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NAMD-L: By Author

By Author

3750 messages sorted by: [ date ] [ thread ] [ subject ] [ attachment ]
About this archive

Starting: Thu Jan 03 2013 - 06:24:44 CST
Ending: Tue Dec 30 2014 - 07:38:36 CST

• #ZHENG FULU#
  • The water box shrinks at the start of the MD simulation (Sun Jul 27 2014 - 06:13:52 CDT)
• Aaron Cann
  • NAMD2.9 single-node benchmarks, 0-2 Kepler GPU's. (Tue Apr 30 2013 - 21:17:02 CDT)
• Aaron Larsen
  • 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)
• Aaron Oakley
  • Re: unsubscriber e-mail office pool anybody? (Tue Mar 05 2013 - 07:31:42 CST)
  • Re: Problem with psfgen for Carbohydrates (Mon Jan 28 2013 - 16:53:24 CST)
  • Re: topology file for ligand (Wed Jan 16 2013 - 02:11:07 CST)
• Abhishek TYAGI
  • 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
  • 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)
  • Re: use of colvars to restrain the absolute positions of all atoms in a large system (Wed Jul 10 2013 - 12:11:10 CDT)
  • Re: use of colvars to restrain the absolute positions of all atoms in a large system (Tue Jul 09 2013 - 17:35:31 CDT)
  • use of colvars to restrain the absolute positions of all atoms in a large system (Tue Jul 09 2013 - 17:01:15 CDT)
• Achani K. Yatawara
  • unsubscribe (Sun Jun 23 2013 - 11:39:20 CDT)
• Ada Zhan
  • RE: WHAM analysis for Umbrella sampling (Wed May 01 2013 - 15:10:03 CDT)
  • RE: WHAM analysis for Umbrella sampling (Wed May 01 2013 - 13:59:46 CDT)
  • RE: WHAM analysis for Umbrella sampling (Wed May 01 2013 - 12:20:15 CDT)
  • RE: WHAM analysis for Umbrella sampling (Tue Apr 30 2013 - 17:18:37 CDT)
  • WHAM analysis for Umbrella sampling (Mon Apr 29 2013 - 14:41:37 CDT)
• 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)
• Aditya Ranganathan
  • MMPBSA Energy Calculations using VMD (Post-Processing) (Thu Apr 10 2014 - 08:25:41 CDT)
  • Extent of Sampling possible using classical all-atom MD Simulations (Tue Oct 01 2013 - 08:22:42 CDT)
  • Convergence of Sampling and Deciding on Simulation Length (Tue Jul 16 2013 - 06:08:15 CDT)
  • Re: Suggestions while building a GPU-machine (CUDA) for NAMD use! (Tue May 28 2013 - 04:04:18 CDT)
  • Re: Suggestions while building a GPU-machine (CUDA) for NAMD use! (Tue May 28 2013 - 02:23:39 CDT)
  • Re: Suggestions while building a GPU-machine (CUDA) for NAMD use! (Mon May 27 2013 - 04:35:32 CDT)
  • Suggestions while building a GPU-machine (CUDA) for NAMD use! (Mon May 27 2013 - 03:14:33 CDT)
  • NAMD PBS Parallel Job Error (Mon Mar 04 2013 - 03:44:15 CST)
  • Re: Percentage of Residues in Ramachandran Plot regions versus time of trajectory (Tue Jan 29 2013 - 09:51:31 CST)
  • Re: Percentage of Residues in Ramachandran Plot regions versus time of trajectory (Tue Jan 29 2013 - 04:14:57 CST)
  • Percentage of Residues in Ramachandran Plot regions versus time of trajectory (Sun Jan 27 2013 - 22:45:13 CST)
• Adrian
  • vdwForceSwitching and PME (Wed Jul 24 2013 - 22:48:20 CDT)
  • FullDirect Electrostatics (Tue Jul 23 2013 - 09:51:53 CDT)
  • Minimization/Equilibrium problem, atoms moving too fast (Thu Jul 18 2013 - 15:28:10 CDT)
  • Implicit water with explicit ions (Thu Jul 18 2013 - 13:10:49 CDT)
  • run NAMD command in GPU (Tue Jul 16 2013 - 14:05:17 CDT)
• adrian palacios
  • RE: Minimization/Equilibrium problem, atoms moving too fast (Thu Jul 18 2013 - 20:32:57 CDT)
  • RE: Minimization/Equilibrium problem, atoms moving too fast (Thu Jul 18 2013 - 20:12:05 CDT)
  • RE: Implicit water with explicit ions (Thu Jul 18 2013 - 20:02:36 CDT)
  • RE: Minimization/Equilibrium problem, atoms moving too fast (Thu Jul 18 2013 - 19:58:47 CDT)
• Ajasja LjubetiÄ�
  • 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)
  • Re: Two GPU-based workstation (Thu Nov 07 2013 - 09:36:44 CST)
  • Re: Two GPU-based workstation (Sun Nov 03 2013 - 06:54:26 CST)
  • Re: Extract KE, PE and total energy from log file (Thu Oct 31 2013 - 18:05:37 CDT)
  • Re: reassignTemp question (Tue Oct 29 2013 - 16:26:41 CDT)
  • Re: Two GPU-based workstation (Tue Oct 29 2013 - 08:33:42 CDT)
  • Re: Two GPU-based workstation (Tue Oct 29 2013 - 04:46:23 CDT)
  • Re: Namd options from TCL (Tue Oct 29 2013 - 04:44:50 CDT)
  • Re: Membrane/peptide system. Water moving from one layer to the other ... (Wed Oct 23 2013 - 07:30:36 CDT)
  • Re: Simulation of a protein and calcium ions (Tue Oct 08 2013 - 08:21:38 CDT)
  • Re: Simulation of a protein and calcium ions (Tue Oct 08 2013 - 04:08:56 CDT)
  • Re: Simulation of a protein and calcium ions (Tue Oct 08 2013 - 03:29:28 CDT)
  • Re: abf integrate on two dimensional pmf (Tue Oct 08 2013 - 03:20:52 CDT)
  • Re: Can a small langevinDamping coefficient lead to 'ERROR: atoms moving too fast'? (Mon Aug 26 2013 - 08:49:08 CDT)
  • Re: Colvar cannot be ran on supercomputer newton (Tue Aug 06 2013 - 09:08:25 CDT)
  • Re: Problem regarding the big DCD file (Thu Jul 18 2013 - 12:08:27 CDT)
  • Re: FW: water layer in membrane protein modeling (Thu Jul 18 2013 - 10:00:19 CDT)
  • Re: Resample trajectory files (Mon Jul 15 2013 - 16:02:04 CDT)
  • Re: First meeting with NAMD (Tue Jun 04 2013 - 08:45:44 CDT)
  • Re: Potential of mean force calculation using colvars in NADM 2.9 package (Fri May 17 2013 - 09:41:40 CDT)
  • Re: A larger protein data bank for performance benchmark (Mon May 13 2013 - 12:13:46 CDT)
  • Re: Current bias values (Wed May 08 2013 - 02:54:11 CDT)
  • Re: Are random forces applied at every step (when using the langevin thermostat) ? (Tue Apr 30 2013 - 10:48:46 CDT)
  • Are random forces applied at every step (when using the langevin thermostat) ? (Fri Apr 26 2013 - 15:21:56 CDT)
  • Re: restrain ligand to z-interval (Mon Apr 15 2013 - 08:22:07 CDT)
  • Re: Coordinate vs. time plots (Thu Mar 28 2013 - 07:53:47 CDT)
  • Re: unsubscriber e-mail office pool anybody? (Tue Mar 05 2013 - 08:39:01 CST)
  • Re: ABF thermostats and energy introduced into the system (Wed Feb 27 2013 - 11:29:28 CST)
  • Re: ABF thermostats and energy introduced into the system (Wed Feb 27 2013 - 06:26:39 CST)
  • Re: ABF thermostats and energy introduced into the system (Tue Feb 26 2013 - 03:10:27 CST)
  • Re: ABF thermostats and energy introduced into the system (Tue Feb 26 2013 - 02:52:54 CST)
  • ABF thermostats and energy introduced into the system (Mon Feb 25 2013 - 07:07:39 CST)
  • Re: running NAMD on Amazon EC2? (Thu Feb 14 2013 - 02:39:06 CST)
  • NAMD mailing list unsubscribe instructions (Sun Feb 03 2013 - 11:28:32 CST)
  • Re: Re: AW: AW: CUDA problem? (Wed Jan 16 2013 - 10:04:02 CST)
  • Re: secondary structure analysis (Fri Jan 11 2013 - 03:34:55 CST)
• Ake Sandgren
  • Re: [charm] Charm 6.5.0 compilation issue (Fri Jan 11 2013 - 12:21:43 CST)
• Akshay Bhatnagar
  • 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)
• Albrecht Goez
  • Does NAMD read the PDB element field? (Fri Feb 01 2013 - 02:52:15 CST)
• Alessandro Mascioni
  • Restart files are empy (Sun Jul 21 2013 - 12:24:23 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)
  • Trouble loading frames from large DCD files (Thu Dec 19 2013 - 16:23:30 CST)
• Ali Khanlarkhani
  • Release of ConcatXY (Tue Nov 12 2013 - 16:18:36 CST)
• Alireza Mansouri
  • calculating free energy (Sat Jun 28 2014 - 12:22:40 CDT)
  • Add acetyle and amin Group to peptide (Mon Dec 30 2013 - 03:30:19 CST)
• Aman
  • How to prepare FEP input files for double mutant (Wed Aug 28 2013 - 15:05:19 CDT)
  • excluded interactions (NNB) in psf file for FEP simulations (Tue Aug 27 2013 - 10:16:38 CDT)
• amin_at_imtech.res.in
  • 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)
  • Re: Topology and parameters for nitrate and nitrite ion (Tue Jul 02 2013 - 09:01:19 CDT)
  • Re: Topology and parameters for nitrate and nitrite ion (Mon Jul 01 2013 - 02:39:44 CDT)
  • Re: Topology and parameters for nitrate and nitrite ion (Sun Jun 30 2013 - 23:00:29 CDT)
  • Topology and parameters for nitrate and nitrite ion (Sat Jun 29 2013 - 12:51:39 CDT)
  • Re: (Fri Feb 22 2013 - 00:31:16 CST)
• amit banerjee
  • Require Suggestion (Tue Feb 18 2014 - 23:39:40 CST)
  • Re: simultaneous simulation for protein in water and SMD (Thu Oct 03 2013 - 12:36:23 CDT)
  • simultaneous simulation for protein in water and SMD (Thu Oct 03 2013 - 07:33:04 CDT)
  • Regarding Production Run in NAMD (Wed Jul 10 2013 - 00:14:34 CDT)
• Ana Celia Vila Verde
  • 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)
  • Re: Gold nanoparticle (Thu Sep 26 2013 - 03:22:47 CDT)
  • how does NAMD calculate intramolecular electrostatic interactions between Drude pairs? (Thu Aug 29 2013 - 04:07:02 CDT)
• 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)
• andrea spitaleri
  • Re: vmd-l: About PLUMED with NAMD VMD (Thu Feb 28 2013 - 02:46:34 CST)
• Andreas Förster
  • Re: Unable to read corrupted binary DCD trajectory file (Mon Sep 08 2014 - 09:29:51 CDT)
• Andrei Tudor
  • Replica exchange and colvars - Missing Stage from restart (Sat Sep 14 2013 - 10:04:43 CDT)
  • RE : AW: vmd-l: Occupancy maps (Mon Aug 12 2013 - 10:40:27 CDT)
  • Replica exchange, colvars & harmonic restraints (Mon Jul 29 2013 - 13:36:22 CDT)
• Andrew DeYoung
  • Should I use a precompiled binary? (Fri May 24 2013 - 15:36:41 CDT)
  • Conceptual questions about GPU acceleration (Sat Apr 27 2013 - 11:46:49 CDT)
• Andrew Emerson
  • Re: iDataPlex (Tue Mar 18 2014 - 03:15:30 CDT)
  • Re: NAMD/VMD installation on Linux Clusters with InfiniBand (Mon May 27 2013 - 07:25:19 CDT)
• Andrew Miglino
  • OpenMPI FEP Yields SegFaults and/or infinite dG (Wed Apr 10 2013 - 12:51:05 CDT)
  • FEP OpenMPI Error (Fri Mar 22 2013 - 10:43:43 CDT)
• Andrew Pearson
  • Re: Always 24-way SMP? (Tue Feb 26 2013 - 08:14:52 CST)
  • Re: Always 24-way SMP? (Mon Feb 25 2013 - 11:50:13 CST)
  • Re: Always 24-way SMP? (Mon Feb 25 2013 - 06:28:05 CST)
  • Always 24-way SMP? (Fri Feb 22 2013 - 12:29:58 CST)
• Anilkumar Naik
  • Re: NAMD related (Tue Jun 11 2013 - 02:51:27 CDT)
  • Re: NAMD related (Tue Jun 11 2013 - 02:20:42 CDT)
  • Re: NAMD related (Tue Jun 11 2013 - 02:14:17 CDT)
  • Re: NAMD related (Tue Jun 11 2013 - 01:43:30 CDT)
  • Re: NAMD related (Tue Jun 11 2013 - 00:16:33 CDT)
  • NAMD related (Mon Jun 10 2013 - 06:35:27 CDT)
  • Re: NAMD/VMD installation on Linux Clusters with InfiniBand (Sun May 26 2013 - 00:46:47 CDT)
  • Re: NAMD/VMD installation on Linux Clusters with InfiniBand (Fri May 24 2013 - 08:25:10 CDT)
  • Re: NAMD/VMD installation on Linux Clusters with InfiniBand (Fri May 24 2013 - 04:55:02 CDT)
  • NAMD/VMD installation on Linux Clusters with InfiniBand (Fri May 24 2013 - 08:31:09 CDT)
  • NAMD/VMD installation on Linux Clusters with InfiniBand (Wed May 22 2013 - 11:18:22 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 Chailyan
  • Re: Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT (Thu Sep 19 2013 - 08:40:58 CDT)
  • Re: Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT (Wed Sep 18 2013 - 10:01:10 CDT)
  • Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT (Tue Sep 17 2013 - 11:10:29 CDT)
• Anna Gorska
  • Re: Running NAMD on SGE cluster - multiple modes and cores (Fri Dec 06 2013 - 07:23:29 CST)
  • Re: Running NAMD on SGE cluster - multiple modes and cores (Thu Dec 05 2013 - 04:14:05 CST)
  • Re: Running NAMD on SGE cluster - multiple modes and cores (Thu Dec 05 2013 - 05:09:27 CST)
  • Re: Running NAMD on SGE cluster - multiple modes and cores (Tue Dec 03 2013 - 09:23:30 CST)
  • Running NAMD on SGE cluster - multiple modes and cores (Tue Dec 03 2013 - 05:25:37 CST)
• Anna Modzelewska
  • segmentation fault in accelMD (Mon Jul 28 2014 - 05:56:05 CDT)
• Anurag Sharma
  • RE: how to apply force SMD method on an anisotropic geometry (Fri Jun 21 2013 - 20:47:47 CDT)
  • RE: AW: how to apply force SMD method on an anisotropic geometry (Fri Jun 21 2013 - 20:38:47 CDT)
  • RE: AW: how to apply force SMD method on an anisotropic geometry (Thu Jun 13 2013 - 09:41:24 CDT)
  • how to apply force SMD method on an anisotropic geometry (Wed Jun 12 2013 - 15:39:34 CDT)
  • Error with NAMD Energy (Mon Mar 25 2013 - 13:05:00 CDT)
  • Re: AW: H-bonds cutoff angle criterian. . (Mon Jan 21 2013 - 01:11:46 CST)
  • H-bonds cutoff angle criterian (Sun Jan 20 2013 - 10:54:07 CST)
  • H-bonds cutoff angle criterian (Thu Jan 17 2013 - 20:52:40 CST)
• Arash Azari
  • Re: Why RDF increases as r increase instead of constant (Mon Nov 03 2014 - 01:32:27 CST)
• aravind chandrasekaran
  • Reg loadtotalforces. (Mon Jul 29 2013 - 06:24:31 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)
• Arman Imen
  • (no subject) (Thu Sep 26 2013 - 05:49:15 CDT)
• Aron Broom
  • 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)
  • Re: Re: AW: puzzle of SMD in NAMD-2.9 and pull code in Gromacs (Sun Dec 15 2013 - 00:51:33 CST)
  • Re: AW: puzzle of SMD in NAMD-2.9 and pull code in Gromacs (Thu Dec 12 2013 - 19:25:58 CST)
  • Re: AW: vmd-l: AMD vs. nvidia support (Thu Dec 12 2013 - 09:10:52 CST)
  • Re: One Chain Simulation (Tue Dec 10 2013 - 11:13:50 CST)
  • Re: XY constraints with center of mass movements (Mon Dec 09 2013 - 12:00:33 CST)
  • Re: Asking for Free energy calculation advice (Fri Dec 06 2013 - 11:48:03 CST)
  • Re: Interaction energy definition (Sat Nov 23 2013 - 07:09:54 CST)
  • Re: Interaction energy definition (Fri Nov 22 2013 - 14:57:35 CST)
  • Re: How to replace NAMD electrostatics (Tue Nov 19 2013 - 17:00:16 CST)
  • Re: Why does my volume suddenly expand as I increase temperature. (Mon Nov 11 2013 - 19:12:33 CST)
  • Re: Extract KE, PE and total energy from log file (Thu Oct 31 2013 - 15:39:05 CDT)
  • Re: Two GPU-based workstation (Thu Oct 31 2013 - 12:34:14 CDT)
  • Re: reassignTemp question (Tue Oct 29 2013 - 16:44:52 CDT)
  • Re: reassignTemp question (Tue Oct 29 2013 - 15:40:46 CDT)
  • Re: Running NAMD in multiprocessor single machine (Thu Oct 17 2013 - 19:31:20 CDT)
  • Re: Protein-ligand affinity (Tue Oct 15 2013 - 12:44:33 CDT)
  • Re: Protein-ligand affinity (Mon Oct 14 2013 - 22:16:00 CDT)
  • Re: About restaring Simulation (Sat Oct 05 2013 - 07:10:17 CDT)
  • Re: simultaneous simulation for protein in water and SMD (Thu Oct 03 2013 - 13:02:55 CDT)
  • Re: MD- GPU (Thu Oct 03 2013 - 07:06:24 CDT)
  • Re: cell origin problem (Wed Sep 25 2013 - 14:53:19 CDT)
  • Re: Organic molecule and membrane. NAMD gives fatal error: (Wed Sep 25 2013 - 08:35:14 CDT)
  • Re: About Muticore Linux Ibnstalltion if NAmd (Fri Sep 20 2013 - 23:29:04 CDT)
  • Re: charm-gui membrane builder (Tue Sep 17 2013 - 00:55:57 CDT)
  • Re: MMPBSA calculation using NAMD (Sun Sep 15 2013 - 17:49:19 CDT)
  • Re: NAMD PERFORMANCE ON NVIDIA K20 GPU (Sat Sep 14 2013 - 20:19:23 CDT)
  • Re: How to optimize parameters in command for NAMD CUDA GPU MD calculations? (Thu Sep 12 2013 - 15:41:50 CDT)
  • Regarding the Protein-Ligand Free Energy Tutorial (Wed Sep 11 2013 - 00:39:18 CDT)
  • Re: NAMD CUDA performance (Tue Sep 10 2013 - 14:30:26 CDT)
  • Re: Atom indices in collective variable definition (Fri Sep 06 2013 - 09:47:30 CDT)
  • Re: Simulation of the membrane protein (Wed Sep 04 2013 - 12:26:00 CDT)
  • Re: Non-equilibrium effects in ABF runs (Tue Aug 13 2013 - 15:59:16 CDT)
  • Re: Minimisation issue (Wed Jul 24 2013 - 15:25:06 CDT)
  • Re: Using negatively charged phopspholipids and no neutralization, membrane expands in the xy direction ....... (Wed Jul 24 2013 - 12:03:47 CDT)
  • Re: Restart files are empy (Mon Jul 22 2013 - 08:33:42 CDT)
  • Re: Minimization/Equilibrium problem, atoms moving too fast (Thu Jul 18 2013 - 20:15:47 CDT)
  • Re: Minimization/Equilibrium problem, atoms moving too fast (Thu Jul 18 2013 - 20:05:53 CDT)
  • Re: Minimization/Equilibrium problem, atoms moving too fast (Thu Jul 18 2013 - 16:12:32 CDT)
  • Re: Minimisation problem (Thu Jul 18 2013 - 13:26:52 CDT)
  • Re: Simulation at different time-steps (Tue Jul 16 2013 - 23:47:17 CDT)
  • Re: Convergence of Sampling and Deciding on Simulation Length (Tue Jul 16 2013 - 09:59:15 CDT)
  • Re: dcd to pdb for trajectory analysis (Thu Jul 11 2013 - 09:49:30 CDT)
  • Re: ABF subdividing the reaction coordinate (Wed Jul 10 2013 - 17:44:57 CDT)
  • Re: ABF subdividing the reaction coordinate (Wed Jul 10 2013 - 17:01:01 CDT)
  • Re: ABF subdividing the reaction coordinate (Wed Jul 10 2013 - 16:22:28 CDT)
  • Re: use of colvars to restrain the absolute positions of all atoms in a large system (Tue Jul 09 2013 - 17:18:35 CDT)
  • Re: about interaction between protein and its image in namd simulation (Tue Jul 09 2013 - 13:10:50 CDT)
  • Re: Protein-ligand simulation (Sat Jul 06 2013 - 13:28:15 CDT)
  • Re: Slow vacuum/GBIS simulations (time to completion keeps increasing) (Wed Jul 03 2013 - 07:40:54 CDT)
  • Re: Slow vacuum/GBIS simulations (time to completion keeps increasing) (Wed Jul 03 2013 - 06:12:30 CDT)
  • Re: Simulation of Protein with Ions (Wed Jul 03 2013 - 06:02:21 CDT)
  • Re: Slow vacuum/GBIS simulations (time to completion keeps increasing) (Tue Jul 02 2013 - 13:10:49 CDT)
  • Re: Slow vacuum/GBIS simulations (time to completion keeps increasing) (Tue Jul 02 2013 - 12:45:17 CDT)
  • Re: Insertion of GPCR in the POPC Bilayer (Thu Jun 20 2013 - 16:27:25 CDT)
  • Re: Free Energy Calculation Question (Thu Jun 20 2013 - 16:22:34 CDT)
  • Re: (Thu Jun 20 2013 - 10:19:40 CDT)
  • Re: C++ API (Thu Jun 20 2013 - 01:12:19 CDT)
  • Re: Overestimated PMF (Mon Jun 17 2013 - 14:13:09 CDT)
  • Re: Overestimated PMF (Mon Jun 17 2013 - 11:51:57 CDT)
  • Re: Lipid bilayer tears apart during simulation (Fri Jun 14 2013 - 15:34:31 CDT)
  • Re: Shift (or offset) of the lipid bilayer along Z axis during equilibration (Fri Jun 07 2013 - 20:56:46 CDT)
  • Re: ABF with the RMSD colvar (Fri Jun 07 2013 - 09:50:12 CDT)
  • Re: how to do a vacuum minimization without electrostatics and periodic boundary conditions? (Wed Jun 05 2013 - 10:47:48 CDT)
  • Re: Suggestions while building a GPU-machine (CUDA) for NAMD use! (Tue May 28 2013 - 08:26:01 CDT)
  • Re: Suggestions while building a GPU-machine (CUDA) for NAMD use! (Mon May 27 2013 - 08:09:44 CDT)
  • Re: Help with "ERROR: Constraint failure in RATTLE algorithm for atom XXXX!" (Mon May 20 2013 - 21:38:01 CDT)
  • Re: Suggestions on parameterizing a ligand to simulate in NAMD (Mon May 20 2013 - 14:10:21 CDT)
  • Re: Help with "ERROR: Constraint failure in RATTLE algorithm for atom XXXX!" (Mon May 20 2013 - 14:07:56 CDT)
  • Re: Help with "ERROR: Constraint failure in RATTLE algorithm for atom XXXX!" (Mon May 20 2013 - 11:16:35 CDT)
  • Re: Protein unfolding and Coarse grained (Fri May 17 2013 - 07:44:38 CDT)
  • Re: Potential of mean force calculation using colvars in NADM 2.9 package (Thu May 16 2013 - 07:55:46 CDT)
  • Re: A larger protein data bank for performance benchmark (Mon May 13 2013 - 22:56:35 CDT)
  • Re: restart files not written. (Thu May 09 2013 - 20:52:19 CDT)
  • Re: WHAM analysis for Umbrella sampling (Wed May 01 2013 - 14:12:23 CDT)
  • Re: WHAM analysis for Umbrella sampling (Wed May 01 2013 - 13:09:53 CDT)
  • Re: NAMD2.9 single-node benchmarks, 0-2 Kepler GPU's. (Tue Apr 30 2013 - 23:59:32 CDT)
  • Re: WHAM analysis for Umbrella sampling (Tue Apr 30 2013 - 17:27:57 CDT)
  • Re: WHAM analysis for Umbrella sampling (Mon Apr 29 2013 - 15:17:00 CDT)
  • Re: metadynamics (Fri Apr 26 2013 - 10:19:40 CDT)
  • Re: (Thu Apr 25 2013 - 09:34:41 CDT)
  • Re: binding free energy calculation (Mon Apr 22 2013 - 10:12:45 CDT)
  • Re: cuda error (Fri Mar 29 2013 - 18:40:46 CDT)
  • Re: strange result using implicit solvent (Fri Mar 29 2013 - 12:04:43 CDT)
  • Re: Error in implicit solvent MD (Wed Mar 27 2013 - 15:39:39 CDT)
  • Re: implicit solvent (Wed Mar 27 2013 - 12:30:09 CDT)
  • Re: implicit solvent (Wed Mar 27 2013 - 12:20:30 CDT)
  • Re: (Tue Mar 26 2013 - 13:02:52 CDT)
  • Re: (Mon Mar 25 2013 - 16:48:45 CDT)
  • Re: free energy methods cheat-sheet/comparison chart (Mon Mar 25 2013 - 16:43:54 CDT)
  • Re: free energy methods cheat-sheet/comparison chart (Mon Mar 25 2013 - 14:28:00 CDT)
  • Re: distanceZ - harmonic restraints (Mon Mar 18 2013 - 12:35:47 CDT)
  • Re: smd force is too high (Fri Mar 15 2013 - 12:10:55 CDT)
  • Re: DCD file doubles a monomer (Tue Feb 26 2013 - 12:34:54 CST)
  • Re: Calculate binding free energy (Sun Feb 24 2013 - 22:46:17 CST)
  • Re: center of mass calculation in the tcl interface (Sun Feb 24 2013 - 14:48:38 CST)
  • Re: namd2 CUDA errors for non-superusers in Debian (Thu Feb 14 2013 - 17:31:26 CST)
  • Re: How to split large NAMD DCD file (Thu Jan 24 2013 - 11:06:45 CST)
• arpita agarwal
  • unsubscribe (Sun Jun 23 2013 - 23:12:39 CDT)
• Artem Zhmurov
  • unsubscribe (Sat Mar 02 2013 - 03:12:14 CST)
• Arturas
  • ABF zCoord analog in colvars ? (Wed Jun 05 2013 - 08:41:15 CDT)
  • Re: pump / force application (Thu Apr 11 2013 - 09:14:31 CDT)
  • Re: pump / force application (Thu Apr 11 2013 - 08:54:34 CDT)
  • pump / force application (Thu Apr 11 2013 - 08:19:46 CDT)
  • tcf forces and ccordinate wrapping (Tue Apr 09 2013 - 13:23:21 CDT)
• Asaf Farhi
  • FW: editing the code of the non bonded pair potentials (Fri Aug 30 2013 - 19:54:45 CDT)
  • RE: editing the code of the non bonded pair potentials (Fri Aug 30 2013 - 13:55:21 CDT)
  • FW: editing the code of the non bonded pair potentials (Fri Aug 30 2013 - 13:14:33 CDT)
  • RE: editing the code of the non bonded pair potentials (Fri Aug 30 2013 - 05:26:41 CDT)
  • FW: editing the code of the non bonded pair potentials (Fri Aug 30 2013 - 04:31:44 CDT)
  • editing the code of the non bonded pair potentials (Fri Aug 30 2013 - 04:27:19 CDT)
  • questions regarding the source code in NAMD (Fri Aug 23 2013 - 06:12:59 CDT)
• Asis Jana
  • force field parameter for graphene oxide (Fri Mar 07 2014 - 07:58:34 CST)
• Atanu Maity
  • Problem in creating dummy atom (Fri Nov 01 2013 - 01:43:09 CDT)
  • Re: Problem regarding the big DCD file (Fri Jul 19 2013 - 01:05:08 CDT)
• Austin B. Yongye
  • Potential energy as collective variable (Mon Mar 25 2013 - 10:35:30 CDT)
• Axel Kohlmeyer
  • 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)
  • Re: Add acetyle and amin Group to peptide (Mon Dec 30 2013 - 03:55:11 CST)
  • Re: 50% system CPU usage when parallel running NAMD on Rocks cluster (Wed Dec 18 2013 - 07:04:24 CST)
  • Re: 50% system CPU usage when parallel running NAMD on Rocks cluster (Wed Dec 18 2013 - 01:28:34 CST)
  • Re: Hi (Thu Dec 12 2013 - 09:24:31 CST)
  • Re: AW: vmd-l: AMD vs. nvidia support (Thu Dec 12 2013 - 09:23:37 CST)
  • Re: Re: puzzle of SMD in NAMD-2.9 and pull code in Gromacs (Wed Dec 11 2013 - 00:02:26 CST)
  • Re: puzzle of SMD in NAMD-2.9 and pull code in Gromacs (Tue Dec 10 2013 - 08:22:18 CST)
  • Re: zeroMomentum for water droplet (Tue Dec 03 2013 - 22:38:16 CST)
  • Re: AW: Drifting water molecules (Thu Nov 28 2013 - 04:17:47 CST)
  • Re: Drifting water molecules (Wed Nov 27 2013 - 16:56:17 CST)
  • Re: can i use swap partition to increase ram in namd? (Mon Nov 25 2013 - 09:26:13 CST)
  • Re: diffusion of protein into water box (Mon Nov 25 2013 - 07:13:57 CST)
  • Re: diffusion of protein into water box (Sun Nov 24 2013 - 08:24:47 CST)
  • Re: diffusion of protein into water box (Sun Nov 24 2013 - 08:14:52 CST)
  • Re: How to replace NAMD electrostatics (Thu Nov 21 2013 - 12:02:42 CST)
  • Re: pre residues and ligands interaction (Thu Nov 21 2013 - 06:55:04 CST)
  • Re: How to replace NAMD electrostatics (Tue Nov 19 2013 - 17:03:48 CST)
  • Re: How to replace NAMD electrostatics (Tue Nov 19 2013 - 16:54:29 CST)
  • Re: How to replace NAMD electrostatics (Tue Nov 19 2013 - 16:53:01 CST)
  • Approaching Deadline December 1st 2013 - Advanced LAMMPS and Scientific Software Development Workshop at ICTP in March 2014 (Tue Nov 19 2013 - 03:46:45 CST)
  • Re: Compile NAMD with FFTW3 and MPI (Tue Nov 19 2013 - 02:50:48 CST)
  • Re: NAMD 2.9 install on CLuster mpirun/charmrun with ibverb version ? (Thu Nov 14 2013 - 06:52:52 CST)
  • Re: TclForces and efficient PBC corrections (Tue Nov 12 2013 - 01:37:53 CST)
  • Re: TclForces and efficient PBC corrections (Tue Nov 12 2013 - 01:32:28 CST)
  • Re: Re: Using volmap to calculate the water density around certain residues (Mon Nov 04 2013 - 02:32:22 CST)
  • Re: Mysterious slow down in parallel (Sat Oct 26 2013 - 17:04:11 CDT)
  • Re: NAMD and water models (Wed Oct 23 2013 - 23:22:16 CDT)
  • Re: Simulation of a protein and calcium ions (Wed Oct 09 2013 - 02:45:01 CDT)
  • Re: Simulation of a protein and calcium ions (Tue Oct 08 2013 - 03:29:40 CDT)
  • Re: Lennard Jones (LJ) parameters (Sun Oct 06 2013 - 15:36:22 CDT)
  • Re: simultaneous simulation for protein in water and SMD (Thu Oct 03 2013 - 12:40:05 CDT)
  • Re: simultaneous simulation for protein in water and SMD (Thu Oct 03 2013 - 07:39:03 CDT)
  • Re: Same NAMD files give error in Linux but not in Windows .... (Tue Oct 01 2013 - 03:54:56 CDT)
  • Re: Gold nanoparticle (Wed Sep 25 2013 - 12:37:13 CDT)
  • Re: Gold nanoparticle (Wed Sep 25 2013 - 11:34:39 CDT)
  • Re: delta-G calculation (Thu Sep 19 2013 - 03:09:43 CDT)
  • Re: Equilibration of the membrane bilayers with CUDA-support (Wed Sep 11 2013 - 02:14:13 CDT)
  • Re: Equilibration of the membrane bilayers with CUDA-support (Tue Sep 10 2013 - 09:14:55 CDT)
  • Re: bilayer creation (Mon Sep 09 2013 - 15:15:24 CDT)
  • Re: bilayer creation (Mon Sep 09 2013 - 14:15:56 CDT)
  • Re: explicit NVT simulation (Mon Sep 09 2013 - 13:02:37 CDT)
  • Re: explicit NVT simulation (Mon Sep 09 2013 - 09:06:19 CDT)
  • Re: explicit NVT simulation (Mon Sep 09 2013 - 08:17:45 CDT)
  • Re: parallel code in tclforce script (Fri Sep 06 2013 - 00:48:44 CDT)
  • Re: parallel code in tclforce script (Thu Sep 05 2013 - 02:02:36 CDT)
  • Re: namd scale-up (Wed Sep 04 2013 - 03:00:30 CDT)
  • Re: (Sun Sep 01 2013 - 10:40:27 CDT)
  • Re: FW: editing the code of the non bonded pair potentials (Fri Aug 30 2013 - 14:08:53 CDT)
  • Re: editing the code of the non bonded pair potentials (Fri Aug 30 2013 - 13:59:26 CDT)
  • Re: editing the code of the non bonded pair potentials (Fri Aug 30 2013 - 09:10:35 CDT)
  • Re: editing the code of the non bonded pair potentials (Fri Aug 30 2013 - 04:34:46 CDT)
  • Re: CUDA error memcpy to exclusions: invalid argument (Tue Aug 27 2013 - 05:15:45 CDT)
  • Re: CUDA error memcpy to exclusions: invalid argument (Tue Aug 27 2013 - 04:15:23 CDT)
  • Re: colvars and parallel-tempering with namd2.10 (Tue Aug 13 2013 - 12:07:52 CDT)
  • Re: AW: vmd-l: Occupancy maps (Mon Aug 12 2013 - 01:14:52 CDT)
  • Re: Question about converting velocities DCD to ascii plain text (Sat Aug 03 2013 - 14:38:36 CDT)
  • Re: analyzing NAMD trajectory with NAMD Energy (Mon Jul 29 2013 - 10:42:44 CDT)
  • Re: analyzing NAMD trajectory with NAMD Energy (Mon Jul 29 2013 - 10:31:22 CDT)
  • Re: Water density in the solvate plugin (Fri Jul 26 2013 - 10:58:57 CDT)
  • Re: Problem regarding the big DCD file (Fri Jul 19 2013 - 05:03:22 CDT)
  • CatDCD windows binaries (Fri Jul 19 2013 - 04:56:00 CDT)
  • Re: Problem regarding the big DCD file (Thu Jul 18 2013 - 18:10:51 CDT)
  • Re: Problem regarding the big DCD file (Thu Jul 18 2013 - 12:37:28 CDT)
  • Re: Preventing rotation of a protein (Thu Jul 18 2013 - 11:32:28 CDT)
  • Re: question about NVE ensamble (Thu Jul 18 2013 - 03:13:56 CDT)
  • Re: Unsubscribe (Wed Jul 17 2013 - 16:09:04 CDT)
  • Re: Problem regarding the big DCD file (Tue Jul 16 2013 - 14:12:37 CDT)
  • Re: run NAMD command in GPU (Tue Jul 16 2013 - 14:11:35 CDT)
  • Re: ERROR: Could not translate the value....into a Vector for the option 'cellOrigin' (Mon Jul 15 2013 - 16:25:22 CDT)
  • Re: gromacs to NAMD (Tue Jul 09 2013 - 15:48:45 CDT)
  • Re: Slow vacuum/GBIS simulations (time to completion keeps increasing) (Wed Jul 03 2013 - 06:19:36 CDT)
  • Re: Reaction field treatment (Mon Jul 01 2013 - 00:25:32 CDT)
  • Re: Reaction field treatment (Sat Jun 29 2013 - 08:21:54 CDT)
  • Re: unsubscribe (Sat Jun 29 2013 - 01:56:21 CDT)
  • subscribe (Mon Jun 24 2013 - 15:29:29 CDT)
  • Re: About Namd Installation (Sun Jun 16 2013 - 01:23:15 CDT)
  • Re: NAMD related (Tue Jun 11 2013 - 03:01:12 CDT)
  • Re: NAMD related (Tue Jun 11 2013 - 02:27:51 CDT)
  • Re: Suggestions while building a GPU-machine (CUDA) for NAMD use! (Tue May 28 2013 - 04:40:00 CDT)
  • Re: Suggestions while building a GPU-machine (CUDA) for NAMD use! (Mon May 27 2013 - 04:58:05 CDT)
  • Re: Suggestions while building a GPU-machine (CUDA) for NAMD use! (Mon May 27 2013 - 03:57:15 CDT)
  • Re: NAMD/VMD installation on Linux Clusters with InfiniBand (Sun May 26 2013 - 02:08:46 CDT)
  • Re: NAMD/VMD installation on Linux Clusters with InfiniBand (Fri May 24 2013 - 22:42:08 CDT)
  • Re: NAMD/VMD installation on Linux Clusters with InfiniBand (Fri May 24 2013 - 08:55:42 CDT)
  • Re: AW: Bulk properties of polymers (Wed May 08 2013 - 03:39:25 CDT)
  • Re: Bulk properties of polymers (Wed May 08 2013 - 02:28:50 CDT)
  • Re: How to converse Coarse-Grained structure into all-atom structure (Mon May 06 2013 - 05:09:01 CDT)
  • Re: Conceptual questions about GPU acceleration (Sat Apr 27 2013 - 12:20:06 CDT)
  • Re: metadynamics (Fri Apr 26 2013 - 09:53:41 CDT)
  • Re: floating point reproduceability (Fri Apr 19 2013 - 03:02:11 CDT)
  • Re: minimizer slowly moving atoms with bad contacts downhill (Fri Apr 12 2013 - 03:56:19 CDT)
  • Re: pump / force application (Thu Apr 11 2013 - 08:23:10 CDT)
  • Re: Unsubscribe (Thu Apr 11 2013 - 03:43:00 CDT)
  • Re: Error in distributing the cores for a single processor (Thu Apr 11 2013 - 00:44:20 CDT)
  • Re: NAMD Output files (Thu Apr 11 2013 - 00:35:05 CDT)
  • Re: Error in distributing the cores for a single processor (Thu Apr 11 2013 - 00:33:33 CDT)
  • Re: About Bond Deletion (Thu Apr 11 2013 - 00:32:45 CDT)
  • Re: Sutton-Chen potential (Mon Apr 01 2013 - 04:30:19 CDT)
  • Re: Sutton-Chen potential (Mon Apr 01 2013 - 03:40:43 CDT)
  • Re: implicit solvent (Wed Mar 27 2013 - 11:31:03 CDT)
  • Re: Can protein-water interaction be turned off keeping protein-protein and water-water interactions intact? (Tue Mar 19 2013 - 01:15:42 CDT)
  • Re: Can protein-water interaction be turned off keeping protein-protein and water-water interactions intact? (Tue Mar 19 2013 - 00:04:12 CDT)
  • Re: Effect of phi, psi cross term map (CMAP) correction on result of MD simulation (Wed Mar 13 2013 - 04:20:08 CDT)
  • using stackexchange was: Re: unsubscriber e-mail office pool anybody? (Thu Mar 07 2013 - 03:04:16 CST)
  • Re: unsubscriber e-mail office pool anybody? (Tue Mar 05 2013 - 08:36:45 CST)
  • Re: if{} statements (Tue Mar 05 2013 - 08:15:21 CST)
  • Re: if{} statements (Tue Mar 05 2013 - 07:54:53 CST)
  • unsubscriber e-mail office pool anybody? (Tue Mar 05 2013 - 07:11:44 CST)
  • Re: Very long simulation (Mon Mar 04 2013 - 06:10:43 CST)
  • Re: Single point energy calc with gaussian/namd... log file interpretation (Sat Feb 23 2013 - 02:30:10 CST)
  • Re: running NAMD on Amazon EC2? (Thu Feb 14 2013 - 14:53:56 CST)
  • Re: Generating topology files for crystalline materials (Sun Feb 10 2013 - 16:05:16 CST)
  • Re: Generating topology files for crystalline materials (Sun Feb 10 2013 - 15:11:55 CST)
  • Re: Generating topology files for crystalline materials (Sun Feb 10 2013 - 14:54:45 CST)
  • Re: Generating topology files for crystalline materials (Sun Feb 10 2013 - 12:22:09 CST)
  • Re: namd-I: sub-routine code in NAMD (Thu Jan 03 2013 - 21:05:51 CST)
• AYSEGUL TURUPCU
  • unsubscribe (Mon Jun 24 2013 - 04:22:27 CDT)
  • unsubscribe (Sat Jun 22 2013 - 11:07:04 CDT)
• Azadeh Alavi
  • 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)
• B Hartzoulakis
  • FW: SOLVED: Issues with the "Keep Water Out" tcl script (Fri Jan 04 2013 - 05:14:29 CST)
  • SOLVED: Issues with the "Keep Water Out" tcl script (Fri Jan 04 2013 - 05:01:08 CST)
  • Issues with the "Keep Water Out" tcl script (Thu Jan 03 2013 - 06:15:50 CST)
• Bachir Aoun
  • Lennard Jones (LJ) parameters (Sun Oct 06 2013 - 15:23:36 CDT)
• Bala subramanian
  • 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)
  • Re: Calculating pressure on each direction (Thu Oct 24 2013 - 10:25:20 CDT)
  • Calculating pressure on each direction (Thu Oct 24 2013 - 07:53:07 CDT)
• Basak Isin
  • unsubscribe please! (Fri Aug 02 2013 - 16:35:11 CDT)
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• 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: write pdb (Thu Feb 20 2014 - 00:31:36 CST)
• bdrakuli
  • Re: Non standar solvent (Tue Feb 18 2014 - 11:43:58 CST)
• Beaven, Andrew
  • Changing NAMD XY restraint (Fri Aug 02 2013 - 16:29:05 CDT)
• Behnam Rasti
  • pair interaction energy calculation (Wed Sep 25 2013 - 06:20:35 CDT)
• Benjamin Bouvier
  • Re: Orientation colvar + metadynamics questions (Thu Feb 21 2013 - 07:37:06 CST)
  • Orientation colvar + metadynamics questions (Thu Feb 21 2013 - 04:58:48 CST)
• Benjamin Hill
  • ffTK and phase angles (Thu Jun 19 2014 - 17:43:28 CDT)
  • unsubscribe (Sat Feb 02 2013 - 01:19:58 CST)
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• Benjamin Merget
  • Re: GPUs silently stop working during simulation when oversubscribed (Thu Feb 28 2013 - 04:04:30 CST)
  • GPUs silently stop working during simulation when oversubscribed (Thu Feb 28 2013 - 02:51:39 CST)
• Bennion, Brian
  • 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)
  • RE: VDW energy is negative but total energy is positive (Tue Sep 10 2013 - 10:57:23 CDT)
  • RE: VDW energy is negative but total energy is positive (Mon Sep 09 2013 - 10:25:53 CDT)
  • RE: Should I use a precompiled binary? (Fri May 24 2013 - 15:45:02 CDT)
• bharat gupta
  • Re: Using volmap to calculate the water density around certain residues (Mon Nov 04 2013 - 02:25:22 CST)
• Bhupender Thakur
  • NAMD 2.9 jobs hanging. (Mon Feb 18 2013 - 20:40:14 CST)
• Bikan Tan
  • DNA surrounded by a shell of water in a big box with vacuum (Mon Jan 14 2013 - 11:01:06 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)
• Bin Zhang
  • unsubscribe namd-l (Tue Mar 26 2013 - 13:15:23 CDT)
• BIPLAB NANDI
  • (no subject) (Wed Aug 27 2014 - 22:13:06 CDT)
• bishop_at_latech.edu
  • Re: dcd to pdb for trajectory analysis (Thu Jul 11 2013 - 13:01:33 CDT)
• Blake Mertz
  • Re: namd2 CUDA errors for non-superusers in Debian (Fri Feb 15 2013 - 13:46:39 CST)
  • Re: namd2 CUDA errors for non-superusers in Debian (Fri Feb 15 2013 - 08:42:57 CST)
  • namd2 CUDA errors for non-superusers in Debian (Thu Feb 14 2013 - 16:28:23 CST)
• 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)
  • Re: Preventing rotation of a protein (Wed Jul 17 2013 - 22:05:03 CDT)
• Branko
  • 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)
  • Re: problem in determining atom types and charges for ligand atoms to type in the topology file (Thu Aug 29 2013 - 12:08:30 CDT)
  • Re: NAMD with pbs script (Sun Aug 25 2013 - 10:20:28 CDT)
  • Re: AW: Colvar cannot be ran on supercomputer newton (Wed Aug 07 2013 - 11:25:38 CDT)
  • Re: AW: Colvar cannot be ran on supercomputer newton (Wed Aug 07 2013 - 03:04:23 CDT)
  • Re: Protein-ligand simulation (Sat Jul 06 2013 - 11:49:45 CDT)
  • Re: Two dimensional ABF (Tue Jun 11 2013 - 12:38:19 CDT)
  • Re: First meeting with NAMD (Tue Jun 04 2013 - 08:46:07 CDT)
  • Re: Sevoflurane parameters (psf file) (Fri May 03 2013 - 13:14:27 CDT)
  • Re: strange result using implicit solvent (Fri Mar 29 2013 - 09:41:09 CDT)
  • Re: How to split large NAMD DCD file (Thu Jan 24 2013 - 11:15:17 CST)
  • Re: smd tcl script - problem atoms id (Sun Jan 20 2013 - 16:46:56 CST)
  • smd tcl script - problem atoms id (Sun Jan 20 2013 - 10:37:56 CST)
• Brunner, Robert Kraemer
  • Re: NAMD and NUMA (Fri May 09 2014 - 12:03:53 CDT)
• Bryan Roessler
  • Altering extrabonds forces during MD (Tue Apr 15 2014 - 09:53:02 CDT)
  • Targeted and Steered MD: Why must the initial and targeted PDBs have identical # of atoms? (Mon Aug 26 2013 - 11:24:31 CDT)
  • NAMD exiting on startup phase (Mon Jun 24 2013 - 09:52:36 CDT)
• btreece_at_andrew.cmu.edu
  • running a calculation during simulation (Mon Oct 20 2014 - 16:08:12 CDT)
• buksanbio_at_gmail.com
  • (no subject) (Sat Oct 05 2013 - 16:12:07 CDT)
• Carlos Navarrro Retamal
  • (no subject) (Tue Jul 22 2014 - 11:43:10 CDT)
  • Special constraint on MD simulation (Mon Aug 05 2013 - 04:13:33 CDT)
• Cat Chenal
  • unsuscribe (Thu Apr 10 2014 - 09:49:18 CDT)
  • unsuscribe (Tue Oct 29 2013 - 09:45:33 CDT)
  • unsuscribe (Mon Aug 12 2013 - 10:01:42 CDT)
  • unsuscribe (Thu Aug 08 2013 - 12:20:16 CDT)
  • FATAL ERROR Unknown parameter in charmm parameter file (Mon Jul 01 2013 - 13:19:27 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)
• Cesar Millan
  • Re: charm-gui membrane builder (Sun Sep 08 2013 - 11:51:56 CDT)
  • Re: A larger protein data bank for performance benchmark (Mon May 13 2013 - 11:52:30 CDT)
• Chan Tabris C
  • Compile NAMD with FFTW3 and MPI (Tue Nov 19 2013 - 02:45:00 CST)
• Charles McAnany
  • Phosphorylating a residue with Amber ff (Sat Nov 30 2013 - 12:24:19 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)
• Chen Wei
  • Error when running MIC version of namd on Stampede (Fri Feb 21 2014 - 09:49:38 CST)
• chin chun
  • Mechanical Properties of protein (Thu Oct 30 2014 - 19:18:11 CDT)
• chipot
  • Re: Problem with running FEP calculations (Mon Apr 15 2013 - 00:03:24 CDT)
• Chris Chipot
  • Re: Protein-ligand simulation (Sat Jul 06 2013 - 03:02:05 CDT)
  • Re: Reaction field treatment (Mon Jul 01 2013 - 14:29:56 CDT)
  • Re: Protein-ligand simulation (Mon Jun 24 2013 - 07:02:24 CDT)
  • Re: ABF (Thu May 09 2013 - 01:09:27 CDT)
  • Re: BAR-estimator error of ParseFEP plugin version 1.5 in VMD 1.9.1 (Tue May 07 2013 - 00:44:08 CDT)
  • Re: How to use ParseFEP plugin to carry out FEP analysis for several forward and backward *.fepout files when lambda is from 0 to 1 (Sun May 05 2013 - 02:44:48 CDT)
  • Re: WHAM analysis for Umbrella sampling (Wed May 01 2013 - 12:58:18 CDT)
  • Re: WHAM analysis for Umbrella sampling (Wed May 01 2013 - 02:01:44 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)
  • Re: memory demands of REMD (Thu Mar 07 2013 - 18:19:39 CST)
  • Re: Current CVS broken? (SortedArray.h) (Tue Feb 05 2013 - 13:20:58 CST)
  • Re: NAMD on Stempede (and other MIC Coprocessor systems) (Fri Jan 11 2013 - 15:18:42 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 Jorgensen
  • Fwd: vmd-l: Re: wrapping option in namd (Mon Jun 23 2014 - 04:59:50 CDT)
• Christopher Neale
  • NAMD with Intel Xeon Phi coprocessors ? (Fri Mar 08 2013 - 22:32:06 CST)
• Christopher Rowley
  • vdW-only fep between two ions (Tue Nov 04 2014 - 14:43:08 CST)
• Christopher Von Bargen
  • pairInteractionSelf interaction terms (Thu Nov 07 2013 - 15:22:58 CST)
• Cloud Computing
  • Re: running NAMD on Amazon EC2? (Thu Feb 14 2013 - 14:48:04 CST)
  • Re: running NAMD on Amazon EC2? (Thu Feb 14 2013 - 14:38:38 CST)
  • running NAMD on Amazon EC2? (Wed Feb 13 2013 - 16:05:03 CST)
• Cobalto Tetracloruro
  • Fwd: Pressure in NPT ensamble (Fri May 31 2013 - 11:15:49 CDT)
• Corey Fugate
  • Re: Help with "ERROR: Constraint failure in RATTLE algorithm for atom XXXX!" (Mon May 20 2013 - 17:28:21 CDT)
  • Re: Help with "ERROR: Constraint failure in RATTLE algorithm for atom XXXX!" (Mon May 20 2013 - 11:57:14 CDT)
  • Help with "ERROR: Constraint failure in RATTLE algorithm for atom XXXX!" (Mon May 20 2013 - 11:08:07 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)
• Cruz-Chu Eduardo Roberto
  • RE: Simulation continuously crashes after minimization (Tue Feb 12 2013 - 17:00:57 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)
• Dale l. Schruben
  • RE: free energy methods cheat-sheet/comparison chart (Mon Mar 25 2013 - 21:06:22 CDT)
• Dan F. X. Martingano
  • Re: Umbrella Sampling of Sugar Pseudorotation (Mon Feb 03 2014 - 13:40:08 CST)
• Daniel Abergel
  • converting dcd files to netcdf or ascii (Thu Feb 28 2013 - 07:04:41 CST)
• 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)
• Daniele Gentili
  • namd 2.9 tip4p-2005 (Tue Jan 15 2013 - 06:23:14 CST)
• Danielle Chandler
  • 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)
• 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)
  • Computational Biophysics Workshop using NAMD and VMD, November 18-22, 2013, Urbana, Illinois, USA (Fri Aug 23 2013 - 14:07:30 CDT)
  • Workshop on GPU Programming for Molecular Modeling, August 2-4, 2013, in Urbana, Illinois (Tue Jun 11 2013 - 17:41:43 CDT)
  • 'Hands-on' Workshop on Computational Biophysics using VMD, NAMD, and ProDy, June 10-14, 2013 in Pittsburgh, PA (Fri Mar 08 2013 - 12:08:25 CST)
• David Chin
  • Compiling with Open64 4.5.2.1 for AMD Opteron 6378 (Mon Mar 24 2014 - 10:44:54 CDT)
• David Cohen-Tanugi
  • Water density in the solvate plugin (Fri Jul 26 2013 - 10:50:20 CDT)
• David Hardy
  • 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)
  • Re: zeroMomentum for water droplet (Wed Dec 04 2013 - 09:32:41 CST)
  • Re: Bonds in XPLOR format (Wed Oct 23 2013 - 13:14:23 CDT)
  • Re: src/ComputeNonbondedCUDA.C:1022: error: thread-local storage not supported for this target (Wed Jan 16 2013 - 11:07:48 CST)
• David Huggins
  • Implementing the Virtual Bond Algorithm Using Colvars (Wed Dec 17 2014 - 06:25:33 CST)
  • Energy Correction Term For PME Electrostatics in a Charged Periodic System (Wed Sep 18 2013 - 05:02:52 CDT)
• davide branduardi
  • Re: About PLUMED with NAMD VMD (Wed Feb 27 2013 - 02:41:14 CST)
• dayanidhi mohanta
  • VDW energy is negative but total energy is positive (Fri Sep 06 2013 - 23:18:51 CDT)
• dbaogen
  • Re: Re: AW: puzzle of SMD in NAMD-2.9 and pull code in Gromacs (Thu Dec 12 2013 - 23:58:49 CST)
  • Re: AW: puzzle of SMD in NAMD-2.9 and pull code in Gromacs (Thu Dec 12 2013 - 19:02:30 CST)
  • Re: Re: puzzle of SMD in NAMD-2.9 and pull code in Gromacs (Tue Dec 10 2013 - 20:27:15 CST)
  • puzzle of SMD in NAMD-2.9 and pull code in Gromacs (Tue Dec 10 2013 - 06:02:25 CST)
  • problem of using SMD and TclForces keywords simultaneously (Fri Nov 15 2013 - 02:42:07 CST)
  • Problem of ATP mutated to dATP in solution using FEP method (Mon Aug 05 2013 - 02:14:24 CDT)
  • BAR-estimator error of ParseFEP plugin version 1.5 in VMD 1.9.1 (Tue May 07 2013 - 00:10:40 CDT)
  • How to use ParseFEP plugin to carry out FEP analysis for several forward and backward *.fepout files when lambda is from 0 to 1 (Sat May 04 2013 - 02:23:19 CDT)
  • unrecognizable code in the output file of ParseFEP analysis in VMD 1.9.1 under the Linux system (Sun Apr 28 2013 - 03:11:52 CDT)
  • Effect of phi, psi cross term map (CMAP) correction on result of MD simulation (Wed Mar 13 2013 - 04:13:42 CDT)
• Debashis Kundu
  • Multiple input and output files (Wed Nov 05 2014 - 20:20:37 CST)
• DENILSON FERREIRA DE OLIVEIRA
  • Martini RBCG (Mon Jan 14 2013 - 09:55:51 CST)
• Dennis Lam
  • About NAMD (Tue Jun 25 2013 - 11:20:15 CDT)
• Devang Jane
  • Compile NAMD2.9 on Xeon Phi (Thu Aug 08 2013 - 13:15:38 CDT)
• Devang Sachdev
  • Uncovering the Elusive HIV Capsid with Kepler GPUs Running NAMD & VMD (Tue Jul 02 2013 - 13:25:57 CDT)
  • Aron Broom on NVIDIA CUDA Spotlight (Wed May 22 2013 - 19:59:11 CDT)
• Dhanashree Khanale
  • Unsubscribe (Thu Jun 19 2014 - 03:19:51 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)
• Dmitry Osolodkin
  • Charm 6.5.0 compilation issue (Fri Jan 11 2013 - 07:17:21 CST)
  • Charm 6.5.0 compilation issue (Sun Jan 06 2013 - 13:28:27 CST)
• Dong Luo
  • Re: Method for solvation of protein (Tue Oct 22 2013 - 10:57:17 CDT)
  • Re: NAMD simulation with flag similar to -maxh in Gromacs (Tue Oct 15 2013 - 11:50:45 CDT)
  • Re: running NAMD on Amazon EC2? (Thu Feb 14 2013 - 10:54:21 CST)
• Douglas Houston
  • 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
  • Re: Gold nanoparticle (Thu Sep 26 2013 - 09:42:36 CDT)
  • Re: Gold nanoparticle (Wed Sep 25 2013 - 11:52:48 CDT)
  • Gold nanoparticle (Wed Sep 25 2013 - 11:25:45 CDT)
  • namdenergy and namd (Mon Jun 17 2013 - 08:43:44 CDT)
• Eduard Schreiner
  • Re: DCD file doubles a monomer (Tue Feb 26 2013 - 16:17:34 CST)
• Edward Lyman
  • hey! you! why did my simulation crash? (Wed Mar 26 2014 - 10:42:46 CDT)
  • utilizing mic coprocs on Stampede (Tue Jun 18 2013 - 14:46:47 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)
• Elif Ozkirimli
  • unsubscribe (Sun Feb 03 2013 - 17:34:25 CST)
  • unsubscribe (Fri Feb 01 2013 - 18:37:04 CST)
• Emilia Wu
  • Re: charm-gui membrane builder (Sat Sep 07 2013 - 09:16:19 CDT)
• eprates_at_iqm.unicamp.br
  • Re: AW: AW: AW: Martini RBCG simulation frequently crashing with "atoms moving too fast" (Wed Nov 06 2013 - 11:17:19 CST)
  • Re: AW: AW: Martini RBCG simulation frequently crashing with "atoms moving too fast" (Mon Nov 04 2013 - 09:59:14 CST)
  • Re: AW: Martini RBCG simulation frequently crashing with "atoms moving too fast" (Mon Nov 04 2013 - 08:42:53 CST)
  • Martini RBCG simulation frequently crashing with "atoms moving too fast" (Sun Nov 03 2013 - 11:57:18 CST)
  • simulation crashes frequently with "atoms moving too fast" (Fri Nov 01 2013 - 16:26:57 CDT)
• Eric Hill
  • Re: AW: AW: CUDA problem? (Tue Jan 15 2013 - 01:12:53 CST)
  • Re: How we can merge protein and ligand complex? (Tue Jan 15 2013 - 01:15:22 CST)
• Eric Lang
  • RE: Problem with running FEP calculations (Mon Apr 15 2013 - 20:21:53 CDT)
  • Problem with running FEP calculations (Sun Apr 14 2013 - 18:51:45 CDT)
• Eudes Fileti
  • FEP Error - TCL (Tue Oct 29 2013 - 14:28:17 CDT)
  • Mac OS Binary for NAMD 2.10 (Thu Oct 24 2013 - 06:16:31 CDT)
• Fabien Cailliez
  • total charge of the system - rounding error ? (Mon Apr 15 2013 - 11:59:33 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
  • Protein solvation (Sat May 10 2014 - 12:28:26 CDT)
  • Re: Fwd: Majordomo results (Wed Jan 01 2014 - 14:57:29 CST)
  • problem with Dihedral (Sun Oct 06 2013 - 07:27:01 CDT)
• Fatemeh Omidbeygi
  • RDF calculation of crystal system (Sat Aug 30 2014 - 00:41:02 CDT)
• Felipe Merino
  • 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)
  • Re: How I can to change the force field function in NAMD for protein phi-value analysis (Mon Oct 07 2013 - 09:15:48 CDT)
  • Re: question about NVE ensamble (Thu Jul 18 2013 - 10:33:23 CDT)
  • Atom numbering (Sat Jun 22 2013 - 05:34:53 CDT)
  • Re: Overestimated PMF (Mon Jun 17 2013 - 13:33:13 CDT)
  • Re: Overestimated PMF (Mon Jun 17 2013 - 10:15:07 CDT)
  • Overestimated PMF (Mon Jun 17 2013 - 09:43:07 CDT)
• Fidan Sumbul
  • 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)
  • zinc finger with ASP (Thu Jun 27 2013 - 09:47:22 CDT)
• 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)
  • minimization with symmetry restrain (Fri Dec 13 2013 - 12:31:39 CST)
  • Re: Topology and parameters for nitrate and nitrite ion (Sun Jun 30 2013 - 14:02:06 CDT)
  • Re: Very long simulation (Mon Mar 04 2013 - 17:39:26 CST)
  • Re: How to split large NAMD DCD file (Thu Jan 24 2013 - 11:09:31 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)
• forough askari
  • (no subject) (Sun Jan 27 2013 - 10:06:36 CST)
  • (no subject) (Tue Jan 22 2013 - 16:32:34 CST)
  • (no subject) (Mon Jan 21 2013 - 18:38:10 CST)
• Fotis Baltoumas
  • 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 oteri
  • protein schematic representaton (Mon Jun 10 2013 - 13:23:17 CDT)
  • spectrum simulation (Sun Feb 24 2013 - 14:56:55 CST)
  • Re: transmembrane protein simulation - hydrophobic thickness and NAMD membrane plugin (Mon Feb 18 2013 - 11:31:09 CST)
• Francesco Pietra
  • 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)
  • Fwd: Bug in T-REMD with colvars (Tue Dec 03 2013 - 13:31:24 CST)
  • Fwd: Bug in T-REMD with colvars (Tue Dec 03 2013 - 02:55:43 CST)
  • Bug in T-REMD with colvars (Tue Dec 03 2013 - 01:55:14 CST)
  • Re: PCIexpress 3.0 for MD with NAMD on GPUs (Thu Nov 21 2013 - 05:00:54 CST)
  • Fwd: PCIexpress 3.0 for MD with NAMD on GPUs (Tue Nov 19 2013 - 02:50:42 CST)
  • Fwd: PCIexpress 3.0 for MD with NAMD on GPUs (Mon Nov 18 2013 - 03:13:05 CST)
  • Re: PCIexpress 3.0 for MD with NAMD on GPUs (Mon Nov 18 2013 - 01:31:10 CST)
  • Fwd: PCIexpress 3.0 for MD with NAMD on GPUs (Sun Nov 17 2013 - 09:06:51 CST)
  • Re: PCIexpress 3.0 for MD with NAMD on GPUs (Sun Nov 17 2013 - 04:56:04 CST)
  • Fwd: RE: PCIexpress 3.0 for MD with NAMD on GPUs (Tue Nov 12 2013 - 01:46:45 CST)
  • PCIexpress 3.0 for MD with NAMD on GPUs (Mon Nov 11 2013 - 03:51:02 CST)
  • Re: Restarting T-REMD with colvars (Tue Nov 05 2013 - 13:58:55 CST)
  • Fwd: Restarting T-REMD with colvars (Tue Nov 05 2013 - 01:53:50 CST)
  • Fwd: Restarting T-REMD with colvars (Tue Nov 05 2013 - 01:48:45 CST)
  • Restarting T-REMD with colvars (Mon Nov 04 2013 - 10:19:30 CST)
  • Re: CUDA vd non-CUDA for minimization (Sat Oct 19 2013 - 02:28:50 CDT)
  • CUDA vd non-CUDA for minimization (Fri Oct 18 2013 - 12:13:04 CDT)
  • Re: About the scope of show_replicas.vmd (Fri Sep 20 2013 - 12:39:16 CDT)
  • Re: About the scope of show_replicas.vmd (Fri Sep 20 2013 - 02:33:19 CDT)
  • Re: About the scope of show_replicas.vmd (Thu Sep 19 2013 - 10:53:58 CDT)
  • About the scope of show_replicas.vmd (Thu Sep 19 2013 - 01:48:16 CDT)
  • Does stray PME charges with T-REMD mean insufficient resources and can explicit water abandoned for implicit GB? (Wed Sep 11 2013 - 09:24:59 CDT)
  • Re: Stray PME grid charges on increasing number of replicas and T-range with T-REMD (Tue Sep 10 2013 - 11:34:58 CDT)
  • Fwd: Stray PME grid charges on increasing number of replicas and T-range with T-REMD (Tue Sep 10 2013 - 05:33:03 CDT)
  • Stray PME grid charges on increasing number of replicas and T-range with T-REMD (Tue Sep 10 2013 - 05:24:58 CDT)
  • About a REMD tutorial (Sat Sep 07 2013 - 09:35:51 CDT)
  • Fwd: deca-alanin folding by remd parallel tempering (Wed Sep 04 2013 - 04:35:45 CDT)
  • Error with show_replicas.vmd (Tue Sep 03 2013 - 04:44:55 CDT)
  • Re: colvars and parallel-tempering with namd2.10 (Fri Aug 23 2013 - 02:57:53 CDT)
  • remd restart (Thu Aug 22 2013 - 06:00:40 CDT)
  • Fwd: Low global exclusion count on parallel tempering, not on MD (Thu Aug 22 2013 - 03:32:18 CDT)
  • Fwd: Low global exclusion count on parallel tempering, not on MD (Wed Aug 21 2013 - 11:27:44 CDT)
  • Low global exclusion count on parallel tempering, not on MD (Wed Aug 21 2013 - 10:45:05 CDT)
  • Re: colvars and parallel-tempering with namd2.10 (Mon Aug 19 2013 - 01:46:36 CDT)
  • Re: colvars and parallel-tempering with namd2.10 (Mon Aug 19 2013 - 01:41:12 CDT)
  • Re: colvars and parallel-tempering with namd2.10 (Sat Aug 17 2013 - 11:51:08 CDT)
  • colvars and parallel-tempering with namd2.10 (Mon Aug 12 2013 - 09:54:25 CDT)
  • Re: replica exchange parallel tempering BlueGene/Q (Mon Aug 12 2013 - 02:25:42 CDT)
  • replica exchange parallel tempering BlueGene/Q (Sun Aug 11 2013 - 01:15:04 CDT)
  • namd/bluegeneQ (Mon Aug 05 2013 - 12:48:07 CDT)
  • Fwd: replica exchange and colvars (Wed Jul 31 2013 - 02:49:11 CDT)
  • replica exchange and colvars (Wed Jul 31 2013 - 02:34:05 CDT)
  • Re: Replica exchange on single physical node (Sat Jul 06 2013 - 10:37:43 CDT)
  • Replica exchange on single physical node (Sat Jul 06 2013 - 09:19:42 CDT)
  • Launching namd GPU-MPI vs GPU-binary (Sat Jul 06 2013 - 02:54:00 CDT)
  • REMD-GPU (Thu Jul 04 2013 - 02:36:59 CDT)
  • Fwd: Failure with compilation namd2.9-cuda_plumed1.3_recon (Mon Jun 24 2013 - 04:48:24 CDT)
  • Failure with compilation namd2.9-cuda_plumed1.3_recon (Sat Jun 22 2013 - 12:15:26 CDT)
  • About Fiorin-Klein-Henin recent colvar examples (Fri Jun 21 2013 - 03:50:35 CDT)
  • Any alternative to colvars for minimization? (Thu Jun 06 2013 - 01:36:40 CDT)
  • Does MOLLY really retain bond motion for water? (Sun Jun 02 2013 - 08:45:04 CDT)
  • QM-MM (Fri May 31 2013 - 01:47:47 CDT)
  • Re: namd with ff99sb (Wed May 29 2013 - 01:27:32 CDT)
  • Flags for TIP3 water with NAMD/AMBER FF (Tue May 28 2013 - 10:46:01 CDT)
  • Re: Suggestions while building a GPU-machine (CUDA) for NAMD use! (Tue May 28 2013 - 02:54:47 CDT)
  • Re: Suggestions while building a GPU-machine (CUDA) for NAMD use! (Tue May 28 2013 - 00:55:38 CDT)
  • Selecting GPU for namd2 (Mon May 06 2013 - 02:27:57 CDT)
  • Fe-N bond parameters (Sun Apr 28 2013 - 09:55:16 CDT)
  • Re: metadynamics (Fri Apr 26 2013 - 11:02:19 CDT)
  • Re: metadynamics (Fri Apr 26 2013 - 10:58:40 CDT)
  • metadynamics (Fri Apr 26 2013 - 09:46:12 CDT)
  • Fwd: vmd-l: HEME acting unplanar (Wed Apr 24 2013 - 15:07:54 CDT)
  • Fwd: Inconsistency in fast table energy vs force (Sat Apr 13 2013 - 05:27:01 CDT)
  • Inconsistency in fast table energy vs force (Sat Apr 13 2013 - 02:36:32 CDT)
  • understanding which is which with GPU cards (Sat Apr 06 2013 - 17:17:13 CDT)
  • Fwd: CUDA error in cuda_check_remote_progress on Pe 2 (Sat Apr 06 2013 - 04:49:21 CDT)
  • Fwd: CUDA error in cuda_check_remote_progress on Pe 2 (Fri Apr 05 2013 - 10:04:48 CDT)
  • Fwd: CUDA error in cuda_check_remote_progress on Pe 2 (Fri Apr 05 2013 - 09:58:58 CDT)
  • CUDA error in cuda_check_remote_progress on Pe 2 (Fri Apr 05 2013 - 09:55:44 CDT)
  • Re: vmd-l: FFTK Atom types (Wed Mar 27 2013 - 10:54:21 CDT)
  • FFTK Atom types (Wed Mar 27 2013 - 02:21:13 CDT)
  • Morse potentail with charmm 27 (Sun Mar 24 2013 - 11:04:56 CDT)
  • Fwd: NAMD 2.9 CUDA compilation (Mon Mar 11 2013 - 10:56:51 CDT)
  • NAMD 2.9 CUDA compilation (Mon Mar 11 2013 - 10:40:11 CDT)
  • Fwd: NAMD + PLUMED COMPILATION (Fri Mar 01 2013 - 00:52:14 CST)
  • NAMD + PLUMED COMPILATION (Thu Feb 28 2013 - 11:02:28 CST)
  • (no subject) (Thu Feb 28 2013 - 10:59:57 CST)
  • About PLUMED with NAMD VMD (Wed Feb 27 2013 - 02:16:28 CST)
  • Fwd: About "add solvation" (Mon Jan 21 2013 - 03:49:06 CST)
  • About "add solvation" (Mon Jan 21 2013 - 03:42:54 CST)
• Frank Haverkort
  • Re: error when doing minimization with the charmm Drude FF (Fri Aug 30 2013 - 08:48:43 CDT)
  • error when doing minimization with the charmm Drude FF (Wed Aug 28 2013 - 05:23:49 CDT)
  • understanding the lone pair section of psf files (Thu Aug 22 2013 - 10:44:17 CDT)
  • setting the polarizabilities for the Drude force field (Thu Aug 01 2013 - 06:48:59 CDT)
• Frank Thommen
  • Re: AW: charm++ MPI build errors on LSF Cluster: "Can not compile a MPI program" (Mon Dec 02 2013 - 04:07:42 CST)
  • charm++ MPI build errors on LSF Cluster: "Can not compile a MPI program" (Sat Nov 30 2013 - 14:51:55 CST)
• Fugui
  • Protein unfolding and Coarse grained (Fri May 17 2013 - 06:55:02 CDT)
  • Coarse-grained reverse transformation (Sat May 11 2013 - 10:21:04 CDT)
  • Bad global bond count (Mon May 06 2013 - 15:26:52 CDT)
  • Coarse-Grained fatal error! (Thu May 02 2013 - 07:49:20 CDT)
  • strange result using implicit solvent (Fri Mar 29 2013 - 08:00:04 CDT)
  • Error in implicit solvent MD (Wed Mar 27 2013 - 15:08:19 CDT)
  • implicit solvent (Wed Mar 27 2013 - 11:27:55 CDT)
• Fugui
  • How to converse Coarse-Grained structure into all-atom structure (Mon May 06 2013 - 05:02:10 CDT)
• Fulu Zheng
  • two O atoms in CTER are unusually close (Sat Jul 05 2014 - 02:05:28 CDT)
• FX
  • Re: Fixing Langevin piston to allow off-diagonal stress (and why does the source say "FIX THIS"?) (Wed Mar 06 2013 - 16:36:04 CST)
  • Re: tcl-related segfault in NAMD (Wed Mar 06 2013 - 12:59:37 CST)
  • Re: tcl-related segfault in NAMD (Wed Mar 06 2013 - 10:37:37 CST)
  • tcl-related segfault in NAMD (Wed Mar 06 2013 - 09:32:39 CST)
  • Fixing Langevin piston to allow off-diagonal stress (and why does the source say "FIX THIS"?) (Wed Mar 06 2013 - 04:43:49 CST)
  • Re: Constant pressure energy minimization (Wed Feb 20 2013 - 02:18:43 CST)
  • Constant volume energy minimization (Tue Feb 19 2013 - 16:06:53 CST)
  • Re: Generating topology files for crystalline materials (Sun Feb 10 2013 - 15:58:31 CST)
  • Re: Generating topology files for crystalline materials (Sun Feb 10 2013 - 14:02:16 CST)
  • Generating topology files for crystalline materials (Sun Feb 10 2013 - 12:05:26 CST)
• 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)
  • New empirical force field tools: Release of R.E.D. Server Dev./R.E.D. Python (Fri Nov 22 2013 - 04:18:53 CST)
• Gabriel Jara
  • Re: dcd to pdb for trajectory analysis (Thu Jul 11 2013 - 09:43:16 CDT)
  • Invitation to connect on LinkedIn (Mon Jun 03 2013 - 08:46:22 CDT)
• GALLY Jose Manuel
  • Fwd: Troubles to converge while running bidirectional FEP (Thu Jun 27 2013 - 02:12:24 CDT)
• Ganesh Kamath
  • Question about loading velocity files on VMD (Fri Aug 09 2013 - 10:01:17 CDT)
• Ganesh Shahane
  • (no subject) (Thu Apr 25 2013 - 08:51:59 CDT)
  • (no subject) (Thu Apr 25 2013 - 01:25:29 CDT)
• Gareth Price
  • Minimisation of protein in a water box (Sat Apr 13 2013 - 13:52:01 CDT)
• Geoffrey Kwai Wai Kong
  • MDFF - should hydrogens be included? (Mon Mar 04 2013 - 00:19:26 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)
  • Modify Molecule.C to avoid fatal error? (Thu Nov 28 2013 - 02:26:37 CST)
  • Error with dummy atoms (Wed Nov 27 2013 - 11:07:40 CST)
  • Re: ABF with the RMSD colvar (Fri Jun 07 2013 - 09:43:45 CDT)
  • ABF with the RMSD colvar (Fri Jun 07 2013 - 08:51:22 CDT)
  • Apply torque with NAMD (Tue Feb 12 2013 - 05:30:28 CST)
  • SMD and torque application (Sun Feb 03 2013 - 14:42:09 CST)
• Gergely Gyimesi
  • Re: Unable to read corrupted binary DCD trajectory file (Mon Sep 08 2014 - 09:51:33 CDT)
  • lone pair velocities (Wed Sep 25 2013 - 11:27:48 CDT)
• Giacomo Fiorin
  • 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)
  • Re: obtaining the system force (Tue Dec 24 2013 - 10:51:10 CST)
  • Re: colavrs ABF restart not matching (Tue Dec 10 2013 - 11:40:38 CST)
  • Re: Colvars periodic boundary treatment question (Tue Dec 03 2013 - 16:07:12 CST)
  • Re: ABF: Distances in colvars.traj not identical with VMD exported distances (Tue Oct 29 2013 - 09:33:36 CDT)
  • Re: ABF: Distances in colvars.traj not identical with VMD exported distances (Mon Oct 28 2013 - 16:28:15 CDT)
  • Re: How I can to change the force field function in NAMD for protein phi-value analysis (Mon Oct 07 2013 - 08:30:34 CDT)
  • Re: How to setting tilt component in colvars module (Mon Sep 23 2013 - 09:43:35 CDT)
  • Re: NAMD job submission on Kraken? (Fri Aug 30 2013 - 15:37:56 CDT)
  • Re: eigenvector colvar (Thu Aug 29 2013 - 09:00:56 CDT)
  • Re: colvars and parallel-tempering with namd2.10 (Sun Aug 18 2013 - 10:40:59 CDT)
  • Re: colvars and parallel-tempering with namd2.10 (Tue Aug 13 2013 - 12:00:45 CDT)
  • Re: colvars and parallel-tempering with namd2.10 (Tue Aug 13 2013 - 10:51:39 CDT)
  • Re: Colvars RMSD syntax with a moving reference frame (Fri Aug 02 2013 - 13:17:49 CDT)
  • Re: Replica exchange, colvars & harmonic restraints (Mon Jul 29 2013 - 16:22:56 CDT)
  • Re: pmf command (Thu Jul 25 2013 - 13:00:50 CDT)
  • Re: Unsubscribe (Fri Jul 19 2013 - 13:00:04 CDT)
  • Re: Preventing rotation of a protein (Thu Jul 18 2013 - 11:41:55 CDT)
  • Re: Preventing rotation of a protein (Wed Jul 17 2013 - 21:31:15 CDT)
  • Re: use of colvars to restrain the absolute positions of all atoms in a large system (Tue Jul 09 2013 - 17:16:19 CDT)
  • Re: Simulation in Collective sub-space (Tue Jun 25 2013 - 16:54:04 CDT)
  • Re: Simulation in Collective sub-space (Tue Jun 25 2013 - 08:03:48 CDT)
  • Re: Atom numbering (Sat Jun 22 2013 - 10:41:35 CDT)
  • Re: About Fiorin-Klein-Henin recent colvar examples (Fri Jun 21 2013 - 09:59:06 CDT)
  • collective variables new paper (Mon Jun 17 2013 - 17:48:11 CDT)
  • Re: Overestimated PMF (Mon Jun 17 2013 - 10:10:10 CDT)
  • Re: How to remove center of mass translation of macromolecule (Thu Jun 13 2013 - 20:09:49 CDT)
  • Re: How to remove center of mass translation of macromolecule (Thu Jun 13 2013 - 18:17:00 CDT)
  • Re: abf_integrate (Tue Jun 11 2013 - 15:03:29 CDT)
  • Re: Any alternative to colvars for minimization? (Thu Jun 06 2013 - 08:25:34 CDT)
  • Re: What does "outputSystemForce" output? (Wed Jun 05 2013 - 17:17:04 CDT)
  • Re: What does "outputSystemForce" output? (Wed Jun 05 2013 - 16:49:20 CDT)
  • Re: First meeting with NAMD (Tue Jun 04 2013 - 10:05:52 CDT)
  • Re: First meeting with NAMD (Tue Jun 04 2013 - 09:38:15 CDT)
  • Re: First meeting with NAMD (Mon Jun 03 2013 - 09:16:05 CDT)
  • Re: ABF (Thu Apr 04 2013 - 16:09:15 CDT)
  • Re: ABF (Thu Apr 04 2013 - 11:24:57 CDT)
  • Re: colvars configuration file example (Wed Apr 03 2013 - 15:09:12 CDT)
  • Re: implicit solvent (Wed Mar 27 2013 - 12:26:15 CDT)
  • Re: free energy methods cheat-sheet/comparison chart (Mon Mar 25 2013 - 17:11:29 CDT)
  • Re: Potential energy as collective variable (Mon Mar 25 2013 - 11:55:41 CDT)
  • Re: NAMD + PLUMED COMPILATION (Thu Feb 28 2013 - 11:26:00 CST)
  • Re: colvar keyword ForceNoPBC (Wed Feb 27 2013 - 23:50:16 CST)
  • Re: About PLUMED with NAMD VMD (Wed Feb 27 2013 - 02:39:27 CST)
  • Re: Orientation colvar + metadynamics questions (Thu Feb 21 2013 - 10:10:24 CST)
  • Re: Metadynamics pmf restart (Mon Jan 28 2013 - 14:43:56 CST)
• Gianluca Interlandi
  • 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)
  • Re: Mysterious slow down in parallel (Sun Oct 27 2013 - 01:12:21 CDT)
  • Re: forward (Thu Sep 05 2013 - 21:43:40 CDT)
  • Re: editing the code of the non bonded pair potentials (Fri Aug 30 2013 - 18:33:06 CDT)
  • Re: editing the code of the non bonded pair potentials (Fri Aug 30 2013 - 18:00:08 CDT)
  • Re: Constraint failure in RATTLE algorithm occurs during NAMD simulation with amber force field (Thu Aug 29 2013 - 22:58:38 CDT)
  • LJcorrection (Wed Aug 28 2013 - 01:33:39 CDT)
  • Re: Can a small langevinDamping coefficient lead to 'ERROR: atoms moving too fast'? (Mon Aug 26 2013 - 11:56:47 CDT)
  • Linuxtag (Thu May 16 2013 - 14:38:40 CDT)
  • Re: A larger protein data bank for performance benchmark (Tue May 14 2013 - 00:02:34 CDT)
  • Accelerated MD parameters (Tue Mar 26 2013 - 19:37:56 CDT)
  • Re: Simulation at high pressure (Fri Mar 22 2013 - 15:10:42 CDT)
• Giovanni Settanni
  • building namd on a Cray XE6 with Interlagos procs (Tue May 20 2014 - 09:03:22 CDT)
• Gisella Alfonsino
  • explicit membrane in implicit solvent (Mon Nov 03 2014 - 05:00:36 CST)
• goldwheel87
  • namd-I: sub-routine code in NAMD (Thu Jan 03 2013 - 16:18:27 CST)
• Gordon Wells
  • Re: can't run multiple jobs with multiple gpus (Thu Apr 04 2013 - 19:10:02 CDT)
  • can't run multiple jobs with multiple gpus (Wed Apr 03 2013 - 15:42:44 CDT)
  • Re: FEP on an amino acid ligand (Wed Jan 23 2013 - 17:18:46 CST)
  • Re: FEP on an amino acid ligand (Wed Jan 23 2013 - 14:44:41 CST)
• Gozde Eskici
  • changing damping coefficient during simulation (Tue Mar 18 2014 - 10:20:25 CDT)
• Grace Brannigan
  • Re: Parameter colvars (Mon Oct 06 2014 - 15:56:18 CDT)
  • Re: Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT (Wed Sep 18 2013 - 11:59:02 CDT)
  • Re: charm-gui membrane builder (Sun Sep 08 2013 - 01:02:31 CDT)
  • Re: Can protein-water electrostatic interaction be turned off keeping protein-protein (vdw+elect) and water-water (vdw+elect) interactions intact? (Wed Mar 20 2013 - 08:45:51 CDT)
• Guanglei Cui
  • Re: namd 2.9 tip4p-2005 (Thu Apr 11 2013 - 10:31:33 CDT)
• Gurpreet Kaur Dhindsa
  • 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)
  • Hi (Thu Dec 12 2013 - 09:19:31 CST)
• 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)
  • Re: understanding the lone pair section of psf files (Fri Aug 23 2013 - 12:11:39 CDT)
  • Re: setting the polarizabilities for the Drude force field (Fri Aug 02 2013 - 13:28:46 CDT)
  • Drude polarizable force field (Sat Jul 06 2013 - 02:06:15 CDT)
• Hadi Dinpajooh
  • Re: Kb, Ktheta values for TIP3P water model (Tue Aug 05 2014 - 11:52:44 CDT)
  • Re: setting the polarizabilities for the Drude force field (Thu Aug 01 2013 - 13:39:42 CDT)
• Hailey Bureau
  • Re: explicit NVT simulation (Tue Sep 10 2013 - 10:35:24 CDT)
  • Re: explicit NVT simulation (Mon Sep 09 2013 - 08:07:19 CDT)
  • explicit NVT simulation (Sun Sep 08 2013 - 17:54:26 CDT)
  • question on explicit solvent reproducibility (Thu Sep 05 2013 - 16:31:52 CDT)
• Haleh a
  • Re: Folic acid parameters (Wed Oct 01 2014 - 01:42:20 CDT)
  • Folic acid parameters (Tue Sep 30 2014 - 08:44:38 CDT)
• Haleh Abdizadeh
  • PSF file for a metalloprotein (Mon Dec 09 2013 - 07:29:55 CST)
  • Re: cell origin problem (Wed Sep 25 2013 - 15:06:19 CDT)
  • Re: cell origin problem (Wed Sep 25 2013 - 14:00:49 CDT)
  • cell origin problem (Tue Sep 24 2013 - 09:53:17 CDT)
  • Re: CUDA error memcpy to exclusions: invalid argument (Tue Aug 27 2013 - 05:13:11 CDT)
  • CUDA error memcpy to exclusions: invalid argument (Tue Aug 27 2013 - 04:06:29 CDT)
• hamid mosaddeghi
  • CNT coarse grain (Fri Jan 11 2013 - 06:01:51 CST)
• Hamze Rahimi
  • unsubscribe (Mon Aug 12 2013 - 23:37:05 CDT)
  • unsubscribe (Sun Jun 23 2013 - 12:27:06 CDT)
• hanif mahboobi
  • Protein Dielectric Constant in GBIS (Mon Mar 04 2013 - 12:31:46 CST)
  • Protein Dielectric Constant in GBIS (Fri Mar 01 2013 - 02:58:01 CST)
  • NAMD on Stampede (Wed Feb 27 2013 - 13:46:29 CST)
• Hannes Loeffler
  • 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)
  • Re: MM-PBSA calculation (Wed Nov 06 2013 - 03:25:23 CST)
  • Re: MMPBSA-like analysis (Wed Oct 30 2013 - 08:24:43 CDT)
  • Re: MMPBSA-like analysis (Wed Oct 30 2013 - 06:02:54 CDT)
  • Re: MMPBSA-like analysis (Tue Oct 29 2013 - 04:32:01 CDT)
  • Re: MMPBSA-like analysis (Wed Oct 23 2013 - 02:39:29 CDT)
  • Re: if{} statements (Tue Mar 05 2013 - 07:59:32 CST)
• hannes.loeffler_at_stfc.ac.uk
  • 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
  • question about NVE ensamble (Thu Jul 18 2013 - 01:56:18 CDT)
  • NAMD configuration file (Wed Jul 03 2013 - 17:12:22 CDT)
• 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)
• Himani Raina
  • solvated system for minimization (Mon Apr 22 2013 - 05:31:18 CDT)
  • minimizer slowly moving atoms with bad contacts downhill (Fri Apr 12 2013 - 02:02:17 CDT)
  • Regarding installing Namd 2.9 on windows xp 32 bit system (Tue Feb 26 2013 - 04:08:25 CST)
• 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)
• houyang chen
  • Questions regarding pressure difference (Wed Oct 02 2013 - 08:29:43 CDT)
  • questions regarding pressure difference (Sun Sep 29 2013 - 22:55:10 CDT)
• Huihui Liu
  • accelerated MD parameters for dual boost mode (Thu Oct 31 2013 - 10:04:23 CDT)
  • Free energy calculation of proton transfer with FEP (Sat Apr 27 2013 - 03:49:10 CDT)
• Hyuntae Na
  • Guideline for selecting water box size. (Sun Feb 16 2014 - 18:49:00 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)
• Ivan Mikhaylov
  • Re: What does "outputSystemForce" output? (Wed Jun 05 2013 - 17:14:50 CDT)
  • What does "outputSystemForce" output? (Wed Jun 05 2013 - 16:28:48 CDT)
• Ivana
  • Re: REMD history file and question (Mon Jul 08 2013 - 11:22:36 CDT)
  • Re: Solvent Box (Wed Jun 26 2013 - 12:18:00 CDT)
  • Re: Error in PSF gen (Wed Jun 19 2013 - 10:14:36 CDT)
  • Re: Error in PSF gen (Mon Jun 17 2013 - 14:39:00 CDT)
  • MDFF force threshold (Thu May 02 2013 - 10:07:17 CDT)
  • Re: pump / force application (Thu Apr 11 2013 - 08:23:44 CDT)
  • MDFF volumetric map (Wed Feb 27 2013 - 11:43:03 CST)
• Izhar Karbat
  • catdcd output and .psf file atom count mismatch (Mon May 06 2013 - 17:18:53 CDT)
  • transmembrane protein simulation - hydrophobic thickness and NAMD membrane plugin (Mon Feb 18 2013 - 11:26:30 CST)
• Jack Bulat
  • Re: Problem regarding the psfgen (Mon Jun 10 2013 - 12:21:32 CDT)
  • Re: Problem regarding the psfgen (Fri Jun 07 2013 - 15:51:10 CDT)
  • Re: Problem regarding the psfgen (Fri Jun 07 2013 - 15:02:58 CDT)
  • Re: DNA terminals and charges (Tue Jan 15 2013 - 22:13:24 CST)
• Jacqueline Schmidt
  • Re: smd force is too high (Fri Mar 15 2013 - 12:35:52 CDT)
  • smd force is too high (Fri Mar 15 2013 - 11:25:58 CDT)
  • Re: AW: smd simulation (Thu Feb 28 2013 - 01:12:36 CST)
  • smd simulation (Wed Feb 27 2013 - 08:27:43 CST)
  • center of mass calculation in the tcl interface (Sun Feb 24 2013 - 13:02:21 CST)
• jafar azamat
  • Unsubscribe (Fri Jun 20 2014 - 03:27:10 CDT)
  • Reduce percent use of cpu (Tue Dec 03 2013 - 02:31:53 CST)
  • Question about how much used from CPU? (Mon Nov 18 2013 - 02:50:14 CST)
• JAGODINSKY, JUSTIN
  • Coarse grain parameter files (Fri Jul 12 2013 - 09:47:50 CDT)
  • (no subject) (Fri Jul 12 2013 - 09:12:51 CDT)
• James Starlight
  • 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)
  • Re: Equilibration of the membrane-protein system done in CHARMM-GUI (Thu Nov 14 2013 - 07:32:44 CST)
  • Re: Steered Molecular Dynamics tutorial (Wed Nov 13 2013 - 12:11:57 CST)
  • Steered Molecular Dynamics tutorial (Tue Nov 12 2013 - 03:40:44 CST)
  • Re: Two GPU-based workstation (Mon Nov 11 2013 - 06:55:01 CST)
  • Re: Two GPU-based workstation (Mon Nov 11 2013 - 02:49:05 CST)
  • Re: Two GPU-based workstation (Mon Nov 11 2013 - 02:42:18 CST)
  • Re: Two GPU-based workstation (Sat Nov 09 2013 - 08:53:20 CST)
  • Re: Equilibration of the membrane-protein system done in CHARMM-GUI (Fri Nov 08 2013 - 06:38:26 CST)
  • Re: Accelerated MD in NAMD (Fri Nov 08 2013 - 06:36:51 CST)
  • Re: Two GPU-based workstation (Fri Nov 08 2013 - 05:50:30 CST)
  • Re: Accelerated MD in NAMD (Fri Nov 08 2013 - 00:53:41 CST)
  • Re: Accelerated MD in NAMD (Thu Nov 07 2013 - 13:18:47 CST)
  • Re: Accelerated MD in NAMD (Thu Nov 07 2013 - 06:48:45 CST)
  • Namd energy plugin (Thu Nov 07 2013 - 01:53:52 CST)
  • Re: Accelerated MD in NAMD (Thu Nov 07 2013 - 01:09:45 CST)
  • Re: Two GPU-based workstation (Wed Nov 06 2013 - 23:32:18 CST)
  • Re: Accelerated MD in NAMD (Wed Nov 06 2013 - 23:28:44 CST)
  • Re: Accelerated MD in NAMD (Wed Nov 06 2013 - 12:50:36 CST)
  • Re: Equilibration of the membrane-protein system done in CHARMM-GUI (Wed Nov 06 2013 - 09:02:45 CST)
  • Re: Accelerated MD in NAMD (Wed Nov 06 2013 - 01:29:53 CST)
  • Equilibration of the membrane-protein system done in CHARMM-GUI (Wed Nov 06 2013 - 00:51:22 CST)
  • Re: Two GPU-based workstation (Mon Nov 04 2013 - 04:43:09 CST)
  • Re: Two GPU-based workstation (Mon Nov 04 2013 - 01:52:01 CST)
  • Accelerated MD in NAMD (Sun Nov 03 2013 - 08:17:51 CST)
  • Re: Two GPU-based workstation (Sun Nov 03 2013 - 08:04:02 CST)
  • Re: Two GPU-based workstation (Sun Nov 03 2013 - 02:38:59 CST)
  • Re: charm-gui membrane builder (Fri Nov 01 2013 - 04:23:07 CDT)
  • Re: Two GPU-based workstation (Fri Nov 01 2013 - 02:40:14 CDT)
  • Re: Two GPU-based workstation (Thu Oct 31 2013 - 12:24:16 CDT)
  • Re: Two GPU-based workstation (Wed Oct 30 2013 - 08:12:58 CDT)
  • Re: Two GPU-based workstation (Tue Oct 29 2013 - 08:20:22 CDT)
  • Two GPU-based workstation (Tue Oct 29 2013 - 00:29:43 CDT)
  • Re: Protein-ligand affinity (Wed Oct 16 2013 - 14:42:42 CDT)
  • Re: Protein-ligand affinity (Tue Oct 15 2013 - 15:05:11 CDT)
  • Re: Protein-ligand affinity (Tue Oct 15 2013 - 13:43:30 CDT)
  • Re: Protein-ligand affinity (Tue Oct 15 2013 - 12:42:09 CDT)
  • Protein-ligand affinity (Mon Oct 14 2013 - 13:20:17 CDT)
  • Re: CHARMGUI and ligands parametrisation (Tue Sep 24 2013 - 15:35:09 CDT)
  • CHARMGUI and ligands parametrisation (Tue Sep 24 2013 - 09:38:30 CDT)
  • Re: charm-gui membrane builder (Thu Sep 19 2013 - 01:04:39 CDT)
  • Re: charm-gui membrane builder (Tue Sep 17 2013 - 15:30:31 CDT)
  • Re: charm-gui membrane builder (Tue Sep 17 2013 - 14:32:17 CDT)
  • Re: charm-gui membrane builder (Tue Sep 17 2013 - 12:12:21 CDT)
  • Re: charm-gui membrane builder (Tue Sep 17 2013 - 00:33:30 CDT)
  • Fwd: charm-gui membrane builder (Mon Sep 16 2013 - 07:07:43 CDT)
  • Re: First meeting with NAMD (Fri Sep 13 2013 - 08:41:12 CDT)
  • Re: charm-gui membrane builder (Fri Sep 13 2013 - 02:06:07 CDT)
  • Re: charm-gui membrane builder (Thu Sep 12 2013 - 06:24:51 CDT)
  • Re: charm-gui membrane builder (Wed Sep 11 2013 - 15:15:23 CDT)
  • Re: charm-gui membrane builder (Wed Sep 11 2013 - 12:20:59 CDT)
  • Re: Equilibration of the membrane bilayers with CUDA-support (Wed Sep 11 2013 - 01:31:05 CDT)
  • Re: charm-gui membrane builder (Tue Sep 10 2013 - 11:29:17 CDT)
  • Re: Equilibration of the membrane bilayers with CUDA-support (Tue Sep 10 2013 - 09:06:11 CDT)
  • Re: charm-gui membrane builder (Sun Sep 08 2013 - 23:52:00 CDT)
  • Equilibration of the membrane bilayers with CUDA-support (Mon Sep 09 2013 - 10:16:40 CDT)
  • Re: charm-gui membrane builder (Sun Sep 08 2013 - 11:44:04 CDT)
  • Re: charm-gui membrane builder (Sat Sep 07 2013 - 23:56:42 CDT)
  • Re: charm-gui membrane builder (Sat Sep 07 2013 - 04:04:10 CDT)
  • Re: charm-gui membrane builder (Fri Sep 06 2013 - 15:03:41 CDT)
  • Re: charm-gui membrane builder (Fri Sep 06 2013 - 11:24:56 CDT)
  • charm-gui membrane builder (Fri Sep 06 2013 - 06:21:15 CDT)
  • Re: Simulation of the membrane protein (Thu Sep 05 2013 - 10:52:29 CDT)
  • Re: Simulation of the membrane protein (Thu Sep 05 2013 - 02:48:10 CDT)
  • Re: Simulation of the membrane protein (Thu Sep 05 2013 - 00:35:26 CDT)
  • Simulation of the membrane protein (Wed Sep 04 2013 - 11:16:35 CDT)
  • Restarting simulation (Tue Jul 02 2013 - 00:45:37 CDT)
  • Re: Protein-ligand simulation (Sat Jun 29 2013 - 00:02:32 CDT)
  • Simulation in NPT ensemble (Fri Jun 28 2013 - 15:28:40 CDT)
  • Re: Protein-ligand simulation (Fri Jun 28 2013 - 14:55:55 CDT)
  • Re: Protein-ligand simulation (Fri Jun 28 2013 - 04:21:45 CDT)
  • Re: Protein-ligand simulation (Thu Jun 27 2013 - 23:35:21 CDT)
  • analysis of simulation output (Thu Jun 27 2013 - 13:25:38 CDT)
  • Re: Protein-ligand simulation (Thu Jun 27 2013 - 13:18:59 CDT)
  • Re: Protein-ligand simulation (Thu Jun 27 2013 - 00:16:25 CDT)
  • Re: Protein-ligand simulation (Wed Jun 26 2013 - 00:56:38 CDT)
  • Re: Protein-ligand simulation (Tue Jun 25 2013 - 13:39:02 CDT)
  • Re: Simulation in Collective sub-space (Tue Jun 25 2013 - 13:21:18 CDT)
  • Simulation in Collective sub-space (Tue Jun 25 2013 - 07:52:41 CDT)
  • Re: Protein-ligand simulation (Tue Jun 25 2013 - 00:58:51 CDT)
  • Re: Protein-ligand simulation (Mon Jun 24 2013 - 13:15:51 CDT)
  • Parameters for prosthetic groups (Mon Jun 24 2013 - 06:56:03 CDT)
  • Protein-ligand simulation (Mon Jun 24 2013 - 06:51:46 CDT)
  • Re: First meeting with NAMD (Fri Jun 07 2013 - 00:13:55 CDT)
  • Re: First meeting with NAMD (Thu Jun 06 2013 - 06:31:42 CDT)
  • Re: First meeting with NAMD (Wed Jun 05 2013 - 05:22:28 CDT)
  • First meeting with NAMD (Tue Jun 04 2013 - 09:46:54 CDT)
  • Re: First meeting with NAMD (Tue Jun 04 2013 - 09:33:19 CDT)
  • Re: First meeting with NAMD (Tue Jun 04 2013 - 08:25:06 CDT)
  • Re: First meeting with NAMD (Tue Jun 04 2013 - 03:13:10 CDT)
  • Re: First meeting with NAMD (Mon Jun 03 2013 - 13:08:01 CDT)
  • First meeting with NAMD (Mon Jun 03 2013 - 09:08:58 CDT)
  • Running namd on linux in cpu+gpu mode (Sat Jan 19 2013 - 01:19:53 CST)
• Jan Fredin
  • apoa1 slow Phase 1 (Thu Aug 15 2013 - 16:25:11 CDT)
• Jana, Suvamay
  • xplor psf used for namd (Mon Nov 25 2013 - 20:07:31 CST)
• Jason Swails
  • 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)
  • Re: MMPBSA-like analysis (Tue Oct 22 2013 - 05:01:32 CDT)
  • Re: About the scope of show_replicas.vmd (Thu Sep 19 2013 - 11:19:24 CDT)
  • Re: CHAMBER generated .prmtop file is not compatable with namd2 (Mon Sep 16 2013 - 04:55:09 CDT)
  • Re: Implicit water with explicit ions (Thu Jul 18 2013 - 21:09:27 CDT)
  • Re: Implicit water with explicit ions (Thu Jul 18 2013 - 18:30:49 CDT)
  • pairInteraction and PME (Wed Apr 03 2013 - 15:58:21 CDT)
• JAVAD NOROOZI
  • 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: 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)
  • Re: minimization with symmetry restrain (Fri Dec 13 2013 - 16:48:32 CST)
  • FEP failure - FFTW problem? (Fri Sep 20 2013 - 14:16:37 CDT)
  • Re: All CUDA devices are in prohibited mode, of compute capability 1.0, or otherwise unusable. (Tue Aug 20 2013 - 13:14:27 CDT)
  • Re: Protein-ligand simulation (Sat Jun 29 2013 - 07:53:31 CDT)
  • Re: Protein-ligand simulation (Fri Jun 28 2013 - 17:43:24 CDT)
  • Re: Protein-ligand simulation (Thu Jun 27 2013 - 18:40:15 CDT)
  • Re: Protein-ligand simulation (Wed Jun 26 2013 - 15:21:09 CDT)
  • Re: Protein-ligand simulation (Mon Jun 24 2013 - 18:43:42 CDT)
  • Re: Overestimated PMF (Mon Jun 17 2013 - 11:37:10 CDT)
  • Re: dihedral parameter conversion (Fri May 03 2013 - 00:21:10 CDT)
  • RE: dihedral parameter conversion (Thu May 02 2013 - 09:41:30 CDT)
  • dihedral parameter conversion (Thu May 02 2013 - 08:17:00 CDT)
  • Re: total charge of the system - rounding error ? (Mon Apr 15 2013 - 12:20:09 CDT)
  • Re: NamdMemoryReduction - genCompressedPsf (Wed Apr 03 2013 - 22:50:22 CDT)
  • Re: free energy methods cheat-sheet/comparison chart (Mon Mar 25 2013 - 14:50:04 CDT)
  • unsubscribe (Tue Mar 05 2013 - 09:44:57 CST)
  • Re: ABF thermostats and energy introduced into the system (Wed Feb 27 2013 - 15:29:49 CST)
  • RE: DCD file doubles a monomer (Tue Feb 26 2013 - 20:58:04 CST)
  • Re: DCD file doubles a monomer (Tue Feb 26 2013 - 19:50:08 CST)
  • Re: ABF thermostats and energy introduced into the system (Mon Feb 25 2013 - 16:32:13 CST)
  • Re: FEP on an amino acid ligand (Wed Jan 23 2013 - 18:10:00 CST)
  • Re: FEP on an amino acid ligand (Wed Jan 23 2013 - 16:45:19 CST)
  • Re: FEP on an amino acid ligand (Wed Jan 23 2013 - 11:29:57 CST)
  • Re: FEP on an amino acid ligand (Wed Jan 23 2013 - 11:16:32 CST)
  • Re: FEP on an amino acid ligand (Wed Jan 23 2013 - 08:24:25 CST)
• 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)
• Jeff Comer
  • 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)
  • Re: Accelerated MD in NAMD (Thu Nov 07 2013 - 10:46:59 CST)
  • Re: Accelerated MD in NAMD (Thu Nov 07 2013 - 08:19:53 CST)
  • Accelerated MD in NAMD (Wed Nov 06 2013 - 19:24:58 CST)
  • Re: Accelerated MD in NAMD (Wed Nov 06 2013 - 15:03:00 CST)
  • Re: Accelerated MD in NAMD (Wed Nov 06 2013 - 12:00:29 CST)
  • NAMD on Stempede (and other MIC Coprocessor systems) (Fri Jan 11 2013 - 13:39:37 CST)
• Jeffery Klauda
  • NAMD/MIC & CUDA on Stampede (Wed Jul 16 2014 - 13:28:27 CDT)
• Jeffrey Potoff
  • 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)
  • Re: About Membrane anlysis (Wed Dec 18 2013 - 09:50:03 CST)
  • Re: sn-1 tail order parameter (Thu Jun 27 2013 - 17:01:06 CDT)
  • Re: Tail order parameter (Thu Jun 27 2013 - 11:06:22 CDT)
  • Re: Solvent Box (Wed Jun 26 2013 - 13:10:26 CDT)
  • Re: Insertion of GPCR in the POPC Bilayer (Thu Jun 20 2013 - 20:12:27 CDT)
  • Re: Lipid bilayer tears apart during simulation (Fri Jun 14 2013 - 15:46:10 CDT)
  • Re: free energy methods cheat-sheet/comparison chart (Mon Mar 25 2013 - 15:09:53 CDT)
  • Re: how to convert CHARMM TIP3P to traditional TIP3P (Wed Mar 06 2013 - 09:07:55 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)
• Jesper Madsen
  • chloromethyl ketone patch? (Tue Feb 11 2014 - 16:49:21 CST)
• Jhonatam Cordeiro Rodrigues
  • 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)
• 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)
• Jiawei Xu
  • Re: vmd-l: Suggestions on parameterizing a ligand to simulate in NAMD (Mon May 20 2013 - 14:11:50 CDT)
• Jim Phillips
  • 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)
  • Re: DEVELOPER QUESTION -> NAMD Internal energy unit and TCL interface (Thu Oct 24 2013 - 10:01:30 CDT)
• jinxj
  • pbc problem (Tue Sep 03 2013 - 04:45:06 CDT)
  • writedcd problem (Mon Sep 02 2013 - 09:32:00 CDT)
  • pbc problem (Mon Sep 02 2013 - 04:08:28 CDT)
  • pbc error (Sun Sep 01 2013 - 21:38:48 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)
• Joe Janicki
  • Question about converting velocities DCD to ascii plain text (Sat Aug 03 2013 - 13:24:11 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)
• johan strumpfer
  • Re: Question about NAMD (Mon Jan 28 2013 - 02:02:13 CST)
• John Stone
  • 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)
  • Re: vmd-l: Error with show_replicas.vmd (Tue Sep 03 2013 - 10:57:26 CDT)
  • Re: vmd-l: About PLUMED with NAMD VMD (Wed Feb 27 2013 - 10:10:48 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)
  • Re: PCIexpress 3.0 for MD with NAMD on GPUs (Wed Nov 20 2013 - 10:32:41 CST)
  • ABF calculations in NAMD (Mon Nov 18 2013 - 07:36:58 CST)
  • Re: PCIexpress 3.0 for MD with NAMD on GPUs (Sun Nov 17 2013 - 14:23:22 CST)
  • Re: Steered MD along detected routes (Sat Nov 16 2013 - 10:48:42 CST)
  • Re: Steered MD along detected routes (Sat Nov 16 2013 - 10:46:01 CST)
  • Re: Steered MD along detected routes (Sat Nov 16 2013 - 10:27:38 CST)
  • Steered MD along detected routes (Sat Nov 16 2013 - 05:10:40 CST)
• Jon Kusner
  • Solvent Box (Wed Jun 26 2013 - 12:15:31 CDT)
• 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)
• Jorgen Simonsen
  • not reading improper angle from amber1.5 ff12SB (Sun Jan 27 2013 - 16:06:20 CST)
  • suppressing LBD output (Sat Jan 26 2013 - 21:57:18 CST)
• Jose Borreguero
  • 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)
  • Re: Can a small langevinDamping coefficient lead to 'ERROR: atoms moving too fast'? (Tue Aug 27 2013 - 16:25:38 CDT)
  • Can a small langevinDamping coefficient lead to 'ERROR: atoms moving too fast'? (Mon Aug 26 2013 - 08:24:32 CDT)
  • obtaining cellBasisVectors from SCALE entries in the PDB file (Fri Aug 23 2013 - 10:31:28 CDT)
  • Re: ERROR: Could not translate the value....into a Vector for the option 'cellOrigin' (Mon Jul 15 2013 - 16:35:08 CDT)
  • ERROR: Could not translate the value....into a Vector for the option 'cellOrigin' (Mon Jul 15 2013 - 16:19:31 CDT)
  • how to do a vacuum minimization without electrostatics and periodic boundary conditions? (Wed Jun 05 2013 - 10:20:27 CDT)
  • SOLVED: Fatal Error by charmc.../usr/bin/ld: cannot find -lsrfftw. Please help! (Wed Feb 13 2013 - 12:34:49 CST)
  • Fatal Error by charmc.../usr/bin/ld: cannot find -lsrfftw. Please help! (Tue Feb 12 2013 - 17:26:12 CST)
• 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)
  • Re: BLCR and NAMD (Thu Nov 07 2013 - 22:56:44 CST)
  • Re: Mysterious slow down in parallel (Sun Oct 27 2013 - 00:20:02 CDT)
  • Re: Fwd: Re: [Checkpoint] BLCR and NAMD (Fri Oct 25 2013 - 12:33:29 CDT)
  • Fwd: Re: [Checkpoint] BLCR and NAMD (Wed Oct 23 2013 - 13:46:00 CDT)
• Josh Vermaas
  • 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)
  • Re: editing the code of the non bonded pair potentials (Fri Aug 30 2013 - 14:06:12 CDT)
• 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 José Galano Frutos
  • How I can to change the force field function in NAMD for protein phi-value analysis (Mon Oct 07 2013 - 04:55:44 CDT)
• Juan R. Perilla
  • Re: vmd-l: Accelerated MD (aMD) (Sun Jul 27 2014 - 20:23:00 CDT)
• Juba, Derek
  • RE: How to replace NAMD electrostatics (Thu Nov 21 2013 - 11:41:06 CST)
  • How to replace NAMD electrostatics (Tue Nov 19 2013 - 16:36:20 CST)
• Justin Sanders
  • CUDA Fatal Error While Trying to Run Under Windows 8.1 (Thu Nov 06 2014 - 12:01:58 CST)
• Jérôme Hénin
  • 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)
  • Re: FEP calculations: optimizing the dlambda, number of steps (Thu Dec 12 2013 - 03:05:30 CST)
  • Re: Colvars periodic boundary treatment question (Tue Dec 03 2013 - 12:39:25 CST)
  • Re: pH calculation (Mon Dec 02 2013 - 03:05:46 CST)
  • Re: Colvars periodic boundary treatment question (Sat Nov 30 2013 - 19:04:48 CST)
  • Re: FEP calculations: optimizing the dlambda, number of steps (Fri Nov 22 2013 - 10:49:17 CST)
  • Re: FEP calculations: optimizing the dlambda, number of steps (Fri Nov 22 2013 - 04:21:54 CST)
  • Re: FEP calculations: optimizing the dlambda, number of steps (Tue Nov 19 2013 - 04:25:39 CST)
  • Re: FEP calculations: optimizing the dlambda, number of steps (Mon Nov 18 2013 - 17:32:09 CST)
  • Re: FEP Error - TCL (Tue Nov 12 2013 - 16:17:13 CST)
  • Re: question about setting up FEP calculations (Sat Nov 02 2013 - 04:24:49 CDT)
  • Re: FEP Error - TCL (Wed Oct 30 2013 - 11:07:33 CDT)
  • Re: question about setting up FEP calculations (Fri Oct 18 2013 - 04:33:54 CDT)
  • Re: question about setting up FEP calculations (Tue Oct 15 2013 - 12:00:58 CDT)
  • Re: question about setting up FEP calculations (Tue Oct 15 2013 - 11:29:51 CDT)
  • Re: question about setting up FEP calculations (Tue Oct 15 2013 - 10:44:51 CDT)
  • Re: question about setting up FEP calculations (Mon Oct 14 2013 - 14:32:34 CDT)
  • Re: Accumulating free energy change for applying colvar restraint (Mon Oct 07 2013 - 09:06:15 CDT)
  • Re: Psfgen - bonding terms involving disulfide bridges (Fri Oct 04 2013 - 06:55:47 CDT)
  • Re: Replica exchange and colvars - Missing Stage from restart (Sun Sep 15 2013 - 15:41:54 CDT)
  • Re: explicit NVT simulation (Mon Sep 09 2013 - 08:31:03 CDT)
  • Re: Atom indices in collective variable definition (Fri Sep 06 2013 - 09:56:06 CDT)
  • Re: Linear force ramp increments in ABF (Thu Aug 29 2013 - 14:15:43 CDT)
  • Re: Linear force ramp increments in ABF (Thu Aug 29 2013 - 12:06:49 CDT)
  • Re: colvars and parallel-tempering with namd2.10 (Tue Aug 13 2013 - 09:51:30 CDT)
  • Re: Special constraint on MD simulation (Mon Aug 05 2013 - 12:46:05 CDT)
  • Re: Center of mass motion included in Temperature? (Fri Aug 02 2013 - 15:24:56 CDT)
  • Re: Colvars RMSD syntax with a moving reference frame (Fri Aug 02 2013 - 10:29:12 CDT)
  • Re: Retaining conformation (Thu Jul 18 2013 - 06:01:09 CDT)
  • Re: Preventing rotation of a protein (Thu Jul 18 2013 - 06:00:19 CDT)
  • Re: Free Energy using atomic coordinates as CVs (Fri Jul 12 2013 - 05:12:23 CDT)
  • Re: use of colvars to restrain the absolute positions of all atoms in a large system (Wed Jul 10 2013 - 05:07:16 CDT)
  • Re: Free Energy Calculation Question (Thu Jun 20 2013 - 16:18:57 CDT)
  • Re: How to remove center of mass translation of macromolecule (Mon Jun 17 2013 - 08:51:20 CDT)
  • Re: ABF simulations with barriers (adsorption) (Thu Jun 13 2013 - 04:45:19 CDT)
  • Re: multiple vectors in SMD (Thu Jun 13 2013 - 02:56:44 CDT)
  • Re: AW: how to apply force SMD method on an anisotropic geometry (Thu Jun 13 2013 - 02:54:42 CDT)
  • Re: How to remove center of mass translation of macromolecule (Wed Jun 12 2013 - 04:00:48 CDT)
  • Re: Two dimensional ABF (Tue Jun 11 2013 - 12:35:52 CDT)
  • Re: ABF simulations with barriers (adsorption) (Tue Jun 11 2013 - 07:09:06 CDT)
  • New: Colvars project page (Fri Jun 07 2013 - 11:43:42 CDT)
  • Re: ABF with the RMSD colvar (Fri Jun 07 2013 - 09:07:57 CDT)
  • Re: AW: Any alternative to colvars for minimization? (Thu Jun 06 2013 - 05:07:25 CDT)
  • Re: ABF zCoord analog in colvars ? (Wed Jun 05 2013 - 08:44:16 CDT)
  • Re: A fancy problem in calculating the protonated glutamic acid modelled by adding the patch of GLUP (Fri May 31 2013 - 10:30:01 CDT)
  • Re: Free energy calculations (Tue May 28 2013 - 05:36:55 CDT)
  • Re: Potential of mean force calculation using colvars in NADM 2.9 package (Fri May 17 2013 - 09:56:36 CDT)
  • Re: Potential of mean force calculation using colvars in NADM 2.9 package (Fri May 17 2013 - 09:21:24 CDT)
  • Re: Potential of mean force calculation using colvars in NADM 2.9 package (Thu May 16 2013 - 08:19:57 CDT)
  • Re: AW: Can I define a simulation box but turn off the PBC at the same time? (Mon May 13 2013 - 03:17:29 CDT)
  • Re: Sevoflurane parameters (psf file) (Mon May 06 2013 - 03:42:42 CDT)
  • Re: WHAM analysis for Umbrella sampling (Tue Apr 30 2013 - 04:07:52 CDT)
  • Re: Are random forces applied at every step (when using the langevin thermostat) ? (Mon Apr 29 2013 - 03:58:22 CDT)
  • Re: pump / force application (Thu Apr 11 2013 - 08:38:20 CDT)
  • Re: pump / force application (Thu Apr 11 2013 - 08:15:14 CDT)
  • Re: VDW component: NAMD vs. CHARMM (Thu Apr 04 2013 - 09:56:46 CDT)
  • Re: (Tue Mar 26 2013 - 12:35:01 CDT)
  • Re: (Mon Mar 25 2013 - 16:12:10 CDT)
  • Re: smd force is too high (Mon Mar 18 2013 - 12:07:40 CDT)
  • Re: distanceZ - harmonic restraints (Mon Mar 18 2013 - 12:04:03 CDT)
  • Re: dynamic_cast cannot be done without runtime type information (Mon Mar 11 2013 - 10:31:27 CDT)
  • dynamic_cast cannot be done without runtime type information (Mon Mar 11 2013 - 10:16:24 CDT)
  • Re: tcl-related segfault in NAMD (Wed Mar 06 2013 - 09:33:07 CST)
  • Re: unsubscriber e-mail office pool anybody? (Tue Mar 05 2013 - 07:02:47 CST)
  • Re: ABF thermostats and energy introduced into the system (Mon Feb 25 2013 - 08:01:52 CST)
  • Re: Orientation colvar + metadynamics questions (Thu Feb 21 2013 - 09:21:43 CST)
  • Re: Constant volume energy minimization (Wed Feb 20 2013 - 04:29:50 CST)
  • Re: Apply torque with NAMD (Tue Feb 12 2013 - 07:08:35 CST)
  • Re: FEP on an amino acid ligand (Wed Jan 23 2013 - 08:13:30 CST)
• K Miura
  • Running Charmrun/NAMD with more than 10 processes fails (Tue Dec 16 2014 - 02:53:36 CST)
• k.manzoorolajdad
  • can i use swap partition to increase ram in namd? (Mon Nov 25 2013 - 09:18:15 CST)
  • Re: NAMD with pbs script (Tue Sep 03 2013 - 02:22:54 CDT)
  • NAMD with pbs script (Sun Aug 25 2013 - 09:36:58 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)
  • FEP simulation on membrane protein (Sun Jul 21 2013 - 22:37:44 CDT)
• karthik kumar
  • Free energy calculations (Mon May 27 2013 - 07:47:33 CDT)
  • ABF (Wed May 08 2013 - 23:34:17 CDT)
  • Re: solvated system for minimization (Mon Apr 22 2013 - 05:56:15 CDT)
  • ABF (Mon Apr 15 2013 - 07:38:26 CDT)
  • ABF (Sat Apr 13 2013 - 06:45:12 CDT)
  • ABF (Thu Apr 04 2013 - 10:53:58 CDT)
• karthik s
  • unsubscribe (Tue Mar 05 2013 - 06:54:55 CST)
  • unsubscribe (Fri Mar 01 2013 - 02:50:59 CST)
• 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)
  • Re: colavrs ABF restart not matching (Tue Dec 10 2013 - 12:02:53 CST)
  • colavrs ABF restart not matching (Tue Dec 10 2013 - 11:30:50 CST)
  • Asking for Free energy calculation advice (Thu Dec 05 2013 - 14:18:20 CST)
  • Re: Colvars periodic boundary treatment question (Tue Dec 03 2013 - 15:57:04 CST)
  • Re: Colvars periodic boundary treatment question (Sat Nov 30 2013 - 22:25:46 CST)
  • Colvars periodic boundary treatment question (Sat Nov 30 2013 - 13:12:42 CST)
  • Free Energy Calculation Question (Thu Jun 20 2013 - 15:28:28 CDT)
  • abf_integrate (Tue Jun 11 2013 - 14:54:34 CDT)
• 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)
  • Help regarding PMF with SMD (Thu Aug 01 2013 - 10:06:03 CDT)
• kaushik chakraborty
  • (no subject) (Sun Aug 25 2013 - 11:41:34 CDT)
• Keller Wenger
  • Restart simulation of an equilibrated bilayer with sugar molecules inserted (Sun Mar 17 2013 - 09:51:27 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)
  • Re: Equilibration of the membrane-protein system done in CHARMM-GUI (Wed Nov 06 2013 - 14:03:05 CST)
  • Re: Force Field Parameters for PEG (Wed Nov 06 2013 - 13:27:41 CST)
  • Re: Charge distribution (Fri Nov 01 2013 - 13:52:54 CDT)
  • Re: I have a question about pair interaction energy calculations. (Thu Oct 31 2013 - 13:21:31 CDT)
  • Re: HEME B PARAMETERS (Thu Oct 31 2013 - 13:06:26 CDT)
  • Re: MMPBSA-like analysis (Fri Oct 25 2013 - 15:05:05 CDT)
  • Re: Bonds in XPLOR format (Wed Oct 23 2013 - 13:49:24 CDT)
  • Re: MMPBSA-like analysis (Tue Oct 22 2013 - 11:56:59 CDT)
  • Re: Re: vmd-l: fftk-charges (Mon Oct 21 2013 - 12:53:59 CDT)
  • Re: Simulation results from NVT has a cavity (Mon Oct 21 2013 - 12:25:58 CDT)
  • Re: Error (Mon Oct 21 2013 - 12:17:41 CDT)
  • Re: CUDA vd non-CUDA for minimization (Mon Oct 21 2013 - 11:34:26 CDT)
  • Re: CUDA vd non-CUDA for minimization (Fri Oct 18 2013 - 13:55:00 CDT)
  • Re: [SUSPICIOUS MESSAGE] Reg System Prepartion namd (Thu Oct 17 2013 - 16:15:10 CDT)
  • Re: Peptide insertion into a membrane (Thu Oct 17 2013 - 15:08:10 CDT)
  • Re: Error (Wed Oct 16 2013 - 21:21:20 CDT)
  • Re: get topology and parameter file for the ligand. (Wed Oct 16 2013 - 17:21:38 CDT)
  • Re: Protein-ligand affinity (Tue Oct 15 2013 - 15:51:03 CDT)
  • Re: Protein-ligand affinity (Tue Oct 15 2013 - 15:50:25 CDT)
  • Re: Protein-ligand affinity (Tue Oct 15 2013 - 14:40:50 CDT)
  • Re: About Constraint Failure (Tue Oct 15 2013 - 12:33:23 CDT)
  • Re: About Usage of Topolgy and Parameter (Mon Oct 14 2013 - 11:09:59 CDT)
  • Re: About Usage of Topolgy and Parameter (Mon Oct 14 2013 - 00:26:01 CDT)
  • Re: Simulation of a protein and calcium ions (Tue Oct 08 2013 - 11:37:19 CDT)
  • Re: problem with Dihedral (Sun Oct 06 2013 - 21:42:57 CDT)
  • Re: Biotin force field (Thu Oct 03 2013 - 13:28:51 CDT)
  • Re: reg Parameters (Sun Sep 29 2013 - 14:11:14 CDT)
  • Re: Reg VDw Parameters (Fri Sep 27 2013 - 13:36:47 CDT)
  • Re: Gold nanoparticle (Fri Sep 27 2013 - 13:30:35 CDT)
  • Re: NAMD electrostatic interaction Failure. (Thu Sep 26 2013 - 16:59:20 CDT)
  • Re: NAMD electrostatic interaction Failure. (Wed Sep 25 2013 - 19:32:11 CDT)
  • Re: Organic molecule and membrane. NAMD gives fatal error: (Wed Sep 25 2013 - 12:33:54 CDT)
  • Re: About Muticore Linux Ibnstalltion if NAmd (Tue Sep 24 2013 - 11:32:07 CDT)
  • Re: About the scope of show_replicas.vmd (Tue Sep 24 2013 - 11:19:21 CDT)
  • Re: CHARMGUI and ligands parametrisation (Tue Sep 24 2013 - 10:54:37 CDT)
  • Re: About the scope of show_replicas.vmd (Fri Sep 20 2013 - 12:22:39 CDT)
  • Re: Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT (Wed Sep 18 2013 - 16:52:41 CDT)
  • Re: Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT (Wed Sep 18 2013 - 13:50:04 CDT)
  • Re: namd scale-up (Tue Sep 17 2013 - 18:50:07 CDT)
  • Re: AW: NAMD PERFORMANCE ON NVIDIA K20 GPU (Tue Sep 17 2013 - 18:42:55 CDT)
  • Re: Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT (Tue Sep 17 2013 - 18:20:38 CDT)
  • Re: charm-gui membrane builder (Tue Sep 17 2013 - 14:26:09 CDT)
  • Re: First meeting with NAMD (Fri Sep 13 2013 - 12:19:52 CDT)
  • Re: explicit NVT simulation (Mon Sep 09 2013 - 13:46:20 CDT)
  • Re: explicit NVT simulation (Mon Sep 09 2013 - 12:24:29 CDT)
  • Re: editing the code of the non bonded pair potentials (Fri Aug 30 2013 - 13:47:15 CDT)
  • Re: problem in determining atom types and charges for ligand atoms to type in the topology file (Thu Aug 29 2013 - 16:05:27 CDT)
  • Re: problem in determining atom types and charges for ligand atoms to type in the topology file (Thu Aug 29 2013 - 09:00:58 CDT)
  • Re: making patch (Tue Aug 27 2013 - 19:07:40 CDT)
  • Re: problem in finding atom types for ligand (Tue Aug 27 2013 - 11:02:10 CDT)
  • Re: AW: AW: hi every body, (Thu Aug 22 2013 - 22:30:11 CDT)
  • Re: All CUDA devices are in prohibited mode, of compute capability 1.0, or otherwise unusable. (Thu Aug 15 2013 - 22:25:07 CDT)
  • Re: AW: NBFIX 1-4 scaling term ignored for CHARMM format parameters (Thu Aug 08 2013 - 11:16:59 CDT)
  • Re: Center of mass motion included in Temperature? (Fri Aug 02 2013 - 11:15:09 CDT)
  • Re: setting the polarizabilities for the Drude force field (Fri Aug 02 2013 - 11:01:26 CDT)
  • Re: Water density in the solvate plugin (Mon Jul 29 2013 - 10:34:11 CDT)
  • Re: Re: Using negatively charged phospholipids and no neutralization, membrane expands in the xy direction ....... (Thu Jul 25 2013 - 11:12:23 CDT)
  • Re: Using negatively charged phopspholipids and no neutralization, membrane expands in the xy direction ....... (Wed Jul 24 2013 - 11:07:42 CDT)
  • Re: Problem regarding the big DCD file (Thu Jul 18 2013 - 12:36:34 CDT)
  • Re: Preventing rotation of a protein (Thu Jul 18 2013 - 11:54:15 CDT)
  • Re: Preventing rotation of a protein (Thu Jul 18 2013 - 11:25:43 CDT)
  • Re: NAMD 2.9 ibverbs: Charmrun crashing on checkpoint-restart (Tue Jul 16 2013 - 11:29:09 CDT)
  • Re: Problem with the cross term of C NH1 CT1 C NH1 CT1 C NH1 (Fri Jul 05 2013 - 16:44:06 CDT)
  • Re: Problem with the cross term of C NH1 CT1 C NH1 CT1 C NH1 (Fri Jul 05 2013 - 15:47:58 CDT)
  • Re: Problem with the cross term of C NH1 CT1 C NH1 CT1 C NH1 (Fri Jul 05 2013 - 12:21:20 CDT)
  • Re: Problem with the cross term of C NH1 CT1 C NH1 CT1 C NH1 (Thu Jul 04 2013 - 19:49:35 CDT)
  • Re: Topology and parameters for nitrate and nitrite ion (Tue Jul 02 2013 - 09:17:32 CDT)
  • Re: FATAL ERROR Unknown parameter in charmm parameter file (Mon Jul 01 2013 - 15:07:30 CDT)
  • Re: Topology and parameters for nitrate and nitrite ion (Mon Jul 01 2013 - 14:37:51 CDT)
  • Re: Topology and parameters for nitrate and nitrite ion (Mon Jul 01 2013 - 02:52:28 CDT)
  • Re: Topology and parameters for nitrate and nitrite ion (Sun Jun 30 2013 - 23:47:57 CDT)
  • Re: Topology and parameters for nitrate and nitrite ion (Sun Jun 30 2013 - 19:17:40 CDT)
  • Re: Protein-ligand simulation (Sat Jun 29 2013 - 12:36:32 CDT)
  • Re: Protein-ligand simulation (Fri Jun 28 2013 - 16:12:50 CDT)
  • Re: Protein-ligand simulation (Fri Jun 28 2013 - 12:22:12 CDT)
  • Re: Protein-ligand simulation (Thu Jun 27 2013 - 10:50:25 CDT)
  • Re: Protein-ligand simulation (Wed Jun 26 2013 - 14:07:09 CDT)
  • Re: Protein-ligand simulation (Tue Jun 25 2013 - 14:17:17 CDT)
  • Re: Protein-ligand simulation (Tue Jun 25 2013 - 13:09:27 CDT)
  • Re: Protein-ligand simulation (Mon Jun 24 2013 - 21:51:34 CDT)
• Kevin C Chan
  • 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 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
  • 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)
• Kong, Ren
  • FW: water layer in membrane protein modeling (Thu Jul 18 2013 - 09:24:06 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 (Wed Jul 30 2014 - 09:56:28 CDT)
• Kuldeep Roy
  • Re: Fwd: Majordomo results (Wed Jan 01 2014 - 16:33:22 CST)
• Lane, William
  • RE: RE: PCIexpress 3.0 for MD with NAMD on GPUs (Fri Nov 15 2013 - 02:22:53 CST)
  • NAMD build problems on PowerPC under Red Hat Enterprise (Wed Oct 16 2013 - 11:37:12 CDT)
• Laura
  • unsubscribe (Sun Jun 15 2014 - 12:29:39 CDT)
• lcbllcc_at_gmail.com
  • Re: Gold nanoparticle (Thu Sep 26 2013 - 04:07:26 CDT)
• Leandro Martínez
  • Re: direction of pull in namd (Tue Jan 29 2013 - 10:46:15 CST)
  • Re: direction of pull in namd (Tue Jan 29 2013 - 08:09:01 CST)
• Leili Zhang
  • colvars fatal error (Tue Nov 04 2014 - 22:44:05 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)
• Lewis Martin
  • Sudden jumps during FEP (Thu Feb 28 2013 - 23:16:21 CST)
• Lili Zhang
  • Patch information for 1TUB.pdb in order to use "psfgen" (Tue Dec 10 2013 - 09:21:39 CST)
  • Combining several proteins of the same type together (Mon Oct 14 2013 - 13:54:56 CDT)
  • .psf file in VMD (Thu Oct 03 2013 - 12:10:56 CDT)
  • Problem in SMD "Constant Velocity Pulling" on Ubiquitin example (Thu Oct 03 2013 - 08:53:48 CDT)
  • Problem in running "Constant Velocity Pulling" example (Wed Oct 02 2013 - 12:25:56 CDT)
• linux freaker
  • Re: AW: A larger protein data bank for performance benchmark (Tue May 14 2013 - 01:30:42 CDT)
  • Re: AW: A larger protein data bank for performance benchmark (Tue May 14 2013 - 01:28:23 CDT)
  • Re: AW: A larger protein data bank for performance benchmark (Tue May 14 2013 - 00:58:52 CDT)
  • Re: A larger protein data bank for performance benchmark (Mon May 13 2013 - 21:02:59 CDT)
  • Re: A larger protein data bank for performance benchmark (Mon May 13 2013 - 19:51:51 CDT)
  • A larger protein data bank for performance benchmark (Mon May 13 2013 - 11:49:10 CDT)
  • NAMD post processing analysis.... (Tue Mar 26 2013 - 21:09:31 CDT)
  • Re: (Tue Mar 26 2013 - 12:57:20 CDT)
  • Query regarding NAMD (Sun Mar 24 2013 - 05:13:43 CDT)
• Liqi Feng
  • fail to guess missing coordinates (Tue May 07 2013 - 13:30:21 CDT)
• Liqun Zhang
  • how to fix the problem (Fri Nov 14 2014 - 17:19:37 CST)
  • what to do with this error (Tue Dec 03 2013 - 14:21:34 CST)
  • about interaction between protein and its image in namd simulation (Tue Jul 09 2013 - 12:16:37 CDT)
• 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 Bellucci
  • Re: Gold nanoparticle (Fri Sep 27 2013 - 03:10:09 CDT)
• luca belmonte
  • angles between residues (Tue Dec 30 2014 - 07:38:14 CST)
• Lucas
  • Re: Peptide insertion into a membrane (Thu Oct 17 2013 - 17:33:38 CDT)
  • Re: All CUDA devices are in prohibited mode, of compute capability 1.0, or otherwise unusable. (Thu Aug 15 2013 - 17:26:07 CDT)
  • Re: All CUDA devices are in prohibited mode, of compute capability 1.0, or otherwise unusable. (Thu Aug 15 2013 - 01:53:22 CDT)
  • Re: All CUDA devices are in prohibited mode, of compute capability 1.0, or otherwise unusable. (Wed Aug 14 2013 - 17:09:56 CDT)
  • All CUDA devices are in prohibited mode, of compute capability 1.0, or otherwise unusable. (Tue Aug 13 2013 - 13:06:06 CDT)
  • Exploding vdW energies in automatically generated POPC membranes (Mon May 06 2013 - 15:33:47 CDT)
• Lurong Pan
  • Qh (Thu Sep 11 2014 - 08:22:22 CDT)
  • question about force constant (Fri Jan 03 2014 - 09:02:13 CST)
• Magnus Andersson
  • PMF calculation crashes with constraint failure (Sat Jan 25 2014 - 11:02:11 CST)
  • restrain ligand to z-interval (Mon Apr 15 2013 - 06:29:07 CDT)
  • restrain ligand in z-interval (Mon Apr 15 2013 - 06:37:26 CDT)
• Mahdi Tavakol
  • unsubscribe (Sun Feb 03 2013 - 02:52:04 CST)
• Mamon Hatmal
  • Re: ÅÙÇÏÉ ÊèÌêç: (Tue Dec 03 2013 - 05:14:42 CST)
  • Re: problem in determining atom types and charges for ligand atoms to type in the topology file (Sun Sep 01 2013 - 16:16:38 CDT)
  • Re: problem in determining atom types and charges for ligand atoms to type in the topology file (Thu Aug 29 2013 - 11:28:27 CDT)
  • problem in determining atom types and charges for ligand atoms to type in the topology file (Thu Aug 29 2013 - 06:03:17 CDT)
  • problem in finding atom types for ligand (Tue Aug 27 2013 - 06:54:38 CDT)
• manish kesherwani
  • Re: (Wed Apr 16 2014 - 13:21:34 CDT)
  • (no subject) (Tue Apr 15 2014 - 00:02:12 CDT)
  • Fwd: (Sun Nov 24 2013 - 06:29:35 CST)
• 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)
  • Simulation at different time-steps (Tue Jul 16 2013 - 22:02:58 CDT)
• Maria Bykhovskaia
  • wrapping in two dimensions (Thu Oct 16 2014 - 15:33:34 CDT)
  • wrapping a protein (Wed Aug 20 2014 - 17:40:30 CDT)
  • How to recenter a waterbox with ions around my protein? (Thu Mar 28 2013 - 17:44:06 CDT)
• Maria Kopp
  • I would like to unsubscribe (Wed Sep 10 2014 - 09:04:54 CDT)
  • unsubscribe from mailing list (Mon Jun 17 2013 - 10:24:13 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)
  • Defining colvars groups of atoms for ABF (Wed Aug 21 2013 - 04:13:57 CDT)
• Maria Saeed
  • topology file for ligand (Wed Jan 16 2013 - 01:47:34 CST)
  • How we can merge protein and ligand complex? (Tue Jan 15 2013 - 01:06:20 CST)
  • (no subject) (Tue Jan 15 2013 - 01:03:27 CST)
• Mariana Graterol
  • Subject: Simulated Annealing/ Cooling (Fri Mar 01 2013 - 11:55:21 CST)
• MARK
  • Molecular Shape Searching on GPUs (Mon May 20 2013 - 13:13:55 CDT)
• Mark Cheeseman
  • Unsubscribe (Fri Mar 29 2013 - 23:05:32 CDT)
  • Final link of namd2 executable fails under AIX with xlC compiler (Mon Mar 25 2013 - 17:07:05 CDT)
• MARK PLUMMER
  • 2014 Biophysics Workshop In Aspen Colorado (Tue Jun 11 2013 - 20:39:57 CDT)
  • 2014 Aspen Center for Physics Workshop (Fri May 24 2013 - 14:50:54 CDT)
• Markus Dahlgren
  • Re: analyzing NAMD trajectory with NAMD Energy (Mon Jul 29 2013 - 10:40:54 CDT)
  • analyzing NAMD trajectory with NAMD Energy (Mon Jul 29 2013 - 10:13:42 CDT)
  • Re: dihedral parameter conversion (Thu May 02 2013 - 10:08:51 CDT)
  • Re: dihedral parameter conversion (Thu May 02 2013 - 09:16:36 CDT)
• Marlet Martinez
  • ERROR: Molecule destroyed by fatal error (Mon Jan 27 2014 - 13:31:18 CST)
• Martin, Erik W
  • RE: Why does my volume suddenly expand as I increase temper ature.. . (Tue Nov 12 2013 - 09:14:29 CST)
  • Why does my volume suddenly expand as I increase temperature. (Mon Nov 11 2013 - 17:55:05 CST)
  • RE: regarding editing protonated glutamate in the pdb file via psfgen . . (Tue Nov 05 2013 - 01:38:20 CST)
  • Re: reassignTemp question (Tue Oct 29 2013 - 18:55:08 CDT)
  • reassignTemp question (Tue Oct 29 2013 - 15:26:46 CDT)
  • question about NAMD on Kraken. (Mon Oct 14 2013 - 13:44:10 CDT)
  • NAMD job submission on Kraken? (Fri Aug 30 2013 - 15:36:03 CDT)
  • REMD history file and question (Mon Jul 08 2013 - 10:23:00 CDT)
  • modeling missing loops in starting structures (Tue May 21 2013 - 17:08:06 CDT)
  • colvars configuration file example (Wed Apr 03 2013 - 15:04:41 CDT)
  • RE: memory demands of REMD (Fri Mar 08 2013 - 15:44:50 CST)
  • RE: memory demands of REMD (Thu Mar 07 2013 - 18:27:55 CST)
  • memory demands of REMD (Thu Mar 07 2013 - 16:16:00 CST)
  • remd run command question (Mon Mar 04 2013 - 12:59:56 CST)
  • confines volume effects (Thu Feb 14 2013 - 12:30:39 CST)
  • Re: AW: H-bonds cutoff angle criterian. . (Mon Jan 21 2013 - 01:07:11 CST)
  • NAMD with NVIDIA Quadro K5000? (Tue Jan 15 2013 - 12:15:41 CST)
  • secondary structure analysis (Wed Jan 09 2013 - 14:20:36 CST)
  • RE: reassigning temperatures (Thu Jan 03 2013 - 08:19:24 CST)
• 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)
  • Re: BKS potential (Sat Aug 03 2013 - 13:39:33 CDT)
• Mashayak, Sikandar Yusufoddin
  • local pressure profile for water liquid-vapor (Wed Jul 10 2013 - 10:43:21 CDT)
• Massimiliano Bonomi
  • PLUMED 2.0 announcement (Mon Oct 28 2013 - 06:51:47 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)
  • Re: Topology and parameters for nitrate and nitrite ion (Mon Jul 01 2013 - 06:41:12 CDT)
• Matthew Ralph Adendorff
  • NAMD-SMP-Ibverbs-CUDA assistance (Tue May 13 2014 - 09:25:44 CDT)
  • PREMD in NAMD (Mon Feb 10 2014 - 09:27:15 CST)
  • Adaptive tempering exception error (Sun Nov 17 2013 - 09:52:27 CST)
  • RE: Linear force ramp increments in ABF (Thu Aug 29 2013 - 14:56:30 CDT)
  • RE: Linear force ramp increments in ABF (Thu Aug 29 2013 - 13:40:42 CDT)
  • Linear force ramp increments in ABF (Tue Aug 27 2013 - 12:44:41 CDT)
  • Non-equilibrium effects in ABF runs (Tue Aug 13 2013 - 11:38:57 CDT)
• Maxim Belkin
  • 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)
  • Re: Trouble loading frames from large DCD files (Thu Dec 19 2013 - 16:40:27 CST)
• Maxim Igaev
  • 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: 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)
• Maximilian Ebert
  • Re: ABF: Distances in colvars.traj not identical with VMD exported distances (Tue Oct 29 2013 - 10:02:05 CDT)
  • Re: ABF: Distances in colvars.traj not identical with VMD exported distances (Tue Oct 29 2013 - 07:13:04 CDT)
  • ABF: Distances in colvars.traj not identical with VMD exported distances (Mon Oct 28 2013 - 16:21:45 CDT)
• Maxwell Wesley Terban
  • Generating .psf for amorphous disaccharide (Fri Feb 28 2014 - 13:10:56 CST)
• Mayne, Christopher G
  • 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)
  • Re: Colvars RMSD syntax with a moving reference frame (Fri Aug 02 2013 - 16:38:21 CDT)
  • Colvars RMSD syntax with a moving reference frame (Fri Aug 02 2013 - 10:14:47 CDT)
  • Re: vmd-l: Suggestions on parameterizing a ligand to simulate in NAMD (Mon May 20 2013 - 14:32:42 CDT)
  • Re: vmd-l: FFTK Atom types (Wed Mar 27 2013 - 08:06:05 CDT)
• Mehran Bagheri
  • NAMD electrostatic interaction Failure. (Wed Sep 25 2013 - 08:58:03 CDT)
• MEHRAN MB
  • 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)
  • Re: NAMD electrostatic interaction Failure. (Thu Sep 26 2013 - 17:27:31 CDT)
  • Re: NAMD electrostatic interaction Failure. (Thu Sep 26 2013 - 10:12:16 CDT)
  • NAMD electrostatic interaction Failure (Wed Sep 25 2013 - 10:53:25 CDT)
  • Re: NAMD pressureProfile command (Fri Jul 12 2013 - 12:33:48 CDT)
  • Re: Restarting simulation (Fri Jul 05 2013 - 15:52:04 CDT)
  • Re: fixed atom/Constraint failure in RATTLE algorithm/ (Tue Jun 04 2013 - 10:26:47 CDT)
  • fixed atom/Constraint failure in RATTLE algorithm/ (Fri May 31 2013 - 11:33:03 CDT)
• Melina
  • Re: Locally Enhanced Sampling (Wed Mar 27 2013 - 13:23:06 CDT)
  • Locally Enhanced Sampling (Mon Mar 18 2013 - 12:20:09 CDT)
• Mengyuan Zhu
  • Will there be a NAMD2.9 for IBM AIX UNIX? (Fri Dec 13 2013 - 11:06:48 CST)
  • How to compile NAMD2.9 in IBM AIX UNIX$B!)(B (Thu Dec 12 2013 - 12:24:42 CST)
• 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)
• Mert Gür
  • Re: RMSD calculation (Fri Aug 02 2013 - 22:22:35 CDT)
• 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 Mazack
  • Re: Constant volume energy minimization (Tue Feb 19 2013 - 16:18:00 CST)
  • Re: namd2 CUDA errors for non-superusers in Debian (Fri Feb 15 2013 - 22:55:07 CST)
  • Re: namd2 CUDA errors for non-superusers in Debian (Fri Feb 15 2013 - 08:47:47 CST)
  • Re: Current CVS broken? (SortedArray.h) (Wed Feb 06 2013 - 09:00:43 CST)
  • Re: Current CVS broken? (SortedArray.h) (Tue Feb 05 2013 - 14:24:42 CST)
  • Current CVS broken? (SortedArray.h) (Tue Feb 05 2013 - 12:52:26 CST)
• Michael Purdy
  • Re: Two GPU-based workstation (Tue Jan 14 2014 - 08:05:40 CST)
  • Re: How to split large NAMD DCD file (Thu Jan 24 2013 - 11:06:33 CST)
• Michael Shokhen
  • How to optimize parameters in command for NAMD CUDA GPU MD calculations? (Thu Sep 12 2013 - 14:59:21 CDT)
• Michal Skoczek
  • NAMD 2.9 Changing/Replacing atoms in multiple molecules (Fri Feb 21 2014 - 08:02:41 CST)
  • Problem with replica exchange (Tue Dec 17 2013 - 04:57:38 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
  • 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)
  • zeroMomentum for water droplet (Tue Dec 03 2013 - 17:38:43 CST)
  • Drifting water molecules (Wed Nov 27 2013 - 16:45:10 CST)
  • Separate water coordinates from graphite (Tue Nov 12 2013 - 13:57:01 CST)
  • Re: Extract KE, PE and total energy from log file (Sat Nov 02 2013 - 17:49:06 CDT)
  • Extract KE, PE and total energy from log file (Thu Oct 31 2013 - 15:15:04 CDT)
  • NAMD and water models (Wed Oct 23 2013 - 20:13:17 CDT)
  • Re: Bonds in XPLOR format (Wed Oct 23 2013 - 13:23:10 CDT)
  • Bonds in XPLOR format (Wed Oct 23 2013 - 13:00:05 CDT)
  • Fixed and SMD atoms (Sat Oct 19 2013 - 14:16:47 CDT)
  • Error (Wed Oct 16 2013 - 20:15:29 CDT)
  • Coordinates of Carbon atoms on Graphite (Tue Sep 24 2013 - 11:47:28 CDT)
  • sn-1 tail order parameter (Thu Jun 27 2013 - 16:33:11 CDT)
  • Tail order parameter (Wed Jun 26 2013 - 19:47:11 CDT)
  • (no subject) (Thu Jun 20 2013 - 10:14:07 CDT)
  • Link between simulations (Sat Apr 20 2013 - 15:18:36 CDT)
  • Timeline (Fri Mar 29 2013 - 19:20:41 CDT)
  • Re: Coordinate vs. time plots (Thu Mar 28 2013 - 06:11:44 CDT)
  • (no subject) (Tue Mar 26 2013 - 12:41:35 CDT)
  • Coordinate vs. time plots (Wed Mar 20 2013 - 17:17:46 CDT)
  • Very long simulation (Mon Mar 04 2013 - 05:55:07 CST)
  • RATTLE algorithm (Mon Feb 25 2013 - 17:56:25 CST)
• 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: Sevoflurane parameters (psf file) (Mon May 06 2013 - 13:25:38 CDT)
  • Re: Sevoflurane parameters (psf file) (Fri May 03 2013 - 15:07:00 CDT)
  • Sevoflurane parameters (psf file) (Fri May 03 2013 - 09:41:19 CDT)
• minh nhut
  • forward (Thu Sep 05 2013 - 21:01:00 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: 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
  • (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: 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)
• Moema Monteiro
  • (no subject) (Wed Feb 27 2013 - 15:08:10 CST)
• Mohammad Jomah I Abu Saude (mbusaude)
  • (no subject) (Wed Apr 10 2013 - 17:30:08 CDT)
• Mohan maruthi sena
  • 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)
• 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)
  • RE: TclForces and efficient PBC corrections (Wed Nov 13 2013 - 10:31:31 CST)
  • TclForces and efficient PBC corrections (Mon Nov 11 2013 - 12:02:52 CST)
• Mortaza Aghtar
  • vibrational modes calculation (Mon Sep 23 2013 - 08:55:27 CDT)
• mostafa raeesi
  • velocity manipulation (Thu Oct 16 2014 - 06:37:02 CDT)
• Munir S. Skaf
  • Re: Steered MD along detected routes (Sat Nov 16 2013 - 06:43:08 CST)
  • Re: Cellulose MD simulations (Fri Feb 01 2013 - 07:46:07 CST)
• Mustafa Tekpinar
  • PMF and work distribution (Wed Jun 25 2014 - 05:50:30 CDT)
• Nadeem A. Vellore
  • abf integrate on two dimensional pmf (Mon Oct 07 2013 - 21:25:11 CDT)
  • Two dimensional ABF (Tue Jun 11 2013 - 11:33:02 CDT)
  • colvar keyword ForceNoPBC (Wed Feb 27 2013 - 23:46:09 CST)
  • Re: ABF - distance between two domains (Wed Feb 27 2013 - 15:45:49 CST)
  • ABF - distance between two domains (Wed Feb 27 2013 - 15:12:35 CST)
• Nadia Salami
  • pH calculation (Sun Dec 01 2013 - 23:31:02 CST)
  • Potential energy in the boundaries (Tue Nov 05 2013 - 03:06:50 CST)
  • incorrect bond (Wed Sep 18 2013 - 01:28:59 CDT)
  • incorrect bond (Wed Sep 18 2013 - 01:11:08 CDT)
  • (no subject) (Sun Sep 01 2013 - 10:26:51 CDT)
  • BKS potential (Sat Aug 03 2013 - 12:54:40 CDT)
  • Annealing of SiO (Fri Aug 02 2013 - 23:07:58 CDT)
• namd_chcwaaa_at_yahoo.com.cn
  • How Pressureprofile output are averaged ? (Fri Jan 04 2013 - 23:21:39 CST)
• nan li
  • Re: Interaction energy definition (Fri Nov 22 2013 - 15:21:31 CST)
  • Interaction energy definition (Fri Nov 22 2013 - 14:45:13 CST)
• Narasimhan LOGANATHAN
  • Re: distanceZ - harmonic restraints (Mon Mar 18 2013 - 13:38:55 CDT)
  • Re: distanceZ - harmonic restraints (Mon Mar 18 2013 - 13:37:45 CDT)
  • distanceZ - harmonic restraints (Mon Mar 18 2013 - 12:14:46 CDT)
  • Collective variable data analysis using WHAM (Wed Feb 20 2013 - 11:55:31 CST)
• 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)
• ncskocze_at_cyf-kr.edu.pl
  • NAMD 2.9 Replica-exchange. FATAL ERROR: Unknown command-line option +replicas (Fri Jan 04 2013 - 07:53:16 CST)
• Neelanjana Sengupta
  • harmonic restraints between multiple atom pairs (Mon Nov 03 2014 - 22:42:33 CST)
  • restraining bonds (Sun Aug 31 2014 - 23:50:24 CDT)
  • obtaining the system force (Tue Dec 24 2013 - 00:26:59 CST)
  • Reaction field treatment (Fri Jun 28 2013 - 01:24:08 CDT)
• Neeraj Agrawal
  • Re: NAMD PERFORMANCE ON NVIDIA K20 GPU (Tue Sep 17 2013 - 18:13:34 CDT)
  • NAMD PERFORMANCE ON NVIDIA K20 GPU (Sat Sep 14 2013 - 18:59:08 CDT)
• Nicholas M Glykos
  • 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)
  • Carma v.1.3 available for download (Sun Nov 24 2013 - 04:33:05 CST)
  • [OT] A new method for quantifying convergence of MD simulations (Mon Oct 21 2013 - 12:37:45 CDT)
  • Re: Problem regarding the big DCD file (Sat Jul 20 2013 - 07:29:04 CDT)
  • grcarma : a graphical user interface to carma (Wed Apr 17 2013 - 09:33:24 CDT)
  • Re: confines volume effects (Fri Feb 15 2013 - 04:04:29 CST)
  • Re: secondary structure analysis (Fri Jan 11 2013 - 02:57:26 CST)
• Nicolas Floquet
  • Metadynamics with eigenvector (Mon Aug 25 2014 - 09:40:06 CDT)
  • NAMD 2.9 install on CLuster mpirun/charmrun with ibverb version ? (Thu Nov 14 2013 - 05:17:48 CST)
• nicolas martin
  • 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)
• 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)
  • Re: FEP simulation: protein moving out of water box. (Tue Nov 05 2013 - 21:21:48 CST)
  • Re: About the scope of show_replicas.vmd (Thu Sep 19 2013 - 12:30:05 CDT)
  • Re: About the scope of show_replicas.vmd (Thu Sep 19 2013 - 09:48:11 CDT)
  • Re: Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT (Wed Sep 18 2013 - 10:29:40 CDT)
  • Re: charm-gui membrane builder (Tue Sep 17 2013 - 13:22:45 CDT)
  • Re: Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT (Tue Sep 17 2013 - 11:35:45 CDT)
  • Re: charm-gui membrane builder (Fri Sep 13 2013 - 09:01:51 CDT)
  • Re: charm-gui membrane builder (Thu Sep 12 2013 - 13:08:53 CDT)
  • Re: Simulation of the membrane protein (Thu Sep 05 2013 - 12:23:00 CDT)
  • Re: catdcd error (Mon Aug 19 2013 - 08:26:24 CDT)
  • Re: Incorporating some ions with specific location (Tue Aug 13 2013 - 08:43:04 CDT)
  • Re: vacuum minimisation-reg (Wed Jul 24 2013 - 08:38:49 CDT)
  • Re: Using negatively charged phopspholipids and no neutralization, membrane expands in the xy direction ....... (Wed Jul 24 2013 - 08:45:19 CDT)
  • Re: metadynamics (Fri Apr 26 2013 - 10:17:00 CDT)
  • Re: strange result using implicit solvent (Fri Mar 29 2013 - 08:39:05 CDT)
  • Re: free energy methods cheat-sheet/comparison chart (Mon Mar 25 2013 - 17:06:36 CDT)
  • Re: free energy methods cheat-sheet/comparison chart (Mon Mar 25 2013 - 16:17:06 CDT)
  • Re: NAMD on Stampede (Wed Feb 27 2013 - 14:27:34 CST)
• Nikolaos Glykos
  • Re: Convergence of Sampling and Deciding on Simulation Length (Tue Jul 16 2013 - 12:16:12 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: 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)
  • AW: Trouble loading frames from large DCD files (Fri Dec 20 2013 - 01:52:23 CST)
  • AW: 50% system CPU usage when parallel running NAMD on Rocks cluster (Wed Dec 18 2013 - 02:06:09 CST)
  • AW: Problem with replica exchange (Tue Dec 17 2013 - 05:43:32 CST)
  • AW: 50% system CPU usage when parallel running NAMD on Rocks cluster (Mon Dec 16 2013 - 01:08:54 CST)
  • AW: 50% system CPU usage when parallel running NAMD on Rocks cluster (Mon Dec 16 2013 - 01:07:28 CST)
  • AW: Re: AW: puzzle of SMD in NAMD-2.9 and pull code in Gromacs (Fri Dec 13 2013 - 01:43:43 CST)
  • AW: Re: AW: puzzle of SMD in NAMD-2.9 and pull code in Gromacs (Fri Dec 13 2013 - 00:47:03 CST)
  • AW: vmd-l: AMD vs. nvidia support (Thu Dec 12 2013 - 01:05:22 CST)
  • AW: 50% system CPU usage when parallel running NAMD on Rocks cluster (Tue Dec 10 2013 - 08:19:45 CST)
  • AW: puzzle of SMD in NAMD-2.9 and pull code in Gromacs (Tue Dec 10 2013 - 08:18:03 CST)
  • AW: 50% system CPU usage when parallel running NAMD on Rocks cluster (Mon Dec 09 2013 - 01:19:28 CST)
  • AW: Running NAMD on SGE cluster - multiple modes and cores (Thu Dec 05 2013 - 04:33:12 CST)
  • AW: Running NAMD on SGE cluster - multiple modes and cores (Thu Dec 05 2013 - 04:57:18 CST)
  • AW: Running NAMD on SGE cluster - multiple modes and cores (Thu Dec 05 2013 - 04:06:31 CST)
  • AW: Running NAMD on SGE cluster - multiple modes and cores (Thu Dec 05 2013 - 02:58:07 CST)
  • AW: Running NAMD on SGE cluster - multiple modes and cores (Wed Dec 04 2013 - 07:36:48 CST)
  • AW: Runaway cuda-enabled namd2 processes (Wed Dec 04 2013 - 05:41:20 CST)
  • AW: 50% system CPU usage when parallel running NAMD on Rocks cluster (Tue Dec 03 2013 - 08:47:54 CST)
  • AW: Running NAMD on SGE cluster - multiple modes and cores (Tue Dec 03 2013 - 06:12:08 CST)
  • AW: AW: charm++ MPI build errors on LSF Cluster: "Can not compile a MPI program" (Mon Dec 02 2013 - 05:27:37 CST)
  • AW: charm++ MPI build errors on LSF Cluster: "Can not compile a MPI program" (Mon Dec 02 2013 - 02:05:24 CST)
  • AW: BUG: TCL coorfile command (Mon Dec 02 2013 - 01:43:41 CST)
  • AW: Drifting water molecules (Thu Nov 28 2013 - 02:59:56 CST)
  • Problem regarding the Pre-Minimizer Bad Contacts Removal (Wed Nov 27 2013 - 02:24:28 CST)
  • AW: inconsistency between "Benchmark" and "Timing" output (Tue Nov 26 2013 - 01:08:31 CST)
  • Sherical BC energy conservation (Mon Nov 25 2013 - 03:18:37 CST)
  • AW: NAMD_2.9_Linux-x86_64-ibverbs RUNS on QueenBee RUN TIME VARIATION (Tue Nov 19 2013 - 09:07:42 CST)
  • AW: Question about how much used from CPU? (Tue Nov 19 2013 - 03:06:14 CST)
  • AW: NAMD 2.9 install on CLuster mpirun/charmrun with ibverb version ? (Thu Nov 14 2013 - 06:43:49 CST)
  • AW: Separate water coordinates from graphite (Thu Nov 14 2013 - 06:34:46 CST)
  • AW: Separate water coordinates from graphite (Thu Nov 14 2013 - 01:26:31 CST)
  • AW: Separate water coordinates from graphite (Wed Nov 13 2013 - 04:58:35 CST)
  • AW: TclForces and efficient PBC corrections (Tue Nov 12 2013 - 01:55:16 CST)
  • AW: Why does my volume suddenly expand as I increase temperature. (Tue Nov 12 2013 - 01:23:47 CST)
  • AW: TclForces and efficient PBC corrections (Tue Nov 12 2013 - 01:19:01 CST)
  • AW: Two GPU-based workstation (Mon Nov 11 2013 - 03:26:06 CST)
  • AW: Two GPU-based workstation (Mon Nov 11 2013 - 03:23:53 CST)
  • AW: Two GPU-based workstation (Mon Nov 11 2013 - 01:09:38 CST)
  • AW: Two GPU-based workstation (Thu Nov 07 2013 - 01:51:43 CST)
  • AW: AW: AW: Martini RBCG simulation frequently crashing with "atoms moving too fast" (Tue Nov 05 2013 - 03:04:53 CST)
  • AW: AW: Martini RBCG simulation frequently crashing with "atoms moving too fast" (Mon Nov 04 2013 - 09:02:04 CST)
  • AW: Two GPU-based workstation (Mon Nov 04 2013 - 05:15:06 CST)
  • AW: Two GPU-based workstation (Mon Nov 04 2013 - 02:27:40 CST)
  • AW: Martini RBCG simulation frequently crashing with "atoms moving too fast" (Mon Nov 04 2013 - 01:17:46 CST)
  • AW: Extract KE, PE and total energy from log file (Mon Nov 04 2013 - 01:13:05 CST)
  • AW: Two GPU-based workstation (Mon Nov 04 2013 - 01:04:00 CST)
  • AW: Two GPU-based workstation (Wed Oct 30 2013 - 11:09:44 CDT)
  • AW: Two GPU-based workstation (Tue Oct 29 2013 - 09:46:10 CDT)
  • AW: vmd-l: Creating custom molecule in VMD scripting (Tue Oct 29 2013 - 07:16:46 CDT)
  • AW: Two GPU-based workstation (Tue Oct 29 2013 - 05:00:15 CDT)
  • AW: Two GPU-based workstation (Tue Oct 29 2013 - 04:13:17 CDT)
  • AW: Re: DEVELOPER QUESTION -> NAMD Internal energy unit and TCL interface (Mon Oct 28 2013 - 09:17:36 CDT)
  • AW: Mysterious slow down in parallel (Mon Oct 28 2013 - 01:50:58 CDT)
  • AW: Re: DEVELOPER QUESTION -> NAMD Internal energy unit and TCL interface (Thu Oct 24 2013 - 11:53:37 CDT)
  • AW: Re: DEVELOPER QUESTION -> NAMD Internal energy unit and TCL interface (Thu Oct 24 2013 - 11:51:38 CDT)
  • DEVELOPER QUESTION -> NAMD Internal energy unit and TCL interface (Thu Oct 24 2013 - 01:21:19 CDT)
  • NAMD Internal energy unit (Wed Oct 23 2013 - 05:16:57 CDT)
  • Namd options from TCL (Tue Oct 22 2013 - 10:26:37 CDT)
  • AW: Fixed and SMD atoms (Tue Oct 22 2013 - 03:37:09 CDT)
  • AW: Fixed and SMD atoms (Mon Oct 21 2013 - 01:37:28 CDT)
  • AW: vmd-l: fftk-charges (Mon Oct 21 2013 - 01:23:48 CDT)
  • AW: Error (Thu Oct 17 2013 - 00:38:22 CDT)
  • AW: Pass a runtime parameter into the configuration file (Wed Oct 16 2013 - 00:45:18 CDT)
  • AW: About Constraint Failure (Wed Oct 16 2013 - 00:31:03 CDT)
  • AW: rcmd: socket: All ports in use w/ NAMD_2.9_Linux-x86_64-ibverbs (Mon Oct 14 2013 - 01:15:13 CDT)
  • BUG Report: NAMD 2.10 Nightly Build from 11.Sep (Fri Oct 11 2013 - 06:23:14 CDT)
  • AW: vmd-l: Finding particles that are close (Tue Oct 08 2013 - 06:48:07 CDT)
  • AW: cell origin problem (Thu Sep 26 2013 - 00:59:57 CDT)
  • AW: vmd-l: non-orthorhombic PBCs (Thu Sep 26 2013 - 00:49:18 CDT)
  • AW: Coordinates of Carbon atoms on Graphite (Thu Sep 26 2013 - 00:45:38 CDT)
  • AW: Coordinates of Carbon atoms on Graphite (Wed Sep 25 2013 - 09:16:24 CDT)
  • AW: Coordinates of Carbon atoms on Graphite (Wed Sep 25 2013 - 08:35:15 CDT)
  • AW: Coordinates of Carbon atoms on Graphite (Wed Sep 25 2013 - 00:49:32 CDT)
  • AW: cell origin problem (Wed Sep 25 2013 - 00:44:46 CDT)
  • AW: charm-gui membrane builder (Mon Sep 16 2013 - 09:16:41 CDT)
  • AW: NAMD PERFORMANCE ON NVIDIA K20 GPU (Mon Sep 16 2013 - 02:05:34 CDT)
  • AW: NAMD CUDA performance (Wed Sep 11 2013 - 01:53:54 CDT)
  • AW: explicit NVT simulation (Mon Sep 09 2013 - 01:26:14 CDT)
  • AW: VDW energy is negative but total energy is positive (Mon Sep 09 2013 - 01:14:20 CDT)
  • AW: vmd-l: Error: Maximum number of bonds exceeded (Mon Sep 09 2013 - 01:06:38 CDT)
  • AW: namd scale-up (Fri Sep 06 2013 - 02:09:19 CDT)
  • AW: namd scale-up (Thu Sep 05 2013 - 08:55:10 CDT)
  • AW: namd scale-up (Thu Sep 05 2013 - 07:58:23 CDT)
  • AW: parallel code in tclforce script (Thu Sep 05 2013 - 01:45:08 CDT)
  • AW: namd scale-up (Thu Sep 05 2013 - 01:32:45 CDT)
  • AW: vmd-l: how to enable multiple core rendering? (Thu Sep 05 2013 - 01:01:40 CDT)
  • AW: AW: AW: pbc error (Tue Sep 03 2013 - 04:55:03 CDT)
  • AW: writedcd problem (Tue Sep 03 2013 - 03:47:16 CDT)
  • AW: pbc error (Mon Sep 02 2013 - 01:44:18 CDT)
  • AW: vmd-l: SangbaeLee: question about pbc wrap (Fri Aug 30 2013 - 02:15:30 CDT)
  • WG: questions regarding the source code in NAMD (Wed Aug 28 2013 - 10:49:31 CDT)
  • AW: making patch (Wed Aug 28 2013 - 02:46:00 CDT)
  • AW: problem with ptch ... (Tue Aug 27 2013 - 03:40:58 CDT)
  • AW: vmd-l: matching part of two models (Mon Aug 26 2013 - 04:58:04 CDT)
  • AW: a problem about pbc in a namd trajectory (Mon Aug 26 2013 - 03:44:14 CDT)
  • AW: questions regarding the source code in NAMD (Fri Aug 23 2013 - 06:59:34 CDT)
  • AW: AW: hi every body, (Thu Aug 22 2013 - 04:39:38 CDT)
  • AW: hi every body, (Thu Aug 22 2013 - 02:16:39 CDT)
  • AW: Nvidia GPUs (Wed Aug 21 2013 - 03:22:12 CDT)
  • AW: catdcd error (Mon Aug 19 2013 - 08:53:59 CDT)
  • AW: apoa1 slow Phase 1 (Fri Aug 16 2013 - 00:32:09 CDT)
  • AW: All CUDA devices are in prohibited mode, of compute capability 1.0, or otherwise unusable. (Fri Aug 16 2013 - 00:22:44 CDT)
  • AW: All CUDA devices are in prohibited mode, of compute capability 1.0, or otherwise unusable. (Thu Aug 15 2013 - 02:12:58 CDT)
  • AW: All CUDA devices are in prohibited mode, of compute capability 1.0, or otherwise unusable. (Thu Aug 15 2013 - 00:50:54 CDT)
  • AW: All CUDA devices are in prohibited mode, of compute capability 1.0, or otherwise unusable. (Wed Aug 14 2013 - 00:41:31 CDT)
  • AW: AW: vmd-l: Occupancy maps (Tue Aug 13 2013 - 03:28:25 CDT)
  • AW: AW: vmd-l: Occupancy maps (Mon Aug 12 2013 - 01:47:30 CDT)
  • AW: vmd-l: Occupancy maps (Mon Aug 12 2013 - 00:14:36 CDT)
  • AW: Question about loading velocity files on VMD (Sun Aug 11 2013 - 23:48:35 CDT)
  • AW: NBFIX 1-4 scaling term ignored for CHARMM format parameters (Thu Aug 08 2013 - 00:27:43 CDT)
  • AW: Colvar cannot be ran on supercomputer newton (Wed Aug 07 2013 - 02:18:25 CDT)
  • AW: Colvar cannot be ran on supercomputer newton (Tue Aug 06 2013 - 09:57:32 CDT)
  • AW: running namd in parallel (Fri Aug 02 2013 - 03:43:52 CDT)
  • Center of mass motion included in Temperature? (Thu Aug 01 2013 - 04:53:34 CDT)
  • AW: Replica exchange, colvars & harmonic restraints (Tue Jul 30 2013 - 00:38:02 CDT)
  • AW: (Fri Jun 21 2013 - 03:11:07 CDT)
  • AW: C++ API (Thu Jun 20 2013 - 01:01:53 CDT)
  • AW: how to apply force SMD method on an anisotropic geometry (Thu Jun 13 2013 - 01:56:48 CDT)
  • AW: NAMD related (Mon Jun 10 2013 - 10:24:11 CDT)
  • AW: First meeting with NAMD (Mon Jun 10 2013 - 00:35:06 CDT)
  • AW: DCD writing error on cluster (Mon Jun 10 2013 - 00:48:28 CDT)
  • AW: 回å¤�： Shift (or offset) of the lipid bilayer along Z axis during equilibration (Mon Jun 10 2013 - 00:42:35 CDT)
  • AW: First meeting with NAMD (Thu Jun 06 2013 - 02:23:05 CDT)
  • AW: Any alternative to colvars for minimization? (Thu Jun 06 2013 - 02:27:26 CDT)
  • AW: how to do a vacuum minimization without electrostatics and periodic boundary conditions? (Thu Jun 06 2013 - 02:12:01 CDT)
  • AW: First meeting with NAMD (Tue Jun 04 2013 - 02:16:18 CDT)
  • AW: fixed atom/Constraint failure in RATTLE algorithm/ (Tue Jun 04 2013 - 02:01:10 CDT)
  • AW: Does MOLLY really retain bond motion for water? (Mon Jun 03 2013 - 00:43:15 CDT)
  • AW: fixed atom/Constraint failure in RATTLE algorithm/ (Mon Jun 03 2013 - 00:23:43 CDT)
  • AW: problem with runiing namd through infiniband (Fri May 31 2013 - 01:04:09 CDT)
  • AW: NAMD/VMD installation on Linux Clusters with InfiniBand (Thu May 30 2013 - 05:14:55 CDT)
  • AW: problem with runiing namd through infiniband (Thu May 30 2013 - 05:05:59 CDT)
  • AW: Suggestions while building a GPU-machine (CUDA) for NAMD use! (Wed May 29 2013 - 00:27:44 CDT)
  • AW: problem with runiing namd through infiniband (Wed May 29 2013 - 00:22:58 CDT)
  • AW: NAMD/VMD installation on Linux Clusters with InfiniBand (Thu May 23 2013 - 01:24:51 CDT)
  • AW: Help with "ERROR: Constraint failure in RATTLE algorithm for atom XXXX!" (Tue May 21 2013 - 01:02:42 CDT)
  • AW: Protein unfolding and Coarse grained (Fri May 17 2013 - 07:41:17 CDT)
  • AW: Building crystal polymer (Fri May 17 2013 - 07:39:30 CDT)
  • AW: A larger protein data bank for performance benchmark (Tue May 14 2013 - 10:30:08 CDT)
  • AW: A larger protein data bank for performance benchmark (Tue May 14 2013 - 00:46:34 CDT)
  • AW: Coarse-grained reverse transformation (Mon May 13 2013 - 00:43:00 CDT)
  • AW: Can I define a simulation box but turn off the PBC at the same time? (Mon May 13 2013 - 00:22:55 CDT)
  • AW: Bulk properties of polymers (Wed May 08 2013 - 02:13:56 CDT)
  • AW: catdcd output and .psf file atom count mismatch (Tue May 07 2013 - 00:47:33 CDT)
  • AW: Exploding vdW energies in automatically generated POPC membranes (Tue May 07 2013 - 00:17:36 CDT)
  • AW: Exploding vdW energies in automatically generated POPC membranes (Tue May 07 2013 - 00:16:20 CDT)
  • AW: AW: Coarse-Grained fatal error! (Mon May 06 2013 - 01:09:08 CDT)
  • AW: Coarse-Grained fatal error! (Fri May 03 2013 - 00:25:54 CDT)
  • AW: NAMD2.9 single-node benchmarks, 0-2 Kepler GPU's. (Thu May 02 2013 - 01:13:08 CDT)
  • AW: [SOLVED] Charmrun> error x attaching to node (Tue Apr 30 2013 - 07:09:22 CDT)
  • [SOLVED] Charmrun> error x attaching to node (Tue Apr 30 2013 - 05:09:05 CDT)
  • AW: Are random forces applied at every step (when using the langevin thermostat) ? (Mon Apr 29 2013 - 01:55:37 CDT)
  • AW: Build polymer from monomer (Fri Apr 26 2013 - 01:07:13 CDT)
  • AW: Link between simulations (Wed Apr 24 2013 - 02:09:13 CDT)
  • AW: solvated system for minimization (Mon Apr 22 2013 - 09:14:20 CDT)
  • AW: Link between simulations (Mon Apr 22 2013 - 01:34:43 CDT)
  • AW: AW: Minimisation of protein in a water box (Mon Apr 22 2013 - 01:22:48 CDT)
  • AW: floating point reproduceability (Fri Apr 19 2013 - 02:09:33 CDT)
  • AW: Minimisation of protein in a water box (Fri Apr 19 2013 - 02:03:15 CDT)
  • AW: floating point reproduceability (Thu Apr 18 2013 - 02:15:11 CDT)
  • AW: Minimisation of protein in a water box (Tue Apr 16 2013 - 01:31:31 CDT)
  • AW: Error in distributing the cores for a single processor (Thu Apr 11 2013 - 01:20:57 CDT)
  • AW: About Bond Deletion (Thu Apr 11 2013 - 00:57:43 CDT)
  • AW: NamdMemoryReduction - genCompressedPsf (Fri Mar 22 2013 - 02:28:53 CDT)
  • AW: Coordinate vs. time plots (Thu Mar 21 2013 - 01:49:37 CDT)
  • AW: Can protein-water electrostatic interaction be turned off keeping protein-protein (vdw+elect) and water-water (vdw+elect) interactions intact? (Wed Mar 20 2013 - 02:47:06 CDT)
  • AW: MD crashes at 300K after warm up MD (Wed Mar 20 2013 - 02:36:02 CDT)
  • AW: Can protein-water interaction be turned off keeping protein-protein and water-water interactions intact? (Tue Mar 19 2013 - 10:18:35 CDT)
  • AW: NamdMemoryReduction - genCompressedPsf (Tue Mar 19 2013 - 02:50:33 CDT)
  • AW: Restart simulation of an equilibrated bilayer with sugar molecules inserted (Mon Mar 18 2013 - 01:39:50 CDT)
  • AW: LES very slow (Tue Mar 12 2013 - 01:51:40 CDT)
  • AW: NAMD 2.9 CUDA compilation (Tue Mar 12 2013 - 02:53:06 CDT)
  • AW: NamdMemoryReduction - genCompressedPsf (Tue Mar 12 2013 - 01:58:11 CDT)
  • AW: NAMD 2.9 CUDA compilation (Tue Mar 12 2013 - 01:57:00 CDT)
  • AW: NAMD with Intel Xeon Phi coprocessors ? (Mon Mar 11 2013 - 02:05:28 CDT)
  • AW: NamdMemoryReduction - genCompressedPsf (Mon Mar 11 2013 - 01:56:40 CDT)
  • AW: NamdMemoryReduction - genCompressedPsf (Fri Mar 08 2013 - 01:04:34 CST)
  • AW: LES very slow (Thu Mar 07 2013 - 00:47:59 CST)
  • AW: LES very slow (Wed Mar 06 2013 - 01:03:39 CST)
  • AW: problem in solvating a graphene layer created using VMD-nanotube builder (Tue Mar 05 2013 - 00:18:44 CST)
  • AW: remd run command question (Tue Mar 05 2013 - 00:14:22 CST)
  • AW: LES very slow (Tue Mar 05 2013 - 00:08:42 CST)
  • AW: LES very slow (Mon Mar 04 2013 - 01:27:27 CST)
  • AW: converting dcd files to netcdf or ascii (Thu Feb 28 2013 - 09:05:59 CST)
  • AW: GPUs silently stop working during simulation when oversubscribed (Thu Feb 28 2013 - 05:41:04 CST)
  • AW: GPUs silently stop working during simulation when oversubscribed (Thu Feb 28 2013 - 03:21:00 CST)
  • AW: AW: smd simulation (Thu Feb 28 2013 - 03:10:01 CST)
  • AW: smd simulation (Thu Feb 28 2013 - 00:48:19 CST)
  • AW: LES very slow (Thu Feb 28 2013 - 00:37:07 CST)
  • AW: Always 24-way SMP? (Wed Feb 27 2013 - 01:53:27 CST)
  • AW: Regarding installing Namd 2.9 on windows xp 32 bit system (Wed Feb 27 2013 - 01:30:58 CST)
  • AW: RATTLE algorithm (Wed Feb 27 2013 - 01:24:05 CST)
  • AW: LES very slow (Wed Feb 27 2013 - 01:19:51 CST)
  • AW: LES very slow (Tue Feb 26 2013 - 00:42:30 CST)
  • AW: RATTLE algorithm (Tue Feb 26 2013 - 00:38:53 CST)
  • AW: Always 24-way SMP? (Tue Feb 26 2013 - 00:27:27 CST)
  • AW: Always 24-way SMP? (Mon Feb 25 2013 - 09:06:05 CST)
  • AW: spectrum simulation (Mon Feb 25 2013 - 01:01:05 CST)
  • AW: Always 24-way SMP? (Mon Feb 25 2013 - 00:55:26 CST)
  • AW: (Fri Feb 22 2013 - 00:49:17 CST)
  • AW: Scaling on 64 core nodes? (Fri Feb 15 2013 - 01:43:58 CST)
  • AW: running NAMD on Amazon EC2? (Thu Feb 14 2013 - 01:30:58 CST)
  • AW: ERROR: Constraint failure in RATTLE algorithm for atom 593! (Mon Feb 04 2013 - 09:33:08 CST)
  • AW: Percentage of Residues in Ramachandran Plot regions versus time of trajectory (Tue Jan 29 2013 - 08:27:01 CST)
  • AW: Re: Question about NAMD (Tue Jan 29 2013 - 00:24:26 CST)
  • AW: Percentage of Residues in Ramachandran Plot regions versus time of trajectory (Mon Jan 28 2013 - 00:08:17 CST)
  • AW: Assigning Partial Charges to FE in Active Site Superoxide Dismutase. (Thu Jan 24 2013 - 01:23:18 CST)
  • AW: FEP on an amino acid ligand (Wed Jan 23 2013 - 01:21:09 CST)
  • AW: FEP on an amino acid ligand (Tue Jan 22 2013 - 00:28:38 CST)
  • Remove tjwang@iastate.edu from the list pls (Mon Jan 21 2013 - 00:04:57 CST)
  • AW: Scaling problem: 4 nodes OK, 5 fails to start (Mon Jan 21 2013 - 00:02:25 CST)
  • AW: Running namd on linux in cpu+gpu mode (Sun Jan 20 2013 - 23:52:48 CST)
  • AW: H-bonds cutoff angle criterian (Sun Jan 20 2013 - 23:46:48 CST)
  • AW: Scaling problem: 4 nodes OK, 5 fails to start (Thu Jan 17 2013 - 00:14:37 CST)
  • AW: Re: AW: AW: CUDA problem? (Thu Jan 17 2013 - 00:01:27 CST)
  • AW: Re: AW: AW: CUDA problem? (Wed Jan 16 2013 - 00:21:57 CST)
  • AW: namd 2.9 tip4p-2005 (Wed Jan 16 2013 - 00:01:40 CST)
  • AW: DNA surrounded by a shell of water in a big box with vacuum (Tue Jan 15 2013 - 00:39:59 CST)
  • AW: secondary structure analysis (Thu Jan 10 2013 - 00:16:07 CST)
• Nutan Preety
  • ERROR: Constraint failure in RATTLE algorithm for atom 593! (Mon Feb 04 2013 - 06:26:44 CST)
  • Re: namd-l digest V1 #979 (Mon Feb 04 2013 - 06:18:55 CST)
• oguz gurbulak
  • namd conf file (Sat Sep 21 2013 - 05:52:23 CDT)
  • dcd to pdb for trajectory analysis (Thu Jul 11 2013 - 07:40:11 CDT)
• Ole Juul Andersen
  • Re: Slow vacuum/GBIS simulations (time to completion keeps increasing) (Wed Jul 03 2013 - 07:28:20 CDT)
  • RE: Slow vacuum/GBIS simulations (time to completion keeps increasing) (Wed Jul 03 2013 - 05:06:46 CDT)
  • RE: Slow vacuum/GBIS simulations (time to completion keeps increasing) (Tue Jul 02 2013 - 12:57:14 CDT)
  • Slow vacuum/GBIS simulations (time to completion keeps increasing) (Tue Jul 02 2013 - 12:33:45 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)
• P.-L. Chau
  • Re: NAMD pressureProfile command (Fri Jul 12 2013 - 11:48:30 CDT)
  • pressure profile calculation problem (Fri Jul 12 2013 - 10:47:05 CDT)
  • Re: NAMD pressureProfile command (Thu Jul 11 2013 - 04:05:45 CDT)
  • NAMD pressureProfile command (Thu Jul 04 2013 - 16:52:00 CDT)
  • pressure profile calculations (Thu Jul 04 2013 - 16:43:32 CDT)
• 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)
  • Temperature reassignment (Tue Dec 31 2013 - 11:28:12 CST)
• Paraskevi Gkeka
  • src/ComputeNonbondedCUDA.C:1022: error: thread-local storage not supported for this target (Wed Jan 16 2013 - 10:35:57 CST)
  • src/ComputeNonbondedCUDA.C:1022: error: thread-local storage not supported for this target (Wed Jan 16 2013 - 10:29:52 CST)
• parikshit moitra
  • Question regarding reverse CG to all-atom (Tue Jan 21 2014 - 04:42:04 CST)
• Patriche Simona
  • Cellulose MD simulations (Thu Jan 31 2013 - 04:39:33 CST)
• Patricia Campbell
  • unsubscribe (Sat Jun 29 2013 - 00:21:31 CDT)
  • unsubscribe (Fri Jun 28 2013 - 15:39:45 CDT)
  • unsubscribe (Fri May 03 2013 - 08:57:21 CDT)
  • MD crashes at 300K after warm up MD (Tue Mar 19 2013 - 13:30:23 CDT)
  • DCD file doubles a monomer (Tue Feb 26 2013 - 15:01:18 CST)
  • Re: DCD file doubles a monomer (Tue Feb 26 2013 - 12:13:53 CST)
  • DCD file doubles a monomer (Tue Feb 26 2013 - 12:09:16 CST)
  • Simulation continuously crashes after minimization (Tue Feb 12 2013 - 15:01:37 CST)
  • Simulation continuously crashes after minimization (Tue Feb 12 2013 - 14:52:03 CST)
• Patrick Chiu
  • the dielectric constant use in pairwise interaction energy calculation of ligand and protein (Tue Apr 08 2014 - 08:45:11 CDT)
• Paul Hargrove
  • Re: BLCR and NAMD (Fri Nov 08 2013 - 01:54:48 CST)
• Paul Rigor
  • Re: All CUDA devices are in prohibited mode, of compute capability 1.0, or otherwise unusable. (Thu Aug 15 2013 - 11:15:40 CDT)
• Pavan
  • Re: what to do with this error (Fri Dec 06 2013 - 08:03:31 CST)
• Pavan G
  • Re: 2d periodic box (Sun Mar 31 2013 - 12:50:49 CDT)
  • Re: 2d periodic box (Fri Mar 29 2013 - 08:56:33 CDT)
  • Re: 2d periodic box (Fri Mar 29 2013 - 08:39:59 CDT)
  • 2d periodic box (Wed Mar 27 2013 - 12:51:25 CDT)
• Pedro Swagger
  • Re: pmf command (Thu Jul 25 2013 - 12:35:00 CDT)
  • pmf command (Wed Jul 24 2013 - 15:30:40 CDT)
  • Re: ABF subdividing the reaction coordinate (Wed Jul 10 2013 - 17:15:44 CDT)
  • Re: ABF subdividing the reaction coordinate (Wed Jul 10 2013 - 16:45:15 CDT)
  • ABF subdividing the reaction coordinate (Wed Jul 10 2013 - 16:00:37 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 Jones
  • Re: MMPBSA-like analysis (Tue Oct 22 2013 - 04:21:24 CDT)
  • Re: Preventing rotation of a protein (Wed Jul 17 2013 - 22:06:10 CDT)
• Peter Murphy
  • Re: NAMD Tutorial - Water Sphere - Altering size of water sphere (Mon May 13 2013 - 11:16:20 CDT)
• Peter Reinke
  • tools for Charmm (Thu Feb 20 2014 - 02:39:59 CST)
  • Charmm (Thu Feb 20 2014 - 02:31:35 CST)
• peter.schmidtke_at_fr.netgrs.com
  • RE: Issues with the "Keep Water Out" tcl script (Thu Jan 03 2013 - 09:09:29 CST)
• Peterson J
  • XY constraints with center of mass movements (Mon Dec 09 2013 - 11:29:12 CST)
  • Charge distribution (Fri Nov 01 2013 - 00:28:34 CDT)
  • Segmentation fault - colvar (Mon Sep 16 2013 - 23:02:55 CDT)
  • gromacs to NAMD (Tue Jul 09 2013 - 14:55:46 CDT)
  • Problem during TMD (Wed Jun 26 2013 - 14:59:50 CDT)
  • Using CosntantArea in membrane simulation (Wed Jun 19 2013 - 16:53:06 CDT)
  • query on constraintScaling in NAMD (Fri Jun 14 2013 - 15:47:25 CDT)
  • Re: Lipid bilayer tears apart during simulation (Fri Jun 14 2013 - 15:44:46 CDT)
  • Lipid bilayer tears apart during simulation (Fri Jun 14 2013 - 15:14:02 CDT)
  • FATAL ERROR: Bad global bond count! (Wed Jun 12 2013 - 11:01:23 CDT)
  • Re: Re: vmd-l: Suggestions on parameterizing a ligand to simulate in NAMD (Mon May 20 2013 - 23:48:48 CDT)
  • Suggestions on parameterizing a ligand to simulate in NAMD (Mon May 20 2013 - 13:03:57 CDT)
  • Patching N- and C-Terms and their parameters (Thu May 02 2013 - 18:28:25 CDT)
• 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)
  • BLCR and NAMD (Thu Nov 07 2013 - 22:47:14 CST)
• Pino, James Christopher
  • GPU/CPU workstation optimal simulation parameters for NAMD2.9 performance (Tue Feb 18 2014 - 12:00:34 CST)
• Prathit Chatterjee
  • regarding editing protonated glutamate in the pdb file via psfgen (Tue Nov 05 2013 - 00:53:17 CST)
• Price, Gareth
  • RE: Minimisation of protein in a water box (Thu Apr 18 2013 - 19:15:31 CDT)
• Prija Ponnan
  • Invitation to Submit Review Article Current Protein & Peptide Science (IF: 2.326) (Fri Jun 27 2014 - 06:40:43 CDT)
• Priyanka Purkayastha
  • Unsubscribe (Fri Jul 19 2013 - 01:02:33 CDT)
  • Error in distributing the cores for a single processor (Wed Apr 10 2013 - 23:36:00 CDT)
• Purushottam Dixit
  • unsubscribe (Fri Mar 01 2013 - 11:01:44 CST)
  • unsubscribe (Sun Feb 03 2013 - 07:38:18 CST)
• Q=AF=9B=E8=BF=90=E9=93=96?=
  • Re: Non-equilibrium effects in ABF runs (Fri Aug 16 2013 - 13:28:05 CDT)
• R.J. Swett
  • Re: Force field design (Wed Jul 23 2014 - 23:03:48 CDT)
• raghav singh
  • direction of pull in namd (Tue Jan 29 2013 - 07:18:49 CST)
• Rajan Vatassery
  • Re: Minimisation problem (Thu Jul 18 2013 - 13:14:40 CDT)
  • Re: Problem with the cross term of C NH1 CT1 C NH1 CT1 C NH1 (Fri Jul 05 2013 - 14:16:59 CDT)
  • Re: AW: Minimisation of protein in a water box (Fri Apr 19 2013 - 18:18:28 CDT)
  • Re: Minimisation of protein in a water box (Mon Apr 15 2013 - 12:30:46 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)
  • Re: diffusion of protein into water box (Mon Nov 25 2013 - 02:30:39 CST)
  • Re: diffusion of protein into water box (Sun Nov 24 2013 - 08:21:04 CST)
  • diffusion of protein into water box (Sun Nov 24 2013 - 08:06:27 CST)
  • pre residues and ligands interaction (Thu Nov 21 2013 - 06:48:15 CST)
  • MM-PBSA calculation (Wed Nov 06 2013 - 02:56:43 CST)
  • get topology and parameter file for the ligand. (Wed Oct 16 2013 - 12:14:15 CDT)
  • Re: NAMD_multiprocessor (Sat Sep 28 2013 - 04:40:19 CDT)
  • Re: Insertion of GPCR in the POPC Bilayer (Fri Jun 21 2013 - 03:17:13 CDT)
  • Re: CNT coarse grain (Sat Jan 12 2013 - 03:29:59 CST)
• Ramya Gamini
  • Re: RBCG and NAMD 2.9 (Wed Apr 16 2014 - 14:49:54 CDT)
  • Re: file for fixed atoms is not found! - but the file exist actually (Fri Apr 05 2013 - 00:25:56 CDT)
• Randall Hall
  • Thermodynamic integration questions (Thu Jan 09 2014 - 12:16:03 CST)
• Randy J. Zauhar
  • Accumulating free energy change for applying colvar restraint (Mon Oct 07 2013 - 08:50:07 CDT)
  • Atom indices in collective variable definition (Fri Sep 06 2013 - 09:40:09 CDT)
• ransun
  • Re: long running sim dies (Mon Oct 13 2014 - 09:12:33 CDT)
• rasti
  • problem with ptch ... (Mon Aug 26 2013 - 15:21:36 CDT)
  • problem with using patch LINK ... (Sun Aug 25 2013 - 07:54:50 CDT)
  • problem with using patch LINK ... (Sat Aug 24 2013 - 07:50:16 CDT)
  • hi every body, (Wed Aug 21 2013 - 17:19:05 CDT)
• rasti_at_ut.ac.ir
  • (no subject) (Fri Sep 20 2013 - 05:19:37 CDT)
  • delta-G calculation (Thu Sep 19 2013 - 03:02:33 CDT)
  • making patch (Tue Aug 27 2013 - 18:41:06 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)
  • One Chain Simulation (Tue Dec 10 2013 - 11:06:10 CST)
  • NAMD Output files (Tue Apr 09 2013 - 08:02:26 CDT)
  • Re: Simulation at high pressure (Sat Mar 23 2013 - 13:45:25 CDT)
  • Simulation at high pressure (Fri Mar 22 2013 - 14:20:49 CDT)
  • Amorphous Structure code or builder (Thu Feb 28 2013 - 14:47:14 CST)
  • Simulated Annealing/ Cooling (Tue Feb 26 2013 - 09:43:32 CST)
  • Epoxy CHARMM (Thu Feb 21 2013 - 18:11:41 CST)
  • Simulated Annealing for a polymer (Mon Feb 04 2013 - 13:13:54 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)
• Rebecca Swett
  • Re: A larger protein data bank for performance benchmark (Mon May 13 2013 - 20:52:17 CDT)
  • Re: file for fixed atoms is not found! - but the file exist actually (Fri Apr 05 2013 - 09:23:54 CDT)
  • Scaling on 64 core nodes? (Thu Feb 14 2013 - 08:37:44 CST)
• Rehan Zafar
  • unsuscribe (Tue Oct 29 2013 - 11:30:35 CDT)
  • Patching protein with phosphoserine, phosphothreonine and phosphotyrosine patches (Thu Sep 12 2013 - 03:41:08 CDT)
  • DCD writing error on cluster (Sun Jun 09 2013 - 14:01:44 CDT)
• 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)
  • Re: MMPBSA-like analysis (Wed Oct 23 2013 - 01:19:40 CDT)
  • Re: MMPBSA-like analysis (Tue Oct 22 2013 - 11:12:52 CDT)
  • MMPBSA-like analysis (Tue Oct 22 2013 - 02:04:49 CDT)
  • Re: namd scale-up (Wed Sep 18 2013 - 01:16:09 CDT)
  • Re: namd scale-up (Sat Sep 14 2013 - 00:26:51 CDT)
  • Re: namd scale-up (Fri Sep 06 2013 - 01:25:53 CDT)
  • Re: namd scale-up (Thu Sep 05 2013 - 08:30:40 CDT)
  • Re: namd scale-up (Thu Sep 05 2013 - 03:47:19 CDT)
  • namd scale-up (Wed Sep 04 2013 - 02:43:24 CDT)
  • catdcd error (Mon Aug 19 2013 - 07:15:04 CDT)
  • running namd in parallel (Thu Aug 01 2013 - 23:39:02 CDT)
  • Re: vacuum minimisation-reg (Thu Jul 25 2013 - 02:40:42 CDT)
  • vacuum minimisation-reg (Wed Jul 24 2013 - 02:37:12 CDT)
  • minimization does not converge (Mon Jul 08 2013 - 11:43:27 CDT)
• Reza
  • Re: Psfgen - bonding terms involving disulfide bridges (Fri Oct 04 2013 - 09:32:46 CDT)
  • Psfgen - bonding terms involving disulfide bridges (Sun Sep 22 2013 - 22:26:33 CDT)
  • Re: PSF files and long atom name (Mon Jun 10 2013 - 19:45:48 CDT)
  • PSF files and long atom name (Sun Jun 09 2013 - 14:40:17 CDT)
• 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 Wood
  • error message (Tue Jun 03 2014 - 19:13:26 CDT)
  • Re: bilayer creation (Mon Sep 09 2013 - 15:50:18 CDT)
  • Re: bilayer creation (Mon Sep 09 2013 - 14:58:39 CDT)
  • bilayer creation (Mon Sep 09 2013 - 14:00:43 CDT)
• Riley Workman
  • PMF from ABF simulation not plateauing (Thu May 08 2014 - 12:08:13 CDT)
  • Retaining conformation (Wed Jul 17 2013 - 14:52:44 CDT)
  • (no subject) (Mon Mar 25 2013 - 15:07:09 CDT)
  • unsubscribe (Fri Mar 01 2013 - 10:59:39 CST)
  • Metadynamics pmf restart (Mon Jan 28 2013 - 12:18:48 CST)
• Robert Elder
  • Re: Replica-exchange metadynamics scripts (Thu Feb 14 2013 - 18:29:53 CST)
• 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)
• rodolfo gonzalez
  • Re: vmd-l: fftk-charges (Mon Oct 21 2013 - 01:57:55 CDT)
• Roman Shirokov
  • Re:ERROR IN TIP4P WATER SIMULATION IN NAMD2.9 (Tue Sep 03 2013 - 16:44:57 CDT)
• 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)
  • Re: Patch information for 1TUB.pdb in order to use "psfgen" (Tue Dec 10 2013 - 10:07:22 CST)
  • Re: PSF file for a metalloprotein (Mon Dec 09 2013 - 09:57:32 CST)
  • Re: Force Field Parameters for PEG (Wed Nov 06 2013 - 13:58:57 CST)
  • Force Field Parameters for PEG (Wed Nov 06 2013 - 12:21:46 CST)
  • Re: Mysterious slow down in parallel (Sat Oct 26 2013 - 22:06:49 CDT)
  • Mysterious slow down in parallel (Sat Oct 26 2013 - 10:05:13 CDT)
  • Re: Running NAMD in multiprocessor single machine (Thu Oct 17 2013 - 16:28:02 CDT)
  • Running NAMD in multiprocessor single machine (Thu Oct 17 2013 - 16:02:58 CDT)
  • Ligand in association with water (Mon Mar 25 2013 - 09:40:44 CDT)
  • Assigning Partial Charges to FE in Active Site Superoxide Dismutase. (Wed Jan 23 2013 - 13:39:04 CST)
  • Using CNS parameter file to create NAMD topology and parameter files (Wed Jan 23 2013 - 13:21:35 CST)
• 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)
• rukman kesh
  • unsubscribe (Fri Mar 01 2013 - 05:32:54 CST)
• Ryan McGreevy
  • Re: AW: Question about accelerated MD (Wed Mar 26 2014 - 11:19:17 CDT)
• Saaz Sakrikar
  • Re: Nonstandard ligand-DNA system (Tue Jun 11 2013 - 16:47:13 CDT)
  • Nucleic acid-small molecule system (Fri Jun 07 2013 - 01:45:49 CDT)
• Sadegh Faramarzi Ganjabad
  • 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)
  • HEME B PARAMETERS (Wed Oct 30 2013 - 02:30:09 CDT)
• Sagar Gore
  • MD- GPU (Thu Oct 03 2013 - 06:51:02 CDT)
• Sahu, Indra
  • Repelling extracellular regions of the protein from membrane in NAMD MD simulation (Sat Feb 09 2013 - 14:58:24 CST)
  • Repelling extracellular regions of the protein from membrane in NAMD MD simulation (Sun Feb 10 2013 - 11:43:43 CST)
• Sai Kumar Ramadugu
  • Polarizability Question! (Wed Feb 20 2013 - 11:46:06 CST)
  • Problem with psfgen for Carbohydrates (Mon Jan 28 2013 - 13:28:06 CST)
• Salvatore Mario Cosseddu
  • Citating colvars module (Tue Jan 21 2014 - 11:20:50 CST)
  • Are coordinates in the tclForces module loaded as wrapped? (Tue Apr 16 2013 - 05:12:08 CDT)
  • My calcforces does not work properly after a unknown point of the simulation. (Wed Mar 13 2013 - 15:35:11 CDT)
  • How to get cell information from within calcforces in TclForces (Fri Feb 08 2013 - 17:35:52 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)
• Sanket Avinash Deshmukh
  • Reverse coarse-graining Error: CG Builder (Fri Dec 13 2013 - 00:42:25 CST)
• Santosh Kumar Chaudhary
  • 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
  • Re: Problem with the cross term of C NH1 CT1 C NH1 CT1 C NH1 (Fri Jul 05 2013 - 14:03:08 CDT)
• Sebastián Gutiérrez
  • Nucleic acid stains parameters (Mon Aug 25 2014 - 10:37:04 CDT)
• Shaikh Abdul Rajjak
  • Building crystal polymer (Fri May 17 2013 - 00:59:09 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
  • .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)
• 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)
• sheida bagherzadeh
  • Re: bks potential (Sat Jul 06 2013 - 05:00:08 CDT)
  • bks potential (Mon Jul 01 2013 - 02:15:13 CDT)
• shivani nanda
  • unsubscribe (Sun Feb 03 2013 - 11:02:57 CST)
  • unsubscribe (Sun Feb 03 2013 - 11:02:28 CST)
• Shomesankar Bhunia
  • Re: NAMD_multiprocessor (Sat Sep 28 2013 - 03:15:11 CDT)
  • NAMD_multiprocessor (Sat Sep 28 2013 - 03:08:23 CDT)
• Shubhra Ghosh Dastidar
  • Re: Two GPU-based workstation (Tue Oct 29 2013 - 01:53:16 CDT)
  • Error while running the infiniband version. (Wed Jun 12 2013 - 07:52:36 CDT)
  • Re: problem with runiing namd through infiniband (Thu May 30 2013 - 05:15:40 CDT)
  • Re: problem with runiing namd through infiniband (Wed May 29 2013 - 07:41:47 CDT)
  • Re: problem with runiing namd through infiniband (Wed May 29 2013 - 05:13:10 CDT)
  • problem with runiing namd through infiniband (Tue May 28 2013 - 02:15:15 CDT)
  • VDW component: NAMD vs. CHARMM (Thu Apr 04 2013 - 09:20:23 CDT)
  • unsubscribe (Fri Mar 01 2013 - 03:27:30 CST)
• shunzhou Wan
  • bugs in NAMD_TI script? (Wed Jul 31 2013 - 11:57:28 CDT)
• 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)
  • Re: FEP calculations: optimizing the dlambda, number of steps (Thu Dec 12 2013 - 09:37:22 CST)
  • Re: FEP calculations: optimizing the dlambda, number of steps (Wed Dec 11 2013 - 15:37:08 CST)
  • Re: FEP calculations: optimizing the dlambda, number of steps (Wed Dec 11 2013 - 15:00:01 CST)
  • Re: FEP calculations: optimizing the dlambda, number of steps (Tue Dec 10 2013 - 10:28:10 CST)
  • Re: FEP calculations: optimizing the dlambda, number of steps (Tue Dec 03 2013 - 17:12:43 CST)
  • Re: FEP calculations: optimizing the dlambda, number of steps (Fri Nov 22 2013 - 12:09:37 CST)
  • Re: FEP calculations: optimizing the dlambda, number of steps (Fri Nov 22 2013 - 11:01:18 CST)
  • Re: FEP calculations: optimizing the dlambda, number of steps (Fri Nov 22 2013 - 10:32:44 CST)
  • Re: FEP calculations: optimizing the dlambda, number of steps (Thu Nov 21 2013 - 13:33:34 CST)
  • Re: FEP calculations: optimizing the dlambda, number of steps (Mon Nov 18 2013 - 23:21:35 CST)
  • Re: FEP calculations: optimizing the dlambda, number of steps (Mon Nov 18 2013 - 12:56:19 CST)
  • Re: FEP calculations: optimizing the dlambda, number of steps (Mon Nov 18 2013 - 11:44:59 CST)
  • FEP calculations: optimizing the dlambda, number of steps (Fri Nov 15 2013 - 14:41:13 CST)
  • FEP calculations: optimizing the dlambda, number of steps (Fri Nov 15 2013 - 15:02:06 CST)
  • Re: question about setting up FEP calculations (Thu Nov 14 2013 - 15:25:45 CST)
  • Re: question about setting up FEP calculations (Fri Nov 01 2013 - 10:14:36 CDT)
  • Re: question about setting up FEP calculations (Fri Oct 18 2013 - 11:44:41 CDT)
  • Re: question about setting up FEP calculations (Wed Oct 16 2013 - 16:21:09 CDT)
  • Re: question about setting up FEP calculations (Tue Oct 15 2013 - 11:53:12 CDT)
  • Re: question about setting up FEP calculations (Tue Oct 15 2013 - 11:21:51 CDT)
  • Re: question about setting up FEP calculations (Mon Oct 14 2013 - 20:01:48 CDT)
  • question about setting up FEP calculations (Mon Oct 14 2013 - 10:48:46 CDT)
  • Assigning atom serial number after the first 99999 atoms (Fri Aug 30 2013 - 11:07:49 CDT)
• Sijia (Scarlett) Dong
  • problem with restraining a dihedral angle (Mon Aug 12 2013 - 18:55:33 CDT)
• Sindu
  • Geometric center of a residue over time (Wed Jul 24 2013 - 05:33:32 CDT)
  • Re: AW: Bulk properties of polymers (Wed May 08 2013 - 03:46:35 CDT)
  • Re: Bulk properties of polymers (Wed May 08 2013 - 03:33:15 CDT)
  • Re: AW: Bulk properties of polymers (Wed May 08 2013 - 02:33:18 CDT)
  • Bulk properties of polymers (Tue May 07 2013 - 23:34:20 CDT)
  • Re: AW: Build polymer from monomer (Fri Apr 26 2013 - 01:22:46 CDT)
  • Build polymer from monomer (Thu Apr 25 2013 - 23:48:17 CDT)
  • Parameter file for DGEBA (Mon Mar 25 2013 - 03:56:40 CDT)
• Siri Søndergaard
  • Current bias values (Wed May 01 2013 - 20:39:50 CDT)
  • LES very slow (Mon Feb 25 2013 - 18:00:02 CST)
  • DNA terminals and charges (Tue Jan 15 2013 - 20:45:40 CST)
• 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)
• Sneha Menon
  • Switching function while using AMBER force field (Wed Jan 09 2013 - 04:03:09 CST)
• snoze pa
  • How to split large NAMD DCD file (Thu Jan 24 2013 - 10:49:58 CST)
• Sofya Lushchekina
  • Colvars keyword problem (Mon May 05 2014 - 09:32:11 CDT)
• somedatta pal
  • Re: Can protein-water electrostatic interaction be turned off keeping protein-protein (vdw+elect) and water-water (vdw+elect) interactions intact? (Thu Mar 21 2013 - 23:49:13 CDT)
  • Re: Can protein-water electrostatic interaction be turned off keeping protein-protein (vdw+elect) and water-water (vdw+elect) interactions intact? (Wed Mar 20 2013 - 00:37:21 CDT)
  • how to switch off protein-water electrostatic interaction keeping the protein-water vdw interactions intact (Tue Mar 19 2013 - 02:57:09 CDT)
  • Fwd: Can protein-water interaction be turned off keeping protein-protein and water-water interactions intact? (Tue Mar 19 2013 - 02:54:35 CDT)
  • Re: Can protein-water interaction be turned off keeping protein-protein and water-water interactions intact? (Tue Mar 19 2013 - 00:35:22 CDT)
  • Can protein-water interaction be turned off keeping protein-protein and water-water interactions intact? (Mon Mar 18 2013 - 23:58:43 CDT)
  • protein-water interactions (Mon Mar 18 2013 - 12:40:31 CDT)
• Spencer, Jacob
  • Difficulties with using the "rescalevels" command every MD timestep (Thu Jan 09 2014 - 09:48:37 CST)
• Sridhar Kumar Kannam
  • 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)
  • ABF historyFile and distFile (Thu Aug 29 2013 - 22:58:33 CDT)
  • Re: file for fixed atoms is not found! - but the file exist actually (Fri Apr 05 2013 - 01:24:44 CDT)
  • file for fixed atoms is not found! - but the file exist actually (Thu Apr 04 2013 - 21:33:52 CDT)
  • Re: NamdMemoryReduction - genCompressedPsf (Thu Apr 04 2013 - 00:24:09 CDT)
  • problem with inorganic builder genCompressedPsf (Wed Apr 03 2013 - 01:05:07 CDT)
  • Re: NamdMemoryReduction - genCompressedPsf (Wed Apr 03 2013 - 01:00:06 CDT)
  • Re: NamdMemoryReduction - genCompressedPsf (Wed Apr 03 2013 - 00:05:39 CDT)
  • Re: NamdMemoryReduction - genCompressedPsf (Thu Mar 21 2013 - 23:31:06 CDT)
  • Re: NamdMemoryReduction - genCompressedPsf (Mon Mar 11 2013 - 17:18:12 CDT)
  • NamdMemoryReduction - genCompressedPsf (Sun Mar 10 2013 - 16:10:42 CDT)
  • NamdMemoryReduction - genCompressedPsf (Thu Mar 07 2013 - 21:39:20 CST)
  • problem in solvating a graphene layer created using VMD-nanotube builder (Mon Mar 04 2013 - 21:37:15 CST)
  • topology/parameter files for biotin (Tue Feb 19 2013 - 21:27:48 CST)
• stefano pieraccini
  • Re: unsubscribe (Tue Jun 25 2013 - 09:54:47 CDT)
• Stephan Grein
  • 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)
  • Incorporating some ions with specific location (Tue Aug 13 2013 - 03:04:10 CDT)
  • Simulation of Protein with Ions (Wed Jul 03 2013 - 02:47:03 CDT)
  • C++ API (Wed Jun 19 2013 - 08:20:11 CDT)
• Stephan Matthias Grein
  • Re: Simulation of a protein and calcium ions (Wed Oct 09 2013 - 02:39:27 CDT)
  • Re: Simulation of a protein and calcium ions (Tue Oct 08 2013 - 04:49:53 CDT)
  • Simulation of a protein and ions (Tue Oct 08 2013 - 03:29:05 CDT)
  • Simulation of a protein and calcium ions (Tue Oct 08 2013 - 03:15:44 CDT)
• Steven Mike
  • Re: eigenvector colvar (Thu Aug 29 2013 - 13:24:41 CDT)
  • eigenvector colvar (Wed Aug 28 2013 - 23:14:49 CDT)
• Stober, Spencer T
  • Adaptive tempering floating point exception (Fri Oct 18 2013 - 13:21:03 CDT)
  • Adaptive tempering floating point exception (Fri Sep 27 2013 - 09:56:10 CDT)
  • Single point energy calc with gaussian/namd... log file interpretation (Fri Feb 22 2013 - 16:31:01 CST)
  • RE: Scaling problem: 4 nodes OK, 5 fails to start (Thu Jan 17 2013 - 08:31:53 CST)
  • Scaling problem: 4 nodes OK, 5 fails to start (Wed Jan 16 2013 - 13:39:08 CST)
  • Scaling problem: 4 nodes OK, 5 nodes fail (Wed Jan 16 2013 - 13:46:07 CST)
• Subbarao Kanchi
  • 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)
  • Re: cuda error (Mon Apr 08 2013 - 03:37:11 CDT)
  • Re: cuda error (Sat Mar 30 2013 - 10:53:13 CDT)
  • cuda error (Fri Mar 29 2013 - 12:36:50 CDT)
  • how to convert CHARMM TIP3P to traditional TIP3P (Wed Mar 06 2013 - 05:56:27 CST)
  • Re: question regarding interaction parameters (Thu Jan 24 2013 - 12:36:57 CST)
  • question regarding interaction parameters (Thu Jan 24 2013 - 09:52:42 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
  • CHAMBER generated .prmtop file is not compatable with namd2 (Sun Sep 15 2013 - 23:51:48 CDT)
  • MMPBSA calculation using NAMD (Wed Sep 11 2013 - 07:37:57 CDT)
• 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)
  • Re: Equilibration of the membrane-protein system done in CHARMM-GUI (Wed Nov 06 2013 - 09:29:54 CST)
  • Re: Equilibration of the membrane-protein system done in CHARMM-GUI (Wed Nov 06 2013 - 08:07:25 CST)
  • Re: Bonds in XPLOR format (Wed Oct 23 2013 - 13:28:27 CDT)
  • Re: CHARMGUI and ligands parametrisation (Tue Sep 24 2013 - 10:34:40 CDT)
  • Re: Reg Membrane Builder (Wed Sep 18 2013 - 12:26:06 CDT)
  • Re: charm-gui membrane builder (Wed Sep 11 2013 - 17:41:02 CDT)
  • Re: charm-gui membrane builder (Wed Sep 11 2013 - 13:32:58 CDT)
  • Re: charm-gui membrane builder (Sun Sep 08 2013 - 08:35:10 CDT)
  • Re: charm-gui membrane builder (Fri Sep 06 2013 - 15:13:45 CDT)
  • Re: charm-gui membrane builder (Fri Sep 06 2013 - 07:39:34 CDT)
  • Re: CHARMM-c36, glycans and RATTLE (Thu Aug 15 2013 - 09:31:26 CDT)
  • Re: CHARMM-c36, glycans and RATTLE (Thu Aug 15 2013 - 01:09:40 CDT)
  • Re: colvars and parallel-tempering with namd2.10 (Tue Aug 13 2013 - 11:17:44 CDT)
  • Re: colvars and parallel-tempering with namd2.10 (Tue Aug 13 2013 - 10:29:08 CDT)
  • Re: colvars and parallel-tempering with namd2.10 (Mon Aug 12 2013 - 10:29:23 CDT)
  • NBFIX 1-4 scaling term ignored for CHARMM format parameters (Wed Aug 07 2013 - 15:21:33 CDT)
• sunyeping
  • 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)
  • TOTLAL2, POTENTIAL abd aMD (Mon Sep 30 2013 - 03:11:43 CDT)
  • Constraint failure in RATTLE algorithm occurs during NAMD simulation with amber force field (Thu Aug 29 2013 - 21:32:22 CDT)
• sunyeping_at_aliyun.com
  • thernodynamics integration in NAMD (Sat Jul 27 2013 - 11:41:09 CDT)
• Suresh
  • Re: catdcd error (Mon Aug 19 2013 - 08:43:35 CDT)
  • Re: Link between simulations (Mon Apr 22 2013 - 01:37:00 CDT)
• suresh satpati
  • ERROR: Constraint failure in RATTLE algorithm for atom 474! (Tue Apr 09 2013 - 00:54:41 CDT)
• sutapa dutta
  • (no subject) (Fri Nov 22 2013 - 05:04:36 CST)
• Tanner, John J.
  • 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)
  • Fwd: NAMD tcouple atoms moving too fast (Thu Jun 06 2013 - 15:04:56 CDT)
  • NAMD "tCouple" option (Wed Apr 17 2013 - 15:56:54 CDT)
• Teerapong Pirojsirikul
  • code implementation based on NAMD source code (Thu May 29 2014 - 17:39:21 CDT)
  • Re: Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT (Wed Sep 18 2013 - 15:45:54 CDT)
  • Re: Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT (Wed Sep 18 2013 - 12:20:24 CDT)
  • Re: parallel code in tclforce script (Thu Sep 05 2013 - 18:48:42 CDT)
  • parallel code in tclforce script (Wed Sep 04 2013 - 22:03:15 CDT)
  • Free Energy using atomic coordinates as CVs (Thu Jul 11 2013 - 17:59:31 CDT)
  • Re: How to remove center of mass translation of macromolecule (Thu Jun 13 2013 - 20:56:29 CDT)
  • Re: How to remove center of mass translation of macromolecule (Thu Jun 13 2013 - 19:40:23 CDT)
  • Re: How to remove center of mass translation of macromolecule (Thu Jun 13 2013 - 17:38:07 CDT)
  • How to remove center of mass translation of macromolecule (Wed Jun 12 2013 - 03:05:36 CDT)
  • How to write dcd file within Tclforce script (Wed Feb 20 2013 - 17:56:31 CST)
• Thomas Albers
  • Re: PCIexpress 3.0 for MD with NAMD on GPUs (Sat Nov 16 2013 - 09:58:22 CST)
  • Nvidia GPUs (Tue Aug 20 2013 - 13:27:28 CDT)
  • Re: Preventing rotation of a protein (Thu Jul 18 2013 - 11:21:30 CDT)
  • Preventing rotation of a protein (Wed Jul 17 2013 - 21:18:16 CDT)
  • Tetraphenylphosphonium (Mon Mar 25 2013 - 12:19:31 CDT)
  • Re: FEP on an amino acid ligand (Wed Jan 23 2013 - 09:30:36 CST)
  • Re: FEP on an amino acid ligand (Wed Jan 23 2013 - 07:36:36 CST)
  • Re: FEP on an amino acid ligand (Tue Jan 22 2013 - 16:36:59 CST)
  • FEP on an amino acid ligand (Mon Jan 21 2013 - 19:44:20 CST)
• Thomas Brian
  • Re: pressure profile freezing (Wed May 22 2013 - 12:41:52 CDT)
  • pressure profile freezing (Wed May 22 2013 - 11:57:59 CDT)
  • Re: floating point reproduceability (Thu Apr 18 2013 - 23:28:31 CDT)
  • floating point reproduceability (Wed Apr 17 2013 - 17:08:34 CDT)
• Thomas C. Bishop
  • 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)
  • NAMD_2.9_Linux-x86_64-ibverbs RUNS on QueenBee RUN TIME VARIATION (Tue Nov 19 2013 - 08:06:31 CST)
  • rcmd: socket: All ports in use w/ NAMD_2.9_Linux-x86_64-ibverbs (Sun Oct 13 2013 - 22:29:51 CDT)
  • Re: Nvidia GPUs (Tue Aug 20 2013 - 14:22:10 CDT)
  • Re: free energy methods cheat-sheet/comparison chart (Mon Mar 25 2013 - 14:56:11 CDT)
  • free energy methods cheat-sheet/comparison chart (Mon Mar 25 2013 - 13:49:16 CDT)
  • Re: if{} statements (Tue Mar 05 2013 - 08:07:02 CST)
  • if{} statements (Tue Mar 05 2013 - 07:46:29 CST)
• Thomas Evangelidis
  • 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)
  • Re: About Membrane anlysis (Wed Dec 18 2013 - 10:45:52 CST)
  • membrane bilayer crosses the z axis boundaries of the box and separates into two layers (Wed Dec 11 2013 - 14:29:33 CST)
  • Re: Accelerated MD in NAMD (Thu Nov 07 2013 - 09:59:39 CST)
  • Re: Accelerated MD in NAMD (Thu Nov 07 2013 - 04:32:04 CST)
  • Re: Accelerated MD in NAMD (Wed Nov 06 2013 - 15:21:52 CST)
  • accelerated MD and External Electric Field (Tue Nov 05 2013 - 07:10:24 CST)
  • Re: Protein-ligand affinity (Tue Oct 15 2013 - 14:43:39 CDT)
  • Re: modeling missing loops in starting structures (Tue May 21 2013 - 17:12:44 CDT)
  • Re: Link between simulations (Wed Apr 24 2013 - 04:30:12 CDT)
  • Re: How to recenter a waterbox with ions around my protein? (Fri Mar 29 2013 - 08:47:33 CDT)
• thomas lemmin
  • MARTINI Bad global angle count (Mon Mar 25 2013 - 04:40:07 CDT)
• Tian Li
  • problems about new molecule parameterization (Thu Jan 30 2014 - 22:28:36 CST)
  • membrane protein simulation lipid bilayer question (Wed Oct 02 2013 - 19:48:35 CDT)
  • Margin setup (Fri Aug 30 2013 - 08:37:03 CDT)
  • Colvar cannot be ran on supercomputer newton (Tue Aug 06 2013 - 08:35:44 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)
• Tim.Ho_at_csiro.au
  • Runaway cuda-enabled namd2 processes (Tue Dec 03 2013 - 21:31:42 CST)
• Tina Stokelj
  • (no subject) (Thu Apr 11 2013 - 00:07:11 CDT)
  • unsubscribe (Sat Feb 02 2013 - 00:02:14 CST)
• Titis Sekar Humani
  • Re: AW: (Fri Feb 22 2013 - 00:57:11 CST)
  • (no subject) (Fri Feb 22 2013 - 00:05:07 CST)
• TREIKALIS Antons
  • Umbrella Sampling Replica Exchange Simulations (Sat Jul 13 2013 - 11:24:12 CDT)
• Tristan Croll
  • 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)
  • Poor scaling in NAMD simulations (Fri Nov 08 2013 - 22:11:41 CST)
  • HMMM model (Wed Oct 30 2013 - 22:51:50 CDT)
  • RE: Targeted and Steered MD: Why must the initial and targeted PDBs have identical # of atoms? (Tue Aug 27 2013 - 19:27:26 CDT)
  • General query re: symmetry restraints (Mon Aug 19 2013 - 22:33:02 CDT)
  • RE: CHARMM-c36, glycans and RATTLE (Fri Aug 16 2013 - 06:26:33 CDT)
  • RE: CHARMM-c36, glycans and RATTLE (Fri Aug 16 2013 - 05:51:17 CDT)
  • RE: CHARMM-c36, glycans and RATTLE (Thu Aug 15 2013 - 04:13:59 CDT)
  • RE: CHARMM-c36, glycans and RATTLE (Thu Aug 15 2013 - 01:23:50 CDT)
  • RE: CHARMM-c36, glycans and RATTLE (Thu Aug 15 2013 - 01:05:32 CDT)
  • CHARMM-c36, glycans and RATTLE (Wed Aug 14 2013 - 23:50:36 CDT)
  • Re: Retaining conformation (Sat Jul 20 2013 - 05:15:17 CDT)
  • RE: Minimization/Equilibrium problem, atoms moving too fast (Thu Jul 18 2013 - 21:08:02 CDT)
  • RE: Minimization/Equilibrium problem, atoms moving too fast (Thu Jul 18 2013 - 20:23:35 CDT)
  • RE: NAMD 2.9 ibverbs: Charmrun crashing on checkpoint-restart (Wed Jul 17 2013 - 19:02:25 CDT)
  • RE: NAMD 2.9 ibverbs: Charmrun crashing on checkpoint-restart (Tue Jul 16 2013 - 02:40:08 CDT)
  • RE: NAMD 2.9 ibverbs: Charmrun crashing on checkpoint-restart (Tue Jul 16 2013 - 00:59:49 CDT)
  • RE: NAMD 2.9 ibverbs: Charmrun crashing on checkpoint-restart (Tue Jul 16 2013 - 01:05:19 CDT)
  • NAMD 2.9 ibverbs: Charmrun crashing on checkpoint-restart (Tue Jul 16 2013 - 00:14:36 CDT)
• Tugba Nogay
  • pbc wrap (Fri Aug 02 2013 - 14:52:23 CDT)
• Uday Midya
  • ERROR IN TIP4P WATER SIMULATION IN NAMD2.9 (Sun Aug 11 2013 - 07:09:05 CDT)
  • ERROR IN TIP4P WATER SIMULATION IN NAMD2.9 (Sun Aug 11 2013 - 02:19:47 CDT)
• 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)
• Van Ngo
  • unsubscribe (Wed Mar 13 2013 - 18:23:14 CDT)
• Vanessa Gameiro
  • restrain noe's in random.inp (Tue Dec 03 2013 - 04:12:38 CST)
• vapour
  • Re: Phosphorylating a residue with Amber ff (Tue Dec 03 2013 - 17:29:31 CST)
• Vasumathi Velachi
  • psf generation error (Fri Mar 08 2013 - 13:26:14 CST)
• venkata agasthya
  • FEP simulation: protein moving out of water box. (Tue Nov 05 2013 - 19:39:51 CST)
  • Minimisation issue (Wed Jul 24 2013 - 15:12:06 CDT)
  • Minimisation problem (Thu Jul 18 2013 - 12:42:08 CDT)
• Vibhor Agrawal
  • Implementation of ELASTIC NETWORK model in NAMD (Fri Aug 23 2013 - 10:57:17 CDT)
  • Normal Mode Analysis in NAMD (Thu Aug 15 2013 - 09:06:09 CDT)
  • RMSD calculation (Fri Aug 02 2013 - 21:44:47 CDT)
  • Re: Problem regarding the big DCD file (Thu Jul 18 2013 - 11:42:23 CDT)
  • Problem regarding the big DCD file (Tue Jul 16 2013 - 14:07:40 CDT)
  • RE: NAMD 2.9 ibverbs: Charmrun crashing on checkpoint-restart (Tue Jul 16 2013 - 01:18:44 CDT)
  • Re: NAMD 2.9 ibverbs: Charmrun crashing on checkpoint-restart (Tue Jul 16 2013 - 00:56:33 CDT)
  • Resample trajectory files (Mon Jul 15 2013 - 15:52:58 CDT)
  • Re: Problem with the cross term of C NH1 CT1 C NH1 CT1 C NH1 (Fri Jul 05 2013 - 14:44:31 CDT)
  • Re: Problem with the cross term of C NH1 CT1 C NH1 CT1 C NH1 (Thu Jul 04 2013 - 21:28:54 CDT)
  • Problem with the cross term of C NH1 CT1 C NH1 CT1 C NH1 (Thu Jul 04 2013 - 02:31:27 CDT)
  • Re: Solvent Box (Wed Jun 26 2013 - 12:19:54 CDT)
  • Re: Insertion of GPCR in the POPC Bilayer (Fri Jun 21 2013 - 11:34:22 CDT)
  • Insertion of GPCR in the POPC Bilayer (Thu Jun 20 2013 - 15:29:20 CDT)
  • Re: Error in PSF gen (Tue Jun 18 2013 - 22:36:32 CDT)
  • Fwd: Error in PSF gen (Mon Jun 17 2013 - 11:48:27 CDT)
  • Error in PSF gen (Sat Jun 15 2013 - 21:18:13 CDT)
  • Re: Problem regarding the psfgen (Sat Jun 08 2013 - 14:17:52 CDT)
  • Re: Problem regarding the psfgen (Fri Jun 07 2013 - 15:33:38 CDT)
  • Problem regarding the psfgen (Fri Jun 07 2013 - 14:55:28 CDT)
• Victor
  • Re: editing the code of the non bonded pair potentials (Fri Aug 30 2013 - 18:19:04 CDT)
  • Re: editing the code of the non bonded pair potentials (Fri Aug 30 2013 - 14:29:58 CDT)
  • Re: problem with using patch LINK ... (Sun Aug 25 2013 - 11:28:45 CDT)
  • Re: Implementation of ELASTIC NETWORK model in NAMD (Fri Aug 23 2013 - 12:29:01 CDT)
  • Re: problem with restraining a dihedral angle (Tue Aug 13 2013 - 19:19:59 CDT)
  • Re: Basic question about impropers (Wed Jun 19 2013 - 11:29:11 CDT)
• Victor Ovchinnikov
  • Re: pmf command (Thu Jul 25 2013 - 12:56:52 CDT)
  • Re: question regarding interaction parameters (Thu Jan 24 2013 - 10:37:22 CST)
• Vidhya Sankar
  • 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)
  • About Namd Compilation (Sat Dec 28 2013 - 11:12:02 CST)
  • About Membrane anlysis (Wed Dec 18 2013 - 09:09:22 CST)
  • About Free energy tutorial for Membrane-Protein system (Sun Dec 15 2013 - 03:26:34 CST)
  • About Psfgen for cyclic peptide (Sun Nov 03 2013 - 00:08:11 CDT)
  • About Constraint Failure (Tue Oct 15 2013 - 04:57:04 CDT)
  • Re: About Usage of Topolgy and Parameter (Mon Oct 14 2013 - 08:24:20 CDT)
  • About Usage of Topolgy and Parameter (Sun Oct 13 2013 - 06:59:39 CDT)
  • Reg Lack of Lack of VDW parameters (Wed Oct 09 2013 - 10:57:58 CDT)
  • About restaring Simulation (Sat Oct 05 2013 - 02:56:01 CDT)
  • reg Parameters (Sun Sep 29 2013 - 08:35:10 CDT)
  • Reg Reading of files durin simulation (Sat Sep 28 2013 - 03:52:32 CDT)
  • Reg VDw Parameters (Fri Sep 27 2013 - 11:18:30 CDT)
  • About Muticore Linux Ibnstalltion if NAmd (Fri Sep 20 2013 - 22:50:38 CDT)
  • Regarding Membrane Builder (Fri Sep 20 2013 - 08:40:51 CDT)
  • Reg Membrane Builder (Wed Sep 18 2013 - 12:08:59 CDT)
  • About Psfgen for membrane (Wed Sep 18 2013 - 10:56:30 CDT)
  • About Namd Installation (Sun Jun 16 2013 - 00:14:04 CDT)
  • About Bond Deletion (Wed Apr 10 2013 - 22:12:33 CDT)
• Villalain Boullon, Jose
  • Membrane/peptide system. Water moving from one layer to the other ... (Wed Oct 23 2013 - 05:46:00 CDT)
  • Peptide insertion into a membrane (Thu Oct 17 2013 - 07:44:47 CDT)
  • Same NAMD files give error in Linux but not in Windows .... (Tue Oct 01 2013 - 03:49:55 CDT)
  • Organic molecule and membrane. NAMD gives fatal error: (Wed Sep 25 2013 - 08:27:59 CDT)
  • Re: Using negatively charged phospholipids and no neutralization, membrane expands in the xy direction ....... (Thu Jul 25 2013 - 05:52:05 CDT)
  • Using negatively charged phopspholipids and no neutralization, membrane expands in the xy direction ....... (Wed Jul 24 2013 - 03:37:20 CDT)
• Vince Cho
  • Distance Constraints in ABF Simulation (Wed Dec 25 2013 - 05:31:26 CST)
• Viswanath Pasumarthi
  • 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
  • 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)
  • inconsistency between "Benchmark" and "Timing" output (Mon Nov 25 2013 - 09:08:58 CST)
• Vlastimil Zíma
  • 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)
  • Re: NAMD CUDA performance (Wed Sep 11 2013 - 04:04:08 CDT)
  • NAMD CUDA performance (Tue Sep 10 2013 - 07:59:41 CDT)
  • Namd and CUDA on Debian Wheezy (Tue Feb 12 2013 - 07:11:38 CST)
• Walter Rocchia
  • Computational Electrostatics for Biological Application (CEBA'13) - July 1-3 2013 - Genoa - Italy (Fri Apr 19 2013 - 04:59:23 CDT)
• Wang
  • not fatal error but no more information (Thu Apr 04 2013 - 13:50:17 CDT)
• Wasut Pornpatcharapong
  • Questions on calling external program to calculate force with NAMD (Mon Feb 10 2014 - 15:41:48 CST)
• Wenhao Liu
  • Basic question about impropers (Tue Jun 18 2013 - 18:30:12 CDT)
• Wesley Lay
  • *** glibc detected *** namd2: invalid fastbin entry (free) (Thu May 22 2014 - 15:19:11 CDT)
• Wonpil Im
  • Re: Inquiry about lipid membrane simulation (Wed Jun 18 2014 - 14:53:31 CDT)
• XAvier Periole
  • Re: Martini 2.2 and ElNeDyn in NAMD (Thu Jul 18 2013 - 03:30:00 CDT)
  • Martini 2.2 and ElNeDyn in NAMD (Wed Jul 03 2013 - 12:29:16 CDT)
• Xiaodong Pang
  • Evaluate energy of "protein + two closest ions" (Tue Aug 06 2013 - 17:25:45 CDT)
• Xingcheng Lin
  • Method for solvation of protein (Mon Oct 21 2013 - 15:45:16 CDT)
  • Simulation results from NVT has a cavity (Sat Oct 19 2013 - 13:49:12 CDT)
  • Pass a runtime parameter into the configuration file (Tue Oct 15 2013 - 17:55:48 CDT)
  • NAMD simulation with flag similar to -maxh in Gromacs (Tue Oct 15 2013 - 11:30:49 CDT)
• Yan Zhou
  • INCONSISTENCY messages and minimization in toturial 1-2-sphere (Wed Sep 03 2014 - 03:14:30 CDT)
• Yarrow Madrona
  • Re: restart files not written. (Fri May 10 2013 - 14:11:00 CDT)
  • restart files not written. (Thu May 09 2013 - 19:25:57 CDT)
  • HEME acting unplanar (Sun Apr 21 2013 - 17:48:43 CDT)
  • Adding HEME parameters (Sat Mar 09 2013 - 17:54:03 CST)
• Yi Wang, PhD
  • Re: delta-G calculation (Thu Sep 19 2013 - 03:08:28 CDT)
  • Re: Insertion of GPCR in the POPC Bilayer (Thu Jun 20 2013 - 21:09:03 CDT)
  • Re: smd force is too high (Mon Mar 18 2013 - 20:07:26 CDT)
  • Re: smd force is too high (Sat Mar 16 2013 - 09:35:44 CDT)
  • Re: problem in solvating a graphene layer created using VMD-nanotube builder (Mon Mar 04 2013 - 22:10:47 CST)
• Yihua Zhou
  • unsubscribe (Mon Mar 04 2013 - 11:18:09 CST)
• Yize Hu
  • Re: A fancy problem in calculating the protonated glutamic acid modelled by adding the patch of GLUP (Sat Jun 01 2013 - 03:17:27 CDT)
  • A fancy problem in calculating the protonated glutamic acid modelled by adding the patch of GLUP (Fri May 31 2013 - 10:20:52 CDT)
• Yongcheng Zhou
  • 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)
• yp sun
  • multiple vectors in SMD (Mon Jun 10 2013 - 22:35:50 CDT)
  • binding free energy calculation (Sun Apr 21 2013 - 07:42:52 CDT)
  • Calculate binding free energy (Sun Feb 24 2013 - 19:22:08 CST)
• Z
  • 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)
• Zachary Ulissi
  • ABF simulations with barriers (adsorption) (Mon Jun 10 2013 - 12:26:49 CDT)
• Zack Scholl
  • Biotin force field (Thu Oct 03 2013 - 10:44:25 CDT)
• Zailo Leite
  • unsubscribe (Fri Feb 14 2014 - 11:20:04 CST)
• Zeinab Emami
  • 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)
• zhangxing
  • How to apply Symmetry boundary on NAMD (Tue Nov 19 2013 - 17:52:50 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)
  • Re: Sutton-Chen potential (Mon Apr 01 2013 - 22:09:28 CDT)
  • Sutton-Chen potential (Mon Apr 01 2013 - 03:30:55 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)
• Zumot, Elia Nabil
  • RE: NAMD on Stampede (Wed Feb 27 2013 - 14:15:51 CST)
  • RE: transmembrane protein simulation - hydrophobic thickness and NAMD membrane plugin (Mon Feb 18 2013 - 11:49:35 CST)
• º«À×
  • Unsubscribe (Thu Jul 18 2013 - 18:42:07 CDT)
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• 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)
  • Re: How to setting tilt component in colvars module (Mon Sep 23 2013 - 22:54:26 CDT)
  • How to setting tilt component in colvars module (Mon Sep 23 2013 - 01:21:35 CDT)
  • creating coarse grain model with martini force field (Mon Sep 02 2013 - 01:58:10 CDT)
  • Potential of mean force calculation using colvars in NADM 2.9 package (Thu May 16 2013 - 02:06:53 CDT)
• ¼Û ¿¬È£
  • I have a question about pair interaction energy calculations. (Wed Oct 30 2013 - 02:14:32 CDT)
• ½ùÏþ½Ü
  • a problem about pbc in a namd trajectory (Mon Aug 26 2013 - 02:44:23 CDT)
• ¬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)
• ÂÀСӨ
  • the difference of PCA and EDA (Wed Dec 10 2014 - 02:31:30 CST)
  • pThr topology (Tue Feb 18 2014 - 21:05:27 CST)
• 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)
• ç¿�æž—å²½
  • 回å¤�： Shift (or offset) of the lipid bilayer along Z axis during equilibration (Fri Jun 07 2013 - 21:30:12 CDT)
  • Shift (or offset) of the lipid bilayer along Z axis during equilibration (Fri Jun 07 2013 - 20:36:44 CDT)
  • negative VdW energy and Elect energy (Tue Apr 30 2013 - 20:50:17 CDT)
• Ð�лекÑ�андр Северюхин
  • Unsubscribe (Thu Apr 11 2013 - 01:45:51 CDT)
• ÕÔÀöÄÈ
  • Can I define a simulation box but turn off the PBC at the same time? (Thu May 09 2013 - 03:49:48 CDT)
• ÖÜêÇêÀ
  • Re: 50% system CPU usage when parallel running NAMD on Rocks cluster (Wed Dec 18 2013 - 06:43:18 CST)
  • Re: 50% system CPU usage when parallel running NAMD on Rocks cluster (Tue Dec 17 2013 - 08:12:33 CST)
  • Re: 50% system CPU usage when parallel running NAMD on Rocks cluster (Sat Dec 14 2013 - 07:55:47 CST)
  • Re: 50% system CPU usage when parallel running NAMD on Rocks cluster (Tue Dec 10 2013 - 06:51:31 CST)
  • Re: 50% system CPU usage when parallel running NAMD on Rocks cluster (Sun Dec 08 2013 - 09:11:31 CST)
  • 50% system CPU usage when parallel running NAMD on Rocks cluster (Sat Nov 30 2013 - 21:06:18 CST)
  • 50% system CPU usage when parallel running NAMD on Rocks cluster (Tue Dec 03 2013 - 07:43:07 CST)