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NAMD-L: By messages with attachments

By messages with attachments

4086 messages sorted by: [ author ] [ date ] [ thread ] [ subject ]
About this archive

Starting: Mon Jan 02 2012 - 00:44:43 CST
Ending: Tue Dec 31 2013 - 11:28:27 CST

• Re: MMPBSA-like analysis Kenno Vanommeslaeghe (Fri Oct 25 2013 - 15:05:05 CDT)
  1. psf_xplor2charmm (2075 bytes)
• AW: Coordinates of Carbon atoms on Graphite Norman Geist (Wed Sep 25 2013 - 09:16:24 CDT)
  1. graphite2.pdb (7976 bytes)
• Re: Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT Teerapong Pirojsirikul (Wed Sep 18 2013 - 12:20:24 CDT)
  1. toppar_water_ions.mod.str (6353 bytes)
• Re: Replica exchange and colvars - Missing Stage from restart Jérôme Hénin (Sun Sep 15 2013 - 15:41:54 CDT)
  1. fix_uninitialized_nstages.patch (1026 bytes)
• RE: VDW energy is negative but total energy is positive Bennion, Brian (Tue Sep 10 2013 - 10:57:23 CDT)
  1. ATT00001.txt (134 bytes)
• Re: namd scale-up Revthi Sanker (Fri Sep 06 2013 - 01:25:53 CDT)
  1. cpuinfo (14140 bytes)
• Re: NAMD with pbs script k.manzoorolajdad (Tue Sep 03 2013 - 02:22:54 CDT)
  1. 959.cluster.pprc.ir.err (2129 bytes)
  2. 959.cluster.pprc.ir.out (521 bytes)
  3. job.sh (1616 bytes)
  4. nodelist (253 bytes)
  5. out.log (135 bytes)
  6. script.pbs (142 bytes)
• how does NAMD calculate intramolecular electrostatic interactions between Drude pairs? Ana Celia Vila Verde (Thu Aug 29 2013 - 04:07:02 CDT)
  1. 002_dipNON0.zip (8386 bytes)
  2. 001_dip0.zip (10004 bytes)
• making patch rasti_at_ut.ac.ir (Tue Aug 27 2013 - 18:41:06 CDT)
  1. 2 (463 bytes)
• Problem of ATP mutated to dATP in solution using FEP method dbaogen (Mon Aug 05 2013 - 02:14:24 CDT)
  1. clip_image002.gif (3184 bytes)
• pressure profile calculation problem P.-L. Chau (Fri Jul 12 2013 - 10:47:05 CDT)
  1. enecalc.conf (3705 bytes)
  2. dcdanalysis2.conf (3799 bytes)
  3. dcdanalysis2.log (9999 bytes)
• local pressure profile for water liquid-vapor Mashayak, Sikandar Yusufoddin (Wed Jul 10 2013 - 10:43:21 CDT)
  1. namd_forcefield.inp (1560 bytes)
  2. namd_top.inp (983 bytes)
  3. run.conf (2998 bytes)
• FATAL ERROR Unknown parameter in charmm parameter file Cat Chenal (Mon Jul 01 2013 - 13:19:27 CDT)
  1. wb_mineq_v27.namd (2566 bytes)
• Fwd: Troubles to converge while running bidirectional FEP GALLY Jose Manuel (Thu Jun 27 2013 - 02:12:24 CDT)
  1. AspToAsp_dlambda.png (6126 bytes)
  2. AspToAsp_long.png (6121 bytes)
  3. AspToAsp_medium.png (5826 bytes)
  4. AspToAsp_short.png (5795 bytes)
• RE: AW: how to apply force SMD method on an anisotropic geometry Anurag Sharma (Thu Jun 13 2013 - 09:41:24 CDT)
  1. a.jpg (34976 bytes)
• NAMD related Anilkumar Naik (Mon Jun 10 2013 - 06:35:27 CDT)
  1. NAMD_make_config.txt (560 bytes)
  2. PPC-MX64-xlc64_arch.txt (196 bytes)
  3. NAMD_path.txt (617 bytes)
• Building crystal polymer Shaikh Abdul Rajjak (Fri May 17 2013 - 00:59:09 CDT)
  1. topPVDF.in (3003 bytes)
  2. parPVDF.inp (4029 bytes)
  3. pvdf_monomer.pdb (1023 bytes)
• Are coordinates in the tclForces module loaded as wrapped? Salvatore Mario Cosseddu (Tue Apr 16 2013 - 05:12:08 CDT)
  1. spherical_harm.tcl (5161 bytes)
• Re: NamdMemoryReduction - genCompressedPsf Sridhar Kumar Kannam (Thu Mar 21 2013 - 23:31:06 CDT)
  1. 199392.out (4891 bytes)
• My calcforces does not work properly after a unknown point of the simulation. Salvatore Mario Cosseddu (Wed Mar 13 2013 - 15:35:11 CDT)
  1. spherical_harm.tcl (5161 bytes)
• Constant volume energy minimization FX (Tue Feb 19 2013 - 16:06:53 CST)
  1. md.conf (1042 bytes)
• Re: [charm] Charm 6.5.0 compilation issue Ake Sandgren (Fri Jan 11 2013 - 12:21:43 CST)
  1. impi.patch (1158 bytes)
• reassigning temperatures Martin, Erik W (Thu Dec 20 2012 - 11:40:36 CST)
  1. temps.jpg (49762 bytes)
• Re: Alchemical transformations and DDG of point mutations Gianluca Interlandi (Thu Dec 13 2012 - 16:10:45 CST)
  1. vwf_dyn_10ns_fep_extr.jpg (100990 bytes)
• Colvars value is out of boundary DAI, JIAN (Mon Dec 10 2012 - 16:15:45 CST)
  1. md.1.conf (1458 bytes)
  2. colvars.tcl (690 bytes)
• pressure profile calculations upayan baul (Sat Nov 17 2012 - 04:55:59 CST)
  1. 15-20ns.conf (2892 bytes)
  2. 15-20ns-ewald.conf (1914 bytes)
• Errors compiling namd with CUDA Martin, Erik W (Tue Nov 13 2012 - 10:15:53 CST)
  1. cuda-errors.txt (18194 bytes)
• RE: A bug in replica.namd? Ada Zhan (Thu Nov 08 2012 - 13:32:39 CST)
  1. replica_mod.namd (5920 bytes)
• Re: unreasonably high temp/pressure Martin, Erik W (Wed Oct 24 2012 - 14:33:41 CDT)
  1. press.jpg (58942 bytes)
  2. pack.temp.conf (2630 bytes)
• Re: unreasonably high temp/pressure Martin, Erik W (Wed Oct 24 2012 - 10:34:57 CDT)
  1. tip4-run.test.conf (2737 bytes)
• [MetaD; namd 2.9] Pmf output file problem once the CV boundaries are reached, even using "expandBoundaries on" Salvatore Mario Cosseddu (Fri Sep 07 2012 - 07:49:36 CDT)
  1. temperedMetaDPMF.png (20435 bytes)
  2. colvar.traj.png (19329 bytes)
• Rückruf: scnb value to prevent VDWs scaling Norman Geist (Thu Sep 06 2012 - 08:10:22 CDT)
  1. winmail.dat (1177 bytes)
• NAMD 2.9 with CUDA runs Ashley Chew (Fri Aug 31 2012 - 04:02:48 CDT)
  1. image003.png (35649 bytes)
• Re: inputPrefix in ABF Branko (Thu Aug 16 2012 - 04:02:32 CDT)
  1. 24diiPrcolvsec (710 bytes)
• peculiar scaling on the GPU Ajasja LjubetiÄ� (Tue Jul 31 2012 - 09:06:50 CDT)
  1. 00001.log (15128 bytes)
• problem with NAMD surface area calculation (LCPO) -- fixed Clayton (Mon Jul 23 2012 - 10:08:35 CDT)
  1. formula.png (27770 bytes)
• testing digest demime - please ignore #2 Jim Phillips (Tue Jul 03 2012 - 19:59:09 CDT)
  1. foo (0 bytes)
• testing digest demime - please ignore Jim Phillips (Tue Jul 03 2012 - 17:50:18 CDT)
  1. foo (0 bytes)
• Re: Atoms moving too fast only with CUDA version. amin_at_imtech.res.in (Wed Jun 27 2012 - 01:34:28 CDT)
  1. equil_mod.conf (2113 bytes)
• Workshop for Computational Chemistry & Physics MARK PLUMMER (Wed Jun 20 2012 - 15:17:27 CDT)
  1. Advertising_Statement_for_2013_ACP_Workshop_final.docx (17252 bytes)
• Negative surface area? David Minh (Fri Jun 15 2012 - 09:08:12 CDT)
  1. NAMD_Test.tar.gz (29505 bytes)
• namd simulation:protein,ligand,lipid,water and ions Marlet Martinez (Wed Jun 13 2012 - 18:44:40 CDT)
  1. 02.log (8253 bytes)
• NAMD-INCONSISTENCY IN SCOR jose correa (Tue Jun 12 2012 - 17:23:00 CDT)
  1. 02.log (8253 bytes)
• Workshop - Computational Molecular Physics of Non-Bonded Bio-Molecular Interactions MARK PLUMMER (Mon Jun 11 2012 - 17:14:51 CDT)
  1. Advertising_Statement_for_2013_ACP_Workshop_final.docx (17224 bytes)
• RE: AW: compress PSF into INTER Cruz-Chu Eduardo Roberto (Thu Jun 07 2012 - 07:02:35 CDT)
  1. eg07PSF4.namd (4492 bytes)
  2. 03_memOptcompiled.log (5692 bytes)
  3. 02_compiled.log (3912 bytes)
  4. 01_download.log (3896 bytes)
• RE: compress PSF into INTER Cruz-Chu Eduardo Roberto (Thu Jun 07 2012 - 04:20:56 CDT)
  1. MinProtPSF.log (3991 bytes)
• compress PSF into INTER Cruz-Chu Eduardo Roberto (Wed Jun 06 2012 - 13:37:34 CDT)
  1. MinPSF.namd (4486 bytes)
• Re: Issues with 'Gyration' in Colvars module Shaon Chakrabarti (Sat Jun 02 2012 - 14:29:52 CDT)
  1. colvars_abf.conf (338 bytes)
  2. test.colvars.traj (709 bytes)
• Issues with 'Gyration' in Colvars module Jérôme Hénin (Fri May 25 2012 - 13:20:49 CDT)
  1. colvarcomp_distances.C (30863 bytes)
• Re: Issues with 'Gyration' in Colvars module Shaon Chakrabarti (Wed May 23 2012 - 17:11:13 CDT)
  1. molecule.colvars.traj (1147 bytes)
  2. colvars_abf.conf (293 bytes)
• stereo-chemical inversion during MD Gordon Wells (Mon May 07 2012 - 12:01:24 CDT)
  1. LGlu_autopsf.pdb (1472 bytes)
  2. LGlu_distorted.pdb (2923 bytes)
• Re: namd and x-plor Jernej Zidar (Sat Apr 14 2012 - 08:16:08 CDT)
  1. smime.p7s (2077 bytes)
• Re: PDB sugar unit residue name Massimiliano Porrini (Fri Mar 30 2012 - 07:06:15 CDT)
  1. AGLCNA.pdb (865 bytes)
  2. aglcna.pgn (755 bytes)
• Re: PDB sugar unit residue name Massimiliano Porrini (Thu Mar 29 2012 - 14:05:04 CDT)
  1. AGLCNA.pdb (865 bytes)
  2. aglcna.pgn (755 bytes)
• conf file question Molecular Dynamics (Wed Mar 21 2012 - 04:19:57 CDT)
  1. namd.conf (1421 bytes)
• Re: Compiling NAMD on NICS Kraken Jernej Zidar (Thu Mar 08 2012 - 23:42:09 CST)
  1. smime.p7s (2077 bytes)
• Re: R: restart file Namd Namd (Mon Feb 27 2012 - 02:42:32 CST)
  1. file.conf (1488 bytes)
• Re: Analysis of FEP output file Chris Chipot (Thu Feb 16 2012 - 07:35:12 CST)
  1. parseFEP.tcl (138547 bytes)
• Re: Trouble using rotateReference, centerRefrence and refPositionsGroup in the colvar module Giacomo Fiorin (Tue Feb 07 2012 - 16:57:33 CST)
  1. quaternion2rmatrix.tcl (1997 bytes)
• rigidBonds water option Hasan haska (Thu Feb 02 2012 - 01:48:22 CST)
  1. namd.conf (3175 bytes)
• Re: Harmonic Constrain like MMFP in CHARMM Vahid Mirjalili (Fri Jan 20 2012 - 19:41:28 CST)
  1. rmsd (380 bytes)
• target pressure value Namd Namd (Tue Jan 17 2012 - 06:32:45 CST)
  1. pressurefile.gif (20610 bytes)
• target pressure value Namd Namd (Tue Jan 17 2012 - 06:30:20 CST)
  1. pressure.jpeg (20610 bytes)
• Re: Controlling fans on a GTX 560 ti Axel Kohlmeyer (Mon Jan 16 2012 - 19:29:26 CST)
  1. gpu-fans.tar.gz (2050 bytes)
• Problem running NAMD 2.8 with ibverbs Moritz Schlarb (Fri Jan 06 2012 - 09:29:18 CST)
  1. alanin.log (1477 bytes)

Last message date: Tue Dec 31 2013 - 11:28:27 CST
Archived on: Tue Dec 31 2013 - 23:24:09 CST

4086 messages sorted by: [ author ] [ date ] [ thread ] [ subject ]
About this archive