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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)
- FEP calculations - membrane protein Luba Simhaev (Thu Dec 31 2020 - 02:45:38 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)
- [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 ROPÓN-PALACIOS G. (Sat Dec 26 2020 - 15:32:44 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: Ambiguity among number of residues as counted in VMD and PyMol for RMSF Peter Freddolino (Mon Dec 28 2020 - 23:44:34 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 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 - 08:04:13 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 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 - 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)
- Question about Radius of hexagon; Seke Keretsu (Thu Dec 24 2020 - 00:33:17 CST)
- Query regarding 'Protein:ligand Standard Binding Free Energies' tutorial Faisal, H M Nasrullah (Tue Dec 22 2020 - 14:39:15 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)
- 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)
- path CV Stefano Guglielmo (Fri Dec 18 2020 - 08:48:27 CST)
- Assessing total time of run in NAMD Mi Yang (Thu Dec 17 2020 - 12:50:33 CST)
- Force field for Li-ion batteries electrolytes based on ionic liquids Mauro Sgroi (Thu Dec 17 2020 - 03:46:32 CST)
- Installation with tcl Arturo Fernandez (Wed Dec 16 2020 - 16:22:33 CST)
- Water wrapping in the QMMM simulations Alex Balaeff (Mon Dec 14 2020 - 17:27:11 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)
- NAMD QM/MM multi nodes performance bad Chunli Yan (Sun Dec 13 2020 - 20:47:15 CST)
- Question Colvar o tclforces ROPÓN-PALACIOS G. (Sat Dec 12 2020 - 13:15:23 CST)
- Centre of mass distance in ABF Aashish Bhatt (Sat Dec 12 2020 - 02:15:46 CST)
- About the well-tempered metadynamics convergence.. zeynab hosseini (Thu Dec 10 2020 - 12:49:14 CST)
- NAMD3: how to get the best performance in one gpu node? Siyoung Kim (Wed Dec 09 2020 - 03:00:02 CST)
- Fep setup membrane protein-Drug complex ROPÓN-PALACIOS G. (Tue Dec 08 2020 - 13:20:41 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)
- NAMD3 segfault while writing restart files David Sept (Sat Dec 05 2020 - 11:09:55 CST)
- Membrana-protein-lig protocol ROPÓN-PALACIOS G. (Fri Dec 04 2020 - 12:42:24 CST)
- Hydrogen Mass Repartitioning McGuire, Kelly (Thu Dec 03 2020 - 21:04:50 CST)
- RE: Hydrogen Mass Repartitioning Mohammed umar Sheriff (Thu Dec 03 2020 - 21:35:10 CST)
- Re: Hydrogen Mass Repartitioning Gumbart, JC (Thu Dec 03 2020 - 21:57:23 CST)
- AW: Hydrogen Mass Repartitioning Norman Geist (Fri Dec 04 2020 - 03:00:59 CST)
- RE: Hydrogen Mass Repartitioning James Kress (Fri Dec 04 2020 - 17:32:44 CST)
- Re: Hydrogen Mass Repartitioning Rafael Bernardi (Sat Dec 05 2020 - 14:27:45 CST)
- RE: Hydrogen Mass Repartitioning James Kress (Sat Dec 05 2020 - 15:43:49 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)
- CPU vs GPU Question McGuire, Kelly (Wed Dec 02 2020 - 16:51:37 CST)
- Re: CPU vs GPU Question Bennion, Brian (Wed Dec 02 2020 - 17:05:50 CST)
- Re: CPU vs GPU Question McGuire, Kelly (Thu Dec 03 2020 - 21:05:05 CST)
- Re: CPU vs GPU Question McGuire, Kelly (Wed Dec 09 2020 - 01:14:47 CST)
- Re: CPU vs GPU Question Bennion, Brian (Wed Dec 09 2020 - 10:21:54 CST)
- Re: Re: CPU vs GPU Question Gumbart, JC (Wed Dec 09 2020 - 14:56:23 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 - 16:19:41 CST)
- Re: Re: CPU vs GPU Question McGuire, Kelly (Wed Dec 09 2020 - 16:27:36 CST)
- Re: Re: CPU vs GPU Question Rafael Bernardi (Wed Dec 09 2020 - 23:26:20 CST)
- Re: Re: CPU vs GPU Question Bennion, Brian (Wed Dec 09 2020 - 23:35:11 CST)
- Re: Re: CPU vs GPU Question McGuire, Kelly (Wed Dec 09 2020 - 16:36:06 CST)
- Re: Re: CPU vs GPU Question vermaasj (Wed Dec 09 2020 - 18:23:32 CST)
- Re: Re: CPU vs GPU Question McGuire, Kelly (Thu Dec 10 2020 - 19:27:16 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 - 19:40:46 CST)
- Re: Re: CPU vs GPU Question Rafael Bernardi (Thu Dec 10 2020 - 21:39:48 CST)
- Re: CPU vs GPU Question Mohammed umar Sheriff (Sat Dec 05 2020 - 05:33:54 CST)
- Re: CPU vs GPU Question Bennion, Brian (Wed Dec 02 2020 - 17:05:50 CST)
- Termination between Minimization to Equilibration Ramon Mendoza Uriarte (Wed Dec 02 2020 - 13:43:17 CST)
- Re: Termination between Minimization to Equilibration Ramon Mendoza Uriarte (Wed Dec 02 2020 - 18:11:37 CST)
- Re: Re: Termination between Minimization to Equilibration Peter Freddolino (Wed Dec 02 2020 - 19:35:52 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 - 20:07:58 CST)
- Re: Re: Termination between Minimization to Equilibration Ramon Mendoza Uriarte (Thu Dec 03 2020 - 13:40:23 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)
- Advice for Protein Mutation FEP Calculations Matthew Guberman-Pfeffer (Tue Dec 01 2020 - 10:27:43 CST)
- NamdEnergy Nonbonded H-bonds Francesco Pietra (Mon Nov 30 2020 - 11:06:52 CST)
- not getting NAMD multicopy simulation started René Hafner TUK (Mon Nov 23 2020 - 07:22:36 CST)
- Implicit MD is slower than explcit MD! Krishna Vkm (Mon Nov 23 2020 - 05:18:51 CST)
- Cavernous Depressions in Water Box Oscar Bastidas (Sat Nov 21 2020 - 19:22:14 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)
- performing SMD in Z using colvar module Ropón-Palacios G. (Mon Nov 16 2020 - 16:16:33 CST)
- Exit code 127 with QMMM Francesco Pietra (Mon Nov 16 2020 - 10:58:30 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)
- Adding bias potential Peter Rosenquist (Thu Nov 12 2020 - 15:00:38 CST)
- Calculating 2D PMF from 1D eABF simulations using CZAR estimator. Abhishek Acharya (Wed Nov 11 2020 - 13:04:29 CST)
- FEP/λ-REMD Simulation error Alao, John-Paul (Mon Nov 09 2020 - 11:01:26 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)
- Rmsd calculation Asmi Mahmood (Tue Nov 03 2020 - 00:22:54 CST)
- rmsd Asmi Mahmood (Mon Nov 02 2020 - 04:41:35 CST)
- rmsd colvar Stefano Guglielmo (Sun Nov 01 2020 - 10:17:10 CST)
- NPT then NVT simulation in a single config file for water box? Tanooj Shah (Fri Oct 30 2020 - 21:52:19 CDT)
- restart file Constantin Gunkel (Fri Oct 30 2020 - 09:45:17 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)
- model with TIP4 water minimization getting crashed every time Faisal, H M Nasrullah (Tue Oct 27 2020 - 10:04:49 CDT)
- Compile NAMD with PLUMED Jiali Wang (Mon Oct 26 2020 - 22:15:28 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)
- model with TIP4 water minimization getting crashed every time Faisal, H M Nasrullah (Mon Oct 26 2020 - 12:50:33 CDT)
- Running multiple walker metadynamics replicas as a bundle zeynab hosseini (Mon Oct 26 2020 - 07:33:11 CDT)
- Re: Running multiple walker metadynamics replicas as a bundle Josh Vermaas (Mon Oct 26 2020 - 11:04:02 CDT)
- Repulsive wall potential or spherical boundry conditions Almeida-Hernndez, Yasser, Dr. (Fri Oct 23 2020 - 05:13:55 CDT)
- How to Selectively Scale Interactions Matthew Guberman-Pfeffer (Thu Oct 22 2020 - 23:30:47 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)
- NAMD 2.14 fatal error executing tcl script Alsaloum, Matthew (Sun Oct 18 2020 - 21:06:58 CDT)
- well-tempered metadynamics deforms the water box and the system becomes unstable.. zeynab hosseini (Fri Oct 16 2020 - 03:44:27 CDT)
- Re: well-tempered metadynamics deforms the water box and the system becomes unstable.. Giacomo Fiorin (Fri Oct 16 2020 - 09:10:26 CDT)
- Re: well-tempered metadynamics deforms the water box and the system becomes unstable.. zeynab hosseini (Mon Oct 19 2020 - 12:36:07 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: 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 (Wed Oct 21 2020 - 09:47:29 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.. 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 - 13:03:28 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 (Thu Oct 22 2020 - 03:10:38 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 (Fri Oct 23 2020 - 04:21:33 CDT)
- Re: well-tempered metadynamics deforms the water box and the system becomes unstable.. Giacomo Fiorin (Fri Oct 16 2020 - 09:10:26 CDT)
- GPU Acceleration and Drude Simulations Michael Robinson (Fri Oct 16 2020 - 01:23:57 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)
- Targeted MD in NAMD 3.0? Smith, Harper E. (Tue Oct 13 2020 - 11:18:03 CDT)
- A home PC to run NAMD simulations Harish Srinivasan (Sun Oct 11 2020 - 02:02:27 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)
- Quary resgading Adaptive biasing force Aashish Bhatt (Thu Oct 08 2020 - 08:43:44 CDT)
- Transition State Search BY NAMD 辛志宏 (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-Hernndez, Yasser, Dr. (Tue Oct 06 2020 - 03:37:32 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)
- Regarding "lossiness" of namd on GPUs Bassam Haddad (Mon Oct 05 2020 - 16:19:26 CDT)
- psf generation divyabharathi korlepara (Mon Oct 05 2020 - 10:13:35 CDT)
- Drude equilibration Almeida-Hernndez, Yasser, Dr. (Mon Oct 05 2020 - 03:08:48 CDT)
- How to determine the residue of qmLSSRef in QwikMD? 辛志宏 (Sun Oct 04 2020 - 20:28:28 CDT)
- Incorrect restarting velocities Kodituwakku,Dimuthu Nirmani (Fri Oct 02 2020 - 09:53:02 CDT)
- QwikMD--ERROR) Unable to ascertain relative endianness of remote machine 辛志宏 (Fri Oct 02 2020 - 03:18:39 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)
- 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)
- 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 辛志宏 (Tue Sep 22 2020 - 09:42:12 CDT)
- Error running command for QM forces calculation 辛志宏 (Mon Sep 21 2020 - 01:21:20 CDT)
- Farnesylated Cysteine Xu, Shenyuan (Sun Sep 20 2020 - 10:55:46 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)
- 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: 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)
- 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: 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 - 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 - 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 - 13:20:05 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)
- Atom outside of the MSM grid in NVT simulation - Semiperiodic boundaries Guna Mandava (Wed Sep 16 2020 - 21:20:28 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)
- Convert solvated CHARMM PDB + PSF to Amber Gianluca Interlandi (Tue Sep 15 2020 - 20:34:44 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)
- 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)
- Hybrid Coarse Grain/ all atom simulation in NAMD Shadi Rahnama (Sun Sep 13 2020 - 14:18:26 CDT)
- Post processing NAMD trajectory Kodituwakku,Dimuthu Nirmani (Sun Sep 13 2020 - 13:08:14 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 辛志宏 (Sun Sep 13 2020 - 07:52:13 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)
- ERROR: Atoms moving too fast; simulation has become unstable 辛志宏 (Wed Sep 09 2020 - 23:03:53 CDT)
- DRMS Colvar Ethan Croitoru (Wed Sep 09 2020 - 14:25:33 CDT)
- Basics of MD Raman Preet Singh (Tue Sep 08 2020 - 05:10:10 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 辛志宏 (Mon Sep 07 2020 - 03:40:03 CDT)
- Re: Issue regarding to the speed of QM/MM Marcelo C. R. Melo (Mon Sep 07 2020 - 13:11:07 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)
- Replica exchange problem Julian David Baquero Contreras (Wed Sep 02 2020 - 13:13:59 CDT)
- Colvars Harmonic Bias Force Direction Mortimer Hemmit (Wed Sep 02 2020 - 07:28:03 CDT)
- Wrong number of basis-sets stored! 辛志宏 (Tue Sep 01 2020 - 21:10:17 CDT)
- Re: Wrong number of basis-sets stored! Acharya, Atanu (Wed Sep 02 2020 - 00:10:54 CDT)
- Re:Re: Wrong number of basis-sets stored! 辛志宏 (Wed Sep 02 2020 - 09:48:38 CDT)
- Re: Wrong number of basis-sets stored! Acharya, Atanu (Wed Sep 02 2020 - 13:45:48 CDT)
- Re:Re: Wrong number of basis-sets stored! 辛志宏 (Wed Sep 02 2020 - 19:32:23 CDT)
- Re: Re:Re: Wrong number of basis-sets stored! Alex Balaeff (Wed Sep 02 2020 - 20:17:40 CDT)
- Re:Re: Re:Re: Wrong number of basis-sets stored! 辛志宏 (Wed Sep 02 2020 - 21:25:09 CDT)
- Re: Re: Re:Re: Wrong number of basis-sets stored! Alex Balaeff (Wed Sep 02 2020 - 22:08:03 CDT)
- Re:Re: Re: Re:Re: Wrong number of basis-sets stored! 辛志宏 (Thu Sep 03 2020 - 02:41:43 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: Wrong number of basis-sets stored! 辛志宏 (Wed Sep 02 2020 - 09:48:38 CDT)
- Re: Wrong number of basis-sets stored! Acharya, Atanu (Wed Sep 02 2020 - 00:10:54 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)
- Error when using namdplot Kodituwakku,Dimuthu Nirmani (Sat Aug 29 2020 - 18:36:01 CDT)
- Re: Error when using namdplot Peter Freddolino (Sat Aug 29 2020 - 22:26:08 CDT)
- Re: Error when using namdplot Kodituwakku,Dimuthu Nirmani (Sun Aug 30 2020 - 09:18:40 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 - 11:58:07 CDT)
- Re: Error when using namdplot Peter Freddolino (Sun Aug 30 2020 - 23:38:09 CDT)
- Re: Error when using namdplot Kodituwakku,Dimuthu Nirmani (Mon Aug 31 2020 - 07:34:00 CDT)
- Re: Error when using namdplot Kodituwakku,Dimuthu Nirmani (Sun Aug 30 2020 - 09:18:40 CDT)
- Re: Error when using namdplot Kodituwakku,Dimuthu Nirmani (Sun Aug 30 2020 - 09:33:47 CDT)
- Re: Error when using namdplot Peter Freddolino (Sat Aug 29 2020 - 22:26:08 CDT)
- QM atom cannot be fixed in space 辛志宏 (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 Josh Vermaas (Fri Aug 28 2020 - 18:21:18 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)
- 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)
- Error in fftk during bond opt using VMD 1.9.3 Faisal, H M Nasrullah (Mon Aug 17 2020 - 10:08:00 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: 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 - 12:44:55 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: Asymmetric concentration gradient: non-periodic z-boundary for only ions Gumbart, JC (Sat Aug 15 2020 - 20:23:12 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: 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 David Hardy (Thu Aug 27 2020 - 10:16:22 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: Asymmetric concentration gradient: non-periodic z-boundary for only ions Athreya, Nagendra Bala Murali (Tue Aug 25 2020 - 15:06:12 CDT)
- Re: Asymmetric concentration gradient: non-periodic z-boundary for only ions Gumbart, JC (Sat Aug 15 2020 - 20:23:12 CDT)
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- Extra frame at start of each trajectory Ethan Croitoru (Wed Aug 05 2020 - 14:23:47 CDT)
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- Alchemical Transformation for calculation of standard binding free energies Cameron Grant (Wed Aug 05 2020 - 04:44:58 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)
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- 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)
- 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. Michael Von Domaros (Mon Aug 03 2020 - 18:39:14 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)
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- Re: Slow performance over multi-core processor and CUDA build Ashkan Shekaari (Tue Jul 28 2020 - 07:25:29 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 Giacomo Fiorin (Tue Jul 28 2020 - 08:04:52 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 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 Josh Vermaas (Tue Jul 28 2020 - 20:32:26 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)
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- MOPAC output file analysis M. A (Fri Jul 03 2020 - 14:53:05 CDT)
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- 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)
- Re: The HIP version of NAMD gets wrong results when computing on more than one node 张驭洲 (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 - 10:33:14 CDT)
- Re: Re: The HIP version of NAMD gets wrong results when computing on more than one node 张驭洲 (Fri Jul 03 2020 - 23:03:54 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: The HIP version of NAMD gets wrong results when computing on more than one node 张驭洲 (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)
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- Re: how to disable the periodic condition tracking two atom distance Josh Vermaas (Wed Jun 10 2020 - 15:10:35 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: [External Email] Re: how to disable the periodic condition tracking two atom distance Jérôme Hénin (Fri Jun 12 2020 - 12:42:26 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 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 - 13:42:29 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: how to disable the periodic condition tracking two atom distance Josh Vermaas (Wed Jun 10 2020 - 15:10:35 CDT)
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- (no subject) shyam sharma (Mon Jun 08 2020 - 04:29:00 CDT)
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- Re: Error during simulation shyam sharma (Thu Jun 04 2020 - 22:54:10 CDT)
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- System Drifts Along Z-Axis Bassam Haddad (Fri May 29 2020 - 14:36:49 CDT)
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- 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: 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: 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: 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 (Wed May 27 2020 - 13:09:41 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 - 19:11:32 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: 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)
- Negative Forces in SMD Simulations Souvik Dey (Fri May 22 2020 - 16:40:25 CDT)
- Re: Negative Forces in SMD Simulations Gumbart, JC (Tue May 26 2020 - 13:17:03 CDT)
- Re: Negative Forces in SMD Simulations Souvik Dey (Tue May 26 2020 - 13:21:19 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 - 15:22:19 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 - 19:05:54 CDT)
- Re: Negative Forces in SMD Simulations Peter Freddolino (Tue May 26 2020 - 19:24:35 CDT)
- Re: Negative Forces in SMD Simulations Josh Vermaas (Tue May 26 2020 - 19:27:23 CDT)
- Re: Negative Forces in SMD Simulations Pratik Narain Srivastava (Tue May 26 2020 - 13:34:55 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 - 13:21:19 CDT)
- Re: Negative Forces in SMD Simulations Gumbart, JC (Tue May 26 2020 - 13:17:03 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)
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- Negative Forces in SMD Simulations Souvik Dey (Thu May 21 2020 - 16:45:28 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)
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- 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)
- Re: FATAL ERROR: Charge placement error in QM-MM bond. M. A (Mon May 11 2020 - 15:01:49 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: Using NAMD and Orca together -- a QM/MM job David Baker (Thu May 07 2020 - 10:19:43 CDT)
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- Box of Water L- (Mon May 04 2020 - 19:12:03 CDT)
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- qmmm simulation and question for md analysis M. A (Mon Apr 20 2020 - 03:59:45 CDT)
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- Re: FATAL ERROR: Error running command for QM forces calculation. M. A (Fri Apr 17 2020 - 11:53:08 CDT)
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- Re: Error: Number of NGauss expected in AddNewGTOs Francesco Pietra (Thu Apr 16 2020 - 11:52:28 CDT)
- Re: Error: Number of NGauss expected in AddNewGTOs Francesco Pietra (Thu Apr 16 2020 - 12:29:46 CDT)
- Re: Error: Number of NGauss expected in AddNewGTOs Francesco Pietra (Tue Apr 28 2020 - 12:06:01 CDT)
- Error: Number of NGauss expected in AddNewGTOs Francesco Pietra (Thu Apr 16 2020 - 10:09:36 CDT)
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- 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)
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- (no subject) ROPÓN-PALACIOS G. (Tue Apr 14 2020 - 21:25:41 CDT)
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- Re: minimise in restarting first equilibration step Josh Vermaas (Mon Apr 13 2020 - 12:16:35 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 - 12:42:24 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 Khoualdi Asma Feriel (Mon Apr 13 2020 - 13:50:03 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)
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- QMMM param issue Francesco Pietra (Wed Apr 01 2020 - 05:49:53 CDT)
- Re: QMMM param issue Marcelo C. R. Melo (Wed Apr 01 2020 - 09:57:44 CDT)
- Re: QMMM param issue Francesco Pietra (Wed Apr 01 2020 - 11:09:29 CDT)
- Fwd: QMMM param issue Francesco Pietra (Wed Apr 01 2020 - 12:46:17 CDT)
- Re: QMMM param issue Marcelo C. R. Melo (Wed Apr 01 2020 - 13:15:37 CDT)
- Re: QMMM param issue Francesco Pietra (Wed Apr 01 2020 - 16:16:42 CDT)
- Re: QMMM param issue Marcelo C. R. Melo (Wed Apr 01 2020 - 17:05:32 CDT)
- Re: QMMM param issue Francesco Pietra (Thu Apr 02 2020 - 03:30:27 CDT)
- Re: QMMM param issue Josh Vermaas (Thu Apr 02 2020 - 11:41:22 CDT)
- Re: QMMM param issue Francesco Pietra (Fri Apr 03 2020 - 12:48:50 CDT)
- Re: QMMM param issue Marcelo C. R. Melo (Sat Apr 04 2020 - 11:25:27 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)
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- Running on GPU multiple nodes Adupa Vasista (Sun Mar 29 2020 - 04:42:43 CDT)
- Unpredictably Crashes upon Restarting Matthew Guberman-Pfeffer (Fri Mar 27 2020 - 16:56:43 CDT)
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- Error Restarting Simulation Matthew Guberman-Pfeffer (Mon Mar 09 2020 - 12:46:34 CDT)
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- Re: question to run namd2 with multiple CPUs Yu, Tao (Mon Mar 02 2020 - 15:08:04 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 Renfro, Michael (Thu Mar 05 2020 - 10:25:21 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 - 14:26:22 CST)
- Re: question to run namd2 with multiple CPUs Yu, Tao (Mon Mar 02 2020 - 15:08:04 CST)
- Re: question to run namd2 with multiple CPUs Victor Kwan (Thu Mar 05 2020 - 18:33:23 CST)
- Re: question to run namd2 with multiple CPUs Josh Vermaas (Fri Feb 28 2020 - 16:29:09 CST)
- bad angle error!! ROPÓN-PALACIOS G. (Thu Feb 27 2020 - 21:10:45 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)
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- Re: FATAL ERROR: Error in QM-MM bond assignment (NAMD-ORCA) M. A (Tue Feb 25 2020 - 04:23:19 CST)
- The best initial structure of Protein-Protein complex Alireza Mansouri (Mon Feb 24 2020 - 03:54:21 CST)
- Protocol share Ribosome ROPÓN-PALACIOS G. (Fri Feb 21 2020 - 09:05:33 CST)
- Can NAMD 2.13 be build on Charm++ with UCX backend? 张驭洲 (Fri Feb 21 2020 - 03:55:25 CST)
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- (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)
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- Re: Flat-bottom harmonic position restraints using colvars Giacomo Fiorin (Wed Feb 05 2020 - 12:51:05 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 (Mon Feb 10 2020 - 06:14:11 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 David Hardy (Tue Feb 11 2020 - 15:57:40 CST)
- Re: Flat-bottom harmonic position restraints using colvars Daipayan Sarkar (Tue Feb 11 2020 - 16:12:12 CST)
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- Re: Flat-bottom harmonic position restraints using colvars Giacomo Fiorin (Wed Feb 05 2020 - 12:51:05 CST)
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- 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 (Tue Feb 04 2020 - 09:02:41 CST)
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- 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: [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: [External Email] Re: Cations spontaneous binding pathway with PMF calculation? Jiali Wang (Fri Jan 31 2020 - 10:36:51 CST)
- Re: [External Email] Re: Cations spontaneous binding pathway with PMF calculation? Jiali Wang (Fri Jan 31 2020 - 10:14:59 CST)
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- Re: looping on multiple dcds in namd configuration file SHIVAM TIWARI (Fri Nov 15 2019 - 06:25:46 CST)
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- Re: Doubt about ABF and PMF file generation Jérôme Hénin (Mon Nov 18 2019 - 12:18:14 CST)
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- Re: Doubt about ABF and PMF file generation Souvik Sinha (Fri Nov 15 2019 - 00:03:11 CST)
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- Re: How to integrate multiple walkers 2D metadynamics results? Canal de Sebassen (Sat Nov 09 2019 - 19:03:01 CST)
- Re: How to integrate multiple walkers 2D metadynamics results? Sebastian S (Fri Nov 15 2019 - 12:34:57 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? Giacomo Fiorin (Fri Nov 15 2019 - 13:12:00 CST)
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- Re: How to integrate multiple walkers 2D metadynamics results? Giacomo Fiorin (Thu Nov 07 2019 - 17:37:11 CST)
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- RE: charmrun error: Work completion error in sendCq Vermaas, Joshua (Thu Oct 24 2019 - 14:53:53 CDT)
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- Re: Colvars Orientation Question Jérôme Hénin (Wed Jul 03 2019 - 03:53:44 CDT)
- Re: Colvars Orientation Question Xander Gonzalez (Fri Jul 05 2019 - 14:22:34 CDT)
- Re: Colvars Orientation Question Jérôme Hénin (Tue Jul 09 2019 - 04:49:07 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. Joao Ribeiro (Mon Jul 01 2019 - 09:12:22 CDT)
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- does any body know why GPU Acceleration not work on Windows? Milad Lagzian (Fri Jun 28 2019 - 00:13:49 CDT)
- Re: does any body know why GPU Acceleration not work on Windows? Miro Astore (Fri Jun 28 2019 - 00:21:46 CDT)
- Re: does any body know why GPU Acceleration not work on Windows? Pratik Narain Srivastava (Fri Jun 28 2019 - 02:18:04 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? 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 - 03:06:21 CDT)
- Re: does any body know why GPU Acceleration not work on Windows? Bryan Roessler (Fri Jun 28 2019 - 14:52:47 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)
- Re: When using WHAM TO ANALYSIS Giacomo Fiorin (Thu Jun 27 2019 - 15:01:47 CDT)
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- 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)
- OPC Water Model eee ffff (Mon Jun 24 2019 - 05:09:12 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)
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- FATAL ERROR: High global CUDA exclusion count! Sunny (Wed Jun 12 2019 - 12:07:23 CDT)
- FATAL ERROR: High global CUDA exclusion count! Nima Nouri (Wed Jun 12 2019 - 03:20:20 CDT)
- error in compiling namd Kosar Khajeh (Tue Jun 11 2019 - 07:45:38 CDT)
- TMD Partial Fitting Problem mert gölcük (Tue Jun 11 2019 - 07:26:02 CDT)
- Re: we apply a harmonic potential Giacomo Fiorin (Sun Jun 09 2019 - 15:18:55 CDT)
- Problem in Running CUDA-Enabled NAMD Via MOE software Milad Lagzian (Fri Jun 07 2019 - 04:26:04 CDT)
- reg: quenching NAMD trajectory Lara rajam (Thu Jun 06 2019 - 14:39:52 CDT)
- Re: vecsub:two vectors don't have the same size Joao Ribeiro (Thu Jun 06 2019 - 09:21:58 CDT)
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- vecsub:two vectors don't have the same size SHRUTEE JEURKAR (Thu Jun 06 2019 - 02:29:47 CDT)
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- Reg: Solvation box Adupa Vasista (Sun Jun 02 2019 - 03:50:50 CDT)
- Re: Reg: Solvation box Axel Kohlmeyer (Sun Jun 02 2019 - 06:42:45 CDT)
- Re: Reg: Solvation box Adupa Vasista (Sun Jun 02 2019 - 08:03:28 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 - 08:18:33 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 - 08:48:29 CDT)
- Re: Reg: Solvation box Adupa Vasista (Tue Jun 04 2019 - 01:37:20 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: Docking Adupa Vasista (Sat Jun 01 2019 - 05:08:11 CDT)
- Reg: Force Field file Adupa Vasista (Fri May 31 2019 - 01:47:28 CDT)
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- FATAL ERROR: Periodic cell has become too small for original patch grid! Adupa Vasista (Sun May 26 2019 - 07:07:39 CDT)
- (no subject) Adupa Vasista (Sat May 25 2019 - 05:45:51 CDT)
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- "constraint failure in rattle algorithm" soroush ziaei (Tue May 21 2019 - 17:31:21 CDT)
- NAMD with infinite cutoffs? Geist, Norman (Mon Jun 03 2019 - 11:30:24 CDT)
- Re: NAMD with infinite cutoffs? Brian Radak (Mon Jun 03 2019 - 13:21:15 CDT)
- Re: NAMD with infinite cutoffs? Geist, Norman (Mon Jun 03 2019 - 15:45:40 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 - 23:58:49 CDT)
- Re: NAMD with infinite cutoffs? Brian Radak (Tue Jun 04 2019 - 07:59:19 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 - 08:49:36 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)
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- vacuum simulation -Reg Mani Kandan (Sun May 19 2019 - 08:55:02 CDT)
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- 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)
- 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)
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- Big oscillations during QM/MM minimization Pawel Kedzierski (Tue May 07 2019 - 08:53:18 CDT)
- Re: Big oscillations during QM/MM minimization Dawid das (Tue May 07 2019 - 10:07:20 CDT)
- Bug in NAMD (was: Big oscillations during QM/MM minimization) Pawel Kedzierski (Tue Jun 18 2019 - 01:47:24 CDT)
- Re: Bug in NAMD (was: Big oscillations during QM/MM minimization) Brian Radak (Tue Jun 18 2019 - 11:42:02 CDT)
- Re: Bug in NAMD Pawel Kedzierski (Thu Jun 20 2019 - 08:23:43 CDT)
- Re: Bug in NAMD Marcelo C. R. Melo (Thu Jun 20 2019 - 09:46:36 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 Pawel Kedzierski (Fri Jun 21 2019 - 07:01:03 CDT)
- Re: Bug in NAMD Marcelo C. R. Melo (Fri Jun 21 2019 - 11:27:15 CDT)
- Re: Bug in NAMD Pawel Kedzierski (Sat Jun 22 2019 - 04:52:43 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)
- Need help with psfgen : psfgen can't read file.pdb Priyanka Mondal (Mon May 06 2019 - 20:53:03 CDT)
- Re: Need help with psfgen : psfgen can't read file.pdb Victor Kwan (Tue May 07 2019 - 01:46:43 CDT)
- Re: Need help with psfgen : psfgen can't read file.pdb Brian Radak (Tue May 07 2019 - 08:16:01 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)
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- 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)
- Re: " the error of hydrogen group size " Brian Radak (Wed May 01 2019 - 08:51:08 CDT)
- Re: " the error of hydrogen group size " soroush ziaei (Fri May 03 2019 - 05:56:55 CDT)
- Re: " the error of hydrogen group size " soroush ziaei (Fri May 03 2019 - 09:48:06 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 10 2019 - 08:28:44 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 - 09:22:06 CDT)
- Re: " the error of hydrogen group size " soroush ziaei (Fri May 03 2019 - 05:56:55 CDT)
- Re: " the error of hydrogen group size " Brian Radak (Wed May 01 2019 - 08:51:08 CDT)
- FW (1): 71i sudipta.mml (Mon Apr 29 2019 - 04:45:45 CDT)
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- 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)
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- Water Molecule Issue McGuire, Kelly (Wed Apr 24 2019 - 10:03:23 CDT)
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- 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)
- Parameter and Topology File Question Oscar Bastidas (Sun Apr 21 2019 - 04:44:45 CDT)
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- Building of NAMD on the Linux cluster with InfiniBand Арслан Кусмаев (Mon Apr 15 2019 - 06:06:12 CDT)
- changing value of coulomb constant Akshay Prabhakant (Sun Apr 14 2019 - 01:26:40 CDT)
- Electrostatic interaction of 2 ions Fateme Ghadirian (Fri Apr 12 2019 - 09:33:08 CDT)
- Umbrella sampling of a protein through a membrane Villalain Boullon, Jose (Thu Apr 11 2019 - 02:00:51 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)
- FATAL ERROR: CUDA error CudaComputeNonbonded::forceDoneCheck polled 1000000 times over 154.549621 s on Pe 4 (c36.chundoong device 0 pci 0:2:0) 김민재 (Mon Apr 08 2019 - 23:00:38 CDT)
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- Error in PMF Calculations HEMANTH H 18310019 (Thu Apr 04 2019 - 00:21:54 CDT)
- Re: Error in PMF Calculations Jeff Comer (Thu Apr 04 2019 - 07:16:38 CDT)
- Re: Error in PMF Calculations HEMANTH H 18310019 (Thu Apr 04 2019 - 23:39:21 CDT)
- Re: Error in PMF Calculations Jeff Comer (Fri Apr 05 2019 - 08:42:08 CDT)
- Re: Error in PMF Calculations HEMANTH H 18310019 (Tue Apr 09 2019 - 23:42:20 CDT)
- Re: Error in PMF Calculations Souvik Sinha (Wed Apr 10 2019 - 02:02:20 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 - 03:20:21 CDT)
- Re: Error in PMF Calculations Souvik Sinha (Wed Apr 10 2019 - 03:38:22 CDT)
- Re: Error in PMF Calculations HEMANTH H 18310019 (Thu Apr 04 2019 - 23:39:21 CDT)
- Re: Error in PMF Calculations HEMANTH H 18310019 (Tue Apr 23 2019 - 07:06:06 CDT)
- Re: Error in PMF Calculations Jeff Comer (Thu Apr 04 2019 - 07:16:38 CDT)
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- Re: SMD negative forces Joao Ribeiro (Wed Apr 03 2019 - 10:00:17 CDT)
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- Fwd: About changing charge/multiplicity during QM-MM Francesco Pietra (Tue Apr 02 2019 - 09:36:47 CDT)
- Non bonding energy calculation through NAMD varun dewaker (Tue Apr 02 2019 - 03:59:15 CDT)
- Re: Non bonding energy calculation through NAMD Giacomo Fiorin (Tue Apr 02 2019 - 09:00:54 CDT)
- Re: Non bonding energy calculation through NAMD varun dewaker (Thu Apr 11 2019 - 01:46:37 CDT)
- Re: Non bonding energy calculation through NAMD Brian Radak (Thu Apr 11 2019 - 08:56:48 CDT)
- Re: Non bonding energy calculation through NAMD varun dewaker (Fri Apr 12 2019 - 02:29:06 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 - 08:24:39 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 Gumbart, JC (Fri Apr 12 2019 - 13:04:16 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 Pratik Narain Srivastava (Fri Apr 12 2019 - 14:03:43 CDT)
- Re: Non bonding energy calculation through NAMD varun dewaker (Thu Apr 11 2019 - 01:46:37 CDT)
- Re: Non bonding energy calculation through NAMD Giacomo Fiorin (Tue Apr 02 2019 - 09:00:54 CDT)
- Running MD simulation for two molecules 김민재 (Tue Apr 02 2019 - 01:23:45 CDT)
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- TclBC forces on individual atoms Udaya Dahal (Sun Mar 31 2019 - 10:24:52 CDT)
- MAOL ABOUT USAGE OF TCL SCRIPT Vidhya Sankar (Sun Mar 31 2019 - 03:56:29 CDT)
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- TeraChem McGuire, Kelly (Fri Mar 29 2019 - 18:29:18 CDT)
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- 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)
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- REMD using remote GPU John Hamre (Thu Mar 28 2019 - 08:51:21 CDT)
- mail about pbs script Vidhya Sankar (Thu Mar 28 2019 - 06:35:47 CDT)
- how to translate a protein without unfolding Monika Madhavi (Wed Mar 27 2019 - 00:26:29 CDT)
- mail about error in configuration files Vidhya Sankar (Mon Mar 25 2019 - 08:59:01 CDT)
- About changing charge/multiplicity during QM-MM Francesco Pietra (Mon Mar 25 2019 - 02:16:35 CDT)
- Re: About changing charge/multiplicity during QM-MM McGuire, Kelly (Mon Mar 25 2019 - 02:47:14 CDT)
- Re: About changing charge/multiplicity during QM-MM Francesco Pietra (Mon Mar 25 2019 - 09:33:55 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 Gerard Rowe (Mon Apr 08 2019 - 11:26:48 CDT)
- Re: About changing charge/multiplicity during QM-MM Gerard Rowe (Mon Apr 15 2019 - 08:06:52 CDT)
- Re: About changing charge/multiplicity during QM-MM Gerard Rowe (Fri Apr 19 2019 - 07:46:31 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 - 11:09:41 CDT)
- Fwd: About changing charge/multiplicity during QM-MM Francesco Pietra (Mon Mar 25 2019 - 13:20:49 CDT)
- Re: About changing charge/multiplicity during QM-MM Gerard Rowe (Mon Mar 25 2019 - 13:34:09 CDT)
- Re: About changing charge/multiplicity during QM-MM Francesco Pietra (Tue Mar 26 2019 - 11:35:23 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 William Tao (Thu Mar 28 2019 - 12:05:02 CDT)
- Re: About changing charge/multiplicity during QM-MM McGuire, Kelly (Mon Mar 25 2019 - 02:47:14 CDT)
- Solvate with methanol and acetone using free energy methods in NAMD? Defrese, Matthew (Sun Mar 24 2019 - 13:03:52 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: Fastest way to get PSF file for pure QM simulation? Marcelo C. R. Melo (Sat Mar 23 2019 - 12:25:04 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? Joao Ribeiro (Sat Mar 23 2019 - 18:47:12 CDT)
- Re: Fastest way to get PSF file for pure QM simulation? William Tao (Thu Mar 28 2019 - 11:43:29 CDT)
- Re: Fastest way to get PSF file for pure QM simulation? Marcelo C. R. Melo (Sat Mar 23 2019 - 12:25:04 CDT)
- QMMM Frequency Calculation McGuire, Kelly (Thu Mar 21 2019 - 11:55:12 CDT)
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- Average structure using colvars Deepti Karandur (Wed Mar 20 2019 - 15:39:59 CDT)
- what's the latest on using NAMD (and MD in general) for docking? Homeo Morphism (Wed Mar 20 2019 - 13:20:17 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)
- COMmotion -- is it a good practice to turn it on for a restart? Homeo Morphism (Tue Mar 19 2019 - 16:30:02 CDT)
- Unit of Force constant of position restraint Junwoong Yoon (Sun Mar 17 2019 - 23:20:07 CDT)
- Parallel Simulation Question McGuire, Kelly (Sat Mar 16 2019 - 23:30:08 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: vmd-l: ORCA Orbital Bug John Stone (Sat Mar 16 2019 - 01:13:06 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 (Sun Mar 17 2019 - 19:19:48 CDT)
- Re: vmd-l: ORCA Orbital Bug McGuire, Kelly (Sun Mar 17 2019 - 19:58:46 CDT)
- Re: vmd-l: ORCA Orbital Bug McGuire, Kelly (Tue Mar 19 2019 - 12:31:43 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 - 12:40:34 CDT)
- Re: vmd-l: ORCA Orbital Bug McGuire, Kelly (Tue Mar 19 2019 - 12:43:30 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 (Sat Mar 16 2019 - 18:34:51 CDT)
- Re: vmd-l: ORCA Orbital Bug John Stone (Sat Mar 16 2019 - 01:13:06 CDT)
- alculate energy force field L- (Thu Mar 14 2019 - 11:39:24 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)
- 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)
- Re: Colvars: Are the derivatives of optimal rotation matrix wrt atomic coordinates applied implicitly? Jérôme Hénin (Wed Mar 13 2019 - 09:37:31 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? 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 - 10:41:47 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? Jérôme Hénin (Wed Mar 13 2019 - 09:37:31 CDT)
- BUG? reinitatoms on wrapped coordinates occasionally fail with rigidbonds Norman Geist (Wed Mar 13 2019 - 03:05:56 CDT)
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- Research Programmer for VMD/NAMD at UIUC João Ribeiro (Tue Mar 12 2019 - 13:20:11 CDT)
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- [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: Colvars: implement a CV which requires computing minimal RMSDs with respect to multiple different reference frames Jérôme Hénin (Mon Mar 11 2019 - 08:01:07 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 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 (Mon Mar 11 2019 - 22:16:08 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 Jérôme Hénin (Mon Mar 11 2019 - 08:01:07 CDT)
- NAMD support for lone pairs Tabitha Nobel (Thu Mar 07 2019 - 20:26:05 CST)
- Re: NAMD support for lone pairs Brian Radak (Fri Mar 08 2019 - 09:45:39 CST)
- Re: NAMD support for lone pairs Tabitha Nobel (Fri Mar 08 2019 - 11:10:13 CST)
- Re: NAMD support for lone pairs Brian Radak (Mon Mar 11 2019 - 13:41:20 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 - 16:30:56 CDT)
- Re: NAMD support for lone pairs Brian Radak (Mon Mar 11 2019 - 16:39:24 CDT)
- Re: NAMD support for lone pairs Tabitha Nobel (Mon Mar 11 2019 - 18:10:43 CDT)
- Re: NAMD support for lone pairs Tabitha Nobel (Mon Mar 11 2019 - 17:15:45 CDT)
- Re: NAMD support for lone pairs Tabitha Nobel (Mon Mar 11 2019 - 17:19:54 CDT)
- Re: NAMD support for lone pairs Brian Radak (Mon Mar 11 2019 - 17:38:33 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 - 20:01:06 CDT)
- Re: NAMD support for lone pairs Brian Radak (Tue Mar 12 2019 - 07:50:44 CDT)
- Re: NAMD support for lone pairs Gumbart, JC (Tue Mar 12 2019 - 08:35:03 CDT)
- Re: NAMD support for lone pairs Tabitha Nobel (Tue Mar 12 2019 - 11:11:39 CDT)
- Re: NAMD support for lone pairs Brian Radak (Tue Mar 12 2019 - 11:55:21 CDT)
- Re: NAMD support for lone pairs Brian Radak (Fri Mar 08 2019 - 09:45:39 CST)
- NAMD Configuration file error 김민재 (Thu Mar 07 2019 - 00:29:52 CST)
- QM/MM error: The number of QM atoms received is different than expected Haohao Fu (Wed Mar 06 2019 - 21:08:27 CST)
- making new psf file from .prm and pdb file Hadi Rahmaninejad (Tue Mar 05 2019 - 16:59:17 CST)
- Minimization Error 김민재 (Tue Mar 05 2019 - 00:31:36 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)
- "the error of movement of atoms" soroush ziaei (Fri Mar 01 2019 - 11:33:21 CST)
- Parameter Optimization Advice McGuire, Kelly (Fri Mar 01 2019 - 12:13:21 CST)
- Re: Parameter Optimization Advice Brian Radak (Fri Mar 01 2019 - 13:18:15 CST)
- RE: Parameter Optimization Advice Lennart Nilsson (Fri Mar 01 2019 - 13:20:57 CST)
- Re: Parameter Optimization Advice Gumbart, JC (Fri Mar 01 2019 - 23:15:45 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)
- Targeted molecular dynamics domain selection question Aditya Ranganathan (Thu Feb 28 2019 - 17:19:49 CST)
- GolP-CHARMM Mikhail Suyetin (Wed Feb 27 2019 - 10:24:21 CST)
- Fwd: Running NAMD on Linux Cluster 김민재 (Wed Feb 27 2019 - 07:10:34 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)
- 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 김민재 (Tue Feb 26 2019 - 09:22:37 CST)
- Constant Force SMD Question McGuire, Kelly (Mon Feb 25 2019 - 12:25:34 CST)
- colvar restraint simulation Prabir Khatua (Mon Feb 25 2019 - 11:04:33 CST)
- Stochastic velocity rescaling for Free Energy calculations Braden Kelly (Sat Feb 23 2019 - 15:21:37 CST)
- H2 Topology and Parameter files Teja Vanjari (Sat Feb 23 2019 - 11:58:35 CST)
- Lennard-Jones Potential McGuire, Kelly (Sat Feb 23 2019 - 11:34:21 CST)
- Re: Lennard-Jones Potential Victor Kwan (Sat Feb 23 2019 - 11:35:49 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 - 12:00:36 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 - 12:09:01 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 - 12:41:34 CST)
- Re: Lennard-Jones Potential McGuire, Kelly (Sat Feb 23 2019 - 11:37:58 CST)
- Re: Lennard-Jones Potential Kowsar Khajeh (Sat Feb 23 2019 - 11:47:11 CST)
- Re: Lennard-Jones Potential Victor Kwan (Sat Feb 23 2019 - 11:35:49 CST)
- QM-MM NAMD-ORCA broken symmetry Francesco Pietra (Sat Feb 23 2019 - 10:38:42 CST)
- Energy Minimization Simulation 김민재 (Fri Feb 22 2019 - 12:09:38 CST)
- Constant Velocity Pulls McGuire, Kelly (Fri Feb 22 2019 - 09:58:42 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)
- Running NAMD in MPI environment 김민재 (Wed Feb 20 2019 - 09:58:42 CST)
- TIP4P water box 김민재 (Tue Feb 19 2019 - 12:59:01 CST)
- Free energy plot Faramarz Joodaki (Tue Feb 19 2019 - 11:57:20 CST)
- Running QM-MM multinode Francesco Pietra (Sat Feb 16 2019 - 02:12:26 CST)
- QMMM Question McGuire, Kelly (Thu Feb 14 2019 - 11:26:53 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)
- solute scaling does not affect electrostatics (and other quirks) Jeff Comer (Wed Feb 13 2019 - 15:20:02 CST)
- Error running deinterleave_idws.py on FEP simulation output Amy Rice (Wed Feb 13 2019 - 12:42:10 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: About restarting QM-MM simulation Marcelo C. R. Melo (Wed Feb 13 2019 - 12:31:57 CST)
- Re: About restarting QM-MM simulation Eric Smoll (Wed Feb 13 2019 - 12:48:05 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 (Thu Feb 14 2019 - 04:17:35 CST)
- Re: About restarting QM-MM simulation Francesco Pietra (Thu Feb 14 2019 - 08:46:34 CST)
- Re: About restarting QM-MM simulation Gerard Rowe (Thu Feb 14 2019 - 10:38:06 CST)
- Re: About restarting QM-MM simulation Marcelo C. R. Melo (Thu Feb 14 2019 - 11:33:24 CST)
- Re: About restarting QM-MM simulation Francesco Pietra (Thu Feb 14 2019 - 16:34:46 CST)
- Re: About restarting QM-MM simulation Francesco Pietra (Fri Feb 15 2019 - 02:34:56 CST)
- Re: About restarting QM-MM simulation Marcelo C. R. Melo (Sun Feb 17 2019 - 15:26:12 CST)
- Re: About restarting QM-MM simulation francesco.pietra_at_accademialucchese.it (Sun Feb 17 2019 - 15:50:41 CST)
- Fwd: Gromacs to Charmm FF Format Conversion -Reg Mani Kandan (Tue Feb 12 2019 - 09:44:10 CST)
- Gromacs to Charmm FF Format Conversion -Reg Mani Kandan (Tue Feb 12 2019 - 08:12:40 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: reinitatoms Laura Lopes (Fri Feb 08 2019 - 03:38:55 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)
- Using harmonic walls on water molecules Moises Ernesto Romero (Mon Feb 04 2019 - 19:14:39 CST)
- Tuning QM-MM with namd-orca on one cluster node Francesco Pietra (Thu Jan 31 2019 - 12:25:15 CST)
- Re: Tuning QM-MM with namd-orca on one cluster node Marcelo C. R. Melo (Thu Jan 31 2019 - 13:07:53 CST)
- Re: Tuning QM-MM with namd-orca on one cluster node Francesco Pietra (Thu Jan 31 2019 - 15:22:25 CST)
- Fwd: Tuning QM-MM with namd-orca on one cluster node Francesco Pietra (Thu Jan 31 2019 - 15:30:40 CST)
- Re: Fwd: Tuning QM-MM with namd-orca on one cluster node Jim Phillips (Thu Jan 31 2019 - 15:47:35 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: Tuning QM-MM with namd-orca on one cluster node Francesco Pietra (Fri Feb 01 2019 - 09:24:44 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 Marcelo C. R. Melo (Sun Feb 03 2019 - 17:03:54 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 Francesco Pietra (Thu Jan 31 2019 - 15:22:25 CST)
- Re: Tuning QM-MM with namd-orca on one cluster node Marcelo C. R. Melo (Thu Jan 31 2019 - 13:07:53 CST)
- info about gpu hardware Stefano Guglielmo (Thu Jan 31 2019 - 11:12:57 CST)
- Question about colvars Faramarz Joodaki (Wed Jan 30 2019 - 19:06:12 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: 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)
- 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 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 (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 Aravinda Munasinghe (Wed Jan 30 2019 - 20:18:13 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 (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 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)
- 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: run MD simulation in NAMD using stages file strategy or allin one file ? soroush ziaei (Sat Jan 26 2019 - 14:26:04 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)
- 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)
- 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)
- (no subject) jeevan gc (Thu Jan 24 2019 - 16:53:46 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)
- Angle list Ashkan Shekaari (Sat Jan 19 2019 - 07:49:35 CST)
- mdff for EM map with helical symmetry and the asymmetric unit is dimer Zhang Yan (Thu Jan 17 2019 - 21:28:37 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)
- FATAL ERROR with "File exists" Seibold, Steve Allan (Wed Jan 16 2019 - 12:30:48 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)
- 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)
- running NAMD with Slurm Seibold, Steve Allan (Wed Jan 09 2019 - 09:54:21 CST)
- Re: [External] running NAMD with Slurm Sharp, Kim (Wed Jan 09 2019 - 11:15:19 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 - 12:41:20 CST)
- Re: [External] running NAMD with Slurm Seibold, Steve Allan (Wed Jan 09 2019 - 12:52:44 CST)
- Re: [External] running NAMD with Slurm Bennion, Brian (Wed Jan 09 2019 - 12:56:14 CST)
- Re: [External] running NAMD with Slurm Jim Phillips (Mon Jan 14 2019 - 14:29:55 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 on cluster Seibold, Steve Allan (Wed Jan 09 2019 - 09:08:57 CST)
- CHARMM force field for Hydrogen bond? Nasim Rajabi (Mon Jan 07 2019 - 16:15:43 CST)
- Protein Charge Ashkan Shekaari (Mon Jan 07 2019 - 02:24:15 CST)
- Error in using the QMElecEmbed keyword Xi Chen (Fri Jan 04 2019 - 12:13:58 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 Victor Kwan (Thu Jan 03 2019 - 13:19:20 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)
- 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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