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