VMD-L Mailing List

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About this archive

Starting: Thu Dec 19 1996 - 11:40:41 CST
Ending: Wed Sep 20 2017 - 02:37:44 CDT

Unable to visualize the solid isosurfaces Shivanand Malaganvi (Tue Sep 12 2017 - 10:46:00 CDT)
1. RDGfill.vmd (332 bytes)
Cannot show the simulation box lan hoa Trinh (Thu Aug 31 2017 - 17:21:01 CDT)
1. equil.gro (8676 bytes)
Unable to visualize the solid isosurfaces Shivanand Malaganvi (Wed Aug 30 2017 - 07:12:33 CDT)
1. RDGfill.vmd (332 bytes)
Re: Problem loading Amber trajectory Axel Kohlmeyer (Sun Aug 13 2017 - 09:22:54 CDT)
1. 1.png (17975 bytes)
Re: Building HMMM using patch files Vermaas, Joshua (Wed Aug 09 2017 - 18:09:02 CDT)
1. scse.prm (768 bytes)
2. scse.rtf (355 bytes)
Re: FFTk, dihedral optimization Mayne, Christopher G (Sat Jul 29 2017 - 10:10:51 CDT)
1. smime.p7s (1735 bytes)
Re: FFTk, dihedral optimization RAHUL SURESH (Sat Jul 29 2017 - 10:04:57 CDT)
1. errorlog.txt (8468 bytes)
Re: FFTk, dihedral optimization Mayne, Christopher G (Sat Jul 29 2017 - 09:43:05 CDT)
1. smime.p7s (1735 bytes)
Re: ffTK: neutral pyruvate group and charged pyruvate group at beta-D-mannose Mayne, Christopher G (Thu Jul 27 2017 - 22:52:49 CDT)
1. smime.p7s (1735 bytes)
Re: fftk - MM/QM distances not converging Mayne, Christopher G (Mon Jul 24 2017 - 22:28:54 CDT)
1. smime.p7s (1735 bytes)
Re: Building HMMM using patch files Vermaas, Joshua (Thu Jul 20 2017 - 16:35:15 CDT)
1. charmmgui2hmmm.tcl (6854 bytes)
Re: VMD crashed during reading the trajectory file Pawel Kedzierski (Sat Jun 10 2017 - 05:33:58 CDT)
1. pawel_kedzierski.vcf (571 bytes)
Fwd: vmd-1 Sharav Desai (Tue Apr 11 2017 - 03:32:09 CDT)
1. ResNmae.log (1052 bytes)
psfgen giving wrong structure in the autopdb file Harish Srinivasan (Thu Apr 06 2017 - 01:37:29 CDT)
1. dodecylsulphate.rtf (2285 bytes)
2. dodecylsulphate2.pdb (7440 bytes)
3. dodecylsulphate2_autopsf.psf (9768 bytes)
4. dodecylsulphate2_autopsf.pdb (3368 bytes)
Re: psfgen error with charmm36 parameters? Pawel Kedzierski (Wed Apr 05 2017 - 06:23:50 CDT)
1. pawel_kedzierski.vcf (571 bytes)
Re: vicinity analysis Ramon GuixÃ (Fri Mar 31 2017 - 09:06:56 CDT)
1. image.png (10859 bytes)
2. image.png (9066 bytes)
Re: vicinity analysis Ramon GuixÃ (Fri Mar 31 2017 - 05:05:50 CDT)
1. image.png (9066 bytes)
2. image.png (10859 bytes)
Re: vicinity analysis Udit Aswal (Fri Mar 31 2017 - 04:32:20 CDT)
1. image.png (9066 bytes)
2. image.png (10859 bytes)
AW: Building NAMD 2.12 from Source with IB and CUDA Greipel.Joachim_at_mh-hannover.de (Thu Mar 02 2017 - 05:53:58 CST)
1. smime.p7s (5980 bytes)
Building NAMD 2.12 from Source with IB and CUDA Greipel.Joachim_at_mh-hannover.de (Thu Mar 02 2017 - 02:57:01 CST)
1. smime.p7s (5980 bytes)
How to remove rmsd spikes due to PB zoran matovic (Sat Feb 25 2017 - 13:40:12 CST)
1. rmsd_protein.png (22205 bytes)
.gro files written with python script not displayed until strange modification Benjamin Joseph Coscia (Thu Feb 02 2017 - 14:51:44 CST)
1. build.py (20902 bytes)
Re: colvars module Stefano Guglielmo (Mon Jan 30 2017 - 16:05:23 CST)
1. frame_energy_output (10255 bytes)
Running out of memory due to multiple mol addfile's (?) Alexander Balaeff (Fri Jan 27 2017 - 00:03:15 CST)
1. RMSD_map.tcl (3165 bytes)
AW: Quad buffered stereo from Quadro M4000 to HDMI monitor Greipel.Joachim_at_mh-hannover.de (Tue Jan 17 2017 - 07:12:12 CST)
1. smime.p7s (5722 bytes)
Analyzing results of simulation done by gromacs maria khan (Fri Jan 13 2017 - 15:44:31 CST)
1. dipole.agr (69 bytes)
2. multiplot.agr (111 bytes)
Re: compiling VMD 1.9.3 with OSPRay support John Stone (Tue Jan 10 2017 - 07:59:38 CST)
1. OSPRayRenderer.C.gz (20734 bytes)
Re: AW: why vmd cannot load the dcd trajectory? Ashar Malik (Tue Jan 10 2017 - 04:18:44 CST)
1. image001.png (8788 bytes)
AW: AW: why vmd cannot load the dcd trajectory? Norman Geist (Tue Jan 10 2017 - 03:18:54 CST)
1. image001.png (8788 bytes)
Re: AW: why vmd cannot load the dcd trajectory? sunyeping (Tue Jan 10 2017 - 03:03:47 CST)
1. part (8788 bytes)
AW: why vmd cannot load the dcd trajectory? Norman Geist (Tue Jan 10 2017 - 02:43:17 CST)
1. image001.png (8788 bytes)
why vmd cannot load the dcd trajectory? sunyeping (Tue Jan 10 2017 - 01:06:08 CST)
1. part (8788 bytes)
Some macOS code simplification FX (Fri Dec 02 2016 - 07:42:09 CST)
1. vmd_macos.diff (12504 bytes)
Re: X3D render NewRibbons only in blue Jean Richelle (Fri Nov 25 2016 - 08:59:19 CST)
1. signature.asc (204 bytes)
Re: Close contacts upon solvation of XYZ file. Pawel Kedzierski (Fri Nov 25 2016 - 03:20:37 CST)
1. pawel_kedzierski.vcf (571 bytes)
Re: VMD problems on Linux Cinnamon Mint (Sarah) Madaras ErzsÃ©bet (Fri Nov 25 2016 - 02:12:59 CST)
1. .vmdrc (1813 bytes)
Re: Close contacts upon solvation of XYZ file. Pawel Kedzierski (Fri Nov 25 2016 - 01:27:57 CST)
1. pawel_kedzierski.vcf (571 bytes)
Re: X3D render NewRibbons only in blue Jean Richelle (Thu Nov 24 2016 - 10:04:44 CST)
1. signature.asc (204 bytes)
X3D render NewRibbons only in blue Jean Richelle (Wed Nov 23 2016 - 00:19:29 CST)
1. signature.asc (204 bytes)
error loading PDB Anna Lohning (Tue Nov 22 2016 - 00:56:00 CST)
1. Picture__Device_Independent_Bitmap__1.jpg (1024 bytes)
2. Picture__Device_Independent_Bitmap__2.jpg (998 bytes)
3. Picture__Device_Independent_Bitmap__3.jpg (1011 bytes)
4. Picture__Device_Independent_Bitmap__4.jpg (1014 bytes)
5. Picture__Device_Independent_Bitmap__5.jpg (964 bytes)
6. Picture__Device_Independent_Bitmap__6.jpg (1000 bytes)
7. Picture__Device_Independent_Bitmap__7.jpg (971 bytes)
8. Picture__Device_Independent_Bitmap__8.jpg (3454 bytes)
Re: MD movie making of fluent movements Ajasja LjubetiÄ (Fri Nov 04 2016 - 05:54:32 CDT)
1. image.png (14415 bytes)
The new molecule file browser M K (Fri Oct 28 2016 - 20:51:59 CDT)
1. browser.png (21997 bytes)
Re: using vslab in vmd Anjela Manandhar (Mon Aug 15 2016 - 09:45:56 CDT)
1. .vmdrc (614 bytes)
Re: VMD window turning black with Nvidia 3d vision on ASUS monitor Matic Kisovec (Thu Jul 14 2016 - 01:53:27 CDT)
1. matic_kisovec.vcf (348 bytes)
Re: VMD called from python hangs on Windows Pawel Kedzierski (Wed Jul 13 2016 - 03:46:22 CDT)
1. pawel_kedzierski.vcf (571 bytes)
VMD called from python hangs on Windows Pawel Kedzierski (Mon Jul 11 2016 - 15:35:40 CDT)
1. pawel_kedzierski.vcf (571 bytes)
Re: Installing VMD-1.9.2 in Ubuntu 16.04-32bit Matic Kisovec (Mon Jul 04 2016 - 06:09:12 CDT)
1. matic_kisovec.vcf (348 bytes)
Re: generating autopsf Pawel Kedzierski (Tue Jun 28 2016 - 15:10:23 CDT)
1. pawel_kedzierski.vcf (571 bytes)
generating autopsf Tahmina Akter (Tue Jun 28 2016 - 13:07:20 CDT)
1. 06-28_14:01:26.png (15335 bytes)
ffTK fitting dihedrals Seth Axen (Tue May 17 2016 - 13:23:41 CDT)
1. multiplot.png (25517 bytes)
Re: Re: FFTK dihedral fitting Mohan maruthi sena (Thu Mar 31 2016 - 22:55:00 CDT)
1. test1.png (11648 bytes)
FFTK dihedral fitting Mohan maruthi sena (Wed Mar 30 2016 - 09:37:49 CDT)
1. test_ml.png (3519 bytes)
Re: How to work on multiple pdbs by tcl script? Ajasja LjubetiÄ (Tue Mar 22 2016 - 05:26:44 CDT)
1. clone_reps.tcl (1727 bytes)
Re: default drawing style Pawel Kedzierski (Fri Mar 18 2016 - 05:44:07 CDT)
1. pawel_kedzierski.vcf (571 bytes)
Fwd: ISQBP 2016 meeting - registration opened! Vlad Cojocaru (Mon Mar 14 2016 - 03:13:37 CDT)
1. Attached_Message_Part (135 bytes)
Re: default drawing style Pawel Kedzierski (Fri Mar 11 2016 - 02:43:29 CST)
1. pawel_kedzierski.vcf (571 bytes)
NAMD 2.11 Cuda does not work with Quadro FX 3800 Greipel.Joachim_at_mh-hannover.de (Thu Mar 10 2016 - 01:57:06 CST)
1. smime.p7s (5649 bytes)
AW: WG: vmd and proxy settings Greipel.Joachim_at_mh-hannover.de (Thu Mar 03 2016 - 01:12:02 CST)
1. smime.p7s (5649 bytes)
WG: vmd and proxy settings Greipel.Joachim_at_mh-hannover.de (Wed Mar 02 2016 - 03:58:28 CST)
1. smime.p7s (5649 bytes)
AW: vmd and proxy settings Greipel.Joachim_at_mh-hannover.de (Wed Mar 02 2016 - 03:42:26 CST)
1. smime.p7s (5649 bytes)
AW: vmd and proxy settings Greipel.Joachim_at_mh-hannover.de (Wed Mar 02 2016 - 01:21:53 CST)
1. smime.p7s (5649 bytes)
vmd and proxy settings Greipel.Joachim_at_mh-hannover.de (Tue Mar 01 2016 - 05:59:03 CST)
1. smime.p7s (5649 bytes)
RE: Unable to access config file Richard Wood (Fri Dec 11 2015 - 11:32:04 CST)
1. image.png (13390 bytes)
Re: Unable to access config file Ajasja LjubetiÄ (Fri Dec 11 2015 - 11:24:18 CST)
1. image.png (13390 bytes)
Re: Unable to access config file Pawel Kedzierski (Fri Dec 11 2015 - 03:52:26 CST)
1. pawel_kedzierski.vcf (571 bytes)
RE: Problem visualizing a pdbqt file generated by AutoDockTools Bennion, Brian (Wed Dec 02 2015 - 17:41:25 CST)
1. forJohn.pdbqt (7760 bytes)
FFTK dihedral scan Chitrak Gupta (Wed Nov 18 2015 - 08:07:57 CST)
1. Fitting.pdf (5915 bytes)
Re: what is difference between "TOTAL", Q=80=9cTOTAL2=22_and_=22POTENTIAL=22_in_the_VMD_plugin_NAMD_Plo?= t? Pawel Kedzierski (Mon Nov 09 2015 - 04:09:48 CST)
1. pawel_kedzierski.vcf (571 bytes)
Re: Charge optimization in ffTK Pawel Kedzierski (Thu Nov 05 2015 - 02:04:17 CST)
1. pawel_kedzierski.vcf (571 bytes)
Re: Problem of VMD in ubuntu 14.04 Pawel Kedzierski (Fri Oct 23 2015 - 08:31:27 CDT)
1. pawel_kedzierski.vcf (571 bytes)
Re: Problem of VMD in ubuntu 14.04 Pawel Kedzierski (Fri Oct 23 2015 - 06:43:31 CDT)
1. pawel_kedzierski.vcf (571 bytes)
Re: Problem of VMD in ubuntu 14.04 Pawel Kedzierski (Fri Oct 23 2015 - 03:17:14 CDT)
1. pawel_kedzierski.vcf (571 bytes)
VMD: Problems loading PDB Files from behind a proxy server Greipel.Joachim_at_mh-hannover.de (Fri Oct 23 2015 - 01:15:53 CDT)
1. smime.p7s (5649 bytes)
Re: Problems with S-Adenosyl-L-Methionine / SAM Topology & Parameter for MD simulations Pawel Kedzierski (Sun Oct 11 2015 - 08:33:33 CDT)
1. pawel_kedzierski.vcf (571 bytes)
Problems with S-Adenosyl-L-Methionine / SAM Topology & Parameter for MD simulations Daan Mevius (Sun Oct 11 2015 - 06:20:19 CDT)
1. SET-Crystalstructure-original-nowater_autopsf-solvate-namd.out.txt (4363 bytes)
2. SET-Crystalstructure-original-nowater_autopsf-solvate-namd.namd.txt (1971 bytes)
3. paper-SAMplusfluo-topologyrtf.txt (3134 bytes)
4. paper-parameters.txt (1647 bytes)
Re: FFTK Bond optimization Chitrak Gupta (Fri Sep 25 2015 - 15:43:45 CDT)
1. multiplot.pdf (7323 bytes)
ffTK: Charge optimization Amy Rice (Thu Sep 17 2015 - 14:39:05 CDT)
1. m_arginine_files.zip (4423 bytes)
Re: How to extract data from NAMD log file for viscosity calculation Pawel Kedzierski (Wed Aug 19 2015 - 09:23:22 CDT)
1. pawel_kedzierski.vcf (571 bytes)
VMD movie error Kshatresh Dutta Dubey (Tue Aug 04 2015 - 17:00:51 CDT)
1. error.log (989 bytes)
RE: Generating PSF for several proteins in one shot Matthew Stewart (Fri Jul 24 2015 - 01:25:58 CDT)
1. image001.jpg (7339 bytes)
vmd error xMDFF CPMAS Chen (Thu Jun 11 2015 - 14:34:51 CDT)
1. step1.log (3358 bytes)
2. step1.namd (1807 bytes)
very high vdw and electrostatic energy for bulk urea molecules Subrata Paul (Tue May 19 2015 - 01:04:43 CDT)
1. 05-19_01:40:10.png (16839 bytes)
Re: Running 64-bit Linux VMD in VMWare VM on Windows 8.1 64-bit Host Machine Matic Kisovec (Fri May 15 2015 - 10:53:33 CDT)
1. matic_kisovec.vcf (348 bytes)
Re: AW: Problem with assignation of secondary structure in VMD Matic Kisovec (Thu May 07 2015 - 07:48:28 CDT)
1. matic_kisovec.vcf (348 bytes)
Re: AW: Problem with assignation of secondary structure in VMD Matic Kisovec (Thu May 07 2015 - 00:41:07 CDT)
1. matic_kisovec.vcf (348 bytes)
Problem with assignation of secondary structure in VMD Matic Kisovec (Wed May 06 2015 - 06:29:20 CDT)
1. matic_kisovec.vcf (348 bytes)
Re: Error on fftk while optimizing bonded parameters Hyunjin Kim (Mon May 04 2015 - 11:37:38 CDT)
1. ba.log (1304 bytes)
Re: Setting up a truncation cutoff fro volumetric data Axel Kohlmeyer (Tue Apr 28 2015 - 10:41:55 CDT)
1. trimcube.c.gz (3087 bytes)
Re: Error saying "too many open files" Monika Madhavi (Mon Apr 20 2015 - 01:56:32 CDT)
1. tracemol.tcl (2513 bytes)
Valbond and NAMD zoran (Thu Apr 16 2015 - 07:11:37 CDT)
1. zoran_matovic_matovic.vcf (763 bytes)
Re: using namdstats.tcl John Stone (Sat Apr 11 2015 - 13:13:26 CDT)
1. namdstats.tcl (3794 bytes)
VMD 1.9.3 alpha Matic Kisovec (Fri Mar 27 2015 - 07:58:47 CDT)
1. matic_kisovec.vcf (348 bytes)
Problem with generating psf and pdb files of metalloprotein made up of two fragments zoran (Thu Mar 26 2015 - 13:45:59 CDT)
1. zoran_matovic_matovi__.vcf (763 bytes)
Re: Hydration Shell RDF -- VMD Nomenclature Needed Jim Parker (Mon Mar 02 2015 - 21:20:19 CST)
1. image003.jpg (5149 bytes)
Hydration Shell RDF -- VMD Nomenclature Needed Phelan Jr., Frederick R. Dr. (Mon Feb 23 2015 - 15:31:03 CST)
1. image003.jpg (5149 bytes)
FFTK scan torsions question Elena Lilkova (Tue Feb 17 2015 - 07:46:06 CST)
1. model_charges.psf (8384 bytes)
2. opt.pdb (2287 bytes)
3. for_optimization_ba.par (3227 bytes)
FW: Feature request: read environment to set FreeVR lib, include paths Stock, Mark (Fri Feb 13 2015 - 12:07:56 CST)
1. mstockvmd.patch (1218 bytes)
Re: NAMDEnergy fails to locate supporting files Viswanath Pasumarthi (Thu Feb 12 2015 - 03:15:21 CST)
1. IntEnergy.tcl (229 bytes)
2. temp.namd (942 bytes)
3. temp.log (3655 bytes)
Re: VMD Segmentation fault (core dumped) Matic Kisovec (Thu Jan 29 2015 - 05:51:02 CST)
1. matic_kisovec.vcf (348 bytes)
VMD Segmentation fault (core dumped) Matic Kisovec (Wed Jan 28 2015 - 09:53:11 CST)
1. matic_kisovec.vcf (348 bytes)
Re: Re: FFTK work's with molecules containing new atom types zoran (Tue Dec 16 2014 - 09:42:00 CST)
1. obp.pdb (2783 bytes)
FFTK work's with molecules containing new atom types zoran (Mon Dec 15 2014 - 17:57:28 CST)
1. zoran_matovic_matovic.vcf (763 bytes)
Re: How find water mediated hydrogen bond zoran (Thu Dec 11 2014 - 06:26:39 CST)
1. zoran_matovic_matovi__.vcf (763 bytes)
fftk-bonded-opt problem zoran (Thu Dec 11 2014 - 03:30:25 CST)
1. zoran_matovic_matovi__.vcf (763 bytes)
fftk problem - opt_bonded zoran (Mon Dec 08 2014 - 06:39:38 CST)
1. zoran_matovic_matovi__.vcf (763 bytes)
2. opt.pdb (2052 bytes)
3. log.log (8667 bytes)
Re: Fwd: namd-l: Why RDF increases as r increase instead of constant Nifeng Guo hui (Mon Nov 03 2014 - 15:29:25 CST)
1. name_OH.png (7083 bytes)
Re: Fwd: namd-l: Why RDF increases as r increase instead of constant Nifeng Guo hui (Sun Nov 02 2014 - 22:19:43 CST)
1. RDF.png (7444 bytes)
Fwd: namd-l: Why RDF increases as r increase instead of constant Nifeng Guo hui (Sun Nov 02 2014 - 16:01:29 CST)
1. RDF.png (9094 bytes)
Compiling VMD for Windows 64bit Nima Nouri (Fri Oct 03 2014 - 15:08:15 CDT)
1. image.png (14318 bytes)
Problem with TIP3 angles during phosphorylation Thierry Oscar Wambo (Fri Sep 26 2014 - 08:04:18 CDT)
1. Error (2584 bytes)
Solvate Plugin: Why "Rotate to minimize volume" along 2 instead of 3 axes? Sebastian Stolzenberg (Mon Sep 22 2014 - 09:59:35 CDT)
1. solvate_rotate_zx_vs_solvate_rotate_zxy.tcl (2144 bytes)
using vmd to apply symmetry operators part 2 Bennion, Brian (Thu Sep 18 2014 - 17:21:43 CDT)
1. unitCellCalcs.png (363295 bytes)
strange behavior of render command Philippe Bopp (Thu Aug 28 2014 - 10:57:33 CDT)
1. test5.tga (18 bytes)
2. input.tcl (86 bytes)
3. carfiles.vmd (24745 bytes)
Re: MDFF simulations Ryan McGreevy (Tue Aug 12 2014 - 11:31:31 CDT)
1. move_dx.tcl (1342 bytes)
Re: color scale definitions with more than three colors? John Stone (Thu Jul 31 2014 - 12:58:37 CDT)
1. matlab_colorscale.tcl (13793 bytes)
Re: .obj Oddity Darrell Kuykendall (Thu Jul 24 2014 - 13:57:16 CDT)
1. Ethylene_log_vmd.zip (20192 bytes)
Fwd: Visualizing the displacement vector karthik kumar (Fri Jul 04 2014 - 09:28:07 CDT)
1. VIB1.log (19250 bytes)
Re: How do i merge files with mergemols Ashish .Chauniyal (Thu May 01 2014 - 05:39:14 CDT)
1. log (2662 bytes)
2. jointhem.tcl (519 bytes)
Re: Changing the Font size of the XYZ Logo Mehdi Eftekhari (Fri Apr 11 2014 - 12:00:25 CDT)
1. 11-2014_9-24-13_PM.jpg (4329 bytes)
ffTK generated Gaussian file puts "atoms too close" and Gaussian fails to run Jim Parker (Fri Apr 04 2014 - 05:42:33 CDT)
1. opt.pdb (6212 bytes)
2. DON-HA.gau (5109 bytes)
Fedora 20 x86_64 + ibus + sazanami fonts + GNOME => VMD 1.9.1 crashes René Genz (Sun Mar 09 2014 - 08:51:55 CDT)
1. 191-on-Fedora20.tar.gz (2973 bytes)
Compile VMD saeed (Wed Mar 05 2014 - 09:52:59 CST)
1. Makefile (13319 bytes)
Re: Security problem? Olaf Lenz (Fri Feb 21 2014 - 03:20:39 CST)
1. vmd.patch (926 bytes)
RDF calculation . Juita (Mon Jan 13 2014 - 18:27:09 CST)
1. 33ps.out.xyz (12407 bytes)
Issues with tachyon internal renderer Tyler Smith (Fri Jan 03 2014 - 14:19:36 CST)
1. dynamic_CCE_movie_TachyonInternal.cpp (5352 bytes)
2. dynamic_CCE_movie_snapshot.cpp (5311 bytes)
Re: Domain Error while using ParseFEP plugin Shyno Mathew (Mon Dec 09 2013 - 11:01:38 CST)
1. error.log (906 bytes)
Re: Domain Error while using ParseFEP plugin Shyno Mathew (Sun Dec 08 2013 - 22:40:58 CST)
1. errornew.log (906 bytes)
script to draw lines between labelled atoms david MARTROU (Wed Nov 27 2013 - 07:30:07 CST)
1. draw_line_between_labelled_atom.tcl (1713 bytes)
script to draw lines between labelled atoms david MARTROU (Wed Nov 27 2013 - 05:26:21 CST)
1. draw_line_between_labelled_atom.tcl (1672 bytes)
Re: "measure symmetry" and SymmetryTools fail to find simple symmetry FX (Fri Nov 22 2013 - 07:13:43 CST)
1. symmetry.diff (3252 bytes)
issues rendering images Tyler Smith (Mon Nov 18 2013 - 18:40:48 CST)
1. Tachyon_Internal_error.txt (2258 bytes)
2. snapshot_error.txt (1801 bytes)
genetaring psf file for HEME ( hemoglobin) Ramin Ekhteiari (Tue Nov 05 2013 - 03:15:07 CST)
1. new.zip (7234 bytes)
RE: writing PDB Matthew Stewart (Thu Oct 24 2013 - 18:30:51 CDT)
1. image001.jpg (7339 bytes)
psfgen forces to apply terminils to peptide Wanzhi Qiu (Thu Oct 10 2013 - 00:11:40 CDT)
1. c1_fix.pdb (4680 bytes)
Finding particles that are close Olaf Lenz (Tue Oct 08 2013 - 03:31:45 CDT)
1. olenz.vcf (409 bytes)
Re: viewing bond between two hydrogens on a water molecule Axel Kohlmeyer (Mon Oct 07 2013 - 10:25:03 CDT)
1. fixamberwater.tcl (903 bytes)
Re: Incompatible cubefiles (G09revD.01 cubegen) Axel Kohlmeyer (Tue Sep 24 2013 - 04:59:00 CDT)
1. cubeplugin.so.gz (17883 bytes)
making patch rasti_at_ut.ac.ir (Tue Aug 27 2013 - 18:41:06 CDT)
1. 2 (463 bytes)
Re: remove vmd in ubuntu Olaf Lenz (Mon Jul 29 2013 - 01:50:58 CDT)
1. olenz.vcf (409 bytes)
AW: WG: VMD mismatch between CUDA runtime and GPU driver Greipel.Joachim_at_mh-hannover.de (Fri Jul 19 2013 - 01:04:54 CDT)
1. smime.p7s (5531 bytes)
WG: VMD mismatch between CUDA runtime and GPU driver Greipel.Joachim_at_mh-hannover.de (Thu Jul 18 2013 - 02:24:18 CDT)
1. smime.p7s (5531 bytes)
VMD mismatch between CUDA runtime and GPU driver Greipel.Joachim_at_mh-hannover.de (Thu Jul 18 2013 - 02:01:31 CDT)
1. smime.p7s (5531 bytes)
VMD shows there's a H-BOND between Carbon and Hydrogen? Hovakim Grabski (Sat Jun 29 2013 - 05:47:02 CDT)
1. smime.p7s (1484 bytes)
RE: dynamic cross correlation map Mark Cunningham (Wed May 15 2013 - 10:58:17 CDT)
1. cross_corr2.tcl (9656 bytes)
2. ccplot.m (1397 bytes)
3. build_index.m (4697 bytes)
4. build_reg.m (2708 bytes)
5. read_ccmat.m (745 bytes)
6. parse_head.m (459 bytes)
7. rpimage.m (1957 bytes)
Re: ellipsoidal particles Axel Kohlmeyer (Mon Apr 22 2013 - 02:42:08 CDT)
1. ellipsoid.tcl (5459 bytes)
Re: problem about displaying hbond in periodic box Axel Kohlmeyer (Tue Apr 16 2013 - 04:41:53 CDT)
1. 1.png (18192 bytes)
problem about displaying hbond in periodic box yi (Tue Apr 16 2013 - 04:22:06 CDT)
1. 1.png (18192 bytes)
Re: Disable display resetview Axel Kohlmeyer (Thu Apr 04 2013 - 02:17:46 CDT)
1. reload.tcl (1278 bytes)
bug in xsfplugin [patch included] Roberto Guerra (Sat Mar 30 2013 - 19:55:43 CDT)
1. a.xsf (200 bytes)
2. b.xsf (233 bytes)
Re: FFTK... and now gaussian version or QMtool problem PaweÅ‚ KÄ™dzierski (Thu Mar 28 2013 - 09:25:50 CDT)
1. qmtool01.patch (460 bytes)
atomselect within a loop Yohann Morille (Mon Mar 18 2013 - 06:17:15 CDT)
1. pdbbfactormodif.tcl (806 bytes)
2. test.pdb (1383 bytes)
RE: how to plot per-atom field variable peter.schmidtke_at_fr.netgrs.com (Mon Jan 07 2013 - 02:56:30 CST)
1. loadInteractionEnergiesToVMD.tcl (1174 bytes)
cant open .car file Erik (Fri Nov 30 2012 - 12:25:30 CST)
1. O2.car (1855 bytes)
Re: Question regarding dihedral fitting using fftk Erik (Fri Nov 30 2012 - 12:24:42 CST)
1. O2.car (1855 bytes)
Re: How do I make sure the normals value of trinorms? Axel Kohlmeyer (Thu Nov 29 2012 - 08:36:17 CST)
1. ellipsoid.tcl (5459 bytes)
Re: vmd cause linux system freezes randomly Kasra Fattah (Wed Nov 07 2012 - 23:03:50 CST)
1. glxinfo.txt (18893 bytes)
How to disable CUDA in VMD 1.9.1? Joakim Swedberg (Sun Sep 16 2012 - 21:48:38 CDT)
1. image001.jpg (9583 bytes)
Re: Python plans Olaf Lenz (Wed Jul 25 2012 - 03:07:49 CDT)
1. olenz.vcf (409 bytes)
Re: Secondary Structure Issue John Stone (Wed Jul 18 2012 - 09:57:28 CDT)
1. fillasn.c (17044 bytes)
Re: periodic bonds in vmd Olaf Lenz (Tue Jul 17 2012 - 14:15:45 CDT)
1. olenz.vcf (409 bytes)
Building unit cell from asymmetric unit Sebastián Gutiérrez (Wed Jul 04 2012 - 17:16:32 CDT)
1. 300Kmod.pdb (2763 bytes)
Re: Running ProcupinePlot script Ban Arn (Fri Jun 22 2012 - 11:53:33 CDT)
1. procupine_plot.tcl (10732 bytes)
generating psf files for bicarbonate Traci Clymer (Fri Jun 22 2012 - 09:13:36 CDT)
1. BCT_VMD.pdb (466 bytes)
2. bct.pgn (145 bytes)
Workshop for Computational Chemistry and Physics MARK PLUMMER (Wed Jun 20 2012 - 15:20:40 CDT)
1. Advertising_Statement_for_2013_ACP_Workshop_final.docx (17252 bytes)
Workshop - Computational Molecular Physics of Non-Bonded Bio-Molecular Interactions MARK PLUMMER (Mon Jun 11 2012 - 17:16:47 CDT)
1. Advertising_Statement_for_2013_ACP_Workshop_final.docx (17224 bytes)
Re: Drawing an ellipsoid John Stone (Thu Jun 07 2012 - 15:11:19 CDT)
1. ellipse.tcl (3260 bytes)
hbonds vs time Subrata Paul (Thu May 31 2012 - 10:40:13 CDT)
1. numHbonds.dat (1164 bytes)
Re: Fw: pbc-box Olaf Lenz (Tue May 22 2012 - 02:42:45 CDT)
1. olenz.vcf (376 bytes)
2. signature.asc (263 bytes)
N-methylated amino acid topologies Joakim Swedberg (Wed May 02 2012 - 19:20:41 CDT)
1. image001.jpg (9583 bytes)
writing pair/bond/angle/dihedral information for lammps input winardi, erik (Sun Apr 29 2012 - 17:17:14 CDT)
1. 2p_6f.car (3321 bytes)
Re:Problem with generating psf using CGENFF amin_at_imtech.res.in (Fri Apr 27 2012 - 22:46:21 CDT)
1. ign-cgenff.rtf (15102 bytes)
2. ign.psf (9477 bytes)
3. ign.pdb (3368 bytes)
4. ign.pgn (197 bytes)
Re:Problem with generating psf using CGENFF amin_at_imtech.res.in (Fri Apr 27 2012 - 22:35:16 CDT)
1. ign-cgenff.rtf (15102 bytes)
2. ign.psf (9477 bytes)
3. ign.pdb (3368 bytes)
Problem with generating psf using CGENFF amin_at_imtech.res.in (Thu Apr 26 2012 - 04:42:40 CDT)
1. ign-cgenff.rtf (15102 bytes)
2. ign.psf (9477 bytes)
3. ign.pdb (3368 bytes)
4. ign.pgn (197 bytes)
Misfunction of some plugins if compiled Vlastimil ZÃma (Tue Apr 17 2012 - 12:28:10 CDT)
1. 04-17_19:17:04.png (8622 bytes)
problems with MDFF Gregorio Fernandez (Fri Apr 06 2012 - 02:42:22 CDT)
1. error_file.log (5097 bytes)
Re: starting tkcon Olaf Lenz (Wed Mar 21 2012 - 11:56:20 CDT)
1. olenz.vcf (376 bytes)
2. signature.asc (263 bytes)
How to change the python include and linkage path in configure script Haw-Zan Goh (Mon Feb 27 2012 - 12:15:06 CST)
1. _2_.html (2870 bytes)
mono2poly question Joseph Bylund (Sun Feb 26 2012 - 23:24:00 CST)
1. signature.asc (555 bytes)
pdb reader/writer appears to corrupt pdb output Bennion, Brian (Thu Feb 16 2012 - 14:49:06 CST)
1. temp1.pdb (1895 bytes)
2. temp2.pdb (1971 bytes)
charge visualization niladri patra (Tue Feb 07 2012 - 18:41:37 CST)
1. vmd.xyz (1051 bytes)
Re: Coloring by RMSD during trajectory John Stone (Thu Feb 02 2012 - 00:00:15 CST)
1. residue_rmsd.tcl (1556 bytes)
Re: VMD 1.9.1 beta 2 to be posted tonight... Ajasja LjubetiÄ (Thu Jan 26 2012 - 03:04:29 CST)
1. image.png (16672 bytes)
Use "Metal complexes/FeS-clusters" in VMD paratool Jiajian Li (Wed Jan 18 2012 - 16:01:10 CST)
1. base_mol.pdb (4025 bytes)
Re: VMD 1.9.1 beta 1 posted for download... Bjoern Olausson (Tue Jan 03 2012 - 01:32:26 CST)
1. signature.asc (199 bytes)
Re: Change Color Scale John Stone (Wed Dec 21 2011 - 15:09:09 CST)
1. matlab_colorscale.tcl (13781 bytes)
Re: Protein-ligand contact Dong Luo (Wed Dec 21 2011 - 11:13:26 CST)
1. contactFreq.tcl (1908 bytes)
Re: Povray renders labels always centered Bjoern Olausson (Tue Dec 13 2011 - 09:31:52 CST)
1. signature.asc (199 bytes)
Povray renders labels always centered Bjoern Olausson (Mon Dec 12 2011 - 01:37:04 CST)
1. signature.asc (199 bytes)
Re: TCL strangeness Ben Roberts (Thu Dec 08 2011 - 21:17:45 CST)
1. smime.p7s (2595 bytes)
Re: Rendering long and high-quality movies from VMD Bjoern Olausson (Wed Dec 07 2011 - 10:58:01 CST)
1. signature.asc_ (199 bytes)
Re: convertind dcd to xyz file Thomas Bishop (Mon Dec 05 2011 - 08:54:11 CST)
1. dcd2pdb.vmd (671 bytes)
Improve OFF plugin: handle colors FX (Mon Dec 05 2011 - 07:20:06 CST)
1. offplugin.C (10255 bytes)
2. tri.off (55 bytes)
3. cube.off (156 bytes)
Re: VMD never finishes reading vis. state file, stalls and hoggs CPU Bjoern Olausson (Wed Nov 30 2011 - 10:11:53 CST)
1. signature.asc_ (199 bytes)
Re: VMD never finishes reading vis. state file, stalls and hoggs CPU Bjoern Olausson (Mon Nov 28 2011 - 02:54:17 CST)
1. signature.asc_ (199 bytes)
Re: VMD never finishes reading vis. state file, stalls and hoggs CPU Bjoern Olausson (Fri Nov 25 2011 - 05:36:26 CST)
1. signature.asc_ (199 bytes)
VMD never finishes reading vis. state file, stalls and hoggs CPU Bjoern Olausson (Fri Nov 25 2011 - 00:51:07 CST)
1. signature.asc_ (199 bytes)
clip plane and cpk / VdW Philippe Bopp / temporary (Wed Nov 23 2011 - 04:48:33 CST)
1. clip.problem.jpg (15976 bytes)
Re: RMSD Tool failes with MOL ID > 999 Bjoern Olausson (Tue Nov 15 2011 - 02:38:34 CST)
1. signature.asc_ (199 bytes)
Re: pbc wrap Olaf Lenz (Mon Nov 14 2011 - 09:57:04 CST)
1. olenz.vcf (388 bytes)
2. signature.asc (263 bytes)
Re: Re: Save "Visulaization State" from within Tk Console Bjoern Olausson (Mon Nov 14 2011 - 01:17:02 CST)
1. signature.asc_ (199 bytes)
Re: Save "Visulaization State" from within Tk Console Bjoern Olausson (Fri Nov 11 2011 - 07:48:03 CST)
1. signature.asc_ (199 bytes)
Save "Visulaization State" from within Tk Console Bjoern Olausson (Fri Nov 11 2011 - 07:41:18 CST)
1. signature.asc_ (199 bytes)
RMSD Tool failes with MOL ID > 999 Bjoern Olausson (Fri Nov 11 2011 - 05:52:11 CST)
1. signature.asc_ (199 bytes)
Re: namd-l: SASA of PBD files sajad falsafi (Sat Sep 03 2011 - 14:38:17 CDT)
1. sasa.tcl (1565 bytes)
Re: loading a trajectory where particles aren't conservd Axel Kohlmeyer (Wed Aug 31 2011 - 15:42:14 CDT)
1. correct.xyz (5458 bytes)
Re: loading a trajectory where particles aren't conservd Chris Knorowski (Wed Aug 31 2011 - 15:35:04 CDT)
1. bcc.xyz (5464 bytes)
pdb naming convention to get ribbon representation Casey Johnson (Wed Aug 31 2011 - 09:08:11 CDT)
1. PBLG5.pdb (4816 bytes)
Re: Fw: Lammps Output data format Axel Kohlmeyer (Tue Aug 30 2011 - 12:45:15 CDT)
1. find_products.tcl (2482 bytes)
Re: convert pdb format to normal pdb format Bjoern Olausson (Wed Aug 24 2011 - 06:10:45 CDT)
1. signature.asc_ (199 bytes)
RMSD calculator extension George Tzotzos (Tue Aug 23 2011 - 08:59:19 CDT)
1. error_log (866 bytes)
Fwd: Dowser plugin: Error message George Tzotzos (Mon Aug 22 2011 - 16:34:31 CDT)
1. dowser_error (1136 bytes)
Re: Turning Label Info output off in vmd console Sebastián Gutiérrez (Fri Aug 19 2011 - 15:21:02 CDT)
1. gauche_DOT_bigdcd.tcl (2073 bytes)
Re: how to wrap a protein with periodic waters Olaf Lenz (Mon Aug 15 2011 - 02:43:51 CDT)
1. olenz.vcf (376 bytes)
How to cionize DNA? example needed! Bikan Tan (Mon Aug 08 2011 - 18:59:19 CDT)
1. 2GC_Bdna.pdb.pdb (9972 bytes)
about psf file generation safron saif (Mon Aug 01 2011 - 07:22:08 CDT)
1. swcntdef.pdb (20004 bytes)
2. cnt.inp (115 bytes)
3. cnt.pgn (221 bytes)
Re: Understand a script Bjoern Olausson (Thu Jul 28 2011 - 03:28:41 CDT)
1. signature.asc_ (199 bytes)
Re: Understand a script Bjoern Olausson (Mon Jul 25 2011 - 10:05:59 CDT)
1. signature.asc_ (199 bytes)
Re: File as video Bjoern Olausson (Tue Jul 05 2011 - 03:33:13 CDT)
1. signature.asc_ (199 bytes)
Patchlet for MacOS 32/64-bit compilation FX (Sat Jul 02 2011 - 05:13:21 CDT)
1. mac.diff (986 bytes)
A patch for OFF import and a question about representation of surfaces FX (Sat Jul 02 2011 - 05:08:08 CDT)
1. off.diff (14507 bytes)
2. mushroom.off (16606 bytes)
can not compile VMD plugin hongphuc nguyen (Wed Jun 22 2011 - 22:15:55 CDT)
1. script.py (5176 bytes)
Re: saving dcd with less frames Bjoern Olausson (Tue Jun 07 2011 - 05:27:58 CDT)
1. signature.asc_ (199 bytes)
submit VMD_SS script sajad falsafi (Fri Jun 03 2011 - 11:35:20 CDT)
1. attachments_2011_06_03.zip (1234 bytes)
submit VMD_SS script sajad falsafi (Fri Jun 03 2011 - 00:59:22 CDT)
1. VMD_SS.tcl (2557 bytes)
2. VMD_SS.txt (477 bytes)
measure fit - wrong alignment Eduardo Oliveira (Thu May 26 2011 - 05:56:40 CDT)
1. pdb1.pdb (312 bytes)
2. pdb2.pdb (312 bytes)
Re: pbctools plugin & protein-bound ligand Olaf Lenz (Wed May 25 2011 - 02:01:11 CDT)
1. olenz.vcf (376 bytes)
Re: size for render Bjoern Olausson (Tue May 24 2011 - 06:34:49 CDT)
1. signature.asc_ (199 bytes)
Re: pbc unwrap not complete Olaf Lenz (Mon May 23 2011 - 04:57:38 CDT)
1. olenz.vcf (376 bytes)
Re: color atom by stress Shaorui Yang (Sat May 21 2011 - 21:10:17 CDT)
1. dump.tension (340 bytes)
Re: hi to all Bjoern Olausson (Thu May 19 2011 - 04:15:26 CDT)
1. signature.asc_ (199 bytes)
Re: pbc wrap Olaf Lenz (Mon May 16 2011 - 03:14:25 CDT)
1. olenz.vcf (376 bytes)
Re: PhD position in Computational Structural Biology at MPI Muenster Olaf Lenz (Sun May 15 2011 - 10:34:40 CDT)
1. olenz.vcf (409 bytes)
Re: command for volume slice? Olaf Lenz (Wed May 11 2011 - 09:11:32 CDT)
1. olenz.vcf (376 bytes)
Re: trajectory of water within 5 A of protein Eduard Schreiner (Tue May 10 2011 - 09:51:13 CDT)
1. ww_nearest.tcl (2369 bytes)
2. get_closest.tcl (471 bytes)
Re: CAVE and Flystick control John Stone (Wed May 04 2011 - 15:15:20 CDT)
1. .vmdsensors (1531 bytes)
Problem with cartoon and secondary structure Francisco José Taberner Sanchis (Tue May 03 2011 - 05:13:18 CDT)
1. image001.jpg (3026 bytes)
VMD Movie Generator problem with "Image smoothing" set Bjoern Olausson (Mon May 02 2011 - 06:26:54 CDT)
1. signature.asc_ (199 bytes)
Re: fit dcd is not converging mohan maruthi sena (Fri Apr 22 2011 - 03:52:48 CDT)
1. fitframes.tcl (949 bytes)
Re: fit dcd is not converging John Stone (Thu Apr 21 2011 - 12:15:30 CDT)
1. fitframes1.tcl (966 bytes)
Re: fit dcd is not converging mohan maruthi sena (Thu Apr 21 2011 - 11:49:02 CDT)
1. fitframes1.tcl (977 bytes)
fit dcd is not converging mohan maruthi sena (Thu Apr 21 2011 - 04:10:07 CDT)
1. fitframes.tcl (949 bytes)
Re: Replica Exchange Olaf Lenz (Fri Apr 15 2011 - 04:18:17 CDT)
1. olenz.vcf (376 bytes)
Re: recenter Olaf Lenz (Tue Apr 05 2011 - 02:29:57 CDT)
1. olenz.vcf (376 bytes)
Re: recenter Olaf Lenz (Mon Apr 04 2011 - 02:11:25 CDT)
1. olenz.vcf (376 bytes)
How to create bonds in VMD? Saketh Bharadwaja (Fri Apr 01 2011 - 11:07:21 CDT)
1. VMDInputFile.xyz (21053 bytes)
Generate a PSF file for small, simple molecules THANH NGUYEN (Mon Mar 28 2011 - 19:11:42 CDT)
1. APTES.pdb (2215 bytes)
2. APTES.mol (2267 bytes)
Re: Color wheel gradient John Stone (Thu Mar 24 2011 - 22:14:38 CDT)
1. matlab_colorscale.tcl (13781 bytes)
VMD 1.9 builds on MACOSXX86_64 Joshua A. Anderson (Tue Mar 22 2011 - 08:55:00 CDT)
1. Update-launcher-script-to-look-for-correct-executabl.patch (1083 bytes)
2. Add-missing-.r-file.patch (871 bytes)
3. Fix-bug-where-size_range-was-undefined.patch (1173 bytes)
Hbond rendering issue with VMD 1.9 Nicolas Sapay (Fri Mar 18 2011 - 04:58:27 CDT)
1. nicolas_sapay.vcf (333 bytes)
Re: MSD calculation from VMD RMSD plugin. Axel Kohlmeyer (Wed Mar 16 2011 - 14:23:30 CDT)
1. calcmsd.tcl (1944 bytes)
Re: Triclinic boxes in VMD using the LAMMPS file format Olaf Lenz (Thu Mar 10 2011 - 07:44:14 CST)
1. olenz.vcf (376 bytes)
Re: Zero box vector Olaf Lenz (Thu Mar 10 2011 - 07:07:35 CST)
1. olenz.vcf (376 bytes)
VMD and Kinect Olaf Lenz (Wed Mar 09 2011 - 05:30:16 CST)
1. olenz.vcf (388 bytes)
Re: Installing VMD 1.8.7 on i686/SL5 Olaf Lenz (Wed Mar 02 2011 - 08:31:01 CST)
1. olenz.vcf (409 bytes)
Re: Drawing Bonds in Periodic structure Olaf Lenz (Tue Mar 01 2011 - 03:06:06 CST)
1. olenz.vcf (388 bytes)
Re: Re: VMD 1.9 beta 1 posted for download... Bjoern Olausson (Thu Feb 17 2011 - 05:37:48 CST)
1. signature.asc_ (199 bytes)
only one model is displayed Joyce Tan (Fri Feb 11 2011 - 09:56:39 CST)
1. fit.pdb (2330 bytes)
How to use VMD script "PorcupinePlot.tcl" B.M.B. Vanschouwen (Mon Jan 31 2011 - 10:46:55 CST)
1. PorcupinePlot.tcl (10260 bytes)
Re: GLSL with ATI 5750 in Mac OS X 10.6 / 64-bit build Joshua A. Anderson (Thu Jan 27 2011 - 06:35:56 CST)
1. patch_commit_7e4de34f2520.patch (511 bytes)
2. patch_commit_a9869b4dd8ad.patch (1096 bytes)
RE: Issues with Paratools and Gaussian Ali, Rejwan (Wed Jan 12 2011 - 12:13:54 CST)
1. 7_h_ad.txt (1871 bytes)
RE: Issues with Paratools and Gaussian Ali, Rejwan (Wed Jan 12 2011 - 11:54:33 CST)
1. 7_H_add.com (1871 bytes)
VTF trajectory from coarse grained ESPReSo simulations. Visualization in Windows. Dudo (Wed Jan 12 2011 - 06:41:27 CST)
1. vtf2lammps.f90 (3072 bytes)
Re: regarding counting water molecules Joshua Adelman (Wed Dec 22 2010 - 07:26:33 CST)
1. water.tcl (1243 bytes)
Re: missing fragments in molefacture Peter Freddolino (Tue Nov 30 2010 - 19:25:50 CST)
1. phospho.zip (359 bytes)
Re: Headtracking software Ajasja LjubetiÄ (Tue Nov 16 2010 - 09:00:27 CST)
1. remote_ctl.tcl (3679 bytes)
Re: Vega ZZ DCD trajectory crashes VMD Ajasja LjubetiÄ (Tue Nov 09 2010 - 06:56:26 CST)
1. DCD_fix_for_VMD.c (2952 bytes)
2. DCD_fix_for_VMD.rtf (494 bytes)
Re: IED 2.02 and VMD 1.8.7 Jérôme Hénin (Wed Nov 03 2010 - 05:44:06 CDT)
1. ied.py.gz (6590 bytes)
namd-I : Constraint failure in RATTLE algorithm for atom 268 surendra jain (Thu Oct 28 2010 - 23:39:30 CDT)
1. equil3_conf (4323 bytes)
Vega ZZ DCD trajectory crashes VMD Ajasja LjubetiÄ (Tue Oct 19 2010 - 09:21:44 CDT)
1. CMTS_VAC.psf (9742 bytes)
2. CMTS_VAC.relaxed.dcd (3300 bytes)
protein breaks into parts after converting trajectory file to pdb file Joyce Tan (Mon Sep 27 2010 - 04:58:48 CDT)
1. 6ns.jpeg (14514 bytes)
Clarification on solvent box sizing Ian Stokes-Rees (Wed Sep 22 2010 - 14:42:30 CDT)
1. ijstokes.vcf (381 bytes)
Re: Mouse event listener John Stone (Sun Sep 19 2010 - 19:32:23 CDT)
1. callbacks.tcl (2576 bytes)
Re: vasp POSCAR plugin John Stone (Sun Sep 19 2010 - 19:26:47 CDT)
1. vaspposcarplugin.c (13006 bytes)
vmd display water molecules error Cun Zhang (Fri Sep 17 2010 - 02:37:03 CDT)
1. vmd_water_error.png (10384 bytes)
Re: Draw a box cell for a crystal Bjoern Olausson (Wed Sep 15 2010 - 08:19:32 CDT)
1. signature.asc_ (199 bytes)
DCD Based on a parameter Pat Yee (Thu Aug 26 2010 - 09:01:51 CDT)
1. dcd_export.tcl (633 bytes)
2. frames.dat (387 bytes)
Re: Conversion into POVRay coordinates Nicolas Sapay (Fri Aug 06 2010 - 08:41:47 CDT)
1. nicolas_sapay.vcf (333 bytes)
Re: Conversion into POVRay coordinates John Stone (Thu Aug 05 2010 - 17:06:54 CDT)
1. glowlights.tcl (5799 bytes)
Conversion into POVRay coordinates Nicolas Sapay (Wed Aug 04 2010 - 04:01:20 CDT)
1. nicolas_sapay.vcf (333 bytes)
Re: multiseq/stamp alignment of coiled coil bundle and homo-dimer Ian Stokes-Rees (Fri Jul 30 2010 - 13:14:47 CDT)
1. ijstokes.vcf (381 bytes)
Focal blur with Tachyon Nicolas Sapay (Fri Jul 30 2010 - 03:13:49 CDT)
1. nicolas_sapay.vcf (333 bytes)
Re: multiseq/stamp alignment of coiled coil bundle and homo-dimer Ian Stokes-Rees (Tue Jul 27 2010 - 16:54:53 CDT)
1. ijstokes.vcf (381 bytes)
multiseq/stamp alignment of coiled coil bundle and homo-dimer Ian Stokes-Rees (Tue Jul 27 2010 - 14:37:02 CDT)
1. ijstokes.vcf (381 bytes)
Re: PC suitable for visualisation of large systems, maximum namuber of atoms in a .pdb file Ian Stokes-Rees (Wed Jul 21 2010 - 12:20:56 CDT)
1. ijstokes.vcf (381 bytes)
Re: PC suitable for visualisation of large systems, maximum namuber of atoms in a .pdb file Ian Stokes-Rees (Wed Jul 21 2010 - 07:07:51 CDT)
1. ijstokes.vcf (381 bytes)
Re: VMD failure of RMSD Traj Tool, time index on each rendered frame, and crash John Stone (Tue Jul 20 2010 - 10:39:53 CDT)
1. frameupdate.vmd (717 bytes)
Re: compilation of vmd 1.8.7 source Ian Stokes-Rees (Tue Jul 20 2010 - 10:07:45 CDT)
1. ijstokes.vcf (381 bytes)
Adding other online PDB data bases to VMD Ian Stokes-Rees (Fri Jul 16 2010 - 18:46:31 CDT)
1. ijstokes.vcf (381 bytes)
Re: Building VMD on OS X 10.6 with Python and CUDA support Ian Stokes-Rees (Fri Jul 16 2010 - 02:41:24 CDT)
1. ijstokes.vcf (381 bytes)
Re: Building VMD on OS X 10.6 with Python and CUDA support Ian Stokes-Rees (Fri Jul 16 2010 - 02:24:38 CDT)
1. ijstokes.vcf (381 bytes)
Building VMD on OS X 10.6 with Python and CUDA support Ian Stokes-Rees (Thu Jul 15 2010 - 22:44:34 CDT)
1. ijstokes.vcf (381 bytes)
Re: color charmm dcd by kinetic energy Bjoern Olausson (Tue Jul 06 2010 - 02:51:24 CDT)
1. signature.asc_ (199 bytes)
Re: VMD / Tachyon Questions John Stone (Thu Jul 01 2010 - 10:58:26 CDT)
1. glowlights.tcl (5799 bytes)
Re: structure file for big molecules Nicholas Musolino (Sun Jun 20 2010 - 20:23:50 CDT)
1. atom_uniq.awk (710 bytes)
Re: Hydrophobic interaction Nicolas Sapay (Fri Jun 18 2010 - 08:25:09 CDT)
1. nicolas_sapay.vcf (333 bytes)
Re: Retrieving the Cremer-Pople parameters Nicolas Sapay (Mon Jun 07 2010 - 04:05:01 CDT)
1. nicolas_sapay.vcf (333 bytes)
Retrieving the Cremer-Pople parameters Nicolas Sapay (Fri Jun 04 2010 - 03:46:30 CDT)
1. nicolas_sapay.vcf (333 bytes)
Re: Tcl-wrapped "lightweight plugin" in C++ Jérôme Hénin (Thu Jun 03 2010 - 07:56:51 CDT)
1. array.tar.gz (1105 bytes)
Re: Visualize intersection of overlapping spheres? Bjoern Olausson (Thu Jun 03 2010 - 02:24:02 CDT)
1. signature.asc_ (199 bytes)
Re: CAN ANY ONE HELP ME vani panguluri (Wed Jun 02 2010 - 11:44:33 CDT)
1. vmd.txt (4532 bytes)
Visualize intersection of overlapping spheres? Bjoern Olausson (Wed Jun 02 2010 - 06:51:56 CDT)
1. signature.asc_ (199 bytes)
Re: Modelling program that does hydrogen adjust Bjoern Olausson (Fri May 28 2010 - 06:14:24 CDT)
1. signature.asc_ (199 bytes)
LAMMPS trajectory file Anna Ceguerra (Mon May 10 2010 - 21:12:28 CDT)
1. 2steps-RL0_1.lammpstrj (783 bytes)
Re: Creating AVI movies Bjoern Olausson (Mon May 10 2010 - 08:37:58 CDT)
1. signature.asc_ (199 bytes)
Re: How to remove hydrogens from a pdb file? Bjoern Olausson (Fri May 07 2010 - 02:41:51 CDT)
1. signature.asc_ (199 bytes)
G(r) tcl script not including intramolecular correlations Hall, Lisa Michelle (Thu May 06 2010 - 18:12:49 CDT)
1. date_ (1659 bytes)
Using RMSD in colvar Stefan Franzen (Mon May 03 2010 - 08:48:10 CDT)
1. ubq_ws_cv.inp (566 bytes)
Re: Coloring atoms based on timeframe range? Bjoern Olausson (Fri Apr 23 2010 - 04:01:19 CDT)
1. signature.asc_ (199 bytes)
Re: Coloring atoms based on timeframe range? Bjoern Olausson (Thu Apr 22 2010 - 10:41:46 CDT)
1. signature.asc_ (199 bytes)
Coloring atoms based on timeframe range? Bjoern Olausson (Thu Apr 22 2010 - 08:51:34 CDT)
1. signature.asc_ (199 bytes)
Re: High quality movies, bmp frames and videomach=poor quality Bjoern Olausson (Wed Apr 21 2010 - 08:34:00 CDT)
1. signature.asc_ (199 bytes)
how to pick certain water molecular from a .mdcrd ÅÓÑ©ÇÛ Pang Xueqin (Tue Apr 13 2010 - 01:37:16 CDT)
1. _______1_.vcf (1243 bytes)
Re: question about vmd use Bjoern Olausson (Mon Apr 12 2010 - 06:16:42 CDT)
1. signature.asc_ (199 bytes)
AutoHotkey script for managing VMD windows Ajasja LjubetiÄ (Fri Apr 09 2010 - 07:56:42 CDT)
1. VMD_layout.ahk (3252 bytes)
2. vmd_here.png (12126 bytes)
3. vmd_here.reg (438 bytes)
Turn off initial VMD animation and "menu tkcon on" problem Ajasja LjubetiÄ (Fri Apr 09 2010 - 07:18:57 CDT)
1. vmd.rc (1867 bytes)
Re: Way to change ColorScale Method to single color gradient? Bjoern Olausson (Thu Apr 08 2010 - 02:18:05 CDT)
1. signature.asc_ (199 bytes)
Re: Way to change ColorScale Method to single color gradient? Bjoern Olausson (Wed Apr 07 2010 - 08:05:07 CDT)
1. signature.asc_ (199 bytes)
Way to change ColorScale Method to single color gradient? Bjoern Olausson (Wed Apr 07 2010 - 03:33:18 CDT)
1. signature.asc_ (199 bytes)
(no subject) Irene Newhouse (Mon Mar 29 2010 - 15:12:41 CDT)
1. apo1a6grun_ils.tcl (4990 bytes)
Wrapping membrane to center of PBC-Box Bjoern Olausson (Tue Mar 23 2010 - 12:06:31 CDT)
1. signature.asc_ (199 bytes)
properly applying patches to create DPPC Ronald Salesky (Wed Mar 10 2010 - 18:33:59 CST)
1. palm1.pdb (3946 bytes)
2. palm2.pdb (3946 bytes)
3. pcgl.pdb (2978 bytes)
Re: Question Regarding User-Defined Trajectories John Stone (Mon Mar 08 2010 - 09:37:25 CST)
1. ethanol.xyz (570 bytes)
2. ethanoltrj.xyz (5691 bytes)
Porcupine update Carsten Olbrich (Wed Feb 17 2010 - 03:03:27 CST)
1. PorcupinePlot.tcl (10260 bytes)
psfgen generates 0 atom .psf file Ronald Salesky (Fri Feb 12 2010 - 19:41:10 CST)
1. sds.pdb (3437 bytes)
Re: Blank thumbnails and non-working snapshots John Stone (Tue Feb 09 2010 - 10:07:31 CST)
1. viewmaster.tcl.gz (9506 bytes)
problem with generating PSF file for guanine based molecule Parisa Akhski (Sun Feb 07 2010 - 11:51:03 CST)
1. modell.pdb (7258 bytes)
Re: Trouble building VMD 1.8.7 on Mac OS X John Stone (Wed Feb 03 2010 - 15:55:51 CST)
1. vmdmac.r.gz (207 bytes)
autopsf generator need at least one atom error Ronald Salesky (Sun Jan 24 2010 - 12:29:12 CST)
1. agctvega.pdb (13513 bytes)
Fwd: Re: allowing negative 'resid' numbers in selection strings Vlad Cojocaru (Fri Jan 08 2010 - 09:10:02 CST)
1. part (3755 bytes)
Fwd: Failure of AutoSCFBuilder to recognize all monomers Francesco Pietra (Sun Jan 03 2010 - 09:24:22 CST)
1. attachment.txt (887 bytes)
Failure of AutoSCFBuilder to recognize all monomers Francesco Pietra (Sun Jan 03 2010 - 04:54:24 CST)
1. attachment.txt (887 bytes)
superimposed structure leila karami (Sun Dec 20 2009 - 08:46:03 CST)
1. f.pdb (28503 bytes)
Re: VMD on AIX --- successful build, failed execution John Stone (Wed Dec 16 2009 - 10:56:56 CST)
1. TclTextInterp.C (19188 bytes)
Re: PBC + DCD wrap/unwrap Olaf Lenz (Tue Dec 15 2009 - 03:38:55 CST)
1. signature.asc_ (198 bytes)
Re: porcupine plots for PC1 Carsten Olbrich (Thu Dec 10 2009 - 04:43:03 CST)
1. PorcupinePlot.tcl (10354 bytes)
Re: A VMD script to emulate the Matlab "jet" colorscale John Stone (Wed Dec 09 2009 - 11:48:11 CST)
1. matlab_colorscale.tcl (13781 bytes)
A VMD script to emulate the Matlab "jet" colorscale John Stone (Tue Dec 08 2009 - 16:49:40 CST)
1. matlab_colorscale.tcl (1145 bytes)
FW: VMD 1.8.7 build with VRPN 7.23 Mark Cunningham (Mon Dec 07 2009 - 14:09:59 CST)
1. vmdbuild.tar.gz (25395 bytes)
Re: building VMD is tricky -please help Axel Kohlmeyer (Tue Dec 01 2009 - 18:31:54 CST)
1. fedora.spec (16813 bytes)
destroyed molecule sarah k (Sat Nov 21 2009 - 06:57:32 CST)
1. 65.pdb (2292 bytes)
2. 65qm.top (11208 bytes)
3. 65.pdb (2292 bytes)
4. 65_autopsf.pdb (2292 bytes)
paratool problem sarah k (Wed Nov 18 2009 - 23:43:52 CST)
1. 65.pdb (2292 bytes)
2. 65qm.top (11208 bytes)
Re: Lipid Order Parameter Sebastian Stolzenberg (Sat Nov 07 2009 - 16:49:42 CST)
1. calc_op.tcl (4340 bytes)
Re: running under Shell using VMD Nicolas Sapay (Tue Nov 03 2009 - 05:07:45 CST)
1. nicolas_sapay.vcf (391 bytes)
Re: Cuda an a cluster ? John Stone (Thu Oct 22 2009 - 11:04:45 CDT)
1. startcuda (1710 bytes)
Re: text timer in vmd animations John Stone (Mon Oct 05 2009 - 22:22:10 CDT)
1. frameupdate.vmd (717 bytes)
Overlaying 2 structures madura_at_duq.edu (Fri Sep 25 2009 - 15:55:05 CDT)
1. mol0.pdb (247 bytes)
2. mol1.pdb (245 bytes)
Re: tinkerxyz Joshua D. Moore (Sat Aug 29 2009 - 02:26:29 CDT)
1. system.inc (1839 bytes)
2. dcdtotinkerxyz.f (6627 bytes)
VMD: 1.8.7 win32 opengl runtime error Guanglei Cui (Fri Aug 21 2009 - 09:14:56 CDT)
1. screenshot.jpg (17233 bytes)
Re: Rendering polyhedra with POV-Ray Nicolas Sapay (Tue Aug 18 2009 - 11:11:35 CDT)
1. nicolas_sapay.vcf (391 bytes)
Re: Rendering polyhedra with POV-Ray Nicolas Sapay (Tue Aug 18 2009 - 10:54:44 CDT)
1. nicolas_sapay.vcf (391 bytes)
Re: Problem: VMD 1.8.7 beta 5 does not launch on AIX Stanislav Polonsky (Fri Jul 24 2009 - 13:24:45 CDT)
1. graycol.gif (105 bytes)
2. pic20695.gif (1255 bytes)
3. ecblank.gif (45 bytes)
Re: Problem: VMD 1.8.7 beta 5 does not launch on AIX Axel Kohlmeyer (Fri Jul 24 2009 - 09:22:09 CDT)
1. vmd.csh (11427 bytes)
2. vmd.sh (10937 bytes)
Re: Problem: volumetric data coloring fails on AIX5_64 with GXT6500 OpenGL renderer Stanislav Polonsky (Thu Jul 23 2009 - 16:42:37 CDT)
1. graycol.gif (105 bytes)
2. pic27353.gif (1255 bytes)
3. ecblank.gif (45 bytes)
Re: Problem: volumetric data coloring fails on AIX5_64 with GXT6500 OpenGL renderer Stanislav Polonsky (Thu Jul 23 2009 - 12:21:14 CDT)
1. graycol.gif (105 bytes)
2. pic21869.gif (1255 bytes)
3. ecblank.gif (45 bytes)
Re: Problem: volumetric data coloring fails on AIX5_64 with GXT6500 OpenGL renderer Stanislav Polonsky (Thu Jul 23 2009 - 10:39:36 CDT)
1. graycol.gif (105 bytes)
2. pic06285.gif (1255 bytes)
3. ecblank.gif (45 bytes)
Re: Disable the set output Nicolas Sapay (Thu Jul 23 2009 - 09:28:13 CDT)
1. nicolas_sapay.vcf (391 bytes)
Re: Problem: volumetric data coloring fails on AIX5_64 with GXT6500 OpenGL renderer Stanislav Polonsky (Mon Jul 20 2009 - 16:19:05 CDT)
1. graycol.gif (105 bytes)
2. pic13008.gif (1255 bytes)
3. ecblank.gif (45 bytes)
Re: Problem: volumetric data coloring fails on AIX5_64 with GXT6500 OpenGL renderer Stanislav Polonsky (Mon Jul 20 2009 - 13:16:31 CDT)
1. graycol.gif (105 bytes)
2. pic30527.gif (1255 bytes)
3. ecblank.gif (45 bytes)
Re: Problem: volumetric data coloring fails on AIX5_64 with GXT6500 OpenGL renderer Stanislav Polonsky (Mon Jul 20 2009 - 11:40:40 CDT)
1. graycol.gif (105 bytes)
2. pic26374.gif (1255 bytes)
3. ecblank.gif (45 bytes)
.xst file disagrees with pbctools/.dcd file - what are the limitations of pbctools? Patrick Kiley (Wed Jul 15 2009 - 05:05:01 CDT)
1. 1.png (12836 bytes)
Re: Curious about analytical capabilities of VMD Bjoern Olausson (Mon Jul 06 2009 - 07:10:37 CDT)
1. signature.asc_ (199 bytes)
Re: Curious about analytical capabilities of VMD Bjoern Olausson (Wed Jul 01 2009 - 07:19:39 CDT)
1. signature.asc_ (199 bytes)
Re: Curious about analytical capabilities of VMD Bjoern Olausson (Mon Jun 29 2009 - 05:29:33 CDT)
1. signature.asc_ (199 bytes)
Curious about analytical capabilities of VMD Bjoern Olausson (Fri Jun 26 2009 - 03:48:05 CDT)
1. signature.asc_ (199 bytes)
Re: Memory allocation problem Axel Kohlmeyer (Mon Jun 15 2009 - 10:00:02 CDT)
1. debug_atomselect.tcl.gz (2445 bytes)
Re: Transparency settings John Stone (Fri Jun 12 2009 - 10:32:15 CDT)
1. glowlights.tcl (5122 bytes)
Re: Transparency settings Bjoern Olausson (Thu Jun 11 2009 - 06:09:15 CDT)
1. signature.asc_ (199 bytes)
Re: Transparency settings Bjoern Olausson (Wed Jun 10 2009 - 10:29:08 CDT)
1. signature.asc_ (199 bytes)
Transparency settings Bjoern Olausson (Wed Jun 10 2009 - 09:13:13 CDT)
1. signature.asc_ (199 bytes)
debugging tool for atomselect Axel Kohlmeyer (Thu Jun 04 2009 - 17:05:10 CDT)
1. debug_atomselect.tcl (6166 bytes)
Re: Energy John Stone (Wed Jun 03 2009 - 22:04:04 CDT)
1. namdplot.tcl (16672 bytes)
Heat capacity zizi moradi (Sun May 24 2009 - 16:39:45 CDT)
1. heat_capacity.xls (76800 bytes)
Re: "Determine file type" list is far too long... Axel Kohlmeyer (Sun May 24 2009 - 11:40:33 CDT)
1. vmdrc.tcl.gz (1377 bytes)
VMD 1.8.7b3 and desktop effects on Fedora 10 Nicolas Sapay (Wed May 20 2009 - 07:48:33 CDT)
1. nicolas_sapay.vcf (391 bytes)
VMD 1.8.7 beta 1 posted for download... John Stone (Wed Apr 29 2009 - 15:06:27 CDT)
1. README (12062 bytes)
Re: cvs plugins do not compile because of errors in the sgsmooth.C John Stone (Tue Mar 31 2009 - 13:34:05 CDT)
1. sgsmooth.C (17062 bytes)
Re: problem while integrating bigdcd into a namespace John Stone (Thu Mar 05 2009 - 22:36:23 CST)
1. callbacks.tcl (2576 bytes)
2. watchcallbacks.tcl (1484 bytes)
Re: selection by residue Nicolas (Thu Mar 05 2009 - 10:34:05 CST)
1. nsapay.vcf (311 bytes)
Re: Outline rendering style with Tachyon Nicolas (Tue Mar 03 2009 - 16:04:17 CST)
1. nsapay.vcf (311 bytes)
info for computational chemistry awards, please forward Carlos Simmerling (Fri Feb 20 2009 - 10:22:27 CST)
1. gradstudentawards.txt (2268 bytes)
2. HPaward.asstprof.txt (2436 bytes)
multiplot : integration of undrawing command (?) Nadja Lederer (Thu Feb 05 2009 - 05:14:43 CST)
1. multiplot.tcl (47940 bytes)
[patch] potential CUDA acceleration - load-balancing on different CUDA devices Martin Aumüller (Wed Jan 28 2009 - 06:35:19 CST)
1. cuda-potential-balance.diff (3360 bytes)
Re: Test builds of VMD 1.8.7 using Tcl/Tk 8.5.x... Axel Kohlmeyer (Tue Jan 20 2009 - 17:31:19 CST)
1. vmd_completion.dat (3513 bytes)
Re: Calculating acyl chain order parameter profile on phospholipid vesicles dimka (Tue Jan 13 2009 - 10:28:43 CST)
1. orderparam2.tcl (4693 bytes)
Re: how to prevent view reset on data load Axel Kohlmeyer (Sun Nov 30 2008 - 05:46:45 CST)
1. reload_wait.tcl.gz (578 bytes)
Re: Other color scales than the predefined ones? John Stone (Thu Nov 27 2008 - 09:36:40 CST)
1. colorscale.tcl (1003 bytes)
[patch] Autodetection of formats supported by openbabel FX (Thu Nov 20 2008 - 05:07:17 CST)
1. 1.diff (5724 bytes)
RE: B factor calculation Aaron.Oakley_at_csiro.au (Tue Nov 04 2008 - 16:27:02 CST)
1. bfactor.tcl (4022 bytes)
RE: Problem in text mode Wei Huang (Thu Oct 16 2008 - 00:58:55 CDT)
1. tilt.tcl (3889 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)
question about sscache qwang_at_mail.uh.edu (Sun Sep 28 2008 - 19:33:02 CDT)
1. hel.tcl (1915 bytes)
question about sscache qwang_at_mail.uh.edu (Fri Sep 26 2008 - 14:00:07 CDT)
1. hel.tcl (1915 bytes)
Re: psf file generation: once again Peter Freddolino (Thu Sep 25 2008 - 08:12:34 CDT)
1. mac.tbz (1852 bytes)
Re: Gromacs reading: Why scaling?? Nicolas (Thu Jul 31 2008 - 19:32:16 CDT)
1. nsapay.vcf (309 bytes)
Re: VMD with amber rst7 and parm7 files Axel Kohlmeyer (Thu Jul 31 2008 - 09:02:29 CDT)
1. fixamberwater.tcl (903 bytes)
Re: Creating a VMD movie from a Tcl script John Stone (Tue Jul 22 2008 - 13:51:41 CDT)
1. vmdmovie17a1.tar.gz (12223 bytes)
2. textmovie.tcl (378 bytes)
Re: Problem writing trajectory to "crd" (Amber) format? Axel Kohlmeyer (Wed Jul 16 2008 - 09:31:59 CDT)
1. no-eol-fix.diff (831 bytes)
Fwd: memory overflow problem of Tcl scripting when dealing with trajectories(sorry for cross mailing...) bo liu (Wed Jul 16 2008 - 03:18:43 CDT)
1. dipole_profile.tcl (6794 bytes)
Re: speed of movie Axel Kohlmeyer (Sun Jul 13 2008 - 15:49:02 CDT)
1. gen_render.tcl (928 bytes)
Re: contour plots Subramanian Vaitheeswaran (Thu Jul 10 2008 - 10:02:58 CDT)
1. contour_plot.gnu (1554 bytes)
2. contour.dat (1095 bytes)
The maximal size which can be displayed by VMD? Fred (Rui FENG) (Wed Jul 02 2008 - 16:06:18 CDT)
1. circle.pdb (10939 bytes)
Re: Error using namdstat.tcl script Axel Kohlmeyer (Mon Jun 30 2008 - 11:42:26 CDT)
1. namdstats.tcl.gz (1082 bytes)
Re: Re: PSF works in NAMD but not in VMD Esben A. Gad (Mon Jun 23 2008 - 07:20:08 CDT)
1. temp.namd (840 bytes)
Re: render "color by volume" Nicolas Sapay (Tue Jun 17 2008 - 17:11:45 CDT)
1. nsapay.vcf (283 bytes)
Re: specify a rtf file when generating a psf file. Nicolas Sapay (Tue Jun 17 2008 - 15:28:34 CDT)
1. nsapay.vcf (283 bytes)
Re: opening gromacs .gro file gives warning messsage and does not display the molecule Nicolas Sapay (Tue Jun 17 2008 - 13:51:36 CDT)
1. nsapay.vcf (283 bytes)
specify a rtf file when generating a psf file. Nicolas Sapay (Tue Jun 17 2008 - 13:46:22 CDT)
1. nsapay.vcf (283 bytes)
problem with namdstats.tcl sudipta sinha (Sun Jun 15 2008 - 01:51:11 CDT)
1. namdstats.tcl (3456 bytes)
Re: User defined charges with PMEpot Nicolas (Thu Jun 12 2008 - 23:08:24 CDT)
1. nsapay.vcf (309 bytes)
User defined charges with PMEpot Nicolas Sapay (Thu Jun 12 2008 - 18:24:57 CDT)
1. nsapay.vcf (283 bytes)
measure hbonds problem politr_at_huji.ac.il (Fri May 30 2008 - 10:59:28 CDT)
1. F1.jpg (8706 bytes)
hydrogen bonds politr_at_huji.ac.il (Fri May 30 2008 - 06:05:12 CDT)
1. F1.jpg (8706 bytes)
Energy plot script Alexandre A. Vakhrouchev (Wed May 14 2008 - 22:11:19 CDT)
1. plot_energy.sh.gz (1205 bytes)
bigdcd v2.0 testers needed... Axel Kohlmeyer (Wed May 07 2008 - 15:21:47 CDT)
1. bigdcd_v2.tcl (4260 bytes)
Re: bug in the g(r) evaluation? cipitaua_at_gmail.com (Tue Apr 22 2008 - 11:06:14 CDT)
1. Si10.xyz (278 bytes)
RE: warnings during plugin build Cojocaru,Vlad (Mon Apr 21 2008 - 18:35:21 CDT)
1. config_mod.log (1782 bytes)
RE: warnings during plugin build Cojocaru,Vlad (Sun Apr 20 2008 - 12:37:39 CDT)
1. config (7204 bytes)
RE: warnings during plugin build Axel Kohlmeyer (Sat Apr 19 2008 - 18:40:41 CDT)
1. mods.diff.gz (3155 bytes)
RE: warnings during plugin build Cojocaru,Vlad (Sat Apr 19 2008 - 17:53:58 CDT)
1. makeSURF.log (18820 bytes)
Re: Insall Problem VMD Linux 1.8.6 Part II! Axel Kohlmeyer (Sun Apr 06 2008 - 23:50:58 CDT)
1. vmd.sh.gz (3263 bytes)
About Tcl command zhjjvmd (Sat Apr 05 2008 - 20:58:15 CDT)
1. pdbofactor.tcl (822 bytes)
VMD 3D stereo hardware Alba Colet Subirachs (Thu Mar 06 2008 - 03:16:25 CST)
1. details00000.txt (213 bytes)
Re: couldn't fork child process: not enough memory jrui_at_ci.uc.pt (Fri Feb 22 2008 - 08:41:54 CST)
1. ADP01.mol2 (2205 bytes)
2. ADP03.mol2 (2205 bytes)
3. ADP07.mol2 (2205 bytes)
Re: VASP CHGCAR Axel Kohlmeyer (Thu Feb 21 2008 - 17:18:50 CST)
1. vaspchgcarplugin.c (10254 bytes)
Fwd: spacial distribution function L. Michel Espinoza-Fonseca (Tue Feb 19 2008 - 18:54:53 CST)
1. hc-3-129-gr.png (9914 bytes)
Re: X_ChangeProperty: BadValue (integer parameter out of range for operation) 0x40 Guanglei Cui (Tue Jan 08 2008 - 14:40:43 CST)
1. xorg.conf (3787 bytes)
saltbr plugging problem: too many open files Amaury Pupo Meriño (Fri Dec 21 2007 - 09:31:07 CST)
1. saltbr.diff (72 bytes)
VMD movie from XYZ coordinate if file has two type of atoms] Anil Kumar (Tue Dec 11 2007 - 04:20:07 CST)
1. 2 (6023 bytes)
Re: SpaceNavigator John Stone (Tue Dec 04 2007 - 22:57:22 CST)
1. printtool.patch (748 bytes)
Re: Rainbow color scheme for VolumeSlice / Volume John Stone (Tue Dec 04 2007 - 18:03:05 CST)
1. colorscale.tcl (1492 bytes)
Re: combine.tcl membrane plugin Francesco Pietra (Thu Nov 15 2007 - 09:50:36 CST)
1. combine.log.tar.bz2 (15005 bytes)
Re: combine.tcl membrane plugin Francesco Pietra (Thu Nov 15 2007 - 03:15:33 CST)
1. combine.log.tar.bz2 (1204 bytes)
problems with atomselect: missing selection Philipp Schön (Mon Nov 12 2007 - 05:23:32 CST)
1. smime.p7s (1764 bytes)
Re: cloning a molecule Axel Kohlmeyer (Mon Nov 05 2007 - 00:35:27 CST)
1. backup.tcl (4572 bytes)
Re: Alignment John Stone (Sun Nov 04 2007 - 13:53:06 CST)
1. mybigdcd.tcl (2476 bytes)
Re: Problem with bigdcd Himanshu Khandelia (Fri Oct 19 2007 - 12:25:56 CDT)
1. mybigdcd.tcl (2475 bytes)
Is catdcd running on Windows? Philipp Schön (Wed Oct 17 2007 - 03:45:54 CDT)
1. smime.p7s (1764 bytes)
Re: Cube Files - proportion of the electron density Axel Kohlmeyer (Sun Oct 07 2007 - 18:14:00 CDT)
1. trimcube.c (10144 bytes)
Re: Storing multiple values in the user field John Stone (Fri Sep 28 2007 - 17:12:51 CDT)
1. extrauserdata.patch (10190 bytes)
2. extrausercolor.vmd (973 bytes)
Re: residue selection: conflict between resid and residue Nicolas Sapay (Fri Sep 21 2007 - 16:04:56 CDT)
1. nsapay.vcf (283 bytes)
Re: residue selection: conflict between resid and residue Nicolas Sapay (Fri Sep 21 2007 - 15:14:23 CDT)
1. nsapay.vcf (283 bytes)
residue selection: conflict between resid and residue Nicolas Sapay (Fri Sep 21 2007 - 13:22:45 CDT)
1. nsapay.vcf (283 bytes)
Problem generating PSF file for decalanine...any help? Santanu Chatterjee (Wed Sep 19 2007 - 18:24:38 CDT)
1. alanine.pdb (5616 bytes)
VMD analysis using NAMD plot Philipp Schön (Wed Aug 29 2007 - 05:47:01 CDT)
1. smime.p7s (1764 bytes)
TIP5P jestin mandumpal (Sun Aug 26 2007 - 23:41:03 CDT)
1. tip5p.pdb (433 bytes)
2. tip5p.top (310 bytes)
Increasing use of RAM even if I put unset/delete for selections! Due to use of arrays? Philipp Schön (Tue Aug 14 2007 - 05:28:13 CDT)
1. smime.p7s (1764 bytes)
how to make user input during runtime of a tcl program using TkConsole? Philipp Schön (Fri Aug 10 2007 - 10:14:46 CDT)
1. smime.p7s (1764 bytes)
package require Tcl 8.5 => ::tcl::mathfunc:: Philipp Schön (Thu Aug 09 2007 - 10:56:09 CDT)
1. smime.p7s (1764 bytes)
Re: Problems to load Gaussian .log file in Paratool Jan Saam (Tue Jul 31 2007 - 11:05:34 CDT)
1. paratool_hessian.tcl (23920 bytes)
puzzling psfgen problem with deleted atoms coming back Irene Newhouse (Fri Jul 13 2007 - 16:47:05 CDT)
1. LSTa.pdb (5539 bytes)
2. lsta.pgn (279 bytes)
3. top_kitsink.inp (220721 bytes)
Re: vmd residue position snoze pa (Wed Jul 25 2007 - 14:54:16 CDT)
1. X.pdb (2551 bytes)
Reading a pdbqt file (generated from AutoDock) Arneh Babakhani (Thu Jul 19 2007 - 18:01:01 CDT)
1. Molecule.pdb (2424 bytes)
2. Molecule.pdbqt (1416 bytes)
calculation limit of gofr? Philipp Schön (Thu Jul 05 2007 - 10:16:00 CDT)
1. smime.p7s (1764 bytes)
atom serial number Francesco Pietra (Sun Jul 01 2007 - 02:33:20 CDT)
1. sustiva.pdb (1710 bytes)
Using VMD just to plot some coordinates from a mathematical/geometrical model Arneh Babakhani (Fri Jun 22 2007 - 17:51:35 CDT)
1. MyNodes.pdb (293 bytes)
Mail System Error - Returned Mail The Post Office (Wed Jun 20 2007 - 12:17:09 CDT)
1. attachment.zip (1370 bytes)
Script to rendering ANISOU records in VMD Aaron Oakley (Tue Jun 19 2007 - 21:22:51 CDT)
1. draw_anisou.tcl (6472 bytes)
Re: Simple TCL/Tk question Robert Brunner (Fri Jun 08 2007 - 14:55:20 CDT)
1. PGP.sig (187 bytes)
how to visualize Charmm generated files ThuZar Lwin (Wed Jun 06 2007 - 16:38:54 CDT)
1. melitinin.psf (2285701 bytes)
Re: CCL: show ruler in VMD John Stone (Fri Jun 01 2007 - 14:11:07 CDT)
1. ruler.tcl (3673 bytes)
Order Parameter Script for changing bilayer normal Richard Swenson (Fri Jun 01 2007 - 09:21:07 CDT)
1. tiltednormaltest.tcl (19726 bytes)
pqr files---- Raul Araya (Tue May 29 2007 - 16:46:49 CDT)
1. Wt_70.pqr (427665 bytes)
(no subject) Lechuga, Javier (Fri May 25 2007 - 08:10:27 CDT)
1. Coordinates.tcl (142 bytes)
Re: questions about developing a plugin Axel Kohlmeyer (Thu May 24 2007 - 08:02:33 CDT)
1. orig.tar.gz (20018 bytes)
(no subject) Lechuga, Javier (Thu May 17 2007 - 09:40:07 CDT)
1. DPPC.pdb (10732 bytes)
2. PsfGen_DPPC.tcl (196 bytes)
3. top_all27_lipid.rtf (113499 bytes)
Re: namd-l: how to use measure hbonds to calculate occupancy of all hbonds in simulation? Dong Luo (Wed May 16 2007 - 11:44:01 CDT)
1. hbond_occupancy.tcl (2711 bytes)
Re: namd-l: 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: namd-l: 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 Axel Kohlmeyer (Fri May 11 2007 - 07:46:23 CDT)
1. air.pdb (75 bytes)
2. air.psf (336 bytes)
rms fitting problem Myunggi Yi (Wed May 02 2007 - 16:34:04 CDT)
1. rms.agr (52368 bytes)
Visualization and reading problems Marcelo Puiatti (Fri Apr 27 2007 - 18:12:44 CDT)
1. solv.png (64716 bytes)
2. 2.png (81426 bytes)
3. cambio_de_lugar.pdf (14195 bytes)
GLSL rendering problems (??) Nichols A. Romero (Tue Apr 24 2007 - 15:40:57 CDT)
1. glxinfo (8005 bytes)
Re: how to reset a timed out connection John Stone (Tue Apr 24 2007 - 14:57:41 CDT)
1. rsyncPDB.sh (1903 bytes)
Re: Variable number of atoms in xyz file Axel Kohlmeyer (Tue Apr 24 2007 - 09:21:45 CDT)
1. split_xyz.pl (390 bytes)
Re: .xyz to .dcd using catdcd Ekta Khurana (Mon Apr 16 2007 - 14:34:47 CDT)
1. try.xyz (1597155 bytes)
Re: GLSL rendering problems Nichols A. Romero (Thu Apr 05 2007 - 15:07:14 CDT)
1. glxinfo (9578 bytes)
Re: Problem with Reading Binary ccp4 File Generated by CHARMM Leonardo Trabuco (Thu Apr 05 2007 - 14:55:07 CDT)
1. mapab2.ccp4 (525724 bytes)
Problem with Reading Binary ccp4 File Generated by CHARMM rossi_at_york.cuny.edu (Thu Apr 05 2007 - 11:32:02 CDT)
1. tcr.pdb (261784 bytes)
2. mapab.ccp4 (525724 bytes)
[vmd-l] Graduate assistanship in Bioinformatics at NCSA Gloria Rendon (Wed Mar 28 2007 - 17:45:25 CDT)
1. BSW_grad_assistantship_job_descriptionv1.4.pdf (21681 bytes)
Re: How to superimpose trajectories Kailee (Thu Mar 22 2007 - 10:04:44 CDT)
1. example.jpg (37498 bytes)
2. snap.jpg (54513 bytes)
Re: Scripts to unwrap PBC from REMD trajectory Olaf Lenz (Fri Mar 16 2007 - 03:57:59 CDT)
1. pbcjoin.tcl (1573 bytes)
Re: Scripts to unwrap PBC from REMD trajectory Olaf Lenz (Fri Mar 16 2007 - 02:52:57 CDT)
1. 2.0.tar.gz (15717 bytes)
OmpF biological unit Adrian Kaats (Thu Mar 15 2007 - 18:58:17 CDT)
1. 2OMF.pdb1.gz (170370 bytes)
Re: reading charmm files Axel Kohlmeyer (Mon Mar 05 2007 - 11:56:34 CST)
1. fixamberwater.tcl (903 bytes)
Re: New Molecule (or Load Data) resets viewpoint of Display. Why? Axel Kohlmeyer (Mon Mar 05 2007 - 05:24:25 CST)
1. reload.tcl (1244 bytes)
Re: vmd/gaussian cubes Axel Kohlmeyer (Fri Mar 02 2007 - 11:48:20 CST)
1. iso.tcl (2737 bytes)
Re: Same pdb file, different image hamdi (Fri Feb 23 2007 - 03:02:57 CST)
1. dyn2HIU.pdb (25203 bytes)
2. 2HIU1.pdb (24886 bytes)
Same pdb file, different image Hai-Jun Su (Thu Feb 22 2007 - 22:11:27 CST)
1. dyn2HIU.pdb (26148 bytes)
2. 2HIU1.pdb (24886 bytes)
3. snapshot.JPG (18812 bytes)
Re: Strange MOL2 export Mario Valle (Mon Feb 19 2007 - 09:12:33 CST)
1. ferrocene.mol2 (2527 bytes)
2. ferrocene.pdb (1577 bytes)
Strange MOL2 export Mario Valle (Sat Feb 17 2007 - 12:21:42 CST)
1. VANADATE.mol2 (3460 bytes)
Assigning Color Codes for stress/force in .xyz trajectory files Adrian Koh (Fri Feb 09 2007 - 00:08:26 CST)
1. kohsj.vcf (398 bytes)
Re: about CHARMM electrostaic potential John Stone (Mon Feb 05 2007 - 11:03:04 CST)
1. pbeqmap.vmd (14321 bytes)
Regarding com file error Javaria Ahmed (Sun Feb 04 2007 - 23:23:40 CST)
1. paratool_screen_geo_opt_input.bmp (1455542 bytes)
Re: Getting (or changing) molinfo matrices John Stone (Wed Jan 24 2007 - 12:05:08 CST)
1. save_state.tcl (17833 bytes)
script to load dcds from Replica Exchange simulations by Temperature Ana Celia Araujo Vila Verde (Mon Jan 15 2007 - 17:30:44 CST)
1. REselectByTemp.tcl (4990 bytes)
Re: VMD scene information John Stone (Thu Jan 11 2007 - 15:15:22 CST)
1. camfly.tcl (4726 bytes)
2. camsetup.tcl (488 bytes)
create new topology file for new molecule _at_huji.ac.il (Tue Jan 09 2007 - 10:06:25 CST)
1. sorbitol_alone.pdb (130 bytes)
2. one_sorbitol.pdb (2105 bytes)
3. create_osmolite.pgn (274 bytes)
4. top_all27_prot_lipid_ret_csff_adam_spc.rtf (251091 bytes)
sasa by residue alexandra.marques_at_fc.up.pt (Mon Jan 08 2007 - 19:01:04 CST)
1. _sasa_res.tcl (3258 bytes)
Save coordinates from MD simulation Per Jr. Greisen (Thu Jan 04 2007 - 10:55:34 CST)
1. strange_bond.pdb (5605 bytes)
Re: using namdenergy with amber prmtop file Peter Freddolino (Wed Jan 03 2007 - 20:09:29 CST)
1. amber.tcl (63052 bytes)
RE: (); [Fwd: PET force field & topolgy files etc.] wolfinbm_at_uci.edu (Wed Dec 27 2006 - 14:23:22 CST)
1. PET_force_field___topolgy_files_etc..msg (18651 bytes)
2. PETE_good.xbgf (4466 bytes)
vmd questions _at_huji.ac.il (Thu Dec 21 2006 - 05:09:59 CST)
1. create_replica.tcl (5967 bytes)
Voicemail from Pavan Ghatty (5 seconds) pavan.vmd_at_gmail.com (Thu Dec 21 2006 - 18:17:51 CST)
1. part (121 bytes)
Re: VMD 1.8.3 works ok for 64-bit windows, but not VMD 1.8.5 Adrian Koh (Thu Nov 23 2006 - 23:31:49 CST)
1. kohsj.vcf (398 bytes)
VMD 1.8.3 works ok for 64-bit windows, but not VMD 1.8.5 Adrian Koh (Thu Nov 23 2006 - 22:07:27 CST)
1. kohsj.vcf (398 bytes)
Installing VMD Windows version on 64-bit Windows Environment Adrian Koh (Tue Nov 21 2006 - 21:30:01 CST)
1. kohsj.vcf (398 bytes)
VMD 1.8.5 startup Chang, Christopher (Wed Nov 08 2006 - 14:56:37 CST)
1. Christopher_H_Chang.vcf (586 bytes)
Dynamic selection of residues on a trajectory amit_at_mbu.iisc.ernet.in (Tue Nov 07 2006 - 11:07:13 CST)
1. amit.tgz (206635 bytes)
VMD trajectory/structure/coordinate format Olaf Lenz (Thu Oct 26 2006 - 07:28:52 CDT)
1. vtfplugin.c (22580 bytes)
Free Linux Cluster-Building Workshop - 30 Nov 2006 - 01 Dec 2006 Tim Skirvin (Mon Oct 16 2006 - 12:34:13 CDT)
1. part (186 bytes)
Re: Missing main menu Stefan Gerlach (Tue Oct 10 2006 - 04:03:10 CDT)
1. part (190 bytes)
Missing main menu Stefan Gerlach (Mon Oct 09 2006 - 13:12:52 CDT)
1. part (190 bytes)
Re: Question about measure gofr Jennie Thomas (Fri Oct 06 2006 - 15:36:16 CDT)
1. script.tcl (775 bytes)
cutting short a DMPC bilayer in VMD Akshay Patny (Thu Oct 05 2006 - 21:23:43 CDT)
1. dmpc_288.pdb (3351906 bytes)
Re: problem viewing cube files Axel Kohlmeyer (Thu Oct 05 2006 - 10:51:17 CDT)
1. isosurf.vmd (629 bytes)
Re: problem viewing cube files Dr. Seth Olsen (Thu Oct 05 2006 - 03:32:34 CDT)
1. VMDrunner.py (975 bytes)
2. m0c1211s2ss1i90diff.cube (6573752 bytes)
3. test.jpg (31404 bytes)
problem viewing cube files Dr. Seth Olsen (Tue Oct 03 2006 - 21:10:33 CDT)
1. crap.jpg (28722 bytes)
Possible bug in LAMMPS plugin Lutz Maibaum (Mon Oct 02 2006 - 15:10:43 CDT)
1. np1.lammpstrj (77167 bytes)
2. np2.lammpstrj (77167 bytes)
HBonds criterion François-Xavier Coudert (Tue Sep 26 2006 - 11:18:22 CDT)
1. vmd.xyz (64 bytes)
Re: What unit system does VMD use? Dr. Seth Olsen (Thu Sep 21 2006 - 21:50:58 CDT)
1. Angstrom3.jpg (17928 bytes)
2. Angstrom4.jpg (14707 bytes)
Re: What unit system does VMD use? Dr. Seth Olsen (Thu Sep 21 2006 - 21:38:01 CDT)
1. Angstrom2.jpg (4229 bytes)
Re: What unit system does VMD use? Dr. Seth Olsen (Thu Sep 21 2006 - 21:30:53 CDT)
1. SOlsen_vmdrc (1929 bytes)
Re: What unit system does VMD use? Dr. Seth Olsen (Thu Sep 21 2006 - 21:25:09 CDT)
1. VMDAngstrom.py (233 bytes)
2. AngstromScale.pdb (162 bytes)
3. Angstrom.jpg (3528 bytes)
RE: psf for protein Al-Rawi, Ahlam (Tue Sep 19 2006 - 12:03:55 CDT)
1. beta1.pdb (17820 bytes)
Re: protein in membrane daniel aguayo (Wed Sep 13 2006 - 21:32:19 CDT)
1. combine.dav (4404 bytes)
Re: drawing of direction vectors for conformational transition Peter Freddolino (Wed Sep 13 2006 - 17:34:34 CDT)
1. porcplot.tcl (571 bytes)
Re: drawing of direction vectors for conformational transition Axel Kohlmeyer (Wed Sep 13 2006 - 14:18:03 CDT)
1. cavec.tcl (457 bytes)
2. vmd_draw_lib.tcl (5804 bytes)
Re: Labels not appearing with "load state" Ignacio Fernández Galván (Mon Sep 11 2006 - 02:28:23 CDT)
1. test.zip (3554 bytes)
RE: How to produce a graph as the one attached, using VMD? Jiapu.Zhang_at_csiro.au (Sun Sep 10 2006 - 23:49:37 CDT)
1. snap_en.jpg (44638 bytes)
How to produce a graph as the one attached, using VMD? Jiapu.Zhang_at_csiro.au (Sun Sep 10 2006 - 21:32:20 CDT)
1. snap.jpg (44511 bytes)
Opening DCD file >2GB Lechuga, Javier (Sun Sep 10 2006 - 13:35:52 CDT)
1. Error_message.bmp (108598 bytes)
2. View_script.tcl (106 bytes)
Re: How to use bigdcd in vmd batch mode? John Stone (Fri Sep 08 2006 - 16:32:18 CDT)
1. mybigdcd.tcl (2475 bytes)
How to use bigdcd in vmd batch mode? Hamsa Priya Mohana sundaram (Fri Sep 08 2006 - 09:44:45 CDT)
1. boxbig2.tcl (2630 bytes)
imposing period boundary conditions in a simulation with a crystal Ana Celia Araujo Vila Verde (Tue Sep 05 2006 - 11:13:06 CDT)
1. Fig2.jpg (130755 bytes)
2. Fig3.jpg (73614 bytes)
3. fig1.jpg (119154 bytes)
Re: qsub (torque/maui) and vmd Leonardo Trabuco (Mon Sep 04 2006 - 22:47:19 CDT)
1. mybigdcd.tcl (2475 bytes)
Re: looking for VMD draw scripts. John Stone (Fri Sep 01 2006 - 17:03:37 CDT)
1. graphicspick.tcl (1629 bytes)
Re: Dynamic bond calculation John Stone (Tue Aug 29 2006 - 14:27:46 CDT)
1. dynamicreps.tcl (1584 bytes)
Re: spikes in trajectory, problem with the alignment of frames Johannes Müllegger (Thu Aug 24 2006 - 13:50:20 CDT)
1. no_spikes.pdf (19332 bytes)
2. spikes_myscript.pdf (18260 bytes)
3. spikes.pdf (20415 bytes)
Axes dilema griadi_at_utalca.cl (Fri Aug 11 2006 - 18:11:07 CDT)
1. axes_paradox.JPG (287099 bytes)
Re: SASA calculation for a trajectory L. Michel Espinoza-Fonseca (Tue Aug 08 2006 - 21:31:51 CDT)
1. sasa.tcl (272 bytes)
Re: Altering Definition of Molecular Coloring Method Adrian Koh (Mon Jul 31 2006 - 23:18:19 CDT)
1. kohsj.vcf (398 bytes)
Altering Definition of Molecular Coloring Method Adrian Koh (Mon Jul 31 2006 - 05:08:56 CDT)
1. kohsj.vcf (398 bytes)
Re: RDF.tcl griadi_at_utalca.cl (Fri Jul 28 2006 - 17:01:24 CDT)
1. counting_waters.tcl (1199 bytes)
RE: vmd-l digest V1 #579 Mark Harder (Wed Jul 19 2006 - 21:09:08 CDT)
1. image001.gif (145 bytes)
Re: secondary structure assignment Melquiond (Mon Jul 17 2006 - 12:59:39 CDT)
1. test_AM_amber.pdb (74021 bytes)
2. test_AM_amber.prmtop (425261 bytes)
Re: secondary structure assignment Melquiond (Mon Jul 17 2006 - 09:23:03 CDT)
1. test_AM.pdb (27092 bytes)
Re: 3Dconnexion SpaceTraveler works Eugen Leitl (Fri Jul 14 2006 - 03:43:21 CDT)
1. signature.asc (192 bytes)
Re: Missing atom error while atoms exist in pdb Rima Chaudhuri (Thu Jul 06 2006 - 11:46:46 CDT)
1. NL_wb.conf (3423 bytes)
Missing atom error while atoms exist in pdb Rima Chaudhuri (Thu Jul 06 2006 - 11:05:50 CDT)
1. NL63.pdb (181909 bytes)
Re: Movie Maker in VMD kohsj_at_ihpc.a-star.edu.sg (Wed Jul 05 2006 - 12:01:00 CDT)
1. kohsj.vcf (256 bytes)
3Dconnexion SpaceTraveler works Eugen Leitl (Wed Jul 05 2006 - 07:54:46 CDT)
1. signature.asc (192 bytes)
Movie Maker in VMD Adrian Koh (Wed Jul 05 2006 - 04:30:49 CDT)
1. kohsj.vcf (398 bytes)
Re: Renaming Molecule Names in existing .xyz trajectory files Adrian Koh (Tue Jul 04 2006 - 23:07:57 CDT)
1. kohsj.vcf (398 bytes)
Renaming Molecule Names in existing .xyz trajectory files Adrian Koh (Tue Jul 04 2006 - 01:44:28 CDT)
1. kohsj.vcf (398 bytes)
Re: VMD crashed due to: vmd_LINUXAMD64: indirect_vertex_array.c:659: emit_DrawArrays_old: Assertion `elements_per_request >= count' failed Brett Pemberton (Tue Jun 27 2006 - 22:37:59 CDT)
1. signature.asc (190 bytes)
Re: VMD crashed due to: vmd_LINUXAMD64: indirect_vertex_array.c:659: emit_DrawArrays_old: Assertion `elements_per_request >= count' failed Brett Pemberton (Tue Jun 27 2006 - 20:59:56 CDT)
1. signature.asc (190 bytes)
Re: VMD crashed due to: vmd_LINUXAMD64: indirect_vertex_array.c:659: emit_DrawArrays_old: Assertion `elements_per_request >= count' failed Brett Pemberton (Tue Jun 27 2006 - 18:57:15 CDT)
1. signature.asc (190 bytes)
VMD crashed due to: vmd_LINUXAMD64: indirect_vertex_array.c:659: emit_DrawArrays_old: Assertion `elements_per_request >= count' failed Brett Pemberton (Tue Jun 27 2006 - 00:52:41 CDT)
1. signature.asc (190 bytes)
bonds forming during simulation Sandeep Prakash (Mon Jun 26 2006 - 12:59:50 CDT)
1. snap.jpeg (3717174 bytes)
Re: error using Namdenergy Peter Freddolino (Wed Jun 21 2006 - 20:15:21 CDT)
1. namdenergy.tcl (44985 bytes)
Re: error message occurred in RMSD Trajectory Tool John Stone (Thu Jun 22 2006 - 13:53:37 CDT)
1. rmsdtt.tcl (48232 bytes)
Average Structure and RMSD griadi_at_utalca.cl (Wed Jun 21 2006 - 11:28:33 CDT)
1. align_and_average_structure_english.tcl (4757 bytes)
Re: the python library error in VMD when do IED Shulin Zhuang (Thu Jun 15 2006 - 20:55:56 CDT)
1. evec.pev (1354768 bytes)
2. proj.ppj (261296 bytes)
3. fimpca.pdb (104386 bytes)
the python library error in VMD when do IED Shulin Zhuang (Thu Jun 15 2006 - 20:40:23 CDT)
1. Projection_Prolbem.jpg (80732 bytes)
the patch between segments for multiple chains molecule. Moumita Maiti (Fri Jun 02 2006 - 12:14:58 CDT)
1. 1kx5.pgn (1369 bytes)
psf generation Moumita Maiti (Fri Jun 02 2006 - 11:56:17 CDT)
1. 1kx5.pgn (1369 bytes)
Problems with APBS Compatibility Vyom Sharma (Thu Jun 01 2006 - 17:34:04 CDT)
1. sphere.pqr (40081 bytes)
2. my_functions (4727 bytes)
Re: Compilation John Stone (Thu May 25 2006 - 14:35:31 CDT)
1. main.c (3368 bytes)
Re: Solutions for stereo - is CRT technology dead? Eugen Leitl (Mon May 22 2006 - 07:03:57 CDT)
1. signature.asc (192 bytes)
secondary structure assignment Melquiond (Sun May 14 2006 - 15:34:43 CDT)
1. min19778.pdb (13562 bytes)
Re: How to select water near a certain residue if it is outside of the water box? Mgr. Lubos Vrbka (Wed May 10 2006 - 05:52:32 CDT)
1. smime.p7s (2341 bytes)
Re: dlpoly history files in vmd 1.8.4 Mgr. Lubos Vrbka (Fri May 05 2006 - 00:48:51 CDT)
1. smime.p7s (2341 bytes)
Re: dlpoly history files in vmd 1.8.4 Mgr. Lubos Vrbka (Thu May 04 2006 - 01:09:54 CDT)
1. smime.p7s (2341 bytes)
Re: search path and naming conventions for custom TCL scripts Axel Kohlmeyer (Wed May 03 2006 - 10:29:29 CDT)
1. mkidx (44 bytes)
dlpoly history files in vmd 1.8.4 Mgr. Lubos Vrbka (Wed May 03 2006 - 02:26:50 CDT)
1. smime.p7s (2341 bytes)
Re: coloring trajectory depending on coordination number Mgr. Lubos Vrbka (Thu Apr 27 2006 - 05:06:46 CDT)
1. smime.p7s (2341 bytes)
Re: tcl question Mgr. Lubos Vrbka (Wed Apr 26 2006 - 06:29:48 CDT)
1. smime.p7s (2341 bytes)
Re: Problem with wait John Stone (Tue Apr 25 2006 - 12:59:07 CDT)
1. dmm.tcl (1525 bytes)
tcl question Mgr. Lubos Vrbka (Tue Apr 25 2006 - 03:31:16 CDT)
1. smime.p7s (2341 bytes)
question Maria Konstantakaki (Thu Apr 20 2006 - 10:38:20 CDT)
1. final.pdb (1131007 bytes)
a question about ribbon representation yzhou_at_chem.umn.edu (Wed Apr 12 2006 - 15:07:27 CDT)
1. 1Q6Odeladdnew.pdb (306907 bytes)
parameter file for DAD Yu Wang (Fri Apr 07 2006 - 09:18:55 CDT)
1. wy0519.vcf (268 bytes)
Re: latest beta nVidia driver for Windows looks good so far... Eugen Leitl (Tue Apr 04 2006 - 02:04:43 CDT)
1. signature.asc (192 bytes)
WARNING: Coordinates will be rotated to comply ... Peter Hamm (Mon Apr 03 2006 - 08:01:57 CDT)
1. out0.cube (438910 bytes)
Re: how to show biological unit coordiates from PDB using VMD? John Stone (Fri Mar 31 2006 - 16:15:14 CST)
1. mono2poly.tcl (3586 bytes)
Re: how to show biological unit coordiates from PDB using VMD? John Stone (Fri Mar 31 2006 - 15:52:08 CST)
1. mono2poly.tcl (3208 bytes)
Re: stereo on MacG5 with Nvidia GeForce FX 5200 Robert Brunner (Wed Mar 29 2006 - 16:44:12 CST)
1. PGP.sig (187 bytes)
Re: pdb - generation Florian Haberl (Tue Mar 21 2006 - 09:06:57 CST)
1. part (190 bytes)
Poor Hydrogen Placement in AutoPSF Brian Bennion (Fri Mar 17 2006 - 16:39:15 CST)
1. hewl.pdb (80637 bytes)
2. hewl_ionized.pdb (1296772 bytes)
Re: Convert an ascii matrix to an image Jérôme Hénin (Mon Mar 13 2006 - 15:22:11 CST)
1. stride2png.awk (1701 bytes)
changing colours isosurface L. Michel Espinoza-Fonseca (Mon Mar 13 2006 - 10:44:23 CST)
1. qdens.GIF (89432 bytes)
Re: radial distribution Peter Freddolino (Fri Mar 10 2006 - 10:52:38 CST)
1. radden.tcl (998 bytes)
Re: namd-l: Aligning structures Peter Freddolino (Thu Mar 09 2006 - 21:37:05 CST)
1. align_frames.tcl (409 bytes)
Re: pbc and vmd Axel Kohlmeyer (Mon Mar 06 2006 - 01:01:20 CST)
1. moveframes.tcl (624 bytes)
2. set_unitcell.tcl (1029 bytes)
3. pbcwrap.tcl (8933 bytes)
Re: Q:selection of atoms on the surface of a molecule Mgr. Lubos Vrbka (Wed Mar 01 2006 - 00:44:11 CST)
1. _sasa_res.tcl (3052 bytes)
Free Cluster-Building Workshops - 16-17 Mar 2006, 20-21 Apr 2006 Tim Skirvin (Mon Feb 13 2006 - 13:33:09 CST)
1. part (186 bytes)
chain fails Yu Chen (Fri Feb 10 2006 - 14:52:43 CST)
1. 1.pdb (613791 bytes)
Re: vmd installation on the server andrea spitaleri (Tue Jan 31 2006 - 03:25:19 CST)
1. firefox_80x15.png (1063 bytes)
vmd installation on the server andrea spitaleri (Mon Jan 30 2006 - 09:31:46 CST)
1. firefox_80x15.png (1063 bytes)
Changing Graphical Representations Adrian Koh (Wed Jan 25 2006 - 00:15:54 CST)
1. kohsj.vcf (377 bytes)
problem with APBS pqr generation... Ravinder Abrol (Mon Jan 23 2006 - 20:26:17 CST)
1. pdb22.pdb (45897 bytes)
2. pdb22.pqr (39933 bytes)
Adding New Color Definitions to Color Form Adrian Koh (Tue Jan 24 2006 - 03:08:48 CST)
1. kohsj.vcf (377 bytes)
Problem with biotin autopsf Lin (Thu Jan 19 2006 - 22:17:02 CST)
1. temp.top (447350 bytes)
Changing Default Settings for VMD Main Window Adrian Koh (Thu Jan 19 2006 - 05:08:23 CST)
1. kohsj.vcf (377 bytes)
script no reading correct number of frames syma (Thu Jan 12 2006 - 10:03:02 CST)
1. contacts.tcl (504 bytes)
Re: loading a new molecule without changing the view Axel Kohlmeyer (Fri Jan 06 2006 - 14:05:40 CST)
1. reload.tcl (1244 bytes)
Help on MD animation with VMD yuhl (Tue Jan 03 2006 - 17:41:07 CST)
1. yuhl.vcf (122 bytes)
Re: babel compilation error Eugen Leitl (Fri Dec 09 2005 - 11:30:24 CST)
1. signature.asc (190 bytes)
Re: spaceballs, etc. Eugen Leitl (Fri Dec 09 2005 - 03:26:35 CST)
1. signature.asc (190 bytes)
spaceballs, etc. Eugen Leitl (Thu Dec 08 2005 - 16:33:53 CST)
1. signature.asc (190 bytes)
Re: APBS plugin John Stone (Wed Dec 07 2005 - 17:08:21 CST)
1. apbsrun.tcl (61307 bytes)
Re: MSMS problem Michel Sanner (Tue Dec 06 2005 - 15:33:09 CST)
1. msms.i86Linux2.2.5.5 (429944 bytes)
RE: discriminate aromatic ring face Michel Espinoza-Fonseca (Mon Dec 05 2005 - 10:45:47 CST)
1. firefox_80x15.png (1063 bytes)
RE: Uncharged terminal ends? Michel Espinoza-Fonseca (Tue Nov 22 2005 - 05:41:24 CST)
1. good.pdb (2860 bytes)
2. good.psf (8339 bytes)
RE: Uncharged terminal ends? hodak_at_chips.ncsu.edu (Tue Nov 22 2005 - 05:13:43 CST)
1. HG3.pdb (1189 bytes)
2. script.tcl (2894 bytes)
Re: calculate rmsd in a loop:feedback [sorry if you get it twice] Nuno R. L. Ferreira (Fri Nov 18 2005 - 04:10:16 CST)
1. firefox_80x15.png (1063 bytes)
Re: Re: Réf. : calculate rmsd in a loop:feedback [sorry if you get it twice] Nuno R. L. Ferreira (Thu Nov 17 2005 - 04:34:44 CST)
1. firefox_80x15.png (1063 bytes)
Re: calculate rmsd in a loop:feedback [sorry if you get it twice] Nuno R. L. Ferreira (Thu Nov 17 2005 - 03:31:13 CST)
1. firefox_80x15.png (1063 bytes)
illegal mouse mode Axel Kohlmeyer (Fri Nov 11 2005 - 13:33:13 CST)
1. clickme.tcl (748 bytes)
Updating color_scale_bar_new.tcl JOSE MANUEL ROMO HERRERA (Tue Nov 08 2005 - 13:19:08 CST)
1. color_scale_bar_new2.tcl (4807 bytes)
help with modifying script syma (Wed Nov 02 2005 - 11:47:48 CST)
1. newcontacts.tcl (6744 bytes)
[selection problem] When I choose all not 'solvent', one residue is gone?v1.8.3 Stanley Lan (Fri Oct 28 2005 - 11:47:06 CDT)
1. lmmmta1.dat (89979 bytes)
2. lmmsxmd2.dat (596216 bytes)
3. c9s3.pdb (193974 bytes)
Re: add a new file type to VMD on linux(FC4) John Stone (Fri Oct 28 2005 - 10:24:32 CDT)
1. vmfplugin2.C (6292 bytes)
add a new file type to VMD on linux(FC4) baogen duan (Thu Oct 27 2005 - 22:32:59 CDT)
1. vmfplugin.C (5468 bytes)
2. ch3oh.vmf (610 bytes)
Re: removing waters (gramicidin example) Charles McCallum (Thu Oct 27 2005 - 15:46:22 CDT)
1. correct.jpg (15239 bytes)
Re: tcl/python and readline not working Robert Brunner (Thu Oct 27 2005 - 11:09:25 CDT)
1. smime.p7s (2363 bytes)
2. PGP.sig (187 bytes)
Re: Starting v1.8.4a20 vs. v1.8.2a22 Stephen P. Molar, Ph.D. (Thu Oct 20 2005 - 16:12:45 CDT)
1. diff.vmd.txt (108 bytes)
new macs out Eugen Leitl (Wed Oct 19 2005 - 15:10:22 CDT)
1. signature.asc (190 bytes)
Re: Cannot load Gromos96 trajectory file (attached) Axel Kohlmeyer (Mon Oct 17 2005 - 19:37:14 CDT)
1. gromos2dcd.c (19882 bytes)
Re: gamess plugin error of vmd 1.8.4a22 on windows mashaojie163 (Sat Oct 15 2005 - 01:20:40 CDT)
1. ma.tar.gz (737847 bytes)
rdf.tcl one more time bizoniusz_at_o2.pl (Mon Oct 17 2005 - 10:19:28 CDT)
1. RDF.tcl (10382 bytes)
position of protein respect to membrane andrea spitaleri (Mon Sep 26 2005 - 09:35:10 CDT)
1. firefox_80x15.png (1063 bytes)
Re: Ployhedra in VMD Jen-Chang Chen (Mon Sep 26 2005 - 07:56:53 CDT)
1. tetrahedra.gif (1144 bytes)
2. octahedra.gif (1304 bytes)
Re: Lipid Order Parameter Justin Gullingsrud (Fri Sep 23 2005 - 11:13:16 CDT)
1. orderparam2.tcl (4693 bytes)
Re: Import gromos output file into VMD without format conversion? Axel Kohlmeyer (Thu Sep 22 2005 - 07:32:55 CDT)
1. gromos2dcd.c (19882 bytes)
Re: Lipid Order Parameter Justin Gullingsrud (Wed Sep 21 2005 - 12:26:37 CDT)
1. orderparam.tcl (3729 bytes)
Re: problem with coloring surface by electrostatic potential Eugen Leitl (Wed Sep 21 2005 - 03:50:47 CDT)
1. signature.asc (190 bytes)
Re: DCD file format John Stone (Thu Sep 15 2005 - 11:07:50 CDT)
1. dcdplugin.c (35191 bytes)
Re: setting different colors Justin Gullingsrud (Sun Aug 21 2005 - 15:55:04 CDT)
1. colorBySpeed.tcl (749 bytes)
Re: Periodic boundary conditions Justin Gullingsrud (Thu Aug 18 2005 - 13:43:38 CDT)
1. wrap.tcl (1058 bytes)
Re: more precision in inverse trig functions Robert Brunner (Wed Aug 03 2005 - 09:22:21 CDT)
1. smime.p7s (2363 bytes)
2. PGP.sig (187 bytes)
Re: problems to launch VMD 1.83 in MAC os x tiger Robert Brunner (Fri Jul 08 2005 - 15:17:02 CDT)
1. smime.p7s (2363 bytes)
2. PGP.sig (187 bytes)
Re: VMD 1.8.4 test builds, 32-bit and 64-bit AIX5... Ioana Cozmuta (Thu Jun 23 2005 - 17:12:47 CDT)
1. err.vmd (17423 bytes)
autoimd on windows Anna Modzelewska (Mon Jun 20 2005 - 06:40:29 CDT)
1. autoimd.log (2741 bytes)
Strange VMD output Chang, Christopher (Fri Jun 17 2005 - 15:02:57 CDT)
1. 95.pdb (11543 bytes)
2. 96.pdb (11543 bytes)
3. A0095.pdb (76608 bytes)
4. A0096.pdb (76608 bytes)
5. BDanimate.tcl (548 bytes)
6. VMD.strange (1675 bytes)
Re: autoimd error Jordi Cohen (Wed Jun 15 2005 - 13:13:25 CDT)
1. autoimd.log (2423 bytes)
autoimd error Anna Modzelewska (Wed Jun 15 2005 - 09:35:01 CDT)
1. autoimd.log (2423 bytes)
Adding Salt to a system Thomas C. Bishop (Thu May 19 2005 - 10:09:26 CDT)
1. DashOfSalt.vmd (5924 bytes)
Re: VMD does not run on MacOS X 10.4 Tiger Robert Brunner (Mon May 16 2005 - 22:11:18 CDT)
1. smime.p7s (2363 bytes)
GNU-Darwin rides Tiger, packages back on-line proclus_at_gnu-darwin.org (Fri May 06 2005 - 11:05:55 CDT)
1. part (190 bytes)
Error Encountered in making vmdmovie Adrian Koh (Tue May 03 2005 - 02:42:00 CDT)
1. kohsj.vcf (377 bytes)
Color bar in VMD Dan Wright (Fri Apr 22 2005 - 16:23:36 CDT)
1. color_scale_bar_new.tcl (4230 bytes)
Re: a question about get the coordinates in vector form Eugen Leitl (Fri Apr 15 2005 - 15:45:24 CDT)
1. part (199 bytes)
Re: CA-CA distances in a trayectory Luis Gracia (Thu Apr 14 2005 - 15:44:45 CDT)
1. contacts.vmd (4942 bytes)
2. basics.tcl (568 bytes)
Re: CA-CA distances in a trayectory Luis Gracia (Thu Apr 14 2005 - 12:18:00 CDT)
1. contacts.vmd (3963 bytes)
2. basics.tcl (568 bytes)
Re: Customizing VMD Sessions Adrian Koh (Thu Apr 14 2005 - 06:03:41 CDT)
1. kohsj.vcf (377 bytes)
Customizing VMD Sessions Adrian Koh (Thu Apr 14 2005 - 02:49:19 CDT)
1. kohsj.vcf (377 bytes)
Re: Maximum numbers of atoms Nicolas CHARVIN (Wed Apr 06 2005 - 11:10:12 CDT)
1. BigConfig_under_Qmol.gif (180959 bytes)
dynamic coloring Leonor Cruzeiro (Mon Apr 04 2005 - 11:22:02 CDT)
1. color_test1.vmd (2262 bytes)
Re: GRD file format Axel Kohlmeyer (Wed Mar 23 2005 - 01:33:31 CST)
1. trimcube.c (9120 bytes)
New Sharp 3D Notebook Available with Linux Eugen Leitl (Tue Mar 22 2005 - 05:35:19 CST)
1. part (199 bytes)
problem with DPPC topology Alexis Salas (Tue Mar 08 2005 - 14:29:43 CST)
1. dppc_alsalas.pdb (10061 bytes)
2. dppc_4.pdb (10754 bytes)
Re: VMD 1.8.2 and 1.8.3 fail on MacOS X after upgrade to 10.3.8 Alexander Peyser (Wed Mar 02 2005 - 12:45:30 CST)
1. apeyser.vcf (130 bytes)
Re: VMD 1.8.2 and 1.8.3 fail on MacOS X after upgrade to 10.3.8 Robert Brunner (Wed Mar 02 2005 - 10:36:54 CST)
1. PGP.sig (187 bytes)
Re: User colors and povray Alexander Peyser (Wed Feb 23 2005 - 16:01:19 CST)
1. apeyser.vcf (130 bytes)
Re: How to image molecules back into a PBC box? Olaf Lenz (Wed Feb 16 2005 - 03:08:15 CST)
1. olpbcwrap.tcl (4306 bytes)
Defining Bonds in .xyz file format Adrian Koh (Wed Feb 16 2005 - 02:29:09 CST)
1. kohsj.vcf (377 bytes)
Re: slowing the movie animation Axel Kohlmeyer (Mon Feb 14 2005 - 03:45:59 CST)
1. repeat-frame.diff (2989 bytes)
Re: volume shading in 1.8.3b1 ? Axel Kohlmeyer (Mon Feb 07 2005 - 14:27:53 CST)
1. snap.jpg (49478 bytes)
molecular orientation li (Fri Jan 28 2005 - 21:10:26 CST)
1. axis.tcl (6380 bytes)
VMD and CPMD rschurhammer_at_chimie.u-strasbg.fr (Wed Jan 26 2005 - 04:47:23 CST)
1. snap2.jpg (13217 bytes)
which nForce to use? Eugen Leitl (Tue Jan 25 2005 - 03:23:18 CST)
1. part (199 bytes)
Screen corruption Sylvain EDALEINE (Wed Dec 15 2004 - 04:16:22 CST)
1. capture.jpg (333287 bytes)
Re: Virtual Reality and VMD Eugen Leitl (Tue Dec 14 2004 - 10:41:33 CST)
1. part (199 bytes)
Re: [linux-elitists] ATI Radeon support (fwd from deejoe@raccoon.com) Eugen Leitl (Tue Dec 14 2004 - 03:33:02 CST)
1. part (199 bytes)
Re: Thanks :) Garf (Wed Dec 08 2004 - 10:02:08 CST)
1. part (147 bytes)
Re: bridging_waters.tcl error and usage Justin Gullingsrud (Mon Nov 08 2004 - 13:04:00 CST)
1. closewater.tcl (1817 bytes)
Re: bridging_waters.tcl error and usage Justin Gullingsrud (Mon Nov 08 2004 - 12:51:05 CST)
1. closewater.tcl (1984 bytes)
Re: Hi Garf (Fri Nov 05 2004 - 15:29:42 CST)
1. part (127 bytes)
Re: VMD scripting questions Axel Kohlmeyer (Fri Oct 29 2004 - 08:26:48 CDT)
1. with-color.vmd (864 bytes)
Re: Thank you! Garf (Fri Oct 29 2004 - 04:13:47 CDT)
1. part (145 bytes)
Re: error while loading shared libraries: libGLU.so.1 Cheri M Turman (Tue Oct 26 2004 - 15:12:07 CDT)
1. cturman.vcf (336 bytes)
RE: Problems with povray Luis Rosales (Tue Oct 26 2004 - 15:11:53 CDT)
1. 03.png (142488 bytes)
2. 02.png (503476 bytes)
3. 01.png (154053 bytes)
Re: error while loading shared libraries: libGLU.so.1 Cheri M Turman (Tue Oct 26 2004 - 13:37:56 CDT)
1. cturman.vcf (336 bytes)
Re: error while loading shared libraries: libGLU.so.1 Cheri M Turman (Tue Oct 26 2004 - 12:21:29 CDT)
1. cturman.vcf (336 bytes)
Re: error while loading shared libraries: libGLU.so.1 Cheri M Turman (Thu Oct 21 2004 - 14:27:46 CDT)
1. cturman.vcf (336 bytes)
error while loading shared libraries: libGLU.so.1 Cheri M Turman (Thu Oct 21 2004 - 13:24:12 CDT)
1. cturman.vcf (336 bytes)
Re: VMD on Linux Fedora Core 2 Eugen Leitl (Wed Oct 13 2004 - 11:28:18 CDT)
1. part (199 bytes)
Re: measure fit error?? Justin Gullingsrud (Fri Oct 08 2004 - 14:26:10 CDT)
1. rmsd.tcl (1356 bytes)
Re: Changing the atom species during animation John Stone (Wed Sep 15 2004 - 17:56:07 CDT)
1. usercolor.vmd (974 bytes)
RE: Counting number of hydrogen bonds in the representation Ahmet Bakan (Wed Sep 15 2004 - 03:39:56 CDT)
1. hbond.tcl (5158 bytes)
new user: how to load output file Paul Christopher Millett (Sun Sep 05 2004 - 12:04:40 CDT)
1. image002.gif (86 bytes)
2. image001.gif (86 bytes)
Periodic display problem Keith Refson (Tue Aug 24 2004 - 05:34:31 CDT)
1. vmdtest.pdb (3736 bytes)
Re: Trajectory Files John Stone (Mon Aug 09 2004 - 10:08:36 CDT)
1. jsplugin.c (11167 bytes)
2. endianswap.h (4750 bytes)
3. fastio.h (5122 bytes)
Re: Trajectory Files Axel Kohlmeyer (Sun Aug 08 2004 - 13:36:35 CDT)
1. ReadDCD.h (2233 bytes)
2. ReadDCD.c (20408 bytes)
Re: 1.8.3 John Stone (Fri Jul 30 2004 - 14:33:35 CDT)
1. README (12125 bytes)
Extensions to the selection language Olaf Lenz (Thu Jul 22 2004 - 11:08:38 CDT)
1. signature.asc (253 bytes)
Re: Axes are not rotated? Olaf Lenz (Thu Jul 22 2004 - 10:50:06 CDT)
1. signature.asc (253 bytes)
Re: Picking atoms: romoving or changing the position of atoms Olaf Lenz (Tue Jul 20 2004 - 12:11:17 CDT)
1. signature.asc (253 bytes)
Re: FPS indicator color Olaf Lenz (Tue Jul 20 2004 - 12:06:03 CDT)
1. signature.asc (253 bytes)
Axes are not rotated? Olaf Lenz (Mon Jul 19 2004 - 10:12:29 CDT)
1. signature.asc (253 bytes)
FPS indicator color Olaf Lenz (Mon Jul 19 2004 - 10:06:55 CDT)
1. signature.asc (253 bytes)
visualization of electroly solvation shells Axel Kohlmeyer (Mon Jul 19 2004 - 04:09:34 CDT)
1. solv-shell.jpg (94648 bytes)
Re: File Reader Plugin Issues Olaf Lenz (Mon Jul 19 2004 - 06:14:29 CDT)
1. signature.asc (253 bytes)
Re: Picking atoms: romoving or changing the position of atoms Olaf Lenz (Mon Jul 19 2004 - 03:44:44 CDT)
1. signature.asc (253 bytes)
Picking atoms Olaf Lenz (Fri Jul 16 2004 - 10:06:46 CDT)
1. signature.asc (253 bytes)
"Selection not understood" Olaf Lenz (Fri Jul 16 2004 - 09:47:04 CDT)
1. signature.asc (253 bytes)
File Reader Plugin Issues Olaf Lenz (Fri Jul 16 2004 - 09:40:33 CDT)
1. signature.asc (253 bytes)
Default radii and colors Olaf Lenz (Fri Jul 16 2004 - 09:21:03 CDT)
1. signature.asc (253 bytes)
Re: Elliptic molecules Olaf Lenz (Fri Jul 16 2004 - 09:07:36 CDT)
1. signature.asc (253 bytes)
Re: Elliptic molecules Olaf Lenz (Thu Jul 15 2004 - 09:56:21 CDT)
1. signature.asc (253 bytes)
Re: Updated Bonding Connectivity each frame Axel Kohlmeyer (Tue Jul 13 2004 - 15:28:17 CDT)
1. molmovie.vmd (1029 bytes)
Re: [MMTK] Visualization to an image file (fwd from hinsen@cnrs-orleans.fr) Eugen Leitl (Mon Jul 12 2004 - 08:36:58 CDT)
1. part (199 bytes)
Re: visualizing trr files Axel Kohlmeyer (Fri Jun 18 2004 - 13:46:13 CDT)
1. pbcwrap.tcl (8933 bytes)
RE: Torsional Angles Ahmet Bakan (Mon May 31 2004 - 15:54:52 CDT)
1. phi.tcl (932 bytes)
RE: Torsional Angles Ahmet Bakan (Sun May 30 2004 - 19:41:49 CDT)
1. phi.tcl (540 bytes)
Torsional Angles Ahmet Bakan (Wed May 26 2004 - 13:52:53 CDT)
1. minstr.pdb (2823 bytes)
Re: changing the representation of all loaded molecules Axel Kohlmeyer (Thu May 20 2004 - 13:35:08 CDT)
1. clone_reps.tcl (2383 bytes)
2. clonerep.tcl (4326 bytes)
autoionize script amodzelewska_at_dns.iimcb.gov.pl (Sun May 16 2004 - 13:21:58 CDT)
1. ions.top (1176 bytes)
Re: Missing bonds Karsten Suhre (Thu May 06 2004 - 01:44:52 CDT)
1. InGaAs.vmd (4983 bytes)
Missing bonds Min Chin Chai (Wed May 05 2004 - 17:28:28 CDT)
1. InGaAs_QD_small.pdb (46772 bytes)
RE: Selection problem on TkCon Ahmet Bakan (Tue May 04 2004 - 18:57:39 CDT)
1. hbond.tcl (5025 bytes)
RE: Selection problem on TkCon Ahmet Bakan (Tue May 04 2004 - 06:47:55 CDT)
1. hbond.tcl (3554 bytes)
Required Assistance for VMD zaheer qasmi (Sat Apr 17 2004 - 09:16:34 CDT)
1. vmd.jpg (66277 bytes)
Looking for assistance on vmd Dr. Zaheer-ul-Haq Qasmi (Sat Apr 17 2004 - 11:45:53 CDT)
1. vmd.jpg (66277 bytes)
Re: Viewing MD trajectories John Stone (Tue Apr 13 2004 - 15:59:32 CDT)
1. fixed.xyz (126141 bytes)
2. deleteallbonds.tcl (419 bytes)
Re: Viewing MD trajectories John Stone (Tue Apr 13 2004 - 15:12:08 CDT)
1. foo.xyz (55231 bytes)
Re: how to make whole biological unit / virus capsid from pdb BIOMT records John Stone (Tue Apr 06 2004 - 09:59:56 CDT)
1. mergemultiframepdb.tcl (2384 bytes)
Re: startup failure Cheri M Turman (Mon Apr 05 2004 - 12:47:54 CDT)
1. cturman.vcf (336 bytes)
startup failure Cheri M Turman (Fri Apr 02 2004 - 15:29:00 CST)
1. cturman.vcf (336 bytes)
startup errors and variations of installation Cheri M Turman (Thu Apr 01 2004 - 14:43:58 CST)
1. cturman.vcf (336 bytes)
startup failure Cheri M Turman (Thu Apr 01 2004 - 14:24:14 CST)
1. cturman.vcf (336 bytes)
Re: animating drawn objects John Stone (Thu Apr 01 2004 - 13:26:17 CST)
1. frameupdate.vmd (717 bytes)
Re: about dynamical change color of atoms John Stone (Thu Apr 01 2004 - 12:57:33 CST)
1. usercolor.vmd (974 bytes)
Re: JMV Robert Brunner (Wed Mar 31 2004 - 16:36:17 CST)
1. PGP.sig (187 bytes)
Re: xyz to psf John Stone (Wed Mar 24 2004 - 15:47:03 CST)
1. deleteallbonds.tcl (419 bytes)
Re: coloring method User John Stone (Mon Mar 22 2004 - 11:18:35 CST)
1. usercolor.vmd (974 bytes)
Re: coloring of trajectory John Stone (Thu Mar 11 2004 - 14:29:47 CST)
1. usercolor.vmd (974 bytes)
Formation of a gold layer lmfok_at_acae.cuhk.edu.hk (Mon Mar 08 2004 - 20:41:33 CST)
1. au.pdb (4991 bytes)
Using VMD for non-atomic simulations? Olaf Lenz (Wed Mar 03 2004 - 03:51:39 CST)
1. signature.asc (253 bytes)
Re: Color error on loading Olaf Lenz (Wed Mar 03 2004 - 03:12:02 CST)
1. signature.asc (253 bytes)
Re: repitition of residue numbers in LIPIDS Jim Phillips (Mon Feb 16 2004 - 17:55:50 CST)
1. lipids.vmd (1990 bytes)
Re: Some pdb file contains many frames : How Can I retrieve all in a frame... John Stone (Mon Feb 16 2004 - 17:25:36 CST)
1. mergemultiframepdb.tcl (2384 bytes)
Re: any body else have VMD problems with Linux + ATI FireGL X1-256p + fglrx-glc22-4.3.0-3.7.0 Dallas Warren (Wed Feb 11 2004 - 17:14:28 CST)
1. XF86Config.txt (2338 bytes)
Re: Spatial Distributionb Functions Oliver Beckstein (Thu Feb 05 2004 - 12:35:41 CST)
1. plt.h (907 bytes)
2. plt.c (2424 bytes)
Re: Helical Tilt Angle Justin Gullingsrud (Wed Jan 28 2004 - 11:23:15 CST)
1. fit_angle.tcl (3964 bytes)
Hi phubbard_at_post.its.mcw.edu (Sun Jan 18 2004 - 22:09:47 CST)
1. part (150 bytes)
Re: PBC Axel Kohlmeyer (Tue Jan 06 2004 - 12:19:50 CST)
1. set_unitcell.tcl (1029 bytes)
Re: vmdmovie in OS X.3 Robert Brunner (Mon Nov 24 2003 - 19:26:44 CST)
1. PGP.sig (187 bytes)
Re: vmdmovie in OS X.3 Robert Brunner (Mon Nov 24 2003 - 19:15:34 CST)
1. PGP.sig (187 bytes)
AMBER (old ?) nucleic acids names not recognised Teletchéa Stéphane (Fri Nov 21 2003 - 03:57:04 CST)
1. signature.asc (190 bytes)
Re: Naming in XmGrace Teletchéa Stéphane (Thu Nov 20 2003 - 11:16:41 CST)
1. signature.asc (190 bytes)
Re: Naming in XmGrace Teletchéa Stéphane (Thu Nov 20 2003 - 06:53:21 CST)
1. signature.asc (190 bytes)
Re: Naming in XmGrace Teletchéa Stéphane (Thu Nov 20 2003 - 02:54:12 CST)
1. signature.asc (190 bytes)
Re: Naming in XmGrace Teletchéa Stéphane (Wed Nov 19 2003 - 11:01:41 CST)
1. signature.asc (190 bytes)
Re: Eugen Leitl (Wed Nov 19 2003 - 04:13:28 CST)
1. part (199 bytes)
(no subject) Dongsheng Zhang (Tue Nov 18 2003 - 17:24:20 CST)
1. md4e0001.pdb (2200133 bytes)
2. md4a.psf (2048411 bytes)
Re: Naming in XmGrace Teletchéa Stéphane (Tue Nov 18 2003 - 10:39:08 CST)
1. signature.asc (190 bytes)
Re: Naming in XmGrace John Stone (Tue Nov 18 2003 - 10:05:04 CST)
1. graphlabels.tcl (2613 bytes)
Naming in XmGrace Teletchéa Stéphane (Tue Nov 18 2003 - 07:03:10 CST)
1. signature.asc (190 bytes)
Re: Highlighting nearest atom ? (wrt to a tool) Eugen Leitl (Wed Nov 12 2003 - 04:22:51 CST)
1. part (199 bytes)
Re: POV-Ray Tauna Rignall (Tue Nov 11 2003 - 11:19:33 CST)
1. spin_test.0001.dat (8628132 bytes)
Re: VMD and Mandrake Linux 9.1 Teletchéa Stéphane (Fri Nov 07 2003 - 06:08:23 CST)
1. signature.asc (190 bytes)
ribbon representation Darui Xu (Fri Oct 17 2003 - 11:28:31 CDT)
1. mu2ribbon.wrl (261100 bytes)
Re: water sphere John Stone (Tue Oct 07 2003 - 14:40:53 CDT)
1. watersphere.vmd (1495 bytes)
convert pdb to psf FOK LO MING (Tue Sep 30 2003 - 03:54:34 CDT)
1. Au.pdb (4625 bytes)
Re: spacemice John Stone (Tue Sep 23 2003 - 13:25:41 CDT)
1. vrpn.cfg (14153 bytes)
2. vrpn_Tracker.cfg (272 bytes)
3. .vmdsensors (1776 bytes)
Re: saving bond-length information Axel Kohlmeyer (Thu Sep 11 2003 - 06:36:48 CDT)
1. graph.pl (989 bytes)
2. genfulldihedrallists.tcl (1835 bytes)
Re: compile VMD on freebsd 4.8 brad noyes (Tue Sep 09 2003 - 21:05:44 CDT)
1. lpthread.txt (967 bytes)
2. nolpthread.txt (897 bytes)
3. lpth.txt (959 bytes)
psfgen Oded Kleifeld (Mon Aug 25 2003 - 19:50:26 CDT)
1. IMSTP.gif (494 bytes)
Re: Amber prmtop/inpcrd files Teletchéa Stéphane (Thu Jul 31 2003 - 15:44:32 CDT)
1. signature.asc (190 bytes)
Re: Amber prmtop/inpcrd files Teletchéa Stéphane (Thu Jul 31 2003 - 12:49:27 CDT)
1. signature.asc (190 bytes)
Re: Some improvements for 1.8.2 Teletchéa Stéphane (Fri Jul 25 2003 - 21:06:37 CDT)
1. signature.asc (190 bytes)
Some improvements for 1.8.2 Teletchéa Stéphane (Fri Jul 25 2003 - 19:55:17 CDT)
1. signature.asc (190 bytes)
render to png, and ppm Brad Noyes (Sun Jul 13 2003 - 20:47:15 CDT)
1. png.patch (6552 bytes)
2. ppm.patch (5558 bytes)
Re: Visualizing CURVES output Teletchéa Stéphane (Fri Jun 20 2003 - 06:36:12 CDT)
1. signature.asc (190 bytes)
Re: helix axis for A-RNA Teletchéa Stéphane (Tue Jun 10 2003 - 08:11:35 CDT)
1. signature.asc (190 bytes)
Re: VMD Error! Teletchéa Stéphane (Tue Jun 10 2003 - 02:06:50 CDT)
1. signature.asc (190 bytes)
Re: VMD Error! Teletchéa Stéphane (Tue Jun 10 2003 - 01:40:55 CDT)
1. signature.asc (190 bytes)
Re: IMD interface code and endianness Marc Baaden (Fri May 30 2003 - 08:39:14 CDT)
1. unat.pdb (103 bytes)
Wrapping atoms around unit cell boundaries John Stone (Thu May 22 2003 - 10:14:18 CDT)
1. pbcwrap.tcl (10144 bytes)
Re: Wait command in Win2000 John Stone (Fri Apr 11 2003 - 17:24:22 CDT)
1. DNA_vmd.vmd (2429 bytes)
Re: atom velocity arrows John Stone (Wed Mar 12 2003 - 15:24:31 CST)
1. nmm.tcl (1825 bytes)
2. ala1.nmm (493 bytes)
Bugfix: new save_state.tcl for VMD 1.8 installations... John Stone (Fri Jan 31 2003 - 14:02:44 CST)
1. save_state.tcl (10874 bytes)
Re: stereo display on NVIDIA Quadro4 750 XGL Magnus Kreth (Mon Jan 13 2003 - 09:32:28 CST)
1. glxinfo.out (7951 bytes)
Re: can VMD display a box? Marc Baaden (Thu Nov 28 2002 - 07:26:05 CST)
1. box.pl (826 bytes)
Re: VMD 1.7.1 on HPUX John Stone (Thu Sep 05 2002 - 14:02:38 CDT)
1. zoomseq.tcl.gz (11093 bytes)
Re: Secondary structure Robert Campbell (Fri Aug 23 2002 - 12:13:44 CDT)
1. vmd_use_stride_ss (3092 bytes)
Re: [Contribute] transparent MacOS X icon for VMD MengJuei Hsieh (Fri Aug 16 2002 - 20:54:41 CDT)
1. VMDicon.icns (23156 bytes)
[Contribute] transparent MacOS X icon for VMD MengJuei Hsieh (Wed Aug 14 2002 - 19:15:49 CDT)
1. VMDicon.icns (24567 bytes)
Re: viewing insight trajectories with vmd John Stone (Tue Jun 25 2002 - 15:15:22 CDT)
1. crdplugin.c (4627 bytes)
MacOS native version resource attach info... John Stone (Mon Jun 24 2002 - 11:46:10 CDT)
1. vmdmac.r (370 bytes)
Re: Animating Trajectories/NAMD Output files Barry Isralewitz (Wed May 08 2002 - 11:01:26 CDT)
1. drag.tcl (8234 bytes)
Re: Animating Trajectories/NAMD Output files Barry Isralewitz (Tue May 07 2002 - 22:15:21 CDT)
1. drag.tcl (8220 bytes)
Which drawing method is used in the picture? Anna Aagaard (Tue Apr 09 2002 - 14:40:17 CDT)
1. winmail.dat (1676 bytes)
Re: strange bond Nguyen Hoang Phuong (Wed Apr 03 2002 - 10:20:54 CST)
1. xxx_1.pdb (3634 bytes)
2. xxx_2.pdb (3634 bytes)
Announce: ZoomSeq -- sequence browser for VMD Barry Isralewitz (Thu Dec 28 2000 - 14:54:20 CST)
1. zoomseq.txt (15488 bytes)

Last message date: Wed Sep 20 2017 - 02:37:44 CDT
Archived on: Mon Sep 25 2017 - 02:07:52 CDT

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