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NAMD-L: By messages with attachments

By messages with attachments

2588 messages sorted by: [ author ] [ date ] [ thread ] [ subject ]
About this archive

Starting: Sat Jan 02 2016 - 22:55:30 CST
Ending: Sat Dec 30 2017 - 12:48:03 CST

• Re: Script for Terachem QMMM Haohao Fu (Thu Dec 14 2017 - 07:13:47 CST)
  1. namd_xtb.py (7810 bytes)
• Free MD simulation (Production run) Roshan Shrestha (Fri Sep 08 2017 - 02:32:50 CDT)
  1. sim_free.namd (2202 bytes)
• No minimized system after running minimization in NAMD Roshan Shrestha (Thu Sep 07 2017 - 09:17:02 CDT)
  1. minimization.conf (2176 bytes)
• Production run after equilibration Roshan Shrestha (Tue Aug 29 2017 - 05:38:00 CDT)
  1. equil.conf (2968 bytes)
• Re: make psf error for ligand Natasha Gupta (Fri Aug 25 2017 - 05:37:38 CDT)
  1. rscb.pdb (3397 bytes)
  2. mkpsf.log (17478 bytes)
  3. mkpsf1.tcl (1509 bytes)
• Re: Creating psf file for ligand Roshan Shrestha (Thu Aug 24 2017 - 12:58:07 CDT)
  1. ZINC05.mol2 (7086 bytes)
  2. ZNC05.pdb (4428 bytes)
• Re: Creating psf file for ligand Roshan Shrestha (Sat Aug 12 2017 - 09:38:59 CDT)
  1. 8093.mol2 (6453 bytes)
  2. convert_out.pdb (8219 bytes)
• Re: veldcdfile command Jérôme Hénin (Thu Jun 29 2017 - 07:11:45 CDT)
  1. veldcdfile.patch (1747 bytes)
• Re: veldcdfile command Giacomo Fiorin (Wed Jun 28 2017 - 13:36:43 CDT)
  1. veldcdfile.patch (1521 bytes)
• Re: veldcdfile command Jérôme Hénin (Wed Jun 28 2017 - 11:41:21 CDT)
  1. veldcdfile.patch (2328 bytes)
• Re: veldcdfile command Jérôme Hénin (Wed Jun 28 2017 - 11:05:58 CDT)
  1. veldcdfile.patch (1524 bytes)
• Re: coarse-grained simulations with errors "Atoms moving too fast" and "low global exclusion" Yaxin An (Fri Jun 09 2017 - 10:38:33 CDT)
  1. image.png (3514 bytes)
  2. image.png (3444 bytes)
  3. image.png (275 bytes)
  4. image.png (117 bytes)
• Keeping potassium ions out of an area during equilibration Charles Hoying (Mon Jun 05 2017 - 22:57:40 CDT)
  1. keep_water_out.tcl (8617 bytes)
• Re: namd 2.12 and plumed 2.3 Vermaas, Joshua (Tue May 02 2017 - 10:22:01 CDT)
  1. combineddiff.txt (9994 bytes)
• compilation of NAMD 2.12 fails Vlad Cojocaru (Thu Apr 27 2017 - 10:02:19 CDT)
  1. 6.7.1_openmpi-2.1.0_gnu-4.8.5.log (67172 bytes)
• psfgen giving wrong structure in the autopdb file Harish Srinivasan (Thu Apr 06 2017 - 01:37:29 CDT)
  1. dodecylsulphate.rtf (2285 bytes)
  2. dodecylsulphate2.pdb (7440 bytes)
  3. dodecylsulphate2_autopsf.psf (9768 bytes)
  4. dodecylsulphate2_autopsf.pdb (3368 bytes)
• patch hem_chandra_at_iitg.ernet.in (Mon Mar 27 2017 - 23:28:53 CDT)
  1. boc.str (3914 bytes)
  2. wwl.pdb (2666 bytes)
• Problem in NAMD QMMM Kshatresh Dutta Dubey (Sat Mar 25 2017 - 13:37:25 CDT)
  1. out.log (10344 bytes)
  2. config.ORCA.namd (5398 bytes)
• Re: AW: Scaling behaviour of NAMD on hosts with GPU accelrators Maxime Boissonneault (Fri Mar 24 2017 - 06:42:04 CDT)
  1. benchmark_scaling_namd20150917_k80.csv (1174 bytes)
• Re: problems mutating HID to TYR for free energy calculations Nehad Elsalamouny (Tue Mar 07 2017 - 16:50:32 CST)
  1. h2y.rtf (8720 bytes)
  2. ATT00001.htm (6395 bytes)
• problems mutating HID to TYR for free energy calculations Nehad Elsalamouny (Tue Mar 07 2017 - 04:27:28 CST)
  1. xxxx.pdb (1554 bytes)
  2. ATT00001.htm (215 bytes)
  3. h2y.pdb (2880 bytes)
  4. ATT00002.htm (516 bytes)
• AW: vmd-l: Building NAMD 2.12 from Source with IB and CUDA Greipel.Joachim_at_mh-hannover.de (Thu Mar 02 2017 - 05:53:58 CST)
  1. smime.p7s (5980 bytes)
• Regarding Error on HB2 Obayed Ullah (Mon Feb 20 2017 - 18:48:56 CST)
  1. trif_ionized_min_dynamic.conf (1892 bytes)
• Re: Npt lipid simulation with electrostatics 2 Life Sciences Inc (Fri Feb 17 2017 - 11:04:12 CST)
  1. volume.jpg (27833 bytes)
• Re: Npt lipid simulation with electrostatics 2 Life Sciences Inc (Fri Feb 17 2017 - 10:52:36 CST)
  1. volume.jpg (27833 bytes)
• Compiling charm/NAMD with an alternative gcc, e.g. gcc 6.x Greipel.Joachim_at_mh-hannover.de (Mon Feb 06 2017 - 08:54:08 CST)
  1. smime.p7s (5980 bytes)
• Solvation free energy difference of alchemical transformation of K+ into Na+ Abhishek Kumar Singh (Tue Jan 10 2017 - 05:09:01 CST)
  1. derivate_vs___values (255 bytes)
• dcd to pdb conversion Srijita Paul (Wed Jan 04 2017 - 06:18:21 CST)
  1. dcdtopdb.tcl (271 bytes)
• NAMD_2.12b1 build on Cray XC40 is failing Ianni, James C CTR USARMY RDECOM ARL (US) (Mon Dec 12 2016 - 14:35:32 CST)
  1. smime.p7s (5430 bytes)
• Minimization error Santanu Santra (Tue Dec 06 2016 - 23:00:04 CST)
  1. xxxxx.conf (1953 bytes)
• How to create 3'-3' phosphodiester linkage for a DNA. Susmita Ghosh (Mon Nov 28 2016 - 23:50:26 CST)
  1. image.png (20003 bytes)
• Re: A common tool to read the output of NAMD run Ajasja Ljubetič (Mon Nov 28 2016 - 08:34:47 CST)
  1. to-ener.py (1242 bytes)
• REMD kaushik chakraborty (Wed Nov 23 2016 - 13:58:51 CST)
  1. ubq_ww_pcv1.conf (1135 bytes)
  2. replica.conf (593 bytes)
• Re: Generate psf file in x-plor format Nehad Elsalamouny (Thu Nov 17 2016 - 14:44:40 CST)
  1. xxxx.psf (24093 bytes)
  2. ATT00001.htm (2591 bytes)
• RE: visualizing and analyzing long simulation Deng, Jinxia (Nancy) (Mon Oct 10 2016 - 10:51:42 CDT)
  1. image001.png (25350 bytes)
• Re: question regarding rmsd Leandro Martínez (Wed Oct 05 2016 - 15:58:39 CDT)
  1. rmsd.png (13568 bytes)
• RE: question regarding rmsd Radak, Brian K (Wed Oct 05 2016 - 15:39:01 CDT)
  1. rmsd.png (13568 bytes)
• Re: question regarding rmsd Dhiraj Srivastava (Wed Oct 05 2016 - 14:02:32 CDT)
  1. rmsd.png (13568 bytes)
• Re: question regarding rmsd Pardis Tabaee (Wed Oct 05 2016 - 13:34:41 CDT)
  1. rmsd.png (13568 bytes)
• RE: question regarding rmsd Radak, Brian K (Wed Oct 05 2016 - 11:18:12 CDT)
  1. rmsd.png (13568 bytes)
• Re: question regarding rmsd Roshan Shrestha (Wed Oct 05 2016 - 11:07:09 CDT)
  1. rmsd.png (13568 bytes)
• Re: question regarding rmsd Pardis Tabaee (Wed Oct 05 2016 - 10:55:01 CDT)
  1. rmsd.png (13568 bytes)
• question regarding rmsd Dhiraj Srivastava (Tue Oct 04 2016 - 16:07:43 CDT)
  1. rmsd.png (13568 bytes)
• convert .xyz file in .psf file for non-protein molecule grenier_at_cinam.univ-mrs.fr (Thu Sep 08 2016 - 10:20:03 CDT)
  1. azacalix.xyz (3360 bytes)
• PMF Calculation Crystal Liu (Fri Aug 12 2016 - 19:15:46 CDT)
  1. 08-12_at_2.14.31_PM.png (7861 bytes)
  2. 08-12_at_3.37.50_PM.png (27699 bytes)
• namd2 seg fault NAMD_2.11_Source Linux-x86_64-g++ Doug Stetner (Tue Jul 12 2016 - 22:51:40 CDT)
  1. signature.asc (843 bytes)
• Regarding radial distribution function graph siddharth kamal (Thu Jun 16 2016 - 08:31:23 CDT)
  1. O.eps (21785 bytes)
• Colvars: Unable to restrict rotation and translation along y and z axes Sourav Ray (Wed May 18 2016 - 07:22:00 CDT)
  1. ref.pdb (57587 bytes)
• ffTK fitting dihedrals Seth Axen (Tue May 17 2016 - 01:36:02 CDT)
  1. multiplot.png (25517 bytes)
• Re: Srijita Paul (Tue May 10 2016 - 08:41:10 CDT)
  1. nvt.namd (2960 bytes)
  2. npt_eq.namd (3306 bytes)
• (no subject) Srijita Paul (Sat Apr 16 2016 - 00:06:47 CDT)
  1. top_urea.rtf (889 bytes)
• Re: AW: problem with +devices using nikolaev_at_spbau.ru (Tue Apr 05 2016 - 07:41:17 CDT)
  1. CPUINFO (46690 bytes)
• Re: Running multi-node jobs on Sun Grid Engine Sourav Ray (Tue Apr 05 2016 - 00:19:23 CDT)
  1. Sun_Grid_Engine.sh (470 bytes)
• Running multi-node jobs on Sun Grid Engine Sourav Ray (Sun Apr 03 2016 - 10:49:30 CDT)
  1. _single_node.sh (469 bytes)
  2. PBS.sh (1324 bytes)
  3. Other.sh (840 bytes)
• Occasional performance slow down using NAMD with Xeon Phi Mattia Felice Palermo (Fri Apr 01 2016 - 09:53:37 CDT)
  1. avg_load.pdf (6988 bytes)
  2. max_load.pdf (7584 bytes)
• NAMD 2.11 CUDA freezes on windows 8 Ajasja Ljubetič (Wed Mar 16 2016 - 13:08:59 CDT)
  1. COMPUTER-A-NAMD.2.10-CUDA-WORKS.txt (11196 bytes)
  2. COMPUTER-A-NAMD.2.11-WORKS.txt (9424 bytes)
  3. COMPUTER-A-NAMD.2.11-CUDA-NOT_WORKING.txt (10608 bytes)
• WG: vmd-l: NAMD 2.11 Cuda does not work with Quadro FX 3800 Greipel.Joachim_at_mh-hannover.de (Mon Mar 14 2016 - 04:47:28 CDT)
  1. smime.p7s (5649 bytes)
• Fwd: ISQBP 2016 meeting - registration opened! Vlad Cojocaru (Mon Mar 14 2016 - 03:13:10 CDT)
  1. Attached_Message_Part (135 bytes)
• AW: vmd-l: NAMD 2.11 Cuda does not work with Quadro FX 3800 Greipel.Joachim_at_mh-hannover.de (Fri Mar 11 2016 - 01:47:27 CST)
  1. smime.p7s (5649 bytes)
• Energy gradient in colvars.state file Carlo Guardiani (Mon Feb 29 2016 - 13:09:31 CST)
  1. Energy_Gradients.agr (17708 bytes)
• Re: Replica Exchange US, Colvar suggestion Abhishek TYAGI (Sat Feb 13 2016 - 22:39:29 CST)
  1. _amp__X1f610.png (459 bytes)
• Replica Exchange US, Colvar suggestion Abhishek TYAGI (Sat Feb 13 2016 - 01:07:38 CST)
  1. 1.conf (16132 bytes)
  2. colvars.conf (309 bytes)
• bond energy high Ipsita Basu (Wed Feb 03 2016 - 05:15:35 CST)
  1. file (4177 bytes)
• RE: [Non-DoD Source] AW: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) Downs, Andrew S CTR USARMY ARL (US) (Tue Jan 12 2016 - 14:04:36 CST)
  1. winmail.dat (8793 bytes)
• RE: [Non-DoD Source] AW: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) Downs, Andrew S CTR USARMY ARL (US) (Tue Jan 12 2016 - 09:44:54 CST)
  1. winmail.dat (8009 bytes)
• RE: [Non-DoD Source] AW: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) Downs, Andrew S CTR USARMY ARL (US) (Tue Jan 12 2016 - 07:27:59 CST)
  1. winmail.dat (7333 bytes)
• Re: Regarding system forces in NAMD sruthi c k (Fri Jan 08 2016 - 06:14:08 CST)
  1. Histogram.eps (20972 bytes)
  2. Av_system_force.eps (21181 bytes)
• Fwd: Regarding system forces in NAMD sruthi c k (Fri Jan 08 2016 - 03:38:26 CST)
  1. Histogram.eps (20972 bytes)
  2. Av_system_force.eps (21181 bytes)

Last message date: Sat Dec 30 2017 - 12:48:03 CST
Archived on: Sun Dec 31 2017 - 23:21:55 CST

2588 messages sorted by: [ author ] [ date ] [ thread ] [ subject ]
About this archive