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NAMD-L: By Author

By Author

4370 messages sorted by: [ date ] [ thread ] [ subject ] [ attachment ]
About this archive

Starting: Fri Jan 01 2010 - 09:55:54 CST
Ending: Sat Dec 31 2011 - 05:23:47 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 set the right PME parameters for amber's prmtop and inpcrd files? (Wed Jan 26 2011 - 04:34:33 CST)
  • How to set the right PME parameters for amber's prmtop and inpcrd files? (Wed Jan 26 2011 - 04:17:32 CST)
  • 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)
• Aakash C R
  • (no subject) (Sat Aug 28 2010 - 04:35:48 CDT)
  • REGARDING Topology file (Fri Apr 09 2010 - 16:57:31 CDT)
• AB
  • about D amino acid (Fri Jul 29 2011 - 03:50:16 CDT)
  • is there any difference between non-constrained equilibrium and normal MD production? (Mon Jul 25 2011 - 13:04:35 CDT)
  • how to generate transparent figures? (Sat Jul 23 2011 - 09:59:07 CDT)
  • how to calculate partial charge for ligand based on CHARMM principle? (Thu Jul 21 2011 - 11:49:39 CDT)
• Ada Sedova
  • aligning two molecules by principal axes of inertia using measure.c (Mon Jun 20 2011 - 08:18:41 CDT)
• Ada Zhan
  • RE: question on residue rmsd.tcl (Mon Jun 06 2011 - 14:25:36 CDT)
  • RE: question on residue rmsd.tcl (Thu Jun 02 2011 - 14:06:00 CDT)
  • RE: heat annealing conf file (Thu Jun 02 2011 - 14:02:06 CDT)
  • 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
  • Forcefield for simulating peptide with heparin!!!! (Mon May 02 2011 - 07:24:56 CDT)
  • 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)
• Adrian Jasiñski
  • NAG simulation problem with CPS (Wed Jan 05 2011 - 05:36:00 CST)
• Agostino Bruno
  • Problem with Targeted molecular dynamics (Sun Feb 28 2010 - 10:07:25 CST)
• Ahlam Al-Rawi
  • Invitation to connect on LinkedIn (Thu Sep 15 2011 - 16:11:12 CDT)
• ais_at_fh.huji.ac.il
  • water box deformation (Wed Feb 09 2011 - 09:47:27 CST)
• Ajasja LjubetiÄ�
  • Re: Trouble running NAMD on win7 (Mon Sep 26 2011 - 03:09:19 CDT)
  • Re: SMD (Mon Sep 12 2011 - 04:07:52 CDT)
  • Re: mean square displacement (Mon Sep 05 2011 - 08:22:55 CDT)
  • Re: Suspend NAMD (to RAM) (Sat Jul 30 2011 - 09:44:23 CDT)
  • Re: Dividing a 2D ABF simulations into regions (on nodes with different speeds) (Fri Jul 29 2011 - 11:56:17 CDT)
  • Dividing a 2D ABF simulations into regions (on nodes with different speeds) (Fri Jul 29 2011 - 04:44:38 CDT)
  • Re: DPPC membrane (Thu Jul 28 2011 - 05:21:10 CDT)
  • Re: Setting integrator parameters for ABF (Wed Jul 27 2011 - 14:01:31 CDT)
  • Setting integrator parameters for ABF (Wed Jul 27 2011 - 12:49:24 CDT)
  • Re: Controlling fans on a GTX 560 ti (Fri Jul 22 2011 - 09:12:29 CDT)
  • Controlling fans on a GTX 560 ti (Fri Jul 22 2011 - 05:24:26 CDT)
  • Suspend NAMD (to RAM) (Wed Jul 20 2011 - 17:10:06 CDT)
  • Re: Win64-MPI (Tue Jul 12 2011 - 08:24:28 CDT)
  • Re: Fixed COM (Tue Jul 12 2011 - 08:11:04 CDT)
  • Re: Fixed COM (Mon Jul 11 2011 - 14:37:43 CDT)
  • Re: Difference between cwd and cd (Wed Jul 06 2011 - 08:59:30 CDT)
  • Re: membrane simulation ERROR rattle algorithm (Wed Jul 06 2011 - 06:37:10 CDT)
  • Transferring environment variables when using charmrun (Wed Jul 06 2011 - 05:08:54 CDT)
  • Difference between cwd and cd (Wed Jul 06 2011 - 04:43:43 CDT)
  • Re: membrane simulation ERROR rattle algorithm (Tue Jul 05 2011 - 13:40:44 CDT)
  • Re: membrane simulation ERROR rattle algorithm (Tue Jul 05 2011 - 12:54:40 CDT)
  • Re: membrane simulation ERROR rattle algorithm (Tue Jul 05 2011 - 12:01:53 CDT)
  • Re: Win64-MPI (Tue Jul 05 2011 - 02:11:25 CDT)
  • Re: vmd-l: protein-water RDF (Mon Jun 27 2011 - 03:33:13 CDT)
  • Re: vmd-l: protein-water RDF (Mon Jun 27 2011 - 03:29:44 CDT)
  • Re: CUDA limitations (Fri Jun 24 2011 - 07:37:13 CDT)
  • Re: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR C H (ATOMS 2 1) (Fri Jun 24 2011 - 03:46:18 CDT)
  • Re: slow heating md (Thu Jun 23 2011 - 06:32:24 CDT)
  • Re: aligning two molecules by principal axes of inertia using measure.c (Mon Jun 20 2011 - 09:40:20 CDT)
  • Re: rescaling velocity (Fri Jun 17 2011 - 13:14:32 CDT)
  • Re: NAMD crashes with OpenMPI/OpenMX (Fri Jun 17 2011 - 05:10:06 CDT)
  • Re: hi all (Thu Jun 16 2011 - 07:29:53 CDT)
  • Re: NAMD crashes with OpenMPI/OpenMX (Thu Jun 16 2011 - 06:23:36 CDT)
  • Re: cuda error cudastreamcreate (Tue Jun 14 2011 - 08:23:23 CDT)
  • Re: changing solventDielectric in GBIS (Mon Jun 13 2011 - 07:50:42 CDT)
  • Re: max number of CPU PEs per GPU? (Fri Jun 10 2011 - 15:17:43 CDT)
  • Re: max number of CPU PEs per GPU? (Fri Jun 10 2011 - 06:50:44 CDT)
  • Re: CUDA limitations (Thu Jun 09 2011 - 15:32:09 CDT)
  • Re: CthCreate failed to create fiber (Thu Jun 09 2011 - 15:29:25 CDT)
  • Re: CthCreate failed to create fiber (Tue Jun 07 2011 - 13:57:00 CDT)
  • Re: Advice on buying GPUs (Mon Jun 06 2011 - 06:39:31 CDT)
  • Re: Alpha P.M.F. with NAMD 2.8 (Fri Jun 03 2011 - 07:05:47 CDT)
  • Re: Advice on buying GPUs (Thu Jun 02 2011 - 03:13:10 CDT)
  • Advice on buying GPUs (Wed Jun 01 2011 - 09:43:24 CDT)
  • Re: NAMD crashes when writing restart file and dcdfreq is 1 (Tue May 24 2011 - 07:25:25 CDT)
  • Re: error in the orientationAngle (Sun May 22 2011 - 05:48:29 CDT)
  • Re: NAMD crashes when writing restart file and dcdfreq is 1 (Fri May 20 2011 - 05:25:31 CDT)
  • NAMD crashes when writing restart file and dcdfreq is 1 (Fri May 20 2011 - 05:16:30 CDT)
  • Re: CUDA limitations (Fri May 13 2011 - 07:00:49 CDT)
  • Re: ABF simulation with extendedLagrangian on keeps crashing (Thu May 12 2011 - 03:55:03 CDT)
  • CUDA limitations (Thu May 12 2011 - 03:07:02 CDT)
  • Re: what will be the best way to simulate substrate interaction only within a binding pocket of a large protein. (Tue May 10 2011 - 15:57:58 CDT)
  • Re: A newer version of win32 libraries (Tue May 10 2011 - 15:55:06 CDT)
  • Re: print center of mass (Tue May 10 2011 - 11:10:48 CDT)
  • A newer version of win32 libraries (Mon May 09 2011 - 07:35:47 CDT)
  • Re: ABF simulation with extendedLagrangian on keeps crashing (Thu May 05 2011 - 15:50:34 CDT)
  • Re: ABF simulation with extendedLagrangian on keeps crashing (Thu May 05 2011 - 03:38:16 CDT)
  • Re: ABF simulation with extendedLagrangian on keeps crashing (Wed May 04 2011 - 06:31:58 CDT)
  • Re: alpha pmf (Wed May 04 2011 - 03:04:14 CDT)
  • Re: ABF simulation with extendedLagrangian on keeps crashing (Tue May 03 2011 - 11:02:12 CDT)
  • Re: ABF simulation with extendedLagrangian on keeps crashing (Tue May 03 2011 - 08:11:26 CDT)
  • Re: ABF simulation with extendedLagrangian on keeps crashing (Fri Apr 22 2011 - 09:27:24 CDT)
  • Re: ABF simulation with extendedLagrangian on keeps crashing (Fri Apr 22 2011 - 03:34:29 CDT)
  • Re: ABF simulation with extendedLagrangian on keeps crashing (Thu Apr 21 2011 - 06:30:47 CDT)
  • Re: ABF simulation with extendedLagrangian on keeps crashing (Tue Apr 19 2011 - 12:05:23 CDT)
  • Re: ABF simulation with extendedLagrangian on keeps crashing (Tue Apr 19 2011 - 11:05:09 CDT)
  • ABF simulation with extendedLagrangian on keeps crashing (Tue Apr 19 2011 - 10:55:57 CDT)
  • Reduce the frequency of load balancer output (Tue Apr 19 2011 - 09:23:04 CDT)
  • Re: problem in restarting (Thu Apr 14 2011 - 10:28:19 CDT)
  • NAMD feture request (Wed Apr 13 2011 - 09:46:07 CDT)
  • Re: Incompatibility between colvars and tclforces? (Wed Mar 30 2011 - 06:21:23 CDT)
  • Re: GBIS and ABF (Mon Mar 28 2011 - 11:34:07 CDT)
  • Re: Rotate two linked proteins against each other and calculate energy profile (Mon Mar 28 2011 - 09:30:28 CDT)
  • Re: Advisable limit on the number of quadrants a 2D ABF simulation can be split. (Mon Mar 28 2011 - 09:06:40 CDT)
  • Re: GBIS and ABF (Mon Mar 28 2011 - 08:37:36 CDT)
  • Re: vmd-l: How to maximize the VMD display window (Fri Mar 25 2011 - 07:48:24 CDT)
  • Advisable limit on the number of quadrants a 2D ABF simulation can be split. (Fri Mar 25 2011 - 04:52:09 CDT)
  • Re: how to write the bond across the cell boundary (Fri Mar 25 2011 - 03:44:41 CDT)
  • Re: question about force information (Thu Mar 24 2011 - 14:22:10 CDT)
  • Re: GBIS and ABF (Wed Mar 23 2011 - 14:17:48 CDT)
  • Re: how obtain .xst form .dcd file? (Wed Mar 23 2011 - 14:11:27 CDT)
  • Re: Rotate two linked proteins against each other and calculate energy profile (Mon Mar 21 2011 - 03:43:55 CDT)
  • Re: Rotate two linked proteins against each other and calculate energy profile (Tue Mar 15 2011 - 16:56:39 CDT)
  • Re: colvars PMF history problem (Wed Mar 09 2011 - 03:40:18 CST)
  • Re: Job scheduling (managing) software recommendation (Wed Mar 09 2011 - 03:15:41 CST)
  • Re: Job scheduling (managing) software recommendation (Mon Mar 07 2011 - 15:13:48 CST)
  • Re: colvars PMF history problem (Mon Mar 07 2011 - 15:01:08 CST)
  • Re: colvars PMF history problem (Mon Mar 07 2011 - 14:50:06 CST)
  • colvars PMF history problem (Mon Mar 07 2011 - 08:43:08 CST)
  • Job scheduling (managing) software recommendation (Mon Mar 07 2011 - 05:36:42 CST)
  • Re: membrane equilibration (Fri Mar 04 2011 - 05:09:19 CST)
  • Re: energy jump between minimization and simulation (Wed Feb 16 2011 - 03:27:53 CST)
  • New colvar feature request -- angleXY (Mon Feb 14 2011 - 07:19:46 CST)
  • Re: Equilibration when splitting an ABF calculation (Fri Jan 28 2011 - 06:26:58 CST)
  • Re: Equilibration when splitting an ABF calculation (Thu Jan 27 2011 - 08:48:48 CST)
  • Equilibration when splitting an ABF calculation (Thu Jan 27 2011 - 06:25:04 CST)
  • Re: bond lengths angles in namd (Thu Jan 27 2011 - 07:14:26 CST)
  • Re: Feature request for the colvars module -- TCL syntax (Mon Jan 24 2011 - 08:16:01 CST)
  • Re: distance calculation between atoms of two segments (Sat Jan 22 2011 - 13:48:54 CST)
  • Re: Various practical colvar module related questions (Thu Jan 20 2011 - 09:12:30 CST)
  • Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein (Wed Jan 19 2011 - 10:01:42 CST)
  • Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein (Wed Jan 19 2011 - 06:53:41 CST)
  • Various practical colvar module related questions (Tue Jan 18 2011 - 11:31:46 CST)
  • Re: Feature request for the colvars module -- TCL syntax (Tue Jan 18 2011 - 11:44:54 CST)
  • Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein (Tue Jan 18 2011 - 08:40:56 CST)
  • Re: Feature request for the colvars module -- TCL syntax (Tue Jan 18 2011 - 07:17:54 CST)
  • Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein (Mon Jan 17 2011 - 09:56:28 CST)
  • Feature request for the colvars module -- TCL syntax (Mon Jan 17 2011 - 09:26:47 CST)
  • Re: Running bias exchange metadynamics simulations with NAMD (Mon Jan 17 2011 - 08:40:11 CST)
  • Re: Running bias exchange metadynamics simulations with NAMD (Fri Jan 14 2011 - 09:31:49 CST)
  • Re: Running bias exchange metadynamics simulations with NAMD (Sun Jan 02 2011 - 15:03:48 CST)
  • 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)
• Ajasja Ljubetiè
  • Re: Advice on buying GPUs (Thu Jun 02 2011 - 09:46:55 CDT)
  • Re: Advice on buying GPUs (Thu Jun 02 2011 - 08:27:47 CDT)
  • Re: ABF simulation with extendedLagrangian on keeps crashing (Wed Apr 20 2011 - 09:22:21 CDT)
  • Re: ABF simulation with extendedLagrangian on keeps crashing (Tue Apr 19 2011 - 12:43:12 CDT)
  • Re: colvars PMF history problem (Mon Mar 07 2011 - 09:43:02 CST)
  • Re: New colvar feature request -- angleXY (Mon Feb 14 2011 - 16:04:27 CST)
  • Re: New colvar feature request -- angleXY (Mon Feb 14 2011 - 10:13:28 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)
• alamng_at_uci.edu
  • Replica Exchange (Fri Apr 15 2011 - 04:35:47 CDT)
• AlbertAlbert
  • where can I find parameters for t-BuO(C=O)NH-? (Tue Jul 12 2011 - 12:33:39 CDT)
  • does any body have the parameter file for aldehyde group? (Fri Jul 08 2011 - 01:34:22 CDT)
• albus hawking
  • Relationship between High temperature and the boiling point of water (Wed Aug 17 2011 - 13:29:56 CDT)
  • NAMD-l: Get the PDB file from Steered Molecular Dynamics output files (Tue Jun 14 2011 - 22:56:55 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)
• Alessandro Cembran
  • NAMD on Shared Memory (Altix UV 1000) (Thu Dec 02 2010 - 18:11:45 CST)
• Alex
  • Differences between ABF and metadynamics (Tue Sep 13 2011 - 05:13:34 CDT)
• Alex Curutiu
  • specific heat - instability (Sun Aug 15 2010 - 05:49:52 CDT)
• alex digenova bravo
  • Re: new error in NAMD2.8b1 with fixedAtoms (Fri May 13 2011 - 23:19:54 CDT)
• Alex Liu
  • Fw: topology file for nucleic acids including ammonium ion (Mon Mar 21 2011 - 16:40:55 CDT)
  • Fix atoms-Colvars (Thu Jan 06 2011 - 15:46:14 CST)
  • Distance XY-colvars (Tue Jan 04 2011 - 15:56:56 CST)
  • .colvars.state file in ABF (Mon Jan 03 2011 - 15:53:45 CST)
  • 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
  • Re: Relative RMSD constraint (Wed Aug 17 2011 - 02:31:56 CDT)
  • Truncated octahedron - unwrapping the trajectory etc (Tue Aug 16 2011 - 21:46:22 CDT)
  • 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)
• Alexandra Nemkevich
  • (no subject) (Thu Feb 03 2011 - 04:30:50 CST)
• 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
  • Possibility of modifying the non-bonded terms of the potential (Fri Jul 08 2011 - 16:58:44 CDT)
• Ali Khanlarkhani
  • NAMD on PS3 (Sat Aug 06 2011 - 11:02:22 CDT)
  • Fixed COM (Mon Jul 11 2011 - 13:30:32 CDT)
• alpertunga daðcan
  • CMAP dimension limited to 24 dimensions (Thu Mar 18 2010 - 21:42:03 CDT)
• amit banerjee
  • Re: Pico scale to nanoscale simulation....alteration if .conf files required (Mon Jul 25 2011 - 07:42:35 CDT)
  • Pico scale to nanoscale simulation....alteration if .conf files required (Sun Jul 17 2011 - 21:28:43 CDT)
  • Help required for nanoscale simulation (Wed Jul 13 2011 - 03:03:45 CDT)
  • Re: question on residue rmsd.tcl (Mon Jun 06 2011 - 00:18:48 CDT)
  • question on residue rmsd.tcl (Wed Jun 01 2011 - 22:49:17 CDT)
  • problem in distance.tcl (Wed Jun 01 2011 - 22:37:42 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)
• Ana Celia Vila Verde
  • example psf and pdb files for simulations with tip4p (Wed Mar 02 2011 - 12:21:44 CST)
  • using TIP4P 2005 in namd (Wed Feb 23 2011 - 11:57:03 CST)
• anas .
  • Building PSF file for protein with ions (Wed Sep 01 2010 - 05:22:50 CDT)
• Andrea Holfelder
  • Re: Margin Value in NAMD (Thu Sep 01 2011 - 03:09:09 CDT)
  • Re: Margin Value in NAMD (Wed Aug 31 2011 - 23:57:36 CDT)
  • Re: Dock a metal ion into a peptide/protein (Wed Aug 31 2011 - 21:51:27 CDT)
  • Margin Value in NAMD (Wed Aug 31 2011 - 21:42:05 CDT)
  • Dock a metal ion into a peptide/protein (Wed Aug 31 2011 - 14:29:39 CDT)
  • HETATM vs ATOM in .pdb file (Wed Aug 31 2011 - 04:56:35 CDT)
  • SASA of PBD files (Sat Aug 20 2011 - 04:11:25 CDT)
  • (no subject) (Thu Aug 18 2011 - 04:59:05 CDT)
  • RHDO lattice as a PBC unit Cell in NAMD (Thu Aug 18 2011 - 04:59:59 CDT)
  • PME Grid Settings and its significance relative to a cutoff value (Tue Aug 16 2011 - 15:07:14 CDT)
• 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 Colubri
  • Re: changing solventDielectric in GBIS (Mon Jun 13 2011 - 08:17:36 CDT)
  • changing solventDielectric in GBIS (Mon Jun 13 2011 - 07:36:41 CDT)
• Andres Morales
  • Andres Morales sent you a little gift (Sun Apr 11 2010 - 20:33:49 CDT)
• Andres Morales N
  • Area per lipid error (Mon Oct 17 2011 - 21:12:33 CDT)
  • Periodic cell has become too small for original patch grid!â€� (Thu Sep 29 2011 - 23:52:39 CDT)
  • RE: Temperature during membrane equilibration (Fri Sep 09 2011 - 20:57:36 CDT)
  • RE: Temperature during membrane equilibration (Thu Sep 08 2011 - 18:33:47 CDT)
  • Temperature during membrane equilibration (Wed Sep 07 2011 - 23:57:10 CDT)
  • Using 'Alignment to principal axes ' (Mon Aug 29 2011 - 00:38:44 CDT)
  • RE: Lipid bilayer equilibration: Periodic cell has become too small for original patch grid! (Mon Aug 08 2011 - 17:20:56 CDT)
  • Lipid bilayer equilibration: Periodic cell has become too small for original patch grid! (Sun Aug 07 2011 - 21:00:38 CDT)
  • RE: System net charge (Thu Aug 04 2011 - 23:43:11 CDT)
  • RE: System net charge (Tue Aug 02 2011 - 19:20:38 CDT)
  • System net charge (Fri Jul 29 2011 - 03:25:11 CDT)
  • RE: DPPC membrane (Fri Jul 29 2011 - 03:16:50 CDT)
  • DPPC membrane (Thu Jul 28 2011 - 01:29:36 CDT)
  • Membranes (Tue Jul 19 2011 - 15:46:54 CDT)
  • Equilibration (Tue Jul 19 2011 - 13:39:37 CDT)
  • RE: Bactenecine (Wed Mar 16 2011 - 14:22:09 CDT)
  • Bactenecine (Mon Mar 14 2011 - 23:11:05 CDT)
  • 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)
• Andrew Emerson
  • Re: Get number of timesteps from DCD via script (Tue Feb 08 2011 - 08:00:07 CST)
  • Re: REMD with IBM SP6 LoadLeveler (Mon Jan 24 2011 - 02:24:58 CST)
  • 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)
• Andy Somogyi
  • Memory leak patch (Tue Aug 23 2011 - 09:20:09 CDT)
  • Blue Waters (Tue Aug 09 2011 - 10:18:49 CDT)
  • Re: NAMD on PS3 (Sat Aug 06 2011 - 13:16:20 CDT)
  • Molecule2.C (Thu Jul 21 2011 - 11:45:11 CDT)
  • NAMD chares (Mon Jul 11 2011 - 10:35:17 CDT)
• 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: Help With colvars/abf Please (Sun Jan 30 2011 - 11:00:38 CST)
  • Help With colvars/abf Please (Sun Jan 30 2011 - 07:09:41 CST)
• Anirban Ghosh
  • Bioinformatics Symposium at C-DAC, Pune (Fri Sep 03 2010 - 00:41:23 CDT)
• Anna Dejardin
  • psfgen error (Wed Feb 03 2010 - 07:35:54 CST)
• Anna James
  • PBB File Format/Setup for PBC (Fri Aug 19 2011 - 07:24:11 CDT)
  • RE: (Tue Aug 16 2011 - 12:23:05 CDT)
  • RE: (Tue Aug 16 2011 - 09:20:49 CDT)
  • RE: (Tue Aug 16 2011 - 08:48:51 CDT)
  • (no subject) (Tue Aug 16 2011 - 08:38:14 CDT)
• Anthony Rey
  • Quick TCl scripting question (Wed Sep 21 2011 - 20:57:07 CDT)
  • Re: Bonds are too long after simulation (Wed Sep 07 2011 - 22:48:37 CDT)
  • Bonds are too long after simulation (Wed Sep 07 2011 - 10:32:11 CDT)
• 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)
• Anurag Sethi
  • Re: metadynamics combined with PCV (Fri Jun 03 2011 - 14:11:54 CDT)
  • metadynamics combined with PCV (Fri Jun 03 2011 - 12:14:18 CDT)
  • Re: dcd to trr using catdcd (Tue Mar 22 2011 - 02:03:56 CDT)
• Aoife Fogarty
  • Re: (NAMD2.7b1) loadtotalforces gives output even when there are no forces in system (Tue Mar 15 2011 - 13:15:04 CDT)
  • (NAMD2.7b1) loadtotalforces gives output even when there are no forces in system (Mon Mar 07 2011 - 03:43:14 CST)
• Arash Azari
  • ERROR: CUDA-enabled NAMD requires at least one patch per process (Wed Apr 27 2011 - 23:49:56 CDT)
• Armen H. Poghosyan
  • About viscosity calculation (Sun Feb 21 2010 - 18:22:12 CST)
• Aron Broom
  • Re: Umbrella sampling-NAMD (Fri Dec 16 2011 - 09:46:39 CST)
  • Re: Umbrella sampling-NAMD (Thu Dec 15 2011 - 14:14:05 CST)
  • Re: Umbrella sampling-NAMD (Thu Dec 15 2011 - 11:11:04 CST)
  • Re: cell size (Tue Dec 13 2011 - 10:03:58 CST)
  • Re: tclforces and extrabonds (Mon Dec 12 2011 - 11:30:36 CST)
  • Re: correlation functions (Sat Dec 10 2011 - 08:54:56 CST)
  • Re: Peptide planarity Dihedral angle restraints (Thu Dec 08 2011 - 21:11:20 CST)
  • Re: Calculation of distance traveled by an atom (Tue Dec 06 2011 - 02:43:34 CST)
  • Re: Calculation of distance traveled by an atom (Mon Dec 05 2011 - 17:38:33 CST)
  • Re: OpenCL and AMD GPUs (Thu Nov 24 2011 - 15:53:33 CST)
  • Re: Scaled forces, colvars and harmonic con/restraints (Wed Nov 23 2011 - 14:36:42 CST)
  • Re: HEME and Cystein instead of His (Wed Nov 23 2011 - 14:02:42 CST)
  • Re: Re: Predicting the binding affinity and anion (Wed Nov 23 2011 - 12:46:33 CST)
  • Re: OpenCL and AMD GPUs (Wed Nov 23 2011 - 09:06:13 CST)
  • OpenCL and AMD GPUs (Tue Nov 22 2011 - 22:04:13 CST)
• Artem Zhmurov
  • Re: dcd files (Sun May 22 2011 - 16:52:19 CDT)
  • Re: NAMD starts AMBER calculation only from 3rd run (Mon Mar 01 2010 - 14:47:14 CST)
• Arturas
  • Re: tabulatd potentials (Thu Dec 29 2011 - 14:11:43 CST)
  • tabulatd potentials (Thu Dec 29 2011 - 13:09:17 CST)
• Arun Kumar Subramanian
  • what will be the best way to simulate substrate interaction only within a binding pocket of a large protein. (Sat May 07 2011 - 21:20:29 CDT)
• Arvind Kannan
  • CUDA on GPU Cluster (Fri Aug 19 2011 - 17:31:06 CDT)
  • Segmentation Faults on Mac OS X Lion (Mon Jul 25 2011 - 16:48:21 CDT)
  • Segmentation Faults on Mac OS X Lion (Mon Jul 25 2011 - 16:39:31 CDT)
• 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: Constraint failure; simulation has become unstable (Sat Jan 08 2011 - 08:05:15 CST)
  • Re: Constraint failure; simulation has become unstable (Fri Jan 07 2011 - 15:04:08 CST)
  • 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)
• atsuiai_at_aim.com
  • Re: Dangling Bonds? (Thu Sep 29 2011 - 08:45:39 CDT)
  • Re: Dangling Bonds? (Thu Sep 29 2011 - 06:23:55 CDT)
  • Dangling Bonds? (Wed Sep 28 2011 - 17:35:12 CDT)
• 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)
• Austin B. Yongye
  • Low global exclusion count errors (Wed Jul 13 2011 - 13:10:10 CDT)
  • Low global exclusion count (Tue Jul 12 2011 - 15:08:51 CDT)
  • Filtered mail? (Tue Jul 12 2011 - 09:04:32 CDT)
  • 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)
• avl211_at_lehigh.edu
  • Issue with NAMD Not understand (Fri Nov 12 2010 - 12:29:32 CST)
• Axel Kohlmeyer
  • Re: Re: Generating .tpr file using NAMD files (Mon Dec 19 2011 - 11:59:35 CST)
  • Re: New physical understanding. (Sat Dec 17 2011 - 13:42:31 CST)
  • Re: New physical understanding. (Fri Dec 16 2011 - 05:47:48 CST)
  • Re: cell size (Tue Dec 13 2011 - 10:00:43 CST)
  • Re: cell size (Tue Dec 13 2011 - 08:21:18 CST)
  • Re: Calculation of distance traveled by an atom (Mon Dec 05 2011 - 23:22:53 CST)
  • Re: Calculation of distance traveled by an atom (Mon Dec 05 2011 - 17:36:58 CST)
  • Re: Coulomb 1-4 interactions (Fri Dec 02 2011 - 10:21:36 CST)
  • Re: cpu-gpu vs cpu (Tue Nov 29 2011 - 10:19:50 CST)
  • Re: cpu-gpu vs cpu (Tue Nov 29 2011 - 07:41:51 CST)
  • Re: charmrun constantly hanging (Sat Nov 26 2011 - 10:06:22 CST)
  • Re: charmrun constantly hanging (Fri Nov 25 2011 - 08:27:08 CST)
  • Re: OpenCL and AMD GPUs (Wed Nov 23 2011 - 10:23:06 CST)
  • Re: OpenCL and AMD GPUs (Wed Nov 23 2011 - 09:52:47 CST)
  • Re: Re: Predicting the binding affinity and anion (Wed Nov 23 2011 - 07:37:19 CST)
  • Re: OpenCL and AMD GPUs (Wed Nov 23 2011 - 05:07:52 CST)
  • Re: namd force field (Tue Nov 22 2011 - 08:05:08 CST)
  • Re: AW: namd-ibverbs fails to start (Tue Nov 22 2011 - 08:02:12 CST)
  • Re: Assertion failed in file @ KRAKEN (Wed Nov 09 2011 - 11:00:04 CST)
  • Re: membrane simulation at high Temp (Fri Nov 04 2011 - 19:08:22 CDT)
  • Re: Running NAMD CUDA (Fri Nov 04 2011 - 15:16:45 CDT)
  • Re: Use of RBCG to convert multiple frames from atomistic trajectory to Coarse grained (Tue Nov 01 2011 - 14:59:27 CDT)
  • Re: NAMD on KRAKEN (Fri Oct 28 2011 - 08:03:35 CDT)
  • Re: NAMD on KRAKEN (Fri Oct 28 2011 - 04:43:59 CDT)
  • Re: PMF (Tue Oct 25 2011 - 07:23:21 CDT)
  • Re: * CGtool force field * (Sun Oct 23 2011 - 16:16:47 CDT)
  • Re: * CGtool force field * (Sat Oct 22 2011 - 14:36:38 CDT)
  • Re: * CGtool force field * (Sat Oct 22 2011 - 12:47:47 CDT)
  • Re: how to visualize an alchemical FEP transformation?? (Sat Oct 22 2011 - 11:33:47 CDT)
  • Re: coloring method in VMD (Thu Oct 20 2011 - 18:21:30 CDT)
  • Re: how to visualize an alchemical FEP transformation?? (Thu Oct 20 2011 - 16:42:02 CDT)
  • Re: how to visualize an alchemical FEP transformation?? (Thu Oct 20 2011 - 14:02:59 CDT)
  • Re: Using CHARMM Compatible Amber Parameters (Thu Oct 20 2011 - 11:34:33 CDT)
  • Re: how to visualize an alchemical FEP transformation?? (Thu Oct 20 2011 - 09:02:34 CDT)
  • Re: Question about silver nanoparticle simulation (Wed Oct 19 2011 - 09:26:27 CDT)
  • Re: tclforces- tcl extension written in c and built with swig (Mon Oct 17 2011 - 18:43:08 CDT)
  • Re: rigid bonds (Fri Oct 14 2011 - 09:27:34 CDT)
  • Re: How to write a dcd in fortran? (Mon Oct 03 2011 - 18:13:20 CDT)
  • Re: How to write a dcd in fortran? (Mon Oct 03 2011 - 14:13:03 CDT)
  • Re: How to write a dcd in fortran? (Mon Oct 03 2011 - 13:26:54 CDT)
  • Re: Periodic cell has become too small for original patch grid!â€� (Fri Sep 30 2011 - 08:06:26 CDT)
  • Re: Dangling Bonds? (Wed Sep 28 2011 - 17:58:18 CDT)
  • Re: Quick TCl scripting question (Wed Sep 21 2011 - 21:09:50 CDT)
  • Re: NAMD running on windows HPC question (Tue Sep 20 2011 - 11:27:23 CDT)
  • Re: Infiniband and commodity hardware (Sun Sep 18 2011 - 02:38:48 CDT)
  • Re: TopoTools for tpr file (Fri Sep 09 2011 - 10:44:42 CDT)
  • Re: Bonds are too long after simulation (Wed Sep 07 2011 - 13:18:26 CDT)
  • Re: mean square displacement (Mon Sep 05 2011 - 08:42:03 CDT)
  • Re: POPC membrane model in pH 4 (Sat Sep 03 2011 - 09:50:08 CDT)
  • Re: HETATM vs ATOM in .pdb file (Wed Aug 31 2011 - 06:16:16 CDT)
  • Re: about extrabonds restrain (Tue Aug 30 2011 - 08:06:04 CDT)
  • Re: SMD-extension (Fri Aug 26 2011 - 08:20:28 CDT)
  • Re: Heating /Equilibration (Fri Aug 26 2011 - 08:16:29 CDT)
  • (no subject) (Tue Aug 23 2011 - 09:37:15 CDT)
  • Re: PME Grid Settings and its significance relative to a cutoff value (Fri Aug 19 2011 - 13:05:26 CDT)
  • Re: AW: Multinode NAMD CUDA GPU Selection (Fri Aug 19 2011 - 06:33:28 CDT)
  • Re: Multinode NAMD CUDA GPU Selection (Thu Aug 18 2011 - 10:39:18 CDT)
  • Re: vmd-l: Re: MMTools (Wed Aug 17 2011 - 20:28:28 CDT)
  • Re: MMTools (Wed Aug 17 2011 - 10:15:50 CDT)
  • Re: (Tue Aug 16 2011 - 08:43:00 CDT)
  • Re: Batch Mode MD simulation Script for NAMD (Fri Aug 12 2011 - 07:53:13 CDT)
  • Re: sodium ion in water (Thu Aug 11 2011 - 00:36:08 CDT)
  • Re: Solvation in VMD using Non Standard Solvent System (Wed Aug 10 2011 - 07:47:35 CDT)
  • Re: error: expected floating-point number but got (Thu Aug 04 2011 - 10:29:08 CDT)
  • Re: namd-I: cionize problem in vmd (Fri Jul 29 2011 - 11:23:56 CDT)
  • Re: Dividing a 2D ABF simulations into regions (on nodes with different speeds) (Fri Jul 29 2011 - 08:34:33 CDT)
  • Re: Controlling fans on a GTX 560 ti (Fri Jul 22 2011 - 09:19:59 CDT)
  • Re: Controlling fans on a GTX 560 ti (Fri Jul 22 2011 - 08:56:17 CDT)
  • Re: namd files (Wed Jul 20 2011 - 08:48:08 CDT)
  • Re: tesla 2050 benchmark (Tue Jul 12 2011 - 14:04:00 CDT)
  • Re: temperature-TS with NAMDplot (Fri Jul 08 2011 - 08:09:57 CDT)
  • Re: Transferring environment variables when using charmrun (Wed Jul 06 2011 - 07:47:46 CDT)
  • Re: Difference between cwd and cd (Wed Jul 06 2011 - 07:49:18 CDT)
  • Re: membrane simulation ERROR rattle algorithm (Tue Jul 05 2011 - 13:05:18 CDT)
  • Re: Cannot find bond parameters (Tue Jun 28 2011 - 11:09:12 CDT)
  • Re: slow heating md (Thu Jun 23 2011 - 09:06:01 CDT)
  • Re: cuda error cudastreamcreate. SOLVED (probably) (Thu Jun 16 2011 - 04:40:03 CDT)
  • Re: cuda error cudastreamcreate. SOLVED (probably) (Wed Jun 15 2011 - 09:51:33 CDT)
  • Re: NAMD crashes with OpenMPI/OpenMX (Tue Jun 14 2011 - 13:25:23 CDT)
  • Re: namd ( please help me!!! ) (Mon Jun 13 2011 - 14:36:24 CDT)
  • Re: Iron Oxide and Arsenic (Sat Jun 11 2011 - 17:53:28 CDT)
  • Re: Iron Oxide and Arsenic (Sat Jun 11 2011 - 17:38:21 CDT)
  • Re: Iron Oxide and Arsenic (Sat Jun 11 2011 - 17:16:06 CDT)
  • Re: Compiling NAMD for CUDA (Sat Jun 11 2011 - 16:43:28 CDT)
  • Re: AMD-PhenomII-1075_GTX470 NAMD-CUDA performance (Mon Jun 06 2011 - 06:57:35 CDT)
  • Re: Advice on buying GPUs (Mon Jun 06 2011 - 06:50:16 CDT)
  • Re: AMD-PhenomII-1075_GTX470 NAMD-CUDA performance (Mon Jun 06 2011 - 06:29:38 CDT)
  • Re: AMD-PhenomII-1075_GTX470 NAMD-CUDA performance (Mon Jun 06 2011 - 05:50:24 CDT)
  • Re: conf file script ( help needed ) (Fri Jun 03 2011 - 08:45:27 CDT)
  • Re: Fwd: Fwd: hi (Thu Jun 02 2011 - 12:52:25 CDT)
  • Re: Advice on buying GPUs (Thu Jun 02 2011 - 09:06:08 CDT)
  • Re: Re: Periodic Boundary conditions (Thu Jun 02 2011 - 06:19:54 CDT)
  • Re: Advice on buying GPUs (Thu Jun 02 2011 - 06:17:14 CDT)
  • Re: Fail to Run VMD (Tue May 31 2011 - 13:57:24 CDT)
  • Re: Script Help (Sun May 29 2011 - 18:58:44 CDT)
  • Re: Joining PSF Files (Tue May 24 2011 - 09:08:32 CDT)
  • Re: Joining PSF Files (Tue May 24 2011 - 09:00:57 CDT)
  • Re: Problem building NAMD (multiple definitions) (Mon May 23 2011 - 17:41:37 CDT)
  • Re: Problem building NAMD (multiple definitions) (Mon May 23 2011 - 17:12:21 CDT)
  • Re: dcd files (Sun May 22 2011 - 09:15:48 CDT)
  • Re: dcd files (Sun May 22 2011 - 09:10:29 CDT)
  • Re: simulation box (Fri May 20 2011 - 11:33:20 CDT)
  • Re: simulation box (Fri May 20 2011 - 11:25:36 CDT)
  • Re: Is there any difference between SMD and tclForces? (Wed May 18 2011 - 20:34:13 CDT)
  • Re: CUDA simulation memory usage (Wed May 18 2011 - 08:29:18 CDT)
  • Re: trajectory_path.tcl (Tue May 17 2011 - 09:38:19 CDT)
  • Re: Automatic GPU selection in NAMD ? (Tue May 17 2011 - 07:19:44 CDT)
  • Re: Re: ç­”å¤�: compilation of namd (Thu May 12 2011 - 08:34:14 CDT)
  • Re: Re: ç­”å¤�: compilation of namd (Thu May 12 2011 - 04:53:58 CDT)
  • Re: Re: ç­”å¤�: compilation of namd (Wed May 11 2011 - 11:16:29 CDT)
  • Re: ç­”å¤�: compilation of namd (Tue May 10 2011 - 22:14:26 CDT)
  • Re: REMD across gpus (Tue May 10 2011 - 15:52:42 CDT)
  • Re: REMD across gpus (Tue May 10 2011 - 15:05:06 CDT)
  • Re: print center of mass (Tue May 10 2011 - 11:01:35 CDT)
  • Re: AMD Multicore + CUDA Benchmarks, are them ok ? (Thu May 05 2011 - 08:57:18 CDT)
  • Re: AMD Multicore + CUDA Benchmarks, are them ok ? (Thu May 05 2011 - 08:47:56 CDT)
  • Re: run tests with CUDA (Mon May 02 2011 - 16:55:18 CDT)
  • Re: Add bonds and topology file problem (Sun May 01 2011 - 15:52:30 CDT)
  • Re: pbc wrap option for x,y,z lengths (Mon Apr 25 2011 - 09:22:29 CDT)
  • Re: pbc wrap option for x,y,z lengths (Sun Apr 24 2011 - 14:53:20 CDT)
  • Re: pbc wrap option for x,y,z lengths (Sun Apr 24 2011 - 13:00:10 CDT)
  • Re: pbc wrap option for x,y,z lengths (Sat Apr 23 2011 - 03:37:20 CDT)
  • Re: pbc wrap option for x,y,z lengths (Fri Apr 22 2011 - 22:21:56 CDT)
  • Re: GeForce vs Tesla GPUs for high performance computing (Thu Apr 14 2011 - 14:57:16 CDT)
  • Re: GeForce vs Tesla GPUs for high performance computing (Thu Apr 14 2011 - 14:23:50 CDT)
  • Re: problem in restarting (Thu Apr 14 2011 - 11:42:59 CDT)
  • Re: Help building a desktop for namd (Thu Apr 14 2011 - 08:37:20 CDT)
  • Re: problem in restarting (Thu Apr 14 2011 - 08:29:24 CDT)
  • Re: Help building a desktop for namd (Wed Apr 13 2011 - 17:22:03 CDT)
  • Re: about rigid bonds (Wed Apr 13 2011 - 10:38:19 CDT)
  • Re: Recent Geforce Cuda GPU cards(GT 440, GTX 560ti) (Wed Apr 13 2011 - 09:25:58 CDT)
  • Re: Replica Exchange Simulations on Blue Gene/P (Tue Apr 12 2011 - 10:03:16 CDT)
  • Re: Help building a desktop for namd (Mon Apr 11 2011 - 16:34:22 CDT)
  • Re: Help building a desktop for namd (Mon Apr 11 2011 - 15:06:33 CDT)
  • Re: Help building a desktop for namd (Mon Apr 11 2011 - 12:55:34 CDT)
  • Re: Help building a desktop for namd (Sun Apr 10 2011 - 12:52:59 CDT)
  • Re: SMD simulation: stop applying force during simulation? (Fri Apr 08 2011 - 07:46:54 CDT)
  • Re: Abe versus Lincoln (Thu Apr 07 2011 - 16:18:09 CDT)
  • Re: Abe versus Lincoln (Thu Apr 07 2011 - 14:21:33 CDT)
  • Re: Abe versus Lincoln (Thu Apr 07 2011 - 13:46:34 CDT)
  • Re: NAMD speed on MPICH2 Ubuntu 64 bit Cluster (Wed Apr 06 2011 - 16:22:48 CDT)
  • Re: NAMD speed on MPICH2 Ubuntu 64 bit Cluster (Wed Apr 06 2011 - 12:06:41 CDT)
  • Re: NPT simulations in NAMD (Tue Apr 05 2011 - 08:09:26 CDT)
  • Re: gromacs analysis tools (Sun Apr 03 2011 - 14:28:04 CDT)
  • Re: Multi node run causes "CUDA error cudaStreamCreate" (Fri Apr 01 2011 - 16:10:00 CDT)
  • Re: Multi node run causes "CUDA error cudaStreamCreate" (Fri Apr 01 2011 - 15:02:18 CDT)
  • Re: NAMD_CVS_Source (Wed Mar 30 2011 - 17:27:04 CDT)
  • Re: The biggest system simulated on one TESLA C2050 ? (Wed Mar 30 2011 - 14:42:56 CDT)
  • Re: how to write the bond across the cell boundary (Fri Mar 25 2011 - 08:17:05 CDT)
  • Re: namd and Fedora14 (Tue Mar 22 2011 - 08:44:21 CDT)
  • Re: rule of thumb for dcd sampling frequency? (Mon Mar 21 2011 - 14:12:00 CDT)
  • Re: ABF colvar error-capped nanotube interaction (Sun Mar 20 2011 - 12:13:43 CDT)
  • Re: ABF colvar error-capped nanotube interaction (Sat Mar 19 2011 - 12:02:53 CDT)
  • Re: Multiple runs of NAMD highly take fluctuating times (Wed Mar 16 2011 - 00:36:28 CDT)
  • Re: Keyword "lower" not supported...colvars (Sat Mar 12 2011 - 16:02:38 CST)
  • Re: creating .psf file for a nanotube (Fri Mar 11 2011 - 08:26:58 CST)
  • Re: creating .psf file for a nanotube (Fri Mar 11 2011 - 05:18:57 CST)
  • Re: topology file for nanotube (Thu Mar 10 2011 - 08:11:13 CST)
  • Re: topology file for nanotube (Thu Mar 10 2011 - 04:43:37 CST)
  • Re: topology file for nanotube (Thu Mar 10 2011 - 04:38:27 CST)
  • Re: colvars PMF history problem (Mon Mar 07 2011 - 17:56:05 CST)
  • Re: colvars PMF history problem (Mon Mar 07 2011 - 10:03:24 CST)
  • Re: Job scheduling (managing) software recommendation (Mon Mar 07 2011 - 09:16:38 CST)
  • Re: colvars PMF history problem (Mon Mar 07 2011 - 09:27:19 CST)
  • Re: Problem with SPC/E water simulation (Fri Mar 04 2011 - 15:50:13 CST)
  • Re: membrane equilibration (Thu Mar 03 2011 - 20:42:59 CST)
  • Re: membrane equilibration (Thu Mar 03 2011 - 13:43:48 CST)
  • Re: NAMD2.7 on BluegeneL hang at "LDB: Central LB being created..." (Wed Mar 02 2011 - 22:32:28 CST)
  • Re: Positional restraints - Dielectric constant (Wed Mar 02 2011 - 11:39:39 CST)
  • Re: namd at ranger(tacc) (Thu Feb 24 2011 - 15:20:02 CST)
  • Re: Computing interaction energies in namd (Tue Feb 22 2011 - 19:07:11 CST)
  • Re: timing variation during 256core run on abe.ncsa.uiuc.edu (Tue Feb 22 2011 - 11:06:26 CST)
  • Re: timing variation during 256core run on abe.ncsa.uiuc.edu (Mon Feb 21 2011 - 15:07:50 CST)
  • Re: Calculation of IR spectra using VMD IRspec Plug-in (Sun Feb 20 2011 - 12:40:41 CST)
  • Re: Get number of timesteps from DCD via script (Wed Feb 09 2011 - 08:43:21 CST)
  • Re: Get number of timesteps from DCD via script (Wed Feb 09 2011 - 07:43:17 CST)
  • Re: mainboard-power source for GPU (Tue Jan 25 2011 - 06:36:57 CST)
  • Re: increasing MAX_EXCLUSIONS (Wed Jan 19 2011 - 16:42:29 CST)
  • Re: Feature request for the colvars module -- TCL syntax (Tue Jan 18 2011 - 09:09:54 CST)
  • Re: Can DCD trajectory files contain only protein but water surround (Thu Jan 13 2011 - 19:57:05 CST)
  • Re: Constraint failure; simulation has become unstable (Mon Jan 10 2011 - 08:49:07 CST)
  • Re: water sphere (Thu Jan 06 2011 - 08:18:57 CST)
  • 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)
• Azat Mukhametov
  • Re: Question about end of log file (Mon May 30 2011 - 21:53:50 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)
• Babban Mia
  • Heating /Equilibration (Fri Aug 26 2011 - 05:20:23 CDT)
  • Heating /Equilibration (Wed Aug 24 2011 - 02:56:37 CDT)
  • Re: Heating in NAMD (Sun Aug 21 2011 - 06:06:25 CDT)
  • Re: Heating in NAMD (Sat Aug 20 2011 - 05:37:53 CDT)
  • Re: Restarting MD (Disabling Checklist) (Fri Aug 19 2011 - 06:50:04 CDT)
  • Restarting MD (Disabling Checklist) (Thu Aug 18 2011 - 10:58:55 CDT)
  • Heating in NAMD (Thu Aug 18 2011 - 10:13:08 CDT)
  • Re: (Tue Aug 16 2011 - 09:41:58 CDT)
  • Re: Periodic Boundary Condition for a 630 Amino Acid Protein (Sun Aug 14 2011 - 09:19:18 CDT)
  • Periodic Boundary Condition for a 630 Amino Acid Protein (Sun Aug 14 2011 - 08:15:28 CDT)
  • Re: Batch Mode MD simulation Script for NAMD (Sat Aug 13 2011 - 07:36:56 CDT)
  • .COOR TO PDB FILE (Sat Aug 13 2011 - 01:11:48 CDT)
  • Re: Batch Mode MD simulation Script for NAMD (Fri Aug 12 2011 - 13:55:03 CDT)
  • Re: Batch Mode MD simulation Script for NAMD (Fri Aug 12 2011 - 12:59:45 CDT)
  • Re: Batch Mode MD simulation Script for NAMD (Fri Aug 12 2011 - 12:06:28 CDT)
  • Re: Batch Mode MD simulation Script for NAMD (Fri Aug 12 2011 - 05:46:32 CDT)
  • Batch Mode MD simulation Script for NAMD (Thu Aug 11 2011 - 18:56:19 CDT)
  • Re: Topology file for ethanol (Wed Aug 10 2011 - 23:35:37 CDT)
  • Topology file for ethanol (Wed Aug 10 2011 - 22:58:19 CDT)
  • Solvation in VMD using Non Standard Solvent System (Wed Aug 10 2011 - 07:35:32 CDT)
  • Re: Explicit Solvent Sytem (40% Ethanol + 60% Water) (Wed Aug 10 2011 - 04:49:20 CDT)
  • Re: Explicit Solvent Sytem (40% Ethanol + 60% Water) (Tue Aug 09 2011 - 09:42:26 CDT)
  • Explicit Solvent Sytem (40% Ethanol + 60% Water) (Tue Aug 09 2011 - 01:20:20 CDT)
• 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
  • clustering of trajectory (Tue Jul 05 2011 - 09:46:24 CDT)
  • 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)
• 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)
• 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)
• Bennion, Brian
  • Hints for building namd2.8 on charm++ ibverbs layer? (Fri Sep 02 2011 - 18:06:15 CDT)
  • question on modifyAppliedForces() (Fri Apr 22 2011 - 12:11:27 CDT)
  • RE: forces on fixed atoms (Wed Feb 16 2011 - 18:04:30 CST)
  • forces on fixed atoms (Wed Feb 16 2011 - 16:01:44 CST)
  • RE: NAMD-l: energy jump between minimization and simulation (Wed Feb 16 2011 - 13:48:34 CST)
  • RE: energy jump between minimization and simulation (Wed Feb 16 2011 - 10:58:33 CST)
  • 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)
• bharat gupta
  • Re: Predicting the binding affinity and anion (Wed Nov 23 2011 - 07:23:29 CST)
  • protein moving out during npt equilibration (Wed Jul 13 2011 - 10:48:48 CDT)
  • Re: Re: Protein moving out of box during npt simulation (Tue Jul 05 2011 - 21:25:04 CDT)
  • Re: Re: Protein moving out of box during npt simulation (Tue Jul 05 2011 - 03:40:59 CDT)
  • Re: Protein moving out of box during npt simulation (Tue Jul 05 2011 - 00:33:30 CDT)
  • Re: distortion of some bonds during structure preparation (Mon Jul 04 2011 - 03:36:39 CDT)
  • Hi: some doubt about nvt and npt equilibration (Sun Jul 03 2011 - 20:36:19 CDT)
  • Re: NPT equilibration (Fri Jul 01 2011 - 04:04:56 CDT)
  • Re: Fatal Error Periodic cell has become too small for original patch grid (Fri Jul 01 2011 - 00:59:56 CDT)
  • Re: Final production run in MD (Thu Jun 30 2011 - 18:42:23 CDT)
  • Re: Equilibration - NVT & NPT (Thu Jun 30 2011 - 01:36:56 CDT)
  • Re: Equilibration (Wed Jun 29 2011 - 01:06:10 CDT)
  • Re: Energy minimization (Tue Jun 28 2011 - 18:49:01 CDT)
  • Re: patch for phosphotyrosine residue (Tue Jun 21 2011 - 20:53:38 CDT)
  • Fwd: phosphotyrosine (Mon Jun 20 2011 - 00:29:04 CDT)
  • Re: phosphotyrosine (Sun Jun 19 2011 - 19:26:37 CDT)
  • 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)
• BIN ZHANG
  • free energy perturbation (Wed Jan 05 2011 - 02:07:57 CST)
  • 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)
• Bishop, Thomas C
  • RE: timing variation during 256core run on abe.ncsa.uiuc.edu (Tue Feb 22 2011 - 10:14:30 CST)
• Bjoern Olausson
  • Re: membrane system (Thu Sep 22 2011 - 03:10:00 CDT)
  • Re: membrane system (Wed Sep 21 2011 - 05:02:08 CDT)
  • Re: Fwd: Re : Setting up a membrane simulation (Tue Sep 20 2011 - 05:43:30 CDT)
  • Re: Fwd: Re : Setting up a membrane simulation (Tue Sep 20 2011 - 04:27:23 CDT)
  • Re: Setting up a membrane simulation (Fri Sep 16 2011 - 07:13:56 CDT)
  • Re: HETATM vs ATOM in .pdb file (Wed Aug 31 2011 - 06:20:55 CDT)
  • Logfile flooded with "The last position output [...]" when IMDon is used. (Tue Aug 23 2011 - 04:32:47 CDT)
  • Re: AW: Letzte Hilfe (Tue Aug 16 2011 - 06:17:36 CDT)
  • Re: Denaturation via increased temperature (Mon Aug 15 2011 - 06:11:17 CDT)
  • Re: Denaturation via increased temperature (Mon Aug 15 2011 - 04:31:25 CDT)
  • Denaturation via increased temperature (Mon Aug 15 2011 - 04:11:06 CDT)
  • Re: Lipid bilayer equilibration: Periodic cell has become too small for original patch grid! (Wed Aug 10 2011 - 02:49:01 CDT)
  • Re: Lipid bilayer equilibration: Periodic cell has become too small for original patch grid! (Mon Aug 08 2011 - 02:57:08 CDT)
  • Re: how to generate transparent figures? (Mon Jul 25 2011 - 04:04:58 CDT)
  • Re: Yan: analysis question (Fri Jul 22 2011 - 03:01:05 CDT)
  • Re: PME or not PME? What happens if PME is turned off? (Wed Jul 20 2011 - 03:03:10 CDT)
  • Re: analysis question (Tue Jul 19 2011 - 05:43:34 CDT)
  • Re: PME or not PME? What happens if PME is turned off? (Tue Jul 19 2011 - 01:48:50 CDT)
  • PME or not PME? What happens if PME is turned off? (Mon Jul 18 2011 - 04:10:08 CDT)
  • Re: temperature-TS with NAMDplot (Fri Jul 08 2011 - 09:07:43 CDT)
  • Re: temperature-TS with NAMDplot (Fri Jul 08 2011 - 06:30:09 CDT)
  • Re: Implicit solvent simulation (Fri Jul 08 2011 - 05:57:03 CDT)
  • Re: Re: Protein moving out of box during npt simulation (Fri Jul 08 2011 - 02:50:29 CDT)
  • Re: Re: Protein moving out of box during npt simulation (Tue Jul 05 2011 - 04:22:50 CDT)
  • Re: NAMD crashes with OpenMPI/OpenMX (Thu Jun 16 2011 - 07:40:07 CDT)
  • Re: about log file (Thu Jun 09 2011 - 05:02:36 CDT)
  • Re: water equilibration (Mon Jun 06 2011 - 09:12:33 CDT)
  • Re: the meaning of " 5-ZEROS" " 9-ZEROS" in the DCD file (Tue May 24 2011 - 03:44:23 CDT)
  • Typo in NAMD 2.8b2 output for Accelerated MD (Thu May 19 2011 - 07:25:51 CDT)
  • Re: hi (Thu May 19 2011 - 04:29:14 CDT)
  • Re: NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 (Thu May 19 2011 - 04:00:33 CDT)
  • Re: NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 (Wed May 18 2011 - 08:44:48 CDT)
  • Re: NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 (Mon May 16 2011 - 13:45:14 CDT)
  • Re: NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 (Mon May 16 2011 - 04:02:51 CDT)
  • Re: NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 (Sat May 14 2011 - 01:12:57 CDT)
  • Re: NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 (Fri May 13 2011 - 13:10:46 CDT)
  • Re: NAMD2.7 on BluegeneL hang at "LDB: Central LB being created..." (Fri May 13 2011 - 02:47:16 CDT)
  • NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 (Thu May 12 2011 - 17:20:09 CDT)
  • Re: Re: Re: q=AD=94=E5=A4=8D=3A_namd-l=3A_compilation_of?= namd (Thu May 12 2011 - 11:13:21 CDT)
  • Re: Re: Re: q=AD=94=E5=A4=8D=3A_namd-l=3A_compilation_of?= namd (Thu May 12 2011 - 09:58:47 CDT)
  • Re: Re: q=AD=94=E5=A4=8D=3A_namd-l=3A_compilation_of?= namd (Thu May 12 2011 - 08:11:57 CDT)
  • Re: Re: q=AD=94=E5=A4=8D=3A_namd-l=3A_compilation_of?= namd (Thu May 12 2011 - 02:45:49 CDT)
  • Re: Accelerated MD: question about dual boost mode (Tue May 10 2011 - 10:17:59 CDT)
  • Re: Accelerated MD: question about dual boost mode (Tue May 10 2011 - 07:32:13 CDT)
  • Re: 'cutting' colvars.traj file (Tue May 03 2011 - 08:34:21 CDT)
  • Re: 'cutting' colvars.traj file (Tue May 03 2011 - 05:45:23 CDT)
  • Re: 'cutting' colvars.traj file (Wed Apr 27 2011 - 05:53:41 CDT)
  • Re: NVT setup for monolayer (Thu Apr 14 2011 - 02:17:35 CDT)
  • NVT setup for monolayer (Thu Apr 07 2011 - 08:24:32 CDT)
  • Re: Rotate two linked proteins against each other and calculate energy profile (Tue Mar 29 2011 - 10:16:12 CDT)
  • Re: Rotate two linked proteins against each other and calculate energy profile (Mon Mar 28 2011 - 16:46:29 CDT)
  • Re: Rotate two linked proteins against each other and calculate energy profile (Mon Mar 28 2011 - 16:00:25 CDT)
  • Re: Rotate two linked proteins against each other and calculate energy profile (Mon Mar 28 2011 - 11:36:13 CDT)
  • Re: Rotate two linked proteins against each other and calculate energy profile (Mon Mar 28 2011 - 11:18:09 CDT)
  • Re: GBIS and ABF (Mon Mar 28 2011 - 09:56:41 CDT)
  • Re: Rotate two linked proteins against each other and calculate energy profile (Mon Mar 28 2011 - 07:49:23 CDT)
  • Re: GBIS and ABF (Mon Mar 28 2011 - 02:45:46 CDT)
  • Re: GBIS and ABF (Wed Mar 23 2011 - 06:57:32 CDT)
  • Re: GBIS and ABF (Wed Mar 23 2011 - 09:32:43 CDT)
  • Re: GBIS and ABF (Wed Mar 23 2011 - 07:04:29 CDT)
  • Re: GBIS question and possible Bug for colvar "outputSystemForce" declaration in NAMD CVS-2011-03-03 (Wed Mar 23 2011 - 07:06:21 CDT)
  • Re: GBIS question and possible Bug for colvar "outputSystemForce" declaration in NAMD CVS-2011-03-03 (Wed Mar 23 2011 - 03:18:22 CDT)
  • Re: GBIS and ABF (Tue Mar 22 2011 - 18:13:18 CDT)
  • GBIS question and possible Bug for colvar "outputSystemForce" declaration in NAMD CVS-2011-03-03 (Tue Mar 22 2011 - 17:56:09 CDT)
  • Re: Rotate two linked proteins against each other and calculate energy profile (Sun Mar 20 2011 - 11:03:32 CDT)
  • Rotate two linked proteins against each other and calculate energy profile (Tue Mar 15 2011 - 14:20:00 CDT)
  • Re: Accelerated MD documentation? (Tue Mar 15 2011 - 10:47:21 CDT)
  • Re: Accelerated MD documentation? (Tue Mar 15 2011 - 08:59:48 CDT)
  • psfgen - any version capable of reading extended PSF files? (Fri Feb 11 2011 - 05:47:05 CST)
  • Re: Get number of timesteps from DCD via script (Thu Feb 10 2011 - 03:52:44 CST)
  • FEP - Protein binding to Membrane surface (Thu Feb 10 2011 - 03:50:37 CST)
  • Re: Get number of timesteps from DCD via script (Wed Feb 09 2011 - 08:05:42 CST)
  • Re: Get number of timesteps from DCD via script (Wed Feb 09 2011 - 08:32:13 CST)
  • Re: Get number of timesteps from DCD via script (Wed Feb 09 2011 - 06:37:20 CST)
  • Re: Get number of timesteps from DCD via script (Tue Feb 08 2011 - 05:24:29 CST)
  • Get number of timesteps from DCD via script (Mon Feb 07 2011 - 06:52:39 CST)
  • 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)
• 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)
• Bo Liu
  • Re: Can I do protein-ligand docking using NAMD? (Wed Feb 16 2011 - 00:30:54 CST)
  • Re: non-zero charge (Wed Jan 19 2011 - 16:31:22 CST)
  • 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)
• Bob Masong
  • Error with "namd" (Wed Oct 26 2011 - 00:01:21 CDT)
  • Error with ubqp.pdb in NAMD tutorial (Mon Oct 24 2011 - 22:43:46 CDT)
• Boyang Wang
  • Re: Coarse-Graining MD don't work perfect as expected (Fri Dec 30 2011 - 03:57:44 CST)
  • Re: scaling (Fri Dec 30 2011 - 03:56:03 CST)
  • Fwd: about md in npt (Wed Dec 28 2011 - 02:54:01 CST)
  • Re: New physical understanding. (Sat Dec 17 2011 - 21:24:21 CST)
  • Re: New physical understanding. (Sat Dec 17 2011 - 08:52:28 CST)
  • Re: New physical understanding. (Fri Dec 16 2011 - 06:56:42 CST)
  • New physical understanding. (Fri Dec 16 2011 - 00:39:27 CST)
  • Re: correlation functions (Sat Dec 10 2011 - 18:03:53 CST)
  • Re: Peptide planarity Dihedral angle restraints (Thu Dec 08 2011 - 20:17:02 CST)
  • Re: Minimization doesn't stop when converged (Sat Oct 08 2011 - 01:25:24 CDT)
  • Re: Minimization doesn't stop when converged (Fri Oct 07 2011 - 03:56:01 CDT)
  • Re: Re: How to evaluate the area per lipid and thickness of the lipid bilayer in a membrane-protein system? (Thu Aug 25 2011 - 02:32:01 CDT)
  • Re: How to evaluate the area per lipid and thickness of the lipid bilayer in a membrane-protein system? (Thu Aug 25 2011 - 01:41:51 CDT)
  • Re: vmd-l: Re: MMTools (Thu Aug 18 2011 - 00:15:02 CDT)
  • How to set improper dihedral for trans-double bond. (Mon Nov 29 2010 - 06:15:16 CST)
• Branko
  • Re: collective variable calculation from dcd file (Wed Dec 21 2011 - 15:38:39 CST)
  • Re: collective variable calculation from dcd file (Wed Dec 21 2011 - 15:15:06 CST)
  • Re: MMTools for analysis (Sat Dec 10 2011 - 10:21:06 CST)
  • Re: paper/articule on colvars module (Tue Nov 29 2011 - 04:16:42 CST)
  • Re: Lipid as residues topology (Tue Nov 01 2011 - 05:59:43 CDT)
  • Re: GBIS and hydrophobic term, in replay to Jerome and David discussion (Sun Oct 23 2011 - 09:55:27 CDT)
  • GBIS and hydrophobic term, in replay to Jerome and David discussion (Sun Oct 23 2011 - 09:36:17 CDT)
  • Re: GBIS and hydrophobic solvation (Mon Oct 10 2011 - 10:11:42 CDT)
  • phosphorilated serine (Sat Sep 17 2011 - 11:01:42 CDT)
  • Re: Dock a metal ion into a peptide/protein (Thu Sep 01 2011 - 04:09:16 CDT)
  • Re: Dock a metal ion into a peptide/protein (Wed Aug 31 2011 - 15:28:17 CDT)
  • low dielectric constants in GBIS (Tue Aug 16 2011 - 15:41:04 CDT)
  • Fwd: Re: Explicit Solvent Sytem (40% Ethanol + 60% Water) (Tue Aug 09 2011 - 13:29:52 CDT)
  • Re: Minimization is taking a lot of computing time. (Tue Aug 09 2011 - 12:42:17 CDT)
  • Re: formyl and ethanolamide parameters and topology (Fri Jun 24 2011 - 03:52:32 CDT)
  • atom select within hbond analysis (Tue Jun 07 2011 - 07:40:09 CDT)
  • Re PMF (Sat May 28 2011 - 12:18:22 CDT)
  • Re: 'cutting' colvars.traj file (Tue May 03 2011 - 06:41:34 CDT)
  • Re: 'cutting' colvars.traj file (Tue May 03 2011 - 05:55:42 CDT)
  • Re: 'cutting' colvars.traj file (Sat Apr 23 2011 - 13:07:20 CDT)
  • 'cutting' colvars.traj file (Sat Apr 23 2011 - 12:28:58 CDT)
  • Re: partial charges for organic ligands (Sat Mar 26 2011 - 16:09:35 CDT)
  • Re: partial charges for organic ligands (Sat Mar 26 2011 - 12:42:32 CDT)
  • Re: GBIS and ABF (Tue Mar 22 2011 - 17:16:54 CDT)
  • Re: rule of thumb for dcd sampling frequency? (Tue Mar 22 2011 - 04:47:29 CDT)
  • Re: rule of thumb for dcd sampling frequency? (Mon Mar 21 2011 - 14:13:51 CDT)
  • html manual 2.8, ref 46 and some GBIS questions (Sun Mar 20 2011 - 09:05:27 CDT)
  • Re: GBIS and ABF (Fri Mar 18 2011 - 04:53:00 CDT)
  • GBIS and ABF (Thu Mar 17 2011 - 15:50:40 CDT)
  • Fwd: Re: Bactenecine (Wed Mar 16 2011 - 16:35:57 CDT)
  • maximum number of atoms per patch (Sun Feb 27 2011 - 12:21:56 CST)
  • Re: Calculation of IR spectra using VMD IRspec Plug-in (Sat Feb 19 2011 - 11:54:48 CST)
  • Benchmark for NAMD2.7 (curent version) (Wed Jan 05 2011 - 14:19:19 CST)
  • 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)
• Branko2
  • Re: Fwd: Installing NAMD on windows (Sat Dec 04 2010 - 11:25:29 CST)
• Brian Novak
  • Re: Removing some water from a .dcd file or .coor file (Sat Mar 27 2010 - 10:27:27 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)
• Bruno Luís Pinto de Oliveira
  • help in a FEP restart? (Sat Nov 26 2011 - 10:15:13 CST)
  • RE: HEME and Cystein instead of His (Wed Nov 23 2011 - 14:33:39 CST)
  • RE: how to visualize an alchemical FEP transformation?? (Sat Oct 22 2011 - 12:31:01 CDT)
  • RE: how to visualize an alchemical FEP transformation?? (Sat Oct 22 2011 - 09:58:42 CDT)
  • RE: how to visualize an alchemical FEP transformation?? (Thu Oct 20 2011 - 16:19:38 CDT)
  • RE: how to visualize an alchemical FEP transformation?? (Thu Oct 20 2011 - 15:10:28 CDT)
  • RE: how to visualize an alchemical FEP transformation?? (Thu Oct 20 2011 - 13:28:13 CDT)
  • how to visualize an alchemical FEP transformation?? (Thu Oct 20 2011 - 06:27:47 CDT)
  • RE: Force Vector Between Two Atoms (Sat Oct 08 2011 - 04:25:40 CDT)
  • RE: Help in reverse Free Energy perturbation - hysteresis (Tue Oct 04 2011 - 14:29:34 CDT)
  • Help in reverse Free Energy perturbation - hysteresis (Mon Oct 03 2011 - 05:24:58 CDT)
  • Help in FEP backward/reverse calculation (Thu Sep 22 2011 - 14:36:38 CDT)
  • help in FEP calculations : analysis/confirmation of results (Thu Sep 08 2011 - 13:59:23 CDT)
  • help in FEP calculations_binding free energy difference between 2 inhibitors (Mon Sep 05 2011 - 13:08:58 CDT)
  • help in FEP calculations_binding free energy difference between 2 inhibitors (Thu Sep 01 2011 - 10:04:41 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)
• Bryan Roessler
  • TMD and binary coordinate files (Wed Sep 28 2011 - 16:40:49 CDT)
• Buddhadev Maiti
  • (no subject) (Fri Oct 28 2011 - 22:14:30 CDT)
  • ForceConstant in Umbrella Sampling (Fri Oct 28 2011 - 12:38:24 CDT)
  • The Nudged Elastic Band Approach to Find the Lowest Energy Pathway Between two States (Tue May 24 2011 - 22:14:14 CDT)
  • Umbrella Sampling (Tue May 17 2011 - 21:52:38 CDT)
  • NAMD_2.7_AIX-POWER-MPI (Sun May 01 2011 - 21:28:41 CDT)
  • ABF calculation using RMSD (Mon Apr 25 2011 - 22:14:39 CDT)
  • problem for simulation of membrane protein system (Tue Apr 12 2011 - 11:06:30 CDT)
  • (no subject) (Mon Apr 11 2011 - 14:27:13 CDT)
  • (no subject) (Fri Apr 08 2011 - 10:45:19 CDT)
  • ABF Restart (Thu Mar 17 2011 - 21:46:37 CDT)
  • ABF calculation using RMSD (Wed Feb 16 2011 - 21:04:11 CST)
  • Force constant for Umbrella Sampling (Mon Feb 14 2011 - 19:19:02 CST)
  • ABF calculation using RMSD (Mon Feb 14 2011 - 19:08:32 CST)
  • 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)
• Burgess, Don E
  • tesla 2050 benchmark (Tue Jul 12 2011 - 13:56:45 CDT)
  • Recent Geforce Cuda GPU cards(GT 440, GTX 560ti) (Wed Apr 13 2011 - 08:21:15 CDT)
  • NBFIX support in CUDA NAMD (Mon Jan 24 2011 - 20:41:26 CST)
  • NBFIX for carbonyl atoms and potassium ions -- User Defined Force -- CUDA (Mon Jan 17 2011 - 15:35:28 CST)
• 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)
• 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)
• Cem Meydan
  • Waterbox used in minimization? (Thu May 13 2010 - 07:25:30 CDT)
• Chandra Ramananjara
  • (no subject) (Tue Nov 22 2011 - 12:31:08 CST)
  • (no subject) (Tue Nov 22 2011 - 06:53:15 CST)
  • (no subject) (Sun May 15 2011 - 12:32:07 CDT)
  • (no subject) (Thu May 12 2011 - 19:58:21 CDT)
  • (no subject) (Sun May 08 2011 - 09:37:04 CDT)
  • (no subject) (Sat May 07 2011 - 14:00:37 CDT)
• Chao Zhang
  • Different types of constraints at the same time (Thu Jul 15 2010 - 14:05:30 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)
• charlie
  • questions about the heat diffusion calculation in the tutorial (Sun May 22 2011 - 11:57:56 CDT)
  • large load rate using implicit solvent (Sun May 08 2011 - 20:45:10 CDT)
  • how to apply different temperature simultaneously to different atoms in the same system (Wed Apr 27 2011 - 02:41:08 CDT)
  • A namd2.8b1 bug ? (Wed Apr 27 2011 - 02:23:56 CDT)
  • restart problem (Wed Jan 05 2011 - 02:07:48 CST)
  • 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
  • unsubcribe (Wed Jan 05 2011 - 10:49:54 CST)
  • Re: Umbrella Sampling Methodology (Wed Aug 18 2010 - 11:39:17 CDT)
  • Umbrella Sampling Methodology (Mon Aug 16 2010 - 06:23:15 CDT)
• Chathurika Abeyrathne
  • Re: vmd-l: Re: MMTools (Wed Aug 17 2011 - 21:07:21 CDT)
  • Re: vmd-l: Re: MMTools (Wed Aug 17 2011 - 19:02:46 CDT)
  • MMTools (Tue Aug 16 2011 - 20:03:45 CDT)
  • Temperature bath (Mon Aug 01 2011 - 02:20:15 CDT)
  • Methanol - Autocorrelation of total dipole moment (Sat Jun 25 2011 - 03:36:06 CDT)
• Chen, Zhihong (chenz2)
  • unsubscribe (Thu Mar 31 2011 - 13:02:05 CDT)
  • (no subject) (Wed Jan 05 2011 - 18:43:15 CST)
  • 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)
• Chewning, Joseph
  • Compiled Windows HPC version. (Tue Oct 04 2011 - 07:04:31 CDT)
  • CUDA compiled code for Windows HPC (Wed Sep 28 2011 - 14:52:29 CDT)
  • RE: NAMD running on windows HPC question (Tue Sep 20 2011 - 08:34:51 CDT)
  • NAMD running on windows HPC question (Tue Sep 20 2011 - 07:58:43 CDT)
• Chirag Vora
  • Re: help in FEP calculations_binding free energy difference between 2 inhibitors (Mon Sep 05 2011 - 16:36:04 CDT)
• Chris Chipot
  • Re: help in a FEP restart? (Sat Nov 26 2011 - 10:51:57 CST)
  • Re: Sampling schemes with FEP (Thu Oct 20 2011 - 09:16:34 CDT)
  • Re: Help in reverse Free Energy perturbation - hysteresis (Wed Oct 05 2011 - 01:10:24 CDT)
  • Re: Help in reverse Free Energy perturbation - hysteresis (Mon Oct 03 2011 - 07:05:16 CDT)
  • Re: How to calculate Binding Free energy in NAMD (Sat Jun 18 2011 - 07:51:20 CDT)
  • Re: vmd-l: ParseFEP output errors (Mon Apr 11 2011 - 11:40:10 CDT)
  • Re: vmd: ParseFEP plot mistake (Tue Mar 29 2011 - 07:06:46 CDT)
  • Re: Domain error ParseFEP (Fri Mar 25 2011 - 09:57:19 CDT)
  • Re: Domain error ParseFEP (Fri Mar 25 2011 - 09:41:25 CDT)
  • Re: New NAMD version 2011-03-03 uses (Thu Mar 17 2011 - 13:43:44 CDT)
  • Re: New NAMD version 2011-03-03 uses (Thu Mar 17 2011 - 13:09:30 CDT)
  • Re: New NAMD version 2011-03-03 uses (Tue Mar 15 2011 - 17:37:15 CDT)
  • Re: New NAMD version 2011-03-03 uses (Tue Mar 15 2011 - 10:00:17 CDT)
  • 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)
• Chris Harrison
  • Re: New physical understanding. (Fri Dec 16 2011 - 09:20:53 CST)
  • Re: Umbrella sampling-NAMD (Thu Dec 15 2011 - 14:07:36 CST)
  • Re: Peptide planarity Dihedral angle restraints (Fri Dec 09 2011 - 00:27:29 CST)
  • Re: xplor-formated parameters (Tue Dec 06 2011 - 12:41:05 CST)
  • Re: ERROR: Atoms moving too fast; (Fri Nov 11 2011 - 13:03:52 CST)
  • Re: membrane simulation at high Temp (Fri Nov 04 2011 - 19:01:07 CDT)
  • Re: membrane simulation at high Temp (Fri Nov 04 2011 - 18:58:11 CDT)
  • Re: Reading files for multiple threaded simulations (Wed Nov 02 2011 - 01:57:36 CDT)
  • Re: selection of cholesterol molecules (Wed Nov 02 2011 - 00:06:35 CDT)
  • Re: (Mon Oct 31 2011 - 15:24:19 CDT)
  • Re: ForceConstant in Umbrella Sampling (Fri Oct 28 2011 - 18:10:40 CDT)
  • Re: installing namd on ibm cluster (powerpc) (Fri Oct 28 2011 - 17:35:07 CDT)
  • Re: question about namd simulation on protein in tip4p water box (Fri Oct 28 2011 - 13:43:51 CDT)
  • Re: PME and net charge in the system (Thu Oct 27 2011 - 12:12:46 CDT)
  • Re: * CGtool force field * (Sat Oct 22 2011 - 17:02:37 CDT)
  • Re: how to visualize an alchemical FEP transformation?? (Sat Oct 22 2011 - 12:48:16 CDT)
  • Re: how to visualize an alchemical FEP transformation?? (Thu Oct 20 2011 - 18:02:32 CDT)
  • Re: how to visualize an alchemical FEP transformation?? (Thu Oct 20 2011 - 15:21:59 CDT)
  • Re: tclforces- tcl extension written in c and built with swig (Mon Oct 17 2011 - 18:46:36 CDT)
  • Re: Restarting protein system simulation using different ligand (Sun Oct 16 2011 - 18:41:55 CDT)
  • Re: rsh not working (Wed Oct 12 2011 - 10:08:27 CDT)
  • Re: ABF with Alpha colvar can't be used on supercomputer? (Thu Sep 29 2011 - 10:11:32 CDT)
  • Re: FATAL ERROR: Low global exclusion count! System unstable or pairlistdist or cutoff too small. (Mon Aug 29 2011 - 20:07:33 CDT)
  • Re: FATAL ERROR: Low global exclusion count! System unstable or pairlistdist or cutoff too small. (Mon Aug 29 2011 - 19:35:42 CDT)
  • Re: RNA simulation (Mon Aug 29 2011 - 19:23:07 CDT)
  • Re: FATAL ERROR: Low global exclusion count! System unstable or pairlistdist or cutoff too small. (Mon Aug 29 2011 - 11:50:00 CDT)
  • Re: PME or not PME? What happens if PME is turned off? (Wed Aug 03 2011 - 14:48:12 CDT)
  • Re: TIP4P water model (Thu Jul 21 2011 - 16:54:33 CDT)
  • Re: PME or not PME? What happens if PME is turned off? (Tue Jul 19 2011 - 14:45:48 CDT)
  • Re: Equilibration (Tue Jul 19 2011 - 14:42:06 CDT)
  • Re: free energy of binding (Thu Jul 07 2011 - 17:12:34 CDT)
  • Re: RBCG water simulation (Fri May 27 2011 - 12:49:08 CDT)
  • Re: SMD of three atom at a time (Fri May 20 2011 - 12:22:09 CDT)
  • Re: Typo in NAMD 2.8b2 output for Accelerated MD (Thu May 19 2011 - 09:32:11 CDT)
  • Re: multilevel summation in NAMD (Wed Apr 06 2011 - 21:56:19 CDT)
  • Re: namd and Fedora14 (Tue Mar 29 2011 - 04:36:36 CDT)
  • Re: namd and Fedora14 (Tue Mar 29 2011 - 04:33:39 CDT)
  • Re: implementing RBCG (Tue Mar 22 2011 - 21:25:54 CDT)
  • Re: Am I using the right version for accelerated MD? (Tue Mar 22 2011 - 16:11:35 CDT)
  • Re: namd and Fedora14 (Tue Mar 22 2011 - 08:08:28 CDT)
  • Re: Accelerated MD documentation? (Sat Mar 19 2011 - 00:15:15 CDT)
  • Re: New NAMD version 2011-03-03 uses (Thu Mar 17 2011 - 13:53:08 CDT)
  • Re: New NAMD version 2011-03-03 uses (Tue Mar 15 2011 - 13:18:56 CDT)
  • Re: New NAMD version 2011-03-03 uses (Tue Mar 15 2011 - 10:48:04 CDT)
  • Re: Accelerated MD documentation? (Tue Mar 15 2011 - 09:28:35 CDT)
  • Re: Accelerated MD documentation? (Tue Mar 15 2011 - 09:22:55 CDT)
  • Re: Keyword "lower" not supported...colvars (Sat Mar 12 2011 - 20:52:30 CST)
  • Re: NAMD2.7 on BluegeneL hang at "LDB: Central LB being created..." (Thu Mar 03 2011 - 20:08:20 CST)
  • Re: membrane equilibration (Thu Mar 03 2011 - 18:10:06 CST)
  • Re: NAMD2.7 on BluegeneL hang at "LDB: Central LB being created..." (Thu Mar 03 2011 - 00:41:50 CST)
  • Re: I need help with this (Fri Feb 11 2011 - 12:08:56 CST)
  • Re: I need help with this (Fri Feb 11 2011 - 12:44:42 CST)
  • Re: job termination (Fri Feb 11 2011 - 11:50:20 CST)
  • Re: I need help with this (Fri Feb 11 2011 - 11:42:41 CST)
  • Re: Get number of timesteps from DCD via script (Mon Feb 07 2011 - 12:34:25 CST)
  • Re: Question regarding NAMD membrane tutorial (Thu Feb 03 2011 - 18:32:04 CST)
  • Re: Strange (very large) atom motions (Thu Feb 03 2011 - 18:18:24 CST)
  • Re: Problems compiling NAMD on 8-core Mac (Mon Jan 31 2011 - 22:49:39 CST)
  • Re: Problems compiling NAMD on 8-core Mac (Mon Jan 31 2011 - 16:44:23 CST)
  • Re: Question regarding NAMD membrane tutorial (Mon Jan 31 2011 - 11:11:43 CST)
  • Re: topology for DNA (Fri Jan 28 2011 - 07:59:06 CST)
  • Re: peptide structure (Sun Jan 23 2011 - 10:10:08 CST)
  • Re: the meaning of reassignFreq and reassignTemp (Sun Jan 23 2011 - 09:51:01 CST)
  • Re: discrete energy value after restart (Sun Jan 23 2011 - 10:00:07 CST)
  • Re: Protein-DNA simulations (Wed Jan 19 2011 - 21:24:43 CST)
  • Re: non-zero charge (Wed Jan 19 2011 - 21:08:22 CST)
  • Re: Feature request for the colvars module -- TCL syntax (Mon Jan 17 2011 - 11:00:22 CST)
  • Re: NAMD initial coordinate file (Mon Jan 10 2011 - 06:27:07 CST)
  • 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)
• Christian Jorgensen
  • vmd-l: No APBS output: 'cannot access output file' error (Mon Jul 18 2011 - 18:44:07 CDT)
  • Minimisation algorithm (Thu May 19 2011 - 18:31:03 CDT)
  • vmd-l: ParseFEP output errors (Mon Apr 11 2011 - 11:27:08 CDT)
  • RE: vmd-l: No probability distribution plot in ParseFEP (Fri Apr 01 2011 - 04:09:12 CDT)
  • vmd-l: No probability distribution plot in ParseFEP (Thu Mar 31 2011 - 13:24:27 CDT)
  • RE: vmd: ParseFEP plot mistake (Tue Mar 29 2011 - 10:08:35 CDT)
  • vmd: ParseFEP plot mistake (Tue Mar 29 2011 - 04:45:07 CDT)
  • RE: Domain error ParseFEP (Fri Mar 25 2011 - 09:42:29 CDT)
  • Domain error ParseFEP (Fri Mar 25 2011 - 09:14:02 CDT)
  • RE: New NAMD version 2011-03-03 uses (Thu Mar 17 2011 - 13:34:44 CDT)
  • RE: New NAMD version 2011-03-03 uses (Thu Mar 17 2011 - 12:58:03 CDT)
  • New NAMD version 2011-03-03 uses (Tue Mar 15 2011 - 09:52:27 CDT)
  • PME for electrostatics and cutoff for vdW? (Thu Feb 10 2011 - 11:07:53 CST)
  • RE: Missing angle parameters NH1 CT1 NH1 (Fri Jan 21 2011 - 12:01:09 CST)
  • Missing angle parameters NH1 CT1 NH1 (Fri Jan 21 2011 - 04:39:07 CST)
  • 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)
• christos.lamprakis_at_dcb.unibe.ch
  • set dummyAtom position changing (Fri Apr 01 2011 - 09:44:39 CDT)
  • dissociated quartz SiO2 groups in surface (Tue Dec 14 2010 - 05:39:59 CST)
• Clark Zhang
  • how to define the numsteps in ABF or metadynamics simulation? (Wed Jul 06 2011 - 23:08:50 CDT)
• cnu gromacs
  • NAMD 2.8 job submission script for queenbee (Mon Jul 25 2011 - 18:29:51 CDT)
  • msd calculation for lipid bilayers (Thu May 05 2011 - 14:22:24 CDT)
• Cojocaru, Vlad
  • RE: Fwd: RAMD Setting parameter TclForces from script failed (Mon Mar 28 2011 - 16:55:44 CDT)
  • RE: RAMD Setting parameter TclForces from script failed (Mon Mar 28 2011 - 16:55:14 CDT)
  • RE: RAMD Setting parameter TclForces from script failed (Mon Mar 28 2011 - 14:20:56 CDT)
• 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)
• Cole Gleason
  • unsubscribe (Thu May 19 2011 - 09:37:36 CDT)
  • 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)
• Cosseddu, Salvatore
  • RE: bigdcd file help (Mon Jul 04 2011 - 04:11:55 CDT)
• Courtney Taylor
  • Pair interaction and thermo integration (Mon Aug 01 2011 - 09:32:38 CDT)
  • 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)
• Craig Jolley
  • Strange (very large) atom motions (Thu Feb 03 2011 - 17:14:42 CST)
• 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)
• Cristhian Boetsch
  • Re: Tcl issue with config script (Fri Jun 17 2011 - 10:13:25 CDT)
  • Re: RBCG water simulation (Fri Jun 03 2011 - 07:22:38 CDT)
  • RBCG water simulation (Fri May 27 2011 - 12:17:38 CDT)
• Cristina Rodríguez
  • How to write gradual heating config files (Mon Feb 14 2011 - 19:08:07 CST)
  • 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)
• Cruz-Chu Eduardo Roberto
  • Re: System net charge (Thu Aug 04 2011 - 03:28:45 CDT)
  • Re: Quartz modelling (Thu Jul 28 2011 - 03:20:53 CDT)
  • Re: I need help with this (Thu Feb 10 2011 - 02:51:43 CST)
• D70039
  • different values of "1-4scaling" in a system (Wed Jun 16 2010 - 06:00:06 CDT)
• da xue
  • Setting PME Grid Size (Tue Mar 29 2011 - 20:28:26 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)
• Dan J Martingano
  • Loadleveler Script on Bluegene for NAMD (Fri Jul 02 2010 - 22:48:42 CDT)
• Daniel Aguayo
  • Re: TopoTools for tpr file (Fri Sep 09 2011 - 10:46:33 CDT)
  • Re: Re: vmd-l: CHARMM parameters for Mn 2+ ion (Fri Mar 25 2011 - 14:45:15 CDT)
  • Re: Turning off Electrostatics Completely (Mon Mar 07 2011 - 11:53:55 CST)
  • 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)
• Daniel Hornburg
  • (no subject) (Tue Mar 16 2010 - 07:17:02 CDT)
  • (no subject) (Tue Mar 16 2010 - 06:19:40 CDT)
• Daniel Svozil
  • mmView - a tool for mmCIF exploration (Tue Dec 06 2011 - 05:38:35 CST)
• Danny Xu
  • GBIS on GPU? (Thu Aug 04 2011 - 11:51:57 CDT)
  • Re: max number of CPU PEs per GPU? (Sat Jun 11 2011 - 00:49:10 CDT)
  • Re: max number of CPU PEs per GPU? (Fri Jun 10 2011 - 22:34:34 CDT)
  • Re: max number of CPU PEs per GPU? (Fri Jun 10 2011 - 11:20:13 CDT)
  • max number of CPU PEs per GPU? (Fri Jun 10 2011 - 01:17:53 CDT)
• Darko Stefanovski
  • Re: GPU-CPU small-scale machine for NAMD (Tue May 17 2011 - 12:10:31 CDT)
  • Running NAMD parallel on two machines with 3 CUDAs (Thu May 05 2011 - 11:53:40 CDT)
• David A. Horita
  • RE: namd 2.7 iverbs error 93620 attaching to node (Fri Dec 03 2010 - 11:42:46 CST)
• David Brandon
  • 'Hands-On' Workshop on Computational Biophysics using VMD and NAMD, February 11-15, 2012 in Urbana, Illinois (Thu Nov 17 2011 - 13:46:56 CST)
  • 'Hands-On' Workshop on Computational Biophysics using VMD and NAMD, October 17-21, 2011, Bremen, Germany (Fri Jul 29 2011 - 14:13:05 CDT)
  • "Hands-On" Workshop on Computational Biophysics, March 21-25, 2011, Atlanta, GA, USA (Tue Dec 21 2010 - 14:34:17 CST)
• David Hardy
  • Re: SWM4-NDP Simulation (Wed Aug 24 2011 - 18:49:22 CDT)
  • Re: ewald method (Fri Mar 25 2011 - 10:27:11 CDT)
  • 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)
• David Hemmendinger
  • namd-ibverbs fails to start (Fri Nov 18 2011 - 21:39:20 CST)
• David Huggins
  • Re: Keeping rigidBonds during Minimization (Mon Sep 12 2011 - 12:20:28 CDT)
  • Keeping rigidBonds during Minimization (Wed Aug 31 2011 - 19:05:05 CDT)
  • SWM4-NDP Simulation (Wed Aug 24 2011 - 14:49:33 CDT)
  • NAMD with TIP5P water (Tue Jun 21 2011 - 13:24:49 CDT)
  • TIP5P water simulation (Thu May 26 2011 - 15:57:25 CDT)
  • Langevin Buffer Region (Wed Feb 16 2011 - 04:19:51 CST)
  • Setting Up A Langevin Buffer Region (Wed Feb 16 2011 - 04:30:44 CST)
• 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
  • Problem with NAMD 2.8 (but not in 2.7) : Endless loop repeating "The last position output ..." (Wed Jun 08 2011 - 09:00:34 CDT)
  • NAMD with GPU error : "Number of VDW types exceeds CUDA LJ_TABLE_SIZE" (Fri May 27 2011 - 06:12:42 CDT)
  • Re: Automatic GPU selection in NAMD ? (Thu May 19 2011 - 04:42:39 CDT)
  • Re: Automatic GPU selection in NAMD ? (Tue May 17 2011 - 09:35:57 CDT)
  • Re: Automatic GPU selection in NAMD ? (Tue May 17 2011 - 06:02:29 CDT)
  • Re: Automatic GPU selection in NAMD ? (Tue May 17 2011 - 05:34:21 CDT)
  • Automatic GPU selection in NAMD ? (Tue May 17 2011 - 04:58:56 CDT)
  • AMD Multicore + CUDA Benchmarks, are them ok ? (Thu May 05 2011 - 04:08:30 CDT)
  • 4 x Opteron 12-core or 4 x Xeon 8-core ? (Thu Jan 20 2011 - 05:59:13 CST)
• David Rogers
  • (no subject) (Mon Aug 22 2011 - 20:25:04 CDT)
  • Accessing Colvars Within NAMD TCL (Thu Jun 30 2011 - 10:28:33 CDT)
  • (no subject) (Mon Apr 11 2011 - 22:26:09 CDT)
• David Tanner
  • Re: GBIS and hydrophobic solvation (Thu Oct 13 2011 - 13:40:32 CDT)
  • Re: SASA of PBD files (Thu Aug 25 2011 - 08:47:31 CDT)
  • Re: Implicit solvent (Mon Jun 27 2011 - 09:04:24 CDT)
  • Does GB Implicit Solvent handle explicit ions? (Sun Apr 17 2011 - 06:39:19 CDT)
  • Re: implicit solvent job error in NAMD2.8b1 (Tue Apr 05 2011 - 11:35:49 CDT)
  • Re: implicit solvent job error in NAMD2.8b1 (Mon Apr 04 2011 - 16:34:11 CDT)
  • Re: Generalized Born implicit solvent model in 2.8b1 (Wed Mar 30 2011 - 12:04:20 CDT)
  • Re: GBIS not compatible with CUDA at this time (Tue Mar 22 2011 - 14:21:09 CDT)
  • Re: GBIS synamics (Wed Mar 02 2011 - 07:56:59 CST)
  • Re: Turning off Electrostatics Completely (Thu Feb 24 2011 - 18:50:56 CST)
  • Re: Parameter in configuration NVE or NPT (Wed Feb 16 2011 - 08:37:31 CST)
  • 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)
• Davide Branduardi
  • Re: Compiling NAMD 2.7 with the PLUMED patch (Thu Jan 06 2011 - 17:42:56 CST)
• Davide Vanzo/FS/VCU
  • Problem with SPC/E water simulation (Fri Mar 04 2011 - 15:07:42 CST)
• DDR
  • Installation of NAMD & charm - fatal errors (Sat Mar 27 2010 - 18:23:25 CDT)
• Demet Akten
  • coarse-grained MD (Fri Feb 11 2011 - 03:34:56 CST)
  • temperature range for residue-based CG (Mon Jan 17 2011 - 08:02:59 CST)
  • 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)
• 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)
• Dimitrios Tragoudaras
  • rigid body (Thu Oct 20 2011 - 12:33:45 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)
• divya nayar
  • Na ion, Cl ion in TIP4P (Thu Sep 15 2011 - 02:42:54 CDT)
  • sodium ion in water (Thu Aug 11 2011 - 00:17:27 CDT)
  • Trp-cage folding simulation (Thu Jul 28 2011 - 00:09:07 CDT)
  • finding water around protein (Thu Jun 23 2011 - 00:59:56 CDT)
  • Coulombic component of configurational energy (Tue May 24 2011 - 03:12:24 CDT)
  • 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)
• dklose_at_uni-osnabrueck.de
  • new error in NAMD2.8b1 with fixedAtoms (Tue Apr 19 2011 - 11:45:25 CDT)
• Dong Luo
  • Re: "Constraint failure in RATTLE algorithm" when restart FEP (Mon Aug 01 2011 - 10:50:27 CDT)
  • Re: "Constraint failure in RATTLE algorithm" when restart FEP (Fri Jul 29 2011 - 14:36:44 CDT)
  • "Constraint failure in RATTLE algorithm" when restart FEP (Thu Jul 28 2011 - 12:21:28 CDT)
  • Re: free energy of binding (Thu Jul 07 2011 - 10:50:07 CDT)
  • Re: NAMD 2.7/2.8b1 and BlueGeneL (Wed Apr 13 2011 - 16:46:00 CDT)
  • Re: Replica Exchange Simulations on Blue Gene/P (Tue Apr 12 2011 - 09:54:31 CDT)
  • Re: NAMD2.7 on BluegeneL hang at "LDB: Central LB being created..." (Tue Apr 12 2011 - 09:44:09 CDT)
  • NAMD 2.7/2.8b1 and BlueGeneL (Tue Mar 29 2011 - 11:00:22 CDT)
  • Re: NAMD2.7 on BluegeneL hang at "LDB: Central LB being created..." (Fri Mar 04 2011 - 10:40:54 CST)
  • Re: NAMD2.7 on BluegeneL hang at "LDB: Central LB being created..." (Fri Mar 04 2011 - 08:08:38 CST)
  • Re: NAMD2.7 on BluegeneL hang at "LDB: Central LB being created..." (Thu Mar 03 2011 - 19:59:10 CST)
  • NAMD2.7 on BluegeneL hang at "LDB: Central LB being created..." (Wed Mar 02 2011 - 21:42:57 CST)
  • 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)
• dota alexiou
  • VMD inorganic builder plugin (Thu Mar 17 2011 - 05:36:31 CDT)
  • 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)
• 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)
• Dropbox
  • I M wants to share "legis_2011" with you (Fri Jun 03 2011 - 15:20:24 CDT)
• Edroaldo Lummertz da Rocha
  • MARTINI parameters and Bead definitions (Fri Jun 03 2011 - 18:56:49 CDT)
  • Build .pdb and .psf after coarse graining results in errors (Thu May 19 2011 - 13:37:15 CDT)
  • Add bonds and topology file problem (Sun May 01 2011 - 16:57:16 CDT)
  • Add bonds and topology file problem (Sun May 01 2011 - 15:20:01 CDT)
  • Re: Gold nanoparticle and 1-octanethiol (Thu Apr 28 2011 - 19:07:44 CDT)
  • Re: Gold nanoparticle and 1-octanethiol (Wed Apr 27 2011 - 07:01:52 CDT)
  • Gold nanoparticle and 1-octanethiol (Mon Apr 25 2011 - 13:14:22 CDT)
• Eduard Schreiner
  • Re: about D amino acid (Fri Jul 29 2011 - 04:27:39 CDT)
  • Re: Membrane protein simulaton (Fri Jan 14 2011 - 19:08:43 CST)
  • 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)
• Eduardo Cruz-Chu
  • output forces with tclBC (Mon Mar 28 2011 - 04:33:15 CDT)
  • Re: topology for DNA (Fri Jan 28 2011 - 08:23:33 CST)
  • Re: Atom movement within a range of Z value (Tue May 11 2010 - 15:45:59 CDT)
• Edward Lyman
  • Re: About Columb energy of 2 ions in Vacuum (Tue Aug 23 2011 - 19:47:25 CDT)
  • Re: infrequent rattle failure with charmm36 (Wed Apr 20 2011 - 09:50:37 CDT)
  • infrequent rattle failure with charmm36 (Wed Apr 20 2011 - 08:47:59 CDT)
  • building a MARTINI bilayer (Wed Apr 21 2010 - 12:41:35 CDT)
  • coarse-grained model building (Mon Apr 05 2010 - 13:12:50 CDT)
• ehenriques_at_qui.uc.pt
  • Re: Automatic PSF Builder Problem (Sat Mar 12 2011 - 10:49:05 CST)
  • 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)
• Ehsan Ban
  • Re: Is it possible to print out the force of one specific atom? (Wed Nov 23 2011 - 15:45:49 CST)
  • Re: Using CHARMM Compatible Amber Parameters (Sun Oct 23 2011 - 12:57:03 CDT)
  • Using CHARMM Compatible Amber Parameters (Wed Oct 19 2011 - 20:10:30 CDT)
  • Re: Force Vector Between Two Atoms (Mon Oct 10 2011 - 01:19:55 CDT)
  • Force Vector Between Two Atoms (Fri Oct 07 2011 - 17:14:02 CDT)
  • Re: force question (Thu Sep 22 2011 - 05:18:34 CDT)
  • Re: SMD-extension (Fri Aug 26 2011 - 08:36:10 CDT)
  • Re: Moving an atom 1A0 in one timestep then running MD for 10,000 timesteps while holding that one atom fixed (Mon Aug 15 2011 - 00:01:22 CDT)
  • Re: .COOR TO PDB FILE (Sat Aug 13 2011 - 02:47:27 CDT)
  • Moving an atom 1A0 in one timestep then running MD for 10,000 timesteps while holding that one atom fixed (Fri Jul 29 2011 - 12:40:27 CDT)
• Eli Fine
  • Abnormal EOF Error in Extra Bonds File (Tue Apr 26 2011 - 14:22:11 CDT)
• 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)
• Emily Chen
  • "didn't find VdW parameter for atom type NH3" error (Tue Jun 29 2010 - 07:06:33 CDT)
• Enrico Guarnera
  • Re: Re: Namd-I: Implicit solvent problem (Wed Jul 20 2011 - 11:22:46 CDT)
  • Generalized Born implicit solvent model in 2.8b1 (Wed Mar 30 2011 - 09:40:45 CDT)
• Eric H. Lee
  • Re: Running namd on Mac OS (Tue Jul 20 2010 - 13:06:51 CDT)
• Eric Perim
  • Hello! (Wed Mar 17 2010 - 07:45:19 CDT)
• Erica Smith
  • parameter file for DMPC lipid and protein system but with CHARMM36 lipids (Mon Jan 03 2011 - 21:53:59 CST)
• Erik Nordgren
  • Re: Temperature during membrane equilibration (Fri Sep 09 2011 - 11:17:53 CDT)
  • Re: Heating in NAMD (Fri Aug 19 2011 - 12:52:31 CDT)
  • Re: PME Grid Settings and its significance relative to a cutoff value (Fri Aug 19 2011 - 12:38:34 CDT)
  • Re: nitrogen in namd (Wed Jul 27 2011 - 14:49:04 CDT)
  • Re: Pico scale to nanoscale simulation....alteration if .conf files required (Tue Jul 26 2011 - 20:54:30 CDT)
  • Re: Membranes (Thu Jul 21 2011 - 20:54:46 CDT)
  • Re: Equilibration (Thu Jul 21 2011 - 20:44:38 CDT)
  • Re: Pico scale to nanoscale simulation....alteration if .conf files required (Thu Jul 21 2011 - 20:22:25 CDT)
  • Re: Memory leak and crash before first step (Sun Jul 10 2011 - 04:02:05 CDT)
  • Re: Patch link (Sun Jul 10 2011 - 03:27:51 CDT)
  • (no subject) (Mon Apr 11 2011 - 21:38:33 CDT)
  • 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)
• Erik Santiso
  • Re: how obtain .xst form .dcd file? (Wed Mar 23 2011 - 17:24:16 CDT)
  • 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)
• Ernesto Vargas
  • coordNum colvar with dummyAtom (Mon Dec 19 2011 - 18:56:40 CST)
• esmael
  • Re: PME or not PME? What happens if PME is turned off? (Tue Aug 02 2011 - 18:54:03 CDT)
  • water sphere plus dielectric (Wed Jul 27 2011 - 14:11:20 CDT)
  • alchDecouple (Fri Jul 22 2011 - 19:10:59 CDT)
  • Re: rescaling velocity (Fri Jun 17 2011 - 13:04:10 CDT)
  • rescaling velocity (Wed Jun 15 2011 - 18:17:58 CDT)
• Eva Gonzalez Noya
  • tclforces- tcl extension written in c and built with swig (Mon Oct 17 2011 - 18:30:33 CDT)
  • Re: RE: NAMD-l: energy jump between minimization and simulation (Wed Feb 16 2011 - 16:37:09 CST)
  • Re: energy jump between minimization and simulation (Wed Feb 16 2011 - 13:15:01 CST)
  • Re: energy jump between minimization and simulation (Wed Feb 16 2011 - 10:14:45 CST)
  • energy jump between minimization and simulation (Tue Feb 15 2011 - 18:06:25 CST)
  • energy jump running a simulation after minimization (Tue Feb 15 2011 - 17:23:07 CST)
  • energy jump running a simulation after minimization (Tue Feb 15 2011 - 16:37:59 CST)
• 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)
• 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)
• felmerino_at_uchile.cl
  • Re: AW: glycosaminoglycan with GLYCAM06 in amber format (Wed Dec 21 2011 - 12:44:08 CST)
  • Re: namd force field (Tue Nov 22 2011 - 12:14:28 CST)
  • Re: does any body have the parameter file for aldehyde group? (Fri Jul 08 2011 - 01:44:15 CDT)
  • Re: Iron Oxide and Arsenic (Sat Jun 11 2011 - 17:48:57 CDT)
  • Re: alpha pmf (Wed May 04 2011 - 02:37:06 CDT)
  • Re: SMD for two steered directions (Sun Apr 17 2011 - 13:53:35 CDT)
  • Re: NCS (Tue Feb 15 2011 - 20:22:38 CST)
  • Re: I need help with this (Fri Feb 11 2011 - 10:35:52 CST)
  • Re: water box deformation (Wed Feb 09 2011 - 12:57:23 CST)
  • Re: Proposed Feature in Targeted MD (Mon Jan 31 2011 - 20:20:04 CST)
  • 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)
• 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)
• 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)
• flavio seixas
  • Re: RMSD trajectory (Sat Nov 19 2011 - 08:44:40 CST)
  • RMSD trajectory (Fri Nov 18 2011 - 14:09:15 CST)
  • Re: restraining residues in NAMD (Wed Sep 28 2011 - 17:32:27 CDT)
  • Re: Bonds are too long after simulation (Wed Sep 07 2011 - 13:10:13 CDT)
  • Patch at AutoPsfBuilder (Sun Sep 04 2011 - 14:17:38 CDT)
  • Re: convert pdb format to normal pdb format (Wed Aug 24 2011 - 18:05:18 CDT)
  • Re: Lipid bilayer equilibration: Periodic cell has become too small for original patch grid! (Mon Aug 08 2011 - 21:12:24 CDT)
  • Re: Patch link (Mon Jul 11 2011 - 10:16:54 CDT)
  • Patch link (Fri Jul 08 2011 - 14:11:38 CDT)
  • Re: formyl and ethanolamide parameters and topology (Thu Jun 23 2011 - 21:58:27 CDT)
  • Re: formyl and ethanolamide parameters and topology (Thu Jun 23 2011 - 12:08:58 CDT)
  • Re: conf file script ( help needed ) (Mon Jun 06 2011 - 07:02:41 CDT)
  • Re: conf file script ( help needed ) (Sat Jun 04 2011 - 07:53:08 CDT)
  • Script Help (Sun May 29 2011 - 18:16:51 CDT)
  • NADPH topology (Fri May 27 2011 - 08:58:17 CDT)
  • Namdstats.tcl (Tue May 10 2011 - 14:51:13 CDT)
  • angles (Thu Mar 31 2011 - 15:57:33 CDT)
  • Re: namd and Fedora14 (Mon Mar 28 2011 - 08:55:57 CDT)
  • namd and Fedora14 (Tue Mar 22 2011 - 07:28:27 CDT)
  • Re: NCS (Wed Feb 16 2011 - 18:42:38 CST)
  • Re: NCS (Tue Feb 15 2011 - 17:20:49 CST)
  • Re: NCS (Tue Feb 15 2011 - 05:04:33 CST)
  • NCS (Mon Feb 14 2011 - 14:09:35 CST)
  • 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)
• 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)
• francesco oteri
  • Re: iron sulphur cluster parametrization (Thu Oct 13 2011 - 09:03:43 CDT)
  • iron sulphur cluster parametrization (Thu Oct 06 2011 - 09:24:31 CDT)
  • Re: Namd-I: Implicit solvent problem (Wed Jun 29 2011 - 16:17:21 CDT)
  • Re: last frame and restart are different (Thu May 19 2011 - 15:50:06 CDT)
  • last frame and restart are different (Thu May 19 2011 - 11:12:22 CDT)
  • implicit solvent and cuda (Mon May 02 2011 - 16:03:15 CDT)
  • multilevel summation in NAMD (Wed Apr 06 2011 - 17:32:49 CDT)
  • Re: gromacs analysis tools (Sun Apr 03 2011 - 13:47:19 CDT)
  • Re: Job scheduling (managing) software recommendation (Mon Mar 07 2011 - 06:30:53 CST)
  • GBIS synamics (Wed Mar 02 2011 - 05:02:29 CST)
  • Re: increasing MAX_EXCLUSIONS (Thu Jan 20 2011 - 09:56:35 CST)
  • increasing MAX_EXCLUSIONS (Wed Jan 19 2011 - 16:07:05 CST)
  • 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
  • cpu-gpu vs cpu (Tue Nov 29 2011 - 00:44:10 CST)
  • minimization and gradient trend (Mon Oct 31 2011 - 03:57:10 CDT)
  • cellBasisvectors/.xsc fixing/colvars while running amber ff (Fri Oct 21 2011 - 13:13:57 CDT)
  • Re: Running AMBER FF with NAMD 2.8-CUDA (Wed Oct 19 2011 - 09:23:32 CDT)
  • Running AMBER FF with NAMD 2.8-CUDA (Wed Oct 19 2011 - 08:14:59 CDT)
  • Fwd: rigid bonds (Fri Oct 14 2011 - 09:44:14 CDT)
  • rigid bonds (Fri Oct 14 2011 - 09:24:41 CDT)
  • Epsilon, Rmin for copper ions (Sat Sep 24 2011 - 03:55:34 CDT)
  • Fwd: Solved stream files and paratool (Fri Sep 23 2011 - 10:13:06 CDT)
  • stream files and paratool (Fri Sep 23 2011 - 03:10:52 CDT)
  • nvidia cuda driver version (Fri Aug 05 2011 - 08:44:44 CDT)
  • About fastest CUDA cards (Fri Jul 29 2011 - 04:09:37 CDT)
  • SOLVED: Failure to run namd-cuda with gtx-470 (Fri Jul 22 2011 - 09:56:34 CDT)
  • Re: free energy of binding (Thu Jul 07 2011 - 16:50:12 CDT)
  • free energy of binding (Thu Jul 07 2011 - 04:52:38 CDT)
  • Re: Failure to run namd-cuda with gtx-470 (Thu Jul 07 2011 - 01:57:25 CDT)
  • Re: Failure to run namd-cuda with gtx-470 (Wed Jul 06 2011 - 16:18:53 CDT)
  • Failure to run namd-cuda with gtx-470 (Wed Jul 06 2011 - 10:44:38 CDT)
  • Fwd: nvidia 275.09.07 driver. SOLVED, NO DRIVER PROBLEM (Thu Jun 30 2011 - 14:49:56 CDT)
  • nvidia 275.09.07 driver (Thu Jun 30 2011 - 03:24:48 CDT)
  • Re: vmd-l: Re: Fwd: "cuda error cudastreamcreate", (Fri Jun 17 2011 - 02:36:49 CDT)
  • Re: Fwd: "cuda error cudastreamcreate", (Fri Jun 17 2011 - 00:50:05 CDT)
  • Re: cuda error cudastreamcreate. SOLVED (probably) (Thu Jun 16 2011 - 00:57:15 CDT)
  • Fwd: cuda error cudastreamcreate. SOLVED (probably) (Wed Jun 15 2011 - 09:43:28 CDT)
  • Fwd: cuda error cudastreamcreate. SOLVED (probably) (Wed Jun 15 2011 - 02:45:26 CDT)
  • cuda error cudastreamcreate (Tue Jun 14 2011 - 00:45:37 CDT)
  • Fwd: AMD-PhenomII-1075_GTX470 NAMD-CUDA performance (Mon Jun 06 2011 - 04:30:46 CDT)
  • Fwd: AMD-PhenomII-1075_GTX470 NAMD-CUDA performance (Mon Jun 06 2011 - 04:15:44 CDT)
  • AMD-PhenomII-1075_GTX470 NAMD-CUDA performance (Mon Jun 06 2011 - 02:54:52 CDT)
  • GPU-CPU small-scale machine for NAMD (Mon May 16 2011 - 03:45:37 CDT)
  • Fwd: ramd seed (Thu Apr 07 2011 - 08:41:08 CDT)
  • Fwd: Wrong exit from RAMD runs (Tue Apr 05 2011 - 15:34:19 CDT)
  • Wrong exit from RAMD runs (Tue Apr 05 2011 - 03:11:29 CDT)
  • Fwd: Incompatibility between colvars and tclforces? (Wed Mar 30 2011 - 12:32:53 CDT)
  • Re: Fwd: Incompatibility between colvars and tclforces? (Thu Mar 31 2011 - 02:45:10 CDT)
  • Re: Incompatibility between colvars and tclforces? (Wed Mar 30 2011 - 11:29:15 CDT)
  • Re: Incompatibility between colvars and tclforces? (Wed Mar 30 2011 - 09:06:13 CDT)
  • Incompatibility between colvars and tclforces? (Wed Mar 30 2011 - 05:04:02 CDT)
  • Re: RAMD Setting parameter TclForces from script failed (Tue Mar 29 2011 - 06:09:40 CDT)
  • Re: RAMD Setting parameter TclForces from script failed (Tue Mar 29 2011 - 02:51:19 CDT)
  • Re: RAMD Setting parameter TclForces from script failed (Mon Mar 28 2011 - 16:09:55 CDT)
  • Fwd: RAMD Setting parameter TclForces from script failed (Mon Mar 28 2011 - 15:37:24 CDT)
  • Fwd: RAMD Setting parameter TclForces from script failed (Mon Mar 28 2011 - 15:19:57 CDT)
  • Re: RAMD Setting parameter TclForces from script failed (Mon Mar 28 2011 - 14:43:34 CDT)
  • Re: RAMD Setting parameter TclForces from script failed (Mon Mar 28 2011 - 09:50:31 CDT)
  • RAMD Setting parameter TclForces from script failed (Mon Mar 28 2011 - 05:26:21 CDT)
  • Fwd: ramd firstRamdAtom (Mon Mar 28 2011 - 03:15:56 CDT)
  • ramd firstRamdAtom (Mon Mar 28 2011 - 02:22:20 CDT)
  • Re: partial charges for organic ligands (Sat Mar 26 2011 - 15:23:05 CDT)
  • partial charges for organic ligands (Sat Mar 26 2011 - 11:45:26 CDT)
  • Re: Accelerated MD documentation? (Tue Mar 15 2011 - 10:20:18 CDT)
  • Setting up values in distance colvar (Sun Mar 13 2011 - 12:49:51 CDT)
  • Fwd: Keyword "lower" not supported...colvars (Sun Mar 13 2011 - 05:37:41 CDT)
  • Keyword "lower" not supported...colvars (Sat Mar 12 2011 - 11:16:19 CST)
  • Re: BOUNCE namd-l@ks.uiuc.edu: Message too long (>40000 chars) (Fri Mar 11 2011 - 11:46:30 CST)
  • Re: Fwd: vmd-l: Re: hBond colvars and patching (Fri Mar 11 2011 - 09:07:20 CST)
  • Fwd: vmd-l: Re: hBond colvars and patching (Tue Mar 08 2011 - 00:34:36 CST)
  • Re: vmd-l: Re: hBond colvars and patching (Mon Mar 07 2011 - 10:04:37 CST)
  • Re: hBond colvars and patching (Mon Mar 07 2011 - 00:12:54 CST)
  • hBond colvars and patching (Sun Mar 06 2011 - 14:05:47 CST)
  • Fwd: hBond component in colvars and patching (Sun Mar 06 2011 - 02:36:10 CST)
  • hBond component in colvars and patching (Sat Mar 05 2011 - 14:38:45 CST)
  • Model system spherical sieve (Fri Mar 04 2011 - 14:28:32 CST)
  • Positional restraints - Dielectric constant (Wed Mar 02 2011 - 10:56:18 CST)
  • binaryrestart/binaryoutput problem (Tue Mar 01 2011 - 02:54:26 CST)
  • Fwd: binaryrestart/binaryoutput problem (Tue Mar 01 2011 - 02:56:29 CST)
  • mainboard-power source for GPU (Tue Jan 25 2011 - 01:47:42 CST)
  • 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)
• 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)
• gaborekt_at_duq.edu
  • Turning off Electrostatics Completely (Thu Feb 24 2011 - 16:05:41 CST)
• Gabriel Jara
  • (no subject) (Tue Nov 22 2011 - 06:59:12 CST)
  • 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)
• Gary M. Skinner
  • unsubscribe (Mon May 09 2011 - 03:31:45 CDT)
  • FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT (Thu Apr 07 2011 - 07:17:14 CDT)
• Gayatri Rathod
  • Cannot find bond parameters (Tue Jun 28 2011 - 11:03:45 CDT)
• gbellesia_at_chem.ucsb.edu
  • Re: namd job crashed (Mon Feb 01 2010 - 11:29:33 CST)
• George Khelashvili
  • How to restraint angle in NAMD (Fri Oct 01 2010 - 21:32:29 CDT)
• George M Giambasu
  • Re: Sticking TIP4P water molecules AMBER (Mon Dec 19 2011 - 10:16:56 CST)
• George Madalin Giambasu
  • Re: Problem with NAMD2.8 & prmtop files made with AMBER11/AmberTools1.5 (Wed Sep 28 2011 - 19:04:22 CDT)
  • online guide for using amber ff in NAMD (Wed Aug 03 2011 - 11:18:10 CDT)
  • 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)
• Germain Salvato Vallverdu
  • Re: vmd-l: RMSD Question (Mon Nov 29 2010 - 02:56:05 CST)
• Giacomo Fiorin
  • Re: coordNum colvar with dummyAtom (Thu Dec 22 2011 - 17:41:20 CST)
  • Re: paper/articule on colvars module (Tue Nov 29 2011 - 01:12:39 CST)
  • Re: Scaled forces, colvars and harmonic con/restraints (Wed Nov 23 2011 - 14:40:34 CST)
  • Re: Scaled forces, colvars and harmonic con/restraints (Wed Nov 23 2011 - 09:28:50 CST)
  • Re: Extra bonds-ABF (Mon Nov 07 2011 - 11:01:22 CST)
  • Re: membrane simulation at high Temp (Fri Nov 04 2011 - 16:56:12 CDT)
  • Re: cellBasisvectors/.xsc fixing/colvars while running amber ff (Fri Oct 21 2011 - 17:06:43 CDT)
  • Re: ABF & distanceZ projection axis (Wed Sep 21 2011 - 19:22:36 CDT)
  • Re: restraint with colvars mocule (Mon Sep 12 2011 - 11:23:57 CDT)
  • Re: colvar restrain of water in lipid system (Mon Aug 29 2011 - 11:06:44 CDT)
  • Re: colvar restrain of water in lipid system (Mon Aug 29 2011 - 09:36:39 CDT)
  • Re: combining metadynamics simulations (Fri Aug 26 2011 - 09:18:01 CDT)
  • Re: distanceXY colvar-ABF (Sun Aug 21 2011 - 12:28:07 CDT)
  • Re: colvars, discontinuous rotation (Wed Jul 27 2011 - 21:20:41 CDT)
  • Re: Setting integrator parameters for ABF (Wed Jul 27 2011 - 14:10:17 CDT)
  • Re: Setting integrator parameters for ABF (Wed Jul 27 2011 - 13:12:46 CDT)
  • Re: Suspend NAMD (to RAM) (Wed Jul 20 2011 - 20:41:27 CDT)
  • Re: protein moving out during npt equilibration (Wed Jul 13 2011 - 10:54:10 CDT)
  • Re: Colvars "tilt" component force constant units for WHAM (Tue Jul 12 2011 - 23:19:31 CDT)
  • Re: how to define the numsteps in ABF or metadynamics simulation? (Tue Jul 12 2011 - 15:06:17 CDT)
  • Re: metadynamics combined with PCV (Fri Jun 03 2011 - 12:28:53 CDT)
  • Re: Alpha P.M.F. with NAMD 2.8 (Fri Jun 03 2011 - 07:16:05 CDT)
  • Re: error in the orientationAngle (Sat May 21 2011 - 09:47:49 CDT)
  • Re: hi (Wed May 18 2011 - 10:28:48 CDT)
  • Re: what will be the best way to simulate substrate interaction only within a binding pocket of a large protein. (Tue May 10 2011 - 15:20:18 CDT)
  • Re: alpha pmf (Mon May 09 2011 - 16:05:19 CDT)
  • Re: ABF simulation with extendedLagrangian on keeps crashing (Thu May 05 2011 - 16:22:09 CDT)
  • Re: alpha pmf (Thu May 05 2011 - 09:31:51 CDT)
  • Re: question about rotation force in SMD (Wed Apr 27 2011 - 10:00:33 CDT)
  • Re: ABF calculation using RMSD (Mon Apr 25 2011 - 22:26:54 CDT)
  • Re: Can I set a range to limit the ABF (Wed Apr 20 2011 - 11:25:44 CDT)
  • Re: ABF simulation with extendedLagrangian on keeps crashing (Wed Apr 20 2011 - 11:22:37 CDT)
  • Re: ABF simulation with extendedLagrangian on keeps crashing (Tue Apr 19 2011 - 11:41:55 CDT)
  • Re: question on the center of mass calculation in colvar (Sat Apr 16 2011 - 10:33:23 CDT)
  • Re: Error: keyword "group1" is not supported, or not recognized in this context. (Fri Apr 15 2011 - 11:02:03 CDT)
  • Re: NAMD feture request (Wed Apr 13 2011 - 10:17:27 CDT)
  • Re: problem for simulation of membrane protein system (Tue Apr 12 2011 - 11:30:39 CDT)
  • Re: protein on solid surface (Fri Apr 08 2011 - 11:21:33 CDT)
  • Re: Why NAMD writes colvars step by step (Sat Apr 02 2011 - 19:38:26 CDT)
  • Re: Why NAMD writes colvars step by step (Fri Apr 01 2011 - 21:10:15 CDT)
  • Re: angles (Thu Mar 31 2011 - 18:05:28 CDT)
  • Re: Incompatibility between colvars and tclforces? (Wed Mar 30 2011 - 11:20:08 CDT)
  • Re: GBIS and ABF (Mon Mar 28 2011 - 10:08:00 CDT)
  • Re: GBIS and ABF (Mon Mar 28 2011 - 10:09:55 CDT)
  • Re: GBIS question and possible Bug for colvar "outputSystemForce" declaration in NAMD CVS-2011-03-03 (Tue Mar 22 2011 - 21:07:53 CDT)
  • Re: A "strange" observation during ColVar calculations (Mon Mar 21 2011 - 15:46:27 CDT)
  • Re: ABF colvar error-capped nanotube interaction (Sat Mar 19 2011 - 13:54:37 CDT)
  • Re: GBIS and ABF (Thu Mar 17 2011 - 20:02:37 CDT)
  • Re: Fwd: vmd-l: Re: hBond colvars and patching (Fri Mar 11 2011 - 11:40:06 CST)
  • Re: hBond colvars and patching (Sun Mar 06 2011 - 22:57:04 CST)
  • Re: Positional restraints - Dielectric constant (Wed Mar 02 2011 - 13:42:33 CST)
  • Re: New colvar feature request -- angleXY (Mon Feb 14 2011 - 17:07:05 CST)
  • Re: New colvar feature request -- angleXY (Mon Feb 14 2011 - 09:43:33 CST)
  • Re: (Thu Feb 03 2011 - 10:49:22 CST)
  • Re: Distance XY-colvars (Wed Jan 05 2011 - 16:12:32 CST)
  • Re: Running bias exchange metadynamics simulations with NAMD (Mon Jan 03 2011 - 18:13:21 CST)
  • 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)
• Gianluca Interlandi
  • Re: What is the proper value of TMDk in TMD simulations? (Mon Oct 24 2011 - 11:03:37 CDT)
  • PBC Wrap + TMD (Mon Oct 10 2011 - 14:02:58 CDT)
  • Re: free energy of binding (Thu Jul 07 2011 - 17:29:18 CDT)
  • Re: free energy of binding (Thu Jul 07 2011 - 17:08:55 CDT)
  • Re: Namd-I: Implicit solvent problem (Wed Jun 29 2011 - 17:49:51 CDT)
  • Re: Namd-I: Implicit solvent problem (Wed Jun 29 2011 - 16:31:49 CDT)
  • Re: Question about equilibration (Wed Jun 15 2011 - 14:18:43 CDT)
  • Re: Question about equilibration (Wed Jun 15 2011 - 14:03:57 CDT)
  • Re: Does GB Implicit Solvent handle explicit ions? (Sun Apr 17 2011 - 22:43:37 CDT)
  • Re: GeForce vs Tesla GPUs for high performance computing (Thu Apr 14 2011 - 14:48:58 CDT)
  • Re: Help building a desktop for namd (Wed Apr 13 2011 - 17:06:53 CDT)
  • Re: Help building a desktop for namd (Mon Apr 11 2011 - 16:25:26 CDT)
  • Re: Help building a desktop for namd (Mon Apr 11 2011 - 16:21:27 CDT)
  • Re: Help building a desktop for namd (Mon Apr 11 2011 - 14:41:28 CDT)
  • Re: Abe versus Lincoln (Thu Apr 07 2011 - 16:55:51 CDT)
  • Re: Abe versus Lincoln (Thu Apr 07 2011 - 15:40:11 CDT)
  • Re: Abe versus Lincoln (Thu Apr 07 2011 - 13:57:41 CDT)
  • Re: Abe versus Lincoln (Thu Apr 07 2011 - 13:50:45 CDT)
  • Abe versus Lincoln (Thu Apr 07 2011 - 13:22:37 CDT)
  • Re: NAMD 2.7 released (Thu Mar 17 2011 - 17:58:46 CDT)
  • NAMD + Plumed on Abe (Fri Feb 25 2011 - 00:03:17 CST)
  • Re: accuracy of measurement (Mon Feb 21 2011 - 22:11:43 CST)
  • CHARMM General Force Field (CGENFF) (Wed Feb 16 2011 - 18:56:33 CST)
  • Re: Compiling NAMD 2.7 with the PLUMED patch (Thu Jan 06 2011 - 17:41:23 CST)
  • Compiling NAMD 2.7 with the PLUMED patch (Thu Jan 06 2011 - 16:55:03 CST)
  • 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)
• Giovanni Bellesia
  • Re: collective variable calculation from dcd file (Wed Dec 21 2011 - 15:20:27 CST)
  • collective variable calculation from dcd file (Wed Dec 21 2011 - 14:44:47 CST)
  • combining metadynamics simulations (Fri Aug 26 2011 - 08:40:29 CDT)
  • Restarting an alchemic FEP calculation (Mon Jun 27 2011 - 09:32:25 CDT)
  • Re: protein on solid surface (Fri Apr 08 2011 - 13:45:31 CDT)
  • protein on solid surface (Fri Apr 08 2011 - 09:48:50 CDT)
• Giovanni Nico
  • usage of NAMD with AMBER commands (Tue Jun 15 2010 - 11:51:08 CDT)
• Giovanni Settanni
  • Re: Namd-I: Implicit solvent problem (Thu Jun 30 2011 - 01:56:13 CDT)
• Gmail
  • Unsubscribe (Mon Sep 12 2011 - 14:33:58 CDT)
• Gong Xiaojing
  • About matdcd (Sat Apr 03 2010 - 21:23:39 CDT)
• GONZALEZ NOYA, EVA
  • CT1 terminal patch for THR (Mon Mar 07 2011 - 14:47:57 CST)
• Goutham
  • minimization gradient question (Thu Feb 04 2010 - 19:20:32 CST)
• 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)
• Grazia Cottone
  • Re: slow heating md (Thu Jun 23 2011 - 08:33:37 CDT)
  • Re: dcd files (Sun May 22 2011 - 15:14:41 CDT)
  • Re: pentacoordinate heme (Tue Mar 08 2011 - 16:58:27 CST)
  • pentacoordinate heme (Sun Mar 06 2011 - 09:43:02 CST)
  • ligand parameters (Wed Oct 20 2010 - 06:43:23 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)
• 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
  • Re: Replica exchange MD with NAMD with SGE.... (Wed Jul 13 2011 - 17:50:57 CDT)
  • FATAL error when run Replica Exchange Method on Franklin (Thu May 12 2011 - 14:03:58 CDT)
  • Error when run Replica Exchange Method on Ranger (Thu May 12 2011 - 14:13:59 CDT)
  • 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
  • (no subject) (Thu Nov 03 2011 - 03:01:19 CDT)
  • (no subject) (Thu Nov 03 2011 - 03:00:22 CDT)
  • installing namd on ibm cluster (powerpc) (Fri Oct 28 2011 - 15:14:02 CDT)
  • fftw libraries for ppc (Wed Oct 19 2011 - 22:04:42 CDT)
  • Re: water equilibration (Tue Jun 07 2011 - 15:14:51 CDT)
  • FATAL ERROR: CAN'T FIND CROSSTERM PARAMETERS FOR CC NH1 CT1 C NH1 CT1 C NH1 (Sat Nov 06 2010 - 02:41:31 CDT)
• HAMID -
  • Re: * CGtool force field * (Wed Oct 26 2011 - 08:47:39 CDT)
  • Re: * CGtool force field * (Sun Oct 23 2011 - 03:09:03 CDT)
  • Re: * CGtool force field * (Sat Oct 22 2011 - 14:11:14 CDT)
  • * CGtool force field * (Sat Oct 22 2011 - 12:00:19 CDT)
  • RBCG electrostatic term (Thu Oct 20 2011 - 12:43:33 CDT)
  • RBCG water (Thu Oct 13 2011 - 17:45:14 CDT)
  • Re: membrane simulation and mobility of lipids - blocking ion channel (Thu Sep 29 2011 - 04:57:10 CDT)
  • Re: membrane simulation and mobility of lipids - blocking ion channel (Thu Sep 29 2011 - 04:33:48 CDT)
  • Re: ABF & distanceZ projection axis more (Thu Sep 22 2011 - 05:36:32 CDT)
  • Re: save the last frame as a pdb file using dcd file (Thu Sep 22 2011 - 03:08:25 CDT)
  • ABF & distanceZ projection axis more (Thu Sep 22 2011 - 03:05:07 CDT)
  • Re: ABF & distanceZ projection axis (Thu Sep 22 2011 - 01:20:02 CDT)
  • ABF & distanceZ projection axis (Wed Sep 21 2011 - 16:15:45 CDT)
  • ABF results interpretation (Wed Sep 21 2011 - 10:22:38 CDT)
• hamid mosaddeghi
  • build a layer (Wed Aug 25 2010 - 07:58:46 CDT)
• hamze rahimi
  • convert pdb format to normal pdb format (Wed Aug 24 2011 - 04:48:09 CDT)
  • MD condition (Sun Aug 14 2011 - 05:02:36 CDT)
  • zinc-finger protein simulation (Mon Jul 18 2011 - 06:55:08 CDT)
  • problem with MD (Tue Feb 15 2011 - 00:25:25 CST)
  • problem with cuda version (Wed Dec 08 2010 - 12:30:23 CST)
  • run NAMD_2.7B2 (Sat Jan 02 2010 - 00:58:42 CST)
• Hannes Loeffler
  • interpretation of timing data in output (Fri Jun 24 2011 - 04:29:42 CDT)
  • 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)
• 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)
• Haque-Student,STW, Farhadul
  • Trouble running NAMD on win7 (Sun Sep 25 2011 - 23:44:14 CDT)
• harish vashisth
  • Re: TClforce (Thu Oct 20 2011 - 12:29:14 CDT)
  • Re: implicit solvent job error in NAMD2.8b1 (Mon Apr 04 2011 - 17:14:20 CDT)
  • implicit solvent job error in NAMD2.8b1 (Mon Apr 04 2011 - 15:47:33 CDT)
  • Re: help needed (Tue Mar 01 2011 - 10:00:46 CST)
  • 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)
• Harshad Joshi
  • Simulating more than 20 Million atom system (Mon Feb 21 2011 - 16:01:47 CST)
• Hasan haska
  • about md in npt (Wed Dec 28 2011 - 02:18:30 CST)
  • equilibrate the system in NPT (Mon Dec 26 2011 - 13:57:37 CST)
  • Interfaces in NAMD (Sat Dec 17 2011 - 14:20:25 CST)
  • Re: cell size (Wed Dec 14 2011 - 06:41:10 CST)
  • Re: cell size (Tue Dec 13 2011 - 09:47:50 CST)
  • cell size (Tue Dec 13 2011 - 08:10:49 CST)
  • equilibrate water molecules (Thu Nov 24 2011 - 01:43:38 CST)
  • different velocities problem (Tue Oct 25 2011 - 01:28:22 CDT)
  • namd 2.8 new feature (Thu Sep 22 2011 - 08:37:27 CDT)
  • Re: force question (Thu Sep 22 2011 - 05:36:47 CDT)
  • force question (Thu Sep 22 2011 - 02:50:18 CDT)
  • TopoTools for tpr file (Fri Sep 09 2011 - 09:01:44 CDT)
  • namd files (Wed Jul 20 2011 - 08:17:34 CDT)
  • slow heating md (Thu Jun 23 2011 - 06:11:51 CDT)
  • NPT simulations in NAMD (Tue Apr 05 2011 - 07:31:52 CDT)
  • charmm 19 parameters (Fri Mar 25 2011 - 09:49:24 CDT)
  • ewald method (Fri Mar 25 2011 - 09:49:57 CDT)
  • ewald method (Fri Mar 25 2011 - 09:45:45 CDT)
  • charmm 19 parameters (Fri Mar 25 2011 - 09:38:41 CDT)
  • NAMD installation (Mon Oct 04 2010 - 05:25:06 CDT)
• Haydee Valdes
  • restraining residues in NAMD (Wed Sep 28 2011 - 10:59:20 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)
• Henriette Elisabeth Autzen
  • Impropers in Charmm and OPLS (Tue Jun 14 2011 - 08:33:58 CDT)
• hgrabner
  • error codes: 255 (Wed Oct 20 2010 - 03:57:07 CDT)
• 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
  • combining thermodynamic integration with replica exchange in NAMD (Mon Jul 25 2011 - 10:05:50 CDT)
  • Re: (NAMD2.7b1) loadtotalforces gives output even when there are no forces in system (Mon Mar 07 2011 - 07:10:09 CST)
  • 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)
• Hyonseok Hwang
  • question on the center of mass calculation in colvar (Sat Apr 16 2011 - 09:57:16 CDT)
  • parallel scaling issues (Wed Jul 21 2010 - 09:11:18 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)
• imran.1.618_at_gmail.com
  • RE: Hello (Sat Oct 15 2011 - 00:32:59 CDT)
• Indrajit Deb
  • Problem on periodic boundary condition (Wed Feb 24 2010 - 07:25:28 CST)
• ipsita basu
  • membrane system (Wed Sep 21 2011 - 01:30:00 CDT)
  • image centering problem (Thu Aug 11 2011 - 00:41:20 CDT)
  • problem in restarting (Thu Apr 14 2011 - 02:11:24 CDT)
  • psf problem (Sat Mar 12 2011 - 04:33:39 CST)
  • psf problem (Fri Mar 11 2011 - 08:24:10 CST)
  • job termination (Fri Feb 11 2011 - 00:46:17 CST)
  • Re: peptide structure (Thu Jan 27 2011 - 02:29:21 CST)
  • peptide structure (Tue Jan 18 2011 - 23:05:34 CST)
  • 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)
• Irene Newhouse
  • Problem with NAMD2.8 & prmtop files made with AMBER11/AmberTools1.5 (Wed Sep 28 2011 - 15:40:24 CDT)
  • RE: topology for monophosphate (Wed Apr 06 2011 - 14:02:30 CDT)
  • topology for monophosphate (Tue Apr 05 2011 - 15:25:52 CDT)
  • RE: rule of thumb for dcd sampling frequency? (Tue Mar 22 2011 - 13:00:28 CDT)
  • rule of thumb for dcd sampling frequency? (Mon Mar 21 2011 - 13:26:25 CDT)
  • compiling NAMD w. infiniband (Fri Jun 04 2010 - 16:21:37 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)
• ishiikai08_at_yahoo.co.jp
  • Periodic Boundary conditions (Mon Jun 20 2011 - 06:11:49 CDT)
  • Re:Re: Periodic Boundary conditions (Thu Jun 02 2011 - 03:14:12 CDT)
  • Periodic Boundary conditions (Tue May 31 2011 - 21:57:03 CDT)
• Ismail, Mohd F.
  • RE: Batch Mode MD simulation Script for NAMD (Fri Aug 12 2011 - 14:40:31 CDT)
  • RE: Batch Mode MD simulation Script for NAMD (Fri Aug 12 2011 - 13:07:59 CDT)
  • RE: Explicit Solvent Sytem (40% Ethanol + 60% Water) (Tue Aug 09 2011 - 13:02:19 CDT)
  • Get restart file (restart.coor) from DCD (Mon Mar 28 2011 - 17:41:56 CDT)
  • NAMD on GPU (Sun Mar 20 2011 - 21:24:09 CDT)
  • NAMD initial coordinate file (Fri Jan 07 2011 - 00:10:47 CST)
• Ivan Vyalov
  • Re: FEP with flattened free energy surface? (Fri Apr 08 2011 - 15:48:09 CDT)
  • Re: FEP with flattened free energy surface? (Fri Apr 08 2011 - 14:12:38 CDT)
  • FEP with flattened free energy surface? (Wed Apr 06 2011 - 04:49:50 CDT)
• Jacopo Sgrignani
  • Steered dynamics (Fri Nov 11 2011 - 04:56:32 CST)
  • NOE (Tue Sep 20 2011 - 07:27:09 CDT)
  • SMD (Thu Sep 15 2011 - 07:12:26 CDT)
  • SMD (Mon Sep 12 2011 - 02:53:30 CDT)
  • Lingand Unbinding using SMD (Mon Aug 15 2011 - 02:19:17 CDT)
  • trajectory_path.tcl (Tue May 17 2011 - 09:16:47 CDT)
  • print center of mass (Tue May 10 2011 - 10:54:09 CDT)
  • 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)
• jafar azamat
  • PMF (Tue Oct 25 2011 - 06:52:28 CDT)
  • umbrella sampling by NAMD (Tue Jun 14 2011 - 06:27:45 CDT)
  • PMF (Tue May 24 2011 - 00:47:30 CDT)
  • PMF calculation (Mon May 23 2011 - 07:31:13 CDT)
• 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)
• Jaime Gonzalez
  • Debug NAMD with CharmDebug (Tue Jul 20 2010 - 03:41:45 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)
• Jan H. Meinke
  • Replica Exchange Simulations on Blue Gene/P (Tue Apr 12 2011 - 07:09:32 CDT)
• Jane Ren
  • NAMD Tutorial Problem (Thu Jan 06 2011 - 13:19:50 CST)
  • 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 vinod
  • Re: charmrun constantly hanging (Sat Nov 26 2011 - 01:06:22 CST)
  • charmrun constantly hanging (Fri Nov 25 2011 - 00:59:35 CST)
  • 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)
• 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)
• jaya c.jose
  • Implicit solvent simulation (Fri Jul 08 2011 - 05:35:40 CDT)
  • 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: Steered dynamics (Sat Nov 12 2011 - 01:18:06 CST)
  • RE: improper angle (Sat Nov 12 2011 - 01:14:09 CST)
  • RE: ABF with Alpha colvar can't be used on supercomputer? (Thu Sep 29 2011 - 08:05:19 CDT)
  • Re: ABF with Alpha colvar can't be used on supercomputer? (Thu Sep 29 2011 - 01:05:53 CDT)
  • Re: about extrabonds restrain (Tue Aug 30 2011 - 08:41:35 CDT)
  • RE: About Columb energy of 2 ions in Vacuum (Fri Aug 26 2011 - 01:37:05 CDT)
  • Re: Batch Mode MD simulation Script for NAMD (Sat Aug 13 2011 - 08:45:56 CDT)
  • Re: .COOR TO PDB FILE (Sat Aug 13 2011 - 01:29:04 CDT)
  • RE: Minimization is taking a lot of computing time. (Wed Aug 10 2011 - 00:52:16 CDT)
  • RE: Custom CHARMM forcefield usage problem (Wed Aug 10 2011 - 00:00:55 CDT)
  • Re: colvars, discontinuous rotation (Wed Jul 27 2011 - 23:27:23 CDT)
  • colvars, discontinuous rotation (Wed Jul 27 2011 - 20:41:30 CDT)
  • RE: using colvars for bending modulus? (Wed Jul 27 2011 - 01:40:24 CDT)
  • using colvars for bending modulus? (Tue Jul 26 2011 - 15:43:50 CDT)
  • Re: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR C H (ATOMS 2 1) (Thu Jun 23 2011 - 16:17:59 CDT)
  • patch needed for tuple is missing (Sat Jun 18 2011 - 23:49:47 CDT)
  • colvars orientation problem appears in 2.8 only? (Thu Apr 28 2011 - 18:41:17 CDT)
  • Re: Can paratools really parametrize a structure? Is it really finished? (Mon Feb 28 2011 - 13:31:16 CST)
  • RE: Can paratools really parametrize a structure? Is it really finished? (Mon Feb 28 2011 - 11:23:54 CST)
  • RE: maximum number of atoms per patch (Sun Feb 27 2011 - 12:34:36 CST)
  • Re: Computing interaction energies in namd (Tue Feb 22 2011 - 14:48:51 CST)
  • RE: ABF calculation using RMSD (Wed Feb 16 2011 - 21:24:01 CST)
  • RE: Can I do protein-ligand docking using NAMD? (Wed Feb 16 2011 - 01:08:36 CST)
  • Re: question from a tutorial (Thu Jan 20 2011 - 14:29:23 CST)
  • RE: NAMD CUDA error message (Fri Jan 14 2011 - 11:46:39 CST)
  • Re: restart problem (Wed Jan 05 2011 - 14:23:32 CST)
  • RE: NAG simulation problem with CPS (Wed Jan 05 2011 - 08:04:24 CST)
  • RE: parameter file for DMPC lipid and protein system but with CHARMM36 lipids (Mon Jan 03 2011 - 23:34:18 CST)
  • 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)
• JC S
  • Run-time system modification (Mon Nov 22 2010 - 23:38:54 CST)
• Jeff Wereszczynski
  • Re: free energy of binding (Thu Jul 07 2011 - 18:27:55 CDT)
  • Re: Setting up aMD simulation of a membrane protein (Fri Apr 01 2011 - 11:00:23 CDT)
  • Re: Accelerated MD: question about dual boost mode (Thu Mar 31 2011 - 17:07:07 CDT)
  • Re: New NAMD version 2011-03-03 uses (Tue Mar 15 2011 - 11:49:28 CDT)
  • Compiling NAMD on Cray XE6 (Mon Feb 28 2011 - 11:38:48 CST)
  • 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)
• Jeffery Klauda
  • TIP4P with NPT (Thu Nov 18 2010 - 12:44:56 CST)
• Jeffrey J. Potoff
  • Re: (Tue Aug 16 2011 - 09:35:20 CDT)
  • Re: initial structures for md simulations (Wed Feb 16 2011 - 09:02:13 CST)
  • 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: Re: Generating .tpr file using NAMD files (Mon Dec 19 2011 - 12:05:56 CST)
  • Re: Pressure Problems, Excessively High Readings (Wed Nov 09 2011 - 04:02:30 CST)
  • Re: TopoTools for tpr file (Fri Sep 09 2011 - 11:09:22 CDT)
  • Re: Relationship between High temperature and the boiling point of water (Thu Aug 18 2011 - 09:22:36 CDT)
  • Re: (Tue Aug 16 2011 - 09:45:33 CDT)
  • Re: Batch Mode MD simulation Script for NAMD (Fri Aug 12 2011 - 06:45:12 CDT)
  • Re: minimization problem (Tue Aug 09 2011 - 07:16:08 CDT)
  • Re: Lipid bilayer equilibration: Periodic cell has become too small for original patch grid! (Mon Aug 08 2011 - 21:12:39 CDT)
  • Re: water equilibration (Fri Aug 05 2011 - 09:32:23 CDT)
  • Re: nitrogen in namd (Wed Jul 27 2011 - 15:51:57 CDT)
  • Re: how to calculate partial charge for ligand based on CHARMM principle? (Thu Jul 21 2011 - 12:02:49 CDT)
  • Re: free energy of binding (Thu Jul 07 2011 - 17:16:02 CDT)
  • Re: Joining PSF Files (Tue May 24 2011 - 09:04:53 CDT)
  • Re: simulation box (Fri May 20 2011 - 11:36:57 CDT)
  • Re: Help building a desktop for namd (Thu Apr 14 2011 - 00:07:16 CDT)
  • Re: problem for simulation of membrane protein system (Tue Apr 12 2011 - 11:29:25 CDT)
  • Re: membrane equilibration (Thu Mar 03 2011 - 19:58:11 CST)
  • Re: membrane simulation Constraint failure in RATTLE algorithm (Wed Feb 16 2011 - 22:18:57 CST)
  • Re: membrane simulation Constraint failure in RATTLE algorithm (Wed Feb 16 2011 - 14:58:38 CST)
  • Re: water box deformation (Wed Feb 09 2011 - 10:51:41 CST)
  • 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)
• Jens K. Munk
  • Lipid as residues topology (Tue Nov 01 2011 - 05:35:37 CDT)
  • Re: Error with ubqp.pdb in NAMD tutorial (Tue Oct 25 2011 - 02:10:22 CDT)
  • FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CT2 CT1 CT2 (ATOMS 107 98 100) (Sun Oct 23 2011 - 14:39:24 CDT)
• jeremy adler
  • Re: membrane equilibration (Thu Mar 03 2011 - 18:30:46 CST)
  • Re: membrane equilibration (Thu Mar 03 2011 - 17:03:18 CST)
  • membrane equilibration (Thu Mar 03 2011 - 13:02:57 CST)
• Jernej Zidar
  • Re: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CT2 CT1 CT2 (ATOMS 107 98 100) (Sun Oct 23 2011 - 19:45:56 CDT)
  • Re: Using CHARMM Compatible Amber Parameters (Wed Oct 19 2011 - 20:22:46 CDT)
  • Re: refphrasing of the question for equilibration script (Fri Sep 30 2011 - 03:50:35 CDT)
  • Re: an important question for equilibration script (Thu Sep 29 2011 - 18:42:58 CDT)
  • Re: Trouble running NAMD on win7 (Mon Sep 26 2011 - 03:42:19 CDT)
  • Re: Denaturation via increased temperature (Mon Aug 15 2011 - 04:38:55 CDT)
  • Re: Batch Mode MD simulation Script for NAMD (Fri Aug 12 2011 - 08:03:21 CDT)
  • Re: Mixed TIP3/TIP4 Waters (Thu Aug 11 2011 - 07:28:29 CDT)
  • Re: Custom CHARMM forcefield usage problem (Tue Aug 09 2011 - 23:47:30 CDT)
  • Custom CHARMM forcefield usage problem (Tue Aug 09 2011 - 23:12:04 CDT)
  • Re: vmd-l: CHARMM parameters for Mn 2+ ion (Fri Mar 25 2011 - 12:57:00 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)
• Jesper Soerensen
  • NAMD ibverbs not working on new cluster (Wed Jan 20 2010 - 03:11:35 CST)
• Jesper Sørensen
  • RE: CUDA simulation memory usage (Thu May 19 2011 - 03:11:41 CDT)
  • RE: CUDA simulation memory usage (Wed May 18 2011 - 07:23:28 CDT)
  • RE: CUDA simulation memory usage (Wed May 18 2011 - 06:14:51 CDT)
  • RE: CUDA simulation memory usage (Wed May 18 2011 - 05:55:59 CDT)
  • CUDA simulation memory usage (Wed May 18 2011 - 05:03:17 CDT)
• Jesper Sørensen
  • RE: Segmentation Faults on Mac OS X Lion (Tue Jul 26 2011 - 03:40:33 CDT)
  • RE: CUDA simulation memory usage (Wed May 18 2011 - 08:41:34 CDT)
  • Automatic GPU selection in NAMD ? (Tue May 17 2011 - 06:17:43 CDT)
  • RE: Automatic GPU selection in NAMD ? (Tue May 17 2011 - 05:41:03 CDT)
  • RE: Automatic GPU selection in NAMD ? (Tue May 17 2011 - 05:05:27 CDT)
• Jian Dai
  • tclforces and extrabonds (Mon Dec 12 2011 - 10:13:16 CST)
• Jian Liu
  • Re: namd log file (Fri Oct 07 2011 - 19:14:39 CDT)
  • Re: Lingand Unbinding using SMD (Mon Aug 15 2011 - 03:28:37 CDT)
  • 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)
• 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)
• 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)
• Jiao, Dian NMN (-EXP)
  • Re: membrane simulation at high Temp (Fri Nov 04 2011 - 17:38:56 CDT)
  • membrane simulation at high Temp (Fri Nov 04 2011 - 16:50:20 CDT)
  • Constraint failure during equalibration (Tue Sep 13 2011 - 12:45:50 CDT)
  • Constraint failure during equalibration (Tue Sep 13 2011 - 12:55:22 CDT)
• 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 Phillips
  • Re: nitrogen in namd (Thu Jul 28 2011 - 11:57:05 CDT)
  • Re: nitrogen in namd (Wed Jul 27 2011 - 15:07:25 CDT)
  • Re: NAMD 2.8 on Cray XE6 segfaulting (Tue Jul 26 2011 - 16:14:34 CDT)
  • Re: Segmentation Faults on Mac OS X Lion (Tue Jul 26 2011 - 15:46:30 CDT)
  • Re: NAMD 2.8 on Cray XE6 segfaulting (Tue Jul 26 2011 - 11:58:34 CDT)
  • Re: Molecule2.C (Tue Jul 26 2011 - 11:36:33 CDT)
  • Re: NAMD 2.8 job submission script for queenbee (Tue Jul 26 2011 - 11:13:57 CDT)
  • Re: NAMD 2.8 on Cray XE6 segfaulting (Tue Jul 26 2011 - 11:05:30 CDT)
  • Re: control distance between solvent and solute (Wed Jul 20 2011 - 11:57:16 CDT)
  • Re: interpretation of timing data in output (Wed Jul 20 2011 - 11:47:04 CDT)
  • Re: simulated annealing protocol (Wed Jul 20 2011 - 11:31:19 CDT)
  • Re: how to get the energy in vacuum of a molecule in NAMD (Wed Jul 20 2011 - 11:25:59 CDT)
  • expect NAMD survey emails this week (Tue Jul 19 2011 - 11:51:22 CDT)
  • Re: Low global exclusion count errors (Mon Jul 18 2011 - 17:00:02 CDT)
  • Re: NAMD chares (Mon Jul 18 2011 - 16:47:44 CDT)
  • Re: Memory leak and crash before first step (Mon Jul 18 2011 - 16:26:38 CDT)
  • Re: Re: Equilibration (Mon Jul 18 2011 - 16:01:26 CDT)
  • Re: patch needed for tuple is missing (Mon Jul 18 2011 - 15:35:28 CDT)
  • Re: Re: patch for phosphotyrosine residue (Wed Jun 22 2011 - 10:46:17 CDT)
  • Re: rescaling velocity (Fri Jun 17 2011 - 13:16:44 CDT)
  • Re: NAMD-l: Get the PDB file from Steered Molecular Dynamics output files (Fri Jun 17 2011 - 13:14:11 CDT)
  • Re: REMD exchange ratios (Fri Jun 17 2011 - 12:43:19 CDT)
  • Re: rescaling velocity (Fri Jun 17 2011 - 12:45:44 CDT)
  • Re: Channel flow equilibration (Wed Jun 15 2011 - 17:02:10 CDT)
  • Re: AW: AW: NAMD crashes with OpenMPI/OpenMX (Wed Jun 15 2011 - 11:25:34 CDT)
  • Re: AW: AW: AW: NAMD crashes with OpenMPI/OpenMX (Wed Jun 15 2011 - 11:17:47 CDT)
  • Re: NAMD crashes with OpenMPI/OpenMX (Tue Jun 14 2011 - 11:33:35 CDT)
  • Re: cuda error cudastreamcreate (Tue Jun 14 2011 - 11:02:33 CDT)
  • Re: max number of CPU PEs per GPU? (Sat Jun 11 2011 - 14:12:35 CDT)
  • Re: max number of CPU PEs per GPU? (Fri Jun 10 2011 - 15:15:19 CDT)
  • Re: Problem with NAMD 2.8 (but not in 2.7) : Endless loop repeating "The last position output ..." (Thu Jun 09 2011 - 10:53:46 CDT)
  • Re: water equilibration (Wed Jun 08 2011 - 14:40:03 CDT)
  • Re: CthCreate failed to create fiber (Tue Jun 07 2011 - 18:02:21 CDT)
  • Re: CthCreate failed to create fiber (Fri Jun 03 2011 - 11:42:44 CDT)
  • Re: Periodic Boundary Condition in NAMD (Fri Jun 03 2011 - 09:57:38 CDT)
  • Re: lengthening time-step with constraints causes RMSD "jump" (Thu Jun 02 2011 - 15:36:33 CDT)
  • Re: lengthening time-step with constraints causes RMSD "jump" (Thu Jun 02 2011 - 11:11:28 CDT)
  • Re: Periodic Boundary conditions (Wed Jun 01 2011 - 13:08:55 CDT)
  • Re: restart a simulation (Tue May 31 2011 - 15:00:23 CDT)
  • NAMD 2.8 released (Tue May 31 2011 - 14:55:34 CDT)
  • Re: Question about end of log file (Sun May 29 2011 - 22:37:30 CDT)
  • Re: Truncated octahedron box issues (?) (Thu May 26 2011 - 22:59:06 CDT)
  • Re: about conf file (Thu May 26 2011 - 09:55:14 CDT)
  • Re: PSF and PDB file for SWM4 water models (Thu May 26 2011 - 09:39:22 CDT)
  • Re: NAMD crashes when writing restart file and dcdfreq is 1 (Thu May 26 2011 - 09:12:02 CDT)
  • Re: Truncated octahedron box issues (?) (Wed May 25 2011 - 13:57:05 CDT)
  • Re: restart with constraints causes RMSD "jump" (Wed May 25 2011 - 13:40:21 CDT)
  • Re: restart with constraints causes RMSD "jump" (Wed May 25 2011 - 11:31:29 CDT)
  • Re: Development plan of NAMD? (Tue May 24 2011 - 13:54:09 CDT)
  • Re: NAMD crashes when writing restart file and dcdfreq is 1 (Tue May 24 2011 - 13:39:51 CDT)
  • Re: Problem building NAMD (multiple definitions) (Mon May 23 2011 - 17:57:27 CDT)
  • Re: Problem building NAMD (multiple definitions) (Mon May 23 2011 - 17:08:21 CDT)
  • Re: dcd files (Sun May 22 2011 - 14:53:45 CDT)
  • Re: Minimisation algorithm (Sun May 22 2011 - 14:49:16 CDT)
  • Re: dcd files (Sun May 22 2011 - 14:38:55 CDT)
  • Re: NAMD crashes when writing restart file and dcdfreq is 1 (Fri May 20 2011 - 17:06:32 CDT)
  • Re: NAMD crashes when writing restart file and dcdfreq is 1 (Fri May 20 2011 - 08:45:46 CDT)
  • NAMD 2.8b3 released (Thu May 19 2011 - 16:28:04 CDT)
  • Re: last frame and restart are different (Thu May 19 2011 - 14:02:25 CDT)
  • Re: NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 (Wed May 18 2011 - 17:58:16 CDT)
  • Re: hi (Wed May 18 2011 - 17:52:49 CDT)
  • Re: CUDA simulation memory usage (Wed May 18 2011 - 17:37:45 CDT)
  • Re: Automatic GPU selection in NAMD ? (Wed May 18 2011 - 13:22:57 CDT)
  • Re: GPU-CPU small-scale machine for NAMD (Wed May 18 2011 - 12:48:52 CDT)
  • Re: NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 (Tue May 17 2011 - 13:21:49 CDT)
  • Re: NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 (Fri May 13 2011 - 14:52:53 CDT)
  • Re: CUDA limitations (Fri May 13 2011 - 09:02:36 CDT)
  • Re: REMD segmentation fault (Fri May 13 2011 - 08:52:47 CDT)
  • Re: REMD segmentation fault (Fri May 13 2011 - 08:30:08 CDT)
  • Re: NAMD2.7 on BluegeneL hang at "LDB: Central LB being created..." (Fri May 13 2011 - 08:18:37 CDT)
  • Re: AW: Corrupt dcd files (Thu May 12 2011 - 17:20:36 CDT)
  • Re: CUDA limitations (Thu May 12 2011 - 12:45:44 CDT)
  • Re: Re: Re: ç­”å¤�: compilation of namd (Thu May 12 2011 - 12:32:28 CDT)
  • NAMD 2.8b2 released (Wed May 11 2011 - 17:15:43 CDT)
  • Re: Re: ç­”å¤�: compilation of namd (Wed May 11 2011 - 10:53:59 CDT)
  • Re: question on modifyAppliedForces() (Tue May 10 2011 - 21:31:42 CDT)
  • Re: A namd2.8b1 bug ? (Tue May 10 2011 - 21:02:49 CDT)
  • Re: Q=AD=94=E5=A4=8D:__compilation_of_namd?= (Tue May 10 2011 - 20:32:27 CDT)
  • Re: implicit solvent and cuda (Tue May 10 2011 - 20:24:17 CDT)
  • Re: Abnormal EOF Error in Extra Bonds File (Tue May 10 2011 - 20:15:18 CDT)
  • Re: new error in NAMD2.8b1 with fixedAtoms (Tue May 10 2011 - 20:01:25 CDT)
  • Re: Reduce the frequency of load balancer output (Tue May 10 2011 - 19:12:30 CDT)
  • Re: Replica Exchange (Tue May 10 2011 - 18:59:03 CDT)
  • Re: A newer version of win32 libraries (Tue May 10 2011 - 14:39:25 CDT)
  • Re: Oh dear, 'namd2 invoked oom-killer' ... (Fri Apr 15 2011 - 11:34:14 CDT)
  • Re: problem in restarting (Fri Apr 15 2011 - 08:06:56 CDT)
  • Re: NAMD2.7 on BluegeneL hang at "LDB: Central LB being created..." (Wed Apr 13 2011 - 10:39:41 CDT)
  • Re: about rigid bonds (Wed Apr 13 2011 - 10:32:07 CDT)
  • Re: Re: (Wed Apr 13 2011 - 10:19:45 CDT)
  • Re: Help building a desktop for namd (Wed Apr 13 2011 - 10:17:27 CDT)
  • Re: NVT setup for monolayer (Wed Apr 13 2011 - 10:09:49 CDT)
  • Re: Fwd: Wrong exit from RAMD runs (Wed Apr 13 2011 - 10:02:18 CDT)
  • Re: Fwd: Wrong exit from RAMD runs (Wed Apr 13 2011 - 09:59:25 CDT)
  • Re: external forces (Wed Apr 13 2011 - 09:47:03 CDT)
  • Re: The biggest system simulated on one TESLA C2050 ? (Wed Apr 13 2011 - 09:37:46 CDT)
  • Re: Network version gives inconsistent wall clock timings (Wed Apr 13 2011 - 09:04:46 CDT)
  • Re: Setting PME Grid Size (Wed Apr 13 2011 - 08:55:23 CDT)
  • Re: NAMD 2.7/2.8b1 and BlueGeneL (Wed Apr 13 2011 - 08:46:26 CDT)
  • Re: Velocity distribution (Wed Apr 13 2011 - 08:38:58 CDT)
  • Re: RAMD Setting parameter TclForces from script failed (Wed Apr 13 2011 - 08:33:57 CDT)
  • Re: NAMD speed on MPICH2 Ubuntu 64 bit Cluster (Wed Apr 06 2011 - 17:01:31 CDT)
  • Re: Multi node run causes "CUDA error cudaStreamCreate" (Wed Apr 06 2011 - 16:17:02 CDT)
  • Re: Fwd: RAMD Setting parameter TclForces from script failed (Mon Mar 28 2011 - 16:49:25 CDT)
  • Re: RAMD Setting parameter TclForces from script failed (Mon Mar 28 2011 - 14:33:32 CDT)
  • Re: Net forces on each atom can be written to PDB in NAMD 2.8b1 (Mon Mar 28 2011 - 12:00:59 CDT)
  • NAMD 2.8b1 released (Sun Mar 27 2011 - 12:25:13 CDT)
  • Re: Why are the pressures in my box of water systematically off? (Sun Mar 27 2011 - 10:04:35 CDT)
  • Re: namd at ranger(tacc) (Thu Feb 24 2011 - 15:36:18 CST)
  • Re: Problems compiling NAMD on 8-core Mac (Tue Feb 01 2011 - 09:26:54 CST)
  • Re: Problems compiling NAMD on 8-core Mac (Mon Jan 31 2011 - 16:39:49 CST)
  • 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)
• 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)
• jiyong
  • Relative RMSD constraint (Wed Aug 17 2011 - 02:00:57 CDT)
• Jiyong Park
  • colvar and tclForces with CUDA (Sun Sep 25 2011 - 02:02:29 CDT)
• jnsong
  • how to get the energy in vacuum of a molecule in NAMD (Wed Jun 22 2011 - 08:36:40 CDT)
  • How to calculate Binding Free energy in NAMD (Sat Jun 18 2011 - 01:00:49 CDT)
  • the meaning of " 5-ZEROS" " 9-ZEROS" in the DCD file (Tue May 24 2011 - 03:12:57 CDT)
  • Re: AW: question about wrap atoms to its original coordinates (Thu May 19 2011 - 21:31:54 CDT)
  • question about wrap atoms to its original coordinates (Wed May 18 2011 - 00:06:20 CDT)
  • question about rotation force in SMD (Wed Apr 27 2011 - 09:34:09 CDT)
  • 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)
• Joakim Swedberg
  • Charmm parameters for (Wed Apr 28 2010 - 21:47:03 CDT)
• Joe Yelk
  • Multiple dihedral parameters in X-PLOR format (Tue Oct 18 2011 - 17:46:57 CDT)
• johan strumpfer
  • Re: Segmentation violation with adaptive tempering. (Mon Nov 21 2011 - 12:04:38 CST)
  • Re: Segmentation violation with adaptive tempering. (Mon Nov 21 2011 - 12:20:28 CST)
  • Re: improper angle (Fri Nov 11 2011 - 06:21:38 CST)
  • Re: Pressure Problems, Excessively High Readings (Tue Nov 08 2011 - 21:13:23 CST)
  • Re: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CT2 CT1 CT2 (ATOMS 107 98 100) (Sun Oct 23 2011 - 16:42:07 CDT)
  • Re: Using CHARMM Compatible Amber Parameters (Wed Oct 19 2011 - 22:57:48 CDT)
  • Re: Restart from anywhere in DCD trajectory (Mon Oct 03 2011 - 17:16:57 CDT)
  • Re: restraining residues in NAMD (Wed Sep 28 2011 - 19:44:34 CDT)
  • Re: NAMD running on windows HPC question (Tue Sep 20 2011 - 08:30:51 CDT)
  • Re: NAMD running on windows HPC question (Tue Sep 20 2011 - 08:46:51 CDT)
  • Re: Margin Value in NAMD (Thu Sep 01 2011 - 00:35:30 CDT)
  • Re: Margin Value in NAMD (Wed Aug 31 2011 - 22:56:39 CDT)
  • Re: SMD-extension (Fri Aug 26 2011 - 07:26:18 CDT)
  • Re: PBB File Format/Setup for PBC (Fri Aug 19 2011 - 17:41:04 CDT)
  • Re: temperature-TS with NAMDplot (Fri Jul 08 2011 - 07:23:44 CDT)
  • Re: Hi: some doubt about nvt and npt equilibration (Sun Jul 03 2011 - 20:53:47 CDT)
  • Re: Re: Equilibration (Wed Jun 29 2011 - 01:25:35 CDT)
  • Re: Re: phosphotyrosine (Mon Jun 20 2011 - 06:30:03 CDT)
  • Re: Question about equilibration (Wed Jun 15 2011 - 13:22:56 CDT)
  • Re: Question about equilibration (Wed Jun 15 2011 - 13:10:10 CDT)
  • Re: Question about equilibration (Wed Jun 15 2011 - 11:27:45 CDT)
  • Re: Question about equilibration (Wed Jun 15 2011 - 11:48:06 CDT)
  • Re: Question about equilibration (Wed Jun 15 2011 - 11:19:17 CDT)
  • Re: Impropers in Charmm and OPLS (Tue Jun 14 2011 - 10:01:13 CDT)
  • Re: A question on Jarkynski equation (Tue Jun 14 2011 - 09:51:22 CDT)
  • Re: water equilibration (Tue Jun 07 2011 - 11:20:16 CDT)
  • Re: water equilibration (Tue Jun 07 2011 - 09:44:33 CDT)
  • Re: water equilibration (Mon Jun 06 2011 - 08:59:05 CDT)
  • Re: PBC (Fri Jun 03 2011 - 12:09:55 CDT)
  • Re: PBC (Wed Jun 01 2011 - 12:19:04 CDT)
  • Re: PBC (Wed Jun 01 2011 - 11:03:04 CDT)
  • Re: compilation of namd (Fri May 06 2011 - 09:09:35 CDT)
  • Re: FATAL ERROR: Bad global angle count! (Sun Apr 24 2011 - 16:16:52 CDT)
  • Re: Abe versus Lincoln (Thu Apr 07 2011 - 16:23:16 CDT)
  • Re: Abe versus Lincoln (Thu Apr 07 2011 - 13:40:13 CDT)
  • Re: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT (Thu Apr 07 2011 - 09:23:02 CDT)
  • Re: external forces (Mon Apr 04 2011 - 11:07:02 CDT)
  • Re: partial charges for organic ligands (Sat Mar 26 2011 - 12:40:48 CDT)
  • Re: "FATAL ERROR: Bad global improper count" revisited (Tue Mar 22 2011 - 12:41:42 CDT)
  • Re: Bactenecine (Wed Mar 16 2011 - 15:54:46 CDT)
  • Re: moving inner wall of nanotube with outer wall fixed (Tue Mar 15 2011 - 12:01:36 CDT)
• Johann Morr
  • Generating binvelocities, bincoordinates, and extendedSystem files (AMBER) (Sat Feb 13 2010 - 23:01:32 CST)
• John Baker
  • NAMD FEP - Bad Hydrogen group size (Wed Dec 07 2011 - 05:38:11 CST)
• John Stone
  • Re: vmd-l: Parse Fep plugin error (Fri Dec 23 2011 - 10:47:56 CST)
  • Re: vmd-l: Re: Fwd: "cuda error cudastreamcreate", (Fri Jun 17 2011 - 01:22:50 CDT)
• Jorgen Simonsen
  • membrane simulation and mobility of lipids - blocking ion channel (Wed Sep 28 2011 - 09:07:50 CDT)
  • convergence and stability of simulation (Mon Aug 15 2011 - 14:08:29 CDT)
  • patch becoming too small (Tue Aug 09 2011 - 01:14:33 CDT)
  • FATAL ERROR: Setting parameter fixedAtomsFile from script failed! (Fri Jul 15 2011 - 15:55:26 CDT)
  • Re: membrane simulation ERROR rattle algorithm (Wed Jul 06 2011 - 03:36:22 CDT)
  • Re: membrane simulation ERROR rattle algorithm (Tue Jul 05 2011 - 12:41:49 CDT)
  • membrane simulation ERROR rattle algorithm (Tue Jul 05 2011 - 10:13:57 CDT)
  • formyl and ethanolamide parameters and topology (Thu Jun 23 2011 - 09:52:18 CDT)
  • FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR C H (ATOMS 2 1) (Thu Jun 23 2011 - 08:51:52 CDT)
  • 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)
• 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
  • Cu+2 parameters (Wed Jan 26 2011 - 07:36:59 CST)
  • 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)
• Joseph Antoine Garate
  • Parse Fep plugin error (Fri Dec 23 2011 - 08:27:39 CST)
• Joshua Adelman
  • Re: about md in npt (Wed Dec 28 2011 - 07:55:02 CST)
  • Re: RMSD trajectory (Fri Nov 18 2011 - 14:21:46 CST)
  • Re: Questions (Mon Oct 10 2011 - 21:54:49 CDT)
  • Re: Restarting MD (Disabling Checklist) (Fri Aug 19 2011 - 07:18:17 CDT)
  • Re: Periodic Boundary Condition for a 630 Amino Acid Protein (Sun Aug 14 2011 - 08:46:11 CDT)
  • Re: gromacs analysis tools (Sun Apr 03 2011 - 10:45:16 CDT)
  • Re: NCS (Tue Feb 15 2011 - 20:28:36 CST)
  • Re: NCS (Tue Feb 15 2011 - 11:51:46 CST)
  • Re: Constraint failure; simulation has become unstable (Sat Jan 08 2011 - 09:49:18 CST)
  • Re: Constraint failure; simulation has become unstable (Fri Jan 07 2011 - 18:18:05 CST)
  • 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)
• Joshua D. Moore
  • Re: How to write a dcd in fortran? (Mon Oct 03 2011 - 15:56:57 CDT)
  • Re: Get restart file (restart.coor) from DCD (Mon Mar 28 2011 - 20:18:11 CDT)
  • Re: Problem with SPC/E water simulation (Fri Mar 04 2011 - 17:54:20 CST)
  • Re: Get number of timesteps from DCD via script (Wed Feb 09 2011 - 08:40:27 CST)
  • Re: Get number of timesteps from DCD via script (Wed Feb 09 2011 - 06:41:06 CST)
  • Re: Get number of timesteps from DCD via script (Tue Feb 08 2011 - 17:01:32 CST)
  • Re: Get number of timesteps from DCD via script (Tue Feb 08 2011 - 16:56:02 CST)
  • Re: Format of namd restartfile *.coor, *.vel) (2nd try ;) ) (Thu Nov 18 2010 - 18:27:22 CST)
• 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)
• Juan Antonio Raygoza Garay
  • RNA simulation (Fri Aug 26 2011 - 15:38:38 CDT)
• juan du
  • Membrane simulation, Box X,Y enlarge, Z shrink and membrane thickness shrink (Tue Jun 07 2011 - 18:27:25 CDT)
  • 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)
• Jun Zhang
  • Re: Evaluated heat capacities via NAMD are larger than experimental values (Wed Oct 26 2011 - 19:00:18 CDT)
  • Re: clustering of trajectory (Tue Jul 05 2011 - 20:18:16 CDT)
  • Re: A question on Jarkynski equation (Wed Jun 15 2011 - 00:25:17 CDT)
  • Re: A question on Jarkynski equation (Tue Jun 14 2011 - 23:03:53 CDT)
  • A question on Jarkynski equation (Mon Jun 13 2011 - 22:01:59 CDT)
  • Is there any difference between SMD and tclForces? (Wed May 18 2011 - 20:29:07 CDT)
  • RE: deca-Ala simulations with different cutoff produce different results (Mon May 16 2011 - 03:47:44 CDT)
  • deca-Ala simulations with different cutoff produce different results (Mon May 16 2011 - 00:48:36 CDT)
  • Re: NAMD on GPU (Mon Mar 21 2011 - 19:45:10 CDT)
  • Technique issue with free energy calculation on GPU (Tue Mar 01 2011 - 08:24:59 CST)
  • Re£º Can DCD trajectory files contain only protein but water surround (Thu Jan 13 2011 - 19:22:10 CST)
  • 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)
• Jérôme Hénin
  • Re: collective variable calculation from dcd file (Thu Dec 22 2011 - 05:20:15 CST)
  • Re: Umbrella sampling-NAMD (Thu Dec 15 2011 - 11:07:04 CST)
  • Re: tclforces and extrabonds (Mon Dec 12 2011 - 11:30:47 CST)
  • Re: NAMD FEP - Bad Hydrogen group size (Wed Dec 07 2011 - 06:54:01 CST)
  • Re: stochastical boundary conditions in NAMD (Wed Dec 07 2011 - 04:39:41 CST)
  • Re: Scaled forces, colvars and harmonic con/restraints (Thu Nov 24 2011 - 08:18:07 CST)
  • Re: Scaled forces, colvars and harmonic con/restraints (Thu Nov 24 2011 - 06:33:58 CST)
  • Re: Scaled forces, colvars and harmonic con/restraints (Thu Nov 24 2011 - 03:51:51 CST)
  • Re: Scaled forces, colvars and harmonic con/restraints (Wed Nov 23 2011 - 10:41:58 CST)
  • Re: fullSamples in ABF: applied at restart? (Mon Nov 21 2011 - 04:11:06 CST)
  • Re: fullSamples in ABF: applied at restart? (Mon Nov 21 2011 - 02:10:10 CST)
  • Re: Fwd: restrain on COM (Sat Nov 19 2011 - 10:48:41 CST)
  • Re: Umbrella sampling (Thu Nov 17 2011 - 03:29:23 CST)
  • Re: different velocities problem (Tue Oct 25 2011 - 02:10:14 CDT)
  • Re: What is the proper value of TMDk in TMD simulations? (Mon Oct 24 2011 - 03:02:43 CDT)
  • Re: GBIS and hydrophobic term, in replay to Jerome and David discussion (Sun Oct 23 2011 - 09:43:08 CDT)
  • Re: About "alchDecouple" in FEP (Sat Oct 22 2011 - 11:51:27 CDT)
  • Re: Boundary potential of colvar alpha not working? (Thu Oct 13 2011 - 10:23:41 CDT)
  • Re: Boundary potential of colvar alpha not working? (Thu Oct 13 2011 - 08:54:35 CDT)
  • Re: Boundary potential of colvar alpha not working? (Thu Oct 13 2011 - 07:14:53 CDT)
  • GBIS and hydrophobic solvation (Mon Oct 10 2011 - 07:24:50 CDT)
  • Re: Minimization doesn't stop when converged (Fri Oct 07 2011 - 05:27:13 CDT)
  • Re: Help in reverse Free Energy perturbation - hysteresis (Mon Oct 03 2011 - 06:49:46 CDT)
  • Re: ABF with Alpha colvar can't be used on supercomputer? (Thu Sep 29 2011 - 09:56:46 CDT)
  • Re: ABF with Alpha colvar can't be used on supercomputer? (Thu Sep 29 2011 - 05:04:42 CDT)
  • Re: how to use variables in colvar configuration file (Fri Sep 23 2011 - 13:23:55 CDT)
  • Re: Help in FEP backward/reverse calculation (Fri Sep 23 2011 - 03:22:52 CDT)
  • Re: ABF & distanceZ projection axis more (Thu Sep 22 2011 - 04:33:02 CDT)
  • Re: force question (Thu Sep 22 2011 - 04:32:45 CDT)
  • Re: ABF question (Wed Sep 21 2011 - 07:01:50 CDT)
  • Re: membrane system (Wed Sep 21 2011 - 03:47:16 CDT)
  • Re: membrane system (Wed Sep 21 2011 - 02:44:42 CDT)
  • Re: NOE (Tue Sep 20 2011 - 08:17:30 CDT)
  • Re: time step and total simulation time in conf file (Wed Sep 14 2011 - 10:53:43 CDT)
  • Re: Differences between ABF and metadynamics (Tue Sep 13 2011 - 08:45:17 CDT)
  • Re: Differences between ABF and metadynamics (Tue Sep 13 2011 - 05:43:39 CDT)
  • Re: question about Distance XY (Tue Sep 13 2011 - 02:50:13 CDT)
  • Re: Keeping rigidBonds during Minimization (Mon Sep 12 2011 - 18:09:58 CDT)
  • Re: restraint with colvars mocule (Mon Sep 12 2011 - 10:08:47 CDT)
  • Re: restraint with colvars mocule (Mon Sep 12 2011 - 04:48:33 CDT)
  • Re: Component distanceZ-ABF (Tue Sep 06 2011 - 04:27:44 CDT)
  • Re: Component distanceZ-ABF (Mon Sep 05 2011 - 10:56:06 CDT)
  • Re: Component distanceZ-ABF (Fri Sep 02 2011 - 16:19:53 CDT)
  • Re: colvar restrain of water in lipid system (Mon Aug 29 2011 - 11:17:47 CDT)
  • Re: dummyAtom-ABF (Fri Aug 26 2011 - 10:32:20 CDT)
  • Re: About Columb energy of 2 ions in Vacuum (Fri Aug 26 2011 - 04:30:54 CDT)
  • Re: using colvars for bending modulus? (Wed Jul 27 2011 - 03:12:33 CDT)
  • Re: using colvars for bending modulus? (Wed Jul 27 2011 - 01:29:59 CDT)
  • Re: alchDecouple (Mon Jul 25 2011 - 15:19:14 CDT)
  • Re: alchDecouple (Sat Jul 23 2011 - 02:44:36 CDT)
  • Re: PME or not PME? What happens if PME is turned off? (Mon Jul 18 2011 - 15:27:09 CDT)
  • Re: how to define the numsteps in ABF or metadynamics simulation? (Sat Jul 16 2011 - 10:57:21 CDT)
  • Re: Filtered mail? (Tue Jul 12 2011 - 10:19:41 CDT)
  • Re: Possibility of modifying the non-bonded terms of the potential (Sat Jul 09 2011 - 03:34:36 CDT)
  • Re: Re: Final production run in MD (Fri Jul 01 2011 - 02:31:04 CDT)
  • Re: Accessing Colvars Within NAMD TCL (Thu Jun 30 2011 - 12:05:01 CDT)
  • Re: Restarting an alchemic FEP calculation (Mon Jun 27 2011 - 11:03:55 CDT)
  • Re: restraining groups of atoms (Mon Jun 20 2011 - 07:56:06 CDT)
  • Re: A question on Jarkynski equation (Tue Jun 14 2011 - 09:09:13 CDT)
  • Re: umbrella sampling by NAMD (Tue Jun 14 2011 - 07:31:53 CDT)
  • Re: A question on Jarkynski equation (Tue Jun 14 2011 - 03:43:55 CDT)
  • Re: vmd-l: measure fit - wrong alignment (Thu May 26 2011 - 13:09:29 CDT)
  • Re: Umbrella Sampling (Wed May 18 2011 - 09:40:25 CDT)
  • Re: ABF simulation with extendedLagrangian on keeps crashing (Thu May 12 2011 - 04:36:20 CDT)
  • Re: ABF atom selection (Tue May 10 2011 - 09:59:08 CDT)
  • Re: alpha pmf (Tue May 10 2011 - 03:37:24 CDT)
  • Re: ABF atom selection (Sun May 08 2011 - 11:41:09 CDT)
  • Re: alpha pmf (Fri May 06 2011 - 07:58:37 CDT)
  • Re: ABF simulation with extendedLagrangian on keeps crashing (Thu May 05 2011 - 17:02:56 CDT)
  • Re: ABF simulation with extendedLagrangian on keeps crashing (Thu May 05 2011 - 10:23:23 CDT)
  • Re: alpha pmf (Wed May 04 2011 - 04:17:16 CDT)
  • Re: ABF simulation with extendedLagrangian on keeps crashing (Tue May 03 2011 - 10:23:17 CDT)
  • Re: non-bonded potential in NAMD (Sat Apr 30 2011 - 17:28:14 CDT)
  • Re: colvars orientation problem appears in 2.8 only? (Fri Apr 29 2011 - 06:16:55 CDT)
  • Re: ABF simulation with extendedLagrangian on keeps crashing (Fri Apr 22 2011 - 15:38:07 CDT)
  • Re: ABF simulation with extendedLagrangian on keeps crashing (Thu Apr 21 2011 - 09:43:21 CDT)
  • Re: SMD for two steered directions (Sun Apr 17 2011 - 14:31:36 CDT)
  • Re: question on the center of mass calculation in colvar (Sat Apr 16 2011 - 10:55:11 CDT)
  • Re: problem in restarting (Thu Apr 14 2011 - 09:52:59 CDT)
  • Re: FEP with flattened free energy surface? (Sat Apr 09 2011 - 01:18:19 CDT)
  • Re: FEP with flattened free energy surface? (Fri Apr 08 2011 - 15:05:30 CDT)
  • Re: FEP with flattened free energy surface? (Wed Apr 06 2011 - 11:45:29 CDT)
  • Re: Why NAMD writes colvars step by step (Sat Apr 02 2011 - 02:34:02 CDT)
  • New collective variable: biolRel (Fri Apr 01 2011 - 09:01:53 CDT)
  • Re: Fwd: Incompatibility between colvars and tclforces? (Thu Mar 31 2011 - 03:25:18 CDT)
  • Re: Incompatibility between colvars and tclforces? (Wed Mar 30 2011 - 10:23:45 CDT)
  • Re: Incompatibility between colvars and tclforces? (Wed Mar 30 2011 - 06:23:42 CDT)
  • Re: Rotate two linked proteins against each other and calculate energy profile (Tue Mar 29 2011 - 07:03:14 CDT)
  • Re: Rotate two linked proteins against each other and calculate energy profile (Mon Mar 28 2011 - 15:50:44 CDT)
  • Re: Rotate two linked proteins against each other and calculate energy profile (Mon Mar 28 2011 - 15:43:46 CDT)
  • Re: Rotate two linked proteins against each other and calculate energy profile (Mon Mar 28 2011 - 11:07:43 CDT)
  • Re: A "strange" observation during ColVar calculations (Mon Mar 28 2011 - 09:51:21 CDT)
  • Re: Advisable limit on the number of quadrants a 2D ABF simulation can be split. (Mon Mar 28 2011 - 09:42:33 CDT)
  • Re: A "strange" observation during ColVar calculations (Mon Mar 28 2011 - 08:33:42 CDT)
  • Re: Advisable limit on the number of quadrants a 2D ABF simulation can be split. (Fri Mar 25 2011 - 06:25:30 CDT)
  • Re: GBIS and ABF (Thu Mar 24 2011 - 10:01:43 CDT)
  • Re: GBIS and ABF (Thu Mar 24 2011 - 05:39:52 CDT)
  • Re: GBIS and ABF (Wed Mar 23 2011 - 12:10:15 CDT)
  • Re: GBIS question and possible Bug for colvar "outputSystemForce" declaration in NAMD CVS-2011-03-03 (Wed Mar 23 2011 - 05:39:51 CDT)
  • Re: A "strange" observation during ColVar calculations (Tue Mar 22 2011 - 11:30:56 CDT)
  • Re: ABF Restart (Fri Mar 18 2011 - 04:08:34 CDT)
  • Re: Setting up values in distance colvar (Sun Mar 13 2011 - 14:45:43 CDT)
  • Re: colvars PMF history problem (Tue Mar 08 2011 - 22:55:42 CST)
  • Re: Computing interaction energies in namd (Wed Feb 23 2011 - 03:42:14 CST)
  • Re: forces on fixed atoms (Thu Feb 17 2011 - 03:31:32 CST)
  • Re: forces on fixed atoms (Wed Feb 16 2011 - 17:58:28 CST)
  • Re: Setting Up A Langevin Buffer Region (Wed Feb 16 2011 - 06:34:58 CST)
  • Re: NCS (Tue Feb 15 2011 - 12:27:12 CST)
  • Re: ABF calculation using RMSD (Tue Feb 15 2011 - 04:46:25 CST)
  • Re: New colvar feature request -- angleXY (Mon Feb 14 2011 - 10:06:45 CST)
  • Re: ABF reproducibility (Mon Feb 14 2011 - 06:29:40 CST)
  • Re: SMD negative forces (Fri Feb 11 2011 - 03:24:54 CST)
  • Re: Mirror Image Energy Discrepency (Thu Feb 10 2011 - 13:01:33 CST)
  • Re: Mirror Image Energy Discrepency (Wed Feb 09 2011 - 14:40:06 CST)
  • Re: Abf force output (Wed Feb 09 2011 - 07:30:16 CST)
  • Re: Abf force output (Wed Feb 09 2011 - 03:25:59 CST)
  • Re: ABF question (sampling and colvars output file) (Mon Feb 07 2011 - 11:16:28 CST)
  • Re: ABF question (sampling and colvars output file) (Mon Feb 07 2011 - 04:20:28 CST)
  • Re: (Thu Feb 03 2011 - 11:13:22 CST)
  • Re: Proposed Feature in Targeted MD (Mon Jan 31 2011 - 16:39:37 CST)
  • Re: Help With colvars/abf Please (Sun Jan 30 2011 - 09:10:50 CST)
  • Re: Equilibration when splitting an ABF calculation (Fri Jan 28 2011 - 06:44:32 CST)
  • Re: Equilibration when splitting an ABF calculation (Thu Jan 27 2011 - 08:08:12 CST)
  • Re: bond lengths angles in namd (Thu Jan 27 2011 - 06:55:28 CST)
  • Re: Missing angle parameters NH1 CT1 NH1 (Fri Jan 21 2011 - 11:01:56 CST)
  • Re: Missing angle parameters NH1 CT1 NH1 (Fri Jan 21 2011 - 06:44:14 CST)
  • Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein (Thu Jan 20 2011 - 08:07:36 CST)
  • Re: Various practical colvar module related questions (Wed Jan 19 2011 - 09:46:23 CST)
  • Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein (Wed Jan 19 2011 - 09:23:03 CST)
  • Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein (Mon Jan 17 2011 - 11:44:24 CST)
  • Re: Running bias exchange metadynamics simulations with NAMD (Mon Jan 17 2011 - 10:35:20 CST)
  • Re: Feature request for the colvars module -- TCL syntax (Mon Jan 17 2011 - 11:52:23 CST)
  • Re: Running bias exchange metadynamics simulations with NAMD (Fri Jan 14 2011 - 10:37:17 CST)
  • Re: Fix atoms-Colvars (Fri Jan 07 2011 - 13:04:10 CST)
  • Re: free energy perturbation (Wed Jan 05 2011 - 12:07:39 CST)
  • Re: free energy perturbation (Wed Jan 05 2011 - 07:39:37 CST)
  • Re: .colvars.state file in ABF (Wed Jan 05 2011 - 07:15:45 CST)
  • Re: Running bias exchange metadynamics simulations with NAMD (Sat Jan 01 2011 - 15:48:06 CST)
  • 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)
• kakali sen
  • remove translation of protein under spherical boundary conditions (Fri Aug 19 2011 - 04:39:24 CDT)
  • dihedral rotation with ABF (Sun Apr 10 2011 - 12:48:17 CDT)
  • writing back coordinates of waters that cross the unit cell (Thu Nov 25 2010 - 08:29:09 CST)
• Kalyan Pulipaka
  • Check out my photos on Facebook (Sat Oct 02 2010 - 21:57:26 CDT)
• kamal Kishor Thakur
  • regarding vmd (Thu Jun 02 2011 - 01:28:36 CDT)
• kanchi subbarao rao
  • Re: problem regarding charmm parameter file of carbon nano tube (Mon Nov 21 2011 - 09:52:36 CST)
  • Fwd: problem regarding charmm parameter file of carbon nano tube (Mon Nov 21 2011 - 05:07:50 CST)
  • problem regarding charmm parameter file of carbon nano tube (Sun Nov 20 2011 - 16:43:01 CST)
  • membrane moving up in simulation box (Mon Oct 17 2011 - 01:09:17 CDT)
  • Fwd: membrane moving up in simulation box (Thu Oct 13 2011 - 06:26:12 CDT)
  • Fwd: membrane moving up in simulation box (Thu Oct 13 2011 - 04:54:15 CDT)
  • membrane moving up in simulation box (Thu Oct 13 2011 - 01:54:32 CDT)
  • hi (Thu Jul 14 2011 - 12:31:06 CDT)
  • hi (Wed Jul 13 2011 - 13:47:30 CDT)
  • Fwd: hi all (Thu Jun 16 2011 - 07:16:22 CDT)
  • Fwd: hi all (Wed Jun 15 2011 - 11:46:09 CDT)
  • hi all (Wed Jun 15 2011 - 04:14:04 CDT)
  • Fwd: Fwd: hi (Thu Jun 02 2011 - 12:44:27 CDT)
  • Fwd: Fwd: hi (Wed Jun 01 2011 - 13:32:41 CDT)
  • Fwd: hi (Tue May 31 2011 - 05:10:32 CDT)
  • hi (Wed May 18 2011 - 03:43:25 CDT)
• Kang Hee Cho
  • control distance between solvent and solute (Fri Jul 15 2011 - 20:07:56 CDT)
  • reassignFreq expression and relation with SMD (Thu Mar 31 2011 - 10:56:47 CDT)
  • rescaling and reassignment parameter (Mon Feb 07 2011 - 22:35:44 CST)
  • water content (Thu Jan 27 2011 - 23:18:24 CST)
  • the meaning and effect of reassignFreq and reassignTemp (Tue Jan 25 2011 - 08:46:39 CST)
  • the meaning of reassignFreq and reassignTemp (Sat Jan 22 2011 - 04:28:22 CST)
  • discrete energy value after restart (Thu Jan 20 2011 - 21:25:46 CST)
• Kartheek
  • Minimization is taking a lot of computing time. (Tue Aug 09 2011 - 06:06:57 CDT)
  • Minimization is taking a lot of computing time. (Fri Aug 05 2011 - 04:53:42 CDT)
• Katherine Parra
  • unsubscribe (Tue Oct 12 2010 - 16:58:06 CDT)
  • unsubscribe (Wed Sep 15 2010 - 09:42:24 CDT)
• Keith Battle
  • Mixed TIP3/TIP4 Waters (Thu Aug 11 2011 - 06:29:18 CDT)
  • Mirror Image Energy Discrepency (Wed Feb 09 2011 - 13:23:28 CST)
  • 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)
• Kevin Kastner
  • Restarting protein system simulation using different ligand (Thu Oct 13 2011 - 12:22:41 CDT)
• Kevin Littrell
  • Questions (Mon Oct 10 2011 - 21:20:37 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)
• KONG Xian
  • Error with tclBC to induce shear flow (Thu Oct 20 2011 - 20:59:42 CDT)
• koushik.k
  • Re: Umbrella sampling (Wed Nov 16 2011 - 22:18:59 CST)
• Kristopher Opron
  • RE: Tcl issue with config script (Fri Jun 17 2011 - 15:40:31 CDT)
• Kwee Hong
  • non-zero charge (Wed Jan 19 2011 - 10:17:45 CST)
  • 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)
• La Fosca
  • Re: anomalous behaviour of ASPP and GLUP during MD run (Thu Feb 25 2010 - 09:04:29 CST)
• Lachele Foley (Lists)
  • Re: glycosaminoglycan with GLYCAM06 in amber format (Tue Dec 20 2011 - 08:53:59 CST)
• Lada Biedermannová
  • freeEnergy parsing error (Wed Apr 27 2011 - 09:08:46 CDT)
  • 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)
• lam nguyen
  • coloring method in VMD (Thu Oct 20 2011 - 18:19:14 CDT)
  • Re: How to write a dcd in fortran? (Mon Oct 03 2011 - 18:03:37 CDT)
  • Re: How to write a dcd in fortran? (Mon Oct 03 2011 - 14:07:47 CDT)
  • How to write a dcd in fortran? (Mon Oct 03 2011 - 13:21:36 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)
• Leandro Martínez
  • Re: SMD (Thu Sep 15 2011 - 07:21:15 CDT)
  • (solved) charmrun: ssh_exchange_identification: Connection closed by remote host (Fri Sep 02 2011 - 14:44:24 CDT)
  • 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)
• Lei Shi
  • namd at ranger(tacc) (Thu Feb 24 2011 - 12:56:29 CST)
• Lela Vukovic
  • NAMDEnergy Plugin - setting PMEGridSize / mesh density (Wed May 11 2011 - 14:48:51 CDT)
  • 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)
• Leonardo Herrera
  • Re: paper/articule on colvars module (Tue Nov 29 2011 - 13:59:02 CST)
  • paper/articule on colvars module (Mon Nov 28 2011 - 19:35:37 CST)
  • Re: Why NAMD writes colvars step by step (Sat Apr 02 2011 - 19:22:23 CDT)
  • Why NAMD writes colvars step by step (Fri Apr 01 2011 - 19:04:21 CDT)
  • Why NAMD writes colvars step by step (Fri Apr 01 2011 - 17:06:03 CDT)
  • NAMD_CVS_Source (Wed Mar 30 2011 - 16:43:52 CDT)
  • 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)
• 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)
• Lewyn Li
  • Re: Consecutive Simulations (Thu Feb 25 2010 - 10:08:47 CST)
• 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)
• Ling Wu
  • unit of force constant for dihedral angle restrain with extrabonds command (Thu Oct 13 2011 - 15:43:13 CDT)
  • how to use variables in colvar configuration file (Fri Sep 23 2011 - 12:26:08 CDT)
  • Re: restraint with colvars mocule (Mon Sep 12 2011 - 09:53:21 CDT)
  • restraint with colvars mocule (Sun Sep 11 2011 - 16:25:39 CDT)
  • Re: AW: about extrabonds restrain (Tue Aug 30 2011 - 07:58:25 CDT)
  • about extrabonds restrain (Mon Aug 29 2011 - 16:22:53 CDT)
  • Re: colvar restrain of water in lipid system (Mon Aug 29 2011 - 09:55:45 CDT)
  • colvar restrain of water in lipid system (Mon Aug 29 2011 - 09:13:58 CDT)
  • colvar restrain of water in lipid system (Fri Aug 26 2011 - 14:44:21 CDT)
• Liqun Zhang
  • question about namd simulation on protein in tip4p water box (Fri Oct 28 2011 - 13:14:36 CDT)
• Lisa Brown
  • how to convert X_PLOR to CHARMM? (Fri Mar 25 2011 - 11:01:26 CDT)
  • CHARMM parameters for Mn 2+ ion (Fri Mar 25 2011 - 10:43:45 CDT)
  • question from a tutorial (Thu Jan 20 2011 - 14:17:29 CST)
  • 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)
• 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)
• liupeng012_at_mail.nankai.edu.cn
  • parameter for TFA (trifluoroacetic acid) (Fri May 13 2011 - 03:36:55 CDT)
  • Re: vmd-l: No probability distribution plot in ParseFEP (Thu Mar 31 2011 - 21:08:46 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)
• Luca Bellucci
  • REMD with IBM SP6 LoadLeveler (Sat Jan 22 2011 - 11:45:31 CST)
  • Adding special VdW parameters (Sat Dec 25 2010 - 10:04:55 CST)
• Luca Muccioli
  • Re: Fwd: help to improve the script to predict mean square displacement (Fri Mar 12 2010 - 17:08:31 CST)
• lucie delemotte
  • Current status of polarizable force fields in NAMD (Wed Feb 16 2011 - 04:37:03 CST)
  • NAMD stalled at startup phase 0 when working on a large numbr of processors (Wed Mar 24 2010 - 13:07:44 CDT)
• M Mahjour
  • fixing group of atoms, Proper for manipualation (Wed Apr 13 2011 - 17:06:43 CDT)
• M.Raviprasad
  • RE: Calculation of distance traveled by an atom (Mon Dec 05 2011 - 23:11:19 CST)
  • RE: Calculation of distance traveled by an atom (Mon Dec 05 2011 - 23:19:54 CST)
  • Calculation of distance traveled by an atom (Mon Dec 05 2011 - 14:54:27 CST)
• 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
  • Query about switch function using AMBER ff99SB forcefield and NAMD simulation code (Tue Jul 19 2011 - 06:41:25 CDT)
  • 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)
• 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)
• Mao Mao
  • Channel flow equilibration (Wed Jun 15 2011 - 11:46:26 CDT)
  • restart a simulation (Tue May 31 2011 - 14:50:22 CDT)
• Marc Baaden
  • Re: AW: Corrupt dcd files (Sun May 15 2011 - 06:28:38 CDT)
  • Re: AW: Corrupt dcd files (Sat May 14 2011 - 16:23:30 CDT)
  • Corrupt dcd files (Wed May 11 2011 - 11:15:55 CDT)
  • 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)
• Marc Charendoff
  • Automatic PSF Builder Problem (Fri Mar 11 2011 - 10:43:15 CST)
  • psfgen - ACE cap on PRO (Thu Mar 10 2011 - 19:07:33 CST)
• Marcello Sega
  • Re: Re: namd 2.7b2 or later - amberff/prmtop causes segfault during startup phase (Sat Apr 03 2010 - 19:35:01 CDT)
• Marco Sant
  • improper angle (Fri Nov 11 2011 - 02:34:42 CST)
  • Re: nitrogen in namd (Sun Jul 31 2011 - 05:47:18 CDT)
  • nitrogen in namd (Wed Jul 27 2011 - 04:47:15 CDT)
• Marcos Sotomayor
  • Re: membrane moving up in simulation box (Mon Oct 17 2011 - 01:58:17 CDT)
• Marek Maly
  • The biggest system simulated on one TESLA C2050 ? (Wed Mar 30 2011 - 13:30:11 CDT)
• Maria Kamm
  • TIP5P-model (Thu Jul 14 2011 - 19:07:48 CDT)
• Maria Musgaard
  • SV: restart simulation writing in the same .dcd file. (Sat Jul 02 2011 - 03:03:26 CDT)
• Marie N
  • Lipid and protein interactions (Fri Feb 19 2010 - 17:25:29 CST)
• 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)
• Markus K. Dahlgren
  • Re: Bonds are too long after simulation (Wed Sep 07 2011 - 12:54:16 CDT)
  • velocity error during steered MD (Tue Apr 26 2011 - 09:08:32 CDT)
  • Re: infrequent rattle failure with charmm36 (Wed Apr 20 2011 - 09:30:11 CDT)
  • "FATAL ERROR: Bad global improper count" revisited (Tue Mar 22 2011 - 10:42:49 CDT)
  • Re: Missing angle parameters CT3 CT3 CT3 (Tue Nov 02 2010 - 07:38:08 CDT)
• Markus Metz
  • differences in multiprocessor energy minimization results (Wed Aug 17 2011 - 11:44:19 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 1.3 available (Wed Nov 09 2011 - 09:05:09 CST)
  • 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)
• Massimiliano Porrini
  • Re: AW: glycosaminoglycan with GLYCAM06 in amber format (Thu Dec 22 2011 - 11:12:10 CST)
  • Re: glycosaminoglycan with GLYCAM06 in amber format (Tue Dec 20 2011 - 09:46:18 CST)
  • Re: glycosaminoglycan with GLYCAM06 in amber format (Tue Dec 20 2011 - 08:55:58 CST)
  • Re: glycosaminoglycan with GLYCAM06 in amber format (Mon Dec 19 2011 - 05:04:40 CST)
  • glycosaminoglycan with GLYCAM06 in amber format (Sun Dec 18 2011 - 10:44:48 CST)
  • Re: FATAL ERROR: Low global exclusion count! System unstable or pairlistdist or cutoff too small. (Mon Aug 29 2011 - 14:26:06 CDT)
  • FATAL ERROR: Low global exclusion count! System unstable or pairlistdist or cutoff too small. (Mon Aug 29 2011 - 09:36:55 CDT)
  • Re: simulated annealing protocol (Wed Jul 20 2011 - 12:25:18 CDT)
  • Re: a bundle of coor files (Tue Jul 05 2011 - 10:34:16 CDT)
  • Re: a bundle of coor files (Sat Jul 02 2011 - 20:16:05 CDT)
  • a bundle of coor files (Sat Jul 02 2011 - 13:21:56 CDT)
  • Implicit solvent (Mon Jun 27 2011 - 06:35:00 CDT)
  • simulated annealing protocol (Tue Jun 21 2011 - 07:41:00 CDT)
  • restraining groups of atoms (Mon Jun 20 2011 - 07:03:09 CDT)
  • REMD exchange ratios (Fri Jun 17 2011 - 08:47:48 CDT)
  • Re: Truncated octahedron box issues (?) (Thu May 26 2011 - 14:00:49 CDT)
  • Truncated octahedron box issues (?) (Wed May 25 2011 - 10:38:03 CDT)
  • Re: REMD segmentation fault (Fri May 13 2011 - 08:41:09 CDT)
  • REMD segmentation fault (Fri May 13 2011 - 07:58:45 CDT)
  • Re: REMD across gpus (Tue May 10 2011 - 15:29:36 CDT)
  • REMD across gpus (Sun May 08 2011 - 06:02:19 CDT)
  • REMD across gpus (Mon May 09 2011 - 09:28:51 CDT)
  • REMD across gpus (Fri May 06 2011 - 07:39:56 CDT)
  • Re: run tests with CUDA (Wed May 04 2011 - 11:45:09 CDT)
  • run tests with CUDA (Mon May 02 2011 - 16:25:17 CDT)
• Matteo Rotter
  • Re: rsh not working (Tue Oct 11 2011 - 13:37:26 CDT)
  • Re: Re: Namd-I: Implicit solvent problem (Wed Jul 20 2011 - 16:06:29 CDT)
  • Re: Namd-I: Implicit solvent problem (Wed Jul 20 2011 - 11:04:03 CDT)
  • external forces (Mon Apr 04 2011 - 08:13:24 CDT)
• matziast_at_med.uth.gr
  • Low global exclusion count (Tue Nov 08 2011 - 04:23:47 CST)
  • script for equilibration (Sun Oct 02 2011 - 04:19:19 CDT)
  • refphrasing of the question for equilibration script (Fri Sep 30 2011 - 04:16:27 CDT)
  • refphrasing of the question for equilibration script (Fri Sep 30 2011 - 03:43:13 CDT)
  • an important question for equilibration script (Thu Sep 29 2011 - 15:44:58 CDT)
  • 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
  • Evaluated heat capacities via NAMD are larger than experimental values (Wed Oct 26 2011 - 13:44:35 CDT)
  • 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)
• Michael Di Domenico
  • GPU heavy models? (Tue Dec 14 2010 - 08:03:52 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 LeVine
  • FEP for GLY and PRO Mutations (Mon Jul 26 2010 - 10:10:28 CDT)
• Michael S. Sellers (Cont, ARL/WMRD)
  • Re: NAMDEnergy Plugin - setting PMEGridSize / mesh density (Wed May 11 2011 - 15:29:25 CDT)
  • Re: Multi node run causes "CUDA error cudaStreamCreate" (Fri Apr 01 2011 - 16:27:08 CDT)
  • Re: Multi node run causes "CUDA error cudaStreamCreate" (Fri Apr 01 2011 - 15:46:21 CDT)
  • Multi node run causes "CUDA error cudaStreamCreate" (Fri Apr 01 2011 - 12:32:35 CDT)
  • Re: namd and Fedora14 (Mon Mar 28 2011 - 09:12:47 CDT)
  • Re: namd and Fedora14 (Mon Mar 28 2011 - 09:16:51 CDT)
  • Re: rule of thumb for dcd sampling frequency? (Tue Mar 22 2011 - 15:56:17 CDT)
  • GBIS not compatible with CUDA at this time (Tue Mar 22 2011 - 13:27:48 CDT)
  • Re: namd and Fedora14 (Tue Mar 22 2011 - 10:10:02 CDT)
  • 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 Zimmermann
  • subscribe namd-l (Wed Mar 23 2011 - 13:24:38 CDT)
  • implementing RBCG (Tue Mar 22 2011 - 15:11:30 CDT)
  • 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)
• Michel Espinoza-Fonseca
  • Re: anomalous behaviour of ASPP and GLUP during MD run (Thu Feb 25 2010 - 10:51:36 CST)
• Michelle Kuttel
  • Re: Scaled forces, colvars and harmonic con/restraints (Thu Nov 24 2011 - 09:39:56 CST)
  • Re: Scaled forces, colvars and harmonic con/restraints (Thu Nov 24 2011 - 07:24:58 CST)
  • Re: Scaled forces, colvars and harmonic con/restraints (Wed Nov 23 2011 - 23:31:14 CST)
  • Re: Scaled forces, colvars and harmonic con/restraints (Wed Nov 23 2011 - 23:33:26 CST)
  • Re: Scaled forces, colvars and harmonic con/restraints (Wed Nov 23 2011 - 14:03:22 CST)
  • Re: Is it possible to print out the force of one specific atom? (Wed Nov 23 2011 - 08:45:22 CST)
  • Re: Scaled forces, colvars and harmonic con/restraints (Wed Nov 23 2011 - 08:16:58 CST)
  • Scaled forces, colvars and harmonic con/restraints (Mon Nov 21 2011 - 04:45:39 CST)
• Mikhail Suyetin
  • Re: Charmm parameter for H2 gas (Wed Jun 29 2011 - 05:00:05 CDT)
  • Calculation of IR spectra using VMD IRspec Plug-in (Thu Feb 17 2011 - 01:22:00 CST)
  • 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)
• 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)
• Minh, David D.
  • Re: Problems compiling NAMD on 8-core Mac (Tue Feb 01 2011 - 11:28:43 CST)
  • Re: Problems compiling NAMD on 8-core Mac (Tue Feb 01 2011 - 00:23:07 CST)
  • Re: Problems compiling NAMD on 8-core Mac (Mon Jan 31 2011 - 17:44:01 CST)
  • Re: Proposed Feature in Targeted MD (Mon Jan 31 2011 - 15:34:48 CST)
  • Re: Proposed Feature in Targeted MD (Mon Jan 31 2011 - 15:33:42 CST)
  • Proposed Feature in Targeted MD (Mon Jan 31 2011 - 13:12:38 CST)
  • Problems compiling NAMD on 8-core Mac (Mon Jan 31 2011 - 12:25:40 CST)
• Miroslav Hodak
  • Re: Problem building NAMD (multiple definitions) (Mon May 23 2011 - 18:14:35 CDT)
  • Re: Problem building NAMD (multiple definitions) (Mon May 23 2011 - 17:49:59 CDT)
  • Re: Problem building NAMD (multiple definitions) (Mon May 23 2011 - 17:38:47 CDT)
  • Problem building NAMD (multiple definitions) (Mon May 23 2011 - 05:47:08 CDT)
• mjyang
  • stochastical boundary conditions in NAMD (Tue Dec 06 2011 - 19:24:17 CST)
  • how to write out the dcd file by vmd python command? (Mon Feb 21 2011 - 08:53:58 CST)
  • distance calculation between atoms of two segments (Sat Jan 22 2011 - 10:51:00 CST)
  • 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)
• MOhan maruthi sena
  • SMD-extension (Fri Aug 26 2011 - 05:18:25 CDT)
• Mohd Farid Ismail
  • Re: NAMD initial coordinate file (Thu Jan 13 2011 - 12:40:03 CST)
  • 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)
• Molecular Dynamics
  • correlation functions (Sat Dec 10 2011 - 05:18:50 CST)
  • namd force field (Tue Nov 22 2011 - 06:21:16 CST)
  • velocity information (Fri Sep 23 2011 - 08:20:29 CDT)
  • mean square displacement (Mon Sep 05 2011 - 08:15:28 CDT)
  • TIP4P water model (Wed Jul 20 2011 - 07:34:47 CDT)
  • temperature-TS with NAMDplot (Fri Jul 08 2011 - 05:44:50 CDT)
  • about log file (Thu Jun 09 2011 - 04:30:30 CDT)
  • Ä°lt: Re: heat annealing conf file (Fri Jun 03 2011 - 09:57:07 CDT)
  • conf file script ( help needed ) (Fri Jun 03 2011 - 08:37:57 CDT)
  • heat annealing conf file (Thu Jun 02 2011 - 05:26:17 CDT)
  • dcd files (Sun May 22 2011 - 08:02:48 CDT)
  • non-bonded potential in NAMD (Sat Apr 30 2011 - 15:06:58 CDT)
  • topology and parameter files (Sat Apr 16 2011 - 07:13:28 CDT)
  • gromacs analysis tools (Sun Apr 03 2011 - 04:33:14 CDT)
  • gromacs analysis tools (Sun Apr 03 2011 - 04:54:35 CDT)
• mon_sharma_at_research.iiit.ac.in
  • Re: NAMDenergy calculations for nucleic acid systems (Sat Apr 16 2011 - 08:18:17 CDT)
  • NAMDenergy calculations for nucleic acid systems (Sat Apr 16 2011 - 03:22:37 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)
• murffyp_at_gmail.com
  • hello (Tue Jun 21 2011 - 07:54:59 CDT)
  • hi (Sun May 22 2011 - 23:14:11 CDT)
• Myunggi Yi
  • unsubscribe namd-l (Fri Aug 27 2010 - 21:01:19 CDT)
  • StepsPerCycle (Wed Feb 03 2010 - 09:33:08 CST)
• 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 Namd
  • MMTools for analysis (Sat Dec 10 2011 - 05:07:19 CST)
  • install NAMD 2.8 v (Mon Oct 10 2011 - 05:50:53 CDT)
  • namd log file (Fri Oct 07 2011 - 07:20:02 CDT)
  • Re : AW: save the last frame as a pdb file using dcd file (Thu Sep 22 2011 - 03:33:05 CDT)
  • save the last frame as a pdb file using dcd file (Thu Sep 22 2011 - 02:02:53 CDT)
  • time step and total simulation time in conf file (Wed Sep 14 2011 - 09:41:00 CDT)
  • analysis question (Tue Jul 19 2011 - 04:32:06 CDT)
  • namd ( please help me!!! ) (Mon Jun 13 2011 - 14:29:40 CDT)
  • force field (Mon Jun 13 2011 - 03:36:04 CDT)
• Narasimhan LOGANATHAN
  • Re: minimization problem (Tue Aug 09 2011 - 08:21:37 CDT)
  • minimization problem (Tue Aug 09 2011 - 07:00:28 CDT)
  • Re: AW: water equilibration (Fri Aug 05 2011 - 07:53:22 CDT)
  • water equilibration (Fri Aug 05 2011 - 05:41:27 CDT)
  • Re: water equilibration (Thu Aug 04 2011 - 03:25:07 CDT)
  • Re: water equilibration (Tue Aug 02 2011 - 08:42:11 CDT)
  • Re: water equilibration (Wed Jun 08 2011 - 05:17:17 CDT)
  • Re: water equilibration (Tue Jun 07 2011 - 11:15:10 CDT)
  • Re: water equilibration (Tue Jun 07 2011 - 09:03:23 CDT)
  • Re: water equilibration (Mon Jun 06 2011 - 08:55:39 CDT)
  • water equilibration (Mon Jun 06 2011 - 08:07:38 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)
• Neelanjana Sengupta
  • scaling (Wed Dec 28 2011 - 22:56:45 CST)
  • Re: fullSamples in ABF: applied at restart? (Mon Nov 21 2011 - 02:51:55 CST)
  • fullSamples in ABF: applied at restart? (Sun Nov 20 2011 - 22:19:00 CST)
  • fullSamples in ABF: applied at restart? (Sun Nov 20 2011 - 22:14:15 CST)
  • Re: rsh not working (Wed Oct 12 2011 - 02:29:16 CDT)
  • rsh not working (Tue Oct 11 2011 - 00:58:27 CDT)
  • Ib version and nodelist (Mon Aug 22 2011 - 00:36:09 CDT)
  • Re: dcd to trr using catdcd (Tue Mar 22 2011 - 00:11:33 CDT)
  • dcd to trr using catdcd (Mon Mar 21 2011 - 05:44:39 CDT)
  • specify acceptance ratio in REMD (Thu Mar 17 2011 - 01:47:32 CDT)
  • topology for DNA (Fri Jan 28 2011 - 06:28:03 CST)
  • 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)
• 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: Sticking TIP4P water molecules AMBER (Mon Dec 19 2011 - 04:58:13 CST)
  • Re: cpu-gpu vs cpu (Tue Nov 29 2011 - 09:28:34 CST)
  • Re: OpenCL and AMD GPUs (Wed Nov 23 2011 - 01:01:20 CST)
  • Re: Segmentation violation with adaptive tempering. (Mon Nov 21 2011 - 12:11:45 CST)
  • Segmentation violation with adaptive tempering. (Sun Nov 20 2011 - 05:13:02 CST)
  • Carma v.1.1 released. (Thu Oct 27 2011 - 12:54:24 CDT)
  • Re: Running AMBER FF with NAMD 2.8-CUDA (Wed Oct 19 2011 - 10:06:08 CDT)
  • Re: Running AMBER FF with NAMD 2.8-CUDA (Wed Oct 19 2011 - 08:37:15 CDT)
  • Re: save the last frame as a pdb file using dcd file (Thu Sep 22 2011 - 03:10:21 CDT)
  • 'firsttimestep' treated as signed integer ? (Mon Aug 22 2011 - 12:01:26 CDT)
  • Re: how to generate transparent figures? (Sat Jul 23 2011 - 10:47:54 CDT)
  • Re: Suspend NAMD (to RAM) (Thu Jul 21 2011 - 01:20:14 CDT)
  • Re: bigdcd file help (Tue Jul 05 2011 - 13:35:43 CDT)
  • Re: clustering of trajectory (Tue Jul 05 2011 - 09:57:50 CDT)
  • Re: AMD Multicore + CUDA Benchmarks, are them ok ? (Thu May 05 2011 - 04:31:52 CDT)
  • Re: run tests with CUDA (Tue May 03 2011 - 03:09:12 CDT)
  • Re: Oh dear, 'namd2 invoked oom-killer' ... (Fri Apr 15 2011 - 12:16:06 CDT)
  • Oh dear, 'namd2 invoked oom-killer' ... (Fri Apr 15 2011 - 09:55:35 CDT)
  • Re: colvars PMF history problem (Mon Mar 07 2011 - 11:14:40 CST)
  • Re: Job scheduling (managing) software recommendation (Mon Mar 07 2011 - 07:50:07 CST)
  • Re: NCS (Wed Feb 16 2011 - 03:18:29 CST)
  • 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)
• 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)
• 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
  • (no subject) (Tue May 03 2011 - 11:51:42 CDT)
  • Re: namd 2.7b2 or later - amberff/prmtop causes segfault during startup phase (Wed Feb 24 2010 - 06:49:47 CST)
• Nicolás Pérez
  • CG parameters from dcd file for protein CG modelling (Sun Feb 27 2011 - 13:32:18 CST)
• Nikhil Kumar Mittal
  • RE: Resend - ERROR: Atoms moving too fast; (Fri Nov 11 2011 - 20:02:51 CST)
  • Resend - ERROR: Atoms moving too fast; (Fri Nov 11 2011 - 19:56:39 CST)
  • ERROR: Atoms moving too fast; (Fri Nov 11 2011 - 12:10:52 CST)
• Nikita Vakula
  • Quartz modelling (Thu Jul 28 2011 - 00:46:05 CDT)
• Nikolaos Glykos
  • Re: RMSD trajectory (Fri Nov 18 2011 - 14:32:41 CST)
  • Re: NAMD running on windows HPC question (Tue Sep 20 2011 - 08:23:34 CDT)
  • Re: Truncated octahedron box issues Q=3F=29?= (Wed May 25 2011 - 12:19:03 CDT)
  • Re: Truncated octahedron box issues Q=3F=29?= (Wed May 25 2011 - 12:15:44 CDT)
  • Re: rule of thumb for dcd sampling frequency? (Mon Mar 21 2011 - 14:51:09 CDT)
  • Re: colvars PMF history problem (Mon Mar 07 2011 - 16:54:35 CST)
  • Re: NCS (Tue Feb 15 2011 - 13:59:45 CST)
  • 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)
• Niraj kumar
  • Dear friend (Sun May 22 2011 - 20:29:53 CDT)
• 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)
• Norman Geist
  • AW: glycosaminoglycan with GLYCAM06 in amber format (Wed Dec 21 2011 - 00:51:03 CST)
  • AW: glycosaminoglycan with GLYCAM06 in amber format (Wed Dec 21 2011 - 00:54:50 CST)
  • AW: glycosaminoglycan with GLYCAM06 in amber format (Tue Dec 20 2011 - 06:45:32 CST)
  • AW: Sticking TIP4P water molecules AMBER (Tue Dec 20 2011 - 00:33:08 CST)
  • AW: glycosaminoglycan with GLYCAM06 in amber format (Mon Dec 19 2011 - 07:35:58 CST)
  • Sticking TIP4P water molecules AMBER (Mon Dec 19 2011 - 04:33:25 CST)
  • AW: glycosaminoglycan with GLYCAM06 in amber format (Mon Dec 19 2011 - 00:45:19 CST)
  • AW: cell size (Thu Dec 15 2011 - 00:16:59 CST)
  • AW: Peptide planarity Dihedral angle restraints (Fri Dec 09 2011 - 00:18:47 CST)
  • AW: stochastical boundary conditions in NAMD (Wed Dec 07 2011 - 00:38:58 CST)
  • AW: installing namd on ibm cluster (powerpc) (Mon Dec 05 2011 - 03:30:48 CST)
  • AW: installing namd on ibm cluster (powerpc) (Mon Dec 05 2011 - 00:29:43 CST)
  • AW: AW: AW: AW: namd-ibverbs fails to start (Thu Nov 24 2011 - 00:15:52 CST)
  • AW: AW: (Wed Nov 23 2011 - 01:25:12 CST)
  • AW: AW: (Wed Nov 23 2011 - 00:59:15 CST)
  • AW: AW: (Wed Nov 23 2011 - 01:00:42 CST)
  • AW: AW: namd-ibverbs fails to start (Wed Nov 23 2011 - 00:16:28 CST)
  • AW: AW: AW: namd-ibverbs fails to start (Wed Nov 23 2011 - 00:09:41 CST)
  • AW: (Wed Nov 23 2011 - 00:01:50 CST)
  • AW: AW: namd-ibverbs fails to start (Tue Nov 22 2011 - 00:47:00 CST)
  • AW: AW: namd-ibverbs fails to start (Tue Nov 22 2011 - 00:49:46 CST)
  • AW: Reading files for multiple threaded simulations (Fri Nov 04 2011 - 02:28:50 CDT)
  • AW: Reading files for multiple threaded simulations (Thu Nov 03 2011 - 02:26:05 CDT)
  • AW: Reading files for multiple threaded simulations (Wed Nov 02 2011 - 01:45:32 CDT)
  • AW: Error with "namd" (Wed Oct 26 2011 - 02:05:17 CDT)
  • AW: Minimization doesn't stop when converged (Fri Oct 07 2011 - 04:54:47 CDT)
  • Minimization doesn't stop when converged (Fri Oct 07 2011 - 03:48:36 CDT)
  • AW: script for equilibration (Tue Oct 04 2011 - 00:18:04 CDT)
  • AW: AW: save the last frame as a pdb file using dcd file (Thu Sep 22 2011 - 04:33:07 CDT)
  • AW: save the last frame as a pdb file using dcd file (Thu Sep 22 2011 - 03:15:43 CDT)
  • AW: Infiniband and commodity hardware (Mon Sep 19 2011 - 01:03:41 CDT)
  • AW: Constraint failure during equalibration (Wed Sep 14 2011 - 00:31:59 CDT)
  • AW: AW: about extrabonds restrain (Wed Aug 31 2011 - 00:05:47 CDT)
  • AW: about extrabonds restrain (Tue Aug 30 2011 - 01:18:37 CDT)
  • AW: Ib version and nodelist (Mon Aug 22 2011 - 00:50:56 CDT)
  • AW: CUDA on GPU Cluster (Mon Aug 22 2011 - 00:47:16 CDT)
  • AW: Multinode NAMD CUDA GPU Selection (Fri Aug 19 2011 - 00:53:31 CDT)
  • AW: Multinode NAMD CUDA GPU Selection (Fri Aug 19 2011 - 00:22:56 CDT)
  • Multinode NAMD CUDA GPU Selection (Thu Aug 18 2011 - 01:25:00 CDT)
  • AW: Batch Mode MD simulation Script for NAMD (Mon Aug 15 2011 - 00:29:43 CDT)
  • AW: Letzte Hilfe (Mon Aug 15 2011 - 07:16:39 CDT)
  • AW: .COOR TO PDB FILE (Mon Aug 15 2011 - 00:34:58 CDT)
  • AW: Batch Mode MD simulation Script for NAMD (Mon Aug 15 2011 - 00:34:15 CDT)
  • AW: Batch Mode MD simulation Script for NAMD (Fri Aug 12 2011 - 07:02:29 CDT)
  • AW: Batch Mode MD simulation Script for NAMD (Fri Aug 12 2011 - 00:47:19 CDT)
  • AW: Minimization is taking a lot of computing time. (Wed Aug 10 2011 - 01:21:10 CDT)
  • AW: Minimization is taking a lot of computing time. (Wed Aug 10 2011 - 00:44:55 CDT)
  • AW: patch becoming too small (Tue Aug 09 2011 - 02:41:19 CDT)
  • AW: nvidia cuda driver version (Mon Aug 08 2011 - 00:04:40 CDT)
  • AW: water equilibration (Fri Aug 05 2011 - 05:56:04 CDT)
  • AW: Minimization is taking a lot of computing time. (Fri Aug 05 2011 - 05:54:49 CDT)
  • AW: Namd-I: namd compiling problem (Thu Aug 04 2011 - 00:33:59 CDT)
  • AW: Namd-I: namd compiling problem (Wed Aug 03 2011 - 00:23:52 CDT)
  • AW: Win64-MPI (Tue Jul 12 2011 - 08:20:11 CDT)
  • AW: temperature-TS with NAMDplot (Fri Jul 08 2011 - 06:02:14 CDT)
  • AW: free energy of binding (Thu Jul 07 2011 - 05:35:07 CDT)
  • AW: Re: Protein moving out of box during npt simulation (Tue Jul 05 2011 - 01:15:20 CDT)
  • AW: Re: NPT equilibration (Fri Jul 01 2011 - 05:50:23 CDT)
  • AW: Re: NPT equilibration (Fri Jul 01 2011 - 05:49:38 CDT)
  • AW: Re: Equilibration (Wed Jun 29 2011 - 04:08:26 CDT)
  • AW: Re: Equilibration (Wed Jun 29 2011 - 04:04:42 CDT)
  • AW: Re: Equilibration (Wed Jun 29 2011 - 01:39:13 CDT)
  • AW: aligning two molecules by principal axes of inertia using measure.c (Mon Jun 20 2011 - 09:30:02 CDT)
  • AW: NAMD crashes with OpenMPI/OpenMX (Mon Jun 20 2011 - 00:36:54 CDT)
  • AW: AW: AW: NAMD crashes with OpenMPI/OpenMX (Wed Jun 15 2011 - 10:37:47 CDT)
  • AW: AW: NAMD crashes with OpenMPI/OpenMX (Wed Jun 15 2011 - 09:37:40 CDT)
  • AW: AW: NAMD crashes with OpenMPI/OpenMX (Wed Jun 15 2011 - 01:01:25 CDT)
  • AW: water is forming bonds between oxigens (Wed Jun 15 2011 - 01:05:35 CDT)
  • AW: max number of CPU PEs per GPU? (Fri Jun 10 2011 - 06:25:45 CDT)
  • AW: max number of CPU PEs per GPU? (Fri Jun 10 2011 - 02:56:30 CDT)
  • AW: Problem with NAMD 2.8 (but not in 2.7) : Endless loop repeating "The last position output ..." (Thu Jun 09 2011 - 00:44:01 CDT)
  • AW: Multiple Runs in a Single Conf File (Thu Jun 09 2011 - 00:40:18 CDT)
  • AW: Problem with NAMD 2.8 (but not in 2.7) : Endless loop repeating "The last position output ..." (Thu Jun 09 2011 - 00:36:44 CDT)
  • AW: Problem with NAMD 2.8 (but not in 2.7) : Endless loop repeating "The last position output ..." (Thu Jun 09 2011 - 00:26:13 CDT)
  • AW: Multiple Runs in a Single Conf File (Wed Jun 08 2011 - 03:27:54 CDT)
  • AW: AMD-PhenomII-1075_GTX470 NAMD-CUDA performance (Mon Jun 06 2011 - 06:49:06 CDT)
  • AW: AMD-PhenomII-1075_GTX470 NAMD-CUDA performance (Mon Jun 06 2011 - 07:22:45 CDT)
  • AW: AMD-PhenomII-1075_GTX470 NAMD-CUDA performance (Mon Jun 06 2011 - 06:11:18 CDT)
  • AW: AMD-PhenomII-1075_GTX470 NAMD-CUDA performance (Mon Jun 06 2011 - 04:51:31 CDT)
  • Development plan of NAMD? (Tue May 24 2011 - 02:03:37 CDT)
  • AW: AW: AW: question about wrap atoms to its original coordinates (Mon May 23 2011 - 01:03:53 CDT)
  • My benchmark results with TeslaC2050 (Fri May 20 2011 - 01:02:36 CDT)
  • AW: AW: question about wrap atoms to its original coordinates (Fri May 20 2011 - 00:04:48 CDT)
  • AW: AW: Automatic GPU selection in NAMD ? (Thu May 19 2011 - 01:41:37 CDT)
  • AW: CUDA simulation memory usage (Wed May 18 2011 - 07:10:58 CDT)
  • AW: question about wrap atoms to its original coordinates (Wed May 18 2011 - 00:34:33 CDT)
  • AW: Automatic GPU selection in NAMD ? (Wed May 18 2011 - 00:24:45 CDT)
  • AW: deca-Ala simulations with different cutoff produce different results (Mon May 16 2011 - 04:20:58 CDT)
  • RE: deca-Ala simulations with different cutoff produce different results (Mon May 16 2011 - 02:12:40 CDT)
  • AW: Corrupt dcd files (Thu May 12 2011 - 01:53:23 CDT)
  • AW: Corrupt dcd files (Thu May 12 2011 - 01:51:56 CDT)
  • AW: Corrupt dcd files (Thu May 12 2011 - 01:46:51 CDT)
  • AW: AW: Running NAMD parallel on two machines with 3 CUDAs (Fri May 06 2011 - 01:36:20 CDT)
  • AW: compilation of namd (Fri May 06 2011 - 01:16:56 CDT)
  • AW: compilation of namd (Fri May 06 2011 - 00:46:01 CDT)
  • AW: Running NAMD parallel on two machines with 3 CUDAs (Fri May 06 2011 - 00:41:11 CDT)
  • AW: Running NAMD parallel on two machines with 3 CUDAs (Fri May 06 2011 - 00:36:27 CDT)
  • WG: Abnormal EOF Error in Extra Bonds File (Mon May 02 2011 - 06:48:41 CDT)
  • Re: NAMD speed on MPICH2 Ubuntu 64 bit Cluster (Fri Apr 15 2011 - 07:46:00 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
  • Coulomb 1-4 interactions (Fri Dec 02 2011 - 10:11:24 CST)
  • Density Profile in VMD (Mon Sep 05 2011 - 02:30:50 CDT)
  • about charmm force field (Fri Jun 10 2011 - 09:55:26 CDT)
  • prm and top files for charmm19 force field (Fri Jun 03 2011 - 09:22:47 CDT)
  • about conf file (Thu May 26 2011 - 09:11:29 CDT)
  • about rigid bonds (Wed Apr 13 2011 - 03:39:34 CDT)
  • Net forces on each atom can be written to PDB in NAMD 2.8b1 (Mon Mar 28 2011 - 04:53:55 CDT)
  • Net forces on each atom can be written to PDB in NAMD 2.8b1 (Mon Mar 28 2011 - 04:06:05 CDT)
  • question about force information (Thu Mar 24 2011 - 06:02:14 CDT)
  • question about force information (Thu Mar 24 2011 - 04:43:20 CDT)
  • initial structures for md simulations (Wed Feb 16 2011 - 07:52:26 CST)
  • initial structures for md simulations (Wed Feb 16 2011 - 06:22:11 CST)
  • bond lengths angles in namd (Thu Jan 27 2011 - 06:35:34 CST)
  • bond lengths angles in namd (Thu Jan 27 2011 - 05:43:09 CST)
  • 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)
• opronkri_at_msu.edu
  • Tcl issue with config script (Fri Jun 17 2011 - 00:06:53 CDT)
• Osman Yogurtcu
  • Re: question about force information (Thu Mar 24 2011 - 09:56:25 CDT)
• P.-L. Chau
  • intermittent non-execution of NAMD on tesla (Mon Nov 21 2011 - 04:09:04 CST)
  • Re: lengthening time-step with constraints causes RMSD "jump" (Thu Jun 02 2011 - 16:03:53 CDT)
  • Re: lengthening time-step with constraints causes RMSD "jump" (Thu Jun 02 2011 - 11:23:34 CDT)
  • lengthening time-step with constraints causes RMSD "jump" (Thu Jun 02 2011 - 06:53:05 CDT)
  • Re: restart with constraints causes RMSD "jump" (Wed May 25 2011 - 12:56:41 CDT)
  • restart with constraints causes RMSD "jump" (Wed May 25 2011 - 07:24:11 CDT)
• 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
  • RE: Umbrella sampling-NAMD (Fri Dec 16 2011 - 09:29:27 CST)
  • RE: Umbrella sampling-NAMD (Thu Dec 15 2011 - 12:51:57 CST)
  • Umbrella sampling-NAMD (Thu Dec 15 2011 - 09:24:36 CST)
  • Umbrella sampling (Wed Nov 16 2011 - 15:12:17 CST)
  • Extra bonds-ABF (Mon Nov 07 2011 - 10:53:18 CST)
  • RE: Component distanceZ-ABF (Mon Sep 05 2011 - 13:07:26 CDT)
  • RE: Component distanceZ-ABF (Mon Sep 05 2011 - 09:42:17 CDT)
  • Component distanceZ-ABF (Fri Sep 02 2011 - 11:21:56 CDT)
  • dummyAtom-ABF (Fri Aug 26 2011 - 09:57:13 CDT)
  • distanceXY colvar-ABF (Sun Aug 21 2011 - 09:05:16 CDT)
  • RE: Fixed COM (Mon Jul 11 2011 - 13:52:21 CDT)
  • RE: ABF atom selection (Tue May 10 2011 - 09:16:29 CDT)
  • ABF atom selection (Sat May 07 2011 - 18:14:24 CDT)
  • ABF atom selection question (Thu May 05 2011 - 21:50:00 CDT)
  • ABF reproducibility (Sun Feb 13 2011 - 15:08:26 CST)
  • RE: ABF question (sampling and colvars output file) (Mon Feb 07 2011 - 14:27:03 CST)
  • ABF question (sampling and colvars output file) (Sun Feb 06 2011 - 15:20:47 CST)
  • ABF question (sampling and colvars output file) (Tue Feb 01 2011 - 10:27:43 CST)
  • .colvars.state file in ABF (Tue Jan 04 2011 - 15:51:09 CST)
  • concatenate pmf files in colvars (Sat Jan 01 2011 - 12:23:06 CST)
  • 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
  • Sampling schemes with FEP (Thu Oct 20 2011 - 08:13:19 CDT)
  • 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
  • Re: Win64-MPI (Tue Jul 12 2011 - 08:08:14 CDT)
  • Win64-MPI (Tue Jul 05 2011 - 02:04:17 CDT)
  • Gibbs potential (Mon Jun 06 2011 - 10:10:01 CDT)
  • CthCreate failed to create fiber (Fri Jun 03 2011 - 08:52:28 CDT)
  • 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 wintrode
  • Accelerated MD: question about dual boost mode (Thu Mar 31 2011 - 15:01:49 CDT)
  • Am I using the right version for accelerated MD? (Tue Mar 22 2011 - 15:34:29 CDT)
  • Accelerated MD documentation? (Tue Mar 15 2011 - 08:05:19 CDT)
  • 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)
• PAUL NEWMAN
  • Assertion failed in file @ KRAKEN (Wed Nov 09 2011 - 10:07:07 CST)
  • Re: NAMD on KRAKEN (Fri Oct 28 2011 - 07:55:01 CDT)
  • NAMD on KRAKEN (Fri Oct 28 2011 - 02:04:00 CDT)
  • water is forming bonds between oxigens (Tue Jun 14 2011 - 16:36:33 CDT)
  • Re: Joining PSF Files (Tue May 24 2011 - 09:04:24 CDT)
  • Joining PSF Files (Tue May 24 2011 - 08:58:24 CDT)
  • Re: dcd files (Sun May 22 2011 - 14:46:57 CDT)
  • Re: dcd files (Sun May 22 2011 - 08:24:15 CDT)
  • Re: simulation box (Fri May 20 2011 - 11:30:43 CDT)
  • Re: simulation box (Fri May 20 2011 - 11:11:52 CDT)
  • simulation box (Fri May 20 2011 - 10:39:48 CDT)
  • Re: FATAL ERROR: Bad global angle count! (Sat Apr 23 2011 - 22:04:37 CDT)
  • FATAL ERROR: Bad global angle count! (Fri Apr 22 2011 - 19:42:02 CDT)
• 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)
• 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)
• pawan raghav
  • Nice paper on MD Simulations (Sat Sep 10 2011 - 13:37:00 CDT)
• Payel Das
  • Proline hybrid topology file for FEP (Fri Aug 20 2010 - 19:54:28 CDT)
• Pedro Gonnet
  • Re: Memory leak and crash before first step (Tue Jul 12 2011 - 15:00:45 CDT)
  • Re: Memory leak and crash before first step (Tue Jul 05 2011 - 08:25:34 CDT)
  • Memory leak and crash before first step (Fri Jun 24 2011 - 14:28:08 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
  • Unpredictable crash at runtime (Fri Mar 18 2011 - 03:14:22 CDT)
  • NVE crash (Wed Apr 28 2010 - 10:30:09 CDT)
• Pellegrini Eric
  • Heating in NPT (Mon Sep 19 2011 - 07:44:04 CDT)
  • Re : Setting up a membrane simulation (Mon Sep 19 2011 - 02:09:58 CDT)
  • Setting up a membrane simulation (Fri Sep 16 2011 - 02:52:05 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)
• pepe barrientos
  • Thermodynamic integration questions (Tue Dec 06 2011 - 10:39:38 CST)
• Pete Kekenes-Huskey
  • namd2_ti.pl Modification of non-creatable array value attempted, subscript -49999 (Tue Sep 06 2011 - 17:22:26 CDT)
• Peter Freddolino
  • Re: NAMDenergy calculations for nucleic acid systems (Sat Apr 16 2011 - 05:48:31 CDT)
  • Re: implementing RBCG (Wed Mar 23 2011 - 20:19:09 CDT)
  • Re: implementing RBCG (Tue Mar 22 2011 - 21:17:32 CDT)
  • Re: psfgen - ACE cap on PRO (Thu Mar 10 2011 - 19:59:14 CST)
  • Re: Fwd: vmd-l: Re: hBond colvars and patching (Tue Mar 08 2011 - 13:48:53 CST)
  • Re: vmd-l: Re: hBond colvars and patching (Mon Mar 07 2011 - 17:08:23 CST)
  • Re: vmd-l: Re: hBond colvars and patching (Mon Mar 07 2011 - 09:19:20 CST)
  • Re: example psf and pdb files for simulations with tip4p (Wed Mar 02 2011 - 13:28:48 CST)
  • Re: namd at ranger(tacc) (Thu Feb 24 2011 - 17:02:27 CST)
  • 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)
• 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)
• 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] Regarding Compiling in Redhat linux. (Wed Aug 03 2011 - 09:30:01 CDT)
  • Re: [ppl] Compliling NAMD in RedHat (Tue Aug 02 2011 - 10:10:18 CDT)
  • Re: [ppl] Help Regarding NAMD Application Testing (Mon Mar 21 2011 - 09:00:13 CDT)
  • Re: [ppl] NAMD at linux on sparc (Sun Feb 06 2011 - 21:18:32 CST)
  • Re: [ppl] error compiling charm-6.2.2 for bluegenep-xlc (Wed Oct 27 2010 - 23:14:34 CDT)
• Philip Peartree
  • Velocity distribution (Tue Mar 29 2011 - 05:45:30 CDT)
  • 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)
• 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)
• Pletezhov Alexandr
  • accuracy of measurement (Mon Feb 21 2011 - 17:14:16 CST)
  • Output of forces (Thu Dec 02 2010 - 06:04:46 CST)
• poker_at_physics.usyd.edu.au
  • Re: TClforce (Thu Oct 20 2011 - 21:22:25 CDT)
  • Re: slow heating md (Thu Jun 23 2011 - 20:00:54 CDT)
  • Re: formyl and ethanolamide parameters and topology (Thu Jun 23 2011 - 19:11:57 CDT)
  • Re: Fwd: phosphotyrosine (Mon Jun 20 2011 - 01:42:49 CDT)
  • 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)
• politr_at_fh.huji.ac.il
  • NAMD energy plugin (Thu Jul 28 2011 - 04:22:42 CDT)
• prasun kumar
  • unsubscribe (Mon Feb 01 2010 - 12:00:49 CST)
• Prathit Chatterjee
  • Re: Re: Alpha P.M.F. with NAMD 2.8 (Fri Jun 03 2011 - 07:55:52 CDT)
  • Alpha P.M.F. with NAMD 2.8 (Fri Jun 03 2011 - 06:21:46 CDT)
  • Re: error in the orientationAngle (Sun May 22 2011 - 05:01:55 CDT)
  • error in the orientationAngle (Sat May 21 2011 - 03:51:10 CDT)
  • Re: alpha pmf (Sat May 07 2011 - 00:33:28 CDT)
  • Re: alpha pmf (Fri May 06 2011 - 05:54:55 CDT)
  • Re: alpha pmf (Thu May 05 2011 - 01:21:02 CDT)
  • alpha pmf (Wed May 04 2011 - 00:55:40 CDT)
  • Re: parameter file for DMPC lipid and protein system but with CHARMM36 lipids (Tue Jan 04 2011 - 01:14:10 CST)
  • problem regarding rattle algorithm (Fri Dec 31 2010 - 02:29:43 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
  • Pressure Calculation (Fri Sep 02 2011 - 12:43:25 CDT)
  • 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)
• 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)
• Purushottam Dixit
  • unsubscribe (Mon Jan 31 2011 - 20:59:01 CST)
• pxq_at_dicp.ac.cn
  • can RHDO crystal shape works in NAMD (Fri Jul 01 2011 - 01:33:14 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)
• QFrank_X=2E_V=E1zquez=22?=
  • QM/MM (Mon Apr 11 2011 - 18:23:26 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)
• 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)
• raghav singh
  • Re: what is wrong with this pdb to simulate with NAMD (Fri Oct 14 2011 - 12:04:20 CDT)
  • DNA terminal Patch / How could I retain the primes in DNA (Tue Jul 05 2011 - 03:23:21 CDT)
• Rajan Vatassery
  • Re: Pressure Problems, Excessively High Readings (Mon Nov 14 2011 - 01:14:41 CST)
  • Pressure Problems, Excessively High Readings (Tue Nov 08 2011 - 20:43:10 CST)
  • Re: FATAL ERROR: Setting parameter fixedAtomsFile from script failed! (Fri Jul 15 2011 - 16:43:04 CDT)
  • Re: TIP5P-model (Thu Jul 14 2011 - 20:30:00 CDT)
  • Re: a bundle of coor files (Sat Jul 02 2011 - 16:26:32 CDT)
  • Re: Multiple Runs in a Single Conf File (Wed Jun 08 2011 - 09:53:55 CDT)
  • Multiple Runs in a Single Conf File (Wed Jun 08 2011 - 03:00:55 CDT)
  • Question about end of log file (Sun May 29 2011 - 14:14:34 CDT)
  • 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)
• rajitha rajeshwar
  • Fwd: Generating .tpr file using NAMD files (Mon Dec 19 2011 - 03:05:34 CST)
• rajitha tatikonda
  • Re: Generating .tpr file using NAMD files (Mon Dec 19 2011 - 00:32:56 CST)
• 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 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)
• Ranyere Deyler
  • restart simulation writing in the same .dcd file. (Sat Jul 02 2011 - 02:25:51 CDT)
  • Re: topology file for nanotube (Thu Mar 10 2011 - 02:10:13 CST)
  • Re: Can paratools really parametrize a structure? Is it really finished? (Mon Feb 28 2011 - 13:28:30 CST)
  • Can paratools really parametrize a structure? Is it really finished? (Mon Feb 28 2011 - 10:56:35 CST)
  • Paratool`s error reading single point calculation. (Sat Feb 26 2011 - 00:50:59 CST)
  • 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)
• Raul Araya
  • Re: HEME and Cystein instead of His (Wed Nov 23 2011 - 14:25:37 CST)
  • HEME and Cystein instead of His (Wed Nov 23 2011 - 13:10:36 CST)
  • dextran and or poly-D-glucosamine topology (Fri Nov 04 2011 - 16:58:34 CDT)
  • Setting up aMD simulation of a membrane protein (Fri Apr 01 2011 - 09:05:32 CDT)
  • Accelerated MD with membrane embedded proteins. (Mon Mar 28 2011 - 13:45:36 CDT)
  • Using RAMD for studiying conformational changes in proteins (Thu Mar 24 2011 - 15:23:39 CDT)
  • Replica exchange MD with NAMD with SGE.... (Fri Feb 25 2011 - 15:14:19 CST)
  • 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)
• Ravinder Abrol
  • TIP4P/Ice usage in NAMD (Tue Aug 24 2010 - 03:22:17 CDT)
• Reichert, David
  • RE: Question about equilibration (Wed Jun 15 2011 - 14:21:33 CDT)
  • restarting a simulation ? (Fri Mar 05 2010 - 13:17:14 CST)
• 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)
• Richard Wood
  • two NAMD questions (Wed Nov 09 2011 - 22:31:18 CST)
  • Re: free energy of binding (Thu Jul 07 2011 - 18:56:48 CDT)
  • Re: slow heating md (Thu Jun 23 2011 - 08:13:25 CDT)
  • Re: Question about equilibration (Wed Jun 15 2011 - 14:12:14 CDT)
  • Re: Question about equilibration (Wed Jun 15 2011 - 13:47:59 CDT)
  • Re: Question about equilibration (Wed Jun 15 2011 - 13:16:00 CDT)
  • Re: Question about equilibration (Wed Jun 15 2011 - 12:35:44 CDT)
  • Re: partial charges for organic ligands (Sat Mar 26 2011 - 22:18:50 CDT)
  • Re: rule of thumb for dcd sampling frequency? (Mon Mar 21 2011 - 18:43:30 CDT)
  • help needed (Tue Mar 01 2011 - 09:25:51 CST)
  • Another PSF question... (Tue Feb 15 2011 - 16:13:13 CST)
  • Re: I need help with this (Fri Feb 11 2011 - 12:39:57 CST)
  • Re: I need help with this (Fri Feb 11 2011 - 12:00:11 CST)
  • Re: I need help with this (Fri Feb 11 2011 - 11:07:42 CST)
  • Re: I need help with this (Fri Feb 11 2011 - 06:07:23 CST)
  • Re: Mirror Image Energy Discrepency (Wed Feb 09 2011 - 16:42:18 CST)
  • I need help with this (Wed Feb 09 2011 - 13:01:25 CST)
• Rick Calloway
  • Pressure Questions (Wed Feb 10 2010 - 08:16:50 CST)
• riya david
  • monolayere (Fri Jul 30 2010 - 14:29:48 CDT)
• Robert Brunner
  • Re: VMD inorganic builder plugin (Thu Mar 17 2011 - 14:17:48 CDT)
• Robert Elder
  • Re: Colvars "tilt" component force constant units for WHAM (Fri Jul 22 2011 - 11:06:16 CDT)
  • Colvars "tilt" component force constant units for WHAM (Tue Jul 12 2011 - 16:36:55 CDT)
  • Colvars "tilt" component force constant units for WHAM (Tue Jul 12 2011 - 16:48:48 CDT)
  • 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)
• Robert McCarrick
  • Re: NAMD speed on MPICH2 Ubuntu 64 bit Cluster (Thu Apr 07 2011 - 09:06:03 CDT)
  • Re: NAMD speed on MPICH2 Ubuntu 64 bit Cluster (Wed Apr 06 2011 - 15:50:11 CDT)
  • Re: NAMD speed on MPICH2 Ubuntu 64 bit Cluster (Wed Apr 06 2011 - 11:19:16 CDT)
  • NAMD speed on MPICH2 Ubuntu 64 bit Cluster (Tue Apr 05 2011 - 13:51:55 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)
• rohan uttarwar
  • Use of RBCG to convert multiple frames from atomistic trajectory to Coarse grained (Tue Nov 01 2011 - 13:13:20 CDT)
  • Problem while using MARTINI force field with NAMD 2.8 (Tue Jul 12 2011 - 11:42:14 CDT)
  • Error while using larger timesteps in Coarse grained Simulation of Polymer (Fri Mar 04 2011 - 15:53:56 CST)
• 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)
• 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)
• Roy Kim
  • Resources for trying out NVIDIA GPUs for free with NAMD (Wed Aug 18 2010 - 12:22:09 CDT)
• Ryan McGreevy
  • Proposed Feature in Targeted MD (Wed Feb 02 2011 - 12:48:58 CST)
• S Richmond
  • Re: SMD negative forces (Thu Feb 10 2011 - 15:32:35 CST)
  • Re: SMD negative forces (Mon Feb 07 2011 - 17:37:09 CST)
  • SMD negative forces (Fri Feb 04 2011 - 10:39:44 CST)
• S.Archana
  • Protein-DNA simulations (Mon Jan 17 2011 - 04:41:27 CST)
• Sabyashachi Mishra
  • abf_integrate (Wed Aug 04 2010 - 04:50:08 CDT)
  • selective rigidbonds (Fri May 21 2010 - 04:29:57 CDT)
• sajad falsafi
  • Re: two NAMD questions (Wed Nov 09 2011 - 23:16:18 CST)
  • Re: membrane simulation ERROR rattle algorithm (Tue Jul 05 2011 - 11:44:10 CDT)
  • Re: bigdcd file help (Mon Jul 04 2011 - 08:52:36 CDT)
  • Re: atom select within hbond analysis (Tue Jun 07 2011 - 09:21:09 CDT)
  • Re: Gibbs potential (Tue Jun 07 2011 - 02:14:40 CDT)
• sakthi kumaran
  • Re: ABF colvar error-capped nanotube interaction (Sun Mar 20 2011 - 11:26:04 CDT)
  • Re: ABF colvar error-capped nanotube interaction (Sun Mar 20 2011 - 01:55:30 CDT)
  • ABF colvar error-capped nanotube interaction (Sat Mar 19 2011 - 11:12:57 CDT)
  • Re: targeted molecular dynamics (Thu Mar 17 2011 - 09:08:25 CDT)
  • targeted molecular dynamics (Thu Mar 17 2011 - 01:28:59 CDT)
  • moving inner wall of nanotube with outer wall fixed (Tue Mar 15 2011 - 04:29:02 CDT)
  • Re: creating .psf file for a nanotube (Fri Mar 11 2011 - 06:34:36 CST)
  • Re: creating .psf file for a nanotube (Fri Mar 11 2011 - 05:13:34 CST)
  • creating .psf file for a nanotube (Fri Mar 11 2011 - 02:36:02 CST)
  • topology file for nanotube (Thu Mar 10 2011 - 00:57:44 CST)
• Salvador H-V
  • Problems Bionanotechnology Tutorial (Fri Oct 21 2011 - 22:19:01 CDT)
  • Re: How to evaluate the area per lipid and thickness of the lipid bilayer in a membrane-protein system? (Thu Aug 25 2011 - 11:12:49 CDT)
  • Re: Iron Oxide and Arsenic (Sat Jun 11 2011 - 17:25:25 CDT)
  • Iron Oxide and Arsenic (Sat Jun 11 2011 - 17:09:20 CDT)
  • GeForce vs Tesla GPUs for high performance computing (Thu Apr 14 2011 - 13:58:30 CDT)
  • Re: Help building a desktop for namd (Wed Apr 13 2011 - 11:34:18 CDT)
  • Re: Help building a desktop for namd (Mon Apr 11 2011 - 12:22:01 CDT)
  • Help building a desktop for namd (Sun Apr 10 2011 - 12:40:05 CDT)
• Salvatore Mario Cosseddu
  • Re: PME and net charge in the system (Thu Oct 27 2011 - 12:20:26 CDT)
  • PME and net charge in the system (Thu Oct 27 2011 - 12:00:12 CDT)
  • Re: membrane simulation ERROR rattle algorithm (Wed Jul 06 2011 - 06:15:46 CDT)
• saman amiri
  • Re: restart simulation writing in the same .dcd file. (Sat Jul 02 2011 - 10:00:29 CDT)
  • Re: Re: Equilibration (Thu Jun 30 2011 - 02:53:42 CDT)
  • Re: Re: Equilibration (Wed Jun 29 2011 - 16:05:11 CDT)
  • SWM4 water model simulation (Mon Jun 27 2011 - 12:27:34 CDT)
  • SWM4 water model simulation (Fri Jun 17 2011 - 16:07:14 CDT)
  • PSF and PDB file for SWM4 water models (Thu May 26 2011 - 07:37:04 CDT)
• Samy Hamdouche
  • Re: Computing interaction energies in namd (Tue Feb 22 2011 - 18:21:46 CST)
  • Computing interaction energies in namd (Tue Feb 22 2011 - 14:40:31 CST)
  • Computing several pair interactions (Tue Feb 15 2011 - 18:11:25 CST)
• 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
  • water sphere (Thu Jan 06 2011 - 03:14:01 CST)
  • 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)
• Sara baretller
  • Namd / gromacs (Tue Aug 16 2011 - 09:17:41 CDT)
• sathish kumar gurupatham
  • unsubscribe namd-l (Sat Aug 28 2010 - 14:07:25 CDT)
  • unsubscribe (Mon Apr 19 2010 - 09:25:06 CDT)
• Saumya
  • Analysis of Results of only Lipid Bilayer Simulations (Wed May 19 2010 - 05:22:06 CDT)
• sciencekey
  • NAMD for windows cannot run correctly according to namd tutorials (Tue Apr 05 2011 - 04:00:11 CDT)
• 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)
• scott stensland
  • Re: regarding vmd (Thu Jun 02 2011 - 08:59:15 CDT)
• Sebastian Maximilian Wilhelm
  • NAMDenergy electrostatic energies (Mon Feb 28 2011 - 10:41:03 CST)
• 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)
• 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
  • calculating energy term from extrabonds (Mon Feb 07 2011 - 23:50:43 CST)
  • calculating energy term from extrabonds (Mon Feb 07 2011 - 20:08:33 CST)
  • determining force constant in exterbonds (harmonic potential) (Sat Feb 05 2011 - 10:09:50 CST)
  • Re: Parallel replicas? (Fri Mar 12 2010 - 10:51:05 CST)
• Sellers, Michael S. (Cont, ARL/WMRD)
  • extending namd / shared library build (UNCLASSIFIED) (Fri Oct 29 2010 - 08:23:41 CDT)
• Seren Soner
  • IBverbs charmrun problem (Tue Mar 08 2011 - 05:41:33 CST)
  • Error on closing binary file (Thu Jan 13 2011 - 06:42:50 CST)
• Shen, Han
  • error: expected floating-point number but got (Thu Aug 04 2011 - 10:21:32 CDT)
  • Can I set a range to limit the ABF (Wed Apr 20 2011 - 10:24:46 CDT)
  • Error: keyword "group1" is not supported, or not recognized in this context. (Fri Apr 15 2011 - 09:14:11 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)
• Sibel Cakan
  • Reverse Mapping of RBCG Model (Thu Mar 31 2011 - 06:20:08 CDT)
  • Reverse Mapping of RBCG Model (Thu Mar 31 2011 - 03:51:57 CDT)
  • Coarse_Graining tempetrature (Fri Jan 28 2011 - 09:12:43 CST)
  • Coarse_Graining tempetrature (Fri Jan 28 2011 - 08:31:02 CST)
  • CG_MD temperature (Fri Jan 28 2011 - 07:52:15 CST)
• sibel.cakan
  • FATAL ERROR: Unable to open binary file (Thu Jul 14 2011 - 05:34:57 CDT)
  • CG-MD high electrostatic energy values (Fri Jun 24 2011 - 03:40:32 CDT)
  • question about v2.8 (Tue Jun 07 2011 - 09:01:58 CDT)
• 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
  • Re: difference between run and minimize (Wed Sep 14 2011 - 10:05:56 CDT)
  • Re: difference between run and minimize (Wed Sep 14 2011 - 10:02:03 CDT)
  • difference between run and minimize (Fri Sep 09 2011 - 16:01:55 CDT)
  • Re: Re: Protein moving out of box during npt simulation (Thu Jul 07 2011 - 10:02:09 CDT)
  • Re: membrane simulation ERROR rattle algorithm (Wed Jul 06 2011 - 10:06:03 CDT)
  • Re: bigdcd file help (Tue Jul 05 2011 - 13:19:06 CDT)
  • Re: Re: Protein moving out of box during npt simulation (Tue Jul 05 2011 - 10:00:23 CDT)
  • Re: bigdcd file help (Tue Jul 05 2011 - 09:56:15 CDT)
  • bigdcd file help (Mon Jul 04 2011 - 01:29:23 CDT)
  • Re: Re: Equilibration (Wed Jun 29 2011 - 18:00:48 CDT)
  • Re: Question about equilibration (Thu Jun 16 2011 - 17:33:37 CDT)
  • Re: Question about equilibration (Wed Jun 15 2011 - 12:06:57 CDT)
  • Re: Question about equilibration (Wed Jun 15 2011 - 11:38:17 CDT)
  • Re: Question about equilibration (Wed Jun 15 2011 - 11:20:04 CDT)
  • Re: Question about equilibration (Wed Jun 15 2011 - 11:07:51 CDT)
  • Question about equilibration (Wed Jun 15 2011 - 11:02:53 CDT)
  • Re: namd ( please help me!!! ) (Mon Jun 13 2011 - 15:12:19 CDT)
  • Protein distort during equilibration (Mon Jun 13 2011 - 10:22:10 CDT)
  • Re: SMD of three atom at a time (Wed Jun 01 2011 - 08:14:39 CDT)
  • SMD of three atom at a time (Fri May 20 2011 - 11:32:03 CDT)
  • NAMD question (Fri May 13 2011 - 16:34:16 CDT)
  • NAMD cell dimension increasing in Z direction, problem with periodic cell (Fri Apr 15 2011 - 13:23:53 CDT)
  • Re: membrane simulation Constraint failure in RATTLE algorithm (Thu Feb 17 2011 - 10:00:44 CST)
  • Re: membrane simulation Constraint failure in RATTLE algorithm (Wed Feb 16 2011 - 17:51:32 CST)
  • Re: membrane simulation Constraint failure in RATTLE algorithm (Wed Feb 16 2011 - 14:43:06 CST)
  • membrane simulation Constraint failure in RATTLE algorithm (Wed Feb 16 2011 - 12:15:11 CST)
  • Parameter in configuration NVE or NPT (Tue Feb 15 2011 - 11:17:03 CST)
  • Re: Tetramer protein complex (Mon Feb 14 2011 - 15:01:31 CST)
  • Re: NCS (Mon Feb 14 2011 - 15:09:33 CST)
  • Tetramer protein complex (Sun Feb 13 2011 - 00:54:34 CST)
  • Re: Question regarding NAMD membrane tutorial (Wed Feb 02 2011 - 13:03:38 CST)
  • Question regarding NAMD membrane tutorial (Mon Jan 31 2011 - 10:49:07 CST)
  • Membrane protein simulaton (Fri Jan 14 2011 - 18:19:24 CST)
  • NAMD CUDA error message (Fri Jan 14 2011 - 11:37:54 CST)
  • 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)
• Song, Hyundeok (songhk)
  • RE: question about Distance XY (Tue Sep 13 2011 - 09:10:07 CDT)
  • question about Distance XY (Mon Sep 12 2011 - 23:27:05 CDT)
  • 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)
• Soran
  • NAMD OPLS Parameters (Thu Nov 04 2010 - 16:57:56 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)
• Stan Skafidas
  • Compiling Namd on MAC with Cuda (Wed Aug 10 2011 - 07:16:49 CDT)
• Stefan Franzen
  • CG parameterization problem (Tue Apr 26 2011 - 05:07:32 CDT)
  • Coarse Graining problem resolved (Tue Apr 26 2011 - 05:32:21 CDT)
  • Coarse Graining setup question (Tue Apr 26 2011 - 05:13:23 CDT)
  • 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
  • Re: Abf force output (Wed Feb 09 2011 - 04:12:50 CST)
  • Abf force output (Tue Feb 08 2011 - 20:58:39 CST)
  • 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)
• Steven Cox
  • Running NAMD CUDA (Fri Nov 04 2011 - 15:06:31 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)
• 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)
• superdirac
  • the unit of dipole moment in the calculation of dielectric constant. (Sun Apr 25 2010 - 21:58:11 CDT)
• 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
  • Fwd: restrain on COM (Fri Nov 18 2011 - 23:33:09 CST)
  • selection of cholesterol molecules (Tue Nov 01 2011 - 23:54:06 CDT)
  • TClforce (Thu Oct 20 2011 - 03:11:01 CDT)
  • charmm force field (Thu Feb 03 2011 - 21:55:22 CST)
  • volume calculation (Tue Feb 01 2011 - 04:02:48 CST)
  • 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)
• S¨¢ndor Kov¨¢cs
  • Re: force field for replica exchange with NAMD (Thu Oct 28 2010 - 17:47:21 CDT)
• Sándor Kovács
  • Re: hi (Thu Jul 14 2011 - 14:19:52 CDT)
  • Re: namd at ranger(tacc) (Thu Feb 24 2011 - 16:46:41 CST)
• TAEJIN KIM
  • Control DCD file (Mon Jun 07 2010 - 17:09:20 CDT)
• TAO WANG
  • Q=AD=94=E5=A4=8D:_=E7=AD=94=E5=A4=8D:__compilation_of_n?= amd (Tue May 10 2011 - 20:42:49 CDT)
  • Q=AD=94=E5=A4=8D:__compilation_of_namd?= (Mon May 09 2011 - 01:27:12 CDT)
  • Q=AD=94=E5=A4=8D:__compilation_of_namd?= (Sun May 08 2011 - 19:34:03 CDT)
  • ??: compilation of namd (Fri May 06 2011 - 00:56:41 CDT)
  • compilation of namd (Thu May 05 2011 - 21:08:37 CDT)
• 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)
• THANH NGUYEN
  • SMD simulation: stop applying force during simulation? (Thu Apr 07 2011 - 22:05:35 CDT)
• Thomas Albers
  • Cluster on commodity hardware (Mon Oct 31 2011 - 12:37:30 CDT)
  • Infiniband and commodity hardware (Sat Sep 17 2011 - 14:59:20 CDT)
  • Re: NAMD crashes with OpenMPI/OpenMX (Sun Jun 19 2011 - 21:32:42 CDT)
  • Re: AW: AW: NAMD crashes with OpenMPI/OpenMX (Wed Jun 15 2011 - 10:01:00 CDT)
  • Re: AW: NAMD crashes with OpenMPI/OpenMX (Wed Jun 15 2011 - 09:10:28 CDT)
  • Re: NAMD crashes with OpenMPI/OpenMX (Tue Jun 14 2011 - 13:04:29 CDT)
  • NAMD crashes with OpenMPI/OpenMX (Mon Jun 13 2011 - 11:50:35 CDT)
  • Re: Compiling NAMD for CUDA (Sat Jun 11 2011 - 21:53:56 CDT)
  • Compiling NAMD for CUDA (Sat Jun 11 2011 - 16:23:01 CDT)
• Thomas Bishop
  • Re: correlation functions (Mon Dec 12 2011 - 07:54:06 CST)
  • Re: OpenCL and AMD GPUs (Wed Nov 23 2011 - 10:09:43 CST)
  • Generalized Born calcs (Tue Aug 16 2011 - 14:53:17 CDT)
  • Re: NAMD 2.8 job submission script for queenbee: ManyJobs (Tue Jul 26 2011 - 08:46:29 CDT)
• 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
  • timing variation during 256core run on abe.ncsa.uiuc.edu (Mon Feb 21 2011 - 13:52:56 CST)
  • 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)
• Thomas Evangelidis
  • Re: NAMD feture request (Wed Apr 13 2011 - 12:06:57 CDT)
  • 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 Freeman
  • Re: Psfgen Errors for C-type Heme (Tue Mar 01 2011 - 14:15:56 CST)
  • Psfgen Errors for C-type Heme (Mon Feb 28 2011 - 13:46:04 CST)
• 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)
• Tibbitt, Jeffrey A.
  • unsubscribe (Tue Jul 12 2011 - 19:32:21 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)
• Tim Robinson
  • NAMD 2.8 on Cray XE6 segfaulting (Tue Jul 26 2011 - 05:46:01 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)
• Tom Sisan
  • Re: Why are the pressures in my box of water systematically off? (Thu Mar 31 2011 - 17:04:03 CDT)
  • Re: Why are the pressures in my box of water systematically off? (Wed Mar 30 2011 - 12:40:58 CDT)
  • Why are the pressures in my box of water systematically off? (Thu Mar 24 2011 - 18:33:39 CDT)
• 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)
• Udaysankar Midya
  • GPRESSURE becomes nan in TIP4P simulation (Sat Dec 31 2011 - 05:23:35 CST)
• 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
  • Uma wants to chat (Thu Mar 03 2011 - 07:33:27 CST)
• 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)
• V.Ovchinnikov
  • Re: using TIP4P 2005 in namd (Wed Feb 23 2011 - 15:54:26 CST)
  • Re: Proposed Feature in Targeted MD (Mon Jan 31 2011 - 15:53:38 CST)
  • Re: Proposed Feature in Targeted MD (Mon Jan 31 2011 - 15:14:15 CST)
• Van Ngo
  • Periodic Boundary Condition in NAMD (Thu Jun 02 2011 - 23:55:08 CDT)
  • modify NAMD code for Lee-Edwards boundary conditions and compute stress tensor (Tue Apr 26 2011 - 19:17:47 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)
• Vijay Vammi
  • Re: Peptide planarity Dihedral angle restraints (Fri Dec 09 2011 - 00:47:00 CST)
  • Re: Peptide planarity Dihedral angle restraints (Thu Dec 08 2011 - 21:20:23 CST)
  • Peptide planarity Dihedral angle restraints (Thu Dec 08 2011 - 20:07:12 CST)
  • Re: Accelerated Molecular Dynamics (Wed Nov 02 2011 - 20:42:07 CDT)
  • Re: Accelerated Molecular Dynamics (Tue Oct 25 2011 - 23:45:32 CDT)
  • Re: Accelerated Molecular Dynamics (Tue Oct 25 2011 - 21:04:49 CDT)
  • Accelerated Molecular Dynamics (Tue Oct 25 2011 - 16:11:54 CDT)
• Vlad Cojocaru
  • PhD position in Computational Structural Biology at MPI Muenster (Fri May 13 2011 - 04:47:24 CDT)
  • Re: Fwd: Wrong exit from RAMD runs (Thu Apr 14 2011 - 03:08:54 CDT)
  • Re: Fwd: Incompatibility between colvars and tclforces? (Thu Mar 31 2011 - 05:12:10 CDT)
  • Re: Fwd: Incompatibility between colvars and tclforces? (Thu Mar 31 2011 - 02:27:40 CDT)
  • Re: RAMD Setting parameter TclForces from script failed (Tue Mar 29 2011 - 04:59:25 CDT)
  • Re: RAMD Setting parameter TclForces from script failed (Mon Mar 28 2011 - 08:45:49 CDT)
  • Re: Using RAMD for studiying conformational changes in proteins (Thu Mar 24 2011 - 17:59:22 CDT)
  • 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)
• Wang Yi
  • Re: restraining groups of atoms (Mon Jun 20 2011 - 08:54:13 CDT)
  • Re: A question on Jarkynski equation (Tue Jun 14 2011 - 08:11:46 CDT)
  • Re: water equilibration (Mon Jun 06 2011 - 08:42:26 CDT)
  • Re: 'cutting' colvars.traj file (Sat Apr 23 2011 - 12:54:15 CDT)
  • Re: Incompatibility between colvars and tclforces? (Wed Mar 30 2011 - 09:16:25 CDT)
  • Re: A "strange" observation during ColVar calculations (Mon Mar 28 2011 - 08:40:51 CDT)
  • Re: A "strange" observation during ColVar calculations (Tue Mar 22 2011 - 12:54:29 CDT)
  • Re: A "strange" observation during ColVar calculations (Mon Mar 21 2011 - 15:58:17 CDT)
  • A "strange" observation during ColVar calculations (Mon Mar 21 2011 - 13:49:45 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
  • Re: Constraint failure; simulation has become unstable (Sat Jan 08 2011 - 08:29:37 CST)
  • Re: Constraint failure; simulation has become unstable (Sat Jan 08 2011 - 07:53:11 CST)
  • Constraint failure; simulation has become unstable (Fri Jan 07 2011 - 14:42:46 CST)
  • Re: Constraint failure; simulation has become unstable (Fri Jan 07 2011 - 15:18:20 CST)
  • Re: Constraint failure; simulation has become unstable (Fri Jan 07 2011 - 15:25:23 CST)
  • 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)
• Wenhao Liu
  • Re: Is it possible to print out the force of one specific atom? (Wed Nov 23 2011 - 08:59:10 CST)
  • Is it possible to print out the force of one specific atom? (Wed Nov 23 2011 - 08:29:23 CST)
• wenhao_at_uchicago.edu
  • Re: About "alchDecouple" in FEP (Sun Oct 23 2011 - 07:47:26 CDT)
  • About "alchDecouple" in FEP (Sat Oct 22 2011 - 10:47:14 CDT)
  • can we run FEP calculation in water sphere? (Fri Sep 09 2011 - 03:21:01 CDT)
  • RE: About Columb energy of 2 ions in Vacuum (Fri Aug 26 2011 - 02:30:48 CDT)
  • About Columb energy of 2 ions in Vacuum (Thu Aug 25 2011 - 18:02:04 CDT)
  • Re: About Columb energy of 2 ions in Vacuum (Tue Aug 23 2011 - 22:32:08 CDT)
  • Re: About Columb energy of 2 ions in Vacuum (Tue Aug 23 2011 - 22:30:29 CDT)
  • About Columb energy of 2 ions in Vacuum (Tue Aug 23 2011 - 17:28:04 CDT)
• Werner Crous
  • Re: PBC (Thu Jun 02 2011 - 04:18:38 CDT)
  • Re: PBC (Thu Jun 02 2011 - 04:05:41 CDT)
  • PBC (Wed Jun 01 2011 - 05:09:27 CDT)
  • 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)
• wood irene
  • Re: how obtain .xst form .dcd file? (Wed Mar 23 2011 - 12:59:01 CDT)
  • how obtain .xst form .dcd file? (Mon Mar 21 2011 - 09:25:47 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)
• Xueqing Zou
  • Re: simulating DNA using namd:: (Tue Apr 20 2010 - 09:48:46 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: vdw parameter of metal ion (Thu Jun 02 2011 - 07:34:20 CDT)
  • Re: vdw parameter of metal ion (Thu Jun 02 2011 - 07:32:41 CDT)
  • 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)
• yandong Huang
  • Switching function for cut-off method (Wed Mar 30 2011 - 08:54:09 CDT)
  • switching function (Wed Mar 23 2011 - 22:52:32 CDT)
  • Can DCD trajectory files contain only protein but water surround (Thu Jan 13 2011 - 08:44:10 CST)
• Yang Gao
  • force field for 2-methyl-2,4-pentanediol (MPD) (Tue May 10 2011 - 10:40:40 CDT)
  • 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)
• Yao Xiao
  • Question about silver nanoparticle simulation (Wed Oct 19 2011 - 08:37:23 CDT)
• yashodhan karandikar
  • Network version gives inconsistent wall clock timings (Wed Mar 30 2011 - 08:39:15 CDT)
  • Re: Multiple runs of NAMD highly take fluctuating times (Wed Mar 16 2011 - 00:48:27 CDT)
  • Multiple runs of NAMD highly take fluctuating times (Tue Mar 15 2011 - 23:06:59 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)
• Ye Yang
  • Namd-I: A question about constant force pulling of a group of atoms (Thu Sep 01 2011 - 10:16:18 CDT)
  • Re: Namd-I: namd compiling problem (Wed Aug 03 2011 - 10:46:13 CDT)
  • Namd-I: namd compiling problem (Tue Aug 02 2011 - 22:28:05 CDT)
  • Re: namd-I: cionize problem in vmd (Mon Aug 01 2011 - 11:36:26 CDT)
  • namd-I: cionize problem in vmd (Fri Jul 29 2011 - 11:17:10 CDT)
  • Re: Namd-I: Implicit solvent problem (Wed Jun 29 2011 - 17:44:55 CDT)
  • Re: Namd-I: Implicit solvent problem (Wed Jun 29 2011 - 17:38:54 CDT)
  • Namd-I: Implicit solvent problem (Wed Jun 29 2011 - 16:07:55 CDT)
  • namd-I: Problems with Namd coarsegrain and Gromacs top file (Wed Jun 15 2011 - 14:50:23 CDT)
  • Namd-1: problems using increment of temperature during simulation (Sun Feb 27 2011 - 14:27:16 CST)
  • Hi, I am a new user of Namd, and I met some problems using increment of temperature during simulation (Fri Feb 25 2011 - 13:40:43 CST)
• Yi He
  • Re: Reading files for multiple threaded simulations (Wed Nov 02 2011 - 11:00:11 CDT)
  • Reading files for multiple threaded simulations (Tue Nov 01 2011 - 12:16:52 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 Wang
  • Re: Accelerated Molecular Dynamics (Tue Oct 25 2011 - 18:03:33 CDT)
  • Re: Setting up aMD simulation of a membrane protein (Fri Apr 01 2011 - 13:59:01 CDT)
• ying yu
  • a question about modifying the NAMD input file (Mon Oct 25 2010 - 12:06:50 CDT)
• Yingzhe Liu
  • How to simulate a charged surface (Wed Jun 22 2011 - 02:53:56 CDT)
  • How to simulate a charged surface (Thu Jun 23 2011 - 05:43:49 CDT)
  • 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)
• yudaqi
  • Re: AW: update: segmentation faults with AMBER topology and RAMD tcl scripts (Wed Feb 24 2010 - 06:37:25 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)
• Yun Luo
  • Re: Boundary potential of colvar alpha not working? (Thu Oct 13 2011 - 08:21:15 CDT)
  • Re: Boundary potential of colvar alpha not working? (Thu Oct 13 2011 - 09:03:46 CDT)
  • Boundary potential of colvar alpha not working? (Wed Oct 12 2011 - 09:34:27 CDT)
  • Re: ABF with Alpha colvar can't be used on supercomputer? (Thu Sep 29 2011 - 14:25:57 CDT)
  • ABF with Alpha colvar can't be used on supercomputer? (Wed Sep 28 2011 - 15:38:02 CDT)
• Zack Scholl
  • Restart from anywhere in DCD trajectory (Mon Oct 03 2011 - 13:19:41 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)
• Zhao Lina
  • Charmm parameter for H2 gas (Wed Jun 29 2011 - 04:41:15 CDT)
• zhjpan_at_mail.ustc.edu.cn
  • Re: Re: POPC membrane model in pH 4 (Sat Sep 03 2011 - 10:12:06 CDT)
  • POPC membrane model in pH 4 (Sat Sep 03 2011 - 09:36:58 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)
• Zumot, Elia Nabil
  • RE: pbc wrap option for x,y,z lengths (Sun Apr 24 2011 - 19:38:43 CDT)
  • RE: pbc wrap option for x,y,z lengths (Sun Apr 24 2011 - 14:44:06 CDT)
  • RE: pbc wrap option for x,y,z lengths (Sun Apr 24 2011 - 12:51:16 CDT)
  • RE: pbc wrap option for x,y,z lengths (Fri Apr 22 2011 - 22:52:11 CDT)
  • pbc wrap option for x,y,z lengths (Fri Apr 22 2011 - 14:03:29 CDT)
  • 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)
• 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)
• Àî¼Ñ¼ü
  • Fail to Run VMD (Tue May 31 2011 - 13:53:07 CDT)
  • Can I do protein-ligand docking using NAMD? (Tue Feb 15 2011 - 23:32:03 CST)
• ÁõÏþ¹â
  • FW: namd cuda with geforce 470 (fermi) gpu fatal error at runtime (Sun Jun 06 2010 - 06:50:56 CDT)
• ä¿žç¿”
  • Re: force field for replica exchange with NAMD (Thu Oct 28 2010 - 17:56:58 CDT)
• 常姗燕
  • What is the proper value of TMDk in TMD simulations? (Sun Oct 23 2011 - 23:21:19 CDT)
  • SMD for two steered directions (Sun Apr 17 2011 - 09:51:12 CDT)
• 张勇
  • Re: Re: How to evaluate the area per lipid and thickness of the lipid bilayer in a membrane-protein system? (Thu Aug 25 2011 - 02:26:50 CDT)
• 张鋆
  • (no subject) (Fri Apr 16 2010 - 22:04:17 CDT)
• ÅÓ´ºÀö
  • vdw value in parameter file (Mon Jun 20 2011 - 02:26:06 CDT)
  • vdw parameter of metal ion (Tue May 31 2011 - 04:49:55 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)
• æ�Žä½³é”®
  • Using VMD paratool (Mon Jul 11 2011 - 16:24:12 CDT)
• 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)
• Íõ—²
  • how to write the bond across the cell boundary (Fri Mar 25 2011 - 01:52:15 CDT)
  • 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)
• ÐìÖÓºÓ
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