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NAMD-L: By Author

By Author

1983 messages sorted by: [ date ] [ thread ] [ subject ] [ attachment ]
About this archive

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

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