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NAMD-L: By messages with attachments

By messages with attachments

2851 messages sorted by: [ author ] [ date ] [ thread ] [ subject ]
About this archive

Starting: Fri Jan 02 2004 - 12:06:46 CST
Ending: Wed Dec 28 2005 - 17:21:37 CST

• FATAL ERROR: unknown floating-point error, errno = 4 Manori Indira Jayasinghe (Thu Dec 22 2005 - 23:16:41 CST)
  1. md_zero.namd (3685 bytes)
• Re: define abf1 and abf2 for CM of water and CM of molecule Manori Indira Jayasinghe (Wed Dec 21 2005 - 11:26:37 CST)
  1. md_zero.namd (3680 bytes)
• Errors: Periodic cell became too small for original patch grid & Setting parameter binaryoutput from script failed! Nitin Bhardwaj (Sun Nov 13 2005 - 12:26:35 CST)
  1. popc_s.conf (1703 bytes)
• Re: ABF Simulation Jérôme Hénin (Fri Oct 28 2005 - 04:05:52 CDT)
  1. vectors.tcl (10343 bytes)
• scaling issue Robert Bjornson (Fri Oct 21 2005 - 15:56:13 CDT)
  1. prod2.namd (2773 bytes)
  2. apoa1.namd (851 bytes)
• Re: namdplot: command not found Robert Brunner (Thu Oct 13 2005 - 15:11:37 CDT)
  1. smime.p7s (2363 bytes)
  2. PGP.sig (187 bytes)
• Re: namdplot: command not found bo baker (Tue Oct 11 2005 - 18:56:10 CDT)
  1. namdplot (3535 bytes)
• Re: namdplot: command not found Robert Brunner (Tue Oct 11 2005 - 10:32:00 CDT)
  1. smime.p7s (2363 bytes)
  2. PGP.sig (187 bytes)
• RE: autoionize & namd2 Michel Espinoza-Fonseca (Thu Sep 22 2005 - 02:51:08 CDT)
  1. test.in (1882 bytes)
• problem when heating the system Phoenix (Mon Aug 29 2005 - 23:07:42 CDT)
  1. heat.cfg (1198 bytes)
• ERROR: Margin is too small (BUG?) Mauricio Carrillo Tripp (Wed Aug 03 2005 - 10:02:42 CDT)
  1. mini-heat.namd (2288 bytes)
• Re: Report on a trajectory incompatibility between NAMD and CHARMM: Unfolding and RDFs NAVEEN P MICHAUD AGRAWAL (Fri Jul 29 2005 - 23:30:23 CDT)
  1. dcdcellfix.tar (102400 bytes)
• Velocity after heating mustapha.hamdi_at_ensi-bourges.fr (Mon Jul 18 2005 - 06:56:03 CDT)
  1. position_restrained.log (13533 bytes)
• Re: Runnig same config file many times Mauricio Carrillo Tripp (Fri Jul 15 2005 - 17:33:48 CDT)
  1. namd.csh (513 bytes)
• RE: Adding Misc. Potentials (e.g. spherical/repulsive restraints/constraints ) JC Gumbart (Wed Jun 29 2005 - 11:18:23 CDT)
  1. keep_water_out.tcl (7635 bytes)
• Re: catdcd and dcdunitcell Jérôme Hénin (Tue Jun 28 2005 - 09:14:32 CDT)
  1. catdcd.gz (12558 bytes)
• autoimd on windows Anna Modzelewska (Mon Jun 20 2005 - 06:40:29 CDT)
  1. autoimd.log (2741 bytes)
• How to conservate energy during NVE simulations??? Leonardo Sepulveda Durán (Wed Jun 15 2005 - 20:55:29 CDT)
  1. equil_data1_TempPresTotEn.pdf (48858 bytes)
• Re: Multiple Harmonic Constraints Sascha Tayefeh (Thu Jun 09 2005 - 08:28:52 CDT)
  1. sascha.vcf (372 bytes)
• Multiple Harmonic Constraints Sascha Tayefeh (Thu Jun 09 2005 - 02:31:38 CDT)
  1. sascha.vcf (372 bytes)
• config files Mark A. Hallman (Tue Jun 07 2005 - 12:17:35 CDT)
  1. minimize.namd (882 bytes)
• Re: NADP problem Hemant Kushwaha (Fri Jun 03 2005 - 22:07:08 CDT)
  1. nadp.top (11769 bytes)
• Re: NADP problem Hemant Kushwaha (Fri Jun 03 2005 - 08:28:56 CDT)
  1. nadp.top (11768 bytes)
• about *.psf ËïæÃæà(Thu May 26 2005 - 23:59:07 CDT)
  1. lig1.gif (3592 bytes)
• Re: Re: Simulated Annealing Config Leonardo Sepulveda Durán (Tue May 24 2005 - 14:55:49 CDT)
  1. ubq.conf (3346 bytes)
• What's wrong with my namd2 Xiaoqing Wang (Sun May 15 2005 - 07:01:13 CDT)
  1. 8 (959438 bytes)
• Re: Leandro Martínez (Fri Apr 08 2005 - 13:50:34 CDT)
  1. atomnames.f (3102 bytes)
• Re: NMAD job abnormally killed with PBS Chris Samuel (Wed Apr 06 2005 - 22:32:01 CDT)
  1. part (190 bytes)
• Re: FATAL ERROR: Stale NFS file handle Chris Samuel (Wed Apr 06 2005 - 22:29:59 CDT)
  1. part (190 bytes)
• RATTLE and DNA Nicholas M Glykos (Tue Apr 05 2005 - 05:33:48 CDT)
  1. heat.namd (3877 bytes)
  2. equi.namd (2125 bytes)
• Re: problem running namd Chris Samuel (Mon Apr 04 2005 - 18:10:58 CDT)
  1. part (190 bytes)
• Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC Chris Samuel (Wed Mar 30 2005 - 00:05:44 CST)
  1. part (190 bytes)
• Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC Chris Samuel (Sun Mar 20 2005 - 20:04:50 CST)
  1. part (190 bytes)
• Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC Chris Samuel (Thu Mar 17 2005 - 23:23:24 CST)
  1. part (190 bytes)
• Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC Chris Samuel (Wed Mar 16 2005 - 00:06:21 CST)
  1. part (190 bytes)
• Re: G5 clusters Gengbin Zheng (Tue Mar 08 2005 - 12:44:25 CST)
  1. apoa1_bench.png (12517 bytes)
• Re: segmentation violation!! Robert Brunner (Tue Jan 18 2005 - 11:05:00 CST)
  1. PGP.sig (187 bytes)
• multiple jobs on a cluster Cheri M Turman (Wed Jan 12 2005 - 15:55:42 CST)
  1. cturman.vcf (336 bytes)
• about MCTI output mashaojie163 (Mon Dec 27 2004 - 01:29:36 CST)
  1. clip_image002.gif (168 bytes)
  2. clip_image002.gif (315 bytes)
  3. clip_image002.gif (168 bytes)
  4. clip_image002.gif (147 bytes)
• FATAL ERROR: Asymmetric water molecule ? Gaurav Sharma (Tue Dec 21 2004 - 14:58:11 CST)
  1. output.log (3898 bytes)
• Re: How I can run two simulations one after an other Michael Grabe (Tue Dec 14 2004 - 15:15:36 CST)
  1. md_script (841 bytes)
  2. fep_script (665 bytes)
• Re: Variation of results in iterations Robert Brunner (Mon Dec 06 2004 - 21:15:00 CST)
  1. PGP.sig (187 bytes)
• Re: NAMD on Xeon EM64T Chris Samuel (Thu Dec 02 2004 - 22:18:39 CST)
  1. part (190 bytes)
• Re: NAMD Source Robert Brunner (Fri Nov 19 2004 - 10:54:16 CST)
  1. PGP.sig (187 bytes)
• Rif: Re: Rif: Re: Rif: Re: Rif: Re: linux cluster trouble max (Fri Nov 19 2004 - 03:47:01 CST)
  1. IMSTP.gif (494 bytes)
  2. namd.out (27427 bytes)
• linux cluster trouble max (Tue Nov 16 2004 - 04:44:36 CST)
  1. IMSTP.gif (494 bytes)
• Rif: Re: linux cluster trouble max (Wed Nov 10 2004 - 03:00:42 CST)
  1. IMSTP.gif (494 bytes)
• Re: Sample Configuratiion files Cheri M Turman (Wed Nov 03 2004 - 19:47:25 CST)
  1. cturman.vcf (336 bytes)
• Re: System minimization: fail after 199 steps Charles Danko (Wed Nov 03 2004 - 11:53:06 CST)
  1. minimize.namd (2698 bytes)
• Tcl dihedral restraints in CG minimisation Ben Roberts (Tue Nov 02 2004 - 17:01:28 CST)
  1. restraints.tcl (13840 bytes)
• Re: [Periodic Boundary]: from charmm to namd Sascha Tayefeh (Tue Nov 02 2004 - 12:46:02 CST)
  1. sascha.vcf (397 bytes)
• [Periodic Boundary]: from charmm to namd Sascha Tayefeh (Tue Nov 02 2004 - 09:08:42 CST)
  1. sascha.vcf (397 bytes)
• HEM residue in NAMD Peter Bazeley (Tue Nov 02 2004 - 02:23:50 CST)
  1. 2D6H_fixed_heme_bak.pdb (6068 bytes)
• FK506 ligand topology file(1FKF) MERIC AYSE OVACIK (Thu Oct 28 2004 - 05:29:21 CDT)
  1. part (824 bytes)
• Re: Compilation on an Opteron Server SuSE Linux Enterprise System Version 8 Chris Samuel (Wed Oct 20 2004 - 18:05:49 CDT)
  1. part (190 bytes)
• Re: NAMD on Linux cluster with Myrinet Chris Samuel (Mon Oct 18 2004 - 23:02:27 CDT)
  1. part (190 bytes)
• bug report and stray pme Cheri M Turman (Mon Oct 18 2004 - 16:23:42 CDT)
  1. cturman.vcf (336 bytes)
• [Fwd: counterion software] Cetin Baloglu (Sun Oct 10 2004 - 23:55:20 CDT)
  1. cetinb.vcf (342 bytes)
• counterion software Cetin Baloglu (Sun Oct 10 2004 - 23:51:56 CDT)
  1. cetinb.vcf (342 bytes)
• Fw: Constraint failure in RATTLE algorithm Zhong Wenyu (Sun Sep 19 2004 - 02:14:27 CDT)
  1. open4.namd (2190 bytes)
  2. open4.log (19290 bytes)
• Re: Compilation on Opteron Chris Samuel (Thu Aug 26 2004 - 00:04:07 CDT)
  1. part (190 bytes)
• RE: radial distribution function Liu, Zhanwu (Fri Aug 13 2004 - 08:40:51 CDT)
  1. RDF.tcl (10381 bytes)
• Re: Need to add Hydrogens to over 300 distinct PDB's Edward Patrick Obrien (Wed Aug 11 2004 - 13:05:33 CDT)
  1. Add_Atoms_to_PDBs.pl (3307 bytes)
• HYP files Ivan Vinogradov (Tue Aug 03 2004 - 12:55:52 CDT)
  1. top_hyp.inp (2006 bytes)
  2. par_hyp.inp (351 bytes)
• charm++ MPICH and Myrinet Mauricio Carrillo Tripp (Mon Jul 26 2004 - 17:34:53 CDT)
  1. 01.log (11715 bytes)
• Warning: Not all atoms have unique coordinates. Shirley Hui (Thu Jul 08 2004 - 09:25:13 CDT)
  1. cpc.conf (2926 bytes)
• Re: icc compilation problem Chris Samuel (Sun Jul 04 2004 - 20:41:14 CDT)
  1. part (190 bytes)
• Re: icc compilation problem Chris Samuel (Thu Jul 01 2004 - 18:11:57 CDT)
  1. part (190 bytes)
• pmf error mashaojie163 (Mon Jun 21 2004 - 10:17:20 CDT)
  1. pmf.conf (2407 bytes)
  2. run.log (700 bytes)
• Simulated Annealing Config Ahmet Bakan (Tue Jun 15 2004 - 08:24:59 CDT)
  1. SA.JPG (42098 bytes)
  2. namd.run (909 bytes)
• Re: Force Calculation in NAMD Gadi Oron (Sun May 23 2004 - 02:37:27 CDT)
  1. 8859-8 (2126 bytes)
• Why Vmd didn't show the Pt-Cl bond myang (Wed May 19 2004 - 18:46:31 CDT)
  1. K2PtCl6_less.pdb (1865 bytes)
• autoionize script amodzelewska_at_dns.iimcb.gov.pl (Sun May 16 2004 - 13:21:58 CDT)
  1. ions.top (1176 bytes)
• installing on beowulf cluster Cheri M Turman (Sun May 09 2004 - 19:58:25 CDT)
  1. cturman.vcf (336 bytes)
• installing on beowulf cluster Cheri M Turman (Thu May 06 2004 - 13:38:16 CDT)
  1. cturman.vcf (336 bytes)
• Re: ,log and .out files with namd running on mac os x (panther) Arieana Moore (Wed May 05 2004 - 17:30:28 CDT)
  1. cnt_mod3.out (5817 bytes)
  2. cnt_mod3.conf (2999 bytes)
• RE: Binding free energy of a protein complex Ahmet Bakan (Mon May 03 2004 - 06:02:29 CDT)
  1. hbond.tcl (3461 bytes)
• problems with namdplot fixed by using new plotting program Cheri M Turman (Tue Apr 27 2004 - 16:34:42 CDT)
  1. cturman.vcf (336 bytes)
• temperature question in logfile Cheri M Turman (Tue Apr 20 2004 - 17:13:28 CDT)
  1. cturman.vcf (336 bytes)
• Re: still problems with namdplot Gadi Oron (Sun Apr 18 2004 - 01:51:42 CDT)
  1. 8859-8 (3707 bytes)
  2. 8859-8 (3688 bytes)
• still problems with namdplot Cheri M Turman (Thu Apr 15 2004 - 14:13:57 CDT)
  1. cturman.vcf (336 bytes)
• Re: More NAMD/gm2 problems Chris Samuel (Wed Mar 31 2004 - 00:40:36 CST)
  1. charmc.patch (349 bytes)
  2. mpicc.h (200 bytes)
  3. mpicc.sh (538 bytes)
• A tool to set up alchemical FEP transformations Jérôme Hénin (Mon Mar 29 2004 - 10:27:12 CST)
  1. alchemify.tar.gz (20572 bytes)
• Re: CP3-NH3 error Tim Isgro (Thu Mar 04 2004 - 13:56:44 CST)
  1. HERGpsfgen.txt (508 bytes)
• Re: Minimization with CHARMM Tim Isgro (Mon Feb 09 2004 - 17:04:13 CST)
  1. sample.conf (4331 bytes)
• RE: minimization problem - "Bad global exclusion count,possible error!" Frances Leung (Fri Jan 30 2004 - 02:52:09 CST)
  1. psfgen_log.txt (52161 bytes)
• minimization problem - "Bad global exclusion count, possible error!" Frances Leung (Thu Jan 29 2004 - 19:25:27 CST)
  1. minimize_log.txt (15543 bytes)
• Parameters and topologies for aa at different protonation states Bartosz Dobrzelecki (Fri Jan 23 2004 - 06:45:26 CST)
  1. signature.asc (190 bytes)
• missing atoms warnings for psfgen Frances Leung (Mon Jan 19 2004 - 21:47:33 CST)
  1. psflog.txt (142065 bytes)
• Potential Terms AHMET BAKAN (Mon Jan 05 2004 - 12:20:02 CST)
  1. 2_Theory.fm.anc.gif (13045 bytes)
• alchemical free energy perturbation AMIT PALIWAL (Mon Jan 05 2004 - 00:37:05 CST)
  1. growth.namd (1866 bytes)
  2. system.fep (450 bytes)

Last message date: Wed Dec 28 2005 - 17:21:37 CST
Archived on: Wed Feb 29 2012 - 15:40:16 CST

2851 messages sorted by: [ author ] [ date ] [ thread ] [ subject ]
About this archive