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NAMD-L: By Author

By Author

2588 messages sorted by: [ date ] [ thread ] [ subject ] [ attachment ]
About this archive

Starting: Sat Jan 02 2016 - 22:55:30 CST
Ending: Sat Dec 30 2017 - 12:48:03 CST

• #YEO JINGJIE#
  • Compilation of NAMD for CUDA and replica exchange (Fri Apr 29 2016 - 13:53:44 CDT)
• 'Patrick Welche'
  • Re: velocity computation (Mon Feb 08 2016 - 08:34:19 CST)
• Abhaysinh Gaikwad
  • RMSD colvar not working in NAMD2.12 Linux version (Tue Nov 07 2017 - 21:46:28 CST)
  • Re: Constraining and imparting motion to a geometry (Thu Sep 07 2017 - 14:35:01 CDT)
  • Constraining and imparting motion to a geometry (Fri Sep 01 2017 - 14:47:21 CDT)
  • Re: Steered Molecular Dynamics (Tue Aug 29 2017 - 10:25:19 CDT)
  • Steered Molecular Dynamics (Thu Aug 24 2017 - 13:28:49 CDT)
• Abhishek Kumar Singh
  • Re: Solvation free energy difference of alchemical transformation of K+ into Na+ (Wed Jan 11 2017 - 00:39:11 CST)
  • Solvation free energy difference of alchemical transformation of K+ into Na+ (Tue Jan 10 2017 - 05:09:01 CST)
  • Solvation free energy difference of alchemical transformation of K+ into Na+ (Mon Jan 09 2017 - 00:09:32 CST)
  • Solvation free energy difference of alchemical transformation of K+ into Na+ (Sun Jan 08 2017 - 22:12:34 CST)
• Abhishek TYAGI
  • Re: namd-l digest V1 #2289 (Wed Oct 25 2017 - 05:42:24 CDT)
  • Re: FATAL ERROR: cuda_check_progress polled 1000000 times over ... (Tue Oct 24 2017 - 06:42:32 CDT)
  • Re: Modifying the equilibrium distance for a specific region of carbon nanotube in the parameter file (Mon Dec 26 2016 - 08:59:58 CST)
  • Re: NAMD How to calculate ns/day (Thu Dec 08 2016 - 01:38:04 CST)
  • Re: Problem with minimization (Thu Oct 27 2016 - 06:13:10 CDT)
  • Re: Query regarding parameter file generation of non standard residue (Thu Sep 08 2016 - 06:37:37 CDT)
  • Re: Adsorption energy of protein in vacuum (Mon May 23 2016 - 19:52:56 CDT)
  • Re: Adsorption energy of protein in vacuum (Sun May 22 2016 - 22:46:38 CDT)
  • Re: (Sat May 07 2016 - 07:45:54 CDT)
  • Re: Replica Exchange US, Colvar suggestion (Sat Feb 13 2016 - 22:39:29 CST)
  • Replica Exchange US, Colvar suggestion (Sat Feb 13 2016 - 01:07:38 CST)
  • Re: Enabling GPU for Replica exchange umbrella sampling (Mon Jan 25 2016 - 01:49:23 CST)
  • Re: Enabling GPU for Replica exchange umbrella sampling (Sat Jan 23 2016 - 13:05:26 CST)
  • Re: Enabling GPU for Replica exchange umbrella sampling (Thu Jan 21 2016 - 22:02:59 CST)
  • Enabling GPU for REUS (Wed Jan 20 2016 - 21:12:50 CST)
• Abraham A. Gutierrez Hernandez
  • FATAL ERROR CUDA error during equilibration using NAMD (Tue Aug 30 2016 - 18:27:38 CDT)
• Adrien Cerdan
  • SMP instructions for multi-node calculation on POWER 8 + P100 (Wed Nov 22 2017 - 10:09:51 CST)
• Ahmad Kiani Karanji
  • RATTLE error with lipid bilayer system (Tue Nov 21 2017 - 13:08:46 CST)
• Ajasja LjubetiÄ�
  • Re: displacement of protein (Fri Sep 22 2017 - 02:29:00 CDT)
  • Re: No minimized system after running minimization in NAMD (Thu Sep 07 2017 - 09:38:18 CDT)
  • Re: Coarse Grain of a Calcium Binding Protein (Wed Aug 09 2017 - 10:51:34 CDT)
  • Re: Simulating SDS molecules (Fri Jun 30 2017 - 09:20:08 CDT)
  • Re: restraining selected atom's z coordinates (Sun May 14 2017 - 01:51:03 CDT)
  • Re: [NAMD] Problem with colvar "tilt" (Fri May 12 2017 - 13:41:54 CDT)
  • Re: NAMD-2.12 handful of issues with CUDA (Fri Mar 10 2017 - 05:14:10 CST)
  • Re: colvars: Error: Feature unavailable:compute total collective force only from one group center (Thu Feb 23 2017 - 01:36:03 CST)
  • Re: multiple replicas metadynamics (Mon Jan 09 2017 - 23:55:38 CST)
  • Re: not a number error (Mon Jan 09 2017 - 07:39:15 CST)
  • Re: Re: Re: RMSD based PMF calculation with umbrella sampling (Fri Dec 30 2016 - 10:46:39 CST)
  • Re: Returning energy values from .log file. (Thu Dec 08 2016 - 02:30:28 CST)
  • Re: NAMD How to calculate ns/day (Wed Dec 07 2016 - 16:59:45 CST)
  • Re: Returning energy values from .log file. (Wed Dec 07 2016 - 14:41:54 CST)
  • Re: A common tool to read the output of NAMD run (Mon Nov 28 2016 - 08:34:47 CST)
  • Re: Minimization failing on one machine only (Sat Oct 15 2016 - 01:50:29 CDT)
  • Re: Gradual Heating Periodic Error (Tue Sep 13 2016 - 09:15:38 CDT)
  • Re: Energy minimization in NAMD (Tue Aug 09 2016 - 11:27:41 CDT)
  • Re: Energy minimization in NAMD (Tue Aug 09 2016 - 04:24:08 CDT)
  • Re: Energy minimization in NAMD (Mon Aug 08 2016 - 15:54:58 CDT)
  • Re: How to replace NAMD Eletrostatic Forces (Fri Aug 05 2016 - 02:46:00 CDT)
  • Re: Equilibration and production run (Mon May 16 2016 - 03:23:29 CDT)
  • Re: size of water box and cellbasisvectors (Wed Mar 30 2016 - 08:08:14 CDT)
  • NAMD 2.11 CUDA freezes on windows 8 (Wed Mar 16 2016 - 13:08:59 CDT)
  • Re: installing NAMD 2.11 (Wed Mar 09 2016 - 07:38:39 CST)
  • Re: applying constant force only within certain part of simulation cell? (Thu Mar 03 2016 - 15:27:35 CST)
  • Re: PBC in lipid bilayer: receptor vs. ligand (Wed Jan 27 2016 - 09:21:11 CST)
  • Re: (Wed Jan 27 2016 - 03:39:04 CST)
• Akshay Bhatnagar
  • Equilibration using NPT and Production run using NVE ensemble (Thu Apr 27 2017 - 07:47:29 CDT)
  • is NVE ensemble for production run justified? (Tue Mar 21 2017 - 00:13:19 CDT)
  • Re: (Fri Apr 22 2016 - 02:30:13 CDT)
• Albers, Thomas
  • minimum CUDA compute capability required for NAMD2.12 (Sat Sep 23 2017 - 16:03:24 CDT)
  • ABF for dihedrals (Thu Aug 03 2017 - 12:48:24 CDT)
• Alexander Adams
  • PACE CG Model (Fri Jul 28 2017 - 12:53:24 CDT)
  • NAMD on UCSD Comet (Mon Jul 03 2017 - 13:26:48 CDT)
• Ali Khanlarkhani
  • Introducing PDBManip (Tue Aug 16 2016 - 10:10:05 CDT)
• Aliasghar Alizadeh-Mojarad
  • Re: Having problem with restarting colvar distance, (Fri Dec 29 2017 - 14:46:29 CST)
  • Having problem with restarting colvar distance, (Fri Dec 29 2017 - 02:10:07 CST)
  • Re: REMD using NAMD 2.13 (Wed Nov 22 2017 - 17:14:40 CST)
  • Re: REMD using NAMD 2.13 (Sat Nov 18 2017 - 18:03:41 CST)
  • REMD using NAMD 2.13 (Fri Nov 17 2017 - 18:02:46 CST)
  • much larger diameter of ssDNA, (Sat Jun 04 2016 - 04:22:41 CDT)
• Allen, Caley R
  • RE: SMD restraints (Tue Nov 15 2016 - 13:30:17 CST)
  • SMD restraints (Mon Nov 14 2016 - 15:14:09 CST)
  • Re: Fatal Error: vdw atom type CC3161 (Wed Aug 03 2016 - 13:46:17 CDT)
  • Fatal Error: vdw atom type CC3161 (Wed Aug 03 2016 - 09:53:37 CDT)
  • Re: SMD Constant velocity pulling (Wed Jul 27 2016 - 13:38:19 CDT)
  • group selection in TCL script for use in NAMD (Wed Jul 27 2016 - 13:35:05 CDT)
  • Re: TCL Scripting for Force Calculations (Mon May 02 2016 - 14:08:17 CDT)
  • TCL Scripting for Force Calculations (Mon May 02 2016 - 10:48:56 CDT)
• Allison, Jane
  • PhD and postdoctoral positions in biomolecular simulation (Thu Jan 07 2016 - 19:01:29 CST)
• Amali Guruge
  • Using Gromacs topology in NAMD (Sun Nov 12 2017 - 22:19:43 CST)
  • Re: Psf file generation with Gromacs Parameters (Thu Nov 09 2017 - 19:45:28 CST)
  • NAMD job termination (Wed Nov 08 2017 - 21:01:25 CST)
  • Re: Psf file generation with Gromacs Parameters (Wed Nov 08 2017 - 17:17:14 CST)
  • Psf file generation with Gromacs Parameters (Mon Nov 06 2017 - 19:53:58 CST)
  • Some water molecules are missing in psf (Thu Nov 02 2017 - 17:33:06 CDT)
• amit kumar
  • FAD parameter and topology files (Tue Sep 19 2017 - 23:12:39 CDT)
  • Regarding: Free energy of alchemical transformation of K + and Na + (Fri Jan 06 2017 - 05:09:35 CST)
  • Regarding Trajectory files (Sun Dec 25 2016 - 23:18:26 CST)
• Amy Rice
  • Re: Pulling protein through membrane without changing the position of membrane (Thu May 11 2017 - 12:05:37 CDT)
  • Problem with alpha colvar in NAMD 2.12b1 (Thu Dec 08 2016 - 15:23:16 CST)
  • Re: ion escapes the channel during US simulation (Wed Aug 31 2016 - 10:40:16 CDT)
  • Re: Dynamics of an interface Water/Hexane (Wed Apr 13 2016 - 11:32:09 CDT)
• Ana Celia Vila Verde
  • Re: The use of NPT or NVT ensemble to observe dynamical parameters (Mon Jan 02 2017 - 04:13:20 CST)
  • Re: Half of the structure goes out of the simulation box! (Fri Sep 30 2016 - 07:31:03 CDT)
  • Re: Adsorption energy of protein in vacuum (Sat May 21 2016 - 04:17:54 CDT)
  • Re: How to use a proper force constant to decrease computational cost while keeping calculation precision? (Wed Apr 20 2016 - 03:03:08 CDT)
  • Re: LJ Parameters for Au and S and harmonic constraints (Fri Apr 08 2016 - 02:55:45 CDT)
  • Re: restart a job (Thu Apr 07 2016 - 02:43:32 CDT)
  • Re: water box has a weird shape (Thu Apr 07 2016 - 02:40:47 CDT)
• Andrey KALINICHEV
  • Re: AW: High pressure calculations (Sat Feb 04 2017 - 05:54:36 CST)
• Angelo Rossi
  • Re: Hybrid QM/MM NAMD: Problem Reading Extended psf files -- But some good news too (Wed Apr 26 2017 - 11:00:24 CDT)
  • Hybrid QM/MM NAMD: Problem Reading Extended psf files -- But some good news too (Wed Apr 26 2017 - 08:06:03 CDT)
  • NAMD 2.12 released (Mon Dec 26 2016 - 15:53:42 CST)
• Aron Broom
  • Re: Energy minimization (Tue Aug 16 2016 - 09:57:04 CDT)
  • Re: Generalized Born solvation models supported by NAMD (Tue Aug 02 2016 - 09:41:09 CDT)
  • Re: Generalized Born solvation models supported by NAMD (Fri Jul 29 2016 - 14:24:21 CDT)
  • Re: Generalized Born solvation models supported by NAMD (Fri Jul 29 2016 - 12:25:49 CDT)
  • Re: Generalized Born solvation models supported by NAMD (Fri Jul 29 2016 - 10:55:51 CDT)
  • Re: PMF with ABF for ion channels in a spherical molecule (Fri Jul 01 2016 - 18:42:21 CDT)
  • Re: PMF with ABF for ion channels in a spherical molecule (Tue Jun 28 2016 - 16:37:49 CDT)
  • Re: PMF with ABF for ion channels in a spherical molecule (Tue Jun 28 2016 - 15:57:14 CDT)
  • Re: PMF with ABF for ion channels in a spherical molecule (Sun Jun 26 2016 - 15:13:36 CDT)
  • Re: Tesla K80 vs 3 x GTX 980Ti (Sun Jun 26 2016 - 15:07:13 CDT)
  • Re: water box has a weird shape (Wed Apr 06 2016 - 13:41:04 CDT)
  • Re: maximum coordinate is negative for z (Fri Apr 01 2016 - 12:16:52 CDT)
• arpita agarwal
  • Re: Replica exchange (Fri Apr 22 2016 - 02:54:50 CDT)
  • Replica exchange (Thu Apr 21 2016 - 00:43:44 CDT)
  • Regarding Bionanotechnology tutorial (Wed Apr 13 2016 - 20:07:26 CDT)
• Art
  • Re: tclBC relective boundaries (Fri Jan 29 2016 - 17:27:02 CST)
  • tclBC relective boundaries (Fri Jan 29 2016 - 13:51:17 CST)
• Arthur Oliveira Vale
  • RE: REG Protein inserion in to membrane bi layear (Thu Jun 22 2017 - 10:27:47 CDT)
  • Simulating Protein Entering membrane (Sun Jun 18 2017 - 20:14:32 CDT)
• Arthur Vale
  • Simulating Protein/Membrane interface with pre-equiliibrated lipid bilayer (Wed Aug 23 2017 - 18:58:59 CDT)
  • FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CG321 CTL3 (ATOMS 8773 8776) (Thu Jul 20 2017 - 20:08:28 CDT)
• asaffarhi_at_post.tau.ac.il
  • introduction to research on free energies (Fri Jan 20 2017 - 09:34:05 CST)
• ashika torikora
  • Should you cap C and N termini? (Thu Feb 18 2016 - 07:09:10 CST)
• Atanu Maity
  • Re: atom selection error (Mon Dec 11 2017 - 08:30:55 CST)
  • NAMD Acceleration using P100 (GP-GPU) accelerator (Tue Feb 07 2017 - 03:25:52 CST)
  • K40 benchmark problem in NAMD (Thu Nov 17 2016 - 01:27:04 CST)
  • GPU acceleration using K40 and k80 (Wed Sep 14 2016 - 00:32:00 CDT)
  • Re: Restart multiple walker ABF (Mon May 23 2016 - 01:13:10 CDT)
  • Re: Restart multiple walker ABF (Sun May 22 2016 - 23:55:32 CDT)
  • Re: Restart multiple walker ABF (Thu May 19 2016 - 03:36:30 CDT)
  • Restart multiple walker ABF (Thu May 19 2016 - 03:32:24 CDT)
• Athreya, Nagendra Bala Murali
  • Multiple Electric Field simulation (Wed Mar 01 2017 - 15:13:37 CST)
  • DNA not translocating under electric field (Wed Nov 30 2016 - 21:20:55 CST)
• Atsutoshi Okabe
  • About parseFEP error (Wed Feb 03 2016 - 08:01:21 CST)
• Axel Kohlmeyer
  • Re: NAMD with multiple molecules (Thu Aug 17 2017 - 10:15:15 CDT)
  • Re: Questions on implementing new collective variable in colvars. (Mon Jun 12 2017 - 22:38:48 CDT)
  • Re: NVE simulations in NAMD - the right choice of timesteps and parameters (Tue Nov 29 2016 - 10:16:11 CST)
  • Re: NAMD breaks with wrong timestep (Fri Oct 21 2016 - 10:54:00 CDT)
  • Re: mail reg compilation of mdenergy (Wed Oct 19 2016 - 14:27:04 CDT)
  • Re: convert .xyz file in .psf file for non-protein molecule (Thu Sep 08 2016 - 10:41:07 CDT)
  • Re: Equivalent of gromacs' "rdd" option (Mon Jul 25 2016 - 10:16:08 CDT)
  • Re: LJ parameters for Pd surface (Fri May 06 2016 - 08:36:59 CDT)
  • Re: Running a test simulation using GPU only (without any CPU core) (Thu Apr 28 2016 - 10:40:38 CDT)
  • Re: Opinions on Haptic Feedback Devices with NAMD/VMD (Fri Mar 25 2016 - 08:52:33 CDT)
• Azadeh Alavi
  • Re: Metadynamics simulation (Thu Jan 05 2017 - 06:39:34 CST)
  • Metadynamics simulation (Tue Jan 03 2017 - 09:00:43 CST)
  • Re: PMF decompostion (Mon Sep 12 2016 - 13:34:22 CDT)
  • PMF decompostion (Mon Sep 12 2016 - 06:49:50 CDT)
  • NBFIX parameters for Calcium ion (Thu Jun 09 2016 - 04:49:04 CDT)
  • Re: segmentation fault in ABF simulations (Mon Jan 25 2016 - 12:31:10 CST)
  • Re: segmentation fault in ABF simulations (Mon Jan 25 2016 - 12:11:58 CST)
  • Re: segmentation fault in ABF simulations (Mon Jan 25 2016 - 11:00:26 CST)
  • segmentation fault in ABF simulations (Mon Jan 25 2016 - 07:58:49 CST)
• Azadeh Alavizargar
  • Bias-exchange metadynamics (Fri Nov 17 2017 - 05:07:56 CST)
  • Re: Colvar distance xy to restrain ions (Fri Jan 13 2017 - 15:00:16 CST)
  • Re: Colvar distance xy to restrain ions (Thu Jan 12 2017 - 04:30:42 CST)
  • Colvar distance xy to restrain ions (Thu Jan 12 2017 - 02:42:25 CST)
• B.W.J. Irwin
  • Re: Solvation free energy difference of alchemical transformation of K+ into Na+ (Tue Jan 10 2017 - 09:09:52 CST)
  • Re: Regarding: Free energy of alchemical transformation of K + and Na + (Fri Jan 06 2017 - 08:50:24 CST)
  • Re: Low global exclusion count error (Fri Dec 02 2016 - 04:43:49 CST)
  • RE: Is it possible to perform NVT FEP on a fluid system? (Tue Aug 09 2016 - 11:23:58 CDT)
  • Is it possible to perform NVT FEP on a fluid system? (Tue Aug 09 2016 - 05:22:08 CDT)
• Bala subramanian
  • Re: query on OuputTotalforce Vs OnesiteTotal force ? (Wed Nov 30 2016 - 07:39:14 CST)
  • query on OuputTotalforce Vs OnesiteTotal force ? (Tue Nov 29 2016 - 09:39:39 CST)
  • Query on colvar distanceZ (Sat Nov 19 2016 - 08:18:57 CST)
• Bassam Haddad
  • Re: Which NAMD-Build for my local HPC? (Tue Oct 31 2017 - 15:50:19 CDT)
  • Which NAMD-Build for my local HPC? (Tue Oct 31 2017 - 13:34:12 CDT)
  • Re: Steered Molecular Dynamics (Fri Aug 25 2017 - 12:38:14 CDT)
  • Re: two stage equilibration in single configuration file (Thu Aug 03 2017 - 12:29:53 CDT)
  • Re: namd 2.12 and plumed 2.3 (Wed Apr 26 2017 - 10:48:55 CDT)
  • Best NAMD distribution for COEUS cluster? (Thu Apr 13 2017 - 15:27:10 CDT)
• Bata Zsófia
  • Amber force filed input failure on GPU (Wed Oct 25 2017 - 10:40:06 CDT)
• bay__gulf618_at_sina.com
  • Re: Lennard-Jones potential in coarse grained MD (Sat Jan 30 2016 - 01:19:17 CST)
  • »Ø¸´: about User-Defined Forces (Mon Jan 18 2016 - 05:23:00 CST)
• Ben Adams
  • Define a colvar from other colvars (Thu Dec 14 2017 - 13:50:29 CST)
  • Re: problem with minimization and calculation of force on a fixed atom (Fri Sep 01 2017 - 11:01:49 CDT)
  • Re: problem with minimization and calculation of force on a fixed atom (Fri Sep 01 2017 - 10:36:21 CDT)
  • problem with minimization and calculation of force on a fixed atom (Thu Aug 31 2017 - 17:03:21 CDT)
  • Re: extracting force on a single atom (Thu Aug 31 2017 - 10:11:19 CDT)
  • Re: extracting force on a single atom (Thu Aug 31 2017 - 10:03:04 CDT)
  • Re: extracting force on a single atom (Thu Aug 31 2017 - 08:38:05 CDT)
  • extracting force on a single atom (Wed Aug 30 2017 - 19:18:49 CDT)
• Ben Fritch
  • Opinions on Haptic Feedback Devices with NAMD/VMD (Fri Mar 25 2016 - 08:37:31 CDT)
  • Opinions on Haptic Feedback Devices with NAMD/VMD (Thu Mar 24 2016 - 14:29:02 CDT)
• Ben Lowe
  • Re: Calculating electrostatic force from NAMD trajectory (Fri Jul 07 2017 - 02:14:30 CDT)
  • Calculating electrostatic force from NAMD trajectory (Mon Jul 03 2017 - 21:35:50 CDT)
  • Selecting atoms in NAMD .conf file and time-varying electric field (Wed Mar 01 2017 - 15:42:55 CST)
• Benjamin Brown
  • PME vs. cutoff with switching function (Fri Jun 17 2016 - 10:25:44 CDT)
• Benjamin Hill
  • ATP - CGENFF (Tue Jun 07 2016 - 19:34:15 CDT)
  • cgenff (Mon Jun 06 2016 - 14:48:30 CDT)
  • Re: No parameter for ribose ring, Charmm 27 (Sun May 29 2016 - 11:12:07 CDT)
  • Re: No parameter for ribose ring, Charmm 27 (Fri May 27 2016 - 05:51:40 CDT)
  • No parameter for ribose ring, Charmm 27 (Thu May 26 2016 - 17:18:43 CDT)
• Benjamin Rousseau
  • Proper combination of langevinHydrogen with rigidbonds (Thu Aug 31 2017 - 10:31:31 CDT)
• Benjamin.Haberl_at_physik.uni-muenchen.de
  • MDFF with two symmetry groups (Tue May 17 2016 - 14:48:19 CDT)
• Bennion, Brian
  • RE: Concatenating log files (Wed Sep 06 2017 - 11:50:53 CDT)
  • RE: performance of NAMD SMP MPI version (Thu May 25 2017 - 13:45:13 CDT)
  • RE: MPIRUN SLURM SCRIPT (Tue May 09 2017 - 13:07:08 CDT)
  • Re: Slurm Script for Multi Node Run (Mon Apr 17 2017 - 11:52:58 CDT)
  • RE: Specify number of water molecules:simulation set up in VMD (Fri Mar 10 2017 - 13:34:56 CST)
  • Re: colvars: Error: Feature unavailable:compute total collective force only from one group center (Mon Feb 27 2017 - 17:36:53 CST)
  • Re: colvars: Error: Feature unavailable:compute total collective force only from one group center (Fri Feb 24 2017 - 10:33:28 CST)
  • RE: colvars: Error: Feature unavailable:compute total collective force only from one group center (Thu Feb 23 2017 - 14:58:54 CST)
  • RE: colvars: Error: Feature unavailable:compute total collective force only from one group center (Thu Feb 23 2017 - 14:35:22 CST)
  • Re: colvars: Error: Feature unavailable:compute total collective force only from one group center (Thu Feb 23 2017 - 10:38:39 CST)
  • colvars: Error: Feature unavailable:compute total collective force only from one group center (Wed Feb 22 2017 - 18:17:44 CST)
  • Re: PDB file creation (Wed Feb 08 2017 - 11:23:57 CST)
  • RE: Query regarding parameter file generation of non standard residue (Thu Sep 08 2016 - 11:07:13 CDT)
  • download stmv files for benchmarking (Wed Jun 01 2016 - 14:29:22 CDT)
  • RE: Constraint failure in RATTLE algorithm for atom 6! (Tue Apr 26 2016 - 16:29:09 CDT)
• Benz, Max
  • NAMD with multiple molecules (Thu Aug 17 2017 - 10:09:17 CDT)
• Bhati, Agastya
  • Re: Implementation of sortreplicas executable for restarted REST2 simulations (Thu Oct 12 2017 - 09:00:27 CDT)
  • Re: Implementation of sortreplicas executable for restarted REST2 simulations (Thu Oct 12 2017 - 06:50:40 CDT)
  • Re: Implementation of sortreplicas executable for restarted REST2 simulations (Wed Oct 11 2017 - 14:50:46 CDT)
  • REST2 simulations: Corecting shifted dcd files! (Wed Oct 11 2017 - 14:36:14 CDT)
  • Implementation of sortreplicas executable for restarted REST2 simulations (Wed Oct 11 2017 - 14:12:44 CDT)
• Bob Faith
  • Defining colvars based on a region (Mon Mar 20 2017 - 19:48:00 CDT)
• Bogdan Marekha
  • Re: Define a colvar from other colvars (Thu Dec 14 2017 - 14:53:11 CST)
  • Periodic molecules in NAMD (Wed Dec 13 2017 - 05:13:54 CST)
  • Re: colvars/rmsd: Error: definition for atom group "atoms" not found. (Sun Dec 03 2017 - 06:35:28 CST)
  • nan for Drude's LP in distance-like colvars (Fri Nov 24 2017 - 10:44:01 CST)
• Boonstra, S.
  • Re: CHARMRUN ERROR (Thu May 11 2017 - 15:03:38 CDT)
  • Re: Type of solvent water molecules (Wed Apr 19 2017 - 05:20:31 CDT)
  • Re: Scaling behaviour of NAMD on hosts with GPU accelrators (Fri Mar 24 2017 - 06:41:19 CDT)
  • CPU/GPU energy difference (Mon Feb 27 2017 - 05:08:28 CST)
• Boyang Wang
  • Re: (Tue Jul 19 2016 - 23:33:49 CDT)
• Branko
  • Fwd: namd on Windows 10 (Fri Feb 05 2016 - 08:13:51 CST)
  • namd on Windows 10 (Thu Feb 04 2016 - 12:24:14 CST)
  • Re: Aoid protein to reach periodic boundary (Tue Jan 12 2016 - 05:41:21 CST)
• Brian Radak
  • Re: gbsa (Wed Dec 20 2017 - 11:57:24 CST)
  • Re: atom selection error (Mon Dec 11 2017 - 11:14:36 CST)
  • Re: atom selection error (Fri Dec 08 2017 - 10:41:57 CST)
  • Re: missing parameters. (Mon Nov 20 2017 - 08:33:41 CST)
  • Re: REMD using NAMD 2.13 (Mon Nov 20 2017 - 08:29:29 CST)
  • Re: missing parameters. (Wed Nov 15 2017 - 08:10:46 CST)
  • flat and smooth energy? (Mon Oct 23 2017 - 14:07:13 CDT)
  • Re: convergence criterion of free energy perturbation (FEP) simulations for pKa calculation (Fri Oct 06 2017 - 14:28:56 CDT)
  • Re: convergence criterion of free energy perturbation (FEP) simulations for pKa calculation (Fri Oct 06 2017 - 14:11:27 CDT)
  • Re: convergence criterion of free energy perturbation (FEP) simulations for pKa calculation (Thu Oct 05 2017 - 15:30:28 CDT)
  • Re: NAMDEnergy with xtc file (Thu Oct 05 2017 - 07:39:03 CDT)
  • Re: What is the exact form of the harmonic potential used by the NAMD "constraints" option? (Tue Sep 19 2017 - 11:39:05 CDT)
  • Re: What is the exact form of the harmonic potential used by the NAMD "constraints" option? (Tue Sep 19 2017 - 08:30:20 CDT)
  • Re: Ion type in NAMD Implicit solvent model for ionizing the system (Wed Sep 13 2017 - 09:59:27 CDT)
  • Re: Concatenating log files (Wed Sep 06 2017 - 11:32:02 CDT)
  • Re: Production run after equilibration (Tue Aug 29 2017 - 10:10:44 CDT)
  • Re: calculate cumulative dG (Tue Aug 29 2017 - 10:08:25 CDT)
  • Re: raising temperature after equiliobration (Mon Aug 28 2017 - 09:12:40 CDT)
  • Re: difference between constraining,restraining and fixing the atoms (Fri Aug 04 2017 - 09:34:22 CDT)
  • Re: Setting up softcore parameters for FEP (Thu Aug 03 2017 - 13:03:29 CDT)
  • Re: two stage equilibration in single configuration file (Thu Aug 03 2017 - 12:45:14 CDT)
  • Re: Setting up softcore parameters for FEP (Thu Aug 03 2017 - 12:02:47 CDT)
  • Re: Setting up softcore parameters for FEP (Thu Aug 03 2017 - 08:20:36 CDT)
  • Re: Problems running FEP on Lenovo NextScale KNL (Thu Jul 27 2017 - 15:55:21 CDT)
  • Re: Problems running FEP on Lenovo NextScale KNL (Wed Jul 26 2017 - 14:45:22 CDT)
  • Re: Problems running FEP on Lenovo NextScale KNL (Wed Jul 26 2017 - 10:04:22 CDT)
  • Re: Error in thermodynamic integration for calculating ligand absolute binding free energy (Mon Jul 17 2017 - 15:55:21 CDT)
  • Re: Segmentation fault error with 'nan' pressure and energy (Wed May 31 2017 - 18:24:19 CDT)
  • Re: Fatal error in the simulation of a water box (Wed May 31 2017 - 08:33:47 CDT)
  • Re: pKa calculation with thermodynamic integration (TI) (Tue May 30 2017 - 09:23:34 CDT)
  • Re: Equilibrium Energies (Tue May 23 2017 - 15:18:59 CDT)
  • Re: pKa calculation with thermodynamic integration (TI) (Tue May 23 2017 - 09:32:14 CDT)
  • Re: pKa calculation with thermodynamic integration (TI) (Thu May 11 2017 - 10:27:25 CDT)
  • Re: Type of solvent water molecules (Tue Apr 18 2017 - 16:56:02 CDT)
  • Re: is NVE ensemble for production run justified? (Tue Mar 21 2017 - 09:44:52 CDT)
  • Re: problems mutating HID to TYR for free energy calculations (Tue Mar 07 2017 - 17:02:27 CST)
  • Re: pairInteraction commands (Mon Feb 20 2017 - 08:19:54 CST)
  • Re: Calculating gradient of the potential (force field) on each atom. (Fri Jan 13 2017 - 11:34:11 CST)
  • Re: Solvation free energy difference of alchemical transformation of K+ into Na+ (Wed Jan 11 2017 - 10:20:21 CST)
  • Re: Solvation free energy difference of alchemical transformation of K+ into Na+ (Mon Jan 09 2017 - 10:11:47 CST)
  • Re: very small cell (Sun Jan 08 2017 - 18:59:15 CST)
  • Re: Studying Folding of 870 Small Peptides. Computationally Feasible? (Mon Dec 19 2016 - 09:32:10 CST)
  • Re: Writing number of atoms in a specific group to a file (Fri Dec 16 2016 - 12:11:04 CST)
  • Re: psfgen - pdbalias when using readpsf (Thu Dec 15 2016 - 14:48:01 CST)
  • psfgen - pdbalias when using readpsf (Thu Dec 15 2016 - 14:28:56 CST)
  • Re: protonating ASP and GLU (Tue Dec 13 2016 - 13:20:27 CST)
  • Re: protonating ASP and GLU (Tue Dec 13 2016 - 08:27:28 CST)
  • Re: Energy output values (Tue Dec 06 2016 - 13:35:47 CST)
  • Re: selectively assign HIE or HID for HIS residues (Mon Dec 05 2016 - 22:13:09 CST)
  • Re: Getting cluster with defined criteria (Sun Dec 04 2016 - 17:54:21 CST)
  • Re: Low global exclusion count error (Fri Dec 02 2016 - 09:25:30 CST)
  • Re: NVE simulations in NAMD - the right choice of timesteps and parameters (Tue Nov 29 2016 - 12:52:15 CST)
  • Re: NVE simulations in NAMD - the right choice of timesteps and parameters (Tue Nov 29 2016 - 10:04:53 CST)
  • Re: Are there features NOT or POORLY supported on GPU ? (Mon Nov 14 2016 - 14:46:40 CST)
  • Re: Are there features NOT or POORLY supported on GPU ? (Mon Nov 14 2016 - 14:24:13 CST)
  • Re: AW: Trigger DCD frame from TCL? (Wed Nov 09 2016 - 07:34:48 CST)
  • Re: Trigger DCD frame from TCL? (Tue Nov 08 2016 - 09:22:24 CST)
  • Re: Parameters for determining run time (Tue Nov 08 2016 - 09:18:15 CST)
  • multiple run commands freeze when using MTS? (Thu Nov 03 2016 - 15:45:40 CDT)
  • Re: Diagnosing CUDA (non)performance (Mon Oct 31 2016 - 13:37:13 CDT)
  • Re: AW: Turning off and back on fixed atoms (Sat Oct 29 2016 - 12:04:57 CDT)
  • Re: Using NAMD with NMR structure (Mon Oct 24 2016 - 09:02:02 CDT)
  • Re: NAMD breaks with wrong timestep (Fri Oct 21 2016 - 15:20:19 CDT)
  • Re: NAMD breaks with wrong timestep (Fri Oct 21 2016 - 10:41:46 CDT)
  • Collecting average energies via Tcl callback? (Thu Oct 13 2016 - 11:19:40 CDT)
  • Re: Switch function equation (Mon Oct 03 2016 - 21:16:58 CDT)
  • Re: Oxidized cysteine parameters for CHARMM36 (Fri Sep 30 2016 - 09:35:08 CDT)
  • Re: Autocorrelation function of Rg goes down without fluctuation around zero (Wed Sep 07 2016 - 09:17:03 CDT)
  • Re: Autocorrelation function of Rg goes down without fluctuation around zero (Tue Sep 06 2016 - 16:43:30 CDT)
  • Re: NAMD Question: Generating ensemble of structures (Thu Sep 01 2016 - 08:44:10 CDT)
  • Re: Autocorrelation function of Rg goes down without fluctuation around zero (Tue Aug 23 2016 - 14:28:36 CDT)
  • Re: Autocorrelation function of Rg goes down without fluctuation around zero (Tue Aug 23 2016 - 13:59:31 CDT)
  • Re: NAMD equilibrium step (Tue Aug 23 2016 - 13:55:47 CDT)
  • Re: how to rerun a namd trajectory in order to complement the missing snapshots? (Fri Aug 19 2016 - 07:54:54 CDT)
  • Re: Autocorrelation function of Rg goes down without fluctuation around zero (Thu Aug 18 2016 - 11:37:31 CDT)
  • Re: Autocorrelation function of Rg goes down without fluctuation around zero (Thu Aug 18 2016 - 11:20:22 CDT)
  • Re: Autocorrelation function of Rg goes down without fluctuation around zero (Thu Aug 18 2016 - 11:00:16 CDT)
  • Re: Autocorrelation function of Rg goes down without fluctuation around zero (Thu Aug 18 2016 - 10:21:30 CDT)
  • Re: Autocorrelation function of Rg goes down without fluctuation around zero (Thu Aug 18 2016 - 09:47:02 CDT)
  • Re: PMF Calculation (Sun Aug 14 2016 - 16:36:06 CDT)
  • Re: psfgen: creating segments without extra hydrogens? (Sun Aug 14 2016 - 16:39:59 CDT)
  • Re: How to replace NAMD Eletrostatic Forces (Thu Aug 04 2016 - 15:17:17 CDT)
  • Re: LJcorrection option in NAMD (Wed Jun 22 2016 - 17:22:07 CDT)
  • Re: LJcorrection option in NAMD (Wed Jun 22 2016 - 17:04:02 CDT)
  • Re: LJcorrection option in NAMD (Tue Jun 21 2016 - 07:36:06 CDT)
  • Re: RMSD (Thu Jun 16 2016 - 14:11:29 CDT)
  • Re: RMSD (Thu Jun 16 2016 - 13:51:46 CDT)
  • Re: How can I find the proper number of solvent molecules in the simulation? (Mon Jun 06 2016 - 09:49:42 CDT)
  • Re: Excessively high dE_avg values in FEP output (NAMD CVS) (Fri May 20 2016 - 07:47:33 CDT)
  • Re: Excessively high dE_avg values in FEP output (NAMD CVS) (Wed May 18 2016 - 13:25:44 CDT)
  • Re: Conversion from c6 and c12 = 0 to sigma epsilon (Sat May 14 2016 - 15:39:48 CDT)
  • Re: gradual heating problem (Sun May 08 2016 - 11:04:31 CDT)
  • Re: water box and padding (Mon May 02 2016 - 09:54:43 CDT)
  • Re: Running a test simulation using GPU only (without any CPU core) (Thu Apr 28 2016 - 10:00:42 CDT)
  • Re: CHARMM36 and TIP3 (Tue Apr 26 2016 - 13:57:05 CDT)
  • Re: Alchemify Possibilities (Mon Apr 25 2016 - 11:15:19 CDT)
  • Re: Why wrapped and unwrapped trajectories show different energies over the time? (Sun Apr 24 2016 - 09:03:07 CDT)
  • Re: Simulated annealing error (Thu Apr 07 2016 - 15:34:51 CDT)
  • Re: simulated annealing (Thu Apr 07 2016 - 10:00:03 CDT)
  • Re: Constraint failure in RATTLE algorithm for atom 538 (Tue Apr 05 2016 - 10:04:40 CDT)
  • Re: AW: AW: AW: why does the transition seem to be irreversible in aMD (Tue Apr 05 2016 - 09:42:27 CDT)
  • Re: Lowe-Andersen, Langevin and velocity rescaling thermostats (lipid bilayers) (Mon Apr 04 2016 - 09:44:37 CDT)
  • Re: Making NAMD aware of Tcl packages? (Thu Mar 31 2016 - 16:12:20 CDT)
  • Re: Making NAMD aware of Tcl packages? (Thu Mar 31 2016 - 10:20:42 CDT)
  • Making NAMD aware of Tcl packages? (Thu Mar 31 2016 - 10:11:07 CDT)
  • Re: AW: "Jump" in Energy and Volume graphs of my MD (Thu Mar 31 2016 - 07:56:32 CDT)
  • Re: AW: Tcl script for simulated tempering? (Tue Mar 15 2016 - 08:14:11 CDT)
  • Re: Fwd: Urey-Bradley parameters (Mon Mar 14 2016 - 10:25:22 CDT)
• Brunner, Robert Kraemer
  • Re: [Non-DoD Source] AW: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) (Tue Jan 12 2016 - 14:31:36 CST)
• Bryan Roessler
  • Re: Using 3 GPUs (but not 2) causes energy and temperatures to rise extremely fast in NAMD 2.12 (Thu Feb 16 2017 - 12:10:23 CST)
  • Using 3 GPUs (but not 2) causes energy and temperatures to rise extremely fast in NAMD 2.12 (Tue Feb 07 2017 - 19:55:59 CST)
  • Re: Re: Inconsistency between NAMD 2.11 and NAMD 2.12 (Fri Feb 03 2017 - 14:47:27 CST)
  • Re: Re: Inconsistency between NAMD 2.11 and NAMD 2.12 (Fri Feb 03 2017 - 14:17:51 CST)
  • Re: Inconsistency between NAMD 2.11 and NAMD 2.12 (Tue Jan 31 2017 - 10:12:07 CST)
  • Re: Inconsistency between NAMD 2.11 and NAMD 2.12 (Tue Jan 31 2017 - 09:47:30 CST)
  • Inconsistency between NAMD 2.11 and NAMD 2.12 (Tue Jan 31 2017 - 00:52:22 CST)
• Bylund, Tatsiana (NIH/NIAID) [F]
  • restart namd calculations (Tue Jan 12 2016 - 16:55:09 CST)
• Carlo Guardiani
  • Electric field simulation: eFieldNormalized (Tue Nov 28 2017 - 13:53:57 CST)
  • Re: Metadynamics state file (Mon Feb 20 2017 - 13:20:05 CST)
  • Metadynamics state file (Fri Feb 17 2017 - 06:53:31 CST)
  • FEP double annihilation (Fri Sep 23 2016 - 13:28:30 CDT)
  • Energy gradient in colvars.state file (Mon Feb 29 2016 - 13:09:31 CST)
• Carlos Simmerling
  • ACS COMP Division awards deadline this week (Wed Sep 28 2016 - 11:34:52 CDT)
• Charles Hoying
  • Keeping potassium ions out of an area during equilibration (Mon Jun 05 2017 - 22:57:40 CDT)
• Chenyi L
  • The adaptTemp and Temp in Adaptive tempering (Thu Jul 07 2016 - 19:51:03 CDT)
• Chitrak Gupta
  • Re: REMD using NAMD 2.13 (Sat Nov 18 2017 - 17:58:53 CST)
  • Re: NAMD job termination (Wed Nov 08 2017 - 21:17:25 CST)
  • sortreplicas on Stampede 2 (Mon Oct 16 2017 - 14:34:15 CDT)
  • Re: Fwd: About wall clock time (Mon Oct 16 2017 - 08:48:38 CDT)
  • Re: Implementation of sortreplicas executable for restarted REST2 simulations (Thu Oct 12 2017 - 08:21:09 CDT)
  • Re: Implementation of sortreplicas executable for restarted REST2 simulations (Wed Oct 11 2017 - 20:20:24 CDT)
  • Re: Implementation of sortreplicas executable for restarted REST2 simulations (Wed Oct 11 2017 - 14:32:54 CDT)
  • Re: NAMD on Stampede 2 (Fri Oct 06 2017 - 11:04:16 CDT)
  • Re: NAMD on Stampede 2 (Fri Oct 06 2017 - 08:32:30 CDT)
  • NAMD on Stampede 2 (Thu Oct 05 2017 - 18:23:05 CDT)
  • Re: [NAMD] Running NAMD in Stampede2 (Sun Oct 01 2017 - 19:21:52 CDT)
  • Re: Ion type in NAMD Implicit solvent model for ionizing the system (Wed Sep 13 2017 - 09:26:11 CDT)
  • Re: Compiling NAMD on stampede 2. (Fri Jul 21 2017 - 12:20:38 CDT)
  • Re: Compiling NAMD on stampede 2. (Thu Jul 20 2017 - 11:29:37 CDT)
  • Re: Compiling NAMD on stampede 2. (Thu Jul 20 2017 - 11:09:29 CDT)
  • Compiling NAMD on stampede 2. (Wed Jul 19 2017 - 17:47:07 CDT)
  • Re: How to set setting periodic boundary condition (Fri Jul 07 2017 - 09:54:54 CDT)
  • Re: GaMD in NAMD (Mon Jun 19 2017 - 08:43:37 CDT)
  • Re: GaMD in NAMD (Sun Jun 18 2017 - 14:57:20 CDT)
  • Re: GaMD in NAMD (Sun Jun 18 2017 - 09:20:11 CDT)
  • GaMD in NAMD (Sat Jun 17 2017 - 15:16:18 CDT)
  • Re: colvars to restrain peptide close to lipid (Sat May 20 2017 - 16:10:35 CDT)
  • Re: Custum made residue addition (Fri Apr 28 2017 - 08:11:31 CDT)
  • Re: colvars to restrain peptide close to lipid (Thu Apr 27 2017 - 15:11:17 CDT)
  • Re: Custum made residue addition (Thu Apr 27 2017 - 14:46:27 CDT)
  • Fwd: colvars to restrain peptide close to lipid (Wed Apr 26 2017 - 17:22:37 CDT)
  • Re: colvars to restrain peptide close to lipid (Wed Apr 26 2017 - 15:15:10 CDT)
  • colvars to restrain peptide close to lipid (Wed Apr 26 2017 - 15:01:23 CDT)
  • Re: colvars not scaling well in NAMD 2.10 (Fri Feb 24 2017 - 11:46:32 CST)
  • colvars not scaling well in NAMD 2.10 (Thu Feb 23 2017 - 17:25:14 CST)
  • REST2 patch for NAMD 2.12 (Fri Feb 17 2017 - 14:49:07 CST)
  • Re: PDB file creation (Wed Feb 08 2017 - 11:27:29 CST)
  • Re: PDB file creation (Wed Feb 08 2017 - 08:46:20 CST)
  • Re: Returning energy values from .log file. (Wed Dec 07 2016 - 14:36:57 CST)
  • Re: How to continue RMSD of previous production simulation (Fri Dec 02 2016 - 12:43:05 CST)
  • Re: Fatal Error: vdw atom type CC3161 (Wed Aug 03 2016 - 10:11:51 CDT)
  • Re: Generalized Born solvation models supported by NAMD (Tue Aug 02 2016 - 17:54:08 CDT)
  • Re: Generalized Born solvation models supported by NAMD (Fri Jul 29 2016 - 16:05:02 CDT)
  • performance drop during run (Fri Jul 29 2016 - 10:41:32 CDT)
  • Re: (Wed Jun 01 2016 - 13:03:34 CDT)
  • Re: (Wed Jun 01 2016 - 08:57:57 CDT)
  • Re: (Tue May 10 2016 - 13:57:03 CDT)
  • Re: (Mon May 09 2016 - 11:07:14 CDT)
  • Re: (Sat Apr 23 2016 - 23:19:09 CDT)
  • Re: Few doubt on the numbers implying in REMD simulation (Tue Apr 12 2016 - 10:00:21 CDT)
  • Re: (Fri Apr 08 2016 - 16:40:46 CDT)
  • Re: (Fri Apr 08 2016 - 10:01:07 CDT)
  • Re: Constraint failure in RATTLE algorithm for atom 538 (Tue Apr 05 2016 - 11:04:08 CDT)
  • Re: Constraint failure in RATTLE algorithm for atom 538 (Tue Apr 05 2016 - 10:10:44 CDT)
  • Re: varying two colvar distances simultaneously (Fri Mar 25 2016 - 17:20:57 CDT)
  • Re: varying two colvar distances simultaneously (Fri Mar 25 2016 - 10:58:08 CDT)
  • varying two colvar distances simultaneously (Thu Mar 24 2016 - 16:49:06 CDT)
  • Re: installing NAMD 2.11 (Thu Mar 10 2016 - 11:30:44 CST)
  • Re: calculating replica exchange acceptance ratio (Wed Jan 27 2016 - 04:18:38 CST)
  • Re: calculating replica exchange acceptance ratio (Mon Jan 25 2016 - 09:58:31 CST)
  • Re: calculating replica exchange acceptance ratio (Mon Jan 25 2016 - 09:51:48 CST)
  • Re: calculating replica exchange acceptance ratio (Mon Jan 25 2016 - 02:54:15 CST)
  • calculating replica exchange acceptance ratio (Sun Jan 24 2016 - 23:16:09 CST)
  • Re: Replica Exchange (Tue Jan 19 2016 - 14:40:20 CST)
• Chris Butch
  • Script for Terachem QMMM (Thu Dec 14 2017 - 03:29:17 CST)
• Chris Chipot
  • Klaus Schulten Memorial Issue (http://pubs.acs.org/toc/jpcbfk/121/15) (Thu Apr 20 2017 - 12:10:34 CDT)
  • Re: On-the-fly eABF: Problem with the tcl script. (Thu Jan 26 2017 - 07:20:13 CST)
• Chris Goedde
  • NAMD Energies (Wed Dec 14 2016 - 13:13:01 CST)
  • Re: Are there features NOT or POORLY supported on GPU ? (Mon Nov 14 2016 - 14:30:16 CST)
  • Diagnosing CUDA (non)performance (Mon Oct 31 2016 - 07:48:31 CDT)
  • Re: Minimization failing on one machine only (Fri Oct 21 2016 - 14:11:42 CDT)
  • Minimization failing on one machine only (Fri Oct 14 2016 - 15:34:10 CDT)
  • unix path length limits for namd (Sun May 01 2016 - 17:10:34 CDT)
• Christian Jorgensen
  • Drude minimization does not converge (Fri Jan 13 2017 - 10:16:08 CST)
  • Re: Drude minimization does not converge (Fri Jan 13 2017 - 13:21:39 CST)
  • Re: Drude minimization does not converge (Fri Jan 13 2017 - 11:26:39 CST)
  • Drude minimization does not converge (Fri Jan 13 2017 - 10:19:03 CST)
• Chun Heung Wong
  • Re: Unable to run CUDA NAMD but able to run non-CUDA version on Windows (Sat Dec 16 2017 - 07:22:29 CST)
  • Unable to run CUDA NAMD but able to run non-CUDA version on Windows (Sat Dec 16 2017 - 06:50:06 CST)
• Constanza Galaz Araya
  • NAMD QM/MM (Tue Nov 14 2017 - 10:08:45 CST)
• Crystal Liu
  • PMF Calculation (Fri Aug 12 2016 - 19:15:46 CDT)
• d.ronika_at_iitg.ernet.in
  • query in the equilibration step (Thu Sep 08 2016 - 07:32:32 CDT)
  • NAMD equilibrium step (Mon Aug 22 2016 - 00:34:01 CDT)
  • Re: AW: Energy minimization (Wed Aug 17 2016 - 05:09:01 CDT)
  • Energy minimization (Mon Aug 15 2016 - 00:05:12 CDT)
  • (no subject) (Tue Jul 19 2016 - 22:52:43 CDT)
• Daipayan Sarkar
  • How to sample pressure from NAMD log file. (Thu Sep 21 2017 - 22:16:54 CDT)
  • Re: Build NAMD with CUDA for unix workstation (centos 7) (Wed Sep 20 2017 - 03:04:32 CDT)
  • Build NAMD with CUDA for unix workstation (centos 7) (Wed Sep 20 2017 - 01:54:25 CDT)
  • Movie in VMD (Sat Aug 26 2017 - 22:56:24 CDT)
• daniel aguayo
  • Re: GPU configuration suggestions (Tue Mar 22 2016 - 06:59:16 CDT)
• Daniel Möller
  • AW: Movie in VMD (Sun Aug 27 2017 - 08:13:39 CDT)
  • AW: Simulation of metalo-binding proteins (Wed Nov 23 2016 - 15:52:53 CST)
  • AW: Simulation runs only in background (Wed Jun 01 2016 - 04:44:55 CDT)
• Daniela Rivas
  • Re: "Jump" in Energy and Volume graphs of my MD (Thu Mar 31 2016 - 11:21:03 CDT)
  • Re: "Jump" in Energy and Volume graphs of my MD (Wed Mar 30 2016 - 15:49:01 CDT)
  • "Jump" in Energy and Volume graphs of my MD (Wed Mar 30 2016 - 15:04:07 CDT)
• Danilo Di Maio
  • Re: The reason for the formation of bubbles in heating stage (Mon Jan 09 2017 - 09:09:58 CST)
• Danny Xu
  • Automate QwikMD set up for a large number of NAMD jobs? (Tue Dec 20 2016 - 15:24:36 CST)
• Darya Fadavi
  • Re: namd2.exe has stopped working, NAMD Energy (Thu Feb 02 2017 - 19:44:09 CST)
  • namd2.exe has stopped working, NAMD Energy (Wed Feb 01 2017 - 12:31:15 CST)
• david gae
  • Re: Gradual Heating Periodic Error (Tue Sep 13 2016 - 12:03:07 CDT)
  • Re: Gradual Heating Periodic Error (Tue Sep 13 2016 - 09:27:25 CDT)
• David Hardy
  • Fwd: Klaus Schulten Memorial Symposium, registration and accommodation (Thu Oct 05 2017 - 15:29:08 CDT)
  • Re: minimum CUDA compute capability required for NAMD2.12 (Sun Sep 24 2017 - 10:31:29 CDT)
  • Re: pairInteraction and PME? (Tue Sep 12 2017 - 11:05:23 CDT)
  • Re: Molecule-based Electrostatics Cutoff? (Mon Sep 11 2017 - 17:21:11 CDT)
  • Re: NAMD-2.12 CUDA2 and PMECUDA problems (Wed Aug 30 2017 - 11:05:47 CDT)
  • Re: vmd-l: 780Ti and NAMD2 (Wed Aug 30 2017 - 10:21:40 CDT)
  • Re: Periodic cell too small with GPUs, not with pur CPUs (Fri Aug 25 2017 - 21:34:38 CDT)
  • Re: "Periodic cell has become too small for original patch grid!" with membrane system on GPU (Fri Aug 25 2017 - 14:39:24 CDT)
  • Re: Periodic cell too small with GPUs, not with pur CPUs (Fri Aug 25 2017 - 14:31:31 CDT)
  • Re: Software for molecular electrostatic calculations (Thu Aug 17 2017 - 13:28:19 CDT)
  • Re: difference between .vel and .vel.restart (Thu Aug 17 2017 - 13:25:02 CDT)
  • Re: Running NAMD on Intel OmniPath (Fri Jul 28 2017 - 10:29:37 CDT)
  • Re: Running NAMD on Intel OmniPath (Thu Jul 27 2017 - 16:36:47 CDT)
  • Re: Running NAMD on Intel OmniPath (Thu Jul 27 2017 - 14:18:47 CDT)
  • Re: Periodic cell too small with GPUs, not with pur CPUs (Tue Jul 18 2017 - 17:05:00 CDT)
  • Re: Periodic cell too small with GPUs, not with pur CPUs (Wed Jul 05 2017 - 11:02:14 CDT)
  • Re: GaMD in NAMD (Sun Jun 18 2017 - 11:02:19 CDT)
  • Re: Center of mass drift (Fri Jun 02 2017 - 12:35:12 CDT)
  • Re: NAMD crashes when Multilevel Summation Method (MSM) is on (Tue May 30 2017 - 11:11:07 CDT)
  • Re: compilation of NAMD 2.12 fails (Fri Apr 28 2017 - 10:41:18 CDT)
  • Re: compilation of NAMD 2.12 fails (Fri Apr 28 2017 - 10:15:04 CDT)
  • Re: compilation of NAMD 2.12 fails (Thu Apr 27 2017 - 12:36:35 CDT)
  • Re: Explanation of parameters for NBTABLE's tabulated external file? (Wed Mar 22 2017 - 14:17:09 CDT)
  • Re: Explanation of parameters for NBTABLE's tabulated external file? (Wed Mar 22 2017 - 14:09:17 CDT)
  • Re: Minimization failing on one machine only (Fri Oct 21 2016 - 15:16:47 CDT)
  • Re: mail reg compilation of mdenergy (Wed Oct 19 2016 - 14:11:32 CDT)
  • Re: "Jump" in Energy and Volume graphs of my MD (Fri Apr 01 2016 - 12:09:44 CDT)
• David Huggins
  • Molecule-based Electrostatics Cutoff? (Mon Sep 11 2017 - 16:58:59 CDT)
  • Re: More FEP using separated topologies (Fri Apr 28 2017 - 03:28:55 CDT)
  • Re: More FEP using separated topologies (Tue Apr 25 2017 - 14:10:06 CDT)
  • Re: Neutralize a box for FEP (Wed Apr 12 2017 - 13:05:05 CDT)
  • Neutralize a box for FEP (Wed Apr 12 2017 - 10:30:20 CDT)
  • More FEP using separated topologies (Fri May 27 2016 - 15:21:01 CDT)
  • Re: Alchemify Possibilities (Tue Apr 26 2016 - 09:28:15 CDT)
  • Alchemify Possibilities (Mon Apr 25 2016 - 11:03:10 CDT)
• dayanidhi mohanta
  • Intramolecular interaction energy of protein in vacuum from NAMD simualtions (Sat Jul 09 2016 - 08:26:13 CDT)
• Debaditya Mukherjee
  • (no subject) (Tue Mar 21 2017 - 23:38:56 CDT)
  • (no subject) (Fri Mar 10 2017 - 23:40:50 CST)
  • (no subject) (Wed Mar 08 2017 - 22:52:17 CST)
• Deng, Jinxia (Nancy)
  • specify H-bond in CGMD (Thu Mar 09 2017 - 08:42:14 CST)
  • restraint backbone to keep secondary structure in coarse grain MD (Wed Nov 09 2016 - 10:42:46 CST)
  • fix disulfide bond in coarse grain(CG) model for NAMD (Mon Oct 24 2016 - 11:46:11 CDT)
  • fix disulfide bridge in coarse grain MD (Wed Oct 19 2016 - 11:54:59 CDT)
  • RE: visualizing and analyzing long simulation (Mon Oct 10 2016 - 10:51:42 CDT)
  • truncated text RE: external computational power for NAMD (Thu May 26 2016 - 12:59:40 CDT)
  • external computational power for NAMD (Thu May 26 2016 - 12:02:54 CDT)
  • RE: Parameters for HS(CH2)11NH2 (Sun May 22 2016 - 14:03:37 CDT)
  • external HPC resource (Thu Feb 18 2016 - 10:23:36 CST)
  • MD trajectory analysis (Thu Jan 28 2016 - 13:02:14 CST)
  • multipld .dcd analysis by VMD (Wed Jan 20 2016 - 13:53:21 CST)
  • solvent other than water (Wed Jan 06 2016 - 12:17:11 CST)
• Dharmeshkumar Patel
  • Aoid protein to reach periodic boundary (Mon Jan 11 2016 - 18:15:16 CST)
• Dhiraj Srivastava
  • Fwd: enhanced sampling of domain motion, GSAfold (Mon Jul 03 2017 - 16:33:17 CDT)
  • enhanced sampling of domain motion, GSAfold (Sat Jul 01 2017 - 23:49:00 CDT)
  • visualizing and analyzing long simulation (Mon Oct 10 2016 - 10:41:53 CDT)
  • Re: question regarding rmsd (Wed Oct 05 2016 - 14:02:32 CDT)
  • question regarding rmsd (Tue Oct 04 2016 - 16:07:43 CDT)
  • stripping off water from DCD file except structural water (Sun Oct 02 2016 - 22:57:24 CDT)
  • dcd file frame number (Thu Sep 29 2016 - 22:22:54 CDT)
  • gradual heating problem (Sun May 08 2016 - 10:27:39 CDT)
  • heating in NPT ensemble (Thu May 05 2016 - 17:39:35 CDT)
  • water box and padding (Sat Apr 30 2016 - 11:40:53 CDT)
  • minimization, heating, equilibration and production run in one script (Thu Apr 28 2016 - 10:05:55 CDT)
  • Autoionize and topology (Tue Apr 26 2016 - 22:07:04 CDT)
  • Re: CHARMM36 and TIP3 (Tue Apr 26 2016 - 17:01:10 CDT)
  • CHARMM36 and TIP3 (Tue Apr 26 2016 - 13:37:49 CDT)
  • Amino acid as ligand (Mon Apr 25 2016 - 12:22:24 CDT)
  • Sugar phosphate topology and parameter (Thu Apr 14 2016 - 00:32:55 CDT)
• dhirajks_at_gmail.com
  • Enhanced sampling of domain motion and gsafold (Mon Jul 03 2017 - 19:18:38 CDT)
  • Re: question regarding rmsd (Thu Oct 06 2016 - 17:37:23 CDT)
  • Re: question regarding rmsd (Wed Oct 05 2016 - 11:03:41 CDT)
  • Equilibration and production run (Mon May 16 2016 - 01:25:32 CDT)
  • PMEProcessors setting on one node (Sun May 08 2016 - 21:22:54 CDT)
  • Re: gradual heating problem (Sun May 08 2016 - 11:21:13 CDT)
• divyabharathi korlepara
  • Re: Two parameter file in NAMD configuration file (Wed Jun 14 2017 - 00:01:04 CDT)
  • Two parameter file in NAMD configuration file (Fri Jun 09 2017 - 02:58:16 CDT)
• Dmitri Priimak
  • NAMD DCD file format (Fri Jun 09 2017 - 01:47:36 CDT)
• Doug Stetner
  • namd2 seg fault NAMD_2.11_Source Linux-x86_64-g++ (Tue Jul 12 2016 - 22:51:40 CDT)
• Douglas Houston
  • ABF with alpha colvar? (Sat Jan 21 2017 - 11:30:49 CST)
• Downs, Andrew S CTR USARMY ARL (US)
  • RE: [Non-DoD Source] RE: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) (Thu Jan 14 2016 - 09:24:50 CST)
  • RE: [Non-DoD Source] AW: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) (Tue Jan 12 2016 - 14:04:36 CST)
  • RE: [Non-DoD Source] AW: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) (Tue Jan 12 2016 - 09:44:54 CST)
  • RE: [Non-DoD Source] AW: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) (Tue Jan 12 2016 - 07:27:59 CST)
  • Compilation error across Intel 14,15 and 16 (UNCLASSIFIED) (Mon Jan 11 2016 - 13:10:19 CST)
• Dr. Eddie
  • Running 2.12 (Fri Oct 13 2017 - 19:56:46 CDT)
  • Optimizing namd run (Wed Oct 11 2017 - 13:04:29 CDT)
  • Re: Tutorial example of replica exchange (Fri Mar 11 2016 - 09:35:03 CST)
  • Re: Tutorial example of replica exchange (Thu Mar 10 2016 - 12:26:19 CST)
  • Re: Tutorial example of replica exchange (Thu Mar 10 2016 - 09:46:50 CST)
  • Tutorial example of replica exchange (Tue Mar 08 2016 - 16:55:34 CST)
  • Replica Exchange (Tue Jan 19 2016 - 10:35:00 CST)
• Dushyant Sahoo
  • Define spheres using NAMD (Sun Feb 19 2017 - 12:17:37 CST)
• Eduard Schreiner
  • Re: Type of solvent water molecules (Tue Apr 18 2017 - 16:21:01 CDT)
• Emerson Macedo
  • PDB File of Primary structure and Simulation (Fri Sep 02 2016 - 11:19:18 CDT)
  • psfgen: creating segments without extra hydrogens? (Sat Aug 13 2016 - 13:58:49 CDT)
  • Re: How to replace NAMD Eletrostatic Forces (Fri Aug 05 2016 - 10:45:12 CDT)
  • How to replace NAMD Eletrostatic Forces (Thu Aug 04 2016 - 13:15:38 CDT)
• Emmanuel MOUTOUSSAMY
  • Re: On-the-fly eABF: Problem with the tcl script. (Fri Jan 27 2017 - 02:58:38 CST)
  • On-the-fly eABF: Problem with the tcl script. (Thu Jan 26 2017 - 06:06:52 CST)
• Eric A Brenner
  • Re: Studying Folding of 870 Small Peptides. Computationally Feasible? (Sat Dec 17 2016 - 19:02:39 CST)
  • Studying Folding of 870 Small Peptides. Computationally Feasible? (Sat Dec 17 2016 - 12:35:59 CST)
• Eric Germaneau
  • Re: AW: Testing NAMD scalability (Mon Mar 21 2016 - 03:15:06 CDT)
• Eric Lang
  • NPT simulations with PLUMED in NAMD (Wed Nov 15 2017 - 07:58:27 CST)
• Eric Pederson
  • Implicit solvent no non-bonded pairing (Thu Mar 16 2017 - 19:41:51 CDT)
• Eric Smoll
  • Question about new NAMD QM/MM code (Sun May 07 2017 - 22:08:08 CDT)
  • Bond-jitter/Total-energy-spikes during energy minimization in vacuum (Mon May 01 2017 - 02:58:10 CDT)
• Eric Weine
  • Topology Command in VMD (Thu Jun 09 2016 - 19:27:39 CDT)
  • Using Mergestructs (Tue May 31 2016 - 14:09:46 CDT)
• Erik Nordgren
  • strange diffs in energy output of NAMD 2.9 vs. 2.11 (Fri Feb 03 2017 - 14:05:23 CST)
• Estefanía Hugo
  • displacement of protein (Thu Sep 21 2017 - 09:08:19 CDT)
• Faramarz Joodaki
  • Re: Cross-term (CMAP) (Sat Jul 08 2017 - 07:25:27 CDT)
  • Cross-term (CMAP) (Fri Jul 07 2017 - 18:04:48 CDT)
  • Re: Fatal Error in NAMD (Thu Mar 30 2017 - 12:54:13 CDT)
  • Re: Fatal Error in NAMD (Thu Mar 30 2017 - 12:24:20 CDT)
  • Fatal Error in NAMD (Thu Mar 30 2017 - 12:14:51 CDT)
  • Switch function equation (Sun Oct 02 2016 - 23:57:40 CDT)
  • Energy minimization in NAMD (Mon Aug 08 2016 - 11:37:45 CDT)
  • Re: how to reassign dcdfreq?? (Wed Jul 13 2016 - 08:02:23 CDT)
  • Re: how to reassign dcdfreq?? (Wed Jul 13 2016 - 08:01:09 CDT)
  • how to reassign dcdfreq?? (Mon Jul 11 2016 - 22:17:54 CDT)
  • Re: I cannot make MD simulation constant in pressure (Mon May 23 2016 - 22:44:21 CDT)
  • Re: I cannot make MD simulation constant in pressure (Mon May 23 2016 - 18:29:14 CDT)
  • I cannot make MD simulation constant in pressure (Mon May 23 2016 - 14:41:54 CDT)
• Farhad Jahanfar
  • How to continue RMSD of previous production simulation (Fri Dec 02 2016 - 12:21:36 CST)
• faride badalkhani
  • Re: AW: High pressure calculations (Sat Feb 04 2017 - 06:11:52 CST)
  • Re: High pressure calculations (Fri Feb 03 2017 - 13:23:34 CST)
  • High pressure calculations (Fri Feb 03 2017 - 10:10:39 CST)
  • How to calculate the number of solvent molecules for simulations in a specified pressure (Wed Feb 01 2017 - 04:33:55 CST)
  • Re: NVT and NPT simulationd (Thu Dec 15 2016 - 14:38:24 CST)
  • Re: NVT and NPT simulationd (Wed Dec 14 2016 - 12:14:08 CST)
  • Re: NVT and NPT simulationd (Wed Dec 14 2016 - 11:09:40 CST)
  • NVT and NPT simulationd (Tue Dec 13 2016 - 23:50:53 CST)
  • Low global exclusion count error (Thu Dec 01 2016 - 15:21:03 CST)
  • Low global exclusion count errors! (Thu Nov 24 2016 - 10:28:53 CST)
  • Half of the structure goes out of the simulation box! (Fri Sep 30 2016 - 05:18:51 CDT)
  • Simulated annealing, in solvent or in vacuum? (Thu Sep 08 2016 - 14:21:26 CDT)
  • Re: Autocorrelation function of Rg goes down without fluctuation around zero (Wed Sep 07 2016 - 01:14:08 CDT)
  • The needed time for a MD simulation (Mon Sep 05 2016 - 10:11:08 CDT)
  • Re: Autocorrelation function of Rg goes down without fluctuation around zero (Mon Sep 05 2016 - 06:03:13 CDT)
  • Re: Autocorrelation function of Rg goes down without fluctuation around zero (Tue Aug 23 2016 - 14:16:28 CDT)
  • Re: Autocorrelation function of Rg goes down without fluctuation around zero (Mon Aug 22 2016 - 07:34:17 CDT)
  • Re: Autocorrelation function of Rg goes down without fluctuation around zero (Fri Aug 19 2016 - 04:00:59 CDT)
  • Re: Autocorrelation function of Rg goes down without fluctuation around zero (Thu Aug 18 2016 - 13:50:23 CDT)
  • Re: Autocorrelation function of Rg goes down without fluctuation around zero (Thu Aug 18 2016 - 11:31:05 CDT)
  • Re: Autocorrelation function of Rg goes down without fluctuation around zero (Thu Aug 18 2016 - 11:27:39 CDT)
  • Re: Autocorrelation function of Rg goes down without fluctuation around zero (Thu Aug 18 2016 - 11:16:57 CDT)
  • Re: Autocorrelation function of Rg goes down without fluctuation around zero (Thu Aug 18 2016 - 10:31:53 CDT)
  • Re: Autocorrelation function of Rg goes down without fluctuation around zero (Thu Aug 18 2016 - 10:16:34 CDT)
  • Autocorrelation function of Rg goes down without fluctuation around zero (Thu Aug 18 2016 - 04:21:07 CDT)
  • Potential per TS looks wierd (Mon Jun 27 2016 - 13:18:33 CDT)
  • Re: RMSD (Thu Jun 16 2016 - 14:13:40 CDT)
  • Re: RMSD (Thu Jun 16 2016 - 14:02:43 CDT)
  • RMSD (Thu Jun 16 2016 - 12:42:32 CDT)
  • Building PSF for the system prepared by Packmol (Thu Jun 09 2016 - 09:27:31 CDT)
  • An script for ACF (Tue Jun 07 2016 - 16:37:13 CDT)
  • How can I find the proper number of solvent molecules in the simulation? (Mon Jun 06 2016 - 09:25:50 CDT)
  • autocorrelation function (Thu Jun 02 2016 - 09:06:04 CDT)
  • non-standard solvants (Wed Jun 01 2016 - 11:55:28 CDT)
  • hyper-branched polymers (Tue May 24 2016 - 09:24:41 CDT)
  • running simulations in successive steps (Mon May 16 2016 - 17:31:31 CDT)
  • parameterization of cations (Wed May 04 2016 - 11:28:59 CDT)
  • parameterizing a new solvent (Tue May 03 2016 - 08:54:06 CDT)
  • Dihedral missing (Thu Apr 28 2016 - 17:54:15 CDT)
  • Re: Constraint failure in RATTLE algorithm for atom 6! (Tue Apr 26 2016 - 16:47:59 CDT)
  • Re: Constraint failure in RATTLE algorithm for atom 6! (Tue Apr 26 2016 - 16:46:40 CDT)
  • Re: Constraint failure in RATTLE algorithm for atom 6! (Tue Apr 26 2016 - 16:22:02 CDT)
  • Constraint failure in RATTLE algorithm for atom 6! (Mon Apr 25 2016 - 10:42:52 CDT)
  • cell basis vectors (Wed Apr 20 2016 - 13:59:11 CDT)
  • simulation of hyperbranched polymers (Tue Apr 19 2016 - 07:54:49 CDT)
  • initial structure (Mon Apr 18 2016 - 10:17:30 CDT)
  • initial structure (Fri Apr 15 2016 - 14:18:03 CDT)
  • Bad initial structure? (Thu Apr 14 2016 - 13:50:14 CDT)
  • Re: Polymer moves to the edge of water box during the simulation (Thu Apr 14 2016 - 09:56:07 CDT)
  • Re: Polymer moves to the edge of water box during the simulation (Wed Apr 13 2016 - 12:55:28 CDT)
  • Re: Polymer moves to the edge of water box during the simulation (Wed Apr 13 2016 - 08:32:29 CDT)
  • Re: Polymer moves to the edge of water box during the simulation (Tue Apr 12 2016 - 17:02:19 CDT)
  • Polymer moves to the edge of water box during the simulation (Tue Apr 12 2016 - 16:49:21 CDT)
  • Simulated annealing error (Thu Apr 07 2016 - 13:13:38 CDT)
  • simulated annealing (Thu Apr 07 2016 - 08:14:10 CDT)
  • water box has a weird shape (Wed Apr 06 2016 - 13:21:28 CDT)
  • simulated annealing (Wed Apr 06 2016 - 11:24:30 CDT)
  • Re: Constraint failure in RATTLE algorithm for atom 538 (Tue Apr 05 2016 - 10:18:25 CDT)
  • Constraint failure in RATTLE algorithm for atom 538 (Tue Apr 05 2016 - 09:57:30 CDT)
  • Dihedral parameter missing (Mon Apr 04 2016 - 16:26:03 CDT)
  • Re: Stray PME grid charges detected (Mon Apr 04 2016 - 13:02:51 CDT)
  • Stray PME grid charges detected (Sun Apr 03 2016 - 12:49:18 CDT)
  • Re: maximum coordinate is negative for z (Fri Apr 01 2016 - 12:23:38 CDT)
  • maximum coordinate is negative for z (Fri Apr 01 2016 - 12:14:17 CDT)
  • segmentation fault (core dumped) (Wed Mar 30 2016 - 16:24:26 CDT)
  • Fwd: problem with angle parameters (Wed Mar 30 2016 - 10:01:22 CDT)
  • problem with angle parameters (Wed Mar 30 2016 - 09:01:20 CDT)
  • size of water box and cellbasisvectors (Wed Mar 30 2016 - 07:51:14 CDT)
  • Parameterizing residues of a polymer (Tue Mar 22 2016 - 12:47:57 CDT)
  • Parameterizing residues of a polymer (Tue Mar 22 2016 - 09:17:46 CDT)
  • Basic validation of CGenFF (Mon Mar 21 2016 - 07:31:05 CDT)
  • CGENFF validation (Fri Mar 18 2016 - 15:12:56 CDT)
  • Re: charge group (Fri Mar 18 2016 - 13:36:14 CDT)
  • Re: charge group (Fri Mar 18 2016 - 11:23:39 CDT)
  • charge group (Fri Mar 18 2016 - 10:56:42 CDT)
  • Fwd: Appropriate FF for a specific solvent (Fri Mar 18 2016 - 10:53:15 CDT)
  • Appropriate FF for a specific solvent (Thu Mar 17 2016 - 10:48:57 CDT)
  • Fwd: Urey-Bradley parameters (Mon Mar 14 2016 - 07:20:08 CDT)
  • Urey-Bradley parameters (Fri Mar 11 2016 - 09:10:39 CST)
  • problem with bringing down the pressure (Thu Mar 10 2016 - 11:31:36 CST)
  • equilibration error (Wed Mar 09 2016 - 15:22:25 CST)
  • cellBasisVectors (Wed Mar 09 2016 - 10:27:53 CST)
  • Re: installing NAMD 2.11 (Wed Mar 09 2016 - 07:54:23 CST)
  • installing NAMD 2.11 (Wed Mar 09 2016 - 07:32:46 CST)
  • INTERNAL COORDINATES (Tue Mar 01 2016 - 07:52:09 CST)
  • Combination of top_all36_cgenff with top_all36_prot (Mon Feb 29 2016 - 15:03:31 CST)
• Farideh Badalkhani Khamseh
  • restart a job (Wed Apr 06 2016 - 11:57:49 CDT)
• Felipe Merino
  • Re: NVE simulations in NAMD - the right choice of timesteps and parameters (Tue Nov 29 2016 - 07:03:45 CST)
  • Recover the PMF along an unbiased CV (Thu Jan 14 2016 - 16:11:37 CST)
  • Re: Aoid protein to reach periodic boundary (Tue Jan 12 2016 - 06:13:43 CST)
• Felix W.-H. Weng
  • XPLOR format PSF file for small molecules (Sun Apr 24 2016 - 11:21:45 CDT)
• fhh2626_at_gmail.com
  • Re: value of langevinTemp in case of binvelocities (Thu Aug 10 2017 - 02:13:20 CDT)
  • Re: Re: I don't have any eabf output file. (Wed Jul 26 2017 - 01:47:09 CDT)
• Fidan Sumbul
  • Re: problem in writing the coor files (Tue Nov 07 2017 - 02:55:40 CST)
  • problem in writing the coor files (Mon Nov 06 2017 - 11:11:28 CST)
  • Re: RMSD of backbone changes rapidly at the beginning of production run (Fri Nov 03 2017 - 06:27:42 CDT)
• Florian Blanc
  • Re: Error on Settle.C when compiling NAMD with Intel Compiler (Thu Nov 09 2017 - 11:00:09 CST)
  • Re: Error on Settle.C when compiling NAMD with Intel Compiler (Thu Oct 26 2017 - 12:34:06 CDT)
  • Error on Settle.C when compiling NAMD with Intel Compiler (Wed Oct 25 2017 - 15:26:57 CDT)
  • Re: Water atoms' explosion out of solvate box in my RBCG simulation on NAMD (Mon Oct 23 2017 - 06:03:14 CDT)
  • Re: extracting force on a single atom (Thu Aug 31 2017 - 10:07:59 CDT)
  • Re: Syntax for replicaRecv (Tue Aug 08 2017 - 05:13:50 CDT)
  • Re: Syntax for replicaRecv (Mon Aug 07 2017 - 08:47:02 CDT)
  • Syntax for replicaRecv (Fri Aug 04 2017 - 10:17:27 CDT)
• Fotis Baltoumas
  • Re: Psf file generation with Gromacs Parameters (Wed Nov 08 2017 - 17:43:42 CST)
  • Re: NAMDEnergy with xtc file (Thu Oct 05 2017 - 05:29:44 CDT)
  • Re: Building namd 2.12 from source an ARM64 architecture (Wed Sep 27 2017 - 18:15:36 CDT)
  • Re: difference between constraining,restraining and fixing the atoms (Thu Aug 03 2017 - 23:33:22 CDT)
  • Re: Lipid_bilayer_area_per_lipid_problem_using_NPT_CharmmForcefield (Fri Jul 07 2017 - 02:22:06 CDT)
  • Re: problem to generate LPS PSF file using PSFGEN (Fri Mar 17 2017 - 05:03:42 CDT)
  • Re: Separate switchdist for electrostatic interactions (Mon Nov 21 2016 - 09:54:33 CST)
  • Re: fix disulfide bridge in coarse grain MD (Wed Oct 19 2016 - 12:36:11 CDT)
  • Re: Martini CG models parameters errors (Mon Sep 26 2016 - 14:58:52 CDT)
  • Re: Equivalent of gromacs' "rdd" option (Mon Jul 25 2016 - 10:26:05 CDT)
  • Re: Equivalent of gromacs' "rdd" option (Mon Jul 25 2016 - 10:08:18 CDT)
  • Re: Equivalent of gromacs' "rdd" option (Fri Jul 22 2016 - 11:05:50 CDT)
  • Re: Coarse Grain Angle Parameter Issue (Sat Jun 18 2016 - 00:23:37 CDT)
  • Re: Coarse-grained simulation with Polarizable Water crashing (Sat May 21 2016 - 17:14:36 CDT)
  • Re: TIP4P/2005 par file by Jordi Faraudo (Sat Jan 09 2016 - 12:13:01 CST)
• Francesca Lønstad Bleken
  • transition metal parameters (Fri Jun 24 2016 - 02:19:01 CDT)
• Francesco Pietra
  • tcl used for binary compilation (Mon Dec 18 2017 - 14:26:30 CST)
  • Re: About the performance of RAMD (Sat Nov 11 2017 - 00:46:49 CST)
  • About the performance of RAMD (Fri Nov 10 2017 - 10:55:42 CST)
  • Too many iterations in routine jacobi during FEP (Wed Sep 06 2017 - 01:36:16 CDT)
  • Re: How to get the right density of a methane system (Sat Aug 12 2017 - 01:07:54 CDT)
  • Re: Are KNL a good choice for classical MD? (Sun Aug 06 2017 - 03:04:31 CDT)
  • Fwd: Are KNL a good choice for classical MD? (Sat Aug 05 2017 - 02:42:31 CDT)
  • Re: Are KNL a good choice for classical MD? (Sat Aug 05 2017 - 02:02:09 CDT)
  • Are KNL a good choice for classical MD? (Fri Aug 04 2017 - 15:51:48 CDT)
  • Re: Periodic cell too small with GPUs, not with pur CPUs (Fri Aug 04 2017 - 06:44:37 CDT)
  • Does FEP really run on Knights Landing? (Thu Jul 27 2017 - 11:44:13 CDT)
  • Re: Problems running FEP on Lenovo NextScale KNL (Thu Jul 27 2017 - 01:27:24 CDT)
  • Re: Problems running FEP on Lenovo NextScale KNL (Wed Jul 26 2017 - 10:27:20 CDT)
  • Problems running FEP on Lenovo NextScale KNL (Wed Jul 26 2017 - 09:23:19 CDT)
  • Re: Too many iterations in routine jacobi. (Sun Jul 23 2017 - 01:58:42 CDT)
  • Too many iterations in routine jacobi. (Fri Jul 21 2017 - 12:06:45 CDT)
  • Re: Periodic cell too small with GPUs, not with pur CPUs (Mon Jul 17 2017 - 09:09:20 CDT)
  • Re: ABF: umbrella_int.awk (Sat Jul 15 2017 - 08:45:00 CDT)
  • Re: ABF: umbrella_int.awk (Sat Jul 15 2017 - 03:36:33 CDT)
  • Re: ABF: umbrella_int.awk (Fri Jul 14 2017 - 03:39:48 CDT)
  • ABF: umbrella_int.awk (Thu Jul 13 2017 - 10:32:40 CDT)
  • Re: ABF FEP with multichain receptor (Tue Jul 11 2017 - 11:28:48 CDT)
  • Fwd: ABF FEP with multichain receptor (Tue Jul 11 2017 - 01:20:12 CDT)
  • Fwd: ABF FEP with multichain receptor (Mon Jul 10 2017 - 05:25:30 CDT)
  • Re: ABF FEP with multichain receptor (Sun Jul 09 2017 - 00:44:14 CDT)
  • Re: ABF FEP with multichain receptor (Sat Jul 08 2017 - 11:08:41 CDT)
  • ABF FEP with multichain receptor (Fri Jul 07 2017 - 10:21:52 CDT)
  • Re: Fwd: Atoms too fast/periodic cell too small with ABF protein-ligand (Thu Jul 06 2017 - 01:15:50 CDT)
  • Re: Fwd: Atoms too fast/periodic cell too small with ABF protein-ligand (Wed Jul 05 2017 - 11:03:05 CDT)
  • Periodic cell too small with GPUs, not with pur CPUs (Wed Jul 05 2017 - 02:09:14 CDT)
  • Re: Fwd: Atoms too fast/periodic cell too small with ABF protein-ligand (Thu Jun 29 2017 - 08:47:59 CDT)
  • Fwd: About the robustness of ABF and FEB protein-ligand (Wed Jun 28 2017 - 09:47:59 CDT)
  • About the robustness of ABF and FEB protein-ligand (Wed Jun 28 2017 - 09:40:15 CDT)
  • Re: Fwd: Atoms too fast/periodic cell too small with ABF protein-ligand (Tue Jun 27 2017 - 02:46:38 CDT)
  • Fwd: Atoms too fast/periodic cell too small with ABF protein-ligand (Mon Jun 26 2017 - 11:24:59 CDT)
  • Fwd: Atoms too fast/periodic cell too small with ABF protein-ligand (Mon Jun 26 2017 - 05:28:49 CDT)
  • Atoms too fast/periodic cell too small with ABF protein-ligand (Sun Jun 25 2017 - 05:56:01 CDT)
  • Fwd: measuring Euler angles and polar angles (Sat Jun 24 2017 - 01:22:17 CDT)
  • Re: measuring Euler angles and polar angles (Fri Jun 23 2017 - 12:06:18 CDT)
  • Re: measuring Euler angles and polar angles (Fri Jun 23 2017 - 09:55:31 CDT)
  • measuring Euler angles and polar angles (Thu Jun 22 2017 - 12:01:39 CDT)
  • Re: GaMD in NAMD (Mon Jun 19 2017 - 00:36:19 CDT)
  • Re: GaMD in NAMD (Sun Jun 18 2017 - 01:04:59 CDT)
  • about GaMD reweighting (Tue Jun 06 2017 - 10:58:40 CDT)
  • Howto gaussian accelerated MD (Tue May 16 2017 - 09:34:11 CDT)
  • Re: ++idlepoll (Mon Feb 06 2017 - 02:37:33 CST)
  • Re: AW: High pressure calculations (Sat Feb 04 2017 - 06:00:53 CST)
  • Re: basis set for QM-MM dft (Thu Jan 26 2017 - 01:19:29 CST)
  • basis set for QM-MM dft (Wed Jan 25 2017 - 09:15:43 CST)
  • Re: QM-MM ORCA Charm++ error Could not find QM output file (Thu Jan 19 2017 - 11:56:20 CST)
  • Re: QM-MM ORCA Charm++ error Could not find QM output file (Tue Jan 17 2017 - 12:10:52 CST)
  • QM-MM ORCA Charm++ error Could not find QM output file (Mon Jan 16 2017 - 01:55:38 CST)
  • Fwd: Re: Charm++ fatal error with QM-MM MOPAC (Sun Jan 15 2017 - 02:53:17 CST)
  • Re: Re: Charm++ fatal error with QM-MM MOPAC (Sun Jan 15 2017 - 01:55:20 CST)
  • Re: Charm++ fatal error with QM-MM MOPAC (Tue Jan 10 2017 - 10:50:58 CST)
  • Re: Re: Charm++ fatal error with QM-MM MOPAC (Tue Jan 10 2017 - 10:40:39 CST)
  • Charm++ fatal error with QM-MM MOPAC (Tue Jan 10 2017 - 01:56:35 CST)
  • QM-MM flooding potential (Tue Jan 03 2017 - 01:40:20 CST)
  • Fwd: (1) Failure running QM-MM with ORCA and (2) problems preparing input with transition metals (Mon Jan 02 2017 - 04:54:19 CST)
  • (1) Failure running QM-MM with ORCA and (2) problems preparing input with transition metals (Mon Jan 02 2017 - 01:38:54 CST)
  • Fwd: Problems running NAMD QM-MM with ORCA 3.0.3 (Fri Dec 30 2016 - 03:51:10 CST)
  • Problems running NAMD QM-MM with ORCA 3.0.3 (Fri Dec 30 2016 - 03:24:04 CST)
  • Fwd: NAMD 2.12 released (Wed Dec 28 2016 - 02:12:14 CST)
  • Fwd: NAMD 2.12 released (Wed Dec 28 2016 - 02:10:55 CST)
  • Re: NAMD 2.12 released (Tue Dec 27 2016 - 01:40:40 CST)
  • Re: NAMD 2.12 released (Mon Dec 26 2016 - 04:17:27 CST)
  • Re: Simulation of metalo-binding proteins (Thu Nov 24 2016 - 14:41:58 CST)
  • About pbc (Tue Nov 08 2016 - 15:10:56 CST)
  • Drude Prepper error in genic (Mon Jun 13 2016 - 01:33:15 CDT)
  • Help about Drude Prepper (Tue Jun 07 2016 - 10:06:48 CDT)
  • Re: H-bonds in charmm36 with namd2.11 (Tue May 24 2016 - 04:30:13 CDT)
  • Fwd: H-bonds in charmm36 with namd2.11 (Sun May 22 2016 - 01:46:52 CDT)
  • Re: H-bonds in charmm36 with namd2.11 (Sun May 22 2016 - 01:43:55 CDT)
  • H-bonds in charmm36 with namd2.11 (Fri May 20 2016 - 16:18:22 CDT)
  • Re: Re: vmd-l: CHARMM36 alleged missing CC CT1 NH2 angle params (Tue May 17 2016 - 11:43:05 CDT)
  • Re: Re: vmd-l: CHARMM36 alleged missing CC CT1 NH2 angle params (Mon May 16 2016 - 08:54:45 CDT)
  • Re: vmd-l: CHARMM36 alleged missing CC CT1 NH2 angle params (Mon May 16 2016 - 08:54:31 CDT)
  • Re: vmd-l: CHARMM36 alleged missing CC CT1 NH2 angle params (Mon May 16 2016 - 04:30:29 CDT)
  • CHARMM36 alleged missing CC CT1 NH2 angle params (Mon May 16 2016 - 02:45:55 CDT)
  • Mixing all_36_cgenff with all_36_prot (Sat Mar 26 2016 - 13:02:27 CDT)
  • restarting simulation (Mon Mar 14 2016 - 09:45:44 CDT)
• Fırat Yılmaz
  • Re: run namd cuda with srun. (Wed Jun 21 2017 - 03:36:09 CDT)
  • run namd cuda with srun. (Tue Jun 20 2017 - 16:03:29 CDT)
  • missing binary operator before token "(" (Thu Jun 15 2017 - 02:30:12 CDT)
• Gabriel Jara
  • Re: unbinding free energy using ABF (Fri Jul 01 2016 - 16:13:32 CDT)
  • unbinding free energy using ABF (Thu Jun 30 2016 - 13:25:27 CDT)
• Gergely Gyimesi
  • Oxidized cysteine parameters for CHARMM36 (Fri Sep 30 2016 - 08:40:04 CDT)
• Giacomo Fiorin
  • Re: reconstructing pmf (Tue Dec 19 2017 - 18:24:46 CST)
  • Re: reconstructing pmf (Tue Dec 19 2017 - 10:27:09 CST)
  • Re: reconstructing pmf (Tue Dec 19 2017 - 08:08:03 CST)
  • Re: reconstructing pmf (Mon Dec 18 2017 - 19:40:03 CST)
  • Re: tcl used for binary compilation (Mon Dec 18 2017 - 14:32:23 CST)
  • Re: Define a colvar from other colvars (Thu Dec 14 2017 - 14:57:56 CST)
  • Re: Re: metadynamics run in NAMD or using plumed in NAMD (Fri Dec 08 2017 - 12:19:43 CST)
  • Re: Free energy did not converge by using ABF (Fri Dec 08 2017 - 09:27:21 CST)
  • Re: Re: metadynamics run in NAMD or using plumed in NAMD (Fri Dec 08 2017 - 07:08:36 CST)
  • Re: nvt vs nve file (Mon Dec 04 2017 - 12:21:34 CST)
  • Re: Colvar Error (Mon Dec 04 2017 - 08:03:05 CST)
  • Re: Electric field simulation: eFieldNormalized (Wed Nov 29 2017 - 08:48:05 CST)
  • Re: nan for Drude's LP in distance-like colvars (Fri Nov 24 2017 - 12:31:37 CST)
  • Re: Bias-exchange metadynamics (Sun Nov 19 2017 - 17:30:49 CST)
  • Re: missing parameters. (Thu Nov 16 2017 - 06:19:04 CST)
  • Re: Running multiple-replicas metadynamics (Tue Nov 14 2017 - 09:07:43 CST)
  • Re: About the performance of RAMD (Fri Nov 10 2017 - 13:14:40 CST)
  • Re: Running multiple-replicas metadynamics (Thu Nov 09 2017 - 17:45:50 CST)
  • Re: Error on Settle.C when compiling NAMD with Intel Compiler (Thu Nov 09 2017 - 16:12:41 CST)
  • Re: Running multiple-replicas metadynamics (Wed Nov 08 2017 - 16:50:17 CST)
  • Re: Running multiple-replicas metadynamics (Wed Nov 08 2017 - 15:49:54 CST)
  • Re: Running multiple-replicas metadynamics (Wed Nov 08 2017 - 05:58:38 CST)
  • Re: RMSD colvar not working in NAMD2.12 Linux version (Wed Nov 08 2017 - 05:40:19 CST)
  • Re: Running multiple-replicas metadynamics (Sun Nov 05 2017 - 10:17:13 CST)
  • Re: Some water molecules are missing in psf (Fri Nov 03 2017 - 08:49:48 CDT)
  • Re: Which NAMD-Build for my local HPC? (Wed Nov 01 2017 - 08:30:27 CDT)
  • Re: Fwd: About wall clock time (Fri Oct 27 2017 - 08:39:25 CDT)
  • Re: [NAMD] Too many collective variables? (Thu Oct 26 2017 - 15:34:51 CDT)
  • Re: Error on Settle.C when compiling NAMD with Intel Compiler (Thu Oct 26 2017 - 13:56:26 CDT)
  • Re: Stack Traceback problem in colvar restrain (Wed Oct 25 2017 - 12:19:16 CDT)
  • Re: Stack Traceback problem in colvar restrain (Wed Oct 25 2017 - 10:55:59 CDT)
  • Re: building system with or without water for metadynamics (Tue Oct 17 2017 - 21:34:55 CDT)
  • Re: Fwd: About wall clock time (Tue Oct 17 2017 - 09:25:13 CDT)
  • Re: colvars: Did the orthogonality requirements of colvars change in ABF? (Mon Oct 16 2017 - 21:43:40 CDT)
  • Re: Fwd: About wall clock time (Mon Oct 16 2017 - 12:16:29 CDT)
  • Re: NAMD on Stampede 2 (Fri Oct 06 2017 - 09:08:35 CDT)
  • Re: Constrain on DNA when using ABF for protein-DNA system (Fri Oct 06 2017 - 08:15:40 CDT)
  • Re: NAMD on Stampede 2 (Fri Oct 06 2017 - 07:50:50 CDT)
  • Re: ion moving laterally during Umbrella Sampling? (Wed Oct 04 2017 - 12:05:39 CDT)
  • Re: ion moving laterally during Umbrella Sampling? (Tue Oct 03 2017 - 15:16:01 CDT)
  • Re: colvars: keepFreeEnergyFiles doesn't work in latest colvars version (Sat Sep 30 2017 - 12:32:26 CDT)
  • Re: What is the exact form of the harmonic potential used by the NAMD "constraints" option? (Tue Sep 19 2017 - 12:23:46 CDT)
  • Re: Dihedral colvar (Fri Sep 08 2017 - 14:54:44 CDT)
  • Re: applying constant force on water molecules in a particular direction (Wed Sep 06 2017 - 07:08:34 CDT)
  • Re: Regular vs US sampling runs. (Thu Aug 31 2017 - 21:34:56 CDT)
  • Re: restarting and continuing - difference (Mon Aug 14 2017 - 09:16:24 CDT)
  • Re: replica_bias and colvars (Sat Aug 12 2017 - 13:29:48 CDT)
  • Re: simulation crashing in 2nd stage equilibration (Fri Aug 11 2017 - 08:31:53 CDT)
  • Re: simulation crashing in 2nd stage equilibration (Fri Aug 11 2017 - 07:57:11 CDT)
  • Re: replica_bias and colvars (Thu Aug 10 2017 - 21:10:21 CDT)
  • Re: replica_bias and colvars (Thu Aug 10 2017 - 15:25:35 CDT)
  • Re: replica_bias and colvars (Thu Aug 10 2017 - 12:51:26 CDT)
  • Re: Software for molecular electrostatic calculations (Thu Aug 10 2017 - 08:15:28 CDT)
  • Re: finding atoms in protein-lipid system having electrostatic interaction (Wed Aug 09 2017 - 14:19:26 CDT)
  • Re: Software for molecular electrostatic calculations (Wed Aug 09 2017 - 14:16:54 CDT)
  • Re: ABF for dihedrals (Thu Aug 03 2017 - 12:53:19 CDT)
  • Re: How to calculate free energy to unbias colvars restraint? (Sat Jul 29 2017 - 09:51:01 CDT)
  • Re: How to calculate free energy to unbias colvars restraint? (Fri Jul 28 2017 - 19:10:59 CDT)
  • Re: PACE CG Model (Fri Jul 28 2017 - 13:23:43 CDT)
  • Re: Running NAMD on Intel OmniPath (Thu Jul 27 2017 - 17:53:52 CDT)
  • Re: Running NAMD on Intel OmniPath (Thu Jul 27 2017 - 14:33:38 CDT)
  • Re: polymer (Thu Jul 27 2017 - 08:14:01 CDT)
  • Re: Too many iterations in routine jacobi. (Fri Jul 21 2017 - 12:49:56 CDT)
  • Re: Compiling NAMD on stampede 2. (Fri Jul 21 2017 - 12:47:07 CDT)
  • Re: Compiling NAMD on stampede 2. (Thu Jul 20 2017 - 11:45:18 CDT)
  • Re: Compiling NAMD on stampede 2. (Thu Jul 20 2017 - 11:20:29 CDT)
  • Re: Compiling NAMD on stampede 2. (Wed Jul 19 2017 - 20:14:30 CDT)
  • Re: Simulation of the mechanical stress in NAMD (Mon Jul 17 2017 - 13:15:14 CDT)
  • Re: Simulation of the mechanical stress in NAMD (Mon Jul 17 2017 - 07:49:49 CDT)
  • Re: ABF: umbrella_int.awk (Sat Jul 15 2017 - 07:04:13 CDT)
  • Re: ABF: umbrella_int.awk (Fri Jul 14 2017 - 08:21:10 CDT)
  • Re: ABF: umbrella_int.awk (Fri Jul 14 2017 - 08:20:15 CDT)
  • Re: Collective variable remains at zero during Umbrella Sampling (Mon Jul 10 2017 - 21:46:53 CDT)
  • Re: Fwd: Atoms too fast/periodic cell too small with ABF protein-ligand (Wed Jul 05 2017 - 11:30:59 CDT)
  • Re: Simulating SDS molecules (Fri Jun 30 2017 - 09:27:36 CDT)
  • Re: veldcdfile command (Wed Jun 28 2017 - 13:36:43 CDT)
  • Re: Fwd: Atoms too fast/periodic cell too small with ABF protein-ligand (Wed Jun 28 2017 - 11:35:19 CDT)
  • Re: Fwd: Atoms too fast/periodic cell too small with ABF protein-ligand (Mon Jun 26 2017 - 11:32:58 CDT)
  • Re: measuring Euler angles and polar angles (Fri Jun 23 2017 - 10:00:36 CDT)
  • Re: measuring Euler angles and polar angles (Thu Jun 22 2017 - 12:18:00 CDT)
  • Re: Defining custom Colvars to measure pmf with Umbrella Sampling (Thu Jun 22 2017 - 09:15:21 CDT)
  • Re: Defining custom Colvars to measure pmf with Umbrella Sampling (Tue Jun 20 2017 - 21:49:26 CDT)
  • Re: Colvars wall boundaries for CoordNum (Thu Jun 08 2017 - 19:42:46 CDT)
  • Re: Querries on eABF (Tue May 30 2017 - 08:12:30 CDT)
  • Re: colvars to restrain peptide close to lipid (Sun May 21 2017 - 11:31:42 CDT)
  • Re: colvar distanceInv not propagated with a harmonic moving restraint in NAMD 2.12 (Tue May 16 2017 - 12:18:18 CDT)
  • Re: colvar distanceInv not propagated with a harmonic moving restraint in NAMD 2.12 (Tue May 16 2017 - 09:39:59 CDT)
  • Re: [NAMD] Outputting PMF at half the time using Metadynamics (Sun May 14 2017 - 22:20:14 CDT)
  • Re: [NAMD] Problem with colvar "tilt" (Fri May 12 2017 - 14:00:25 CDT)
  • Re: [NAMD] Problem with colvar "tilt" (Fri May 12 2017 - 08:43:41 CDT)
  • Re: namd 2.12 and plumed 2.3 (Tue May 02 2017 - 09:45:17 CDT)
  • Re: namd 2.12 and plumed 2.3 (Tue May 02 2017 - 08:38:06 CDT)
  • Re: Free energy calculation under external bias, (e)ABF/US/etc (Mon May 01 2017 - 10:10:18 CDT)
  • Re: colvars to restrain peptide close to lipid (Thu Apr 27 2017 - 15:13:14 CDT)
  • Re: Kinetic energy outputs (Thu Apr 27 2017 - 08:50:37 CDT)
  • Re: colvars to restrain peptide close to lipid (Wed Apr 26 2017 - 18:46:50 CDT)
  • Re: Can large number of atoms define in colvariables reduce the computational speed in adaptive biased force (ABF) simulation via lowering the GPU utility? (Wed Apr 26 2017 - 13:34:12 CDT)
  • Re: namd 2.12 and plumed 2.3 (Wed Apr 26 2017 - 12:01:51 CDT)
  • Re: Shear flow simulation setup (Wed Apr 26 2017 - 09:47:21 CDT)
  • Re: What to cite for CHARMM22 (Tue Apr 18 2017 - 12:42:19 CDT)
  • Re: how to have large coordinate values in the "coordinates PDB" file (Mon Apr 17 2017 - 14:05:40 CDT)
  • Re: patch (Fri Mar 31 2017 - 07:49:16 CDT)
  • Re: Fatal Error in NAMD (Thu Mar 30 2017 - 12:20:26 CDT)
  • Workshop on MD simulation software design (Tue Mar 21 2017 - 13:42:55 CDT)
  • Re: Defining colvars based on a region (Mon Mar 20 2017 - 20:00:09 CDT)
  • Re: Question about applying external force (Mon Mar 06 2017 - 16:23:57 CST)
  • Re: Question about applying external force (Mon Mar 06 2017 - 15:40:38 CST)
  • Re: colvars: Error: Feature unavailable:compute total collective force only from one group center (Wed Mar 01 2017 - 02:04:00 CST)
  • Re: colvars not scaling well in NAMD 2.10 (Thu Feb 23 2017 - 21:58:43 CST)
  • Re: colvars: Error: Feature unavailable:compute total collective force only from one group center (Thu Feb 23 2017 - 21:50:08 CST)
  • Re: colvars: Error: Feature unavailable:compute total collective force only from one group center (Thu Feb 23 2017 - 14:44:00 CST)
  • Re: colvars: Error: Feature unavailable:compute total collective force only from one group center (Thu Feb 23 2017 - 03:10:20 CST)
  • Re: Metadynamics state file (Thu Feb 23 2017 - 03:09:17 CST)
  • Re: Metadynamics state file (Fri Feb 17 2017 - 12:22:05 CST)
  • Re: about colvar module in NAMD (Wed Feb 01 2017 - 12:49:24 CST)
  • Re: about colvar module in NAMD (Wed Feb 01 2017 - 12:34:57 CST)
  • Re: about colvar module in NAMD (Wed Feb 01 2017 - 12:31:36 CST)
  • Re: [NAMD] Using as collective variable the minimum of a set of distances (Mon Jan 30 2017 - 17:07:07 CST)
  • Re: how do I restart umbrella sampling calculations? (Tue Jan 24 2017 - 16:09:13 CST)
  • Re: how do I restart umbrella sampling calculations? (Tue Jan 24 2017 - 15:20:38 CST)
  • Re: how do I restart umbrella sampling calculations? (Tue Jan 24 2017 - 14:50:41 CST)
  • Re: [NAMD] Using ABF to study separation of two molecules (Mon Jan 23 2017 - 09:15:16 CST)
  • Re: [NAMD] Using ABF to study separation of two molecules (Mon Jan 23 2017 - 08:43:26 CST)
  • Re: minimizing each structure of a DCD file (Sun Jan 22 2017 - 11:28:05 CST)
  • Re: ABF with alpha colvar? (Sat Jan 21 2017 - 15:21:21 CST)
  • Re: dihedral colvar (Tue Jan 17 2017 - 20:47:39 CST)
  • Re: multiple replicas metadynamics (Tue Jan 10 2017 - 15:40:43 CST)
  • Re: multiple replicas metadynamics (Tue Jan 10 2017 - 11:37:00 CST)
  • Re: How to perform REMD of a system a membrane-protein system? (Tue Jan 10 2017 - 10:09:04 CST)
  • Re: How to restart metadynamics in namd (Mon Jan 09 2017 - 00:11:17 CST)
  • Re: How to restart metadynamics in namd (Sun Jan 08 2017 - 23:59:54 CST)
  • Re: multiple replicas metadynamics (Sun Jan 08 2017 - 17:37:21 CST)
  • Re: Metadynamics simulation (Thu Jan 05 2017 - 09:51:08 CST)
  • Re: Metadynamics simulation (Wed Jan 04 2017 - 12:16:25 CST)
  • Re: Running IMD with TMD (domain restraints) (Wed Jan 04 2017 - 08:36:46 CST)
  • Re: How to perform REMD of a system a membrane-protein system? (Wed Jan 04 2017 - 08:24:18 CST)
  • Re: Query regarding colvar distanceZ (Tue Dec 27 2016 - 13:20:42 CST)
  • Re: Problem with using autoPSF on TMCL lipid (Fri Dec 16 2016 - 11:18:21 CST)
  • Re: NAMD Energies (Wed Dec 14 2016 - 13:53:02 CST)
  • Re: NAMD Energies (Wed Dec 14 2016 - 13:47:16 CST)
  • Re: using colvars to constrain two atoms in a direction (Wed Dec 14 2016 - 11:11:00 CST)
  • Re: using colvars to constrain two atoms in a direction (Wed Dec 14 2016 - 10:49:31 CST)
  • Re: using colvars to constrain two atoms in a direction (Wed Dec 14 2016 - 10:40:57 CST)
  • Re: using colvars to constrain two atoms in a direction (Wed Dec 14 2016 - 10:22:39 CST)
  • Re: protonating ASP and GLU (Tue Dec 13 2016 - 13:06:05 CST)
  • Re: Problem with alpha colvar in NAMD 2.12b1 (Fri Dec 09 2016 - 17:14:34 CST)
  • Re: Setting up symmetry restraints in a homo-dimer with non-equal number of residues (Fri Dec 09 2016 - 12:34:43 CST)
  • Re: Problem with alpha colvar in NAMD 2.12b1 (Thu Dec 08 2016 - 16:04:41 CST)
  • Re: query on OuputTotalforce Vs OnesiteTotal force ? (Tue Nov 29 2016 - 10:20:36 CST)
  • Re: query on OuputTotalforce Vs OnesiteTotal force ? (Tue Nov 29 2016 - 10:14:34 CST)
  • Re: Query on colvar distanceZ (Mon Nov 21 2016 - 11:10:57 CST)
  • Re: Crashes with dihedral PC (Tue Nov 15 2016 - 22:40:17 CST)
  • Re: SMD restraints (Tue Nov 15 2016 - 13:17:17 CST)
  • Re: Queries regarding metadynamics and .pmf visualization (Tue Nov 15 2016 - 10:40:15 CST)
  • Re: SMD restraints (Mon Nov 14 2016 - 15:59:07 CST)
  • Re: SMD restraints (Mon Nov 14 2016 - 15:17:59 CST)
  • Re: NAMD2.12b1 and CUDA (Thu Nov 10 2016 - 11:09:04 CST)
  • Re: Re: no response from mail list (Tue Nov 01 2016 - 09:36:49 CDT)
  • Re: is it possible to restrict the access of ions to certain volume? (Mon Oct 31 2016 - 15:43:34 CDT)
  • Re: Tcl clock (Wed Oct 05 2016 - 10:58:47 CDT)
  • Re: Running REMD (Mon Sep 19 2016 - 11:22:52 CDT)
  • Re: Umbrella sampling colvars DistanceZ deviates a lot (Wed Sep 14 2016 - 08:32:43 CDT)
  • Re: Umbrella sampling colvars DistanceZ deviates a lot (Tue Sep 13 2016 - 15:16:14 CDT)
  • Re: Umbrella sampling colvars DistanceZ deviates a lot (Tue Sep 13 2016 - 11:23:56 CDT)
  • Re: interpretation of eigenvec colvar? (Tue Aug 23 2016 - 20:29:37 CDT)
  • Re: How to replace NAMD Eletrostatic Forces (Fri Aug 05 2016 - 09:45:05 CDT)
  • Re: metadynamics and pmf file (Tue Jul 05 2016 - 16:29:10 CDT)
  • Re: namd2 or charmrun ++local ? (Fri Jun 17 2016 - 13:18:48 CDT)
  • Re: Colvars order in the pmf file (Mon Jun 06 2016 - 09:57:38 CDT)
  • Re: Umbrella sampling of 2 CNT's taking distance as collective variable (Wed Jun 01 2016 - 05:07:50 CDT)
  • Re: FES analysis (Tue May 24 2016 - 16:00:51 CDT)
  • Re: Colvars: Unable to restrict rotation and translation along y and z axes (Fri May 20 2016 - 10:33:27 CDT)
  • Re: Colvars: Unable to restrict rotation and translation along y and z axes (Wed May 18 2016 - 08:23:14 CDT)
  • Re: Excessively high dE_avg values in FEP output (NAMD CVS) (Mon May 16 2016 - 18:51:55 CDT)
  • Re: Colvars crossing "upperboundary" limit (Tue May 10 2016 - 15:25:18 CDT)
  • Re: rotation angle (Wed Apr 20 2016 - 13:51:43 CDT)
  • Re: ERROR: ofstream_namd::close() called when file is not open (Mon Apr 18 2016 - 07:36:01 CDT)
  • Re: ERROR: ofstream_namd::close() called when file is not open (Mon Apr 18 2016 - 06:40:09 CDT)
  • Re: Corrfunc output not generated (Thu Apr 14 2016 - 17:41:44 CDT)
  • Re: Corrfunc output not generated (Tue Apr 12 2016 - 22:00:04 CDT)
  • Re: Corrfunc output not generated (Tue Apr 12 2016 - 16:16:00 CDT)
  • Re: Metadynamics simulation with Radius of Gyration and RMSD variation - 2 (Mon Apr 11 2016 - 10:08:14 CDT)
  • Re: Metadynamics simulation with Radius of Gyration and RMSD variation - 1 (Mon Apr 11 2016 - 10:02:45 CDT)
  • Re: Steered MD diminishing distances (Sat Apr 02 2016 - 20:56:34 CDT)
  • Re: Making NAMD aware of Tcl packages? (Thu Mar 31 2016 - 11:36:20 CDT)
  • Re: Making NAMD aware of Tcl packages? (Thu Mar 31 2016 - 10:17:30 CDT)
  • Re: varying two colvar distances simultaneously (Fri Mar 25 2016 - 17:22:37 CDT)
  • Re: varying two colvar distances simultaneously (Thu Mar 24 2016 - 16:53:46 CDT)
  • Re: segmentation error (Fri Mar 04 2016 - 10:54:29 CST)
  • Re: Energy gradient in colvars.state file (Mon Feb 29 2016 - 14:25:35 CST)
  • Re: Replica Exchange US, Colvar suggestion (Sat Feb 13 2016 - 13:21:00 CST)
  • Re: Regarding system forces in NAMD (Fri Jan 08 2016 - 08:36:45 CST)
  • Re: Regarding system forces in NAMD (Thu Jan 07 2016 - 09:18:35 CST)
  • Re: Regarding system forces in NAMD (Thu Jan 07 2016 - 09:14:45 CST)
  • Re: Regarding system forces in NAMD (Thu Jan 07 2016 - 09:10:39 CST)
• Gianluca Interlandi
  • Re: Should you cap C and N termini? (Thu Feb 18 2016 - 12:57:24 CST)
• giulia palermo
  • MDFF based on known EM maps (Tue Jun 28 2016 - 12:08:12 CDT)
  • rotation angle (Wed Apr 20 2016 - 12:25:16 CDT)
  • Steered MD diminishing distances (Sat Apr 02 2016 - 20:29:14 CDT)
  • problem in running targeted MD (Wed Feb 24 2016 - 19:56:11 CST)
• Goedde, Chris
  • Re: namd2.exe has stopped working, NAMD Energy (Wed Feb 01 2017 - 14:45:02 CST)
• Grace Brannigan
  • Re: Neutralize a box for FEP (Wed Apr 12 2017 - 13:08:16 CDT)
  • Re: LJcorrection option in NAMD (Mon Jun 27 2016 - 06:41:33 CDT)
  • Re: LJcorrection option in NAMD (Tue Jun 21 2016 - 13:03:24 CDT)
• Grant Schauer
  • namdenergy and bigdcd (Thu Jun 02 2016 - 23:58:23 CDT)
• Greipel.Joachim_at_mh-hannover.de
  • AW: vmd-l: Building NAMD 2.12 from Source with IB and CUDA (Thu Mar 02 2017 - 05:53:58 CST)
  • Compiling charm/NAMD with an alternative gcc, e.g. gcc 6.x (Mon Feb 06 2017 - 08:54:08 CST)
  • WG: vmd-l: NAMD 2.11 Cuda does not work with Quadro FX 3800 (Mon Mar 14 2016 - 04:47:28 CDT)
  • AW: vmd-l: NAMD 2.11 Cuda does not work with Quadro FX 3800 (Fri Mar 11 2016 - 01:47:27 CST)
• grenier_at_cinam.univ-mrs.fr
  • RE: convert .xyz file in .psf file for non-protein molecule (Fri Sep 09 2016 - 02:51:25 CDT)
  • convert .xyz file in .psf file for non-protein molecule (Thu Sep 08 2016 - 10:20:03 CDT)
• Götz, Alexander
  • Solvent box fluctuations (Mon Mar 27 2017 - 11:56:09 CDT)
  • Re: NAMD breaks with wrong timestep (Sat Oct 22 2016 - 10:19:42 CDT)
• Götz, Alexander
  • AW: Solvent box fluctuations (Wed Mar 29 2017 - 03:37:59 CDT)
  • NAMD breaks with wrong timestep (Fri Oct 21 2016 - 08:23:33 CDT)
• Haleh a
  • adaptive biasing force with RMSD colvar (Thu Mar 17 2016 - 11:39:45 CDT)
• Hamed Fadaei
  • Re: Writing number of atoms in a specific group to a file (Fri Dec 16 2016 - 12:52:06 CST)
  • Writing number of atoms in a specific group to a file (Fri Dec 16 2016 - 11:35:24 CST)
  • Re: using colvars to constrain two atoms in a direction (Wed Dec 14 2016 - 11:02:37 CST)
  • Re: using colvars to constrain two atoms in a direction (Wed Dec 14 2016 - 10:34:08 CST)
  • using colvars to constrain two atoms in a direction (Wed Dec 14 2016 - 10:15:20 CST)
• Hannes Loeffler
  • Re: pKa calculation with thermodynamic integration (TI) (Wed May 17 2017 - 03:37:52 CDT)
  • Re: Solvation free energy difference of alchemical transformation of K+ into Na+ (Tue Jan 10 2017 - 09:59:35 CST)
  • Re: Solvation free energy difference of alchemical transformation of K+ into Na+ (Tue Jan 10 2017 - 06:15:02 CST)
  • Re: Solvation free energy difference of alchemical transformation of K+ into Na+ (Mon Jan 09 2017 - 01:55:35 CST)
• Hao Dong
  • energy difference between HSE and HSD (Mon May 08 2017 - 23:48:48 CDT)
  • performance of GPU calculations (Sun Nov 06 2016 - 21:11:40 CST)
• Haohao
  • Re: Re: I don't have any eabf output file. (Tue Jul 25 2017 - 06:20:33 CDT)
  • Re: Re: I don't have any eabf output file. (Tue Jul 25 2017 - 06:14:48 CDT)
• Haohao Fu
  • Re: (Fri Dec 29 2017 - 21:36:33 CST)
  • Re: colvars: Error: keyword "translatereference" is not supported, or not recognized in this context. (Sun Dec 17 2017 - 23:54:10 CST)
  • Re: Script for Terachem QMMM (Thu Dec 14 2017 - 07:13:47 CST)
  • Re: Periodic molecules in NAMD (Wed Dec 13 2017 - 22:14:16 CST)
  • Re: problem in writing the coor files (Mon Nov 06 2017 - 23:27:01 CST)
  • Re: Psf file generation with Gromacs Parameters (Mon Nov 06 2017 - 23:22:05 CST)
  • Re: Build NAMD with CUDA for unix workstation (centos 7) (Wed Sep 20 2017 - 03:25:16 CDT)
  • Re: Build NAMD with CUDA for unix workstation (centos 7) (Wed Sep 20 2017 - 02:22:17 CDT)
  • Re: The number of QM atoms received is different than expected (Fri Sep 08 2017 - 04:23:59 CDT)
  • The number of QM atoms received is different than expected (Fri Sep 08 2017 - 04:01:24 CDT)
  • Re: QM atoms outside the PBC boundary in QM/MM calculation (Sun Sep 03 2017 - 08:56:44 CDT)
  • QM atoms outside the PBC boundary in QM/MM calculation (Sat Sep 02 2017 - 21:55:26 CDT)
  • Re: Gyration in colvars doesn't work with eABF. (Thu Jun 15 2017 - 02:17:55 CDT)
• Hardy, David Joseph
  • Re: Gradual Heating Periodic Error (Tue Sep 13 2016 - 14:13:52 CDT)
• Harish Srinivasan
  • psfgen giving wrong structure in the autopdb file (Thu Apr 06 2017 - 01:37:29 CDT)
  • Choice of bromide ion LJ parameters (Tue Mar 07 2017 - 07:03:16 CST)
  • Re: readable output of gbis.coor (Sat Jan 07 2017 - 01:58:23 CST)
  • The use of NPT or NVT ensemble to observe dynamical parameters (Mon Jan 02 2017 - 02:27:50 CST)
  • Re: Regarding Trajectory files (Mon Dec 26 2016 - 23:44:52 CST)
  • Re: Regarding Trajectory files (Mon Dec 26 2016 - 23:44:03 CST)
  • NVE simulations in NAMD - the right choice of timesteps and parameters (Tue Nov 29 2016 - 04:54:32 CST)
  • A common tool to read the output of NAMD run (Mon Nov 28 2016 - 06:28:00 CST)
  • Switch off rescale temperature after some number of timesteps (Wed Oct 26 2016 - 01:05:50 CDT)
• Hartling, Kathryn
  • TIP4P water with flexible bonds (Wed May 18 2016 - 14:32:24 CDT)
• hem_chandra_at_iitg.ernet.in
  • wrong pdb struvture generated while using patch (Fri Apr 07 2017 - 02:06:11 CDT)
  • patch (Fri Mar 31 2017 - 04:03:15 CDT)
  • patch (Mon Mar 27 2017 - 23:28:53 CDT)
  • gbis for acetonitrile (Sat Mar 11 2017 - 00:40:15 CST)
  • readable output of gbis.coor (Sat Jan 07 2017 - 00:43:19 CST)
  • MD using implicit solvent (Fri Dec 30 2016 - 05:51:58 CST)
• Hemanth Vemuri
  • Collective variable remains at zero during Umbrella Sampling (Sun Jul 09 2017 - 23:59:18 CDT)
  • Re: Defining custom Colvars to measure pmf with Umbrella Sampling (Thu Jun 22 2017 - 01:34:15 CDT)
  • Re: Defining custom Colvars to measure pmf with Umbrella Sampling (Thu Jun 22 2017 - 00:26:31 CDT)
  • Defining custom Colvars to measure pmf with Umbrella Sampling (Tue Jun 20 2017 - 00:25:29 CDT)
• Horia Jalily Hasani
  • Re: REMD and sortreplicas program (Tue Sep 13 2016 - 10:34:22 CDT)
  • Re: REMD and sortreplicas program (Mon Sep 12 2016 - 11:21:55 CDT)
  • Re: REMD and sortreplicas program (Thu Sep 08 2016 - 12:22:39 CDT)
  • REMD and sortreplicas program (Wed Sep 07 2016 - 19:10:49 CDT)
  • Re: AW: Replica Exchange: Equilibrating at each temperature (Tue Jun 07 2016 - 11:21:09 CDT)
  • Re: AW: Replica Exchange: Equilibrating at each temperature (Thu Jun 02 2016 - 10:59:56 CDT)
  • Re: Replica Exchange: Equilibrating at each temperature (Tue May 31 2016 - 11:18:08 CDT)
  • Replica Exchange: Equilibrating at each temperature (Mon May 30 2016 - 11:28:24 CDT)
• HOUSTON Douglas
  • Re: AW: REMD on HPC (Tue Mar 07 2017 - 02:33:29 CST)
  • REMD on HPC (Mon Mar 06 2017 - 08:15:25 CST)
• Hyun
  • topology file for the residue CSO (Fri Jun 23 2017 - 11:43:38 CDT)
  • Re: Charm++ supports RoCE ? (Mon Mar 20 2017 - 22:22:40 CDT)
  • Charm++ supports RoCE ? (Thu Mar 16 2017 - 18:06:01 CDT)
  • generating nodelist and error (Thu Mar 16 2017 - 10:10:19 CDT)
• Ianni, James C CTR USARMY RDECOM ARL (US)
  • NAMD_2.12b1 build on Cray XC40 is failing (Mon Dec 12 2016 - 14:35:32 CST)
• Ipsita Basu
  • bond energy high (Wed Feb 03 2016 - 05:15:35 CST)
• Isaac Twelves
  • Water permeation through aquaporin-Z (Fri Jul 07 2017 - 13:04:37 CDT)
• istamkos_at_auth.gr
  • Re: Building namd 2.12 from source an ARM64 architecture (Fri Sep 29 2017 - 17:38:21 CDT)
  • Building namd 2.12 from source an ARM64 architecture (Wed Sep 27 2017 - 17:06:00 CDT)
  • Protein trapped on an edge of the simulation cell using C36 force field (Tue Jul 11 2017 - 03:15:51 CDT)
  • Protein trapped on an edge of the simulation cell using C36 force field (Tue Jul 04 2017 - 01:25:13 CDT)
• Ivaylo Nikolaev Ivanov
  • Ph.D. positions available (Tue May 17 2016 - 10:10:41 CDT)
  • Postdoc position available (Tue May 17 2016 - 10:05:18 CDT)
• Jackson Cavett
  • NAMD Equil Config (Thu Sep 22 2016 - 07:24:53 CDT)
  • Re: Gradual Heating Periodic Error (Tue Sep 13 2016 - 15:39:42 CDT)
  • Re: Gradual Heating Periodic Error (Tue Sep 13 2016 - 10:32:22 CDT)
  • Re: Gradual Heating Periodic Error (Tue Sep 13 2016 - 09:01:43 CDT)
  • Gradual Heating Periodic Error (Tue Sep 13 2016 - 08:34:30 CDT)
• Jacob Usadi
  • Enhanced sampling methods for oligomers (Fri Oct 20 2017 - 15:33:34 CDT)
• Jamal Zanjani
  • constant velocity pulling (Thu Mar 31 2016 - 06:04:18 CDT)
• James Starlight
  • Radial pair distribution function for internal water analysis (Thu Aug 31 2017 - 05:49:39 CDT)
  • Functional role of the internal water channel within the receptor (Tue Aug 08 2017 - 07:42:07 CDT)
  • "Periodic cell has become too small for original patch grid!" with membrane system on GPU (Thu Jul 20 2017 - 06:03:29 CDT)
  • Simulation of the mechanical stress in NAMD (Mon Jul 17 2017 - 02:55:30 CDT)
  • Re: Shear flow simulation setup (Thu Apr 27 2017 - 07:09:25 CDT)
  • Shear flow simulation setup (Wed Apr 26 2017 - 08:51:54 CDT)
  • Re: Simulation of metalo-binding proteins (Thu Nov 24 2016 - 14:44:03 CST)
  • Re: Simulation of metalo-binding proteins (Thu Nov 24 2016 - 14:01:08 CST)
  • Simulation of metalo-binding proteins (Wed Nov 23 2016 - 13:52:38 CST)
  • Shear Stress modelling in NAMD (Sun Sep 11 2016 - 05:12:26 CDT)
• Jan Brezovsky
  • Positions for Ph.D. candidates in biomolecular modeling (Thu Feb 02 2017 - 05:30:48 CST)
• Jan Fredin
  • NAMD How to calculate ns/day (Wed Dec 07 2016 - 16:02:16 CST)
• jashnvareh 1395
  • Modifying equilibrium distance for part of carbon nanotubes in parameter file (Tue Dec 27 2016 - 02:55:42 CST)
  • Modifying equilibrium distance for a specific region of carbon nanotube in the parameter file (Mon Dec 26 2016 - 08:30:59 CST)
• Jason Swails
  • Re: Why wrapped and unwrapped trajectories show different energies over the time? (Sun Apr 24 2016 - 00:23:50 CDT)
  • Re: Replica Exchange (Tue Jan 19 2016 - 15:06:24 CST)
• JC Gumbart
  • Re: [NAMD] Question about patches (Tue Dec 26 2017 - 09:26:12 CST)
  • Re: [NAMD] Question about patches (Sun Dec 24 2017 - 15:16:10 CST)
  • Re: margin and pressure in CUDA version (Wed Sep 27 2017 - 12:55:49 CDT)
  • margin and pressure in CUDA version (Wed Sep 27 2017 - 11:48:52 CDT)
  • Re: Periodic cell too small with GPUs, not with pur CPUs (Sat Aug 26 2017 - 08:11:13 CDT)
  • Re: Periodic cell too small with GPUs, not with pur CPUs (Fri Aug 25 2017 - 17:09:49 CDT)
  • Re: replica_bias and colvars (Sat Aug 12 2017 - 06:49:35 CDT)
  • Re: replica_bias and colvars (Thu Aug 10 2017 - 16:17:21 CDT)
  • replica_bias and colvars (Thu Aug 10 2017 - 12:07:45 CDT)
  • Re: Studying Folding of 870 Small Peptides. Computationally Feasible? (Sat Dec 17 2016 - 19:18:46 CST)
  • Re: Studying Folding of 870 Small Peptides. Computationally Feasible? (Sat Dec 17 2016 - 18:48:50 CST)
  • Re: Problem with alpha colvar in NAMD 2.12b1 (Fri Dec 09 2016 - 16:58:23 CST)
  • Re: CHARMM22-STAR force field for NAMD (Tue Nov 01 2016 - 21:28:04 CDT)
  • Re: interpretation of eigenvec colvar? (Tue Aug 23 2016 - 22:12:48 CDT)
  • interpretation of eigenvec colvar? (Tue Aug 23 2016 - 20:02:37 CDT)
  • Re: unbinding free energy using ABF (Tue Jul 05 2016 - 18:28:59 CDT)
  • Re: unbinding free energy using ABF (Thu Jun 30 2016 - 15:51:09 CDT)
  • Re: PME vs. cutoff with switching function (Mon Jun 27 2016 - 00:33:36 CDT)
  • Re: Tesla K80 vs 3 x GTX 980Ti (Mon Jun 27 2016 - 00:26:31 CDT)
  • Re: LJcorrection option in NAMD (Mon Jun 27 2016 - 00:23:12 CDT)
  • Re: ATP - CGENFF (Thu Jun 09 2016 - 09:36:37 CDT)
  • Re: No parameter for ribose ring, Charmm 27 (Mon May 30 2016 - 07:19:44 CDT)
  • Re: setting up simulation in vmd using charmm 36 forcefield (Mon May 30 2016 - 07:29:44 CDT)
  • Re: No parameter for ribose ring, Charmm 27 (Fri May 27 2016 - 14:14:17 CDT)
  • Re: No parameter for ribose ring, Charmm 27 (Thu May 26 2016 - 18:42:52 CDT)
  • namd leaves zombie processes on nodes? (Mon May 23 2016 - 10:01:45 CDT)
  • Re: H-bonds in charmm36 with namd2.11 (Mon May 23 2016 - 08:59:24 CDT)
  • Re: H-bonds in charmm36 with namd2.11 (Sat May 21 2016 - 18:44:09 CDT)
  • Re: Re: vmd-l: CHARMM36 alleged missing CC CT1 NH2 angle params (Tue May 17 2016 - 09:29:52 CDT)
  • Re: excluding non-bonded interactions between two proteins (Wed May 04 2016 - 19:04:43 CDT)
  • excluding non-bonded interactions between two proteins (Wed May 04 2016 - 18:16:26 CDT)
  • Re: NAMD 2.11 released (Tue Jan 05 2016 - 16:16:03 CST)
• Jean-François Fabre
  • Missing atom type for hydroperoxide (Tue Jun 14 2016 - 10:48:55 CDT)
  • Dynamics of an interface Water/Hexane (Wed Apr 13 2016 - 07:54:17 CDT)
• jeevan gc
  • Re: Regular vs US sampling runs. (Fri Sep 01 2017 - 16:32:20 CDT)
  • Re: Regular vs US sampling runs. (Fri Sep 01 2017 - 11:32:27 CDT)
  • Re: Regular vs US sampling runs. (Thu Aug 31 2017 - 20:13:38 CDT)
  • Regular vs US sampling runs. (Thu Aug 31 2017 - 18:23:43 CDT)
  • Re: GaMD in NAMD (Sun Jun 18 2017 - 10:49:40 CDT)
  • Re: SMD Constant velocity pulling (Wed Jul 27 2016 - 16:45:19 CDT)
• Jeff Comer
  • Re: reconstructing pmf (Tue Dec 19 2017 - 12:52:21 CST)
  • Re: reconstructing pmf (Tue Dec 19 2017 - 09:20:57 CST)
  • Re: How to pull protein-Monomer from DNA using ABF without any force on DNA? (Tue Jun 13 2017 - 13:37:05 CDT)
  • Re: Error regarding missing angles between perturbed groups for fep calculation (Thu May 25 2017 - 16:16:18 CDT)
  • Re: Querries on eABF (Thu May 25 2017 - 16:06:33 CDT)
  • Re: verbs-smp on a single node (Mon May 01 2017 - 11:22:48 CDT)
  • Re: colvars to restrain peptide close to lipid (Wed Apr 26 2017 - 15:31:33 CDT)
  • verbs-smp on a single node (Wed Apr 26 2017 - 15:13:40 CDT)
  • Re: Scaling behaviour of NAMD on hosts with GPU accelrators (Thu Mar 23 2017 - 12:24:23 CDT)
  • Re: Constraining bonds that aren't hydrogens - splitPatch usefulness ? (Wed Mar 22 2017 - 08:56:57 CDT)
  • Re: TMD: initial and targeted structure does not have same number of atoms (Tue Mar 07 2017 - 10:15:39 CST)
  • Re: Npt lipid simulation with electrostatics 2 (Fri Feb 17 2017 - 10:31:43 CST)
  • Re: Constraint bonds that does not include hydrogrens (Thu Dec 22 2016 - 13:24:30 CST)
  • Re: Constraint bonds that does not include hydrogrens (Thu Dec 22 2016 - 09:38:50 CST)
  • Re: Problem with using autoPSF on TMCL lipid (Fri Dec 16 2016 - 10:40:17 CST)
  • Re: About pbc (Tue Nov 15 2016 - 17:40:12 CST)
  • Re: NPT with graphene (Tue Nov 15 2016 - 08:10:57 CST)
  • Re: NAMD2.12b1 and CUDA (Thu Nov 10 2016 - 17:23:04 CST)
  • NAMD2.12b1 and CUDA (Thu Nov 10 2016 - 09:09:50 CST)
  • Re: graphene with proteins (Mon Sep 26 2016 - 15:18:07 CDT)
  • Re: Graphene Oxide Parameter File (Sat Aug 20 2016 - 16:25:07 CDT)
  • Re: Exit Command Failure (Thu Jun 23 2016 - 08:45:54 CDT)
  • Re: Applying "selectionRule" in Multiple Walker ABF (Wed Jun 22 2016 - 09:49:31 CDT)
  • Re: Free energy calculation using MM-GBSA with NAMD (Wed Jun 15 2016 - 09:10:21 CDT)
  • Re: I cannot make MD simulation constant in pressure (Mon May 23 2016 - 16:06:17 CDT)
  • Re: Adsorption energy of protein in vacuum (Mon May 23 2016 - 12:02:17 CDT)
  • Re: Restart multiple walker ABF (Thu May 19 2016 - 15:58:22 CDT)
  • Re: TIP4P water with flexible bonds (Wed May 18 2016 - 17:03:53 CDT)
  • Combining Drude structures (Mon May 16 2016 - 16:25:32 CDT)
  • Re: Coarse-grained simulation with Polarizable Water crashing (Mon May 16 2016 - 12:04:43 CDT)
  • Re: (Sun May 08 2016 - 20:19:44 CDT)
  • Re: water box and padding (Mon May 02 2016 - 11:10:45 CDT)
  • Re: Constraint failure in RATTLE algorithm for atom 6! (Tue Apr 26 2016 - 16:14:50 CDT)
  • Re: (Wed Apr 13 2016 - 08:32:23 CDT)
  • Re: (Tue Apr 12 2016 - 08:56:29 CDT)
  • Re: LJ Parameters for Au and S and harmonic constraints (Fri Apr 08 2016 - 12:52:50 CDT)
  • Re: Lowe-Andersen, Langevin and velocity rescaling thermostats (lipid bilayers) (Wed Apr 06 2016 - 08:49:16 CDT)
  • Re: AW: "Jump" in Energy and Volume graphs of my MD (Thu Mar 31 2016 - 08:44:50 CDT)
  • Re: æ�¥è‡ª"ZOU Changling" <zoucl@ihep.ac.cn>的邮件 (Thu Mar 03 2016 - 11:22:49 CST)
  • Re: PBC in lipid bilayer: receptor vs. ligand (Thu Jan 28 2016 - 12:38:45 CST)
  • LSU SuperMIC (Tue Jan 19 2016 - 16:21:39 CST)
  • Re: Aoid protein to reach periodic boundary (Tue Jan 12 2016 - 09:30:36 CST)
  • Re: solvent other than water (Wed Jan 06 2016 - 13:39:14 CST)
  • Re: NAMD 2.11 released (Wed Jan 06 2016 - 08:35:12 CST)
• Jeffrey Potoff
  • RE: Free energy did not converge by using ABF (Fri Dec 08 2017 - 13:22:44 CST)
  • RE: Is it possible to perform NVT FEP on a fluid system? (Tue Aug 09 2016 - 12:10:10 CDT)
• Jessen Lucas
  • Re: Re: How to get ideal alpha-helical, ω-shaped γ-turn, and turn/310-helix conformations (Tue Feb 07 2017 - 10:58:22 CST)
  • Re: How to get ideal alpha-helical, ω-shaped γ-turn, and turn/310-helix conformations (Tue Feb 07 2017 - 09:28:21 CST)
  • Re: about colvar module in NAMD (Wed Feb 01 2017 - 13:01:24 CST)
  • Re: about colvar module in NAMD (Wed Feb 01 2017 - 13:00:04 CST)
  • about colvar module in NAMD (Wed Feb 01 2017 - 11:47:41 CST)
  • How to get ideal alpha-helical, ω-shaped γ-turn, and turn/310-helix conformations (Thu Jan 12 2017 - 20:09:30 CST)
• Jim
  • Free energy calculation under external bias, (e)ABF/US/etc (Fri Apr 28 2017 - 20:25:57 CDT)
  • Standard Output: Benchmark vs Timing (Fri Apr 07 2017 - 17:31:55 CDT)
• Jim Phillips
  • NAMD 2.12 released (Fri Dec 23 2016 - 12:57:34 CST)
  • Re: NAMD_CUDA (Tue Dec 20 2016 - 23:30:12 CST)
  • Re: 2.11 how to remove charmrun remote-shell options (Tue Dec 20 2016 - 23:29:12 CST)
  • Re: selectively assign HIE or HID for HIS residues (Tue Dec 06 2016 - 16:08:47 CST)
  • Re: Low global exclusion count errors! (Tue Dec 06 2016 - 15:59:34 CST)
  • Re: AW: NAMD 2.11 on CRAY XK with CPU+GPU (Tue Dec 06 2016 - 15:54:31 CST)
  • Re: NAMD2.12b1 and CUDA (Thu Nov 10 2016 - 16:20:31 CST)
  • Re: AW: Trigger DCD frame from TCL? (Wed Nov 09 2016 - 16:48:00 CST)
  • NAMD 2.12b1 released (Thu Nov 03 2016 - 17:06:48 CDT)
  • NAMD survey starting (Tue Mar 15 2016 - 13:34:00 CDT)
  • Re: AW: vmd-l: NAMD 2.11 Cuda does not work with Quadro FX 3800 (Fri Mar 11 2016 - 09:45:19 CST)
• jing liang
  • performance of NAMD on KNL (Fri Sep 29 2017 - 15:10:04 CDT)
  • performance of NAMD SMP MPI version (Thu May 25 2017 - 13:38:10 CDT)
• Jiyong Park
  • Crashes with dihedral PC (Tue Nov 15 2016 - 20:28:32 CST)
• Jodi Ann Hadden
  • Hands-On Workshop on Integrative Modeling and Simulations (Wed Nov 16 2016 - 11:28:03 CST)
  • Hands-On Workshop on Computational Biophysics: November 14-18 in Atlanta, GA (Thu Sep 29 2016 - 00:27:31 CDT)
  • Hands-On Workshop on Computational Biophysics: October 17-21 in Urbana, IL (Fri Sep 16 2016 - 15:35:45 CDT)
  • Hands-On Workshop on Computational Biophysics: October 17-21 in Urbana, IL (Wed Sep 07 2016 - 18:06:53 CDT)
  • Hands-On Workshop on Computational Biophysics: November 14-18 in Atlanta, GA (Tue Aug 16 2016 - 15:41:22 CDT)
  • Hands-On Workshop on Computational Biophysics: October 17-21 in Urbana, IL (Tue Aug 16 2016 - 15:21:32 CDT)
  • NAMD Developer Workshop: May 26-27 in Chicago, IL (Fri Apr 15 2016 - 13:14:22 CDT)
  • Hands-On Workshop on Computational Biophysics: June 6-10 in Pittsburgh, PA (Wed Mar 09 2016 - 14:34:10 CST)
  • NAMD Developer Workshop: May 26-27 in Chicago, IL (Wed Mar 09 2016 - 14:31:56 CST)
• John Green
  • Re: TMD without alignment (Wed Aug 09 2017 - 17:27:25 CDT)
  • TMD without alignment (Fri Aug 04 2017 - 13:27:31 CDT)
  • Re: Setting up softcore parameters for FEP (Thu Aug 03 2017 - 12:49:20 CDT)
  • Re: Setting up softcore parameters for FEP (Thu Aug 03 2017 - 11:38:37 CDT)
  • Setting up softcore parameters for FEP (Wed Aug 02 2017 - 16:18:32 CDT)
• John Stone
  • Re: vmd-l: Inconsistent atom count (Tue Jul 05 2016 - 12:54:26 CDT)
• Josh Vermaas
  • Re: Topology Command in VMD (Mon Jun 13 2016 - 08:22:33 CDT)
  • Re: restart file - langevin options removed? (Thu Apr 28 2016 - 15:16:41 CDT)
  • Re: Running a test simulation using GPU only (without any CPU core) (Thu Apr 28 2016 - 10:09:28 CDT)
  • Re: Autoionize and topology (Wed Apr 27 2016 - 08:11:15 CDT)
  • Re: CHARMM36 and TIP3 (Tue Apr 26 2016 - 19:49:04 CDT)
  • Re: Polymer moves to the edge of water box during the simulation (Wed Apr 13 2016 - 08:02:36 CDT)
  • Re: Polymer moves to the edge of water box during the simulation (Tue Apr 12 2016 - 16:54:35 CDT)
  • Re: Dihedral parameter missing (Mon Apr 04 2016 - 16:30:27 CDT)
  • Re: charge group (Fri Mar 18 2016 - 11:36:21 CDT)
  • Re: charge group (Fri Mar 18 2016 - 11:10:51 CDT)
  • Re: AW: vmd-l: NAMD 2.11 Cuda does not work with Quadro FX 3800 (Fri Mar 11 2016 - 09:29:09 CST)
  • Re: problem with bringing down the pressure (Thu Mar 10 2016 - 19:26:12 CST)
  • Re: Tutorial example of replica exchange (Thu Mar 10 2016 - 10:04:07 CST)
  • Re: INTERNAL COORDINATES (Tue Mar 01 2016 - 08:28:33 CST)
  • Re: Non respect of sequence of commands in command file (Fri Feb 12 2016 - 11:04:28 CST)
  • Re: PBC in lipid bilayer: receptor vs. ligand (Thu Jan 28 2016 - 11:09:08 CST)
  • Re: PBC in lipid bilayer: receptor vs. ligand (Thu Jan 28 2016 - 09:43:21 CST)
  • Re: PBC in lipid bilayer: receptor vs. ligand (Wed Jan 27 2016 - 09:22:40 CST)
  • Re: compute capability (Mon Jan 25 2016 - 09:52:37 CST)
• Joshua .
  • Re: Periodic cell too small with GPUs, not with pur CPUs (Wed Jul 05 2017 - 09:39:40 CDT)
• João Ribeiro
  • Re: Creating psf file for ligand (Thu Aug 24 2017 - 13:19:32 CDT)
  • "Hands-on" Workshop on Enhanced Sampling and Free-Energy Calculation at Urbana, IL (Mon Jul 17 2017 - 14:45:43 CDT)
  • "Hands-on" Workshop on Enhanced Sampling and Free-Energy Calculation at Urbana, IL (Tue Jun 27 2017 - 13:46:57 CDT)
  • NAMD developer workshop - Chicago, May 22-23, 2017 (Tue Apr 25 2017 - 07:45:59 CDT)
  • NAMD developer workshop - Chicago, May 22-23, 2017 (Tue Apr 18 2017 - 07:45:04 CDT)
  • TCBG Live Computational Biophysics Workshop Lectures (Mon Apr 17 2017 - 09:13:24 CDT)
  • TCBG Live Computational Biophysics Workshop Lectures (Mon Apr 10 2017 - 08:24:13 CDT)
• João Ribeiro KS
  • Hands-On Workshop on Computational Biophysics: May 30 - June 2 in Pittsburgh, PA (Wed Mar 22 2017 - 10:15:40 CDT)
  • Workshop on Computational Biophysics, Urbana, IL: Application Deadline March 10th (Sat Mar 04 2017 - 15:56:47 CST)
  • NAMD developer workshop at Chicago IL, May 22-23, 2017 (Fri Feb 24 2017 - 19:23:08 CST)
  • Re: Hands-On Workshop on Computational Biophysics: April 17-21 in Urbana, IL (Fri Feb 24 2017 - 09:11:34 CST)
  • Hands-On Workshop on Computational Biophysics: April 17-21 in Urbana, IL (Fri Feb 17 2017 - 16:57:13 CST)
• Jyoti Sharma
  • Fwd: facing problem while downloading NAMD (Fri Dec 22 2017 - 03:24:19 CST)
  • facing problem while downloading NAMD (Fri Dec 22 2017 - 03:20:26 CST)
• Jérôme Hénin
  • Re: Having problem with restarting colvar distance, (Fri Dec 29 2017 - 04:34:56 CST)
  • Re: Free energy did not converge by using ABF (Fri Dec 08 2017 - 06:39:06 CST)
  • Re: Colvar Error (Mon Dec 04 2017 - 12:19:31 CST)
  • Re: Improper section for parameterization (Tue Nov 21 2017 - 07:26:17 CST)
  • Re: RMSD colvar not working in NAMD2.12 Linux version (Wed Nov 08 2017 - 05:12:12 CST)
  • Re: colvars: Did the orthogonality requirements of colvars change in ABF? (Tue Oct 17 2017 - 08:23:44 CDT)
  • Re: Constrain on DNA when using ABF for protein-DNA system (Fri Oct 06 2017 - 07:52:43 CDT)
  • Re: What is the exact form of the harmonic potential used by the NAMD "constraints" option? (Tue Sep 19 2017 - 13:03:04 CDT)
  • Re: applying constant force on water molecules in a particular direction (Mon Sep 11 2017 - 05:12:50 CDT)
  • Re: Dihedral colvar (Fri Sep 08 2017 - 08:53:28 CDT)
  • Re: Constraining and imparting motion to a geometry (Fri Sep 08 2017 - 03:56:55 CDT)
  • Re: Constraining and imparting motion to a geometry (Mon Sep 04 2017 - 07:42:47 CDT)
  • Re: Dihedral colvar (Mon Sep 04 2017 - 07:40:26 CDT)
  • Re: problem with minimization and calculation of force on a fixed atom (Fri Sep 01 2017 - 11:23:23 CDT)
  • Re: problem with minimization and calculation of force on a fixed atom (Fri Sep 01 2017 - 11:02:52 CDT)
  • Re: problem with minimization and calculation of force on a fixed atom (Fri Sep 01 2017 - 10:48:49 CDT)
  • Re: problem with minimization and calculation of force on a fixed atom (Thu Aug 31 2017 - 17:36:54 CDT)
  • Re: Proper combination of langevinHydrogen with rigidbonds (Thu Aug 31 2017 - 10:43:12 CDT)
  • Re: extracting force on a single atom (Thu Aug 31 2017 - 10:25:18 CDT)
  • Re: extracting force on a single atom (Thu Aug 31 2017 - 08:46:28 CDT)
  • Re: extracting force on a single atom (Thu Aug 31 2017 - 05:37:13 CDT)
  • Re: ABF vs Umbrella Sampling entrance barrier heights discrepancy (Thu Aug 10 2017 - 14:11:42 CDT)
  • Re: TMD without alignment (Sun Aug 06 2017 - 04:23:42 CDT)
  • Re: difference between constraining,restraining and fixing the atoms (Sun Aug 06 2017 - 10:20:51 CDT)
  • Re: ABF vs Umbrella Sampling entrance barrier heights discrepancy (Sun Aug 06 2017 - 10:17:44 CDT)
  • Re: Free energy calculation under external bias, (e)ABF/US/etc (Fri Jul 28 2017 - 12:17:05 CDT)
  • Re: ABF: umbrella_int.awk (Thu Jul 13 2017 - 13:14:33 CDT)
  • Re: Querries on eABF (Wed Jul 12 2017 - 07:24:14 CDT)
  • Re: ABF FEP with multichain receptor (Tue Jul 11 2017 - 11:52:23 CDT)
  • Re: ABF FEP with multichain receptor (Tue Jul 11 2017 - 08:12:51 CDT)
  • Re: Maintaining PBC on Collective Variables (Mon Jul 10 2017 - 08:20:55 CDT)
  • Re: ABF FEP with multichain receptor (Sat Jul 08 2017 - 15:07:36 CDT)
  • Re: ABF FEP with multichain receptor (Sat Jul 08 2017 - 05:46:31 CDT)
  • Re: veldcdfile command (Thu Jun 29 2017 - 07:11:45 CDT)
  • Re: veldcdfile command (Thu Jun 29 2017 - 05:12:26 CDT)
  • Re: veldcdfile command (Wed Jun 28 2017 - 11:41:21 CDT)
  • Re: veldcdfile command (Wed Jun 28 2017 - 11:05:58 CDT)
  • Re: measuring Euler angles and polar angles (Fri Jun 23 2017 - 10:04:46 CDT)
  • Re: Questions on implementing new collective variable in colvars. (Wed Jun 14 2017 - 07:26:16 CDT)
  • Re: principal axes in colvars (Wed Jun 14 2017 - 07:23:30 CDT)
  • Re: Questions on implementing new collective variable in colvars. (Tue Jun 13 2017 - 10:32:23 CDT)
  • Re: Querries on eABF (Tue May 30 2017 - 23:10:42 CDT)
  • Re: Querries on eABF (Tue May 30 2017 - 07:54:55 CDT)
  • Re: Querries on eABF (Fri May 26 2017 - 10:30:46 CDT)
  • Re: colvar distanceInv not propagated with a harmonic moving restraint in NAMD 2.12 (Tue May 16 2017 - 09:08:46 CDT)
  • Re: [NAMD] Problem with colvar "tilt" (Mon May 15 2017 - 08:42:37 CDT)
  • Re: energy difference between HSE and HSD (Tue May 09 2017 - 11:28:52 CDT)
  • Re: energy difference between HSE and HSD (Tue May 09 2017 - 10:51:00 CDT)
  • Re: Free energy calculation under external bias, (e)ABF/US/etc (Tue May 02 2017 - 05:07:29 CDT)
  • Re: Querries on eABF (Thu Apr 27 2017 - 16:00:31 CDT)
  • Re: More FEP using separated topologies (Wed Apr 26 2017 - 05:27:27 CDT)
  • Re: How to calculate 2d surface energy surface on segmented adaptive biased force (ABF) simulations (Tue Apr 18 2017 - 04:47:22 CDT)
  • Re: How to calculate 2d surface energy surface on segmented adaptive biased force (ABF) simulations (Mon Apr 17 2017 - 15:22:36 CDT)
  • Re: Error : components of colvar "alpha" does not support system force calculation (Fri Apr 07 2017 - 07:06:36 CDT)
  • Re: Some questions about the orthogonality of colvars in ABF. (Wed Mar 15 2017 - 07:26:23 CDT)
  • Re: A problem in ABF simulation (Mon Mar 13 2017 - 17:04:00 CDT)
  • Re: Question about applying external force (Mon Mar 06 2017 - 14:23:24 CST)
  • Re: colvars not scaling well in NAMD 2.10 (Thu Feb 23 2017 - 17:36:52 CST)
  • Re: Questions on creating constraints in NAMD (Tue Feb 21 2017 - 09:51:20 CST)
  • Re: question about Steered Molecular Dynamics (Wed Feb 15 2017 - 17:11:42 CST)
  • Re: Re: How to get ideal alpha-helical, ω-shaped γ-turn, and turn/310-helix conformations (Tue Feb 07 2017 - 10:43:53 CST)
  • Re: [NAMD] Using as collective variable the minimum of a set of distances (Sun Jan 29 2017 - 10:25:38 CST)
  • Re: How to get ideal alpha-helical, ω-shaped γ-turn, and turn/310-helix conformations (Fri Jan 13 2017 - 02:57:13 CST)
  • Re: Colvar distance xy to restrain ions (Thu Jan 12 2017 - 04:40:41 CST)
  • Re: Colvar distance xy to restrain ions (Thu Jan 12 2017 - 04:09:12 CST)
  • Re: Re: Re: RMSD based PMF calculation with umbrella sampling (Fri Dec 30 2016 - 07:49:17 CST)
  • Re: RMSD based PMF calculation with umbrella sampling (Thu Dec 22 2016 - 05:06:35 CST)
  • Re: A problem in ABF simulation (Wed Dec 14 2016 - 10:29:51 CST)
  • Re: query on OuputTotalforce Vs OnesiteTotal force ? (Tue Nov 29 2016 - 10:12:44 CST)
  • Re: A problem in ABF simulation (Tue Nov 29 2016 - 08:16:02 CST)
  • Re: tclBC during SMD and ABF simulations (Mon Nov 28 2016 - 12:45:48 CST)
  • Re: Simulation of metalo-binding proteins (Wed Nov 23 2016 - 14:11:44 CST)
  • Re: Coordinate DCD file was not created during restart of adaptive biasing force simulation using colvars. (Thu Sep 22 2016 - 14:34:27 CDT)
  • Re: Coordinate DCD file was not created during restart of adaptive biasing force simulation using colvars. (Thu Sep 22 2016 - 05:04:25 CDT)
  • Re: PMF calculation input files (Wed Aug 24 2016 - 15:22:47 CDT)
  • Re: How to replace NAMD Eletrostatic Forces (Thu Aug 04 2016 - 17:21:40 CDT)
  • Re: get seed (Fri Jul 01 2016 - 12:39:28 CDT)
  • Re: LJcorrection option in NAMD (Tue Jun 21 2016 - 09:48:12 CDT)
  • Re: Colvar orientation and CoG (Fri Jun 17 2016 - 04:43:06 CDT)
  • Re: Colvars order in the pmf file (Mon Jun 06 2016 - 11:18:51 CDT)
  • Re: Umbrella sampling of 2 CNT's taking distance as collective variable (Wed Jun 01 2016 - 10:26:27 CDT)
  • Re: More FEP using separated topologies (Fri May 27 2016 - 23:00:20 CDT)
  • Re: Excessively high dE_avg values in FEP output (NAMD CVS) (Fri May 20 2016 - 10:25:03 CDT)
  • Re: Some questions on the Deca-Alanine ABF tutorial (Fri May 20 2016 - 08:07:03 CDT)
  • Re: Some questions on the Deca-Alanine ABF tutorial (Fri May 20 2016 - 07:35:22 CDT)
  • Re: Some questions on the Deca-Alanine ABF tutorial (Thu May 19 2016 - 02:31:14 CDT)
  • Re: Some questions on the Deca-Alanine ABF tutorial (Wed May 18 2016 - 05:49:56 CDT)
  • Re: Excessively high dE_avg values in FEP output (NAMD CVS) (Tue May 17 2016 - 14:44:52 CDT)
  • Re: Some questions on the Deca-Alanine ABF tutorial (Tue May 17 2016 - 10:33:03 CDT)
  • Re: TCL Scripting for Force Calculations (Mon May 02 2016 - 11:37:19 CDT)
  • Re: Re: accessing values of 'extendedLagrangian' fictious degree of freedom (Fri Apr 29 2016 - 04:37:36 CDT)
  • Re: accessing values of 'extendedLagrangian' fictious degree of freedom (Wed Apr 27 2016 - 04:24:18 CDT)
  • Re: Alchemify Possibilities (Mon Apr 25 2016 - 11:31:32 CDT)
  • Re: Restarting ABF (Wed Mar 23 2016 - 04:28:51 CDT)
  • Re: adaptive biasing force with RMSD colvar (Sun Mar 20 2016 - 05:49:54 CDT)
  • Re: segmentation fault in ABF simulations (Mon Jan 25 2016 - 12:47:00 CST)
  • Re: segmentation fault in ABF simulations (Mon Jan 25 2016 - 12:23:01 CST)
  • Re: segmentation fault in ABF simulations (Mon Jan 25 2016 - 11:08:22 CST)
  • Re: segmentation fault in ABF simulations (Mon Jan 25 2016 - 08:14:47 CST)
  • Re: Recover the PMF along an unbiased CV (Thu Jan 14 2016 - 17:38:51 CST)
  • Re: Aoid protein to reach periodic boundary (Tue Jan 12 2016 - 05:34:22 CST)
  • Re: Regarding system forces in NAMD (Thu Jan 07 2016 - 08:37:07 CST)
  • Re: Regarding merging of .grad files obtained from ABF simulations (Thu Jan 07 2016 - 04:07:17 CST)
• Karson Bader
  • System temperature check of specific atoms , sys temp of only coupled atoms? (Thu Jul 21 2016 - 15:36:13 CDT)
  • Output temperature not agreeing with tcouple temperature (Fri May 13 2016 - 12:07:52 CDT)
• Karteek Bejagam
  • Problem with running on multiple nodes (Wed May 31 2017 - 11:33:48 CDT)
  • Re: lipid centering (Tue Apr 11 2017 - 13:26:05 CDT)
  • Re: Constraint bonds that does not include hydrogrens (Fri Dec 30 2016 - 18:14:17 CST)
  • Re: Constraint bonds that does not include hydrogrens (Thu Dec 22 2016 - 10:00:08 CST)
  • Constraint bonds that does not include hydrogrens (Wed Dec 21 2016 - 23:00:55 CST)
  • Re: A problem in ABF simulation (Tue Nov 29 2016 - 12:14:44 CST)
  • Re: Query on colvar distanceZ (Sat Nov 19 2016 - 10:12:36 CST)
• Kashish Punjani
  • Converting x,y,z coordinates to dcd file (Sun Jun 11 2017 - 12:44:18 CDT)
  • Umbrella sampling of 2 CNT's taking distance as collective variable (Wed Jun 01 2016 - 01:16:45 CDT)
• kaushik chakraborty
  • REMD (Wed Nov 23 2016 - 13:58:51 CST)
• Kenneth Huang
  • Re: (Tue Jul 26 2016 - 08:09:12 CDT)
  • Re: LSU SuperMIC (Tue Jan 19 2016 - 17:15:39 CST)
• Keshab Thapa
  • SMD: constant velocity output analysis (Develop force and displacement plot) (Mon Nov 13 2017 - 17:20:38 CST)
• Kevin C Chan
  • Re: Segmentation fault during water MD (Tue Apr 25 2017 - 06:59:07 CDT)
  • Continuing SMD from restart files (Wed Apr 19 2017 - 08:20:03 CDT)
  • Re: Umbrella sampling colvars DistanceZ deviates a lot (Tue Sep 13 2016 - 23:10:21 CDT)
  • Umbrella sampling colvars DistanceZ deviates a lot (Tue Sep 13 2016 - 11:19:08 CDT)
• Kevin Chun Chan
  • Continuing SMD from restart files (Mon Apr 24 2017 - 08:32:18 CDT)
• Kostas Malavazos
  • NAMD related theoretical questions (Wed Jul 20 2016 - 12:33:11 CDT)
  • Re: namd on Windows 10 (Thu Feb 04 2016 - 14:14:09 CST)
• Kowsar Khajeh
  • Re: error - parameter file for fluorine on a benzene ring (Wed Aug 23 2017 - 17:38:42 CDT)
• Kraus, Sebastian
  • Scaling behaviour of NAMD on hosts with GPU accelrators (Thu Mar 23 2017 - 11:18:14 CDT)
• krishna
  • (no subject) (Mon Aug 29 2016 - 03:03:21 CDT)
  • (no subject) (Tue Jul 26 2016 - 00:56:38 CDT)
• Kshatresh Dutta Dubey
  • Problem in NAMD QMMM (Sat Mar 25 2017 - 13:37:25 CDT)
• Lara rajam
  • error during minimization (Mon Feb 27 2017 - 13:07:44 CST)
  • Re: torsional restrain (Thu Feb 23 2017 - 15:23:31 CST)
  • Re: torsional restrain (Thu Feb 23 2017 - 11:56:45 CST)
  • torsional restrain (Thu Feb 23 2017 - 10:14:21 CST)
  • restraints and constraints in NAMD (Tue Feb 21 2017 - 17:42:40 CST)
• Laura Joana
  • write first point into (vel)dcd file (Mon Jul 03 2017 - 07:11:37 CDT)
  • Re: veldcdfile command (Mon Jul 03 2017 - 06:13:06 CDT)
  • Re: veldcdfile command (Fri Jun 30 2017 - 07:38:02 CDT)
  • Re: veldcdfile command (Wed Jun 28 2017 - 14:26:17 CDT)
  • Re: veldcdfile command (Wed Jun 28 2017 - 14:25:35 CDT)
  • Re: veldcdfile command (Wed Jun 28 2017 - 13:09:28 CDT)
  • veldcdfile command (Wed Jun 28 2017 - 09:59:45 CDT)
  • Re: Tcl clock (Wed Oct 05 2016 - 10:42:00 CDT)
  • Tcl clock (Tue Oct 04 2016 - 14:10:12 CDT)
  • Inconsistent atom count (Tue Jul 05 2016 - 12:04:44 CDT)
  • get seed (Fri Jul 01 2016 - 11:52:46 CDT)
  • namd2 or charmrun ++local ? (Fri Jun 17 2016 - 11:35:05 CDT)
  • firstTimestep error message (Mon May 23 2016 - 05:55:51 CDT)
• Laurent Chaloin
  • Re: Replica Exchange US, Colvar suggestion (Sat Feb 13 2016 - 02:02:24 CST)
  • Re: Replica Exchange US, Colvar suggestion (Sat Feb 13 2016 - 01:53:46 CST)
• Leandro Martínez
  • Re: question regarding rmsd (Wed Oct 05 2016 - 15:58:39 CDT)
• Lennart Nilsson
  • RE: [NAMD] Question about patches (Tue Dec 26 2017 - 04:43:30 CST)
  • RE: [NAMD] Question about patches (Mon Dec 25 2017 - 09:17:51 CST)
  • Re: missing parameters. (Mon Nov 20 2017 - 11:54:32 CST)
  • RE: What is the exact form of the harmonic potential used by the NAMD "constraints" option? (Tue Sep 19 2017 - 12:29:33 CDT)
  • RE: DNA capping (Fri Jun 02 2017 - 09:10:04 CDT)
  • RE: Autocorrelation function of Rg goes down without fluctuation around zero (Fri Aug 19 2016 - 01:42:03 CDT)
  • RE: Autocorrelation function of Rg goes down without fluctuation around zero (Thu Aug 18 2016 - 13:29:40 CDT)
  • RE: No parameter for ribose ring, Charmm 27 (Fri May 27 2016 - 15:28:43 CDT)
  • No parameter for ribose ring, Charmm 27 (Fri May 27 2016 - 05:42:02 CDT)
• Life Sciences Inc
  • Re: Npt lipid simulation with electrostatics 2 (Fri Feb 17 2017 - 11:04:12 CST)
  • Re: Npt lipid simulation with electrostatics 2 (Fri Feb 17 2017 - 10:52:36 CST)
  • Npt lipid simulation with electrostatics 2 (Thu Feb 16 2017 - 16:46:32 CST)
  • Fixing COM of one atom in selection and letting the other move (Tue Feb 14 2017 - 12:15:00 CST)
  • Re: restart a job (Wed Apr 06 2016 - 12:40:28 CDT)
• Loison Claire
  • Lowe-Andersen, Langevin and velocity rescaling thermostats (lipid bilayers) (Mon Apr 04 2016 - 07:16:22 CDT)
• Luba Simhaev
  • Movement of chloride ions during MD (Sun Oct 08 2017 - 06:21:53 CDT)
  • Cascade MDFF (Thu Mar 09 2017 - 02:34:08 CST)
  • MDFF simulations in membrane environment (Wed Feb 22 2017 - 06:15:09 CST)
• luca belmonte
  • Re: Simulation of metalo-binding proteins (Fri Nov 25 2016 - 06:47:10 CST)
  • Re: transition metal parameters (Fri Jun 24 2016 - 03:04:02 CDT)
• M. Wong
  • Re: Center of mass drift (Sat Jun 03 2017 - 04:44:18 CDT)
  • Center of mass drift (Fri Jun 02 2017 - 04:10:50 CDT)
  • Fatal error in the simulation of a water box (Wed May 31 2017 - 04:04:38 CDT)
• Ma'Mon Hatmal
  • steepest descent (Tue Nov 08 2016 - 08:58:30 CST)
  • problem in minimization (Tue Nov 08 2016 - 00:01:28 CST)
  • Problem with minimization (Thu Oct 27 2016 - 05:22:52 CDT)
• Madhulika Gupta
  • Re: SMD simulation problem (Sun May 22 2016 - 10:59:18 CDT)
  • Re: Adsorption energy of protein in vacuum (Sat May 21 2016 - 10:20:34 CDT)
  • Adsorption energy of protein in vacuum (Fri May 20 2016 - 06:01:05 CDT)
  • LJ parameters for Pd surface (Fri May 06 2016 - 08:33:03 CDT)
  • SMD in NAMD (Sat Apr 23 2016 - 05:15:34 CDT)
  • Ru surface potential (Mon Apr 11 2016 - 03:52:26 CDT)
  • Re: LJ Parameters for Au and S and harmonic constraints (Fri Apr 08 2016 - 03:24:34 CDT)
  • LJ Parameters for Au and S and harmonic constraints (Fri Apr 08 2016 - 02:18:29 CDT)
• Mahad Gatti
  • RE: Martini CG models parameters errors (Wed Sep 28 2016 - 05:40:51 CDT)
  • RE: Martini CG models parameters errors (Mon Sep 26 2016 - 04:01:32 CDT)
  • Martini CG models parameters errors (Thu Sep 22 2016 - 10:07:34 CDT)
• mahdi K
  • Ligand jump out of the protein through NPT ensemle runs (Fri Nov 25 2016 - 06:40:31 CST)
• Mahdi Tavakol
  • Maximum dihedral angle (Sun Jul 31 2016 - 03:19:16 CDT)
• Mahdiye Azadpour
  • Msd (Sat Jul 23 2016 - 23:21:09 CDT)
• Mahrukh Imtiaz
  • RE: Query regarding parameter file generation of non standard residue (Thu Sep 08 2016 - 11:22:31 CDT)
  • Re: Query regarding parameter file generation of non standard residue (Thu Sep 08 2016 - 11:01:22 CDT)
  • Query regarding parameter file generation of non standard residue (Thu Sep 08 2016 - 04:54:35 CDT)
  • Re: Query regarding parameter file generation of non standard residue (Thu Sep 08 2016 - 02:36:31 CDT)
  • Query regarding parameter file generation of non standard residue (Thu Sep 08 2016 - 00:12:37 CDT)
  • Query regarding parameter file generation of a non standard residue (Wed Sep 07 2016 - 15:12:14 CDT)
  • Repulsion of lipid bilayer during equilibration (Fri Jul 22 2016 - 05:00:41 CDT)
• Mahya Hemmat
  • Re: external HPC resource (Thu Feb 18 2016 - 17:10:12 CST)
• Maksym Korablyov
  • did anyone built NAMD with PLUMED on XSEDE (Thu Sep 01 2016 - 09:36:07 CDT)
• Malay Ranjan Biswal
  • Re: Maintaining PBC on Collective Variables (Thu Jul 13 2017 - 11:49:15 CDT)
  • Maintaining PBC on Collective Variables (Mon Jul 10 2017 - 08:17:30 CDT)
• Marawan Hussien
  • Error in thermodynamic integration for calculating ligand absolute binding free energy (Mon Jul 17 2017 - 11:45:22 CDT)
• Marcelo C. R. Melo
  • Re: Script for Terachem QMMM (Thu Dec 14 2017 - 15:45:59 CST)
  • Re: NAMD QM/MM (Tue Nov 14 2017 - 11:39:49 CST)
  • Re: QM/MM With Mopac Error (Fri Sep 15 2017 - 07:36:26 CDT)
  • Re: QM/MM Parallel Computing With Orca (Tue Sep 12 2017 - 09:45:08 CDT)
  • Re: Hybrid QM/MM NAMD: Problem Reading Extended psf files -- But some good news too (Wed Apr 26 2017 - 09:32:15 CDT)
  • Re: basis set for QM-MM dft (Wed Jan 25 2017 - 13:18:36 CST)
  • Re: QM-MM ORCA Charm++ error Could not find QM output file (Fri Jan 20 2017 - 08:33:18 CST)
  • Re: QM-MM ORCA Charm++ error Could not find QM output file (Tue Jan 17 2017 - 15:58:58 CST)
  • Re: Re: Charm++ fatal error with QM-MM MOPAC (Tue Jan 17 2017 - 15:52:04 CST)
  • Re: QM-MM ORCA Charm++ error Could not find QM output file (Mon Jan 16 2017 - 16:17:19 CST)
  • Re: Re: Charm++ fatal error with QM-MM MOPAC (Mon Jan 16 2017 - 15:52:41 CST)
  • Re: Charm++ fatal error with QM-MM MOPAC (Tue Jan 10 2017 - 08:11:02 CST)
• Marco Antonio Ramirez Martinez
  • (no subject) (Thu Mar 23 2017 - 13:23:33 CDT)
• Marco Sant
  • Re: NAMD2.11 DCD HEADER PROBLEM (Wed Sep 14 2016 - 06:37:02 CDT)
  • NAMD2.11 DCD HEADER PROBLEM (Wed Sep 14 2016 - 05:35:31 CDT)
• Maria Bykhovskaia
  • Re: NAMD for Stampede2 (Wed Aug 09 2017 - 20:21:20 CDT)
  • NAMD for Stampede2 (Wed Aug 09 2017 - 10:26:57 CDT)
• Marisol Oswald
  • Slurm Run on supercomputer (Sun Jan 22 2017 - 18:21:01 CST)
  • Linux Ubuntu Workstation Networks: Charmrun> error attaching to node '192.168.1.8': Timeout waiting for node-program to connect (Fri Dec 30 2016 - 18:51:28 CST)
  • NAMD running on a Cluster of Ubuntu Linux (Sun Oct 09 2016 - 18:37:55 CDT)
  • Graphene Oxide Parameter File (Sat Aug 20 2016 - 14:25:38 CDT)
• MARK
  • Have GPU-accelerated NAMD Questions? Join us for a Live Webinar (Fri May 20 2016 - 13:07:08 CDT)
  • NAMD Recipe for Success with GPUs! (Thu May 05 2016 - 11:35:42 CDT)
• Mark Berger
  • Recipe for Success - GPU accelerated NAMD (Wed May 04 2016 - 19:25:24 CDT)
• Mark Hilge
  • Re: Setting up symmetry restraints in a homo-dimer with non-equal number of residues (Mon Dec 12 2016 - 16:55:07 CST)
  • Setting up symmetry restraints in a homo-dimer with non-equal number of residues (Fri Dec 09 2016 - 00:17:19 CST)
• Marlon Sidore
  • Re: FATAL ERROR: Duplicate bond when going from nvt to npt (Mon Oct 09 2017 - 04:04:17 CDT)
  • Constraining bonds that aren't hydrogens - splitPatch usefulness ? (Wed Mar 22 2017 - 07:08:50 CDT)
  • Constraining bonds that don't include hydrogens (Thu Jan 05 2017 - 08:11:06 CST)
  • FATAL ERROR: Duplicate bond when going from nvt to npt (Mon Dec 12 2016 - 04:02:17 CST)
  • Re: Equivalent of gromacs' "rdd" option (Mon Jul 25 2016 - 10:44:48 CDT)
  • Re: Equivalent of gromacs' "rdd" option (Mon Jul 25 2016 - 02:56:06 CDT)
  • Re: Equivalent of gromacs' "rdd" option (Fri Jul 22 2016 - 10:16:57 CDT)
  • Equivalent of gromacs' "rdd" option (Fri Jul 22 2016 - 10:12:47 CDT)
  • Re: how to reassign dcdfreq?? (Wed Jul 13 2016 - 03:35:52 CDT)
  • Re: Applying "selectionRule" in Multiple Walker ABF (Wed Jun 22 2016 - 11:00:32 CDT)
  • Re: Colvars order in the pmf file (Mon Jun 06 2016 - 10:49:01 CDT)
  • Colvars order in the pmf file (Mon Jun 06 2016 - 09:14:53 CDT)
  • Re: Simulation runs only in background (Wed Jun 01 2016 - 04:09:16 CDT)
• Martin, Erik W
  • charmm parameters for buffer molecules (Fri Apr 07 2017 - 15:10:46 CDT)
  • protein stability in a membrane and SMD (Fri Feb 17 2017 - 17:14:31 CST)
• matthew reeves
  • Kinetic energy outputs (Thu Apr 27 2017 - 06:29:38 CDT)
  • Energy values (Fri Apr 14 2017 - 16:49:54 CDT)
  • pairInteraction commands (Sun Feb 19 2017 - 16:39:27 CST)
  • Re: PDB file creation (Wed Feb 08 2017 - 11:14:13 CST)
  • PDB file creation (Tue Feb 07 2017 - 17:52:08 CST)
  • Returning energy values from .log file. (Wed Dec 07 2016 - 14:16:44 CST)
  • Energy output values (Tue Dec 06 2016 - 13:16:00 CST)
  • Charmm++ error (Sun Nov 20 2016 - 11:29:25 CST)
• Mattia Felice Palermo
  • Occasional performance slow down using NAMD with Xeon Phi (Fri Apr 01 2016 - 09:53:37 CDT)
• Mauro Lapelosa
  • Re: Running NAMD on Intel OmniPath (Thu Jul 27 2017 - 13:06:24 CDT)
• Maxim Belkin
  • Re: (Mon May 09 2016 - 09:38:23 CDT)
  • Re: restart file - langevin options removed? (Thu Apr 28 2016 - 15:36:52 CDT)
  • Re: restart file - langevin options removed? (Thu Apr 28 2016 - 15:17:35 CDT)
  • Re: restart file - langevin options removed? (Thu Apr 28 2016 - 15:00:57 CDT)
  • Re: Dynamics of an interface Water/Hexane (Fri Apr 15 2016 - 07:39:43 CDT)
  • Re: maximum coordinate is negative for z (Fri Apr 01 2016 - 12:21:05 CDT)
  • Re: force units conversion (Fri Mar 25 2016 - 14:12:22 CDT)
  • Re: force units conversion (Fri Mar 25 2016 - 10:42:40 CDT)
  • Re: periodic boundary condition in XY, hard wall in Z - errors (Tue Mar 15 2016 - 15:50:18 CDT)
  • Re: periodic boundary condition in XY, hard wall in Z - errors (Mon Mar 14 2016 - 11:24:35 CDT)
  • Re: periodic boundary condition in XY, hard wall in Z - errors (Fri Mar 11 2016 - 15:31:50 CST)
  • Re: periodic boundary condition in XY, hard wall in Z - errors (Fri Mar 11 2016 - 14:39:06 CST)
  • Re: periodic boundary condition in XY, hard wall in Z - errors (Fri Mar 11 2016 - 14:34:35 CST)
  • Re: periodic boundary condition in XY, hard wall in Z - errors (Thu Mar 10 2016 - 15:58:45 CST)
• Maxime Boissonneault
  • Re: Running NAMD on Intel OmniPath (Thu Jul 27 2017 - 13:47:54 CDT)
  • Running NAMD on Intel OmniPath (Thu Jul 27 2017 - 13:00:04 CDT)
  • Re: AW: Scaling behaviour of NAMD on hosts with GPU accelrators (Fri Mar 24 2017 - 06:42:04 CDT)
• Mayne, Christopher G
  • Re: Tcl clock (Wed Oct 05 2016 - 09:51:15 CDT)
• md_at_novamechanics.com
  • Problem with namd2 execution on Windows GPU version (Fri Mar 17 2017 - 15:57:26 CDT)
• Mehdi Bagherpour
  • Constrain on DNA when using ABF for protein-DNA system (Thu Oct 05 2017 - 13:25:33 CDT)
  • How to pull protein-Monomer from DNA using ABF without any force on DNA? (Tue Jun 13 2017 - 12:30:29 CDT)
• MEHRAN MB
  • Re: Problems with wrapAll (Fri Jul 22 2016 - 11:35:12 CDT)
• Mert Gür
  • Re: Is GPU double-precision floating point performance important for NAMD? (Fri Jun 03 2016 - 09:20:42 CDT)
  • Is GPU double-precision floating point performance important for NAMD? (Thu Jun 02 2016 - 16:48:07 CDT)
• Michael LeVine
  • pairInteraction and PME? (Mon Sep 11 2017 - 19:20:59 CDT)
• Michelle Kuttel
  • Namd 2.12 error with Nvidia M2090 cards (Thu Aug 03 2017 - 03:30:21 CDT)
• Mihaela Drenscko
  • lipid centering (Tue Apr 11 2017 - 13:08:24 CDT)
  • Re: multiple replicas metadynamics (Tue Jan 10 2017 - 14:57:55 CST)
  • Re: multiple replicas metadynamics (Mon Jan 09 2017 - 16:20:34 CST)
  • Re: multiple replicas metadynamics (Mon Jan 09 2017 - 16:02:45 CST)
  • multiple replicas metadynamics (Fri Jan 06 2017 - 20:24:46 CST)
  • COORDINATE DCD FILE WAS NOT CREATED (Thu Sep 15 2016 - 15:42:20 CDT)
  • Energy increase with fixed atoms in POPC membrane (Wed Feb 17 2016 - 16:27:15 CST)
• Mohaddeseh Habibzadeh
  • Re: AW: not a number in NAMD log file (Wed Jan 18 2017 - 06:44:58 CST)
  • not a number in NAMD log file (Tue Jan 17 2017 - 00:31:55 CST)
  • The reason for the formation of bubbles in heating stage (Mon Jan 09 2017 - 08:16:51 CST)
  • Re: not a number error (Mon Jan 09 2017 - 08:07:12 CST)
  • not a number error (Mon Jan 09 2017 - 01:53:08 CST)
• Mohammad Hassan Khatami
  • making glucose chains using charmm36 (Mon Jul 24 2017 - 13:29:18 CDT)
• Mohan maruthi sena
  • Simulation crashes on GPU (Tue Oct 24 2017 - 05:25:10 CDT)
• Monika Madhavi
  • Gradual cooling of the system (Sun Dec 24 2017 - 22:27:27 CST)
  • Change pressure during simulation (Wed Nov 15 2017 - 01:07:39 CST)
  • Re: RMSD of backbone changes rapidly at the beginning of production run (Fri Nov 03 2017 - 18:45:34 CDT)
  • Re: RMSD of backbone changes rapidly at the beginning of production run (Thu Nov 02 2017 - 17:28:24 CDT)
  • RMSD of backbone changes rapidly at the beginning of production run (Thu Nov 02 2017 - 04:52:11 CDT)
  • How to set the configuration file for a NVE simulation (Mon Sep 04 2017 - 19:02:29 CDT)
  • Re: How to get the right density of a methane system (Fri Aug 25 2017 - 03:29:17 CDT)
  • How to get the right density of a methane system (Fri Aug 11 2017 - 21:56:51 CDT)
  • Topology and parameter files for liquid methane (Wed Aug 31 2016 - 00:24:24 CDT)
  • Re: TIP4P/2005 par file by Jordi Faraudo (Sat Jan 09 2016 - 14:38:50 CST)
  • TIP4P/2005 par file by Jordi Faraudo (Sat Jan 09 2016 - 07:16:17 CST)
• mrinal patel
  • regarding constant velocity steered molecular dynamics (Wed Feb 08 2017 - 04:07:24 CST)
• msa5
  • Pressure Profile. (Thu Nov 17 2016 - 11:06:48 CST)
  • Dear NAMD users (Thu Nov 03 2016 - 17:18:00 CDT)
  • Hi All (Tue Nov 01 2016 - 22:06:01 CDT)
• Natalia Ostrowska
  • Gradual cooling of the system (Mon Dec 25 2017 - 02:23:11 CST)
  • Re: [NAMD] Question about patches (Mon Dec 25 2017 - 01:58:35 CST)
• Natasha Gupta
  • minimization error (Fri Sep 08 2017 - 19:48:14 CDT)
  • -nan values and fatal error (Thu Sep 07 2017 - 11:24:29 CDT)
  • FATAL ERROR: Singular matrix in routine ludcmp (Fri Sep 01 2017 - 18:41:24 CDT)
  • Re: error - atom type not in psf (Fri Sep 01 2017 - 02:28:46 CDT)
  • error - atom type not in psf (Thu Aug 31 2017 - 05:56:15 CDT)
  • Re: make psf error for ligand (Fri Aug 25 2017 - 05:37:38 CDT)
  • Re: make psf error for ligand (Wed Aug 23 2017 - 17:35:34 CDT)
  • make psf error for ligand (Wed Aug 23 2017 - 16:46:55 CDT)
  • error - parameter file for fluorine on a benzene ring (Wed Aug 23 2017 - 15:07:08 CDT)
• Nathan Lim
  • FEP/REMD with NAMD2.11 - missing alchLambda? (Wed Apr 06 2016 - 20:42:58 CDT)
• Natnael Doilicho
  • Parameters for HS(CH2)11NH2 (Fri May 20 2016 - 19:06:55 CDT)
• Nehad Elsalamouny
  • FATAL ERROR: Bad global improper count! (Fri Dec 15 2017 - 23:53:33 CST)
  • Re: calculate cumulative dG (Wed Aug 30 2017 - 19:20:09 CDT)
  • calculate cumulative dG (Tue Aug 29 2017 - 00:18:16 CDT)
  • Re: problems mutating HID to TYR for free energy calculations (Tue Mar 07 2017 - 17:39:37 CST)
  • Re: problems mutating HID to TYR for free energy calculations (Tue Mar 07 2017 - 16:50:32 CST)
  • problems mutating HID to TYR for free energy calculations (Tue Mar 07 2017 - 04:27:28 CST)
  • Re: protonating ASP and GLU (Tue Dec 13 2016 - 12:48:35 CST)
  • protonating ASP and GLU (Tue Dec 13 2016 - 05:58:51 CST)
  • Re: selectively assign HIE or HID for HIS residues (Tue Dec 06 2016 - 15:03:47 CST)
  • selectively assign HIE or HID for HIS residues (Mon Dec 05 2016 - 20:19:44 CST)
  • Re: Generate psf file in x-plor format (Thu Nov 17 2016 - 19:04:06 CST)
  • Re: Generate psf file in x-plor format (Thu Nov 17 2016 - 16:59:53 CST)
  • Re: Generate psf file in x-plor format (Thu Nov 17 2016 - 14:44:40 CST)
  • Generate psf file in x-plor format (Thu Nov 17 2016 - 06:07:39 CST)
• Nehir NALINCI
  • polymer (Thu Jul 27 2017 - 03:02:49 CDT)
  • generating topology file (Mon Apr 24 2017 - 07:25:06 CDT)
  • generating topology file (Sat Apr 15 2017 - 03:09:07 CDT)
  • (no subject) (Thu Dec 08 2016 - 01:06:44 CST)
• NEHÄ°R NALINCI
  • Re: nvt vs nve file (Tue Dec 05 2017 - 00:42:47 CST)
  • nvt vs nve file (Mon Dec 04 2017 - 12:11:27 CST)
  • Re: missing parameters. (Mon Nov 20 2017 - 05:32:44 CST)
  • Re: missing parameters. (Thu Nov 16 2017 - 01:28:42 CST)
  • missing parameters. (Wed Nov 15 2017 - 06:53:06 CST)
• Nicholas M Glykos
  • Re: AW: NAMD-2.12 CUDA2 and PMECUDA problems (Wed Aug 30 2017 - 03:05:17 CDT)
  • Carma/grcarma v.1.7 released. (Mon Mar 06 2017 - 10:31:26 CST)
  • 2.12, cufft problems on a GTX 1070 ? (Sun Jan 01 2017 - 03:56:32 CST)
• Nicholas M. Glykos
  • Re: NAMD-2.12 CUDA2 and PMECUDA problems (Tue Aug 29 2017 - 12:54:40 CDT)
  • Re: 2.12, cufft problems on a GTX 1070 ? [SOLVED] (Wed Jan 11 2017 - 12:51:54 CST)
  • Re: Studying Folding of 870 Small Peptides. Computationally Feasible? (Mon Dec 19 2016 - 03:36:15 CST)
  • CHARMM22-STAR force field for NAMD (Tue Nov 01 2016 - 13:15:48 CDT)
  • CHARMM22-STAR force field for NAMD (Tue Nov 01 2016 - 13:07:39 CDT)
• Nicholus Bhattacharjee
  • Re: DNA capping (Fri Jun 02 2017 - 09:57:41 CDT)
  • Re: DNA capping (Fri Jun 02 2017 - 07:38:24 CDT)
  • Re: DNA capping (Fri Jun 02 2017 - 07:09:08 CDT)
  • DNA capping (Thu Jun 01 2017 - 04:11:48 CDT)
  • Need help with TCL script (Mon Nov 14 2016 - 13:10:13 CST)
  • Re: WHY!!! num_runs should be divisible by runs_per_frame * frames_per_restart -->REMD (Wed May 04 2016 - 10:07:53 CDT)
  • WHY!!! num_runs should be divisible by runs_per_frame * frames_per_restart -->REMD (Fri Apr 22 2016 - 08:21:46 CDT)
  • Few doubt on the numbers implying in REMD simulation (Tue Apr 12 2016 - 07:06:42 CDT)
  • Few doubt on the numbers implying in REMD simulatio (Thu Apr 07 2016 - 03:34:44 CDT)
  • Few doubt on the numbers implying in REMD simulation (Tue Apr 05 2016 - 10:00:50 CDT)
• Nicolas Martin
  • Re: Running REMD (Wed Sep 21 2016 - 03:26:18 CDT)
  • Running REMD (Wed Sep 14 2016 - 03:10:55 CDT)
  • Colvar orientation and CoG (Thu Jun 16 2016 - 09:02:28 CDT)
• Nielsen, Steven
  • RE: Free energy did not converge by using ABF (Fri Dec 08 2017 - 15:01:55 CST)
  • RE: How to get the right density of a methane system (Fri Aug 11 2017 - 23:38:18 CDT)
  • RE: [NAMD] How to build and simulate a periodic DNA in NAMD (Sat May 06 2017 - 13:49:13 CDT)
  • how to have large coordinate values in the "coordinates PDB" file (Mon Apr 17 2017 - 13:33:37 CDT)
• Nikhil Maroli
  • Re: make psf error for ligand (Thu Aug 24 2017 - 12:44:45 CDT)
  • Re: Creating psf file for ligand (Wed Aug 23 2017 - 10:07:59 CDT)
  • Re: Creating psf file for ligand (Mon Aug 21 2017 - 12:33:07 CDT)
  • NAMD performance monitor (Tue Jan 17 2017 - 06:42:41 CST)
  • water permeation through nanotube in lipid bilayer (Fri Jul 29 2016 - 07:18:45 CDT)
  • Tesla K80 vs 3 x GTX 980Ti (Sat Jun 25 2016 - 11:24:25 CDT)
  • Tesla K80 vs 3 x GTX 980ti (Sat Jun 25 2016 - 08:02:25 CDT)
  • Re: GPU configuration suggestions (Tue Mar 22 2016 - 04:31:33 CDT)
  • GPU configuration suggestions (Tue Mar 22 2016 - 00:52:25 CDT)
  • Equilibration fails for long time ,NPT (Sun Jan 03 2016 - 11:42:32 CST)
• nikolaev_at_spbau.ru
  • Segmentation fault during water MD (Tue Apr 18 2017 - 09:37:10 CDT)
  • Re: AW: problem with +devices using (Tue Apr 05 2016 - 07:41:17 CDT)
  • problem with +devices using (Tue Apr 05 2016 - 06:35:23 CDT)
• Nisler, Collin R.
  • QM/MM With Mopac Error (Wed Sep 13 2017 - 15:27:19 CDT)
  • Re: QM/MM Parallel Computing With Orca (Tue Sep 12 2017 - 11:08:47 CDT)
  • QM/MM Parallel Computing With Orca (Tue Sep 12 2017 - 09:12:59 CDT)
  • Coarse Grain of a Calcium Binding Protein (Wed Aug 09 2017 - 10:31:24 CDT)
  • Coarse Grain Angle Parameter Issue (Fri Jun 17 2016 - 22:37:42 CDT)
• Norman Geist
  • AW: Change pressure during simulation (Wed Nov 15 2017 - 01:28:06 CST)
  • AW: building system with or without water for metadynamics (Wed Oct 18 2017 - 01:35:32 CDT)
  • AW: NAMD-2.12 CUDA2 and PMECUDA problems (Fri Sep 01 2017 - 03:23:28 CDT)
  • AW: AW: NAMD-2.12 CUDA2 and PMECUDA problems (Wed Aug 30 2017 - 03:47:53 CDT)
  • AW: NAMD-2.12 CUDA2 and PMECUDA problems (Wed Aug 30 2017 - 02:13:41 CDT)
  • NAMD-2.12 CUDA2 and PMECUDA problems (Mon Aug 28 2017 - 05:54:58 CDT)
  • AW: Organic Solvent & Water Simulation (Wed Jun 21 2017 - 02:31:42 CDT)
  • AW: Scaling behaviour of NAMD on hosts with GPU accelerators (Fri Mar 24 2017 - 08:25:52 CDT)
  • AW: Scaling behaviour of NAMD on hosts with GPU accelrators (Fri Mar 24 2017 - 05:47:39 CDT)
  • AW: Scaling behaviour of NAMD on hosts with GPU accelrators (Fri Mar 24 2017 - 05:35:00 CDT)
  • AW: Scaling behaviour of NAMD on hosts with GPU accelrators (Fri Mar 24 2017 - 05:27:46 CDT)
  • AW: NAMD-2.12 handful of issues with CUDA (Fri Mar 10 2017 - 05:41:10 CST)
  • AW: NAMD-2.12 handful of issues with CUDA (Fri Mar 10 2017 - 04:55:47 CST)
  • NAMD-2.12 handful of issues with CUDA (Fri Mar 10 2017 - 03:16:13 CST)
  • AW: REMD on HPC (Mon Mar 06 2017 - 09:26:00 CST)
  • AW: FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE (Fri Feb 10 2017 - 05:34:40 CST)
  • AW: question about GPU (Wed Feb 08 2017 - 02:24:53 CST)
  • AW: FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE (Wed Feb 08 2017 - 02:22:17 CST)
  • AW: question about GPU (Tue Feb 07 2017 - 03:15:30 CST)
  • AW: question about GPU (Mon Feb 06 2017 - 09:47:28 CST)
  • AW: ++idlepoll (Mon Feb 06 2017 - 02:15:12 CST)
  • AW: High pressure calculations (Sat Feb 04 2017 - 05:33:49 CST)
  • AW: AW: AW: not a number in NAMD log file (Mon Jan 30 2017 - 01:44:14 CST)
  • AW: not a number in NAMD log file (Wed Jan 18 2017 - 01:14:12 CST)
  • AW: NAMD performance monitor (Wed Jan 18 2017 - 01:10:26 CST)
  • GBIS intrinsic radii set from aber parm7 (Fri Dec 16 2016 - 02:04:15 CST)
  • AW: NVT and NPT simulationd (Thu Dec 15 2016 - 02:20:28 CST)
  • AW: NVT and NPT simulationd (Wed Dec 14 2016 - 01:33:16 CST)
  • AW: How to continue RMSD of previous production simulation (Sat Dec 03 2016 - 05:45:35 CST)
  • AW: How to continue RMSD of previous production simulation (Sat Dec 03 2016 - 05:51:18 CST)
  • AW: Amber forcefield in namd simulation in parallel version (Fri Dec 02 2016 - 01:59:20 CST)
  • AW: Amber forcefield in namd simulation in parallel version (Thu Dec 01 2016 - 07:58:00 CST)
  • AW: Running gromacs in namd (Thu Dec 01 2016 - 01:06:23 CST)
  • AW: NAMD 2.11 on CRAY XK with CPU+GPU (Thu Dec 01 2016 - 01:04:38 CST)
  • AW: Running gromacs in namd (Wed Nov 30 2016 - 02:45:09 CST)
  • AW: Running gromacs in namd (Tue Nov 29 2016 - 01:36:48 CST)
  • AW: NPT with graphene (Tue Nov 15 2016 - 03:04:09 CST)
  • AW: AW: Trigger DCD frame from TCL? (Thu Nov 10 2016 - 02:09:22 CST)
  • AW: Trigger DCD frame from TCL? (Wed Nov 09 2016 - 02:48:33 CST)
  • AW: Trigger DCD frame from TCL? (Wed Nov 09 2016 - 02:05:50 CST)
  • Trigger DCD frame from TCL? (Tue Nov 08 2016 - 09:12:04 CST)
  • AW: Turning off and back on fixed atoms (Fri Oct 28 2016 - 04:40:22 CDT)
  • AW: vmd-l: Error connecting to localhost on port 3000 and IMD connection ended unexpectedly; connection terminated. (Thu Oct 27 2016 - 07:50:19 CDT)
  • Turning off and back on fixed atoms (Thu Oct 27 2016 - 05:14:28 CDT)
  • AW: Re: AW: Reason: FATAL ERROR: Unknown command-line option ++local (Tue Oct 11 2016 - 00:33:25 CDT)
  • AW: NAMD running on a Cluster of Ubuntu Linux (Mon Oct 10 2016 - 01:27:59 CDT)
  • AW: Reason: FATAL ERROR: Unknown command-line option ++local (Mon Oct 10 2016 - 01:24:44 CDT)
  • AW: NAMD2.11 DCD HEADER PROBLEM (Thu Sep 15 2016 - 01:09:39 CDT)
  • AW: REMD and sortreplicas program (Tue Sep 13 2016 - 01:19:34 CDT)
  • AW: REMD and sortreplicas program (Mon Sep 12 2016 - 01:38:01 CDT)
  • AW: REMD and sortreplicas program (Mon Sep 12 2016 - 01:05:39 CDT)
  • AW: REMD and sortreplicas program (Thu Sep 08 2016 - 01:41:21 CDT)
  • AW: FATAL ERROR CUDA error during equilibration using NAMD (Thu Sep 01 2016 - 01:15:55 CDT)
  • AW: NAMD Question: Generating ensemble of structures (Wed Aug 31 2016 - 01:29:49 CDT)
  • AW: Energy minimization (Tue Aug 16 2016 - 23:53:20 CDT)
  • AW: How to replace NAMD Eletrostatic Forces (Fri Aug 05 2016 - 02:33:51 CDT)
  • Possible bug in DCD writer, number of frames not in NSET but in 5-ZEROS (Wed Jul 06 2016 - 07:26:01 CDT)
  • AW: Is GPU double-precision floating point performance important for NAMD? (Fri Jun 03 2016 - 01:49:06 CDT)
  • AW: AW: Replica Exchange: Equilibrating at each temperature (Fri Jun 03 2016 - 01:39:54 CDT)
  • AW: Replica Exchange: Equilibrating at each temperature (Thu Jun 02 2016 - 01:33:55 CDT)
  • AW: Replica Exchange: Equilibrating at each temperature (Tue May 31 2016 - 08:41:23 CDT)
  • AW: Replica Exchange: Equilibrating at each temperature (Tue May 31 2016 - 04:24:52 CDT)
  • AW: Re: AW: AW: AW: why does the transition seem to be irreversible in aMD (Tue May 24 2016 - 00:57:09 CDT)
  • AW: Re: AW: AW: AW: why does the transition seem to be irreversible in aMD (Mon May 23 2016 - 08:42:04 CDT)
  • AW: AW: problem with +devices using (Tue Apr 05 2016 - 08:21:37 CDT)
  • AW: problem with +devices using (Tue Apr 05 2016 - 07:09:22 CDT)
  • AW: AW: AW: why does the transition seem to be irreversible in aMD (Tue Apr 05 2016 - 04:31:27 CDT)
  • AW: AW: why does the transition seem to be irreversible in aMD (Tue Apr 05 2016 - 03:06:43 CDT)
  • AW: why does the transition seem to be irreversible in aMD (Tue Apr 05 2016 - 02:29:42 CDT)
  • AW: Running multi-node jobs on Sun Grid Engine (Mon Apr 04 2016 - 05:32:12 CDT)
  • AW: Running multi-node jobs on Sun Grid Engine (Mon Apr 04 2016 - 01:50:27 CDT)
  • AW: Occasional performance slow down using NAMD with Xeon Phi (Mon Apr 04 2016 - 01:47:27 CDT)
  • AW: "Jump" in Energy and Volume graphs of my MD (Thu Mar 31 2016 - 01:00:46 CDT)
  • AW: GPU configuration suggestions (Tue Mar 22 2016 - 05:20:52 CDT)
  • AW: GPU configuration suggestions (Tue Mar 22 2016 - 04:26:39 CDT)
  • AW: GPU configuration suggestions (Tue Mar 22 2016 - 03:44:44 CDT)
  • AW: GPU configuration suggestions (Tue Mar 22 2016 - 02:28:40 CDT)
  • AW: AW: Testing NAMD scalability (Mon Mar 21 2016 - 03:31:30 CDT)
  • AW: Testing NAMD scalability (Mon Mar 21 2016 - 02:45:31 CDT)
  • AW: AW: Tcl script for simulated tempering? (Wed Mar 16 2016 - 05:10:14 CDT)
  • AW: AW: Tcl script for simulated tempering? (Tue Mar 15 2016 - 10:21:11 CDT)
  • AW: Tcl script for simulated tempering? (Tue Mar 15 2016 - 02:53:21 CDT)
  • AW: Tutorial example of replica exchange (Thu Mar 10 2016 - 16:53:22 CST)
  • AW: vmd-l: NAMD 2.11 Cuda does not work with Quadro FX 3800 (Thu Mar 10 2016 - 16:43:55 CST)
  • AW: Tutorial example of replica exchange (Thu Mar 10 2016 - 02:03:38 CST)
  • AW: periodic boundary condition in XY, hard wall in Z - errors (Thu Mar 10 2016 - 01:05:33 CST)
  • AW: selection error in forces script (Tue Mar 08 2016 - 01:35:26 CST)
  • AW: applying constant force only within certain part of simulation cell? (Fri Mar 04 2016 - 02:27:49 CST)
  • AW: problem in running targeted MD (Mon Feb 29 2016 - 01:37:21 CST)
  • AW: À´×Ô"ZOU Changling" <zoucl@ihep.ac.cn>µÄÓʼþ (Fri Feb 26 2016 - 06:10:11 CST)
  • AW: problem in running targeted MD (Fri Feb 26 2016 - 01:57:15 CST)
  • AW: problem in running targeted MD (Thu Feb 25 2016 - 01:38:33 CST)
  • AW: Energy increase with fixed atoms in POPC membrane (Mon Feb 22 2016 - 02:04:39 CST)
  • AW: Energy increase with fixed atoms in POPC membrane (Fri Feb 19 2016 - 01:47:51 CST)
  • AW: Energy increase with fixed atoms in POPC membrane (Thu Feb 18 2016 - 02:03:09 CST)
  • AW: vmd-l: moving atoms and updating distances (Mon Feb 15 2016 - 00:11:47 CST)
  • AW: velocity computation (Tue Feb 09 2016 - 02:22:54 CST)
  • AW: velocity computation (Mon Feb 08 2016 - 00:51:46 CST)
  • AW: Re: tclBC relective boundaries (Mon Feb 01 2016 - 00:10:45 CST)
  • AW: PBC in lipid bilayer: receptor vs. ligand (Wed Jan 27 2016 - 09:35:05 CST)
  • AW: calculating replica exchange acceptance ratio (Tue Jan 26 2016 - 08:03:40 CST)
  • AW: calculating replica exchange acceptance ratio (Mon Jan 25 2016 - 05:51:31 CST)
  • AW: calculating replica exchange acceptance ratio (Mon Jan 25 2016 - 04:37:56 CST)
  • AW: PBC BUG in coorfile + pair interaction (Mon Jan 25 2016 - 02:33:18 CST)
  • AW: calculating replica exchange acceptance ratio (Mon Jan 25 2016 - 01:13:51 CST)
  • AW: Enabling GPU for Replica exchange umbrella sampling (Mon Jan 25 2016 - 01:06:05 CST)
  • AW: Enabling GPU for Replica exchange umbrella sampling (Fri Jan 22 2016 - 03:09:24 CST)
  • AW: Re: Enabling GPU for Replica exchange umbrella sampling (Fri Jan 22 2016 - 03:07:59 CST)
  • AW: PBC BUG in coorfile + pair interaction (Thu Jan 21 2016 - 04:32:33 CST)
  • PBC BUG in coorfile + pair interaction (Thu Jan 21 2016 - 03:50:59 CST)
  • AW: [Non-DoD Source] AW: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) (Wed Jan 13 2016 - 02:17:01 CST)
  • AW: [Non-DoD Source] AW: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) (Tue Jan 12 2016 - 13:23:21 CST)
  • AW: [Non-DoD Source] AW: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) (Tue Jan 12 2016 - 08:31:52 CST)
  • AW: Compilation error across Intel 14,15 and 16 (UNCLASSIFIED) (Tue Jan 12 2016 - 02:16:38 CST)
• Obayed Ullah
  • Regarding Error on HB2 (Mon Feb 20 2017 - 18:48:56 CST)
• Oleksii Zdorevskyi
  • analyze NAMD trajectory in Curves+ (Mon Mar 06 2017 - 11:46:03 CST)
  • question about Steered Molecular Dynamics (Wed Feb 15 2017 - 08:38:22 CST)
• Olya Kravchenko
  • excluding ions based on mass (Wed Oct 04 2017 - 14:38:44 CDT)
  • Re: ion moving laterally during Umbrella Sampling? (Wed Oct 04 2017 - 11:48:43 CDT)
  • ion moving laterally during Umbrella Sampling? (Tue Oct 03 2017 - 12:45:09 CDT)
  • Re: ABF vs Umbrella Sampling entrance barrier heights discrepancy (Thu Aug 10 2017 - 12:45:48 CDT)
  • ABF vs Umbrella Sampling entrance barrier heights discrepancy (Wed Aug 02 2017 - 13:39:16 CDT)
  • Re: how do I restart umbrella sampling calculations? (Wed Jan 25 2017 - 09:19:10 CST)
  • Re: how do I restart umbrella sampling calculations? (Tue Jan 24 2017 - 16:11:17 CST)
  • Re: how do I restart umbrella sampling calculations? (Tue Jan 24 2017 - 15:44:32 CST)
  • Re: how do I restart umbrella sampling calculations? (Tue Jan 24 2017 - 15:14:55 CST)
  • how do I restart umbrella sampling calculations? (Tue Jan 24 2017 - 14:39:12 CST)
  • Re: Colvar distance xy to restrain ions (Thu Jan 12 2017 - 10:39:00 CST)
  • Re: tclBC during SMD and ABF simulations (Mon Nov 28 2016 - 19:44:01 CST)
  • tclBC during SMD and ABF simulations (Mon Nov 28 2016 - 12:36:47 CST)
  • Re: is it possible to restrict the access of ions to certain volume? (Mon Oct 31 2016 - 15:55:28 CDT)
  • is it possible to restrict the access of ions to certain volume? (Mon Oct 31 2016 - 15:28:40 CDT)
  • Re: ion escapes the channel during US simulation (Thu Sep 01 2016 - 10:17:08 CDT)
  • Re: ion escapes the channel during US simulation (Thu Sep 01 2016 - 09:03:14 CDT)
  • ion escapes the channel during US simulation (Tue Aug 30 2016 - 16:17:26 CDT)
  • targetCenters in Umbrella Sampling (Wed Aug 24 2016 - 17:50:36 CDT)
  • Re: PMF calculation input files (Wed Aug 24 2016 - 16:23:30 CDT)
  • Re: PMF calculation input files (Tue Aug 23 2016 - 10:01:05 CDT)
  • Re: PMF calculation input files (Mon Aug 22 2016 - 15:10:57 CDT)
  • PMF calculation input files (Mon Aug 22 2016 - 10:30:28 CDT)
  • how to not overwrite a modified file? (while producing coordinates for ABF/US windows) (Sat Aug 06 2016 - 07:18:56 CDT)
  • is there a way to prevent ions from entering the channel? (Thu Jul 21 2016 - 12:56:57 CDT)
  • Re: PMF with ABF for ion channels in a spherical molecule (Fri Jul 01 2016 - 15:50:15 CDT)
  • Re: PMF with ABF for ion channels in a spherical molecule (Tue Jun 28 2016 - 16:20:13 CDT)
  • Re: PMF with ABF for ion channels in a spherical molecule (Tue Jun 28 2016 - 15:35:53 CDT)
  • PMF with ABF for ion channels in a spherical molecule (Fri Jun 24 2016 - 17:01:13 CDT)
  • Re: restart file - langevin options removed? (Thu Apr 28 2016 - 15:59:09 CDT)
  • Re: restart file - langevin options removed? (Thu Apr 28 2016 - 15:28:57 CDT)
  • Re: restart file - langevin options removed? (Thu Apr 28 2016 - 15:13:00 CDT)
  • restart file - langevin options removed? (Thu Apr 28 2016 - 14:49:45 CDT)
  • Re: Constraint failure in RATTLE algorithm for atom 538 (Tue Apr 05 2016 - 10:29:38 CDT)
  • force units conversion (Thu Mar 24 2016 - 14:15:05 CDT)
  • Re: periodic boundary condition in XY, hard wall in Z - errors (Tue Mar 15 2016 - 14:48:58 CDT)
  • Re: periodic boundary condition in XY, hard wall in Z - errors (Fri Mar 11 2016 - 21:42:23 CST)
  • Re: periodic boundary condition in XY, hard wall in Z - errors (Fri Mar 11 2016 - 14:57:55 CST)
  • Re: periodic boundary condition in XY, hard wall in Z - errors (Thu Mar 10 2016 - 20:01:12 CST)
  • Re: periodic boundary condition in XY, hard wall in Z - errors (Thu Mar 10 2016 - 11:21:00 CST)
  • periodic boundary condition in XY, hard wall in Z - errors (Wed Mar 09 2016 - 21:23:05 CST)
  • Re: selection error in forces script (Tue Mar 08 2016 - 00:08:00 CST)
  • selection error in forces script (Mon Mar 07 2016 - 23:02:34 CST)
  • applying constant force only within certain part of simulation cell? (Thu Mar 03 2016 - 14:00:33 CST)
• Oscar Bastidas
  • Re: make psf error for ligand (Thu Aug 24 2017 - 13:26:58 CDT)
  • Re: make psf error for ligand (Wed Aug 23 2017 - 17:59:27 CDT)
  • Organic Solvent & Water Simulation (Tue Jun 20 2017 - 15:15:05 CDT)
  • Type of solvent water molecules (Tue Apr 18 2017 - 16:05:06 CDT)
  • What to cite for CHARMM22 (Tue Apr 18 2017 - 12:37:04 CDT)
  • Charm++ Fatal Error Question (Mon Feb 20 2017 - 11:36:53 CST)
  • Protein Penetrating Water Box (Sun Jan 29 2017 - 03:15:25 CST)
  • Re: Parameters for determining run time (Tue Nov 08 2016 - 15:33:00 CST)
  • Parameters for determining run time (Mon Nov 07 2016 - 16:10:34 CST)
  • Re: no response from mail list (Mon Oct 31 2016 - 20:16:50 CDT)
  • NAMD Execution Error (Sun Oct 30 2016 - 18:46:19 CDT)
  • NAMD Question: NAMD Message "364"-What does it mean? (Thu Oct 27 2016 - 03:34:17 CDT)
  • NAMD Question: How to run on 2-chain system (Wed Oct 26 2016 - 20:08:18 CDT)
  • Using NAMD with NMR structure (Sun Oct 23 2016 - 02:00:14 CDT)
  • NAMD Question: Generating ensemble of structures (Wed Aug 31 2016 - 00:52:20 CDT)
• P.-L. Chau
  • NAMD parallelisation / patch grid (Tue Dec 27 2016 - 04:37:15 CST)
  • NAMD 2.11 on CRAY XK with CPU+GPU (Wed Nov 30 2016 - 17:47:07 CST)
• Panagiota Kyriakou
  • Re: How to perform REMD of a system a membrane-protein system? (Mon Jan 09 2017 - 16:34:03 CST)
  • How to perform REMD of a system a membrane-protein system? (Tue Jan 03 2017 - 18:38:54 CST)
• Pardis Tabaee
  • Re: Using NAMD with NMR structure (Mon Oct 24 2016 - 16:02:48 CDT)
  • Re: Using NAMD with NMR structure (Mon Oct 24 2016 - 11:26:09 CDT)
  • Re: Using NAMD with NMR structure (Mon Oct 24 2016 - 11:20:26 CDT)
  • Re: Using NAMD with NMR structure (Mon Oct 24 2016 - 06:13:04 CDT)
  • Re: question regarding rmsd (Wed Oct 05 2016 - 13:34:41 CDT)
  • Re: question regarding rmsd (Wed Oct 05 2016 - 10:55:01 CDT)
  • Re: Re: vmd-l: CHARMM36 alleged missing CC CT1 NH2 angle params (Fri May 20 2016 - 11:12:24 CDT)
  • Re: Some questions on the Deca-Alanine ABF tutorial (Fri May 20 2016 - 09:52:09 CDT)
  • Re: Some questions on the Deca-Alanine ABF tutorial (Fri May 20 2016 - 10:01:13 CDT)
  • Re: Problem with the cross term of C NH1 CT1 C NH1 CT1 C NH1 (Fri May 06 2016 - 08:05:10 CDT)
  • Re: ------------- Processor 0 Exiting: Called CmiAbort ------------ (Thu Mar 17 2016 - 12:09:43 CDT)
• parinaz bashirbanaem
  • question about point substitution A→U (Sat Dec 30 2017 - 12:47:43 CST)
  • question about GPU (Mon Feb 06 2017 - 09:00:53 CST)
• Patrick Welche
  • velocity computation (Fri Feb 05 2016 - 13:05:25 CST)
• Payel Das
  • Postdoctoral opening in biomolecular modeling at IBM (Mon Mar 21 2016 - 16:38:19 CDT)
• Peter Freddolino
  • Re: atom selection error (Mon Dec 11 2017 - 14:26:26 CST)
  • Re: atom selection error (Mon Dec 11 2017 - 00:38:19 CST)
  • Re: atom selection error (Mon Dec 11 2017 - 00:24:47 CST)
  • Re: atom selection error (Fri Dec 08 2017 - 11:54:00 CST)
  • Re: atom selection error (Fri Dec 08 2017 - 07:59:51 CST)
  • Re: NAMD energy run in VMD (Tue Nov 21 2017 - 13:02:07 CST)
  • Re: RMSD of backbone changes rapidly at the beginning of production run (Thu Nov 02 2017 - 20:25:17 CDT)
  • Re: RMSD of backbone changes rapidly at the beginning of production run (Thu Nov 02 2017 - 09:02:13 CDT)
  • Re: FAD parameter and topology files (Tue Sep 19 2017 - 23:41:42 CDT)
  • Re: minimization error (Sat Sep 09 2017 - 22:51:23 CDT)
  • Re: coarse-grained simulations with errors "Atoms moving too fast" and "low global exclusion" (Fri Jun 09 2017 - 10:10:21 CDT)
  • Re: psfgen giving wrong structure in the autopdb file (Thu Apr 06 2017 - 19:50:01 CDT)
  • Re: Studying Folding of 870 Small Peptides. Computationally Feasible? (Sat Dec 17 2016 - 22:04:38 CST)
  • Re: psfgen - pdbalias when using readpsf (Thu Dec 15 2016 - 15:37:40 CST)
  • Re: psfgen - pdbalias when using readpsf (Thu Dec 15 2016 - 15:03:23 CST)
  • Re: psfgen - pdbalias when using readpsf (Thu Dec 15 2016 - 14:40:40 CST)
  • Re: NAMD Energies (Wed Dec 14 2016 - 13:54:52 CST)
  • Re: Parameters for determining run time (Tue Nov 08 2016 - 15:10:04 CST)
  • Re: Parameters for determining run time (Mon Nov 07 2016 - 21:21:51 CST)
  • Re: no response from mail list (Mon Oct 31 2016 - 20:36:12 CDT)
  • Re: Using NAMD with NMR structure (Sun Oct 23 2016 - 05:55:08 CDT)
  • Re: I cannot make MD simulation constant in pressure (Mon May 23 2016 - 22:56:48 CDT)
  • Re: I cannot make MD simulation constant in pressure (Mon May 23 2016 - 21:01:23 CDT)
  • Re: vmd-l: CHARMM36 alleged missing CC CT1 NH2 angle params (Mon May 16 2016 - 07:46:47 CDT)
  • Re: excluding non-bonded interactions between two proteins (Wed May 04 2016 - 19:14:34 CDT)
  • Re: excluding non-bonded interactions between two proteins (Wed May 04 2016 - 18:41:18 CDT)
  • Re: WHY!!! num_runs should be divisible by runs_per_frame * frames_per_restart -->REMD (Tue May 03 2016 - 11:08:17 CDT)
  • Re: (Fri Apr 22 2016 - 12:26:51 CDT)
  • Re: (Tue Apr 19 2016 - 10:03:52 CDT)
  • Re: (Sat Apr 16 2016 - 20:14:41 CDT)
  • Re: "Jump" in Energy and Volume graphs of my MD (Thu Mar 31 2016 - 09:13:46 CDT)
  • Re: "Jump" in Energy and Volume graphs of my MD (Wed Mar 30 2016 - 19:33:49 CDT)
  • Re: "Jump" in Energy and Volume graphs of my MD (Wed Mar 30 2016 - 15:56:22 CDT)
  • Re: "Jump" in Energy and Volume graphs of my MD (Wed Mar 30 2016 - 15:23:46 CDT)
  • Re: Basic validation of CGenFF (Mon Mar 21 2016 - 08:19:53 CDT)
  • Re: Problems in NAMD's code about real implementation of function named ComputeNonbondedUtil:calc_pair_energy (Sat Jan 30 2016 - 21:00:17 CST)
• Peter Mawanga
  • Re: Query regarding colvar distanceZ (Tue Dec 27 2016 - 20:47:16 CST)
  • Re: Query regarding colvar distanceZ (Tue Dec 27 2016 - 19:07:07 CST)
  • Re: Query regarding colvar distanceZ (Mon Dec 26 2016 - 11:39:48 CST)
  • Re: Query regarding colvar distanceZ (Mon Dec 26 2016 - 09:17:34 CST)
  • Re: Query regarding colvar distanceZ (Mon Dec 26 2016 - 09:07:18 CST)
  • Query regarding colvar distanceZ (Mon Dec 26 2016 - 06:57:57 CST)
  • Getting cluster with defined criteria (Sun Dec 04 2016 - 07:05:35 CST)
  • Separate switchdist for electrostatic interactions (Mon Nov 21 2016 - 06:17:18 CST)
• philippe Bourly
  • Free energy (eABF): negative RMSD and harmonic restraints. (Wed Aug 02 2017 - 11:45:56 CDT)
  • Re: Re: I don't have any eabf output file. (Tue Jul 25 2017 - 07:23:34 CDT)
  • Re: I don't have any eabf output file. (Tue Jul 25 2017 - 05:20:51 CDT)
  • I don't have any eabf output file. (Fri Jul 21 2017 - 13:46:39 CDT)
  • Re: eABF - Fullsamples and windows merging (Fri Jul 21 2017 - 12:54:03 CDT)
  • eABF - Fullsamples and windows merging (Wed Jul 19 2017 - 08:41:56 CDT)
• Prabhakar Bhimalapuram
  • Re: accessing values of 'extendedLagrangian' fictious degree of freedom (Thu Apr 28 2016 - 12:23:36 CDT)
  • accessing values of 'extendedLagrangian' fictious degree of freedom (Tue Apr 26 2016 - 22:01:58 CDT)
• Pragya Priyadarshini
  • water permeability calculation using NAMD trajectories (Tue Dec 13 2016 - 22:39:41 CST)
• Prapasiri Pongprayoon
  • Re: Running multiple-replicas metadynamics (Wed Nov 08 2017 - 15:37:51 CST)
  • Re: Running multiple-replicas metadynamics (Mon Nov 06 2017 - 16:35:51 CST)
  • Running multiple-replicas metadynamics (Fri Nov 03 2017 - 18:30:11 CDT)
• PRITI ROY
  • Re: Stack Traceback problem in colvar restrain (Thu Oct 26 2017 - 07:35:09 CDT)
  • Re: Stack Traceback problem in colvar restrain (Wed Oct 25 2017 - 12:11:52 CDT)
  • Stack Traceback problem in colvar restrain (Wed Oct 25 2017 - 07:46:57 CDT)
  • Re: Dihedral colvar (Fri Sep 08 2017 - 14:33:45 CDT)
  • Re: Dihedral colvar (Fri Sep 08 2017 - 13:55:01 CDT)
  • Re: Dihedral colvar (Fri Sep 08 2017 - 08:44:31 CDT)
  • Dihedral colvar (Mon Sep 04 2017 - 06:08:00 CDT)
  • Re: FATAL ERROR: Duplicate bond (Tue Mar 21 2017 - 08:25:08 CDT)
• Puneet
  • NAMD installation (Sat Nov 26 2016 - 01:41:14 CST)
• quo.physics_at_gmail.com
  • Re: multiple replicas metadynamics (Tue Jan 10 2017 - 05:57:27 CST)
• R. Charbel MAROUN
  • HBB2-pol (Fri Mar 25 2016 - 09:01:46 CDT)
  • Non respect of sequence of commands in command file (Fri Feb 12 2016 - 05:11:39 CST)
  • Re: PBC in lipid bilayer: receptor vs. ligand (Mon Feb 01 2016 - 10:39:06 CST)
  • Re: PBC in lipid bilayer: receptor vs. ligand (Thu Jan 28 2016 - 11:59:14 CST)
  • Re: PBC in lipid bilayer: receptor vs. ligand (Thu Jan 28 2016 - 11:03:17 CST)
  • Re: PBC in lipid bilayer: receptor vs. ligand (Thu Jan 28 2016 - 05:26:33 CST)
  • PBC in lipid bilayer: receptor vs. ligand (Wed Jan 27 2016 - 07:54:34 CST)
• Rabeta Yeasmin
  • Re: Re: metadynamics run in NAMD or using plumed in NAMD (Fri Dec 08 2017 - 12:39:49 CST)
  • Re: Re: metadynamics run in NAMD or using plumed in NAMD (Fri Dec 08 2017 - 12:14:11 CST)
  • Re: metadynamics run in NAMD or using plumed in NAMD (Fri Dec 08 2017 - 02:06:22 CST)
  • Re: metadynamics run in NAMD or using plumed in NAMD (Fri Dec 08 2017 - 01:53:49 CST)
  • metadynamics run in NAMD or using plumed in NAMD (Thu Dec 07 2017 - 17:49:22 CST)
  • building system with or without water for metadynamics (Tue Oct 17 2017 - 16:52:38 CDT)
  • Sample umbrella sampling input file (Fri Oct 06 2017 - 17:14:02 CDT)
  • How to get 3D figure of solvent accessible surface area from APBS output (Fri Aug 11 2017 - 17:18:54 CDT)
  • Re: Software for molecular electrostatic calculations (Thu Aug 10 2017 - 10:31:58 CDT)
  • Re: Software for molecular electrostatic calculations (Wed Aug 09 2017 - 16:44:01 CDT)
  • finding atoms in protein-lipid system having electrostatic interaction (Wed Aug 09 2017 - 13:32:35 CDT)
  • Software for molecular electrostatic calculations (Wed Aug 09 2017 - 13:03:49 CDT)
  • Problem in running wham (Fri Aug 04 2017 - 10:41:06 CDT)
  • Harmonic force Keyword "centers" significance (Wed Jun 21 2017 - 17:40:43 CDT)
  • Setting up the range for movement of protein in umbrella sampling (Fri Jun 16 2017 - 16:21:55 CDT)
  • Re: namd-l digest V1 #2196 (Fri Jun 09 2017 - 15:40:37 CDT)
  • Umbrella Sampling colvar file parameters (Thu Jun 08 2017 - 12:20:16 CDT)
  • Restraining the mass centre coordinate during Umbrella Sampling (Wed Jun 07 2017 - 10:46:57 CDT)
  • Restring the coordinate during Umbrella Sampling (Tue Jun 06 2017 - 16:13:08 CDT)
  • Writing pdb file for a particular frame (Tue May 16 2017 - 18:18:33 CDT)
  • Re: Pulling protein through membrane without changing the position of membrane (Mon May 15 2017 - 13:23:22 CDT)
  • Re: restraining selected atom's z coordinates (Mon May 15 2017 - 13:19:33 CDT)
  • restraining selected atom's z coordinates (Sat May 13 2017 - 19:17:26 CDT)
  • Pulling protein through membrane without changing the position of membrane (Thu May 11 2017 - 11:51:44 CDT)
  • Specify number of water molecules:simulation set up in VMD (Fri Mar 10 2017 - 13:21:31 CST)
  • Re: TMD: initial and targeted structure does not have same number of atoms (Wed Mar 08 2017 - 10:20:26 CST)
  • TMD: initial and targeted structure does not have same number of atoms (Tue Mar 07 2017 - 09:42:58 CST)
  • setting up simulation in vmd using charmm 36 forcefield (Fri May 27 2016 - 16:28:38 CDT)
• Radak, Brian K
  • Re: topology file for the residue CSO (Fri Jun 23 2017 - 13:10:51 CDT)
  • Re: Defining custom Colvars to measure pmf with Umbrella Sampling (Wed Jun 21 2017 - 11:16:49 CDT)
  • Re: Defining custom Colvars to measure pmf with Umbrella Sampling (Wed Jun 21 2017 - 11:01:08 CDT)
  • Re: FEP with ExtraBonds (Mon Jun 12 2017 - 16:13:31 CDT)
  • Re: Two parameter file in NAMD configuration file (Fri Jun 09 2017 - 09:39:46 CDT)
  • Re: about GaMD reweighting (Tue Jun 06 2017 - 11:29:09 CDT)
  • RE: Center of mass drift (Fri Jun 02 2017 - 10:10:01 CDT)
  • RE: pKa calculation with thermodynamic integration (TI) (Wed May 24 2017 - 13:29:59 CDT)
  • RE: pKa calculation with thermodynamic integration (TI) (Wed May 24 2017 - 11:35:50 CDT)
  • RE: pKa calculation with thermodynamic integration (TI) (Wed May 17 2017 - 09:54:39 CDT)
  • RE: energy difference between HSE and HSD (Tue May 09 2017 - 11:12:14 CDT)
  • RE: energy difference between HSE and HSD (Tue May 09 2017 - 10:43:49 CDT)
  • RE: pKa calculation with thermodynamic integration (TI) (Tue May 09 2017 - 10:41:52 CDT)
  • RE: More FEP using separated topologies (Wed Apr 26 2017 - 09:59:47 CDT)
  • RE: Neutralize a box for FEP (Wed Apr 12 2017 - 13:17:46 CDT)
  • RE: Neutralize a box for FEP (Wed Apr 12 2017 - 11:14:26 CDT)
  • RE: problems mutating HID to TYR for free energy calculations (Tue Mar 07 2017 - 09:49:38 CST)
  • RE: analyze NAMD trajectory in Curves+ (Mon Mar 06 2017 - 12:03:25 CST)
  • RE: Npt lipid simulation with electrostatics 2 (Fri Feb 17 2017 - 09:26:20 CST)
  • RE: PSFgen failed to guess coordinate due to bad angle CD CG HG2 (Fri Feb 10 2017 - 09:36:22 CST)
  • RE: PSFgen failed to guess coordinate due to bad angle CD CG HG2 (Thu Feb 09 2017 - 10:58:59 CST)
  • RE: regarding constant velocity steered molecular dynamics (Wed Feb 08 2017 - 11:48:09 CST)
  • RE: Compiling charm/NAMD with an alternative gcc, e.g. gcc 6.x (Mon Feb 06 2017 - 11:27:58 CST)
  • RE: Energy Gradient Plotting (Wed Jan 18 2017 - 11:19:04 CST)
  • RE: Solvation free energy difference of alchemical transformation of K+ into Na+ (Tue Jan 10 2017 - 14:28:57 CST)
  • RE: Solvation free energy difference of alchemical transformation of K+ into Na+ (Tue Jan 10 2017 - 12:27:07 CST)
  • RE: dcd to pdb conversion (Wed Jan 04 2017 - 10:43:35 CST)
  • RE: NAMD Energies (Wed Dec 14 2016 - 13:42:36 CST)
  • RE: FATAL ERROR: Duplicate bond when going from nvt to npt (Mon Dec 12 2016 - 09:33:46 CST)
  • RE: Returning energy values from .log file. (Wed Dec 07 2016 - 15:19:49 CST)
  • RE: Turning off and back on fixed atoms (Thu Oct 27 2016 - 12:05:27 CDT)
  • RE: Switch off rescale temperature after some number of timesteps (Wed Oct 26 2016 - 11:12:36 CDT)
  • RE: question regarding rmsd (Wed Oct 05 2016 - 15:39:01 CDT)
  • RE: question regarding rmsd (Wed Oct 05 2016 - 11:18:12 CDT)
  • RE: Wrapall on or off? (Tue Sep 27 2016 - 10:50:33 CDT)
  • RE: PMF decompostion (Mon Sep 12 2016 - 12:31:48 CDT)
  • RE: convert .xyz file in .psf file for non-protein molecule (Thu Sep 08 2016 - 12:39:04 CDT)
  • RE: Is it possible to perform NVT FEP on a fluid system? (Tue Aug 09 2016 - 10:22:59 CDT)
  • RE: Is it possible to perform NVT FEP on a fluid system? (Tue Aug 09 2016 - 11:51:05 CDT)
  • RE: Msd (Mon Jul 25 2016 - 12:48:13 CDT)
  • RE: how to reassign dcdfreq?? (Tue Jul 12 2016 - 13:22:08 CDT)
  • RE: Missing atom type for hydroperoxide (Tue Jun 14 2016 - 12:58:25 CDT)
  • RE: Building PSF for the system prepared by Packmol (Thu Jun 09 2016 - 14:16:46 CDT)
  • RE: Excessively high dE_avg values in FEP output (NAMD CVS) (Fri May 20 2016 - 11:58:43 CDT)
  • RE: gradual heating problem (Mon May 09 2016 - 10:12:01 CDT)
  • RE: heating in NPT ensemble (Fri May 06 2016 - 10:04:07 CDT)
  • RE: Constraint failure in RATTLE algorithm for atom 6! (Tue Apr 26 2016 - 16:40:45 CDT)
  • RE: Constraint failure in RATTLE algorithm for atom 6! (Tue Apr 26 2016 - 16:26:30 CDT)
  • RE: How to use a proper force constant to decrease computational cost while keeping calculation precision? (Wed Apr 20 2016 - 16:22:09 CDT)
  • Unexpected(?) callback behavior when minimizing before MD (Tue Apr 12 2016 - 16:02:34 CDT)
  • RE: problem with angle parameters (Wed Mar 30 2016 - 11:09:12 CDT)
  • instantaneous pressure and temp change for multiple run calls? (Tue Mar 22 2016 - 13:21:53 CDT)
  • RE: AW: Tcl script for simulated tempering? (Wed Mar 16 2016 - 10:17:07 CDT)
  • RE: AW: Tcl script for simulated tempering? (Tue Mar 15 2016 - 13:01:56 CDT)
  • Tcl script for simulated tempering? (Fri Mar 11 2016 - 16:12:21 CST)
• Randy J. Zauhar
  • Re: Questions on creating constraints in NAMD (Sat Mar 11 2017 - 13:01:17 CST)
  • RE: Questions on creating constraints in NAMD (Tue Feb 21 2017 - 10:07:18 CST)
  • Questions on creating constraints in NAMD (Tue Feb 21 2017 - 09:03:21 CST)
• Raul Araya
  • (no subject) (Tue Jan 03 2017 - 14:22:09 CST)
• Renfro, Michael
  • Re: Fwd: About wall clock time (Mon Oct 16 2017 - 08:18:27 CDT)
  • RFC: shell scripts and support functions for NAMD on Slurm (including GPU and Infiniband) (Mon Sep 04 2017 - 13:57:54 CDT)
• Reza Salari
  • Re: Excessively high dE_avg values in FEP output (NAMD CVS) (Thu May 19 2016 - 16:21:08 CDT)
  • Re: Excessively high dE_avg values in FEP output (NAMD CVS) (Tue May 17 2016 - 14:20:32 CDT)
  • Excessively high dE_avg values in FEP output (NAMD CVS) (Mon May 16 2016 - 16:29:32 CDT)
  • Excessively high dE_avg values in FEP output (NAMD CVS) (Mon May 16 2016 - 12:42:27 CDT)
• Richard
  • Re: NAMD2.9-ERROR: Constraint failure in RATTLE algorithm for atom! (Fri Aug 25 2017 - 23:03:00 CDT)
• Richard Overstreet
  • Re: NAMD job termination (Wed Nov 08 2017 - 21:08:32 CST)
  • Re: coarse-grained simulations with errors "Atoms moving too fast" and "low global exclusion" (Fri Jun 09 2017 - 09:45:06 CDT)
  • Re: Segmentation fault error with 'nan' pressure and energy (Tue May 30 2017 - 16:41:33 CDT)
  • Re: namd2.exe has stopped working, NAMD Energy (Thu Feb 02 2017 - 20:46:29 CST)
  • Re: A common tool to read the output of NAMD run (Mon Nov 28 2016 - 08:08:03 CST)
  • Re: NPT with graphene (Mon Nov 14 2016 - 15:03:43 CST)
  • NPT with graphene (Mon Nov 14 2016 - 11:29:27 CST)
  • Re: Parameters for determining run time (Mon Nov 07 2016 - 19:12:59 CST)
  • Re: visualizing and analyzing long simulation (Mon Oct 10 2016 - 11:48:28 CDT)
  • Re: Half of the structure goes out of the simulation box! (Fri Sep 30 2016 - 06:25:19 CDT)
• Rik Chakraborty
  • Re: Fwd: About wall clock time (Thu Oct 26 2017 - 23:09:27 CDT)
  • Fwd: About wall clock time (Mon Oct 16 2017 - 01:20:40 CDT)
• Robert Sawko
  • Spawning too many gpu processes on the first node (Thu Dec 01 2016 - 13:10:12 CST)
  • NAMD GPU+ibverbs on multiple nodes: timeout problems (Thu Nov 17 2016 - 05:51:21 CST)
• Roshan Shrestha
  • Re: facing problem while downloading NAMD (Fri Dec 22 2017 - 03:40:20 CST)
  • Re: nvt vs nve file (Mon Dec 04 2017 - 18:20:49 CST)
  • Re: Ion type in NAMD Implicit solvent model for ionizing the system (Wed Sep 13 2017 - 00:49:39 CDT)
  • Re: Free MD simulation (Production run) (Fri Sep 08 2017 - 02:36:04 CDT)
  • Free MD simulation (Production run) (Fri Sep 08 2017 - 02:32:50 CDT)
  • No minimized system after running minimization in NAMD (Thu Sep 07 2017 - 09:17:02 CDT)
  • Re: Concatenating log files (Wed Sep 06 2017 - 12:00:34 CDT)
  • Re: Concatenating log files (Wed Sep 06 2017 - 11:39:06 CDT)
  • Concatenating log files (Wed Sep 06 2017 - 11:07:51 CDT)
  • Re: How to set the configuration file for a NVE simulation (Mon Sep 04 2017 - 19:59:40 CDT)
  • Production run after equilibration (Tue Aug 29 2017 - 05:38:00 CDT)
  • Re: Creating psf file for ligand (Thu Aug 24 2017 - 12:58:07 CDT)
  • Re: Creating psf file for ligand (Sat Aug 12 2017 - 09:38:59 CDT)
  • Creating psf file for ligand (Sat Aug 12 2017 - 09:34:29 CDT)
  • Re: Creating psf file DNA (Thu Jul 06 2017 - 17:53:51 CDT)
  • Creating psf file DNA (Thu Jul 06 2017 - 11:47:54 CDT)
  • Re: question regarding rmsd (Wed Oct 05 2016 - 11:07:09 CDT)
  • Re: Simulated annealing, in solvent or in vacuum? (Fri Sep 09 2016 - 03:17:37 CDT)
  • SMD Constant velocity pulling (Wed Jul 27 2016 - 12:59:49 CDT)
  • Permeation of liquid through Silicon Dioxide Crystal (Fri Jun 10 2016 - 07:30:00 CDT)
  • Simulation runs only in background (Wed Jun 01 2016 - 03:44:15 CDT)
  • Re: Conversion from GROMACS .top .itp to CHARMM .psf .par combo (Sat May 28 2016 - 10:04:08 CDT)
  • Re: truncated text RE: external computational power for NAMD (Thu May 26 2016 - 21:35:39 CDT)
  • Binding energy of organic molecules/small peptides on the surface of Silicon Dioxide (Thu May 26 2016 - 10:29:01 CDT)
• Ryan McGreevy
  • Re: Cascade MDFF (Thu Mar 09 2017 - 10:53:42 CST)
  • Re: Cascade MDFF (Thu Mar 09 2017 - 08:25:56 CST)
  • Re: MDFF simulations in membrane environment (Thu Feb 23 2017 - 08:33:24 CST)
  • Re: MDFF simulations in membrane environment (Wed Feb 22 2017 - 09:28:04 CST)
  • Re: Setting up symmetry restraints in a homo-dimer with non-equal number of residues (Fri Dec 09 2016 - 12:46:04 CST)
  • Re: MDFF based on known EM maps (Tue Jun 28 2016 - 12:20:46 CDT)
• Sachin Natesh
  • Re: Lipid Bilayer Shearing (Tue Aug 16 2016 - 13:01:45 CDT)
  • Lipid Bilayer Shearing (Tue Aug 16 2016 - 12:01:15 CDT)
• Sadegh Faramarzi Ganjabad
  • Restarting FEP calculations (Mon Oct 23 2017 - 15:10:55 CDT)
  • Re: convergence criterion of free energy perturbation (FEP) simulations for pKa calculation (Fri Oct 06 2017 - 14:19:56 CDT)
  • Re: convergence criterion of free energy perturbation (FEP) simulations for pKa calculation (Fri Oct 06 2017 - 14:04:39 CDT)
  • convergence criterion of free energy perturbation (FEP) simulations for pKa calculation (Thu Oct 05 2017 - 13:36:07 CDT)
  • Re: Segmentation fault error with 'nan' pressure and energy (Tue Jun 06 2017 - 14:07:24 CDT)
  • Re: Segmentation fault error with 'nan' pressure and energy (Thu Jun 01 2017 - 13:05:09 CDT)
  • Re: Re: Segmentation fault error with 'nan' pressure and energy (Wed May 31 2017 - 13:37:09 CDT)
  • Re: Segmentation fault error with 'nan' pressure and energy (Tue May 30 2017 - 16:48:09 CDT)
  • Segmentation fault error with 'nan' pressure and energy (Tue May 30 2017 - 16:17:12 CDT)
  • Re: pKa calculation with thermodynamic integration (TI) (Tue May 30 2017 - 13:12:23 CDT)
  • Re: pKa calculation with thermodynamic integration (TI) (Mon May 29 2017 - 15:45:10 CDT)
  • Re: pKa calculation with thermodynamic integration (TI) (Wed May 24 2017 - 13:16:46 CDT)
  • Re: pKa calculation with thermodynamic integration (TI) (Wed May 24 2017 - 10:48:29 CDT)
  • Re: pKa calculation with thermodynamic integration (TI) (Tue May 23 2017 - 01:04:17 CDT)
  • psfgen readpsf error with no more explanation (Wed May 17 2017 - 15:58:37 CDT)
  • Re: pKa calculation with thermodynamic integration (TI) (Wed May 17 2017 - 02:00:11 CDT)
  • Re: pKa calculation with thermodynamic integration (TI) (Wed May 10 2017 - 19:36:16 CDT)
  • pKa calculation with thermodynamic integration (TI) (Mon May 08 2017 - 14:59:06 CDT)
• saeed amini
  • minimizing each structure of a DCD file (Sun Jan 22 2017 - 07:21:23 CST)
• Sahoo, Dushyant
  • How to define spheres of different sizes and their spatial constrains using NAMD? (Tue Feb 21 2017 - 02:40:33 CST)
• Saleh AlKhalifa
  • Lipid bilayer and ligand interactions (Sun Feb 26 2017 - 08:47:58 CST)
  • Re: Protein Penetrating Water Box (Sun Jan 29 2017 - 14:02:05 CST)
• salehesam101 .
  • Re: Protein Penetrating Water Box (Sun Jan 29 2017 - 20:07:08 CST)
  • Problem with using autoPSF on TMCL lipid (Fri Dec 16 2016 - 10:11:47 CST)
• salehesam_at_gmail.com
  • Re: Drude minimization does not converge (Fri Jan 13 2017 - 10:36:41 CST)
• Samuel Bowerman
  • NAMD Implicit GB Parameters (Mon Feb 01 2016 - 12:41:03 CST)
• Sana Saeed
  • NAMD_CUDA (Thu Dec 15 2016 - 20:23:18 CST)
• Sanjib Paul
  • Re: applying constant force on water molecules in a particular direction (Mon Sep 11 2017 - 01:22:48 CDT)
  • applying constant force on water molecules in a particular direction (Wed Sep 06 2017 - 06:14:16 CDT)
• Santanu Santra
  • Minimization error (Tue Dec 06 2016 - 23:00:04 CST)
  • Re: Amber forcefield in namd simulation in parallel version (Fri Dec 02 2016 - 00:05:35 CST)
  • Re: Amber forcefield in namd simulation in parallel version (Thu Dec 01 2016 - 23:00:45 CST)
  • Amber forcefield in namd simulation in parallel version (Thu Dec 01 2016 - 06:36:24 CST)
  • (no subject) (Mon Oct 31 2016 - 23:22:58 CDT)
• Sarah Sweger
  • Exit Command Failure (Thu Jun 23 2016 - 08:01:09 CDT)
• Sarath Josh M.K
  • PSFgen failed to guess coordinate due to bad angle CD CG HG2 (Thu Feb 09 2017 - 03:19:39 CST)
• Scott Brozell
  • Re: CHARMRUN ERROR (Fri May 19 2017 - 11:17:18 CDT)
  • Re: CHARMRUN ERROR (Thu May 18 2017 - 13:28:52 CDT)
  • Re: 2.11 how to remove charmrun remote-shell options (Tue Dec 20 2016 - 19:05:08 CST)
  • charmc rpath (Thu Jan 21 2016 - 22:04:41 CST)
  • 2.11 how to remove charmrun remote-shell options (Wed Jan 13 2016 - 12:04:54 CST)
• Seibold, Steve Allan
  • Re: Incorporate aluminum oxide monolayer (Wed Apr 12 2017 - 09:47:43 CDT)
• sem ciccioni
  • clarification (Mon Apr 18 2016 - 16:21:08 CDT)
• Seth Axen
  • ffTK fitting dihedrals (Tue May 17 2016 - 01:36:02 CDT)
• Shadrina Maria
  • NAMD crashes when Multilevel Summation Method (MSM) is on (Tue May 30 2017 - 10:12:46 CDT)
• Shahee Islam
  • Re: atom selection error (Tue Dec 12 2017 - 01:31:22 CST)
  • Re: atom selection error (Mon Dec 11 2017 - 00:52:18 CST)
  • Re: atom selection error (Mon Dec 11 2017 - 00:33:38 CST)
  • Re: atom selection error (Mon Dec 11 2017 - 00:04:47 CST)
  • Re: atom selection error (Fri Dec 08 2017 - 08:22:51 CST)
  • atom selection error (Fri Dec 08 2017 - 02:33:19 CST)
  • Re: (Mon Dec 04 2017 - 03:57:36 CST)
  • (no subject) (Fri Dec 01 2017 - 02:28:17 CST)
• Shambo Hore
  • ION CHANNEL gating mechanism (Sat Sep 03 2016 - 05:42:46 CDT)
  • namd "WARNING: ignoring command" problem (Tue May 31 2016 - 12:11:35 CDT)
  • SMD simulation problem. (Sun May 29 2016 - 20:15:57 CDT)
  • SMD simulation problem (Sun May 22 2016 - 10:37:52 CDT)
• Shannon, Gareth Bayley. (ARC-SS)[UNIVERSITIES SPACE RESEARCH ASSOCIATION]
  • FEP with ExtraBonds (Mon Jun 12 2017 - 15:30:59 CDT)
  • RE: Error regarding missing angles between perturbed groups for fep calculation (Fri May 26 2017 - 17:03:36 CDT)
  • RE: Error regarding missing angles between perturbed groups for fep calculation (Thu May 25 2017 - 16:24:08 CDT)
  • Error regarding missing angles between perturbed groups for fep calculation (Thu May 25 2017 - 10:49:32 CDT)
  • Running Charmm36 (Fri Apr 08 2016 - 19:04:49 CDT)
  • Restarting ABF (Tue Mar 22 2016 - 13:45:51 CDT)
• Shikha Sharma
  • Re: NAMD How to calculate ns/day (Wed Dec 07 2016 - 23:01:44 CST)
• Shyam Saladi
  • Re: unix path length limits for namd (Sun May 01 2016 - 19:21:27 CDT)
• Siddharth Girdhar
  • Simulating SDS molecules (Fri Jun 30 2017 - 09:11:08 CDT)
• siddharth kamal
  • Regarding radial distribution function graph (Thu Jun 16 2016 - 08:31:23 CDT)
• Sneha M
  • NAMDEnergy with xtc file (Thu Oct 05 2017 - 05:11:37 CDT)
• Sneha Menon
  • Free energy calculation using MM-GBSA with NAMD (Wed Jun 15 2016 - 05:50:41 CDT)
• sonia ziada
  • Re: K40 benchmark problem in NAMD (Thu Nov 17 2016 - 01:54:59 CST)
  • Re: Are there features NOT or POORLY supported on GPU ? (Tue Nov 15 2016 - 01:34:34 CST)
  • Are there features NOT or POORLY supported on GPU ? (Mon Nov 14 2016 - 04:11:43 CST)
• Sonu Kumar
  • Shrinking a polymer to match its density using pbc (Wed Sep 28 2016 - 10:21:11 CDT)
  • Shrinking a molecule (Colvars and Constant Pressure not working) (Mon Aug 22 2016 - 15:21:48 CDT)
  • Re: Problems with wrapAll (Fri Jul 22 2016 - 13:08:33 CDT)
  • Re: Problems with wrapAll (Fri Jul 22 2016 - 06:58:13 CDT)
  • Problems with wrapAll (Thu Jul 21 2016 - 00:52:55 CDT)
• sonu2kd_at_gmail.com
  • Re: dcd to pdb conversion (Wed Jan 04 2017 - 06:26:49 CST)
• Sourav Pal
  • Re: Writing pdb file for a particular frame (Tue May 16 2017 - 22:18:31 CDT)
  • (no subject) (Mon Oct 03 2016 - 02:44:00 CDT)
• Sourav Ray
  • Re: Charmm++ error (Sun Nov 20 2016 - 17:12:02 CST)
  • Re: Charmm++ error (Sun Nov 20 2016 - 17:10:44 CST)
  • Re: NAMD2.11 DCD HEADER PROBLEM (Wed Sep 14 2016 - 06:10:20 CDT)
  • Re: Umbrella sampling colvars DistanceZ deviates a lot (Tue Sep 13 2016 - 15:22:47 CDT)
  • Re: Unable to compile Tachyon on Sun Grid Engine (Sat Jun 04 2016 - 08:03:44 CDT)
  • Re: Unable to compile Tachyon on Sun Grid Engine (Sat Jun 04 2016 - 05:59:00 CDT)
  • Unable to compile Tachyon on Sun Grid Engine (Sat Jun 04 2016 - 04:20:29 CDT)
  • Conversion from GROMACS .top .itp to CHARMM .psf .par combo (Sat May 28 2016 - 10:00:54 CDT)
  • Re: Coarse-grained simulation with Polarizable Water crashing (Sat May 21 2016 - 11:39:42 CDT)
  • Re: Colvars: Unable to restrict rotation and translation along y and z axes (Fri May 20 2016 - 01:31:38 CDT)
  • Colvars: Unable to restrict rotation and translation along y and z axes (Wed May 18 2016 - 07:22:00 CDT)
  • Error associated with protected variable initialization: Nightly Build version (Tue May 17 2016 - 13:50:54 CDT)
  • Re: Coarse-grained simulation with Polarizable Water crashing (Mon May 16 2016 - 15:31:14 CDT)
  • Particle Mesh Ewald with Martini (Mon May 16 2016 - 10:55:14 CDT)
  • Re: Coarse-grained simulation with Polarizable Water crashing (Sun May 15 2016 - 17:08:31 CDT)
  • Coarse-grained simulation with Polarizable Water crashing (Sun May 15 2016 - 16:34:18 CDT)
  • Conversion from c6 and c12 = 0 to sigma epsilon (Sat May 14 2016 - 06:29:49 CDT)
  • Martini polarizable water topology and/or psf file (Thu May 12 2016 - 17:30:57 CDT)
  • Colvars crossing "upperboundary" limit (Thu May 05 2016 - 05:33:26 CDT)
  • Re: Running a test simulation using GPU only (without any CPU core) (Thu Apr 28 2016 - 10:04:29 CDT)
  • Running a test simulation using GPU only (without any CPU core) (Thu Apr 28 2016 - 09:40:00 CDT)
  • Corrfunc output not generated (Mon Apr 11 2016 - 12:38:39 CDT)
  • Re: Metadynamics simulation with Radius of Gyration and RMSD variation - 2 (Mon Apr 11 2016 - 11:10:57 CDT)
  • Re: Metadynamics simulation with Radius of Gyration and RMSD variation - 2 (Sat Apr 09 2016 - 14:53:15 CDT)
  • Metadynamics simulation with Radius of Gyration and RMSD variation - 2 (Sat Apr 09 2016 - 12:11:53 CDT)
  • Metadynamics simulation with Radius of Gyration and RMSD variation - 1 (Sat Apr 09 2016 - 12:03:36 CDT)
  • Re: Running multi-node jobs on Sun Grid Engine (Tue Apr 05 2016 - 00:19:23 CDT)
  • Re: Stray PME grid charges detected (Mon Apr 04 2016 - 13:12:41 CDT)
  • Wrapping molecules in a NAMD simulation (Mon Apr 04 2016 - 08:23:02 CDT)
  • Re: Stray PME grid charges detected (Mon Apr 04 2016 - 05:26:56 CDT)
  • Re: Running multi-node jobs on Sun Grid Engine (Mon Apr 04 2016 - 04:39:57 CDT)
  • Running multi-node jobs on Sun Grid Engine (Sun Apr 03 2016 - 10:49:30 CDT)
• Souvik Sinha
  • Re: Colvar Error (Mon Dec 04 2017 - 12:34:36 CST)
  • Re: Colvar Error (Mon Dec 04 2017 - 08:37:09 CST)
  • Colvar Error (Mon Dec 04 2017 - 07:33:12 CST)
  • Re: extracting avarage pdb from dcd file (Mon Sep 11 2017 - 10:19:51 CDT)
  • Re: Querries on eABF (Sat Jul 15 2017 - 07:39:34 CDT)
  • Re: Querries on eABF (Wed Jul 12 2017 - 07:34:46 CDT)
  • Re: Querries on eABF (Wed Jul 12 2017 - 07:15:51 CDT)
  • Re: Keeping potassium ions out of an area during equilibration (Wed Jun 07 2017 - 01:37:38 CDT)
  • Re: Querries on eABF (Tue May 30 2017 - 11:01:09 CDT)
  • Re: Querries on eABF (Tue May 30 2017 - 07:37:19 CDT)
  • Re: Querries on eABF (Tue May 30 2017 - 02:51:31 CDT)
  • Re: Querries on eABF (Fri May 26 2017 - 10:53:04 CDT)
  • Re: Querries on eABF (Fri May 26 2017 - 00:45:37 CDT)
  • Re: Querries on eABF (Thu May 25 2017 - 05:02:32 CDT)
  • Re: Querries on eABF (Wed Apr 26 2017 - 06:17:03 CDT)
  • Querries on eABF (Wed Apr 26 2017 - 01:40:21 CDT)
  • Error : components of colvar "alpha" does not support system force calculation (Fri Apr 07 2017 - 03:47:11 CDT)
  • Re: Applying "selectionRule" in Multiple Walker ABF (Thu Jun 23 2016 - 03:07:13 CDT)
  • Re: Applying "selectionRule" in Multiple Walker ABF (Tue May 31 2016 - 01:27:08 CDT)
  • Applying "selectionRule" in Multiple Walker ABF (Fri May 27 2016 - 09:43:28 CDT)
  • PMF calculation using ABF (Tue May 10 2016 - 08:57:52 CDT)
  • Re: ERROR: ofstream_namd::close() called when file is not open (Mon Apr 18 2016 - 06:54:37 CDT)
  • ERROR: ofstream_namd::close() called when file is not open (Mon Apr 18 2016 - 02:36:33 CDT)
• Srijita Paul
  • NAMD energy run in VMD (Tue Nov 21 2017 - 09:43:08 CST)
  • extracting avarage pdb from dcd file (Mon Sep 11 2017 - 00:48:06 CDT)
  • Re: dcd to pdb conversion (Wed Jan 04 2017 - 13:05:28 CST)
  • dcd to pdb conversion (Wed Jan 04 2017 - 06:18:21 CST)
  • (no subject) (Tue May 31 2016 - 23:29:11 CDT)
  • (no subject) (Tue May 31 2016 - 05:03:47 CDT)
  • Re: (Tue May 10 2016 - 08:41:10 CDT)
  • (no subject) (Sat May 07 2016 - 06:17:48 CDT)
  • Re: (Fri Apr 22 2016 - 05:39:12 CDT)
  • (no subject) (Fri Apr 22 2016 - 01:19:21 CDT)
  • (no subject) (Sat Apr 16 2016 - 00:06:47 CDT)
  • (no subject) (Wed Apr 13 2016 - 07:08:28 CDT)
  • (no subject) (Tue Apr 12 2016 - 07:33:41 CDT)
  • (no subject) (Fri Apr 08 2016 - 08:00:25 CDT)
  • Packing of different system (Thu Apr 07 2016 - 10:51:32 CDT)
  • (no subject) (Tue Jan 26 2016 - 23:06:12 CST)
  • (no subject) (Tue Jan 26 2016 - 23:02:28 CST)
  • (no subject) (Wed Jan 06 2016 - 22:25:56 CST)
• sruthi c k
  • Re: Regarding system forces in NAMD (Fri Jan 08 2016 - 06:14:08 CST)
  • Fwd: Regarding system forces in NAMD (Fri Jan 08 2016 - 03:38:26 CST)
  • Re: Regarding system forces in NAMD (Thu Jan 07 2016 - 11:43:49 CST)
  • Re: Regarding system forces in NAMD (Thu Jan 07 2016 - 09:13:57 CST)
  • Regarding system forces in NAMD (Thu Jan 07 2016 - 06:49:51 CST)
  • Re: Regarding merging of .grad files obtained from ABF simulations (Thu Jan 07 2016 - 04:31:11 CST)
  • Regarding merging of .grad files obtained from ABF simulations (Thu Jan 07 2016 - 01:49:18 CST)
• Stefano Guglielmo
  • Re: gbsa (Wed Dec 20 2017 - 15:57:21 CST)
  • Re: reconstructing pmf (Wed Dec 20 2017 - 01:55:15 CST)
  • gbsa (Tue Dec 19 2017 - 19:55:21 CST)
  • Re: reconstructing pmf (Tue Dec 19 2017 - 18:17:35 CST)
  • Re: reconstructing pmf (Tue Dec 19 2017 - 02:48:53 CST)
  • reconstructing pmf (Mon Dec 18 2017 - 18:24:15 CST)
  • GAAMP (Mon Jul 10 2017 - 06:55:21 CDT)
  • principal axes in colvars (Wed Jun 14 2017 - 06:28:44 CDT)
  • Re: dihedral colvar (Wed Jan 18 2017 - 01:43:48 CST)
  • dihedral colvar (Tue Jan 17 2017 - 19:11:09 CST)
  • metadynamics and pmf file (Mon Jul 04 2016 - 19:43:23 CDT)
  • FES analysis (Tue May 24 2016 - 15:46:21 CDT)
  • segmentation error (Fri Mar 04 2016 - 04:15:01 CST)
  • Constraint failure in RATTLE algorithm (Tue Mar 01 2016 - 19:18:05 CST)
  • plumed (Sun Feb 28 2016 - 10:21:32 CST)
  • compute capability (Sun Jan 24 2016 - 17:15:43 CST)
• Steve Chou
  • Re: Using NAMD with NMR structure (Mon Oct 24 2016 - 13:18:34 CDT)
• Steven Cohen
  • Running IMD with TMD (domain restraints) (Mon Jan 02 2017 - 10:43:09 CST)
• Steven Neumann
  • performance on ~1.5 million atoms system (Mon Apr 17 2017 - 00:42:12 CDT)
• Stober, Spencer T
  • RE: Hybrid QM/MM in NAMD 2.12 with Gaussian (Wed Apr 19 2017 - 10:44:18 CDT)
  • Hybrid QM/MM in NAMD 2.12 with Gaussian (Tue Apr 18 2017 - 10:24:03 CDT)
• Strahs, Dr. Daniel Bernard
  • Re: DNA capping (Fri Jun 02 2017 - 10:01:52 CDT)
  • Re: DNA capping (Fri Jun 02 2017 - 07:30:57 CDT)
• Subbarao Kanchi
  • Re: Running gromacs in namd (Thu Dec 01 2016 - 01:42:24 CST)
  • Re: Running gromacs in namd (Thu Dec 01 2016 - 00:27:37 CST)
  • Re: Running gromacs in namd (Tue Nov 29 2016 - 04:25:06 CST)
  • Running gromacs in namd (Tue Nov 29 2016 - 00:30:37 CST)
  • Re: Collecting average energies via Tcl callback? (Thu Oct 13 2016 - 19:20:39 CDT)
• sunyeping
  • Re: Calculating electrostatic force from NAMD trajectory (Mon Jul 03 2017 - 21:42:56 CDT)
  • Re: Can large number of atoms define in colvariables reduce the computational speed in adaptive biased force (ABF) simulation via lowering the GPU utility? (Thu Apr 27 2017 - 00:34:49 CDT)
  • Can large number of atoms define in colvariables reduce the computational speed in adaptive biased force (ABF) simulation via lowering the GPU utility? (Wed Apr 26 2017 - 12:51:17 CDT)
  • Re: How to calculate 2d surface energy surface on segmented adaptive biased force (ABF) simulations (Mon Apr 17 2017 - 21:06:19 CDT)
  • How to calculate 2d surface energy surface on segmented adaptive biased force (ABF) simulations (Mon Apr 17 2017 - 05:54:46 CDT)
  • cuda errors when running NAMD (Fri Mar 03 2017 - 18:51:34 CST)
  • fatal error in running namd/2.12 (Wed Jan 11 2017 - 07:46:01 CST)
  • FATAL ERROR: cuda_check_progress polled 1000000 times over 101.178648 s on step 6418536 (Thu Dec 01 2016 - 17:27:36 CST)
  • “Cannot compile C++ programs with mpicxx" error when compiling charm-6.7 (Sun Nov 20 2016 - 13:22:02 CST)
  • Re: no response from mail list (Mon Oct 31 2016 - 20:32:18 CDT)
  • no response from mail list (Mon Oct 31 2016 - 19:23:09 CDT)
  • Re: AW: Reason: FATAL ERROR: Unknown command-line option ++local (Mon Oct 10 2016 - 21:55:27 CDT)
  • Wrapall on or off? (Tue Sep 27 2016 - 00:14:49 CDT)
  • how to rerun a namd trajectory in order to complement the missing snapshots? (Thu Aug 18 2016 - 22:35:51 CDT)
  • aMD doesn't work when some atoms are fixed (Mon Jul 18 2016 - 20:41:34 CDT)
  • Why does the water box collapse in an aMD (Mon Jun 13 2016 - 21:11:00 CDT)
  • Re: AW: Re: AW: AW: AW: why does the transition seem to be irreversible in aMD (Wed May 25 2016 - 00:48:18 CDT)
  • Re: AW: AW: AW: why does the transition seem to be irreversible in aMD (Mon May 23 2016 - 03:53:37 CDT)
  • Re: Some questions on the Deca-Alanine ABF tutorial (Thu May 19 2016 - 22:41:05 CDT)
  • Re: Some questions on the Deca-Alanine ABF tutorial (Wed May 18 2016 - 20:29:46 CDT)
  • Re: Some questions on the Deca-Alanine ABF tutorial (Wed May 18 2016 - 03:06:08 CDT)
  • Some questions on the Deca-Alanine ABF tutorial (Mon May 16 2016 - 04:19:33 CDT)
  • Re: AW: AW: why does the transition seem to be irreversible in aMD (Tue Apr 05 2016 - 04:10:59 CDT)
  • Re: AW: why does the transition seem to be irreversible in aMD (Tue Apr 05 2016 - 02:47:39 CDT)
  • why does the transition seem to be irreversible in aMD (Mon Apr 04 2016 - 22:21:00 CDT)
  • GBIS error (Sat Jan 02 2016 - 22:55:10 CST)
• Suresh Ghimire
  • (no subject) (Fri Dec 29 2017 - 19:57:56 CST)
  • (no subject) (Fri Dec 22 2017 - 09:54:23 CST)
• Susmita Ghosh
  • Ion type in NAMD Implicit solvent model for ionizing the system (Wed Sep 13 2017 - 00:31:50 CDT)
  • Re: MPIRUN SLURM SCRIPT (Tue May 09 2017 - 05:39:23 CDT)
  • How to create 3'-3' phosphodiester linkage for a DNA. (Mon Nov 28 2016 - 23:50:26 CST)
• t.shivam_at_iitg.ernet.in
  • raising temperature after equiliobration (Sat Aug 26 2017 - 02:20:20 CDT)
  • Re: NAMD with multiple molecules (Thu Aug 17 2017 - 22:51:58 CDT)
  • restarting and continuing - difference (Mon Aug 14 2017 - 09:05:03 CDT)
  • Re: simulation crashing in 2nd stage equilibration (Fri Aug 11 2017 - 08:20:42 CDT)
  • simulation crashing in 2nd stage equilibration (Fri Aug 11 2017 - 06:32:32 CDT)
  • Re: value of langevinTemp in case of binvelocities (Thu Aug 10 2017 - 04:41:10 CDT)
  • difference between .vel and .vel.restart (Thu Aug 10 2017 - 04:39:49 CDT)
  • value of langevinTemp in case of binvelocities (Thu Aug 10 2017 - 02:05:43 CDT)
  • difference between constraining,restraining and fixing the atoms (Fri Aug 04 2017 - 01:25:23 CDT)
  • two stage equilibration in single configuration file (Thu Aug 03 2017 - 01:03:46 CDT)
• Tabris Chun Chan
  • Re: Umbrella sampling colvars DistanceZ deviates a lot (Tue Sep 13 2016 - 12:27:25 CDT)
• Taejin Kim
  • Manganese force field (Fri Mar 18 2016 - 14:07:35 CDT)
• Teerapong Pirojsirikul
  • Re: Amber forcefield in namd simulation in parallel version (Fri Dec 02 2016 - 03:30:11 CST)
• ThatMind TV
  • Water atoms' explosion out of solvate box in my RBCG simulation on NAMD (Mon Oct 23 2017 - 05:57:39 CDT)
• The Cromicus Productions
  • Re: [NAMD] Question about patches (Mon Dec 25 2017 - 18:04:43 CST)
  • Re: [NAMD] Question about patches (Mon Dec 25 2017 - 17:53:36 CST)
  • Re: [NAMD] Question about patches (Mon Dec 25 2017 - 17:29:06 CST)
  • [NAMD] Question about patches (Sun Dec 24 2017 - 03:49:07 CST)
  • Re: [NAMD] Patch 5MC2 (Thu Nov 30 2017 - 12:25:55 CST)
  • [NAMD] Patch 5MC2 (Wed Nov 29 2017 - 17:45:16 CST)
  • [NAMD] Too many collective variables? (Thu Oct 26 2017 - 15:11:19 CDT)
  • [NAMD] Running NAMD in Stampede2 (Fri Sep 29 2017 - 14:59:34 CDT)
  • [NAMD] Simulations in guanidinium chloride (Tue Sep 12 2017 - 15:57:13 CDT)
  • [NAMD] File Missing in Nanopore Tutorial (Mon Sep 11 2017 - 22:38:23 CDT)
  • Re: [NAMD] How to build and simulate a periodic DNA in NAMD (Sun Jun 18 2017 - 17:47:39 CDT)
  • Re: [NAMD] How to build and simulate a periodic DNA in NAMD (Tue Jun 13 2017 - 05:42:00 CDT)
  • Re: [NAMD] How to build and simulate a periodic DNA in NAMD (Fri Jun 09 2017 - 12:31:08 CDT)
  • [NAMD] Outputting PMF at half the time using Metadynamics (Sun May 14 2017 - 14:04:32 CDT)
  • Re: [NAMD] Problem with colvar "tilt" (Fri May 12 2017 - 13:29:17 CDT)
  • [NAMD] Problem with colvar "tilt" (Fri May 12 2017 - 08:34:33 CDT)
  • Re: [NAMD] How to build and simulate a periodic DNA in NAMD (Sun May 07 2017 - 00:03:43 CDT)
  • Re: [NAMD] How to build and simulate a periodic DNA in NAMD (Sat May 06 2017 - 23:30:26 CDT)
  • Re: [NAMD] How to build and simulate a periodic DNA in NAMD (Sat May 06 2017 - 19:02:57 CDT)
  • [NAMD] How to build and simulate a periodic DNA in NAMD (Sat May 06 2017 - 13:14:34 CDT)
  • Incorporate aluminum oxide monolayer (Tue Apr 11 2017 - 14:50:37 CDT)
  • Re: Question about applying external force (Mon Mar 06 2017 - 18:27:20 CST)
  • Re: Question about applying external force (Mon Mar 06 2017 - 15:59:25 CST)
  • Re: Question about applying external force (Mon Mar 06 2017 - 15:32:36 CST)
  • Question about applying external force (Mon Mar 06 2017 - 13:56:30 CST)
  • [NAMD] Obtain dynamical matrix away from equilibrium (Thu Feb 09 2017 - 12:02:35 CST)
  • Re: FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE (Thu Feb 09 2017 - 12:01:55 CST)
  • FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE (Tue Feb 07 2017 - 17:43:40 CST)
  • Re: [NAMD] Using as collective variable the minimum of a set of distances (Mon Jan 30 2017 - 16:53:34 CST)
  • [NAMD] Using as collective variable the minimum of a set of distances (Sat Jan 28 2017 - 17:07:52 CST)
  • Re: [NAMD] Using ABF to study separation of two molecules (Mon Jan 23 2017 - 09:12:39 CST)
  • [NAMD] Using ABF to study separation of two molecules (Mon Jan 23 2017 - 01:00:48 CST)
• Theodora Teddy
  • Improper section for parameterization (Tue Nov 21 2017 - 07:20:59 CST)
  • Equilibrium Energies (Tue May 23 2017 - 11:10:19 CDT)
• Thomas C. Bishop
  • Remembering Klaus Schulten (Tue Nov 01 2016 - 09:33:31 CDT)
• Thomas Evangelidis
  • Re: Generalized Born solvation models supported by NAMD (Fri Jul 29 2016 - 13:18:08 CDT)
  • Re: Generalized Born solvation models supported by NAMD (Fri Jul 29 2016 - 11:20:46 CDT)
  • Generalized Born solvation models supported by NAMD (Fri Jul 29 2016 - 10:26:13 CDT)
• Tien Huynh
  • Post Doctoral Fellow Opening at IBM for Biomolecular Modeling (Tue Apr 05 2016 - 18:30:43 CDT)
• Tim.Ho_at_csiro.au
  • FATAL ERROR running apoa1 with NAMD 2.12 (Wed Apr 05 2017 - 01:53:26 CDT)
  • RE: RE: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) (Thu Jan 14 2016 - 22:02:44 CST)
  • RE: [Non-DoD Source] RE: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) (Thu Jan 14 2016 - 16:00:28 CST)
  • RE: Compilation error across Intel 14,15 and 16 (UNCLASSIFIED) (Wed Jan 13 2016 - 22:28:53 CST)
• Tom King
  • (no subject) (Fri Dec 09 2016 - 16:43:07 CST)
• Toon Verstraelen
  • Downloads are .tar files but have .tar.gz extension (Thu Nov 09 2017 - 05:07:26 CST)
• Tristan Croll
  • Re: Mixing all_36_cgenff with all_36_prot (Mon Mar 28 2016 - 14:36:33 CDT)
  • Re: Energy increase with fixed atoms in POPC membrane (Fri Feb 19 2016 - 10:51:52 CST)
  • Re: velocity computation (Tue Feb 09 2016 - 03:04:40 CST)
  • Re: velocity computation (Mon Feb 08 2016 - 12:33:16 CST)
• Vermaas, Joshua
  • Re: reconstructing pmf (Mon Dec 18 2017 - 18:35:31 CST)
  • Re: Define a colvar from other colvars (Thu Dec 14 2017 - 14:40:22 CST)
  • Re: Periodic molecules in NAMD (Wed Dec 13 2017 - 12:18:31 CST)
  • Re: atom selection error (Mon Dec 11 2017 - 11:28:09 CST)
  • Re: Free energy did not converge by using ABF (Thu Dec 07 2017 - 19:23:53 CST)
  • Re: nvt vs nve file (Mon Dec 04 2017 - 12:26:59 CST)
  • Re: (Fri Dec 01 2017 - 08:35:31 CST)
  • Re: RATTLE error with lipid bilayer system (Tue Nov 21 2017 - 14:22:05 CST)
  • Re: missing parameters. (Mon Nov 20 2017 - 11:08:47 CST)
  • Re: REMD using NAMD 2.13 (Fri Nov 17 2017 - 18:16:43 CST)
  • Re: Running multiple-replicas metadynamics (Fri Nov 03 2017 - 19:05:18 CDT)
  • Re: Some water molecules are missing in psf (Thu Nov 02 2017 - 18:13:28 CDT)
  • Re: RMSD of backbone changes rapidly at the beginning of production run (Thu Nov 02 2017 - 17:59:45 CDT)
  • Re: Error on Settle.C when compiling NAMD with Intel Compiler (Wed Oct 25 2017 - 16:01:57 CDT)
  • Re: building system with or without water for metadynamics (Tue Oct 17 2017 - 19:06:12 CDT)
  • Re: Running 2.12 (Mon Oct 16 2017 - 12:07:07 CDT)
  • Re: Optimizing namd run (Wed Oct 11 2017 - 14:14:01 CDT)
  • Re: Sample umbrella sampling input file (Fri Oct 06 2017 - 17:35:33 CDT)
  • Re: NAMD on Stampede 2 (Fri Oct 06 2017 - 10:43:59 CDT)
  • Re: performance of NAMD on KNL (Fri Sep 29 2017 - 16:49:40 CDT)
  • Re: Building namd 2.12 from source an ARM64 architecture (Wed Sep 27 2017 - 18:09:31 CDT)
  • Re: Dihedral colvar (Fri Sep 08 2017 - 14:06:25 CDT)
  • Re: -nan values and fatal error (Thu Sep 07 2017 - 12:15:51 CDT)
  • Re: Concatenating log files (Wed Sep 06 2017 - 11:14:52 CDT)
  • Re: error - atom type not in psf (Fri Sep 01 2017 - 16:06:53 CDT)
  • Re: Regular vs US sampling runs. (Fri Sep 01 2017 - 11:53:11 CDT)
  • Re: error - atom type not in psf (Fri Sep 01 2017 - 11:36:19 CDT)
  • Re: Regular vs US sampling runs. (Thu Aug 31 2017 - 18:56:17 CDT)
  • Re: error - atom type not in psf (Thu Aug 31 2017 - 17:49:48 CDT)
  • Re: error - atom type not in psf (Thu Aug 31 2017 - 11:25:10 CDT)
  • Re: Creating psf file DNA (Wed Aug 30 2017 - 10:11:27 CDT)
  • Re: Simulating Protein/Membrane interface with pre-equiliibrated lipid bilayer (Wed Aug 23 2017 - 19:16:51 CDT)
  • Re: replica_bias and colvars (Thu Aug 10 2017 - 12:58:27 CDT)
  • Re: NAMD for Stampede2 (Wed Aug 09 2017 - 17:45:00 CDT)
  • Re: Are KNL a good choice for classical MD? (Fri Aug 04 2017 - 16:34:28 CDT)
  • Re: Namd 2.12 error with Nvidia M2090 cards (Thu Aug 03 2017 - 11:45:40 CDT)
  • Re: two stage equilibration in single configuration file (Thu Aug 03 2017 - 11:38:18 CDT)
  • Re: Configuration of new HPC Cluster for NAMD and GROMACS (Mon Jul 31 2017 - 13:57:50 CDT)
  • Re: NAMD 2.12 multicore CUDA on Ubuntu 16.04 with NVIDIA Tesla M10 produces segmentation fault (Tue Jul 18 2017 - 14:10:20 CDT)
  • Re: Maintaining PBC on Collective Variables (Mon Jul 10 2017 - 12:49:11 CDT)
  • Re: Creating psf file DNA (Thu Jul 06 2017 - 18:02:37 CDT)
  • Re: Creating psf file DNA (Thu Jul 06 2017 - 12:33:05 CDT)
  • Re: REG Protein inserion in to membrane bi layear (Thu Jun 22 2017 - 12:25:00 CDT)
  • Re: Harmonic force Keyword "centers" significance (Wed Jun 21 2017 - 17:49:20 CDT)
  • Re: Defining custom Colvars to measure pmf with Umbrella Sampling (Wed Jun 21 2017 - 11:06:57 CDT)
  • Re: REG Protein inserion in to membrane bi layear (Tue Jun 20 2017 - 10:49:51 CDT)
  • Re: Simulating Protein Entering membrane (Mon Jun 19 2017 - 12:01:45 CDT)
  • Re: [NAMD] How to build and simulate a periodic DNA in NAMD (Tue Jun 13 2017 - 12:09:32 CDT)
  • Re: Two parameter file in NAMD configuration file (Mon Jun 12 2017 - 10:20:44 CDT)
  • Re: Converting x,y,z coordinates to dcd file (Mon Jun 12 2017 - 10:17:24 CDT)
  • Re: Re: namd-l digest V1 #2196 (Fri Jun 09 2017 - 17:07:05 CDT)
  • Re: [NAMD] How to build and simulate a periodic DNA in NAMD (Fri Jun 09 2017 - 12:42:49 CDT)
  • Re: Two parameter file in NAMD configuration file (Fri Jun 09 2017 - 12:00:01 CDT)
  • Re: Umbrella Sampling colvar file parameters (Thu Jun 08 2017 - 12:32:44 CDT)
  • Re: Keeping potassium ions out of an area during equilibration (Wed Jun 07 2017 - 12:15:45 CDT)
  • Re: Keeping potassium ions out of an area during equilibration (Tue Jun 06 2017 - 11:59:46 CDT)
  • Re: Segmentation fault error with 'nan' pressure and energy (Tue May 30 2017 - 17:14:16 CDT)
  • Re: Error regarding missing angles between perturbed groups for fep calculation (Fri May 26 2017 - 17:09:53 CDT)
  • Re: Error regarding missing angles between perturbed groups for fep calculation (Thu May 25 2017 - 17:29:59 CDT)
  • Re: psfgen readpsf error with no more explanation (Wed May 17 2017 - 16:12:41 CDT)
  • Re: restraining selected atom's z coordinates (Mon May 15 2017 - 11:30:55 CDT)
  • Re: pKa calculation with thermodynamic integration (TI) (Thu May 11 2017 - 11:52:48 CDT)
  • Re: MPIRUN SLURM SCRIPT (Tue May 09 2017 - 10:48:25 CDT)
  • Re: pKa calculation with thermodynamic integration (TI) (Mon May 08 2017 - 17:01:05 CDT)
  • Re: namd 2.12 and plumed 2.3 (Tue May 02 2017 - 10:22:01 CDT)
  • Re: compilation of NAMD 2.12 fails (Thu Apr 27 2017 - 11:37:08 CDT)
  • Re: namd 2.12 and plumed 2.3 (Wed Apr 26 2017 - 11:43:41 CDT)
  • Re: how to have large coordinate values in the "coordinates PDB" file (Mon Apr 17 2017 - 14:03:15 CDT)
  • Re: performance on ~1.5 million atoms system (Mon Apr 17 2017 - 10:33:04 CDT)
  • Re: Energy values (Fri Apr 14 2017 - 17:57:56 CDT)
  • Re: lipid centering (Tue Apr 11 2017 - 13:23:05 CDT)
  • Re: Standard Output: Benchmark vs Timing (Sun Apr 09 2017 - 20:58:47 CDT)
  • Re: Solvent box fluctuations (Mon Mar 27 2017 - 12:13:37 CDT)
  • Re: Explanation of parameters for NBTABLE's tabulated external file? (Wed Mar 22 2017 - 13:09:02 CDT)
  • Re: Re: problems mutating HID to TYR for free energy calculations (Wed Mar 08 2017 - 09:45:49 CST)
  • Re: AW: REMD on HPC (Mon Mar 06 2017 - 09:47:23 CST)
  • Re: torsional restrain (Thu Feb 23 2017 - 12:02:18 CST)
  • Re: torsional restrain (Thu Feb 23 2017 - 11:09:02 CST)
  • Re: restraints and constraints in NAMD (Wed Feb 22 2017 - 11:57:14 CST)
  • Re: Regarding Error on HB2 (Tue Feb 21 2017 - 11:28:49 CST)
  • Re: Fixing COM of one atom in selection and letting the other move (Thu Feb 16 2017 - 10:58:32 CST)
  • Re: Fixing COM of one atom in selection and letting the other move (Tue Feb 14 2017 - 18:12:38 CST)
  • Re: PDB file creation (Wed Feb 08 2017 - 11:37:22 CST)
  • Re: High pressure calculations (Fri Feb 03 2017 - 11:15:04 CST)
  • Re: how do I restart umbrella sampling calculations? (Tue Jan 24 2017 - 16:26:39 CST)
  • Re: how do I restart umbrella sampling calculations? (Tue Jan 24 2017 - 14:57:36 CST)
  • Re: NAMD performance monitor (Tue Jan 17 2017 - 10:47:33 CST)
  • Re: MD using implicit solvent (Fri Dec 30 2016 - 11:03:05 CST)
  • Re: Query regarding colvar distanceZ (Tue Dec 27 2016 - 19:14:06 CST)
  • Re: Query regarding colvar distanceZ (Mon Dec 26 2016 - 10:49:38 CST)
  • Re: Query regarding colvar distanceZ (Mon Dec 26 2016 - 08:12:23 CST)
  • Re: Writing number of atoms in a specific group to a file (Fri Dec 16 2016 - 13:12:22 CST)
  • Re: psfgen - pdbalias when using readpsf (Thu Dec 15 2016 - 15:26:11 CST)
  • Re: (Thu Dec 08 2016 - 10:17:25 CST)
  • Re: Minimization error (Wed Dec 07 2016 - 11:36:44 CST)
  • Re: selectively assign HIE or HID for HIS residues (Tue Dec 06 2016 - 11:03:38 CST)
  • Re: REMD (Thu Nov 24 2016 - 11:07:06 CST)
  • Re: Generate psf file in x-plor format (Thu Nov 17 2016 - 18:56:55 CST)
  • Re: Generate psf file in x-plor format (Thu Nov 17 2016 - 14:56:01 CST)
  • Re: Generate psf file in x-plor format (Thu Nov 17 2016 - 09:47:42 CST)
  • Re: SMD restraints (Mon Nov 14 2016 - 16:26:01 CST)
  • Re: Need help with TCL script (Mon Nov 14 2016 - 14:17:08 CST)
  • Re: Parameters for determining run time (Mon Nov 07 2016 - 18:43:03 CST)
  • Re: NAMD Execution Error (Mon Oct 31 2016 - 14:09:02 CDT)
  • Re: NAMD breaks with wrong timestep (Fri Oct 21 2016 - 10:49:22 CDT)
  • Re: Martini CG models parameters errors (Mon Sep 26 2016 - 10:48:56 CDT)
  • Re: Martini CG models parameters errors (Thu Sep 22 2016 - 10:36:40 CDT)
  • Re: Query regarding parameter file generation of non standard residue (Thu Sep 08 2016 - 11:19:05 CDT)
  • Re: Query regarding parameter file generation of a non standard residue (Wed Sep 07 2016 - 16:49:15 CDT)
  • Re: ion escapes the channel during US simulation (Thu Sep 01 2016 - 10:27:16 CDT)
  • Re: ion escapes the channel during US simulation (Thu Sep 01 2016 - 09:44:22 CDT)
  • Re: targetCenters in Umbrella Sampling (Wed Aug 24 2016 - 18:04:31 CDT)
  • Re: PMF calculation input files (Tue Aug 23 2016 - 11:02:01 CDT)
  • Re: PMF calculation input files (Mon Aug 22 2016 - 16:27:34 CDT)
  • Re: PMF calculation input files (Mon Aug 22 2016 - 11:23:58 CDT)
  • Re: AW: Energy minimization (Wed Aug 17 2016 - 10:55:14 CDT)
  • Re: Lipid Bilayer Shearing (Tue Aug 16 2016 - 13:06:52 CDT)
  • Re: Lipid Bilayer Shearing (Tue Aug 16 2016 - 12:25:06 CDT)
  • Re: Problems with wrapAll (Fri Jul 22 2016 - 11:55:30 CDT)
  • Re: Problems with wrapAll (Thu Jul 21 2016 - 11:14:48 CDT)
• Victor Kwan
  • colvars: Error: keyword "translatereference" is not supported, or not recognized in this context. (Sun Dec 17 2017 - 22:35:33 CST)
  • Re: colvars/rmsd: Error: definition for atom group "atoms" not found. (Sun Dec 03 2017 - 15:15:38 CST)
  • colvars/rmsd: Error: definition for atom group "atoms" not found. (Sun Dec 03 2017 - 05:12:06 CST)
• Victor Ovchinnikov
  • Re: Error on Settle.C when compiling NAMD with Intel Compiler (Wed Oct 25 2017 - 15:59:42 CDT)
  • Re: (Thu Mar 23 2017 - 16:34:22 CDT)
• Victoria Lim
  • Re: What is the exact form of the harmonic potential used by the NAMD "constraints" option? (Tue Sep 19 2017 - 12:39:34 CDT)
  • Re: What is the exact form of the harmonic potential used by the NAMD "constraints" option? (Tue Sep 19 2017 - 11:33:46 CDT)
  • What is the exact form of the harmonic potential used by the NAMD "constraints" option? (Tue Sep 19 2017 - 01:37:21 CDT)
  • Re: How to calculate free energy to unbias colvars restraint? (Fri Jul 28 2017 - 19:17:33 CDT)
  • How to calculate free energy to unbias colvars restraint? (Fri Jul 28 2017 - 18:56:44 CDT)
• Vidhya Sankar
  • Issues about Keep_water_out.tcl acript (Fri Aug 18 2017 - 10:25:55 CDT)
  • Reg membrane assembly (Thu Aug 17 2017 - 00:37:42 CDT)
  • reg diffusion of water molecules (Sat Aug 12 2017 - 23:51:25 CDT)
  • How to set setting periodic boundary condition (Thu Jul 06 2017 - 07:43:56 CDT)
  • Reg seeting of periodic boundary condition (Tue Jun 20 2017 - 11:56:59 CDT)
  • REG Protein inserion in to membrane bi layear (Tue Jun 20 2017 - 05:05:39 CDT)
  • Reg seeting of periodic boundary condition (Wed Jun 14 2017 - 21:59:27 CDT)
  • mail reg membrane tutorial (Sat Feb 18 2017 - 23:34:54 CST)
  • Re: mail reg compilation of mdenergy (Tue Oct 25 2016 - 20:20:07 CDT)
  • mail reg compilation of mdenergy (Wed Oct 19 2016 - 12:08:12 CDT)
• Vlad Cojocaru
  • Re: Constrain on DNA when using ABF for protein-DNA system (Fri Oct 06 2017 - 08:28:43 CDT)
  • Re: Constrain on DNA when using ABF for protein-DNA system (Fri Oct 06 2017 - 08:08:33 CDT)
  • Re: colvar distanceInv not propagated with a harmonic moving restraint in NAMD 2.12 (Tue May 16 2017 - 10:50:10 CDT)
  • Re: colvar distanceInv not propagated with a harmonic moving restraint in NAMD 2.12 (Tue May 16 2017 - 09:36:38 CDT)
  • Re: colvar distanceInv not propagated with a harmonic moving restraint in NAMD 2.12 (Tue May 16 2017 - 08:20:31 CDT)
  • colvar distanceInv not propagated with a harmonic moving restraint in NAMD 2.12 (Mon May 15 2017 - 04:18:28 CDT)
  • Re: namd 2.12 and plumed 2.3 (Tue May 02 2017 - 10:33:34 CDT)
  • Re: namd 2.12 and plumed 2.3 (Tue May 02 2017 - 09:00:14 CDT)
  • Re: namd 2.12 and plumed 2.3 (Tue May 02 2017 - 08:12:22 CDT)
  • Re: compilation of NAMD 2.12 fails (Fri Apr 28 2017 - 10:36:12 CDT)
  • Re: compilation of NAMD 2.12 fails (Fri Apr 28 2017 - 10:24:18 CDT)
  • Re: compilation of NAMD 2.12 fails (Fri Apr 28 2017 - 10:23:24 CDT)
  • Re: compilation of NAMD 2.12 fails (Fri Apr 28 2017 - 09:14:58 CDT)
  • compilation of NAMD 2.12 fails (Thu Apr 27 2017 - 10:02:19 CDT)
  • Re: namd 2.12 and plumed 2.3 (Wed Apr 26 2017 - 11:23:54 CDT)
  • namd 2.12 and plumed 2.3 (Wed Apr 26 2017 - 05:20:28 CDT)
  • Re: NVE simulations in NAMD - the right choice of timesteps and parameters (Tue Nov 29 2016 - 11:09:40 CST)
  • Early bird extended! ISQBP2016 meeting - Bergen Norway (Mon Apr 18 2016 - 14:35:38 CDT)
  • 2016 ISQBP Meeting: early registration / abstract submission deadline approaching (Thu Mar 17 2016 - 03:49:47 CDT)
  • Fwd: ISQBP 2016 meeting - registration opened! (Mon Mar 14 2016 - 03:13:10 CDT)
  • Re: Should you cap C and N termini? (Thu Feb 18 2016 - 09:31:56 CST)
• vlad.cojocaru_at_mpi-muenster.mpg.de
  • Re: About the performance of RAMD (Fri Nov 10 2017 - 13:38:17 CST)
  • Re: namd 2.12 and plumed 2.3 (Tue May 02 2017 - 11:50:02 CDT)
• Vogel, Alexander
  • Re: Configuration of new HPC Cluster for NAMD and GROMACS (Tue Aug 01 2017 - 05:45:57 CDT)
  • Configuration of new HPC Cluster for NAMD and GROMACS (Mon Jul 31 2017 - 05:36:30 CDT)
• Wang, X. Y.
  • How to restart metadynamics in namd (Sun Jan 08 2017 - 22:29:41 CST)
  • Re: Re: RMSD based PMF calculation with umbrella sampling (Fri Dec 30 2016 - 06:03:02 CST)
  • RMSD based PMF calculation with umbrella sampling (Thu Dec 22 2016 - 04:26:21 CST)
• Wasut Pornpatcharapong
  • Colvars wall boundaries for CoordNum (Thu Jun 08 2017 - 19:27:50 CDT)
  • Re: Explanation of parameters for NBTABLE's tabulated external file? (Wed Mar 22 2017 - 16:59:19 CDT)
  • Re: Explanation of parameters for NBTABLE's tabulated external file? (Wed Mar 22 2017 - 13:56:15 CDT)
  • Explanation of parameters for NBTABLE's tabulated external file? (Wed Mar 22 2017 - 12:55:12 CDT)
  • Calculating gradient of the potential (force field) on each atom. (Thu Jan 12 2017 - 17:37:55 CST)
• Wei Jiang
  • Post-doc position at ALCF - HPC post-doc in Computational Materials (Fri Apr 07 2017 - 10:18:55 CDT)
• Wilson,Michael
  • Re: NAMD 2.12 multicore CUDA on Ubuntu 16.04 with NVIDIA Tesla M10 produces segmentation fault (Tue Jul 18 2017 - 15:18:28 CDT)
  • NAMD 2.12 multicore CUDA on Ubuntu 16.04 with NVIDIA Tesla M10 produces segmentation fault (Tue Jul 18 2017 - 13:57:16 CDT)
• wliu
  • How to use a proper force constant to decrease computational cost while keeping calculation precision? (Wed Apr 20 2016 - 02:18:01 CDT)
• Wright, David
  • NAMD 2.12 using CUDA 8.0 (Thu Apr 20 2017 - 08:40:28 CDT)
• Yan Shen
  • test area method to calculate surface tension (Thu Feb 25 2016 - 15:05:45 CST)
• Yaxin An
  • Re: namd-l digest V1 #2316 (Fri Dec 08 2017 - 09:06:19 CST)
  • Re: Free energy did not converge by using ABF (Fri Dec 08 2017 - 08:57:01 CST)
  • Free energy did not converge by using ABF (Thu Dec 07 2017 - 17:22:31 CST)
  • Re: coarse-grained simulations with errors "Atoms moving too fast" and "low global exclusion" (Fri Jun 09 2017 - 10:38:33 CDT)
  • coarse-grained simulations with errors "Atoms moving too fast" and "low global exclusion" (Fri Jun 09 2017 - 09:39:28 CDT)
• yeguoqiao
  • Problems in NAMD's code about real implementation of function named ComputeNonbondedUtil:calc_pair_energy (Fri Jan 29 2016 - 09:05:31 CST)
• Yi Huizhan
  • performance is more poor for namd 2.12 (Wed Sep 13 2017 - 22:25:13 CDT)
• yjcoshc
  • Re: metadynamics run in NAMD or using plumed in NAMD (Thu Dec 07 2017 - 19:22:06 CST)
  • Re: colvars: Did the orthogonality requirements of colvars change in ABF? (Mon Oct 16 2017 - 22:23:06 CDT)
  • colvars: Did the orthogonality requirements of colvars change in ABF? (Mon Oct 16 2017 - 20:20:29 CDT)
  • colvars: keepFreeEnergyFiles doesn't work in latest colvars version (Fri Sep 29 2017 - 21:38:13 CDT)
  • Gyration in colvars doesn't work with eABF. (Wed Jun 14 2017 - 06:49:51 CDT)
  • Re: Questions on implementing new collective variable in colvars. (Tue Jun 13 2017 - 20:36:32 CDT)
  • Re: Questions on implementing new collective variable in colvars. (Mon Jun 12 2017 - 22:48:26 CDT)
  • Questions on implementing new collective variable in colvars. (Mon Jun 12 2017 - 22:14:35 CDT)
  • Re: Some questions about the orthogonality of colvars in ABF. (Wed Mar 15 2017 - 08:39:58 CDT)
  • Some questions about the orthogonality of colvars in ABF. (Wed Mar 15 2017 - 07:11:46 CDT)
• yjcoshc_at_gmail.com
  • Re: colvars: keepFreeEnergyFiles doesn't work in latest colvars version (Sat Sep 30 2017 - 22:41:30 CDT)
  • Q=9B=9E=E5=A4=8D:__Free_energy_(eABF):_ne?= gative RMSD and harmonic restraints. (Wed Aug 02 2017 - 20:00:22 CDT)
  • Re: I don't have any eabf output file. (Tue Jul 25 2017 - 05:06:44 CDT)
  • Re: eABF - Fullsamples and windows merging (Wed Jul 19 2017 - 09:01:40 CDT)
  • Re: ABF: umbrella_int.awk (Sat Jul 15 2017 - 07:02:33 CDT)
  • Re: Querries on eABF (Tue May 30 2017 - 20:18:40 CDT)
  • Re: namd 2.12 and plumed 2.3 (Tue May 02 2017 - 11:02:33 CDT)
  • Re: Free energy calculation under external bias, (e)ABF/US/etc (Tue May 02 2017 - 04:15:21 CDT)
• Yongcheng Zhou
  • Re: Lennard-Jones potential in coarse grained MD (Sun Jan 31 2016 - 00:16:37 CST)
  • Lennard-Jones potential in coarse grained MD (Sat Jan 30 2016 - 00:36:20 CST)
• yousef nademi
  • Re: Lipid_bilayer_area_per_lipid_problem_using_NPT_CharmmForcefield (Fri Jul 07 2017 - 17:50:40 CDT)
  • Lipid_bilayer_area_per_lipid_problem_using_NPT_CharmmForcefield (Thu Jul 06 2017 - 20:49:48 CDT)
• Yue Qian
  • LJcorrection option in NAMD (Mon Jun 20 2016 - 17:09:04 CDT)
• Zach Bonham
  • Coordinate DCD file was not created during restart of adaptive biasing force simulation using colvars. (Wed Sep 21 2016 - 15:15:45 CDT)
• Zahra Mohammadi
  • Re: namd-l digest V1 #2289 (Wed Oct 25 2017 - 02:58:36 CDT)
  • FATAL ERROR: cuda_check_progress polled 1000000 times over ... (Tue Oct 24 2017 - 06:12:55 CDT)
• Zeina Salman
  • Re: graphene with proteins (Mon Sep 26 2016 - 16:02:36 CDT)
  • graphene with proteins (Sun Sep 25 2016 - 19:42:51 CDT)
• Zeki Zeybek
  • Re: CHARMRUN ERROR (Thu May 18 2017 - 13:38:26 CDT)
  • Re: CHARMRUN ERROR (Thu May 18 2017 - 02:27:27 CDT)
  • Re: CHARMRUN ERROR (Fri May 12 2017 - 02:05:13 CDT)
  • CHARMRUN ERROR (Thu May 11 2017 - 02:39:43 CDT)
  • Re: MPIRUN SLURM SCRIPT (Tue May 09 2017 - 11:00:07 CDT)
  • Re: MPIRUN SLURM SCRIPT (Tue May 09 2017 - 10:58:29 CDT)
  • Re: MPIRUN SLURM SCRIPT (Tue May 09 2017 - 06:02:20 CDT)
  • MPIRUN SLURM SCRIPT (Tue May 09 2017 - 05:08:22 CDT)
  • Custum made residue addition (Thu Apr 27 2017 - 08:08:17 CDT)
  • Slurm Script for Multi Node Run (Sun Apr 16 2017 - 11:42:41 CDT)
  • FFTK Determination of Dihedrals to be Scanned (Sun Feb 26 2017 - 08:20:30 CST)
  • Re: ++idlepoll (Mon Feb 06 2017 - 02:59:51 CST)
  • ++idlepoll (Mon Feb 06 2017 - 01:21:19 CST)
  • Energy Gradient Plotting (Wed Jan 18 2017 - 02:19:03 CST)
• zeynab hoseyni
  • Fwd: Modifying the equilibrium distance for a specific region of carbon nanotube in the parameter file (Mon Dec 26 2016 - 06:45:28 CST)
  • Fwd: Modifying the equilibrium distance for a specific region of carbon nanotube in the parameter file (Sun Dec 25 2016 - 14:31:53 CST)
  • Modifying the equilibrium distance for a specific region of carbon nanotube in the parameter file (Sun Dec 25 2016 - 12:51:46 CST)
  • Why wrapped and unwrapped trajectories show different energies over the time? (Sat Apr 23 2016 - 21:22:04 CDT)
• zeynab mohamad hoseyni
  • Modifying the equilibrium distance for a specific region of carbon nanotube in the parameter file (Sun Dec 25 2016 - 12:46:28 CST)
  • Why wrapped and unwrapped trajectories show different energies over time? (Sat Apr 23 2016 - 09:30:08 CDT)
• Zhao Qin
  • Re: multipld .dcd analysis by VMD (Thu Jan 21 2016 - 12:40:25 CST)
• zmhoseyni
  • Fw (5): zmhoseyni (Mon Dec 19 2016 - 13:47:30 CST)
• ZOU Changling
  • Q=B4=D7=D4"ZOU_Changling"_<zoucl@ihep.ac.cn>=B5=C4=D3=CA=BC=FE?= (Mon Feb 29 2016 - 02:43:31 CST)
  • Re: AW: À´×Ô"ZOU Changling" <zoucl@ihep.ac.cn>µÄÓʼþ (Sun Feb 28 2016 - 19:36:06 CST)
  • Q=B4=D7=D4"ZOU_Changling"_<zoucl@ihep.ac.cn>=B5=C4=D3=CA=BC=FE?= (Fri Feb 26 2016 - 05:20:03 CST)
• §³henyi
  • The adaptTemp and Temp in Adaptive tempering (Thu Jun 09 2016 - 15:17:25 CDT)
• ¸ß¾ü
  • about User-Defined Forces (Mon Jan 18 2016 - 03:28:31 CST)
• ÀîÎľê
  • The question about Network calculation (Thu Jun 23 2016 - 03:28:47 CDT)
• Éric Germaneau
  • Re: Running multi-node jobs on Sun Grid Engine (Sun Apr 03 2016 - 20:34:20 CDT)
  • Re: dynamic_cast & runtime type information (Wed Mar 23 2016 - 19:43:44 CDT)
  • Re: AW: AW: Testing NAMD scalability (Mon Mar 21 2016 - 22:20:54 CDT)
  • Testing NAMD scalability (Fri Mar 18 2016 - 20:31:31 CDT)
  • dynamic_cast & runtime type information (Fri Mar 18 2016 - 11:46:10 CDT)
• 孙业平
  • Reason: FATAL ERROR: Unknown command-line option ++local (Sun Oct 09 2016 - 14:09:47 CDT)
• 宋瑞ç�©
  • A problem in ABF simulation (Wed Dec 14 2016 - 05:45:28 CST)
  • A problem in ABF simulation (Tue Nov 29 2016 - 04:28:21 CST)
• å°�澤å�‹
  • very small cell (Fri Jan 06 2017 - 20:29:34 CST)
• 王茜茜
  • Re: NAMD2.9-ERROR: Constraint failure in RATTLE algorithm for atom! (Tue Sep 05 2017 - 05:23:02 CDT)
  • NAMD2.9-ERROR: Constraint failure in RATTLE algorithm for atom! (Fri Aug 25 2017 - 22:47:16 CDT)
  • NAMD2.9-ERROR: Constraint failure in RATTLE algorithm for atom! (Fri Aug 25 2017 - 22:33:43 CDT)
• 黄å§�姮
  • Targeted MD, "Biased atoms" and "Fitted atoms", RMSD (Wed Nov 29 2017 - 07:27:15 CST)
• 송연호
  • Re: problem to generate LPS PSF file using PSFGEN (Mon Mar 20 2017 - 19:22:29 CDT)
  • problem to generate LPS PSF file using PSFGEN (Thu Mar 16 2017 - 23:19:36 CDT)