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Tutorial-l Mailing List

358 messages sorted by: [ date ] [ thread ] [ subject ] [ attachment ]
About this archive

Starting: Thu Jul 14 2005 - 12:24:32 CDT
Ending: Mon May 23 2022 - 18:54:52 CDT

• a-yermakova_at_northwestern.edu
  • Minimizing and Equilibrating (Mon Jul 17 2006 - 13:12:52 CDT)
• aabusaleh
  • QwikMD protonation (Mon Jan 13 2020 - 15:44:26 CST)
• Aaron Osysko
  • How to track distances between molecules while running molecular dynamics? (Fri May 23 2008 - 13:54:39 CDT)
• Abdul Kadir Mukarram
  • Re: NAMD Compiling Problems (Tue Nov 04 2014 - 05:29:18 CST)
  • NAMD Compiling Problems (Mon Nov 03 2014 - 02:55:15 CST)
• Abhishek TYAGI
  • Re: DNA not translocating - Nanopore tutorial (Fri Dec 16 2016 - 22:56:22 CST)
  • ERROR: One-dimensionalumbrellareplica-exchange sampling (Fri Dec 18 2015 - 03:37:28 CST)
  • One-dimensionalumbrellareplica-exchange sampling (Tue Dec 15 2015 - 22:43:52 CST)
• abojovschi_at_ict.swin.edu.au
  • specific heat of ubiquinone (Mon Aug 08 2005 - 19:08:15 CDT)
  • NAMD-tutorial - specific heat of ubiquinone (Tue Aug 02 2005 - 21:08:02 CDT)
• Adult Dating
  • Re: new stuff (Fri Oct 14 2016 - 17:26:31 CDT)
• Albert
  • a question about PME grid size (Fri Mar 23 2012 - 03:35:21 CDT)
  • equilibrium error for membrane system (Thu Mar 22 2012 - 09:27:33 CDT)
• Alejandro Ortega
  • DCD file (Fri Mar 07 2008 - 12:10:10 CST)
• Alexander Gonzalez
  • Colvars Orientation Question (Mon Jul 01 2019 - 14:29:07 CDT)
• Alia Sagatova
  • FATAL error (Mon May 13 2013 - 20:33:55 CDT)
• Alireza Mansouri
  • (no subject) (Sat Mar 01 2014 - 06:49:49 CST)
  • (no subject) (Mon Dec 30 2013 - 02:01:17 CST)
  • (no subject) (Tue Dec 17 2013 - 00:37:00 CST)
• Alisha \
  • FEP tutorial-molecule from step 6 will not load (Mon Mar 19 2012 - 01:25:37 CDT)
• amin_at_imtech.res.in
  • Simulations with alpha methylated amino acids (Wed Mar 14 2012 - 10:24:58 CDT)
• Ana Celia Araujo Vila Verde
  • RE: script for hbond time series (fwd) (Wed Mar 21 2007 - 11:00:46 CDT)
  • RE: (Mon Jan 29 2007 - 13:59:12 CST)
  • RE: a question about small molecule (Mon Jan 29 2007 - 10:59:42 CST)
  • suggestions for improving NAMD tutorial (Sat Dec 17 2005 - 14:23:01 CST)
• Anna Dejardin
  • Re: FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE (Mon Jun 15 2009 - 06:55:07 CDT)
  • Re: FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE (Mon Jun 15 2009 - 03:49:20 CDT)
  • Re: FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE (Fri May 15 2009 - 08:34:15 CDT)
  • FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE (Thu May 14 2009 - 07:24:42 CDT)
• Antoniya Aleksandrova
  • Membrane Tutorial Images (Sun Jul 14 2013 - 09:42:37 CDT)
• arpita agarwal
  • Regarding Bionanotechnology Tutorial (Tue Apr 12 2016 - 22:26:52 CDT)
• Athreya, Nagendra Bala Murali
  • RE: DNA not translocating - Nanopore tutorial (Tue Jan 31 2017 - 11:24:50 CST)
  • RE: DNA not translocating - Nanopore tutorial (Fri Dec 16 2016 - 12:20:15 CST)
  • RE: DNA not translocating - Nanopore tutorial (Mon Dec 05 2016 - 16:27:21 CST)
  • DNA not translocating - Nanopore tutorial (Wed Nov 30 2016 - 20:46:29 CST)
• Aurijit Sarkar
  • CHARMM36 compatible hybrid topology file (Thu Sep 24 2015 - 14:41:36 CDT)
• Basheer Subei
  • Re: Why does the Nanopore Tutorial not reuse the equilibrated structures when combining the DNA and nanopore? (Sun Aug 24 2014 - 16:40:31 CDT)
  • Why does the Nanopore Tutorial not reuse the equilibrated structures when combining the DNA and nanopore? (Fri Aug 22 2014 - 19:35:18 CDT)
• baxy
  • SMD Analysis (Sat May 12 2007 - 15:14:21 CDT)
  • problems retriving log file (Sat May 12 2007 - 03:03:57 CDT)
• Ben Joseph Cuyacot
  • RDF (Wed Sep 17 2014 - 21:51:52 CDT)
  • Radial Distribution Function (Wed Sep 17 2014 - 07:15:04 CDT)
• Bharath Rajeswaran
  • something wrong with the topology file of cellob01 (Thu Jun 24 2010 - 07:13:39 CDT)
  • Regarding patches (Wed Jun 23 2010 - 04:52:13 CDT)
  • regarding unknown residue type (Thu Jun 10 2010 - 11:25:58 CDT)
  • regarding polymers (Wed Jun 02 2010 - 04:31:51 CDT)
  • Re.PSF file in VMD (Fri May 28 2010 - 04:20:58 CDT)
• Biljana
  • Problem (Sun Nov 05 2006 - 17:24:49 CST)
• Brian Teague
  • NAMD bionanotechnology tutorial: scultor.tcl switches handedness (Thu Oct 16 2008 - 18:27:10 CDT)
• brosbam_at_berkeley.edu
  • residues for purple bacteria non protein (Mon Jul 14 2008 - 20:15:11 CDT)
• Bruno Rodrigues
  • Re: Problem with NAMD Ubiquitin Tutorial Step4 (Tue Feb 01 2011 - 05:28:53 CST)
• Büttner, Markus
  • NAMD-Tutorial: Curve-fitting for the diffusion constant (Wed Jan 13 2021 - 02:47:21 CST)
• C. Parry
  • Re: Volume (Fri Dec 01 2006 - 18:02:17 CST)
  • Volume (Thu Nov 30 2006 - 09:22:24 CST)
• Carles Corbi Verge
  • NANMA free energy surface vacuum map problems (Fri Oct 29 2010 - 06:50:23 CDT)
  • ABF tutorial. NANMA free energy surface vacumm map problems (Fri Oct 29 2010 - 06:23:24 CDT)
• Chris Harrison
  • Fwd: help (Tue Apr 17 2012 - 19:23:54 CDT)
  • Re: Can not download AmberTools-tcbg_molefmod-1.5.tar.bz2 (Mon Apr 16 2012 - 08:42:26 CDT)
  • Re: Can not download AmberTools-tcbg_molefmod-1.5.tar.bz2 (Mon Apr 16 2012 - 05:38:00 CDT)
  • Re: Problem with NAMD Ubiquitin Tutorial Step4 (Mon Jan 31 2011 - 23:02:01 CST)
  • Re: Unable to generate PSF file due to an unparametrized methyl histidine (Tue Jul 28 2009 - 20:41:03 CDT)
  • Re: lysozyme simulation (Wed Jul 22 2009 - 16:06:15 CDT)
  • Re: troubles with generating pdb with hydrogens (Thu Jul 09 2009 - 15:49:42 CDT)
  • Re: FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE (Mon Jun 15 2009 - 08:01:00 CDT)
  • Re: FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE (Mon Jun 15 2009 - 06:32:56 CDT)
• Chris Malajczuk
  • RBCG using MARTINI Force Field in NAMD - Bad global angler count! (Mon Dec 16 2013 - 02:00:24 CST)
• Chunli Yan
  • scalar and non scalar colvar in NAMD12 (Wed Jul 26 2017 - 16:21:02 CDT)
• Colm Herbert
  • Dead links in Modeling Nanopores for Sequencing DNA tutorial (Sat Jan 03 2015 - 10:48:42 CST)
• Connie Wang
  • ABF Tutorial-Methane Hydration (Thu Aug 11 2011 - 20:41:14 CDT)
• Corey Fugate
  • Text Mode on OS 10.5 (Fri Nov 27 2009 - 20:59:51 CST)
  • troubles with generating pdb with hydrogens (Thu Jul 09 2009 - 13:51:59 CDT)
  • empty rmsd.dat file (Thu Feb 19 2009 - 13:41:03 CST)
  • Fatal Error in Tutorial Configuration File (Sun Feb 01 2009 - 22:04:33 CST)
• Courtney Taylor
  • Minimization problem in FEP tutorial (Mon Sep 20 2010 - 13:55:06 CDT)
  • RDF for all atoms in multiple frames (Thu Jun 18 2009 - 16:56:07 CDT)
• Cuong Nguyen
  • Protein structure distorted after Energy minimization with NAMD (Wed Oct 08 2014 - 20:37:26 CDT)
• Deniz Wong
  • questions on NAMD (Fri Aug 24 2007 - 01:32:24 CDT)
• DL Lynch
  • Gramicidin A tutorial question (Fri Nov 03 2006 - 06:57:27 CST)
• Drew buschhorn
  • Nanotubes tutorial - coorList(577) no such element (Mon Feb 15 2010 - 22:56:16 CST)
• Dudas, Balint
  • Re: NAMD-QM/MM: "QM forces are not compatible with CUDA at this time" (Thu Jun 14 2018 - 04:31:18 CDT)
  • NAMD-QM/MM: "QM forces are not compatible with CUDA at this time" (Wed Jun 13 2018 - 04:42:41 CDT)
• Ebenezer Owusu-Ansah
  • FATAL ERROR :'( (Wed Nov 27 2013 - 12:46:32 CST)
• Eduard Schreiner
  • Re: Problem with NAMD Ubiquitin Tutorial Step4 (Mon Jan 31 2011 - 22:38:54 CST)
• Ehsan Ban
  • Errror in Running Ubiquitin Tutorial on page 22 (Mon Apr 11 2011 - 07:21:54 CDT)
• Ehsan Nikbin
  • Residue-Based Coarse-Graining (Mon Dec 02 2013 - 09:24:19 CST)
• Epie Emmanuel Njumbe
  • Building water boxes (Mon Jul 04 2011 - 08:03:35 CDT)
• Erik Sanchez
  • ✔hey! oh wow (Tue Nov 14 2017 - 19:08:13 CST)
• esserlo_at_helix.nih.gov
  • mem-tutorial FATAL ERROR: ATOM TYPE OSLP (Mon Mar 13 2017 - 10:16:27 CDT)
• Eva Gonzalez Noya
  • running a simulation after minimization (Tue Feb 15 2011 - 16:15:52 CST)
• Faisal, H M Nasrullah
  • MDFF tutorial is not working (Thu Aug 20 2020 - 09:10:01 CDT)
  • Any tutorial/manual for Dowser for membrane protein modeling (Tue Aug 18 2020 - 08:39:16 CDT)
• Fletcher Quick
  • porsche design is your style; (Thu Jun 18 2009 - 14:18:17 CDT)
• Fotis Baltoumas
  • Re: NAMD-QM/MM: "QM forces are not compatible with CUDA at this time" (Wed Jun 13 2018 - 05:09:35 CDT)
  • Re: mem-tutorial FATAL ERROR: ATOM TYPE OSLP (Mon Mar 13 2017 - 13:22:46 CDT)
  • Re: mem-tutorial FATAL ERROR: ATOM TYPE OSLP (Mon Mar 13 2017 - 11:56:01 CDT)
  • Re: Martini parameters from RBCG tutorial (Thu Jan 26 2017 - 09:07:10 CST)
• Frymier, Paul D
  • Newb question (Wed Jan 07 2015 - 14:54:49 CST)
• Grace Shen
  • RE: [NAMD] Question about vmdtext (Mon Oct 24 2005 - 09:33:17 CDT)
• Greg Tietjen
  • Issue with molefacture (Mon Apr 16 2012 - 21:36:10 CDT)
• Greipel.Joachim_at_mh-hannover.de
  • IMD-Tutorial (alanine) does not work with CUDA support - Atoms moving too fast (Thu Jun 28 2012 - 01:25:07 CDT)
• GUO HAO
  • a question about small molecule (Mon Jan 29 2007 - 10:50:08 CST)
  • a basic question on NAMD (Thu Jan 25 2007 - 17:52:12 CST)
• gurunath katagi
  • (no subject) (Tue Jan 20 2009 - 08:31:39 CST)
  • (no subject) (Wed Dec 10 2008 - 11:32:08 CST)
• Hall McDull
  • Three questions about bonds accross the boundary (Mon Apr 16 2012 - 00:03:05 CDT)
• Hicks, Stephanie N.
  • (no subject) (Mon Apr 17 2017 - 15:57:34 CDT)
• HOCHEOL LIM
  • How to get final state structure from FEP (Thu Dec 20 2018 - 08:22:12 CST)
• Hoffmann
  • [NAMD] Question about vmdtext (Sun Oct 23 2005 - 17:09:29 CDT)
• Hossein Mohammadiarani
  • Protein:ligand standard binding free energies (Thu Jan 26 2017 - 12:00:13 CST)
• Houyang Chen
  • questions regarding pressure difference (Wed Oct 02 2013 - 08:36:43 CDT)
  • RE: a question regarding eField calculation (Thu Apr 25 2013 - 13:43:03 CDT)
  • a question regarding eField calculation (Thu Apr 25 2013 - 13:04:13 CDT)
  • How can i write psf for nanotubes?Thanks. (Thu Jan 22 2009 - 14:23:20 CST)
• Hugo Hearn
  • yay Re: useful information for you (Sun Sep 03 2017 - 17:43:45 CDT)
• Hui Zhu
  • HYDROGEN BONDS? (Tue Jun 12 2007 - 04:41:43 CDT)
• Hyundeok Song
  • membrane at Gramicidin channel (Mon Aug 11 2008 - 11:18:54 CDT)
  • the button on the labled AS (Mon May 12 2008 - 10:53:36 CDT)
• Jake Michaelson
  • QM/MM tutorial (Wed Jan 25 2006 - 15:09:48 CST)
  • qm/mm in namd? (Wed Jan 25 2006 - 15:05:51 CST)
• javacfish
  • What is the means of system-min.conf in the Residue-Based Coarse tutorial? (Tue Apr 17 2012 - 11:18:30 CDT)
  • Can not download AmberTools-tcbg_molefmod-1.5.tar.bz2 (Mon Apr 16 2012 - 02:11:08 CDT)
• JC Gumbart
  • Re: a question regarding eField calculation (Thu Apr 25 2013 - 13:27:02 CDT)
  • Re: equilibrium error for membrane system (Fri Mar 23 2012 - 09:36:16 CDT)
  • Re: Problem with NAMD Ubiquitin Tutorial Running Simulation Step 1.4.2 (Wed Mar 02 2011 - 23:49:11 CST)
  • Re: Minimization problem in FEP tutorial (Mon Sep 20 2010 - 16:24:38 CDT)
  • Re: Minimization problem in FEP tutorial (Mon Sep 20 2010 - 15:07:28 CDT)
  • RE: membrane protein tutorial (Thu Aug 12 2010 - 00:00:55 CDT)
  • RE: Regarding patches (Wed Jun 23 2010 - 07:36:35 CDT)
  • Re: regarding unknown residue type (Fri Jun 11 2010 - 12:23:03 CDT)
  • Re: regarding unknown residue type (Thu Jun 10 2010 - 14:49:15 CDT)
  • RE: tutorial is not working (Wed Jun 02 2010 - 00:25:33 CDT)
  • Re: namd (Tue Apr 13 2010 - 13:56:51 CDT)
  • RE: namd could't use mutiple CPU (Wed Apr 07 2010 - 07:50:07 CDT)
  • Re: Biotechnology Tutorial -- Total Energy during Ion Transport (Sun Mar 14 2010 - 19:12:03 CDT)
  • RE: empty rmsd.dat file (Mon Feb 23 2009 - 00:55:11 CST)
  • Re: Fatal Error in Tutorial Configuration File (Mon Feb 02 2009 - 12:34:37 CST)
  • Re: (Wed Dec 10 2008 - 16:16:25 CST)
  • Re: User-defined forces in NAMD (Mon Oct 06 2008 - 12:03:17 CDT)
  • Re: namd-l: PMEGridSize (Fri Oct 03 2008 - 21:53:25 CDT)
  • Re: membrane at Gramicidin channel (Mon Aug 11 2008 - 16:28:10 CDT)
  • Re: parallel computing - namd (Tue Jul 01 2008 - 14:04:07 CDT)
  • Re: How to track distances between molecules while running molecular dynamics? (Mon May 26 2008 - 11:17:49 CDT)
  • Re: ubuquitin tutorial-FATAL ERROR: BAD IMPROPER FORMAT IN CHARMM PARAMETER FILE (Wed May 14 2008 - 15:56:24 CDT)
  • Re: ubuquitin tutorial-FATAL ERROR: BAD IMPROPER FORMAT IN CHARMM PARAMETER FILE (Tue May 13 2008 - 14:13:13 CDT)
  • Re: the button on the labled AS (Mon May 12 2008 - 14:08:41 CDT)
  • Re: RMSD for water sphere simulation of ubiquitin in tutorial (Tue Apr 01 2008 - 22:37:45 CDT)
  • Re: Enquires (Thu Mar 13 2008 - 15:16:28 CDT)
  • Re: Reagarding Stretching alanine (Fri Oct 26 2007 - 11:18:21 CDT)
  • RE: Questions (Thu Oct 04 2007 - 01:00:04 CDT)
  • Re: Problems encountered in namd tutorials (Mon Sep 17 2007 - 21:29:54 CDT)
  • Re: water molecule (Thu Aug 02 2007 - 14:42:37 CDT)
  • Re: water molecule (Tue Jul 31 2007 - 15:15:15 CDT)
  • RE: problems retriving log file (Sat May 12 2007 - 10:48:14 CDT)
  • Re: Shrink periodic box (Mon Apr 23 2007 - 17:23:11 CDT)
• jd42687_at_comcast.net
  • NAMD Simulation (Sat Jan 16 2016 - 10:05:22 CST)
• Jeff Comer
  • Re: DNA not translocating - Nanopore tutorial (Thu Dec 01 2016 - 09:14:21 CST)
  • Re: Newb question (Wed Jan 07 2015 - 15:13:53 CST)
  • Re: NAMD Compiling Problems (Mon Nov 03 2014 - 08:19:39 CST)
  • Re: Why does the Nanopore Tutorial not reuse the equilibrated structures when combining the DNA and nanopore? (Sat Aug 23 2014 - 13:16:22 CDT)
  • Re: Why does the Nanopore Tutorial not reuse the equilibrated structures when combining the DNA and nanopore? (Sat Aug 23 2014 - 12:43:41 CDT)
• Jeffrey Potoff
  • RBCG Tutorial: Inconsistency in MARTINI parameters (Tue Apr 14 2015 - 08:48:16 CDT)
• Jenni Carvajal
  • Biotechnology Tutorial -- Total Energy during Ion Transport (Sun Mar 14 2010 - 18:45:30 CDT)
• Jeronimo Terrones
  • Water Permeation Through Nanotubes -- Atoms Moving Too Fast!!! (Wed Oct 11 2017 - 10:19:44 CDT)
• Joao Ribeiro
  • Re: QwikMD protonation (Tue Jan 21 2020 - 09:22:52 CST)
• Joseph Alia
  • Fwd: Minimizing and Equilibrating (Thu May 12 2011 - 08:18:22 CDT)
• Joseph R. Vella
  • Problem with NAMD Ubiquitin Tutorial Running Simulation Step 1.4.2 (Tue Mar 01 2011 - 19:47:24 CST)
  • Problem with NAMD Ubiquitin Tutorial Step4 (Mon Jan 31 2011 - 22:18:28 CST)
• João Ribeiro
  • Re: How to get final state structure from FEP (Thu Dec 20 2018 - 23:05:10 CST)
  • Re: Re. 'OT' parameter in CHARMM36 (Tue Dec 11 2018 - 09:17:20 CST)
  • Re: Issue with keep_water_out script - mem-tutorial (Mon Nov 26 2018 - 09:26:06 CST)
  • Re: Replica-Exchange Umbrella Sampling Won't Start on Laptop (Mon Oct 08 2018 - 09:22:31 CDT)
• Junichi Kishikawa
  • mdff-tutorial: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT (Mon Feb 19 2018 - 01:10:31 CST)
• Kalas, Vasilios
  • Calculation of the Maxwell-Boltzmann Distribution (Sat Aug 02 2014 - 19:13:35 CDT)
• Katherine Parra
  • User-defined forces in NAMD (Mon Oct 06 2008 - 10:35:17 CDT)
• Kevin KNOOPS
  • membrane protein tutorial (Tue Aug 10 2010 - 10:05:21 CDT)
• Laura
  • Structure file generation problems (Mon Oct 28 2013 - 10:41:13 CDT)
• Leonardo Darre
  • alchemical tranformation input file (Wed Apr 15 2015 - 17:10:33 CDT)
• leuven
  • Re: NAMD couldn't use mutiple CPU (Thu Apr 08 2010 - 04:09:15 CDT)
  • NAMD couldn't use mutiple CPU (Thu Apr 08 2010 - 02:23:07 CDT)
  • namd could't use mutiple CPU (Wed Apr 07 2010 - 04:34:44 CDT)
• Levi Morrison
  • NAMD 2.9 CUDA: lateral pressure profiling (Tue Nov 20 2012 - 17:30:50 CST)
• Liu\.Y\.Z
  • a problem about topology and parameter information (Sun Oct 21 2007 - 20:16:35 CDT)
  • (no subject) (Wed Sep 26 2007 - 21:06:32 CDT)
• Lorenzo Fabbri
  • Issue with keep_water_out script - mem-tutorial (Sat Nov 24 2018 - 02:38:08 CST)
• mahesh kulharia
  • Gramicidin tutorial - par-extraterms.inp file needed (Wed Nov 12 2008 - 04:08:52 CST)
• Mai Suan Li
  • Re: Problem (Fri Dec 01 2006 - 20:18:02 CST)
  • Re: Problem (Sat Nov 25 2006 - 20:25:29 CST)
  • NAMD: configuaration file for equilibration with non-periodic BC (Wed Nov 15 2006 - 04:39:49 CST)
  • Re: Problem (Mon Nov 06 2006 - 20:03:05 CST)
• Maria Sanchez Farran
  • RMSD for water sphere simulation of ubiquitin in tutorial (Mon Mar 31 2008 - 08:12:27 CDT)
• María Pedrosa
  • RBCG tutorial: Problem when reading the DSSP file (Sun Dec 27 2020 - 17:21:36 CST)
• Matthew Ambrosia
  • velocity DCD file data retrieval (Wed Sep 17 2008 - 01:48:02 CDT)
• Mersch, Kacey
  • Re: Pair Interaction Calculation (Thu Oct 22 2020 - 15:30:16 CDT)
  • Pair Interaction Calculation (Thu Oct 22 2020 - 14:40:06 CDT)
• Michael Bach
  • trajectory analysis (fwd) (Fri Aug 24 2007 - 10:45:56 CDT)
  • RE: script for hbond time series (fwd) (Wed Mar 21 2007 - 14:08:23 CDT)
  • script for hbond time series (fwd) (Wed Mar 21 2007 - 10:29:41 CDT)
  • RE: NAMD tutorial for Windows problem reading pgn file from vmd tkconsole (fwd) (Thu Nov 09 2006 - 16:30:48 CST)
  • NAMD tutorial for Windows problem reading pgn file from vmd tkconsole (fwd) (Thu Nov 09 2006 - 16:30:33 CST)
  • Re: Welcome to tutorial-l (Wed Jul 20 2005 - 16:04:14 CDT)
  • Welcome to tutorial-l (Tue Jul 19 2005 - 16:51:49 CDT)
• Mina Ebrahimy
  • ionize water box by add ions plugin (Wed Sep 19 2018 - 09:30:53 CDT)
• Mohammadi Pezhman
  • Error (IMD connection windows)in strech the Alanin tururial (Wed Jul 16 2014 - 07:06:32 CDT)
• Monika Sharma
  • Question regarding loss of translational entropy calculation in FEP tutorial (Fri Jan 17 2014 - 13:27:39 CST)
• Ms. Nabila Tahreen
  • tutorial is not working (Tue Jun 01 2010 - 23:47:08 CDT)
• mvitod
  • problems with smd.tcl script (Tue Jan 22 2013 - 12:52:30 CST)
• nadia salami
  • (no subject) (Sat Aug 03 2013 - 00:38:04 CDT)
• Nandhini Sokkalingam
  • alchemical FEP question (Thu Dec 18 2008 - 16:08:54 CST)
• Navid Azadi
  • Reference for force field used in "Simulation of Water Permeation Through Nanotubes" (Mon Sep 28 2009 - 02:32:47 CDT)
• nikki strickland
  • Helices analysis (Wed Nov 30 2005 - 04:48:14 CST)
• Nima Nouri
  • Bionanotechnology Tutorial: FATAL ERROR (Sat Nov 28 2020 - 02:36:58 CST)
• Olivier Beyens
  • Re: Protein:lingand standard binding free energy tutorial: theory question (Thu Jul 29 2021 - 07:11:06 CDT)
  • Protein:lingand standard binding free energy tutorial: theory question (Tue Jul 20 2021 - 09:25:51 CDT)
• Panagiota Kyriakou
  • Martini parameters from RBCG tutorial (Wed Jan 25 2017 - 19:21:53 CST)
• Patrick Chiu
  • namd question (Mon Jul 11 2011 - 15:39:45 CDT)
• Pavel Mironov
  • lysozyme simulation (Fri Jul 17 2009 - 11:56:22 CDT)
• Per Jr. Greisen
  • Reagarding Stretching alanine (Fri Oct 26 2007 - 05:38:28 CDT)
• Peter Bender
  • test (Fri Dec 19 2008 - 06:48:16 CST)
  • test (Fri Dec 19 2008 - 05:17:26 CST)
• Peter Freddolino
  • Re: FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE (Mon Jun 15 2009 - 07:12:15 CDT)
  • Re: FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE (Fri May 15 2009 - 09:44:57 CDT)
  • Re: FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE (Thu May 14 2009 - 07:31:41 CDT)
  • Re: pressure profile namd (Wed Jun 11 2008 - 09:01:57 CDT)
  • Re: SMD Analysis (Sat May 12 2007 - 16:10:10 CDT)
  • Re: SMD Analysis (Sat May 12 2007 - 16:07:48 CDT)
• Peter Murphy
  • Re: NAMD Tutorial - Water Sphere - Altering size of water sphere (Mon May 13 2013 - 11:16:20 CDT)
  • NAMD Tutorial - Water Sphere - Altering size of water sphere (Wed May 08 2013 - 07:06:37 CDT)
• Prapasiri Pongprayoon
  • How to set up Multiple-replicas metadynamics (Thu Nov 02 2017 - 23:35:59 CDT)
• Prashanth Athri
  • Ligand-Protein turorial (Wed Jun 14 2006 - 09:05:53 CDT)
• Qiang Zhong
  • Can I use FEP in NAMD for reaction of ATP with Kinase? (Sun Jul 22 2007 - 03:23:02 CDT)
  • free energy,energy,entropy calculation for pushing ATP to active site of kinase! (Sun Jul 22 2007 - 03:20:16 CDT)
• Rabab Toubar
  • Re: namd-l: PMEGridSize (Fri Oct 03 2008 - 15:22:19 CDT)
  • PMEGridSize (Thu Oct 02 2008 - 13:55:04 CDT)
• Rahul Nori
  • Re: Problems with running simulation for the first time (Mon Jan 07 2013 - 12:24:25 CST)
  • Problems with running simulation for the first time (Mon Jan 07 2013 - 12:00:47 CST)
• Ramon Mendoza Uriarte
  • Re: One-dimensional replica-exchange umbrella sampling tutorial help (Fri Oct 23 2020 - 20:30:56 CDT)
  • One-dimensional replica-exchange umbrella sampling tutorial help (Tue Sep 29 2020 - 18:36:46 CDT)
• Rangeen Salih
  • (no subject) (Mon Feb 10 2014 - 08:49:01 CST)
• Rawan Al Nsour
  • Keep water out.tcl (Tue Jun 14 2011 - 22:20:44 CDT)
• Resham Regmi
  • calculation of Gibbs free energy (Tue Apr 03 2018 - 13:22:15 CDT)
• Ribi Akbar
  • How to extract protein coordinates after equilibration or production MD (Mon May 23 2022 - 18:54:41 CDT)
  • ABF: how to obtain the pdb file for each window (Mon May 16 2022 - 08:27:54 CDT)
  • first time step (Tue May 03 2022 - 07:57:32 CDT)
• RICARDO VAZQUEZ
  • Minimizing and Equilibrating (Fri May 20 2011 - 22:09:08 CDT)
  • Minimizing and Equilibrating (Wed May 11 2011 - 22:04:04 CDT)
  • parallel computing - namd (Tue Jul 01 2008 - 13:48:43 CDT)
• Richard Meyer
  • Error extracting SMD output in TkCounsel (Mon Oct 13 2014 - 09:53:05 CDT)
• Rita Leite
  • Questions (Mon Jul 17 2006 - 04:05:21 CDT)
• Robert Coffman
  • Re: first time step (Tue May 03 2022 - 19:48:04 CDT)
• Roberta Rostagno
  • Re: ubuquitin tutorial-FATAL ERROR: BAD IMPROPER FORMAT IN CHARMM PARAMETER FILE (Wed May 14 2008 - 02:00:20 CDT)
• roberta.rostagno
  • ubuquitin tutorial-FATAL ERROR: BAD IMPROPER FORMAT IN CHARMM PARAMETER FILE (Tue May 13 2008 - 05:37:07 CDT)
• Rocco Caliandro
  • problem with heme protein simulation (Mon May 03 2010 - 11:49:27 CDT)
• Rogan Carr
  • Re: regarding polymers (Wed Jun 02 2010 - 10:15:41 CDT)
  • Re: Enquires (Tue Sep 25 2007 - 12:51:29 CDT)
  • Re: Enquires (Mon Sep 24 2007 - 15:10:11 CDT)
  • Re: HYDROGEN BONDS? (Wed Jun 13 2007 - 13:15:26 CDT)
• Sandra Rennebaum, Biochemisches Inst.
  • Berendsen- two baths (Tue Aug 11 2009 - 01:53:32 CDT)
• santhu kumar
  • molecular dynamic simmulation help (Thu Jan 12 2006 - 04:53:05 CST)
• saravana
  • basic question (Sun Mar 11 2007 - 18:52:30 CDT)
  • hydrophobic part of the solvent accessible surface area -request (Mon Mar 05 2007 - 22:10:50 CST)
  • com velocity ? (Tue Feb 06 2007 - 18:05:08 CST)
• saravana prakash
  • nanotube -psf (Tue May 11 2010 - 22:31:57 CDT)
  • pressure profile namd (Wed Jun 11 2008 - 07:09:44 CDT)
• Sathish Gurupatham
  • water molecule (Tue Jul 31 2007 - 11:09:27 CDT)
• Schwartz, Noah
  • Replica-Exchange Umbrella Sampling Won't Start on Laptop (Sat Oct 06 2018 - 15:31:41 CDT)
• sciencekey
  • how to run molecular dynamics simulation in different pH? (Thu Jun 12 2014 - 07:36:34 CDT)
• Seah Harold
  • Enquires (Wed Mar 12 2008 - 10:47:35 CDT)
  • Enquires (Wed Feb 20 2008 - 00:56:16 CST)
  • Enquires (Sun Feb 10 2008 - 22:41:45 CST)
  • Enquires (Wed Jan 16 2008 - 03:38:52 CST)
  • Questions (Wed Oct 03 2007 - 22:03:36 CDT)
  • Enquiries (Tue Oct 02 2007 - 20:33:11 CDT)
  • Enquires (Tue Sep 25 2007 - 11:14:47 CDT)
  • Enquires (Mon Sep 24 2007 - 10:53:48 CDT)
  • Problems encountered in namd tutorials (Mon Sep 17 2007 - 21:25:11 CDT)
• Shaghayegh Vafaei
  • Creating pdb and psf file (Wed Jun 23 2010 - 14:39:53 CDT)
• sharvil kaware
  • Cell basis vector (Fri Jun 11 2010 - 16:10:15 CDT)
  • Only Water & Acetone evaporation. (Sun Mar 14 2010 - 20:09:13 CDT)
  • Only water simulation (Thu Mar 04 2010 - 20:20:53 CST)
  • Querry (Thu Mar 04 2010 - 20:10:52 CST)
• SHAUNAK BADANI
  • Regarding Tutorial : String method with swarms of trajectories: A tutorial for free-energy calculations along a minimum-action path (Tue Oct 15 2019 - 14:24:57 CDT)
• SHIVAM TIWARI
  • how to search for existing topology (Fri Jan 29 2021 - 22:51:09 CST)
  • Re: rules for grouping atoms (Thu Jan 28 2021 - 10:38:22 CST)
  • rules for grouping atoms (Thu Jan 28 2021 - 09:13:34 CST)
  • basis for creating a group (Wed Jan 27 2021 - 06:52:55 CST)
• simon chapman
  • opening namd-tutorial-files (Mon Oct 02 2017 - 16:04:31 CDT)
• Simon Wheeler
  • Installing NAMD in Windows10 (Tue Jan 08 2019 - 04:51:03 CST)
• Sourmaidou, Damiani
  • minimization command (Wed Jan 23 2008 - 12:35:49 CST)
  • C NH1 C minimization error (Thu Jan 17 2008 - 06:43:18 CST)
• Sridhar Kumar Kannam
  • Residue-Based Coarse-Graining; (Wed Aug 13 2014 - 00:58:50 CDT)
  • Electrostatic Maps and Ion Conduction, Z-slice axis and rotation (Mon Jan 06 2014 - 07:19:48 CST)
  • Re: Modeling Nanopores for Sequencing DNA - genCompressedPsf (Thu Apr 04 2013 - 21:26:57 CDT)
  • Modeling Nanopores for Sequencing DNA - genCompressedPsf (Wed Apr 03 2013 - 18:03:55 CDT)
• stinger
  • good news (Sun Aug 07 2016 - 21:58:13 CDT)
• subbu813
  • (no subject) (Wed Aug 14 2013 - 01:41:38 CDT)
• Subbusinger N
  • namd simulation for solids without solvation (Thu Nov 13 2014 - 00:08:33 CST)
  • dcd file uploading problem (Thu Dec 05 2013 - 06:02:32 CST)
  • Rmsd plot (Thu Nov 28 2013 - 03:31:12 CST)
  • rmsd.dat file (Wed Nov 27 2013 - 06:09:30 CST)
  • getting rmsd plot (Tue Nov 26 2013 - 23:59:37 CST)
  • rmsd plot (Wed Nov 06 2013 - 23:17:39 CST)
• Sujata Sovani
  • SBCG - Error loating-point value too small to represent (Fri Nov 06 2009 - 14:19:22 CST)
  • Minimization and equilibration - Configuration file FF parameters (Wed Jul 29 2009 - 12:10:09 CDT)
  • Unable to generate PSF file due to an unparametrized methyl histidine (Tue Jul 28 2009 - 18:01:18 CDT)
• suneyna bansal
  • namd (Fri Aug 06 2010 - 02:30:12 CDT)
  • namd (Thu May 13 2010 - 05:07:55 CDT)
  • namd (Tue Apr 13 2010 - 05:02:38 CDT)
• Süleyman Selim
  • Fwd: Charm++ fatal error: FATAL ERROR: BAD ANGLE FORMAT IN CHARMM PARAMETER FILE LINE=*DIHEDRALS* (Mon Nov 21 2016 - 07:06:33 CST)
• Takuro UDAGAWA
  • keep_water_out.tcl in Membrane proteins tutorial (Mon Dec 05 2011 - 04:37:40 CST)
• Teng, Teng
  • Force calculation along a DNA strand in DNA origami structure (Wed Nov 18 2020 - 15:14:29 CST)
• Tim Skirvin
  • Re: Testing (Thu Jul 14 2005 - 12:25:48 CDT)
  • Testing (Thu Jul 14 2005 - 12:24:31 CDT)
• Timothy Isgro
  • Re: Water density in a periodic box (Sat Mar 17 2007 - 16:37:00 CDT)
  • Re: hydrophobic part of the solvent accessible surface area -request (Fri Mar 16 2007 - 14:49:43 CDT)
  • Re: Water density in a periodic box (Fri Mar 16 2007 - 12:55:34 CDT)
  • Re: Center of mass analysis for a DCD trajectory (Sat Feb 17 2007 - 16:18:54 CST)
  • Re: com velocity ? (Fri Feb 16 2007 - 11:56:48 CST)
  • Re: gofr calculation (Fri Feb 16 2007 - 11:45:31 CST)
  • Re: Re: (Tue Jan 30 2007 - 19:41:01 CST)
  • Re: (Mon Jan 29 2007 - 15:04:22 CST)
  • Re: a basic question on NAMD (Thu Jan 25 2007 - 22:46:31 CST)
  • Re: Problem (Fri Dec 01 2006 - 14:45:09 CST)
  • Re: The format of BOND table in a topology file (Tue Nov 07 2006 - 16:53:16 CST)
  • Re: Problem (Tue Nov 07 2006 - 16:25:43 CST)
  • Re: Problem (Mon Nov 06 2006 - 09:14:34 CST)
  • Re: Gramicidin A tutorial question (Fri Nov 03 2006 - 14:33:18 CST)
  • Re: making psf file (Mon Aug 21 2006 - 19:09:20 CDT)
  • Re: namd-l: Minimizing and Equilibrating (Tue Jul 18 2006 - 12:19:23 CDT)
  • Re: Questions (Mon Jul 17 2006 - 11:19:02 CDT)
  • Re: Ligand-Protein turorial (Wed Jun 14 2006 - 15:13:22 CDT)
  • Re: molecular dynamic simmulation help (Tue Mar 07 2006 - 21:12:42 CST)
  • Re: qm/mm in namd? (Tue Mar 07 2006 - 20:49:30 CST)
  • Re: suggestions for improving NAMD tutorial (Tue Mar 07 2006 - 20:02:29 CST)
• Troels Emtekær Linnet
  • Re: Looking for gnuplot plot files (Thu Mar 10 2011 - 15:06:17 CST)
  • Looking for gnuplot plot files (Fri Jan 07 2011 - 02:07:47 CST)
• TYAGI Abhishek
  • Structure (psf) file is in CHARMM format; XPLOR format required (Sat Dec 28 2013 - 03:57:56 CST)
  • Problem in designing .tcl, .inp, .prm (Wed Nov 06 2013 - 01:30:11 CST)
• valentina.romano_at_unibas.ch
  • Problem with NAMDtutorial (Wed Sep 26 2012 - 11:48:28 CDT)
• Villalain Boullon, Jose
  • Membrane and water: from a rectangular box to a cicle box (Wed Jun 05 2013 - 03:25:01 CDT)
• wahn_at_uiuc.edu
  • FATAL ERROR: Periodic cell has become too small (Wed May 16 2007 - 14:30:02 CDT)
  • Water density in a periodic box (Wed Mar 14 2007 - 14:46:20 CDT)
  • Re: Center of mass analysis for a DCD trajectory (Sun Feb 18 2007 - 12:31:53 CST)
  • Center of mass analysis for a DCD trajectory (Fri Feb 16 2007 - 13:09:06 CST)
  • gofr calculation (Tue Feb 06 2007 - 18:21:50 CST)
  • (no subject) (Mon Jan 29 2007 - 13:42:54 CST)
  • (no subject) (Mon Jan 29 2007 - 13:42:13 CST)
• Won-Young Ahn
  • Shrink periodic box (Mon Apr 23 2007 - 12:35:34 CDT)
  • The format of BOND table in a topology file (Tue Nov 07 2006 - 14:22:53 CST)
  • The format of BOND table in a topology file (Tue Nov 07 2006 - 14:20:08 CST)
  • making psf file (Mon Aug 14 2006 - 11:17:49 CDT)
• yp sun
  • Constraint failure in RATTLE algorithm (Mon Dec 17 2012 - 00:26:58 CST)
• zeynab hosseini
  • Umbrella sampling of AA and CNT dissociation, pmf doesn't flatten & reduces over large distances... (Wed Apr 15 2020 - 00:08:45 CDT)
• Zhang, Jiong (MU-Student)
  • build four arranged cnt (Tue Mar 11 2014 - 10:38:59 CDT)
• Катерина Коц
  • String method with swarms of trajectories (Fri Apr 29 2016 - 01:44:31 CDT)
• 대학ì›�/ì�¼ë°˜ëŒ€í•™ì›� ìƒ�명과학부
  • Heme PSF file generation and hydrogen peroxide parameter files (Wed Dec 12 2018 - 20:35:20 CST)
  • Re. 'OT' parameter in CHARMM36 (Mon Dec 10 2018 - 19:58:16 CST)
  • Free Energy Perturbation (Mon Dec 10 2018 - 00:51:33 CST)
  • Targeted Molecular Dynamics (Sat Dec 08 2018 - 09:50:22 CST)

Last message date: Mon May 23 2022 - 18:54:52 CDT
Archived on: Thu Jul 21 2022 - 18:40:04 CDT

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