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NAMD-L: By messages with attachments

By messages with attachments

3942 messages sorted by: [ author ] [ date ] [ thread ] [ subject ]
About this archive

Starting: Mon Jan 02 2006 - 18:54:15 CST
Ending: Thu Dec 27 2007 - 12:55:11 CST

• Re: Segmentation violation when running without an internet connection Robert Brunner (Thu Dec 20 2007 - 14:45:41 CST)
  1. smime.p7s (2417 bytes)
• Re: problems replicating a DOPC membrane Richard Swenson (Thu Nov 29 2007 - 14:57:35 CST)
  1. cla_psf.tcl (383 bytes)
  2. dopc_psf.tcl (783 bytes)
  3. fix.tcl (1075 bytes)
  4. reformat.sh (951 bytes)
  5. sod_psf.tcl (379 bytes)
  6. system_psf.tcl (545 bytes)
  7. water_psf.tcl (520 bytes)
• Re: Is there solution to numerical inaccuracy Alok Juneja (Fri Nov 23 2007 - 12:14:01 CST)
  1. comparision.pdf (6353 bytes)
  2. B1-B2.pdf (2997 bytes)
• Re: Replica Exchange NAMD John R. Dowdle (Mon Nov 19 2007 - 20:16:43 CST)
  1. signature.asc (190 bytes)
• heat flux when using langevin dynamics Philipp Schön (Thu Nov 01 2007 - 09:12:56 CDT)
  1. smime.p7s (1764 bytes)
• Errors during equilibration: segmentation fault and bad global exclusion count Ambrish (Tue Oct 23 2007 - 01:45:05 CDT)
  1. equil_mode2.namd (2817 bytes)
• (no subject) ramya narasimhan (Tue Oct 23 2007 - 00:45:16 CDT)
  1. resmd.conf (1590 bytes)
• Molecule drifts and high average RMSD per residue Ambrish (Mon Oct 08 2007 - 11:02:49 CDT)
  1. npt_model1.namd (1635 bytes)
• question regarding nearest-image resolution in NAMD Vincent Kraeutler (Mon Sep 03 2007 - 03:23:24 CDT)
  1. signature.asc (250 bytes)
• Re: Recommended solvation box size Vincent Kraeutler (Wed Aug 29 2007 - 07:46:48 CDT)
  1. signature.asc (250 bytes)
• Re: Re: pressure vs density tip3p Vincent Kraeutler (Mon Aug 27 2007 - 16:55:47 CDT)
  1. signature.asc (250 bytes)
• Re: pressure vs density tip3p Roy Kimura (Mon Aug 27 2007 - 16:04:24 CDT)
  1. roy.kimura.vcf (262 bytes)
• pressure vs density tip3p Roy Kimura (Mon Aug 27 2007 - 15:54:40 CDT)
  1. roy.kimura.vcf (262 bytes)
• Re: setting solvent density during solvation jestin mandumpal (Mon Aug 27 2007 - 01:05:32 CDT)
  1. tip5p.top (310 bytes)
  2. tip5p.pdb (433 bytes)
• Re: How to implement an additional interaction potential? Vincent Kraeutler (Thu Aug 23 2007 - 07:53:05 CDT)
  1. signature.asc (250 bytes)
• How to implement an additional interaction potential? Philipp Schön (Thu Aug 23 2007 - 07:00:12 CDT)
  1. smime.p7s (1764 bytes)
• Re: energy drift in NVE Vincent Kraeutler (Mon Aug 20 2007 - 02:22:49 CDT)
  1. signature.asc (250 bytes)
• Code question: Partitioning the patch contents into water and non-water Vincent Kraeutler (Fri Aug 17 2007 - 04:01:24 CDT)
  1. signature.asc (250 bytes)
• Re: Re: NAMD: Exiting Prematurely Vincent Kraeutler (Wed Aug 15 2007 - 14:06:44 CDT)
  1. signature.asc (250 bytes)
• How to avoid => ERROR: Step 100920 cell rescaling factor limited. Philipp Schön (Mon Aug 13 2007 - 07:28:39 CDT)
  1. smime.p7s (1764 bytes)
• Re: Storage of large files Vincent Kraeutler (Thu Aug 09 2007 - 04:03:32 CDT)
  1. signature.asc (250 bytes)
• Re: Is very slow heating "bad"? Vincent Kraeutler (Sat Aug 04 2007 - 11:06:11 CDT)
  1. signature.asc (250 bytes)
• no effect on velocity scaling Philipp Schön (Fri Aug 03 2007 - 02:36:19 CDT)
  1. smime.p7s (1764 bytes)
• Re: Steered MD with NAMD? Vincent Kraeutler (Thu Aug 02 2007 - 14:47:06 CDT)
  1. signature.asc (250 bytes)
• Re: Can NAMD be used as for general Newtonian mechanics simulations? Vincent Kraeutler (Sat Jul 28 2007 - 07:11:27 CDT)
  1. signature.asc (250 bytes)
• Re: Question regarding NAMD nonbonded routines Vincent Kraeutler (Fri Jul 27 2007 - 12:57:28 CDT)
  1. signature.asc (250 bytes)
• Re: Help Needed>Compiling source namd mpi enabled for a linux cluster Vincent Kraeutler (Fri Jul 27 2007 - 03:47:40 CDT)
  1. signature.asc (250 bytes)
• Re: Question regarding NAMD nonbonded routines Vincent Kraeutler (Thu Jul 26 2007 - 12:27:29 CDT)
  1. signature.asc (250 bytes)
• Question regarding NAMD nonbonded routines Vincent Kraeutler (Wed Jul 25 2007 - 11:55:40 CDT)
  1. signature.asc (250 bytes)
• A serious problem of NAMD output. Wang, Boyang (Tue Jul 24 2007 - 17:35:08 CDT)
  1. rotlectr0.psf (424 bytes)
• Re: ATP molecule snoze pa (Thu Jul 19 2007 - 12:40:35 CDT)
  1. ATP.pdb (5022 bytes)
• Restarting calculation missmatches Alexandre A. Vakhrouchev (Thu Jul 19 2007 - 00:59:36 CDT)
  1. vz_avg.png (4590 bytes)
• Re: removing waters from big dcd files Dong Luo (Mon Jul 16 2007 - 23:00:25 CDT)
  1. DCDframe.zip (20082 bytes)
• balck box: what is the coupling constant when using langenvinFile? Philipp Schön (Fri Jul 13 2007 - 06:53:38 CDT)
  1. smime.p7s (1764 bytes)
• TCL: force not a vector Peter Jones (Tue Jul 10 2007 - 21:39:04 CDT)
  1. tcl_forces_E (3276 bytes)
• Problems with using multiple Tclforces scripts sequentially maria goranovic (Tue Jul 10 2007 - 12:46:48 CDT)
  1. cons196.tcl (1600 bytes)
• can i somehow use reassigntemp for selected atoms only? Philipp Schön (Tue Jul 10 2007 - 11:06:51 CDT)
  1. smime.p7s (1764 bytes)
• Did anybody really use TIP4P? Alessio Alexiadis (Mon Jul 09 2007 - 09:52:47 CDT)
  1. TIP4P.zip (2608 bytes)
• Re: Re: Installing NAMD 2.6 on SMP machine... charm++ install errors Claudio Redaelli (Fri Jul 06 2007 - 04:14:39 CDT)
  1. LINUX_PWR5.tar.gz (2606 bytes)
• Re: ABF restrain alex digenova bravo (Thu Jul 05 2007 - 11:48:12 CDT)
  1. ABF.dat (5959 bytes)
• Re: Count protein solvent HBs? Dong Luo (Thu Jul 05 2007 - 09:21:36 CDT)
  1. hbonds.tcl (20260 bytes)
• problem with periodic boundaries Philipp Schön (Tue Jul 03 2007 - 10:13:04 CDT)
  1. smime.p7s (1764 bytes)
• Re: Changing loop to helix: restraining about 20 dihedral angles Jerome Henin (Sun Jun 24 2007 - 11:37:53 CDT)
  1. dummy.tcl (287 bytes)
• negative force shivam ghosh (Fri Jun 22 2007 - 00:42:24 CDT)
  1. ft_min0.pdf (7665 bytes)
• namd-l-outgoing2@halifax.ks.uiuc.edu sanghyuk_at_ewha.ac.kr (Wed Jun 20 2007 - 12:03:59 CDT)
  1. attachment.zip (1352 bytes)
• Re: Re: heat diffusion calculation QJos=E9_R=2E_Sabino=22?= (Mon Jun 18 2007 - 14:11:17 CDT)
  1. jrsabino.vcf (511 bytes)
• Re: Energy shift during simulation Cesar Luis Avila (Tue May 29 2007 - 09:53:31 CDT)
  1. energy.png (23524 bytes)
• basic pdb file run with namd and vmd Kayode Karunwi (Wed May 23 2007 - 16:05:01 CDT)
  1. alanine.pdb (1139 bytes)
  2. alanine.pgn.txt (168 bytes)
  3. alanine2.pdb (1092 bytes)
  4. alanine2.psf (3169 bytes)
  5. alanine2_wb.pdb (17412 bytes)
  6. alanine2_ws.pdb (1092 bytes)
  7. wat_sphere_alanine.tcl.txt (2089 bytes)
• Minimization Rita Cassia (Wed May 16 2007 - 12:19:51 CDT)
  1. ind.conf (4874 bytes)
• Re: how to use measure hbonds to calculate occupancy of all hbonds in simulation? lnubiofox (Wed May 16 2007 - 09:57:51 CDT)
  1. hbondoccupancy.txt (1148 bytes)
• Re: how to use measure hbonds to calculate occupancy of all hbonds in simulation? Dong Luo (Tue May 15 2007 - 18:27:01 CDT)
  1. hbond.tcl (2269 bytes)
• Re: files for air Jeffrey J. Potoff (Fri May 11 2007 - 07:21:20 CDT)
  1. h2s.pdb (270 bytes)
  2. build.tcl (132 bytes)
• Re: query about wrapped coordinates Gianluca Interlandi (Fri May 04 2007 - 14:54:20 CDT)
  1. DOC_unwrap.html (1140 bytes)
  2. unwrap.tcl (4957 bytes)
• abrupt deviation in rmsd values Monika Sharma (Wed May 02 2007 - 10:35:38 CDT)
  1. rmsd.dat (9927 bytes)
• Re: dcd binary file format Jeffrey A Tibbitt (Tue May 01 2007 - 16:57:47 CDT)
  1. syspart_dcd2 (6668 bytes)
• Re: Pressure Discrepancy Morad Alawneh (Fri Apr 20 2007 - 12:30:37 CDT)
  1. acf_pressure.pdf (2827 bytes)
• Re: Pressure Discrepancy Morad Alawneh (Fri Apr 20 2007 - 10:56:07 CDT)
  1. acf_pressure.pdf (22361 bytes)
• Re: Pressure Discrepancy Morad Alawneh (Tue Apr 03 2007 - 11:39:08 CDT)
  1. acf_pressure.pdf (17244 bytes)
• It doesn't work with using amber files. Hidekazu WATANABE (Thu Mar 29 2007 - 07:09:25 CDT)
  1. r800.new.pdb (3641 bytes)
• Help !!! ERROR: Atoms mooving too fast Juan Diaz (Tue Mar 27 2007 - 18:21:05 CDT)
  1. eq_npt_8.txt (3320 bytes)
• Re: Simulation explodes as soon as minimization starts "GRADIENT TOLERANCE: nan" namd vmd (Thu Mar 22 2007 - 07:55:00 CDT)
  1. top.inp.inp (929 bytes)
• Premature stop paco ty (Thu Mar 08 2007 - 03:57:15 CST)
  1. logfile.txt (7131 bytes)
• RDF.tcl question Jianhui Tian (Wed Feb 21 2007 - 12:43:24 CST)
  1. RDF.tcl (10381 bytes)
• Temperature problem Al-Rawi, Ahlam (Tue Feb 13 2007 - 14:05:35 CST)
  1. equ1.conf (1602 bytes)
• RE: DMPC psf. Lea Thøgersen (Fri Feb 09 2007 - 16:33:01 CST)
  1. DMPC.pdbalias (1281 bytes)
• "atoms moving too fast" error in bilayer simulation Himanshu Khandelia (Fri Feb 02 2007 - 07:31:53 CST)
  1. pope.in (1688 bytes)
• minimizing bad system: bad global excl. count Himanshu Khandelia (Tue Jan 23 2007 - 11:32:41 CST)
  1. config.in (1548 bytes)
• Stray PME grid charges detected Simon Watson (Tue Jan 09 2007 - 12:06:53 CST)
  1. eq0.conf (1234 bytes)
• 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)

Last message date: Thu Dec 27 2007 - 12:55:11 CST
Archived on: Wed Feb 29 2012 - 15:45:45 CST

3942 messages sorted by: [ author ] [ date ] [ thread ] [ subject ]
About this archive