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NAMD-L: By Author

By Author

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

Starting: Sat Jan 01 2022 - 00:55:09 CST
Ending: Tue Dec 13 2022 - 12:14:18 CST

• Acharya, Atanu
  • Re: Missing cphrst file in incomplete run (Mon Mar 14 2022 - 13:48:58 CDT)
  • Missing cphrst file in incomplete run (Fri Mar 11 2022 - 16:52:02 CST)
• Adrita Chakraborty
  • Re: Calculation of interprotein contacts between two proteins (Thu Apr 21 2022 - 08:54:13 CDT)
  • Re: Calculation of interprotein contacts between two proteins (Thu Apr 21 2022 - 04:18:05 CDT)
  • Calculation of interprotein contacts between two proteins (Tue Apr 19 2022 - 09:13:10 CDT)
• Ajian
  • RE: FATAL ERROR: sed: can't read restraints/dihe.txt: No suchfile or directory (Tue Jan 11 2022 - 22:59:51 CST)
  • FATAL ERROR: sed: can't read restraints/dihe.txt: No such file or directory (Tue Jan 11 2022 - 18:12:54 CST)
• Alexander Adams
  • Re: Tool for Repositioning disordered loop: TMD (Thu Jan 27 2022 - 04:07:07 CST)
  • Tool for Repositioning disordered loop: TMD (Mon Jan 24 2022 - 11:01:36 CST)
• Alexandre Suman de Araújo
  • Namd 2.14 CUDA not working on Geforce 2080Ti (Sat Sep 10 2022 - 07:46:00 CDT)
  • Problems to run namd2-cuda on alienware m15 R6 (Fri May 13 2022 - 07:26:27 CDT)
• Almeida-Hernández, Yasser, Dr.
  • Restarting a simulation (Mon Jul 25 2022 - 04:20:55 CDT)
  • NAMD3 benchmark (Mon May 09 2022 - 03:12:16 CDT)
  • Re: Running NAMD Singularity container on GPU multinode cluster with Omnipath (Fri Jan 21 2022 - 07:17:19 CST)
  • Running NAMD Singularity container on GPU multinode cluster with Omnipath (Fri Jan 21 2022 - 03:14:42 CST)
• Anastasia Saar
  • setting forceRAMD (Thu Jun 16 2022 - 16:32:14 CDT)
• Andrew Michael Erly
  • qmLSS for Non-Water Solvents (Mon Nov 14 2022 - 15:28:54 CST)
• Angel Tamez
  • PBC and Alignment issues (Wed Apr 20 2022 - 16:03:33 CDT)
• Angelo Rossi
  • Re: Ficoll/Dextran CHARMM Force Field (Tue Aug 23 2022 - 12:58:38 CDT)
  • Re: Ficoll/Dextran CHARMM Force Field (Tue Aug 23 2022 - 08:55:42 CDT)
• Anirvinya Gururajan
  • Alchemical FEP simulation (Wed Nov 16 2022 - 23:58:31 CST)
  • Re: Error while simulating on NAMD (Tue Mar 22 2022 - 02:27:05 CDT)
  • Re: Error while simulating on NAMD (Mon Mar 21 2022 - 08:53:39 CDT)
  • Error while simulating on NAMD (Sun Mar 20 2022 - 16:16:25 CDT)
• Ankita Kandalkar
  • Error: Constraint failure in RATTLE algorithm for atom 5298 (Fri Oct 14 2022 - 05:20:57 CDT)
• Antonio Frances Monerris
  • Re: CPU multinode NAMD 2.14 execution (Tue Sep 20 2022 - 04:57:46 CDT)
  • Re: CPU multinode NAMD 2.14 execution (Mon Sep 19 2022 - 12:01:27 CDT)
  • Re: CPU multinode NAMD 2.14 execution (Mon Sep 19 2022 - 10:58:01 CDT)
  • CPU multinode NAMD 2.14 execution (Mon Sep 19 2022 - 09:40:37 CDT)
• Anup Prasad
  • Re: Regarding minimization of a protein (Mon Mar 28 2022 - 04:30:39 CDT)
• Ashkan Shekaari
  • Re: Tool for Repositioning disordered loop: TMD (Wed Jan 26 2022 - 10:42:33 CST)
• Ashutosh Shandilya
  • MW-eABF error: specified 1 reference frames, but gspath requires at least 2 frames (Thu Feb 17 2022 - 11:16:46 CST)
  • multiple-walker eABF run input (Tue Feb 15 2022 - 23:59:59 CST)
  • eABF run issue: czar.grad file not covering the reaction coordinates (Thu Feb 10 2022 - 10:20:59 CST)
• Axel Kohlmeyer
  • Re: Advice on choice of NAMD to install for CUDA/GPU support (Mon Sep 12 2022 - 12:51:14 CDT)
  • Re: pdb file from a particular configuration (Tue Jun 28 2022 - 04:55:38 CDT)
  • Re: pdb file from a particular configuration (Tue Jun 28 2022 - 04:53:09 CDT)
• Bassam Haddad
  • Re: Very High RMSD Value from NAMD Simulation (Wed May 11 2022 - 14:42:25 CDT)
• Bennion, Brian
  • Re: How to handle large pdbs in namd? (Thu Mar 03 2022 - 18:18:24 CST)
  • Re: How to handle large pdbs in namd? (Thu Mar 03 2022 - 17:13:58 CST)
• Bibekananda Rabha
  • smd simulation using gaff parameter (Thu Jan 27 2022 - 07:59:46 CST)
  • SMD simulation (Wed Jan 26 2022 - 03:41:04 CST)
• Brian Radak
  • Re: When should I use NTER and NNEU as a patch? (Wed Oct 12 2022 - 13:47:03 CDT)
  • Re: Reading CHARMM36 .str topology error (Thu Sep 08 2022 - 11:04:17 CDT)
• brian.radak_at_gmail.com
  • Fwd: Error while analyzing testcph.log file by using pynamd (Wed Sep 07 2022 - 08:25:46 CDT)
  • Re: Missing cphrst file in incomplete run (Sat Mar 12 2022 - 13:05:44 CST)
• Bunzeki Kilolo (Mme)
  • Re: NAMD can not run 5.6 million system with amber prmtop (Fri Nov 04 2022 - 12:57:17 CDT)
  • Re: pdb file from a particular configuration (Tue Jun 28 2022 - 04:10:02 CDT)
• Chunli Yan
  • NAMD can not run 5.6 million system with amber prmtop (Fri Nov 04 2022 - 12:44:22 CDT)
• Collin Nisler
  • Applying Constraints for ABF Calculations (Wed Dec 07 2022 - 18:47:54 CST)
  • Discontinuity in SMD Forces (Mon Dec 05 2022 - 13:52:59 CST)
  • Interrupted Writing Restart Files (Fri Dec 02 2022 - 10:21:14 CST)
  • Issue Combining PSF and PDB Files (Sun Nov 13 2022 - 19:35:31 CST)
  • Use of Targeted MD vs. Colvars (Wed Oct 19 2022 - 12:04:15 CDT)
  • Creating a New Patch for RNA (Sun Sep 04 2022 - 17:04:15 CDT)
• Daipayan Sarkar
  • Re: Alchemical FEP simulation (Sat Nov 19 2022 - 08:10:18 CST)
  • Re: Alchemical FEP simulation (Thu Nov 17 2022 - 07:02:39 CST)
  • Re: Issue Combining PSF and PDB Files (Sun Nov 13 2022 - 21:11:06 CST)
  • Re: Query regarding performance (Tue Oct 25 2022 - 10:09:16 CDT)
  • Re: Query regarding performance (Tue Oct 25 2022 - 05:16:55 CDT)
  • Re: Query regarding performance (Tue Oct 04 2022 - 06:46:10 CDT)
• Dalhaimer, Paul Matthew
  • Re: S-S bond (Sun Feb 20 2022 - 19:03:16 CST)
  • S-S bond (Sun Feb 20 2022 - 08:06:16 CST)
• David Hardy
  • NAMD and VMD programmer positions (Fri Sep 09 2022 - 18:35:41 CDT)
  • Re: Considering switching to NAMD3 (Fri Jun 24 2022 - 10:28:19 CDT)
  • NAMD 3.0alpha12 released (Fri Jun 24 2022 - 10:26:56 CDT)
• Deepshikha Ghosh 19310001
  • Re: Regarding minimization of a protein (Mon Mar 28 2022 - 05:32:58 CDT)
  • Re: Regarding minimization of a protein (Mon Mar 28 2022 - 05:24:51 CDT)
  • Regarding minimization of a protein (Mon Mar 28 2022 - 04:01:24 CDT)
• Derman Basturk
  • When should I use NTER and NNEU as a patch? (Wed Oct 12 2022 - 12:46:17 CDT)
• Diego Gomes
  • Re: QwikMD QM Tut - FATAL ERROR: Error running command for QM forces calculation. (Fri Sep 09 2022 - 13:39:49 CDT)
• Do, Hung Nguyen
  • Re: Error compiling NAMD 2.15 Source Code (Mon Apr 11 2022 - 12:54:24 CDT)
  • Error compiling NAMD 2.15 Source Code (Tue Apr 05 2022 - 22:15:30 CDT)
• Ebru Çetin
  • Snakemake with NAMD (Tue Jun 28 2022 - 17:04:06 CDT)
• Eduardo R Cruz-Chu
  • Re: NAMD can not run 5.6 million system with amber prmtop (Fri Nov 04 2022 - 14:12:44 CDT)
• Efthymiou, Christos
  • Very High RMSD Value from NAMD Simulation (Wed May 11 2022 - 14:19:37 CDT)
• fhh2626_at_gmail.com
  • Re: ABF Free Energy Calculation (Tue Oct 04 2022 - 01:43:42 CDT)
  • CUDA error cudaCreateTextureObject (Thu Jul 28 2022 - 23:36:48 CDT)
  • Re: Re: Chain identifiers in NAMD simulation (Thu Apr 07 2022 - 21:11:42 CDT)
  • Re: Chain identifiers in NAMD simulation (Wed Apr 06 2022 - 06:17:46 CDT)
• Francesco Coppola
  • NAMDenergy (Mon May 16 2022 - 13:41:19 CDT)
• Francesco Pietra
  • CUDA error cudaStreamSynchronize(stream) and CUDA error in ComputeBondedCUDA (Thu Nov 17 2022 - 10:19:43 CST)
  • Parameters for naturally modified nucleotides (Mon Nov 14 2022 - 11:48:04 CST)
  • Re: Restarting namd-mopac QMMM (Sat Feb 12 2022 - 12:44:34 CST)
  • Restarting namd-mopac QMMM (Sat Feb 12 2022 - 10:42:50 CST)
  • Puzzle with "small molecule" ligand structure in nucleotide environments (Sun Feb 06 2022 - 01:59:52 CST)
  • Re: No xyz and scfp files in QMMM ORCA output (Sat Feb 05 2022 - 02:45:30 CST)
  • No xyz and scfp files in QMMM ORCA output (Mon Jan 31 2022 - 08:27:45 CST)
  • QMMM analysis on downloaded ORCA /0 (Mon Jan 31 2022 - 07:54:04 CST)
  • Fwd: Problems with charmm36 modified nucleotides for psfgen and namd (Thu Jan 20 2022 - 08:43:12 CST)
  • Fwd: Problems with charmm36 modified nucleotides for psfgen and namd (Thu Jan 20 2022 - 08:31:36 CST)
  • Problems with charmm36 modified nucleotides for psfgen and namd (Thu Jan 20 2022 - 08:26:48 CST)
  • Where to find top_all36_cgenff.rtf/prm version 4.5? (Wed Jan 19 2022 - 08:39:20 CST)
  • Fwd: Fwd: nvidia issue with namd12 Debian 11 (Tue Jan 18 2022 - 03:18:06 CST)
  • Re: Fwd: nvidia issue with namd12 Debian 11 (Mon Jan 17 2022 - 14:50:14 CST)
  • Fwd: nvidia issue with namd12 Debian 11 (Mon Jan 17 2022 - 03:36:38 CST)
  • nvidia issue with namd12 Debian 11 (Mon Jan 17 2022 - 03:15:17 CST)
• GAGANJYOT KAUR BAKSHI
  • NAMD Simulations (Tue Nov 29 2022 - 20:23:28 CST)
• Gauri Tekbahadur Thapa
  • RAMD error (Sun May 15 2022 - 05:55:18 CDT)
• Gauri Thapa
  • Re: RAMD error (Tue May 17 2022 - 02:21:32 CDT)
• Geist, Norman
  • Re: Re: namd-l digest V1 #3281 (Tue Sep 13 2022 - 01:40:34 CDT)
  • Re: Re: namd-l digest V1 #3281 (Tue Sep 13 2022 - 00:31:43 CDT)
  • Re: Re: namd-l digest V1 #3281 (Tue Sep 13 2022 - 00:22:22 CDT)
  • Re: to rigidify bonds without hydrogen (about suggestion http://jeffcomer.us/downloads.html) (Mon Aug 29 2022 - 06:11:32 CDT)
  • Re: to rigidify bonds without hydrogen (about suggestion http://jeffcomer.us/downloads.html) (Mon Aug 29 2022 - 06:09:21 CDT)
  • Re: BUG: ReplicaUniformPatchGrid namd-2.14 (Tue May 31 2022 - 07:36:47 CDT)
  • BUG: ReplicaUniformPatchGrid namd-2.14 (Tue May 31 2022 - 01:29:34 CDT)
  • CheckpointStore command (Mon May 30 2022 - 01:22:34 CDT)
  • Re: Applying unidirectional pressure on a membrane protein system (Sat May 28 2022 - 02:19:50 CDT)
  • Re: Applying pressure on membrane protein system (Thu May 12 2022 - 00:26:04 CDT)
  • Re: (Thu Apr 14 2022 - 00:42:06 CDT)
• Gerald Keller
  • namd3-alpha13 on CentOS7 (Sun Jul 31 2022 - 03:39:13 CDT)
  • Considering switching to NAMD3 (Tue May 17 2022 - 10:18:27 CDT)
• Ghazanfari, Sarah
  • Question (Thu Apr 14 2022 - 15:11:26 CDT)
• Giacomo Fiorin
  • Re: Applying Constraints for ABF Calculations (Tue Dec 13 2022 - 12:12:50 CST)
  • Re: Density over time (Tue Nov 29 2022 - 10:44:22 CST)
  • Re: Gradual heating (Mon Nov 21 2022 - 08:09:57 CST)
  • Re: Gradual heating (Mon Nov 21 2022 - 07:59:16 CST)
  • Re: equilibrating a system using restraints (Thu Nov 17 2022 - 07:54:23 CST)
  • Re: Use of Targeted MD vs. Colvars (Wed Oct 19 2022 - 14:25:43 CDT)
  • Re: No performance improvement with NAMD 3.0 alpha8 over namd 2.14 cuda (Fri Sep 09 2022 - 11:17:23 CDT)
  • Re: Low performance in SMwST simulations (Fri Aug 26 2022 - 03:29:20 CDT)
  • Re: Simulating a system with an imaginary barrier (Mon Aug 22 2022 - 04:35:03 CDT)
  • Re: Error (Thu Jul 14 2022 - 08:57:19 CDT)
  • Re: Anvil Purdue (Thu Jun 16 2022 - 15:31:44 CDT)
  • Re: BUG: ReplicaUniformPatchGrid namd-2.14 (Tue May 31 2022 - 10:35:48 CDT)
  • Re: Colvar vs. SMD (Wed Mar 16 2022 - 10:22:06 CDT)
  • Re: Colvar vs. SMD (Wed Mar 16 2022 - 09:41:02 CDT)
  • Re: NAMD3 runs failing with no error - XST failing to load and jumping to negative timestep (Thu Mar 10 2022 - 08:26:38 CST)
  • Re: << Tool to create NAMD input for non biological system >> (Thu Mar 03 2022 - 14:02:57 CST)
  • Re: << Tool to create NAMD input for non biological system >> (Thu Mar 03 2022 - 10:52:00 CST)
  • Re: FATAL ERROR: CudaTileListKernel::buildTileLists, (Tue Mar 01 2022 - 08:47:11 CST)
  • Re: FATAL ERROR: CudaTileListKernel::buildTileLists, (Tue Mar 01 2022 - 08:45:03 CST)
  • Re: namd3 (Mon Feb 21 2022 - 09:46:01 CST)
  • Re: S-S bond (Sun Feb 20 2022 - 18:35:50 CST)
  • Re: NAMD hangs with replica option (Fri Feb 11 2022 - 07:22:50 CST)
  • Re: Running NAMD Singularity container on GPU multinode cluster with Omnipath (Fri Jan 21 2022 - 07:51:33 CST)
  • Re: Running NAMD Singularity container on GPU multinode cluster with Omnipath (Fri Jan 21 2022 - 06:51:11 CST)
  • Re: FATAL ERROR: sed: can't read restraints/dihe.txt: No suchfile or directory (Wed Jan 12 2022 - 08:32:55 CST)
  • Re: NAMD hangs with replica option (Wed Jan 12 2022 - 08:32:14 CST)
  • Re: NAMD hangs with replica option (Mon Jan 10 2022 - 13:26:53 CST)
  • Re: NAMD hangs with replica option (Mon Jan 10 2022 - 10:22:13 CST)
• Gisele Strieder Philippsen
  • namd3 (Mon Feb 21 2022 - 07:19:37 CST)
• GIUSEPPE LEONARDO LICARI
  • Optimal choice of NVIDIA GPU to run NAMD3 (Sat Aug 06 2022 - 05:48:44 CDT)
• Gumbart, JC
  • Re: Chain identifiers in NAMD simulation (Fri Apr 08 2022 - 11:26:02 CDT)
  • Re: Chain identifiers in NAMD simulation (Thu Apr 07 2022 - 13:36:38 CDT)
• Hemanth Haridas
  • Re: Tool for Repositioning disordered loop: TMD (Wed Jan 26 2022 - 21:37:11 CST)
• hgkrug1_at_gmail.com
  • Advice on choice of NAMD to install for CUDA/GPU support (Mon Sep 12 2022 - 12:24:43 CDT)
  • Re: QwikMD QM Tut - FATAL ERROR: Error running command for QM forces calculation. (Mon Sep 12 2022 - 05:36:33 CDT)
  • Re: QwikMD QM Tut - FATAL ERROR: Error running command for QM forces calculation. (Mon Sep 12 2022 - 02:34:16 CDT)
  • QwikMD QM Tut - FATAL ERROR: Error running command for QM forces calculation. (Fri Sep 09 2022 - 03:30:09 CDT)
  • QwikMD QM Tut - FATAL ERROR: Error running command for QM forces calculation. (Fri Sep 09 2022 - 03:20:53 CDT)
  • Re: QwikMD QM Tut - FATAL ERROR: Error running command for QM forces calculation. (Thu Sep 08 2022 - 12:49:42 CDT)
  • QwikMD QM Tut - FATAL ERROR: Error running command for QM forces calculation. (Mon Sep 05 2022 - 04:46:39 CDT)
  • Re: QwikMD QM Tut - FATAL ERROR: Error running command for QM forces calculation. (Mon Sep 05 2022 - 00:58:26 CDT)
  • QwikMD QM Tut - FATAL ERROR: Error running command for QM forces calculation. (Sun Sep 04 2022 - 01:16:02 CDT)
  • Re: Error: [1]+ Segmentation fault (core dumped) (Tue Aug 30 2022 - 08:40:25 CDT)
  • Error: [1]+ Segmentation fault (core dumped) (Tue Aug 30 2022 - 05:47:14 CDT)
• Hocine El Khaoudi enyoury
  • Re: Density over time (Tue Nov 29 2022 - 11:00:40 CST)
  • Density over time (Tue Nov 29 2022 - 10:18:59 CST)
  • Re: Gradual heating (Wed Nov 23 2022 - 04:47:30 CST)
  • Re: Gradual heating (Mon Nov 21 2022 - 08:01:38 CST)
  • Gradual heating (Mon Nov 21 2022 - 05:54:22 CST)
• Hrishikesh Dhondge
  • Decomposing the free energy contributions (Fri Oct 07 2022 - 03:51:53 CDT)
  • Re: Unable to run NAMD3.0 on 2 GPUs simultaneously (Mon May 02 2022 - 04:54:59 CDT)
  • Re: Calculation of interprotein contacts between two proteins (Tue Apr 26 2022 - 10:19:33 CDT)
  • Re: Calculation of interprotein contacts between two proteins (Thu Apr 21 2022 - 06:09:16 CDT)
  • Re: PBC and Alignment issues (Thu Apr 21 2022 - 02:47:54 CDT)
  • Re: Calculation of interprotein contacts between two proteins (Wed Apr 20 2022 - 01:08:35 CDT)
  • Re: Native and nonnative contacts (Mon Apr 11 2022 - 04:26:44 CDT)
  • Native and nonnative contacts (Mon Apr 11 2022 - 03:31:08 CDT)
  • Chain identifiers in NAMD simulation (Wed Apr 06 2022 - 05:00:09 CDT)
  • Re: Error while simulating on NAMD (Tue Mar 22 2022 - 01:40:27 CDT)
• I. Camps
  • Re: << Tool to create NAMD input for non biological system >> (Thu Mar 03 2022 - 13:46:30 CST)
  • << Tool to create NAMD input for non biological system >> (Wed Mar 02 2022 - 19:43:55 CST)
• Ian Bongalonta
  • Reading CHARMM36 .str topology error (Wed Sep 07 2022 - 20:29:39 CDT)
• Ingrid Bernardes Santana Martins
  • Re: Didn't find vdW parameter for stop type HB1 Error (Wed Apr 13 2022 - 09:15:15 CDT)
  • Re: Didn't find vdW parameter for stop type HB1 Error (Mon Apr 11 2022 - 16:56:05 CDT)
• Ivaylo Nikolaev Ivanov
  • postdoctoral position in molecular modeling (Mon Apr 04 2022 - 10:54:21 CDT)
• Jeff Comer
  • Re: Fwd: Irregular spontaneous membrane bending even in the absence of protein (Sun Sep 11 2022 - 15:38:29 CDT)
  • Re: Ficoll/Dextran CHARMM Force Field (Tue Aug 23 2022 - 12:08:07 CDT)
  • Re: question about namd3 performance (Fri Jul 22 2022 - 13:07:38 CDT)
  • Re: Colvar vs. SMD (Mon Mar 21 2022 - 09:21:39 CDT)
• Jie Shi
  • Re: Re: namd-l digest V1 #3281 (Wed Sep 14 2022 - 11:00:34 CDT)
  • Re: Re: namd-l digest V1 #3281 (Tue Sep 13 2022 - 02:03:35 CDT)
  • Re: Re: namd-l digest V1 #3281 (Tue Sep 13 2022 - 00:36:48 CDT)
  • Re: Re: namd-l digest V1 #3281 (Tue Sep 13 2022 - 00:28:30 CDT)
  • Re: Re: namd-l digest V1 #3281 (Mon Sep 12 2022 - 17:17:12 CDT)
  • Re: Fwd: Irregular spontaneous membrane bending even in the absence of protein (Sun Sep 11 2022 - 19:55:38 CDT)
  • Fwd: Irregular spontaneous membrane bending even in the absence of protein (Sun Sep 11 2022 - 10:36:09 CDT)
• jing liang
  • Re: QM/MM CASSCF shows strange symbols in the input file (Fri Nov 04 2022 - 06:34:48 CDT)
  • QM/MM CASSCF shows strange symbols in the input file (Thu Nov 03 2022 - 03:15:31 CDT)
  • QM/MM time-dependent DFT simulations (Fri Aug 12 2022 - 15:23:39 CDT)
  • Re: NAMD hangs with replica option (Fri Feb 11 2022 - 03:21:27 CST)
  • Re: NAMD hangs with replica option (Wed Jan 12 2022 - 03:21:22 CST)
  • Re: NAMD hangs with replica option (Mon Jan 10 2022 - 13:12:53 CST)
  • NAMD hangs with replica option (Sun Jan 09 2022 - 13:34:38 CST)
• Joey Farrell
  • Re: ABF Free Energy Calculation (Wed Oct 05 2022 - 16:16:26 CDT)
  • ABF Free Energy Calculation (Tue Oct 04 2022 - 01:12:52 CDT)
  • Re: ABF Non-Uniform Zcount (Tue May 03 2022 - 19:13:03 CDT)
  • Re: ABF Non-Uniform Zcount (Tue Apr 26 2022 - 11:38:16 CDT)
  • ABF Non-Uniform Zcount (Mon Apr 25 2022 - 23:33:51 CDT)
• joseph pareti
  • weighted ensemble algorithm (Wed Mar 09 2022 - 13:42:43 CST)
• Josh Vermaas
  • Re: Interrupted Writing Restart Files (Fri Dec 02 2022 - 12:24:18 CST)
  • Re: Gradual heating (Mon Nov 21 2022 - 09:04:53 CST)
  • Re: NAMD3, GPU and slurm: FATAL ERROR: CUDA error cudaFree (Sat Nov 05 2022 - 16:09:43 CDT)
  • Re: MMPBSA Question (Thu Sep 22 2022 - 14:15:36 CDT)
  • Re: CPU multinode NAMD 2.14 execution (Mon Sep 19 2022 - 12:15:03 CDT)
  • Re: CPU multinode NAMD 2.14 execution (Mon Sep 19 2022 - 11:25:59 CDT)
  • Re: CPU multinode NAMD 2.14 execution (Mon Sep 19 2022 - 10:21:52 CDT)
  • Re: Creating a New Patch for RNA (Mon Sep 05 2022 - 05:39:14 CDT)
  • Re: restart glitch - return to original structure (Fri Apr 15 2022 - 16:00:16 CDT)
  • Re: Error compiling NAMD 2.15 Source Code (Thu Apr 07 2022 - 15:41:22 CDT)
  • Re: Error while simulating on NAMD (Mon Mar 21 2022 - 08:22:58 CDT)
  • Re: Simulation running slow (1ns/day) (Thu Mar 17 2022 - 10:30:10 CDT)
  • Re: NAMD hangs with replica option (Mon Jan 10 2022 - 08:35:49 CST)
• Jérôme Hénin
  • Re: ABF Non-Uniform Zcount (Wed Apr 27 2022 - 08:40:35 CDT)
  • Re: Colvar vs. SMD (Wed Mar 16 2022 - 09:28:17 CDT)
  • Re: Inconsistent PMF profile of Ionized polymer (Mon Jan 17 2022 - 12:28:48 CST)
• Kartik Tulsian
  • GPU requirements for CUDA enabled NAMD (Sat Oct 15 2022 - 03:24:59 CDT)
• Kartikey Pandey
  • Heating a system or applying force with some function of timestep in simulation (Sun Jul 17 2022 - 22:35:05 CDT)
• Kevin Chan
  • Compute atom/residue-based interactions on-the-fly (Tue Apr 26 2022 - 02:14:59 CDT)
• Kosar Khajeh
  • Re: TIP4P Simulation Scripts (Tue Jul 05 2022 - 22:50:47 CDT)
• Krithika Unmesh
  • equilibrating a system using restraints (Thu Nov 17 2022 - 00:52:06 CST)
• Luis Cebamanos
  • Wrong number of p (Wed Oct 12 2022 - 09:32:51 CDT)
  • Utilizing all GPUs on multi-node environment (Fri Jan 14 2022 - 10:57:51 CST)
• Marcelo C. R. Melo
  • Re: QM/MM CASSCF shows strange symbols in the input file (Thu Nov 03 2022 - 14:41:24 CDT)
  • Re: QMMM Question (Tue Oct 18 2022 - 16:33:00 CDT)
  • Re: how to properly calculate the interaction between the QM and MM region (Mon Oct 17 2022 - 11:42:47 CDT)
  • Re: How to qm/mm calculations with NAMD-QChem (Mon May 02 2022 - 18:51:55 CDT)
  • Re: How to qm/mm calculations with NAMD-QChem (Mon May 02 2022 - 16:08:22 CDT)
  • Re: How to qm/mm calculations with NAMD-QChem (Sun May 01 2022 - 22:50:09 CDT)
  • Re: Restarting namd-mopac QMMM (Sat Feb 12 2022 - 15:47:44 CST)
  • Re: Restarting namd-mopac QMMM (Sat Feb 12 2022 - 11:46:50 CST)
  • Re: No xyz and scfp files in QMMM ORCA output (Mon Jan 31 2022 - 12:28:49 CST)
• Mare Libero
  • FATAL ERROR: Atom 1 has bad hydrogen group size. Check for duplicate bonds. (Sun Jan 23 2022 - 17:30:15 CST)
• Maria Bykhovskaia
  • Anvil Purdue (Thu Jun 16 2022 - 15:59:54 CDT)
  • glutathione, Charmm 36 (Fri May 20 2022 - 17:27:29 CDT)
• Mcguire, Kelly
  • QMMM Update (Thu Oct 20 2022 - 20:29:15 CDT)
  • Re: QMMM Question (Tue Oct 18 2022 - 23:45:09 CDT)
  • QMMM Question (Mon Oct 17 2022 - 14:38:54 CDT)
  • Re: MMPBSA Question (Sat Oct 01 2022 - 20:12:39 CDT)
  • Re: MMPBSA Question (Thu Sep 22 2022 - 14:40:43 CDT)
  • MMPBSA Question (Thu Sep 22 2022 - 12:56:44 CDT)
  • Atoms Per Patch Question (Thu Mar 24 2022 - 16:27:56 CDT)
  • Re: NAMD CUDA Error (Sat Mar 12 2022 - 19:29:13 CST)
  • NAMD CUDA Error (Sat Mar 12 2022 - 19:26:33 CST)
  • Re: Minimization Crashing Implicit Solvent (Fri Feb 18 2022 - 16:49:04 CST)
  • Minimization Crashing Implicit Solvent (Fri Feb 18 2022 - 14:30:28 CST)
  • Multiple Jobs (Sun Feb 06 2022 - 02:43:46 CST)
  • SMD Question (Wed Jan 12 2022 - 22:13:20 CST)
• Md Zobayer Hossain
  • Re: Applying unidirectional pressure on a membrane protein system (Sat May 28 2022 - 05:37:17 CDT)
  • Using non bonded energy table option (Mon Feb 21 2022 - 13:39:44 CST)
• Meng Shen
  • Customized revision of NAMD (Thu Aug 11 2022 - 09:56:06 CDT)
• Michelle Kuttel
  • Re: Ficoll/Dextran CHARMM Force Field (Wed Aug 24 2022 - 02:48:36 CDT)
• Mike McCallum
  • Re: Multiple Jobs (Sun Feb 06 2022 - 10:29:07 CST)
• Monika Kumari
  • Re: The parameter error in the NAMD Energy of VMD (Wed Nov 30 2022 - 03:15:59 CST)
  • Re: NAMD Energy Plugin giving incorrect energies (Mon Oct 10 2022 - 00:57:02 CDT)
  • Re: NAMD Energy Plugin giving incorrect energies (Mon Oct 03 2022 - 00:08:59 CDT)
  • NAMD Energy Plugin giving incorrect energies (Tue Sep 27 2022 - 09:40:23 CDT)
  • Re: Simulating a system with an imaginary barrier (Tue Aug 23 2022 - 05:02:41 CDT)
  • Simulating a system with an imaginary barrier (Thu Aug 18 2022 - 08:48:21 CDT)
• Monika Madhavi
  • Applying a force to a molecule in water (Sat Jan 01 2022 - 00:54:40 CST)
• Moumita Saharay
  • Re: FATAL ERROR: sed: can't read restraints/dihe.txt: No such file or directory (Tue Jan 11 2022 - 21:59:56 CST)
• Mükerrem TüfekçioÄŸlu
  • Low performance in SMwST simulations (Thu Aug 25 2022 - 15:29:57 CDT)
  • Force and RMSD Values for TMD (Thu Jun 30 2022 - 15:13:37 CDT)
• Natalia Ostrowska
  • Re: Using non bonded energy table option (Tue Feb 22 2022 - 05:12:25 CST)
• Nicholus Bhattacharjee
  • Re: Query regarding performance (Tue Oct 25 2022 - 10:14:54 CDT)
  • Re: Query regarding performance (Tue Oct 25 2022 - 07:43:04 CDT)
  • Re: Query regarding performance (Tue Oct 25 2022 - 03:21:39 CDT)
  • Re: Query regarding performance (Tue Oct 04 2022 - 04:07:28 CDT)
  • Query regarding performance (Mon Oct 03 2022 - 03:13:19 CDT)
  • Steered molecular dynamics simulations of peptide with non standard amino acid using GAFF parameter (Sat Feb 05 2022 - 03:30:16 CST)
  • Steered molecular dynamics simulations of peptide with non standard amino acid using GAFF parameter (Wed Feb 02 2022 - 23:29:33 CST)
  • Steered molecular dynamics simulations of peptide with non standard amino acid using GAFF parameter (Sun Jan 30 2022 - 01:30:58 CST)
• Nicole Richardson
  • NAMD3 runs failing with no error - XST failing to load and jumping to negative timestep (Thu Mar 10 2022 - 01:44:29 CST)
• Nur Afiqah Ahmad
  • RE: Error (Thu Jul 14 2022 - 20:44:20 CDT)
  • Re: Error (Thu Jul 14 2022 - 08:50:42 CDT)
  • Re: Error (Thu Jul 14 2022 - 08:46:56 CDT)
  • Error (Thu Jul 14 2022 - 08:16:30 CDT)
• Oleksii Zdorevskyi
  • Re: how to properly calculate the interaction between the QM and MM region (Fri Oct 21 2022 - 05:29:37 CDT)
  • how to properly calculate the interaction between the QM and MM region (Fri Oct 14 2022 - 04:59:58 CDT)
• PaweÅ‚ KÄ™dzierski
  • Re: The parameter error in the NAMD Energy of VMD (Wed Nov 30 2022 - 03:57:16 CST)
• Peter Freddolino
  • Re: NAMD Energy Plugin giving incorrect energies (Sun Oct 16 2022 - 15:53:21 CDT)
  • Re: NAMD Energy Plugin giving incorrect energies (Sun Oct 02 2022 - 14:23:34 CDT)
  • Re: Using non bonded energy table option (Mon Feb 21 2022 - 22:43:24 CST)
  • Re: namd slurm getting error (Mon Feb 14 2022 - 07:44:07 CST)
  • Re: namd slurm getting error (Mon Feb 14 2022 - 07:43:14 CST)
  • Re: FATAL ERROR: Atom 1 has bad hydrogen group size. Check for duplicate bonds. (Sun Jan 23 2022 - 18:26:03 CST)
• Peter Starrs
  • QMMM write forces for a single step (run 0) (Thu Feb 10 2022 - 19:23:23 CST)
• Polly Ren
  • Ficoll/Dextran CHARMM Force Field (Mon Aug 22 2022 - 14:14:27 CDT)
• Pradeepti Kampani
  • Re: Angle parameter errors (Wed Jan 05 2022 - 02:08:15 CST)
• Raman Preet Singh
  • Re: namd-l digest V1 #3281 (Mon Sep 12 2022 - 03:55:06 CDT)
  • Re: namd-l digest V1 #3272 (Tue Aug 23 2022 - 07:03:28 CDT)
  • Restraints to maintain shape of particle (Tue Mar 08 2022 - 05:24:47 CST)
• Randall Hall
  • NAMD on apple M1 processor (Mon Aug 08 2022 - 12:35:24 CDT)
• René Hafner TUK
  • Re: Query regarding performance (Tue Oct 04 2022 - 04:44:45 CDT)
  • Re: Query regarding performance (Tue Oct 04 2022 - 03:45:24 CDT)
  • Re: Error while simulating on NAMD (Mon Mar 21 2022 - 17:28:55 CDT)
• Ribi Akbar
  • Re: charmm-gui namd inputs not working namd (Sun Jul 17 2022 - 16:30:34 CDT)
  • Re: pdb file from a particular configuration (Tue Jun 28 2022 - 04:54:48 CDT)
  • Re: pdb file from a particular configuration (Tue Jun 28 2022 - 04:24:52 CDT)
  • pdb file from a particular configuration (Tue Jun 28 2022 - 02:49:17 CDT)
  • How to extract coordinates from trajectories (Tue May 24 2022 - 11:45:06 CDT)
• RonitS Chem
  • Re: How to qm/mm calculations with NAMD-QChem (Tue May 03 2022 - 16:39:56 CDT)
  • Re: How to qm/mm calculations with NAMD-QChem (Mon May 02 2022 - 17:48:06 CDT)
  • How to qm/mm calculations with NAMD-QChem (Sun May 01 2022 - 18:05:03 CDT)
• ROPÓN-PALACIOS G.
  • COLVAR moving restraint (Fri Mar 18 2022 - 10:05:05 CDT)
  • Fullsamples ABF choice (Thu Mar 03 2022 - 17:00:57 CST)
  • Re: mail about Charmm++ (Sat Jan 29 2022 - 15:02:52 CST)
• Roshan Shrestha
  • Re: How could I select a range of ATOMS by using VMD Program? (Fri Nov 04 2022 - 17:28:32 CDT)
• Rudy Richardson
  • Re: MMPBSA Question (Thu Sep 22 2022 - 16:36:11 CDT)
• Rulong Ma
  • The parameter error in the NAMD Energy of VMD (Tue Nov 29 2022 - 12:02:19 CST)
  • Re: NAMD3 failed to run longer than 4.2μs. (Fri Nov 11 2022 - 14:58:51 CST)
  • NAMD3 failed to run longer than 4.2μs. (Fri Nov 11 2022 - 12:09:02 CST)
• Ruturaj warake
  • (no subject) (Thu Jul 14 2022 - 09:11:55 CDT)
  • Re: Simulation running slow (1ns/day) (Thu Mar 17 2022 - 07:52:23 CDT)
• s) Lucy McEvoy
  • (s) Lucy McEvoy wants to share the file input files.zip with you (Wed Apr 13 2022 - 05:45:23 CDT)
  • (s) Lucy McEvoy wants to share the file input files.zip with you (Wed Apr 13 2022 - 05:45:23 CDT)
  • Re: Didn't find vdW parameter for stop type HB1 Error (Tue Apr 12 2022 - 11:25:13 CDT)
  • Didn't find vdW parameter for stop type HB1 Error (Mon Apr 11 2022 - 13:14:45 CDT)
• SARBAJIT LAYEK
  • (no subject) (Wed Apr 13 2022 - 10:31:02 CDT)
• Seibold, Steve Allan
  • RE: Colvar vs. SMD (Tue Mar 22 2022 - 08:17:33 CDT)
  • RE: Colvar vs. SMD (Wed Mar 16 2022 - 10:50:04 CDT)
  • RE: Colvar vs. SMD (Wed Mar 16 2022 - 10:18:38 CDT)
  • Colvar vs. SMD (Wed Mar 16 2022 - 08:21:47 CDT)
• Shadi Rahnama
  • Re: Error in Using Tabulated FF (Tue Dec 13 2022 - 05:16:41 CST)
• Shiv Seshan
  • TIP4P Simulation Scripts (Tue Jul 05 2022 - 18:10:42 CDT)
• SHIVAM TIWARI
  • Re: No performance improvement with NAMD 3.0 alpha8 over namd 2.14 cuda (Sat Sep 10 2022 - 01:45:25 CDT)
  • Re: No performance improvement with NAMD 3.0 alpha8 over namd 2.14 cuda (Fri Sep 09 2022 - 10:44:58 CDT)
  • No performance improvement with NAMD 3.0 alpha8 over namd 2.14 cuda (Fri Sep 09 2022 - 03:21:36 CDT)
  • Re: error while running simulation with NAMD3.0alpha12 and 13 (Tue Aug 30 2022 - 10:45:19 CDT)
  • error while running simulation with NAMD3.0alpha12 and 13 (Tue Aug 30 2022 - 06:26:34 CDT)
  • Re: CUDA error cudaMalloc during running namd (Thu Aug 25 2022 - 11:36:02 CDT)
  • CUDA error cudaMalloc during running namd (Thu Aug 25 2022 - 07:30:04 CDT)
  • How to get best performance (Tue Apr 26 2022 - 01:18:31 CDT)
• shreya bhattacharya
  • Hybrid FEP topology for Nucleotides (Tue Dec 13 2022 - 06:34:38 CST)
  • FATAL ERROR: SequencerCUDA: Atoms moving too fast error in FEP simulation in NAMD3 (Sat Sep 10 2022 - 02:31:01 CDT)
  • Fatal error during running FEP simulations (Fri Sep 09 2022 - 00:30:15 CDT)
  • Re: Error (Thu Jul 14 2022 - 08:53:40 CDT)
  • Re: Error (Thu Jul 14 2022 - 08:42:42 CDT)
  • How to prepare the topology file for nucleotide FEP in NAMD? (Thu Jul 14 2022 - 08:39:13 CDT)
• Smith, Harper E.
  • NAMD3 Multi-GPU features? (Tue Nov 29 2022 - 16:40:50 CST)
• Sruthi Sundaresan
  • Re: Applying unidirectional pressure on a membrane protein system (Sat May 28 2022 - 04:49:49 CDT)
  • Applying unidirectional pressure on a membrane protein system (Sat May 28 2022 - 01:38:36 CDT)
  • Applying pressure on membrane protein system (Thu May 12 2022 - 00:08:42 CDT)
  • Re: Unable to run NAMD3.0 on 2 GPUs simultaneously (Mon May 02 2022 - 06:56:26 CDT)
  • Unable to run NAMD3.0 on 2 GPUs simultaneously (Mon May 02 2022 - 04:33:13 CDT)
  • Re: Simulation running slow (1ns/day) (Wed Apr 27 2022 - 04:36:22 CDT)
  • Re: Simulation running slow (1ns/day) (Tue Apr 26 2022 - 08:25:07 CDT)
  • Re: Simulation running slow (1ns/day) (Tue Apr 26 2022 - 07:41:20 CDT)
  • Re: Simulation running slow (1ns/day) (Thu Mar 17 2022 - 07:57:43 CDT)
  • Simulation running slow (1ns/day) (Thu Mar 17 2022 - 07:46:27 CDT)
• Strahs, Dr. Daniel Bernard
  • Re: restart glitch - return to original structure (Fri Apr 15 2022 - 16:07:48 CDT)
  • restart glitch - return to original structure (Fri Apr 15 2022 - 13:04:04 CDT)
• Sungho Han
  • [namd3 alpha9] FATAL ERROR: Low global CUDA exclusion count! (781005 vs 781007) System unstable or pairlistdist or cutoff too small. (Fri Mar 18 2022 - 11:35:22 CDT)
• SYEDA SABIHA SULTANA LUBNA .
  • NAMD analysis (Tue Jan 25 2022 - 02:21:27 CST)
• Thérèse Malliavin
  • NAMD3, GPU and slurm: FATAL ERROR: CUDA error cudaFree (Sat Nov 05 2022 - 09:46:16 CDT)
• Tue Boesen
  • Re: How to handle large pdbs in namd? (Thu Mar 03 2022 - 19:15:52 CST)
  • Re: How to handle large pdbs in namd? (Thu Mar 03 2022 - 18:03:53 CST)
  • How to handle large pdbs in namd? (Thu Mar 03 2022 - 16:40:41 CST)
  • Re: FATAL ERROR: CudaTileListKernel::buildTileLists, (Tue Mar 01 2022 - 10:52:46 CST)
  • FATAL ERROR: CudaTileListKernel::buildTileLists, (Tue Mar 01 2022 - 01:14:10 CST)
• Vermaas, Josh
  • Re: NAMD3 failed to run longer than 4.2μs. (Fri Nov 11 2022 - 14:00:45 CST)
  • Postdoctoral positions at Michigan State (Fri Nov 04 2022 - 07:43:24 CDT)
  • Re: GPU requirements for CUDA enabled NAMD (Mon Oct 17 2022 - 09:48:08 CDT)
  • Re: No performance improvement with NAMD 3.0 alpha8 over namd 2.14 cuda (Fri Sep 09 2022 - 09:51:34 CDT)
  • Re: error while running simulation with NAMD3.0alpha12 and 13 (Tue Aug 30 2022 - 10:55:05 CDT)
  • Re: error while running simulation with NAMD3.0alpha12 and 13 (Tue Aug 30 2022 - 08:56:34 CDT)
  • Re: CUDA error cudaMalloc during running namd (Thu Aug 25 2022 - 11:13:54 CDT)
  • Re: Error (Thu Jul 14 2022 - 08:54:47 CDT)
  • Re: Error (Thu Jul 14 2022 - 08:39:39 CDT)
  • Re: Force and RMSD Values for TMD (Thu Jun 30 2022 - 16:05:10 CDT)
  • Re: Simulation running slow (1ns/day) (Tue Apr 26 2022 - 08:29:28 CDT)
  • Re: Simulation running slow (1ns/day) (Tue Apr 26 2022 - 08:23:59 CDT)
  • Re: /tmp/slurmd/job8440949/slurm_script: line 31: mpirun: command not found (Mon Feb 14 2022 - 08:55:00 CST)
  • Re: Multiple Jobs (Sun Feb 06 2022 - 10:52:58 CST)
  • Re: mail about Charmm++ (Sun Jan 30 2022 - 08:59:26 CST)
  • Re: Fwd: nvidia issue with namd12 Debian 11 (Mon Jan 17 2022 - 12:24:31 CST)
  • Re: Building NAMD3 (Thu Jan 06 2022 - 15:17:37 CST)
  • Re: Building NAMD3 (Thu Jan 06 2022 - 14:33:15 CST)
• Victor Hue
  • Inconsistent PMF profile of Ionized polymer (Fri Jan 14 2022 - 11:44:55 CST)
• Victor Kwan
  • Re: namd3-alpha13 on CentOS7 (Mon Aug 01 2022 - 14:01:10 CDT)
  • Re: ABF Non-Uniform Zcount (Tue Apr 26 2022 - 09:37:28 CDT)
  • Re: How to handle large pdbs in namd? (Fri Mar 04 2022 - 14:33:01 CST)
• Vidhya Sankar
  • mail about Charmm++ (Sat Jan 29 2022 - 11:00:25 CST)
• Yoshio Alarcon Lopez
  • Re: GPU requirements for CUDA enabled NAMD (Sat Oct 15 2022 - 11:49:50 CDT)
  • Re: CUDA error cudaMalloc during running namd (Sun Aug 28 2022 - 13:01:36 CDT)
• zeynab hosseini
  • Re: to rigidify bonds without hydrogen (about suggestion http://jeffcomer.us/downloads.html) (Mon Aug 29 2022 - 06:38:56 CDT)
  • to rigidify bonds without hydrogen (about suggestion http://jeffcomer.us/downloads.html) (Mon Aug 29 2022 - 05:59:11 CDT)
  • Creating a parameter file for SiC nanotube (Fri Aug 26 2022 - 11:46:36 CDT)
• Ä°mren Bayıl
  • How could I select a range of ATOMS by using VMD Program? (Fri Nov 04 2022 - 17:24:37 CDT)
  • how to continue namd md simulation (Fri Jul 22 2022 - 16:49:56 CDT)
  • charmm-gui namd inputs not working namd (Sun Jul 17 2022 - 16:23:47 CDT)
  • using amber force field in namd simulation (Wed Jun 29 2022 - 05:32:57 CDT)
  • minimization in water not running ! (Sat May 21 2022 - 09:38:44 CDT)
  • Namd with slurm getting error (Thu May 19 2022 - 10:11:02 CDT)
  • Namd with slurm getting error (Thu May 19 2022 - 06:27:38 CDT)
  • namd slurm error (Thu Feb 24 2022 - 16:48:23 CST)
  • /tmp/slurmd/job8440949/slurm_script: line 31: mpirun: command not found (Mon Feb 14 2022 - 08:27:35 CST)
  • namd slurm getting error (Mon Feb 14 2022 - 06:57:44 CST)
  • namd slurm getting error (Mon Feb 14 2022 - 06:38:32 CST)
  • Unable to open binary file md_equ_300.out.rst.vel (Mon Feb 07 2022 - 02:27:59 CST)
  • Unable to open binary file md_equ_300.out.rst.vel (Sat Feb 05 2022 - 04:09:31 CST)
  • Unable to open binary file md_equ_300.out.rst.vel (Fri Feb 04 2022 - 05:20:06 CST)
  • FATAL ERROR: Cannot specify both an initial temperature and a velocity file (Thu Feb 03 2022 - 18:27:28 CST)
• 王è�ªé¢–
  • How can I convert XPLOR-DCD file to plain CSV file (Fri Dec 02 2022 - 01:00:04 CST)
• ì�¼ë°˜ëŒ€í•™ì›� ìƒ�명과학부
  • question about namd3 performance (Fri Jul 22 2022 - 02:55:45 CDT)

Last message date: Tue Dec 13 2022 - 12:14:18 CST
Archived on: Tue Dec 13 2022 - 14:32:44 CST

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