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NAMD-L: By messages with attachments

By messages with attachments

3750 messages sorted by: [ author ] [ date ] [ thread ] [ subject ]
About this archive

Starting: Thu Jan 03 2013 - 06:24:44 CST
Ending: Tue Dec 30 2014 - 07:38:36 CST

• Re: Colvar: minimal distance between 2 groups of atoms Ajasja Ljubetič (Mon Nov 17 2014 - 11:30:45 CST)
  1. part (9260 bytes)
  2. part (29688 bytes)
• Re: Colvar: minimal distance between 2 groups of atoms Ajasja Ljubetič (Mon Nov 17 2014 - 10:28:20 CST)
  1. image.png (9260 bytes)
  2. image.png (29688 bytes)
• Re: vmd-l: making psf files Zeinab Emami (Mon Oct 13 2014 - 04:55:06 CDT)
  1. Ethane_e.pdb (1722 bytes)
• 2-residue patch for Asn-Lys side chain amide bond Kenno Vanommeslaeghe (Fri Jul 25 2014 - 12:20:46 CDT)
  1. dkam.str (1845 bytes)
• 2-residue patch for hydrocarbon staple Kenno Vanommeslaeghe (Thu Jul 24 2014 - 15:48:52 CDT)
  1. k2hc7staple.str (5414 bytes)
• Loading and analysis of DCD file (~300 MB) Stephan Grein (Thu Jul 24 2014 - 06:18:45 CDT)
  1. low_wrappers.tcl (5423 bytes)
• AW: Should PME be used for electrostatic interaction energy calculations? Norman Geist (Thu Jun 19 2014 - 02:46:48 CDT)
  1. ng_n07_cutoff9_noPME.dcd.png (13760 bytes)
  2. ng_n07_cutoff9_withPME.dcd.png (9137 bytes)
• Constraint failure in RATTLE algorithm Douglas Houston (Wed Jun 18 2014 - 12:29:48 CDT)
  1. mdrun.conf (3559 bytes)
• Re: About electrostatic treatment Mo Chen (Fri May 30 2014 - 19:39:31 CDT)
  1. gromacs.jpg (19641 bytes)
• Re: FixedAtoms and Reference group in spinangle colvar nicolas martin (Thu May 22 2014 - 07:06:08 CDT)
  1. spin-dihe-EB.png (102797 bytes)
• Re: Teflon New Residue Kenno Vanommeslaeghe (Fri May 02 2014 - 12:21:09 CDT)
  1. perfluorohexane.mol2 (1108 bytes)
  2. perfluorohexane_cgenff.str (4109 bytes)
  3. perfluorohexane_adjust_ch.str (3828 bytes)
• Re: Help to solve the error Flora Chettiar (Thu Mar 27 2014 - 01:47:09 CDT)
  1. config_file_of_vmd_namd.txt (2958 bytes)
• Require Suggestion amit banerjee (Tue Feb 18 2014 - 23:39:40 CST)
  1. Consensus_ws_eq.log (5707 bytes)
  2. Consensus_ws_eq.conf (2583 bytes)
• Re: AW: Dihedrals multiplicity! Anna Borlsky (Sat Feb 15 2014 - 04:34:49 CST)
  1. cou.par (9196 bytes)
  2. cou.top (7604 bytes)
• unsubscribe Zailo Leite (Fri Feb 14 2014 - 11:20:04 CST)
  1. 0x202F0355.asc (1736 bytes)
• Re: ABF simulations Aron Broom (Mon Feb 10 2014 - 11:20:54 CST)
  1. jpg.counts.abf_low.jpeg (18203 bytes)
  2. jpg.pmfs_low.jpeg (22856 bytes)
• Re: AW: Re: Various questions Douglas Houston (Tue Feb 04 2014 - 07:26:05 CST)
  1. GetNAMDdims.ksh (1213 bytes)
• 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)

Last message date: Tue Dec 30 2014 - 07:38:36 CST
Archived on: Wed Dec 31 2014 - 23:23:11 CST

3750 messages sorted by: [ author ] [ date ] [ thread ] [ subject ]
About this archive