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NAMD-L: By messages with attachments

By messages with attachments

16073 messages sorted by: [ author ] [ date ] [ thread ] [ subject ]
About this archive

Starting: Mon Sep 08 2003 - 09:54:14 CDT
Ending: Wed Feb 29 2012 - 01:22:45 CST

• 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)
• Re: vmd-l: Parse Fep plugin error John Stone (Fri Dec 23 2011 - 10:47:56 CST)
  1. parseFEP.tcl (127449 bytes)
• Segmentation violation with adaptive tempering. Nicholas M Glykos (Sun Nov 20 2011 - 05:13:02 CST)
  1. LOG_segmentation_violation (12172 bytes)
  2. LOG_normal (17424 bytes)
• Fwd: restrain on COM Swarna M Patra (Fri Nov 18 2011 - 23:33:09 CST)
  1. run_conf2 (3744 bytes)
  2. restrain2.tcl (3415 bytes)
• Re: Umbrella sampling koushik.k (Wed Nov 16 2011 - 22:18:59 CST)
  1. hist.png (12438 bytes)
• different velocities problem Hasan haska (Tue Oct 25 2011 - 01:28:22 CDT)
  1. velocity.dat (3006 bytes)
• Re: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CT2 CT1 CT2 (ATOMS 107 98 100) Jernej Zidar (Sun Oct 23 2011 - 19:45:56 CDT)
  1. smime.p7s (2077 bytes)
• Re: Using CHARMM Compatible Amber Parameters Jernej Zidar (Wed Oct 19 2011 - 20:22:46 CDT)
  1. smime.p7s (2077 bytes)
• Re: ABF with Alpha colvar can't be used on supercomputer? Jérôme Hénin (Thu Sep 29 2011 - 09:56:46 CDT)
  1. colvaratoms.C.patch.gz (220 bytes)
• Re: membrane system Bjoern Olausson (Thu Sep 22 2011 - 03:10:00 CDT)
  1. signature.asc_ (199 bytes)
• ABF & distanceZ projection axis more HAMID - (Thu Sep 22 2011 - 03:05:07 CDT)
  1. ABFpic.pdf (17510 bytes)
• Re: membrane system Bjoern Olausson (Wed Sep 21 2011 - 05:02:08 CDT)
  1. signature.asc_ (199 bytes)
• Re: Fwd: Re : Setting up a membrane simulation Bjoern Olausson (Tue Sep 20 2011 - 05:43:30 CDT)
  1. signature.asc_ (199 bytes)
• Re: Fwd: Re : Setting up a membrane simulation Bjoern Olausson (Tue Sep 20 2011 - 04:27:23 CDT)
  1. signature.asc_ (199 bytes)
• Re: Setting up a membrane simulation Bjoern Olausson (Fri Sep 16 2011 - 07:13:56 CDT)
  1. signature.asc_ (199 bytes)
• Re: HETATM vs ATOM in .pdb file Bjoern Olausson (Wed Aug 31 2011 - 06:20:55 CDT)
  1. signature.asc_ (199 bytes)
• Logfile flooded with "The last position output [...]" when IMDon is used. Bjoern Olausson (Tue Aug 23 2011 - 04:32:47 CDT)
  1. signature.asc_ (199 bytes)
• AW: CUDA on GPU Cluster Norman Geist (Mon Aug 22 2011 - 00:47:16 CDT)
  1. provide (74 bytes)
• Re: AW: Letzte Hilfe Bjoern Olausson (Tue Aug 16 2011 - 06:17:36 CDT)
  1. signature.asc_ (199 bytes)
• Re: Denaturation via increased temperature Bjoern Olausson (Mon Aug 15 2011 - 06:11:17 CDT)
  1. signature.asc_ (199 bytes)
• Re: Denaturation via increased temperature Bjoern Olausson (Mon Aug 15 2011 - 04:31:25 CDT)
  1. signature.asc_ (199 bytes)
• Denaturation via increased temperature Bjoern Olausson (Mon Aug 15 2011 - 04:11:06 CDT)
  1. signature.asc_ (199 bytes)
• Re: Lipid bilayer equilibration: Periodic cell has become too small for original patch grid! Bjoern Olausson (Wed Aug 10 2011 - 02:49:01 CDT)
  1. signature.asc_ (199 bytes)
• Re: Lipid bilayer equilibration: Periodic cell has become too small for original patch grid! Bjoern Olausson (Mon Aug 08 2011 - 02:57:08 CDT)
  1. signature.asc_ (199 bytes)
• Re: NAMD 2.8 job submission script for queenbee: ManyJobs Thomas Bishop (Tue Jul 26 2011 - 08:46:29 CDT)
  1. qb.tcsh (714 bytes)
  2. qb.tcsh (1011 bytes)
• Re: how to generate transparent figures? Bjoern Olausson (Mon Jul 25 2011 - 04:04:58 CDT)
  1. signature.asc_ (199 bytes)
• Re: Yan: analysis question Bjoern Olausson (Fri Jul 22 2011 - 03:01:05 CDT)
  1. signature.asc_ (199 bytes)
• Re: PME or not PME? What happens if PME is turned off? Bjoern Olausson (Wed Jul 20 2011 - 03:03:10 CDT)
  1. signature.asc_ (199 bytes)
• Re: analysis question Bjoern Olausson (Tue Jul 19 2011 - 05:43:34 CDT)
  1. signature.asc_ (199 bytes)
• PME or not PME? What happens if PME is turned off? Bjoern Olausson (Mon Jul 18 2011 - 04:10:08 CDT)
  1. signature.asc_ (199 bytes)
• Help required for nanoscale simulation amit banerjee (Wed Jul 13 2011 - 03:03:45 CDT)
  1. conf_file_for_picoscale_simulation.conf (2457 bytes)
• Problem while using MARTINI force field with NAMD 2.8 rohan uttarwar (Tue Jul 12 2011 - 11:42:14 CDT)
  1. equil.conf (3212 bytes)
  2. par_cg_hexdecane.inp (1042 bytes)
• tesla 2050 benchmark Burgess, Don E (Tue Jul 12 2011 - 13:56:45 CDT)
  1. 09.log (15340 bytes)
• Re: temperature-TS with NAMDplot Bjoern Olausson (Fri Jul 08 2011 - 09:07:43 CDT)
  1. signature.asc_ (199 bytes)
• Re: temperature-TS with NAMDplot Bjoern Olausson (Fri Jul 08 2011 - 06:30:09 CDT)
  1. signature.asc_ (199 bytes)
• Re: Implicit solvent simulation Bjoern Olausson (Fri Jul 08 2011 - 05:57:03 CDT)
  1. signature.asc_ (199 bytes)
• Re: Re: Protein moving out of box during npt simulation Bjoern Olausson (Fri Jul 08 2011 - 02:50:29 CDT)
  1. signature.asc_ (199 bytes)
• Re: Re: Protein moving out of box during npt simulation Bjoern Olausson (Tue Jul 05 2011 - 04:22:50 CDT)
  1. signature.asc_ (199 bytes)
• simulated annealing protocol Massimiliano Porrini (Tue Jun 21 2011 - 07:41:00 CDT)
  1. SA.conf (3005 bytes)
• Re: NAMD crashes with OpenMPI/OpenMX Bjoern Olausson (Thu Jun 16 2011 - 07:40:07 CDT)
  1. signature.asc_ (199 bytes)
• Re: about log file Bjoern Olausson (Thu Jun 09 2011 - 05:02:36 CDT)
  1. signature.asc_ (199 bytes)
• AW: AMD-PhenomII-1075_GTX470 NAMD-CUDA performance Norman Geist (Mon Jun 06 2011 - 06:49:06 CDT)
  1. teslac2050.png (38201 bytes)
• Re: water equilibration Bjoern Olausson (Mon Jun 06 2011 - 09:12:33 CDT)
  1. signature.asc_ (199 bytes)
• Re: NAMD crashes when writing restart file and dcdfreq is 1 Ajasja LjubetiÄ� (Tue May 24 2011 - 07:25:25 CDT)
  1. CRASH.sh (402 bytes)
• Re: the meaning of " 5-ZEROS" " 9-ZEROS" in the DCD file Bjoern Olausson (Tue May 24 2011 - 03:44:23 CDT)
  1. signature.asc_ (199 bytes)
• Re: dcd files Artem Zhmurov (Sun May 22 2011 - 16:52:19 CDT)
  1. dcdio.c (6885 bytes)
  2. dcdio.h (735 bytes)
• error in the orientationAngle Prathit Chatterjee (Sat May 21 2011 - 03:51:10 CDT)
  1. npt01.out (10866 bytes)
• Typo in NAMD 2.8b2 output for Accelerated MD Bjoern Olausson (Thu May 19 2011 - 07:25:51 CDT)
  1. signature.asc_ (199 bytes)
• Re: hi Bjoern Olausson (Thu May 19 2011 - 04:29:14 CDT)
  1. signature.asc_ (199 bytes)
• Re: NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 Bjoern Olausson (Thu May 19 2011 - 04:00:33 CDT)
  1. signature.asc_ (199 bytes)
• Re: NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 Bjoern Olausson (Mon May 16 2011 - 04:02:51 CDT)
  1. signature.asc_ (199 bytes)
• Re: REMD segmentation fault Massimiliano Porrini (Fri May 13 2011 - 08:41:09 CDT)
  1. restart_1.out (15933 bytes)
• REMD segmentation fault Massimiliano Porrini (Fri May 13 2011 - 07:58:45 CDT)
  1. error.dat (4782 bytes)
• Re: NAMD2.7 on BluegeneL hang at "LDB: Central LB being created..." Bjoern Olausson (Fri May 13 2011 - 02:47:16 CDT)
  1. signature.asc_ (199 bytes)
• Re: Re: Re: q=AD=94=E5=A4=8D=3A_namd-l=3A_compilation_of?= namd Bjoern Olausson (Thu May 12 2011 - 11:13:21 CDT)
  1. signature.asc_ (199 bytes)
• Re: Re: Re: q=AD=94=E5=A4=8D=3A_namd-l=3A_compilation_of?= namd Bjoern Olausson (Thu May 12 2011 - 09:58:47 CDT)
  1. signature.asc_ (199 bytes)
• Re: Re: q=AD=94=E5=A4=8D=3A_namd-l=3A_compilation_of?= namd Bjoern Olausson (Thu May 12 2011 - 08:11:57 CDT)
  1. signature.asc_ (199 bytes)
• Re: ABF simulation with extendedLagrangian on keeps crashing Ajasja LjubetiÄ� (Thu May 12 2011 - 03:55:03 CDT)
  1. tp.in (1612 bytes)
• Re: Re: q=AD=94=E5=A4=8D=3A_namd-l=3A_compilation_of?= namd Bjoern Olausson (Thu May 12 2011 - 02:45:49 CDT)
  1. signature.asc_ (199 bytes)
• Re: NAMDEnergy Plugin - setting PMEGridSize / mesh density Michael S. Sellers (Cont, ARL/WMRD) (Wed May 11 2011 - 15:29:25 CDT)
  1. smime.p7s (10449 bytes)
• Re: Accelerated MD: question about dual boost mode Bjoern Olausson (Tue May 10 2011 - 10:17:59 CDT)
  1. signature.asc_ (199 bytes)
• Re: Accelerated MD: question about dual boost mode Bjoern Olausson (Tue May 10 2011 - 07:32:13 CDT)
  1. signature.asc_ (199 bytes)
• Re: ABF simulation with extendedLagrangian on keeps crashing Jérôme Hénin (Thu May 05 2011 - 10:23:23 CDT)
  1. angle_ABF.tar.gz (9698 bytes)
• Re: 'cutting' colvars.traj file Bjoern Olausson (Tue May 03 2011 - 08:34:21 CDT)
  1. signature.asc_ (199 bytes)
• Re: 'cutting' colvars.traj file Bjoern Olausson (Tue May 03 2011 - 05:45:23 CDT)
  1. signature.asc_ (199 bytes)
• run tests with CUDA Massimiliano Porrini (Mon May 02 2011 - 16:25:17 CDT)
  1. dynamix.conf (1984 bytes)
• Re: 'cutting' colvars.traj file Bjoern Olausson (Wed Apr 27 2011 - 05:53:41 CDT)
  1. signature.asc_ (199 bytes)
• Re: ABF simulation with extendedLagrangian on keeps crashing Ajasja LjubetiÄ� (Tue Apr 19 2011 - 12:05:23 CDT)
  1. tp.00001.colvars.traj.zip (5223 bytes)
• Re: NVT setup for monolayer Bjoern Olausson (Thu Apr 14 2011 - 02:17:35 CDT)
  1. signature.asc_ (199 bytes)
• Re: Help building a desktop for namd Axel Kohlmeyer (Mon Apr 11 2011 - 15:06:33 CDT)
  1. namd-scale.pdf (16882 bytes)
• NVT setup for monolayer Bjoern Olausson (Thu Apr 07 2011 - 08:24:32 CDT)
  1. signature.asc_ (199 bytes)
• Fwd: Wrong exit from RAMD runs Francesco Pietra (Tue Apr 05 2011 - 15:34:19 CDT)
  1. ramd.wrong.output.txt (2932 bytes)
• Wrong exit from RAMD runs Francesco Pietra (Tue Apr 05 2011 - 03:11:29 CDT)
  1. ramd.wrong.output.txt (2932 bytes)
• Re: Multi node run causes "CUDA error cudaStreamCreate" Michael S. Sellers (Cont, ARL/WMRD) (Fri Apr 01 2011 - 15:46:21 CDT)
  1. smime.p7s (10449 bytes)
• Re: Why are the pressures in my box of water systematically off? Tom Sisan (Wed Mar 30 2011 - 12:40:58 CDT)
  1. w233pressures.png (25062 bytes)
• Re: Rotate two linked proteins against each other and calculate energy profile Bjoern Olausson (Tue Mar 29 2011 - 10:16:12 CDT)
  1. signature.asc_ (199 bytes)
• Re: Rotate two linked proteins against each other and calculate energy profile Jérôme Hénin (Tue Mar 29 2011 - 07:03:14 CDT)
  1. periodicity-update.tar.gz (25108 bytes)
• Re: Rotate two linked proteins against each other and calculate energy profile Bjoern Olausson (Mon Mar 28 2011 - 11:36:13 CDT)
  1. signature.asc_ (199 bytes)
• Re: Rotate two linked proteins against each other and calculate energy profile Bjoern Olausson (Mon Mar 28 2011 - 11:18:09 CDT)
  1. signature.asc_ (199 bytes)
• Re: GBIS and ABF Bjoern Olausson (Mon Mar 28 2011 - 09:56:41 CDT)
  1. signature.asc_ (199 bytes)
• Re: namd and Fedora14 Michael S. Sellers (Cont, ARL/WMRD) (Mon Mar 28 2011 - 09:16:51 CDT)
  1. smime.p7s (10449 bytes)
• Re: namd and Fedora14 Michael S. Sellers (Cont, ARL/WMRD) (Mon Mar 28 2011 - 09:12:47 CDT)
  1. smime.p7s (10449 bytes)
• Re: Rotate two linked proteins against each other and calculate energy profile Bjoern Olausson (Mon Mar 28 2011 - 07:49:23 CDT)
  1. signature.asc_ (199 bytes)
• Re: GBIS and ABF Bjoern Olausson (Mon Mar 28 2011 - 02:45:46 CDT)
  1. signature.asc_ (199 bytes)
• Re: GBIS and ABF Bjoern Olausson (Wed Mar 23 2011 - 06:57:32 CDT)
  1. signature.asc_ (199 bytes)
• Re: GBIS and ABF Bjoern Olausson (Wed Mar 23 2011 - 09:32:43 CDT)
  1. signature.asc_ (199 bytes)
• Re: GBIS question and possible Bug for colvar "outputSystemForce" declaration in NAMD CVS-2011-03-03 Bjoern Olausson (Wed Mar 23 2011 - 07:06:21 CDT)
  1. signature.asc_ (199 bytes)
• Re: GBIS and ABF Bjoern Olausson (Wed Mar 23 2011 - 07:04:29 CDT)
  1. signature.asc_ (199 bytes)
• Re: GBIS question and possible Bug for colvar "outputSystemForce" declaration in NAMD CVS-2011-03-03 Bjoern Olausson (Wed Mar 23 2011 - 03:18:22 CDT)
  1. signature.asc_ (199 bytes)
• Re: GBIS and ABF Bjoern Olausson (Tue Mar 22 2011 - 18:13:18 CDT)
  1. signature.asc_ (199 bytes)
• GBIS question and possible Bug for colvar "outputSystemForce" declaration in NAMD CVS-2011-03-03 Bjoern Olausson (Tue Mar 22 2011 - 17:56:09 CDT)
  1. signature.asc_ (199 bytes)
• Re: rule of thumb for dcd sampling frequency? Michael S. Sellers (Cont, ARL/WMRD) (Tue Mar 22 2011 - 15:56:17 CDT)
  1. smime.p7s (10449 bytes)
• GBIS not compatible with CUDA at this time Michael S. Sellers (Cont, ARL/WMRD) (Tue Mar 22 2011 - 13:27:48 CDT)
  1. smime.p7s (10449 bytes)
• Re: namd and Fedora14 Michael S. Sellers (Cont, ARL/WMRD) (Tue Mar 22 2011 - 10:10:02 CDT)
  1. smime.p7s (10449 bytes)
• Re: Accelerated MD documentation? Bjoern Olausson (Tue Mar 15 2011 - 10:47:21 CDT)
  1. signature.asc_ (199 bytes)
• Re: Accelerated MD documentation? Bjoern Olausson (Tue Mar 15 2011 - 08:59:48 CDT)
  1. signature.asc_ (199 bytes)
• Re: BOUNCE namd-l@ks.uiuc.edu: Message too long (>40000 chars) Francesco Pietra (Fri Mar 11 2011 - 11:46:30 CST)
  1. 371.jpg (11413 bytes)
  2. 427.jpg (5969 bytes)
• Re: vmd-l: Re: hBond colvars and patching Francesco Pietra (Mon Mar 07 2011 - 10:04:37 CST)
  1. asp.jpg (37881 bytes)
• Re: membrane equilibration Ajasja LjubetiÄ� (Fri Mar 04 2011 - 05:09:19 CST)
  1. psfregen.vmd (1863 bytes)
• Re: Psfgen Errors for C-type Heme Thomas Freeman (Tue Mar 01 2011 - 14:15:56 CST)
  1. top_c_heme.inp (28026 bytes)
• maximum number of atoms per patch Branko (Sun Feb 27 2011 - 12:21:56 CST)
  1. voda2.namd (2438 bytes)
• psfgen - any version capable of reading extended PSF files? Bjoern Olausson (Fri Feb 11 2011 - 05:47:05 CST)
  1. signature.asc_ (199 bytes)
• job termination ipsita basu (Fri Feb 11 2011 - 00:46:17 CST)
  1. input.doc (12800 bytes)
• Re: Get number of timesteps from DCD via script Bjoern Olausson (Thu Feb 10 2011 - 03:52:44 CST)
  1. signature.asc_ (199 bytes)
• FEP - Protein binding to Membrane surface Bjoern Olausson (Thu Feb 10 2011 - 03:50:37 CST)
  1. signature.asc_ (199 bytes)
• Re: Get number of timesteps from DCD via script Bjoern Olausson (Wed Feb 09 2011 - 08:32:13 CST)
  1. signature.asc_ (199 bytes)
• Re: Get number of timesteps from DCD via script Bjoern Olausson (Wed Feb 09 2011 - 08:05:42 CST)
  1. signature.asc_ (199 bytes)
• Re: Get number of timesteps from DCD via script Bjoern Olausson (Wed Feb 09 2011 - 06:37:20 CST)
  1. signature.asc_ (199 bytes)
• Re: Get number of timesteps from DCD via script Bjoern Olausson (Tue Feb 08 2011 - 05:24:29 CST)
  1. signature.asc_ (199 bytes)
• Get number of timesteps from DCD via script Bjoern Olausson (Mon Feb 07 2011 - 06:52:39 CST)
  1. signature.asc_ (199 bytes)
• Re: Feature request for the colvars module -- TCL syntax Ajasja LjubetiÄ� (Mon Jan 24 2011 - 08:16:01 CST)
  1. example.rar (10313 bytes)
• The outputs of REMD were suspended Yingzhe Liu (Sun Dec 19 2010 - 08:21:11 CST)
  1. fold_alanin.job0.0.log (11467 bytes)
  2. REMD.log (1454 bytes)
• jobs get stuck using NAMDv2.7 and stop producing output in the log-file harish vashisth (Fri Dec 17 2010 - 10:20:10 CST)
  1. job_files.tgz (8274 bytes)
• how to generate the topology and parameter file for ligand jnsong (Thu Dec 16 2010 - 07:45:52 CST)
  1. 11.jpg (17458 bytes)
• how to generate topology and parameter file for ligand jnsong (Thu Dec 16 2010 - 07:40:38 CST)
  1. 11.jpg (17458 bytes)
• Re: periodic boundary conditions in namd energy calculation Michael S. Sellers (Cont, ARL/WMRD) (Tue Nov 30 2010 - 14:06:09 CST)
  1. smime.p7s (10435 bytes)
• Creating a NAMD Shared Library -> Undefined Symbols in Charm libs Michael S. Sellers (Cont, ARL/WMRD) (Mon Nov 29 2010 - 15:22:40 CST)
  1. smime.p7s (10435 bytes)
• Creating a NAMD Shared Library -> Undefined Symbols in Charm libs Michael S. Sellers (Cont, ARL/WMRD) (Mon Nov 29 2010 - 15:07:21 CST)
  1. smime.p7s (10435 bytes)
• How to set improper dihedral for trans-double bond. Boyang Wang (Mon Nov 29 2010 - 06:15:16 CST)
  1. trans.pdb (560 bytes)
• Re: Allowed CMAP dimensions Ajasja LjubetiÄ� (Fri Nov 26 2010 - 10:23:23 CST)
  1. CMAPInterpolate.rar (13992 bytes)
• FATAL ERROR: CAN'T FIND CROSSTERM PARAMETERS FOR CC NH1 CT1 C NH1 CT1 C NH1 Gurunath Katagi (Sat Nov 06 2010 - 02:41:31 CDT)
  1. a.pdb (2840 bytes)
• extending namd / shared library build (UNCLASSIFIED) Sellers, Michael S. (Cont, ARL/WMRD) (Fri Oct 29 2010 - 08:23:41 CDT)
  1. smime.p7s (5716 bytes)
• Constraint failure in RATTLE algorithm for atom 268 surendra jain (Fri Oct 29 2010 - 04:54:38 CDT)
  1. equil3_conf (4323 bytes)
• Fwd: minimization problem ipsita basu (Fri Oct 29 2010 - 00:25:58 CDT)
  1. input.doc (14848 bytes)
• RE: force field for replica exchange with NAMD ÓáÏè (Thu Oct 28 2010 - 15:40:52 CDT)
  1. re.out (8332 bytes)
  2. fold_synuclein.conf (2698 bytes)
  3. synuclein_base.namd (271 bytes)
  4. re2.out (6780 bytes)
• minimization problem ipsita basu (Wed Oct 27 2010 - 01:00:23 CDT)
  1. input.doc (14848 bytes)
• a question about modifying the NAMD input file ying yu (Mon Oct 25 2010 - 12:06:50 CDT)
  1. revized_siliconmechanicstest.namd (5708 bytes)
• Re: Is the DCD file size consistent for consecutive runs? Bjoern Olausson (Fri Oct 08 2010 - 11:30:36 CDT)
  1. signature.asc_ (199 bytes)
• (no subject) ipsita basu (Fri Oct 08 2010 - 06:00:41 CDT)
  1. input.doc (14848 bytes)
• Re: Is the DCD file size consistent for consecutive runs? Bjoern Olausson (Fri Oct 08 2010 - 04:27:54 CDT)
  1. signature.asc_ (199 bytes)
• Re: Is the DCD file size consistent for consecutive runs? Bjoern Olausson (Thu Oct 07 2010 - 06:40:17 CDT)
  1. signature.asc_ (199 bytes)
• Is the DCD file size consistent for consecutive runs? Bjoern Olausson (Wed Oct 06 2010 - 03:36:04 CDT)
  1. signature.asc_ (199 bytes)
• reg_membrane_peptide_interaction lara lara (Sat Sep 25 2010 - 04:24:09 CDT)
  1. codes.pgn (1118 bytes)
• Re: NAMD Energy types Lada Biedermannová (Thu Sep 09 2010 - 03:51:12 CDT)
  1. temp.namd (671 bytes)
  2. temp.pdb (1971 bytes)
• restarting simulation sara (Sun Aug 29 2010 - 03:18:07 CDT)
  1. c8_2CNT_wb_eq.conf (3119 bytes)
• WorkDistrib: Recursive bisection fails,invoking least-load algorithm Swarna M Patra (Tue Aug 24 2010 - 11:42:45 CDT)
  1. min_conf1 (3807 bytes)
• Re: Re: psf creating for carbon nanotube Jian Liu (Mon Aug 16 2010 - 00:23:54 CDT)
  1. nanotube.tcl (1446 bytes)
• LJ correction in NAMD2.7b3 Thomas C. Bishop (Thu Aug 12 2010 - 14:05:04 CDT)
  1. http:__www.ks.uiuc.edu_Research_namd_2.7b3_ug_img19.png (0 bytes)
  2. http:__www.ks.uiuc.edu_Research_namd_2.7b3_ug_img20.png (0 bytes)
• Reading NAMD coor files in CHARMM -> Fail for 64Bit Bjoern Olausson (Wed Aug 11 2010 - 06:57:27 CDT)
  1. signature.asc_ (199 bytes)
• Re: question regarding warning. Bjoern Olausson (Mon Aug 09 2010 - 03:13:58 CDT)
  1. signature.asc_ (199 bytes)
• Re: RetinalTop Bjoern Olausson (Tue Aug 03 2010 - 02:57:26 CDT)
  1. signature.asc_ (199 bytes)
• Re: RetinalTop Bjoern Olausson (Mon Aug 02 2010 - 09:49:32 CDT)
  1. signature.asc_ (199 bytes)
• Re: Using CHARMM-GUI membrane builder with NAMD Bjoern Olausson (Mon Aug 02 2010 - 08:21:07 CDT)
  1. signature.asc_ (199 bytes)
• Re: Using CHARMM-GUI membrane builder with NAMD Ajasja LjubetiÄ� (Mon Aug 02 2010 - 07:59:54 CDT)
  1. membrane_lipid_restraint.str (1541 bytes)
• Re: Using CHARMM-GUI membrane builder with NAMD Bjoern Olausson (Mon Aug 02 2010 - 06:56:14 CDT)
  1. signature.asc_ (199 bytes)
• Re: Using CHARMM-GUI membrane builder with NAMD Bjoern Olausson (Mon Aug 02 2010 - 02:37:09 CDT)
  1. signature.asc_ (199 bytes)
• Re: how to submit job on a HPC equipped with infiniband Bjoern Olausson (Mon Jul 26 2010 - 04:31:55 CDT)
  1. signature.asc_ (199 bytes)
• Re: 1us simulation of 80k atom system -- how much gross structure movement is expected? Ian Stokes-Rees (Mon Jul 19 2010 - 20:06:05 CDT)
  1. ijstokes.vcf (381 bytes)
• problem wuth solvate plugin Mikhail Suyetin (Mon Jul 12 2010 - 05:53:28 CDT)
  1. h2.top (8337 bytes)
  2. h2.pdb (132 bytes)
  3. h2.psf (531 bytes)
  4. group-8-2.pdb (717 bytes)
  5. group-8-2.psf (1584 bytes)
  6. multiplication.tcl (1611 bytes)
• Re: Helix tilt Bjoern Olausson (Tue Jul 06 2010 - 10:59:54 CDT)
  1. signature.asc_ (199 bytes)
• Re: namd2 still works but without any new messages in log file Bjoern Olausson (Thu Jul 01 2010 - 09:27:47 CDT)
  1. signature.asc_ (199 bytes)
• NAMD terminates prematurely without error. Ajasja LjubetiÄ� (Wed Jun 23 2010 - 02:41:24 CDT)
  1. i18c_20ns.1.d.log (8692 bytes)
  2. i18c_20ns.1.conf (3124 bytes)
  3. i18c_20ns.1.restart.conf (3132 bytes)
• Query regarding ABF Tutorial on Methane Hydration Navendu bhatnagar (Tue Jun 22 2010 - 14:52:41 CDT)
  1. window1.in (404 bytes)
  2. equil.conf (3384 bytes)
  3. 5b-off.pmf (886 bytes)
• charges in psf and in namd (or vmd) fett_at_vtr.net (Wed Jun 02 2010 - 11:12:07 CDT)
  1. toluene.top (967 bytes)
  2. toluene.psf (3604 bytes)
  3. toluene.pdb (1235 bytes)
• Re: Sudden crash - any clue about the cause? --> wc[0] status 12 wc[i].opcode 0 Bjoern Olausson (Wed Jun 02 2010 - 10:13:32 CDT)
  1. signature.asc_ (199 bytes)
• Sudden crash - any clue about the cause? --> wc[0] status 12 wc[i].opcode 0 Bjoern Olausson (Wed Jun 02 2010 - 08:32:24 CDT)
  1. signature.asc_ (199 bytes)
• Re: Run simulation in NAMD using files generated by CHARMM-GUI Bjoern Olausson (Tue Jun 01 2010 - 03:22:25 CDT)
  1. signature.asc_ (199 bytes)
• Drift of the center of mass of lipid bilayer Dai, Jian1 (Mon May 24 2010 - 13:26:39 CDT)
  1. production4.conf (1482 bytes)
• Re: error : atom moving too fast Bjoern Olausson (Thu May 06 2010 - 06:34:45 CDT)
  1. signature.asc_ (199 bytes)
• error : atom moving too fast ipsita basu (Wed May 05 2010 - 01:10:33 CDT)
  1. input.doc (15360 bytes)
• Using RMSD in colvar Stefan Franzen (Mon May 03 2010 - 17:42:18 CDT)
  1. ubq_ws_cv.inp (566 bytes)
• FW: ammonia to methane/ c/o Jerome Henin Dale l. Schruben (Mon Apr 26 2010 - 21:18:01 CDT)
  1. psfNH3.pgn (317 bytes)
  2. top_ammonia.inp (632 bytes)
  3. NH3.pdb (237 bytes)
  4. psfCH4.pgn (412 bytes)
  5. top_methane.inp (765 bytes)
  6. CH4.pdb (238 bytes)
• the unit of dipole moment in the calculation of dielectric constant. superdirac (Sun Apr 25 2010 - 21:58:11 CDT)
  1. 26-10-56-12_.jpg (20382 bytes)
• FW: ammonia to methane/ c/o Jerome Henin Dale l. Schruben (Fri Apr 23 2010 - 10:19:19 CDT)
  1. psfNH3.pgn (317 bytes)
  2. top_ammonia.inp (632 bytes)
  3. NH3.pdb (237 bytes)
  4. psfCH4.pgn (412 bytes)
  5. top_methane.inp (765 bytes)
  6. CH4.pdb (238 bytes)
• FW: ammonia to methane/DISREGARD this post-changes to files below make methane work now Dale l. Schruben (Wed Apr 07 2010 - 22:36:49 CDT)
  1. psfNH3.pgn (317 bytes)
  2. top_ammonia.inp (632 bytes)
  3. NH3.pdb (237 bytes)
  4. psfCH4.pgn (412 bytes)
  5. top_methane.inp (765 bytes)
  6. CH4.pdb (238 bytes)
• ammonia to methane Dale l. Schruben (Wed Apr 07 2010 - 11:37:10 CDT)
  1. psfNH3.pgn (317 bytes)
  2. top_ammonia.inp (632 bytes)
  3. NH3.pdb (237 bytes)
  4. psfCH4.pgn (412 bytes)
  5. top_methane.inp (765 bytes)
  6. CH4.pdb (238 bytes)
• Re: About matdcd Mert Gür (Sun Apr 04 2010 - 04:20:50 CDT)
  1. -static--liam_sitting_bottomleft.jpg (9536 bytes)
• NAMD CUDA bahare bamdad (Tue Mar 16 2010 - 03:23:04 CDT)
  1. log (233281 bytes)
  2. sample.conf (3264 bytes)
• anomalous behaviour of ASPP and GLUP during MD run Andreini Matteo (Thu Feb 25 2010 - 08:24:45 CST)
  1. logosienabiotech_trasparente_piccolo3d6c.gif (1477 bytes)
• anomalous behaviour of ASPP and GLUP during MD run Andreini Matteo (Thu Feb 25 2010 - 02:31:45 CST)
  1. logosienabiotech_trasparente_piccolo489c.gif (1477 bytes)
• Re: AW: update: segmentation faults with AMBER topology and RAMD tcl scripts Balazs Jojart (Wed Feb 24 2010 - 01:52:26 CST)
  1. output.tar (30720 bytes)
• Re: namd 2.7b2 or later - amberff/prmtop causes segfault during startup phase Nicolas Sapay (Wed Feb 24 2010 - 06:49:47 CST)
  1. nicolas_sapay.vcf (333 bytes)
• running tcl scripting ipsita basu (Tue Feb 23 2010 - 04:26:05 CST)
  1. combine.tcl.htm (5377 bytes)
• RE: atom charges for protonated carboxyl termini Peter Jones (Mon Feb 22 2010 - 18:46:25 CST)
  1. date_ (1096 bytes)
• tutorial-l: Nanotubes tutorial - coorList(577) no such element Drew buschhorn (Thu Feb 18 2010 - 00:45:24 CST)
  1. log.txt (9288 bytes)
• error in scripting ipsita basu (Tue Feb 16 2010 - 05:26:07 CST)
  1. script.txt (3393 bytes)
• how to get .coor .vel and .xsc for a .dcd file ÅÓÑ©ÇÛ Pang Xueqin (Wed Jan 27 2010 - 08:42:44 CST)
  1. _______1_.vcf (1243 bytes)
• reading dcd file ipsita basu (Mon Jan 25 2010 - 03:20:39 CST)
  1. script.txt_ (3419 bytes)
• scripting problem ipsita basu (Mon Jan 25 2010 - 00:15:51 CST)
  1. script1.doc (6933 bytes)
• scripting error ipsita basu (Thu Jan 21 2010 - 23:36:02 CST)
  1. script.doc (3420 bytes)
• error of the energy output when equilibration xyhu1127 (Thu Jan 14 2010 - 19:17:18 CST)
  1. 1uy6_eq2.conf (2744 bytes)
• Re: Number of MC steps in ABF integrate gives entirely diferent surfaces Jerome Henin (Thu Jan 14 2010 - 05:00:18 CST)
  1. integrate.tar.gz (5363 bytes)
• Re: ABF questions Austin B. Yongye (Tue Jan 05 2010 - 16:19:57 CST)
  1. atom_based_01.dat (4543 bytes)
  2. 1.emin_colvar.conf (931 bytes)
  3. colVarfile.txt (533 bytes)
• gradual increase in the temperature after minimization gurunath katagi (Wed Dec 09 2009 - 12:21:34 CST)
  1. protein.conf (3213 bytes)
  2. protein1.conf (3310 bytes)
• Re: FreeEnergy: Not enough steps to complete pfm & mcti blocks priyodorshi satpati (Thu Nov 26 2009 - 03:19:48 CST)
  1. test_const.namd (3223 bytes)
  2. test_const.log (8350 bytes)
• Signal: segmentation violation gurunath katagi (Fri Nov 20 2009 - 15:20:16 CST)
  1. protein.conf (3209 bytes)
  2. sge_16.sh (572 bytes)
• Re: Simultaneous water and protein minimization jkmann_at_buffalo.edu (Thu Nov 19 2009 - 15:07:54 CST)
  1. swemt_water_min.conf (3198 bytes)
  2. swemt_protein_min_and_dynamics.conf (3202 bytes)
• Generating psf for NPC1 Joshua Lioi (Thu Nov 19 2009 - 10:45:07 CST)
  1. gkh.pgn (850 bytes)
• Re: Will MPICH2 work for NAMD? and the best way to build/compile NAMD to exploit my hardware resource? Bjoern Olausson (Fri Nov 13 2009 - 03:39:32 CST)
  1. signature.asc_ (199 bytes)
• Re: Formating of logfile Bjoern Olausson (Fri Nov 13 2009 - 02:55:02 CST)
  1. signature.asc_ (199 bytes)
• Re: Will MPICH2 work for NAMD? Bjoern Olausson (Wed Nov 11 2009 - 07:07:47 CST)
  1. signature.asc_ (199 bytes)
• Formating of logfile Bjoern Olausson (Wed Nov 11 2009 - 07:07:34 CST)
  1. signature.asc_ (199 bytes)
• Formating of logfile Bjoern Olausson (Wed Nov 11 2009 - 06:58:44 CST)
  1. signature.asc_ (199 bytes)
• Re: Will MPICH2 work for NAMD? Bjoern Olausson (Tue Nov 10 2009 - 02:52:03 CST)
  1. signature.asc_ (199 bytes)
• Re: Is it a bug? TCL Script may Lead to Overflow Fred (Rui FENG) (Sat Nov 07 2009 - 15:31:29 CST)
  1. tclscript.zip (21695 bytes)
• Error in Minimization Ale Gomez (Sat Nov 07 2009 - 10:45:24 CST)
  1. preparacion.tcl (7205 bytes)
  2. bacmin.conf (2360 bytes)
• Re: ibverbs crash Bjoern Olausson (Wed Nov 04 2009 - 08:38:25 CST)
  1. ibverbs.c (92079 bytes)
  2. signature.asc_ (199 bytes)
• Re: ibverbs crash Bjoern Olausson (Wed Nov 04 2009 - 04:06:48 CST)
  1. signature.asc_ (199 bytes)
• Re: ibverbs crash Bjoern Olausson (Wed Nov 04 2009 - 08:38:45 CST)
  1. signature.asc_ (199 bytes)
• issues with AutoPSF for a cyclodextrin CHINDEA Vlad (Thu Oct 29 2009 - 18:32:50 CDT)
  1. amidon4.pdb (16877 bytes)
• Re: Fullerene topology Luca Muccioli (Wed Oct 28 2009 - 10:55:11 CDT)
  1. C60.tpg (2634 bytes)
  2. C60.pdb (4624 bytes)
• About NAN error cong chen (Fri Sep 18 2009 - 01:35:51 CDT)
  1. water-10-npt.log (2175362 bytes)
  2. water-10-npt.conf (3439 bytes)
• Re: Regarding ABF Simulation Jagan Mohan (Tue Sep 15 2009 - 00:10:48 CDT)
  1. eqf_inp_back (2020 bytes)
• Re: Constraint failure in RATTLE algorithm - shouldn't a rerun fail at the same step? Bjoern Olausson (Thu Sep 10 2009 - 05:38:18 CDT)
  1. signature.asc_ (199 bytes)
• Re: Constraint failure in RATTLE algorithm - shouldn't a rerun fail at the same step? Bjoern Olausson (Thu Sep 10 2009 - 05:26:00 CDT)
  1. signature.asc_ (199 bytes)
• Constraint failure in RATTLE algorithm - shouldn't a rerun fail at the same step? Bjoern Olausson (Tue Sep 08 2009 - 03:12:04 CDT)
  1. signature.asc_ (199 bytes)
• Constraint failure in RATTLE algorithm - shouldn't a rerun fail at the same step? Bjoern Olausson (Tue Sep 08 2009 - 03:13:02 CDT)
  1. signature.asc_ (199 bytes)
• Re-posting - Methylated Histidine topology file Sujata Sovani (Mon Aug 31 2009 - 12:47:16 CDT)
  1. MeHIS2.doc (24064 bytes)
• Methylated Histidine topology file Sujata Sovani (Mon Aug 31 2009 - 12:38:03 CDT)
  1. MeHIS2.doc (24064 bytes)
• hole on the surface of the waterbox Mert Gür (Fri Aug 28 2009 - 05:08:09 CDT)
  1. molcom.conf (1599 bytes)
• Postdoc position in biomolecular simulation Ivaylo Ivanov (Wed Aug 26 2009 - 16:40:02 CDT)
  1. positions.pdf (11803 bytes)
• Re: charm++ how to handle SMP/Multicore Bjoern Olausson (Thu Aug 20 2009 - 11:41:16 CDT)
  1. signature.asc_ (199 bytes)
• restating simuation and periodic cell conditions gurunath katagi (Tue Aug 18 2009 - 03:23:20 CDT)
  1. protein.conf (3955 bytes)
• Re: Error with GUI NAMD Energy snoze pa (Mon Aug 10 2009 - 11:32:53 CDT)
  1. namdlog.pl (924 bytes)
• FEP implementation in NAMD 2.6 vs. 2.7b1 Dan Bolintineanu (Tue Jul 28 2009 - 16:50:37 CDT)
  1. ethane3.namd (2350 bytes)
• NAMD 2.7b1 with APBS/iAPBS Bjoern Olausson (Wed Jul 22 2009 - 02:56:07 CDT)
  1. signature.asc_ (199 bytes)
• Minimization problem of a protein-DNA complex with namd sudipta (Sun Jul 12 2009 - 02:21:36 CDT)
  1. pro_dna_new_cc.in (5103 bytes)
  2. pro_dna_minimization.conf (2790 bytes)
• Re: Value for "firsttimestep" when restarting MD Bjoern Olausson (Thu Jul 02 2009 - 04:05:23 CDT)
  1. signature.asc_ (199 bytes)
• RE: ABF simulations Branko (Tue Jun 23 2009 - 14:52:42 CDT)
  1. Example.tif (13176 bytes)
• Postdoc position in biomolecular simulation Ivaylo, Ivanov (Sat Jun 13 2009 - 02:08:07 CDT)
  1. positions.pdf (21058 bytes)
• Postdoc position in biomolecular simulation Ivaylo, Ivanov (Sat Jun 13 2009 - 01:37:55 CDT)
  1. positions.pdf (21058 bytes)
• FATAL ERROR: Bad global exclusion count! KIRTANA S (Mon Jun 01 2009 - 12:37:38 CDT)
  1. parameter.rtf (2239 bytes)
  2. psf.rtf (7629 bytes)
• regd: my parameter file KIRTANA S (Fri May 29 2009 - 16:05:26 CDT)
  1. par_all27_prot_lipid.inp (759 bytes)
  2. psf.rtf (7629 bytes)
• Re: water tail correction Floris Buelens (Fri May 22 2009 - 05:40:00 CDT)
  1. LJcorrection.diff (5368 bytes)
  2. LJcorrection_validation.txt (6002 bytes)
• Need help to generate ubq-get-energy.conf Mert Gür (Wed May 13 2009 - 10:06:55 CDT)
  1. 1EJG.conf (1674 bytes)
• Re: Make NAMD2.7b1 with cuda bug? Axel Kohlmeyer (Wed May 13 2009 - 10:03:44 CDT)
  1. back_end.diff.gz (455 bytes)
• Which compiler-suite was used... Bjoern Olausson (Tue May 12 2009 - 07:26:00 CDT)
  1. signature.asc_ (199 bytes)
• Re: Value for "firsttimestep" when restarting MD Bjoern Olausson (Tue May 05 2009 - 12:45:56 CDT)
  1. signature.asc_ (199 bytes)
• Re: dummy atom mass changed yun luo (Tue May 05 2009 - 12:19:05 CDT)
  1. memb2_fep.png (7043 bytes)
• Re: dummy atom mass changed Jerome Henin (Tue May 05 2009 - 10:43:48 CDT)
  1. lambda.png (16558 bytes)
• Value for "firsttimestep" when restarting MD Bjoern Olausson (Tue May 05 2009 - 09:50:42 CDT)
  1. signature.asc_ (199 bytes)
• regarding simulation prasun kumar (Tue May 05 2009 - 08:48:00 CDT)
  1. dna1.conf (3202 bytes)
• structure problem Ahlam Al-Rawi (Wed Apr 22 2009 - 12:22:29 CDT)
  1. corey.pdb (23316 bytes)
• Re: Unfavorable anti conformation after GLUP patching? Sebastian Stolzenberg (Thu Apr 16 2009 - 11:00:17 CDT)
  1. pmf.tcl (224 bytes)
• Re: how to do: FEP e2?, a protonating mutation? Sébastien Légaré (Thu Apr 09 2009 - 10:48:06 CDT)
  1. glud1.txt (3053 bytes)
• how to do: FEP e2?, a protonating mutation? Sebastian Stolzenberg (Tue Apr 07 2009 - 19:15:19 CDT)
  1. GLU2GLUP.pdf (25541 bytes)
• About CUDA version of NAMD 2.7 B1 wang (Wed Mar 25 2009 - 00:57:33 CDT)
  1. c00jsw00.vcf (879 bytes)
• acridine orange Rudra Banerjee (Thu Mar 19 2009 - 23:54:50 CDT)
  1. ao.pdf (4692 bytes)
• Re: Reference file for the constraining force in Umbrella Sampling Mert Gür (Sat Mar 14 2009 - 07:10:35 CDT)
  1. molcom.conf (4009 bytes)
• Re: topology and parameter file for FAD Schreiner Eduard (Sun Mar 01 2009 - 01:52:09 CST)
  1. Dagger.gif (105 bytes)
  2. Dagger.gif (105 bytes)
• Re: cgmd stability wang (Wed Feb 25 2009 - 21:43:41 CST)
  1. c00jsw00.vcf (879 bytes)
• Re: cgmd stability wang (Mon Feb 23 2009 - 23:49:47 CST)
  1. c00jsw00.vcf (864 bytes)
• RE: Autopsf error with a modified top file CHINDEA Vlad (Fri Feb 20 2009 - 19:28:28 CST)
  1. para.pdb (1585 bytes)
• (no subject) gurunath katagi (Fri Feb 20 2009 - 06:08:37 CST)
  1. sample.txt (8722 bytes)
  2. protein.conf (3925 bytes)
• Re: cgmd stability wang (Thu Feb 19 2009 - 03:15:56 CST)
  1. c00jsw00.vcf (879 bytes)
• Autopsf error with a modified top file CHINDEA Vlad (Wed Feb 18 2009 - 15:17:52 CST)
  1. top_para.inp (10344 bytes)
• tcl script fett_at_vtr.net (Mon Feb 02 2009 - 21:31:04 CST)
  1. kineticv2.tcl (3299 bytes)
• (no subject) OZGE ENGIN (Wed Jan 28 2009 - 03:29:03 CST)
  1. udp.psf (14881 bytes)
• Re: Inorganic compounds Chris Harrison (Wed Jan 14 2009 - 23:25:19 CST)
  1. image002.jpg (3133 bytes)
• Inorganic compounds Casey,Richard (Thu Jan 08 2009 - 12:20:34 CST)
  1. image002.jpg (3133 bytes)
  2. 4.jpg (30468 bytes)
• Re: namdcvs Achani.K.Yatawara_at_Dartmouth.edu (Mon Jan 05 2009 - 13:32:34 CST)
  1. massage (17679 bytes)
• Re: namd cvs compilation BIN ZHANG (Mon Dec 01 2008 - 11:59:39 CST)
  1. 1.conf (2321 bytes)
• H-bond occupancy in nucleic acids Tianjiao Wang (Thu Nov 20 2008 - 10:08:27 CST)
  1. hbonds.tcl (20260 bytes)
• ABF:problems with calculating Free Energy Profile supram_at_nankai.edu.cn (Sun Nov 16 2008 - 20:55:39 CST)
  1. bcdlglu.abf (14219 bytes)
• NAMD Simulation error Anirban Ghosh (Fri Nov 14 2008 - 02:36:16 CST)
  1. CG.conf (2737 bytes)
• NAMD Simulation error Anirban Ghosh (Wed Nov 12 2008 - 22:41:07 CST)
  1. CG.conf (2737 bytes)
• Re: Atoms moving too fast OR constraint failure in RATTLE algorithm Diego Alejandro Vargas (Sat Nov 08 2008 - 17:31:30 CST)
  1. ser39ala_wb_mn.xst (2047 bytes)
  2. ser39ala_wb_eq.xst (172 bytes)
• Re: ABF - using gyration Jerome Henin (Tue Oct 28 2008 - 15:11:43 CDT)
  1. abf_script.tcl (21731 bytes)
  2. gyration.tcl (2758 bytes)
• ABF backbone dihedral Sébastien Légaré (Tue Oct 28 2008 - 11:44:21 CDT)
  1. helix.tcl (8212 bytes)
• Backbone dihedral ABF Sébastien Légaré (Tue Oct 28 2008 - 11:50:02 CDT)
  1. helix.tcl (8212 bytes)
• Using NAMD to calculate pair energy with many subset permutations brmorgan_at_clarku.edu (Wed Oct 15 2008 - 13:08:42 CDT)
  1. energy_batch.namd (2557 bytes)
• Problem with creating psf file from structure made by inorganic builder Anneta Tzampazi (Fri Oct 03 2008 - 04:43:19 CDT)
  1. pyramida.top (317 bytes)
• FW: psf generation for a small non-peptide molecule - again CHINDEA Vlad (Mon Sep 29 2008 - 17:21:16 CDT)
  1. azi.pdb (11017 bytes)
  2. unk_azi.xbgf (1974 bytes)
• Namd water density jouko_at_uchicago.edu (Mon Sep 22 2008 - 21:36:11 CDT)
  1. bakforeq.conf.md (4458 bytes)
• Re: need help on CG modelling Nicolas Sapay (Mon Sep 22 2008 - 13:59:16 CDT)
  1. nsapay.vcf (283 bytes)
• Re: need help on CG modelling Nicolas Sapay (Mon Sep 22 2008 - 12:34:47 CDT)
  1. nsapay.vcf (283 bytes)
• TCL Forces : OUT OF MEMORY BIN ZHANG (Fri Sep 12 2008 - 13:38:17 CDT)
  1. derv.tcl (6532 bytes)
  2. wham_1d.tcl (2613 bytes)
• NAMD compilation / TACC Ranger Arturas Ziemys (Thu Aug 28 2008 - 11:25:14 CDT)
  1. Ranger-2.log.gz (5595 bytes)
• Re: How to write gradual heating config file Hyundeok Song (Mon Aug 25 2008 - 19:30:26 CDT)
  1. heat7.ps (14452 bytes)
• Re: unwanted bonds in .pdb file while using molefacture Subhashis Biswas (Wed Aug 06 2008 - 14:23:23 CDT)
  1. GCTiO2.pdb (9872 bytes)
• Constraining center of mass of monomers S.K. Ghosh (Wed Jul 16 2008 - 17:45:57 CDT)
  1. smd.tcl (1548 bytes)
• memory overflow problem of Tcl scripting when dealing with trajectories bo liu (Wed Jul 16 2008 - 03:16:31 CDT)
  1. dipole_profile.tcl (6794 bytes)
• Re: Rise in Total Energy in NVE S.K. Ghosh (Wed Jul 09 2008 - 10:25:35 CDT)
  1. energy.log (719 bytes)
• Running minimization, heating and FEP simulation within the same configuration file. Jawahar Neelankatan (Tue Jun 24 2008 - 20:28:21 CDT)
  1. min_heat_eq_FEP.conf (2590 bytes)
• Different Hbonds values on different machines using same script for same trajectories sunita gupta (Mon Jun 09 2008 - 02:29:57 CDT)
  1. hbonds.tcl (20260 bytes)
  2. hbonds1.txt (4685 bytes)
  3. hbonds2.txt (2876 bytes)
• Bond energy become Zero!!! Ming (Thu Jun 05 2008 - 04:17:01 CDT)
  1. CH4.top (2802 bytes)
  2. CH4.par (4084 bytes)
  3. CH4_try.psf (1092 bytes)
  4. CH4_try.pdb (452 bytes)
• Re: The correct topology/parameter file and pgn S.K. Ghosh (Wed Jun 04 2008 - 13:48:41 CDT)
  1. btn.inp (2912 bytes)
• Problem with TclBC when run in more than one processor fett_at_vtr.net (Wed Jun 04 2008 - 12:08:57 CDT)
  1. eF_water_test.conf (3874 bytes)
• Re: Error Parsing Config File MIke S (Mon May 26 2008 - 15:46:19 CDT)
  1. trial.conf (5718 bytes)
• Energy plot script Alexandre A. Vakhrouchev (Wed May 14 2008 - 22:11:19 CDT)
  1. plot_energy.sh.gz (1205 bytes)
• What does "cellOrigin" really mean? bo liu (Wed Apr 23 2008 - 05:48:45 CDT)
  1. pic1.JPG (21336 bytes)
• What does "cellOrigin" really mean? bo liu (Fri Apr 18 2008 - 09:38:56 CDT)
  1. pic1.JPG (21336 bytes)
• FEP: FATAL ERROR: Periodic cell has become too small for original patch grid! List (Wed Mar 12 2008 - 13:29:38 CDT)
  1. fep.conf (2878 bytes)
• NAMD stops running without error messages or termination Yinglong Miao (Mon Mar 03 2008 - 17:18:12 CST)
  1. NAMD.tcl (1904 bytes)
• protein_RNA simulation sripad chandan (Sat Mar 01 2008 - 08:43:22 CST)
  1. xmin.conf (2396 bytes)
  2. comp.pgn.txt (703 bytes)
• namd_minimize sripad chandan (Sun Feb 24 2008 - 10:51:47 CST)
  1. 1tbc_c_ws_eq.conf (1278 bytes)
• Alchemical FEP NAMD tutorial - problems with reproducing the results Jawahar Neelankatan (Mon Feb 18 2008 - 21:25:54 CST)
  1. tyr2ala.pdb (4637 bytes)
• ABF question Matthew Davies (Wed Feb 13 2008 - 11:00:44 CST)
  1. abf.dat (660 bytes)
• Re: catDCD 32 bit Vs. 64 bit Version Philip Peartree (Thu Feb 07 2008 - 09:28:15 CST)
  1. dcd_convert.tcl (202 bytes)
• how to minimize the energy of a protein using CHARMM FF in NAMD Kalyan chaitanya (Thu Feb 07 2008 - 09:29:08 CST)
  1. input-file.doc (26624 bytes)
  2. standard_parameter_file.txt (706 bytes)
• Tests not running for Charm++ Myrinet with MPICH-MX brmorgan_at_clarku.edu (Wed Jan 23 2008 - 14:35:05 CST)
  1. mach.sh (939 bytes)
• 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)
• 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)
• Simulating RNA+PROTEIN complexes Bartosz Dobrzelecki (Fri Dec 19 2003 - 14:30:23 CST)
  1. signature.asc (190 bytes)
• Re: Help! unstable simulation - ARG go nuts... Gadi Oron (Tue Dec 16 2003 - 09:33:25 CST)
  1. snap.png (53801 bytes)
• Re: Help! unstable simulation. Alexandre Vakhrouchev (Fri Dec 12 2003 - 03:16:55 CST)
  1. psf.log (5144 bytes)
• simulated annealing script Cheri M Turman (Thu Sep 25 2003 - 13:15:10 CDT)
  1. cturman.vcf (336 bytes)
• Re: Re: seg fault and namdplot problem Cheri M Turman (Mon Sep 22 2003 - 18:58:30 CDT)
  1. cturman.vcf (336 bytes)
• Re: seg fault and namdplot problem Cheri M Turman (Mon Sep 22 2003 - 16:22:46 CDT)
  1. cturman.vcf (336 bytes)
• segmentation fault Cheri M Turman (Tue Sep 16 2003 - 14:12:43 CDT)
  1. W1A1_wb.log (15255 bytes)
  2. cturman.vcf (336 bytes)

Last message date: Wed Feb 29 2012 - 01:22:45 CST
Archived on: Wed Feb 29 2012 - 05:24:56 CST

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