Tutorial-l Mailing List

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About this archive

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

JC Gumbart (Wed Dec 10 2008 - 16:16:25 CST)

Timothy Isgro (Tue Jan 30 2007 - 19:41:01 CST)

Timothy Isgro (Mon Jan 29 2007 - 15:04:22 CST)

Ana Celia Araujo Vila Verde (Mon Jan 29 2007 - 13:59:12 CST)

(no subject)
- Hicks, Stephanie N. (Mon Apr 17 2017 - 15:57:34 CDT)
- Alireza Mansouri (Sat Mar 01 2014 - 06:49:49 CST)
- Rangeen Salih (Mon Feb 10 2014 - 08:49:01 CST)
- Alireza Mansouri (Mon Dec 30 2013 - 02:01:17 CST)
- Alireza Mansouri (Tue Dec 17 2013 - 00:37:00 CST)
- subbu813 (Wed Aug 14 2013 - 01:41:38 CDT)
- nadia salami (Sat Aug 03 2013 - 00:38:04 CDT)
- gurunath katagi (Tue Jan 20 2009 - 08:31:39 CST)
- gurunath katagi (Wed Dec 10 2008 - 11:32:08 CST)
- Liu\.Y\.Z (Wed Sep 26 2007 - 21:06:32 CDT)
- wahn_at_uiuc.edu (Mon Jan 29 2007 - 13:42:54 CST)
- wahn_at_uiuc.edu (Mon Jan 29 2007 - 13:42:13 CST)
[NAMD] Question about vmdtext
- Grace Shen (Mon Oct 24 2005 - 09:33:17 CDT)
- Hoffmann (Sun Oct 23 2005 - 17:09:29 CDT)
a basic question on NAMD
- Timothy Isgro (Thu Jan 25 2007 - 22:46:31 CST)
- GUO HAO (Thu Jan 25 2007 - 17:52:12 CST)
a problem about topology and parameter information
- Liu\.Y\.Z (Sun Oct 21 2007 - 20:16:35 CDT)
a question about PME grid size
- Albert (Fri Mar 23 2012 - 03:35:21 CDT)
a question about small molecule
- Ana Celia Araujo Vila Verde (Mon Jan 29 2007 - 10:59:42 CST)
- GUO HAO (Mon Jan 29 2007 - 10:50:08 CST)
a question regarding eField calculation
- Houyang Chen (Thu Apr 25 2013 - 13:43:03 CDT)
- JC Gumbart (Thu Apr 25 2013 - 13:27:02 CDT)
- Houyang Chen (Thu Apr 25 2013 - 13:04:13 CDT)
ABF Tutorial-Methane Hydration
- Connie Wang (Thu Aug 11 2011 - 20:41:14 CDT)
ABF tutorial. NANMA free energy surface vacumm map problems
- Carles Corbi Verge (Fri Oct 29 2010 - 06:23:24 CDT)
ABF: how to obtain the pdb file for each window
- Ribi Akbar (Mon May 16 2022 - 08:27:54 CDT)
alchemical FEP question
- Nandhini Sokkalingam (Thu Dec 18 2008 - 16:08:54 CST)
alchemical tranformation input file
- Leonardo Darre (Wed Apr 15 2015 - 17:10:33 CDT)
Any tutorial/manual for Dowser for membrane protein modeling
- Faisal, H M Nasrullah (Tue Aug 18 2020 - 08:39:16 CDT)
basic question
- saravana (Sun Mar 11 2007 - 18:52:30 CDT)
basis for creating a group
- SHIVAM TIWARI (Wed Jan 27 2021 - 06:52:55 CST)
Berendsen- two baths
- Sandra Rennebaum, Biochemisches Inst. (Tue Aug 11 2009 - 01:53:32 CDT)
Bionanotechnology Tutorial: FATAL ERROR
- Nima Nouri (Sat Nov 28 2020 - 02:36:58 CST)
Biotechnology Tutorial -- Total Energy during Ion Transport
- JC Gumbart (Sun Mar 14 2010 - 19:12:03 CDT)
- Jenni Carvajal (Sun Mar 14 2010 - 18:45:30 CDT)
build four arranged cnt
- Zhang, Jiong (MU-Student) (Tue Mar 11 2014 - 10:38:59 CDT)
Building water boxes
- Epie Emmanuel Njumbe (Mon Jul 04 2011 - 08:03:35 CDT)
C NH1 C minimization error
- Sourmaidou, Damiani (Thu Jan 17 2008 - 06:43:18 CST)
calculation of Gibbs free energy
- Resham Regmi (Tue Apr 03 2018 - 13:22:15 CDT)
Calculation of the Maxwell-Boltzmann Distribution
- Kalas, Vasilios (Sat Aug 02 2014 - 19:13:35 CDT)
Can I use FEP in NAMD for reaction of ATP with Kinase?
- Qiang Zhong (Sun Jul 22 2007 - 03:23:02 CDT)
Can not download AmberTools-tcbg_molefmod-1.5.tar.bz2
- Chris Harrison (Mon Apr 16 2012 - 08:42:26 CDT)
- Chris Harrison (Mon Apr 16 2012 - 05:38:00 CDT)
- javacfish (Mon Apr 16 2012 - 02:11:08 CDT)
Cell basis vector
- sharvil kaware (Fri Jun 11 2010 - 16:10:15 CDT)
Center of mass analysis for a DCD trajectory
- wahn_at_uiuc.edu (Sun Feb 18 2007 - 12:31:53 CST)
- Timothy Isgro (Sat Feb 17 2007 - 16:18:54 CST)
- wahn_at_uiuc.edu (Fri Feb 16 2007 - 13:09:06 CST)
CHARMM36 compatible hybrid topology file
- Aurijit Sarkar (Thu Sep 24 2015 - 14:41:36 CDT)
Colvars Orientation Question
- Alexander Gonzalez (Mon Jul 01 2019 - 14:29:07 CDT)
com velocity ?
- Timothy Isgro (Fri Feb 16 2007 - 11:56:48 CST)
- saravana (Tue Feb 06 2007 - 18:05:08 CST)
Constraint failure in RATTLE algorithm
- yp sun (Mon Dec 17 2012 - 00:26:58 CST)
Creating pdb and psf file
- Shaghayegh Vafaei (Wed Jun 23 2010 - 14:39:53 CDT)
DCD file
- Alejandro Ortega (Fri Mar 07 2008 - 12:10:10 CST)
dcd file uploading problem
- Subbusinger N (Thu Dec 05 2013 - 06:02:32 CST)
Dead links in Modeling Nanopores for Sequencing DNA tutorial
- Colm Herbert (Sat Jan 03 2015 - 10:48:42 CST)
DNA not translocating - Nanopore tutorial
- Athreya, Nagendra Bala Murali (Tue Jan 31 2017 - 11:24:50 CST)
- Abhishek TYAGI (Fri Dec 16 2016 - 22:56:22 CST)
- Athreya, Nagendra Bala Murali (Fri Dec 16 2016 - 12:20:15 CST)
- Athreya, Nagendra Bala Murali (Mon Dec 05 2016 - 16:27:21 CST)
- Jeff Comer (Thu Dec 01 2016 - 09:14:21 CST)
- Athreya, Nagendra Bala Murali (Wed Nov 30 2016 - 20:46:29 CST)
Electrostatic Maps and Ion Conduction, Z-slice axis and rotation
- Sridhar Kumar Kannam (Mon Jan 06 2014 - 07:19:48 CST)
empty rmsd.dat file
- JC Gumbart (Mon Feb 23 2009 - 00:55:11 CST)
- Corey Fugate (Thu Feb 19 2009 - 13:41:03 CST)
Enquires
- JC Gumbart (Thu Mar 13 2008 - 15:16:28 CDT)
- Seah Harold (Wed Mar 12 2008 - 10:47:35 CDT)
- Seah Harold (Wed Feb 20 2008 - 00:56:16 CST)
- Seah Harold (Sun Feb 10 2008 - 22:41:45 CST)
- Seah Harold (Wed Jan 16 2008 - 03:38:52 CST)
- Rogan Carr (Tue Sep 25 2007 - 12:51:29 CDT)
- Seah Harold (Tue Sep 25 2007 - 11:14:47 CDT)
- Rogan Carr (Mon Sep 24 2007 - 15:10:11 CDT)
- Seah Harold (Mon Sep 24 2007 - 10:53:48 CDT)
Enquiries
- Seah Harold (Tue Oct 02 2007 - 20:33:11 CDT)
equilibrium error for membrane system
- JC Gumbart (Fri Mar 23 2012 - 09:36:16 CDT)
- Albert (Thu Mar 22 2012 - 09:27:33 CDT)
Error (IMD connection windows)in strech the Alanin tururial
- Mohammadi Pezhman (Wed Jul 16 2014 - 07:06:32 CDT)
Error extracting SMD output in TkCounsel
- Richard Meyer (Mon Oct 13 2014 - 09:53:05 CDT)
ERROR: One-dimensionalumbrellareplica-exchange sampling
- Abhishek TYAGI (Fri Dec 18 2015 - 03:37:28 CST)
Errror in Running Ubiquitin Tutorial on page 22
- Ehsan Ban (Mon Apr 11 2011 - 07:21:54 CDT)
FATAL error
- Alia Sagatova (Mon May 13 2013 - 20:33:55 CDT)
FATAL ERROR :'(
- Ebenezer Owusu-Ansah (Wed Nov 27 2013 - 12:46:32 CST)
Fatal Error in Tutorial Configuration File
- JC Gumbart (Mon Feb 02 2009 - 12:34:37 CST)
- Corey Fugate (Sun Feb 01 2009 - 22:04:33 CST)
FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
- Chris Harrison (Mon Jun 15 2009 - 08:01:00 CDT)
- Peter Freddolino (Mon Jun 15 2009 - 07:12:15 CDT)
- Anna Dejardin (Mon Jun 15 2009 - 06:55:07 CDT)
- Chris Harrison (Mon Jun 15 2009 - 06:32:56 CDT)
- Anna Dejardin (Mon Jun 15 2009 - 03:49:20 CDT)
- Peter Freddolino (Fri May 15 2009 - 09:44:57 CDT)
- Anna Dejardin (Fri May 15 2009 - 08:34:15 CDT)
- Peter Freddolino (Thu May 14 2009 - 07:31:41 CDT)
- Anna Dejardin (Thu May 14 2009 - 07:24:42 CDT)
FATAL ERROR: Periodic cell has become too small
- wahn_at_uiuc.edu (Wed May 16 2007 - 14:30:02 CDT)
FEP tutorial-molecule from step 6 will not load
- Alisha \ (Mon Mar 19 2012 - 01:25:37 CDT)
first time step
- Robert Coffman (Tue May 03 2022 - 19:48:04 CDT)
- Ribi Akbar (Tue May 03 2022 - 07:57:32 CDT)
Force calculation along a DNA strand in DNA origami structure
- Teng, Teng (Wed Nov 18 2020 - 15:14:29 CST)
Free Energy Perturbation
- ëŒ€í•™ì›/ì¼ë°˜ëŒ€í•™ì› ìƒëª…ê³¼í•™ë¶€ (Mon Dec 10 2018 - 00:51:33 CST)
free energy,energy,entropy calculation for pushing ATP to active site of kinase!
- Qiang Zhong (Sun Jul 22 2007 - 03:20:16 CDT)
Fwd: Charm++ fatal error: FATAL ERROR: BAD ANGLE FORMAT IN CHARMM PARAMETER FILE LINE=*DIHEDRALS*
- SÃ¼leyman Selim (Mon Nov 21 2016 - 07:06:33 CST)
Fwd: help
- Chris Harrison (Tue Apr 17 2012 - 19:23:54 CDT)
Fwd: Minimizing and Equilibrating
- Joseph Alia (Thu May 12 2011 - 08:18:22 CDT)
getting rmsd plot
- Subbusinger N (Tue Nov 26 2013 - 23:59:37 CST)
gofr calculation
- Timothy Isgro (Fri Feb 16 2007 - 11:45:31 CST)
- wahn_at_uiuc.edu (Tue Feb 06 2007 - 18:21:50 CST)
good news
- stinger (Sun Aug 07 2016 - 21:58:13 CDT)
Gramicidin A tutorial question
- Timothy Isgro (Fri Nov 03 2006 - 14:33:18 CST)
- DL Lynch (Fri Nov 03 2006 - 06:57:27 CST)
Gramicidin tutorial - par-extraterms.inp file needed
- mahesh kulharia (Wed Nov 12 2008 - 04:08:52 CST)
Helices analysis
- nikki strickland (Wed Nov 30 2005 - 04:48:14 CST)
Heme PSF file generation and hydrogen peroxide parameter files
- ëŒ€í•™ì›/ì¼ë°˜ëŒ€í•™ì› ìƒëª…ê³¼í•™ë¶€ (Wed Dec 12 2018 - 20:35:20 CST)
How can i write psf for nanotubes?Thanks.
- houyang chen (Thu Jan 22 2009 - 14:23:20 CST)
How to extract protein coordinates after equilibration or production MD
- Ribi Akbar (Mon May 23 2022 - 18:54:41 CDT)
How to get final state structure from FEP
- JoÃ£o Ribeiro (Thu Dec 20 2018 - 23:05:10 CST)
- HOCHEOL LIM (Thu Dec 20 2018 - 08:22:12 CST)
how to run molecular dynamics simulation in different pH?
- sciencekey (Thu Jun 12 2014 - 07:36:34 CDT)
how to search for existing topology
- SHIVAM TIWARI (Fri Jan 29 2021 - 22:51:09 CST)
How to set up Multiple-replicas metadynamics
- Prapasiri Pongprayoon (Thu Nov 02 2017 - 23:35:59 CDT)
How to track distances between molecules while running molecular dynamics?
- JC Gumbart (Mon May 26 2008 - 11:17:49 CDT)
- Aaron Osysko (Fri May 23 2008 - 13:54:39 CDT)
HYDROGEN BONDS?
- Rogan Carr (Wed Jun 13 2007 - 13:15:26 CDT)
- Hui Zhu (Tue Jun 12 2007 - 04:41:43 CDT)
hydrophobic part of the solvent accessible surface area -request
- Timothy Isgro (Fri Mar 16 2007 - 14:49:43 CDT)
- saravana (Mon Mar 05 2007 - 22:10:50 CST)
IMD-Tutorial (alanine) does not work with CUDA support - Atoms moving too fast
- Greipel.Joachim_at_mh-hannover.de (Thu Jun 28 2012 - 01:25:07 CDT)
Installing NAMD in Windows10
- Simon Wheeler (Tue Jan 08 2019 - 04:51:03 CST)
ionize water box by add ions plugin
- Mina Ebrahimy (Wed Sep 19 2018 - 09:30:53 CDT)
Issue with keep_water_out script - mem-tutorial
- JoÃ£o Ribeiro (Mon Nov 26 2018 - 09:26:06 CST)
- Lorenzo Fabbri (Sat Nov 24 2018 - 02:38:08 CST)
Issue with molefacture
- Greg Tietjen (Mon Apr 16 2012 - 21:36:10 CDT)
Keep water out.tcl
- Rawan Al Nsour (Tue Jun 14 2011 - 22:20:44 CDT)
keep_water_out.tcl in Membrane proteins tutorial
- Takuro UDAGAWA (Mon Dec 05 2011 - 04:37:40 CST)
Ligand-Protein turorial
- Timothy Isgro (Wed Jun 14 2006 - 15:13:22 CDT)
- Prashanth Athri (Wed Jun 14 2006 - 09:05:53 CDT)
Looking for gnuplot plot files
- Troels Emtekær Linnet (Thu Mar 10 2011 - 15:06:17 CST)
- Troels Emtekær Linnet (Fri Jan 07 2011 - 02:07:47 CST)
lysozyme simulation
- Chris Harrison (Wed Jul 22 2009 - 16:06:15 CDT)
- Pavel Mironov (Fri Jul 17 2009 - 11:56:22 CDT)
making psf file
- Timothy Isgro (Mon Aug 21 2006 - 19:09:20 CDT)
- Won-Young Ahn (Mon Aug 14 2006 - 11:17:49 CDT)
Martini parameters from RBCG tutorial
- Fotis Baltoumas (Thu Jan 26 2017 - 09:07:10 CST)
- Panagiota Kyriakou (Wed Jan 25 2017 - 19:21:53 CST)
MDFF tutorial is not working
- Faisal, H M Nasrullah (Thu Aug 20 2020 - 09:10:01 CDT)
mdff-tutorial: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT
- Junichi Kishikawa (Mon Feb 19 2018 - 01:10:31 CST)
mem-tutorial FATAL ERROR: ATOM TYPE OSLP
- Fotis Baltoumas (Mon Mar 13 2017 - 13:22:46 CDT)
- Fotis Baltoumas (Mon Mar 13 2017 - 11:56:01 CDT)
- esserlo_at_helix.nih.gov (Mon Mar 13 2017 - 10:16:27 CDT)
Membrane and water: from a rectangular box to a cicle box
- Villalain Boullon, Jose (Wed Jun 05 2013 - 03:25:01 CDT)
membrane at Gramicidin channel
- JC Gumbart (Mon Aug 11 2008 - 16:28:10 CDT)
- Hyundeok Song (Mon Aug 11 2008 - 11:18:54 CDT)
membrane protein tutorial
- JC Gumbart (Thu Aug 12 2010 - 00:00:55 CDT)
- Kevin KNOOPS (Tue Aug 10 2010 - 10:05:21 CDT)
Membrane Tutorial Images
- Antoniya Aleksandrova (Sun Jul 14 2013 - 09:42:37 CDT)
Minimization and equilibration - Configuration file FF parameters
- Sujata Sovani (Wed Jul 29 2009 - 12:10:09 CDT)
minimization command
- Sourmaidou, Damiani (Wed Jan 23 2008 - 12:35:49 CST)
Minimization problem in FEP tutorial
- JC Gumbart (Mon Sep 20 2010 - 16:24:38 CDT)
- JC Gumbart (Mon Sep 20 2010 - 15:07:28 CDT)
- Courtney Taylor (Mon Sep 20 2010 - 13:55:06 CDT)
Minimizing and Equilibrating
- RICARDO VAZQUEZ (Fri May 20 2011 - 22:09:08 CDT)
- RICARDO VAZQUEZ (Wed May 11 2011 - 22:04:04 CDT)
- a-yermakova_at_northwestern.edu (Mon Jul 17 2006 - 13:12:52 CDT)
Modeling Nanopores for Sequencing DNA - genCompressedPsf
- Sridhar Kumar Kannam (Thu Apr 04 2013 - 21:26:57 CDT)
- Sridhar Kumar Kannam (Wed Apr 03 2013 - 18:03:55 CDT)
molecular dynamic simmulation help
- Timothy Isgro (Tue Mar 07 2006 - 21:12:42 CST)
- santhu kumar (Thu Jan 12 2006 - 04:53:05 CST)
namd
- suneyna bansal (Fri Aug 06 2010 - 02:30:12 CDT)
- suneyna bansal (Thu May 13 2010 - 05:07:55 CDT)
- JC Gumbart (Tue Apr 13 2010 - 13:56:51 CDT)
- suneyna bansal (Tue Apr 13 2010 - 05:02:38 CDT)
NAMD 2.9 CUDA: lateral pressure profiling
- Levi Morrison (Tue Nov 20 2012 - 17:30:50 CST)
NAMD bionanotechnology tutorial: scultor.tcl switches handedness
- Brian Teague (Thu Oct 16 2008 - 18:27:10 CDT)
NAMD Compiling Problems
- Abdul Kadir Mukarram (Tue Nov 04 2014 - 05:29:18 CST)
- Jeff Comer (Mon Nov 03 2014 - 08:19:39 CST)
- Abdul Kadir Mukarram (Mon Nov 03 2014 - 02:55:15 CST)
namd could't use mutiple CPU
- JC Gumbart (Wed Apr 07 2010 - 07:50:07 CDT)
- leuven (Wed Apr 07 2010 - 04:34:44 CDT)
NAMD couldn't use mutiple CPU
- leuven (Thu Apr 08 2010 - 04:09:15 CDT)
- leuven (Thu Apr 08 2010 - 02:23:07 CDT)
namd question
- Patrick Chiu (Mon Jul 11 2011 - 15:39:45 CDT)
NAMD Simulation
- jd42687_at_comcast.net (Sat Jan 16 2016 - 10:05:22 CST)
namd simulation for solids without solvation
- Subbusinger N (Thu Nov 13 2014 - 00:08:33 CST)
NAMD Tutorial - Water Sphere - Altering size of water sphere
- Peter Murphy (Mon May 13 2013 - 11:16:20 CDT)
- Peter Murphy (Wed May 08 2013 - 07:06:37 CDT)
NAMD tutorial for Windows problem reading pgn file from vmd tkconsole (fwd)
- Michael Bach (Thu Nov 09 2006 - 16:30:48 CST)
- Michael Bach (Thu Nov 09 2006 - 16:30:33 CST)
namd-l: Minimizing and Equilibrating
- Timothy Isgro (Tue Jul 18 2006 - 12:19:23 CDT)
namd-l: PMEGridSize
- JC Gumbart (Fri Oct 03 2008 - 21:53:25 CDT)
- Rabab Toubar (Fri Oct 03 2008 - 15:22:19 CDT)
NAMD-QM/MM: "QM forces are not compatible with CUDA at this time"
- Dudas, Balint (Thu Jun 14 2018 - 04:31:18 CDT)
- Fotis Baltoumas (Wed Jun 13 2018 - 05:09:35 CDT)
- Dudas, Balint (Wed Jun 13 2018 - 04:42:41 CDT)
NAMD-tutorial - specific heat of ubiquinone
- abojovschi_at_ict.swin.edu.au (Tue Aug 02 2005 - 21:08:02 CDT)
NAMD-Tutorial: Curve-fitting for the diffusion constant
- Büttner, Markus (Wed Jan 13 2021 - 02:47:21 CST)
NAMD: configuaration file for equilibration with non-periodic BC
- Mai Suan Li (Wed Nov 15 2006 - 04:39:49 CST)
NANMA free energy surface vacuum map problems
- Carles Corbi Verge (Fri Oct 29 2010 - 06:50:23 CDT)
nanotube -psf
- saravana prakash (Tue May 11 2010 - 22:31:57 CDT)
Nanotubes tutorial - coorList(577) no such element
- Drew buschhorn (Mon Feb 15 2010 - 22:56:16 CST)
new stuff
- Adult Dating (Fri Oct 14 2016 - 17:26:31 CDT)
Newb question
- Jeff Comer (Wed Jan 07 2015 - 15:13:53 CST)
- Frymier, Paul D (Wed Jan 07 2015 - 14:54:49 CST)
One-dimensional replica-exchange umbrella sampling tutorial help
- Ramon Mendoza Uriarte (Fri Oct 23 2020 - 20:30:56 CDT)
- Ramon Mendoza Uriarte (Tue Sep 29 2020 - 18:36:46 CDT)
One-dimensionalumbrellareplica-exchange sampling
- Abhishek TYAGI (Tue Dec 15 2015 - 22:43:52 CST)
Only Water & Acetone evaporation.
- sharvil kaware (Sun Mar 14 2010 - 20:09:13 CDT)
Only water simulation
- sharvil kaware (Thu Mar 04 2010 - 20:20:53 CST)
opening namd-tutorial-files
- simon chapman (Mon Oct 02 2017 - 16:04:31 CDT)
Pair Interaction Calculation
- Mersch, Kacey (Thu Oct 22 2020 - 15:30:16 CDT)
- Mersch, Kacey (Thu Oct 22 2020 - 14:40:06 CDT)
parallel computing - namd
- JC Gumbart (Tue Jul 01 2008 - 14:04:07 CDT)
- RICARDO VAZQUEZ (Tue Jul 01 2008 - 13:48:43 CDT)
PMEGridSize
- Rabab Toubar (Thu Oct 02 2008 - 13:55:04 CDT)
porsche design is your style;
- Fletcher Quick (Thu Jun 18 2009 - 14:18:17 CDT)
pressure profile namd
- Peter Freddolino (Wed Jun 11 2008 - 09:01:57 CDT)
- saravana prakash (Wed Jun 11 2008 - 07:09:44 CDT)
Problem
- Mai Suan Li (Fri Dec 01 2006 - 20:18:02 CST)
- Timothy Isgro (Fri Dec 01 2006 - 14:45:09 CST)
- Mai Suan Li (Sat Nov 25 2006 - 20:25:29 CST)
- Timothy Isgro (Tue Nov 07 2006 - 16:25:43 CST)
- Mai Suan Li (Mon Nov 06 2006 - 20:03:05 CST)
- Timothy Isgro (Mon Nov 06 2006 - 09:14:34 CST)
- Biljana (Sun Nov 05 2006 - 17:24:49 CST)
Problem in designing .tcl, .inp, .prm
- TYAGI Abhishek (Wed Nov 06 2013 - 01:30:11 CST)
problem with heme protein simulation
- Rocco Caliandro (Mon May 03 2010 - 11:49:27 CDT)
Problem with NAMD Ubiquitin Tutorial Running Simulation Step 1.4.2
- JC Gumbart (Wed Mar 02 2011 - 23:49:11 CST)
- Joseph R. Vella (Tue Mar 01 2011 - 19:47:24 CST)
Problem with NAMD Ubiquitin Tutorial Step4
- Bruno Rodrigues (Tue Feb 01 2011 - 05:28:53 CST)
- Chris Harrison (Mon Jan 31 2011 - 23:02:01 CST)
- Eduard Schreiner (Mon Jan 31 2011 - 22:38:54 CST)
- Joseph R. Vella (Mon Jan 31 2011 - 22:18:28 CST)
Problem with NAMDtutorial
- valentina.romano_at_unibas.ch (Wed Sep 26 2012 - 11:48:28 CDT)
Problems encountered in namd tutorials
- JC Gumbart (Mon Sep 17 2007 - 21:29:54 CDT)
- Seah Harold (Mon Sep 17 2007 - 21:25:11 CDT)
problems retriving log file
- JC Gumbart (Sat May 12 2007 - 10:48:14 CDT)
- baxy (Sat May 12 2007 - 03:03:57 CDT)
Problems with running simulation for the first time
- Rahul Nori (Mon Jan 07 2013 - 12:24:25 CST)
- Rahul Nori (Mon Jan 07 2013 - 12:00:47 CST)
problems with smd.tcl script
- mvitod (Tue Jan 22 2013 - 12:52:30 CST)
Protein structure distorted after Energy minimization with NAMD
- Cuong Nguyen (Wed Oct 08 2014 - 20:37:26 CDT)
Protein:ligand standard binding free energies
- Hossein Mohammadiarani (Thu Jan 26 2017 - 12:00:13 CST)
Protein:lingand standard binding free energy tutorial: theory question
- Olivier Beyens (Thu Jul 29 2021 - 07:11:06 CDT)
- Olivier Beyens (Tue Jul 20 2021 - 09:25:51 CDT)
qm/mm in namd?
- Timothy Isgro (Tue Mar 07 2006 - 20:49:30 CST)
- Jake Michaelson (Wed Jan 25 2006 - 15:05:51 CST)
QM/MM tutorial
- Jake Michaelson (Wed Jan 25 2006 - 15:09:48 CST)
Querry
- sharvil kaware (Thu Mar 04 2010 - 20:10:52 CST)
Question regarding loss of translational entropy calculation in FEP tutorial
- Monika Sharma (Fri Jan 17 2014 - 13:27:39 CST)
Questions
- JC Gumbart (Thu Oct 04 2007 - 01:00:04 CDT)
- Seah Harold (Wed Oct 03 2007 - 22:03:36 CDT)
- Timothy Isgro (Mon Jul 17 2006 - 11:19:02 CDT)
- Rita Leite (Mon Jul 17 2006 - 04:05:21 CDT)
questions on NAMD
- Deniz Wong (Fri Aug 24 2007 - 01:32:24 CDT)
questions regarding pressure difference
- Houyang Chen (Wed Oct 02 2013 - 08:36:43 CDT)
QwikMD protonation
- Joao Ribeiro (Tue Jan 21 2020 - 09:22:52 CST)
- aabusaleh (Mon Jan 13 2020 - 15:44:26 CST)
Radial Distribution Function
- Ben Joseph Cuyacot (Wed Sep 17 2014 - 07:15:04 CDT)
RBCG Tutorial: Inconsistency in MARTINI parameters
- Jeffrey Potoff (Tue Apr 14 2015 - 08:48:16 CDT)
RBCG tutorial: Problem when reading the DSSP file
- MarÃa Pedrosa (Sun Dec 27 2020 - 17:21:36 CST)
RBCG using MARTINI Force Field in NAMD - Bad global angler count!
- Chris Malajczuk (Mon Dec 16 2013 - 02:00:24 CST)
RDF
- Ben Joseph Cuyacot (Wed Sep 17 2014 - 21:51:52 CDT)
RDF for all atoms in multiple frames
- Courtney Taylor (Thu Jun 18 2009 - 16:56:07 CDT)
Re. 'OT' parameter in CHARMM36
- JoÃ£o Ribeiro (Tue Dec 11 2018 - 09:17:20 CST)
- ëŒ€í•™ì›/ì¼ë°˜ëŒ€í•™ì› ìƒëª…ê³¼í•™ë¶€ (Mon Dec 10 2018 - 19:58:16 CST)
Re.PSF file in VMD
- Bharath Rajeswaran (Fri May 28 2010 - 04:20:58 CDT)
Reagarding Stretching alanine
- JC Gumbart (Fri Oct 26 2007 - 11:18:21 CDT)
- Per Jr. Greisen (Fri Oct 26 2007 - 05:38:28 CDT)
Reference for force field used in "Simulation of Water Permeation Through Nanotubes"
- Navid Azadi (Mon Sep 28 2009 - 02:32:47 CDT)
Regarding Bionanotechnology Tutorial
- arpita agarwal (Tue Apr 12 2016 - 22:26:52 CDT)
Regarding patches
- JC Gumbart (Wed Jun 23 2010 - 07:36:35 CDT)
- Bharath Rajeswaran (Wed Jun 23 2010 - 04:52:13 CDT)
regarding polymers
- Rogan Carr (Wed Jun 02 2010 - 10:15:41 CDT)
- Bharath Rajeswaran (Wed Jun 02 2010 - 04:31:51 CDT)
Regarding Tutorial : String method with swarms of trajectories: A tutorial for free-energy calculations along a minimum-action path
- SHAUNAK BADANI (Tue Oct 15 2019 - 14:24:57 CDT)
regarding unknown residue type
- JC Gumbart (Fri Jun 11 2010 - 12:23:03 CDT)
- JC Gumbart (Thu Jun 10 2010 - 14:49:15 CDT)
- Bharath Rajeswaran (Thu Jun 10 2010 - 11:25:58 CDT)
Replica-Exchange Umbrella Sampling Won't Start on Laptop
- JoÃ£o Ribeiro (Mon Oct 08 2018 - 09:22:31 CDT)
- Schwartz, Noah (Sat Oct 06 2018 - 15:31:41 CDT)
Residue-Based Coarse-Graining
- Ehsan Nikbin (Mon Dec 02 2013 - 09:24:19 CST)
Residue-Based Coarse-Graining;
- Sridhar Kumar Kannam (Wed Aug 13 2014 - 00:58:50 CDT)
residues for purple bacteria non protein
- brosbam_at_berkeley.edu (Mon Jul 14 2008 - 20:15:11 CDT)
RMSD for water sphere simulation of ubiquitin in tutorial
- JC Gumbart (Tue Apr 01 2008 - 22:37:45 CDT)
- Maria Sanchez Farran (Mon Mar 31 2008 - 08:12:27 CDT)
Rmsd plot
- Subbusinger N (Thu Nov 28 2013 - 03:31:12 CST)
- Subbusinger N (Wed Nov 06 2013 - 23:17:39 CST)
rmsd.dat file
- Subbusinger N (Wed Nov 27 2013 - 06:09:30 CST)
rules for grouping atoms
- SHIVAM TIWARI (Thu Jan 28 2021 - 10:38:22 CST)
- SHIVAM TIWARI (Thu Jan 28 2021 - 09:13:34 CST)
running a simulation after minimization
- Eva Gonzalez Noya (Tue Feb 15 2011 - 16:15:52 CST)
SBCG - Error loating-point value too small to represent
- Sujata Sovani (Fri Nov 06 2009 - 14:19:22 CST)
scalar and non scalar colvar in NAMD12
- Chunli Yan (Wed Jul 26 2017 - 16:21:02 CDT)
script for hbond time series (fwd)
- Michael Bach (Wed Mar 21 2007 - 14:08:23 CDT)
- Ana Celia Araujo Vila Verde (Wed Mar 21 2007 - 11:00:46 CDT)
- Michael Bach (Wed Mar 21 2007 - 10:29:41 CDT)
Shrink periodic box
- JC Gumbart (Mon Apr 23 2007 - 17:23:11 CDT)
- Won-Young Ahn (Mon Apr 23 2007 - 12:35:34 CDT)
Simulations with alpha methylated amino acids
- amin_at_imtech.res.in (Wed Mar 14 2012 - 10:24:58 CDT)
SMD Analysis
- Peter Freddolino (Sat May 12 2007 - 16:10:10 CDT)
- Peter Freddolino (Sat May 12 2007 - 16:07:48 CDT)
- baxy (Sat May 12 2007 - 15:14:21 CDT)
something wrong with the topology file of cellob01
- Bharath Rajeswaran (Thu Jun 24 2010 - 07:13:39 CDT)
specific heat of ubiquinone
- abojovschi_at_ict.swin.edu.au (Mon Aug 08 2005 - 19:08:15 CDT)
String method with swarms of trajectories
- ÐšÐ°Ñ‚ÐµÑ€Ð¸Ð½Ð° ÐšÐ¾Ñ† (Fri Apr 29 2016 - 01:44:31 CDT)
Structure (psf) file is in CHARMM format; XPLOR format required
- TYAGI Abhishek (Sat Dec 28 2013 - 03:57:56 CST)
Structure file generation problems
- Laura (Mon Oct 28 2013 - 10:41:13 CDT)
suggestions for improving NAMD tutorial
- Timothy Isgro (Tue Mar 07 2006 - 20:02:29 CST)
- Ana Celia Araujo Vila Verde (Sat Dec 17 2005 - 14:23:01 CST)
Targeted Molecular Dynamics
- ëŒ€í•™ì›/ì¼ë°˜ëŒ€í•™ì› ìƒëª…ê³¼í•™ë¶€ (Sat Dec 08 2018 - 09:50:22 CST)
test
- Peter Bender (Fri Dec 19 2008 - 06:48:16 CST)
- Peter Bender (Fri Dec 19 2008 - 05:17:26 CST)
Testing
- Tim Skirvin (Thu Jul 14 2005 - 12:25:48 CDT)
- Tim Skirvin (Thu Jul 14 2005 - 12:24:31 CDT)
Text Mode on OS 10.5
- Corey Fugate (Fri Nov 27 2009 - 20:59:51 CST)
the button on the labled AS
- JC Gumbart (Mon May 12 2008 - 14:08:41 CDT)
- Hyundeok Song (Mon May 12 2008 - 10:53:36 CDT)
The format of BOND table in a topology file
- Timothy Isgro (Tue Nov 07 2006 - 16:53:16 CST)
- Won-Young Ahn (Tue Nov 07 2006 - 14:22:53 CST)
- Won-Young Ahn (Tue Nov 07 2006 - 14:20:08 CST)
Three questions about bonds accross the boundary
- Hall McDull (Mon Apr 16 2012 - 00:03:05 CDT)
trajectory analysis (fwd)
- Michael Bach (Fri Aug 24 2007 - 10:45:56 CDT)
troubles with generating pdb with hydrogens
- Chris Harrison (Thu Jul 09 2009 - 15:49:42 CDT)
- Corey Fugate (Thu Jul 09 2009 - 13:51:59 CDT)
tutorial is not working
- JC Gumbart (Wed Jun 02 2010 - 00:25:33 CDT)
- Ms. Nabila Tahreen (Tue Jun 01 2010 - 23:47:08 CDT)
ubuquitin tutorial-FATAL ERROR: BAD IMPROPER FORMAT IN CHARMM PARAMETER FILE
- JC Gumbart (Wed May 14 2008 - 15:56:24 CDT)
- Roberta Rostagno (Wed May 14 2008 - 02:00:20 CDT)
- JC Gumbart (Tue May 13 2008 - 14:13:13 CDT)
- roberta.rostagno (Tue May 13 2008 - 05:37:07 CDT)
Umbrella sampling of AA and CNT dissociation, pmf doesn't flatten & reduces over large distances...
- zeynab hosseini (Wed Apr 15 2020 - 00:08:45 CDT)
Unable to generate PSF file due to an unparametrized methyl histidine
- Chris Harrison (Tue Jul 28 2009 - 20:41:03 CDT)
- Sujata Sovani (Tue Jul 28 2009 - 18:01:18 CDT)
useful information for you
- Hugo Hearn (Sun Sep 03 2017 - 17:43:45 CDT)
User-defined forces in NAMD
- JC Gumbart (Mon Oct 06 2008 - 12:03:17 CDT)
- Katherine Parra (Mon Oct 06 2008 - 10:35:17 CDT)
velocity DCD file data retrieval
- Matthew Ambrosia (Wed Sep 17 2008 - 01:48:02 CDT)
Volume
- C. Parry (Fri Dec 01 2006 - 18:02:17 CST)
- C. Parry (Thu Nov 30 2006 - 09:22:24 CST)
Water density in a periodic box
- Timothy Isgro (Sat Mar 17 2007 - 16:37:00 CDT)
- Timothy Isgro (Fri Mar 16 2007 - 12:55:34 CDT)
- wahn_at_uiuc.edu (Wed Mar 14 2007 - 14:46:20 CDT)
water molecule
- JC Gumbart (Thu Aug 02 2007 - 14:42:37 CDT)
- JC Gumbart (Tue Jul 31 2007 - 15:15:15 CDT)
- Sathish Gurupatham (Tue Jul 31 2007 - 11:09:27 CDT)
Water Permeation Through Nanotubes -- Atoms Moving Too Fast!!!
- Jeronimo Terrones (Wed Oct 11 2017 - 10:19:44 CDT)
Welcome to tutorial-l
- Michael Bach (Wed Jul 20 2005 - 16:04:14 CDT)
- Michael Bach (Tue Jul 19 2005 - 16:51:49 CDT)
What is the means of system-min.conf in the Residue-Based Coarse tutorial?
- javacfish (Tue Apr 17 2012 - 11:18:30 CDT)
Why does the Nanopore Tutorial not reuse the equilibrated structures when combining the DNA and nanopore?
- Basheer Subei (Sun Aug 24 2014 - 16:40:31 CDT)
- Jeff Comer (Sat Aug 23 2014 - 13:16:22 CDT)
- Jeff Comer (Sat Aug 23 2014 - 12:43:41 CDT)
- Basheer Subei (Fri Aug 22 2014 - 19:35:18 CDT)
âœ”hey! oh wow
- Erik Sanchez (Tue Nov 14 2017 - 19:08:13 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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