NAMD-L: By Thread
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About this archive
Starting: Fri Jan 02 2009 - 02:55:43 CST
Ending: Fri Dec 31 2010 - 20:32:36 CST
- Force field for PDMS Yingzhe Liu (Fri Dec 31 2010 - 20:32:20 CST)
- problem regarding rattle algorithm Prathit Chatterjee (Fri Dec 31 2010 - 02:29:43 CST)
- Running bias exchange metadynamics simulations with NAMD Ajasja Ljubeti膷 (Thu Dec 30 2010 - 16:13:13 CST)
- colvars-history file J閞鬽e H閚in (Wed Dec 29 2010 - 02:24:17 CST)
- help with the equilibration script matziast_at_med.uth.gr (Tue Dec 28 2010 - 16:31:44 CST)
- Colvars-history file Alex Liu (Sat Dec 25 2010 - 18:39:21 CST)
- Unsubscribe Pri... (Mon Dec 27 2010 - 23:03:02 CST)
- About plumed installation problem in NAMD_2.6_AIX-POWER-MPI Buddhadev Maiti (Mon Dec 27 2010 - 21:30:38 CST)
- structure of an equilibration script matziast_at_med.uth.gr (Sun Dec 26 2010 - 07:23:53 CST)
- equilibration script from restart files matziast_at_med.uth.gr (Sun Dec 26 2010 - 06:24:16 CST)
- Adding special VdW parameters Luca Bellucci (Sat Dec 25 2010 - 10:04:55 CST)
- NBFIX and cuda Jacopo Sgrignani (Wed Dec 22 2010 - 03:13:48 CST)
- "Hands-On" Workshop on Computational Biophysics, March 21-25, 2011, Atlanta, GA, USA David Brandon (Tue Dec 21 2010 - 14:34:17 CST)
- compiling namd gpu Jacopo Sgrignani (Tue Dec 21 2010 - 03:13:57 CST)
- ABF on NAMD 2.7b3 Alex Liu (Mon Dec 20 2010 - 15:03:22 CST)
- Why do different versions of NAMD deserve different simulation results? 何毓辉 (Mon Dec 20 2010 - 06:03:03 CST)
- The outputs of REMD were suspended Yingzhe Liu (Sun Dec 19 2010 - 08:21:11 CST)
- Problem with topology file Christian Jorgensen (Sat Dec 18 2010 - 07:35:25 CST)
- counting h-bond in system with vmd sara (Fri Dec 17 2010 - 15:10:21 CST)
- Zcoord for ABF Parisa Akhski (Fri Dec 17 2010 - 13:22:49 CST)
- Re: vmd-l: why atom positions are reset after readpsf, coordpdb commands? Jim Phillips (Fri Dec 17 2010 - 10:58:39 CST)
- FEP VdW and electrostatic decoupling parameters Christian Jorgensen (Fri Dec 17 2010 - 10:21:39 CST)
- jobs get stuck using NAMDv2.7 and stop producing output in the log-file harish vashisth (Fri Dec 17 2010 - 10:20:10 CST)
- par_all36_cgenff.prm with NAMD2.7 - problem of file reading Branko (Fri Dec 17 2010 - 09:19:44 CST)
- NAMD cal with AMBER forces: Polarizable parameters in AMBER Xiao Ju Zhang (Thu Dec 16 2010 - 13:21:01 CST)
- a cv-smd puzzle charlie (Thu Dec 16 2010 - 10:09:55 CST)
- a cv-smd puzzle Charlie (Thu Dec 16 2010 - 09:21:43 CST)
- unsubscribe namd-l sripad chandan (Thu Dec 16 2010 - 09:04:49 CST)
- how to get topology and parameter file for ligand jnsong (Thu Dec 16 2010 - 08:58:07 CST)
- how to generate the topology and parameter file for ligand jnsong (Thu Dec 16 2010 - 07:45:52 CST)
- how to generate topology and parameter file for ligand jnsong (Thu Dec 16 2010 - 07:40:38 CST)
- Which compiler is used for the official (windows) NAMD binaries Ajasja Ljubeti膷 (Thu Dec 16 2010 - 07:09:52 CST)
- questions about smd Charlie (Wed Dec 15 2010 - 22:37:33 CST)
- questions about smd Charlie (Wed Dec 15 2010 - 21:42:56 CST)
- some questions about smd Charlie (Wed Dec 15 2010 - 21:03:17 CST)
- some questions about smd Charlie (Wed Dec 15 2010 - 20:08:45 CST)
- problem with cuda version hamze rahimi (Wed Dec 08 2010 - 12:30:23 CST)
- Constraint failures and TI electrostatic calcs Courtney Taylor (Mon Dec 06 2010 - 13:26:52 CST)
- Interaction potentials W-S Evgeniya Volkova (Wed Dec 15 2010 - 08:13:40 CST)
- Asking for some sample PDB and PSF files of carbon nanotube 何毓辉 (Wed Dec 15 2010 - 04:19:22 CST)
- Re: Asking for some sample PDB and PSF files of carbon nanotube Leandro Mart韓ez (Wed Dec 15 2010 - 04:55:59 CST)
- RE: Asking for some sample PDB and PSF files of carbon nanotube JC Gumbart (Wed Dec 15 2010 - 10:52:32 CST)
- Re: Asking for some sample PDB and PSF files of carbon nanotube Axel Kohlmeyer (Wed Dec 15 2010 - 10:52:08 CST)
- memory allocation failed on processor 0 matziast_at_med.uth.gr (Wed Dec 15 2010 - 04:07:02 CST)
- Simultaneous FEP simulation of two distinct residues Christian Jorgensen (Tue Dec 14 2010 - 13:44:10 CST)
- GPU heavy models? Michael Di Domenico (Tue Dec 14 2010 - 08:03:52 CST)
- dissociated quartz SiO2 groups in surface christos.lamprakis_at_dcb.unibe.ch (Tue Dec 14 2010 - 05:39:59 CST)
- input file for memory optimised version Stefano Pieraccini (Tue Dec 14 2010 - 03:43:12 CST)
- questions about user defined potential in NAMD Chen, Zhihong (chenz2) (Mon Dec 13 2010 - 15:48:47 CST)
- How were the output files of the Replica Exchange Method sorted? Guoxiong Su (Sun Dec 12 2010 - 14:11:37 CST)
- Adding extra bond Francesco Oteri (Sun Dec 12 2010 - 04:22:05 CST)
- Problem when using psfgen Christian Jorgensen (Sat Dec 11 2010 - 14:56:06 CST)
- plotting potential energy Kwee Hong (Thu Dec 09 2010 - 03:37:04 CST)
- ABF questions (Concatenate output files/force constant) Parisa Akhski (Wed Dec 08 2010 - 17:57:40 CST)
- Using ABF to explore the conformational space of a spin label attached to a membrane protein Ajasja Ljubeti膷 (Wed Dec 08 2010 - 10:31:16 CST)
- Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein Branko (Wed Dec 08 2010 - 11:09:53 CST)
- Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein J閞鬽e H閚in (Wed Dec 08 2010 - 16:16:58 CST)
- Using ABF to explore the conformational space of a spin label attached to a membrane protein Ajasja Ljubeti膷 (Wed Dec 15 2010 - 07:21:54 CST)
- Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein J閞鬽e H閚in (Wed Dec 15 2010 - 09:31:20 CST)
- Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein Ajasja Ljubeti膷 (Wed Dec 15 2010 - 10:34:43 CST)
- Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein J閞鬽e H閚in (Wed Dec 15 2010 - 11:07:20 CST)
- Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein Ajasja Ljubeti膷 (Thu Dec 16 2010 - 07:04:19 CST)
- Re: Using ABF to explore the conformational space of a spin label attached to a membrane protein J閞鬽e H閚in (Thu Dec 16 2010 - 07:47:42 CST)
- Using ABF to explore the conformational space of a spin label attached to a membrane protein Ajasja Ljubeti膷 (Wed Dec 15 2010 - 07:21:54 CST)
- SHAKE convergence property for CUDA and nonCUDA NAMD Jun Zhang (Wed Dec 08 2010 - 06:54:10 CST)
- SHAKE convergence property for CUDA and nonCUDA NAMD Jun Zhang (Wed Dec 08 2010 - 05:59:53 CST)
- Problem of running NAMD Yingzhe Liu (Wed Dec 08 2010 - 04:37:45 CST)
- Free energy perturbation (FEP) hybrid pdb file Christian Jorgensen (Tue Dec 07 2010 - 21:36:31 CST)
- Problem of running NAMD Yingzhe Liu (Tue Dec 07 2010 - 05:16:35 CST)
- Fwd: Installing NAMD on windows bharat gupta (Sat Dec 04 2010 - 02:07:05 CST)
- ABF question Parisa Akhski (Fri Dec 03 2010 - 09:16:07 CST)
- nodelist file for concurrent execution of 2 nodes Thomas Evangelidis (Fri Dec 03 2010 - 05:08:28 CST)
- NAMD on Shared Memory (Altix UV 1000) Alessandro Cembran (Thu Dec 02 2010 - 18:11:45 CST)
- trajectory in temperature from Replica Exchange MD Guoxiong Su (Thu Dec 02 2010 - 13:45:04 CST)
- Lowe-Andersen thermostat J閞鬽e H閚in (Thu Dec 02 2010 - 09:12:12 CST)
- Output of forces Pletezhov Alexandr (Thu Dec 02 2010 - 06:04:46 CST)
- SMD constant velocity pulling B. Nandy (Thu Dec 02 2010 - 00:21:32 CST)
- Restart, discontinuity of energy juan du (Wed Dec 01 2010 - 09:56:51 CST)
- SMD constant velocity pulling B. Nandy (Wed Dec 01 2010 - 03:51:45 CST)
- Re: SMD constant velocity pulling J閞鬽e H閚in (Wed Dec 01 2010 - 05:35:29 CST)
- Re: SMD constant velocity pulling Gianluca Interlandi (Wed Dec 01 2010 - 10:36:07 CST)
- Re: SMD constant velocity pulling Gianluca Interlandi (Wed Dec 01 2010 - 12:49:50 CST)
- Re: SMD constant velocity pulling J閞鬽e H閚in (Wed Dec 01 2010 - 16:55:20 CST)
- Re: SMD constant velocity pulling Gianluca Interlandi (Wed Dec 01 2010 - 17:22:40 CST)
- Re: SMD constant velocity pulling B. Nandy (Wed Dec 01 2010 - 23:17:37 CST)
- Re: SMD constant velocity pulling Gianluca Interlandi (Thu Dec 02 2010 - 01:38:59 CST)
- Re: SMD constant velocity pulling J閞鬽e H閚in (Wed Dec 01 2010 - 05:35:29 CST)
- SMD constant velocity pulling B. Nandy (Wed Dec 01 2010 - 02:51:41 CST)
- Jarzinsky's equation Gianluca Interlandi (Wed Dec 01 2010 - 01:54:57 CST)
- problem in generating psf file Alex Liu (Tue Nov 30 2010 - 09:12:36 CST)
- switching function for electrostaic interaction divya nayar (Tue Nov 30 2010 - 10:13:58 CST)
- RBCG dota alexiou (Tue Nov 30 2010 - 02:44:51 CST)
- periodic boundary conditions in namd energy calculation Lan Hua (Mon Nov 29 2010 - 15:52:43 CST)
- Creating a NAMD Shared Library -> Undefined Symbols in Charm libs Michael S. Sellers (Cont, ARL/WMRD) (Mon Nov 29 2010 - 15:22:40 CST)
- Creating a NAMD Shared Library -> Undefined Symbols in Charm libs Michael S. Sellers (Cont, ARL/WMRD) (Mon Nov 29 2010 - 15:07:21 CST)
- wrapping problem Buddhadev Maiti (Mon Nov 29 2010 - 13:41:38 CST)
- CUDA error in NAMD 2.7: Increase MAX_EXCLUSIONS Amodeo, Pietro (Fri Nov 26 2010 - 11:21:22 CST)
- Local elevation method in NAMD? Cristina Rodr韌uez (Thu Nov 25 2010 - 16:54:12 CST)
- crash jp2854_at_columbia.edu (Mon Nov 29 2010 - 11:18:24 CST)
- restart ABF Parisa Akhski (Mon Nov 29 2010 - 10:43:26 CST)
- How to set improper dihedral for trans-double bond. Boyang Wang (Mon Nov 29 2010 - 06:15:16 CST)
- pair interaction energy for 2 water molecules divya nayar (Mon Nov 29 2010 - 04:00:14 CST)
- RMSD Question snoze pa (Sun Nov 28 2010 - 11:08:25 CST)
- Re: pair interaction of water molecules divya nayar (Sun Nov 28 2010 - 08:54:43 CST)
- system density Kwee Hong (Sat Nov 27 2010 - 05:18:19 CST)
- CUDA error in NAMD 2.7: Increase MAX_EXCLUSIONS Pietro Amodeo (Fri Nov 26 2010 - 18:07:46 CST)
- Update to CUDA error in NAMD 2.7: Increase MAX_EXCLUSIONS: problem persists and CPU-only MD scales poorly Pietro Amodeo (Mon Dec 27 2010 - 14:01:04 CST)
- Errata to: Update to CUDA error in NAMD 2.7: Increase MAX_EXCLUSIONS: problem persists and CPU-only MD scales poorly Pietro Amodeo (Mon Dec 27 2010 - 14:20:03 CST)
- Re: Errata to: Update to CUDA error in NAMD 2.7: Increase MAX_EXCLUSIONS: problem persists and CPU-only MD scales poorly Axel Kohlmeyer (Tue Dec 28 2010 - 03:46:37 CST)
- Re: Errata to: Update to CUDA error in NAMD 2.7: Increase MAX_EXCLUSIONS: problem persists and CPU-only MD scales poorly Pietro Amodeo (Tue Dec 28 2010 - 05:45:16 CST)
- Errata to: Update to CUDA error in NAMD 2.7: Increase MAX_EXCLUSIONS: problem persists and CPU-only MD scales poorly Pietro Amodeo (Mon Dec 27 2010 - 14:20:03 CST)
- Update to CUDA error in NAMD 2.7: Increase MAX_EXCLUSIONS: problem persists and CPU-only MD scales poorly Pietro Amodeo (Mon Dec 27 2010 - 14:01:04 CST)
- Local elevation method in NAMD? Cristina Rodr韌uez (Fri Nov 26 2010 - 12:07:20 CST)
- "GroupPressure no" resulting in negative pressure outputs Sebastian Stolzenberg (Thu Nov 25 2010 - 13:51:13 CST)
- Constant pressure Kwee Hong (Thu Nov 25 2010 - 10:29:29 CST)
- writing back coordinates of waters that cross the unit cell kakali sen (Thu Nov 25 2010 - 08:29:09 CST)
- subtlety with PSFGEN - angle/dihedral regeneration Erik Nordgren (Wed Nov 24 2010 - 20:55:06 CST)
- Zcoord-1atom for ABF Parisa Akhski (Wed Nov 24 2010 - 16:11:16 CST)
- Warning about PSF file Alexander Predeus (Wed Nov 24 2010 - 15:27:22 CST)
- reloadCharges command Wendy Gonz醠ez (Wed Nov 24 2010 - 13:35:07 CST)
- morse potentials in NAMD revisited Thomas C. Bishop (Wed Nov 24 2010 - 11:29:05 CST)
- ERROR: Atoms moving too fast with RBCG model wenchangyu2006_at_gmail.com (Wed Nov 24 2010 - 10:00:57 CST)
- Restart, RMSD increase juan du (Wed Nov 24 2010 - 08:58:05 CST)
- Restart RMSD increase juan du (Wed Nov 24 2010 - 07:54:45 CST)
- pair interaction of water molecules divya nayar (Wed Nov 24 2010 - 03:41:13 CST)
- Allowed CMAP dimensions Ajasja Ljubeti膷 (Tue Nov 23 2010 - 11:07:33 CST)
- Distance Restraint Jacopo Sgrignani (Tue Nov 23 2010 - 10:23:27 CST)
- MOnte carlo simulation Ramya Narasimhan (Tue Nov 23 2010 - 01:04:10 CST)
- Namd with Amber ff for RNA minimization Irina Tuszynska (Tue Nov 23 2010 - 00:43:56 CST)
- Re: Namd with Amber ff for RNA minimization J閞鬽e H閚in (Tue Nov 23 2010 - 02:14:20 CST)
- Re: Namd with Amber ff for RNA minimization Irina Tuszynska (Tue Nov 23 2010 - 05:29:33 CST)
- Re: Namd with Amber ff for RNA minimization Hannes Loeffler (Tue Nov 23 2010 - 07:28:26 CST)
- Re: Namd with Amber ff for RNA minimization Irina Tuszynska (Tue Nov 23 2010 - 09:37:59 CST)
- namd 2.7 iverbs error 93620 attaching to node Thomas C. Bishop (Tue Nov 23 2010 - 12:11:38 CST)
- RE: namd 2.7 iverbs error 93620 attaching to node David A. Horita (Fri Dec 03 2010 - 11:42:46 CST)
- Re: Namd with Amber ff for RNA minimization Irina Tuszynska (Tue Nov 23 2010 - 05:29:33 CST)
- Re: Namd with Amber ff for RNA minimization J閞鬽e H閚in (Tue Nov 23 2010 - 02:14:20 CST)
- Run-time system modification JC S (Mon Nov 22 2010 - 23:38:54 CST)
- Different Dielectric constant value for different segment Madhurima Jana (Mon Nov 22 2010 - 07:48:39 CST)
- how best to build a GPU-accelerated desktop machine for NAMD? Erik Nordgren (Fri Nov 19 2010 - 20:08:48 CST)
- Need help preventing hydration of the lipid-protein interface in my system Maggie Pruitt (Fri Nov 19 2010 - 09:46:45 CST)
- atom type matziast_at_med.uth.gr (Fri Nov 19 2010 - 06:21:47 CST)
- atom type matziast_at_med.uth.gr (Fri Nov 19 2010 - 05:03:28 CST)
- TIP4P with NPT Jeffery Klauda (Thu Nov 18 2010 - 12:44:56 CST)
- Format of namd restartfile *.coor, *.vel) (2nd try ;) ) henri mone (Thu Nov 18 2010 - 10:05:15 CST)
- psf of insulin sara (Wed Nov 17 2010 - 10:27:20 CST)
- Bad Global Exclusion Count Errors in (Relatively) Simple System Jason Richard Mick (Tue Nov 16 2010 - 18:32:49 CST)
- MD simulations increasing electrostatic potential of a certain residue Wendy Gonz醠ez (Tue Nov 16 2010 - 16:35:06 CST)
- berendsen thermostat divya nayar (Mon Nov 15 2010 - 08:15:37 CST)
- simulating Acetylated lysine substrate complex SUBHA KALYAANAMOORTHY (Sun Nov 14 2010 - 23:12:11 CST)
- pair interaction calculations dhacademic (Sun Nov 14 2010 - 09:51:40 CST)
- the usage of ++nodelist and ++local jnsong (Sun Nov 14 2010 - 06:25:21 CST)
- VdW parameters for Zn and Fe in metalloproteins Erik Nordgren (Fri Nov 12 2010 - 22:05:33 CST)
- Issue with NAMD Not understand avl211_at_lehigh.edu (Fri Nov 12 2010 - 12:29:32 CST)
- Interactive MD driver/controller software no longer in beta Axel Kohlmeyer (Fri Nov 12 2010 - 09:41:59 CST)
- Restart simulation Henri Mone (Thu Nov 11 2010 - 19:54:39 CST)
- Minimization does not converge Christian Jorgensen (Thu Nov 11 2010 - 17:42:42 CST)
- Ions conversion from atomic model to coarse grained model 周文昌 (Wed Nov 10 2010 - 11:41:41 CST)
- NAMD FEP and GPU TJ Mustard (Tue Nov 09 2010 - 13:26:26 CST)
- Using NAMD for Metropolis Monte Carlo conformational searches Ajasja Ljubeti膷 (Tue Nov 09 2010 - 09:12:29 CST)
- Re: Using NAMD for Metropolis Monte Carlo conformational searches Axel Kohlmeyer (Tue Nov 09 2010 - 10:06:58 CST)
- Re: Using NAMD for Metropolis Monte Carlo conformational searches Ajasja Ljubeti膷 (Wed Nov 10 2010 - 04:04:31 CST)
- Re: Using NAMD for Metropolis Monte Carlo conformational searches Ajasja Ljubeti膷 (Wed Nov 10 2010 - 04:22:53 CST)
- Re: Using NAMD for Metropolis Monte Carlo conformational searches Axel Kohlmeyer (Wed Nov 10 2010 - 09:10:02 CST)
- Re: Using NAMD for Metropolis Monte Carlo conformational searches Marc Baaden (Thu Nov 25 2010 - 06:26:43 CST)
- Re: Using NAMD for Metropolis Monte Carlo conformational searches Ajasja Ljubeti膷 (Wed Nov 10 2010 - 04:04:31 CST)
- Re: Using NAMD for Metropolis Monte Carlo conformational searches Axel Kohlmeyer (Tue Nov 09 2010 - 10:06:58 CST)
- NAMDv2.7 stops producing output in the log-file--any help? harish vashisth (Tue Nov 09 2010 - 08:24:22 CST)
- residue based coarse-grained simulation Demet Akten (Tue Nov 09 2010 - 07:03:05 CST)
- Free-energy perturbation in NAMD: Evaluation of electrostatic and van der Waals terms Christian Jorgensen (Mon Nov 08 2010 - 16:23:51 CST)
- FEP and GPU TJ Mustard (Mon Nov 08 2010 - 15:06:51 CST)
- salt bridge Swarna M Patra (Mon Nov 08 2010 - 02:09:21 CST)
- finding appropriate topology file for polymers masoumeh ozmaeian (Sun Nov 07 2010 - 08:45:23 CST)
- FATAL ERROR: CAN'T FIND CROSSTERM PARAMETERS FOR CC NH1 CT1 C NH1 CT1 C NH1 Gurunath Katagi (Sat Nov 06 2010 - 02:41:31 CDT)
- Recover high precision coordinates from binary .coor file Rajan Vatassery (Fri Nov 05 2010 - 19:37:48 CDT)
- Issue with Load Balancing Al-Ali, Hassan (Fri Nov 05 2010 - 10:15:52 CDT)
- NAMD OPLS Parameters Soran (Thu Nov 04 2010 - 16:57:56 CDT)
- Question for Developers: NAMD 2.7 performance issues and Questions about Compiling harish vashisth (Thu Nov 04 2010 - 05:43:49 CDT)
- Release of R.E.D. Server 2.0 FyD (Thu Nov 04 2010 - 04:50:36 CDT)
- about Hydrogen Bond correlation function Jun Zhang (Thu Nov 04 2010 - 00:55:28 CDT)
- NAMD 2.7 performance issues and Questions about Compiling David Lee Braun (Wed Nov 03 2010 - 15:27:58 CDT)
- Re: vmd-l: Asymmetric water molecule J閞鬽e H閚in (Wed Nov 03 2010 - 05:03:40 CDT)
- problems with temperature control Pegah Khalili (Wed Nov 03 2010 - 04:35:50 CDT)
- problems with temperature control Pegah Khalili (Wed Nov 03 2010 - 04:28:59 CDT)
- Error in configuration file Christian Jorgensen (Tue Nov 02 2010 - 11:33:12 CDT)
- Missing angle parameters CT3 CT3 CT3 Christian Jorgensen (Mon Nov 01 2010 - 18:12:06 CDT)
- MINIMIZER SLOWLY MOVING 810 ATOMS WITH BAD CONTACTS DOWNHILL nishtha mishra (Sat Oct 30 2010 - 08:40:36 CDT)
- namd install ipsita basu (Mon Nov 01 2010 - 05:53:21 CDT)
- rmsd divya nayar (Mon Nov 01 2010 - 03:30:11 CDT)
- MINIMIZER SLOWLY MOVING 810 ATOMS WITH BAD CONTACTS DOWNHILL nishtha.mishra (Mon Nov 01 2010 - 02:27:18 CDT)
- MINIMIZER SLOWLY MOVING 810 ATOMS WITH BAD CONTACTS DOWNHILL nishtha.mishra (Mon Nov 01 2010 - 02:18:06 CDT)
- Radius of gyration Dhanashree Khanale (Sat Oct 30 2010 - 08:43:22 CDT)
- H-bond and salt bridge between protein dimer surendra jain (Sat Oct 30 2010 - 07:17:55 CDT)
- script for calculation of an rmsd matziast_at_med.uth.gr (Sat Oct 30 2010 - 03:41:41 CDT)
- How to generate the tcouple file for NAMD runs? a a (Fri Oct 29 2010 - 22:45:42 CDT)
- extending namd / shared library build (UNCLASSIFIED) Sellers, Michael S. (Cont, ARL/WMRD) (Fri Oct 29 2010 - 08:23:41 CDT)
- NANMA free energy surface vacuum map problems Carles Corbi Verge (Fri Oct 29 2010 - 08:03:54 CDT)
- Re: NANMA free energy surface vacuum map problems J閞鬽e H閚in (Fri Oct 29 2010 - 09:33:37 CDT)
- Re: NANMA free energy surface vacuum map problems Carles Corbi Verge (Mon Nov 01 2010 - 06:16:36 CDT)
- Re: NANMA free energy surface vacuum map problems JC Gumbart (Mon Nov 01 2010 - 20:33:14 CDT)
- Re: NANMA free energy surface vacuum map problems J閞鬽e H閚in (Tue Nov 02 2010 - 05:40:08 CDT)
- RE: NANMA free energy surface vacuum map problems JC Gumbart (Tue Nov 02 2010 - 07:23:30 CDT)
- Re: NANMA free energy surface vacuum map problems J閞鬽e H閚in (Tue Nov 02 2010 - 08:18:30 CDT)
- Re: NANMA free energy surface vacuum map problems Carles Corbi Verge (Thu Nov 04 2010 - 09:37:34 CDT)
- Re: NANMA free energy surface vacuum map problems Carles Corbi Verge (Mon Nov 01 2010 - 06:16:36 CDT)
- Re: NANMA free energy surface vacuum map problems J閞鬽e H閚in (Fri Oct 29 2010 - 09:33:37 CDT)
- Constraint failure in RATTLE algorithm for atom 268 Ajasja Ljubeti膷 (Fri Oct 29 2010 - 05:46:16 CDT)
- Constraint failure in RATTLE algorithm for atom 268 surendra jain (Fri Oct 29 2010 - 04:54:38 CDT)
- questions about ABF simulations mjyang (Thu Oct 28 2010 - 13:26:59 CDT)
- Force field for replica Xiang Yu (Thu Oct 28 2010 - 09:12:25 CDT)
- force field for replica exchange with NAMD Xiang Yu (Wed Oct 27 2010 - 23:06:32 CDT)
- Enthalpy calculation divya nayar (Thu Oct 28 2010 - 10:12:00 CDT)
- Least squares fitting of frames of trajectory divya nayar (Wed Oct 27 2010 - 23:01:29 CDT)
- Charmrun: error on request socket-- Kwee Hong (Wed Oct 27 2010 - 12:08:11 CDT)
- build nanoparticle sara (Wed Oct 27 2010 - 11:10:58 CDT)
- Symmetry in NAMD, how to achieve during a MD simulation? Wendy Gonz醠ez (Wed Oct 27 2010 - 10:46:03 CDT)
- global and internal motion of protein divya nayar (Wed Oct 27 2010 - 02:39:04 CDT)
- minimization problem ipsita basu (Wed Oct 27 2010 - 01:00:23 CDT)
- protein fixed in simulation divya nayar (Wed Oct 27 2010 - 00:53:56 CDT)
- error compiling charm-6.2.2 for bluegenep-xlc hannes.loeffler_at_stfc.ac.uk (Tue Oct 26 2010 - 14:22:50 CDT)
- coordinate not the same between the input and frame 0 Kwee Hong (Tue Oct 26 2010 - 03:27:25 CDT)
- a question about modifying the NAMD input file ying yu (Mon Oct 25 2010 - 12:06:50 CDT)
- Warning: Bad global exclusion count, possible error! Kwee Hong (Sun Oct 24 2010 - 22:07:39 CDT)
- getting desired angle Kwee Hong (Sat Oct 23 2010 - 03:49:23 CDT)
- NAMD with missing residues snoze pa (Fri Oct 22 2010 - 15:46:34 CDT)
- potential functions in NAMD oguz gurbulak (Fri Oct 22 2010 - 04:22:45 CDT)
- Strange vdw_dU/dl values in thermodynamic integration Hugh Heldenbrand (Thu Oct 21 2010 - 19:37:25 CDT)
- Cube vs. Truncated Octahedron Performance Alexander Predeus (Thu Oct 21 2010 - 17:04:42 CDT)
- Relaxed dihedral scans (or how to constrain a dihedral angle to a changing value). Ajasja Ljubeti膷 (Thu Oct 21 2010 - 08:45:43 CDT)
- Enhance electrostatic interactions? Wendy Gonz醠ez (Thu Oct 21 2010 - 07:32:46 CDT)
- Angle in parameter file Christian Jorgensen (Thu Oct 21 2010 - 06:08:03 CDT)
- the storage format of the coordinate binary file in NAMD jnsong (Thu Oct 21 2010 - 03:55:27 CDT)
- how to cenvert NAMD binary coordinate file to text file jnsong (Thu Oct 21 2010 - 02:27:06 CDT)
- Re: how to cenvert NAMD binary coordinate file to text file OiniL (Thu Oct 21 2010 - 03:15:16 CDT)
- Re: how to cenvert NAMD binary coordinate file to text file Ajasja Ljubeti膷 (Thu Oct 21 2010 - 03:24:19 CDT)
- Re: how to cenvert NAMD binary coordinate file to text file Hannes Loeffler (Thu Oct 21 2010 - 04:48:59 CDT)
- ligand parameters grazia cottone (Wed Oct 20 2010 - 06:43:23 CDT)
- psfgen gives wrong psf file Christian Jorgensen (Wed Oct 20 2010 - 04:32:56 CDT)
- error codes: 255 hgrabner (Wed Oct 20 2010 - 03:57:07 CDT)
- PME Kappa and Non-bonded Cutoff Alexander Predeus (Tue Oct 19 2010 - 18:20:12 CDT)
- NAMD 2.7 released Jim Phillips (Tue Oct 19 2010 - 14:57:57 CDT)
- Tcl script in NAMD divya nayar (Tue Oct 19 2010 - 08:21:48 CDT)
- Amber topology in CUDA NAMD - can it be done? Benjamin Bouvier (Tue Oct 19 2010 - 07:27:48 CDT)
- Changing functions without recompiling Cole Gleason (Mon Oct 18 2010 - 16:53:32 CDT)
- rotation question jp d (Mon Oct 18 2010 - 16:35:55 CDT)
- Denied permission on dcd file preventing simulation Christian Jorgensen (Mon Oct 18 2010 - 09:32:07 CDT)
- High RMSD of Coarse grain Protein sunita gupta (Mon Oct 18 2010 - 06:52:18 CDT)
- CHARMM Lorentz-berthelot mixing rules divya nayar (Mon Oct 18 2010 - 05:21:52 CDT)
- expansion of solvation box at high temperature mjyang (Sun Oct 17 2010 - 04:41:25 CDT)
- top file for CNT sara (Sun Oct 17 2010 - 03:10:13 CDT)
- expansion of solvation box at high temperature mjyang (Sun Oct 17 2010 - 02:03:31 CDT)
- Re: expansion of solvation box at high temperature Nicholas Musolino (Sun Oct 17 2010 - 08:29:06 CDT)
- RE: expansion of solvation box at high temperature mjyang (Sun Oct 17 2010 - 10:18:26 CDT)
- Re: expansion of solvation box at high temperature Nicholas Musolino (Sun Oct 17 2010 - 10:27:40 CDT)
- RE: expansion of solvation box at high temperature mjyang (Sun Oct 17 2010 - 10:56:15 CDT)
- Re: expansion of solvation box at high temperature Jeffrey Potoff (Sun Oct 17 2010 - 11:44:53 CDT)
- Re: expansion of solvation box at high temperature Joshua Adelman (Sun Oct 17 2010 - 12:25:19 CDT)
- RE: expansion of solvation box at high temperature Jim Phillips (Mon Oct 18 2010 - 11:32:18 CDT)
- RE: expansion of solvation box at high temperature mjyang (Mon Oct 18 2010 - 22:31:13 CDT)
- RE: expansion of solvation box at high temperature mjyang (Sun Oct 17 2010 - 10:18:26 CDT)
- Re: expansion of solvation box at high temperature Nicholas Musolino (Sun Oct 17 2010 - 08:29:06 CDT)
- Re: hexane Jian Liu (Sat Oct 16 2010 - 20:32:09 CDT)
- hexane lara lara (Sat Oct 16 2010 - 04:00:09 CDT)
- Conjugate gradient reference Philip Peartree (Fri Oct 15 2010 - 10:33:16 CDT)
- change force field in NAMD Chen, Zhihong (chenz2) (Fri Oct 15 2010 - 09:51:04 CDT)
- change force field in NAMD Chen, Zhihong (chenz2) (Fri Oct 15 2010 - 09:50:14 CDT)
- tmd log file matziast_at_med.uth.gr (Fri Oct 15 2010 - 06:35:37 CDT)
- script for targeted molecular dynamics matziast_at_med.uth.gr (Fri Oct 15 2010 - 03:15:20 CDT)
- targeted molecular dynamics matziast_at_med.uth.gr (Thu Oct 14 2010 - 17:22:30 CDT)
- Restraint on XY Plane Peixi Zhu (Thu Oct 14 2010 - 16:12:30 CDT)
- Assigning partial charges in topology file Christian Jorgensen (Thu Oct 14 2010 - 13:57:30 CDT)
- Restart MD from a certain point? Wendy Gonz醠ez (Thu Oct 14 2010 - 07:45:48 CDT)
- simulation time instead of frames Kwee Hong (Thu Oct 14 2010 - 06:05:47 CDT)
- Namd using Charmm restart files Courtney Taylor (Wed Oct 13 2010 - 16:55:00 CDT)
- High RMSD in Coarse Grain Simulation of Protein sunita gupta (Wed Oct 13 2010 - 03:06:22 CDT)
- unsubscribe Katherine Parra (Tue Oct 12 2010 - 16:58:06 CDT)
- Modification of Colvar Module Components Alexander Predeus (Tue Oct 12 2010 - 15:44:20 CDT)
- Langevin process in NAMD tutorial yi jiang (Mon Oct 11 2010 - 11:14:22 CDT)
- Re: Langevin process in NAMD tutorial Axel Kohlmeyer (Mon Oct 11 2010 - 12:21:04 CDT)
- Regarding answering questions in a forum. Re: Langevin process in NAMD tutorial Basak Isin (Mon Oct 11 2010 - 14:56:17 CDT)
- Re: Regarding answering questions in a forum. Re: Langevin process in NAMD tutorial Axel Kohlmeyer (Mon Oct 11 2010 - 15:16:21 CDT)
- Re: Regarding answering questions in a forum. Re: Langevin process in NAMD tutorial Basak Isin (Mon Oct 11 2010 - 15:44:42 CDT)
- Re: Regarding answering questions in a forum. Re: Langevin process in NAMD tutorial Gianluca Interlandi (Mon Oct 11 2010 - 16:56:03 CDT)
- Re: Regarding answering questions in a forum. Re: Langevin process in NAMD tutorial Basak Isin (Mon Oct 11 2010 - 18:11:14 CDT)
- Re: Regarding answering questions in a forum. Re: Langevin process in NAMD tutorial Axel Kohlmeyer (Mon Oct 11 2010 - 18:54:28 CDT)
- Re: Regarding answering questions in a forum. Re: Langevin process in NAMD tutorial yi jiang (Mon Oct 11 2010 - 20:42:05 CDT)
- Re: Regarding answering questions in a forum. Re: Langevin process in NAMD tutorial Jim Phillips (Wed Oct 13 2010 - 09:46:57 CDT)
- Regarding answering questions in a forum. Re: Langevin process in NAMD tutorial Basak Isin (Mon Oct 11 2010 - 14:56:17 CDT)
- Re: Langevin process in NAMD tutorial Axel Kohlmeyer (Mon Oct 11 2010 - 12:21:04 CDT)
- 2 Stray PME grid charges detected possible bug 2.7b2 Branko (Sun Oct 10 2010 - 11:12:09 CDT)
- Stray PME grid charges detected possible bug 2.7b2 Branko (Sun Oct 10 2010 - 10:54:11 CDT)
- Comparision of GPU and multi-CPUs version of NAMD Jianing Song (Sun Oct 10 2010 - 09:51:54 CDT)
- how to improve the occupation of GPU with NAMD-2.7b3-CUDA Jianing Song (Sun Oct 10 2010 - 09:43:58 CDT)
- unsubscribe Asmita Gupta (Fri Oct 08 2010 - 10:56:18 CDT)
- Re: problem caused by cluster? Jim Phillips (Fri Oct 08 2010 - 08:34:23 CDT)
- (no subject) ipsita basu (Fri Oct 08 2010 - 06:00:41 CDT)
- Flushing memory into output file Parisa Akhski (Thu Oct 07 2010 - 11:58:46 CDT)
- change force field in NAMD Chen, Zhihong (chenz2) (Thu Oct 07 2010 - 09:49:45 CDT)
- Alchemical FEP tutorial files Christian Jorgensen (Thu Oct 07 2010 - 06:55:09 CDT)
- Carma v.1.0 released. Nicholas M Glykos (Wed Oct 06 2010 - 06:14:15 CDT)
- Is the DCD file size consistent for consecutive runs? Bjoern Olausson (Wed Oct 06 2010 - 03:36:04 CDT)
- Re: Is the DCD file size consistent for consecutive runs? Bjoern Olausson (Thu Oct 07 2010 - 06:40:17 CDT)
- Re: Is the DCD file size consistent for consecutive runs? Axel Kohlmeyer (Thu Oct 07 2010 - 10:07:53 CDT)
- Re: Is the DCD file size consistent for consecutive runs? Bjoern Olausson (Fri Oct 08 2010 - 04:27:54 CDT)
- Re: Is the DCD file size consistent for consecutive runs? Bjoern Olausson (Fri Oct 08 2010 - 11:30:36 CDT)
- Re: Is the DCD file size consistent for consecutive runs? Bjoern Olausson (Thu Oct 07 2010 - 06:40:17 CDT)
- ADENOSINE-5-DIPHOSPHORIBOSE topology Raul Araya (Tue Oct 05 2010 - 20:56:42 CDT)
- problem caused by cluster? Kwee Hong (Tue Oct 05 2010 - 20:17:50 CDT)
- Minimization problem on cluster Swarna M Patra (Mon Oct 04 2010 - 23:09:07 CDT)
- change force field in NAMD Chen, Zhihong (chenz2) (Mon Oct 04 2010 - 14:11:11 CDT)
- unable to open binary file Kwee Hong (Mon Oct 04 2010 - 09:00:10 CDT)
- NAMD installation Hasan haska (Mon Oct 04 2010 - 05:25:06 CDT)
- Check out my photos on Facebook Kalyan Pulipaka (Sat Oct 02 2010 - 21:57:26 CDT)
- How to restraint angle in NAMD George Khelashvili (Fri Oct 01 2010 - 21:32:29 CDT)
- Fermi NVidia jose correa (Thu Sep 30 2010 - 09:13:47 CDT)
- NAMD and Gromacs oguz gurbulak (Thu Sep 30 2010 - 06:36:51 CDT)
- FFTW and NAMD problems during compiling on BluegeneL I. Vyalov (Wed Sep 29 2010 - 05:00:55 CDT)
- (馀 耘唾) I. Vyalov (Wed Sep 29 2010 - 04:46:48 CDT)
- Re: How to analysis RAMD data? Vlad Cojocaru (Wed Sep 29 2010 - 02:26:28 CDT)
- How to analysis RAMD data? asknamd asknamd (Tue Sep 28 2010 - 13:43:33 CDT)
- Selection of alchElecLambdaStart Courtney Taylor (Tue Sep 28 2010 - 10:50:24 CDT)
- metadynamics simulations slow down and down OiniL (Sat Sep 25 2010 - 23:06:17 CDT)
- reg_membrane_peptide_interaction lara lara (Sat Sep 25 2010 - 04:24:09 CDT)
- flexible-cell constant pressure not supported in CUDA Jianing Song (Fri Sep 24 2010 - 19:50:26 CDT)
- NAMD error message snoze pa (Fri Sep 24 2010 - 17:04:45 CDT)
- change force field in NAMD Chen, Zhihong (chenz2) (Fri Sep 24 2010 - 14:36:09 CDT)
- Colvars: Using "Alpha" Component Alexander Predeus (Thu Sep 23 2010 - 19:26:31 CDT)
- Re: Colvars: Using "Alpha" Component J閞鬽e H閚in (Fri Sep 24 2010 - 03:27:40 CDT)
- Re: Colvars: Using "Alpha" Component Alexander Predeus (Fri Sep 24 2010 - 13:25:31 CDT)
- Re: Colvars: Using "Alpha" Component Giacomo Fiorin (Fri Sep 24 2010 - 15:48:59 CDT)
- Re: Colvars: Using "Alpha" Component Alexander Predeus (Fri Sep 24 2010 - 16:10:46 CDT)
- Re: Colvars: Using "Alpha" Component Giacomo Fiorin (Fri Sep 24 2010 - 16:35:44 CDT)
- Re: Colvars: Using "Alpha" Component Alexander Predeus (Fri Sep 24 2010 - 16:56:21 CDT)
- Re: Colvars: Using "Alpha" Component Giacomo Fiorin (Fri Sep 24 2010 - 17:01:27 CDT)
- Re: Colvars: Using "Alpha" Component Alexander Predeus (Fri Sep 24 2010 - 13:25:31 CDT)
- Re: Colvars: Using "Alpha" Component J閞鬽e H閚in (Fri Sep 24 2010 - 03:27:40 CDT)
- Accelerated MD? patrick wintrode (Thu Sep 23 2010 - 09:44:41 CDT)
- Colvars and COM restraints for protein+membrane; plus a minor bug Marc Baaden (Thu Sep 23 2010 - 09:24:59 CDT)
- about protein phosphorylation Zhang, Jiong (MU-Student) (Wed Sep 22 2010 - 11:59:36 CDT)
- (no subject) fereshteh moradi (Wed Sep 22 2010 - 04:59:49 CDT)
- unsubscribe Asmita Gupta (Wed Sep 22 2010 - 03:17:24 CDT)
- configuration file Demet Akten (Wed Sep 22 2010 - 02:51:48 CDT)
- ion concentration in residue-based coarse-grained model Demet Akten (Wed Sep 22 2010 - 02:49:01 CDT)
- membrane tutorial. Swarna M Patra (Wed Sep 22 2010 - 01:44:23 CDT)
- NAMD 2.7b4 released Jim Phillips (Tue Sep 21 2010 - 21:38:22 CDT)
- (no subject) Zhang, Jiong (MU-Student) (Tue Sep 21 2010 - 20:01:38 CDT)
- RBCG-dcd files dota alexiou (Tue Sep 21 2010 - 16:40:00 CDT)
- Colvars in NAMD 2.7b4 J閞鬽e H閚in (Tue Sep 21 2010 - 07:06:29 CDT)
- total charge correction Chen, Zhihong (chenz2) (Fri Sep 17 2010 - 11:33:38 CDT)
- Why NAMD run Slow down Ramin Omidvar (Fri Sep 17 2010 - 11:32:07 CDT)
- ewald self energy Chen, Zhihong (chenz2) (Thu Sep 16 2010 - 15:12:07 CDT)
- Re: Low temperature Molecular Dynamics Mert G黵 (Thu Sep 16 2010 - 14:49:01 CDT)
- tcl script for saving .coor of each frame from dcd file Madhurima Jana (Wed Sep 15 2010 - 23:51:41 CDT)
- unsubscribe Katherine Parra (Wed Sep 15 2010 - 09:42:24 CDT)
- Re: Problem facing during Solvation of Coarse Grain Model Peter Freddolino (Tue Sep 14 2010 - 18:59:54 CDT)
- Low temperature Molecular Dynamics Mert G黵 (Tue Sep 14 2010 - 15:42:53 CDT)
- replica exchange trans cis isomerisme Jorgen Simonsen (Sat Sep 11 2010 - 03:02:30 CDT)
- degrees of freedom Jorgen Simonsen (Sat Sep 11 2010 - 00:26:10 CDT)
- psfgen problem, not generating angles/dihedrals Rajan Vatassery (Fri Sep 10 2010 - 23:33:42 CDT)
- AMBER force field in NAMD Patargias, George (Fri Sep 10 2010 - 09:48:01 CDT)
- beta column Swarna M Patra (Fri Sep 10 2010 - 00:57:04 CDT)
- parameters for Glutathione and BSO Raul Araya (Thu Sep 09 2010 - 11:44:38 CDT)
- NAMD Energy types Lada Biedermannov (Wed Sep 08 2010 - 04:16:30 CDT)
- Re: NAMD Energy types Peter Freddolino (Wed Sep 08 2010 - 19:19:02 CDT)
- Re: NAMD Energy types Lada Biedermannov (Thu Sep 09 2010 - 03:51:12 CDT)
- Re: NAMD Energy types Peter Freddolino (Thu Sep 09 2010 - 07:04:49 CDT)
- Re: NAMD Energy types Lada Biedermannov (Thu Sep 09 2010 - 08:16:44 CDT)
- Re: NAMD Energy types Peter Freddolino (Thu Sep 09 2010 - 20:40:15 CDT)
- Re: NAMD Energy types Jim Phillips (Fri Sep 17 2010 - 14:39:29 CDT)
- Re: NAMD Energy types Peter Freddolino (Fri Sep 17 2010 - 18:20:55 CDT)
- Re: NAMD Energy types Lada Biedermannov (Thu Sep 09 2010 - 03:51:12 CDT)
- Re: NAMD Energy types Peter Freddolino (Wed Sep 08 2010 - 19:19:02 CDT)
- Q=B4=D7=D4crazylyf@163.com=B5=C4=D3=CA=BC=FE?= crazylyf (Tue Sep 07 2010 - 22:17:50 CDT)
- problem on pair interaction Chen, Zhihong (chenz2) (Tue Sep 07 2010 - 15:49:04 CDT)
- Acceptance ratio of REMD simulation jaya c.jose (Tue Sep 07 2010 - 05:47:04 CDT)
- user-defined energy function Ramya Narasimhan (Mon Sep 06 2010 - 04:53:47 CDT)
- question on hydrogen bond Kwee Hong (Sun Sep 05 2010 - 22:40:40 CDT)
- FATAL ERROR: Couldn't open DCD file equil0.dcd: No such file or directory henri mone (Sun Sep 05 2010 - 10:16:27 CDT)
- Bad atom ID in extra bond file Kwee Hong (Sat Sep 04 2010 - 03:10:25 CDT)
- problem in cgsolvate.tcl while adding CG water to the system sunita gupta (Sat Sep 04 2010 - 02:52:12 CDT)
- solute movement in periodic box Mark M Huntress (Fri Sep 03 2010 - 09:53:38 CDT)
- script for energy minimization of a .dcd file sudipta (Fri Sep 03 2010 - 02:39:22 CDT)
- Bioinformatics Symposium at C-DAC, Pune Anirban Ghosh (Fri Sep 03 2010 - 00:41:23 CDT)
- simulation cell enlarging too much after restart Parisa Akhski (Thu Sep 02 2010 - 17:26:40 CDT)
- Minimization convergence Wendy Gonz醠ez (Thu Sep 02 2010 - 15:55:19 CDT)
- Does "rigidbond off" work instead of "rigidbonds none" Mert G黵 (Thu Sep 02 2010 - 15:03:21 CDT)
- 1-4 pair generation Jianhui Tian (Thu Sep 02 2010 - 13:12:42 CDT)
- g(r) calculation for CNT sara (Thu Sep 02 2010 - 04:34:48 CDT)
- NAMD Cuda NBFIX Terms Jane Ren (Wed Sep 01 2010 - 20:21:20 CDT)
- Building PSF file for protein with ions anas . (Wed Sep 01 2010 - 05:22:50 CDT)
- Charmm carbohydrate force field Jianhui Tian (Tue Aug 31 2010 - 13:09:58 CDT)
- Force constant scaling guardiani_at_fi.infn.it (Tue Aug 31 2010 - 09:45:14 CDT)
- FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. dhacademic (Tue Aug 31 2010 - 08:25:35 CDT)
- Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. J閞鬽e H閚in (Tue Aug 31 2010 - 10:22:06 CDT)
- Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. dhacademic (Fri Sep 03 2010 - 12:30:57 CDT)
- Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. dhacademic (Fri Sep 03 2010 - 23:26:49 CDT)
- Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. J閞鬽e H閚in (Sat Sep 04 2010 - 02:50:54 CDT)
- Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. dhacademic (Mon Sep 06 2010 - 03:29:31 CDT)
- Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. J閞鬽e H閚in (Mon Sep 06 2010 - 10:14:25 CDT)
- Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. dhacademic (Mon Sep 06 2010 - 10:29:38 CDT)
- Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. Giacomo Fiorin (Mon Sep 06 2010 - 14:10:06 CDT)
- Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. dhacademic (Mon Sep 06 2010 - 17:26:29 CDT)
- Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. Giacomo Fiorin (Tue Sep 07 2010 - 11:23:35 CDT)
- Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. dhacademic (Tue Sep 07 2010 - 15:31:07 CDT)
- Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. Giacomo Fiorin (Wed Sep 08 2010 - 16:28:50 CDT)
- Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. dhacademic (Wed Sep 08 2010 - 17:07:09 CDT)
- Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. dhacademic (Wed Sep 08 2010 - 16:46:37 CDT)
- Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. J閞鬽e H閚in (Thu Sep 09 2010 - 11:06:33 CDT)
- Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. dhacademic (Fri Sep 10 2010 - 14:11:23 CDT)
- Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. J閞鬽e H閚in (Sat Sep 11 2010 - 04:02:52 CDT)
- Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. dhacademic (Fri Sep 03 2010 - 12:30:57 CDT)
- Re: FATAL ERROR: Due to a design error, GlobalMasterServer does not support individual atom requests from multiple global force clients on parallel runs. J閞鬽e H閚in (Tue Aug 31 2010 - 10:22:06 CDT)
- protein shifts out of water box Kwee Hong (Tue Aug 31 2010 - 05:20:53 CDT)
- CatDCD installation bkziervogel_at_uchicago.edu (Mon Aug 30 2010 - 11:24:04 CDT)
- cholestrerol Swarna M Patra (Mon Aug 30 2010 - 04:29:38 CDT)
- claen water Swarna M Patra (Sun Aug 29 2010 - 22:28:22 CDT)
- restarting simulation sara (Sun Aug 29 2010 - 03:18:07 CDT)
- Protonation Andres Morales N (Sat Aug 28 2010 - 21:11:49 CDT)
- Unsubscribe namd-l udbhav ojha (Sat Aug 28 2010 - 16:20:45 CDT)
- unsubscribe namd-l sathish kumar gurupatham (Sat Aug 28 2010 - 14:07:25 CDT)
- problem at applying patch Kwee Hong (Sat Aug 28 2010 - 12:58:21 CDT)
- charge calculation Kwee Hong (Sat Aug 28 2010 - 09:09:12 CDT)
- unsubscribe namd-l sripad chandan (Sat Aug 28 2010 - 09:08:12 CDT)
- (no subject) Aakash C R (Sat Aug 28 2010 - 04:35:48 CDT)
- unsubscribe namd-l udbhav ojha (Sat Aug 28 2010 - 02:23:20 CDT)
- VdW and fixatoms Ranyere Deyler (Sat Aug 28 2010 - 00:07:06 CDT)
- unsubscribe namd-l Myunggi Yi (Fri Aug 27 2010 - 21:01:19 CDT)
- FEP substrate transformation with common moiety Sebastian Stolzenberg (Fri Aug 27 2010 - 20:35:01 CDT)
- write out the snapshot from MD trajectory mjyang (Fri Aug 27 2010 - 04:59:32 CDT)
- Version 2.7 problems! Wendy Gonz醠ez (Thu Aug 26 2010 - 11:55:47 CDT)
- build a layer hamid mosaddeghi (Wed Aug 25 2010 - 07:58:46 CDT)
- build a wall sara (Wed Aug 25 2010 - 11:01:39 CDT)
- WorkDistrib: Recursive bisection fails,invoking least-load algorithm Swarna M Patra (Tue Aug 24 2010 - 11:42:45 CDT)
- problem with water Swarna M Patra (Tue Aug 24 2010 - 11:26:45 CDT)
- water escape Swarna M Patra (Tue Aug 24 2010 - 10:38:31 CDT)
- TIP4P/Ice usage in NAMD Ravinder Abrol (Tue Aug 24 2010 - 03:22:17 CDT)
- possible bug with NAMD Energy plugin Zumot, Elia Nabil (Mon Aug 23 2010 - 15:19:07 CDT)
- Proline hybrid topology file for FEP Payel Das (Fri Aug 20 2010 - 19:54:28 CDT)
- ABF calculations: Jacobian term describing geometry entropy chengh_at_ringo.chem.pitt.edu (Mon Aug 23 2010 - 08:13:37 CDT)
- problem at maintaining geometry coordinate Kwee Hong (Mon Aug 23 2010 - 02:22:53 CDT)
- Does CHARMM stabilize alpha helices? Rabab Toubar (Sat Aug 21 2010 - 15:58:24 CDT)
- zeroMomentum for SMD Ihsan Omur Akdag (Fri Aug 20 2010 - 05:58:18 CDT)
- About the solvate package c00jsw00 (Thu Aug 19 2010 - 22:25:31 CDT)
- specific site-ion LJ parameters and CHARMM general force field 鏋楁槦闆 (Thu Aug 19 2010 - 05:53:55 CDT)
- my problem was solved zhangliqun (Wed Aug 18 2010 - 15:39:36 CDT)
- Resources for trying out NVIDIA GPUs for free with NAMD Roy Kim (Wed Aug 18 2010 - 12:22:09 CDT)
- change solvent Leandro Mart韓ez (Wed Aug 18 2010 - 11:36:59 CDT)
- change solvent sara (Wed Aug 18 2010 - 10:26:20 CDT)
- zeroMomentum for SMD 輍san 謒黵 Akda (Wed Aug 18 2010 - 07:29:45 CDT)
- interaction-energy balaji nagarajan (Wed Aug 18 2010 - 05:15:03 CDT)
- problem at maintaining geometry coordinate Kwee Hong (Tue Aug 17 2010 - 22:48:35 CDT)
- about recentering of namd trajectory zhangliqun (Tue Aug 17 2010 - 10:50:54 CDT)
- Re: parameter file for carbon nanotube Jian Liu (Mon Aug 16 2010 - 23:53:56 CDT)
- Applying a positional restraint with colvars module bkziervogel_at_uchicago.edu (Mon Aug 16 2010 - 12:06:24 CDT)
- Dowser with RESIDUE LYR Ale Gomez (Mon Aug 16 2010 - 12:02:18 CDT)
- Umbrella Sampling Methodology Charlie Forde (Mon Aug 16 2010 - 06:23:15 CDT)
- parameter file for carbon nanotube sara (Mon Aug 16 2010 - 10:34:53 CDT)
- Re: psf creating for carbon nanotube Jian Liu (Sun Aug 15 2010 - 07:40:32 CDT)
- specific heat - instability Alex Curutiu (Sun Aug 15 2010 - 05:49:52 CDT)
- psf creating for carbon nanotube sara (Sun Aug 15 2010 - 02:48:36 CDT)
- Modifying a peptide and introducing residues Aditya Ranganathan (Sat Aug 14 2010 - 05:57:28 CDT)
- Re: how to save a DCD file without water in NAMD ? Lisa Brown (Fri Aug 13 2010 - 08:06:36 CDT)
- "Hands-On" Workshop on Computational Biophysics, November 1-5, 2010 & November 29-December 3, 2010 in Urbana, IL TCBG Workshops (Thu Aug 12 2010 - 17:04:39 CDT)
- how to save a DCD file without water in NAMD ? Lisa Brown (Thu Aug 12 2010 - 15:00:40 CDT)
- grid-based correction map yandong Huang (Thu Aug 12 2010 - 08:52:33 CDT)
- Enthalpy calculation from NPT simulation sudipta (Wed Aug 11 2010 - 13:54:16 CDT)
- ABF problem with gyration radius/Cl and Br Branko (Wed Aug 11 2010 - 07:25:41 CDT)
- Reading NAMD coor files in CHARMM -> Fail for 64Bit Bjoern Olausson (Wed Aug 11 2010 - 06:57:27 CDT)
- Mysterious Formation of Solvent Spheres Charles Zhao (Wed Aug 11 2010 - 01:32:52 CDT)
- Re: Mysterious Formation of Solvent Spheres Axel Kohlmeyer (Wed Aug 11 2010 - 05:23:36 CDT)
- Re: Mysterious Formation of Solvent Spheres Charles Zhao (Wed Aug 11 2010 - 11:42:16 CDT)
- Re: Mysterious Formation of Solvent Spheres Thomas C. Bishop (Wed Aug 11 2010 - 13:48:10 CDT)
- Re: Mysterious Formation of Solvent Spheres Charles Zhao (Wed Aug 11 2010 - 15:23:53 CDT)
- Re: Mysterious Formation of Solvent Spheres Charles Zhao (Wed Aug 11 2010 - 18:19:07 CDT)
- Re: Mysterious Formation of Solvent Spheres Axel Kohlmeyer (Wed Aug 11 2010 - 05:23:36 CDT)
- FEP calculation is doing nothing sudipta (Tue Aug 10 2010 - 10:09:29 CDT)
- positive total energy C. Navarro (Tue Aug 10 2010 - 08:48:59 CDT)
- restart from different snap shots Jorgen Simonsen (Tue Aug 10 2010 - 06:05:25 CDT)
- version of namd to install Jorgen Simonsen (Mon Aug 09 2010 - 04:47:43 CDT)
- question regarding warning. Kwee Hong (Mon Aug 09 2010 - 02:28:16 CDT)
- Reason of FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT Mert G黵 (Sat Aug 07 2010 - 10:20:19 CDT)
- Re: Reason of FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT Mert G黵 (Sat Aug 07 2010 - 11:39:13 CDT)
- Re: Reason of FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT Axel Kohlmeyer (Sat Aug 07 2010 - 13:10:15 CDT)
- Re: Reason of FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT Mert G黵 (Sat Aug 07 2010 - 15:12:15 CDT)
- Re: Reason of FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT Axel Kohlmeyer (Sat Aug 07 2010 - 15:28:29 CDT)
- Re: Reason of FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT Mert G黵 (Mon Aug 09 2010 - 08:14:39 CDT)
- Re: Reason of FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT Axel Kohlmeyer (Sat Aug 07 2010 - 13:10:15 CDT)
- Re: Reason of FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT felmerino_at_uchile.cl (Sat Aug 07 2010 - 19:13:59 CDT)
- Re: Reason of FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT Mert G黵 (Sat Aug 07 2010 - 11:39:13 CDT)
- reinitvels vs restart.vel Dhiraj Srivastava (Fri Aug 06 2010 - 15:06:05 CDT)
- CHARMM FF parameters for O2 Gas m.raviprasad_at_ndsu.edu (Fri Aug 06 2010 - 14:39:11 CDT)
- last call for 2.7b3 bug reports! Jim Phillips (Fri Aug 06 2010 - 09:59:00 CDT)
- Constraints on the plane and on the atom positions (in the same simulation) Ajasja Ljubeti膷 (Fri Aug 06 2010 - 03:15:16 CDT)
- Problems with AutoPSF flavio seixas (Wed Aug 04 2010 - 21:20:26 CDT)
- abf_integrate Sabyashachi Mishra (Wed Aug 04 2010 - 04:50:08 CDT)
- Interface analisis Leonardo Herrera (Tue Aug 03 2010 - 12:20:00 CDT)
- heating and binvelocities Dhiraj Srivastava (Tue Aug 03 2010 - 11:26:36 CDT)
- Specifying Values for Rotating Constraints Megan Scoppa (Tue Aug 03 2010 - 11:09:54 CDT)
- flashmob namd Ramon Rocha (Tue Aug 03 2010 - 10:52:15 CDT)
- NAMD Pair Interactions Finite Box Size Correction Hok-Hei Tam (Tue Aug 03 2010 - 09:58:53 CDT)
- coarse graining ipsita basu (Tue Aug 03 2010 - 04:43:20 CDT)
- RetinalTop Ale Gomez (Mon Aug 02 2010 - 00:47:44 CDT)
- RetinalTop Ale Gomez (Mon Aug 02 2010 - 08:52:10 CDT)
- Re: RetinalTop Bjoern Olausson (Mon Aug 02 2010 - 09:49:32 CDT)
- Re: RetinalTop Ale Gomez (Mon Aug 02 2010 - 10:15:41 CDT)
- Re: RetinalTop Ale Gomez (Mon Aug 02 2010 - 11:07:52 CDT)
- Re: RetinalTop Ale Gomez (Mon Aug 02 2010 - 20:00:49 CDT)
- Re: RetinalTop Ale Gomez (Mon Aug 02 2010 - 22:53:13 CDT)
- Re: RetinalTop Bjoern Olausson (Tue Aug 03 2010 - 02:57:26 CDT)
- Re: RetinalTop tillmann.utesch_at_mail.tu-berlin.de (Tue Aug 03 2010 - 03:23:22 CDT)
- Re: RetinalTop Ale Gomez (Tue Aug 03 2010 - 11:22:19 CDT)
- Re: RetinalTop Ale Gomez (Wed Aug 04 2010 - 11:47:09 CDT)
- Re: RetinalTop Bjoern Olausson (Mon Aug 02 2010 - 09:49:32 CDT)
- RetinalTop Ale Gomez (Mon Aug 02 2010 - 08:52:10 CDT)
- (no subject) fereshteh moradi (Sun Aug 01 2010 - 23:25:34 CDT)
- Problems installing NAMD Bruno Rodrigues (Sat Jul 31 2010 - 01:12:12 CDT)
- monolayere riya david (Fri Jul 30 2010 - 14:29:48 CDT)
- Using CHARMM-GUI membrane builder with NAMD Ajasja Ljubeti膷 (Fri Jul 30 2010 - 09:17:36 CDT)
- Re: Using CHARMM-GUI membrane builder with NAMD Bjoern Olausson (Mon Aug 02 2010 - 02:37:09 CDT)
- Re: Using CHARMM-GUI membrane builder with NAMD Ajasja Ljubeti膷 (Mon Aug 02 2010 - 03:43:53 CDT)
- Re: Using CHARMM-GUI membrane builder with NAMD Bjoern Olausson (Mon Aug 02 2010 - 06:56:14 CDT)
- Re: Using CHARMM-GUI membrane builder with NAMD Axel Kohlmeyer (Mon Aug 02 2010 - 07:45:53 CDT)
- Re: Using CHARMM-GUI membrane builder with NAMD Bjoern Olausson (Mon Aug 02 2010 - 08:21:07 CDT)
- Re: Using CHARMM-GUI membrane builder with NAMD Ajasja Ljubeti膷 (Mon Aug 02 2010 - 07:59:54 CDT)
- Re: Using CHARMM-GUI membrane builder with NAMD Ajasja Ljubeti膷 (Mon Aug 02 2010 - 03:43:53 CDT)
- Re: Using CHARMM-GUI membrane builder with NAMD Bjoern Olausson (Mon Aug 02 2010 - 02:37:09 CDT)
- Pressure is not constant in NPT ensemble Parisa Akhski (Thu Jul 29 2010 - 14:01:05 CDT)
- Z-direction shrinking crazylyf (Thu Jul 29 2010 - 03:33:11 CDT)
- Interaction energy difference m.raviprasad_at_ndsu.edu (Wed Jul 28 2010 - 22:42:07 CDT)
- Namd 2.6 on ubuntu 9.10 oguz gurbulak (Wed Jul 28 2010 - 14:22:09 CDT)
- Running namd on multiple win32 nodes Ajasja Ljubeti膷 (Wed Jul 28 2010 - 04:42:20 CDT)
- Pressure parameter in minimization Parisa Akhski (Tue Jul 27 2010 - 16:31:03 CDT)
- structure breaking ipsita basu (Tue Jul 27 2010 - 00:36:35 CDT)
- FEP for GLY and PRO Mutations Michael LeVine (Mon Jul 26 2010 - 10:10:28 CDT)
- Re: how to submit job on a HPC equipped with infiniband Bjoern Olausson (Mon Jul 26 2010 - 04:31:55 CDT)
- how to submit job on a HPC equipped with infiniband liupeng012 (Mon Jul 26 2010 - 02:59:34 CDT)
- dihedral terms for a parameter file Basak Isin (Sun Jul 25 2010 - 17:09:09 CDT)
- Running namd on Apple's XGrid Ido Gan (Sun Jul 25 2010 - 02:16:44 CDT)
- tclforces: measure distances in NAMD 2.6b2 ? Sebastian Stolzenberg (Sat Jul 24 2010 - 21:46:51 CDT)
- NAMD time connect out on multi-computers Nicolas Floquet (Fri Jul 23 2010 - 07:00:12 CDT)
- RAMD patch in NAMD CVS Vlad Cojocaru (Fri Jul 23 2010 - 04:18:15 CDT)
- Deprotonated Lys Dhiraj Srivastava (Thu Jul 22 2010 - 21:13:50 CDT)
- Running NAMD on SGI Altix system Ronald Salesky (Thu Jul 22 2010 - 15:13:31 CDT)
- "gradient tolerance" for minimization Parisa Akhski (Thu Jul 22 2010 - 11:29:19 CDT)
- Timeout waiting for node-program to connect Nicolas Floquet (Wed Jul 21 2010 - 10:43:02 CDT)
- parallel scaling issues Hyonseok Hwang (Wed Jul 21 2010 - 09:11:18 CDT)
- dual all-atom/coarse grain simulation Keith Battle (Tue Jul 20 2010 - 15:52:30 CDT)
- constraintScaling to gradually release harmonic restraints during minimization Scott Boyken (Tue Jul 20 2010 - 15:22:08 CDT)
- Running namd on Mac OS Patargias, George (Tue Jul 20 2010 - 12:25:04 CDT)
- namd development mailing list? Nicholas Musolino (Tue Jul 20 2010 - 12:09:38 CDT)
- pair interaction self in 2.7b3 Kimura, Roy (Tue Jul 20 2010 - 09:28:48 CDT)
- Debug NAMD with CharmDebug Jaime Gonzalez (Tue Jul 20 2010 - 03:41:45 CDT)
- running namd faster ipsita basu (Tue Jul 20 2010 - 00:55:34 CDT)
- 1us simulation of 80k atom system -- how much gross structure movement is expected? Ian Stokes-Rees (Mon Jul 19 2010 - 12:18:55 CDT)
- Re: 1us simulation of 80k atom system -- how much gross structure movement is expected? Francesco Oteri (Mon Jul 19 2010 - 13:39:54 CDT)
- Re: 1us simulation of 80k atom system -- how much gross structure movement is expected? Peter Freddolino (Mon Jul 19 2010 - 18:52:20 CDT)
- Re: 1us simulation of 80k atom system -- how much gross structure movement is expected? Ian Stokes-Rees (Mon Jul 19 2010 - 20:06:05 CDT)
- Re: 1us simulation of 80k atom system -- how much gross structure movement is expected? Axel Kohlmeyer (Mon Jul 19 2010 - 21:03:22 CDT)
- Re: 1us simulation of 80k atom system -- how much gross structure movement is expected? Branko (Tue Jul 20 2010 - 07:58:01 CDT)
- Re: 1us simulation of 80k atom system -- how much gross structure movement is expected? Peter Freddolino (Mon Jul 19 2010 - 20:52:48 CDT)
- Re: 1us simulation of 80k atom system -- how much gross structure movement is expected? Ian Stokes-Rees (Mon Jul 19 2010 - 20:06:05 CDT)
- Re: 1us simulation of 80k atom system -- how much gross structure movement is expected? Andrew Emerson (Tue Jul 20 2010 - 05:09:05 CDT)
- Extract trajectory from replica exchange simulation Shi, Chuanyin (Mon Jul 19 2010 - 09:19:21 CDT)
- Re: CPU GPU comparison francesco oteri (Fri Jul 16 2010 - 03:13:17 CDT)
- alchemy FEP query Madhurima Jana (Fri Jul 16 2010 - 01:05:44 CDT)
- pairinteractionself in 2.7b3 Kimura, Roy (Thu Jul 15 2010 - 14:33:04 CDT)
- Different types of constraints at the same time Chao Zhang (Thu Jul 15 2010 - 14:05:30 CDT)
- mutation of DNA sudipta (Thu Jul 15 2010 - 05:57:46 CDT)
- CPU GPU comparison francesco oteri (Tue Jul 13 2010 - 11:47:05 CDT)
- RBCG doty alexiou (Tue Jul 13 2010 - 02:42:53 CDT)
- Running problem with NAMD2.7b lixb07_at_lzu.cn (Mon Jul 12 2010 - 21:01:40 CDT)
- Cartesian vs dihedral angle space PCA patrick wintrode (Mon Jul 12 2010 - 10:12:29 CDT)
- headgroup area calculation ipsita basu (Mon Jul 12 2010 - 07:33:47 CDT)
- about DCD file format document Jun Zhang (Mon Jul 12 2010 - 06:43:02 CDT)
- problem wuth solvate plugin Mikhail Suyetin (Mon Jul 12 2010 - 05:53:28 CDT)
- the problem with NAMD2.7b lixb07_at_lzu.cn (Mon Jul 12 2010 - 05:13:41 CDT)
- NAMD checkpoint mechanism. Michael Harney (Fri Jul 09 2010 - 15:38:46 CDT)
- Bin Coordinate file to pdb Philip Peartree (Thu Jul 08 2010 - 15:50:34 CDT)
- FATAL ERROR: Asymmetric water molecule found??? This can't be right. Jorgen Simonsen (Wed Jul 07 2010 - 17:34:44 CDT)
- Release of the R.E.D.-III.4 tools FyD (Wed Jul 07 2010 - 02:04:36 CDT)
- (no subject) Melanie Santos Marrero (Tue Jul 06 2010 - 15:35:18 CDT)
- NAMD 2.7b3 released Jim Phillips (Tue Jul 06 2010 - 13:45:58 CDT)
- Helix tilt stefhoor (Tue Jul 06 2010 - 09:29:42 CDT)
- save trajectory only for two residues wenchangyu2006_at_gmail.com (Tue Jul 06 2010 - 08:13:42 CDT)
- residue based CG method doty alexiou (Tue Jul 06 2010 - 06:22:30 CDT)
- How can I connect different structures between them using VMD and NAMD? Patriche Simona (Sun Jul 04 2010 - 19:45:15 CDT)
- O-PHOSPHOTYROSINE link to DNA base pair. q md (Sun Jul 04 2010 - 02:37:44 CDT)
- hydration in membrane-protein simulations dhacademic (Sat Jul 03 2010 - 10:20:23 CDT)
- Loadleveler Script on Bluegene for NAMD Dan J Martingano (Fri Jul 02 2010 - 22:48:42 CDT)
- Help: NAMD on cluster; nodes reject multiple connections David Kelly (Thu Jul 01 2010 - 00:33:11 CDT)
- namd2 still works but without any new messages in log file lixb07_at_lzu.cn (Thu Jul 01 2010 - 07:21:18 CDT)
- Dihedral angle potential energy function Ajasja Ljubeti膷 (Thu Jul 01 2010 - 05:07:27 CDT)
- NAMD with Replica Exchange Simulations on Teragrid Shi, Chuanyin (Thu Jul 01 2010 - 00:17:45 CDT)
- "didn't find VdW parameter for atom type NH3" error Emily Chen (Tue Jun 29 2010 - 07:06:33 CDT)
- parameters for graphene nanoribbons annealed by hydrogen 何毓辉 (Tue Jun 29 2010 - 03:09:15 CDT)
- OPENING EXTENDED SYSTEM TRAJECTORY FILE Parisa Akhski (Mon Jun 28 2010 - 13:47:39 CDT)
- regarding parameter and topology files for a new molecule ajay singh (Mon Jun 28 2010 - 02:31:26 CDT)
- How do I connect the non-overlwindows of ABF's results? Aurum Bai (Sun Jun 27 2010 - 23:14:38 CDT)
- modification of CHARMM force field lixb07_at_lzu.cn (Fri Jun 25 2010 - 20:05:56 CDT)
- How to calculate binding free energy of a protein-DNA complex by using NAMD? sudipta (Fri Jun 25 2010 - 11:14:38 CDT)
- ABF question Parisa Akhski (Thu Jun 24 2010 - 16:03:15 CDT)
- Query regarding ABF Tutorial on Methane Hydration Navendu bhatnagar (Thu Jun 24 2010 - 12:38:42 CDT)
- NAMD terminates prematurely without error. Ajasja Ljubeti膷 (Wed Jun 23 2010 - 02:41:24 CDT)
- Simulation configuration file not accesible listowel agyarko (Tue Jun 22 2010 - 15:30:59 CDT)
- Query regarding ABF Tutorial on Methane Hydration Navendu bhatnagar (Tue Jun 22 2010 - 14:52:41 CDT)
- ABF question Parisa Akhski (Tue Jun 22 2010 - 13:06:55 CDT)
- ABF question Parisa Akhski (Tue Jun 22 2010 - 11:43:06 CDT)
- standard state correction of delta G from a PMF Elio Cino (Tue Jun 22 2010 - 10:06:30 CDT)
- Multi-step MD in a single .conf file Jun Zhang (Mon Jun 21 2010 - 19:02:22 CDT)
- waterbox changes shape during steered molecular dynamics Mert G黵 (Mon Jun 21 2010 - 14:50:58 CDT)
- waterbox changes shape during steered molecular dynamics Mert G黵 (Mon Jun 21 2010 - 14:13:21 CDT)
- error during charm-6.1.3 building Mikhail Suyetin (Mon Jun 21 2010 - 13:40:04 CDT)
- impose restraint on the internal coordinate of protein dhacademic (Mon Jun 21 2010 - 13:43:58 CDT)
- (no subject) Jun Zhang (Mon Jun 21 2010 - 08:13:01 CDT)
- a question about NAMD TI 鏋楁槦闆 (Sun Jun 20 2010 - 22:26:48 CDT)
- Hepl whit colvar subrutiene Leonardo Herrera (Fri Jun 18 2010 - 16:11:19 CDT)
- phosphate parameters BIN ZHANG (Fri Jun 18 2010 - 12:42:18 CDT)
- Reply: couldn磘 find rsh program Jun Zhang (Thu Jun 17 2010 - 19:03:41 CDT)
- couldn磘 find rsh program jose correa (Thu Jun 17 2010 - 14:39:56 CDT)
- NAMD parralel processor windows Ramin Omidvar (Thu Jun 17 2010 - 13:25:54 CDT)
- Distance constraint Nicolas Floquet (Thu Jun 17 2010 - 03:30:45 CDT)
- different values of "1-4scaling" in a system D70039 (Wed Jun 16 2010 - 06:00:06 CDT)
- Minimization messes up C terminal Pavan G (Wed Jun 16 2010 - 10:32:42 CDT)
- pairinteractions Thomas C. Bishop (Tue Jun 15 2010 - 17:34:27 CDT)
- usage of NAMD with AMBER commands Giovanni Nico (Tue Jun 15 2010 - 11:51:08 CDT)
- Regarding NAMD algorithm jani vinod (Tue Jun 15 2010 - 07:38:29 CDT)
- Re: Help with cys unprotonated ehenriques_at_qui.uc.pt (Tue Jun 15 2010 - 05:08:55 CDT)
- Help with cys unprotonated Leonardo Herrera (Mon Jun 14 2010 - 20:24:39 CDT)
- colvars don't run with minimization ... Leonardo Herrera (Mon Jun 14 2010 - 19:44:21 CDT)
- Possible way of performing a temperature gradient?? Ranyere Deyler (Sun Jun 13 2010 - 23:19:10 CDT)
- Workshop on GPU Programming for Molecular Modeling, August 6-8, 2010, at the Beckman Institute in Urbana, Illinois TCBG Workshops (Fri Jun 11 2010 - 17:28:26 CDT)
- colvars: Error: in parsing "centers" Leonardo Herrera (Thu Jun 10 2010 - 19:25:16 CDT)
- NAMD on Ranger at Teragrid Zumot, Elia Nabil (Thu Jun 10 2010 - 15:08:16 CDT)
- Balancer and singularities ... Nicholas M Glykos (Thu Jun 10 2010 - 10:52:05 CDT)
- rough edges of energy landscape when running ABF crazylyf (Thu Jun 10 2010 - 09:34:56 CDT)
- Protein in a Lipid Membrane Ale Gomez (Thu Jun 10 2010 - 05:22:33 CDT)
- Could namd use the method ONIOM of Gaussian? Aurum Bai (Thu Jun 10 2010 - 04:51:29 CDT)
- Re: parameter format for REMD simulations Neelanjana Sengupta (Thu Jun 10 2010 - 04:00:41 CDT)
- Dreiding parameters fereshteh moradi (Wed Jun 09 2010 - 07:17:21 CDT)
- where do I find info about freeEnergy ? Leonardo Herrera (Tue Jun 08 2010 - 13:28:15 CDT)
- colvar atom syntax Michael Zimmermann (Tue Jun 08 2010 - 13:11:29 CDT)
- Re: colvar atom syntax Giacomo Fiorin (Tue Jun 08 2010 - 15:01:41 CDT)
- Re: colvar atom syntax Michael Zimmermann (Thu Jun 10 2010 - 15:15:41 CDT)
- Re: colvar atom syntax Michael Zimmermann (Thu Jun 10 2010 - 15:40:53 CDT)
- Re: Re: colvar atom syntax Giacomo Fiorin (Thu Jun 10 2010 - 17:20:18 CDT)
- Re: Re: colvar atom syntax Michael Zimmermann (Tue Jun 15 2010 - 15:59:09 CDT)
- Re: Re: colvar atom syntax J閞鬽e H閚in (Wed Jun 16 2010 - 07:24:51 CDT)
- Re: Re: colvar atom syntax Michael Zimmermann (Wed Jun 16 2010 - 10:24:50 CDT)
- Re: Re: colvar atom syntax Giacomo Fiorin (Wed Jun 16 2010 - 11:20:33 CDT)
- Re: Re: colvar atom syntax J閞鬽e H閚in (Wed Jun 16 2010 - 11:42:09 CDT)
- TIP4P water in AMBER parm7 format fails with 2010-06-07 nightly build Hugh Heldenbrand (Tue Jun 08 2010 - 10:30:41 CDT)
- gradient tolerance Ramya Narasimhan (Tue Jun 08 2010 - 05:48:11 CDT)
- Regarding temperature accelerated MD Ramya Narasimhan (Tue Jun 08 2010 - 05:32:34 CDT)
- Fatal error when running ABF simulation crazylyf (Tue Jun 08 2010 - 01:00:01 CDT)
- Fwd: error : atom moving too fast ipsita basu (Tue Jun 08 2010 - 00:20:24 CDT)
- Control DCD file TAEJIN KIM (Mon Jun 07 2010 - 17:09:20 CDT)
- RDF.tcl selections Rabab Toubar (Mon Jun 07 2010 - 13:40:56 CDT)
- distance colvar Neelanjana Sengupta (Mon Jun 07 2010 - 03:07:51 CDT)
- compiling NAMD w. infiniband Irene Newhouse (Fri Jun 04 2010 - 16:21:37 CDT)
- rotational restrains Ziemys, Arturas (Fri Jun 04 2010 - 13:34:18 CDT)
- Problem with extraBonds Leonardo Herrera (Thu Jun 03 2010 - 20:23:32 CDT)
- Appropriate dcdfreq Philip Peartree (Thu Jun 03 2010 - 15:33:53 CDT)
- Minimization at higher temperature Rabab Toubar (Thu Jun 03 2010 - 14:08:37 CDT)
- Wrong energies in CUDA version Jeff Wereszczynski (Thu Jun 03 2010 - 11:45:13 CDT)
- help whit distance restraint Leonardo Herrera (Wed Jun 02 2010 - 17:37:57 CDT)
- charges in psf and in namd (or vmd) fett_at_vtr.net (Wed Jun 02 2010 - 11:12:07 CDT)
- Sudden crash - any clue about the cause? --> wc[0] status 12 wc[i].opcode 0 Bjoern Olausson (Wed Jun 02 2010 - 08:32:24 CDT)
- Run simulation in NAMD using files generated by CHARMM-GUI Dai, Jian1 (Tue Jun 01 2010 - 00:09:27 CDT)
- Dowser Basak Isin (Sat May 29 2010 - 19:25:37 CDT)
- multistep minimization with different constraint Mengchen Pu (Fri May 28 2010 - 06:29:34 CDT)
- are tclForces included in minimization? Michael Zimmermann (Fri May 28 2010 - 00:41:26 CDT)
- new NAMD user ABF setup question Elio Cino (Thu May 27 2010 - 14:10:04 CDT)
- Re: new NAMD user ABF setup question Giacomo Fiorin (Thu May 27 2010 - 16:27:02 CDT)
- Re: new NAMD user ABF setup question Elio Cino (Fri May 28 2010 - 07:48:03 CDT)
- Re: new NAMD user ABF setup question Giacomo Fiorin (Fri May 28 2010 - 09:03:59 CDT)
- Re: new NAMD user ABF setup question J閞鬽e H閚in (Sat May 29 2010 - 05:06:50 CDT)
- Re: new NAMD user ABF setup question Elio Cino (Mon May 31 2010 - 09:57:21 CDT)
- Re: new NAMD user ABF setup question Chris Chipot (Mon May 31 2010 - 10:29:53 CDT)
- Re: new NAMD user ABF setup question Felipe Merino (Tue Jun 01 2010 - 20:15:53 CDT)
- Re: new NAMD user ABF setup question J閞鬽e H閚in (Wed Jun 02 2010 - 09:53:05 CDT)
- Re: new NAMD user ABF setup question Elio Cino (Fri May 28 2010 - 07:48:03 CDT)
- Re: new NAMD user ABF setup question Giacomo Fiorin (Thu May 27 2010 - 16:27:02 CDT)
- monitoring instantaneous kinetic energy of a subsystem Rocchia Walter (Thu May 27 2010 - 06:52:16 CDT)
- multiplicity of dihedrals matziast_at_med.uth.gr (Thu May 27 2010 - 03:02:16 CDT)
- Temperature gradient! Ranyere Deyler (Wed May 26 2010 - 22:35:35 CDT)
- K25 NIH award Gianluca Interlandi (Wed May 26 2010 - 19:45:33 CDT)
- backbone restraints Michael Zimmermann (Wed May 26 2010 - 10:46:09 CDT)
- NAMD 2.7b2 versy slow on multiple nodes Laurent Chaloin (Tue May 25 2010 - 16:30:51 CDT)
- parameter file for CHARMM matziast_at_med.uth.gr (Tue May 25 2010 - 16:05:09 CDT)
- namd cuda with geforce 470 (fermi) gpu fatal error at runtime Phil Greer (Tue May 25 2010 - 13:52:41 CDT)
- RE: ABF question Patrick Yee (Tue May 25 2010 - 13:38:33 CDT)
- ABF (NAMD 2.7x) speed ? Ziemys, Arturas (Tue May 25 2010 - 09:51:33 CDT)
- ABF question Ziemys, Arturas (Tue May 25 2010 - 08:51:39 CDT)
- Question about Tcl/customising the colvar module poker_at_physics.usyd.edu.au (Tue May 25 2010 - 04:25:34 CDT)
- New NVIDIA GPU C2050 Richard Owczarzy (Tue May 25 2010 - 00:29:24 CDT)
- Drift of the center of mass of lipid bilayer Dai, Jian1 (Mon May 24 2010 - 13:26:39 CDT)
- Two questions about essential dynamics Jun Zhang (Mon May 24 2010 - 06:48:34 CDT)
- Problems about FEP simulation Yang Gao (Fri May 21 2010 - 11:03:08 CDT)
- Re: Error in running minimization m.raviprasad_at_ndsu.edu (Fri May 21 2010 - 09:27:08 CDT)
- Difference between the two Dowsers Ning Zhang (Fri May 21 2010 - 05:26:37 CDT)
- Error in running minimization Prija Ponnan (Fri May 21 2010 - 05:24:58 CDT)
- selective rigidbonds Sabyashachi Mishra (Fri May 21 2010 - 04:29:57 CDT)
- requirements for running the precompiled Linux-x86_64-ibverbs Guanglei Cui (Thu May 20 2010 - 08:49:26 CDT)
- Phi MD Rabab Toubar (Thu May 20 2010 - 08:07:45 CDT)
- How to solve the out of cell box for long time in Periodic Boundary Conditions? Aurum Bai (Wed May 19 2010 - 21:06:38 CDT)
- Constraint Failure in SMD simulation Ramin Omidvar (Wed May 19 2010 - 11:51:20 CDT)
- Analysis of Results of only Lipid Bilayer Simulations Saumya (Wed May 19 2010 - 05:22:06 CDT)
- PLUMED release 1.2.0 available Massimiliano Bonomi (Tue May 18 2010 - 06:47:05 CDT)
- Input/output error 王棽 (Tue May 18 2010 - 01:55:20 CDT)
- duplicate residue key ALA will be ignored Mert G黵 (Mon May 17 2010 - 16:42:59 CDT)
- (no subject) Mert G黵 (Mon May 17 2010 - 16:11:22 CDT)
- ABF in various simulations stefhoor (Mon May 17 2010 - 08:30:36 CDT)
- Re: ABF in various simulations Patrick Yee (Mon May 17 2010 - 10:47:58 CDT)
- Re: ABF in various simulations stefhoor (Mon May 17 2010 - 11:31:03 CDT)
- Re: ABF in various simulations Robert Elder (Mon May 17 2010 - 14:42:30 CDT)
- Re: ABF in various simulations stefhoor (Mon May 17 2010 - 15:18:57 CDT)
- Re: ABF in various simulations Robert Elder (Mon May 17 2010 - 18:43:41 CDT)
- Re: ABF in various simulations Giacomo Fiorin (Mon May 17 2010 - 21:17:32 CDT)
- Re: ABF in various simulations stefhoor (Mon May 17 2010 - 11:31:03 CDT)
- Re: ABF in various simulations J閞鬽e H閚in (Mon May 17 2010 - 11:08:28 CDT)
- Re: ABF in various simulations Patrick Yee (Mon May 17 2010 - 10:47:58 CDT)
- trouble running metalloprotein simulation from literature Sibo Lin (Sat May 15 2010 - 14:44:40 CDT)
- Generate psf files from Scott Feller's lipid coordinates Dai, Jian1 (Sat May 15 2010 - 13:46:36 CDT)
- Acetyl group patch for lysine residue Prija Ponnan (Sat May 15 2010 - 08:19:51 CDT)
- About RMSD based PMF's Felipe Merino (Thu May 13 2010 - 23:03:44 CDT)
- TCBG "Hands-on" Workshop on Computational Biophysics, July 12-16, 2010, at San Diego TCBG Workshops (Thu May 13 2010 - 16:33:11 CDT)
- Compiling NAMD under SGE and OpenMPI Gabriel Jara (Thu May 13 2010 - 11:34:49 CDT)
- Waterbox used in minimization? Cem Meydan (Thu May 13 2010 - 07:25:30 CDT)
- FEP yields the same results for forward and backward computation! Jun Zhang (Wed May 12 2010 - 22:38:44 CDT)
- protein unfolding no increase in conf energy Odysseas Axillews (Wed May 12 2010 - 05:25:24 CDT)
- Atom movement within a range of Z value muniyamuthu.raviprasad_at_ndsu.edu (Tue May 11 2010 - 14:47:15 CDT)
- a gap in flowing water fereshteh moradi (Tue May 11 2010 - 06:45:31 CDT)
- psfgen creates too many bonds in a distorted Fe4S4 cluster Sibo Lin (Mon May 10 2010 - 22:50:00 CDT)
- mininization do not go on flavio seixas (Sun May 09 2010 - 08:58:19 CDT)
- blank between nanotube and the bulk water fereshteh moradi (Fri May 07 2010 - 23:29:22 CDT)
- installation of namd without tcl and fftw ipsita basu (Mon May 10 2010 - 06:11:39 CDT)
- Timestep 594 flavio seixas (Sun May 09 2010 - 09:39:36 CDT)
- looking for topology and parameters of methamphetamine Liao Chen (Sun May 09 2010 - 08:47:46 CDT)
- Free energy calculation yields strange results Jun Zhang (Sun May 09 2010 - 07:53:36 CDT)
- ReassignFreq script fail!! Ranyere Deyler (Sat May 08 2010 - 03:10:14 CDT)
- How I can insert de harmonic restraint? Leonardo Herrera (Fri May 07 2010 - 15:33:18 CDT)
- Nightly build version: Parallel IO can not be used with langevin On Yudong Sun (Fri May 07 2010 - 06:21:57 CDT)
- Re: Nightly build version: Parallel IO can not be used with langevin On Yudong Sun (Wed May 19 2010 - 07:01:51 CDT)
- Re: Nightly build version: Parallel IO can not be used with langevin On Gabriel Jara (Wed May 19 2010 - 07:46:18 CDT)
- Re: Nightly build version: Parallel IO can not be used with langevin On Bryan Holland (Wed May 19 2010 - 09:21:25 CDT)
- Re: Nightly build version: Parallel IO can not be used with langevin On Bryan Holland (Wed May 19 2010 - 10:21:59 CDT)
- Re: Nightly build version: Parallel IO can not be used with langevin On Yudong Sun (Wed May 19 2010 - 07:01:51 CDT)
- Best tool to use to generate a custom (patched) polypeptide PDB? Jason Richard Mick (Thu May 06 2010 - 17:23:54 CDT)
- NAMD 2.7b1 distanceDir Guanglei Cui (Thu May 06 2010 - 13:03:34 CDT)
- Re: error : atom moving too fast muniyamuthu.raviprasad_at_ndsu.edu (Wed May 05 2010 - 09:58:50 CDT)
- Re: error : atom moving too fast ipsita basu (Thu May 06 2010 - 05:32:13 CDT)
- Re: error : atom moving too fast muniyamuthu.raviprasad_at_ndsu.edu (Wed May 19 2010 - 09:40:00 CDT)
- error : atom moving too fast ipsita basu (Wed May 05 2010 - 01:10:33 CDT)
- high atom velocity Mark M Huntress (Tue May 04 2010 - 14:36:56 CDT)
- Using RMSD in colvar Stefan Franzen (Mon May 03 2010 - 17:42:18 CDT)
- Particle Mesh Ewald question (from the tutorial) Stefan Franzen (Mon May 03 2010 - 17:39:38 CDT)
- RE: TMD simulations Andres Morales N (Mon May 03 2010 - 21:25:29 CDT)
- TMD simulations Andres Morales N (Fri Apr 30 2010 - 02:52:52 CDT)
- langevinhydrogen on with rigidbonds water Mark M Huntress (Fri Apr 30 2010 - 11:29:55 CDT)
- colvar: coordnum output Neelanjana Sengupta (Fri Apr 30 2010 - 05:34:29 CDT)
- software/algorithm to cluster protein conformations Basak Isin (Thu Apr 29 2010 - 17:51:59 CDT)
- NAMD complain about gromacs ff parameter ATOMTYPES definition 王棽 (Wed Apr 28 2010 - 22:36:10 CDT)
- Charmm parameters for Joakim Swedberg (Wed Apr 28 2010 - 21:47:03 CDT)
- NVE crash pellegrini (Wed Apr 28 2010 - 10:30:09 CDT)
- Dielectric Constant ydhuang2727 (Tue Apr 27 2010 - 20:23:11 CDT)
- Re: Dielectric Constant Axel Kohlmeyer (Wed Apr 28 2010 - 11:17:58 CDT)
- Re:Re: Dielectric Constant ydhuang2727 (Wed Apr 28 2010 - 22:54:30 CDT)
- Re: Re: Dielectric Constant Axel Kohlmeyer (Wed Apr 28 2010 - 23:44:20 CDT)
- Re: Re: Dielectric Constant Axel Kohlmeyer (Thu Apr 29 2010 - 00:06:18 CDT)
- Re:Re: Re: Dielectric Constant ydhuang2727 (Thu Apr 29 2010 - 01:19:46 CDT)
- Re: Re: Dielectric Constant J閞鬽e H閚in (Thu Apr 29 2010 - 02:59:42 CDT)
- Re:Re: Re: Dielectric Constant ydhuang2727 (Thu Apr 29 2010 - 07:39:49 CDT)
- Re: Re: Re: Dielectric Constant Axel Kohlmeyer (Thu Apr 29 2010 - 08:34:36 CDT)
- Re: Re: Re: Dielectric Constant J閞鬽e H閚in (Thu Apr 29 2010 - 10:06:57 CDT)
- TMD SCRIPT Sebastian Stolzenberg (Thu Apr 29 2010 - 11:11:42 CDT)
- Re:Re: Re: Re: Dielectric Constant ydhuang2727 (Thu Apr 29 2010 - 20:59:23 CDT)
- Re: Re: Re: Re: Dielectric Constant Axel Kohlmeyer (Thu Apr 29 2010 - 21:34:42 CDT)
- Re:Re: Re: Re: Re: Dielectric Constant ydhuang2727 (Sat May 01 2010 - 08:03:01 CDT)
- Re: Re:Re: Re: Re: Re: Dielectric Constant Axel Kohlmeyer (Sat May 01 2010 - 13:22:10 CDT)
- Re: Re: Re:Re: Re: Re: Re: Dielectric Constant Axel Kohlmeyer (Tue May 04 2010 - 08:03:08 CDT)
- Re:Re: Dielectric Constant ydhuang2727 (Wed Apr 28 2010 - 22:54:30 CDT)
- Re: Dielectric Constant Axel Kohlmeyer (Wed Apr 28 2010 - 11:17:58 CDT)
- evaluating energy in a trajectory of variable box size? Jose Borreguero (Tue Apr 27 2010 - 14:04:11 CDT)
- the unit of dipole moment in the calculation of dielectric constant. superdirac (Sun Apr 25 2010 - 21:58:11 CDT)
- something is wrong with my equilibration Ning Zhang (Sun Apr 25 2010 - 21:52:10 CDT)
- VRPN driver for Novint Falcon haptic device available - Looking for testers Axel Kohlmeyer (Fri Apr 23 2010 - 16:03:08 CDT)
- Dihedral parameters for side-chains? Igor Petrik (Fri Apr 23 2010 - 11:50:30 CDT)
- lipids moving crazylyf (Thu Apr 22 2010 - 21:05:33 CDT)
- Re: help J閞鬽e H閚in (Thu Apr 22 2010 - 16:44:58 CDT)
- error while running config file Asmita Gupta (Thu Apr 22 2010 - 13:41:29 CDT)
- Running REMD with CHARMM f.f. jaya c.jose (Thu Apr 22 2010 - 06:37:05 CDT)
- Re: topology file for dissacharides with psfgen Milton Sonoda (Thu Apr 22 2010 - 00:11:03 CDT)
- topology file for dissacharides with psfgen Milton Sonoda (Wed Apr 21 2010 - 23:38:56 CDT)
- NAMD CONFIG FILE:: Asmita Gupta (Wed Apr 21 2010 - 12:50:51 CDT)
- building a MARTINI bilayer Edward Lyman (Wed Apr 21 2010 - 12:41:35 CDT)
- setting transfer rate in IMD protocol Magdalena Gruziel (Wed Apr 21 2010 - 09:22:22 CDT)
- the total energy of single H2O molecule uu zhu (Wed Apr 21 2010 - 09:11:45 CDT)
- colvar for PMF calculation Navendu bhatnagar (Tue Apr 20 2010 - 18:02:28 CDT)
- simulating dna Asmita Gupta (Tue Apr 20 2010 - 12:02:36 CDT)
- simulating DNA using namd:: Asmita Gupta (Tue Apr 20 2010 - 07:07:34 CDT)
- Running REMD with CHARMM f.f. jaya c.jose (Tue Apr 20 2010 - 06:52:58 CDT)
- unsubscribe sathish kumar gurupatham (Mon Apr 19 2010 - 09:25:06 CDT)
- ABF: moving system in Z direction sefer baday (Mon Apr 19 2010 - 08:49:09 CDT)
- Re: ABF: moving system in Z direction J閞鬽e H閚in (Mon Apr 19 2010 - 11:20:35 CDT)
- Re: ABF: moving system in Z direction Giacomo Fiorin (Mon Apr 19 2010 - 12:16:08 CDT)
- Re: ABF: moving system in Z direction sefer baday (Tue Apr 20 2010 - 04:58:51 CDT)
- Re: ABF: moving system in Z direction Giacomo Fiorin (Tue Apr 20 2010 - 09:06:52 CDT)
- NAMD2.7/MEtadynamics simulation analysis disparity neville forlemu (Thu Apr 29 2010 - 13:30:42 CDT)
- Re: NAMD2.7/MEtadynamics simulation analysis disparity felmerino_at_uchile.cl (Thu Apr 29 2010 - 20:49:34 CDT)
- Re: NAMD2.7/MEtadynamics simulation analysis disparity neville forlemu (Fri Apr 30 2010 - 09:20:41 CDT)
- Re: NAMD2.7/MEtadynamics simulation analysis disparity Giacomo Fiorin (Fri Apr 30 2010 - 09:16:17 CDT)
- Re: ABF: moving system in Z direction sefer baday (Tue Apr 20 2010 - 04:58:51 CDT)
- Q=B4=D7=D4y=5Fja@163.com=B5=C4=D3=CA=BC=FE?= y_ja (Mon Apr 19 2010 - 02:09:29 CDT)
- unsubscribe Falgun Shah (Sun Apr 18 2010 - 22:53:44 CDT)
- modifying velocities within global master Nicholas Musolino (Sun Apr 18 2010 - 16:42:51 CDT)
- re a problem with "Charging a spherical ion" Jun Zhang (Sun Apr 18 2010 - 03:21:38 CDT)
- unsubscribe shivam ghosh (Sat Apr 17 2010 - 21:10:14 CDT)
- (no subject) 寮犻媶 (Fri Apr 16 2010 - 22:04:17 CDT)
- colvar: atom group defn. fails Neelanjana Sengupta (Fri Apr 16 2010 - 05:29:29 CDT)
- ABF non-uniform sampling Patrick Yee (Thu Apr 15 2010 - 22:19:45 CDT)
- FATAL ERROR: ABNORMAL EOF FOUND-buffer Jignesh Patel (Thu Apr 15 2010 - 15:11:55 CDT)
- How to use harmonic restraint parameter for 2 selection of atoms 王棽 (Thu Apr 15 2010 - 02:00:06 CDT)
- which one is better to use - fixed atoms or constraints? Jignesh Patel (Wed Apr 14 2010 - 12:09:07 CDT)
- Implementation of Martini CG FF in NAMD Liao Chuan (Wed Apr 14 2010 - 11:25:50 CDT)
- file writing stopped francesco oteri (Wed Apr 14 2010 - 03:34:59 CDT)
- colvars: free energy change with rmsd Neelanjana Sengupta (Wed Apr 14 2010 - 00:54:08 CDT)
- colvars error running ABF Patrick Yee (Tue Apr 13 2010 - 20:47:21 CDT)
- Performance peoblem about NAMD-CUDA benchmarks xiaoguang liu (Sun Apr 11 2010 - 06:53:16 CDT)
- Re: Performance peoblem about NAMD-CUDA benchmarks Biff Forbush (Mon Apr 12 2010 - 14:42:37 CDT)
- calculate side-chain dihedral/torsion angles Ajasja Ljubeti膷 (Mon Apr 12 2010 - 02:40:47 CDT)
- Andres Morales sent you a little gift Andres Morales (Sun Apr 11 2010 - 20:33:49 CDT)
- get total force on a group of atoms within GlobalMasterSMD Liao Chen (Sun Apr 11 2010 - 19:02:16 CDT)
- How to get PMF from SMD with colvars Jian Liu (Sat Apr 10 2010 - 03:45:05 CDT)
- (no subject) #SHEPHERDSON IGNATIUS MARK# (Fri Apr 09 2010 - 20:24:37 CDT)
- REGARDING Topology file Aakash C R (Fri Apr 09 2010 - 16:57:31 CDT)
- Job restart neville forlemu (Fri Apr 09 2010 - 16:39:57 CDT)
- LES dcd file split Dong Luo (Fri Apr 09 2010 - 15:09:08 CDT)
- Can AMBER topology be used in NAMD-CUDA? Lela Vukovic (Fri Apr 09 2010 - 14:54:08 CDT)
- selecting potential binding cavities with MD Thomas Evangelidis (Fri Apr 09 2010 - 14:11:21 CDT)
- Regarding ligand forcefield Jignesh Patel (Thu Apr 08 2010 - 14:13:15 CDT)
- A problem of the forces-tutorial 张宁 (Thu Apr 08 2010 - 07:18:33 CDT)
- Ionize script Tommy Kahn (Wed Apr 07 2010 - 18:35:55 CDT)
- ammonia to methane Dale l. Schruben (Wed Apr 07 2010 - 11:37:10 CDT)
- for your suggestions on Pressure Control of transmembrane protein (GPCR) 庞雪芹 Pang Xueqin (Wed Apr 07 2010 - 03:30:20 CDT)
- how to ensure molecules adopt their favor orientations in SMD simulation crazylyf (Tue Apr 06 2010 - 22:39:11 CDT)
- Postdoc Position available Angela Weiss (Tue Apr 06 2010 - 10:35:04 CDT)
- NAMD/VMD Research Programmer Position available Angela Weiss (Tue Apr 06 2010 - 08:41:21 CDT)
- NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance. Priyan Amaras (Tue Apr 06 2010 - 11:36:25 CDT)
- OPLS mixing rules fett_at_vtr.net (Tue Apr 06 2010 - 09:40:05 CDT)
- problem with NVT using TIP4P jampani srinivas (Tue Apr 06 2010 - 09:26:09 CDT)
- coarse-grained model building Edward Lyman (Mon Apr 05 2010 - 13:12:50 CDT)
- Size of Timestep Aditya Ranganathan (Mon Apr 05 2010 - 06:33:48 CDT)
- NAMD on GPU bahare bamdad (Sun Apr 04 2010 - 09:38:00 CDT)
- Generate missing atoms of a coarse grained structure Mert G黵 (Sun Apr 04 2010 - 04:40:13 CDT)
- Re: Generate missing atoms of a coarse grained structure Peter Freddolino (Sun Apr 04 2010 - 07:55:56 CDT)
- About matdcd Gong Xiaojing (Sat Apr 03 2010 - 21:23:39 CDT)
- NPT simulation schemes Philip Peartree (Fri Apr 02 2010 - 18:04:55 CDT)
- CmiAbort+0x5f Demet Akten (Fri Apr 02 2010 - 05:25:54 CDT)
- Installation problem on Win64 Kwee Hong (Fri Apr 02 2010 - 04:46:28 CDT)
- Periodic cell has become too small for original patch grid! Philip Peartree (Thu Apr 01 2010 - 09:27:16 CDT)
- Re: Periodic cell has become too small for original patch grid! snoze pa (Fri Apr 02 2010 - 13:33:35 CDT)
- Re: Periodic cell has become too small for original patch grid! Philip Peartree (Fri Apr 02 2010 - 15:36:54 CDT)
- Re: Periodic cell has become too small for original patch grid! Jeff Wereszczynski (Fri Apr 02 2010 - 17:05:50 CDT)
- Re: Periodic cell has become too small for original patch grid! Philip Peartree (Fri Apr 02 2010 - 18:06:43 CDT)
- Re: Periodic cell has become too small for original patch grid! Philip Peartree (Tue Apr 06 2010 - 09:52:59 CDT)
- Re: Periodic cell has become too small for original patch grid! snoze pa (Tue Apr 06 2010 - 10:26:09 CDT)
- Re: Periodic cell has become too small for original patch grid! Jeffrey J. Potoff (Tue Apr 06 2010 - 11:18:24 CDT)
- Re: Periodic cell has become too small for original patch grid! Philip Peartree (Tue Apr 06 2010 - 16:19:15 CDT)
- Re: Periodic cell has become too small for original patch grid! Philip Peartree (Tue Apr 06 2010 - 17:56:17 CDT)
- Re: Periodic cell has become too small for original patch grid! Philip Peartree (Fri Apr 02 2010 - 15:36:54 CDT)
- Re: Periodic cell has become too small for original patch grid! snoze pa (Fri Apr 02 2010 - 13:33:35 CDT)
- questions about Constant Pressure Control (variable volume) 娴锋竻 姊 (Thu Apr 01 2010 - 02:18:11 CDT)
- how to set pH crazylyf (Wed Mar 31 2010 - 05:23:58 CDT)
- ABF Simulation Crash from TCL script Patrick Yee (Tue Mar 30 2010 - 17:10:49 CDT)
- Parameter file problem udbhav ojha (Tue Mar 30 2010 - 14:54:23 CDT)
- How to confirm water box is big enough? Jin Liu (Tue Mar 30 2010 - 14:29:15 CDT)
- Problem in energy minimization using Fixatoms or Constraints Ranyere Deyler (Tue Mar 30 2010 - 12:52:09 CDT)
- Re: altering residues in .pdb files muniyamuthu.raviprasad_at_ndsu.edu (Mon Mar 29 2010 - 11:20:08 CDT)
- ABF Displacement Patrick Yee (Sat Mar 27 2010 - 14:42:18 CDT)
- NAMD in TACC lonestar snoze pa (Mon Mar 29 2010 - 10:51:57 CDT)
- psf file error udbhav ojha (Mon Mar 29 2010 - 08:47:36 CDT)
- rigid molecule Mark M Huntress (Sun Mar 28 2010 - 15:34:30 CDT)
- Calculating interaction energy in NAMD DimitryASuplatov (Sun Mar 28 2010 - 04:28:52 CDT)
- Installation of NAMD & charm - fatal errors DDR (Sat Mar 27 2010 - 18:23:25 CDT)
- altering residues in .pdb files Thomas Kahn (Fri Mar 26 2010 - 18:34:53 CDT)
- Atom type for protonated pyridine N Branko (Fri Mar 26 2010 - 02:24:16 CDT)
- NAMD regression test suite? Ronald Salesky (Fri Mar 26 2010 - 11:46:59 CDT)
- colvar error Ferenc 謙v鰏, PhD (Fri Mar 26 2010 - 04:45:27 CDT)
- Atom type for protonated pyridine N Branko (Fri Mar 26 2010 - 02:31:59 CDT)
- NAMD with two GPUs Priyan Amaras (Wed Mar 24 2010 - 21:35:46 CDT)
- NAMD stalled at startup phase 0 when working on a large numbr of processors lucie delemotte (Wed Mar 24 2010 - 13:07:44 CDT)
- Pressure profile calculation problem wenchangyu2006_at_gmail.com (Tue Mar 23 2010 - 15:38:56 CDT)
- STRIDE Structure Assignment and Ramachandran Plot Beta Strand allowed regions Aditya Ranganathan (Tue Mar 23 2010 - 01:36:42 CDT)
- Fwd: STRIDE Question from article "Interpeptide interactions induce helix to strand structural transition in Abeta peptides" Aditya Ranganathan (Tue Mar 23 2010 - 01:34:47 CDT)
- No. of processors in the namd command. Priyan Amaras (Mon Mar 22 2010 - 21:13:55 CDT)
- CHARM parameter file needed for simple organic molecules like Methanol, Formamide, Chloroform, TCE, Toluene MD. ZILLUR RAHMAN (Sun Mar 21 2010 - 22:07:46 CDT)
- request help- namd error abortion stack error Odysseas Axillews (Sun Mar 21 2010 - 20:24:30 CDT)
- Cationic Dummy Atom models Hok-Hei Tam (Sun Mar 21 2010 - 16:31:39 CDT)
- Error: This application has requested the Runtime to terminate it in an unusual way: Please contact the application's support team for more information" after specifying the namd2.exe path Mary Newcomb (Fri Mar 19 2010 - 16:17:27 CDT)
- CMAP dimension limited to 24 dimensions alpertunga da餭an (Thu Mar 18 2010 - 21:42:03 CDT)
- request help- namd error abortion stack error Odysseas Axillews (Thu Mar 18 2010 - 21:21:44 CDT)
- water "flying out of the box" 鏋楁槦闆 (Fri Mar 19 2010 - 06:06:30 CDT)
- Allowed CMAP dimensions in NAMD A D (Thu Mar 18 2010 - 20:11:24 CDT)
- CMAP dimensions in NAMD A D (Thu Mar 18 2010 - 19:07:43 CDT)
- Removing some water from a .dcd file or .coor file Rabab Toubar (Wed Mar 17 2010 - 15:36:14 CDT)
- Hello! Eric Perim (Wed Mar 17 2010 - 07:45:19 CDT)
- Could namd support the ATI-GPU Aurum Bai (Wed Mar 17 2010 - 07:35:34 CDT)
- free energy changes of one subunit Lixia Jin Day (Tue Mar 16 2010 - 13:39:55 CDT)
- Fixatoms minimization problem!! Ranyere Deyler (Tue Mar 16 2010 - 12:45:57 CDT)
- NAMD CUDA bahare bamdad (Tue Mar 16 2010 - 03:23:04 CDT)
- simulating TIP4P with NAMD 2.7b2 Guillaume Stirnemann (Tue Mar 16 2010 - 08:33:48 CDT)
- CUDA error memcpy to exclusions: invalid argument Priyan Amaras (Tue Mar 16 2010 - 09:37:28 CDT)
- (no subject) Daniel Hornburg (Tue Mar 16 2010 - 07:17:02 CDT)
- (no subject) Daniel Hornburg (Tue Mar 16 2010 - 06:19:40 CDT)
- What is the Potential Energy of a Protein in Namdenergy Mert G黵 (Tue Mar 16 2010 - 05:51:39 CDT)
- benchmarking on Cray XT4 Hannes Loeffler (Tue Mar 16 2010 - 05:50:17 CDT)
- How to get information of computing time for LJ calculation and pair list generation Hideya Nakamura (Mon Mar 15 2010 - 12:08:20 CDT)
- patch missing residues BIN ZHANG (Mon Mar 15 2010 - 15:42:49 CDT)
- Problem in minimization, Energy "-1.#IND" and bad dcd file. Ranyere Deyler (Sun Mar 14 2010 - 17:36:19 CDT)
- Problem in minimization, Energy "-1.#IND" and bad dcd file. Ranyere Deyler (Sun Mar 14 2010 - 17:28:58 CDT)
- FATAL ERROR:BAD GLOBAL EXCLUSION COUNT:Please help Werner Crous (Sat Mar 13 2010 - 10:22:47 CST)
- Fwd: help to improve the script to predict mean square displacement jampani srinivas (Fri Mar 12 2010 - 14:51:55 CST)
- segmentation faults with AMBER topology Ibrahim Abou Hamad (Fri Mar 12 2010 - 13:39:59 CST)
- Problem Compiling NAMD (version 2.7b2) Michael Homa (Fri Mar 12 2010 - 12:06:34 CST)
- question about NAMD Pengcheng Yin (Thu Mar 11 2010 - 19:20:21 CST)
- run multiple walkers Naiyin Yu (Thu Mar 11 2010 - 16:15:33 CST)
- Parallel replicas? Jason Russler (Thu Mar 11 2010 - 14:40:41 CST)
- Re: vmd-l: water molecules around proteins Axel Kohlmeyer (Thu Mar 11 2010 - 11:49:50 CST)
- highthroughput NAMD Thomas C. Bishop (Thu Mar 11 2010 - 11:25:35 CST)
- high pressure tillmann.utesch_at_mail.tu-berlin.de (Thu Mar 11 2010 - 06:01:06 CST)
- NAMD CUDA bahare bamdad (Thu Mar 11 2010 - 03:11:21 CST)
- colvars fixes Giacomo Fiorin (Tue Mar 09 2010 - 19:36:08 CST)
- Regenerating a .dcd file Rabab Toubar (Mon Mar 08 2010 - 14:02:15 CST)
- script for lipid density Demet Akten (Mon Mar 08 2010 - 05:34:39 CST)
- Error: atom group "group1" is set, but has no definition Jagan Mohan (Mon Mar 08 2010 - 00:05:08 CST)
- Unstable atoms Ale Gomez (Sat Mar 06 2010 - 23:00:30 CST)
- Water Box Shape Changing during NVT Simulation! Aditya Ranganathan (Fri Mar 05 2010 - 21:59:26 CST)
- Re: Water Box Shape Changing during NVT Simulation! Pablo Campomanes (Fri Mar 05 2010 - 22:50:53 CST)
- Re: Water Box Shape Changing during NVT Simulation! Pablo Campomanes (Sat Mar 06 2010 - 11:50:45 CST)
- Re: Water Box Shape Changing during NVT Simulation! Ronald Salesky (Mon Mar 08 2010 - 11:46:24 CST)
- Re: Water Box Shape Changing during NVT Simulation! Axel Kohlmeyer (Mon Mar 08 2010 - 12:39:16 CST)
- Re: Water Box Shape Changing during NVT Simulation! Jeffrey J. Potoff (Mon Mar 08 2010 - 15:05:10 CST)
- Re: Water Box Shape Changing during NVT Simulation! Axel Kohlmeyer (Tue Mar 09 2010 - 03:38:09 CST)
- Re: Water Box Shape Changing during NVT Simulation! Pablo Campomanes (Sat Mar 06 2010 - 11:50:45 CST)
- Re: Water Box Shape Changing during NVT Simulation! Pablo Campomanes (Fri Mar 05 2010 - 22:50:53 CST)
- RE: RAMD scripts version 4.1 Cojocaru,Vlad (Fri Mar 05 2010 - 13:56:20 CST)
- restarting a simulation ? Reichert, David (Fri Mar 05 2010 - 13:17:14 CST)
- Distance Analysis for Constant Force Pulling for kinesin neck linker Patriche Simona (Fri Mar 05 2010 - 05:44:37 CST)
- tcl forces and tcl 8.5 Vlad Cojocaru (Fri Mar 05 2010 - 03:19:16 CST)
- RAMD scripts version 4.1 Vlad Cojocaru (Fri Mar 05 2010 - 03:08:51 CST)
- Warning: DUPLICATE ANGLE ENTRY FOR CPH1-NR1-CPH2 PREVIOUS VALUES Jignesh Patel (Thu Mar 04 2010 - 11:29:03 CST)
- isopropanol parameters? Jose Borreguero (Thu Mar 04 2010 - 09:24:58 CST)
- segmentation fault with AMBER topology (cvs code 03.03.2010) Cojocaru,Vlad (Thu Mar 04 2010 - 05:28:38 CST)
- update: segmentation faults with AMBER topology (cvscode 03 Mar 2010) Vlad Cojocaru (Thu Mar 04 2010 - 07:43:09 CST)
- Volume of the Solution used for MD simulation Aditya Ranganathan (Thu Mar 04 2010 - 06:32:57 CST)
- Alchemical calculations in CUDA version of NAMD? Lela Vukovic (Wed Mar 03 2010 - 11:33:36 CST)
- job script for Kraken Zumot, Elia Nabil (Wed Mar 03 2010 - 09:14:15 CST)
- error jbp087_at_gmail.com (Tue Mar 02 2010 - 23:48:53 CST)
- creating an output file from a dcd file Rabab Toubar (Tue Mar 02 2010 - 10:34:15 CST)
- RE: cell basis vector restart Mark M Huntress (Tue Mar 02 2010 - 09:51:21 CST)
- wrapping ions Bala subramanian (Tue Mar 02 2010 - 03:05:45 CST)
- cell basis vector restart Mark M Huntress (Mon Mar 01 2010 - 16:47:47 CST)
- electrostatic vs van der waals Mark M Huntress (Mon Mar 01 2010 - 09:57:35 CST)
- NAMD starts AMBER calculation only from 3rd run Q=C1=D2=D8=D1_=FB=C1=CC=C1=C5=D7=C1?= (Mon Mar 01 2010 - 09:38:43 CST)
- Dihedral angle energy in silica block Jindal Shah (Sun Feb 28 2010 - 21:51:15 CST)
- Problem with Targeted molecular dynamics Agostino Bruno (Sun Feb 28 2010 - 10:07:25 CST)
- multiple trajectories Bala subramanian (Fri Feb 26 2010 - 10:50:38 CST)
- Issue attaching to nodes Bryan Holland (Thu Feb 25 2010 - 10:24:13 CST)
- Consecutive Simulations Keith Battle (Thu Feb 25 2010 - 09:25:33 CST)
- Explicit Water System Condensing Keith Battle (Thu Feb 25 2010 - 09:17:53 CST)
- anomalous behaviour of ASPP and GLUP during MD run Andreini Matteo (Thu Feb 25 2010 - 08:24:45 CST)
- anomalous behaviour of ASPP and GLUP during MD run Andreini Matteo (Thu Feb 25 2010 - 02:31:45 CST)
- psfgen errors tpreeprem3_at_gatech.edu (Thu Feb 25 2010 - 00:37:46 CST)
- Problem on periodic boundary condition Indrajit Deb (Wed Feb 24 2010 - 07:25:28 CST)
- Fwd: Coarse Graining Problem Aditya Ranganathan (Wed Feb 24 2010 - 05:59:51 CST)
- psfgen error Syed Kashif Zafar (Tue Feb 23 2010 - 22:44:21 CST)
- update: segmentation faults with AMBER topology and RAMD tcl scripts Vlad Cojocaru (Tue Feb 23 2010 - 08:31:27 CST)
- running tcl scripting ipsita basu (Tue Feb 23 2010 - 04:26:05 CST)
- about NAMD nonbonded routines (Tue Feb 23 2010 - 02:55:29 CST)
- atom charges for protonated carboxyl termini Zumot, Elia Nabil (Mon Feb 22 2010 - 14:48:59 CST)
- sucrose top/par Ziemys, Arturas (Mon Feb 22 2010 - 13:41:14 CST)
- version of tcl in binary builds Francesco Pietra (Mon Feb 22 2010 - 10:53:08 CST)
- Re: version of tcl in binary builds Francesco Pietra (Mon Feb 22 2010 - 11:38:22 CST)
- Re: version of tcl in binary builds Giacomo Fiorin (Tue Feb 23 2010 - 01:52:23 CST)
- RAMD scripts and tcl version Vlad Cojocaru (Tue Feb 23 2010 - 02:37:25 CST)
- Re: RAMD scripts and tcl version Balazs Jojart (Tue Feb 23 2010 - 03:33:24 CST)
- Re: RAMD scripts and tcl version Vlad Cojocaru (Tue Feb 23 2010 - 03:45:44 CST)
- Re: RAMD scripts and tcl version Balazs Jojart (Tue Feb 23 2010 - 04:27:03 CST)
- Re: RAMD scripts and tcl version George Madalin Giambasu (Tue Feb 23 2010 - 09:52:30 CST)
- Re: version of tcl in binary builds Giacomo Fiorin (Tue Feb 23 2010 - 01:52:23 CST)
- Re: version of tcl in binary builds Francesco Pietra (Mon Feb 22 2010 - 11:38:22 CST)
- NAMD running error bahare bamdad (Mon Feb 22 2010 - 09:38:37 CST)
- Re: About the err of "distanceZ"! Jian Liu (Mon Feb 22 2010 - 07:57:37 CST)
- About the err of "distanceZ"! Aurum Bai (Mon Feb 22 2010 - 03:28:31 CST)
- The problem of annihilating the solute in the aqueous Aurum Bai (Mon Feb 22 2010 - 00:47:45 CST)
- namd 2.7b2 or later - amberff/prmtop causes segfault during startup phase George Madalin Giambasu (Sun Feb 21 2010 - 18:01:43 CST)
- Re: namd 2.7b2 or later - amberff/prmtop causes segfault during startup phase Vlad Cojocaru (Mon Feb 22 2010 - 01:31:07 CST)
- Re: namd 2.7b2 or later - amberff/prmtop causes segfault during startup phase Philipp M. (Mon Feb 22 2010 - 05:23:20 CST)
- Re: namd 2.7b2 or later - amberff/prmtop causes segfault during startup phase Nicolas Sapay (Wed Feb 24 2010 - 06:49:47 CST)
- Re: namd 2.7b2 or later - amberff/prmtop causes segfault during startup phase Vlad Cojocaru (Wed Mar 31 2010 - 07:02:07 CDT)
- About the err of "Constraint failure" Aurum Bai (Sun Feb 21 2010 - 03:13:25 CST)
- About "equilibrate.conf' of FEP tutorial Aurum Bai (Sat Feb 20 2010 - 07:15:58 CST)
- Lipid and protein interactions Marie N (Fri Feb 19 2010 - 17:25:29 CST)
- Parameters/topology entries for non-standard nucleotides Thomas Kahn (Fri Feb 19 2010 - 16:14:33 CST)
- Is two colvars file output possible during single simulation (ABF/2.7b) Branko (Fri Feb 19 2010 - 10:51:10 CST)
- Re: Is two colvars file output possible during single simulation (ABF/2.7b) Giacomo Fiorin (Fri Feb 19 2010 - 18:45:48 CST)
- Re: Is two colvars file output possible during single simulation (ABF/2.7b) Giacomo Fiorin (Fri Feb 19 2010 - 18:44:21 CST)
- Re: Is two colvars file output possible during single simulation (ABF/2.7b) Jerome Henin (Sat Feb 20 2010 - 10:05:26 CST)
- Drude polarizability parameters Igor Petrik (Fri Feb 19 2010 - 06:09:57 CST)
- reading prameter file ipsita basu (Fri Feb 19 2010 - 03:58:16 CST)
- Re: namd trouble Joshua Adelman (Thu Feb 18 2010 - 07:08:46 CST)
- Re: tutorial-l: Nanotubes tutorial - coorList(577) no such element Jian Liu (Thu Feb 18 2010 - 04:09:25 CST)
- tutorial-l: Nanotubes tutorial - coorList(577) no such element Drew buschhorn (Thu Feb 18 2010 - 00:45:24 CST)
- trouble in dynamics Sweta Ramachandran (Wed Feb 17 2010 - 23:18:48 CST)
- calculation van der Waals force field parameters Mikhail Suyetin (Wed Feb 17 2010 - 13:27:50 CST)
- Fwd: electric field unit conversion Mikhail Suyetin (Wed Feb 17 2010 - 11:25:21 CST)
- coordinates and cells Andreas F鰎ster (Wed Feb 17 2010 - 11:00:54 CST)
- Windows binaries of NAMD 2.72b supports CUDA? Mohd Farid Ismail (Wed Feb 17 2010 - 09:52:16 CST)
- electric field unit conversion Ziemys, Arturas (Wed Feb 17 2010 - 09:45:46 CST)
- Problem of compiling Version Nightly Build (2010-02-16) Shulin Zhuang (Tue Feb 16 2010 - 18:28:30 CST)
- bonded FAD topology file Demet Akten (Tue Feb 16 2010 - 07:23:13 CST)
- error in scripting ipsita basu (Tue Feb 16 2010 - 05:26:07 CST)
- installation of namd ipsita basu (Tue Feb 16 2010 - 04:00:23 CST)
- Large protein translation during minimization Rachel Ruskin (Mon Feb 15 2010 - 16:24:20 CST)
- Can't find C-PDB bond parameters Francesco Pietra (Mon Feb 15 2010 - 03:46:29 CST)
- CAN'T FIND BOND PARAMETERS FOR BOND C - CPB IN PARAMETER FILES Francesco Pietra (Sun Feb 14 2010 - 10:26:01 CST)
- Generating binvelocities, bincoordinates, and extendedSystem files (AMBER) Johann Morr (Sat Feb 13 2010 - 23:01:32 CST)
- installation of namd in parallel mode ipsita basu (Sat Feb 13 2010 - 01:40:28 CST)
- Job Offer Jim Phillips (Fri Feb 12 2010 - 20:21:33 CST)
- Topology files Thomas Kahn (Fri Feb 12 2010 - 17:13:48 CST)
- apologize for the typo Bennion, Brian (Fri Feb 12 2010 - 13:13:30 CST)
- RE: Questions about lattice information in NAMD2.7b2 Bennion, Brian (Fri Feb 12 2010 - 12:42:45 CST)
- water-molecules/coordenates jose correa (Thu Feb 11 2010 - 13:19:01 CST)
- The accuracy of FEP calculation chengh_at_ringo.chem.pitt.edu (Thu Feb 11 2010 - 09:58:20 CST)
- SMD normal vector snoze pa (Wed Feb 10 2010 - 17:48:00 CST)
- Crashing ibverbs binary of NAMD_2.7b2 Philipp M. (Wed Feb 10 2010 - 10:58:03 CST)
- Pressure Questions Rick Calloway (Wed Feb 10 2010 - 08:16:50 CST)
- Fatal Error by charmc - Compiling NAMD_2.7b2_Source philipp.coloc_at_gmx.de (Wed Feb 10 2010 - 04:59:30 CST)
- Re: Problem compiling namd philipp.coloc_at_gmx.de (Wed Feb 10 2010 - 03:53:21 CST)
- Bringing UMA-type mainboards to TESLA Francesco Pietra (Tue Feb 09 2010 - 15:59:16 CST)
- SMD and langevin dynamics snoze pa (Sat Feb 06 2010 - 19:00:15 CST)
- FW: Parallel Simulations #SHEPHERDSON IGNATIUS MARK# (Sat Feb 06 2010 - 09:56:55 CST)
- Re: apoa1 bencmark for 2.7 MPI compiled Branko (Fri Feb 05 2010 - 16:02:29 CST)
- apoa1 bencmark for 2.7 MPI compiled Branko (Fri Feb 05 2010 - 13:00:21 CST)
- Simulations with NAMD Santanu Chatterjee (Fri Feb 05 2010 - 10:37:44 CST)
- Changing the Potential Energy Function Hok-Hei Tam (Thu Feb 04 2010 - 22:08:41 CST)
- minimization gradient question Goutham (Thu Feb 04 2010 - 19:20:32 CST)
- NAMD on Ranger neville forlemu (Wed Feb 03 2010 - 17:57:14 CST)
- Definitions of certain routine names in source Bennion, Brian (Wed Feb 03 2010 - 17:01:52 CST)
- Plumed and NAMD neville forlemu (Wed Feb 03 2010 - 12:45:37 CST)
- StepsPerCycle Myunggi Yi (Wed Feb 03 2010 - 09:33:08 CST)
- psfgen error Anna Dejardin (Wed Feb 03 2010 - 07:35:54 CST)
- saving psf ipsita basu (Tue Feb 02 2010 - 00:53:38 CST)
- Questions about thermodynamic integration in NAMD 2.7b2 Jeffrey J. Potoff (Mon Feb 01 2010 - 14:27:22 CST)
- IMD VMD NAMD adding frames Scooter Willis (Mon Feb 01 2010 - 13:35:37 CST)
- unsubscribe prasun kumar (Mon Feb 01 2010 - 12:00:49 CST)
- firsttimestep in NAMD snoze pa (Mon Feb 01 2010 - 11:31:42 CST)
- namd job crashed Bala subramanian (Mon Feb 01 2010 - 10:55:23 CST)
- Re: dcd] Branko (Mon Feb 01 2010 - 10:59:57 CST)
- water structure ipsita basu (Mon Feb 01 2010 - 05:40:54 CST)
- dcd ipsita basu (Mon Feb 01 2010 - 03:27:17 CST)
- Info: Attempting to read FFTW data from FFTW_NAMD_2.7b1_Linux-Itanium-MPI-Altix.txt Bala subramanian (Mon Feb 01 2010 - 03:12:04 CST)
- analysis of dcd ipsita basu (Sun Jan 31 2010 - 22:58:41 CST)
- Parameter File Scooter Willis (Sun Jan 31 2010 - 21:19:32 CST)
- Tcl Forces error Brittany Morgan (Thu Jan 28 2010 - 19:39:16 CST)
- ERROR: Constraint failure in RATTLE algorithm for atom snoze pa (Sun Jan 31 2010 - 12:41:16 CST)
- langevinTemp and system temperature snoze pa (Fri Jan 29 2010 - 09:30:07 CST)
- Tcl Forces error Brittany Morgan (Thu Jan 28 2010 - 20:00:10 CST)
- implicit solvent with iapbs BIN ZHANG (Thu Jan 28 2010 - 01:33:38 CST)
- Magnesium Ions Placement Thomas Kahn (Wed Jan 27 2010 - 19:18:02 CST)
- how to get .coor .vel and .xsc for a .dcd file 庞雪芹 Pang Xueqin (Wed Jan 27 2010 - 08:42:44 CST)
- velocities from a DCD file Raul Araya (Wed Jan 27 2010 - 08:01:00 CST)
- the maximum numbers of atoms in NAMD? uu zhu (Wed Jan 27 2010 - 06:19:58 CST)
- problem whit comand "COM" Leonardo Herrera (Tue Jan 26 2010 - 20:21:19 CST)
- Announcement: TCBG workshop at Pittsburgh Supercomputing Center May 10-14, 2010 TCBG Workshops (Tue Jan 26 2010 - 13:41:36 CST)
- PLUMED tutorial announcement Massimiliano Bonomi (Tue Jan 26 2010 - 02:38:12 CST)
- Re: colvar module question BIN ZHANG (Tue Jan 26 2010 - 01:32:50 CST)
- Re: colvar module question Giacomo Fiorin (Tue Jan 26 2010 - 08:18:15 CST)
- ABF question Austin B. Yongye (Tue Jan 26 2010 - 17:07:05 CST)
- Re: ABF question J閞鬽e H閚in (Wed Jan 27 2010 - 04:18:13 CST)
- Solute moves outside of solvent box Austin B. Yongye (Thu Jan 28 2010 - 12:28:37 CST)
- Re: Solute moves outside of solvent box Jeffrey J. Potoff (Thu Jan 28 2010 - 12:55:08 CST)
- Re: Solute moves outside of solvent box Jeffrey J. Potoff (Tue Feb 02 2010 - 10:26:09 CST)
- Re: colvar module question BIN ZHANG (Tue Jan 26 2010 - 23:54:19 CST)
- ABF question Austin B. Yongye (Tue Jan 26 2010 - 17:07:05 CST)
- Re: colvar module question Giacomo Fiorin (Tue Jan 26 2010 - 08:18:15 CST)
- colvar module question BIN ZHANG (Mon Jan 25 2010 - 15:09:24 CST)
- problems with NAMD plot and .DCD file parsons_at_umbi.umd.edu (Mon Jan 25 2010 - 11:35:13 CST)
- reading dcd file ipsita basu (Mon Jan 25 2010 - 03:20:39 CST)
- scripting problem ipsita basu (Mon Jan 25 2010 - 00:15:51 CST)
- NAMD on AMD Istanbul versus intel Nehalem with infiniband Vlad Cojocaru (Fri Jan 22 2010 - 07:56:11 CST)
- Colvar on 2.7b2 win vs Linux MPI instalation Branko (Fri Jan 22 2010 - 14:28:30 CST)
- NAMD on AMD Istanbul versus intel Nehalem with infiniband Vlad Cojocaru (Fri Jan 22 2010 - 08:47:58 CST)
- scripting error ipsita basu (Thu Jan 21 2010 - 23:36:02 CST)
- NAMD on linux Lixia Jin Day (Thu Jan 21 2010 - 10:55:57 CST)
- protein unfolding jose correa (Thu Jan 21 2010 - 08:57:06 CST)
- Erratic behavior of TclBC in parallel J閞鬽e H閚in (Thu Jan 21 2010 - 08:38:35 CST)
- protein unfolding jose correa (Thu Jan 21 2010 - 07:29:13 CST)
- simulation error ipsita basu (Thu Jan 21 2010 - 00:13:46 CST)
- Re: Fwd: suitable motherboards for both graphical visualization and NAMD-CUDA computation? Biff Forbush (Wed Jan 20 2010 - 20:32:06 CST)
- suitable motherboards for both graphical visualization and NAMD-CUDA computation? Lela Vukovic (Wed Jan 20 2010 - 14:56:45 CST)
- Re: Reply:Re: How to convert the GROMOS parameter unit into charmm22 style J閞鬽e H閚in (Wed Jan 20 2010 - 07:05:37 CST)
- NAMD ibverbs not working on new cluster Jesper Soerensen (Wed Jan 20 2010 - 03:11:35 CST)
- How to convert the GROMOS parameter unit into charmm22 style 王棽 (Wed Jan 20 2010 - 00:24:27 CST)
- Regarding Periodic Boundary Jagan Mohan (Tue Jan 19 2010 - 23:45:44 CST)
- Simulation question snoze pa (Tue Jan 19 2010 - 11:26:06 CST)
- (Infiniband-related?) NAMD 2.7b2 (ibverbs x86_64) runtime error during a MD run Pietro Amodeo (Tue Jan 19 2010 - 05:03:21 CST)
- starting namd ipsita basu (Tue Jan 19 2010 - 04:50:41 CST)
- units of position coordinate velocity coordinate and timestep in .dcd and .veldcd file sudipta (Tue Jan 19 2010 - 04:57:58 CST)
- Center of Mass Harmonic Potentials Keith Battle (Mon Jan 18 2010 - 18:59:25 CST)
- convergence of ABF Jorgen Simonsen (Sun Jan 17 2010 - 20:42:30 CST)
- harmonic constraint when equilibrate the system Naiyin Yu (Sun Jan 17 2010 - 00:32:57 CST)
- error of the energy output when equilibration xyhu1127 (Thu Jan 14 2010 - 19:17:18 CST)
- Excluding interactions? Charles Zhao (Thu Jan 14 2010 - 19:46:57 CST)
- Number of MC steps in ABF integrate gives entirely diferent surfaces Branko (Thu Jan 14 2010 - 04:42:14 CST)
- Strange behavior of NAMD 2.7b1 Alexandre Suman de Araujo (Wed Jan 13 2010 - 12:25:49 CST)
- starting a job ipsita basu (Wed Jan 13 2010 - 04:39:34 CST)
- Problem compiling namd Philipp M. (Mon Jan 11 2010 - 07:19:43 CST)
- NAMD-CUDA benchmarks, dual GTX295, dual Xeon Nehalem system Biff Forbush (Sat Jan 09 2010 - 22:16:41 CST)
- CPU usage when exec function is used daniel aguayo (Fri Jan 08 2010 - 14:48:42 CST)
- release of RAMD scripts for NAMD 2.6 and 2.7 Vlad Cojocaru (Fri Jan 08 2010 - 05:52:52 CST)
- colvarsInput filename problem BIN ZHANG (Wed Jan 06 2010 - 19:51:43 CST)
- CUDA-NAMD hangs -- check the Northbridge temp! Biff Forbush (Tue Jan 05 2010 - 21:51:51 CST)
- ABF questions Austin B. Yongye (Tue Jan 05 2010 - 10:27:47 CST)
- NAMD-FEP tutorial-alchemify problem Lisa Brown (Tue Jan 05 2010 - 09:21:41 CST)
- run NAMD_2.7B2 hamze rahimi (Sat Jan 02 2010 - 00:58:42 CST)
- CMAP in NAMD output Yang MIngjun (Mon Jan 04 2010 - 01:50:47 CST)
- Re: Definition of two colvars for ABF Branko (Fri Jan 01 2010 - 09:58:30 CST)
- Definition of two colvars for ABF Branko (Wed Dec 30 2009 - 14:41:20 CST)
- How to get the coordinate of a certain atom with tcl in the config file? 王棽 (Mon Dec 28 2009 - 04:14:23 CST)
- useconstantarea Francesco Pietra (Mon Dec 28 2009 - 03:35:48 CST)
- subscribe 王棽 (Mon Dec 28 2009 - 02:56:07 CST)
- dmpc bilayer Syed Kashif Zafar (Sun Dec 27 2009 - 15:10:26 CST)
- CG equilibration recurring crashes Francesco Pietra (Sun Dec 27 2009 - 08:47:12 CST)
- How to read trajectory within CHARMM generated by NAMD Yang MIngjun (Sun Dec 27 2009 - 01:36:53 CST)
- Re: How to read trajectory within CHARMM generated by NAMD Axel Kohlmeyer (Sun Dec 27 2009 - 02:36:30 CST)
- Fw: Re: Re: How to read trajectory within CHARMM generated by NAMD Yang MIngjun (Sun Dec 27 2009 - 20:06:44 CST)
- Re: Fw: Re: Re: How to read trajectory within CHARMM generated by NAMD Axel Kohlmeyer (Mon Dec 28 2009 - 02:46:34 CST)
- RE: Fw: Re: Re: How to read trajectory within CHARMM generated by NAMD David A. Horita (Mon Dec 28 2009 - 08:33:31 CST)
- Re: RE: Fw: Re: Re: How to read trajectory within CHARMM generated by NAMD Yang MIngjun (Thu Dec 31 2009 - 04:18:13 CST)
- Re: How to read trajectory within CHARMM generated by NAMD Dimitar V Pachov (Mon Dec 28 2009 - 11:52:59 CST)
- Fw: Re: Re: How to read trajectory within CHARMM generated by NAMD Yang MIngjun (Sun Dec 27 2009 - 20:06:44 CST)
- Re: How to read trajectory within CHARMM generated by NAMD gaillard_at_chimie.u-strasbg.fr (Mon Dec 28 2009 - 08:44:16 CST)
- Re: How to read trajectory within CHARMM generated by NAMD Axel Kohlmeyer (Sun Dec 27 2009 - 02:36:30 CST)
- Periodic cell has become too small Francesco Pietra (Thu Dec 24 2009 - 03:35:52 CST)
- problems compiling charm and NAMD on intel cluster using MPI over ethernet Corenflos, Steven (Wed Dec 23 2009 - 23:48:28 CST)
- hi Segun Jung (Wed Dec 23 2009 - 00:59:44 CST)
- How to acetylate at the N terminus and amidate at the C terminus ydhuang2727 (Tue Dec 22 2009 - 21:10:45 CST)
- NAMD 2.7b2 new features Myunggi Yi (Tue Dec 22 2009 - 14:16:49 CST)
- SelectConstraints problem priyodorshi satpati (Tue Dec 22 2009 - 08:43:15 CST)
- namd: Running namd on a node on cluster Rabab Toubar (Tue Dec 22 2009 - 06:44:21 CST)
- reassignFreq script Francesco Pietra (Mon Dec 21 2009 - 11:33:33 CST)
- NAMD 2.7b2 with CUDA and infinband Jyh-Shyong (Sun Dec 20 2009 - 23:03:37 CST)
- how to output the velocity for one selected atom in the system chengh_at_ringo.chem.pitt.edu (Sat Dec 19 2009 - 10:49:54 CST)
- Does amber force field in NAMD 2.7b2 work stable? yudaqi (Fri Dec 18 2009 - 21:02:50 CST)
- How to prevent cg water entering a membrane Francesco Pietra (Fri Dec 18 2009 - 16:49:55 CST)
- error in install NAMD_2.7b2_Linux-x86_64-CUDA hamze rahimi (Fri Dec 18 2009 - 06:59:43 CST)
- ABF - sequence of MD runs Krishnan, Marimuthu (Thu Dec 17 2009 - 21:55:59 CST)
- defined path for NAMD2 hamze rahimi (Thu Dec 17 2009 - 06:45:56 CST)
- NAMD on current CPUs J閞鬽e H閚in (Thu Dec 17 2009 - 08:34:22 CST)
- Problem generating psf file in psfgen Ranyere Deyler (Wed Dec 16 2009 - 23:20:57 CST)
- How to obtain the system force on a fixed atom chengh_at_ringo.chem.pitt.edu (Wed Dec 16 2009 - 08:40:37 CST)
- Re: How to obtain the system force on a fixed atom Roman Petrenko (Wed Dec 16 2009 - 09:34:36 CST)
- Re: How to obtain the system force on a fixed atom J閞鬽e H閚in (Wed Dec 16 2009 - 10:38:55 CST)
- documentation on parallel implementation Paul Rigor (uci) (Wed Dec 16 2009 - 08:33:03 CST)
- force constant in abf configuration file Madhurima Jana (Tue Dec 15 2009 - 23:01:02 CST)
- conf file for coarse grained simulation Francesco Pietra (Sun Dec 13 2009 - 15:08:59 CST)
- Fwd: conf file for coarse grained simulation Francesco Pietra (Mon Dec 14 2009 - 02:19:52 CST)
- Re: Fwd: conf file for coarse grained simulation Axel Kohlmeyer (Tue Dec 15 2009 - 02:17:45 CST)
- Re: Fwd: conf file for coarse grained simulation Francesco Pietra (Tue Dec 15 2009 - 02:40:55 CST)
- Re: vmd-l: Re: Fwd: conf file for coarse grained simulation Peter Freddolino (Tue Dec 15 2009 - 10:45:27 CST)
- Re: Fwd: conf file for coarse grained simulation Francesco Pietra (Tue Dec 15 2009 - 10:01:30 CST)
- Re: vmd-l: Re: Fwd: conf file for coarse grained simulation Axel Kohlmeyer (Tue Dec 15 2009 - 11:16:14 CST)
- Re: vmd-l: Re: Fwd: conf file for coarse grained simulation Francesco Pietra (Wed Dec 16 2009 - 02:13:59 CST)
- Fwd: vmd-l: Re: Fwd: conf file for coarse grained simulation Francesco Pietra (Wed Dec 16 2009 - 03:01:27 CST)
- Re: Fwd: vmd-l: Re: Fwd: conf file for coarse grained simulation Peter Freddolino (Wed Dec 16 2009 - 15:46:39 CST)
- Re: Fwd: vmd-l: Re: Fwd: conf file for coarse grained simulation Peter Freddolino (Wed Dec 16 2009 - 18:49:13 CST)
- Re: Fwd: conf file for coarse grained simulation Axel Kohlmeyer (Tue Dec 15 2009 - 02:17:45 CST)
- Re: conf file for coarse grained simulation Peter Freddolino (Mon Dec 14 2009 - 19:15:57 CST)
- Fwd: conf file for coarse grained simulation Francesco Pietra (Mon Dec 14 2009 - 02:19:52 CST)
- reference of ewald method Hidekazu WATANABE (Sun Dec 13 2009 - 06:02:27 CST)
- ABF error calculation Valeria M. (Fri Dec 11 2009 - 09:57:25 CST)
- Re: vmd-l: namd CG minimization error: unable to find angle parameters for nxg nxx nxg Francesco Pietra (Fri Dec 11 2009 - 09:52:43 CST)
- namd CG minimization error: unable to find angle parameters for nxg nxx nxg Francesco Pietra (Thu Dec 10 2009 - 10:27:13 CST)
- Re: Request for information regarding ABF in NAMD. J閞鬽e H閚in (Fri Dec 11 2009 - 08:51:35 CST)
- MD papers Corey Fugate (Thu Dec 10 2009 - 15:25:31 CST)
- unsubscribe Rajiv Abhyankar (Thu Dec 10 2009 - 00:35:13 CST)
- About "Visualization and Analysis of CPMD data with VMD" tutorial Aurum Bai (Wed Dec 09 2009 - 21:43:44 CST)
- "-Wno-long-double" linking error David Tanner (Wed Dec 09 2009 - 14:24:14 CST)
- Fwd: vmd-l: Restraints on coarse grained model Francesco Pietra (Wed Dec 09 2009 - 03:07:36 CST)
- Free Energy Calculation of a protein Mert G黵 (Wed Dec 09 2009 - 14:19:42 CST)
- Re: Free Energy Calculation of a protein Pu Tian (Wed Dec 09 2009 - 15:53:35 CST)
- Re: Free Energy Calculation of a protein Mert G黵 (Thu Dec 10 2009 - 03:14:28 CST)
- Re: Free Energy Calculation of a protein Mert G黵 (Thu Dec 10 2009 - 03:48:22 CST)
- Re: Free Energy Calculation of a protein S閎astien L間ar (Thu Dec 10 2009 - 14:19:01 CST)
- Re: Free Energy Calculation of a protein Mert G黵 (Tue Dec 15 2009 - 02:48:31 CST)
- Re: Free Energy Calculation of a protein Axel Kohlmeyer (Tue Dec 15 2009 - 03:40:07 CST)
- Re: Free Energy Calculation of a protein Mert G黵 (Wed Dec 16 2009 - 08:41:50 CST)
- Re: Free Energy Calculation of a protein Mert G黵 (Thu Dec 10 2009 - 03:14:28 CST)
- Re: Free Energy Calculation of a protein Pu Tian (Wed Dec 09 2009 - 15:53:35 CST)
- gradual increase in the temperature after minimization gurunath katagi (Wed Dec 09 2009 - 12:21:34 CST)
- 'dSmooth' no longer in the ABF procedure? Hugh Martin (Wed Dec 09 2009 - 09:08:30 CST)
- Re: What is LINK Patch? Jian Liu (Mon Dec 07 2009 - 23:42:48 CST)
- PSFGEN Hyun Chul Lee (Mon Dec 07 2009 - 15:36:44 CST)
- What is LINK Patch? Myunggi Yi (Mon Dec 07 2009 - 13:47:20 CST)
- Running a simulation with coarse-grained protein in membrane Francesco Pietra (Mon Dec 07 2009 - 12:36:16 CST)
- About the Nucleic Acid parameter and protein parameters Aurum Bai (Sun Dec 06 2009 - 05:59:36 CST)
- Could namd realizes the QM-MM method? Aurum Bai (Fri Dec 04 2009 - 01:31:32 CST)
- (no subject) Jim Parker (Thu Dec 03 2009 - 21:48:51 CST)
- pressure profile Ziemys, Arturas (Thu Dec 03 2009 - 16:22:41 CST)
- constraints doty alexiou (Thu Dec 03 2009 - 15:06:49 CST)
- (no subject) Jim Parker (Thu Dec 03 2009 - 07:13:58 CST)
- [Solved] Re: TclForces and getstep Jim Parker (Thu Dec 03 2009 - 07:10:12 CST)
- which portions of NAMD are CUDA accelerated? Paul Rigor (uci) (Wed Dec 02 2009 - 20:00:27 CST)
- Re: which portions of NAMD are CUDA accelerated? Axel Kohlmeyer (Wed Dec 02 2009 - 22:09:38 CST)
- Re: which portions of NAMD are CUDA accelerated? Biff Forbush (Thu Dec 03 2009 - 20:29:16 CST)
- Re: which portions of NAMD are CUDA accelerated? Paul Rigor (uci-ics) (Fri Dec 04 2009 - 21:59:12 CST)
- Re: which portions of NAMD are CUDA accelerated? Wenyu Zhong (Wed Dec 09 2009 - 00:29:25 CST)
- RE: which portions of NAMD are CUDA accelerated? Tian, Pu (NIH/NIDDK) [C] (Wed Dec 09 2009 - 08:08:28 CST)
- Re: which portions of NAMD are CUDA accelerated? Wenyu Zhong (Wed Dec 09 2009 - 23:45:54 CST)
- Re: which portions of NAMD are CUDA accelerated? Paul Rigor (uci) (Wed Dec 16 2009 - 03:57:36 CST)
- Re: which portions of NAMD are CUDA accelerated? Biff Forbush (Thu Dec 03 2009 - 20:29:16 CST)
- Re: which portions of NAMD are CUDA accelerated? Axel Kohlmeyer (Wed Dec 02 2009 - 22:09:38 CST)
- Incorrect Atom Count Charles Zhao (Wed Dec 02 2009 - 15:53:51 CST)
- TclForces and getstep Jim Parker (Wed Dec 02 2009 - 00:33:37 CST)
- How are the SMD atoms connected to the center of mass Mert G黵 (Tue Dec 01 2009 - 07:31:47 CST)
- Small discrepancy in Kinetic Energy after restarting the simulation Mert G黵 (Tue Dec 01 2009 - 03:10:30 CST)
- RMSD for individual residue gurunath katagi (Mon Nov 30 2009 - 11:55:34 CST)
- rigidTolerance question snoze pa (Sun Nov 29 2009 - 19:06:15 CST)
- psfgen fails to set coords for all atoms Blake Mertz (Fri Nov 27 2009 - 15:06:47 CST)
- adding constraints doty alexiou (Thu Nov 26 2009 - 15:40:09 CST)
- Re: FreeEnergy: Not enough steps to complete pfm & mcti blocks priyodorshi satpati (Thu Nov 26 2009 - 03:19:48 CST)
- stopping protein rotation with colvars David A. Horita (Wed Nov 25 2009 - 13:55:56 CST)
- FreeEnergy: Not enough steps to complete pfm & mcti blocks priyodorshi satpati (Wed Nov 25 2009 - 09:31:15 CST)
- Re: Multiplicity of Parameters for dihedral bond exceeded Ajasja Ljubeti膷 (Wed Nov 25 2009 - 03:42:35 CST)
- Re: Re: vmd-l: problems with CG protein-lipidbilayer-water system Francesco Pietra (Sun Nov 22 2009 - 15:32:18 CST)
- problems with CG protein-lipidbilayer-water system Francesco Pietra (Sat Nov 21 2009 - 12:00:54 CST)
- maximum number of devices supported per namd process Paul Rigor (uci) (Mon Nov 23 2009 - 21:45:08 CST)
- Difference between Linux-x86_64-TCP and Linux-x86_64 Lee Wei Yang (Mon Nov 23 2009 - 16:33:12 CST)
- GeForce vs. Tesla Tian, Pu (NIH/NIDDK) [C] (Mon Nov 23 2009 - 10:01:13 CST)
- Stray PME grid charges detected: colvars Vamshi Gangupomu (Mon Nov 23 2009 - 09:44:39 CST)
- Signal: segmentation violation gurunath katagi (Fri Nov 20 2009 - 15:20:16 CST)
- help with running namd-cuda for the tutorials Paul Rigor (uci) (Fri Nov 20 2009 - 10:24:20 CST)
- Finer details of an ABF/colvar simulation Hugh Martin (Fri Nov 20 2009 - 09:10:08 CST)
- Fwd: error in scripting ipsita basu (Thu Nov 19 2009 - 23:33:25 CST)
- simulation configuration file not accesible - other reasons CHINDEA Vlad (Thu Nov 19 2009 - 16:46:23 CST)
- Generating psf for NPC1 Joshua Lioi (Thu Nov 19 2009 - 10:45:07 CST)
- Fwd: error in scripting ipsita basu (Thu Nov 19 2009 - 03:28:03 CST)
- iAPBS 1.0.0 released Robert Konecny (Wed Nov 18 2009 - 22:55:24 CST)
- Unimportant bug in output xst file writing process A D (Wed Nov 18 2009 - 18:18:37 CST)
- Simultaneous water and protein minimization jkmann_at_buffalo.edu (Wed Nov 18 2009 - 15:58:22 CST)
- calculation of periodic box Michael Thomas (Tue Nov 17 2009 - 22:16:05 CST)
- NAMD file limitation in Win32 - windows XP Richard Owczarzy (Tue Nov 17 2009 - 11:51:52 CST)
- Error: failed on end of segment with RBCG Francesco Pietra (Sun Nov 15 2009 - 03:18:57 CST)
- error in scripting ipsita basu (Mon Nov 16 2009 - 00:47:57 CST)
- Segmentation Violation: colvars Vamshi Gangupomu (Sun Nov 15 2009 - 05:32:42 CST)
- The MD of aquaporin in NAMD Ning Zhang (Sat Nov 14 2009 - 01:31:31 CST)
- NAMD 2.7b2 Released Jim Phillips (Fri Nov 13 2009 - 17:03:52 CST)
- CUDA-accelarated NAMD does not use the video card? Lee Wei Yang (Fri Nov 13 2009 - 16:55:15 CST)
- Re: Will MPICH2 work for NAMD? and the best way to build/compile NAMD to exploit my hardware resource? Bjoern Olausson (Fri Nov 13 2009 - 03:39:32 CST)
- Re: Formating of logfile Bjoern Olausson (Fri Nov 13 2009 - 02:55:02 CST)
- NAMD 2.7b1 Performance loss with CUDA 2.3 Joakim Swedberg (Thu Nov 12 2009 - 20:07:23 CST)
- Memory keep increasing. Ming (Thu Nov 12 2009 - 06:14:05 CST)
- Re: Memory keep increasing. Axel Kohlmeyer (Thu Nov 12 2009 - 07:36:00 CST)
- NAMD bonded energy function BIN ZHANG (Thu Nov 12 2009 - 01:23:16 CST)
- 32 bit + 64 bit mixed architecture problem Yogesh Aher (Wed Nov 11 2009 - 10:17:27 CST)
- Formating of logfile Bjoern Olausson (Wed Nov 11 2009 - 07:07:34 CST)
- Formating of logfile Bjoern Olausson (Wed Nov 11 2009 - 06:58:44 CST)
- RBCG tutorial Francesco Pietra (Wed Nov 11 2009 - 03:08:03 CST)
- FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT gurunath katagi (Tue Nov 10 2009 - 12:08:13 CST)
- Retrieving standard deviation values while using collective variables (ABF) Hugh Martin (Tue Nov 10 2009 - 05:55:53 CST)
- Re: Retrieving standard deviation values while using collective variables (ABF) Jerome Henin (Tue Nov 10 2009 - 10:52:34 CST)
- Re: Retrieving standard deviation values while using collective variables (ABF) Hugh Martin (Thu Nov 26 2009 - 07:38:13 CST)
- Re: Retrieving standard deviation values while using collective variables (ABF) Jerome Henin (Thu Nov 26 2009 - 09:04:19 CST)
- Re: Retrieving standard deviation values while using collective variables (ABF) Hugh Martin (Thu Nov 26 2009 - 09:30:21 CST)
- Is it possible to run replica exchange simulation on BlueGeneL? Dong Luo (Fri Feb 12 2010 - 11:47:21 CST)
- Re: Retrieving standard deviation values while using collective variables (ABF) Hugh Martin (Thu Nov 26 2009 - 07:38:13 CST)
- Re: Retrieving standard deviation values while using collective variables (ABF) Jerome Henin (Tue Nov 10 2009 - 10:52:34 CST)
- scripiting problem ipsita basu (Tue Nov 10 2009 - 01:30:51 CST)
- Harmonic restraint parameters Bernardo Sosa Padilla Araujo (Mon Nov 09 2009 - 13:49:37 CST)
- Will MPICH2 work for NAMD? Lee Wei Yang (Mon Nov 09 2009 - 12:37:58 CST)
- Automatic namd 2.7b1 installation DimitryASuplatov (Mon Nov 09 2009 - 11:36:22 CST)
- fixing the protein during minimization Mert G黵 (Mon Nov 09 2009 - 08:22:24 CST)
- dielectric constant assignment Rajiv Abhyankar (Mon Nov 09 2009 - 06:22:04 CST)
- missing libraries for NAMD 2.7 on Linux cluster? Erik Nordgren (Sat Nov 07 2009 - 01:09:17 CST)
- Re: angle in colvars Dimitar V Pachov (Sun Nov 08 2009 - 22:17:20 CST)
- angle in colvars Felipe Merino (Sun Nov 08 2009 - 21:52:10 CST)
- Fwd: Error in Minimization Ale Gomez (Sun Nov 08 2009 - 09:15:02 CST)
- water box size gurunath katagi (Sun Nov 08 2009 - 07:23:41 CST)
- Error in Minimization Ale Gomez (Sat Nov 07 2009 - 10:45:24 CST)
- Is it a bug? TCL Script may Lead to Overflow Fred (Rui FENG) (Sat Nov 07 2009 - 03:09:28 CST)
- Tuning NAMD CUDA? Ronald Salesky (Fri Nov 06 2009 - 18:07:14 CST)
- strange error from NAMD with CUDA t s (Thu Nov 05 2009 - 13:55:14 CST)
- NAMD-problem jose correa (Thu Nov 05 2009 - 17:29:30 CST)
- Atom constraint in certain direction Priyan Amaras (Thu Nov 05 2009 - 11:15:31 CST)
- molecular dynamics simulation ipsita basu (Thu Nov 05 2009 - 04:35:33 CST)
- Running NAMD w/ CUDA under Linux Ronald Salesky (Wed Nov 04 2009 - 21:23:30 CST)
- Read dcd file and calculate (distance/constraint energy Vs snapshots) using NAMD priyodorshi satpati (Wed Nov 04 2009 - 11:05:33 CST)
- Re: ibverbs crash Bjoern Olausson (Wed Nov 04 2009 - 08:38:45 CST)
- TIP4P Luca Mammucari (Tue Nov 03 2009 - 17:07:10 CST)
- TIP4P topology Luca Bellucci (Tue Nov 03 2009 - 14:24:04 CST)
- ibverbs crash David A. Horita (Tue Nov 03 2009 - 14:17:17 CST)
- (no subject) l.mammucari_at_tin.it (Mon Nov 02 2009 - 15:47:14 CST)
- (no subject) Luca M. (Mon Nov 02 2009 - 14:33:36 CST)
- Abnormal EOF found -buffer=*END* Patrick Yee (Mon Nov 02 2009 - 12:35:52 CST)
- PMEGridSpacing DimitryASuplatov (Sat Oct 31 2009 - 05:46:04 CDT)
- How to apply an unsteady magnetic field? fereshteh moradi (Sun Oct 25 2009 - 01:52:29 CDT)
- Namd benchmark problem Sangamesh B (Thu Oct 22 2009 - 10:29:17 CDT)
- Namd benchmark problem Sangamesh B (Sat Oct 24 2009 - 02:12:05 CDT)
- Re: Namd benchmark problem Axel Kohlmeyer (Sat Oct 24 2009 - 11:30:45 CDT)
- Re: Namd benchmark problem Sangamesh B (Sun Oct 25 2009 - 01:46:29 CDT)
- Re: Namd benchmark problem Joshua Adelman (Sun Oct 25 2009 - 08:18:23 CDT)
- Re: Namd benchmark problem Axel Kohlmeyer (Sun Oct 25 2009 - 15:48:23 CDT)
- Re: Namd benchmark problem Bernardo Sosa Padilla Araujo (Mon Oct 26 2009 - 00:10:25 CDT)
- Re: Namd benchmark problem Nicholas M Glykos (Mon Oct 26 2009 - 04:57:22 CDT)
- Re: Namd benchmark problem Axel Kohlmeyer (Mon Oct 26 2009 - 08:26:03 CDT)
- Re: Namd benchmark problem Nicholas M Glykos (Mon Oct 26 2009 - 09:14:36 CDT)
- Re: Namd benchmark problem Axel Kohlmeyer (Mon Oct 26 2009 - 09:45:46 CDT)
- Re: Namd benchmark problem Nicholas M Glykos (Mon Oct 26 2009 - 10:08:01 CDT)
- Re: Namd benchmark problem Axel Kohlmeyer (Mon Oct 26 2009 - 08:16:55 CDT)
- Re: Namd benchmark problem Axel Kohlmeyer (Sat Oct 24 2009 - 11:30:45 CDT)
- Namd benchmark problem Sangamesh B (Sat Oct 24 2009 - 02:12:05 CDT)
- Molecular dynamics of multiple organic molecules with NAMD B (Thu Oct 22 2009 - 09:39:06 CDT)
- Error on renaming file: Permission denied Stephen Hicks (Mon Jun 04 2007 - 00:38:28 CDT)
- Hydrogen molecule model Mikhail Suyetin (Fri Oct 30 2009 - 10:42:19 CDT)
- issues with AutoPSF for a cyclodextrin CHINDEA Vlad (Thu Oct 29 2009 - 18:32:50 CDT)
- RAMD in NAMD; bugs and new version 4.0 Vlad Cojocaru (Thu Oct 29 2009 - 11:13:39 CDT)
- About APBS calculation 獼 (Thu Oct 29 2009 - 09:22:48 CDT)
- Using restraints DimitryASuplatov (Wed Oct 28 2009 - 10:55:44 CDT)
- Re: NAMD2.7 scaling problems DimitryASuplatov (Wed Oct 28 2009 - 08:30:44 CDT)
- NAMD2.7 scaling problems DimitryASuplatov (Wed Oct 28 2009 - 04:06:13 CDT)
- abnormal water surface after nvt and npt for POPC membrane pxq 庞雪芹 (Tue Oct 27 2009 - 19:57:58 CDT)
- order parameter, lipid segments as vectors Raul Araya (Tue Oct 27 2009 - 08:48:32 CDT)
- Tcl forces Myunggi Yi (Mon Oct 26 2009 - 13:12:50 CDT)
- Modeling familial amyloidotic polyneuropathy drmartin_at_fizyka.umk.pl (Mon Oct 26 2009 - 07:04:03 CDT)
- Random Expulsion MD (REMD) kristian krantz (Mon Oct 26 2009 - 06:07:11 CDT)
- namd cvs memory leak? BIN ZHANG (Thu Oct 22 2009 - 18:12:08 CDT)
- Pair interaction runtime analysis skipping dcd frames lucie delemotte (Thu Oct 22 2009 - 09:30:08 CDT)
- fresh file not ready to read? BIN ZHANG (Thu Oct 22 2009 - 01:46:10 CDT)
- Modification of equlibrated simulation box namd_chcwaaa_at_yahoo.com.cn (Wed Oct 21 2009 - 00:36:37 CDT)
- Re: CG bead definition BIN ZHANG (Tue Oct 20 2009 - 15:12:04 CDT)
- unsubscribe Vinit Rege (Tue Oct 20 2009 - 13:26:56 CDT)
- Fwd: vmd-l: CG bead definition BIN ZHANG (Tue Oct 20 2009 - 11:19:30 CDT)
- COARSE GRAINED WATER MODEL Valeria Marquez (Tue Oct 20 2009 - 08:52:10 CDT)
- smd output (v2.6) David A. Horita (Mon Oct 19 2009 - 12:04:05 CDT)
- Water Sphere Solvation Peter Murphy (Sun Oct 18 2009 - 08:41:38 CDT)
- Tolerance for SHAKE Nicholas M Glykos (Sun Oct 18 2009 - 07:58:20 CDT)
- zeroMomentum command A D (Fri Oct 16 2009 - 18:29:08 CDT)
- tcl force Seungho Choe (Fri Oct 16 2009 - 16:34:58 CDT)
- Tcl forces Myunggi Yi (Fri Oct 16 2009 - 15:06:45 CDT)
- ATP and Stream files Luis Agullo (LAB) (Fri Oct 16 2009 - 03:39:30 CDT)
- Slow heating in namd Pavan G (Thu Oct 15 2009 - 09:10:02 CDT)
- Ionization with VMD Luis Agullo (LAB) (Thu Oct 15 2009 - 09:07:13 CDT)
- ATP and Stream files Luis Agullo (LAB) (Thu Oct 15 2009 - 07:49:58 CDT)
- spontaneous system explosion after 2 ns of normal run Roman Petrenko (Wed Oct 14 2009 - 22:57:34 CDT)
- Re: spontaneous system explosion after 2 ns of normal run Roman Petrenko (Wed Oct 14 2009 - 23:09:36 CDT)
- Re: spontaneous system explosion after 2 ns of normal run Luis Agullo (LAB) (Thu Oct 15 2009 - 08:40:06 CDT)
- Re: spontaneous system explosion after 2 ns of normal run Axel Kohlmeyer (Thu Oct 15 2009 - 10:01:00 CDT)
- Re: spontaneous system explosion after 2 ns of normal run Roman Petrenko (Thu Oct 15 2009 - 10:22:44 CDT)
- Re: spontaneous system explosion after 2 ns of normal run Axel Kohlmeyer (Thu Oct 15 2009 - 11:15:23 CDT)
- Re: spontaneous system explosion after 2 ns of normal run daniel aguayo (Thu Oct 15 2009 - 19:46:12 CDT)
- Re: spontaneous system explosion after 2 ns of normal run Roman Petrenko (Sun Oct 18 2009 - 22:59:08 CDT)
- Fullerene topology Austin B. Yongye (Mon Oct 26 2009 - 13:40:17 CDT)
- Simulation crash due to charmrun error Rukman Hertadi (Tue Oct 27 2009 - 03:38:20 CDT)
- Re: Fullerene topology Luca Muccioli (Wed Oct 28 2009 - 10:55:11 CDT)
- Re: Fullerene topology Austin B. Yongye (Wed Oct 28 2009 - 11:41:49 CDT)
- Re: Fullerene topology Luca Muccioli (Wed Oct 28 2009 - 15:31:38 CDT)
- Re: spontaneous system explosion after 2 ns of normal run Jian Liu (Mon Oct 19 2009 - 01:45:24 CDT)
- Re: spontaneous system explosion after 2 ns of normal run Roman Petrenko (Thu Oct 15 2009 - 10:22:44 CDT)
- center of mass of dummyAtom in colvar BIN ZHANG (Wed Oct 14 2009 - 16:57:13 CDT)
- Unusual bond between residues: 0 (none) and 1 (protein) Song, Hyundeok (songhk) (Wed Oct 14 2009 - 11:33:15 CDT)
- How to fix relative position of a group Yang (Tue Oct 13 2009 - 15:40:53 CDT)
- Re: How to fix relative position of a group JC Gumbart (Tue Oct 13 2009 - 19:27:40 CDT)
- Re: PRESSURE, GPRESSURE, PRESSAVG, and GPRESSAVG Sebastian Stolzenberg (Wed Nov 04 2009 - 18:10:32 CST)
- Re: Re: PRESSURE, GPRESSURE, PRESSAVG, and GPRESSAVG Sebastian Stolzenberg (Sat Nov 07 2009 - 12:33:32 CST)
- temperature calculations from velocities in NAMD? Sebastian Stolzenberg (Sat Nov 07 2009 - 13:32:41 CST)
- Re: temperature calculations from velocities in NAMD? Axel Kohlmeyer (Sat Nov 07 2009 - 14:21:40 CST)
- Re: temperature calculations from velocities in NAMD? Sebastian Stolzenberg (Sat Nov 07 2009 - 16:31:48 CST)
- Re: temperature calculations from velocities in NAMD? Axel Kohlmeyer (Sat Nov 07 2009 - 16:55:13 CST)
- Re: temperature calculations from velocities in NAMD? Sebastian Stolzenberg (Sat Nov 07 2009 - 19:49:18 CST)
- Re: temperature calculations from velocities in NAMD? Sebastian Stolzenberg (Sat Nov 07 2009 - 20:13:55 CST)
- Re: temperature calculations from velocities in NAMD? Axel Kohlmeyer (Sun Nov 08 2009 - 11:17:20 CST)
- Re: temperature calculations from velocities in NAMD? Sebastian Stolzenberg (Sun Nov 08 2009 - 19:24:12 CST)
- Re: temperature calculations from velocities in NAMD? Axel Kohlmeyer (Sun Nov 08 2009 - 19:33:18 CST)
- Re: temperature calculations from velocities in NAMD? Sebastian Stolzenberg (Tue Nov 10 2009 - 23:00:44 CST)
- temperature from binary velocities file Sebastian Stolzenberg (Mon Dec 14 2009 - 14:59:42 CST)
- Re: temperature from binary velocities file Sebastian Stolzenberg (Tue Dec 15 2009 - 09:41:23 CST)
- Re: PRESSURE, GPRESSURE, PRESSAVG, and GPRESSAVG Sebastian Stolzenberg (Wed Nov 04 2009 - 18:10:32 CST)
- Re: How to fix relative position of a group JC Gumbart (Tue Oct 13 2009 - 19:27:40 CDT)
- size of integration step Jorgen Simonsen (Tue Oct 13 2009 - 10:44:47 CDT)
- Incorrect Atom Count in binary file Yogesh Aher (Tue Oct 13 2009 - 03:42:44 CDT)
- Generation of average trajectory mon_sharma_at_research.iiit.ac.in (Mon Oct 12 2009 - 02:26:02 CDT)
- restraining the COM of a group of atoms BIN ZHANG (Fri Oct 09 2009 - 19:19:56 CDT)
- Lennard-Jones potential in CHARMM Lixia Jin Day (Thu Oct 08 2009 - 16:19:16 CDT)
- nonbonded potential BIN ZHANG (Thu Oct 08 2009 - 00:19:30 CDT)
- about restart namd_chcwaaa_at_yahoo.com.cn (Thu Oct 08 2009 - 06:46:07 CDT)
- NAMD CUDA release steve.kaminski_at_mail.tu-berlin.de (Wed Oct 07 2009 - 16:01:12 CDT)
- followup question on error calculation in ABF Giovanni Bellesia (Wed Oct 07 2009 - 13:50:55 CDT)
- Tcl force Chaloin Laurent (Wed Oct 07 2009 - 05:22:01 CDT)
- How to put a COM restraint on a membrane protein? A D (Tue Oct 06 2009 - 18:03:25 CDT)
- constraint energy contributions Michael Thomas (Tue Oct 06 2009 - 06:33:25 CDT)
- PCA Calculation Anirban Ghosh (Tue Oct 06 2009 - 00:13:08 CDT)
- R.E.D.-III.3 tools release - q4md-forcefieldtools.org FyD (Sun Oct 04 2009 - 09:37:06 CDT)
- running namd in parallel Jorgen Simonsen (Sat Oct 03 2009 - 16:18:57 CDT)
- CMAP w/ D-amino acid Ziemys, Arturas (Fri Oct 02 2009 - 10:51:24 CDT)
- Changing the atomtype of a particle on the fly BIN ZHANG (Fri Oct 02 2009 - 01:15:07 CDT)
- error termination Sridhar Vaddadi (Fri Oct 02 2009 - 11:08:02 CDT)
- Minimisation Protocol Philip Peartree (Fri Oct 02 2009 - 11:36:49 CDT)
- Re: Changing the atomtype of a particle on the fly Axel Kohlmeyer (Fri Oct 02 2009 - 13:09:12 CDT)
- Re: Changing the atomtype of a particle on the fly Axel Kohlmeyer (Fri Oct 02 2009 - 13:30:57 CDT)
- Re: Changing the atomtype of a particle on the fly BIN ZHANG (Fri Oct 02 2009 - 13:50:21 CDT)
- Re: Changing the atomtype of a particle on the fly Axel Kohlmeyer (Fri Oct 02 2009 - 14:57:43 CDT)
- Re: Changing the atomtype of a particle on the fly daniel aguayo (Sun Oct 04 2009 - 18:59:00 CDT)
- Re: Changing the atomtype of a particle on the fly Axel Kohlmeyer (Mon Oct 05 2009 - 02:14:41 CDT)
- NAMD 2.7b1 on Lonestar Jufang Shan (Mon Oct 05 2009 - 10:44:23 CDT)
- Re: Changing the atomtype of a particle on the fly Axel Kohlmeyer (Fri Oct 02 2009 - 13:30:57 CDT)
- questions regarding new single node box for NAMD: re components, CUDA, Fermi Biff Forbush (Thu Oct 01 2009 - 17:27:06 CDT)
- RE: questions regarding new single node box for NAMD: re components, CUDA, Fermi Richard Owczarzy (Fri Oct 02 2009 - 10:42:12 CDT)
- Re: questions regarding new single node box for NAMD: re components, CUDA, Fermi Axel Kohlmeyer (Fri Oct 02 2009 - 12:51:26 CDT)
- Re: questions regarding new single node box for NAMD: re components, CUDA, Fermi Biff Forbush (Sun Oct 04 2009 - 20:37:43 CDT)
- Re: questions regarding new single node box for NAMD: re components, CUDA, Fermi Axel Kohlmeyer (Mon Oct 05 2009 - 02:01:47 CDT)
- NAMD benchmark results for dual-Nehalem, was Re: questions regarding new single node box for NAMD: re components, CUDA, Fermi Biff Forbush (Wed Dec 09 2009 - 20:53:00 CST)
- Re: NAMD benchmark results for dual-Nehalem, was Re: questions regarding new single node box for NAMD: re components, CUDA, Fermi Axel Kohlmeyer (Thu Dec 10 2009 - 00:52:52 CST)
- Re: NAMD benchmark results for dual-Nehalem, was Re: questions regarding new single node box for NAMD: re components, CUDA, Fermi Biff Forbush (Thu Dec 10 2009 - 19:47:58 CST)
- Re: NAMD benchmark results for dual-Nehalem, was Re: questions regarding new single node box for NAMD: re components, CUDA, Fermi Dow Hurst (Thu Dec 10 2009 - 05:14:54 CST)
- Re: NAMD benchmark results for dual-Nehalem, was Re: questions regarding new single node box for NAMD: re components, CUDA, Fermi Biff Forbush (Thu Dec 10 2009 - 19:57:02 CST)
- Re: NAMD benchmark results for dual-Nehalem, was Re: questions regarding new single node box for NAMD: re components, CUDA, Fermi Gengbin Zheng (Thu Dec 10 2009 - 11:54:33 CST)
- Re: questions regarding new single node box for NAMD: re components, CUDA, Fermi Biff Forbush (Sun Oct 04 2009 - 20:37:43 CDT)
- Loop Andres Morales N (Thu Oct 01 2009 - 07:59:27 CDT)
- heating a system Bernardo Sosa Padilla Araujo (Thu Oct 01 2009 - 11:51:10 CDT)
- ABF + LES Ziemys, Arturas (Thu Oct 01 2009 - 11:45:38 CDT)
- namd2.7b1, tip4p, and dummies Edward Lyman (Wed Sep 30 2009 - 13:56:47 CDT)
- Re: vmd-l: namd2.7b1, tip4p, and dummies Joshua D. Moore (Wed Sep 30 2009 - 05:24:34 CDT)
- NAMD 2.7b1 ABF + free energy windows Reichert, David (Tue Sep 29 2009 - 15:33:48 CDT)
- g(r) GUI Plugin problem Branko (Tue Sep 29 2009 - 05:32:03 CDT)
- a timing question; 206,000atoms > 512cores not good Thomas C. Bishop (Mon Sep 28 2009 - 12:17:07 CDT)
- Why is the temperature set different in the membrane proteins tutorial? FengXian Zheng (Sat Sep 26 2009 - 19:58:28 CDT)
- NAMD2.7b1 performance Myunggi Yi (Fri Sep 25 2009 - 08:54:33 CDT)
- Namd not detecting my CUDA enabled GPU nicolabrisotto (Thu Sep 24 2009 - 11:07:35 CDT)
- where can I find the file: cornell.rtf (in bionano tutorial) Jian Liu (Thu Sep 24 2009 - 02:03:38 CDT)
- How the seed influences the molecular dynamics simulations? Agostino (Wed Sep 23 2009 - 04:15:26 CDT)
- extracting info from output files Rajiv Abhyankar (Tue Sep 22 2009 - 13:26:08 CDT)
- Re: extracting info from output files Axel Kohlmeyer (Tue Sep 22 2009 - 14:03:12 CDT)
- Re: extracting info from output files Giacomo Fiorin (Tue Sep 22 2009 - 15:12:05 CDT)
- Re: extracting info from output files Rajiv Abhyankar (Tue Sep 22 2009 - 17:56:19 CDT)
- RE: extracting info from output files Zumot, Elia Nabil (Tue Sep 22 2009 - 16:22:40 CDT)
- Precision of Coordinate data Rick Calloway (Tue Sep 22 2009 - 12:08:34 CDT)
- Re: Precision of Coordinate data Axel Kohlmeyer (Tue Sep 22 2009 - 13:22:47 CDT)
- help requested Sridhar Vaddadi (Wed Sep 23 2009 - 11:23:36 CDT)
- topology files Sridhar Vaddadi (Wed Sep 23 2009 - 13:59:02 CDT)
- Re: topology files Ramya Gamini (Wed Sep 23 2009 - 17:17:28 CDT)
- RE: topology files Sridhar Vaddadi (Wed Sep 23 2009 - 17:37:20 CDT)
- RE: topology files Sridhar Vaddadi (Thu Sep 24 2009 - 13:17:26 CDT)
- Re: topology files Axel Kohlmeyer (Thu Sep 24 2009 - 14:16:17 CDT)
- psfgen Sridhar Vaddadi (Wed Sep 23 2009 - 17:11:37 CDT)
- RE: pdb file Sridhar Vaddadi (Thu Sep 24 2009 - 11:34:38 CDT)
- topology files Sridhar Vaddadi (Wed Sep 23 2009 - 13:59:02 CDT)
- Do top_all27_prot_na.inp and cornell.prm share the same naming rules of atom types? 何毓辉 (Tue Sep 22 2009 - 02:51:56 CDT)
- GPU Selection in NAMD CUDA Ron Stubbs (Mon Sep 21 2009 - 14:56:42 CDT)
- adding specific forces between atoms Michael Zimmermann (Mon Sep 21 2009 - 15:44:48 CDT)
- Kemp elimination substrate charmm parameters Bernardo Sosa Padilla Araujo (Mon Sep 21 2009 - 15:41:01 CDT)
- Regarding Lipid Order Parameter Calculation Jagan Mohan (Mon Sep 21 2009 - 00:54:18 CDT)
- ABF calculation - normalization of the PMF Giovanni Bellesia (Sat Sep 19 2009 - 16:59:46 CDT)
- Replay to Parametrizing a novel residue] Branko (Fri Sep 18 2009 - 13:58:11 CDT)
- Parametrizing a novel residue Q=C1=D2=D8=D1_=FB=C1=CC=C1=C5=D7=C1?= (Fri Sep 18 2009 - 10:25:18 CDT)
- About NAN error cong chen (Fri Sep 18 2009 - 01:35:51 CDT)
- How to access velocity coordinates from within TclForces script Patrick Hogan (Thu Sep 17 2009 - 14:43:21 CDT)
- how to get psf files of DNA but not RNA with psfgen? 何毓辉 (Thu Sep 17 2009 - 06:25:02 CDT)
- can't load forces in tclforces James Servantie (Thu Sep 17 2009 - 05:54:21 CDT)
- AlF4 Laurent Chaloin (Thu Sep 17 2009 - 04:54:14 CDT)
- scripts for starting namd with condor John Wise (Wed Sep 16 2009 - 17:06:26 CDT)
- FAD topology and parameters of FAD jose correa (Wed Sep 16 2009 - 11:21:58 CDT)
- how to use volmap analysing a series of dcd. liupeng012_at_mail.nankai.edu.cn (Wed Sep 16 2009 - 08:39:50 CDT)
- Re: NVT with truncated octahedron or with sphere? Werner Crous (Wed Sep 16 2009 - 06:04:31 CDT)
- FATAL ERROR: Couldn't open DCD file ubq_wb_eq.dcd: No such file or directory Bernardo Sosa Padilla Araujo (Tue Sep 15 2009 - 18:26:25 CDT)
- NVT with truncated octahedron or with sphere? Werner Crous (Tue Sep 15 2009 - 03:03:06 CDT)
- Temperature rescaling vs. reassignment Luis Agullo (LAB) (Tue Sep 15 2009 - 09:26:48 CDT)
- Visit my Netlog profile Moumita Maiti (Tue Sep 15 2009 - 00:07:31 CDT)
- question about FEP soft-core yun luo (Mon Sep 14 2009 - 15:03:16 CDT)
- Re: CUDA-accelerated NAMD does not support NBFIX parameters [RESOLVED] H閏tor Urbina (Mon Sep 14 2009 - 07:24:35 CDT)
- Regarding ABF Simulation Jagan Mohan (Mon Sep 14 2009 - 04:48:19 CDT)
- CUDA-accelerated NAMD does not support NBFIX parameters H閏tor Urbina (Sun Sep 13 2009 - 13:47:33 CDT)
- Saving a subset of atoms Austin B. Yongye (Fri Sep 11 2009 - 12:32:44 CDT)
- Regarding NAMD CPU usage Amr Zeinalabideen Majul (Fri Sep 11 2009 - 08:22:08 CDT)
- atomic structure of some surfaces Roman Petrenko (Thu Sep 10 2009 - 19:57:14 CDT)
- FAD-parameters jose correa (Thu Sep 10 2009 - 13:50:33 CDT)
- [off topic] The mailing list's mailer ... Nicholas M Glykos (Wed Sep 09 2009 - 12:50:58 CDT)
- Implicit membrane models Austin B. Yongye (Wed Sep 09 2009 - 09:03:53 CDT)
- Constraint failure in RATTLE algorithm - shouldn't a rerun fail at the same step? Bjoern Olausson (Tue Sep 08 2009 - 03:12:04 CDT)
- problems of "Stray PME grid charges" pxq 庞雪芹 (Tue Sep 08 2009 - 09:40:44 CDT)
- Constraint failure in RATTLE algorithm - shouldn't a rerun fail at the same step? Bjoern Olausson (Tue Sep 08 2009 - 03:13:02 CDT)
- (no subject) Jim Phillips (Tue Sep 08 2009 - 17:21:54 CDT)
- PMF: free energy calcs in "grow" phase? Sebastian Stolzenberg (Fri Sep 04 2009 - 15:57:00 CDT)
- CAN'T FIND DIHEDRAL PARAMETERS FOR CN8B CN7 ON5 HN5 Sujata Sovani (Fri Sep 04 2009 - 15:35:56 CDT)
- Re: vmd-l: rmsd matrix Cesar Millan (Thu Sep 03 2009 - 11:23:20 CDT)
- Membrane simulations Austin B. Yongye (Tue Sep 01 2009 - 10:24:36 CDT)
- CHARMM to NAMD Yang MIngjun (Tue Sep 01 2009 - 09:03:13 CDT)
- Re-posting - Methylated Histidine topology file Sujata Sovani (Mon Aug 31 2009 - 12:47:16 CDT)
- Methylated Histidine topology file Sujata Sovani (Mon Aug 31 2009 - 12:38:03 CDT)
- Periodic boundary conditions in membrane simulation jouko_at_uchicago.edu (Mon Aug 31 2009 - 11:56:22 CDT)
- Doubts and problem in ABF simulations Paulo Cesar Telles de Souza (Mon Aug 31 2009 - 11:00:57 CDT)
- PMF via constrained dynamics in NAMD satya work (Mon Aug 31 2009 - 09:01:43 CDT)
- for your suggestions on Pressure Control of transmembrane protein (GPCR) pxq 庞雪芹 (Sun Aug 30 2009 - 22:18:47 CDT)
- Cuda benchmarks namd2.7b1 - effects of configuration parameters and hardware. Mike Kuiper (Sun Aug 30 2009 - 03:54:57 CDT)
- Re: Cuda benchmarks namd2.7b1 - effects of configuration parameters and hardware. Gianluca Interlandi (Sun Aug 30 2009 - 14:11:25 CDT)
- Re: Cuda benchmarks namd2.7b1 - effects of configuration parameters and hardware. Roman Petrenko (Sun Aug 30 2009 - 16:06:26 CDT)
- Aslos End'tasa (Fri Aug 28 2009 - 11:55:17 CDT)
- hole on the surface of the waterbox Mert G黵 (Fri Aug 28 2009 - 05:08:09 CDT)
- Re: hole on the surface of the waterbox Ana Vila Verde (Fri Aug 28 2009 - 05:54:06 CDT)
- Re: hole on the surface of the waterbox Mert G黵 (Fri Aug 28 2009 - 06:12:25 CDT)
- Re: hole on the surface of the waterbox Ana Vila Verde (Fri Aug 28 2009 - 06:19:41 CDT)
- Re: hole on the surface of the waterbox Mert G黵 (Fri Aug 28 2009 - 07:20:09 CDT)
- Re: hole on the surface of the waterbox Ana Vila Verde (Fri Aug 28 2009 - 07:26:14 CDT)
- Re: hole on the surface of the waterbox Mert G黵 (Fri Aug 28 2009 - 07:36:16 CDT)
- Re: hole on the surface of the waterbox Ana Vila Verde (Fri Aug 28 2009 - 07:48:35 CDT)
- Re: hole on the surface of the waterbox Mert G黵 (Fri Aug 28 2009 - 13:45:03 CDT)
- Re: hole on the surface of the waterbox Mert G黵 (Fri Aug 28 2009 - 06:12:25 CDT)
- Re: hole on the surface of the waterbox Nicholas M Glykos (Fri Aug 28 2009 - 07:38:00 CDT)
- Re: hole on the surface of the waterbox Ana Vila Verde (Fri Aug 28 2009 - 05:54:06 CDT)
- ERROR: Constraint failure in RATTLE algorithm for atom 9080! gurunath katagi (Fri Aug 28 2009 - 00:16:01 CDT)
- Tesla Utilization -- NAMD 2.7b1 Ron Stubbs (Thu Aug 27 2009 - 13:06:19 CDT)
- ABF 'Xi' log output producing strange results Hugh Martin (Thu Aug 27 2009 - 10:30:22 CDT)
- Running a simulation with a protein and a sugar pellegrini (Thu Aug 27 2009 - 04:06:48 CDT)
- how to set up force parameters of a novel residue? He Yuhui (Thu Aug 27 2009 - 02:37:12 CDT)
- Postdoc position in biomolecular simulation Ivaylo Ivanov (Wed Aug 26 2009 - 16:40:02 CDT)
- question on forces / theory Ziemys, Arturas (Tue Aug 25 2009 - 22:07:07 CDT)
- fixed atoms pdb Mark M Huntress (Mon Aug 24 2009 - 17:13:20 CDT)
- multi-cluster configuration Piotr Kopta (Mon Aug 24 2009 - 16:18:42 CDT)
- Parameters for esters Jorgen Simonsen (Mon Aug 24 2009 - 11:55:08 CDT)
- About DPD 獼 (Sun Aug 23 2009 - 09:52:59 CDT)
- SMD on membrane protein. Yoav Beck (Sun Aug 23 2009 - 09:04:55 CDT)
- Alignment of velocity dcd file Mert G黵 (Sat Aug 22 2009 - 15:03:10 CDT)
- FATAL ERROR: ABNORMAL EOF FOUND - buffer=*0 0 0* FengXian Zheng (Fri Aug 21 2009 - 10:14:38 CDT)
- Questions from new user 獼 (Thu Aug 20 2009 - 21:57:05 CDT)
- Force extension from SMD log file snoze pa (Thu Aug 20 2009 - 17:25:20 CDT)
- Re: ABF Colvars Configuration File Neelanjana Sengupta (Thu Aug 20 2009 - 09:21:41 CDT)
- unbinding SMD skill question Sangbae Lee (Wed Aug 19 2009 - 15:24:59 CDT)
- protocol to start MD jose correa (Wed Aug 19 2009 - 09:27:29 CDT)
- glibc runtime errors on BlueGeneP occur only if running the cvs code (18.08) and not namd 2.6 Vlad Cojocaru (Wed Aug 19 2009 - 05:38:47 CDT)
- About the namd tutorial err Aurum Bai (Tue Aug 18 2009 - 23:55:01 CDT)
- how to save pdb file after "moveby" command in VMD? He Yuhui (Tue Aug 18 2009 - 21:33:42 CDT)
- glibc detected : corrupted double-linked list: 0xa4657ad8 Vlad Cojocaru (Tue Aug 18 2009 - 05:15:55 CDT)
- Re: glibc detected : corrupted double-linked list: 0xa4657ad8 Vlad Cojocaru (Tue Aug 18 2009 - 05:44:58 CDT)
- Re: glibc detected : corrupted double-linked list: 0xa4657ad8 George Madalin Giambasu (Tue Aug 18 2009 - 12:05:22 CDT)
- RE: glibc detected : corrupted double-linked list: 0xa4657ad8 Cojocaru,Vlad (Tue Aug 18 2009 - 15:52:59 CDT)
- Re: glibc detected : corrupted double-linked list: 0xa4657ad8 Vlad Cojocaru (Wed Aug 19 2009 - 02:17:55 CDT)
- Re: glibc detected : corrupted double-linked list: 0xa4657ad8 Vlad Cojocaru (Wed Aug 19 2009 - 02:46:08 CDT)
- Re: glibc detected : corrupted double-linked list: 0xa4657ad8 Vlad Cojocaru (Wed Aug 19 2009 - 04:43:40 CDT)
- Re: glibc detected : corrupted double-linked list: 0xa4657ad8 George Madalin Giambasu (Tue Aug 18 2009 - 12:05:22 CDT)
- Re: glibc detected : corrupted double-linked list: 0xa4657ad8 Vlad Cojocaru (Tue Aug 18 2009 - 05:44:58 CDT)
- Berendsen, explicit water Sandra Rennebaum, Biochemisches Inst. (Tue Aug 18 2009 - 04:54:07 CDT)
- restating simuation and periodic cell conditions gurunath katagi (Tue Aug 18 2009 - 03:23:20 CDT)
- what is the charge of sulfur on thiol? He Yuhui (Mon Aug 17 2009 - 01:38:01 CDT)
- Colvars Configuration File Neelanjana Sengupta (Sat Aug 15 2009 - 02:16:19 CDT)
- (is there) a dependence of dynamics on WRAPPING satya work (Sat Aug 15 2009 - 01:33:26 CDT)
- Restarting ABF Branko (Thu Aug 13 2009 - 11:05:18 CDT)
- Re: About SMD Roman Petrenko (Thu Aug 13 2009 - 10:33:34 CDT)
- FATAL ERROR: Tried to find atom type on node other than node 0 Yoav Beck (Thu Aug 13 2009 - 09:21:38 CDT)
- Re: FATAL ERROR: Tried to find atom type on node other than node 0 yzliu (Sat Aug 15 2009 - 11:06:10 CDT)
- Re: FATAL ERROR: Tried to find atom type on node other than node 0 Yoav Beck (Mon Aug 17 2009 - 05:04:48 CDT)
- Re: FATAL ERROR: Tried to find atom type on node other than node 0 Narender Singh Maan (Mon Aug 17 2009 - 08:43:41 CDT)
- Re: FATAL ERROR: Tried to find atom type on node other than node 0 Chris Harrison (Mon Aug 17 2009 - 09:44:35 CDT)
- Minimization issue. Yoav Beck (Mon Aug 17 2009 - 10:20:41 CDT)
- Re: Minimization issue. Schreiner Eduard (Mon Aug 17 2009 - 10:33:57 CDT)
- Re: Minimization issue. Chris Harrison (Mon Aug 17 2009 - 10:43:24 CDT)
- Re: Minimization issue. Chris Harrison (Tue Aug 18 2009 - 10:51:20 CDT)
- Re: Minimization issue. Yoav Beck (Wed Aug 19 2009 - 07:11:21 CDT)
- Re: FATAL ERROR: Tried to find atom type on node other than node 0 Yoav Beck (Mon Aug 17 2009 - 05:04:48 CDT)
- Re: FATAL ERROR: Tried to find atom type on node other than node 0 yzliu (Sat Aug 15 2009 - 11:06:10 CDT)
- Bug advisory: ABF integration tool Jerome Henin (Wed Aug 12 2009 - 17:49:24 CDT)
- Kanamycin topology DimitryASuplatov (Wed Aug 12 2009 - 12:16:33 CDT)
- symmetric behavior Narender Singh Maan (Wed Aug 12 2009 - 09:16:39 CDT)
- can we control the number and distribution of solvate molecular pxq 庞雪芹 (Wed Aug 12 2009 - 02:21:23 CDT)
- About "Parameterizing a Novel Residue" tutorial problem Aurum Bai (Wed Aug 12 2009 - 00:18:09 CDT)
- About SMD Yang MIngjun (Tue Aug 11 2009 - 22:11:51 CDT)
- solvate plugin with solvent other than water dalton banks (Tue Aug 11 2009 - 15:02:13 CDT)
- bonding in periodic boundary conditions d b (Tue Aug 11 2009 - 15:05:08 CDT)
- Berendsen- two baths Sandra Rennebaum, Biochemisches Inst. (Tue Aug 11 2009 - 01:55:10 CDT)
- SMD with force applied to two seperate molecules Elia Zumot (Tue Aug 11 2009 - 10:09:17 CDT)
- how to simulate a protein-ligand complex ? ydhuang2727 (Tue Aug 11 2009 - 08:29:25 CDT)
- namd-SMD constant Force missing smdatom location snoze pa (Mon Aug 10 2009 - 14:40:51 CDT)
- Steered Molecular Dynamics for more than one atom gaurav bhatti (Mon Aug 10 2009 - 13:55:10 CDT)
- Clarification regarding some finer details in ABF simulations Hugh Martin (Mon Aug 10 2009 - 12:33:47 CDT)
- combining segments d b (Mon Aug 10 2009 - 09:06:51 CDT)
- increase the temperature step by step after minimization gurunath katagi (Mon Aug 10 2009 - 00:27:03 CDT)
- how to write a command to close vmd in shell script? He Yuhui (Sun Aug 09 2009 - 22:21:34 CDT)
- On naming rules in force-field parameter files? He Yuhui (Sun Aug 09 2009 - 20:12:21 CDT)
- charm++ how to handle SMP/Multicore Bjoern Olausson (Sun Aug 09 2009 - 17:01:48 CDT)
- ABF question (free energy partition) Lei Shi (Sun Aug 09 2009 - 11:36:10 CDT)
- namd27: tclforces activate TI calculation by default George Madalin Giambasu (Sat Aug 08 2009 - 16:12:34 CDT)
- Re: Cell Data in DCD files - CHARMM compatibility Dimitar V Pachov (Fri Aug 07 2009 - 19:50:30 CDT)
- Error with GUI NAMD Energy Elia Zumot (Fri Aug 07 2009 - 16:45:23 CDT)
- SMD and Temperature control snoze pa (Fri Aug 07 2009 - 15:25:51 CDT)
- NAMD performance with 10GbE interconnect Prakash Velayutham (Fri Aug 07 2009 - 15:02:55 CDT)
- NAMD FFTW question? snoze pa (Fri Aug 07 2009 - 11:17:58 CDT)
- What is the different between "periodic boundary ,spherical harmonic boundary and cylindrical harmonic boundary conditions"? Aurum Bai (Fri Aug 07 2009 - 11:04:50 CDT)
- Would my simulation setting a铿ect the result? About the parameter "fixedAtomsForces" wayj86 wayj86 (Fri Aug 07 2009 - 05:51:42 CDT)
- NAMDenergy: does rewrite temp files at different timesteps Neelanjana Sengupta (Fri Aug 07 2009 - 00:18:14 CDT)
- cutoffs in direct and indirect space used in PME? dimka (Thu Aug 06 2009 - 23:13:05 CDT)
- Continuing simulation after constraint failure error? Sujata Sovani (Thu Aug 06 2009 - 11:59:28 CDT)
- Re: Proteine-membrane simulation. Yoav Beck (Thu Aug 06 2009 - 07:46:05 CDT)
- Defining Temperature for Langevin for Namd restart. Amr Zeinalabideen Majul (Wed Aug 05 2009 - 14:20:15 CDT)
- Re: Defining Temperature for Langevin for Namd restart. Roman Petrenko (Wed Aug 05 2009 - 15:13:57 CDT)
- Re: Defining Temperature for Langevin for Namd restart. Gianluca Interlandi (Wed Aug 05 2009 - 16:35:14 CDT)
- Re: frozen water Oxygens Chris Harrison (Wed Aug 05 2009 - 09:01:24 CDT)
- SMD output : which col represents force, second or last snoze pa (Wed Aug 05 2009 - 11:42:42 CDT)
- SMD output : which col represents force, second or last snoze pa (Wed Aug 05 2009 - 11:25:35 CDT)
- Re: SMD output : which col represents force, second or last Roman Petrenko (Wed Aug 05 2009 - 12:05:16 CDT)
- RE: SMD output : which col represents force, second or last Sadhu, Shubho (NIH/NCI) [F] (Wed Aug 05 2009 - 12:19:27 CDT)
- Re: SMD output : which col represents force, second or last David Tanner (Wed Aug 05 2009 - 12:03:30 CDT)
- Re: SMD output : which col represents force, second or last Gianluca Interlandi (Wed Aug 05 2009 - 13:10:34 CDT)
- Re: SMD output : which col represents force, second or last Chris Harrison (Wed Aug 05 2009 - 12:27:08 CDT)
- water molecules in channel protein Narender Singh Maan (Wed Aug 05 2009 - 10:57:50 CDT)
- Re: recalculating energy using dcd file Rabab Toubar (Wed Aug 05 2009 - 09:43:44 CDT)
- How to do a complex dynamics simulation ydhuang2727 (Wed Aug 05 2009 - 03:25:10 CDT)
- Simulating molecules in bulk water & VMD installation problems Vincent Su (Tue Aug 04 2009 - 14:27:38 CDT)
- SMD restrain point in NAMD snoze pa (Tue Aug 04 2009 - 11:40:05 CDT)
- frozen water Oxygens Mark M Huntress (Tue Aug 04 2009 - 11:13:12 CDT)
- Proteine-membrane simulation. Yoav Beck (Tue Aug 04 2009 - 10:08:55 CDT)
- Does Berendsen increase viscosity of water? Gianluca Interlandi (Tue Aug 04 2009 - 00:36:38 CDT)
- A script for performing calculations divided by quanta Mikhail Suyetin (Mon Aug 03 2009 - 08:26:28 CDT)
- The steps in protein and membrane simulation Narender Singh Maan (Sat Aug 01 2009 - 23:23:49 CDT)
- NAMD water sphere problem snoze pa (Fri Jul 31 2009 - 17:19:12 CDT)
- how to use ethanol as solvent in namd for MD simulations ? Wang Yf (Fri Jul 31 2009 - 04:06:55 CDT)
- compilation error "could not set locale" with intel 11.0 Vlad Cojocaru (Fri Jul 31 2009 - 03:03:53 CDT)
- Steered Molecular Dynamics gaurav bhatti (Fri Jul 31 2009 - 00:33:50 CDT)
- How to calculate free energy for conformational change Lixia Jin Day (Thu Jul 30 2009 - 16:46:07 CDT)
- CUDA Linux-x86 doesn't compile Sadhu, Shubho (NIH/NCI) [F] (Thu Jul 30 2009 - 09:06:04 CDT)
- how to generate DNA psf files? He Yuhui (Wed Jul 29 2009 - 21:04:27 CDT)
- Different ensembles in the same system Eric Perim (Wed Jul 29 2009 - 14:48:39 CDT)
- THERMODYNAMIC INTEGRATION ON in namd 2.7b1 compiled 24.07 when TCL forces active Vlad Cojocaru (Wed Jul 29 2009 - 05:03:27 CDT)
- Unable to generate PSF file due to an unparametrized component Sujata Sovani (Tue Jul 28 2009 - 16:33:09 CDT)
- (no subject) Sujata Sovani (Tue Jul 28 2009 - 17:02:30 CDT)
- FEP implementation in NAMD 2.6 vs. 2.7b1 Dan Bolintineanu (Tue Jul 28 2009 - 16:50:37 CDT)
- Equilibration "substraction" from obtained PMF from MD Branko (Tue Jul 28 2009 - 16:32:00 CDT)
- Using preprotonated structure with NAMD DimitryASuplatov (Tue Jul 28 2009 - 09:48:18 CDT)
- PLUMED release 1.1.0 available Massimiliano Bonomi (Tue Jul 28 2009 - 03:12:27 CDT)
- use tclForce and tclBC together? yun luo (Mon Jul 27 2009 - 20:14:45 CDT)
- error running namd Bernardo Sosa Padilla Araujo (Mon Jul 27 2009 - 16:37:17 CDT)
- hydroxyls in phosphate group collapsing Yvonne.Westermaier_at_unige.ch (Mon Jul 27 2009 - 09:41:20 CDT)
- Group forces in tclForces Benjamin Bouvier (Mon Jul 27 2009 - 06:02:12 CDT)
- Re: An outlier appear on the curve of RMSD wayj86 wayj86 (Sun Jul 26 2009 - 20:42:13 CDT)
- How to set magnitude of cellBasisVector? Aurum Bai (Fri Jul 24 2009 - 00:52:19 CDT)
- An outlier appear on the curve of RMSD wayj86 wayj86 (Thu Jul 23 2009 - 22:37:04 CDT)
- how to run namd2.7b1 on multiple nodes Roman Petrenko (Thu Jul 23 2009 - 17:48:19 CDT)
- RE: PMEGridSize Rabab Toubar (Thu Jul 23 2009 - 15:13:03 CDT)
- NAMD documentation regarding compiling Thomas C. Bishop (Thu Jul 23 2009 - 15:25:19 CDT)
- RescaleFreq of temperature =1? Mikhail Suyetin (Thu Jul 23 2009 - 09:48:54 CDT)
- NAMD CUDA on dual Nvidia 295 GPUs David Chalmers (Thu Jul 23 2009 - 07:20:34 CDT)
- Re: NAMD CUDA on dual Nvidia 295 GPUs Axel Kohlmeyer (Thu Jul 23 2009 - 08:04:42 CDT)
- RE: NAMD CUDA on dual Nvidia 295 GPUs Sadhu, Shubho (NIH/NCI) [F] (Thu Jul 23 2009 - 09:11:48 CDT)
- Re: RE: NAMD CUDA on dual Nvidia 295 GPUs Axel Kohlmeyer (Thu Jul 23 2009 - 10:02:45 CDT)
- RE: RE: NAMD CUDA on dual Nvidia 295 GPUs Sadhu, Shubho (NIH/NCI) [F] (Thu Jul 23 2009 - 12:14:42 CDT)
- RE: RE: NAMD CUDA on dual Nvidia 295 GPUs Axel Kohlmeyer (Thu Jul 23 2009 - 12:28:24 CDT)
- NAMD CUDA performance degradation Thomas C. Bishop (Thu Jul 23 2009 - 14:31:10 CDT)
- Re: NAMD CUDA performance degradation Axel Kohlmeyer (Thu Jul 23 2009 - 15:19:16 CDT)
- Re: RE: NAMD CUDA on dual Nvidia 295 GPUs Axel Kohlmeyer (Thu Jul 23 2009 - 10:02:45 CDT)
- maximum residues using AMBER parm with NAMD benc_at_bsc.es (Wed Jul 22 2009 - 05:09:17 CDT)
- NAMD installation Bernardo Sosa Padilla Araujo (Wed Jul 22 2009 - 17:33:15 CDT)
- NAMD 2.7b1 with APBS/iAPBS Bjoern Olausson (Wed Jul 22 2009 - 02:56:07 CDT)
- Measuring the molarity Rabab Toubar (Wed Jul 22 2009 - 15:16:58 CDT)
- inconsistence in NAMD and AMBER energy Yi Shang (Mon Jul 20 2009 - 18:31:47 CDT)
- Re: inconsistence in NAMD and AMBER energy Goutham (Tue Jul 21 2009 - 01:13:48 CDT)
- Re: inconsistence in NAMD and AMBER energy Floris Buelens (Tue Jul 21 2009 - 02:11:51 CDT)
- Re: inconsistence in NAMD and AMBER energy Thomas C. Bishop (Tue Jul 21 2009 - 09:33:35 CDT)
- Re: inconsistence in NAMD and AMBER energy Yi Shang (Tue Jul 21 2009 - 09:56:04 CDT)
- Re: inconsistence in NAMD and AMBER energy Thomas C. Bishop (Tue Jul 21 2009 - 10:14:28 CDT)
- Re: inconsistence in NAMD and AMBER energy Yi Shang (Tue Jul 21 2009 - 10:22:45 CDT)
- Re: inconsistence in NAMD and AMBER energy: AMBER truncted octahedron Vlad Cojocaru (Tue Jul 21 2009 - 11:08:40 CDT)
- Re: inconsistence in NAMD and AMBER energy: AMBER truncted octahedron Thomas C. Bishop (Tue Jul 21 2009 - 11:30:35 CDT)
- Re: inconsistence in NAMD and AMBER energy: AMBER truncted octahedron Vlad Cojocaru (Wed Jul 22 2009 - 04:44:45 CDT)
- Re: inconsistence in NAMD and AMBER energy Thomas C. Bishop (Tue Jul 21 2009 - 11:11:39 CDT)
- Re: inconsistence in NAMD and AMBER energy Floris Buelens (Tue Jul 21 2009 - 10:57:41 CDT)
- Re: inconsistence in NAMD and AMBER energy Yi Shang (Tue Jul 21 2009 - 11:04:18 CDT)
- Re: inconsistence in NAMD and AMBER energy George Madalin Giambasu (Tue Jul 21 2009 - 11:27:03 CDT)
- Re: inconsistence in NAMD and AMBER energy Thomas C. Bishop (Tue Jul 21 2009 - 09:33:35 CDT)
- ABF tutorial sudipta (Mon Jul 20 2009 - 08:57:54 CDT)
- on NAMD simulation of DNA translocation through nanopores yuhuihe_at_ime.pku.edu.cn (Sun Jul 19 2009 - 07:27:55 CDT)
- about compile namd2.7 liupeng012 (Sun Jul 19 2009 - 05:58:05 CDT)
- CPU USAGE mahmoud mirzaei (Sat Jul 18 2009 - 11:14:10 CDT)
- Re: CPU USAGE Axel Kohlmeyer (Sat Jul 18 2009 - 11:50:25 CDT)
- Re: CPU USAGE mahmoud mirzaei (Sat Jul 18 2009 - 23:07:26 CDT)
- RE: CPU USAGE JC Gumbart (Sun Jul 19 2009 - 00:16:30 CDT)
- RE: CPU USAGE mahmoud (Sun Jul 19 2009 - 04:15:08 CDT)
- Re: CPU USAGE Benjamin Bouvier (Sun Jul 19 2009 - 04:51:32 CDT)
- Re: CPU USAGE Nicholas M Glykos (Sun Jul 19 2009 - 06:57:56 CDT)
- Re: CPU USAGE Axel Kohlmeyer (Sun Jul 19 2009 - 11:15:14 CDT)
- Re: CPU USAGE mahmoud mirzaei (Sat Jul 18 2009 - 23:07:26 CDT)
- Re: CPU USAGE Axel Kohlmeyer (Sat Jul 18 2009 - 11:50:25 CDT)
- NAMD 2.7b1 Jianhui Tian (Fri Jul 17 2009 - 10:52:28 CDT)
- NAMD hanging on GPU Sadhu, Shubho (NIH/NCI) [F] (Fri Jul 17 2009 - 08:00:21 CDT)
- Reassign Temp during the Production Run twshen (Thu Jul 16 2009 - 12:04:03 CDT)
- Grid Forces documentation Hugh Martin (Thu Jul 16 2009 - 08:02:04 CDT)
- VMD-Installation problems jose correa (Wed Jul 15 2009 - 19:16:35 CDT)
- molecule jumps from one site to the other? uu zhu (Mon Jul 13 2009 - 21:11:52 CDT)
- Implementation of graphite walls Sabine Leroch (Mon Jul 13 2009 - 07:36:05 CDT)
- Fwd: one atom off in the minimization result Chris Harrison (Sun Jul 12 2009 - 18:23:10 CDT)
- Re: Tried to find atom type on node other than node 0 Narender Singh Maan (Mon Jul 13 2009 - 10:46:47 CDT)
- Bad global exclusion count Yogesh Aher (Mon Jul 13 2009 - 05:57:18 CDT)
- Fwd: PROBLEM OF INSTALLATION OF NAMD ipsita basu (Sun Jul 12 2009 - 23:28:30 CDT)
- Fwd: Minimization problem of a protein-DNA complex with namd Chris Harrison (Sun Jul 12 2009 - 18:23:40 CDT)
- one atom off in the minimization result mgssal (Sun Jul 12 2009 - 03:22:46 CDT)
- Minimization problem of a protein-DNA complex with namd sudipta (Sun Jul 12 2009 - 02:21:36 CDT)
- Fwd: 99999999.9999 as vander waals energy Chris Harrison (Sat Jul 11 2009 - 19:38:30 CDT)
- Simulating Protonated base pairs of RNA Monika Sharma (Sat Jul 11 2009 - 07:07:29 CDT)
- pdbalias for PO4 residue gurunath katagi (Sat Jul 11 2009 - 01:09:29 CDT)
- 99999999.9999 as vander waals energy Uma Mageshwari (Sat Jul 11 2009 - 00:18:19 CDT)
- SMD working only at high velocity Elia Zumot (Fri Jul 10 2009 - 13:20:33 CDT)
- Intel 11 compilers Xavier Deupi (Fri Jul 10 2009 - 08:52:58 CDT)
- protein folding doty alexiou (Fri Jul 10 2009 - 03:00:37 CDT)
- bug or custom? BIN ZHANG (Thu Jul 09 2009 - 13:00:44 CDT)
- Fwd: Tried to find atom type on node other than node 0 Chris Harrison (Thu Jul 09 2009 - 09:45:23 CDT)
- Tried to find atom type on node other than node 0 Narender Singh Maan (Thu Jul 09 2009 - 09:00:44 CDT)
- Re: Generation of .psf file of DNA Jian Liu (Thu Jul 09 2009 - 07:43:21 CDT)
- Re: namd hangs or exits with segmentation faults on opteron cluster with infiniband Vlad Cojocaru (Thu Jul 09 2009 - 06:59:31 CDT)
- Another strange error: MStream checksums do not agree Vlad Cojocaru (Thu Jul 09 2009 - 03:05:13 CDT)
- Generation of .psf file of DNA sudipta (Thu Jul 09 2009 - 01:53:25 CDT)
- bicarbonate parameters Brian R Novak (Wed Jul 08 2009 - 13:31:28 CDT)
- FATAL ERROR: Sorry, combined TI and FEP is not implemented Vlad Cojocaru (Wed Jul 08 2009 - 05:41:00 CDT)
- LES problem Irene Newhouse (Tue Jul 07 2009 - 00:30:50 CDT)
- Fatal Error Help Goutham (Mon Jul 06 2009 - 16:10:18 CDT)
- Translocation problem while attempting to use ABF Hugh Martin (Mon Jul 06 2009 - 10:39:38 CDT)
- END: No log file Luis Agullo (LAB) (Mon Jul 06 2009 - 09:56:15 CDT)
- No log file Luis Agullo (LAB) (Mon Jul 06 2009 - 08:41:14 CDT)
- protein collapsing problem ydhuang2727 (Sun Jul 05 2009 - 20:12:38 CDT)
- Re: Re: namd2.7b1 slower with openmpi 1.3.2 than namd2.6 withopenmpi 1.2.6 liupeng012 (Sat Jul 04 2009 - 21:17:15 CDT)
- about psfgen emilia.l.wu (Sat Jul 04 2009 - 08:59:44 CDT)
- implicit solvent model in NAMD? Yinglong Miao (Fri Jul 03 2009 - 15:18:17 CDT)
- namd hangs or exits with segmentation faults on opteron cluster with infiniband Vlad Cojocaru (Fri Jul 03 2009 - 08:16:28 CDT)
- Hardware for NAMD / VMD machine Olve Peersen (Fri Jul 03 2009 - 01:26:11 CDT)
- ERROR! Explicit exclusions or fluctuating charges not supported, atom ignored. emilia wu (Thu Jul 02 2009 - 18:35:32 CDT)
- NAMD_ti.pl Philip Fowler (Wed Jul 01 2009 - 06:45:31 CDT)
- Par and Top files for BCL Kov醕s, S醤dor 羋醡 (Thu Jul 02 2009 - 12:08:08 CDT)
- namd2.7b1 slower with openmpi 1.3.2 than namd2.6 with openmpi 1.2.6 Vlad Cojocaru (Thu Jul 02 2009 - 10:41:23 CDT)
- nose-hoover David A. Horita (Wed Jul 01 2009 - 10:36:30 CDT)
- NAMD_ti.pl Philip Fowler (Wed Jul 01 2009 - 07:50:26 CDT)
- NAMD Installation mahmoud (Wed Jul 01 2009 - 02:53:51 CDT)
- location of the SMD source code Liang (Tue Jun 30 2009 - 13:17:48 CDT)
- Hi,all, the parameters for Strain uu zhu (Tue Jun 30 2009 - 01:32:26 CDT)
- GPGPU Programming summer school at University of Tennessee, Aug 10-14. Axel Kohlmeyer (Mon Jun 29 2009 - 14:43:11 CDT)
- namd cvs 26.06.09, tcl 8.5, loadcoords Vlad Cojocaru (Mon Jun 29 2009 - 09:10:46 CDT)
- Modeling of Gramicidin A Jian Liu (Mon Jun 29 2009 - 08:08:41 CDT)
- Protein collpasing problem! ydhuang2727 (Mon Jun 29 2009 - 01:12:47 CDT)
- defenestrate Peter Freddolino (Sun Jun 28 2009 - 15:20:11 CDT)
- unsubscribe Anna Blice-Baum (Sun Jun 28 2009 - 14:40:10 CDT)
- unsubscribe wavedalla\_at_libero\.it (Sun Jun 28 2009 - 09:49:09 CDT)
- Can I use another solvent rather than TI3P model in namd for MD simulations ? Wang Yf (Sat Jun 27 2009 - 22:30:04 CDT)
- the recent flood of unsubscribe requests Axel Kohlmeyer (Sat Jun 27 2009 - 10:07:28 CDT)
- unsubscribe Ariovaldo de Souza Junior (Sat Jun 27 2009 - 09:25:57 CDT)
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- unsubscribe Vinit Rege (Fri Jun 26 2009 - 22:27:45 CDT)
- unsubscribe Hatley, Jade M (Fri Jun 26 2009 - 19:02:48 CDT)
- colvars: Error: undefined output or restart file. Bonnie Merchant (Fri Jun 26 2009 - 13:41:42 CDT)
- My protein went out of the water box in SMD. Would it have a bad effect on the result? wayj86 wayj86 (Fri Jun 26 2009 - 03:02:46 CDT)
- Grid Forces gbellesia_at_chem.ucsb.edu (Thu Jun 25 2009 - 15:31:19 CDT)
- Does NAMD have any capability to assign coordiantes to novel sequences? Amr Zeinalabideen Majul (Thu Jun 25 2009 - 10:34:43 CDT)
- protein collapsing problem! ydhuang2727 (Thu Jun 25 2009 - 00:08:29 CDT)
- regarding positioning of protein molecule prasun kumar (Wed Jun 24 2009 - 17:39:15 CDT)
- bugfixes in the colvars module (ABF, metadynamics etc.) Giacomo Fiorin (Wed Jun 24 2009 - 16:00:27 CDT)
- Re: launch NAMD from tcl script J Liu (Wed Jun 24 2009 - 08:58:47 CDT)
- launch NAMD from tcl script Floris Buelens (Wed Jun 24 2009 - 06:55:06 CDT)
- Total energy of a residue Mert G黵 (Tue Jun 23 2009 - 10:08:12 CDT)
- Re: 2.7b metadynamics ::hBond component :: folding of a single helix in water Ali Emileh (Mon Jun 22 2009 - 14:23:57 CDT)
- Pair interaction : Energy values are zero Navendu bhatnagar (Sun Jun 21 2009 - 16:01:45 CDT)
- FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR NH3 HC NH3 gurunath katagi (Sat Jun 20 2009 - 12:59:51 CDT)
- VMD/NAMD two identical molecules solvate in a water sphere David Jiang (Sat Jun 20 2009 - 11:02:49 CDT)
- Re: VMD/NAMD two identical molecules solvate in a water sphere Eric H. Lee (Sat Jun 20 2009 - 12:46:25 CDT)
- Re: VMD/NAMD two identical molecules solvate in a water sphere Joshua Adelman (Sat Jun 20 2009 - 12:21:49 CDT)
- Re: VMD/NAMD two identical molecules solvate in a water sphere David Jiang (Tue Jun 23 2009 - 10:27:07 CDT)
- Re: VMD/NAMD two identical molecules solvate in a water sphere Peter Freddolino (Tue Jun 23 2009 - 11:17:54 CDT)
- Re: VMD/NAMD two identical molecules solvate in a water sphere David Jiang (Tue Jun 23 2009 - 11:34:04 CDT)
- Re: VMD/NAMD two identical molecules solvate in a water sphere Peter Freddolino (Tue Jun 23 2009 - 12:06:21 CDT)
- Re: VMD/NAMD two identical molecules solvate in a water sphere David Jiang (Tue Jun 23 2009 - 14:02:48 CDT)
- Re: VMD/NAMD two identical molecules solvate in a water sphere Peter Freddolino (Tue Jun 23 2009 - 14:11:15 CDT)
- Re: VMD/NAMD two identical molecules solvate in a water sphere David Jiang (Tue Jun 23 2009 - 10:27:07 CDT)
- Developing a neutral arginine patch in a topology file urmit shah (Fri Jun 19 2009 - 17:54:19 CDT)
- Re: Reassign temp bay__gulf618_at_sina.com (Wed Jun 17 2009 - 20:44:15 CDT)
- Reassign temp Marcelo Puiatti (Wed Jun 17 2009 - 15:27:18 CDT)
- collective variables Jarrod Nickel (Wed Jun 17 2009 - 11:07:26 CDT)
- How is dG caluclated from dE during FEP? Michael Thomas (Wed Jun 17 2009 - 06:51:31 CDT)
- Re: Re: Thermodynamic integration script - where is it? Floris Buelens (Tue Jun 16 2009 - 02:37:44 CDT)
- to run NAMD on a PC Lixia Jin Day (Mon Jun 15 2009 - 12:59:08 CDT)
- need advices for running NAMD efficiently. Lixia Jin Day (Mon Jun 15 2009 - 12:44:55 CDT)
- Postdoc position in biomolecular simulation Ivaylo, Ivanov (Sat Jun 13 2009 - 02:08:07 CDT)
- Postdoc position in biomolecular simulation Ivaylo, Ivanov (Sat Jun 13 2009 - 01:37:55 CDT)
- Histamine topology file r charbel maroun (Fri Jun 12 2009 - 11:32:35 CDT)
- regarding psfgen algorithm prasun kumar (Fri Jun 12 2009 - 03:22:04 CDT)
- What decides the pulling direction in SMD? 李璀 (Fri Jun 12 2009 - 02:35:15 CDT)
- Force Constant Units Kamilla Kopec (Wed Jun 10 2009 - 12:08:24 CDT)
- compile NAMD with TCP and SMP sudipta (Wed Jun 10 2009 - 00:19:18 CDT)
- ABF simulations Sumanth Jamadagni (Tue Jun 09 2009 - 21:08:10 CDT)
- question about repeating output text ershela.durresi_at_yale.edu (Tue Jun 09 2009 - 05:58:20 CDT)
- How to set the parameters for two different baths in one molecule? uu zhu (Mon Jun 08 2009 - 20:14:36 CDT)
- Bug advisory: RMSD and ABF Jerome Henin (Mon Jun 08 2009 - 17:55:10 CDT)
- Problem namd2 and mpich2 sudipta (Mon Jun 08 2009 - 01:40:58 CDT)
- Read DCD file in Java Kejun (Kevin) Dong (Sat Jun 06 2009 - 00:39:27 CDT)
- regarding protein-protein interaction prasun kumar (Fri Jun 05 2009 - 02:51:37 CDT)
- Re: regarding protein-protein interaction Marcin Krol (Fri Jun 05 2009 - 03:23:13 CDT)
- Re: regarding protein-protein interaction L. Michel Espinoza-Fonseca (Fri Jun 05 2009 - 03:19:43 CDT)
- Re: regarding protein-protein interaction Benjamin Bouvier (Fri Jun 05 2009 - 03:50:21 CDT)
- Re: regarding protein-protein interaction Joshua Adelman (Fri Jun 05 2009 - 10:41:44 CDT)
- protein folding cg doty alexiou (Fri Jun 05 2009 - 01:21:16 CDT)
- Please disregard the spam "Lei sent you private photos on Tagged :)" Lei Shi (Thu Jun 04 2009 - 17:04:05 CDT)
- tclforces and minimization Roman Petrenko (Thu Jun 04 2009 - 16:42:27 CDT)
- abf with colvars example David A. Horita (Thu Jun 04 2009 - 12:53:20 CDT)
- Charmrun/INTEL MAC/2.7 Grabe, Michael David (Thu Jun 04 2009 - 09:21:21 CDT)
- Exclusions and CUDA Benjamin Bouvier (Thu Jun 04 2009 - 03:40:22 CDT)
- NAMD on GPU xiaojing gong (Thu Jun 04 2009 - 02:53:18 CDT)
- namd 2.7b1 on infiniband about the error : stack Traceback liupeng012 (Thu Jun 04 2009 - 00:10:32 CDT)
- Measuring protein diffusion: results too small? Stephen Hicks (Wed Jun 03 2009 - 16:49:03 CDT)
- lamboot -v nodelist Yogesh Aher (Wed Jun 03 2009 - 09:49:15 CDT)
- compile namd2.7b1 on infiniband liupeng012 (Tue Jun 02 2009 - 21:43:16 CDT)
- Namd lite Goutham (Tue Jun 02 2009 - 19:54:21 CDT)
- 2.7b metadynamics ::alpha module :: folding of a single helix in water Ali Emileh (Tue Jun 02 2009 - 18:39:25 CDT)
- Re: 2.7b metadynamics ::alpha module :: folding of a single helix in water Giacomo Fiorin (Fri Jun 05 2009 - 10:53:48 CDT)
- Re: 2.7b metadynamics ::alpha module :: folding of a single helix in water Ali Emileh (Tue Jun 09 2009 - 11:52:19 CDT)
- Re: 2.7b metadynamics ::alpha module :: folding of a single helix in water Giacomo Fiorin (Tue Jun 09 2009 - 12:24:39 CDT)
- Re: 2.7b metadynamics ::alpha module :: folding of a single helix in water Ali Emileh (Tue Jun 09 2009 - 18:02:12 CDT)
- Re: 2.7b metadynamics ::alpha module :: folding of a single helix in water Giacomo Fiorin (Wed Jun 10 2009 - 08:57:38 CDT)
- Re: 2.7b metadynamics ::alpha module :: folding of a single helix in water Ali Emileh (Wed Jul 22 2009 - 21:18:11 CDT)
- Re: 2.7b metadynamics ::alpha module :: folding of a single helix in water Giacomo Fiorin (Mon Jul 27 2009 - 11:52:44 CDT)
- Re: 2.7b metadynamics ::alpha module :: folding of a single helix in water Ali Emileh (Tue Jun 09 2009 - 11:52:19 CDT)
- Re: 2.7b metadynamics ::alpha module :: folding of a single helix in water Giacomo Fiorin (Fri Jun 05 2009 - 10:53:48 CDT)
- Fwd: RESP and CHARMM r charbel maroun (Tue Jun 02 2009 - 08:35:17 CDT)
- IMD, Hostname and Port Nano Group (Tue Jun 02 2009 - 07:40:01 CDT)
- force output of pairInteraction BIN ZHANG (Mon Jun 01 2009 - 17:20:07 CDT)
- Rescale Temperature when velocity of COM is not zero Fred (Rui FENG) (Mon Jun 01 2009 - 15:12:05 CDT)
- Re: Thermodynamic integration script - where is it? Lela Vukovic (Mon Jun 01 2009 - 12:52:38 CDT)
- FATAL ERROR: Bad global exclusion count! KIRTANA S (Mon Jun 01 2009 - 12:37:38 CDT)
- flipdcd Michael Kreim (Sat May 30 2009 - 07:12:34 CDT)
- Regd: Error KIRTANA S (Sun May 31 2009 - 22:52:15 CDT)
- regd: my parameter file KIRTANA S (Fri May 29 2009 - 16:05:26 CDT)
- Regd :parameter file KIRTANA S (Fri May 29 2009 - 15:56:04 CDT)
- visualize energy on a structure Michael Zimmermann (Fri May 29 2009 - 12:20:24 CDT)
- using amber topology and parameter files in NAMD KIRTANA S (Fri May 29 2009 - 12:16:54 CDT)
- water molecules "collapse" during equilibration enz1+_at_pitt.edu (Fri May 29 2009 - 11:38:06 CDT)
- FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE Yogesh Aher (Fri May 29 2009 - 09:34:13 CDT)
- electric field along z-direction Roman Petrenko (Wed May 27 2009 - 16:21:27 CDT)
- unknown path type LSN 周文昌 (Tue May 26 2009 - 07:48:49 CDT)
- TMD for moving ion across membrane yun luo (Mon May 25 2009 - 12:10:59 CDT)
- Software to Mutate DNA sunita gupta (Mon May 25 2009 - 08:39:51 CDT)
- NAMD 2.7b1 running & performance issues Marius Micluta (Mon May 25 2009 - 06:13:07 CDT)
- Force on multiple atoms in ABF Mert G黵 (Sun May 24 2009 - 11:26:16 CDT)
- Postdoctoral Position in Scientific Computing VMD NAMD Postdoc Position (Sat May 23 2009 - 13:41:27 CDT)
- Offset for frame ids in dcd trajectory DimitryASuplatov (Sat May 23 2009 - 11:11:09 CDT)
- Warning: Not all atoms have unique coordinates Jarrod Nickel (Fri May 22 2009 - 14:08:34 CDT)
- GridForces methodology in NAMD 2.7b1 Giovanni Bellesia (Fri May 22 2009 - 13:26:16 CDT)
- triazol parameters Ziemys, Arturas (Thu May 21 2009 - 16:01:53 CDT)
- NAMD2.6 - 1D Periodic Boundary and PME - FATAL ERROR: PME requires periodic boundary conditions. Greg Guthe (Thu May 21 2009 - 15:32:47 CDT)
- selectively write atom coordinates on-the-fly Vasudevan V (Thu May 21 2009 - 11:29:35 CDT)
- Harmonically constrained simulations Sumanth Jamadagni (Thu May 21 2009 - 10:00:13 CDT)
- calculating energy for large log files gurunath katagi (Thu May 21 2009 - 02:30:40 CDT)
- Fw: NAMD 2.7b1 running problem bay__gulf618_at_sina.com (Wed May 20 2009 - 20:10:15 CDT)
- NAMD Tuning page on the wiki vs. NAMD/CUDA Dow_Hurst (Wed May 20 2009 - 18:09:21 CDT)
- tmao molecule Vasudevan V (Wed May 20 2009 - 09:43:40 CDT)
- Free energy of conformational change Branko (Wed May 20 2009 - 06:15:57 CDT)
- NAMD 2.7b1 running problem 周文昌 (Wed May 20 2009 - 05:19:19 CDT)
- calculating forces from dcd trajectory BIN ZHANG (Wed May 20 2009 - 02:18:26 CDT)
- namd-openmosix jose correa (Tue May 19 2009 - 07:29:49 CDT)
- REMD on AIX5.3 Florian Janetzko (Tue May 19 2009 - 06:44:34 CDT)
- How to minimize our model by SD using namd Ahmad Firoz (Tue May 19 2009 - 00:33:01 CDT)
- Periodic Forcing Functions Rick Calloway (Mon May 18 2009 - 16:50:42 CDT)
- NAMD infiniband performance Guanglei Cui (Mon May 18 2009 - 16:10:55 CDT)
- Re: NAMD infiniband performance Lev Lafayette (Tue May 19 2009 - 01:31:47 CDT)
- Re: NAMD infiniband performance Guanglei Cui (Tue May 19 2009 - 08:56:00 CDT)
- Re: NAMD infiniband performance Axel Kohlmeyer (Tue May 19 2009 - 10:00:11 CDT)
- Re: NAMD infiniband performance Guanglei Cui (Tue May 19 2009 - 11:06:09 CDT)
- Re: NAMD infiniband performance Guanglei Cui (Tue May 19 2009 - 11:04:39 CDT)
- Re: NAMD infiniband performance Axel Kohlmeyer (Tue May 19 2009 - 17:13:50 CDT)
- Re: NAMD infiniband performance Guanglei Cui (Mon Jun 01 2009 - 15:15:23 CDT)
- Re: NAMD infiniband performance Axel Kohlmeyer (Mon Jun 01 2009 - 15:54:17 CDT)
- Re: NAMD infiniband performance Guanglei Cui (Mon Jun 01 2009 - 21:27:07 CDT)
- Re: NAMD infiniband performance Axel Kohlmeyer (Mon Jun 01 2009 - 21:58:49 CDT)
- Re: NAMD infiniband performance Guanglei Cui (Tue May 19 2009 - 08:56:00 CDT)
- Re: NAMD infiniband performance Lev Lafayette (Tue May 19 2009 - 01:31:47 CDT)
- about limitdist cong chen (Mon May 18 2009 - 06:11:48 CDT)
- Error running NAMD on CUDA jani sahil (Mon May 18 2009 - 03:34:11 CDT)
- the external electric field vector uu zhu (Mon May 18 2009 - 01:56:29 CDT)
- exclude 1-2 doty alexiou (Fri May 15 2009 - 01:55:09 CDT)
- charm++ build problem Yogesh (Thu May 14 2009 - 08:24:42 CDT)
- TMD biasing Felipe Merino (Thu May 14 2009 - 06:23:23 CDT)
- peptides on surface Jorgen Simonsen (Wed May 13 2009 - 13:16:51 CDT)
- Need help to generate ubq-get-energy.conf Mert G黵 (Wed May 13 2009 - 10:06:55 CDT)
- Re: Need help to generate ubq-get-energy.conf Peter Freddolino (Wed May 13 2009 - 12:03:55 CDT)
- Re: Need help to generate ubq-get-energy.conf Mert G黵 (Wed May 13 2009 - 15:49:24 CDT)
- Re: Need help to generate ubq-get-energy.conf Peter Freddolino (Wed May 13 2009 - 15:55:29 CDT)
- Re: Need help to generate ubq-get-energy.conf Mert G黵 (Thu May 14 2009 - 02:01:27 CDT)
- Re: Need help to generate ubq-get-energy.conf Eric H. Lee (Thu May 14 2009 - 02:52:20 CDT)
- Re: Need help to generate ubq-get-energy.conf Mert G黵 (Thu May 14 2009 - 05:43:46 CDT)
- Re: Need help to generate ubq-get-energy.conf Peter Freddolino (Thu May 14 2009 - 10:33:10 CDT)
- Re: Need help to generate ubq-get-energy.conf Mert G黵 (Thu May 14 2009 - 13:00:57 CDT)
- Re: Need help to generate ubq-get-energy.conf Peter Freddolino (Thu May 14 2009 - 11:33:57 CDT)
- Re: Need help to generate ubq-get-energy.conf Mert G黵 (Wed May 13 2009 - 15:49:24 CDT)
- Re: Need help to generate ubq-get-energy.conf Peter Freddolino (Wed May 13 2009 - 12:03:55 CDT)
- Make NAMD2.7b1 with cuda bug? Lev Lafayette (Tue May 12 2009 - 22:48:04 CDT)
- Re: Make NAMD2.7b1 with cuda bug? Roman Petrenko (Wed May 13 2009 - 08:56:02 CDT)
- Re: Make NAMD2.7b1 with cuda bug? Charles Taylor (Wed May 13 2009 - 09:29:27 CDT)
- Re: Make NAMD2.7b1 with cuda bug? Jim Phillips (Wed May 13 2009 - 11:58:30 CDT)
- Re: Make NAMD2.7b1 with cuda bug? Gengbin Zheng (Wed May 13 2009 - 12:09:03 CDT)
- Re: Make NAMD2.7b1 with cuda bug? Jim Phillips (Wed May 13 2009 - 13:41:29 CDT)
- Re: Make NAMD2.7b1 with cuda bug? Gengbin Zheng (Wed May 13 2009 - 15:47:44 CDT)
- Re: Make NAMD2.7b1 with cuda bug? Lev Lafayette (Thu May 14 2009 - 01:12:41 CDT)
- Re: Make NAMD2.7b1 with cuda bug? jani sahil (Fri May 15 2009 - 03:00:35 CDT)
- Re: Make NAMD2.7b1 with cuda bug? jani sahil (Fri May 15 2009 - 04:23:17 CDT)
- Re: Make NAMD2.7b1 with cuda bug? Roman Petrenko (Wed May 13 2009 - 08:56:02 CDT)
- changing protonation states for a pdb with more than a single polypeptide Elia Zomot (Tue May 12 2009 - 18:47:41 CDT)
- PSF file KIRTANA S (Tue May 12 2009 - 14:29:05 CDT)
- exclude 1-2 or 1-4? doty alexiou (Tue May 12 2009 - 09:56:31 CDT)
- Which compiler-suite was used... Bjoern Olausson (Tue May 12 2009 - 07:26:00 CDT)
- Asymmetric water molecule found Jorgen Simonsen (Tue May 12 2009 - 05:00:45 CDT)
- namd-cuda-intel vs. namd-intel Roman Petrenko (Tue May 12 2009 - 00:32:58 CDT)
- Re: namd-cuda-intel vs. namd-intel Axel Kohlmeyer (Tue May 12 2009 - 06:24:04 CDT)
- Calculating displacement in a system with periodic boundary Fred (Rui FENG) (Mon May 11 2009 - 23:26:21 CDT)
- Re: Calculating displacement in a system with periodic boundary Joshua Adelman (Mon May 11 2009 - 23:44:23 CDT)
- Re: Calculating displacement in a system with periodic boundary Eric H. Lee (Mon May 11 2009 - 23:49:25 CDT)
- Re: Calculating displacement in a system with periodic boundary Fred (Rui FENG) (Tue May 12 2009 - 01:07:22 CDT)
- Re: Calculating displacement in a system with periodic boundary Eric H. Lee (Tue May 12 2009 - 01:15:56 CDT)
- Re: Calculating displacement in a system with periodic boundary Fred (Rui FENG) (Tue May 12 2009 - 01:37:58 CDT)
- Re: Calculating displacement in a system with periodic boundary BIN ZHANG (Tue May 12 2009 - 02:25:48 CDT)
- Re: Calculating displacement in a system with periodic boundary Fred (Rui FENG) (Tue May 12 2009 - 02:52:49 CDT)
- Re: Calculating displacement in a system with periodic boundary Fred (Rui FENG) (Tue May 12 2009 - 01:07:22 CDT)
- FEP on 2.7b1 Christopher Hartshorn (Mon May 11 2009 - 15:38:37 CDT)
- collective variable space PMF, including biasing potential terms? Sebastian Stolzenberg (Wed May 13 2009 - 14:48:05 CDT)
- Re: collective variable space PMF, including biasing potential terms? Jerome Henin (Wed May 13 2009 - 16:23:49 CDT)
- Re: collective variable space PMF, including biasing potential terms? Roman Petrenko (Wed May 13 2009 - 17:00:49 CDT)
- Re: collective variable space PMF, including biasing potential terms? Chris Chipot (Wed May 13 2009 - 17:37:04 CDT)
- Re: collective variable space PMF, including biasing potential terms? Roman Petrenko (Wed May 13 2009 - 17:45:29 CDT)
- Re: collective variable space PMF, including biasing potential terms? Axel Kohlmeyer (Wed May 13 2009 - 17:52:30 CDT)
- Re: collective variable space PMF, including biasing potential terms? Chris Chipot (Wed May 13 2009 - 18:16:54 CDT)
- NAMD 2.7b1: metadynamics+tclForces => "... design error, GlobalMasterServer..." Sebastian Stolzenberg (Thu May 14 2009 - 16:41:16 CDT)
- Re: NAMD 2.7b1: metadynamics+tclForces => "... design error, GlobalMasterServer..." Giacomo Fiorin (Thu May 14 2009 - 19:23:19 CDT)
- mercury ion parameters? Sebastian Stolzenberg (Sat May 23 2009 - 11:12:04 CDT)
- Re: collective variable space PMF, including biasing potential terms? Giacomo Fiorin (Wed May 13 2009 - 16:38:56 CDT)
- Re: collective variable space PMF, including biasing potential terms? Jerome Henin (Wed May 13 2009 - 16:23:49 CDT)
- collective variable space PMF, including biasing potential terms? Sebastian Stolzenberg (Wed May 13 2009 - 14:48:05 CDT)
- SiCortex with Pathscale Christopher Hartshorn (Sat May 09 2009 - 19:52:29 CDT)
- ERROR: Multiple definitions of 'LangevinPiston' roberta.rostagno (Mon May 11 2009 - 07:15:42 CDT)
- ERROR: Multiple definitions of 'LangevinPiston' roberta.rostagno (Mon May 11 2009 - 07:38:38 CDT)
- Re: ERROR: Multiple definitions of 'LangevinPiston' Peter Freddolino (Mon May 11 2009 - 08:09:40 CDT)
- Re: ERROR: Multiple definitions of 'LangevinPiston' roberta.rostagno (Mon May 11 2009 - 08:20:29 CDT)
- Re: ERROR: Multiple definitions of 'LangevinPiston' Peter Freddolino (Mon May 11 2009 - 12:11:57 CDT)
- Re: ERROR: Multiple definitions of 'LangevinPiston' roberta.rostagno (Tue May 12 2009 - 03:02:45 CDT)
- Re: ERROR: Multiple definitions of 'LangevinPiston' Peter Freddolino (Tue May 12 2009 - 06:41:29 CDT)
- Re: ERROR: Multiple definitions of 'LangevinPiston' roberta.rostagno (Thu May 14 2009 - 04:02:29 CDT)
- Re: ERROR: Multiple definitions of 'LangevinPiston' Peter Freddolino (Thu May 14 2009 - 10:19:28 CDT)
- Re: ERROR: Multiple definitions of 'LangevinPiston' Roberta Rostagno (Fri May 15 2009 - 02:19:09 CDT)
- Re: ERROR: Multiple definitions of 'LangevinPiston' Peter Freddolino (Fri May 15 2009 - 05:54:11 CDT)
- Re: ERROR: Multiple definitions of 'LangevinPiston' roberta.rostagno (Wed May 20 2009 - 09:44:02 CDT)
- Re: ERROR: Multiple definitions of 'LangevinPiston' Peter Freddolino (Wed May 20 2009 - 09:59:45 CDT)
- ERROR: Stray PME grid charges detected roberta.rostagno (Mon May 25 2009 - 04:34:11 CDT)
- Re: ERROR: Multiple definitions of 'LangevinPiston' roberta.rostagno (Mon May 11 2009 - 08:20:29 CDT)
- Re: ERROR: Multiple definitions of 'LangevinPiston' Peter Freddolino (Mon May 11 2009 - 08:09:40 CDT)
- lipid bi-layer and SiO2 Raul Araya (Fri May 08 2009 - 14:36:41 CDT)
- NAMD with CUDA Prakash Velayutham (Thu May 07 2009 - 13:06:04 CDT)
- HW - HW IN PARAMETER FILES Jorgen Simonsen (Thu May 07 2009 - 06:17:19 CDT)
- water models and some questions fett_at_vtr.net (Thu May 07 2009 - 06:02:39 CDT)
- running namd2.7 problem ydhuang2727 (Thu May 07 2009 - 01:23:46 CDT)
- force-field for cy3, cy5 dyes Roman Petrenko (Wed May 06 2009 - 19:26:54 CDT)
- (no subject) Wang,Ying (Wed May 06 2009 - 13:50:12 CDT)
- diffusion / fex peptide problem Benjamin Stauch (Wed May 06 2009 - 10:24:16 CDT)
- fatal error: tried to assign bond index before all parameter files were read Jorgen Simonsen (Wed May 06 2009 - 05:36:16 CDT)
- umbrella sampling script Hyundeok Song (Tue May 05 2009 - 17:30:28 CDT)
- Langevin damping coefficient Gianluca Interlandi (Tue May 05 2009 - 16:49:30 CDT)
- Postdoc position in computational biophysics and nanotechnology Aleksei Aksimentiev (Tue May 05 2009 - 14:34:04 CDT)
- Re: Value for "firsttimestep" when restarting MD Bjoern Olausson (Tue May 05 2009 - 12:45:56 CDT)
- Value for "firsttimestep" when restarting MD Bjoern Olausson (Tue May 05 2009 - 09:50:42 CDT)
- regarding simulation prasun kumar (Tue May 05 2009 - 08:48:00 CDT)
- DCOLVARS_DEBUG George Madalin Giambasu (Mon May 04 2009 - 22:49:17 CDT)
- truncated octahedral daniel aguayo (Mon May 04 2009 - 20:21:37 CDT)
- geomtery optimization with namd Roman Petrenko (Mon May 04 2009 - 16:18:03 CDT)
- dummy atom mass changed yun luo (Mon May 04 2009 - 14:54:27 CDT)
- Re: dummy atom mass changed Chris Harrison (Mon May 04 2009 - 15:33:57 CDT)
- Re: dummy atom mass changed yun luo (Mon May 04 2009 - 16:24:59 CDT)
- Re: dummy atom mass changed Jerome Henin (Mon May 04 2009 - 17:39:22 CDT)
- Re: dummy atom mass changed daniel aguayo (Mon May 04 2009 - 19:53:14 CDT)
- Re: dummy atom mass changed Chris Harrison (Mon May 04 2009 - 22:24:32 CDT)
- Re: dummy atom mass changed daniel aguayo (Tue May 05 2009 - 10:18:39 CDT)
- Re: dummy atom mass changed Jerome Henin (Tue May 05 2009 - 10:43:48 CDT)
- Re: dummy atom mass changed yun luo (Tue May 05 2009 - 11:49:06 CDT)
- Re: dummy atom mass changed yun luo (Tue May 05 2009 - 12:19:05 CDT)
- Re: dummy atom mass changed Chris Harrison (Tue May 05 2009 - 12:53:00 CDT)
- Re: dummy atom mass changed yun luo (Tue May 05 2009 - 15:26:46 CDT)
- Re: dummy atom mass changed yun luo (Wed May 06 2009 - 11:50:06 CDT)
- Re: dummy atom mass changed Chris Harrison (Wed May 06 2009 - 13:09:26 CDT)
- Re: dummy atom mass changed Floris Buelens (Thu May 07 2009 - 05:09:36 CDT)
- Re: dummy atom mass changed yun luo (Thu May 07 2009 - 11:18:43 CDT)
- Re: dummy atom mass changed yun luo (Tue May 12 2009 - 11:10:11 CDT)
- Re: dummy atom mass changed Jerome Henin (Tue May 12 2009 - 11:51:55 CDT)
- Re: dummy atom mass changed yun luo (Mon May 04 2009 - 16:24:59 CDT)
- Re: dummy atom mass changed Chris Harrison (Mon May 04 2009 - 15:33:57 CDT)
- Regarding amber parameters using NAMD Jorgen Simonsen (Mon May 04 2009 - 03:22:27 CDT)
- NAMD 2.7b1 and clustermatic Gianluca Interlandi (Sun May 03 2009 - 19:26:08 CDT)
- NPAT - NPgT ensemble Bjoern Olausson (Sat May 02 2009 - 07:43:34 CDT)
- CGMD ? Hydrophobic scale BIN ZHANG (Fri May 01 2009 - 17:00:12 CDT)
- Force Fields Goutham (Fri May 01 2009 - 00:36:09 CDT)
- FreeEnergy and minimization Roman Petrenko (Thu Apr 30 2009 - 23:31:55 CDT)
- crash with more than 96 processors (v2.7b1) Grace Brannigan (Thu Apr 30 2009 - 14:49:58 CDT)
- Setting PME Grid DimitryASuplatov (Thu Apr 30 2009 - 11:13:46 CDT)
- two independent groups of constraints Marcin Krol (Thu Apr 30 2009 - 07:44:41 CDT)
- Energy minimization failure DimitryASuplatov (Thu Apr 30 2009 - 05:23:31 CDT)
- running problem ydhuang2727 (Thu Apr 30 2009 - 05:08:22 CDT)
- NAMD 2.7b1 on NCSA Abe Gianluca Interlandi (Wed Apr 29 2009 - 22:16:32 CDT)
- Re: NAMD 2.7b1 on NCSA Abe Peter Freddolino (Thu Apr 30 2009 - 06:41:50 CDT)
- Re: NAMD 2.7b1 on NCSA Abe Gianluca Interlandi (Thu Apr 30 2009 - 12:15:37 CDT)
- topology and parameter files for guanidinium ion Payel Das (Thu Apr 30 2009 - 15:04:48 CDT)
- Re: topology and parameter files for guanidinium ion Peter Freddolino (Thu Apr 30 2009 - 16:32:21 CDT)
- Re: NAMD 2.7b1 on NCSA Abe Peter Freddolino (Thu Apr 30 2009 - 20:11:27 CDT)
- Re: NAMD 2.7b1 on NCSA Abe Gianluca Interlandi (Thu Apr 30 2009 - 22:58:09 CDT)
- Re: NAMD 2.7b1 on NCSA Abe Peter Freddolino (Fri May 01 2009 - 06:41:23 CDT)
- Re: NAMD 2.7b1 on NCSA Abe Gianluca Interlandi (Fri May 01 2009 - 12:18:05 CDT)
- Re: NAMD 2.7b1 on NCSA Abe Gianluca Interlandi (Tue May 05 2009 - 16:53:27 CDT)
- Re: NAMD 2.7b1 on NCSA Abe Gianluca Interlandi (Thu Apr 30 2009 - 12:15:37 CDT)
- Re: NAMD 2.7b1 on NCSA Abe Peter Freddolino (Thu Apr 30 2009 - 06:41:50 CDT)
- Benzene PSF Matt Krems (Wed Apr 29 2009 - 19:04:27 CDT)
- protein shifts out of the water box Eric Userlist (Wed Apr 29 2009 - 18:52:16 CDT)
- FEP tutorial graph question Christopher Hartshorn (Wed Apr 29 2009 - 15:35:27 CDT)
- Re: FEP tutorial graph question Chris Harrison (Wed Apr 29 2009 - 16:17:07 CDT)
- Re: FEP tutorial graph question Jerome Henin (Wed Apr 29 2009 - 18:36:35 CDT)
- cell on namd 2.7b1 alessandro.venturelli_at_univr.it (Wed Apr 29 2009 - 08:10:01 CDT)
- water tail correction Floris Buelens (Wed Apr 29 2009 - 05:51:55 CDT)
- Re: water tail correction Peter Freddolino (Wed Apr 29 2009 - 07:09:45 CDT)
- Re: water tail correction Peter Freddolino (Wed Apr 29 2009 - 10:26:24 CDT)
- Re: water tail correction Floris Buelens (Fri May 22 2009 - 05:40:00 CDT)
- Re: water tail correction Peter Freddolino (Fri May 22 2009 - 13:34:16 CDT)
- Re: water tail correction Floris Buelens (Mon May 25 2009 - 15:51:16 CDT)
- Re: water tail correction Peter Freddolino (Tue May 26 2009 - 14:17:03 CDT)
- Re: water tail correction Floris Buelens (Wed May 27 2009 - 03:16:33 CDT)
- Re: water tail correction Peter Freddolino (Thu May 28 2009 - 13:12:04 CDT)
- Re: water tail correction Peter Freddolino (Fri May 22 2009 - 16:16:59 CDT)
- Re: water tail correction Floris Buelens (Fri May 22 2009 - 05:40:00 CDT)
- how to set initial velocity? uu zhu (Tue Apr 28 2009 - 21:27:37 CDT)
- force-field for ATP Roman Petrenko (Tue Apr 28 2009 - 18:55:05 CDT)
- System expands: CCL4 simulation; NPT(Langevin Piston) satya work (Tue Apr 28 2009 - 16:10:32 CDT)
- crash with more than 96 processors (v2.7b1) Grace Brannigan (Tue Apr 28 2009 - 14:16:07 CDT)
- biotin parameters and topology Brian R Novak (Tue Apr 28 2009 - 12:37:53 CDT)
- +1 offset to VMD index file? DimitryASuplatov (Tue Apr 28 2009 - 08:40:33 CDT)
- Optimizing configuration option for fast calculations DimitryASuplatov (Tue Apr 28 2009 - 07:16:00 CDT)
- Adding a new bond to CHARMM DimitryASuplatov (Sat Apr 25 2009 - 08:23:19 CDT)
- Yet another NAMD speed concerns DimitryASuplatov (Sat Apr 25 2009 - 04:44:44 CDT)
- compile NAMD 2.7b1 on Intel Xeon(R) infiniband cluster 娴锋竻 姊 (Sat Apr 25 2009 - 01:44:24 CDT)
- Copper parameters for CHARMM DimitryASuplatov (Fri Apr 24 2009 - 11:02:50 CDT)
- how to install NAMD on suse10_ppc64 without xlc bay__gulf618_at_sina.com (Fri Apr 24 2009 - 05:18:04 CDT)
- Namd and MM-PBSA Esteban Gabriel Vega Hissi (Thu Apr 23 2009 - 10:42:49 CDT)
- unsubscribe Matthew Ambrosia (Thu Apr 23 2009 - 09:08:56 CDT)
- Compile Problem xiaojing gong (Thu Apr 23 2009 - 07:42:51 CDT)
- lipidmonolayer balaji nagarajan (Wed Apr 22 2009 - 14:58:25 CDT)
- mapping of force vectors during SMD Jeff Forbes (Wed Apr 22 2009 - 13:42:23 CDT)
- structure problem Ahlam Al-Rawi (Wed Apr 22 2009 - 12:22:29 CDT)
- Constraints in NAMD DimitryASuplatov (Wed Apr 22 2009 - 09:50:37 CDT)
- FATAL ERROR: Periodic cell has become too small for original patch grid! DimitryASuplatov (Wed Apr 22 2009 - 01:44:45 CDT)
- VDW distance in energy minimized conformation Lixia Jin Day (Tue Apr 21 2009 - 17:11:42 CDT)
- can I change coordinate before restart? Mark M Huntress (Tue Apr 21 2009 - 16:03:55 CDT)
- 2.7b1 + CUDA + STMV Charles Taylor (Tue Apr 21 2009 - 09:25:44 CDT)
- tip4p on namd 2.7b fett_at_vtr.net (Tue Apr 21 2009 - 07:45:40 CDT)
- Re: tip4p on namd 2.7b Peter Freddolino (Tue Apr 21 2009 - 09:36:39 CDT)
- Re: tip4p on namd 2.7b Guanglei Cui (Wed Apr 22 2009 - 10:52:19 CDT)
- Re: tip4p on namd 2.7b Peter Freddolino (Wed Apr 22 2009 - 12:19:33 CDT)
- Re: tip4p on namd 2.7b Guanglei Cui (Wed Apr 22 2009 - 16:17:57 CDT)
- PARAM22 and CMAP correction Gianluca Interlandi (Wed Apr 22 2009 - 13:30:48 CDT)
- Re: PARAM22 and CMAP correction Eric H. Lee (Wed Apr 22 2009 - 22:34:19 CDT)
- NAMD 2.7b1 on Abe Gianluca Interlandi (Sat Apr 25 2009 - 12:17:06 CDT)
- soft-core FEP in namd 2.7b Sebastian Stolzenberg (Fri May 08 2009 - 11:57:10 CDT)
- recent papers on MD gotchas with PRNG seeds Brian Bennion (Fri May 08 2009 - 14:20:39 CDT)
- Re: recent papers on MD gotchas with PRNG seeds Peter Freddolino (Sat May 09 2009 - 17:22:43 CDT)
- Re: soft-core FEP in namd 2.7b Chris Harrison (Fri May 08 2009 - 16:14:44 CDT)
- Re: soft-core FEP in namd 2.7b Sebastian Stolzenberg (Sun May 10 2009 - 10:36:47 CDT)
- Re: soft-core FEP in namd 2.7b Jerome Henin (Sun May 10 2009 - 11:50:25 CDT)
- Re: soft-core FEP in namd 2.7b Sebastian Stolzenberg (Sun May 10 2009 - 21:29:32 CDT)
- Re: soft-core FEP in namd 2.7b Jerome Henin (Sun May 10 2009 - 22:19:52 CDT)
- Re: soft-core FEP in namd 2.7b yun luo (Mon May 11 2009 - 12:31:49 CDT)
- Re: soft-core FEP in namd 2.7b Jerome Henin (Mon May 11 2009 - 16:39:37 CDT)
- Re: tip4p on namd 2.7b Guanglei Cui (Wed Apr 22 2009 - 10:52:19 CDT)
- Re: tip4p on namd 2.7b Peter Freddolino (Tue Apr 21 2009 - 09:36:39 CDT)
- Parallel TMD (2.7b) dies : "MPICH internal error" Ali Emileh (Mon Apr 20 2009 - 11:00:11 CDT)
- Re: compiling error of NAMD2.7b1 Joachim Hein (Mon Apr 20 2009 - 06:05:38 CDT)
- Re: compiling error of NAMD2.7b1 BIN ZHANG (Mon Apr 20 2009 - 12:30:17 CDT)
- Re: compiling error of NAMD2.7b1 Peter Freddolino (Mon Apr 20 2009 - 13:12:01 CDT)
- Re: compiling error of NAMD2.7b1 Joachim Hein (Mon Apr 20 2009 - 13:22:11 CDT)
- Re: compiling error of NAMD2.7b1 Peter Freddolino (Mon Apr 20 2009 - 14:49:07 CDT)
- Re: compiling error of NAMD2.7b1 BIN ZHANG (Mon Apr 20 2009 - 13:41:01 CDT)
- Re: compiling error of NAMD2.7b1 Peter Freddolino (Mon Apr 20 2009 - 14:47:09 CDT)
- Re: compiling error of NAMD2.7b1 Joachim Hein (Tue Apr 21 2009 - 04:18:14 CDT)
- Re: compiling error of NAMD2.7b1 Joachim Hein (Mon Apr 20 2009 - 12:53:59 CDT)
- Re: compiling error of NAMD2.7b1 Peter Freddolino (Mon Apr 20 2009 - 13:12:01 CDT)
- Re: compiling error of NAMD2.7b1 BIN ZHANG (Mon Apr 20 2009 - 12:30:17 CDT)
- Peptide in Membrane Environment: loosing water from one leaflet Praveen Agrawal (Mon Apr 20 2009 - 05:53:23 CDT)
- Metadynamics in NAMD 周文昌 (Mon Apr 20 2009 - 05:50:42 CDT)
- Cylindrical harmonic BC and constraintScaling Elsa Fernanda de Sousa Henriques (Mon Apr 20 2009 - 05:22:25 CDT)
- Pressure coupling and system heating DimitryASuplatov (Mon Apr 20 2009 - 03:38:36 CDT)
- NAMD and new sugar parameter set Gianluca Interlandi (Mon Apr 20 2009 - 00:42:14 CDT)
- I can't keep my pulling directions the same with the SMD vector Mert G黵 (Sun Apr 19 2009 - 07:56:00 CDT)
- Re: I can't keep my pulling directions the same with the SMD vector Chris Harrison (Sun Apr 19 2009 - 10:25:14 CDT)
- Re: I can't keep my pulling directions the same with the SMD vector Mert G黵 (Sun Apr 19 2009 - 11:10:11 CDT)
- Re: I can't keep my pulling directions the same with the SMD vector Chris Harrison (Sun Apr 19 2009 - 18:27:24 CDT)
- Re: I can't keep my pulling directions the same with the SMD vector Mert G黵 (Mon Apr 20 2009 - 03:16:39 CDT)
- Re: I can't keep my pulling directions the same with the SMD vector Axel Kohlmeyer (Mon Apr 20 2009 - 08:41:22 CDT)
- Re: I can't keep my pulling directions the same with the SMD vector Mert G黵 (Tue Apr 21 2009 - 02:49:19 CDT)
- Re: I can't keep my pulling directions the same with the SMD vector Axel Kohlmeyer (Tue Apr 21 2009 - 07:27:50 CDT)
- Re: I can't keep my pulling directions the same with the SMD vector Mert G黵 (Sun Apr 19 2009 - 11:10:11 CDT)
- Re: I can't keep my pulling directions the same with the SMD vector Chris Harrison (Sun Apr 19 2009 - 10:25:14 CDT)
- compiling error of NAMD2.7b1 zhngbn_at_gmail.com (Sun Apr 19 2009 - 03:02:44 CDT)
- restart REMD simulation Segun Jung (Sat Apr 18 2009 - 21:32:55 CDT)
- cvs logs BIN ZHANG (Fri Apr 17 2009 - 13:53:54 CDT)
- RE: display all frames simultaneously Luis Gracia (Fri Apr 17 2009 - 00:35:29 CDT)
- Speeding up: Dummy constructions for aromatics or hydrogens DimitryASuplatov (Fri Apr 17 2009 - 12:11:27 CDT)
- NAMD 2.7b1 on Ranger/MPI Problems? Jeff Wereszczynski (Fri Apr 17 2009 - 00:56:30 CDT)
- display all frames simultaneously Samuel Coulbourn Flores 鑺卞北 (Thu Apr 16 2009 - 21:35:59 CDT)
- How to set the parameters for C60? uu zhu (Thu Apr 16 2009 - 05:06:37 CDT)
- Dihedral Restraints during MD simulation Matthieu Wilhelm (Wed Apr 15 2009 - 12:33:04 CDT)
- NAMD 1.7b1 quits writing files/hangs Jason Russler (Wed Apr 15 2009 - 08:00:49 CDT)
- elastic network BIN ZHANG (Tue Apr 14 2009 - 18:10:37 CDT)
- How can I fix lipid lateral area in membrane simulation? Leonardo Herrera (Tue Apr 14 2009 - 12:39:38 CDT)
- 4 sequential jobs work on laptops, but only first one works on supercomputer JT (Mon Apr 13 2009 - 18:00:49 CDT)
- Selectively write atoms to dcd files DimitryASuplatov (Mon Apr 13 2009 - 12:20:01 CDT)
- Water is boiling with namd and charmm DimitryASuplatov (Mon Apr 13 2009 - 09:27:54 CDT)
- Fwd: psf file creation gurunath katagi (Sun Apr 12 2009 - 19:43:48 CDT)
- Error : DIDN'T FIND vdW PARAMETER FOR ATOM TYPE C11 Goutham (Sat Apr 11 2009 - 00:54:22 CDT)
- Keyword to start FEP calculation in NAMD 2.7b1 govardhan reddy (Fri Apr 10 2009 - 15:22:30 CDT)
- PCA Analysis of CGMD Anirban Ghosh (Thu Apr 09 2009 - 07:23:04 CDT)
- Re: PCA Analysis of CGMD Joshua Adelman (Thu Apr 09 2009 - 10:28:06 CDT)
- RE: PCA Analysis of CGMD Anirban Ghosh (Fri Apr 10 2009 - 04:08:25 CDT)
- RE: PCA Analysis of CGMD Rogan Carr (Fri Apr 10 2009 - 09:47:35 CDT)
- Re: PCA Analysis of CGMD Joshua Adelman (Fri Apr 10 2009 - 10:20:04 CDT)
- Re: PCA Analysis of CGMD Anirban (Wed Apr 15 2009 - 14:44:29 CDT)
- Re: PCA Analysis of CGMD Joshua Adelman (Wed Apr 15 2009 - 09:45:53 CDT)
- Re: PCA Analysis of CGMD Anirban (Wed Apr 15 2009 - 15:42:44 CDT)
- Re: PCA Analysis of CGMD Joshua Adelman (Wed Apr 15 2009 - 10:35:00 CDT)
- Re: PCA Analysis of CGMD Giacomo Fiorin (Wed Apr 15 2009 - 11:20:39 CDT)
- RE: PCA Analysis of CGMD Anirban Ghosh (Fri Apr 10 2009 - 04:08:25 CDT)
- Re: PCA Analysis of CGMD Joshua Adelman (Thu Apr 09 2009 - 10:28:06 CDT)
- soft-core potential for FEP felmerino_at_uchile.cl (Wed Apr 08 2009 - 17:46:33 CDT)
- TMD RMSD problem Elif Ozkirimli (Wed Apr 08 2009 - 15:21:16 CDT)
- Evaluating kinetic energy from a modified DCD file Mert G黵 (Wed Apr 08 2009 - 14:33:05 CDT)
- Re: Evaluating kinetic energy from a modified DCD file Peter Freddolino (Wed Apr 08 2009 - 15:15:00 CDT)
- Re: Evaluating kinetic energy from a modified DCD file Mert G黵 (Wed Apr 08 2009 - 16:57:01 CDT)
- Re: Evaluating kinetic energy from a modified DCD file JT (Fri Apr 10 2009 - 11:36:52 CDT)
- Re: Evaluating kinetic energy from a modified DCD file Mert G黵 (Fri Apr 10 2009 - 12:52:08 CDT)
- RE: Evaluating kinetic energy from a modified DCD file Tibbitt, Jeffrey A. (Fri Apr 10 2009 - 15:03:24 CDT)
- RE: Evaluating kinetic energy from a modified DCD file JT (Sat Apr 11 2009 - 03:47:57 CDT)
- Re: Evaluating kinetic energy from a modified DCD file Mert G黵 (Sun Apr 12 2009 - 08:11:21 CDT)
- Re: Evaluating kinetic energy from a modified DCD file Peter Freddolino (Wed Apr 08 2009 - 15:15:00 CDT)
- problem namd2-MPICH jose correa (Wed Apr 08 2009 - 14:05:09 CDT)
- Compiling NAMD on Ranger shayan_at_msu.edu (Wed Apr 08 2009 - 07:33:26 CDT)
- erergy gradient tolerance in Configuration Files uu zhu (Wed Apr 08 2009 - 05:55:49 CDT)
- constraints dota (Wed Apr 08 2009 - 04:23:40 CDT)
- Writing 3 subsequent timesteps to the DCD file Mert G黵 (Tue Apr 07 2009 - 06:24:18 CDT)
- Re: Writing 3 subsequent timesteps to the DCD file Axel Kohlmeyer (Tue Apr 07 2009 - 07:45:54 CDT)
- Re: Writing 3 subsequent timesteps to the DCD file Mert G黵 (Wed Apr 08 2009 - 04:44:09 CDT)
- Re: Writing 3 subsequent timesteps to the DCD file Axel Kohlmeyer (Wed Apr 08 2009 - 08:23:26 CDT)
- Re: Writing 3 subsequent timesteps to the DCD file David Hardy (Wed Apr 08 2009 - 09:33:40 CDT)
- Re: Writing 3 subsequent timesteps to the DCD file Axel Kohlmeyer (Wed Apr 08 2009 - 10:26:17 CDT)
- Re: Writing 3 subsequent timesteps to the DCD file Mert G黵 (Wed Apr 08 2009 - 13:40:43 CDT)
- Re: Writing 3 subsequent timesteps to the DCD file Mert G黵 (Wed Apr 08 2009 - 14:36:45 CDT)
- Re: Writing 3 subsequent timesteps to the DCD file Grace Brannigan (Wed Apr 08 2009 - 17:36:19 CDT)
- Re: Writing 3 subsequent timesteps to the DCD file Mert G黵 (Fri Apr 10 2009 - 10:24:23 CDT)
- Re: Writing 3 subsequent timesteps to the DCD file Axel Kohlmeyer (Fri Apr 10 2009 - 12:02:06 CDT)
- Re: Writing 3 subsequent timesteps to the DCD file Giacomo Fiorin (Wed Apr 08 2009 - 10:22:46 CDT)
- Re: Writing 3 subsequent timesteps to the DCD file Axel Kohlmeyer (Wed Apr 08 2009 - 08:23:26 CDT)
- outputname and restartname Neelanjana Sengupta (Tue Apr 07 2009 - 01:45:19 CDT)
- NAMD job dies on 2-quad core server vivek.viv.sharma_at_gmail.com (Sun Apr 05 2009 - 23:45:28 CDT)
- Re: NAMD job dies on 2-quad core server Axel Kohlmeyer (Mon Apr 06 2009 - 08:44:54 CDT)
- Re: Re: NAMD job dies on 2-quad core server vivek.viv.sharma_at_gmail.com (Thu Apr 09 2009 - 01:44:01 CDT)
- Re: Re: NAMD job dies on 2-quad core server Axel Kohlmeyer (Thu Apr 09 2009 - 09:03:24 CDT)
- Re: NAMD job dies on 2-quad core server Gengbin Zheng (Thu Apr 09 2009 - 10:22:04 CDT)
- Re: Re: NAMD job dies on 2-quad core server vivek.viv.sharma_at_gmail.com (Thu Apr 09 2009 - 22:32:12 CDT)
- Re: NAMD job dies on 2-quad core server Gengbin Zheng (Thu Apr 09 2009 - 23:14:31 CDT)
- Re: Re: NAMD job dies on 2-quad core server vivek.viv.sharma_at_gmail.com (Thu Apr 09 2009 - 01:44:01 CDT)
- Re: NAMD job dies on 2-quad core server Axel Kohlmeyer (Mon Apr 06 2009 - 08:44:54 CDT)
- lammps input data file accomp lin (Sun Apr 05 2009 - 21:44:56 CDT)
- how to install namd in windows xp balaji nagarajan (Sat Apr 04 2009 - 01:11:00 CDT)
- Exiting prematurely BIN ZHANG (Fri Apr 03 2009 - 02:22:28 CDT)
- regarding implicit solvent models ramya narasimhan (Fri Apr 03 2009 - 01:59:57 CDT)
- psf file creation gurunath katagi (Fri Apr 03 2009 - 00:41:24 CDT)
- Jarzynski equality and the pull direction in SMD Paulo Cesar Telles de Souza (Thu Apr 02 2009 - 19:00:40 CDT)
- NAMD 2.7b1 on Athlon64 Gigabit MPI - Compile Error "src/Settle.C:153: error: 慱mm_cvtsd_f64 was not declared in this scope" Greg Guthe (Thu Apr 02 2009 - 18:50:44 CDT)
- .inter.bin files? Joachim Hein (Thu Apr 02 2009 - 10:24:20 CDT)
- PSF/top/inp for joint charmm/amber benchmark Andrew Fant (Tue Mar 31 2009 - 17:03:48 CDT)
- RAMD in NAMD Vlad Cojocaru (Wed Apr 01 2009 - 03:24:52 CDT)
- how to config two different files for fixed atoms karthik s (Tue Mar 31 2009 - 06:54:10 CDT)
- smd direction Wang,Ying (Mon Mar 30 2009 - 10:04:28 CDT)
- NAMD 2.7b1 on Teragrid Ali Emileh (Mon Mar 30 2009 - 09:55:33 CDT)
- Pulling atoms in different directions Rahul Bhowmik (Sun Mar 29 2009 - 15:59:01 CDT)
- Error generating file.psf for cholesterol, missing coordinates in file.pdb. Leonardo Herrera (Sun Mar 29 2009 - 14:56:20 CDT)
- NAMD is too slow?! DimitryASuplatov (Sun Mar 29 2009 - 04:37:39 CDT)
- Interactive protonation DimitryASuplatov (Sat Mar 28 2009 - 16:46:51 CDT)
- NAMD and CFF forcefields C. Denise Enekwa (Sat Mar 28 2009 - 13:22:36 CDT)
- modifying a nucleobase jfgaff_at_ncsu.edu (Sat Mar 28 2009 - 09:05:01 CDT)
- use of tiElecLambdaStart (NAMD 2.7b1) brmorgan_at_clarku.edu (Fri Mar 27 2009 - 11:00:51 CDT)
- Re: use of tiElecLambdaStart (NAMD 2.7b1) Chris Harrison (Fri Mar 27 2009 - 14:33:04 CDT)
- Re: use of tiElecLambdaStart (NAMD 2.7b1) Chris Harrison (Fri Mar 27 2009 - 15:45:41 CDT)
- Re: use of tiElecLambdaStart (NAMD 2.7b1) Jerome Henin (Fri Mar 27 2009 - 16:32:31 CDT)
- Re: use of tiElecLambdaStart (NAMD 2.7b1) brmorgan_at_clarku.edu (Mon Mar 30 2009 - 13:21:34 CDT)
- Re: use of tiElecLambdaStart (NAMD 2.7b1) Floris Buelens (Tue Mar 31 2009 - 04:29:56 CDT)
- Re: use of tiElecLambdaStart (NAMD 2.7b1) Chris Harrison (Fri Mar 27 2009 - 14:33:04 CDT)
- NAMD and multi-rail IB for improved latency Dow Hurst (Thu Mar 26 2009 - 21:55:13 CDT)
- BUILDING BPTI jose correa (Thu Mar 26 2009 - 14:53:43 CDT)
- NAMD 2.7b1 on SGI Altix 330 David McGiven (Thu Mar 26 2009 - 08:50:31 CDT)
- Free energy of conformational change Lixia Jin Day (Wed Mar 25 2009 - 15:21:19 CDT)
- Scale for Potential Bond Parameter Mohamed Seyam (Wed Mar 25 2009 - 14:32:28 CDT)
- MINIMIZER SLOWLY MOVING ATOMS WITH BAD CONTACTS DOWNHILL David Tanner (Wed Mar 25 2009 - 12:47:44 CDT)
- TMD on tRNA does not converge Segun Jung (Wed Mar 25 2009 - 11:13:21 CDT)
- Rosetta Academic Training Webinar Nir London (Wed Mar 25 2009 - 11:09:54 CDT)
- processor counts FFT and NAMD Bishop, Thomas C (Wed Mar 25 2009 - 10:42:43 CDT)
- NAMD 2.7b1 release Jim Phillips (Wed Mar 25 2009 - 10:16:18 CDT)
- phosphoserine simulation using toppar files and NAMD hgrabner (Wed Mar 25 2009 - 06:55:56 CDT)
- About CUDA version of NAMD 2.7 B1 wang (Wed Mar 25 2009 - 00:57:33 CDT)
- Gromacs simulation not running in NAMD abhijit ramachandran (Mon Mar 23 2009 - 21:19:32 CDT)
- alanine dipeptide: no dihdral energy terms? Sebastian Stolzenberg (Mon Mar 23 2009 - 22:33:03 CDT)
- Re: alanine dipeptide: no dihdral energy terms? Peter Freddolino (Mon Mar 23 2009 - 22:45:01 CDT)
- Re: alanine dipeptide: no dihdral energy terms? Sebastian Stolzenberg (Thu Mar 26 2009 - 19:21:04 CDT)
- Re: alanine dipeptide: no dihdral energy terms? Peter Freddolino (Fri Mar 27 2009 - 14:42:54 CDT)
- how to do: FEP e2?, a protonating mutation? Sebastian Stolzenberg (Tue Apr 07 2009 - 19:15:19 CDT)
- Re: how to do: FEP e2?, a protonating mutation? S閎astien L間ar (Thu Apr 09 2009 - 10:48:06 CDT)
- Unfavorable anti conformation after GLUP patching? Sebastian Stolzenberg (Tue Apr 14 2009 - 19:13:21 CDT)
- Re: Unfavorable anti conformation after GLUP patching? S閎astien L間ar (Wed Apr 15 2009 - 22:06:14 CDT)
- Re: Unfavorable anti conformation after GLUP patching? Sebastian Stolzenberg (Thu Apr 16 2009 - 11:00:17 CDT)
- Re: Re: Unfavorable anti conformation after GLUP patching? S茅bastien L茅gar茅 (Sat Apr 18 2009 - 21:43:22 CDT)
- Re: how to do: FEP e2?, a protonating mutation? S茅bastien L茅gar茅 (Wed Apr 15 2009 - 22:32:27 CDT)
- Re: alanine dipeptide: no dihdral energy terms? Peter Freddolino (Mon Mar 23 2009 - 22:45:01 CDT)
- Re: Gromacs simulation not running in NAMD Peter Freddolino (Mon Mar 23 2009 - 22:43:27 CDT)
- alanine dipeptide: no dihdral energy terms? Sebastian Stolzenberg (Mon Mar 23 2009 - 22:33:03 CDT)
- polymer topology file accomp lin (Mon Mar 23 2009 - 07:41:38 CDT)
- Re: vmd-l: GTP topology file Peter Freddolino (Fri Mar 20 2009 - 12:03:01 CDT)
- GTP topology file tiziano gallo cassarino (Fri Mar 20 2009 - 08:47:23 CDT)
- acridine orange Rudra Banerjee (Thu Mar 19 2009 - 23:54:50 CDT)
- Re: FW: NAMD 2.6, AMD64, MVAPICH2 compile error Thomas C. Bishop (Thu Mar 19 2009 - 16:31:27 CDT)
- how to use constraints properly Roman Petrenko (Thu Mar 19 2009 - 13:38:24 CDT)
- Using Amber FF in NAMD Joshua Adelman (Wed Mar 18 2009 - 18:13:33 CDT)
- Amber ff99sb force-field in namd Joshua Adelman (Wed Mar 18 2009 - 17:25:13 CDT)
- PRESSURE, GPRESSURE, PRESSAVG, and GPRESSAVG Dennis Glass (Wed Mar 18 2009 - 11:13:12 CDT)
- cg protein folding doty alexiou (Wed Mar 18 2009 - 09:51:17 CDT)
- bracket in the log file Lei Zhang (Tue Mar 17 2009 - 16:29:07 CDT)
- how to get rid of TCL messages in namd.log from tclForcesScript Roman Petrenko (Fri Mar 13 2009 - 18:45:21 CDT)
- alchemical fep amber topology George Madalin Giambasu (Fri Mar 13 2009 - 13:55:22 CDT)
- Reference file for the constraining force in Umbrella Sampling Mert G黵 (Thu Mar 12 2009 - 18:02:24 CDT)
- FEP restart? Christopher Hartshorn (Wed Mar 11 2009 - 19:34:59 CDT)
- FATAL ERROR: Duplicate bond 鐠 鏉 (Wed Mar 11 2009 - 02:45:17 CDT)
- Selectively turning off electrostatic interactions govardhan reddy (Wed Mar 11 2009 - 11:36:57 CDT)
- Re: Selectively turning off electrostatic interactions JC Gumbart (Wed Mar 11 2009 - 12:07:03 CDT)
- Re: Selectively turning off electrostatic interactions Chris Harrison (Wed Mar 11 2009 - 15:28:46 CDT)
- Re: some problem about ABF Jerome Henin (Wed Mar 11 2009 - 09:18:14 CDT)
- FW: Water density of water Box Shahid Qamar (Wed Mar 11 2009 - 07:07:15 CDT)
- Problems with OPLS in NAMD Kalavera_at_gmx.net (Wed Mar 11 2009 - 04:32:56 CDT)
- some problem about ABF liupeng012 (Wed Mar 11 2009 - 03:59:53 CDT)
- Error running simulation on KRAKEN XT5 harish vashisth (Tue Mar 10 2009 - 18:49:03 CDT)
- How to get the acceptance ratio in REMD Yunlang Li (Mon Mar 09 2009 - 16:59:50 CDT)
- Problem to generate water segments and lipid reading in membrane Leonardo Herrera (Tue Mar 10 2009 - 05:18:15 CDT)
- Problem to generate water segments and lipid reading in membrane Leonardo Herrera (Tue Mar 10 2009 - 05:17:36 CDT)
- problem about NAMD compile liupeng012 (Tue Mar 10 2009 - 03:15:27 CDT)
- How to use lset inside tclforces/calc_forces Cameron Abrams (Mon Mar 09 2009 - 09:00:51 CDT)
- REX simulations on lonestar or ranger Giovanni Bellesia (Mon Mar 09 2009 - 13:59:57 CDT)
- PME and fixed atoms questions Christopher Hartshorn (Mon Mar 09 2009 - 13:31:52 CDT)
- Re: about the memery lock in openMPI on infiniband 刘鹏 (Mon Mar 09 2009 - 04:27:11 CDT)
- about the memery lock in openMPI on infiniband 刘鹏 (Sun Mar 08 2009 - 03:55:40 CDT)
- job submission script on KRAKEN @ NICS harish vashisth (Fri Mar 06 2009 - 22:22:50 CST)
- Building NAMD for Opteron Cluster with ICC Chris Share (Fri Mar 06 2009 - 21:53:02 CST)
- FATAL ERROR: FixedAtoms may not be enabled in a script Dolan, Michael (NIH/NIAID) [C] (Fri Mar 06 2009 - 11:32:52 CST)
- how to use hydrogen bond parameter during minimization and simulation prasun kumar (Thu Mar 05 2009 - 23:27:47 CST)
- Job submission to Lonestar on TACC Ali Emileh (Wed Mar 04 2009 - 17:19:03 CST)
- about calculation of PMF from SMD trajectories (with pasted smd_config_file) Falgun Shah (Wed Mar 04 2009 - 12:04:52 CST)
- about calculation of PMF from SMD trajectories Falgun Shah (Wed Mar 04 2009 - 11:58:52 CST)
- removing water from big dcd files jose correa (Tue Mar 03 2009 - 20:36:24 CST)
- regarding topology file generation prasun kumar (Tue Mar 03 2009 - 04:55:16 CST)
- Re: tutorial for calculation of PMF using namd Hyundeok Song (Mon Mar 02 2009 - 23:46:21 CST)
- help running NAMD energy at multiple stable temperatures (newbie) Marie N (Mon Mar 02 2009 - 23:32:04 CST)
- tutorial for calculation of PMF using namd Falgun Shah (Mon Mar 02 2009 - 22:44:15 CST)
- Coordinate Output in both binary and ASCII. Or converting binary to ASCII in the command line Hugh Martin (Mon Mar 02 2009 - 10:09:56 CST)
- Minimization convergence issue Brittany Morgan (Mon Mar 02 2009 - 09:59:21 CST)
- Re: Minimization convergence issue Peter Freddolino (Mon Mar 02 2009 - 10:29:32 CST)
- RE: Minimization convergence issue Brittany Morgan (Mon Mar 02 2009 - 10:53:55 CST)
- RE: Minimization convergence issue Brittany Morgan (Wed Mar 04 2009 - 13:36:38 CST)
- Re: Minimization convergence issue Chris Harrison (Wed Mar 04 2009 - 19:41:06 CST)
- RE: Minimization convergence issue Brittany Morgan (Thu Mar 05 2009 - 07:56:47 CST)
- Re: Minimization convergence issue Chris Harrison (Thu Mar 05 2009 - 17:05:51 CST)
- Re: Minimization convergence issue Christopher Gillespie (Thu Mar 05 2009 - 12:04:02 CST)
- RE: Minimization convergence issue Brittany Morgan (Thu Mar 05 2009 - 12:46:28 CST)
- RE: Minimization convergence issue Brittany Morgan (Mon Mar 02 2009 - 10:53:55 CST)
- Re: Minimization convergence issue Peter Freddolino (Mon Mar 02 2009 - 10:29:32 CST)
- topology and parameter file for FAD Demet Akten (Sat Feb 28 2009 - 08:40:31 CST)
- How can I find topology and parameter files for heterocyclic, heteroaromatic, halogens and sugar compounds Lisa Brown (Fri Feb 27 2009 - 11:02:51 CST)
- error in writing restart files Ruchi Sachdeva (Fri Feb 27 2009 - 03:55:30 CST)
- paramater about Amphotericin B 刘鹏 (Fri Feb 27 2009 - 03:25:46 CST)
- Topology files Corey Fugate (Thu Feb 26 2009 - 16:08:38 CST)
- PLUMED release 1.0.0 available Massimiliano Bonomi (Thu Feb 26 2009 - 07:12:04 CST)
- Background load problem Anirban Ghosh (Thu Feb 26 2009 - 03:34:53 CST)
- Re: Background load problem Peter Freddolino (Thu Feb 26 2009 - 07:50:36 CST)
- Re: Background load problem Anirban (Thu Feb 26 2009 - 08:15:04 CST)
- Re: Background load problem Nicholas M Glykos (Thu Feb 26 2009 - 09:29:58 CST)
- Re: Background load problem Axel Kohlmeyer (Thu Feb 26 2009 - 10:13:06 CST)
- Re: Background load problem Peter Freddolino (Thu Feb 26 2009 - 11:45:00 CST)
- Re: Background load problem Anirban (Fri Feb 27 2009 - 03:38:16 CST)
- Re: Background load problem Peter Freddolino (Fri Feb 27 2009 - 15:10:29 CST)
- Re: Background load problem Anirban (Thu Feb 26 2009 - 08:15:04 CST)
- Re: Background load problem Peter Freddolino (Thu Feb 26 2009 - 07:50:36 CST)
- loading of large dcd files sripad chandan (Wed Feb 25 2009 - 23:54:58 CST)
- charm27 forcefield_topology Falgun Shah (Wed Feb 25 2009 - 11:02:02 CST)
- Re: vmd-l: Membrane builder ?'s Christopher Hartshorn (Tue Feb 24 2009 - 00:47:57 CST)
- FEP anomaly? Christopher Hartshorn (Mon Feb 23 2009 - 12:53:15 CST)
- how to do a MD of small part of a protein, using namd? Lisa Brown (Mon Feb 23 2009 - 10:23:43 CST)
- smd force vs time Falgun Shah (Sun Feb 22 2009 - 13:31:07 CST)
- solution for generating IC CHINDEA Vlad (Sat Feb 21 2009 - 17:20:11 CST)
- Re: A beginner's question for using NAMD to do cell membrane simulation and molecular transportation Ramya Gamini (Sat Feb 21 2009 - 15:34:24 CST)
- A beginner's question for using NAMD to do cell membrane simulation and molecular transportation Xu Dong (Sat Feb 21 2009 - 14:23:49 CST)
- memory optimised version and exclusion check Joachim Hein (Fri Feb 20 2009 - 13:48:24 CST)
- (no subject) gurunath katagi (Fri Feb 20 2009 - 06:08:37 CST)
- Can I get the pressure value in a cube? Fred (Rui FENG) (Thu Feb 19 2009 - 22:12:35 CST)
- NAMD CVS Luis Cunha (Thu Feb 19 2009 - 18:01:39 CST)
- Re: Constant pressure simulation: can I get the changed volume? Fred (Rui FENG) (Thu Feb 19 2009 - 04:26:50 CST)
- Constant pressure simulation: can I get the changed volume? Fred (Rui FENG) (Thu Feb 19 2009 - 01:52:55 CST)
- LD with explicit water molecules ramya narasimhan (Wed Feb 18 2009 - 22:14:40 CST)
- cgmd stability BIN ZHANG (Wed Feb 18 2009 - 17:13:14 CST)
- Autopsf error with a modified top file CHINDEA Vlad (Wed Feb 18 2009 - 15:17:52 CST)
- Re: Autopsf error with a modified top file Peter Freddolino (Wed Feb 18 2009 - 15:24:59 CST)
- RE: Autopsf error with a modified top file CHINDEA Vlad (Thu Feb 19 2009 - 18:15:45 CST)
- Re: Autopsf error with a modified top file Peter Freddolino (Thu Feb 19 2009 - 19:52:52 CST)
- RE: Autopsf error with a modified top file CHINDEA Vlad (Fri Feb 20 2009 - 19:28:28 CST)
- Re: Autopsf error with a modified top file Peter Freddolino (Fri Feb 20 2009 - 23:19:22 CST)
- RE: Autopsf error with a modified top file CHINDEA Vlad (Sat Feb 21 2009 - 06:04:19 CST)
- RE: Autopsf error with a modified top file CHINDEA Vlad (Thu Feb 19 2009 - 18:15:45 CST)
- Re: Autopsf error with a modified top file Peter Freddolino (Wed Feb 18 2009 - 15:24:59 CST)
- fail to run replica exchange on more than one node Linchen Gong (Wed Feb 18 2009 - 01:31:24 CST)
- Thiol on gold simulation in NAMD S.K. Ghosh (Tue Feb 17 2009 - 14:14:36 CST)
- Re: Thiol on gold simulation in NAMD Axel Kohlmeyer (Tue Feb 17 2009 - 14:54:51 CST)
- how can i get the energy of a molecule of a whole system? Wang,Ying (Tue Feb 17 2009 - 10:30:11 CST)
- Problem running NAMD on ranger@TACC shayan_at_msu.edu (Tue Feb 17 2009 - 07:01:27 CST)
- Forces on Atoms and Potential Energy Mohamed Seyam (Mon Feb 16 2009 - 13:57:01 CST)
- unsubscribe Vinit Rege (Mon Feb 16 2009 - 12:07:11 CST)
- log file from 3 different protein simulations sripad chandan (Mon Feb 16 2009 - 05:50:36 CST)
- Re: FEP/binding free energy difference WT vs Mut Chris Harrison (Fri Feb 13 2009 - 17:57:21 CST)
- FEP/binding free energy difference WT vs Mut Luis Cunha (Fri Feb 13 2009 - 16:43:27 CST)
- Membrane Proteins Tutorial Marcos Sotomayor (Fri Feb 13 2009 - 16:25:15 CST)
- unsubscribe Lee, Se I (Thu Feb 12 2009 - 13:26:01 CST)
- ligand flies away from binding pocket Osman Yogurtcu (Thu Feb 12 2009 - 11:39:04 CST)
- namd ubuntu-instalation jose correa (Thu Feb 12 2009 - 09:23:15 CST)
- (no subject) gurunath katagi (Thu Feb 12 2009 - 03:13:47 CST)
- namd cvs compilation with a maximum number of cores to run on Vlad Cojocaru (Thu Feb 12 2009 - 03:11:50 CST)
- Re: namd cvs compilation with a maximum number of cores to run on Peter Freddolino (Thu Feb 12 2009 - 08:32:59 CST)
- Re: namd cvs compilation with a maximum number of cores to run on Vlad Cojocaru (Thu Feb 12 2009 - 09:04:14 CST)
- Re: namd cvs compilation with a maximum number of cores to run on Peter Freddolino (Thu Feb 12 2009 - 09:41:27 CST)
- Re: namd cvs compilation with a maximum number of cores to run on Axel Kohlmeyer (Thu Feb 12 2009 - 10:35:05 CST)
- Re: namd cvs compilation with a maximum number of cores to run on Andrew Emerson (Fri Feb 13 2009 - 03:36:30 CST)
- Re: namd cvs compilation with a maximum number of cores to run on Axel Kohlmeyer (Fri Feb 13 2009 - 07:21:33 CST)
- Re: namd cvs compilation with a maximum number of cores to run on Vlad Cojocaru (Thu Feb 12 2009 - 09:04:14 CST)
- Re: namd cvs compilation with a maximum number of cores to run on Peter Freddolino (Thu Feb 12 2009 - 08:32:59 CST)
- reg dynamics hari prasad (Thu Feb 12 2009 - 01:58:55 CST)
- (力格 绝澜) Taeho Kim (Wed Feb 11 2009 - 22:29:19 CST)
- pressure profile calculations Grace Brannigan (Wed Feb 11 2009 - 16:58:06 CST)
- cuda 1.0 binaries on cuda 1.1 Roman Petrenko (Wed Feb 11 2009 - 13:47:32 CST)
- Need Charmm FF for Gangliosides bo liu (Wed Feb 11 2009 - 11:36:19 CST)
- (no subject) gurunath katagi (Wed Feb 11 2009 - 10:49:16 CST)
- center of mass for SMD Falgun Shah (Tue Feb 10 2009 - 17:52:06 CST)
- How to specify processors for running VMD on a cluster? Yinglong Miao (Tue Feb 10 2009 - 10:45:27 CST)
- tmd algorithm Elif Ozkirimli (Tue Feb 10 2009 - 09:22:58 CST)
- Periodic boundary condition in a membrane simulation Eric Hu (Mon Feb 09 2009 - 17:28:38 CST)
- any experiences with executing parallel NAMD in a NAMD simulation Yinglong Miao (Mon Feb 09 2009 - 15:59:07 CST)
- Re: any experiences with executing parallel NAMD in a NAMD simulation Peter Freddolino (Mon Feb 09 2009 - 16:26:39 CST)
- Re: any experiences with executing parallel NAMD in a NAMD simulation Yinglong Miao (Mon Feb 09 2009 - 19:56:44 CST)
- Re: any experiences with executing parallel NAMD in a NAMD simulation Peter Freddolino (Mon Feb 09 2009 - 22:13:43 CST)
- Re: any experiences with executing parallel NAMD in a NAMD simulation Yinglong Miao (Mon Feb 09 2009 - 22:26:37 CST)
- Re: any experiences with executing parallel NAMD in a NAMD simulation Peter Freddolino (Tue Feb 10 2009 - 09:26:02 CST)
- Re: any experiences with executing parallel NAMD in a NAMD simulation Yinglong Miao (Tue Feb 10 2009 - 10:13:56 CST)
- Re: any experiences with executing parallel NAMD in a NAMD simulation Peter Freddolino (Tue Feb 10 2009 - 12:45:34 CST)
- Re: any experiences with executing parallel NAMD in a NAMD simulation Yinglong Miao (Mon Feb 09 2009 - 19:56:44 CST)
- Re: any experiences with executing parallel NAMD in a NAMD simulation Peter Freddolino (Mon Feb 09 2009 - 16:26:39 CST)
- Take a look at jaxtr! Sudipta Sinha (Sun Feb 08 2009 - 22:20:40 CST)
- Accessing atoms and velocities during NVE run Nd S (Fri Feb 06 2009 - 10:57:02 CST)
- eucb - beta testers wanted for trajectory analysis program Athanassios Stavrakoudis (Thu Feb 05 2009 - 18:18:08 CST)
- "Hands-On" Workshop on Computational Biophysics, July 6-10 and August 10-14, 2009 TCBG Workshop (Thu Feb 05 2009 - 15:52:30 CST)
- Fwd:Re: TCL: divide by zero supram_at_nankai.edu.cn (Thu Feb 05 2009 - 10:28:45 CST)
- TCL: divide by zero supram_at_nankai.edu.cn (Thu Feb 05 2009 - 10:08:11 CST)
- TCL: divide by zero supram_at_nankai.edu.cn (Thu Feb 05 2009 - 06:26:11 CST)
- Fwd:Re: ABF-Zcoord: 刘育 (Wed Feb 04 2009 - 22:04:40 CST)
- Fatal error in configuration file Corey Fugate (Wed Feb 04 2009 - 21:05:36 CST)
- ABF:restraint in free energy calculation in Zcoord-method 刘育 (Tue Feb 03 2009 - 22:15:42 CST)
- Variable results for the same simulation Nd S (Tue Feb 03 2009 - 12:18:24 CST)
- ABF-Zcoord: 刘育 (Tue Feb 03 2009 - 07:29:23 CST)
- tcl script fett_at_vtr.net (Mon Feb 02 2009 - 21:31:04 CST)
- generating xsc and vel files David A. Horita (Mon Feb 02 2009 - 10:29:29 CST)
- Correlation matrix of the Ca atoms sripad chandan (Sun Feb 01 2009 - 22:46:14 CST)
- Re: Correlation matrix of the Ca atoms Joshua Adelman (Sun Feb 01 2009 - 23:22:07 CST)
- Re: Correlation matrix of the Ca atoms Nicholas M Glykos (Mon Feb 02 2009 - 02:17:39 CST)
- FEP with fixed explicit environment? Sebastian Stolzenberg (Thu Mar 12 2009 - 18:50:32 CDT)
- Re: FEP with fixed explicit environment? Chris Harrison (Thu Mar 12 2009 - 22:05:24 CDT)
- Re: FEP with fixed explicit environment? Sebastian Stolzenberg (Fri Mar 13 2009 - 10:58:32 CDT)
- Re: FEP with fixed explicit environment? Sebastian Stolzenberg (Fri Mar 13 2009 - 16:42:35 CDT)
- FEP with fixed explicit environment? Sebastian Stolzenberg (Sun Mar 15 2009 - 12:03:28 CDT)
- Re: FEP with fixed explicit environment? Sebastian Stolzenberg (Tue Mar 17 2009 - 13:21:12 CDT)
- Re: FEP with fixed explicit environment? Peter Freddolino (Tue Mar 17 2009 - 14:10:07 CDT)
- multiple FEP experiments in one NAMD-FEP run? Sebastian Stolzenberg (Tue Mar 17 2009 - 15:51:14 CDT)
- Re: multiple FEP experiments in one NAMD-FEP run? Peter Freddolino (Wed Mar 18 2009 - 15:42:27 CDT)
- tclforces included in the NAMD-FEP \delta_G values? Sebastian Stolzenberg (Thu Mar 19 2009 - 13:11:10 CDT)
- Re: tclforces included in the NAMD-FEP \delta_G values? Jerome Henin (Thu Mar 19 2009 - 15:47:32 CDT)
- alchemify with CMAP? Sebastian Stolzenberg (Thu Apr 16 2009 - 19:11:53 CDT)
- Re: alchemify with CMAP? Chris Chipot (Thu Apr 16 2009 - 19:21:19 CDT)
- Re: alchemify with CMAP? Jerome Henin (Thu Apr 16 2009 - 19:21:51 CDT)
- Re: Re: alchemify with CMAP? S閎astien L間ar (Fri Apr 17 2009 - 11:01:08 CDT)
- Re: Re: alchemify with CMAP? Jerome Henin (Fri Apr 17 2009 - 14:44:11 CDT)
- Re: Re: alchemify with CMAP? Jerome Henin (Mon Apr 20 2009 - 11:42:05 CDT)
- FEP with fixed explicit environment? Sebastian Stolzenberg (Thu Mar 12 2009 - 18:51:05 CDT)
- FEP with fixed explicit environment? Sebastian Stolzenberg (Thu Mar 12 2009 - 18:50:32 CDT)
- combining abf reaction path Arturas Ziemys (Sat Jan 31 2009 - 12:20:55 CST)
- pdb and rmsd Falgun Shah (Fri Jan 30 2009 - 13:46:42 CST)
- Aligning the distance between two centroids with an axis Mert G黵 (Fri Jan 30 2009 - 04:02:55 CST)
- Re: Aligning the distance between two centroids with an axis Nicholas M Glykos (Fri Jan 30 2009 - 05:08:19 CST)
- Re: Aligning the distance between two centroids with an axis Grace Brannigan (Fri Jan 30 2009 - 10:01:55 CST)
- Re: Aligning the distance between two centroids with an axis Chris Harrison (Fri Jan 30 2009 - 21:31:43 CST)
- FEP on NAMD2.6 versus latest CVS NAMD build Christopher Hartshorn (Fri Jan 30 2009 - 00:54:54 CST)
- running NAMD on Kraken Cray-XT4 Xu, Jiancong (Thu Jan 29 2009 - 15:44:58 CST)
- New open() for DCDs in v.2.6 ? Nicholas M Glykos (Thu Jan 29 2009 - 11:34:37 CST)
- loading large dcd files sripad chandan (Thu Jan 29 2009 - 04:30:29 CST)
- asymmetric water found! OZGE ENGIN (Wed Jan 28 2009 - 07:26:07 CST)
- value 9999999.99999 during simulation uma mageshwari (Wed Jan 28 2009 - 04:11:57 CST)
- alpha character error in the psf file OZGE ENGIN (Wed Jan 28 2009 - 03:30:26 CST)
- (no subject) OZGE ENGIN (Wed Jan 28 2009 - 03:29:03 CST)
- how to add ions to a system uma mageshwari (Wed Jan 28 2009 - 03:18:19 CST)
- how to add ions to a system uma mageshwari (Wed Jan 28 2009 - 01:57:09 CST)
- how to add ions to a system uma mageshwari (Wed Jan 28 2009 - 01:08:12 CST)
- Rosetta Academic Training Workshop Nir London (Tue Jan 27 2009 - 07:04:42 CST)
- NAMD on a virtual grid Benjamin Bouvier (Mon Jan 26 2009 - 09:38:30 CST)
- RMSD and merging trajectories Falgun Shah (Sat Jan 24 2009 - 17:20:27 CST)
- Stratification schemes Chris Chipot (Sat Jan 24 2009 - 16:28:37 CST)
- NADP jose correa (Fri Jan 23 2009 - 18:43:07 CST)
- Re: some recommendations for parametrizing new molecules required CHINDEA Vlad (Fri Jan 23 2009 - 16:30:16 CST)
- Re: problems-protein minimization jose correa (Fri Jan 23 2009 - 14:27:59 CST)
- problems-protein minimization jose correa (Fri Jan 23 2009 - 12:40:22 CST)
- some recommendations for parametrizing new molecules required CHINDEA Vlad (Fri Jan 23 2009 - 03:31:04 CST)
- Re: some recommendations for parametrizing new molecules required Christopher Gillespie (Fri Jan 23 2009 - 07:36:30 CST)
- Re: some recommendations for parametrizing new molecules required Axel Kohlmeyer (Fri Jan 23 2009 - 09:20:50 CST)
- Re: some recommendations for parametrizing new molecules required JC Gumbart (Fri Jan 23 2009 - 11:17:09 CST)
- use of berendsenPressure during heating Falgun Shah (Thu Jan 22 2009 - 22:22:29 CST)
- abf convergence problems Jorgen Simonsen (Thu Jan 22 2009 - 11:16:36 CST)
- I: Running Charm++ over MPI does not work andy.mastellone_at_alice.it (Thu Jan 22 2009 - 08:23:58 CST)
- Running Charm++ over MPI does not work andy.mastellone_at_alice.it (Thu Jan 22 2009 - 07:20:28 CST)
- Hexafluoro-2-propanol (HFIP) force parameters Dong Luo (Wed Jan 21 2009 - 15:04:43 CST)
- Re: CUDA version status Dow_Hurst (Wed Jan 21 2009 - 13:12:32 CST)
- IBVerbs NAMD build segfaults Jason Russler (Wed Jan 21 2009 - 08:47:28 CST)
- double-wide sampling with soft-core S閎astien L間ar (Tue Jan 20 2009 - 14:27:32 CST)
- Re: double-wide sampling with soft-core Jerome Henin (Wed Jan 21 2009 - 16:02:24 CST)
- Re: double-wide sampling with soft-core Chris Chipot (Wed Jan 21 2009 - 17:32:52 CST)
- Re: double-wide sampling with soft-core Floris Buelens (Thu Jan 22 2009 - 04:58:40 CST)
- Re: double-wide sampling with soft-core Chris Harrison (Thu Jan 22 2009 - 11:21:15 CST)
- Re: double-wide sampling with soft-core Peter Freddolino (Thu Jan 22 2009 - 11:34:07 CST)
- Re: double-wide sampling with soft-core Floris Buelens (Thu Jan 22 2009 - 12:02:36 CST)
- Re: double-wide sampling with soft-core Chris Chipot (Thu Jan 22 2009 - 12:23:55 CST)
- Re: double-wide sampling with soft-core Floris Buelens (Thu Jan 22 2009 - 13:25:19 CST)
- Re: double-wide sampling with soft-core Jerome Henin (Thu Jan 22 2009 - 11:35:39 CST)
- Re: double-wide sampling with soft-core Chris Harrison (Thu Jan 22 2009 - 11:48:23 CST)
- Re: double-wide sampling with soft-core Jerome Henin (Wed Jan 21 2009 - 16:02:24 CST)
- CUDA version status Dow Hurst (Tue Jan 20 2009 - 12:39:20 CST)
- (no subject) gurunath katagi (Tue Jan 20 2009 - 08:25:06 CST)
- Single vs. Double precision Neelanjana Sengupta (Mon Jan 19 2009 - 05:27:27 CST)
- The limit of atom number on Blue Gene/L Fred (Rui FENG) (Mon Jan 19 2009 - 02:09:15 CST)
- TMD comments Michael Feig (Fri Jan 16 2009 - 23:06:07 CST)
- syntax error in expression "(": premature end of expression - namdstats CHINDEA Vlad (Fri Jan 16 2009 - 17:08:54 CST)
- Problems deciphering fepout Christopher Hartshorn (Fri Jan 16 2009 - 16:28:21 CST)
- SMD output dimka (Fri Jan 16 2009 - 12:59:43 CST)
- SMD output Dmitry Lupyan (Thu Jan 15 2009 - 16:50:08 CST)
- ABF calculation with TclForces script in the configuration file govardhan reddy (Fri Jan 16 2009 - 09:18:40 CST)
- advice on van Hove Arturas Ziemys (Thu Jan 15 2009 - 12:08:40 CST)
- Energy drif in NVE ensemble eprates_at_iqm.unicamp.br (Thu Jan 15 2009 - 11:51:54 CST)
- dielectric parameter? BIN ZHANG (Thu Jan 15 2009 - 01:10:36 CST)
- problem in fitting Maxwell-Boltzmann distribution CHINDEA Vlad (Wed Jan 14 2009 - 17:08:48 CST)
- Re: problem in fitting Maxwell-Boltzmann distribution JC Gumbart (Wed Jan 14 2009 - 19:00:12 CST)
- RE: problem in fitting Maxwell-Boltzmann distribution CHINDEA Vlad (Thu Jan 15 2009 - 06:39:47 CST)
- Re: problem in fitting Maxwell-Boltzmann distribution Peter Freddolino (Thu Jan 15 2009 - 08:22:19 CST)
- RE: problem in fitting Maxwell-Boltzmann distribution CHINDEA Vlad (Fri Jan 16 2009 - 13:30:26 CST)
- Re: problem in fitting Maxwell-Boltzmann distribution Peter Freddolino (Fri Jan 16 2009 - 13:48:27 CST)
- RE: problem in fitting Maxwell-Boltzmann distribution CHINDEA Vlad (Thu Jan 15 2009 - 06:39:47 CST)
- Re: problem in fitting Maxwell-Boltzmann distribution JC Gumbart (Wed Jan 14 2009 - 19:00:12 CST)
- error during heating of the minimized system: (please reply!) Falgun Shah (Wed Jan 14 2009 - 01:08:28 CST)
- question about cellBasisVector*? BIN ZHANG (Tue Jan 13 2009 - 00:13:25 CST)
- Creating bonds during a run Marcin S. (Mon Jan 12 2009 - 09:41:23 CST)
- Question on mutator in VMD Jianping Lin (Sun Jan 11 2009 - 17:00:54 CST)
- Re: compiling NAMD failed on windows with Cygwin accomp lin (Fri Jan 09 2009 - 22:06:37 CST)
- binary trajectories karthik s (Fri Jan 09 2009 - 04:53:54 CST)
- NAMD disk writes and quota overflow Jeff Forbes (Thu Jan 08 2009 - 15:45:05 CST)
- how to save output file in plain text? Segun Jung (Thu Jan 08 2009 - 15:09:02 CST)
- Re: tclforces: switch from md with external forces to standard md Peter Freddolino (Thu Jan 08 2009 - 13:38:05 CST)
- Re: tclforces: switch from md with external forces to standard md Jerome Henin (Fri Jan 09 2009 - 10:24:24 CST)
- Single or double precision? mm148881 (Thu Jan 08 2009 - 13:09:21 CST)
- Inorganic compounds Casey,Richard (Thu Jan 08 2009 - 12:20:34 CST)
- FATAL ERROR: Setting parameter constraints from script failed! Do Nhu Trang (Thu Jan 08 2009 - 09:57:28 CST)
- Re: FATAL ERROR: Setting parameter constraints from script failed! Axel Kohlmeyer (Thu Jan 08 2009 - 10:58:05 CST)
- Re: FATAL ERROR: Setting parameter constraints from script failed! Joshua Adelman (Thu Jan 08 2009 - 11:14:24 CST)
- Re: FATAL ERROR: Setting parameter constraints from script failed! Do Nhu Trang (Fri Jan 09 2009 - 08:31:02 CST)
- Re: FATAL ERROR: Setting parameter constraints from script failed! Axel Kohlmeyer (Fri Jan 09 2009 - 08:54:26 CST)
- Re: FATAL ERROR: Setting parameter constraints from script failed! Do Nhu Trang (Fri Jan 09 2009 - 10:17:02 CST)
- Re: FATAL ERROR: Setting parameter constraints from script failed! Joshua Adelman (Thu Jan 08 2009 - 11:14:24 CST)
- Re: FATAL ERROR: Setting parameter constraints from script failed! Axel Kohlmeyer (Thu Jan 08 2009 - 10:58:05 CST)
- tcl forces interface Vlad Cojocaru (Wed Jan 07 2009 - 04:36:13 CST)
- Gradient tolerance nan for A three-atom simulation accomp lin (Mon Jan 05 2009 - 23:09:41 CST)
- RE: Gradient tolerance nan for A three-atom simulation JC Gumbart (Mon Jan 05 2009 - 23:24:35 CST)
- RE: Gradient tolerance nan for A three-atom simulation accomp lin (Tue Jan 06 2009 - 22:20:18 CST)
- Re: Gradient tolerance nan for A three-atom simulation Peter Freddolino (Thu Jan 08 2009 - 13:19:39 CST)
- Re: Gradient tolerance nan for A three-atom simulation accomp lin (Fri Jan 09 2009 - 02:51:43 CST)
- Re: Gradient tolerance nan for A three-atom simulation Peter Freddolino (Fri Jan 09 2009 - 16:14:33 CST)
- Re: Gradient tolerance nan for A three-atom simulation Peter Freddolino (Fri Jan 09 2009 - 16:14:48 CST)
- Re: Gradient tolerance nan for A three-atom simulation BIN ZHANG (Mon Jan 12 2009 - 12:03:52 CST)
- Re: Gradient tolerance nan for A three-atom simulation Peter Freddolino (Mon Jan 12 2009 - 12:17:49 CST)
- RE: Gradient tolerance nan for A three-atom simulation accomp lin (Tue Jan 06 2009 - 22:20:18 CST)
- RE: Gradient tolerance nan for A three-atom simulation JC Gumbart (Mon Jan 05 2009 - 23:24:35 CST)
- Re: namdcvs Achani.K.Yatawara_at_Dartmouth.edu (Mon Jan 05 2009 - 13:32:34 CST)
- Re: Re: namdcvs Peter Freddolino (Mon Jan 05 2009 - 13:51:02 CST)
- Re: Re: namdcvs Peter Freddolino (Mon Jan 05 2009 - 14:02:58 CST)
- Re: Re: namdcvs BIN ZHANG (Mon Jan 05 2009 - 14:12:59 CST)
- Problem with number of steps > 1000000 Anirban Ghosh (Mon Jan 05 2009 - 07:52:55 CST)
- Re: FEP simulations? Christopher Hartshorn (Mon Jan 05 2009 - 03:20:53 CST)
- Re: gpu pressure control Chris Harrison (Sun Jan 04 2009 - 12:23:48 CST)
- Re: base stacking analysis of the trajectory of a nucleic acids simulation Chris Harrison (Sun Jan 04 2009 - 12:12:07 CST)
- Confira meu perfil no Facebook Ariovaldo De Souza Junior (Sat Jan 03 2009 - 12:31:41 CST)
- How to get over with the error "Atoms moving too fast; simulation has become unstable and Exiting prematurely sunita gupta (Fri Jan 02 2009 - 03:58:37 CST)
- Re: namdcvs Re: how to apply restraints for phi and psi for alpha helix regions Leonardo Trabuco (Fri Jan 02 2009 - 02:55:40 CST)
Last message date: Fri Dec 31 2010 - 20:32:36 CST
Archived on: Wed Feb 29 2012 - 15:54:54 CST
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