NAMD-L: By Date

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NAMD-L: By Date

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About this archive

Starting: Tue Jan 01 2019 - 03:25:13 CST
Ending: Thu Dec 31 2020 - 22:29:33 CST

namdEnergy empy output file Khoualdi Asma Feriel (Thu Dec 31 2020 - 22:29:18 CST)
Re: about geometrical restrain protein on membrane Liqun Zhang (Thu Dec 31 2020 - 15:55:27 CST)
Re: Cavernous Depressions in Water Box Oscar Bastidas (Thu Dec 31 2020 - 15:26:31 CST)
Re: about geometrical restrain protein on membrane Giacomo Fiorin (Thu Dec 31 2020 - 13:08:40 CST)
Re: about geometrical restrain protein on membrane vermaasj (Thu Dec 31 2020 - 12:08:06 CST)
Re: about geometrical restrain protein on membrane Liqun Zhang (Thu Dec 31 2020 - 12:04:59 CST)
Re: about geometrical restrain protein on membrane vermaasj (Thu Dec 31 2020 - 09:06:35 CST)
FEP calculations - membrane protein Luba Simhaev (Thu Dec 31 2020 - 02:45:38 CST)
Re: namdEnergy execution issue -path for namd2 in server Pratik Narain Srivastava (Thu Dec 31 2020 - 00:17:02 CST)
namdEnergy execution issue -path for namd2 in server Khoualdi Asma Feriel (Wed Dec 30 2020 - 23:23:08 CST)
about geometrical restrain protein on membrane Liqun Zhang (Wed Dec 30 2020 - 21:30:37 CST)
Re: Ambiguity among number of residues as counted in VMD and PyMol for RMSF Peter Freddolino (Wed Dec 30 2020 - 12:52:19 CST)
Re: Ambiguity among number of residues as counted in VMD and PyMol for RMSF Mi Yang (Wed Dec 30 2020 - 11:17:23 CST)
Re: Ambiguity among number of residues as counted in VMD and PyMol for RMSF Mi Yang (Wed Dec 30 2020 - 08:04:13 CST)
Re: Ambiguity among number of residues as counted in VMD and PyMol for RMSF varun dewaker (Wed Dec 30 2020 - 01:45:49 CST)
Re: Ambiguity among number of residues as counted in VMD and PyMol for RMSF Mi Yang (Wed Dec 30 2020 - 01:27:03 CST)
Re: Ambiguity among number of residues as counted in VMD and PyMol for RMSF Peter Freddolino (Mon Dec 28 2020 - 23:44:34 CST)
[NAMD] Example of submission script on Comet/Stampede GPUs Sebastian S (Mon Dec 28 2020 - 12:58:27 CST)
Force Field Parametrization Ramon Mendoza Uriarte (Sun Dec 27 2020 - 19:08:44 CST)
Charmm hybrid topology ROPÃ“N-PALACIOS G. (Sat Dec 26 2020 - 15:32:44 CST)
Re: Question about Radius of hexagon; Ramon Mendoza Uriarte (Thu Dec 24 2020 - 13:54:06 CST)
Ambiguity among number of residues as counted in VMD and PyMol for RMSF Mi Yang (Thu Dec 24 2020 - 13:02:23 CST)
Re: ERROR: Atoms moving too fast; simulation has become unstable (2 atoms on patch 42 pe 18). Ashkan Shekaari (Thu Dec 24 2020 - 03:31:57 CST)
Re: ERROR: Atoms moving too fast; simulation has become unstable (2 atoms on patch 42 pe 18). Mi Yang (Thu Dec 24 2020 - 02:44:32 CST)
Question about Radius of hexagon; Seke Keretsu (Thu Dec 24 2020 - 00:33:17 CST)
Re: SMD on Intermembrane Helices Alex Balaeff (Tue Dec 22 2020 - 20:57:43 CST)
Re: Query regarding 'Protein:ligand Standard Binding Free Energies' tutorial Faisal, H M Nasrullah (Tue Dec 22 2020 - 20:52:34 CST)
Re: SMD on Intermembrane Helices Gumbart, JC (Tue Dec 22 2020 - 20:45:09 CST)
Re: Query regarding 'Protein:ligand Standard Binding Free Energies' tutorial Gumbart, JC (Tue Dec 22 2020 - 20:43:36 CST)
Query regarding 'Protein:ligand Standard Binding Free Energies' tutorial Faisal, H M Nasrullah (Tue Dec 22 2020 - 14:39:15 CST)
Re: SMD on Intermembrane Helices Bassam Haddad (Tue Dec 22 2020 - 11:36:36 CST)
Re: FATAL ERROR: can't read "boxtype" Bassam Haddad (Tue Dec 22 2020 - 11:31:23 CST)
Re: SMD on Intermembrane Helices Ashkan Shekaari (Tue Dec 22 2020 - 11:32:32 CST)
Re: SMD on Intermembrane Helices Ashkan Shekaari (Tue Dec 22 2020 - 11:30:54 CST)
SMD on Intermembrane Helices Ethan Croitoru (Tue Dec 22 2020 - 11:15:45 CST)
FATAL ERROR: can't read "boxtype" Seke Keretsu (Sun Dec 20 2020 - 20:24:37 CST)
Re: ERROR: Atoms moving too fast; simulation has become unstable (2 atoms on patch 42 pe 18). Roshan Shrestha (Sat Dec 19 2020 - 08:12:30 CST)
ERROR: Atoms moving too fast; simulation has become unstable (2 atoms on patch 42 pe 18). Mi Yang (Sat Dec 19 2020 - 08:07:11 CST)
Re: Question Colvar o tclforces ROPÃ“N-PALACIOS G. (Fri Dec 18 2020 - 17:31:34 CST)
Re: path CV Stefano Guglielmo (Fri Dec 18 2020 - 11:22:05 CST)
Re: path CV Giacomo Fiorin (Fri Dec 18 2020 - 10:35:30 CST)
path CV Stefano Guglielmo (Fri Dec 18 2020 - 08:48:27 CST)
Re: Assessing total time of run in NAMD Josh Vermaas (Fri Dec 18 2020 - 07:52:09 CST)
Re: Assessing total time of run in NAMD Mi Yang (Fri Dec 18 2020 - 07:38:23 CST)
Re: Centre of mass distance in ABF Aashish Bhatt (Thu Dec 17 2020 - 23:07:59 CST)
Re: Assessing total time of run in NAMD Ingrid Bernardes Santana Martins (Thu Dec 17 2020 - 13:18:23 CST)
Assessing total time of run in NAMD Mi Yang (Thu Dec 17 2020 - 12:50:33 CST)
Re: Centre of mass distance in ABF Giacomo Fiorin (Thu Dec 17 2020 - 09:03:45 CST)
Re: Centre of mass distance in ABF Giacomo Fiorin (Thu Dec 17 2020 - 08:38:08 CST)
Force field for Li-ion batteries electrolytes based on ionic liquids Mauro Sgroi (Thu Dec 17 2020 - 03:46:32 CST)
Re: Installation with tcl Josh Vermaas (Wed Dec 16 2020 - 16:50:53 CST)
Installation with tcl Arturo Fernandez (Wed Dec 16 2020 - 16:22:33 CST)
Re: NAMD QM/MM multi nodes performance bad Francesco Pietra (Tue Dec 15 2020 - 03:37:34 CST)
Re: Water wrapping in the QMMM simulations Alex Balaeff (Mon Dec 14 2020 - 20:13:27 CST)
Re: Water wrapping in the QMMM simulations Marcelo C. R. Melo (Mon Dec 14 2020 - 18:53:57 CST)
Water wrapping in the QMMM simulations Alex Balaeff (Mon Dec 14 2020 - 17:27:11 CST)
RE: NAMD QM/MM multi nodes performance bad James Kress (Mon Dec 14 2020 - 13:21:33 CST)
Re: I frequently get FATAL ERROR: Unable to open text file clc_test.equil.1.colvars.state: File exists when running across multiple nodes Prince, Chandler (Mon Dec 14 2020 - 11:24:57 CST)
Re: NAMD QM/MM multi nodes performance bad Josh Vermaas (Mon Dec 14 2020 - 09:43:03 CST)
Re: I frequently get FATAL ERROR: Unable to open text file clc_test.equil.1.colvars.state: File exists when running across multiple nodes Giacomo Fiorin (Mon Dec 14 2020 - 08:35:16 CST)
I frequently get FATAL ERROR: Unable to open text file clc_test.equil.1.colvars.state: File exists when running across multiple nodes Prince, Chandler (Mon Dec 14 2020 - 08:20:48 CST)
Re: NAMD QM/MM multi nodes performance bad Chunli Yan (Sun Dec 13 2020 - 22:21:52 CST)
Re: NAMD QM/MM multi nodes performance bad Josh Vermaas (Sun Dec 13 2020 - 21:53:31 CST)
NAMD QM/MM multi nodes performance bad Chunli Yan (Sun Dec 13 2020 - 20:47:15 CST)
Question Colvar o tclforces ROPÃ“N-PALACIOS G. (Sat Dec 12 2020 - 13:15:23 CST)
Re: Centre of mass distance in ABF Giacomo Fiorin (Sat Dec 12 2020 - 09:17:32 CST)
Centre of mass distance in ABF Aashish Bhatt (Sat Dec 12 2020 - 02:15:46 CST)
Re: Re: CPU vs GPU Question Rafael Bernardi (Thu Dec 10 2020 - 21:39:48 CST)
Re: Re: CPU vs GPU Question McGuire, Kelly (Thu Dec 10 2020 - 19:40:46 CST)
Re: Re: CPU vs GPU Question Rafael Bernardi (Thu Dec 10 2020 - 19:35:32 CST)
Re: Re: CPU vs GPU Question McGuire, Kelly (Thu Dec 10 2020 - 19:27:16 CST)
Re: About the well-tempered metadynamics convergence.. Giacomo Fiorin (Thu Dec 10 2020 - 13:36:44 CST)
Re: About the well-tempered metadynamics convergence.. zeynab hosseini (Thu Dec 10 2020 - 13:01:48 CST)
About the well-tempered metadynamics convergence.. zeynab hosseini (Thu Dec 10 2020 - 12:49:14 CST)
Re: namd QM/MM on oak ridge ANDES cluster Marcelo C. R. Melo (Thu Dec 10 2020 - 11:06:02 CST)
Re: Re: CPU vs GPU Question Bennion, Brian (Wed Dec 09 2020 - 23:35:11 CST)
Re: Re: CPU vs GPU Question Rafael Bernardi (Wed Dec 09 2020 - 23:26:20 CST)
Re: Re: CPU vs GPU Question vermaasj (Wed Dec 09 2020 - 18:23:32 CST)
Re: Re: CPU vs GPU Question McGuire, Kelly (Wed Dec 09 2020 - 16:36:06 CST)
Re: Re: CPU vs GPU Question McGuire, Kelly (Wed Dec 09 2020 - 16:27:36 CST)
Re: Re: CPU vs GPU Question Gumbart, JC (Wed Dec 09 2020 - 16:19:41 CST)
Re: Re: CPU vs GPU Question McGuire, Kelly (Wed Dec 09 2020 - 16:15:28 CST)
Re: Re: CPU vs GPU Question Gumbart, JC (Wed Dec 09 2020 - 14:56:23 CST)
Re: CPU vs GPU Question Bennion, Brian (Wed Dec 09 2020 - 10:21:54 CST)
Re: NAMD3: how to get the best performance in one gpu node? vermaasj (Wed Dec 09 2020 - 10:18:41 CST)
NAMD3: how to get the best performance in one gpu node? Siyoung Kim (Wed Dec 09 2020 - 03:00:02 CST)
Re: CPU vs GPU Question McGuire, Kelly (Wed Dec 09 2020 - 01:14:47 CST)
Fep setup membrane protein-Drug complex ROPÃ“N-PALACIOS G. (Tue Dec 08 2020 - 13:20:41 CST)
Re: Free Energy Pertubation simulation set-up ROPÃ“N-PALACIOS G. (Sun Dec 06 2020 - 23:33:51 CST)
namd QM/MM on oak ridge ANDES cluster Chunli Yan (Sun Dec 06 2020 - 19:14:06 CST)
Free Energy Pertubation simulation set-up alli suliat (Sun Dec 06 2020 - 18:19:23 CST)
RE: Hydrogen Mass Repartitioning James Kress (Sat Dec 05 2020 - 15:43:49 CST)
Re: Hydrogen Mass Repartitioning Rafael Bernardi (Sat Dec 05 2020 - 14:27:45 CST)
NAMD3 segfault while writing restart files David Sept (Sat Dec 05 2020 - 11:09:55 CST)
Re: CPU vs GPU Question Mohammed umar Sheriff (Sat Dec 05 2020 - 05:33:54 CST)
RE: Hydrogen Mass Repartitioning James Kress (Fri Dec 04 2020 - 17:32:44 CST)
Membrana-protein-lig protocol ROPÃ“N-PALACIOS G. (Fri Dec 04 2020 - 12:42:24 CST)
AW: Hydrogen Mass Repartitioning Norman Geist (Fri Dec 04 2020 - 03:00:59 CST)
Re: Hydrogen Mass Repartitioning Gumbart, JC (Thu Dec 03 2020 - 21:57:23 CST)
RE: Hydrogen Mass Repartitioning Mohammed umar Sheriff (Thu Dec 03 2020 - 21:35:10 CST)
Re: CPU vs GPU Question McGuire, Kelly (Thu Dec 03 2020 - 21:05:05 CST)
Hydrogen Mass Repartitioning McGuire, Kelly (Thu Dec 03 2020 - 21:04:50 CST)
Re: Re: Termination between Minimization to Equilibration Ramon Mendoza Uriarte (Thu Dec 03 2020 - 13:40:23 CST)
Re: Restarting QMMM Francesco Pietra (Thu Dec 03 2020 - 04:42:26 CST)
Re: Re: Termination between Minimization to Equilibration Peter Freddolino (Wed Dec 02 2020 - 20:07:58 CST)
Re: Re: Termination between Minimization to Equilibration Ramon Mendoza Uriarte (Wed Dec 02 2020 - 19:48:32 CST)
Re: Re: Termination between Minimization to Equilibration Peter Freddolino (Wed Dec 02 2020 - 19:35:52 CST)
Re: Termination between Minimization to Equilibration Ramon Mendoza Uriarte (Wed Dec 02 2020 - 18:11:37 CST)
Re: CPU vs GPU Question Bennion, Brian (Wed Dec 02 2020 - 17:05:50 CST)
CPU vs GPU Question McGuire, Kelly (Wed Dec 02 2020 - 16:51:37 CST)
Re: Restarting QMMM Marcelo C. R. Melo (Wed Dec 02 2020 - 14:44:45 CST)
Termination between Minimization to Equilibration Ramon Mendoza Uriarte (Wed Dec 02 2020 - 13:43:17 CST)
Re: Advice for Protein Mutation FEP Calculations Brian Radak (Tue Dec 01 2020 - 13:45:16 CST)
Advice for Protein Mutation FEP Calculations Matthew Guberman-Pfeffer (Tue Dec 01 2020 - 10:27:43 CST)
Re: NamdEnergy Nonbonded H-bonds Peter Freddolino (Mon Nov 30 2020 - 19:28:16 CST)
Re: Compile NAMD on Windows 64 bit; nocuda, multicore Mortimer Hemmit (Mon Nov 30 2020 - 14:39:09 CST)
NamdEnergy Nonbonded H-bonds Francesco Pietra (Mon Nov 30 2020 - 11:06:52 CST)
Re: Implicit MD is slower than explcit MD! Aravinda Munasinghe (Sun Nov 29 2020 - 09:01:30 CST)
Re: not getting NAMD multicopy simulation started Josh Vermaas (Wed Nov 25 2020 - 13:22:55 CST)
Re: not getting NAMD multicopy simulation started Josh Vermaas (Wed Nov 25 2020 - 10:11:58 CST)
Implicit MD is slower than explcit MD! Krishna Vkm (Mon Nov 23 2020 - 05:18:51 CST)
Re: Cavernous Depressions in Water Box Alex Balaeff (Sun Nov 22 2020 - 12:21:45 CST)
Re: Cavernous Depressions in Water Box Peter Freddolino (Sat Nov 21 2020 - 21:14:01 CST)
Cavernous Depressions in Water Box Oscar Bastidas (Sat Nov 21 2020 - 19:22:14 CST)
Re: regarding constant PH simulation zahra nabavi (Fri Nov 20 2020 - 11:15:36 CST)
Re: regarding constant PH simulation Brian Radak (Fri Nov 20 2020 - 07:31:12 CST)
Re: regarding constant PH simulation Jeff Comer (Thu Nov 19 2020 - 21:25:24 CST)
regarding constant PH simulation zahra nabavi (Thu Nov 19 2020 - 21:07:35 CST)
Restarting QMMM Francesco Pietra (Thu Nov 19 2020 - 05:13:41 CST)
Re: Calculating 2D PMF from 1D eABF simulations using CZAR estimator. Abhishek Acharya (Thu Nov 19 2020 - 00:02:49 CST)
Re: Exit code 127 with QMMM Francesco Pietra (Tue Nov 17 2020 - 14:13:29 CST)
Re: Exit code 127 with QMMM Marcelo C. R. Melo (Tue Nov 17 2020 - 12:18:36 CST)
Re: Exit code 127 with QMMM Francesco Pietra (Tue Nov 17 2020 - 03:25:07 CST)
performing SMD in Z using colvar module RopÃ³n-Palacios G. (Mon Nov 16 2020 - 16:16:33 CST)
Re: Calculating 2D PMF from 1D eABF simulations using CZAR estimator. JÃ©rÃ´me HÃ©nin (Mon Nov 16 2020 - 14:10:50 CST)
Re: Setting up QM-MM with homotrimer Francesco Pietra (Mon Nov 16 2020 - 11:54:04 CST)
Re: NAMD took more than 1 day on 36 cpu to complete 1ns simulation for a 77000 system Peter Freddolino (Mon Nov 16 2020 - 11:40:28 CST)
Re: Exit code 127 with QMMM Marcelo C. R. Melo (Mon Nov 16 2020 - 11:26:49 CST)
Re: NAMD took more than 1 day on 36 cpu to complete 1ns simulation for a 77000 system Josh Vermaas (Mon Nov 16 2020 - 11:13:36 CST)
Exit code 127 with QMMM Francesco Pietra (Mon Nov 16 2020 - 10:58:30 CST)
Re: NAMD took more than 1 day on 36 cpu to complete 1ns simulation for a 77000 system Josh Vermaas (Mon Nov 16 2020 - 10:01:54 CST)
NAMD took more than 1 day on 36 cpu to complete 1ns simulation for a 77000 system Seke Keretsu (Mon Nov 16 2020 - 01:55:06 CST)
IMD simulation RopÃ³n-Palacios G. (Thu Nov 12 2020 - 19:03:23 CST)
Re: Adding bias potential Pang, Yui Tik (Thu Nov 12 2020 - 15:25:58 CST)
Adding bias potential Peter Rosenquist (Thu Nov 12 2020 - 15:00:38 CST)
Re: Calculating 2D PMF from 1D eABF simulations using CZAR estimator. Abhishek Acharya (Wed Nov 11 2020 - 16:13:39 CST)
Re: Calculating 2D PMF from 1D eABF simulations using CZAR estimator. JÃ©rÃ´me HÃ©nin (Wed Nov 11 2020 - 13:53:36 CST)
Calculating 2D PMF from 1D eABF simulations using CZAR estimator. Abhishek Acharya (Wed Nov 11 2020 - 13:04:29 CST)
Re: FEP/Î»-REMD Simulation error RopÃ³n-Palacios G. (Mon Nov 09 2020 - 14:30:01 CST)
Re: FEP/Î»-REMD Simulation error Alao, John-Paul (Mon Nov 09 2020 - 13:00:39 CST)
Re: FEP/Î»-REMD Simulation error ROPÃ“N-PALACIOS G. (Mon Nov 09 2020 - 12:51:31 CST)
FEP/Î»-REMD Simulation error Alao, John-Paul (Mon Nov 09 2020 - 11:01:26 CST)
Re: psf generation for multiple trehalose molecules Ritu Arora (Mon Nov 09 2020 - 10:33:55 CST)
Re: psf generation for multiple trehalose molecules Ritu Arora (Mon Nov 09 2020 - 04:12:07 CST)
Re: psf generation for multiple trehalose molecules Peter Freddolino (Mon Nov 09 2020 - 00:08:01 CST)
Re: psf generation for multiple trehalose molecules Ritu Arora (Sun Nov 08 2020 - 21:46:15 CST)
Re: psf generation for multiple trehalose molecules Josh Vermaas (Sun Nov 08 2020 - 20:13:20 CST)
psf generation for multiple trehalose molecules Ritu Arora (Sun Nov 08 2020 - 18:24:15 CST)
Setting up QM-MM with homotrimer Francesco Pietra (Thu Nov 05 2020 - 10:52:27 CST)
model with TIP4 water minimization getting crashed every time Faisal, H M Nasrullah (Wed Nov 04 2020 - 10:47:22 CST)
Re: Rmsd calculation Asmi Mahmood (Wed Nov 04 2020 - 04:12:00 CST)
Re: Rmsd calculation Atanu Maity (Tue Nov 03 2020 - 19:42:33 CST)
Rmsd calculation Asmi Mahmood (Tue Nov 03 2020 - 00:22:54 CST)
Re: NPT then NVT simulation in a single config file for water box? Hemanth Haridas (Tue Nov 03 2020 - 00:27:18 CST)
Re: rmsd colvar Giacomo Fiorin (Mon Nov 02 2020 - 08:57:31 CST)
rmsd Asmi Mahmood (Mon Nov 02 2020 - 04:41:35 CST)
rmsd colvar Stefano Guglielmo (Sun Nov 01 2020 - 10:17:10 CST)
Re: NPT then NVT simulation in a single config file for water box? Tanooj Shah (Sun Nov 01 2020 - 09:36:15 CST)
NPT then NVT simulation in a single config file for water box? Tanooj Shah (Fri Oct 30 2020 - 21:52:19 CDT)
Re: restart file Peter Freddolino (Fri Oct 30 2020 - 10:43:03 CDT)
restart file Constantin Gunkel (Fri Oct 30 2020 - 09:45:17 CDT)
Re: model with TIP4 water minimization getting crashed every time Faisal, H M Nasrullah (Thu Oct 29 2020 - 17:02:44 CDT)
Re: Problem Peter Freddolino (Thu Oct 29 2020 - 06:57:17 CDT)
Problem Constantin Gunkel (Wed Oct 28 2020 - 20:15:43 CDT)
model with TIP4 water minimization getting crashed every time Faisal, H M Nasrullah (Wed Oct 28 2020 - 09:44:24 CDT)
Re: Running multiple walker metadynamics replicas as a bundle zeynab hosseini (Wed Oct 28 2020 - 06:18:55 CDT)
Re: Running multiple walker metadynamics replicas as a bundle zeynab hosseini (Wed Oct 28 2020 - 04:02:35 CDT)
Re: Running multiple walker metadynamics replicas as a bundle zeynab hosseini (Wed Oct 28 2020 - 04:01:19 CDT)
RE: Can Namd 2.14 and genpsf 2.0 process halogen bonds? Pang, Yui Tik (Tue Oct 27 2020 - 13:00:14 CDT)
model with TIP4 water minimization getting crashed every time Faisal, H M Nasrullah (Tue Oct 27 2020 - 10:04:49 CDT)
Re: MM/QM with namd Asmi Mahmood (Tue Oct 27 2020 - 09:58:58 CDT)
Re: MM/QM with namd Marcelo C. R. Melo (Tue Oct 27 2020 - 09:39:21 CDT)
Re: MM/QM with namd Asmi Mahmood (Tue Oct 27 2020 - 04:37:40 CDT)
Compile NAMD with PLUMED Jiali Wang (Mon Oct 26 2020 - 22:15:28 CDT)
Re: Peter Freddolino (Mon Oct 26 2020 - 19:16:57 CDT)
Re: Jeff Comer (Mon Oct 26 2020 - 18:37:05 CDT)
Re: Josh Vermaas (Mon Oct 26 2020 - 18:21:20 CDT)
Can Namd 2.14 and genpsf 2.0 process halogen bonds? Nan Li (Mon Oct 26 2020 - 17:15:06 CDT)
(no subject) Mersch, Kacey (Mon Oct 26 2020 - 16:33:00 CDT)
Re: Running multiple walker metadynamics replicas as a bundle Giacomo Fiorin (Mon Oct 26 2020 - 13:49:10 CDT)
model with TIP4 water minimization getting crashed every time Faisal, H M Nasrullah (Mon Oct 26 2020 - 12:50:33 CDT)
Re: Running multiple walker metadynamics replicas as a bundle Josh Vermaas (Mon Oct 26 2020 - 11:04:02 CDT)
Running multiple walker metadynamics replicas as a bundle zeynab hosseini (Mon Oct 26 2020 - 07:33:11 CDT)
Re: Repulsive wall potential or spherical boundry conditions Almeida-Hernández, Yasser, Dr. (Fri Oct 23 2020 - 12:58:25 CDT)
Re: Repulsive wall potential or spherical boundry conditions Giacomo Fiorin (Fri Oct 23 2020 - 10:31:17 CDT)
Repulsive wall potential or spherical boundry conditions Almeida-Hernández, Yasser, Dr. (Fri Oct 23 2020 - 05:13:55 CDT)
Re: well-tempered metadynamics deforms the water box and the system becomes unstable.. zeynab hosseini (Fri Oct 23 2020 - 04:21:33 CDT)
How to Selectively Scale Interactions Matthew Guberman-Pfeffer (Thu Oct 22 2020 - 23:30:47 CDT)
Re: well-tempered metadynamics deforms the water box and the system becomes unstable.. Giacomo Fiorin (Thu Oct 22 2020 - 15:45:17 CDT)
Re: well-tempered metadynamics deforms the water box and the system becomes unstable.. zeynab hosseini (Thu Oct 22 2020 - 03:10:38 CDT)
Re: well-tempered metadynamics deforms the water box and the system becomes unstable.. Giacomo Fiorin (Wed Oct 21 2020 - 14:08:35 CDT)
Re: well-tempered metadynamics deforms the water box and the system becomes unstable.. zeynab hosseini (Wed Oct 21 2020 - 13:03:28 CDT)
Re: well-tempered metadynamics deforms the water box and the system becomes unstable.. Giacomo Fiorin (Wed Oct 21 2020 - 10:26:15 CDT)
Re: well-tempered metadynamics deforms the water box and the system becomes unstable.. zeynab hosseini (Wed Oct 21 2020 - 09:59:40 CDT)
Re: well-tempered metadynamics deforms the water box and the system becomes unstable.. zeynab hosseini (Wed Oct 21 2020 - 09:47:29 CDT)
Re: Protein:ligand standard binding free energies clarification question JC Gumbart (Tue Oct 20 2020 - 23:33:22 CDT)
Velocity MAP calculation in VMD Abhijit Gogoi (Wed Oct 21 2020 - 03:59:13 CDT)
Protein:ligand standard binding free energies clarification question Ethan Croitoru (Tue Oct 20 2020 - 21:14:53 CDT)
Re: well-tempered metadynamics deforms the water box and the system becomes unstable.. Giacomo Fiorin (Tue Oct 20 2020 - 16:01:43 CDT)
Re: well-tempered metadynamics deforms the water box and the system becomes unstable.. zeynab hosseini (Tue Oct 20 2020 - 15:33:10 CDT)
Re: NAMD 2.14 fatal error executing tcl script Alsaloum, Matthew (Tue Oct 20 2020 - 11:10:20 CDT)
Re: NAMD 2.14 fatal error executing tcl script Josh Vermaas (Mon Oct 19 2020 - 14:01:33 CDT)
Re: well-tempered metadynamics deforms the water box and the system becomes unstable.. Giacomo Fiorin (Mon Oct 19 2020 - 13:34:20 CDT)
Re: well-tempered metadynamics deforms the water box and the system becomes unstable.. zeynab hosseini (Mon Oct 19 2020 - 12:36:07 CDT)
NAMD 2.14 fatal error executing tcl script Alsaloum, Matthew (Sun Oct 18 2020 - 21:06:58 CDT)
Re: MM/QM with namd Marcelo C. R. Melo (Fri Oct 16 2020 - 11:37:33 CDT)
Re: MM/QM with namd jing liang (Fri Oct 16 2020 - 09:38:48 CDT)
Re: well-tempered metadynamics deforms the water box and the system becomes unstable.. Giacomo Fiorin (Fri Oct 16 2020 - 09:10:26 CDT)
well-tempered metadynamics deforms the water box and the system becomes unstable.. zeynab hosseini (Fri Oct 16 2020 - 03:44:27 CDT)
GPU Acceleration and Drude Simulations Michael Robinson (Fri Oct 16 2020 - 01:23:57 CDT)
Re: MM/QM with namd Marcelo C. R. Melo (Thu Oct 15 2020 - 12:02:38 CDT)
MM/QM with namd Asmi Mahmood (Thu Oct 15 2020 - 08:04:32 CDT)
NAMD QM/MM simulations jing liang (Thu Oct 15 2020 - 03:18:48 CDT)
Re: Targeted MD in NAMD 3.0? Josh Vermaas (Wed Oct 14 2020 - 09:28:14 CDT)
Re: Targeted MD in NAMD 3.0? Giacomo Fiorin (Wed Oct 14 2020 - 09:15:30 CDT)
RE: A home PC to run NAMD simulations Sanjay Hari (Tue Oct 13 2020 - 15:03:07 CDT)
Targeted MD in NAMD 3.0? Smith, Harper E. (Tue Oct 13 2020 - 11:18:03 CDT)
Re: A home PC to run NAMD simulations Adupa Vasista (Sun Oct 11 2020 - 04:13:12 CDT)
A home PC to run NAMD simulations Harish Srinivasan (Sun Oct 11 2020 - 02:02:27 CDT)
Re: Question about PBC and RMSD Pratik Narain Srivastava (Sat Oct 10 2020 - 03:22:28 CDT)
Question about PBC and RMSD alli suliat (Sat Oct 10 2020 - 00:31:11 CDT)
Formation of nanoparticle ligand complex Yuvam Bhateja (Fri Oct 09 2020 - 14:09:30 CDT)
Re: REUS zeynab hosseini (Fri Oct 09 2020 - 13:51:32 CDT)
Re: Quary resgading Adaptive biasing force Giacomo Fiorin (Thu Oct 08 2020 - 09:36:35 CDT)
Quary resgading Adaptive biasing force Aashish Bhatt (Thu Oct 08 2020 - 08:43:44 CDT)
Re: COLVARs for Cremer-Pople puckering parameters in NAMD Metadynamics JÃ©rÃ´me HÃ©nin (Wed Oct 07 2020 - 05:26:59 CDT)
Re: Transition State Search BY NAMD Pawel Kedzierski (Wed Oct 07 2020 - 02:57:04 CDT)
Transition State Search BY NAMD è¾›å¿—å® (Wed Oct 07 2020 - 02:26:58 CDT)
amber force field divyabharathi korlepara (Tue Oct 06 2020 - 23:51:49 CDT)
COLVARs for Cremer-Pople puckering parameters in NAMD Metadynamics Chythra J N (Tue Oct 06 2020 - 21:57:46 CDT)
shifting of ions from -z to +z in a single frame(1ps) Basanta Acharya (Tue Oct 06 2020 - 21:54:07 CDT)
Ligand coated Silver Nanoparticle. Yuvam Bhateja (Tue Oct 06 2020 - 11:19:02 CDT)
CHARMM36 to Drude conversion for NAMD Almeida-Hernández, Yasser, Dr. (Tue Oct 06 2020 - 03:37:32 CDT)
Re: psf generation Pratik Narain Srivastava (Tue Oct 06 2020 - 01:37:04 CDT)
Re: NAMD doesn't use my CUDA enabled GPU Pratik Narain Srivastava (Tue Oct 06 2020 - 01:36:01 CDT)
Re: Optimum time for md run in i3 laptop Pratik Narain Srivastava (Tue Oct 06 2020 - 01:35:06 CDT)
Optimum time for md run in i3 laptop achchirangeebi (Tue Oct 06 2020 - 01:30:55 CDT)
NAMD doesn't use my CUDA enabled GPU Rimon Riju (Tue Oct 06 2020 - 01:17:45 CDT)
Re: psf generation divyabharathi korlepara (Tue Oct 06 2020 - 00:45:24 CDT)
Re: Regarding "lossiness" of namd on GPUs Bassam Haddad (Mon Oct 05 2020 - 16:30:50 CDT)
Re: Regarding "lossiness" of namd on GPUs Victor Kwan (Mon Oct 05 2020 - 16:26:54 CDT)
Re: Regarding "lossiness" of namd on GPUs Josh Vermaas (Mon Oct 05 2020 - 16:26:29 CDT)
Regarding "lossiness" of namd on GPUs Bassam Haddad (Mon Oct 05 2020 - 16:19:26 CDT)
Re: psf generation Ashkan Shekaari (Mon Oct 05 2020 - 13:52:43 CDT)
Re: psf generation Josh Vermaas (Mon Oct 05 2020 - 11:51:24 CDT)
Re: psf generation Sanjay Hari (Mon Oct 05 2020 - 10:31:16 CDT)
psf generation divyabharathi korlepara (Mon Oct 05 2020 - 10:13:35 CDT)
Re: Drude equilibration Almeida-Hernández, Yasser, Dr. (Mon Oct 05 2020 - 03:46:46 CDT)
Re: Drude equilibration Almeida-Hernández, Yasser, Dr. (Mon Oct 05 2020 - 03:35:52 CDT)
Drude equilibration Almeida-Hernández, Yasser, Dr. (Mon Oct 05 2020 - 03:08:48 CDT)
How to determine the residue of qmLSSRef in QwikMD? è¾›å¿—å® (Sun Oct 04 2020 - 20:28:28 CDT)
Re: renumbering and rewriting a trajectory Kodituwakku,Dimuthu Nirmani (Sat Oct 03 2020 - 22:12:05 CDT)
Re:Re: QwikMD--ERROR) Unable to ascertain relative endianness of remote machine è¾›å¿—å® (Sat Oct 03 2020 - 07:19:56 CDT)
Re:Re: QwikMD--ERROR) Unable to ascertain relative endianness of remote machine è¾›å¿—å® (Fri Oct 02 2020 - 20:47:05 CDT)
Re: QwikMD--ERROR) Unable to ascertain relative endianness of remote machine Victor Kwan (Fri Oct 02 2020 - 19:23:36 CDT)
Incorrect restarting velocities Kodituwakku,Dimuthu Nirmani (Fri Oct 02 2020 - 09:53:02 CDT)
Re: renumbering and rewriting a trajectory Kodituwakku,Dimuthu Nirmani (Fri Oct 02 2020 - 09:28:13 CDT)
Re: TMD questions - refined Nadia Elghobashi-Meinhardt (Fri Oct 02 2020 - 03:54:52 CDT)
QwikMD--ERROR) Unable to ascertain relative endianness of remote machine è¾›å¿—å® (Fri Oct 02 2020 - 03:18:39 CDT)
Re: TMD questions - refined Ashkan Shekaari (Thu Oct 01 2020 - 09:14:33 CDT)
TMD questions - refined Nadia Elghobashi-Meinhardt (Thu Oct 01 2020 - 08:59:18 CDT)
renumbering and rewriting a trajectory Kodituwakku,Dimuthu Nirmani (Wed Sep 30 2020 - 10:30:25 CDT)
REUS Ashkan Shekaari (Mon Sep 28 2020 - 11:37:29 CDT)
WHAM Ashkan Shekaari (Mon Sep 28 2020 - 08:40:02 CDT)
TMD config parameters Nadia Elghobashi-Meinhardt (Fri Sep 25 2020 - 02:48:06 CDT)
VMD nc file problem Seibold, Steve Allan (Thu Sep 24 2020 - 09:20:51 CDT)
Re: Farnesylated Cysteine Xu, Shenyuan (Wed Sep 23 2020 - 20:39:05 CDT)
Re: NAMD trajectory with MMPBSA.py I. Camps (Wed Sep 23 2020 - 09:54:08 CDT)
Re: namd3 on centos 6 Giacomo Fiorin (Wed Sep 23 2020 - 09:40:04 CDT)
NAMD trajectory with MMPBSA.py Asmi Mahmood (Wed Sep 23 2020 - 09:36:52 CDT)
REMD Problem Anup Prasad (Wed Sep 23 2020 - 05:47:08 CDT)
Re: namd3 on centos 6 Pratik Narain Srivastava (Wed Sep 23 2020 - 02:48:21 CDT)
Re: Getting high performance on multi-copy (replica) GPU simulations Victor Zhao (Wed Sep 23 2020 - 00:04:27 CDT)
Re: Getting high performance on multi-copy (replica) GPU simulations Josh Vermaas (Tue Sep 22 2020 - 13:04:26 CDT)
Getting high performance on multi-copy (replica) GPU simulations Victor Zhao (Tue Sep 22 2020 - 11:12:58 CDT)
Regarding to the parameters of QwikMD è¾›å¿—å® (Tue Sep 22 2020 - 09:42:12 CDT)
Re: namd3 on centos 6 Axel Kohlmeyer (Mon Sep 21 2020 - 17:34:24 CDT)
Re: Replica exchange problem Julian David Baquero Contreras (Mon Sep 21 2020 - 16:54:35 CDT)
RE: namd3 on centos 6 Sanjay Hari (Mon Sep 21 2020 - 16:46:36 CDT)
Re: Replica exchange problem Josh Vermaas (Mon Sep 21 2020 - 15:36:19 CDT)
Re: Farnesylated Cysteine Josh Vermaas (Mon Sep 21 2020 - 11:23:35 CDT)
Error running command for QM forces calculation è¾›å¿—å® (Mon Sep 21 2020 - 01:21:20 CDT)
Re: namd3 on centos 6 Victor Kwan (Sun Sep 20 2020 - 13:07:50 CDT)
Farnesylated Cysteine Xu, Shenyuan (Sun Sep 20 2020 - 10:55:46 CDT)
Re: namd3 on centos 6 Pratik Narain Srivastava (Sat Sep 19 2020 - 09:04:24 CDT)
namd3 on centos 6 Boyan Bonev (Sat Sep 19 2020 - 07:49:07 CDT)
(no subject) shyam sharma (Fri Sep 18 2020 - 04:20:27 CDT)
(no subject) shyam sharma (Fri Sep 18 2020 - 03:58:41 CDT)
Re: Convert solvated CHARMM PDB + PSF to Amber Michael Robinson (Fri Sep 18 2020 - 02:22:16 CDT)
Re: Convert solvated CHARMM PDB + PSF to Amber Gianluca Interlandi (Thu Sep 17 2020 - 20:00:59 CDT)
Re: Output of harmonic restrains effect in alchemical route of protein-ligand binding free energy calculation Giacomo Fiorin (Thu Sep 17 2020 - 16:48:19 CDT)
Re: Output of harmonic restrains effect in alchemical route of protein-ligand binding free energy calculation Faisal, H M Nasrullah (Thu Sep 17 2020 - 16:07:10 CDT)
Re: Output of harmonic restrains effect in alchemical route of protein-ligand binding free energy calculation Giacomo Fiorin (Thu Sep 17 2020 - 14:42:53 CDT)
Re: Output of harmonic restrains effect in alchemical route of protein-ligand binding free energy calculation Faisal, H M Nasrullah (Thu Sep 17 2020 - 13:20:05 CDT)
Re: NAN in output of aMD Ritu Arora (Thu Sep 17 2020 - 10:54:33 CDT)
Re: Output of harmonic restrains effect in alchemical route of protein-ligand binding free energy calculation Giacomo Fiorin (Thu Sep 17 2020 - 10:40:50 CDT)
Output of harmonic restrains effect in alchemical route of protein-ligand binding free energy calculation Faisal, H M Nasrullah (Thu Sep 17 2020 - 10:07:35 CDT)
Re: Convert solvated CHARMM PDB + PSF to Amber Michael Robinson (Wed Sep 16 2020 - 23:08:52 CDT)
Atom outside of the MSM grid in NVT simulation - Semiperiodic boundaries Guna Mandava (Wed Sep 16 2020 - 21:20:28 CDT)
Re: NAN in output of aMD Giacomo Fiorin (Wed Sep 16 2020 - 16:25:36 CDT)
MD simulation of a molecule with a halogen Federico Rui (Wed Sep 16 2020 - 11:22:17 CDT)
simulated annealing Stefano Guglielmo (Wed Sep 16 2020 - 10:53:09 CDT)
Re: Post processing NAMD trajectory Kodituwakku,Dimuthu Nirmani (Tue Sep 15 2020 - 20:46:39 CDT)
Convert solvated CHARMM PDB + PSF to Amber Gianluca Interlandi (Tue Sep 15 2020 - 20:34:44 CDT)
Re: Re: AMBER input and REST2 leads to crash Victor Zhao (Tue Sep 15 2020 - 17:33:54 CDT)
Re: NAN in output of aMD Ritu Arora (Tue Sep 15 2020 - 13:26:11 CDT)
Re: Re: AMBER input and REST2 leads to crash David Hardy (Tue Sep 15 2020 - 12:26:55 CDT)
Re: Support for drudeNbthole on CUDA version of NAMD David Hardy (Tue Sep 15 2020 - 12:06:22 CDT)
Re: Re: AMBER input and REST2 leads to crash Victor Zhao (Tue Sep 15 2020 - 12:01:43 CDT)
Re: AMBER input and REST2 leads to crash Victor Zhao (Tue Sep 15 2020 - 11:04:16 CDT)
Parameters and topology files regarding arsorite(ASO3 - - -) Basanta Acharya (Tue Sep 15 2020 - 07:29:51 CDT)
(no subject) Basanta Acharya (Tue Sep 15 2020 - 07:27:03 CDT)
Re: NAN in output of aMD HEMANTH H (Tue Sep 15 2020 - 00:55:59 CDT)
AMBER input and REST2 leads to crash Victor Zhao (Tue Sep 15 2020 - 00:53:42 CDT)
NAN in output of aMD Ritu Arora (Mon Sep 14 2020 - 09:33:03 CDT)
Re: Post processing NAMD trajectory Alex Balaeff (Sun Sep 13 2020 - 21:26:34 CDT)
Re: Post processing NAMD trajectory Josh Vermaas (Sun Sep 13 2020 - 15:56:12 CDT)
Re: Post processing NAMD trajectory Josh Vermaas (Sun Sep 13 2020 - 15:55:57 CDT)
Hybrid Coarse Grain/ all atom simulation in NAMD Shadi Rahnama (Sun Sep 13 2020 - 14:18:26 CDT)
Re: Equilibration of a solvated CNT using C36 Axel Kohlmeyer (Sun Sep 13 2020 - 13:14:18 CDT)
Post processing NAMD trajectory Kodituwakku,Dimuthu Nirmani (Sun Sep 13 2020 - 13:08:14 CDT)
Re: toppar_water_ions.str NAMD format for last version of C36 (on July 2020) zeynab hosseini (Sun Sep 13 2020 - 10:47:16 CDT)
Re: toppar_water_ions.str NAMD format for last version of C36 (on July 2020) Josh Vermaas (Sun Sep 13 2020 - 10:45:31 CDT)
Equilibration of a solvated CNT using C36 zeynab hosseini (Sun Sep 13 2020 - 09:01:52 CDT)
FATAL ERROR: Error running command for QM forces calculation è¾›å¿—å® (Sun Sep 13 2020 - 07:52:13 CDT)
Re: toppar_water_ions.str NAMD format for last version of C36 (on July 2020) zeynab hosseini (Wed Sep 02 2020 - 07:03:11 CDT)
Re: toppar_water_ions.str NAMD format for last version of C36 (on July 2020) Josh Vermaas (Sat Sep 12 2020 - 16:44:27 CDT)
toppar_water_ions.str NAMD format for last version of C36 (on July 2020) zeynab hosseini (Tue Sep 01 2020 - 13:29:11 CDT)
Re: Umbrella sampling of AA and CNT dissociation, pmf doesn't flatten & reduces over large distances... zeynab hosseini (Tue Sep 01 2020 - 12:52:30 CDT)
Re:Re: ERROR: Atoms moving too fast; simulation has become unstable è¾›å¿—å® (Thu Sep 10 2020 - 04:35:27 CDT)
Re: ERROR: Atoms moving too fast; simulation has become unstable Natalia Ostrowska (Thu Sep 10 2020 - 03:40:27 CDT)
ERROR: Atoms moving too fast; simulation has become unstable è¾›å¿—å® (Wed Sep 09 2020 - 23:03:53 CDT)
Re: DRMS Colvar Giacomo Fiorin (Wed Sep 09 2020 - 14:55:47 CDT)
DRMS Colvar Ethan Croitoru (Wed Sep 09 2020 - 14:25:33 CDT)
Re:Re: Re: Re: Issue regarding to the speed of QM/MM è¾›å¿—å® (Tue Sep 08 2020 - 20:46:24 CDT)
Re: Re: Re: Issue regarding to the speed of QM/MM Marcelo C. R. Melo (Tue Sep 08 2020 - 20:32:05 CDT)
Re: Basics of MD JC Gumbart (Tue Sep 08 2020 - 13:51:42 CDT)
RE: Basics of MD Lennart Nilsson (Tue Sep 08 2020 - 13:05:28 CDT)
Re: Basics of MD JC Gumbart (Tue Sep 08 2020 - 11:46:16 CDT)
Re: Basics of MD Peter Freddolino (Tue Sep 08 2020 - 10:17:37 CDT)
Re: Re: Issue regarding to the speed of QM/MM Marcelo C. R. Melo (Tue Sep 08 2020 - 08:27:36 CDT)
Re:Re: Issue regarding to the speed of QM/MM è¾›å¿—å® (Tue Sep 08 2020 - 07:20:57 CDT)
Basics of MD Raman Preet Singh (Tue Sep 08 2020 - 05:10:10 CDT)
Re: Issue regarding to the speed of QM/MM Axel Kohlmeyer (Mon Sep 07 2020 - 14:09:51 CDT)
Re: Issue regarding to the speed of QM/MM Marcelo C. R. Melo (Mon Sep 07 2020 - 13:47:09 CDT)
Re: Issue regarding to the speed of QM/MM Alex Balaeff (Mon Sep 07 2020 - 13:36:29 CDT)
Re: Issue regarding to the speed of QM/MM Marcelo C. R. Melo (Mon Sep 07 2020 - 13:11:07 CDT)
Re: How to treat electrostatics in crystal lattice MD simulation Peter Freddolino (Mon Sep 07 2020 - 09:46:13 CDT)
How to treat electrostatics in crystal lattice MD simulation Matthew Guberman-Pfeffer (Mon Sep 07 2020 - 07:02:17 CDT)
Issue regarding to the speed of QM/MM è¾›å¿—å® (Mon Sep 07 2020 - 03:40:03 CDT)
<< Setting the simulation time parameters >> I. Camps (Sat Sep 05 2020 - 13:44:17 CDT)
<< Conformational sampling with NAMD >> I. Camps (Sat Sep 05 2020 - 12:54:13 CDT)
Support for drudeNbthole on CUDA version of NAMD HEMANTH H (Sat Sep 05 2020 - 02:15:51 CDT)
xMDFF Error Joey Farrell (Thu Sep 03 2020 - 23:19:47 CDT)
ABF Not Sampling Whole Window Ethan Croitoru (Thu Sep 03 2020 - 18:35:15 CDT)
Re: Re:Re: Re: Re:Re: Wrong number of basis-sets stored! Alex Balaeff (Thu Sep 03 2020 - 11:31:51 CDT)
Re:Re: Re: Re:Re: Wrong number of basis-sets stored! è¾›å¿—å® (Thu Sep 03 2020 - 02:41:43 CDT)
Re: Re: Re:Re: Wrong number of basis-sets stored! Alex Balaeff (Wed Sep 02 2020 - 22:08:03 CDT)
Re: Asymmetric concentration gradient: non-periodic z-boundary for only ions Athreya, Nagendra Bala Murali (Wed Sep 02 2020 - 21:35:55 CDT)
Re:Re: Re:Re: Wrong number of basis-sets stored! è¾›å¿—å® (Wed Sep 02 2020 - 21:25:09 CDT)
Re: Re:Re: Wrong number of basis-sets stored! Alex Balaeff (Wed Sep 02 2020 - 20:17:40 CDT)
Re: Colvars Harmonic Bias Force Direction Mortimer Hemmit (Wed Sep 02 2020 - 20:02:03 CDT)
Re:Re: Wrong number of basis-sets stored! è¾›å¿—å® (Wed Sep 02 2020 - 19:32:23 CDT)
Re: Replica exchange problem Josh Vermaas (Wed Sep 02 2020 - 17:10:12 CDT)
Re: Wrong number of basis-sets stored! Acharya, Atanu (Wed Sep 02 2020 - 13:45:48 CDT)
Replica exchange problem Julian David Baquero Contreras (Wed Sep 02 2020 - 13:13:59 CDT)
Re:Re: Wrong number of basis-sets stored! è¾›å¿—å® (Wed Sep 02 2020 - 09:48:38 CDT)
Colvars Harmonic Bias Force Direction Mortimer Hemmit (Wed Sep 02 2020 - 07:28:03 CDT)
Re: PME in PairInteraction Calculations Matthew Guberman-Pfeffer (Wed Sep 02 2020 - 01:01:25 CDT)
Re: Wrong number of basis-sets stored! Acharya, Atanu (Wed Sep 02 2020 - 00:10:54 CDT)
Re: Re: Re: QM atom cannot be fixed in space Alex Balaeff (Tue Sep 01 2020 - 23:47:18 CDT)
Wrong number of basis-sets stored! è¾›å¿—å® (Tue Sep 01 2020 - 21:10:17 CDT)
Re: PME in PairInteraction Calculations Peter Freddolino (Tue Sep 01 2020 - 00:23:26 CDT)
PME in PairInteraction Calculations Matthew Guberman-Pfeffer (Tue Sep 01 2020 - 00:01:51 CDT)
Problems in sharing of replicas in REMD Anup Prasad (Mon Aug 31 2020 - 18:03:59 CDT)
Re: Error when using namdplot Kodituwakku,Dimuthu Nirmani (Mon Aug 31 2020 - 07:34:00 CDT)
Re: Re: QM atom cannot be fixed in space Alex Balaeff (Mon Aug 31 2020 - 00:41:26 CDT)
Re: Error when using namdplot Peter Freddolino (Sun Aug 30 2020 - 23:38:09 CDT)
Re: Error when using namdplot Kodituwakku,Dimuthu Nirmani (Sun Aug 30 2020 - 11:58:07 CDT)
Re: Error when using namdplot Peter Freddolino (Sun Aug 30 2020 - 11:55:03 CDT)
Re: Error when using namdplot Kodituwakku,Dimuthu Nirmani (Sun Aug 30 2020 - 09:33:47 CDT)
Re: Error when using namdplot Kodituwakku,Dimuthu Nirmani (Sun Aug 30 2020 - 09:18:40 CDT)
Re: Error when using namdplot Peter Freddolino (Sat Aug 29 2020 - 22:26:08 CDT)
Error when using namdplot Kodituwakku,Dimuthu Nirmani (Sat Aug 29 2020 - 18:36:01 CDT)
Re: QM atom cannot be fixed in space Alex Balaeff (Sat Aug 29 2020 - 09:29:48 CDT)
QM atom cannot be fixed in space è¾›å¿—å® (Sat Aug 29 2020 - 07:51:21 CDT)
Re: Re: The HIP version of NAMD gets wrong results when computing on more than one node å¼ é©æ´² (Fri Aug 28 2020 - 23:36:12 CDT)
Re: : Re: The HIP version of NAMD gets wrong results when computing on more than one node Josh Vermaas (Fri Aug 28 2020 - 18:21:18 CDT)
Re: Asymmetric concentration gradient: non-periodic z-boundary for only ions David Hardy (Thu Aug 27 2020 - 10:16:22 CDT)
Re: Asymmetric concentration gradient: non-periodic z-boundary for only ions JC Gumbart (Tue Aug 25 2020 - 19:27:34 CDT)
Re: Asymmetric concentration gradient: non-periodic z-boundary for only ions Athreya, Nagendra Bala Murali (Tue Aug 25 2020 - 15:06:12 CDT)
Re: Problem with BEUS in NAMD 2.14 Giacomo Fiorin (Mon Aug 24 2020 - 14:42:34 CDT)
Problem with BEUS in NAMD 2.14 David Tang (Mon Aug 24 2020 - 14:29:10 CDT)
Re: namd-l digest V1 #2927 Raman Preet Singh (Mon Aug 24 2020 - 01:45:58 CDT)
Re: Simulation Crash SMD Coarse-Grained Victor Kwan (Sun Aug 23 2020 - 10:44:55 CDT)
Re: Running NAMD - 2.14 - SMP - Verbs - CUDA Victor Kwan (Sun Aug 23 2020 - 10:42:05 CDT)
Re: QM/MM simulations with live solvent Marcelo C. R. Melo (Fri Aug 21 2020 - 09:51:26 CDT)
Re: Running NAMD - 2.14 - SMP - Verbs - CUDA Bassam Haddad (Thu Aug 20 2020 - 16:56:36 CDT)
Re: QM/MM simulations with live solvent Oleksii Zdorevskyi (Thu Aug 20 2020 - 08:43:52 CDT)
Running NAMD - 2.14 - SMP - Verbs - CUDA Bassam Haddad (Wed Aug 19 2020 - 20:56:19 CDT)
Simulation Crash SMD Coarse-Grained Ethan Croitoru (Wed Aug 19 2020 - 15:24:01 CDT)
JS plugin issues when constructing large systems Cavalleri A. (Mon Aug 17 2020 - 13:37:22 CDT)
Re: Re: namd-l digest V1 #2923 Asmi Mahmood (Mon Aug 17 2020 - 10:50:18 CDT)
Re: Re: namd-l digest V1 #2923 Peter Freddolino (Mon Aug 17 2020 - 10:41:57 CDT)
Error in fftk during bond opt using VMD 1.9.3 Faisal, H M Nasrullah (Mon Aug 17 2020 - 10:08:00 CDT)
Re: Re: namd-l digest V1 #2923 JC Gumbart (Mon Aug 17 2020 - 06:44:34 CDT)
AW: Re: namd-l digest V1 #2923 Norman Geist (Mon Aug 17 2020 - 03:14:07 CDT)
Re: Re: namd-l digest V1 #2923 Pratik Narain Srivastava (Mon Aug 17 2020 - 02:49:19 CDT)
Re: Re: namd-l digest V1 #2923 Asmi Mahmood (Mon Aug 17 2020 - 02:36:33 CDT)
Re: namd-l digest V1 #2923 Raman Preet Singh (Mon Aug 17 2020 - 01:47:09 CDT)
Low simulation speed with 24 processors Asmi Mahmood (Sun Aug 16 2020 - 12:39:26 CDT)
Hi Asmi Mahmood (Sun Aug 16 2020 - 12:38:21 CDT)
Re: Asymmetric concentration gradient: non-periodic z-boundary for only ions Gumbart, JC (Sat Aug 15 2020 - 20:23:12 CDT)
Re: vmd-l: PME boolean HEMANTH H (Fri Aug 14 2020 - 03:20:48 CDT)
Resuming / Resubmitting RAMD simulations on a HPC Gerald Keller (Thu Aug 13 2020 - 02:51:37 CDT)
Annealing stepin QwikMD of VMD soodabeh ghaffari (Wed Aug 12 2020 - 17:50:01 CDT)
Re: ABF protocol to calculate PMF Rukhsar Ali (Wed Aug 12 2020 - 14:12:48 CDT)
Re: ABF protocol to calculate PMF Giacomo Fiorin (Wed Aug 12 2020 - 13:36:21 CDT)
Re: ABF protocol to calculate PMF Giacomo Fiorin (Wed Aug 12 2020 - 13:20:17 CDT)
Re: ABF protocol to calculate PMF Rukhsar Ali (Wed Aug 12 2020 - 12:44:55 CDT)
RE: Restarting aborted NAMD run Raman Preet Singh (Wed Aug 12 2020 - 12:40:45 CDT)
ABF protocol to calculate PMF Rukhsar Ali (Wed Aug 12 2020 - 11:13:53 CDT)
Asymmetric concentration gradient: non-periodic z-boundary for only ions Athreya, Nagendra Bala Murali (Tue Aug 11 2020 - 19:50:48 CDT)
RE: Cuboid water box issues Raman Preet Singh (Tue Aug 11 2020 - 13:28:55 CDT)
POSTDOCTORAL POSITION at CFM/MPC (Donostia, San Sebastian - SPAIN) Aritz Leonardo Liceranzu (Mon Aug 10 2020 - 17:04:46 CDT)
Re: Postdoctoral opening at MSU Shailesh Kumar Panday (Sat Aug 08 2020 - 21:05:46 CDT)
Re: QM/MM simulations with live solvent Marcelo C. R. Melo (Fri Aug 07 2020 - 15:34:00 CDT)
Re: Cuboid water box issues Peter Freddolino (Fri Aug 07 2020 - 15:16:50 CDT)
Re: Cuboid water box issues Josh Vermaas (Fri Aug 07 2020 - 13:46:30 CDT)
Cuboid water box issues Raman Preet Singh (Fri Aug 07 2020 - 13:29:06 CDT)
Postdoctoral opening at MSU Josh Vermaas (Thu Aug 06 2020 - 09:46:56 CDT)
QM/MM simulations with live solvent Oleksii Zdorevskyi (Thu Aug 06 2020 - 05:15:26 CDT)
Re: Possible issue with NAMD_2.13_Linux-x86_64-multicore-CUDA version for Drude support JC Gumbart (Wed Aug 05 2020 - 15:44:38 CDT)
Re: Extra frame at start of each trajectory Josh Vermaas (Wed Aug 05 2020 - 14:33:43 CDT)
Extra frame at start of each trajectory Ethan Croitoru (Wed Aug 05 2020 - 14:23:47 CDT)
Possible issue with NAMD_2.13_Linux-x86_64-multicore-CUDA version for Drude support HEMANTH H (Wed Aug 05 2020 - 10:11:08 CDT)
Re: RAMD seed number Aashish Bhatt (Wed Aug 05 2020 - 05:31:11 CDT)
Alchemical Transformation for calculation of standard binding free energies Cameron Grant (Wed Aug 05 2020 - 04:44:58 CDT)
Re: [3.0alpha5] Low global CUDA exclusion count. System is stable without cudaSOAIntegrate or without rigidBonds. Michael Von Domaros (Mon Aug 03 2020 - 18:39:14 CDT)
Senior Investigator/ Investigator Position (Molecular Dynamics) at Silicon Therapeutics Joao Ribeiro (Mon Aug 03 2020 - 12:51:52 CDT)
Senior Investigator/ Investigator Position (Quantum Mechanics) at Silicon Therapeutics Joao Ribeiro (Mon Aug 03 2020 - 07:50:06 CDT)
Re: [3.0alpha5] Low global CUDA exclusion count. System is stable without cudaSOAIntegrate or without rigidBonds. yjcoshc (Fri Jul 31 2020 - 14:43:11 CDT)
Parameters for molecular N2 Raman Preet Singh (Fri Jul 31 2020 - 13:29:47 CDT)
Re: [3.0alpha5] Low global CUDA exclusion count. System is stable without cudaSOAIntegrate or without rigidBonds. Michael Von Domaros (Fri Jul 31 2020 - 11:01:46 CDT)
Re: [3.0alpha5] Low global CUDA exclusion count. System is stable without cudaSOAIntegrate or without rigidBonds. yjcoshc (Thu Jul 30 2020 - 20:17:40 CDT)
[3.0alpha5] Low global CUDA exclusion count. System is stable without cudaSOAIntegrate or without rigidBonds. Michael Von Domaros (Thu Jul 30 2020 - 18:43:15 CDT)
CUDA Error Roshan Shrestha (Wed Jul 29 2020 - 13:22:36 CDT)
Re: error with namd2_ti.pl script Mateusz Bieniek (Wed Jul 29 2020 - 09:14:53 CDT)
Re: Slow performance over multi-core processor and CUDA build Josh Vermaas (Tue Jul 28 2020 - 20:32:26 CDT)
Re: error with namd2_ti.pl script Qasim Pars (Tue Jul 28 2020 - 15:01:12 CDT)
Re: Slow performance over multi-core processor and CUDA build Josh Vermaas (Tue Jul 28 2020 - 14:28:59 CDT)
Re: Slow performance over multi-core processor and CUDA build Joseph Farran (Tue Jul 28 2020 - 12:41:18 CDT)
Re: Slow performance over multi-core processor and CUDA build Roshan Shrestha (Tue Jul 28 2020 - 11:36:36 CDT)
Re: Slow performance over multi-core processor and CUDA build Giacomo Fiorin (Tue Jul 28 2020 - 08:04:52 CDT)
AW: Slow performance over multi-core processor and CUDA build Norman Geist (Tue Jul 28 2020 - 07:36:02 CDT)
Re: Slow performance over multi-core processor and CUDA build Ashkan Shekaari (Tue Jul 28 2020 - 07:25:29 CDT)
Slow performance over multi-core processor and CUDA build Roshan Shrestha (Tue Jul 28 2020 - 05:01:14 CDT)
Re: NAMD on 24 threads Pratik Narain Srivastava (Mon Jul 27 2020 - 12:10:53 CDT)
Re: NAMD on 24 threads Ashkan Shekaari (Mon Jul 27 2020 - 07:03:54 CDT)
NAMD on 24 threads Asmi Mahmood (Mon Jul 27 2020 - 04:06:28 CDT)
Re: error with namd2_ti.pl script yjcoshc (Sun Jul 26 2020 - 12:58:50 CDT)
error with namd2_ti.pl script Qasim Pars (Sat Jul 25 2020 - 23:42:22 CDT)
NAMD CUDA specification Asmi Mahmood (Sat Jul 25 2020 - 01:33:55 CDT)
Missing frames in DCD header when continue from segment without DCD output Maximilian Ebert (Fri Jul 24 2020 - 15:30:32 CDT)
PhD Position In Computational Structural Biology Of Membrane Proteins Marawan Hussien (Thu Jul 23 2020 - 17:49:08 CDT)
Re: FATAL ERROR: EOF ENCOUNTERED WHILE READING BONDS FROM PSF FILE Josh Vermaas (Thu Jul 23 2020 - 13:19:16 CDT)
FATAL ERROR: EOF ENCOUNTERED WHILE READING BONDS FROM PSF FILE Jose Correa (Thu Jul 23 2020 - 12:28:07 CDT)
Re: FATAL ERROR: must have same number of LP hosts as lone pairs yjcoshc (Wed Jul 22 2020 - 16:51:03 CDT)
FATAL ERROR: must have same number of LP hosts as lone pairs Selemon Bekele (Wed Jul 22 2020 - 16:33:33 CDT)
Re: TI alchemical transformation of a ring atom: small partial charge difference affects strongly dG Mateusz Bieniek (Tue Jul 21 2020 - 07:33:17 CDT)
Re: TI alchemical transformation of a ring atom: small partial charge difference affects strongly dG Peter Freddolino (Sun Jul 19 2020 - 20:54:13 CDT)
TI alchemical transformation of a ring atom: small partial charge difference affects strongly dG Mateusz Bieniek (Sat Jul 18 2020 - 09:30:33 CDT)
Re: Free-energy of association of transmembrane helices Giacomo Fiorin (Sat Jul 18 2020 - 07:36:17 CDT)
Free-energy of association of transmembrane helices Ethan Croitoru (Fri Jul 17 2020 - 20:05:40 CDT)
obtaining the viscosity of mixture from NAMD output file Kosar Khajeh (Thu Jul 16 2020 - 08:13:30 CDT)
issues with QMMM and parameters Francesco Pietra (Wed Jul 15 2020 - 02:23:43 CDT)
obtaining the viscosity of mixture from NAMD output file Kosar Khajeh (Wed Jul 15 2020 - 02:21:23 CDT)
NAMD overestimates the hydration free energy with Drude force field Qasim Pars (Tue Jul 14 2020 - 12:10:01 CDT)
Re: Degrees of Freedom in REST2 JC Gumbart (Sun Jul 12 2020 - 18:13:31 CDT)
Degrees of Freedom in REST2 Alex Hummels (Sun Jul 12 2020 - 13:31:49 CDT)
Re: Dcd file abnormal termination please help Kushal Roy (Sun Jul 12 2020 - 12:05:21 CDT)
Re: Restarting aborted NAMD run Alex Balaeff (Sun Jul 12 2020 - 10:50:38 CDT)
Re: Restarting aborted NAMD run Adupa Vasista (Sun Jul 12 2020 - 10:05:41 CDT)
Re: Dcd file abnormal termination please help Chandni Tiwari (Sun Jul 12 2020 - 08:27:40 CDT)
Dcd file abnormal termination please help Kushal Roy (Sun Jul 12 2020 - 06:43:28 CDT)
Restarting aborted NAMD run Raman Preet Singh (Sun Jul 12 2020 - 03:56:22 CDT)
Dynamic switching GPU/CPU minimization Maximilian Ebert (Sat Jul 11 2020 - 08:49:50 CDT)
Pair interaction calculations of the QM/MM system Alex Balaeff (Tue Jul 07 2020 - 18:44:21 CDT)
Re: Re: scripts to generate initial boxes of solvents Francesco Pietra (Mon Jul 06 2020 - 10:25:06 CDT)
Re: Re: scripts to generate initial boxes of solvents Josh Vermaas (Mon Jul 06 2020 - 10:18:03 CDT)
Re: Re: scripts to generate initial boxes of solvents Francesco Pietra (Mon Jul 06 2020 - 10:01:03 CDT)
Re: scripts to generate initial boxes of solvents Josh Vermaas (Sun Jul 05 2020 - 14:51:48 CDT)
Re: Equilibrated boxes of organic solvents Josh Vermaas (Sun Jul 05 2020 - 14:02:20 CDT)
Re: Equilibrated boxes of organic solvents Joseph Farran (Sun Jul 05 2020 - 10:34:44 CDT)
Re: Equilibrated boxes of organic solvents Francesco Pietra (Sun Jul 05 2020 - 09:27:40 CDT)
Re: Equilibrated boxes of organic solvents Josh Vermaas (Sat Jul 04 2020 - 22:57:46 CDT)
Equilibrated boxes of organic solvents Francesco Pietra (Sat Jul 04 2020 - 11:46:15 CDT)
Re: Re: The HIP version of NAMD gets wrong results when computing on more than one node Josh Vermaas (Fri Jul 03 2020 - 23:17:09 CDT)
Re: Re: The HIP version of NAMD gets wrong results when computing on more than one node å¼ é©æ´² (Fri Jul 03 2020 - 23:03:54 CDT)
MOPAC output file analysis M. A (Fri Jul 03 2020 - 14:53:05 CDT)
Re: The HIP version of NAMD gets wrong results when computing on more than one node Josh Vermaas (Fri Jul 03 2020 - 10:33:14 CDT)
Re: The HIP version of NAMD gets wrong results when computing on more than one node å¼ é©æ´² (Fri Jul 03 2020 - 06:36:12 CDT)
Re: The HIP version of NAMD gets wrong results when computing on more than one node Josh Vermaas (Fri Jul 03 2020 - 05:54:33 CDT)
The HIP version of NAMD gets wrong results when computing on more than one node å¼ é©æ´² (Fri Jul 03 2020 - 04:58:16 CDT)
Re: Questions about soluteScalingFactor in REST2 Geist, Norman (Fri Jul 03 2020 - 04:34:41 CDT)
Questions about soluteScalingFactor in REST2 Alex Hummels (Thu Jul 02 2020 - 17:19:11 CDT)
Re: CpHMD: Warning when building atom of unknown mass (psfgen) Brian Radak (Tue Jun 30 2020 - 18:18:30 CDT)
CpHMD: Warning when building atom of unknown mass (psfgen) Aalap Parikh (Tue Jun 30 2020 - 15:35:37 CDT)
Re: RAMD seed number Aashish Bhatt (Tue Jun 30 2020 - 01:02:58 CDT)
Re: RAMD seed number Josh Vermaas (Mon Jun 29 2020 - 17:26:59 CDT)
RAMD seed number Aashish Bhatt (Mon Jun 29 2020 - 08:31:10 CDT)
Re: NAMD configuration file error HEMANTH H (Mon Jun 29 2020 - 02:40:50 CDT)
Re: NAMD configuration file error HEMANTH H (Sun Jun 28 2020 - 21:06:26 CDT)
Re: Patch bond not formed Josh Vermaas (Sun Jun 28 2020 - 17:33:31 CDT)
Re: Patch bond not formed Kodituwakku,Dimuthu Nirmani (Sun Jun 28 2020 - 16:46:19 CDT)
Re: Patch bond not formed Josh Vermaas (Sun Jun 28 2020 - 16:42:45 CDT)
NAMD configuration file error Ratnika Sharma (Sun Jun 28 2020 - 15:45:27 CDT)
Patch bond not formed Kodituwakku,Dimuthu Nirmani (Sun Jun 28 2020 - 00:58:56 CDT)
Re: How to best use GPUs Itamar Kass (Thu Jun 25 2020 - 12:20:37 CDT)
Re: How to best use GPUs Josh Vermaas (Thu Jun 25 2020 - 11:10:51 CDT)
Re: How to restart a FEP simulation Qasim Pars (Thu Jun 25 2020 - 08:03:45 CDT)
Re: How to best use GPUs Giacomo Fiorin (Thu Jun 25 2020 - 07:51:45 CDT)
How to best use GPUs Itamar Kass (Thu Jun 25 2020 - 05:06:46 CDT)
How to restart a FEP simulation Qasim Pars (Thu Jun 25 2020 - 02:37:46 CDT)
npt simulation where only one of the dimensions is fixed Oleksii Zdorevskyi (Wed Jun 24 2020 - 01:29:50 CDT)
Re: Protein-ligand complex Pratik Narain Srivastava (Tue Jun 23 2020 - 09:56:45 CDT)
Protein-ligand complex Raman Preet Singh (Tue Jun 23 2020 - 08:47:56 CDT)
Re: how does NAMD know which residue to (de)couple Chris Chipot (Mon Jun 22 2020 - 02:22:06 CDT)
Re: how does NAMD know which residue to (de)couple Qasim Pars (Sun Jun 21 2020 - 23:32:28 CDT)
Re: how does NAMD know which residue to (de)couple Michael Robinson (Sun Jun 21 2020 - 21:26:06 CDT)
how does NAMD know which residue to (de)couple Qasim Pars (Sun Jun 21 2020 - 17:28:19 CDT)
Warning: DUPLICATE ANGLE/BOND/DIHEDRAL ENTRY FOR ............... Indrajit Deb (Wed Jun 17 2020 - 00:03:18 CDT)
Re: [External Email] Re: how to disable the periodic condition tracking two atom distance Jiali Wang (Fri Jun 12 2020 - 13:42:29 CDT)
Re: [External Email] Re: how to disable the periodic condition tracking two atom distance Josh Vermaas (Fri Jun 12 2020 - 13:41:22 CDT)
Re: [External Email] Re: how to disable the periodic condition tracking two atom distance Jiali Wang (Fri Jun 12 2020 - 13:10:20 CDT)
Re: [External Email] Re: how to disable the periodic condition tracking two atom distance JÃ©rÃ´me HÃ©nin (Fri Jun 12 2020 - 12:42:26 CDT)
Re: [External Email] Re: how to disable the periodic condition tracking two atom distance Jiali Wang (Thu Jun 11 2020 - 11:49:54 CDT)
Re: Transforming ORCA data to CHARMM format GIUSEPPE LEONARDO LICARI (Thu Jun 11 2020 - 08:58:22 CDT)
Transforming ORCA data to CHARMM format Peter Mawanga (Thu Jun 11 2020 - 06:32:40 CDT)
how to run flexible fitting for structure with helical symmetry Zhang Yan (Thu Jun 11 2020 - 03:24:31 CDT)
Re: how to disable the periodic condition tracking two atom distance Josh Vermaas (Wed Jun 10 2020 - 15:10:35 CDT)
how to disable the periodic condition tracking two atom distance Jiali Wang (Wed Jun 10 2020 - 12:54:51 CDT)
ERROR: Atoms (still) moving too fast Justine Raymond (Wed Jun 10 2020 - 09:23:34 CDT)
CPU/GPU Distribution Youssef Elmougy (Tue Jun 09 2020 - 16:44:59 CDT)
(no subject) shyam sharma (Mon Jun 08 2020 - 04:29:00 CDT)
How can I analyse QMMM log file? M. A (Sun Jun 07 2020 - 02:43:55 CDT)
Psfgen, Disulfide Linkages, and the Drude Polarizable Force Field Michael Robinson (Fri Jun 05 2020 - 03:31:05 CDT)
Re: Error during simulation shyam sharma (Thu Jun 04 2020 - 22:54:10 CDT)
Bond between custom ligand and protein sidechain McGuire, Kelly (Thu Jun 04 2020 - 20:05:51 CDT)
Re: Non-SLI GPUs in NAMD Josh Vermaas (Thu Jun 04 2020 - 14:59:36 CDT)
Non-SLI GPUs in NAMD Raman Preet Singh (Thu Jun 04 2020 - 12:56:58 CDT)
Re: System Drifts Along Z-Axis Bassam Haddad (Sun May 31 2020 - 16:56:05 CDT)
Re: System Drifts Along Z-Axis Giacomo Fiorin (Sun May 31 2020 - 16:25:07 CDT)
Re: System Drifts Along Z-Axis Bassam Haddad (Sun May 31 2020 - 16:16:52 CDT)
Re: Files from "Hands-on" Workshop on Structural DNA Nanotechnology at Urbana Sebastian S (Sun May 31 2020 - 15:13:33 CDT)
Re: Question about QMMM simulation M. A (Sun May 31 2020 - 15:03:04 CDT)
Re: Files from "Hands-on" Workshop on Structural DNA Nanotechnology at Urbana Aksimentiev, Aleksei (Sun May 31 2020 - 14:51:36 CDT)
Re: System Drifts Along Z-Axis Bassam Haddad (Sun May 31 2020 - 14:09:37 CDT)
Re: System Drifts Along Z-Axis Peter Freddolino (Sun May 31 2020 - 13:35:00 CDT)
Re: Files from "Hands-on" Workshop on Structural DNA Nanotechnology at Urbana Sebastian S (Sun May 31 2020 - 11:58:40 CDT)
Comparison of electric field between MD simulation and Experiments Mani Kandan (Sun May 31 2020 - 11:47:55 CDT)
Re: Question about QMMM simulation Giacomo Fiorin (Sun May 31 2020 - 11:02:50 CDT)
Re: Files from "Hands-on" Workshop on Structural DNA Nanotechnology at Urbana Aksimentiev, Aleksei (Sun May 31 2020 - 09:27:31 CDT)
Re: Drude polarizable force field Victor Kwan (Sun May 31 2020 - 09:22:27 CDT)
Question about QMMM simulation M. A (Sun May 31 2020 - 06:31:38 CDT)
Drude polarizable force field NicolÃ¡s Marcelo Rozas Castro (Sun May 31 2020 - 04:13:43 CDT)
Files from "Hands-on" Workshop on Structural DNA Nanotechnology at Urbana Sebastian S (Sun May 31 2020 - 00:20:07 CDT)
System Drifts Along Z-Axis Bassam Haddad (Fri May 29 2020 - 14:36:49 CDT)
Re: Is there a way to stop a MD run before the END_OF_RUN timestep? Cardenas, Alfredo E (Wed May 27 2020 - 19:11:32 CDT)
Re: Is there a way to stop a MD run before the END_OF_RUN timestep? Josh Vermaas (Wed May 27 2020 - 16:00:44 CDT)
Re: Is there a way to stop a MD run before the END_OF_RUN timestep? Cardenas, Alfredo E (Wed May 27 2020 - 13:09:41 CDT)
Re: Negative Forces in SMD Simulations Josh Vermaas (Tue May 26 2020 - 19:27:23 CDT)
Re: Negative Forces in SMD Simulations Peter Freddolino (Tue May 26 2020 - 19:24:35 CDT)
Re: Negative Forces in SMD Simulations Souvik Dey (Tue May 26 2020 - 19:05:54 CDT)
Re: Negative Forces in SMD Simulations Peter Freddolino (Tue May 26 2020 - 15:42:59 CDT)
Re: Negative Forces in SMD Simulations Souvik Dey (Tue May 26 2020 - 15:25:04 CDT)
Re: Negative Forces in SMD Simulations Souvik Dey (Tue May 26 2020 - 15:22:19 CDT)
Re: error: minimizer slowly moving xxx atoms with bad contacts downhill Giacomo Fiorin (Tue May 26 2020 - 15:16:08 CDT)
Re: Is there a way to stop a MD run before the END_OF_RUN timestep? Giacomo Fiorin (Tue May 26 2020 - 15:14:19 CDT)
Re: Is there a way to stop a MD run before the END_OF_RUN timestep? Cardenas, Alfredo E (Tue May 26 2020 - 14:44:22 CDT)
Re: Negative Forces in SMD Simulations Pratik Narain Srivastava (Tue May 26 2020 - 13:34:55 CDT)
Re: error: minimizer slowly moving xxx atoms with bad contacts downhill Ceren Ciraci (Tue May 26 2020 - 13:33:09 CDT)
Re: Negative Forces in SMD Simulations Peter Freddolino (Tue May 26 2020 - 13:30:11 CDT)
Re: Negative Forces in SMD Simulations Souvik Dey (Tue May 26 2020 - 13:21:19 CDT)
Re: Negative Forces in SMD Simulations Gumbart, JC (Tue May 26 2020 - 13:17:03 CDT)
Re: error: minimizer slowly moving xxx atoms with bad contacts downhill Giacomo Fiorin (Tue May 26 2020 - 10:50:43 CDT)
error: minimizer slowly moving xxx atoms with bad contacts downhill Ceren Ciraci (Tue May 26 2020 - 10:45:45 CDT)
Specifying a pull direction with COLVARS Selemon Bekele (Mon May 25 2020 - 23:52:47 CDT)
Re: Is there a way to stop a MD run before the END_OF_RUN timestep? Josh Vermaas (Mon May 25 2020 - 17:35:40 CDT)
Re: Re: Setting up / Running NAMD on HPC Victor Kwan (Mon May 25 2020 - 16:54:55 CDT)
Re: Re: Setting up / Running NAMD on HPC Josh Vermaas (Mon May 25 2020 - 16:44:10 CDT)
Re: Re: Setting up / Running NAMD on HPC Gerald Keller (Mon May 25 2020 - 14:17:40 CDT)
Re: Setting up / Running NAMD on HPC Renfro, Michael (Mon May 25 2020 - 09:23:50 CDT)
Setting up / Running NAMD on HPC Gerald Keller (Mon May 25 2020 - 03:56:34 CDT)
Is there a way to stop a MD run before the END_OF_RUN timestep? Cardenas, Alfredo E (Mon May 25 2020 - 00:35:20 CDT)
Re: solvation with SWM4 water model RopÃ³n-Palacios G. (Sun May 24 2020 - 14:51:36 CDT)
Re: Fwd: Inquiry regarding benchmark simulations John Stone (Sat May 23 2020 - 02:15:28 CDT)
Re: solvation with SWM4 water model HEMANTH H (Fri May 22 2020 - 20:42:58 CDT)
Re: Dcdfreq Variable Value Question Mortimer Hemmit (Fri May 22 2020 - 17:28:59 CDT)
Negative Forces in SMD Simulations Souvik Dey (Fri May 22 2020 - 16:40:25 CDT)
Re: solvation with SWM4 water model Qasim Pars (Fri May 22 2020 - 15:42:13 CDT)
Dcdfreq Variable Value Question Oscar Bastidas (Fri May 22 2020 - 15:23:45 CDT)
NAMD 3.0 alpha, operating system requirements Nicholas M. Glykos (Fri May 22 2020 - 13:19:02 CDT)
Re: solvation with SWM4 water model Giacomo Fiorin (Fri May 22 2020 - 09:47:43 CDT)
Re: solvation with SWM4 water model HEMANTH H (Fri May 22 2020 - 09:26:15 CDT)
solvation with SWM4 water model Qasim Pars (Thu May 21 2020 - 19:37:21 CDT)
Re: Negative Forces in SMD Simulations Josh Vermaas (Thu May 21 2020 - 18:16:52 CDT)
Negative Forces in SMD Simulations Souvik Dey (Thu May 21 2020 - 16:45:28 CDT)
Re: Format of 'dcdfreq' field in conf file Oscar Bastidas (Thu May 21 2020 - 01:19:05 CDT)
Re: Format of 'dcdfreq' field in conf file Axel Kohlmeyer (Thu May 21 2020 - 01:19:26 CDT)
Format of 'dcdfreq' field in conf file Oscar Bastidas (Thu May 21 2020 - 01:09:00 CDT)
Fwd: Inquiry regarding benchmark simulations David Hardy (Wed May 20 2020 - 17:15:38 CDT)
Issue in reading the soluteScalingFile for REST2 GILLET Natacha (Sat May 16 2020 - 01:56:52 CDT)
how to set the input file for the free energy calculations with CHARMM Drude force field Qasim Pars (Fri May 15 2020 - 17:36:33 CDT)
Fwd: FATAL ERROR: Charge placement error in QM-MM bond. M. A (Thu May 14 2020 - 05:39:54 CDT)
Re: FATAL ERROR: Charge placement error in QM-MM bond. M. A (Mon May 11 2020 - 15:01:49 CDT)
Re: Replica exchange on GPU with OPA network and Slurm Geist, Norman (Mon May 11 2020 - 05:24:54 CDT)
Replica exchange on GPU with OPA network and Slurm Thibaut Very (Mon May 11 2020 - 03:20:50 CDT)
FATAL ERROR: Charge placement error in QM-MM bond. M. A (Mon May 11 2020 - 01:43:20 CDT)
Re: qmmm simulation and question for md analysis M. A (Sat May 09 2020 - 01:55:18 CDT)
Re: Using NAMD and Orca together -- a QM/MM job David Baker (Thu May 07 2020 - 10:19:43 CDT)
Using NAMD and Orca together -- a QM/MM job David Baker (Thu May 07 2020 - 06:12:57 CDT)
Fwd: Bypassing MM parameterization of ligand in QMMM Francesco Pietra (Wed May 06 2020 - 03:10:29 CDT)
Bypassing MM parameterization of ligand in QMMM Francesco Pietra (Wed May 06 2020 - 02:49:55 CDT)
Re: Langevin dynamics and random seeds Peter Freddolino (Tue May 05 2020 - 19:20:39 CDT)
Re: Box of Water Josh Vermaas (Tue May 05 2020 - 18:09:35 CDT)
Re: NAMD job takes long time to finish 1 ns equilibration Giacomo Fiorin (Tue May 05 2020 - 17:46:54 CDT)
Langevin dynamics and random seeds Morgan Packer (Tue May 05 2020 - 17:30:54 CDT)
NAMD job takes long time to finish 1 ns equilibration Khoualdi Asma Feriel (Tue May 05 2020 - 14:57:27 CDT)
Re: Box of Water Oscar Bastidas (Tue May 05 2020 - 14:51:44 CDT)
Re: Rattle algorithm error: when to minimise Khoualdi Asma Feriel (Tue May 05 2020 - 14:49:42 CDT)
Re: actual production MD Oscar Bastidas (Tue May 05 2020 - 14:44:50 CDT)
Re: actual production MD L- (Tue May 05 2020 - 07:41:43 CDT)
Parametrization of zinc ion (+2) in using CHARMM force field. varun dewaker (Tue May 05 2020 - 00:26:12 CDT)
pbc correction for nve unwrap trajectory aiming calculation of diffusion coefficient Santanu Santra (Mon May 04 2020 - 23:54:19 CDT)
Re: Box of Water HEMANTH H (Mon May 04 2020 - 21:53:07 CDT)
actual production MD L- (Mon May 04 2020 - 20:01:10 CDT)
Box of Water L- (Mon May 04 2020 - 19:12:03 CDT)
Re: DCD File Not Generating Oscar Bastidas (Sat May 02 2020 - 15:50:36 CDT)
Re: DCD File Not Generating Oscar Bastidas (Sat May 02 2020 - 15:35:17 CDT)
Re: DCD File Not Generating Josh Vermaas (Sat May 02 2020 - 10:12:44 CDT)
Re: DCD File Not Generating Michael Robinson (Sat May 02 2020 - 08:14:51 CDT)
Re: DCD File Not Generating Oscar Bastidas (Sat May 02 2020 - 05:31:03 CDT)
Re: DCD File Not Generating Ashkan Shekaari (Sat May 02 2020 - 05:30:42 CDT)
Re: DCD File Not Generating Aashish Bhatt (Sat May 02 2020 - 05:21:53 CDT)
DCD File Not Generating Oscar Bastidas (Sat May 02 2020 - 05:08:10 CDT)
Re: When to use a semicolon in a *.conf file? Oscar Bastidas (Thu Apr 30 2020 - 22:28:25 CDT)
Re: Patch grid too small error in first production run Khoualdi Asma Feriel (Thu Apr 30 2020 - 12:16:01 CDT)
Re: When to use a semicolon in a *.conf file? Josh Vermaas (Thu Apr 30 2020 - 07:50:12 CDT)
When to use a semicolon in a *.conf file? Oscar Bastidas (Wed Apr 29 2020 - 23:14:07 CDT)
Re: Error: Number of NGauss expected in AddNewGTOs Francesco Pietra (Wed Apr 29 2020 - 01:59:05 CDT)
Re: Error: Number of NGauss expected in AddNewGTOs Pawel Kedzierski (Tue Apr 28 2020 - 15:10:01 CDT)
Re: Error: Number of NGauss expected in AddNewGTOs Francesco Pietra (Tue Apr 28 2020 - 12:06:01 CDT)
Re: Run NAMD without GPU Josh Vermaas (Sun Apr 26 2020 - 07:29:45 CDT)
Run NAMD without GPU L- (Sun Apr 26 2020 - 06:33:50 CDT)
Re: qmmm simulation and question for md analysis Francesco Pietra (Mon Apr 20 2020 - 05:16:02 CDT)
qmmm simulation and question for md analysis M. A (Mon Apr 20 2020 - 03:59:45 CDT)
Re: Patch grid too small error in first production run Josh Vermaas (Sun Apr 19 2020 - 20:19:53 CDT)
Re: Patch grid too small error in first production run Ashkan Shekaari (Sun Apr 19 2020 - 18:10:32 CDT)
Re: Patch grid too small error in first production run Josh Vermaas (Sun Apr 19 2020 - 16:51:22 CDT)
Patch grid too small error in first production run Khoualdi Asma Feriel (Sun Apr 19 2020 - 14:29:06 CDT)
Receptor-ligand binding energy from QMMM Francesco Pietra (Sat Apr 18 2020 - 03:52:40 CDT)
Re: Issues with vdW for non existing atom JC Gumbart (Fri Apr 17 2020 - 18:07:46 CDT)
Re: FATAL ERROR: Error running command for QM forces calculation. M. A (Fri Apr 17 2020 - 12:06:08 CDT)
Re: FATAL ERROR: Error running command for QM forces calculation. M. A (Fri Apr 17 2020 - 11:53:08 CDT)
Re: Issues with vdW for non existing atom Francesco Pietra (Fri Apr 17 2020 - 04:01:17 CDT)
Re: Issues with vdW for non existing atom JC Gumbart (Thu Apr 16 2020 - 23:15:34 CDT)
Fw: Re: Issue about replica-exchangeumbrella sampling by 16 threads è¾›å¿—å® (Thu Apr 16 2020 - 19:40:50 CDT)
Re: Umbrella sampling of AA and CNT dissociation, pmf doesn't flatten & reduces over large distances... Giacomo Fiorin (Thu Apr 16 2020 - 13:05:59 CDT)
Re: Error: Number of NGauss expected in AddNewGTOs Francesco Pietra (Thu Apr 16 2020 - 12:29:46 CDT)
Fwd: Error: Number of NGauss expected in AddNewGTOs Francesco Pietra (Thu Apr 16 2020 - 11:55:50 CDT)
Re: Error: Number of NGauss expected in AddNewGTOs Francesco Pietra (Thu Apr 16 2020 - 11:52:28 CDT)
Re: Issue about replica-exchangeumbrella sampling by 16 threads Josh Vermaas (Thu Apr 16 2020 - 11:33:00 CDT)
Re: Error: Number of NGauss expected in AddNewGTOs Francesco Pietra (Thu Apr 16 2020 - 10:42:25 CDT)
Fwd: Error: Number of NGauss expected in AddNewGTOs Francesco Pietra (Thu Apr 16 2020 - 10:17:09 CDT)
Error: Number of NGauss expected in AddNewGTOs Francesco Pietra (Thu Apr 16 2020 - 10:09:36 CDT)
Re: Umbrella sampling of AA and CNT dissociation, pmf doesn't flatten & reduces over large distances... Giacomo Fiorin (Thu Apr 16 2020 - 09:13:14 CDT)
Issue about replica-exchangeumbrella sampling by 16 threads è¾›å¿—å® (Thu Apr 16 2020 - 04:12:37 CDT)
Umbrella sampling of AA and CNT dissociation, pmf doesn't flatten & reduces over large distances... zeynab hosseini (Wed Apr 15 2020 - 00:07:27 CDT)
Re: Issues with vdW for non existing atom Francesco Pietra (Wed Apr 15 2020 - 15:55:35 CDT)
Re: Issues with vdW for non existing atom Pratik Narain Srivastava (Wed Apr 15 2020 - 10:48:04 CDT)
Issues with vdW for non existing atom Francesco Pietra (Wed Apr 15 2020 - 10:29:14 CDT)
(no subject) ROPÃ“N-PALACIOS G. (Tue Apr 14 2020 - 21:25:41 CDT)
Re: minimise in restarting first equilibration step Khoualdi Asma Feriel (Mon Apr 13 2020 - 13:50:03 CDT)
Re: minimise in restarting first equilibration step Giacomo Fiorin (Mon Apr 13 2020 - 12:54:03 CDT)
Re: minimise in restarting first equilibration step Josh Vermaas (Mon Apr 13 2020 - 12:42:24 CDT)
Re: minimise in restarting first equilibration step Khoualdi Asma Feriel (Mon Apr 13 2020 - 12:24:18 CDT)
Re: minimise in restarting first equilibration step Josh Vermaas (Mon Apr 13 2020 - 12:16:35 CDT)
minimise in restarting first equilibration step Khoualdi Asma Feriel (Mon Apr 13 2020 - 09:37:29 CDT)
Re: QwikMD Error: child killed: unknown signal Joao Ribeiro KS (Mon Apr 13 2020 - 09:25:39 CDT)
Compile NAMD on Windows 64 bit; nocuda, multicore Mortimer Hemmit (Sun Apr 12 2020 - 17:36:46 CDT)
QwikMD Error: child killed: unknown signal Frank Lam (Sun Apr 12 2020 - 13:29:06 CDT)
Re: .coor and .vel output files not generated Khoualdi Asma Feriel (Fri Apr 10 2020 - 11:12:24 CDT)
Re: rmsd colvars atom definition Francesco Pietra (Fri Apr 10 2020 - 05:33:54 CDT)
rmsd colvars atom definition Francesco Pietra (Fri Apr 10 2020 - 01:44:55 CDT)
Re: .coor and .vel output files not generated Khoualdi Asma Feriel (Fri Apr 10 2020 - 00:35:08 CDT)
Re: .coor and .vel output files not generated JC Gumbart (Thu Apr 09 2020 - 23:05:41 CDT)
Re: .coor and .vel output files not generated Josh Vermaas (Thu Apr 09 2020 - 21:46:58 CDT)
.coor and .vel output files not generated Khoualdi Asma Feriel (Thu Apr 09 2020 - 21:32:20 CDT)
Re: Error generating files with QwikMD Joao Ribeiro KS (Thu Apr 09 2020 - 09:20:48 CDT)
Forces in QM/MM calculations nikolaev_at_spbau.ru (Wed Apr 08 2020 - 12:57:07 CDT)
FATAL ERROR: Error running command for QM forces calculation. M. A (Tue Apr 07 2020 - 10:31:12 CDT)
Re: PSF for Cyclic-Branched Peptides Aravinda Munasinghe (Sun Apr 05 2020 - 19:46:40 CDT)
PSF for Cyclic-Branched Peptides Hendrik SchrÃ¶der (Sun Apr 05 2020 - 17:20:18 CDT)
Error generating files with QwikMD Marcos Verissimo Alves (Sun Apr 05 2020 - 00:33:57 CDT)
Fwd: fatal error: error in qm-mm bond assignment mariano spivak (Sat Apr 04 2020 - 11:40:19 CDT)
Re: QMMM param issue Marcelo C. R. Melo (Sat Apr 04 2020 - 11:25:27 CDT)
Re: QMMM param issue Francesco Pietra (Fri Apr 03 2020 - 12:48:50 CDT)
Re: difference between numsteps and run in step4_equilibration.inp Mortimer Hemmit (Thu Apr 02 2020 - 18:50:12 CDT)
Re: difference between numsteps and run in step4_equilibration.inp Josh Vermaas (Thu Apr 02 2020 - 16:00:34 CDT)
Re: difference between numsteps and run in step4_equilibration.inp soodabeh ghaffari (Thu Apr 02 2020 - 15:57:49 CDT)
Re: difference between numsteps and run in step4_equilibration.inp Giacomo Fiorin (Thu Apr 02 2020 - 15:56:37 CDT)
difference between numsteps and run in step4_equilibration.inp soodabeh ghaffari (Thu Apr 02 2020 - 14:39:05 CDT)
Re: QMMM param issue Josh Vermaas (Thu Apr 02 2020 - 11:41:22 CDT)
Re: QMMM param issue Francesco Pietra (Thu Apr 02 2020 - 03:30:27 CDT)
Re: converting gromacs topology file to namd Josh Vermaas (Wed Apr 01 2020 - 18:21:55 CDT)
converting gromacs topology file to namd Hadi Rahmaninejad (Wed Apr 01 2020 - 17:11:40 CDT)
Re: QMMM param issue Marcelo C. R. Melo (Wed Apr 01 2020 - 17:05:32 CDT)
Re: QMMM param issue Francesco Pietra (Wed Apr 01 2020 - 16:16:42 CDT)
Re: [External] how i can utilize 4 GPU in simulation with poor performance Sharp, Kim (Wed Apr 01 2020 - 14:00:15 CDT)
Re: QMMM param issue Marcelo C. R. Melo (Wed Apr 01 2020 - 13:15:37 CDT)
Re: how i can utilize 4 GPU in simulation with poor performance Giacomo Fiorin (Wed Apr 01 2020 - 13:11:37 CDT)
Fwd: QMMM param issue Francesco Pietra (Wed Apr 01 2020 - 12:46:17 CDT)
how i can utilize 4 GPU in simulation with poor performance L- (Wed Apr 01 2020 - 11:30:13 CDT)
MDFF chirality restrain error - measure imprp: empty atom index Indrajit Deb (Wed Apr 01 2020 - 11:15:57 CDT)
Re: QMMM param issue Francesco Pietra (Wed Apr 01 2020 - 11:09:29 CDT)
Re: QMMM param issue Marcelo C. R. Melo (Wed Apr 01 2020 - 09:57:44 CDT)
QMMM param issue Francesco Pietra (Wed Apr 01 2020 - 05:49:53 CDT)
Re: using an Amber topology with OPC water model in NAMD Vlad Cojocaru (Tue Mar 31 2020 - 18:20:00 CDT)
Re: using an Amber topology with OPC water model in NAMD Victor Kwan (Tue Mar 31 2020 - 15:34:57 CDT)
using an Amber topology with OPC water model in NAMD Vlad Cojocaru (Tue Mar 31 2020 - 13:38:42 CDT)
Collaboration offer Raman Preet Singh (Mon Mar 30 2020 - 08:01:54 CDT)
Re: Running on GPU multiple nodes Adupa Vasista (Sun Mar 29 2020 - 21:34:14 CDT)
Re: Running on GPU multiple nodes Josh Vermaas (Sun Mar 29 2020 - 17:47:49 CDT)
Re: Running on GPU multiple nodes Adupa Vasista (Sun Mar 29 2020 - 14:22:05 CDT)
Re: Running on GPU multiple nodes Renfro, Michael (Sun Mar 29 2020 - 08:15:16 CDT)
Running on GPU multiple nodes Adupa Vasista (Sun Mar 29 2020 - 04:42:43 CDT)
Re: Unpredictably Crashes upon Restarting Matthew Guberman-Pfeffer (Fri Mar 27 2020 - 18:00:32 CDT)
Re: Unpredictably Crashes upon Restarting Victor Kwan (Fri Mar 27 2020 - 17:32:01 CDT)
Re: How to fix mutex error Victor Kwan (Fri Mar 27 2020 - 17:28:56 CDT)
Unpredictably Crashes upon Restarting Matthew Guberman-Pfeffer (Fri Mar 27 2020 - 16:56:43 CDT)
Re: How to fix mutex error Matthew Guberman-Pfeffer (Fri Mar 27 2020 - 16:36:38 CDT)
Lipids generated by VMD could not use "coordpdb" to read jiali wang (Thu Mar 26 2020 - 23:42:27 CDT)
Fw: How to avoid producing a huge DCD file? è¾›å¿—å® (Tue Mar 24 2020 - 02:35:00 CDT)
Re: How to avoid producing a huge DCD file? Julio Maia (Tue Mar 24 2020 - 00:09:00 CDT)
Re: How to avoid producing a huge DCD file? HEMANTH H (Mon Mar 23 2020 - 23:19:19 CDT)
How to avoid producing a huge DCD file? è¾›å¿—å® (Mon Mar 23 2020 - 22:15:53 CDT)
Re: How to fix mutex error Victor Kwan (Sun Mar 22 2020 - 20:01:15 CDT)
How to fix mutex error Matthew Guberman-Pfeffer (Sat Mar 21 2020 - 22:51:27 CDT)
Re: Technical specifications for the V100 and GTX gpu cards Souvik Sinha (Fri Mar 20 2020 - 01:18:32 CDT)
Re: Re: NAMD performance Stefano Guglielmo (Thu Mar 19 2020 - 11:47:04 CDT)
Antw: Re: NAMD performance Gerald Keller (Thu Mar 19 2020 - 11:21:26 CDT)
Re: NAMD performance Josh Vermaas (Thu Mar 19 2020 - 10:59:06 CDT)
Re: NAMD performance Stefano Guglielmo (Thu Mar 19 2020 - 10:35:53 CDT)
Re: acetylene Josh Vermaas (Wed Mar 18 2020 - 09:47:07 CDT)
acetylene Mikhail Suyetin (Wed Mar 18 2020 - 06:56:47 CDT)
Re: NGRP NST2 Selemon Bekele (Tue Mar 17 2020 - 14:51:04 CDT)
RE: NGRP NST2 Lennart Nilsson (Tue Mar 17 2020 - 12:46:38 CDT)
NGRP NST2 Selemon Bekele (Tue Mar 17 2020 - 12:13:20 CDT)
Re: Technical specifications for the V100 and GTX gpu cards Axel Kohlmeyer (Tue Mar 17 2020 - 06:32:59 CDT)
Technical specifications for the V100 and GTX gpu cards Souvik Sinha (Tue Mar 17 2020 - 03:26:28 CDT)
Re: Pair interaction calculation is not supported in CUDA version Adupa Vasista (Sun Mar 15 2020 - 23:48:52 CDT)
Re: Pair interaction calculation is not supported in CUDA version Josh Vermaas (Sun Mar 15 2020 - 14:58:45 CDT)
Re: vmd-l: Pair interaction calculation is not supported in CUDA version Adupa Vasista (Sun Mar 15 2020 - 13:01:44 CDT)
Pair interaction calculation is not supported in CUDA version Adupa Vasista (Sun Mar 15 2020 - 12:10:53 CDT)
Re: FATAL ERROR: Error in QM-MM bond assignment (NAMD-ORCA) M. A (Sat Mar 14 2020 - 17:17:37 CDT)
NAMD error : alloc_mempool_block: posix_memalign failed Himanshu Joshi (Fri Mar 13 2020 - 15:51:51 CDT)
Does NAMD have unit tests or how can I confirm the correctness of the simulation results of NAMD? å¼ é©æ´² (Tue Mar 10 2020 - 20:29:34 CDT)
Stability issues with POPC membrane using Drude force field Batuhan Kav (Tue Mar 10 2020 - 05:08:14 CDT)
Re: Error Restarting Simulation Oscar Bastidas (Mon Mar 09 2020 - 15:00:52 CDT)
Error Restarting Simulation Matthew Guberman-Pfeffer (Mon Mar 09 2020 - 12:46:34 CDT)
Different Velocity or Margin Errors for Restarted Simulation Matthew Guberman-Pfeffer (Mon Mar 09 2020 - 09:08:14 CDT)
Re: FATAL ERROR: Error in QM-MM bond assignment (NAMD-ORCA) M. A (Sun Mar 08 2020 - 05:09:07 CDT)
Re: FATAL ERROR: Error in QM-MM bond assignment (NAMD-ORCA) M. A (Sun Mar 08 2020 - 04:30:03 CDT)
Re: question to run namd2 with multiple CPUs Victor Kwan (Thu Mar 05 2020 - 18:33:23 CST)
Re: NAMD performance Josh Vermaas (Thu Mar 05 2020 - 15:03:07 CST)
Re: question to run namd2 with multiple CPUs Renfro, Michael (Thu Mar 05 2020 - 14:26:22 CST)
Re: NAMD performance Victor Kwan (Thu Mar 05 2020 - 11:18:09 CST)
Re: question to run namd2 with multiple CPUs Yu, Tao (Thu Mar 05 2020 - 10:46:41 CST)
Re: question to run namd2 with multiple CPUs Renfro, Michael (Thu Mar 05 2020 - 10:25:21 CST)
NAMD performance Stefano Guglielmo (Thu Mar 05 2020 - 09:05:31 CST)
Re: adding peptide constraint in NAMD configuration file Josh Vermaas (Wed Mar 04 2020 - 09:22:20 CST)
Re: adding peptide constraint in NAMD configuration file Giacomo Fiorin (Wed Mar 04 2020 - 08:55:20 CST)
Re: adding peptide constraint in NAMD configuration file soodabeh ghaffari (Wed Mar 04 2020 - 08:44:22 CST)
MD with 3-site CO model Nadia Elghobashi-Meinhardt (Wed Mar 04 2020 - 08:24:51 CST)
Re: adding peptide constraint in NAMD configuration file Giacomo Fiorin (Wed Mar 04 2020 - 08:03:49 CST)
adding peptide constraint in NAMD configuration file soodabeh ghaffari (Tue Mar 03 2020 - 22:49:20 CST)
Re: question to run namd2 with multiple CPUs Josh Vermaas (Mon Mar 02 2020 - 15:30:03 CST)
Re: question to run namd2 with multiple CPUs Yu, Tao (Mon Mar 02 2020 - 15:08:04 CST)
Re: QM/MM error in the charges Aashish Bhatt (Mon Mar 02 2020 - 08:15:03 CST)
Re: bad angle error!! ROPÃ“N-PALACIOS G. (Fri Feb 28 2020 - 19:40:22 CST)
Re: bad angle error!! Mortimer Hemmit (Fri Feb 28 2020 - 18:42:37 CST)
Re: bad angle error!! ROPÃ“N-PALACIOS G. (Fri Feb 28 2020 - 18:06:54 CST)
Re: bad angle error!! Josh Vermaas (Fri Feb 28 2020 - 16:44:18 CST)
Re: question to run namd2 with multiple CPUs Josh Vermaas (Fri Feb 28 2020 - 16:29:09 CST)
question to run namd2 with multiple CPUs Yu, Tao (Fri Feb 28 2020 - 16:10:20 CST)
Re: bad angle error!! ROPÃ“N-PALACIOS G. (Fri Feb 28 2020 - 14:51:44 CST)
Re: QM/MM error in the charges Pawel Kedzierski (Fri Feb 28 2020 - 08:06:44 CST)
Re: bad angle error!! Josh Vermaas (Fri Feb 28 2020 - 07:53:17 CST)
Re: QM/MM error in the charges Josh Vermaas (Fri Feb 28 2020 - 07:50:26 CST)
Re: QM/MM error in the charges Aashish Bhatt (Fri Feb 28 2020 - 06:44:06 CST)
bad angle error!! ROPÃ“N-PALACIOS G. (Thu Feb 27 2020 - 21:10:45 CST)
Re: Issue with preparing QM-MM Victor Kwan (Thu Feb 27 2020 - 16:26:39 CST)
Re: Issue with preparing QM-MM Francesco Pietra (Thu Feb 27 2020 - 16:02:54 CST)
Re: Issue with preparing QM-MM Victor Kwan (Thu Feb 27 2020 - 14:41:17 CST)
Re: Issue with preparing QM-MM Francesco Pietra (Thu Feb 27 2020 - 14:28:19 CST)
Issue with preparing QM-MM Francesco Pietra (Thu Feb 27 2020 - 12:32:58 CST)
Re: QM/MM error in the charges Josh Vermaas (Thu Feb 27 2020 - 09:00:50 CST)
QM/MM error in the charges Aashish Bhatt (Thu Feb 27 2020 - 04:14:45 CST)
Re: AW: vmd-l: How to increase the number of core ROPÃ“N-PALACIOS G. (Wed Feb 26 2020 - 09:46:54 CST)
AW: vmd-l: How to increase the number of core Norman Geist (Wed Feb 26 2020 - 01:59:33 CST)
Swarms of Trajectrories MPI NAMD Run Ebru Ã‡etin (Tue Feb 25 2020 - 10:15:37 CST)
Re: FATAL ERROR: Error in QM-MM bond assignment (NAMD-ORCA) M. A (Tue Feb 25 2020 - 04:23:19 CST)
Re: The best initial structure of Protein-Protein complex ROPÃ“N-PALACIOS G. (Mon Feb 24 2020 - 09:54:28 CST)
The best initial structure of Protein-Protein complex Alireza Mansouri (Mon Feb 24 2020 - 03:54:21 CST)
Protocol share Ribosome ROPÃ“N-PALACIOS G. (Fri Feb 21 2020 - 09:05:33 CST)
Re: Can NAMD 2.13 be build on Charm++ with UCX backend? Giacomo Fiorin (Fri Feb 21 2020 - 06:30:26 CST)
Re: Francesco Pietra (Wed Feb 19 2020 - 01:36:55 CST)
Re: Abhijit Gogoi (Wed Feb 19 2020 - 02:25:32 CST)
Re: Josh Vermaas (Tue Feb 18 2020 - 15:37:22 CST)
Bad global bond count! Francesco Pietra (Tue Feb 18 2020 - 15:07:46 CST)
(no subject) Francesco Pietra (Tue Feb 18 2020 - 15:05:34 CST)
FATAL ERROR: Error in QM-MM bond assignment (NAMD-ORCA) M. A (Sat Feb 15 2020 - 23:45:11 CST)
Re: Flat-bottom harmonic position restraints using colvars Daipayan Sarkar (Wed Feb 12 2020 - 19:24:22 CST)
Re: Flat-bottom harmonic position restraints using colvars Daipayan Sarkar (Tue Feb 11 2020 - 16:12:12 CST)
Re: Flat-bottom harmonic position restraints using colvars David Hardy (Tue Feb 11 2020 - 15:57:40 CST)
Conformation Sampling tutorial: factor of 2 in monitor.sh Alexander Adams (Tue Feb 11 2020 - 13:24:21 CST)
Re: Flat-bottom harmonic position restraints using colvars Daipayan Sarkar (Mon Feb 10 2020 - 20:41:47 CST)
Re: Flat-bottom harmonic position restraints using colvars Giacomo Fiorin (Mon Feb 10 2020 - 06:14:11 CST)
Re: Re: FATAL ERROR in protein minimization by drude model : UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1 Joao Ribeiro (Thu Feb 06 2020 - 10:42:41 CST)
Re: Re: FATAL ERROR in protein minimization by drude model : UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1 Santanu Santra (Thu Feb 06 2020 - 09:50:39 CST)
Re: Re: FATAL ERROR in protein minimization by drude model : UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1 Santanu Santra (Thu Feb 06 2020 - 00:28:01 CST)
Re: [External] Re: Hydrogen bond energy for TIP3 water Randy J. Zauhar (Wed Feb 05 2020 - 19:13:41 CST)
Re: Hydrogen bond energy for TIP3 water Randy J. Zauhar (Wed Feb 05 2020 - 18:25:20 CST)
Re: [External] Re: Hydrogen bond energy for TIP3 water Sharp, Kim (Wed Feb 05 2020 - 17:45:57 CST)
Re: Hydrogen bond energy for TIP3 water Randy J. Zauhar (Wed Feb 05 2020 - 16:49:02 CST)
Re: Hydrogen bond energy for TIP3 water Victor Kwan (Wed Feb 05 2020 - 15:58:15 CST)
Hydrogen bond energy for TIP3 water Randy J. Zauhar (Wed Feb 05 2020 - 14:34:38 CST)
Re: Flat-bottom harmonic position restraints using colvars Daipayan Sarkar (Wed Feb 05 2020 - 13:34:38 CST)
Re: Flat-bottom harmonic position restraints using colvars Giacomo Fiorin (Wed Feb 05 2020 - 12:51:05 CST)
Flat-bottom harmonic position restraints using colvars Daipayan Sarkar (Wed Feb 05 2020 - 12:12:29 CST)
Re: Re: FATAL ERROR in protein minimization by drude model : UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1 Joao Ribeiro (Wed Feb 05 2020 - 09:18:50 CST)
Re: Re: FATAL ERROR in protein minimization by drude model : UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1 Santanu Santra (Wed Feb 05 2020 - 08:10:34 CST)
mail about cuda exculssion count Vidhya Sankar (Wed Feb 05 2020 - 06:28:37 CST)
Re: Re: problem with TIP4P on nightly version Monika Madhavi (Tue Feb 04 2020 - 22:08:33 CST)
Re: Re: FATAL ERROR in protein minimization by drude model : UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1 Joao Ribeiro (Tue Feb 04 2020 - 09:02:41 CST)
Re: Re: FATAL ERROR in protein minimization by drude model : UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1 Santanu Santra (Mon Feb 03 2020 - 22:43:31 CST)
Re: Re: FATAL ERROR in protein minimization by drude model : UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1 Joao Ribeiro (Mon Feb 03 2020 - 10:07:57 CST)
Re: Re: FATAL ERROR in protein minimization by drude model : UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1 Joao Ribeiro (Mon Feb 03 2020 - 09:50:27 CST)
Re: FATAL ERROR in protein minimization by drude model : UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1 Santanu Santra (Sun Feb 02 2020 - 22:04:18 CST)
FATAL ERROR in protein minimization by drude model : UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1 Santanu Santra (Sun Feb 02 2020 - 22:00:48 CST)
Re: Re: problem with TIP4P on nightly version Brian Radak (Sun Feb 02 2020 - 14:31:58 CST)
Re: [External Email] Re: [External Email] Re: [External Email] Re: Cations spontaneous binding pathway with PMF calculation? Jiali Wang (Fri Jan 31 2020 - 10:36:51 CST)
Re: [External Email] Re: [External Email] Re: Cations spontaneous binding pathway with PMF calculation? Giacomo Fiorin (Fri Jan 31 2020 - 10:35:02 CST)
Re: [External Email] Re: [External Email] Re: Cations spontaneous binding pathway with PMF calculation? Jiali Wang (Fri Jan 31 2020 - 10:30:02 CST)
Re: [External Email] Re: Cations spontaneous binding pathway with PMF calculation? Giacomo Fiorin (Fri Jan 31 2020 - 10:18:48 CST)
Re: [External Email] Re: Cations spontaneous binding pathway with PMF calculation? Jiali Wang (Fri Jan 31 2020 - 10:14:59 CST)
Re: Re: problem with TIP4P on nightly version Peter Freddolino (Fri Jan 31 2020 - 09:49:56 CST)
Re: Cations spontaneous binding pathway with PMF calculation? Giacomo Fiorin (Fri Jan 31 2020 - 09:22:02 CST)
Cations spontaneous binding pathway with PMF calculation? Jiali Wang (Fri Jan 31 2020 - 08:32:52 CST)
Re: problem with TIP4P on nightly version Laura Lopes (Fri Jan 31 2020 - 08:11:25 CST)
problem with TIP4P on nightly version Laura Lopes (Fri Jan 31 2020 - 04:22:42 CST)
Solvent Heating with Rigid Bonds ben estimated.com (Sun Jan 26 2020 - 22:07:34 CST)
Why very large force reported at the starting point of constant velocity SMD run in NAMD log file? Shadi Rahnama (Sat Jan 25 2020 - 14:56:57 CST)
Re: Amber14 in NAMD 2.13 Brian Radak (Sat Jan 25 2020 - 10:00:20 CST)
Re: Analysis of force applied to a certain atom Giacomo Fiorin (Fri Jan 24 2020 - 08:58:42 CST)
Re: Topology and parameter files for flavonoid compounds Giacomo Fiorin (Fri Jan 24 2020 - 06:08:20 CST)
Re: log file Alexei Rossokhin (Fri Jan 24 2020 - 01:11:08 CST)
Topology and parameter files for flavonoid compounds Shruthi M (116011752017) Res/Bio-Tech (Fri Jan 24 2020 - 00:42:52 CST)
Re: GaMD with nucleotides Miao, Yinglong (Thu Jan 23 2020 - 13:42:09 CST)
Re: vmd-l: NAMD and VMD Armv8-A Giacomo Fiorin (Thu Jan 23 2020 - 09:37:59 CST)
GaMD with nucleotides Francesco Pietra (Thu Jan 23 2020 - 09:30:57 CST)
Re: Analysis of force applied to a certain atom Giacomo Fiorin (Thu Jan 23 2020 - 09:17:59 CST)
Analysis of force applied to a certain atom nikolaev_at_spbau.ru (Thu Jan 23 2020 - 09:12:27 CST)
Amber14 in NAMD 2.13 nikolaev_at_spbau.ru (Thu Jan 23 2020 - 08:57:23 CST)
Fwd: GaMD config file Francesco Pietra (Tue Jan 21 2020 - 03:26:23 CST)
spontaneous binding pathway with PMF calculation? Jiali Wang (Mon Jan 20 2020 - 21:42:47 CST)
GaMD config file Francesco Pietra (Mon Jan 20 2020 - 15:43:10 CST)
Workshop on Free Energy calculations in Muenster March 11-13 2020 Vlad Cojocaru (Fri Jan 17 2020 - 03:33:13 CST)
Re: modelling an aqueous solution of protein+hydrogen peroxide Lucas Neumann (Wed Jan 15 2020 - 18:27:29 CST)
modelling an aqueous solution of protein+hydrogen peroxide Artur Hermano (Wed Jan 15 2020 - 17:50:41 CST)
Re: log file Pang, Yui Tik (Wed Jan 15 2020 - 13:58:47 CST)
Re: log file Alexei Rossokhin (Wed Jan 15 2020 - 04:44:16 CST)
Re: log file Pang, Yui Tik (Tue Jan 14 2020 - 17:32:11 CST)
Re: log file Alexei Rossokhin (Tue Jan 14 2020 - 10:10:19 CST)
Re: harmonic-restraints/colvars Francesco Pietra (Tue Jan 14 2020 - 09:42:43 CST)
Re: log file Giacomo Fiorin (Tue Jan 14 2020 - 08:54:10 CST)
log file Alexei Rossokhin (Tue Jan 14 2020 - 08:36:53 CST)
harmonic-restraints/colvars Francesco Pietra (Tue Jan 14 2020 - 03:44:06 CST)
How to protonate GLU Kaique Gracia De SÃ¡ Billotta (Fri Jan 10 2020 - 11:56:05 CST)
Unable to calculate SMD for amber topology Aashish Bhatt (Fri Jan 10 2020 - 08:33:10 CST)
Measuring Kinetic Energy of Solvent ben estimated.com (Tue Jan 07 2020 - 17:00:00 CST)
Order of Minimizing/Heating/Equilibrating ben estimated.com (Tue Jan 07 2020 - 16:33:51 CST)
Re: LIE protocol in QM/MM Marcelo C. R. Melo (Fri Jan 03 2020 - 11:26:04 CST)
LIE protocol in QM/MM Shahar Keinan (Fri Jan 03 2020 - 07:25:04 CST)
Support of recent Amber force field Haohao Fu (Mon Dec 30 2019 - 20:11:54 CST)
Antw: Re: slow down when running 2 simulations on 1 node Gerald Keller (Sun Dec 29 2019 - 07:29:48 CST)
Re: slow down when running 2 simulations on 1 node Miro Astore (Fri Dec 27 2019 - 16:42:25 CST)
Re: slow down when running 2 simulations on 1 node Bryan Roessler (Fri Dec 27 2019 - 11:58:06 CST)
AW: slow down when running 2 simulations on 1 node Norman Geist (Wed Dec 18 2019 - 06:06:18 CST)
Re: slow down when running 2 simulations on 1 node Gerald Keller (Wed Dec 18 2019 - 05:33:21 CST)
Cuda Geordano Palacios (Tue Dec 17 2019 - 11:59:56 CST)
Re: slow down when running 2 simulations on 1 node David Hardy (Mon Dec 16 2019 - 12:36:12 CST)
Gradual minimization Geordano Palacios (Sat Dec 14 2019 - 10:00:16 CST)
Re: slow down when running 2 simulations on 1 node Gerald Keller (Sat Dec 14 2019 - 09:51:09 CST)
Ion concentration and aggregation problem of the nuclear protein simulations kilincc18_at_itu.edu.tr (Fri Dec 13 2019 - 09:19:07 CST)
Re: Protein:ligand standard binding free energies Abhijit Gogoi (Fri Dec 13 2019 - 10:51:27 CST)
Re: slow down when running 2 simulations on 1 node Giacomo Fiorin (Thu Dec 12 2019 - 13:26:28 CST)
Re: slow down when running 2 simulations on 1 node Julio Maia (Thu Dec 12 2019 - 13:13:01 CST)
Re: slow down when running 2 simulations on 1 node Henrik Schopmans (Thu Dec 12 2019 - 12:58:26 CST)
Re: fatal error regarding parameters mohammad goodarzi (Thu Dec 12 2019 - 09:55:08 CST)
Re: slow down when running 2 simulations on 1 node Victor Kwan (Thu Dec 12 2019 - 08:03:10 CST)
Re: slow down when running 2 simulations on 1 node Gerald Keller (Thu Dec 12 2019 - 05:18:47 CST)
Re: slow down when running 2 simulations on 1 node Miro Astore (Thu Dec 12 2019 - 04:10:05 CST)
Re: Protein:ligand standard binding free energies SHIVAM TIWARI (Thu Dec 12 2019 - 03:50:46 CST)
Re: fatal error regarding parameters Adupa Vasista (Thu Dec 12 2019 - 02:40:47 CST)
slow down when running 2 simulations on 1 node Gerald Keller (Thu Dec 12 2019 - 02:09:14 CST)
RE: Protein:ligand standard binding free energies Sanjay Hari (Wed Dec 11 2019 - 13:29:49 CST)
Re: Protein:ligand standard binding free energies mohammad goodarzi (Wed Dec 11 2019 - 12:37:52 CST)
Re: Protein:ligand standard binding free energies mohammad goodarzi (Wed Dec 11 2019 - 12:33:15 CST)
RE: fatal error regarding parameters Vermaas, Joshua (Wed Dec 11 2019 - 12:28:56 CST)
Re: Protein:ligand standard binding free energies Joao Ribeiro (Wed Dec 11 2019 - 11:37:58 CST)
Re: Protein:ligand standard binding free energies Chris Chipot (Wed Dec 11 2019 - 11:28:37 CST)
Re: fatal error regarding parameters mohammad goodarzi (Wed Dec 11 2019 - 11:22:15 CST)
Protein:ligand standard binding free energies mohammad goodarzi (Wed Dec 11 2019 - 11:12:13 CST)
Re: fatal error regarding parameters Adupa Vasista (Wed Dec 11 2019 - 01:51:15 CST)
RE: fatal error regarding parameters Vermaas, Joshua (Tue Dec 10 2019 - 18:09:24 CST)
Re: fatal error regarding parameters Chandni Tiwari (Tue Dec 10 2019 - 17:55:12 CST)
Re: fatal error regarding parameters mohammad goodarzi (Tue Dec 10 2019 - 12:15:01 CST)
Re: Running multiple walker metadynamics on Stampede2 Giacomo Fiorin (Tue Dec 10 2019 - 12:01:12 CST)
Re: fatal error regarding parameters Adupa Vasista (Tue Dec 10 2019 - 11:28:22 CST)
fatal error regarding parameters mohammad goodarzi (Tue Dec 10 2019 - 11:04:21 CST)
Regarding PCA SHOBHIT JAIN . (Mon Dec 09 2019 - 23:51:00 CST)
Re: vivek nani (Thu Dec 05 2019 - 10:17:12 CST)
Re: Gustavo Olivos (Thu Dec 05 2019 - 09:35:48 CST)
Re: Aravinda Munasinghe (Thu Dec 05 2019 - 09:33:27 CST)
Hybrid AA/CG for a transmembrane protein system Alison de Sousa RebouÃ§as (Thu Dec 05 2019 - 08:58:37 CST)
(no subject) vivek nani (Thu Dec 05 2019 - 03:43:47 CST)
Re: Running multiple walker metadynamics on Stampede2 Sebastian S (Wed Dec 04 2019 - 21:44:38 CST)
Re: gamd restart file in namd 2.13 Aravinda Munasinghe (Wed Dec 04 2019 - 10:54:20 CST)
Re: gamd restart file in namd 2.13 Pang, Yui Tik (Wed Dec 04 2019 - 09:55:30 CST)
Re: Simulation of sodium dodecyl sulfate Mikhail Suyetin (Wed Dec 04 2019 - 09:51:10 CST)
RE: Running multiple walker metadynamics on Stampede2 Vermaas, Joshua (Tue Dec 03 2019 - 11:15:58 CST)
gamd restart file in namd 2.13 Aravinda Munasinghe (Tue Dec 03 2019 - 08:17:20 CST)
Running multiple walker metadynamics on Stampede2 Sebastian S (Mon Dec 02 2019 - 22:43:09 CST)
Re: rigid body simulation with NAMD Jovan Dragelj (Fri Nov 29 2019 - 12:36:07 CST)
Re: rigid body simulation with NAMD Jovan Dragelj (Fri Nov 29 2019 - 02:46:04 CST)
Re: rigid body simulation with NAMD Victor Kwan (Thu Nov 28 2019 - 15:53:27 CST)
rigid body simulation with NAMD Jovan Dragelj (Thu Nov 28 2019 - 15:16:38 CST)
Re: Problem with compiling vmd from source code Victor Kwan (Wed Nov 27 2019 - 11:06:46 CST)
Problem with compiling vmd from source code Oleksii (Wed Nov 27 2019 - 09:29:40 CST)
Re: Colvar orientation of polymer Henrik Schopmans (Wed Nov 27 2019 - 00:48:13 CST)
Re: Multi canonical ensemble method Takeru KAMEDA (Wed Nov 27 2019 - 00:19:06 CST)
Re: Colvar orientation of polymer Giacomo Fiorin (Tue Nov 26 2019 - 13:16:04 CST)
Colvar orientation of polymer Henrik Schopmans (Tue Nov 26 2019 - 12:53:21 CST)
Re: PCA calculations Poonam Pandey (Tue Nov 26 2019 - 10:25:16 CST)
PCA calculations SHOBHIT JAIN . (Sat Nov 23 2019 - 22:02:58 CST)
Re: use Colvars to track four group of pair atoms distance at same time? yjcoshc_at_gmail.com (Fri Nov 22 2019 - 20:42:11 CST)
Re: use Colvars to track four group of pair atoms distance at same time? Jiali Wang (Fri Nov 22 2019 - 19:56:18 CST)
Re: use Colvars to track four group of pair atoms distance at same time? yjcoshc_at_gmail.com (Fri Nov 22 2019 - 13:23:13 CST)
use Colvars to track four group of pair atoms distance at same time? Jiali Wang (Fri Nov 22 2019 - 12:59:32 CST)
Re: NAMD-QM/MM TUTORIAL: Atoms moving too fast error M. A (Fri Nov 22 2019 - 09:43:20 CST)
Re: Job submission error for NAMD-2.13 ( version netlrts with cuda-10.0) using Torque job scheduler Daipayan Sarkar (Tue Nov 19 2019 - 15:19:10 CST)
Re: Job submission error for NAMD-2.13 ( version netlrts with cuda-10.0) using Torque job scheduler Victor Kwan (Tue Nov 19 2019 - 14:57:56 CST)
Job submission error for NAMD-2.13 ( version netlrts with cuda-10.0) using Torque job scheduler Daipayan Sarkar (Tue Nov 19 2019 - 14:49:51 CST)
Re: Error in the collective variables Victor Kwan (Tue Nov 19 2019 - 14:27:41 CST)
Re: Error in the collective variables Giacomo Fiorin (Tue Nov 19 2019 - 14:21:53 CST)
RE: Simulation of sodium dodecyl sulfate Vermaas, Joshua (Tue Nov 19 2019 - 13:12:04 CST)
Error in the collective variables Jiali Wang (Tue Nov 19 2019 - 12:48:25 CST)
Re: Simulation of sodium dodecyl sulfate Giacomo Fiorin (Tue Nov 19 2019 - 11:56:56 CST)
Re: Simulation of sodium dodecyl sulfate Mikhail Suyetin (Tue Nov 19 2019 - 10:56:16 CST)
Re: Doubt about ABF and PMF file generation Souvik Sinha (Mon Nov 18 2019 - 12:52:52 CST)
Re: Doubt about ABF and PMF file generation Souvik Sinha (Mon Nov 18 2019 - 12:26:33 CST)
Re: looping on multiple dcds in namd configuration file SHIVAM TIWARI (Sat Nov 16 2019 - 07:50:38 CST)
Re: How to integrate multiple walkers 2D metadynamics results? Sebastian S (Fri Nov 15 2019 - 18:29:23 CST)
Re: Selected cofactor in final output Giacomo Fiorin (Fri Nov 15 2019 - 13:14:29 CST)
Re: How to integrate multiple walkers 2D metadynamics results? Giacomo Fiorin (Fri Nov 15 2019 - 13:12:00 CST)
Re: How to integrate multiple walkers 2D metadynamics results? Sebastian S (Fri Nov 15 2019 - 12:39:29 CST)
Re: How to integrate multiple walkers 2D metadynamics results? Sebastian S (Fri Nov 15 2019 - 12:34:57 CST)
RE: looping on multiple dcds in namd configuration file Vermaas, Joshua (Fri Nov 15 2019 - 11:26:19 CST)
Re: How to integrate multiple walkers 2D metadynamics results? Canal de Sebassen (Fri Nov 15 2019 - 11:25:34 CST)
Selected cofactor in final output Aashish Bhatt (Fri Nov 15 2019 - 08:47:32 CST)
Re: looping on multiple dcds in namd configuration file SHIVAM TIWARI (Fri Nov 15 2019 - 06:25:46 CST)
Re: looping on multiple dcds in namd configuration file Miro Astore (Fri Nov 15 2019 - 05:22:34 CST)
Re: looping on multiple dcds in namd configuration file SHIVAM TIWARI (Fri Nov 15 2019 - 00:59:51 CST)
Re: looping on multiple dcds in namd configuration file Miro Astore (Fri Nov 15 2019 - 00:44:37 CST)
looping on multiple dcds in namd configuration file SHIVAM TIWARI (Fri Nov 15 2019 - 00:33:23 CST)
Re: Doubt about ABF and PMF file generation Souvik Sinha (Fri Nov 15 2019 - 00:03:11 CST)
RE: Simulation of sodium dodecyl sulfate Vermaas, Joshua (Thu Nov 14 2019 - 10:46:05 CST)
Simulation of sodium dodecyl sulfate Mikhail Suyetin (Thu Nov 14 2019 - 08:00:33 CST)
Doubt about ABF and PMF file generation Ercalary . (Mon Nov 11 2019 - 14:15:55 CST)
Doubt about abf and pmf file generation Constanza Galaz Araya (Mon Nov 11 2019 - 12:41:26 CST)
Re: NAMD-QM/MM TUTORIAL: Atoms moving too fast error Marcelo C. R. Melo (Mon Nov 11 2019 - 09:50:36 CST)
Re: Harmonic restrains Miro Astore (Sun Nov 10 2019 - 22:07:15 CST)
Re: Harmonic restrains Zhang Yan (Sun Nov 10 2019 - 20:42:45 CST)
NAMD-QM/MM TUTORIAL: Atoms moving too fast error M. A (Sun Nov 10 2019 - 03:50:49 CST)
Re: Harmonic restrains Miro Astore (Sat Nov 09 2019 - 19:25:30 CST)
Re: How to integrate multiple walkers 2D metadynamics results? Canal de Sebassen (Sat Nov 09 2019 - 19:03:01 CST)
Re: Harmonic restrains Miro Astore (Sat Nov 09 2019 - 03:17:41 CST)
Re: Harmonic restrains Miro Astore (Sat Nov 09 2019 - 03:08:36 CST)
Harmonic restrains Zhang Yan (Sat Nov 09 2019 - 02:20:49 CST)
Re: Performance on GPU Anup Prasad (Fri Nov 08 2019 - 05:35:37 CST)
Re: How to integrate multiple walkers 2D metadynamics results? Giacomo Fiorin (Thu Nov 07 2019 - 17:37:11 CST)
How to integrate multiple walkers 2D metadynamics results? Canal de Sebassen (Thu Nov 07 2019 - 17:04:15 CST)
Re: Homologous structure as stating flexible fitting model Miro Astore (Wed Nov 06 2019 - 21:09:12 CST)
Re: Homologous structure as stating flexible fitting model Zhang Yan (Wed Nov 06 2019 - 20:39:23 CST)
Re: Multi canonical ensemble method Giacomo Fiorin (Wed Nov 06 2019 - 13:32:45 CST)
RE: Performance on GPU Vermaas, Joshua (Wed Nov 06 2019 - 09:00:41 CST)
Re: Multi canonical ensemble method Takeru KAMEDA (Wed Nov 06 2019 - 03:58:33 CST)
Re: Homologous structure as stating flexible fitting model Miro Astore (Wed Nov 06 2019 - 01:27:56 CST)
Homologous structure as stating flexible fitting model Zhang Yan (Wed Nov 06 2019 - 01:10:55 CST)
Re: Performance on GPU Anup Prasad (Tue Nov 05 2019 - 23:40:27 CST)
flexible fitting for helical structure Zhang Yan (Tue Nov 05 2019 - 20:01:28 CST)
RE: Performance on GPU Vermaas, Joshua (Tue Nov 05 2019 - 11:33:02 CST)
Performance on GPU Anup Prasad (Tue Nov 05 2019 - 07:29:58 CST)
Re: Multi canonical ensemble method Giacomo Fiorin (Tue Nov 05 2019 - 07:18:49 CST)
Re: Differences between z-gradient and gradient in ABF simulation JÃ©rÃ´me HÃ©nin (Mon Nov 04 2019 - 07:12:57 CST)
Re: auto psf file generation Chandni Tiwari (Mon Nov 04 2019 - 03:04:24 CST)
auto psf file generation Zhang Yan (Mon Nov 04 2019 - 02:52:05 CST)
running pair interaction analysis multiple dcds in sequence in single run SHIVAM TIWARI (Fri Nov 01 2019 - 09:59:54 CDT)
FATAL ERROR: FOUND ISOLATED LONE PAIR Nibedita Ray Chaudhuri (Fri Nov 01 2019 - 07:35:49 CDT)
Re: Multi canonical ensemble method Giacomo Fiorin (Wed Oct 30 2019 - 09:22:58 CDT)
Re: Multi canonical ensemble method Takeru KAMEDA (Wed Oct 30 2019 - 00:26:28 CDT)
Re: Should a pairlist warning concern me? Victor Kwan (Mon Oct 28 2019 - 09:35:55 CDT)
Differences between z-gradient and gradient in ABF simulation Surbhi patel (Mon Oct 28 2019 - 06:23:06 CDT)
Should a pairlist warning concern me? Henrik Schopmans (Mon Oct 28 2019 - 05:59:10 CDT)
Re: Need help with errors in REST2 sample file Han, Yuwei (Mon Oct 28 2019 - 02:28:15 CDT)
Re: RE: charmrun error: Work completion error in sendCq Julio Maia (Thu Oct 24 2019 - 16:05:50 CDT)
RE: RE: charmrun error: Work completion error in sendCq Vermaas, Joshua (Thu Oct 24 2019 - 15:40:47 CDT)
Re: RE: charmrun error: Work completion error in sendCq Julio Maia (Thu Oct 24 2019 - 15:30:24 CDT)
RE: charmrun error: Work completion error in sendCq Vermaas, Joshua (Thu Oct 24 2019 - 14:53:53 CDT)
Re: Need help with errors in REST2 sample file Han, Yuwei (Wed Oct 23 2019 - 00:23:49 CDT)
Re: Need help with errors in REST2 sample file Chitrak Gupta (Tue Oct 22 2019 - 22:47:44 CDT)
Re: Need help with errors in REST2 sample file Chandni Tiwari (Tue Oct 22 2019 - 17:47:16 CDT)
Need help with errors in REST2 sample file Han, Yuwei (Mon Oct 21 2019 - 22:28:46 CDT)
RE: charmrun error: Work completion error in sendCq Pang, Yui Tik (Sat Oct 19 2019 - 16:26:33 CDT)
RE: charmrun error: Work completion error in sendCq Vermaas, Joshua (Sat Oct 19 2019 - 15:55:11 CDT)
charmrun error: Work completion error in sendCq Pang, Yui Tik (Sat Oct 19 2019 - 11:10:07 CDT)
RE: ERROR During MPI run Vermaas, Joshua (Tue Oct 15 2019 - 11:13:19 CDT)
Reduce verbosity during minimization Sanjay Hari (Sat Oct 12 2019 - 17:55:04 CDT)
RE: ERROR During MPI run Vermaas, Joshua (Sat Oct 12 2019 - 16:38:24 CDT)
ERROR During MPI run SHOBHIT JAIN . (Sat Oct 12 2019 - 00:18:54 CDT)
Re: Segfault during NAMD compilation with GCC 8.3 fabricio (Thu Oct 10 2019 - 18:18:35 CDT)
Segfault during NAMD compilation with GCC 8.3 Marcelo C. R. Melo (Thu Oct 10 2019 - 17:58:12 CDT)
Re: Error while runing simulation for protein docking SHOBHIT JAIN . (Thu Oct 10 2019 - 01:38:51 CDT)
Re: vmd-l: query on how to allow the protein to interact with the water molecules Joao Ribeiro (Tue Oct 08 2019 - 09:01:51 CDT)
RE: psfgen error protein-ligand Pavel Kostadinov (Tue Oct 08 2019 - 08:17:46 CDT)
RE: psfgen error protein-ligand Vermaas, Joshua (Mon Oct 07 2019 - 10:03:53 CDT)
RE: Error while runing simulation for protein docking Vermaas, Joshua (Mon Oct 07 2019 - 09:50:44 CDT)
Error while runing simulation for protein docking SHOBHIT JAIN . (Sun Oct 06 2019 - 15:01:24 CDT)
Re: psfgen error protein-ligand Pavel Kostadinov (Sat Oct 05 2019 - 11:17:07 CDT)
Re: psfgen error protein-ligand Adupa Vasista (Fri Oct 04 2019 - 10:41:31 CDT)
Re: psfgen error protein-ligand Joao Ribeiro (Fri Oct 04 2019 - 10:29:39 CDT)
Re: Distance restraints Paula Mihaljevic-Juric (Fri Oct 04 2019 - 07:35:59 CDT)
Re: Distance restraints Giacomo Fiorin (Fri Oct 04 2019 - 07:01:46 CDT)
Re: Regarding psf generation SHOBHIT JAIN . (Fri Oct 04 2019 - 07:06:52 CDT)
psfgen error protein-ligand Pavel Kostadinov (Fri Oct 04 2019 - 02:42:08 CDT)
Distance restraints Paula Mihaljevic-Juric (Fri Oct 04 2019 - 02:21:47 CDT)
FATAL ERROR: PBC Raha YS (Thu Oct 03 2019 - 14:20:40 CDT)
Re: namd on AWS Milad Lagzian (Thu Oct 03 2019 - 00:39:20 CDT)
Re: namd on AWS Miro Astore (Wed Oct 02 2019 - 15:47:38 CDT)
RE: namd on AWS Sanjay Hari (Wed Oct 02 2019 - 11:00:55 CDT)
Re: Regarding psf generation Joao Ribeiro (Wed Oct 02 2019 - 10:21:48 CDT)
GBIS parameters Paula Mihaljevic-Juric (Wed Oct 02 2019 - 09:57:40 CDT)
Fwd: namd on AWS Miro Astore (Tue Oct 01 2019 - 22:46:56 CDT)
Re: Regarding psf generation Joao Ribeiro (Tue Oct 01 2019 - 09:10:29 CDT)
Re: namd on AWS Sanjay Hari (Tue Oct 01 2019 - 05:42:15 CDT)
namd on AWS Miro Astore (Tue Oct 01 2019 - 00:02:14 CDT)
Re: Regarding psf generation Joao Ribeiro (Mon Sep 30 2019 - 12:54:46 CDT)
Re: protein movement Giacomo Fiorin (Mon Sep 30 2019 - 07:11:08 CDT)
Doubt in generating Ficoll 70 Hard Sphere for Coarse Grain Simulation SHOBHIT JAIN . (Mon Sep 30 2019 - 07:00:17 CDT)
Re: Regarding Hard sphere Roshan Shrestha (Mon Sep 30 2019 - 02:39:00 CDT)
Regarding psf generation SHOBHIT JAIN . (Mon Sep 30 2019 - 02:39:04 CDT)
Regarding Hard sphere SHOBHIT JAIN . (Mon Sep 30 2019 - 02:34:28 CDT)
Multi canonical ensemble method Takeru KAMEDA (Sun Sep 29 2019 - 21:19:47 CDT)
RE: protein movement Vermaas, Joshua (Sun Sep 29 2019 - 16:32:03 CDT)
protein movement Mahdi Mousaei (Sun Sep 29 2019 - 14:58:30 CDT)
RE: SMwST RATTLE Algorithm Vermaas, Joshua (Wed Sep 25 2019 - 09:42:53 CDT)
Re: parameters and topology for Deacylcortivazol (DAC) Victor Kwan (Wed Sep 25 2019 - 05:23:53 CDT)
parameters and topology for Deacylcortivazol (DAC) Ester 94 (Wed Sep 25 2019 - 03:48:11 CDT)
SMwST RATTLE Algorithm Xander Gonzalez (Tue Sep 24 2019 - 16:28:24 CDT)
Re: vmd-l: Re: Is there someway to render protein picture without background color? John Stone (Thu Sep 19 2019 - 10:13:52 CDT)
MAIL ABOUT INTRODUCING NEW residue Vidhya Sankar (Thu Sep 19 2019 - 08:27:09 CDT)
AW: vmd-l: Re: Is there someway to render protein picture without background color? Norman Geist (Thu Sep 19 2019 - 04:13:05 CDT)
Re: vmd-l: Re: Is there someway to render protein picture without background color? John Stone (Wed Sep 18 2019 - 10:18:52 CDT)
Re: vmd-l: Re: Is there someway to render protein picture without background color? jiali wang (Wed Sep 18 2019 - 10:14:28 CDT)
Re: vmd-l: Re: Is there someway to render protein picture without background color? John Stone (Tue Sep 17 2019 - 16:11:48 CDT)
Accelerated MD with transmembrane protein Alison de Sousa RebouÃ§as (Tue Sep 17 2019 - 13:48:46 CDT)
Re: Barostat dimension rescaling under semi-isotropic pressure coupling conditions Victor Kwan (Mon Sep 16 2019 - 17:24:41 CDT)
Barostat dimension rescaling under semi-isotropic pressure coupling conditions Milka Doktorova (Mon Sep 16 2019 - 16:56:45 CDT)
RE: Amber topology for mutation Vermaas, Joshua (Mon Sep 16 2019 - 13:22:25 CDT)
Re: Amber topology for mutation Victor Kwan (Mon Sep 16 2019 - 12:42:12 CDT)
Amber topology for mutation Aashish Bhatt (Mon Sep 16 2019 - 10:40:50 CDT)
Re: Brian Radak (Sun Sep 15 2019 - 18:00:36 CDT)
(no subject) SHOBHIT JAIN . (Sun Sep 15 2019 - 14:36:29 CDT)
Re: Is there someway to render protein picture without background color? Jiali Wang (Sun Sep 15 2019 - 09:58:40 CDT)
Re: Is there someway to render protein picture without background color? Chandni Tiwari (Sun Sep 15 2019 - 02:16:43 CDT)
Re: Is there someway to render protein picture without background color? Roshan Shrestha (Sat Sep 14 2019 - 23:44:28 CDT)
Re: Is there someway to render protein picture without background color? Jiali Wang (Sat Sep 14 2019 - 21:19:50 CDT)
Re: Is there someway to render protein picture without background color? Chitrak Gupta (Sat Sep 14 2019 - 20:52:08 CDT)
Is there someway to render protein picture without background color? jiali wang (Sat Sep 14 2019 - 20:25:54 CDT)
Heating problem for protein/ligand complex Alessandro Ruda (Fri Sep 13 2019 - 13:31:56 CDT)
Re: Pulling only one half of a harmonic restraint Miro Astore (Fri Sep 13 2019 - 04:26:13 CDT)
Pulling only one half of a harmonic restraint Miro Astore (Fri Sep 13 2019 - 03:02:44 CDT)
Re: Salvation of non-orthogonal box HEMANTH H 18310019 (Thu Sep 12 2019 - 21:38:40 CDT)
Salvation of non-orthogonal box Yousefi, Raziyeh (Thu Sep 12 2019 - 13:43:56 CDT)
Regarding FICOLL 70 & PEG20000 SHOBHIT JAIN . (Thu Sep 12 2019 - 05:55:53 CDT)
Re: veccross implementation in tclforces Victor Kwan (Wed Sep 11 2019 - 17:59:58 CDT)
Re: veccross implementation in tclforces Victor Kwan (Wed Sep 11 2019 - 17:48:49 CDT)
veccross implementation in tclforces Daniel Strahs (Wed Sep 11 2019 - 16:55:53 CDT)
Periodic boundary condition Weitao Wang (Wed Sep 11 2019 - 16:08:05 CDT)
Re: Regarding number of water molecule Srijita Paul (Tue Sep 10 2019 - 01:19:07 CDT)
Regarding number of water molecule SHOBHIT JAIN . (Tue Sep 10 2019 - 01:14:45 CDT)
Re: Running NAMD on Amazon AMI Ryan McGreevy (Wed Sep 04 2019 - 13:22:04 CDT)
Running NAMD on Amazon AMI Sanjay Hari (Wed Sep 04 2019 - 13:05:12 CDT)
RE: Namd Vermaas, Joshua (Tue Sep 03 2019 - 09:49:40 CDT)
Namd Joey Gehring (Mon Sep 02 2019 - 20:35:08 CDT)
Re: RDF of hydroxide ion in a water box Haohao Fu (Mon Sep 02 2019 - 01:19:31 CDT)
Protein Deformity in Implicit Solvent Simulation Athena Xue (Sun Sep 01 2019 - 18:46:48 CDT)
RE: Fwd: running NAMD with AMBER inputs Vermaas, Joshua (Sun Sep 01 2019 - 14:50:36 CDT)
Re: RDF of hydroxide ion in a water box RonitS Chem (Sun Sep 01 2019 - 14:10:43 CDT)
Fwd: running NAMD with AMBER inputs Rui Chen (Sun Sep 01 2019 - 13:13:12 CDT)
Re: nan (Not a number) error in meta-eABF simulation Dhiman Ray (Sun Sep 01 2019 - 03:11:02 CDT)
Re: nan (Not a number) error in meta-eABF simulation Haohao Fu (Sun Sep 01 2019 - 01:18:03 CDT)
nan (Not a number) error in meta-eABF simulation Dhiman Ray (Sat Aug 31 2019 - 22:00:39 CDT)
Re: Thermodynamic Integration document Brian Radak (Sat Aug 31 2019 - 14:32:38 CDT)
Thermodynamic Integration document Aashish Bhatt (Sat Aug 31 2019 - 04:26:30 CDT)
Re: NAMD configuration file Victor Kwan (Thu Aug 29 2019 - 19:52:03 CDT)
Re: NAMD configuration file Rui Chen (Thu Aug 29 2019 - 19:32:43 CDT)
Re: Hamiltonian Replica exchange configuration file neha rana (Thu Aug 29 2019 - 18:18:09 CDT)
RE: Hamiltonian Replica exchange configuration file Vermaas, Joshua (Thu Aug 29 2019 - 17:47:54 CDT)
Hamiltonian Replica exchange configuration file neha rana (Thu Aug 29 2019 - 15:57:50 CDT)
NAMD configuration file Rui Chen (Tue Aug 27 2019 - 15:54:59 CDT)
Re: pairlist question Jiali Wang (Mon Aug 26 2019 - 10:41:02 CDT)
Postdoctoral researcher position in computational virology. Juan R. Perilla (Mon Aug 26 2019 - 10:37:58 CDT)
pairlist question Rui Chen (Mon Aug 26 2019 - 10:26:27 CDT)
heating Rui Chen (Sat Aug 24 2019 - 11:16:21 CDT)
RDF of hydroxide ion in a water box RonitS Chem (Thu Aug 22 2019 - 21:15:18 CDT)
SMD for understanding the proximity of two atoms Roshan Shrestha (Wed Aug 21 2019 - 10:47:01 CDT)
Re: Can't set multiple harmonic restrains in colvar module Lucas Neumann (Wed Aug 21 2019 - 09:18:39 CDT)
Re: DNA won't translocate through graphene nanopore Canal de Sebassen (Tue Aug 20 2019 - 23:37:50 CDT)
Re: DNA won't translocate through graphene nanopore Mohsen Farshad (Tue Aug 20 2019 - 20:54:21 CDT)
Re: DNA won't translocate through graphene nanopore Priyanka Mondal (Tue Aug 20 2019 - 20:02:50 CDT)
Re: DNA won't translocate through graphene nanopore Canal de Sebassen (Tue Aug 20 2019 - 19:43:37 CDT)
RE: question about SMD Vermaas, Joshua (Tue Aug 20 2019 - 14:55:31 CDT)
question about SMD Maria Bykhovskaia (Tue Aug 20 2019 - 14:44:32 CDT)
DNA won't translocate through graphene nanopore Priyanka Mondal (Tue Aug 20 2019 - 14:04:52 CDT)
Re: Mailing list for Postdoctoral opportunities in Simulations Karteek Bejagam (Tue Aug 20 2019 - 01:36:20 CDT)
Mailing list for Postdoctoral opportunities in Simulations Peter Mawanga (Tue Aug 20 2019 - 01:24:38 CDT)
Re: Can't set multiple harmonic restrains in colvar module Victor Kwan (Mon Aug 19 2019 - 15:06:23 CDT)
RE: Can't set multiple harmonic restrains in colvar module Vermaas, Joshua (Mon Aug 19 2019 - 13:37:46 CDT)
Can't set multiple harmonic restrains in colvar module Lucas Neumann (Mon Aug 19 2019 - 12:44:28 CDT)
Re: AMBER force field parameters Victor Kwan (Fri Aug 16 2019 - 16:35:12 CDT)
Swarms Errors Xander Gonzalez (Fri Aug 16 2019 - 13:10:45 CDT)
(no subject) vivek nani (Fri Aug 16 2019 - 02:01:18 CDT)
Re: REST and Periodic Cell Issues Jeff Comer (Thu Aug 15 2019 - 17:04:22 CDT)
Re: REST and Periodic Cell Issues Giacomo Fiorin (Thu Aug 15 2019 - 08:53:14 CDT)
Re: REST and Periodic Cell Issues Gumbart, JC (Thu Aug 15 2019 - 08:39:56 CDT)
Re: Standard binding free energy protein-ligand (ABF) Giacomo Fiorin (Thu Aug 15 2019 - 08:14:09 CDT)
Re: Standard binding free energy protein-ligand (ABF) philippe Bourly (Thu Aug 15 2019 - 07:04:44 CDT)
Re: Standard binding free energy protein-ligand (ABF) Haohao Fu (Thu Aug 15 2019 - 06:22:07 CDT)
Standard binding free energy protein-ligand (ABF) philippe Bourly (Thu Aug 15 2019 - 06:10:48 CDT)
Standard binding free energy protein-ligand (ABF) philippe Bourly (Thu Aug 15 2019 - 06:03:33 CDT)
Compiler and version used by jenkins to test patch sets Marcelo C. R. Melo (Tue Aug 13 2019 - 08:49:53 CDT)
REST and Periodic Cell Issues Stix, Robyn (NIH/NHLBI) [F] (Mon Aug 12 2019 - 08:34:51 CDT)
ABF and Kinetic Barriers McGuire, Kelly (Sun Aug 11 2019 - 19:26:00 CDT)
Re: AMBER force field parameters Victor Kwan (Thu Aug 08 2019 - 06:51:07 CDT)
constraint-force constant Rui Chen (Tue Aug 06 2019 - 21:28:06 CDT)
Re: Computational electrophysiology Gumbart, JC (Tue Aug 06 2019 - 20:21:49 CDT)
AMBER force field parameters Rui Chen (Tue Aug 06 2019 - 16:22:06 CDT)
Re: Computational electrophysiology Giacomo Fiorin (Mon Aug 05 2019 - 07:56:25 CDT)
Computational electrophysiology Villalain Boullon, Jose (Mon Aug 05 2019 - 06:09:47 CDT)
Same timestep for my simulation run is coming more than once and in random order in the log file Chandni Tiwari (Sun Aug 04 2019 - 09:25:36 CDT)
Re: Re: FATAL ERROR: Must have either an initial temperature or a velocity file è¾›å¿—å® (Sun Aug 04 2019 - 07:22:13 CDT)
RE: mpirun was unable to find the specified executable file Vermaas, Joshua (Fri Aug 02 2019 - 12:16:11 CDT)
Re: mpirun was unable to find the specified executable file Adupa Vasista (Fri Aug 02 2019 - 11:29:28 CDT)
Re: mpirun was unable to find the specified executable file Roshan Shrestha (Fri Aug 02 2019 - 10:13:24 CDT)
Re: mpirun was unable to find the specified executable file mariano spivak (Fri Aug 02 2019 - 10:01:38 CDT)
mpirun was unable to find the specified executable file Adupa Vasista (Fri Aug 02 2019 - 08:24:05 CDT)
Re: FATAL ERROR: Must have either an initial temperature or a velocity file Joao Ribeiro (Thu Aug 01 2019 - 08:55:49 CDT)
Re: Re: FATAL ERROR: Must have either an initial temperature or a velocity file è¾›å¿—å® (Tue Jul 30 2019 - 20:50:47 CDT)
Re: FATAL ERROR: Must have either an initial temperature or a velocity file Joao Ribeiro (Tue Jul 30 2019 - 10:27:55 CDT)
Re: FATAL ERROR: Must have either an initial temperature or a velocity file Joao Ribeiro (Tue Jul 30 2019 - 09:16:13 CDT)
Orientation Colvars Question Xander Gonzalez (Mon Jul 29 2019 - 17:17:27 CDT)
Re: FATAL ERROR: Must have either an initial temperature or a velocity file Joao Ribeiro (Mon Jul 29 2019 - 09:03:36 CDT)
RE: FATAL ERROR: Must have either an initial temperature or a velocity file Vermaas, Joshua (Sun Jul 28 2019 - 14:40:58 CDT)
FATAL ERROR: Must have either an initial temperature or a velocity file è¾›å¿—å® (Sat Jul 27 2019 - 22:48:17 CDT)
Multi-node job errors Anup Prasad (Sat Jul 27 2019 - 02:34:00 CDT)
Some questions about restrained-ensemble molecular dynamics (reMD) TeYu Kao (Wed Jul 24 2019 - 21:13:03 CDT)
Re: namdstats.tcl problem Jeff Comer (Wed Jul 24 2019 - 20:56:53 CDT)
namdstats.tcl problem Rui Chen (Wed Jul 24 2019 - 17:24:46 CDT)
Re: Acceptable Timescale fro NAMD Oscar Bastidas (Wed Jul 24 2019 - 14:32:03 CDT)
Re: Acceptable Timescale fro NAMD Axel Kohlmeyer (Wed Jul 24 2019 - 14:22:32 CDT)
Re: Acceptable Timescale fro NAMD Oscar Bastidas (Wed Jul 24 2019 - 13:49:34 CDT)
question Mandana Tarakamesamani (Wed Jul 24 2019 - 13:39:20 CDT)
Re: Calculating Interaction Energies Using NAMD Energy Plugin Peter Freddolino (Wed Jul 24 2019 - 13:23:51 CDT)
Re: Acceptable Timescale fro NAMD Bassam Haddad (Wed Jul 24 2019 - 13:20:48 CDT)
Acceptable Timescale fro NAMD Oscar Bastidas (Wed Jul 24 2019 - 12:33:38 CDT)
Calculating Interaction Energies Using NAMD Energy Plugin Joanna Zienkiewicz (Wed Jul 24 2019 - 11:41:58 CDT)
Re: Simulation crashes during annealing the reverted all-atom structure Peter Freddolino (Wed Jul 24 2019 - 00:17:22 CDT)
Hydrogen mass repartitioning and 4-fs time steps in NAMD Gumbart, JC (Fri Jul 19 2019 - 11:34:28 CDT)
Re: Issue With CatDCD in Dynamical Network Tutorial Victor Kwan (Mon Jul 15 2019 - 09:45:04 CDT)
Re: Simulation crashes during annealing the reverted all-atom structure Peter Freddolino (Sat Jul 13 2019 - 22:09:46 CDT)
Simulation crashes during annealing the reverted all-atom structure Rabeta Yeasmin (Fri Jul 12 2019 - 16:11:25 CDT)
GLA (Î³-carboxyglutamic acid) topology for CHARMM36 Raul Araya (Fri Jul 12 2019 - 09:00:15 CDT)
Error in running NAMD on a cluster Monika Madhavi (Fri Jul 12 2019 - 08:36:21 CDT)
RE: PMF calculation Mahdi Mousaei (Thu Jul 11 2019 - 15:59:42 CDT)
Re: PMF calculation Giacomo Fiorin (Thu Jul 11 2019 - 15:28:20 CDT)
RE: PMF calculation Mahdi Mousaei (Thu Jul 11 2019 - 15:11:32 CDT)
Re: PMF calculation Souvik Sinha (Thu Jul 11 2019 - 15:08:08 CDT)
PMF calculation Mahdi Mousaei (Thu Jul 11 2019 - 14:14:37 CDT)
Does umbrella sampling need same sampling steps for each windows? jiali wang (Thu Jul 11 2019 - 12:59:32 CDT)
String Method with Swarms of Trajectories (SMwST) Performance Alexander Adams (Thu Jul 11 2019 - 10:43:25 CDT)
New version of Molefacture -small molecule modeling tool- posted Joao Ribeiro (Wed Jul 10 2019 - 16:59:50 CDT)
Issue With CatDCD in Dynamical Network Tutorial Nisler, Collin R. (Wed Jul 10 2019 - 15:50:14 CDT)
Re: Colvars Orientation Question Giacomo Fiorin (Wed Jul 10 2019 - 13:28:16 CDT)
Fwd: Colvars Orientation Question Xander Gonzalez (Wed Jul 10 2019 - 13:18:33 CDT)
Re: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CG2O4 CG311 (ATOMS 1220 1222) Aravinda Munasinghe (Wed Jul 10 2019 - 06:57:20 CDT)
Re: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CG2O4 CG311 (ATOMS 1220 1222) Nirmitee Mulgaonkar (Wed Jul 10 2019 - 01:02:53 CDT)
Re: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CG2O4 CG311 (ATOMS 1220 1222) Aravinda Munasinghe (Tue Jul 09 2019 - 22:00:31 CDT)
FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CG2O4 CG311 (ATOMS 1220 1222) Nirmitee Mulgaonkar (Tue Jul 09 2019 - 20:23:49 CDT)
Reminder NAMD Developer Meeting 2019 giuseppe_at_ks.uiuc.edu (Tue Jul 09 2019 - 10:54:29 CDT)
Re: EPW "ATOMS Moving too fast" Bowman, Jacob (Tue Jul 09 2019 - 09:52:34 CDT)
Re: EPW "ATOMS Moving too fast" Peter Freddolino (Tue Jul 09 2019 - 09:24:44 CDT)
Re: EPW "ATOMS Moving too fast" Natalia Ostrowska (Tue Jul 09 2019 - 03:29:26 CDT)
Re: AutoPSF charge generation Srijita Paul (Tue Jul 09 2019 - 00:18:29 CDT)
Re: Velocity unit soroush ziaei (Mon Jul 08 2019 - 15:55:30 CDT)
EPW "ATOMS Moving too fast" Bowman, Jacob (Mon Jul 08 2019 - 15:26:40 CDT)
Re: AutoPSF charge generation Peter Freddolino (Sat Jul 06 2019 - 21:00:48 CDT)
AutoPSF charge generation Adupa Vasista (Sat Jul 06 2019 - 04:28:55 CDT)
Re: Colvars Orientation Question Xander Gonzalez (Fri Jul 05 2019 - 14:22:34 CDT)
Re: Re: vmd-l: Getting the topology,PSF files Adupa Vasista (Fri Jul 05 2019 - 00:04:32 CDT)
Re: Re: vmd-l: Getting the topology,PSF files Pratik Narain Srivastava (Thu Jul 04 2019 - 23:54:54 CDT)
Re: Re: vmd-l: Getting the topology,PSF files Adupa Vasista (Thu Jul 04 2019 - 23:22:37 CDT)
Re: vmd-l: Getting the topology,PSF files Peter Freddolino (Thu Jul 04 2019 - 17:09:41 CDT)
Getting the topology,PSF files Adupa Vasista (Thu Jul 04 2019 - 14:54:25 CDT)
Re: Colvars Orientation Question Xander Gonzalez (Tue Jul 02 2019 - 16:46:11 CDT)
Re: Colvars Orientation Question Giacomo Fiorin (Mon Jul 01 2019 - 19:01:39 CDT)
Re: readmol2 warning: non-unique atoms were renamed. Adupa Vasista (Mon Jul 01 2019 - 15:12:29 CDT)
Colvars Orientation Question Alexander Gonzalez (Mon Jul 01 2019 - 14:59:26 CDT)
Re: readmol2 warning: non-unique atoms were renamed. Joao Ribeiro (Mon Jul 01 2019 - 09:12:22 CDT)
readmol2 warning: non-unique atoms were renamed. Adupa Vasista (Sat Jun 29 2019 - 11:30:25 CDT)
Re: does any body know why GPU Acceleration not work on Windows? Bryan Roessler (Fri Jun 28 2019 - 14:52:47 CDT)
Re: Reload molecular topology for amber files? David Hardy (Fri Jun 28 2019 - 12:12:57 CDT)
AW: does any body know why GPU Acceleration not work on Windows? Norman Geist (Fri Jun 28 2019 - 03:06:21 CDT)
Re: does any body know why GPU Acceleration not work on Windows? Milad Lagzian (Fri Jun 28 2019 - 02:36:16 CDT)
AW: does any body know why GPU Acceleration not work on Windows? Norman Geist (Fri Jun 28 2019 - 02:22:53 CDT)
Re: does any body know why GPU Acceleration not work on Windows? Pratik Narain Srivastava (Fri Jun 28 2019 - 02:18:04 CDT)
Re: does any body know why GPU Acceleration not work on Windows? Miro Astore (Fri Jun 28 2019 - 00:21:46 CDT)
does any body know why GPU Acceleration not work on Windows? Milad Lagzian (Fri Jun 28 2019 - 00:13:49 CDT)
Re: Re: When using WHAM TO ANALYSIS Jiali Wang (Thu Jun 27 2019 - 15:10:40 CDT)
Re: When using WHAM TO ANALYSIS Giacomo Fiorin (Thu Jun 27 2019 - 15:01:47 CDT)
Re: Velocity unit Victor Kwan (Thu Jun 27 2019 - 14:09:19 CDT)
Reload molecular topology for amber files? Norman Geist (Thu Jun 27 2019 - 06:52:49 CDT)
AW: Velocity unit Norman Geist (Thu Jun 27 2019 - 06:06:54 CDT)
Velocity unit Ashkan Shekaari (Thu Jun 27 2019 - 05:47:38 CDT)
Re: Standard Error Calcuation Giacomo Fiorin (Wed Jun 26 2019 - 17:20:57 CDT)
Standard Error Calcuation Mahdi Mousaei (Wed Jun 26 2019 - 17:01:15 CDT)
Re: Question about PMF calculation Giacomo Fiorin (Tue Jun 25 2019 - 11:14:19 CDT)
Re: CUDA acceleration on Windows 10 doesn't work Sunny (Tue Jun 25 2019 - 02:06:25 CDT)
Re: OPC Water Model Brian Radak (Mon Jun 24 2019 - 09:06:32 CDT)
Re: OPC Water Model Peter Freddolino (Mon Jun 24 2019 - 07:18:10 CDT)
Re: CUDA acceleration on Windows 10 doesn't work Milad Lagzian (Mon Jun 24 2019 - 07:09:44 CDT)
OPC Water Model eee ffff (Mon Jun 24 2019 - 05:09:12 CDT)
Re: CUDA acceleration on Windows 10 doesn't work Sunny (Sat Jun 22 2019 - 21:42:58 CDT)
Re: Bug in NAMD Pawel Kedzierski (Sat Jun 22 2019 - 04:52:43 CDT)
Re: Bug in NAMD Marcelo C. R. Melo (Fri Jun 21 2019 - 11:27:15 CDT)
Re: Bug in NAMD Pawel Kedzierski (Fri Jun 21 2019 - 07:01:03 CDT)
Re: Bug in NAMD (was: Big oscillations during QM/MM minimization) Pawel Kedzierski (Thu Jun 20 2019 - 10:35:11 CDT)
Re: Bug in NAMD (was: Big oscillations during QM/MM minimization) Pawel Kedzierski (Thu Jun 20 2019 - 10:11:19 CDT)
Re: Bug in NAMD Marcelo C. R. Melo (Thu Jun 20 2019 - 09:46:36 CDT)
Re: Bug in NAMD Pawel Kedzierski (Thu Jun 20 2019 - 08:23:43 CDT)
CUDA acceleration on Windows 10 doesn't work Maximilian Ebert (Thu Jun 20 2019 - 02:43:05 CDT)
NAMD on Windows 10 with huge performance drop after 39 CPUs Maximilian Ebert (Thu Jun 20 2019 - 02:41:41 CDT)
Immediate postdoc opening in Bio-molecular simulation, University of Alberta, Canada Marawan Hussien (Wed Jun 19 2019 - 19:17:55 CDT)
NAMD Developer Meeting 2019 giuseppe_at_ks.uiuc.edu (Wed Jun 19 2019 - 17:13:31 CDT)
Attachments allowed? Maximilian Ebert (Wed Jun 19 2019 - 11:20:13 CDT)
Re: compiling infiniband version of NAMD Aravinda Munasinghe (Wed Jun 19 2019 - 10:17:07 CDT)
compiling infiniband version of NAMD Kosar Khajeh (Wed Jun 19 2019 - 07:41:27 CDT)
Re: Bug in NAMD (was: Big oscillations during QM/MM minimization) Brian Radak (Tue Jun 18 2019 - 11:42:02 CDT)
Re: Big oscillations during QM/MM minimization mariano spivak (Tue Jun 18 2019 - 09:57:34 CDT)
Bug in NAMD (was: Big oscillations during QM/MM minimization) Pawel Kedzierski (Tue Jun 18 2019 - 01:47:24 CDT)
Re: colvar setting, targetcenters not working jiali wang (Mon Jun 17 2019 - 09:20:41 CDT)
colvar setting, targetcenters not working Jiali Wang (Sun Jun 16 2019 - 20:16:49 CDT)
FATAL ERROR: High global CUDA exclusion count! Sunny (Wed Jun 12 2019 - 12:07:23 CDT)
Re: TMD Partial Fitting Problem mert gÃ¶lcÃ¼k (Wed Jun 12 2019 - 09:32:07 CDT)
FATAL ERROR: High global CUDA exclusion count! Nima Nouri (Wed Jun 12 2019 - 03:20:20 CDT)
Re: TMD Partial Fitting Problem Gumbart, JC (Tue Jun 11 2019 - 18:53:35 CDT)
RE: error in compiling namd Vermaas, Joshua (Tue Jun 11 2019 - 08:00:46 CDT)
error in compiling namd Kosar Khajeh (Tue Jun 11 2019 - 07:45:38 CDT)
TMD Partial Fitting Problem mert gÃ¶lcÃ¼k (Tue Jun 11 2019 - 07:26:02 CDT)
Re: we apply a harmonic potential Giacomo Fiorin (Mon Jun 10 2019 - 12:38:36 CDT)
Re: we apply a harmonic potential Giacomo Fiorin (Sun Jun 09 2019 - 15:18:55 CDT)
Re: Prevent DNA denaturation Takeru KAMEDA (Fri Jun 07 2019 - 08:27:26 CDT)
Re: Problem in Running CUDA-Enabled NAMD Via MOE software Victor Kwan (Fri Jun 07 2019 - 08:21:02 CDT)
Problem in Running CUDA-Enabled NAMD Via MOE software Milad Lagzian (Fri Jun 07 2019 - 04:26:04 CDT)
Re: reg: quenching NAMD trajectory Brian Radak (Thu Jun 06 2019 - 16:37:56 CDT)
Re: reg: quenching NAMD trajectory Lara rajam (Thu Jun 06 2019 - 14:47:22 CDT)
Re: reg: quenching NAMD trajectory Pratik Narain Srivastava (Thu Jun 06 2019 - 14:44:39 CDT)
reg: quenching NAMD trajectory Lara rajam (Thu Jun 06 2019 - 14:39:52 CDT)
Re: Prevent DNA denaturation Ryan McGreevy (Thu Jun 06 2019 - 10:36:45 CDT)
Re: Prevent DNA denaturation Brian Radak (Thu Jun 06 2019 - 10:27:29 CDT)
Re: vecsub:two vectors don't have the same size Joao Ribeiro (Thu Jun 06 2019 - 09:21:58 CDT)
Re: Prevent DNA denaturation Priyanka Mondal (Thu Jun 06 2019 - 08:17:29 CDT)
Prevent DNA denaturation Takeru KAMEDA (Thu Jun 06 2019 - 03:40:48 CDT)
vecsub:two vectors don't have the same size SHRUTEE JEURKAR (Thu Jun 06 2019 - 02:29:47 CDT)
Re: multiplot: Data vector empty, ignoring plot! Adupa Vasista (Wed Jun 05 2019 - 09:20:17 CDT)
Re: multiplot: Data vector empty, ignoring plot! Joao Ribeiro (Wed Jun 05 2019 - 08:51:25 CDT)
Re: multiplot: Data vector empty, ignoring plot! Pratik Narain Srivastava (Wed Jun 05 2019 - 08:41:45 CDT)
Re: multiplot: Data vector empty, ignoring plot! Adupa Vasista (Wed Jun 05 2019 - 08:36:39 CDT)
Re: multiplot: Data vector empty, ignoring plot! Roshan Shrestha (Wed Jun 05 2019 - 08:29:35 CDT)
Re: multiplot: Data vector empty, ignoring plot! Adupa Vasista (Wed Jun 05 2019 - 08:26:20 CDT)
Re: multiplot: Data vector empty, ignoring plot! Pratik Narain Srivastava (Wed Jun 05 2019 - 08:26:30 CDT)
multiplot: Data vector empty, ignoring plot! Adupa Vasista (Wed Jun 05 2019 - 08:18:01 CDT)
Re: NAMD with infinite cutoffs? Brian Radak (Tue Jun 04 2019 - 08:49:36 CDT)
AW: NAMD with infinite cutoffs? Norman Geist (Tue Jun 04 2019 - 08:40:09 CDT)
Re: NAMD with infinite cutoffs? Brian Radak (Tue Jun 04 2019 - 07:59:19 CDT)
Re: Reg: Solvation box Adupa Vasista (Tue Jun 04 2019 - 01:37:20 CDT)
RE: NAMD with infinite cutoffs? Geist, Norman (Mon Jun 03 2019 - 23:58:49 CDT)
RE: NAMD with infinite cutoffs? Vermaas, Joshua (Mon Jun 03 2019 - 17:01:53 CDT)
Re: NAMD with infinite cutoffs? Geist, Norman (Mon Jun 03 2019 - 15:45:40 CDT)
Re: NAMD with infinite cutoffs? Brian Radak (Mon Jun 03 2019 - 13:21:15 CDT)
NAMD with infinite cutoffs? Geist, Norman (Mon Jun 03 2019 - 11:30:24 CDT)
Re: Reg: Solvation box Adupa Vasista (Sun Jun 02 2019 - 08:48:29 CDT)
Re: Reg: Solvation box Jim Parker (Sun Jun 02 2019 - 08:28:21 CDT)
Re: Reg: Solvation box Adupa Vasista (Sun Jun 02 2019 - 08:18:33 CDT)
Re: Reg: Solvation box Pratik Narain Srivastava (Sun Jun 02 2019 - 08:13:06 CDT)
Re: Reg: Solvation box Adupa Vasista (Sun Jun 02 2019 - 08:03:28 CDT)
Re: Reg: Solvation box Axel Kohlmeyer (Sun Jun 02 2019 - 06:42:45 CDT)
Reg: Solvation box Adupa Vasista (Sun Jun 02 2019 - 03:50:50 CDT)
Re: Reg: Docking Pratik Narain Srivastava (Sat Jun 01 2019 - 07:06:54 CDT)
Reg: Docking Adupa Vasista (Sat Jun 01 2019 - 05:08:11 CDT)
Re: Reg: Force Field file Adupa Vasista (Fri May 31 2019 - 01:57:09 CDT)
Re: Reg: Force Field file Roshan Shrestha (Fri May 31 2019 - 01:59:25 CDT)
Re: Reg: Force Field file Adupa Vasista (Fri May 31 2019 - 01:50:57 CDT)
Re: Reg: Force Field file Pratik Narain Srivastava (Fri May 31 2019 - 01:53:13 CDT)
Reg: Force Field file Adupa Vasista (Fri May 31 2019 - 01:47:28 CDT)
Distortion in Structure Minimization HEMANTH H 18310019 (Mon May 27 2019 - 02:01:58 CDT)
Re: FATAL ERROR: Periodic cell has become too small for original patch grid! HEMANTH H 18310019 (Sun May 26 2019 - 21:38:33 CDT)
Re: FATAL ERROR: Periodic cell has become too small for original patch grid! Aravinda Munasinghe (Sun May 26 2019 - 13:29:41 CDT)
FATAL ERROR: Periodic cell has become too small for original patch grid! Adupa Vasista (Sun May 26 2019 - 07:07:39 CDT)
Re: how to switch off hydrogen bonds in TIP4P/2005 water Jeff Comer (Sat May 25 2019 - 15:11:19 CDT)
Re: how to switch off hydrogen bonds in TIP4P/2005 water Axel Kohlmeyer (Sat May 25 2019 - 12:50:45 CDT)
Re: Ingrid Bernardes Santana Martins (Sat May 25 2019 - 06:49:03 CDT)
Re: Axel Kohlmeyer (Sat May 25 2019 - 06:24:15 CDT)
Re: Axel Kohlmeyer (Sat May 25 2019 - 06:17:28 CDT)
Re: Ingrid Bernardes Santana Martins (Sat May 25 2019 - 06:05:29 CDT)
(no subject) Adupa Vasista (Sat May 25 2019 - 05:45:51 CDT)
how to switch off hydrogen bonds in TIP4P/2005 water Monika Madhavi (Fri May 24 2019 - 08:43:59 CDT)
"constraint failure in rattle algorithm" soroush ziaei (Tue May 21 2019 - 17:31:21 CDT)
Running broken-symmetry with namd-orca Francesco Pietra (Tue May 21 2019 - 10:59:29 CDT)
Re: PME with Implicit solvent - Reg Jeff Comer (Mon May 20 2019 - 17:03:04 CDT)
Re: PME with Implicit solvent - Reg Brian Radak (Mon May 20 2019 - 13:55:21 CDT)
Re: compiling NAMD 2.13 make error Priyanka Mondal (Mon May 20 2019 - 13:22:17 CDT)
Re: PME with Implicit solvent - Reg Mani Kandan (Mon May 20 2019 - 12:58:53 CDT)
Re: PME with Implicit solvent - Reg Brian Radak (Mon May 20 2019 - 12:51:40 CDT)
PME with Implicit solvent - Reg Mani Kandan (Mon May 20 2019 - 08:58:32 CDT)
Re: vacuum simulation -Reg Mani Kandan (Sun May 19 2019 - 11:23:23 CDT)
Re: vacuum simulation -Reg Subbarao Kanchi (Sun May 19 2019 - 10:32:33 CDT)
Re: vacuum simulation -Reg Mani Kandan (Sun May 19 2019 - 10:27:47 CDT)
Re: vacuum simulation -Reg Subbarao Kanchi (Sun May 19 2019 - 09:33:18 CDT)
Re: vacuum simulation -Reg Mani Kandan (Sun May 19 2019 - 09:27:36 CDT)
Re: vacuum simulation -Reg Ashkan Shekaari (Sun May 19 2019 - 09:08:11 CDT)
vacuum simulation -Reg Mani Kandan (Sun May 19 2019 - 08:55:02 CDT)
catalysis mechnism of ATPase sunyeping (Sun May 19 2019 - 06:30:07 CDT)
Re: compiling NAMD 2.13 make error Giacomo Fiorin (Sat May 18 2019 - 14:46:52 CDT)
compiling NAMD 2.13 make error Kosar Khajeh (Sat May 18 2019 - 04:37:44 CDT)
Compiler segfault when building 2.13 with GCC 8.x fabricio (Wed May 15 2019 - 13:51:28 CDT)
Re: Make error in compiling NAMD source code Priyanka Mondal (Wed May 15 2019 - 09:52:16 CDT)
Make error in compiling NAMD source code Kosar Khajeh (Wed May 15 2019 - 04:21:50 CDT)
MD without water - Reg Mani Kandan (Mon May 13 2019 - 13:11:31 CDT)
Re: " the error of hydrogen group size " soroush ziaei (Fri May 10 2019 - 09:22:06 CDT)
RE: " the error of hydrogen group size " Lennart Nilsson (Fri May 10 2019 - 08:47:12 CDT)
Re: " the error of hydrogen group size " soroush ziaei (Fri May 10 2019 - 08:28:44 CDT)
AW: patch for cystein bond Bernitzky, Cornelius Constantin Maria (Thu May 09 2019 - 03:48:07 CDT)
RE: patch for cystein bond Lennart Nilsson (Wed May 08 2019 - 15:10:34 CDT)
RE: patch for cystein bond Vermaas, Joshua (Wed May 08 2019 - 13:37:31 CDT)
Re: patch for cystein bond Brian Radak (Wed May 08 2019 - 13:15:27 CDT)
patch for cystein bond Bernitzky, Cornelius Constantin Maria (Wed May 08 2019 - 09:28:01 CDT)
Re: Need help with psfgen : psfgen can't read file.pdb Joao Ribeiro (Tue May 07 2019 - 10:53:30 CDT)
Re: Need help with psfgen : psfgen can't read file.pdb Brian Radak (Tue May 07 2019 - 10:44:39 CDT)
Re: Big oscillations during QM/MM minimization Dawid das (Tue May 07 2019 - 10:07:20 CDT)
Re: Need help with psfgen : psfgen can't read file.pdb Priyanka Mondal (Tue May 07 2019 - 10:05:37 CDT)
Big oscillations during QM/MM minimization Pawel Kedzierski (Tue May 07 2019 - 08:53:18 CDT)
Re: Need help with psfgen : psfgen can't read file.pdb Brian Radak (Tue May 07 2019 - 08:16:01 CDT)
Re: Need help with psfgen : psfgen can't read file.pdb Victor Kwan (Tue May 07 2019 - 01:46:43 CDT)
Need help with psfgen : psfgen can't read file.pdb Priyanka Mondal (Mon May 06 2019 - 20:53:03 CDT)
Re: " the error of hydrogen group size " Brian Radak (Fri May 03 2019 - 12:37:25 CDT)
Re: " the error of hydrogen group size " soroush ziaei (Fri May 03 2019 - 09:48:06 CDT)
Re: orca_plot asking .xyz file from QM-MM Francesco Pietra (Fri May 03 2019 - 08:18:43 CDT)
Re: " the error of hydrogen group size " soroush ziaei (Fri May 03 2019 - 05:56:55 CDT)
Re: Question McGuire, Kelly (Thu May 02 2019 - 14:04:31 CDT)
Re: Question Brian Radak (Thu May 02 2019 - 13:59:15 CDT)
orca_plot asking .xyz file from QM-MM Francesco Pietra (Thu May 02 2019 - 13:03:16 CDT)
Question McGuire, Kelly (Thu May 02 2019 - 12:10:41 CDT)
Re: How to extend an ABF simulation ? Giacomo Fiorin (Wed May 01 2019 - 09:43:54 CDT)
Re: " the error of hydrogen group size " Brian Radak (Wed May 01 2019 - 08:51:08 CDT)
Re: How to extend an ABF simulation ? philippe Bourly (Wed May 01 2019 - 02:55:29 CDT)
How do I add passivated H-atom to ZGNR Priyanka Mondal (Tue Apr 30 2019 - 11:43:20 CDT)
Re: How to extend an ABF simulation ? horacio poblete (Tue Apr 30 2019 - 10:36:49 CDT)
How to extend an ABF simulation ? philippe Bourly (Tue Apr 30 2019 - 10:19:38 CDT)
MD Simulations with GROMACS/NAMD/AMBER/VMD: Seasonal School in Stockholm 10-13 June Joao Ribeiro (Tue Apr 30 2019 - 09:43:46 CDT)
" the error of hydrogen group size " soroush ziaei (Tue Apr 30 2019 - 04:25:57 CDT)
FW (1): 71i sudipta.mml (Mon Apr 29 2019 - 04:45:45 CDT)
Error in the NAMD Tutorial Ashkan Shekaari (Sat Apr 27 2019 - 08:39:21 CDT)
Re: Number of QM Atoms Error McGuire, Kelly (Fri Apr 26 2019 - 18:18:04 CDT)
Postdoc Position at Penn in Chromosome Modeling Hemant Kumar (Fri Apr 26 2019 - 13:41:25 CDT)
Re: vmd-l: Bugs and Questions McGuire, Kelly (Thu Apr 25 2019 - 14:25:02 CDT)
Re: vmd-l: Bugs and Questions Joao Ribeiro (Thu Apr 25 2019 - 14:22:44 CDT)
Re: vmd-l: Bugs and Questions McGuire, Kelly (Thu Apr 25 2019 - 14:15:36 CDT)
Re: vmd-l: Bugs and Questions Joao Ribeiro (Thu Apr 25 2019 - 14:14:17 CDT)
Re: vmd-l: Bugs and Questions McGuire, Kelly (Thu Apr 25 2019 - 14:10:36 CDT)
Re: vmd-l: Bugs and Questions Joao Ribeiro (Thu Apr 25 2019 - 13:39:32 CDT)
Bugs and Questions McGuire, Kelly (Thu Apr 25 2019 - 10:14:02 CDT)
Number of QM Atoms Error McGuire, Kelly (Wed Apr 24 2019 - 18:19:45 CDT)
Re: Water Molecule Issue McGuire, Kelly (Wed Apr 24 2019 - 12:54:01 CDT)
Re: Water Molecule Issue McGuire, Kelly (Wed Apr 24 2019 - 10:12:29 CDT)
Water Molecule Issue McGuire, Kelly (Wed Apr 24 2019 - 10:03:23 CDT)
RE: Umbrella Sampling in PLUMED + NAMD Vermaas, Joshua (Tue Apr 23 2019 - 09:53:12 CDT)
Adding H-bonds to neutralize GNR built using Nanotube Builder in VMD Priyanka Mondal (Tue Apr 23 2019 - 09:30:26 CDT)
Re: Error in PMF Calculations HEMANTH H 18310019 (Tue Apr 23 2019 - 07:06:06 CDT)
RE: Umbrella Sampling in PLUMED + NAMD Vermaas, Joshua (Mon Apr 22 2019 - 11:50:56 CDT)
Umbrella Sampling in PLUMED + NAMD Mikhail Suyetin (Mon Apr 22 2019 - 01:33:04 CDT)
Enthalpy Question McGuire, Kelly (Mon Apr 22 2019 - 00:19:09 CDT)
Re: Parameter and Topology File Question Brian Radak (Sun Apr 21 2019 - 12:30:49 CDT)
Re: Parameter and Topology File Question Victor Kwan (Sun Apr 21 2019 - 07:35:53 CDT)
Parameter and Topology File Question Oscar Bastidas (Sun Apr 21 2019 - 04:44:45 CDT)
Re: Problem with namd 2.13 constant pH molecular dynamics, HSD residue. Brian Radak (Fri Apr 19 2019 - 08:33:04 CDT)
Problem with namd 2.13 constant pH molecular dynamics, HSD residue. Ingrid Bernardes Santana Martins (Fri Apr 19 2019 - 08:01:32 CDT)
Re: About changing charge/multiplicity during QM-MM Gerard Rowe (Fri Apr 19 2019 - 07:46:31 CDT)
Re: Tutorial McGuire, Kelly (Thu Apr 18 2019 - 18:06:25 CDT)
Re: Tutorial Marcelo C. R. Melo (Thu Apr 18 2019 - 14:33:24 CDT)
Tutorial McGuire, Kelly (Thu Apr 18 2019 - 12:42:17 CDT)
Re: Re: Error while equilibrating AGNR nanopore + DNA system Victor Kwan (Tue Apr 16 2019 - 06:02:50 CDT)
Re: Error while equilibrating AGNR nanopore + DNA system Priyanka Mondal (Mon Apr 15 2019 - 12:27:31 CDT)
Re: Building of NAMD on the Linux cluster with InfiniBand Aravinda Munasinghe (Mon Apr 15 2019 - 10:41:08 CDT)
Re: changing value of coulomb constant Brian Radak (Mon Apr 15 2019 - 09:51:36 CDT)
Error while equilibrating AGNR nanopore + DNA system Priyanka Mondal (Mon Apr 15 2019 - 09:45:52 CDT)
Re: changing value of coulomb constant Gumbart, JC (Mon Apr 15 2019 - 09:05:29 CDT)
Re: About changing charge/multiplicity during QM-MM Gerard Rowe (Mon Apr 15 2019 - 08:06:52 CDT)
Building of NAMD on the Linux cluster with InfiniBand ÐÑ€ÑÐ»Ð°Ð½ ÐšÑƒÑÐ¼Ð°ÐµÐ² (Mon Apr 15 2019 - 06:06:12 CDT)
Re: changing value of coulomb constant Brian Radak (Sun Apr 14 2019 - 11:47:16 CDT)
changing value of coulomb constant Akshay Prabhakant (Sun Apr 14 2019 - 01:26:40 CDT)
Re: Non bonding energy calculation through NAMD Pratik Narain Srivastava (Fri Apr 12 2019 - 14:03:43 CDT)
Re: Non bonding energy calculation through NAMD Peter Freddolino (Fri Apr 12 2019 - 14:02:34 CDT)
Re: Non bonding energy calculation through NAMD Gumbart, JC (Fri Apr 12 2019 - 13:04:16 CDT)
Re: Electrostatic interaction of 2 ions Fateme Ghadirian (Fri Apr 12 2019 - 12:39:54 CDT)
Re: Electrostatic interaction of 2 ions Brian Radak (Fri Apr 12 2019 - 10:07:36 CDT)
Electrostatic interaction of 2 ions Fateme Ghadirian (Fri Apr 12 2019 - 09:33:08 CDT)
Re: Umbrella sampling of a protein through a membrane Giacomo Fiorin (Fri Apr 12 2019 - 09:12:38 CDT)
Re: Non bonding energy calculation through NAMD Brian Radak (Fri Apr 12 2019 - 08:58:45 CDT)
Re: Non bonding energy calculation through NAMD varun dewaker (Fri Apr 12 2019 - 08:24:39 CDT)
Re: Non bonding energy calculation through NAMD Brian Radak (Fri Apr 12 2019 - 07:49:32 CDT)
Re: Non bonding energy calculation through NAMD varun dewaker (Fri Apr 12 2019 - 02:29:06 CDT)
RE: Umbrella sampling of a protein through a membrane Villalain Boullon, Jose (Fri Apr 12 2019 - 01:49:24 CDT)
RE: Umbrella sampling of a protein through a membrane Villalain Boullon, Jose (Fri Apr 12 2019 - 01:40:34 CDT)
Re: Umbrella sampling of a protein through a membrane Victor Kwan (Thu Apr 11 2019 - 23:04:59 CDT)
Re: Umbrella sampling of a protein through a membrane Gumbart, JC (Thu Apr 11 2019 - 22:59:10 CDT)
Re: Non bonding energy calculation through NAMD Brian Radak (Thu Apr 11 2019 - 08:56:48 CDT)
Umbrella sampling of a protein through a membrane Villalain Boullon, Jose (Thu Apr 11 2019 - 02:00:51 CDT)
Re: Non bonding energy calculation through NAMD varun dewaker (Thu Apr 11 2019 - 01:46:37 CDT)
Python Wrapper Bug McGuire, Kelly (Thu Apr 11 2019 - 01:08:33 CDT)
QM/MM internal energies Shahar Keinan (Wed Apr 10 2019 - 15:18:19 CDT)
Re: Error in PMF Calculations Souvik Sinha (Wed Apr 10 2019 - 03:38:22 CDT)
Re: Error in PMF Calculations Souvik Sinha (Wed Apr 10 2019 - 03:20:21 CDT)
Re: Error in PMF Calculations HEMANTH H 18310019 (Wed Apr 10 2019 - 01:59:53 CDT)
Re: Error in PMF Calculations Souvik Sinha (Wed Apr 10 2019 - 02:02:20 CDT)
Re: Error in PMF Calculations HEMANTH H 18310019 (Tue Apr 09 2019 - 23:42:20 CDT)
FATAL ERROR: CUDA error CudaComputeNonbonded::forceDoneCheck polled 1000000 times over 154.549621 s on Pe 4 (c36.chundoong device 0 pci 0:2:0) ê¹€ë¯¼ìž¬ (Mon Apr 08 2019 - 23:00:38 CDT)
Re: About changing charge/multiplicity during QM-MM Gerard Rowe (Mon Apr 08 2019 - 11:26:48 CDT)
Re: Pointcharge file in QM/MM setup with ORCA Acharya, Atanu (Mon Apr 08 2019 - 09:18:58 CDT)
Re: Merge File Question McGuire, Kelly (Sun Apr 07 2019 - 00:47:23 CDT)
Merge File Question McGuire, Kelly (Fri Apr 05 2019 - 19:36:08 CDT)
Re: Error in PMF Calculations Jeff Comer (Fri Apr 05 2019 - 08:42:08 CDT)
Re: Error in PMF Calculations HEMANTH H 18310019 (Thu Apr 04 2019 - 23:39:21 CDT)
Re: Pointcharge file in QM/MM setup with ORCA Marcelo C. R. Melo (Thu Apr 04 2019 - 15:05:07 CDT)
Re: Error in PMF Calculations Jeff Comer (Thu Apr 04 2019 - 07:16:38 CDT)
Error in PMF Calculations HEMANTH H 18310019 (Thu Apr 04 2019 - 00:21:54 CDT)
TeraChem QMMM McGuire, Kelly (Wed Apr 03 2019 - 17:42:13 CDT)
Re: [NAMD] How to decompose REUS results into electrostatic and van der Waals contributions Jeff Comer (Wed Apr 03 2019 - 15:10:03 CDT)
Pointcharge file in QM/MM setup with ORCA Acharya, Atanu (Wed Apr 03 2019 - 15:05:00 CDT)
Re: [NAMD] How to decompose REUS results into electrostatic and van der Waals contributions Gumbart, JC (Wed Apr 03 2019 - 14:52:38 CDT)
RE: [NAMD] How to decompose REUS results into electrostatic and van der Waals contributions Vermaas, Joshua (Wed Apr 03 2019 - 11:24:50 CDT)
Re: SMD negative forces Joao Ribeiro (Wed Apr 03 2019 - 10:18:06 CDT)
Re: SMD negative forces Joao Ribeiro (Wed Apr 03 2019 - 10:00:17 CDT)
Re: inputPrefix merge error ABF Abhishek TYAGI (Wed Apr 03 2019 - 09:55:00 CDT)
Re: Running MD simulation for two molecules ê¹€ë¯¼ìž¬ (Wed Apr 03 2019 - 01:44:46 CDT)
[NAMD] How to decompose REUS results into electrostatic and van der Waals contributions Canal de Sebassen (Tue Apr 02 2019 - 19:25:08 CDT)
RE: position restraint only certain residues during minimization Vermaas, Joshua (Tue Apr 02 2019 - 12:17:08 CDT)
RE: Running MD simulation for two molecules Vermaas, Joshua (Tue Apr 02 2019 - 12:14:33 CDT)
Re: inputPrefix merge error ABF Giacomo Fiorin (Tue Apr 02 2019 - 12:02:25 CDT)
Re: position restraint only certain residues during minimization Brian Radak (Tue Apr 02 2019 - 11:31:49 CDT)
position restraint only certain residues during minimization Akshay Prabhakant (Tue Apr 02 2019 - 11:14:57 CDT)
Re: About changing charge/multiplicity during QM-MM Gerard Rowe (Tue Apr 02 2019 - 11:14:57 CDT)
Re: inputPrefix merge error ABF Jeff Comer (Tue Apr 02 2019 - 11:03:54 CDT)
Fwd: About changing charge/multiplicity during QM-MM Francesco Pietra (Tue Apr 02 2019 - 09:36:47 CDT)
Re: Non bonding energy calculation through NAMD Giacomo Fiorin (Tue Apr 02 2019 - 09:00:54 CDT)
Non bonding energy calculation through NAMD varun dewaker (Tue Apr 02 2019 - 03:59:15 CDT)
Running MD simulation for two molecules ê¹€ë¯¼ìž¬ (Tue Apr 02 2019 - 01:23:45 CDT)
Re: inputPrefix merge error ABF Abhishek TYAGI (Mon Apr 01 2019 - 22:29:42 CDT)
Re: inputPrefix merge error ABF Jeff Comer (Mon Apr 01 2019 - 15:36:02 CDT)
Re: TeraChem McGuire, Kelly (Mon Apr 01 2019 - 13:54:58 CDT)
Re: TeraChem Gerard Rowe (Mon Apr 01 2019 - 13:39:51 CDT)
Re: TeraChem McGuire, Kelly (Mon Apr 01 2019 - 13:25:39 CDT)
Re: TeraChem Gerard Rowe (Mon Apr 01 2019 - 13:19:39 CDT)
Re: TclBC forces on individual atoms Udaya Dahal (Mon Apr 01 2019 - 11:56:49 CDT)
RE: TclBC forces on individual atoms Vermaas, Joshua (Mon Apr 01 2019 - 11:49:34 CDT)
inputPrefix merge error ABF Abhishek TYAGI (Sun Mar 31 2019 - 23:46:47 CDT)
TclBC forces on individual atoms Udaya Dahal (Sun Mar 31 2019 - 10:24:52 CDT)
Re: MAOL ABOUT USAGE OF TCL SCRIPT Giacomo Fiorin (Sun Mar 31 2019 - 10:01:33 CDT)
MAOL ABOUT USAGE OF TCL SCRIPT Vidhya Sankar (Sun Mar 31 2019 - 03:56:29 CDT)
Re: TeraChem McGuire, Kelly (Sat Mar 30 2019 - 14:21:51 CDT)
Re: TeraChem McGuire, Kelly (Sat Mar 30 2019 - 14:20:18 CDT)
Re: TeraChem Brian Radak (Sat Mar 30 2019 - 14:13:47 CDT)
Re: Restart Annealing McGuire, Kelly (Sat Mar 30 2019 - 13:48:45 CDT)
Restart Annealing McGuire, Kelly (Sat Mar 30 2019 - 12:09:34 CDT)
TeraChem McGuire, Kelly (Fri Mar 29 2019 - 18:29:18 CDT)
QMMM 1 Node vs Multinode McGuire, Kelly (Fri Mar 29 2019 - 14:48:31 CDT)
AW: mpi with NAMD Norman Geist (Fri Mar 29 2019 - 09:42:17 CDT)
Re: mpi with NAMD John Hamre (Fri Mar 29 2019 - 09:38:55 CDT)
AW: mpi with NAMD Norman Geist (Fri Mar 29 2019 - 09:29:10 CDT)
mpi with NAMD John Hamre (Fri Mar 29 2019 - 09:19:09 CDT)
mail about tcl script Vidhya Sankar (Fri Mar 29 2019 - 08:52:34 CDT)
SMD negative forces Seibold, Steve Allan (Fri Mar 29 2019 - 08:37:03 CDT)
Machinefile Question McGuire, Kelly (Thu Mar 28 2019 - 19:34:43 CDT)
Re: About changing charge/multiplicity during QM-MM Francesco Pietra (Thu Mar 28 2019 - 16:19:01 CDT)
Re: About changing charge/multiplicity during QM-MM Francesco Pietra (Thu Mar 28 2019 - 15:04:14 CDT)
Re: About changing charge/multiplicity during QM-MM William Tao (Thu Mar 28 2019 - 12:05:02 CDT)
Re: About changing charge/multiplicity during QM-MM Francesco Pietra (Thu Mar 28 2019 - 11:49:48 CDT)
Re: Fastest way to get PSF file for pure QM simulation? William Tao (Thu Mar 28 2019 - 11:43:29 CDT)
REMD using remote GPU John Hamre (Thu Mar 28 2019 - 08:51:21 CDT)
Re: mail about pbs script John Hamre (Thu Mar 28 2019 - 08:49:41 CDT)
mail about pbs script Vidhya Sankar (Thu Mar 28 2019 - 06:35:47 CDT)
Re: how to translate a protein without unfolding Karteek Bejagam (Wed Mar 27 2019 - 00:46:45 CDT)
how to translate a protein without unfolding Monika Madhavi (Wed Mar 27 2019 - 00:26:29 CDT)
Re: About changing charge/multiplicity during QM-MM Gerard Rowe (Tue Mar 26 2019 - 16:24:05 CDT)
Re: About changing charge/multiplicity during QM-MM Francesco Pietra (Tue Mar 26 2019 - 11:35:23 CDT)
Re: mail about error in configuration files Brian Radak (Mon Mar 25 2019 - 14:53:39 CDT)
Re: About changing charge/multiplicity during QM-MM Gerard Rowe (Mon Mar 25 2019 - 13:34:09 CDT)
Fwd: About changing charge/multiplicity during QM-MM Francesco Pietra (Mon Mar 25 2019 - 13:20:49 CDT)
RE: mail about error in configuration files Vermaas, Joshua (Mon Mar 25 2019 - 12:03:53 CDT)
Re: Re: Solvate with methanol and acetone using free energy methods in NAMD? Brian Radak (Mon Mar 25 2019 - 11:44:08 CDT)
Re: About changing charge/multiplicity during QM-MM Francesco Pietra (Mon Mar 25 2019 - 11:09:41 CDT)
Re: About changing charge/multiplicity during QM-MM Gerard Rowe (Mon Mar 25 2019 - 09:52:18 CDT)
Re: About changing charge/multiplicity during QM-MM Francesco Pietra (Mon Mar 25 2019 - 09:33:55 CDT)
mail about error in configuration files Vidhya Sankar (Mon Mar 25 2019 - 08:59:01 CDT)
Re: About changing charge/multiplicity during QM-MM McGuire, Kelly (Mon Mar 25 2019 - 02:47:14 CDT)
About changing charge/multiplicity during QM-MM Francesco Pietra (Mon Mar 25 2019 - 02:16:35 CDT)
Re: Solvate with methanol and acetone using free energy methods in NAMD? Braden Kelly (Sun Mar 24 2019 - 14:49:40 CDT)
Re: Fastest way to get PSF file for pure QM simulation? William Tao (Sun Mar 24 2019 - 13:33:03 CDT)
Solvate with methanol and acetone using free energy methods in NAMD? Defrese, Matthew (Sun Mar 24 2019 - 13:03:52 CDT)
Re: Fastest way to get PSF file for pure QM simulation? Joao Ribeiro (Sat Mar 23 2019 - 18:47:12 CDT)
Re: Fastest way to get PSF file for pure QM simulation? William Tao (Sat Mar 23 2019 - 14:32:12 CDT)
Re: Fastest way to get PSF file for pure QM simulation? Marcelo C. R. Melo (Sat Mar 23 2019 - 12:25:04 CDT)
Re: Constraint failure in rattle algorithm for some atoms, simulation becomes unstable Brian Radak (Fri Mar 22 2019 - 11:20:26 CDT)
Re: Constraint failure in rattle algorithm for some atoms, simulation becomes unstable Giacomo Fiorin (Fri Mar 22 2019 - 08:08:24 CDT)
Constraint failure in rattle algorithm for some atoms, simulation becomes unstable Akshay Prabhakant (Fri Mar 22 2019 - 05:01:55 CDT)
Fastest way to get PSF file for pure QM simulation? William Tao (Thu Mar 21 2019 - 21:27:42 CDT)
Re: QMMM Frequency Calculation Francesco Pietra (Thu Mar 21 2019 - 17:05:16 CDT)
Re: QMMM Frequency Calculation McGuire, Kelly (Thu Mar 21 2019 - 15:17:44 CDT)
Re: QMMM Frequency Calculation McGuire, Kelly (Thu Mar 21 2019 - 12:25:34 CDT)
RE: QMMM Frequency Calculation Bennion, Brian (Thu Mar 21 2019 - 12:07:18 CDT)
QMMM Frequency Calculation McGuire, Kelly (Thu Mar 21 2019 - 11:55:12 CDT)
Re: what's the latest on using NAMD (and MD in general) for docking? Homeo Morphism (Thu Mar 21 2019 - 02:04:27 CDT)
Re: what's the latest on using NAMD (and MD in general) for docking? Thomas Evangelidis (Wed Mar 20 2019 - 18:42:16 CDT)
Colvar not working in NAMD2.12 Linux version Mukta Sharma (Wed Mar 20 2019 - 18:01:45 CDT)
Average structure using colvars Deepti Karandur (Wed Mar 20 2019 - 15:39:59 CDT)
Re: how to make a .Dx file trajectory to showing the Electrostatic Maps or ion concentration video? Giacomo Fiorin (Wed Mar 20 2019 - 14:42:13 CDT)
what's the latest on using NAMD (and MD in general) for docking? Homeo Morphism (Wed Mar 20 2019 - 13:20:17 CDT)
Re: how to make a .Dx file trajectory to showing the Electrostatic Maps or ion concentration video? Giacomo Fiorin (Wed Mar 20 2019 - 08:10:44 CDT)
how to make a .Dx file trajectory to showing the Electrostatic Maps or ion concentration video? jiali wang (Tue Mar 19 2019 - 20:00:55 CDT)
Re: COMmotion -- is it a good practice to turn it on for a restart? Brian Radak (Tue Mar 19 2019 - 17:03:02 CDT)
COMmotion -- is it a good practice to turn it on for a restart? Homeo Morphism (Tue Mar 19 2019 - 16:30:02 CDT)
Re: Parallel Simulation Question Gerard Rowe (Tue Mar 19 2019 - 14:59:03 CDT)
Re: Parallel Simulation Question McGuire, Kelly (Tue Mar 19 2019 - 14:22:44 CDT)
Re: need help in study the effect of mutation, L- (Tue Mar 19 2019 - 14:14:03 CDT)
Re: Parallel Simulation Question Gerard Rowe (Tue Mar 19 2019 - 13:39:52 CDT)
Re: vmd-l: ORCA Orbital Bug John Stone (Tue Mar 19 2019 - 13:04:58 CDT)
Re: vmd-l: ORCA Orbital Bug McGuire, Kelly (Tue Mar 19 2019 - 12:43:30 CDT)
Re: vmd-l: ORCA Orbital Bug McGuire, Kelly (Tue Mar 19 2019 - 12:40:34 CDT)
Re: vmd-l: ORCA Orbital Bug John Stone (Tue Mar 19 2019 - 12:39:43 CDT)
Re: vmd-l: ORCA Orbital Bug McGuire, Kelly (Tue Mar 19 2019 - 12:31:43 CDT)
Re: Parallel Simulation Question McGuire, Kelly (Mon Mar 18 2019 - 22:57:23 CDT)
RE: Unit of Force constant of position restraint Vermaas, Joshua (Mon Mar 18 2019 - 11:59:53 CDT)
Unit of Force constant of position restraint Junwoong Yoon (Sun Mar 17 2019 - 23:20:07 CDT)
Re: vmd-l: ORCA Orbital Bug McGuire, Kelly (Sun Mar 17 2019 - 19:58:46 CDT)
Re: vmd-l: ORCA Orbital Bug John Stone (Sun Mar 17 2019 - 19:19:48 CDT)
Parallel Simulation Question McGuire, Kelly (Sat Mar 16 2019 - 23:30:08 CDT)
Re: vmd-l: ORCA Orbital Bug McGuire, Kelly (Sat Mar 16 2019 - 18:34:51 CDT)
Re: vmd-l: ORCA Orbital Bug John Stone (Sat Mar 16 2019 - 01:13:06 CDT)
Re: Re: ORCA NAMD Parallel McGuire, Kelly (Fri Mar 15 2019 - 17:22:08 CDT)
Re: Re: ORCA NAMD Parallel Marcelo C. R. Melo (Fri Mar 15 2019 - 16:20:58 CDT)
need help in study the effect of mutation, L- (Fri Mar 15 2019 - 13:01:00 CDT)
ORCA Orbital Bug McGuire, Kelly (Fri Mar 15 2019 - 11:02:30 CDT)
Re: QMMM ORCA Error McGuire, Kelly (Fri Mar 15 2019 - 10:54:43 CDT)
Re: ORCA NAMD Parallel McGuire, Kelly (Fri Mar 15 2019 - 10:53:25 CDT)
Re: QMMM ORCA Error Gerard Rowe (Fri Mar 15 2019 - 09:47:34 CDT)
Re: ORCA NAMD Parallel Gerard Rowe (Fri Mar 15 2019 - 09:45:30 CDT)
alculate energy force field L- (Thu Mar 14 2019 - 11:39:24 CDT)
RE: "the error of movement of atoms" soroush ziaei (Thu Mar 14 2019 - 03:36:25 CDT)
RE: "the error of movement of atoms" soroush ziaei (Thu Mar 14 2019 - 02:59:31 CDT)
ORCA NAMD Parallel McGuire, Kelly (Thu Mar 14 2019 - 02:51:09 CDT)
QMMM ORCA Error McGuire, Kelly (Thu Mar 14 2019 - 01:50:24 CDT)
Re: Re: Didn't Find vdw parameter QMMM McGuire, Kelly (Thu Mar 14 2019 - 01:48:03 CDT)
Re: BUG? reinitatoms on wrapped coordinates occasionally fail with rigidbonds Jim Phillips (Wed Mar 13 2019 - 13:43:16 CDT)
Re: Re: Didn't Find vdw parameter QMMM Jim Phillips (Wed Mar 13 2019 - 13:35:58 CDT)
Re: Re: Didn't Find vdw parameter QMMM Brian Radak (Wed Mar 13 2019 - 10:59:15 CDT)
Re: Colvars: Are the derivatives of optimal rotation matrix wrt atomic coordinates applied implicitly? yjcoshc_at_gmail.com (Wed Mar 13 2019 - 10:41:47 CDT)
Re: Colvars: Are the derivatives of optimal rotation matrix wrt atomic coordinates applied implicitly? Giacomo Fiorin (Wed Mar 13 2019 - 10:39:20 CDT)
Re: Colvars: Are the derivatives of optimal rotation matrix wrt atomic coordinates applied implicitly? yjcoshc_at_gmail.com (Wed Mar 13 2019 - 10:08:55 CDT)
Re: Colvars: Are the derivatives of optimal rotation matrix wrt atomic coordinates applied implicitly? JÃ©rÃ´me HÃ©nin (Wed Mar 13 2019 - 09:37:31 CDT)
Colvars: Are the derivatives of optimal rotation matrix wrt atomic coordinates applied implicitly? yjcoshc_at_gmail.com (Wed Mar 13 2019 - 08:01:04 CDT)
BUG? reinitatoms on wrapped coordinates occasionally fail with rigidbonds Norman Geist (Wed Mar 13 2019 - 03:05:56 CDT)
Re: Didn't Find vdw parameter QMMM McGuire, Kelly (Tue Mar 12 2019 - 22:13:43 CDT)
Didn't Find vdw parameter QMMM McGuire, Kelly (Tue Mar 12 2019 - 21:41:31 CDT)
Research Programmer for VMD/NAMD at UIUC JoÃ£o Ribeiro (Tue Mar 12 2019 - 13:20:11 CDT)
Zero PME pencils found Alex Saad-Falcon (Tue Mar 12 2019 - 12:43:03 CDT)
Re: NAMD support for lone pairs Brian Radak (Tue Mar 12 2019 - 11:55:21 CDT)
Re: NAMD support for lone pairs Tabitha Nobel (Tue Mar 12 2019 - 11:11:39 CDT)
Re: NAMD support for lone pairs Gumbart, JC (Tue Mar 12 2019 - 08:35:03 CDT)
Re: NAMD support for lone pairs Brian Radak (Tue Mar 12 2019 - 07:50:44 CDT)
Re: Any NAMD-Working Small Organic Molecule Gumbart, JC (Mon Mar 11 2019 - 23:57:11 CDT)
Re: Colvars: implement a CV which requires computing minimal RMSDs with respect to multiple different reference frames yjcoshc (Mon Mar 11 2019 - 22:16:08 CDT)
Re: NAMD support for lone pairs Tabitha Nobel (Mon Mar 11 2019 - 20:01:06 CDT)
Any NAMD-Working Small Organic Molecule Alex Saad-Falcon (Mon Mar 11 2019 - 19:35:17 CDT)
Re: NAMD support for lone pairs Brian Radak (Mon Mar 11 2019 - 19:27:48 CDT)
Re: NAMD support for lone pairs Tabitha Nobel (Mon Mar 11 2019 - 18:10:43 CDT)
Re: NAMD support for lone pairs Brian Radak (Mon Mar 11 2019 - 17:38:33 CDT)
Re: NAMD support for lone pairs Tabitha Nobel (Mon Mar 11 2019 - 17:19:54 CDT)
Re: NAMD support for lone pairs Tabitha Nobel (Mon Mar 11 2019 - 17:15:45 CDT)
Re: NAMD support for lone pairs Brian Radak (Mon Mar 11 2019 - 16:39:24 CDT)
Re: NAMD support for lone pairs Brian Radak (Mon Mar 11 2019 - 16:30:56 CDT)
Re: NAMD support for lone pairs Tabitha Nobel (Mon Mar 11 2019 - 16:02:11 CDT)
Re: NAMD support for lone pairs Brian Radak (Mon Mar 11 2019 - 13:41:20 CDT)
Re: Colvars: implement a CV which requires computing minimal RMSDs with respect to multiple different reference frames Giacomo Fiorin (Mon Mar 11 2019 - 10:39:31 CDT)
Re: Colvars: implement a CV which requires computing minimal RMSDs with respect to multiple different reference frames yjcoshc_at_gmail.com (Mon Mar 11 2019 - 08:50:17 CDT)
Re: Colvars: implement a CV which requires computing minimal RMSDs with respect to multiple different reference frames JÃ©rÃ´me HÃ©nin (Mon Mar 11 2019 - 08:01:07 CDT)
Re: info about gpu hardware Stefano Guglielmo (Sun Mar 10 2019 - 03:38:15 CDT)
[namd] Help with sortreplicas Canal de Sebassen (Sat Mar 09 2019 - 13:01:49 CST)
Colvars: implement a CV which requires computing minimal RMSDs with respect to multiple different reference frames yjcoshc (Fri Mar 08 2019 - 19:41:00 CST)
Re: NAMD support for lone pairs Gumbart, JC (Fri Mar 08 2019 - 18:18:28 CST)
Re: NAMD support for lone pairs Brian Radak (Fri Mar 08 2019 - 14:14:36 CST)
Re: NAMD support for lone pairs Tabitha Nobel (Fri Mar 08 2019 - 11:10:13 CST)
Re: FATAL ERROR: Error in QM-MM bond assignment; bonded QM atoms with occupancy=1 Marcelo C. R. Melo (Fri Mar 08 2019 - 10:51:43 CST)
Re: Re: QM/MM error: The number of QM atoms received is different than expected Marcelo C. R. Melo (Fri Mar 08 2019 - 10:44:33 CST)
Re: NAMD support for lone pairs Brian Radak (Fri Mar 08 2019 - 09:45:39 CST)
NAMD support for lone pairs Tabitha Nobel (Thu Mar 07 2019 - 20:26:05 CST)
RE: NAMD Configuration file error Jim Phillips (Thu Mar 07 2019 - 11:13:51 CST)
Re: NAMD Configuration file error ê¹€ë¯¼ìž¬ (Thu Mar 07 2019 - 10:23:14 CST)
RE: NAMD Configuration file error Vermaas, Joshua (Thu Mar 07 2019 - 10:03:26 CST)
NAMD Configuration file error ê¹€ë¯¼ìž¬ (Thu Mar 07 2019 - 00:29:52 CST)
Re: QM/MM error: The number of QM atoms received is different than expected Haohao Fu (Wed Mar 06 2019 - 21:11:46 CST)
QM/MM error: The number of QM atoms received is different than expected Haohao Fu (Wed Mar 06 2019 - 21:08:27 CST)
RE: making new psf file from .prm and pdb file Vermaas, Joshua (Tue Mar 05 2019 - 21:01:40 CST)
making new psf file from .prm and pdb file Hadi Rahmaninejad (Tue Mar 05 2019 - 16:59:17 CST)
Re: Minimization Error ê¹€ë¯¼ìž¬ (Tue Mar 05 2019 - 05:02:52 CST)
Re: Minimization Error Pratik Narain Srivastava (Tue Mar 05 2019 - 01:01:22 CST)
Minimization Error ê¹€ë¯¼ìž¬ (Tue Mar 05 2019 - 00:31:36 CST)
Re: restrict atoms to cross a boundary Udaya Dahal (Mon Mar 04 2019 - 15:59:57 CST)
Re: restrict atoms to cross a boundary Giacomo Fiorin (Mon Mar 04 2019 - 15:50:04 CST)
restrict atoms to cross a boundary Udaya Dahal (Mon Mar 04 2019 - 13:42:09 CST)
FATAL ERROR: Error in QM-MM bond assignment; bonded QM atoms with occupancy=1 shreyas supekar (Mon Mar 04 2019 - 05:53:17 CST)
Re: Parameter Optimization Advice Roshan Shrestha (Fri Mar 01 2019 - 23:26:16 CST)
Re: Parameter Optimization Advice Gumbart, JC (Fri Mar 01 2019 - 23:22:28 CST)
Re: Parameter Optimization Advice Gumbart, JC (Fri Mar 01 2019 - 23:15:45 CST)
RE: "the error of movement of atoms" Vermaas, Joshua (Fri Mar 01 2019 - 16:21:35 CST)
Re: "the error of movement of atoms" Brian Radak (Fri Mar 01 2019 - 16:17:57 CST)
Re: Parameter Optimization Advice McGuire, Kelly (Fri Mar 01 2019 - 15:09:12 CST)
"the error of movement of atoms" soroush ziaei (Fri Mar 01 2019 - 11:33:21 CST)
Re: Parameter Optimization Advice Brian Radak (Fri Mar 01 2019 - 13:57:15 CST)
RE: Parameter Optimization Advice Vermaas, Joshua (Fri Mar 01 2019 - 13:54:23 CST)
Re: Parameter Optimization Advice McGuire, Kelly (Fri Mar 01 2019 - 13:42:39 CST)
RE: Parameter Optimization Advice Vermaas, Joshua (Fri Mar 01 2019 - 13:36:15 CST)
Re: Parameter Optimization Advice McGuire, Kelly (Fri Mar 01 2019 - 13:34:22 CST)
Re: Parameter Optimization Advice McGuire, Kelly (Fri Mar 01 2019 - 13:31:22 CST)
RE: Parameter Optimization Advice Lennart Nilsson (Fri Mar 01 2019 - 13:20:57 CST)
Re: Parameter Optimization Advice Brian Radak (Fri Mar 01 2019 - 13:18:15 CST)
Parameter Optimization Advice McGuire, Kelly (Fri Mar 01 2019 - 12:13:21 CST)
RE: Targeted molecular dynamics domain selection question Vermaas, Joshua (Fri Mar 01 2019 - 12:05:50 CST)
Re: Multiple Constraints Equilibration Giacomo Fiorin (Fri Mar 01 2019 - 11:56:53 CST)
Re: Multiple Constraints Equilibration Brian Radak (Fri Mar 01 2019 - 11:28:33 CST)
solvating silica Hadi Rahmaninejad (Fri Mar 01 2019 - 09:36:13 CST)
Multiple Constraints Equilibration McGuire, Kelly (Thu Feb 28 2019 - 19:30:52 CST)
RE: Targeted molecular dynamics domain selection question Vermaas, Joshua (Thu Feb 28 2019 - 18:52:29 CST)
Targeted molecular dynamics domain selection question Aditya Ranganathan (Thu Feb 28 2019 - 17:19:49 CST)
Re: strange benchmark results -- how would you explain them and what would you advice? Homeo Morphism (Thu Feb 28 2019 - 11:43:55 CST)
Re: Running NAMD on Linux Cluster ê¹€ë¯¼ìž¬ (Wed Feb 27 2019 - 18:45:34 CST)
Re: GolP-CHARMM horacio poblete (Wed Feb 27 2019 - 14:06:03 CST)
Re: Running NAMD on Linux Cluster Jim Phillips (Wed Feb 27 2019 - 13:57:49 CST)
Re: Running NAMD on Linux Cluster ê¹€ë¯¼ìž¬ (Wed Feb 27 2019 - 12:51:05 CST)
RE: Running NAMD on Linux Cluster Vermaas, Joshua (Wed Feb 27 2019 - 12:26:52 CST)
Re: Running NAMD on Linux Cluster Aravinda Munasinghe (Wed Feb 27 2019 - 12:03:35 CST)
GolP-CHARMM Mikhail Suyetin (Wed Feb 27 2019 - 10:24:21 CST)
Re: problem with solvating a structure Hadi Rahmaninejad (Wed Feb 27 2019 - 10:04:07 CST)
Fwd: Running NAMD on Linux Cluster ê¹€ë¯¼ìž¬ (Wed Feb 27 2019 - 07:10:34 CST)
AW: strange benchmark results -- how would you explain them and what would you advice? Norman Geist (Wed Feb 27 2019 - 04:57:12 CST)
Re: problem with solvating a structure Udaya Dahal (Tue Feb 26 2019 - 15:38:45 CST)
Re: problem with solvating a structure JoÃ£o Ribeiro (Tue Feb 26 2019 - 15:33:42 CST)
Re: problem with solvating a structure JoÃ£o Ribeiro (Tue Feb 26 2019 - 14:48:12 CST)
problem with solvating a structure Hadi Rahmaninejad (Tue Feb 26 2019 - 14:40:05 CST)
problem with solvating a structure Hadi Rahmaninejad (Tue Feb 26 2019 - 14:32:28 CST)
Re: Running NAMD on Linux Cluster Aravinda Munasinghe (Tue Feb 26 2019 - 14:06:13 CST)
patch for threonine (THP2). L- (Tue Feb 26 2019 - 12:46:15 CST)
strange benchmark results -- how would you explain them and what would you advice? Homeo Morphism (Tue Feb 26 2019 - 11:38:13 CST)
Running NAMD on Linux Cluster ê¹€ë¯¼ìž¬ (Tue Feb 26 2019 - 09:22:37 CST)
Re: colvar restraint simulation Prabir Khatua (Mon Feb 25 2019 - 13:52:39 CST)
Constant Force SMD Question McGuire, Kelly (Mon Feb 25 2019 - 12:25:34 CST)
Re: Stochastic velocity rescaling for Free Energy calculations Brian Radak (Mon Feb 25 2019 - 12:05:22 CST)
Re: colvar restraint simulation Giacomo Fiorin (Mon Feb 25 2019 - 11:40:17 CST)
RE: colvar restraint simulation Vermaas, Joshua (Mon Feb 25 2019 - 11:35:05 CST)
colvar restraint simulation Prabir Khatua (Mon Feb 25 2019 - 11:04:33 CST)
Re: Fwd: QM-MM NAMD-ORCA broken symmetry Marcelo C. R. Melo (Mon Feb 25 2019 - 10:23:20 CST)
Re: Fwd: QM-MM NAMD-ORCA broken symmetry Gerard Rowe (Mon Feb 25 2019 - 08:52:58 CST)
Stochastic velocity rescaling for Free Energy calculations Braden Kelly (Sat Feb 23 2019 - 15:21:37 CST)
Fwd: QM-MM NAMD-ORCA broken symmetry Francesco Pietra (Sat Feb 23 2019 - 14:34:22 CST)
Re: Lennard-Jones Potential Victor Kwan (Sat Feb 23 2019 - 12:41:34 CST)
Re: Lennard-Jones Potential McGuire, Kelly (Sat Feb 23 2019 - 12:11:08 CST)
Re: Lennard-Jones Potential Victor Kwan (Sat Feb 23 2019 - 12:09:01 CST)
Re: Lennard-Jones Potential McGuire, Kelly (Sat Feb 23 2019 - 12:02:18 CST)
Re: Lennard-Jones Potential Victor Kwan (Sat Feb 23 2019 - 12:00:36 CST)
H2 Topology and Parameter files Teja Vanjari (Sat Feb 23 2019 - 11:58:35 CST)
Re: Lennard-Jones Potential Kowsar Khajeh (Sat Feb 23 2019 - 11:47:11 CST)
Re: Lennard-Jones Potential McGuire, Kelly (Sat Feb 23 2019 - 11:37:58 CST)
Re: Lennard-Jones Potential Victor Kwan (Sat Feb 23 2019 - 11:35:49 CST)
Lennard-Jones Potential McGuire, Kelly (Sat Feb 23 2019 - 11:34:21 CST)
QM-MM NAMD-ORCA broken symmetry Francesco Pietra (Sat Feb 23 2019 - 10:38:42 CST)
Re: Constant Velocity Pulls McGuire, Kelly (Fri Feb 22 2019 - 13:12:56 CST)
Re: Constant Velocity Pulls Brian Radak (Fri Feb 22 2019 - 13:06:09 CST)
Re: Constant Velocity Pulls McGuire, Kelly (Fri Feb 22 2019 - 12:58:37 CST)
RE: Energy Minimization Simulation Vermaas, Joshua (Fri Feb 22 2019 - 12:55:37 CST)
RE: Constant Velocity Pulls Vermaas, Joshua (Fri Feb 22 2019 - 12:51:41 CST)
Energy Minimization Simulation ê¹€ë¯¼ìž¬ (Fri Feb 22 2019 - 12:09:38 CST)
Constant Velocity Pulls McGuire, Kelly (Fri Feb 22 2019 - 09:58:42 CST)
Re: Utilising the GPU in NAMD((NVIDIA CUDA acceleration) in windows Darin Lory (Thu Feb 21 2019 - 16:52:52 CST)
RE: Utilising the GPU in NAMD((NVIDIA CUDA acceleration) in windows Vermaas, Joshua (Thu Feb 21 2019 - 12:24:15 CST)
Re: Utilising the GPU in NAMD((NVIDIA CUDA acceleration) in windows Roessler, Bryan C (Thu Feb 21 2019 - 09:32:46 CST)
Utilising the GPU in NAMD((NVIDIA CUDA acceleration) in windows Denish Poudyal (Thu Feb 21 2019 - 08:59:29 CST)
Constant Velocity SMD Question McGuire, Kelly (Thu Feb 21 2019 - 01:32:02 CST)
Re: Running NAMD in MPI environment Jim Phillips (Wed Feb 20 2019 - 11:04:09 CST)
Running NAMD in MPI environment ê¹€ë¯¼ìž¬ (Wed Feb 20 2019 - 09:58:42 CST)
Re: Free energy plot Miao, Yinglong (Tue Feb 19 2019 - 21:34:04 CST)
Re: TIP4P water box Peter Freddolino (Tue Feb 19 2019 - 21:03:02 CST)
Re: Free energy plot Roshan Shrestha (Tue Feb 19 2019 - 19:31:12 CST)
Re: Running QM-MM multinode Francesco Pietra (Tue Feb 19 2019 - 14:25:32 CST)
TIP4P water box ê¹€ë¯¼ìž¬ (Tue Feb 19 2019 - 12:59:01 CST)
Free energy plot Faramarz Joodaki (Tue Feb 19 2019 - 11:57:20 CST)
Re: Running QM-MM multinode Gerard Rowe (Tue Feb 19 2019 - 11:25:59 CST)
Re: About restarting QM-MM simulation francesco.pietra_at_accademialucchese.it (Sun Feb 17 2019 - 15:50:41 CST)
Re: About restarting QM-MM simulation Marcelo C. R. Melo (Sun Feb 17 2019 - 15:26:12 CST)
Re: Running QM-MM multinode Francesco Pietra (Sun Feb 17 2019 - 01:41:05 CST)
Re: Error running deinterleave_idws.py on FEP simulation output Brian Radak (Sat Feb 16 2019 - 13:18:44 CST)
Re: Running QM-MM multinode Bennion, Brian (Sat Feb 16 2019 - 12:03:19 CST)
Running QM-MM multinode Francesco Pietra (Sat Feb 16 2019 - 02:12:26 CST)
Re: Error running deinterleave_idws.py on FEP simulation output Amy Rice (Fri Feb 15 2019 - 16:13:04 CST)
Re: About restarting QM-MM simulation Francesco Pietra (Fri Feb 15 2019 - 02:34:56 CST)
Re: vmd-l: PDB structures of peptides Aravinda Munasinghe (Thu Feb 14 2019 - 18:26:40 CST)
Re: About restarting QM-MM simulation Francesco Pietra (Thu Feb 14 2019 - 16:34:46 CST)
Re: QMMM Question McGuire, Kelly (Thu Feb 14 2019 - 14:06:11 CST)
Re: QMMM Question Brian Radak (Thu Feb 14 2019 - 13:04:50 CST)
Re: Dual topology FEP for anions Brian Radak (Thu Feb 14 2019 - 12:11:47 CST)
Re: About restarting QM-MM simulation Marcelo C. R. Melo (Thu Feb 14 2019 - 11:33:24 CST)
QMMM Question McGuire, Kelly (Thu Feb 14 2019 - 11:26:53 CST)
Re: About restarting QM-MM simulation Gerard Rowe (Thu Feb 14 2019 - 10:38:06 CST)
RE: Dual topology FEP for anions Vermaas, Joshua (Thu Feb 14 2019 - 09:59:17 CST)
Re: About restarting QM-MM simulation Francesco Pietra (Thu Feb 14 2019 - 08:46:34 CST)
Re: About restarting QM-MM simulation Francesco Pietra (Thu Feb 14 2019 - 04:17:35 CST)
PDB structures of peptides Mikhail Suyetin (Thu Feb 14 2019 - 03:05:15 CST)
Dual topology FEP for anions Hristina Zhekova (Wed Feb 13 2019 - 18:57:12 CST)
Re: About restarting QM-MM simulation Marcelo C. R. Melo (Wed Feb 13 2019 - 16:20:33 CST)
solute scaling does not affect electrostatics (and other quirks) Jeff Comer (Wed Feb 13 2019 - 15:20:02 CST)
Re: About restarting QM-MM simulation Francesco Pietra (Wed Feb 13 2019 - 14:47:45 CST)
Re: About restarting QM-MM simulation Francesco Pietra (Wed Feb 13 2019 - 14:47:13 CST)
Re: Force constant for Umbrella sampling and WHAM Udaya Dahal (Wed Feb 13 2019 - 13:08:44 CST)
Re: About restarting QM-MM simulation Eric Smoll (Wed Feb 13 2019 - 12:48:05 CST)
Error running deinterleave_idws.py on FEP simulation output Amy Rice (Wed Feb 13 2019 - 12:42:10 CST)
Re: About restarting QM-MM simulation Marcelo C. R. Melo (Wed Feb 13 2019 - 12:31:57 CST)
RE: Force constant for Umbrella sampling and WHAM Vermaas, Joshua (Wed Feb 13 2019 - 12:24:51 CST)
Re: Force constant for Umbrella sampling and WHAM Giacomo Fiorin (Wed Feb 13 2019 - 12:19:47 CST)
Force constant for Umbrella sampling and WHAM Udaya Dahal (Wed Feb 13 2019 - 12:07:42 CST)
About restarting QM-MM simulation Francesco Pietra (Wed Feb 13 2019 - 09:32:54 CST)
Re: Gromacs to Charmm FF Format Conversion -Reg Mani Kandan (Tue Feb 12 2019 - 10:40:15 CST)
Re: CSVR + eABF, system temperature set to zero Michael von Domaros (Tue Feb 12 2019 - 16:38:01 CST)
RE: Gromacs to Charmm FF Format Conversion -Reg Vermaas, Joshua (Tue Feb 12 2019 - 10:34:53 CST)
Re: Large number of simulations in parallel using replica exchange. Brian Radak (Tue Feb 12 2019 - 10:32:28 CST)
Re: info about gpu hardware Roessler, Bryan C (Tue Feb 12 2019 - 09:47:57 CST)
Fwd: Gromacs to Charmm FF Format Conversion -Reg Mani Kandan (Tue Feb 12 2019 - 09:44:10 CST)
RE: Gromacs to Charmm FF Format Conversion -Reg Lennart Nilsson (Tue Feb 12 2019 - 09:40:18 CST)
Re: Gromacs to Charmm FF Format Conversion -Reg Roessler, Bryan C (Tue Feb 12 2019 - 09:23:28 CST)
Gromacs to Charmm FF Format Conversion -Reg Mani Kandan (Tue Feb 12 2019 - 08:12:40 CST)
Re: CSVR + eABF, system temperature set to zero Giacomo Fiorin (Tue Feb 12 2019 - 07:19:53 CST)
AW: Large number of simulations in parallel using replica exchange. Norman Geist (Tue Feb 12 2019 - 01:54:14 CST)
Re: CSVR + eABF, system temperature set to zero Giacomo Fiorin (Mon Feb 11 2019 - 22:15:47 CST)
Re: Large number of simulations in parallel using replica exchange. Giacomo Fiorin (Mon Feb 11 2019 - 22:06:38 CST)
Re: Large number of simulations in parallel using replica exchange. Aravinda Munasinghe (Mon Feb 11 2019 - 21:44:41 CST)
Re: Sending REUS simulations to Stampede Canal de Sebassen (Mon Feb 11 2019 - 21:25:31 CST)
Re: Sending REUS simulations to Stampede Giacomo Fiorin (Mon Feb 11 2019 - 21:02:55 CST)
Sending REUS simulations to Stampede Canal de Sebassen (Mon Feb 11 2019 - 19:39:24 CST)
CSVR + eABF, system temperature set to zero Michael von Domaros (Mon Feb 11 2019 - 18:51:37 CST)
Large number of simulations in parallel using replica exchange. Dipak Balasaheb Sanap (Mon Feb 11 2019 - 14:52:26 CST)
Re: Maximum Timestep for NAMD Prakash Saud (Sun Feb 10 2019 - 09:59:51 CST)
Re: jeevan gc (Sun Feb 10 2019 - 09:52:26 CST)
Re: Using harmonic walls on water molecules Moises Ernesto Romero (Fri Feb 08 2019 - 15:23:45 CST)
Re: Maximum Timestep for NAMD Aravinda Munasinghe (Fri Feb 08 2019 - 09:07:55 CST)
Re: reinitatoms Brian Radak (Fri Feb 08 2019 - 07:51:25 CST)
Re: reinitatoms Laura Lopes (Fri Feb 08 2019 - 03:38:55 CST)
AW: MSM grid values Norman Geist (Fri Feb 08 2019 - 03:04:28 CST)
AW: MSM grid values Norman Geist (Fri Feb 08 2019 - 02:59:55 CST)
Re: MSM grid values Denish Poudyal (Thu Feb 07 2019 - 19:46:23 CST)
Re: Maximum Timestep for NAMD Giacomo Fiorin (Thu Feb 07 2019 - 15:57:46 CST)
Re: Maximum Timestep for NAMD Giacomo Fiorin (Thu Feb 07 2019 - 15:37:58 CST)
Re: Maximum Timestep for NAMD Braden Kelly (Thu Feb 07 2019 - 15:34:48 CST)
RE: Maximum Timestep for NAMD Vermaas, Joshua (Thu Feb 07 2019 - 15:02:20 CST)
Re: Maximum Timestep for NAMD Richard Overstreet (Thu Feb 07 2019 - 14:51:30 CST)
Re: MSM grid values David Hardy (Thu Feb 07 2019 - 14:43:02 CST)
RE: Maximum Timestep for NAMD Bennion, Brian (Thu Feb 07 2019 - 14:41:57 CST)
Maximum Timestep for NAMD Alex Saad-Falcon (Thu Feb 07 2019 - 14:24:30 CST)
MSM grid values Denish Poudyal (Wed Feb 06 2019 - 23:15:24 CST)
RE: Using harmonic walls on water molecules Vermaas, Joshua (Mon Feb 04 2019 - 19:50:52 CST)
Using harmonic walls on water molecules Moises Ernesto Romero (Mon Feb 04 2019 - 19:14:39 CST)
Re: Tuning QM-MM with namd-orca on one cluster node Francesco Pietra (Mon Feb 04 2019 - 01:54:31 CST)
Re: Tuning QM-MM with namd-orca on one cluster node Marcelo C. R. Melo (Sun Feb 03 2019 - 17:03:54 CST)
Fwd: Tuning QM-MM with namd-orca on one cluster node Francesco Pietra (Sat Feb 02 2019 - 03:07:47 CST)
Re: Tuning QM-MM with namd-orca on one cluster node Francesco Pietra (Fri Feb 01 2019 - 09:24:44 CST)
Re: Fwd: Tuning QM-MM with namd-orca on one cluster node Francesco Pietra (Fri Feb 01 2019 - 09:10:40 CST)
Re: Tuning QM-MM with namd-orca on one cluster node Marcelo C. R. Melo (Thu Jan 31 2019 - 16:41:35 CST)
Re: Fwd: Tuning QM-MM with namd-orca on one cluster node Jim Phillips (Thu Jan 31 2019 - 15:47:35 CST)
Fwd: Tuning QM-MM with namd-orca on one cluster node Francesco Pietra (Thu Jan 31 2019 - 15:30:40 CST)
Re: Tuning QM-MM with namd-orca on one cluster node Francesco Pietra (Thu Jan 31 2019 - 15:22:25 CST)
RE: info about gpu hardware Vermaas, Joshua (Thu Jan 31 2019 - 13:35:54 CST)
Re: Tuning QM-MM with namd-orca on one cluster node Marcelo C. R. Melo (Thu Jan 31 2019 - 13:07:53 CST)
Tuning QM-MM with namd-orca on one cluster node Francesco Pietra (Thu Jan 31 2019 - 12:25:15 CST)
info about gpu hardware Stefano Guglielmo (Thu Jan 31 2019 - 11:12:57 CST)
Re: pre compiled charmm-6.8.2 for namd2.13 nightly version compilation for multiple GPU node simulations Aravinda Munasinghe (Thu Jan 31 2019 - 08:58:00 CST)
Re: pre compiled charmm-6.8.2 for namd2.13 nightly version compilation for multiple GPU node simulations Giacomo Fiorin (Thu Jan 31 2019 - 08:50:46 CST)
Re: pre compiled charmm-6.8.2 for namd2.13 nightly version compilation for multiple GPU node simulations Aravinda Munasinghe (Wed Jan 30 2019 - 20:18:13 CST)
Re: Question about colvars Faramarz Joodaki (Wed Jan 30 2019 - 19:29:31 CST)
RE: Question about colvars Vermaas, Joshua (Wed Jan 30 2019 - 19:19:56 CST)
Question about colvars Faramarz Joodaki (Wed Jan 30 2019 - 19:06:12 CST)
Re: pre compiled charmm-6.8.2 for namd2.13 nightly version compilation for multiple GPU node simulations Aravinda Munasinghe (Wed Jan 30 2019 - 17:17:56 CST)
Re: pre compiled charmm-6.8.2 for namd2.13 nightly version compilation for multiple GPU node simulations Jim Phillips (Wed Jan 30 2019 - 16:34:39 CST)
Re: pre compiled charmm-6.8.2 for namd2.13 nightly version compilation for multiple GPU node simulations Aravinda Munasinghe (Tue Jan 29 2019 - 22:32:06 CST)
RE: pre compiled charmm-6.8.2 for namd2.13 nightly version compilation for multiple GPU node simulations Vermaas, Joshua (Tue Jan 29 2019 - 11:42:29 CST)
pre compiled charmm-6.8.2 for namd2.13 nightly version compilation for multiple GPU node simulations Aravinda Munasinghe (Tue Jan 29 2019 - 10:37:15 CST)
Re: hbond restraint simulation Prabir Khatua (Mon Jan 28 2019 - 15:40:36 CST)
RE: hbond restraint simulation Vermaas, Joshua (Mon Jan 28 2019 - 15:23:57 CST)
RE: "-nan" free energy from WHAM analysis Vermaas, Joshua (Mon Jan 28 2019 - 09:37:24 CST)
Re: gaussian aMD with iE=2 (setting E threshold at maximum) Vlad Cojocaru (Mon Jan 28 2019 - 09:26:31 CST)
Re: gaussian aMD with iE=2 (setting E threshold at maximum) Miao, Yinglong (Mon Jan 28 2019 - 09:02:37 CST)
Re: hbond restraint simulation Prabir Khatua (Sun Jan 27 2019 - 16:33:59 CST)
"-nan" free energy from WHAM analysis Junwoong Yoon (Sun Jan 27 2019 - 12:11:58 CST)
Re: gaussian aMD with iE=2 (setting E threshold at maximum) Vlad Cojocaru (Sun Jan 27 2019 - 06:00:02 CST)
RE: run MD simulation in NAMD using stages file strategy or allin one file ? soroush ziaei (Sat Jan 26 2019 - 14:26:04 CST)
Re: gaussian aMD with iE=2 (setting E threshold at maximum) Miao, Yinglong (Sat Jan 26 2019 - 13:23:41 CST)
Re: run MD simulation in NAMD using stages file strategy or all in one file ? L- (Sat Jan 26 2019 - 10:59:20 CST)
Re: jeevan gc (Sat Jan 26 2019 - 09:45:22 CST)
RE: hbond restraint simulation Vermaas, Joshua (Fri Jan 25 2019 - 16:01:31 CST)
RE: Phosphotyrosine Parameters/Toplogy Lennart Nilsson (Fri Jan 25 2019 - 14:35:51 CST)
RE: hbond restraint simulation Vermaas, Joshua (Fri Jan 25 2019 - 14:09:52 CST)
RE: Phosphotyrosine Parameters/Toplogy Vermaas, Joshua (Fri Jan 25 2019 - 13:57:26 CST)
hbond restraint simulation Prabir Khatua (Fri Jan 25 2019 - 13:19:24 CST)
Phosphotyrosine Parameters/Toplogy Alex Saad-Falcon (Fri Jan 25 2019 - 12:10:14 CST)
RE: Vermaas, Joshua (Fri Jan 25 2019 - 11:59:35 CST)
gaussian aMD with iE=2 (setting E threshold at maximum) Vlad Cojocaru (Fri Jan 25 2019 - 07:32:43 CST)
Re: AW: restarting Gaussian accelerated MD fails Vlad Cojocaru (Fri Jan 25 2019 - 04:48:50 CST)
Re: restarting Gaussian accelerated MD fails Vlad Cojocaru (Fri Jan 25 2019 - 04:11:03 CST)
(no subject) jeevan gc (Thu Jan 24 2019 - 16:53:46 CST)
Re: restarting Gaussian accelerated MD fails Miao, Yinglong (Tue Jan 22 2019 - 14:10:21 CST)
Re: mdff for EM map with helical symmetry and the asymmetric unit is dimer Ryan McGreevy (Tue Jan 22 2019 - 14:07:55 CST)
Re: restarting Gaussian accelerated MD fails Vlad Cojocaru (Tue Jan 22 2019 - 02:56:58 CST)
Modifying LJ Potential -Reg Mani Kandan (Sat Jan 19 2019 - 22:24:07 CST)
Re: Angle list Ashkan Shekaari (Sat Jan 19 2019 - 09:19:00 CST)
RE: Angle list soroush ziaei (Sat Jan 19 2019 - 08:55:27 CST)
Angle list Ashkan Shekaari (Sat Jan 19 2019 - 07:49:35 CST)
Re: RE: FATAL ERROR with "File exists" Seibold, Steve Allan (Fri Jan 18 2019 - 09:37:24 CST)
mdff for EM map with helical symmetry and the asymmetric unit is dimer Zhang Yan (Thu Jan 17 2019 - 21:28:37 CST)
Re: RE: FATAL ERROR with "File exists" Zhang Yan (Thu Jan 17 2019 - 21:16:17 CST)
RE: RE: FATAL ERROR with "File exists" Vermaas, Joshua (Thu Jan 17 2019 - 12:36:28 CST)
RE: Graphene psf file soroush ziaei (Thu Jan 17 2019 - 08:23:01 CST)
Re: RE: FATAL ERROR with "File exists" Zhang Yan (Wed Jan 16 2019 - 21:03:57 CST)
pre compiled namd2.13 version nightly build for Linux-x86_64-verbs-smp-CUDA or help with compiling charm++ Aravinda Munasinghe (Wed Jan 16 2019 - 20:16:26 CST)
RE: FATAL ERROR with "File exists" Vermaas, Joshua (Wed Jan 16 2019 - 13:51:51 CST)
FATAL ERROR with "File exists" Seibold, Steve Allan (Wed Jan 16 2019 - 12:30:48 CST)
Re: Several issues (possible bugs) in REST2 - soluteScalingFile & langevinTemp Jim Phillips (Tue Jan 15 2019 - 16:57:42 CST)
Several issues (possible bugs) in REST2 - soluteScalingFile & langevinTemp Aravinda Munasinghe (Tue Jan 15 2019 - 15:31:04 CST)
QM-MM and transition elements Francesco Pietra (Tue Jan 15 2019 - 11:20:39 CST)
mistakes in the user guide in the accelerated MD section ? Vlad Cojocaru (Tue Jan 15 2019 - 07:29:02 CST)
Re: [External] running NAMD with Slurm Jim Phillips (Mon Jan 14 2019 - 14:29:55 CST)
Re: Graphene psf file Victor Kwan (Mon Jan 14 2019 - 13:42:06 CST)
Re: Extracting velocities from veldcd file Prakash Saud (Mon Jan 14 2019 - 07:46:51 CST)
Re: Extracting velocities from veldcd file Roshan Shrestha (Mon Jan 14 2019 - 07:36:39 CST)
Extracting velocities from veldcd file ARNAB MUKHERJEE (Mon Jan 14 2019 - 07:01:09 CST)
Graphene psf file Ashkan Shekaari (Wed Jan 09 2019 - 13:14:03 CST)
Re: [External] running NAMD with Slurm Bennion, Brian (Wed Jan 09 2019 - 12:56:14 CST)
Re: [External] running NAMD with Slurm Seibold, Steve Allan (Wed Jan 09 2019 - 12:52:44 CST)
Re: [External] running NAMD with Slurm Sharp, Kim (Wed Jan 09 2019 - 12:41:20 CST)
Re: running NAMD with Slurm on cluster Victor Kwan (Wed Jan 09 2019 - 12:05:07 CST)
Re: [External] running NAMD with Slurm Bennion, Brian (Wed Jan 09 2019 - 11:57:54 CST)
Re: [External] running NAMD with Slurm Sharp, Kim (Wed Jan 09 2019 - 11:15:19 CST)
running NAMD with Slurm Seibold, Steve Allan (Wed Jan 09 2019 - 09:54:21 CST)
Re: [External] running NAMD with Slurm on cluster Sharp, Kim (Wed Jan 09 2019 - 09:30:32 CST)
running NAMD with Slurm on cluster Seibold, Steve Allan (Wed Jan 09 2019 - 09:08:57 CST)
Re: CHARMM force field for Hydrogen bond? Ashkan Shekaari (Tue Jan 08 2019 - 13:58:19 CST)
Re: Running QM-MM MOPAC on a cluster Francesco Pietra (Tue Jan 08 2019 - 11:06:27 CST)
Re: CHARMM force field for Hydrogen bond? HEMANTH H 18310019 (Mon Jan 07 2019 - 20:59:58 CST)
CHARMM force field for Hydrogen bond? Nasim Rajabi (Mon Jan 07 2019 - 16:15:43 CST)
Re: Error in using the QMElecEmbed keyword Marcelo C. R. Melo (Mon Jan 07 2019 - 13:07:28 CST)
Re: Wrong result in running QM/MM simulation with a small test system Marcelo C. R. Melo (Mon Jan 07 2019 - 12:55:52 CST)
Re: Running QM-MM MOPAC on a cluster Jim Phillips (Mon Jan 07 2019 - 10:40:56 CST)
Re: Protein Charge Brian Radak (Mon Jan 07 2019 - 10:39:28 CST)
Re: Protein Charge Peter Freddolino (Mon Jan 07 2019 - 10:17:32 CST)
Re: Protein Charge Ashkan Shekaari (Mon Jan 07 2019 - 07:42:25 CST)
RE: Protein Charge soroush ziaei (Mon Jan 07 2019 - 07:37:06 CST)
Protein Charge Ashkan Shekaari (Mon Jan 07 2019 - 02:24:15 CST)
Re: unable to open restart.colvars Giacomo Fiorin (Fri Jan 04 2019 - 13:10:26 CST)
Re: Running QM-MM MOPAC on a cluster Francesco Pietra (Fri Jan 04 2019 - 12:28:32 CST)
Error in using the QMElecEmbed keyword Xi Chen (Fri Jan 04 2019 - 12:13:58 CST)
Re: unable to open restart.colvars Francesco Pietra (Fri Jan 04 2019 - 11:16:08 CST)
Wrong result in running QM/MM simulation with a small test system Xi Chen (Thu Jan 03 2019 - 20:17:29 CST)
Re: unable to open restart.colvars Giacomo Fiorin (Thu Jan 03 2019 - 13:57:50 CST)
Re: unable to open restart.colvars Victor Kwan (Thu Jan 03 2019 - 13:19:20 CST)
Re: ERROR: Constraint failure in RATTLE algorithm for atom 232! ERROR: Constraint failure; simulation has become unstable. Roshan Shrestha (Thu Jan 03 2019 - 01:08:21 CST)
ERROR: Constraint failure in RATTLE algorithm for atom 232! ERROR: Constraint failure; simulation has become unstable. Denish Poudyal (Wed Jan 02 2019 - 23:48:59 CST)
Re: Running QM-MM MOPAC on a cluster Jim Phillips (Wed Jan 02 2019 - 16:40:46 CST)
CG simulation of water molecules -Reg Mani Kandan (Wed Jan 02 2019 - 14:06:46 CST)
Re: QM-MM with MOPAC Marcelo C. R. Melo (Wed Jan 02 2019 - 09:33:25 CST)
Re: Running QM-MM MOPAC on a cluster Francesco Pietra (Tue Jan 01 2019 - 03:24:43 CST)

Last message date: Thu Dec 31 2020 - 22:29:33 CST
Archived on: Thu Dec 31 2020 - 23:17:15 CST

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