NAMD-L: By Author
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About this archive
Starting: Sat Jan 01 2011 - 12:21:40 CST
Ending: Mon Dec 31 2012 - 14:36:03 CST
- a a
- Aaron Cann
- Aaron Oakley
- AB
- Ada Sedova
- Ada Zhan
- Adam Skelton
- Adebayo Adeleke via LinkedIn
- Adeleke Adebayo Abayomi
- Aditya Ranganathan
- Adrian Jasiñski
- Ahlam Al-Rawi
- ais_at_fh.huji.ac.il
- Ajasja LjubetiÄ
- Re: dump specific atom positions into a txt file during the simulation (Fri Aug 31 2012 - 03:44:42 CDT)
- Re: Atoms Gone Missing after Generalized Born Implicit Solvent Equilibration (Mon Jul 16 2012 - 01:25:10 CDT)
- Re: Trouble using rotateReference, centerRefrence and refPositionsGroup in the colvar module (Thu Feb 09 2012 - 12:05:19 CST)
- Re: Trouble using rotateReference, centerRefrence and refPositionsGroup in the colvar module (Mon Feb 06 2012 - 16:55:26 CST)
- Re: Trouble using rotateReference, centerRefrence and refPositionsGroup in the colvar module (Mon Feb 06 2012 - 15:04:56 CST)
- Re: Trouble using rotateReference, centerRefrence and refPositionsGroup in the colvar module (Thu Feb 02 2012 - 09:06:37 CST)
- Re: Trouble using rotateReference, centerRefrence and refPositionsGroup in the colvar module (Wed Feb 01 2012 - 03:44:26 CST)
- Trouble using rotateReference, centerRefrence and refPositionsGroup in the colvar module (Tue Jan 31 2012 - 08:30:05 CST)
- Re: Dividing a 2D ABF simulations into regions (on nodes with different speeds) (Fri Jul 29 2011 - 11:56:17 CDT)
- Dividing a 2D ABF simulations into regions (on nodes with different speeds) (Fri Jul 29 2011 - 04:44:38 CDT)
- Re: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR C H (ATOMS 2 1) (Fri Jun 24 2011 - 03:46:18 CDT)
- Re: aligning two molecules by principal axes of inertia using measure.c (Mon Jun 20 2011 - 09:40:20 CDT)
- Re: what will be the best way to simulate substrate interaction only within a binding pocket of a large protein. (Tue May 10 2011 - 15:57:58 CDT)
- Re: Rotate two linked proteins against each other and calculate energy profile (Mon Mar 28 2011 - 09:30:28 CDT)
- Re: Advisable limit on the number of quadrants a 2D ABF simulation can be split. (Mon Mar 28 2011 - 09:06:40 CDT)
- Advisable limit on the number of quadrants a 2D ABF simulation can be split. (Fri Mar 25 2011 - 04:52:09 CDT)
- Re: Rotate two linked proteins against each other and calculate energy profile (Mon Mar 21 2011 - 03:43:55 CDT)
- Re: Rotate two linked proteins against each other and calculate energy profile (Tue Mar 15 2011 - 16:56:39 CDT)
- Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein (Wed Jan 19 2011 - 10:01:42 CST)
- Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein (Wed Jan 19 2011 - 06:53:41 CST)
- Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein (Tue Jan 18 2011 - 08:40:56 CST)
- Ajasja Ljubetiè
- Ajith Rathnaweera Rajapaksha Mudalige
- Aksimentiev, Oleksii
- alamng_at_uci.edu
- Albert
- AlbertAlbert
- albus hawking
- Alex
- alex digenova bravo
- Alex Liu
- Alex Smith
- Alexander Predeus
- Alexandra Nemkevich
- Ali Emileh
- Ali Ghaffaari
- Ali Khanlarkhani
- Alisha \
- amin_at_imtech.res.in
- amit banerjee
- Re: Pico scale to nanoscale simulation....alteration if .conf files required (Mon Jul 25 2011 - 07:42:35 CDT)
- amit majhi
- Ana Celia Vila Verde
- anaome_at_fundp.ac.be
- Andrea Holfelder
- Andreas Förster
- Andres Colubri
- Andres Morales N
- RE: Lipid bilayer equilibration: Periodic cell has become too small for original patch grid! (Mon Aug 08 2011 - 17:20:56 CDT)
- Andrew Emerson
- Andrey
- Andy Somogyi
- Angelo Rossi
- Anirban Ghosh
- Anna James
- Anthony Rey
- Anurag Sethi
- Aoife Fogarty
- Arash Azari
- Aron Broom
- Re: Unexplained segmentation faults in NAMD 2.9 using CUDA and GBIS (Thu Nov 29 2012 - 17:01:23 CST)
- Re: metadynamics/ABF simulations using collective variables - issues with restarting the calculations (Tue Nov 13 2012 - 13:58:29 CST)
- Re: metadynamics/ABF simulations using collective variables - issues with restarting the calculations (Tue Nov 13 2012 - 10:47:52 CST)
- Re: FATAL ERROR: CUDA error in cudaGetDeviceCount on Pe 0 (thomasASUS): CUDA driver version is insufficient for CUDA runtime version (Mon Oct 22 2012 - 10:10:54 CDT)
- Re: NAMD (and VMD) fail to read simple AMBER prmtop file (and it's not the SCEE and SCNB flags) (Sun Oct 21 2012 - 18:37:56 CDT)
- Re: using colvar for umbrella sampling between two carbon nanotubes in aqueous dispersion (Thu Sep 20 2012 - 12:58:35 CDT)
- Re: Atoms Gone Missing after Generalized Born Implicit Solvent Equilibration (Mon Jul 16 2012 - 16:59:22 CDT)
- Re: Atoms Gone Missing after Generalized Born Implicit Solvent Equilibration (Mon Jul 16 2012 - 16:27:34 CDT)
- Re: Atoms Gone Missing after Generalized Born Implicit Solvent Equilibration (Sun Jul 15 2012 - 20:31:26 CDT)
- Re: running simulations on different machines with different versions of NAMD (Fri Jun 15 2012 - 05:38:20 CDT)
- Re: rigidBonds water and langevinHydrogen off are INCOMPATIBLE when using a solute with hdyrogens (Fri Mar 02 2012 - 10:51:16 CST)
- Re: rigidBonds water and langevinHydrogen off are INCOMPATIBLE when using a solute with hdyrogens (Thu Mar 01 2012 - 15:06:29 CST)
- Re: what restraint can I use to prevent membrane diffusion on the Z-axis? (Wed Feb 29 2012 - 16:46:05 CST)
- rigidBonds water and langevinHydrogen off are INCOMPATIBLE when using a solute with hdyrogens (Tue Feb 28 2012 - 21:58:25 CST)
- Re: what restraint can I use to prevent membrane diffusion on the Z-axis? (Tue Feb 28 2012 - 16:46:23 CST)
- Artem Zhmurov
- Arturas
- Arun Kumar Subramanian
- Arvind Kannan
- Ashley Chew
- Ashwin C.V.
- Athanassios Stavrakoudis
- atsuiai_at_aim.com
- Austin B. Yongye
- Axel Kohlmeyer
- Re: connect a spring between all the atoms present in pdb structure (Sat Aug 04 2012 - 13:21:27 CDT)
- Re: vmd-l: connect a spring between all the atoms present in pdb structure (Sat Aug 04 2012 - 13:20:05 CDT)
- Re: Atoms Gone Missing after Generalized Born Implicit Solvent Equilibration (Mon Jul 16 2012 - 15:46:51 CDT)
- Re: Simultaneous calculation on CPU-only nodes and CPU/GPU node (with or without rCUDA) (Mon May 28 2012 - 17:19:42 CDT)
- Re: Simultaneous calculation on CPU-only nodes and CPU/GPU node (with or without rCUDA) (Mon May 28 2012 - 14:58:53 CDT)
- Re: Simultaneous calculation on CPU-only nodes and CPU/GPU node (with or without rCUDA) (Fri May 25 2012 - 05:39:37 CDT)
- Re: Sufficiently large values for 'firsttimestep' can lead to immediate simulation abort. (Sun Apr 08 2012 - 12:38:10 CDT)
- Re: what restraint can I use to prevent membrane diffusion on the Z-axis? (Wed Feb 29 2012 - 16:53:59 CST)
- Re: ATTENTION: 0031-408 4 tasks allocated by LoadLeveler, continuing (Tue Jan 10 2012 - 14:21:26 CST)
- Re: Use of RBCG to convert multiple frames from atomistic trajectory to Coarse grained (Tue Nov 01 2011 - 14:59:27 CDT)
- Re: PME Grid Settings and its significance relative to a cutoff value (Fri Aug 19 2011 - 13:05:26 CDT)
- Re: Dividing a 2D ABF simulations into regions (on nodes with different speeds) (Fri Jul 29 2011 - 08:34:33 CDT)
- Re: NAMD2.7 on BluegeneL hang at "LDB: Central LB being created..." (Wed Mar 02 2011 - 22:32:28 CST)
- Azat Mukhametov
- Babban Mia
- Badoo
- Bala subramanian
- baogen duan
- Basak Isin
- Benjamin Merget
- Re: Simultaneous calculation on CPU-only nodes and CPU/GPU node (with or without rCUDA) (Sun May 27 2012 - 09:10:59 CDT)
- Bennion, Brian
- bharat gupta
- Re: Replica Exchange Discrete Molecular Dynamics for structure based models (Tue Jan 03 2012 - 00:48:16 CST)
- Bin Zhang
- Bishop, Thomas C
- Bjoern Olausson
- Logfile flooded with "The last position output [...]" when IMDon is used. (Tue Aug 23 2011 - 04:32:47 CDT)
- Re: Lipid bilayer equilibration: Periodic cell has become too small for original patch grid! (Wed Aug 10 2011 - 02:49:01 CDT)
- Re: Lipid bilayer equilibration: Periodic cell has become too small for original patch grid! (Mon Aug 08 2011 - 02:57:08 CDT)
- Re: NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 (Thu May 19 2011 - 04:00:33 CDT)
- Re: NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 (Wed May 18 2011 - 08:44:48 CDT)
- Re: NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 (Mon May 16 2011 - 13:45:14 CDT)
- Re: NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 (Mon May 16 2011 - 04:02:51 CDT)
- Re: NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 (Sat May 14 2011 - 01:12:57 CDT)
- Re: NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 (Fri May 13 2011 - 13:10:46 CDT)
- Re: NAMD2.7 on BluegeneL hang at "LDB: Central LB being created..." (Fri May 13 2011 - 02:47:16 CDT)
- NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 (Thu May 12 2011 - 17:20:09 CDT)
- Re: Rotate two linked proteins against each other and calculate energy profile (Tue Mar 29 2011 - 10:16:12 CDT)
- Re: Rotate two linked proteins against each other and calculate energy profile (Mon Mar 28 2011 - 16:46:29 CDT)
- Re: Rotate two linked proteins against each other and calculate energy profile (Mon Mar 28 2011 - 16:00:25 CDT)
- Re: Rotate two linked proteins against each other and calculate energy profile (Mon Mar 28 2011 - 11:36:13 CDT)
- Re: Rotate two linked proteins against each other and calculate energy profile (Mon Mar 28 2011 - 11:18:09 CDT)
- Re: Rotate two linked proteins against each other and calculate energy profile (Mon Mar 28 2011 - 07:49:23 CDT)
- Re: GBIS question and possible Bug for colvar "outputSystemForce" declaration in NAMD CVS-2011-03-03 (Wed Mar 23 2011 - 07:06:21 CDT)
- Re: GBIS question and possible Bug for colvar "outputSystemForce" declaration in NAMD CVS-2011-03-03 (Wed Mar 23 2011 - 03:18:22 CDT)
- GBIS question and possible Bug for colvar "outputSystemForce" declaration in NAMD CVS-2011-03-03 (Tue Mar 22 2011 - 17:56:09 CDT)
- Re: Rotate two linked proteins against each other and calculate energy profile (Sun Mar 20 2011 - 11:03:32 CDT)
- Blake Mertz
- Bo Liu
- Bob Masong
- bond.james
- Boyang Wang
- Re: Using TCLforces to rescale force(s) on particular atom(s) --- loadtotalforces, addforce and previous/current timestep issue (Thu Jan 19 2012 - 17:45:41 CST)
- Re: surfaceTensionTarget - Surface Tension per interface or per bilayer (Wed Jan 11 2012 - 08:30:17 CST)
- Re: how does namd handle violations of the minimum image convention? (Tue Jan 10 2012 - 21:45:04 CST)
- Re: Re: How to evaluate the area per lipid and thickness of the lipid bilayer in a membrane-protein system? (Thu Aug 25 2011 - 02:32:01 CDT)
- Branko
- Re: RMSD collective variable - Different atons to align and to calculate RMSD (Tue Feb 07 2012 - 12:49:37 CST)
- Re: GBIS and hydrophobic term, in replay to Jerome and David discussion (Sun Oct 23 2011 - 09:55:27 CDT)
- Brett T. Hannigan
- Bruno Luís Pinto de Oliveira
- Bryan Roessler
- Buddhadev Maiti
- Burgess, Don E
- c jepson
- Cade Markegard
- Caitlin Scott
- candy deck
- Carlos Sosa
- Cesar Millan
- Chandra Ramananjara
- chang
- charlie
- Charlie Forde
- Chathurika Abeyrathne
- Chen, Zhihong (chenz2)
- Chewning, Joseph
- Chiara Cosenza unina
- Chiara.cosenza
- Chirag Vora
- Chris Chipot
- Re: question about relative binding free energy calculation method using FEP (Sat Nov 24 2012 - 09:54:46 CST)
- Chris Harrison
- Re: FATAL ERROR: CUDA error in cudaGetDeviceCount on Pe 0 (thomasASUS): CUDA driver version is insufficient for CUDA runtime version (Sat Sep 22 2012 - 10:23:16 CDT)
- Re: FATAL ERROR: CUDA error in cudaGetDeviceCount on Pe 0 (thomasASUS): CUDA driver version is insufficient for CUDA runtime version (Sat Sep 22 2012 - 09:03:42 CDT)
- Re: FATAL ERROR: CUDA error in cudaGetDeviceCount on Pe 0 (thomasASUS): CUDA driver version is insufficient for CUDA runtime version (Sat Sep 22 2012 - 07:56:34 CDT)
- Re: Need help preventing hydration of the lipid-protein interface in my system (Thu May 03 2012 - 18:31:50 CDT)
- Re: what restraint can I use to prevent membrane diffusion on the Z-axis? (Sat Feb 25 2012 - 11:59:43 CST)
- Re: RMSD collective variable - Different atons to align and to calculate RMSD (Thu Feb 02 2012 - 13:54:55 CST)
- Re: FATAL ERROR: Low global exclusion count! System unstable or pairlistdist or cutoff too small. (Mon Aug 29 2011 - 20:07:33 CDT)
- Re: FATAL ERROR: Low global exclusion count! System unstable or pairlistdist or cutoff too small. (Mon Aug 29 2011 - 19:35:42 CDT)
- Re: FATAL ERROR: Low global exclusion count! System unstable or pairlistdist or cutoff too small. (Mon Aug 29 2011 - 11:50:00 CDT)
- Re: NAMD2.7 on BluegeneL hang at "LDB: Central LB being created..." (Thu Mar 03 2011 - 20:08:20 CST)
- chris liopiri
- Christian Jorgensen
- Christopher Rowley
- christos.lamprakis_at_dcb.unibe.ch
- Clark Zhang
- Clayton
- cnu gromacs
- Cojocaru, Vlad
- Cole Gleason
- Cosseddu, Salvatore
- Courtney Taylor
- Craig Jolley
- Cristhian Boetsch
- Cristina Rodríguez
- Cruz-Chu Eduardo Roberto
- da xue
- DAI, JIAN
- Damián Montaldo
- Daniel Aguayo
- Daniel Svozil
- Danny Xu
- Darko Stefanovski
- David Brandon
- 'Hands-On' Workshop on Computational Biophysics using VMD and NAMD, October 22-26, 2012 in Urbana, Illinois (Mon Jul 09 2012 - 14:29:08 CDT)
- David Hardy
- David Hemmendinger
- David Huggins
- David McGiven
- Problem with NAMD 2.8 (but not in 2.7) : Endless loop repeating "The last position output ..." (Wed Jun 08 2011 - 09:00:34 CDT)
- David Minh
- David Rogers
- David Tanner
- Davide Branduardi
- Davide Vanzo/FS/VCU
- dbaogen
- Demet Akten
- Dhiraj Srivastava
- Dimitrios Tragoudaras
- divya nayar
- dklose_at_uni-osnabrueck.de
- Dmitry Osolodkin
- Dong Luo
- Re: NAMD2.7 on BluegeneL hang at "LDB: Central LB being created..." (Tue Apr 12 2011 - 09:44:09 CDT)
- Re: NAMD2.7 on BluegeneL hang at "LDB: Central LB being created..." (Fri Mar 04 2011 - 10:40:54 CST)
- Re: NAMD2.7 on BluegeneL hang at "LDB: Central LB being created..." (Fri Mar 04 2011 - 08:08:38 CST)
- dongsheng lei
- dota alexiou
- Dr. Eddie
- dream
- Dropbox
- Edroaldo Lummertz da Rocha
- Eduard Schreiner
- Eduardo Cruz-Chu
- Edward Lyman
- ehenriques_at_qui.uc.pt
- Ehsan Ban
- Eli Fine
- Enrico Guarnera
- Eric H. Lee
- Erica Smith
- Erik Nordgren
- Re: PME Grid Settings and its significance relative to a cutoff value (Fri Aug 19 2011 - 12:38:34 CDT)
- Re: Pico scale to nanoscale simulation....alteration if .conf files required (Tue Jul 26 2011 - 20:54:30 CDT)
- Erik Santiso
- Ernesto Vargas
- esmael
- Eun Kim
- Eva Gonzalez Noya
- Evgeny Bulat
- Fabien Archambault
- Family Xu
- farzad kiani
- Felipe Merino
- felmerino_at_uchile.cl
- flavio seixas
- Florian Mrugalla
- forough askari
- francesco oteri
- Francesco Pietra
- Alchemical protein transformation with a group of (non proteic) atoms bound to two amino acids (Mon Aug 06 2012 - 02:36:47 CDT)
- Re: Re: vmd-l: FFTK VMD plugin issue (arising from VECSCALE TCL issues of either NAMD or VMD ?) (Tue Jun 05 2012 - 12:54:05 CDT)
- FFTK VMD plugin issue (arising from VECSCALE TCL issues of either NAMD or VMD ?) (Tue Jun 05 2012 - 02:16:40 CDT)
- Re: Simultaneous calculation on CPU-only nodes and CPU/GPU node (with or without rCUDA) (Tue May 29 2012 - 00:10:08 CDT)
- Frederik Heurlin Aidt
- FyD
- gaborekt_at_duq.edu
- Gabriel Jara
- Ganesh Kamath
- Gareth Shannon
- Gary M. Skinner
- Gayatri Rathod
- George M Giambasu
- George Madalin Giambasu
- Germán Andrés Miño
- Giacomo Fiorin
- Re: [MetaD; namd 2.9] Pmf output file problem once the CV boundaries are reached, even using "expandBoundaries on" (Tue Nov 20 2012 - 18:41:02 CST)
- Re: metadynamics/ABF simulations using collective variables - issues with restarting the calculations (Wed Nov 14 2012 - 18:26:29 CST)
- Re: metadynamics/ABF simulations using collective variables - issues with restarting the calculations (Tue Nov 13 2012 - 14:11:05 CST)
- Re: [MetaD; namd 2.9] Pmf output file problem once the CV boundaries are reached, even using "expandBoundaries on" (Fri Sep 07 2012 - 11:38:08 CDT)
- Re: Trouble using rotateReference, centerRefrence and refPositionsGroup in the colvar module (Tue Feb 07 2012 - 16:57:33 CST)
- Re: Question about "Free Energy of Conformational Change Calculations" (Mon Feb 06 2012 - 11:13:21 CST)
- Re: Trouble using rotateReference, centerRefrence and refPositionsGroup in the colvar module (Thu Feb 02 2012 - 17:02:08 CST)
- Re: RMSD collective variable - Different atons to align and to calculate RMSD (Thu Feb 02 2012 - 13:52:49 CST)
- Re: Trouble using rotateReference, centerRefrence and refPositionsGroup in the colvar module (Wed Feb 01 2012 - 19:31:53 CST)
- Re: Trouble using rotateReference, centerRefrence and refPositionsGroup in the colvar module (Tue Jan 31 2012 - 12:28:24 CST)
- Re: Using TCLforces to rescale force(s) on particular atom(s) --- loadtotalforces, addforce and previous/current timestep issue (Thu Jan 19 2012 - 11:56:00 CST)
- Re: what will be the best way to simulate substrate interaction only within a binding pocket of a large protein. (Tue May 10 2011 - 15:20:18 CDT)
- Re: Error: keyword "group1" is not supported, or not recognized in this context. (Fri Apr 15 2011 - 11:02:03 CDT)
- Gianluca Interlandi
- Giovanni Bellesia
- Giovanni Settanni
- Giulia
- Gmail
- GONZALEZ NOYA, EVA
- Gordon Wells
- Grace Brannigan
- Grant Schauer
- Grazia Cottone
- Guanglei Cui
- Gungor Ozer
- Guoxiong Su
- Gurunath Katagi
- Hall McDull
- HAMID -
- Re: membrane simulation and mobility of lipids - blocking ion channel (Thu Sep 29 2011 - 04:57:10 CDT)
- Hamze Rahimi
- Hannes Loeffler
- hannes.loeffler_at_stfc.ac.uk
- Haque-Student,STW, Farhadul
- harish vashisth
- Harris, Robert C.
- Harshad Joshi
- Hasan haska
- Haydee Valdes
- Henriette Elisabeth Autzen
- Hugh Heldenbrand
- Huihui Liu
- Hyonseok Hwang
- Hyuntae Na
- imran.1.618_at_gmail.com
- ipsita basu
- Irene Newhouse
- Isaure Chauvot de Beauchêne
- ishiikai08_at_yahoo.co.jp
- Ismail, Mohd F.
- Ivan Vyalov
- Iyer, Ravishankar K
- Jacopo Sgrignani
- Jacqueline Schmidt
- Re: dump specific atom positions into a txt file during the simulation (Fri Aug 31 2012 - 07:33:40 CDT)
- jafar azamat
- Jan H. Meinke
- Jane Ren
- jani vinod
- javacfish
- jaya c.jose
- JC Gumbart
- Re: 回å¤: Re: question about relative binding free energy calculation method using FEP (Sun Nov 25 2012 - 00:46:48 CST)
- Re: vmd-l: FFTK VMD plugin issue (arising from VECSCALE TCL issues of either NAMD or VMD ?) (Tue Jun 05 2012 - 09:22:10 CDT)
- RE: About the correction of charging two ion water box by using FEP (Sat Jun 02 2012 - 07:43:15 CDT)
- Re: About the correction of charging two ion water box by using FEP (Mon May 28 2012 - 17:15:35 CDT)
- RE: About the correction of charging two ion water box by using FEP (Mon May 28 2012 - 08:41:56 CDT)
- Re: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR C H (ATOMS 2 1) (Thu Jun 23 2011 - 16:17:59 CDT)
- Re: Can paratools really parametrize a structure? Is it really finished? (Mon Feb 28 2011 - 13:31:16 CST)
- Jeff Wereszczynski
- Jeffrey J. Potoff
- Jeffrey Potoff
- Re: Relationship between High temperature and the boiling point of water (Thu Aug 18 2011 - 09:22:36 CDT)
- Re: Lipid bilayer equilibration: Periodic cell has become too small for original patch grid! (Mon Aug 08 2011 - 21:12:39 CDT)
- Jens K. Munk
- jeremy adler
- Jeremy Parlin
- Jernej Zidar
- jesmin jahan
- Jesper Sørensen
- Jesper Sørensen
- Jian Dai
- Jian Liu
- Jiao, Dian NMN (-EXP)
- Jim Phillips
- Re: Re: NAMD 2.9b2-cuda does not scale well compared to NAMD 2.8 (solved) (Fri Apr 27 2012 - 14:10:20 CDT)
- Re: rigidBonds water and langevinHydrogen off are INCOMPATIBLE when using a solute with hdyrogens (Thu Mar 01 2012 - 14:47:48 CST)
- Re: NAMD-l: Get the PDB file from Steered Molecular Dynamics output files (Fri Jun 17 2011 - 13:14:11 CDT)
- Re: Problem with NAMD 2.8 (but not in 2.7) : Endless loop repeating "The last position output ..." (Thu Jun 09 2011 - 10:53:46 CDT)
- Re: NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 (Wed May 18 2011 - 17:58:16 CDT)
- Re: NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 (Tue May 17 2011 - 13:21:49 CDT)
- Re: NAMD 2.7/2.8b2 stuck - [0] processControlPoints() haveControlPointChangeCallback=0 frameworkShouldAdvancePhase=0 (Fri May 13 2011 - 14:52:53 CDT)
- Re: NAMD2.7 on BluegeneL hang at "LDB: Central LB being created..." (Fri May 13 2011 - 08:18:37 CDT)
- jiyong
- Jiyong Park
- jnsong
- Joe Yelk
- johan strumpfer
- John Baker
- John Doe
- John Jumper
- John Stone
- Jon Fuller
- Jon Phillips
- Jorge Hernandez Cobos
- Jorgen Simonsen
- Jose Borreguero
- NAMD (and VMD) fail to read simple AMBER prmtop file (and it's not the SCEE and SCNB flags) (Sat Oct 20 2012 - 15:55:51 CDT)
- Re: what restraint can I use to prevent membrane diffusion on the Z-axis? (Wed Feb 29 2012 - 16:38:44 CST)
- jose correa
- Joseph Antoine Garate
- Joshua Adelman
- Joshua D. Moore
- Juan Antonio Raygoza Garay
- juan du
- Jun Zhang
- Re: Evaluated heat capacities via NAMD are larger than experimental values (Wed Oct 26 2011 - 19:00:18 CDT)
- RE: deca-Ala simulations with different cutoff produce different results (Mon May 16 2011 - 03:47:44 CDT)
- Jérôme Hénin
- Jérôme Hénin
- Re: metadynamics/ABF simulations using collective variables - issues with restarting the calculations (Tue Nov 13 2012 - 10:21:19 CST)
- Re: using colvar for umbrella sampling between two carbon nanotubes in aqueous dispersion (Thu Sep 20 2012 - 12:45:49 CDT)
- Re: using colvar for umbrella sampling between two carbon nanotubes in aqueous dispersion (Thu Sep 20 2012 - 11:59:47 CDT)
- Re: Trouble using rotateReference, centerRefrence and refPositionsGroup in the colvar module (Fri Feb 03 2012 - 05:20:31 CST)
- Re: RMSD collective variable - Different atons to align and to calculate RMSD (Thu Feb 02 2012 - 15:40:47 CST)
- Re: surfaceTensionTarget - Surface Tension per interface or per bilayer (Wed Jan 11 2012 - 09:18:39 CST)
- Re: GBIS and hydrophobic term, in replay to Jerome and David discussion (Sun Oct 23 2011 - 09:43:08 CDT)
- Re: Rotate two linked proteins against each other and calculate energy profile (Tue Mar 29 2011 - 07:03:14 CDT)
- Re: Rotate two linked proteins against each other and calculate energy profile (Mon Mar 28 2011 - 15:50:44 CDT)
- Re: Rotate two linked proteins against each other and calculate energy profile (Mon Mar 28 2011 - 15:43:46 CDT)
- Re: Rotate two linked proteins against each other and calculate energy profile (Mon Mar 28 2011 - 11:07:43 CDT)
- Re: Advisable limit on the number of quadrants a 2D ABF simulation can be split. (Mon Mar 28 2011 - 09:42:33 CDT)
- Re: Advisable limit on the number of quadrants a 2D ABF simulation can be split. (Fri Mar 25 2011 - 06:25:30 CDT)
- Re: GBIS question and possible Bug for colvar "outputSystemForce" declaration in NAMD CVS-2011-03-03 (Wed Mar 23 2011 - 05:39:51 CDT)
- Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein (Thu Jan 20 2011 - 08:07:36 CST)
- Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein (Wed Jan 19 2011 - 09:23:03 CST)
- kakali sen
- kamal Kishor Thakur
- kanchi subbarao rao
- Fwd: what restraint can I use to prevent membrane diffusion on the Z-axis? (Tue Feb 28 2012 - 13:50:50 CST)
- Re: what restraint can I use to prevent membrane diffusion on the Z-axis? (Tue Feb 28 2012 - 11:58:49 CST)
- Re: what restraint can I use to prevent membrane diffusion on the Z-axis? (Mon Feb 27 2012 - 22:49:02 CST)
- Kang Hee Cho
- Kapil jain
- Kartheek
- Kasam, Vinod
- Katrin Stöbener
- Kei Sit
- Kei-ichi Okazaki
- Keith Battle
- Kevin Kastner
- Kevin Littrell
- khalil ghafarian
- Kiarash Hosseini
- Koivuniemi Artturi
- KONG Xian
- koushik.k
- Kovacs, Sandor
- Kristopher Opron
- Kwee Hong
- Lachele Foley (Lists)
- Lada Biedermannová
- lam nguyen
- Lawson, John W. (ARC-TSM)
- lcbllcc_at_gmail.com
- Leandro Martínez
- lecan
- Lei Shi
- Lela Vukovic
- Leonardo Herrera
- Lindong Weng
- Ling Wu
- Liqun Zhang
- Lisa Brown
- liupeng012_at_mail.nankai.edu.cn
- Luca Bellucci
- lucie delemotte
- Luthur Cheung
- M Mahjour
- M.Raviprasad
- Madhulika Gupta
- Madhurima Jana
- Mallajosyula, Sairam
- Mao Mao
- Marc Baaden
- Marc Charendoff
- Marc Gordon
- Marcel UJI (IMAP)
- Marco Sant
- Marcos Sotomayor
- Marek Maly
- Maria Antonieta Sanchez Farran
- Maria Bykhovskaia
- Maria Kamm
- Maria Musgaard
- Maria Pikoula
- Maria Saeed
- Mariana Graterol
- Marimuthu Krishnan
- Re: metadynamics/ABF simulations using collective variables - issues with restarting the calculations (Wed Nov 14 2012 - 18:22:48 CST)
- Re: metadynamics/ABF simulations using collective variables - issues with restarting the calculations (Tue Nov 13 2012 - 13:47:41 CST)
- Mark Abraham
- Mark Cunningham
- MARK PLUMMER
- Workshop - Computational Molecular Physics of Non-Bonded Bio-Molecular Interactions (Mon Jun 11 2012 - 17:14:51 CDT)
- Mark Triger
- Markus Dahlgren
- Markus K. Dahlgren
- Markus Metz
- Marlet Martinez
- Martin, Erik W
- María Antonieta Sánchez Farrán
- Massimiliano Bonomi
- Massimiliano Porrini
- Re: FATAL ERROR: Low global exclusion count! System unstable or pairlistdist or cutoff too small. (Mon Aug 29 2011 - 14:26:06 CDT)
- Matteo Pappalardo
- Matteo Rotter
- Matthew B. Roark
- matziast_at_med.uth.gr
- Maximilian Ebert
- Mayne, Christopher G
- Mert Gür
- Michael Galloway
- Michael Purdy
- Michael S. Sellers (Cont, ARL/WMRD)
- Michael Zimmermann
- Michel Espinoza-Fonseca
- Michelle Kuttel
- Miguel Ángel Mompeán García
- Mikhail Suyetin
- Minh, David D.
- Miroslav Hodak
- Mithun Biswas
- mj_aghaei_at_aut.ac.ir
- mjyang
- MOHAMMAD JAVAD AGHAEI
- Mohammad Jomah Ibraheem Ali Abu Saude (mbusaude)
- mohan maruthi sena
- Mohd Farid Ismail
- Molecular Dynamics
- mon_sharma_at_research.iiit.ac.in
- Monika Madhavi
- Moritz Schlarb
- Mortaza Aghtar
- mpahleva_at_abo.fi
- murffyp_at_gmail.com
- nabaneeta mukhopadhyay
- Namd Namd
- Narasimhan LOGANATHAN
- Neelanjana Sengupta
- Nicholas M Glykos
- Nicolas Sapay
- Nicolás Pérez
- Nikhil Kumar Mittal
- Nikita chopra
- Nikita Vakula
- Niklaus Johner
- Nikolaos Glykos
- Re: Sufficiently large values for 'firsttimestep' can lead to immediate simulation abort. (Sun Apr 08 2012 - 13:08:59 CDT)
- Niraj kumar
- Norman Geist
- AW: Unexplained segmentation faults in NAMD 2.9 using CUDA and GBIS (Fri Nov 30 2012 - 00:32:14 CST)
- AW: FATAL ERROR: CUDA error in cudaGetDeviceCount on Pe 0 (thomasASUS): CUDA driver version is insufficient for CUDA runtime version (Tue Oct 23 2012 - 01:04:04 CDT)
- AW: FATAL ERROR: CUDA error in cudaGetDeviceCount on Pe 0 (thomasASUS): CUDA driver version is insufficient for CUDA runtime version (Tue Oct 23 2012 - 00:37:16 CDT)
- AW: FATAL ERROR: CUDA error in cudaGetDeviceCount on Pe 0 (thomasASUS): CUDA driver version is insufficient for CUDA runtime version (Mon Oct 22 2012 - 01:01:02 CDT)
- AW: RE: FATAL ERROR: CUDA error in cudaGetDeviceCount on Pe 0 (thomasASUS): CUDA driver version is insufficient for CUDA runtime version (Mon Sep 24 2012 - 00:19:08 CDT)
- AW: Please read: fatal error namd 2.7b1 for Win32 Memory allocation failed on processor > 0 (Tue Aug 28 2012 - 02:00:12 CDT)
- AW: Simultaneous calculation on CPU-only nodes and CPU/GPU node (with or without rCUDA) (Tue May 29 2012 - 01:05:16 CDT)
- AW: AW: Simultaneous calculation on CPU-only nodes and CPU/GPU node (with or without rCUDA) (Tue May 29 2012 - 00:59:55 CDT)
- AW: Simultaneous calculation on CPU-only nodes and CPU/GPU node (with or without rCUDA) (Fri May 25 2012 - 01:10:17 CDT)
- AW: Linux-x86_64-CUDA version 2.8 on CentOS-5 x86_64 non local user issue? (Mon Mar 26 2012 - 00:43:17 CDT)
- AW: Linux-x86_64-CUDA version 2.8 on CentOS-5 x86_64 non local user issue? (Fri Mar 23 2012 - 02:09:28 CDT)
- AW: Linux-x86_64-CUDA version 2.8 on CentOS-5 x86_64 non local user issue? (Wed Mar 21 2012 - 02:02:41 CDT)
- AW: Linux-x86_64-CUDA version 2.8 on CentOS-5 x86_64 non local user issue? (Tue Mar 20 2012 - 01:36:34 CDT)
- AW: what restraint can I use to prevent membrane diffusion on the Z-axis? (Tue Feb 28 2012 - 00:42:24 CST)
- AW: aligning two molecules by principal axes of inertia using measure.c (Mon Jun 20 2011 - 09:30:02 CDT)
- AW: Problem with NAMD 2.8 (but not in 2.7) : Endless loop repeating "The last position output ..." (Thu Jun 09 2011 - 00:44:01 CDT)
- AW: Problem with NAMD 2.8 (but not in 2.7) : Endless loop repeating "The last position output ..." (Thu Jun 09 2011 - 00:36:44 CDT)
- AW: Problem with NAMD 2.8 (but not in 2.7) : Endless loop repeating "The last position output ..." (Thu Jun 09 2011 - 00:26:13 CDT)
- AW: deca-Ala simulations with different cutoff produce different results (Mon May 16 2011 - 04:20:58 CDT)
- oguz gurbulak
- Okazaki, Keiichi (NIH/NIDDK) [F]
- Olgun Guvench
- opronkri_at_msu.edu
- Osman Yogurtcu
- Osman, Roman
- P Fajer
- P.-L. Chau
- Paraskevi Gkeka
- Parisa Akhski
- Patargias, George
- Patriche Simona
- Patrick Chiu
- patrick wintrode
- PAUL NEWMAN
- Paulo Cesar Telles de Souza
- Re: RMSD collective variable - Different atons to align and to calculate RMSD (Tue Feb 07 2012 - 11:53:47 CST)
- pawan raghav
- Payne, Christy
- Pedro Armando Ojeda May
- Pedro Gonnet
- pellegrini
- Pellegrini Eric
- pepe barrientos
- Pete Kekenes-Huskey
- Peter Freddolino
- Peter Jones
- peter.schmidtke_at_fr.netgrs.com
- Phil Miller
- Philip Peartree
- Pletezhov Alexandr
- poker_at_physics.usyd.edu.au
- politr_at_fh.huji.ac.il
- Prathit Chatterjee
- Priyan Amaras
- Purushottam Dixit
- Puspita Halder
- pxq_at_dicp.ac.cn
- QFrank_X=2E_V=E1zquez=22?=
- Quick, Ross
- R. Charbel Maroun
- Raghav
- raghav singh
- Rajan Vatassery
- rajitha rajeshwar
- rajitha tatikonda
- Ramesh Cheerla
- Ramin Ekhteiari
- Ramya Gamini
- Ranyere Deyler
- Re: Can paratools really parametrize a structure? Is it really finished? (Mon Feb 28 2011 - 13:28:30 CST)
- Raul Araya
- Reichert, David
- Richard Wood
- Robert Brunner
- Robert Elder
- Robert Johnson
- Robert McCarrick
- Roberts, Jason
- rohan uttarwar
- Roy Fernando
- Re: Atoms Gone Missing after Generalized Born Implicit Solvent Equilibration (Mon Jul 16 2012 - 16:43:04 CDT)
- Re: Atoms Gone Missing after Generalized Born Implicit Solvent Equilibration (Mon Jul 16 2012 - 15:03:53 CDT)
- Rui Zhang
- rukman kesh
- Ryan McGreevy
- S Richmond
- S.Archana
- sai nitin
- sajad falsafi
- Sajad Falsafi-Zadeh
- sakthi kumaran
- Salvador H-V
- Salvatore Mario Cosseddu
- saman amiri
- Samuel Flores
- Samy Hamdouche
- Sandeep Patel
- sanxing.xu_at_gmail.com
- sara
- Sara baretller
- sciencekey
- scott davis
- scott stensland
- Sean T Kigerl
- Sebastian Maximilian Wilhelm
- Sebastian Stolzenberg
- Seetha Pothapragada
- Segun Jung
- Sereda, Yuriy Vladimirovich
- Seren Soner
- Sergei
- Sergey
- Shaon Chakrabarti
- Shen, Han
- Sheng, Zi-Zhang
- Shomesankar Bhunia
- Shubhra Ghosh Dastidar
- Shyno Mathew
- Sibel Cakan
- sibel.cakan
- simone bardwell
- Siri Søndergaard
- Sneha Menon
- snoze pa
- Song, Hyundeok (songhk)
- SONY kaur
- Sridhar Kumar Kannam
- Stan Skafidas
- Stefan Franzen
- Stefanos Anogiannakis
- stefhoor
- Stephen Holmes
- Steven Cox
- Steven W Rick
- subbarao kanchi
- SUBHA KALYAANAMOORTHY
- sudipta
- superdirac
- Suranga Edirisinghe
- Swarna M Patra
- Syed Kashif Zafar
- Sándor Kovács
- Takuro Udagawa
- TAO WANG
- Taruna Gupta
- TCBG Workshop
- THANH NGUYEN
- Theresa H
- Thomas Albers
- Re: Re: NAMD 2.9b2-cuda does not scale well compared to NAMD 2.8 (solved) (Sun Apr 29 2012 - 08:33:54 CDT)
- Thomas Bishop
- Thomas Brian
- Thomas C. Bishop
- Thomas Evangelidis
- Re: FATAL ERROR: CUDA error in cudaGetDeviceCount on Pe 0 (thomasASUS): CUDA driver version is insufficient for CUDA runtime version (Mon Oct 22 2012 - 16:42:57 CDT)
- Re: FATAL ERROR: CUDA error in cudaGetDeviceCount on Pe 0 (thomasASUS): CUDA driver version is insufficient for CUDA runtime version (Sat Oct 20 2012 - 11:46:53 CDT)
- Re: RE: FATAL ERROR: CUDA error in cudaGetDeviceCount on Pe 0 (thomasASUS): CUDA driver version is insufficient for CUDA runtime version (Thu Sep 27 2012 - 06:08:04 CDT)
- Re: RE: FATAL ERROR: CUDA error in cudaGetDeviceCount on Pe 0 (thomasASUS): CUDA driver version is insufficient for CUDA runtime version (Sun Sep 23 2012 - 11:33:31 CDT)
- Re: FATAL ERROR: CUDA error in cudaGetDeviceCount on Pe 0 (thomasASUS): CUDA driver version is insufficient for CUDA runtime version (Sat Sep 22 2012 - 10:32:11 CDT)
- Re: FATAL ERROR: CUDA error in cudaGetDeviceCount on Pe 0 (thomasASUS): CUDA driver version is insufficient for CUDA runtime version (Sat Sep 22 2012 - 10:09:11 CDT)
- Re: FATAL ERROR: CUDA error in cudaGetDeviceCount on Pe 0 (thomasASUS): CUDA driver version is insufficient for CUDA runtime version (Sat Sep 22 2012 - 08:19:11 CDT)
- Thomas Freeman
- Thomas Lemmin
- Tibbitt, Jeffrey A.
- tillmann.utesch_at_mail.tu-berlin.de
- Tim Robinson
- Tina Stokelj
- Tom Coles
- Tom Sisan
- Tristan Croll
- Tru Huynh
- Re: Linux-x86_64-CUDA version 2.8 on CentOS-5 x86_64 non local user issue? (Wed Mar 28 2012 - 09:48:15 CDT)
- Re: Linux-x86_64-CUDA version 2.8 on CentOS-5 x86_64 non local user issue? (Wed Mar 28 2012 - 09:10:26 CDT)
- Re: Linux-x86_64-CUDA version 2.8 on CentOS-5 x86_64 non local user issue? (Sat Mar 24 2012 - 18:03:28 CDT)
- Re: Linux-x86_64-CUDA version 2.8 on CentOS-5 x86_64 non local user issue? (Thu Mar 22 2012 - 14:28:54 CDT)
- Tugba Nogay
- Udaysankar Midya
- Uma
- upayan baul
- V.Ovchinnikov
- Vahid Mirjalili
- Van Ngo
- Vasudevan V
- Victor Ovchinnikov
- Vidhya Sankar
- Vignesh
- Vijay Vammi
- Vincent Leroux
- Vlad Cojocaru
- Vlastimil ZÃma
- Wang
- Wang Yi
- Wanzhi Qiu
- Webber
- Wendy González
- Wenhao Liu
- wenhao_at_uchicago.edu
- Wenyu Zhong
- Werner Crous
- Win Liu
- wood irene
- Xavier Bidault
- Xi Cheng
- Xiaohu Li
- yandong Huang
- yandong Huang
- Yang Gao
- Yao Xiao
- yashodhan karandikar
- Ye Yang
- Yi He
- Yi Wang
- Yim, Keun Soo
- Yingzhe Liu
- yp sun
- ypg
- Yun Luo
- Yuqi Liu
- Zachary Ulissi
- Zack Scholl
- Zhao Lina
- zhjpan_at_mail.ustc.edu.cn
- Zhuyi Xue
- Zumot, Elia Nabil
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Last message date: Mon Dec 31 2012 - 14:36:03 CST
Archived on: Mon Dec 31 2012 - 23:22:24 CST
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