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NAMD-L: By Author

By Author

2690 messages sorted by: [ date ] [ thread ] [ subject ] [ attachment ]
About this archive

Starting: Sun Jan 01 2017 - 04:00:35 CST
Ending: Mon Dec 31 2018 - 09:42:31 CST

• Aashish Bhatt
  • FEP atom velocity. (Mon Aug 20 2018 - 01:10:35 CDT)
  • Vibration Analysis Script (Fri Aug 03 2018 - 05:16:24 CDT)
  • Re: AMBER NetCDF file for Simulation (Thu Jun 07 2018 - 02:02:31 CDT)
  • AMBER NetCDF file for Simulation (Wed Jun 06 2018 - 07:33:10 CDT)
  • Re: FAD topology and parameters (Mon Feb 19 2018 - 09:46:16 CST)
  • Error Regarding minimization (Tue Jan 30 2018 - 09:36:37 CST)
• Abhaysinh Gaikwad
  • Simulation of imprinting process in NAMD (Tue Jan 30 2018 - 10:52:50 CST)
  • Stress calculation (Mon Jan 29 2018 - 10:04:34 CST)
  • Re: Stress calculation (Sun Jan 28 2018 - 15:50:37 CST)
  • Stress calculation (Tue Jan 16 2018 - 09:03:15 CST)
  • 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)
• Abhijit Gogoi
  • Re: (Mon Jul 23 2018 - 22:54:06 CDT)
  • (no subject) (Fri Jul 20 2018 - 01:15:37 CDT)
• Abhishek Kumar Singh
  • Regarding free energy (Sun Dec 09 2018 - 22:30:57 CST)
  • Re: Total charge problem (Sat Jul 07 2018 - 11:42:15 CDT)
  • Re: Total charge problem (Thu Jul 05 2018 - 13:29:40 CDT)
  • Total charge problem (Wed Jul 04 2018 - 07:50:36 CDT)
  • 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: Fix aminoacids - error (Sun Nov 04 2018 - 06:33:55 CST)
  • Re: Query for coarse grain system (Wed Apr 11 2018 - 00:39:49 CDT)
  • Re: Query for coarse grain system (Mon Apr 09 2018 - 12:17:06 CDT)
  • Re: Query for coarse grain system (Mon Apr 09 2018 - 08:42:35 CDT)
  • Re: Query for coarse grain system (Thu Apr 05 2018 - 10:23:18 CDT)
  • Query for coarse grain system (Thu Apr 05 2018 - 09:53:36 CDT)
  • 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)
• Adrien Cerdan
  • SMP instructions for multi-node calculation on POWER 8 + P100 (Wed Nov 22 2017 - 10:09:51 CST)
• Agisilaos Chantzis
  • Setting up QM/MM calculations with QwikMD without the GUI (Fri Oct 05 2018 - 11:20:54 CDT)
  • Re: Cutoff radius for electrostatic embedding in QM/MM calculations (Mon Sep 10 2018 - 12:41:25 CDT)
  • Cutoff radius for electrostatic embedding in QM/MM calculations (Wed Sep 05 2018 - 10:21:23 CDT)
  • Re: QM/MM MD and the qmParamPDB file (Thu Aug 16 2018 - 04:25:56 CDT)
  • QM/MM MD and the qmParamPDB file (Wed Aug 15 2018 - 07:48:40 CDT)
• Ahmad Kiani
  • Dielectric Constant in the gas phase (Fri Feb 09 2018 - 11:47:08 CST)
  • Re: Missing Parameters For H3O+ (Wed Jan 24 2018 - 09:27:28 CST)
  • Missing Parameters For H3O+ (Tue Jan 23 2018 - 12:13:00 CST)
  • UNABLE TO FIND ANGLE PARAMETERS FOR CD OH1 CD (ATOMS 282 284 282) (Tue Jan 16 2018 - 11:13:20 CST)
• Ahmad Kiani Karanji
  • RATTLE error with lipid bilayer system (Tue Nov 21 2017 - 13:08:46 CST)
• Ajasja LjubetiÄ�
  • Re: Isomerization between runs (Wed Aug 01 2018 - 06:40:19 CDT)
  • Re: Strange Bond Behavior Question (Sat Jun 23 2018 - 04:54:04 CDT)
  • Re: Re: vmd-l: Large number of harmonic distance restraints (Tue May 29 2018 - 11:36:46 CDT)
  • Re: mail reg Namd compilation (Mon May 28 2018 - 03:58:48 CDT)
  • Re: Get NAMD version from the tcl script interface (Wed May 09 2018 - 10:43:11 CDT)
  • Re: Get NAMD version from the tcl script interface (Wed May 09 2018 - 10:06:48 CDT)
  • Re: ffTK Without Using Gaussian (Tue Mar 20 2018 - 15:35:40 CDT)
  • Re: Residue Charges (Fri Mar 02 2018 - 08:55:31 CST)
  • 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)
• 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)
• Aksimentiev, Aleksei
  • Re: Creating an infinite graphene sheet (Sun May 13 2018 - 12:38:52 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)
• Alex Saad-Falcon
  • Microtubule Simulation (Wed May 30 2018 - 17:13:40 CDT)
  • ffTK Without Using Gaussian (Tue Mar 20 2018 - 10:49:48 CDT)
  • AutoPSF Error (Mon Mar 12 2018 - 10:40:47 CDT)
  • Simulating a Binding Event (Tue Mar 06 2018 - 11:53:54 CST)
  • Residue Charges (Fri Mar 02 2018 - 08:35:30 CST)
  • Simple PME Question (Mon Feb 19 2018 - 10:04:54 CST)
• Alexander Adams
  • Re: accelMDdihe is not working properly in NAMD after commit e3e849639982dcba9a60c6072c81fdb7cba69759 (Tue Aug 07 2018 - 11:43:30 CDT)
  • Re: GaMD in NAMD (Wed Jun 13 2018 - 23:15:12 CDT)
  • Re: Selective accelerated MD in NAMD (Sat Apr 07 2018 - 07:00:37 CDT)
  • Re: Selective accelerated MD in NAMD (Fri Apr 06 2018 - 15:36:59 CDT)
  • Selective accelerated MD in NAMD (Fri Apr 06 2018 - 14:08:43 CDT)
  • PACE CG Model (Fri Jul 28 2017 - 12:53:24 CDT)
  • NAMD on UCSD Comet (Mon Jul 03 2017 - 13:26:48 CDT)
• Alfonso Gijón
  • Re: How to simulate flexible water with TIP4P potential? (Wed Oct 03 2018 - 13:13:59 CDT)
  • How to simulate flexible water with TIP4P potential? (Wed Oct 03 2018 - 08:15:12 CDT)
• Ali Mehdizadeh Rahimi
  • Ewald size-dependence correction in FEP simulation of an electric dipole (Wed Sep 12 2018 - 19:34:37 CDT)
• Aliasghar Alizadeh-Mojarad
  • Re: Having problem with restarting colvar distance, (Wed Jan 03 2018 - 13:44:19 CST)
  • Re: Having problem with restarting colvar distance, (Wed Jan 03 2018 - 10:35:52 CST)
  • 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)
• Alice Zheng
  • Membrane Simulation (Tue Oct 30 2018 - 20:58:03 CDT)
• 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)
• Amy Rice
  • Re: Pulling protein through membrane without changing the position of membrane (Thu May 11 2017 - 12:05:37 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)
• 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)
• ANIRBAN MANDAL
  • Restrict drift of Graphene sheet in X-Y plane using Colvars (Mon Mar 26 2018 - 05:04:55 CDT)
  • Low global CUDA exclusion count! (9592 vs 9618) (Tue Mar 13 2018 - 04:39:31 CDT)
• Antonio Vila Sanjurjo
  • xMDFF: model file is not given (Fri May 25 2018 - 07:00:32 CDT)
• 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)
• Artur Hermano
  • adaptive biasing force (Wed Oct 24 2018 - 14:08:35 CDT)
  • nonuniform sampling in ABF (Tue Jun 12 2018 - 10:28:28 CDT)
  • Re: (Sat Mar 17 2018 - 16:41:44 CDT)
  • statistical error in ABF calculations (Wed Mar 14 2018 - 10:27:15 CDT)
  • trouble with colvars module (Thu Feb 01 2018 - 12:48:02 CST)
• asaffarhi_at_post.tau.ac.il
  • introduction to research on free energies (Fri Jan 20 2017 - 09:34:05 CST)
• Asghar Razavi
  • Re: Is there really no way of automating pair interaction calculations without invoking NAMD for each pdb file separately? (Fri Nov 02 2018 - 08:30:21 CDT)
  • Is there really no way of automating pair interaction calculations without invoking NAMD for each pdb file separately? (Thu Nov 01 2018 - 11:43:30 CDT)
  • How does NAMD calculate AccumulatedWork when using RMSD colvar? (Thu Apr 12 2018 - 12:29:19 CDT)
• Ashkan Shekaari
  • Re: C36 force field (Tue Dec 11 2018 - 11:21:24 CST)
  • Re: C36 force field (Tue Dec 11 2018 - 11:16:31 CST)
  • C36 force field (Tue Dec 11 2018 - 07:34:38 CST)
  • Positive energy for protein (Mon Dec 03 2018 - 08:20:58 CST)
  • Positive energy values for protein (Sat Dec 01 2018 - 07:43:48 CST)
  • Magnetic field (Thu Nov 22 2018 - 07:22:46 CST)
  • Nano-bio interaction in NAMD (Tue Oct 23 2018 - 10:01:09 CDT)
• Ashutosh Shandilya
  • Re: Bad global bond count! (48842 vs 48843) (Tue Apr 10 2018 - 11:41:32 CDT)
  • Re: periodic cell has become too small for original patch grid (Tue Mar 06 2018 - 15:41:54 CST)
  • UNABLE TO FIND ANGLE PARAMETERS FOR CT OS HO (ATOMS 23662 23661 23656) (Fri Mar 02 2018 - 13:55:43 CST)
  • periodic cell has become too small for original patch grid (Fri Mar 02 2018 - 13:55:10 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)
• Athreya, Nagendra Bala Murali
  • Multiple Electric Field simulation (Wed Mar 01 2017 - 15:13:37 CST)
• Axel Kohlmeyer
  • Re: Different cell vectors - Reg (Mon Sep 17 2018 - 05:09:27 CDT)
  • Re: Different cell vectors - Reg (Mon Sep 17 2018 - 04:49:10 CDT)
  • Re: Random Velocities Question (Tue Jul 03 2018 - 22:37:39 CDT)
  • Re: vmd-l: Large number of harmonic distance restraints (Tue May 29 2018 - 11:26:36 CDT)
  • Re: (Thu Apr 26 2018 - 10:19:18 CDT)
  • Re: (Thu Apr 26 2018 - 10:04:58 CDT)
  • Re: (Thu Apr 26 2018 - 08:50:28 CDT)
  • Re: Query for coarse grain system (Mon Apr 09 2018 - 09:22:11 CDT)
  • Re: NAMD Simulation in a laptop (Sun Mar 25 2018 - 21:07:13 CDT)
  • 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)
• Aysima Hacisuleyman
  • Re: Phosphorylated Residues (Wed Jun 27 2018 - 05:54:02 CDT)
  • QwikMD SMD force calculation (Mon Feb 05 2018 - 04:00:02 CST)
• Azadeh Alavi
  • Re: Metadynamics simulation (Thu Jan 05 2017 - 06:39:34 CST)
  • Metadynamics simulation (Tue Jan 03 2017 - 09:00:43 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)
• Bartlomiej Tywoniuk
  • Negative step number (Sat Apr 28 2018 - 14:03:54 CDT)
• Bassam Haddad
  • Re: E-field to Voltage - Reg (Fri Oct 05 2018 - 14:57:54 CDT)
  • Re: About CUDA version (Tue Sep 25 2018 - 14:04:14 CDT)
  • Re: Colvars Restraint Question (Thu Jun 21 2018 - 12:33:58 CDT)
  • Re: Running on GPU (Mon Mar 12 2018 - 14:33:58 CDT)
  • Re: Ways to find water molecules passing through the water channel in lipid bilayer (Thu Jan 18 2018 - 18:46:46 CST)
  • 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)
• Battocchio, Giovanni
  • NAMD 2.13 and RTX2080Ti (Thu Nov 22 2018 - 06:52:57 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 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 Rousseau
  • Proper combination of langevinHydrogen with rigidbonds (Thu Aug 31 2017 - 10:31:31 CDT)
• Bennion, Brian
  • Re: Parallel Jobs (Thu Dec 06 2018 - 15:01:48 CST)
  • Re: Parallel Jobs (Thu Dec 06 2018 - 14:51:38 CST)
  • 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)
• 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)
• Braden Kelly
  • NAMD QM/MM alchemical free energy change capabilities? (Mon Nov 26 2018 - 22:07:33 CST)
• Brian Radak
  • Re: User force field with FEP? (Tue Dec 11 2018 - 14:02:12 CST)
  • Re: Regarding free energy (Mon Dec 10 2018 - 11:47:27 CST)
  • Re: NAMD QM/MM alchemical free energy change capabilities? (Tue Nov 27 2018 - 08:26:34 CST)
  • Re: Minimization Question (Mon Nov 12 2018 - 20:41:26 CST)
  • Re: Minimization Question (Mon Nov 12 2018 - 13:45:43 CST)
  • Re: FEP Rattle Error (Mon Nov 12 2018 - 12:11:41 CST)
  • Re: Setting alchElecLambdaStart 1.0 parameter for FEP calculations (Mon Nov 12 2018 - 12:01:45 CST)
  • Re: creating topology for a unique structure (Thu Nov 08 2018 - 09:55:53 CST)
  • Re: Langevin Dynamics Coefficient Value -Reg (Tue Nov 06 2018 - 13:34:00 CST)
  • Re: Error with D-amino acids mid-sequence using NAMD 2.12/2.13b2 and CHARMm36 (Mon Nov 05 2018 - 11:18:56 CST)
  • Re: creating topology for a unique structure (Mon Nov 05 2018 - 10:49:48 CST)
  • Re: Is there really no way of automating pair interaction calculations without invoking NAMD for each pdb file separately? (Fri Nov 02 2018 - 09:28:21 CDT)
  • Re: detecting vanishing atoms in zero.fep (Thu Nov 01 2018 - 16:59:58 CDT)
  • Re: detecting vanishing atoms in zero.fep (Wed Oct 31 2018 - 09:06:15 CDT)
  • Re: detecting vanishing atoms in zero.fep (Sun Oct 28 2018 - 10:39:22 CDT)
  • Re: Alchdecouple for dihedral/improper terms (Sun Oct 28 2018 - 10:34:04 CDT)
  • Re: the fep error in third part of config file (Thu Oct 18 2018 - 15:10:31 CDT)
  • Fwd: the fep error in third part of config file (Wed Oct 17 2018 - 09:14:48 CDT)
  • Re: the fep error in third part of config file (Mon Oct 15 2018 - 14:17:23 CDT)
  • Re: How to simulate flexible water with TIP4P potential? (Wed Oct 03 2018 - 16:46:21 CDT)
  • Re: How to simulate flexible water with TIP4P potential? (Wed Oct 03 2018 - 09:34:42 CDT)
  • Re: SWM4-NDP PSF File (Thu Sep 27 2018 - 21:22:26 CDT)
  • Re: SWM4-NDP PSF File (Thu Sep 27 2018 - 08:41:10 CDT)
  • Re: Do firsttimestep, numsteps and run have maximum values? (Wed Sep 19 2018 - 09:32:29 CDT)
  • Re: Ewald size-dependence correction in FEP simulation of an electric dipole (Fri Sep 14 2018 - 09:37:16 CDT)
  • Re: energy calculation with namdenergy (Wed Sep 05 2018 - 08:18:56 CDT)
  • Re: Unexpected Energy values - Reg (Wed Sep 05 2018 - 08:15:40 CDT)
  • Re: Re: Error NPT simulation - Need Urgent Help - Reg (Fri Aug 31 2018 - 09:22:48 CDT)
  • Re: Question: constant-pH to standard MD (Fri Aug 24 2018 - 10:16:30 CDT)
  • Re: CGenFF 4.1 lone pairs (Wed Aug 22 2018 - 17:37:57 CDT)
  • Re: ERROR in multiple walker metadynamics simulation (Tue Aug 21 2018 - 09:05:31 CDT)
  • Re: FEP atom velocity. (Mon Aug 20 2018 - 13:15:01 CDT)
  • Re: ParseFEP error with FEP in segments at different lambda schedule (Wed Aug 01 2018 - 06:53:18 CDT)
  • Re: Problems with temperature control. (Tue Jul 31 2018 - 14:57:09 CDT)
  • Re: Problems with temperature control. (Tue Jul 31 2018 - 12:57:43 CDT)
  • Re: Rattle error with lateral pressure calculations (Tue Jul 31 2018 - 12:41:31 CDT)
  • Re: Problems with temperature control. (Tue Jul 31 2018 - 06:56:59 CDT)
  • Re: Problems with temperature control. (Mon Jul 30 2018 - 13:31:20 CDT)
  • Re: Problems with temperature control. (Mon Jul 30 2018 - 08:41:29 CDT)
  • Re: Rattle error with lateral pressure calculations (Mon Jul 30 2018 - 08:29:44 CDT)
  • Re: Rattle error with lateral pressure calculations (Sat Jul 28 2018 - 12:17:53 CDT)
  • Re: NAMD Error (Tue Jul 17 2018 - 16:32:50 CDT)
  • Re: NAMD Error (Tue Jul 17 2018 - 15:17:16 CDT)
  • Re: Decreasing performance of cluster running FEP (Sat Jul 14 2018 - 09:24:47 CDT)
  • Re: Decreasing performance of cluster running FEP (Thu Jul 12 2018 - 09:24:19 CDT)
  • Re: ABF Asymmetry (Tue Jul 10 2018 - 07:26:07 CDT)
  • Re: ABF Asymmetry (Mon Jul 09 2018 - 20:17:02 CDT)
  • Re: Distorted peptide bond with new residue (Thu Jul 05 2018 - 19:23:06 CDT)
  • Re: At high cutoff: "ERROR: CALCULATED VDWA FORCE MAY NOT MATCH ENERGY! POSSIBLE BUG!" (Sun Jul 01 2018 - 12:21:03 CDT)
  • Re: Strange Bond Behavior Question (Fri Jun 22 2018 - 16:12:30 CDT)
  • Re: "block" module for NAMD (Fri Jun 22 2018 - 08:22:10 CDT)
  • Re: namd mpi (Fri Jun 22 2018 - 08:20:16 CDT)
  • Re: mail reg constraint force (Fri Jun 22 2018 - 08:14:08 CDT)
  • Re: Colvars Restraint Question (Thu Jun 21 2018 - 15:01:39 CDT)
  • Re: Colvars Restraint Question (Thu Jun 21 2018 - 14:01:23 CDT)
  • Re: non uniform attempts distribution in constant pH MD (Wed Jun 13 2018 - 10:27:59 CDT)
  • Re: AMBER NetCDF file for Simulation (Thu Jun 07 2018 - 09:18:39 CDT)
  • Re: AMBER NetCDF file for Simulation (Wed Jun 06 2018 - 09:12:17 CDT)
  • Re: enhanced sampling of flexible tail (Tue Jun 05 2018 - 16:16:15 CDT)
  • Re: namd2_ti.pl Error: Modification of non-creatable array value attempted (Mon Jun 04 2018 - 08:14:11 CDT)
  • Re: Re: vmd-l: Large number of harmonic distance restraints (Tue May 29 2018 - 12:37:00 CDT)
  • Re: Solutescaling not working with Amber files (Tue May 29 2018 - 09:47:15 CDT)
  • Re: Are there plans on thermostat groups? (Wed May 16 2018 - 12:52:09 CDT)
  • Re: Are there plans on thermostat groups? (Wed May 16 2018 - 10:24:00 CDT)
  • Re: FEP slowdown during execution (Mon May 14 2018 - 15:14:01 CDT)
  • Re: Problem generating pdb psf of ATP (Mon May 14 2018 - 11:35:17 CDT)
  • Re: Get NAMD version from the tcl script interface (Wed May 09 2018 - 10:38:36 CDT)
  • Re: Get NAMD version from the tcl script interface (Wed May 09 2018 - 09:36:44 CDT)
  • Re: FEP & node/core number (Mon May 07 2018 - 08:38:37 CDT)
  • Re: Missing cphrst file (Mon May 07 2018 - 08:36:38 CDT)
  • Re: Re: vmd-l: Fwd: FEP with intermediary segments (Fri May 04 2018 - 15:46:56 CDT)
  • Re: Re: vmd-l: Fwd: FEP with intermediary segments (Fri May 04 2018 - 11:04:10 CDT)
  • Re: How to solve the segmentation faults in compiling NAMD to build and test the Charm++/Converse library (MPI version)? (Fri May 04 2018 - 08:05:21 CDT)
  • Re: vmd-l: Fwd: FEP with intermediary segments (Fri May 04 2018 - 08:01:28 CDT)
  • Re: (Thu May 03 2018 - 08:40:03 CDT)
  • Re: FEP & node/core number (Tue May 01 2018 - 11:58:04 CDT)
  • Re: (Thu Apr 26 2018 - 09:05:49 CDT)
  • Re: Re: vmd-l: PSFGEN 1.6.4 autogenerate PATCH keyword not available (Tue Apr 24 2018 - 11:23:47 CDT)
  • Re: vmd-l: PSFGEN 1.6.4 autogenerate PATCH keyword not available (Tue Apr 24 2018 - 07:34:01 CDT)
  • Re: Question about "useConstantArea" in puresure control model (Mon Apr 23 2018 - 11:20:26 CDT)
  • Re: Question about "useConstantArea" in puresure control model (Mon Apr 23 2018 - 07:38:42 CDT)
  • Re: FEP slowdown (Mon Apr 23 2018 - 07:34:47 CDT)
  • Re: How to interpret Thermodynamic Integration output (Thu Apr 19 2018 - 09:15:32 CDT)
  • Re: vmd-l: Re: Re: Bug with FEP? (Tue Apr 17 2018 - 09:42:46 CDT)
  • Re: vmd-l: Re: Re: Bug with FEP? (Mon Apr 16 2018 - 11:31:45 CDT)
  • Re: Re: Bug with FEP? (Fri Apr 13 2018 - 10:03:17 CDT)
  • Re: Re: Bad global bond count! (48842 vs 48843) (Tue Apr 10 2018 - 12:50:45 CDT)
  • Re: Proper use of psfgen "mutate"? (Tue Apr 10 2018 - 09:41:54 CDT)
  • Proper use of psfgen "mutate"? (Tue Apr 10 2018 - 08:58:47 CDT)
  • Re: ParseFEP error with FEP in segments at different lambda schedule (Tue Apr 10 2018 - 07:56:40 CDT)
  • Re: Fatty Acid Topology (Sun Apr 01 2018 - 09:01:48 CDT)
  • Re: Using PBC tools for a cubic and a rectangular box (Tue Mar 27 2018 - 09:03:55 CDT)
  • Re: Using PBC tools for a cubic and a rectangular box (Tue Mar 27 2018 - 08:09:43 CDT)
  • Re: vmd-l: [VMD-NAMD] Question about Dipole of DNA / Dipole Moment Watcher Plugin (Fri Mar 23 2018 - 10:59:05 CDT)
  • Re: vmd-l: Fwd: ParseFEP for restating FEP (Fri Mar 23 2018 - 10:48:17 CDT)
  • Re: How to interpret Thermodynamic Integration output (Fri Mar 23 2018 - 10:30:26 CDT)
  • Re: (Mon Mar 19 2018 - 07:58:36 CDT)
  • Re: (Sun Mar 18 2018 - 15:27:05 CDT)
  • Re: (Fri Mar 16 2018 - 09:26:38 CDT)
  • Re: (Thu Mar 15 2018 - 08:24:07 CDT)
  • Re: Python based tool for analysis of DCD trajectories (Fri Mar 09 2018 - 08:41:16 CST)
  • Re: Hydrogen Mass Repartitioning in NAMD (Thu Mar 08 2018 - 09:00:04 CST)
  • Re: Hydrogen Mass Repartitioning in NAMD (Thu Mar 08 2018 - 08:44:24 CST)
  • Re: Thermodynamic integration output analysis (Wed Mar 07 2018 - 07:59:18 CST)
  • Re: vmd-l: Fwd: parseFEP domain error (Mon Mar 05 2018 - 15:43:15 CST)
  • Re: UNABLE TO FIND ANGLE PARAMETERS FOR CT OS HO (ATOMS 23662 23661 23656) (Fri Mar 02 2018 - 14:29:26 CST)
  • Re: FEP minimum requirements (Thu Mar 01 2018 - 08:18:27 CST)
  • Re: How to interpret Thermodynamic Integration output (Tue Feb 27 2018 - 13:00:48 CST)
  • Re: How to interpret Thermodynamic Integration output (Sun Feb 25 2018 - 12:45:10 CST)
  • Re: Ligand atoms moving too fast with FEP (Tue Feb 20 2018 - 10:21:48 CST)
  • Re: Ligand atoms moving too fast with FEP (Tue Feb 20 2018 - 09:24:04 CST)
  • Re: Simple PME Question (Mon Feb 19 2018 - 11:04:12 CST)
  • Re: PME Tolerance (Mon Feb 19 2018 - 11:02:23 CST)
  • Re: Question on making 'reversible' solvated simulation (Mon Feb 19 2018 - 11:00:20 CST)
  • Re: Ligand atoms moving too fast with FEP (Fri Feb 16 2018 - 07:47:18 CST)
  • Re: Ligand atoms moving too fast with FEP (Thu Feb 15 2018 - 08:27:42 CST)
  • Re: Question on making 'reversible' solvated simulation (Mon Feb 12 2018 - 10:00:18 CST)
  • Re: Dielectric Constant in the gas phase (Fri Feb 09 2018 - 13:15:16 CST)
  • Re: Error Regarding minimization (Tue Jan 30 2018 - 09:51:13 CST)
  • Re: Calculate energy of a residue using NAMD energy (Tue Jan 30 2018 - 09:18:44 CST)
  • Re: Question on restraint behavior when part of system decouples (Mon Jan 29 2018 - 11:19:00 CST)
  • Re: Missing Parameters For H3O+ (Wed Jan 24 2018 - 09:05:36 CST)
  • Re: reinitatoms (Fri Jan 12 2018 - 14:20:14 CST)
  • 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)
• Bruno Cuevas Zuviría
  • Re: Unusual WT-Metadynamics gaussians heights (Tue Nov 13 2018 - 10:16:51 CST)
  • Unusual WT-Metadynamics gaussians heights (Mon Nov 12 2018 - 04:25:08 CST)
• Bryan Roessler
  • Spectre/Meltdown patch performance hits (Thu May 24 2018 - 09:34:00 CDT)
  • 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)
• Carla Gómez Santiago
  • Periodic cell basis too small for GridForce (Sun May 27 2018 - 09:29:30 CDT)
  • PBC and restraints (Wed May 23 2018 - 11:05:06 CDT)
• Carlo Guardiani
  • Setting up amorphous SiO2 slab (Tue Apr 24 2018 - 12:52:20 CDT)
  • 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)
• Chang Sun
  • Re: Vectors and indexing in VMD (Tue Jan 23 2018 - 10:35:35 CST)
• Charles Hoying
  • FATAL ERROR: Unable to access config file temp14.conf (Thu Aug 16 2018 - 20:44:17 CDT)
  • Keeping potassium ions out of an area during equilibration (Mon Jun 05 2017 - 22:57:40 CDT)
• Charline FAGNEN
  • Pressure ? High values ; Pressavg Gpressavg ? value of first step of restart very different from the last of the previous MD (Tue Jan 09 2018 - 10:09:16 CST)
• Chitrak Gupta
  • Re: GaMD in NAMD (Wed Jun 13 2018 - 22:04:51 CDT)
  • Re: Selective accelerated MD in NAMD (Sat Apr 07 2018 - 09:42:25 CDT)
  • Re: Selective accelerated MD in NAMD (Fri Apr 06 2018 - 17:42:15 CDT)
  • Re: Different resid in pdb fie but showing same molecule in VMD (Fri Jan 12 2018 - 19:00:01 CST)
  • 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)
• Chris Borchert
  • g++ 5.3 fails on 2.12/2.13b1 with CUDA 8.0 (Thu Oct 04 2018 - 15:59:10 CDT)
• Chris Butch
  • Script for Terachem QMMM (Thu Dec 14 2017 - 03:29:17 CST)
• Chris Chipot
  • Re: Fwd: FEP protein-ligand tutorial 2017 unclear section (Sat May 05 2018 - 09:28:27 CDT)
  • Re: ParseFEP error with FEP in segments at different lambda schedule (Sun Apr 08 2018 - 08:58:34 CDT)
  • Re: Fwd: parseFEP domain error (Mon Mar 05 2018 - 17:25:57 CST)
  • 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)
• 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: Double-defined segid, resid for more than 9999 id's (Wed Feb 07 2018 - 10:59:28 CST)
  • Double-defined segid, resid for more than 9999 id's (Fri Feb 02 2018 - 10:17:30 CST)
  • Vectors and indexing in VMD (Tue Jan 23 2018 - 06:16:00 CST)
  • 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)
• 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 Möller
  • AW: Aromatic rings don't maintain the planarity during the heating (Fri May 04 2018 - 11:23:24 CDT)
  • AW: Movie in VMD (Sun Aug 27 2017 - 08:13:39 CDT)
• Danilo Di Maio
  • Re: The reason for the formation of bubbles in heating stage (Mon Jan 09 2017 - 09:09:58 CST)
• Darin Lory
  • Re: tar.gz incorrect firmat? (Wed Dec 05 2018 - 15:01:08 CST)
  • Re: Way to wget or curl download the precompiled NAMD? (Fri Nov 09 2018 - 10:02:09 CST)
  • Re: Way to wget or curl download the precompiled NAMD? (Thu Nov 08 2018 - 16:19:33 CST)
  • Way to wget or curl download the precompiled NAMD? (Thu Nov 08 2018 - 15:13:22 CST)
  • (no subject) (Fri Oct 26 2018 - 11:22:41 CDT)
• 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 Hardy
  • Re: Binding free energy tutorial (Sun Oct 28 2018 - 11:47:37 CDT)
  • Re: Binding free energy tutorial (Sat Oct 27 2018 - 15:34:24 CDT)
  • Re: (Sat Oct 27 2018 - 04:22:03 CDT)
  • Re: Binding free energy tutorial (Sat Oct 27 2018 - 03:15:30 CDT)
  • Re: git rid of it (Fri Oct 19 2018 - 15:17:49 CDT)
  • Re: Affinity (Tue Oct 16 2018 - 17:27:30 CDT)
  • Re: How to simulate flexible water with TIP4P potential? (Wed Oct 03 2018 - 10:35:58 CDT)
  • Re: SWM4-NDP PSF File (Fri Sep 28 2018 - 10:35:46 CDT)
  • Re: SWM4-NDP PSF File (Thu Sep 27 2018 - 18:07:09 CDT)
  • Re: Do firsttimestep, numsteps and run have maximum values? (Wed Sep 19 2018 - 10:04:28 CDT)
  • Re: Rattle algorithm Constraint failure - Reg (Fri Sep 07 2018 - 09:31:19 CDT)
  • Re: Error NPT simulation - Need Urgent Help - Reg (Wed Aug 29 2018 - 12:01:46 CDT)
  • Re: restarting Gaussian accelerated MD fails (Wed Aug 08 2018 - 11:35:44 CDT)
  • Re: accelMDdihe is not working properly in NAMD after commit e3e849639982dcba9a60c6072c81fdb7cba69759 (Wed Aug 08 2018 - 11:26:50 CDT)
  • Re: Re: QM/MM with Orca: Memory allocation failed (Thu Jul 26 2018 - 14:33:03 CDT)
  • Re: (Thu Jun 07 2018 - 14:18:06 CDT)
  • Re: mail reg Namd compilation (Tue May 29 2018 - 11:38:42 CDT)
  • Re: accelMDdihe is not working properly in NAMD after commit e3e849639982dcba9a60c6072c81fdb7cba69759 (Thu May 17 2018 - 10:46:00 CDT)
  • Re: NAMD-CUDA GPU workload (Mon Apr 02 2018 - 11:33:06 CDT)
  • Re: Segmentation fault for the tutorial (Wed Mar 07 2018 - 10:51:44 CST)
  • 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)
• David Huggins
  • Setting alchElecLambdaStart 1.0 parameter for FEP calculations (Fri Nov 09 2018 - 12:08:51 CST)
  • Alchdecouple for dihedral/improper terms (Sat Oct 27 2018 - 10:21:26 CDT)
  • 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)
• Dawid das
  • Re: re-centering the molecule while restarting the run (Fri Apr 13 2018 - 15:18:06 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)
• deep deep
  • patch ID error (Wed Mar 21 2018 - 15:18:04 CDT)
• Deng, Jinxia (Nancy)
  • specify H-bond in CGMD (Thu Mar 09 2017 - 08:42:14 CST)
• Denish Poudyal
  • Re: Problem generating pdb psf of ATP (Mon May 14 2018 - 04:55:05 CDT)
  • Enabling charmrun in NAMD simulation (Wed Apr 25 2018 - 01:00:35 CDT)
  • Meaning of warning in output log file (Wed Mar 28 2018 - 02:57:23 CDT)
  • Re: NAMD Simulation in a laptop (Sun Mar 25 2018 - 23:34:38 CDT)
  • Re: NAMD Simulation in a laptop (Sun Mar 25 2018 - 21:37:28 CDT)
  • NAMD Simulation in a laptop (Sun Mar 25 2018 - 20:56:44 CDT)
• Dhiraj Srivastava
  • Re: parameter file for ACE and CT3 cap (Mon Sep 03 2018 - 11:59:40 CDT)
  • parameter file for ACE and CT3 cap (Sun Sep 02 2018 - 19:45:14 CDT)
  • Re: PCA and vector (Sat Jun 16 2018 - 13:03:57 CDT)
  • PCA and vector (Fri Jun 15 2018 - 13:59:07 CDT)
  • Re: GaMD in NAMD (Thu Jun 14 2018 - 07:40:52 CDT)
  • Re: GaMD in NAMD (Wed Jun 13 2018 - 23:51:07 CDT)
  • Re: GaMD in NAMD (Wed Jun 13 2018 - 22:09:46 CDT)
  • GaMD in NAMD (Wed Jun 13 2018 - 21:54:19 CDT)
  • enhanced sampling of flexible tail (Tue Jun 05 2018 - 16:02:08 CDT)
  • temperature accelerated molecular dynamics (Thu May 31 2018 - 23:59:35 CDT)
  • distance filter during data analysis (Tue May 08 2018 - 23:43:39 CDT)
  • Re: SMD with colvar not working (Tue Apr 24 2018 - 11:12:17 CDT)
  • Re: SMD with colvar not working (Tue Apr 24 2018 - 11:02:29 CDT)
  • Re: SMD with colvar not working (Tue Apr 24 2018 - 10:45:24 CDT)
  • SMD with colvar not working (Tue Apr 24 2018 - 00:21:43 CDT)
  • long simulation and error "integer value too large" (Fri Apr 20 2018 - 23:24:23 CDT)
  • Re: colvar with moving frame of reference (Tue Apr 17 2018 - 13:39:23 CDT)
  • Re: colvar with moving frame of reference (Mon Apr 16 2018 - 14:24:41 CDT)
  • colvar with moving frame of reference (Mon Apr 16 2018 - 13:29:53 CDT)
  • re-centering the molecule while restarting the run (Fri Apr 13 2018 - 13:27:30 CDT)
  • Re: calculation of helical axis in NAMD (Mon Apr 09 2018 - 10:29:11 CDT)
  • Re: calculation of helical axis in NAMD (Sun Apr 08 2018 - 17:41:48 CDT)
  • calculation of helical axis in NAMD (Sat Apr 07 2018 - 01:01:20 CDT)
  • Re: Steered MD simulation with pull and rotation (Mon Apr 02 2018 - 09:24:36 CDT)
  • Steered MD simulation with pull and rotation (Wed Mar 28 2018 - 14:23:08 CDT)
  • 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)
• dhirajks
  • RE: long simulation and error "integer value too large" (Sat Apr 21 2018 - 09:04:42 CDT)
• dhirajks_at_gmail.com
  • Enhanced sampling of domain motion and gsafold (Mon Jul 03 2017 - 19:18:38 CDT)
• Diego Gomes
  • [ REST2 ] Possible bug on NAMD example (Thu Nov 22 2018 - 07:06:41 CST)
• Dipak Balasaheb Sanap
  • Re: ffTK torsion scan convergence using Gaussian. (Tue Nov 13 2018 - 20:14:40 CST)
  • Re: ffTK torsion scan convergence using Gaussian. (Tue Nov 13 2018 - 20:07:02 CST)
  • ffTK torsion scan convergence using Gaussian. (Mon Nov 12 2018 - 18:08:12 CST)
  • Gaussian Dihedral Scan Log files visualization. (Sat Nov 03 2018 - 21:47:47 CDT)
  • FFtK Tutorial (Urey-Bradley angles error). (Fri Oct 26 2018 - 14:20:59 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)
• Douglas Houston
  • ABF with alpha colvar? (Sat Jan 21 2017 - 11:30:49 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)
• Dushyant Sahoo
  • Define spheres using NAMD (Sun Feb 19 2017 - 12:17:37 CST)
• Ebru Çetin
  • Re: FEP Rattle Error (Mon Nov 12 2018 - 13:30:08 CST)
  • FEP Rattle Error (Sun Nov 11 2018 - 17:07:51 CST)
• Eduard Schreiner
  • Re: Type of solvent water molecules (Tue Apr 18 2017 - 16:21:01 CDT)
• Ekaterina Sobakinskaja
  • Re: ABF, rigid bonds and constraints (Fri Jul 06 2018 - 10:06:21 CDT)
  • ABF, rigid bonds and constraints (Fri Jul 06 2018 - 05:23:10 CDT)
  • Q=9E=D1=82=D0=B2=D0=B5=D1=82:=20Re:=20=20none?= quilibrium SMD with fixed atoms (Wed Jan 24 2018 - 13:58:29 CST)
  • nonequilibrium SMD with fixed atoms (Wed Jan 24 2018 - 09:27:28 CST)
• 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 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)
• Erik Nordgren
  • strange diffs in energy output of NAMD 2.9 vs. 2.11 (Fri Feb 03 2017 - 14:05:23 CST)
• Esmael Jafari Haddadian
  • Re: Angle of lone pair in TIP4P 2005 simulation (Tue May 08 2018 - 19:18:23 CDT)
• Estefanía Hugo
  • displacement of protein (Thu Sep 21 2017 - 09:08:19 CDT)
• Faramarz Joodaki
  • Re: How to add a C code to NAMD properly? (Tue Dec 18 2018 - 09:37:25 CST)
  • Re: How to add a C code to NAMD properly? (Sun Dec 16 2018 - 11:59:19 CST)
  • Re: How to add a C code to NAMD properly? (Sun Dec 16 2018 - 11:50:41 CST)
  • Re: NAMD compiling problem (Thu Dec 06 2018 - 14:08:52 CST)
  • NAMD compiling problem (Thu Dec 06 2018 - 10:59:17 CST)
  • Re: How to add a C code to NAMD properly? (Wed Dec 05 2018 - 19:51:57 CST)
  • Re: How to add a C code to NAMD properly? (Wed Dec 05 2018 - 18:39:07 CST)
  • Re: How to add a C code to NAMD properly? (Tue Nov 27 2018 - 16:10:46 CST)
  • How to add a C code to NAMD properly? (Fri Nov 23 2018 - 12:58:39 CST)
  • 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)
• 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)
• Fateme Ghadirian
  • Re: RE: Hard wall on Z direction for ions (Tue May 15 2018 - 03:28:02 CDT)
  • Hard wall on Z direction for ions (Mon May 14 2018 - 09:06:31 CDT)
• fhh2626
  • re: Nano-bio interaction in NAMD (Tue Oct 23 2018 - 10:22:52 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
  • Right NAMD version (Tue Sep 18 2018 - 06:00:36 CDT)
  • 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: colvars selecting frames (Thu Feb 01 2018 - 10:21:18 CST)
  • Re: Trouble with NAMD Win64-CUDA 2.12 on my new PC (Mon Jan 22 2018 - 11:29:45 CST)
  • 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: NAMD/VMD installation for Windows 10 (Mon Nov 19 2018 - 10:59:48 CST)
  • Re: mail reg Namd compilation (Mon May 28 2018 - 04:14:34 CDT)
  • Re: Fatty Acid Topology (Mon Apr 02 2018 - 12:46:54 CDT)
  • Re: Atom velocity error in coarse grained simulation using MARTINI (Sun Apr 01 2018 - 06:07:58 CDT)
  • Re: ffTK Without Using Gaussian (Tue Mar 20 2018 - 12:59:34 CDT)
  • Re: Re: simulation becomes unstable in residue base coarse grained system (Tue Feb 13 2018 - 06:13:14 CST)
  • 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)
• Francesco Pietra
  • unable to open restart.colvars (Mon Dec 31 2018 - 01:47:21 CST)
  • QM-MM with MOPAC (Mon Dec 31 2018 - 01:32:04 CST)
  • Re: Running QM-MM MOPAC on a cluster (Fri Dec 21 2018 - 13:17:13 CST)
  • Re: Running QM-MM MOPAC on a cluster (Mon Dec 17 2018 - 15:22:11 CST)
  • Fwd: Question on restraints with MM-GBSA (Sun Dec 16 2018 - 13:28:47 CST)
  • Question on restraints with MM-GBSA (Sun Dec 16 2018 - 04:47:36 CST)
  • Re: Running QM-MM MOPAC on a cluster (Sun Dec 16 2018 - 01:47:41 CST)
  • Running QM-MM MOPAC on a cluster (Fri Dec 14 2018 - 04:21:04 CST)
  • Re: tar.gz incorrect firmat? (Thu Dec 06 2018 - 02:58:05 CST)
  • tar.gz incorrect firmat? (Wed Dec 05 2018 - 14:51:50 CST)
  • Re: Is there a problem of ORCA running for NAMD MPI? (Tue Nov 20 2018 - 09:32:34 CST)
  • Is there a problem of ORCA running for NAMD MPI? (Tue Nov 20 2018 - 03:35:17 CST)
  • Fwd: Running QM-MM tutorial on a cluster (Sun Nov 18 2018 - 00:44:44 CST)
  • Running QM-MM tutorial on a cluster (Sat Nov 17 2018 - 13:30:02 CST)
  • Re: parameter request for PRES bonding (Tue Oct 30 2018 - 09:16:39 CDT)
  • Re: parameter request for PRES bonding (Mon Oct 29 2018 - 02:07:38 CDT)
  • Fwd: parameter request for PRES bonding (Sat Oct 27 2018 - 02:29:39 CDT)
  • parameter request for PRES bonding (Sat Oct 27 2018 - 02:27:05 CDT)
  • Fwd: Sudden /\A drop in last FEP window (Tue Aug 14 2018 - 23:44:06 CDT)
  • Re: Sudden /\A drop in last FEP window (Mon Aug 06 2018 - 09:30:28 CDT)
  • Re: ParseFEP error with FEP in segments at different lambda schedule (Sat Aug 04 2018 - 08:21:10 CDT)
  • Re: ParseFEP error with FEP in segments at different lambda schedule (Wed Aug 01 2018 - 09:10:54 CDT)
  • Re: ParseFEP error with FEP in segments at different lambda schedule (Wed Aug 01 2018 - 05:40:22 CDT)
  • Fwd: Sudden /\A drop in last FEP window (Sat Jul 28 2018 - 05:30:07 CDT)
  • Fwd: Sudden /\A drop in last FEP window (Fri Jul 27 2018 - 03:13:46 CDT)
  • Re: Sudden /\A drop in last FEP window (Thu Jul 26 2018 - 12:54:12 CDT)
  • Sudden /\A drop in last FEP window (Thu Jul 26 2018 - 10:34:06 CDT)
  • Re: Decreasing performance of cluster running FEP (Sat Jul 14 2018 - 10:57:38 CDT)
  • Re: Decreasing performance of cluster running FEP (Thu Jul 12 2018 - 01:58:45 CDT)
  • Re: Decreasing performance of cluster running FEP (Wed Jul 11 2018 - 16:31:55 CDT)
  • Decreasing performance of cluster running FEP (Wed Jul 11 2018 - 00:29:51 CDT)
  • Re: GaMD in NAMD (Thu Jun 14 2018 - 01:05:52 CDT)
  • Sudden drop of /\A in ParseFEP.log near lamda 1.0 (Wed Jun 06 2018 - 00:58:11 CDT)
  • FEP performance (Mon May 28 2018 - 10:05:01 CDT)
  • Fwd: FEP slowdown during execution (Sat May 12 2018 - 01:12:35 CDT)
  • FEP slowdown during execution (Sat May 12 2018 - 01:10:39 CDT)
  • Fwd: FEP & node/core number (Mon May 07 2018 - 09:34:14 CDT)
  • Fwd: FEP & node/core number (Mon May 07 2018 - 08:19:22 CDT)
  • Re: Fwd: FEP protein-ligand tutorial 2017 unclear section (Mon May 07 2018 - 08:03:34 CDT)
  • Re: Fwd: FEP protein-ligand tutorial 2017 unclear section (Sat May 05 2018 - 01:43:17 CDT)
  • Re: Re: vmd-l: Fwd: FEP with intermediary segments (Sat May 05 2018 - 01:21:23 CDT)
  • Re: Re: vmd-l: Fwd: FEP with intermediary segments (Fri May 04 2018 - 15:00:22 CDT)
  • Re: Fwd: FEP protein-ligand tutorial 2017 unclear section (Fri May 04 2018 - 14:47:42 CDT)
  • Re: Re: vmd-l: Fwd: FEP with intermediary segments (Fri May 04 2018 - 10:51:45 CDT)
  • Fwd: FEP protein-ligand tutorial 2017 unclear section (Fri May 04 2018 - 00:39:24 CDT)
  • Fwd: FEP with intermediary segments (Fri May 04 2018 - 00:37:18 CDT)
  • FEP protein-ligand tutorial 2017 unclear section (Wed May 02 2018 - 14:51:14 CDT)
  • Re: FEP & node/core number (Wed May 02 2018 - 00:53:44 CDT)
  • FEP & node/core number (Mon Apr 30 2018 - 10:36:26 CDT)
  • FEP with intermediary segments (Thu Apr 26 2018 - 10:20:21 CDT)
  • Re: FEP slowdown (Tue Apr 24 2018 - 08:51:02 CDT)
  • FEP slowdown (Sat Apr 21 2018 - 10:34:58 CDT)
  • Re: vmd-l: Re: Re: Bug with FEP? (Tue Apr 17 2018 - 00:05:38 CDT)
  • Re: Re: Bug with FEP? (Sun Apr 15 2018 - 02:48:10 CDT)
  • Re: Bug with FEP? (Fri Apr 13 2018 - 02:49:14 CDT)
  • Bug with FEP? (Thu Apr 12 2018 - 15:28:31 CDT)
  • Re: vmd-l: Proper use of psfgen "mutate"? (Tue Apr 10 2018 - 09:20:20 CDT)
  • ParseFEP error with FEP in segments at different lambda schedule (Sun Apr 08 2018 - 08:46:35 CDT)
  • Re: vmd-l: Fwd: ParseFEP for restating FEP (Fri Mar 23 2018 - 15:31:58 CDT)
  • Fwd: ParseFEP for restating FEP (Fri Mar 23 2018 - 09:00:15 CDT)
  • ParseFEP for restating FEP (Fri Mar 23 2018 - 02:05:41 CDT)
  • Re: Fwd: parseFEP domain error (Wed Mar 07 2018 - 08:39:49 CST)
  • Fwd: parseFEP domain error (Mon Mar 05 2018 - 14:17:56 CST)
  • Fwd: parseFEP domain error (Sat Mar 03 2018 - 11:44:06 CST)
  • FEP minimum requirements (Thu Mar 01 2018 - 03:05:22 CST)
  • Re: Ligand atoms moving too fast with FEP (Tue Feb 20 2018 - 10:10:50 CST)
  • Fwd: Ligand atoms moving too fast with FEP (Tue Feb 20 2018 - 09:23:05 CST)
  • Fwd: Ligand atoms moving too fast with FEP (Tue Feb 20 2018 - 02:08:17 CST)
  • Fwd: Ligand atoms moving too fast with FEP (Tue Feb 20 2018 - 01:58:37 CST)
  • Re: Ligand atoms moving too fast with FEP (Fri Feb 16 2018 - 09:31:08 CST)
  • Re: Ligand atoms moving too fast with FEP (Thu Feb 15 2018 - 09:47:51 CST)
  • Ligand atoms moving too fast with FEP (Thu Feb 15 2018 - 02:00:39 CST)
  • 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)
• 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)
• Geo Reuter
  • Angle of lone pair in TIP4P 2005 simulation (Tue May 08 2018 - 19:08:34 CDT)
  • Equilibrated TIP4P_2005 Waterbox (Tue May 01 2018 - 15:09:53 CDT)
• Gerard Rowe
  • Re: Is there a problem of ORCA running for NAMD MPI? (Tue Nov 20 2018 - 08:12:49 CST)
  • Re: Minimization Question (Tue Nov 13 2018 - 07:54:53 CST)
  • Re: Minimization Question (Mon Nov 12 2018 - 13:08:00 CST)
  • Re: QM/MM Question (Tue Nov 06 2018 - 13:17:42 CST)
  • Re: QM/MM Question (Mon Nov 05 2018 - 16:19:08 CST)
  • Re: QM/MM Question (Mon Nov 05 2018 - 13:41:11 CST)
  • Re: QM/MM Question (Mon Nov 05 2018 - 07:32:06 CST)
  • Re: ORCA GPUs (Fri Nov 02 2018 - 12:56:39 CDT)
  • Re: ORCA GPUs (Fri Nov 02 2018 - 09:14:41 CDT)
  • Re: ORCA QMMM (Thu Nov 01 2018 - 16:26:34 CDT)
  • Re: ORCA QMMM (Tue Oct 30 2018 - 07:42:20 CDT)
  • MOPAC Point Charges (Mon Aug 20 2018 - 12:29:36 CDT)
  • SegFault in QM/MM run (Wed Aug 01 2018 - 08:59:37 CDT)
  • Re: QM/MM with Orca: Memory allocation failed (Tue Jul 24 2018 - 10:55:53 CDT)
  • QM/MM with Orca: Memory allocation failed (Wed Jul 18 2018 - 17:18:33 CDT)
• Giacomo Fiorin
  • Re: How to add a C code to NAMD properly? (Wed Dec 19 2018 - 13:45:21 CST)
  • Re: How to add a C code to NAMD properly? (Sun Dec 16 2018 - 22:36:26 CST)
  • Re: User force field with FEP? (Tue Dec 11 2018 - 14:16:10 CST)
  • Re: User force field with FEP? (Tue Dec 11 2018 - 13:44:33 CST)
  • Re: NAMD compiling problem (Thu Dec 06 2018 - 11:12:27 CST)
  • Re: NAMD compiling problem (Thu Dec 06 2018 - 11:11:25 CST)
  • Re: ERROR TOLERANCE (Wed Dec 05 2018 - 13:51:42 CST)
  • Re: Unusual WT-Metadynamics gaussians heights (Tue Nov 13 2018 - 13:50:47 CST)
  • Re: Unusual WT-Metadynamics gaussians heights (Tue Nov 13 2018 - 07:44:58 CST)
  • Re: Error with D-amino acids mid-sequence using NAMD 2.12/2.13b2 and CHARMm36 (Mon Nov 05 2018 - 13:13:06 CST)
  • Re: Error with D-amino acids mid-sequence using NAMD 2.12/2.13b2 and CHARMm36 (Mon Nov 05 2018 - 11:36:47 CST)
  • Re: NVIDIA Quadro(R) GV100 card for NAMD studies (Mon Nov 05 2018 - 07:29:48 CST)
  • Re: NVIDIA Quadro(R) GV100 card for NAMD studies (Fri Nov 02 2018 - 06:48:30 CDT)
  • Re: Binding free energy tutorial (Sun Oct 28 2018 - 10:20:50 CDT)
  • Re: Positive VDW energies (Thu Oct 25 2018 - 16:32:50 CDT)
  • Re: constant temprature for vacuum condition in namd file (Fri Oct 19 2018 - 14:26:48 CDT)
  • Re: ABF Window Boundaries (Fri Oct 19 2018 - 10:35:27 CDT)
  • Re: Colvars and distance restraint for umbrella sampling (Tue Oct 16 2018 - 19:31:15 CDT)
  • Re: E-field to Voltage - Reg (Fri Oct 05 2018 - 11:43:51 CDT)
  • Re: calculating non bonded energy using namdenergy (Thu Sep 20 2018 - 09:49:14 CDT)
  • Re: Right NAMD version (Tue Sep 18 2018 - 08:19:50 CDT)
  • Re: Re: namd simulation input file setting from NPT to NVT (Mon Sep 10 2018 - 11:25:54 CDT)
  • Re: Weird PBC wrapping (Thu Aug 30 2018 - 08:41:54 CDT)
  • Re: Three bonds with water in vmd from NAMD DCD (Tue Aug 21 2018 - 10:04:42 CDT)
  • Re: Periodic cell has become too small for original patch grid (Mon Aug 13 2018 - 07:00:35 CDT)
  • Re: Which one is more reliable to use in umbrella sampling- .traj data or vmd script data (Fri Aug 03 2018 - 13:03:11 CDT)
  • Re: Which one is more reliable to use in umbrella sampling- .traj data or vmd script data (Thu Aug 02 2018 - 22:33:16 CDT)
  • Re: Multi-dimensional PMF (Fri Jul 27 2018 - 22:49:55 CDT)
  • Re: Re: Multiple Colvars (Wed Jul 25 2018 - 18:03:21 CDT)
  • Re: Multiple Colvars (Tue Jul 24 2018 - 22:28:57 CDT)
  • Re: overlapping windows in ABF (Tue Jul 24 2018 - 22:24:52 CDT)
  • Re: (Mon Jul 23 2018 - 17:09:14 CDT)
  • Re: ABF Questions (Mon Jul 23 2018 - 08:27:06 CDT)
  • Re: ABF Questions (Sat Jul 21 2018 - 13:44:52 CDT)
  • Re: [NAMD] Define time-dependent grid force (Fri Jul 20 2018 - 21:29:25 CDT)
  • Re: Question about the fundamentals of MD and WHAM (Fri Jul 20 2018 - 07:42:40 CDT)
  • Re: Is QM/MM compatible with Colvars? (Thu Jul 19 2018 - 16:24:07 CDT)
  • Re: ABF simulations with singularities? (Mon Jul 09 2018 - 13:00:03 CDT)
  • Re: PMF calculation using CPU and GPU (Fri Jun 08 2018 - 08:55:15 CDT)
  • Re: NAMD+PLUMED (Mon Jun 04 2018 - 06:48:05 CDT)
  • Re: [NAMD] Apply an electric field only in a specific region (Mon Jun 04 2018 - 06:33:27 CDT)
  • Re: NAMD+PLUMED (Sat Jun 02 2018 - 16:25:26 CDT)
  • Re: Re: vmd-l: Large number of harmonic distance restraints (Tue May 29 2018 - 12:53:52 CDT)
  • Re: run different simulation of the same system by using different initial velocities (Thu May 24 2018 - 08:22:46 CDT)
  • Re: restrain lateral movement during ABF (Thu May 17 2018 - 17:06:02 CDT)
  • Re: How to create multiple molecules using psfgen (Wed May 16 2018 - 07:06:12 CDT)
  • Re: dummyAtom in distance colvar in ABF calculations (Mon May 14 2018 - 18:49:02 CDT)
  • Re: Creating an infinite graphene sheet (Sun May 13 2018 - 10:53:39 CDT)
  • Re: dummyAtom in distance colvar in ABF calculations (Sun May 13 2018 - 10:16:35 CDT)
  • Re: Creating an infinite graphene sheet (Sun May 13 2018 - 10:08:46 CDT)
  • Re: Creating an infinite graphene sheet (Sat May 12 2018 - 13:19:11 CDT)
  • Re: Get NAMD version from the tcl script interface (Wed May 09 2018 - 06:50:57 CDT)
  • Re: Fwd: FEP protein-ligand tutorial 2017 unclear section (Fri May 04 2018 - 17:04:28 CDT)
  • Re: Continuing metadynamics run (Fri May 04 2018 - 10:59:30 CDT)
  • Re: Colvars alternative recommendations (Mon Apr 30 2018 - 10:34:58 CDT)
  • Re: Colvars alternative recommendations (Mon Apr 30 2018 - 09:31:57 CDT)
  • Re: (Thu Apr 26 2018 - 09:12:42 CDT)
  • Re: (Thu Apr 26 2018 - 08:35:29 CDT)
  • Re: colvar with moving frame of reference (Mon Apr 16 2018 - 15:03:08 CDT)
  • Re: How does NAMD calculate AccumulatedWork when using RMSD colvar? (Thu Apr 12 2018 - 16:14:53 CDT)
  • Re: How does NAMD calculate AccumulatedWork when using RMSD colvar? (Thu Apr 12 2018 - 14:54:13 CDT)
  • Re: How does NAMD calculate AccumulatedWork when using RMSD colvar? (Thu Apr 12 2018 - 14:49:04 CDT)
  • Re: scriptedColvarForces doesn't work in recent NAMD builds (Thu Apr 12 2018 - 11:55:59 CDT)
  • Re: scriptedColvarForces doesn't work in recent NAMD builds (Wed Apr 11 2018 - 15:09:13 CDT)
  • Re: Query for coarse grain system (Mon Apr 09 2018 - 09:02:23 CDT)
  • Re: colvars: make an extended CV periodic (Fri Apr 06 2018 - 13:05:07 CDT)
  • Re: Query for coarse grain system (Thu Apr 05 2018 - 10:27:16 CDT)
  • Re: Query for coarse grain system (Thu Apr 05 2018 - 10:17:47 CDT)
  • Re: Steered MD simulation with pull and rotation (Mon Apr 02 2018 - 10:40:56 CDT)
  • Re: Using restraint on the dye using radius of gyration value in namd (Mon Apr 02 2018 - 10:40:18 CDT)
  • Re: Steered MD simulation with pull and rotation (Thu Mar 29 2018 - 06:37:55 CDT)
  • Re: Using PBC tools for a cubic and a rectangular box (Tue Mar 27 2018 - 09:18:17 CDT)
  • Re: Using PBC tools for a cubic and a rectangular box (Tue Mar 27 2018 - 08:35:54 CDT)
  • Re: colvars: Questions about the metadynamics hillWIdth option. (Wed Mar 21 2018 - 08:55:11 CDT)
  • Re: Selecting waters from dynamics trajectory (Tue Mar 20 2018 - 17:05:43 CDT)
  • Re: ffTK Without Using Gaussian (Tue Mar 20 2018 - 15:43:43 CDT)
  • Re: (Mon Mar 19 2018 - 08:08:23 CDT)
  • Re: statistical error in ABF calculations (Mon Mar 19 2018 - 06:35:42 CDT)
  • Re: statistical error in ABF calculations (Thu Mar 15 2018 - 20:04:38 CDT)
  • Re: colvars: How to implement a collective variable of vector type? (Wed Mar 14 2018 - 08:26:48 CDT)
  • Re: colvars: How to implement a collective variable of vector type? (Tue Mar 13 2018 - 09:07:18 CDT)
  • Re: colvars: How to implement a collective variable of vector type? (Mon Mar 12 2018 - 07:13:52 CDT)
  • Re: colvars: How to implement a collective variable of vector type? (Sun Mar 11 2018 - 07:05:09 CDT)
  • Re: Functionality of wrapWater and wrapAll commands for periodic simulations (Wed Mar 07 2018 - 07:35:30 CST)
  • Re: Re: How to set up a window distance of 2 angstroms in Umbrella sampling (Mon Mar 05 2018 - 07:38:59 CST)
  • Re: Build for CUDA support (Sat Mar 03 2018 - 10:10:35 CST)
  • Re: namd2 GPU error (Wed Feb 14 2018 - 08:32:21 CST)
  • Re: Re: simulation becomes unstable in residue base coarse grained system (Mon Feb 12 2018 - 09:20:04 CST)
  • Re: Re: simulation becomes unstable in residue base coarse grained system (Mon Feb 12 2018 - 08:38:15 CST)
  • Re: Dielectric Constant in the gas phase (Fri Feb 09 2018 - 12:19:09 CST)
  • Re: NAMD run on Intel hyperthreaded cores (Tue Feb 06 2018 - 13:54:50 CST)
  • Re: Holding molecules on one side of membrane (Sun Feb 04 2018 - 09:07:30 CST)
  • Re: trouble with colvars module (Thu Feb 01 2018 - 12:54:34 CST)
  • Re: colvars selecting frames (Thu Feb 01 2018 - 10:03:14 CST)
  • Re: Calculation of Diffusion coefficient (Mon Jan 29 2018 - 10:43:27 CST)
  • Re: Stress calculation (Mon Jan 29 2018 - 10:17:58 CST)
  • Re: Calculation of Diffusion coefficient (Mon Jan 29 2018 - 10:02:19 CST)
  • Re: Replica exchange simulation with GPU Accelaration (Fri Jan 26 2018 - 13:18:17 CST)
  • Re: Replica exchange simulation with GPU Accelaration (Fri Jan 26 2018 - 12:32:55 CST)
  • Re: Replica exchange simulation with GPU Accelaration (Fri Jan 26 2018 - 09:12:28 CST)
  • Re: Replica exchange simulation with GPU Accelaration (Thu Jan 25 2018 - 08:22:24 CST)
  • Re: nonequilibrium SMD with fixed atoms (Wed Jan 24 2018 - 10:11:18 CST)
  • Re: Missing Parameters For H3O+ (Wed Jan 24 2018 - 08:41:47 CST)
  • Re: Ways to find water molecules passing through the water channel in lipid bilayer (Thu Jan 18 2018 - 18:54:48 CST)
  • Re: Ways to find water molecules passing through the water channel in lipid bilayer (Thu Jan 18 2018 - 18:38:33 CST)
  • Re: acceptor (Thu Jan 18 2018 - 06:50:07 CST)
  • Re: Stress calculation (Wed Jan 17 2018 - 10:42:31 CST)
  • Re: acceptor (Wed Jan 17 2018 - 10:20:34 CST)
  • Re: SMD: Combined Constant Velocity and Constant Force method (Thu Jan 11 2018 - 15:56:28 CST)
  • Re: Having problem with restarting colvar distance, (Wed Jan 03 2018 - 11:02:00 CST)
  • 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)
• Giorgio Amendola
  • Thermodynamic integration output analysis (Wed Mar 07 2018 - 05:57:08 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)
• 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)
• Gumbart, James C
  • Re: ffTK torsion scan convergence using Gaussian. (Tue Nov 13 2018 - 20:04:59 CST)
  • Re: ffTK torsion scan convergence using Gaussian. (Tue Nov 13 2018 - 19:56:23 CST)
  • Re: Binding free energy tutorial (Wed Nov 07 2018 - 12:16:06 CST)
  • Re: Error with D-amino acids mid-sequence using NAMD 2.12/2.13b2 and CHARMm36 (Mon Nov 05 2018 - 14:17:46 CST)
  • Re: parameter request for PRES bonding (Mon Oct 29 2018 - 13:07:40 CDT)
  • Re: Colvars and distance restraint for umbrella sampling (Wed Oct 17 2018 - 10:49:11 CDT)
  • Re: Colvars and distance restraint for umbrella sampling (Wed Oct 17 2018 - 10:27:01 CDT)
• Götz, Alexander
  • Solvent box fluctuations (Mon Mar 27 2017 - 11:56:09 CDT)
• Götz, Alexander
  • AW: Solvent box fluctuations (Wed Mar 29 2017 - 03:37:59 CDT)
• 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)
• 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: Using 4-site water model in NAMD (Sun Sep 16 2018 - 22:20:33 CDT)
  • Using 4-site water model in NAMD (Sun Sep 16 2018 - 20:05:23 CDT)
  • Re: ABF Question (Fri Jun 29 2018 - 01:29:23 CDT)
  • Re: nonuniform sampling in ABF (Tue Jun 12 2018 - 11:25:39 CDT)
  • Re: Python based tool for analysis of DCD trajectories (Fri Mar 09 2018 - 00:52:15 CST)
  • Re: (Sun Jan 07 2018 - 21:02:01 CST)
  • 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)
• Harish Srinivasan
  • CMIAbort Error (Fri Apr 06 2018 - 05:38:39 CDT)
  • Python based tool for analysis of DCD trajectories (Thu Mar 08 2018 - 23:46:32 CST)
  • Re: Functionality of wrapWater and wrapAll commands for periodic simulations (Wed Mar 07 2018 - 23:11:19 CST)
  • Functionality of wrapWater and wrapAll commands for periodic simulations (Wed Mar 07 2018 - 05:34:08 CST)
  • 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)
• Hazard, E. Starr
  • bpti example compiled source charmrun++ does not launch (Thu Nov 01 2018 - 09:31:05 CDT)
  • Couldn't open DCD file (Wed Oct 31 2018 - 14:19:30 CDT)
• Hazel, Anthony J
  • Re: "Child killed: segmentation violation" error when running QM/MM minimization in QwikMD (Tue Jun 26 2018 - 17:48:31 CDT)
  • Re: "Child killed: segmentation violation" error when running QM/MM minimization in QwikMD (Tue Jun 26 2018 - 17:48:08 CDT)
  • "Child killed: segmentation violation" error when running QM/MM minimization in QwikMD (Tue Jun 26 2018 - 17:17:28 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)
• HEMANTH H 18310019
  • Error in NAMD Simulations -Drude (Mon Dec 24 2018 - 00:24:23 CST)
  • Re: C36 force field (Tue Dec 11 2018 - 08:41:47 CST)
  • Re: CHARMM36 parameters for nucelobases (Sat Nov 10 2018 - 07:14:49 CST)
  • Re: error in (runfepmin) (Sun Oct 21 2018 - 23:13:26 CDT)
  • Temperature Fluctuations in Drude Simulations - NAMD (Thu Oct 04 2018 - 23:39:14 CDT)
• 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)
• horacio poblete
  • Re: Setting up GPU workstation advice (Mon Jan 08 2018 - 07:17:52 CST)
• 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
  • Re: Martini CG parameter errors for lipids (Sun May 06 2018 - 08:52:44 CDT)
  • 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)
• 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)
• Ivan
  • Converting GromacsForce File to NAMD using GromacsTopFile.C (Tue Jul 17 2018 - 06:25:58 CDT)
  • Included Topology (.itp) in gromacs to parameter file for NAMD (Tue Jul 03 2018 - 03:40:29 CDT)
• Jacob Usadi
  • Wrapping multimeric protein issues (Wed Dec 12 2018 - 17:51:55 CST)
  • REMD restart tcl script meaning? (Tue Jul 24 2018 - 12:51:06 CDT)
  • Cleaving and capping protein with autopsf leads to parameter errors upon running NAMD (Wed May 02 2018 - 00:14:40 CDT)
  • Enhanced sampling methods for oligomers (Fri Oct 20 2017 - 15:33:34 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)
• Jan Brezovsky
  • Ph.D. candidate position in biomolecular modeling or bioinformatics (Wed Jul 04 2018 - 05:33:36 CDT)
  • Ph.D. and Post-doc positions in molecular simulations and structural bioinformatics (Mon Mar 05 2018 - 11:10:28 CST)
  • Ph.D. and Post-doc positions in molecular simulations and structural bioinformatics (Sun Feb 11 2018 - 15:59:31 CST)
  • Positions for Ph.D. candidates in biomolecular modeling (Thu Feb 02 2017 - 05:30:48 CST)
• jashnvareh 1395
  • Which parameters to use in the MD simulation of defected carbon nanotube/graphene? (Sun May 27 2018 - 03:10:25 CDT)
  • Re: Creating an infinite graphene sheet (Sat May 19 2018 - 20:23:17 CDT)
  • Re: Creating an infinite graphene sheet (Wed May 16 2018 - 00:54:03 CDT)
  • Re: Creating an infinite graphene sheet (Sun May 13 2018 - 11:23:54 CDT)
  • Re: Creating an infinite graphene sheet (Sun May 13 2018 - 10:34:11 CDT)
  • Re: Creating an infinite graphene sheet (Sun May 13 2018 - 02:27:42 CDT)
  • Re: Creating an infinite graphene sheet (Sun May 13 2018 - 02:13:13 CDT)
  • Re: Creating an infinite graphene sheet (Sun May 13 2018 - 02:11:07 CDT)
  • Creating an infinite graphene sheet (Sat May 12 2018 - 10:34:09 CDT)
• JC Gumbart
  • Re: Multi-dimensional PMF (Sat Jul 28 2018 - 09:48:08 CDT)
  • Re: CHARMM FF parameters for FE-S bond in CYP450 (Tue Jul 17 2018 - 16:54:12 CDT)
  • Re: Consulting about buying new hardware (GPU) (Tue Jul 10 2018 - 09:45:27 CDT)
  • Re: Fwd: FEP protein-ligand tutorial 2017 unclear section (Sat May 05 2018 - 07:20:13 CDT)
  • Re: Fwd: FEP protein-ligand tutorial 2017 unclear section (Fri May 04 2018 - 10:43:47 CDT)
  • Re: RE: Regarding Topology and Parameterization (Wed Apr 11 2018 - 13:12:32 CDT)
  • Re: ffTK Without Using Gaussian (Tue Mar 20 2018 - 14:37:35 CDT)
  • Re: (Mon Mar 19 2018 - 19:13:33 CDT)
  • Re: Hydrogen Mass Repartitioning in NAMD (Thu Mar 08 2018 - 09:36:43 CST)
  • Hydrogen Mass Repartitioning in NAMD (Wed Mar 07 2018 - 17:31:32 CST)
  • Re: Coarse-grained umbrella sampling for POPS-protein system (Sat Feb 24 2018 - 08:39:07 CST)
  • Re: Hamiltonian Replica Exchange MD in NAMD (Thu Jan 18 2018 - 18:02:37 CST)
  • 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)
• jeevan gc
  • Re: CHARMM FF parameters for FE-S bond in CYP450 (Wed Jul 18 2018 - 11:20:37 CDT)
  • Re: CHARMM FF parameters for FE-S bond in CYP450 (Tue Jul 17 2018 - 18:43:50 CDT)
  • CHARMM FF parameters for FE-S bond in CYP450 (Tue Jul 17 2018 - 16:39:50 CDT)
  • 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)
• Jeff Comer
  • Re: Nano-bio interaction in NAMD (Wed Oct 24 2018 - 16:23:33 CDT)
  • Re: adaptive biasing force (Wed Oct 24 2018 - 16:00:02 CDT)
  • Re: Standard density -reg (Wed Oct 24 2018 - 15:50:32 CDT)
  • CGenFF 4.1 lone pairs (Wed Aug 22 2018 - 13:56:30 CDT)
  • Re: Multi-dimensional PMF (Fri Jul 27 2018 - 18:39:37 CDT)
  • Re: scriptedColvarForces doesn't work in recent NAMD builds (Thu Apr 12 2018 - 08:14:26 CDT)
  • scriptedColvarForces doesn't work in recent NAMD builds (Wed Apr 11 2018 - 11:04:53 CDT)
  • Re: Fatty Acid Topology (Mon Apr 02 2018 - 09:14:32 CDT)
  • Re: Replica exchange simulation with GPU Accelaration (Fri Jan 26 2018 - 15:46:57 CST)
  • Re: Setting up GPU workstation advice (Mon Jan 08 2018 - 10:04:52 CST)
  • 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)
• Jeffrey Potoff
  • RE: Free energy did not converge by using ABF (Fri Dec 08 2017 - 13:22:44 CST)
• 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)
• Jeyaram R A
  • Pair interaction energies: TCL error -reg (Thu Feb 08 2018 - 01:32:44 CST)
• Jiali Wang
  • question when apply external electric field (Sat Aug 04 2018 - 16:43:04 CDT)
• 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
  • Re: Running QM-MM MOPAC on a cluster (Mon Dec 31 2018 - 09:42:27 CST)
  • Re: Running QM-MM MOPAC on a cluster (Tue Dec 18 2018 - 16:03:22 CST)
  • Re: Running QM-MM MOPAC on a cluster (Mon Dec 17 2018 - 09:12:25 CST)
  • Re: Running QM-MM MOPAC on a cluster (Fri Dec 14 2018 - 09:29:51 CST)
  • Re: [ REST2 ] Possible bug on NAMD example (Mon Nov 26 2018 - 11:19:57 CST)
  • Re: Building with GCC on Ubuntu 18 (Mon Nov 12 2018 - 09:08:30 CST)
  • RE: Building with GCC on Ubuntu 18 (Fri Nov 09 2018 - 16:17:41 CST)
  • Re: Way to wget or curl download the precompiled NAMD? (Fri Nov 09 2018 - 09:31:17 CST)
  • Re: bpti example compiled source charmrun++ does not launch (Thu Nov 01 2018 - 11:33:45 CDT)
  • Re: FFtK Tutorial (Urey-Bradley angles error). (Thu Nov 01 2018 - 01:31:51 CDT)
  • Re: Couldn't open DCD file (Wed Oct 31 2018 - 15:33:06 CDT)
  • Re: Membrane Simulation (Wed Oct 31 2018 - 12:15:59 CDT)
  • Re: multi-node mpiexec issue (Wed Oct 24 2018 - 16:08:40 CDT)
• jing liang
  • Re: Binding free energy tutorial (Wed Nov 07 2018 - 08:17:44 CST)
  • Re: Binding free energy tutorial (Wed Oct 31 2018 - 04:31:13 CDT)
  • Binding free energy tutorial (Fri Oct 26 2018 - 14:37:51 CDT)
  • Re: NAMD+PLUMED (Sun Jun 03 2018 - 05:15:09 CDT)
  • NAMD+PLUMED (Sat Jun 02 2018 - 13:34:26 CDT)
  • 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)
• Joey Gehring
  • NAMD/VMD installation for Windows 10 (Mon Nov 19 2018 - 10:27:22 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)
• Josep Ivan Balaguer Molins
  • Re: Problems with temperature control. (Wed Aug 01 2018 - 12:34:30 CDT)
  • Re: Problems with temperature control. (Tue Jul 31 2018 - 10:54:40 CDT)
  • Re: Problems with temperature control. (Tue Jul 31 2018 - 06:37:49 CDT)
  • Re: Problems with temperature control. (Tue Jul 31 2018 - 01:24:58 CDT)
  • Re: Problems with temperature control. (Mon Jul 30 2018 - 09:41:32 CDT)
  • Problems with temperature control. (Mon Jul 30 2018 - 05:21:09 CDT)
• Joshua .
  • Re: Periodic cell too small with GPUs, not with pur CPUs (Wed Jul 05 2017 - 09:39:40 CDT)
• jozs2019_at_uni.sydney.edu.au
  • Re: Difference between REMD replica temperature and actual temperature (Tue May 29 2018 - 18:19:31 CDT)
  • Difference between REMD replica temperature and actual temperature (Mon May 28 2018 - 21:03:05 CDT)
• João Ribeiro
  • Re: C36 force field (Tue Dec 11 2018 - 10:55:00 CST)
  • Re: C36 force field (Tue Dec 11 2018 - 09:23:31 CST)
  • Re: FFtK Tutorial (Urey-Bradley angles error). (Wed Oct 31 2018 - 12:05:35 CDT)
  • Re: Setting up QM/MM calculations with QwikMD without the GUI (Fri Oct 05 2018 - 13:44:31 CDT)
  • First "Hands-On" Workshop on Structural DNA Nanotechnology (Mon Sep 24 2018 - 09:13:30 CDT)
  • Re: vmd-l: Enhanced Sampling and Free-Energy Calculations Lectures (Wed Sep 12 2018 - 08:56:28 CDT)
  • Enhanced Sampling and Free-Energy Calculations Lectures (Mon Sep 10 2018 - 12:02:42 CDT)
  • Re: parameter file for ACE and CT3 cap (Tue Sep 04 2018 - 08:02:57 CDT)
  • Research Programmer Positions Available (Fri Aug 10 2018 - 13:29:41 CDT)
  • "Hands-on" Workshop on Enhanced Sampling and Free-Energy Calculation at Urbana, IL, September 10-14, 2018 (Mon Jul 30 2018 - 16:15:45 CDT)
  • Re: Reg autioionize plugin (Mon Jul 30 2018 - 09:09:24 CDT)
  • Re: mail about autoionize plugin (Fri Jul 27 2018 - 08:07:33 CDT)
  • Re: Qwikmd ABF Question (Mon Jul 09 2018 - 08:18:48 CDT)
  • Re: Qwikmd ABF Question (Thu Jul 05 2018 - 13:16:01 CDT)
  • Re: Qwikmd ABF Question (Thu Jul 05 2018 - 08:03:31 CDT)
  • Re: Qwikmd ABF Question (Wed Jul 04 2018 - 19:25:30 CDT)
  • Re: Qwikmd ABF Question (Wed Jul 04 2018 - 08:08:10 CDT)
  • Re: QwikMD Question (Thu Jun 28 2018 - 12:08:13 CDT)
  • Re: "Child killed: segmentation violation" error when running QM/MM minimization in QwikMD (Wed Jun 27 2018 - 09:47:41 CDT)
  • Re: "Child killed: segmentation violation" error when running QM/MM minimization in QwikMD (Tue Jun 26 2018 - 18:16:11 CDT)
  • Re: "Child killed: segmentation violation" error when running QM/MM minimization in QwikMD (Tue Jun 26 2018 - 17:53:38 CDT)
  • Re: "Child killed: segmentation violation" error when running QM/MM minimization in QwikMD (Tue Jun 26 2018 - 17:41:48 CDT)
  • Re: Strange Bond Behavior Question (Fri Jun 22 2018 - 16:08:07 CDT)
  • Re: NAMD Developer Workshop at Urbana IL, June 11-12, 2018 (Wed May 02 2018 - 09:17:31 CDT)
  • Re: Energy Minimization failure for mutants (Mon Apr 30 2018 - 09:24:35 CDT)
  • NAMD Developer Workshop at Urbana IL, June 11-12, 2018 (Tue Apr 24 2018 - 08:57:57 CDT)
  • TCBG Workshop lecture videos (Sat Apr 07 2018 - 10:45:12 CDT)
  • "'Hands-on" Workshop on Computational Biophysics at Pittsburgh, PA, May 21-25, 2018 (Fri Mar 16 2018 - 15:47:15 CDT)
  • Re: "Hands-On" Workshop on QM/MM Simulations at Urbana, IL, April 5-7, 2018 (Tue Feb 27 2018 - 08:08:16 CST)
  • "Hands-on" Workshop on Enhanced Sampling and Free-Energy Calculation at Urbana, IL, September 10-14, 2018 (Wed Feb 07 2018 - 10:46:51 CST)
  • NAMD Developer Workshop at Urbana IL, June 11-12, 2018 (Wed Feb 07 2018 - 10:46:41 CST)
  • "Hands-On" Workshop on QM/MM Simulations at Urbana, IL, April 5-7, 2018 (Wed Feb 07 2018 - 10:44:57 CST)
  • 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)
• Julian Müller
  • SWM4-NDP PSF File (Thu Sep 27 2018 - 02:48:10 CDT)
• Julio Maia
  • Re: Building with GCC on Ubuntu 18 (Thu Nov 08 2018 - 11:26:36 CST)
  • Re: Re: ORCA GPUs (Fri Nov 02 2018 - 13:13:21 CDT)
• Jumin Lee
  • Jobs and Evens in CHARMM-GUI (Mon Feb 05 2018 - 16:00:01 CST)
• Junwoong Yoon
  • Re: Umbrella Sampling input parameters (Mon Jul 23 2018 - 23:18:58 CDT)
  • Question about the fundamentals of MD and WHAM (Thu Jul 19 2018 - 15:52:43 CDT)
  • Re: Umbrella Sampling input parameters (Thu Jul 12 2018 - 17:45:19 CDT)
  • Umbrella Sampling input parameters (Tue Jul 10 2018 - 01:55:16 CDT)
  • Re: ABF simulations with singularities? (Mon Jul 09 2018 - 15:11:48 CDT)
  • Re: ABF simulations with singularities? (Mon Jul 09 2018 - 12:58:31 CDT)
  • Re: ABF simulations with singularities? (Mon Jul 09 2018 - 12:52:09 CDT)
  • ABF simulations with singularities? (Thu Jul 05 2018 - 20:55:29 CDT)
• 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: Constant Force Pull (Thu Dec 13 2018 - 09:39:28 CST)
  • Re: Constant Force Pull (Thu Dec 13 2018 - 07:06:12 CST)
  • Re: Wrapping multimeric protein issues (Thu Dec 13 2018 - 06:56:02 CST)
  • Re: How to add a C code to NAMD properly? (Mon Nov 26 2018 - 06:27:24 CST)
  • Re: Building with GCC on Ubuntu 18 (Tue Nov 13 2018 - 07:29:35 CST)
  • Re: Building with GCC on Ubuntu 18 (Mon Nov 12 2018 - 09:14:01 CST)
  • Re: Building with GCC on Ubuntu 18 (Mon Nov 12 2018 - 07:45:37 CST)
  • Re: Building with GCC on Ubuntu 18 (Fri Nov 09 2018 - 07:00:43 CST)
  • Building with GCC on Ubuntu 18 (Thu Nov 08 2018 - 11:18:05 CST)
  • Re: ABF Window Boundaries (Sun Oct 21 2018 - 17:28:15 CDT)
  • Re: ABF Window Boundaries (Fri Oct 19 2018 - 02:59:37 CDT)
  • Re: ABF Question (Thu Sep 27 2018 - 04:35:25 CDT)
  • Re: Sudden /\A drop in last FEP window (Fri Aug 17 2018 - 04:39:12 CDT)
  • Re: 1-D ABF and Compressibility (Tue Jul 31 2018 - 00:43:50 CDT)
  • Re: 1-D ABF and Compressibility (Mon Jul 30 2018 - 16:14:56 CDT)
  • Re: Sudden /\A drop in last FEP window (Sat Jul 28 2018 - 08:41:19 CDT)
  • Re: Multi-dimensional PMF (Fri Jul 27 2018 - 11:53:05 CDT)
  • Re: Multi-dimensional PMF (Fri Jul 27 2018 - 10:16:44 CDT)
  • Re: Multi-dimensional PMF (Fri Jul 27 2018 - 02:45:20 CDT)
  • Re: Sudden /\A drop in last FEP window (Thu Jul 26 2018 - 11:48:07 CDT)
  • Re: Dual Topology in FEP Calculations - How to Calculate Electrostatics and van der Waals Free Energies Separately? (Tue Jul 24 2018 - 02:55:40 CDT)
  • Re: overlapping windows in ABF (Mon Jul 23 2018 - 16:16:55 CDT)
  • Re: Dual Topology in FEP Calculations - How to Calculate Electrostatics and van der Waals Free Energies Separately? (Mon Jul 23 2018 - 16:12:28 CDT)
  • Re: (Mon Jul 23 2018 - 16:10:50 CDT)
  • Re: (Sat Jul 21 2018 - 06:06:53 CDT)
  • Re: ABF Questions (Sat Jul 21 2018 - 06:03:39 CDT)
  • Re: Dual Topology in FEP Calculations - How to Calculate Electrostatics and van der Waals Free Energies Separately? (Sat Jul 21 2018 - 05:58:02 CDT)
  • Re: Umbrella Sampling input parameters (Thu Jul 19 2018 - 18:01:06 CDT)
  • Re: ABF Asymmetry (Tue Jul 10 2018 - 07:59:54 CDT)
  • Re: ABF, rigid bonds and constraints (Fri Jul 06 2018 - 06:03:00 CDT)
  • Re: ABF simulations with singularities? (Fri Jul 06 2018 - 02:18:34 CDT)
  • Re: Hydronium parameters (Tue Jun 26 2018 - 11:09:07 CDT)
  • Re: merging abf trajectories with different number of colvars (Thu Jun 21 2018 - 05:21:17 CDT)
  • Re: PCA and vector (Sat Jun 16 2018 - 09:13:37 CDT)
  • Re: nonuniform sampling in ABF (Tue Jun 12 2018 - 17:09:56 CDT)
  • Re: merging abf trajectories with different number of colvars (Mon Jun 04 2018 - 07:22:34 CDT)
  • Re: restrain lateral movement during ABF (Thu May 17 2018 - 08:03:50 CDT)
  • Re: FEP & node/core number (Mon May 07 2018 - 08:39:21 CDT)
  • Re: (Thu Apr 26 2018 - 08:56:08 CDT)
  • Re: (Thu Apr 26 2018 - 07:20:11 CDT)
  • Re: SMD with colvar not working (Tue Apr 24 2018 - 12:50:47 CDT)
  • Re: SMD with colvar not working (Tue Apr 24 2018 - 11:04:24 CDT)
  • Re: SMD with colvar not working (Tue Apr 24 2018 - 10:56:46 CDT)
  • Re: SMD with colvar not working (Tue Apr 24 2018 - 04:27:49 CDT)
  • Re: colvar with moving frame of reference (Tue Apr 17 2018 - 16:18:29 CDT)
  • Re: scriptedColvarForces doesn't work in recent NAMD builds (Wed Apr 11 2018 - 12:12:26 CDT)
  • Re: scriptedColvarForces doesn't work in recent NAMD builds (Wed Apr 11 2018 - 11:26:58 CDT)
  • Re: Proper use of psfgen "mutate"? (Tue Apr 10 2018 - 09:23:20 CDT)
  • Re: calculation of helical axis in NAMD (Mon Apr 09 2018 - 10:21:26 CDT)
  • Re: colvars: make an extended CV periodic (Sun Apr 08 2018 - 09:46:23 CDT)
  • Re: colvars: make an extended CV periodic (Fri Apr 06 2018 - 12:47:56 CDT)
  • Re: Restrict drift of Graphene sheet in X-Y plane using Colvars (Mon Mar 26 2018 - 07:01:01 CDT)
  • Re: colvars: How to implement a collective variable of vector type? (Sun Mar 11 2018 - 16:54:15 CDT)
  • Re: Handling of nonbonded lists in PSF - please clarify (Sun Feb 25 2018 - 15:10:11 CST)
  • Re: Alchemify? (Mon Feb 19 2018 - 09:32:33 CST)
  • Re: Question on making 'reversible' solvated simulation (Sun Feb 11 2018 - 04:56:22 CST)
  • Re: NAMD run on Intel hyperthreaded cores (Tue Feb 06 2018 - 06:31:10 CST)
  • Re: colvars selecting frames (Thu Feb 01 2018 - 10:42:17 CST)
  • Re: colvars selecting frames (Thu Feb 01 2018 - 06:32:00 CST)
  • Re: colvars selecting frames (Wed Jan 31 2018 - 03:22:22 CST)
  • Re: Question on restraint behavior when part of system decouples (Mon Jan 29 2018 - 16:20:22 CST)
  • Re: Question on restraint behavior when part of system decouples (Mon Jan 29 2018 - 13:52:07 CST)
  • Re: Question on restraint behavior when part of system decouples (Mon Jan 29 2018 - 09:53:51 CST)
  • Re: Setting up GPU workstation advice (Mon Jan 08 2018 - 07:27:50 CST)
  • Re: Having problem with restarting colvar distance, (Wed Jan 03 2018 - 10:38:26 CST)
  • 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)
• 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)
• Kashish Punjani
  • Converting x,y,z coordinates to dcd file (Sun Jun 11 2017 - 12:44:18 CDT)
• Keshab Thapa
  • SMD: Combined Constant Velocity and Constant Force method (Thu Jan 11 2018 - 15:51:18 CST)
  • 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)
• Kevin Chun Chan
  • Continuing SMD from restart files (Mon Apr 24 2017 - 08:32:18 CDT)
• Kinkini Jayasundara
  • Diffusion Coefficient calculation (Fri Sep 28 2018 - 20:48:39 CDT)
  • Re: Hydronium parameters (Tue Jun 26 2018 - 11:10:31 CDT)
  • Hydronium parameters (Tue Jun 26 2018 - 10:49:03 CDT)
• Kooshul S. Jhaveri
  • namd2_ti.pl Error: Modification of non-creatable array value attempted (Sun Jun 03 2018 - 11:34:09 CDT)
• Kowsar Khajeh
  • velocity.pdb and velocity unit in NAMD (Tue Jul 24 2018 - 01:07:13 CDT)
  • Re: Equilibration in NPT simulation (Wed Jul 04 2018 - 10:46:47 CDT)
  • Re: electric field- forces in NAMD source code (Sat Jun 16 2018 - 06:17:31 CDT)
  • electric field- forces in NAMD source code (Sat Jun 16 2018 - 02:25:29 CDT)
  • Re: [NAMD] Apply an electric field only in a specific region (Mon Jun 04 2018 - 02:46:12 CDT)
  • Fwd: pressure in interfacial tension (Sun Jan 28 2018 - 21:18:39 CST)
  • 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)
• Kshatresh Dutta Dubey
  • Problem in NAMD QMMM (Sat Mar 25 2017 - 13:37:25 CDT)
• L-
  • run MD simulation in NAMD using stages file strategy or all in one file ? (Thu Dec 13 2018 - 10:12:13 CST)
  • Re: ERROR TOLERANCE (Wed Dec 05 2018 - 14:00:47 CST)
  • ERROR TOLERANCE (Wed Dec 05 2018 - 13:32:42 CST)
• 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
  • problem with minimizer (Wed Jun 20 2018 - 07:53:41 CDT)
  • Re: reinitatoms (Thu Jan 11 2018 - 10:36:31 CST)
  • reinitatoms (Thu Jan 11 2018 - 08:26:28 CST)
  • 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)
• Laura Tiessler
  • Re: (Thu Jun 14 2018 - 13:38:28 CDT)
  • (no subject) (Thu Jun 07 2018 - 06:24:00 CDT)
• Lennart Nilsson
  • RE: CHARMM36 parameters for nucelobases (Sat Nov 10 2018 - 10:57:04 CST)
  • RE: CHARMM36 parameters for nucelobases (Sat Nov 10 2018 - 10:24:29 CST)
  • RE: parameter request for PRES bonding (Tue Oct 30 2018 - 09:31:59 CDT)
  • RE: Re: vmd-l: PSFGEN 1.6.4 autogenerate PATCH keyword not available (Tue Apr 24 2018 - 12:45:26 CDT)
  • 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)
• Lesli Oiling Mark
  • PME Tolerance (Mon Feb 19 2018 - 10:03:48 CST)
• Lewis J Martin
  • Re: Consulting about buying new hardware (GPU) (Wed Jul 11 2018 - 18:13:10 CDT)
  • Re: NAMD-CUDA GPU workload (Thu Apr 05 2018 - 19:50:09 CDT)
• Lewis Martin
  • Setting up GPU workstation advice (Sun Jan 07 2018 - 20:28:49 CST)
• LIAO Mingling
  • How to solve the segmentation faults in compiling NAMD to build and test the Charm++/Converse library (MPI version)? (Fri May 04 2018 - 07:07:13 CDT)
• Life Sciences Inc
  • Using restraint on the dye using radius of gyration value in namd (Mon Apr 02 2018 - 09:26:47 CDT)
  • 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)
• 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)
• Lutimba Stuart
  • Re: Simulating a Binding Event (Tue Mar 06 2018 - 12:44:52 CST)
  • Re: How to set up a window distance of 2 angstroms in Umbrella sampling (Mon Mar 05 2018 - 03:40:10 CST)
  • Re: Coarse-grained umbrella sampling for POPS-protein system (Fri Feb 23 2018 - 18:02:53 CST)
  • Re: Error in the Continuation TMD simulation Run. (Wed Feb 21 2018 - 13:49:36 CST)
• M RCC
  • PBC error. Amber force field in NAMD (Tue Sep 25 2018 - 06:35:53 CDT)
  • Critical isofrom selectivity in molecular dynamics (Mon Sep 24 2018 - 06:23:14 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)
• Mahmood Naderan
  • Affinity (Tue Oct 16 2018 - 15:20:52 CDT)
  • Re: About CUDA version (Tue Sep 25 2018 - 14:43:33 CDT)
  • About CUDA version (Tue Sep 25 2018 - 13:22:21 CDT)
  • mscs.pdb (Tue Mar 13 2018 - 11:03:33 CDT)
  • Re: Running on GPU (Mon Mar 12 2018 - 14:47:35 CDT)
  • Running on GPU (Mon Mar 12 2018 - 14:22:31 CDT)
  • Re: Segmentation fault for the tutorial (Wed Mar 07 2018 - 14:24:31 CST)
  • Re: Segmentation fault for the tutorial (Wed Mar 07 2018 - 12:02:02 CST)
  • Re: Segmentation fault for the tutorial (Wed Mar 07 2018 - 11:38:44 CST)
  • Re: Segmentation fault for the tutorial (Wed Mar 07 2018 - 09:48:08 CST)
  • Re: Segmentation fault for the tutorial (Wed Mar 07 2018 - 01:33:55 CST)
  • Re: Segmentation fault for the tutorial (Tue Mar 06 2018 - 13:58:56 CST)
  • Segmentation fault for the tutorial (Tue Mar 06 2018 - 13:06:11 CST)
  • Re: Build for CUDA support (Sat Mar 03 2018 - 10:35:06 CST)
  • Build for CUDA support (Sat Mar 03 2018 - 08:22:47 CST)
• 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)
• Mani Kandan
  • Coarse Grained simulation of silicon nitride nanopore - Reg (Fri Dec 28 2018 - 13:35:58 CST)
  • Langevin Dynamics Coefficient Value -Reg (Tue Nov 06 2018 - 11:30:09 CST)
  • Re: Standard density -reg (Wed Oct 24 2018 - 23:30:55 CDT)
  • Standard density -reg (Wed Oct 24 2018 - 02:07:44 CDT)
  • Re: E-field to Voltage - Reg (Fri Oct 05 2018 - 21:49:03 CDT)
  • Re: E-field to Voltage - Reg (Fri Oct 05 2018 - 12:40:26 CDT)
  • E-field to Voltage - Reg (Fri Oct 05 2018 - 09:58:19 CDT)
  • Re: Constraint failure in Highly charged system - Reg (Sun Sep 23 2018 - 23:23:50 CDT)
  • Constraint failure in Highly charged system - Reg (Thu Sep 20 2018 - 23:33:16 CDT)
  • Re: Different cell vectors - Reg (Mon Sep 17 2018 - 04:56:25 CDT)
  • Different cell vectors - Reg (Mon Sep 17 2018 - 04:45:10 CDT)
  • Rattle algorithm Constraint failure - Reg (Fri Sep 07 2018 - 05:46:59 CDT)
  • Unexpected Energy values - Reg (Wed Sep 05 2018 - 07:07:29 CDT)
  • Re: Error NPT simulation - Need Urgent Help - Reg (Fri Aug 31 2018 - 08:38:44 CDT)
  • Error NPT simulation - Need Urgent Help - Reg (Wed Aug 29 2018 - 11:35:02 CDT)
  • Induced Electric filed and Electrostatics - Reg (Sun Aug 19 2018 - 02:54:45 CDT)
  • E-filed to individual channel in parallel system - Reg (Tue Jul 17 2018 - 12:09:57 CDT)
  • Re: Equilibration in NPT simulation (Wed Jul 04 2018 - 11:59:38 CDT)
  • Re: Equilibration in NPT simulation (Wed Jul 04 2018 - 11:30:50 CDT)
  • Equilibration in NPT simulation (Wed Jul 04 2018 - 10:25:19 CDT)
  • Re: NAMD SMP version warning - Reg (Wed Jul 04 2018 - 09:59:35 CDT)
  • NAMD SMP version warning - Reg (Wed Jul 04 2018 - 04:57:40 CDT)
  • Problem in NAMD memory optimized version - Reg (Mon Jul 02 2018 - 11:02:37 CDT)
  • Better way to fix the atom -Reg (Fri Jun 22 2018 - 10:51:57 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: Is there a problem of ORCA running for NAMD MPI? (Tue Nov 20 2018 - 11:21:58 CST)
  • Re: QM/MM Error (Tue Oct 30 2018 - 12:15:42 CDT)
  • Re: Cutoff radius for electrostatic embedding in QM/MM calculations (Mon Sep 10 2018 - 11:53:13 CDT)
  • Re: MOPAC Point Charges (Mon Aug 20 2018 - 16:40:46 CDT)
  • Re: QM/MM MD and the qmParamPDB file (Wed Aug 15 2018 - 22:43:27 CDT)
  • Re: Re: QM/MM with Orca: Memory allocation failed (Tue Jul 24 2018 - 16:28:01 CDT)
  • Re: QM/MM with Orca: Memory allocation failed (Thu Jul 19 2018 - 09:51:25 CDT)
  • Re: Issue using qwikMD with an uncommon cofactor (Thu May 31 2018 - 17:55:02 CDT)
  • 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 kadowaki
  • FAD topology and parameters (Mon Feb 19 2018 - 09:23:53 CST)
• 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)
• Marlon Sidore
  • Re: all-atom to coarse-grained system (Sat Feb 03 2018 - 14:04:34 CST)
  • 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)
• 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)
• Mauro Lapelosa
  • Re: Running NAMD on Intel OmniPath (Thu Jul 27 2017 - 13:06:24 CDT)
• 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)
• McGuire, Kelly
  • MOPAC Plugin Update (Mon Dec 17 2018 - 14:01:13 CST)
  • Re: Constant Force Pull (Thu Dec 13 2018 - 10:33:13 CST)
  • Constant Force Pull (Thu Dec 13 2018 - 03:44:18 CST)
  • Re: Parallel Jobs (Thu Dec 06 2018 - 14:54:30 CST)
  • Parallel Jobs (Thu Dec 06 2018 - 14:36:45 CST)
  • Water Transport (Thu Nov 29 2018 - 13:34:54 CST)
  • Re: Minimization Question (Tue Nov 13 2018 - 09:39:49 CST)
  • Re: Minimization Question (Mon Nov 12 2018 - 20:52:19 CST)
  • Re: Minimization Question (Mon Nov 12 2018 - 19:50:51 CST)
  • Re: Minimization Question (Mon Nov 12 2018 - 15:37:01 CST)
  • Re: Minimization Question (Mon Nov 12 2018 - 15:35:57 CST)
  • Minimization Question (Sun Nov 11 2018 - 19:46:19 CST)
  • Re: Concatenate Outputs (Sat Nov 10 2018 - 14:52:45 CST)
  • Concatenate Outputs (Fri Nov 09 2018 - 14:12:21 CST)
  • Re: QM/MM Question (Tue Nov 06 2018 - 15:52:41 CST)
  • Re: QM/MM Question (Tue Nov 06 2018 - 13:40:14 CST)
  • Re: QM/MM Question (Mon Nov 05 2018 - 21:23:11 CST)
  • Re: QM/MM Question (Mon Nov 05 2018 - 13:46:39 CST)
  • Re: QM/MM Question (Mon Nov 05 2018 - 12:14:02 CST)
  • Re: QM/MM Question (Mon Nov 05 2018 - 11:13:45 CST)
  • QM/MM Question (Sun Nov 04 2018 - 12:59:51 CST)
  • qmSecProc Proper Use (Fri Nov 02 2018 - 15:02:00 CDT)
  • Re: ORCA GPUs (Fri Nov 02 2018 - 13:04:20 CDT)
  • Re: ORCA GPUs (Fri Nov 02 2018 - 12:58:08 CDT)
  • ORCA GPUs (Thu Nov 01 2018 - 20:48:47 CDT)
  • Re: ORCA QMMM (Thu Nov 01 2018 - 20:46:10 CDT)
  • Re: ORCA QMMM (Thu Nov 01 2018 - 14:45:51 CDT)
  • Re: ORCA QMMM (Thu Nov 01 2018 - 14:42:34 CDT)
  • Re: QM/MM Error (Tue Oct 30 2018 - 12:43:50 CDT)
  • Re: ORCA QMMM (Tue Oct 30 2018 - 09:46:11 CDT)
  • ORCA QMMM (Mon Oct 29 2018 - 17:41:25 CDT)
  • QM/MM Error (Mon Oct 29 2018 - 00:01:25 CDT)
  • QM/MM Question (Sun Oct 28 2018 - 21:53:59 CDT)
  • Re: ABF Window Boundaries (Fri Oct 19 2018 - 10:34:38 CDT)
  • Re: ABF Window Boundaries (Fri Oct 19 2018 - 10:32:41 CDT)
  • ABF Window Boundaries (Fri Oct 19 2018 - 02:45:07 CDT)
  • ABF Question (Wed Sep 26 2018 - 21:32:54 CDT)
  • Re: 1-D ABF and Compressibility (Mon Jul 30 2018 - 17:14:49 CDT)
  • 1-D ABF and Compressibility (Mon Jul 30 2018 - 14:44:53 CDT)
  • Re: Multi-dimensional PMF (Fri Jul 27 2018 - 23:25:11 CDT)
  • Re: Multi-dimensional PMF (Fri Jul 27 2018 - 13:07:51 CDT)
  • Re: Multi-dimensional PMF (Fri Jul 27 2018 - 12:04:34 CDT)
  • Re: Multi-dimensional PMF (Fri Jul 27 2018 - 10:38:58 CDT)
  • Re: Multi-dimensional PMF (Fri Jul 27 2018 - 09:58:43 CDT)
  • Multi-dimensional PMF (Thu Jul 26 2018 - 16:40:28 CDT)
  • Re: Multiple Colvars (Wed Jul 25 2018 - 10:26:46 CDT)
  • Re: Multiple Colvars (Wed Jul 25 2018 - 09:32:31 CDT)
  • Multiple Colvars (Tue Jul 24 2018 - 15:38:22 CDT)
  • Re: ABF Questions (Sat Jul 21 2018 - 14:06:51 CDT)
  • Re: ABF Questions (Sat Jul 21 2018 - 09:52:31 CDT)
  • Re: ABF Questions (Fri Jul 20 2018 - 21:20:25 CDT)
  • ABF Questions (Fri Jul 20 2018 - 21:13:43 CDT)
  • Re: ABF Asymmetry (Tue Jul 10 2018 - 12:20:05 CDT)
  • Re: ABF Asymmetry (Tue Jul 10 2018 - 00:11:43 CDT)
  • ABF Asymmetry (Mon Jul 09 2018 - 16:48:51 CDT)
  • Re: Qwikmd ABF Question (Thu Jul 05 2018 - 10:48:41 CDT)
  • Re: Qwikmd ABF Question (Wed Jul 04 2018 - 19:35:02 CDT)
  • Re: Qwikmd ABF Question (Wed Jul 04 2018 - 18:44:26 CDT)
  • Re: Qwikmd ABF Question (Wed Jul 04 2018 - 11:21:57 CDT)
  • Re: Qwikmd ABF Question (Wed Jul 04 2018 - 11:21:21 CDT)
  • Qwikmd ABF Question (Wed Jul 04 2018 - 02:42:39 CDT)
  • Re: Random Velocities Question (Tue Jul 03 2018 - 22:46:05 CDT)
  • Random Velocities Question (Tue Jul 03 2018 - 22:09:44 CDT)
  • ABF Question (Thu Jun 28 2018 - 23:59:03 CDT)
  • QwikMD Question (Thu Jun 28 2018 - 10:34:17 CDT)
  • Re: Colvars Restraint Question (Mon Jun 25 2018 - 12:15:44 CDT)
  • Re: Colvars Restraint Question (Sun Jun 24 2018 - 23:20:31 CDT)
  • Re: vmd-l: Re: Strange Bond Behavior Question (Fri Jun 22 2018 - 21:27:04 CDT)
  • Re: Strange Bond Behavior Question (Fri Jun 22 2018 - 16:52:49 CDT)
  • Re: Strange Bond Behavior Question (Fri Jun 22 2018 - 16:17:28 CDT)
  • Strange Bond Behavior Question (Fri Jun 22 2018 - 15:42:20 CDT)
  • Re: Colvars Restraint Question (Thu Jun 21 2018 - 16:45:39 CDT)
  • Re: Colvars Restraint Question (Thu Jun 21 2018 - 15:46:49 CDT)
  • Re: Colvars Restraint Question (Thu Jun 21 2018 - 15:04:41 CDT)
  • Re: Colvars Restraint Question (Thu Jun 21 2018 - 14:53:17 CDT)
  • Re: Colvars Restraint Question (Thu Jun 21 2018 - 13:43:18 CDT)
  • Colvars Restraint Question (Thu Jun 21 2018 - 12:01:18 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)
• Miao, Yinglong
  • Re: restarting Gaussian accelerated MD fails (Fri Aug 03 2018 - 16:58:34 CDT)
  • Re: GaMD in NAMD (Thu Jun 14 2018 - 08:46:45 CDT)
• Michael LeVine
  • pairInteraction and PME? (Mon Sep 11 2017 - 19:20:59 CDT)
• michael zhenin
  • Re: Consulting about buying new hardware (GPU) (Sun Jul 15 2018 - 06:47:22 CDT)
  • Consulting about buying new hardware (GPU) (Tue Jul 10 2018 - 03:44:31 CDT)
• Michail Lazaratos
  • Weird PBC wrapping (Thu Aug 30 2018 - 05:41:11 CDT)
  • Isomerization between runs (Wed Aug 01 2018 - 04:56:01 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)
• Miraj Naik
  • RE: namd2 GPU error (Tue Feb 20 2018 - 05:22:16 CST)
  • namd2 GPU error (Tue Feb 13 2018 - 22:43:10 CST)
• Miyu Tamura
  • ERROR in multiple walker metadynamics simulation (Tue Aug 21 2018 - 01:30:09 CDT)
• 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
  • calculating non bonded energy using namdenergy (Wed Sep 19 2018 - 22:19:16 CDT)
  • energy calculation with namdenergy (Wed Sep 05 2018 - 07:32:00 CDT)
  • Re: Angle of lone pair in TIP4P 2005 simulation (Tue May 08 2018 - 22:17:16 CDT)
  • Re: Using PBC tools for a cubic and a rectangular box (Wed Mar 28 2018 - 23:07:41 CDT)
  • Using PBC tools for a cubic and a rectangular box (Tue Mar 27 2018 - 05:34:10 CDT)
  • Re: Calculate energy of a residue using NAMD energy (Fri Feb 02 2018 - 01:05:47 CST)
  • Re: Calculate energy of a residue using NAMD energy (Thu Feb 01 2018 - 22:51:37 CST)
  • Re: Calculate energy of a residue using NAMD energy (Thu Feb 01 2018 - 18:08:15 CST)
  • Re: Calculate energy of a residue using NAMD energy (Wed Jan 31 2018 - 17:25:13 CST)
  • Re: Calculate energy of a residue using NAMD energy (Tue Jan 30 2018 - 17:41:28 CST)
  • Calculate energy of a residue using NAMD energy (Mon Jan 29 2018 - 21:22:19 CST)
  • 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)
• mrinal patel
  • regarding constant velocity steered molecular dynamics (Wed Feb 08 2017 - 04:07:24 CST)
• Nassar, Omneya
  • Re: Binding free energy tutorial (Wed Nov 07 2018 - 08:56:56 CST)
  • Re: Using 4-site water model in NAMD (Sun Sep 16 2018 - 22:35:57 CDT)
  • Re: Using 4-site water model in NAMD (Sun Sep 16 2018 - 22:05:37 CDT)
  • Re: Using 4-site water model in NAMD (Sun Sep 16 2018 - 22:04:00 CDT)
  • Re: regarding umbrella sampling simulation (Fri Sep 14 2018 - 23:47:27 CDT)
  • Re: Ewald size-dependence correction in FEP simulation of an electric dipole (Fri Sep 14 2018 - 08:02:04 CDT)
  • Re: Ewald size-dependence correction in FEP simulation of an electric dipole (Fri Sep 14 2018 - 07:47:39 CDT)
  • RE: Ewald size-dependence correction in FEP simulation of an electric dipole (Thu Sep 13 2018 - 21:54:08 CDT)
  • RE: Ewald size-dependence correction in FEP simulation of an electric dipole (Wed Sep 12 2018 - 23:16:02 CDT)
  • Re: Dual Topology in FEP Calculations - How to Calculate Electrostatics and van der Waals Free Energies Separately? (Tue Jul 24 2018 - 07:29:13 CDT)
  • Re: Dual Topology in FEP Calculations - How to Calculate Electrostatics and van der Waals Free Energies Separately? (Sat Jul 21 2018 - 07:58:40 CDT)
  • Dual Topology in FEP Calculations - How to Calculate Electrostatics and van der Waals Free Energies Separately? (Fri Jul 20 2018 - 15:04:17 CDT)
• Natalia Ostrowska
  • Re: Three bonds with water in vmd from NAMD DCD (Wed Aug 22 2018 - 04:27:42 CDT)
  • 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)
• Nate Walkins
  • Update particle position iteratively in between steps (Sun Jun 03 2018 - 09:55:29 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)
• 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)
• 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)
• 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)
• Nick Guros
  • Lowe-Andersen Thermostat Speed (Fri Mar 16 2018 - 13:59:43 CDT)
• Nick Palmer
  • Positive VDW energies (Thu Oct 25 2018 - 14:54:58 CDT)
  • Re: Distorted peptide bond with new residue (Thu Jul 05 2018 - 17:39:25 CDT)
  • Re: Distorted peptide bond with new residue (Thu Jul 05 2018 - 17:00:25 CDT)
  • Distorted peptide bond with new residue (Thu Jul 05 2018 - 16:18:28 CDT)
• Nielsen, Steven
  • Re: Is there really no way of automating pair interaction calculations without invoking NAMD for each pdb file separately? (Thu Nov 01 2018 - 12:30:21 CDT)
  • 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)
• nikolaev_at_spbau.ru
  • Segmentation fault during water MD (Tue Apr 18 2017 - 09:37:10 CDT)
• Nisler, Collin R.
  • Fatty Acid Topology (Fri Mar 30 2018 - 21:25:30 CDT)
  • 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)
• Norman Geist
  • AW: Bad structure after converting the coarse grained last frame to all-atom (Fri Sep 21 2018 - 01:08:00 CDT)
  • AW: Weird PBC wrapping (Fri Aug 31 2018 - 01:58:11 CDT)
  • AW: AW: AW: Periodic cell has become too small for original patch grid (Wed Aug 15 2018 - 09:52:28 CDT)
  • AW: AW: AW: Periodic cell has become too small for original patch grid (Wed Aug 15 2018 - 09:52:13 CDT)
  • AW: AW: Periodic cell has become too small for original patch grid (Wed Aug 15 2018 - 05:52:38 CDT)
  • AW: Periodic cell has become too small for original patch grid (Tue Aug 14 2018 - 01:28:06 CDT)
  • AW: NAMD SMP version warning - Reg (Wed Jul 04 2018 - 09:42:45 CDT)
  • AW: NAMD SMP version warning - Reg (Wed Jul 04 2018 - 05:18:45 CDT)
  • AW: NAMD SMP version warning - Reg (Wed Jul 04 2018 - 05:12:46 CDT)
  • AW: AW: How to run a TCL proc at every step in NAMD using callback command? (Thu Jun 14 2018 - 04:13:18 CDT)
  • AW: How to run a TCL proc at every step in NAMD using callback command? (Thu Jun 14 2018 - 03:38:08 CDT)
  • BUG: ReplicaUniformPatchGrids and "output" command namd-2.13NB (Thu Jun 07 2018 - 01:56:47 CDT)
  • Solutescaling not working with Amber files (Tue May 29 2018 - 06:06:57 CDT)
  • Info on solutescaling (Tue May 29 2018 - 02:13:27 CDT)
  • AW: Difference between REMD replica temperature and actual temperature (Tue May 29 2018 - 02:12:11 CDT)
  • AW: Difference between REMD replica temperature and actual temperature (Tue May 29 2018 - 02:08:12 CDT)
  • AW: Are there plans on thermostat groups? (Thu May 17 2018 - 02:25:49 CDT)
  • Are there plans on thermostat groups? (Wed May 16 2018 - 09:56:01 CDT)
  • AW: Low global CUDA exclusion count! (9592 vs 9618) (Tue Mar 13 2018 - 06:05:46 CDT)
  • AW: Low global CUDA exclusion count! (9592 vs 9618) (Tue Mar 13 2018 - 05:56:25 CDT)
  • AW: Hydrogen Mass Repartitioning in NAMD (Thu Mar 08 2018 - 08:53:24 CST)
  • AW: periodic cell has become too small for original patch grid (Tue Mar 06 2018 - 01:50:42 CST)
  • AW: periodic cell has become too small for original patch grid (Mon Mar 05 2018 - 02:17:25 CST)
  • 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)
• 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)
• Oleksiy Kovtun
  • Re: reverting atoms introduced by name into standard PDB ones (Mon May 14 2018 - 07:44:15 CDT)
  • reverting atoms introduced by name into standard PDB ones (Mon May 14 2018 - 04:45:43 CDT)
• Olya Kravchenko
  • Re: overlapping windows in ABF (Tue Jul 24 2018 - 18:37:44 CDT)
  • overlapping windows in ABF (Mon Jul 23 2018 - 09:52:39 CDT)
  • Re: merging abf trajectories with different number of colvars (Thu Jun 21 2018 - 11:22:26 CDT)
  • Re: merging abf trajectories with different number of colvars (Thu Jun 21 2018 - 09:19:17 CDT)
  • Re: merging abf trajectories with different number of colvars (Wed Jun 20 2018 - 13:18:11 CDT)
  • merging abf trajectories with different number of colvars (Thu May 31 2018 - 11:13:50 CDT)
  • Re: "non-numeric floating-point value" error while using distanceXY (Wed May 30 2018 - 11:40:18 CDT)
  • "non-numeric floating-point value" error while using distanceXY (Wed May 30 2018 - 09:06:00 CDT)
  • Re: restrain lateral movement during ABF (Fri May 18 2018 - 08:37:24 CDT)
  • Re: restrain lateral movement during ABF (Thu May 17 2018 - 16:47:13 CDT)
  • restrain lateral movement during ABF (Wed May 16 2018 - 16:34:48 CDT)
  • Re: dummyAtom in distance colvar in ABF calculations (Mon May 14 2018 - 12:37:20 CDT)
  • Re: dummyAtom in distance colvar in ABF calculations (Mon May 14 2018 - 10:26:55 CDT)
  • dummyAtom in distance colvar in ABF calculations (Sat May 12 2018 - 16:44:16 CDT)
  • Re: water box tilts during equilibration (Fri Apr 27 2018 - 20:31:52 CDT)
  • water box tilts during equilibration (Fri Apr 27 2018 - 17:51:39 CDT)
  • 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)
• Omid Bavi
  • Re: accelMDbdihe is not working properly in NAMD after commit e3e849639982dcba9a60c6072c81fdb7cba69759 (Tue Aug 07 2018 - 13:49:39 CDT)
  • Holding molecules on one side of membrane (Sun Feb 04 2018 - 07:14:26 CST)
• Onur SerçinoÄŸlu
  • Re: Calculate energy of a residue using NAMD energy (Thu Feb 01 2018 - 06:06:08 CST)
• Oscar Bastidas
  • Phosphorylated Residues (Tue Jun 26 2018 - 23:29:07 CDT)
  • 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)
• 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)
• 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)
• Peter Freddolino
  • Re: Is there really no way of automating pair interaction calculations without invoking NAMD for each pdb file separately? (Thu Nov 01 2018 - 15:45:16 CDT)
  • Re: Bad structure after converting the coarse grained last frame to all-atom (Thu Sep 20 2018 - 11:14:35 CDT)
  • Re: calculating non bonded energy using namdenergy (Thu Sep 20 2018 - 11:13:50 CDT)
  • Re: Bad structure after converting the coarse grained last frame to all-atom (Wed Sep 19 2018 - 20:52:15 CDT)
  • Re: Bad structure after converting the coarse grained last frame to all-atom (Tue Sep 18 2018 - 12:26:59 CDT)
  • Re: Bad structure after converting the coarse grained last frame to all-atom (Mon Sep 17 2018 - 15:58:31 CDT)
  • Re: Using 4-site water model in NAMD (Sun Sep 16 2018 - 22:11:44 CDT)
  • Re: Broken Structure after reverting coarse-grained system to all-atom system (Tue Jul 10 2018 - 09:07:44 CDT)
  • Re: Equilibration in NPT simulation (Wed Jul 04 2018 - 13:37:31 CDT)
  • Re: Problem in generating psf (Thu May 31 2018 - 07:31:46 CDT)
  • Re: Angle of lone pair in TIP4P 2005 simulation (Tue May 08 2018 - 23:06:55 CDT)
  • Re: Angle of lone pair in TIP4P 2005 simulation (Tue May 08 2018 - 20:37:19 CDT)
  • Re: Cleaving and capping protein with autopsf leads to parameter errors upon running NAMD (Wed May 02 2018 - 00:23:22 CDT)
  • Re: Reverting coarse-grain system to all-atom system (Mon Apr 16 2018 - 16:05:39 CDT)
  • Re: Reverting coarse-grain system to all-atom system (Mon Apr 16 2018 - 10:43:49 CDT)
  • Re: Reverting coarse-grain system to all-atom system (Sun Apr 15 2018 - 19:57:33 CDT)
  • Re: AutoPSF Error (Mon Mar 12 2018 - 12:22:35 CDT)
  • Re: Calculate energy of a residue using NAMD energy (Mon Feb 05 2018 - 00:42:43 CST)
  • Re: Calculate energy of a residue using NAMD energy (Thu Feb 01 2018 - 22:59:57 CST)
  • Re: Calculate energy of a residue using NAMD energy (Thu Feb 01 2018 - 21:59:53 CST)
  • Re: Calculate energy of a residue using NAMD energy (Tue Jan 30 2018 - 20:51:50 CST)
  • 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)
• philippe Bourly
  • CZAR Estimator: grad file (Tue Apr 24 2018 - 03:38:49 CDT)
  • 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)
• 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)
• quo.physics_at_gmail.com
  • Re: multiple replicas metadynamics (Tue Jan 10 2017 - 05:57:27 CST)
• Rabeta Yeasmin
  • Calculating hydrophilic and hydrophobic Solvent Accessible Surface Area (Mon Oct 15 2018 - 10:26:45 CDT)
  • Re: Bad structure after converting the coarse grained last frame to all-atom (Thu Sep 20 2018 - 09:58:39 CDT)
  • Re: Bad structure after converting the coarse grained last frame to all-atom (Wed Sep 19 2018 - 13:00:29 CDT)
  • Re: Bad structure after converting the coarse grained last frame to all-atom (Tue Sep 18 2018 - 13:36:40 CDT)
  • Re: Bad structure after converting the coarse grained last frame to all-atom (Tue Sep 18 2018 - 10:58:25 CDT)
  • Bad structure after converting the coarse grained last frame to all-atom (Mon Sep 17 2018 - 11:50:49 CDT)
  • atom moving fast error in Coarse grained simulation: even reduced the time step (Mon Aug 06 2018 - 14:30:40 CDT)
  • Re: Which one is more reliable to use in umbrella sampling- .traj data or vmd script data (Fri Aug 03 2018 - 10:41:28 CDT)
  • Which one is more reliable to use in umbrella sampling- .traj data or vmd script data (Thu Aug 02 2018 - 16:24:35 CDT)
  • Re: Broken Structure after reverting coarse-grained system to all-atom system (Tue Jul 10 2018 - 09:46:07 CDT)
  • Broken Structure after reverting coarse-grained system to all-atom system (Mon Jul 09 2018 - 13:38:42 CDT)
  • Bond parameter error for the system which has been converted using residue-based coarse-grained method (Wed Jul 04 2018 - 15:25:24 CDT)
  • Continuing metadynamics run (Fri May 04 2018 - 10:25:08 CDT)
  • Re: Reverting coarse-grain system to all-atom system (Tue Apr 17 2018 - 10:49:55 CDT)
  • Re: Reverting coarse-grain system to all-atom system (Mon Apr 16 2018 - 10:41:11 CDT)
  • Reverting coarse-grain system to all-atom system (Sun Apr 15 2018 - 18:49:21 CDT)
  • metadynamics problem (Mon Mar 26 2018 - 11:39:28 CDT)
  • Coarse-grained umbrella sampling for POPS-protein system (Fri Feb 23 2018 - 17:53:53 CST)
  • Lipid bilayer deformed during coarse grain simulation (Fri Feb 09 2018 - 10:58:19 CST)
  • Re: all-atom to coarse-grained system (Mon Feb 05 2018 - 11:23:20 CST)
  • Re: all-atom to coarse-grained system (Fri Feb 02 2018 - 15:43:57 CST)
  • all-atom to coarse-grained system (Thu Feb 01 2018 - 15:29:45 CST)
  • Re: Ways to find water molecules passing through the water channel in lipid bilayer (Fri Jan 19 2018 - 13:13:31 CST)
  • Re: Ways to find water molecules passing through the water channel in lipid bilayer (Thu Jan 18 2018 - 18:43:06 CST)
  • Tilting angle of lipid calculation (Thu Jan 18 2018 - 18:29:44 CST)
  • Ways to find water molecules passing through the water channel in lipid bilayer (Thu Jan 18 2018 - 18:19:29 CST)
  • Re: Different resid in pdb fie but showing same molecule in VMD (Mon Jan 15 2018 - 01:57:54 CST)
  • Different resid in pdb fie but showing same molecule in VMD (Fri Jan 12 2018 - 17:42:14 CST)
  • metadynamics reaction coordinate (Wed Jan 03 2018 - 11:42:57 CST)
  • 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)
• 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)
• Rakesh K
  • Atom velocity error in coarse grained simulation using MARTINI (Sat Mar 31 2018 - 10:16:39 CDT)
• rakesh kumar
  • FEP/REMD (ERROR: 'alchLambda' is a required configuration option) (Wed Feb 07 2018 - 03:25:17 CST)
• Randy J. Zauhar
  • Re: User force field with FEP? (Tue Dec 11 2018 - 14:01:04 CST)
  • User force field with FEP? (Tue Dec 11 2018 - 13:27:00 CST)
  • Re: Selecting waters from dynamics trajectory (Wed Mar 21 2018 - 11:08:46 CDT)
  • Selecting waters from dynamics trajectory (Tue Mar 20 2018 - 16:47:38 CDT)
  • Handling of nonbonded lists in PSF - please clarify (Sun Feb 25 2018 - 14:42:10 CST)
  • Re: Question on making 'reversible' solvated simulation (Mon Feb 19 2018 - 12:42:36 CST)
  • Re: Question on making 'reversible' solvated simulation (Sun Feb 18 2018 - 17:01:27 CST)
  • Re: Question on making 'reversible' solvated simulation (Sun Feb 18 2018 - 16:54:20 CST)
  • Re: Question on making 'reversible' solvated simulation (Sat Feb 17 2018 - 11:20:48 CST)
  • Re: Question on making 'reversible' solvated simulation (Sun Feb 11 2018 - 12:52:18 CST)
  • Question on making 'reversible' solvated simulation (Sat Feb 10 2018 - 12:15:37 CST)
  • Re: Question on restraint behavior when part of system decouples (Mon Jan 29 2018 - 13:24:45 CST)
  • Question on restraint behavior when part of system decouples (Mon Jan 29 2018 - 09:19:28 CST)
  • 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)
• Rene Hamburger UNI KL
  • Equilibration of membrane water system (pressure in NVT) (Fri Oct 26 2018 - 02:32:38 CDT)
• Renfro, Michael
  • Re: What NAMD version to obtain (Wed Dec 19 2018 - 15:08:37 CST)
  • Re: problems running GPU-accelerated namd (Sun Dec 09 2018 - 10:07:21 CST)
  • Re: Parallel Jobs (Thu Dec 06 2018 - 15:05:19 CST)
  • Re: bpti example compiled source charmrun++ does not launch (Thu Nov 01 2018 - 10:14:24 CDT)
  • Re: Build for CUDA support (Sat Mar 03 2018 - 10:03:26 CST)
  • Re: Replica exchange simulation with GPU Accelaration (Thu Jan 25 2018 - 13:40:28 CST)
  • 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)
• Richard
  • Re: NAMD2.9-ERROR: Constraint failure in RATTLE algorithm for atom! (Fri Aug 25 2017 - 23:03:00 CDT)
• Richard Overstreet
  • Re: NAMD Simulation in a laptop (Sun Mar 25 2018 - 23:26:24 CDT)
  • NAMD 2.12 Volta Compatibility (Sat Feb 03 2018 - 13:24:45 CST)
  • 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)
• 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)
• Rohit Modee
  • Re: AW: AW: Periodic cell has become too small for original patch grid (Wed Aug 15 2018 - 06:06:12 CDT)
  • Re: AW: Periodic cell has become too small for original patch grid (Wed Aug 15 2018 - 04:34:52 CDT)
  • Periodic cell has become too small for original patch grid (Mon Aug 13 2018 - 03:26:13 CDT)
• Roshan Shrestha
  • Re: Enabling charmrun in NAMD simulation (Wed Apr 25 2018 - 02:11:53 CDT)
  • Re: Enabling charmrun in NAMD simulation (Wed Apr 25 2018 - 02:10:27 CDT)
  • Re: (Sat Jan 06 2018 - 09:56:26 CST)
  • 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)
• Ryan McGreevy
  • Re: the instance type selection for NAMD simulation in Amason marketplace (Mon Oct 15 2018 - 08:45:31 CDT)
  • Re: Periodic cell basis too small for GridForce (Mon May 28 2018 - 11:42:01 CDT)
  • Re: xMDFF: model file is not given (Fri May 25 2018 - 10:31:56 CDT)
  • 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)
• Ryuzo Azuma
  • multi-node mpiexec issue (Fri Aug 31 2018 - 11:44:26 CDT)
• Sadegh Faramarzi Ganjabad
  • Re: Rattle error with lateral pressure calculations (Thu Aug 02 2018 - 13:28:52 CDT)
  • Re: Rattle error with lateral pressure calculations (Sun Jul 29 2018 - 22:18:39 CDT)
  • Rattle error with lateral pressure calculations (Tue Jul 24 2018 - 17:24:17 CDT)
  • Re: How to interpret Thermodynamic Integration output (Mon Apr 23 2018 - 11:01:02 CDT)
  • Re: How to interpret Thermodynamic Integration output (Wed Apr 18 2018 - 14:57:56 CDT)
  • Re: How to interpret Thermodynamic Integration output (Thu Mar 22 2018 - 14:13:03 CDT)
  • Re: How to interpret Thermodynamic Integration output (Tue Feb 27 2018 - 12:26:17 CST)
  • How to interpret Thermodynamic Integration output (Fri Feb 23 2018 - 18:09:19 CST)
  • ParseFEP error (Sat Feb 17 2018 - 23:39:52 CST)
  • 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)
• salehesam_at_gmail.com
  • Re: Drude minimization does not converge (Fri Jan 13 2017 - 10:36:41 CST)
• san kumar
  • regarding umbrella sampling simulation (Fri Sep 14 2018 - 23:11:54 CDT)
• 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)
• Sanket Deshmukh
  • Requesting abstracts for MRS Fall 2018 Symposium BM03: Multiscale Modeling of Soft Materials and Interfaces (Thu Jun 07 2018 - 09:22:42 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
  • git rid of it (Fri Oct 19 2018 - 14:21:57 CDT)
  • Re: How to solve the segmentation faults in compiling NAMD to build and test the Charm++/Converse library (MPI version)? (Fri May 04 2018 - 11:17:32 CDT)
  • Re: CHARMRUN ERROR (Fri May 19 2017 - 11:17:18 CDT)
  • Re: CHARMRUN ERROR (Thu May 18 2017 - 13:28:52 CDT)
• Seibold, Steve Allan
  • What NAMD version to obtain (Wed Dec 19 2018 - 14:35:12 CST)
  • Three bonds with water in vmd from NAMD DCD (Tue Aug 21 2018 - 09:17:43 CDT)
  • Re: Incorporate aluminum oxide monolayer (Wed Apr 12 2017 - 09:47:43 CDT)
• Serena Vittorio
  • run different simulation of the same system by using different initial velocities (Thu May 24 2018 - 07:35:39 CDT)
  • Re: AW: Aromatic rings don't maintain the planarity during the heating (Fri May 04 2018 - 11:51:39 CDT)
  • Aromatic rings don't maintain the planarity during the heating (Fri May 04 2018 - 11:14:30 CDT)
• sesha surya vara prasad reddy karri
  • Re: NVIDIA Quadro(R) GV100 card for NAMD studies (Fri Nov 02 2018 - 07:05:04 CDT)
  • NVIDIA Quadro(R) GV100 card for NAMD studies (Fri Nov 02 2018 - 05:58:41 CDT)
• Shadrina Maria
  • NAMD crashes when Multilevel Summation Method (MSM) is on (Tue May 30 2017 - 10:12:46 CDT)
• Shahee Islam
  • Re: Re: simulation becomes unstable in residue base coarse grained system (Tue Feb 13 2018 - 06:56:10 CST)
  • Re: Re: simulation becomes unstable in residue base coarse grained system (Tue Feb 13 2018 - 05:53:23 CST)
  • Re: Re: simulation becomes unstable in residue base coarse grained system (Mon Feb 12 2018 - 09:27:03 CST)
  • Re: Re: simulation becomes unstable in residue base coarse grained system (Mon Feb 12 2018 - 09:05:04 CST)
  • Re: simulation becomes unstable in residue base coarse grained system (Sun Feb 11 2018 - 23:08:42 CST)
  • having problem with disulfide bond (Thu Jan 04 2018 - 05:48:38 CST)
  • 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)
• 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)
• Sharp, Kim
  • Re: Residue Charges (Fri Mar 02 2018 - 08:49:05 CST)
• Shivangi Nangia
  • CHARMM36 parameters for nucelobases (Sat Nov 10 2018 - 07:03:34 CST)
• Shriya Bansal
  • NAMD Error (Tue Jul 17 2018 - 14:45:26 CDT)
• shyam sharma
  • Error during simulation (Wed Jun 13 2018 - 06:27:46 CDT)
  • (no subject) (Thu Apr 26 2018 - 07:02:17 CDT)
  • (no subject) (Fri Mar 09 2018 - 02:02:09 CST)
• Siddharth Girdhar
  • Simulating SDS molecules (Fri Jun 30 2017 - 09:11:08 CDT)
• SM Bargeen A Turzo
  • QMMM FEP (Thu Jun 28 2018 - 14:38:31 CDT)
  • SM Bargeen A Turzo wants to share the file Min_error with you (Wed May 02 2018 - 21:43:51 CDT)
  • (no subject) (Wed May 02 2018 - 21:43:45 CDT)
  • Energy Minimization failure for mutants (Sun Apr 29 2018 - 22:36:54 CDT)
  • Re: RE: Regarding Topology and Parameterization (Wed Apr 11 2018 - 14:25:22 CDT)
  • Re: RE: Regarding Topology and Parameterization (Wed Apr 11 2018 - 14:16:12 CDT)
  • Regarding Topology and Parameterization (Tue Apr 10 2018 - 18:51:35 CDT)
• Sneha M
  • NAMDEnergy with xtc file (Thu Oct 05 2017 - 05:11:37 CDT)
• Sonibare, Kolawole
  • Converting a mixture system from NAMD to LAMMPS (Thu Aug 16 2018 - 12:14:56 CDT)
  • Re: Segmentation fault (Wed May 23 2018 - 16:49:04 CDT)
  • Segmentation fault (Wed May 23 2018 - 13:41:03 CDT)
  • How to create multiple molecules using psfgen (Tue May 15 2018 - 17:32:32 CDT)
• sonu2kd_at_gmail.com
  • Re: dcd to pdb conversion (Wed Jan 04 2017 - 06:26:49 CST)
• soroush ziaei
  • Re: creating topology for a unique structure (Thu Nov 08 2018 - 14:29:17 CST)
  • creating topology for a unique structure (Wed Nov 07 2018 - 11:05:08 CST)
  • creating topology for a unique structure (Sun Nov 04 2018 - 02:02:03 CST)
  • detecting vanishing atoms in zero.fep (Thu Nov 01 2018 - 18:03:12 CDT)
  • detecting vanishing atoms in zero.fep (Thu Nov 01 2018 - 15:39:07 CDT)
  • detecting vanishing atoms in zero.fep (Sat Oct 27 2018 - 16:37:20 CDT)
  • error in (runfepmin) (Sun Oct 21 2018 - 18:02:24 CDT)
  • constant temprature for vacuum condition in namd file (Fri Oct 19 2018 - 14:19:53 CDT)
  • vacuum condition in config file (Fri Oct 19 2018 - 13:58:37 CDT)
  • Re: the fep error in third part of config file (Thu Oct 18 2018 - 04:13:08 CDT)
  • the fep error in third part of config file (Mon Oct 15 2018 - 09:50:25 CDT)
• Sourav Pal
  • Re: Writing pdb file for a particular frame (Tue May 16 2017 - 22:18:31 CDT)
• Souvik Sinha
  • Re: merging abf trajectories with different number of colvars (Thu Jun 21 2018 - 10:05:30 CDT)
  • Re: PMF calculation using CPU and GPU (Fri Jun 08 2018 - 10:04:51 CDT)
  • PMF calculation using CPU and GPU (Fri Jun 08 2018 - 08:36:27 CDT)
  • Re: distance filter during data analysis (Wed May 09 2018 - 00:53:43 CDT)
  • Re: (Tue Feb 13 2018 - 06:32:42 CST)
  • Re: Pair interaction energies: TCL error -reg (Thu Feb 08 2018 - 07:32:26 CST)
  • Re: NAMD run on Intel hyperthreaded cores (Tue Feb 06 2018 - 14:17:50 CST)
  • Re: NAMD run on Intel hyperthreaded cores (Tue Feb 06 2018 - 08:20:43 CST)
  • NAMD run on Intel hyperthreaded cores (Tue Feb 06 2018 - 02:41:49 CST)
  • Re: Calculation of Diffusion coefficient (Mon Jan 29 2018 - 11:13:55 CST)
  • Re: Calculation of Diffusion coefficient (Mon Jan 29 2018 - 10:35:57 CST)
  • Calculation of Diffusion coefficient (Mon Jan 29 2018 - 08:01:13 CST)
  • Re: Replica exchange simulation with GPU Accelaration (Mon Jan 29 2018 - 05:30:39 CST)
  • Re: Replica exchange simulation with GPU Accelaration (Fri Jan 26 2018 - 23:20:14 CST)
  • Re: Replica exchange simulation with GPU Accelaration (Fri Jan 26 2018 - 13:35:12 CST)
  • Re: Replica exchange simulation with GPU Accelaration (Fri Jan 26 2018 - 13:02:56 CST)
  • Re: Replica exchange simulation with GPU Accelaration (Fri Jan 26 2018 - 12:24:27 CST)
  • Re: Replica exchange simulation with GPU Accelaration (Thu Jan 25 2018 - 12:59:26 CST)
  • Replica exchange simulation with GPU Accelaration (Thu Jan 25 2018 - 03:02:15 CST)
  • 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)
• Srijita Paul
  • Problem in generating psf (Thu May 31 2018 - 01:25:39 CDT)
  • Problem generating pdb psf of ATP (Mon May 14 2018 - 02:33:43 CDT)
  • Re: (Mon Mar 19 2018 - 14:54:36 CDT)
  • Re: (Mon Mar 19 2018 - 14:54:36 CDT)
  • Re: (Mon Mar 19 2018 - 04:16:13 CDT)
  • (no subject) (Fri Mar 16 2018 - 14:14:22 CDT)
  • (no subject) (Fri Mar 16 2018 - 06:40:03 CDT)
  • (no subject) (Fri Mar 16 2018 - 05:54:30 CDT)
  • (no subject) (Thu Mar 15 2018 - 06:44:21 CDT)
  • Re: (Fri Feb 16 2018 - 06:42:56 CST)
  • (no subject) (Tue Feb 13 2018 - 05:06:51 CST)
  • 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)
• Stefano Guglielmo
  • namd mpi (Fri Jun 22 2018 - 07:46:27 CDT)
  • Re: psf from parmed (Fri Jun 08 2018 - 09:20:59 CDT)
  • psf from parmed (Fri Jun 08 2018 - 08:09:16 CDT)
  • torsion scan (Thu Apr 19 2018 - 18:30:00 CDT)
  • Re: colvars selecting frames (Tue Feb 20 2018 - 14:54:20 CST)
  • Re: colvars selecting frames (Thu Feb 01 2018 - 06:06:41 CST)
  • colvars selecting frames (Tue Jan 30 2018 - 19:37:54 CST)
  • 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)
• 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)
• Strenic Computations
  • VMD/NMAD on AWS (Sat Mar 17 2018 - 18:50:17 CDT)
• sunyeping
  • the instance type selection for NAMD simulation in Amason marketplace (Mon Oct 15 2018 - 07:09:54 CDT)
  • 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)
• Suresh Ghimire
  • unit dipole moment vector (Fri May 11 2018 - 02:58:09 CDT)
  • variation of pressure (Thu Apr 19 2018 - 05:31:57 CDT)
  • effect of acceptors (Sun Apr 01 2018 - 10:44:37 CDT)
  • parameter (Sat Feb 24 2018 - 07:40:24 CST)
  • minimization (Sat Jan 27 2018 - 01:29:00 CST)
  • acceptor (Wed Jan 17 2018 - 00:02:10 CST)
  • accepter (Tue Jan 16 2018 - 23:51:20 CST)
  • (no subject) (Sun Jan 14 2018 - 07:31:05 CST)
  • (no subject) (Sun Jan 07 2018 - 04:09:05 CST)
  • (no subject) (Sat Jan 06 2018 - 09:46:20 CST)
  • (no subject) (Mon Jan 01 2018 - 09:14:36 CST)
  • (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)
• 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)
• 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] Running REUS in many nodes (Tue Nov 20 2018 - 18:40:55 CST)
  • [NAMD] Running REUS in many nodes (Tue Nov 20 2018 - 16:12:01 CST)
  • Re: [NAMD] Define time-dependent grid force (Thu Jul 26 2018 - 18:57:14 CDT)
  • [NAMD] Define time-dependent grid force (Fri Jul 20 2018 - 12:52:13 CDT)
  • Re: E-filed to individual channel in parallel system - Reg (Fri Jul 20 2018 - 12:48:21 CDT)
  • Re: [NAMD] Apply an electric field only in a specific region (Tue Jun 19 2018 - 03:41:15 CDT)
  • [NAMD] Apply an electric field only in a specific region (Mon Jun 04 2018 - 01:39:28 CDT)
  • Re: unit dipole moment vector (Fri May 11 2018 - 13:11:13 CDT)
  • Re: vmd-l: [VMD-NAMD] Question about Dipole of DNA / Dipole Moment Watcher Plugin (Sun Mar 25 2018 - 20:31:45 CDT)
  • [VMD-NAMD] Question about Dipole of DNA / Dipole Moment Watcher Plugin (Thu Mar 22 2018 - 18:17:30 CDT)
  • [NAMD] Units of Efieldfreq (Wed Jan 31 2018 - 23:23:16 CST)
  • 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)
• thiagorrg UFC
  • Martini CG parameter errors for lipids (Wed May 02 2018 - 12:00:05 CDT)
• Thomas C. Bishop
  • PSFGEN 1.6.4 autogenerate PATCH keyword not available (Mon Apr 23 2018 - 19:57:47 CDT)
• Tim.Ho_at_csiro.au
  • FATAL ERROR running apoa1 with NAMD 2.12 (Wed Apr 05 2017 - 01:53:26 CDT)
• Toon Verstraelen
  • Downloads are .tar files but have .tar.gz extension (Thu Nov 09 2017 - 05:07:26 CST)
• Travis Hesketh
  • Error with D-amino acids mid-sequence using NAMD 2.12/2.13b2 and CHARMm36 (Mon Nov 05 2018 - 10:04:49 CST)
• Tyler Wied
  • "block" module for NAMD (Fri Jun 22 2018 - 07:56:56 CDT)
• Udaya Dahal
  • Re: Colvars and distance restraint for umbrella sampling (Wed Oct 17 2018 - 10:58:13 CDT)
  • Re: Colvars and distance restraint for umbrella sampling (Wed Oct 17 2018 - 10:41:00 CDT)
  • Re: Colvars and distance restraint for umbrella sampling (Tue Oct 16 2018 - 19:41:21 CDT)
  • Colvars and distance restraint for umbrella sampling (Tue Oct 16 2018 - 19:08:07 CDT)
• varun dewaker
  • Regarding free energy calculation (Mon Mar 26 2018 - 02:39:54 CDT)
• Vermaas, Joshua
  • RE: What NAMD version to obtain (Wed Dec 19 2018 - 17:14:33 CST)
  • RE: Wrapping multimeric protein issues (Wed Dec 12 2018 - 18:10:57 CST)
  • RE: problems running GPU-accelerated namd (Mon Dec 10 2018 - 12:10:06 CST)
  • RE: Parallel Jobs (Thu Dec 06 2018 - 15:21:18 CST)
  • RE: Problems about constraint (conskcol) in umbrella sampling conf file (Wed Nov 21 2018 - 11:46:56 CST)
  • RE: [NAMD] Running REUS in many nodes (Tue Nov 20 2018 - 16:51:32 CST)
  • RE: Building with GCC on Ubuntu 18 (Mon Nov 12 2018 - 11:34:11 CST)
  • RE: Building with GCC on Ubuntu 18 (Fri Nov 09 2018 - 12:42:37 CST)
  • RE: Way to wget or curl download the precompiled NAMD? (Thu Nov 08 2018 - 15:37:21 CST)
  • RE: Building with GCC on Ubuntu 18 (Thu Nov 08 2018 - 11:50:54 CST)
  • RE: Gaussian Dihedral Scan Log files visualization. (Mon Nov 05 2018 - 12:10:48 CST)
  • RE: Membrane Simulation (Wed Oct 31 2018 - 12:49:17 CDT)
  • RE: parameter request for PRES bonding (Sun Oct 28 2018 - 18:09:06 CDT)
  • RE: Positive VDW energies (Thu Oct 25 2018 - 18:29:47 CDT)
  • RE: error in (runfepmin) (Mon Oct 22 2018 - 13:51:10 CDT)
  • RE: vacuum condition in config file (Fri Oct 19 2018 - 14:08:18 CDT)
  • RE: Calculating hydrophilic and hydrophobic Solvent Accessible Surface Area (Mon Oct 15 2018 - 10:35:25 CDT)
  • RE: Mismatch in atom number between psf and dcd files (Fri Sep 28 2018 - 11:23:05 CDT)
  • RE: About CUDA version (Tue Sep 25 2018 - 15:06:54 CDT)
  • RE: PBC error. Amber force field in NAMD (Tue Sep 25 2018 - 11:35:42 CDT)
  • RE: Best water model (Thu Sep 20 2018 - 08:50:50 CDT)
  • RE: namd simulation input file setting from NPT to NVT (Thu Sep 06 2018 - 16:04:20 CDT)
  • RE: FATAL ERROR: Unable to access config file temp14.conf (Fri Aug 17 2018 - 13:15:46 CDT)
  • RE: Which one is more reliable to use in umbrella sampling- .traj data or vmd script data (Fri Aug 03 2018 - 13:55:43 CDT)
  • RE: Isomerization between runs (Wed Aug 01 2018 - 06:10:27 CDT)
  • RE: Problems with temperature control. (Tue Jul 31 2018 - 14:18:35 CDT)
  • RE: Multi-dimensional PMF (Fri Jul 27 2018 - 14:43:26 CDT)
  • RE: Multi-dimensional PMF (Fri Jul 27 2018 - 11:27:45 CDT)
  • RE: Multiple Colvars (Tue Jul 24 2018 - 16:59:23 CDT)
  • RE: Umbrella Sampling input parameters (Tue Jul 24 2018 - 09:45:08 CDT)
  • RE: Question about the fundamentals of MD and WHAM (Fri Jul 20 2018 - 11:35:19 CDT)
  • RE: Umbrella Sampling input parameters (Thu Jul 19 2018 - 15:53:25 CDT)
  • RE: NAMD Error (Wed Jul 18 2018 - 07:45:36 CDT)
  • RE: Umbrella Sampling input parameters (Fri Jul 13 2018 - 20:30:39 CDT)
  • RE: Decreasing performance of cluster running FEP (Wed Jul 11 2018 - 18:23:23 CDT)
  • RE: Included Topology (.itp) in gromacs to parameter file for NAMD (Wed Jul 11 2018 - 18:18:44 CDT)
  • RE: Decreasing performance of cluster running FEP (Wed Jul 11 2018 - 12:21:07 CDT)
  • RE: Included Topology (.itp) in gromacs to parameter file for NAMD (Wed Jul 11 2018 - 12:16:11 CDT)
  • RE: Umbrella Sampling input parameters (Tue Jul 10 2018 - 05:40:51 CDT)
  • RE: Distorted peptide bond with new residue (Thu Jul 05 2018 - 17:05:54 CDT)
  • RE: Distorted peptide bond with new residue (Thu Jul 05 2018 - 16:34:02 CDT)
  • RE: Total charge problem (Thu Jul 05 2018 - 15:22:24 CDT)
  • RE: Total charge problem (Wed Jul 04 2018 - 11:51:09 CDT)
  • RE: Random Velocities Question (Tue Jul 03 2018 - 22:37:39 CDT)
  • RE: Included Topology (.itp) in gromacs to parameter file for NAMD (Tue Jul 03 2018 - 11:51:12 CDT)
  • RE: Colvars Restraint Question (Mon Jun 25 2018 - 12:18:16 CDT)
  • RE: Colvars Restraint Question (Mon Jun 25 2018 - 12:01:53 CDT)
  • RE: Colvars Restraint Question (Thu Jun 21 2018 - 16:02:54 CDT)
  • RE: Colvars Restraint Question (Thu Jun 21 2018 - 15:22:10 CDT)
  • RE: [NAMD] Apply an electric field only in a specific region (Tue Jun 19 2018 - 08:41:14 CDT)
  • RE: (Fri Jun 15 2018 - 04:34:48 CDT)
  • RE: mail about non bonded parameters (Wed Jun 13 2018 - 05:13:09 CDT)
  • RE: psf from parmed (Fri Jun 08 2018 - 09:30:11 CDT)
  • RE: psf from parmed (Fri Jun 08 2018 - 09:03:43 CDT)
  • RE: NAMD+PLUMED (Sat Jun 02 2018 - 22:03:22 CDT)
  • RE: mail about error in namd compilation (Fri Jun 01 2018 - 11:05:15 CDT)
  • RE: run different simulation of the same system by using different initial velocities (Thu May 24 2018 - 08:28:06 CDT)
  • RE: Are there plans on thermostat groups? (Wed May 16 2018 - 11:33:10 CDT)
  • RE: Creating an infinite graphene sheet (Wed May 16 2018 - 08:30:50 CDT)
  • RE: How to create multiple molecules using psfgen (Tue May 15 2018 - 19:47:10 CDT)
  • RE: How to create multiple molecules using psfgen (Tue May 15 2018 - 18:18:25 CDT)
  • RE: RE: Hard wall on Z direction for ions (Tue May 15 2018 - 08:36:16 CDT)
  • RE: Hard wall on Z direction for ions (Mon May 14 2018 - 10:57:10 CDT)
  • RE: reverting atoms introduced by name into standard PDB ones (Mon May 14 2018 - 07:55:45 CDT)
  • RE: reverting atoms introduced by name into standard PDB ones (Mon May 14 2018 - 07:31:44 CDT)
  • RE: Creating an infinite graphene sheet (Sun May 13 2018 - 13:58:05 CDT)
  • RE: Creating an infinite graphene sheet (Sat May 12 2018 - 16:27:42 CDT)
  • RE: Angle of lone pair in TIP4P 2005 simulation (Tue May 08 2018 - 19:57:31 CDT)
  • RE: Equilibrated TIP4P_2005 Waterbox (Tue May 01 2018 - 15:54:14 CDT)
  • RE: Negative step number (Sat Apr 28 2018 - 23:07:17 CDT)
  • RE: water box tilts during equilibration (Fri Apr 27 2018 - 20:17:10 CDT)
  • RE: Re: vmd-l: PSFGEN 1.6.4 autogenerate PATCH keyword not available (Tue Apr 24 2018 - 12:08:20 CDT)
  • RE: Re: vmd-l: PSFGEN 1.6.4 autogenerate PATCH keyword not available (Tue Apr 24 2018 - 10:59:35 CDT)
  • RE: Question about "useConstantArea" in puresure control model (Mon Apr 23 2018 - 10:54:23 CDT)
  • RE: Question about "useConstantArea" in puresure control model (Sat Apr 21 2018 - 13:49:08 CDT)
  • RE: long simulation and error "integer value too large" (Sat Apr 21 2018 - 08:45:51 CDT)
  • RE: torsion scan (Thu Apr 19 2018 - 18:49:48 CDT)
  • RE: colvar with moving frame of reference (Mon Apr 16 2018 - 14:08:06 CDT)
  • RE: Regarding Topology and Parameterization (Wed Apr 11 2018 - 11:02:35 CDT)
  • RE: calculation of helical axis in NAMD (Sun Apr 08 2018 - 18:28:10 CDT)
  • RE: calculation of helical axis in NAMD (Sat Apr 07 2018 - 10:01:45 CDT)
  • Re: Meaning of warning in output log file (Wed Mar 28 2018 - 09:53:41 CDT)
  • Re: NAMD Simulation in a laptop (Mon Mar 26 2018 - 13:42:06 CDT)
  • Re: Running on GPU (Mon Mar 12 2018 - 14:46:57 CDT)
  • Re: Python based tool for analysis of DCD trajectories (Fri Mar 09 2018 - 12:28:42 CST)
  • Re: Segmentation fault for the tutorial (Wed Mar 07 2018 - 12:30:36 CST)
  • Re: periodic cell has become too small for original patch grid (Tue Mar 06 2018 - 15:53:00 CST)
  • Re: Segmentation fault for the tutorial (Tue Mar 06 2018 - 14:27:43 CST)
  • Re: How to interpret Thermodynamic Integration output (Sun Feb 25 2018 - 17:23:39 CST)
  • Re: (Sun Feb 18 2018 - 12:09:02 CST)
  • Re: namd2 GPU error (Wed Feb 14 2018 - 12:14:28 CST)
  • Re: (Tue Feb 13 2018 - 13:41:42 CST)
  • Re: Dielectric Constant in the gas phase (Fri Feb 09 2018 - 12:18:33 CST)
  • Re: Holding molecules on one side of membrane (Mon Feb 05 2018 - 11:18:56 CST)
  • Re: all-atom to coarse-grained system (Fri Feb 02 2018 - 15:55:35 CST)
  • Re: Double-defined segid, resid for more than 9999 id's (Fri Feb 02 2018 - 14:26:07 CST)
  • Re: Ways to find water molecules passing through the water channel in lipid bilayer (Fri Jan 19 2018 - 13:37:56 CST)
  • Re: Hamiltonian Replica Exchange MD in NAMD (Thu Jan 18 2018 - 16:14:04 CST)
  • Re: UNABLE TO FIND ANGLE PARAMETERS FOR CD OH1 CD (ATOMS 282 284 282) (Tue Jan 16 2018 - 13:54:29 CST)
  • 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)
• Victor Kwan
  • Re: problems running GPU-accelerated namd (Mon Dec 10 2018 - 09:14:02 CST)
  • Re: Ewald size-dependence correction in FEP simulation of an electric dipole (Thu Sep 13 2018 - 10:57:31 CDT)
  • Re: parameter file for ACE and CT3 cap (Mon Sep 03 2018 - 11:52:35 CDT)
  • Re: Total charge problem (Fri Jul 06 2018 - 18:50:36 CDT)
  • At high cutoff: "ERROR: CALCULATED VDWA FORCE MAY NOT MATCH ENERGY! POSSIBLE BUG!" (Sat Jun 30 2018 - 15:35:08 CDT)
  • Re: problem with minimizer (Wed Jun 20 2018 - 11:04:50 CDT)
  • Re: Error during simulation (Thu Jun 14 2018 - 12:22:45 CDT)
  • Re: Equilibrated TIP4P_2005 Waterbox (Tue May 01 2018 - 19:25:34 CDT)
  • Re: Meaning of warning in output log file (Tue Apr 17 2018 - 14:10:33 CDT)
  • Re: all-atom to coarse-grained system (Fri Feb 02 2018 - 14:03:39 CST)
  • Re: Missing Parameters For H3O+ (Tue Jan 23 2018 - 22:16:11 CST)
  • Re: Missing Parameters For H3O+ (Tue Jan 23 2018 - 22:03:20 CST)
  • Re: UNABLE TO FIND ANGLE PARAMETERS FOR CD OH1 CD (ATOMS 282 284 282) (Wed Jan 17 2018 - 11:59:44 CST)
  • 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
  • Reg Membrane simulation (Mon Dec 03 2018 - 07:43:58 CST)
  • Reg membrane hydration (Thu Sep 13 2018 - 21:01:39 CDT)
  • Need help preventing hydration of the lipid-protein interface (Mon Sep 10 2018 - 07:38:50 CDT)
  • Need help preventing hydration of the lipid-protein using tcl script (Mon Sep 10 2018 - 07:34:34 CDT)
  • Reg autioionize plugin (Sat Jul 28 2018 - 01:19:09 CDT)
  • mail about autoionize plugin (Thu Jul 26 2018 - 08:34:43 CDT)
  • reg nan error in namd (Tue Jul 24 2018 - 21:00:50 CDT)
  • MAIL about namd velocity error (Tue Jul 24 2018 - 09:08:08 CDT)
  • mail about usage of water tcl script in membrane (Sat Jun 23 2018 - 08:09:26 CDT)
  • mail reg constraint force (Fri Jun 22 2018 - 07:04:54 CDT)
  • mail about constraints in namd configuration file (Thu Jun 21 2018 - 07:52:17 CDT)
  • mail about non bonded parameters (Mon Jun 11 2018 - 20:58:09 CDT)
  • Mail about force field parameters (Thu Jun 07 2018 - 21:25:38 CDT)
  • mail about error in namd compilation (Fri Jun 01 2018 - 03:08:09 CDT)
  • MAIL REG NAMD PBS SCRIPT on mpi cluster (Thu May 31 2018 - 23:15:09 CDT)
  • Mail from vidhyasankar (Tue May 29 2018 - 22:10:49 CDT)
  • mail reg Namd compilation (Mon May 28 2018 - 03:06:06 CDT)
  • 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)
• Villalain Boullon, Jose
  • Fix aminoacids - error (Sun Nov 04 2018 - 03:18:23 CST)
• Vlad Cojocaru
  • restarting Gaussian accelerated MD fails (Fri Aug 03 2018 - 07:00:30 CDT)
  • 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)
• 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)
• 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)
• William Tao
  • Fwd: Is QM/MM compatible with Colvars? (Thu Jul 19 2018 - 16:20:43 CDT)
  • Is QM/MM compatible with Colvars? (Thu Jul 19 2018 - 16:16:35 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)
• Wintrode, Patrick
  • RE: Mismatch in atom number between psf and dcd files (Mon Oct 01 2018 - 14:11:24 CDT)
  • Mismatch in atom number between psf and dcd files (Fri Sep 28 2018 - 10:04:11 CDT)
• Wright, David
  • NAMD 2.12 using CUDA 8.0 (Thu Apr 20 2017 - 08:40:28 CDT)
• Yasser Bruno Ruiz Blanco
  • Question: constant-pH to standard MD (Fri Aug 24 2018 - 02:34:43 CDT)
  • non uniform attempts distribution in constant pH MD (Wed Jun 13 2018 - 06:04:10 CDT)
  • Missing cphrst file (Mon May 07 2018 - 07:59:15 CDT)
• 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)
• Yi Huizhan
  • performance is more poor for namd 2.12 (Wed Sep 13 2017 - 22:25:13 CDT)
• Yi Lun Lee
  • Using center of mass to calculate the radial distribution function (Fri Nov 09 2018 - 11:37:36 CST)
  • Surface Tension calculation (Fri Oct 19 2018 - 15:33:58 CDT)
  • Re: namd simulation input file setting from NPT to NVT (Mon Sep 10 2018 - 11:19:14 CDT)
  • namd simulation input file setting from NPT to NVT (Thu Sep 06 2018 - 15:31:10 CDT)
  • How to make water stay in the Z direction? (Wed Aug 08 2018 - 11:26:11 CDT)
  • convert a 3d system into a 2d system (Fri Aug 03 2018 - 11:51:03 CDT)
• yjcoshc
  • Re: How to add a C code to NAMD properly? (Wed Dec 05 2018 - 19:45:11 CST)
  • Re: How to add a C code to NAMD properly? (Tue Nov 27 2018 - 19:44:25 CST)
  • Re: How to add a C code to NAMD properly? (Sat Nov 24 2018 - 19:20:22 CST)
  • Do firsttimestep, numsteps and run have maximum values? (Tue Sep 18 2018 - 20:42:05 CDT)
  • Re: AW: How to run a TCL proc at every step in NAMD using callback command? (Thu Jun 14 2018 - 04:06:40 CDT)
  • How to run a TCL proc at every step in NAMD using callback command? (Thu Jun 14 2018 - 03:10:32 CDT)
  • Re: temperature accelerated molecular dynamics (Fri Jun 01 2018 - 01:54:18 CDT)
  • accelMDdihe is not working properly in NAMD after commit e3e849639982dcba9a60c6072c81fdb7cba69759 (Tue May 15 2018 - 20:59:09 CDT)
  • NAMD hangs at "Load balancer assumes all CPUs are same." when runs on an infiniband cluster. (Mon May 14 2018 - 22:08:46 CDT)
  • Re: Get NAMD version from the tcl script interface (Wed May 09 2018 - 19:51:23 CDT)
  • Get NAMD version from the tcl script interface (Wed May 09 2018 - 03:36:18 CDT)
  • Re: CZAR Estimator: grad file (Tue Apr 24 2018 - 04:07:20 CDT)
  • colvars: make an extended CV periodic (Thu Apr 05 2018 - 22:42:01 CDT)
  • colvars: Questions about the metadynamics hillWIdth option. (Wed Mar 21 2018 - 02:39:09 CDT)
  • Re: colvars: How to implement a collective variable of vector type? (Wed Mar 14 2018 - 04:13:19 CDT)
  • Re: colvars: How to implement a collective variable of vector type? (Tue Mar 13 2018 - 03:12:51 CDT)
  • Re: colvars: How to implement a collective variable of vector type? (Mon Mar 12 2018 - 05:01:52 CDT)
  • Re: colvars: How to implement a collective variable of vector type? (Mon Mar 12 2018 - 02:32:56 CDT)
  • colvars: How to implement a collective variable of vector type? (Sat Mar 10 2018 - 03:27:54 CST)
  • 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: How to add a C code to NAMD properly? (Sat Dec 15 2018 - 19:33:28 CST)
  • Re: Do firsttimestep, numsteps and run have maximum values? (Wed Sep 19 2018 - 09:52:56 CDT)
  • Re: colvars: make an extended CV periodic (Mon Apr 09 2018 - 08:22:31 CDT)
  • Re: colvars: make an extended CV periodic (Fri Apr 06 2018 - 21:21:12 CDT)
  • 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)
• Youngwoo Woo
  • Hamiltonian Replica Exchange MD in NAMD (Thu Jan 18 2018 - 16:01:28 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)
• Yu Zhou
  • NAMD-CUDA GPU workload (Mon Apr 02 2018 - 10:11:51 CDT)
  • Trouble with NAMD Win64-CUDA 2.12 on my new PC (Mon Jan 22 2018 - 11:24:26 CST)
• Zachary Ulissi
  • Re: Colvars alternative recommendations (Mon Apr 30 2018 - 09:50:35 CDT)
  • Colvars alternative recommendations (Mon Apr 30 2018 - 08:57:27 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)
• 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)
• å°�澤å�‹
  • very small cell (Fri Jan 06 2017 - 20:29:34 CST)
• 张锦途
  • Question about "useConstantArea" in puresure control model (Sat Apr 21 2018 - 11:00:31 CDT)
• æ�Žè€€
  • problems running GPU-accelerated namd (Sun Dec 09 2018 - 02:02:36 CST)
  • Problems about constraint (conskcol) in umbrella sampling conf file (Wed Nov 21 2018 - 09:44:53 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)
• 董超
  • Re: TCBG Workshop lecture videosðŸ˜�😚😚 (Sun Apr 08 2018 - 14:21:02 CDT)
• 黄å§�姮
  • Targeted MD, "Biased atoms" and "Fitted atoms", RMSD (Wed Nov 29 2017 - 07:27:15 CST)
• 김민재
  • Best water model (Thu Sep 20 2018 - 07:54:34 CDT)
• 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)