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NAMD-L: By Author

By Author

3174 messages sorted by: [ date ] [ thread ] [ subject ] [ attachment ]
About this archive

Starting: Wed Jan 01 2014 - 05:18:45 CST
Ending: Tue Dec 29 2015 - 07:12:19 CST

• #ZHENG FULU#
  • The water box shrinks at the start of the MD simulation (Sun Jul 27 2014 - 06:13:52 CDT)
• Aaron Larsen
  • Re: sausage plot for a namd trajectory in vmd (Fri Jul 31 2015 - 05:44:17 CDT)
  • Re: atom types in PSF/PRM/RTF (Fri May 22 2015 - 07:34:37 CDT)
  • Error during Opt. Charges while using FF Took Kit (Wed May 20 2015 - 16:38:19 CDT)
  • Best Practices for Nucleobase Parameterization (Mon May 18 2015 - 11:30:22 CDT)
  • Re: optimising namd ibverb runs (Mon May 18 2015 - 08:48:18 CDT)
  • PSFgen with RNA-like nucleotide monophosphates (Wed May 06 2015 - 11:01:26 CDT)
  • Re: (Tue Jul 22 2014 - 11:38:27 CDT)
  • Re: Rapid and accurate parameterization of new molecules in CHARMM (Tue May 27 2014 - 19:22:22 CDT)
  • Rapid and accurate parameterization of new molecules in CHARMM (Tue May 27 2014 - 08:21:06 CDT)
  • Re: AW: moving out of the box (Fri Feb 14 2014 - 09:10:36 CST)
  • Re: moving out of the box (Thu Feb 13 2014 - 14:39:04 CST)
  • RSMDTT keyword for nucleic acids (Wed Feb 05 2014 - 14:43:13 CST)
  • Umbrella sampling using colvarconfig file with dihedrals (Wed Feb 05 2014 - 11:07:23 CST)
  • Re: Umbrella Sampling of Sugar Pseudorotation (Mon Feb 03 2014 - 15:47:38 CST)
  • Umbrella Sampling of Sugar Pseudorotation (Mon Feb 03 2014 - 13:32:45 CST)
• Abhishek TYAGI
  • Re: À´×Ô"ZOU Changling" <zoucl@ihep.ac.cn>µÄÓʼþ (Wed Nov 25 2015 - 07:03:45 CST)
  • Re: Re: Fw: À´×Ô"ZOU Changling" <zoucl@ihep.ac.cn>µÄÓʼþ (Wed Nov 18 2015 - 20:12:47 CST)
  • Re: Fw: À´×Ô"ZOU Changling" <zoucl@ihep.ac.cn>µÄÓʼþ (Wed Nov 18 2015 - 09:45:45 CST)
  • Re: Including two parameters for protein-ligand simulation (Wed Oct 28 2015 - 01:59:21 CDT)
  • Re: Solvation free energy calculation with MM/GBSA (Thu Sep 24 2015 - 07:40:43 CDT)
  • Re: Solvation free energy calculation with MM/GBSA (Thu Sep 24 2015 - 07:13:20 CDT)
  • Re: simulating graphene sheets (with bonds across boundaries) with water (Tue Sep 15 2015 - 18:58:52 CDT)
  • Re: simulating graphene sheets (with bonds across boundaries) with water (Mon Sep 14 2015 - 19:28:04 CDT)
  • Re: node file for NAMD (Fri Sep 11 2015 - 22:55:16 CDT)
  • Re: wrapping in NVT (Wed Jul 22 2015 - 00:27:02 CDT)
  • wrapping in NVT (Tue Jul 21 2015 - 22:59:52 CDT)
  • TIP4P water for MD (Mon Apr 13 2015 - 07:44:51 CDT)
  • Re: timestep querry (Thu Apr 02 2015 - 23:07:39 CDT)
  • Re: timestep querry (Wed Apr 01 2015 - 11:15:49 CDT)
  • timestep querry (Wed Apr 01 2015 - 10:28:12 CDT)
  • number of close contacts and contact area (Sun Mar 22 2015 - 04:37:57 CDT)
  • Re: DCD Error (Thu Mar 19 2015 - 03:59:56 CDT)
  • Re: DCD Error (Wed Mar 18 2015 - 10:13:07 CDT)
  • Re: DCD Error (Wed Mar 18 2015 - 09:51:17 CDT)
  • Re: DCD Error (Wed Mar 18 2015 - 09:29:42 CDT)
  • DCD Error (Wed Mar 18 2015 - 06:23:58 CDT)
  • Re: equilibrate the bulk water system (Fri Mar 13 2015 - 09:49:20 CDT)
  • Re: namd simulation (Thu Mar 05 2015 - 04:46:29 CST)
  • Re: question about CUDA-enabled (Sun Nov 30 2014 - 02:57:53 CST)
  • Re: question about CUDA-enabled (Sat Nov 29 2014 - 11:04:55 CST)
  • Re: NAMD on SLURM (Wed Nov 12 2014 - 21:07:16 CST)
  • NAMD on SLURM (Wed Nov 05 2014 - 23:30:20 CST)
  • Graphene simualtion (Mon Oct 20 2014 - 03:28:51 CDT)
  • RE: Force field design (Wed Jul 23 2014 - 19:57:40 CDT)
  • RE: Force field design (Wed Jul 23 2014 - 00:23:36 CDT)
  • RE: Force field design (Tue Jul 22 2014 - 23:04:23 CDT)
  • RE: Force field design (Tue Jul 22 2014 - 05:40:00 CDT)
  • RE: Force field design (Sat Jul 19 2014 - 07:44:53 CDT)
  • Force field design (Tue Jul 15 2014 - 11:55:35 CDT)
  • RE: CUDA error in cuda_check_local_progress (Thu Apr 17 2014 - 04:23:44 CDT)
  • RE: CUDA error in cuda_check_local_progress (Thu Apr 17 2014 - 04:07:36 CDT)
  • CUDA error in cuda_check_local_progress (Thu Apr 17 2014 - 02:41:11 CDT)
• Abir Ganguly
  • Re: Calculating RMSF per residue (Tue Apr 21 2015 - 02:58:40 CDT)
  • Calculating RMSF per residue (Mon Apr 20 2015 - 12:58:24 CDT)
  • COLVAR related quesion (Tue Mar 11 2014 - 16:06:20 CDT)
  • Re: ABF simulations (Thu Feb 13 2014 - 22:50:10 CST)
  • ABF simulations (Sat Feb 08 2014 - 15:38:01 CST)
• Adam Kells
  • Nanotube tutorial (Fri Jul 04 2014 - 13:19:33 CDT)
  • Invalid command error (Mon Jun 30 2014 - 06:49:07 CDT)
• Adam Moser
  • memory problem (Fri Jun 20 2014 - 15:01:30 CDT)
• Adelman, Joshua Lev
  • Re: namd-I: How to assume the thickness of membrane when applying external Electric field ? (Tue Jan 13 2015 - 08:36:01 CST)
• Aditya Chattopadhyay
  • Reg. restarting a Thermodynamic Integration Run (Mon Jan 12 2015 - 09:32:26 CST)
• Aditya Ranganathan
  • Atomselect within radial pair distribution function g(r) (Wed Sep 30 2015 - 03:55:37 CDT)
  • Re: Automatic PSF builder for cyclic peptide (Sun Sep 20 2015 - 08:20:24 CDT)
  • Re: Aggregation related analysis scripts (Wed Feb 25 2015 - 01:13:42 CST)
  • Aggregation related analysis scripts (Tue Feb 24 2015 - 02:28:10 CST)
  • Putting multiple copies of peptide in a box (Tue Feb 17 2015 - 03:39:14 CST)
  • Analysis plugins for Martini Coarse Grained protein simulations (Sat Feb 07 2015 - 03:55:33 CST)
  • MMPBSA Energy Calculations using VMD (Post-Processing) (Thu Apr 10 2014 - 08:25:41 CDT)
• Ajasja LjubetiÄ�
  • Re: NAMD 2.11 released (Thu Dec 24 2015 - 02:35:34 CST)
  • Re: about deca alanine tutorial setup (Mon Nov 02 2015 - 16:14:28 CST)
  • Re: vmd-l: gromacs to charmm conversion (Fri Oct 23 2015 - 03:28:28 CDT)
  • Re: Minimization without MD (Thu Jul 16 2015 - 17:18:20 CDT)
  • Re: NAMD workflows <- : Re: call "NAMD" from another program (Fri Jul 10 2015 - 02:50:31 CDT)
  • Re: velocity IO with psfgen? (Thu Feb 26 2015 - 10:37:55 CST)
  • Re: vmd-l: vmd-I: Fatal Error: Unable to Open CHARMM Parameter File (Tue Feb 03 2015 - 07:06:43 CST)
  • Re: inconsistency in ABF results for helix unfolding (Wed Jan 28 2015 - 04:05:37 CST)
  • Inspiration for most efficient implementation of coarse grained forcefield. (Mon Dec 15 2014 - 12:08:03 CST)
  • Re: tilt colvar (Mon Nov 24 2014 - 09:27:37 CST)
  • Re: Colvar: minimal distance between 2 groups of atoms (Mon Nov 17 2014 - 11:30:45 CST)
  • Re: Colvar: minimal distance between 2 groups of atoms (Mon Nov 17 2014 - 10:28:20 CST)
  • Re: running a calculation during simulation (Tue Oct 21 2014 - 02:52:21 CDT)
  • Re: velocity manipulation (Thu Oct 16 2014 - 08:24:34 CDT)
  • Re: Colvars simulation running slow? (Wed Sep 10 2014 - 19:58:48 CDT)
  • Re: I would like to unsubscribe (Wed Sep 10 2014 - 10:03:21 CDT)
  • Re: Unable to read corrupted binary DCD trajectory file (Mon Sep 08 2014 - 12:26:27 CDT)
  • Re: Unable to read corrupted binary DCD trajectory file (Mon Sep 08 2014 - 09:51:03 CDT)
  • Re: AW: Using nodelist file causes namd to hang (Wed Aug 27 2014 - 12:32:53 CDT)
  • Re: NAMD 2.10 Manual (Fri Aug 22 2014 - 03:30:05 CDT)
  • Re: Loading and analysis of DCD file (~300 MB) (Thu Jul 24 2014 - 09:30:12 CDT)
  • Re: (Tue Jul 22 2014 - 13:18:02 CDT)
  • Re: accelerated MD as the engine for loop refirement (Wed Jul 09 2014 - 15:22:15 CDT)
  • Re: PMF and work distribution (Thu Jun 26 2014 - 08:05:48 CDT)
  • Re: How to apply a magnetic field with NAMD (Tue Jun 24 2014 - 16:52:06 CDT)
  • Using position-dependent diffusion to simulate long colvars trajectories (Thu Apr 03 2014 - 07:36:28 CDT)
  • Re: moving out of the box (Thu Feb 13 2014 - 10:08:36 CST)
  • Re: Log file is not being updated (Mon Feb 10 2014 - 05:53:39 CST)
• Akshata Rudrapatna
  • Re: FATAL ERROR: Low global exclusion count! (Wed Feb 18 2015 - 18:32:03 CST)
  • Re: namd-1: Simulation Terminating Early (Mon Feb 09 2015 - 20:54:55 CST)
  • namd-1: Simulation Terminating Early (Sat Feb 07 2015 - 15:06:33 CST)
  • Re: namd-1: Fatal Error: Unable to Open CHARMM Parameter File (Thu Feb 05 2015 - 06:32:40 CST)
  • namd-1: Fatal Error: Unable to Open CHARMM Parameter File (Tue Feb 03 2015 - 14:43:55 CST)
• Akshay Bhatnagar
  • Reg: topology file amidated and acetylated disulfide bridged Cystine (Fri Apr 10 2015 - 05:05:42 CDT)
  • Re: Reg: solvating in a non-standard solvent (Wed Mar 25 2015 - 02:38:00 CDT)
  • Re: Reg: solvating in a non-standard solvent (Thu Mar 19 2015 - 23:38:24 CDT)
  • Re: Reg: solvating in a non-standard solvent (Thu Mar 19 2015 - 01:40:55 CDT)
  • Reg: solvating in a non-standard solvent (Wed Mar 18 2015 - 01:29:20 CDT)
  • Re: Reg: simulating an amino acid in dichloromethane (Mon Jan 05 2015 - 06:46:07 CST)
  • Reg: simulating an amino acid in dichloromethane (Fri Jan 02 2015 - 23:18:45 CST)
  • Reg: QM/MM calculations in NAMD (Mon Nov 10 2014 - 07:05:40 CST)
  • Reg: dielectric constant calculations in NAMD (Fri Oct 31 2014 - 00:51:24 CDT)
  • Reg: error in log file (Tue Oct 21 2014 - 20:36:48 CDT)
  • Re: Reg: minimization (Thu Sep 25 2014 - 04:52:40 CDT)
  • Re: Reg: minimization (Thu Sep 25 2014 - 04:51:52 CDT)
  • Reg: minimization (Wed Sep 24 2014 - 23:35:16 CDT)
  • Fwd: Reg: solvation in DMSO (Wed Sep 03 2014 - 02:36:04 CDT)
  • Reg: solvation in DMSO (Mon Sep 01 2014 - 00:01:44 CDT)
  • Reg: LangevinPistonDecay and LangevinPistonPeriod (Thu Jul 24 2014 - 02:04:25 CDT)
  • Reg: deciding cell basis vector (Mon Jul 21 2014 - 08:57:57 CDT)
  • Reg : MD simulation with DMSO instead of water (Tue Jun 17 2014 - 06:04:58 CDT)
  • Reg: movement of protein outside box (Mon Jun 09 2014 - 20:46:56 CDT)
  • Re: Reg: deformation of water box during equilibration (Fri Jun 06 2014 - 21:15:30 CDT)
  • Reg: deformation of water box during equilibration (Fri Jun 06 2014 - 11:35:34 CDT)
  • Re: Density of water box (Tue Jun 03 2014 - 07:26:41 CDT)
  • Density of water box (Tue Jun 03 2014 - 05:22:00 CDT)
• Aksimentiev, Oleksii
  • Postdoc in Theoretical and Computational Biophysics (Mon Jun 08 2015 - 11:51:11 CDT)
• Alex Utev (CMP)
  • Using the CHARMM36 forcefield with NAMD (Wed Apr 23 2014 - 11:15:08 CDT)
  • How to stop omega trans-cis switching (Mon Mar 03 2014 - 12:11:25 CST)
  • How to stop omega trans-cis switching (Mon Mar 03 2014 - 12:10:08 CST)
• Alexander Tzanov
  • Re: Re: run on sungle node (Wed Jun 24 2015 - 13:37:01 CDT)
  • Re: run on sungle node (Wed Jun 24 2015 - 11:03:24 CDT)
  • run on sungle node (Wed Jun 24 2015 - 09:56:18 CDT)
  • Re: NAMD slows at startup phase 1 smp problem (Thu Jan 15 2015 - 10:05:16 CST)
• Alireza Mansouri
  • calculating free energy (Sat Jun 28 2014 - 12:22:40 CDT)
• Amin Dehkharghani
  • WHICH VERSION OF NAMD SHOULD I INSTALL ON MY SYSTEM? (Sun Mar 01 2015 - 14:58:08 CST)
• amin_at_imtech.res.in
  • Re: Add ions/molecules different from Autoionize defaults (Fri Dec 25 2015 - 07:16:46 CST)
  • Re: AW: AW: AW: warnings while using amber files (Mon Jan 05 2015 - 07:34:30 CST)
  • Re: AW: AW: warnings while using amber files (Mon Jan 05 2015 - 04:39:58 CST)
  • Re: AW: warnings while using amber files (Mon Jan 05 2015 - 02:50:52 CST)
  • Re: warnings while using amber files (Thu Dec 25 2014 - 21:54:38 CST)
  • warnings while using amber files (Thu Dec 25 2014 - 05:14:20 CST)
  • constraint file from amber prmtop/inpcrd (Sat May 24 2014 - 14:32:55 CDT)
• amit banerjee
  • regarding PME grid setting problem (Sun Jan 04 2015 - 18:31:44 CST)
  • Require Suggestion (Tue Feb 18 2014 - 23:39:40 CST)
• Amitkumar Majhi
  • pdb files to dcd (Tue Nov 03 2015 - 14:33:21 CST)
• Amy Rice
  • Re: problem restarting multiple walker metadynamics (Thu Apr 02 2015 - 14:54:56 CDT)
  • Re: problem restarting multiple walker metadynamics (Mon Mar 30 2015 - 13:23:24 CDT)
  • Re: problem restarting multiple walker metadynamics (Fri Mar 27 2015 - 11:48:02 CDT)
  • Re: problem restarting multiple walker metadynamics (Thu Mar 19 2015 - 17:44:25 CDT)
  • Re: problem restarting multiple walker metadynamics (Thu Mar 19 2015 - 17:24:29 CDT)
  • Re: problem restarting multiple walker metadynamics (Thu Mar 12 2015 - 17:26:10 CDT)
  • Re: problem restarting multiple walker metadynamics (Wed Mar 11 2015 - 22:49:51 CDT)
  • problem restarting multiple walker metadynamics (Wed Mar 11 2015 - 14:59:46 CDT)
• Ana Celia Vila Verde
  • Re: how does NAMD calculate intramolecular electrostatic interactions between Drude pairs? (Thu Nov 26 2015 - 01:13:38 CST)
  • Re: how does NAMD calculate intramolecular electrostatic interactions between Drude pairs? (Mon Nov 23 2015 - 09:27:00 CST)
  • simulation options available with GPU (Tue Sep 16 2014 - 02:52:51 CDT)
  • simulation options available with GPU (Tue Sep 16 2014 - 02:58:28 CDT)
  • Re: Density of water box (Tue Jun 03 2014 - 06:29:02 CDT)
  • Re: peptide tends to migrate out the water box (Fri Apr 18 2014 - 02:12:40 CDT)
  • Re: RDF calculation with NAMD (Tue Jan 21 2014 - 11:23:57 CST)
  • subscribe namd-l (Tue Jan 21 2014 - 11:22:15 CST)
• Andras Borosy
  • automatic extraction of RMSD values of the heavy atoms of residues from NAMD output? (Mon Aug 04 2014 - 05:32:53 CDT)
  • running Linux-x86_64-multicore precompiled version at 2 hexa-core CPUs? (Thu Jul 17 2014 - 09:27:46 CDT)
• Andre Ribeiro
  • energy groups in NAMD (Fri Mar 06 2015 - 14:22:34 CST)
  • energy groups in NAMD (Fri Mar 06 2015 - 14:23:14 CST)
• Andreas Förster
  • Re: Unable to read corrupted binary DCD trajectory file (Mon Sep 08 2014 - 09:29:51 CDT)
• Andrew Emerson
  • Re: iDataPlex (Tue Mar 18 2014 - 03:15:30 CDT)
• André Farias de Moura
  • Re: Topology and parameters for Sodium dodecanoate (Tue Nov 03 2015 - 12:57:34 CST)
• Anjela Manandhar
  • UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT (Mon Jul 13 2015 - 15:58:55 CDT)
• AnkiReddy katha
  • Re: OPLS force field in NAMD (Sat Jun 20 2015 - 16:17:31 CDT)
  • OPLS force-field in NAMD (Thu May 07 2015 - 02:12:03 CDT)
  • atoms sequence in improper, OPLS, TOPOTOOLS, CHARMM (Thu May 07 2015 - 06:17:27 CDT)
  • Re: OPLS in NAMD (Thu May 07 2015 - 04:40:47 CDT)
  • OPLS in NAMD (Thu May 07 2015 - 04:17:23 CDT)
• Anna Borlsky
  • Re: AW: Dihedrals multiplicity! (Tue Feb 18 2014 - 03:11:42 CST)
  • Re: AW: Dihedrals multiplicity! (Sat Feb 15 2014 - 11:51:16 CST)
  • Re: AW: Dihedrals multiplicity! (Sat Feb 15 2014 - 04:34:49 CST)
  • Dihedrals multiplicity! (Thu Feb 13 2014 - 09:24:46 CST)
  • non-planarity problem! NOE restraints! (Thu Feb 13 2014 - 09:22:43 CST)
  • useGroupPressure (Fri Jan 10 2014 - 17:09:32 CST)
  • periodic boundary conditions (Fri Jan 10 2014 - 15:27:34 CST)
• Anna Modzelewska
  • segmentation fault in accelMD (Mon Jul 28 2014 - 05:56:05 CDT)
• Arash Azari
  • Re: Why RDF increases as r increase instead of constant (Mon Nov 03 2014 - 01:32:27 CST)
• Ardavan Mehdizadeh
  • Re: Add ions/molecules different from Autoionize defaults (Fri Dec 25 2015 - 12:28:43 CST)
  • Re: Add ions/molecules different from Autoionize defaults (Thu Dec 24 2015 - 07:37:39 CST)
  • Add ions/molecules different from Autoionize defaults (Thu Dec 24 2015 - 07:37:01 CST)
  • Add ions/molecules different from Autoionize defaults (Wed Dec 23 2015 - 12:05:36 CST)
  • Re: Reverse Coarse Graining using VMD CG Builder (Wed Oct 21 2015 - 10:41:55 CDT)
  • Reverse Coarse Graining using VMD CG Builder (Wed Oct 21 2015 - 03:15:35 CDT)
• Ariel Talavera Perez
  • Re: AW: moving out of the box (Thu Feb 20 2014 - 07:48:07 CST)
  • Re: AW: moving out of the box (Mon Feb 17 2014 - 06:51:36 CST)
  • Re: AW: moving out of the box (Mon Feb 17 2014 - 04:39:29 CST)
  • Re: AW: moving out of the box (Fri Feb 14 2014 - 08:38:01 CST)
  • moving out of the box (Thu Feb 13 2014 - 09:57:16 CST)
• Arijit Ghosh
  • Which Binary to use? (Fri Apr 24 2015 - 00:10:49 CDT)
  • How to save a structure after minimizing for 1000 steps? (Thu Apr 23 2015 - 16:15:40 CDT)
  • Enerygy Minimization of a homology modelled structure in NAMD (Tue Mar 31 2015 - 22:46:49 CDT)
  • Enerygy Minimization of a homology modelled structure in NAMD (Mon Mar 30 2015 - 00:21:35 CDT)
  • Enerygy Minimization of a homology modelled structure in NAMD (Sun Mar 29 2015 - 21:16:03 CDT)
• Aron Broom
  • Re: DOF during alchemical simulations (Thu Nov 26 2015 - 12:28:27 CST)
  • Re: call "NAMD" from another program (Thu Jul 09 2015 - 17:59:08 CDT)
  • Re: How to save a structure after minimizing for 1000 steps? (Thu Apr 23 2015 - 16:28:47 CDT)
  • Re: Calculating RMSF per residue (Mon Apr 20 2015 - 15:59:23 CDT)
  • Re: Calculation of PMF between protein domains NAMD (Fri Apr 17 2015 - 18:00:09 CDT)
  • Re: Calculation of PMF between protein domains NAMD (Fri Apr 17 2015 - 17:57:48 CDT)
  • Re: timestep querry (Wed Apr 01 2015 - 10:51:31 CDT)
  • Re: Dihedral calculation with colvars (Wed Mar 11 2015 - 23:17:09 CDT)
  • Re: Umbrella sampling tilt with respect to Z-axis (Wed Oct 08 2014 - 18:54:44 CDT)
  • Re: Molecular Dynamics of Rigid Linear Molecules in NAMD. (Sun Sep 28 2014 - 10:25:13 CDT)
  • Re: expected speed up after fixing atoms? (Wed Sep 24 2014 - 14:07:32 CDT)
  • Re: expected speed up after fixing atoms? (Wed Sep 24 2014 - 13:10:45 CDT)
  • Re: Implicit solvent lipid bilayer simulation in NAMD. (Wed Sep 17 2014 - 13:54:57 CDT)
  • Re: GBIS CUDA not yet compatible with fixed atoms (Fri Sep 05 2014 - 16:50:39 CDT)
  • Re: Silent crash NAMD-multicore-CUDA (Tue Aug 19 2014 - 11:17:04 CDT)
  • Re: "Beefier" benchmark (Tue Aug 19 2014 - 11:15:29 CDT)
  • Re: Silent crash NAMD-multicore-CUDA (Wed Jul 30 2014 - 17:50:54 CDT)
  • Re: Rule of thumb for equilibration (Mon Jul 28 2014 - 09:59:04 CDT)
  • Re: ABF/colvar error in NAMD2.9 (Tue Jul 22 2014 - 13:08:48 CDT)
  • Re: (Tue Jul 22 2014 - 12:36:33 CDT)
  • Re: ABF/colvar error in NAMD2.9 (Tue Jul 22 2014 - 12:32:06 CDT)
  • Re: ABF/colvar error in NAMD2.9 (Tue Jul 22 2014 - 11:30:49 CDT)
  • Re: Cost of a colvar calculation (Tue Jul 22 2014 - 10:56:45 CDT)
  • Re: Inquiry about forceConstant (Mon Jul 21 2014 - 15:12:06 CDT)
  • Re: Reg: deciding cell basis vector (Mon Jul 21 2014 - 12:39:39 CDT)
  • Re: Force field design (Tue Jul 15 2014 - 21:58:07 CDT)
  • Re: Restraints between ion and small molecule (Mon Jul 14 2014 - 21:13:44 CDT)
  • Re: (Mon Jul 14 2014 - 13:18:14 CDT)
  • Re: variable force constant (Thu Jul 10 2014 - 13:00:32 CDT)
  • Re: calculating free energy (Sat Jun 28 2014 - 15:53:02 CDT)
  • Re: Restraints between ion and small molecule (Thu Jun 26 2014 - 13:55:13 CDT)
  • Re: Constraint failure in RATTLE algorithm (Sun Jun 22 2014 - 23:02:28 CDT)
  • Re: Constraint failure in RATTLE algorithm (Thu Jun 19 2014 - 09:15:49 CDT)
  • Re: Constraint failure in RATTLE algorithm (Thu Jun 19 2014 - 10:37:59 CDT)
  • Re: Constraint failure in RATTLE algorithm (Wed Jun 18 2014 - 14:07:04 CDT)
  • Re: Merging the two files...... (Tue Jun 17 2014 - 10:58:22 CDT)
  • Re: Merging the two files...... (Tue Jun 17 2014 - 10:44:36 CDT)
  • Re: Reg: movement of protein outside box (Mon Jun 09 2014 - 22:09:28 CDT)
  • Re: Reg: deformation of water box during equilibration (Fri Jun 06 2014 - 22:28:02 CDT)
  • Re: Reg: deformation of water box during equilibration (Fri Jun 06 2014 - 12:37:30 CDT)
  • Re: Fixed atoms. (Thu Jun 05 2014 - 17:03:12 CDT)
  • Re: Ion Au+3 simulation (Wed Jun 04 2014 - 16:00:23 CDT)
  • Re: NAMD energy plugin (Wed Jun 04 2014 - 13:34:51 CDT)
  • Re: Ion Au+3 simulation (Tue Jun 03 2014 - 16:21:52 CDT)
  • Re: NAMD-GPU (Wed May 14 2014 - 09:54:20 CDT)
  • Re: PMF from ABF simulation not plateauing (Thu May 08 2014 - 13:56:37 CDT)
  • Re: Collective Variables to Restrain Ions Away From Protein (Sun Apr 20 2014 - 00:27:37 CDT)
  • Re: Collective Variables to Restrain Ions Away From Protein (Thu Apr 17 2014 - 23:15:35 CDT)
  • Re: (Tue Apr 15 2014 - 13:47:48 CDT)
  • Re: Fwd: TCL command "run" erratic (Sun Mar 16 2014 - 15:58:34 CDT)
  • Re: NAMD 2.9 quits early without error message. (Fri Mar 07 2014 - 17:31:37 CST)
  • Re: Force Field Parameters for PEG (Mon Feb 24 2014 - 10:29:42 CST)
  • Re: Guideline for selecting water box size. (Sun Feb 16 2014 - 19:12:30 CST)
  • Re: Volume Entry (Sun Feb 16 2014 - 15:28:27 CST)
  • Re: Volume Entry (Sun Feb 16 2014 - 13:57:33 CST)
  • Re: AW: moving out of the box (Fri Feb 14 2014 - 13:25:54 CST)
  • Re: ABF simulations (Fri Feb 14 2014 - 07:34:46 CST)
  • Re: ABF simulations (Mon Feb 10 2014 - 11:20:54 CST)
  • Re: PMEGridSizeX (number of grid points) is very small. (Wed Feb 05 2014 - 15:10:53 CST)
  • Re: Umbrella sampling using colvarconfig file with dihedrals (Wed Feb 05 2014 - 11:27:27 CST)
  • Re: Question regarding loss of translational entropy calculation in FEP tutorial (Tue Feb 04 2014 - 14:22:31 CST)
  • Re: Umbrella Sampling of Sugar Pseudorotation (Mon Feb 03 2014 - 15:01:34 CST)
  • Re: Steering colvars to defined points in space (Sun Jan 26 2014 - 19:23:56 CST)
• Art
  • vdw parameter error | atom type <-> name problem (Wed Mar 11 2015 - 14:03:38 CDT)
• Ashar Malik
  • Re: vmd-l: Number of pdb and psf atoms are not the same! (Wed Dec 16 2015 - 09:57:47 CST)
• Asis Jana
  • force field parameter for graphene oxide (Fri Mar 07 2014 - 07:58:34 CST)
• Asma el-magboub
  • Re: Create psf file (Mon Jun 22 2015 - 18:43:13 CDT)
  • NAMD "unable to find improper parameters" (Thu Jan 22 2015 - 21:32:09 CST)
• Atanu Maity
  • query for system size in pmf calculation (Fri Nov 20 2015 - 05:24:47 CST)
  • Re: DCD Error (Wed Mar 18 2015 - 23:32:32 CDT)
• Avisek Das
  • RE: Using the multi-copy version of NAMD on a linux workstation (Mon Jun 01 2015 - 12:22:46 CDT)
  • Using the multi-copy version of NAMD on a linux workstation (Fri May 29 2015 - 14:43:18 CDT)
• Axel Kohlmeyer
  • Re: Re: Fw: æ�¥è‡ª"ZOU Changling" <zoucl@ihep.ac.cn>的邮件 (Wed Nov 18 2015 - 20:15:49 CST)
  • Re: Problem with tcl intepreter (Thu Oct 29 2015 - 19:54:34 CDT)
  • Re: Dielectric constant of water from MSM and PME simulations (Fri Oct 23 2015 - 09:47:38 CDT)
  • Re: Regarding FFTW routines usage in NAMD (Tue Oct 20 2015 - 08:10:09 CDT)
  • Re: simulating graphene sheets (with bonds across boundaries) with water (Tue Sep 15 2015 - 19:22:27 CDT)
  • Re: feature request: external initiated clean exit (Fri Aug 21 2015 - 17:03:32 CDT)
  • Re: Interrupted Molecular Dynamics Simulation (Tue Jul 28 2015 - 10:53:28 CDT)
  • Re: not able to view trajectory in VMD (Fri Jun 26 2015 - 13:04:20 CDT)
  • Re: Re: run on sungle node (Wed Jun 24 2015 - 11:16:34 CDT)
  • Re: Weird Bond In Non-Polar Tail (Thu Jun 18 2015 - 10:45:06 CDT)
  • Re: Why the Lennard−Jones parameters E for anions are usually larger than cations? (Mon Jun 15 2015 - 05:36:16 CDT)
  • Re: Using a different potential with NAMD (Fri Jun 12 2015 - 09:39:47 CDT)
  • Re: Restarting trajectories (Wed May 20 2015 - 11:07:56 CDT)
  • Re: Restarting trajectories (Wed May 20 2015 - 10:49:11 CDT)
  • Re: Different trajectories with and without restarting (Sat May 16 2015 - 00:06:27 CDT)
  • Re: Different trajectories with and without restarting (Fri May 15 2015 - 18:26:53 CDT)
  • Re: Error applying PME to simulation set up (Wed May 13 2015 - 08:00:00 CDT)
  • School on Molecular Dynamics and Enhanced Sampling Methods @ Temple University July 6-10, 2015 (Fri May 08 2015 - 11:28:54 CDT)
  • Re: atom ID in VMD and NAMD (Mon May 04 2015 - 07:25:49 CDT)
  • Re: atom ID in VMD and NAMD (Mon May 04 2015 - 07:04:22 CDT)
  • GPU Programming workshop @ ICTP: deadline extended for participants not requiring visa and financial support (Tue Mar 24 2015 - 14:17:40 CDT)
  • Re: equilibrate the bulk water system (Sun Mar 15 2015 - 21:30:06 CDT)
  • Re: NAMD warning: Randomization of stack point is turned on in kernal, thread migration may not work! (Thu Mar 05 2015 - 11:40:42 CST)
  • Re: Maximum limit for "run" parameter (Wed Feb 18 2015 - 17:15:30 CST)
  • Re: Extracting data (Wed Feb 04 2015 - 08:24:25 CST)
  • Re: problem with water molecules angle in MD simulation (Fri Jan 30 2015 - 05:32:06 CST)
  • Re: NAMD Non-features (Wed Jan 21 2015 - 15:54:49 CST)
  • Re: NAMD Non-features (Wed Jan 21 2015 - 05:31:57 CST)
  • Re: NAMD Non-features (Wed Jan 21 2015 - 05:24:41 CST)
  • Re: namd-I: How to assume the thickness of membrane when applying external Electric field ? (Tue Jan 13 2015 - 07:21:49 CST)
  • Re: Asking help on results of our GPU benchmark (Mon Jan 05 2015 - 10:36:24 CST)
  • Re: information about simulation speed (Tue Dec 02 2014 - 17:07:15 CST)
  • Re: information about simulation speed (Tue Dec 02 2014 - 16:53:44 CST)
  • Re: question about CUDA-enabled (Sat Nov 29 2014 - 19:22:55 CST)
  • Re: Atomselect for coor, vel, xsc (Fri Nov 14 2014 - 09:02:47 CST)
  • Re: Multiple input and output files (Wed Nov 05 2014 - 21:51:44 CST)
  • Re: 1-5 Intramolecular repulsions (Wed Nov 05 2014 - 15:12:43 CST)
  • Re: SMD constant velocity not constant (Wed Oct 29 2014 - 20:04:28 CDT)
  • Re: velocity manipulation (Thu Oct 16 2014 - 08:21:17 CDT)
  • Re: VRPN compilation error (Tue Oct 14 2014 - 08:54:12 CDT)
  • Re: Does NAMD have some way to test the result? (Fri Oct 03 2014 - 22:17:05 CDT)
  • Re: Molecular Dynamics of Rigid Linear Molecules in NAMD. (Sun Sep 28 2014 - 13:31:59 CDT)
  • Re: Reg: minimization (Wed Sep 24 2014 - 23:44:35 CDT)
  • Re: Is there any point in running NAMD over an ethernet-linked cluster? (Mon Sep 22 2014 - 01:22:11 CDT)
  • Re: Alignment (Thu Sep 04 2014 - 07:53:23 CDT)
  • Re: Fixing atoms while equilibration (Mon Sep 01 2014 - 08:14:37 CDT)
  • Re: Fixing atoms while equilibration (Mon Sep 01 2014 - 07:48:34 CDT)
  • Re: NAMD energy minimization (Sun Aug 31 2014 - 14:51:10 CDT)
  • Re: RDF calculation of crystal system (Sat Aug 30 2014 - 01:49:16 CDT)
  • Re: Kb, Ktheta values for TIP3P water model (Tue Aug 12 2014 - 14:26:05 CDT)
  • Re: Kb, Ktheta values for TIP3P water model (Tue Aug 12 2014 - 12:27:25 CDT)
  • Re: Kb, Ktheta values for TIP3P water model (Mon Aug 11 2014 - 06:40:43 CDT)
  • Re: Kb, Ktheta values for TIP3P water model (Wed Aug 06 2014 - 15:48:57 CDT)
  • Re: Kb, Ktheta values for TIP3P water model (Wed Aug 06 2014 - 15:28:23 CDT)
  • Re: Kb, Ktheta values for TIP3P water model (Wed Aug 06 2014 - 14:11:01 CDT)
  • Re: Kb, Ktheta values for TIP3P water model (Tue Aug 05 2014 - 14:59:14 CDT)
  • Re: Kb, Ktheta values for TIP3P water model (Tue Aug 05 2014 - 14:28:04 CDT)
  • Re: Kb, Ktheta values for TIP3P water model (Thu Jul 31 2014 - 14:14:43 CDT)
  • Re: Force field design (Thu Jul 24 2014 - 14:35:11 CDT)
  • Re: Force field design (Wed Jul 23 2014 - 22:06:21 CDT)
  • RE: Force field design (Wed Jul 23 2014 - 05:13:16 CDT)
  • Re: Force field design (Tue Jul 22 2014 - 23:36:30 CDT)
  • Re: Force field design (Tue Jul 22 2014 - 11:14:16 CDT)
  • Re: Cost of a colvar calculation (Tue Jul 22 2014 - 11:02:47 CDT)
  • School on Molecular Dynamics with NAMD and LAMMPS in Philadelphia, August 18-22 2014 (Thu Jul 17 2014 - 14:48:33 CDT)
  • Re: running Linux-x86_64-multicore precompiled version at 2 hexa-core CPUs? (Thu Jul 17 2014 - 09:35:59 CDT)
  • Re: Invalid command error (Mon Jun 30 2014 - 07:44:41 CDT)
  • Re: How to apply a magnetic field with NAMD (Tue Jun 24 2014 - 19:43:42 CDT)
  • Re: NAMD on CRAY XE6m-200: dynamic linking in tcl not working (Fri Jun 20 2014 - 14:36:37 CDT)
  • Re: Constraint failure in RATTLE algorithm (Wed Jun 18 2014 - 13:23:05 CDT)
  • Re: Reg : MD simulation with DMSO instead of water (Tue Jun 17 2014 - 06:12:55 CDT)
  • Re: boron nitride nanotube (Thu Jun 12 2014 - 05:46:33 CDT)
  • Re: change in pdb.. (Wed Jun 11 2014 - 20:55:34 CDT)
  • Re: NAMD_2.9_Linux-x86_64-multicore-CUDA Segfaults (Wed Jun 11 2014 - 03:13:56 CDT)
  • Re: NAMD_2.9_Linux-x86_64-multicore-CUDA Segfaults (Wed Jun 11 2014 - 02:42:48 CDT)
  • Re: boron nitride nanotube (Mon Jun 09 2014 - 04:19:24 CDT)
  • Re: Ion Au+3 simulation (Tue Jun 03 2014 - 15:49:35 CDT)
  • Re: Ion Au+3 simulation (Tue Jun 03 2014 - 14:38:35 CDT)
  • Re: IMPROPER PARAMETERS FOR CA CA CA CA (Mon May 26 2014 - 16:47:44 CDT)
  • Re: NAMD-GPU (Wed May 14 2014 - 07:51:37 CDT)
  • Re: Scaling solvent-solute intermolecular interactions (Tue May 13 2014 - 15:17:53 CDT)
  • Re: Scaling solvent-solute intermolecular interactions (Tue May 13 2014 - 13:56:02 CDT)
  • Re: NAMD-Lite (Tue Apr 15 2014 - 18:22:54 CDT)
  • Re: NAMD-Lite (Tue Apr 15 2014 - 17:42:32 CDT)
  • Re: Nanotube Simulation (Mon Apr 14 2014 - 13:53:53 CDT)
  • Re: Nanotube Simulation (Fri Apr 11 2014 - 17:41:04 CDT)
  • Re: Nanotube Simulation (Fri Apr 11 2014 - 14:55:16 CDT)
  • Re: Nanotube Simulation (Fri Apr 11 2014 - 13:30:47 CDT)
  • Re: Nanotube Simulation (Fri Apr 11 2014 - 12:05:50 CDT)
  • Re: Nanotube Simulation (Fri Apr 11 2014 - 03:36:44 CDT)
  • Re: SHAKE or RATTLE algorithm (Fri Apr 04 2014 - 15:44:45 CDT)
  • Re: residue_rmsd.tcl segmentation fault (Fri Apr 04 2014 - 04:12:38 CDT)
  • Re: residue_rmsd.tcl segmentation fault (Fri Apr 04 2014 - 03:03:55 CDT)
  • Re: Multiple dihedral with multiplicity of 7 greater than max of 6 (Wed Apr 02 2014 - 13:52:18 CDT)
  • Re: Monitoring progress of an ongoing molecular dynamics simulation (Fri Mar 07 2014 - 10:49:34 CST)
  • Re: VDW energy: positive or negative? (Tue Mar 04 2014 - 17:28:08 CST)
  • Re: Apply magnetic field through TCLBC (Mon Mar 03 2014 - 11:46:25 CST)
  • Re: Force Field Parameters for PEG (Mon Feb 24 2014 - 10:49:58 CST)
  • Re: ´ð¸´£ºRE£º NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance (Mon Feb 24 2014 - 04:34:22 CST)
  • Re: RE£º NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance (Sun Feb 23 2014 - 21:26:40 CST)
  • Re: NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance (Sun Feb 23 2014 - 20:57:18 CST)
  • Re: NAMD 2.9 Changing/Replacing atoms in multiple molecules (Fri Feb 21 2014 - 08:11:33 CST)
  • Re: Polarization effect of gold cluster (Tue Feb 18 2014 - 06:32:07 CST)
  • Re: ERROR: CALCULATED VDWA FORCE MAY NOT MATCH ENERGY! POSSIBLE BUG! (Mon Feb 17 2014 - 21:39:00 CST)
  • Re: ERROR: CALCULATED VDWA FORCE MAY NOT MATCH ENERGY! POSSIBLE BUG! (Mon Feb 17 2014 - 17:26:41 CST)
  • Re: atomselect option for extracting protein-ligand complex (Mon Feb 17 2014 - 16:22:38 CST)
  • Re: Volume Entry (Sun Feb 16 2014 - 17:33:03 CST)
  • Re: Volume Entry (Sun Feb 16 2014 - 13:51:37 CST)
  • Re: psf file does not contain cross-terms (Sun Feb 16 2014 - 12:10:01 CST)
  • Re: Volume Entry (Sun Feb 16 2014 - 10:38:13 CST)
  • Re: Volume Entry (Mon Feb 10 2014 - 11:09:18 CST)
  • Re: Volume Entry (Mon Feb 10 2014 - 10:45:37 CST)
  • Re: Volume Entry (Mon Feb 10 2014 - 10:12:49 CST)
  • Re: Interactive molecular dynamics question (Sun Feb 09 2014 - 17:13:15 CST)
  • Re: Structure size limitation in NAMD (Wed Jan 29 2014 - 21:00:46 CST)
  • Re: ERROR: Molecule destroyed by fatal error (Mon Jan 27 2014 - 13:37:58 CST)
  • Re: About Warning in compilation of Namd (Sat Jan 04 2014 - 06:21:55 CST)
• Azadeh Alavi
  • Re: how to get the restart files from the dcd file? (Mon Dec 21 2015 - 07:10:47 CST)
  • Re: how to get the restart files from the dcd file? (Sun Dec 20 2015 - 14:30:07 CST)
  • how to get the restart files from the dcd file? (Sun Dec 20 2015 - 03:02:36 CST)
  • problem with equilibration of membrane-protein system (Sat Feb 14 2015 - 05:35:59 CST)
  • A problem in ABF simulations (Sat Nov 22 2014 - 05:50:03 CST)
  • multiple harmonic constrains (Sat Nov 08 2014 - 01:36:16 CST)
  • efficient way to apply time-dependent electric field (Thu Sep 04 2014 - 05:38:12 CDT)
• Baker D.J.
  • NAMD 2.10 on IBM POWER(8) machines (Thu Jun 25 2015 - 07:00:49 CDT)
• Bala subramanian
  • ABF with external electric field (Tue Mar 31 2015 - 10:42:24 CDT)
  • Re: temperature for lipid-protein assembly (Mon Jul 28 2014 - 12:46:39 CDT)
  • Re: temperature for lipid-protein assembly (Mon Jul 28 2014 - 12:08:15 CDT)
  • Re: temperature for lipid-protein assembly (Mon Jul 28 2014 - 12:06:34 CDT)
  • temperature for lipid-protein assembly (Mon Jul 28 2014 - 10:19:10 CDT)
• Basheer
  • Re: using CHARMM-format Amber parameters in NAMD (Wed Aug 20 2014 - 22:15:22 CDT)
• Basheer Subei
  • using CHARMM-format Amber parameters in NAMD (Tue Aug 19 2014 - 19:16:43 CDT)
• BATUHAN KAV
  • Re: Log file is not being updated (Thu Feb 13 2014 - 11:05:13 CST)
  • Re: Log file is not being updated (Mon Feb 10 2014 - 06:44:08 CST)
  • Re: Log file is not being updated (Mon Feb 10 2014 - 06:01:41 CST)
  • Log file is not being updated (Mon Feb 10 2014 - 05:41:07 CST)
• bay__gulf618_at_sina.com
  • Re: PSF for CYCLIC PEPTIDE : (Sat Sep 26 2015 - 21:26:01 CDT)
  • Re: call "NAMD" from another program (Sat Jul 11 2015 - 22:21:09 CDT)
  • Why the Lennard−Jones parameters E for anions are usually larger than cations? (Mon Jun 15 2015 - 04:02:44 CDT)
  • Re: write pdb (Thu Feb 20 2014 - 00:31:36 CST)
• bdrakuli
  • Re: Non standar solvent (Tue Feb 18 2014 - 11:43:58 CST)
• begüm alaybeyoÄŸlu
  • Re: RATTLE Error During Minimization of Charmm Gui Generated Bilayer (Wed Dec 16 2015 - 10:21:17 CST)
  • Re: RATTLE Error During Minimization of Charmm Gui Generated Bilayer (Wed Dec 16 2015 - 03:46:10 CST)
  • RATTLE Error During Minimization of Charmm Gui Generated Bilayer (Tue Dec 15 2015 - 10:27:48 CST)
  • Using colvars for biasing potential in Umbrella Sampling (Wed Jan 07 2015 - 10:01:17 CST)
• Belkin, Maxim
  • Re: Problem with tcl intepreter (Tue Nov 03 2015 - 10:53:53 CST)
• Benjamin Hill
  • ffTK and phase angles (Thu Jun 19 2014 - 17:43:28 CDT)
• Bennion, Brian
  • RE: Parameterizing a novel peptide (Tue Sep 15 2015 - 11:15:56 CDT)
  • RE: parameters problem in sulfated molecules (Tue Sep 01 2015 - 12:27:17 CDT)
  • RE: error in writing colvars state file (Thu Jun 04 2015 - 16:30:07 CDT)
  • error in writing colvars state file (Thu Jun 04 2015 - 16:24:44 CDT)
  • RE: Restarting trajectories (Wed May 20 2015 - 14:38:43 CDT)
  • RE: Restarting trajectories (Wed May 20 2015 - 10:42:46 CDT)
  • RE: namd-l digest V1 #1668 (Mon May 04 2015 - 10:42:12 CDT)
  • RE: Problems in running AutoIMD (Fri May 01 2015 - 11:00:35 CDT)
  • RE: performance question (Tue Apr 28 2015 - 15:06:13 CDT)
  • RE: proper order for par files in namd (solved) (Fri Apr 24 2015 - 18:21:22 CDT)
  • proper order for par files in namd (Fri Apr 24 2015 - 17:05:16 CDT)
  • RE: Re: Problems to parametrize molecules (Fri Apr 24 2015 - 14:02:59 CDT)
  • RE: Re: Problems to parametrize molecules (Fri Apr 24 2015 - 13:46:52 CDT)
  • RE: Re: Problems to parametrize molecules (Fri Apr 24 2015 - 12:27:51 CDT)
  • RE: Problems to parametrize molecules (Wed Apr 15 2015 - 15:44:53 CDT)
  • RE: Problems to parametrize molecules (Wed Apr 15 2015 - 13:04:21 CDT)
  • RE: Problems to parametrize molecules (Tue Apr 14 2015 - 15:57:28 CDT)
  • RE: Problems to parametrize molecules (Tue Apr 14 2015 - 15:45:41 CDT)
  • namd ibverbs compile target (Tue Oct 28 2014 - 18:04:52 CDT)
  • RE: Monitoring progress of an ongoing molecular dynamics simulation (Fri Mar 07 2014 - 11:44:01 CST)
  • runaway minimizations (Thu Feb 20 2014 - 12:06:54 CST)
  • RE: Runaway positive feedback when minimizing large systems (was: strange glitches when performing energy minimization in MDFF simulations) (Thu Feb 20 2014 - 11:53:31 CST)
  • RE: Runaway positive feedback when minimizing large systems (was: strange glitches when performing energy minimization in MDFF simulations) (Wed Feb 12 2014 - 10:57:12 CST)
  • RE: PMEGridSizeX (number of grid points) is very small. (Wed Feb 05 2014 - 12:28:37 CST)
  • RE: recent comparison of NAMD to other MD engines (Fri Jan 24 2014 - 12:59:21 CST)
  • recent comparison of NAMD to other MD engines (Wed Jan 22 2014 - 18:22:03 CST)
• Bin He
  • APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11) (Thu Nov 13 2014 - 01:53:42 CST)
  • Re: Why CPU Usage is low when I run ibverbs-smp-cuda version NAMD (Tue Nov 11 2014 - 06:19:06 CST)
  • Re: Why CPU Usage is low when I run ibverbs-smp-cuda version NAMD (Mon Nov 10 2014 - 13:51:15 CST)
  • Why CPU Usage is low when I run ibverbs-smp-cuda version NAMD (Sat Nov 08 2014 - 01:24:32 CST)
• BIPLAB NANDI
  • (no subject) (Wed Aug 27 2014 - 22:13:06 CDT)
• bmaiti_at_andrew.cmu.edu
  • Point group symmetry (Mon Apr 07 2014 - 18:20:08 CDT)
• Boshra Moradi
  • choose the best equilibrium arrangement of water molecules (Tue May 06 2014 - 16:55:17 CDT)
  • (no subject) (Tue May 06 2014 - 16:35:44 CDT)
  • slice of water box (Wed Apr 09 2014 - 17:13:12 CDT)
  • REMD (Tue Feb 18 2014 - 02:08:53 CST)
• Boyang Wang
  • Re: (Thu Feb 20 2014 - 00:53:46 CST)
  • (no subject) (Thu Feb 20 2014 - 00:05:03 CST)
• Branko
  • Re: NAMD 2.11 released (Tue Dec 22 2015 - 16:19:37 CST)
  • Re: energy output (Wed Dec 09 2015 - 11:51:45 CST)
  • Re: modify input file for production phase MD (Fri Dec 04 2015 - 11:50:53 CST)
  • Fwd: Re: about deca alanine tutorial setup (Mon Nov 02 2015 - 16:26:57 CST)
  • Re: Performing MD simulations with protein and halide ions (iodide, bromide, chloride) (Sat Oct 17 2015 - 15:42:11 CDT)
  • Re: Performing MD simulations with protein and halide ions (iodide, bromide, chloride) (Sat Oct 17 2015 - 14:35:37 CDT)
  • Re: Problem with iron ion (FE2+) (Mon Aug 24 2015 - 13:40:17 CDT)
  • Re: Problem with iron ion (FE2+) (Mon Aug 24 2015 - 13:09:01 CDT)
  • Re: nvt input file (Fri Jul 17 2015 - 08:44:24 CDT)
  • statistical error of mean force in (NAMD) ABF calculations (Wed Jul 01 2015 - 05:09:48 CDT)
  • Re: Remembering resid (Thu Jun 18 2015 - 08:54:40 CDT)
  • Re: Combining parameter files from CHARMM (Mon Jun 15 2015 - 07:39:49 CDT)
  • Fwd: Re: Combining parameter files from CHARMM (Mon Jun 15 2015 - 05:12:57 CDT)
  • Re: Combining parameter files from CHARMM (Fri Jun 05 2015 - 05:17:56 CDT)
  • startup phase 1 for benchmark (Tue May 12 2015 - 09:29:28 CDT)
  • Re: energy minimization in namd (Thu Apr 23 2015 - 11:57:06 CDT)
  • Re: Dipole Moment Watcher, Ibuprofen (Tue Mar 31 2015 - 04:12:14 CDT)
  • Re: Reg: solvating in a non-standard solvent (Wed Mar 18 2015 - 07:19:45 CDT)
  • namd-1: Fatal Error: Unable to Open CHARMM Parameter File (Tue Feb 03 2015 - 16:14:32 CST)
  • NAMD 2.10 with multiple-replica support (Sat Jan 31 2015 - 14:06:06 CST)
  • Re: Histidine C-H---O hydrogen bonding (Thu Jan 29 2015 - 12:53:52 CST)
  • Re: using NAMD with CHARMM36 ff (Sun Jan 18 2015 - 11:46:38 CST)
  • Re: Reg: simulating an amino acid in dichloromethane (Mon Jan 05 2015 - 05:39:13 CST)
  • Re: CUDA Fatal Error While Trying to Run Under Windows 8.1 (Thu Nov 06 2014 - 12:15:59 CST)
  • Re: Unable to read corrupted binary DCD trajectory file (Mon Sep 08 2014 - 09:13:35 CDT)
  • Re: Cost of a colvar calculation (Wed Jul 23 2014 - 07:45:31 CDT)
  • Re: Cost of a colvar calculation (Tue Jul 22 2014 - 07:44:04 CDT)
  • Fwd: Re: (Mon Jul 14 2014 - 13:24:43 CDT)
  • Re: Reg: deformation of water box during equilibration (Sat Jun 07 2014 - 05:05:35 CDT)
• Brian Radak
  • Re: free energy changes via FEP method (Wed Dec 16 2015 - 12:15:10 CST)
  • "implausibly old time stamp" for charm++ 6.7 in CVS (Wed Dec 16 2015 - 11:42:29 CST)
  • Re: vmd-l: PRES and water-ions issues with charmm36 (Thu Dec 10 2015 - 15:58:49 CST)
  • buffer overflow with long file paths in psfgen in NAMD 2.11b2? (Tue Dec 08 2015 - 15:54:28 CST)
  • Re: Overflow in LJcorrection? (Thu Dec 03 2015 - 16:26:19 CST)
  • Re: Overflow in LJcorrection? (Thu Dec 03 2015 - 16:15:59 CST)
  • Re: Overflow in LJcorrection? (Thu Dec 03 2015 - 16:10:59 CST)
  • Re: Overflow in LJcorrection? (Thu Dec 03 2015 - 15:59:27 CST)
  • Overflow in LJcorrection? (Thu Dec 03 2015 - 15:45:38 CST)
  • Re: DOF during alchemical simulations (Tue Dec 01 2015 - 10:08:08 CST)
  • Re: DOF during alchemical simulations (Mon Nov 30 2015 - 12:30:33 CST)
  • Re: accelerated MD new variant (Mon Nov 30 2015 - 09:48:36 CST)
  • Re: DOF during alchemical simulations (Mon Nov 30 2015 - 09:36:55 CST)
  • DOF during alchemical simulations (Wed Nov 25 2015 - 10:31:11 CST)
  • Crazy rigid water molecules (Thu Nov 19 2015 - 15:40:55 CST)
  • Re: Lennard-Jones and Electrostatic Forces and Energies (Tue Oct 27 2015 - 08:50:27 CDT)
  • Re: Rigid bonds and non-bonded energy (Tue Oct 20 2015 - 12:52:34 CDT)
  • Re: Rigid bonds and non-bonded energy (Tue Oct 20 2015 - 10:33:51 CDT)
  • Re: Regarding significance of days per ns (days/ns) parameter in NAMD benchmark (Tue Oct 20 2015 - 09:46:32 CDT)
  • Re: Rigid bonds and non-bonded energy (Mon Oct 19 2015 - 14:40:51 CDT)
  • Re: Rigid bonds and non-bonded energy (Fri Oct 16 2015 - 17:42:34 CDT)
  • Re: MD Simulation of accelerated MD using GPU (Mon Oct 12 2015 - 20:01:24 CDT)
  • Re: LJ Parameters on hydrogen for TIP4P water models (Tue Sep 29 2015 - 14:52:44 CDT)
  • LJcorrection + switching? (Tue Sep 01 2015 - 09:31:34 CDT)
  • Error in TI derivatives for staggered lambda scaling? (Tue Jul 21 2015 - 13:41:28 CDT)
  • Debugging and Force Checking? (Mon Jul 20 2015 - 09:32:44 CDT)
  • Re: does fixedAtoms modify velocities? (Tue Jul 07 2015 - 12:48:23 CDT)
  • does fixedAtoms modify velocities? (Tue Jul 07 2015 - 12:25:32 CDT)
  • Attempting modification to accumulate "Langevin heat" (Tue Jun 30 2015 - 10:43:40 CDT)
  • Re: energy minimization in namd (Thu Apr 23 2015 - 11:51:26 CDT)
  • Re: timestep querry (Thu Apr 02 2015 - 14:17:47 CDT)
  • Re: pressure value (Sun Mar 29 2015 - 15:30:42 CDT)
  • Fwd: FW: NAMD (Wed Mar 25 2015 - 11:35:27 CDT)
  • accelMD and GBIS? (Fri Feb 27 2015 - 18:15:13 CST)
  • Re: vmd-l: Re: velocity IO with psfgen? (Thu Feb 26 2015 - 11:42:22 CST)
  • Re: velocity IO with psfgen? (Thu Feb 26 2015 - 10:56:57 CST)
  • velocity IO with psfgen? (Thu Feb 26 2015 - 09:41:04 CST)
  • compile psfgen as shared object or Tcl package? (Wed Feb 18 2015 - 15:47:27 CST)
  • Re: making dipeptides with psfgen - CMAP terms? (Tue Feb 17 2015 - 16:10:49 CST)
  • Re: making dipeptides with psfgen - CMAP terms? (Tue Feb 17 2015 - 12:06:54 CST)
  • making dipeptides with psfgen - CMAP terms? (Tue Feb 17 2015 - 09:42:59 CST)
  • on-the-fly parameter introspection (Thu Feb 05 2015 - 13:54:51 CST)
  • Re: Could I run aMD in Drude force field? (Thu Feb 05 2015 - 13:50:15 CST)
  • Re: Alchemy Shift Coefficient at Low Density Regime (TI) (Thu Feb 05 2015 - 13:44:14 CST)
  • Re: LJcorrection and alchemy? (Fri Jan 30 2015 - 14:15:01 CST)
  • LJcorrection and alchemy? (Fri Jan 30 2015 - 12:10:53 CST)
  • Re: Is it possible to rename atoms with psfgen? (Fri Jan 30 2015 - 10:35:43 CST)
  • Is it possible to rename atoms with psfgen? (Wed Jan 28 2015 - 09:54:16 CST)
• Brunner, Robert Kraemer
  • Re: NAMD and NUMA (Fri May 09 2014 - 12:03:53 CDT)
• Bryan Roessler
  • Re: OutputAccumulatedWork...where's the output? (Mon Dec 14 2015 - 12:41:08 CST)
  • OutputAccumulatedWork...where's the output? (Sun Dec 13 2015 - 19:36:26 CST)
  • Re: Problem with tcl intepreter (Thu Oct 29 2015 - 20:06:58 CDT)
  • Re: Problem with tcl intepreter (Thu Oct 29 2015 - 20:00:31 CDT)
  • Problem with tcl intepreter (Thu Oct 29 2015 - 19:24:53 CDT)
  • Re: Parameterizing a novel peptide (Tue Sep 15 2015 - 12:06:12 CDT)
  • Parameterizing a novel peptide (Fri Sep 11 2015 - 17:14:05 CDT)
  • "UNABLE TO FIND BOND PARAMETERS" but bond is defined in stream file (Fri Sep 04 2015 - 00:07:49 CDT)
  • Altering extrabonds forces during MD (Tue Apr 15 2014 - 09:53:02 CDT)
• btreece_at_andrew.cmu.edu
  • Re: Different trajectories with and without restarting (Fri May 15 2015 - 18:26:09 CDT)
  • Parallelization of External Program Forces (Tue Mar 24 2015 - 18:49:26 CDT)
  • Re: DCD Error (Wed Mar 18 2015 - 10:05:58 CDT)
  • Re: DCD Error (Wed Mar 18 2015 - 09:27:28 CDT)
  • tclBCArgs, passing floating point lists (Thu Jan 22 2015 - 14:03:21 CST)
  • running a calculation during simulation (Mon Oct 20 2014 - 16:08:12 CDT)
• Bärwinkel, Tom
  • non-bonded energy of individual atoms (Fri Jun 12 2015 - 09:17:46 CDT)
• Carlos Navarrro Retamal
  • (no subject) (Tue Jul 22 2014 - 11:43:10 CDT)
• Cat Chenal
  • unsuscribe (Thu Apr 10 2014 - 09:49:18 CDT)
• Cenk Denktas
  • FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR C NH3 (ATOMS 105 107) (Fri Jul 25 2014 - 15:30:40 CDT)
  • autopsf (patch) (Tue Jul 15 2014 - 12:41:48 CDT)
• Charan Thota
  • Grid forces visualisation (Wed Feb 11 2015 - 06:13:12 CST)
• Charles Whidborne
  • SMD constant velocity not constant (Wed Oct 29 2014 - 19:25:08 CDT)
  • SMD pulling speed (Sat Sep 27 2014 - 20:45:48 CDT)
  • Setting constraints for SMD simulation (Mon Sep 15 2014 - 20:20:39 CDT)
  • problems running ABF simulation (Tue Sep 02 2014 - 00:37:40 CDT)
  • ABF hBond (Mon Aug 25 2014 - 02:52:45 CDT)
  • ABF simulation, free energy to remove a DNA strand (Tue Aug 05 2014 - 01:54:14 CDT)
• Charlesworth, Henry
  • what exactly is the form of the cosine angle potential? (Fri Jul 17 2015 - 08:08:50 CDT)
• Chen Wei
  • Error when running MIC version of namd on Stampede (Fri Feb 21 2014 - 09:49:38 CST)
• Chen, Po-chia
  • New web server for setup of membrane simulation systems (Sun Feb 08 2015 - 06:17:35 CST)
• chin chun
  • Mechanical Properties of protein (Thu Oct 30 2014 - 19:18:11 CDT)
• Chitrak Gupta
  • Re: RATTLE Error During Minimization of Charmm Gui Generated Bilayer (Fri Dec 18 2015 - 09:08:27 CST)
  • Re: RATTLE Error During Minimization of Charmm Gui Generated Bilayer (Wed Dec 16 2015 - 11:23:39 CST)
  • Re: RATTLE Error During Minimization of Charmm Gui Generated Bilayer (Wed Dec 16 2015 - 09:21:07 CST)
  • Re: RATTLE Error During Minimization of Charmm Gui Generated Bilayer (Tue Dec 15 2015 - 12:46:36 CST)
  • Re: NAMD on TACC (Darter) (Thu Dec 10 2015 - 17:35:15 CST)
  • Re: energy output (Wed Dec 09 2015 - 11:47:57 CST)
  • Re: NAMD on TACC (Darter) (Wed Dec 09 2015 - 07:49:53 CST)
  • Re: NAMD on TACC (Darter) (Tue Dec 08 2015 - 22:19:12 CST)
  • NAMD on TACC (Darter) (Tue Dec 08 2015 - 18:16:29 CST)
  • Re: error when use Charmm_Gui prepared *.inp for NAMD (Thu Dec 03 2015 - 08:49:59 CST)
  • Re: error reading colvars.conf in REUS (Mon Nov 16 2015 - 08:42:08 CST)
  • Re: error reading colvars.conf in REUS (Tue Nov 10 2015 - 20:18:11 CST)
  • error reading colvars.conf in REUS (Thu Nov 05 2015 - 16:45:48 CST)
  • Re: constraint failure in Rattle algorithm for atom 54134 (Mon Oct 26 2015 - 13:01:16 CDT)
  • Re: constraint failure in Rattle algorithm for atom 54134 (Mon Oct 26 2015 - 09:10:59 CDT)
  • Re: constraint failure in Rattle algorithm for atom 54134 (Mon Oct 26 2015 - 08:31:44 CDT)
  • Re: Atomselect within radial pair distribution function g(r) (Wed Sep 30 2015 - 08:09:16 CDT)
  • Re: Interrupted Molecular Dynamics Simulation (Tue Jul 28 2015 - 09:34:21 CDT)
  • Re: Interrupted Molecular Dynamics Simulation (Mon Jul 27 2015 - 12:29:25 CDT)
  • Re: Re: I can not run fixed protein in membrane with NAMD (Mon Jun 29 2015 - 14:41:11 CDT)
  • Re: Pressure coupling options (Sun Jun 28 2015 - 15:54:05 CDT)
  • Re: Remembering resid (Thu Jun 18 2015 - 08:52:08 CDT)
  • Re: How to save a structure after minimizing for 1000 steps? (Thu Apr 23 2015 - 16:35:58 CDT)
  • Re: energy minimization in namd (Thu Apr 23 2015 - 11:44:51 CDT)
  • bilayer simulation keeps crashing (Tue Apr 14 2015 - 10:00:27 CDT)
• Chola Regmi
  • Re: Metadynamics: writeHillsTrajectory (Thu Jul 30 2015 - 16:48:15 CDT)
  • Metadynamics: writeHillsTrajectory (Thu Jul 30 2015 - 16:37:53 CDT)
  • Re: Calculation of PMF between protein domains NAMD (Wed May 13 2015 - 18:14:49 CDT)
  • Re: Calculation of PMF between protein domains NAMD (Fri Apr 17 2015 - 18:50:25 CDT)
  • Calculation of PMF between protein domains NAMD (Fri Apr 17 2015 - 17:26:03 CDT)
• Chris Chipot
  • Re: string method in NAMD 2.10 (Tue Sep 22 2015 - 10:46:28 CDT)
  • Re: string method in NAMD 2.10 (Tue Sep 22 2015 - 10:26:53 CDT)
  • Re: Equilibration for a reverse FEP run (Thu Apr 23 2015 - 10:04:32 CDT)
  • Re: Alchemical FEP calculation involving glycine (Tue Mar 10 2015 - 05:59:57 CDT)
• Chris Harrison
  • Re: Interactive molecular dynamics question (Sun Feb 09 2014 - 17:00:27 CST)
  • Re: Structure size limitation in NAMD (Wed Jan 29 2014 - 23:41:09 CST)
• Chris Ing
  • Re: accelerated MD as the engine for loop refirement (Mon Jul 14 2014 - 16:53:07 CDT)
  • Collective Variables to Restrain Ions Away From Protein (Thu Apr 17 2014 - 18:36:06 CDT)
• Christian Bope Domilongo
  • Re: Getting residue mapping correpond to bead using SBCG (Shape based CG) Model in Coarse Grain Builder VMD (Fri Jan 09 2015 - 09:18:32 CST)
  • Getting residue mapping correpond to bead using SBCG (Shape based CG) Model in Coarse Grain Builder VMD (Fri Jan 09 2015 - 04:31:44 CST)
• Christian Jorgensen
  • Re: PSF generated with PSFGEN [problem in CP2K] - Problem with CGenFF naming? (Thu Feb 12 2015 - 13:01:13 CST)
  • PSF generated with PSFGEN [problem in CP2K] - Problem with CGenFF naming? (Thu Feb 12 2015 - 10:16:00 CST)
  • Fwd: vmd-l: Re: wrapping option in namd (Mon Jun 23 2014 - 04:59:50 CDT)
• Christopher Rowley
  • vdW-only fep between two ions (Tue Nov 04 2014 - 14:43:08 CST)
• clarkzhy
  • Re: Re: 1-4scaling for glycosylated protein using AMBER/GLYCAM FF in NAMD (Tue Mar 17 2015 - 21:18:48 CDT)
  • 1-4scaling for glycosylated protein using AMBER/GLYCAM FF in NAMD (Tue Mar 17 2015 - 20:33:41 CDT)
• Cosseddu, Salvatore
  • RE: how to get cell vectors in tcl forces script (Thu Mar 13 2014 - 13:11:01 CDT)
  • RE: how to get cell vectors in tcl forces script (Wed Mar 12 2014 - 09:01:35 CDT)
  • RE: how to get cell vectors in tcl forces script (Wed Mar 12 2014 - 07:05:43 CDT)
  • RE: Regarding colvar distancez (Sat Mar 08 2014 - 07:44:39 CST)
  • RE: Monitoring progress of an ongoing molecular dynamics simulation (Fri Mar 07 2014 - 10:57:59 CST)
  • RE: Monitoring progress of an ongoing molecular dynamics simulation (Fri Mar 07 2014 - 10:43:29 CST)
  • RE: Monitoring progress of an ongoing molecular dynamics simulation (Fri Mar 07 2014 - 08:21:35 CST)
• cuiyoutian_at_163.com
  • 崔幼æ�¬ 自动回å¤�: Multiple input and output files (Wed Nov 05 2014 - 20:20:37 CST)
  • 崔幼æ�¬ 自动回å¤�: Re: 1-5 Intramolecular repulsions (Wed Nov 05 2014 - 15:12:43 CST)
• Dan F. X. Martingano
  • Re: Umbrella Sampling of Sugar Pseudorotation (Mon Feb 03 2014 - 13:40:08 CST)
• daneshkaftroody_v_at_mech.sharif.ir
  • How occupancy relates to force in SMD (Mon Nov 02 2015 - 10:41:11 CST)
• Daniel Möller
  • AW: feature request: external initiated clean exit (Fri Aug 21 2015 - 19:21:54 CDT)
• Daniel Möller
  • feature request: external initiated clean exit (Fri Aug 21 2015 - 07:37:02 CDT)
• Daniel Strahs
  • MPICH 3 with Namd2/Charm (Mon Oct 13 2014 - 18:04:45 CDT)
• Daniel Torrente
  • Re: Atom selection in Tcl Force script with Amber partop file (Fri Aug 15 2014 - 18:21:23 CDT)
  • Re: Atom selection in Tcl Force script with Amber partop file (Fri Aug 15 2014 - 19:01:23 CDT)
  • Re: Atom selection in Tcl Force script with Amber partop file (Fri Aug 15 2014 - 18:25:23 CDT)
  • Atom selection in Tcl Force script with Amber partop file (Fri Aug 15 2014 - 12:25:49 CDT)
  • Loss of Translational entropy calculation in FEP (Wed Jul 30 2014 - 16:57:08 CDT)
  • Re: Restraints between ion and small molecule (Mon Jul 14 2014 - 20:51:55 CDT)
  • Restraints between ion and small molecule (Thu Jun 26 2014 - 11:53:49 CDT)
  • Re: Ion Au+3 simulation (Tue Jun 03 2014 - 16:17:38 CDT)
  • Re: Ion Au+3 simulation (Tue Jun 03 2014 - 15:17:15 CDT)
  • Ion Au+3 simulation (Tue Jun 03 2014 - 13:31:40 CDT)
• Daniela Rivas
  • Re: Problem with iron ion (FE2+) (Mon Aug 24 2015 - 13:16:15 CDT)
  • Problem with iron ion (FE2+) (Mon Aug 24 2015 - 12:51:59 CDT)
  • Re: Interrupted Molecular Dynamics Simulation (Wed Jul 29 2015 - 10:25:29 CDT)
  • Re: Interrupted Molecular Dynamics Simulation (Tue Jul 28 2015 - 09:45:07 CDT)
  • Re: Interrupted Molecular Dynamics Simulation (Mon Jul 27 2015 - 19:21:00 CDT)
  • Interrupted Molecular Dynamics Simulation (Mon Jul 27 2015 - 10:32:29 CDT)
• Danielle Chandler
  • Announcement: Hands-On Workshop On Computational Biophysics (Wed Jan 07 2015 - 12:30:35 CST)
  • Announcement: Hands-On Workshop On Computational Biophysics (Wed Dec 17 2014 - 10:24:50 CST)
  • Announcement: Hands-On Workshop On Computational Biophysics (Tue Oct 07 2014 - 11:30:07 CDT)
  • Announcement: Hands-On Workshop On Computational Biophysics (Wed Aug 27 2014 - 13:05:05 CDT)
  • Announcement: Hands-On Workshop On Computational Biophysics (Tue Aug 12 2014 - 09:31:17 CDT)
• Danielle Grodi
  • Weird Bond In Non-Polar Tail (Thu Jun 18 2015 - 10:15:53 CDT)
  • FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CTL2 OC301 (ATOMS 25 45) (Fri Jun 12 2015 - 13:39:30 CDT)
• Danilo Di Maio
  • Re: strange behavior of ABF (Tue Apr 14 2015 - 12:48:13 CDT)
  • strange behavior of ABF (Tue Apr 14 2015 - 05:41:24 CDT)
• David Brandon
  • Workshop on Very Large System Simulation Workshop, Urbana, IL, August 11-15, 2014 (Sat May 17 2014 - 18:22:07 CDT)
  • Workshop on GPU Programming for Molecular Modeling, in Urbana, Illinois, July 22-24, 2014 (Fri Apr 18 2014 - 16:49:02 CDT)
  • "Hands-on" Workshop on Computational Biophysics at Lake Tahoe, August 4-8, 2014 (Thu Apr 03 2014 - 11:17:33 CDT)
• David Chin
  • NAMD 2.10 with MVAPICH2-GDR? (Thu Jan 15 2015 - 08:41:04 CST)
  • Compiling with Open64 4.5.2.1 for AMD Opteron 6378 (Mon Mar 24 2014 - 10:44:54 CDT)
• David Hardy
  • Re: Trouble using the extForces parameters (Sat Apr 11 2015 - 12:05:49 CDT)
  • Re: Algorithm used by NAMD (Fri Apr 03 2015 - 11:18:46 CDT)
  • Re: namd-1: Fatal Error: Unable to Open CHARMM Parameter File (Tue Feb 03 2015 - 15:54:49 CST)
  • Re: namd-1: Fatal Error: Unable to Open CHARMM Parameter File (Tue Feb 03 2015 - 15:32:57 CST)
  • Re: GBIS using CUDA enabled NAMD (Wed Sep 10 2014 - 14:46:22 CDT)
  • Re: About electrostatic treatment (Sat May 31 2014 - 12:01:34 CDT)
  • Re: SHAKE or RATTLE algorithm (Fri Apr 04 2014 - 16:28:54 CDT)
  • Re: problem compiling NAMD (Tue Feb 25 2014 - 12:39:11 CST)
  • Re: problem compiling NAMD (Mon Feb 24 2014 - 13:18:32 CST)
  • Re: PBC only along the z axis. (Fri Jan 03 2014 - 17:18:47 CST)
• David Huggins
  • FEP using separated topologies (Thu Nov 12 2015 - 07:46:54 CST)
  • Implementing the Virtual Bond Algorithm Using Colvars (Wed Dec 17 2014 - 06:25:33 CST)
• Dawid das
  • Message about timing in *log file. (Sun Feb 01 2015 - 05:05:39 CST)
  • System unstable after turning electric field on. (Tue Jan 27 2015 - 11:26:50 CST)
  • PMEGridSize and parameters controlling electrostatic interactions. (Sat Jan 24 2015 - 13:48:44 CST)
• Debashis Kundu
  • Usage of velDCDfile and forceDCDfile keywords in viscosity calculations (Mon Dec 14 2015 - 00:34:56 CST)
  • Multiple input and output files (Wed Nov 05 2014 - 20:20:37 CST)
• Deng, Jinxia (Nancy)
  • RE: energy output (Wed Dec 09 2015 - 13:12:11 CST)
  • energy output (Wed Dec 09 2015 - 11:39:14 CST)
  • RE: multiple output .dcd files?? (Tue Dec 08 2015 - 08:43:02 CST)
  • multiple output .dcd files?? (Mon Dec 07 2015 - 14:56:53 CST)
  • modify input file for production phase MD (Fri Dec 04 2015 - 11:31:26 CST)
  • RE: error when use Charmm_Gui prepared *.inp for NAMD (Thu Dec 03 2015 - 09:52:20 CST)
  • error when use Charmm_Gui prepared *.inp for NAMD (Thu Dec 03 2015 - 08:37:14 CST)
• Dhanashree Khanale
  • Unsubscribe (Thu Jun 19 2014 - 03:19:51 CDT)
• Dhiraj Srivastava
  • fructose 1,6 bisphosphate forcefield parameters. (Wed Dec 02 2015 - 00:06:45 CST)
  • energy minimization (Mon Apr 20 2015 - 21:57:55 CDT)
  • slow heating of system (Sun Apr 19 2015 - 00:55:58 CDT)
• Dian Jiao
  • How to parametrize new atom types in Namd (Fri Jan 17 2014 - 15:44:50 CST)
  • RDF calculation with NAMD (Tue Jan 14 2014 - 15:05:32 CST)
• Diksha Dubey
  • Restraints on the outer solutes (Mon Dec 28 2015 - 03:39:00 CST)
• divya nayar
  • Temperature assignment REMD (Sat Jan 03 2015 - 08:36:05 CST)
• Dong Luo
  • Re: How to let NAMD terminate automatically at a given time (Mon Mar 02 2015 - 09:27:22 CST)
• Douglas Houston
  • Re: Problem running REMD simulation (Tue Aug 25 2015 - 04:16:55 CDT)
  • Re: Is there any point in running NAMD over an ethernet-linked cluster? (Thu Apr 16 2015 - 05:10:12 CDT)
  • Re: AW: FATAL ERROR: seek failed while writing DCD file: No such file or directory (Fri Dec 19 2014 - 08:40:04 CST)
  • Re: FATAL ERROR: seek failed while writing DCD file: No such file or directory (Fri Dec 19 2014 - 08:33:31 CST)
  • Re: AW: FATAL ERROR: seek failed while writing DCD file: No such file or directory (Fri Dec 19 2014 - 02:12:48 CST)
  • FATAL ERROR: seek failed while writing DCD file: No such file or directory (Thu Dec 18 2014 - 14:39:51 CST)
  • Re: AW: About NAMD (Wed Nov 26 2014 - 05:28:39 CST)
  • Re: About NAMD (Tue Nov 18 2014 - 09:32:59 CST)
  • Re: Is there any point in running NAMD over an ethernet-linked cluster? (Mon Sep 22 2014 - 00:23:41 CDT)
  • Is there any point in running NAMD over an ethernet-linked cluster? (Sat Sep 20 2014 - 06:18:25 CDT)
  • Re: Using nodelist file causes namd to hang (Sat Sep 20 2014 - 06:14:29 CDT)
  • Re: AW: Using nodelist file causes namd to hang (Thu Sep 18 2014 - 05:35:30 CDT)
  • Re: AW: AW: AW: Using nodelist file causes namd to hang (Thu Aug 28 2014 - 07:54:30 CDT)
  • Re: AW: AW: Using nodelist file causes namd to hang (Thu Aug 28 2014 - 05:43:48 CDT)
  • Re: AW: Using nodelist file causes namd to hang (Wed Aug 27 2014 - 12:47:24 CDT)
  • Re: AW: Using nodelist file causes namd to hang (Wed Aug 27 2014 - 09:30:42 CDT)
  • Re: Constraint failure in RATTLE algorithm (Tue Jul 01 2014 - 04:29:38 CDT)
  • RE: Constraint failure in RATTLE algorithm (Fri Jun 27 2014 - 09:29:42 CDT)
  • Re: AW: AW: Using nodelist file causes namd to hang (Tue Jun 24 2014 - 08:42:20 CDT)
  • Re: Constraint failure in RATTLE algorithm (Fri Jun 20 2014 - 08:31:56 CDT)
  • Re: AW: Using nodelist file causes namd to hang (Fri Jun 20 2014 - 05:00:05 CDT)
  • Re: Using nodelist file causes namd to hang (Thu Jun 19 2014 - 12:25:25 CDT)
  • Re: Constraint failure in RATTLE algorithm (Thu Jun 19 2014 - 09:51:33 CDT)
  • Re: AW: AW: AW: AW: Using nodelist file causes namd to hang (Thu Jun 19 2014 - 04:56:28 CDT)
  • Re: Constraint failure in RATTLE algorithm (Thu Jun 19 2014 - 05:26:53 CDT)
  • Constraint failure in RATTLE algorithm (Wed Jun 18 2014 - 12:29:48 CDT)
  • Re: AW: AW: AW: Using nodelist file causes namd to hang (Wed Jun 18 2014 - 07:57:59 CDT)
  • Re: AW: AW: Using nodelist file causes namd to hang (Wed Jun 18 2014 - 07:24:00 CDT)
  • Re: AW: Using nodelist file causes namd to hang (Fri Jun 13 2014 - 12:17:15 CDT)
  • Re: AW: AW: Using nodelist file causes namd to hang (Mon Jun 02 2014 - 04:50:40 CDT)
  • Re: AW: AW: Using nodelist file causes namd to hang (Wed Apr 09 2014 - 06:16:35 CDT)
  • Re: Using nodelist file causes namd to hang (Wed Apr 09 2014 - 04:49:17 CDT)
  • Re: AW: Using nodelist file causes namd to hang (Wed Apr 09 2014 - 04:28:37 CDT)
  • Re: Using nodelist file causes namd to hang (Tue Apr 08 2014 - 08:50:15 CDT)
  • Re: AW: Using nodelist file causes namd to hang (Tue Apr 08 2014 - 07:21:19 CDT)
  • Re: AW: AW: Using nodelist file causes namd to hang (Tue Apr 08 2014 - 07:13:42 CDT)
  • Re: AW: Using nodelist file causes namd to hang (Tue Apr 08 2014 - 05:52:52 CDT)
  • Using nodelist file causes namd to hang (Tue Apr 08 2014 - 04:29:34 CDT)
  • Re: Monitoring progress of an ongoing molecular dynamics simulation (Fri Mar 07 2014 - 08:55:47 CST)
  • CHARMM36 and NAMD (Tue Feb 18 2014 - 04:02:38 CST)
  • Re: AW: Re: Various questions (Tue Feb 04 2014 - 07:26:05 CST)
  • Re: Various questions (Mon Feb 03 2014 - 03:52:42 CST)
  • Re: Various questions (Wed Jan 22 2014 - 08:31:03 CST)
  • Re: AW: Various questions (Wed Jan 22 2014 - 04:30:17 CST)
  • Various questions (Tue Jan 21 2014 - 09:42:14 CST)
• Dr. Eddie
  • Sampling frequency (Mon Aug 31 2015 - 14:02:46 CDT)
• dream
  • Could I run aMD in Drude force field? (Thu Feb 05 2015 - 02:14:04 CST)
• Duster, Adam
  • Trouble using the extForces parameters (Sat Apr 11 2015 - 04:11:42 CDT)
• eBiothon Admin Team
  • eBiothon platform (Mon Aug 03 2015 - 10:07:36 CDT)
• Ebru Çetin
  • Getting Infinity in Calculation of Free Energy using SMD (Tue Jun 23 2015 - 00:23:19 CDT)
• Edward Lyman
  • hey! you! why did my simulation crash? (Wed Mar 26 2014 - 10:42:46 CDT)
• Eifler, Jay Q. (UMKC-Student)
  • (no subject) (Mon Jul 14 2014 - 13:05:36 CDT)
  • question (Mon Mar 31 2014 - 11:47:16 CDT)
• Emad Tajkhorshid
  • Re: Restarting trajectories (Wed May 20 2015 - 12:32:12 CDT)
  • Re: Announcement: 'Hands On' Workshop on Computational Biophysics (Berkeley, CA, Aug 3-7, 2015) (Wed May 20 2015 - 00:43:55 CDT)
• eprates_at_iqm.unicamp.br
  • Re: Histidine C-H---O hydrogen bonding (Thu Jan 29 2015 - 11:39:57 CST)
  • Re: Histidine C-H---O hydrogen bonding (Thu Jan 29 2015 - 11:36:33 CST)
  • Histidine C-H---O hydrogen bonding (Thu Jan 29 2015 - 09:03:17 CST)
• Ern Seang Ong
  • Charm++ warning> fences and atomic operations not available in native assembly (Thu Aug 20 2015 - 02:56:40 CDT)
  • RE: namd-l digest V1 #1668 (Sun May 03 2015 - 23:14:28 CDT)
  • Problems in running AutoIMD (Thu Apr 30 2015 - 23:33:47 CDT)
• Evandro Semighini
  • Re: Topology for drugs to do MD after docking (Wed Oct 21 2015 - 11:48:21 CDT)
  • Re: Controlling water diffusion (Sun Jul 19 2015 - 21:42:17 CDT)
  • Re: Controlling water diffusion (Fri Jul 17 2015 - 07:44:36 CDT)
  • Controlling water diffusion (Thu Jul 16 2015 - 14:21:50 CDT)
  • Re: Re: Problems to parametrize molecules (Fri Apr 24 2015 - 14:26:50 CDT)
  • Re: Re: Problems to parametrize molecules (Fri Apr 24 2015 - 13:58:25 CDT)
  • Re: Re: Problems to parametrize molecules (Fri Apr 24 2015 - 13:54:33 CDT)
  • Re: Re: Problems to parametrize molecules (Fri Apr 24 2015 - 12:49:31 CDT)
  • Re: Re: Problems to parametrize molecules (Fri Apr 24 2015 - 10:04:37 CDT)
  • Re: Re: Problems to parametrize molecules (Sun Apr 19 2015 - 18:47:21 CDT)
  • Re: Problems to parametrize molecules (Thu Apr 16 2015 - 15:28:23 CDT)
  • Re: Problems to parametrize molecules (Thu Apr 16 2015 - 14:53:54 CDT)
  • Re: Problems to parametrize molecules (Wed Apr 15 2015 - 15:37:12 CDT)
  • Re: Problems to parametrize molecules (Tue Apr 14 2015 - 15:51:17 CDT)
  • Problems to parametrize molecules (Tue Apr 14 2015 - 15:30:03 CDT)
• Faezeh Mottaghitalab
  • Re: How to apply a magnetic field with NAMD (Wed Jun 25 2014 - 15:40:43 CDT)
  • How to apply a magnetic field with NAMD (Tue Jun 24 2014 - 16:00:48 CDT)
  • Re: error while making psf file for bacteriorhodopsin system (Fri May 09 2014 - 13:10:55 CDT)
  • error while making psf file for bacteriorhodopsin system (Thu May 08 2014 - 15:11:26 CDT)
  • error : segmentation fault (Wed Jan 01 2014 - 05:18:30 CST)
  • Fwd: Majordomo results (Wed Jan 01 2014 - 05:19:11 CST)
• farzad kiani
  • Re: Atoms moving too fast; simulation has become unstable (Mon Aug 31 2015 - 06:17:38 CDT)
  • Re: OPLS force field in NAMD (Sat Jun 20 2015 - 15:28:39 CDT)
  • Protein solvation (Sat May 10 2014 - 12:28:26 CDT)
  • Re: Fwd: Majordomo results (Wed Jan 01 2014 - 14:57:29 CST)
• Fatemeh Omidbeygi
  • RDF calculation of crystal system (Sat Aug 30 2014 - 00:41:02 CDT)
• Felipe Merino
  • Re: Would it be possible to continue a simulation from any snapshot of a trajectory? (Thu Nov 12 2015 - 03:33:05 CST)
  • Re: Interrupted Molecular Dynamics Simulation (Tue Jul 28 2015 - 10:34:17 CDT)
  • Re: Interrupted Molecular Dynamics Simulation (Tue Jul 28 2015 - 02:03:00 CDT)
  • Re: FEP method- Free energy of solvation of ligand (Wed Jul 22 2015 - 03:07:32 CDT)
  • Re: nvt run error (Tue Jul 21 2015 - 03:28:40 CDT)
  • Re: FEP, big variations in dG within a window (Mon Jan 05 2015 - 10:27:30 CST)
  • Re: How to setup a system with two pulling directions (Thu Apr 17 2014 - 10:38:06 CDT)
  • Re: Accelerated MD with transmembrane protein (Fri Apr 11 2014 - 03:27:09 CDT)
  • accelerated MD log (Mon Mar 31 2014 - 03:57:30 CDT)
  • Re: AW: moving out of the box (Sat Feb 15 2014 - 04:50:15 CST)
• Fidan Sumbul
  • Re: Biasing potential of a Metadynamics Simulation (Tue Oct 27 2015 - 14:38:16 CDT)
  • Biasing potential of a Metadynamics Simulation (Tue Oct 27 2015 - 13:05:02 CDT)
  • Re: Error in Metadynamics Simulation (Fri Oct 23 2015 - 06:08:40 CDT)
  • Error in Metadynamics Simulation (Wed Oct 21 2015 - 16:31:30 CDT)
  • Bias-exchange metadynamics (Sun Oct 18 2015 - 18:16:34 CDT)
  • Re: Hamiltonian Replica Exchange MD Simulation in NAMD (Tue Jan 27 2015 - 14:07:31 CST)
  • Hamiltonian Replica Exchange MD Simulation in NAMD (Fri Jan 23 2015 - 13:04:19 CST)
  • Re: Can NAMD does Langevin Dynamics Simulation (Thu Nov 13 2014 - 10:41:39 CST)
  • Can NAMD does Langevin Dynamics Simulation (Wed Nov 12 2014 - 14:48:25 CST)
• flavio seixas
  • Re: AW: (Wed Nov 26 2014 - 09:53:23 CST)
  • (no subject) (Tue Nov 25 2014 - 19:13:24 CST)
  • Re: FAD topology and parameters (Mon Feb 17 2014 - 06:01:14 CST)
• Floquet Nicolas
  • Metadynamics test along eigenvector (Tue Aug 26 2014 - 02:58:00 CDT)
• Flora Chettiar
  • Re: Help to solve the error (Thu Mar 27 2014 - 01:47:09 CDT)
  • Help to solve the error (Wed Mar 26 2014 - 04:00:46 CDT)
• Fotis Baltoumas
  • Re: NAMD Anisotropic pressure control (Fri Sep 18 2015 - 09:50:14 CDT)
  • Re: what exactly is the form of the cosine angle potential? (Fri Jul 17 2015 - 08:47:55 CDT)
  • Re: Mail reg Parameter file (Mon Apr 20 2015 - 08:48:36 CDT)
  • PACE Force Field and NAMD 2.10 (Thu Mar 12 2015 - 06:18:07 CDT)
  • Re: Analysis plugins for Martini Coarse Grained protein simulations (Sat Feb 07 2015 - 05:25:50 CST)
  • Targeted MD and the MARTINI Coarse-Grained Force Field (Fri Feb 06 2015 - 10:06:55 CST)
  • Re: Restart heating (Fri Jan 16 2015 - 12:26:09 CST)
  • Re: the difference of PCA and EDA (Wed Dec 10 2014 - 05:36:43 CST)
  • Simulation of a membrane protein with large extracellular domains (Thu Nov 13 2014 - 07:30:54 CST)
  • Re: Folic acid parameters (Tue Sep 30 2014 - 10:06:43 CDT)
  • Re: parameter and topology files for martini polarizable water (Thu Jul 10 2014 - 04:17:31 CDT)
  • Should PME be used for electrostatic interaction energy calculations? (Wed Jun 18 2014 - 12:59:16 CDT)
  • Re: MMPBSA Energy Calculations using VMD (Post-Processing) (Thu Apr 10 2014 - 10:09:00 CDT)
  • Re: Excluding non bonded interactions between segments (Tue Apr 08 2014 - 07:08:40 CDT)
  • Re: Excluding non bonded interactions between segments (Tue Apr 08 2014 - 06:57:35 CDT)
  • Excluding non bonded interactions between segments (Wed Apr 02 2014 - 07:40:29 CDT)
  • Generalized Born Implicit solvation with implicit membrane (Fri Mar 14 2014 - 08:28:45 CDT)
• Francesco Pietra
  • Re: NAMD 2.11 released (Thu Dec 24 2015 - 01:22:37 CST)
  • Re: vmd-l: Number of pdb and psf atoms are not the same! (Wed Dec 16 2015 - 10:14:12 CST)
  • Number of pdb and psf atoms are not the same! (Wed Dec 16 2015 - 09:23:41 CST)
  • Re: vmd-l: Re: VMD-NAMD and PDB element column (Mon Dec 14 2015 - 14:52:18 CST)
  • Re: vmd-l: Re: VMD-NAMD and PDB element column (Mon Dec 14 2015 - 14:42:21 CST)
  • Re: vmd-l: Re: VMD-NAMD and PDB element column (Sun Dec 13 2015 - 15:59:37 CST)
  • Re: vmd-l: Re: VMD-NAMD and PDB element column (Sun Dec 13 2015 - 13:39:11 CST)
  • VMD-NAMD and PDB element column (Sat Dec 12 2015 - 09:09:55 CST)
  • Re: Problems with GLUP and ASPP with CHARMM36 (Fri Dec 11 2015 - 09:35:48 CST)
  • Re: Problems with GLUP and ASPP with CHARMM36 (Fri Dec 11 2015 - 09:21:34 CST)
  • Problems with GLUP and ASPP with CHARMM36 (Fri Dec 11 2015 - 05:07:03 CST)
  • PRES and water-ions issues with charmm36 (Thu Dec 10 2015 - 15:30:14 CST)
  • Re: anionic cysteine (Wed Dec 09 2015 - 04:13:54 CST)
  • anionic cysteine (Tue Dec 08 2015 - 08:50:19 CST)
  • namd2.22b CUDA Phi (Sat Dec 05 2015 - 01:06:49 CST)
  • Re: Fwd: TIP4P and CHARMM27 (Thu Dec 03 2015 - 12:19:58 CST)
  • Re: Fwd: TIP4P and CHARMM27 (Wed Dec 02 2015 - 11:47:58 CST)
  • Re: Fwd: TIP4P and CHARMM27 (Tue Dec 01 2015 - 03:22:31 CST)
  • Re: Fwd: TIP4P and CHARMM27 (Fri Nov 27 2015 - 15:54:56 CST)
  • Re: Fwd: TIP4P and CHARMM27 (Fri Nov 27 2015 - 11:35:25 CST)
  • Re: Fwd: TIP4P and CHARMM27 (Fri Nov 27 2015 - 10:18:28 CST)
  • Fwd: TIP4P and CHARMM27 (Fri Nov 27 2015 - 09:17:35 CST)
  • Re: OPLSAA to CHARMM (Fri Nov 06 2015 - 00:59:02 CST)
  • OPLSAA to CHARMM (Thu Nov 05 2015 - 10:21:42 CST)
  • Re: Fwd: ANGLE PARAMETERS FOR NH3 HC NH3 (Tue Oct 27 2015 - 13:33:59 CDT)
  • Fwd: ANGLE PARAMETERS FOR NH3 HC NH3 (Tue Oct 27 2015 - 11:19:48 CDT)
  • ANGLE PARAMETERS FOR NH3 HC NH3 (Tue Oct 27 2015 - 11:12:20 CDT)
  • gromacs to charmm conversion (Fri Oct 23 2015 - 02:34:15 CDT)
  • about "small molecules" in OPLS-AAM FF (Wed Oct 07 2015 - 16:14:12 CDT)
  • Recomposing the system splitted by periodicity (Thu Jun 11 2015 - 04:34:57 CDT)
  • Re: Simulated Annealing with many frequent restarts (Fri May 01 2015 - 01:21:28 CDT)
  • Fwd: No steric clashes, still not minimizing (Wed Mar 11 2015 - 12:28:44 CDT)
  • No steric clashes, still not minimizing (Wed Mar 11 2015 - 06:38:40 CDT)
  • Phi vs GPU (Wed Feb 04 2015 - 01:52:43 CST)
  • Re: Fwd: Local minima on minimiztion with colvars (Thu Jan 22 2015 - 02:55:09 CST)
  • Fwd: Local minima on minimiztion with colvars (Wed Jan 21 2015 - 13:01:33 CST)
  • Local minima on minimiztion with colvars (Wed Jan 21 2015 - 12:45:14 CST)
  • Re: problems running amber parm7 (Tue Jan 20 2015 - 01:56:02 CST)
  • Re: problems running amber parm7 (Tue Jan 20 2015 - 01:25:17 CST)
  • problems running amber parm7 (Mon Jan 19 2015 - 13:03:44 CST)
  • Restart heating (Fri Jan 16 2015 - 12:04:33 CST)
  • Re: Fwd: colvars: keyword "name" is not supported, or not recognized in this context. (Thu Jan 15 2015 - 10:54:47 CST)
  • Fwd: colvars: keyword "name" is not supported, or not recognized in this context. (Thu Jan 15 2015 - 10:10:14 CST)
  • colvars: keyword "name" is not supported, or not recognized in this context. (Thu Jan 15 2015 - 09:52:16 CST)
  • Re: Failure MD with par7/rst7 amber input (Fri Jan 09 2015 - 02:31:55 CST)
  • Failure MD with par7/rst7 amber input (Wed Jan 07 2015 - 02:55:16 CST)
  • Re: Fwd: Cannot find colvar dih1 (dih colvars) (Wed Dec 24 2014 - 05:53:54 CST)
  • Fwd: Cannot find colvar dih1 (dih colvars) (Tue Dec 23 2014 - 15:01:39 CST)
  • Fwd: Cannot find colvar dih1 (dih colvars) (Tue Dec 23 2014 - 14:23:04 CST)
  • Cannot find colvar dih1 (dih colvars) (Tue Dec 23 2014 - 11:15:31 CST)
  • CGenFF atom type N- (Mon Nov 24 2014 - 02:55:04 CST)
  • Misleading failure of VMD with charge/CGenFF from waterbox (Sun Nov 23 2014 - 03:21:38 CST)
  • Fwd: Fwd: vmd-l: Re: problems with in text mode towards pdf and pdb files (Sat Nov 22 2014 - 02:45:10 CST)
  • Fwd: vmd-l: Re: problems with in text mode towards pdf and pdb files (Fri Nov 21 2014 - 10:42:05 CST)
  • Re: problems with in text mode towards pdf and pdb files (Fri Nov 21 2014 - 10:06:28 CST)
  • Re: problems with in text mode towards pdf and pdb files (Fri Nov 21 2014 - 09:39:56 CST)
  • problems with in text mode towards pdf and pdb files (Fri Nov 21 2014 - 09:09:52 CST)
  • Re: Dioxygen atom type with CHARMM36 (Wed Nov 12 2014 - 01:17:44 CST)
  • Re: Dioxygen atom type with CHARMM36 (Tue Nov 11 2014 - 13:34:13 CST)
  • Re: Dioxygen atom type with CHARMM36 (Tue Nov 11 2014 - 11:19:17 CST)
  • SOD topology with CHARMM36 (Tue Nov 11 2014 - 11:02:22 CST)
  • Dioxygen atom type with CHARMM36 (Tue Nov 11 2014 - 10:11:00 CST)
  • Dioxygen params charmm36 (Wed Oct 29 2014 - 16:27:17 CDT)
  • Re: NAMD and usable FFs (Fri Oct 17 2014 - 03:12:48 CDT)
  • Re: NAMD and usable FFs (Thu Oct 16 2014 - 16:41:59 CDT)
  • Re: NAMD and usable FFs (Thu Oct 16 2014 - 12:59:10 CDT)
  • NAMD and usable FFs (Wed Oct 15 2014 - 04:34:31 CDT)
  • Re: REMD on IBM iDataPlex DX360M3 (Tue Jul 08 2014 - 12:14:10 CDT)
  • Fwd: REMD on IBM iDataPlex DX360M3 (Tue Jul 08 2014 - 00:41:54 CDT)
  • Re: REMD on IBM iDataPlex DX360M3 (Thu Jul 03 2014 - 09:42:41 CDT)
  • Re: REMD on IBM iDataPlex DX360M3 (Thu Jul 03 2014 - 04:53:32 CDT)
  • REMD on IBM iDataPlex DX360M3 (Thu Jul 03 2014 - 01:15:21 CDT)
  • Re: peptide tends to migrate out the water box (Fri Apr 18 2014 - 03:14:49 CDT)
  • peptide tends to migrate out the water box (Thu Apr 17 2014 - 17:02:01 CDT)
  • Re: Accelerated MD with transmembrane protein (Sat Apr 12 2014 - 08:24:00 CDT)
  • Re: Accelerated MD with transmembrane protein (Fri Apr 11 2014 - 12:16:40 CDT)
  • Re: Accelerated MD with transmembrane protein (Fri Apr 11 2014 - 11:39:10 CDT)
  • Re: remd across gpus (Mon Mar 31 2014 - 02:41:24 CDT)
  • Re: Constraint failure in RATTLE (Mon Mar 31 2014 - 02:29:48 CDT)
  • Fwd: Constraint failure in RATTLE (Sun Mar 30 2014 - 03:07:50 CDT)
  • Constraint failure in RATTLE (Sun Mar 30 2014 - 02:31:54 CDT)
  • accelMD on GPUs (Sat Mar 29 2014 - 02:38:58 CDT)
  • remd across gpus (Sat Mar 29 2014 - 02:29:12 CDT)
  • Re: iDataPlex (Tue Mar 18 2014 - 04:03:29 CDT)
  • iDataPlex (Mon Mar 17 2014 - 13:12:32 CDT)
  • Re: Fwd: TCL command "run" erratic (Mon Mar 17 2014 - 02:22:26 CDT)
  • Fwd: TCL command "run" erratic (Sun Mar 16 2014 - 14:57:53 CDT)
  • Fwd: TCL command "run" erratic (Sun Mar 16 2014 - 14:48:12 CDT)
  • TCL command "run" erratic (Sun Mar 16 2014 - 14:40:09 CDT)
  • Fwd: Failure of namd2.10 in keeping trace of cell in t-remd (Tue Feb 18 2014 - 12:45:35 CST)
  • Failure of namd2.10 in keeping trace of cell in t-remd (Tue Feb 18 2014 - 05:44:34 CST)
  • Re: colvars with replica exchange molecular dynamics (Fri Jan 31 2014 - 01:38:21 CST)
  • Fwd: colvars with replica exchange molecular dynamics (Thu Jan 30 2014 - 04:38:47 CST)
  • Fwd: colvars with replica exchange molecular dynamics (Wed Jan 29 2014 - 10:40:22 CST)
  • Re: colvars with replica exchange molecular dynamics (Tue Jan 14 2014 - 02:25:19 CST)
  • colvars with replica exchange molecular dynamics (Mon Jan 13 2014 - 14:29:41 CST)
• Fransiska Kurniawan
  • Create psf file (Sat Jun 20 2015 - 17:56:52 CDT)
  • CHARMM parameter file (Wed Apr 15 2015 - 04:11:00 CDT)
  • Topology and Parameter File (Mon Mar 09 2015 - 01:52:36 CDT)
• Fulu Zheng
  • two O atoms in CTER are unusually close (Sat Jul 05 2014 - 02:05:28 CDT)
• FyD
  • Empirical force fields: release of R.E.D. Server Dev./PyRED Nov. 2014 (Tue Dec 09 2014 - 02:43:22 CST)
  • Empirical force fields: release new version of RED Server Dev/PyRED (Mon May 05 2014 - 06:07:18 CDT)
• g_at_ut#@m!
  • FEP Restart file (Wed Jan 21 2015 - 08:26:15 CST)
• Gaurab Sarkar
  • Viscosity Calculation using EMD (Mon Dec 14 2015 - 13:22:02 CST)
• George Patargias
  • VRPN cannot connect to Falcon (Wed Oct 15 2014 - 04:58:11 CDT)
  • VRPN compilation error (Tue Oct 14 2014 - 08:43:59 CDT)
  • Re: ABF with the RMSD colvar (Mon Sep 29 2014 - 05:25:01 CDT)
  • Re: ABF with the RMSD colvar (Mon Sep 22 2014 - 06:21:45 CDT)
  • Re: ABF with the RMSD colvar (Fri Sep 19 2014 - 10:12:40 CDT)
  • Re: ABF with the RMSD colvar (Wed Sep 17 2014 - 06:43:44 CDT)
  • Re: Cost of a colvar calculation (Wed Jul 23 2014 - 01:33:23 CDT)
  • Cost of a colvar calculation (Tue Jul 22 2014 - 06:27:52 CDT)
  • Re: Steered MD with the RMSD colvar (Thu Jul 03 2014 - 06:26:19 CDT)
  • Re: Steered MD with the RMSD colvar (Mon May 19 2014 - 05:01:12 CDT)
  • Re: ABF with the RMSD colvar (Fri Apr 25 2014 - 05:20:31 CDT)
  • Re: ABF with the RMSD colvar (Wed Apr 16 2014 - 05:14:05 CDT)
  • ABF with the RMSD colvar (Tue Apr 15 2014 - 05:22:46 CDT)
• Gergely Gyimesi
  • Re: Unable to read corrupted binary DCD trajectory file (Mon Sep 08 2014 - 09:51:33 CDT)
• Giacomo Fiorin
  • Re: OutputAccumulatedWork...where's the output? (Mon Dec 14 2015 - 13:32:17 CST)
  • Re: OutputAccumulatedWork...where's the output? (Mon Dec 14 2015 - 10:55:36 CST)
  • Re: query for system size in pmf calculation (Fri Nov 20 2015 - 08:52:35 CST)
  • Re: ABF calculations - reaction coordinate (Mon Nov 16 2015 - 20:30:56 CST)
  • Re: Bubble in water during membrane simulations (Mon Nov 16 2015 - 09:48:42 CST)
  • Re: Free energy profiles in ABF tutorial (Mon Nov 16 2015 - 07:52:31 CST)
  • Re: error reading colvars.conf in REUS (Wed Nov 11 2015 - 11:00:21 CST)
  • Re: error reading colvars.conf in REUS (Fri Nov 06 2015 - 14:41:42 CST)
  • Re: ABF error on NAMD 2.10 (Mon Nov 02 2015 - 08:51:52 CST)
  • Re: ABF error on NAMD 2.10 (Mon Nov 02 2015 - 07:49:46 CST)
  • Re: Biasing potential of a Metadynamics Simulation (Tue Oct 27 2015 - 15:55:13 CDT)
  • Re: Biasing potential of a Metadynamics Simulation (Tue Oct 27 2015 - 13:14:06 CDT)
  • Re: Error in Metadynamics Simulation (Thu Oct 22 2015 - 15:41:57 CDT)
  • Re: keyword "outputaccumulatedwork" is not supported, or not recognized in this context. (Wed Oct 14 2015 - 06:33:28 CDT)
  • Re: Regarding biasTemperature used in Well-tempered metadynamics (Tue Oct 06 2015 - 09:01:52 CDT)
  • Re: NAMD 2.10 Building from Source (Thu Jul 09 2015 - 16:05:02 CDT)
  • Re: polymerization simulations (Thu Jul 09 2015 - 15:51:38 CDT)
  • Re: NAMD 2.10 Building from Source (Thu Jul 09 2015 - 15:45:32 CDT)
  • Re: Multiple-replicas metadynamics / Well-tempered metadynamics (Fri Jun 12 2015 - 14:21:15 CDT)
  • Re: Calculating the spin angle collective variable value (Mon May 11 2015 - 08:57:41 CDT)
  • Re: Calculating the spin angle collective variable value (Mon May 11 2015 - 08:40:34 CDT)
  • Re: Calculation of PMF between protein domains NAMD (Fri Apr 17 2015 - 17:48:33 CDT)
  • Re: problem restarting multiple walker metadynamics (Wed Apr 01 2015 - 15:05:30 CDT)
  • Re: ABF with external electric field (Tue Mar 31 2015 - 13:16:15 CDT)
  • Re: problem restarting multiple walker metadynamics (Sat Mar 28 2015 - 17:50:19 CDT)
  • Re: angle between 2 vectors as collective variable (Thu Mar 26 2015 - 10:16:25 CDT)
  • Re: angle between 2 vectors as collective variable (Thu Mar 26 2015 - 09:58:26 CDT)
  • Re: problem restarting multiple walker metadynamics (Thu Mar 19 2015 - 18:39:06 CDT)
  • Re: problem restarting multiple walker metadynamics (Thu Mar 19 2015 - 17:26:27 CDT)
  • Re: problem restarting multiple walker metadynamics (Sun Mar 15 2015 - 10:47:17 CDT)
  • Re: problem restarting multiple walker metadynamics (Sun Mar 15 2015 - 10:45:14 CDT)
  • Re: Dihedral calculation with colvars (Fri Mar 13 2015 - 10:05:20 CDT)
  • Re: Colvar with variable axis (Thu Mar 12 2015 - 08:25:54 CDT)
  • Re: Colvar with variable axis (Thu Mar 12 2015 - 06:23:31 CDT)
  • Re: problem restarting multiple walker metadynamics (Wed Mar 11 2015 - 18:29:36 CDT)
  • Re: Dihedral definition in NAMD (Wed Mar 11 2015 - 03:13:27 CDT)
  • Re: Dihedral definition in NAMD (Tue Mar 10 2015 - 18:46:42 CDT)
  • Re: Dihedral definition in NAMD (Tue Mar 10 2015 - 09:49:00 CDT)
  • Re: Dihedral definition in NAMD (Tue Mar 10 2015 - 09:33:15 CDT)
  • Re: Dihedral definition in NAMD (Tue Mar 10 2015 - 06:28:26 CDT)
  • Re: inconsistency in ABF results for helix unfolding (Wed Jan 28 2015 - 14:52:54 CST)
  • Re: colvars and drude don't play nice? (Fri Jan 16 2015 - 11:04:44 CST)
  • Re: colvars and drude don't play nice? (Wed Jan 14 2015 - 10:07:23 CST)
  • Re: colvars and drude don't play nice? (Tue Jan 13 2015 - 18:31:38 CST)
  • Re: colvars angle centerReference (Wed Jan 07 2015 - 14:00:02 CST)
  • Re: Using colvars for biasing potential in Umbrella Sampling (Wed Jan 07 2015 - 10:08:11 CST)
  • Re: Implementing the Virtual Bond Algorithm Using Colvars (Thu Dec 18 2014 - 19:37:06 CST)
  • Re: colvars angle centerReference (Wed Dec 10 2014 - 08:44:22 CST)
  • Re: question about FEP for amphiphile in lipid bilayer (Wed Dec 10 2014 - 08:41:25 CST)
  • Re: colvars angle centerReference (Tue Dec 09 2014 - 21:54:55 CST)
  • Re: colvars angle centerReference (Tue Dec 09 2014 - 18:35:22 CST)
  • Re: Choosing of windows and width for Umbrella Sampling (Mon Dec 08 2014 - 08:29:49 CST)
  • Re: Colvars error (Tue Nov 25 2014 - 08:53:58 CST)
  • Re: tilt colvar (Mon Nov 24 2014 - 16:53:25 CST)
  • Re: tilt colvar (Mon Nov 24 2014 - 09:34:32 CST)
  • Re: tilt colvar (Fri Nov 21 2014 - 11:35:25 CST)
  • Re: carboxyl NBFIX on proteins (Thu Nov 20 2014 - 10:05:10 CST)
  • Re: Colvar: minimal distance between 2 groups of atoms (Mon Nov 17 2014 - 08:49:18 CST)
  • Re: Umbrella sampling tilt with respect to Z-axis (Wed Oct 08 2014 - 15:45:04 CDT)
  • Re: Parameter colvars (Tue Oct 07 2014 - 13:04:53 CDT)
  • Re: Parameter colvars (Mon Oct 06 2014 - 15:25:06 CDT)
  • Re: Parameter colvars (Mon Oct 06 2014 - 07:03:38 CDT)
  • Re: Parameter colvars (Mon Oct 06 2014 - 06:27:23 CDT)
  • Re: Parameter colvars (Mon Oct 06 2014 - 05:45:41 CDT)
  • Re: PCL dcd files (Mon Sep 29 2014 - 12:10:07 CDT)
  • Re: SMD pulling speed (Sat Sep 27 2014 - 21:16:15 CDT)
  • Re: I would like to unsubscribe (Wed Sep 10 2014 - 09:21:11 CDT)
  • Re: problems running ABF simulation (Tue Sep 02 2014 - 02:45:26 CDT)
  • Re: Metadynamics test along eigenvector (Tue Aug 26 2014 - 10:07:34 CDT)
  • Re: ABF hBond (Mon Aug 25 2014 - 10:18:12 CDT)
  • Re: Metadynamics with eigenvector (Mon Aug 25 2014 - 10:17:22 CDT)
  • Re: Cost of a colvar calculation (Tue Jul 22 2014 - 17:31:23 CDT)
  • Re: PMF calculations between membrane and nano particle simulations (Mon Jul 07 2014 - 18:05:06 CDT)
  • Re: PMF calculations between membrane and nano particle simulations (Thu Jul 03 2014 - 16:34:33 CDT)
  • Re: PMF and work distribution (Wed Jun 25 2014 - 12:12:52 CDT)
  • Re: Steered MD with the RMSD colvar (Wed May 21 2014 - 17:52:54 CDT)
  • Re: COLVAR metadynamics: center of mass of atoms crossing simulation box (Tue May 20 2014 - 11:41:56 CDT)
  • Re: running Multiple-replicas metadynamics (Fri May 16 2014 - 14:00:41 CDT)
  • Re: FixedAtoms and Reference group in spinangle colvar (Sun May 11 2014 - 17:27:29 CDT)
  • Re: ABF with the RMSD colvar (Fri Apr 25 2014 - 09:41:54 CDT)
  • Re: ABF with the RMSD colvar (Wed Apr 16 2014 - 13:41:54 CDT)
  • Re: ABF with the RMSD colvar (Tue Apr 15 2014 - 10:06:44 CDT)
  • Re: Collective variable module (Fri Apr 11 2014 - 12:49:20 CDT)
  • Re: Collective variable module (Thu Apr 10 2014 - 14:06:18 CDT)
  • Re: Collective variable module (Thu Apr 10 2014 - 12:03:27 CDT)
  • Re: Spinangle with refgroup : Warning: discontinuous rotation! (Thu Apr 10 2014 - 08:56:01 CDT)
  • Re: Spinangle with refgroup : Warning: discontinuous rotation! (Thu Apr 10 2014 - 08:34:25 CDT)
  • Re: Spinangle with refgroup : Warning: discontinuous rotation! (Wed Apr 09 2014 - 11:18:13 CDT)
  • Re: Spinangle with refgroup : Warning: discontinuous rotation! (Mon Apr 07 2014 - 19:54:30 CDT)
  • Re: COLVAR related quesion (Tue Mar 11 2014 - 16:19:24 CDT)
  • Re: ABF simulation fails with "FATAL ERROR: Low global exclusion count!" (Tue Feb 25 2014 - 20:19:28 CST)
  • Re: Umbrella sampling using colvarconfig file with dihedrals (Wed Feb 05 2014 - 11:25:36 CST)
  • Re: colvars with replica exchange molecular dynamics (Thu Jan 30 2014 - 17:32:47 CST)
  • Re: PMF calculation crashes with constraint failure (Sun Jan 26 2014 - 15:37:10 CST)
  • Re: recent comparison of NAMD to other MD engines (Wed Jan 22 2014 - 20:38:29 CST)
  • Re: Citating colvars module (Tue Jan 21 2014 - 11:12:55 CST)
  • Re: colvars with replica exchange molecular dynamics (Mon Jan 13 2014 - 15:17:25 CST)
  • Re: whidth value of orientation in colvars (Fri Jan 10 2014 - 16:20:45 CST)
  • Re: whidth value of orientation in colvars (Thu Jan 09 2014 - 07:31:15 CST)
• Gianluca Interlandi
  • Re: free energy changes via FEP method (Wed Dec 16 2015 - 12:49:26 CST)
  • Re: Changing Boundary conditions from PBC to non-periodic (Thu Nov 19 2015 - 14:30:16 CST)
  • Re: AW: stepspercycle (Mon Oct 19 2015 - 12:31:23 CDT)
  • stepspercycle (Sun Oct 18 2015 - 20:20:26 CDT)
  • Re: BONDS vs DOUBLE in topology file (Fri Oct 09 2015 - 12:42:43 CDT)
  • BONDS vs DOUBLE in topology file (Fri Oct 09 2015 - 00:42:05 CDT)
  • Re: namd ibverbs (Thu Jul 16 2015 - 17:09:40 CDT)
  • Re: namd ibverbs (Thu Jul 16 2015 - 16:20:34 CDT)
  • Re: namd ibverbs (Thu Jul 16 2015 - 16:06:37 CDT)
  • Re: namd ibverbs (Thu Jul 16 2015 - 15:56:14 CDT)
  • Re: namd ibverbs (Thu Jul 16 2015 - 15:31:34 CDT)
  • -xHost (Mon Jul 06 2015 - 13:08:37 CDT)
  • running multicore version on a 2-CPU node (Sat Jul 04 2015 - 15:33:25 CDT)
  • multicore vs ibverbs (Sat Jul 04 2015 - 12:52:40 CDT)
  • Assessing convergence in FEP calculations (Thu Aug 28 2014 - 14:00:08 CDT)
  • Re: (Thu Aug 28 2014 - 00:16:37 CDT)
  • Window for FEP calculations (Tue Aug 26 2014 - 19:35:33 CDT)
  • Re: Force field design (Thu Jul 24 2014 - 14:22:41 CDT)
  • Re: Force field design (Wed Jul 23 2014 - 23:30:58 CDT)
  • RE: Force field design (Wed Jul 16 2014 - 00:32:49 CDT)
  • Re: Force field design (Tue Jul 15 2014 - 22:32:35 CDT)
  • Re: accelerated MD as the engine for loop refirement (Tue Jul 15 2014 - 02:05:30 CDT)
  • Re: (Mon Jul 14 2014 - 13:26:57 CDT)
  • Re: accelerated MD as the engine for loop refirement (Thu Jul 10 2014 - 17:59:24 CDT)
  • Re: accelerated MD as the engine for loop refirement (Wed Jul 09 2014 - 15:08:17 CDT)
  • Re: AW: Xeon vs i7 and ECC vs SDRAM (Wed Jun 25 2014 - 01:14:48 CDT)
  • Re: Xeon vs i7 and ECC vs SDRAM (Tue Jun 24 2014 - 23:07:02 CDT)
  • Xeon vs i7 and ECC vs SDRAM (Tue Jun 24 2014 - 20:02:49 CDT)
  • Re: NAMD-Lite (Tue Apr 15 2014 - 18:16:50 CDT)
  • Re: FEP error using CUDA (Sun Apr 13 2014 - 23:14:03 CDT)
  • Re: tools for Charmm (Thu Feb 20 2014 - 13:15:51 CST)
  • Re: tools for Charmm (Thu Feb 20 2014 - 12:08:24 CST)
  • Re: Charmm (Thu Feb 20 2014 - 12:10:22 CST)
• Giovanni Settanni
  • building namd on a Cray XE6 with Interlagos procs (Tue May 20 2014 - 09:03:22 CDT)
• Gisella Alfonsino
  • about langevin dynamics (Sun Mar 08 2015 - 05:36:28 CDT)
  • explicit membrane in implicit solvent (Mon Nov 03 2014 - 05:00:36 CST)
• gmail
  • Re: inconsistency in ABF results for helix unfolding (Wed Jan 28 2015 - 03:49:54 CST)
• Gozde Eskici
  • changing damping coefficient during simulation (Tue Mar 18 2014 - 10:20:25 CDT)
• Grace Brannigan
  • Re: DOF during alchemical simulations (Mon Nov 30 2015 - 14:45:55 CST)
  • Re: DOF during alchemical simulations (Mon Nov 30 2015 - 12:05:36 CST)
  • Re: Parameter colvars (Mon Oct 06 2014 - 15:56:18 CDT)
• Grzegorz Nawrocki
  • Re: Rigid bonds and non-bonded energy (Wed Oct 21 2015 - 08:29:22 CDT)
  • Re: Rigid bonds and non-bonded energy (Tue Oct 20 2015 - 11:09:20 CDT)
  • Re: Rigid bonds and non-bonded energy (Tue Oct 20 2015 - 10:11:42 CDT)
  • Rigid bonds and non-bonded energy (Fri Oct 16 2015 - 16:39:48 CDT)
  • Re: Restarting trajectories (Thu May 21 2015 - 09:10:28 CDT)
  • Re: Restarting trajectories (Wed May 20 2015 - 14:24:08 CDT)
  • Re: Different trajectories with and without restarting (Mon May 18 2015 - 15:04:17 CDT)
  • Re: Different trajectories with and without restarting (Fri May 15 2015 - 21:08:40 CDT)
  • Different trajectories with and without restarting (Fri May 15 2015 - 18:09:57 CDT)
• Gurpreet Kaur Dhindsa
  • Algorithm used by NAMD (Thu Apr 02 2015 - 09:55:36 CDT)
  • unsubscribe (Wed Nov 12 2014 - 19:04:28 CST)
  • Root mean square deviation.......... (Tue Aug 12 2014 - 12:58:38 CDT)
  • Fatal error.. (Sun Jun 22 2014 - 17:32:16 CDT)
  • Merging the two files...... (Tue Jun 17 2014 - 10:00:09 CDT)
  • Re: change in pdb.. (Wed Jun 11 2014 - 20:34:29 CDT)
  • change in pdb.. (Wed Jun 11 2014 - 09:39:31 CDT)
  • change in pdb.. (Sat Jun 07 2014 - 18:37:41 CDT)
  • Fixed atoms. (Thu Jun 05 2014 - 16:15:05 CDT)
• Hadi
  • Re: Kb, Ktheta values for TIP3P water model (Sun Aug 10 2014 - 22:29:55 CDT)
  • Re: Kb, Ktheta values for TIP3P water model (Sun Aug 10 2014 - 20:59:58 CDT)
  • Re: Kb, Ktheta values for TIP3P water model (Thu Aug 07 2014 - 17:15:09 CDT)
  • Re: Kb, Ktheta values for TIP3P water model (Thu Aug 07 2014 - 12:36:33 CDT)
  • Re: Kb, Ktheta values for TIP3P water model (Wed Aug 06 2014 - 17:39:50 CDT)
  • Re: Kb, Ktheta values for TIP3P water model (Wed Aug 06 2014 - 16:07:27 CDT)
  • Re: Kb, Ktheta values for TIP3P water model (Wed Aug 06 2014 - 15:40:22 CDT)
  • Re: Kb, Ktheta values for TIP3P water model (Wed Aug 06 2014 - 14:41:58 CDT)
  • Re: Kb, Ktheta values for TIP3P water model (Wed Aug 06 2014 - 13:57:26 CDT)
  • Re: Kb, Ktheta values for TIP3P water model (Tue Aug 05 2014 - 14:49:48 CDT)
  • Re: Kb, Ktheta values for TIP3P water model (Tue Aug 05 2014 - 14:10:14 CDT)
  • Re: Kb, Ktheta values for TIP3P water model (Tue Aug 05 2014 - 02:14:00 CDT)
  • Re: Kb, Ktheta values for TIP3P water model (Tue Jul 29 2014 - 17:59:19 CDT)
  • PME: The Excluded Coulombic Interactions (Fri Mar 21 2014 - 22:56:50 CDT)
• Hadi Dinpajooh
  • Re: Kb, Ktheta values for TIP3P water model (Tue Aug 05 2014 - 11:52:44 CDT)
• Haleh a
  • Re: free energy changes via FEP method (Thu Dec 17 2015 - 05:42:15 CST)
  • free energy changes via FEP method (Tue Dec 15 2015 - 09:59:10 CST)
  • Free energy profiles in ABF tutorial (Mon Nov 16 2015 - 06:35:30 CST)
  • Re: ABF error on NAMD 2.10 (Mon Nov 02 2015 - 08:45:29 CST)
  • ABF error on NAMD 2.10 (Mon Nov 02 2015 - 05:55:59 CST)
  • Re: Folic acid parameters (Wed Oct 01 2014 - 01:42:20 CDT)
  • Folic acid parameters (Tue Sep 30 2014 - 08:44:38 CDT)
• Hannes Loeffler
  • Re: DOF during alchemical simulations (Tue Dec 01 2015 - 08:19:00 CST)
  • Re: atom types in PSF/PRM/RTF (Thu May 28 2015 - 13:19:14 CDT)
  • atom types in PSF/PRM/RTF (Fri May 22 2015 - 04:42:45 CDT)
  • Re: the difference of PCA and EDA (Wed Dec 10 2014 - 05:59:37 CST)
  • Re: alchemical free energy simulations with parmtop (Mon Dec 01 2014 - 03:20:17 CST)
  • alchemical free energy simulations with parmtop (Tue Jun 17 2014 - 04:35:59 CDT)
  • Re: recent comparison of NAMD to other MD engines (Thu Jan 23 2014 - 04:05:18 CST)
• hannes.loeffler_at_stfc.ac.uk
  • RE: FEP method- Free energy of solvation of ligand (Wed Jul 22 2015 - 03:10:42 CDT)
  • RE: atom types in PSF/PRM/RTF (Sun May 31 2015 - 07:43:34 CDT)
  • RE: How to let NAMD terminate automatically at a given time (Mon Mar 02 2015 - 14:17:16 CST)
  • RE: How to let NAMD terminate automatically at a given time (Mon Mar 02 2015 - 13:19:08 CST)
  • RE: setting up namd simulation in IBM Blue Gene/L (Thu Dec 18 2014 - 01:43:11 CST)
  • RE: setting up namd simulation in IBM Blue Gene/L (Thu Dec 18 2014 - 01:36:36 CST)
  • RE: setting up namd simulation in IBM Blue Gene/L (Wed Dec 17 2014 - 07:07:23 CST)
  • RE: Re: alchemical free energy simulations with parmtop (Thu Dec 04 2014 - 11:52:49 CST)
  • RE: Re: alchemical free energy simulations with parmtop (Tue Dec 02 2014 - 12:39:41 CST)
  • RE: AW: Dihedrals multiplicity! (Mon Feb 17 2014 - 11:43:47 CST)
  • RE: Membrane and NPAT (Mon Feb 17 2014 - 10:53:49 CST)
  • RE: AW: Dihedrals multiplicity! (Sun Feb 16 2014 - 02:34:16 CST)
• Harish Vashisth
  • Re: ABF/colvar error in NAMD2.9 (Tue Jul 22 2014 - 14:39:15 CDT)
  • Re: ABF/colvar error in NAMD2.9 (Tue Jul 22 2014 - 13:00:04 CDT)
  • ABF/colvar error in NAMD2.9 (Tue Jul 22 2014 - 11:23:13 CDT)
  • Re: NAMD on CRAY XE6m-200: dynamic linking in tcl not working (Fri Jun 20 2014 - 18:49:59 CDT)
  • Re: NAMD on CRAY XE6m-200: dynamic linking in tcl not working (Fri Jun 20 2014 - 15:17:34 CDT)
  • NAMD on CRAY XE6m-200: dynamic linking in tcl not working (Fri Jun 20 2014 - 14:07:31 CDT)
• Harris, Robert C.
  • computing forces on atoms by postprocessing a dcd file generated with FEP enabled (Wed Sep 03 2014 - 14:05:40 CDT)
• Hasan haska
  • energy minimization in namd (Thu Apr 23 2015 - 11:29:43 CDT)
  • problem about namdstats.tcl (Wed Apr 01 2015 - 01:34:32 CDT)
  • pressure value (Sun Mar 29 2015 - 14:23:28 CDT)
  • about hydrogen bond analysis (Tue Mar 24 2015 - 16:07:08 CDT)
  • Re: equilibrate the bulk water system (Sat Mar 14 2015 - 14:38:03 CDT)
  • Re: equilibrate the bulk water system (Fri Mar 13 2015 - 06:57:15 CDT)
  • equilibrate the bulk water system (Tue Mar 10 2015 - 16:51:30 CDT)
  • configuration file question (Thu Feb 26 2015 - 16:49:55 CST)
• Hassan Kianinejad
  • NAMD-Lite (Tue Apr 15 2014 - 17:22:56 CDT)
  • medwater config (Fri Apr 04 2014 - 19:15:32 CDT)
  • running benchmarks on NAMD-Lite (Fri Mar 14 2014 - 17:35:21 CDT)
  • compiling namd-lite (Thu Mar 06 2014 - 19:08:28 CST)
  • compiling namd-lite (Thu Mar 06 2014 - 18:55:54 CST)
  • benchmark info (Thu Feb 27 2014 - 16:34:08 CST)
  • problem compiling NAMD (Mon Feb 24 2014 - 10:48:51 CST)
• HERBERT MAX VENTHUR PEÂ¥A
  • FEP utility for binding estimation (Mon Sep 14 2015 - 10:35:17 CDT)
• Hongbo Du
  • RE: water-protein interation (Fri Nov 14 2014 - 09:03:37 CST)
  • RE: slice of water box (Wed Apr 09 2014 - 20:22:04 CDT)
  • RE: Problems with energy minimization (Wed Apr 09 2014 - 10:17:08 CDT)
  • RE: the dielectric constant use in pairwise interaction energy calculation of ligand and protein (Tue Apr 08 2014 - 10:01:01 CDT)
  • RE: how to get cell vectors in tcl forces script (Thu Mar 13 2014 - 11:32:32 CDT)
  • RE: Apply magnetic field through TCLBC (Mon Mar 03 2014 - 16:23:55 CST)
  • Apply magnetic field through TCLBC (Fri Feb 28 2014 - 11:22:04 CST)
• horacio poblete
  • GPU Multinodes problem (Wed Feb 18 2015 - 15:59:07 CST)
• Hossein Mohammadiarani
  • Re: Format of colvars.state (Wed Aug 26 2015 - 18:05:19 CDT)
  • Format of colvars.state (Mon Aug 24 2015 - 12:53:14 CDT)
• Hugo Siles
  • FATAL ERROR: Unable to access config file ubq_ws_eq.log (Thu Nov 12 2015 - 16:40:41 CST)
• Hyuntae Na
  • Guideline for selecting water box size. (Sun Feb 16 2014 - 18:49:00 CST)
• ibrahim khalil
  • polarizable carbon nanotubes (Tue Apr 21 2015 - 11:00:36 CDT)
• Igaev, Maxim
  • multiple thermostats in adaptive tempering (Wed Feb 18 2015 - 11:20:52 CST)
• Istvan Jonyer
  • NAMD on Rescale (Mon Mar 10 2014 - 20:22:10 CDT)
  • Re: namd-l digest V1 #1282 (Fri Jan 17 2014 - 14:04:39 CST)
• Ivan Gregoretti
  • Re: [ANN] MDTraj 1.0: Trajectory Analysis in Python (Tue Sep 09 2014 - 12:09:49 CDT)
  • Re: Cost of a colvar calculation (Tue Jul 22 2014 - 08:41:41 CDT)
  • Re: Cost of a colvar calculation (Tue Jul 22 2014 - 07:33:14 CDT)
  • Re: NAMD-2.9:Help needed on how to write to different DCD files in a single running NAMD simulation?? (Thu Jun 26 2014 - 08:34:16 CDT)
  • Re: change in pdb.. (Wed Jun 11 2014 - 10:29:05 CDT)
  • Re: Help to solve the error (Thu Mar 27 2014 - 07:20:50 CDT)
  • Re: Help to solve the error (Wed Mar 26 2014 - 17:11:58 CDT)
  • Re: wrapping option in namd (Wed Mar 19 2014 - 21:58:30 CDT)
  • Re: NAMD 2.9 quits early without error message. (Mon Mar 10 2014 - 18:45:17 CDT)
  • Re: NAMD 2.9 quits early without error message. (Fri Mar 07 2014 - 11:46:54 CST)
  • NAMD 2.9 quits early without error message. (Fri Mar 07 2014 - 11:36:17 CST)
  • Re: Monitoring progress of an ongoing molecular dynamics simulation (Fri Mar 07 2014 - 10:57:31 CST)
  • Re: Monitoring progress of an ongoing molecular dynamics simulation (Fri Mar 07 2014 - 09:08:44 CST)
  • Re: Monitoring progress of an ongoing molecular dynamics simulation (Fri Mar 07 2014 - 08:52:43 CST)
  • Monitoring progress of an ongoing molecular dynamics simulation (Fri Mar 07 2014 - 08:08:11 CST)
  • Re: How to maintain Density constant? (Thu Mar 06 2014 - 10:34:43 CST)
  • Re: How to maintain Density constant? (Thu Mar 06 2014 - 07:23:29 CST)
  • Re: problem compiling NAMD (Tue Feb 25 2014 - 13:23:23 CST)
• jafar azamat
  • Unsubscribe (Fri Jun 20 2014 - 03:27:10 CDT)
• James Starlight
  • NetworkView plugin for the non-namd trajectories (Tue Apr 14 2015 - 09:34:57 CDT)
  • Calculation of the water inside of protein during trajectory (Tue Feb 03 2015 - 09:51:07 CST)
  • Re: [External] Boost value in aMD simulation (Fri Aug 22 2014 - 11:54:05 CDT)
  • Re: [External] Boost value in aMD simulation (Tue Aug 19 2014 - 13:45:58 CDT)
  • Re: [External] Boost value in aMD simulation (Tue Aug 19 2014 - 04:56:58 CDT)
  • Re: [External] Boost value in aMD simulation (Mon Aug 18 2014 - 03:25:53 CDT)
  • Re: [External] Boost value in aMD simulation (Thu Jul 24 2014 - 01:13:09 CDT)
  • Re: [External] Boost value in aMD simulation (Wed Jul 23 2014 - 15:32:53 CDT)
  • Re: [External] Boost value in aMD simulation (Wed Jul 23 2014 - 14:24:45 CDT)
  • Boost value in aMD simulation (Wed Jul 23 2014 - 06:30:12 CDT)
  • Re: accelerated MD as the engine for loop refirement (Mon Jul 14 2014 - 05:16:46 CDT)
  • Re: accelerated MD as the engine for loop refirement (Sun Jul 13 2014 - 14:05:10 CDT)
  • Re: accelerated MD as the engine for loop refirement (Sat Jul 12 2014 - 09:28:21 CDT)
  • Re: accelerated MD as the engine for loop refirement (Thu Jul 10 2014 - 04:39:17 CDT)
  • accelerated MD as the engine for loop refirement (Wed Jul 09 2014 - 14:39:08 CDT)
  • Re: MMPBSA Energy Calculations using VMD (Post-Processing) (Mon Apr 21 2014 - 14:27:38 CDT)
  • Re: MMPBSA Energy Calculations using VMD (Post-Processing) (Mon Apr 14 2014 - 04:23:01 CDT)
  • Re: MMPBSA Energy Calculations using VMD (Post-Processing) (Mon Apr 14 2014 - 00:56:50 CDT)
  • Re: MMPBSA Energy Calculations using VMD (Post-Processing) (Sat Apr 12 2014 - 01:53:35 CDT)
  • Simulation crash during NPT equilibration (Fri Apr 11 2014 - 05:58:17 CDT)
  • Re: Problems with energy minimization (Thu Apr 10 2014 - 05:32:48 CDT)
  • Re: Problems with energy minimization (Wed Apr 09 2014 - 09:38:21 CDT)
  • Problems with energy minimization (Wed Apr 09 2014 - 09:07:28 CDT)
  • Re: Restoring simulation from the previous run (Wed Mar 19 2014 - 09:38:18 CDT)
  • Restoring simulation from the previous run (Wed Mar 19 2014 - 03:32:31 CDT)
  • Detection of Internal water along MD trajectory (Mon Mar 17 2014 - 04:14:38 CDT)
  • Cross-correlation analysis in multidomain proteins (Thu Mar 13 2014 - 05:32:22 CDT)
  • Re: Accelerated MD in NAMD (Sat Mar 08 2014 - 09:24:47 CST)
  • Tct script for energy estimation (Mon Jan 20 2014 - 03:16:23 CST)
  • Reassure fluctuations in course of simulation (Mon Jan 20 2014 - 03:19:51 CST)
  • Re: Two GPU-based workstation (Tue Jan 14 2014 - 04:45:38 CST)
• Jason Swails
  • Re: Overflow in LJcorrection? (Sat Dec 05 2015 - 07:54:57 CST)
  • Re: Overflow in LJcorrection? (Thu Dec 03 2015 - 16:18:40 CST)
  • Re: Overflow in LJcorrection? (Thu Dec 03 2015 - 16:15:15 CST)
  • Re: Overflow in LJcorrection? (Thu Dec 03 2015 - 16:04:28 CST)
  • Re: Overflow in LJcorrection? (Thu Dec 03 2015 - 15:55:30 CST)
  • Re: Running constant pH molecular dynamics (CpHMD) (Thu Jul 09 2015 - 20:05:36 CDT)
  • Re: atom types in PSF/PRM/RTF (Thu May 28 2015 - 13:55:44 CDT)
  • Re: .inpcrd to .pdb (Sun Dec 21 2014 - 20:04:39 CST)
  • Re: Implicit solvent lipid bilayer simulation in NAMD. (Wed Sep 17 2014 - 13:47:53 CDT)
  • Re: NAMD_energy_plot (Tue Jul 22 2014 - 17:22:29 CDT)
  • Re: (Tue Jul 22 2014 - 12:06:31 CDT)
  • Re: Scaling solvent-solute intermolecular interactions (Wed May 14 2014 - 10:20:57 CDT)
  • Re: Scaling solvent-solute intermolecular interactions (Tue May 13 2014 - 16:57:14 CDT)
  • Re: full electrostatics and pairlistdist (Wed Apr 16 2014 - 08:27:34 CDT)
  • Re: MMPBSA Energy Calculations using VMD (Post-Processing) (Mon Apr 14 2014 - 13:02:08 CDT)
  • Re: MMPBSA Energy Calculations using VMD (Post-Processing) (Mon Apr 14 2014 - 07:31:05 CDT)
  • Re: MMPBSA Energy Calculations using VMD (Post-Processing) (Mon Apr 14 2014 - 07:26:59 CDT)
  • Re: MMPBSA Energy Calculations using VMD (Post-Processing) (Sat Apr 12 2014 - 06:53:32 CDT)
  • Re: VDW energy: positive or negative? (Tue Mar 04 2014 - 20:04:38 CST)
• JAVAD NOROOZI
  • Dipole Moment Watcher, Ibuprofen (Tue Mar 31 2015 - 01:01:46 CDT)
  • NAMD Source, Molecule.c , Mass Critaria (Wed Feb 18 2015 - 12:55:25 CST)
  • Compressibility of Berendesen Barostat (Simulations Near Critical Point) (Fri Feb 13 2015 - 00:37:42 CST)
  • LangevinPistonPeriod (Simulation Near Critical Point) (Tue Feb 10 2015 - 03:15:23 CST)
  • Alchemy Shift Coefficient at Low Density Regime (TI) (Wed Feb 04 2015 - 02:58:15 CST)
  • Re: NAMD Non-features (Wed Jan 21 2015 - 15:24:43 CST)
  • NAMD Non-features (Wed Jan 21 2015 - 01:54:50 CST)
  • Re: AW: Periodic Box Dimension (WrapAll is on) (Tue Jan 20 2015 - 01:37:18 CST)
  • Periodic Box Dimension (WrapAll is on) (Mon Jan 19 2015 - 23:55:19 CST)
  • Multiple Dihedral in CHARMM parameters (Mon Jan 19 2015 - 01:19:37 CST)
  • Multiple Tcouple (Mon Jan 12 2015 - 03:35:01 CST)
  • Tempreture Profile along z axis (Thu Jan 08 2015 - 03:23:12 CST)
  • Problem with Kinetic Energy of Atomselection (Wed Jan 07 2015 - 00:53:38 CST)
  • Probelm with Lone Pairs on TIP4 model (Tue Jan 06 2015 - 04:07:23 CST)
  • Multiple tcouple (Nonequilbirium molecular dynamics) (Tue Jan 06 2015 - 03:51:07 CST)
  • Lone Pair on H2S (Tue Dec 30 2014 - 06:05:39 CST)
  • Lone Pair on H2S (Tue Dec 30 2014 - 06:05:40 CST)
  • Lone Pair on H2S (Sat Dec 27 2014 - 09:42:25 CST)
  • Loading Velocity DCD file (Wed Dec 17 2014 - 13:23:20 CST)
  • Extracting Kinetic Energy of Certain Atoms (Wed Dec 17 2014 - 03:19:09 CST)
  • Molecular Dynamics of Rigid Linear Molecules in NAMD. (Sun Sep 28 2014 - 00:44:28 CDT)
  • alchElecLambdaStart (Thermodynamic Integration) (Fri Jun 06 2014 - 13:55:28 CDT)
  • FEP is in kj/mol (Sun Apr 27 2014 - 08:32:33 CDT)
  • TI analysis script (Sat Apr 19 2014 - 08:16:18 CDT)
  • Step size in FEP calculation (Tue Apr 15 2014 - 23:21:35 CDT)
  • Free Energy Calculation Using Thermodynamic Integration (Mon Mar 17 2014 - 02:06:08 CDT)
  • FEP result analysis (Sat Mar 01 2014 - 03:37:29 CST)
  • Free Energy Perturbation (Tue Feb 25 2014 - 00:36:30 CST)
  • Widom test particle insertion in NAMD (Mon Feb 17 2014 - 00:40:08 CST)
  • Non standar solvent (Sat Feb 15 2014 - 06:52:17 CST)
  • Solvation in non standard solvent (Fri Feb 14 2014 - 05:58:59 CST)
• Javier Cáceres Delpiano
  • Movie of a channel trajectory (Sat Apr 05 2014 - 22:26:21 CDT)
• JC Gumbart
  • Re: The script of Umbrella sampling (Fri Dec 25 2015 - 12:49:51 CST)
  • Re: Re: vmd-l: Fwd: Inviting applications for a new PhD program in Quantitative Biosciences at Georgia Tech (Fri Sep 11 2015 - 10:08:07 CDT)
  • Fwd: Inviting applications for a new PhD program in Quantitative Biosciences at Georgia Tech (Wed Sep 09 2015 - 18:15:34 CDT)
  • Fwd: Inviting applications for a new PhD program in Quantitative Biosciences at Georgia Tech (Wed Sep 09 2015 - 10:13:31 CDT)
  • Re: inconsistency in ABF results for helix unfolding (Wed Jan 28 2015 - 15:40:30 CST)
  • Re: Hamiltonian Replica Exchange MD Simulation in NAMD (Tue Jan 27 2015 - 08:52:42 CST)
  • Re: using NAMD with CHARMM36 ff (Sun Jan 18 2015 - 12:32:35 CST)
  • Re: using NAMD with CHARMM36 ff (Sat Jan 17 2015 - 19:36:55 CST)
  • Re: colvars and drude don't play nice? (Sat Jan 17 2015 - 15:34:43 CST)
  • Re: colvars and drude don't play nice? (Wed Jan 14 2015 - 09:58:28 CST)
  • colvars and drude don't play nice? (Tue Jan 13 2015 - 18:08:42 CST)
  • Re: tilt colvar (Tue Dec 02 2014 - 18:30:22 CST)
  • Re: tilt colvar (Mon Nov 24 2014 - 17:57:44 CST)
  • Re: tilt colvar (Mon Nov 24 2014 - 14:42:43 CST)
  • Re: tilt colvar (Sat Nov 22 2014 - 08:10:23 CST)
  • Re: tilt colvar (Fri Nov 21 2014 - 18:12:31 CST)
  • tilt colvar (Fri Nov 21 2014 - 11:09:55 CST)
  • colvars replica exchange oddity (Tue Oct 14 2014 - 22:27:07 CDT)
  • Re: expected speed up after fixing atoms? (Wed Sep 24 2014 - 14:15:54 CDT)
  • Re: FEP, Ewald size-dependence charge correction (Sat Sep 13 2014 - 18:38:44 CDT)
  • Re: Kb, Ktheta values for TIP3P water model (Thu Jul 31 2014 - 16:24:06 CDT)
  • Re: Kb, Ktheta values for TIP3P water model (Wed Jul 30 2014 - 10:27:16 CDT)
  • Re: Inquiry about lipid membrane simulation (Wed Jun 18 2014 - 19:48:17 CDT)
  • RE: Rapid and accurate parameterization of new molecules in CHARMM (Tue May 27 2014 - 09:19:40 CDT)
  • Re: Generating .psf for amorphous disaccharide (Sat Mar 01 2014 - 21:41:45 CST)
  • Re: recent comparison of NAMD to other MD engines (Thu Jan 23 2014 - 11:14:22 CST)
• jc guo
  • Re: global does not work in configuration and callback function (Sat Oct 24 2015 - 08:51:33 CDT)
  • global does not work in configuration and callback function (Sat Oct 24 2015 - 01:46:21 CDT)
  • about re install (Tue Oct 20 2015 - 01:20:08 CDT)
  • about command replicaRecv and replicaSend (Mon Oct 19 2015 - 02:09:43 CDT)
  • about replica exchange (Fri Oct 16 2015 - 10:43:23 CDT)
  • about replica exchange example in lib of 2.10 NAMD (Fri Oct 16 2015 - 00:11:18 CDT)
• Jean-Patrick Francoia
  • Re: Topology for lysine bouding in Epsilon (Wed May 07 2014 - 04:40:11 CDT)
  • Re: Topology for lysine bouding in Epsilon (Tue May 06 2014 - 13:38:43 CDT)
  • Topology for lysine bouding in Epsilon (Mon May 05 2014 - 12:11:23 CDT)
• jeevan gc
  • Re: MD Simulation of accelerated MD using GPU (Fri Oct 16 2015 - 08:25:29 CDT)
  • Re: MD Simulation of accelerated MD using GPU (Wed Oct 14 2015 - 16:21:36 CDT)
  • MD Simulation of accelerated MD using GPU (Mon Oct 12 2015 - 17:19:15 CDT)
  • MD Simulation of accelerated MD using GPU (Mon Oct 12 2015 - 17:07:39 CDT)
• Jeff Comer
  • Re: NAMD 2.11 released (Wed Dec 23 2015 - 19:38:21 CST)
  • Re: how to get the restart files from the dcd file? (Sun Dec 20 2015 - 12:46:16 CST)
  • Re: how to get the restart files from the dcd file? (Sun Dec 20 2015 - 12:06:17 CST)
  • NAMD 2.11b1 multicore CUDA: Incorrect number of exclusions (Thu Dec 03 2015 - 14:20:42 CST)
  • recommendations for a fast multicore workstation (Tue Nov 24 2015 - 11:56:54 CST)
  • Re: NAMD 2.11b1 released (Tue Nov 10 2015 - 13:18:06 CST)
  • Re: about replica exchange example in lib of 2.10 NAMD (Tue Oct 20 2015 - 20:10:00 CDT)
  • Re: about replica exchange (Fri Oct 16 2015 - 16:17:13 CDT)
  • Re: Solvation free energy calculation with MM/GBSA (Thu Sep 24 2015 - 08:27:26 CDT)
  • Re: Error in NAMD Controller Class Reference- Adaptive Tempering (Fri Sep 11 2015 - 08:12:15 CDT)
  • Re: Error in NAMD Controller Class Reference- Adaptive Tempering (Fri Sep 11 2015 - 08:10:02 CDT)
  • Re: Sampling frequency (Tue Sep 01 2015 - 08:40:14 CDT)
  • Re: statistical error of mean force in (NAMD) ABF calculations (Thu Jul 02 2015 - 09:09:38 CDT)
  • Re: Colvars Boundary potentials do not look harmonic (Wed Jun 03 2015 - 11:54:28 CDT)
  • Re: where can I find the parameter file for chlorophenols? (Mon May 25 2015 - 14:35:46 CDT)
  • Re: Calculation of PMF between protein domains NAMD (Fri Apr 17 2015 - 18:22:17 CDT)
  • Re: ABF with external electric field (Tue Mar 31 2015 - 11:41:35 CDT)
  • Re: pressure value (Sun Mar 29 2015 - 16:54:09 CDT)
  • Re: Restraining angle between bond vector and coordinate vector (Mon Mar 23 2015 - 18:17:18 CDT)
  • Re: Reg: solvating in a non-standard solvent (Thu Mar 19 2015 - 09:02:10 CDT)
  • Re: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OC2D2 (Wed Mar 18 2015 - 17:35:39 CDT)
  • Re: Reg: solvating in a non-standard solvent (Wed Mar 18 2015 - 09:44:12 CDT)
  • Re: How to let NAMD terminate automatically at a given time (Mon Mar 02 2015 - 13:58:14 CST)
  • Re: WHICH VERSION OF NAMD SHOULD I INSTALL ON MY SYSTEM? (Mon Mar 02 2015 - 10:45:28 CST)
  • Re: scaling non-bonded interactiion parameter for specific pairs (Fri Feb 27 2015 - 13:58:31 CST)
  • Re: configuration file question (Thu Feb 26 2015 - 17:34:09 CST)
  • Re: Aggregation related analysis scripts (Tue Feb 24 2015 - 15:39:12 CST)
  • Re: FATAL ERROR: Low global exclusion count! (Wed Feb 18 2015 - 18:59:28 CST)
  • Re: Grid forces visualisation (Wed Feb 11 2015 - 08:16:41 CST)
  • Re: Extracting data (Wed Feb 04 2015 - 08:39:33 CST)
  • Re: Extracting data (Wed Feb 04 2015 - 07:56:42 CST)
  • Re: error running min (Tue Feb 03 2015 - 08:32:57 CST)
  • Re: System unstable after turning electric field on. (Tue Jan 27 2015 - 14:04:26 CST)
  • Re: System unstable after turning electric field on. (Tue Jan 27 2015 - 13:22:38 CST)
  • Re: PMEGridSize and parameters controlling electrostatic interactions. (Sun Jan 25 2015 - 18:11:17 CST)
  • Re: NAMD Non-features (Wed Jan 21 2015 - 09:35:27 CST)
  • Re: Getting residue mapping correpond to bead using SBCG (Shape based CG) Model in Coarse Grain Builder VMD (Fri Jan 09 2015 - 08:23:03 CST)
  • Re: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS (Wed Jan 07 2015 - 20:15:30 CST)
  • Re: Reg: simulating an amino acid in dichloromethane (Sat Jan 03 2015 - 00:34:17 CST)
  • Re: Fwd: Cannot find colvar dih1 (dih colvars) (Tue Dec 23 2014 - 15:35:37 CST)
  • Re: Is it so different when setting reinitvels or not? (Wed Dec 17 2014 - 05:45:09 CST)
  • Re: colvars angle centerReference (Wed Dec 10 2014 - 09:22:10 CST)
  • Re: colvars angle centerReference (Wed Dec 10 2014 - 08:41:06 CST)
  • Re: colvars angle centerReference (Tue Dec 09 2014 - 21:41:26 CST)
  • colvars angle centerReference (Fri Dec 05 2014 - 15:00:44 CST)
  • Re: information about simulation speed (Tue Dec 02 2014 - 18:09:54 CST)
  • Re: A problem in ABF simulations (Mon Nov 24 2014 - 11:44:45 CST)
  • Re: carboxyl NBFIX on proteins (Thu Nov 20 2014 - 10:46:35 CST)
  • carboxyl NBFIX on proteins (Thu Nov 20 2014 - 09:18:45 CST)
  • Re: about the vdw Interpolation calculation in NAMD source code (Thu Nov 20 2014 - 08:20:54 CST)
  • Re: how to fix the problem (Sat Nov 15 2014 - 08:33:54 CST)
  • Re: how to fix the problem (Fri Nov 14 2014 - 20:02:44 CST)
  • Re: how to fix the problem (Fri Nov 14 2014 - 20:02:09 CST)
  • Re: Can NAMD does Langevin Dynamics Simulation (Thu Nov 13 2014 - 15:11:10 CST)
  • Re: Can NAMD does Langevin Dynamics Simulation (Thu Nov 13 2014 - 14:37:13 CST)
  • Re: Can NAMD does Langevin Dynamics Simulation (Wed Nov 12 2014 - 16:37:31 CST)
  • Re: multiple harmonic constrains (Sat Nov 08 2014 - 14:54:50 CST)
  • Re: Annealing process of silica with excluded block (Mon Sep 15 2014 - 09:30:57 CDT)
• Jeff Wereszczynski
  • Re: is the aMD implementation compatible with AMBER force fields (Wed Jun 18 2014 - 13:14:11 CDT)
  • Re: Accelerated MD with transmembrane protein (Fri Apr 11 2014 - 11:50:20 CDT)
  • Re: Accelerated MD with transmembrane protein (Fri Apr 11 2014 - 07:19:20 CDT)
• Jeffery Klauda
  • NAMD/MIC & CUDA on Stampede (Wed Jul 16 2014 - 13:28:27 CDT)
• Jeffrey Potoff
  • Re: energy output (Wed Dec 09 2015 - 11:56:45 CST)
  • Re: error when use Charmm_Gui prepared *.inp for NAMD (Thu Dec 03 2015 - 08:44:53 CST)
  • Re: Patch-size Error (not like the other ones) (Fri Jul 24 2015 - 13:38:52 CDT)
  • Re: 1-5 Intramolecular repulsions (Wed Nov 05 2014 - 12:51:02 CST)
  • Re: Dihedrals multiplicity! (Thu Feb 13 2014 - 11:34:16 CST)
  • Re: Dihedrals multiplicity! (Thu Feb 13 2014 - 10:51:12 CST)
  • Re: Calculating density for a molecule (Fri Feb 07 2014 - 13:17:17 CST)
  • Re: MD simulation Patch grid errors (Mon Jan 13 2014 - 22:34:42 CST)
  • Re: MD simulation Patch grid errors (Tue Jan 07 2014 - 18:03:29 CST)
• Jenny lou
  • String method in NAMD 2.10b1? (Mon Oct 06 2014 - 12:58:17 CDT)
• jeremy adler
  • 11/22/2014 6:32:52 PM (Sat Nov 22 2014 - 00:32:52 CST)
  • jeremy adler (Thu Oct 23 2014 - 06:21:43 CDT)
• Jerome Karp
  • Re: extendedLagrangian for non-scalar colvar (Thu Dec 10 2015 - 12:05:51 CST)
  • extendedLagrangian for non-scalar colvar (Thu Dec 10 2015 - 10:45:27 CST)
  • Re: string method in NAMD 2.10 (Tue Sep 22 2015 - 11:44:37 CDT)
  • Re: string method in NAMD 2.10 (Tue Sep 22 2015 - 10:39:30 CDT)
  • Re: string method in NAMD 2.10 (Tue Sep 22 2015 - 10:05:05 CDT)
  • string method in NAMD 2.10 (Mon Sep 21 2015 - 10:49:42 CDT)
• Jerry Karp
  • string method in NAMD 2.10 (Mon Sep 21 2015 - 10:46:45 CDT)
• Jesper Madsen
  • chloromethyl ketone patch? (Tue Feb 11 2014 - 16:49:21 CST)
• Jessen Lucas
  • about deca alanine tutorial setup (Mon Nov 02 2015 - 15:22:16 CST)
  • Re: replica exchange module (Tue Oct 27 2015 - 03:42:23 CDT)
  • Re: replica exchange module (Mon Oct 26 2015 - 22:49:20 CDT)
  • Re: replica exchange module (Mon Oct 26 2015 - 03:25:46 CDT)
  • Re: replica exchange module (Mon Oct 26 2015 - 02:25:49 CDT)
  • replica exchange module (Mon Oct 26 2015 - 01:29:43 CDT)
• Jhonatam Cordeiro Rodrigues
  • Re: How to calculate the temperature for a subset of my simulation (Tue Oct 20 2015 - 13:47:53 CDT)
  • Re: How to calculate the temperature for a subset of my simulation (Tue Oct 20 2015 - 12:20:46 CDT)
  • How to calculate the temperature for a subset of my simulation (Mon Oct 19 2015 - 15:08:27 CDT)
  • Re: Assigning different temperatures to simulation (Thu Apr 03 2014 - 15:24:09 CDT)
  • Re: Assigning different temperatures to simulation (Wed Apr 02 2014 - 00:42:17 CDT)
  • Assigning different temperatures to simulation (Tue Apr 01 2014 - 15:29:36 CDT)
• Jian Dai
  • Questions about lambda scheme in free energy perturbation (Tue Feb 24 2015 - 08:59:57 CST)
• Jiann George Pazhamalil
  • Re: MD simulation Patch grid errors (Mon Jan 13 2014 - 21:37:41 CST)
  • MD simulation Patch grid errors (Tue Jan 07 2014 - 17:33:06 CST)
• Jim Phillips
  • Re: NAMD 2.11 released (Tue Dec 22 2015 - 21:37:31 CST)
  • NAMD 2.11 released (Tue Dec 22 2015 - 10:38:50 CST)
  • Re: "implausibly old time stamp" for charm++ 6.7 in CVS (Mon Dec 21 2015 - 10:04:11 CST)
  • Re: MD simulation of Linear Molecules (like 2-butyne£© (Sat Dec 19 2015 - 21:53:01 CST)
  • RE: SMP NAMD reports threads greater than physical cores, even when distributed to other nodes (Sat Dec 19 2015 - 21:39:50 CST)
  • RE: SMP NAMD reports threads greater than physical cores, even when distributed to other nodes (Fri Dec 18 2015 - 09:38:15 CST)
  • Re: ERROR in CUDA run (Thu Dec 17 2015 - 19:50:54 CST)
  • Re: RATTLE Error During Minimization of Charmm Gui Generated Bilayer (Thu Dec 17 2015 - 19:49:32 CST)
  • Re: vmd-l: Re: VMD-NAMD and PDB element column (Mon Dec 14 2015 - 09:04:21 CST)
  • Re: vmd-l: Re: VMD-NAMD and PDB element column (Sun Dec 13 2015 - 14:32:38 CST)
  • Re: VMD-NAMD and PDB element column (Sun Dec 13 2015 - 12:17:57 CST)
  • Re: NAMD on TACC (Darter) (Thu Dec 10 2015 - 10:03:56 CST)
  • Re: NAMD on TACC (Darter) (Tue Dec 08 2015 - 22:41:19 CST)
  • Re: NAMD on TACC (Darter) (Tue Dec 08 2015 - 22:15:15 CST)
  • Re: buffer overflow with long file paths in psfgen in NAMD 2.11b2? (Tue Dec 08 2015 - 16:41:22 CST)
  • Re: multiple output .dcd files?? (Mon Dec 07 2015 - 16:43:12 CST)
  • Re: Overflow in LJcorrection? (Mon Dec 07 2015 - 16:35:27 CST)
  • NAMD 2.11b2 released (Sun Dec 06 2015 - 22:01:09 CST)
  • Re: namd2.22b CUDA Phi (Sat Dec 05 2015 - 08:50:57 CST)
  • Re: NAMD 2.11b1 multicore CUDA: Incorrect number of exclusions (Fri Dec 04 2015 - 16:52:30 CST)
  • Re: Fwd: TIP4P and CHARMM27 (Mon Nov 30 2015 - 16:21:44 CST)
  • Re: Re: Re: Re: NAMD 2.11b1 released (Fri Nov 27 2015 - 20:10:42 CST)
  • Re: Which namd to use (Fri Nov 20 2015 - 11:11:30 CST)
  • Re: Which namd to use (Fri Nov 20 2015 - 08:02:36 CST)
  • Re: NAMD2.11 source code not compiling (Wed Nov 18 2015 - 09:21:13 CST)
  • Re: Can't start SMP NAMD - Problem clearly is in front of the monitor (Tue Nov 17 2015 - 12:45:51 CST)
  • Re: AW: time per step during GPU-accelerated Implicit Solvent calculations (Mon Nov 16 2015 - 08:55:26 CST)
  • Re: NAMD 2.11 CUDA forces IBverbs (Fri Nov 13 2015 - 08:31:50 CST)
  • Re: Re: Re: NAMD 2.11b1 released (Thu Nov 12 2015 - 22:41:32 CST)
  • Re: FATAL ERROR: Unable to access config file ubq_ws_eq.log (Thu Nov 12 2015 - 22:45:32 CST)
  • Re: NAMD 2.11b1 released (Thu Nov 12 2015 - 11:15:27 CST)
  • Re: Re: NAMD 2.11b1 released (Thu Nov 12 2015 - 06:55:42 CST)
  • Re: On-the-fly modification of tclforces script? (Tue Nov 10 2015 - 09:53:42 CST)
  • NAMD 2.11b1 released (Tue Nov 10 2015 - 09:39:44 CST)
  • Re: AW: Compilation of NAMD from Source (Cray XC40) (Tue Oct 13 2015 - 17:00:08 CDT)
  • Re: Compilation of NAMD from Source (Cray XC40) (Tue Oct 13 2015 - 10:03:39 CDT)
  • Re: optimising namd ibverb runs (Wed May 20 2015 - 12:28:37 CDT)
  • Re: +p option on Windows 7 (Wed May 20 2015 - 11:58:13 CDT)
  • Re: error while running namd on CRAY XC40 machine (Mon Mar 23 2015 - 13:59:47 CDT)
  • Re: Maximum limit for "run" parameter (Wed Feb 18 2015 - 17:49:41 CST)
  • Re: GPU Multinodes problem (Wed Feb 18 2015 - 17:36:26 CST)
  • Re: Maximum limit for "run" parameter (Wed Feb 18 2015 - 17:10:36 CST)
  • Re: making dipeptides with psfgen - CMAP terms? (Tue Feb 17 2015 - 13:53:04 CST)
  • Re: GBIS in NAMD 2.10 CUDA with IMD (Sat Feb 14 2015 - 12:18:25 CST)
  • Re: PSF generated with PSFGEN [problem in CP2K] - Problem with CGenFF naming? (Thu Feb 12 2015 - 12:32:42 CST)
  • Re: GBIS in NAMD 2.10 CUDA with IMD (Thu Feb 12 2015 - 12:29:25 CST)
  • Re: GBIS in NAMD 2.10 CUDA with IMD (Wed Feb 11 2015 - 10:51:31 CST)
  • Re: namd-1: Simulation Terminating Early (Mon Feb 09 2015 - 13:33:09 CST)
  • Re: on-the-fly parameter introspection (Mon Feb 09 2015 - 13:18:02 CST)
  • Re: Residue number changed to hexadecimal string (Fri Feb 06 2015 - 00:38:00 CST)
  • Re: Editing Patch Grid Dimensions (Thu Feb 05 2015 - 10:32:28 CST)
  • Re: namd-1: Fatal Error: Unable to Open CHARMM Parameter File (Tue Feb 03 2015 - 18:48:35 CST)
  • Re: Message about timing in *log file. (Mon Feb 02 2015 - 00:15:09 CST)
  • Re: NAMD 2.10 with multiple-replica support (Mon Feb 02 2015 - 00:11:26 CST)
  • Re: Is it possible to rename atoms with psfgen? (Thu Jan 29 2015 - 13:11:46 CST)
  • Re: tclBCArgs, passing floating point lists (Thu Jan 22 2015 - 14:27:15 CST)
  • Re: colvars and drude don't play nice? (Fri Jan 16 2015 - 16:57:58 CST)
  • Re: NAMD 2.10 with MVAPICH2-GDR? (Fri Jan 16 2015 - 16:54:35 CST)
  • Re: NAMD slows at startup phase 1 smp problem (Thu Jan 15 2015 - 14:20:58 CST)
  • Re: NAMD slows at startup phase 1 smp problem (Wed Jan 14 2015 - 17:16:19 CST)
  • Re: Tempreture Profile along z axis (Thu Jan 08 2015 - 10:48:58 CST)
  • Re: setting up namd simulation in IBM Blue Gene/L (Fri Dec 19 2014 - 12:55:33 CST)
  • Re: Error compiling NAMD2.9 after patching with PLUMED2.1 (Tue Dec 16 2014 - 09:22:04 CST)
  • Re: Inspiration for most efficient implementation of coarse grained forcefield. (Tue Dec 16 2014 - 09:30:40 CST)
  • Re: Error compiling NAMD2.9 after patching with PLUMED2.1 (Mon Dec 15 2014 - 08:37:26 CST)
  • NAMD 2.10 released (Fri Dec 12 2014 - 16:35:38 CST)
  • Re: Info: Pairlistdist is too small for 3 computes during timestep 115001 (Fri Dec 12 2014 - 15:49:06 CST)
  • Re: colvars angle centerReference (Wed Dec 10 2014 - 07:31:11 CST)
  • RE: Re: alchemical free energy simulations with parmtop (Fri Dec 05 2014 - 14:49:55 CST)
  • RE: Re: alchemical free energy simulations with parmtop (Thu Dec 04 2014 - 11:09:22 CST)
  • Re: Re: alchemical free energy simulations with parmtop (Tue Dec 02 2014 - 12:06:40 CST)
  • Re: running NAMD in parallel (Sat Nov 29 2014 - 16:51:06 CST)
  • Re: Fwd: vmd-l: Re: problems with in text mode towards pdf and pdb files (Fri Nov 21 2014 - 12:50:22 CST)
  • Re: Fwd: vmd-l: Re: problems with in text mode towards pdf and pdb files (Fri Nov 21 2014 - 10:54:20 CST)
  • Re: problems with in text mode towards pdf and pdb files (Fri Nov 21 2014 - 09:56:11 CST)
  • Re: problems with in text mode towards pdf and pdb files (Fri Nov 21 2014 - 09:29:35 CST)
  • Re: Re: about the vdw Interpolation calculation in NAMD source code (Thu Nov 20 2014 - 16:00:29 CST)
  • Re: about the vdw Interpolation calculation in NAMD source code (Thu Nov 20 2014 - 08:29:27 CST)
  • NAMD 2.10b2 released (Mon Nov 17 2014 - 14:22:52 CST)
  • Re: Simulation of a membrane protein with large extracellular domains (Thu Nov 13 2014 - 16:05:08 CST)
  • Re: APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11) (Thu Nov 13 2014 - 15:47:52 CST)
  • Re: AW: FATAL ERROR: error parsing config file while executing <feff> (Mon Nov 10 2014 - 16:00:19 CST)
  • Re: AW: FATAL ERROR: error parsing config file while executing <feff> (Mon Nov 10 2014 - 15:44:39 CST)
  • Re: CUDA Fatal Error While Trying to Run Under Windows 8.1 (Thu Nov 06 2014 - 13:00:35 CST)
  • Re: Multiple input and output files (Thu Nov 06 2014 - 12:50:36 CST)
  • Re: Reg: error in log file (Thu Oct 30 2014 - 10:46:01 CDT)
  • Re: which namd versions compatible with CUDA 5.5 and other CUDA woes (Fri Sep 26 2014 - 17:25:29 CDT)
  • Re: getting different dihedral energy with two identical backbones (Fri Sep 26 2014 - 17:18:24 CDT)
  • Re: GBIS using CUDA enabled NAMD (Wed Sep 10 2014 - 16:32:32 CDT)
  • Re: AW: AW: Question to NAMD source (Mon Sep 08 2014 - 08:43:00 CDT)
  • Re: GBIS CUDA not yet compatible with fixed atoms (Fri Sep 05 2014 - 15:16:04 CDT)
  • Re: AW: Question to NAMD source (Fri Sep 05 2014 - 14:34:55 CDT)
  • Re: Question to NAMD source (Thu Sep 04 2014 - 11:25:48 CDT)
  • Re: efficient way to apply time-dependent electric field (Thu Sep 04 2014 - 11:18:00 CDT)
  • Re: Combining interleaved and top posting is considered harmful. (Thu Aug 28 2014 - 11:29:10 CDT)
  • Re: (Tue Aug 26 2014 - 10:38:36 CDT)
  • Re: NAMD 2.10b1 CUDA PME offload (Tue Aug 26 2014 - 10:22:48 CDT)
  • NAMD 2.10b1 released (Mon Aug 25 2014 - 07:49:51 CDT)
  • posting from Yahoo addresses disabled (Tue Apr 08 2014 - 17:45:15 CDT)
• jing liang
  • applying a force to some atoms (Sat Jun 27 2015 - 06:22:02 CDT)
• Jo, Sunhwan
  • Re: Cost of a colvar calculation (Tue Jul 22 2014 - 19:02:20 CDT)
  • Re: Cost of a colvar calculation (Tue Jul 22 2014 - 13:06:12 CDT)
• Joaquim Rui de Castro Rodrigues
  • RE: change in pdb.. (Wed Jun 11 2014 - 13:03:18 CDT)
• Joel Moniz
  • Re: AW: Regarding NAMD and MD simulations (Tue Jul 08 2014 - 22:17:19 CDT)
  • Regarding NAMD and MD simulations (Mon Jul 07 2014 - 01:42:04 CDT)
• John Stone
  • Re: vmd-l: Re: On-the-fly modification of tclforces script? (Fri Nov 13 2015 - 20:17:53 CST)
  • Re: vmd-l: Re: On-the-fly modification of tclforces script? (Fri Nov 13 2015 - 19:05:34 CST)
  • Re: vmd-l: script error (Fri Oct 02 2015 - 10:10:56 CDT)
  • Re: vmd-l: Which VMD AND NAMD should install (Tue Sep 22 2015 - 14:07:17 CDT)
  • Re: vmd-l: Re: velocity IO with psfgen? (Thu Feb 26 2015 - 12:47:52 CST)
  • Re: vmd-l: Re: velocity IO with psfgen? (Thu Feb 26 2015 - 11:03:15 CST)
  • Re: vmd-l: velocity IO with psfgen? (Thu Feb 26 2015 - 10:24:36 CST)
  • Re: vmd-l: GBIS in NAMD 2.10 CUDA with IMD (Wed Feb 11 2015 - 10:03:39 CST)
  • Re: vmd-l: NAMD energy calculation (Mon Jun 30 2014 - 22:59:28 CDT)
  • Re: vmd-l: citing SODIUM program (Tue Jan 14 2014 - 09:19:27 CST)
• John Xi
  • Re: How to setup a system with two pulling directions (Thu Apr 17 2014 - 19:48:39 CDT)
  • How to setup a system with two pulling directions (Wed Apr 16 2014 - 19:32:27 CDT)
  • Re: AW: residue_rmsd.tcl segmentation fault (Fri Apr 04 2014 - 07:04:45 CDT)
  • residue_rmsd.tcl segmentation fault (Thu Apr 03 2014 - 21:49:05 CDT)
• Johny Telecaster
  • Re: Two GPU-based workstation (Mon Mar 17 2014 - 02:38:56 CDT)
  • Accelerated Molecular Dynamics logs (Sat Mar 08 2014 - 09:37:05 CST)
• Jonasson Gabriella
  • FEP, big variations in dG within a window (Mon Jan 05 2015 - 09:44:31 CST)
• Jonathan Phillips
  • Re: full electrostatics and pairlistdist (Fri Apr 18 2014 - 05:51:02 CDT)
  • full electrostatics and pairlistdist (Mon Apr 14 2014 - 16:25:04 CDT)
• Jose Borreguero
  • Re: problems compiling NAMD with mpicxx from mvapich2 (Mon Jan 26 2015 - 08:27:41 CST)
  • problems compiling NAMD with mpicxx from mvapich2 (Sat Jan 24 2015 - 11:49:02 CST)
  • Newbie GPU user, please help with my submission line (Thu Oct 02 2014 - 14:03:24 CDT)
  • Re: expected speed up after fixing atoms? (Wed Sep 24 2014 - 14:26:06 CDT)
  • Re: expected speed up after fixing atoms? (Wed Sep 24 2014 - 13:41:02 CDT)
  • expected speed up after fixing atoms? (Wed Sep 24 2014 - 12:44:48 CDT)
• Joseph Farran
  • Re: AW: NAMD and NUMA (Thu May 08 2014 - 11:33:25 CDT)
  • Re: AW: NAMD and NUMA (Thu May 08 2014 - 11:28:46 CDT)
  • NAMD and NUMA (Wed May 07 2014 - 13:54:51 CDT)
• Josh Vermaas
  • Re: Add ions/molecules different from Autoionize defaults (Sun Dec 27 2015 - 06:25:50 CST)
  • Re: Problems with GLUP and ASPP with CHARMM36 (Fri Dec 11 2015 - 09:25:11 CST)
  • Re: Problems with GLUP and ASPP with CHARMM36 (Fri Dec 11 2015 - 08:45:00 CST)
  • Re: error when use Charmm_Gui prepared *.inp for NAMD (Thu Dec 03 2015 - 08:50:36 CST)
  • Re: pdb files to dcd (Tue Nov 03 2015 - 14:40:53 CST)
  • Re: Problem with tcl intepreter (Thu Oct 29 2015 - 19:45:12 CDT)
  • Re: Fwd: ANGLE PARAMETERS FOR NH3 HC NH3 (Tue Oct 27 2015 - 11:24:47 CDT)
  • Re: How to calculate the temperature for a subset of my simulation (Tue Oct 20 2015 - 14:03:32 CDT)
  • Re: NAMD - wrap atoms, not center of mass (Fri Oct 16 2015 - 10:48:35 CDT)
  • Re: BONDS vs DOUBLE in topology file (Fri Oct 09 2015 - 09:46:07 CDT)
  • Re: charm36 for ATP and MG (Tue Sep 08 2015 - 11:13:19 CDT)
  • Re: "UNABLE TO FIND BOND PARAMETERS" but bond is defined in stream file (Fri Sep 04 2015 - 10:29:38 CDT)
  • Re: Problem with iron ion (FE2+) (Mon Aug 24 2015 - 14:17:20 CDT)
  • Re: backbone constraint (Wed Jul 22 2015 - 08:59:48 CDT)
  • Re: extra bonds (Fri Jul 03 2015 - 09:08:25 CDT)
  • Re: extra bonds (Thu Jul 02 2015 - 09:48:22 CDT)
  • Re: Pressure coupling options (Sat Jun 27 2015 - 19:36:17 CDT)
  • Re: Re: run on sungle node (Wed Jun 24 2015 - 11:14:16 CDT)
  • Re: Combining parameter files from CHARMM (Mon Jun 15 2015 - 11:10:43 CDT)
  • Re: Force-field for DOPI lipid (Sun May 24 2015 - 08:27:46 CDT)
  • Re: atom types in PSF/PRM/RTF (Fri May 22 2015 - 09:55:44 CDT)
  • Re: Restarting trajectories (Wed May 20 2015 - 11:07:42 CDT)
  • Re: Calculation of PMF between protein domains NAMD (Fri Apr 17 2015 - 17:54:37 CDT)
  • Re: Calculation of PMF between protein domains NAMD (Fri Apr 17 2015 - 17:43:49 CDT)
  • Re: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OC2D2 (Wed Mar 18 2015 - 17:42:03 CDT)
  • Re: DCD Error (Wed Mar 18 2015 - 10:06:43 CDT)
  • Re: DCD Error (Wed Mar 18 2015 - 09:36:52 CDT)
  • Re: Reg: solvating in a non-standard solvent (Wed Mar 18 2015 - 09:08:24 CDT)
  • Re: Dihedral definition in NAMD (Tue Mar 10 2015 - 13:32:12 CDT)
  • Re: Dihedral definition in NAMD (Tue Mar 10 2015 - 09:30:21 CDT)
  • Re: Dihedral definition in NAMD (Tue Mar 10 2015 - 09:14:27 CDT)
  • Re: Histidine C-H---O hydrogen bonding (Thu Jan 29 2015 - 09:21:27 CST)
  • Re: Re: Constant Pressure, Variable Volume, Minimization (Thu Dec 18 2014 - 13:17:35 CST)
  • Re: Transferring bond list to new molecule (Wed Dec 17 2014 - 08:18:18 CST)
  • Re: query about the cross term in psf (Sat Dec 06 2014 - 14:22:32 CST)
  • Re: query about the cross term in psf (Sat Dec 06 2014 - 13:49:06 CST)
  • Re: information about simulation speed (Tue Dec 02 2014 - 17:08:55 CST)
  • Re: Fwd: vmd-l: Re: problems with in text mode towards pdf and pdb files (Fri Nov 21 2014 - 10:54:56 CST)
  • Re: Atomselect for coor, vel, xsc (Fri Nov 14 2014 - 08:58:29 CST)
  • Re: Simulation of a membrane protein with large extracellular domains (Thu Nov 13 2014 - 08:35:43 CST)
  • Re: SOD topology with CHARMM36 (Tue Nov 11 2014 - 11:08:26 CST)
  • Re: Multiple input and output files (Wed Nov 05 2014 - 20:54:02 CST)
  • Re: running a calculation during simulation (Mon Oct 20 2014 - 16:38:57 CDT)
  • Re: NAMD and usable FFs (Thu Oct 16 2014 - 13:05:27 CDT)
  • Re: NAMD and usable FFs (Wed Oct 15 2014 - 09:20:08 CDT)
  • Re: Problem with running namdenergy plugin from text interface (Mon Sep 22 2014 - 15:09:10 CDT)
• Joshua Adelman
  • Re: how to quantify and visualize the flow of water into a protein (Tue Jul 08 2014 - 19:36:02 CDT)
• jostmey .
  • Re: Alchemical FEP calculation involving glycine (Wed Mar 11 2015 - 17:57:02 CDT)
  • Alchemical FEP calculation involving glycine (Mon Mar 09 2015 - 23:58:31 CDT)
  • Re: Alchemical FEP calculations in Implicit Solvent (Mon Feb 23 2015 - 14:45:13 CST)
  • Re: Alchemical FEP calculations in Implicit Solvent (Mon Feb 23 2015 - 13:21:57 CST)
  • Alchemical FEP calculations in Implicit Solvent (Mon Feb 23 2015 - 13:04:15 CST)
• José Villalaín
  • Membrane and NPAT (Mon Feb 17 2014 - 04:49:08 CST)
• Joyce Yang
  • Re: getting different dihedral energy with two identical backbones (Mon Sep 29 2014 - 21:15:54 CDT)
  • getting different dihedral energy with two identical backbones (Wed Sep 24 2014 - 16:45:52 CDT)
• Juan R. Perilla
  • Re: vmd-l: Accelerated MD (aMD) (Sun Jul 27 2014 - 20:23:00 CDT)
• Julian Gamboa
  • Re: charm36 for ATP and MG (Tue Sep 08 2015 - 11:19:03 CDT)
• Justin Sanders
  • CUDA Fatal Error While Trying to Run Under Windows 8.1 (Thu Nov 06 2014 - 12:01:58 CST)
• Jérôme Hénin
  • Re: extendedLagrangian for non-scalar colvar (Thu Dec 10 2015 - 11:18:39 CST)
  • Re: Determining the PMF with Adaptive Biasing Forces (Tue Dec 08 2015 - 09:09:58 CST)
  • Re: DOF during alchemical simulations (Fri Nov 27 2015 - 03:31:25 CST)
  • Re: DOF during alchemical simulations (Thu Nov 26 2015 - 12:00:01 CST)
  • Re: FEP using separated topologies (Thu Nov 12 2015 - 08:48:12 CST)
  • Re: ABF error on NAMD 2.10 (Mon Nov 02 2015 - 07:47:25 CST)
  • Re: keyword "outputaccumulatedwork" is not supported, or not recognized in this context. (Thu Oct 15 2015 - 01:43:25 CDT)
  • Re: keyword "outputaccumulatedwork" is not supported, or not recognized in this context. (Wed Oct 14 2015 - 05:14:41 CDT)
  • Re: keyword "outputaccumulatedwork" is not supported, or not recognized in this context. (Wed Oct 14 2015 - 05:05:54 CDT)
  • Re: Outward tilting which colvar to use (Thu Oct 01 2015 - 07:11:45 CDT)
  • Re: NAMD Anisotropic pressure control (Fri Sep 18 2015 - 09:44:50 CDT)
  • Re: Thermodynamic integration question (Mon Sep 07 2015 - 01:44:15 CDT)
  • Re: Format of colvars.state (Thu Aug 27 2015 - 04:27:00 CDT)
  • Re: Format of colvars.state (Mon Aug 24 2015 - 13:04:50 CDT)
  • Re: Tilt angle clockwise rotation (Wed Jul 22 2015 - 11:04:55 CDT)
  • Re: Debugging and Force Checking? (Mon Jul 20 2015 - 12:42:20 CDT)
  • Re: applying a force to some atoms (Sun Jun 28 2015 - 15:54:42 CDT)
  • Re: RE: error in writing colvars state file (Fri Jun 05 2015 - 05:33:07 CDT)
  • Re: Colvars Boundary potentials do not look harmonic (Wed Jun 03 2015 - 10:15:04 CDT)
  • Re: NAMD nightly build compilation (Thu May 07 2015 - 09:11:53 CDT)
  • Re: atom ID in VMD and NAMD (Mon May 04 2015 - 04:52:06 CDT)
  • Re: Patches for namd 2.10 (Fri Apr 24 2015 - 04:38:39 CDT)
  • Re: strange behavior of ABF (Tue Apr 14 2015 - 07:06:47 CDT)
  • Re: Daily cron stalls running NAMD outputs (Wed Apr 08 2015 - 03:16:22 CDT)
  • Re: Minimisation not converged (Thu Apr 02 2015 - 06:52:36 CDT)
  • Re: Minimisation not converged (Wed Apr 01 2015 - 02:14:12 CDT)
  • Re: Enerygy Minimization of a homology modelled structure in NAMD (Wed Apr 01 2015 - 02:07:59 CDT)
  • Re: Restraining angle between bond vector and coordinate vector (Mon Mar 23 2015 - 15:45:02 CDT)
  • Re: Dihedral calculation with colvars (Fri Mar 13 2015 - 09:42:21 CDT)
  • Re: Colvar with variable axis (Thu Mar 12 2015 - 08:53:45 CDT)
  • Re: Dihedral calculation with colvars (Thu Mar 12 2015 - 06:29:22 CDT)
  • Re: Dihedral calculation with colvars (Thu Mar 12 2015 - 05:27:07 CDT)
  • Re: Alchemical FEP calculation involving glycine (Thu Mar 12 2015 - 04:26:18 CDT)
  • Re: How to let NAMD terminate automatically at a given time (Mon Mar 02 2015 - 11:12:40 CST)
  • Re: Questions about lambda scheme in free energy perturbation (Tue Feb 24 2015 - 16:18:21 CST)
  • Re: Aggregation related analysis scripts (Tue Feb 24 2015 - 09:39:01 CST)
  • Re: about angles in coordination complexes (Mon Jan 26 2015 - 10:50:35 CST)
  • Re: about angles in coordination complexes (Mon Jan 26 2015 - 10:20:37 CST)
  • Re: about angles in coordination complexes (Mon Jan 26 2015 - 09:56:07 CST)
  • Re: FEP Restart file (Wed Jan 21 2015 - 08:57:20 CST)
  • Re: NAMD Non-features (Wed Jan 21 2015 - 04:38:17 CST)
  • Re: Multiple Dihedral in CHARMM parameters (Mon Jan 19 2015 - 04:57:07 CST)
  • Re: Fwd: colvars: keyword "name" is not supported, or not recognized in this context. (Thu Jan 15 2015 - 10:34:22 CST)
  • Re: is there a method equivalent to conformational flooding in NAMD 2.10 (Mon Jan 12 2015 - 04:44:58 CST)
  • Re: Inspiration for most efficient implementation of coarse grained forcefield. (Mon Dec 15 2014 - 15:41:22 CST)
  • Re: colvar DistanceZ (Wed Nov 26 2014 - 07:35:37 CST)
  • Re: colvar DistanceZ (Wed Nov 26 2014 - 05:07:19 CST)
  • Re: tilt colvar (Mon Nov 24 2014 - 15:09:14 CST)
  • Re: tilt colvar (Mon Nov 24 2014 - 08:46:48 CST)
  • Re: tilt colvar (Sat Nov 22 2014 - 06:00:10 CST)
  • Re: Colvar: minimal distance between 2 groups of atoms (Mon Nov 17 2014 - 13:13:07 CST)
  • Re: Colvar: minimal distance between 2 groups of atoms (Mon Nov 17 2014 - 10:07:38 CST)
  • Re: colvars fatal error (Wed Nov 05 2014 - 02:54:43 CST)
  • Re: running a calculation during simulation (Tue Oct 21 2014 - 04:03:13 CDT)
  • Re: Parameter colvars (Mon Oct 06 2014 - 10:01:52 CDT)
  • Re: Does NAMD have some way to test the result? (Sat Oct 04 2014 - 04:20:57 CDT)
  • Re: FATAL ERROR: Setting parameter colvars from script failed! (Tue Sep 30 2014 - 13:28:48 CDT)
  • Re: FATAL ERROR: Setting parameter colvars from script failed! (Tue Sep 30 2014 - 13:04:27 CDT)
  • Re: FATAL ERROR: Setting parameter colvars from script failed! (Tue Sep 30 2014 - 10:17:02 CDT)
  • Re: ABF with the RMSD colvar (Mon Sep 22 2014 - 08:37:00 CDT)
  • Re: ABF with the RMSD colvar (Fri Sep 19 2014 - 10:46:45 CDT)
  • Re: ABF with the RMSD colvar (Wed Sep 17 2014 - 07:13:05 CDT)
  • Re: Colvars simulation running slow? (Wed Sep 10 2014 - 02:13:00 CDT)
  • Re: ABF simulation, free energy to remove a DNA strand (Tue Aug 05 2014 - 03:15:46 CDT)
  • Re: (Tue Jul 22 2014 - 12:21:26 CDT)
  • Re: (Tue Jul 22 2014 - 11:57:54 CDT)
  • Re: ABF/colvar error in NAMD2.9 (Tue Jul 22 2014 - 11:56:06 CDT)
  • Re: ABF/colvar error in NAMD2.9 (Tue Jul 22 2014 - 11:29:47 CDT)
  • Re: Cost of a colvar calculation (Tue Jul 22 2014 - 11:20:56 CDT)
  • Re: Cost of a colvar calculation (Tue Jul 22 2014 - 07:43:30 CDT)
  • Re: Cost of a colvar calculation (Tue Jul 22 2014 - 06:56:42 CDT)
  • Re: Inquiry about forceConstant (Tue Jul 22 2014 - 04:37:30 CDT)
  • Re: FixedAtoms and Reference group in spinangle colvar (Thu May 22 2014 - 07:00:25 CDT)
  • Re: FixedAtoms and Reference group in spinangle colvar (Fri May 09 2014 - 13:53:56 CDT)
  • Re: PMF from ABF simulation not plateauing (Thu May 08 2014 - 17:37:20 CDT)
  • Re: Colvars keyword problem (Mon May 05 2014 - 10:01:03 CDT)
  • Re: Excluding non bonded interactions between segments (Tue Apr 08 2014 - 06:56:22 CDT)
  • Re: Excluding non bonded interactions between segments (Wed Apr 02 2014 - 08:09:21 CDT)
  • Re: Assigning different temperatures to simulation (Wed Apr 02 2014 - 03:16:30 CDT)
  • Re: Assigning different temperatures to simulation (Wed Apr 02 2014 - 02:35:40 CDT)
  • Re: question (Mon Mar 31 2014 - 12:26:01 CDT)
  • Re: ABF simulation fails with "FATAL ERROR: Low global exclusion count!" (Fri Feb 28 2014 - 11:58:59 CST)
  • Re: Free Energy Perturbation (Thu Feb 27 2014 - 07:05:00 CST)
  • Re: ABF force distribution (Thu Feb 27 2014 - 06:59:48 CST)
• K Miura
  • Residue number changed to hexadecimal string (Thu Feb 05 2015 - 23:34:24 CST)
  • Running Charmrun/NAMD with more than 10 processes fails (Tue Dec 16 2014 - 02:53:36 CST)
• Kanzliersch, Lukas
  • Verification of NAMD Results (Wed Aug 05 2015 - 15:32:38 CDT)
• Kapil jain
  • Accelerated molecular dynamics: Energy value in output file (Tue Aug 19 2014 - 23:53:20 CDT)
  • Re: Energy term in output file of Accelerated dynamics (Sun Aug 10 2014 - 21:39:32 CDT)
  • Energy term in output file of Accelerated dynamics (Fri Aug 08 2014 - 02:14:56 CDT)
• Kasra Fattah
  • Re: ABF force distribution (Sat Mar 01 2014 - 18:20:11 CST)
  • ABF force distribution (Thu Feb 13 2014 - 14:56:42 CST)
• Katherine Parra
  • Unsubscribe (Wed Sep 10 2014 - 09:12:24 CDT)
  • Unsubscribe (Sun Aug 10 2014 - 11:30:22 CDT)
• Katherine Parra Pulido
  • CAN'T FIND DIHEDRAL PARAMETERS FOR CPH1 NR2 FE NPH (Mon Jan 06 2014 - 23:33:49 CST)
• Kenneth Huang
  • Re: MD Simulation of accelerated MD using GPU (Mon Oct 12 2015 - 20:09:26 CDT)
• Kenno Vanommeslaeghe
  • Re: namd simulation for solids withoy solvation (Thu Nov 13 2014 - 11:50:51 CST)
  • Re: Dioxygen atom type with CHARMM36 (Tue Nov 11 2014 - 14:19:40 CST)
  • Re: Dioxygen atom type with CHARMM36 (Tue Nov 11 2014 - 12:46:48 CST)
  • Re: SOD topology with CHARMM36 (Tue Nov 11 2014 - 12:27:08 CST)
  • Re: Dioxygen atom type with CHARMM36 (Tue Nov 11 2014 - 11:07:25 CST)
  • Re: 1-5 Intramolecular repulsions (Wed Nov 05 2014 - 12:33:12 CST)
  • Re: explicit membrane in implicit solvent (Mon Nov 03 2014 - 10:46:24 CST)
  • Re: Why RDF increases as r increase instead of constant (Sun Nov 02 2014 - 18:25:41 CST)
  • Re: Why RDF increases as r increase instead of constant (Sun Nov 02 2014 - 12:38:04 CST)
  • Re: NAMD and usable FFs (Fri Oct 17 2014 - 11:15:18 CDT)
  • Re: NAMD and usable FFs (Thu Oct 16 2014 - 17:53:13 CDT)
  • Re: NAMD and usable FFs (Thu Oct 16 2014 - 13:45:05 CDT)
  • Re: NAMD and usable FFs (Thu Oct 16 2014 - 13:37:11 CDT)
  • Re: Re: vmd-l: making psf files (Mon Oct 13 2014 - 12:18:31 CDT)
  • Re: Folic acid parameters (Tue Sep 30 2014 - 11:37:03 CDT)
  • Re: Folic acid parameters (Tue Sep 30 2014 - 10:43:21 CDT)
  • Re: Molecular Dynamics of Rigid Linear Molecules in NAMD. (Sun Sep 28 2014 - 14:00:43 CDT)
  • Re: Molecular Dynamics of Rigid Linear Molecules in NAMD. (Sun Sep 28 2014 - 13:06:06 CDT)
  • Re: expected speed up after fixing atoms? (Wed Sep 24 2014 - 14:06:46 CDT)
  • Re: Implicit solvent lipid bilayer simulation in NAMD. (Thu Sep 18 2014 - 15:39:49 CDT)
  • Re: Unable to read corrupted binary DCD trajectory file (Mon Sep 08 2014 - 16:38:48 CDT)
  • Re: Unable to read corrupted binary DCD trajectory file (Mon Sep 08 2014 - 13:08:11 CDT)
  • Re: Unable to read corrupted binary DCD trajectory file (Mon Sep 08 2014 - 11:56:01 CDT)
  • Re: Fwd: Reg: solvation in DMSO (Wed Sep 03 2014 - 14:43:59 CDT)
  • Re: restraining bonds (Tue Sep 02 2014 - 11:04:37 CDT)
  • Re: Fixing atoms while equilibration (Mon Sep 01 2014 - 10:52:07 CDT)
  • Re: restraining bonds (Mon Sep 01 2014 - 10:37:17 CDT)
  • Re: Nucleic acid stains parameters (Mon Aug 25 2014 - 10:56:26 CDT)
  • Re: using CHARMM-format Amber parameters in NAMD (Wed Aug 20 2014 - 10:27:20 CDT)
  • Re: NVT, NPT, order & combination (Tue Aug 19 2014 - 12:17:27 CDT)
  • Re: Kb, Ktheta values for TIP3P water model (Tue Aug 12 2014 - 13:31:04 CDT)
  • Re: Kb, Ktheta values for TIP3P water model (Mon Aug 11 2014 - 14:08:41 CDT)
  • Re: Kb, Ktheta values for TIP3P water model (Sun Aug 10 2014 - 23:16:19 CDT)
  • Re: Kb, Ktheta values for TIP3P water model (Sun Aug 10 2014 - 22:10:43 CDT)
  • Re: Kb, Ktheta values for TIP3P water model (Sun Aug 10 2014 - 17:49:01 CDT)
  • Re: Kb, Ktheta values for TIP3P water model (Thu Aug 07 2014 - 15:08:39 CDT)
  • Re: Kb, Ktheta values for TIP3P water model (Thu Aug 07 2014 - 10:50:24 CDT)
  • Re: Kb, Ktheta values for TIP3P water model (Wed Aug 06 2014 - 17:28:12 CDT)
  • Re: Kb, Ktheta values for TIP3P water model (Tue Aug 05 2014 - 15:00:49 CDT)
  • Re: Kb, Ktheta values for TIP3P water model (Tue Aug 05 2014 - 14:29:22 CDT)
  • Re: Kb, Ktheta values for TIP3P water model (Tue Aug 05 2014 - 13:41:12 CDT)
  • Re: Kb, Ktheta values for TIP3P water model (Tue Aug 05 2014 - 09:54:35 CDT)
  • Re: Intermolecular potential energy function in NAMD (Fri Aug 01 2014 - 11:41:46 CDT)
  • Re: Kb, Ktheta values for TIP3P water model (Thu Jul 31 2014 - 17:28:09 CDT)
  • Re: Kb, Ktheta values for TIP3P water model (Thu Jul 31 2014 - 14:03:00 CDT)
  • Re: Kb, Ktheta values for TIP3P water model (Tue Jul 29 2014 - 23:21:58 CDT)
  • Re: temperature for lipid-protein assembly (Mon Jul 28 2014 - 13:33:00 CDT)
  • Re: temperature for lipid-protein assembly (Mon Jul 28 2014 - 12:40:18 CDT)
  • Re: temperature for lipid-protein assembly (Mon Jul 28 2014 - 10:57:41 CDT)
  • Re: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR C NH3 (ATOMS 105 107) (Fri Jul 25 2014 - 16:44:15 CDT)
  • 2-residue patch for Asn-Lys side chain amide bond (Fri Jul 25 2014 - 12:20:46 CDT)
  • 2-residue patch for hydrocarbon staple (Thu Jul 24 2014 - 15:48:52 CDT)
  • Re: Force field design (Thu Jul 24 2014 - 11:12:18 CDT)
  • Re: Force field design (Wed Jul 23 2014 - 18:20:53 CDT)
  • Re: (Tue Jul 22 2014 - 11:58:25 CDT)
  • Re: Force field design (Tue Jul 22 2014 - 10:40:37 CDT)
  • Re: Force field design (Mon Jul 21 2014 - 10:47:12 CDT)
  • Re: Subject: Re: Subject: Re:Re: New partial charges after patching (Wed Jul 16 2014 - 12:53:47 CDT)
  • Re: Re: NADH topology file (Wed Jul 16 2014 - 12:39:02 CDT)
  • Re: Force field design (Wed Jul 16 2014 - 12:24:29 CDT)
  • Re: Force field design (Wed Jul 16 2014 - 12:06:23 CDT)
  • Re: NADH topology file (Tue Jul 15 2014 - 09:44:10 CDT)
  • Re: (Mon Jul 14 2014 - 15:58:25 CDT)
  • Re: Subject: Re:Re: New partial charges after patching (Fri Jul 11 2014 - 12:19:21 CDT)
  • Re: accelerated MD as the engine for loop refirement (Thu Jul 10 2014 - 17:32:38 CDT)
  • Re: two O atoms in CTER are unusually close (Thu Jul 10 2014 - 17:28:08 CDT)
  • Re: Constraint failure in RATTLE algorithm (Fri Jun 27 2014 - 10:37:19 CDT)
  • Re: Restraints between ion and small molecule (Thu Jun 26 2014 - 14:43:47 CDT)
  • Re: Restraints between ion and small molecule (Thu Jun 26 2014 - 13:21:42 CDT)
  • Re: Restraints between ion and small molecule (Thu Jun 26 2014 - 13:16:31 CDT)
  • Re: AW: Xeon vs i7 and ECC vs SDRAM (Wed Jun 25 2014 - 10:26:26 CDT)
  • Re: How to apply a magnetic field with NAMD (Wed Jun 25 2014 - 10:08:11 CDT)
  • Re: ffTK and phase angles (Thu Jun 19 2014 - 20:01:05 CDT)
  • Re: Subject: Re:Re: New partial charges after patching (Thu Jun 19 2014 - 10:11:28 CDT)
  • Re: Inquiry about lipid membrane simulation (Wed Jun 18 2014 - 14:02:52 CDT)
  • Re: Inquiry about lipid membrane simulation (Wed Jun 18 2014 - 10:20:24 CDT)
  • Re: Reg : MD simulation with DMSO instead of water (Tue Jun 17 2014 - 13:13:02 CDT)
  • Re: New partial charges after patching (Mon Jun 16 2014 - 10:23:02 CDT)
  • Re: About converting NAMD dcd file into CHARMM dcd file (Fri Jun 13 2014 - 21:18:52 CDT)
  • Re: Ion Au+3 simulation (Thu Jun 05 2014 - 17:27:37 CDT)
  • Re: NAMD energy plugin (Wed Jun 04 2014 - 14:16:48 CDT)
  • Re: NAMD energy plugin (Wed Jun 04 2014 - 14:10:39 CDT)
  • Re: Ion Au+3 simulation (Wed Jun 04 2014 - 10:32:46 CDT)
  • Re: Rapid and accurate parameterization of new molecules in CHARMM (Wed May 28 2014 - 10:35:07 CDT)
  • Re: Rapid and accurate parameterization of new molecules in CHARMM (Tue May 27 2014 - 17:58:42 CDT)
  • Re: IMPROPER PARAMETERS FOR CA CA CA CA (Mon May 26 2014 - 16:42:29 CDT)
  • Re: Polymer Layer/ Cutoff (Thu May 15 2014 - 18:00:42 CDT)
  • Re: Polymer Layer/ Cutoff (Thu May 15 2014 - 14:34:00 CDT)
  • Re: Polymer Layer/ Cutoff (Thu May 15 2014 - 11:58:43 CDT)
  • Re: AW: NAMD and NUMA (Mon May 12 2014 - 12:06:53 CDT)
  • Re: Using the CHARMM36 forcefield with NAMD (Fri May 09 2014 - 11:50:45 CDT)
  • Re: AW: AW: NAMD and NUMA (Fri May 09 2014 - 11:45:09 CDT)
  • Re: error while making psf file for bacteriorhodopsin system (Fri May 09 2014 - 11:38:08 CDT)
  • Re: error while making psf file for bacteriorhodopsin system (Thu May 08 2014 - 15:57:52 CDT)
  • Re: Getting extra atoms by Patching! (Thu May 08 2014 - 12:38:10 CDT)
  • Re: Setting up membrane protein simulation from existing conformation? (Wed May 07 2014 - 14:44:00 CDT)
  • Re: Topology for lysine bouding in Epsilon (Wed May 07 2014 - 10:33:16 CDT)
  • Re: Topology for lysine bouding in Epsilon (Tue May 06 2014 - 14:04:37 CDT)
  • Re: Patch to connect monomers code (Tue May 06 2014 - 13:33:49 CDT)
  • Re: Topology for lysine bouding in Epsilon (Tue May 06 2014 - 13:06:38 CDT)
  • Re: Topology for lysine bouding in Epsilon (Mon May 05 2014 - 15:07:31 CDT)
  • Re: Force field for sulfated tyrosines (Mon May 05 2014 - 13:11:47 CDT)
  • Re: Patch to connect monomers code (Mon May 05 2014 - 13:11:36 CDT)
  • Re: Getting extra atoms by Patching! (Mon May 05 2014 - 11:45:48 CDT)
  • Re: Teflon New Residue (Fri May 02 2014 - 12:21:09 CDT)
  • Re: Using the CHARMM36 forcefield with NAMD (Wed Apr 23 2014 - 12:28:33 CDT)
  • Re: peptide tends to migrate out the water box (Fri Apr 18 2014 - 10:27:09 CDT)
  • Re: (Tue Apr 15 2014 - 12:14:07 CDT)
  • Re: Nanotube Simulation (Tue Apr 15 2014 - 12:13:14 CDT)
  • Re: Nanotube Simulation (Mon Apr 14 2014 - 12:33:58 CDT)
  • Re: MMPBSA Energy Calculations using VMD (Post-Processing) (Mon Apr 14 2014 - 12:24:33 CDT)
  • Re: Nanotube Simulation (Fri Apr 11 2014 - 17:18:18 CDT)
  • Re: Multiple dihedral with multiplicity of 7 greater than max of 6 (Wed Apr 02 2014 - 14:05:49 CDT)
  • Re: force field parameter for graphene oxide (Fri Mar 07 2014 - 11:28:50 CST)
  • Re: How to maintain Density constant? (Thu Mar 06 2014 - 12:39:08 CST)
  • Re: How to maintain Density constant? (Thu Mar 06 2014 - 10:55:28 CST)
  • Re: How to maintain Density constant? (Thu Mar 06 2014 - 09:57:24 CST)
  • Re: VDW energy: positive or negative? (Wed Mar 05 2014 - 17:21:12 CST)
  • Re: How to maintain Density constant? (Wed Mar 05 2014 - 16:51:30 CST)
  • Re: VDW energy: positive or negative? (Tue Mar 04 2014 - 19:14:15 CST)
  • Re: VDW energy: positive or negative? (Tue Mar 04 2014 - 17:50:50 CST)
  • Re: How to stop omega trans-cis switching (Mon Mar 03 2014 - 13:01:10 CST)
  • Re: Apply magnetic field through TCLBC (Mon Mar 03 2014 - 11:33:06 CST)
  • Re: NAMD 2.9 Changing/Replacing atoms in multiple molecules (Fri Feb 21 2014 - 12:38:25 CST)
  • Re: tools for Charmm (Thu Feb 20 2014 - 14:06:28 CST)
  • Re: tools for Charmm (Thu Feb 20 2014 - 13:59:02 CST)
  • Re: tools for Charmm (Thu Feb 20 2014 - 13:05:13 CST)
  • Re: Charmm (Thu Feb 20 2014 - 12:53:55 CST)
  • Re: Charmm (Thu Feb 20 2014 - 10:40:41 CST)
  • Re: AW: Dihedrals multiplicity! (Thu Feb 20 2014 - 10:35:55 CST)
  • Re: tools for Charmm (Thu Feb 20 2014 - 10:16:40 CST)
  • Re: CHARMM36 and NAMD (Tue Feb 18 2014 - 20:23:37 CST)
  • Re: AW: Dihedrals multiplicity! (Tue Feb 18 2014 - 20:12:14 CST)
  • Re: FAD topology and parameters (Tue Feb 18 2014 - 20:01:28 CST)
  • Re: AW: Dihedrals multiplicity! (Mon Feb 17 2014 - 12:44:19 CST)
  • Re: AW: Dihedrals multiplicity! (Mon Feb 17 2014 - 10:56:29 CST)
  • Re: Membrane and NPAT (Mon Feb 17 2014 - 10:43:03 CST)
  • Re: AW: Dihedrals multiplicity! (Sun Feb 16 2014 - 12:45:16 CST)
  • Re: AW: Dihedrals multiplicity! (Sat Feb 15 2014 - 22:15:33 CST)
  • Re: AW: Dihedrals multiplicity! (Sat Feb 15 2014 - 11:30:42 CST)
  • Re: AW: moving out of the box (Fri Feb 14 2014 - 13:15:37 CST)
  • Re: AW: Dihedrals multiplicity! (Thu Feb 13 2014 - 19:48:12 CST)
  • Re: AW: Dihedrals multiplicity! (Thu Feb 13 2014 - 17:53:49 CST)
• Kevin C Chan
  • Bubble in water during membrane simulations (Mon Nov 16 2015 - 02:12:29 CST)
  • SMD or moving contraints (Thu Oct 15 2015 - 21:50:20 CDT)
  • Re: namd ibverbs (Thu Jul 23 2015 - 05:38:49 CDT)
  • Compilation with OpenMPI (Mon Jul 20 2015 - 05:02:10 CDT)
  • Compilation with OpenMPI (Tue Jul 14 2015 - 00:11:38 CDT)
  • Compilation with OpenMPI (Sun Jul 12 2015 - 01:13:30 CDT)
  • Pressure coupling options (Fri Jun 26 2015 - 23:32:05 CDT)
  • Minimisation goes to several values (Thu Jun 25 2015 - 11:32:10 CDT)
  • Re: Remembering resid (Thu Jun 18 2015 - 11:48:50 CDT)
  • Remembering resid (Thu Jun 18 2015 - 08:42:34 CDT)
  • Re: Combining parameter files from CHARMM (Mon Jun 15 2015 - 07:29:36 CDT)
  • Re: Combining parameter files from CHARMM (Mon Jun 15 2015 - 03:08:06 CDT)
  • Combining parameter files from CHARMM (Fri Jun 05 2015 - 04:51:13 CDT)
  • Force-field for DOPI lipid (Sat May 23 2015 - 13:58:30 CDT)
  • Re: Minimisation not converged (Wed Apr 01 2015 - 22:26:19 CDT)
  • Minimisation not converged (Wed Apr 01 2015 - 01:20:37 CDT)
  • Re: Dihedral calculation with colvars (Thu Mar 12 2015 - 06:13:00 CDT)
  • Re: Dihedral calculation with colvars (Thu Mar 12 2015 - 01:20:46 CDT)
  • Dihedral calculation with colvars (Wed Mar 11 2015 - 23:05:45 CDT)
  • Re: Dihedral definition in NAMD (Wed Mar 11 2015 - 05:03:54 CDT)
  • Re: Dihedral definition in NAMD (Tue Mar 10 2015 - 22:22:34 CDT)
  • Re: Dihedral definition in NAMD (Tue Mar 10 2015 - 13:13:00 CDT)
  • Re: Dihedral definition in NAMD (Tue Mar 10 2015 - 09:24:23 CDT)
  • Re: Dihedral definition in NAMD (Tue Mar 10 2015 - 06:52:53 CDT)
  • Dihedral definition in NAMD (Tue Mar 10 2015 - 06:19:16 CDT)
  • Re: Choosing of windows and width for Umbrella Sampling (Mon Dec 08 2014 - 09:39:46 CST)
  • Choosing of windows and width for Umbrella Sampling (Mon Dec 08 2014 - 06:48:19 CST)
  • Re: colvar DistanceZ (Wed Nov 26 2014 - 20:32:24 CST)
  • Re: colvar DistanceZ (Wed Nov 26 2014 - 07:25:03 CST)
  • Re: Colvars error (Tue Nov 25 2014 - 21:11:41 CST)
  • colvar DistanceZ (Tue Nov 25 2014 - 21:03:55 CST)
  • Re: Colvars error (Tue Nov 25 2014 - 05:11:55 CST)
  • Re: Colvars error (Tue Nov 25 2014 - 00:57:45 CST)
  • Colvars error (Tue Nov 25 2014 - 00:10:05 CST)
  • Re: Atomselect for coor, vel, xsc (Fri Nov 21 2014 - 04:20:16 CST)
  • Atomselect for coor, vel, xsc (Thu Nov 13 2014 - 22:49:02 CST)
  • Umbrella Sampling in NAMD (Thu Nov 13 2014 - 10:25:13 CST)
  • Improving MDFF results (Mon Oct 20 2014 - 22:15:59 CDT)
  • Re: NADH topology file (Wed Jul 16 2014 - 01:51:22 CDT)
  • NADH topology file (Tue Jul 15 2014 - 05:41:51 CDT)
  • About asterisk in IC statements in topology files (Tue Jul 08 2014 - 02:30:25 CDT)
• Kevin Chan
  • Re: Bubble in water during membrane simulations (Mon Nov 16 2015 - 10:41:21 CST)
• Kevin Chun Chan
  • Re: Improving MDFF results (Tue Oct 21 2014 - 10:56:00 CDT)
• Kevin Kastner
  • Re: Accelerated MD with transmembrane protein (Fri Apr 11 2014 - 13:06:28 CDT)
  • Accelerated MD with transmembrane protein (Thu Apr 10 2014 - 13:40:26 CDT)
• Khaled Barakat
  • coarse-grained simulation: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR C5M P5 (ATOMS 1 2) (Sun Mar 23 2014 - 22:44:02 CDT)
• Kipp Johnson
  • Re: Protein solvation (Sat May 10 2014 - 15:38:26 CDT)
• KK R
  • Topology and parameter files for some engineered residues (Wed Nov 19 2014 - 09:31:33 CST)
  • atomselect option for extracting protein-ligand complex (Mon Feb 17 2014 - 16:16:43 CST)
• Klas Karis
  • Can't find documentation of known bug in NAMD 2.9 (Mon Apr 13 2015 - 12:02:25 CDT)
  • Re: parameter and topology files for martini polarizable water (Thu Jul 10 2014 - 12:11:35 CDT)
  • parameter and topology files for martini polarizable water (Wed Jul 09 2014 - 18:30:23 CDT)
• Kostas Malavazos
  • Van der Waals and Electrostatic Forces - CUDA (Tue Nov 10 2015 - 11:11:37 CST)
  • Lennard-Jones and Electrostatic Forces and Energies (Mon Oct 26 2015 - 13:54:28 CDT)
  • ApoA1 simulation (Wed Oct 21 2015 - 05:21:28 CDT)
  • Compile NAMD - Projections (Wed Oct 14 2015 - 11:45:04 CDT)
• Kshatresh Dutta Dubey
  • Re: query about the cross term in psf (Sat Dec 06 2014 - 14:12:31 CST)
  • query about the cross term in psf (Sat Dec 06 2014 - 13:31:42 CST)
  • Re: information about simulation speed (Tue Dec 02 2014 - 17:45:32 CST)
  • Re: information about simulation speed (Tue Dec 02 2014 - 17:35:14 CST)
  • Re: information about simulation speed (Tue Dec 02 2014 - 17:22:28 CST)
  • Re: information about simulation speed (Tue Dec 02 2014 - 17:04:31 CST)
  • information about simulation speed (Tue Dec 02 2014 - 16:50:11 CST)
  • running NAMD in parallel (Fri Nov 28 2014 - 19:29:43 CST)
• Kukol, Andreas
  • +p option on Windows 7 (Fri May 15 2015 - 05:07:55 CDT)
  • +p option on Windows 7 (Wed Jul 30 2014 - 09:56:28 CDT)
• Kuldeep Roy
  • Re: Fwd: Majordomo results (Wed Jan 01 2014 - 16:33:22 CST)
• Kumar, Amit
  • Segmentation Fault - Debug (Mon Oct 05 2015 - 09:13:14 CDT)
  • RE: NAMD 2.10 Building from Source (Thu Jul 09 2015 - 16:02:07 CDT)
  • NAMD 2.10 Building from Source (Thu Jul 09 2015 - 15:28:07 CDT)
  • NAMD Repeated failures launching tasks (Mon May 11 2015 - 13:47:40 CDT)
• L. Signorile
  • polymerization simulations (Thu Jul 09 2015 - 13:06:51 CDT)
• Lachele Foley
  • Re: Re: 1-4scaling for glycosylated protein using AMBER/GLYCAM FF in NAMD (Tue Mar 17 2015 - 21:46:19 CDT)
  • Re: 1-4scaling for glycosylated protein using AMBER/GLYCAM FF in NAMD (Tue Mar 17 2015 - 21:15:41 CDT)
• Lara rajam
  • ERROR in CUDA run (Thu Dec 17 2015 - 08:50:49 CST)
  • Re: patching SO3 group to GAG (Thu Sep 03 2015 - 22:45:34 CDT)
  • patching SO3 group to GAG (Thu Sep 03 2015 - 19:13:21 CDT)
  • parameters problem in sulfated molecules (Tue Sep 01 2015 - 12:12:42 CDT)
  • heparin (Sat Aug 29 2015 - 18:48:08 CDT)
  • restart error (Mon Jul 20 2015 - 10:15:23 CDT)
  • Re: extra bonds (Thu Jul 02 2015 - 12:35:14 CDT)
  • extra bonds (Thu Jul 02 2015 - 09:20:59 CDT)
  • not able to view trajectory in VMD (Fri Jun 26 2015 - 12:55:01 CDT)
• Laura
  • unsubscribe (Sun Jun 15 2014 - 12:29:39 CDT)
• Leili Zhang
  • colvars fatal error (Tue Nov 04 2014 - 22:44:05 CST)
• Lela Vukovic
  • Second Announcement: ‘Hands On’ Workshop on Computational Biophysics (Berkeley, CA, Aug 3-7, 2015) (Tue Jun 16 2015 - 12:04:27 CDT)
  • Announcement: Workshop on Simulation Based Drug Discovery (San Diego, CA, Sept 21-25, 2015) (Fri Jun 12 2015 - 21:06:22 CDT)
  • Announcement: ‘Hands On’ Workshop on Computational Biophysics (Berkeley, CA, Aug 3-7, 2015) (Wed May 20 2015 - 00:06:46 CDT)
  • Announcement: ‘Hands On’ Workshop on Computational Biophysics (Odense, Denmark, Oct 12-16, 2015) (Wed May 06 2015 - 01:39:55 CDT)
  • Announcement: ‘Hands On’ Workshop on Computational Biophysics (Lake Tahoe, CA, Aug 3-7, 2015) (Tue Mar 24 2015 - 15:50:58 CDT)
  • Announcement: ‘Hands On’ Workshop on Computational Biophysics (Pittsburgh, PA, June 1-5, 2015) (Wed Mar 04 2015 - 13:07:25 CST)
  • Announcement: "Hands-On" Workshop on Computational Biophysics in Urbana, IL (April 6-10,2015) (Mon Feb 16 2015 - 14:44:55 CST)
• Lenin Domínguez
  • Re: grcarma : a graphical user interface to carma (Sun Jan 05 2014 - 18:20:50 CST)
• Leonardo Darre
  • Re: question about FEP for amphiphile in lipid bilayer (Wed Dec 10 2014 - 09:20:51 CST)
  • question about FEP for amphiphile in lipid bilayer (Wed Dec 10 2014 - 08:08:27 CST)
• Leonardo Herrera
  • Running constant pH molecular dynamics (CpHMD) (Thu Jul 09 2015 - 19:00:02 CDT)
• Lewis Martin
  • Can NAMD handle two different LJ cutoffs in a single simulation? (Mon Sep 14 2015 - 23:17:36 CDT)
• Life Sciences Inc
  • Re: constraint failure in Rattle algorithm for atom 54134 (Mon Oct 26 2015 - 13:37:42 CDT)
  • constraint failure in Rattle algorithm for atom 54134 (Sun Oct 25 2015 - 19:42:57 CDT)
• Liqun Zhang
  • how to fix the problem (Fri Nov 14 2014 - 17:19:37 CST)
• Lorenz Ripka
  • Re: COLVAR metadynamics: center of mass of atoms crossing simulation box (Fri May 23 2014 - 07:35:23 CDT)
  • COLVAR metadynamics: center of mass of atoms crossing simulation box (Mon May 19 2014 - 03:44:36 CDT)
  • COLVAR metadynamics: center of mass of atoms crossing simulation box (Mon May 19 2014 - 07:17:47 CDT)
• Lu Hong
  • RE: exchange force constants (Mon Jul 21 2014 - 11:25:25 CDT)
  • exchange force constants (Mon Jul 21 2014 - 08:50:24 CDT)
  • variable force constant (Thu Jul 10 2014 - 12:34:58 CDT)
• luca belmonte
  • concerning paratools (Thu Dec 03 2015 - 04:36:04 CST)
  • sausage plot for a namd trajectory in vmd (Fri Jul 31 2015 - 05:01:02 CDT)
  • Re: about angles in coordination complexes (Wed Feb 04 2015 - 04:37:28 CST)
  • Re: about angles in coordination complexes (Mon Jan 26 2015 - 11:51:11 CST)
  • Re: about angles in coordination complexes (Mon Jan 26 2015 - 10:55:10 CST)
  • Re: about angles in coordination complexes (Mon Jan 26 2015 - 10:28:17 CST)
  • Re: about angles in coordination complexes (Mon Jan 26 2015 - 10:02:27 CST)
  • Re: about angles in coordination complexes (Mon Jan 26 2015 - 09:28:16 CST)
  • about angles in coordination complexes (Mon Jan 26 2015 - 08:39:17 CST)
  • angles between residues (Tue Dec 30 2014 - 07:38:14 CST)
• Lucía Díaz
  • substrate and membrane protein (Mon Nov 02 2015 - 08:03:28 CST)
• Lurong Pan
  • Qh (Thu Sep 11 2014 - 08:22:22 CDT)
  • question about force constant (Fri Jan 03 2014 - 09:02:13 CST)
• Ma'Mon Hatmal
  • call "NAMD" from another program (Thu Jul 09 2015 - 17:53:24 CDT)
  • (no subject) (Thu Feb 05 2015 - 06:32:09 CST)
• Madhulika Gupta
  • Re: NAMD2.11 source code not compiling (Fri Nov 20 2015 - 01:20:05 CST)
  • Re: NAMD2.11 source code not compiling (Wed Nov 18 2015 - 10:31:55 CST)
  • NAMD2.11 source code not compiling (Wed Nov 18 2015 - 02:47:38 CST)
• Madhusoodanan M.R
  • topology & force field parameters for Sorbitan monooleate (span 80) (Tue Jan 06 2015 - 20:32:39 CST)
• Magnus Andersson
  • PMF calculation crashes with constraint failure (Sat Jan 25 2014 - 11:02:11 CST)
• Mahdi Tavakol
  • SMD with PBC (Thu Dec 24 2015 - 00:22:36 CST)
  • LangevinDamping Coefficient for MARTINI (Wed Dec 23 2015 - 05:33:48 CST)
  • Changing Boundary conditions from PBC to non-periodic (Thu Nov 19 2015 - 12:30:23 CST)
  • Output to a file (Mon Oct 05 2015 - 01:31:55 CDT)
  • Re: NAMD Anisotropic pressure control (Fri Sep 18 2015 - 11:51:29 CDT)
  • NAMD Anisotropic pressure control (Fri Sep 18 2015 - 08:50:04 CDT)
• Mahya Hemmat
  • Hybrid coarse-grained/all-atom simulation (Mon Sep 28 2015 - 14:25:24 CDT)
  • Error: Constraint failure in RATTLE algorithm for atom 5380! in NAMD (Mon Jul 06 2015 - 11:06:39 CDT)
• Mai Aamer
  • Multiple NAMD calculations on windows (Mon Nov 02 2015 - 16:40:06 CST)
  • model.conf (Thu Jul 09 2015 - 17:09:01 CDT)
• manish kesherwani
  • Re: DCD Error (Wed Mar 18 2015 - 08:10:18 CDT)
  • Re: (Wed Apr 16 2014 - 13:21:34 CDT)
  • (no subject) (Tue Apr 15 2014 - 00:02:12 CDT)
• maral hassani
  • Constant velocity SMD (Tue Jun 09 2015 - 07:14:16 CDT)
• Marawan Hussien
  • Immediate PhD Opening Computational Structural Biology Of Membrane Proteins (Thu Apr 09 2015 - 19:18:53 CDT)
  • Immediate Postdoctoral Position Opening (Thu Apr 09 2015 - 18:10:32 CDT)
  • Immediate Postdoctoral Position Opening (Sun Mar 22 2015 - 16:08:16 CDT)
• Mare Libero
  • Re: AW: Question about accelerated MD (Wed Mar 26 2014 - 11:35:38 CDT)
  • Re: AW: Question about accelerated MD (Wed Mar 26 2014 - 10:12:13 CDT)
  • Question about accelerated MD (Tue Mar 25 2014 - 17:14:27 CDT)
  • Interactive molecular dynamics question (Sun Feb 09 2014 - 15:05:51 CST)
• Maria Bykhovskaia
  • using NAMD with CHARMM36 ff (Sat Jan 17 2015 - 19:26:29 CST)
  • wrapping in two dimensions (Thu Oct 16 2014 - 15:33:34 CDT)
  • wrapping a protein (Wed Aug 20 2014 - 17:40:30 CDT)
• Maria Kopp
  • I would like to unsubscribe (Wed Sep 10 2014 - 09:04:54 CDT)
• Maria Pikoula
  • Re: ABF simulation fails with "FATAL ERROR: Low global exclusion count!" (Fri Feb 28 2014 - 12:50:27 CST)
  • Re: ABF simulation fails with "FATAL ERROR: Low global exclusion count!" (Fri Feb 28 2014 - 11:42:47 CST)
  • ABF simulation fails with "FATAL ERROR: Low global exclusion count!" (Tue Feb 25 2014 - 11:02:24 CST)
• Marlet Martinez
  • ERROR: Molecule destroyed by fatal error (Mon Jan 27 2014 - 13:31:18 CST)
• Marlon Sidore
  • Re: keyword "outputaccumulatedwork" is not supported, or not recognized in this context. (Wed Oct 14 2015 - 05:12:16 CDT)
  • Coarse grained instability: atoms moving too fast (Mon Oct 05 2015 - 06:47:41 CDT)
  • Re: Calculating the spin angle collective variable value (Mon May 11 2015 - 09:06:46 CDT)
  • Re: Calculating the spin angle collective variable value (Mon May 11 2015 - 08:48:51 CDT)
  • Calculating the spin angle collective variable value (Mon May 11 2015 - 03:51:38 CDT)
• maryam atabay
  • question about CUDA-enabled (Sat Nov 29 2014 - 10:19:49 CST)
  • question about CUDA-enabled (Tue Nov 25 2014 - 01:05:32 CST)
  • Fwd: question about CUDA-enabled (Mon Nov 24 2014 - 05:08:04 CST)
• Maryam Sayadi
  • Instability in thermodynamic integration (Sun Feb 16 2014 - 14:04:12 CST)
• Marzieh Alishahi
  • Re: Annealing process of silica with excluded block (Mon Sep 15 2014 - 09:40:21 CDT)
  • Annealing process of silica with excluded block (Fri Sep 12 2014 - 10:22:51 CDT)
• Massimiliano Porrini
  • Re: Constraint failure in RATTLE (Mon Mar 31 2014 - 11:48:38 CDT)
  • Re: Constraint failure in RATTLE (Sun Mar 30 2014 - 06:49:34 CDT)
• Matthew Ralph Adendorff
  • Processing 64-window FEP (Sun May 10 2015 - 08:44:08 CDT)
  • RE: Equilibration for a reverse FEP run (Thu Apr 23 2015 - 10:16:08 CDT)
  • Equilibration for a reverse FEP run (Thu Apr 23 2015 - 09:54:41 CDT)
  • NAMD-SMP-Ibverbs-CUDA assistance (Tue May 13 2014 - 09:25:44 CDT)
  • PREMD in NAMD (Mon Feb 10 2014 - 09:27:15 CST)
• Mattia Felice Palermo
  • Dielectric constant of water from MSM and PME simulations (Fri Oct 23 2015 - 08:57:37 CDT)
  • (no subject) (Wed Oct 21 2015 - 04:07:03 CDT)
• Maxim Belkin
  • Re: Restarting trajectories (Wed May 20 2015 - 11:11:33 CDT)
  • Re: Simulated Annealing with many frequent restarts (Fri May 01 2015 - 11:49:41 CDT)
  • Re: Simulated Annealing with many frequent restarts (Fri May 01 2015 - 11:18:21 CDT)
  • Re: Simulated Annealing with many frequent restarts (Fri May 01 2015 - 09:46:21 CDT)
  • Re: slow heating of system (Sun Apr 19 2015 - 04:08:03 CDT)
  • Re: Reg: solvating in a non-standard solvent (Thu Mar 19 2015 - 12:06:38 CDT)
  • Re: Reg: solvating in a non-standard solvent (Thu Mar 19 2015 - 11:59:28 CDT)
  • Re: DCD Error (Wed Mar 18 2015 - 10:06:34 CDT)
  • Re: equilibrate the bulk water system (Fri Mar 13 2015 - 11:28:35 CDT)
  • Re: vmd-l: Re: velocity IO with psfgen? (Thu Feb 26 2015 - 12:14:24 CST)
  • Re: PMEGridSize and parameters controlling electrostatic interactions. (Sun Jan 25 2015 - 21:20:58 CST)
  • Re: PMEGridSize and parameters controlling electrostatic interactions. (Sat Jan 24 2015 - 14:11:59 CST)
  • Re: Fwd: Cannot find colvar dih1 (dih colvars) (Tue Dec 23 2014 - 15:59:09 CST)
  • Re: Mechanical Properties of protein (Thu Oct 30 2014 - 20:27:58 CDT)
  • Re: running a calculation during simulation (Mon Oct 20 2014 - 18:00:03 CDT)
  • Re: wrapping a protein (Wed Aug 20 2014 - 17:53:46 CDT)
  • Re: Atom selection in Tcl Force script with Amber partop file (Fri Aug 15 2014 - 18:33:18 CDT)
  • Re: Atom selection in Tcl Force script with Amber partop file (Fri Aug 15 2014 - 16:48:12 CDT)
  • Re: Kb, Ktheta values for TIP3P water model (Tue Aug 12 2014 - 23:11:43 CDT)
  • Re: Kb, Ktheta values for TIP3P water model (Mon Aug 11 2014 - 18:05:41 CDT)
  • Re: automatic extraction of RMSD values of the heavy atoms of residues from NAMD output? (Mon Aug 04 2014 - 11:25:15 CDT)
  • Re: Calculating the force needed to constrain a protein (Fri Jul 18 2014 - 11:43:27 CDT)
  • Re: NAMD/MIC & CUDA on Stampede (Thu Jul 17 2014 - 13:32:27 CDT)
  • Re: NAMD/MIC & CUDA on Stampede (Wed Jul 16 2014 - 15:44:34 CDT)
  • Re: how to quantify and visualize the flow of water into a protein (Tue Jul 08 2014 - 19:20:12 CDT)
  • Re: how to quantify and visualize the flow of water into a protein (Tue Jul 08 2014 - 18:40:15 CDT)
  • Re: Fixed atoms. (Thu Jun 05 2014 - 17:14:48 CDT)
  • Re: TclForces wrapmode FATAL ERROR: Setting parameter wrapmode from script failed (Wed May 07 2014 - 16:15:22 CDT)
  • Re: PMEGridSizeX (number of grid points) is very small. (Wed Feb 05 2014 - 12:44:35 CST)
• Maxim Igaev
  • Re: atom ID in VMD and NAMD (Mon May 04 2015 - 07:18:38 CDT)
  • Re: atom ID in VMD and NAMD (Mon May 04 2015 - 06:47:09 CDT)
  • atom ID in VMD and NAMD (Mon May 04 2015 - 03:16:09 CDT)
  • Re: anisotropic pressure control (Wed Nov 26 2014 - 05:10:09 CST)
  • Re: anisotropic pressure control (Wed Nov 26 2014 - 04:04:49 CST)
  • Fw: anisotropic pressure control (Wed Nov 26 2014 - 03:47:41 CST)
  • anisotropic pressure control (Wed Nov 26 2014 - 02:48:51 CST)
• Maxime Boissonneault
  • Re: Which namd to use (Fri Nov 20 2015 - 08:13:58 CST)
  • Which namd to use (Fri Nov 20 2015 - 07:29:45 CST)
  • Reducing the amount of work being done on CPU (Tue Sep 01 2015 - 09:48:24 CDT)
  • Re: namd ibverbs (Thu Jul 16 2015 - 16:43:06 CDT)
  • Re: namd ibverbs (Thu Jul 16 2015 - 15:59:19 CDT)
  • Re: namd ibverbs (Thu Jul 16 2015 - 15:50:36 CDT)
  • namd ibverbs (Thu Jul 16 2015 - 12:59:50 CDT)
  • Re: AW: FATAL ERROR: seek failed while writing DCD file: No such file or directory (Fri Dec 19 2014 - 08:18:38 CST)
  • Re: AW: AW: AW: AW: FATAL ERROR: PME offload requires exactly one CUDA device per process. (Mon Aug 25 2014 - 07:34:34 CDT)
  • Re: AW: AW: AW: FATAL ERROR: PME offload requires exactly one CUDA device per process. (Fri Aug 22 2014 - 08:59:26 CDT)
  • Re: AW: AW: FATAL ERROR: PME offload requires exactly one CUDA device per process. (Fri Aug 22 2014 - 08:22:43 CDT)
  • FATAL ERROR: PME offload requires exactly one CUDA device per process. (Fri Aug 22 2014 - 06:40:06 CDT)
  • SMP vs Multicore (Thu Aug 21 2014 - 09:26:43 CDT)
  • Re: AW: AW: AW: "Beefier" benchmark (Thu Aug 21 2014 - 09:04:42 CDT)
  • Re: AW: AW: "Beefier" benchmark (Thu Aug 21 2014 - 07:32:10 CDT)
  • Re: AW: "Beefier" benchmark (Wed Aug 20 2014 - 09:20:15 CDT)
  • Re: "Beefier" benchmark (Tue Aug 19 2014 - 11:14:31 CDT)
  • "Beefier" benchmark (Tue Aug 19 2014 - 10:48:30 CDT)
  • Re: AW: AW: Hybrid MPI + Multicore + Cuda build (Thu Aug 14 2014 - 11:53:16 CDT)
  • Re: AW: Hybrid MPI + Multicore + Cuda build (Thu Aug 14 2014 - 07:19:37 CDT)
  • Hybrid MPI + Multicore + Cuda build (Wed Aug 13 2014 - 11:46:59 CDT)
• Maxwell Wesley Terban
  • Generating .psf for amorphous disaccharide (Fri Feb 28 2014 - 13:10:56 CST)
• Mayne, Christopher G
  • Re: concerning paratools (Thu Dec 03 2015 - 14:11:52 CST)
  • Re: Topology and parameters for Sodium dodecanoate (Wed Nov 04 2015 - 08:05:46 CST)
  • Re: vmd-l: Topology for drugs to do MD after docking (Wed Oct 21 2015 - 14:44:18 CDT)
  • Re: Parameterizing a novel peptide (Mon Sep 14 2015 - 21:38:04 CDT)
  • Re: Parameterizing a novel peptide (Mon Sep 14 2015 - 08:48:57 CDT)
  • Re: Create psf file (Mon Jun 22 2015 - 10:01:23 CDT)
  • FFTK - error (Mon Jun 08 2015 - 11:56:34 CDT)
  • Best Practices for Nucleobase Parameterization (Wed May 20 2015 - 08:12:55 CDT)
  • proper order for par files in namd (Fri May 01 2015 - 09:21:11 CDT)
  • Re: Re: Problems to parametrize molecules (Fri Apr 24 2015 - 14:22:55 CDT)
  • Re: Re: Problems to parametrize molecules (Fri Apr 24 2015 - 13:53:01 CDT)
  • Re: Re: Problems to parametrize molecules (Sun Apr 19 2015 - 18:59:20 CDT)
  • Re: Problems to parametrize molecules (Fri Apr 17 2015 - 11:16:16 CDT)
  • Re: vmd-l: ffTK problem: OPT.Charges (Fri Nov 07 2014 - 10:51:57 CST)
  • Re: Re: ffTK problem: initial parameter fiel is viod of atoms! (Mon Oct 20 2014 - 11:45:39 CDT)
  • Re: ffTK problem: initial parameter fiel is viod of atoms! (Mon Oct 20 2014 - 09:55:55 CDT)
  • Re: Force field design (Tue Jul 22 2014 - 09:01:58 CDT)
  • Re: Force field design (Wed Jul 16 2014 - 10:46:48 CDT)
• MEHRAN MB
  • Re: scaling non-bonded interactiion parameter for specific pairs (Fri Feb 27 2015 - 14:01:29 CST)
  • scaling non-bonded interactiion parameter for specific pairs (Fri Feb 27 2015 - 13:15:11 CST)
  • Re: Alchemical FEP calculations in Implicit Solvent (Mon Feb 23 2015 - 13:08:56 CST)
  • Re: inconsistency in ABF results for helix unfolding (Wed Jan 28 2015 - 14:50:14 CST)
  • inconsistency in ABF results for helix unfolding (Tue Jan 27 2015 - 17:09:19 CST)
  • Re: I would like to unsubscribe (Wed Sep 10 2014 - 09:19:54 CDT)
  • Re: Silent crash NAMD-multicore-CUDA (Tue Aug 19 2014 - 11:06:34 CDT)
  • Re: Silent crash NAMD-multicore-CUDA (Thu Jul 31 2014 - 18:27:55 CDT)
  • Silent crash NAMD-multicore-CUDA (Wed Jul 30 2014 - 17:23:10 CDT)
  • Re: NAMD energy plugin (Wed Jun 04 2014 - 15:16:09 CDT)
  • Re: Nanotube Simulation (Fri Apr 11 2014 - 13:33:31 CDT)
  • Re: vmd-l: Re: wrapping option in namd (Tue Apr 01 2014 - 21:44:36 CDT)
  • Re: Adding hydrogen atoms to the crystall structure (Tue Feb 18 2014 - 15:54:55 CST)
  • Re: ABF force distribution (Tue Feb 18 2014 - 10:50:59 CST)
  • Re: ABF simulations (Tue Feb 18 2014 - 10:38:25 CST)
  • Re: Non standar solvent (Tue Feb 18 2014 - 10:12:26 CST)
  • Re: Adding hydrogen atoms to the crystall structure (Tue Feb 18 2014 - 10:10:53 CST)
  • Re: AW: moving out of the box (Mon Feb 17 2014 - 11:48:44 CST)
  • Re: unsubscribe (Fri Feb 14 2014 - 11:33:01 CST)
• Merrill, Dante
  • Patch-size Error (not like the other ones) (Fri Jul 24 2015 - 13:14:28 CDT)
• Mert Gür
  • Re: Transferring bond list to new molecule (Wed Dec 17 2014 - 18:06:05 CST)
  • Transferring bond list to new molecule (Tue Dec 16 2014 - 23:17:02 CST)
• Michael Bellucci
  • RE: Scaling solvent-solute intermolecular interactions (Wed May 14 2014 - 08:50:36 CDT)
  • RE: Scaling solvent-solute intermolecular interactions (Tue May 13 2014 - 15:09:06 CDT)
  • Scaling solvent-solute intermolecular interactions (Tue May 13 2014 - 13:34:13 CDT)
• Michael Bokoch
  • Hexagonal cell instability during lipid bilayer sim in NAMD 2.9 (Mon Jul 07 2014 - 21:42:54 CDT)
• Michael Feig
  • RE: Restarting trajectories (Wed May 20 2015 - 11:18:12 CDT)
  • RE: Restarting trajectories (Wed May 20 2015 - 10:59:07 CDT)
  • Restarting trajectories (Wed May 20 2015 - 02:47:08 CDT)
  • Restarting trajectories (Wed May 20 2015 - 03:01:37 CDT)
  • Re: REMD on GPU cluster (Tue Apr 14 2015 - 08:00:16 CDT)
  • REMD on GPU cluster (Mon Apr 13 2015 - 17:09:05 CDT)
• Michael Purdy
  • Re: Two GPU-based workstation (Tue Jan 14 2014 - 08:05:40 CST)
• Michael Yuchi
  • How to output CCC per residue from MDFF (Thu Apr 23 2015 - 21:48:11 CDT)
• Michal Skoczek
  • NAMD 2.9 Changing/Replacing atoms in multiple molecules (Fri Feb 21 2014 - 08:02:41 CST)
• Michel van der List
  • RE: Running CUDA-enabled NAMD on multiple nodes without InfiniBand? (Wed Dec 03 2014 - 12:06:03 CST)
  • Running CUDA-enabled NAMD on multiple nodes without InfiniBand? (Mon Dec 01 2014 - 08:40:46 CST)
• Michelle Kuttel
  • Re: Getting extra atoms by Patching! (Sat May 03 2014 - 01:11:50 CDT)
• Mihaela Drenscko
  • Re: Incorrect atom count in binary file (Wed Feb 18 2015 - 07:34:15 CST)
  • Incorrect atom count in binary file (Tue Feb 17 2015 - 18:59:43 CST)
  • FATAL ERROR: UNABLE TO FIND BOND PARAMETERS (Wed Jan 07 2015 - 19:58:27 CST)
  • Error on write to binary file (Mon Dec 22 2014 - 18:02:54 CST)
  • FATAL ERROR: error parsing config file while executing <feff> (Sun Nov 09 2014 - 11:39:11 CST)
  • FATAL ERROR: Setting parameter colvars from script failed! (Tue Sep 30 2014 - 09:27:18 CDT)
  • Fwd: PCL dcd files (Mon Sep 29 2014 - 11:38:30 CDT)
  • PCL dcd files (Mon Sep 29 2014 - 11:09:40 CDT)
• Mike Makowski
  • Re: Molecular Dynamics of Rigid Linear Molecules in NAMD. (Sun Sep 28 2014 - 06:50:36 CDT)
  • Re: Molecular Dynamics of Rigid Linear Molecules in NAMD. (Sun Sep 28 2014 - 03:03:10 CDT)
  • Re: using CHARMM-format Amber parameters in NAMD (Tue Aug 19 2014 - 23:34:13 CDT)
  • Re: Running NAMD via GROMACS topology (Sun Aug 10 2014 - 18:05:21 CDT)
  • Running NAMD via GROMACS topology (Sun Aug 10 2014 - 17:44:35 CDT)
• Mikhail Suyetin
  • Re: Re: NH4+ params (Sat Oct 24 2015 - 11:56:15 CDT)
  • NH4+ params (Fri Oct 23 2015 - 16:38:55 CDT)
• Milica UtjeÅ¡anović
  • Ispopetide bond (Fri Oct 02 2015 - 14:30:04 CDT)
• Miro Hodak
  • Re: Nanotube Simulation (Fri Apr 11 2014 - 13:13:32 CDT)
  • Re: Nanotube Simulation (Fri Apr 11 2014 - 11:56:59 CDT)
  • Nanotube Simulation (Thu Apr 10 2014 - 18:02:56 CDT)
• Miss. State
  • Re: Constant Pressure, Variable Volume, Minimization (Thu Dec 18 2014 - 13:01:05 CST)
  • ERROR: CALCULATED VDWA FORCE MAY NOT MATCH ENERGY! POSSIBLE BUG! (Mon Feb 17 2014 - 17:05:09 CST)
• Mitchell Gleed
  • Re: replica exchange and GPU acceleration (Mon Jul 13 2015 - 01:32:14 CDT)
  • Re: replica exchange and GPU acceleration (Sun Jul 12 2015 - 22:36:54 CDT)
  • Re: replica exchange and GPU acceleration (Sat Jul 04 2015 - 10:49:22 CDT)
  • Re: replica exchange and GPU acceleration (Wed Jul 01 2015 - 11:01:50 CDT)
  • replica exchange and GPU acceleration (Tue Jun 30 2015 - 18:09:27 CDT)
  • Re: Colvar with variable axis (Thu Mar 12 2015 - 10:49:21 CDT)
  • Re: Colvar with variable axis (Thu Mar 12 2015 - 07:59:56 CDT)
  • Colvar with variable axis (Thu Mar 12 2015 - 06:01:56 CDT)
  • Re: Multicore-CUDA NAMD output hangs (Tue Mar 03 2015 - 10:34:20 CST)
  • Multicore-CUDA NAMD output hangs (Wed Feb 18 2015 - 15:12:21 CST)
  • Re: NAMD on SLURM (Wed Nov 12 2014 - 12:57:16 CST)
  • Re: Umbrella sampling tilt with respect to Z-axis (Wed Oct 08 2014 - 18:07:00 CDT)
  • Umbrella sampling tilt with respect to Z-axis (Wed Oct 08 2014 - 15:38:29 CDT)
• Mitul Saha
  • "Unknown command-line option +replicas" (Mon Mar 02 2015 - 23:33:11 CST)
  • Maximum limit for "run" parameter (Tue Feb 17 2015 - 18:50:38 CST)
  • (no subject) (Tue Jul 22 2014 - 11:27:04 CDT)
  • Re: Bad global crossterm count! (Tue Jul 08 2014 - 16:48:51 CDT)
  • Bad global crossterm count! (Tue Jul 08 2014 - 16:46:17 CDT)
• Mo Chen
  • Re: about hydrogen bond analysis (Tue Mar 24 2015 - 16:19:37 CDT)
  • Re: Inquiry about forceConstant (Mon Jul 21 2014 - 16:57:15 CDT)
  • Re: Inquiry about forceConstant (Mon Jul 21 2014 - 15:23:06 CDT)
  • Inquiry about forceConstant (Mon Jul 21 2014 - 15:03:30 CDT)
  • Re: how to quantify and visualize the flow of water into a protein (Tue Jul 08 2014 - 19:43:35 CDT)
  • Re: Inquiry about lipid membrane simulation (Wed Jun 18 2014 - 14:25:16 CDT)
  • Inquiry about lipid membrane simulation (Tue Jun 17 2014 - 20:57:59 CDT)
  • About converting NAMD dcd file into CHARMM dcd file (Fri Jun 13 2014 - 18:41:30 CDT)
  • Re: About electrostatic treatment (Fri May 30 2014 - 19:39:31 CDT)
  • About electrostatic treatment (Fri May 30 2014 - 19:35:50 CDT)
• Mohan maruthi sena
  • ABF calculations - reaction coordinate (Mon Nov 16 2015 - 19:15:15 CST)
  • FEP method- Free energy of solvation of ligand (Wed Jul 22 2015 - 02:25:40 CDT)
  • FFTK - error (Sat Jun 06 2015 - 18:35:44 CDT)
  • namd coulomb conversion factor (Sat Sep 27 2014 - 01:09:43 CDT)
  • Namd grid forces -distance between molecule and surface (Fri Jun 27 2014 - 05:20:29 CDT)
  • keeping Crystal angles constant (Wed Jan 15 2014 - 12:03:58 CST)
• Mona Habibi
  • NAMD/VMD: generating psf for Abeta, ACE patch (Tue Sep 15 2015 - 15:31:37 CDT)
• Monika Madhavi
  • Re: simulating TIP5P water (Mon Oct 12 2015 - 05:10:35 CDT)
  • Re: simulating TIP5P water (Mon Oct 12 2015 - 03:44:50 CDT)
  • simulating TIP5P water (Fri Oct 09 2015 - 05:29:35 CDT)
  • Re: namd simulation with TIP5P (Fri Oct 02 2015 - 01:16:41 CDT)
  • simulating tip5p water (Thu Oct 01 2015 - 23:36:51 CDT)
  • Re: Atoms moving too fast; simulation has become unstable (Mon Sep 21 2015 - 00:58:32 CDT)
  • Re: Atoms moving too fast; simulation has become unstable (Thu Sep 17 2015 - 22:58:12 CDT)
  • Re: Atoms moving too fast; simulation has become unstable (Thu Sep 17 2015 - 04:42:40 CDT)
  • Atoms moving too fast; simulation has become unstable (Mon Aug 31 2015 - 05:42:48 CDT)
• Monika Sharma
  • FEP of water molecule in binding pocket (Wed May 28 2014 - 15:35:33 CDT)
  • Question regarding loss of translational entropy calculation in FEP tutorial (Tue Feb 04 2014 - 14:05:49 CST)
  • Question regarding loss of translational entropy calculation in FEP tutorial (Sun Jan 19 2014 - 11:32:02 CST)
• Morgan, Brittany
  • RE: Re: vmd-l: NAMD energy calculation (Wed Jul 02 2014 - 11:58:22 CDT)
  • RE: Re: vmd-l: NAMD energy calculation (Tue Jul 01 2014 - 09:26:44 CDT)
  • RE: Problems with energy minimization (Wed Apr 09 2014 - 10:20:05 CDT)
  • RE: NAMD 2.9 quits early without error message. (Fri Mar 07 2014 - 11:45:15 CST)
  • RE: How to maintain Density constant? (Thu Mar 06 2014 - 12:26:02 CST)
  • RE: How to maintain Density constant? (Thu Mar 06 2014 - 11:41:12 CST)
• mostafa raeesi
  • velocity manipulation (Thu Oct 16 2014 - 06:37:02 CDT)
• Mustafa Tekpinar
  • PMF and work distribution (Wed Jun 25 2014 - 05:50:30 CDT)
• nader zabarjad
  • Re: namd-l digest V1 #1726 (Sun Aug 02 2015 - 10:41:55 CDT)
• nam kim
  • how to create two namd jobs in a single script with 2 x dual cuda gpus? (Sat Aug 01 2015 - 16:36:15 CDT)
  • Re: how to create two namd jobs in a single script with 2 x dual cuda gpus? (Sat Aug 01 2015 - 16:33:04 CDT)
• naresh kumar
  • Re: Collective variable module (Mon Apr 14 2014 - 10:11:37 CDT)
  • Re: Collective variable module (Fri Apr 11 2014 - 12:01:32 CDT)
  • Re: Collective variable module (Thu Apr 10 2014 - 12:54:02 CDT)
  • Collective variable module (Thu Apr 10 2014 - 11:36:07 CDT)
• Natalie Esther Smith
  • PMETolerance (Tue Apr 08 2014 - 23:07:52 CDT)
• Natnael Doilicho
  • Re: Self-Assemble Monolayer--Periodic Boundary Conditions (Wed Oct 01 2014 - 16:14:52 CDT)
  • Self-Assemble Monolayer--Periodic Boundary Conditions (Mon Sep 29 2014 - 18:03:18 CDT)
  • Constraining two sets of atoms (Tue Sep 16 2014 - 12:06:38 CDT)
• Neelanjana Sengupta
  • Re: Solvation free energy calculation with MM/GBSA (Fri Sep 25 2015 - 07:36:50 CDT)
  • Re: Solvation free energy calculation with MM/GBSA (Thu Sep 24 2015 - 07:37:04 CDT)
  • Solvation free energy calculation with MM/GBSA (Wed Sep 23 2015 - 06:51:28 CDT)
  • harmonic restraints between multiple atom pairs (Mon Nov 03 2014 - 22:42:33 CST)
  • restraining bonds (Sun Aug 31 2014 - 23:50:24 CDT)
• Nicholas M Glykos
  • Re: Adaptive tempering implementation in NAMD differs (Fri Sep 25 2015 - 04:36:52 CDT)
  • Carma v.1.4 released. (Mon Oct 27 2014 - 06:09:24 CDT)
  • Re: Is there any point in running NAMD over an ethernet-linked cluster? (Mon Sep 22 2014 - 03:40:59 CDT)
  • Re: Is there any point in running NAMD over an ethernet-linked cluster? (Sun Sep 21 2014 - 13:21:53 CDT)
  • Combining interleaved and top posting is considered harmful. (Thu Aug 28 2014 - 11:11:40 CDT)
• Nicholas M. Glykos
  • Re: Adaptive tempering implementation in NAMD differs (Wed Sep 23 2015 - 05:45:40 CDT)
• Nicholus Bhattacharjee
  • Re: Problem running REMD simulation (Thu Aug 27 2015 - 03:00:31 CDT)
  • Re: Problem running REMD simulation (Tue Aug 25 2015 - 04:59:07 CDT)
  • Problem running REMD simulation (Tue Aug 25 2015 - 03:01:36 CDT)
  • Problem running REMD simulation (Thu Aug 20 2015 - 03:47:33 CDT)
• Nicolas Floquet
  • Metadynamics with eigenvector (Mon Aug 25 2014 - 09:40:06 CDT)
• Nicolas Martin
  • Outward tilting which colvar to use (Thu Oct 01 2015 - 05:13:01 CDT)
  • Tilt angle clockwise rotation (Wed Jul 22 2015 - 08:34:47 CDT)
  • Re: FixedAtoms and Reference group in spinangle colvar (Thu May 22 2014 - 07:06:08 CDT)
  • Re: FixedAtoms and Reference group in spinangle colvar (Thu May 22 2014 - 06:21:02 CDT)
  • Re: FixedAtoms and Reference group in spinangle colvar (Sun May 11 2014 - 16:52:42 CDT)
  • FixedAtoms and Reference group in spinangle colvar (Fri May 09 2014 - 09:01:28 CDT)
  • Re: Spinangle with refgroup : Warning: discontinuous rotation! (Thu Apr 10 2014 - 09:04:21 CDT)
  • Re: Spinangle with refgroup : Warning: discontinuous rotation! (Thu Apr 10 2014 - 08:40:18 CDT)
  • Re: Spinangle with refgroup : Warning: discontinuous rotation! (Thu Apr 10 2014 - 08:30:44 CDT)
  • Re: Spinangle with refgroup : Warning: discontinuous rotation! (Wed Apr 09 2014 - 10:41:35 CDT)
  • Spinangle with refgroup : Warning: discontinuous rotation! (Mon Apr 07 2014 - 11:33:58 CDT)
  • Spinangle with refgroup : Warning: discontinuous rotation! (Mon Apr 07 2014 - 11:32:49 CDT)
  • Spinangle with refgroup : Warning: discontinuous rotation! (Mon Apr 07 2014 - 11:33:50 CDT)
• Nifeng Guo hui
  • Why RDF increases as r increase instead of constant (Sat Nov 01 2014 - 17:07:32 CDT)
• Nikhil Maroli
  • Including two parameters for protein-ligand simulation (Wed Oct 28 2015 - 01:52:30 CDT)
  • GPU accelerated MD (Fri Oct 23 2015 - 04:12:24 CDT)
  • Topology for drugs to do MD after docking (Wed Oct 21 2015 - 11:40:04 CDT)
  • Re: Re: vmd-l: script error (Sat Oct 03 2015 - 02:44:17 CDT)
  • Cyclic peptide Nanotube (Fri Oct 02 2015 - 08:52:59 CDT)
  • script error (Fri Oct 02 2015 - 08:44:13 CDT)
  • PSF for cyclic peptide nanotube (Fri Oct 02 2015 - 08:36:47 CDT)
  • psf for cyclic peptide nanotube:psf ready for one ring but required for 8 ring (Sat Sep 26 2015 - 06:50:31 CDT)
  • PSF for CYCLIC PEPTIDE : (Sat Sep 26 2015 - 05:45:17 CDT)
  • Automatic PSF builder for cyclic peptide (Sun Sep 20 2015 - 07:04:36 CDT)
  • Which VMD AND NAMD should install (Sat Sep 19 2015 - 01:57:30 CDT)
• Niklaus Johner
  • Re: PCL dcd files (Tue Sep 30 2014 - 01:15:25 CDT)
  • Re: ABF/colvar error in NAMD2.9 (Tue Jul 22 2014 - 13:32:12 CDT)
• Nithyanan Annamalai
  • Structure size limitation in NAMD (Wed Jan 29 2014 - 20:36:54 CST)
• Nizar Masbukhin
  • Replica Exchange Simulation in NAMD Precompiled binary in single node. (Thu Oct 16 2014 - 17:09:05 CDT)
  • Performance difference of prcompiled binary VS source code (Mon Oct 13 2014 - 19:23:43 CDT)
• Norman Geist
  • AW: ERROR in CUDA run (Thu Dec 17 2015 - 09:24:20 CST)
  • AW: Re: Re: Re: NAMD 2.11b1 released (Fri Nov 27 2015 - 01:22:44 CST)
  • AW: Changing Boundary conditions from PBC to non-periodic (Fri Nov 20 2015 - 01:52:26 CST)
  • AW: time per step during GPU-accelerated Implicit Solvent calculations (Mon Nov 16 2015 - 01:52:00 CST)
  • NAMD 2.11 CUDA forces IBverbs (Fri Nov 13 2015 - 06:00:18 CST)
  • AW: On-the-fly modification of tclforces script? (Tue Nov 10 2015 - 04:18:02 CST)
  • AW: 16 total processes killed (some possibly by mpirun during cleanup) (Tue Nov 03 2015 - 00:25:15 CST)
  • AW: replica exchange module (Tue Oct 27 2015 - 03:08:42 CDT)
  • AW: replica exchange module (Mon Oct 26 2015 - 03:21:01 CDT)
  • AW: replica exchange module (Mon Oct 26 2015 - 02:11:47 CDT)
  • AW: global does not work in configuration and callback function (Sat Oct 24 2015 - 08:30:48 CDT)
  • AW: GPU accelerated MD (Fri Oct 23 2015 - 05:00:05 CDT)
  • AW: Re: AW: Why the computational speed does not increase with the increase of GPUs? (Fri Oct 23 2015 - 03:49:49 CDT)
  • AW: Why the computational speed does not increase with the increase of GPUs? (Thu Oct 22 2015 - 02:27:54 CDT)
  • AW: How to calculate the temperature for a subset of my simulation (Wed Oct 21 2015 - 02:24:09 CDT)
  • AW: Regarding significance of days per ns (days/ns) parameter in NAMD benchmark (Tue Oct 20 2015 - 03:53:51 CDT)
  • AW: Regarding significance of days per ns (days/ns) parameter in NAMD benchmark (Tue Oct 20 2015 - 01:29:19 CDT)
  • AW: How to calculate the temperature for a subset of my simulation (Tue Oct 20 2015 - 01:23:57 CDT)
  • AW: about command replicaRecv and replicaSend (Mon Oct 19 2015 - 02:43:43 CDT)
  • AW: stepspercycle (Mon Oct 19 2015 - 01:25:18 CDT)
  • AW: Reducing the amount of work being done on CPU (Tue Sep 01 2015 - 12:47:56 CDT)
  • AW: Problem running REMD simulation (Thu Aug 27 2015 - 03:42:10 CDT)
  • AW: Problem running REMD simulation (Tue Aug 25 2015 - 03:50:15 CDT)
  • AW: AW: Regarding NAMD installation (Mon Aug 17 2015 - 05:22:11 CDT)
  • AW: Regarding NAMD installation (Mon Aug 17 2015 - 04:32:19 CDT)
  • RE: "missing operator at _@_ in expression" for if statement (Tue Jul 28 2015 - 01:33:01 CDT)
  • RE: Patch-size Error (not like the other ones) (Mon Jul 27 2015 - 02:32:33 CDT)
  • RE: replica exchange and GPU acceleration (Mon Jul 13 2015 - 00:51:11 CDT)
  • RE: replica exchange and GPU acceleration (Mon Jul 06 2015 - 01:38:11 CDT)
  • RE: replica exchange and GPU acceleration (Fri Jul 03 2015 - 03:16:17 CDT)
  • RE: replica exchange and GPU acceleration (Wed Jul 01 2015 - 02:13:56 CDT)
  • RE: Using the multi-copy version of NAMD on a linux workstation (Mon Jun 01 2015 - 02:43:36 CDT)
  • RE: optimising namd ibverb runs (Mon May 18 2015 - 08:16:11 CDT)
  • RE: +p option on Windows 7 (Mon May 18 2015 - 02:39:30 CDT)
  • RE: Error applying PME to simulation set up (Wed May 13 2015 - 05:08:45 CDT)
  • RE: performance question (Wed Apr 29 2015 - 03:24:46 CDT)
  • RE: performance question (Tue Apr 28 2015 - 02:51:06 CDT)
  • RE: Which Binary to use? (Mon Apr 27 2015 - 01:59:17 CDT)
  • RE: Is there any point in running NAMD over an ethernet-linked cluster? (Thu Apr 16 2015 - 10:39:38 CDT)
  • RE: REMD on GPU cluster (Tue Apr 14 2015 - 11:01:49 CDT)
  • RE: REMD on GPU cluster (Tue Apr 14 2015 - 02:10:03 CDT)
  • RE: Restarting NAMD simulation (Thu Mar 12 2015 - 09:13:14 CDT)
  • RE: equilibrate the bulk water system (Wed Mar 11 2015 - 02:03:46 CDT)
  • RE: about langevin dynamics (Mon Mar 09 2015 - 01:44:18 CDT)
  • RE: BUG: NAMD-2.10 CUDA REMD segfault with TCL exec randomly (Wed Mar 04 2015 - 04:40:07 CST)
  • BUG: NAMD-2.10 CUDA REMD segfault with TCL exec randomly (Wed Mar 04 2015 - 01:47:42 CST)
  • RE: "Unknown command-line option +replicas" (Tue Mar 03 2015 - 08:35:47 CST)
  • RE: How to let NAMD terminate automatically at a given time (Tue Mar 03 2015 - 02:35:36 CST)
  • RE: Incorrect atom count in binary file (Wed Feb 18 2015 - 03:13:52 CST)
  • RE: namd-1: Simulation Terminating Early (Mon Feb 09 2015 - 03:09:57 CST)
  • RE: (Thu Feb 05 2015 - 07:55:53 CST)
  • AW: problem with water molecules angle in MD simulation (Thu Jan 29 2015 - 01:56:18 CST)
  • AW: problem with water molecules angle in MD simulation (Wed Jan 28 2015 - 10:50:47 CST)
  • AW: problem with water molecules angle in MD simulation (Wed Jan 28 2015 - 04:08:53 CST)
  • AW: problem with water molecules angle in MD simulation (Tue Jan 27 2015 - 02:28:18 CST)
  • AW: about angles in coordination complexes (Tue Jan 27 2015 - 02:23:29 CST)
  • AW: about angles in coordination complexes (Mon Jan 26 2015 - 09:24:39 CST)
  • AW: problem with water molecules angle in MD simulation (Mon Jan 26 2015 - 02:43:41 CST)
  • AW: problems compiling NAMD with mpicxx from mvapich2 (Mon Jan 26 2015 - 02:36:17 CST)
  • AW: about compiling NAMD using intel icc and impi (Fri Jan 23 2015 - 04:59:43 CST)
  • AW: problems running amber parm7 (Tue Jan 20 2015 - 02:10:44 CST)
  • AW: AW: Periodic Box Dimension (WrapAll is on) (Tue Jan 20 2015 - 02:07:47 CST)
  • AW: problems running amber parm7 (Tue Jan 20 2015 - 01:38:30 CST)
  • AW: Periodic Box Dimension (WrapAll is on) (Tue Jan 20 2015 - 00:39:59 CST)
  • AW: problems running amber parm7 (Tue Jan 20 2015 - 00:19:40 CST)
  • AW: NAMD slows at startup phase 1 smp problem (Tue Jan 13 2015 - 05:52:43 CST)
  • AW: NAMD slows at startup phase 1 smp problem (Tue Jan 13 2015 - 05:50:39 CST)
  • AW: NAMD slows at startup phase 1 smp problem (Tue Jan 13 2015 - 01:22:03 CST)
  • AW: is there a method equivalent to conformational flooding in NAMD 2.10 (Mon Jan 12 2015 - 00:53:25 CST)
  • AW: Tempreture Profile along z axis (Fri Jan 09 2015 - 02:23:04 CST)
  • AW: Failure MD with par7/rst7 amber input (Wed Jan 07 2015 - 03:28:15 CST)
  • AW: Probelm with Lone Pairs on TIP4 model (Tue Jan 06 2015 - 05:34:59 CST)
  • AW: Asking help on results of our GPU benchmark (Mon Jan 05 2015 - 00:37:40 CST)
  • AW: AW: AW: AW: warnings while using amber files (Mon Jan 05 2015 - 08:56:36 CST)
  • AW: AW: AW: warnings while using amber files (Mon Jan 05 2015 - 06:35:46 CST)
  • AW: AW: warnings while using amber files (Mon Jan 05 2015 - 03:19:13 CST)
  • AW: Temperature assignment REMD (Mon Jan 05 2015 - 01:29:55 CST)
  • AW: regarding PME grid setting problem (Mon Jan 05 2015 - 00:48:11 CST)
  • AW: warnings while using amber files (Mon Jan 05 2015 - 00:42:51 CST)
  • AW: error parsing config file while executing (Mon Jan 05 2015 - 00:26:37 CST)
  • AW: Asking help on results of our GPU benchmark (Tue Dec 23 2014 - 02:34:58 CST)
  • AW: Error on write to binary file (Tue Dec 23 2014 - 02:42:04 CST)
  • AW: Asking help on results of our GPU benchmark (Mon Dec 22 2014 - 01:16:12 CST)
  • AW: FATAL ERROR: seek failed while writing DCD file: No such file or directory (Fri Dec 19 2014 - 00:35:26 CST)
  • AW: Asking help on results of our GPU benchmark (Fri Dec 19 2014 - 00:30:22 CST)
  • AW: Asking help on results of our GPU benchmark (Thu Dec 18 2014 - 02:39:51 CST)
  • AW: Loading Velocity DCD file (Thu Dec 18 2014 - 02:31:16 CST)
  • AW: Running Charmrun/NAMD with more than 10 processes fails (Tue Dec 16 2014 - 04:06:49 CST)
  • AW: Running CUDA-enabled NAMD on multiple nodes without InfiniBand? (Thu Dec 04 2014 - 01:08:09 CST)
  • AW: information about simulation speed (Wed Dec 03 2014 - 02:31:26 CST)
  • AW: Running CUDA-enabled NAMD on multiple nodes without InfiniBand? (Mon Dec 01 2014 - 09:19:24 CST)
  • AW: question about CUDA-enabled (Mon Dec 01 2014 - 02:56:08 CST)
  • AW: question about CUDA-enabled (Mon Dec 01 2014 - 02:05:20 CST)
  • AW: anisotropic pressure control (Wed Nov 26 2014 - 05:04:20 CST)
  • AW: anisotropic pressure control (Wed Nov 26 2014 - 03:22:31 CST)
  • AW: (Wed Nov 26 2014 - 02:26:35 CST)
  • AW: About NAMD (Wed Nov 19 2014 - 01:10:11 CST)
  • AW: Why CPU Usage is low when I run ibverbs-smp-cuda version NAMD (Tue Nov 11 2014 - 07:03:53 CST)
  • AW: Why CPU Usage is low when I run ibverbs-smp-cuda version NAMD (Tue Nov 11 2014 - 02:48:52 CST)
  • AW: FATAL ERROR: error parsing config file while executing <feff> (Mon Nov 10 2014 - 08:20:48 CST)
  • AW: Reg: QM/MM calculations in NAMD (Mon Nov 10 2014 - 08:12:44 CST)
  • AW: FATAL ERROR: error parsing config file while executing <feff> (Mon Nov 10 2014 - 00:56:24 CST)
  • AW: Why CPU Usage is low when I run ibverbs-smp-cuda version NAMD (Mon Nov 10 2014 - 00:53:15 CST)
  • AW: NAMD error LInux 3.11.10-21-desktop kernel AMD opternon 6272 (Thu Nov 06 2014 - 01:43:36 CST)
  • AW: wrapping in two dimensions (Mon Oct 20 2014 - 01:14:02 CDT)
  • AW: wrapping in two dimensions (Fri Oct 17 2014 - 02:21:07 CDT)
  • AW: velocity manipulation (Thu Oct 16 2014 - 08:26:37 CDT)
  • AW: velocity manipulation (Thu Oct 16 2014 - 08:11:59 CDT)
  • AW: velocity manipulation (Thu Oct 16 2014 - 07:27:28 CDT)
  • AW: question about '+devices' (Wed Oct 08 2014 - 02:13:08 CDT)
  • AW: vmd-l: Stray PME grid (Wed Oct 01 2014 - 02:27:31 CDT)
  • AW: Self-Assemble Monolayer--Periodic Boundary Conditions (Tue Sep 30 2014 - 01:38:57 CDT)
  • AW: Reg: minimization (Thu Sep 25 2014 - 05:23:26 CDT)
  • Re: AW: Using nodelist file causes namd to hang (Thu Sep 18 2014 - 12:32:23 CDT)
  • AW: AW: Question to NAMD source (Mon Sep 08 2014 - 04:40:10 CDT)
  • AW: AW: Question to NAMD source (Mon Sep 08 2014 - 01:19:49 CDT)
  • AW: Question to NAMD source (Fri Sep 05 2014 - 01:32:29 CDT)
  • Question to NAMD source (Thu Sep 04 2014 - 08:02:31 CDT)
  • AW: Fixing atoms while equilibration (Mon Sep 01 2014 - 02:26:11 CDT)
  • AW: ibverb&&smp build NAMD (Mon Sep 01 2014 - 02:17:13 CDT)
  • AW: AW: AW: Using nodelist file causes namd to hang (Thu Aug 28 2014 - 06:08:47 CDT)
  • AW: AW: Using nodelist file causes namd to hang (Thu Aug 28 2014 - 02:47:58 CDT)
  • AW: ibverb&&smp build NAMD (Thu Aug 28 2014 - 05:25:13 CDT)
  • AW: NAMD 2.10b1 CUDA PME offload (Tue Aug 26 2014 - 10:24:50 CDT)
  • NAMD 2.10b1 CUDA PME offload (Tue Aug 26 2014 - 09:25:48 CDT)
  • Siginificant speedup by updating nvidia driver (Mon Aug 25 2014 - 11:06:38 CDT)
  • AW: AW: AW: AW: FATAL ERROR: PME offload requires exactly one CUDA device per process. (Mon Aug 25 2014 - 01:07:21 CDT)
  • AW: AW: AW: FATAL ERROR: PME offload requires exactly one CUDA device per process. (Fri Aug 22 2014 - 08:56:32 CDT)
  • AW: NAMD 2.10 Manual (Fri Aug 22 2014 - 08:46:07 CDT)
  • AW: AW: FATAL ERROR: PME offload requires exactly one CUDA device per process. (Fri Aug 22 2014 - 08:21:25 CDT)
  • NAMD 2.10 Manual (Fri Aug 22 2014 - 03:14:47 CDT)
  • AW: AW: AW: "Beefier" benchmark (Thu Aug 21 2014 - 08:43:05 CDT)
  • AW: AW: "Beefier" benchmark (Thu Aug 21 2014 - 03:04:01 CDT)
  • AW: "Beefier" benchmark (Wed Aug 20 2014 - 01:38:51 CDT)
  • AW: AW: AW: Hybrid MPI + Multicore + Cuda build (Fri Aug 15 2014 - 00:39:36 CDT)
  • AW: AW: Hybrid MPI + Multicore + Cuda build (Thu Aug 14 2014 - 08:14:30 CDT)
  • AW: Hybrid MPI + Multicore + Cuda build (Thu Aug 14 2014 - 02:13:32 CDT)
  • AW: Running NAMD via GROMACS topology (Mon Aug 11 2014 - 00:33:15 CDT)
  • AW: Regarding Temperature calculation from velocity trajectory of NAMD-2.9 (Fri Jul 11 2014 - 02:51:44 CDT)
  • AW: Regarding Temperature calculation from velocity trajectory of NAMD-2.9 (Thu Jul 10 2014 - 05:08:50 CDT)
  • AW: REMD on IBM iDataPlex DX360M3 (Wed Jul 09 2014 - 02:24:27 CDT)
  • AW: REMD on IBM iDataPlex DX360M3 (Tue Jul 08 2014 - 01:12:46 CDT)
  • AW: Regarding NAMD and MD simulations (Mon Jul 07 2014 - 02:48:08 CDT)
  • AW: REMD on IBM iDataPlex DX360M3 (Thu Jul 03 2014 - 05:42:02 CDT)
  • AW: REMD on IBM iDataPlex DX360M3 (Thu Jul 03 2014 - 05:38:48 CDT)
  • AW: REMD on IBM iDataPlex DX360M3 (Thu Jul 03 2014 - 04:28:46 CDT)
  • AW: AW: Xeon vs i7 and ECC vs SDRAM (Thu Jun 26 2014 - 00:59:13 CDT)
  • AW: AW: Xeon vs i7 and ECC vs SDRAM (Wed Jun 25 2014 - 01:47:38 CDT)
  • AW: Xeon vs i7 and ECC vs SDRAM (Wed Jun 25 2014 - 00:31:47 CDT)
  • AW: AW: AW: Using nodelist file causes namd to hang (Tue Jun 24 2014 - 08:50:06 CDT)
  • AW: paricle type in residue based coarse graining of NAMD (Tue Jun 24 2014 - 03:13:21 CDT)
  • AW: Fatal error.. (Mon Jun 23 2014 - 03:33:27 CDT)
  • AW: AW: Using nodelist file causes namd to hang (Fri Jun 20 2014 - 05:15:02 CDT)
  • AW: Using nodelist file causes namd to hang (Fri Jun 20 2014 - 02:25:11 CDT)
  • AW: AW: AW: AW: AW: Using nodelist file causes namd to hang (Thu Jun 19 2014 - 05:09:43 CDT)
  • AW: AW: AW: AW: Using nodelist file causes namd to hang (Thu Jun 19 2014 - 02:19:03 CDT)
  • AW: Should PME be used for electrostatic interaction energy calculations? (Thu Jun 19 2014 - 02:46:48 CDT)
  • AW: Constraint failure in RATTLE algorithm (Thu Jun 19 2014 - 02:29:16 CDT)
  • AW: Should PME be used for electrostatic interaction energy calculations? (Thu Jun 19 2014 - 02:25:49 CDT)
  • AW: AW: AW: Using nodelist file causes namd to hang (Wed Jun 18 2014 - 07:52:29 CDT)
  • AW: AW: Using nodelist file causes namd to hang (Mon Jun 16 2014 - 02:19:28 CDT)
  • AW: AW: How to refer to side-chain via tcl-force scripting? (Fri Jun 13 2014 - 03:26:33 CDT)
  • AW: Reg: movement of protein outside box (Fri Jun 13 2014 - 03:09:20 CDT)
  • AW: How to refer to side-chain via tcl-force scripting? (Fri Jun 13 2014 - 02:56:03 CDT)
  • AW: How to refer to side-chain via tcl-force scripting? (Fri Jun 13 2014 - 02:53:41 CDT)
  • AW: NAMD_2.9_Linux-x86_64-multicore-CUDA Segfaults (Wed Jun 11 2014 - 03:07:21 CDT)
  • AW: Reg: movement of protein outside box (Tue Jun 10 2014 - 07:26:58 CDT)
  • AW: Reg: movement of protein outside box (Tue Jun 10 2014 - 02:47:32 CDT)
  • AW: NAMD-2.9:Help needed on how to write to different DCD files in a single running NAMD simulation?? (Tue Jun 10 2014 - 02:43:11 CDT)
  • AW: NAMD Multicore CUDA usage (Tue Jun 10 2014 - 02:33:13 CDT)
  • AW: Reg: deformation of water box during equilibration (Tue Jun 10 2014 - 02:23:04 CDT)
  • AW: coordinates in namd (Tue Jun 03 2014 - 01:40:14 CDT)
  • AW: NAMD-SMP-Ibverbs-CUDA assistance (Wed May 14 2014 - 00:42:51 CDT)
  • AW: NAMD and NUMA (Mon May 12 2014 - 01:12:54 CDT)
  • AW: AW: NAMD and NUMA (Fri May 09 2014 - 02:11:19 CDT)
  • AW: TclForces wrapmode FATAL ERROR: Setting parameter wrapmode from script failed (Thu May 08 2014 - 01:54:10 CDT)
  • AW: NAMD and NUMA (Thu May 08 2014 - 01:53:12 CDT)
  • TclForces wrapmode FATAL ERROR: Setting parameter wrapmode from script failed (Tue May 06 2014 - 05:49:45 CDT)
  • AW: How to extract the .coor, .vel and .xsc files for a conformation in the middle of trajectory (Tue Apr 29 2014 - 02:21:20 CDT)
  • AW: How to extract the .coor, .vel and .xsc files for a conformation in the middle of trajectory (Tue Apr 29 2014 - 02:20:33 CDT)
  • AW: CUDA error in cuda_check_local_progress (Tue Apr 22 2014 - 00:39:49 CDT)
  • AW: CUDA error in cuda_check_local_progress (Thu Apr 17 2014 - 04:50:10 CDT)
  • AW: CUDA error in cuda_check_local_progress (Thu Apr 17 2014 - 03:21:44 CDT)
  • AW: Re: Persistent margin errors (Wed Apr 16 2014 - 07:49:47 CDT)
  • AW: Simulation crash during NPT equilibration (Fri Apr 11 2014 - 06:31:49 CDT)
  • AW: slice of water box (Thu Apr 10 2014 - 01:46:05 CDT)
  • AW: AW: AW: Using nodelist file causes namd to hang (Wed Apr 09 2014 - 07:09:53 CDT)
  • AW: AW: Using nodelist file causes namd to hang (Wed Apr 09 2014 - 05:53:50 CDT)
  • AW: Using nodelist file causes namd to hang (Wed Apr 09 2014 - 05:28:51 CDT)
  • AW: Using nodelist file causes namd to hang (Wed Apr 09 2014 - 00:21:40 CDT)
  • AW: AW: AW: Using nodelist file causes namd to hang (Tue Apr 08 2014 - 07:30:15 CDT)
  • AW: AW: Using nodelist file causes namd to hang (Tue Apr 08 2014 - 06:22:41 CDT)
  • AW: Using nodelist file causes namd to hang (Tue Apr 08 2014 - 05:06:03 CDT)
  • AW: Movie of a channel trajectory (Mon Apr 07 2014 - 02:05:25 CDT)
  • AW: residue_rmsd.tcl segmentation fault (Fri Apr 04 2014 - 03:18:08 CDT)
  • AW: residue_rmsd.tcl segmentation fault (Fri Apr 04 2014 - 02:53:45 CDT)
  • AW: Assigning different temperatures to simulation (Wed Apr 02 2014 - 02:45:57 CDT)
  • Random segfault for MPI based REMD at startup (Wed Apr 02 2014 - 00:34:20 CDT)
  • AW: Assigning different temperatures to simulation (Wed Apr 02 2014 - 00:06:08 CDT)
  • AW: Assigning different temperatures to simulation (Wed Apr 02 2014 - 00:02:58 CDT)
  • AW: Constraint failure in RATTLE (Tue Apr 01 2014 - 00:11:28 CDT)
  • AW: remd across gpus (Mon Mar 31 2014 - 04:13:21 CDT)
  • AW: Constraint failure in RATTLE (Mon Mar 31 2014 - 00:43:09 CDT)
  • AW: remd across gpus (Mon Mar 31 2014 - 00:39:03 CDT)
  • AW: Question about accelerated MD (Wed Mar 26 2014 - 02:34:20 CDT)
  • Improve scaling for large amount of fixed atoms (Wed Mar 19 2014 - 03:19:38 CDT)
  • AW: how to get cell vectors in tcl forces script (Thu Mar 13 2014 - 08:34:58 CDT)
  • AW: how to get cell vectors in tcl forces script (Wed Mar 12 2014 - 09:59:12 CDT)
  • AW: how to get cell vectors in tcl forces script (Wed Mar 12 2014 - 07:54:50 CDT)
  • AW: how to get cell vectors in tcl forces script (Wed Mar 12 2014 - 02:29:43 CDT)
  • AW: AW: benchmark info (Fri Mar 07 2014 - 01:40:25 CST)
  • AW: benchmark info (Fri Feb 28 2014 - 01:18:46 CST)
  • AW: RE: Runaway positive feedback when minimizing large systems (was: strange glitches when performing energy minimization in MDFF simulations) (Fri Feb 21 2014 - 01:34:55 CST)
  • AW: (Thu Feb 20 2014 - 00:41:55 CST)
  • AW: Require Suggestion (Wed Feb 19 2014 - 01:42:09 CST)
  • AW: GPU/CPU workstation optimal simulation parameters for NAMD2.9 performance (Wed Feb 19 2014 - 01:38:53 CST)
  • AW: REMD (Tue Feb 18 2014 - 02:59:07 CST)
  • AW: Job script for multi node job (Fri Feb 14 2014 - 06:03:47 CST)
  • AW: Job script for multi node job (Fri Feb 14 2014 - 05:12:56 CST)
  • AW: moving out of the box (Thu Feb 13 2014 - 14:24:53 CST)
  • AW: Dihedrals multiplicity! (Thu Feb 13 2014 - 14:23:52 CST)
  • AW: moving out of the box (Thu Feb 13 2014 - 14:21:26 CST)
  • AW: RE: Strange glitches when performing energy minimization in MDFF simulations (Wed Feb 12 2014 - 01:53:40 CST)
  • AW: Log file is not being updated (Mon Feb 10 2014 - 07:32:10 CST)
  • AW: Log file is not being updated (Mon Feb 10 2014 - 06:42:06 CST)
  • AW: Re: Various questions (Mon Feb 03 2014 - 04:34:48 CST)
  • AW: recent comparison of NAMD to other MD engines (Fri Jan 24 2014 - 13:22:51 CST)
  • AW: recent comparison of NAMD to other MD engines (Fri Jan 24 2014 - 01:01:04 CST)
  • AW: recent comparison of NAMD to other MD engines (Thu Jan 23 2014 - 01:32:54 CST)
  • AW: Various questions (Wed Jan 22 2014 - 02:42:07 CST)
  • AW: Question regarding reverse CG to all-atom (Tue Jan 21 2014 - 06:18:10 CST)
  • AW: keeping Crystal angles constant (Thu Jan 16 2014 - 02:36:51 CST)
  • AW: keeping Crystal angles constant (Thu Jan 16 2014 - 02:13:08 CST)
• oguz gurbulak
  • OPLS/AA force field (Wed Aug 05 2015 - 09:00:01 CDT)
  • bond lengths and angles constraints (Tue Jun 23 2015 - 10:04:53 CDT)
  • OPLS force field in NAMD (Sat Jun 20 2015 - 11:43:02 CDT)
  • question about restart conf file (Sun Apr 26 2015 - 07:10:44 CDT)
  • restart simulation (Thu Apr 23 2015 - 09:22:38 CDT)
  • TIP4P topology and parameter files (Sun Apr 19 2015 - 05:18:41 CDT)
  • bond angle and dihedral values (Thu Mar 26 2015 - 03:55:03 CDT)
• Osvalds Verners
  • Re: running Multiple-replicas metadynamics (Fri May 16 2014 - 14:21:28 CDT)
  • running Multiple-replicas metadynamics (Fri May 16 2014 - 13:01:08 CDT)
• Otello Maria Roscioni
  • Re: Dielectric constant of water from MSM and PME simulations (Mon Oct 26 2015 - 12:29:02 CDT)
• Ozge Sensoy
  • dual-boost aMD and the dV value in the output file (Sun Jan 18 2015 - 14:00:47 CST)
• PANAGIOTA KYRIAKOU
  • Re: VDW energy: positive or negative? (Tue Mar 04 2014 - 18:24:54 CST)
  • VDW energy: positive or negative? (Tue Mar 04 2014 - 17:20:53 CST)
  • Re: Temperature reassignment (Wed Jan 01 2014 - 18:17:40 CST)
• Panel Nicolas (M.)
  • Re: Colvars Boundary potentials do not look harmonic (Thu Jun 04 2015 - 08:08:49 CDT)
  • Colvars Boundary potentials do not look harmonic (Wed Jun 03 2015 - 10:00:53 CDT)
  • Truncated octahedron : Problems in PBC when reading a dcd file with NAMD (Mon Mar 16 2015 - 11:18:00 CDT)
• Parag Khuraswar
  • node file for NAMD (Fri Sep 11 2015 - 08:02:54 CDT)
  • node file for NAMD (Tue Sep 01 2015 - 23:28:06 CDT)
  • RE: feature request: external initiated clean exit (Fri Aug 21 2015 - 07:58:53 CDT)
• parikshit moitra
  • Question regarding reverse CG to all-atom (Tue Jan 21 2014 - 04:42:04 CST)
• Patrick Chiu
  • the dielectric constant use in pairwise interaction energy calculation of ligand and protein (Tue Apr 08 2014 - 08:45:11 CDT)
• Payal Chatterjee
  • Re: vmd-l: Re: Including two parameters for protein-ligand simulation (Wed Oct 28 2015 - 03:08:16 CDT)
• Payel Das
  • Updated Link: Postdoc positions available at IBM (bio-molecular modeling and MD) (Mon Mar 16 2015 - 10:50:46 CDT)
  • Postdoc positions available at IBM (bio-molecular modeling and MD) (Mon Mar 16 2015 - 09:15:05 CDT)
• Per Larsson
  • Dual boost accelerated md energy parameters? (Mon May 12 2014 - 13:54:48 CDT)
  • Re: Setting up membrane protein simulation from existing conformation? (Wed May 07 2014 - 15:12:53 CDT)
  • Setting up membrane protein simulation from existing conformation? (Wed May 07 2014 - 14:17:41 CDT)
• Peter Freddolino
  • Re: Add ions/molecules different from Autoionize defaults (Sun Dec 27 2015 - 22:04:00 CST)
  • Re: Add ions/molecules different from Autoionize defaults (Sat Dec 26 2015 - 21:12:23 CST)
  • Re: Add ions/molecules different from Autoionize defaults (Thu Dec 24 2015 - 08:45:43 CST)
  • Re: Overflow in LJcorrection? (Sat Dec 05 2015 - 21:15:12 CST)
  • Re: Overflow in LJcorrection? (Sat Dec 05 2015 - 17:57:22 CST)
  • Re: Overflow in LJcorrection? (Thu Dec 03 2015 - 15:55:49 CST)
  • Re: Fwd: TIP4P and CHARMM27 (Wed Dec 02 2015 - 12:51:43 CST)
  • Re: Fwd: TIP4P and CHARMM27 (Fri Nov 27 2015 - 11:37:48 CST)
  • Re: Fwd: TIP4P and CHARMM27 (Fri Nov 27 2015 - 10:26:05 CST)
  • Re: Fwd: TIP4P and CHARMM27 (Fri Nov 27 2015 - 09:41:00 CST)
  • Re: Reverse Coarse Graining using VMD CG Builder (Wed Oct 21 2015 - 11:25:44 CDT)
  • Re: Reverse Coarse Graining using VMD CG Builder (Wed Oct 21 2015 - 10:49:38 CDT)
  • Re: Reverse Coarse Graining using VMD CG Builder (Wed Oct 21 2015 - 07:29:13 CDT)
  • Re: simulating TIP5P water (Sat Oct 10 2015 - 21:33:50 CDT)
  • Re: LJ Parameters on hydrogen for TIP4P water models (Wed Sep 30 2015 - 08:14:45 CDT)
  • Re: LJ Parameters on hydrogen for TIP4P water models (Tue Sep 29 2015 - 13:25:07 CDT)
  • Re: Atoms moving too fast; simulation has become unstable (Mon Sep 21 2015 - 07:53:14 CDT)
  • Re: Atoms moving too fast; simulation has become unstable (Thu Sep 17 2015 - 23:01:32 CDT)
  • Re: Atoms moving too fast; simulation has become unstable (Thu Sep 17 2015 - 21:44:09 CDT)
  • Re: LJcorrection + switching? (Tue Sep 15 2015 - 20:11:32 CDT)
  • Re: Parameterizing a novel peptide (Mon Sep 14 2015 - 22:00:56 CDT)
  • Re: Parameterizing a novel peptide (Mon Sep 14 2015 - 21:08:55 CDT)
  • Re: patching SO3 group to GAG (Thu Sep 03 2015 - 20:36:45 CDT)
  • Re: parameters problem in sulfated molecules (Tue Sep 01 2015 - 12:25:02 CDT)
  • Re: Atoms moving too fast; simulation has become unstable (Mon Aug 31 2015 - 08:30:48 CDT)
  • Re: Problem running REMD simulation (Wed Aug 26 2015 - 08:28:57 CDT)
  • Re: Problem running REMD simulation (Tue Aug 25 2015 - 23:25:00 CDT)
  • Re: feature request: external initiated clean exit (Fri Aug 21 2015 - 20:04:42 CDT)
  • Re: feature request: external initiated clean exit (Fri Aug 21 2015 - 17:09:40 CDT)
  • Re: feature request: external initiated clean exit (Fri Aug 21 2015 - 16:47:55 CDT)
  • Re: feature request: external initiated clean exit (Fri Aug 21 2015 - 16:44:27 CDT)
  • Re: Controlling water diffusion (Sun Jul 19 2015 - 21:13:15 CDT)
  • Re: Controlling water diffusion (Thu Jul 16 2015 - 21:54:49 CDT)
  • Re: OPLS force field in NAMD (Sat Jun 20 2015 - 22:20:00 CDT)
  • Re: Using a different potential with NAMD (Fri Jun 12 2015 - 09:25:32 CDT)
  • running with replica exchange on stampede (Sun May 24 2015 - 21:40:09 CDT)
• Peter Reinke
  • tools for Charmm (Thu Feb 20 2014 - 02:39:59 CST)
  • Charmm (Thu Feb 20 2014 - 02:31:35 CST)
• Phil Greer
  • Re: "Beefier" benchmark (Tue Aug 19 2014 - 11:30:38 CDT)
  • Re: "Beefier" benchmark (Tue Aug 19 2014 - 11:10:28 CDT)
  • Re: Job script for multi node job (Fri Feb 14 2014 - 09:04:37 CST)
• Phil Miller
  • Re: About Tcl8.3 error in namd2.8 (Wed Jan 01 2014 - 09:33:57 CST)
• Phillips, Carolyn L.
  • Simulation Box Rescaling (Tue May 05 2015 - 18:02:28 CDT)
  • Re: Simulated Annealing with many frequent restarts (Fri May 01 2015 - 11:24:13 CDT)
  • Re: Simulated Annealing with many frequent restarts (Fri May 01 2015 - 10:16:43 CDT)
  • Simulated Annealing with many frequent restarts (Thu Apr 30 2015 - 18:51:19 CDT)
• Pino, James Christopher
  • GPU/CPU workstation optimal simulation parameters for NAMD2.9 performance (Tue Feb 18 2014 - 12:00:34 CST)
• Pragya Priyadarshini
  • Re: AW: Regarding NAMD installation (Mon Aug 17 2015 - 04:38:29 CDT)
  • Regarding NAMD installation (Mon Aug 17 2015 - 02:45:13 CDT)
• Prathit Chatterjee
  • Re: Running two molecule coarse-grained simulation (Thu Apr 16 2015 - 11:37:21 CDT)
  • Re: Running two molecule coarse-grained simulation (Wed Apr 15 2015 - 09:24:32 CDT)
  • Re: Restarting an abruptly interrupted simulation (Tue Mar 17 2015 - 02:03:52 CDT)
• Prija Ponnan
  • Invitation to Submit Review Article Current Protein & Peptide Science (IF: 2.326) (Fri Jun 27 2014 - 06:40:43 CDT)
• Puneet Singh
  • Regarding FFTW routines usage in NAMD (Tue Oct 20 2015 - 07:39:50 CDT)
  • Regarding significance of days per ns (days/ns) parameter in NAMD benchmark (Tue Oct 20 2015 - 01:01:24 CDT)
  • NAMD hybrid configuration: Atoms moving too fast error (Mon Jul 27 2015 - 06:41:38 CDT)
  • segmentation fault when running with mpirun (Fri Jul 24 2015 - 08:05:23 CDT)
• Purushottam Dixit
  • Re: Interrupted Molecular Dynamics Simulation (Tue Jul 28 2015 - 09:51:22 CDT)
• Qing Li
  • Fwd: all atom equilibrium of yeast PGK simulation with NAMD (Tue Feb 03 2015 - 21:14:36 CST)
• Qing Lv
  • Re:Re: How to let NAMD terminate automatically at a given time (Mon Mar 02 2015 - 22:20:40 CST)
• R.J. Swett
  • Re: Force field design (Wed Jul 23 2014 - 23:03:48 CDT)
• R.L. Ma
  • Re: I can not run fixed protein in membrane with NAMD (Sat Jun 27 2015 - 21:27:18 CDT)
• Radhika Anoop
  • Re: charm36 for ATP and MG (Wed Sep 09 2015 - 05:09:39 CDT)
  • charm36 for ATP and MG (Tue Sep 08 2015 - 00:55:48 CDT)
• Raed Ahmed Abdelsalam Shalaby
  • RE: Create psf file (Mon Jun 22 2015 - 05:54:32 CDT)
• Ramin Ekhteiari
  • "BAK" format files (Mon Nov 24 2014 - 06:52:20 CST)
  • Accelerated MD (aMD) (Sat Jul 26 2014 - 06:06:25 CDT)
  • membrane lipid involvement of cholesterol (Sat Jul 26 2014 - 03:14:38 CDT)
  • Re: accelerated MD as the engine for loop refirement (Tue Jul 15 2014 - 01:30:12 CDT)
  • NAMD energy plugin - dielectric constant (Mon Jul 07 2014 - 14:59:42 CDT)
  • namd-slurm file (Wed Jul 02 2014 - 10:08:31 CDT)
  • Re: Re: vmd-l: NAMD energy calculation (Tue Jul 01 2014 - 12:07:47 CDT)
  • NAMD energy calculation (Wed Jun 25 2014 - 11:45:33 CDT)
  • Re: NAMD energy plugin (Wed Jun 04 2014 - 13:55:23 CDT)
  • NAMD energy plugin (Wed Jun 04 2014 - 12:45:36 CDT)
  • NAMD-GPU (Wed May 14 2014 - 07:19:10 CDT)
  • SHAKE or RATTLE algorithm (Fri Apr 04 2014 - 15:08:04 CDT)
  • 6 equilibration steps at charmm gui server (Thu Apr 03 2014 - 04:32:58 CDT)
• Ramya Gamini
  • Re: RBCG and NAMD 2.9 (Wed Apr 16 2014 - 14:49:54 CDT)
• Randall Hall
  • Thermodynamic integration question (Sat Sep 05 2015 - 23:28:57 CDT)
  • Thermodynamic integration questions (Thu Jan 09 2014 - 12:16:03 CST)
• ransun
  • Re: long running sim dies (Mon Oct 13 2014 - 09:12:33 CDT)
• Raul Araya
  • Martini forcefield RBCG and ENM (Fri Aug 15 2014 - 10:05:01 CDT)
  • RBCG and NAMD 2.9 (Wed Apr 16 2014 - 13:21:43 CDT)
• Ravi Abrol
  • NAMD Multicore CUDA usage (Fri Jun 06 2014 - 14:20:10 CDT)
• Rawan Al Nsour
  • Re: Polymer Layer/ Cutoff (Thu May 15 2014 - 16:13:58 CDT)
  • Polymer Layer/ Cutoff (Thu May 15 2014 - 11:19:21 CDT)
  • Patch to connect monomers code (Sun May 04 2014 - 12:15:12 CDT)
  • Re: Teflon New Residue (Fri May 02 2014 - 11:10:38 CDT)
  • Teflon New Residue (Fri May 02 2014 - 09:57:57 CDT)
  • Multiple dihedral with multiplicity of 7 greater than max of 6 (Wed Apr 02 2014 - 13:44:33 CDT)
  • Multiple dihedral with multiplicity of 7 greater than max of 6 (Wed Apr 02 2014 - 13:38:53 CDT)
  • Re: Volume Entry (Sun Feb 16 2014 - 16:36:04 CST)
  • Re: Volume Entry (Sun Feb 16 2014 - 15:16:44 CST)
  • Re: Volume Entry (Sun Feb 16 2014 - 13:08:05 CST)
  • Re: Volume Entry (Sun Feb 16 2014 - 10:29:18 CST)
  • Re: Volume Entry (Mon Feb 10 2014 - 11:04:06 CST)
  • Volume Entry (Mon Feb 10 2014 - 10:08:19 CST)
  • Specific Heat Calculation (Fri Feb 07 2014 - 20:56:14 CST)
  • PMEGridSizeX (number of grid points) is very small. (Wed Feb 05 2014 - 12:00:57 CST)
• Rebecca Lindsey
  • Re: 1-5 Intramolecular repulsions (Wed Nov 05 2014 - 13:07:49 CST)
  • 1-5 Intramolecular repulsions (Wed Nov 05 2014 - 11:54:40 CST)
• Research Jubilant
  • non-neutralized system (Wed Jun 04 2014 - 10:29:47 CDT)
  • coordinates in namd (Mon Jun 02 2014 - 23:34:52 CDT)
  • Re: vmd-l: Re: wrapping option in namd (Wed Mar 19 2014 - 22:38:16 CDT)
  • wrapping option in namd (Wed Mar 19 2014 - 21:34:57 CDT)
  • Calculating density for a molecule (Fri Feb 07 2014 - 11:36:41 CST)
• Revthi Sanker
  • Re: create psf file without hydrogens (Fri Nov 21 2014 - 03:23:19 CST)
  • create psf file without hydrogens (Thu Nov 20 2014 - 12:26:48 CST)
• Richard Wood
  • RE: vmd-l: membrane lipid involvement of cholesterol (Sat Jul 26 2014 - 09:07:57 CDT)
  • RE: vmd-l: membrane lipid involvement of cholesterol (Sat Jul 26 2014 - 06:26:59 CDT)
• Richard Overstreet
  • PME Seg Fault (Mon Aug 10 2015 - 09:11:27 CDT)
  • Re: wrapping in NVT (Wed Jul 22 2015 - 01:05:30 CDT)
  • Re: WHICH VERSION OF NAMD SHOULD I INSTALL ON MY SYSTEM? (Sun Mar 01 2015 - 16:56:39 CST)
• Richard Wood
  • error message (Tue Jun 03 2014 - 19:13:26 CDT)
• Richter, Stefan
  • AW: Compilation of NAMD from Source (Cray XC40) (Tue Oct 13 2015 - 13:10:44 CDT)
  • Compilation of NAMD from Source (Cray XC40) (Tue Oct 13 2015 - 09:26:06 CDT)
• Riley Workman
  • PMF from ABF simulation not plateauing (Thu May 08 2014 - 12:08:13 CDT)
• Robert McGibbon
  • [ANN] MDTraj 1.0: Trajectory Analysis in Python (Mon Sep 08 2014 - 17:19:00 CDT)
• Robert Wohlhueter
  • Re: which namd versions compatible with CUDA 5.5 and other CUDA woes (Sun Sep 28 2014 - 12:00:17 CDT)
  • which namd versions compatible with CUDA 5.5 and other CUDA woes (Mon Sep 22 2014 - 13:39:19 CDT)
• rocwhite168
  • Re: 1-5 Intramolecular repulsions (Wed Nov 05 2014 - 14:55:05 CST)
  • Re: 1-5 Intramolecular repulsions (Wed Nov 05 2014 - 13:02:55 CST)
• Roy Fernando
  • Simulation Do not Run in the Cluster (Sun Sep 21 2014 - 12:16:44 CDT)
  • Re: NAMD 2.9 quits early without error message. (Sat Mar 08 2014 - 10:03:21 CST)
  • Re: How to maintain Density constant? (Thu Mar 06 2014 - 12:03:37 CST)
  • Re: How to maintain Density constant? (Thu Mar 06 2014 - 11:28:23 CST)
  • How to maintain Density constant? (Wed Mar 05 2014 - 15:43:59 CST)
  • Re: Force Field Parameters for PEG (Mon Feb 24 2014 - 10:48:08 CST)
  • Re: Force Field Parameters for PEG (Mon Feb 24 2014 - 10:22:47 CST)
  • Re: Non standar solvent (Tue Feb 18 2014 - 10:49:10 CST)
  • Liquid Simulation Failure (Fri Jan 24 2014 - 18:54:44 CST)
  • Re: CAN'T FIND DIHEDRAL PARAMETERS FOR CPH1 NR2 FE NPH (Tue Jan 07 2014 - 08:05:22 CST)
• rswett_at_chem.wayne.edu
  • Looking for benchmarks on k80's (Thu Aug 13 2015 - 10:40:45 CDT)
• Rubén Granero
  • Re: Error compiling NAMD2.9 after patching with PLUMED2.1 (Tue Dec 16 2014 - 12:07:45 CST)
  • Re: Error compiling NAMD2.9 after patching with PLUMED2.1 (Tue Dec 16 2014 - 07:39:02 CST)
  • Error compiling NAMD2.9 after patching with PLUMED2.1 (Mon Dec 15 2014 - 06:47:27 CST)
• Ryan Gordon
  • Re: Editing Patch Grid Dimensions (Thu Feb 05 2015 - 12:08:20 CST)
  • Editing Patch Grid Dimensions (Thu Feb 05 2015 - 10:00:28 CST)
  • NAMD slows at startup phase 1 smp problem (Mon Jan 12 2015 - 12:24:31 CST)
• Ryan McGreevy
  • Re: How to output CCC per residue from MDFF (Thu Apr 23 2015 - 22:15:49 CDT)
  • Re: AW: Question about accelerated MD (Wed Mar 26 2014 - 11:19:17 CDT)
• Sachin Natesh
  • Re: Adaptive tempering implementation in NAMD differs (Thu Sep 24 2015 - 20:28:36 CDT)
  • Re: Adaptive tempering implementation in NAMD differs (Wed Sep 23 2015 - 10:28:05 CDT)
  • Adaptive tempering implementation in NAMD differs from original paper? (Tue Sep 22 2015 - 19:45:22 CDT)
  • Error in NAMD Controller Class Reference- Adaptive Tempering (Thu Sep 10 2015 - 19:13:41 CDT)
  • Adaptive Tempering - Velocity Rescaling (Mon Aug 31 2015 - 09:45:16 CDT)
• Sadegh Faramarzi Ganjabad
  • Topology and parameters for Sodium dodecanoate (Tue Nov 03 2015 - 11:21:45 CST)
  • Re: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OC2D2 (Wed Mar 18 2015 - 17:50:58 CDT)
  • FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OC2D2 (Wed Mar 18 2015 - 16:47:50 CDT)
  • Subject: RE: Re:Subject: Re: Subject: Re:Re: New partial charges after patching (Tue Jul 22 2014 - 06:28:57 CDT)
  • Subject: Re: Subject: Re: Subject: Re:Re: New partial charges after patching (Tue Jul 22 2014 - 05:04:09 CDT)
  • Re:Subject: Re: Subject: Re:Re: New partial charges after patching (Wed Jul 16 2014 - 01:27:52 CDT)
  • Subject: Re:Re: New partial charges after patching (Thu Jun 19 2014 - 03:21:33 CDT)
  • New partial charges after patching (Sat Jun 14 2014 - 04:15:47 CDT)
  • Fwd: Getting extra atoms by Patching! (Thu May 08 2014 - 15:49:14 CDT)
  • Getting extra atoms by Patching! (Fri May 02 2014 - 18:51:31 CDT)
  • FEP error using CUDA (Sun Apr 13 2014 - 22:42:12 CDT)
• Salvatore Mario Cosseddu
  • Citating colvars module (Tue Jan 21 2014 - 11:20:50 CST)
• Samoylova, Olga M.
  • RE: Nanotube Simulation (Tue Apr 15 2014 - 12:50:06 CDT)
  • RE: Nanotube Simulation (Tue Apr 15 2014 - 09:49:31 CDT)
• Samuel Bowerman
  • NAMD CVS_CUDA ERROR: "all CUDA-capable devices are busy or unavailable" (Mon Aug 11 2014 - 11:50:45 CDT)
• sananda chatterjee
  • NAMD_energy_plot (Tue Jul 22 2014 - 17:08:56 CDT)
• Sandhyaa Subramanian
  • Re: FATAL ERROR: Low global exclusion count! (9231 vs 9270) System unstable or pairlistdist or cutoff too small. (Wed Sep 03 2014 - 02:37:32 CDT)
  • FATAL ERROR: Low global exclusion count! (9231 vs 9270) System unstable or pairlistdist or cutoff too small. (Wed Sep 03 2014 - 02:34:06 CDT)
  • FATAL ERROR: Low global exclusion count! (9231 vs 9270) System unstable or pairlistdist or cutoff too small. (Sat Aug 30 2014 - 09:06:14 CDT)
• Sanjana Anil Kumar Nair
  • running namd gpu version (Sat Aug 29 2015 - 05:21:41 CDT)
• Santosh Kumar Chaudhary
  • Re: error while running namd on CRAY XC40 machine (Fri Mar 27 2015 - 01:00:51 CDT)
  • error while running namd on CRAY XC40 machine (Sun Mar 22 2015 - 02:40:31 CDT)
  • Re: setting up namd simulation in IBM Blue Gene/L (Sat Dec 20 2014 - 01:53:14 CST)
  • problem in installation of charm-6.4.0 in bluegeneL] (Fri Dec 19 2014 - 05:49:45 CST)
  • RE: setting up namd simulation in IBM Blue Gene/L (Thu Dec 18 2014 - 00:09:48 CST)
  • setting up namd simulation in IBM Blue Gene/L (Wed Dec 17 2014 - 06:21:17 CST)
  • Info: Pairlistdist is too small for 3 computes during timestep 115001 (Fri Dec 12 2014 - 10:34:41 CST)
• Sebastian Stolzenberg
  • Re: FEP, Ewald size-dependence charge correction (Fri Sep 12 2014 - 13:21:10 CDT)
  • Re: FEP, Ewald size-dependence charge correction (Sun Sep 07 2014 - 10:23:17 CDT)
  • FEP, Ewald size-dependence charge correction (Tue Sep 02 2014 - 15:12:17 CDT)
• Sebastián Gutiérrez
  • Nucleic acid stains parameters (Mon Aug 25 2014 - 10:37:04 CDT)
• sena
  • Re: mail reg parameters (Fri Dec 25 2015 - 22:29:17 CST)
• Seth Axen
  • Re: Restraining angle between bond vector and coordinate vector (Wed Mar 25 2015 - 19:01:40 CDT)
  • Restraining angle between bond vector and coordinate vector (Mon Mar 23 2015 - 15:26:37 CDT)
• Shailesh Pandey
  • problem in calculating binding energy using MMGBSA with namd-2.9 (Mon Sep 01 2014 - 07:31:34 CDT)
  • Re: Regarding Temperature calculation from velocity trajectory of NAMD-2.9 (Fri Jul 11 2014 - 06:14:59 CDT)
  • Fwd: Regarding Temperature calculation from velocity trajectory of NAMD-2.9 (Thu Jul 10 2014 - 09:31:03 CDT)
  • Regarding Temperature calculation from velocity trajectory of NAMD-2.9 (Thu Jul 10 2014 - 04:30:20 CDT)
  • Re: NAMD-2.9:Help needed on how to write to different DCD files in a single running NAMD simulation?? (Thu Jun 26 2014 - 04:41:49 CDT)
  • NAMD-2.9:Help needed on how to write to different DCD files in a single running NAMD simulation?? (Mon Jun 09 2014 - 12:54:03 CDT)
• Shalton Evans
  • 16 total processes killed (some possibly by mpirun during cleanup) (Mon Nov 02 2015 - 14:34:13 CST)
  • .inpcrd to .pdb (Sun Dec 21 2014 - 13:56:30 CST)
  • (no subject) (Sat Aug 09 2014 - 23:00:48 CDT)
  • unsubscribe (Sun May 11 2014 - 19:18:39 CDT)
  • ERROR: CALCULATED VDWA/B FORCES DOES NOT MATCH ENERGY (Mon Feb 03 2014 - 21:13:41 CST)
• Shane.OMahony
  • Calculating the force needed to constrain a protein (Fri Jul 18 2014 - 11:18:05 CDT)
• Shanshan Wu
  • namd simulation with TIP5P (Tue Feb 03 2015 - 18:36:34 CST)
• Shaon Chakrabarti
  • Force field for sulfated tyrosines (Sun May 04 2014 - 21:35:38 CDT)
• Sharmon
  • Regarding free energy cost incurred by using pseudo bonds (Thu Jul 10 2014 - 13:29:29 CDT)
• Shayon Bhattacharya
  • Re: LJ Parameters on hydrogen for TIP4P water models (Wed Sep 30 2015 - 16:39:45 CDT)
  • Re: LJ Parameters on hydrogen for TIP4P water models (Tue Sep 29 2015 - 14:04:44 CDT)
  • LJ Parameters on hydrogen for TIP4P water models (Tue Sep 29 2015 - 10:20:36 CDT)
• Shoresh
  • Re: problem with water molecules angle in MD simulation (Tue Jan 27 2015 - 10:30:54 CST)
• Shoresh Shafei
  • Re: problem with water molecules angle in MD simulation (Fri Jan 30 2015 - 02:28:17 CST)
  • problem with water molecules angle in MD simulation (Sun Jan 25 2015 - 19:06:23 CST)
• Shyno Mathew
  • Re: Restarting an FEP simulation (Sat Mar 22 2014 - 14:00:06 CDT)
  • Re: Restarting an FEP simulation (Mon Mar 10 2014 - 11:58:02 CDT)
  • Restarting an FEP simulation (Wed Mar 05 2014 - 12:43:48 CST)
  • citing SODIUM program (Sat Jan 04 2014 - 10:45:36 CST)
• siddharth kamal
  • Regarding problem in psfgen of heparin (Fri Oct 02 2015 - 14:20:15 CDT)
  • Re: parameters problem in sulfated molecules (Wed Sep 02 2015 - 08:33:11 CDT)
  • Fwd: Regarding problem in generating psf file of heparin and heparan sulfate (Thu Jul 16 2015 - 07:44:46 CDT)
• Simon Kit Sang Chu
  • "missing operator at _@_ in expression" for if statement (Mon Jul 27 2015 - 19:39:51 CDT)
  • VDW energy diverged & VMD functions applied on cluster (Sat Jul 18 2015 - 16:37:54 CDT)
  • Minimization without MD (Thu Jul 16 2015 - 15:37:39 CDT)
  • Minimization without MD (Thu Jul 16 2015 - 16:21:40 CDT)
• Siva Dasetty
  • Re: Implicit solvent lipid bilayer simulation in NAMD. (Wed Sep 17 2014 - 13:23:53 CDT)
  • Re: GBIS using CUDA enabled NAMD (Wed Sep 17 2014 - 09:36:03 CDT)
  • GBIS using CUDA enabled NAMD (Tue Sep 09 2014 - 18:59:01 CDT)
  • Re: GBIS CUDA not yet compatible with fixed atoms (Fri Sep 05 2014 - 18:01:13 CDT)
  • Re: GBIS CUDA not yet compatible with fixed atoms (Fri Sep 05 2014 - 15:24:45 CDT)
  • GBIS CUDA not yet compatible with fixed atoms (Fri Sep 05 2014 - 10:03:12 CDT)
  • SASA calculation (Thu Sep 04 2014 - 09:03:56 CDT)
  • Re: Fixing atoms while equilibration (Mon Sep 01 2014 - 08:07:59 CDT)
  • Re: Fixing atoms while equilibration (Mon Sep 01 2014 - 07:33:57 CDT)
  • NAMD energy minimization (Sun Aug 31 2014 - 14:30:56 CDT)
  • Fixing atoms while equilibration (Fri Aug 29 2014 - 20:12:21 CDT)
• Sofya Lushchekina
  • Colvars keyword problem (Mon May 05 2014 - 09:32:11 CDT)
• Sourav Purohit
  • Rotating Constraints (Tue Feb 24 2015 - 14:23:26 CST)
• Sourav Ray
  • Re: vmd-l: Including two parameters for protein-ligand simulation (Wed Oct 28 2015 - 02:20:04 CDT)
  • Re: NAMD - wrap atoms, not center of mass (Fri Oct 16 2015 - 10:27:09 CDT)
  • Re: node file for NAMD (Sat Sep 12 2015 - 01:13:32 CDT)
  • Re: node file for NAMD (Sat Sep 12 2015 - 01:11:30 CDT)
  • Re: Re: vmd-l: Fwd: Inviting applications for a new PhD program in Quantitative Biosciences at Georgia Tech (Fri Sep 11 2015 - 11:15:47 CDT)
  • Re: vmd-l: Fwd: Inviting applications for a new PhD program in Quantitative Biosciences at Georgia Tech (Wed Sep 09 2015 - 22:51:54 CDT)
  • Re: Atoms moving too fast; simulation has become unstable (Mon Aug 31 2015 - 06:29:30 CDT)
  • Re: Regarding NAMD installation (Mon Aug 17 2015 - 02:53:00 CDT)
  • Re: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CTL2 OC301 (ATOMS 25 45) (Fri Jun 12 2015 - 13:49:00 CDT)
  • Re: Announcement: 'Hands On' Workshop on Computational Biophysics (Berkeley, CA, Aug 3-7, 2015) (Wed May 20 2015 - 00:33:00 CDT)
  • Re: Error applying PME to simulation set up (Wed May 13 2015 - 06:02:51 CDT)
  • Error applying PME to simulation set up (Wed May 13 2015 - 04:24:41 CDT)
  • Re: Which Binary to use? (Fri Apr 24 2015 - 00:45:44 CDT)
  • Re: Running two molecule coarse-grained simulation (Thu Apr 16 2015 - 06:27:30 CDT)
  • Re: Running two molecule coarse-grained simulation (Wed Apr 15 2015 - 09:05:43 CDT)
  • Re: Running two molecule coarse-grained simulation (Wed Apr 15 2015 - 05:51:29 CDT)
  • Running two molecule coarse-grained simulation (Wed Apr 15 2015 - 05:39:18 CDT)
  • Restarting an abruptly interrupted simulation (Tue Mar 17 2015 - 01:30:21 CDT)
  • Re: Updated Link: Postdoc positions available at IBM (bio-molecular modeling and MD) (Mon Mar 16 2015 - 12:30:29 CDT)
  • Re: Restarting NAMD simulation (Thu Mar 12 2015 - 09:16:26 CDT)
  • Restarting NAMD simulation (Thu Mar 12 2015 - 08:30:27 CDT)
• Souvik Sinha
  • Re: Determining the PMF with Adaptive Biasing Forces (Tue Dec 08 2015 - 01:42:34 CST)
• Spencer, Jacob
  • Difficulties with using the "rescalevels" command every MD timestep (Thu Jan 09 2014 - 09:48:37 CST)
• Sridhar Kumar Kannam
  • Re: keyword "outputaccumulatedwork" is not supported, or not recognized in this context. (Thu Oct 15 2015 - 02:24:52 CDT)
  • Re: keyword "outputaccumulatedwork" is not supported, or not recognized in this context. (Thu Oct 15 2015 - 00:54:00 CDT)
  • Re: keyword "outputaccumulatedwork" is not supported, or not recognized in this context. (Wed Oct 14 2015 - 05:41:58 CDT)
  • keyword "outputaccumulatedwork" is not supported, or not recognized in this context. (Tue Oct 13 2015 - 23:39:14 CDT)
  • solvate plugin watsize value (Wed Feb 26 2014 - 20:40:46 CST)
  • Re: About Number of atoms in fixed atoms PDB doesn't match coordinate PDB (Sat Jan 25 2014 - 23:49:47 CST)
  • Re: PBC only along the z axis. (Sat Jan 04 2014 - 18:25:28 CST)
  • PBC only along the z axis. (Thu Jan 02 2014 - 21:46:58 CST)
• Srijita Paul
  • DIDN'T FIND vdW PARAMETER FOR ATOM TYPE SG3O1 (Fri Dec 25 2015 - 00:41:47 CST)
  • (no subject) (Tue Dec 22 2015 - 00:06:49 CST)
• Sriram Adhyapak
  • The 2 NAMD tests "Alanin" and "tclforces" fail to run with "Atoms moving too fast" error (Mon Jul 27 2015 - 20:36:14 CDT)
• Stanislav Q=A0imko?=
  • NAMD - wrap atoms, not center of mass (Fri Oct 16 2015 - 10:20:28 CDT)
• Stefan Richter
  • Re: Compile NAMD - Projections (Thu Oct 15 2015 - 04:40:44 CDT)
  • Re: Compilation of NAMD from Source (Cray XC40) (Wed Oct 14 2015 - 04:38:17 CDT)
• Stephan Grein
  • Re: Extracting data (Thu Feb 05 2015 - 03:44:29 CST)
  • Re: Extracting data (Wed Feb 04 2015 - 05:56:47 CST)
  • Extracting data (Wed Feb 04 2015 - 05:55:37 CST)
  • Set exact molarity in cell (Thu Aug 28 2014 - 09:08:42 CDT)
  • H-Bond measurements (Thu Aug 14 2014 - 01:57:40 CDT)
  • Analysis problem (Data vector empty) (Tue Jul 29 2014 - 04:06:27 CDT)
  • Rule of thumb for equilibration (Mon Jul 28 2014 - 09:45:43 CDT)
  • Re: Loading and analysis of DCD file (~300 MB) (Thu Jul 24 2014 - 07:02:53 CDT)
  • Re: Loading and analysis of DCD file (~300 MB) (Thu Jul 24 2014 - 06:45:54 CDT)
  • Loading and analysis of DCD file (~300 MB) (Thu Jul 24 2014 - 06:18:45 CDT)
• Stojanoski, Vlatko
  • Re: Performing MD simulations with protein and halide ions (iodide, bromide, chloride) (Sat Oct 17 2015 - 15:49:19 CDT)
  • Re: Performing MD simulations with protein and halide ions (iodide, bromide, chloride) (Sat Oct 17 2015 - 15:31:43 CDT)
  • Performing MD simulations with protein and halide ions (iodide, bromide, chloride) (Sat Oct 17 2015 - 14:05:29 CDT)
• Subbarao Kanchi
  • Re: NAMD (Tue Mar 24 2015 - 01:48:39 CDT)
  • Re: Info: Pairlistdist is too small for 3 computes during timestep 115001 (Fri Dec 12 2014 - 16:26:26 CST)
  • Re: Colvars error (Tue Nov 25 2014 - 06:30:36 CST)
  • Re: Colvars error (Tue Nov 25 2014 - 02:08:45 CST)
  • Re: Implicit solvent lipid bilayer simulation in NAMD. (Wed Sep 17 2014 - 14:27:10 CDT)
  • Re: Implicit solvent lipid bilayer simulation in NAMD. (Wed Sep 17 2014 - 13:41:34 CDT)
  • Implicit solvent lipid bilayer simulation in NAMD. (Wed Sep 17 2014 - 12:04:44 CDT)
  • Re: PMF calculations between membrane and nano particle simulations (Tue Jul 08 2014 - 01:01:15 CDT)
  • Re: PMF calculations between membrane and nano particle simulations (Thu Jul 03 2014 - 17:46:24 CDT)
  • PMF calculations between membrane and nano particle simulations (Thu Jul 03 2014 - 15:58:23 CDT)
  • Re: Problems with energy minimization (Wed Apr 09 2014 - 09:14:55 CDT)
  • Electronic density profile of lipid bilayer. (Sun Apr 06 2014 - 20:32:54 CDT)
  • Regarding colvar distancez (Sat Mar 08 2014 - 05:00:28 CST)
  • Re: Job script for multi node job (Fri Feb 14 2014 - 08:24:13 CST)
  • Re: Job script for multi node job (Fri Feb 14 2014 - 05:22:55 CST)
  • Job script for multi node job (Fri Feb 14 2014 - 04:20:16 CST)
  • Re: PBC only along the z axis. (Fri Jan 03 2014 - 00:18:53 CST)
• Subbusinger N
  • Re: namd simulation for solids withoy solvation (Fri Nov 14 2014 - 00:20:24 CST)
  • namd simulation for solids withoy solvation (Thu Nov 13 2014 - 00:02:42 CST)
• sudipta.mml
  • (no subject) (Sat Aug 02 2014 - 20:01:46 CDT)
  • (no subject) (Mon Jul 07 2014 - 01:08:12 CDT)
• Sunhwan Jo
  • Re: exchange force constants (Mon Jul 21 2014 - 09:30:08 CDT)
  • Re: Force field design (Wed Jul 16 2014 - 07:37:19 CDT)
  • Re: Inquiry about lipid membrane simulation (Wed Jun 18 2014 - 14:46:56 CDT)
  • Re: 6 equilibration steps at charmm gui server (Thu Apr 03 2014 - 09:34:23 CDT)
  • Re: Question regarding loss of translational entropy calculation in FEP tutorial (Tue Feb 04 2014 - 14:47:17 CST)
• sunyeping
  • Re: Re: Re: NAMD 2.11b1 released (Thu Nov 26 2015 - 23:26:33 CST)
  • Re: Would it be possible to continue a simulation from any snapshot of a trajectory? (Thu Nov 12 2015 - 20:57:20 CST)
  • Re: Re: NAMD 2.11b1 released (Thu Nov 12 2015 - 20:29:18 CST)
  • Would it be possible to continue a simulation from any snapshot of a trajectory? (Thu Nov 12 2015 - 02:45:51 CST)
  • Re: NAMD 2.11b1 released (Thu Nov 12 2015 - 02:39:43 CST)
  • Re: AW: Why the computational speed does not increase with the increase of GPUs? (Fri Oct 23 2015 - 02:57:48 CDT)
  • Why the computational speed does not increase with the increase of GPUs? (Wed Oct 21 2015 - 22:18:17 CDT)
  • About the TMDInitialRMSD parameter in targeted molecular dynamics (Tue Oct 20 2015 - 12:06:22 CDT)
  • Re: about re install (Tue Oct 20 2015 - 02:09:33 CDT)
  • Several questions about targeted molecular dynamics (Mon Oct 19 2015 - 04:54:09 CDT)
  • Can NAMD simulation solve the problem of coordinate clash in a structural model? (Sun Apr 12 2015 - 21:19:18 CDT)
  • Re: Can NAMD simulation solve the problem of coordinate clash in a structural model? (Sun Apr 12 2015 - 21:18:30 CDT)
  • water-protein interation (Fri Nov 14 2014 - 02:32:11 CST)
  • Re：tutorial-l: Protein structure distorted after Energy minimization with NAMD (Wed Oct 08 2014 - 21:58:02 CDT)
  • RE： The water box shrinks at the start of the MD simulation (Sun Jul 27 2014 - 19:19:15 CDT)
  • RE： RE： Re: RE： NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance (Wed Mar 12 2014 - 09:42:34 CDT)
  • aa_ref-monomer-noh.dcd file in the tutorial of shape-based coarse grained (SBCG) simulation (Mon Mar 10 2014 - 20:01:13 CDT)
  • aa_ref-monomer-noh.dcd in shape-based coarse grained simulation (Sat Mar 08 2014 - 20:09:26 CST)
  • ç­”å¤�：RE： NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance (Mon Feb 24 2014 - 03:37:02 CST)
  • RE： Re: RE： NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance (Mon Feb 24 2014 - 03:32:06 CST)
  • RE： NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance (Sun Feb 23 2014 - 21:13:52 CST)
  • NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance (Sun Feb 23 2014 - 20:29:02 CST)
• sunyzero
  • Energy decomposition analyse in NAMD (Mon Dec 28 2015 - 20:23:28 CST)
  • The script of Umbrella sampling (Tue Dec 22 2015 - 03:33:13 CST)
  • Re:Re: Determining the PMF with Adaptive Biasing Forces (Tue Dec 08 2015 - 22:00:19 CST)
  • Determining the PMF with Adaptive Biasing Forces (Mon Dec 07 2015 - 23:48:55 CST)
  • Determining the PMF with Adaptive Biasing Forces (Mon Dec 07 2015 - 20:02:35 CST)
• Syed Kashif Zafar
  • My Plight (Wed Feb 18 2015 - 18:28:19 CST)
• Tanner, John J.
  • Re: Histidine C-H---O hydrogen bonding (Thu Jan 29 2015 - 12:51:42 CST)
  • Re: FAD topology and parameters (Mon Feb 17 2014 - 10:15:52 CST)
  • FAD topology and parameters (Sun Feb 16 2014 - 15:30:38 CST)
• Tao Qu
  • NAMD Pressure profile calculations (Wed Apr 02 2014 - 15:43:59 CDT)
• Teerapong Pirojsirikul
  • code implementation based on NAMD source code (Thu May 29 2014 - 17:39:21 CDT)
• Thanassis Silis
  • optimising namd ibverb runs (Mon May 18 2015 - 06:48:03 CDT)
  • RE: output files are not stored when running namd-2.10 ibverbs (Fri May 08 2015 - 05:07:50 CDT)
  • output files are not stored when running namd-2.10 ibverbs (Thu May 07 2015 - 10:29:26 CDT)
• Thomas Albers
  • Re: AW: time per step during GPU-accelerated Implicit Solvent calculations (Wed Nov 18 2015 - 08:38:07 CST)
  • time per step during GPU-accelerated Implicit Solvent calculations (Sun Nov 15 2015 - 19:11:26 CST)
  • Re: NH4+ params (Sat Oct 24 2015 - 09:26:17 CDT)
  • aMD and GPU acceleration (Thu Oct 22 2015 - 13:53:09 CDT)
• Thomas C Bishop
  • NAMD workflows <- : Re: call "NAMD" from another program (Fri Jul 10 2015 - 02:38:00 CDT)
• Thomas C. Bishop
  • Re: sausage plot for a namd trajectory in vmd (Tue Aug 11 2015 - 10:30:23 CDT)
  • Re: performance question (Tue Apr 28 2015 - 15:53:42 CDT)
  • Re: performance question (Tue Apr 28 2015 - 14:32:16 CDT)
  • performance question (Mon Apr 27 2015 - 15:54:10 CDT)
  • Re: NAMD error LInux 3.11.10-21-desktop kernel AMD opternon 6272 (Tue Nov 11 2014 - 12:41:11 CST)
  • NAMD error LInux 3.11.10-21-desktop kernel AMD opternon 6272 (Wed Nov 05 2014 - 09:48:15 CST)
  • long running sim dies (Mon Oct 13 2014 - 08:29:43 CDT)
  • Re: ABF simulation, free energy to remove a DNA strand (Tue Aug 05 2014 - 10:17:07 CDT)
  • Re: Nanotube Simulation (Mon Apr 14 2014 - 08:24:22 CDT)
  • Re: Nanotube Simulation (Fri Apr 11 2014 - 14:44:08 CDT)
• Thomas Evangelidis
  • Re: string method in NAMD 2.10 (Tue Sep 22 2015 - 05:31:34 CDT)
  • Re: string method in NAMD 2.10 (Tue Sep 22 2015 - 05:29:16 CDT)
  • Re: is there a method equivalent to conformational flooding in NAMD 2.10 (Mon Jan 12 2015 - 04:32:17 CST)
  • is there a method equivalent to conformational flooding in NAMD 2.10 (Sun Jan 11 2015 - 07:43:36 CST)
  • Fwd: [External] Boost value in aMD simulation (Thu Aug 21 2014 - 06:05:05 CDT)
  • Fwd: [External] Boost value in aMD simulation (Tue Aug 19 2014 - 05:24:17 CDT)
  • Re: [External] Boost value in aMD simulation (Mon Aug 18 2014 - 04:21:25 CDT)
  • Fwd: membrane lipid involvement of cholesterol (Sat Jul 26 2014 - 06:39:30 CDT)
  • Re: Accelerated MD (aMD) (Sat Jul 26 2014 - 06:38:20 CDT)
  • Re: Force field design (Thu Jul 24 2014 - 14:31:31 CDT)
  • Re: [External] Boost value in aMD simulation (Wed Jul 23 2014 - 16:37:47 CDT)
  • Re: [External] Boost value in aMD simulation (Wed Jul 23 2014 - 15:02:25 CDT)
  • Re: how to quantify and visualize the flow of water into a protein (Tue Jul 08 2014 - 19:12:40 CDT)
  • Re: how to quantify and visualize the flow of water into a protein (Tue Jul 08 2014 - 19:04:01 CDT)
  • how to quantify and visualize the flow of water into a protein (Tue Jul 08 2014 - 18:20:48 CDT)
  • Re: Should PME be used for electrostatic interaction energy calculations? (Thu Jun 19 2014 - 02:38:50 CDT)
  • Re: is the aMD implementation compatible with AMBER force fields (Wed Jun 18 2014 - 18:20:00 CDT)
  • is the aMD implementation compatible with AMBER force fields (Wed Jun 18 2014 - 06:20:06 CDT)
  • Re: Dual boost accelerated md energy parameters? (Mon May 12 2014 - 14:11:45 CDT)
  • Re: AW: Question about accelerated MD (Wed Mar 26 2014 - 10:36:51 CDT)
  • Re: Generalized Born Implicit solvation with implicit membrane (Fri Mar 14 2014 - 14:22:36 CDT)
  • Re: how to get cell vectors in tcl forces script (Thu Mar 13 2014 - 11:47:28 CDT)
  • Re: how to get cell vectors in tcl forces script (Thu Mar 13 2014 - 06:11:48 CDT)
  • Re: how to get cell vectors in tcl forces script (Wed Mar 12 2014 - 09:26:46 CDT)
  • how to get cell vectors in tcl forces script (Tue Mar 11 2014 - 15:14:17 CDT)
  • Re: Adding hydrogen atoms to the crystall structure (Tue Feb 18 2014 - 16:04:23 CST)
  • Re: Adding hydrogen atoms to the crystall structure (Tue Feb 18 2014 - 14:56:21 CST)
  • Re: Adding hydrogen atoms to the crystall structure (Tue Feb 18 2014 - 10:44:56 CST)
  • Re: MD simulation Patch grid errors (Tue Jan 14 2014 - 02:19:55 CST)
  • Re: MD simulation Patch grid errors (Tue Jan 07 2014 - 17:56:32 CST)
  • Re: Temperature reassignment (Thu Jan 02 2014 - 09:53:35 CST)
  • Re: Temperature reassignment (Wed Jan 01 2014 - 09:27:57 CST)
• Tian Li
  • problems about new molecule parameterization (Thu Jan 30 2014 - 22:28:36 CST)
• Tien Huynh
  • Re: NAMD 2.11b1 released (Thu Nov 12 2015 - 11:24:00 CST)
  • Re: NAMD 2.11b1 released (Tue Nov 10 2015 - 11:10:25 CST)
  • namd 2.10 crashes when using more than 1 CPU for FEP simulation (Tue Oct 27 2015 - 21:58:14 CDT)
• tillmann.utesch_at_mailbox.tu-berlin.de
  • (no subject) (Wed Nov 26 2014 - 03:20:51 CST)
  • Re: Loading and analysis of DCD file (~300 MB) (Thu Jul 24 2014 - 07:00:09 CDT)
• Tom Coles
  • RE: SMP NAMD reports threads greater than physical cores, even when distributed to other nodes (Fri Dec 18 2015 - 15:16:01 CST)
  • SMP NAMD reports threads greater than physical cores, even when distributed to other nodes (Thu Dec 17 2015 - 10:26:20 CST)
• Tomek StÄ™pniewski
  • Re: Parameterizing a novel peptide (Fri Sep 11 2015 - 18:16:27 CDT)
• Tristan Croll
  • Re: Add ions/molecules different from Autoionize defaults (Tue Dec 29 2015 - 07:12:10 CST)
  • Re: anionic cysteine (Wed Dec 09 2015 - 04:23:03 CST)
  • Re: anionic cysteine (Tue Dec 08 2015 - 22:00:12 CST)
  • Re: vmd-l: Re: On-the-fly modification of tclforces script? (Fri Nov 13 2015 - 19:28:39 CST)
  • Re: On-the-fly modification of tclforces script? (Fri Nov 13 2015 - 18:14:28 CST)
  • Re: On-the-fly modification of tclforces script? (Fri Nov 13 2015 - 16:48:21 CST)
  • Re: NAMD 2.11b1 released (Wed Nov 11 2015 - 20:11:00 CST)
  • Re: On-the-fly modification of tclforces script? (Tue Nov 10 2015 - 16:03:38 CST)
  • Re: On-the-fly modification of tclforces script? (Tue Nov 10 2015 - 04:27:19 CST)
  • On-the-fly modification of tclforces script? (Tue Nov 10 2015 - 03:01:19 CST)
  • Weird psfgen bug? (Fri Oct 30 2015 - 03:22:06 CDT)
  • RE: Fwd: ANGLE PARAMETERS FOR NH3 HC NH3 (Wed Oct 28 2015 - 20:36:08 CDT)
  • RE: constraint failure in Rattle algorithm for atom 54134 (Mon Oct 26 2015 - 01:59:47 CDT)
  • Triple-hybrid topology? (Tue Oct 06 2015 - 19:26:07 CDT)
  • Re: Regarding problem in psfgen of heparin (Tue Oct 06 2015 - 18:44:21 CDT)
  • RE: Regarding problem in psfgen of heparin (Mon Oct 05 2015 - 23:00:32 CDT)
  • Re: NAMD/VMD: generating psf for Abeta, ACE patch (Tue Sep 15 2015 - 17:53:20 CDT)
  • Re: Problem with iron ion (FE2+) (Tue Aug 25 2015 - 03:56:51 CDT)
  • Instability in harmonic restraints when equilibrating large systems (Fri Jul 24 2015 - 16:52:05 CDT)
  • Re: Recomposing the system splitted by periodicity (Thu Jun 11 2015 - 23:22:50 CDT)
  • Re: Can NAMD simulation solve the problem of coordinate clash in a structural model? (Fri Apr 17 2015 - 16:50:07 CDT)
  • Re: GBIS in NAMD 2.10 CUDA with IMD (Sun Feb 15 2015 - 20:38:40 CST)
  • Re: GBIS in NAMD 2.10 CUDA with IMD (Wed Feb 11 2015 - 15:09:11 CST)
  • GBIS in NAMD 2.10 CUDA with IMD (Wed Feb 11 2015 - 04:18:11 CST)
  • Re: problem with water molecules angle in MD simulation (Fri Jan 30 2015 - 02:43:42 CST)
  • Re: problem with water molecules angle in MD simulation (Fri Jan 30 2015 - 02:25:32 CST)
  • Re: using NAMD with CHARMM36 ff (Wed Jan 21 2015 - 01:37:05 CST)
  • Re: Running CUDA on a laptop (Tue Jan 13 2015 - 19:14:31 CST)
  • Running CUDA on a laptop (Tue Jan 13 2015 - 18:29:59 CST)
  • NAMD 2.10b1: occasional corrupted frame in binary dcd output (Tue Dec 23 2014 - 16:39:46 CST)
  • Re: create psf file without hydrogens (Thu Nov 20 2014 - 14:22:06 CST)
  • RE: harmonic restraints between multiple atom pairs (Mon Nov 03 2014 - 23:20:09 CST)
  • Re: Improving MDFF results (Tue Oct 21 2014 - 14:22:31 CDT)
  • RE: Improving MDFF results (Tue Oct 21 2014 - 00:36:21 CDT)
  • Re: long running sim dies (Mon Oct 13 2014 - 14:36:37 CDT)
  • RE: Colvars simulation running slow? (Wed Sep 10 2014 - 19:51:15 CDT)
  • RE: Colvars simulation running slow? (Wed Sep 10 2014 - 17:15:35 CDT)
  • Colvars simulation running slow? (Tue Sep 09 2014 - 20:31:06 CDT)
  • RE: FATAL ERROR: Low global exclusion count! (9231 vs 9270) System unstable or pairlistdist or cutoff too small. (Wed Sep 03 2014 - 02:26:27 CDT)
  • RE: FATAL ERROR: Low global exclusion count! (9231 vs 9270) System unstable or pairlistdist or cutoff too small. (Tue Sep 02 2014 - 17:27:20 CDT)
  • RE: restraining bonds (Mon Sep 01 2014 - 01:09:05 CDT)
  • RE: restraining bonds (Mon Sep 01 2014 - 00:57:28 CDT)
  • RE: restraining bonds (Mon Sep 01 2014 - 00:45:22 CDT)
  • RE: Re:Subject: Re: Subject: Re:Re: New partial charges after patching (Wed Jul 16 2014 - 18:44:39 CDT)
  • RE: accelerated MD as the engine for loop refirement (Mon Jul 14 2014 - 18:18:05 CDT)
  • RE: accelerated MD as the engine for loop refirement (Mon Jul 14 2014 - 00:40:11 CDT)
  • RE: Constraint failure in RATTLE algorithm (Sat Jun 21 2014 - 18:43:43 CDT)
  • RE: Constraint failure in RATTLE algorithm (Wed Jun 18 2014 - 20:29:08 CDT)
  • RE: AW: AW: How to refer to side-chain via tcl-force scripting? (Sat Jun 14 2014 - 01:09:39 CDT)
  • RE: How to refer to side-chain via tcl-force scripting? (Fri Jun 13 2014 - 02:08:51 CDT)
  • RE: coordinates in namd (Tue Jun 03 2014 - 02:25:49 CDT)
  • RE: Rapid and accurate parameterization of new molecules in CHARMM (Tue May 27 2014 - 17:23:07 CDT)
  • Re: Improve scaling for large amount of fixed atoms (Wed Mar 19 2014 - 21:15:40 CDT)
  • RE: How to maintain Density constant? (Thu Mar 06 2014 - 16:30:43 CST)
  • Symmetry restraints break IMD handshaking (Tue Feb 25 2014 - 21:23:26 CST)
  • Re: NAMD 2.9 Changing/Replacing atoms in multiple molecules (Fri Feb 21 2014 - 16:04:43 CST)
  • Re: AW: RE: Runaway positive feedback when minimizing large systems (was: strange glitches when performing energy minimization in MDFF simulations) (Fri Feb 21 2014 - 01:44:39 CST)
  • RE: Runaway positive feedback when minimizing large systems (was: strange glitches when performing energy minimization in MDFF simulations) (Thu Feb 20 2014 - 17:52:22 CST)
  • RE: Runaway positive feedback when minimizing large systems (was: strange glitches when performing energy minimization in MDFF simulations) (Wed Feb 19 2014 - 17:53:43 CST)
  • RE: Runaway positive feedback when minimizing large systems (was: strange glitches when performing energy minimization in MDFF simulations) (Wed Feb 12 2014 - 17:51:13 CST)
  • Re: AW: RE: Strange glitches when performing energy minimization in MDFF simulations (Wed Feb 12 2014 - 02:22:47 CST)
  • RE: RE: Strange glitches when performing energy minimization in MDFF simulations (Tue Feb 11 2014 - 18:41:53 CST)
  • Runaway positive feedback when minimizing large systems (was: strange glitches when performing energy minimization in MDFF simulations) (Tue Feb 11 2014 - 20:07:59 CST)
  • Re: RE: Strange glitches when performing energy minimization in MDFF simulations (Tue Feb 11 2014 - 15:33:28 CST)
  • RE: Strange glitches when performing energy minimization in MDFF simulations (Mon Feb 10 2014 - 18:24:37 CST)
  • RE: Strange glitches when performing energy minimization in MDFF simulations (Mon Feb 10 2014 - 00:20:57 CST)
  • Strange glitches when performing energy minimization in MDFF simulations (Sun Feb 09 2014 - 23:49:41 CST)
  • RE: Steering colvars to defined points in space (Sun Jan 26 2014 - 22:44:09 CST)
  • Steering colvars to defined points in space (Sun Jan 26 2014 - 18:10:03 CST)
  • RE: recent comparison of NAMD to other MD engines (Fri Jan 24 2014 - 02:44:05 CST)
  • RE: Temperature reassignment (Sun Jan 12 2014 - 21:32:03 CST)
• ukulililixl
  • question about '+devices' (Wed Oct 08 2014 - 01:06:50 CDT)
  • Does NAMD have some way to test the result? (Fri Oct 03 2014 - 21:50:52 CDT)
  • Re: ibverb&&smp build NAMD (Fri Aug 29 2014 - 06:41:21 CDT)
  • ibverb&&smp build NAMD (Thu Aug 28 2014 - 04:30:47 CDT)
  • (no subject) (Tue Aug 26 2014 - 01:22:20 CDT)
  • question in NAMD with icc & cuda (Mon Aug 25 2014 - 06:40:48 CDT)
• upayan baul
  • Re: simulating graphene sheets (with bonds across boundaries) with water (Wed Sep 16 2015 - 05:40:38 CDT)
  • Re: simulating graphene sheets (with bonds across boundaries) with water (Tue Sep 15 2015 - 06:57:20 CDT)
  • simulating graphene sheets (with bonds across boundaries) with water (Mon Sep 14 2015 - 06:59:00 CDT)
• Urszula Uciechowska
  • FATAL ERROR: Incorrect atom count in binary file min.coor (Fri Jul 24 2015 - 03:27:31 CDT)
  • backbone constraint (Wed Jul 22 2015 - 02:59:37 CDT)
  • nvt run error (Tue Jul 21 2015 - 02:54:10 CDT)
  • nvt input file (Fri Jul 17 2015 - 08:25:21 CDT)
  • protein-DNA complex (Thu Jul 16 2015 - 09:40:25 CDT)
  • namd simulation (Tue Mar 03 2015 - 08:20:25 CST)
  • single strand DNA in hairpin conformation (Thu Feb 12 2015 - 03:14:55 CST)
  • preparing dsDNA (Fri Feb 06 2015 - 05:58:43 CST)
  • error running min (Tue Feb 03 2015 - 08:23:28 CST)
• Vibhor Agrawal
  • Re: Restraints on the outer solutes (Mon Dec 28 2015 - 03:50:57 CST)
  • Re: PME Seg Fault (Mon Aug 10 2015 - 11:31:56 CDT)
• Victor Ovchinnikov
  • Re: vmd-l: Re: VMD-NAMD and PDB element column (Mon Dec 14 2015 - 16:27:41 CST)
  • Re: vmd-l: Re: VMD-NAMD and PDB element column (Mon Dec 14 2015 - 09:47:54 CST)
• Vidhya Sankar
  • mail reg parameters (Fri Dec 25 2015 - 20:51:57 CST)
  • mail reg DCD error (Sun May 03 2015 - 09:44:50 CDT)
  • Mail reg Parameter file (Mon Apr 20 2015 - 07:57:34 CDT)
  • About Number of atoms in fixed atoms PDB doesn't match coordinate PDB (Sat Jan 25 2014 - 21:01:01 CST)
  • About Psfgen error for Lipid molecules (Sun Jan 19 2014 - 07:29:51 CST)
  • About Warning in compilation of Namd (Sat Jan 04 2014 - 03:41:57 CST)
  • About Tcl8.3 error in namd2.8 (Wed Jan 01 2014 - 08:20:20 CST)
• Vijay L. Roy
  • Subscribe (Tue Oct 06 2015 - 01:22:14 CDT)
  • Regarding biasTemperature used in Well-tempered metadynamics (Tue Oct 06 2015 - 01:49:12 CDT)
• VINAYAK BHAT
  • Generating solvent models. (Sun Jul 05 2015 - 04:06:27 CDT)
• Viswanath Pasumarthi
  • Spikes in the Energy Plot (Mon Feb 09 2015 - 02:26:08 CST)
  • Re: Unable to read corrupted binary DCD trajectory file (Mon Sep 08 2014 - 15:27:12 CDT)
  • Re: Unable to read corrupted binary DCD trajectory file (Mon Sep 08 2014 - 10:38:45 CDT)
  • Re: Unable to read corrupted binary DCD trajectory file (Mon Sep 08 2014 - 09:43:47 CDT)
  • Re: Unable to read corrupted binary DCD trajectory file (Mon Sep 08 2014 - 09:38:31 CDT)
  • Unable to read corrupted binary DCD trajectory file (Mon Sep 08 2014 - 09:04:32 CDT)
  • Installation Protocol of NAMD on Linux Cluster (Thu Aug 21 2014 - 14:46:27 CDT)
  • Re: Kb, Ktheta values for TIP3P water model (Wed Aug 13 2014 - 02:27:24 CDT)
  • Re: Kb, Ktheta values for TIP3P water model (Tue Aug 12 2014 - 14:11:40 CDT)
  • Re: Kb, Ktheta values for TIP3P water model (Tue Aug 12 2014 - 12:19:00 CDT)
  • Re: Kb, Ktheta values for TIP3P water model (Mon Aug 11 2014 - 12:56:00 CDT)
  • Intermolecular potential energy function in NAMD (Fri Aug 01 2014 - 06:31:21 CDT)
  • Kb, Ktheta values for TIP3P water model (Tue Jul 29 2014 - 16:38:28 CDT)
• Vlad Cojocaru
  • Re: accelerated MD new variant (Mon Nov 30 2015 - 10:00:35 CST)
  • accelerated MD new variant (Sun Nov 29 2015 - 03:53:20 CST)
  • Re: Compilation of NAMD from Source (Cray XC40) (Tue Oct 13 2015 - 15:04:02 CDT)
  • Re: protein-DNA complex (Thu Jul 16 2015 - 10:59:19 CDT)
  • Re: NAMD nightly build compilation (Fri May 08 2015 - 04:11:52 CDT)
  • Re: NAMD nightly build compilation (Fri May 08 2015 - 03:12:16 CDT)
  • Re: NAMD nightly build compilation (Thu May 07 2015 - 08:40:00 CDT)
  • Re: NetworkView plugin for the non-namd trajectories (Tue Apr 14 2015 - 10:13:47 CDT)
  • Re: angle between 2 vectors as collective variable (Thu Mar 26 2015 - 11:04:09 CDT)
  • Re: angle between 2 vectors as collective variable (Thu Mar 26 2015 - 10:03:36 CDT)
  • angle between 2 vectors as collective variable (Thu Mar 26 2015 - 09:17:41 CDT)
  • Re: NAMD nightly build compilation (Tue Mar 24 2015 - 12:51:47 CDT)
  • NAMD nightly build compilation (Tue Mar 24 2015 - 12:07:03 CDT)
  • LAST CALL: Free Energy Workshop, Münster, March 9-11, 2015 (Tue Feb 03 2015 - 14:34:42 CST)
  • Free Energy Workshop, Münster, March 9-11, 2015 (Fri Jan 09 2015 - 03:19:04 CST)
  • Free Energy Workshop, Münster, March 9-11Q_2015?= (Fri Dec 19 2014 - 12:02:00 CST)
  • Re: Colvar: minimal distance between 2 groups of atoms (Tue Nov 18 2014 - 03:40:53 CST)
  • Re: Colvar: minimal distance between 2 groups of atoms (Mon Nov 17 2014 - 12:12:42 CST)
  • Re: Colvar: minimal distance between 2 groups of atoms (Mon Nov 17 2014 - 10:49:57 CST)
  • Re: Colvar: minimal distance between 2 groups of atoms (Mon Nov 17 2014 - 10:14:58 CST)
  • Re: Colvar: minimal distance between 2 groups of atoms (Mon Nov 17 2014 - 09:57:37 CST)
  • Colvar: minimal distance between 2 groups of atoms (Mon Nov 17 2014 - 07:41:31 CST)
  • Re: MMPBSA Energy Calculations using VMD (Post-Processing) (Sat Apr 12 2014 - 03:46:19 CDT)
  • Call for participation: ISQBP Meeting, Telluride 15-19.06.2014 (Mon Mar 10 2014 - 11:38:09 CDT)
• Vlastimil Zíma
  • Re: Daily cron stalls running NAMD outputs (Wed Apr 08 2015 - 02:41:23 CDT)
  • Re: Daily cron stalls running NAMD outputs (Wed Apr 01 2015 - 07:08:28 CDT)
  • Daily cron stalls running NAMD outputs (Wed Apr 01 2015 - 03:04:26 CDT)
  • NAMD_2.9_Linux-x86_64-multicore-CUDA Segfaults (Wed Jun 11 2014 - 02:36:44 CDT)
  • Re: Persistent margin errors (Wed Apr 16 2014 - 05:28:56 CDT)
  • Persistent margin errors (Wed Feb 26 2014 - 06:38:23 CST)
• Vogel, Alexander
  • Can't start SMP NAMD - Problem clearly is in front of the monitor (Tue Nov 17 2015 - 03:18:05 CST)
• Vy Phan
  • namd-I: How to assume the thickness of membrane when applying external Electric field ? (Tue Jan 13 2015 - 00:20:31 CST)
• Wade, Alex
  • Using a different potential with NAMD (Fri Jun 12 2015 - 09:08:48 CDT)
• Wasut Pornpatcharapong
  • Questions on calling external program to calculate force with NAMD (Mon Feb 10 2014 - 15:41:48 CST)
• Wesley Lay
  • *** glibc detected *** namd2: invalid fastbin entry (free) (Thu May 22 2014 - 15:19:11 CDT)
• wliu
  • Problem on merging multi-psf files into one (Sun Oct 18 2015 - 07:52:11 CDT)
• Wonpil Im
  • Re: Inquiry about lipid membrane simulation (Wed Jun 18 2014 - 14:53:31 CDT)
• Xiaoge Wang
  • run NAMD 2.10 on Xeon Phi machine (Tue Jul 28 2015 - 12:50:23 CDT)
• Xiaokang Liu
  • the method to move freely in one direction like a rigid body (Mon May 25 2015 - 05:46:40 CDT)
• XSC
  • about compiling NAMD using intel icc and impi (Fri Jan 23 2015 - 04:00:29 CST)
• Yan Zhou
  • Re: Temperature assignment REMD (Mon Jan 05 2015 - 02:27:56 CST)
  • INCONSISTENCY messages and minimization in toturial 1-2-sphere (Wed Sep 03 2014 - 03:14:30 CDT)
• yandong Huang
  • LCPO parameters P1-P4 (Sat Jan 31 2015 - 13:24:55 CST)
  • LCPO parameters P1-P4 (Mon Jan 26 2015 - 12:30:21 CST)
• Yarrow Madrona
  • NAMD warning: Randomization of stack point is turned on in kernal, thread migration may not work! (Thu Mar 05 2015 - 10:58:11 CST)
• Yerko Escalona
  • Multiple-replicas metadynamics / Well-tempered metadynamics (Fri Jun 12 2015 - 14:15:39 CDT)
• Yongcheng Zhou
  • FATAL ERROR: Low global exclusion count! (Wed Feb 18 2015 - 18:29:33 CST)
  • adjust water box size in RBCG (Sun Feb 01 2015 - 16:03:54 CST)
  • paricle type in residue based coarse graining of NAMD (Mon Jun 23 2014 - 09:14:12 CDT)
  • paricle type in residue based coarse graining of NAMD (Mon Jun 23 2014 - 14:37:16 CDT)
• Yunhui Peng
  • Problems when running FEP for mutation ASP to GLY (Fri Apr 17 2015 - 13:53:03 CDT)
• Z
  • electrostatics cutoff parameters (Mon Jun 08 2015 - 09:06:00 CDT)
  • Reverse osmosis simulation (Thu Jan 22 2015 - 05:09:24 CST)
  • Re: Parameter colvars (Mon Oct 06 2014 - 22:05:28 CDT)
  • Re: Parameter colvars (Mon Oct 06 2014 - 11:20:41 CDT)
  • Re: Parameter colvars (Mon Oct 06 2014 - 09:47:28 CDT)
  • Re: Parameter colvars (Mon Oct 06 2014 - 07:02:28 CDT)
  • Re: Parameter colvars (Mon Oct 06 2014 - 06:55:44 CDT)
  • Re: Parameter colvars (Mon Oct 06 2014 - 05:56:07 CDT)
  • Parameter colvars (Mon Oct 06 2014 - 05:26:21 CDT)
  • Re: boron nitride nanotube (Thu Jun 12 2014 - 05:28:33 CDT)
  • boron nitride nanotube (Mon Jun 09 2014 - 02:58:02 CDT)
  • IMPROPER PARAMETERS FOR CA CA CA CA (Sat May 24 2014 - 10:50:49 CDT)
• Zailo Leite
  • unsubscribe (Fri Feb 14 2014 - 11:20:04 CST)
• Zeinab Emami
  • OpenGL Display Window, "Key 2", SMD with NAMD (Sun Dec 20 2015 - 11:57:52 CST)
  • Steered NAMD using AMBER Forcefield [Config File] (Sun Jan 18 2015 - 10:07:51 CST)
  • Re: Re: vmd-l: ffTK problem: OPT.Charges (Fri Nov 07 2014 - 11:13:04 CST)
  • ffTK problem: OPT.Charges (Fri Nov 07 2014 - 09:14:15 CST)
  • Re: Re: ffTK problem: initial parameter fiel is viod of atoms! (Mon Oct 20 2014 - 11:33:25 CDT)
  • ffTK problem: initial parameter file is void of of atoms! (Thu Oct 16 2014 - 04:15:55 CDT)
  • ffTK problem: initial parameter fiel is viod of atoms! (Wed Oct 15 2014 - 07:42:57 CDT)
  • Re: vmd-l: making psf files (Mon Oct 13 2014 - 04:55:06 CDT)
  • How to Amend a PBD file for NAMD (Wed Oct 01 2014 - 09:27:15 CDT)
  • Alignment (Thu Sep 04 2014 - 07:12:14 CDT)
  • NVT, NPT, order & combination (Tue Aug 19 2014 - 03:23:26 CDT)
  • Hwo to switch from NPT to NVT (Fri Aug 15 2014 - 07:14:05 CDT)
  • Hwo to switch from NPT to NVT (Fri Aug 15 2014 - 07:12:39 CDT)
• zeynab mohamad hoseyni
  • Re: Problem with running namdenergy plugin from text interface (Mon Sep 22 2014 - 22:29:26 CDT)
  • Problem with running namdenergy plugin from text interface (Mon Sep 22 2014 - 14:53:04 CDT)
  • Re: AW: AW: How to refer to side-chain via tcl-force scripting? (Mon Jun 16 2014 - 11:20:46 CDT)
  • improving tclforce efficiency, getting "Signal: segmentation violation" error (Sun Jun 15 2014 - 20:18:11 CDT)
  • Re: AW: AW: How to refer to side-chain via tcl-force scripting? (Sat Jun 14 2014 - 09:03:09 CDT)
  • Re: AW: AW: How to refer to side-chain via tcl-force scripting? (Fri Jun 13 2014 - 23:01:42 CDT)
  • Re: AW: How to refer to side-chain via tcl-force scripting? (Fri Jun 13 2014 - 03:21:08 CDT)
  • How to refer to side-chain via tcl-force scripting? (Fri Jun 13 2014 - 00:53:12 CDT)
  • How to extract the .coor, .vel and .xsc files for a conformation in the middle of trajectory (Mon Apr 28 2014 - 23:12:57 CDT)
  • FATAL ERROR: Setting parameter tclForces from script failed! (Tue Apr 22 2014 - 02:43:23 CDT)
  • FATAL ERROR: EOF ENCOUNTERED READING CROSS-TERMS FROM PSF FILE (Thu Feb 20 2014 - 13:31:50 CST)
  • About keep_water_out.tcl (Thu Feb 20 2014 - 05:21:23 CST)
  • Re: Adding hydrogen atoms to the crystall structure (Tue Feb 18 2014 - 14:30:00 CST)
  • protein-membrane interface hydration (Tue Feb 18 2014 - 13:37:30 CST)
  • psf file does not contain cross-terms (Sun Feb 16 2014 - 12:00:30 CST)
  • Adding hydrogen atoms to the crystall structure (Sun Feb 16 2014 - 09:54:40 CST)
  • Determining HIS protonation state using PropKa vmd plug-in (Tue Feb 11 2014 - 06:30:09 CST)
  • Hydration of protein-lipid interface (Mon Feb 03 2014 - 10:27:20 CST)
  • How to solvate a protein using C36 and not C27 (Sat Jan 25 2014 - 11:08:14 CST)
  • How to solvate a protein using C36 and not C27 (Sat Jan 25 2014 - 10:48:31 CST)
• Zhao Lina
  • Re: Is it so different when setting reinitvels or not? (Wed Dec 17 2014 - 19:31:49 CST)
  • Is it so different when setting reinitvels or not? (Wed Dec 17 2014 - 00:03:25 CST)
  • Re: Polarization effect of gold cluster (Fri Feb 21 2014 - 06:30:34 CST)
  • Polarization effect of gold cluster (Tue Feb 18 2014 - 06:20:20 CST)
• Zhe Wu
  • Re: Dielectric constant of water from MSM and PME simulations (Fri Oct 23 2015 - 10:46:41 CDT)
  • Re: Dielectric constant of water from MSM and PME simulations (Fri Oct 23 2015 - 10:31:04 CDT)
  • Re: (Wed Oct 21 2015 - 14:16:02 CDT)
• Zheng Fulu
  • The water box shrinks at the start of the MD simulation (Sun Jul 27 2014 - 13:53:55 CDT)
• zmhoseyni
  • (no subject) (Thu Jul 03 2014 - 22:36:44 CDT)
  • (no subject) (Wed Jul 02 2014 - 00:25:31 CDT)
  • (no subject) (Wed May 21 2014 - 04:48:25 CDT)
  • (no subject) (Mon May 19 2014 - 04:18:48 CDT)
• ZOU Changling
  • Q=B4=D7=D4"ZOU_Changling"_<zoucl@ihep.ac.cn>=B5=C4=D3=CA=BC=FE?= (Wed Nov 25 2015 - 06:39:26 CST)
  • Re: Re: Fw: À´×Ô"ZOU Changling" <zoucl@ihep.ac.cn>µÄÓʼþ (Wed Nov 18 2015 - 19:34:42 CST)
  • Fw: À´×Ô"ZOU Changling" <zoucl@ihep.ac.cn>µÄÓʼþ (Wed Nov 18 2015 - 02:43:26 CST)
  • Fw: Fw: À´×Ô"ZOU Changling" <zoucl@ihep.ac.cn>µÄÓʼþ (Wed Nov 18 2015 - 02:40:15 CST)
  • Fw: À´×Ô"ZOU Changling" <zoucl@ihep.ac.cn>µÄÓʼþ (Wed Nov 18 2015 - 00:26:54 CST)
  • Q=B4=D7=D4"ZOU_Changling"_<zoucl@ihep.ac.cn>=B5=C4=D3=CA=BC=FE?= (Wed Nov 18 2015 - 00:25:35 CST)
  • NAMD-Replica exchange (Wed May 27 2015 - 04:31:28 CDT)
• ¶¡êÏ
  • Can 'nonbonded interaction parameters' be ignored in the parameter file? (Tue May 26 2015 - 20:43:52 CDT)
  • where can I find the parameter file for chlorophenols? (Sun May 24 2015 - 08:30:15 CDT)
• ¼­¿ëÀÏ
  • Re: whidth value of orientation in colvars (Thu Jan 09 2014 - 18:28:22 CST)
  • whidth value of orientation in colvars (Thu Jan 09 2014 - 02:27:59 CST)
• ¬Óíï¿
  • Re: Re: Re: about the vdw Interpolation calculation in NAMD source code (Thu Nov 20 2014 - 20:35:48 CST)
  • Re: Re: about the vdw Interpolation calculation in NAMD source code (Thu Nov 20 2014 - 09:32:10 CST)
  • about the vdw Interpolation calculation in NAMD source code (Thu Nov 20 2014 - 02:44:40 CST)
  • The short range nonbonbed force charge after load balancing (Sun Jun 15 2014 - 04:57:43 CDT)
• ÂÀÇç
  • How to let NAMD terminate automatically at a given time (Fri Feb 27 2015 - 20:02:18 CST)
• ÂÀСӨ
  • Q=B4=D7=D4"=C2=C0=D0=A1=D3=A8"_<lv-xy11@mail?= s.tsinghua.edu.cn>µÄÓʼþ (Fri Sep 25 2015 - 09:19:53 CDT)
  • free energy calculation along image index in us (Wed Jun 24 2015 - 02:27:35 CDT)
  • the difference of PCA and EDA (Wed Dec 10 2014 - 02:31:30 CST)
  • pThr topology (Tue Feb 18 2014 - 21:05:27 CST)
• Ã…ke Sandgren
  • Re: Patches for namd 2.10 (Fri Apr 24 2015 - 06:06:53 CDT)
  • Patches for namd 2.10 (Fri Apr 24 2015 - 01:09:35 CDT)
• 周文昌
  • Re: Asking help on results of our GPU benchmark (Tue Dec 23 2014 - 14:05:30 CST)
  • Re: Asking help on results of our GPU benchmark (Mon Dec 22 2014 - 12:11:18 CST)
  • Re: Asking help on results of our GPU benchmark (Fri Dec 19 2014 - 16:06:33 CST)
  • Re: Asking help on results of our GPU benchmark (Thu Dec 18 2014 - 13:24:59 CST)
  • Asking help on results of our GPU benchmark (Wed Dec 17 2014 - 15:13:24 CST)
• 孙业平
  • Fw: vmd-l: what is difference between "TOTAL", “TOTAL2" and "POTENTIAL" in the VMD plugin NAMD Plot? (Mon Nov 09 2015 - 06:49:42 CST)
• 岡部篤俊
  • Lambda-exchange multiple-copy alchemical free energy calculations (Tue Aug 18 2015 - 09:54:40 CDT)
• ԬС¾§
  • Re: Re: MD simulation of Linear Molecules (like 2-butyne£© (Mon Dec 21 2015 - 20:30:09 CST)
  • MD simulation of Linear Molecules (like 2-butyne£© (Fri Dec 18 2015 - 20:26:26 CST)