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NAMD-L: By messages with attachments

By messages with attachments

3455 messages sorted by: [ author ] [ date ] [ thread ] [ subject ]
About this archive

Starting: Sat Jan 01 2005 - 14:57:24 CST
Ending: Fri Dec 29 2006 - 23:10:16 CST

• Simulating the orientation of detergent and lipid molecules around a membrane protein, bacteriorhodopsin Nathan H. Cho (Wed Dec 20 2006 - 20:59:20 CST)
  1. CHAPSO_H.pdb (8304 bytes)
• Is it equilibrated? taojinwuhan_at_sohu.com (Mon Dec 04 2006 - 01:45:49 CST)
  1. _____Microsoft_Word_____.doc (41472 bytes)
• error message in free energy pert. OMAR NABEEL ALY DEMERDASH (Sun Nov 26 2006 - 23:36:23 CST)
  1. 2eck_chrmv157_fep.conf (3179 bytes)
• LINE=*CMAP* regafan_at_usc.es (Wed Nov 22 2006 - 08:32:24 CST)
  1. min.log.gz (1221 bytes)
• ABF (fwd) Matthew Davies (Tue Nov 14 2006 - 07:40:30 CST)
  1. MHC_10_20.dat (2460 bytes)
  2. MHC_15_20.dat (1260 bytes)
• equilibration of protein Dhiraj Srivastava (Wed Nov 01 2006 - 12:31:17 CST)
  1. RMSD.doc (34816 bytes)
• Question about ABF Gaurav Sharma (Wed Oct 25 2006 - 18:03:13 CDT)
  1. ABF.doc (31744 bytes)
• Re: Warnings of psfgen Vishal Kopardé (Wed Oct 25 2006 - 17:09:15 CDT)
  1. pastedGraphic.pdf (25458 bytes)
• Warnings of psfgen Vishal Kopardé (Wed Oct 25 2006 - 08:37:30 CDT)
  1. out2 (18463 bytes)
• Re: phi and psi dihedral restraints luca (Mon Oct 23 2006 - 15:07:25 CDT)
  1. esempio_tcl_force.txt (2184 bytes)
• Multiple tclForcesScript Morad Alawneh (Sat Oct 14 2006 - 14:53:28 CDT)
  1. cylindrical_restraint.tcl (5593 bytes)
  2. spherical_restraint.tcl (5398 bytes)
• Re: "wrapAll on" with a complex Jerome Henin (Thu Oct 05 2006 - 22:08:18 CDT)
  1. DOC_unwrap.html (1140 bytes)
  2. unwrap.tcl (4957 bytes)
• Re: DPPC.Pdb file needed Elsa S. Henriques (Tue Sep 05 2006 - 08:42:29 CDT)
  1. DPPC.crd (9254 bytes)
• DPPC.Pdb file needed Lechuga, Javier (Mon Sep 04 2006 - 11:27:49 CDT)
  1. DPPC.pdb (9102 bytes)
• Re: CoordinateTransformation Sting (Sun Sep 03 2006 - 20:17:21 CDT)
  1. align_axis.tcl.txt (496 bytes)
• questions regarding output data of an ABF simulation Anahita Tafvizi (Mon Aug 07 2006 - 15:27:34 CDT)
  1. cons-dir.namd (12984 bytes)
• Re: RDF.tcl griadi_at_utalca.cl (Fri Jul 28 2006 - 17:01:24 CDT)
  1. counting_waters.tcl (1199 bytes)
• simulation crashing with nan Jackie (Wed Jul 26 2006 - 08:49:56 CDT)
  1. Problem.doc (25088 bytes)
• Re: psfgen gets ATP chiral atoms wrong Peter Freddolino (Tue Jul 25 2006 - 10:44:11 CDT)
  1. fixed.tgz (2937 bytes)
• Re: Queries on patches, GDP-topology Leonardo Trabuco (Mon Jul 24 2006 - 14:20:17 CDT)
  1. top_gdp.rtf (2707 bytes)
• Angle 2, Where is the problem [IMPORTANT] linefinc (Mon Jun 19 2006 - 11:50:41 CDT)
  1. co2.zip (25033 bytes)
• Lipid bilayer center go away from center of system. ghg_at_xalt.am (Sun Jun 18 2006 - 10:10:38 CDT)
  1. NPT.conf (3364 bytes)
• RE: Factorization in PMEGridSize JC Gumbart (Wed Jun 07 2006 - 09:25:24 CDT)
  1. image001.gif (339 bytes)
• the patch between segments for multiple chains molecule. Moumita Maiti (Fri Jun 02 2006 - 12:14:58 CDT)
  1. 1kx5.pgn (1369 bytes)
• Large energy fluctuation Sting (Mon May 30 2005 - 21:44:44 CDT)
  1. minimize.int (1261 bytes)
• Large energy fluctuation Sting (Fri Apr 08 2005 - 07:09:07 CDT)
  1. minimize.int (1261 bytes)
• questions regrading ABF Jan Saam (Mon May 29 2006 - 10:47:48 CDT)
  1. alanine.dat (1711 bytes)
• LDB problem on Dual Atlon64 X2 Sebastian Wasilewski (Wed May 17 2006 - 17:07:17 CDT)
  1. smime.p7s (3122 bytes)
• Re: namd: adding water molecules Mgr. Lubos Vrbka (Fri May 12 2006 - 00:51:02 CDT)
  1. smime.p7s (2341 bytes)
• periodic cell too small genie lfs (Wed May 10 2006 - 04:48:44 CDT)
  1. second.namd (2067 bytes)
  2. third.namd (2042 bytes)
  3. fourth.namd (2013 bytes)
• Re: why pressure is fluctuating so much Mgr. Lubos Vrbka (Fri Apr 28 2006 - 00:40:45 CDT)
  1. smime.p7s (2341 bytes)
• scaling NAMD2.6B1 on IBM P5 Thomas C. Bishop (Tue Apr 25 2006 - 14:44:33 CDT)
  1. dyn.NN.conf (2233 bytes)
• error related to tcl boundary forces gbellesia_at_chem.ucsb.edu (Tue Apr 25 2006 - 00:52:38 CDT)
  1. kffe.conf (2726 bytes)
• Re: NAMD-L: question about harmonic constraints JC Gumbart (Tue Apr 11 2006 - 17:41:08 CDT)
  1. cv_deca.tcl (2165 bytes)
• error about tclForcesScript xiaojing gong (Mon Apr 10 2006 - 09:21:13 CDT)
  1. min_2.log (3130 bytes)
• parameter file for DAD Yu Wang (Fri Apr 07 2006 - 09:18:55 CDT)
  1. wy0519.vcf (268 bytes)
• Simulation failed during the stage of heat Shulin Zhuang (Thu Mar 23 2006 - 23:58:15 CST)
  1. heating.namd (2255 bytes)
• Re: area per lipid for a protein embedded membrane system Nicolas Sapay (Sat Mar 11 2006 - 04:42:32 CST)
  1. area.tar.gz (6398 bytes)
• Re: Aligning structures Peter Freddolino (Thu Mar 09 2006 - 21:37:05 CST)
  1. align_frames.tcl (409 bytes)
• Re: Spherical harmonic restraint Morad Alawneh (Thu Mar 02 2006 - 13:25:39 CST)
  1. keep_water_out.tcl (7636 bytes)
• question on membrane crushing Longzhu Shen (Thu Mar 02 2006 - 15:18:09 CST)
  1. eqmd.in (2610 bytes)
• Re: Alchemical Free Energy Perturbation jsachs_at_mail.csb.yale.edu (Wed Mar 01 2006 - 15:31:07 CST)
  1. asa_dual.pdb (3076 bytes)
  2. asa_alchemify.psf (10667 bytes)
  3. fep.namd (1538 bytes)
• Alchemical Free Energy Perturbation Jawahar Neelankatan (Sat Feb 25 2006 - 00:40:02 CST)
  1. fep.conf (1779 bytes)
  2. ion.fep (214 bytes)
• Alchemical Free Energy Perturbation Jawahar Neelankatan (Sat Feb 25 2006 - 01:36:29 CST)
  1. fep.conf (1779 bytes)
  2. ion.fep (214 bytes)
• Free Cluster-Building Workshops - 16-17 Mar 2006, 20-21 Apr 2006 Tim Skirvin (Mon Feb 13 2006 - 14:41:24 CST)
  1. part (186 bytes)
• Fwd: Water Box size snoze pa (Fri Feb 10 2006 - 10:58:27 CST)
  1. namdmin.png (90535 bytes)
  2. namd1ns.png (97173 bytes)
• pairInteractionSelf Yu Wang (Fri Feb 10 2006 - 03:19:34 CST)
  1. wy0519.vcf (268 bytes)
• Re: Saving coordinates of each frame into one separate .pdb file from a 100-frame .dcd file. Carlos Simoes (Sat Jan 21 2006 - 11:04:54 CST)
  1. splitmultiframepdb2files.tcl (781 bytes)
• Re: velocity error, still bo baker (Wed Jan 11 2006 - 16:20:37 CST)
  1. NPT2-011006.conf (1213 bytes)
  2. NPT3-011006.conf (1233 bytes)
• velocity error, still bo baker (Tue Jan 10 2006 - 15:20:58 CST)
  1. NPT1-011006.conf (1213 bytes)
• same random numbers?? Shahid Qamar (Fri Jan 06 2006 - 15:49:01 CST)
  1. random.txt (959 bytes)
• Re: velocity error bo baker (Thu Jan 05 2006 - 18:02:35 CST)
  1. NPT1.conf (1214 bytes)
  2. 4.log (9250 bytes)
• Re: Energy Plugin bo baker (Wed Jan 04 2006 - 16:26:24 CST)
  1. namdplot (3535 bytes)
  2. 2 (3662 bytes)
• velocity error bo baker (Wed Jan 04 2006 - 13:12:45 CST)
  1. 3.log (9853 bytes)
  2. NPT.conf (1385 bytes)
• 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)

Last message date: Fri Dec 29 2006 - 23:10:16 CST
Archived on: Wed Feb 29 2012 - 15:43:00 CST

3455 messages sorted by: [ author ] [ date ] [ thread ] [ subject ]
About this archive