (Fri Apr 16 2010 - 22:04:17 CDT)
• ÅÓÑ©ÇÛ Pang Xueqin
  • for your suggestions on Pressure Control of transmembrane protein (GPCR) (Wed Apr 07 2010 - 03:30:20 CDT)
  • how to get .coor .vel and .xsc for a .dcd file (Wed Jan 27 2010 - 08:42:44 CST)
• 林星雨
  • specific site-ion LJ parameters and CHARMM general force field (Thu Aug 19 2010 - 05:53:55 CDT)
  • Re: a question about NAMD TI (Mon Jun 21 2010 - 04:17:57 CDT)
  • a question about NAMD TI (Sun Jun 20 2010 - 22:26:48 CDT)
  • water "flying out of the box" (Fri Mar 19 2010 - 06:06:30 CDT)
• 海清 æ¢�
  • questions about Constant Pressure Control (variable volume) (Thu Apr 01 2010 - 02:18:11 CDT)
  • compile NAMD 2.7b1 on Intel Xeon(R) infiniband cluster (Sat Apr 25 2009 - 01:44:24 CDT)
• ç’€ æ�Ž
  • FATAL ERROR: Duplicate bond (Wed Mar 11 2009 - 02:45:17 CDT)
• Íõ—²
  • Input/output error (Tue May 18 2010 - 01:55:20 CDT)
  • NAMD complain about gromacs ff parameter ATOMTYPES definition (Wed Apr 28 2010 - 22:36:10 CDT)
  • How to use harmonic restraint parameter for 2 selection of atoms (Thu Apr 15 2010 - 02:00:06 CDT)
  • How to convert the GROMOS parameter unit into charmm22 style (Wed Jan 20 2010 - 00:24:27 CST)
  • How to get the coordinate of a certain atom with tcl in the config file? (Mon Dec 28 2009 - 04:14:23 CST)
  • subscribe (Mon Dec 28 2009 - 02:56:07 CST)
• ÓáÏè
  • RE: force field for replica exchange with NAMD (Thu Oct 28 2010 - 15:40:52 CDT)
• ÕÅÄþ
  • A problem of the forces-tutorial (Thu Apr 08 2010 - 07:18:33 CDT)
• ÖÜÎIJý
  • Ions conversion from atomic model to coarse grained model (Wed Nov 10 2010 - 11:41:41 CST)
  • unknown path type LSN (Tue May 26 2009 - 07:48:49 CDT)
  • NAMD 2.7b1 running problem (Wed May 20 2009 - 05:19:19 CDT)
  • Metadynamics in NAMD (Mon Apr 20 2009 - 05:50:42 CDT)
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