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NAMD-L: By messages with attachments

By messages with attachments

4370 messages sorted by: [ author ] [ date ] [ thread ] [ subject ]
About this archive

Starting: Fri Jan 01 2010 - 09:55:54 CST
Ending: Sat Dec 31 2011 - 05:23:47 CST

• 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)

Last message date: Sat Dec 31 2011 - 05:23:47 CST
Archived on: Wed Feb 29 2012 - 15:58:04 CST

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